def phase_plot(halo, output_dir=".", phase_args=None, phase_kwargs=None):
r"""
Make a phase plot for the halo object.
Parameters
----------
halo : Halo object
The Halo object to be provided by the HaloCatalog.
output_dir : string
Name of directory where profile data will be written. The full path will be
the output_dir of the halo catalog concatenated with this directory.
Default : "."
phase_args : list
List of arguments to be given to PhasePlot.
phase_kwargs : dict
Dictionary of keyword arguments to be given to PhasePlot.
"""
if phase_args is None:
phase_args = []
if phase_kwargs is None:
phase_kwargs = {}
try:
plot = PhasePlot(halo.data_object, *phase_args, **phase_kwargs)
plot.save(os.path.join(halo.halo_catalog.output_dir, output_dir,
"halo_%06d" % halo.quantities["particle_identifier"]))
except ValueError:
return
def test_profile_data():
tmpdir = make_tempdir()
curdir = os.getcwd()
os.chdir(tmpdir)
ds = data_dir_load(enzotiny)
ad = ds.all_data()
profile_1d = create_profile(ad,
"density",
"temperature",
weight_field="cell_mass")
fn = profile_1d.save_as_dataset()
full_fn = os.path.join(tmpdir, fn)
prof_1d_ds = load(full_fn)
compare_unit_attributes(ds, prof_1d_ds)
assert isinstance(prof_1d_ds, YTProfileDataset)
for field in profile_1d.standard_deviation:
assert_array_equal(
profile_1d.standard_deviation[field],
prof_1d_ds.profile.standard_deviation["data", field[1]],
)
p1 = ProfilePlot(prof_1d_ds.data,
"density",
"temperature",
weight_field="cell_mass")
p1.save()
yield YTDataFieldTest(full_fn, "temperature", geometric=False)
yield YTDataFieldTest(full_fn, "x", geometric=False)
yield YTDataFieldTest(full_fn, "density", geometric=False)
profile_2d = create_profile(
ad,
["density", "temperature"],
"cell_mass",
weight_field=None,
n_bins=(128, 128),
)
fn = profile_2d.save_as_dataset()
full_fn = os.path.join(tmpdir, fn)
prof_2d_ds = load(full_fn)
compare_unit_attributes(ds, prof_2d_ds)
assert isinstance(prof_2d_ds, YTProfileDataset)
p2 = PhasePlot(prof_2d_ds.data,
"density",
"temperature",
"cell_mass",
weight_field=None)
p2.save()
yield YTDataFieldTest(full_fn, "density", geometric=False)
yield YTDataFieldTest(full_fn, "x", geometric=False)
yield YTDataFieldTest(full_fn, "temperature", geometric=False)
yield YTDataFieldTest(full_fn, "y", geometric=False)
yield YTDataFieldTest(full_fn, "cell_mass", geometric=False)
os.chdir(curdir)
if tmpdir != ".":
shutil.rmtree(tmpdir)
def test_old_profile_data():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
ds = data_dir_load(enzotiny)
ad = ds.all_data()
profile_1d = create_profile(
ad,
("gas", "density"),
("gas", "temperature"),
weight_field=("gas", "cell_mass"),
)
fn = "DD0046_Profile1D.h5"
full_fn = os.path.join(ytdata_dir, fn)
prof_1d_ds = data_dir_load(full_fn)
compare_unit_attributes(ds, prof_1d_ds)
assert isinstance(prof_1d_ds, YTProfileDataset)
for field in profile_1d.standard_deviation:
assert_array_equal(
profile_1d.standard_deviation[field],
prof_1d_ds.profile.standard_deviation["data", field[1]],
)
p1 = ProfilePlot(
prof_1d_ds.data,
("gas", "density"),
("gas", "temperature"),
weight_field=("gas", "cell_mass"),
)
p1.save()
yield YTDataFieldTest(full_fn, ("gas", "temperature"), geometric=False)
yield YTDataFieldTest(full_fn, ("index", "x"), geometric=False)
yield YTDataFieldTest(full_fn, ("gas", "density"), geometric=False)
fn = "DD0046_Profile2D.h5"
full_fn = os.path.join(ytdata_dir, fn)
prof_2d_ds = data_dir_load(full_fn)
compare_unit_attributes(ds, prof_2d_ds)
