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DEPR: remove HaloCatalogCallback, let it migrate to yt_astro_analysis
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@neutrinoceros
neutrinoceros committed Oct 17, 2021
1 parent bc7c44a commit b000819
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12 changes: 0 additions & 12 deletions doc/source/cookbook/halo_plotting.py
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1 change: 0 additions & 1 deletion doc/source/reference/api/api.rst
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Expand Up @@ -683,7 +683,6 @@ See also :ref:`callbacks`.
~yt.visualization.plot_modifications.ContourCallback
~yt.visualization.plot_modifications.CuttingQuiverCallback
~yt.visualization.plot_modifications.GridBoundaryCallback
~yt.visualization.plot_modifications.HaloCatalogCallback
~yt.visualization.plot_modifications.ImageLineCallback
~yt.visualization.plot_modifications.LinePlotCallback
~yt.visualization.plot_modifications.MagFieldCallback
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54 changes: 0 additions & 54 deletions doc/source/visualizing/callbacks.rst
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Expand Up @@ -390,60 +390,6 @@ Overplot Cell Edges
slc.annotate_cell_edges()
slc.save()

.. _annotate-halos:

Overplot Halo Annotations
~~~~~~~~~~~~~~~~~~~~~~~~~

.. function:: annotate_halos(self, halo_catalog, circle_args=None, \
width=None, annotate_field=None, \
radius_field='virial_radius', \
center_field_prefix="particle_position", \
text_args=None, factor=1.0)

(This is a proxy for
:class:`~yt.visualization.plot_modifications.HaloCatalogCallback`.)

Accepts a :class:`~yt_astro_analysis.halo_analysis.halo_catalog.HaloCatalog`
and plots a circle at the location of each halo with the radius of the
circle corresponding to the virial radius of the halo. Also accepts a
:ref:`loaded halo catalog dataset <halo-catalog-data>` or a data
container from a halo catalog dataset. If ``width`` is set
to None (default) all halos are plotted, otherwise it accepts a tuple in
the form (1.0, ‘Mpc’) to only display halos that fall within a slab with
width ``width`` centered on the center of the plot data. The appearance of
the circles can be changed with the circle_kwargs dictionary, which is
supplied to the Matplotlib patch Circle. One can label each of the halos
with the annotate_field, which accepts a field contained in the halo catalog
to add text to the plot near the halo (example: ``annotate_field=
'particle_mass'`` will write the halo mass next to each halo, whereas
``'particle_identifier'`` shows the halo number). The size of the circles is
found from the field ``radius_field`` which is ``'virial_radius'`` by
default. If another radius has been found as part of your halo analysis
workflow, you can save that field and use it as the ``radius_field`` to
change the size of the halos. The position of each halo is determined using
``center_field_prefix`` in the following way. If ``'particle_position'``
is the value of ``center_field_prefix`` as is the default, the x value of
the halo position is stored in the field ``'particle_position_x'``, y is
``'particle_position_y'``, and z is ``'particle_position_z'``. If you have
stored another set of coordinates for each halo as part of your halo
analysis as fields such as ``'halo_position_x'``, you can use these fields
to determine halo position by passing ``'halo_position'`` to
``center_field_prefix``. font_kwargs contains the arguments controlling the
text appearance of the annotated field. Factor is the number the virial
radius is multiplied by for plotting the circles. Ex: ``factor=2.0`` will
plot circles with twice the radius of each halo virial radius.

.. python-script::

import yt

data_ds = yt.load("Enzo_64/RD0006/RedshiftOutput0006")
halos_ds = yt.load("rockstar_halos/halos_0.0.bin")

prj = yt.ProjectionPlot(data_ds, "z", ("gas", "density"))
prj.annotate_halos(halos_ds, annotate_field="particle_identifier")
prj.save()

.. _annotate-image-line:

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249 changes: 0 additions & 249 deletions yt/visualization/plot_modifications.py
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Expand Up @@ -6,10 +6,8 @@
import matplotlib
import numpy as np

from yt.data_objects.data_containers import YTDataContainer
from yt.data_objects.level_sets.clump_handling import Clump
from yt.data_objects.selection_objects.cut_region import YTCutRegion
from yt.data_objects.static_output import Dataset
from yt.frontends.ytdata.data_structures import YTClumpContainer
from yt.funcs import is_sequence, mylog, validate_width_tuple
from yt.geometry.geometry_handler import is_curvilinear
Expand All @@ -25,7 +23,6 @@
pixelize_off_axis_cartesian,
)
from yt.utilities.math_utils import periodic_ray
from yt.utilities.on_demand_imports import NotAModule
from yt.visualization.image_writer import apply_colormap

callback_registry = {}
Expand Down Expand Up @@ -1784,252 +1781,6 @@ def __call__(self, plot):
super().__call__(plot)


class HaloCatalogCallback(PlotCallback):
"""
Plots circles at the locations of all the halos
in a halo catalog with radii corresponding to the
virial radius of each halo.
