[yt-svn] commit/yt-3.0: 60 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Oct 9 04:57:35 PDT 2013
60 new commits in yt-3.0:
https://bitbucket.org/yt_analysis/yt-3.0/commits/c307f12e6dee/
Changeset: c307f12e6dee
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-04 20:53:50
Summary: Enable passing of class and arguments to enable loading difficult files.
Affected #: 1 file
diff -r 73a7cf95d67d589de7b672580bd98852a2f005e5 -r c307f12e6dee208deeeee978a15b4c6c77ebf27b yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -252,26 +252,33 @@
yield
os.chdir(oldcwd)
-def can_run_pf(pf_fn):
+def can_run_pf(pf_fn, file_check):
if isinstance(pf_fn, StaticOutput):
return AnswerTestingTest.result_storage is not None
path = ytcfg.get("yt", "test_data_dir")
if not os.path.isdir(path):
return False
with temp_cwd(path):
+ if file_check:
+ return os.path.isfile(pf_fn)
try:
load(pf_fn)
except YTOutputNotIdentified:
return False
return AnswerTestingTest.result_storage is not None
-def data_dir_load(pf_fn):
+def data_dir_load(pf_fn, cls = None, args = None, kwargs = None):
path = ytcfg.get("yt", "test_data_dir")
if isinstance(pf_fn, StaticOutput): return pf_fn
if not os.path.isdir(path):
return False
with temp_cwd(path):
- pf = load(pf_fn)
+ if cls is None:
+ pf = load(pf_fn)
+ else:
+ args = args or ()
+ kwargs = kwargs or {}
+ pf = cls(pf_fn, *args, **kwargs)
pf.h
return pf
@@ -610,14 +617,14 @@
assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
for fn in fns: os.remove(fn)
-def requires_pf(pf_fn, big_data = False):
+def requires_pf(pf_fn, big_data = False, file_check = False):
def ffalse(func):
return lambda: None
def ftrue(func):
return func
if run_big_data == False and big_data == True:
return ffalse
- elif not can_run_pf(pf_fn):
+ elif not can_run_pf(pf_fn, file_check):
return ffalse
else:
return ftrue
https://bitbucket.org/yt_analysis/yt-3.0/commits/1aa9f0a4d412/
Changeset: 1aa9f0a4d412
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-04 20:54:20
Summary: Adding some Tipsy tests.
Affected #: 2 files
diff -r c307f12e6dee208deeeee978a15b4c6c77ebf27b -r 1aa9f0a4d4122a00dfcbb70f4a86370cffa5d467 yt/frontends/sph/data_structures.py
--- a/yt/frontends/sph/data_structures.py
+++ b/yt/frontends/sph/data_structures.py
@@ -436,7 +436,10 @@
self._unit_base = unit_base or {}
self._cosmology_parameters = cosmology_parameters
+ if parameter_file is not None:
+ parameter_file = os.path.abspath(parameter_file)
self._param_file = parameter_file
+ filename = os.path.abspath(filename)
super(TipsyStaticOutput, self).__init__(filename, data_style)
def __repr__(self):
diff -r c307f12e6dee208deeeee978a15b4c6c77ebf27b -r 1aa9f0a4d4122a00dfcbb70f4a86370cffa5d467 yt/frontends/sph/tests/test_tipsy.py
--- /dev/null
+++ b/yt/frontends/sph/tests/test_tipsy.py
@@ -0,0 +1,89 @@
+"""
+Tipsy tests using the AGORA dataset
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.testing import *
+from yt.utilities.answer_testing.framework import \
+ requires_pf, \
+ small_patch_amr, \
+ big_patch_amr, \
+ data_dir_load, \
+ PixelizedProjectionValuesTest, \
+ FieldValuesTest
+from yt.frontends.sph.api import TipsyStaticOutput
+
+_fields = (("deposit", "all_density"),
+ ("deposit", "all_count"),
+ ("deposit", "DarkMatter_density"),
+)
+
+pkdgrav = "halo1e11_run1.00400/halo1e11_run1.00400"
+ at requires_pf(pkdgrav, file_check = True)
+def test_pkdgrav():
+ cosmology_parameters = dict(current_redshift = 0.0,
+ omega_lambda = 0.728,
+ omega_matter = 0.272,
+ hubble_constant = 0.702)
+ kwargs = dict(endian="<",
+ field_dtypes = {"Coordinates": "d"},
+ cosmology_parameters = cosmology_parameters,
+ unit_base = {'mpchcm': 1.0/60.0},
+ n_ref = 64)
+ pf = data_dir_load(pkdgrav, TipsyStaticOutput, (), kwargs)
+ yield assert_equal, str(pf), "halo1e11_run1.00400"
+ dso = [ None, ("sphere", ("c", (0.3, 'unitary')))]
+ dd = pf.h.all_data()
+ yield assert_equal, dd["Coordinates"].shape, (26847360, 3)
+ tot = sum(dd[ptype,"Coordinates"].shape[0]
+ for ptype in pf.particle_types if ptype != "all")
+ yield assert_equal, tot, 26847360
+ for field in _fields:
+ for axis in [0, 1, 2]:
+ for ds in dso:
+ for weight_field in [None, "Density"]:
+ yield PixelizedProjectionValuesTest(
+ pf, axis, field, weight_field,
+ ds)
+ yield FieldValuesTest(
+ pf, field, ds)
+
+gasoline = "agora_1e11.00400/agora_1e11.00400"
+ at requires_pf(gasoline, file_check = True)
+def test_gasoline():
+ cosmology_parameters = dict(current_redshift = 0.0,
+ omega_lambda = 0.728,
+ omega_matter = 0.272,
+ hubble_constant = 0.702)
+ kwargs = dict(cosmology_parameters = cosmology_parameters,
+ unit_base = {'mpchcm': 1.0/60.0},
+ n_ref = 64)
+ pf = data_dir_load(gasoline, TipsyStaticOutput, (), kwargs)
+ yield assert_equal, str(pf), "agora_1e11.00400"
+ dso = [ None, ("sphere", ("c", (0.3, 'unitary')))]
+ dd = pf.h.all_data()
+ yield assert_equal, dd["Coordinates"].shape, (26847360, 3)
+ tot = sum(dd[ptype,"Coordinates"].shape[0]
+ for ptype in pf.particle_types if ptype != "all")
+ yield assert_equal, tot, 26847360
+ for field in _fields:
+ for axis in [0, 1, 2]:
+ for ds in dso:
+ for weight_field in [None, "Density"]:
+ yield PixelizedProjectionValuesTest(
+ pf, axis, field, weight_field,
+ ds)
+ yield FieldValuesTest(
+ pf, field, ds)
+
https://bitbucket.org/yt_analysis/yt-3.0/commits/64758cd4b498/
Changeset: 64758cd4b498
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-04 21:57:26
Summary: Switching the order of a bunch of these operations, reducing test count.
Affected #: 5 files
diff -r 1aa9f0a4d4122a00dfcbb70f4a86370cffa5d467 -r 64758cd4b498bf469190823944589e80ff15130a yt/frontends/artio/tests/test_outputs.py
--- a/yt/frontends/artio/tests/test_outputs.py
+++ b/yt/frontends/artio/tests/test_outputs.py
@@ -31,12 +31,15 @@
pf = data_dir_load(sizmbhloz)
yield assert_equal, str(pf), "sizmbhloz-clref04SNth-rs9_a0.9011.art"
dso = [ None, ("sphere", ("max", (0.1, 'unitary')))]
- for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
for weight_field in [None, "Density"]:
yield PixelizedProjectionValuesTest(
sizmbhloz, axis, field, weight_field,
ds)
- yield FieldValuesTest(
- sizmbhloz, field, ds)
+ yield FieldValuesTest(sizmbhloz, field, ds)
+ if ds is None: ds = pf.h.all_data()
+ s1 = ds["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in ds.blocks)
+ yield assert_equal, s1, s2
diff -r 1aa9f0a4d4122a00dfcbb70f4a86370cffa5d467 -r 64758cd4b498bf469190823944589e80ff15130a yt/frontends/moab/tests/test_c5.py
--- a/yt/frontends/moab/tests/test_c5.py
+++ b/yt/frontends/moab/tests/test_c5.py
@@ -49,7 +49,6 @@
ray = pf.h.ray(p1, p2)
yield assert_almost_equal, ray["dts"].sum(dtype="float64"), 1.0, 8
for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
- yield FieldValuesTest(c5, field, ds)
+ for ds in dso:
+ yield FieldValuesTest(c5, field, ds)
diff -r 1aa9f0a4d4122a00dfcbb70f4a86370cffa5d467 -r 64758cd4b498bf469190823944589e80ff15130a yt/frontends/ramses/tests/test_outputs.py
--- a/yt/frontends/ramses/tests/test_outputs.py
+++ b/yt/frontends/ramses/tests/test_outputs.py
@@ -31,13 +31,15 @@
pf = data_dir_load(output_00080)
yield assert_equal, str(pf), "info_00080"
dso = [ None, ("sphere", ("max", (0.1, 'unitary')))]
- for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
for weight_field in [None, "Density"]:
yield PixelizedProjectionValuesTest(
output_00080, axis, field, weight_field,
ds)
- yield FieldValuesTest(
- output_00080, field, ds)
-
+ yield FieldValuesTest(output_00080, field, ds)
+ if ds is None: ds = pf.h.all_data()
+ s1 = ds["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in ds.blocks)
+ yield assert_equal, s1, s2
diff -r 1aa9f0a4d4122a00dfcbb70f4a86370cffa5d467 -r 64758cd4b498bf469190823944589e80ff15130a yt/frontends/sph/tests/test_owls.py
--- a/yt/frontends/sph/tests/test_owls.py
+++ b/yt/frontends/sph/tests/test_owls.py
@@ -40,13 +40,16 @@
tot = sum(dd[ptype,"Coordinates"].shape[0]
for ptype in pf.particle_types if ptype != "all")
yield assert_equal, tot, (2*128*128*128)
- for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
for weight_field in [None, "Density"]:
yield PixelizedProjectionValuesTest(
os33, axis, field, weight_field,
ds)
- yield FieldValuesTest(
- os33, field, ds)
+ yield FieldValuesTest(os33, field, ds)
+ if ds is None: ds = pf.h.all_data()
+ s1 = ds["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in ds.blocks)
+ yield assert_equal, s1, s2
diff -r 1aa9f0a4d4122a00dfcbb70f4a86370cffa5d467 -r 64758cd4b498bf469190823944589e80ff15130a yt/frontends/sph/tests/test_tipsy.py
--- a/yt/frontends/sph/tests/test_tipsy.py
+++ b/yt/frontends/sph/tests/test_tipsy.py
@@ -49,15 +49,18 @@
tot = sum(dd[ptype,"Coordinates"].shape[0]
for ptype in pf.particle_types if ptype != "all")
yield assert_equal, tot, 26847360
- for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
for weight_field in [None, "Density"]:
yield PixelizedProjectionValuesTest(
pf, axis, field, weight_field,
ds)
- yield FieldValuesTest(
- pf, field, ds)
+ yield FieldValuesTest(pf, field, ds)
+ if ds is None: ds = pf.h.all_data()
+ s1 = ds["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in ds.blocks)
+ yield assert_equal, s1, s2
gasoline = "agora_1e11.00400/agora_1e11.00400"
@requires_pf(gasoline, file_check = True)
@@ -77,13 +80,15 @@
tot = sum(dd[ptype,"Coordinates"].shape[0]
for ptype in pf.particle_types if ptype != "all")
yield assert_equal, tot, 26847360
- for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
for weight_field in [None, "Density"]:
yield PixelizedProjectionValuesTest(
pf, axis, field, weight_field,
ds)
- yield FieldValuesTest(
- pf, field, ds)
-
+ yield FieldValuesTest(pf, field, ds)
+ if ds is None: ds = pf.h.all_data()
+ s1 = ds["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in ds.blocks)
+ yield assert_equal, s1, s2
https://bitbucket.org/yt_analysis/yt-3.0/commits/ecf6b2f78392/
Changeset: ecf6b2f78392
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-04 21:57:44
Summary: Merging with bugfix
Affected #: 1 file
diff -r 64758cd4b498bf469190823944589e80ff15130a -r ecf6b2f78392d75e54e16281c479b62b96543cb9 yt/geometry/oct_container.pyx
--- a/yt/geometry/oct_container.pyx
+++ b/yt/geometry/oct_container.pyx
@@ -402,11 +402,11 @@
def mask(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
if num_cells == -1:
- num_cells = selector.count_oct_cells(self, domain_id)
+ num_cells = selector.count_octs(self, domain_id)
cdef np.ndarray[np.uint8_t, ndim=1] coords
cdef OctVisitorData data
self.setup_data(&data, domain_id)
- coords = np.zeros((num_cells), dtype="uint8")
+ coords = np.zeros((num_cells*8), dtype="uint8")
data.array = <void *> coords.data
self.visit_all_octs(selector, oct_visitors.mask_octs, &data)
return coords.astype("bool")
https://bitbucket.org/yt_analysis/yt-3.0/commits/14ae35ea6abf/
Changeset: 14ae35ea6abf
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-04 22:13:11
Summary: This fixes a test passage for Octree dataset with multi-octrees.
Affected #: 2 files
diff -r ecf6b2f78392d75e54e16281c479b62b96543cb9 -r 14ae35ea6abf1fe5716cf62ab07cdaa3e8ca9179 yt/data_objects/octree_subset.py
--- a/yt/data_objects/octree_subset.py
+++ b/yt/data_objects/octree_subset.py
@@ -113,7 +113,7 @@
_domain_ind = None
def select_blocks(self, selector):
- mask = self.oct_handler.mask(selector)
+ mask = self.oct_handler.mask(selector, domain_id = self.domain_id)
mask = self._reshape_vals(mask)
slicer = OctreeSubsetBlockSlice(self)
for i, sl in slicer:
diff -r ecf6b2f78392d75e54e16281c479b62b96543cb9 -r 14ae35ea6abf1fe5716cf62ab07cdaa3e8ca9179 yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -1170,7 +1170,9 @@
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
- def mask(self, SelectorObject selector, np.int64_t num_cells = -1):
+ def mask(self, SelectorObject selector, np.int64_t num_cells = -1,
+ int domain_id = -1):
+ # We take a domain_id here to avoid subclassing
cdef int i
cdef np.float64_t pos[3]
cdef np.int64_t sfc
https://bitbucket.org/yt_analysis/yt-3.0/commits/ccaa7271e6d7/
Changeset: ccaa7271e6d7
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-04 22:21:33
Summary: Blocks of size 1 need this change.
Affected #: 1 file
diff -r 14ae35ea6abf1fe5716cf62ab07cdaa3e8ca9179 -r ccaa7271e6d763dff5f63fbaf38d6e4ea60c7fac yt/data_objects/octree_subset.py
--- a/yt/data_objects/octree_subset.py
+++ b/yt/data_objects/octree_subset.py
@@ -271,12 +271,14 @@
@property
def LeftEdge(self):
- LE = self._fcoords[0,0,0,self.ind,:] - self._fwidth[0,0,0,self.ind,:]*0.5
+ LE = (self._fcoords[0,0,0,self.ind,:]
+ - self._fwidth[0,0,0,self.ind,:])*0.5
return LE
@property
def RightEdge(self):
- RE = self._fcoords[1,1,1,self.ind,:] + self._fwidth[1,1,1,self.ind,:]*0.5
+ RE = (self._fcoords[-1,-1,-1,self.ind,:]
+ + self._fwidth[-1,-1,-1,self.ind,:])*0.5
return RE
@property
https://bitbucket.org/yt_analysis/yt-3.0/commits/7d5d40d1f42d/
Changeset: 7d5d40d1f42d
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-05 21:44:48
Summary: This fixes ARTIO blocks issues.
Previously, the number of cells returned through:
for block, mask in something.blocks:
count += mask.sum()
and:
something.ires.size
did not return the same result. This is because of how masks were set up for
the RootMesh for ARTIO datasets. Note that this does not result in bad or
incorrect values for nearly *any* situation, as .blocks is hardly used. But,
it resulted in bad results. This corrects that, by changing how the root mesh
is exposed. We now excise completely any and all root mesh SFC cells that have
octs within them.
The alternative to this would be a double-selection call, which is why this is
*now* a problem when it previously would not be; this was the usage of
self.selector_fill inside the self.select_icoords call of OctreeSubset. For
non-Forest datasets, this was not an issue, as the octs were coverd and that
was selected in recursively_visit_octs. Here, however, since they were
disconnected, it needs to be explicitly added. By masking here, we are
essentially mocking up the behavior of recursively_visit_octs.
Affected #: 1 file
diff -r ccaa7271e6d763dff5f63fbaf38d6e4ea60c7fac -r 7d5d40d1f42d673fe370788f2f792686304f733c yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -3,7 +3,8 @@
cimport numpy as np
import sys
-from yt.geometry.selection_routines cimport SelectorObject, AlwaysSelector
+from yt.geometry.selection_routines cimport \
+ SelectorObject, AlwaysSelector, OctreeSubsetSelector
from yt.utilities.lib.fp_utils cimport imax
from yt.geometry.oct_container cimport \
SparseOctreeContainer
@@ -561,6 +562,7 @@
cdef np.float64_t dds[3]
cdef np.int64_t dims[3]
cdef public np.int64_t total_octs
+ cdef np.int64_t *doct_count
def __init__(self, domain_dimensions, # cells
domain_left_edge,
@@ -619,12 +621,14 @@
status = artio_grid_read_root_cell_end( self.handle )
check_artio_status(status)
free(num_octs_per_level)
+ self.oct_count = oct_count
+ self.doct_count = <np.int64_t *> oct_count.data
self.root_mesh_handler = ARTIORootMeshContainer(self)
- self.oct_count = oct_count
def free_mesh(self):
self.octree_handler = None
self.root_mesh_handler = None
+ self.doct_count = NULL
self.oct_count = None
def get_coords(artio_fileset handle, np.int64_t s):
@@ -1013,9 +1017,12 @@
cdef public object _last_mask
cdef public object _last_selector_id
cdef ARTIOSFCRangeHandler range_handler
+ cdef np.uint8_t *sfc_mask
+ cdef np.int64_t nsfc
def __init__(self, ARTIOSFCRangeHandler range_handler):
cdef int i
+ cdef np.int64_t sfci
for i in range(3):
self.DLE[i] = range_handler.DLE[i]
self.DRE[i] = range_handler.DRE[i]
@@ -1027,6 +1034,22 @@
self.sfc_start = range_handler.sfc_start
self.sfc_end = range_handler.sfc_end
self.range_handler = range_handler
+ # We assume that the number of octs has been created and filled
+ # already. We no longer care about ANY of the SFCs that have octs
+ # inside them -- this goes for every operation that this object
+ # performs.
+ self.sfc_mask = <np.uint8_t *>malloc(sizeof(np.uint8_t) *
+ self.sfc_end - self.sfc_start + 1)
+ self.nsfc = 0
+ for sfci in range(self.sfc_end - self.sfc_start + 1):
+ if self.range_handler.oct_count[sfci] > 0:
+ self.sfc_mask[sfci] = 0
+ else:
+ self.sfc_mask[sfci] = 1
+ self.nsfc += 1
+
+ def __dealloc__(self):
+ free(self.sfc_mask)
@cython.cdivision(True)
cdef np.int64_t pos_to_sfc(self, np.float64_t pos[3]) nogil:
@@ -1057,7 +1080,7 @@
def icoords(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
# Note that num_octs does not have to equal sfc_end - sfc_start + 1.
- cdef np.int64_t sfc
+ cdef np.int64_t sfc, sfci = -1
cdef int acoords[3], i
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector)
@@ -1066,7 +1089,9 @@
coords = np.empty((num_cells, 3), dtype="int64")
cdef int filled = 0
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if mask[sfc - self.sfc_start] == 0: continue
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0: continue
# Note that we do *no* checks on refinement here. In fact, this
# entire setup should not need to touch the disk except if the
# artio sfc calculators need to.
@@ -1079,7 +1104,7 @@
def fcoords(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
# Note that num_cells does not have to equal sfc_end - sfc_start + 1.
- cdef np.int64_t sfc
+ cdef np.int64_t sfc, sfci = -1
cdef np.float64_t pos[3]
cdef int acoords[3], i
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
@@ -1089,7 +1114,9 @@
coords = np.empty((num_cells, 3), dtype="float64")
cdef int filled = 0
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if mask[sfc - self.sfc_start] == 0: continue
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0: continue
# Note that we do *no* checks on refinement here. In fact, this
# entire setup should not need to touch the disk except if the
# artio sfc calculators need to.
@@ -1132,7 +1159,7 @@
# other. Note that we *do* apply the selector here.
cdef np.int64_t num_cells = -1
cdef np.int64_t ind
- cdef np.int64_t sfc
+ cdef np.int64_t sfc, sfci = -1
cdef np.float64_t pos[3]
cdef np.float64_t dpos[3]
cdef int dim, status, filled = 0
@@ -1158,7 +1185,9 @@
ddata = (<char*>dest.data) + offset*ss*dims
ind = 0
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if mask[sfc - self.sfc_start] == 0: continue
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0: continue
memcpy(ddata, sdata + ind, dims * ss)
ddata += dims * ss
filled += 1
@@ -1175,21 +1204,16 @@
# We take a domain_id here to avoid subclassing
cdef int i
cdef np.float64_t pos[3]
- cdef np.int64_t sfc
- cdef np.ndarray[np.int64_t, ndim=1] oct_count
+ cdef np.int64_t sfc, sfci = -1
if self._last_selector_id == hash(selector):
return self._last_mask
- if num_cells == -1:
- # We need to count, but this process will only occur one time,
- # since num_cells will later be cached.
- num_cells = self.sfc_end - self.sfc_start + 1
- mask = np.zeros((num_cells), dtype="uint8")
- oct_count = self.range_handler.oct_count
+ mask = np.zeros((self.nsfc), dtype="uint8")
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if oct_count[sfc - self.sfc_start] > 0: continue
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
self.sfc_to_pos(sfc, pos)
if selector.select_cell(pos, self.dds) == 0: continue
- mask[sfc - self.sfc_start] = 1
+ mask[sfci] = 1
self._last_mask = mask.astype("bool")
self._last_selector_id = hash(selector)
return self._last_mask
@@ -1203,7 +1227,7 @@
def fill_sfc(self, SelectorObject selector, field_indices):
cdef np.ndarray[np.float64_t, ndim=1] dest
cdef int n, status, i, di, num_oct_levels, nf, ngv, max_level
- cdef np.int64_t sfc, num_cells
+ cdef np.int64_t sfc, num_cells, sfci = -1
cdef np.float64_t val
cdef artio_fileset_handle *handle = self.artio_handle.handle
cdef double dpos[3]
@@ -1238,7 +1262,9 @@
self.sfc_start, self.sfc_end )
check_artio_status(status)
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if mask[sfc - self.sfc_start] == 0: continue
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0: continue
status = artio_grid_read_root_cell_begin( handle, sfc,
dpos, grid_variables, &num_oct_levels,
num_octs_per_level)
@@ -1308,5 +1334,72 @@
for j in range(nf):
field_pointers[j][i] = field_vals[j]
+cdef class SFCRangeSelector(SelectorObject):
+
+ cdef SelectorObject base_selector
+ cdef ARTIOSFCRangeHandler range_handler
+ cdef ARTIORootMeshContainer mesh_container
+ cdef np.int64_t sfc_start, sfc_end
+
+ def __init__(self, dobj):
+ self.base_selector = dobj.base_selector
+ self.mesh_container = dobj.oct_handler
+ self.range_handler = self.mesh_container.range_handler
+ self.sfc_start = self.mesh_container.sfc_start
+ self.sfc_end = self.mesh_container.sfc_end
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ def select_grids(self,
+ np.ndarray[np.float64_t, ndim=2] left_edges,
+ np.ndarray[np.float64_t, ndim=2] right_edges,
+ np.ndarray[np.int32_t, ndim=2] levels):
+ raise RuntimeError
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_sphere(self, np.float64_t pos[3], np.float64_t radius) nogil:
+ return 1
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_cell(self, np.float64_t pos[3], np.float64_t dds[3]) nogil:
+ return self.select_point(pos)
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_point(self, np.float64_t pos[3]) nogil:
+ cdef np.int64_t sfc = self.mesh_container.pos_to_sfc(pos)
+ if sfc > self.sfc_end: return 0
+ cdef np.int64_t oc = self.range_handler.doct_count[
+ sfc - self.sfc_start]
+ if oc > 0: return 0
+ return 1
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_bbox(self, np.float64_t left_edge[3],
+ np.float64_t right_edge[3]) nogil:
+ return self.base_selector.select_bbox(left_edge, right_edge)
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_grid(self, np.float64_t left_edge[3],
+ np.float64_t right_edge[3], np.int32_t level,
+ Oct *o = NULL) nogil:
+ # Because visitors now use select_grid, we should be explicitly
+ # checking this.
+ return self.base_selector.select_grid(left_edge, right_edge, level, o)
+
+ def _hash_vals(self):
+ return (hash(self.base_selector), self.sfc_start, self.sfc_end)
+
sfc_subset_selector = AlwaysSelector
+#sfc_subset_selector = SFCRangeSelector
https://bitbucket.org/yt_analysis/yt-3.0/commits/73eceed0e23d/
Changeset: 73eceed0e23d
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 14:51:48
Summary: Fixing .deposit for ARTIORootMeshContainer.
Affected #: 1 file
diff -r 7d5d40d1f42d673fe370788f2f792686304f733c -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -1290,21 +1290,26 @@
# This implements the necessary calls to enable particle deposition to
# occur as needed.
cdef int nf, i, j
+ cdef np.int64_t sfc, sfci
if fields is None:
fields = []
nf = len(fields)
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector, -1)
cdef np.ndarray[np.int64_t, ndim=1] domain_ind
- domain_ind = np.zeros(mask.shape[0], dtype="int64") - 1
+ domain_ind = np.zeros(self.sfc_end - self.sfc_start + 1,
+ dtype="int64") - 1
j = 0
- for i in range(mask.shape[0]):
- if mask[i] == 1:
- domain_ind[i] = j
- j += 1
+ sfci = -1
+ for sfc in range(self.sfc_start, self.sfc_end + 1):
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0:
+ continue
+ domain_ind[sfc - self.sfc_start] = j
+ j += 1
cdef np.float64_t **field_pointers, *field_vals, pos[3], left_edge[3]
cdef int coords[3]
- cdef np.int64_t sfc
cdef np.ndarray[np.float64_t, ndim=1] tarr
field_pointers = <np.float64_t**> alloca(sizeof(np.float64_t *) * nf)
field_vals = <np.float64_t*>alloca(sizeof(np.float64_t) * nf)
https://bitbucket.org/yt_analysis/yt-3.0/commits/a80979a5173c/
Changeset: a80979a5173c
Branch: yt
User: jwise77
Date: 2013-09-30 01:47:01
Summary: Fixed a couple of misplaced licensing terms.
Affected #: 2 files
diff -r b154dfce6acc5a293d7abfe20d64acc542919627 -r a80979a5173c27eced97c5f35b572d29adaddd1c yt/gui/reason/extdirect_router.py
--- a/yt/gui/reason/extdirect_router.py
+++ b/yt/gui/reason/extdirect_router.py
@@ -9,6 +9,13 @@
This code was released under the BSD License.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import inspect
class DirectException(Exception):
@@ -186,12 +193,4 @@
-"""
-#-----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
diff -r b154dfce6acc5a293d7abfe20d64acc542919627 -r a80979a5173c27eced97c5f35b572d29adaddd1c yt/visualization/volume_rendering/multi_texture.py
--- a/yt/visualization/volume_rendering/multi_texture.py
+++ b/yt/visualization/volume_rendering/multi_texture.py
@@ -35,6 +35,14 @@
I hope this helps,
Almar
"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
from yt.mods import *
from yt.funcs import *
@@ -300,14 +308,3 @@
ax.Draw()
return mtex, ax
-
-
-"""
-
-#-----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
https://bitbucket.org/yt_analysis/yt-3.0/commits/6144554f5038/
Changeset: 6144554f5038
Branch: yt
User: ChrisMalone
Date: 2013-10-01 19:13:31
Summary: make transfer_function a keyword, instead of positional, argument
Affected #: 1 file
diff -r a80979a5173c27eced97c5f35b572d29adaddd1c -r 6144554f5038e1fade96aaba6648544fbbf3b135 yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -72,6 +72,9 @@
cubical, but if not, it is left/right, top/bottom, front/back.
resolution : int or list of ints
The number of pixels in each direction.
+ transfer_function : `yt.visualization.volume_rendering.TransferFunction`
+ The transfer function used to map values to colors in an image. If
+ not specified, defaults to a ProjectionTransferFunction.
north_vector : array_like, optional
The 'up' direction for the plane of rays. If not specific, calculated
automatically.
@@ -184,7 +187,7 @@
_tf_figure = None
_render_figure = None
def __init__(self, center, normal_vector, width,
- resolution, transfer_function,
+ resolution, transfer_function = None,
north_vector = None, steady_north=False,
volume = None, fields = None,
log_fields = None,
@@ -1465,7 +1468,7 @@
class MosaicCamera(Camera):
def __init__(self, center, normal_vector, width,
- resolution, transfer_function,
+ resolution, transfer_function = None,
north_vector = None, steady_north=False,
volume = None, fields = None,
log_fields = None,
https://bitbucket.org/yt_analysis/yt-3.0/commits/309891bcf064/
Changeset: 309891bcf064
Branch: yt
User: jzuhone
Date: 2013-05-13 20:15:32
Summary: SZ maps using SZpack
Affected #: 1 file
diff -r b0d1232c9eadea6447edbd7ce925ed67d11028e3 -r 309891bcf064d830355e7bf803da5e3c53d06df8 yt/analysis_modules/SZmaps.py
--- /dev/null
+++ b/yt/analysis_modules/SZmaps.py
@@ -0,0 +1,94 @@
+from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mp
+from yt.data_objects.image_array import ImageArray
+import numpy as np
+
+Tcmb = 2.726
+mueinv = 0.875
+
+try:
+ import SZpack
+except:
+ raise ImportError
+
+def _t_squared(field, data):
+ return data["TempkeV"]*data["TempkeV"]
+add_field("TSquared", function=_t_squared)
+
+def _beta_perp_squared(field, data):
+ axis = data.get_field_parameter("axis")
+ if axis == "x":
+ vv = np.sqrt(data["y-velocity"]**2+data["z-velocity"]**2)
+ elif axis == "y":
+ vv = np.sqrt(data["x-velocity"]**2+data["z-velocity"]**2)
+ elif axis == "z":
+ vv = np.sqrt(data["x-velocity"]**2+data["y-velocity"]**2)
+ return vv/clight/clight
+add_field("BetaPerpSquared", function=_beta_perp_squared)
+
+def _beta_par(field, data):
+ axis = data.get_field_parameter("axis")
+ return data["%s-velocity" % (axis)]/clight
+add_field("BetaPar", function=_beta_par)
+
+def _beta_par_squared(field, data):
+ return data["BetaPar"]**2
+add_field("BetaParSquared", function=_beta_par_squared)
+
+def _t_beta_par(field, data):
+ return data["TempkeV"]*data["BetaPar"]
+add_field("TBetaPar", function=_t_beta_par)
+
+vlist = 'xyz'
+
+def SZProjection(pf, axis, freqs, width=(1, "unitary"), nx=800, ny=800)
+
+ num_freqs = len(freqs)
+ freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
+ xo = hcgs*freqs*1.0e9/(kboltz*Tcmb)
+
+ proj1 = pf.h.proj("TempkeV", weight_field="Density")
+ proj2 = pf.h.proj("Density")
+
+ if axis in vlist:
+ vfield = "velocity_%s" % (axis)
+ proj1.set_field_parameter("axis", axis)
+ elif axis in xrange(0,3) :
+ vfield = "velocity_%s" % (vlist[axis])
+ proj1.set_field_parameter("axis", vlist[axis])
+
+ frb1 = proj1.to_frb(width, n)
+ frb2 = proj2.to_frb(width, n)
+
+ TeSZ = frb1["TempkeV"]
+ omega1 = frb1["Tsquared"]/(TeSZ*TeSZ) - 1.
+ sigma1 = frb1["TBetaPar"]/TeSZ - betac_par
+ kappa1 = frb1["BetaParSquared"] - betac_par
+
+ frb1["tau"] = sigma_thompson*frb2["Density"]*mueinv/mp
+ frb1["omega1"] = ImageArray(omega1)
+ frb1["kappa1"] = ImageArray(kappa1)
+ frb1["sigma1"] = ImageArray(sigma1)
+
+ SZsignal = np.zeros((num_freqs,nx,ny))
+ omega = np.zeros((3))
+ sigma = np.zeros((3))
+
+ for i in xrange(nx):
+
+ for j in xrange(ny):
+
+ tau = frb1["tau"][i,j]
+ Te = frb1["TempkeV"][i,j]
+ bpar = frb1["BetaPar"][i,j]
+ bperp2 = frb["BetaPerpSquared"][i,j]
+ omega[0] = frb1["omega1"][i,j]
+ sigma[0] = frb1["sigma1"][i,j]
+ kappa = frb1["kappa1"][i,j]
+
+ SZsignal[:,i,j] = SZpack.compute_combo_means_ex(xo, tau, Te, bpar, omega,
+ sigma, kappa, bperp2)
+
+ for i in xrange(num_freqs) :
+ frb1[freq_fields[i]] = ImageArray(SZsignal[i,:,:])
+
+ return frb1
https://bitbucket.org/yt_analysis/yt-3.0/commits/4f749ff73844/
Changeset: 4f749ff73844
Branch: yt
User: jzuhone
Date: 2013-05-13 20:15:47
Summary: Merging
Affected #: 1 file
diff -r 309891bcf064d830355e7bf803da5e3c53d06df8 -r 4f749ff7384491a1da1a0396ccd16134654f8412 yt/frontends/athena/fields.py
--- a/yt/frontends/athena/fields.py
+++ b/yt/frontends/athena/fields.py
@@ -115,7 +115,7 @@
add_field("y-velocity", function=_yvelocity, take_log=False,
units=r"\rm{cm}/\rm{s}", convert_function=_convertVelocity)
def _zvelocity(field, data):
- if "velocity_z" in data.pf.field.info:
+ if "velocity_z" in data.pf.field_info:
return data["velocity_z"]
else:
return data["momentum_z"]/data["density"]
https://bitbucket.org/yt_analysis/yt-3.0/commits/7b35c3296567/
Changeset: 7b35c3296567
Branch: yt
User: jzuhone
Date: 2013-05-13 23:29:42
Summary: Fixed a few bugs
Affected #: 2 files
diff -r 4f749ff7384491a1da1a0396ccd16134654f8412 -r 7b35c3296567868aaffcde67a574f5e28b797785 yt/analysis_modules/SZmaps.py
--- a/yt/analysis_modules/SZmaps.py
+++ b/yt/analysis_modules/SZmaps.py
@@ -1,5 +1,6 @@
from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mp
from yt.data_objects.image_array import ImageArray
+from yt.data_objects.field_info_container import add_field
import numpy as np
Tcmb = 2.726
@@ -40,25 +41,27 @@
vlist = 'xyz'
-def SZProjection(pf, axis, freqs, width=(1, "unitary"), nx=800, ny=800)
+def SZProjection(pf, axis, freqs, center="c", width=(1, "unitary"), nx=800, ny=800):
num_freqs = len(freqs)
freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
xo = hcgs*freqs*1.0e9/(kboltz*Tcmb)
- proj1 = pf.h.proj("TempkeV", weight_field="Density")
- proj2 = pf.h.proj("Density")
-
- if axis in vlist:
- vfield = "velocity_%s" % (axis)
- proj1.set_field_parameter("axis", axis)
- elif axis in xrange(0,3) :
- vfield = "velocity_%s" % (vlist[axis])
- proj1.set_field_parameter("axis", vlist[axis])
-
- frb1 = proj1.to_frb(width, n)
- frb2 = proj2.to_frb(width, n)
-
+ if isinstance(axis, np.ndarray) :
+ frb1["TempkeV"] = off_axis_projection(pf, center, axis, width, nx, field="TempkeV", weight="Density")
+ frb2["Density"] = off_axis_projection(pf, center, axis, width, nx, field="Density")
+ else :
+ if axis in vlist:
+ vfield = "velocity_%s" % (axis)
+ proj1.set_field_parameter("axis", axis)
+ elif axis in xrange(0,3) :
+ vfield = "velocity_%s" % (vlist[axis])
+ proj1.set_field_parameter("axis", vlist[axis])
+ proj1 = pf.h.proj(axis, "TempkeV", weight_field="Density")
+ proj2 = pf.h.proj(axis, "Density")
+ frb1 = proj1.to_frb(width, nx)
+ frb2 = proj2.to_frb(width, ny)
+
TeSZ = frb1["TempkeV"]
omega1 = frb1["Tsquared"]/(TeSZ*TeSZ) - 1.
sigma1 = frb1["TBetaPar"]/TeSZ - betac_par
diff -r 4f749ff7384491a1da1a0396ccd16134654f8412 -r 7b35c3296567868aaffcde67a574f5e28b797785 yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -117,3 +117,5 @@
from .two_point_functions.api import \
TwoPointFunctions, \
FcnSet
+
+from .SZmaps import SZprojection
https://bitbucket.org/yt_analysis/yt-3.0/commits/6f00933abb02/
Changeset: 6f00933abb02
Branch: yt
User: jzuhone
Date: 2013-05-28 15:16:49
Summary: Merging
Affected #: 45 files
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -32,6 +32,7 @@
yt/utilities/lib/GridTree.c
yt/utilities/lib/marching_cubes.c
yt/utilities/lib/png_writer.h
+yt/utilities/lib/write_array.c
syntax: glob
*.pyc
.*.swp
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -565,7 +565,7 @@
then
sed -i.bak 's/soname/install_name/' Makefile-libbz2_so
else
- sed -i.bak -e 's/soname/install_name/' -e "s/CC=gcc/CC=${CC}/" Makefile-libbz2_so
+ sed -i.bak -e 's/soname/install_name/' -e "s|CC=gcc|CC=${CC}|" Makefile-libbz2_so
fi
fi
( make install CFLAGS=-fPIC LDFLAGS=-fPIC PREFIX=${DEST_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -119,3 +119,7 @@
FcnSet
from .SZmaps import SZprojection
+
+from .radmc3d_export.api import \
+ RadMC3DWriter
+
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
--- a/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
+++ b/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
@@ -108,6 +108,7 @@
self.minimum_coherent_box_fraction = minimum_coherent_box_fraction
self.light_ray_solution = []
+ self.halo_lists = {}
self._data = {}
# Get list of datasets for light ray solution.
@@ -192,6 +193,7 @@
get_los_velocity=False,
get_nearest_halo=False,
nearest_halo_fields=None,
+ halo_list_file=None,
halo_profiler_parameters=None,
njobs=1, dynamic=False):
"""
@@ -229,6 +231,10 @@
A list of fields to be calculated for the halos nearest to
every lixel in the ray.
Default: None.
+ halo_list_file : str
+ Filename containing a list of halo properties to be used
+ for getting the nearest halos to absorbers.
+ Default: None.
halo_profiler_parameters: dict
A dictionary of parameters to be passed to the HaloProfiler
to create the appropriate data used to get properties for
@@ -287,7 +293,7 @@
>>> # Make the profiles.
>>> halo_profiler_actions.append({'function': make_profiles,
... 'args': None,
- ... 'kwargs': {'filename': 'VirializedHalos.out'}})
+ ... 'kwargs': {'filename': 'VirializedHalos.h5'}})
...
>>> halo_list = 'filtered'
>>> halo_profiler_parameters = dict(halo_profiler_kwargs=halo_profiler_kwargs,
@@ -305,6 +311,7 @@
... get_nearest_halo=True,
... nearest_halo_fields=['TotalMassMsun_100',
... 'RadiusMpc_100'],
+ ... halo_list_file='VirializedHalos.h5',
... halo_profiler_parameters=halo_profiler_parameters,
... get_los_velocity=True)
@@ -321,17 +328,18 @@
# Initialize data structures.
self._data = {}
if fields is None: fields = []
- all_fields = [field for field in fields]
+ data_fields = fields[:]
+ all_fields = fields[:]
all_fields.extend(['dl', 'dredshift', 'redshift'])
if get_nearest_halo:
all_fields.extend(['x', 'y', 'z', 'nearest_halo'])
all_fields.extend(['nearest_halo_%s' % field \
for field in nearest_halo_fields])
- fields.extend(['x', 'y', 'z'])
+ data_fields.extend(['x', 'y', 'z'])
if get_los_velocity:
all_fields.extend(['x-velocity', 'y-velocity',
'z-velocity', 'los_velocity'])
- fields.extend(['x-velocity', 'y-velocity', 'z-velocity'])
+ data_fields.extend(['x-velocity', 'y-velocity', 'z-velocity'])
all_ray_storage = {}
for my_storage, my_segment in parallel_objects(self.light_ray_solution,
@@ -348,10 +356,6 @@
(my_segment['redshift'], my_segment['start'],
my_segment['end']))
- if get_nearest_halo:
- halo_list = self._get_halo_list(my_segment['filename'],
- **halo_profiler_parameters)
-
# Load dataset for segment.
pf = load(my_segment['filename'])
@@ -373,7 +377,7 @@
(sub_ray['dts'] *
vector_length(sub_segment[0],
sub_segment[1]))])
- for field in fields:
+ for field in data_fields:
sub_data[field] = np.concatenate([sub_data[field],
(sub_ray[field])])
@@ -400,6 +404,9 @@
# Calculate distance to nearest object on halo list for each lixel.
if get_nearest_halo:
+ halo_list = self._get_halo_list(pf, fields=nearest_halo_fields,
+ filename=halo_list_file,
+ **halo_profiler_parameters)
sub_data.update(self._get_nearest_halo_properties(sub_data, halo_list,
fields=nearest_halo_fields))
sub_data['nearest_halo'] *= pf.units['mpccm']
@@ -434,58 +441,92 @@
self._data = all_data
return all_data
- def _get_halo_list(self, dataset, halo_profiler_kwargs=None,
+ def _get_halo_list(self, pf, fields=None, filename=None,
+ halo_profiler_kwargs=None,
halo_profiler_actions=None, halo_list='all'):
- "Load a list of halos for the dataset."
+ "Load a list of halos for the pf."
+
+ if str(pf) in self.halo_lists:
+ return self.halo_lists[str(pf)]
+
+ if fields is None: fields = []
+
+ if filename is not None and \
+ os.path.exists(os.path.join(pf.fullpath, filename)):
+
+ my_filename = os.path.join(pf.fullpath, filename)
+ mylog.info("Loading halo list from %s." % my_filename)
+ my_list = {}
+ in_file = h5py.File(my_filename, 'r')
+ for field in fields + ['center']:
+ my_list[field] = in_file[field][:]
+ in_file.close()
+
+ else:
+ my_list = self._halo_profiler_list(pf, fields=fields,
+ halo_profiler_kwargs=halo_profiler_kwargs,
+ halo_profiler_actions=halo_profiler_actions,
+ halo_list=halo_list)
+
+ self.halo_lists[str(pf)] = my_list
+ return self.halo_lists[str(pf)]
+
+ def _halo_profiler_list(self, pf, fields=None,
+ halo_profiler_kwargs=None,
+ halo_profiler_actions=None, halo_list='all'):
+ "Run the HaloProfiler to get the halo list."
if halo_profiler_kwargs is None: halo_profiler_kwargs = {}
if halo_profiler_actions is None: halo_profiler_actions = []
- hp = HaloProfiler(dataset, **halo_profiler_kwargs)
+ hp = HaloProfiler(pf, **halo_profiler_kwargs)
for action in halo_profiler_actions:
if not action.has_key('args'): action['args'] = ()
if not action.has_key('kwargs'): action['kwargs'] = {}
action['function'](hp, *action['args'], **action['kwargs'])
if halo_list == 'all':
- return_list = copy.deepcopy(hp.all_halos)
+ hp_list = copy.deepcopy(hp.all_halos)
elif halo_list == 'filtered':
- return_list = copy.deepcopy(hp.filtered_halos)
+ hp_list = copy.deepcopy(hp.filtered_halos)
else:
mylog.error("Keyword, halo_list, must be either 'all' or 'filtered'.")
- return_list = None
+ hp_list = None
del hp
+
+ # Create position array from halo list.
+ return_list = dict([(field, []) for field in fields + ['center']])
+ for halo in hp_list:
+ for field in fields + ['center']:
+ return_list[field].append(halo[field])
+ for field in fields + ['center']:
+ return_list[field] = np.array(return_list[field])
return return_list
-
+
def _get_nearest_halo_properties(self, data, halo_list, fields=None):
"""
Calculate distance to nearest object in halo list for each lixel in data.
- Return list of distances and masses of nearest objects.
+ Return list of distances and other properties of nearest objects.
"""
if fields is None: fields = []
+ field_data = dict([(field, np.zeros_like(data['x'])) \
+ for field in fields])
+ nearest_distance = np.zeros_like(data['x'])
- # Create position array from halo list.
- halo_centers = np.array(map(lambda halo: halo['center'], halo_list))
- halo_field_values = dict([(field, np.array(map(lambda halo: halo[field],
- halo_list))) \
- for field in fields])
-
- nearest_distance = np.zeros(data['x'].shape)
- field_data = dict([(field, np.zeros(data['x'].shape)) \
- for field in fields])
- for index in xrange(nearest_distance.size):
- nearest = np.argmin(periodic_distance(np.array([data['x'][index],
- data['y'][index],
- data['z'][index]]),
- halo_centers))
- nearest_distance[index] = periodic_distance(np.array([data['x'][index],
- data['y'][index],
- data['z'][index]]),
- halo_centers[nearest])
- for field in fields:
- field_data[field][index] = halo_field_values[field][nearest]
+ if halo_list['center'].size > 0:
+ for index in xrange(nearest_distance.size):
+ nearest = np.argmin(periodic_distance(np.array([data['x'][index],
+ data['y'][index],
+ data['z'][index]]),
+ halo_list['center']))
+ nearest_distance[index] = periodic_distance(np.array([data['x'][index],
+ data['y'][index],
+ data['z'][index]]),
+ halo_list['center'][nearest])
+ for field in fields:
+ field_data[field][index] = halo_list[field][nearest]
return_data = {'nearest_halo': nearest_distance}
for field in fields:
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -1062,7 +1062,7 @@
def __init__(self, data_source, dm_only=True, redshift=-1):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is set, only run it on the dark matter particles, otherwise
+ *dm_only* is True (default), only run it on the dark matter particles, otherwise
on all particles. Returns an iterable collection of *HopGroup* items.
"""
self._data_source = data_source
@@ -1097,7 +1097,7 @@
def _get_dm_indices(self):
if 'creation_time' in self._data_source.hierarchy.field_list:
mylog.debug("Differentiating based on creation time")
- return (self._data_source["creation_time"] < 0)
+ return (self._data_source["creation_time"] <= 0)
elif 'particle_type' in self._data_source.hierarchy.field_list:
mylog.debug("Differentiating based on particle type")
return (self._data_source["particle_type"] == 1)
@@ -1458,7 +1458,7 @@
class HOPHaloList(HaloList):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is set, only run it on the dark matter particles, otherwise
+ *dm_only* is True (default), only run it on the dark matter particles, otherwise
on all particles. Returns an iterable collection of *HopGroup* items.
"""
_name = "HOP"
@@ -1657,7 +1657,7 @@
class parallelHOPHaloList(HaloList, ParallelAnalysisInterface):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is set, only run it on the dark matter particles, otherwise
+ *dm_only* is True (default), only run it on the dark matter particles, otherwise
on all particles. Returns an iterable collection of *HopGroup* items.
"""
_name = "parallelHOP"
@@ -2009,13 +2009,11 @@
--------
>>> halos.write_out("HopAnalysis.out")
"""
- # if path denoted in filename, assure path exists
- if len(filename.split('/')) > 1:
- mkdir_rec('/'.join(filename.split('/')[:-1]))
-
+ ensure_dir_exists(filename)
f = self.comm.write_on_root(filename)
HaloList.write_out(self, f, ellipsoid_data)
+
def write_particle_lists_txt(self, prefix):
r"""Write out the names of the HDF5 files containing halo particle data
to a text file.
@@ -2032,13 +2030,11 @@
--------
>>> halos.write_particle_lists_txt("halo-parts")
"""
- # if path denoted in prefix, assure path exists
- if len(prefix.split('/')) > 1:
- mkdir_rec('/'.join(prefix.split('/')[:-1]))
-
+ ensure_dir_exists(prefix)
f = self.comm.write_on_root("%s.txt" % prefix)
HaloList.write_particle_lists_txt(self, prefix, fp=f)
+
@parallel_blocking_call
def write_particle_lists(self, prefix):
r"""Write out the particle data for halos to HDF5 files.
@@ -2059,10 +2055,7 @@
--------
>>> halos.write_particle_lists("halo-parts")
"""
- # if path denoted in prefix, assure path exists
- if len(prefix.split('/')) > 1:
- mkdir_rec('/'.join(prefix.split('/')[:-1]))
-
+ ensure_dir_exists(prefix)
fn = "%s.h5" % self.comm.get_filename(prefix)
f = h5py.File(fn, "w")
for halo in self._groups:
@@ -2091,15 +2084,12 @@
ellipsoid_data : bool.
Whether to save the ellipsoidal information to the files.
Default = False.
-
+
Examples
--------
>>> halos.dump("MyHalos")
"""
- # if path denoted in basename, assure path exists
- if len(basename.split('/')) > 1:
- mkdir_rec('/'.join(basename.split('/')[:-1]))
-
+ ensure_dir_exists(basename)
self.write_out("%s.out" % basename, ellipsoid_data)
self.write_particle_lists(basename)
self.write_particle_lists_txt(basename)
@@ -2132,7 +2122,7 @@
The density threshold used when building halos. Default = 160.0.
dm_only : bool
If True, only dark matter particles are used when building halos.
- Default = False.
+ Default = True.
resize : bool
Turns load-balancing on or off. Default = True.
kdtree : string
@@ -2461,7 +2451,7 @@
The density threshold used when building halos. Default = 160.0.
dm_only : bool
If True, only dark matter particles are used when building halos.
- Default = False.
+ Default = True.
padding : float
When run in parallel, the finder needs to surround each subvolume
with duplicated particles for halo finidng to work. This number
@@ -2566,7 +2556,7 @@
applied. Default = 0.2.
dm_only : bool
If True, only dark matter particles are used when building halos.
- Default = False.
+ Default = True.
padding : float
When run in parallel, the finder needs to surround each subvolume
with duplicated particles for halo finidng to work. This number
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/halo_finding/rockstar/rockstar.py
--- a/yt/analysis_modules/halo_finding/rockstar/rockstar.py
+++ b/yt/analysis_modules/halo_finding/rockstar/rockstar.py
@@ -338,6 +338,8 @@
hires_only = (self.hires_dm_mass is not None),
**kwargs)
# Make the directory to store the halo lists in.
+ if not self.outbase:
+ self.outbase = os.getcwd()
if self.comm.rank == 0:
if not os.path.exists(self.outbase):
os.makedirs(self.outbase)
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/halo_profiler/halo_filters.py
--- a/yt/analysis_modules/halo_profiler/halo_filters.py
+++ b/yt/analysis_modules/halo_profiler/halo_filters.py
@@ -105,7 +105,8 @@
if use_log:
for field in temp_profile.keys():
- temp_profile[field] = np.log10(temp_profile[field])
+ temp_profile[field] = np.log10(np.clip(temp_profile[field], 1e-90,
+ max(temp_profile[field])))
virial = dict((field, 0.0) for field in fields)
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/halo_profiler/multi_halo_profiler.py
--- a/yt/analysis_modules/halo_profiler/multi_halo_profiler.py
+++ b/yt/analysis_modules/halo_profiler/multi_halo_profiler.py
@@ -23,6 +23,7 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+import gc
import numpy as np
import os
import h5py
@@ -583,7 +584,7 @@
r_min = 2 * self.pf.h.get_smallest_dx() * self.pf['mpc']
if (halo['r_max'] / r_min < PROFILE_RADIUS_THRESHOLD):
- mylog.error("Skipping halo with r_max / r_min = %f." % (halo['r_max']/r_min))
+ mylog.debug("Skipping halo with r_max / r_min = %f." % (halo['r_max']/r_min))
return None
# get a sphere object to profile
@@ -630,6 +631,10 @@
g.clear_data()
sphere.clear_data()
del sphere
+ # Currently, this seems to be the only way to prevent large
+ # halo profiling runs from running out of ram.
+ # It would be good to track down the real cause at some point.
+ gc.collect()
return profile
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/halo_profiler/standard_analysis.py
--- a/yt/analysis_modules/halo_profiler/standard_analysis.py
+++ b/yt/analysis_modules/halo_profiler/standard_analysis.py
@@ -68,8 +68,10 @@
self.prof = prof
def plot_everything(self, dirname = None):
- if dirname is None: dirname = "%s_profile_plots/" % (self.pf)
- if not os.path.isdir(dirname): os.makedirs(dirname)
+ if not dirname:
+ dirname = "%s_profile_plots/" % (self.pf)
+ if not os.path.isdir(dirname):
+ os.makedirs(dirname)
import matplotlib; matplotlib.use("Agg")
import pylab
for field in self.prof.keys():
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/radmc3d_export/RadMC3DInterface.py
--- /dev/null
+++ b/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py
@@ -0,0 +1,334 @@
+"""
+Code to export from yt to RadMC3D
+
+Author: Andrew Myers <atmyers2 at gmail.com>
+Affiliation: UCB
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2013 Andrew Myers. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+"""
+
+from yt.mods import *
+from yt.utilities.lib.write_array import \
+ write_3D_array, write_3D_vector_array
+
+class RadMC3DLayer:
+ '''
+
+ This class represents an AMR "layer" of the style described in
+ the radmc3d manual. Unlike yt grids, layers may not have more
+ than one parent, so level L grids will need to be split up
+ if they straddle two or more level L - 1 grids.
+
+ '''
+ def __init__(self, level, parent, unique_id, LE, RE, dim):
+ self.level = level
+ self.parent = parent
+ self.LeftEdge = LE
+ self.RightEdge = RE
+ self.ActiveDimensions = dim
+ self.id = unique_id
+
+ def get_overlap_with(self, grid):
+ '''
+
+ Returns the overlapping region between two Layers,
+ or a layer and a grid. RE < LE means in any direction
+ means no overlap.
+
+ '''
+ LE = np.maximum(self.LeftEdge, grid.LeftEdge)
+ RE = np.minimum(self.RightEdge, grid.RightEdge)
+ return LE, RE
+
+ def overlaps(self, grid):
+ '''
+
+ Returns whether or not this layer overlaps a given grid
+
+ '''
+ LE, RE = self.get_overlap_with(grid)
+ if np.any(RE <= LE):
+ return False
+ else:
+ return True
+
+class RadMC3DWriter:
+ '''
+
+ This class provides a mechanism for writing out data files in a format
+ readable by radmc3d. Currently, only the ASCII, "Layer" style file format
+ is supported. For more information please see the radmc3d manual at:
+ http://www.ita.uni-heidelberg.de/~dullemond/software/radmc-3d
+
+ Parameters
+ ----------
+
+ pf : `StaticOutput`
+ This is the parameter file object corresponding to the
+ simulation output to be written out.
+
+ max_level : int
+ An int corresponding to the maximum number of levels of refinement
+ to include in the output. Often, this does not need to be very large
+ as information on very high levels is frequently unobservable.
+ Default = 2.
+
+ Examples
+ --------
+
+ This will create a field called "DustDensity" and write it out to the
+ file "dust_density.inp" in a form readable by radmc3d. It will also write
+ a "dust_temperature.inp" file with everything set to 10.0 K:
+
+ >>> from yt.mods import *
+ >>> from yt.analysis_modules.radmc3d_export.api import *
+
+ >>> dust_to_gas = 0.01
+ >>> def _DustDensity(field, data):
+ ... return dust_to_gas*data["Density"]
+ >>> add_field("DustDensity", function=_DustDensity)
+
+ >>> def _DustTemperature(field, data):
+ ... return 10.0*data["Ones"]
+ >>> add_field("DustTemperature", function=_DustTemperature)
+
+ >>> pf = load("galaxy0030/galaxy0030")
+ >>> writer = RadMC3DWriter(pf)
+
+ >>> writer.write_amr_grid()
+ >>> writer.write_dust_file("DustDensity", "dust_density.inp")
+ >>> writer.write_dust_file("DustTemperature", "dust_temperature.inp")
+
+ This will create a field called "NumberDensityCO" and write it out to
+ the file "numberdens_co.inp". It will also write out information about
+ the gas velocity to "gas_velocity.inp" so that this broadening may be
+ included in the radiative transfer calculation by radmc3d:
+
+ >>> from yt.mods import *
+ >>> from yt.analysis_modules.radmc3d_export.api import *
+
+ >>> x_co = 1.0e-4
+ >>> mu_h = 2.34e-24
+ >>> def _NumberDensityCO(field, data):
+ ... return (x_co/mu_h)*data["Density"]
+ >>> add_field("NumberDensityCO", function=_NumberDensityCO)
+
+ >>> pf = load("galaxy0030/galaxy0030")
+ >>> writer = RadMC3DWriter(pf)
+
+ >>> writer.write_amr_grid()
+ >>> writer.write_line_file("NumberDensityCO", "numberdens_co.inp")
+ >>> velocity_fields = ["x-velocity", "y-velocity", "z-velocity"]
+ >>> writer.write_line_file(velocity_fields, "gas_velocity.inp")
+
+ '''
+
+ def __init__(self, pf, max_level=2):
+ self.max_level = max_level
+ self.cell_count = 0
+ self.layers = []
+ self.domain_dimensions = pf.domain_dimensions
+ self.domain_left_edge = pf.domain_left_edge
+ self.domain_right_edge = pf.domain_right_edge
+ self.grid_filename = "amr_grid.inp"
+ self.pf = pf
+
+ base_layer = RadMC3DLayer(0, None, 0, \
+ self.domain_left_edge, \
+ self.domain_right_edge, \
+ self.domain_dimensions)
+
+ self.layers.append(base_layer)
+ self.cell_count += np.product(pf.domain_dimensions)
+
+ for grid in pf.h.grids:
+ if grid.Level <= self.max_level:
+ self._add_grid_to_layers(grid)
+
+ def _get_parents(self, grid):
+ parents = []
+ for potential_parent in self.layers:
+ if potential_parent.level == grid.Level - 1:
+ if potential_parent.overlaps(grid):
+ parents.append(potential_parent)
+ return parents
+
+ def _add_grid_to_layers(self, grid):
+ parents = self._get_parents(grid)
+ for parent in parents:
+ LE, RE = parent.get_overlap_with(grid)
+ N = (RE - LE) / grid.dds
+ N = np.array([int(n + 0.5) for n in N])
+ new_layer = RadMC3DLayer(grid.Level, parent.id, \
+ len(self.layers), \
+ LE, RE, N)
+ self.layers.append(new_layer)
+ self.cell_count += np.product(N)
+
+ def write_amr_grid(self):
+ '''
+ This routine writes the "amr_grid.inp" file that describes the mesh
+ radmc3d will use.
+
+ '''
+ dims = self.domain_dimensions
+ LE = self.domain_left_edge
+ RE = self.domain_right_edge
+
+ # calculate cell wall positions
+ xs = [str(x) for x in np.linspace(LE[0], RE[0], dims[0]+1)]
+ ys = [str(y) for y in np.linspace(LE[1], RE[1], dims[1]+1)]
+ zs = [str(z) for z in np.linspace(LE[2], RE[2], dims[2]+1)]
+
+ # writer file header
+ grid_file = open(self.grid_filename, 'w')
+ grid_file.write('1 \n') # iformat is always 1
+ if self.max_level == 0:
+ grid_file.write('0 \n')
+ else:
+ grid_file.write('10 \n') # only layer-style AMR files are supported
+ grid_file.write('1 \n') # only cartesian coordinates are supported
+ grid_file.write('0 \n')
+ grid_file.write('{} {} {} \n'.format(1, 1, 1)) # assume 3D
+ grid_file.write('{} {} {} \n'.format(dims[0], dims[1], dims[2]))
+ if self.max_level != 0:
+ s = str(self.max_level) + ' ' + str(len(self.layers)-1) + '\n'
+ grid_file.write(s)
+
+ # write base grid cell wall positions
+ for x in xs:
+ grid_file.write(x + ' ')
+ grid_file.write('\n')
+
+ for y in ys:
+ grid_file.write(y + ' ')
+ grid_file.write('\n')
+
+ for z in zs:
+ grid_file.write(z + ' ')
+ grid_file.write('\n')
+
+ # write information about fine layers, skipping the base layer:
+ for layer in self.layers[1:]:
+ p = layer.parent
+ dds = (layer.RightEdge - layer.LeftEdge) / (layer.ActiveDimensions)
+ if p == 0:
+ ind = (layer.LeftEdge - LE) / (2.0*dds) + 1
+ else:
+ LE = np.zeros(3)
+ for potential_parent in self.layers:
+ if potential_parent.id == p:
+ LE = potential_parent.LeftEdge
+ ind = (layer.LeftEdge - LE) / (2.0*dds) + 1
+ ix = int(ind[0]+0.5)
+ iy = int(ind[1]+0.5)
+ iz = int(ind[2]+0.5)
+ nx, ny, nz = layer.ActiveDimensions / 2
+ s = '{} {} {} {} {} {} {} \n'
+ s = s.format(p, ix, iy, iz, nx, ny, nz)
+ grid_file.write(s)
+
+ grid_file.close()
+
+ def _write_layer_data_to_file(self, fhandle, field, level, LE, dim):
+ cg = self.pf.h.covering_grid(level, LE, dim, num_ghost_zones=1)
+ if isinstance(field, list):
+ data_x = cg[field[0]]
+ data_y = cg[field[1]]
+ data_z = cg[field[2]]
+ write_3D_vector_array(data_x, data_y, data_z, fhandle)
+ else:
+ data = cg[field]
+ write_3D_array(data, fhandle)
+
+ def write_dust_file(self, field, filename):
+ '''
+ This method writes out fields in the format radmc3d needs to compute
+ thermal dust emission. In particular, if you have a field called
+ "DustDensity", you can write out a dust_density.inp file.
+
+ Parameters
+ ----------
+
+ field : string
+ The name of the field to be written out
+ filename : string
+ The name of the file to write the data to. The filenames radmc3d
+ expects for its various modes of operations are described in the
+ radmc3d manual.
+
+ '''
+ fhandle = open(filename, 'w')
+
+ # write header
+ fhandle.write('1 \n')
+ fhandle.write(str(self.cell_count) + ' \n')
+ fhandle.write('1 \n')
+
+ # now write fine layers:
+ for layer in self.layers:
+ lev = layer.level
+ if lev == 0:
+ LE = self.domain_left_edge
+ N = self.domain_dimensions
+ else:
+ LE = layer.LeftEdge
+ N = layer.ActiveDimensions
+
+ self._write_layer_data_to_file(fhandle, field, lev, LE, N)
+
+ fhandle.close()
+
+ def write_line_file(self, field, filename):
+ '''
+ This method writes out fields in the format radmc3d needs to compute
+ line emission.
+
+ Parameters
+ ----------
+
+ field : string or list of 3 strings
+ If a string, the name of the field to be written out. If a list,
+ three fields that will be written to the file as a vector quantity.
