[yt-svn] commit/yt: 4 new changesets
Bitbucket
commits-noreply at bitbucket.org
Thu Nov 8 07:29:26 PST 2012
4 new commits in yt:
https://bitbucket.org/yt_analysis/yt/changeset/1575fdb073cb/
changeset: 1575fdb073cb
branch: yt
user: samskillman
date: 2012-11-07 21:29:55
summary: Some upgrades for the fixed resolution buffer and image array.
affected #: 1 file
diff -r 3972786cc04e9e66747a2f49196675e45ee66408 -r 1575fdb073cb3ca41e5fb424e0823623cf550df8 yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -407,8 +407,9 @@
self.data_source[item],
self.buff_size[0], self.buff_size[1],
self.bounds).transpose()
- self[item] = buff
- return buff
+ ia = ImageArray(buff, info=self._get_info(item))
+ self[item] = ia
+ return ia
class OffAxisProjectionFixedResolutionBuffer(FixedResolutionBuffer):
@@ -430,7 +431,8 @@
weight=ds.weight_field, volume=ds.volume,
no_ghost=ds.no_ghost, interpolated=ds.interpolated,
north_vector=ds.north_vector)
- self[item] = buff.swapaxes(0,1)
- return buff
+ ia = ImageArray(buff.swapaxes(0,1), info=self._get_info(item))
+ self[item] = ia
+ return ia
https://bitbucket.org/yt_analysis/yt/changeset/e5fabbeb8385/
changeset: e5fabbeb8385
branch: yt
user: samskillman
date: 2012-11-08 05:38:42
summary: Adding assert_allclose for testing.
affected #: 1 file
diff -r 1575fdb073cb3ca41e5fb424e0823623cf550df8 -r e5fabbeb838531c827baa5acf54e2b4aaed84785 yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -26,7 +26,8 @@
from yt.funcs import *
from numpy.testing import assert_array_equal, assert_almost_equal, \
assert_approx_equal, assert_array_almost_equal, assert_equal, \
- assert_array_less, assert_string_equal, assert_array_almost_equal_nulp
+ assert_array_less, assert_string_equal, assert_array_almost_equal_nulp,\
+ assert_allclose
def assert_rel_equal(a1, a2, decimals):
# We have nan checks in here because occasionally we have fields that get
https://bitbucket.org/yt_analysis/yt/changeset/ced3cc36250b/
changeset: ced3cc36250b
branch: yt
user: samskillman
date: 2012-11-08 05:39:11
summary: Merging
affected #: 9 files
diff -r e5fabbeb838531c827baa5acf54e2b4aaed84785 -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 yt/frontends/enzo/simulation_handling.py
--- a/yt/frontends/enzo/simulation_handling.py
+++ b/yt/frontends/enzo/simulation_handling.py
@@ -478,7 +478,7 @@
self.parameters['TopGridRank'] = 3
self.parameters['DomainLeftEdge'] = np.zeros(self.parameters['TopGridRank'])
self.parameters['DomainRightEdge'] = np.ones(self.parameters['TopGridRank'])
- self.parameters['Refineby'] = 2 # technically not the enzo default
+ self.parameters['RefineBy'] = 2 # technically not the enzo default
self.parameters['StopCycle'] = 100000
self.parameters['dtDataDump'] = 0.
self.parameters['CycleSkipDataDump'] = 0.
