[yt-svn] commit/yt: 12 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Sep 7 11:10:14 PDT 2016
12 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/053e35273f81/
Changeset: 053e35273f81
Branch: yt
User: a_gilbert
Date: 2016-08-14 01:50:24+00:00
Summary: Updated origin input to accept floats or ints specifying xloc or yloc. Also updated docs accordingly.
Affected #: 2 files
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r 053e35273f81771c2075d9ea012024b72af679bc yt/visualization/base_plot_types.py
--- a/yt/visualization/base_plot_types.py
+++ b/yt/visualization/base_plot_types.py
@@ -357,6 +357,7 @@
self._toggle_colorbar(True)
return self
+
def get_multi_plot(nx, ny, colorbar = 'vertical', bw = 4, dpi=300,
cbar_padding = 0.4):
r"""Construct a multiple axes plot object, with or without a colorbar, into
@@ -440,3 +441,5 @@
ax.clear()
cbars.append(ax)
return fig, tr, cbars
+
+
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r 053e35273f81771c2075d9ea012024b72af679bc yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -396,18 +396,20 @@
Parameters
----------
- origin : string or length 1, 2, or 3 sequence of strings
+ origin : string or length 1, 2, or 3 sequence of strings or ints/floats
+ and strings.
The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings. In the
- first index the y-location is given by 'lower', 'upper', or 'center'.
- The second index is the x-location, given as 'left', 'right', or
- 'center'. Finally, the whether the origin is applied in 'domain'
- space, plot 'window' space or 'native' simulation coordinate system
- is given. For example, both 'upper-right-domain' and ['upper',
- 'right', 'domain'] place the origin in the upper right hand
- corner of domain space. If x or y are not given, a value is inferred.
- For instance, 'left-domain' corresponds to the lower-left hand corner
- of the simulation domain, 'center-domain' corresponds to the center
+ represented by '-' separated string or a tuple of strings or a mixed
+ tuple. In the first index the y-location is given by 'lower',
+ 'upper', or 'center' or a float or int. The second index is the
+ x-location, given as 'left', 'right', or 'center' or a float or int.
+ Finally, the whether the origin is applied in 'domain' space, plot
+ 'window' space or 'native' simulation coordinate system is given.
+ For example, both 'upper-right-domain' and ['upper', 'right',
+ 'domain'] place the origin in the upper right hand corner of domain
+ space. If x or y are not given, a value is inferred. For instance,
+ 'left-domain' corresponds to the lower-left hand corner of the
+ simulation domain, 'center-domain' corresponds to the center
of the simulation domain, or 'center-window' for the center of the
plot window. Further examples:
@@ -422,6 +424,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ (xloc, yloc, coord_sys) (0.5, 0.5, 'domain')
================================== ============================
"""
@@ -650,6 +653,9 @@
def _setup_origin(self):
origin = self.origin
axis_index = self.data_source.axis
+ xc = None
+ yc = None
+
if isinstance(origin, string_types):
origin = tuple(origin.split('-'))[:3]
if 1 == len(origin):
@@ -659,6 +665,9 @@
origin = (o0map[origin[0]],) + origin
elif 2 == len(origin) and origin[0] in set(['lower','upper','center']):
origin = (origin[0], 'center', origin[-1])
+ elif 2 == len(origin) and type(origin[0]) in set([int, float]):
+ xc = origin[0]
+ yc = origin[1]
assert origin[-1] in ['window', 'domain', 'native']
if origin[2] == 'window':
@@ -677,33 +686,42 @@
else:
mylog.warn("origin = {0}".format(origin))
msg = \
- ('origin keyword "{0}" not recognized, must declare "domain" '
- 'or "center" as the last term in origin.').format(self.origin)
+ ('origin keyword "{0}" not recognized, must declare "domain" '
+ 'or "center" as the last term in origin.').format(self.origin)
raise RuntimeError(msg)
+ if xc is None and yc is None:
+ if origin[0] == 'lower':
+ yc = yllim
+ elif origin[0] == 'upper':
+ yc = yrlim
+ elif origin[0] == 'center':
+ yc = (yllim + yrlim)/2.0
+ else:
+ mylog.warn("origin = {0}".format(origin))
+ msg = ('origin keyword "{0}" not recognized, must declare "lower" '
+ '"upper" or "center" as the first term in origin.')
+ msg = msg.format(self.origin)
+ raise RuntimeError(msg)
- if origin[0] == 'lower':
- yc = yllim
- elif origin[0] == 'upper':
- yc = yrlim
- elif origin[0] == 'center':
- yc = (yllim + yrlim)/2.0
- else:
- mylog.warn("origin = {0}".format(origin))
- msg = ('origin keyword "{0}" not recognized, must declare "lower" '
- '"upper" or "center" as the first term in origin.')
- msg = msg.format(self.origin)
- raise RuntimeError(msg)
+ if origin[1] == 'left':
+ xc = xllim
+ elif origin[1] == 'right':
+ xc = xrlim
+ elif origin[1] == 'center':
+ xc = (xllim + xrlim)/2.0
+ else:
+ mylog.warn("origin = {0}".format(origin))
+ msg = ('origin keyword "{0}" not recognized, must declare "left" '
+ '"right" or "center" as the second term in origin.')
+ msg = msg.format(self.origin)
+ raise RuntimeError(msg)
- if origin[1] == 'left':
- xc = xllim
- elif origin[1] == 'right':
- xc = xrlim
- elif origin[1] == 'center':
- xc = (xllim + xrlim)/2.0
- else:
- mylog.warn("origin = {0}".format(origin))
- msg = ('origin keyword "{0}" not recognized, must declare "left" '
- '"right" or "center" as the second term in origin.')
+ x_in_bounds = xc >= xllim and xc <= xrlim
+ y_in_bounds = yc >= yllim and yc <= yrlim
+
+ if not x_in_bounds and not y_in_bounds:
+ msg = ('orgin inputs not in bounds of specified coordinate sytem' +
+ 'domain.')
msg = msg.format(self.origin)
raise RuntimeError(msg)
@@ -807,12 +825,12 @@
ia = ImageArray(ia)
else:
ia = image
- self.plots[f] = WindowPlotMPL(
- ia, self._field_transform[f].name,
- self._field_transform[f].func,
- self._colormaps[f], extent, zlim,
- self.figure_size, font_size,
- self.aspect, fig, axes, cax)
+ self.plots[f] = WindowPlotMPL(
+ ia, self._field_transform[f].name,
+ self._field_transform[f].func,
+ self._colormaps[f], extent, zlim,
+ self.figure_size, font_size,
+ self.aspect, fig, axes, cax)
if not self._right_handed:
ax = self.plots[f].axes
@@ -1195,25 +1213,22 @@
units are assumed, for example (0.2, 0.3) requests a plot that has an
x width of 0.2 and a y width of 0.3 in code units. If units are
provided the resulting plot axis labels will use the supplied units.
- axes_unit : A string
- The name of the unit for the tick labels on the x and y axes.
- Defaults to None, which automatically picks an appropriate unit.
- If axes_unit is '1', 'u', or 'unitary', it will not display the
- units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings
+ origin : string or length 1, 2, or 3 sequence of strings or ints/floats
+ and strings.
The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings. In the
- first index the y-location is given by 'lower', 'upper', or 'center'.
- The second index is the x-location, given as 'left', 'right', or
- 'center'. Finally, whether the origin is applied in 'domain'
- space, plot 'window' space or 'native' simulation coordinate system
- is given. For example, both 'upper-right-domain' and ['upper',
- 'right', 'domain'] place the origin in the upper right hand
- corner of domain space. If x or y are not given, a value is inferred.
- For instance, the default location 'center-window' corresponds to
- the center of the plot window, 'left-domain' corresponds to the
- lower-left hand corner of the simulation domain, or 'center-domain'
- for the center of the simulation domain. Further examples:
+ represented by '-' separated string or a tuple of strings or a mixed
+ tuple. In the first index the y-location is given by 'lower',
+ 'upper', or 'center' or a float or int. The second index is the
+ x-location, given as 'left', 'right', or 'center' or a float or int.
+ Finally, the whether the origin is applied in 'domain' space, plot
+ 'window' space or 'native' simulation coordinate system is given.
+ For example, both 'upper-right-domain' and ['upper', 'right',
+ 'domain'] place the origin in the upper right hand corner of domain
+ space. If x or y are not given, a value is inferred. For instance,
+ 'left-domain' corresponds to the lower-left hand corner of the
+ simulation domain, 'center-domain' corresponds to the center
+ of the simulation domain, or 'center-window' for the center of the
+ plot window. Further examples:
================================== ============================
format example
@@ -1226,7 +1241,13 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ (xloc, yloc, coord_sys) (0.5, 0.5, 'domain')
================================== ============================
+ axes_unit : A string
+ The name of the unit for the tick labels on the x and y axes.
+ Defaults to None, which automatically picks an appropriate unit.
+ If axes_unit is '1', 'u', or 'unitary', it will not display the
+ units, and only show the axes name.
right_handed : boolean
Whether the implicit east vector for the image generated is set to make a right
handed coordinate system with a normal vector, the direction of the
@@ -1340,18 +1361,20 @@
Defaults to None, which automatically picks an appropriate unit.
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings
+ origin : string or length 1, 2, or 3 sequence of strings or ints/floats
+ and strings.
The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings. In the
- first index the y-location is given by 'lower', 'upper', or 'center'.
- The second index is the x-location, given as 'left', 'right', or
- 'center'. Finally, whether the origin is applied in 'domain'
- space, plot 'window' space or 'native' simulation coordinate system
- is given. For example, both 'upper-right-domain' and ['upper',
- 'right', 'domain'] place the origin in the upper right hand
- corner of domain space. If x or y are not given, a value is inferred.
- For instance, 'left-domain' corresponds to the lower-left hand corner
- of the simulation domain, 'center-domain' corresponds to the center
+ represented by '-' separated string or a tuple of strings or a mixed
+ tuple. In the first index the y-location is given by 'lower',
+ 'upper', or 'center' or a float or int. The second index is the
+ x-location, given as 'left', 'right', or 'center' or a float or int.
+ Finally, the whether the origin is applied in 'domain' space, plot
+ 'window' space or 'native' simulation coordinate system is given.
+ For example, both 'upper-right-domain' and ['upper', 'right',
+ 'domain'] place the origin in the upper right hand corner of domain
+ space. If x or y are not given, a value is inferred. For instance,
+ 'left-domain' corresponds to the lower-left hand corner of the
+ simulation domain, 'center-domain' corresponds to the center
of the simulation domain, or 'center-window' for the center of the
plot window. Further examples:
@@ -1366,6 +1389,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ (xloc, yloc, coord_sys) (0.5, 0.5, 'domain')
================================== ============================
right_handed : boolean
Whether the implicit east vector for the image generated is set to make a right
@@ -1840,22 +1864,22 @@
Defaults to None, which automatically picks an appropriate unit.
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings
- The location of the origin of the plot coordinate system for
- `AxisAlignedSlicePlot` objects; for `OffAxisSlicePlot` objects,
- this parameter is discarded. This is represented by '-' separated
- string or a tuple of strings. In the first index the y-location is
- given by 'lower', 'upper', or 'center'. The second index is the
- x-location, given as 'left', 'right', or 'center'. Finally,
- whether the origin is applied in 'domain' space, plot 'window' space
- or 'native' simulation coordinate system is given. For example, both
- 'upper-right-domain' and ['upper', 'right', 'domain'] place the
- origin in the upper right hand corner of domain space. If x or y are
- not given, a value is inferred. For instance, 'left-domain'
- corresponds to the lower-left hand corner of the simulation domain,
- 'center-domain' corresponds to the center of the simulation domain,
- or 'center-window' for the center of the plot window. Further
- examples:
+ origin : string or length 1, 2, or 3 sequence of strings or ints/floats
+ and strings.
+ The location of the origin of the plot coordinate system. This is
+ represented by '-' separated string or a tuple of strings or a mixed
+ tuple. In the first index the y-location is given by 'lower',
+ 'upper', or 'center' or a float or int. The second index is the
+ x-location, given as 'left', 'right', or 'center' or a float or int.
+ Finally, the whether the origin is applied in 'domain' space, plot
+ 'window' space or 'native' simulation coordinate system is given.
+ For example, both 'upper-right-domain' and ['upper', 'right',
+ 'domain'] place the origin in the upper right hand corner of domain
+ space. If x or y are not given, a value is inferred. For instance,
+ 'left-domain' corresponds to the lower-left hand corner of the
+ simulation domain, 'center-domain' corresponds to the center
+ of the simulation domain, or 'center-window' for the center of the
+ plot window. Further examples:
================================== ============================
format example
@@ -1868,6 +1892,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ (xloc, yloc, coord_sys) (0.5, 0.5, 'domain')
================================== ============================
north_vector : a sequence of floats
A vector defining the 'up' direction in the `OffAxisSlicePlot`; not
https://bitbucket.org/yt_analysis/yt/commits/d0fbd865c310/
Changeset: d0fbd865c310
Branch: yt
User: a_gilbert
Date: 2016-08-14 15:56:28+00:00
Summary: Updating from comment suggestions.
Affected #: 1 file
diff -r 053e35273f81771c2075d9ea012024b72af679bc -r d0fbd865c310c1e7ed3fc5c77925d0d2c8e1b4a9 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -665,7 +665,7 @@
origin = (o0map[origin[0]],) + origin
elif 2 == len(origin) and origin[0] in set(['lower','upper','center']):
origin = (origin[0], 'center', origin[-1])
- elif 2 == len(origin) and type(origin[0]) in set([int, float]):
+ elif 3 == len(origin) and isinstance(origin[0], (int, float)):
xc = origin[0]
yc = origin[1]
assert origin[-1] in ['window', 'domain', 'native']
https://bitbucket.org/yt_analysis/yt/commits/bc35afa585d4/
Changeset: bc35afa585d4
Branch: yt
User: a_gilbert
Date: 2016-08-14 17:38:12+00:00
Summary: Fixing sloppy errors.
Affected #: 1 file
diff -r d0fbd865c310c1e7ed3fc5c77925d0d2c8e1b4a9 -r bc35afa585d4cb0bffa5d85452efb074280ffa97 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -825,12 +825,12 @@
ia = ImageArray(ia)
else:
ia = image
- self.plots[f] = WindowPlotMPL(
- ia, self._field_transform[f].name,
- self._field_transform[f].func,
- self._colormaps[f], extent, zlim,
- self.figure_size, font_size,
- self.aspect, fig, axes, cax)
+ self.plots[f] = WindowPlotMPL(
+ ia, self._field_transform[f].name,
+ self._field_transform[f].func,
+ self._colormaps[f], extent, zlim,
+ self.figure_size, font_size,
+ self.aspect, fig, axes, cax)
if not self._right_handed:
ax = self.plots[f].axes
https://bitbucket.org/yt_analysis/yt/commits/d7a290297082/
Changeset: d7a290297082
Branch: yt
User: a_gilbert
Date: 2016-08-16 18:41:12+00:00
Summary: Updated docs to originals with extra note for new valid input format
Affected #: 1 file
diff -r bc35afa585d4cb0bffa5d85452efb074280ffa97 -r d7a2902970829d2b2085a0f976a5b571bb7216fb yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -396,36 +396,37 @@
Parameters
----------
- origin : string or length 1, 2, or 3 sequence of strings or ints/floats
- and strings.
- The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings or a mixed
- tuple. In the first index the y-location is given by 'lower',
- 'upper', or 'center' or a float or int. The second index is the
- x-location, given as 'left', 'right', or 'center' or a float or int.
- Finally, the whether the origin is applied in 'domain' space, plot
- 'window' space or 'native' simulation coordinate system is given.
- For example, both 'upper-right-domain' and ['upper', 'right',
- 'domain'] place the origin in the upper right hand corner of domain
- space. If x or y are not given, a value is inferred. For instance,
- 'left-domain' corresponds to the lower-left hand corner of the
- simulation domain, 'center-domain' corresponds to the center
- of the simulation domain, or 'center-window' for the center of the
- plot window. Further examples:
+ origin : string or length 1, 2, or 3 sequence of strings.