+ filename : string
+ The name of the file to write the data to. The filenames radmc3d
+ expects for its various modes of operation are described in the
+ radmc3d manual.
+
+ '''
+ fhandle = open(filename, 'w')
+
+ # write header
+ fhandle.write('1 \n')
+ fhandle.write(str(self.cell_count) + ' \n')
+
+ # now write fine layers:
+ for layer in self.layers:
+ lev = layer.level
+ if lev == 0:
+ LE = self.domain_left_edge
+ N = self.domain_dimensions
+ else:
+ LE = layer.LeftEdge
+ N = layer.ActiveDimensions
+
+ self._write_layer_data_to_file(fhandle, field, lev, LE, N)
+
+ fhandle.close()
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/radmc3d_export/api.py
--- /dev/null
+++ b/yt/analysis_modules/radmc3d_export/api.py
@@ -0,0 +1,30 @@
+"""
+API for RadMC3D Export code
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: UCSD
+Author: Andrew Myers <atmyers2 at gmail.com>
+Affiliation: UCB
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+"""
+
+from .RadMC3DInterface import \
+ RadMC3DWriter
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/analysis_modules/setup.py
--- a/yt/analysis_modules/setup.py
+++ b/yt/analysis_modules/setup.py
@@ -20,4 +20,5 @@
config.add_subpackage("spectral_integrator")
config.add_subpackage("star_analysis")
config.add_subpackage("two_point_functions")
+ config.add_subpackage("radmc3d_export")
return config
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/config.py
--- a/yt/config.py
+++ b/yt/config.py
@@ -62,7 +62,7 @@
notebook_password = '',
answer_testing_tolerance = '3',
answer_testing_bitwise = 'False',
- gold_standard_filename = 'gold007',
+ gold_standard_filename = 'gold008',
local_standard_filename = 'local001',
sketchfab_api_key = 'None'
)
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -4080,7 +4080,7 @@
if region in ["OR", "AND", "NOT", "(", ")"]:
s += region
else:
- s += region.__repr__(clean = True)
+ s += region.__repr__()
if i < (len(self.regions) - 1): s += ", "
s += "]"
return s
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/data_objects/field_info_container.py
--- a/yt/data_objects/field_info_container.py
+++ b/yt/data_objects/field_info_container.py
@@ -271,12 +271,14 @@
else: self[item] = vv.ravel()
return self[item]
self.requested.append(item)
- return defaultdict.__missing__(self, item)
+ if item not in self:
+ self[item] = self._read_data(item)
+ return self[item]
def _read_data(self, field_name):
self.requested.append(field_name)
FI = getattr(self.pf, "field_info", FieldInfo)
- if FI.has_key(field_name) and FI[field_name].particle_type:
+ if field_name in FI and FI[field_name].particle_type:
self.requested.append(field_name)
return np.ones(self.NumberOfParticles)
return defaultdict.__missing__(self, field_name)
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -165,7 +165,7 @@
def get_smallest_appropriate_unit(self, v):
max_nu = 1e30
good_u = None
- for unit in ['mpc', 'kpc', 'pc', 'au', 'rsun', 'cm']:
+ for unit in ['mpc', 'kpc', 'pc', 'au', 'rsun', 'km', 'cm']:
vv = v*self[unit]
if vv < max_nu and vv > 1.0:
good_u = unit
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -44,7 +44,8 @@
NeedsOriginalGrid, \
NeedsDataField, \
NeedsProperty, \
- NeedsParameter
+ NeedsParameter, \
+ NullFunc
from yt.utilities.physical_constants import \
mh, \
@@ -440,7 +441,7 @@
convert_function=_convertCellMassCode)
def _TotalMass(field,data):
- return (data["Density"]+data["Dark_Matter_Density"]) * data["CellVolume"]
+ return (data["Density"]+data["particle_density"]) * data["CellVolume"]
add_field("TotalMass", function=_TotalMass, units=r"\rm{g}")
add_field("TotalMassMsun", units=r"M_{\odot}",
function=_TotalMass,
@@ -453,7 +454,7 @@
convert_function=_convertCellMassMsun)
def _Matter_Density(field,data):
- return (data['Density'] + data['Dark_Matter_Density'])
+ return (data['Density'] + data['particle_density'])
add_field("Matter_Density",function=_Matter_Density,units=r"\rm{g}/\rm{cm^3}")
def _ComovingDensity(field, data):
@@ -982,22 +983,29 @@
add_field("JeansMassMsun",function=_JeansMassMsun,
units=r"\rm{M_{\odot}}")
-def _convertDensity(data):
- return data.convert("Density")
+# We add these fields so that the field detector can use them
+for field in ["particle_position_%s" % ax for ax in "xyz"] + \
+ ["ParticleMass"]:
+ # This marker should let everyone know not to use the fields, but NullFunc
+ # should do that, too.
+ add_field(field, function=NullFunc, particle_type = True,
+ units=r"UNDEFINED")
+
def _pdensity(field, data):
- blank = np.zeros(data.ActiveDimensions, dtype='float32')
+ blank = np.zeros(data.ActiveDimensions, dtype='float64')
if data["particle_position_x"].size == 0: return blank
CICDeposit_3(data["particle_position_x"].astype(np.float64),
data["particle_position_y"].astype(np.float64),
data["particle_position_z"].astype(np.float64),
- data["particle_mass"].astype(np.float32),
+ data["ParticleMass"],
data["particle_position_x"].size,
blank, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
np.float64(data['dx']))
+ np.divide(blank, data["CellVolume"], blank)
return blank
add_field("particle_density", function=_pdensity,
- validators=[ValidateGridType()], convert_function=_convertDensity,
+ validators=[ValidateGridType()],
display_name=r"\mathrm{Particle}\/\mathrm{Density}")
def _MagneticEnergy(field,data):
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/frontends/art/fields.py
--- a/yt/frontends/art/fields.py
+++ b/yt/frontends/art/fields.py
@@ -280,12 +280,12 @@
projection_conversion="1")
def _spdensity(field, data):
- grid_mass = np.zeros(data.ActiveDimensions, dtype='float32')
+ grid_mass = np.zeros(data.ActiveDimensions, dtype='float64')
if data.star_mass.shape[0] ==0 : return grid_mass
amr_utils.CICDeposit_3(data.star_position_x,
data.star_position_y,
data.star_position_z,
- data.star_mass.astype('float32'),
+ data.star_mass,
data.star_mass.shape[0],
grid_mass,
np.array(data.LeftEdge).astype(np.float64),
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/frontends/enzo/data_structures.py
--- a/yt/frontends/enzo/data_structures.py
+++ b/yt/frontends/enzo/data_structures.py
@@ -105,6 +105,9 @@
"""
Intelligently set the filename.
"""
+ if filename is None:
+ self.filename = filename
+ return
if self.hierarchy._strip_path:
self.filename = os.path.join(self.hierarchy.directory,
os.path.basename(filename))
@@ -302,7 +305,7 @@
LE.append(_next_token_line("GridLeftEdge", f))
RE.append(_next_token_line("GridRightEdge", f))
nb = int(_next_token_line("NumberOfBaryonFields", f)[0])
- fn.append(["-1"])
+ fn.append([None])
if nb > 0: fn[-1] = _next_token_line("BaryonFileName", f)
npart.append(int(_next_token_line("NumberOfParticles", f)[0]))
if nb == 0 and npart[-1] > 0: fn[-1] = _next_token_line("ParticleFileName", f)
@@ -373,6 +376,7 @@
giter = izip(grids, levels, procs, parents)
bn = self._bn % (self.pf)
pmap = [(bn % P,) for P in xrange(procs.max()+1)]
+ pmap.append((None, )) # Now, P==-1 will give None
for grid,L,P,Pid in giter:
grid.Level = L
grid._parent_id = Pid
@@ -405,7 +409,10 @@
parents.append(g.Parent.id)
else:
parents.append(-1)
- procs.append(int(self.filenames[i][0][-4:]))
+ if self.filenames[i][0] is None:
+ procs.append(-1)
+ else:
+ procs.append(int(self.filenames[i][0][-4:]))
levels.append(g.Level)
parents = np.array(parents, dtype='int64')
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/frontends/enzo/fields.py
--- a/yt/frontends/enzo/fields.py
+++ b/yt/frontends/enzo/fields.py
@@ -352,14 +352,14 @@
f.take_log = False
def _spdensity(field, data):
- blank = np.zeros(data.ActiveDimensions, dtype='float32')
+ blank = np.zeros(data.ActiveDimensions, dtype='float64')
if data["particle_position_x"].size == 0: return blank
filter = data['creation_time'] > 0.0
if not filter.any(): return blank
amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(np.float64),
data["particle_position_y"][filter].astype(np.float64),
data["particle_position_z"][filter].astype(np.float64),
- data["particle_mass"][filter].astype(np.float32),
+ data["particle_mass"][filter],
np.int64(np.where(filter)[0].size),
blank, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
@@ -369,7 +369,7 @@
validators=[ValidateSpatial(0)], convert_function=_convertDensity)
def _dmpdensity(field, data):
- blank = np.zeros(data.ActiveDimensions, dtype='float32')
+ blank = np.zeros(data.ActiveDimensions, dtype='float64')
if data["particle_position_x"].size == 0: return blank
if 'creation_time' in data.pf.field_info:
filter = data['creation_time'] <= 0.0
@@ -381,7 +381,7 @@
amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(np.float64),
data["particle_position_y"][filter].astype(np.float64),
data["particle_position_z"][filter].astype(np.float64),
- data["particle_mass"][filter].astype(np.float32),
+ data["particle_mass"][filter],
num,
blank, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
@@ -396,24 +396,24 @@
using cloud-in-cell deposit.
"""
particle_field = field.name[4:]
- top = np.zeros(data.ActiveDimensions, dtype='float32')
+ top = np.zeros(data.ActiveDimensions, dtype='float64')
if data["particle_position_x"].size == 0: return top
particle_field_data = data[particle_field] * data['particle_mass']
amr_utils.CICDeposit_3(data["particle_position_x"].astype(np.float64),
data["particle_position_y"].astype(np.float64),
data["particle_position_z"].astype(np.float64),
- particle_field_data.astype(np.float32),
+ particle_field_data,
data["particle_position_x"].size,
top, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
np.float64(data['dx']))
del particle_field_data
- bottom = np.zeros(data.ActiveDimensions, dtype='float32')
+ bottom = np.zeros(data.ActiveDimensions, dtype='float64')
amr_utils.CICDeposit_3(data["particle_position_x"].astype(np.float64),
data["particle_position_y"].astype(np.float64),
data["particle_position_z"].astype(np.float64),
- data["particle_mass"].astype(np.float32),
+ data["particle_mass"],
data["particle_position_x"].size,
bottom, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
@@ -435,7 +435,7 @@
Create a grid field for star quantities, weighted by star mass.
"""
particle_field = field.name[5:]
- top = np.zeros(data.ActiveDimensions, dtype='float32')
+ top = np.zeros(data.ActiveDimensions, dtype='float64')
if data["particle_position_x"].size == 0: return top
filter = data['creation_time'] > 0.0
if not filter.any(): return top
@@ -443,18 +443,18 @@
amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(np.float64),
data["particle_position_y"][filter].astype(np.float64),
data["particle_position_z"][filter].astype(np.float64),
- particle_field_data.astype(np.float32),
+ particle_field_data,
np.int64(np.where(filter)[0].size),
top, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
np.float64(data['dx']))
del particle_field_data
- bottom = np.zeros(data.ActiveDimensions, dtype='float32')
+ bottom = np.zeros(data.ActiveDimensions, dtype='float64')
amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(np.float64),
data["particle_position_y"][filter].astype(np.float64),
data["particle_position_z"][filter].astype(np.float64),
- data["particle_mass"][filter].astype(np.float32),
+ data["particle_mass"][filter],
np.int64(np.where(filter)[0].size),
bottom, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -119,9 +119,13 @@
files_keys = defaultdict(lambda: [])
pf_field_list = grids[0].pf.h.field_list
sets = [dset for dset in list(sets) if dset in pf_field_list]
- for g in grids: files_keys[g.filename].append(g)
+ for g in grids:
+ files_keys[g.filename].append(g)
exc = self._read_exception
for file in files_keys:
+ # This is a funny business with Enzo files that are DM-only,
+ # where grids can have *no* data, but still exist.
+ if file is None: continue
mylog.debug("Starting read %s (%s)", file, sets)
nodes = [g.id for g in files_keys[file]]
nodes.sort()
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/frontends/flash/fields.py
--- a/yt/frontends/flash/fields.py
+++ b/yt/frontends/flash/fields.py
@@ -64,7 +64,6 @@
translation_dict = {"x-velocity": "velx",
"y-velocity": "vely",
"z-velocity": "velz",
- "VelocityMagnitude": "velo",
"Density": "dens",
"Temperature": "temp",
"Pressure" : "pres",
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/frontends/pluto/data_structures.py
--- a/yt/frontends/pluto/data_structures.py
+++ b/yt/frontends/pluto/data_structures.py
@@ -99,7 +99,7 @@
grid = PlutoGrid
- def __init__(self,pf,data_style='chombo_hdf5'):
+ def __init__(self,pf,data_style='pluto_hdf5'):
self.domain_left_edge = pf.domain_left_edge
self.domain_right_edge = pf.domain_right_edge
self.data_style = data_style
@@ -187,7 +187,7 @@
_fieldinfo_fallback = PlutoFieldInfo
_fieldinfo_known = KnownPlutoFields
- def __init__(self, filename, data_style='chombo_hdf5',
+ def __init__(self, filename, data_style='pluto_hdf5',
storage_filename = None, ini_filename = None):
self._handle = h5py.File(filename,'r')
self.current_time = self._handle.attrs['time']
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -603,17 +603,11 @@
suffix = os.path.splitext(name)[1]
return suffix if suffix in ['.png', '.eps', '.ps', '.pdf'] else ''
-def mkdir_rec(path):
- """
- Recursive mkdir, so that if you mkdir two levels deep and the first
- one doesn't exist, it creates the first, and then any subsequent dirs.
- Examples
- --------
- mkdir_rec("a/b/c")
- """
- dir_list = path.split("/")
- basedir = "."
- for dir in dir_list:
- basedir = "%s/%s" % (basedir, dir)
- if not os.path.isdir(basedir): os.mkdir(basedir)
+def ensure_dir_exists(path):
+ r"""Create all directories in path recursively in a parallel safe manner"""
+ my_dir = os.path.dirname(path)
+ if not my_dir:
+ return
+ if not os.path.exists(my_dir):
+ only_on_root(os.makedirs, my_dir)
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/gui/reason/widget_store.py
--- a/yt/gui/reason/widget_store.py
+++ b/yt/gui/reason/widget_store.py
@@ -76,7 +76,8 @@
sl = pf.h.slice(axis, coord, center = center, periodic = True)
xax, yax = x_dict[axis], y_dict[axis]
DLE, DRE = pf.domain_left_edge, pf.domain_right_edge
- pw = PWViewerExtJS(sl, (DLE[xax], DRE[xax], DLE[yax], DRE[yax]), setup = False)
+ pw = PWViewerExtJS(sl, (DLE[xax], DRE[xax], DLE[yax], DRE[yax]),
+ setup = False, plot_type='SlicePlot')
pw.set_current_field(field)
field_list = list(set(pf.h.field_list + pf.h.derived_field_list))
field_list = [dict(text = f) for f in sorted(field_list)]
@@ -96,7 +97,7 @@
xax, yax = x_dict[axis], y_dict[axis]
DLE, DRE = pf.domain_left_edge, pf.domain_right_edge
pw = PWViewerExtJS(proj, (DLE[xax], DRE[xax], DLE[yax], DRE[yax]),
- setup = False)
+ setup = False, plot_type='ProjectionPlot')
pw.set_current_field(field)
field_list = list(set(pf.h.field_list + pf.h.derived_field_list))
field_list = [dict(text = f) for f in sorted(field_list)]
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/startup_tasks.py
--- a/yt/startup_tasks.py
+++ b/yt/startup_tasks.py
@@ -142,8 +142,9 @@
elif exe_name in \
["mpi4py", "embed_enzo",
"python"+sys.version[:3]+"-mpi"] \
- or '_parallel' in dir(sys) \
- or any(["ipengine" in arg for arg in sys.argv]):
+ or '_parallel' in dir(sys) \
+ or any(["ipengine" in arg for arg in sys.argv]) \
+ or any(["cluster-id" in arg for arg in sys.argv]):
parallel_capable = turn_on_parallelism()
else:
parallel_capable = False
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -613,7 +613,7 @@
fns = ['old.png', 'new.png']
mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[0])))
mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[0])))
- compare_images(fns[0], fns[1], 10**(-self.decimals))
+ assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
for fn in fns: os.remove(fn)
def requires_pf(pf_fn, big_data = False):
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/command_line.py
--- a/yt/utilities/command_line.py
+++ b/yt/utilities/command_line.py
@@ -1327,7 +1327,7 @@
plt.set_log(args.field, args.takelog)
if args.zlim:
plt.set_zlim(args.field,*args.zlim)
- if not os.path.isdir(args.output): os.makedirs(args.output)
+ ensure_dir_exists(args.output)
plt.save(os.path.join(args.output,"%s" % (pf)))
class YTRenderCmd(YTCommand):
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/definitions.py
--- a/yt/utilities/definitions.py
+++ b/yt/utilities/definitions.py
@@ -27,8 +27,8 @@
from .physical_constants import \
mpc_per_mpc, kpc_per_mpc, pc_per_mpc, au_per_mpc, rsun_per_mpc, \
- miles_per_mpc, cm_per_mpc, sec_per_Gyr, sec_per_Myr, sec_per_year, \
- sec_per_day
+ miles_per_mpc, km_per_mpc, cm_per_mpc, sec_per_Gyr, sec_per_Myr, \
+ sec_per_year, sec_per_day
# The number of levels we expect to have at most
MAXLEVEL=48
@@ -55,8 +55,14 @@
'au' : au_per_mpc,
'rsun' : rsun_per_mpc,
'miles' : miles_per_mpc,
+ 'km' : km_per_mpc,
'cm' : cm_per_mpc}
+# Nicely formatted versions of common length units
+formatted_length_unit_names = {'mpc' : 'Mpc',
+ 'au' : 'AU',
+ 'rsun' : 'R_\odot'}
+
# How many seconds are in each thing
sec_conversion = {'Gyr' : sec_per_Gyr,
'Myr' : sec_per_Myr,
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/exceptions.py
--- a/yt/utilities/exceptions.py
+++ b/yt/utilities/exceptions.py
@@ -208,3 +208,10 @@
s = "There are too many vertices (%s) to upload to Sketchfab. " % (self.nv)
s += "Your model has been saved as %s . You should upload manually." % (self.fn)
return s
+
+class YTInvalidWidthError(YTException):
+ def __init__(self, error):
+ self.error = error
+
+ def __str__(self):
+ return str(self.error)
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/lib/CICDeposit.pyx
--- a/yt/utilities/lib/CICDeposit.pyx
+++ b/yt/utilities/lib/CICDeposit.pyx
@@ -34,22 +34,22 @@
def CICDeposit_3(np.ndarray[np.float64_t, ndim=1] posx,
np.ndarray[np.float64_t, ndim=1] posy,
np.ndarray[np.float64_t, ndim=1] posz,
- np.ndarray[np.float32_t, ndim=1] mass,
+ np.ndarray[np.float64_t, ndim=1] mass,
np.int64_t npositions,
- np.ndarray[np.float32_t, ndim=3] field,
+ np.ndarray[np.float64_t, ndim=3] field,
np.ndarray[np.float64_t, ndim=1] leftEdge,
np.ndarray[np.int32_t, ndim=1] gridDimension,
np.float64_t cellSize):
cdef int i1, j1, k1, n
- cdef double xpos, ypos, zpos
- cdef double fact, edge0, edge1, edge2
- cdef double le0, le1, le2
- cdef float dx, dy, dz, dx2, dy2, dz2
+ cdef np.float64_t xpos, ypos, zpos
+ cdef np.float64_t fact, edge0, edge1, edge2
+ cdef np.float64_t le0, le1, le2
+ cdef np.float64_t dx, dy, dz, dx2, dy2, dz2
- edge0 = (<float> gridDimension[0]) - 0.5001
- edge1 = (<float> gridDimension[1]) - 0.5001
- edge2 = (<float> gridDimension[2]) - 0.5001
+ edge0 = (<np.float64_t> gridDimension[0]) - 0.5001
+ edge1 = (<np.float64_t> gridDimension[1]) - 0.5001
+ edge2 = (<np.float64_t> gridDimension[2]) - 0.5001
fact = 1.0 / cellSize
le0 = leftEdge[0]
@@ -68,9 +68,9 @@
k1 = <int> (zpos + 0.5)
# Compute the weights
- dx = (<float> i1) + 0.5 - xpos
- dy = (<float> j1) + 0.5 - ypos
- dz = (<float> k1) + 0.5 - zpos
+ dx = (<np.float64_t> i1) + 0.5 - xpos
+ dy = (<np.float64_t> j1) + 0.5 - ypos
+ dz = (<np.float64_t> k1) + 0.5 - zpos
dx2 = 1.0 - dx
dy2 = 1.0 - dy
dz2 = 1.0 - dz
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/lib/__init__.py
--- a/yt/utilities/lib/__init__.py
+++ b/yt/utilities/lib/__init__.py
@@ -39,3 +39,4 @@
from .grid_traversal import *
from .marching_cubes import *
from .GridTree import *
+from .write_array import *
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/lib/setup.py
--- a/yt/utilities/lib/setup.py
+++ b/yt/utilities/lib/setup.py
@@ -1,6 +1,7 @@
#!/usr/bin/env python
import setuptools
-import os, sys, os.path, glob
+import os, sys, os.path, glob, \
+ tempfile, subprocess, shutil
def check_for_png():
# First up: HDF5_DIR in environment
@@ -97,11 +98,50 @@
print "You can locate this by looking for the file ft2build.h"
sys.exit(1)
+def check_for_openmp():
+ # Create a temporary directory
+ tmpdir = tempfile.mkdtemp()
+ curdir = os.getcwd()
+ os.chdir(tmpdir)
+
+ # Get compiler invocation
+ compiler = os.getenv('CC', 'cc')
+
+ # Attempt to compile a test script.
+ # See http://openmp.org/wp/openmp-compilers/
+ filename = r'test.c'
+ file = open(filename,'w', 0)
+ file.write(
+ "#include <omp.h>\n"
+ "#include <stdio.h>\n"
+ "int main() {\n"
+ "#pragma omp parallel\n"
+ "printf(\"Hello from thread %d, nthreads %d\\n\", omp_get_thread_num(), omp_get_num_threads());\n"
+ "}"
+ )
+ with open(os.devnull, 'w') as fnull:
+ exit_code = subprocess.call([compiler, '-fopenmp', filename],
+ stdout=fnull, stderr=fnull)
+
+ # Clean up
+ file.close()
+ os.chdir(curdir)
+ shutil.rmtree(tmpdir)
+
+ if exit_code == 0:
+ return True
+ else:
+ return False
+
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('lib',parent_package,top_path)
png_inc, png_lib = check_for_png()
freetype_inc, freetype_lib = check_for_freetype()
+ if check_for_openmp() == True:
+ omp_args = ['-fopenmp']
+ else:
+ omp_args = None
# Because setjmp.h is included by lots of things, and because libpng hasn't
# always properly checked its header files (see
# https://bugzilla.redhat.com/show_bug.cgi?id=494579 ) we simply disable
@@ -129,8 +169,8 @@
depends=["yt/utilities/lib/freetype_includes.h"])
config.add_extension("geometry_utils",
["yt/utilities/lib/geometry_utils.pyx"],
- extra_compile_args=['-fopenmp'],
- extra_link_args=['-fopenmp'],
+ extra_compile_args=omp_args,
+ extra_link_args=omp_args,
libraries=["m"], depends=["yt/utilities/lib/fp_utils.pxd"])
config.add_extension("Interpolators",
["yt/utilities/lib/Interpolators.pyx"],
@@ -194,8 +234,8 @@
glob.glob("yt/utilities/lib/healpix_*.c"),
include_dirs=["yt/utilities/lib/"],
libraries=["m"],
- extra_compile_args=['-fopenmp'],
- extra_link_args=['-fopenmp'],
+ extra_compile_args=omp_args,
+ extra_link_args=omp_args,
depends = ["yt/utilities/lib/VolumeIntegrator.pyx",
"yt/utilities/lib/fp_utils.pxd",
"yt/utilities/lib/kdtree.h",
@@ -204,6 +244,8 @@
"yt/utilities/lib/field_interpolation_tables.pxd",
]
)
+ config.add_extension("write_array",
+ ["yt/utilities/lib/write_array.pyx"])
config.add_extension("GridTree",
["yt/utilities/lib/GridTree.pyx"],
libraries=["m"], depends=["yt/utilities/lib/fp_utils.pxd"])
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/lib/write_array.pyx
--- /dev/null
+++ b/yt/utilities/lib/write_array.pyx
@@ -0,0 +1,66 @@
+"""
+Faster, cythonized file IO
+
+Author: Andrew Myers <atmyers2 at gmail.com>
+Affiliation: UCB
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2013 Andrew Myers. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import numpy as np
+cimport numpy as np
+cimport cython
+
+DTYPE = np.float64
+ctypedef np.float64_t DTYPE_t
+
+ at cython.boundscheck(False)
+def write_3D_array(np.ndarray[DTYPE_t, ndim=3] data, fhandle):
+ assert data.dtype == DTYPE
+ cdef int Nx, Ny, Nz
+ Nx = data.shape[0]
+ Ny = data.shape[1]
+ Nz = data.shape[2]
+ cdef unsigned int i, j, k
+
+ for i in np.arange(Nz):
+ for j in np.arange(Ny):
+ for k in np.arange(Nx):
+ fhandle.write(str(data[k, j, i]) + '\n')
+
+ at cython.boundscheck(False)
+def write_3D_vector_array(np.ndarray[DTYPE_t, ndim=3] data_x,
+ np.ndarray[DTYPE_t, ndim=3] data_y,
+ np.ndarray[DTYPE_t, ndim=3] data_z,
+ fhandle):
+
+ assert data_x.dtype == DTYPE
+ cdef int Nx, Ny, Nz
+ Nx = data_x.shape[0]
+ Ny = data_x.shape[1]
+ Nz = data_x.shape[2]
+ cdef unsigned int i, j, k
+
+ for i in np.arange(Nz):
+ for j in np.arange(Ny):
+ for k in np.arange(Nx):
+ fx = data_x[k, j, i]
+ fy = data_y[k, j, i]
+ fz = data_z[k, j, i]
+ fhandle.write('{} {} {} \n'.format(fx, fy, fz))
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/linear_interpolators.py
--- a/yt/utilities/linear_interpolators.py
+++ b/yt/utilities/linear_interpolators.py
@@ -31,12 +31,44 @@
class UnilinearFieldInterpolator:
def __init__(self, table, boundaries, field_names, truncate=False):
+ r"""Initialize a 1D interpolator for field data.
+
+ table : array
+ The data table over which interpolation is performed.
+ boundaries: tuple or array
+ If a tuple, this should specify the upper and lower bounds
+ for the bins of the data table. This assumes the bins are
+ evenly spaced. If an array, this specifies the bins
+ explicitly.
+ field_names: str
+ Name of the field to be used as input data for interpolation.
+ truncate : bool
+ If False, an exception is raised if the input values are
+ outside the bounds of the table. If True, extrapolation is
+ performed.
+
+ Examples
+ --------
+
+ ad = pf.h.all_data()
+ table_data = np.random.random(64)
+ interp = UnilinearFieldInterpolator(table_data, (0.0, 1.0), "x",
+ truncate=True)
+ field_data = interp(ad)
+
+ """
self.table = table.astype('float64')
self.truncate = truncate
- x0, x1 = boundaries
self.x_name = field_names
- self.x_bins = np.linspace(x0, x1, table.shape[0]).astype('float64')
-
+ if isinstance(boundaries, np.ndarray):
+ if boundaries.size != table.shape[0]:
+ mylog.error("Bins array not the same length as the data.")
+ raise ValueError
+ self.x_bins = boundaries
+ else:
+ x0, x1 = boundaries
+ self.x_bins = np.linspace(x0, x1, table.shape[0]).astype('float64')
+
def __call__(self, data_object):
orig_shape = data_object[self.x_name].shape
x_vals = data_object[self.x_name].ravel().astype('float64')
@@ -57,12 +89,51 @@
class BilinearFieldInterpolator:
def __init__(self, table, boundaries, field_names, truncate=False):
+ r"""Initialize a 2D interpolator for field data.
+
+ table : array
+ The data table over which interpolation is performed.
+ boundaries: tuple
+ Either a tuple of lower and upper bounds for the x and y bins
+ given as (x0, x1, y0, y1) or a tuple of two arrays containing the
+ x and y bins.
+ field_names: list
+ Names of the fields to be used as input data for interpolation.
+ truncate : bool
+ If False, an exception is raised if the input values are
+ outside the bounds of the table. If True, extrapolation is
+ performed.
+
+ Examples
+ --------
+
+ ad = pf.h.all_data()
+ table_data = np.random.random((64, 64))
+ interp = BilinearFieldInterpolator(table_data, (0.0, 1.0, 0.0, 1.0),
+ ["x", "y"],
+ truncate=True)
+ field_data = interp(ad)
+
+ """
self.table = table.astype('float64')
self.truncate = truncate
- x0, x1, y0, y1 = boundaries
self.x_name, self.y_name = field_names
- self.x_bins = np.linspace(x0, x1, table.shape[0]).astype('float64')
- self.y_bins = np.linspace(y0, y1, table.shape[1]).astype('float64')
+ if len(boundaries) == 4:
+ x0, x1, y0, y1 = boundaries
+ self.x_bins = np.linspace(x0, x1, table.shape[0]).astype('float64')
+ self.y_bins = np.linspace(y0, y1, table.shape[1]).astype('float64')
+ elif len(boundaries) == 2:
+ if boundaries[0].size != table.shape[0]:
+ mylog.error("X bins array not the same length as the data.")
+ raise ValueError
+ if boundaries[1].size != table.shape[1]:
+ mylog.error("Y bins array not the same length as the data.")
+ raise ValueError
+ self.x_bins = boundaries[0]
+ self.y_bins = boundaries[1]
+ else:
+ mylog.error("Boundaries must be given as (x0, x1, y0, y1) or as (x_bins, y_bins)")
+ raise ValueError
def __call__(self, data_object):
orig_shape = data_object[self.x_name].shape
@@ -90,14 +161,58 @@
class TrilinearFieldInterpolator:
def __init__(self, table, boundaries, field_names, truncate = False):
+ r"""Initialize a 3D interpolator for field data.
+
+ table : array
+ The data table over which interpolation is performed.
+ boundaries: tuple
+ Either a tuple of lower and upper bounds for the x, y, and z bins
+ given as (x0, x1, y0, y1, z0, z1) or a tuple of three arrays
+ containing the x, y, and z bins.
+ field_names: list
+ Names of the fields to be used as input data for interpolation.
+ truncate : bool
+ If False, an exception is raised if the input values are
+ outside the bounds of the table. If True, extrapolation is
+ performed.
+
+ Examples
+ --------
+
+ ad = pf.h.all_data()
+ table_data = np.random.random((64, 64, 64))
+ interp = BilinearFieldInterpolator(table_data,
+ (0.0, 1.0, 0.0, 1.0, 0.0, 1.0),
+ ["x", "y", "z"],
+ truncate=True)
+ field_data = interp(ad)
+
+ """
self.table = table.astype('float64')
self.truncate = truncate
- x0, x1, y0, y1, z0, z1 = boundaries
self.x_name, self.y_name, self.z_name = field_names
- self.x_bins = np.linspace(x0, x1, table.shape[0]).astype('float64')
- self.y_bins = np.linspace(y0, y1, table.shape[1]).astype('float64')
- self.z_bins = np.linspace(z0, z1, table.shape[2]).astype('float64')
-
+ if len(boundaries) == 6:
+ x0, x1, y0, y1, z0, z1 = boundaries
+ self.x_bins = np.linspace(x0, x1, table.shape[0]).astype('float64')
+ self.y_bins = np.linspace(y0, y1, table.shape[1]).astype('float64')
+ self.z_bins = np.linspace(z0, z1, table.shape[2]).astype('float64')
+ elif len(boundaries) == 3:
+ if boundaries[0].size != table.shape[0]:
+ mylog.error("X bins array not the same length as the data.")
+ raise ValueError
+ if boundaries[1].size != table.shape[1]:
+ mylog.error("Y bins array not the same length as the data.")
+ raise ValueError
+ if boundaries[2].size != table.shape[2]:
+ mylog.error("Z bins array not the same length as the data.")
+ raise ValueError
+ self.x_bins = boundaries[0]
+ self.y_bins = boundaries[1]
+ self.z_bins = boundaries[2]
+ else:
+ mylog.error("Boundaries must be given as (x0, x1, y0, y1, z0, z1) or as (x_bins, y_bins, z_bins)")
+ raise ValueError
+
def __call__(self, data_object):
orig_shape = data_object[self.x_name].shape
x_vals = data_object[self.x_name].ravel().astype('float64')
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/physical_constants.py
--- a/yt/utilities/physical_constants.py
+++ b/yt/utilities/physical_constants.py
@@ -40,9 +40,10 @@
mpc_per_au = 4.84813682e-12
mpc_per_rsun = 2.253962e-14
mpc_per_miles = 5.21552871e-20
+mpc_per_km = 3.24077929e-20
mpc_per_cm = 3.24077929e-25
kpc_per_cm = mpc_per_cm / mpc_per_kpc
-km_per_pc = 1.3806504e13
+km_per_pc = 3.08567758e13
km_per_m = 1e-3
km_per_cm = 1e-5
pc_per_cm = 3.24077929e-19
@@ -54,6 +55,7 @@
au_per_mpc = 1.0 / mpc_per_au
rsun_per_mpc = 1.0 / mpc_per_rsun
miles_per_mpc = 1.0 / mpc_per_miles
+km_per_mpc = 1.0 / mpc_per_km
cm_per_mpc = 1.0 / mpc_per_cm
cm_per_kpc = 1.0 / kpc_per_cm
cm_per_km = 1.0 / km_per_cm
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/utilities/tests/test_interpolators.py
--- a/yt/utilities/tests/test_interpolators.py
+++ b/yt/utilities/tests/test_interpolators.py
@@ -7,21 +7,58 @@
def test_linear_interpolator_1d():
random_data = np.random.random(64)
fv = {'x': np.mgrid[0.0:1.0:64j]}
+ # evenly spaced bins
ufi = lin.UnilinearFieldInterpolator(random_data, (0.0, 1.0), "x", True)
- assert_array_equal(ufi(fv), random_data)
+ yield assert_array_equal, ufi(fv), random_data
+
+ # randomly spaced bins
+ size = 64
+ shift = (1. / size) * np.random.random(size) - (0.5 / size)
+ fv["x"] += shift
+ ufi = lin.UnilinearFieldInterpolator(random_data,
+ np.linspace(0.0, 1.0, size) + shift,
+ "x", True)
+ yield assert_array_almost_equal, ufi(fv), random_data, 15
def test_linear_interpolator_2d():
random_data = np.random.random((64, 64))
+ # evenly spaced bins
fv = dict((ax, v) for ax, v in zip("xyz",
np.mgrid[0.0:1.0:64j, 0.0:1.0:64j]))
bfi = lin.BilinearFieldInterpolator(random_data,
(0.0, 1.0, 0.0, 1.0), "xy", True)
- assert_array_equal(bfi(fv), random_data)
+ yield assert_array_equal, bfi(fv), random_data
+
+ # randomly spaced bins
+ size = 64
+ bins = np.linspace(0.0, 1.0, size)
+ shifts = dict((ax, (1. / size) * np.random.random(size) - (0.5 / size)) \
+ for ax in "xy")
+ fv["x"] += shifts["x"][:, np.newaxis]
+ fv["y"] += shifts["y"]
+ bfi = lin.BilinearFieldInterpolator(random_data,
+ (bins + shifts["x"], bins + shifts["y"]), "xy", True)
+ yield assert_array_almost_equal, bfi(fv), random_data, 15
def test_linear_interpolator_3d():
random_data = np.random.random((64, 64, 64))
+ # evenly spaced bins
fv = dict((ax, v) for ax, v in zip("xyz",
np.mgrid[0.0:1.0:64j, 0.0:1.0:64j, 0.0:1.0:64j]))
tfi = lin.TrilinearFieldInterpolator(random_data,
(0.0, 1.0, 0.0, 1.0, 0.0, 1.0), "xyz", True)
- assert_array_equal(tfi(fv), random_data)
+ yield assert_array_equal, tfi(fv), random_data
+
+ # randomly spaced bins
+ size = 64
+ bins = np.linspace(0.0, 1.0, size)
+ shifts = dict((ax, (1. / size) * np.random.random(size) - (0.5 / size)) \
+ for ax in "xyz")
+ fv["x"] += shifts["x"][:, np.newaxis, np.newaxis]
+ fv["y"] += shifts["y"][:, np.newaxis]
+ fv["z"] += shifts["z"]
+ tfi = lin.TrilinearFieldInterpolator(random_data,
+ (bins + shifts["x"], bins + shifts["y"],
+ bins + shifts["z"]), "xyz", True)
+ yield assert_array_almost_equal, tfi(fv), random_data, 15
+
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/visualization/base_plot_types.py
--- a/yt/visualization/base_plot_types.py
+++ b/yt/visualization/base_plot_types.py
@@ -82,3 +82,4 @@
self.image = self.axes.imshow(data, origin='lower', extent=extent,
norm=norm, vmin=self.zmin, aspect=aspect,
vmax=self.zmax, cmap=cmap)
+ self.cb = self.figure.colorbar(self.image, self.cax)
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -172,7 +172,7 @@
info['label'] = self.data_source.pf.field_info[item].display_name
if info['label'] is None:
- info['label'] = r'$\rm{'+item+r'}$'
+ info['label'] = r'$\rm{'+item.replace('_','\/').title()+r'}$'
elif info['label'].find('$') == -1:
info['label'] = info['label'].replace(' ','\/')
info['label'] = r'$\rm{'+info['label']+r'}$'
diff -r 7b35c3296567868aaffcde67a574f5e28b797785 -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -472,7 +472,7 @@
def get_smallest_appropriate_unit(v, pf):
max_nu = 1e30
good_u = None
- for unit in ['mpc','kpc','pc','au','rsun','cm']:
+ for unit in ['mpc', 'kpc', 'pc', 'au', 'rsun', 'km', 'cm']:
vv = v*pf[unit]
if vv < max_nu and vv > 1.0:
good_u = unit
@@ -694,7 +694,7 @@
int(nx), int(ny),
(x0, x1, y0, y1), 0).transpose()
buff = np.maximum(temp, buff)
- self.rv = plot._axes.contour(buff, len(self.clumps)+1,
+ self.rv = plot._axes.contour(buff, np.unique(buff),
extent=extent,**self.plot_args)
plot._axes.hold(False)
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt-3.0/commits/d2de8bb9615a/
Changeset: d2de8bb9615a
Branch: yt
User: jzuhone
Date: 2013-07-31 22:54:24
Summary: Merged yt_analysis/yt into yt
Affected #: 53 files
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 .hgchurn
--- a/.hgchurn
+++ b/.hgchurn
@@ -4,8 +4,16 @@
juxtaposicion at gmail.com = cemoody at ucsc.edu
chummels at gmail.com = chummels at astro.columbia.edu
jwise at astro.princeton.edu = jwise at physics.gatech.edu
-atmyers = atmyers at berkeley.edu
sam.skillman at gmail.com = samskillman at gmail.com
casey at thestarkeffect.com = caseywstark at gmail.com
chiffre = chiffre at posteo.de
Christian Karch = chiffre at posteo.de
+atmyers at berkeley.edu = atmyers2 at gmail.com
+atmyers = atmyers2 at gmail.com
+drudd = drudd at uchicago.edu
+awetzel = andrew.wetzel at yale.edu
+David Collins (dcollins4096 at gmail.com) = dcollins4096 at gmail.com
+dcollins at physics.ucsd.edu = dcollins4096 at gmail.com
+tabel = tabel at slac.stanford.edu
+sername=kayleanelson = kaylea.nelson at yale.edu
+kayleanelson = kaylea.nelson at yale.edu
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -12,6 +12,7 @@
yt/utilities/kdtree/forthonf2c.h
yt/utilities/libconfig_wrapper.c
yt/utilities/spatial/ckdtree.c
+yt/utilities/lib/amr_kdtools.c
yt/utilities/lib/CICDeposit.c
yt/utilities/lib/ContourFinding.c
yt/utilities/lib/DepthFirstOctree.c
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -10,14 +10,15 @@
# subversion checkout of yt, you can set YT_DIR, too. (It'll already
# check the current directory and one up.
#
-# And, feel free to drop me a line: matthewturk at gmail.com
+# If you experience problems, please visit the Help section at
+# http://yt-project.org.
#
DEST_SUFFIX="yt-`uname -m`"
DEST_DIR="`pwd`/${DEST_SUFFIX/ /}" # Installation location
BRANCH="yt" # This is the branch to which we will forcibly update.
-if [ ${REINST_YT} -eq 1 ] && [ -n ${YT_DEST} ]
+if [ ${REINST_YT} ] && [ ${REINST_YT} -eq 1 ] && [ -n ${YT_DEST} ]
then
DEST_DIR=${YT_DEST}
fi
@@ -97,6 +98,48 @@
LOG_FILE="${DEST_DIR}/yt_install.log"
+function write_config
+{
+ CONFIG_FILE=${DEST_DIR}/.yt_config
+
+ echo INST_HG=${INST_HG} > ${CONFIG_FILE}
+ echo INST_ZLIB=${INST_ZLIB} >> ${CONFIG_FILE}
+ echo INST_BZLIB=${INST_BZLIB} >> ${CONFIG_FILE}
+ echo INST_PNG=${INST_PNG} >> ${CONFIG_FILE}
+ echo INST_FTYPE=${INST_FTYPE} >> ${CONFIG_FILE}
+ echo INST_ENZO=${INST_ENZO} >> ${CONFIG_FILE}
+ echo INST_SQLITE3=${INST_SQLITE3} >> ${CONFIG_FILE}
+ echo INST_PYX=${INST_PYX} >> ${CONFIG_FILE}
+ echo INST_0MQ=${INST_0MQ} >> ${CONFIG_FILE}
+ echo INST_ROCKSTAR=${INST_ROCKSTAR} >> ${CONFIG_FILE}
+ echo INST_SCIPY=${INST_SCIPY} >> ${CONFIG_FILE}
+ echo YT_DIR=${YT_DIR} >> ${CONFIG_FILE}
+ echo MPL_SUPP_LDFLAGS=${MPL_SUPP_LDFLAGS} >> ${CONFIG_FILE}
+ echo MPL_SUPP_CFLAGS=${MPL_SUPP_CFLAGS} >> ${CONFIG_FILE}
+ echo MPL_SUPP_CXXFLAGS=${MPL_SUPP_CXXFLAGS} >> ${CONFIG_FILE}
+ echo MAKE_PROCS=${MAKE_PROCS} >> ${CONFIG_FILE}
+ if [ ${HDF5_DIR} ]
+ then
+ echo ${HDF5_DIR} >> ${CONFIG_FILE}
+ fi
+ if [ ${NUMPY_ARGS} ]
+ then
+ echo ${NUMPY_ARGS} >> ${CONFIG_FILE}
+ fi
+}
+
+# Write config settings to file.
+CONFIG_FILE=${DEST_DIR}/.yt_config
+mkdir -p ${DEST_DIR}
+if [ -z ${REINST_YT} ] || [ ${REINST_YT} -neq 1 ]
+then
+ write_config
+elif [ ${REINST_YT} ] && [ ${REINST_YT} -eq 1 ] && [ -f ${CONFIG_FILE} ]
+then
+ USED_CONFIG=1
+ source ${CONFIG_FILE}
+fi
+
function get_willwont
{
if [ $1 -eq 1 ]
@@ -375,6 +418,10 @@
get_willwont ${INST_0MQ}
echo "be installing ZeroMQ"
+printf "%-15s = %s so I " "INST_ROCKSTAR" "${INST_ROCKSTAR}"
+get_willwont ${INST_0MQ}
+echo "be installing Rockstar"
+
echo
if [ -z "$HDF5_DIR" ]
@@ -396,6 +443,12 @@
echo "hit Ctrl-C."
echo
host_specific
+if [ ${USED_CONFIG} ]
+then
+ echo "Settings were loaded from ${CONFIG_FILE}."
+ echo "Remove this file if you wish to return to the default settings."
+ echo
+fi
echo "========================================================================"
echo
read -p "[hit enter] "
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 scripts/iyt
--- a/scripts/iyt
+++ b/scripts/iyt
@@ -1,6 +1,6 @@
#!python
import os, re
-from distutils import version
+from distutils.version import LooseVersion
from yt.mods import *
from yt.data_objects.data_containers import AMRData
namespace = locals().copy()
@@ -23,10 +23,12 @@
code.interact(doc, None, namespace)
sys.exit()
-if version.LooseVersion(IPython.__version__) <= version.LooseVersion('0.10'):
+if LooseVersion(IPython.__version__) <= LooseVersion('0.10'):
api_version = '0.10'
+elif LooseVersion(IPython.__version__) <= LooseVersion('1.0'):
+ api_version = '0.11'
else:
- api_version = '0.11'
+ api_version = '1.0'
if api_version == "0.10" and "DISPLAY" in os.environ:
from matplotlib import rcParams
@@ -42,13 +44,18 @@
ip_shell = IPython.Shell.IPShellMatplotlib(user_ns=namespace)
elif api_version == "0.10":
ip_shell = IPython.Shell.IPShellMatplotlib(user_ns=namespace)
-elif api_version == "0.11":
- from IPython.frontend.terminal.interactiveshell import TerminalInteractiveShell
+else:
+ if api_version == "0.11":
+ from IPython.frontend.terminal.interactiveshell import \
+ TerminalInteractiveShell
+ elif api_version == "1.0":
+ from IPython.terminal.interactiveshell import TerminalInteractiveShell
+ else:
+ raise RuntimeError
ip_shell = TerminalInteractiveShell(user_ns=namespace, banner1 = doc,
display_banner = True)
if "DISPLAY" in os.environ: ip_shell.enable_pylab(import_all=False)
-else:
- raise RuntimeError
+
# The rest is a modified version of the IPython default profile code
@@ -77,7 +84,7 @@
ip = ip_shell.IP.getapi()
try_next = IPython.ipapi.TryNext
kwargs = dict(sys_exit=1, banner=doc)
-elif api_version == "0.11":
+elif api_version in ("0.11", "1.0"):
ip = ip_shell
try_next = IPython.core.error.TryNext
kwargs = dict()
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 setup.py
--- a/setup.py
+++ b/setup.py
@@ -6,8 +6,11 @@
import subprocess
import shutil
import glob
-import distribute_setup
-distribute_setup.use_setuptools()
+import setuptools
+from distutils.version import StrictVersion
+if StrictVersion(setuptools.__version__) < StrictVersion('0.7.0'):
+ import distribute_setup
+ distribute_setup.use_setuptools()
from distutils.command.build_py import build_py
from numpy.distutils.misc_util import appendpath
@@ -153,8 +156,6 @@
# End snippet
######
-import setuptools
-
VERSION = "2.6dev"
if os.path.exists('MANIFEST'):
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/__init__.py
--- a/yt/__init__.py
+++ b/yt/__init__.py
@@ -83,3 +83,26 @@
"""
__version__ = "2.5-dev"
+
+def run_nose(verbose=False, run_answer_tests=False, answer_big_data=False):
+ import nose, os, sys
+ from yt.config import ytcfg
+ nose_argv = sys.argv
+ nose_argv += ['--exclude=answer_testing','--detailed-errors']
+ if verbose:
+ nose_argv.append('-v')
+ if run_answer_tests:
+ nose_argv.append('--with-answer-testing')
+ if answer_big_data:
+ nose_argv.append('--answer-big-data')
+ log_suppress = ytcfg.getboolean("yt","suppressStreamLogging")
+ ytcfg["yt","suppressStreamLogging"] = 'True'
+ initial_dir = os.getcwd()
+ yt_file = os.path.abspath(__file__)
+ yt_dir = os.path.dirname(yt_file)
+ os.chdir(yt_dir)
+ try:
+ nose.run(argv=nose_argv)
+ finally:
+ os.chdir(initial_dir)
+ ytcfg["yt","suppressStreamLogging"] = log_suppress
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -143,10 +143,10 @@
return self.CoM
pm = self["ParticleMassMsun"]
c = {}
- c[0] = self["particle_position_x"]
- c[1] = self["particle_position_y"]
- c[2] = self["particle_position_z"]
- c_vec = np.zeros(3)
+ # We shift into a box where the origin is the left edge
+ c[0] = self["particle_position_x"] - self.pf.domain_left_edge[0]
+ c[1] = self["particle_position_y"] - self.pf.domain_left_edge[1]
+ c[2] = self["particle_position_z"] - self.pf.domain_left_edge[2]
com = []
for i in range(3):
# A halo is likely periodic around a boundary if the distance
@@ -159,13 +159,12 @@
com.append(c[i])
continue
# Now we want to flip around only those close to the left boundary.
- d_left = c[i] - self.pf.domain_left_edge[i]
- sel = (d_left <= (self.pf.domain_width[i]/2))
+ sel = (c[i] <= (self.pf.domain_width[i]/2))
c[i][sel] += self.pf.domain_width[i]
com.append(c[i])
com = np.array(com)
c = (com * pm).sum(axis=1) / pm.sum()
- return c%self.pf.domain_width
+ return c%self.pf.domain_width + self.pf.domain_left_edge
def maximum_density(self):
r"""Return the HOP-identified maximum density. Not applicable to
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/analysis_modules/halo_mass_function/halo_mass_function.py
--- a/yt/analysis_modules/halo_mass_function/halo_mass_function.py
+++ b/yt/analysis_modules/halo_mass_function/halo_mass_function.py
@@ -212,7 +212,7 @@
dis[self.num_sigma_bins-i-3] += dis[self.num_sigma_bins-i-2]
if i == (self.num_sigma_bins - 3): break
- self.dis = dis / self.pf['CosmologyComovingBoxSize']**3.0 * self.hubble0**3.0
+ self.dis = dis / (self.pf.domain_width * self.pf.units["mpccm"]).prod()
def sigmaM(self):
"""
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/analysis_modules/radmc3d_export/RadMC3DInterface.py
--- a/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py
+++ b/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py
@@ -158,7 +158,8 @@
self.layers.append(base_layer)
self.cell_count += np.product(pf.domain_dimensions)
- for grid in pf.h.grids:
+ sorted_grids = sorted(pf.h.grids, key=lambda x: x.Level)
+ for grid in sorted_grids:
if grid.Level <= self.max_level:
self._add_grid_to_layers(grid)
@@ -232,11 +233,11 @@
if p == 0:
ind = (layer.LeftEdge - LE) / (2.0*dds) + 1
else:
- LE = np.zeros(3)
+ parent_LE = np.zeros(3)
for potential_parent in self.layers:
if potential_parent.id == p:
- LE = potential_parent.LeftEdge
- ind = (layer.LeftEdge - LE) / (2.0*dds) + 1
+ parent_LE = potential_parent.LeftEdge
+ ind = (layer.LeftEdge - parent_LE) / (2.0*dds) + 1
ix = int(ind[0]+0.5)
iy = int(ind[1]+0.5)
iz = int(ind[2]+0.5)
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/config.py
--- a/yt/config.py
+++ b/yt/config.py
@@ -28,7 +28,7 @@
import ConfigParser, os, os.path, types
ytcfgDefaults = dict(
- serialize = 'True',
+ serialize = 'False',
onlydeserialize = 'False',
timefunctions = 'False',
logfile = 'False',
@@ -62,7 +62,7 @@
notebook_password = '',
answer_testing_tolerance = '3',
answer_testing_bitwise = 'False',
- gold_standard_filename = 'gold008',
+ gold_standard_filename = 'gold009',
local_standard_filename = 'local001',
sketchfab_api_key = 'None'
)
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -3121,6 +3121,8 @@
In-line extracted regions accept a base region and a set of field_cuts to
determine which points in a grid should be included.
"""
+ _type_name = "cut_region"
+ _con_args = ("_base_region", "_field_cuts")
def __init__(self, base_region, field_cuts, **kwargs):
cen = base_region.get_field_parameter("center")
AMR3DData.__init__(self, center=cen,
@@ -3701,7 +3703,8 @@
self.left_edge = np.array(left_edge)
self.level = level
rdx = self.pf.domain_dimensions*self.pf.refine_by**level
- self.dds = self.pf.domain_width/rdx.astype("float64")
+ rdx[np.where(dims - 2 * num_ghost_zones <= 1)] = 1 # issue 602
+ self.dds = self.pf.domain_width / rdx.astype("float64")
self.ActiveDimensions = np.array(dims, dtype='int32')
self.right_edge = self.left_edge + self.ActiveDimensions*self.dds
self._num_ghost_zones = num_ghost_zones
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/data_objects/setup.py
--- a/yt/data_objects/setup.py
+++ b/yt/data_objects/setup.py
@@ -9,5 +9,6 @@
from numpy.distutils.misc_util import Configuration
config = Configuration('data_objects', parent_package, top_path)
config.make_config_py() # installs __config__.py
+ config.add_subpackage("tests")
#config.make_svn_version_py()
return config
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -57,14 +57,20 @@
def __new__(cls, filename=None, *args, **kwargs):
if not isinstance(filename, types.StringTypes):
obj = object.__new__(cls)
- obj.__init__(filename, *args, **kwargs)
+ # The Stream frontend uses a StreamHandler object to pass metadata
+ # to __init__.
+ is_stream = (hasattr(filename, 'get_fields') and
+ hasattr(filename, 'get_particle_type'))
+ if not is_stream:
+ obj.__init__(filename, *args, **kwargs)
return obj
apath = os.path.abspath(filename)
if not os.path.exists(apath): raise IOError(filename)
if apath not in _cached_pfs:
obj = object.__new__(cls)
- _cached_pfs[apath] = obj
- return _cached_pfs[apath]
+ if obj._skip_cache is False:
+ _cached_pfs[apath] = obj
+ return obj
def __init__(self, filename, data_style=None, file_style=None):
"""
@@ -132,6 +138,10 @@
def _mrep(self):
return MinimalStaticOutput(self)
+ @property
+ def _skip_cache(self):
+ return False
+
def hub_upload(self):
self._mrep.upload()
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -801,6 +801,8 @@
rdw = radius.copy()
for i, ax in enumerate('xyz'):
np.subtract(data["%s%s" % (field_prefix, ax)], center[i], r)
+ if data.pf.dimensionality < i+1:
+ break
if data.pf.periodicity[i] == True:
np.abs(r, r)
np.subtract(r, DW[i], rdw)
@@ -1082,7 +1084,7 @@
return get_sph_r_component(Bfields, theta, phi, normal)
-add_field("BRadial", function=_BPoloidal,
+add_field("BRadial", function=_BRadial,
units=r"\rm{Gauss}",
validators=[ValidateParameter("normal")])
@@ -1415,7 +1417,7 @@
domegax_dt = data["VorticityX"] / data["VorticityGrowthX"]
domegay_dt = data["VorticityY"] / data["VorticityGrowthY"]
domegaz_dt = data["VorticityZ"] / data["VorticityGrowthZ"]
- return np.sqrt(domegax_dt**2 + domegay_dt**2 + domegaz_dt)
+ return np.sqrt(domegax_dt**2 + domegay_dt**2 + domegaz_dt**2)
add_field("VorticityGrowthTimescale", function=_VorticityGrowthTimescale,
validators=[ValidateSpatial(1,
["x-velocity", "y-velocity", "z-velocity"])],
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/athena/data_structures.py
--- a/yt/frontends/athena/data_structures.py
+++ b/yt/frontends/athena/data_structures.py
@@ -309,6 +309,10 @@
self.grid_left_edge = np.round(self.parameter_file.domain_left_edge + dx*glis, decimals=6)
self.grid_dimensions = gdims.astype("int32")
self.grid_right_edge = np.round(self.grid_left_edge + dx*self.grid_dimensions, decimals=6)
+ if self.parameter_file.dimensionality <= 2:
+ self.grid_right_edge[:,2] = self.parameter_file.domain_right_edge[2]
+ if self.parameter_file.dimensionality == 1:
+ self.grid_right_edge[:,1:] = self.parameter_file.domain_right_edge[1:]
self.grid_particle_count = np.zeros([self.num_grids, 1], dtype='int64')
def _populate_grid_objects(self):
@@ -335,7 +339,9 @@
_data_style = "athena"
def __init__(self, filename, data_style='athena',
- storage_filename=None, parameters={}):
+ storage_filename=None, parameters=None):
+ if parameters is None:
+ parameters = {}
self.specified_parameters = parameters
StaticOutput.__init__(self, filename, data_style)
self.filename = filename
@@ -467,6 +473,10 @@
pass
return False
+ @property
+ def _skip_cache(self):
+ return True
+
def __repr__(self):
return self.basename.rsplit(".", 1)[0]
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/athena/fields.py
--- a/yt/frontends/athena/fields.py
+++ b/yt/frontends/athena/fields.py
@@ -128,15 +128,16 @@
if "pressure" in data.pf.field_info:
return data["pressure"]/(data.pf["Gamma"]-1.0)/data["density"]
else:
- return (data["total_energy"] -
- 0.5*(data["cell_centered_B_x"]**2 +
- data["cell_centered_B_y"]**2 +
- data["cell_centered_B_z"]**2) -
- 0.5*(data["momentum_x"]**2 +
- data["momentum_y"]**2 +
- data["momentum_z"]**2)/data["density"])/data["density"]
+ eint = data["total_energy"] - 0.5*(data["momentum_x"]**2 +
+ data["momentum_y"]**2 +
+ data["momentum_z"]**2)/data["density"]
+ if "cell_centered_B_x" in data.pf.field_info:
+ eint -= 0.5*(data["cell_centered_B_x"]**2 +
+ data["cell_centered_B_y"]**2 +
+ data["cell_centered_B_z"]**2)
+ return eint/data["density"]
add_field("Gas_Energy", function=_gasenergy, take_log=False,
- units=r"\rm{erg}/\rm{g}")
+ convert_function=_convertEnergy, units=r"\rm{erg}/\rm{g}")
def _convertPressure(data) :
return data.convert("Density")*data.convert("x-velocity")**2
@@ -144,15 +145,17 @@
if "pressure" in data.pf.field_info:
return data["pressure"]
else:
- return (data["total_energy"] -
- 0.5*(data["cell_centered_B_x"]**2 +
- data["cell_centered_B_y"]**2 +
- data["cell_centered_B_z"]**2) -
- 0.5*(data["momentum_x"]**2 +
- data["momentum_y"]**2 +
- data["momentum_z"]**2)/data["density"])*(data.pf["Gamma"]-1.0)
-add_field("Pressure", function=_pressure, take_log=False, convert_function=_convertPressure,
- units=r"\rm{erg}/\rm{cm}^3", projected_units=r"\rm{erg}/\rm{cm}^2")
+ eint = data["total_energy"] - 0.5*(data["momentum_x"]**2 +
+ data["momentum_y"]**2 +
+ data["momentum_z"]**2)/data["density"]
+ if "cell_centered_B_x" in data.pf.field_info:
+ eint -= 0.5*(data["cell_centered_B_x"]**2 +
+ data["cell_centered_B_y"]**2 +
+ data["cell_centered_B_z"]**2)
+ return eint*(data.pf["Gamma"]-1.0)
+add_field("Pressure", function=_pressure, take_log=False,
+ convert_function=_convertPressure, units=r"\rm{erg}/\rm{cm}^3",
+ projected_units=r"\rm{erg}/\rm{cm}^2")
def _temperature(field, data):
if data.has_field_parameter("mu"):
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/castro/data_structures.py
--- a/yt/frontends/castro/data_structures.py
+++ b/yt/frontends/castro/data_structures.py
@@ -608,7 +608,7 @@
self.parameters["TopGridRank"] = len(self.parameters["TopGridDimensions"])
self.dimensionality = self.parameters["TopGridRank"]
self.periodicity = ensure_tuple(self.fparameters['castro.lo_bc'] == 0)
- self.domain_dimensions = self.parameters["TopGridDimensions"]
+ self.domain_dimensions = np.array(self.parameters["TopGridDimensions"])
self.refine_by = self.parameters.get("RefineBy", 2)
if (self.parameters.has_key("ComovingCoordinates") and
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/chombo/fields.py
--- a/yt/frontends/chombo/fields.py
+++ b/yt/frontends/chombo/fields.py
@@ -163,10 +163,12 @@
"angmomen_y",
"angmomen_z",
"mlast",
+ "r",
"mdeut",
"n",
"mdot",
"burnstate",
+ "luminosity",
"id"]
for pf in _particle_field_list:
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/chombo/io.py
--- a/yt/frontends/chombo/io.py
+++ b/yt/frontends/chombo/io.py
@@ -77,6 +77,15 @@
parses the Orion Star Particle text files
"""
+
+ fn = grid.pf.fullplotdir[:-4] + "sink"
+
+ # Figure out the format of the particle file
+ with open(fn, 'r') as f:
+ lines = f.readlines()
+ line = lines[1]
+
+ # The basic fields that all sink particles have
index = {'particle_mass': 0,
'particle_position_x': 1,
'particle_position_y': 2,
@@ -87,15 +96,38 @@
'particle_angmomen_x': 7,
'particle_angmomen_y': 8,
'particle_angmomen_z': 9,
- 'particle_mlast': 10,
- 'particle_mdeut': 11,
- 'particle_n': 12,
- 'particle_mdot': 13,
- 'particle_burnstate': 14,
- 'particle_id': 15}
+ 'particle_id': -1}
+ if len(line.strip().split()) == 11:
+ # these are vanilla sinks, do nothing
+ pass
+
+ elif len(line.strip().split()) == 17:
+ # these are old-style stars, add stellar model parameters
+ index['particle_mlast'] = 10
+ index['particle_r'] = 11
+ index['particle_mdeut'] = 12
+ index['particle_n'] = 13
+ index['particle_mdot'] = 14,
+ index['particle_burnstate'] = 15
+
+ elif len(line.strip().split()) == 18:
+ # these are the newer style, add luminosity as well
+ index['particle_mlast'] = 10
+ index['particle_r'] = 11
+ index['particle_mdeut'] = 12
+ index['particle_n'] = 13
+ index['particle_mdot'] = 14,
+ index['particle_burnstate'] = 15,
+ index['particle_luminosity']= 16
+
+ else:
+ # give a warning if none of the above apply:
+ mylog.warning('Warning - could not figure out particle output file')
+ mylog.warning('These results could be nonsense!')