diff -r e5fabbeb838531c827baa5acf54e2b4aaed84785 -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 yt/frontends/flash/fields.py
--- a/yt/frontends/flash/fields.py
+++ b/yt/frontends/flash/fields.py
@@ -99,8 +99,8 @@
add_field(fn1.split("_")[0] + "_Density",
function=_get_density(fn1), take_log=True,
display_name="%s\/Density" % fn1.split("_")[0],
- units = r"\rm{g}/\rm{cm}^3",
- projected_units = r"\rm{g}/\rm{cm}^2",
+ units = r"\rm{g}/\rm{cm}^{3}",
+ projected_units = r"\rm{g}/\rm{cm}^{2}",
)
def _get_convert(fname):
@@ -110,8 +110,8 @@
add_flash_field("dens", function=NullFunc, take_log=True,
convert_function=_get_convert("dens"),
- units=r"\rm{g}/\rm{cm}^3",
- projected_units = r"\rm{g}/\rm{cm}^2"),
+ units=r"\rm{g}/\rm{cm}^{3}",
+ projected_units = r"\rm{g}/\rm{cm}^{2}"),
add_flash_field("velx", function=NullFunc, take_log=False,
convert_function=_get_convert("velx"),
units=r"\rm{cm}/\rm{s}")
@@ -159,10 +159,10 @@
units = r"\rm{K}")
add_flash_field("pres", function=NullFunc, take_log=True,
convert_function=_get_convert("pres"),
- units=r"\rm{erg}\//\/\rm{cm}^{3}")
+ units=r"\rm{erg}/\rm{cm}^{3}")
add_flash_field("pden", function=NullFunc, take_log=True,
convert_function=_get_convert("pden"),
- units=r"\rm{g}/\rm{cm}^3")
+ units=r"\rm{g}/\rm{cm}^{3}")
add_flash_field("magx", function=NullFunc, take_log=False,
convert_function=_get_convert("magx"),
units = r"\mathrm{Gau\ss}")
@@ -174,7 +174,7 @@
units = r"\mathrm{Gau\ss}")
add_flash_field("magp", function=NullFunc, take_log=True,
convert_function=_get_convert("magp"),
- units = r"\rm{erg}\//\/\rm{cm}^{3}")
+ units = r"\rm{erg}/\rm{cm}^{3}")
add_flash_field("divb", function=NullFunc, take_log=False,
convert_function=_get_convert("divb"),
units = r"\mathrm{Gau\ss}\/\rm{cm}")
@@ -186,10 +186,10 @@
units=r"\rm{ratio\/of\/specific\/heats}")
add_flash_field("gpot", function=NullFunc, take_log=False,
convert_function=_get_convert("gpot"),
- units=r"\rm{ergs\//\/g}")
+ units=r"\rm{ergs}/\rm{g}")
add_flash_field("gpol", function=NullFunc, take_log=False,
convert_function=_get_convert("gpol"),
- units = r"\rm{ergs\//\/g}")
+ units = r"\rm{ergs}/\rm{g}")
add_flash_field("flam", function=NullFunc, take_log=False,
convert_function=_get_convert("flam"))
diff -r e5fabbeb838531c827baa5acf54e2b4aaed84785 -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 yt/frontends/stream/api.py
--- a/yt/frontends/stream/api.py
+++ b/yt/frontends/stream/api.py
@@ -29,7 +29,8 @@
StreamHierarchy, \
StreamStaticOutput, \
StreamHandler, \
- load_uniform_grid
+ load_uniform_grid, \
+ load_amr_grids
from .fields import \
KnownStreamFields, \
diff -r e5fabbeb838531c827baa5acf54e2b4aaed84785 -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -395,3 +395,103 @@
for unit in mpc_conversion.keys():
spf.units[unit] = mpc_conversion[unit] * box_in_mpc
return spf
+
+def load_amr_grids(grid_data, domain_dimensions, sim_unit_to_cm, bbox=None,
+ sim_time=0.0, number_of_particles=0):
+ r"""Load a set of grids of data into yt as a
+ :class:`~yt.frontends.stream.data_structures.StreamHandler`.
+
+ This should allow a sequence of grids of varying resolution of data to be
+ loaded directly into yt and analyzed as would any others. This comes with
+ several caveats:
+ * Units will be incorrect unless the data has already been converted to
+ cgs.
+ * Some functions may behave oddly, and parallelism will be
+ disappointing or non-existent in most cases.
+ * Particles may be difficult to integrate.
+ * No consistency checks are performed on the hierarchy
+
+ Parameters
+ ----------
+ grid_data : list of dicts
+ This is a list of dicts. Each dict must have entries "left_edge",
+ "right_edge", "dimensions", "level", and then any remaining entries are
+ assumed to be fields. This will be modified in place and can't be
+ assumed to be static..