+ The location of the origin of the plot coordinate system. This
+ is typically represented by a '-' separated string or a tuple of
+ strings. In the first index the y-location is given by 'lower',
+ 'upper', or 'center'. The second index is the x-location, given as
+ 'left', 'right', or 'center'. Finally, the whether the origin is
+ applied in 'domain' space, plot 'window' space or 'native'
+ simulation coordinate system is given. For example, both
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the
+ origin in the upper right hand corner of domain space. If x or y
+ are not given, a value is inferred. For instance, 'left-domain'
+ corresponds to the lower-left hand corner of the simulation domain,
+ 'center-domain' corresponds to the center of the simulation domain,
+ or 'center-window' for the center of the plot window. In the event
+ that none of these options place the origin in a desired location,
+ a sequence of two numeric types and a string specifying the
+ coordinate space can be given.Further examples:
- ================================== ============================
- format example
- ================================== ============================
- '{space}' 'domain'
- '{xloc}-{space}' 'left-window'
- '{yloc}-{space}' 'upper-domain'
- '{yloc}-{xloc}-{space}' 'lower-right-window'
- ('{space}',) ('window',)
- ('{xloc}', '{space}') ('right', 'domain')
- ('{yloc}', '{space}') ('lower', 'window')
- ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, coord_sys) (0.5, 0.5, 'domain')
- ================================== ============================
+ ================================== ============================
+ format example
+ ================================== ============================
+ '{space}' 'domain'
+ '{xloc}-{space}' 'left-window'
+ '{yloc}-{space}' 'upper-domain'
+ '{yloc}-{xloc}-{space}' 'lower-right-window'
+ ('{space}',) ('window',)
+ ('{xloc}', '{space}') ('right', 'domain')
+ ('{yloc}', '{space}') ('lower', 'window')
+ ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ (xloc, yloc, coord_sys) (0.23, 0.5, 'domain')
+ ================================== ============================
"""
self.origin = origin
@@ -1213,22 +1214,23 @@
units are assumed, for example (0.2, 0.3) requests a plot that has an
x width of 0.2 and a y width of 0.3 in code units. If units are
provided the resulting plot axis labels will use the supplied units.
- origin : string or length 1, 2, or 3 sequence of strings or ints/floats
- and strings.
- The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings or a mixed
- tuple. In the first index the y-location is given by 'lower',
- 'upper', or 'center' or a float or int. The second index is the
- x-location, given as 'left', 'right', or 'center' or a float or int.
- Finally, the whether the origin is applied in 'domain' space, plot
- 'window' space or 'native' simulation coordinate system is given.
- For example, both 'upper-right-domain' and ['upper', 'right',
- 'domain'] place the origin in the upper right hand corner of domain
- space. If x or y are not given, a value is inferred. For instance,
- 'left-domain' corresponds to the lower-left hand corner of the
- simulation domain, 'center-domain' corresponds to the center
- of the simulation domain, or 'center-window' for the center of the
- plot window. Further examples:
+ origin : string or length 1, 2, or 3 sequence of strings.
+ The location of the origin of the plot coordinate system. This
+ is typically represented by a '-' separated string or a tuple of
+ strings. In the first index the y-location is given by 'lower',
+ 'upper', or 'center'. The second index is the x-location, given as
+ 'left', 'right', or 'center'. Finally, the whether the origin is
+ applied in 'domain' space, plot 'window' space or 'native'
+ simulation coordinate system is given. For example, both
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the origin
+ in the upper right hand corner of domain space. If x or y are not given,
+ a value is inferred. For instance, 'left-domain' corresponds to the
+ lower-left hand corner of the simulation domain, 'center-domain'
+ corresponds to the center of the simulation domain, or 'center-window'
+ for the center of the plot window. In the event that none of these
+ options place the origin in a desired location, a sequence of two
+ numeric types and a string specifying the coordinate space can be
+ given.Further examples:
================================== ============================
format example
@@ -1241,7 +1243,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, coord_sys) (0.5, 0.5, 'domain')
+ (xloc, yloc, coord_sys) (0.23, 0.5, 'domain')
================================== ============================
axes_unit : A string
The name of the unit for the tick labels on the x and y axes.
@@ -1361,22 +1363,23 @@
Defaults to None, which automatically picks an appropriate unit.
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings or ints/floats
- and strings.
- The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings or a mixed
- tuple. In the first index the y-location is given by 'lower',
- 'upper', or 'center' or a float or int. The second index is the
- x-location, given as 'left', 'right', or 'center' or a float or int.
- Finally, the whether the origin is applied in 'domain' space, plot
- 'window' space or 'native' simulation coordinate system is given.
- For example, both 'upper-right-domain' and ['upper', 'right',
- 'domain'] place the origin in the upper right hand corner of domain
- space. If x or y are not given, a value is inferred. For instance,
- 'left-domain' corresponds to the lower-left hand corner of the
- simulation domain, 'center-domain' corresponds to the center
- of the simulation domain, or 'center-window' for the center of the
- plot window. Further examples:
+ origin : string or length 1, 2, or 3 sequence of strings.
+ The location of the origin of the plot coordinate system. This
+ is typically represented by a '-' separated string or a tuple of
+ strings. In the first index the y-location is given by 'lower',
+ 'upper', or 'center'. The second index is the x-location, given as
+ 'left', 'right', or 'center'. Finally, the whether the origin is
+ applied in 'domain' space, plot 'window' space or 'native'
+ simulation coordinate system is given. For example, both
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the origin
+ in the upper right hand corner of domain space. If x or y are not given,
+ a value is inferred. For instance, 'left-domain' corresponds to the
+ lower-left hand corner of the simulation domain, 'center-domain'
+ corresponds to the center of the simulation domain, or 'center-window'
+ for the center of the plot window. In the event that none of these
+ options place the origin in a desired location, a sequence of two
+ numeric types and a string specifying the coordinate space can be
+ given.Further examples:
================================== ============================
format example
@@ -1389,7 +1392,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, coord_sys) (0.5, 0.5, 'domain')
+ (xloc, yloc, coord_sys) (0.23, 0.5, 'domain')
================================== ============================
right_handed : boolean
Whether the implicit east vector for the image generated is set to make a right
@@ -1864,22 +1867,24 @@
Defaults to None, which automatically picks an appropriate unit.
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings or ints/floats
- and strings.
- The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings or a mixed
- tuple. In the first index the y-location is given by 'lower',
- 'upper', or 'center' or a float or int. The second index is the
- x-location, given as 'left', 'right', or 'center' or a float or int.
- Finally, the whether the origin is applied in 'domain' space, plot
- 'window' space or 'native' simulation coordinate system is given.
- For example, both 'upper-right-domain' and ['upper', 'right',
- 'domain'] place the origin in the upper right hand corner of domain
- space. If x or y are not given, a value is inferred. For instance,
- 'left-domain' corresponds to the lower-left hand corner of the
- simulation domain, 'center-domain' corresponds to the center
- of the simulation domain, or 'center-window' for the center of the
- plot window. Further examples:
+ origin : string or length 1, 2, or 3 sequence of strings.
+ The location of the origin of the plot coordinate system for
+ `AxisAlignedSlicePlot` objects; for `OffAxisSlicePlot` objects this
+ parameter is discarded. This is typically represented by a '-' separated
+ string or a tuple of strings. In the first index the y-location
+ is given by 'lower', 'upper', or 'center'. The second index is the
+ x-location, given as 'left', 'right', or 'center'. Finally, the whether
+ the origin is applied in 'domain' space, plot 'window' space or 'native'
+ simulation coordinate system is given. For example, both
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the origin
+ in the upper right hand corner of domain space. If x or y are not given,
+ a value is inferred. For instance, 'left-domain' corresponds to the
+ lower-left hand corner of the simulation domain, 'center-domain'
+ corresponds to the center of the simulation domain, or 'center-window'
+ for the center of the plot window. In the event that none of these
+ options place the origin in a desired location, a sequence of two
+ numeric types and a string specifying the coordinate space can be given.
+ Further examples:
================================== ============================
format example
@@ -1892,7 +1897,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, coord_sys) (0.5, 0.5, 'domain')
+ (xloc, yloc, coord_sys) (0.23, 0.5, 'domain')
================================== ============================
north_vector : a sequence of floats
A vector defining the 'up' direction in the `OffAxisSlicePlot`; not
https://bitbucket.org/yt_analysis/yt/commits/6bff2e984ee3/
Changeset: 6bff2e984ee3
Branch: yt
User: a_gilbert
Date: 2016-08-16 22:05:38+00:00
Summary: Updated docs, added a test for origin parameters.
Affected #: 2 files
diff -r d7a2902970829d2b2085a0f976a5b571bb7216fb -r 6bff2e984ee33d88b567ae6e03364d4c5093e012 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -425,7 +425,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, coord_sys) (0.23, 0.5, 'domain')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
================================== ============================
"""
@@ -1215,11 +1215,11 @@
x width of 0.2 and a y width of 0.3 in code units. If units are
provided the resulting plot axis labels will use the supplied units.
origin : string or length 1, 2, or 3 sequence of strings.
- The location of the origin of the plot coordinate system. This
- is typically represented by a '-' separated string or a tuple of
- strings. In the first index the y-location is given by 'lower',
- 'upper', or 'center'. The second index is the x-location, given as
- 'left', 'right', or 'center'. Finally, the whether the origin is
+ The location of the origin of the plot coordinate system. This
+ is typically represented by a '-' separated string or a tuple of
+ strings. In the first index the y-location is given by 'lower',
+ 'upper', or 'center'. The second index is the x-location, given as
+ 'left', 'right', or 'center'. Finally, the whether the origin is
applied in 'domain' space, plot 'window' space or 'native'
simulation coordinate system is given. For example, both
'upper-right-domain' and ['upper', 'right', 'domain'] place the origin
@@ -1229,7 +1229,7 @@
corresponds to the center of the simulation domain, or 'center-window'
for the center of the plot window. In the event that none of these
options place the origin in a desired location, a sequence of two
- numeric types and a string specifying the coordinate space can be
+ numeric types and a string specifying the coordinate space can be
given.Further examples:
================================== ============================
@@ -1243,7 +1243,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, coord_sys) (0.23, 0.5, 'domain')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
================================== ============================
axes_unit : A string
The name of the unit for the tick labels on the x and y axes.
@@ -1364,11 +1364,11 @@
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
origin : string or length 1, 2, or 3 sequence of strings.
- The location of the origin of the plot coordinate system. This
- is typically represented by a '-' separated string or a tuple of
- strings. In the first index the y-location is given by 'lower',
- 'upper', or 'center'. The second index is the x-location, given as
- 'left', 'right', or 'center'. Finally, the whether the origin is
+ The location of the origin of the plot coordinate system. This
+ is typically represented by a '-' separated string or a tuple of
+ strings. In the first index the y-location is given by 'lower',
+ 'upper', or 'center'. The second index is the x-location, given as
+ 'left', 'right', or 'center'. Finally, the whether the origin is
applied in 'domain' space, plot 'window' space or 'native'
simulation coordinate system is given. For example, both
'upper-right-domain' and ['upper', 'right', 'domain'] place the origin
@@ -1378,7 +1378,7 @@
corresponds to the center of the simulation domain, or 'center-window'
for the center of the plot window. In the event that none of these
options place the origin in a desired location, a sequence of two
- numeric types and a string specifying the coordinate space can be
+ numeric types and a string specifying the coordinate space can be
given.Further examples:
================================== ============================
@@ -1392,7 +1392,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, coord_sys) (0.23, 0.5, 'domain')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
================================== ============================
right_handed : boolean
Whether the implicit east vector for the image generated is set to make a right
@@ -1418,13 +1418,13 @@
"mip" : pick out the maximum value of the field in the line of sight.
- "sum" : This method is the same as integrate, except that it does not
- multiply by a path length when performing the integration, and is
+ "sum" : This method is the same as integrate, except that it does not
+ multiply by a path length when performing the integration, and is
just a straight summation of the field along the given axis. WARNING:
This should only be used for uniform resolution grid datasets, as other
datasets may result in unphysical images.
proj_style : string
- The method of projection--same as method keyword. Deprecated as of
+ The method of projection--same as method keyword. Deprecated as of
version 3.0.2. Please use method instead.
window_size : float
The size of the window in inches. Set to 8 by default.
@@ -1897,7 +1897,7 @@
('{xloc}', '{space}') ('right', 'domain')
('{yloc}', '{space}') ('lower', 'window')
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, coord_sys) (0.23, 0.5, 'domain')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
================================== ============================
north_vector : a sequence of floats
A vector defining the 'up' direction in the `OffAxisSlicePlot`; not
diff -r d7a2902970829d2b2085a0f976a5b571bb7216fb -r 6bff2e984ee33d88b567ae6e03364d4c5093e012 yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -115,7 +115,6 @@
((0, 'code_length'), (1, 'code_length')),
((0, 'code_length'), (1, 'code_length')),
((1, 'code_length'), (1, 'code_length')),
- None,
),
0.2 : (
((0.4, 'code_length'), (0.6, 'code_length')),
@@ -444,3 +443,28 @@
assert_raises(
YTInvalidFieldType, object, ds, normal, field_name_list)
+def test_setup_origin():
+ origin_inputs = ('domain', 'left-window', 'center-domain',
+ 'lower-right-window',
+ ('window',), ('right', 'domain'), ('lower', 'window'),
+ ('lower', 'right', 'window'), (0.5, 0.5, 'domain'))
+ w=(10, 'cm')
+
+ ds = fake_random_ds(32, length_unit=100.0)
+ generated_limits = []
+ correct_limits = [[(45.0, 50.0), (45.0, 50.0)],
+ [(0.0, 10.0), (0.0, 10.0)],
+ [(-5.0, 5.0), (-5.0, 5.0)],
+ [(-10.0, 0), (0, 10.0)],
+ [(0.0, 10.0), (0.0, 10.0)],
+ [(-55.0, -45.0), (-55.0, -45.0)],
+ [(-5.0, 5.0), (0.0, 10.0)],
+ [(-10.0, 0), (0, 10.0)],
+ [(-5.0, 5.0), (-5.0, 5.0)]
+ ]
+ for o in origin_inputs:
+ slc = SlicePlot(ds, 2, 'density', width=w, origin=o)
+ ax = slc.plots['density'].axes
+ generated_limits.append([ax.get_xlim(), ax.get_ylim()])
+
+ yield assert_equal, generated_limits, correct_limits
https://bitbucket.org/yt_analysis/yt/commits/15192426c13f/
Changeset: 15192426c13f
Branch: yt
User: a_gilbert
Date: 2016-08-16 22:59:16+00:00
Summary: Updating, accidently removed an argument from WIDTH_SPECS
Affected #: 1 file
diff -r 6bff2e984ee33d88b567ae6e03364d4c5093e012 -r 15192426c13fca9fc50c134e08356d8f79e4def0 yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -115,6 +115,7 @@
((0, 'code_length'), (1, 'code_length')),
((0, 'code_length'), (1, 'code_length')),
((1, 'code_length'), (1, 'code_length')),
+ None
),
0.2 : (
((0.4, 'code_length'), (0.6, 'code_length')),
https://bitbucket.org/yt_analysis/yt/commits/22498343c4ca/
Changeset: 22498343c4ca
Branch: yt
User: a_gilbert
Date: 2016-08-16 23:09:55+00:00
Summary: Debugging.
Affected #: 1 file
diff -r 15192426c13fca9fc50c134e08356d8f79e4def0 -r 22498343c4cab8eda5b12f47f63c3c3fa0e3515b yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -115,7 +115,7 @@
((0, 'code_length'), (1, 'code_length')),
((0, 'code_length'), (1, 'code_length')),
((1, 'code_length'), (1, 'code_length')),
- None
+ None,
),
0.2 : (
((0.4, 'code_length'), (0.6, 'code_length')),
https://bitbucket.org/yt_analysis/yt/commits/49c57c71b73e/
Changeset: 49c57c71b73e
Branch: yt
User: a_gilbert
Date: 2016-08-17 03:02:13+00:00
Summary: Added capacity for tuple of numeric and string unit specifier. Fixed testing.
Affected #: 2 files
diff -r 22498343c4cab8eda5b12f47f63c3c3fa0e3515b -r 49c57c71b73ee727e34b877f2ca5a8d2cdbbe05e yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -156,7 +156,8 @@
Parameters
----------
- data_source : :class:`yt.data_objects.construction_data_containers.YTQuadTreeProj` or :class:`yt.data_objects.selection_data_containers.YTSlice`
+ data_source : :class:`yt.data_objects.construction_data_containers.YTQuadTreeProj`
+ or :class:`yt.data_objects.selection_data_containers.YTSlice`
This is the source to be pixelized, which can be a projection or a
slice. (For cutting planes, see
`yt.visualization.fixed_resolution.ObliqueFixedResolutionBuffer`.)
@@ -396,8 +397,8 @@
Parameters
----------
- origin : string or length 1, 2, or 3 sequence of strings.
- The location of the origin of the plot coordinate system. This
+ origin : string or length 1, 2, or 3 sequence.