Note, this functionality requires the yt_astro_analysis
package. See https://yt-astro-analysis.readthedocs.io/
for more information.
Parameters
----------
halo_catalog : Dataset, DataContainer,
or ~yt.analysis_modules.halo_analysis.halo_catalog.HaloCatalog
The object containing halos to be overplotted. This can
be a HaloCatalog object, a loaded halo catalog dataset,
or a data container from a halo catalog dataset.
circle_args : list
Contains the arguments controlling the
appearance of the circles, supplied to the
Matplotlib patch Circle.
width : tuple
The width over which to select halos to plot,
useful when overplotting to a slice plot. Accepts
a tuple in the form (1.0, 'Mpc').
annotate_field : str
A field contained in the
halo catalog to add text to the plot near the halo.
Example: annotate_field = 'particle_mass' will
write the halo mass next to each halo.
radius_field : str
A field contained in the halo
catalog to set the radius of the circle which will
surround each halo. Default: 'virial_radius'.
center_field_prefix : str
Accepts a field prefix which will
be used to find the fields containing the coordinates
of the center of each halo. Ex: 'particle_position'
will result in the fields 'particle_position_x' for x
'particle_position_y' for y, and 'particle_position_z'
for z. Default: 'particle_position'.
text_args : dict
Contains the arguments controlling the text
appearance of the annotated field.
factor : float
A number the virial radius is multiplied by for
plotting the circles. Ex: factor = 2.0 will plot
circles with twice the radius of each halo virial radius.
Examples
--------
>>> import yt
>>> dds = yt.load("Enzo_64/DD0043/data0043")
>>> hds = yt.load("rockstar_halos/halos_0.0.bin")
>>> p = yt.ProjectionPlot(
... dds, "x", ("gas", "density"), weight_field=("gas", "density")
... )
>>> p.annotate_halos(hds)
>>> p.save()
>>> # plot a subset of all halos
>>> import yt
>>> dds = yt.load("Enzo_64/DD0043/data0043")
>>> hds = yt.load("rockstar_halos/halos_0.0.bin")
>>> # make a region half the width of the box
>>> dregion = dds.box(
... dds.domain_center - 0.25 * dds.domain_width,
... dds.domain_center + 0.25 * dds.domain_width,
... )
>>> hregion = hds.box(
... hds.domain_center - 0.25 * hds.domain_width,
... hds.domain_center + 0.25 * hds.domain_width,
... )
>>> p = yt.ProjectionPlot(
... dds,
... "x",
... ("gas", "density"),
... weight_field=("gas", "density"),
... data_source=dregion,
... width=0.5,
... )
>>> p.annotate_halos(hregion)
>>> p.save()
>>> # plot halos from a HaloCatalog
>>> import yt
>>> from yt.extensions.astro_analysis.halo_analysis.api import HaloCatalog
>>> dds = yt.load("Enzo_64/DD0043/data0043")
>>> hds = yt.load("rockstar_halos/halos_0.0.bin")
>>> hc = HaloCatalog(data_ds=dds, halos_ds=hds)
>>> p = yt.ProjectionPlot(
... dds, "x", ("gas", "density"), weight_field=("gas", "density")
... )
>>> p.annotate_halos(hc)
>>> p.save()
"""

_type_name = "halos"
region = None
_descriptor = None
_supported_geometries = ("cartesian", "spectral_cube")

def __init__(
self,
halo_catalog,
circle_args=None,
circle_kwargs=None,
width=None,
annotate_field=None,
radius_field="virial_radius",
center_field_prefix="particle_position",
text_args=None,
font_kwargs=None,
factor=1.0,
):

try:
from yt_astro_analysis.halo_analysis.api import HaloCatalog
except ImportError:
HaloCatalog = NotAModule("yt_astro_analysis")

PlotCallback.__init__(self)
def_circle_args = {"edgecolor": "white", "facecolor": "None"}
def_text_args = {"color": "white"}

if isinstance(halo_catalog, YTDataContainer):
self.halo_data = halo_catalog
elif isinstance(halo_catalog, Dataset):
self.halo_data = halo_catalog.all_data()
elif isinstance(halo_catalog, HaloCatalog):
if halo_catalog.data_source.ds == halo_catalog.halos_ds:
self.halo_data = halo_catalog.data_source
else:
self.halo_data = halo_catalog.halos_ds.all_data()
else:
raise RuntimeError(
"halo_catalog argument must be a HaloCatalog object, "
+ "a dataset, or a data container."