assert isinstance(prof_2d_ds, YTProfileDataset)
p2 = PhasePlot(
prof_2d_ds.data,
("gas", "density"),
("gas", "temperature"),
("gas", "cell_mass"),
weight_field=None,
)
p2.save()
yield YTDataFieldTest(full_fn, ("gas", "density"), geometric=False)
yield YTDataFieldTest(full_fn, ("index", "x"), geometric=False)
yield YTDataFieldTest(full_fn, ("gas", "temperature"), geometric=False)
yield YTDataFieldTest(full_fn, ("index", "y"), geometric=False)
yield YTDataFieldTest(full_fn, ("gas", "cell_mass"), geometric=False)
os.chdir(curdir)
shutil.rmtree(tmpdir)
def setUpClass(cls):
fields = ('density', 'temperature', 'velocity_x', 'velocity_y',
'velocity_z')
units = ('g/cm**3', 'K', 'cm/s', 'cm/s', 'cm/s')
test_ds = fake_random_ds(64, fields=fields, units=units)
regions = [
test_ds.region([0.5] * 3, [0.4] * 3, [0.6] * 3),
test_ds.all_data()
]
profiles = []
phases = []
pr_fields = [('density', 'temperature'), ('density', 'velocity_x'),
('temperature', 'cell_mass'), ('density', 'radius'),
('velocity_magnitude', 'cell_mass')]
ph_fields = [('density', 'temperature', 'cell_mass'),
('density', 'velocity_x', 'cell_mass'),
('radius', 'temperature', 'velocity_magnitude')]
for reg in regions:
for x_field, y_field in pr_fields:
profiles.append(ProfilePlot(reg, x_field, y_field))
profiles.append(
ProfilePlot(reg,
x_field,
y_field,
fractional=True,
accumulation=True))
p1d = create_profile(reg, x_field, y_field)
profiles.append(ProfilePlot.from_profiles(p1d))
for x_field, y_field, z_field in ph_fields:
# set n_bins to [16, 16] since matplotlib's postscript
# renderer is slow when it has to write a lot of polygons
phases.append(
PhasePlot(reg,
x_field,
y_field,
z_field,
x_bins=16,
y_bins=16))
phases.append(
PhasePlot(reg,
x_field,
y_field,
z_field,
fractional=True,
accumulation=True,
x_bins=16,
y_bins=16))
p2d = create_profile(reg, [x_field, y_field],
z_field,
n_bins=[16, 16])
phases.append(PhasePlot.from_profile(p2d))
cls.profiles = profiles
cls.phases = phases
cls.ds = test_ds
def test_profile_data():
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
ds = data_dir_load(enzotiny)
ad = ds.all_data()
profile_1d = create_profile(ad,
"density",
"temperature",
weight_field="cell_mass")
fn = profile_1d.save_as_dataset()
full_fn = os.path.join(tmpdir, fn)
prof_1d_ds = load(full_fn)
compare_unit_attributes(ds, prof_1d_ds)
assert isinstance(prof_1d_ds, YTProfileDataset)
p1 = ProfilePlot(prof_1d_ds.data,
"density",
"temperature",
weight_field="cell_mass")
p1.save()
yield YTDataFieldTest(full_fn, "temperature", geometric=False)
yield YTDataFieldTest(full_fn, "x", geometric=False)
yield YTDataFieldTest(full_fn, "density", geometric=False)
profile_2d = create_profile(ad, ["density", "temperature"],
"cell_mass",
weight_field=None,
n_bins=(128, 128))
fn = profile_2d.save_as_dataset()
full_fn = os.path.join(tmpdir, fn)
prof_2d_ds = load(full_fn)
compare_unit_attributes(ds, prof_2d_ds)
assert isinstance(prof_2d_ds, YTProfileDataset)
p2 = PhasePlot(prof_2d_ds.data,
"density",
"temperature",
"cell_mass",
weight_field=None)
p2.save()
yield YTDataFieldTest(full_fn, "density", geometric=False)
yield YTDataFieldTest(full_fn, "x", geometric=False)
yield YTDataFieldTest(full_fn, "temperature", geometric=False)
yield YTDataFieldTest(full_fn, "y", geometric=False)
yield YTDataFieldTest(full_fn, "cell_mass", geometric=False)
os.chdir(curdir)
shutil.rmtree(tmpdir)
def plot(self):
r"""
This returns a :class:~yt.visualization.profile_plotter.PhasePlot with
the fields that have been added to this object.