+ The location of the origin of the plot coordinate system. This
is typically represented by a '-' separated string or a tuple of
strings. In the first index the y-location is given by 'lower',
'upper', or 'center'. The second index is the x-location, given as
@@ -411,22 +412,24 @@
'center-domain' corresponds to the center of the simulation domain,
or 'center-window' for the center of the plot window. In the event
that none of these options place the origin in a desired location,
- a sequence of two numeric types and a string specifying the
- coordinate space can be given.Further examples:
+ a sequence of tuples and a string specifying the
+ coordinate space can be given. If plain numeric types are input,
+ units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
- '{space}' 'domain'
- '{xloc}-{space}' 'left-window'
- '{yloc}-{space}' 'upper-domain'
- '{yloc}-{xloc}-{space}' 'lower-right-window'
- ('{space}',) ('window',)
- ('{xloc}', '{space}') ('right', 'domain')
- ('{yloc}', '{space}') ('lower', 'window')
- ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
- ================================== ============================
+ ================================== ============================
+ format example
+ ================================== ============================
+ '{space}' 'domain'
+ '{xloc}-{space}' 'left-window'
+ '{yloc}-{space}' 'upper-domain'
+ '{yloc}-{xloc}-{space}' 'lower-right-window'
+ ('{space}',) ('window',)
+ ('{xloc}', '{space}') ('right', 'domain')
+ ('{yloc}', '{space}') ('lower', 'window')
+ ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ ((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
+ ================================== ============================
"""
self.origin = origin
@@ -667,8 +670,12 @@
elif 2 == len(origin) and origin[0] in set(['lower','upper','center']):
origin = (origin[0], 'center', origin[-1])
elif 3 == len(origin) and isinstance(origin[0], (int, float)):
- xc = origin[0]
- yc = origin[1]
+ xc = self.ds.quan(origin[0], 'code_length')
+ yc = self.ds.quan(origin[1], 'code_length')
+ elif 3 == len(origin) and isinstance(origin[0], tuple):
+ xc = YTQuantity(origin[0][0], origin[0][1])
+ xc = YTQuantity(origin[1][0], origin[0][1])
+
assert origin[-1] in ['window', 'domain', 'native']
if origin[2] == 'window':
@@ -1214,7 +1221,7 @@
units are assumed, for example (0.2, 0.3) requests a plot that has an
x width of 0.2 and a y width of 0.3 in code units. If units are
provided the resulting plot axis labels will use the supplied units.
- origin : string or length 1, 2, or 3 sequence of strings.
+ origin : string or length 1, 2, or 3 sequence.
The location of the origin of the plot coordinate system. This
is typically represented by a '-' separated string or a tuple of
strings. In the first index the y-location is given by 'lower',
@@ -1222,29 +1229,31 @@
'left', 'right', or 'center'. Finally, the whether the origin is
applied in 'domain' space, plot 'window' space or 'native'
simulation coordinate system is given. For example, both
- 'upper-right-domain' and ['upper', 'right', 'domain'] place the origin
- in the upper right hand corner of domain space. If x or y are not given,
- a value is inferred. For instance, 'left-domain' corresponds to the
- lower-left hand corner of the simulation domain, 'center-domain'
- corresponds to the center of the simulation domain, or 'center-window'
- for the center of the plot window. In the event that none of these
- options place the origin in a desired location, a sequence of two
- numeric types and a string specifying the coordinate space can be
- given.Further examples:
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the
+ origin in the upper right hand corner of domain space. If x or y
+ are not given, a value is inferred. For instance, 'left-domain'
+ corresponds to the lower-left hand corner of the simulation domain,
+ 'center-domain' corresponds to the center of the simulation domain,
+ or 'center-window' for the center of the plot window. In the event
+ that none of these options place the origin in a desired location,
+ a sequence of tuples and a string specifying the
+ coordinate space can be given. If plain numeric types are input,
+ units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
- '{space}' 'domain'
- '{xloc}-{space}' 'left-window'
- '{yloc}-{space}' 'upper-domain'
- '{yloc}-{xloc}-{space}' 'lower-right-window'
- ('{space}',) ('window',)
- ('{xloc}', '{space}') ('right', 'domain')
- ('{yloc}', '{space}') ('lower', 'window')
- ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
- ================================== ============================
+ ================================== ============================
+ format example
+ ================================== ============================
+ '{space}' 'domain'
+ '{xloc}-{space}' 'left-window'
+ '{yloc}-{space}' 'upper-domain'
+ '{yloc}-{xloc}-{space}' 'lower-right-window'
+ ('{space}',) ('window',)
+ ('{xloc}', '{space}') ('right', 'domain')
+ ('{yloc}', '{space}') ('lower', 'window')
+ ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ ((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
+ ================================== ============================
axes_unit : A string
The name of the unit for the tick labels on the x and y axes.
Defaults to None, which automatically picks an appropriate unit.
@@ -1363,7 +1372,7 @@
Defaults to None, which automatically picks an appropriate unit.
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings.
+ origin : string or length 1, 2, or 3 sequence.
The location of the origin of the plot coordinate system. This
is typically represented by a '-' separated string or a tuple of
strings. In the first index the y-location is given by 'lower',
@@ -1371,29 +1380,32 @@
'left', 'right', or 'center'. Finally, the whether the origin is
applied in 'domain' space, plot 'window' space or 'native'
simulation coordinate system is given. For example, both
- 'upper-right-domain' and ['upper', 'right', 'domain'] place the origin
- in the upper right hand corner of domain space. If x or y are not given,
- a value is inferred. For instance, 'left-domain' corresponds to the
- lower-left hand corner of the simulation domain, 'center-domain'
- corresponds to the center of the simulation domain, or 'center-window'
- for the center of the plot window. In the event that none of these
- options place the origin in a desired location, a sequence of two
- numeric types and a string specifying the coordinate space can be
- given.Further examples:
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the
+ origin in the upper right hand corner of domain space. If x or y
+ are not given, a value is inferred. For instance, 'left-domain'
+ corresponds to the lower-left hand corner of the simulation domain,
+ 'center-domain' corresponds to the center of the simulation domain,
+ or 'center-window' for the center of the plot window. In the event
+ that none of these options place the origin in a desired location,
+ a sequence of tuples and a string specifying the
+ coordinate space can be given. If plain numeric types are input,
+ units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
- '{space}' 'domain'
- '{xloc}-{space}' 'left-window'
- '{yloc}-{space}' 'upper-domain'
- '{yloc}-{xloc}-{space}' 'lower-right-window'
- ('{space}',) ('window',)
- ('{xloc}', '{space}') ('right', 'domain')
- ('{yloc}', '{space}') ('lower', 'window')
- ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
- ================================== ============================
+ ================================== ============================
+ format example
+ ================================== ============================
+ '{space}' 'domain'
+ '{xloc}-{space}' 'left-window'
+ '{yloc}-{space}' 'upper-domain'
+ '{yloc}-{xloc}-{space}' 'lower-right-window'
+ ('{space}',) ('window',)
+ ('{xloc}', '{space}') ('right', 'domain')
+ ('{yloc}', '{space}') ('lower', 'window')
+ ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ ((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
+ ================================== ============================
+
right_handed : boolean
Whether the implicit east vector for the image generated is set to make a right
handed coordinate system with the direction of the
@@ -1867,38 +1879,40 @@
Defaults to None, which automatically picks an appropriate unit.
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings.
+ origin : string or length 1, 2, or 3 sequence.
The location of the origin of the plot coordinate system for
- `AxisAlignedSlicePlot` objects; for `OffAxisSlicePlot` objects this
- parameter is discarded. This is typically represented by a '-' separated
- string or a tuple of strings. In the first index the y-location
- is given by 'lower', 'upper', or 'center'. The second index is the
- x-location, given as 'left', 'right', or 'center'. Finally, the whether
- the origin is applied in 'domain' space, plot 'window' space or 'native'
- simulation coordinate system is given. For example, both
- 'upper-right-domain' and ['upper', 'right', 'domain'] place the origin
- in the upper right hand corner of domain space. If x or y are not given,
- a value is inferred. For instance, 'left-domain' corresponds to the
- lower-left hand corner of the simulation domain, 'center-domain'
- corresponds to the center of the simulation domain, or 'center-window'
- for the center of the plot window. In the event that none of these
- options place the origin in a desired location, a sequence of two
- numeric types and a string specifying the coordinate space can be given.
- Further examples:
+ `AxisAlignedSlicePlot` object; for `OffAxisSlicePlot` objects this
+ parameter is discarded. This is typically represented by a '-'
+ separated string or a tuple of strings. In the first index the
+ y-location is given by 'lower', 'upper', or 'center'. The second index
+ is the x-location, given as 'left', 'right', or 'center'. Finally, the
+ whether the origin is applied in 'domain' space, plot 'window' space or
+ 'native' simulation coordinate system is given. For example, both
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the
+ origin in the upper right hand corner of domain space. If x or y
+ are not given, a value is inferred. For instance, 'left-domain'
+ corresponds to the lower-left hand corner of the simulation domain,
+ 'center-domain' corresponds to the center of the simulation domain,
+ or 'center-window' for the center of the plot window. In the event
+ that none of these options place the origin in a desired location,
+ a sequence of tuples and a string specifying the
+ coordinate space can be given. If plain numeric types are input,
+ units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
- '{space}' 'domain'
- '{xloc}-{space}' 'left-window'
- '{yloc}-{space}' 'upper-domain'
- '{yloc}-{xloc}-{space}' 'lower-right-window'
- ('{space}',) ('window',)
- ('{xloc}', '{space}') ('right', 'domain')
- ('{yloc}', '{space}') ('lower', 'window')
- ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
- ================================== ============================
+ ================================== ============================
+ format example
+ ================================== ============================
+ '{space}' 'domain'
+ '{xloc}-{space}' 'left-window'
+ '{yloc}-{space}' 'upper-domain'
+ '{yloc}-{xloc}-{space}' 'lower-right-window'
+ ('{space}',) ('window',)
+ ('{xloc}', '{space}') ('right', 'domain')
+ ('{yloc}', '{space}') ('lower', 'window')
+ ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ ((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
+ ================================== ============================
north_vector : a sequence of floats
A vector defining the 'up' direction in the `OffAxisSlicePlot`; not
used in `AxisAlignedSlicePlot`. This option sets the orientation of the
diff -r 22498343c4cab8eda5b12f47f63c3c3fa0e3515b -r 49c57c71b73ee727e34b877f2ca5a8d2cdbbe05e yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -448,7 +448,8 @@
origin_inputs = ('domain', 'left-window', 'center-domain',
'lower-right-window',
('window',), ('right', 'domain'), ('lower', 'window'),
- ('lower', 'right', 'window'), (0.5, 0.5, 'domain'))
+ ('lower', 'right', 'window'), (0.5, 0.5, 'domain'),
+ ((50, 'cm'), (50, 'cm'), 'domain'))
w=(10, 'cm')
ds = fake_random_ds(32, length_unit=100.0)
@@ -462,10 +463,11 @@
[(-5.0, 5.0), (0.0, 10.0)],
[(-10.0, 0), (0, 10.0)],
[(-5.0, 5.0), (-5.0, 5.0)]
+ [(-5.0, 5.0), (-5.0, 5.0)]
]
for o in origin_inputs:
slc = SlicePlot(ds, 2, 'density', width=w, origin=o)
ax = slc.plots['density'].axes
generated_limits.append([ax.get_xlim(), ax.get_ylim()])
- yield assert_equal, generated_limits, correct_limits
+ yield assert_array_almost_equal, correct_limits, generated_limits
https://bitbucket.org/yt_analysis/yt/commits/405474784eb3/
Changeset: 405474784eb3
Branch: yt
User: a_gilbert
Date: 2016-08-17 22:01:54+00:00
Summary: Tests are up and running.
Affected #: 2 files
diff -r 49c57c71b73ee727e34b877f2ca5a8d2cdbbe05e -r 405474784eb337baf3aff2acd48b6acc9cbe9281 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -674,7 +674,7 @@
yc = self.ds.quan(origin[1], 'code_length')
elif 3 == len(origin) and isinstance(origin[0], tuple):
xc = YTQuantity(origin[0][0], origin[0][1])
- xc = YTQuantity(origin[1][0], origin[0][1])
+ yc = YTQuantity(origin[1][0], origin[0][1])
assert origin[-1] in ['window', 'domain', 'native']
@@ -761,7 +761,6 @@
if self.aspect is None:
self.aspect = float((self.ds.quan(1.0, unit_y) /
self.ds.quan(1.0, unit_x)).in_cgs())
-
extentx = [(self.xlim[i] - xc).in_units(unit_x) for i in (0, 1)]
extenty = [(self.ylim[i] - yc).in_units(unit_y) for i in (0, 1)]
diff -r 49c57c71b73ee727e34b877f2ca5a8d2cdbbe05e -r 405474784eb337baf3aff2acd48b6acc9cbe9281 yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -445,29 +445,40 @@
YTInvalidFieldType, object, ds, normal, field_name_list)
def test_setup_origin():
- origin_inputs = ('domain', 'left-window', 'center-domain',
+ origin_inputs = ('domain',
+ 'left-window',
+ 'center-domain',
'lower-right-window',
- ('window',), ('right', 'domain'), ('lower', 'window'),
- ('lower', 'right', 'window'), (0.5, 0.5, 'domain'),
+ ('window',),
+ ('right', 'domain'),
+ ('lower', 'window'),
+ ('lower', 'right', 'window'),
+ (0.5, 0.5, 'domain'),
((50, 'cm'), (50, 'cm'), 'domain'))
w=(10, 'cm')
ds = fake_random_ds(32, length_unit=100.0)
generated_limits = []
- correct_limits = [[(45.0, 50.0), (45.0, 50.0)],
- [(0.0, 10.0), (0.0, 10.0)],
- [(-5.0, 5.0), (-5.0, 5.0)],
- [(-10.0, 0), (0, 10.0)],
- [(0.0, 10.0), (0.0, 10.0)],
- [(-55.0, -45.0), (-55.0, -45.0)],
- [(-5.0, 5.0), (0.0, 10.0)],
- [(-10.0, 0), (0, 10.0)],
- [(-5.0, 5.0), (-5.0, 5.0)]
- [(-5.0, 5.0), (-5.0, 5.0)]
+ #lower limit -> llim
+ #upper limit -> ulim
+ # xllim xulim yllim yulim
+ correct_limits = [45.0, 55.0, 45.0, 55.0,
+ 0.0, 10.0, 0.0, 10.0,
+ -5.0, 5.0, -5.0, 5.0,
+ -10.0, 0, 0, 10.0,
+ 0.0, 10.0, 0.0, 10.0,
+ -55.0, -45.0, -55.0, -45.0,
+ -5.0, 5.0, 0.0, 10.0,
+ -10.0, 0, 0, 10.0,
+ -5.0, 5.0, -5.0, 5.0,
+ -5.0, 5.0, -5.0, 5.0
]
for o in origin_inputs:
slc = SlicePlot(ds, 2, 'density', width=w, origin=o)
ax = slc.plots['density'].axes
- generated_limits.append([ax.get_xlim(), ax.get_ylim()])
-
+ xlims = ax.get_xlim()
+ ylims = ax.get_ylim()
+ lims = [xlims[0], xlims[1], ylims[0], ylims[1]]
+ for l in lims:
+ generated_limits.append(l)
yield assert_array_almost_equal, correct_limits, generated_limits
https://bitbucket.org/yt_analysis/yt/commits/a3465e29e8f8/
Changeset: a3465e29e8f8
Branch: yt
User: ngoldbaum
Date: 2016-08-25 15:51:00+00:00
Summary: merging with mainline
Affected #: 56 files
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -23,6 +23,7 @@
yt/geometry/particle_smooth.c
yt/geometry/selection_routines.c
yt/utilities/amr_utils.c
+yt/utilities/lib/autogenerated_element_samplers.c
yt/utilities/kdtree/forthonf2c.h
yt/utilities/libconfig_wrapper.c
yt/utilities/spatial/ckdtree.c
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -3,6 +3,7 @@
include yt/visualization/mapserver/html/leaflet/*.css
include yt/visualization/mapserver/html/leaflet/*.js
include yt/visualization/mapserver/html/leaflet/images/*.png
+include yt/utilities/mesh_types.yaml
exclude scripts/pr_backport.py
recursive-include yt *.py *.pyx *.pxd *.h README* *.txt LICENSE* *.cu
recursive-include doc *.rst *.txt *.py *.ipynb *.png *.jpg *.css *.html
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -1429,25 +1429,24 @@
YT_DEPS+=('netcdf4')
fi
- # Here is our dependency list for yt
- log_cmd conda update --yes conda
+ log_cmd ${DEST_DIR}/bin/conda update --yes conda
log_cmd echo "DEPENDENCIES" ${YT_DEPS[@]}
for YT_DEP in "${YT_DEPS[@]}"; do
echo "Installing $YT_DEP"
- log_cmd conda install --yes ${YT_DEP}
+ log_cmd ${DEST_DIR}/bin/conda install --yes ${YT_DEP}
done
if [ $INST_PY3 -eq 1 ]
then
echo "Installing mercurial"
- log_cmd conda create -y -n py27 python=2.7 mercurial
+ log_cmd ${DEST_DIR}/bin/conda create -y -n py27 python=2.7 mercurial
log_cmd ln -s ${DEST_DIR}/envs/py27/bin/hg ${DEST_DIR}/bin
fi
- log_cmd pip install python-hglib
+ log_cmd ${DEST_DIR}/bin/pip install python-hglib
- log_cmd hg clone https://bitbucket.org/yt_analysis/yt_conda ${DEST_DIR}/src/yt_conda
+ log_cmd ${DEST_DIR}/bin/hg clone https://bitbucket.org/yt_analysis/yt_conda ${DEST_DIR}/src/yt_conda
if [ $INST_EMBREE -eq 1 ]
then
@@ -1474,17 +1473,17 @@
( ${GETFILE} "$PYEMBREE_URL" 2>&1 ) 1>> ${LOG_FILE} || do_exit
log_cmd unzip ${DEST_DIR}/src/master.zip
pushd ${DEST_DIR}/src/pyembree-master &> /dev/null
- log_cmd python setup.py install build_ext -I${DEST_DIR}/include -L${DEST_DIR}/lib
+ log_cmd ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py install build_ext -I${DEST_DIR}/include -L${DEST_DIR}/lib
popd &> /dev/null
fi
if [ $INST_ROCKSTAR -eq 1 ]
then
echo "Building Rockstar"
- ( hg clone http://bitbucket.org/MatthewTurk/rockstar ${DEST_DIR}/src/rockstar/ 2>&1 ) 1>> ${LOG_FILE}
- ROCKSTAR_PACKAGE=$(conda build ${DEST_DIR}/src/yt_conda/rockstar --output)
- log_cmd conda build ${DEST_DIR}/src/yt_conda/rockstar
- log_cmd conda install $ROCKSTAR_PACKAGE
+ ( ${DEST_DIR}/bin/hg clone http://bitbucket.org/MatthewTurk/rockstar ${DEST_DIR}/src/rockstar/ 2>&1 ) 1>> ${LOG_FILE}
+ ROCKSTAR_PACKAGE=$(${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar --output)
+ log_cmd ${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar
+ log_cmd ${DEST_DIR}/bin/conda install $ROCKSTAR_PACKAGE
ROCKSTAR_DIR=${DEST_DIR}/src/rockstar
fi
@@ -1493,20 +1492,20 @@
then
if [ $INST_PY3 -eq 1 ]
then
- log_cmd pip install pyx
+ log_cmd ${DEST_DIR}/bin/pip install pyx
else
- log_cmd pip install pyx==0.12.1
+ log_cmd ${DEST_DIR}/bin/pip install pyx==0.12.1
fi
fi
if [ $INST_YT_SOURCE -eq 0 ]
then
echo "Installing yt"
- log_cmd conda install -c conda-forge --yes yt
+ log_cmd ${DEST_DIR}/bin/conda install -c conda-forge --yes yt
else
echo "Building yt from source"
YT_DIR="${DEST_DIR}/src/yt-hg"
- log_cmd hg clone -r ${BRANCH} https://bitbucket.org/yt_analysis/yt ${YT_DIR}
+ log_cmd ${DEST_DIR}/bin/hg clone -r ${BRANCH} https://bitbucket.org/yt_analysis/yt ${YT_DIR}
if [ $INST_EMBREE -eq 1 ]
then
echo $DEST_DIR > ${YT_DIR}/embree.cfg
@@ -1517,7 +1516,7 @@
ROCKSTAR_LIBRARY_PATH=${DEST_DIR}/lib
fi
pushd ${YT_DIR} &> /dev/null
- ( LIBRARY_PATH=$ROCKSTAR_LIBRARY_PATH python setup.py develop 2>&1) 1>> ${LOG_FILE} || do_exit
+ ( LIBRARY_PATH=$ROCKSTAR_LIBRARY_PATH ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1) 1>> ${LOG_FILE} || do_exit
popd &> /dev/null
fi
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c doc/source/analyzing/analysis_modules/absorption_spectrum.rst
--- a/doc/source/analyzing/analysis_modules/absorption_spectrum.rst
+++ b/doc/source/analyzing/analysis_modules/absorption_spectrum.rst
@@ -116,7 +116,12 @@
Continuum features with optical depths that follow a power law can also be
added. Like adding lines, you must specify details like the wavelength
and the field in the dataset and LightRay that is tied to this feature.