+ domain_dimensions : array_like
+ This is the domain dimensions of the grid
+ sim_unit_to_cm : float
+ Conversion factor from simulation units to centimeters
+ bbox : array_like (xdim:zdim, LE:RE), optional
+ Size of computational domain in units sim_unit_to_cm
+ sim_time : float, optional
+ The simulation time in seconds
+ number_of_particles : int, optional
+ If particle fields are included, set this to the number of particles
+
+ Examples
+ --------
+
+ >>> grid_data = [
+ ... dict(left_edge = [0.0, 0.0, 0.0],
+ ... right_edge = [1.0, 1.0, 1.],
+ ... level = 0,
+ ... dimensions = [32, 32, 32]),
+ ... dict(left_edge = [0.25, 0.25, 0.25],
+ ... right_edge = [0.75, 0.75, 0.75],
+ ... level = 1,
+ ... dimensions = [32, 32, 32])
+ ... ]
+ ...
+ >>> for g in grid_data:
+ ... g["Density"] = np.random.random(g["dimensions"]) * 2**g["level"]
+ ...
+ >>> pf = load_amr_grids(grid_data, [32, 32, 32], 1.0)
+ """
+
+ domain_dimensions = np.array(domain_dimensions)
+ ngrids = len(grid_data)
+ if bbox is None:
+ bbox = np.array([[0.0, 1.0], [0.0, 1.0], [0.0, 1.0]], 'float64')
+ domain_left_edge = np.array(bbox[:, 0], 'float64')
+ domain_right_edge = np.array(bbox[:, 1], 'float64')
+ grid_levels = np.zeros((ngrids, 1), dtype='int32')
+ grid_left_edges = np.zeros((ngrids, 3), dtype="float32")
+ grid_right_edges = np.zeros((ngrids, 3), dtype="float32")
+ grid_dimensions = np.zeros((ngrids, 3), dtype="int32")
+ sfh = StreamDictFieldHandler()
+ for i, g in enumerate(grid_data):
+ grid_left_edges[i,:] = g.pop("left_edge")
+ grid_right_edges[i,:] = g.pop("right_edge")
+ grid_dimensions[i,:] = g.pop("dimensions")
+ grid_levels[i,:] = g.pop("level")
+ sfh[i] = g
+
+ handler = StreamHandler(
+ grid_left_edges,
+ grid_right_edges,
+ grid_dimensions,
+ grid_levels,
+ None, # parent_ids is none
+ number_of_particles*np.ones(ngrids, dtype='int64').reshape(ngrids,1),
+ np.zeros(ngrids).reshape((ngrids,1)),
+ sfh,
+ )
+
+ handler.name = "AMRGridData"
+ handler.domain_left_edge = domain_left_edge
+ handler.domain_right_edge = domain_right_edge
+ handler.refine_by = 2
+ handler.dimensionality = 3
+ handler.domain_dimensions = domain_dimensions
+ handler.simulation_time = sim_time
+ handler.cosmology_simulation = 0
+
+ spf = StreamStaticOutput(handler)
+ spf.units["cm"] = sim_unit_to_cm
+ spf.units['1'] = 1.0
+ spf.units["unitary"] = 1.0
+ box_in_mpc = sim_unit_to_cm / mpc_conversion['cm']
+ for unit in mpc_conversion.keys():
+ spf.units[unit] = mpc_conversion[unit] * box_in_mpc
+ return spf
diff -r e5fabbeb838531c827baa5acf54e2b4aaed84785 -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -23,6 +23,7 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+import __builtin__
import time, types, signal, inspect, traceback, sys, pdb, os
import contextlib
import warnings, struct, subprocess
@@ -310,7 +311,7 @@
maxval = max(maxval, 1)
from yt.config import ytcfg
if ytcfg.getboolean("yt", "suppressStreamLogging") or \
- ytcfg.getboolean("yt", "ipython_notebook") or \
+ "__IPYTHON__" in dir(__builtin__) or \
ytcfg.getboolean("yt", "__withintesting"):
return DummyProgressBar()
elif ytcfg.getboolean("yt", "__withinreason"):
diff -r e5fabbeb838531c827baa5acf54e2b4aaed84785 -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -34,6 +34,7 @@
from yt.testing import *
from yt.config import ytcfg