"""
from yt.visualization.profile_plotter import PhasePlot
return PhasePlot.from_profile(self)
def test_field_access():
ds = fake_random_ds(16)
ad = ds.all_data()
sp = ds.sphere(ds.domain_center, 0.25)
cg = ds.covering_grid(0, ds.domain_left_edge, ds.domain_dimensions)
scg = ds.smoothed_covering_grid(0, ds.domain_left_edge,
ds.domain_dimensions)
sl = ds.slice(0, ds.domain_center[0])
proj = ds.proj(("gas", "density"), 0)
prof = create_profile(ad, ("index", "radius"), ("gas", "density"))
for data_object in [ad, sp, cg, scg, sl, proj, prof]:
assert_equal(data_object["gas", "density"],
data_object[ds.fields.gas.density])
for field in [("gas", "density"), ds.fields.gas.density]:
ad = ds.all_data()
prof = ProfilePlot(ad, ("index", "radius"), field)
phase = PhasePlot(ad, ("index", "radius"), field, ("gas", "cell_mass"))
s = SlicePlot(ds, 2, field)
oas = SlicePlot(ds, [1, 1, 1], field)
p = ProjectionPlot(ds, 2, field)
oap = OffAxisProjectionPlot(ds, [1, 1, 1], field)
for plot_object in [s, oas, p, oap, prof, phase]:
plot_object._setup_plots()
if hasattr(plot_object, "_frb"):
plot_object._frb[field]
def setUpClass(cls):
fields = ('density', 'temperature', 'velocity_x', 'velocity_y',
'velocity_z')
units = ('g/cm**3', 'K', 'cm/s', 'cm/s', 'cm/s')
test_ds = fake_random_ds(64, fields=fields, units=units)
regions = [test_ds.region([0.5]*3, [0.4]*3, [0.6]*3), test_ds.all_data()]
profiles = []
phases = []
pr_fields = [('density', 'temperature'), ('density', 'velocity_x'),
('temperature', 'cell_mass'), ('density', 'radius'),
('velocity_magnitude', 'cell_mass')]
ph_fields = [('density', 'temperature', 'cell_mass'),
('density', 'velocity_x', 'cell_mass'),
('radius', 'temperature', 'velocity_magnitude')]
for reg in regions:
for x_field, y_field in pr_fields:
profiles.append(ProfilePlot(reg, x_field, y_field))
profiles.append(ProfilePlot(reg, x_field, y_field,
fractional=True, accumulation=True))
p1d = create_profile(reg, x_field, y_field)
profiles.append(ProfilePlot.from_profiles(p1d))
for x_field, y_field, z_field in ph_fields:
# set n_bins to [16, 16] since matplotlib's postscript
# renderer is slow when it has to write a lot of polygons
phases.append(PhasePlot(reg, x_field, y_field, z_field,
x_bins=16, y_bins=16))
phases.append(PhasePlot(reg, x_field, y_field, z_field,
fractional=True, accumulation=True,
x_bins=16, y_bins=16))
p2d = create_profile(reg, [x_field, y_field], z_field,
n_bins=[16, 16])
phases.append(PhasePlot.from_profile(p2d))
cls.profiles = profiles
cls.phases = phases
cls.ds = test_ds
def test_phase_plot(self):
fields = ('density', 'temperature', 'velocity_x', 'velocity_y',
'velocity_z')
units = ('g/cm**3', 'K', 'cm/s', 'cm/s', 'cm/s')
test_ds = fake_random_ds(16, fields=fields, units=units)
regions = [
test_ds.region([0.5] * 3, [0.4] * 3, [0.6] * 3),
test_ds.all_data()
]
phases = []
ph_fields = [('density', 'temperature', 'cell_mass'),
('density', 'velocity_x', 'cell_mass'),
('radius', 'temperature', 'velocity_magnitude')]
for reg in regions:
for x_field, y_field, z_field in ph_fields:
# set n_bins to [16, 16] since matplotlib's postscript
# renderer is slow when it has to write a lot of polygons
phases.append(
PhasePlot(reg,
x_field,
y_field,
z_field,
x_bins=16,
y_bins=16))
phases.append(
PhasePlot(reg,
x_field,
y_field,
z_field,
fractional=True,
accumulation=True,
x_bins=16,
y_bins=16))
p2d = create_profile(reg, [x_field, y_field],
z_field,
n_bins=[16, 16])
phases.append(PhasePlot.from_profile(p2d))
pp = PhasePlot(test_ds.all_data(), 'density', 'temperature',
'cell_mass')
pp.set_xlim(0.3, 0.8)
pp.set_ylim(0.4, 0.6)
pp._setup_plots()
xlim = pp.plots['cell_mass'].axes.get_xlim()