-Below, we will add H Lyman continuum.
+The wavelength refers to the location at which the continuum begins to be
+applied to the dataset, and as it moves to lower wavelength values, the
+optical depth value decreases according to the defined power law. The
+normalization value is the column density of the linked field which results
+in an optical depth of 1 at the defined wavelength. Below, we add the hydrogen
+Lyman continuum.
.. code-block:: python
@@ -131,7 +136,7 @@
Making the Spectrum
^^^^^^^^^^^^^^^^^^^
-Once all the lines and continuum are added, it is time to make a spectrum out
+Once all the lines and continuua are added, it is time to make a spectrum out
of some light ray data.
.. code-block:: python
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c setup.py
--- a/setup.py
+++ b/setup.py
@@ -114,6 +114,9 @@
["yt/utilities/spatial/ckdtree.pyx"],
include_dirs=["yt/utilities/lib/"],
libraries=std_libs),
+ Extension("yt.utilities.lib.autogenerated_element_samplers",
+ ["yt/utilities/lib/autogenerated_element_samplers.pyx"],
+ include_dirs=["yt/utilities/lib/"]),
Extension("yt.utilities.lib.bitarray",
["yt/utilities/lib/bitarray.pyx"],
libraries=std_libs),
@@ -193,7 +196,7 @@
"particle_mesh_operations", "depth_first_octree", "fortran_reader",
"interpolators", "misc_utilities", "basic_octree", "image_utilities",
"points_in_volume", "quad_tree", "ray_integrators", "mesh_utilities",
- "amr_kdtools", "lenses",
+ "amr_kdtools", "lenses", "distance_queue"
]
for ext_name in lib_exts:
cython_extensions.append(
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c tests/tests.yaml
--- a/tests/tests.yaml
+++ b/tests/tests.yaml
@@ -67,11 +67,13 @@
local_ytdata_000:
- yt/frontends/ytdata
- local_absorption_spectrum_001:
+ local_absorption_spectrum_004:
- yt/analysis_modules/absorption_spectrum/tests/test_absorption_spectrum.py:test_absorption_spectrum_non_cosmo
+ - yt/analysis_modules/absorption_spectrum/tests/test_absorption_spectrum.py:test_absorption_spectrum_non_cosmo_novpec
- yt/analysis_modules/absorption_spectrum/tests/test_absorption_spectrum.py:test_absorption_spectrum_cosmo
- yt/analysis_modules/absorption_spectrum/tests/test_absorption_spectrum.py:test_absorption_spectrum_non_cosmo_sph
- yt/analysis_modules/absorption_spectrum/tests/test_absorption_spectrum.py:test_absorption_spectrum_cosmo_sph
+ - yt/analysis_modules/absorption_spectrum/tests/test_absorption_spectrum.py:test_absorption_spectrum_with_continuum
local_axialpix_001:
- yt/geometry/coordinates/tests/test_axial_pixelization.py:test_axial_pixelization
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
@@ -203,6 +203,13 @@
input_ds = input_file
field_data = input_ds.all_data()
+ # temperature field required to calculate voigt profile widths
+ if ('temperature' not in input_ds.derived_field_list) and \
+ (('gas', 'temperature') not in input_ds.derived_field_list):
+ raise RuntimeError(
+ "('gas', 'temperature') field required to be present in %s "
+ "for AbsorptionSpectrum to function." % input_file)
+
self.tau_field = np.zeros(self.lambda_field.size)
self.absorbers_list = []
@@ -210,6 +217,7 @@
comm = _get_comm(())
njobs = min(comm.size, len(self.line_list))
+ mylog.info("Creating spectrum")
self._add_lines_to_spectrum(field_data, use_peculiar_velocity,
output_absorbers_file,
subgrid_resolution=subgrid_resolution,
@@ -268,47 +276,96 @@
redshift_eff = ((1 + redshift) * \
(1 + field_data['redshift_dopp'])) - 1.
+ if not use_peculiar_velocity:
+ redshift_eff = redshift
+
return redshift, redshift_eff
def _add_continua_to_spectrum(self, field_data, use_peculiar_velocity,
observing_redshift=0.):
"""
- Add continuum features to the spectrum.
+ Add continuum features to the spectrum. Continuua are recorded as
+ a name, associated field, wavelength, normalization value, and index.
+ Continuua are applied at and below the denoted wavelength, where the
+ optical depth decreases as a power law of desired index. For positive
+ index values, this means optical depth is highest at the denoted
+ wavelength, and it drops with shorter and shorter wavelengths.
+ Consequently, transmitted flux undergoes a discontinuous cutoff at the
+ denoted wavelength, and then slowly increases with decreasing wavelength
+ according to the power law.
"""
# Change the redshifts of continuum sources to account for the
# redshift at which the observer sits
redshift, redshift_eff = self._apply_observing_redshift(field_data,
use_peculiar_velocity, observing_redshift)
- # Only add continuum features down to tau of 1.e-4.
- min_tau = 1.e-3
+ # min_tau is the minimum optical depth value that warrants
+ # accounting for an absorber. for a single absorber, noticeable
+ # continuum effects begin for tau = 1e-3 (leading to transmitted
+ # flux of e^-tau ~ 0.999). but we apply a cutoff to remove
+ # absorbers with insufficient column_density to contribute
+ # significantly to a continuum (see below). because lots of
+ # low column density absorbers can add up to a significant
+ # continuum effect, we normalize min_tau by the n_absorbers.
+ n_absorbers = field_data['dl'].size
+ min_tau = 1.e-3/n_absorbers
for continuum in self.continuum_list:
- column_density = field_data[continuum['field_name']] * field_data['dl']
+
+ # Normalization is in cm**-2, so column density must be as well
+ column_density = (field_data[continuum['field_name']] *
+ field_data['dl']).in_units('cm**-2')
+ if (column_density == 0).all():
+ mylog.info("Not adding continuum %s: insufficient column density" % continuum['label'])
+ continue
# redshift_eff field combines cosmological and velocity redshifts
if use_peculiar_velocity:
delta_lambda = continuum['wavelength'] * redshift_eff
else:
delta_lambda = continuum['wavelength'] * redshift
+
+ # right index of continuum affected area is wavelength itself
this_wavelength = delta_lambda + continuum['wavelength']
- right_index = np.digitize(this_wavelength, self.lambda_field).clip(0, self.n_lambda)
+ right_index = np.digitize(this_wavelength,
+ self.lambda_field).clip(0, self.n_lambda)
+ # left index of continuum affected area wavelength at which
+ # optical depth reaches tau_min
left_index = np.digitize((this_wavelength *
- np.power((min_tau * continuum['normalization'] /
- column_density), (1. / continuum['index']))),
- self.lambda_field).clip(0, self.n_lambda)
+ np.power((min_tau * continuum['normalization'] /
+ column_density),
+ (1. / continuum['index']))),
+ self.lambda_field).clip(0, self.n_lambda)
+ # Only calculate the effects of continuua where normalized
+ # column_density is greater than min_tau
+ # because lower column will not have significant contribution
valid_continuua = np.where(((column_density /
continuum['normalization']) > min_tau) &
(right_index - left_index > 1))[0]
+ if valid_continuua.size == 0:
+ mylog.info("Not adding continuum %s: insufficient column density or out of range" %
+ continuum['label'])
+ continue
+
pbar = get_pbar("Adding continuum - %s [%f A]: " % \
(continuum['label'], continuum['wavelength']),
valid_continuua.size)
+
+ # Tau value is (wavelength / continuum_wavelength)**index /
+ # (column_dens / norm)
+ # i.e. a power law decreasing as wavelength decreases
+
+ # Step through the absorber list and add continuum tau for each to
+ # the total optical depth for all wavelengths
for i, lixel in enumerate(valid_continuua):
- line_tau = np.power((self.lambda_field[left_index[lixel]:right_index[lixel]] /
- this_wavelength[lixel]), continuum['index']) * \
- column_density[lixel] / continuum['normalization']
- self.tau_field[left_index[lixel]:right_index[lixel]] += line_tau
+ cont_tau = \
+ np.power((self.lambda_field[left_index[lixel] :
+ right_index[lixel]] /
+ this_wavelength[lixel]), \
+ continuum['index']) * \
+ (column_density[lixel] / continuum['normalization'])
+ self.tau_field[left_index[lixel]:right_index[lixel]] += cont_tau
pbar.update(i)
pbar.finish()
@@ -333,6 +390,9 @@
# and deposit the lines into the spectrum
for line in parallel_objects(self.line_list, njobs=njobs):
column_density = field_data[line['field_name']] * field_data['dl']
+ if (column_density == 0).all():
+ mylog.info("Not adding line %s: insufficient column density" % line['label'])
+ continue
# redshift_eff field combines cosmological and velocity redshifts
# so delta_lambda gives the offset in angstroms from the rest frame
@@ -376,7 +436,10 @@
cdens = column_density.in_units("cm**-2").d # cm**-2
thermb = thermal_b.in_cgs().d # thermal b coefficient; cm / s
dlambda = delta_lambda.d # lambda offset; angstroms
- vlos = field_data['velocity_los'].in_units("km/s").d # km/s
+ if use_peculiar_velocity:
+ vlos = field_data['velocity_los'].in_units("km/s").d # km/s
+ else:
+ vlos = np.zeros(field_data['temperature'].size)
# When we actually deposit the voigt profile, sometimes we will
# have underresolved lines (ie lines with smaller widths than
@@ -413,6 +476,12 @@
# observed spectrum where it occurs and deposit a voigt profile
for i in parallel_objects(np.arange(n_absorbers), njobs=-1):
+ # if there is a ray element with temperature = 0 or column
+ # density = 0, skip it
+ if (thermal_b[i] == 0.) or (cdens[i] == 0.):
+ pbar.update(i)
+ continue
+
# the virtual window into which the line is deposited initially
# spans a region of 2 coarse spectral bins
# (one on each side of the center_index) but the window
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/analysis_modules/absorption_spectrum/tests/test_absorption_spectrum.py
--- a/yt/analysis_modules/absorption_spectrum/tests/test_absorption_spectrum.py
+++ b/yt/analysis_modules/absorption_spectrum/tests/test_absorption_spectrum.py
@@ -33,7 +33,8 @@
COSMO_PLUS_SINGLE = "enzo_cosmology_plus/RD0009/RD0009"
GIZMO_PLUS = "gizmo_cosmology_plus/N128L16.param"
GIZMO_PLUS_SINGLE = "gizmo_cosmology_plus/snap_N128L16_151.hdf5"
-
+ISO_GALAXY = "IsolatedGalaxy/galaxy0030/galaxy0030"
+FIRE = "FIRE_M12i_ref11/snapshot_600.hdf5"
@requires_file(COSMO_PLUS)
@requires_answer_testing()
@@ -145,6 +146,58 @@
shutil.rmtree(tmpdir)
@requires_file(COSMO_PLUS_SINGLE)
+ at requires_answer_testing()
+def test_absorption_spectrum_non_cosmo_novpec():
+ """
+ This test generates an absorption spectrum from a simple light ray on a
+ grid dataset
+ """
+
+ # Set up in a temp dir
+ tmpdir = tempfile.mkdtemp()
+ curdir = os.getcwd()
+ os.chdir(tmpdir)
+
+ lr = LightRay(COSMO_PLUS_SINGLE)
+
+ ray_start = [0,0,0]
+ ray_end = [1,1,1]
+ lr.make_light_ray(start_position=ray_start, end_position=ray_end,
+ fields=['temperature', 'density', 'H_number_density'],
+ data_filename='lightray.h5', use_peculiar_velocity=False)
+
+ sp = AbsorptionSpectrum(1200.0, 1300.0, 10001)
+
+ my_label = 'HI Lya'
+ field = 'H_number_density'
+ wavelength = 1215.6700 # Angstromss
+ f_value = 4.164E-01
+ gamma = 6.265e+08
+ mass = 1.00794
+
+ sp.add_line(my_label, field, wavelength, f_value,
+ gamma, mass, label_threshold=1.e10)
+
+ wavelength, flux = sp.make_spectrum('lightray.h5',
+ output_file='spectrum.h5',
+ line_list_file='lines.txt',
+ use_peculiar_velocity=False)
+
+ # load just-generated hdf5 file of spectral data (for consistency)
+ data = h5.File('spectrum.h5', 'r')
+
+ for key in data.keys():
+ func = lambda x=key: data[x][:]
+ func.__name__ = "{}_non_cosmo_novpec".format(key)
+ test = GenericArrayTest(None, func)
+ test_absorption_spectrum_non_cosmo_novpec.__name__ = test.description
+ yield test
+
+ # clean up
+ os.chdir(curdir)
+ shutil.rmtree(tmpdir)
+
+ at requires_file(COSMO_PLUS_SINGLE)
def test_equivalent_width_conserved():
"""
This tests that the equivalent width of the optical depth is conserved
@@ -360,3 +413,146 @@
# clean up
os.chdir(curdir)
shutil.rmtree(tmpdir)
+
+ at requires_file(ISO_GALAXY)
+ at requires_answer_testing()
+def test_absorption_spectrum_with_continuum():
+ """
+ This test generates an absorption spectrum from a simple light ray on a
+ grid dataset and adds Lyman alpha and Lyman continuum to it
+ """
+
+ # Set up in a temp dir
+ tmpdir = tempfile.mkdtemp()
+ curdir = os.getcwd()
+ os.chdir(tmpdir)
+
+ ds = load(ISO_GALAXY)
+ lr = LightRay(ds)
+
+ ray_start = ds.domain_left_edge
+ ray_end = ds.domain_right_edge
+ lr.make_light_ray(start_position=ray_start, end_position=ray_end,
+ fields=['temperature', 'density', 'H_number_density'],
+ data_filename='lightray.h5')
+
+ sp = AbsorptionSpectrum(800.0, 1300.0, 5001)
+
+ my_label = 'HI Lya'
+ field = 'H_number_density'
+ wavelength = 1215.6700 # Angstromss
+ f_value = 4.164E-01
+ gamma = 6.265e+08
+ mass = 1.00794
+
+ sp.add_line(my_label, field, wavelength, f_value,
+ gamma, mass, label_threshold=1.e10)
+
+ my_label = 'Ly C'
+ field = 'H_number_density'
+ wavelength = 912.323660 # Angstroms
+ normalization = 1.6e17
+ index = 3.0
+
+ sp.add_continuum(my_label, field, wavelength, normalization, index)
+
+ wavelength, flux = sp.make_spectrum('lightray.h5',
+ output_file='spectrum.h5',
+ line_list_file='lines.txt',
+ use_peculiar_velocity=True)
+
+ # load just-generated hdf5 file of spectral data (for consistency)
+ data = h5.File('spectrum.h5', 'r')
+
+ for key in data.keys():
+ func = lambda x=key: data[x][:]
+ func.__name__ = "{}_continuum".format(key)
+ test = GenericArrayTest(None, func)
+ test_absorption_spectrum_with_continuum.__name__ = test.description
+ yield test
+
+ # clean up
+ os.chdir(curdir)
+ shutil.rmtree(tmpdir)
+
+ at requires_file(FIRE)
+def test_absorption_spectrum_with_zero_field():
+ """
+ This test generates an absorption spectrum with some
+ particle dataset
+ """
+
+ # Set up in a temp dir
+ tmpdir = tempfile.mkdtemp()
+ curdir = os.getcwd()
+ os.chdir(tmpdir)
+
+ ds = load(FIRE)
+ lr = LightRay(ds)
+
+ # Define species and associated parameters to add to continuum
+ # Parameters used for both adding the transition to the spectrum
+ # and for fitting
+ # Note that for single species that produce multiple lines
+ # (as in the OVI doublet), 'numLines' will be equal to the number
+ # of lines, and f,gamma, and wavelength will have multiple values.