from yt.mods import *
+from yt.data_objects.static_output import StaticOutput
import cPickle
from yt.utilities.logger import disable_stream_logging
@@ -75,6 +76,8 @@
ytcfg["yt","__withintesting"] = "True"
AnswerTestingTest.result_storage = \
self.result_storage = defaultdict(dict)
+ if options.compare_name == "SKIP":
+ options.compare_name = None
if options.compare_name is not None:
# Now we grab from our S3 store
if options.compare_name == "latest":
@@ -132,6 +135,8 @@
def can_run_pf(pf_fn):
path = ytcfg.get("yt", "test_data_dir")
+ if isinstance(pf_fn, StaticOutput):
+ return AnswerTestingTest.result_storage is not None
with temp_cwd(path):
try:
load(pf_fn)
@@ -141,26 +146,44 @@
def data_dir_load(pf_fn):
path = ytcfg.get("yt", "test_data_dir")
+ if isinstance(pf_fn, StaticOutput): return pf_fn
with temp_cwd(path):
pf = load(pf_fn)
pf.h
return pf
+def sim_dir_load(sim_fn, path = None, sim_type = "Enzo",
+ find_outputs=False):
+ if path is None and not os.path.exists(sim_fn):
+ raise IOError
+ if os.path.exists(sim_fn) or not path:
+ path = "."
+ with temp_cwd(path):
+ return simulation(sim_fn, sim_type,
+ find_outputs=find_outputs)
+
class AnswerTestingTest(object):
reference_storage = None
+ prefix = ""
def __init__(self, pf_fn):
self.pf = data_dir_load(pf_fn)
def __call__(self):
nv = self.run()
if self.reference_storage is not None:
- dd = self.reference_storage.get(str(self.pf))
+ dd = self.reference_storage.get(self.storage_name)
if dd is None: raise YTNoOldAnswer()
ov = dd[self.description]
self.compare(nv, ov)
else:
ov = None
- self.result_storage[str(self.pf)][self.description] = nv
+ self.result_storage[self.storage_name][self.description] = nv
+
+ @property
+ def storage_name(self):
+ if self.prefix != "":
+ return "%s_%s" % (self.prefix, self.pf)
+ return str(self.pf)
def compare(self, new_result, old_result):
raise RuntimeError
@@ -312,6 +335,22 @@
for k in new_result:
assert_equal(new_result[k], old_result[k])
+class VerifySimulationSameTest(AnswerTestingTest):
+ _type_name = "VerifySimulationSame"
+ _attrs = ()
+
+ def __init__(self, simulation_obj):
+ self.pf = simulation_obj
+
+ def run(self):
+ result = [ds.current_time for ds in self.pf]
+ return result
+
+ def compare(self, new_result, old_result):
+ assert_equal(len(new_result), len(old_result))
+ for i in range(len(new_result)):
+ assert_equal(new_result[i], old_result[i])
+
class GridHierarchyTest(AnswerTestingTest):
_type_name = "GridHierarchy"
_attrs = ()
@@ -353,6 +392,25 @@
for newc, oldc in zip(new_result["children"], old_result["children"]):
assert(newp == oldp)
+def requires_outputlog(path = ".", prefix = ""):
+ def ffalse(func):
+ return lambda: None
+ def ftrue(func):
+ @wraps(func)
+ def fyielder(*args, **kwargs):
+ with temp_cwd(path):
+ for t in func(*args, **kwargs):
+ if isinstance(t, AnswerTestingTest):
+ t.prefix = prefix
+ yield t
+ return fyielder
+ if os.path.exists("OutputLog"):
+ return ftrue
+ with temp_cwd(path):
+ if os.path.exists("OutputLog"):
+ return ftrue
+ return ffalse
+
def requires_pf(pf_fn, big_data = False):
def ffalse(func):
return lambda: None
diff -r e5fabbeb838531c827baa5acf54e2b4aaed84785 -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 yt/utilities/parallel_tools/parallel_analysis_interface.py
