[yt-svn] commit/yt: 6 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Thu Jul 3 10:33:08 PDT 2014
6 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/c305e2747e0a/
Changeset: c305e2747e0a
Branch: yt-3.0
User: hegan
Date: 2014-07-02 23:27:00
Summary: Fixed halo annotation to respect comoving units, and accurately reflect radii
Affected #: 1 file
diff -r 57ecc4cbdf24f36a5d522c983612468861ffde35 -r c305e2747e0a7043061b330c7cc2ef2edc6a4586 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -16,6 +16,7 @@
import numpy as np
import h5py
+from matplotlib.patches import Circle
from yt.funcs import *
from yt.extern.six import add_metaclass
@@ -871,7 +872,8 @@
_descriptor = None
def __init__(self, halo_catalog, col='white', alpha =1,
- width = None, annotate_field = False, font_kwargs = None):
+ width = None, annotate_field = False,
+ font_kwargs = None, factor = 1.0):
PlotCallback.__init__(self)
self.halo_catalog = halo_catalog
@@ -880,6 +882,7 @@
self.width = width
self.annotate_field = annotate_field
self.font_kwargs = font_kwargs
+ self.factor = factor
def __call__(self, plot):
data = plot.data
@@ -898,20 +901,20 @@
plot._axes.hold(True)
# Set up scales for pixel size and original data
- units = 'Mpccm'
pixel_scale = self.pixel_scale(plot)[0]
data_scale = data.pf.length_unit
+ units = data_scale.units
# Convert halo positions to code units of the plotted data
# and then to units of the plotted window
px = halo_data[field_x][:].in_units(units) / data_scale
py = halo_data[field_y][:].in_units(units) / data_scale
px, py = self.convert_to_plot(plot,[px,py])
+
+ # Convert halo radii to a radius in pixels
+ radius = halo_data['virial_radius'][:].in_units(units)
+ radius = radius*pixel_scale*self.factor/data_scale
- # Convert halo radii to a radius in pixels
- radius = halo_data['radius'][:].in_units(units)
- radius = radius*pixel_scale/data_scale
-
if self.width:
pz = halo_data[field_z][:].in_units(units)/data_scale
pz = data.pf.arr(pz, 'code_length')
@@ -927,8 +930,10 @@
py = py[indices]
radius = radius[indices]
- plot._axes.scatter(px, py, edgecolors='None', marker='o',
- s=radius, c=self.color,alpha=self.alpha)
+ for x,y,r in zip(px, py, radius):
+ plot._axes.add_artist(Circle(xy=(x,y),
+ radius = r, color=self.color, alpha=self.alpha))
+
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
plot._axes.hold(False)
https://bitbucket.org/yt_analysis/yt/commits/be426814140e/
Changeset: be426814140e
Branch: yt-3.0
User: hegan
Date: 2014-07-02 23:28:58
Summary: clarifying colors
Affected #: 1 file
diff -r c305e2747e0a7043061b330c7cc2ef2edc6a4586 -r be426814140e54c5fbe87c2392817e07c905e00a yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -932,7 +932,8 @@
for x,y,r in zip(px, py, radius):
plot._axes.add_artist(Circle(xy=(x,y),
- radius = r, color=self.color, alpha=self.alpha))
+ radius = r, facecolor=self.color,
+ edgecolor = 'None', alpha=self.alpha))
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
https://bitbucket.org/yt_analysis/yt/commits/38056c687fb9/
Changeset: 38056c687fb9
Branch: yt-3.0
User: hegan
Date: 2014-07-03 00:28:16
Summary: added circle kwargs and gave sane defaults
Affected #: 1 file
diff -r be426814140e54c5fbe87c2392817e07c905e00a -r 38056c687fb91e5e5fa0d215fb94d112de8b9b3a yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -871,18 +871,19 @@
region = None
_descriptor = None
- def __init__(self, halo_catalog, col='white', alpha =1,
+ def __init__(self, halo_catalog, circle_kwargs = None,
width = None, annotate_field = False,
font_kwargs = None, factor = 1.0):
PlotCallback.__init__(self)
self.halo_catalog = halo_catalog
- self.color = col
- self.alpha = alpha
self.width = width
self.annotate_field = annotate_field
self.font_kwargs = font_kwargs
self.factor = factor
+ if circle_kwargs is None:
+ circle_kwargs = {'edgecolor':'white', 'facecolor':'None'}
+ self.circle_kwargs = circle_kwargs
def __call__(self, plot):
data = plot.data
@@ -932,8 +933,7 @@
for x,y,r in zip(px, py, radius):
plot._axes.add_artist(Circle(xy=(x,y),
- radius = r, facecolor=self.color,
- edgecolor = 'None', alpha=self.alpha))
+ radius = r, **self.circle_kwargs))
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
https://bitbucket.org/yt_analysis/yt/commits/25d1a86cdc86/
Changeset: 25d1a86cdc86
Branch: yt-3.0
User: hegan
Date: 2014-07-03 00:37:03
Summary: added docstring to annotate_halos
Affected #: 1 file
diff -r 38056c687fb91e5e5fa0d215fb94d112de8b9b3a -r 25d1a86cdc869427c672143aac33e2ec69341ea9 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -866,6 +866,31 @@
plot._axes.text(x, y, self.text, **kwargs)
class HaloCatalogCallback(PlotCallback):
+ """
+ annotate_halos(halo_catalog, circle_kwargs=None,
+ width = None, annotate_field=False,
+ font_kwargs = None, factor = 1.0)
+
+ Plots circles at the locations of all the halos
+ in a halo catalog with radii corresponding to the
+ virial radius of each halo.