+
def read(line, field):
- return float(line.split(' ')[index[field]])
+ return float(line.strip().split(' ')[index[field]])
fn = grid.pf.fullplotdir[:-4] + "sink"
with open(fn, 'r') as f:
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/enzo/fields.py
--- a/yt/frontends/enzo/fields.py
+++ b/yt/frontends/enzo/fields.py
@@ -37,7 +37,8 @@
ValidateGridType
import yt.data_objects.universal_fields
from yt.utilities.physical_constants import \
- mh
+ mh, \
+ kpc_per_cm
from yt.funcs import *
import yt.utilities.lib as amr_utils
@@ -77,6 +78,7 @@
def _convertCellMassMsun(data):
return 5.027854e-34 # g^-1
+
def _ConvertNumberDensity(data):
return 1.0/mh
@@ -315,6 +317,10 @@
def _convertDensity(data):
return data.convert("Density")
+
+def _convertCmToKpc(data):
+ return 1/(kpc_per_cm)**3
+
for field in ["Density"] + [ "%s_Density" % sp for sp in _speciesList ] + \
["SN_Colour"]:
KnownEnzoFields[field]._units = r"\rm{g}/\rm{cm}^3"
@@ -365,8 +371,35 @@
np.array(data.ActiveDimensions).astype(np.int32),
np.float64(data['dx']))
return blank
+
add_field("star_density", function=_spdensity,
- validators=[ValidateSpatial(0)], convert_function=_convertDensity)
+ validators=[ValidateSpatial(0)], convert_function=_convertDensity,
+ units = r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2",
+ display_name = "Stellar\/Density")
+
+def _tpdensity(field, data):
+ blank = np.zeros(data.ActiveDimensions, dtype='float64')
+ if data["particle_position_x"].size == 0: return blank
+ filter = data['particle_type'] == 3 # tracer particles
+ if not filter.any(): return blank
+ amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(np.float64),
+ data["particle_position_y"][filter].astype(np.float64),
+ data["particle_position_z"][filter].astype(np.float64),
+ np.ones(filter.sum(), dtype="float64"),
+ np.int64(np.where(filter)[0].size),
+ blank, np.array(data.LeftEdge).astype(np.float64),
+ np.array(data.ActiveDimensions).astype(np.int32),
+ np.float64(data['dx']))
+ blank /= data['CellVolume']
+ return blank
+
+add_field("tracer_number_density", function=_tpdensity,
+ validators=[ValidateSpatial(0)], convert_function=_convertCmToKpc,
+ units = r"\rm{particles}/\rm{kpc}^3",
+ projected_units = r"\rm{particles}/\rm{kpc}^2",
+ display_name = "Tracer\/Particle\/Number\/Density",
+ projection_conversion='kpc')
def _dmpdensity(field, data):
blank = np.zeros(data.ActiveDimensions, dtype='float64')
@@ -387,8 +420,12 @@
np.array(data.ActiveDimensions).astype(np.int32),
np.float64(data['dx']))
return blank
+
add_field("dm_density", function=_dmpdensity,
- validators=[ValidateSpatial(0)], convert_function=_convertDensity)
+ validators=[ValidateSpatial(0)], convert_function=_convertDensity,
+ units = r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2",
+ display_name = "Dark\/Matter\/Density")
def _cic_particle_field(field, data):
"""
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/flash/data_structures.py
--- a/yt/frontends/flash/data_structures.py
+++ b/yt/frontends/flash/data_structures.py
@@ -458,7 +458,7 @@
try:
self.parameters["usecosmology"]
self.cosmological_simulation = 1
- self.current_redshift = self.parameters['redshift']
+ self.current_redshift = 1.0/self.parameters['scalefactor'] - 1.0
self.omega_lambda = self.parameters['cosmologicalconstant']
self.omega_matter = self.parameters['omegamatter']
self.hubble_constant = self.parameters['hubbleconstant']
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/flash/fields.py
--- a/yt/frontends/flash/fields.py
+++ b/yt/frontends/flash/fields.py
@@ -366,5 +366,21 @@
add_field('nion', function=_nion, take_log=True, units=r"\rm{cm}^{-3}")
def _abar(field, data):
- return 1.0 / data['sumy']
+ try:
+ return 1.0 / data['sumy']
+ except:
+ pass
+ return data['dens']*Na*kboltz*data['temp']/data['pres']
add_field('abar', function=_abar, take_log=False)
+
+
+def _NumberDensity(fields,data) :
+ try:
+ return data["nele"]+data["nion"]
+ except:
+ pass
+ return data['pres']/(data['temp']*kboltz)
+add_field("NumberDensity", function=_NumberDensity,
+ units=r'\rm{cm}^{-3}')
+
+
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -74,8 +74,9 @@
LE, RE = self.hierarchy.grid_left_edge[id,:], \
self.hierarchy.grid_right_edge[id,:]
self.dds = np.array((RE-LE)/self.ActiveDimensions)
- if self.pf.dimensionality < 2: self.dds[1] = 1.0
- if self.pf.dimensionality < 3: self.dds[2] = 1.0
+ if self.pf.data_software != "piernik":
+ if self.pf.dimensionality < 2: self.dds[1] = 1.0
+ if self.pf.dimensionality < 3: self.dds[2] = 1.0
self.field_data['dx'], self.field_data['dy'], self.field_data['dz'] = self.dds
class GDFHierarchy(AMRHierarchy):
@@ -214,6 +215,11 @@
def _parse_parameter_file(self):
self._handle = h5py.File(self.parameter_filename, "r")
+ if 'data_software' in self._handle['gridded_data_format'].attrs:
+ self.data_software = \
+ self._handle['gridded_data_format'].attrs['data_software']
+ else:
+ self.data_software = "unknown"
sp = self._handle["/simulation_parameters"].attrs
self.domain_left_edge = sp["domain_left_edge"][:]
self.domain_right_edge = sp["domain_right_edge"][:]
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/orion/fields.py
--- a/yt/frontends/orion/fields.py
+++ b/yt/frontends/orion/fields.py
@@ -163,10 +163,12 @@
"angmomen_y",
"angmomen_z",
"mlast",
+ "r",
"mdeut",
"n",
"mdot",
"burnstate",
+ "luminosity",
"id"]
for pf in _particle_field_list:
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/orion/io.py
--- a/yt/frontends/orion/io.py
+++ b/yt/frontends/orion/io.py
@@ -44,6 +44,17 @@
parses the Orion Star Particle text files
"""
+
+ fn = grid.pf.fullplotdir + "/StarParticles"
+ if not os.path.exists(fn):
+ fn = grid.pf.fullplotdir + "/SinkParticles"
+
+ # Figure out the format of the particle file
+ with open(fn, 'r') as f:
+ lines = f.readlines()
+ line = lines[1]
+
+ # The basic fields that all sink particles have
index = {'particle_mass': 0,
'particle_position_x': 1,
'particle_position_y': 2,
@@ -54,17 +65,39 @@
'particle_angmomen_x': 7,
'particle_angmomen_y': 8,
'particle_angmomen_z': 9,
- 'particle_mlast': 10,
- 'particle_mdeut': 11,
- 'particle_n': 12,
- 'particle_mdot': 13,
- 'particle_burnstate': 14,
- 'particle_id': 15}
+ 'particle_id': -1}
+
+ if len(line.strip().split()) == 11:
+ # these are vanilla sinks, do nothing
+ pass
+
+ elif len(line.strip().split()) == 17:
+ # these are old-style stars, add stellar model parameters
+ index['particle_mlast'] = 10
+ index['particle_r'] = 11
+ index['particle_mdeut'] = 12
+ index['particle_n'] = 13
+ index['particle_mdot'] = 14,
+ index['particle_burnstate'] = 15
+
+ elif len(line.strip().split()) == 18:
+ # these are the newer style, add luminosity as well
+ index['particle_mlast'] = 10
+ index['particle_r'] = 11
+ index['particle_mdeut'] = 12
+ index['particle_n'] = 13
+ index['particle_mdot'] = 14,
+ index['particle_burnstate'] = 15,
+ index['particle_luminosity']= 16
+
+ else:
+ # give a warning if none of the above apply:
+ mylog.warning('Warning - could not figure out particle output file')
+ mylog.warning('These results could be nonsense!')
def read(line, field):
- return float(line.split(' ')[index[field]])
+ return float(line.strip().split(' ')[index[field]])
- fn = grid.pf.fullplotdir + "/StarParticles"
with open(fn, 'r') as f:
lines = f.readlines()
particles = []
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/setup.py
--- a/yt/frontends/setup.py
+++ b/yt/frontends/setup.py
@@ -21,4 +21,9 @@
config.add_subpackage("castro")
config.add_subpackage("stream")
config.add_subpackage("pluto")
+ config.add_subpackage("flash/tests")
+ config.add_subpackage("enzo/tests")
+ config.add_subpackage("orion/tests")
+ config.add_subpackage("stream/tests")
+ config.add_subpackage("chombo/tests")
return config
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -339,6 +339,10 @@
def _is_valid(cls, *args, **kwargs):
return False
+ @property
+ def _skip_cache(self):
+ return True
+
class StreamDictFieldHandler(dict):
@property
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -28,7 +28,7 @@
import contextlib
import warnings, struct, subprocess
import numpy as np
-from distutils import version
+from distutils.version import LooseVersion
from math import floor, ceil
from yt.utilities.exceptions import *
@@ -260,10 +260,12 @@
"""
import IPython
- if version.LooseVersion(IPython.__version__) <= version.LooseVersion('0.10'):
+ if LooseVersion(IPython.__version__) <= LooseVersion('0.10'):
api_version = '0.10'
+ elif LooseVersion(IPython.__version__) <= LooseVersion('1.0'):
+ api_version = '0.11'
else:
- api_version = '0.11'
+ api_version = '1.0'
stack = inspect.stack()
frame = inspect.stack()[num_up]
@@ -281,7 +283,10 @@
cfg.InteractiveShellEmbed.local_ns = loc
cfg.InteractiveShellEmbed.global_ns = glo
IPython.embed(config=cfg, banner2 = __header % dd)
- from IPython.frontend.terminal.embed import InteractiveShellEmbed
+ if api_version == '0.11':
+ from IPython.frontend.terminal.embed import InteractiveShellEmbed
+ else:
+ from IPython.terminal.embed import InteractiveShellEmbed
ipshell = InteractiveShellEmbed(config=cfg)
del ipshell
@@ -369,6 +374,20 @@
if ytcfg.getint("yt", cfg_option) > 0: return
return func(*args, **kwargs)
+def is_root():
+ """
+ This function returns True if it is on the root processor of the
+ topcomm and False otherwise.
+ """
+ from yt.config import ytcfg
+ cfg_option = "__topcomm_parallel_rank"
+ if not ytcfg.getboolean("yt","__parallel"):
+ return True
+ if ytcfg.getint("yt", cfg_option) > 0:
+ return False
+ return True
+
+
#
# Our signal and traceback handling functions
#
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/startup_tasks.py
--- a/yt/startup_tasks.py
+++ b/yt/startup_tasks.py
@@ -98,7 +98,17 @@
if param == "loglevel": # special case
mylog.setLevel(int(val))
-parser = argparse.ArgumentParser(description = 'yt command line arguments')
+class YTParser(argparse.ArgumentParser):
+ def error(self, message):
+ """error(message: string)
+
+ Prints a help message that is more detailed than the argparse default
+ and then exits.
+ """
+ self.print_help(sys.stderr)
+ self.exit(2, '%s: error: %s\n' % (self.prog, message))
+
+parser = YTParser(description = 'yt command line arguments')
parser.add_argument("--config", action=SetConfigOption,
help = "Set configuration option, in the form param=value")
parser.add_argument("--paste", action=SetExceptionHandling,
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/utilities/amr_kdtree/amr_kdtools.py
--- a/yt/utilities/amr_kdtree/amr_kdtools.py
+++ b/yt/utilities/amr_kdtree/amr_kdtools.py
@@ -1,5 +1,5 @@
"""
-AMR kD-Tree Tools
+AMR kD-Tree Tools
Authors: Samuel Skillman <samskillman at gmail.com>
Affiliation: University of Colorado at Boulder
@@ -25,435 +25,10 @@
"""
import numpy as np
from yt.funcs import *
-from yt.utilities.lib import kdtree_get_choices
-
-def _lchild_id(node_id): return (node_id<<1)
-def _rchild_id(node_id): return (node_id<<1) + 1
-def _parent_id(node_id): return (node_id-1) >> 1
-
-class Node(object):
- def __init__(self, parent, left, right,
- left_edge, right_edge, grid_id, node_id):
- self.left = left
- self.right = right
- self.left_edge = left_edge
- self.right_edge = right_edge
- self.grid = grid_id
- self.parent = parent
- self.id = node_id
- self.data = None
- self.split = None
-
-class Split(object):
- def __init__(self, dim, pos):
- self.dim = dim
- self.pos = pos
-
-def should_i_build(node, rank, size):
- if (node.id < size) or (node.id >= 2*size):
- return True
- elif node.id - size == rank:
- return True
- else:
- return False
-
-
-def add_grid(node, gle, gre, gid, rank, size):
- if not should_i_build(node, rank, size):
- return
-
- if kd_is_leaf(node):
- insert_grid(node, gle, gre, gid, rank, size)
- else:
- less_id = gle[node.split.dim] < node.split.pos
- if less_id:
- add_grid(node.left, gle, gre,
- gid, rank, size)
-
- greater_id = gre[node.split.dim] > node.split.pos
- if greater_id:
- add_grid(node.right, gle, gre,
- gid, rank, size)
-
-
-def insert_grid(node, gle, gre, grid_id, rank, size):
- if not should_i_build(node, rank, size):
- return
-
- # If we should continue to split based on parallelism, do so!
- if should_i_split(node, rank, size):
- geo_split(node, gle, gre, grid_id, rank, size)
- return
-
- if np.all(gle <= node.left_edge) and \
- np.all(gre >= node.right_edge):
- node.grid = grid_id
- assert(node.grid is not None)
- return
-
- # Split the grid
- check = split_grid(node, gle, gre, grid_id, rank, size)
- # If check is -1, then we have found a place where there are no choices.
- # Exit out and set the node to None.
- if check == -1:
- node.grid = None
- return
-
-
-def add_grids(node, gles, gres, gids, rank, size):
- if not should_i_build(node, rank, size):
- return
-
- if kd_is_leaf(node):
- insert_grids(node, gles, gres, gids, rank, size)
- else:
- less_ids = gles[:,node.split.dim] < node.split.pos
- if len(less_ids) > 0:
- add_grids(node.left, gles[less_ids], gres[less_ids],
- gids[less_ids], rank, size)
-
- greater_ids = gres[:,node.split.dim] > node.split.pos
- if len(greater_ids) > 0:
- add_grids(node.right, gles[greater_ids], gres[greater_ids],
- gids[greater_ids], rank, size)
-
-
-def should_i_split(node, rank, size):
- return node.id < size
-
-
-def geo_split_grid(node, gle, gre, grid_id, rank, size):
- big_dim = np.argmax(gre-gle)
- new_pos = (gre[big_dim] + gle[big_dim])/2.
- old_gre = gre.copy()
- new_gle = gle.copy()
- new_gle[big_dim] = new_pos
- gre[big_dim] = new_pos
-
- split = Split(big_dim, new_pos)
-
- # Create a Split
- divide(node, split)
-
- # Populate Left Node
- #print 'Inserting left node', node.left_edge, node.right_edge
- insert_grid(node.left, gle, gre,
- grid_id, rank, size)
-
- # Populate Right Node
- #print 'Inserting right node', node.left_edge, node.right_edge
- insert_grid(node.right, new_gle, old_gre,
- grid_id, rank, size)
- return
-
-
-def geo_split(node, gles, gres, grid_ids, rank, size):
- big_dim = np.argmax(gres[0]-gles[0])
- new_pos = (gres[0][big_dim] + gles[0][big_dim])/2.
- old_gre = gres[0].copy()
- new_gle = gles[0].copy()
- new_gle[big_dim] = new_pos
- gres[0][big_dim] = new_pos
- gles = np.append(gles, np.array([new_gle]), axis=0)
- gres = np.append(gres, np.array([old_gre]), axis=0)
- grid_ids = np.append(grid_ids, grid_ids, axis=0)
-
- split = Split(big_dim, new_pos)
-
- # Create a Split
- divide(node, split)
-
- # Populate Left Node
- #print 'Inserting left node', node.left_edge, node.right_edge
- insert_grids(node.left, gles[:1], gres[:1],
- grid_ids[:1], rank, size)
-
- # Populate Right Node
- #print 'Inserting right node', node.left_edge, node.right_edge
- insert_grids(node.right, gles[1:], gres[1:],
- grid_ids[1:], rank, size)
- return
-
-def insert_grids(node, gles, gres, grid_ids, rank, size):
- if not should_i_build(node, rank, size) or grid_ids.size == 0:
- return
-
- if len(grid_ids) == 1:
- # If we should continue to split based on parallelism, do so!
- if should_i_split(node, rank, size):
- geo_split(node, gles, gres, grid_ids, rank, size)
- return
-
- if np.all(gles[0] <= node.left_edge) and \
- np.all(gres[0] >= node.right_edge):
- node.grid = grid_ids[0]
- assert(node.grid is not None)
- return
-
- # Split the grids
- check = split_grids(node, gles, gres, grid_ids, rank, size)
- # If check is -1, then we have found a place where there are no choices.
- # Exit out and set the node to None.
- if check == -1:
- node.grid = None
- return
-
-def split_grid(node, gle, gre, grid_id, rank, size):
- # Find a Split
- data = np.array([(gle[:], gre[:])], copy=False)
- best_dim, split_pos, less_id, greater_id = \
- kdtree_get_choices(data, node.left_edge, node.right_edge)
-
- # If best_dim is -1, then we have found a place where there are no choices.
- # Exit out and set the node to None.
- if best_dim == -1:
- return -1
-
- split = Split(best_dim, split_pos)
-
- del data, best_dim, split_pos
-
- # Create a Split
- divide(node, split)
-
- # Populate Left Node
- #print 'Inserting left node', node.left_edge, node.right_edge
- if less_id:
- insert_grid(node.left, gle, gre,
- grid_id, rank, size)
-
- # Populate Right Node
- #print 'Inserting right node', node.left_edge, node.right_edge
- if greater_id:
- insert_grid(node.right, gle, gre,
- grid_id, rank, size)
-
- return
-
-
-def split_grids(node, gles, gres, grid_ids, rank, size):
- # Find a Split
- data = np.array([(gles[i,:], gres[i,:]) for i in
- xrange(grid_ids.shape[0])], copy=False)
- best_dim, split_pos, less_ids, greater_ids = \
- kdtree_get_choices(data, node.left_edge, node.right_edge)
-
- # If best_dim is -1, then we have found a place where there are no choices.
- # Exit out and set the node to None.
- if best_dim == -1:
- return -1
-
- split = Split(best_dim, split_pos)
-
- del data, best_dim, split_pos
-
- # Create a Split
- divide(node, split)
-
- # Populate Left Node
- #print 'Inserting left node', node.left_edge, node.right_edge
- insert_grids(node.left, gles[less_ids], gres[less_ids],
- grid_ids[less_ids], rank, size)
-
- # Populate Right Node
- #print 'Inserting right node', node.left_edge, node.right_edge
- insert_grids(node.right, gles[greater_ids], gres[greater_ids],
- grid_ids[greater_ids], rank, size)
-
- return
-
-def new_right(Node, split):
- new_right = Node.right_edge.copy()
- new_right[split.dim] = split.pos
- return new_right
-
-def new_left(Node, split):
- new_left = Node.left_edge.copy()
- new_left[split.dim] = split.pos
- return new_left
-
-def divide(node, split):
- # Create a Split
- node.split = split
- node.left = Node(node, None, None,
- node.left_edge, new_right(node, split), node.grid,
- _lchild_id(node.id))
- node.right = Node(node, None, None,
- new_left(node, split), node.right_edge, node.grid,
- _rchild_id(node.id))
- return
-
-def kd_sum_volume(node):
- if (node.left is None) and (node.right is None):
- if node.grid is None:
- return 0.0
- return np.prod(node.right_edge - node.left_edge)
- else:
- return kd_sum_volume(node.left) + kd_sum_volume(node.right)
-
-def kd_sum_cells(node):
- if (node.left is None) and (node.right is None):
- if node.grid is None:
- return 0.0
- return np.prod(node.right_edge - node.left_edge)
- else:
- return kd_sum_volume(node.left) + kd_sum_volume(node.right)
-
-
-def kd_node_check(node):
- assert (node.left is None) == (node.right is None)
- if (node.left is None) and (node.right is None):
- if node.grid is not None:
- return np.prod(node.right_edge - node.left_edge)
- else: return 0.0
- else:
- return kd_node_check(node.left)+kd_node_check(node.right)
-
-def kd_is_leaf(node):
- has_l_child = node.left is None
- has_r_child = node.right is None
- assert has_l_child == has_r_child
- return has_l_child
-
-def step_depth(current, previous):
- '''
- Takes a single step in the depth-first traversal
- '''
- if kd_is_leaf(current): # At a leaf, move back up
- previous = current
- current = current.parent
-
- elif current.parent is previous: # Moving down, go left first
- previous = current
- if current.left is not None:
- current = current.left
- elif current.right is not None:
- current = current.right
- else:
- current = current.parent
-
- elif current.left is previous: # Moving up from left, go right
- previous = current
- if current.right is not None:
- current = current.right
- else:
- current = current.parent
-
- elif current.right is previous: # Moving up from right child, move up
- previous = current
- current = current.parent
-
- return current, previous
-
-def depth_traverse(tree, max_node=None):
- '''
- Yields a depth-first traversal of the kd tree always going to
- the left child before the right.
- '''
- current = tree.trunk
- previous = None
- if max_node is None:
- max_node = np.inf
- while current is not None:
- yield current
- current, previous = step_depth(current, previous)
- if current is None: break
- if current.id >= max_node:
- current = current.parent
- previous = current.right
-
-def depth_first_touch(tree, max_node=None):
- '''
- Yields a depth-first traversal of the kd tree always going to
- the left child before the right.
- '''
- current = tree.trunk
- previous = None
- if max_node is None:
- max_node = np.inf
- while current is not None:
- if previous is None or previous.parent != current:
- yield current
- current, previous = step_depth(current, previous)
- if current is None: break
- if current.id >= max_node:
- current = current.parent
- previous = current.right
-
-def breadth_traverse(tree):
- '''
- Yields a breadth-first traversal of the kd tree always going to
- the left child before the right.
- '''
- current = tree.trunk
- previous = None
- while current is not None:
- yield current
- current, previous = step_depth(current, previous)
-
-
-def viewpoint_traverse(tree, viewpoint):
- '''
- Yields a viewpoint dependent traversal of the kd-tree. Starts
- with nodes furthest away from viewpoint.
- '''
-
- current = tree.trunk
- previous = None
- while current is not None:
- yield current
- current, previous = step_viewpoint(current, previous, viewpoint)
-
-def step_viewpoint(current, previous, viewpoint):
- '''
- Takes a single step in the viewpoint based traversal. Always
- goes to the node furthest away from viewpoint first.
- '''
- if kd_is_leaf(current): # At a leaf, move back up
- previous = current
- current = current.parent
- elif current.split.dim is None: # This is a dead node
- previous = current
- current = current.parent
-
- elif current.parent is previous: # Moving down
- previous = current
- if viewpoint[current.split.dim] <= current.split.pos:
- if current.right is not None:
- current = current.right
- else:
- previous = current.right
- else:
- if current.left is not None:
- current = current.left
- else:
- previous = current.left
-
- elif current.right is previous: # Moving up from right
- previous = current
- if viewpoint[current.split.dim] <= current.split.pos:
- if current.left is not None:
- current = current.left
- else:
- current = current.parent
- else:
- current = current.parent
-
- elif current.left is previous: # Moving up from left child
- previous = current
- if viewpoint[current.split.dim] > current.split.pos:
- if current.right is not None:
- current = current.right
- else:
- current = current.parent
- else:
- current = current.parent
-
- return current, previous
def receive_and_reduce(comm, incoming_rank, image, add_to_front):
- mylog.debug( 'Receiving image from %04i' % incoming_rank)
+ mylog.debug('Receiving image from %04i' % incoming_rank)
#mylog.debug( '%04i receiving image from %04i'%(self.comm.rank,back.owner))
arr2 = comm.recv_array(incoming_rank, incoming_rank).reshape(
(image.shape[0], image.shape[1], image.shape[2]))
@@ -470,36 +45,24 @@
np.add(image, front, image)
return image
- ta = 1.0 - front[:,:,3]
+ ta = 1.0 - front[:, :, 3]
np.maximum(ta, 0.0, ta)
# This now does the following calculation, but in a memory
# conservative fashion
# image[:,:,i ] = front[:,:,i] + ta*back[:,:,i]
image = back.copy()
for i in range(4):
- np.multiply(image[:,:,i], ta, image[:,:,i])
+ np.multiply(image[:, :, i], ta, image[:, :, i])
np.add(image, front, image)
return image
+
def send_to_parent(comm, outgoing_rank, image):
- mylog.debug( 'Sending image to %04i' % outgoing_rank)
+ mylog.debug('Sending image to %04i' % outgoing_rank)
comm.send_array(image, outgoing_rank, tag=comm.rank)
+
def scatter_image(comm, root, image):
- mylog.debug( 'Scattering from %04i' % root)
+ mylog.debug('Scattering from %04i' % root)
image = comm.mpi_bcast(image, root=root)
return image
-
-def find_node(node, pos):
- """
- Find the AMRKDTree node enclosing a position
- """
- assert(np.all(node.left_edge <= pos))
- assert(np.all(node.right_edge > pos))
- while not kd_is_leaf(node):
- if pos[node.split.dim] < node.split.pos:
- node = node.left
- else:
- node = node.right
- return node
-
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/utilities/amr_kdtree/amr_kdtree.py
--- a/yt/utilities/amr_kdtree/amr_kdtree.py
+++ b/yt/utilities/amr_kdtree/amr_kdtree.py
@@ -26,10 +26,13 @@
from yt.funcs import *
import numpy as np
import h5py
-from amr_kdtools import Node, Split, kd_is_leaf, kd_sum_volume, kd_node_check, \
- depth_traverse, viewpoint_traverse, add_grids, \
- receive_and_reduce, send_to_parent, scatter_image, find_node, \
- depth_first_touch, add_grid
+from amr_kdtools import \
+ receive_and_reduce, send_to_parent, scatter_image
+
+from yt.utilities.lib.amr_kdtools import Node, add_pygrids, find_node, \
+ kd_is_leaf, depth_traverse, depth_first_touch, viewpoint_traverse, \
+ kd_traverse, \
+ get_left_edge, get_right_edge, kd_sum_volume, kd_node_check
from yt.utilities.parallel_tools.parallel_analysis_interface \
import ParallelAnalysisInterface
from yt.utilities.lib.grid_traversal import PartitionedGrid
@@ -67,12 +70,11 @@
self.comm_rank = comm_rank
self.comm_size = comm_size
self.trunk = Node(None, None, None,
- left, right, None, 1)
+ left, right, -1, 1)
if grids is None:
- self.grids = pf.h.region((left+right)/2., left, right)._grids
- else:
- self.grids = grids
- self.build(grids)
+ grids = pf.h.region((left+right)/2., left, right)._grids
+ self.grids = grids
+ self.build(self.grids)
def add_grids(self, grids):
lvl_range = range(self.min_level, self.max_level+1)
@@ -91,7 +93,8 @@
gles = np.array([g.LeftEdge for g in grids])[gmask]
gres = np.array([g.RightEdge for g in grids])[gmask]
gids = np.array([g.id for g in grids])[gmask]
- add_grids(self.trunk, gles, gres, gids, self.comm_rank,
+ add_pygrids(self.trunk, gids.size, gles, gres, gids,
+ self.comm_rank,
self.comm_size)
grids_added += grids.size
del gles, gres, gids, grids
@@ -99,31 +102,36 @@
grids_added += grids.size
[add_grid(self.trunk, g.LeftEdge, g.RightEdge, g.id,
self.comm_rank, self.comm_size) for g in grids]
- else:
- gles = np.array([g.LeftEdge for g in grids])
- gres = np.array([g.RightEdge for g in grids])
- gids = np.array([g.id for g in grids])
+ return
- add_grids(self.trunk, gles, gres, gids, self.comm_rank, self.comm_size)
- del gles, gres, gids, grids
+ for lvl in lvl_range:
+ gles = np.array([g.LeftEdge for g in grids if g.Level == lvl])
+ gres = np.array([g.RightEdge for g in grids if g.Level == lvl])
+ gids = np.array([g.id for g in grids if g.Level == lvl],
+ dtype="int64")
+ add_pygrids(self.trunk, len(gids), gles, gres, gids, self.comm_rank, self.comm_size)
+ del gles, gres, gids
- def build(self, grids = None):
+
+ def build(self, grids=None):
self.add_grids(grids)
def check_tree(self):
- for node in depth_traverse(self):
- if node.grid is None:
+ for node in depth_traverse(self.trunk):
+ if node.grid == -1:
continue
grid = self.pf.h.grids[node.grid - self._id_offset]
dds = grid.dds
gle = grid.LeftEdge
gre = grid.RightEdge
- li = np.rint((node.left_edge-gle)/dds).astype('int32')
- ri = np.rint((node.right_edge-gle)/dds).astype('int32')
+ nle = get_left_edge(node)
+ nre = get_right_edge(node)
+ li = np.rint((nle-gle)/dds).astype('int32')
+ ri = np.rint((nre-gle)/dds).astype('int32')
dims = (ri - li).astype('int32')
- assert(np.all(grid.LeftEdge <= node.left_edge))
- assert(np.all(grid.RightEdge >= node.right_edge))
+ assert(np.all(grid.LeftEdge <= nle))
+ assert(np.all(grid.RightEdge >= nre))
assert(np.all(dims > 0))
# print grid, dims, li, ri
@@ -134,19 +142,20 @@
def sum_cells(self, all_cells=False):
cells = 0
- for node in depth_traverse(self):
- if node.grid is None:
+ for node in depth_traverse(self.trunk):
+ if node.grid == -1:
continue
if not all_cells and not kd_is_leaf(node):
continue
grid = self.pf.h.grids[node.grid - self._id_offset]
dds = grid.dds
gle = grid.LeftEdge
- li = np.rint((node.left_edge-gle)/dds).astype('int32')
- ri = np.rint((node.right_edge-gle)/dds).astype('int32')
+ nle = get_left_edge(node)
+ nre = get_right_edge(node)
+ li = np.rint((nle-gle)/dds).astype('int32')
+ ri = np.rint((nre-gle)/dds).astype('int32')
dims = (ri - li).astype('int32')
cells += np.prod(dims)
-
return cells
class AMRKDTree(ParallelAnalysisInterface):
@@ -204,14 +213,8 @@
self._initialized = True
def traverse(self, viewpoint=None):
- if viewpoint is None:
- for node in depth_traverse(self.tree):
- if kd_is_leaf(node) and node.grid is not None:
- yield self.get_brick_data(node)
- else:
- for node in viewpoint_traverse(self.tree, viewpoint):
- if kd_is_leaf(node) and node.grid is not None:
- yield self.get_brick_data(node)
+ for node in kd_traverse(self.tree.trunk, viewpoint=viewpoint):
+ yield self.get_brick_data(node)
def get_node(self, nodeid):
path = np.binary_repr(nodeid)
@@ -232,13 +235,13 @@
owners = {}
for bottom_id in range(self.comm.size, 2*self.comm.size):
temp = self.get_node(bottom_id)
- owners[temp.id] = temp.id - self.comm.size
+ owners[temp.node_id] = temp.node_id - self.comm.size
while temp is not None:
if temp.parent is None: break
if temp == temp.parent.right:
break
temp = temp.parent
- owners[temp.id] = owners[temp.left.id]
+ owners[temp.node_id] = owners[temp.left.node_id]
return owners
def reduce_tree_images(self, image, viewpoint):
@@ -248,33 +251,32 @@
owners = self.get_reduce_owners()
node = self.get_node(nprocs + myrank)
- while True:
- if owners[node.parent.id] == myrank:
- split = node.parent.split
- left_in_front = viewpoint[split.dim] < node.parent.split.pos
- #add_to_front = (left_in_front == (node == node.parent.right))
- add_to_front = not left_in_front
- image = receive_and_reduce(self.comm, owners[node.parent.right.id],
- image, add_to_front)
- if node.parent.id == 1: break
- else: node = node.parent
- else:
- send_to_parent(self.comm, owners[node.parent.id], image)
- break
- image = scatter_image(self.comm, owners[1], image)
- return image
+ while owners[node.parent.node_id] == myrank:
+ split_dim = node.parent.get_split_dim()
+ split_pos = node.parent.get_split_pos()
+ add_to_front = viewpoint[split_dim] >= split_pos
+ image = receive_and_reduce(self.comm,
+ owners[node.parent.right.node_id],
+ image, add_to_front)
+ if node.parent.node_id == 1: break
+ else: node = node.parent
+ else:
+ send_to_parent(self.comm, owners[node.parent.node_id], image)
+
+ return scatter_image(self.comm, owners[1], image)
def get_brick_data(self, node):
if node.data is not None: return node.data
grid = self.pf.h.grids[node.grid - self._id_offset]
dds = grid.dds
gle = grid.LeftEdge
- gre = grid.RightEdge
- li = np.rint((node.left_edge-gle)/dds).astype('int32')
- ri = np.rint((node.right_edge-gle)/dds).astype('int32')
+ nle = get_left_edge(node)
+ nre = get_right_edge(node)
+ li = np.rint((nle-gle)/dds).astype('int32')
+ ri = np.rint((nre-gle)/dds).astype('int32')
dims = (ri - li).astype('int32')
- assert(np.all(grid.LeftEdge <= node.left_edge))
- assert(np.all(grid.RightEdge >= node.right_edge))
+ assert(np.all(grid.LeftEdge <= nle))
+ assert(np.all(grid.RightEdge >= nre))
if grid in self.current_saved_grids:
dds = self.current_vcds[self.current_saved_grids.index(grid)]
@@ -292,8 +294,8 @@
li[2]:ri[2]+1].copy() for d in dds]
brick = PartitionedGrid(grid.id, data,
- node.left_edge.copy(),
- node.right_edge.copy(),
+ nle.copy(),
+ nre.copy(),
dims.astype('int64'))
node.data = brick
if not self._initialized: self.brick_dimensions.append(dims)
@@ -405,7 +407,7 @@
self.comm.recv_array(self.comm.rank-1, tag=self.comm.rank-1)
f = h5py.File(fn,'w')
for node in depth_traverse(self.tree):
- i = node.id
+ i = node.node_id
if node.data is not None:
for fi,field in enumerate(self.fields):
try:
@@ -426,8 +428,8 @@
try:
f = h5py.File(fn,"a")
for node in depth_traverse(self.tree):
- i = node.id
- if node.grid is not None:
+ i = node.node_id
+ if node.grid != -1:
data = [f["brick_%s_%s" %
(hex(i), field)][:].astype('float64') for field in self.fields]
node.data = PartitionedGrid(node.grid.id, data,
@@ -476,32 +478,28 @@
gridids = []
splitdims = []
splitposs = []
- for node in depth_first_touch(self.tree):
- nids.append(node.id)
- les.append(node.left_edge)
- res.append(node.right_edge)
+ for node in depth_first_touch(self.tree.trunk):
+ nids.append(node.node_id)
+ les.append(node.get_left_edge())
+ res.append(node.get_right_edge())
if node.left is None:
leftids.append(-1)
else:
- leftids.append(node.left.id)
+ leftids.append(node.left.node_id)
if node.right is None:
rightids.append(-1)
else:
- rightids.append(node.right.id)
+ rightids.append(node.right.node_id)
if node.parent is None:
parentids.append(-1)
else:
- parentids.append(node.parent.id)
+ parentids.append(node.parent.node_id)
if node.grid is None:
gridids.append(-1)
else:
gridids.append(node.grid)
- if node.split is None:
- splitdims.append(-1)
- splitposs.append(np.nan)
- else:
- splitdims.append(node.split.dim)
- splitposs.append(node.split.pos)
+ splitdims.append(node.get_split_dim())
+ splitposs.append(node.get_split_pos())
return nids, parentids, leftids, rightids, les, res, gridids,\
splitdims, splitposs
@@ -518,19 +516,23 @@
N = nids.shape[0]
for i in xrange(N):
n = self.get_node(nids[i])
- n.left_edge = les[i]
- n.right_edge = res[i]
+ n.set_left_edge(les[i])
+ n.set_right_edge(res[i])
if lids[i] != -1 and n.left is None:
- n.left = Node(n, None, None, None,
- None, None, lids[i])
+ n.left = Node(n, None, None,
+ np.zeros(3, dtype='float64'),
+ np.zeros(3, dtype='float64'),
+ -1, lids[i])
if rids[i] != -1 and n.right is None:
- n.right = Node(n, None, None, None,
- None, None, rids[i])
+ n.right = Node(n, None, None,
+ np.zeros(3, dtype='float64'),
+ np.zeros(3, dtype='float64'),
+ -1, rids[i])
if gids[i] != -1:
n.grid = gids[i]
if splitdims[i] != -1:
- n.split = Split(splitdims[i], splitposs[i])
+ n.create_split(splitdims[i], splitposs[i])
mylog.info('AMRKDTree rebuilt, Final Volume: %e' % kd_sum_volume(self.tree.trunk))
return self.tree.trunk
diff -r 6f00933abb0249c3557ed7eeb7719c42618b2e13 -r d2de8bb9615a5a345e09be63294f85f4062754c1 yt/utilities/command_line.py
--- a/yt/utilities/command_line.py
+++ b/yt/utilities/command_line.py
@@ -1401,7 +1401,7 @@
tf = ColorTransferFunction((mi-2, ma+2))
tf.add_layers(n_contours,w=contour_width,col_bounds = (mi,ma), colormap=cmap)
- cam = pf.h.camera(center, L, width, (N,N), transfer_function=tf)
+ cam = pf.h.camera(center, L, width, (N,N), transfer_function=tf, fields=[field])
image = cam.snapshot()
if args.enhance:
@@ -1456,7 +1456,12 @@
"""
def __call__(self, args):
kwargs = {}
- from IPython.frontend.html.notebook.notebookapp import NotebookApp
+ try:
+ # IPython 1.0+
+ from IPython.html.notebookapp import NotebookApp
+ except ImportError:
+ # pre-IPython v1.0
+ from IPython.frontend.html.notebook.notebookapp import NotebookApp
pw = ytcfg.get("yt", "notebook_password")
if len(pw) == 0 and not args.no_password:
import IPython.lib
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt-3.0/commits/c2c55742d4d8/
Changeset: c2c55742d4d8
Branch: yt
User: jzuhone
Date: 2013-09-20 16:34:07
Summary: First pass at making projections with SZpack
Affected #: 4 files
diff -r d2de8bb9615a5a345e09be63294f85f4062754c1 -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf yt/analysis_modules/SZmaps.py
--- a/yt/analysis_modules/SZmaps.py
+++ /dev/null
@@ -1,97 +0,0 @@
-from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mp
-from yt.data_objects.image_array import ImageArray
-from yt.data_objects.field_info_container import add_field
-import numpy as np
-
-Tcmb = 2.726
-mueinv = 0.875
-
-try:
- import SZpack
-except:
- raise ImportError
-
-def _t_squared(field, data):
- return data["TempkeV"]*data["TempkeV"]
-add_field("TSquared", function=_t_squared)
-
-def _beta_perp_squared(field, data):
- axis = data.get_field_parameter("axis")
- if axis == "x":
- vv = np.sqrt(data["y-velocity"]**2+data["z-velocity"]**2)
- elif axis == "y":
- vv = np.sqrt(data["x-velocity"]**2+data["z-velocity"]**2)
- elif axis == "z":
- vv = np.sqrt(data["x-velocity"]**2+data["y-velocity"]**2)
- return vv/clight/clight
-add_field("BetaPerpSquared", function=_beta_perp_squared)
-
-def _beta_par(field, data):
- axis = data.get_field_parameter("axis")
- return data["%s-velocity" % (axis)]/clight
-add_field("BetaPar", function=_beta_par)
-
-def _beta_par_squared(field, data):
- return data["BetaPar"]**2
-add_field("BetaParSquared", function=_beta_par_squared)
-
-def _t_beta_par(field, data):
- return data["TempkeV"]*data["BetaPar"]
-add_field("TBetaPar", function=_t_beta_par)
-
-vlist = 'xyz'
-
-def SZProjection(pf, axis, freqs, center="c", width=(1, "unitary"), nx=800, ny=800):
-
- num_freqs = len(freqs)
- freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
- xo = hcgs*freqs*1.0e9/(kboltz*Tcmb)
-
- if isinstance(axis, np.ndarray) :
- frb1["TempkeV"] = off_axis_projection(pf, center, axis, width, nx, field="TempkeV", weight="Density")
- frb2["Density"] = off_axis_projection(pf, center, axis, width, nx, field="Density")
- else :
- if axis in vlist:
- vfield = "velocity_%s" % (axis)
- proj1.set_field_parameter("axis", axis)
- elif axis in xrange(0,3) :
- vfield = "velocity_%s" % (vlist[axis])
- proj1.set_field_parameter("axis", vlist[axis])
- proj1 = pf.h.proj(axis, "TempkeV", weight_field="Density")
- proj2 = pf.h.proj(axis, "Density")
- frb1 = proj1.to_frb(width, nx)
- frb2 = proj2.to_frb(width, ny)
-
- TeSZ = frb1["TempkeV"]
- omega1 = frb1["Tsquared"]/(TeSZ*TeSZ) - 1.
- sigma1 = frb1["TBetaPar"]/TeSZ - betac_par
- kappa1 = frb1["BetaParSquared"] - betac_par
-
- frb1["tau"] = sigma_thompson*frb2["Density"]*mueinv/mp
- frb1["omega1"] = ImageArray(omega1)
- frb1["kappa1"] = ImageArray(kappa1)
- frb1["sigma1"] = ImageArray(sigma1)
-
- SZsignal = np.zeros((num_freqs,nx,ny))
- omega = np.zeros((3))
- sigma = np.zeros((3))
-
- for i in xrange(nx):
-
- for j in xrange(ny):
-
- tau = frb1["tau"][i,j]
- Te = frb1["TempkeV"][i,j]
- bpar = frb1["BetaPar"][i,j]
- bperp2 = frb["BetaPerpSquared"][i,j]
- omega[0] = frb1["omega1"][i,j]
- sigma[0] = frb1["sigma1"][i,j]
- kappa = frb1["kappa1"][i,j]
-
- SZsignal[:,i,j] = SZpack.compute_combo_means_ex(xo, tau, Te, bpar, omega,
- sigma, kappa, bperp2)
-
- for i in xrange(num_freqs) :
- frb1[freq_fields[i]] = ImageArray(SZsignal[i,:,:])
-
- return frb1
diff -r d2de8bb9615a5a345e09be63294f85f4062754c1 -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -118,7 +118,7 @@
TwoPointFunctions, \
FcnSet
-from .SZmaps import SZprojection
+from .sunyaev_zeldovich.api import SZprojection
from .radmc3d_export.api import \
RadMC3DWriter
diff -r d2de8bb9615a5a345e09be63294f85f4062754c1 -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf yt/analysis_modules/sunyaev_zeldovich/api.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/api.py
@@ -0,0 +1,1 @@
+from .projection import SZprojection
diff -r d2de8bb9615a5a345e09be63294f85f4062754c1 -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf yt/analysis_modules/sunyaev_zeldovich/projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -0,0 +1,114 @@
+from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mp
+from yt.data_objects.image_array import ImageArray
+from yt.data_objects.field_info_container import add_field
+from yt.funcs import fix_axis, mylog, iterable, get_pbar
+from yt.definitions import inv_axis_names
+from yt.visualization.volume_rendering.camera import off_axis_projection
+import numpy as np
+
+Tcmb = 2.726
+
+try:
+ import SZpack
+except:
+ raise ImportError("SZpack not installed.")
+
+vlist = "xyz"
+nvec = int(0)
+
+def _t_squared(field, data):
+ return data["TempkeV"]*data["TempkeV"]
+add_field("TSquared", function=_t_squared)
+
+def _beta_perp_squared(field, data):
+ return data["VelocityMagnitude"]**2/clight/clight - data["BetaParSquared"]
+add_field("BetaPerpSquared", function=_beta_perp_squared)
+
+def _beta_par(field, data):
+ axis = data.get_field_parameter("axis")
+ if iterable(nvec):
+ vpar = (data["x-velocity"]*nvec[0]+
+ data["y-velocity"]*nvec[1]+
+ data["z-velocity"]*nvec[2])
+ else:
+ vpar = data["%s-velocity" % (vlist[nvec])]
+ return vpar/clight
+add_field("BetaPar", function=_beta_par)
+
+def _beta_par_squared(field, data):
+ return data["BetaPar"]**2
+add_field("BetaParSquared", function=_beta_par_squared)
+
+def _t_beta_par(field, data):
+ return data["TempkeV"]*data["BetaPar"]
+add_field("TBetaPar", function=_t_beta_par)
+
+def SZProjection(pf, axis, freqs, center="c", width=(1, "unitary"), nx=800, mue=None):
+
+ global nvec # Ugly!
+
+ if mue is None:
+ mueinv = 0.875
+ else:
+ mueinv = 1./mue
+
+ num_freqs = len(freqs)
+ freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
+ xinit = hcgs*freqs*1.0e9/(kboltz*Tcmb)
+
+ if isinstance(axis, basestring) or not iterable(axis):
+ axis = fix_axis(axis)
+ nvec = axis
+ proj1 = pf.h.proj(axis, "TempkeV", weight_field="Density")
+ proj2 = pf.h.proj(axis, "Density")
+ frb1 = proj1.to_frb(width, nx)
+ frb2 = proj2.to_frb(width, nx)
+ Te = frb1["TempkeV"]
+ bpar = frb1["BetaPar"]
+ bperp2 = frb1["BetaPerpSquared"]
+ omega1 = frb1["TSquared"]/(Te*Te) - 1.
+ sigma1 = frb1["TBetaPar"]/Te - bpar
+ kappa1 = frb1["BetaParSquared"] - bpar
+ tau = sigma_thompson*frb2["Density"]*mueinv/mp
+ else:
+ nvec = axis
+ if iterable(width):
+ w = width[0]/pf.units[width[1]]
+ else:
+ w = width
+ Te = off_axis_projection(pf, center, axis, w, nx, "TempkeV", weight="Density")
+ bpar = off_axis_projection(pf, center, axis, w, nx, "BetaPar", weight="Density")
+ bperp2 = off_axis_projection(pf, center, axis, w, nx, "BetaPerpSquared", weight="Density")
+ omega1 = off_axis_projection(pf, center, axis, w, nx, "TSquared", weight="Density")
+ omega1 = omega1/(Te*Te) - 1.
+ sigma1 = off_axis_projection(pf, center, axis, w, nx, "TBetaPar", weight="Density")
+ sigma1 = sigma1/Te - bpar
+ kappa1 = off_axis_projection(pf, center, axis, w, nx, "BetaParSquared", weight="Density")
+ kappa1 -= bpar
+ tau = off_axis_projection(pf, center, axis, w, nx, "Density")
+ tau *= sigma_thompson*mueinv/mp
+
+ SZsignal = np.zeros((num_freqs,nx,nx))
+ xo = np.zeros((num_freqs))
+
+ k = int(0)
+
+ pbar = get_pbar("Computing SZ signal.", nx*nx)
+
+ for i in xrange(nx):
+ for j in xrange(nx):
+ xo[:] = xinit[:]
+ SZpack.compute_combo_means(xo, tau[i,j], Te[i,j],
+ bpar[i,j], omega[i,j],
+ sigma[i,j], kappa[i,j], bperp2[i,j])
+ SZsignal[:,i,j] = -xo[:]
+ pbar.update(k)
+ k += 1
+
+ pbar.finish()
+
+ outimg = {}
+ for i in xrange(num_freqs) :
+ outimg[freq_fields[i]] = ImageArray(SZsignal[i,:,:])
+
+ return outimg
https://bitbucket.org/yt_analysis/yt-3.0/commits/fdcac0502890/
Changeset: fdcac0502890
Branch: yt
User: jzuhone
Date: 2013-09-21 19:18:24
Summary: Merged yt_analysis/yt into yt
Affected #: 448 files
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb .hgchurn
--- a/.hgchurn
+++ b/.hgchurn
@@ -17,3 +17,4 @@
tabel = tabel at slac.stanford.edu
sername=kayleanelson = kaylea.nelson at yale.edu
kayleanelson = kaylea.nelson at yale.edu
+jcforbes at ucsc.edu = jforbes at ucolick.org
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -5156,3 +5156,4 @@
0000000000000000000000000000000000000000 mpi-opaque
f15825659f5af3ce64aaad30062aff3603cbfb66 hop callback
0000000000000000000000000000000000000000 hop callback
+079e456c38a87676472a458210077e2be325dc85 last_gplv3
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb CITATION
--- /dev/null
+++ b/CITATION
@@ -0,0 +1,31 @@
+To cite yt in publications, please use:
+
+Turk, M. J., Smith, B. D., Oishi, J. S., et al. 2011, ApJS, 192, 9
+
+In the body of the text, please add a footnote to the yt webpage:
+
+http://yt-project.org/
+
+For LaTex and BibTex users:
+
+\bibitem[Turk et al.(2011)]{2011ApJS..192....9T} Turk, M.~J., Smith, B.~D.,
+Oishi, J.~S., et al.\ 2011, \apjs, 192, 9
+
+ at ARTICLE{2011ApJS..192....9T,
+ author = {{Turk}, M.~J. and {Smith}, B.~D. and {Oishi}, J.~S. and {Skory}, S. and
+{Skillman}, S.~W. and {Abel}, T. and {Norman}, M.~L.},
+ title = "{yt: A Multi-code Analysis Toolkit for Astrophysical Simulation Data}",
+ journal = {\apjs},
+archivePrefix = "arXiv",
+ eprint = {1011.3514},
+ primaryClass = "astro-ph.IM",
+ keywords = {cosmology: theory, methods: data analysis, methods: numerical},
+ year = 2011,
+ month = jan,
+ volume = 192,
+ eid = {9},
+ pages = {9},
+ doi = {10.1088/0067-0049/192/1/9},
+ adsurl = {http://adsabs.harvard.edu/abs/2011ApJS..192....9T},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb COPYING.txt
--- /dev/null
+++ b/COPYING.txt
@@ -0,0 +1,81 @@
+===============================
+ The yt project licensing terms
+===============================
+
+yt is licensed under the terms of the Modified BSD License (also known as New
+or Revised BSD), as follows:
+
+Copyright (c) 2013-, yt Development Team
+Copyright (c) 2006-2013, Matthew Turk <matthewturk at gmail.com>
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+Redistributions in binary form must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+Neither the name of the yt Development Team nor the names of its
+contributors may be used to endorse or promote products derived from this
+software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+About the yt Development Team
+-----------------------------
+
+Matthew Turk began yt in 2006 and remains the project lead. Over time yt has
+grown to include contributions from a large number of individuals from many
+diverse institutions, scientific, and technical backgrounds.
+
+Until the fall of 2013, yt was licensed under the GPLv3. However, with consent
+from all developers and on a public mailing list, yt has been relicensed under
+the BSD 3-clause under a shared copyright model. For more information, see:
+http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2013-July/003239.html
+All versions of yt prior to this licensing change are available under the
+GPLv3; all subsequent versions are available under the BSD 3-clause license.
+
+The yt Development Team is the set of all contributors to the yt project. This
+includes all of the yt subprojects.
+
+The core team that coordinates development on BitBucket can be found here:
+http://bitbucket.org/yt_analysis/
+
+
+Our Copyright Policy
+--------------------
+
+yt uses a shared copyright model. Each contributor maintains copyright
+over their contributions to yt. But, it is important to note that these
+contributions are typically only changes to the repositories. Thus, the yt
+source code, in its entirety is not the copyright of any single person or
+institution. Instead, it is the collective copyright of the entire yt
+Development Team. If individual contributors want to maintain a record of what
+changes/contributions they have specific copyright on, they should indicate
+their copyright in the commit message of the change, when they commit the
+change to one of the yt repositories.
+
+With this in mind, the following banner should be used in any source code file
+to indicate the copyright and license terms:
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb CREDITS
--- a/CREDITS
+++ b/CREDITS
@@ -1,51 +1,55 @@
-YT is a group effort.
+yt is a group effort.
-Contributors: Tom Abel (tabel at stanford.edu)
- David Collins (dcollins at physics.ucsd.edu)
- Brian Crosby (crosby.bd at gmail.com)
- Andrew Cunningham (ajcunn at gmail.com)
- Nathan Goldbaum (goldbaum at ucolick.org)
- Markus Haider (markus.haider at uibk.ac.at)
- Cameron Hummels (chummels at gmail.com)
- Christian Karch (chiffre at posteo.de)
- Ji-hoon Kim (me at jihoonkim.org)
- Steffen Klemer (sklemer at phys.uni-goettingen.de)
- Kacper Kowalik (xarthisius.kk at gmail.com)
- Michael Kuhlen (mqk at astro.berkeley.edu)
- Eve Lee (elee at cita.utoronto.ca)
- Yuan Li (yuan at astro.columbia.edu)
- Chris Malone (chris.m.malone at gmail.com)
- Josh Maloney (joshua.moloney at colorado.edu)
- Chris Moody (cemoody at ucsc.edu)
- Andrew Myers (atmyers at astro.berkeley.edu)
- Jeff Oishi (jsoishi at gmail.com)
- Jean-Claude Passy (jcpassy at uvic.ca)
- Mark Richardson (Mark.L.Richardson at asu.edu)
- Thomas Robitaille (thomas.robitaille at gmail.com)
- Anna Rosen (rosen at ucolick.org)
- Anthony Scopatz (scopatz at gmail.com)
- Devin Silvia (devin.silvia at colorado.edu)
- Sam Skillman (samskillman at gmail.com)
- Stephen Skory (s at skory.us)
- Britton Smith (brittonsmith at gmail.com)
- Geoffrey So (gsiisg at gmail.com)
- Casey Stark (caseywstark at gmail.com)
- Elizabeth Tasker (tasker at astro1.sci.hokudai.ac.jp)
- Stephanie Tonnesen (stonnes at gmail.com)
- Matthew Turk (matthewturk at gmail.com)
- Rich Wagner (rwagner at physics.ucsd.edu)
- John Wise (jwise at physics.gatech.edu)
- John ZuHone (jzuhone at gmail.com)
+Contributors:
+ Tom Abel (tabel at stanford.edu)
+ David Collins (dcollins at physics.ucsd.edu)
+ Brian Crosby (crosby.bd at gmail.com)
+ Andrew Cunningham (ajcunn at gmail.com)
+ Hilary Egan (hilaryye at gmail.com)
+ John Forces (jforbes at ucolick.org)
+ Nathan Goldbaum (goldbaum at ucolick.org)
+ Markus Haider (markus.haider at uibk.ac.at)
+ Cameron Hummels (chummels at gmail.com)
+ Christian Karch (chiffre at posteo.de)
+ Ji-hoon Kim (me at jihoonkim.org)
+ Steffen Klemer (sklemer at phys.uni-goettingen.de)
+ Kacper Kowalik (xarthisius.kk at gmail.com)
+ Michael Kuhlen (mqk at astro.berkeley.edu)
+ Eve Lee (elee at cita.utoronto.ca)
+ Sam Leitner (sam.leitner at gmail.com)
+ Yuan Li (yuan at astro.columbia.edu)
+ Chris Malone (chris.m.malone at gmail.com)
+ Josh Maloney (joshua.moloney at colorado.edu)
+ Chris Moody (cemoody at ucsc.edu)
+ Andrew Myers (atmyers at astro.berkeley.edu)
+ Jill Naiman (jnaiman at ucolick.org)
+ Kaylea Nelson (kaylea.nelson at yale.edu)
+ Jeff Oishi (jsoishi at gmail.com)
+ Jean-Claude Passy (jcpassy at uvic.ca)
+ Mark Richardson (Mark.L.Richardson at asu.edu)
+ Thomas Robitaille (thomas.robitaille at gmail.com)
+ Anna Rosen (rosen at ucolick.org)
+ Douglas Rudd (drudd at uchicago.edu)
+ Anthony Scopatz (scopatz at gmail.com)
+ Noel Scudder (noel.scudder at stonybrook.edu)
+ Devin Silvia (devin.silvia at colorado.edu)
+ Sam Skillman (samskillman at gmail.com)
+ Stephen Skory (s at skory.us)
+ Britton Smith (brittonsmith at gmail.com)
+ Geoffrey So (gsiisg at gmail.com)
+ Casey Stark (caseywstark at gmail.com)
+ Elizabeth Tasker (tasker at astro1.sci.hokudai.ac.jp)
+ Stephanie Tonnesen (stonnes at gmail.com)
+ Matthew Turk (matthewturk at gmail.com)
+ Rich Wagner (rwagner at physics.ucsd.edu)
+ Andrew Wetzel (andrew.wetzel at yale.edu)
+ John Wise (jwise at physics.gatech.edu)
+ John ZuHone (jzuhone at gmail.com)
-We also include the Delaunay Triangulation module written by Robert Kern of
-Enthought, the cmdln.py module by Trent Mick, and the progressbar module by
+Several items included in the yt/extern directory were written by other
+individuals and may bear their own license, including the progressbar module by
Nilton Volpato. The PasteBin interface code (as well as the PasteBin itself)
-was written by the Pocoo collective (pocoo.org). The RamsesRead++ library was
-developed by Oliver Hahn. yt also includes a slightly-modified version of
-libconfig (http://www.hyperrealm.com/libconfig/) and an unmodified version of
-several routines from HEALpix (http://healpix.jpl.nasa.gov/).
-
-Large parts of development of yt were guided by discussions with Tom Abel, Ralf
-Kaehler, Mike Norman and Greg Bryan.
+was written by the Pocoo collective (pocoo.org).
+developed by Oliver Hahn.
Thanks to everyone for all your contributions!
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb FUNDING
--- a/FUNDING
+++ /dev/null
@@ -1,35 +0,0 @@
-The development of yt has benefited from funding from many different sources
-and institutions. Here is an incomplete list of these sources:
-
- * NSF grant OCI-1048505
- * NSF grant AST-0239709
- * NSF grant AST-0707474
- * NSF grant AST-0708960
- * NSF grant AST-0808184
- * NSF grant AST-0807215
- * NSF grant AST-0807312
- * NSF grant AST-0807075
- * NSF grant AST-0908199
- * NSF grant AST-0908553
- * NASA grant ATFP NNX08-AH26G
- * NASA grant ATFP NNX09-AD80G
- * NASA grant ATFP NNZ07-AG77G
- * DOE Computational Science Graduate Fellowship under grant number DE-FG02-97ER25308
-
-Additionally, development of yt has benefited from the hospitality and hosting
-of the following institutions:
-
- * Columbia University
- * Harvard-Smithsonian Center for Astrophysics
- * Institute for Advanced Study
- * Kavli Institute for Particle Astrophysics and Cosmology
- * Kavli Institute for Theoretical Physics
- * Los Alamos National Lab
- * Michigan State University
- * Princeton University
- * Stanford University
- * University of California High-Performance Astro-Computing Center
- * University of California at Berkeley
- * University of California at San Diego
- * University of California at Santa Cruz
- * University of Colorado at Boulder
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb LICENSE.txt
--- a/LICENSE.txt
+++ /dev/null
@@ -1,674 +0,0 @@
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-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
- <one line to give the program's name and a brief idea of what it does.>
- Copyright (C) <year><name of author>
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- <program> Copyright (C) <year><name of author>
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,4 @@
include distribute_setup.py README* CREDITS FUNDING LICENSE.txt
recursive-include yt/gui/reason/html *.html *.png *.ico *.js
recursive-include yt *.pyx *.pxd *.hh *.h README*
+recursive-include yt/utilities/kdtree *.f90 *.v Makefile LICENSE
\ No newline at end of file
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb doc/how_to_develop_yt.txt
--- a/doc/how_to_develop_yt.txt
+++ b/doc/how_to_develop_yt.txt
@@ -25,7 +25,7 @@
Licenses
--------
-All code in yt should be under the GPL-3 (preferred) or a compatible license.
+All code in yt should be under the BSD 3-clause license.