--- a/yt/utilities/parallel_tools/parallel_analysis_interface.py
+++ b/yt/utilities/parallel_tools/parallel_analysis_interface.py
@@ -581,7 +581,9 @@
ncols, size = data.shape
ncols = self.comm.allreduce(ncols, op=MPI.MAX)
if ncols == 0:
- data = np.zeros(0, dtype=dtype) # This only works for
+ data = np.zeros(0, dtype=dtype) # This only works for
+ elif data is None:
+ data = np.zeros((ncols, 0), dtype=dtype)
size = data.shape[-1]
sizes = np.zeros(self.comm.size, dtype='int64')
outsize = np.array(size, dtype='int64')
@@ -1058,3 +1060,49 @@
nextdim = (nextdim + 1) % 3
return cuts
+class GroupOwnership(ParallelAnalysisInterface):
+ def __init__(self, items):
+ ParallelAnalysisInterface.__init__(self)
+ self.num_items = len(items)
+ self.items = items
+ assert(self.num_items >= self.comm.size)
+ self.owned = range(self.comm.size)
+ self.pointer = 0
+ if parallel_capable:
+ communication_system.push_with_ids([self.comm.rank])
+
+ def __del__(self):
+ if parallel_capable:
+ communication_system.pop()
+
+ def inc(self, n = -1):
+ old_item = self.item
+ if n == -1: n = self.comm.size
+ for i in range(n):
+ if self.pointer >= self.num_items - self.comm.size: break
+ self.owned[self.pointer % self.comm.size] += self.comm.size
+ self.pointer += 1
+ if self.item is not old_item:
+ self.switch()
+
+ def dec(self, n = -1):
+ old_item = self.item
+ if n == -1: n = self.comm.size
+ for i in range(n):
+ if self.pointer == 0: break
+ self.owned[(self.pointer - 1) % self.comm.size] -= self.comm.size
+ self.pointer -= 1
+ if self.item is not old_item:
+ self.switch()
+
+ _last = None
+ @property
+ def item(self):
+ own = self.owned[self.comm.rank]
+ if self._last != own:
+ self._item = self.items[own]
+ self._last = own
+ return self._item
+
+ def switch(self):
+ pass
diff -r e5fabbeb838531c827baa5acf54e2b4aaed84785 -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -375,12 +375,10 @@
class StreamlineCallback(PlotCallback):
_type_name = "streamlines"
def __init__(self, field_x, field_y, factor = 16,
- density = 1, arrowsize = 1, arrowstyle = None,
- color = None, normalize = False):
+ density = 1, plot_args=None):
"""
- annotate_streamlines(field_x, field_y, factor = 16, density = 1,
- arrowsize = 1, arrowstyle = None,
- color = None, normalize = False):
+ annotate_streamlines(field_x, field_y, factor = 16,
+ density = 1, plot_args=None):
Add streamlines to any plot, using the *field_x* and *field_y*
from the associated data, skipping every *factor* datapoints like
@@ -392,12 +390,8 @@
self.bv_x = self.bv_y = 0
self.factor = factor
self.dens = density
- self.arrowsize = arrowsize
- if arrowstyle is None : arrowstyle='-|>'
- self.arrowstyle = arrowstyle
- if color is None : color = "#000000"
- self.color = color
- self.normalize = normalize
+ if plot_args is None: plot_args = {}
+ self.plot_args = plot_args
def __call__(self, plot):
x0, x1 = plot.xlim
@@ -421,15 +415,10 @@
plot.data[self.field_y] - self.bv_y,
int(nx), int(ny),
(x0, x1, y0, y1),).transpose()
- X,Y = (na.linspace(xx0,xx1,nx,endpoint=True),
- na.linspace(yy0,yy1,ny,endpoint=True))
- if self.normalize:
- nn = na.sqrt(pixX**2 + pixY**2)
- pixX /= nn
- pixY /= nn
- plot._axes.streamplot(X,Y, pixX, pixY, density=self.dens,
- arrowsize=self.arrowsize, arrowstyle=self.arrowstyle,
- color=self.color, norm=self.normalize)