ylim = pp.plots['cell_mass'].axes.get_ylim()
assert_array_almost_equal(xlim, (0.3, 0.8))
assert_array_almost_equal(ylim, (0.4, 0.6))
phases.append(pp)
phases[0]._repr_html_()
for p in phases:
for fname in TEST_FLNMS:
assert_fname(p.save(fname)[0])
def setUpClass(cls):
fields = ('density', 'temperature', 'velocity_x', 'velocity_y',
'velocity_z')
units = ('g/cm**3', 'K', 'cm/s', 'cm/s', 'cm/s')
test_ds = fake_random_ds(64, fields=fields, units=units)
regions = [
test_ds.region([0.5] * 3, [0.4] * 3, [0.6] * 3),
test_ds.all_data()
]
profiles = []
phases = []
pr_fields = [('density', 'temperature'), ('density', 'velocity_x'),
('temperature', 'cell_mass'), ('density', 'radius'),
('velocity_magnitude', 'cell_mass')]
ph_fields = [('density', 'temperature', 'cell_mass'),
('density', 'velocity_x', 'cell_mass'),
('radius', 'temperature', 'velocity_magnitude')]
for reg in regions:
for x_field, y_field in pr_fields:
profiles.append(ProfilePlot(reg, x_field, y_field))
profiles.append(
ProfilePlot(reg,
x_field,
y_field,
fractional=True,
accumulation=True))
p1d = create_profile(reg, x_field, y_field)
profiles.append(ProfilePlot.from_profiles(p1d))
for x_field, y_field, z_field in ph_fields:
# set n_bins to [16, 16] since matplotlib's postscript
# renderer is slow when it has to write a lot of polygons
phases.append(
PhasePlot(reg,
x_field,
y_field,
z_field,
x_bins=16,
y_bins=16))
phases.append(
PhasePlot(reg,
x_field,
y_field,
z_field,
fractional=True,
accumulation=True,
x_bins=16,
y_bins=16))
p2d = create_profile(reg, [x_field, y_field],
z_field,
n_bins=[16, 16])
phases.append(PhasePlot.from_profile(p2d))
pp = PhasePlot(test_ds.all_data(), 'density', 'temperature',
'cell_mass')
pp.set_xlim(0.3, 0.8)
pp.set_ylim(0.4, 0.6)
pp._setup_plots()
xlim = pp.plots['cell_mass'].axes.get_xlim()
ylim = pp.plots['cell_mass'].axes.get_ylim()
assert_array_almost_equal(xlim, (0.3, 0.8))
assert_array_almost_equal(ylim, (0.4, 0.6))
phases.append(pp)
p1 = create_profile(test_ds.all_data(), 'density', 'temperature')
p2 = create_profile(test_ds.all_data(), 'density', 'velocity_x')
profiles.append(
ProfilePlot.from_profiles([p1, p2],
labels=['temperature', 'velocity']))
cls.profiles = profiles
cls.phases = phases
cls.ds = test_ds
def test_phase_plot():
fields = ("density", "temperature", "velocity_x", "velocity_y",
"velocity_z")
units = ("g/cm**3", "K", "cm/s", "cm/s", "cm/s")
test_ds = fake_random_ds(16, fields=fields, units=units)
regions = [
test_ds.region([0.5] * 3, [0.4] * 3, [0.6] * 3),
test_ds.all_data()
]
phases = []
ph_fields = [
("density", "temperature", "cell_mass"),
("density", "velocity_x", "cell_mass"),
("radius", "temperature", "velocity_magnitude"),
]
for reg in regions:
for x_field, y_field, z_field in ph_fields:
# set n_bins to [16, 16] since matplotlib's postscript
# renderer is slow when it has to write a lot of polygons
phases.append(
PhasePlot(reg, x_field, y_field, z_field, x_bins=16,
y_bins=16))
phases.append(
PhasePlot(
reg,
x_field,
y_field,
z_field,
fractional=True,
accumulation=True,
x_bins=16,
y_bins=16,
))
p2d = create_profile(reg, [x_field, y_field],
z_field,
n_bins=[16, 16])
phases.append(PhasePlot.from_profile(p2d))
pp = PhasePlot(test_ds.all_data(), "density", "temperature", "cell_mass")
pp.set_xlim(0.3, 0.8)
pp.set_ylim(0.4, 0.6)
pp._setup_plots()
xlim = pp.plots["cell_mass"].axes.get_xlim()
ylim = pp.plots["cell_mass"].axes.get_ylim()
assert_array_almost_equal(xlim, (0.3, 0.8))
assert_array_almost_equal(ylim, (0.4, 0.6))
phases.append(pp)
phases[0]._repr_html_()
for idx, plot in enumerate(phases):
test_prefix = f"{plot.plots.keys()}_{idx}"
yield compare(test_ds,
plot,
test_prefix=test_prefix,
test_name="phase_plots")