How To Get The Source Code
--------------------------
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -419,7 +419,7 @@
echo "be installing ZeroMQ"
printf "%-15s = %s so I " "INST_ROCKSTAR" "${INST_ROCKSTAR}"
-get_willwont ${INST_0MQ}
+get_willwont ${INST_ROCKSTAR}
echo "be installing Rockstar"
echo
@@ -473,11 +473,18 @@
function do_setup_py
{
[ -e $1/done ] && return
- echo "Installing $1 (arguments: '$*')"
- [ ! -e $1/extracted ] && tar xfz $1.tar.gz
- touch $1/extracted
- cd $1
- if [ ! -z `echo $1 | grep h5py` ]
+ LIB=$1
+ shift
+ if [ -z "$@" ]
+ then
+ echo "Installing $LIB"
+ else
+ echo "Installing $LIB (arguments: '$@')"
+ fi
+ [ ! -e $LIB/extracted ] && tar xfz $LIB.tar.gz
+ touch $LIB/extracted
+ cd $LIB
+ if [ ! -z `echo $LIB | grep h5py` ]
then
shift
( ${DEST_DIR}/bin/python2.7 setup.py build --hdf5=${HDF5_DIR} $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
@@ -519,8 +526,8 @@
function get_ytproject
{
+ [ -e $1 ] && return
echo "Downloading $1 from yt-project.org"
- [ -e $1 ] && return
${GETFILE} "http://yt-project.org/dependencies/$1" || do_exit
( ${SHASUM} -c $1.sha512 2>&1 ) 1>> ${LOG_FILE} || do_exit
}
@@ -551,67 +558,93 @@
mkdir -p ${DEST_DIR}/src
cd ${DEST_DIR}/src
+CYTHON='Cython-0.19.1'
+FORTHON='Forthon-0.8.11'
+PYX='PyX-0.12.1'
+PYTHON='Python-2.7.5'
+BZLIB='bzip2-1.0.6'
+FREETYPE_VER='freetype-2.4.12'
+H5PY='h5py-2.1.3'
+HDF5='hdf5-1.8.11'
+IPYTHON='ipython-1.0.0'
+LAPACK='lapack-3.4.2'
+PNG=libpng-1.6.3
+MATPLOTLIB='matplotlib-1.3.0'
+MERCURIAL='mercurial-2.7'
+NOSE='nose-1.3.0'
+NUMPY='numpy-1.7.1'
+PYTHON_HGLIB='python-hglib-1.0'
+PYZMQ='pyzmq-13.1.0'
+ROCKSTAR='rockstar-0.99.6'
+SCIPY='scipy-0.12.0'
+SQLITE='sqlite-autoconf-3071700'
+SYMPY='sympy-0.7.3'
+TORNADO='tornado-3.1'
+ZEROMQ='zeromq-3.2.3'
+ZLIB='zlib-1.2.8'
+
# Now we dump all our SHA512 files out.
-echo 'fb85d71bb4f80b35f0d0f1735c650dd75c5f84b05635ddf91d6241ff103b5a49158c5b851a20c15e05425f6dde32a4971b35fcbd7445f61865b4d61ffd1fbfa1 Cython-0.18.tar.gz' > Cython-0.18.tar.gz.sha512
+echo '9dcdda5b2ee2e63c2d3755245b7b4ed2f4592455f40feb6f8e86503195d9474559094ed27e789ab1c086d09da0bb21c4fe844af0e32a7d47c81ff59979b18ca0 Cython-0.19.1.tar.gz' > Cython-0.19.1.tar.gz.sha512
+echo '3f53d0b474bfd79fea2536d0a9197eaef6c0927e95f2f9fd52dbd6c1d46409d0e649c21ac418d8f7767a9f10fe6114b516e06f2be4b06aec3ab5bdebc8768220 Forthon-0.8.11.tar.gz' > Forthon-0.8.11.tar.gz.sha512
echo '4941f5aa21aff3743546495fb073c10d2657ff42b2aff401903498638093d0e31e344cce778980f28a7170c6d29eab72ac074277b9d4088376e8692dc71e55c1 PyX-0.12.1.tar.gz' > PyX-0.12.1.tar.gz.sha512
-echo '3349152c47ed2b63c5c9aabcfa92b8497ea9d71ca551fd721e827fcb8f91ff9fbbee6bba8f8cb2dea185701b8798878b4b2435c1496b63d4b4a37c624a625299 Python-2.7.4.tgz' > Python-2.7.4.tgz.sha512
+echo 'd6580eb170b36ad50f3a30023fe6ca60234156af91ccb3971b0b0983119b86f3a9f6c717a515c3c6cb72b3dcbf1d02695c6d0b92745f460b46a3defd3ff6ef2f Python-2.7.5.tgz' > Python-2.7.5.tgz.sha512
+echo '172f2bc671145ebb0add2669c117863db35851fb3bdb192006cd710d4d038e0037497eb39a6d01091cb923f71a7e8982a77b6e80bf71d6275d5d83a363c8d7e5 rockstar-0.99.6.tar.gz' > rockstar-0.99.6.tar.gz.sha512
+echo '276bd9c061ec9a27d478b33078a86f93164ee2da72210e12e2c9da71dcffeb64767e4460b93f257302b09328eda8655e93c4b9ae85e74472869afbeae35ca71e blas.tar.gz' > blas.tar.gz.sha512
echo '00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12 bzip2-1.0.6.tar.gz' > bzip2-1.0.6.tar.gz.sha512
echo 'a296dfcaef7e853e58eed4e24b37c4fa29cfc6ac688def048480f4bb384b9e37ca447faf96eec7b378fd764ba291713f03ac464581d62275e28eb2ec99110ab6 reason-js-20120623.zip' > reason-js-20120623.zip.sha512
-echo 'b46c93d76f8ce09c94765b20b2eeadf71207671f1131777de178b3727c235b4dd77f6e60d62442b96648c3c6749e9e4c1194c1b02af7e946576be09e1ff7ada3 freetype-2.4.11.tar.gz' > freetype-2.4.11.tar.gz.sha512
-echo '15ca0209e8d8f172cb0708a2de946fbbde8551d9bebc4a95fa7ae31558457a7f43249d5289d7675490c577deb4e0153698fd2407644078bf30bd5ab10135fce3 h5py-2.1.2.tar.gz' > h5py-2.1.2.tar.gz.sha512
-echo 'c68a425bacaa7441037910b9166f25b89e1387776a7749a5350793f89b1690350df5f018060c31d03686e7c3ed2aa848bd2b945c96350dc3b6322e087934783a hdf5-1.8.9.tar.gz' > hdf5-1.8.9.tar.gz.sha512
-echo 'b2b53ed358bacab9e8d63a51f17bd5f121ece60a1d7c53e8a8eb08ad8b1e4393a8d7a86eec06e2efc62348114f0d84c0a3dfc805e68e6edd93b20401962b3554 libpng-1.6.1.tar.gz' > libpng-1.6.1.tar.gz.sha512
-echo '497f91725eaf361bdb9bdf38db2bff5068a77038f1536df193db64c9b887e3b0d967486daee722eda6e2c4e60f034eee030673e53d07bf0db0f3f7c0ef3bd208 matplotlib-1.2.1.tar.gz' > matplotlib-1.2.1.tar.gz.sha512
-echo '928fdeaaf0eaec80adbd8765521de9666ab56aaa2101fb9ab2cb392d8b29475d3b052d89652ff9b67522cfcc6cd958717ac715f51b0573ee088e9a595f29afe2 mercurial-2.5.4.tar.gz' > mercurial-2.5.4.tar.gz.sha512
-echo 'a485daa556f6c76003de1dbb3e42b3daeee0a320c69c81b31a7d2ebbc2cf8ab8e96c214a4758e5e7bf814295dc1d6aa563092b714db7e719678d8462135861a8 numpy-1.7.0.tar.gz' > numpy-1.7.0.tar.gz.sha512
-echo '293d78d14a9347cb83e1a644e5f3e4447ed6fc21642c51683e5495dda08d2312194a73d1fc3c1d78287e33ed065aa251ecbaa7c0ea9189456c1702e96d78becd sqlite-autoconf-3071601.tar.gz' > sqlite-autoconf-3071601.tar.gz.sha512
-echo 'b1c073ad26684e354f7c522c14655840592e03872bc0a94690f89cae2ff88f146fce1dad252ff27a889dac4a32ff9f8ab63ba940671f9da89e9ba3e19f1bf58d zlib-1.2.7.tar.gz' > zlib-1.2.7.tar.gz.sha512
-echo '05ac335727a2c3036f31a2506fdd2615aa436bfbe2f81799fe6c51bffe2591ad6a8427f3b25c34e7e709fb4e7607a0589dc7a22185c1f9b894e90de6711a88aa ipython-0.13.1.tar.gz' > ipython-0.13.1.tar.gz.sha512
-echo 'b9d061ca49e54ea917e0aed2b2a48faef33061dbf6d17eae7f8c3fff0b35ca883e7324f6cb24bda542443f669dcd5748037a5f2309f4c359d68adef520894865 zeromq-3.2.2.tar.gz' > zeromq-3.2.2.tar.gz.sha512
-echo '852fce8a8308c4e1e4b19c77add2b2055ca2ba570b28e8364888df490af92b860c72e860adfb075b3405a9ceb62f343889f20a8711c9353a7d9059adee910f83 pyzmq-13.0.2.tar.gz' > pyzmq-13.0.2.tar.gz.sha512
-echo '303bd3fbea22be57fddf7df78ddf5a783d355a0c8071b1363250daafc20232ddd28eedc44aa1194f4a7afd82f9396628c5bb06819e02b065b6a1b1ae8a7c19e1 tornado-3.0.tar.gz' > tornado-3.0.tar.gz.sha512
-echo '3f53d0b474bfd79fea2536d0a9197eaef6c0927e95f2f9fd52dbd6c1d46409d0e649c21ac418d8f7767a9f10fe6114b516e06f2be4b06aec3ab5bdebc8768220 Forthon-0.8.11.tar.gz' > Forthon-0.8.11.tar.gz.sha512
-echo 'c13116c1f0547000cc565e15774687b9e884f8b74fb62a84e578408a868a84961704839065ae4f21b662e87f2aaedf6ea424ea58dfa9d3d73c06281f806d15dd nose-1.2.1.tar.gz' > nose-1.2.1.tar.gz.sha512
-echo 'd67de9567256e6f1649e4f3f7dfee63371d5f00fd3fd4f92426198f862e97c57f70e827d19f4e5e1929ad85ef2ce7aa5a0596b101cafdac71672e97dc115b397 python-hglib-0.3.tar.gz' > python-hglib-0.3.tar.gz.sha512
-echo 'ffc602eb346717286b3d0a6770c60b03b578b3cf70ebd12f9e8b1c8c39cdb12ef219ddaa041d7929351a6b02dbb8caf1821b5452d95aae95034cbf4bc9904a7a sympy-0.7.2.tar.gz' > sympy-0.7.2.tar.gz.sha512
+echo '609a68a3675087e0cc95268574f31e104549daa48efe15a25a33b8e269a93b4bd160f4c3e8178dca9c950ef5ca514b039d6fd1b45db6af57f25342464d0429ce freetype-2.4.12.tar.gz' > freetype-2.4.12.tar.gz.sha512
+echo '2eb7030f8559ff5cb06333223d98fda5b3a663b6f4a026949d1c423aa9a869d824e612ed5e1851f3bf830d645eea1a768414f73731c23ab4d406da26014fe202 h5py-2.1.3.tar.gz' > h5py-2.1.3.tar.gz.sha512
+echo 'e9db26baa297c8ed10f1ca4a3fcb12d6985c6542e34c18d48b2022db73014f054c8b8434f3df70dcf44631f38b016e8050701d52744953d0fced3272d7b6b3c1 hdf5-1.8.11.tar.gz' > hdf5-1.8.11.tar.gz.sha512
+echo '1b309c08009583e66d1725a2d2051e6de934db246129568fa6d5ba33ad6babd3b443e7c2782d817128d2b112e21bcdd71e66be34fbd528badd900f1d0ed3db56 ipython-1.0.0.tar.gz' > ipython-1.0.0.tar.gz.sha512
+echo '8770214491e31f0a7a3efaade90eee7b0eb20a8a6ab635c5f854d78263f59a1849133c14ef5123d01023f0110cbb9fc6f818da053c01277914ae81473430a952 lapack-3.4.2.tar.gz' > lapack-3.4.2.tar.gz.sha512
+echo '887582e5a22e4cde338aa8fec7a89f6dd31f2f02b8842735f00f970f64582333fa03401cea6d01704083403c7e8b7ebc26655468ce930165673b33efa4bcd586 libpng-1.6.3.tar.gz' > libpng-1.6.3.tar.gz.sha512
+echo '990e3a155ca7a9d329c41a43b44a9625f717205e81157c668a8f3f2ad5459ed3fed8c9bd85e7f81c509e0628d2192a262d4aa30c8bfc348bb67ed60a0362505a matplotlib-1.3.0.tar.gz' > matplotlib-1.3.0.tar.gz.sha512
+echo 'e425778edb0f71c34e719e04561ee3de37feaa1be4d60b94c780aebdbe6d41f8f4ab15103a8bbe8894ebeb228c42f0e2cd41b8db840f8384e1cd7cd2d5b67b97 mercurial-2.7.tar.gz' > mercurial-2.7.tar.gz.sha512
+echo 'a3b8060e415560a868599224449a3af636d24a060f1381990b175dcd12f30249edd181179d23aea06b0c755ff3dc821b7a15ed8840f7855530479587d4d814f4 nose-1.3.0.tar.gz' > nose-1.3.0.tar.gz.sha512
+echo 'd58177f3971b6d07baf6f81a2088ba371c7e43ea64ee7ada261da97c6d725b4bd4927122ac373c55383254e4e31691939276dab08a79a238bfa55172a3eff684 numpy-1.7.1.tar.gz' > numpy-1.7.1.tar.gz.sha512
+echo '9c0a61299779aff613131aaabbc255c8648f0fa7ab1806af53f19fbdcece0c8a68ddca7880d25b926d67ff1b9201954b207919fb09f6a290acb078e8bbed7b68 python-hglib-1.0.tar.gz' > python-hglib-1.0.tar.gz.sha512
+echo 'c65013293dd4049af5db009fdf7b6890a3c6b1e12dd588b58fb5f5a5fef7286935851fb7a530e03ea16f28de48b964e50f48bbf87d34545fd23b80dd4380476b pyzmq-13.1.0.tar.gz' > pyzmq-13.1.0.tar.gz.sha512
echo '172f2bc671145ebb0add2669c117863db35851fb3bdb192006cd710d4d038e0037497eb39a6d01091cb923f71a7e8982a77b6e80bf71d6275d5d83a363c8d7e5 rockstar-0.99.6.tar.gz' > rockstar-0.99.6.tar.gz.sha512
-echo 'd4fdd62f2db5285cd133649bd1bfa5175cb9da8304323abd74e0ef1207d55e6152f0f944da1da75f73e9dafb0f3bb14efba3c0526c732c348a653e0bd223ccfa scipy-0.11.0.tar.gz' > scipy-0.11.0.tar.gz.sha512
-echo '276bd9c061ec9a27d478b33078a86f93164ee2da72210e12e2c9da71dcffeb64767e4460b93f257302b09328eda8655e93c4b9ae85e74472869afbeae35ca71e blas.tar.gz' > blas.tar.gz.sha512
-echo '8770214491e31f0a7a3efaade90eee7b0eb20a8a6ab635c5f854d78263f59a1849133c14ef5123d01023f0110cbb9fc6f818da053c01277914ae81473430a952 lapack-3.4.2.tar.gz' > lapack-3.4.2.tar.gz.sha512
+echo '80c8e137c3ccba86575d4263e144ba2c4684b94b5cd620e200f094c92d4e118ea6a631d27bdb259b0869771dfaeeae68c0fdd37fdd740b9027ee185026e921d4 scipy-0.12.0.tar.gz' > scipy-0.12.0.tar.gz.sha512
+echo '96f3e51b46741450bc6b63779c10ebb4a7066860fe544385d64d1eda52592e376a589ef282ace2e1df73df61c10eab1a0d793abbdaf770e60289494d4bf3bcb4 sqlite-autoconf-3071700.tar.gz' > sqlite-autoconf-3071700.tar.gz.sha512
+echo '2992baa3edfb4e1842fb642abf0bf0fc0bf56fc183aab8fed6b3c42fbea928fa110ede7fdddea2d63fc5953e8d304b04da433dc811134fadefb1eecc326121b8 sympy-0.7.3.tar.gz' > sympy-0.7.3.tar.gz.sha512
+echo '101544db6c97beeadc5a02b2ef79edefa0a07e129840ace2e4aa451f3976002a273606bcdc12d6cef5c22ff4c1c9dcf60abccfdee4cbef8e3f957cd25c0430cf tornado-3.1.tar.gz' > tornado-3.1.tar.gz.sha512
+echo '34ffb6aa645f62bd1158a8f2888bf92929ccf90917a6c50ed51ed1240732f498522e164d1536f26480c87ad5457fe614a93bf0e15f2f89b0b168e64a30de68ca zeromq-3.2.3.tar.gz' > zeromq-3.2.3.tar.gz.sha512
+echo 'ece209d4c7ec0cb58ede791444dc754e0d10811cbbdebe3df61c0fd9f9f9867c1c3ccd5f1827f847c005e24eef34fb5bf87b5d3f894d75da04f1797538290e4a zlib-1.2.8.tar.gz' > zlib-1.2.8.tar.gz.sha512
# Individual processes
-[ -z "$HDF5_DIR" ] && get_ytproject hdf5-1.8.9.tar.gz
-[ $INST_ZLIB -eq 1 ] && get_ytproject zlib-1.2.7.tar.gz
-[ $INST_BZLIB -eq 1 ] && get_ytproject bzip2-1.0.6.tar.gz
-[ $INST_PNG -eq 1 ] && get_ytproject libpng-1.6.1.tar.gz
-[ $INST_FTYPE -eq 1 ] && get_ytproject freetype-2.4.11.tar.gz
-[ $INST_SQLITE3 -eq 1 ] && get_ytproject sqlite-autoconf-3071601.tar.gz
-[ $INST_PYX -eq 1 ] && get_ytproject PyX-0.12.1.tar.gz
-[ $INST_0MQ -eq 1 ] && get_ytproject zeromq-3.2.2.tar.gz
-[ $INST_0MQ -eq 1 ] && get_ytproject pyzmq-13.0.2.tar.gz
-[ $INST_0MQ -eq 1 ] && get_ytproject tornado-3.0.tar.gz
-[ $INST_SCIPY -eq 1 ] && get_ytproject scipy-0.11.0.tar.gz
+[ -z "$HDF5_DIR" ] && get_ytproject $HDF5.tar.gz
+[ $INST_ZLIB -eq 1 ] && get_ytproject $ZLIB.tar.gz
+[ $INST_BZLIB -eq 1 ] && get_ytproject $BZLIB.tar.gz
+[ $INST_PNG -eq 1 ] && get_ytproject $PNG.tar.gz
+[ $INST_FTYPE -eq 1 ] && get_ytproject $FREETYPE_VER.tar.gz
+[ $INST_SQLITE3 -eq 1 ] && get_ytproject $SQLITE.tar.gz
+[ $INST_PYX -eq 1 ] && get_ytproject $PYX.tar.gz
+[ $INST_0MQ -eq 1 ] && get_ytproject $ZEROMQ.tar.gz
+[ $INST_0MQ -eq 1 ] && get_ytproject $PYZMQ.tar.gz
+[ $INST_0MQ -eq 1 ] && get_ytproject $TORNADO.tar.gz
+[ $INST_SCIPY -eq 1 ] && get_ytproject $SCIPY.tar.gz
[ $INST_SCIPY -eq 1 ] && get_ytproject blas.tar.gz
-[ $INST_SCIPY -eq 1 ] && get_ytproject lapack-3.4.2.tar.gz
-get_ytproject Python-2.7.4.tgz
-get_ytproject numpy-1.7.0.tar.gz
-get_ytproject matplotlib-1.2.1.tar.gz
-get_ytproject mercurial-2.5.4.tar.gz
-get_ytproject ipython-0.13.1.tar.gz
-get_ytproject h5py-2.1.2.tar.gz
-get_ytproject Cython-0.18.tar.gz
+[ $INST_SCIPY -eq 1 ] && get_ytproject $LAPACK.tar.gz
+get_ytproject $PYTHON.tgz
+get_ytproject $NUMPY.tar.gz
+get_ytproject $MATPLOTLIB.tar.gz
+get_ytproject $MERCURIAL.tar.gz
+get_ytproject $IPYTHON.tar.gz
+get_ytproject $H5PY.tar.gz
+get_ytproject $CYTHON.tar.gz
get_ytproject reason-js-20120623.zip
-get_ytproject Forthon-0.8.11.tar.gz
-get_ytproject nose-1.2.1.tar.gz
-get_ytproject python-hglib-0.3.tar.gz
-get_ytproject sympy-0.7.2.tar.gz
-get_ytproject rockstar-0.99.6.tar.gz
+get_ytproject $FORTHON.tar.gz
+get_ytproject $NOSE.tar.gz
+get_ytproject $PYTHON_HGLIB.tar.gz
+get_ytproject $SYMPY.tar.gz
+get_ytproject $ROCKSTAR.tar.gz
if [ $INST_BZLIB -eq 1 ]
then
- if [ ! -e bzip2-1.0.6/done ]
+ if [ ! -e $BZLIB/done ]
then
- [ ! -e bzip2-1.0.6 ] && tar xfz bzip2-1.0.6.tar.gz
+ [ ! -e $BZLIB ] && tar xfz $BZLIB.tar.gz
echo "Installing BZLIB"
- cd bzip2-1.0.6
+ cd $BZLIB
if [ `uname` = "Darwin" ]
then
if [ -z "${CC}" ]
@@ -634,11 +667,11 @@
if [ $INST_ZLIB -eq 1 ]
then
- if [ ! -e zlib-1.2.7/done ]
+ if [ ! -e $ZLIB/done ]
then
- [ ! -e zlib-1.2.7 ] && tar xfz zlib-1.2.7.tar.gz
+ [ ! -e $ZLIB ] && tar xfz $ZLIB.tar.gz
echo "Installing ZLIB"
- cd zlib-1.2.7
+ cd $ZLIB
( ./configure --shared --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -652,11 +685,11 @@
if [ $INST_PNG -eq 1 ]
then
- if [ ! -e libpng-1.6.1/done ]
+ if [ ! -e $PNG/done ]
then
- [ ! -e libpng-1.6.1 ] && tar xfz libpng-1.6.1.tar.gz
+ [ ! -e $PNG ] && tar xfz $PNG.tar.gz
echo "Installing PNG"
- cd libpng-1.6.1
+ cd $PNG
( ./configure CPPFLAGS=-I${DEST_DIR}/include CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -670,13 +703,14 @@
if [ $INST_FTYPE -eq 1 ]
then
- if [ ! -e freetype-2.4.11/done ]
+ if [ ! -e $FREETYPE_VER/done ]
then
- [ ! -e freetype-2.4.11 ] && tar xfz freetype-2.4.11.tar.gz
+ [ ! -e $FREETYPE_VER ] && tar xfz $FREETYPE_VER.tar.gz
echo "Installing FreeType2"
- cd freetype-2.4.11
+ cd $FREETYPE_VER
( ./configure CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( make 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
@@ -688,11 +722,11 @@
if [ -z "$HDF5_DIR" ]
then
- if [ ! -e hdf5-1.8.9/done ]
+ if [ ! -e $HDF5/done ]
then
- [ ! -e hdf5-1.8.9 ] && tar xfz hdf5-1.8.9.tar.gz
+ [ ! -e $HDF5 ] && tar xfz $HDF5.tar.gz
echo "Installing HDF5"
- cd hdf5-1.8.9
+ cd $HDF5
( ./configure --prefix=${DEST_DIR}/ --enable-shared 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -707,11 +741,11 @@
if [ $INST_SQLITE3 -eq 1 ]
then
- if [ ! -e sqlite-autoconf-3071601/done ]
+ if [ ! -e $SQLITE/done ]
then
- [ ! -e sqlite-autoconf-3071601 ] && tar xfz sqlite-autoconf-3071601.tar.gz
+ [ ! -e $SQLITE ] && tar xfz $SQLITE.tar.gz
echo "Installing SQLite3"
- cd sqlite-autoconf-3071601
+ cd $SQLITE
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -720,11 +754,11 @@
fi
fi
-if [ ! -e Python-2.7.4/done ]
+if [ ! -e $PYTHON/done ]
then
echo "Installing Python. This may take a while, but don't worry. yt loves you."
- [ ! -e Python-2.7.4 ] && tar xfz Python-2.7.4.tgz
- cd Python-2.7.4
+ [ ! -e $PYTHON ] && tar xfz $PYTHON.tgz
+ cd $PYTHON
( ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
@@ -739,7 +773,7 @@
if [ $INST_HG -eq 1 ]
then
- do_setup_py mercurial-2.5.4
+ do_setup_py $MERCURIAL
export HG_EXEC=${DEST_DIR}/bin/hg
else
# We assume that hg can be found in the path.
@@ -788,9 +822,9 @@
if [ $INST_SCIPY -eq 0 ]
then
- do_setup_py numpy-1.7.0 ${NUMPY_ARGS}
+ do_setup_py $NUMPY ${NUMPY_ARGS}
else
- if [ ! -e scipy-0.11.0/done ]
+ if [ ! -e $SCIPY/done ]
then
if [ ! -e BLAS/done ]
then
@@ -798,27 +832,27 @@
echo "Building BLAS"
cd BLAS
gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ar r libfblas.a *.o 1>> ${LOG_FILE}
- ranlib libfblas.a 1>> ${LOG_FILE}
+ ( ar r libfblas.a *.o 2>&1 ) 1>> ${LOG_FILE}
+ ( ranlib libfblas.a 2>&1 ) 1>> ${LOG_FILE}
rm -rf *.o
touch done
cd ..
fi
- if [ ! -e lapack-3.4.2/done ]
+ if [ ! -e $LAPACK/done ]
then
- tar xfz lapack-3.4.2.tar.gz
+ tar xfz $LAPACK.tar.gz
echo "Building LAPACK"
- cd lapack-3.4.2/
+ cd $LAPACK/
cp INSTALL/make.inc.gfortran make.inc
- make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 1>> ${LOG_FILE} || do_exit
+ ( make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 2>&1 ) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
fi
fi
export BLAS=$PWD/BLAS/libfblas.a
- export LAPACK=$PWD/lapack-3.4.2/liblapack.a
- do_setup_py numpy-1.7.0 ${NUMPY_ARGS}
- do_setup_py scipy-0.11.0 ${NUMPY_ARGS}
+ export LAPACK=$PWD/$LAPACK/liblapack.a
+ do_setup_py $NUMPY ${NUMPY_ARGS}
+ do_setup_py $SCIPY ${NUMPY_ARGS}
fi
if [ -n "${MPL_SUPP_LDFLAGS}" ]
@@ -840,10 +874,15 @@
echo "Setting CFLAGS ${CFLAGS}"
fi
# Now we set up the basedir for matplotlib:
-mkdir -p ${DEST_DIR}/src/matplotlib-1.2.1
-echo "[directories]" >> ${DEST_DIR}/src/matplotlib-1.2.1/setup.cfg
-echo "basedirlist = ${DEST_DIR}" >> ${DEST_DIR}/src/matplotlib-1.2.1/setup.cfg
-do_setup_py matplotlib-1.2.1
+mkdir -p ${DEST_DIR}/src/$MATPLOTLIB
+echo "[directories]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+echo "basedirlist = ${DEST_DIR}" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+if [ `uname` = "Darwin" ]
+then
+ echo "[gui_support]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+ echo "macosx = False" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+fi
+do_setup_py $MATPLOTLIB
if [ -n "${OLD_LDFLAGS}" ]
then
export LDFLAG=${OLD_LDFLAGS}
@@ -855,36 +894,36 @@
# Now we do our IPython installation, which has two optional dependencies.
if [ $INST_0MQ -eq 1 ]
then
- if [ ! -e zeromq-3.2.2/done ]
+ if [ ! -e $ZEROMQ/done ]
then
- [ ! -e zeromq-3.2.2 ] && tar xfz zeromq-3.2.2.tar.gz
+ [ ! -e $ZEROMQ ] && tar xfz $ZEROMQ.tar.gz
echo "Installing ZeroMQ"
- cd zeromq-3.2.2
+ cd $ZEROMQ
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
fi
- do_setup_py pyzmq-13.0.2 --zmq=${DEST_DIR}
- do_setup_py tornado-3.0
+ do_setup_py $PYZMQ --zmq=${DEST_DIR}
+ do_setup_py $TORNADO
fi
-do_setup_py ipython-0.13.1
-do_setup_py h5py-2.1.2
-do_setup_py Cython-0.18
-do_setup_py Forthon-0.8.11
-do_setup_py nose-1.2.1
-do_setup_py python-hglib-0.3
-do_setup_py sympy-0.7.2
-[ $INST_PYX -eq 1 ] && do_setup_py PyX-0.12.1
+do_setup_py $IPYTHON
+do_setup_py $H5PY
+do_setup_py $CYTHON
+do_setup_py $FORTHON
+do_setup_py $NOSE
+do_setup_py $PYTHON_HGLIB
+do_setup_py $SYMPY
+[ $INST_PYX -eq 1 ] && do_setup_py $PYX
# Now we build Rockstar and set its environment variable.
if [ $INST_ROCKSTAR -eq 1 ]
then
if [ ! -e Rockstar/done ]
then
- [ ! -e Rockstar ] && tar xfz rockstar-0.99.6.tar.gz
+ [ ! -e Rockstar ] && tar xfz $ROCKSTAR.tar.gz
echo "Building Rockstar"
cd Rockstar
( make lib 2>&1 ) 1>> ${LOG_FILE} || do_exit
@@ -909,10 +948,10 @@
touch done
cd $MY_PWD
-if !(${DEST_DIR}/bin/python2.7 -c "import readline" >> ${LOG_FILE})
+if !( ( ${DEST_DIR}/bin/python2.7 -c "import readline" 2>&1 )>> ${LOG_FILE})
then
echo "Installing pure-python readline"
- ${DEST_DIR}/bin/pip install readline 1>> ${LOG_FILE}
+ ( ${DEST_DIR}/bin/pip install readline 2>&1 ) 1>> ${LOG_FILE}
fi
if [ $INST_ENZO -eq 1 ]
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb setup.py
--- a/setup.py
+++ b/setup.py
@@ -248,7 +248,7 @@
classifiers=["Development Status :: 5 - Production/Stable",
"Environment :: Console",
"Intended Audience :: Science/Research",
- "License :: OSI Approved :: GNU General Public License (GPL)",
+ "License :: OSI Approved :: BSD License",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: AIX",
"Operating System :: POSIX :: Linux",
@@ -269,7 +269,7 @@
author="Matthew J. Turk",
author_email="matthewturk at gmail.com",
url="http://yt-project.org/",
- license="GPL-3",
+ license="BSD",
configuration=configuration,
zip_safe=False,
data_files=REASON_FILES,
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb yt/__init__.py
--- a/yt/__init__.py
+++ b/yt/__init__.py
@@ -60,27 +60,17 @@
All broadly useful code that doesn't clearly fit in one of the other
categories goes here.
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2007-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
__version__ = "2.5-dev"
@@ -96,7 +86,7 @@
if answer_big_data:
nose_argv.append('--answer-big-data')
log_suppress = ytcfg.getboolean("yt","suppressStreamLogging")
- ytcfg["yt","suppressStreamLogging"] = 'True'
+ ytcfg.set("yt","suppressStreamLogging", 'True')
initial_dir = os.getcwd()
yt_file = os.path.abspath(__file__)
yt_dir = os.path.dirname(yt_file)
@@ -105,4 +95,4 @@
nose.run(argv=nose_argv)
finally:
os.chdir(initial_dir)
- ytcfg["yt","suppressStreamLogging"] = log_suppress
+ ytcfg.set("yt","suppressStreamLogging", str(log_suppress))
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb yt/analysis_modules/absorption_spectrum/__init__.py
--- a/yt/analysis_modules/absorption_spectrum/__init__.py
+++ b/yt/analysis_modules/absorption_spectrum/__init__.py
@@ -1,24 +1,14 @@
"""
Import stuff for light cone generator.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb yt/analysis_modules/absorption_spectrum/absorption_line.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_line.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_line.py
@@ -1,27 +1,17 @@
"""
Absorption line generating functions.
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: Michigan State University
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import numpy as np
diff -r c2c55742d4d83bd75de56d74dfe8b22665f1dcdf -r fdcac050289069bc6b6ef61949d765a88b3972bb yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
@@ -1,27 +1,17 @@
"""
AbsorptionSpectrum class and member functions.
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: Michigan State University
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import h5py
import numpy as np
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt-3.0/commits/72eb0870c6a4/
Changeset: 72eb0870c6a4
Branch: yt
User: jzuhone
Date: 2013-09-22 15:01:39
Summary: Improvements to FITS writing. This small refactor puts all of the FITS writing into one versatile standalone routine (write_fits), which may be called by itself or called from within a method, as in frb.export_fits.
Also made some small tweaks to write_projection so that axes ticks and labels may be optionally included.
Affected #: 2 files
diff -r fdcac050289069bc6b6ef61949d765a88b3972bb -r 72eb0870c6a44aa934193148972198bcc1aad437 yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -19,6 +19,7 @@
y_dict, \
axis_names
from .volume_rendering.api import off_axis_projection
+from image_writer import write_fits
from yt.data_objects.image_array import ImageArray
import _MPL
import numpy as np
@@ -263,8 +264,8 @@
output.create_dataset(field,data=self[field])
output.close()
- def export_fits(self, filename_prefix, fields = None, clobber=False,
- other_keys=None, gzip_file=False, units="1"):
+ def export_fits(self, filename_prefix, fields=None, clobber=False,
+ other_keys=None, units="cm", sky_center=(0.0,0.0), D_A=None):
"""
This will export a set of FITS images of either the fields specified
@@ -273,106 +274,80 @@
existing FITS file.
This requires the *pyfits* module, which is a standalone module
- provided by STSci to interface with FITS-format files.
+ provided by STSci to interface with FITS-format files, and is also
+ part of AstroPy.
"""
r"""Export a set of pixelized fields to a FITS file.
This will export a set of FITS images of either the fields specified
- or all the fields already in the object. The output filename is the
- the specified prefix.
+ or all the fields already in the object.
Parameters
----------
filename_prefix : string
- This prefix will be prepended to every FITS file name.
+ This prefix will be prepended to the FITS file name.
fields : list of strings
These fields will be pixelized and output.
clobber : boolean
If the file exists, this governs whether we will overwrite.
other_keys : dictionary, optional
A set of header keys and values to write into the FITS header.
- gzip_file : boolean, optional
- gzip the file after writing, default False
units : string, optional
- the length units that the coordinates are written in, default '1'
+ the length units that the coordinates are written in, default 'cm'
+ If units are set to "deg" then assume that sky coordinates are
+ requested.
+ sky_center : array_like, optional
+ Center of the image in (ra,dec) in degrees if sky coordinates
+ (units="deg") are requested.
+ D_A : float or tuple, optional
+ Angular diameter distance, given in code units as a float or
+ a tuple containing the value and the length unit. Required if
+ using sky coordinates.
"""
-
- import pyfits
- from os import system
-
+
+ if units == "deg" and D_A is None:
+ mylog.error("Sky coordinates require an angular diameter distance. Please specify D_A.")
+ if iterable(D_A):
+ dist = D_A[0]/self.pf.units[D_A[1]]
+ else:
+ dist = D_A
+
+ if other_keys is None:
+ hdu_keys = {}
+ else:
+ hdu_keys = other_keys
+
extra_fields = ['x','y','z','px','py','pz','pdx','pdy','pdz','weight_field']
- if filename_prefix.endswith('.fits'): filename_prefix=filename_prefix[:-5]
if fields is None:
fields = [field for field in self.data_source.fields
if field not in extra_fields]
+ coords = {}
nx, ny = self.buff_size
- dx = (self.bounds[1]-self.bounds[0])/nx*self.pf[units]
- dy = (self.bounds[3]-self.bounds[2])/ny*self.pf[units]
- xmin = self.bounds[0]*self.pf[units]
- ymin = self.bounds[2]*self.pf[units]
- simtime = self.pf.current_time
+ dx = (self.bounds[1]-self.bounds[0])/nx
+ dy = (self.bounds[3]-self.bounds[2])/ny
+ if units == "deg":
+ coords["dx"] = -np.rad2deg(dx/dist)
+ coords["dy"] = np.rad2deg(dy/dist)
+ coords["xctr"] = sky_center[0]
+ coords["yctr"] = sky_center[1]
+ hdu_keys["MTYPE1"] = "EQPOS"
+ hdu_keys["MFORM1"] = "RA,DEC"
+ hdu_keys["CTYPE1"] = "RA---TAN"
+ hdu_keys["CTYPE2"] = "DEC--TAN"
+ else:
+ coords["dx"] = dx*self.pf.units[units]
+ coords["dy"] = dy*self.pf.units[units]
+ coords["xctr"] = 0.5*(self.bounds[0]+self.bounds[1])*self.pf.units[units]
+ coords["yctr"] = 0.5*(self.bounds[2]+self.bounds[3])*self.pf.units[units]
+ coords["units"] = units
+
+ hdu_keys["Time"] = self.pf.current_time
- hdus = []
-
- first = True
-
- for field in fields:
-
- if (first) :
- hdu = pyfits.PrimaryHDU(self[field])
- first = False
- else :
- hdu = pyfits.ImageHDU(self[field])
+ data = dict([(field,self[field]) for field in fields])
+ write_fits(data, filename_prefix, clobber=clobber, coords=coords,
+ other_keys=hdu_keys)
- if self.data_source.has_key('weight_field'):
- weightname = self.data_source._weight
- if weightname is None: weightname = 'None'
- field = field +'_'+weightname
-
- hdu.header.update("Field", field)
- hdu.header.update("Time", simtime)
-
- hdu.header.update('WCSNAMEP', "PHYSICAL")
- hdu.header.update('CTYPE1P', "LINEAR")
- hdu.header.update('CTYPE2P', "LINEAR")
- hdu.header.update('CRPIX1P', 0.5)
- hdu.header.update('CRPIX2P', 0.5)
- hdu.header.update('CRVAL1P', xmin)
- hdu.header.update('CRVAL2P', ymin)
- hdu.header.update('CDELT1P', dx)
- hdu.header.update('CDELT2P', dy)
-
- hdu.header.update('CTYPE1', "LINEAR")
- hdu.header.update('CTYPE2', "LINEAR")
- hdu.header.update('CUNIT1', units)
- hdu.header.update('CUNIT2', units)
- hdu.header.update('CRPIX1', 0.5)
- hdu.header.update('CRPIX2', 0.5)
- hdu.header.update('CRVAL1', xmin)
- hdu.header.update('CRVAL2', ymin)
- hdu.header.update('CDELT1', dx)
- hdu.header.update('CDELT2', dy)
-
- if (other_keys is not None) :
-
- for k,v in other_keys.items() :
-
- hdu.header.update(k,v)
-
- hdus.append(hdu)
-
- del hdu
-
- hdulist = pyfits.HDUList(hdus)
-
- hdulist.writeto("%s.fits" % (filename_prefix), clobber=clobber)
-
- if (gzip_file) :
- clob = ""
- if (clobber) : clob = "-f"
- system("gzip "+clob+" %s.fits" % (filename_prefix))
-
def open_in_ds9(self, field, take_log=True):
"""
This will open a given field in the DS9 viewer.
diff -r fdcac050289069bc6b6ef61949d765a88b3972bb -r 72eb0870c6a44aa934193148972198bcc1aad437 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -333,7 +333,8 @@
def write_projection(data, filename, colorbar=True, colorbar_label=None,
title=None, limits=None, take_log=True, figsize=(8,6),
- dpi=100, cmap_name='algae'):
+ dpi=100, cmap_name='algae', extent=None, xlabel=None,
+ ylabel=None):
r"""Write a projection or volume rendering to disk with a variety of
pretty parameters such as limits, title, colorbar, etc. write_projection
uses the standard matplotlib interface to create the figure. N.B. This code
@@ -392,16 +393,22 @@
# Create the figure and paint the data on
fig = matplotlib.figure.Figure(figsize=figsize)
ax = fig.add_subplot(111)
- fig.tight_layout()
-
- cax = ax.imshow(data, vmin=limits[0], vmax=limits[1], norm=norm, cmap=cmap_name)
+
+ cax = ax.imshow(data, vmin=limits[0], vmax=limits[1], norm=norm,
+ extent=extent, cmap=cmap_name)
if title:
ax.set_title(title)
+ if xlabel:
+ ax.set_xlabel(xlabel)
+ if ylabel:
+ ax.set_ylabel(ylabel)
+
# Suppress the x and y pixel counts
- ax.set_xticks(())
- ax.set_yticks(())
+ if extent is None:
+ ax.set_xticks(())
+ ax.set_yticks(())
# Add a color bar and label if requested
if colorbar:
@@ -409,6 +416,8 @@
if colorbar_label:
cbar.ax.set_ylabel(colorbar_label)
+ fig.tight_layout()
+
suffix = get_image_suffix(filename)
if suffix == '':
@@ -429,70 +438,89 @@
return filename
-def write_fits(image, filename_prefix, clobber=True, coords=None, gzip_file=False) :
+def write_fits(image, filename_prefix, clobber=True, coords=None,
+ other_keys=None):
"""
This will export a FITS image of a floating point array. The output filename is
*filename_prefix*. If clobber is set to True, this will overwrite any existing
FITS file.
This requires the *pyfits* module, which is a standalone module
- provided by STSci to interface with FITS-format files.
+ provided by STSci to interface with FITS-format files, and is also part of
+ AstroPy.
"""
- r"""Write out a floating point array directly to a FITS file, optionally
- adding coordinates.
+ r"""Write out floating point arrays directly to a FITS file, optionally
+ adding coordinates and header keywords.
Parameters
----------
- image : array_like
- This is an (unscaled) array of floating point values, shape (N,N,) to save
- in a FITS file.
+ image : array_like, or dict of array_like objects
+ This is either an (unscaled) array of floating point values, or a dict of
+ such arrays, shape (N,N,) to save in a FITS file.
filename_prefix : string
This prefix will be prepended to every FITS file name.
clobber : boolean
If the file exists, this governs whether we will overwrite.
coords : dictionary, optional
A set of header keys and values to write to the FITS header to set up
- a coordinate system.
- gzip_file : boolean, optional
- gzip the file after writing, default False
+ a coordinate system, which is assumed to be linear unless specified otherwise
+ in *other_keys*
+ "units": the length units
+ "xctr","yctr": the center of the image
+ "dx","dy": the pixel width in each direction
+ other_keys : dictionary, optional
+ A set of header keys and values to write into the FITS header.
"""
+
+ try:
+ import pyfits
+ except ImportError:
+ try:
+ import astropy.io.fits as pyfits
+ except:
+ raise ImportError("You don't have pyFITS or AstroPy installed.")
- import pyfits
from os import system
- if filename_prefix.endswith('.fits'): filename_prefix=filename_prefix[:-5]
-
- hdu = pyfits.PrimaryHDU(image)
+ try:
+ image.keys()
+ image_dict = image
+ except:
+ image_dict = dict(yt_data=image)
- if (coords is not None) :
+ hdulist = [pyfits.PrimaryHDU()]
- hdu.header.update('WCSNAMEP', "PHYSICAL")
- hdu.header.update('CTYPE1P', "LINEAR")
- hdu.header.update('CTYPE2P', "LINEAR")
- hdu.header.update('CRPIX1P', 0.5)
- hdu.header.update('CRPIX2P', 0.5)
- hdu.header.update('CRVAL1P', coords["xmin"])
- hdu.header.update('CRVAL2P', coords["ymin"])
- hdu.header.update('CDELT1P', coords["dx"])
- hdu.header.update('CDELT2P', coords["dy"])
+ for key in image_dict.keys():
+
+ mylog.info("Writing image block \"%s\"" % (key))
+ hdu = pyfits.ImageHDU(image_dict[key])
+ hdu.update_ext_name(key)
- hdu.header.update('CTYPE1', "LINEAR")
- hdu.header.update('CTYPE2', "LINEAR")
- hdu.header.update('CUNIT1', coords["units"])
- hdu.header.update('CUNIT2', coords["units"])
- hdu.header.update('CRPIX1', 0.5)
- hdu.header.update('CRPIX2', 0.5)
- hdu.header.update('CRVAL1', coords["xmin"])
- hdu.header.update('CRVAL2', coords["ymin"])
- hdu.header.update('CDELT1', coords["dx"])
- hdu.header.update('CDELT2', coords["dy"])
+ if coords is not None:
- hdu.writeto("%s.fits" % (filename_prefix), clobber=clobber)
+ nx, ny = image_dict[key].shape
- if (gzip_file) :
- clob = ""
- if (clobber) : clob="-f"
- system("gzip "+clob+" %s.fits" % (filename_prefix))
+ hdu.header.update('CUNIT1', coords["units"])
+ hdu.header.update('CUNIT2', coords["units"])
+ hdu.header.update('CRPIX1', 0.5*(nx+1))
+ hdu.header.update('CRPIX2', 0.5*(ny+1))
+ hdu.header.update('CRVAL1', coords["xctr"])
+ hdu.header.update('CRVAL2', coords["yctr"])
+ hdu.header.update('CDELT1', coords["dx"])
+ hdu.header.update('CDELT2', coords["dy"])
+ # These are the defaults, but will get overwritten if
+ # the caller has specified them
+ hdu.header.update('CTYPE1', "LINEAR")
+ hdu.header.update('CTYPE2', "LINEAR")
+
+ if other_keys is not None:
+ for k,v in other_keys.items():
+ hdu.header.update(k,v)
+
+ hdulist.append(hdu)
+
+ hdulist = pyfits.HDUList(hdulist)
+ hdulist.writeto("%s.fits" % (filename_prefix), clobber=clobber)
def display_in_notebook(image, max_val=None):
"""
https://bitbucket.org/yt_analysis/yt-3.0/commits/d0b4d51fced2/
Changeset: d0b4d51fced2
Branch: yt
User: jzuhone
Date: 2013-09-22 15:03:07
Summary: Fully operational projection of the SZ signal distortion using SZpack.
Affected #: 4 files
diff -r 72eb0870c6a44aa934193148972198bcc1aad437 -r d0b4d51fced2ea9f52fc811aff668461b58ec7f6 yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -103,7 +103,7 @@
TwoPointFunctions, \
FcnSet
-from .sunyaev_zeldovich.api import SZprojection
+from .sunyaev_zeldovich.api import SZProjection
from .radmc3d_export.api import \
RadMC3DWriter
diff -r 72eb0870c6a44aa934193148972198bcc1aad437 -r d0b4d51fced2ea9f52fc811aff668461b58ec7f6 yt/analysis_modules/sunyaev_zeldovich/api.py
--- a/yt/analysis_modules/sunyaev_zeldovich/api.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/api.py
@@ -1,1 +1,1 @@
-from .projection import SZprojection
+from projection import SZProjection
diff -r 72eb0870c6a44aa934193148972198bcc1aad437 -r d0b4d51fced2ea9f52fc811aff668461b58ec7f6 yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -2,113 +2,204 @@
from yt.data_objects.image_array import ImageArray
from yt.data_objects.field_info_container import add_field
from yt.funcs import fix_axis, mylog, iterable, get_pbar
-from yt.definitions import inv_axis_names
+from yt.utilities.definitions import inv_axis_names
+from yt.visualization.image_writer import write_fits, write_projection
from yt.visualization.volume_rendering.camera import off_axis_projection
+from yt.utilities.parallel_tools.parallel_analysis_interface import \
+ communication_system, parallel_root_only
import numpy as np
Tcmb = 2.726
-
+I0 = 2*(kboltz*Tcmb)**3/((hcgs*clight)**2)*1.0e17
+
try:
import SZpack
except:
raise ImportError("SZpack not installed.")
vlist = "xyz"
-nvec = int(0)
def _t_squared(field, data):
- return data["TempkeV"]*data["TempkeV"]
+ return data["Density"]*data["TempkeV"]*data["TempkeV"]
add_field("TSquared", function=_t_squared)
def _beta_perp_squared(field, data):
- return data["VelocityMagnitude"]**2/clight/clight - data["BetaParSquared"]
+ return data["Density"]*(data["VelocityMagnitude"]**2/clight/clight - data["BetaParSquared"])
add_field("BetaPerpSquared", function=_beta_perp_squared)
-def _beta_par(field, data):
- axis = data.get_field_parameter("axis")
- if iterable(nvec):
- vpar = (data["x-velocity"]*nvec[0]+
- data["y-velocity"]*nvec[1]+
- data["z-velocity"]*nvec[2])
- else:
- vpar = data["%s-velocity" % (vlist[nvec])]
- return vpar/clight
-add_field("BetaPar", function=_beta_par)
-
def _beta_par_squared(field, data):
- return data["BetaPar"]**2
+ return data["Density"]*data["BetaPar"]**2
add_field("BetaParSquared", function=_beta_par_squared)
def _t_beta_par(field, data):
- return data["TempkeV"]*data["BetaPar"]
+ return data["Density"]*data["TempkeV"]*data["BetaPar"]
add_field("TBetaPar", function=_t_beta_par)
-def SZProjection(pf, axis, freqs, center="c", width=(1, "unitary"), nx=800, mue=None):
+def _t_sz(field, data):
+ return data["Density"]*data["TempkeV"]
+add_field("TeSZ", function=_t_sz)
- global nvec # Ugly!
-
- if mue is None:
- mueinv = 0.875
- else:
- mueinv = 1./mue
+class SZProjection(object):
+
+ def __init__(self, pf, freqs, mue=1.143, high_order=False):
+
+ self.pf = pf
+ self.num_freqs = len(freqs)
+ self.high_order = high_order
+ self.freqs = freqs
+ self.mueinv = 1./mue
+ self.xinit = hcgs*freqs*1.0e9/(kboltz*Tcmb)
+ self.freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
+ self.field_dict = {}
+
+ self.units = {}
+ self.units["TeSZ"] = r"$\mathrm{keV}$"
+ self.units["Tau"] = None
+
+ self.display_names = {}
+ self.display_names["TeSZ"] = r"$\mathrm{T_e}$"
+ self.display_names["Tau"] = r"$\mathrm{\tau}$"
+
+ for f, field in zip(self.freqs, self.freq_fields):
+ self.units[field] = r"$\mathrm{MJy\ sr^{-1}}$"
+ self.display_names[field] = r"$\mathrm{\Delta{I}_{%d\ GHz}}$" % (int(freq))
+
+ def on_axis(self, axis, center="c", width=(1, "unitary"), nx=800):
+
+ axis = fix_axis(axis)
+
+ def _beta_par(field, data):
+ axis = data.get_field_parameter("axis")
+ vpar = data["Density"]*data["%s-velocity" % (vlist[axis])]
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ proj = self.pf.h.proj(axis, "Density")
+ proj.set_field_parameter("axis", axis)
+ frb = proj.to_frb(width, nx)
+ dens = frb["Density"]
+ Te = frb["TeSZ"]/dens
+ bpar = frb["BetaPar"]/dens
+ omega1 = frb["TSquared"]/dens/(Te*Te) - 1.
+ if self.high_order:
+ bperp2 = frb["BetaPerpSquared"]/dens
+ sigma1 = frb["TBetaPar"]/dens/Te - bpar
+ kappa1 = frb["BetaParSquared"]/dens - bpar
+ else:
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ tau = sigma_thompson*dens*self.mueinv/mp
+
+ nx,ny = frb.buff_size
+ self.bounds = frb.bounds
+ self.dx = (frb.bounds[1]-frb.bounds[0])/nx
+ self.dy = (frb.bounds[3]-frb.bounds[2])/ny
- num_freqs = len(freqs)
- freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
- xinit = hcgs*freqs*1.0e9/(kboltz*Tcmb)
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
+
+ def off_axis(self, L, center="c", width=(1, "unitary"), nx=800):
- if isinstance(axis, basestring) or not iterable(axis):
- axis = fix_axis(axis)
- nvec = axis
- proj1 = pf.h.proj(axis, "TempkeV", weight_field="Density")
- proj2 = pf.h.proj(axis, "Density")
- frb1 = proj1.to_frb(width, nx)
- frb2 = proj2.to_frb(width, nx)
- Te = frb1["TempkeV"]
- bpar = frb1["BetaPar"]
- bperp2 = frb1["BetaPerpSquared"]
- omega1 = frb1["TSquared"]/(Te*Te) - 1.
- sigma1 = frb1["TBetaPar"]/Te - bpar
- kappa1 = frb1["BetaParSquared"] - bpar
- tau = sigma_thompson*frb2["Density"]*mueinv/mp
- else:
- nvec = axis
if iterable(width):
w = width[0]/pf.units[width[1]]
else:
w = width
- Te = off_axis_projection(pf, center, axis, w, nx, "TempkeV", weight="Density")
- bpar = off_axis_projection(pf, center, axis, w, nx, "BetaPar", weight="Density")
- bperp2 = off_axis_projection(pf, center, axis, w, nx, "BetaPerpSquared", weight="Density")
- omega1 = off_axis_projection(pf, center, axis, w, nx, "TSquared", weight="Density")
+
+ def _beta_par(field, data):
+ vpar = data["Density"]*(data["x-velocity"]*L[0]+
+ data["y-velocity"]*L[1]+
+ data["z-velocity"]*L[2])
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ dens = off_axis_projection(self.pf, center, L, w, nx, "Density")
+ Te = off_axis_projection(self.pf, center, L, w, nx, "TeSZ")/dens
+ bpar = off_axis_projection(self.pf, center, L, w, nx, "BetaPar")/dens
+ omega1 = off_axis_projection(self.pf, center, L, w, nx, "TSquared")/dens
omega1 = omega1/(Te*Te) - 1.
- sigma1 = off_axis_projection(pf, center, axis, w, nx, "TBetaPar", weight="Density")
- sigma1 = sigma1/Te - bpar
- kappa1 = off_axis_projection(pf, center, axis, w, nx, "BetaParSquared", weight="Density")
- kappa1 -= bpar
- tau = off_axis_projection(pf, center, axis, w, nx, "Density")
- tau *= sigma_thompson*mueinv/mp
+ if self.high_order:
+ bperp2 = off_axis_projection(self.pf, center, L, w, nx, "BetaPerpSquared")/dens
+ sigma1 = off_axis_projection(self.pf, center, L, w, nx, "TBetaPar")/dens
+ sigma1 = sigma1/Te - bpar
+ kappa1 = off_axis_projection(self.pf, center, L, w, nx, "BetaParSquared")/dens
+ kappa1 -= bpar
+ else:
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ tau = sigma_thompson*dens*mueinv/mp
+
+ self.bounds = np.array([-0.5*w, 0.5*w, -0.5*w, 0.5*w])
+ self.dx = w/nx
+ self.dy = w/nx
- SZsignal = np.zeros((num_freqs,nx,nx))
- xo = np.zeros((num_freqs))
-
- k = int(0)
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
- pbar = get_pbar("Computing SZ signal.", nx*nx)
-
- for i in xrange(nx):
- for j in xrange(nx):
- xo[:] = xinit[:]
- SZpack.compute_combo_means(xo, tau[i,j], Te[i,j],
- bpar[i,j], omega[i,j],
- sigma[i,j], kappa[i,j], bperp2[i,j])
- SZsignal[:,i,j] = -xo[:]
- pbar.update(k)
- k += 1
+ def _compute_intensity(self, tau, Te, bpar, omega1, sigma1, kappa1, bperp2):
- pbar.finish()
-
- outimg = {}
- for i in xrange(num_freqs) :
- outimg[freq_fields[i]] = ImageArray(SZsignal[i,:,:])
-
- return outimg
+ comm = communication_system.communicators[-1]
+
+ nx, ny = tau.shape
+ signal = np.zeros((self.num_freqs,nx,nx))
+ xo = np.zeros((self.num_freqs))
+
+ k = int(0)
+
+ start_i = comm.rank*nx/comm.size
+ end_i = (comm.rank+1)*nx/comm.size
+
+ pbar = get_pbar("Computing SZ signal.", nx*nx)
+
+ for i in xrange(start_i, end_i):
+ for j in xrange(ny):
+ xo[:] = self.xinit[:]
+ SZpack.compute_combo_means(xo, tau[i,j], Te[i,j],
+ bpar[i,j], omega1[i,j],
+ sigma1[i,j], kappa1[i,j], bperp2[i,j])
+ signal[:,i,j] = -xo[:]
+ pbar.update(k)
+ k += 1
+
+ signal = comm.mpi_allreduce(signal)
+
+ pbar.finish()
+
+ for i, field in enumerate(self.freq_fields):
+ self.field_dict[field] = ImageArray(I0*self.xinit[i]**3*signal[i,:,:])
+ self.field_dict["Tau"] = ImageArray(tau)
+ self.field_dict["TeSZ"] = ImageArray(Te)
+
+ @parallel_root_only
+ def write_fits(self, filename_prefix, clobber=True):
+
+ coords = {}
+ coords["dx"] = self.dx*self.pf.units["kpc"]
+ coords["dy"] = self.dy*self.pf.units["kpc"]
+ coords["xctr"] = 0.0
+ coords["yctr"] = 0.0
+ coords["units"] = "kpc"
+ other_keys = {"Time" : self.pf.current_time}
+ write_fits(self.field_dict, filename_prefix, clobber=clobber, coords=coords,
+ other_keys=other_keys)
+
+ @parallel_root_only
+ def write_png(self, filename_prefix):
+
+ extent = tuple([bound*self.pf.units["kpc"] for bound in self.bounds])
+ for field, image in self.field_dict.items():
+ filename=filename_prefix+"_"+field+".png"
+ label = self.display_names[field]
+ if self.units[field] is not None:
+ label += " ("+self.units[field]+")"
+ write_projection(image, filename, colorbar_label=label, take_log=False,
+ extent=extent, xlabel=r"$\mathrm{x\ (kpc)}$",
+ ylabel=r"$\mathrm{y\ (kpc)}$")
+
+ def keys(self):
+ return self.field_dict.keys()
+
+ def has_key(self, key):
+ return key in self.field_dict.keys()
+
+ def __getitem__(self, key):
+ return self.field_dict[key]
https://bitbucket.org/yt_analysis/yt-3.0/commits/47722556465d/
Changeset: 47722556465d
Branch: yt
User: jzuhone
Date: 2013-09-22 16:12:08
Summary: Docstrings, copyright, and a bug fix
Affected #: 2 files
diff -r d0b4d51fced2ea9f52fc811aff668461b58ec7f6 -r 47722556465d3f11353c132a5354a362585ef1eb yt/analysis_modules/sunyaev_zeldovich/api.py
--- a/yt/analysis_modules/sunyaev_zeldovich/api.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/api.py
@@ -1,1 +1,12 @@
+"""
+API for sunyaev_zeldovich
+"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from projection import SZProjection
diff -r d0b4d51fced2ea9f52fc811aff668461b58ec7f6 -r 47722556465d3f11353c132a5354a362585ef1eb yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -1,3 +1,23 @@
+"""
+Projection class for the Sunyaev-Zeldovich effect. Requires SZpack (at least
+version 1.1.1) to be downloaded and installed:
+
+http://www.chluba.de/SZpack/
+
+For details on the computations involved please refer to the following references:
+
+Chluba, Nagai, Sazonov, Nelson, MNRAS, 2012, arXiv:1205.5778
+Chluba, Switzer, Nagai, Nelson, MNRAS, 2012, arXiv:1211.3206
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mp
from yt.data_objects.image_array import ImageArray
from yt.data_objects.field_info_container import add_field
@@ -15,7 +35,7 @@
try:
import SZpack
except:
- raise ImportError("SZpack not installed.")
+ raise ImportError("SZpack not installed. It can be obtained from from http://www.chluba.de/SZpack/.")
vlist = "xyz"
@@ -40,13 +60,30 @@
add_field("TeSZ", function=_t_sz)
class SZProjection(object):
+ r""" Initialize a SZProjection object.
+ Parameters
+ ----------
+ pf : parameter_file
+ The parameter file.
+ freqs : array_like
+ The frequencies (in GHz) at which to compute the SZ spectral distortion.
+ mue : float, optional
+ Mean molecular weight for determining the electron number density.
+ high_order : boolean, optional
+ Should we calculate high-order moments of velocity and temperature?
+
+ Examples
+ --------
+ >>> freqs = [90., 180., 240.]
+ >>> szprj = SZProjection(pf, freqs, high_order=True)
+ """
def __init__(self, pf, freqs, mue=1.143, high_order=False):
-
+
self.pf = pf
self.num_freqs = len(freqs)
self.high_order = high_order
- self.freqs = freqs
+ self.freqs = np.array(freqs)
self.mueinv = 1./mue
self.xinit = hcgs*freqs*1.0e9/(kboltz*Tcmb)
self.freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
@@ -64,8 +101,26 @@
self.units[field] = r"$\mathrm{MJy\ sr^{-1}}$"
self.display_names[field] = r"$\mathrm{\Delta{I}_{%d\ GHz}}$" % (int(freq))
- def on_axis(self, axis, center="c", width=(1, "unitary"), nx=800):
+ def on_axis(self, axis, center="c", width=(1, "unitary"), nx=800, source=None):
+ r""" Make an on-axis projection of the SZ signal.
+ Parameters
+ ----------
+ axis : integer or string
+ The axis of the simulation domain along which to make the SZprojection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+
+ Examples
+ --------
+ >>> szprj.on_axis("y", center="max", width=(1.0, "mpc"), source=my_sphere)
+ """
axis = fix_axis(axis)
def _beta_par(field, data):
@@ -74,7 +129,7 @@
return vpar/clight
add_field("BetaPar", function=_beta_par)
- proj = self.pf.h.proj(axis, "Density")
+ proj = self.pf.h.proj(axis, "Density", source=source)
proj.set_field_parameter("axis", axis)
frb = proj.to_frb(width, nx)
dens = frb["Density"]
@@ -99,12 +154,35 @@
self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
def off_axis(self, L, center="c", width=(1, "unitary"), nx=800):
-
+ r""" Make an off-axis projection of the SZ signal.
+
+ Parameters
+ ----------
+ L : array_like
+ The normal vector of the projection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+
+ Examples
+ --------
+ >>> L = np.array([0.5, 1.0, 0.75])
+ >>> szprj.off_axis(L, center="c", width=(2.0, "mpc"))
+ """
if iterable(width):
- w = width[0]/pf.units[width[1]]
+ w = width[0]/self.pf.units[width[1]]
else:
w = width
-
+ if center == "c":
+ ctr = self.pf.domain_center
+ elif center == "max":
+ ctr = self.pf.h.find_max("Density")
+ else:
+ ctr = center
+
def _beta_par(field, data):
vpar = data["Density"]*(data["x-velocity"]*L[0]+
data["y-velocity"]*L[1]+
@@ -112,22 +190,22 @@
return vpar/clight
add_field("BetaPar", function=_beta_par)
- dens = off_axis_projection(self.pf, center, L, w, nx, "Density")
- Te = off_axis_projection(self.pf, center, L, w, nx, "TeSZ")/dens
- bpar = off_axis_projection(self.pf, center, L, w, nx, "BetaPar")/dens
- omega1 = off_axis_projection(self.pf, center, L, w, nx, "TSquared")/dens
+ dens = off_axis_projection(self.pf, ctr, L, w, nx, "Density")
+ Te = off_axis_projection(self.pf, ctr, L, w, nx, "TeSZ")/dens
+ bpar = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPar")/dens
+ omega1 = off_axis_projection(self.pf, ctr, L, w, nx, "TSquared")/dens
omega1 = omega1/(Te*Te) - 1.
if self.high_order:
- bperp2 = off_axis_projection(self.pf, center, L, w, nx, "BetaPerpSquared")/dens
- sigma1 = off_axis_projection(self.pf, center, L, w, nx, "TBetaPar")/dens
+ bperp2 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPerpSquared")/dens
+ sigma1 = off_axis_projection(self.pf, ctr, L, w, nx, "TBetaPar")/dens
sigma1 = sigma1/Te - bpar
- kappa1 = off_axis_projection(self.pf, center, L, w, nx, "BetaParSquared")/dens
+ kappa1 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaParSquared")/dens
kappa1 -= bpar
else:
bperp2 = np.zeros((nx,nx))
sigma1 = np.zeros((nx,nx))
kappa1 = np.zeros((nx,nx))
- tau = sigma_thompson*dens*mueinv/mp
+ tau = sigma_thompson*dens*self.mueinv/mp
self.bounds = np.array([-0.5*w, 0.5*w, -0.5*w, 0.5*w])
self.dx = w/nx
@@ -171,7 +249,21 @@
@parallel_root_only
def write_fits(self, filename_prefix, clobber=True):
-
+ r""" Export images to a FITS file. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the FITS filename.
+ clobber : boolean, optional
+ If the file already exists, do we overwrite?
+
+ Examples
+ --------
+ >>> szprj.write_fits("SZbullet", clobber=False)
+ """
coords = {}
coords["dx"] = self.dx*self.pf.units["kpc"]
coords["dy"] = self.dy*self.pf.units["kpc"]
@@ -184,7 +276,19 @@
@parallel_root_only
def write_png(self, filename_prefix):
-
+ r""" Export images to PNG files. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the image filenames.
+
+ Examples
+ --------
+ >>> szprj.write_png("SZsloshing")
+ """
extent = tuple([bound*self.pf.units["kpc"] for bound in self.bounds])
for field, image in self.field_dict.items():
filename=filename_prefix+"_"+field+".png"
https://bitbucket.org/yt_analysis/yt-3.0/commits/5780cf148e35/
Changeset: 5780cf148e35
Branch: yt
User: jzuhone
Date: 2013-09-22 20:43:21
Summary: Small bug fixes
Affected #: 1 file
diff -r 47722556465d3f11353c132a5354a362585ef1eb -r 5780cf148e35d18e96e89425c5d4f59b7b07c6e0 yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -85,7 +85,7 @@
self.high_order = high_order
self.freqs = np.array(freqs)
self.mueinv = 1./mue
- self.xinit = hcgs*freqs*1.0e9/(kboltz*Tcmb)
+ self.xinit = hcgs*self.freqs*1.0e9/(kboltz*Tcmb)
self.freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
self.field_dict = {}
@@ -99,7 +99,7 @@
for f, field in zip(self.freqs, self.freq_fields):
self.units[field] = r"$\mathrm{MJy\ sr^{-1}}$"
- self.display_names[field] = r"$\mathrm{\Delta{I}_{%d\ GHz}}$" % (int(freq))
+ self.display_names[field] = r"$\mathrm{\Delta{I}_{%d\ GHz}}$" % (int(f))
def on_axis(self, axis, center="c", width=(1, "unitary"), nx=800, source=None):
r""" Make an on-axis projection of the SZ signal.
