[yt-svn] commit/yt: 30 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Oct 2 03:10:39 PDT 2013
30 new commits in yt:
https://bitbucket.org/yt_analysis/yt/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/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/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/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/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/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/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 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
- Preamble
-
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-software and other kinds of works.
-
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-share and change all versions of a program--to make sure it remains free
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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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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):
"""
Repository URL: https://bitbucket.org/yt_analysis/yt/
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