+
+ HI_parameters = {
+ 'name': 'HI',
+ 'field': 'H_number_density',
+ 'f': [.4164],
+ 'Gamma': [6.265E8],
+ 'wavelength': [1215.67],
+ 'mass': 1.00794,
+ 'numLines': 1,
+ 'maxN': 1E22, 'minN': 1E11,
+ 'maxb': 300, 'minb': 1,
+ 'maxz': 6, 'minz': 0,
+ 'init_b': 30,
+ 'init_N': 1E14
+ }
+
+ species_dicts = {'HI': HI_parameters}
+
+
+ # Get all fields that need to be added to the light ray
+ fields = [('gas','temperature')]
+ for s, params in species_dicts.items():
+ fields.append(params['field'])
+
+ # With a single dataset, a start_position and
+ # end_position or trajectory must be given.
+ # Trajectory should be given as (r, theta, phi)
+ lr.make_light_ray(
+ start_position=ds.arr([0., 0., 0.], 'unitary'),
+ end_position=ds.arr([1., 1., 1.], 'unitary'),
+ solution_filename='test_lightraysolution.txt',
+ data_filename='test_lightray.h5',
+ fields=fields)
+
+ # Create an AbsorptionSpectrum object extending from
+ # lambda = 900 to lambda = 1800, with 10000 pixels
+ sp = AbsorptionSpectrum(900.0, 1400.0, 50000)
+
+ # Iterate over species
+ for s, params in species_dicts.items():
+ # Iterate over transitions for a single species
+ for i in range(params['numLines']):
+ # Add the lines to the spectrum
+ sp.add_line(
+ s, params['field'],
+ params['wavelength'][i], params['f'][i],
+ params['Gamma'][i], params['mass'],
+ label_threshold=1.e10)
+
+
+ # Make and save spectrum
+ wavelength, flux = sp.make_spectrum(
+ 'test_lightray.h5',
+ output_file='test_spectrum.h5',
+ line_list_file='test_lines.txt',
+ use_peculiar_velocity=True)
+
+ # clean up
+ os.chdir(curdir)
+ shutil.rmtree(tmpdir)
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
--- a/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
+++ b/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
@@ -21,8 +21,6 @@
load
from yt.frontends.ytdata.utilities import \
save_as_dataset
-from yt.units.unit_object import \
- Unit
from yt.units.yt_array import \
YTArray
from yt.utilities.cosmology import \
@@ -391,7 +389,11 @@
# Initialize data structures.
self._data = {}
+ # temperature field is automatically added to fields
if fields is None: fields = []
+ if (('gas', 'temperature') not in fields) and \
+ ('temperature' not in fields):
+ fields.append(('gas', 'temperature'))
data_fields = fields[:]
all_fields = fields[:]
all_fields.extend(['dl', 'dredshift', 'redshift'])
@@ -604,19 +606,18 @@
self.cosmology.t_from_z(ds["current_redshift"])
extra_attrs = {"data_type": "yt_light_ray"}
field_types = dict([(field, "grid") for field in data.keys()])
+
# Only return LightRay elements with non-zero density
- mask_field_units = ['K', 'cm**-3', 'g/cm**3']
- mask_field_units = [Unit(u) for u in mask_field_units]
- for f in data:
- for u in mask_field_units:
- if data[f].units.same_dimensions_as(u):
- mask = data[f] > 0
- if not np.any(mask):
- raise RuntimeError(
- "No zones along light ray with nonzero %s. "
- "Please modify your light ray trajectory." % (f,))
- for key in data.keys():
- data[key] = data[key][mask]
+ if 'temperature' in data: f = 'temperature'
+ if ('gas', 'temperature') in data: f = ('gas', 'temperature')
+ if 'temperature' in data or ('gas', 'temperature') in data:
+ mask = data[f] > 0
+ if not np.any(mask):
+ raise RuntimeError(
+ "No zones along light ray with nonzero %s. "
+ "Please modify your light ray trajectory." % (f,))
+ for key in data.keys():
+ data[key] = data[key][mask]
save_as_dataset(ds, filename, data, field_types=field_types,
extra_attrs=extra_attrs)
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/analysis_modules/particle_trajectories/particle_trajectories.py
--- a/yt/analysis_modules/particle_trajectories/particle_trajectories.py
+++ b/yt/analysis_modules/particle_trajectories/particle_trajectories.py
@@ -11,7 +11,7 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-from yt.data_objects.data_containers import YTFieldData
+from yt.data_objects.field_data import YTFieldData
from yt.data_objects.time_series import DatasetSeries
from yt.utilities.lib.particle_mesh_operations import CICSample_3
from yt.utilities.parallel_tools.parallel_analysis_interface import \
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/construction_data_containers.py
--- a/yt/data_objects/construction_data_containers.py
+++ b/yt/data_objects/construction_data_containers.py
@@ -28,7 +28,8 @@
from yt.data_objects.data_containers import \
YTSelectionContainer1D, \
YTSelectionContainer2D, \
- YTSelectionContainer3D, \
+ YTSelectionContainer3D
+from yt.data_objects.field_data import \
YTFieldData
from yt.funcs import \
ensure_list, \
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -65,6 +65,8 @@
from yt.geometry.selection_routines import \
compose_selector
from yt.extern.six import add_metaclass, string_types
+from yt.data_objects.field_data import YTFieldData
+from yt.data_objects.profiles import create_profile
data_object_registry = {}
@@ -91,12 +93,6 @@
return tr
return save_state
-class YTFieldData(dict):
- """
- A Container object for field data, instead of just having it be a dict.
- """
- pass
-
class RegisteredDataContainer(type):
def __init__(cls, name, b, d):
type.__init__(cls, name, b, d)
@@ -813,8 +809,77 @@
ex = self._compute_extrema(field)
return ex[1] - ex[0]
- def hist(self, field, weight = None, bins = None):
- raise NotImplementedError
+ def profile(self, bin_fields, fields, n_bins=64,
+ extrema=None, logs=None, units=None,
+ weight_field="cell_mass",
+ accumulation=False, fractional=False,
+ deposition='ngp'):
+ r"""
+ Create a 1, 2, or 3D profile object from this data_source.
+
+ The dimensionality of the profile object is chosen by the number of
+ fields given in the bin_fields argument. This simply calls
+ :func:`yt.data_objects.profiles.create_profile`.
+
+ Parameters
+ ----------
+ bin_fields : list of strings
+ List of the binning fields for profiling.
+ fields : list of strings
+ The fields to be profiled.
+ n_bins : int or list of ints
+ The number of bins in each dimension. If None, 64 bins for
+ each bin are used for each bin field.
+ Default: 64.
+ extrema : dict of min, max tuples
+ Minimum and maximum values of the bin_fields for the profiles.
+ The keys correspond to the field names. Defaults to the extrema
+ of the bin_fields of the dataset. If a units dict is provided, extrema
+ are understood to be in the units specified in the dictionary.
+ logs : dict of boolean values
+ Whether or not to log the bin_fields for the profiles.
+ The keys correspond to the field names. Defaults to the take_log
+ attribute of the field.
+ units : dict of strings
+ The units of the fields in the profiles, including the bin_fields.
+ weight_field : str or tuple field identifier
+ The weight field for computing weighted average for the profile
+ values. If None, the profile values are sums of the data in
+ each bin.
+ accumulation : bool or list of bools
+ If True, the profile values for a bin n are the cumulative sum of
+ all the values from bin 0 to n. If -True, the sum is reversed so
+ that the value for bin n is the cumulative sum from bin N (total bins)
+ to n. If the profile is 2D or 3D, a list of values can be given to
+ control the summation in each dimension independently.
+ Default: False.
+ fractional : If True the profile values are divided by the sum of all
+ the profile data such that the profile represents a probability
+ distribution function.
+ deposition : Controls the type of deposition used for ParticlePhasePlots.
+ Valid choices are 'ngp' and 'cic'. Default is 'ngp'. This parameter is
+ ignored the if the input fields are not of particle type.
+
+
+ Examples
+ --------
+
+ Create a 1d profile. Access bin field from profile.x and field
+ data from profile[<field_name>].
+
+ >>> ds = load("DD0046/DD0046")
+ >>> ad = ds.all_data()
+ >>> profile = ad.profile(ad, [("gas", "density")],
+ ... [("gas", "temperature"),
+ ... ("gas", "velocity_x")])
+ >>> print (profile.x)
+ >>> print (profile["gas", "temperature"])
+ >>> plot = profile.plot()
+ """
+ p = create_profile(self, bin_fields, fields, n_bins,
+ extrema, logs, units, weight_field, accumulation,
+ fractional, deposition)
+ return p
def mean(self, field, axis=None, weight='ones'):
r"""Compute the mean of a field, optionally along an axis, with a
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/field_data.py
--- /dev/null
+++ b/yt/data_objects/field_data.py
@@ -0,0 +1,20 @@
+"""
+The YTFieldData object.
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2016, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+class YTFieldData(dict):
+ """
+ A Container object for field data, instead of just having it be a dict.
+ """
+ pass
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/grid_patch.py
--- a/yt/data_objects/grid_patch.py
+++ b/yt/data_objects/grid_patch.py
@@ -17,8 +17,9 @@
import numpy as np
from yt.data_objects.data_containers import \
- YTFieldData, \
YTSelectionContainer
+from yt.data_objects.field_data import \
+ YTFieldData
from yt.geometry.selection_routines import convert_mask_to_indices
import yt.geometry.particle_deposit as particle_deposit
from yt.utilities.exceptions import \
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/octree_subset.py
--- a/yt/data_objects/octree_subset.py
+++ b/yt/data_objects/octree_subset.py
@@ -17,8 +17,9 @@
import numpy as np
from yt.data_objects.data_containers import \
- YTFieldData, \
YTSelectionContainer
+from yt.data_objects.field_data import \
+ YTFieldData
import yt.geometry.particle_deposit as particle_deposit
import yt.geometry.particle_smooth as particle_smooth
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/particle_io.py
--- a/yt/data_objects/particle_io.py
+++ b/yt/data_objects/particle_io.py
@@ -21,11 +21,12 @@
ensure_list, \
mylog
from yt.extern.six import add_metaclass
+from yt.data_objects.field_data import \
+ YTFieldData
particle_handler_registry = defaultdict()
def particle_converter(func):
- from .data_containers import YTFieldData
def save_state(grid):
old_params = grid.field_parameters
old_keys = grid.field_data.keys()
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/profiles.py
--- a/yt/data_objects/profiles.py
+++ b/yt/data_objects/profiles.py
@@ -26,7 +26,9 @@
array_like_field, \
YTQuantity
from yt.units.unit_object import Unit
-from yt.data_objects.data_containers import YTFieldData
+from yt.data_objects.field_data import YTFieldData
+from yt.utilities.exceptions import \
+ YTIllDefinedProfile
from yt.utilities.lib.misc_utilities import \
new_bin_profile1d, \
new_bin_profile2d, \
@@ -453,6 +455,14 @@
def bounds(self):
return ((self.x_bins[0], self.x_bins[-1]),)
+ def plot(self):
+ r"""
+ This returns a :class:~yt.visualization.profile_plotter.ProfilePlot
+ with the fields that have been added to this object.
+ """
+ from yt.visualization.profile_plotter import ProfilePlot
+ return ProfilePlot.from_profiles(self)
+
class Profile1DFromDataset(ProfileNDFromDataset, Profile1D):
"""
A 1D profile object loaded from a ytdata dataset.
@@ -572,6 +582,14 @@
return ((self.x_bins[0], self.x_bins[-1]),
(self.y_bins[0], self.y_bins[-1]))
+ 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)
+
class Profile2DFromDataset(ProfileNDFromDataset, Profile2D):
"""
A 2D profile object loaded from a ytdata dataset.
@@ -928,7 +946,7 @@
data from profile[<field_name>].
>>> ds = load("DD0046/DD0046")
- >>> ad = ds.h.all_data()
+ >>> ad = ds.all_data()
>>> profile = create_profile(ad, [("gas", "density")],
... [("gas", "temperature"),
... ("gas", "velocity_x")])
@@ -940,10 +958,18 @@
fields = ensure_list(fields)
is_pfield = [data_source.ds._get_field_info(f).particle_type
for f in bin_fields + fields]
+ wf = None
+ if weight_field is not None:
+ wf = data_source.ds._get_field_info(weight_field)
+ is_pfield.append(wf.particle_type)
+ wf = wf.name
- if len(bin_fields) == 1:
+ if any(is_pfield) and not all(is_pfield):
+ raise YTIllDefinedProfile(
+ bin_fields, data_source._determine_fields(fields), wf, is_pfield)
+ elif len(bin_fields) == 1:
cls = Profile1D
- elif len(bin_fields) == 2 and np.all(is_pfield):
+ elif len(bin_fields) == 2 and all(is_pfield):
# log bin_fields set to False for Particle Profiles.
# doesn't make much sense for CIC deposition.
# accumulation and fractional set to False as well.
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -889,10 +889,12 @@
return new_unit
def set_code_units(self):
- self._set_code_unit_attributes()
# here we override units, if overrides have been provided.
self._override_code_units()
+ # set attributes like ds.length_unit
+ self._set_code_unit_attributes()
+
self.unit_registry.modify("code_length", self.length_unit)
self.unit_registry.modify("code_mass", self.mass_unit)
self.unit_registry.modify("code_time", self.time_unit)
@@ -932,19 +934,22 @@
def _override_code_units(self):
if len(self.units_override) == 0:
return
- mylog.warning("Overriding code units. This is an experimental and potentially "+
- "dangerous option that may yield inconsistent results, and must be used "+
- "very carefully, and only if you know what you want from it.")