)

self.width = width
self.radius_field = radius_field
self.center_field_prefix = center_field_prefix
self.annotate_field = annotate_field
if circle_kwargs is not None:
circle_args = circle_kwargs
warnings.warn(
"The circle_kwargs keyword is deprecated. Please "
"use the circle_args keyword instead."
)
if font_kwargs is not None:
text_args = font_kwargs
warnings.warn(
"The font_kwargs keyword is deprecated. Please use "
"the text_args keyword instead."
)
if circle_args is None:
circle_args = def_circle_args
self.circle_args = circle_args
if text_args is None:
text_args = def_text_args
self.text_args = text_args
self.factor = factor

def __call__(self, plot):
from matplotlib.patches import Circle

data = plot.data
x0, x1, y0, y1 = self._physical_bounds(plot)
xx0, xx1, yy0, yy1 = self._plot_bounds(plot)

halo_data = self.halo_data
axis_names = plot.data.ds.coordinates.axis_name
xax = plot.data.ds.coordinates.x_axis[data.axis]
yax = plot.data.ds.coordinates.y_axis[data.axis]
field_x = f"{self.center_field_prefix}_{axis_names[xax]}"
field_y = f"{self.center_field_prefix}_{axis_names[yax]}"
field_z = f"{self.center_field_prefix}_{axis_names[data.axis]}"

# Set up scales for pixel size and original data
pixel_scale = self._pixel_scale(plot)[0]
units = plot.xlim[0].units

# Convert halo positions to code units of the plotted data
# and then to units of the plotted window
px = halo_data[("all", field_x)][:].in_units(units)
py = halo_data[("all", field_y)][:].in_units(units)

xplotcenter = (plot.xlim[0] + plot.xlim[1]) / 2
yplotcenter = (plot.ylim[0] + plot.ylim[1]) / 2

xdomaincenter = plot.ds.domain_center[xax]
ydomaincenter = plot.ds.domain_center[yax]

xoffset = xplotcenter - xdomaincenter
yoffset = yplotcenter - ydomaincenter

xdw = plot.ds.domain_width[xax].to(units)
ydw = plot.ds.domain_width[yax].to(units)

modpx = np.mod(px - xoffset, xdw) + xoffset
modpy = np.mod(py - yoffset, ydw) + yoffset

px[modpx != px] = modpx[modpx != px]
py[modpy != py] = modpy[modpy != py]

px, py = self._convert_to_plot(plot, [px, py])

# Convert halo radii to a radius in pixels
radius = halo_data[("all", self.radius_field)][:].in_units(units)
radius = np.array(radius * pixel_scale * self.factor)

if self.width:
pz = halo_data[("all", field_z)][:].in_units("code_length")
c = data.center[data.axis]

# I should catch an error here if width isn't in this form
# but I dont really want to reimplement get_sanitized_width...
width = data.ds.arr(self.width[0], self.width[1]).in_units("code_length")

indices = np.where((pz > c - 0.5 * width) & (pz < c + 0.5 * width))

px = px[indices]
py = py[indices]
radius = radius[indices]

for x, y, r in zip(px, py, radius):
plot._axes.add_artist(Circle(xy=(x, y), radius=r, **self.circle_args))

plot._axes.set_xlim(xx0, xx1)
plot._axes.set_ylim(yy0, yy1)

if self.annotate_field:
annotate_dat = halo_data[("all", self.annotate_field)]
texts = [f"{float(dat):g}" for dat in annotate_dat]
labels = []
for pos_x, pos_y, t in zip(px, py, texts):
labels.append(plot._axes.text(pos_x, pos_y, t, **self.text_args))

# Set the font properties of text from this callback to be
# consistent with other text labels in this figure
self._set_font_properties(plot, labels, **self.text_args)


class ParticleCallback(PlotCallback):
"""
Adds particle positions, based on a thick slab along *axis* with a
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