+ X,Y = (np.linspace(xx0,xx1,nx,endpoint=True),
+ np.linspace(yy0,yy1,ny,endpoint=True))
+ plot._axes.streamplot(X,Y, pixX, pixY, density = self.dens,
+ **self.plot_args)
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
plot._axes.hold(False)
@@ -743,13 +732,18 @@
self.plot_args = plot_args
def __call__(self, plot):
- if len(self.pos) == 3:
+ xx0, xx1 = plot._axes.get_xlim()
+ yy0, yy1 = plot._axes.get_ylim()
+ if np.array(self.pos).shape == (3,):
pos = (self.pos[x_dict[plot.data.axis]],
self.pos[y_dict[plot.data.axis]])
- else: pos = self.pos
+ elif np.array(self.pos).shape == (2,):
+ pos = self.pos
x,y = self.convert_to_plot(plot, pos)
plot._axes.hold(True)
- plot._axes.plot((x,),(y,),self.marker, **self.plot_args)
+ plot._axes.scatter(x,y, marker = self.marker, **self.plot_args)
+ plot._axes.set_xlim(xx0,xx1)
+ plot._axes.set_ylim(yy0,yy1)
plot._axes.hold(False)
class SphereCallback(PlotCallback):
@@ -815,6 +809,7 @@
def __call__(self, plot):
from matplotlib.patches import Circle
+ num = len(self.hop_output[:self.max_number])
for halo in self.hop_output[:self.max_number]:
size = halo.get_size()
if size < self.min_size or size > self.max_size: continue
@@ -831,18 +826,19 @@
(xi, yi) = (x_dict[plot.data.axis], y_dict[plot.data.axis])
(center_x,center_y) = self.convert_to_plot(plot,(center[xi], center[yi]))
- cir = Circle((center_x, center_y), radius, fill=False)
+ color = np.ones(3) * (0.4 * (num - halo.id)/ num) + 0.6
+ cir = Circle((center_x, center_y), radius, fill=False, color=color)
plot._axes.add_patch(cir)
if self.annotate:
if self.print_halo_size:
- plot._axes.text(center_x, center_y, "%s" % size,
- fontsize=self.font_size)
+ plot._axes.text(center_x+radius, center_y+radius, "%s" % size,
+ fontsize=self.font_size, color=color)
elif self.print_halo_mass:
- plot._axes.text(center_x, center_y, "%s" % halo.total_mass(),
- fontsize=self.font_size)
+ plot._axes.text(center_x+radius, center_y+radius, "%s" % halo.total_mass(),
+ fontsize=self.font_size, color=color)
else:
- plot._axes.text(center_x, center_y, "%s" % halo.id,
- fontsize=self.font_size)
+ plot._axes.text(center_x+radius, center_y+radius, "%s" % halo.id,
+ fontsize=self.font_size, color=color)
class HopParticleCallback(PlotCallback):
_type_name = "hop_particles"
@@ -1174,41 +1170,59 @@
'kev': 1e-12 * 7.6e-8 / 6.03,
'mev': 1e-15 * 7.6e-8 / 6.03,
}
+ _bbox_dict = {'boxstyle': 'square,pad=0.6', 'fc': 'white', 'ec': 'black', 'alpha': 1.0}
- def __init__(self, x, y, units=None, format="{time:.3G} {units}", **kwargs):
+ def __init__(self, x, y, units=None, format="{time:.3G} {units}", normalized=False,
+ bbox_dict=None, **kwargs):
"""
- annotate_timestamp(x, y, units=None, format="{time:.3G} {units}", **kwargs)
+ annotate_timestamp(x, y, units=None, format="{time:.3G} {units}", **kwargs,
+ normalized=False, bbox_dict=None)
Adds the current time to the plot at point given by *x* and *y*. If *units*
is given ('s', 'ms', 'ns', etc), it will covert the time to this basis. If
*units* is None, it will attempt to figure out the correct value by which to
scale. The *format* keyword is a template string that will be evaluated and
- displayed on the plot. All other *kwargs* will be passed to the text()
- method on the plot axes. See matplotlib's text() functions for more
- information.