+ mylog.warning(
+ "Overriding code units. This is an experimental and potentially "
+ "dangerous option that may yield inconsistent results, and must be "
+ "used very carefully, and only if you know what you want from it.")
for unit, cgs in [("length", "cm"), ("time", "s"), ("mass", "g"),
- ("velocity","cm/s"), ("magnetic","gauss"), ("temperature","K")]:
+ ("velocity","cm/s"), ("magnetic","gauss"),
+ ("temperature","K")]:
val = self.units_override.get("%s_unit" % unit, None)
if val is not None:
if isinstance(val, YTQuantity):
val = (val.v, str(val.units))
elif not isinstance(val, tuple):
val = (val, cgs)
- u = getattr(self, "%s_unit" % unit)
- mylog.info("Overriding %s_unit: %g %s -> %g %s.", unit, u.v, u.units, val[0], val[1])
+ u = getattr(self, "%s_unit" % unit, None)
+ mylog.info("Overriding %s_unit: %g -> %g %s.",
+ unit, u, val[0], val[1])
setattr(self, "%s_unit" % unit, self.quan(val[0], val[1]))
_arr = None
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/tests/test_profiles.py
--- a/yt/data_objects/tests/test_profiles.py
+++ b/yt/data_objects/tests/test_profiles.py
@@ -8,7 +8,13 @@
from yt.testing import \
fake_random_ds, \
assert_equal, \
+ assert_raises, \
assert_rel_equal
+from yt.utilities.exceptions import \
+ YTIllDefinedProfile
+from yt.visualization.profile_plotter import \
+ ProfilePlot, \
+ PhasePlot
_fields = ("density", "temperature", "dinosaurs", "tribbles")
_units = ("g/cm**3", "K", "dyne", "erg")
@@ -158,3 +164,34 @@
weight_field = None)
p3d.add_fields(["particle_ones"])
yield assert_equal, p3d["particle_ones"].sum(), 32**3
+
+def test_mixed_particle_mesh_profiles():
+ ds = fake_random_ds(32, particles=10)
+ ad = ds.all_data()
+ assert_raises(
+ YTIllDefinedProfile, ProfilePlot, ad, 'radius', 'particle_mass')
+ assert_raises(
+ YTIllDefinedProfile, ProfilePlot, ad, 'radius',
+ ['particle_mass', 'particle_ones'])
+ assert_raises(
+ YTIllDefinedProfile, ProfilePlot, ad, 'radius',
+ ['particle_mass', 'ones'])
+ assert_raises(
+ YTIllDefinedProfile, ProfilePlot, ad, 'particle_radius', 'particle_mass',
+ 'cell_mass')
+ assert_raises(
+ YTIllDefinedProfile, ProfilePlot, ad, 'radius', 'cell_mass',
+ 'particle_ones')
+
+ assert_raises(
+ YTIllDefinedProfile, PhasePlot, ad, 'radius', 'particle_mass',
+ 'velocity_x')
+ assert_raises(
+ YTIllDefinedProfile, PhasePlot, ad, 'particle_radius', 'particle_mass',
+ 'cell_mass')
+ assert_raises(
+ YTIllDefinedProfile, PhasePlot, ad, 'radius', 'cell_mass',
+ 'particle_ones')
+ assert_raises(
+ YTIllDefinedProfile, PhasePlot, ad, 'particle_radius', 'particle_mass',
+ 'particle_ones')
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/data_objects/unstructured_mesh.py
--- a/yt/data_objects/unstructured_mesh.py
+++ b/yt/data_objects/unstructured_mesh.py
@@ -22,8 +22,9 @@
fill_fcoords, fill_fwidths
from yt.data_objects.data_containers import \
- YTFieldData, \
YTSelectionContainer
+from yt.data_objects.field_data import \
+ YTFieldData
import yt.geometry.particle_deposit as particle_deposit
class UnstructuredMesh(YTSelectionContainer):
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -25,7 +25,8 @@
from yt.data_objects.octree_subset import \
OctreeSubset
from yt.funcs import \
- mylog
+ mylog, \
+ setdefaultattr
from yt.geometry.oct_container import \
ARTOctreeContainer
from yt.frontends.art.definitions import \
@@ -243,10 +244,10 @@
mass = aM0 * 1.98892e33
self.cosmological_simulation = True
- self.mass_unit = self.quan(mass, "g*%s" % ng**3)
- self.length_unit = self.quan(box_proper, "Mpc")
- self.velocity_unit = self.quan(velocity, "cm/s")
- self.time_unit = self.length_unit / self.velocity_unit
+ setdefaultattr(self, 'mass_unit', self.quan(mass, "g*%s" % ng**3))
+ setdefaultattr(self, 'length_unit', self.quan(box_proper, "Mpc"))
+ setdefaultattr(self, 'velocity_unit', self.quan(velocity, "cm/s"))
+ setdefaultattr(self, 'time_unit', self.length_unit / self.velocity_unit)
def _parse_parameter_file(self):
"""
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/artio/data_structures.py
--- a/yt/frontends/artio/data_structures.py
+++ b/yt/frontends/artio/data_structures.py
@@ -30,7 +30,8 @@
ARTIOFieldInfo
from yt.funcs import \
- mylog
+ mylog, \
+ setdefaultattr
from yt.geometry.geometry_handler import \
Index, \
YTDataChunk
@@ -39,7 +40,7 @@
Dataset
from yt.data_objects.octree_subset import \
OctreeSubset
-from yt.data_objects.data_containers import \
+from yt.data_objects.field_data import \
YTFieldData
from yt.utilities.exceptions import \
YTParticleDepositionNotImplemented
@@ -354,10 +355,13 @@
self.storage_filename = storage_filename
def _set_code_unit_attributes(self):
- self.mass_unit = self.quan(self.parameters["unit_m"], "g")
- self.length_unit = self.quan(self.parameters["unit_l"], "cm")
- self.time_unit = self.quan(self.parameters["unit_t"], "s")
- self.velocity_unit = self.length_unit / self.time_unit
+ setdefaultattr(
+ self, 'mass_unit', self.quan(self.parameters["unit_m"], "g"))
+ setdefaultattr(
+ self, 'length_unit', self.quan(self.parameters["unit_l"], "cm"))
+ setdefaultattr(
+ self, 'time_unit', self.quan(self.parameters["unit_t"], "s"))
+ setdefaultattr(self, 'velocity_unit', self.length_unit / self.time_unit)
def _parse_parameter_file(self):
# hard-coded -- not provided by headers
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/athena/data_structures.py
--- a/yt/frontends/athena/data_structures.py
+++ b/yt/frontends/athena/data_structures.py
@@ -471,12 +471,15 @@
def _set_code_unit_attributes(self):
"""
- Generates the conversion to various physical _units based on the parameter file
+ Generates the conversion to various physical _units based on the
+ parameter file
"""
if "length_unit" not in self.units_override:
self.no_cgs_equiv_length = True
for unit, cgs in [("length", "cm"), ("time", "s"), ("mass", "g")]:
- # We set these to cgs for now, but they may be overridden later.
+ # We set these to cgs for now, but they may have been overriden
+ if getattr(self, unit+'_unit', None) is not None:
+ continue
mylog.warning("Assuming 1.0 = 1.0 %s", cgs)
setattr(self, "%s_unit" % unit, self.quan(1.0, cgs))
self.magnetic_unit = np.sqrt(4*np.pi * self.mass_unit /
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/athena/tests/test_outputs.py
--- a/yt/frontends/athena/tests/test_outputs.py
+++ b/yt/frontends/athena/tests/test_outputs.py
@@ -49,6 +49,20 @@
test_blast.__name__ = test.description
yield test
+uo_blast = {
+ 'length_unit': (1.0, 'pc'),
+ 'mass_unit': (2.38858753789e-24, 'g/cm**3*pc**3'),
+ 'time_unit': (1.0, 's*pc/km'),
+}
+
+ at requires_file(blast)
+def test_blast_override():
+ # verify that overriding units causes derived unit values to be updated.
+ # see issue #1259
+ ds = load(blast, units_override=uo_blast)
+ assert_equal(float(ds.magnetic_unit.in_units('gauss')),
+ 5.478674679698131e-07)
+
uo_stripping = {"time_unit":3.086e14,
"length_unit":8.0236e22,
"mass_unit":9.999e-30*8.0236e22**3}
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/boxlib/data_structures.py
--- a/yt/frontends/boxlib/data_structures.py
+++ b/yt/frontends/boxlib/data_structures.py
@@ -22,8 +22,9 @@
import numpy as np
from yt.funcs import \
+ ensure_tuple, \
mylog, \
- ensure_tuple
+ setdefaultattr
from yt.data_objects.grid_patch import AMRGridPatch
from yt.extern.six.moves import zip as izip
from yt.geometry.grid_geometry_handler import GridIndex
@@ -608,10 +609,10 @@
self._setup2d()
def _set_code_unit_attributes(self):
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.velocity_unit = self.quan(1.0, "cm/s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm/s"))
def _setup1d(self):
# self._index_class = BoxlibHierarchy1D
@@ -1016,10 +1017,11 @@
self.particle_types_raw = self.particle_types
def _set_code_unit_attributes(self):
- self.mass_unit = self.quan(1.0, "Msun")
- self.time_unit = self.quan(1.0 / 3.08568025e19, "s")
- self.length_unit = self.quan(1.0 / (1 + self.current_redshift), "Mpc")
- self.velocity_unit = self.length_unit / self.time_unit
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "Msun"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0 / 3.08568025e19, "s"))
+ setdefaultattr(self, 'length_unit',
+ self.quan(1.0 / (1 + self.current_redshift), "Mpc"))
+ setdefaultattr(self, 'velocity_unit', self.length_unit / self.time_unit)
def _guess_pcast(vals):
# Now we guess some things about the parameter and its type
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -23,7 +23,9 @@
from stat import \
ST_CTIME
-from yt.funcs import mylog
+from yt.funcs import \
+ mylog, \
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.extern import six
@@ -275,14 +277,19 @@
self.parameters["EOSType"] = -1 # default
def _set_code_unit_attributes(self):
- mylog.warning("Setting code length to be 1.0 cm")
- mylog.warning("Setting code mass to be 1.0 g")
- mylog.warning("Setting code time to be 1.0 s")
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.magnetic_unit = self.quan(np.sqrt(4.*np.pi), "gauss")
- self.velocity_unit = self.length_unit / self.time_unit
+ if not hasattr(self, 'length_unit'):
+ mylog.warning("Setting code length unit to be 1.0 cm")
+ if not hasattr(self, 'mass_unit'):
+ mylog.warning("Setting code mass unit to be 1.0 g")
+ if not hasattr(self, 'time_unit'):
+ mylog.warning("Setting code time unit to be 1.0 s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'magnetic_unit',
+ self.quan(np.sqrt(4.*np.pi), "gauss"))
+ setdefaultattr(self, 'velocity_unit',
+ self.length_unit / self.time_unit)
def _localize(self, f, default):
if f is None:
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/enzo/data_structures.py
--- a/yt/frontends/enzo/data_structures.py
+++ b/yt/frontends/enzo/data_structures.py
@@ -28,7 +28,8 @@
from yt.funcs import \
ensure_list, \
ensure_tuple, \
- get_pbar
+ get_pbar, \
+ setdefaultattr
from yt.config import ytcfg
from yt.data_objects.grid_patch import \
AMRGridPatch
@@ -917,11 +918,12 @@
if box_size is None:
box_size = self.parameters["Physics"]["Cosmology"]\
["CosmologyComovingBoxSize"]
- self.length_unit = self.quan(box_size, "Mpccm/h")
- self.mass_unit = \
- self.quan(k['urho'], 'g/cm**3') * (self.length_unit.in_cgs())**3
- self.time_unit = self.quan(k['utim'], 's')
- self.velocity_unit = self.quan(k['uvel'], 'cm/s')
+ setdefaultattr(self, 'length_unit', self.quan(box_size, "Mpccm/h"))
+ setdefaultattr(
+ self, 'mass_unit',
+ self.quan(k['urho'], 'g/cm**3') * (self.length_unit.in_cgs())**3)
+ setdefaultattr(self, 'time_unit', self.quan(k['utim'], 's'))
+ setdefaultattr(self, 'velocity_unit', self.quan(k['uvel'], 'cm/s'))
else:
if "LengthUnits" in self.parameters:
length_unit = self.parameters["LengthUnits"]
@@ -937,15 +939,16 @@
mylog.warning("Setting 1.0 in code units to be 1.0 s")
length_unit = mass_unit = time_unit = 1.0
- self.length_unit = self.quan(length_unit, "cm")
- self.mass_unit = self.quan(mass_unit, "g")
- self.time_unit = self.quan(time_unit, "s")
- self.velocity_unit = self.length_unit / self.time_unit
+ setdefaultattr(self, 'length_unit', self.quan(length_unit, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(time_unit, "s"))
+ setdefaultattr(
+ self, 'velocity_unit', self.length_unit / self.time_unit)
magnetic_unit = np.sqrt(4*np.pi * self.mass_unit /
(self.time_unit**2 * self.length_unit))
magnetic_unit = np.float64(magnetic_unit.in_cgs())
- self.magnetic_unit = self.quan(magnetic_unit, "gauss")
+ setdefaultattr(self, 'magnetic_unit', self.quan(magnetic_unit, "gauss"))
def cosmology_get_units(self):
"""
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/exodus_ii/data_structures.py
--- a/yt/frontends/exodus_ii/data_structures.py
+++ b/yt/frontends/exodus_ii/data_structures.py
@@ -14,6 +14,8 @@
#-----------------------------------------------------------------------------
import numpy as np
+from yt.funcs import \
+ setdefaultattr
from yt.geometry.unstructured_mesh_handler import \
UnstructuredIndex
from yt.data_objects.unstructured_mesh import \
@@ -163,9 +165,9 @@
# should be set, along with examples of how to set them to standard
# values.
#
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
#
# These can also be set:
# self.velocity_unit = self.quan(1.0, "cm/s")
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/fits/data_structures.py
--- a/yt/frontends/fits/data_structures.py
+++ b/yt/frontends/fits/data_structures.py
@@ -25,8 +25,9 @@
from yt.config import ytcfg
from yt.funcs import \
+ ensure_list, \
mylog, \
- ensure_list
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.geometry.grid_geometry_handler import \
@@ -447,10 +448,10 @@
mylog.warning("No length conversion provided. Assuming 1 = 1 cm.")
length_factor = 1.0
length_unit = "cm"
- self.length_unit = self.quan(length_factor,length_unit)
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.velocity_unit = self.quan(1.0, "cm/s")
+ setdefaultattr(self, 'length_unit', self.quan(length_factor,length_unit))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm/s"))
if "beam_size" in self.specified_parameters:
beam_size = self.specified_parameters["beam_size"]
beam_size = self.quan(beam_size[0], beam_size[1]).in_cgs().value
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/flash/data_structures.py
--- a/yt/frontends/flash/data_structures.py
+++ b/yt/frontends/flash/data_structures.py
@@ -22,7 +22,9 @@
AMRGridPatch
from yt.data_objects.static_output import \
Dataset, ParticleFile
-from yt.funcs import mylog
+from yt.funcs import \
+ mylog, \
+ setdefaultattr
from yt.geometry.grid_geometry_handler import \
GridIndex
from yt.geometry.particle_geometry_handler import \
@@ -246,13 +248,14 @@
else:
length_factor = 1.0
temperature_factor = 1.0
- self.magnetic_unit = self.quan(b_factor, "gauss")
- self.length_unit = self.quan(length_factor, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.velocity_unit = self.quan(1.0, "cm/s")
- self.temperature_unit = self.quan(temperature_factor, "K")
+ setdefaultattr(self, 'magnetic_unit', self.quan(b_factor, "gauss"))
+ setdefaultattr(self, 'length_unit', self.quan(length_factor, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm/s"))
+ setdefaultattr(
+ self, 'temperature_unit', self.quan(temperature_factor, "K"))
def set_code_units(self):
super(FLASHDataset, self).set_code_units()
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/gadget_fof/data_structures.py
--- a/yt/frontends/gadget_fof/data_structures.py
+++ b/yt/frontends/gadget_fof/data_structures.py
@@ -33,7 +33,8 @@
GadgetFOFFieldInfo, \
GadgetFOFHaloFieldInfo
from yt.funcs import \
- only_on_root
+ only_on_root, \
+ setdefaultattr
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.utilities.cosmology import \
@@ -232,7 +233,8 @@
else:
raise RuntimeError
length_unit = _fix_unit_ordering(length_unit)
- self.length_unit = self.quan(length_unit[0], length_unit[1])
+ setdefaultattr(self, 'length_unit',
+ self.quan(length_unit[0], length_unit[1]))
if "velocity" in unit_base:
velocity_unit = unit_base["velocity"]
@@ -244,7 +246,8 @@
else:
velocity_unit = (1e5, "cmcm/s")
velocity_unit = _fix_unit_ordering(velocity_unit)
- self.velocity_unit = self.quan(velocity_unit[0], velocity_unit[1])
+ setdefaultattr(self, 'velocity_unit',
+ self.quan(velocity_unit[0], velocity_unit[1]))