+
+ circle_kwargs: Contains the arguments controlling the
+ appearance of the circles, supplied to the
+ Matplotlib patch Circle.
+ width: 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: 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.
+ font_kwargs: Contains the arguments controlling the text
+ appearance of the annotated field.
+ factor: 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.
+ """
_type_name = 'halos'
region = None
https://bitbucket.org/yt_analysis/yt/commits/2da411ca16e3/
Changeset: 2da411ca16e3
Branch: yt-3.0
User: hegan
Date: 2014-07-03 17:10:36
Summary: making radius stop being a YTarray because of matplotlib bug
Affected #: 1 file
diff -r 25d1a86cdc869427c672143aac33e2ec69341ea9 -r 2da411ca16e3550f11653d2f5f1e48baf17570df yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -939,7 +939,7 @@
# Convert halo radii to a radius in pixels
radius = halo_data['virial_radius'][:].in_units(units)
- radius = radius*pixel_scale*self.factor/data_scale
+ radius = np.array(radius*pixel_scale*self.factor/data_scale)
if self.width:
pz = halo_data[field_z][:].in_units(units)/data_scale
https://bitbucket.org/yt_analysis/yt/commits/a5713a69df23/
Changeset: a5713a69df23
Branch: yt-3.0
User: ngoldbaum
Date: 2014-07-03 19:32:59
Summary: Merged in hegan/yt/yt-3.0 (pull request #991)
Updates to the annotate halos callback
Affected #: 1 file
diff -r 599797ab880b78ea678c7ce63bb4c70b41394620 -r a5713a69df23a99d04e52a66344aadc7c40295a5 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -16,6 +16,7 @@
import numpy as np
import h5py
+from matplotlib.patches import Circle
from yt.funcs import *
from yt.extern.six import add_metaclass
@@ -865,21 +866,49 @@
plot._axes.text(x, y, self.text, **kwargs)
class HaloCatalogCallback(PlotCallback):
+ """
+ annotate_halos(halo_catalog, circle_kwargs=None,
+ width = None, annotate_field=False,
+ font_kwargs = None, factor = 1.0)
+
+ Plots circles at the locations of all the halos
+ in a halo catalog with radii corresponding to the
+ virial radius of each halo.
+
+ circle_kwargs: Contains the arguments controlling the
+ appearance of the circles, supplied to the
+ Matplotlib patch Circle.
+ width: 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: 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.
+ font_kwargs: Contains the arguments controlling the text
+ appearance of the annotated field.
+ factor: 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.
+ """
_type_name = 'halos'
region = None
_descriptor = None
- def __init__(self, halo_catalog, col='white', alpha =1,
- width = None, annotate_field = False, font_kwargs = None):
+ def __init__(self, halo_catalog, circle_kwargs = None,
+ width = None, annotate_field = False,
+ font_kwargs = None, factor = 1.0):
PlotCallback.__init__(self)
self.halo_catalog = halo_catalog
- self.color = col
- self.alpha = alpha
self.width = width
self.annotate_field = annotate_field
self.font_kwargs = font_kwargs
+ self.factor = factor
+ if circle_kwargs is None:
+ circle_kwargs = {'edgecolor':'white', 'facecolor':'None'}
+ self.circle_kwargs = circle_kwargs
def __call__(self, plot):
data = plot.data
@@ -898,20 +927,20 @@
plot._axes.hold(True)
# Set up scales for pixel size and original data
- units = 'Mpccm'
pixel_scale = self.pixel_scale(plot)[0]
data_scale = data.pf.length_unit
+ units = data_scale.units
# Convert halo positions to code units of the plotted data
# and then to units of the plotted window
px = halo_data[field_x][:].in_units(units) / data_scale
py = halo_data[field_y][:].in_units(units) / data_scale
px, py = self.convert_to_plot(plot,[px,py])
+
+ # Convert halo radii to a radius in pixels
+ radius = halo_data['virial_radius'][:].in_units(units)
+ radius = np.array(radius*pixel_scale*self.factor/data_scale)
- # Convert halo radii to a radius in pixels
- radius = halo_data['radius'][:].in_units(units)
- radius = radius*pixel_scale/data_scale
-
if self.width:
pz = halo_data[field_z][:].in_units(units)/data_scale
pz = data.pf.arr(pz, 'code_length')
@@ -927,8 +956,10 @@
py = py[indices]
radius = radius[indices]
- plot._axes.scatter(px, py, edgecolors='None', marker='o',
- s=radius, c=self.color,alpha=self.alpha)
+ for x,y,r in zip(px, py, radius):
+ plot._axes.add_artist(Circle(xy=(x,y),
+ radius = r, **self.circle_kwargs))
+
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
plot._axes.hold(False)
Repository URL: https://bitbucket.org/yt_analysis/yt/
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