[yt-svn] commit/yt: 6 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Mon Nov 30 11:31:46 PST 2015
6 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/f213ceee6357/
Changeset: f213ceee6357
Branch: yt
User: dorislee0309
Date: 2015-11-26 03:52:19+00:00
Summary: fixed casting error for float and int64 multiplication in sdf class
Affected #: 1 file
diff -r 03a54b627189e63eaee9f2bc1d4a36c3ab6b9637 -r f213ceee6357b0aa20b95a8da95ff240a4d15291 yt/frontends/sdf/data_structures.py
--- a/yt/frontends/sdf/data_structures.py
+++ b/yt/frontends/sdf/data_structures.py
@@ -15,10 +15,15 @@
#-----------------------------------------------------------------------------
+import h5py
import numpy as np
import stat
+import weakref
+import struct
+import glob
import time
import os
+import types
import sys
import contextlib
@@ -27,8 +32,14 @@
ParticleIndex
from yt.data_objects.static_output import \
Dataset, ParticleFile
+from yt.utilities.physical_ratios import \
+ cm_per_kpc, \
+ mass_sun_grams, \
+ sec_per_Gyr
from .fields import \
SDFFieldInfo
+from .io import \
+ IOHandlerSDF
from yt.utilities.sdf import \
SDFRead,\
SDFIndex,\
@@ -105,8 +116,10 @@
def _parse_parameter_file(self):
if self.parameter_filename.startswith("http"):
+ print "HTTPSDFREAD"
sdf_class = HTTPSDFRead
else:
+ print "SDFREAD"
sdf_class = SDFRead
self.sdf_container = sdf_class(self.parameter_filename,
header=self.sdf_header)
@@ -133,8 +146,8 @@
-self.parameters.get("R%s" % ax, R0) for ax in 'xyz'])
self.domain_right_edge = np.array([
+self.parameters.get("R%s" % ax, R0) for ax in 'xyz'])
- self.domain_left_edge *= self.parameters.get("a", 1.0)
- self.domain_right_edge *= self.parameters.get("a", 1.0)
+ self.domain_left_edge *= int(self.parameters.get("a", 1.0))
+ self.domain_right_edge *= int(self.parameters.get("a", 1.0))
nz = 1 << self.over_refine_factor
self.domain_dimensions = np.ones(3, "int32") * nz
https://bitbucket.org/yt_analysis/yt/commits/a812c8e6bbaf/
Changeset: a812c8e6bbaf
Branch: yt
User: dorislee0309
Date: 2015-11-26 03:58:44+00:00
Summary: fixed casting error for float and int64 multiplication in sdf class
Affected #: 1 file
diff -r f213ceee6357b0aa20b95a8da95ff240a4d15291 -r a812c8e6bbaf9586b5385571f40029bffd119b29 yt/frontends/sdf/data_structures.py
--- a/yt/frontends/sdf/data_structures.py
+++ b/yt/frontends/sdf/data_structures.py
@@ -116,10 +116,8 @@
def _parse_parameter_file(self):
if self.parameter_filename.startswith("http"):
- print "HTTPSDFREAD"
sdf_class = HTTPSDFRead
else:
- print "SDFREAD"
sdf_class = SDFRead
self.sdf_container = sdf_class(self.parameter_filename,
header=self.sdf_header)
https://bitbucket.org/yt_analysis/yt/commits/2e3a9b236d04/
Changeset: 2e3a9b236d04
Branch: yt
User: dorislee0309
Date: 2015-11-26 04:07:56+00:00
Summary: deleting unnecessary imports