# We set hubble_constant = 1.0 for non-cosmology, so this is safe.
# Default to 1e10 Msun/h if mass is not specified.
@@ -259,7 +262,7 @@
# Sane default
mass_unit = (1.0, "1e10*Msun/h")
mass_unit = _fix_unit_ordering(mass_unit)
- self.mass_unit = self.quan(mass_unit[0], mass_unit[1])
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit[0], mass_unit[1]))
if "time" in unit_base:
time_unit = unit_base["time"]
@@ -267,7 +270,7 @@
time_unit = (unit_base["UnitTime_in_s"], "s")
else:
time_unit = (1., "s")
- self.time_unit = self.quan(time_unit[0], time_unit[1])
+ setdefaultattr(self, 'time_unit', self.quan(time_unit[0], time_unit[1]))
def __repr__(self):
return self.basename.split(".", 1)[0]
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/gamer/data_structures.py
--- a/yt/frontends/gamer/data_structures.py
+++ b/yt/frontends/gamer/data_structures.py
@@ -18,7 +18,9 @@
import numpy as np
import weakref
-from yt.funcs import mylog
+from yt.funcs import \
+ mylog, \
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.geometry.grid_geometry_handler import \
@@ -205,7 +207,7 @@
"Use units_override to specify the units")
for unit, cgs in [("length", "cm"), ("time", "s"), ("mass", "g")]:
- setattr(self, "%s_unit"%unit, self.quan(1.0, cgs))
+ setdefaultattr(self, "%s_unit"%unit, self.quan(1.0, cgs))
if len(self.units_override) == 0:
mylog.warning("Assuming 1.0 = 1.0 %s", cgs)
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -19,7 +19,9 @@
import os
from yt.extern.six import string_types
from yt.funcs import \
- just_one, ensure_tuple
+ ensure_tuple, \
+ just_one, \
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.geometry.grid_geometry_handler import \
@@ -223,17 +225,17 @@
un = unit_name[:-5]
un = un.replace('magnetic', 'magnetic_field', 1)
unit = self.unit_system[un]
- setattr(self, unit_name, self.quan(value, unit))
- setattr(self, unit_name, self.quan(value, unit))
+ setdefaultattr(self, unit_name, self.quan(value, unit))
+ setdefaultattr(self, unit_name, self.quan(value, unit))
if unit_name in h5f["/field_types"]:
if unit_name in self.field_units:
mylog.warning("'field_units' was overridden by 'dataset_units/%s'"
% (unit_name))
self.field_units[unit_name] = str(unit)
else:
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
h5f.close()
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/halo_catalog/data_structures.py
--- a/yt/frontends/halo_catalog/data_structures.py
+++ b/yt/frontends/halo_catalog/data_structures.py
@@ -23,6 +23,8 @@
from .fields import \
HaloCatalogFieldInfo
+from yt.funcs import \
+ setdefaultattr
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.data_objects.static_output import \
@@ -76,10 +78,10 @@
self.parameters.update(hvals)
def _set_code_unit_attributes(self):
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.velocity_unit = self.quan(1.0, "cm / s")
- self.time_unit = self.quan(1.0, "s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm / s"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/moab/data_structures.py
--- a/yt/frontends/moab/data_structures.py
+++ b/yt/frontends/moab/data_structures.py
@@ -19,6 +19,8 @@
import weakref
from yt.data_objects.unstructured_mesh import \
SemiStructuredMesh
+from yt.funcs import \
+ setdefaultattr
from yt.geometry.unstructured_mesh_handler import \
UnstructuredIndex
from yt.data_objects.static_output import \
@@ -78,9 +80,9 @@
def _set_code_unit_attributes(self):
# Almost everything is regarded as dimensionless in MOAB, so these will
# not be used very much or at all.
- self.length_unit = self.quan(1.0, "cm")
- self.time_unit = self.quan(1.0, "s")
- self.mass_unit = self.quan(1.0, "g")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
def _parse_parameter_file(self):
self._handle = h5py.File(self.parameter_filename, "r")
@@ -161,9 +163,9 @@
def _set_code_unit_attributes(self):
# Almost everything is regarded as dimensionless in MOAB, so these will
# not be used very much or at all.
- self.length_unit = self.quan(1.0, "cm")
- self.time_unit = self.quan(1.0, "s")
- self.mass_unit = self.quan(1.0, "g")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
def _parse_parameter_file(self):
# not sure if this import has side-effects so I'm not deleting it
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/owls_subfind/data_structures.py
--- a/yt/frontends/owls_subfind/data_structures.py
+++ b/yt/frontends/owls_subfind/data_structures.py
@@ -24,7 +24,9 @@
from .fields import \
OWLSSubfindFieldInfo
-from yt.funcs import only_on_root
+from yt.funcs import \
+ only_on_root, \
+ setdefaultattr
from yt.utilities.exceptions import \
YTException
from yt.utilities.logger import ytLogger as \
@@ -176,7 +178,8 @@
else:
raise RuntimeError
length_unit = _fix_unit_ordering(length_unit)
- self.length_unit = self.quan(length_unit[0], length_unit[1])
+ setdefaultattr(self, 'length_unit',
+ self.quan(length_unit[0], length_unit[1]))
if "velocity" in unit_base:
velocity_unit = unit_base["velocity"]
@@ -185,7 +188,8 @@
else:
velocity_unit = (1e5, "cm/s")
velocity_unit = _fix_unit_ordering(velocity_unit)
- self.velocity_unit = self.quan(velocity_unit[0], velocity_unit[1])
+ setdefaultattr(self, 'velocity_unit',
+ self.quan(velocity_unit[0], velocity_unit[1]))
# We set hubble_constant = 1.0 for non-cosmology, so this is safe.
# Default to 1e10 Msun/h if mass is not specified.
@@ -200,7 +204,7 @@
# Sane default
mass_unit = (1.0, "1e10*Msun/h")
mass_unit = _fix_unit_ordering(mass_unit)
- self.mass_unit = self.quan(mass_unit[0], mass_unit[1])
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit[0], mass_unit[1]))
if "time" in unit_base:
time_unit = unit_base["time"]
@@ -208,7 +212,7 @@
time_unit = (unit_base["UnitTime_in_s"], "s")
else:
time_unit = (1., "s")
- self.time_unit = self.quan(time_unit[0], time_unit[1])
+ setdefaultattr(self, 'time_unit', self.quan(time_unit[0], time_unit[1]))
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/ramses/data_structures.py
--- a/yt/frontends/ramses/data_structures.py
+++ b/yt/frontends/ramses/data_structures.py
@@ -23,7 +23,8 @@
from yt.extern.six import string_types
from yt.funcs import \
- mylog
+ mylog, \
+ setdefaultattr
from yt.geometry.oct_geometry_handler import \
OctreeIndex
from yt.geometry.geometry_handler import \
@@ -565,17 +566,21 @@
# For now assume an atomic ideal gas with cosmic abundances (x_H = 0.76)
mean_molecular_weight_factor = _X**-1
- self.density_unit = self.quan(density_unit, 'g/cm**3')
- self.magnetic_unit = self.quan(magnetic_unit, "gauss")
- self.pressure_unit = self.quan(pressure_unit, 'dyne/cm**2')
- self.time_unit = self.quan(time_unit, "s")
- self.mass_unit = self.quan(mass_unit, "g")
- self.velocity_unit = self.quan(length_unit, 'cm') / self.time_unit
- self.temperature_unit = (self.velocity_unit**2*mp*
- mean_molecular_weight_factor/kb).in_units('K')
+ setdefaultattr(self, 'density_unit', self.quan(density_unit, 'g/cm**3'))
+ setdefaultattr(self, 'magnetic_unit', self.quan(magnetic_unit, "gauss"))
+ setdefaultattr(self, 'pressure_unit',
+ self.quan(pressure_unit, 'dyne/cm**2'))
+ setdefaultattr(self, 'time_unit', self.quan(time_unit, "s"))
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit, "g"))
+ setdefaultattr(self, 'velocity_unit',
+ self.quan(length_unit, 'cm') / self.time_unit)
+ temperature_unit = (
+ self.velocity_unit**2*mp*mean_molecular_weight_factor/kb)
+ setdefaultattr(self, 'temperature_unit', temperature_unit.in_units('K'))
# Only the length unit get scales by a factor of boxlen
- self.length_unit = self.quan(length_unit * boxlen, "cm")
+ setdefaultattr(self, 'length_unit',
+ self.quan(length_unit * boxlen, "cm"))
def _parse_parameter_file(self):
# hardcoded for now
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/rockstar/data_structures.py
--- a/yt/frontends/rockstar/data_structures.py
+++ b/yt/frontends/rockstar/data_structures.py
@@ -22,12 +22,14 @@
from .fields import \
RockstarFieldInfo
-from yt.utilities.cosmology import Cosmology
-from yt.geometry.particle_geometry_handler import \
- ParticleIndex
from yt.data_objects.static_output import \
Dataset, \
ParticleFile
+from yt.funcs import \
+ setdefaultattr
+from yt.geometry.particle_geometry_handler import \
+ ParticleIndex
+from yt.utilities.cosmology import Cosmology
import yt.utilities.fortran_utils as fpu
from .definitions import \
@@ -92,10 +94,10 @@
def _set_code_unit_attributes(self):
z = self.current_redshift
- self.length_unit = self.quan(1.0 / (1.0+z), "Mpc / h")
- self.mass_unit = self.quan(1.0, "Msun / h")
- self.velocity_unit = self.quan(1.0, "km / s")
- self.time_unit = self.length_unit / self.velocity_unit
+ setdefaultattr(self, 'length_unit', self.quan(1.0 / (1.0+z), "Mpc / h"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "Msun / h"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "km / s"))
+ setdefaultattr(self, 'time_unit', self.length_unit / self.velocity_unit)
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/sdf/data_structures.py
--- a/yt/frontends/sdf/data_structures.py
+++ b/yt/frontends/sdf/data_structures.py
@@ -28,7 +28,8 @@
from yt.data_objects.static_output import \
Dataset, ParticleFile
from yt.funcs import \
- get_requests
+ get_requests, \
+ setdefaultattr
from .fields import \
SDFFieldInfo
from yt.utilities.sdf import \
@@ -177,16 +178,22 @@
return self._midx
def _set_code_unit_attributes(self):
- self.length_unit = self.quan(1.0, self.parameters.get("length_unit", 'kpc'))
- self.velocity_unit = self.quan(1.0, self.parameters.get("velocity_unit", 'kpc/Gyr'))
- self.time_unit = self.quan(1.0, self.parameters.get("time_unit", 'Gyr'))
+ setdefaultattr(
+ self, 'length_unit',
+ self.quan(1.0, self.parameters.get("length_unit", 'kpc')))
+ setdefaultattr(
+ self, 'velocity_unit',
+ self.quan(1.0, self.parameters.get("velocity_unit", 'kpc/Gyr')))
+ setdefaultattr(
+ self, 'time_unit',
+ self.quan(1.0, self.parameters.get("time_unit", 'Gyr')))
mass_unit = self.parameters.get("mass_unit", '1e10 Msun')
if ' ' in mass_unit:
factor, unit = mass_unit.split(' ')
else:
factor = 1.0
unit = mass_unit
- self.mass_unit = self.quan(float(factor), unit)
+ setdefaultattr(self, 'mass_unit', self.quan(float(factor), unit))
@classmethod
def _is_valid(cls, *args, **kwargs):
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -26,7 +26,7 @@
iterable, \
ensure_list
from yt.utilities.io_handler import io_registry
-from yt.data_objects.data_containers import \
+from yt.data_objects.field_data import \
YTFieldData
from yt.data_objects.particle_unions import \
ParticleUnion
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -1004,3 +1004,12 @@
def get_interactivity():
return interactivity
+
+def setdefaultattr(obj, name, value):
+ """Set attribute with *name* on *obj* with *value* if it doesn't exist yet
+
+ Analogous to dict.setdefault
+ """
+ if not hasattr(obj, name):
+ setattr(obj, name, value)
+ return getattr(obj, name)
diff -r 405474784eb337baf3aff2acd48b6acc9cbe9281 -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c yt/geometry/particle_smooth.pxd
--- a/yt/geometry/particle_smooth.pxd
+++ b/yt/geometry/particle_smooth.pxd
@@ -23,15 +23,12 @@
from yt.utilities.lib.fp_utils cimport *
from oct_container cimport Oct, OctAllocationContainer, OctreeContainer
from .particle_deposit cimport kernel_func, get_kernel_func, gind
+from yt.utilities.lib.distance_queue cimport NeighborList, Neighbor_compare, \
+ r2dist, DistanceQueue
cdef extern from "platform_dep.h":
void *alloca(int)
-cdef struct NeighborList
-cdef struct NeighborList:
- np.int64_t pn # Particle number
- np.float64_t r2 # radius**2
-
cdef class ParticleSmoothOperation:
# We assume each will allocate and define their own temporary storage
cdef kernel_func sph_kernel
@@ -39,10 +36,8 @@
cdef np.float64_t DW[3]
cdef int nfields
cdef int maxn
- cdef int curn
cdef bint periodicity[3]
# Note that we are preallocating here, so this is *not* threadsafe.
- cdef NeighborList *neighbors
cdef void (*pos_setup)(np.float64_t ipos[3], np.float64_t opos[3])
cdef void neighbor_process(self, int dim[3], np.float64_t left_edge[3],
np.float64_t dds[3], np.float64_t[:,:] ppos,
@@ -52,7 +47,7 @@
np.int64_t offset, np.float64_t **index_fields,
OctreeContainer octree, np.int64_t domain_id,
int *nsize, np.float64_t[:,:] oct_left_edges,
- np.float64_t[:,:] oct_dds)
+ np.float64_t[:,:] oct_dds, DistanceQueue dq)
cdef int neighbor_search(self, np.float64_t pos[3], OctreeContainer octree,
np.int64_t **nind, int *nsize,
np.int64_t nneighbors, np.int64_t domain_id,
@@ -65,10 +60,7 @@
np.int64_t offset,
np.float64_t **index_fields,
OctreeContainer octree, np.int64_t domain_id,
- int *nsize)
- cdef void neighbor_eval(self, np.int64_t pn, np.float64_t ppos[3],
- np.float64_t cpos[3])
- cdef void neighbor_reset(self)
+ int *nsize, DistanceQueue dq)
cdef void neighbor_find(self,
np.int64_t nneighbors,
np.int64_t *nind,
@@ -78,7 +70,7 @@
np.float64_t[:,:] ppos,
np.float64_t cpos[3],
np.float64_t[:,:] oct_left_edges,
- np.float64_t[:,:] oct_dds)
+ np.float64_t[:,:] oct_dds, DistanceQueue dq)
cdef void process(self, np.int64_t offset, int i, int j, int k,
int dim[3], np.float64_t cpos[3], np.float64_t **fields,
- np.float64_t **index_fields)
+ np.float64_t **index_fields, DistanceQueue dq)
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt/commits/9a37f70cce9d/
Changeset: 9a37f70cce9d
Branch: yt
User: ngoldbaum
Date: 2016-08-25 15:51:32+00:00
Summary: remove yield assert
Affected #: 1 file
diff -r a3465e29e8f821b8e7109ce3b3cfa5534d2cd55c -r 9a37f70cce9dfdab3d8da8f6362c75a9c7e02e36 yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -481,7 +481,7 @@
lims = [xlims[0], xlims[1], ylims[0], ylims[1]]
for l in lims:
generated_limits.append(l)
- yield assert_array_almost_equal, correct_limits, generated_limits
+ assert_array_almost_equal(correct_limits, generated_limits)
def test_frb_regen():
ds = fake_random_ds(32)
https://bitbucket.org/yt_analysis/yt/commits/7e7c3fdd9cc7/
Changeset: 7e7c3fdd9cc7
Branch: yt
User: ngoldbaum
Date: 2016-09-07 18:09:46+00:00
Summary: Merged in a_gilbert/yt (pull request #2340)
Closing Issue #1247: updated origin input to accept floats or ints specifying xloc or yloc.
Affected #: 3 files
diff -r 4bc8ace93fda81e800a2e90c052c431c2d48a01b -r 7e7c3fdd9cc79e65a179d277ae64b345dc30411f yt/visualization/base_plot_types.py
--- a/yt/visualization/base_plot_types.py
+++ b/yt/visualization/base_plot_types.py
@@ -357,6 +357,7 @@
self._toggle_colorbar(True)
return self
+
def get_multi_plot(nx, ny, colorbar = 'vertical', bw = 4, dpi=300,
cbar_padding = 0.4):
r"""Construct a multiple axes plot object, with or without a colorbar, into
@@ -440,3 +441,5 @@
ax.clear()
cbars.append(ax)
return fig, tr, cbars
+
+
diff -r 4bc8ace93fda81e800a2e90c052c431c2d48a01b -r 7e7c3fdd9cc79e65a179d277ae64b345dc30411f yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -156,7 +156,8 @@
Parameters
----------
- data_source : :class:`yt.data_objects.construction_data_containers.YTQuadTreeProj` or :class:`yt.data_objects.selection_data_containers.YTSlice`
+ data_source : :class:`yt.data_objects.construction_data_containers.YTQuadTreeProj`
+ or :class:`yt.data_objects.selection_data_containers.YTSlice`
This is the source to be pixelized, which can be a projection or a
slice. (For cutting planes, see
`yt.visualization.fixed_resolution.ObliqueFixedResolutionBuffer`.)
@@ -397,33 +398,39 @@
Parameters
----------
- origin : string or length 1, 2, or 3 sequence of strings
- The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings. In the
- first index the y-location is given by 'lower', 'upper', or 'center'.
- The second index is the x-location, given as 'left', 'right', or
- 'center'. Finally, the whether the origin is applied in 'domain'
- space, plot 'window' space or 'native' simulation coordinate system
- is given. For example, both 'upper-right-domain' and ['upper',
- 'right', 'domain'] place the origin in the upper right hand
- corner of domain space. If x or y are not given, a value is inferred.
- For instance, 'left-domain' corresponds to the lower-left hand corner
- of the simulation domain, 'center-domain' corresponds to the center
- of the simulation domain, or 'center-window' for the center of the
- plot window. Further examples:
+ origin : string or length 1, 2, or 3 sequence.