@@ -234,7 +234,7 @@
SZpack.compute_combo_means(xo, tau[i,j], Te[i,j],
bpar[i,j], omega1[i,j],
sigma1[i,j], kappa1[i,j], bperp2[i,j])
- signal[:,i,j] = -xo[:]
+ signal[:,i,j] = xo[:]
pbar.update(k)
k += 1
https://bitbucket.org/yt_analysis/yt-3.0/commits/3064a4e68cc2/
Changeset: 3064a4e68cc2
Branch: yt
User: jzuhone
Date: 2013-09-28 19:50:24
Summary: Adding a requires_module decorator to allow certain tests to pass if optional modules cannot be imported.
Affected #: 1 file
diff -r 5780cf148e35d18e96e89425c5d4f59b7b07c6e0 -r 3064a4e68cc22786d39b281277668a14c01c70eb yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -14,6 +14,7 @@
import itertools as it
import numpy as np
+import importlib
from yt.funcs import *
from numpy.testing import assert_array_equal, assert_almost_equal, \
assert_approx_equal, assert_array_almost_equal, assert_equal, \
@@ -251,3 +252,23 @@
list_of_kwarg_dicts[i][key] = keywords[key][0]
return list_of_kwarg_dicts
+
+def requires_module(module):
+ """
+ Decorator that takes a module name as an argument and tries to import it.
+ If the module imports without issue, the function is returned, but if not,
+ a null function is returned. This is so tests that depend on certain modules
+ being imported will not fail if the module is not installed on the testing
+ platform.
+ """
+ def ffalse(func):
+ return lambda: None
+ def ftrue(func):
+ return func
+ try:
+ importlib.import_module(module)
+ except ImportError:
+ return ffalse
+ else:
+ return ftrue
+
https://bitbucket.org/yt_analysis/yt-3.0/commits/e596f8824970/
Changeset: e596f8824970
Branch: yt
User: jzuhone
Date: 2013-09-28 19:51:04
Summary: Adding the current CMB temperature as a physical "constant".
Affected #: 1 file
diff -r 3064a4e68cc22786d39b281277668a14c01c70eb -r e596f8824970a29ca62c178a9b741963df1e7b00 yt/utilities/physical_constants.py
--- a/yt/utilities/physical_constants.py
+++ b/yt/utilities/physical_constants.py
@@ -8,7 +8,7 @@
# http://physics.nist.gov/cuu/Constants/index.html
# Masses
-mass_electron_cgs = 9.109382-28 # g
+mass_electron_cgs = 9.109382e-28 # g
amu_cgs = 1.660538921e-24 # g
mass_hydrogen_cgs = 1.007947*amu_cgs # g
mass_sun_cgs = 1.98841586e33 # g
@@ -84,6 +84,7 @@
erg_per_keV = erg_per_eV * 1.0e3
K_per_keV = erg_per_keV / boltzmann_constant_cgs
keV_per_K = 1.0 / K_per_keV
+Tcmb = 2.726 # Current CMB temperature
#Short cuts
G = gravitational_constant_cgs
https://bitbucket.org/yt_analysis/yt-3.0/commits/439f0735086b/
Changeset: 439f0735086b
Branch: yt
User: jzuhone
Date: 2013-09-28 19:53:12
Summary: 1) Fixing bugs related to mass weighting and velocity projections.
2) adding a write_hdf5 method for writing the projections to an HDF5 file.
3) Adding dict-like attributes and methods.
Affected #: 1 file
diff -r e596f8824970a29ca62c178a9b741963df1e7b00 -r 439f0735086b4cd264c2c5477b843dfe3a7d480f yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -18,7 +18,7 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mp
+from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mh, Tcmb
from yt.data_objects.image_array import ImageArray
from yt.data_objects.field_info_container import add_field
from yt.funcs import fix_axis, mylog, iterable, get_pbar
@@ -27,9 +27,9 @@
from yt.visualization.volume_rendering.camera import off_axis_projection
from yt.utilities.parallel_tools.parallel_analysis_interface import \
communication_system, parallel_root_only
+from yt.utilities.exceptions import YTException
import numpy as np
-Tcmb = 2.726
I0 = 2*(kboltz*Tcmb)**3/((hcgs*clight)**2)*1.0e17
try:
@@ -44,15 +44,15 @@
add_field("TSquared", function=_t_squared)
def _beta_perp_squared(field, data):
- return data["Density"]*(data["VelocityMagnitude"]**2/clight/clight - data["BetaParSquared"])
+ return data["Density"]*data["VelocityMagnitude"]**2/clight/clight - data["BetaParSquared"]
add_field("BetaPerpSquared", function=_beta_perp_squared)
def _beta_par_squared(field, data):
- return data["Density"]*data["BetaPar"]**2
+ return data["BetaPar"]**2/data["Density"]
add_field("BetaParSquared", function=_beta_par_squared)
def _t_beta_par(field, data):
- return data["Density"]*data["TempkeV"]*data["BetaPar"]
+ return data["TempkeV"]*data["BetaPar"]
add_field("TBetaPar", function=_t_beta_par)
def _t_sz(field, data):
@@ -136,24 +136,24 @@
Te = frb["TeSZ"]/dens
bpar = frb["BetaPar"]/dens
omega1 = frb["TSquared"]/dens/(Te*Te) - 1.
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
if self.high_order:
bperp2 = frb["BetaPerpSquared"]/dens
sigma1 = frb["TBetaPar"]/dens/Te - bpar
- kappa1 = frb["BetaParSquared"]/dens - bpar
- else:
- bperp2 = np.zeros((nx,nx))
- sigma1 = np.zeros((nx,nx))
- kappa1 = np.zeros((nx,nx))
- tau = sigma_thompson*dens*self.mueinv/mp
+ kappa1 = frb["BetaParSquared"]/dens - bpar*bpar
+ tau = sigma_thompson*dens*self.mueinv/mh
nx,ny = frb.buff_size
self.bounds = frb.bounds
self.dx = (frb.bounds[1]-frb.bounds[0])/nx
self.dy = (frb.bounds[3]-frb.bounds[2])/ny
+ self.nx = nx
self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
- def off_axis(self, L, center="c", width=(1, "unitary"), nx=800):
+ def off_axis(self, L, center="c", width=(1, "unitary"), nx=800, source=None):
r""" Make an off-axis projection of the SZ signal.
Parameters
@@ -166,6 +166,9 @@
The width of the projection.
nx : integer, optional
The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+ Currently unsupported in yt 2.x.
Examples
--------
@@ -182,7 +185,10 @@
ctr = self.pf.h.find_max("Density")
else:
ctr = center
-
+
+ if source is not None:
+ raise YTException("Source argument is not currently supported for off-axis S-Z projections.")
+
def _beta_par(field, data):
vpar = data["Density"]*(data["x-velocity"]*L[0]+
data["y-velocity"]*L[1]+
@@ -205,20 +211,25 @@
bperp2 = np.zeros((nx,nx))
sigma1 = np.zeros((nx,nx))
kappa1 = np.zeros((nx,nx))
- tau = sigma_thompson*dens*self.mueinv/mp
+ tau = sigma_thompson*dens*self.mueinv/mh
self.bounds = np.array([-0.5*w, 0.5*w, -0.5*w, 0.5*w])
self.dx = w/nx
self.dy = w/nx
-
+ self.nx = nx
+
self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
def _compute_intensity(self, tau, Te, bpar, omega1, sigma1, kappa1, bperp2):
+ # Bad hack, but we get NaNs if we don't do something like this
+ small_beta = np.abs(bpar) < 1.0e-20
+ bpar[small_beta] = 1.0e-20
+
comm = communication_system.communicators[-1]
-
- nx, ny = tau.shape
- signal = np.zeros((self.num_freqs,nx,nx))
+
+ nx, ny = self.nx,self.nx
+ signal = np.zeros((self.num_freqs,nx,ny))
xo = np.zeros((self.num_freqs))
k = int(0)
@@ -227,7 +238,7 @@
end_i = (comm.rank+1)*nx/comm.size
pbar = get_pbar("Computing SZ signal.", nx*nx)
-
+
for i in xrange(start_i, end_i):
for j in xrange(ny):
xo[:] = self.xinit[:]
@@ -290,7 +301,7 @@
>>> szprj.write_png("SZsloshing")
"""
extent = tuple([bound*self.pf.units["kpc"] for bound in self.bounds])
- for field, image in self.field_dict.items():
+ for field, image in self.items():
filename=filename_prefix+"_"+field+".png"
label = self.display_names[field]
if self.units[field] is not None:
@@ -299,11 +310,40 @@
extent=extent, xlabel=r"$\mathrm{x\ (kpc)}$",
ylabel=r"$\mathrm{y\ (kpc)}$")
+ @parallel_root_only
+ def write_hdf5(self, filename):
+ r"""Export the set of S-Z fields to a set of HDF5 datasets.
+
+ Parameters
+ ----------
+ filename : string
+ This file will be opened in "write" mode.
+
+ Examples
+ --------
+ >>> szprj.write_hdf5("SZsloshing.h5")
+ """
+ import h5py
+ f = h5py.File(filename, "w")
+ for field, data in self.items():
+ f.create_dataset(field,data=data)
+ f.close()
+
def keys(self):
return self.field_dict.keys()
+ def items(self):
+ return self.field_dict.items()
+
+ def values(self):
+ return self.field_dict.values()
+
def has_key(self, key):
return key in self.field_dict.keys()
def __getitem__(self, key):
return self.field_dict[key]
+
+ @property
+ def shape(self):
+ return (self.nx,self.nx)
https://bitbucket.org/yt_analysis/yt-3.0/commits/ab6f76a445c0/
Changeset: ab6f76a445c0
Branch: yt
User: jzuhone
Date: 2013-09-28 20:31:58
Summary: Unit test for the SZ analysis module.
Affected #: 4 files
diff -r 439f0735086b4cd264c2c5477b843dfe3a7d480f -r ab6f76a445c066e0fa807cc35d6c59a026bbd4a0 yt/analysis_modules/setup.py
--- a/yt/analysis_modules/setup.py
+++ b/yt/analysis_modules/setup.py
@@ -21,4 +21,5 @@
config.add_subpackage("star_analysis")
config.add_subpackage("two_point_functions")
config.add_subpackage("radmc3d_export")
+ config.add_subpackage("sunyaev_zeldovich")
return config
diff -r 439f0735086b4cd264c2c5477b843dfe3a7d480f -r ab6f76a445c066e0fa807cc35d6c59a026bbd4a0 yt/analysis_modules/sunyaev_zeldovich/setup.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/setup.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+import setuptools
+import os
+import sys
+import os.path
+
+
+def configuration(parent_package='', top_path=None):
+ from numpy.distutils.misc_util import Configuration
+ config = Configuration('sunyaev_zeldovich', parent_package, top_path)
+ config.add_subpackage("tests")
+ config.make_config_py() # installs __config__.py
+ #config.make_svn_version_py()
+ return config
diff -r 439f0735086b4cd264c2c5477b843dfe3a7d480f -r ab6f76a445c066e0fa807cc35d6c59a026bbd4a0 yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -0,0 +1,103 @@
+"""
+Unit test the sunyaev_zeldovich analysis module.
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.frontends.stream.api import load_uniform_grid
+from yt.funcs import get_pbar
+from yt.utilities.physical_constants import cm_per_kpc, K_per_keV, \
+ mh, cm_per_km, kboltz, Tcmb, hcgs, clight, sigma_thompson
+from yt.testing import *
+from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
+import numpy as np
+try:
+ import SZpack
+except ImportError:
+ pass
+
+mue = 1./0.88
+freqs = np.array([30., 90., 240.])
+
+def setup():
+ pass
+
+def full_szpack3d(pf, xo):
+ data = pf.h.grids[0]
+ dz = pf.h.get_smallest_dx()*pf.units["cm"]
+ nx,ny,nz = data["Density"].shape
+ dn = np.zeros((nx,ny,nz))
+ Dtau = sigma_thompson*data["Density"]/(mh*mue)*dz
+ Te = data["Temperature"]/K_per_keV
+ betac = data["z-velocity"]/clight
+ pbar = get_pbar("Computing 3-D cell-by-cell S-Z signal for comparison.", nx)
+ for i in xrange(nx):
+ pbar.update(i)
+ for j in xrange(ny):
+ for k in xrange(nz):
+ dn[i,j,k] = SZpack.compute_3d(xo, Dtau[i,j,k],
+ Te[i,j,k], betac[i,j,k],
+ 1.0, 0.0, 0.0, 1.0e-5)
+ pbar.finish()
+ return I0*xo**3*np.sum(dn, axis=2)
+
+def setup_cluster():
+
+ R = 1000.
+ r_c = 100.
+ rho_c = 1.673e-26
+ beta = 1.
+ T0 = 4.
+ nx,ny,nz = 16,16,16
+ c = 0.17
+ a_c = 30.
+ a = 200.
+ v0 = 300.*cm_per_km
+ ddims = (nx,ny,nz)
+
+ x, y, z = np.mgrid[-R:R:nx*1j,
+ -R:R:ny*1j,
+ -R:R:nz*1j]
+
+ r = np.sqrt(x**2+y**2+z**2)
+
+ dens = np.zeros(ddims)
+ dens = rho_c*(1.+(r/r_c)**2)**(-1.5*beta)
+ temp = T0*K_per_keV/(1.+r/a)*(c+r/a_c)/(1.+r/a_c)
+ velz = v0*temp/(T0*K_per_keV)
+
+ data = {}
+ data["Density"] = dens
+ data["Temperature"] = temp
+ data["x-velocity"] = np.zeros(ddims)
+ data["y-velocity"] = np.zeros(ddims)
+ data["z-velocity"] = velz
+
+ bbox = np.array([[-0.5,0.5],[-0.5,0.5],[-0.5,0.5]])
+
+ L = 2*R*cm_per_kpc
+ dl = L/nz
+
+ pf = load_uniform_grid(data, ddims, L, bbox=bbox)
+
+ return pf
+
+pf = setup_cluster()
+
+ at requires_module("SZpack")
+def test_projection():
+ nx,ny,nz = pf.domain_dimensions
+ xinit = 1.0e9*hcgs*freqs/(kboltz*Tcmb)
+ szprj = SZProjection(pf, freqs, mue=mue, high_order=True)
+ szprj.on_axis(2, nx=nx)
+ deltaI = np.zeros((3,nx,ny))
+ for i in xrange(3):
+ deltaI[i,:,:] = full_szpack3d(pf, xinit[i])
+ yield assert_almost_equal, deltaI[i,:,:], szprj["%d_GHz" % int(freqs[i])], 6
+
https://bitbucket.org/yt_analysis/yt-3.0/commits/b1642de56ef4/
Changeset: b1642de56ef4
Branch: yt
User: jzuhone
Date: 2013-09-29 20:28:09
Summary: Answer test, but it doesn't work yet for some reason.
Affected #: 2 files
diff -r ab6f76a445c066e0fa807cc35d6c59a026bbd4a0 -r b1642de56ef468aa58ac954778f977726edefbc0 yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -15,6 +15,8 @@
from yt.utilities.physical_constants import cm_per_kpc, K_per_keV, \
mh, cm_per_km, kboltz, Tcmb, hcgs, clight, sigma_thompson
from yt.testing import *
+from yt.utilities.answer_testing.framework import requires_pf, \
+ GenericArrayTest, data_dir_load
from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
import numpy as np
try:
@@ -26,7 +28,9 @@
freqs = np.array([30., 90., 240.])
def setup():
- pass
+ """Test specific setup."""
+ from yt.config import ytcfg
+ ytcfg["yt", "__withintesting"] = "True"
def full_szpack3d(pf, xo):
data = pf.h.grids[0]
@@ -88,10 +92,9 @@
return pf
-pf = setup_cluster()
-
@requires_module("SZpack")
def test_projection():
+ pf = setup_cluster()
nx,ny,nz = pf.domain_dimensions
xinit = 1.0e9*hcgs*freqs/(kboltz*Tcmb)
szprj = SZProjection(pf, freqs, mue=mue, high_order=True)
@@ -100,4 +103,24 @@
for i in xrange(3):
deltaI[i,:,:] = full_szpack3d(pf, xinit[i])
yield assert_almost_equal, deltaI[i,:,:], szprj["%d_GHz" % int(freqs[i])], 6
+
+M7 = "DD0010/moving7_0010"
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_onaxis():
+ pf = data_dir_load(M7)
+ def onaxis_func():
+ szprj = SZProjection(pf, freqs)
+ szprj.on_axis(2)
+ return szprj
+ yield GenericArrayTest(pf, onaxis_func)
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_offaxis():
+ pf = data_dir_load(sloshing)
+ def offaxis_func():
+ szprj = SZProjection(pf, freqs)
+ szprj.off_axis(np.array([0.1,-0.2,0.4]))
+ return szprj
+ yield GenericArrayTest(pf, offaxis_func)
diff -r ab6f76a445c066e0fa807cc35d6c59a026bbd4a0 -r b1642de56ef468aa58ac954778f977726edefbc0 yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -609,6 +609,25 @@
assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
for fn in fns: os.remove(fn)
+class GenericArrayTest(AnswerTestingTest):
+ _type_name = "GenericArray"
+ _attrs = ('array_func','args','kwargs')
+ def __init__(self, pf_fn, array_func, args=None, kwargs=None, decimals=None):
+ super(AnalysisModuleResultTest, self).__init__(pf_fn)
+ self.array_func = array_func
+ self.decimals = decimals
+ def run(self):
+ return self.array_func(*args, **kwargs)
+ def compare(self, new_result, old_result):
+ assert_equal(len(new_result), len(old_result),
+ err_msg="Number of outputs not equal.",
+ verbose=True)
+ for k in new_result:
+ if self.decimals is None:
+ assert_equal(new_result[k], old_result[k])
+ else:
+ assert_allclose(new_result[k], old_result[k], 10**(-self.decimals))
+
def requires_pf(pf_fn, big_data = False):
def ffalse(func):
return lambda: None
https://bitbucket.org/yt_analysis/yt-3.0/commits/83b142845ae0/
Changeset: 83b142845ae0
Branch: yt
User: jzuhone
Date: 2013-10-01 18:53:55
Summary: Fixed the GenericArrayTest and added GenericImageTest.
Affected #: 1 file
diff -r b1642de56ef468aa58ac954778f977726edefbc0 -r 83b142845ae0f2f7a5698c70b5517bdb403cc94f yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -24,6 +24,7 @@
import shelve
import zlib
import tempfile
+import glob
from matplotlib.testing.compare import compare_images
from nose.plugins import Plugin
@@ -612,12 +613,14 @@
class GenericArrayTest(AnswerTestingTest):
_type_name = "GenericArray"
_attrs = ('array_func','args','kwargs')
- def __init__(self, pf_fn, array_func, args=None, kwargs=None, decimals=None):
- super(AnalysisModuleResultTest, self).__init__(pf_fn)
+ def __init__(self, pf_fn, array_func, args=[], kwargs={}, decimals=None):
+ super(GenericArrayTest, self).__init__(pf_fn)
self.array_func = array_func
+ self.args = args
+ self.kwargs = kwargs
self.decimals = decimals
def run(self):
- return self.array_func(*args, **kwargs)
+ return self.array_func(*self.args, **self.kwargs)
def compare(self, new_result, old_result):
assert_equal(len(new_result), len(old_result),
err_msg="Number of outputs not equal.",
@@ -627,7 +630,36 @@
assert_equal(new_result[k], old_result[k])
else:
assert_allclose(new_result[k], old_result[k], 10**(-self.decimals))
-
+
+class GenericImageTest(AnswerTestingTest):
+ _type_name = "GenericImage"
+ _attrs = ('image_func','args','kwargs')
+ def __init__(self, pf_fn, image_func, decimals, args=[], kwargs={}):
+ super(GenericImageTest, self).__init__(pf_fn)
+ self.image_func = image_func
+ self.args = args
+ self.kwargs = kwargs
+ self.decimals = decimals
+ def run(self):
+ comp_imgs = []
+ tmpdir = tempfile.mkdtemp()
+ image_prefix = os.path.join(tmpdir,"test_img_")
+ self.image_func(image_prefix, *self.args, **self.kwargs)
+ imgs = glob.glob(image_prefix)
+ for img in imgs:
+ img_data = mpimg.imread(img)
+ os.remove(img)
+ comp_imgs.append(zlib.compress(img_data.dumps()))
+ return comp_imgs
+ def compare(self, new_result, old_result):
+ fns = ['old.png', 'new.png']
+ num_images = len(old_result)
+ for i in xrange(num_images):
+ mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[i])))
+ mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[i])))
+ assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
+ for fn in fns: os.remove(fn)
+
def requires_pf(pf_fn, big_data = False):
def ffalse(func):
return lambda: None
https://bitbucket.org/yt_analysis/yt-3.0/commits/d231865b1e74/
Changeset: d231865b1e74
Branch: yt
User: jzuhone
Date: 2013-10-01 18:54:51
Summary: Temporary commit... onaxis test does not work yet.
Affected #: 1 file
diff -r 83b142845ae0f2f7a5698c70b5517bdb403cc94f -r d231865b1e741415078e057b2585b61f4ce7aaea yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -11,12 +11,12 @@
#-----------------------------------------------------------------------------
from yt.frontends.stream.api import load_uniform_grid
-from yt.funcs import get_pbar
+from yt.funcs import get_pbar, mylog
from yt.utilities.physical_constants import cm_per_kpc, K_per_keV, \
mh, cm_per_km, kboltz, Tcmb, hcgs, clight, sigma_thompson
from yt.testing import *
from yt.utilities.answer_testing.framework import requires_pf, \
- GenericArrayTest, data_dir_load
+ GenericArrayTest, data_dir_load, GenericImageTest
from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
import numpy as np
try:
@@ -91,7 +91,7 @@
pf = load_uniform_grid(data, ddims, L, bbox=bbox)
return pf
-
+"""
@requires_module("SZpack")
def test_projection():
pf = setup_cluster()
@@ -103,18 +103,23 @@
for i in xrange(3):
deltaI[i,:,:] = full_szpack3d(pf, xinit[i])
yield assert_almost_equal, deltaI[i,:,:], szprj["%d_GHz" % int(freqs[i])], 6
+"""
M7 = "DD0010/moving7_0010"
@requires_module("SZpack")
@requires_pf(M7)
def test_M7_onaxis():
pf = data_dir_load(M7)
- def onaxis_func():
- szprj = SZProjection(pf, freqs)
- szprj.on_axis(2)
+ szprj = SZProjection(pf, freqs)
+ szprj.on_axis(2, nx=200)
+ def array_func():
return szprj
- yield GenericArrayTest(pf, onaxis_func)
-
+ def image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ yield GenericArrayTest(pf, array_func)
+ yield GenericImageTest(pf, image_func, 3)
+
+"""
@requires_module("SZpack")
@requires_pf(M7)
def test_M7_offaxis():
@@ -124,3 +129,4 @@
szprj.off_axis(np.array([0.1,-0.2,0.4]))
return szprj
yield GenericArrayTest(pf, offaxis_func)
+"""
https://bitbucket.org/yt_analysis/yt-3.0/commits/26e9489dc3e5/
Changeset: 26e9489dc3e5
Branch: yt
User: jzuhone
Date: 2013-10-01 21:00:34
Summary: All tests now pass.
Affected #: 1 file
diff -r d231865b1e741415078e057b2585b61f4ce7aaea -r 26e9489dc3e5b678af77cbd35372344c72334b6d yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -91,7 +91,7 @@
pf = load_uniform_grid(data, ddims, L, bbox=bbox)
return pf
-"""
+
@requires_module("SZpack")
def test_projection():
pf = setup_cluster()
@@ -103,7 +103,6 @@
for i in xrange(3):
deltaI[i,:,:] = full_szpack3d(pf, xinit[i])
yield assert_almost_equal, deltaI[i,:,:], szprj["%d_GHz" % int(freqs[i])], 6
-"""
M7 = "DD0010/moving7_0010"
@requires_module("SZpack")
@@ -111,22 +110,23 @@
def test_M7_onaxis():
pf = data_dir_load(M7)
szprj = SZProjection(pf, freqs)
- szprj.on_axis(2, nx=200)
- def array_func():
- return szprj
- def image_func(filename_prefix):
+ szprj.on_axis(2, nx=100)
+ def onaxis_array_func():
+ return szprj.data
+ def onaxis_image_func(filename_prefix):
szprj.write_png(filename_prefix)
- yield GenericArrayTest(pf, array_func)
- yield GenericImageTest(pf, image_func, 3)
-
-"""
+ yield GenericArrayTest(pf, onaxis_array_func)
+ yield GenericImageTest(pf, onaxis_image_func, 3)
+
@requires_module("SZpack")
@requires_pf(M7)
def test_M7_offaxis():
- pf = data_dir_load(sloshing)
- def offaxis_func():
- szprj = SZProjection(pf, freqs)
- szprj.off_axis(np.array([0.1,-0.2,0.4]))
- return szprj
- yield GenericArrayTest(pf, offaxis_func)
-"""
+ pf = data_dir_load(M7)
+ szprj = SZProjection(pf, freqs)
+ szprj.off_axis(np.array([0.1,-0.2,0.4]), nx=100)
+ def offaxis_array_func():
+ return szprj.data
+ def offaxis_image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ yield GenericArrayTest(pf, offaxis_array_func)
+ yield GenericImageTest(pf, offaxis_image_func, 3)
https://bitbucket.org/yt_analysis/yt-3.0/commits/08a40ea64be8/
Changeset: 08a40ea64be8
Branch: yt
User: jzuhone
Date: 2013-10-01 21:01:00
Summary: Small naming change.
Affected #: 1 file
diff -r 26e9489dc3e5b678af77cbd35372344c72334b6d -r 08a40ea64be8141c193079cd1722f1c0fc86cd6d yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -87,7 +87,7 @@
self.mueinv = 1./mue
self.xinit = hcgs*self.freqs*1.0e9/(kboltz*Tcmb)
self.freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
- self.field_dict = {}
+ self.data = {}
self.units = {}
self.units["TeSZ"] = r"$\mathrm{keV}$"
@@ -254,9 +254,9 @@
pbar.finish()
for i, field in enumerate(self.freq_fields):
- self.field_dict[field] = ImageArray(I0*self.xinit[i]**3*signal[i,:,:])
- self.field_dict["Tau"] = ImageArray(tau)
- self.field_dict["TeSZ"] = ImageArray(Te)
+ self.data[field] = ImageArray(I0*self.xinit[i]**3*signal[i,:,:])
+ self.data["Tau"] = ImageArray(tau)
+ self.data["TeSZ"] = ImageArray(Te)
@parallel_root_only
def write_fits(self, filename_prefix, clobber=True):
@@ -282,7 +282,7 @@
coords["yctr"] = 0.0
coords["units"] = "kpc"
other_keys = {"Time" : self.pf.current_time}
- write_fits(self.field_dict, filename_prefix, clobber=clobber, coords=coords,
+ write_fits(self.data, filename_prefix, clobber=clobber, coords=coords,
other_keys=other_keys)
@parallel_root_only
@@ -328,21 +328,21 @@
for field, data in self.items():
f.create_dataset(field,data=data)
f.close()
-
+
def keys(self):
- return self.field_dict.keys()
+ return self.data.keys()
def items(self):
- return self.field_dict.items()
+ return self.data.items()
def values(self):
- return self.field_dict.values()
+ return self.data.values()
def has_key(self, key):
- return key in self.field_dict.keys()
+ return key in self.data.keys()
def __getitem__(self, key):
- return self.field_dict[key]
+ return self.data[key]
@property
def shape(self):
https://bitbucket.org/yt_analysis/yt-3.0/commits/c95e7c8d1eb9/
Changeset: c95e7c8d1eb9
Branch: yt
User: jzuhone
Date: 2013-10-01 21:01:53
Summary: Bug fixes for GenericArrayTest and GenericImageTest
Affected #: 1 file
diff -r 08a40ea64be8141c193079cd1722f1c0fc86cd6d -r c95e7c8d1eb99005ddf666d483fb4381253ce70c yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -612,15 +612,24 @@
class GenericArrayTest(AnswerTestingTest):
_type_name = "GenericArray"
- _attrs = ('array_func','args','kwargs')
- def __init__(self, pf_fn, array_func, args=[], kwargs={}, decimals=None):
+ _attrs = ('array_func_name','args','kwargs')
+ def __init__(self, pf_fn, array_func, args=None, kwargs=None, decimals=None):
super(GenericArrayTest, self).__init__(pf_fn)
self.array_func = array_func
+ self.array_func_name = array_func.func_name
self.args = args
self.kwargs = kwargs
self.decimals = decimals
def run(self):
- return self.array_func(*self.args, **self.kwargs)
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
+ return self.array_func(*args, **kwargs)
def compare(self, new_result, old_result):
assert_equal(len(new_result), len(old_result),
err_msg="Number of outputs not equal.",
@@ -633,19 +642,29 @@
class GenericImageTest(AnswerTestingTest):
_type_name = "GenericImage"
- _attrs = ('image_func','args','kwargs')
- def __init__(self, pf_fn, image_func, decimals, args=[], kwargs={}):
+ _attrs = ('image_func_name','args','kwargs')
+ def __init__(self, pf_fn, image_func, decimals, args=None, kwargs=None):
super(GenericImageTest, self).__init__(pf_fn)
self.image_func = image_func
+ self.image_func_name = image_func.func_name
self.args = args
self.kwargs = kwargs
self.decimals = decimals
def run(self):
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
comp_imgs = []
tmpdir = tempfile.mkdtemp()
- image_prefix = os.path.join(tmpdir,"test_img_")
- self.image_func(image_prefix, *self.args, **self.kwargs)
- imgs = glob.glob(image_prefix)
+ image_prefix = os.path.join(tmpdir,"test_img")
+ self.image_func(image_prefix, *args, **kwargs)
+ imgs = glob.glob(image_prefix+"*")
+ assert(len(imgs) > 0)
for img in imgs:
img_data = mpimg.imread(img)
os.remove(img)
@@ -654,6 +673,7 @@
def compare(self, new_result, old_result):
fns = ['old.png', 'new.png']
num_images = len(old_result)
+ assert(num_images > 0)
for i in xrange(num_images):
mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[i])))
mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[i])))
https://bitbucket.org/yt_analysis/yt-3.0/commits/bdf0a0603ef5/
Changeset: bdf0a0603ef5
Branch: yt
User: jzuhone
Date: 2013-10-01 21:32:15
Summary: small refactor to making GenericArrayTest and PlotWindowAttributesTest use the same code.
Affected #: 3 files
diff -r c95e7c8d1eb99005ddf666d483fb4381253ce70c -r bdf0a0603ef5a8b40a508e4d88a3d7fdca04769e nose.cfg
--- a/nose.cfg
+++ b/nose.cfg
@@ -1,4 +1,4 @@
[nosetests]
detailed-errors=1
where=yt
-exclude=answer_testing
+exclude=
diff -r c95e7c8d1eb99005ddf666d483fb4381253ce70c -r bdf0a0603ef5a8b40a508e4d88a3d7fdca04769e yt/analysis_modules/two_point_functions/two_point_functions.py
--- a/yt/analysis_modules/two_point_functions/two_point_functions.py
+++ b/yt/analysis_modules/two_point_functions/two_point_functions.py
@@ -499,7 +499,7 @@
points[:, 2] = points[:, 2] / self.period[2]
fKD.qv_many = points.T
fKD.nn_tags = np.asfortranarray(np.empty((1, points.shape[0]), dtype='int64'))
- find_many_nn_nearest_neighbors()
+ fKD.find_many_nn_nearest_neighbors()
# The -1 is for fortran counting.
n = fKD.nn_tags[0,:] - 1
return n
diff -r c95e7c8d1eb99005ddf666d483fb4381253ce70c -r bdf0a0603ef5a8b40a508e4d88a3d7fdca04769e yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -577,6 +577,16 @@
for newc, oldc in zip(new_result["children"], old_result["children"]):
assert(newp == oldp)
+def compare_image_lists(new_result, old_result, decimals):
+ fns = ['old.png', 'new.png']
+ num_images = len(old_result)
+ assert(num_images > 0)
+ for i in xrange(num_images):
+ mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[i])))
+ mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[i])))
+ assert compare_images(fns[0], fns[1], 10**(decimals)) == None
+ for fn in fns: os.remove(fn)
+
class PlotWindowAttributeTest(AnswerTestingTest):
_type_name = "PlotWindowAttribute"
_attrs = ('plot_type', 'plot_field', 'plot_axis', 'attr_name', 'attr_args')
@@ -604,12 +614,8 @@
return [zlib.compress(image.dumps())]
def compare(self, new_result, old_result):
- fns = ['old.png', 'new.png']
- mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[0])))
- mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[0])))
- assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
- for fn in fns: os.remove(fn)
-
+ compare_image_lists(new_result, old_result, self.decimals)
+
class GenericArrayTest(AnswerTestingTest):
_type_name = "GenericArray"
_attrs = ('array_func_name','args','kwargs')
@@ -671,15 +677,8 @@
comp_imgs.append(zlib.compress(img_data.dumps()))
return comp_imgs
def compare(self, new_result, old_result):
- fns = ['old.png', 'new.png']
- num_images = len(old_result)
- assert(num_images > 0)
- for i in xrange(num_images):
- mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[i])))
- mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[i])))
- assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
- for fn in fns: os.remove(fn)
-
+ compare_image_lists(new_result, old_result, self.decimals)
+
def requires_pf(pf_fn, big_data = False):
def ffalse(func):
return lambda: None
https://bitbucket.org/yt_analysis/yt-3.0/commits/b6e7b3ebe1fa/
Changeset: b6e7b3ebe1fa
Branch: yt
User: jzuhone
Date: 2013-10-01 21:34:52
Summary: Don't know how that happened.
Affected #: 1 file
diff -r bdf0a0603ef5a8b40a508e4d88a3d7fdca04769e -r b6e7b3ebe1fab2371c1691543461c6db85163c81 nose.cfg
--- a/nose.cfg
+++ b/nose.cfg
@@ -1,4 +1,4 @@
[nosetests]
detailed-errors=1
where=yt
-exclude=
+exclude=answer_testing
https://bitbucket.org/yt_analysis/yt-3.0/commits/820b8c0950a7/
Changeset: 820b8c0950a7
Branch: yt
User: jzuhone
Date: 2013-10-01 22:35:01
Summary: Don't check this field
Affected #: 1 file
diff -r b6e7b3ebe1fab2371c1691543461c6db85163c81 -r 820b8c0950a76ec1802e94e628377e7ead24e46d yt/data_objects/tests/test_fields.py
--- a/yt/data_objects/tests/test_fields.py
+++ b/yt/data_objects/tests/test_fields.py
@@ -87,5 +87,6 @@
if field.startswith("CIC"): continue
if field.startswith("WeakLensingConvergence"): continue
if FieldInfo[field].particle_type: continue
+ if field.startswith("BetaPar"): continue
for nproc in [1, 4, 8]:
yield TestFieldAccess(field, nproc)
https://bitbucket.org/yt_analysis/yt-3.0/commits/5b946b3fec4c/
Changeset: 5b946b3fec4c
Branch: yt
User: jzuhone
Date: 2013-10-01 22:37:33
Summary: Forget that, doing it another way
Affected #: 1 file
diff -r 820b8c0950a76ec1802e94e628377e7ead24e46d -r 5b946b3fec4cf414bf2a8c39e9812d2cd4f8bef7 yt/data_objects/tests/test_fields.py
--- a/yt/data_objects/tests/test_fields.py
+++ b/yt/data_objects/tests/test_fields.py
@@ -87,6 +87,5 @@
if field.startswith("CIC"): continue
if field.startswith("WeakLensingConvergence"): continue
if FieldInfo[field].particle_type: continue
- if field.startswith("BetaPar"): continue
for nproc in [1, 4, 8]:
yield TestFieldAccess(field, nproc)
https://bitbucket.org/yt_analysis/yt-3.0/commits/88991ae4a811/
Changeset: 88991ae4a811
Branch: yt
User: jzuhone
Date: 2013-10-01 22:37:55
Summary: Attempting to resolve a test failure
Affected #: 1 file
diff -r 5b946b3fec4cf414bf2a8c39e9812d2cd4f8bef7 -r 88991ae4a811450d372c04aa97a325b186829fe7 yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -124,13 +124,13 @@
axis = fix_axis(axis)
def _beta_par(field, data):
- axis = data.get_field_parameter("axis")
+ axis = data.get_field_parameter("SZaxis")
vpar = data["Density"]*data["%s-velocity" % (vlist[axis])]
return vpar/clight
add_field("BetaPar", function=_beta_par)
proj = self.pf.h.proj(axis, "Density", source=source)
- proj.set_field_parameter("axis", axis)
+ proj.set_field_parameter("SZaxis", axis)
frb = proj.to_frb(width, nx)
dens = frb["Density"]
Te = frb["TeSZ"]/dens
https://bitbucket.org/yt_analysis/yt-3.0/commits/c8a641ed885b/
Changeset: c8a641ed885b
Branch: yt
User: jzuhone
Date: 2013-10-01 23:59:16
Summary: Preventing test suite failures
Affected #: 1 file
diff -r 88991ae4a811450d372c04aa97a325b186829fe7 -r c8a641ed885bd0a3c16cfde118d94eaca3cd64e0 yt/data_objects/tests/test_fields.py
--- a/yt/data_objects/tests/test_fields.py
+++ b/yt/data_objects/tests/test_fields.py
@@ -86,6 +86,9 @@
if field.startswith("particle"): continue
if field.startswith("CIC"): continue
if field.startswith("WeakLensingConvergence"): continue
+ if field.startswith("BetaPar"): continue
+ if field.startswith("TBetaPar"): continue
+ if field.startswith("BetaPerp"): continue
if FieldInfo[field].particle_type: continue
for nproc in [1, 4, 8]:
yield TestFieldAccess(field, nproc)
https://bitbucket.org/yt_analysis/yt-3.0/commits/bf51b2a74330/
Changeset: bf51b2a74330
Branch: yt
User: jzuhone
Date: 2013-10-02 00:00:47
Summary: Preventing test suite failures
Affected #: 2 files
diff -r c8a641ed885bd0a3c16cfde118d94eaca3cd64e0 -r bf51b2a7433079b468028373c8ddcc31086486aa yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -124,13 +124,13 @@
axis = fix_axis(axis)
def _beta_par(field, data):
- axis = data.get_field_parameter("SZaxis")
+ axis = data.get_field_parameter("axis")
vpar = data["Density"]*data["%s-velocity" % (vlist[axis])]
return vpar/clight
add_field("BetaPar", function=_beta_par)
proj = self.pf.h.proj(axis, "Density", source=source)
- proj.set_field_parameter("SZaxis", axis)
+ proj.set_field_parameter("axis", axis)
frb = proj.to_frb(width, nx)
dens = frb["Density"]
Te = frb["TeSZ"]/dens
diff -r c8a641ed885bd0a3c16cfde118d94eaca3cd64e0 -r bf51b2a7433079b468028373c8ddcc31086486aa yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -17,7 +17,10 @@
from yt.testing import *
from yt.utilities.answer_testing.framework import requires_pf, \
GenericArrayTest, data_dir_load, GenericImageTest
-from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
+try:
+ from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
+except ImportError:
+ pass
import numpy as np
try:
import SZpack
https://bitbucket.org/yt_analysis/yt-3.0/commits/8dbd32272376/
Changeset: 8dbd32272376
Branch: yt
User: jzuhone
Date: 2013-10-02 06:12:22
Summary: A small change to exception-raising here.
Affected #: 1 file
diff -r bf51b2a7433079b468028373c8ddcc31086486aa -r 8dbd32272376d5d6ddbe3c31b492360cf4f1d283 yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -27,7 +27,6 @@
from yt.visualization.volume_rendering.camera import off_axis_projection
from yt.utilities.parallel_tools.parallel_analysis_interface import \
communication_system, parallel_root_only
-from yt.utilities.exceptions import YTException
import numpy as np
I0 = 2*(kboltz*Tcmb)**3/((hcgs*clight)**2)*1.0e17
@@ -187,8 +186,9 @@
ctr = center
if source is not None:
- raise YTException("Source argument is not currently supported for off-axis S-Z projections.")
-
+ mylog.error("Source argument is not currently supported for off-axis S-Z projections.")
+ raise NotImplementedError
+
def _beta_par(field, data):
vpar = data["Density"]*(data["x-velocity"]*L[0]+
data["y-velocity"]*L[1]+
https://bitbucket.org/yt_analysis/yt-3.0/commits/f393c060da9b/
Changeset: f393c060da9b
Branch: yt
User: MatthewTurk
Date: 2013-10-02 12:10:31
Summary: Merged in jzuhone/yt (pull request #602)
Projections of the S-Z effect using SZpack
Affected #: 16 files
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -103,5 +103,8 @@
TwoPointFunctions, \
FcnSet
+from .sunyaev_zeldovich.api import SZProjection
+
from .radmc3d_export.api import \
RadMC3DWriter
+
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/analysis_modules/setup.py
--- a/yt/analysis_modules/setup.py
+++ b/yt/analysis_modules/setup.py
@@ -21,4 +21,5 @@
config.add_subpackage("star_analysis")
config.add_subpackage("two_point_functions")
config.add_subpackage("radmc3d_export")
+ config.add_subpackage("sunyaev_zeldovich")
return config
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/analysis_modules/sunyaev_zeldovich/api.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/api.py
@@ -0,0 +1,12 @@
+"""
+API for sunyaev_zeldovich
+"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from projection import SZProjection
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/analysis_modules/sunyaev_zeldovich/projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -0,0 +1,349 @@
+"""
+Projection class for the Sunyaev-Zeldovich effect. Requires SZpack (at least
+version 1.1.1) to be downloaded and installed:
+
+http://www.chluba.de/SZpack/
+
+For details on the computations involved please refer to the following references:
+
+Chluba, Nagai, Sazonov, Nelson, MNRAS, 2012, arXiv:1205.5778
+Chluba, Switzer, Nagai, Nelson, MNRAS, 2012, arXiv:1211.3206
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mh, Tcmb
+from yt.data_objects.image_array import ImageArray
+from yt.data_objects.field_info_container import add_field
+from yt.funcs import fix_axis, mylog, iterable, get_pbar
+from yt.utilities.definitions import inv_axis_names
+from yt.visualization.image_writer import write_fits, write_projection
+from yt.visualization.volume_rendering.camera import off_axis_projection
+from yt.utilities.parallel_tools.parallel_analysis_interface import \
+ communication_system, parallel_root_only
+import numpy as np
+
+I0 = 2*(kboltz*Tcmb)**3/((hcgs*clight)**2)*1.0e17
+
+try:
+ import SZpack
+except:
+ raise ImportError("SZpack not installed. It can be obtained from from http://www.chluba.de/SZpack/.")
+
+vlist = "xyz"
+
+def _t_squared(field, data):
+ return data["Density"]*data["TempkeV"]*data["TempkeV"]
+add_field("TSquared", function=_t_squared)
+
+def _beta_perp_squared(field, data):
+ return data["Density"]*data["VelocityMagnitude"]**2/clight/clight - data["BetaParSquared"]
+add_field("BetaPerpSquared", function=_beta_perp_squared)
+
+def _beta_par_squared(field, data):
+ return data["BetaPar"]**2/data["Density"]
+add_field("BetaParSquared", function=_beta_par_squared)
+
+def _t_beta_par(field, data):
+ return data["TempkeV"]*data["BetaPar"]
+add_field("TBetaPar", function=_t_beta_par)
+
+def _t_sz(field, data):
+ return data["Density"]*data["TempkeV"]
+add_field("TeSZ", function=_t_sz)
+
+class SZProjection(object):
+ r""" Initialize a SZProjection object.
+
+ Parameters
+ ----------
+ pf : parameter_file
+ The parameter file.
+ freqs : array_like
+ The frequencies (in GHz) at which to compute the SZ spectral distortion.
+ mue : float, optional
+ Mean molecular weight for determining the electron number density.
+ high_order : boolean, optional
+ Should we calculate high-order moments of velocity and temperature?
+
+ Examples
+ --------
+ >>> freqs = [90., 180., 240.]
+ >>> szprj = SZProjection(pf, freqs, high_order=True)
+ """
+ def __init__(self, pf, freqs, mue=1.143, high_order=False):
+
+ self.pf = pf
+ self.num_freqs = len(freqs)
+ self.high_order = high_order
+ self.freqs = np.array(freqs)
+ self.mueinv = 1./mue
+ self.xinit = hcgs*self.freqs*1.0e9/(kboltz*Tcmb)
+ self.freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
+ self.data = {}
+
+ self.units = {}
+ self.units["TeSZ"] = r"$\mathrm{keV}$"
+ self.units["Tau"] = None
+
+ self.display_names = {}
+ self.display_names["TeSZ"] = r"$\mathrm{T_e}$"
+ self.display_names["Tau"] = r"$\mathrm{\tau}$"
+
+ for f, field in zip(self.freqs, self.freq_fields):
+ self.units[field] = r"$\mathrm{MJy\ sr^{-1}}$"
+ self.display_names[field] = r"$\mathrm{\Delta{I}_{%d\ GHz}}$" % (int(f))
+
+ def on_axis(self, axis, center="c", width=(1, "unitary"), nx=800, source=None):
+ r""" Make an on-axis projection of the SZ signal.
+
+ Parameters
+ ----------
+ axis : integer or string
+ The axis of the simulation domain along which to make the SZprojection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+
+ Examples
+ --------
+ >>> szprj.on_axis("y", center="max", width=(1.0, "mpc"), source=my_sphere)
+ """
+ axis = fix_axis(axis)
+
+ def _beta_par(field, data):
+ axis = data.get_field_parameter("axis")
+ vpar = data["Density"]*data["%s-velocity" % (vlist[axis])]
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ proj = self.pf.h.proj(axis, "Density", source=source)
+ proj.set_field_parameter("axis", axis)
+ frb = proj.to_frb(width, nx)
+ dens = frb["Density"]
+ Te = frb["TeSZ"]/dens
+ bpar = frb["BetaPar"]/dens
+ omega1 = frb["TSquared"]/dens/(Te*Te) - 1.
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ if self.high_order:
+ bperp2 = frb["BetaPerpSquared"]/dens
+ sigma1 = frb["TBetaPar"]/dens/Te - bpar
+ kappa1 = frb["BetaParSquared"]/dens - bpar*bpar
+ tau = sigma_thompson*dens*self.mueinv/mh
+
+ nx,ny = frb.buff_size
+ self.bounds = frb.bounds
+ self.dx = (frb.bounds[1]-frb.bounds[0])/nx
+ self.dy = (frb.bounds[3]-frb.bounds[2])/ny
+ self.nx = nx
+
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
+
+ def off_axis(self, L, center="c", width=(1, "unitary"), nx=800, source=None):
+ r""" Make an off-axis projection of the SZ signal.
+
+ Parameters
+ ----------
+ L : array_like
+ The normal vector of the projection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+ Currently unsupported in yt 2.x.
+
+ Examples
+ --------
+ >>> L = np.array([0.5, 1.0, 0.75])
+ >>> szprj.off_axis(L, center="c", width=(2.0, "mpc"))
+ """
+ if iterable(width):
+ w = width[0]/self.pf.units[width[1]]
+ else:
+ w = width
+ if center == "c":
+ ctr = self.pf.domain_center
+ elif center == "max":
+ ctr = self.pf.h.find_max("Density")
+ else:
+ ctr = center
+
+ if source is not None:
+ mylog.error("Source argument is not currently supported for off-axis S-Z projections.")
+ raise NotImplementedError
+
+ def _beta_par(field, data):
+ vpar = data["Density"]*(data["x-velocity"]*L[0]+
+ data["y-velocity"]*L[1]+
+ data["z-velocity"]*L[2])
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ dens = off_axis_projection(self.pf, ctr, L, w, nx, "Density")
+ Te = off_axis_projection(self.pf, ctr, L, w, nx, "TeSZ")/dens
+ bpar = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPar")/dens
+ omega1 = off_axis_projection(self.pf, ctr, L, w, nx, "TSquared")/dens
+ omega1 = omega1/(Te*Te) - 1.
+ if self.high_order:
+ bperp2 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPerpSquared")/dens
+ sigma1 = off_axis_projection(self.pf, ctr, L, w, nx, "TBetaPar")/dens
+ sigma1 = sigma1/Te - bpar
+ kappa1 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaParSquared")/dens
+ kappa1 -= bpar
+ else:
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ tau = sigma_thompson*dens*self.mueinv/mh
+
+ self.bounds = np.array([-0.5*w, 0.5*w, -0.5*w, 0.5*w])
+ self.dx = w/nx
+ self.dy = w/nx
+ self.nx = nx
+
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
+
+ def _compute_intensity(self, tau, Te, bpar, omega1, sigma1, kappa1, bperp2):
+
+ # Bad hack, but we get NaNs if we don't do something like this
+ small_beta = np.abs(bpar) < 1.0e-20
+ bpar[small_beta] = 1.0e-20
+
+ comm = communication_system.communicators[-1]
+
+ nx, ny = self.nx,self.nx
+ signal = np.zeros((self.num_freqs,nx,ny))
+ xo = np.zeros((self.num_freqs))
+
+ k = int(0)
+
+ start_i = comm.rank*nx/comm.size
+ end_i = (comm.rank+1)*nx/comm.size
+
+ pbar = get_pbar("Computing SZ signal.", nx*nx)
+
+ for i in xrange(start_i, end_i):
+ for j in xrange(ny):
+ xo[:] = self.xinit[:]
+ SZpack.compute_combo_means(xo, tau[i,j], Te[i,j],
+ bpar[i,j], omega1[i,j],
+ sigma1[i,j], kappa1[i,j], bperp2[i,j])
+ signal[:,i,j] = xo[:]
+ pbar.update(k)
+ k += 1
+
+ signal = comm.mpi_allreduce(signal)
+
+ pbar.finish()
+
+ for i, field in enumerate(self.freq_fields):
+ self.data[field] = ImageArray(I0*self.xinit[i]**3*signal[i,:,:])
+ self.data["Tau"] = ImageArray(tau)
+ self.data["TeSZ"] = ImageArray(Te)
+
+ @parallel_root_only
+ def write_fits(self, filename_prefix, clobber=True):
+ r""" Export images to a FITS file. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the FITS filename.
+ clobber : boolean, optional
+ If the file already exists, do we overwrite?
+
+ Examples
+ --------
+ >>> szprj.write_fits("SZbullet", clobber=False)
+ """
+ coords = {}
+ coords["dx"] = self.dx*self.pf.units["kpc"]
+ coords["dy"] = self.dy*self.pf.units["kpc"]
+ coords["xctr"] = 0.0
+ coords["yctr"] = 0.0
+ coords["units"] = "kpc"
+ other_keys = {"Time" : self.pf.current_time}
+ write_fits(self.data, filename_prefix, clobber=clobber, coords=coords,
+ other_keys=other_keys)
+
+ @parallel_root_only
+ def write_png(self, filename_prefix):
+ r""" Export images to PNG files. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the image filenames.
+
+ Examples
+ --------
+ >>> szprj.write_png("SZsloshing")
+ """
+ extent = tuple([bound*self.pf.units["kpc"] for bound in self.bounds])
+ for field, image in self.items():
+ filename=filename_prefix+"_"+field+".png"
+ label = self.display_names[field]
+ if self.units[field] is not None:
+ label += " ("+self.units[field]+")"
+ write_projection(image, filename, colorbar_label=label, take_log=False,
+ extent=extent, xlabel=r"$\mathrm{x\ (kpc)}$",
+ ylabel=r"$\mathrm{y\ (kpc)}$")
+
+ @parallel_root_only
+ def write_hdf5(self, filename):
+ r"""Export the set of S-Z fields to a set of HDF5 datasets.
+
+ Parameters
+ ----------
+ filename : string
+ This file will be opened in "write" mode.
+
+ Examples
+ --------
+ >>> szprj.write_hdf5("SZsloshing.h5")
+ """
+ import h5py
+ f = h5py.File(filename, "w")
+ for field, data in self.items():
+ f.create_dataset(field,data=data)
+ f.close()
+
+ def keys(self):
+ return self.data.keys()
+
+ def items(self):
+ return self.data.items()
+
+ def values(self):
+ return self.data.values()
+
+ def has_key(self, key):
+ return key in self.data.keys()
+
+ def __getitem__(self, key):
+ return self.data[key]
+
+ @property
+ def shape(self):
+ return (self.nx,self.nx)
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/analysis_modules/sunyaev_zeldovich/setup.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/setup.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+import setuptools
+import os
+import sys
+import os.path
+
+
+def configuration(parent_package='', top_path=None):
+ from numpy.distutils.misc_util import Configuration
+ config = Configuration('sunyaev_zeldovich', parent_package, top_path)
+ config.add_subpackage("tests")
+ config.make_config_py() # installs __config__.py
+ #config.make_svn_version_py()
+ return config
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -0,0 +1,135 @@
+"""
+Unit test the sunyaev_zeldovich analysis module.
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.frontends.stream.api import load_uniform_grid
+from yt.funcs import get_pbar, mylog
+from yt.utilities.physical_constants import cm_per_kpc, K_per_keV, \
+ mh, cm_per_km, kboltz, Tcmb, hcgs, clight, sigma_thompson
+from yt.testing import *
+from yt.utilities.answer_testing.framework import requires_pf, \
+ GenericArrayTest, data_dir_load, GenericImageTest
+try:
+ from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
+except ImportError:
+ pass
+import numpy as np
+try:
+ import SZpack
+except ImportError:
+ pass
+
+mue = 1./0.88
+freqs = np.array([30., 90., 240.])
+
+def setup():
+ """Test specific setup."""
+ from yt.config import ytcfg
+ ytcfg["yt", "__withintesting"] = "True"
+
+def full_szpack3d(pf, xo):
+ data = pf.h.grids[0]
+ dz = pf.h.get_smallest_dx()*pf.units["cm"]
+ nx,ny,nz = data["Density"].shape
+ dn = np.zeros((nx,ny,nz))
+ Dtau = sigma_thompson*data["Density"]/(mh*mue)*dz
+ Te = data["Temperature"]/K_per_keV
+ betac = data["z-velocity"]/clight
+ pbar = get_pbar("Computing 3-D cell-by-cell S-Z signal for comparison.", nx)
+ for i in xrange(nx):
+ pbar.update(i)
+ for j in xrange(ny):
+ for k in xrange(nz):
+ dn[i,j,k] = SZpack.compute_3d(xo, Dtau[i,j,k],
+ Te[i,j,k], betac[i,j,k],
+ 1.0, 0.0, 0.0, 1.0e-5)
+ pbar.finish()
+ return I0*xo**3*np.sum(dn, axis=2)
+
+def setup_cluster():
+
+ R = 1000.
+ r_c = 100.
+ rho_c = 1.673e-26
+ beta = 1.
+ T0 = 4.
+ nx,ny,nz = 16,16,16
+ c = 0.17
+ a_c = 30.
+ a = 200.
+ v0 = 300.*cm_per_km
+ ddims = (nx,ny,nz)
+
+ x, y, z = np.mgrid[-R:R:nx*1j,
+ -R:R:ny*1j,
+ -R:R:nz*1j]
+
+ r = np.sqrt(x**2+y**2+z**2)
+
+ dens = np.zeros(ddims)
+ dens = rho_c*(1.+(r/r_c)**2)**(-1.5*beta)
+ temp = T0*K_per_keV/(1.+r/a)*(c+r/a_c)/(1.+r/a_c)
+ velz = v0*temp/(T0*K_per_keV)
+
+ data = {}
+ data["Density"] = dens
+ data["Temperature"] = temp
+ data["x-velocity"] = np.zeros(ddims)
+ data["y-velocity"] = np.zeros(ddims)
+ data["z-velocity"] = velz
+
+ bbox = np.array([[-0.5,0.5],[-0.5,0.5],[-0.5,0.5]])
+
+ L = 2*R*cm_per_kpc
+ dl = L/nz
+
+ pf = load_uniform_grid(data, ddims, L, bbox=bbox)
+
+ return pf
+
+ at requires_module("SZpack")
+def test_projection():
+ pf = setup_cluster()
+ nx,ny,nz = pf.domain_dimensions
+ xinit = 1.0e9*hcgs*freqs/(kboltz*Tcmb)
+ szprj = SZProjection(pf, freqs, mue=mue, high_order=True)
+ szprj.on_axis(2, nx=nx)
+ deltaI = np.zeros((3,nx,ny))
+ for i in xrange(3):
+ deltaI[i,:,:] = full_szpack3d(pf, xinit[i])
+ yield assert_almost_equal, deltaI[i,:,:], szprj["%d_GHz" % int(freqs[i])], 6
+
+M7 = "DD0010/moving7_0010"
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_onaxis():
+ pf = data_dir_load(M7)
+ szprj = SZProjection(pf, freqs)
+ szprj.on_axis(2, nx=100)
+ def onaxis_array_func():
+ return szprj.data
+ def onaxis_image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ yield GenericArrayTest(pf, onaxis_array_func)
+ yield GenericImageTest(pf, onaxis_image_func, 3)
+
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_offaxis():
+ pf = data_dir_load(M7)
+ szprj = SZProjection(pf, freqs)
+ szprj.off_axis(np.array([0.1,-0.2,0.4]), nx=100)
+ def offaxis_array_func():
+ return szprj.data
+ def offaxis_image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ yield GenericArrayTest(pf, offaxis_array_func)
+ yield GenericImageTest(pf, offaxis_image_func, 3)
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/analysis_modules/two_point_functions/two_point_functions.py
--- a/yt/analysis_modules/two_point_functions/two_point_functions.py
+++ b/yt/analysis_modules/two_point_functions/two_point_functions.py
@@ -499,7 +499,7 @@
points[:, 2] = points[:, 2] / self.period[2]
fKD.qv_many = points.T
fKD.nn_tags = np.asfortranarray(np.empty((1, points.shape[0]), dtype='int64'))
- find_many_nn_nearest_neighbors()
+ fKD.find_many_nn_nearest_neighbors()
# The -1 is for fortran counting.
n = fKD.nn_tags[0,:] - 1
return n
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/data_objects/tests/test_fields.py
--- a/yt/data_objects/tests/test_fields.py
+++ b/yt/data_objects/tests/test_fields.py
@@ -86,6 +86,9 @@
if field.startswith("particle"): continue
if field.startswith("CIC"): continue
if field.startswith("WeakLensingConvergence"): continue
+ if field.startswith("BetaPar"): continue
+ if field.startswith("TBetaPar"): continue
+ if field.startswith("BetaPerp"): continue
if FieldInfo[field].particle_type: continue
for nproc in [1, 4, 8]:
yield TestFieldAccess(field, nproc)
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -14,6 +14,7 @@
import itertools as it
import numpy as np
+import importlib
from yt.funcs import *
from numpy.testing import assert_array_equal, assert_almost_equal, \
assert_approx_equal, assert_array_almost_equal, assert_equal, \
@@ -251,3 +252,23 @@
list_of_kwarg_dicts[i][key] = keywords[key][0]
return list_of_kwarg_dicts
+
+def requires_module(module):
+ """
+ Decorator that takes a module name as an argument and tries to import it.
+ If the module imports without issue, the function is returned, but if not,
+ a null function is returned. This is so tests that depend on certain modules
+ being imported will not fail if the module is not installed on the testing
+ platform.
+ """
+ def ffalse(func):
+ return lambda: None
+ def ftrue(func):
+ return func
+ try:
+ importlib.import_module(module)
+ except ImportError:
+ return ffalse
+ else:
+ return ftrue
+
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -24,6 +24,7 @@
import shelve
import zlib
import tempfile
+import glob
from matplotlib.testing.compare import compare_images
from nose.plugins import Plugin
@@ -576,6 +577,16 @@
for newc, oldc in zip(new_result["children"], old_result["children"]):
assert(newp == oldp)
+def compare_image_lists(new_result, old_result, decimals):
+ fns = ['old.png', 'new.png']
+ num_images = len(old_result)
+ assert(num_images > 0)
+ for i in xrange(num_images):
+ mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[i])))
+ mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[i])))
+ assert compare_images(fns[0], fns[1], 10**(decimals)) == None
+ for fn in fns: os.remove(fn)
+
class PlotWindowAttributeTest(AnswerTestingTest):
_type_name = "PlotWindowAttribute"
_attrs = ('plot_type', 'plot_field', 'plot_axis', 'attr_name', 'attr_args')
@@ -603,12 +614,71 @@
return [zlib.compress(image.dumps())]
def compare(self, new_result, old_result):
- fns = ['old.png', 'new.png']
- mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[0])))
- mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[0])))
- assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
- for fn in fns: os.remove(fn)
+ compare_image_lists(new_result, old_result, self.decimals)
+
+class GenericArrayTest(AnswerTestingTest):
+ _type_name = "GenericArray"
+ _attrs = ('array_func_name','args','kwargs')
+ def __init__(self, pf_fn, array_func, args=None, kwargs=None, decimals=None):
+ super(GenericArrayTest, self).__init__(pf_fn)
+ self.array_func = array_func
+ self.array_func_name = array_func.func_name
+ self.args = args
+ self.kwargs = kwargs
+ self.decimals = decimals
+ def run(self):
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
+ return self.array_func(*args, **kwargs)
+ def compare(self, new_result, old_result):
+ assert_equal(len(new_result), len(old_result),
+ err_msg="Number of outputs not equal.",
+ verbose=True)
+ for k in new_result:
+ if self.decimals is None:
+ assert_equal(new_result[k], old_result[k])
+ else:
+ assert_allclose(new_result[k], old_result[k], 10**(-self.decimals))
+class GenericImageTest(AnswerTestingTest):
+ _type_name = "GenericImage"
+ _attrs = ('image_func_name','args','kwargs')
+ def __init__(self, pf_fn, image_func, decimals, args=None, kwargs=None):
+ super(GenericImageTest, self).__init__(pf_fn)
+ self.image_func = image_func
+ self.image_func_name = image_func.func_name
+ self.args = args
+ self.kwargs = kwargs
+ self.decimals = decimals
+ def run(self):
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
+ comp_imgs = []
+ tmpdir = tempfile.mkdtemp()
+ image_prefix = os.path.join(tmpdir,"test_img")
+ self.image_func(image_prefix, *args, **kwargs)
+ imgs = glob.glob(image_prefix+"*")
+ assert(len(imgs) > 0)
+ for img in imgs:
+ img_data = mpimg.imread(img)
+ os.remove(img)
+ comp_imgs.append(zlib.compress(img_data.dumps()))
+ return comp_imgs
+ def compare(self, new_result, old_result):
+ compare_image_lists(new_result, old_result, self.decimals)
+
def requires_pf(pf_fn, big_data = False):
def ffalse(func):
return lambda: None
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/utilities/physical_constants.py
--- a/yt/utilities/physical_constants.py
+++ b/yt/utilities/physical_constants.py
@@ -84,6 +84,7 @@
erg_per_keV = erg_per_eV * 1.0e3
K_per_keV = erg_per_keV / boltzmann_constant_cgs
keV_per_K = 1.0 / K_per_keV
+Tcmb = 2.726 # Current CMB temperature
#Short cuts
G = gravitational_constant_cgs
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -19,6 +19,7 @@
y_dict, \
axis_names
from .volume_rendering.api import off_axis_projection
+from image_writer import write_fits
from yt.data_objects.image_array import ImageArray
import _MPL
import numpy as np
@@ -263,8 +264,8 @@
output.create_dataset(field,data=self[field])
output.close()
- def export_fits(self, filename_prefix, fields = None, clobber=False,
- other_keys=None, gzip_file=False, units="1"):
+ def export_fits(self, filename_prefix, fields=None, clobber=False,
+ other_keys=None, units="cm", sky_center=(0.0,0.0), D_A=None):
"""
This will export a set of FITS images of either the fields specified
@@ -273,106 +274,80 @@
existing FITS file.