Affected #: 1 file
diff -r a812c8e6bbaf9586b5385571f40029bffd119b29 -r 2e3a9b236d04586c076e137a576ba27696b11057 yt/frontends/sdf/data_structures.py
--- a/yt/frontends/sdf/data_structures.py
+++ b/yt/frontends/sdf/data_structures.py
@@ -15,15 +15,10 @@
#-----------------------------------------------------------------------------
-import h5py
import numpy as np
import stat
-import weakref
-import struct
-import glob
import time
import os
-import types
import sys
import contextlib
@@ -32,14 +27,8 @@
ParticleIndex
from yt.data_objects.static_output import \
Dataset, ParticleFile
-from yt.utilities.physical_ratios import \
- cm_per_kpc, \
- mass_sun_grams, \
- sec_per_Gyr
from .fields import \
SDFFieldInfo
-from .io import \
- IOHandlerSDF
from yt.utilities.sdf import \
SDFRead,\
SDFIndex,\
https://bitbucket.org/yt_analysis/yt/commits/e26493b973e7/
Changeset: e26493b973e7
Branch: yt
User: dorislee0309
Date: 2015-11-26 05:54:05+00:00
Summary: defining dtype for domain_left_edge and domain_right_edge array
Affected #: 1 file
diff -r 2e3a9b236d04586c076e137a576ba27696b11057 -r e26493b973e770fc07f6951659e62668bd2b595b yt/frontends/sdf/data_structures.py
--- a/yt/frontends/sdf/data_structures.py
+++ b/yt/frontends/sdf/data_structures.py
@@ -125,17 +125,16 @@
if None in (self.domain_left_edge, self.domain_right_edge):
R0 = self.parameters['R0']
if 'offset_center' in self.parameters and self.parameters['offset_center']:
- self.domain_left_edge = np.array([0, 0, 0])
+ self.domain_left_edge = np.array([0, 0, 0],dtype=np.float64)
self.domain_right_edge = np.array([
- 2.0 * self.parameters.get("R%s" % ax, R0) for ax in 'xyz'])
+ 2.0 * self.parameters.get("R%s" % ax, R0) for ax in 'xyz'],dtype=np.float64)
else:
self.domain_left_edge = np.array([
- -self.parameters.get("R%s" % ax, R0) for ax in 'xyz'])
+ -self.parameters.get("R%s" % ax, R0) for ax in 'xyz'],dtype=np.float64)
self.domain_right_edge = np.array([
- +self.parameters.get("R%s" % ax, R0) for ax in 'xyz'])
- self.domain_left_edge *= int(self.parameters.get("a", 1.0))
- self.domain_right_edge *= int(self.parameters.get("a", 1.0))
-
+ +self.parameters.get("R%s" % ax, R0) for ax in 'xyz'],dtype=np.float64)
+ self.domain_left_edge *= self.parameters.get("a", 1.0)
+ self.domain_right_edge *= self.parameters.get("a", 1.0)
nz = 1 << self.over_refine_factor
self.domain_dimensions = np.ones(3, "int32") * nz
if "do_periodic" in self.parameters and self.parameters["do_periodic"]:
https://bitbucket.org/yt_analysis/yt/commits/402bc55e4de8/
Changeset: 402bc55e4de8
Branch: yt
User: ngoldbaum
Date: 2015-11-30 19:29:54+00:00
Summary: Fixing tab/spaces issues, breaking up long lines
Affected #: 1 file
diff -r e26493b973e770fc07f6951659e62668bd2b595b -r 402bc55e4de8acb23a61083886d08c762ca53f94 yt/frontends/sdf/data_structures.py