+ displayed on the plot. If *normalized* is true, *x* and *y* are interpreted
+ as normalized plot coordinates (0,0 is lower-left and 1,1 is upper-right)
+ otherwise *x* and *y* are assumed to be in plot coordinates. The *bbox_dict*
+ is an optional dict of arguments for the bbox that frames the timestamp, see
+ matplotlib's text annotation guide for more details. All other *kwargs* will
+ be passed to the text() method on the plot axes. See matplotlib's text()
+ functions for more information.
"""
self.x = x
self.y = y
self.format = format
self.units = units
+ self.normalized = normalized
+ if bbox_dict is not None:
+ self.bbox_dict = bbox_dict
+ else:
+ self.bbox_dict = self._bbox_dict
self.kwargs = {'color': 'w'}
self.kwargs.update(kwargs)
def __call__(self, plot):
if self.units is None:
- t = plot.data.pf.current_time
+ t = plot.data.pf.current_time * plot.data.pf['Time']
scale_keys = ['as', 'fs', 'ps', 'ns', 'us', 'ms', 's']
self.units = 's'
for k in scale_keys:
if t < self._time_conv[k]:
break
self.units = k
- t = plot.data.pf.current_time / self._time_conv[self.units.lower()]
+ t = plot.data.pf.current_time * plot.data.pf['Time']
+ t /= self._time_conv[self.units.lower()]
if self.units == 'us':
self.units = '$\\mu s$'
s = self.format.format(time=t, units=self.units)
plot._axes.hold(True)
- plot._axes.text(self.x, self.y, s, **self.kwargs)
+ if self.normalized:
+ plot._axes.text(self.x, self.y, s, horizontalalignment='center',
+ verticalalignment='center',
+ transform = plot._axes.transAxes, bbox=self.bbox_dict)
+ else:
+ plot._axes.text(self.x, self.y, s, bbox=self.bbox_dict, **self.kwargs)
plot._axes.hold(False)
diff -r e5fabbeb838531c827baa5acf54e2b4aaed84785 -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -60,6 +60,10 @@
axis_labels
from yt.utilities.math_utils import \
ortho_find
+from yt.utilities.parallel_tools.parallel_analysis_interface import \
+ GroupOwnership
+from yt.data_objects.time_series import \
+ TimeSeriesData
def invalidate_data(f):
@wraps(f)
@@ -239,6 +243,10 @@
rendering is used during data deposition.
"""
+ if not hasattr(self, "pf"):
+ self.pf = data_source.pf
+ ts = self._initialize_dataset(self.pf)
+ self.ts = ts
self._initfinished = False
self.center = None
self.plots = {}
@@ -254,6 +262,34 @@
self.set_center(center)
self._initfinished = True
+ def _initialize_dataset(self, ts):
+ if not isinstance(ts, TimeSeriesData):
+ if not iterable(ts): ts = [ts]
+ ts = TimeSeriesData(ts)
+ return ts
+
+ def __iter__(self):
+ for pf in self.ts:
+ mylog.warning("Switching to %s", pf)
+ self._switch_pf(pf)
+ yield self
+
+ def piter(self, *args, **kwargs):
+ for pf in self.ts.piter(*args, **kwargs):
+ self._switch_pf(pf)
+ yield self
+
+ def _switch_pf(self, new_pf):
+ ds = self.data_source
+ name = ds._type_name
+ kwargs = dict((n, getattr(ds, n)) for n in ds._con_args)
+ new_ds = getattr(new_pf.h, name)(**kwargs)
+ self.pf = new_pf
+ self.data_source = new_ds
+ self._data_valid = self._plot_valid = False
+ self._recreate_frb()
+ self._setup_plots()
+
def __getitem__(self, item):
return self.plots[item]
@@ -273,7 +309,6 @@
self._frb._get_data_source_fields()
else:
for key in old_fields: self._frb[key]
- self.pf = self._frb.pf
self._data_valid = True
def _setup_plots(self):