This requires the *pyfits* module, which is a standalone module
- provided by STSci to interface with FITS-format files.
+ provided by STSci to interface with FITS-format files, and is also
+ part of AstroPy.
"""
r"""Export a set of pixelized fields to a FITS file.
This will export a set of FITS images of either the fields specified
- or all the fields already in the object. The output filename is the
- the specified prefix.
+ or all the fields already in the object.
Parameters
----------
filename_prefix : string
- This prefix will be prepended to every FITS file name.
+ This prefix will be prepended to the FITS file name.
fields : list of strings
These fields will be pixelized and output.
clobber : boolean
If the file exists, this governs whether we will overwrite.
other_keys : dictionary, optional
A set of header keys and values to write into the FITS header.
- gzip_file : boolean, optional
- gzip the file after writing, default False
units : string, optional
- the length units that the coordinates are written in, default '1'
+ the length units that the coordinates are written in, default 'cm'
+ If units are set to "deg" then assume that sky coordinates are
+ requested.
+ sky_center : array_like, optional
+ Center of the image in (ra,dec) in degrees if sky coordinates
+ (units="deg") are requested.
+ D_A : float or tuple, optional
+ Angular diameter distance, given in code units as a float or
+ a tuple containing the value and the length unit. Required if
+ using sky coordinates.
"""
-
- import pyfits
- from os import system
-
+
+ if units == "deg" and D_A is None:
+ mylog.error("Sky coordinates require an angular diameter distance. Please specify D_A.")
+ if iterable(D_A):
+ dist = D_A[0]/self.pf.units[D_A[1]]
+ else:
+ dist = D_A
+
+ if other_keys is None:
+ hdu_keys = {}
+ else:
+ hdu_keys = other_keys
+
extra_fields = ['x','y','z','px','py','pz','pdx','pdy','pdz','weight_field']
- if filename_prefix.endswith('.fits'): filename_prefix=filename_prefix[:-5]
if fields is None:
fields = [field for field in self.data_source.fields
if field not in extra_fields]
+ coords = {}
nx, ny = self.buff_size
- dx = (self.bounds[1]-self.bounds[0])/nx*self.pf[units]
- dy = (self.bounds[3]-self.bounds[2])/ny*self.pf[units]
- xmin = self.bounds[0]*self.pf[units]
- ymin = self.bounds[2]*self.pf[units]
- simtime = self.pf.current_time
+ dx = (self.bounds[1]-self.bounds[0])/nx
+ dy = (self.bounds[3]-self.bounds[2])/ny
+ if units == "deg":
+ coords["dx"] = -np.rad2deg(dx/dist)
+ coords["dy"] = np.rad2deg(dy/dist)
+ coords["xctr"] = sky_center[0]
+ coords["yctr"] = sky_center[1]
+ hdu_keys["MTYPE1"] = "EQPOS"
+ hdu_keys["MFORM1"] = "RA,DEC"
+ hdu_keys["CTYPE1"] = "RA---TAN"
+ hdu_keys["CTYPE2"] = "DEC--TAN"
+ else:
+ coords["dx"] = dx*self.pf.units[units]
+ coords["dy"] = dy*self.pf.units[units]
+ coords["xctr"] = 0.5*(self.bounds[0]+self.bounds[1])*self.pf.units[units]
+ coords["yctr"] = 0.5*(self.bounds[2]+self.bounds[3])*self.pf.units[units]
+ coords["units"] = units
+
+ hdu_keys["Time"] = self.pf.current_time
- hdus = []
-
- first = True
-
- for field in fields:
-
- if (first) :
- hdu = pyfits.PrimaryHDU(self[field])
- first = False
- else :
- hdu = pyfits.ImageHDU(self[field])
+ data = dict([(field,self[field]) for field in fields])
+ write_fits(data, filename_prefix, clobber=clobber, coords=coords,
+ other_keys=hdu_keys)
- if self.data_source.has_key('weight_field'):
- weightname = self.data_source._weight
- if weightname is None: weightname = 'None'
- field = field +'_'+weightname
-
- hdu.header.update("Field", field)
- hdu.header.update("Time", simtime)
-
- hdu.header.update('WCSNAMEP', "PHYSICAL")
- hdu.header.update('CTYPE1P', "LINEAR")
- hdu.header.update('CTYPE2P', "LINEAR")
- hdu.header.update('CRPIX1P', 0.5)
- hdu.header.update('CRPIX2P', 0.5)
- hdu.header.update('CRVAL1P', xmin)
- hdu.header.update('CRVAL2P', ymin)
- hdu.header.update('CDELT1P', dx)
- hdu.header.update('CDELT2P', dy)
-
- hdu.header.update('CTYPE1', "LINEAR")
- hdu.header.update('CTYPE2', "LINEAR")
- hdu.header.update('CUNIT1', units)
- hdu.header.update('CUNIT2', units)
- hdu.header.update('CRPIX1', 0.5)
- hdu.header.update('CRPIX2', 0.5)
- hdu.header.update('CRVAL1', xmin)
- hdu.header.update('CRVAL2', ymin)
- hdu.header.update('CDELT1', dx)
- hdu.header.update('CDELT2', dy)
-
- if (other_keys is not None) :
-
- for k,v in other_keys.items() :
-
- hdu.header.update(k,v)
-
- hdus.append(hdu)
-
- del hdu
-
- hdulist = pyfits.HDUList(hdus)
-
- hdulist.writeto("%s.fits" % (filename_prefix), clobber=clobber)
-
- if (gzip_file) :
- clob = ""
- if (clobber) : clob = "-f"
- system("gzip "+clob+" %s.fits" % (filename_prefix))
-
def open_in_ds9(self, field, take_log=True):
"""
This will open a given field in the DS9 viewer.
diff -r 6144554f5038e1fade96aaba6648544fbbf3b135 -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -333,7 +333,8 @@
def write_projection(data, filename, colorbar=True, colorbar_label=None,
title=None, limits=None, take_log=True, figsize=(8,6),
- dpi=100, cmap_name='algae'):
+ dpi=100, cmap_name='algae', extent=None, xlabel=None,
+ ylabel=None):
r"""Write a projection or volume rendering to disk with a variety of
pretty parameters such as limits, title, colorbar, etc. write_projection
uses the standard matplotlib interface to create the figure. N.B. This code
@@ -392,16 +393,22 @@
# Create the figure and paint the data on
fig = matplotlib.figure.Figure(figsize=figsize)
ax = fig.add_subplot(111)
- fig.tight_layout()
-
- cax = ax.imshow(data, vmin=limits[0], vmax=limits[1], norm=norm, cmap=cmap_name)
+
+ cax = ax.imshow(data, vmin=limits[0], vmax=limits[1], norm=norm,
+ extent=extent, cmap=cmap_name)
if title:
ax.set_title(title)
+ if xlabel:
+ ax.set_xlabel(xlabel)
+ if ylabel:
+ ax.set_ylabel(ylabel)
+
# Suppress the x and y pixel counts
- ax.set_xticks(())
- ax.set_yticks(())
+ if extent is None:
+ ax.set_xticks(())
+ ax.set_yticks(())
# Add a color bar and label if requested
if colorbar:
@@ -409,6 +416,8 @@
if colorbar_label:
cbar.ax.set_ylabel(colorbar_label)
+ fig.tight_layout()
+
suffix = get_image_suffix(filename)
if suffix == '':
@@ -429,70 +438,89 @@
return filename
-def write_fits(image, filename_prefix, clobber=True, coords=None, gzip_file=False) :
+def write_fits(image, filename_prefix, clobber=True, coords=None,
+ other_keys=None):
"""
This will export a FITS image of a floating point array. The output filename is
*filename_prefix*. If clobber is set to True, this will overwrite any existing
FITS file.
This requires the *pyfits* module, which is a standalone module
- provided by STSci to interface with FITS-format files.
+ provided by STSci to interface with FITS-format files, and is also part of
+ AstroPy.
"""
- r"""Write out a floating point array directly to a FITS file, optionally
- adding coordinates.
+ r"""Write out floating point arrays directly to a FITS file, optionally
+ adding coordinates and header keywords.
Parameters
----------
- image : array_like
- This is an (unscaled) array of floating point values, shape (N,N,) to save
- in a FITS file.
+ image : array_like, or dict of array_like objects
+ This is either an (unscaled) array of floating point values, or a dict of
+ such arrays, shape (N,N,) to save in a FITS file.
filename_prefix : string
This prefix will be prepended to every FITS file name.
clobber : boolean
If the file exists, this governs whether we will overwrite.
coords : dictionary, optional
A set of header keys and values to write to the FITS header to set up
- a coordinate system.
- gzip_file : boolean, optional
- gzip the file after writing, default False
+ a coordinate system, which is assumed to be linear unless specified otherwise
+ in *other_keys*
+ "units": the length units
+ "xctr","yctr": the center of the image
+ "dx","dy": the pixel width in each direction
+ other_keys : dictionary, optional
+ A set of header keys and values to write into the FITS header.
"""
+
+ try:
+ import pyfits
+ except ImportError:
+ try:
+ import astropy.io.fits as pyfits
+ except:
+ raise ImportError("You don't have pyFITS or AstroPy installed.")
- import pyfits
from os import system
- if filename_prefix.endswith('.fits'): filename_prefix=filename_prefix[:-5]
-
- hdu = pyfits.PrimaryHDU(image)
+ try:
+ image.keys()
+ image_dict = image
+ except:
+ image_dict = dict(yt_data=image)
- if (coords is not None) :
+ hdulist = [pyfits.PrimaryHDU()]
- hdu.header.update('WCSNAMEP', "PHYSICAL")
- hdu.header.update('CTYPE1P', "LINEAR")
- hdu.header.update('CTYPE2P', "LINEAR")
- hdu.header.update('CRPIX1P', 0.5)
- hdu.header.update('CRPIX2P', 0.5)
- hdu.header.update('CRVAL1P', coords["xmin"])
- hdu.header.update('CRVAL2P', coords["ymin"])
- hdu.header.update('CDELT1P', coords["dx"])
- hdu.header.update('CDELT2P', coords["dy"])
+ for key in image_dict.keys():
+
+ mylog.info("Writing image block \"%s\"" % (key))
+ hdu = pyfits.ImageHDU(image_dict[key])
+ hdu.update_ext_name(key)
- hdu.header.update('CTYPE1', "LINEAR")
- hdu.header.update('CTYPE2', "LINEAR")
- hdu.header.update('CUNIT1', coords["units"])
- hdu.header.update('CUNIT2', coords["units"])
- hdu.header.update('CRPIX1', 0.5)
- hdu.header.update('CRPIX2', 0.5)
- hdu.header.update('CRVAL1', coords["xmin"])
- hdu.header.update('CRVAL2', coords["ymin"])
- hdu.header.update('CDELT1', coords["dx"])
- hdu.header.update('CDELT2', coords["dy"])
+ if coords is not None:
- hdu.writeto("%s.fits" % (filename_prefix), clobber=clobber)
+ nx, ny = image_dict[key].shape
- if (gzip_file) :
- clob = ""
- if (clobber) : clob="-f"
- system("gzip "+clob+" %s.fits" % (filename_prefix))
+ hdu.header.update('CUNIT1', coords["units"])
+ hdu.header.update('CUNIT2', coords["units"])
+ hdu.header.update('CRPIX1', 0.5*(nx+1))
+ hdu.header.update('CRPIX2', 0.5*(ny+1))
+ hdu.header.update('CRVAL1', coords["xctr"])
+ hdu.header.update('CRVAL2', coords["yctr"])
+ hdu.header.update('CDELT1', coords["dx"])
+ hdu.header.update('CDELT2', coords["dy"])
+ # These are the defaults, but will get overwritten if
+ # the caller has specified them
+ hdu.header.update('CTYPE1', "LINEAR")
+ hdu.header.update('CTYPE2', "LINEAR")
+
+ if other_keys is not None:
+ for k,v in other_keys.items():
+ hdu.header.update(k,v)
+
+ hdulist.append(hdu)
+
+ hdulist = pyfits.HDUList(hdulist)
+ hdulist.writeto("%s.fits" % (filename_prefix), clobber=clobber)
def display_in_notebook(image, max_val=None):
"""
https://bitbucket.org/yt_analysis/yt-3.0/commits/824ba0b66e92/
Changeset: 824ba0b66e92
Branch: yt
User: xarthisius
Date: 2013-10-02 15:15:39
Summary: Give meaningful names to answer tests
Affected #: 6 files
diff -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc -r 824ba0b66e9229d070e9323032301e061e57a916 yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -29,11 +29,11 @@
mue = 1./0.88
freqs = np.array([30., 90., 240.])
-
+
def setup():
"""Test specific setup."""
from yt.config import ytcfg
- ytcfg["yt", "__withintesting"] = "True"
+ ytcfg["yt", "__withintesting"] = "True"
def full_szpack3d(pf, xo):
data = pf.h.grids[0]
@@ -43,7 +43,7 @@
Dtau = sigma_thompson*data["Density"]/(mh*mue)*dz
Te = data["Temperature"]/K_per_keV
betac = data["z-velocity"]/clight
- pbar = get_pbar("Computing 3-D cell-by-cell S-Z signal for comparison.", nx)
+ pbar = get_pbar("Computing 3-D cell-by-cell S-Z signal for comparison.", nx)
for i in xrange(nx):
pbar.update(i)
for j in xrange(ny):
@@ -67,7 +67,7 @@
a = 200.
v0 = 300.*cm_per_km
ddims = (nx,ny,nz)
-
+
x, y, z = np.mgrid[-R:R:nx*1j,
-R:R:ny*1j,
-R:R:nz*1j]
@@ -87,7 +87,7 @@
data["z-velocity"] = velz
bbox = np.array([[-0.5,0.5],[-0.5,0.5],[-0.5,0.5]])
-
+
L = 2*R*cm_per_kpc
dl = L/nz
@@ -118,9 +118,11 @@
return szprj.data
def onaxis_image_func(filename_prefix):
szprj.write_png(filename_prefix)
- yield GenericArrayTest(pf, onaxis_array_func)
- yield GenericImageTest(pf, onaxis_image_func, 3)
-
+ for test in [GenericArrayTest(pf, onaxis_array_func),
+ GenericImageTest(pf, onaxis_image_func, 3)]:
+ test_M7_onaxis.__name__ = test.description
+ yield test
+
@requires_module("SZpack")
@requires_pf(M7)
def test_M7_offaxis():
@@ -131,5 +133,7 @@
return szprj.data
def offaxis_image_func(filename_prefix):
szprj.write_png(filename_prefix)
- yield GenericArrayTest(pf, offaxis_array_func)
- yield GenericImageTest(pf, offaxis_image_func, 3)
+ for test in [GenericArrayTest(pf, offaxis_array_func),
+ GenericImageTest(pf, offaxis_image_func, 3)]:
+ test_M7_offaxis.__name__ = test.description
+ yield test
diff -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc -r 824ba0b66e9229d070e9323032301e061e57a916 yt/frontends/chombo/tests/test_outputs.py
--- a/yt/frontends/chombo/tests/test_outputs.py
+++ b/yt/frontends/chombo/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(gc)
yield assert_equal, str(pf), "data.0077.3d.hdf5"
for test in small_patch_amr(gc, _fields):
+ test_gc.__name__ = test.description
yield test
tb = "TurbBoxLowRes/data.0005.3d.hdf5"
@@ -37,4 +38,5 @@
pf = data_dir_load(tb)
yield assert_equal, str(pf), "data.0005.3d.hdf5"
for test in small_patch_amr(tb, _fields):
+ test_tb.__name__ = test.description
yield test
diff -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc -r 824ba0b66e9229d070e9323032301e061e57a916 yt/frontends/enzo/tests/test_outputs.py
--- a/yt/frontends/enzo/tests/test_outputs.py
+++ b/yt/frontends/enzo/tests/test_outputs.py
@@ -30,6 +30,7 @@
pf = data_dir_load(m7)
yield assert_equal, str(pf), "moving7_0010"
for test in small_patch_amr(m7, _fields):
+ test_moving7.__name__ = test.description
yield test
g30 = "IsolatedGalaxy/galaxy0030/galaxy0030"
@@ -38,4 +39,5 @@
pf = data_dir_load(g30)
yield assert_equal, str(pf), "galaxy0030"
for test in big_patch_amr(g30, _fields):
+ test_galaxy0030.__name__ = test.description
yield test
diff -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc -r 824ba0b66e9229d070e9323032301e061e57a916 yt/frontends/flash/tests/test_outputs.py
--- a/yt/frontends/flash/tests/test_outputs.py
+++ b/yt/frontends/flash/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(sloshing)
yield assert_equal, str(pf), "sloshing_low_res_hdf5_plt_cnt_0300"
for test in small_patch_amr(sloshing, _fields):
+ test_sloshing.__name__ = test.description
yield test
_fields_2d = ("Temperature", "Density")
@@ -39,4 +40,5 @@
pf = data_dir_load(wt)
yield assert_equal, str(pf), "windtunnel_4lev_hdf5_plt_cnt_0030"
for test in small_patch_amr(wt, _fields_2d):
+ test_wind_tunnel.__name__ = test.description
yield test
diff -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc -r 824ba0b66e9229d070e9323032301e061e57a916 yt/frontends/orion/tests/test_outputs.py
--- a/yt/frontends/orion/tests/test_outputs.py
+++ b/yt/frontends/orion/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(radadvect)
yield assert_equal, str(pf), "plt00000"
for test in small_patch_amr(radadvect, _fields):
+ test_radadvect.__name__ = test.description
yield test
rt = "RadTube/plt00500"
@@ -37,4 +38,5 @@
pf = data_dir_load(rt)
yield assert_equal, str(pf), "plt00500"
for test in small_patch_amr(rt, _fields):
+ test_radtube.__name__ = test.description
yield test
diff -r f393c060da9bdc22d6e28937ba87c8d8347b6dfc -r 824ba0b66e9229d070e9323032301e061e57a916 yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -94,8 +94,10 @@
for ax in 'xyz':
for attr_name in ATTR_ARGS.keys():
for args in ATTR_ARGS[attr_name]:
- yield PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
- args, decimals)
+ test = PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
+ args, decimals)
+ test_attributes.__name__ = test.description
+ yield test
@requires_pf(WT)
https://bitbucket.org/yt_analysis/yt-3.0/commits/da308f4c50c7/
Changeset: da308f4c50c7
Branch: yt
User: samskillman
Date: 2013-06-30 00:22:39
Summary: Add a new TransferFunctionHelper object to help build, plot, and manage a
transfer function. Adds the capability of overplotting a 1D profile (of say,
CellMass) on the transfer function to help guide choices.
Affected #: 2 files
diff -r 8e8bd5b353df99c1510058a7c982329e5212fcfe -r da308f4c50c7b632169cb3e37036a9651c262864 yt/visualization/volume_rendering/transfer_function_helper.py
--- /dev/null
+++ b/yt/visualization/volume_rendering/transfer_function_helper.py
@@ -0,0 +1,216 @@
+"""
+A helper class to build, display, and modify transfer functions for volume
+rendering.
+
+Author: Samuel Skillman <samskillman at gmail.com>
+Affiliation: DOE CSGF, U. of Colorado at Boulder
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2013 Samuel Skillman. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+from yt.funcs import mylog
+from yt.data_objects.profiles import BinnedProfile1D
+from yt.visualization.volume_rendering.api import ColorTransferFunction
+from yt.visualization._mpl_imports import FigureCanvasAgg
+from matplotlib.figure import Figure
+from IPython.core.display import Image
+import cStringIO
+import numpy as np
+
+
+class TransferFunctionHelper(object):
+
+ profiles = {}
+
+ def __init__(self, pf):
+ r"""A transfer function helper.
+
+ This attempts to help set up a good transfer function by finding
+ bounds, handling linear/log options, and displaying the transfer
+ function combined with 1D profiles of rendering quantity.
+
+ Parameters
+ ----------
+ pf: A StaticOutput instance
+ A static output that is currently being rendered. This is used to
+ help set up data bounds.
+
+ Notes
+ -----
+ """
+ self.pf = pf
+ self.field = None
+ self.log = False
+ self.tf = None
+ self.bounds = None
+ self.grey_opacity = True
+
+ def set_bounds(self, bounds=None):
+ """
+ Set the bounds of the transfer function.
+
+ Parameters
+ ----------
+ bounds: array-like, length 2, optional
+ A length 2 list/array in the form [min, max]. These should be the
+ raw values and not the logarithm of the min and max. If bounds is
+ None, the bounds of the data are calculated from all of the data
+ in the dataset. This can be slow for very large datasets.
+ """
+ if bounds is None:
+ self.bounds = \
+ self.pf.h.all_data().quantities['Extrema'](self.field)[0]
+
+ # Do some error checking.
+ assert(len(self.bounds) == 2)
+ if self.log:
+ assert(self.bounds[0] > 0.0)
+ assert(self.bounds[1] > 0.0)
+ return
+
+ def set_field(self, field):
+ """
+ Set the field to be rendered
+
+ Parameters
+ ----------
+ field: string
+ The field to be rendered.
+ """
+ self.field = field
+
+ def set_log(self, log):
+ """
+ Set whether or not the transfer function should be in log or linear
+ space. Also modifies the pf.field_info[field].take_log attribute to
+ stay in sync with this setting.
+
+ Parameters
+ ----------
+ log: boolean
+ Sets whether the transfer function should use log or linear space.
+ """
+ self.log = log
+ self.pf.h
+ self.pf.field_info[self.field].take_log = log
+
+ def build_transfer_function(self):
+ """
+ Builds the transfer function according to the current state of the
+ TransferFunctionHelper.
+
+ Parameters
+ ----------
+ None
+
+ Returns
+ -------
+
+ A ColorTransferFunction object.
+
+ """
+ if self.bounds is None:
+ mylog.info('Calculating data bounds. This may take a while.' +
+ ' Set the .bounds to avoid this.')
+ self.set_bounds()
+
+ if self.log:
+ mi, ma = np.log10(self.bounds[0]), np.log10(self.bounds[1])
+ else:
+ mi, ma = self.bounds
+ self.tf = ColorTransferFunction((mi, ma),
+ grey_opacity=self.grey_opacity,
+ nbins=512)
+ return self.tf
+
+ def plot(self, fn=None, profile_field=None, profile_weight=None):
+ """
+ Save the current transfer function to a bitmap, or display
+ it inline.
+
+ Parameters
+ ----------
+ fn: string, optional
+ Filename to save the image to. If None, the returns an image
+ to an IPython session.
+
+ Returns
+ -------
+
+ If fn is None, will return an image to an IPython notebook.
+
+ """
+ if self.tf is None:
+ self.build_transfer_function()
+ tf = self.tf
+ if self.log:
+ xfunc = np.logspace
+ xmi, xma = np.log10(self.bounds[0]), np.log10(self.bounds[1])
+ else:
+ xfunc = np.linspace
+ xmi, xma = self.bounds
+
+ x = xfunc(xmi, xma, tf.nbins)
+ y = tf.funcs[3].y
+ w = np.append(x[1:]-x[:-1], x[-1]-x[-2])
+ colors = np.array([tf.funcs[0].y, tf.funcs[1].y, tf.funcs[2].y,
+ np.ones_like(x)]).T
+
+ fig = Figure(figsize=[6, 3])
+ canvas = FigureCanvasAgg(fig)
+ ax = fig.add_axes([0.2, 0.2, 0.75, 0.75])
+ ax.bar(x, tf.funcs[3].y, w, edgecolor=[0.0, 0.0, 0.0, 0.0],
+ log=True, color=colors)
+
+ if profile_field is not None:
+ try:
+ prof = self.profiles[self.field]
+ except KeyError:
+ self.setup_profile(profile_field, profile_weight)
+ prof = self.profiles[self.field]
+ ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
+ prof[profile_field].max(), color='w', linewidth=3)
+ ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
+ prof[profile_field].max(), color='k')
+
+ ax.set_xscale({True: 'log', False: 'linear'}[self.log])
+ ax.set_xlim(x.min(), x.max())
+ ax.set_xlabel(self.pf.field_info[self.field].get_label())
+ ax.set_ylabel(r'$\mathrm{alpha}$')
+ ax.set_ylim(y.max()*1.0e-3, y.max()*2)
+
+ if fn is None:
+ f = cStringIO.StringIO()
+ canvas.print_figure(f)
+ f.seek(0)
+ img = f.read()
+ return Image(img)
+ else:
+ fig.savefig(fn)
+
+ def setup_profile(self, profile_field=None, profile_weight=None):
+ if profile_field is None:
+ profile_field = 'CellVolume'
+ prof = BinnedProfile1D(self.pf.h.all_data(), 128, self.field,
+ self.bounds[0], self.bounds[1],
+ log_space=self.log,
+ lazy_reader=False, end_collect=False)
+ prof.add_fields([profile_field], fractional=False,
+ weight=profile_weight)
+ self.profiles[self.field] = prof
+ return
diff -r 8e8bd5b353df99c1510058a7c982329e5212fcfe -r da308f4c50c7b632169cb3e37036a9651c262864 yt/visualization/volume_rendering/transfer_functions.py
--- a/yt/visualization/volume_rendering/transfer_functions.py
+++ b/yt/visualization/volume_rendering/transfer_functions.py
@@ -641,6 +641,8 @@
self.x_bounds[0]))
rel1 = int(self.nbins*(ma - self.x_bounds[0])/(self.x_bounds[1] -
self.x_bounds[0]))
+ rel0 = max(rel0, 0)
+ rel1 = min(rel1, self.nbins-1)
tomap = np.linspace(0.,1.,num=rel1-rel0)
cmap = get_cmap(colormap)
cc = cmap(tomap)
https://bitbucket.org/yt_analysis/yt-3.0/commits/1fb87198e5e9/
Changeset: 1fb87198e5e9
Branch: yt
User: samskillman
Date: 2013-06-30 04:10:52
Summary: Fix in case a profile is then asked for a different field.
Affected #: 1 file
diff -r da308f4c50c7b632169cb3e37036a9651c262864 -r 1fb87198e5e9d7cdf793da6a8150d4b1d2a07092 yt/visualization/volume_rendering/transfer_function_helper.py
--- a/yt/visualization/volume_rendering/transfer_function_helper.py
+++ b/yt/visualization/volume_rendering/transfer_function_helper.py
@@ -183,6 +183,9 @@
except KeyError:
self.setup_profile(profile_field, profile_weight)
prof = self.profiles[self.field]
+ if profile_field not in prof.keys():
+ prof.add_fields([profile_field], fractional=False,
+ weight=profile_weight)
ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
prof[profile_field].max(), color='w', linewidth=3)
ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
https://bitbucket.org/yt_analysis/yt-3.0/commits/a588666af47f/
Changeset: a588666af47f
Branch: yt
User: samskillman
Date: 2013-07-08 22:59:58
Summary: Fixing up the bounds to be respected, working around a matplotlib bug for
logarithmic bar plots, and initializing the profiles more properly.
Affected #: 1 file
diff -r 1fb87198e5e9d7cdf793da6a8150d4b1d2a07092 -r a588666af47f6e39cd931225df084a8633195e14 yt/visualization/volume_rendering/transfer_function_helper.py
--- a/yt/visualization/volume_rendering/transfer_function_helper.py
+++ b/yt/visualization/volume_rendering/transfer_function_helper.py
@@ -35,7 +35,7 @@
class TransferFunctionHelper(object):
- profiles = {}
+ profiles = None
def __init__(self, pf):
r"""A transfer function helper.
@@ -59,6 +59,7 @@
self.tf = None
self.bounds = None
self.grey_opacity = True
+ self.profiles = {}
def set_bounds(self, bounds=None):
"""
@@ -73,8 +74,8 @@
in the dataset. This can be slow for very large datasets.
"""
if bounds is None:
- self.bounds = \
- self.pf.h.all_data().quantities['Extrema'](self.field)[0]
+ bounds = self.pf.h.all_data().quantities['Extrema'](self.field)[0]
+ self.bounds = bounds
# Do some error checking.
assert(len(self.bounds) == 2)
@@ -175,7 +176,7 @@
canvas = FigureCanvasAgg(fig)
ax = fig.add_axes([0.2, 0.2, 0.75, 0.75])
ax.bar(x, tf.funcs[3].y, w, edgecolor=[0.0, 0.0, 0.0, 0.0],
- log=True, color=colors)
+ log=True, color=colors, bottom=[0])
if profile_field is not None:
try:
https://bitbucket.org/yt_analysis/yt-3.0/commits/51157128e185/
Changeset: 51157128e185
Branch: yt
User: MatthewTurk
Date: 2013-10-02 21:32:13
Summary: Merged in samskillman/yt (pull request #538)
Transfer Function Helper
Affected #: 1 file
diff -r 824ba0b66e9229d070e9323032301e061e57a916 -r 51157128e18557c82dc00a9f5853b6bcd361e63a yt/visualization/volume_rendering/transfer_function_helper.py
--- /dev/null
+++ b/yt/visualization/volume_rendering/transfer_function_helper.py
@@ -0,0 +1,220 @@
+"""
+A helper class to build, display, and modify transfer functions for volume
+rendering.
+
+Author: Samuel Skillman <samskillman at gmail.com>
+Affiliation: DOE CSGF, U. of Colorado at Boulder
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2013 Samuel Skillman. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+from yt.funcs import mylog
+from yt.data_objects.profiles import BinnedProfile1D
+from yt.visualization.volume_rendering.api import ColorTransferFunction
+from yt.visualization._mpl_imports import FigureCanvasAgg
+from matplotlib.figure import Figure
+from IPython.core.display import Image
+import cStringIO
+import numpy as np
+
+
+class TransferFunctionHelper(object):
+
+ profiles = None
+
+ def __init__(self, pf):
+ r"""A transfer function helper.
+
+ This attempts to help set up a good transfer function by finding
+ bounds, handling linear/log options, and displaying the transfer
+ function combined with 1D profiles of rendering quantity.
+
+ Parameters
+ ----------
+ pf: A StaticOutput instance
+ A static output that is currently being rendered. This is used to
+ help set up data bounds.
+
+ Notes
+ -----
+ """
+ self.pf = pf
+ self.field = None
+ self.log = False
+ self.tf = None
+ self.bounds = None
+ self.grey_opacity = True
+ self.profiles = {}
+
+ def set_bounds(self, bounds=None):
+ """
+ Set the bounds of the transfer function.
+
+ Parameters
+ ----------
+ bounds: array-like, length 2, optional
+ A length 2 list/array in the form [min, max]. These should be the
+ raw values and not the logarithm of the min and max. If bounds is
+ None, the bounds of the data are calculated from all of the data
+ in the dataset. This can be slow for very large datasets.
+ """
+ if bounds is None:
+ bounds = self.pf.h.all_data().quantities['Extrema'](self.field)[0]
+ self.bounds = bounds
+
+ # Do some error checking.
+ assert(len(self.bounds) == 2)
+ if self.log:
+ assert(self.bounds[0] > 0.0)
+ assert(self.bounds[1] > 0.0)
+ return
+
+ def set_field(self, field):
+ """
+ Set the field to be rendered
+
+ Parameters
+ ----------
+ field: string
+ The field to be rendered.
+ """
+ self.field = field
+
+ def set_log(self, log):
+ """
+ Set whether or not the transfer function should be in log or linear
+ space. Also modifies the pf.field_info[field].take_log attribute to
+ stay in sync with this setting.
+
+ Parameters
+ ----------
+ log: boolean
+ Sets whether the transfer function should use log or linear space.
+ """
+ self.log = log
+ self.pf.h
+ self.pf.field_info[self.field].take_log = log
+
+ def build_transfer_function(self):
+ """
+ Builds the transfer function according to the current state of the
+ TransferFunctionHelper.
+
+ Parameters
+ ----------
+ None
+
+ Returns
+ -------
+
+ A ColorTransferFunction object.
+
+ """
+ if self.bounds is None:
+ mylog.info('Calculating data bounds. This may take a while.' +
+ ' Set the .bounds to avoid this.')
+ self.set_bounds()
+
+ if self.log:
+ mi, ma = np.log10(self.bounds[0]), np.log10(self.bounds[1])
+ else:
+ mi, ma = self.bounds
+ self.tf = ColorTransferFunction((mi, ma),
+ grey_opacity=self.grey_opacity,
+ nbins=512)
+ return self.tf
+
+ def plot(self, fn=None, profile_field=None, profile_weight=None):
+ """
+ Save the current transfer function to a bitmap, or display
+ it inline.
+
+ Parameters
+ ----------
+ fn: string, optional
+ Filename to save the image to. If None, the returns an image
+ to an IPython session.
+
+ Returns
+ -------
+
+ If fn is None, will return an image to an IPython notebook.
+
+ """
+ if self.tf is None:
+ self.build_transfer_function()
+ tf = self.tf
+ if self.log:
+ xfunc = np.logspace
+ xmi, xma = np.log10(self.bounds[0]), np.log10(self.bounds[1])
+ else:
+ xfunc = np.linspace
+ xmi, xma = self.bounds
+
+ x = xfunc(xmi, xma, tf.nbins)
+ y = tf.funcs[3].y
+ w = np.append(x[1:]-x[:-1], x[-1]-x[-2])
+ colors = np.array([tf.funcs[0].y, tf.funcs[1].y, tf.funcs[2].y,
+ np.ones_like(x)]).T
+
+ fig = Figure(figsize=[6, 3])
+ canvas = FigureCanvasAgg(fig)
+ ax = fig.add_axes([0.2, 0.2, 0.75, 0.75])
+ ax.bar(x, tf.funcs[3].y, w, edgecolor=[0.0, 0.0, 0.0, 0.0],
+ log=True, color=colors, bottom=[0])
+
+ if profile_field is not None:
+ try:
+ prof = self.profiles[self.field]
+ except KeyError:
+ self.setup_profile(profile_field, profile_weight)
+ prof = self.profiles[self.field]
+ if profile_field not in prof.keys():
+ prof.add_fields([profile_field], fractional=False,
+ weight=profile_weight)
+ ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
+ prof[profile_field].max(), color='w', linewidth=3)
+ ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
+ prof[profile_field].max(), color='k')
+
+ ax.set_xscale({True: 'log', False: 'linear'}[self.log])
+ ax.set_xlim(x.min(), x.max())
+ ax.set_xlabel(self.pf.field_info[self.field].get_label())
+ ax.set_ylabel(r'$\mathrm{alpha}$')
+ ax.set_ylim(y.max()*1.0e-3, y.max()*2)
+
+ if fn is None:
+ f = cStringIO.StringIO()
+ canvas.print_figure(f)
+ f.seek(0)
+ img = f.read()
+ return Image(img)
+ else:
+ fig.savefig(fn)
+
+ def setup_profile(self, profile_field=None, profile_weight=None):
+ if profile_field is None:
+ profile_field = 'CellVolume'
+ prof = BinnedProfile1D(self.pf.h.all_data(), 128, self.field,
+ self.bounds[0], self.bounds[1],
+ log_space=self.log,
+ lazy_reader=False, end_collect=False)
+ prof.add_fields([profile_field], fractional=False,
+ weight=profile_weight)
+ self.profiles[self.field] = prof
+ return
https://bitbucket.org/yt_analysis/yt-3.0/commits/736abff6337f/
Changeset: 736abff6337f
Branch: yt
User: ngoldbaum
Date: 2013-10-03 00:13:15
Summary: Updating TransferFunctionHelper's license blurb.
Affected #: 1 file
diff -r 51157128e18557c82dc00a9f5853b6bcd361e63a -r 736abff6337f5c1c037638c1ccfac2b6c4ef3508 yt/visualization/volume_rendering/transfer_function_helper.py
--- a/yt/visualization/volume_rendering/transfer_function_helper.py
+++ b/yt/visualization/volume_rendering/transfer_function_helper.py
@@ -2,27 +2,18 @@
A helper class to build, display, and modify transfer functions for volume
rendering.
-Author: Samuel Skillman <samskillman at gmail.com>
-Affiliation: DOE CSGF, U. of Colorado at Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2013 Samuel Skillman. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
from yt.funcs import mylog
from yt.data_objects.profiles import BinnedProfile1D
from yt.visualization.volume_rendering.api import ColorTransferFunction
https://bitbucket.org/yt_analysis/yt-3.0/commits/4628e092abdc/
Changeset: 4628e092abdc
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 15:00:04
Summary: Merging from yt-2.x
Affected #: 25 files
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -103,5 +103,8 @@
TwoPointFunctions, \
FcnSet
+from .sunyaev_zeldovich.api import SZProjection
+
from .radmc3d_export.api import \
RadMC3DWriter
+
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/analysis_modules/setup.py
--- a/yt/analysis_modules/setup.py
+++ b/yt/analysis_modules/setup.py
@@ -21,4 +21,5 @@
config.add_subpackage("star_analysis")
config.add_subpackage("two_point_functions")
config.add_subpackage("radmc3d_export")
+ config.add_subpackage("sunyaev_zeldovich")
return config
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/analysis_modules/sunyaev_zeldovich/api.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/api.py
@@ -0,0 +1,12 @@
+"""
+API for sunyaev_zeldovich
+"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from projection import SZProjection
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/analysis_modules/sunyaev_zeldovich/projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -0,0 +1,349 @@
+"""
+Projection class for the Sunyaev-Zeldovich effect. Requires SZpack (at least
+version 1.1.1) to be downloaded and installed:
+
+http://www.chluba.de/SZpack/
+
+For details on the computations involved please refer to the following references:
+
+Chluba, Nagai, Sazonov, Nelson, MNRAS, 2012, arXiv:1205.5778
+Chluba, Switzer, Nagai, Nelson, MNRAS, 2012, arXiv:1211.3206
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mh, Tcmb
+from yt.data_objects.image_array import ImageArray
+from yt.data_objects.field_info_container import add_field
+from yt.funcs import fix_axis, mylog, iterable, get_pbar
+from yt.utilities.definitions import inv_axis_names
+from yt.visualization.image_writer import write_fits, write_projection
+from yt.visualization.volume_rendering.camera import off_axis_projection
+from yt.utilities.parallel_tools.parallel_analysis_interface import \
+ communication_system, parallel_root_only
+import numpy as np
+
+I0 = 2*(kboltz*Tcmb)**3/((hcgs*clight)**2)*1.0e17
+
+try:
+ import SZpack
+except:
+ raise ImportError("SZpack not installed. It can be obtained from from http://www.chluba.de/SZpack/.")
+
+vlist = "xyz"
+
+def _t_squared(field, data):
+ return data["Density"]*data["TempkeV"]*data["TempkeV"]
+add_field("TSquared", function=_t_squared)
+
+def _beta_perp_squared(field, data):
+ return data["Density"]*data["VelocityMagnitude"]**2/clight/clight - data["BetaParSquared"]
+add_field("BetaPerpSquared", function=_beta_perp_squared)
+
+def _beta_par_squared(field, data):
+ return data["BetaPar"]**2/data["Density"]
+add_field("BetaParSquared", function=_beta_par_squared)
+
+def _t_beta_par(field, data):
+ return data["TempkeV"]*data["BetaPar"]
+add_field("TBetaPar", function=_t_beta_par)
+
+def _t_sz(field, data):
+ return data["Density"]*data["TempkeV"]
+add_field("TeSZ", function=_t_sz)
+
+class SZProjection(object):
+ r""" Initialize a SZProjection object.
+
+ Parameters
+ ----------
+ pf : parameter_file
+ The parameter file.
+ freqs : array_like
+ The frequencies (in GHz) at which to compute the SZ spectral distortion.
+ mue : float, optional
+ Mean molecular weight for determining the electron number density.
+ high_order : boolean, optional
+ Should we calculate high-order moments of velocity and temperature?
+
+ Examples
+ --------
+ >>> freqs = [90., 180., 240.]
+ >>> szprj = SZProjection(pf, freqs, high_order=True)
+ """
+ def __init__(self, pf, freqs, mue=1.143, high_order=False):
+
+ self.pf = pf
+ self.num_freqs = len(freqs)
+ self.high_order = high_order
+ self.freqs = np.array(freqs)
+ self.mueinv = 1./mue
+ self.xinit = hcgs*self.freqs*1.0e9/(kboltz*Tcmb)
+ self.freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
+ self.data = {}
+
+ self.units = {}
+ self.units["TeSZ"] = r"$\mathrm{keV}$"
+ self.units["Tau"] = None
+
+ self.display_names = {}
+ self.display_names["TeSZ"] = r"$\mathrm{T_e}$"
+ self.display_names["Tau"] = r"$\mathrm{\tau}$"
+
+ for f, field in zip(self.freqs, self.freq_fields):
+ self.units[field] = r"$\mathrm{MJy\ sr^{-1}}$"
+ self.display_names[field] = r"$\mathrm{\Delta{I}_{%d\ GHz}}$" % (int(f))
+
+ def on_axis(self, axis, center="c", width=(1, "unitary"), nx=800, source=None):
+ r""" Make an on-axis projection of the SZ signal.
+
+ Parameters
+ ----------
+ axis : integer or string
+ The axis of the simulation domain along which to make the SZprojection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+
+ Examples
+ --------
+ >>> szprj.on_axis("y", center="max", width=(1.0, "mpc"), source=my_sphere)
+ """
+ axis = fix_axis(axis)
+
+ def _beta_par(field, data):
+ axis = data.get_field_parameter("axis")
+ vpar = data["Density"]*data["%s-velocity" % (vlist[axis])]
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ proj = self.pf.h.proj(axis, "Density", source=source)
+ proj.set_field_parameter("axis", axis)
+ frb = proj.to_frb(width, nx)
+ dens = frb["Density"]
+ Te = frb["TeSZ"]/dens
+ bpar = frb["BetaPar"]/dens
+ omega1 = frb["TSquared"]/dens/(Te*Te) - 1.
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ if self.high_order:
+ bperp2 = frb["BetaPerpSquared"]/dens
+ sigma1 = frb["TBetaPar"]/dens/Te - bpar
+ kappa1 = frb["BetaParSquared"]/dens - bpar*bpar
+ tau = sigma_thompson*dens*self.mueinv/mh
+
+ nx,ny = frb.buff_size
+ self.bounds = frb.bounds
+ self.dx = (frb.bounds[1]-frb.bounds[0])/nx
+ self.dy = (frb.bounds[3]-frb.bounds[2])/ny
+ self.nx = nx
+
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
+
+ def off_axis(self, L, center="c", width=(1, "unitary"), nx=800, source=None):
+ r""" Make an off-axis projection of the SZ signal.
+
+ Parameters
+ ----------
+ L : array_like
+ The normal vector of the projection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+ Currently unsupported in yt 2.x.
+
+ Examples
+ --------
+ >>> L = np.array([0.5, 1.0, 0.75])
+ >>> szprj.off_axis(L, center="c", width=(2.0, "mpc"))
+ """
+ if iterable(width):
+ w = width[0]/self.pf.units[width[1]]
+ else:
+ w = width
+ if center == "c":
+ ctr = self.pf.domain_center
+ elif center == "max":
+ ctr = self.pf.h.find_max("Density")
+ else:
+ ctr = center
+
+ if source is not None:
+ mylog.error("Source argument is not currently supported for off-axis S-Z projections.")
+ raise NotImplementedError
+
+ def _beta_par(field, data):
+ vpar = data["Density"]*(data["x-velocity"]*L[0]+
+ data["y-velocity"]*L[1]+
+ data["z-velocity"]*L[2])
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ dens = off_axis_projection(self.pf, ctr, L, w, nx, "Density")
+ Te = off_axis_projection(self.pf, ctr, L, w, nx, "TeSZ")/dens
+ bpar = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPar")/dens
+ omega1 = off_axis_projection(self.pf, ctr, L, w, nx, "TSquared")/dens
+ omega1 = omega1/(Te*Te) - 1.
+ if self.high_order:
+ bperp2 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPerpSquared")/dens
+ sigma1 = off_axis_projection(self.pf, ctr, L, w, nx, "TBetaPar")/dens
+ sigma1 = sigma1/Te - bpar
+ kappa1 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaParSquared")/dens
+ kappa1 -= bpar
+ else:
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ tau = sigma_thompson*dens*self.mueinv/mh
+
+ self.bounds = np.array([-0.5*w, 0.5*w, -0.5*w, 0.5*w])
+ self.dx = w/nx
+ self.dy = w/nx
+ self.nx = nx
+
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
+
+ def _compute_intensity(self, tau, Te, bpar, omega1, sigma1, kappa1, bperp2):
+
+ # Bad hack, but we get NaNs if we don't do something like this
+ small_beta = np.abs(bpar) < 1.0e-20
+ bpar[small_beta] = 1.0e-20
+
+ comm = communication_system.communicators[-1]
+
+ nx, ny = self.nx,self.nx
+ signal = np.zeros((self.num_freqs,nx,ny))
+ xo = np.zeros((self.num_freqs))
+
+ k = int(0)
+
+ start_i = comm.rank*nx/comm.size
+ end_i = (comm.rank+1)*nx/comm.size
+
+ pbar = get_pbar("Computing SZ signal.", nx*nx)
+
+ for i in xrange(start_i, end_i):
+ for j in xrange(ny):
+ xo[:] = self.xinit[:]
+ SZpack.compute_combo_means(xo, tau[i,j], Te[i,j],
+ bpar[i,j], omega1[i,j],
+ sigma1[i,j], kappa1[i,j], bperp2[i,j])
+ signal[:,i,j] = xo[:]
+ pbar.update(k)
+ k += 1
+
+ signal = comm.mpi_allreduce(signal)
+
+ pbar.finish()
+
+ for i, field in enumerate(self.freq_fields):
+ self.data[field] = ImageArray(I0*self.xinit[i]**3*signal[i,:,:])
+ self.data["Tau"] = ImageArray(tau)
+ self.data["TeSZ"] = ImageArray(Te)
+
+ @parallel_root_only
+ def write_fits(self, filename_prefix, clobber=True):
+ r""" Export images to a FITS file. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the FITS filename.
+ clobber : boolean, optional
+ If the file already exists, do we overwrite?
+
+ Examples
+ --------
+ >>> szprj.write_fits("SZbullet", clobber=False)
+ """
+ coords = {}
+ coords["dx"] = self.dx*self.pf.units["kpc"]
+ coords["dy"] = self.dy*self.pf.units["kpc"]
+ coords["xctr"] = 0.0
+ coords["yctr"] = 0.0
+ coords["units"] = "kpc"
+ other_keys = {"Time" : self.pf.current_time}
+ write_fits(self.data, filename_prefix, clobber=clobber, coords=coords,
+ other_keys=other_keys)
+
+ @parallel_root_only
+ def write_png(self, filename_prefix):
+ r""" Export images to PNG files. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the image filenames.
+
+ Examples
+ --------
+ >>> szprj.write_png("SZsloshing")
+ """
+ extent = tuple([bound*self.pf.units["kpc"] for bound in self.bounds])
+ for field, image in self.items():
+ filename=filename_prefix+"_"+field+".png"
+ label = self.display_names[field]
+ if self.units[field] is not None:
+ label += " ("+self.units[field]+")"
+ write_projection(image, filename, colorbar_label=label, take_log=False,
+ extent=extent, xlabel=r"$\mathrm{x\ (kpc)}$",
+ ylabel=r"$\mathrm{y\ (kpc)}$")
+
+ @parallel_root_only
+ def write_hdf5(self, filename):
+ r"""Export the set of S-Z fields to a set of HDF5 datasets.
+
+ Parameters
+ ----------
+ filename : string
+ This file will be opened in "write" mode.
+
+ Examples
+ --------
+ >>> szprj.write_hdf5("SZsloshing.h5")
+ """
+ import h5py
+ f = h5py.File(filename, "w")
+ for field, data in self.items():
+ f.create_dataset(field,data=data)
+ f.close()
+
+ def keys(self):
+ return self.data.keys()
+
+ def items(self):
+ return self.data.items()
+
+ def values(self):
+ return self.data.values()
+
+ def has_key(self, key):
+ return key in self.data.keys()
+
+ def __getitem__(self, key):
+ return self.data[key]
+
+ @property
+ def shape(self):
+ return (self.nx,self.nx)
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/analysis_modules/sunyaev_zeldovich/setup.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/setup.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+import setuptools
+import os
+import sys
+import os.path
+
+
+def configuration(parent_package='', top_path=None):
+ from numpy.distutils.misc_util import Configuration
+ config = Configuration('sunyaev_zeldovich', parent_package, top_path)
+ config.add_subpackage("tests")
+ config.make_config_py() # installs __config__.py
+ #config.make_svn_version_py()
+ return config
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -0,0 +1,139 @@
+"""
+Unit test the sunyaev_zeldovich analysis module.
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.frontends.stream.api import load_uniform_grid
+from yt.funcs import get_pbar, mylog
+from yt.utilities.physical_constants import cm_per_kpc, K_per_keV, \
+ mh, cm_per_km, kboltz, Tcmb, hcgs, clight, sigma_thompson
+from yt.testing import *
+from yt.utilities.answer_testing.framework import requires_pf, \
+ GenericArrayTest, data_dir_load, GenericImageTest
+try:
+ from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
+except ImportError:
+ pass
+import numpy as np
+try:
+ import SZpack
+except ImportError:
+ pass
+
+mue = 1./0.88
+freqs = np.array([30., 90., 240.])
+
+def setup():
+ """Test specific setup."""
+ from yt.config import ytcfg
+ ytcfg["yt", "__withintesting"] = "True"
+
+def full_szpack3d(pf, xo):
+ data = pf.h.grids[0]
+ dz = pf.h.get_smallest_dx()*pf.units["cm"]
+ nx,ny,nz = data["Density"].shape
+ dn = np.zeros((nx,ny,nz))
+ Dtau = sigma_thompson*data["Density"]/(mh*mue)*dz
+ Te = data["Temperature"]/K_per_keV
+ betac = data["z-velocity"]/clight
+ pbar = get_pbar("Computing 3-D cell-by-cell S-Z signal for comparison.", nx)
+ for i in xrange(nx):
+ pbar.update(i)
+ for j in xrange(ny):
+ for k in xrange(nz):
+ dn[i,j,k] = SZpack.compute_3d(xo, Dtau[i,j,k],
+ Te[i,j,k], betac[i,j,k],
+ 1.0, 0.0, 0.0, 1.0e-5)
+ pbar.finish()
+ return I0*xo**3*np.sum(dn, axis=2)
+
+def setup_cluster():
+
+ R = 1000.
+ r_c = 100.
+ rho_c = 1.673e-26
+ beta = 1.
+ T0 = 4.
+ nx,ny,nz = 16,16,16
+ c = 0.17
+ a_c = 30.
+ a = 200.
+ v0 = 300.*cm_per_km
+ ddims = (nx,ny,nz)
+
+ x, y, z = np.mgrid[-R:R:nx*1j,
+ -R:R:ny*1j,
+ -R:R:nz*1j]
+
+ r = np.sqrt(x**2+y**2+z**2)
+
+ dens = np.zeros(ddims)
+ dens = rho_c*(1.+(r/r_c)**2)**(-1.5*beta)
+ temp = T0*K_per_keV/(1.+r/a)*(c+r/a_c)/(1.+r/a_c)
+ velz = v0*temp/(T0*K_per_keV)
+
+ data = {}
+ data["Density"] = dens
+ data["Temperature"] = temp
+ data["x-velocity"] = np.zeros(ddims)
+ data["y-velocity"] = np.zeros(ddims)
+ data["z-velocity"] = velz
+
+ bbox = np.array([[-0.5,0.5],[-0.5,0.5],[-0.5,0.5]])
+
+ L = 2*R*cm_per_kpc
+ dl = L/nz
+
+ pf = load_uniform_grid(data, ddims, L, bbox=bbox)
+
+ return pf
+
+ at requires_module("SZpack")
+def test_projection():
+ pf = setup_cluster()
+ nx,ny,nz = pf.domain_dimensions
+ xinit = 1.0e9*hcgs*freqs/(kboltz*Tcmb)
+ szprj = SZProjection(pf, freqs, mue=mue, high_order=True)
+ szprj.on_axis(2, nx=nx)
+ deltaI = np.zeros((3,nx,ny))
+ for i in xrange(3):
+ deltaI[i,:,:] = full_szpack3d(pf, xinit[i])
+ yield assert_almost_equal, deltaI[i,:,:], szprj["%d_GHz" % int(freqs[i])], 6
+
+M7 = "DD0010/moving7_0010"
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_onaxis():
+ pf = data_dir_load(M7)
+ szprj = SZProjection(pf, freqs)
+ szprj.on_axis(2, nx=100)
+ def onaxis_array_func():
+ return szprj.data
+ def onaxis_image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ for test in [GenericArrayTest(pf, onaxis_array_func),
+ GenericImageTest(pf, onaxis_image_func, 3)]:
+ test_M7_onaxis.__name__ = test.description
+ yield test
+
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_offaxis():
+ pf = data_dir_load(M7)
+ szprj = SZProjection(pf, freqs)
+ szprj.off_axis(np.array([0.1,-0.2,0.4]), nx=100)
+ def offaxis_array_func():
+ return szprj.data
+ def offaxis_image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ for test in [GenericArrayTest(pf, offaxis_array_func),
+ GenericImageTest(pf, offaxis_image_func, 3)]:
+ test_M7_offaxis.__name__ = test.description
+ yield test
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/analysis_modules/two_point_functions/two_point_functions.py
--- a/yt/analysis_modules/two_point_functions/two_point_functions.py
+++ b/yt/analysis_modules/two_point_functions/two_point_functions.py
@@ -498,7 +498,7 @@
points[:, 2] = points[:, 2] / self.period[2]
fKD.qv_many = points.T
fKD.nn_tags = np.asfortranarray(np.empty((1, points.shape[0]), dtype='int64'))
- find_many_nn_nearest_neighbors()
+ fKD.find_many_nn_nearest_neighbors()
# The -1 is for fortran counting.
n = fKD.nn_tags[0,:] - 1
return n
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/frontends/chombo/tests/test_outputs.py
--- a/yt/frontends/chombo/tests/test_outputs.py
+++ b/yt/frontends/chombo/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(gc)
yield assert_equal, str(pf), "data.0077.3d.hdf5"
for test in small_patch_amr(gc, _fields):
+ test_gc.__name__ = test.description
yield test
tb = "TurbBoxLowRes/data.0005.3d.hdf5"
@@ -37,4 +38,5 @@
pf = data_dir_load(tb)
yield assert_equal, str(pf), "data.0005.3d.hdf5"
for test in small_patch_amr(tb, _fields):
+ test_tb.__name__ = test.description
yield test
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/frontends/enzo/tests/test_outputs.py
--- a/yt/frontends/enzo/tests/test_outputs.py
+++ b/yt/frontends/enzo/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(m7)
yield assert_equal, str(pf), "moving7_0010"
for test in small_patch_amr(m7, _fields):
+ test_moving7.__name__ = test.description
yield test
g30 = "IsolatedGalaxy/galaxy0030/galaxy0030"
@@ -37,4 +38,5 @@
pf = data_dir_load(g30)
yield assert_equal, str(pf), "galaxy0030"
for test in big_patch_amr(g30, _fields):
+ test_galaxy0030.__name__ = test.description
yield test
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/frontends/flash/tests/test_outputs.py
--- a/yt/frontends/flash/tests/test_outputs.py
+++ b/yt/frontends/flash/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(sloshing)
yield assert_equal, str(pf), "sloshing_low_res_hdf5_plt_cnt_0300"
for test in small_patch_amr(sloshing, _fields):
+ test_sloshing.__name__ = test.description
yield test
_fields_2d = ("Temperature", "Density")
@@ -39,4 +40,5 @@
pf = data_dir_load(wt)
yield assert_equal, str(pf), "windtunnel_4lev_hdf5_plt_cnt_0030"
for test in small_patch_amr(wt, _fields_2d):
+ test_wind_tunnel.__name__ = test.description
yield test
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/frontends/orion/tests/test_outputs.py
--- a/yt/frontends/orion/tests/test_outputs.py
+++ b/yt/frontends/orion/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(radadvect)
yield assert_equal, str(pf), "plt00000"
for test in small_patch_amr(radadvect, _fields):
+ test_radadvect.__name__ = test.description
yield test
rt = "RadTube/plt00500"
@@ -37,4 +38,5 @@
pf = data_dir_load(rt)
yield assert_equal, str(pf), "plt00500"
for test in small_patch_amr(rt, _fields):
+ test_radtube.__name__ = test.description
yield test
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/gui/reason/extdirect_router.py
--- a/yt/gui/reason/extdirect_router.py
+++ b/yt/gui/reason/extdirect_router.py
@@ -9,6 +9,13 @@
This code was released under the BSD License.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import inspect
class DirectException(Exception):
@@ -186,12 +193,4 @@
-"""
-#-----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -14,6 +14,7 @@
import itertools as it
import numpy as np
+import importlib
from yt.funcs import *
from numpy.testing import assert_array_equal, assert_almost_equal, \
assert_approx_equal, assert_array_almost_equal, assert_equal, \
@@ -252,3 +253,23 @@
list_of_kwarg_dicts[i][key] = keywords[key][0]
return list_of_kwarg_dicts
+
+def requires_module(module):
+ """
+ Decorator that takes a module name as an argument and tries to import it.
+ If the module imports without issue, the function is returned, but if not,
+ a null function is returned. This is so tests that depend on certain modules
+ being imported will not fail if the module is not installed on the testing
+ platform.
+ """
+ def ffalse(func):
+ return lambda: None
+ def ftrue(func):
+ return func
+ try:
+ importlib.import_module(module)
+ except ImportError:
+ return ffalse
+ else:
+ return ftrue
+
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -24,6 +24,7 @@
import shelve
import zlib
import tempfile
+import glob
from matplotlib.testing.compare import compare_images
from nose.plugins import Plugin
@@ -584,6 +585,16 @@
for newc, oldc in zip(new_result["children"], old_result["children"]):
assert(newp == oldp)
+def compare_image_lists(new_result, old_result, decimals):
+ fns = ['old.png', 'new.png']
+ num_images = len(old_result)
+ assert(num_images > 0)
+ for i in xrange(num_images):
+ mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[i])))
+ mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[i])))
+ assert compare_images(fns[0], fns[1], 10**(decimals)) == None
+ for fn in fns: os.remove(fn)
+
class PlotWindowAttributeTest(AnswerTestingTest):
_type_name = "PlotWindowAttribute"
_attrs = ('plot_type', 'plot_field', 'plot_axis', 'attr_name', 'attr_args')
@@ -611,11 +622,71 @@
return [zlib.compress(image.dumps())]
def compare(self, new_result, old_result):
- fns = ['old.png', 'new.png']
- mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[0])))
- mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[0])))
- assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
- for fn in fns: os.remove(fn)
+ compare_image_lists(new_result, old_result, self.decimals)
+
+class GenericArrayTest(AnswerTestingTest):
+ _type_name = "GenericArray"
+ _attrs = ('array_func_name','args','kwargs')
+ def __init__(self, pf_fn, array_func, args=None, kwargs=None, decimals=None):
+ super(GenericArrayTest, self).__init__(pf_fn)
+ self.array_func = array_func
+ self.array_func_name = array_func.func_name
+ self.args = args
+ self.kwargs = kwargs
+ self.decimals = decimals
+ def run(self):
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
+ return self.array_func(*args, **kwargs)
+ def compare(self, new_result, old_result):
+ assert_equal(len(new_result), len(old_result),
+ err_msg="Number of outputs not equal.",
+ verbose=True)
+ for k in new_result:
+ if self.decimals is None:
+ assert_equal(new_result[k], old_result[k])
+ else:
+ assert_allclose(new_result[k], old_result[k], 10**(-self.decimals))
+
+class GenericImageTest(AnswerTestingTest):
+ _type_name = "GenericImage"
+ _attrs = ('image_func_name','args','kwargs')
+ def __init__(self, pf_fn, image_func, decimals, args=None, kwargs=None):
+ super(GenericImageTest, self).__init__(pf_fn)
+ self.image_func = image_func
+ self.image_func_name = image_func.func_name
+ self.args = args
+ self.kwargs = kwargs
+ self.decimals = decimals
+ def run(self):
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
+ comp_imgs = []
+ tmpdir = tempfile.mkdtemp()
+ image_prefix = os.path.join(tmpdir,"test_img")
+ self.image_func(image_prefix, *args, **kwargs)
+ imgs = glob.glob(image_prefix+"*")
+ assert(len(imgs) > 0)
+ for img in imgs:
+ img_data = mpimg.imread(img)
+ os.remove(img)
+ comp_imgs.append(zlib.compress(img_data.dumps()))
+ return comp_imgs
+ def compare(self, new_result, old_result):
+ compare_image_lists(new_result, old_result, self.decimals)
+
def requires_pf(pf_fn, big_data = False, file_check = False):
def ffalse(func):
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/utilities/physical_constants.py
--- a/yt/utilities/physical_constants.py
+++ b/yt/utilities/physical_constants.py
@@ -84,6 +84,7 @@
erg_per_keV = erg_per_eV * 1.0e3
K_per_keV = erg_per_keV / boltzmann_constant_cgs
keV_per_K = 1.0 / K_per_keV
+Tcmb = 2.726 # Current CMB temperature
#Short cuts
G = gravitational_constant_cgs
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -19,6 +19,7 @@
y_dict, \
axis_names
from .volume_rendering.api import off_axis_projection
+from image_writer import write_fits
from yt.data_objects.image_array import ImageArray
from yt.utilities.lib.misc_utilities import \
pixelize_cylinder
@@ -269,8 +270,8 @@
output.create_dataset(field,data=self[field])
output.close()
- def export_fits(self, filename_prefix, fields = None, clobber=False,
- other_keys=None, gzip_file=False, units="1"):
+ def export_fits(self, filename_prefix, fields=None, clobber=False,
+ other_keys=None, units="cm", sky_center=(0.0,0.0), D_A=None):
"""
This will export a set of FITS images of either the fields specified
@@ -279,106 +280,80 @@
existing FITS file.
This requires the *pyfits* module, which is a standalone module
- provided by STSci to interface with FITS-format files.
+ provided by STSci to interface with FITS-format files, and is also
+ part of AstroPy.
"""
r"""Export a set of pixelized fields to a FITS file.
This will export a set of FITS images of either the fields specified
- or all the fields already in the object. The output filename is the
- the specified prefix.
+ or all the fields already in the object.
Parameters
----------
filename_prefix : string
- This prefix will be prepended to every FITS file name.
+ This prefix will be prepended to the FITS file name.
fields : list of strings
These fields will be pixelized and output.
clobber : boolean
If the file exists, this governs whether we will overwrite.
other_keys : dictionary, optional
A set of header keys and values to write into the FITS header.
- gzip_file : boolean, optional
- gzip the file after writing, default False
units : string, optional
- the length units that the coordinates are written in, default '1'
+ the length units that the coordinates are written in, default 'cm'
+ If units are set to "deg" then assume that sky coordinates are
+ requested.
+ sky_center : array_like, optional
+ Center of the image in (ra,dec) in degrees if sky coordinates
+ (units="deg") are requested.
+ D_A : float or tuple, optional
+ Angular diameter distance, given in code units as a float or
+ a tuple containing the value and the length unit. Required if
+ using sky coordinates.
"""
-
- import pyfits
- from os import system
-
+
+ if units == "deg" and D_A is None:
+ mylog.error("Sky coordinates require an angular diameter distance. Please specify D_A.")