--- a/yt/frontends/sdf/data_structures.py
+++ b/yt/frontends/sdf/data_structures.py
@@ -125,16 +125,19 @@
if None in (self.domain_left_edge, self.domain_right_edge):
R0 = self.parameters['R0']
if 'offset_center' in self.parameters and self.parameters['offset_center']:
- self.domain_left_edge = np.array([0, 0, 0],dtype=np.float64)
+ self.domain_left_edge = np.array([0, 0, 0], dtype=np.float64)
self.domain_right_edge = np.array([
- 2.0 * self.parameters.get("R%s" % ax, R0) for ax in 'xyz'],dtype=np.float64)
+ 2.0 * self.parameters.get("R%s" % ax, R0) for ax in 'xyz'],
+ dtype=np.float64)
else:
self.domain_left_edge = np.array([
- -self.parameters.get("R%s" % ax, R0) for ax in 'xyz'],dtype=np.float64)
+ -self.parameters.get("R%s" % ax, R0) for ax in 'xyz'],
+ dtype=np.float64)
self.domain_right_edge = np.array([
- +self.parameters.get("R%s" % ax, R0) for ax in 'xyz'],dtype=np.float64)
- self.domain_left_edge *= self.parameters.get("a", 1.0)
- self.domain_right_edge *= self.parameters.get("a", 1.0)
+ +self.parameters.get("R%s" % ax, R0) for ax in 'xyz'],
+ dtype=np.float64)
+ self.domain_left_edge *= self.parameters.get("a", 1.0)
+ self.domain_right_edge *= self.parameters.get("a", 1.0)
nz = 1 << self.over_refine_factor
self.domain_dimensions = np.ones(3, "int32") * nz
if "do_periodic" in self.parameters and self.parameters["do_periodic"]:
https://bitbucket.org/yt_analysis/yt/commits/64675f402d50/
Changeset: 64675f402d50
Branch: yt
User: ngoldbaum
Date: 2015-11-30 19:31:03+00:00
Summary: Merging
Affected #: 9 files
diff -r 402bc55e4de8acb23a61083886d08c762ca53f94 -r 64675f402d50709159e5400b0a64873f2fc7400a 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
@@ -127,7 +127,7 @@
def onaxis_image_func(filename_prefix):
szprj.write_png(filename_prefix)
for test in [GenericArrayTest(ds, onaxis_array_func),
- GenericImageTest(ds, onaxis_image_func, 3)]:
+ GenericImageTest(ds, onaxis_image_func, 12)]:
test_M7_onaxis.__name__ = test.description
yield test
@@ -142,6 +142,6 @@
def offaxis_image_func(filename_prefix):
szprj.write_png(filename_prefix)
for test in [GenericArrayTest(ds, offaxis_array_func),
- GenericImageTest(ds, offaxis_image_func, 3)]:
+ GenericImageTest(ds, offaxis_image_func, 12)]:
test_M7_offaxis.__name__ = test.description
yield test
diff -r 402bc55e4de8acb23a61083886d08c762ca53f94 -r 64675f402d50709159e5400b0a64873f2fc7400a yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -712,7 +712,27 @@
raise NotImplementedError
def ptp(self, field):
- raise NotImplementedError
+ r"""Compute the range of values (maximum - minimum) of a field.
+
+ This will, in a parallel-aware fashion, compute the "peak-to-peak" of
+ the given field.
+
+ Parameters
+ ----------
+ field : string or tuple of strings
+ The field to average.