+ The location of the origin of the plot coordinate system. This
+ is typically represented by a '-' separated string or a tuple of
+ strings. In the first index the y-location is given by 'lower',
+ 'upper', or 'center'. The second index is the x-location, given as
+ 'left', 'right', or 'center'. Finally, the whether the origin is
+ applied in 'domain' space, plot 'window' space or 'native'
+ simulation coordinate system is given. For example, both
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the
+ origin in the upper right hand corner of domain space. If x or y
+ are not given, a value is inferred. For instance, 'left-domain'
+ corresponds to the lower-left hand corner of the simulation domain,
+ 'center-domain' corresponds to the center of the simulation domain,
+ or 'center-window' for the center of the plot window. In the event
+ that none of these options place the origin in a desired location,
+ a sequence of tuples and a string specifying the
+ coordinate space can be given. If plain numeric types are input,
+ units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
- '{space}' 'domain'
- '{xloc}-{space}' 'left-window'
- '{yloc}-{space}' 'upper-domain'
- '{yloc}-{xloc}-{space}' 'lower-right-window'
- ('{space}',) ('window',)
- ('{xloc}', '{space}') ('right', 'domain')
- ('{yloc}', '{space}') ('lower', 'window')
- ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- ================================== ============================
+ ================================== ============================
+ format example
+ ================================== ============================
+ '{space}' 'domain'
+ '{xloc}-{space}' 'left-window'
+ '{yloc}-{space}' 'upper-domain'
+ '{yloc}-{xloc}-{space}' 'lower-right-window'
+ ('{space}',) ('window',)
+ ('{xloc}', '{space}') ('right', 'domain')
+ ('{yloc}', '{space}') ('lower', 'window')
+ ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ ((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
+ ================================== ============================
"""
self.origin = origin
@@ -651,6 +658,9 @@
def _setup_origin(self):
origin = self.origin
axis_index = self.data_source.axis
+ xc = None
+ yc = None
+
if isinstance(origin, string_types):
origin = tuple(origin.split('-'))[:3]
if 1 == len(origin):
@@ -660,6 +670,13 @@
origin = (o0map[origin[0]],) + origin
elif 2 == len(origin) and origin[0] in set(['lower','upper','center']):
origin = (origin[0], 'center', origin[-1])
+ elif 3 == len(origin) and isinstance(origin[0], (int, float)):
+ xc = self.ds.quan(origin[0], 'code_length')
+ yc = self.ds.quan(origin[1], 'code_length')
+ elif 3 == len(origin) and isinstance(origin[0], tuple):
+ xc = YTQuantity(origin[0][0], origin[0][1])
+ yc = YTQuantity(origin[1][0], origin[0][1])
+
assert origin[-1] in ['window', 'domain', 'native']
if origin[2] == 'window':
@@ -678,33 +695,42 @@
else:
mylog.warn("origin = {0}".format(origin))
msg = \
- ('origin keyword "{0}" not recognized, must declare "domain" '
- 'or "center" as the last term in origin.').format(self.origin)
+ ('origin keyword "{0}" not recognized, must declare "domain" '
+ 'or "center" as the last term in origin.').format(self.origin)
raise RuntimeError(msg)
+ if xc is None and yc is None:
+ if origin[0] == 'lower':
+ yc = yllim
+ elif origin[0] == 'upper':
+ yc = yrlim
+ elif origin[0] == 'center':
+ yc = (yllim + yrlim)/2.0
+ else:
+ mylog.warn("origin = {0}".format(origin))
+ msg = ('origin keyword "{0}" not recognized, must declare "lower" '
+ '"upper" or "center" as the first term in origin.')
+ msg = msg.format(self.origin)
+ raise RuntimeError(msg)
- if origin[0] == 'lower':
- yc = yllim
- elif origin[0] == 'upper':
- yc = yrlim
- elif origin[0] == 'center':
- yc = (yllim + yrlim)/2.0
- else:
- mylog.warn("origin = {0}".format(origin))
- msg = ('origin keyword "{0}" not recognized, must declare "lower" '
- '"upper" or "center" as the first term in origin.')
- msg = msg.format(self.origin)
- raise RuntimeError(msg)
+ if origin[1] == 'left':
+ xc = xllim
+ elif origin[1] == 'right':
+ xc = xrlim
+ elif origin[1] == 'center':
+ xc = (xllim + xrlim)/2.0
+ else:
+ mylog.warn("origin = {0}".format(origin))
+ msg = ('origin keyword "{0}" not recognized, must declare "left" '
+ '"right" or "center" as the second term in origin.')
+ msg = msg.format(self.origin)
+ raise RuntimeError(msg)
- if origin[1] == 'left':
- xc = xllim
- elif origin[1] == 'right':
- xc = xrlim
- elif origin[1] == 'center':
- xc = (xllim + xrlim)/2.0
- else:
- mylog.warn("origin = {0}".format(origin))
- msg = ('origin keyword "{0}" not recognized, must declare "left" '
- '"right" or "center" as the second term in origin.')
+ x_in_bounds = xc >= xllim and xc <= xrlim
+ y_in_bounds = yc >= yllim and yc <= yrlim
+
+ if not x_in_bounds and not y_in_bounds:
+ msg = ('orgin inputs not in bounds of specified coordinate sytem' +
+ 'domain.')
msg = msg.format(self.origin)
raise RuntimeError(msg)
@@ -736,7 +762,6 @@
if self.aspect is None:
self.aspect = float((self.ds.quan(1.0, unit_y) /
self.ds.quan(1.0, unit_x)).in_cgs())
-
extentx = [(self.xlim[i] - xc).in_units(unit_x) for i in (0, 1)]
extenty = [(self.ylim[i] - yc).in_units(unit_y) for i in (0, 1)]
@@ -1196,38 +1221,44 @@
units are assumed, for example (0.2, 0.3) requests a plot that has an
x width of 0.2 and a y width of 0.3 in code units. If units are
provided the resulting plot axis labels will use the supplied units.
+ origin : string or length 1, 2, or 3 sequence.
+ The location of the origin of the plot coordinate system. This
+ is typically represented by a '-' separated string or a tuple of
+ strings. In the first index the y-location is given by 'lower',
+ 'upper', or 'center'. The second index is the x-location, given as
+ 'left', 'right', or 'center'. Finally, the whether the origin is
+ applied in 'domain' space, plot 'window' space or 'native'
+ simulation coordinate system is given. For example, both
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the
+ origin in the upper right hand corner of domain space. If x or y
+ are not given, a value is inferred. For instance, 'left-domain'
+ corresponds to the lower-left hand corner of the simulation domain,
+ 'center-domain' corresponds to the center of the simulation domain,
+ or 'center-window' for the center of the plot window. In the event
+ that none of these options place the origin in a desired location,
+ a sequence of tuples and a string specifying the
+ coordinate space can be given. If plain numeric types are input,
+ units of `code_length` are assumed. Further examples:
+
+ ================================== ============================
+ format example
+ ================================== ============================
+ '{space}' 'domain'
+ '{xloc}-{space}' 'left-window'
+ '{yloc}-{space}' 'upper-domain'
+ '{yloc}-{xloc}-{space}' 'lower-right-window'
+ ('{space}',) ('window',)
+ ('{xloc}', '{space}') ('right', 'domain')
+ ('{yloc}', '{space}') ('lower', 'window')
+ ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ ((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
+ ================================== ============================
axes_unit : A string
The name of the unit for the tick labels on the x and y axes.
Defaults to None, which automatically picks an appropriate unit.
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings
- The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings. In the
- first index the y-location is given by 'lower', 'upper', or 'center'.
- The second index is the x-location, given as 'left', 'right', or
- 'center'. Finally, whether the origin is applied in 'domain'
- space, plot 'window' space or 'native' simulation coordinate system
- is given. For example, both 'upper-right-domain' and ['upper',
- 'right', 'domain'] place the origin in the upper right hand
- corner of domain space. If x or y are not given, a value is inferred.
- For instance, the default location 'center-window' corresponds to
- the center of the plot window, 'left-domain' corresponds to the
- lower-left hand corner of the simulation domain, or 'center-domain'
- for the center of the simulation domain. Further examples:
-
- ================================== ============================
- format example
- ================================== ============================
- '{space}' 'domain'
- '{xloc}-{space}' 'left-window'
- '{yloc}-{space}' 'upper-domain'
- '{yloc}-{xloc}-{space}' 'lower-right-window'
- ('{space}',) ('window',)
- ('{xloc}', '{space}') ('right', 'domain')
- ('{yloc}', '{space}') ('lower', 'window')
- ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- ================================== ============================
right_handed : boolean
Whether the implicit east vector for the image generated is set to make a right
handed coordinate system with a normal vector, the direction of the
@@ -1341,33 +1372,40 @@
Defaults to None, which automatically picks an appropriate unit.
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings
- The location of the origin of the plot coordinate system. This is
- represented by '-' separated string or a tuple of strings. In the
- first index the y-location is given by 'lower', 'upper', or 'center'.
- The second index is the x-location, given as 'left', 'right', or
- 'center'. Finally, whether the origin is applied in 'domain'
- space, plot 'window' space or 'native' simulation coordinate system
- is given. For example, both 'upper-right-domain' and ['upper',
- 'right', 'domain'] place the origin in the upper right hand
- corner of domain space. If x or y are not given, a value is inferred.
- For instance, 'left-domain' corresponds to the lower-left hand corner
- of the simulation domain, 'center-domain' corresponds to the center
- of the simulation domain, or 'center-window' for the center of the
- plot window. Further examples:
+ origin : string or length 1, 2, or 3 sequence.
+ The location of the origin of the plot coordinate system. This
+ is typically represented by a '-' separated string or a tuple of
+ strings. In the first index the y-location is given by 'lower',
+ 'upper', or 'center'. The second index is the x-location, given as
+ 'left', 'right', or 'center'. Finally, the whether the origin is
+ applied in 'domain' space, plot 'window' space or 'native'
+ simulation coordinate system is given. For example, both
+ 'upper-right-domain' and ['upper', 'right', 'domain'] place the
+ origin in the upper right hand corner of domain space. If x or y
+ are not given, a value is inferred. For instance, 'left-domain'
+ corresponds to the lower-left hand corner of the simulation domain,
+ 'center-domain' corresponds to the center of the simulation domain,
+ or 'center-window' for the center of the plot window. In the event
+ that none of these options place the origin in a desired location,
+ a sequence of tuples and a string specifying the
+ coordinate space can be given. If plain numeric types are input,
+ units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
- '{space}' 'domain'
- '{xloc}-{space}' 'left-window'
- '{yloc}-{space}' 'upper-domain'
- '{yloc}-{xloc}-{space}' 'lower-right-window'
- ('{space}',) ('window',)
- ('{xloc}', '{space}') ('right', 'domain')
- ('{yloc}', '{space}') ('lower', 'window')
- ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- ================================== ============================
+ ================================== ============================
+ format example
+ ================================== ============================
+ '{space}' 'domain'
+ '{xloc}-{space}' 'left-window'
+ '{yloc}-{space}' 'upper-domain'
+ '{yloc}-{xloc}-{space}' 'lower-right-window'
+ ('{space}',) ('window',)
+ ('{xloc}', '{space}') ('right', 'domain')
+ ('{yloc}', '{space}') ('lower', 'window')
+ ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ ((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
+ ================================== ============================
+
right_handed : boolean
Whether the implicit east vector for the image generated is set to make a right
handed coordinate system with the direction of the
@@ -1392,13 +1430,13 @@
"mip" : pick out the maximum value of the field in the line of sight.
- "sum" : This method is the same as integrate, except that it does not
- multiply by a path length when performing the integration, and is
+ "sum" : This method is the same as integrate, except that it does not
+ multiply by a path length when performing the integration, and is
just a straight summation of the field along the given axis. WARNING:
This should only be used for uniform resolution grid datasets, as other
datasets may result in unphysical images.
proj_style : string
- The method of projection--same as method keyword. Deprecated as of
+ The method of projection--same as method keyword. Deprecated as of
version 3.0.2. Please use method instead.
window_size : float
The size of the window in inches. Set to 8 by default.
@@ -1841,35 +1879,40 @@
Defaults to None, which automatically picks an appropriate unit.
If axes_unit is '1', 'u', or 'unitary', it will not display the
units, and only show the axes name.
- origin : string or length 1, 2, or 3 sequence of strings
+ origin : string or length 1, 2, or 3 sequence.
The location of the origin of the plot coordinate system for
- `AxisAlignedSlicePlot` objects; for `OffAxisSlicePlot` objects,
- this parameter is discarded. This is represented by '-' separated
- string or a tuple of strings. In the first index the y-location is
- given by 'lower', 'upper', or 'center'. The second index is the
- x-location, given as 'left', 'right', or 'center'. Finally,
- whether the origin is applied in 'domain' space, plot 'window' space
- or 'native' simulation coordinate system is given. For example, both
+ `AxisAlignedSlicePlot` object; for `OffAxisSlicePlot` objects this
+ parameter is discarded. This is typically represented by a '-'
+ separated string or a tuple of strings. In the first index the
+ y-location is given by 'lower', 'upper', or 'center'. The second index
+ is the x-location, given as 'left', 'right', or 'center'. Finally, the
+ whether the origin is applied in 'domain' space, plot 'window' space or
+ 'native' simulation coordinate system is given. For example, both
'upper-right-domain' and ['upper', 'right', 'domain'] place the
- origin in the upper right hand corner of domain space. If x or y are
- not given, a value is inferred. For instance, 'left-domain'
+ origin in the upper right hand corner of domain space. If x or y
+ are not given, a value is inferred. For instance, 'left-domain'
corresponds to the lower-left hand corner of the simulation domain,
'center-domain' corresponds to the center of the simulation domain,
- or 'center-window' for the center of the plot window. Further
- examples:
+ or 'center-window' for the center of the plot window. In the event
+ that none of these options place the origin in a desired location,
+ a sequence of tuples and a string specifying the
+ coordinate space can be given. If plain numeric types are input,
+ units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
- '{space}' 'domain'
- '{xloc}-{space}' 'left-window'
- '{yloc}-{space}' 'upper-domain'
- '{yloc}-{xloc}-{space}' 'lower-right-window'
- ('{space}',) ('window',)
- ('{xloc}', '{space}') ('right', 'domain')
- ('{yloc}', '{space}') ('lower', 'window')
- ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
- ================================== ============================
+ ================================== ============================
+ format example
+ ================================== ============================
+ '{space}' 'domain'
+ '{xloc}-{space}' 'left-window'
+ '{yloc}-{space}' 'upper-domain'
+ '{yloc}-{xloc}-{space}' 'lower-right-window'
+ ('{space}',) ('window',)
+ ('{xloc}', '{space}') ('right', 'domain')
+ ('{yloc}', '{space}') ('lower', 'window')
+ ('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
+ ((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
+ (xloc, yloc, '{space}') (0.23, 0.5, 'domain')
+ ================================== ============================
north_vector : a sequence of floats
A vector defining the 'up' direction in the `OffAxisSlicePlot`; not
used in `AxisAlignedSlicePlot`. This option sets the orientation of the
diff -r 4bc8ace93fda81e800a2e90c052c431c2d48a01b -r 7e7c3fdd9cc79e65a179d277ae64b345dc30411f yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -444,6 +444,44 @@
assert_raises(
YTInvalidFieldType, object, ds, normal, field_name_list)
+def test_setup_origin():
+ origin_inputs = ('domain',
+ 'left-window',
+ 'center-domain',
+ 'lower-right-window',
+ ('window',),
+ ('right', 'domain'),
+ ('lower', 'window'),
+ ('lower', 'right', 'window'),
+ (0.5, 0.5, 'domain'),
+ ((50, 'cm'), (50, 'cm'), 'domain'))
+ w=(10, 'cm')
+
+ ds = fake_random_ds(32, length_unit=100.0)
+ generated_limits = []
+ #lower limit -> llim
+ #upper limit -> ulim
+ # xllim xulim yllim yulim
+ correct_limits = [45.0, 55.0, 45.0, 55.0,
+ 0.0, 10.0, 0.0, 10.0,
+ -5.0, 5.0, -5.0, 5.0,
+ -10.0, 0, 0, 10.0,
+ 0.0, 10.0, 0.0, 10.0,
+ -55.0, -45.0, -55.0, -45.0,
+ -5.0, 5.0, 0.0, 10.0,
+ -10.0, 0, 0, 10.0,
+ -5.0, 5.0, -5.0, 5.0,
+ -5.0, 5.0, -5.0, 5.0
+ ]
+ for o in origin_inputs:
+ slc = SlicePlot(ds, 2, 'density', width=w, origin=o)
+ ax = slc.plots['density'].axes
+ xlims = ax.get_xlim()
+ ylims = ax.get_ylim()
+ lims = [xlims[0], xlims[1], ylims[0], ylims[1]]
+ for l in lims:
+ generated_limits.append(l)
+ assert_array_almost_equal(correct_limits, generated_limits)
def test_frb_regen():
ds = fake_random_ds(32)
Repository URL: https://bitbucket.org/yt_analysis/yt/
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