@@ -783,14 +818,13 @@
except ParseFatalException, err:
raise YTCannotParseFieldDisplayName(f,field_name,str(err))
- try:
- parser.parse(r'$'+md['units']+r'$')
- except ParseFatalException, err:
- raise YTCannotParseUnitDisplayName(f, md['units'],str(err))
-
if md['units'] == None or md['units'] == '':
label = field_name
else:
+ try:
+ parser.parse(r'$'+md['units']+r'$')
+ except ParseFatalException, err:
+ raise YTCannotParseUnitDisplayName(f, md['units'],str(err))
label = field_name+r'$\/\/('+md['units']+r')$'
self.plots[f].cb.set_label(label)
@@ -987,8 +1021,12 @@
>>> p.save('sliceplot')
"""
+ # tHis will handle time series data and controllers
+ ts = self._initialize_dataset(pf)
+ self.ts = ts
+ pf = self.pf = ts[0]
axis = fix_axis(axis)
- (bounds,center) = GetBoundsAndCenter(axis, center, width, pf)
+ (bounds, center) = GetBoundsAndCenter(axis, center, width, pf)
slc = pf.h.slice(axis, center[axis], fields=fields)
PWViewerMPL.__init__(self, slc, bounds, origin=origin)
self.set_axes_unit(axes_unit)
@@ -1069,8 +1107,11 @@
>>> p.save('sliceplot')
"""
+ ts = self._initialize_dataset(pf)
+ self.ts = ts
+ pf = self.pf = ts[0]
axis = fix_axis(axis)
- (bounds,center) = GetBoundsAndCenter(axis,center,width,pf)
+ (bounds, center) = GetBoundsAndCenter(axis, center, width, pf)
proj = pf.h.proj(axis,fields,weight_field=weight_field,max_level=max_level,center=center)
PWViewerMPL.__init__(self,proj,bounds,origin=origin)
self.set_axes_unit(axes_unit)
@@ -1492,4 +1533,3 @@
norm = norm, vmin = self.zmin,
vmax = self.zmax, cmap = cmap)
self.image.axes.ticklabel_format(scilimits=(-4,3))
-
https://bitbucket.org/yt_analysis/yt/changeset/5c4bcee82cc5/
changeset: 5c4bcee82cc5
branch: yt
user: samskillman
date: 2012-11-08 16:26:55
summary: Adding ShockTubeTest to framework.py for enzo testing.
affected #: 1 file
diff -r ced3cc36250bf0cf797ed7b42d56c39498ab0772 -r 5c4bcee82cc5fc730aa3c8d478db82eae801f6a9 yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -452,3 +452,44 @@
yield PixelizedProjectionValuesTest(
pf_fn, axis, field, weight_field,
ds)
+
+class ShockTubeTest(object):
+ def __init__(self, data_file, solution_file, fields,
+ left_edges, right_edges, rtol, atol):
+ self.solution_file = solution_file
+ self.data_file = data_file
+ self.fields = fields
+ self.left_edges = left_edges
+ self.right_edges = right_edges
+ self.rtol = rtol
+ self.atol = atol
+
+ def __call__(self):
+ # Read in the pf
+ pf = load(self.data_file)
+ exact = self.get_analytical_solution()
+
+ ad = pf.h.all_data()
+ position = ad['x']
+ for k in self.fields:
+ field = ad[k]
+ for xmin, xmax in zip(self.left_edges, self.right_edges):
+ mask = (position >= xmin)*(position <= xmax)
+ exact_field = np.interp(position[mask], exact['pos'], exact[k])
+ # yield test vs analytical solution
+ yield assert_allclose, field[mask], exact_field, \
+ self.rtol, self.atol
+
+ def get_analytical_solution(self):
+ # Reads in from file
+ pos, dens, vel, pres, inte = \
+ np.loadtxt(self.solution_file, unpack=True)
+ exact = {}
+ exact['pos'] = pos
+ exact['Density'] = dens
+ exact['x-velocity'] = vel
+ exact['Pressure'] = pres
+ exact['ThermalEnergy'] = inte
+ return exact
+
+
Repository URL: https://bitbucket.org/yt_analysis/yt/
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