+
+ Returns
+ -------
+ Scalar
+
+ Examples
+ --------
+
+ >>> rho_range = reg.ptp("density")
+ """
+ ex = self._compute_extrema(field)
+ return ex[1] - ex[0]
def hist(self, field, weight = None, bins = None):
raise NotImplementedError
diff -r 402bc55e4de8acb23a61083886d08c762ca53f94 -r 64675f402d50709159e5400b0a64873f2fc7400a yt/data_objects/tests/test_numpy_ops.py
--- a/yt/data_objects/tests/test_numpy_ops.py
+++ b/yt/data_objects/tests/test_numpy_ops.py
@@ -73,6 +73,9 @@
q = ad.max("density").v
yield assert_equal, q, ad["density"].max()
+ ptp = ad.ptp("density").v
+ yield assert_equal, ptp, ad["density"].max() - ad["density"].min()
+
p = ad.max("density", axis=1)
p1 = ds.proj("density", 1, data_source=ad, method="mip")
yield assert_equal, p["density"], p1["density"]
diff -r 402bc55e4de8acb23a61083886d08c762ca53f94 -r 64675f402d50709159e5400b0a64873f2fc7400a yt/fields/derived_field.py
--- a/yt/fields/derived_field.py
+++ b/yt/fields/derived_field.py
@@ -88,8 +88,6 @@
self.display_field = display_field
self.particle_type = particle_type
self.vector_field = vector_field
- if output_units is None: output_units = units
- self.output_units = output_units
self._function = function
@@ -112,6 +110,9 @@
raise FieldUnitsError("Cannot handle units '%s' (type %s)." \
"Please provide a string or Unit " \
"object." % (units, type(units)) )
+ if output_units is None:
+ output_units = self.units
+ self.output_units = output_units
def _copy_def(self):
dd = {}
diff -r 402bc55e4de8acb23a61083886d08c762ca53f94 -r 64675f402d50709159e5400b0a64873f2fc7400a yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -51,6 +51,8 @@
import matplotlib.image as mpimg
import yt.visualization.plot_window as pw
+import yt.visualization.particle_plots as particle_plots
+import yt.visualization.profile_plotter as profile_plotter
mylog = logging.getLogger('nose.plugins.answer-testing')
run_big_data = False
@@ -349,11 +351,12 @@
def create_plot(self, ds, plot_type, plot_field, plot_axis, plot_kwargs = None):
# plot_type should be a string
- # plot_args should be a tuple
# plot_kwargs should be a dict
if plot_type is None:
raise RuntimeError('Must explicitly request a plot type')
- cls = getattr(pw, plot_type)
+ cls = getattr(pw, plot_type, None)
+ if cls is None:
+ cls = getattr(particle_plots, plot_type)
plot = cls(*(ds, plot_axis, plot_field), **plot_kwargs)
return plot
@@ -740,6 +743,50 @@
def compare(self, new_result, old_result):
compare_image_lists(new_result, old_result, self.decimals)
+class PhasePlotAttributeTest(AnswerTestingTest):
+ _type_name = "PhasePlotAttribute"
+ _attrs = ('plot_type', 'x_field', 'y_field', 'z_field',
+ 'attr_name', 'attr_args')
+ def __init__(self, ds_fn, x_field, y_field, z_field,
+ attr_name, attr_args, decimals, plot_type='PhasePlot'):
+ super(PhasePlotAttributeTest, self).__init__(ds_fn)
+ self.data_source = self.ds.all_data()
+ self.plot_type = plot_type
+ self.x_field = x_field
+ self.y_field = y_field
+ self.z_field = z_field
+ self.plot_kwargs = {}
+ self.attr_name = attr_name
+ self.attr_args = attr_args
+ self.decimals = decimals
+
+ def create_plot(self, data_source, x_field, y_field, z_field,
+ plot_type, plot_kwargs=None):
+ # plot_type should be a string
+ # plot_kwargs should be a dict
+ if plot_type is None:
+ raise RuntimeError('Must explicitly request a plot type')
+ cls = getattr(profile_plotter, plot_type, None)
+ if cls is None:
+ cls = getattr(particle_plots, plot_type)
+ plot = cls(*(data_source, x_field, y_field, z_field), **plot_kwargs)
+ return plot
+
+ def run(self):
+ plot = self.create_plot(self.data_source, self.x_field, self.y_field,
+ self.z_field, self.plot_type, self.plot_kwargs)
+ attr = getattr(plot, self.attr_name)
+ attr(*self.attr_args[0], **self.attr_args[1])
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ plot.save(name=tmpname)
+ image = mpimg.imread(tmpname)
+ os.remove(tmpname)
+ return [zlib.compress(image.dumps())]
+
+ def compare(self, new_result, old_result):
+ compare_image_lists(new_result, old_result, self.decimals)
+
class GenericArrayTest(AnswerTestingTest):
_type_name = "GenericArray"
_attrs = ('array_func_name','args','kwargs')
diff -r 402bc55e4de8acb23a61083886d08c762ca53f94 -r 64675f402d50709159e5400b0a64873f2fc7400a yt/visualization/tests/test_particle_plot.py
--- a/yt/visualization/tests/test_particle_plot.py
+++ b/yt/visualization/tests/test_particle_plot.py
@@ -20,9 +20,14 @@
from yt.data_objects.profiles import create_profile
from yt.extern.parameterized import parameterized, param
from yt.visualization.tests.test_plotwindow import \
- assert_fname, WIDTH_SPECS
+ assert_fname, WIDTH_SPECS, ATTR_ARGS
from yt.testing import \
fake_particle_ds, assert_array_almost_equal
+from yt.utilities.answer_testing.framework import \
+ requires_ds, \
+ data_dir_load, \
+ PlotWindowAttributeTest, \
+ PhasePlotAttributeTest
from yt.visualization.api import \
ParticleProjectionPlot, ParticlePhasePlot
from yt.units.yt_array import YTArray
@@ -33,6 +38,22 @@
from yt.config import ytcfg
ytcfg["yt", "__withintesting"] = "True"
+# override some of the plotwindow ATTR_ARGS
+PROJ_ATTR_ARGS = ATTR_ARGS.copy()
+PROJ_ATTR_ARGS["set_cmap"] = [(('particle_mass', 'RdBu'), {}),
+ (('particle_mass', 'kamae'), {})]
+PROJ_ATTR_ARGS["set_log"] = [(('particle_mass', False), {})]
+PROJ_ATTR_ARGS["set_zlim"] = [(('particle_mass', 1e-25, 1e-23), {}),
+ (('particle_mass', 1e-25, None),
+ {'dynamic_range': 4})]
+
+PHASE_ATTR_ARGS = {"annotate_text": [(((5e-29, 5e7), "Hello YT"), {}),
+ (((5e-29, 5e7), "Hello YT"), {'color':'b'})],
+ "set_title": [(('particle_mass', 'A phase plot.'), {})],
+ "set_log": [(('particle_mass', False), {})],
+ "set_unit": [(('particle_mass', 'Msun'), {})],
+ "set_xlim": [((-4e7, 4e7), {})],
+ "set_ylim": [((-4e7, 4e7), {})]}
TEST_FLNMS = [None, 'test', 'test.png', 'test.eps',
'test.ps', 'test.pdf']
@@ -59,6 +80,58 @@
['particle_mass', 'particle_ones'])]
+g30 = "IsolatedGalaxy/galaxy0030/galaxy0030"
+
+ at requires_ds(g30, big_data=True)
+def test_particle_projection_answers():
+ '''
+
+ This iterates over the all the plot modification functions in
+ PROJ_ATTR_ARGS. Each time, it compares the images produced by
+ ParticleProjectionPlot to the gold standard.
+
+
+ '''
+
+ plot_field = 'particle_mass'
+ decimals = 12
+ ds = data_dir_load(g30)
+ for ax in 'xyz':
+ for attr_name in PROJ_ATTR_ARGS.keys():
+ for args in PROJ_ATTR_ARGS[attr_name]:
+ test = PlotWindowAttributeTest(ds, plot_field, ax,
+ attr_name,
+ args, decimals,
+ 'ParticleProjectionPlot')
+ test_particle_projection_answers.__name__ = test.description
+ yield test
+
+
+ at requires_ds(g30, big_data=True)
+def test_particle_phase_answers():
+ '''
+
+ This iterates over the all the plot modification functions in
+ PHASE_ATTR_ARGS. Each time, it compares the images produced by
+ ParticlePhasePlot to the gold standard.