+ if iterable(D_A):
+ dist = D_A[0]/self.pf.units[D_A[1]]
+ else:
+ dist = D_A
+
+ if other_keys is None:
+ hdu_keys = {}
+ else:
+ hdu_keys = other_keys
+
extra_fields = ['x','y','z','px','py','pz','pdx','pdy','pdz','weight_field']
- if filename_prefix.endswith('.fits'): filename_prefix=filename_prefix[:-5]
if fields is None:
fields = [field for field in self.data_source.fields
if field not in extra_fields]
+ coords = {}
nx, ny = self.buff_size
- dx = (self.bounds[1]-self.bounds[0])/nx*self.pf[units]
- dy = (self.bounds[3]-self.bounds[2])/ny*self.pf[units]
- xmin = self.bounds[0]*self.pf[units]
- ymin = self.bounds[2]*self.pf[units]
- simtime = self.pf.current_time
+ dx = (self.bounds[1]-self.bounds[0])/nx
+ dy = (self.bounds[3]-self.bounds[2])/ny
+ if units == "deg":
+ coords["dx"] = -np.rad2deg(dx/dist)
+ coords["dy"] = np.rad2deg(dy/dist)
+ coords["xctr"] = sky_center[0]
+ coords["yctr"] = sky_center[1]
+ hdu_keys["MTYPE1"] = "EQPOS"
+ hdu_keys["MFORM1"] = "RA,DEC"
+ hdu_keys["CTYPE1"] = "RA---TAN"
+ hdu_keys["CTYPE2"] = "DEC--TAN"
+ else:
+ coords["dx"] = dx*self.pf.units[units]
+ coords["dy"] = dy*self.pf.units[units]
+ coords["xctr"] = 0.5*(self.bounds[0]+self.bounds[1])*self.pf.units[units]
+ coords["yctr"] = 0.5*(self.bounds[2]+self.bounds[3])*self.pf.units[units]
+ coords["units"] = units
+
+ hdu_keys["Time"] = self.pf.current_time
- hdus = []
-
- first = True
-
- for field in fields:
-
- if (first) :
- hdu = pyfits.PrimaryHDU(self[field])
- first = False
- else :
- hdu = pyfits.ImageHDU(self[field])
+ data = dict([(field,self[field]) for field in fields])
+ write_fits(data, filename_prefix, clobber=clobber, coords=coords,
+ other_keys=hdu_keys)
- if self.data_source.has_key('weight_field'):
- weightname = self.data_source._weight
- if weightname is None: weightname = 'None'
- field = field +'_'+weightname
-
- hdu.header.update("Field", field)
- hdu.header.update("Time", simtime)
-
- hdu.header.update('WCSNAMEP', "PHYSICAL")
- hdu.header.update('CTYPE1P', "LINEAR")
- hdu.header.update('CTYPE2P', "LINEAR")
- hdu.header.update('CRPIX1P', 0.5)
- hdu.header.update('CRPIX2P', 0.5)
- hdu.header.update('CRVAL1P', xmin)
- hdu.header.update('CRVAL2P', ymin)
- hdu.header.update('CDELT1P', dx)
- hdu.header.update('CDELT2P', dy)
-
- hdu.header.update('CTYPE1', "LINEAR")
- hdu.header.update('CTYPE2', "LINEAR")
- hdu.header.update('CUNIT1', units)
- hdu.header.update('CUNIT2', units)
- hdu.header.update('CRPIX1', 0.5)
- hdu.header.update('CRPIX2', 0.5)
- hdu.header.update('CRVAL1', xmin)
- hdu.header.update('CRVAL2', ymin)
- hdu.header.update('CDELT1', dx)
- hdu.header.update('CDELT2', dy)
-
- if (other_keys is not None) :
-
- for k,v in other_keys.items() :
-
- hdu.header.update(k,v)
-
- hdus.append(hdu)
-
- del hdu
-
- hdulist = pyfits.HDUList(hdus)
-
- hdulist.writeto("%s.fits" % (filename_prefix), clobber=clobber)
-
- if (gzip_file) :
- clob = ""
- if (clobber) : clob = "-f"
- system("gzip "+clob+" %s.fits" % (filename_prefix))
-
def open_in_ds9(self, field, take_log=True):
"""
This will open a given field in the DS9 viewer.
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -333,7 +333,8 @@
def write_projection(data, filename, colorbar=True, colorbar_label=None,
title=None, limits=None, take_log=True, figsize=(8,6),
- dpi=100, cmap_name='algae'):
+ dpi=100, cmap_name='algae', extent=None, xlabel=None,
+ ylabel=None):
r"""Write a projection or volume rendering to disk with a variety of
pretty parameters such as limits, title, colorbar, etc. write_projection
uses the standard matplotlib interface to create the figure. N.B. This code
@@ -392,16 +393,22 @@
# Create the figure and paint the data on
fig = matplotlib.figure.Figure(figsize=figsize)
ax = fig.add_subplot(111)
- fig.tight_layout()
-
- cax = ax.imshow(data, vmin=limits[0], vmax=limits[1], norm=norm, cmap=cmap_name)
+
+ cax = ax.imshow(data, vmin=limits[0], vmax=limits[1], norm=norm,
+ extent=extent, cmap=cmap_name)
if title:
ax.set_title(title)
+ if xlabel:
+ ax.set_xlabel(xlabel)
+ if ylabel:
+ ax.set_ylabel(ylabel)
+
# Suppress the x and y pixel counts
- ax.set_xticks(())
- ax.set_yticks(())
+ if extent is None:
+ ax.set_xticks(())
+ ax.set_yticks(())
# Add a color bar and label if requested
if colorbar:
@@ -409,6 +416,8 @@
if colorbar_label:
cbar.ax.set_ylabel(colorbar_label)
+ fig.tight_layout()
+
suffix = get_image_suffix(filename)
if suffix == '':
@@ -429,70 +438,89 @@
return filename
-def write_fits(image, filename_prefix, clobber=True, coords=None, gzip_file=False) :
+def write_fits(image, filename_prefix, clobber=True, coords=None,
+ other_keys=None):
"""
This will export a FITS image of a floating point array. The output filename is
*filename_prefix*. If clobber is set to True, this will overwrite any existing
FITS file.
This requires the *pyfits* module, which is a standalone module
- provided by STSci to interface with FITS-format files.
+ provided by STSci to interface with FITS-format files, and is also part of
+ AstroPy.
"""
- r"""Write out a floating point array directly to a FITS file, optionally
- adding coordinates.
+ r"""Write out floating point arrays directly to a FITS file, optionally
+ adding coordinates and header keywords.
Parameters
----------
- image : array_like
- This is an (unscaled) array of floating point values, shape (N,N,) to save
- in a FITS file.
+ image : array_like, or dict of array_like objects
+ This is either an (unscaled) array of floating point values, or a dict of
+ such arrays, shape (N,N,) to save in a FITS file.
filename_prefix : string
This prefix will be prepended to every FITS file name.
clobber : boolean
If the file exists, this governs whether we will overwrite.
coords : dictionary, optional
A set of header keys and values to write to the FITS header to set up
- a coordinate system.
- gzip_file : boolean, optional
- gzip the file after writing, default False
+ a coordinate system, which is assumed to be linear unless specified otherwise
+ in *other_keys*
+ "units": the length units
+ "xctr","yctr": the center of the image
+ "dx","dy": the pixel width in each direction
+ other_keys : dictionary, optional
+ A set of header keys and values to write into the FITS header.
"""
+
+ try:
+ import pyfits
+ except ImportError:
+ try:
+ import astropy.io.fits as pyfits
+ except:
+ raise ImportError("You don't have pyFITS or AstroPy installed.")
- import pyfits
from os import system
- if filename_prefix.endswith('.fits'): filename_prefix=filename_prefix[:-5]
-
- hdu = pyfits.PrimaryHDU(image)
+ try:
+ image.keys()
+ image_dict = image
+ except:
+ image_dict = dict(yt_data=image)
- if (coords is not None) :
+ hdulist = [pyfits.PrimaryHDU()]
- hdu.header.update('WCSNAMEP', "PHYSICAL")
- hdu.header.update('CTYPE1P', "LINEAR")
- hdu.header.update('CTYPE2P', "LINEAR")
- hdu.header.update('CRPIX1P', 0.5)
- hdu.header.update('CRPIX2P', 0.5)
- hdu.header.update('CRVAL1P', coords["xmin"])
- hdu.header.update('CRVAL2P', coords["ymin"])
- hdu.header.update('CDELT1P', coords["dx"])
- hdu.header.update('CDELT2P', coords["dy"])
+ for key in image_dict.keys():
+
+ mylog.info("Writing image block \"%s\"" % (key))
+ hdu = pyfits.ImageHDU(image_dict[key])
+ hdu.update_ext_name(key)
- hdu.header.update('CTYPE1', "LINEAR")
- hdu.header.update('CTYPE2', "LINEAR")
- hdu.header.update('CUNIT1', coords["units"])
- hdu.header.update('CUNIT2', coords["units"])
- hdu.header.update('CRPIX1', 0.5)
- hdu.header.update('CRPIX2', 0.5)
- hdu.header.update('CRVAL1', coords["xmin"])
- hdu.header.update('CRVAL2', coords["ymin"])
- hdu.header.update('CDELT1', coords["dx"])
- hdu.header.update('CDELT2', coords["dy"])
+ if coords is not None:
- hdu.writeto("%s.fits" % (filename_prefix), clobber=clobber)
+ nx, ny = image_dict[key].shape
- if (gzip_file) :
- clob = ""
- if (clobber) : clob="-f"
- system("gzip "+clob+" %s.fits" % (filename_prefix))
+ hdu.header.update('CUNIT1', coords["units"])
+ hdu.header.update('CUNIT2', coords["units"])
+ hdu.header.update('CRPIX1', 0.5*(nx+1))
+ hdu.header.update('CRPIX2', 0.5*(ny+1))
+ hdu.header.update('CRVAL1', coords["xctr"])
+ hdu.header.update('CRVAL2', coords["yctr"])
+ hdu.header.update('CDELT1', coords["dx"])
+ hdu.header.update('CDELT2', coords["dy"])
+ # These are the defaults, but will get overwritten if
+ # the caller has specified them
+ hdu.header.update('CTYPE1', "LINEAR")
+ hdu.header.update('CTYPE2', "LINEAR")
+
+ if other_keys is not None:
+ for k,v in other_keys.items():
+ hdu.header.update(k,v)
+
+ hdulist.append(hdu)
+
+ hdulist = pyfits.HDUList(hdulist)
+ hdulist.writeto("%s.fits" % (filename_prefix), clobber=clobber)
def display_in_notebook(image, max_val=None):
"""
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -94,8 +94,10 @@
for ax in 'xyz':
for attr_name in ATTR_ARGS.keys():
for args in ATTR_ARGS[attr_name]:
- yield PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
- args, decimals)
+ test = PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
+ args, decimals)
+ test_attributes.__name__ = test.description
+ yield test
@requires_pf(WT)
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -72,6 +72,9 @@
cubical, but if not, it is left/right, top/bottom, front/back.
resolution : int or list of ints
The number of pixels in each direction.
+ transfer_function : `yt.visualization.volume_rendering.TransferFunction`
+ The transfer function used to map values to colors in an image. If
+ not specified, defaults to a ProjectionTransferFunction.
north_vector : array_like, optional
The 'up' direction for the plane of rays. If not specific, calculated
automatically.
@@ -152,7 +155,7 @@
_tf_figure = None
_render_figure = None
def __init__(self, center, normal_vector, width,
- resolution, transfer_function,
+ resolution, transfer_function = None,
north_vector = None, steady_north=False,
volume = None, fields = None,
log_fields = None,
@@ -1425,7 +1428,7 @@
class MosaicCamera(Camera):
def __init__(self, center, normal_vector, width,
- resolution, transfer_function,
+ resolution, transfer_function = None,
north_vector = None, steady_north=False,
volume = None, fields = None,
log_fields = None,
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/visualization/volume_rendering/multi_texture.py
--- a/yt/visualization/volume_rendering/multi_texture.py
+++ b/yt/visualization/volume_rendering/multi_texture.py
@@ -35,6 +35,14 @@
I hope this helps,
Almar
"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
from yt.mods import *
from yt.funcs import *
@@ -300,14 +308,3 @@
ax.Draw()
return mtex, ax
-
-
-"""
-
-#-----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
diff -r 73eceed0e23d36d8e56a0066d15b2be873c704a2 -r 4628e092abdca5ac1b29449e093cbe3887d26c1e yt/visualization/volume_rendering/transfer_function_helper.py
--- /dev/null
+++ b/yt/visualization/volume_rendering/transfer_function_helper.py
@@ -0,0 +1,211 @@
+"""
+A helper class to build, display, and modify transfer functions for volume
+rendering.
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.funcs import mylog
+from yt.data_objects.profiles import BinnedProfile1D
+from yt.visualization.volume_rendering.api import ColorTransferFunction
+from yt.visualization._mpl_imports import FigureCanvasAgg
+from matplotlib.figure import Figure
+from IPython.core.display import Image
+import cStringIO
+import numpy as np
+
+
+class TransferFunctionHelper(object):
+
+ profiles = None
+
+ def __init__(self, pf):
+ r"""A transfer function helper.
+
+ This attempts to help set up a good transfer function by finding
+ bounds, handling linear/log options, and displaying the transfer
+ function combined with 1D profiles of rendering quantity.
+
+ Parameters
+ ----------
+ pf: A StaticOutput instance
+ A static output that is currently being rendered. This is used to
+ help set up data bounds.
+
+ Notes
+ -----
+ """
+ self.pf = pf
+ self.field = None
+ self.log = False
+ self.tf = None
+ self.bounds = None
+ self.grey_opacity = True
+ self.profiles = {}
+
+ def set_bounds(self, bounds=None):
+ """
+ Set the bounds of the transfer function.
+
+ Parameters
+ ----------
+ bounds: array-like, length 2, optional
+ A length 2 list/array in the form [min, max]. These should be the
+ raw values and not the logarithm of the min and max. If bounds is
+ None, the bounds of the data are calculated from all of the data
+ in the dataset. This can be slow for very large datasets.
+ """
+ if bounds is None:
+ bounds = self.pf.h.all_data().quantities['Extrema'](self.field)[0]
+ self.bounds = bounds
+
+ # Do some error checking.
+ assert(len(self.bounds) == 2)
+ if self.log:
+ assert(self.bounds[0] > 0.0)
+ assert(self.bounds[1] > 0.0)
+ return
+
+ def set_field(self, field):
+ """
+ Set the field to be rendered
+
+ Parameters
+ ----------
+ field: string
+ The field to be rendered.
+ """
+ self.field = field
+
+ def set_log(self, log):
+ """
+ Set whether or not the transfer function should be in log or linear
+ space. Also modifies the pf.field_info[field].take_log attribute to
+ stay in sync with this setting.
+
+ Parameters
+ ----------
+ log: boolean
+ Sets whether the transfer function should use log or linear space.
+ """
+ self.log = log
+ self.pf.h
+ self.pf.field_info[self.field].take_log = log
+
+ def build_transfer_function(self):
+ """
+ Builds the transfer function according to the current state of the
+ TransferFunctionHelper.
+
+ Parameters
+ ----------
+ None
+
+ Returns
+ -------
+
+ A ColorTransferFunction object.
+
+ """
+ if self.bounds is None:
+ mylog.info('Calculating data bounds. This may take a while.' +
+ ' Set the .bounds to avoid this.')
+ self.set_bounds()
+
+ if self.log:
+ mi, ma = np.log10(self.bounds[0]), np.log10(self.bounds[1])
+ else:
+ mi, ma = self.bounds
+ self.tf = ColorTransferFunction((mi, ma),
+ grey_opacity=self.grey_opacity,
+ nbins=512)
+ return self.tf
+
+ def plot(self, fn=None, profile_field=None, profile_weight=None):
+ """
+ Save the current transfer function to a bitmap, or display
+ it inline.
+
+ Parameters
+ ----------
+ fn: string, optional
+ Filename to save the image to. If None, the returns an image
+ to an IPython session.
+
+ Returns
+ -------
+
+ If fn is None, will return an image to an IPython notebook.
+
+ """
+ if self.tf is None:
+ self.build_transfer_function()
+ tf = self.tf
+ if self.log:
+ xfunc = np.logspace
+ xmi, xma = np.log10(self.bounds[0]), np.log10(self.bounds[1])
+ else:
+ xfunc = np.linspace
+ xmi, xma = self.bounds
+
+ x = xfunc(xmi, xma, tf.nbins)
+ y = tf.funcs[3].y
+ w = np.append(x[1:]-x[:-1], x[-1]-x[-2])
+ colors = np.array([tf.funcs[0].y, tf.funcs[1].y, tf.funcs[2].y,
+ np.ones_like(x)]).T
+
+ fig = Figure(figsize=[6, 3])
+ canvas = FigureCanvasAgg(fig)
+ ax = fig.add_axes([0.2, 0.2, 0.75, 0.75])
+ ax.bar(x, tf.funcs[3].y, w, edgecolor=[0.0, 0.0, 0.0, 0.0],
+ log=True, color=colors, bottom=[0])
+
+ if profile_field is not None:
+ try:
+ prof = self.profiles[self.field]
+ except KeyError:
+ self.setup_profile(profile_field, profile_weight)
+ prof = self.profiles[self.field]
+ if profile_field not in prof.keys():
+ prof.add_fields([profile_field], fractional=False,
+ weight=profile_weight)
+ ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
+ prof[profile_field].max(), color='w', linewidth=3)
+ ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
+ prof[profile_field].max(), color='k')
+
+ ax.set_xscale({True: 'log', False: 'linear'}[self.log])
+ ax.set_xlim(x.min(), x.max())
+ ax.set_xlabel(self.pf.field_info[self.field].get_label())
+ ax.set_ylabel(r'$\mathrm{alpha}$')
+ ax.set_ylim(y.max()*1.0e-3, y.max()*2)
+
+ if fn is None:
+ f = cStringIO.StringIO()
+ canvas.print_figure(f)
+ f.seek(0)
+ img = f.read()
+ return Image(img)
+ else:
+ fig.savefig(fn)
+
+ def setup_profile(self, profile_field=None, profile_weight=None):
+ if profile_field is None:
+ profile_field = 'CellVolume'
+ prof = BinnedProfile1D(self.pf.h.all_data(), 128, self.field,
+ self.bounds[0], self.bounds[1],
+ log_space=self.log,
+ lazy_reader=False, end_collect=False)
+ prof.add_fields([profile_field], fractional=False,
+ weight=profile_weight)
+ self.profiles[self.field] = prof
+ return
https://bitbucket.org/yt_analysis/yt-3.0/commits/46521c80a5bd/
Changeset: 46521c80a5bd
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 15:29:40
Summary: Refactoring create_obj and upping gold standard name.
Affected #: 6 files
diff -r 4628e092abdca5ac1b29449e093cbe3887d26c1e -r 46521c80a5bd530c809a35e3845cb87d0f1716f1 yt/config.py
--- a/yt/config.py
+++ b/yt/config.py
@@ -52,7 +52,7 @@
notebook_password = '',
answer_testing_tolerance = '3',
answer_testing_bitwise = 'False',
- gold_standard_filename = 'gold310',
+ gold_standard_filename = 'gold311',
local_standard_filename = 'local001',
sketchfab_api_key = 'None',
thread_field_detection = 'False'
diff -r 4628e092abdca5ac1b29449e093cbe3887d26c1e -r 46521c80a5bd530c809a35e3845cb87d0f1716f1 yt/frontends/artio/tests/test_outputs.py
--- a/yt/frontends/artio/tests/test_outputs.py
+++ b/yt/frontends/artio/tests/test_outputs.py
@@ -19,7 +19,8 @@
requires_pf, \
data_dir_load, \
PixelizedProjectionValuesTest, \
- FieldValuesTest
+ FieldValuesTest, \
+ create_obj
from yt.frontends.artio.api import ARTIOStaticOutput
_fields = ("Temperature", "Density", "VelocityMagnitude",
@@ -39,7 +40,7 @@
sizmbhloz, axis, field, weight_field,
ds)
yield FieldValuesTest(sizmbhloz, field, ds)
- if ds is None: ds = pf.h.all_data()
- s1 = ds["Ones"].sum()
- s2 = sum(mask.sum() for block, mask in ds.blocks)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
yield assert_equal, s1, s2
diff -r 4628e092abdca5ac1b29449e093cbe3887d26c1e -r 46521c80a5bd530c809a35e3845cb87d0f1716f1 yt/frontends/ramses/tests/test_outputs.py
--- a/yt/frontends/ramses/tests/test_outputs.py
+++ b/yt/frontends/ramses/tests/test_outputs.py
@@ -19,7 +19,8 @@
requires_pf, \
data_dir_load, \
PixelizedProjectionValuesTest, \
- FieldValuesTest
+ FieldValuesTest, \
+ create_obj
from yt.frontends.artio.api import ARTIOStaticOutput
_fields = ("Temperature", "Density", "VelocityMagnitude",
@@ -39,7 +40,7 @@
output_00080, axis, field, weight_field,
ds)
yield FieldValuesTest(output_00080, field, ds)
- if ds is None: ds = pf.h.all_data()
- s1 = ds["Ones"].sum()
- s2 = sum(mask.sum() for block, mask in ds.blocks)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
yield assert_equal, s1, s2
diff -r 4628e092abdca5ac1b29449e093cbe3887d26c1e -r 46521c80a5bd530c809a35e3845cb87d0f1716f1 yt/frontends/sph/tests/test_owls.py
--- a/yt/frontends/sph/tests/test_owls.py
+++ b/yt/frontends/sph/tests/test_owls.py
@@ -21,7 +21,8 @@
big_patch_amr, \
data_dir_load, \
PixelizedProjectionValuesTest, \
- FieldValuesTest
+ FieldValuesTest, \
+ create_obj
from yt.frontends.sph.api import OWLSStaticOutput
_fields = (("deposit", "all_density"), ("deposit", "all_count"),
@@ -48,8 +49,7 @@
os33, axis, field, weight_field,
ds)
yield FieldValuesTest(os33, field, ds)
- if ds is None: ds = pf.h.all_data()
- s1 = ds["Ones"].sum()
- s2 = sum(mask.sum() for block, mask in ds.blocks)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
yield assert_equal, s1, s2
-
diff -r 4628e092abdca5ac1b29449e093cbe3887d26c1e -r 46521c80a5bd530c809a35e3845cb87d0f1716f1 yt/frontends/sph/tests/test_tipsy.py
--- a/yt/frontends/sph/tests/test_tipsy.py
+++ b/yt/frontends/sph/tests/test_tipsy.py
@@ -21,7 +21,8 @@
big_patch_amr, \
data_dir_load, \
PixelizedProjectionValuesTest, \
- FieldValuesTest
+ FieldValuesTest, \
+ create_obj
from yt.frontends.sph.api import TipsyStaticOutput
_fields = (("deposit", "all_density"),
@@ -57,9 +58,9 @@
pf, axis, field, weight_field,
ds)
yield FieldValuesTest(pf, field, ds)
- if ds is None: ds = pf.h.all_data()
- s1 = ds["Ones"].sum()
- s2 = sum(mask.sum() for block, mask in ds.blocks)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
yield assert_equal, s1, s2
gasoline = "agora_1e11.00400/agora_1e11.00400"
@@ -88,7 +89,7 @@
pf, axis, field, weight_field,
ds)
yield FieldValuesTest(pf, field, ds)
- if ds is None: ds = pf.h.all_data()
- s1 = ds["Ones"].sum()
- s2 = sum(mask.sum() for block, mask in ds.blocks)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
yield assert_equal, s1, s2
diff -r 4628e092abdca5ac1b29449e093cbe3887d26c1e -r 46521c80a5bd530c809a35e3845cb87d0f1716f1 yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -321,15 +321,6 @@
def compare(self, new_result, old_result):
raise RuntimeError
- def create_obj(self, pf, obj_type):
- # obj_type should be tuple of
- # ( obj_name, ( args ) )
- if obj_type is None:
- return pf.h.all_data()
- cls = getattr(pf.h, obj_type[0])
- obj = cls(*obj_type[1])
- return obj
-
def create_plot(self, pf, plot_type, plot_field, plot_axis, plot_kwargs = None):
# plot_type should be a string
# plot_args should be a tuple
@@ -385,7 +376,7 @@
self.decimals = decimals
def run(self):
- obj = self.create_obj(self.pf, self.obj_type)
+ obj = create_obj(self.pf, self.obj_type)
avg = obj.quantities["WeightedAverageQuantity"](self.field,
weight="Ones")
(mi, ma), = obj.quantities["Extrema"](self.field)
@@ -412,7 +403,7 @@
self.decimals = decimals
def run(self):
- obj = self.create_obj(self.pf, self.obj_type)
+ obj = create_obj(self.pf, self.obj_type)
return obj[self.field]
def compare(self, new_result, old_result):
@@ -439,7 +430,7 @@
def run(self):
if self.obj_type is not None:
- obj = self.create_obj(self.pf, self.obj_type)
+ obj = create_obj(self.pf, self.obj_type)
else:
obj = None
if self.pf.domain_dimensions[self.axis] == 1: return None
@@ -480,7 +471,7 @@
def run(self):
if self.obj_type is not None:
- obj = self.create_obj(self.pf, self.obj_type)
+ obj = create_obj(self.pf, self.obj_type)
else:
obj = None
proj = self.pf.h.proj(self.field, self.axis,
@@ -730,6 +721,15 @@
pf_fn, axis, field, weight_field,
ds)
+def create_obj(pf, obj_type):
+ # obj_type should be tuple of
+ # ( obj_name, ( args ) )
+ if obj_type is None:
+ return pf.h.all_data()
+ cls = getattr(pf.h, obj_type[0])
+ obj = cls(*obj_type[1])
+ return obj
+
class AssertWrapper(object):
"""
Used to wrap a numpy testing assertion, in order to provide a useful name
https://bitbucket.org/yt_analysis/yt-3.0/commits/7d65b4e5b1b1/
Changeset: 7d65b4e5b1b1
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 16:01:13
Summary: A few optimizations with considerable payoff for ARTIO.
Affected #: 1 file
diff -r 46521c80a5bd530c809a35e3845cb87d0f1716f1 -r 7d65b4e5b1b10f538f8fe1d3898cb9cb60ce2073 yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -832,6 +832,9 @@
0, fields)
return rv
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+ at cython.cdivision(True)
cdef read_sfc_particles(artio_fileset artio_handle,
np.int64_t sfc_start, np.int64_t sfc_end,
int read_unrefined, fields):
@@ -1015,7 +1018,8 @@
cdef np.uint64_t sfc_start
cdef np.uint64_t sfc_end
cdef public object _last_mask
- cdef public object _last_selector_id
+ cdef public np.int64_t _last_selector_id
+ cdef np.int64_t _last_mask_sum
cdef ARTIOSFCRangeHandler range_handler
cdef np.uint8_t *sfc_mask
cdef np.int64_t nsfc
@@ -1030,7 +1034,8 @@
self.dds[i] = range_handler.dds[i]
self.handle = range_handler.handle
self.artio_handle = range_handler.artio_handle
- self._last_mask = self._last_selector_id = None
+ self._last_mask = None
+ self._last_selector_id = -1
self.sfc_start = range_handler.sfc_start
self.sfc_end = range_handler.sfc_end
self.range_handler = range_handler
@@ -1077,6 +1082,9 @@
cdef int i
return self.mask(selector).sum()
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def icoords(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
# Note that num_octs does not have to equal sfc_end - sfc_start + 1.
@@ -1084,7 +1092,7 @@
cdef int acoords[3], i
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
cdef np.ndarray[np.int64_t, ndim=2] coords
coords = np.empty((num_cells, 3), dtype="int64")
cdef int filled = 0
@@ -1101,6 +1109,9 @@
filled += 1
return coords
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def fcoords(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
# Note that num_cells does not have to equal sfc_end - sfc_start + 1.
@@ -1109,7 +1120,7 @@
cdef int acoords[3], i
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
cdef np.ndarray[np.float64_t, ndim=2] coords
coords = np.empty((num_cells, 3), dtype="float64")
cdef int filled = 0
@@ -1126,23 +1137,29 @@
filled += 1
return coords
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def fwidth(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
cdef int i
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
cdef np.ndarray[np.float64_t, ndim=2] width
width = np.zeros((num_cells, 3), dtype="float64")
for i in range(3):
width[:,i] = self.dds[i]
return width
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def ires(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
cdef np.ndarray[np.int64_t, ndim=1] res
res = np.zeros(num_cells, dtype="int64")
return res
@@ -1176,7 +1193,7 @@
# Note that RAMSES can have partial refinement inside an Oct. This
# means we actually do want the number of Octs, not the number of
# cells.
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
if dims > 1:
dest = np.zeros((num_cells, dims), dtype=source.dtype,
order='C')
@@ -1208,22 +1225,28 @@
if self._last_selector_id == hash(selector):
return self._last_mask
mask = np.zeros((self.nsfc), dtype="uint8")
+ self._last_mask_sum = 0
for sfc in range(self.sfc_start, self.sfc_end + 1):
if self.sfc_mask[sfc - self.sfc_start] == 0: continue
sfci += 1
self.sfc_to_pos(sfc, pos)
if selector.select_cell(pos, self.dds) == 0: continue
mask[sfci] = 1
+ self._last_mask_sum += 1
self._last_mask = mask.astype("bool")
self._last_selector_id = hash(selector)
return self._last_mask
+
def fill_sfc_particles(self, fields):
rv = read_sfc_particles(self.artio_handle,
self.sfc_start, self.sfc_end,
1, fields)
return rv
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def fill_sfc(self, SelectorObject selector, field_indices):
cdef np.ndarray[np.float64_t, ndim=1] dest
cdef int n, status, i, di, num_oct_levels, nf, ngv, max_level
@@ -1238,7 +1261,7 @@
max_level = self.artio_handle.max_level
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector, -1)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
tr = []
for i in range(nf):
tr.append(np.zeros(num_cells, dtype="float64"))
https://bitbucket.org/yt_analysis/yt-3.0/commits/b514603c5fd4/
Changeset: b514603c5fd4
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 17:38:00
Summary: Updating tests for Gasoline
Affected #: 2 files
diff -r 7d65b4e5b1b10f538f8fe1d3898cb9cb60ce2073 -r b514603c5fd4e8833e4e52be43a2ec998ac4a832 yt/frontends/sph/tests/test_tipsy.py
--- a/yt/frontends/sph/tests/test_tipsy.py
+++ b/yt/frontends/sph/tests/test_tipsy.py
@@ -77,10 +77,10 @@
yield assert_equal, str(pf), "agora_1e11.00400"
dso = [ None, ("sphere", ("c", (0.3, 'unitary')))]
dd = pf.h.all_data()
- yield assert_equal, dd["Coordinates"].shape, (26847360, 3)
+ yield assert_equal, dd["Coordinates"].shape, (10550576, 3)
tot = sum(dd[ptype,"Coordinates"].shape[0]
for ptype in pf.particle_types if ptype != "all")
- yield assert_equal, tot, 26847360
+ yield assert_equal, tot, 10550576
for ds in dso:
for field in _fields:
for axis in [0, 1, 2]:
diff -r 7d65b4e5b1b10f538f8fe1d3898cb9cb60ce2073 -r b514603c5fd4e8833e4e52be43a2ec998ac4a832 yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -253,7 +253,7 @@
yield
os.chdir(oldcwd)
-def can_run_pf(pf_fn, file_check):
+def can_run_pf(pf_fn, file_check = False):
if isinstance(pf_fn, StaticOutput):
return AnswerTestingTest.result_storage is not None
path = ytcfg.get("yt", "test_data_dir")
https://bitbucket.org/yt_analysis/yt-3.0/commits/2f750152aa19/
Changeset: 2f750152aa19
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 19:12:39
Summary: Fix for can_run_pf from Kacper.
Affected #: 1 file
diff -r b514603c5fd4e8833e4e52be43a2ec998ac4a832 -r 2f750152aa19f38763b636f7c914a7128e23744f yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -261,7 +261,8 @@
return False
with temp_cwd(path):
if file_check:
- return os.path.isfile(pf_fn)
+ return os.path.isfile(pf_fn) and \
+ AnswerTestingTest.result_storage is not None
try:
load(pf_fn)
except YTOutputNotIdentified:
https://bitbucket.org/yt_analysis/yt-3.0/commits/104a961a811f/
Changeset: 104a961a811f
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 20:45:09
Summary: A few more changes which have medium level impact.
Affected #: 2 files
diff -r 2f750152aa19f38763b636f7c914a7128e23744f -r 104a961a811fe636f7732276297ad709b8828937 yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -123,7 +123,9 @@
void artio_sfc_coords( artio_fileset_handle *handle, int64_t index, int coords[3] ) nogil
cdef void check_artio_status(int status, char *fname="[unknown]"):
- if status!=ARTIO_SUCCESS :
+ if status != ARTIO_SUCCESS:
+ import traceback
+ traceback.print_stack()
callername = sys._getframe().f_code.co_name
nline = sys._getframe().f_lineno
raise RuntimeError('failure with status', status, 'in function',fname,'from caller', callername, nline)
@@ -665,9 +667,11 @@
# this, we will avoid creating it as long as possible.
cdef public artio_fileset artio_handle
+ cdef ARTIOSFCRangeHandler range_handler
cdef np.int64_t level_indices[32]
def __init__(self, ARTIOSFCRangeHandler range_handler):
+ self.range_handler = range_handler
self.artio_handle = range_handler.artio_handle
# Note the final argument is partial_coverage, which indicates whether
# or not an Oct can be partially refined.
@@ -785,6 +789,12 @@
# * Enable preloading during mesh initialization
# * Calculate domain indices on the fly rather than with a
# double-loop to calculate domain_counts
+ # The cons should be in order
+ cdef np.int64_t sfc_start, sfc_end
+ sfc_start = self.domains[0].con_id
+ sfc_end = self.domains[self.num_domains - 1].con_id
+ status = artio_grid_cache_sfc_range(handle, sfc_start, sfc_end )
+ check_artio_status(status)
cdef np.int64_t offset = 0
for si in range(self.num_domains):
sfc = self.domains[si].con_id
@@ -818,6 +828,8 @@
dest[i + offset] = source[oct_ind, cell_inds[i + offset]]
# Now, we offset by the actual number filled here.
offset += domain_counts[si]
+ status = artio_grid_clear_sfc_cache(handle)
+ check_artio_status(status)
free(field_ind)
free(field_vals)
free(grid_variables)
@@ -829,7 +841,7 @@
sfc_start = self.domains[0].con_id
sfc_end = self.domains[self.num_domains - 1].con_id
rv = read_sfc_particles(self.artio_handle, sfc_start, sfc_end,
- 0, fields)
+ 0, fields, self.range_handler.doct_count)
return rv
@cython.boundscheck(False)
@@ -837,7 +849,8 @@
@cython.cdivision(True)
cdef read_sfc_particles(artio_fileset artio_handle,
np.int64_t sfc_start, np.int64_t sfc_end,
- int read_unrefined, fields):
+ int read_unrefined, fields,
+ np.int64_t *doct_count):
cdef int status, ispec, subspecies
cdef np.int64_t sfc, particle, pid, ind, vind
cdef int num_species = artio_handle.num_species
@@ -887,19 +900,12 @@
sfc_start, sfc_end )
check_artio_status(status)
- # We cache so we can figure out if the cell is refined or not.
- status = artio_grid_cache_sfc_range(handle, sfc_start, sfc_end)
- check_artio_status(status)
-
# Pass through once. We want every single particle.
+ cdef np.int64_t c
for sfc in range(sfc_start, sfc_end + 1):
- status = artio_grid_read_root_cell_begin( handle,
- sfc, dpos, NULL, &num_oct_levels, num_octs_per_level)
- check_artio_status(status)
- status = artio_grid_read_root_cell_end(handle)
- check_artio_status(status)
- if read_unrefined == 1 and num_oct_levels > 0: continue
- if read_unrefined == 0 and num_oct_levels == 0: continue
+ c = doct_count[sfc - sfc_start]
+ if read_unrefined == 1 and c > 0: continue
+ if read_unrefined == 0 and c == 0: continue
status = artio_particle_read_root_cell_begin( handle, sfc,
num_particles_per_species )
check_artio_status(status)
@@ -951,13 +957,10 @@
vp.n_s += 1
for sfc in range(sfc_start, sfc_end + 1):
- status = artio_grid_read_root_cell_begin( handle,
- sfc, dpos, NULL, &num_oct_levels, num_octs_per_level)
+ c = doct_count[sfc - sfc_start]
check_artio_status(status)
- status = artio_grid_read_root_cell_end(handle)
- check_artio_status(status)
- if read_unrefined == 1 and num_oct_levels > 0: continue
- if read_unrefined == 0 and num_oct_levels == 0: continue
+ if read_unrefined == 1 and c > 0: continue
+ if read_unrefined == 0 and c == 0: continue
status = artio_particle_read_root_cell_begin( handle, sfc,
num_particles_per_species )
check_artio_status(status)
@@ -993,11 +996,8 @@
status = artio_particle_read_root_cell_end( handle )
check_artio_status(status)
- #status = artio_particle_clear_sfc_cache(handle)
- #check_artio_status(status)
-
- #status = artio_grid_clear_sfc_cache(handle)
- #check_artio_status(status)
+ status = artio_particle_clear_sfc_cache(handle)
+ check_artio_status(status)
free(num_octs_per_level)
free(num_particles_per_species)
@@ -1224,6 +1224,7 @@
cdef np.int64_t sfc, sfci = -1
if self._last_selector_id == hash(selector):
return self._last_mask
+ cdef np.ndarray[np.uint8_t, ndim=1] mask
mask = np.zeros((self.nsfc), dtype="uint8")
self._last_mask_sum = 0
for sfc in range(self.sfc_start, self.sfc_end + 1):
@@ -1241,7 +1242,7 @@
def fill_sfc_particles(self, fields):
rv = read_sfc_particles(self.artio_handle,
self.sfc_start, self.sfc_end,
- 1, fields)
+ 1, fields, self.range_handler.doct_count)
return rv
@cython.boundscheck(False)
@@ -1306,6 +1307,9 @@
free(num_octs_per_level)
return tr
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def deposit(self, ParticleDepositOperation pdeposit,
SelectorObject selector,
np.ndarray[np.float64_t, ndim=2] positions,
diff -r 2f750152aa19f38763b636f7c914a7128e23744f -r 104a961a811fe636f7732276297ad709b8828937 yt/frontends/artio/data_structures.py
--- a/yt/frontends/artio/data_structures.py
+++ b/yt/frontends/artio/data_structures.py
@@ -72,6 +72,7 @@
return self.sfc_end
def fill(self, fields, selector):
+ if len(fields) == 0: return []
handle = self.oct_handler.artio_handle
field_indices = [handle.parameters["grid_variable_labels"].index(
yt_to_art[f]) for (ft, f) in fields]
@@ -88,6 +89,7 @@
return tr
def fill_particles(self, fields):
+ if len(fields) == 0: return {}
art_fields = []
for s, f in fields:
fn = yt_to_art[f]
@@ -127,6 +129,7 @@
def fill(self, fields, selector):
# We know how big these will be.
+ if len(fields) == 0: return []
handle = self.pf._handle
field_indices = [handle.parameters["grid_variable_labels"].index(
yt_to_art[f]) for (ft, f) in fields]
@@ -250,6 +253,8 @@
list_sfc_ranges = self.pf._handle.root_sfc_ranges(
dobj.selector)
ci = []
+ #v = np.array(list_sfc_ranges)
+ #list_sfc_ranges = [ (v.min(), v.max()) ]
for (start, end) in list_sfc_ranges:
range_handler = ARTIOSFCRangeHandler(
self.pf.domain_dimensions,
https://bitbucket.org/yt_analysis/yt-3.0/commits/ab21fdb8513b/
Changeset: ab21fdb8513b
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 21:21:45
Summary: Adding option for max_range to be passed in
Affected #: 1 file
diff -r 104a961a811fe636f7732276297ad709b8828937 -r ab21fdb8513b1f7610b18e78ef9532d7a8d46c60 yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -490,8 +490,7 @@
return (fcoords, ires, data)
- def root_sfc_ranges_all(self) :
- cdef int max_range_size = 1024
+ def root_sfc_ranges_all(self, int max_range_size = 1024) :
cdef int64_t sfc_start, sfc_end
cdef artio_selection *selection
@@ -505,8 +504,8 @@
artio_selection_destroy(selection)
return sfc_ranges
- def root_sfc_ranges(self, SelectorObject selector) :
- cdef int max_range_size = 1024
+ def root_sfc_ranges(self, SelectorObject selector,
+ int max_range_size = 1024):
cdef int coords[3]
cdef int64_t sfc_start, sfc_end
cdef np.float64_t left[3]
@@ -1299,8 +1298,8 @@
status = artio_grid_read_root_cell_end( handle )
check_artio_status(status)
# Now we have all our sources.
- #status = artio_grid_clear_sfc_cache(handle)
- #check_artio_status(status)
+ status = artio_grid_clear_sfc_cache(handle)
+ check_artio_status(status)
free(field_ind)
free(field_vals)
free(grid_variables)
https://bitbucket.org/yt_analysis/yt-3.0/commits/32515ac758a5/
Changeset: 32515ac758a5
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 22:36:06
Summary: A currently oddly-segfaulting optimization for particle counts.
Affected #: 1 file
diff -r ab21fdb8513b1f7610b18e78ef9532d7a8d46c60 -r 32515ac758a5c65330c13c2cb81833fa8b85f17d yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -564,6 +564,7 @@
cdef np.int64_t dims[3]
cdef public np.int64_t total_octs
cdef np.int64_t *doct_count
+ cdef np.int64_t **pcount
def __init__(self, domain_dimensions, # cells
domain_left_edge,
@@ -571,6 +572,7 @@
artio_fileset artio_handle,
sfc_start, sfc_end):
cdef int i
+ cdef np.int64_t sfc
self.sfc_start = sfc_start
self.sfc_end = sfc_end
self.artio_handle = artio_handle
@@ -578,23 +580,39 @@
self.octree_handler = None
self.handle = artio_handle.handle
self.oct_count = None
+ self.pcount = <np.int64_t **> malloc(sizeof(np.int64_t*)
+ * artio_handle.num_species)
+ for i in range(artio_handle.num_species):
+ self.pcount[i] = <np.int64_t*> malloc(sizeof(np.int64_t)
+ * (self.sfc_end - self.sfc_start + 1))
+ for sfc in range(self.sfc_end - self.sfc_start + 1):
+ self.pcount[i][sfc] = 0
for i in range(3):
self.dims[i] = domain_dimensions[i]
self.DLE[i] = domain_left_edge[i]
self.DRE[i] = domain_right_edge[i]
self.dds[i] = (self.DRE[i] - self.DLE[i])/self.dims[i]
+ def __dealloc__(self):
+ cdef int i
+ for i in range(self.artio_handle.num_species):
+ free(self.pcount[i])
+ free(self.pcount)
+
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def construct_mesh(self):
cdef int status, level
- cdef np.int64_t sfc, oc
+ cdef np.int64_t sfc, oc, i
cdef double dpos[3]
cdef int num_oct_levels
cdef int max_level = self.artio_handle.max_level
cdef int *num_octs_per_level = <int *>malloc(
(max_level + 1)*sizeof(int))
+ cdef int num_species = self.artio_handle.num_species
+ cdef int *num_particles_per_species = <int *>malloc(
+ sizeof(int)*num_species)
cdef ARTIOOctreeContainer octree
self.octree_handler = octree = ARTIOOctreeContainer(self)
# We want to pre-allocate an array of root pointers. In the future,
@@ -621,7 +639,30 @@
num_octs_per_level, sfc)
status = artio_grid_read_root_cell_end( self.handle )
check_artio_status(status)
+ status = artio_grid_clear_sfc_cache( self.handle)
+ check_artio_status(status)
+ # Now particles
+ status = artio_particle_cache_sfc_range(self.handle, self.sfc_start,
+ self.sfc_end)
+ check_artio_status(status)
+ for sfc in range(self.sfc_start, self.sfc_end + 1):
+ # Now particles
+ status = artio_particle_read_root_cell_begin( self.handle,
+ sfc, num_particles_per_species )
+ check_artio_status(status)
+
+ for i in range(num_species):
+ self.pcount[i][sfc - self.sfc_start] = \
+ num_particles_per_species[i]
+
+ status = artio_particle_read_root_cell_end( self.handle)
+ check_artio_status(status)
+
+ status = artio_particle_clear_sfc_cache( self.handle)
+ check_artio_status(status)
+
free(num_octs_per_level)
+ free(num_particles_per_species)
self.oct_count = oct_count
self.doct_count = <np.int64_t *> oct_count.data
self.root_mesh_handler = ARTIORootMeshContainer(self)
@@ -840,7 +881,8 @@
sfc_start = self.domains[0].con_id
sfc_end = self.domains[self.num_domains - 1].con_id
rv = read_sfc_particles(self.artio_handle, sfc_start, sfc_end,
- 0, fields, self.range_handler.doct_count)
+ 0, fields, self.range_handler.doct_count,
+ self.range_handler.pcount)
return rv
@cython.boundscheck(False)
@@ -849,7 +891,8 @@
cdef read_sfc_particles(artio_fileset artio_handle,
np.int64_t sfc_start, np.int64_t sfc_end,
int read_unrefined, fields,
- np.int64_t *doct_count):
+ np.int64_t *doct_count,
+ np.int64_t **pcount):
cdef int status, ispec, subspecies
cdef np.int64_t sfc, particle, pid, ind, vind
cdef int num_species = artio_handle.num_species
@@ -895,25 +938,16 @@
vpoints[ispec].n_p = 0
vpoints[ispec].n_s = 0
- status = artio_particle_cache_sfc_range( handle,
- sfc_start, sfc_end )
- check_artio_status(status)
-
# Pass through once. We want every single particle.
- cdef np.int64_t c
+ tp = 0
+ cdef np.int64_t c
for sfc in range(sfc_start, sfc_end + 1):
c = doct_count[sfc - sfc_start]
if read_unrefined == 1 and c > 0: continue
if read_unrefined == 0 and c == 0: continue
- status = artio_particle_read_root_cell_begin( handle, sfc,
- num_particles_per_species )
- check_artio_status(status)
for ispec in range(num_species):
- total_particles[ispec] += num_particles_per_species[ispec]
-
- status = artio_particle_read_root_cell_end( handle )
- check_artio_status(status)
+ total_particles[ispec] += pcount[ispec][sfc - sfc_start]
# Now we allocate our final fields, which will be filled
#for ispec in range(num_species):
@@ -930,30 +964,40 @@
vp = &vpoints[species]
if field == "MASS":
vp.n_mass = 1
- npf64arr = data[(species, field)] = np.zeros(tp, dtype="float64")
+ data[(species, field)] = np.zeros(tp, dtype="float64")
+ npf64arr = data[(species, field)]
# We fill this *now*
npf64arr += params["particle_species_mass"][species]
vp.mass = <np.float64_t*> npf64arr.data
elif field == "PID":
vp.n_pid = 1
- npi64arr = data[(species, field)] = np.zeros(tp, dtype="int64")
+ data[(species, field)] = np.zeros(tp, dtype="int64")
+ npi64arr = data[(species, field)]
vp.pid = <np.int64_t*> npi64arr.data
elif field == "SPECIES":
vp.n_species = 1
- npi8arr = data[(species, field)] = np.zeros(tp, dtype="int8")
+ data[(species, field)] = np.zeros(tp, dtype="int8")
+ npi8arr = data[(species, field)]
# We fill this *now*
npi8arr += species
vp.species = <np.int8_t*> npi8arr.data
elif npri_vars[species] > 0 and field in pri_vars :
- npf64arr = data[(species, field)] = np.zeros(tp, dtype="float64")
+ data[(species, field)] = np.zeros(tp, dtype="float64")
+ npf64arr = data[(species, field)]
vp.p_ind[vp.n_p] = pri_vars.index(field)
vp.pvars[vp.n_p] = <np.float64_t *> npf64arr.data
vp.n_p += 1
elif nsec_vars[species] > 0 and field in sec_vars :
- npf64arr = data[(species, field)] = np.zeros(tp, dtype="float64")
+ data[(species, field)] = np.zeros(tp, dtype="float64")
+ npf64arr = data[(species, field)]
vp.s_ind[vp.n_s] = sec_vars.index(field)
vp.svars[vp.n_s] = <np.float64_t *> npf64arr.data
vp.n_s += 1
+ print "Allocated ", species, field, data[species, field].size
+
+ status = artio_particle_cache_sfc_range( handle,
+ sfc_start, sfc_end )
+ check_artio_status(status)
for sfc in range(sfc_start, sfc_end + 1):
c = doct_count[sfc - sfc_start]
@@ -1241,7 +1285,8 @@
def fill_sfc_particles(self, fields):
rv = read_sfc_particles(self.artio_handle,
self.sfc_start, self.sfc_end,
- 1, fields, self.range_handler.doct_count)
+ 1, fields, self.range_handler.doct_count,
+ self.range_handler.pcount)
return rv
@cython.boundscheck(False)
https://bitbucket.org/yt_analysis/yt-3.0/commits/be6e9372fa06/
Changeset: be6e9372fa06
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-07 22:51:21
Summary: A few fixes, and a major speedup for ARTIO.
Affected #: 1 file
diff -r 32515ac758a5c65330c13c2cb81833fa8b85f17d -r be6e9372fa06490ebc2f690903ad2dfdf3cb6d29 yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -962,7 +962,7 @@
"species_%02u_secondary_variable_labels" % (species,), [])
tp = total_particles[species]
vp = &vpoints[species]
- if field == "MASS":
+ if field == "MASS" and params["particle_species_mass"][species] != 0.0:
vp.n_mass = 1
data[(species, field)] = np.zeros(tp, dtype="float64")
npf64arr = data[(species, field)]
@@ -993,7 +993,6 @@
vp.s_ind[vp.n_s] = sec_vars.index(field)
vp.svars[vp.n_s] = <np.float64_t *> npf64arr.data
vp.n_s += 1
- print "Allocated ", species, field, data[species, field].size
status = artio_particle_cache_sfc_range( handle,
sfc_start, sfc_end )
@@ -1004,6 +1003,11 @@
check_artio_status(status)
if read_unrefined == 1 and c > 0: continue
if read_unrefined == 0 and c == 0: continue
+ c = 0
+ for ispec in range(num_species) :
+ if accessed_species[ispec] == 0: continue
+ c += pcount[ispec][sfc - sfc_start]
+ if c == 0: continue
status = artio_particle_read_root_cell_begin( handle, sfc,
num_particles_per_species )
check_artio_status(status)
https://bitbucket.org/yt_analysis/yt-3.0/commits/7f9535d0a16f/
Changeset: 7f9535d0a16f
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-08 04:14:19
Summary: Cache root mesh data on instantiation and avoid any reloading.
Affected #: 1 file
diff -r be6e9372fa06490ebc2f690903ad2dfdf3cb6d29 -r 7f9535d0a16f4a3a4b60b5d40cd6b0da2e2c2a07 yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -565,6 +565,7 @@
cdef public np.int64_t total_octs
cdef np.int64_t *doct_count
cdef np.int64_t **pcount
+ cdef float **root_mesh_data
def __init__(self, domain_dimensions, # cells
domain_left_edge,
@@ -580,6 +581,7 @@
self.octree_handler = None
self.handle = artio_handle.handle
self.oct_count = None
+ self.root_mesh_data = NULL
self.pcount = <np.int64_t **> malloc(sizeof(np.int64_t*)
* artio_handle.num_species)
for i in range(artio_handle.num_species):
@@ -597,13 +599,16 @@
cdef int i
for i in range(self.artio_handle.num_species):
free(self.pcount[i])
+ for i in range(self.artio_handle.num_grid_variables):
+ free(self.root_mesh_data[i])
free(self.pcount)
+ free(self.root_mesh_data)
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def construct_mesh(self):
- cdef int status, level
+ cdef int status, level, ngv
cdef np.int64_t sfc, oc, i
cdef double dpos[3]
cdef int num_oct_levels
@@ -614,7 +619,14 @@
cdef int *num_particles_per_species = <int *>malloc(
sizeof(int)*num_species)
cdef ARTIOOctreeContainer octree
+ ngv = self.artio_handle.num_grid_variables
+ cdef float *grid_variables = <float *>malloc(
+ ngv * sizeof(float))
self.octree_handler = octree = ARTIOOctreeContainer(self)
+ self.root_mesh_data = <float **>malloc(sizeof(float *) * ngv)
+ for i in range(ngv):
+ self.root_mesh_data[i] = <float *>malloc(sizeof(float) * \
+ self.sfc_end - self.sfc_start + 1)
# We want to pre-allocate an array of root pointers. In the future,
# this will be pre-determined by the ARTIO library. However, because
# realloc plays havoc with our tree searching, we can't utilize an
@@ -627,7 +639,11 @@
check_artio_status(status)
for sfc in range(self.sfc_start, self.sfc_end + 1):
status = artio_grid_read_root_cell_begin( self.handle,
- sfc, dpos, NULL, &num_oct_levels, num_octs_per_level)
+ sfc, dpos, grid_variables, &num_oct_levels,
+ num_octs_per_level)
+ for i in range(ngv):
+ self.root_mesh_data[i][sfc - self.sfc_start] = \
+ grid_variables[i]
check_artio_status(status)
if num_oct_levels > 0:
oc = 0
@@ -661,6 +677,7 @@
status = artio_particle_clear_sfc_cache( self.handle)
check_artio_status(status)
+ free(grid_variables)
free(num_octs_per_level)
free(num_particles_per_species)
self.oct_count = oct_count
@@ -1301,23 +1318,17 @@
cdef int n, status, i, di, num_oct_levels, nf, ngv, max_level
cdef np.int64_t sfc, num_cells, sfci = -1
cdef np.float64_t val
- cdef artio_fileset_handle *handle = self.artio_handle.handle
cdef double dpos[3]
# We duplicate some of the grid_variables stuff here so that we can
# potentially release the GIL
nf = len(field_indices)
ngv = self.artio_handle.num_grid_variables
- max_level = self.artio_handle.max_level
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector, -1)
num_cells = self._last_mask_sum
tr = []
for i in range(nf):
tr.append(np.zeros(num_cells, dtype="float64"))
- cdef int *num_octs_per_level = <int *>malloc(
- (max_level + 1)*sizeof(int))
- cdef float *grid_variables = <float *>malloc(
- ngv * sizeof(float))
cdef int* field_ind = <int*> malloc(
nf * sizeof(int))
cdef np.float64_t **field_vals = <np.float64_t**> malloc(
@@ -1330,29 +1341,18 @@
# First we need to walk the mesh in the file. Then we fill in the dest
# location based on the file index.
cdef int filled = 0
- status = artio_grid_cache_sfc_range(handle,
- self.sfc_start, self.sfc_end )
- check_artio_status(status)
+ cdef float **mesh_data = self.range_handler.root_mesh_data
for sfc in range(self.sfc_start, self.sfc_end + 1):
if self.sfc_mask[sfc - self.sfc_start] == 0: continue
sfci += 1
if mask[sfci] == 0: continue
- status = artio_grid_read_root_cell_begin( handle, sfc,
- dpos, grid_variables, &num_oct_levels,
- num_octs_per_level)
- check_artio_status(status)
for i in range(nf):
- field_vals[i][filled] = grid_variables[field_ind[i]]
+ field_vals[i][filled] = mesh_data[field_ind[i]][
+ sfc - self.sfc_start]
filled += 1
- status = artio_grid_read_root_cell_end( handle )
- check_artio_status(status)
# Now we have all our sources.
- status = artio_grid_clear_sfc_cache(handle)
- check_artio_status(status)
free(field_ind)
free(field_vals)
- free(grid_variables)
- free(num_octs_per_level)
return tr
@cython.boundscheck(False)
https://bitbucket.org/yt_analysis/yt-3.0/commits/d596ac6902a5/
Changeset: d596ac6902a5
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-08 04:31:56
Summary: Making max_range_size a property of the parameter file.
Affected #: 1 file
diff -r 7f9535d0a16f4a3a4b60b5d40cd6b0da2e2c2a07 -r d596ac6902a5294c06a2f9a64a0bb338a3c62702 yt/frontends/artio/data_structures.py
--- a/yt/frontends/artio/data_structures.py
+++ b/yt/frontends/artio/data_structures.py
@@ -170,6 +170,10 @@
self.float_type = np.float64
super(ARTIOGeometryHandler, self).__init__(pf, data_style)
+ @property
+ def max_range(self):
+ return self.parameter_file.max_range
+
def _setup_geometry(self):
mylog.debug("Initializing Geometry Handler empty for now.")
@@ -244,14 +248,15 @@
nz = getattr(dobj, "_num_zones", 0)
if all_data:
mylog.debug("Selecting entire artio domain")
- list_sfc_ranges = self.pf._handle.root_sfc_ranges_all()
+ list_sfc_ranges = self.pf._handle.root_sfc_ranges_all(
+ max_range_size = self.max_range)
elif sfc_start is not None and sfc_end is not None:
mylog.debug("Restricting to %s .. %s", sfc_start, sfc_end)
list_sfc_ranges = [(sfc_start, sfc_end)]
else:
mylog.debug("Running selector on artio base grid")
list_sfc_ranges = self.pf._handle.root_sfc_ranges(
- dobj.selector)
+ dobj.selector, max_range_size = self.max_range)
ci = []
#v = np.array(list_sfc_ranges)
#list_sfc_ranges = [ (v.min(), v.max()) ]
@@ -327,6 +332,7 @@
_fieldinfo_known = KnownARTIOFields
_particle_mass_name = "particle_mass"
_particle_coordinates_name = "Coordinates"
+ max_range = 1024
def __init__(self, filename, data_style='artio',
storage_filename=None):
https://bitbucket.org/yt_analysis/yt-3.0/commits/4ea6055dd0a0/
Changeset: 4ea6055dd0a0
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-08 13:43:39
Summary: Parentheses result in bad allocation.
Affected #: 1 file
diff -r d596ac6902a5294c06a2f9a64a0bb338a3c62702 -r 4ea6055dd0a07519f96828c16b21a55572241129 yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -626,7 +626,7 @@
self.root_mesh_data = <float **>malloc(sizeof(float *) * ngv)
for i in range(ngv):
self.root_mesh_data[i] = <float *>malloc(sizeof(float) * \
- self.sfc_end - self.sfc_start + 1)
+ (self.sfc_end - self.sfc_start + 1))
# We want to pre-allocate an array of root pointers. In the future,
# this will be pre-determined by the ARTIO library. However, because
# realloc plays havoc with our tree searching, we can't utilize an
https://bitbucket.org/yt_analysis/yt-3.0/commits/b4b67d5c46f9/
Changeset: b4b67d5c46f9
Branch: yt-3.0
User: MatthewTurk
Date: 2013-10-08 14:17:05
Summary: Partial deallocation means we can't rely on artio_handle existing.
Affected #: 1 file
diff -r 4ea6055dd0a07519f96828c16b21a55572241129 -r b4b67d5c46f933a3b8e16c2c92bc6eeb68fd5c9b yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -566,6 +566,7 @@
cdef np.int64_t *doct_count
cdef np.int64_t **pcount
cdef float **root_mesh_data
+ cdef np.int64_t nvars[2]
def __init__(self, domain_dimensions, # cells
domain_left_edge,
@@ -584,6 +585,8 @@
self.root_mesh_data = NULL
self.pcount = <np.int64_t **> malloc(sizeof(np.int64_t*)
* artio_handle.num_species)
+ self.nvars[0] = artio_handle.num_species
+ self.nvars[1] = artio_handle.num_grid_variables
for i in range(artio_handle.num_species):
self.pcount[i] = <np.int64_t*> malloc(sizeof(np.int64_t)
* (self.sfc_end - self.sfc_start + 1))
@@ -597,9 +600,9 @@
def __dealloc__(self):
cdef int i
- for i in range(self.artio_handle.num_species):
+ for i in range(self.nvars[0]):
free(self.pcount[i])
- for i in range(self.artio_handle.num_grid_variables):
+ for i in range(self.nvars[1]):
free(self.root_mesh_data[i])
free(self.pcount)
free(self.root_mesh_data)
@@ -619,7 +622,7 @@
cdef int *num_particles_per_species = <int *>malloc(
sizeof(int)*num_species)
cdef ARTIOOctreeContainer octree
- ngv = self.artio_handle.num_grid_variables
+ ngv = self.nvars[1]
cdef float *grid_variables = <float *>malloc(
ngv * sizeof(float))
self.octree_handler = octree = ARTIOOctreeContainer(self)
https://bitbucket.org/yt_analysis/yt-3.0/commits/90e60994750b/
Changeset: 90e60994750b
Branch: yt-3.0
User: xarthisius
Date: 2013-10-09 13:57:26
Summary: Merged in MatthewTurk/yt-3.0 (pull request #111)
Add a few tests and fix errors in ARTIO that cropped up with this.
Affected #: 35 files
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -103,5 +103,8 @@
TwoPointFunctions, \
FcnSet
+from .sunyaev_zeldovich.api import SZProjection
+
from .radmc3d_export.api import \
RadMC3DWriter
+
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/analysis_modules/setup.py
--- a/yt/analysis_modules/setup.py
+++ b/yt/analysis_modules/setup.py
@@ -21,4 +21,5 @@
config.add_subpackage("star_analysis")
config.add_subpackage("two_point_functions")
config.add_subpackage("radmc3d_export")
+ config.add_subpackage("sunyaev_zeldovich")
return config
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/analysis_modules/sunyaev_zeldovich/api.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/api.py
@@ -0,0 +1,12 @@
+"""
+API for sunyaev_zeldovich
+"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from projection import SZProjection
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/analysis_modules/sunyaev_zeldovich/projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -0,0 +1,349 @@
+"""
+Projection class for the Sunyaev-Zeldovich effect. Requires SZpack (at least
+version 1.1.1) to be downloaded and installed:
+
+http://www.chluba.de/SZpack/
+
+For details on the computations involved please refer to the following references:
+
+Chluba, Nagai, Sazonov, Nelson, MNRAS, 2012, arXiv:1205.5778
+Chluba, Switzer, Nagai, Nelson, MNRAS, 2012, arXiv:1211.3206
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mh, Tcmb
+from yt.data_objects.image_array import ImageArray
+from yt.data_objects.field_info_container import add_field
+from yt.funcs import fix_axis, mylog, iterable, get_pbar
+from yt.utilities.definitions import inv_axis_names
+from yt.visualization.image_writer import write_fits, write_projection
+from yt.visualization.volume_rendering.camera import off_axis_projection
+from yt.utilities.parallel_tools.parallel_analysis_interface import \
+ communication_system, parallel_root_only
+import numpy as np
+
+I0 = 2*(kboltz*Tcmb)**3/((hcgs*clight)**2)*1.0e17
+
+try:
+ import SZpack
+except:
+ raise ImportError("SZpack not installed. It can be obtained from from http://www.chluba.de/SZpack/.")
+
+vlist = "xyz"
+
+def _t_squared(field, data):
+ return data["Density"]*data["TempkeV"]*data["TempkeV"]
+add_field("TSquared", function=_t_squared)
+
+def _beta_perp_squared(field, data):
+ return data["Density"]*data["VelocityMagnitude"]**2/clight/clight - data["BetaParSquared"]
+add_field("BetaPerpSquared", function=_beta_perp_squared)
+
+def _beta_par_squared(field, data):
+ return data["BetaPar"]**2/data["Density"]
+add_field("BetaParSquared", function=_beta_par_squared)
+
+def _t_beta_par(field, data):
+ return data["TempkeV"]*data["BetaPar"]
+add_field("TBetaPar", function=_t_beta_par)
+
+def _t_sz(field, data):
+ return data["Density"]*data["TempkeV"]
+add_field("TeSZ", function=_t_sz)
+
+class SZProjection(object):
+ r""" Initialize a SZProjection object.
+
+ Parameters
+ ----------
+ pf : parameter_file
+ The parameter file.
+ freqs : array_like
+ The frequencies (in GHz) at which to compute the SZ spectral distortion.
+ mue : float, optional
+ Mean molecular weight for determining the electron number density.
+ high_order : boolean, optional
+ Should we calculate high-order moments of velocity and temperature?
+
+ Examples
+ --------
+ >>> freqs = [90., 180., 240.]
+ >>> szprj = SZProjection(pf, freqs, high_order=True)
+ """
+ def __init__(self, pf, freqs, mue=1.143, high_order=False):
+
+ self.pf = pf
+ self.num_freqs = len(freqs)
+ self.high_order = high_order
+ self.freqs = np.array(freqs)
+ self.mueinv = 1./mue
+ self.xinit = hcgs*self.freqs*1.0e9/(kboltz*Tcmb)
+ self.freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
+ self.data = {}
+
+ self.units = {}
+ self.units["TeSZ"] = r"$\mathrm{keV}$"
+ self.units["Tau"] = None
+
+ self.display_names = {}
+ self.display_names["TeSZ"] = r"$\mathrm{T_e}$"
+ self.display_names["Tau"] = r"$\mathrm{\tau}$"
+
+ for f, field in zip(self.freqs, self.freq_fields):
+ self.units[field] = r"$\mathrm{MJy\ sr^{-1}}$"
+ self.display_names[field] = r"$\mathrm{\Delta{I}_{%d\ GHz}}$" % (int(f))
+
+ def on_axis(self, axis, center="c", width=(1, "unitary"), nx=800, source=None):
+ r""" Make an on-axis projection of the SZ signal.
+
+ Parameters
+ ----------
+ axis : integer or string
+ The axis of the simulation domain along which to make the SZprojection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+
+ Examples
+ --------
+ >>> szprj.on_axis("y", center="max", width=(1.0, "mpc"), source=my_sphere)
+ """
+ axis = fix_axis(axis)
+
+ def _beta_par(field, data):
+ axis = data.get_field_parameter("axis")
+ vpar = data["Density"]*data["%s-velocity" % (vlist[axis])]
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ proj = self.pf.h.proj(axis, "Density", source=source)
+ proj.set_field_parameter("axis", axis)
+ frb = proj.to_frb(width, nx)
+ dens = frb["Density"]
+ Te = frb["TeSZ"]/dens
+ bpar = frb["BetaPar"]/dens
+ omega1 = frb["TSquared"]/dens/(Te*Te) - 1.
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ if self.high_order:
+ bperp2 = frb["BetaPerpSquared"]/dens
+ sigma1 = frb["TBetaPar"]/dens/Te - bpar
+ kappa1 = frb["BetaParSquared"]/dens - bpar*bpar
+ tau = sigma_thompson*dens*self.mueinv/mh
+
+ nx,ny = frb.buff_size
+ self.bounds = frb.bounds
+ self.dx = (frb.bounds[1]-frb.bounds[0])/nx
+ self.dy = (frb.bounds[3]-frb.bounds[2])/ny
+ self.nx = nx
+
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
+
+ def off_axis(self, L, center="c", width=(1, "unitary"), nx=800, source=None):
+ r""" Make an off-axis projection of the SZ signal.
+
+ Parameters
+ ----------
+ L : array_like
+ The normal vector of the projection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+ Currently unsupported in yt 2.x.
+
+ Examples
+ --------
+ >>> L = np.array([0.5, 1.0, 0.75])
+ >>> szprj.off_axis(L, center="c", width=(2.0, "mpc"))
+ """
+ if iterable(width):
+ w = width[0]/self.pf.units[width[1]]
+ else:
+ w = width
+ if center == "c":
+ ctr = self.pf.domain_center
+ elif center == "max":
+ ctr = self.pf.h.find_max("Density")
+ else:
+ ctr = center
+
+ if source is not None:
+ mylog.error("Source argument is not currently supported for off-axis S-Z projections.")
+ raise NotImplementedError
+
+ def _beta_par(field, data):
+ vpar = data["Density"]*(data["x-velocity"]*L[0]+
+ data["y-velocity"]*L[1]+
+ data["z-velocity"]*L[2])
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ dens = off_axis_projection(self.pf, ctr, L, w, nx, "Density")
+ Te = off_axis_projection(self.pf, ctr, L, w, nx, "TeSZ")/dens
+ bpar = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPar")/dens
+ omega1 = off_axis_projection(self.pf, ctr, L, w, nx, "TSquared")/dens
+ omega1 = omega1/(Te*Te) - 1.
+ if self.high_order:
+ bperp2 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPerpSquared")/dens
+ sigma1 = off_axis_projection(self.pf, ctr, L, w, nx, "TBetaPar")/dens
+ sigma1 = sigma1/Te - bpar
+ kappa1 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaParSquared")/dens
+ kappa1 -= bpar
+ else:
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ tau = sigma_thompson*dens*self.mueinv/mh
+
+ self.bounds = np.array([-0.5*w, 0.5*w, -0.5*w, 0.5*w])
+ self.dx = w/nx
+ self.dy = w/nx
+ self.nx = nx
+
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
+
+ def _compute_intensity(self, tau, Te, bpar, omega1, sigma1, kappa1, bperp2):
+
+ # Bad hack, but we get NaNs if we don't do something like this
+ small_beta = np.abs(bpar) < 1.0e-20
+ bpar[small_beta] = 1.0e-20
+
+ comm = communication_system.communicators[-1]
+
+ nx, ny = self.nx,self.nx
+ signal = np.zeros((self.num_freqs,nx,ny))
+ xo = np.zeros((self.num_freqs))
+
+ k = int(0)
+
+ start_i = comm.rank*nx/comm.size
+ end_i = (comm.rank+1)*nx/comm.size
+
+ pbar = get_pbar("Computing SZ signal.", nx*nx)
+
+ for i in xrange(start_i, end_i):
+ for j in xrange(ny):
+ xo[:] = self.xinit[:]
+ SZpack.compute_combo_means(xo, tau[i,j], Te[i,j],
+ bpar[i,j], omega1[i,j],
+ sigma1[i,j], kappa1[i,j], bperp2[i,j])
+ signal[:,i,j] = xo[:]
+ pbar.update(k)
+ k += 1
+
+ signal = comm.mpi_allreduce(signal)
+
+ pbar.finish()
+
+ for i, field in enumerate(self.freq_fields):
+ self.data[field] = ImageArray(I0*self.xinit[i]**3*signal[i,:,:])
+ self.data["Tau"] = ImageArray(tau)
+ self.data["TeSZ"] = ImageArray(Te)
+
+ @parallel_root_only
+ def write_fits(self, filename_prefix, clobber=True):
+ r""" Export images to a FITS file. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the FITS filename.
+ clobber : boolean, optional
+ If the file already exists, do we overwrite?
+
+ Examples
+ --------
+ >>> szprj.write_fits("SZbullet", clobber=False)
+ """
+ coords = {}
+ coords["dx"] = self.dx*self.pf.units["kpc"]
+ coords["dy"] = self.dy*self.pf.units["kpc"]
+ coords["xctr"] = 0.0
+ coords["yctr"] = 0.0
+ coords["units"] = "kpc"
+ other_keys = {"Time" : self.pf.current_time}
+ write_fits(self.data, filename_prefix, clobber=clobber, coords=coords,
+ other_keys=other_keys)
+
+ @parallel_root_only
+ def write_png(self, filename_prefix):
+ r""" Export images to PNG files. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the image filenames.
+
+ Examples
+ --------
+ >>> szprj.write_png("SZsloshing")
+ """
+ extent = tuple([bound*self.pf.units["kpc"] for bound in self.bounds])
+ for field, image in self.items():
+ filename=filename_prefix+"_"+field+".png"
+ label = self.display_names[field]
+ if self.units[field] is not None:
+ label += " ("+self.units[field]+")"
+ write_projection(image, filename, colorbar_label=label, take_log=False,
+ extent=extent, xlabel=r"$\mathrm{x\ (kpc)}$",
+ ylabel=r"$\mathrm{y\ (kpc)}$")
+
+ @parallel_root_only
+ def write_hdf5(self, filename):
+ r"""Export the set of S-Z fields to a set of HDF5 datasets.
+
+ Parameters
+ ----------
+ filename : string
+ This file will be opened in "write" mode.
+
+ Examples
+ --------
+ >>> szprj.write_hdf5("SZsloshing.h5")
+ """
+ import h5py
+ f = h5py.File(filename, "w")
+ for field, data in self.items():
+ f.create_dataset(field,data=data)
+ f.close()
+
+ def keys(self):
+ return self.data.keys()
+
+ def items(self):
+ return self.data.items()
+
+ def values(self):
+ return self.data.values()
+
+ def has_key(self, key):
+ return key in self.data.keys()
+
+ def __getitem__(self, key):
+ return self.data[key]
+
+ @property
+ def shape(self):
+ return (self.nx,self.nx)
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/analysis_modules/sunyaev_zeldovich/setup.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/setup.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+import setuptools
+import os
+import sys
+import os.path
+
+
+def configuration(parent_package='', top_path=None):
+ from numpy.distutils.misc_util import Configuration
+ config = Configuration('sunyaev_zeldovich', parent_package, top_path)
+ config.add_subpackage("tests")
+ config.make_config_py() # installs __config__.py
+ #config.make_svn_version_py()
+ return config
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -0,0 +1,139 @@
+"""
+Unit test the sunyaev_zeldovich analysis module.
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.frontends.stream.api import load_uniform_grid
+from yt.funcs import get_pbar, mylog
+from yt.utilities.physical_constants import cm_per_kpc, K_per_keV, \
+ mh, cm_per_km, kboltz, Tcmb, hcgs, clight, sigma_thompson
+from yt.testing import *
+from yt.utilities.answer_testing.framework import requires_pf, \
+ GenericArrayTest, data_dir_load, GenericImageTest
+try:
+ from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
+except ImportError:
+ pass
+import numpy as np
+try:
+ import SZpack
+except ImportError:
+ pass
+
+mue = 1./0.88
+freqs = np.array([30., 90., 240.])
+
+def setup():
+ """Test specific setup."""
+ from yt.config import ytcfg
+ ytcfg["yt", "__withintesting"] = "True"
+
+def full_szpack3d(pf, xo):
+ data = pf.h.grids[0]
+ dz = pf.h.get_smallest_dx()*pf.units["cm"]
+ nx,ny,nz = data["Density"].shape
+ dn = np.zeros((nx,ny,nz))
+ Dtau = sigma_thompson*data["Density"]/(mh*mue)*dz
+ Te = data["Temperature"]/K_per_keV
+ betac = data["z-velocity"]/clight
+ pbar = get_pbar("Computing 3-D cell-by-cell S-Z signal for comparison.", nx)
+ for i in xrange(nx):
+ pbar.update(i)
+ for j in xrange(ny):
+ for k in xrange(nz):
+ dn[i,j,k] = SZpack.compute_3d(xo, Dtau[i,j,k],
+ Te[i,j,k], betac[i,j,k],
+ 1.0, 0.0, 0.0, 1.0e-5)
+ pbar.finish()
+ return I0*xo**3*np.sum(dn, axis=2)
+
+def setup_cluster():
+
+ R = 1000.
+ r_c = 100.
+ rho_c = 1.673e-26
+ beta = 1.
+ T0 = 4.
+ nx,ny,nz = 16,16,16
+ c = 0.17
+ a_c = 30.
+ a = 200.
+ v0 = 300.*cm_per_km
+ ddims = (nx,ny,nz)
+
+ x, y, z = np.mgrid[-R:R:nx*1j,
+ -R:R:ny*1j,
+ -R:R:nz*1j]
+
+ r = np.sqrt(x**2+y**2+z**2)
+
+ dens = np.zeros(ddims)
+ dens = rho_c*(1.+(r/r_c)**2)**(-1.5*beta)
+ temp = T0*K_per_keV/(1.+r/a)*(c+r/a_c)/(1.+r/a_c)
+ velz = v0*temp/(T0*K_per_keV)
+
+ data = {}
+ data["Density"] = dens
+ data["Temperature"] = temp
+ data["x-velocity"] = np.zeros(ddims)
+ data["y-velocity"] = np.zeros(ddims)
+ data["z-velocity"] = velz
+
+ bbox = np.array([[-0.5,0.5],[-0.5,0.5],[-0.5,0.5]])
+
+ L = 2*R*cm_per_kpc
+ dl = L/nz
+
+ pf = load_uniform_grid(data, ddims, L, bbox=bbox)
+
+ return pf
+
+ at requires_module("SZpack")
+def test_projection():
+ pf = setup_cluster()
+ nx,ny,nz = pf.domain_dimensions
+ xinit = 1.0e9*hcgs*freqs/(kboltz*Tcmb)
+ szprj = SZProjection(pf, freqs, mue=mue, high_order=True)
+ szprj.on_axis(2, nx=nx)
+ deltaI = np.zeros((3,nx,ny))
+ for i in xrange(3):
+ deltaI[i,:,:] = full_szpack3d(pf, xinit[i])
+ yield assert_almost_equal, deltaI[i,:,:], szprj["%d_GHz" % int(freqs[i])], 6
+
+M7 = "DD0010/moving7_0010"
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_onaxis():
+ pf = data_dir_load(M7)
+ szprj = SZProjection(pf, freqs)
+ szprj.on_axis(2, nx=100)
+ def onaxis_array_func():
+ return szprj.data
+ def onaxis_image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ for test in [GenericArrayTest(pf, onaxis_array_func),
+ GenericImageTest(pf, onaxis_image_func, 3)]:
+ test_M7_onaxis.__name__ = test.description
+ yield test
+
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_offaxis():
+ pf = data_dir_load(M7)
+ szprj = SZProjection(pf, freqs)
+ szprj.off_axis(np.array([0.1,-0.2,0.4]), nx=100)
+ def offaxis_array_func():
+ return szprj.data
+ def offaxis_image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ for test in [GenericArrayTest(pf, offaxis_array_func),
+ GenericImageTest(pf, offaxis_image_func, 3)]:
+ test_M7_offaxis.__name__ = test.description
+ yield test
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/analysis_modules/two_point_functions/two_point_functions.py
--- a/yt/analysis_modules/two_point_functions/two_point_functions.py
+++ b/yt/analysis_modules/two_point_functions/two_point_functions.py
@@ -498,7 +498,7 @@
points[:, 2] = points[:, 2] / self.period[2]
fKD.qv_many = points.T
fKD.nn_tags = np.asfortranarray(np.empty((1, points.shape[0]), dtype='int64'))
- find_many_nn_nearest_neighbors()
+ fKD.find_many_nn_nearest_neighbors()
# The -1 is for fortran counting.
n = fKD.nn_tags[0,:] - 1
return n
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/config.py
--- a/yt/config.py
+++ b/yt/config.py
@@ -52,7 +52,7 @@
notebook_password = '',
answer_testing_tolerance = '3',
answer_testing_bitwise = 'False',
- gold_standard_filename = 'gold310',
+ gold_standard_filename = 'gold311',
local_standard_filename = 'local001',
sketchfab_api_key = 'None',
thread_field_detection = 'False'
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/data_objects/octree_subset.py
--- a/yt/data_objects/octree_subset.py
+++ b/yt/data_objects/octree_subset.py
@@ -113,7 +113,7 @@
_domain_ind = None
def select_blocks(self, selector):
- mask = self.oct_handler.mask(selector)
+ mask = self.oct_handler.mask(selector, domain_id = self.domain_id)
mask = self._reshape_vals(mask)
slicer = OctreeSubsetBlockSlice(self)
for i, sl in slicer:
@@ -271,12 +271,14 @@
@property
def LeftEdge(self):
- LE = self._fcoords[0,0,0,self.ind,:] - self._fwidth[0,0,0,self.ind,:]*0.5
+ LE = (self._fcoords[0,0,0,self.ind,:]
+ - self._fwidth[0,0,0,self.ind,:])*0.5
return LE
@property
def RightEdge(self):
- RE = self._fcoords[1,1,1,self.ind,:] + self._fwidth[1,1,1,self.ind,:]*0.5
+ RE = (self._fcoords[-1,-1,-1,self.ind,:]
+ + self._fwidth[-1,-1,-1,self.ind,:])*0.5
return RE
@property
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -3,7 +3,8 @@
cimport numpy as np
import sys
-from yt.geometry.selection_routines cimport SelectorObject, AlwaysSelector
+from yt.geometry.selection_routines cimport \
+ SelectorObject, AlwaysSelector, OctreeSubsetSelector
from yt.utilities.lib.fp_utils cimport imax
from yt.geometry.oct_container cimport \
SparseOctreeContainer
@@ -122,7 +123,9 @@
void artio_sfc_coords( artio_fileset_handle *handle, int64_t index, int coords[3] ) nogil
cdef void check_artio_status(int status, char *fname="[unknown]"):
- if status!=ARTIO_SUCCESS :
+ if status != ARTIO_SUCCESS:
+ import traceback
+ traceback.print_stack()
callername = sys._getframe().f_code.co_name
nline = sys._getframe().f_lineno
raise RuntimeError('failure with status', status, 'in function',fname,'from caller', callername, nline)
@@ -487,8 +490,7 @@
return (fcoords, ires, data)
- def root_sfc_ranges_all(self) :
- cdef int max_range_size = 1024
+ def root_sfc_ranges_all(self, int max_range_size = 1024) :
cdef int64_t sfc_start, sfc_end
cdef artio_selection *selection
@@ -502,8 +504,8 @@
artio_selection_destroy(selection)
return sfc_ranges
- def root_sfc_ranges(self, SelectorObject selector) :
- cdef int max_range_size = 1024
+ def root_sfc_ranges(self, SelectorObject selector,
+ int max_range_size = 1024):
cdef int coords[3]
cdef int64_t sfc_start, sfc_end
cdef np.float64_t left[3]
@@ -561,6 +563,10 @@
cdef np.float64_t dds[3]
cdef np.int64_t dims[3]
cdef public np.int64_t total_octs
+ cdef np.int64_t *doct_count
+ cdef np.int64_t **pcount
+ cdef float **root_mesh_data
+ cdef np.int64_t nvars[2]
def __init__(self, domain_dimensions, # cells
domain_left_edge,
@@ -568,6 +574,7 @@
artio_fileset artio_handle,
sfc_start, sfc_end):
cdef int i
+ cdef np.int64_t sfc
self.sfc_start = sfc_start
self.sfc_end = sfc_end
self.artio_handle = artio_handle
@@ -575,25 +582,54 @@
self.octree_handler = None
self.handle = artio_handle.handle
self.oct_count = None
+ self.root_mesh_data = NULL
+ self.pcount = <np.int64_t **> malloc(sizeof(np.int64_t*)
+ * artio_handle.num_species)
+ self.nvars[0] = artio_handle.num_species
+ self.nvars[1] = artio_handle.num_grid_variables
+ for i in range(artio_handle.num_species):
+ self.pcount[i] = <np.int64_t*> malloc(sizeof(np.int64_t)
+ * (self.sfc_end - self.sfc_start + 1))
+ for sfc in range(self.sfc_end - self.sfc_start + 1):
+ self.pcount[i][sfc] = 0
for i in range(3):
self.dims[i] = domain_dimensions[i]
self.DLE[i] = domain_left_edge[i]
self.DRE[i] = domain_right_edge[i]
self.dds[i] = (self.DRE[i] - self.DLE[i])/self.dims[i]
+ def __dealloc__(self):
+ cdef int i
+ for i in range(self.nvars[0]):
+ free(self.pcount[i])
+ for i in range(self.nvars[1]):
+ free(self.root_mesh_data[i])
+ free(self.pcount)
+ free(self.root_mesh_data)
+
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def construct_mesh(self):
- cdef int status, level
- cdef np.int64_t sfc, oc
+ cdef int status, level, ngv
+ cdef np.int64_t sfc, oc, i
cdef double dpos[3]
cdef int num_oct_levels
cdef int max_level = self.artio_handle.max_level
cdef int *num_octs_per_level = <int *>malloc(
(max_level + 1)*sizeof(int))
+ cdef int num_species = self.artio_handle.num_species
+ cdef int *num_particles_per_species = <int *>malloc(
+ sizeof(int)*num_species)
cdef ARTIOOctreeContainer octree
+ ngv = self.nvars[1]
+ cdef float *grid_variables = <float *>malloc(
+ ngv * sizeof(float))
self.octree_handler = octree = ARTIOOctreeContainer(self)
+ self.root_mesh_data = <float **>malloc(sizeof(float *) * ngv)
+ for i in range(ngv):
+ self.root_mesh_data[i] = <float *>malloc(sizeof(float) * \
+ (self.sfc_end - self.sfc_start + 1))
# We want to pre-allocate an array of root pointers. In the future,
# this will be pre-determined by the ARTIO library. However, because
# realloc plays havoc with our tree searching, we can't utilize an
@@ -606,7 +642,11 @@
check_artio_status(status)
for sfc in range(self.sfc_start, self.sfc_end + 1):
status = artio_grid_read_root_cell_begin( self.handle,
- sfc, dpos, NULL, &num_oct_levels, num_octs_per_level)
+ sfc, dpos, grid_variables, &num_oct_levels,
+ num_octs_per_level)
+ for i in range(ngv):
+ self.root_mesh_data[i][sfc - self.sfc_start] = \
+ grid_variables[i]
check_artio_status(status)
if num_oct_levels > 0:
oc = 0
@@ -618,13 +658,39 @@
num_octs_per_level, sfc)
status = artio_grid_read_root_cell_end( self.handle )
check_artio_status(status)
+ status = artio_grid_clear_sfc_cache( self.handle)
+ check_artio_status(status)
+ # Now particles
+ status = artio_particle_cache_sfc_range(self.handle, self.sfc_start,
+ self.sfc_end)
+ check_artio_status(status)
+ for sfc in range(self.sfc_start, self.sfc_end + 1):
+ # Now particles
+ status = artio_particle_read_root_cell_begin( self.handle,
+ sfc, num_particles_per_species )
+ check_artio_status(status)
+
+ for i in range(num_species):
+ self.pcount[i][sfc - self.sfc_start] = \
+ num_particles_per_species[i]
+
+ status = artio_particle_read_root_cell_end( self.handle)
+ check_artio_status(status)
+
+ status = artio_particle_clear_sfc_cache( self.handle)
+ check_artio_status(status)
+
+ free(grid_variables)
free(num_octs_per_level)
+ free(num_particles_per_species)
+ self.oct_count = oct_count
+ self.doct_count = <np.int64_t *> oct_count.data
self.root_mesh_handler = ARTIORootMeshContainer(self)
- self.oct_count = oct_count
def free_mesh(self):
self.octree_handler = None
self.root_mesh_handler = None
+ self.doct_count = NULL
self.oct_count = None
def get_coords(artio_fileset handle, np.int64_t s):
@@ -661,9 +727,11 @@
# this, we will avoid creating it as long as possible.
cdef public artio_fileset artio_handle
+ cdef ARTIOSFCRangeHandler range_handler
cdef np.int64_t level_indices[32]
def __init__(self, ARTIOSFCRangeHandler range_handler):
+ self.range_handler = range_handler
self.artio_handle = range_handler.artio_handle
# Note the final argument is partial_coverage, which indicates whether
# or not an Oct can be partially refined.
@@ -781,6 +849,12 @@
# * Enable preloading during mesh initialization
# * Calculate domain indices on the fly rather than with a
# double-loop to calculate domain_counts
+ # The cons should be in order
+ cdef np.int64_t sfc_start, sfc_end
+ sfc_start = self.domains[0].con_id
+ sfc_end = self.domains[self.num_domains - 1].con_id
+ status = artio_grid_cache_sfc_range(handle, sfc_start, sfc_end )
+ check_artio_status(status)
cdef np.int64_t offset = 0
for si in range(self.num_domains):
sfc = self.domains[si].con_id
@@ -814,6 +888,8 @@
dest[i + offset] = source[oct_ind, cell_inds[i + offset]]
# Now, we offset by the actual number filled here.
offset += domain_counts[si]
+ status = artio_grid_clear_sfc_cache(handle)
+ check_artio_status(status)
free(field_ind)
free(field_vals)
free(grid_variables)
@@ -825,12 +901,18 @@
sfc_start = self.domains[0].con_id
sfc_end = self.domains[self.num_domains - 1].con_id
rv = read_sfc_particles(self.artio_handle, sfc_start, sfc_end,
- 0, fields)
+ 0, fields, self.range_handler.doct_count,
+ self.range_handler.pcount)
return rv
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+ at cython.cdivision(True)
cdef read_sfc_particles(artio_fileset artio_handle,
np.int64_t sfc_start, np.int64_t sfc_end,
- int read_unrefined, fields):
+ int read_unrefined, fields,
+ np.int64_t *doct_count,
+ np.int64_t **pcount):
cdef int status, ispec, subspecies
cdef np.int64_t sfc, particle, pid, ind, vind
cdef int num_species = artio_handle.num_species
@@ -876,32 +958,16 @@
vpoints[ispec].n_p = 0
vpoints[ispec].n_s = 0
- status = artio_particle_cache_sfc_range( handle,
- sfc_start, sfc_end )
- check_artio_status(status)
-
- # We cache so we can figure out if the cell is refined or not.
- status = artio_grid_cache_sfc_range(handle, sfc_start, sfc_end)
- check_artio_status(status)
-
# Pass through once. We want every single particle.
+ tp = 0
+ cdef np.int64_t c
for sfc in range(sfc_start, sfc_end + 1):
- status = artio_grid_read_root_cell_begin( handle,
- sfc, dpos, NULL, &num_oct_levels, num_octs_per_level)
- check_artio_status(status)
- status = artio_grid_read_root_cell_end(handle)
- check_artio_status(status)
- if read_unrefined == 1 and num_oct_levels > 0: continue
- if read_unrefined == 0 and num_oct_levels == 0: continue
- status = artio_particle_read_root_cell_begin( handle, sfc,
- num_particles_per_species )
- check_artio_status(status)
+ c = doct_count[sfc - sfc_start]
+ if read_unrefined == 1 and c > 0: continue
+ if read_unrefined == 0 and c == 0: continue
for ispec in range(num_species):
- total_particles[ispec] += num_particles_per_species[ispec]
-
- status = artio_particle_read_root_cell_end( handle )
- check_artio_status(status)
+ total_particles[ispec] += pcount[ispec][sfc - sfc_start]
# Now we allocate our final fields, which will be filled
#for ispec in range(num_species):
@@ -916,41 +982,52 @@
"species_%02u_secondary_variable_labels" % (species,), [])
tp = total_particles[species]
vp = &vpoints[species]
- if field == "MASS":
+ if field == "MASS" and params["particle_species_mass"][species] != 0.0:
vp.n_mass = 1
- npf64arr = data[(species, field)] = np.zeros(tp, dtype="float64")
+ data[(species, field)] = np.zeros(tp, dtype="float64")
+ npf64arr = data[(species, field)]
# We fill this *now*
npf64arr += params["particle_species_mass"][species]
vp.mass = <np.float64_t*> npf64arr.data
elif field == "PID":
vp.n_pid = 1
- npi64arr = data[(species, field)] = np.zeros(tp, dtype="int64")
+ data[(species, field)] = np.zeros(tp, dtype="int64")
+ npi64arr = data[(species, field)]
vp.pid = <np.int64_t*> npi64arr.data
elif field == "SPECIES":
vp.n_species = 1
- npi8arr = data[(species, field)] = np.zeros(tp, dtype="int8")
+ data[(species, field)] = np.zeros(tp, dtype="int8")
+ npi8arr = data[(species, field)]
# We fill this *now*
npi8arr += species
vp.species = <np.int8_t*> npi8arr.data
elif npri_vars[species] > 0 and field in pri_vars :
- npf64arr = data[(species, field)] = np.zeros(tp, dtype="float64")
+ data[(species, field)] = np.zeros(tp, dtype="float64")
+ npf64arr = data[(species, field)]
vp.p_ind[vp.n_p] = pri_vars.index(field)
vp.pvars[vp.n_p] = <np.float64_t *> npf64arr.data
vp.n_p += 1
elif nsec_vars[species] > 0 and field in sec_vars :
- npf64arr = data[(species, field)] = np.zeros(tp, dtype="float64")
+ data[(species, field)] = np.zeros(tp, dtype="float64")
+ npf64arr = data[(species, field)]
vp.s_ind[vp.n_s] = sec_vars.index(field)
vp.svars[vp.n_s] = <np.float64_t *> npf64arr.data
vp.n_s += 1
+ status = artio_particle_cache_sfc_range( handle,
+ sfc_start, sfc_end )
+ check_artio_status(status)
+
for sfc in range(sfc_start, sfc_end + 1):
- status = artio_grid_read_root_cell_begin( handle,
- sfc, dpos, NULL, &num_oct_levels, num_octs_per_level)
+ c = doct_count[sfc - sfc_start]
check_artio_status(status)
- status = artio_grid_read_root_cell_end(handle)
- check_artio_status(status)
- if read_unrefined == 1 and num_oct_levels > 0: continue
- if read_unrefined == 0 and num_oct_levels == 0: continue
+ if read_unrefined == 1 and c > 0: continue
+ if read_unrefined == 0 and c == 0: continue
+ c = 0
+ for ispec in range(num_species) :
+ if accessed_species[ispec] == 0: continue
+ c += pcount[ispec][sfc - sfc_start]
+ if c == 0: continue
status = artio_particle_read_root_cell_begin( handle, sfc,
num_particles_per_species )
check_artio_status(status)
@@ -986,11 +1063,8 @@
status = artio_particle_read_root_cell_end( handle )
check_artio_status(status)
- #status = artio_particle_clear_sfc_cache(handle)
- #check_artio_status(status)
-
- #status = artio_grid_clear_sfc_cache(handle)
- #check_artio_status(status)
+ status = artio_particle_clear_sfc_cache(handle)
+ check_artio_status(status)
free(num_octs_per_level)
free(num_particles_per_species)
@@ -1011,11 +1085,15 @@
cdef np.uint64_t sfc_start
cdef np.uint64_t sfc_end
cdef public object _last_mask
- cdef public object _last_selector_id
+ cdef public np.int64_t _last_selector_id
+ cdef np.int64_t _last_mask_sum
cdef ARTIOSFCRangeHandler range_handler
+ cdef np.uint8_t *sfc_mask
+ cdef np.int64_t nsfc
def __init__(self, ARTIOSFCRangeHandler range_handler):
cdef int i
+ cdef np.int64_t sfci
for i in range(3):
self.DLE[i] = range_handler.DLE[i]
self.DRE[i] = range_handler.DRE[i]
@@ -1023,10 +1101,27 @@
self.dds[i] = range_handler.dds[i]
self.handle = range_handler.handle
self.artio_handle = range_handler.artio_handle
- self._last_mask = self._last_selector_id = None
+ self._last_mask = None
+ self._last_selector_id = -1
self.sfc_start = range_handler.sfc_start
self.sfc_end = range_handler.sfc_end
self.range_handler = range_handler
+ # We assume that the number of octs has been created and filled
+ # already. We no longer care about ANY of the SFCs that have octs
+ # inside them -- this goes for every operation that this object
+ # performs.
+ self.sfc_mask = <np.uint8_t *>malloc(sizeof(np.uint8_t) *
+ self.sfc_end - self.sfc_start + 1)
+ self.nsfc = 0
+ for sfci in range(self.sfc_end - self.sfc_start + 1):
+ if self.range_handler.oct_count[sfci] > 0:
+ self.sfc_mask[sfci] = 0
+ else:
+ self.sfc_mask[sfci] = 1
+ self.nsfc += 1
+
+ def __dealloc__(self):
+ free(self.sfc_mask)
@cython.cdivision(True)
cdef np.int64_t pos_to_sfc(self, np.float64_t pos[3]) nogil:
@@ -1054,19 +1149,24 @@
cdef int i
return self.mask(selector).sum()
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def icoords(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
# Note that num_octs does not have to equal sfc_end - sfc_start + 1.
- cdef np.int64_t sfc
+ cdef np.int64_t sfc, sfci = -1
cdef int acoords[3], i
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
cdef np.ndarray[np.int64_t, ndim=2] coords
coords = np.empty((num_cells, 3), dtype="int64")
cdef int filled = 0
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if mask[sfc - self.sfc_start] == 0: continue
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0: continue
# Note that we do *no* checks on refinement here. In fact, this
# entire setup should not need to touch the disk except if the
# artio sfc calculators need to.
@@ -1076,20 +1176,25 @@
filled += 1
return coords
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def fcoords(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
# Note that num_cells does not have to equal sfc_end - sfc_start + 1.
- cdef np.int64_t sfc
+ cdef np.int64_t sfc, sfci = -1
cdef np.float64_t pos[3]
cdef int acoords[3], i
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
cdef np.ndarray[np.float64_t, ndim=2] coords
coords = np.empty((num_cells, 3), dtype="float64")
cdef int filled = 0
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if mask[sfc - self.sfc_start] == 0: continue
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0: continue
# Note that we do *no* checks on refinement here. In fact, this
# entire setup should not need to touch the disk except if the
# artio sfc calculators need to.
@@ -1099,23 +1204,29 @@
filled += 1
return coords
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def fwidth(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
cdef int i
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
cdef np.ndarray[np.float64_t, ndim=2] width
width = np.zeros((num_cells, 3), dtype="float64")
for i in range(3):
width[:,i] = self.dds[i]
return width
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def ires(self, SelectorObject selector, np.int64_t num_cells = -1,
int domain_id = -1):
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
cdef np.ndarray[np.int64_t, ndim=1] res
res = np.zeros(num_cells, dtype="int64")
return res
@@ -1132,7 +1243,7 @@
# other. Note that we *do* apply the selector here.
cdef np.int64_t num_cells = -1
cdef np.int64_t ind
- cdef np.int64_t sfc
+ cdef np.int64_t sfc, sfci = -1
cdef np.float64_t pos[3]
cdef np.float64_t dpos[3]
cdef int dim, status, filled = 0
@@ -1149,7 +1260,7 @@
# Note that RAMSES can have partial refinement inside an Oct. This
# means we actually do want the number of Octs, not the number of
# cells.
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
if dims > 1:
dest = np.zeros((num_cells, dims), dtype=source.dtype,
order='C')
@@ -1158,7 +1269,9 @@
ddata = (<char*>dest.data) + offset*ss*dims
ind = 0
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if mask[sfc - self.sfc_start] == 0: continue
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0: continue
memcpy(ddata, sdata + ind, dims * ss)
ddata += dims * ss
filled += 1
@@ -1170,56 +1283,55 @@
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
- def mask(self, SelectorObject selector, np.int64_t num_cells = -1):
+ def mask(self, SelectorObject selector, np.int64_t num_cells = -1,
+ int domain_id = -1):
+ # We take a domain_id here to avoid subclassing
cdef int i
cdef np.float64_t pos[3]
- cdef np.int64_t sfc
- cdef np.ndarray[np.int64_t, ndim=1] oct_count
+ cdef np.int64_t sfc, sfci = -1
if self._last_selector_id == hash(selector):
return self._last_mask
- if num_cells == -1:
- # We need to count, but this process will only occur one time,
- # since num_cells will later be cached.
- num_cells = self.sfc_end - self.sfc_start + 1
- mask = np.zeros((num_cells), dtype="uint8")
- oct_count = self.range_handler.oct_count
+ cdef np.ndarray[np.uint8_t, ndim=1] mask
+ mask = np.zeros((self.nsfc), dtype="uint8")
+ self._last_mask_sum = 0
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if oct_count[sfc - self.sfc_start] > 0: continue
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
self.sfc_to_pos(sfc, pos)
if selector.select_cell(pos, self.dds) == 0: continue
- mask[sfc - self.sfc_start] = 1
+ mask[sfci] = 1
+ self._last_mask_sum += 1
self._last_mask = mask.astype("bool")
self._last_selector_id = hash(selector)
return self._last_mask
+
def fill_sfc_particles(self, fields):
rv = read_sfc_particles(self.artio_handle,
self.sfc_start, self.sfc_end,
- 1, fields)
+ 1, fields, self.range_handler.doct_count,
+ self.range_handler.pcount)
return rv
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def fill_sfc(self, SelectorObject selector, field_indices):
cdef np.ndarray[np.float64_t, ndim=1] dest
cdef int n, status, i, di, num_oct_levels, nf, ngv, max_level
- cdef np.int64_t sfc, num_cells
+ cdef np.int64_t sfc, num_cells, sfci = -1
cdef np.float64_t val
- cdef artio_fileset_handle *handle = self.artio_handle.handle
cdef double dpos[3]
# We duplicate some of the grid_variables stuff here so that we can
# potentially release the GIL
nf = len(field_indices)
ngv = self.artio_handle.num_grid_variables
- max_level = self.artio_handle.max_level
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector, -1)
- num_cells = mask.sum()
+ num_cells = self._last_mask_sum
tr = []
for i in range(nf):
tr.append(np.zeros(num_cells, dtype="float64"))
- cdef int *num_octs_per_level = <int *>malloc(
- (max_level + 1)*sizeof(int))
- cdef float *grid_variables = <float *>malloc(
- ngv * sizeof(float))
cdef int* field_ind = <int*> malloc(
nf * sizeof(int))
cdef np.float64_t **field_vals = <np.float64_t**> malloc(
@@ -1232,29 +1344,23 @@
# First we need to walk the mesh in the file. Then we fill in the dest
# location based on the file index.
cdef int filled = 0
- status = artio_grid_cache_sfc_range(handle,
- self.sfc_start, self.sfc_end )
- check_artio_status(status)
+ cdef float **mesh_data = self.range_handler.root_mesh_data
for sfc in range(self.sfc_start, self.sfc_end + 1):
- if mask[sfc - self.sfc_start] == 0: continue
- status = artio_grid_read_root_cell_begin( handle, sfc,
- dpos, grid_variables, &num_oct_levels,
- num_octs_per_level)
- check_artio_status(status)
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0: continue
for i in range(nf):
- field_vals[i][filled] = grid_variables[field_ind[i]]
+ field_vals[i][filled] = mesh_data[field_ind[i]][
+ sfc - self.sfc_start]
filled += 1
- status = artio_grid_read_root_cell_end( handle )
- check_artio_status(status)
# Now we have all our sources.
- #status = artio_grid_clear_sfc_cache(handle)
- #check_artio_status(status)
free(field_ind)
free(field_vals)
- free(grid_variables)
- free(num_octs_per_level)
return tr
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
def deposit(self, ParticleDepositOperation pdeposit,
SelectorObject selector,
np.ndarray[np.float64_t, ndim=2] positions,
@@ -1262,21 +1368,26 @@
# This implements the necessary calls to enable particle deposition to
# occur as needed.
cdef int nf, i, j
+ cdef np.int64_t sfc, sfci
if fields is None:
fields = []
nf = len(fields)
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector, -1)
cdef np.ndarray[np.int64_t, ndim=1] domain_ind
- domain_ind = np.zeros(mask.shape[0], dtype="int64") - 1
+ domain_ind = np.zeros(self.sfc_end - self.sfc_start + 1,
+ dtype="int64") - 1
j = 0
- for i in range(mask.shape[0]):
- if mask[i] == 1:
- domain_ind[i] = j
- j += 1
+ sfci = -1
+ for sfc in range(self.sfc_start, self.sfc_end + 1):
+ if self.sfc_mask[sfc - self.sfc_start] == 0: continue
+ sfci += 1
+ if mask[sfci] == 0:
+ continue
+ domain_ind[sfc - self.sfc_start] = j
+ j += 1
cdef np.float64_t **field_pointers, *field_vals, pos[3], left_edge[3]
cdef int coords[3]
- cdef np.int64_t sfc
cdef np.ndarray[np.float64_t, ndim=1] tarr
field_pointers = <np.float64_t**> alloca(sizeof(np.float64_t *) * nf)
field_vals = <np.float64_t*>alloca(sizeof(np.float64_t) * nf)
@@ -1306,5 +1417,72 @@
for j in range(nf):
field_pointers[j][i] = field_vals[j]
+cdef class SFCRangeSelector(SelectorObject):
+
+ cdef SelectorObject base_selector
+ cdef ARTIOSFCRangeHandler range_handler
+ cdef ARTIORootMeshContainer mesh_container
+ cdef np.int64_t sfc_start, sfc_end
+
+ def __init__(self, dobj):
+ self.base_selector = dobj.base_selector
+ self.mesh_container = dobj.oct_handler
+ self.range_handler = self.mesh_container.range_handler
+ self.sfc_start = self.mesh_container.sfc_start
+ self.sfc_end = self.mesh_container.sfc_end
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ def select_grids(self,
+ np.ndarray[np.float64_t, ndim=2] left_edges,
+ np.ndarray[np.float64_t, ndim=2] right_edges,
+ np.ndarray[np.int32_t, ndim=2] levels):
+ raise RuntimeError
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_sphere(self, np.float64_t pos[3], np.float64_t radius) nogil:
+ return 1
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_cell(self, np.float64_t pos[3], np.float64_t dds[3]) nogil:
+ return self.select_point(pos)
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_point(self, np.float64_t pos[3]) nogil:
+ cdef np.int64_t sfc = self.mesh_container.pos_to_sfc(pos)
+ if sfc > self.sfc_end: return 0
+ cdef np.int64_t oc = self.range_handler.doct_count[
+ sfc - self.sfc_start]
+ if oc > 0: return 0
+ return 1
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_bbox(self, np.float64_t left_edge[3],
+ np.float64_t right_edge[3]) nogil:
+ return self.base_selector.select_bbox(left_edge, right_edge)
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int select_grid(self, np.float64_t left_edge[3],
+ np.float64_t right_edge[3], np.int32_t level,
+ Oct *o = NULL) nogil:
+ # Because visitors now use select_grid, we should be explicitly
+ # checking this.
+ return self.base_selector.select_grid(left_edge, right_edge, level, o)
+
+ def _hash_vals(self):
+ return (hash(self.base_selector), self.sfc_start, self.sfc_end)
+
sfc_subset_selector = AlwaysSelector
+#sfc_subset_selector = SFCRangeSelector
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/artio/data_structures.py
--- a/yt/frontends/artio/data_structures.py
+++ b/yt/frontends/artio/data_structures.py
@@ -72,6 +72,7 @@
return self.sfc_end
def fill(self, fields, selector):
+ if len(fields) == 0: return []
handle = self.oct_handler.artio_handle
field_indices = [handle.parameters["grid_variable_labels"].index(
yt_to_art[f]) for (ft, f) in fields]
@@ -88,6 +89,7 @@
return tr
def fill_particles(self, fields):
+ if len(fields) == 0: return {}
art_fields = []
for s, f in fields:
fn = yt_to_art[f]
@@ -127,6 +129,7 @@
def fill(self, fields, selector):
# We know how big these will be.
+ if len(fields) == 0: return []
handle = self.pf._handle
field_indices = [handle.parameters["grid_variable_labels"].index(
yt_to_art[f]) for (ft, f) in fields]
@@ -167,6 +170,10 @@
self.float_type = np.float64
super(ARTIOGeometryHandler, self).__init__(pf, data_style)
+ @property
+ def max_range(self):
+ return self.parameter_file.max_range
+
def _setup_geometry(self):
mylog.debug("Initializing Geometry Handler empty for now.")
@@ -241,15 +248,18 @@
nz = getattr(dobj, "_num_zones", 0)
if all_data:
mylog.debug("Selecting entire artio domain")
- list_sfc_ranges = self.pf._handle.root_sfc_ranges_all()
+ list_sfc_ranges = self.pf._handle.root_sfc_ranges_all(
+ max_range_size = self.max_range)
elif sfc_start is not None and sfc_end is not None:
mylog.debug("Restricting to %s .. %s", sfc_start, sfc_end)
list_sfc_ranges = [(sfc_start, sfc_end)]
else:
mylog.debug("Running selector on artio base grid")
list_sfc_ranges = self.pf._handle.root_sfc_ranges(
- dobj.selector)
+ dobj.selector, max_range_size = self.max_range)
ci = []
+ #v = np.array(list_sfc_ranges)
+ #list_sfc_ranges = [ (v.min(), v.max()) ]
for (start, end) in list_sfc_ranges:
range_handler = ARTIOSFCRangeHandler(
self.pf.domain_dimensions,
@@ -322,6 +332,7 @@
_fieldinfo_known = KnownARTIOFields
_particle_mass_name = "particle_mass"
_particle_coordinates_name = "Coordinates"
+ max_range = 1024
def __init__(self, filename, data_style='artio',
storage_filename=None):
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/artio/tests/test_outputs.py
--- a/yt/frontends/artio/tests/test_outputs.py
+++ b/yt/frontends/artio/tests/test_outputs.py
@@ -19,7 +19,8 @@
requires_pf, \
data_dir_load, \
PixelizedProjectionValuesTest, \
- FieldValuesTest
+ FieldValuesTest, \
+ create_obj
from yt.frontends.artio.api import ARTIOStaticOutput
_fields = ("Temperature", "Density", "VelocityMagnitude",
@@ -31,12 +32,15 @@
pf = data_dir_load(sizmbhloz)
yield assert_equal, str(pf), "sizmbhloz-clref04SNth-rs9_a0.9011.art"
dso = [ None, ("sphere", ("max", (0.1, 'unitary')))]
- for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
for weight_field in [None, "Density"]:
yield PixelizedProjectionValuesTest(
sizmbhloz, axis, field, weight_field,
ds)
- yield FieldValuesTest(
- sizmbhloz, field, ds)
+ yield FieldValuesTest(sizmbhloz, field, ds)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
+ yield assert_equal, s1, s2
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/chombo/tests/test_outputs.py
--- a/yt/frontends/chombo/tests/test_outputs.py
+++ b/yt/frontends/chombo/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(gc)
yield assert_equal, str(pf), "data.0077.3d.hdf5"
for test in small_patch_amr(gc, _fields):
+ test_gc.__name__ = test.description
yield test
tb = "TurbBoxLowRes/data.0005.3d.hdf5"
@@ -37,4 +38,5 @@
pf = data_dir_load(tb)
yield assert_equal, str(pf), "data.0005.3d.hdf5"
for test in small_patch_amr(tb, _fields):
+ test_tb.__name__ = test.description
yield test
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/enzo/tests/test_outputs.py
--- a/yt/frontends/enzo/tests/test_outputs.py
+++ b/yt/frontends/enzo/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(m7)
yield assert_equal, str(pf), "moving7_0010"
for test in small_patch_amr(m7, _fields):
+ test_moving7.__name__ = test.description
yield test
g30 = "IsolatedGalaxy/galaxy0030/galaxy0030"
@@ -37,4 +38,5 @@
pf = data_dir_load(g30)
yield assert_equal, str(pf), "galaxy0030"
for test in big_patch_amr(g30, _fields):
+ test_galaxy0030.__name__ = test.description
yield test
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/flash/tests/test_outputs.py
--- a/yt/frontends/flash/tests/test_outputs.py
+++ b/yt/frontends/flash/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(sloshing)
yield assert_equal, str(pf), "sloshing_low_res_hdf5_plt_cnt_0300"
for test in small_patch_amr(sloshing, _fields):
+ test_sloshing.__name__ = test.description
yield test
_fields_2d = ("Temperature", "Density")
@@ -39,4 +40,5 @@
pf = data_dir_load(wt)
yield assert_equal, str(pf), "windtunnel_4lev_hdf5_plt_cnt_0030"
for test in small_patch_amr(wt, _fields_2d):
+ test_wind_tunnel.__name__ = test.description
yield test
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/moab/tests/test_c5.py
--- a/yt/frontends/moab/tests/test_c5.py
+++ b/yt/frontends/moab/tests/test_c5.py
@@ -49,7 +49,6 @@
ray = pf.h.ray(p1, p2)
yield assert_almost_equal, ray["dts"].sum(dtype="float64"), 1.0, 8
for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
- yield FieldValuesTest(c5, field, ds)
+ for ds in dso:
+ yield FieldValuesTest(c5, field, ds)
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/orion/tests/test_outputs.py
--- a/yt/frontends/orion/tests/test_outputs.py
+++ b/yt/frontends/orion/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(radadvect)
yield assert_equal, str(pf), "plt00000"
for test in small_patch_amr(radadvect, _fields):
+ test_radadvect.__name__ = test.description
yield test
rt = "RadTube/plt00500"
@@ -37,4 +38,5 @@
pf = data_dir_load(rt)
yield assert_equal, str(pf), "plt00500"
for test in small_patch_amr(rt, _fields):
+ test_radtube.__name__ = test.description
yield test
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/ramses/tests/test_outputs.py
--- a/yt/frontends/ramses/tests/test_outputs.py
+++ b/yt/frontends/ramses/tests/test_outputs.py
@@ -19,7 +19,8 @@
requires_pf, \
data_dir_load, \
PixelizedProjectionValuesTest, \
- FieldValuesTest
+ FieldValuesTest, \
+ create_obj
from yt.frontends.artio.api import ARTIOStaticOutput
_fields = ("Temperature", "Density", "VelocityMagnitude",
@@ -31,13 +32,15 @@
pf = data_dir_load(output_00080)
yield assert_equal, str(pf), "info_00080"
dso = [ None, ("sphere", ("max", (0.1, 'unitary')))]
- for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
for weight_field in [None, "Density"]:
yield PixelizedProjectionValuesTest(
output_00080, axis, field, weight_field,
ds)
- yield FieldValuesTest(
- output_00080, field, ds)
-
+ yield FieldValuesTest(output_00080, field, ds)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
+ yield assert_equal, s1, s2
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/sph/data_structures.py
--- a/yt/frontends/sph/data_structures.py
+++ b/yt/frontends/sph/data_structures.py
@@ -436,7 +436,10 @@
self._unit_base = unit_base or {}
self._cosmology_parameters = cosmology_parameters
+ if parameter_file is not None:
+ parameter_file = os.path.abspath(parameter_file)
self._param_file = parameter_file
+ filename = os.path.abspath(filename)
super(TipsyStaticOutput, self).__init__(filename, data_style)
def __repr__(self):
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/sph/tests/test_owls.py
--- a/yt/frontends/sph/tests/test_owls.py
+++ b/yt/frontends/sph/tests/test_owls.py
@@ -21,7 +21,8 @@
big_patch_amr, \
data_dir_load, \
PixelizedProjectionValuesTest, \
- FieldValuesTest
+ FieldValuesTest, \
+ create_obj
from yt.frontends.sph.api import OWLSStaticOutput
_fields = (("deposit", "all_density"), ("deposit", "all_count"),
@@ -40,13 +41,15 @@
tot = sum(dd[ptype,"Coordinates"].shape[0]
for ptype in pf.particle_types if ptype != "all")
yield assert_equal, tot, (2*128*128*128)
- for field in _fields:
- for axis in [0, 1, 2]:
- for ds in dso:
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
for weight_field in [None, "Density"]:
yield PixelizedProjectionValuesTest(
os33, axis, field, weight_field,
ds)
- yield FieldValuesTest(
- os33, field, ds)
-
+ yield FieldValuesTest(os33, field, ds)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
+ yield assert_equal, s1, s2
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/frontends/sph/tests/test_tipsy.py
--- /dev/null
+++ b/yt/frontends/sph/tests/test_tipsy.py
@@ -0,0 +1,95 @@
+"""
+Tipsy tests using the AGORA dataset
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.testing import *
+from yt.utilities.answer_testing.framework import \
+ requires_pf, \
+ small_patch_amr, \
+ big_patch_amr, \
+ data_dir_load, \
+ PixelizedProjectionValuesTest, \
+ FieldValuesTest, \
+ create_obj
+from yt.frontends.sph.api import TipsyStaticOutput
+
+_fields = (("deposit", "all_density"),
+ ("deposit", "all_count"),
+ ("deposit", "DarkMatter_density"),
+)
+
+pkdgrav = "halo1e11_run1.00400/halo1e11_run1.00400"
+ at requires_pf(pkdgrav, file_check = True)
+def test_pkdgrav():
+ cosmology_parameters = dict(current_redshift = 0.0,
+ omega_lambda = 0.728,
+ omega_matter = 0.272,
+ hubble_constant = 0.702)
+ kwargs = dict(endian="<",
+ field_dtypes = {"Coordinates": "d"},
+ cosmology_parameters = cosmology_parameters,
+ unit_base = {'mpchcm': 1.0/60.0},
+ n_ref = 64)
+ pf = data_dir_load(pkdgrav, TipsyStaticOutput, (), kwargs)
+ yield assert_equal, str(pf), "halo1e11_run1.00400"
+ dso = [ None, ("sphere", ("c", (0.3, 'unitary')))]
+ dd = pf.h.all_data()
+ yield assert_equal, dd["Coordinates"].shape, (26847360, 3)
+ tot = sum(dd[ptype,"Coordinates"].shape[0]
+ for ptype in pf.particle_types if ptype != "all")
+ yield assert_equal, tot, 26847360
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
+ for weight_field in [None, "Density"]:
+ yield PixelizedProjectionValuesTest(
+ pf, axis, field, weight_field,
+ ds)
+ yield FieldValuesTest(pf, field, ds)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
+ yield assert_equal, s1, s2
+
+gasoline = "agora_1e11.00400/agora_1e11.00400"
+ at requires_pf(gasoline, file_check = True)
+def test_gasoline():
+ cosmology_parameters = dict(current_redshift = 0.0,
+ omega_lambda = 0.728,
+ omega_matter = 0.272,
+ hubble_constant = 0.702)
+ kwargs = dict(cosmology_parameters = cosmology_parameters,
+ unit_base = {'mpchcm': 1.0/60.0},
+ n_ref = 64)
+ pf = data_dir_load(gasoline, TipsyStaticOutput, (), kwargs)
+ yield assert_equal, str(pf), "agora_1e11.00400"
+ dso = [ None, ("sphere", ("c", (0.3, 'unitary')))]
+ dd = pf.h.all_data()
+ yield assert_equal, dd["Coordinates"].shape, (10550576, 3)
+ tot = sum(dd[ptype,"Coordinates"].shape[0]
+ for ptype in pf.particle_types if ptype != "all")
+ yield assert_equal, tot, 10550576
+ for ds in dso:
+ for field in _fields:
+ for axis in [0, 1, 2]:
+ for weight_field in [None, "Density"]:
+ yield PixelizedProjectionValuesTest(
+ pf, axis, field, weight_field,
+ ds)
+ yield FieldValuesTest(pf, field, ds)
+ dobj = create_obj(pf, ds)
+ s1 = dobj["Ones"].sum()
+ s2 = sum(mask.sum() for block, mask in dobj.blocks)
+ yield assert_equal, s1, s2
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/gui/reason/extdirect_router.py
--- a/yt/gui/reason/extdirect_router.py
+++ b/yt/gui/reason/extdirect_router.py
@@ -9,6 +9,13 @@
This code was released under the BSD License.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import inspect
class DirectException(Exception):
@@ -186,12 +193,4 @@
-"""
-#-----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -14,6 +14,7 @@
import itertools as it
import numpy as np
+import importlib
from yt.funcs import *
from numpy.testing import assert_array_equal, assert_almost_equal, \
assert_approx_equal, assert_array_almost_equal, assert_equal, \
@@ -252,3 +253,23 @@
list_of_kwarg_dicts[i][key] = keywords[key][0]
return list_of_kwarg_dicts
+
+def requires_module(module):
+ """
+ Decorator that takes a module name as an argument and tries to import it.
+ If the module imports without issue, the function is returned, but if not,
+ a null function is returned. This is so tests that depend on certain modules
+ being imported will not fail if the module is not installed on the testing
+ platform.
+ """
+ def ffalse(func):
+ return lambda: None
+ def ftrue(func):
+ return func
+ try:
+ importlib.import_module(module)
+ except ImportError:
+ return ffalse
+ else:
+ return ftrue
+
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -24,6 +24,7 @@
import shelve
import zlib
import tempfile
+import glob
from matplotlib.testing.compare import compare_images
from nose.plugins import Plugin
@@ -252,26 +253,34 @@
yield
os.chdir(oldcwd)
-def can_run_pf(pf_fn):
+def can_run_pf(pf_fn, file_check = False):
if isinstance(pf_fn, StaticOutput):
return AnswerTestingTest.result_storage is not None
path = ytcfg.get("yt", "test_data_dir")
if not os.path.isdir(path):
return False
with temp_cwd(path):
+ if file_check:
+ return os.path.isfile(pf_fn) and \
+ AnswerTestingTest.result_storage is not None
try:
load(pf_fn)
except YTOutputNotIdentified:
return False
return AnswerTestingTest.result_storage is not None
-def data_dir_load(pf_fn):
+def data_dir_load(pf_fn, cls = None, args = None, kwargs = None):
path = ytcfg.get("yt", "test_data_dir")
if isinstance(pf_fn, StaticOutput): return pf_fn
if not os.path.isdir(path):
return False
with temp_cwd(path):
- pf = load(pf_fn)
+ if cls is None:
+ pf = load(pf_fn)
+ else:
+ args = args or ()
+ kwargs = kwargs or {}
+ pf = cls(pf_fn, *args, **kwargs)
pf.h
return pf
@@ -313,15 +322,6 @@
def compare(self, new_result, old_result):
raise RuntimeError
- def create_obj(self, pf, obj_type):
- # obj_type should be tuple of
- # ( obj_name, ( args ) )
- if obj_type is None:
- return pf.h.all_data()
- cls = getattr(pf.h, obj_type[0])
- obj = cls(*obj_type[1])
- return obj
-
def create_plot(self, pf, plot_type, plot_field, plot_axis, plot_kwargs = None):
# plot_type should be a string
# plot_args should be a tuple
@@ -377,7 +377,7 @@
self.decimals = decimals
def run(self):
- obj = self.create_obj(self.pf, self.obj_type)
+ obj = create_obj(self.pf, self.obj_type)
avg = obj.quantities["WeightedAverageQuantity"](self.field,
weight="Ones")
(mi, ma), = obj.quantities["Extrema"](self.field)
@@ -404,7 +404,7 @@
self.decimals = decimals
def run(self):
- obj = self.create_obj(self.pf, self.obj_type)
+ obj = create_obj(self.pf, self.obj_type)
return obj[self.field]
def compare(self, new_result, old_result):
@@ -431,7 +431,7 @@
def run(self):
if self.obj_type is not None:
- obj = self.create_obj(self.pf, self.obj_type)
+ obj = create_obj(self.pf, self.obj_type)
else:
obj = None
if self.pf.domain_dimensions[self.axis] == 1: return None
@@ -472,7 +472,7 @@
def run(self):
if self.obj_type is not None:
- obj = self.create_obj(self.pf, self.obj_type)
+ obj = create_obj(self.pf, self.obj_type)
else:
obj = None
proj = self.pf.h.proj(self.field, self.axis,
@@ -577,6 +577,16 @@
for newc, oldc in zip(new_result["children"], old_result["children"]):
assert(newp == oldp)
+def compare_image_lists(new_result, old_result, decimals):
+ fns = ['old.png', 'new.png']
+ num_images = len(old_result)
+ assert(num_images > 0)
+ for i in xrange(num_images):
+ mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[i])))
+ mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[i])))
+ assert compare_images(fns[0], fns[1], 10**(decimals)) == None
+ for fn in fns: os.remove(fn)
+
class PlotWindowAttributeTest(AnswerTestingTest):
_type_name = "PlotWindowAttribute"
_attrs = ('plot_type', 'plot_field', 'plot_axis', 'attr_name', 'attr_args')
@@ -604,20 +614,80 @@
return [zlib.compress(image.dumps())]
def compare(self, new_result, old_result):
- fns = ['old.png', 'new.png']
- mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[0])))
- mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[0])))
- assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
- for fn in fns: os.remove(fn)
+ compare_image_lists(new_result, old_result, self.decimals)
-def requires_pf(pf_fn, big_data = False):
+class GenericArrayTest(AnswerTestingTest):
+ _type_name = "GenericArray"
+ _attrs = ('array_func_name','args','kwargs')
+ def __init__(self, pf_fn, array_func, args=None, kwargs=None, decimals=None):
+ super(GenericArrayTest, self).__init__(pf_fn)
+ self.array_func = array_func
+ self.array_func_name = array_func.func_name
+ self.args = args
+ self.kwargs = kwargs
+ self.decimals = decimals
+ def run(self):
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
+ return self.array_func(*args, **kwargs)
+ def compare(self, new_result, old_result):
+ assert_equal(len(new_result), len(old_result),
+ err_msg="Number of outputs not equal.",
+ verbose=True)
+ for k in new_result:
+ if self.decimals is None:
+ assert_equal(new_result[k], old_result[k])
+ else:
+ assert_allclose(new_result[k], old_result[k], 10**(-self.decimals))
+
+class GenericImageTest(AnswerTestingTest):
+ _type_name = "GenericImage"
+ _attrs = ('image_func_name','args','kwargs')
+ def __init__(self, pf_fn, image_func, decimals, args=None, kwargs=None):
+ super(GenericImageTest, self).__init__(pf_fn)
+ self.image_func = image_func
+ self.image_func_name = image_func.func_name
+ self.args = args
+ self.kwargs = kwargs
+ self.decimals = decimals
+ def run(self):
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
+ comp_imgs = []
+ tmpdir = tempfile.mkdtemp()
+ image_prefix = os.path.join(tmpdir,"test_img")
+ self.image_func(image_prefix, *args, **kwargs)
+ imgs = glob.glob(image_prefix+"*")
+ assert(len(imgs) > 0)
+ for img in imgs:
+ img_data = mpimg.imread(img)
+ os.remove(img)
+ comp_imgs.append(zlib.compress(img_data.dumps()))
+ return comp_imgs
+ def compare(self, new_result, old_result):
+ compare_image_lists(new_result, old_result, self.decimals)
+
+
+def requires_pf(pf_fn, big_data = False, file_check = False):
def ffalse(func):
return lambda: None
def ftrue(func):
return func
if run_big_data == False and big_data == True:
return ffalse
- elif not can_run_pf(pf_fn):
+ elif not can_run_pf(pf_fn, file_check):
return ffalse
else:
return ftrue
@@ -652,6 +722,15 @@
pf_fn, axis, field, weight_field,
ds)
+def create_obj(pf, obj_type):
+ # obj_type should be tuple of
+ # ( obj_name, ( args ) )
+ if obj_type is None:
+ return pf.h.all_data()
+ cls = getattr(pf.h, obj_type[0])
+ obj = cls(*obj_type[1])
+ return obj
+
class AssertWrapper(object):
"""
Used to wrap a numpy testing assertion, in order to provide a useful name
diff -r 55bffcd057e21b219fdb8f1091b4ca66d8ec8591 -r 90e60994750b95e412851f6174d3087a0377b5af yt/utilities/physical_constants.py
--- a/yt/utilities/physical_constants.py
+++ b/yt/utilities/physical_constants.py
@@ -84,6 +84,7 @@
erg_per_keV = erg_per_eV * 1.0e3
K_per_keV = erg_per_keV / boltzmann_constant_cgs
keV_per_K = 1.0 / K_per_keV
+Tcmb = 2.726 # Current CMB temperature
#Short cuts
G = gravitational_constant_cgs
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/yt_analysis/yt-3.0/
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