+
+ '''
+
+ decimals = 12
+ ds = data_dir_load(g30)
+
+ x_field = 'particle_velocity_x'
+ y_field = 'particle_velocity_y'
+ z_field = 'particle_mass'
+ for attr_name in PHASE_ATTR_ARGS.keys():
+ for args in PHASE_ATTR_ARGS[attr_name]:
+ test = PhasePlotAttributeTest(ds, x_field, y_field, z_field,
+ attr_name, args, decimals,
+ 'ParticlePhasePlot')
+
+ test_particle_phase_answers.__name__ = test.description
+ yield test
+
class TestParticlePhasePlotSave(unittest.TestCase):
@classmethod
diff -r 402bc55e4de8acb23a61083886d08c762ca53f94 -r 64675f402d50709159e5400b0a64873f2fc7400a yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -182,7 +182,7 @@
def test_attributes():
"""Test plot member functions that aren't callbacks"""
plot_field = 'density'
- decimals = 3
+ decimals = 12
ds = data_dir_load(M7)
for ax in 'xyz':
@@ -200,7 +200,7 @@
@requires_ds(WT)
def test_attributes_wt():
plot_field = 'density'
- decimals = 3
+ decimals = 12
ds = data_dir_load(WT)
ax = 'z'
diff -r 402bc55e4de8acb23a61083886d08c762ca53f94 -r 64675f402d50709159e5400b0a64873f2fc7400a yt/visualization/tests/test_profile_plots.py
--- a/yt/visualization/tests/test_profile_plots.py
+++ b/yt/visualization/tests/test_profile_plots.py
@@ -26,6 +26,46 @@
ProfilePlot, PhasePlot
from yt.visualization.tests.test_plotwindow import \
assert_fname, TEST_FLNMS
+from yt.utilities.answer_testing.framework import \
+ PhasePlotAttributeTest, \
+ requires_ds, \
+ data_dir_load
+
+ATTR_ARGS = {"annotate_text": [(((5e-29, 5e7), "Hello YT"), {}),
+ (((5e-29, 5e7), "Hello YT"), {'color':'b'})],
+
+ "set_title": [(('cell_mass', 'A phase plot.'), {})],
+ "set_log": [(('cell_mass', False), {})],
+ "set_unit": [(('cell_mass', 'Msun'), {})],
+ "set_xlim": [((1e-27, 1e-24), {})],
+ "set_ylim": [((1e2, 1e6), {})]}
+
+
+g30 = "IsolatedGalaxy/galaxy0030/galaxy0030"
+
+ at requires_ds(g30, big_data=True)
+def test_phase_plot_attributes():
+ '''
+
+ This iterates over the all the plot modification functions in
+ ATTR_ARGS. Each time, it compares the images produced by
+ PhasePlot to the gold standard.
+
+
+ '''
+
+ x_field = 'density'
+ y_field = 'temperature'
+ z_field = 'cell_mass'
+ decimals = 12
+ ds = data_dir_load(g30)
+ for ax in 'xyz':
+ for attr_name in ATTR_ARGS.keys():
+ for args in ATTR_ARGS[attr_name]:
+ test = PhasePlotAttributeTest(ds, x_field, y_field, z_field,
+ attr_name, args, decimals)
+ test_phase_plot_attributes.__name__ = test.description
+ yield test
class TestProfilePlotSave(unittest.TestCase):
diff -r 402bc55e4de8acb23a61083886d08c762ca53f94 -r 64675f402d50709159e5400b0a64873f2fc7400a yt/visualization/volume_rendering/tests/test_vr_orientation.py
--- a/yt/visualization/volume_rendering/tests/test_vr_orientation.py
+++ b/yt/visualization/volume_rendering/tests/test_vr_orientation.py
@@ -107,7 +107,7 @@
n_frames = 5
theta = np.pi / n_frames
- decimals = 3
+ decimals = 12
for lens_type in ['plane-parallel', 'perspective']:
frame = 0
Repository URL: https://bitbucket.org/yt_analysis/yt/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
More information about the yt-svn
mailing list