[yt-svn] commit/yt-3.0: 82 new changesets
Bitbucket
commits-noreply at bitbucket.org
Wed Oct 17 13:38:48 PDT 2012
82 new commits in yt-3.0:
https://bitbucket.org/yt_analysis/yt-3.0/changeset/cc994a53e0f2/
changeset: cc994a53e0f2
branch: yt
user: jsoishi
date: 2012-10-04 01:33:02
summary: updated to python 2.7.3
affected #: 1 file
diff -r 59154579b465a3bc1d01723d7b8680526d4b784d -r cc994a53e0f26352b3459657040bfb70b17d8130 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -400,7 +400,7 @@
echo '2c1933ab31246b4f4eba049d3288156e0a72f1730604e3ed7357849967cdd329e4647cf236c9442ecfb06d0aff03e6fc892a7ba2a5c1cf5c011b7ab9c619acec Cython-0.16.tar.gz' > Cython-0.16.tar.gz.sha512
echo '44eea803870a66ff0bab08d13a8b3388b5578ebc1c807d1d9dca0a93e6371e91b15d02917a00b3b20dc67abb5a21dabaf9b6e9257a561f85eeff2147ac73b478 PyX-0.11.1.tar.gz' > PyX-0.11.1.tar.gz.sha512
-echo '1a754d560bfa433f0960ab3b5a62edb5f291be98ec48cf4e5941fa5b84139e200b87a52efbbd6fa4a76d6feeff12439eed3e7a84db4421940d1bbb576f7a684e Python-2.7.2.tgz' > Python-2.7.2.tgz.sha512
+echo 'b981f8464575bb24c297631c87a3b9172312804a0fc14ce1fa7cb41ce2b0d2fd383cd1c816d6e10c36467d18bf9492d6faf557c81c04ff3b22debfa93f30ad0b Python-2.7.3.tgz' > Python-2.7.3.tgz.sha512
echo 'c017d3d59dd324ac91af0edc178c76b60a5f90fbb775cf843e39062f95bd846238f2c53705f8890ed3f34bc0e6e75671a73d13875eb0287d6201cb45f0a2d338 bzip2-1.0.5.tar.gz' > bzip2-1.0.5.tar.gz.sha512
echo 'a296dfcaef7e853e58eed4e24b37c4fa29cfc6ac688def048480f4bb384b9e37ca447faf96eec7b378fd764ba291713f03ac464581d62275e28eb2ec99110ab6 reason-js-20120623.zip' > reason-js-20120623.zip.sha512
echo 'b519218f93946400326e9b656669269ecb3e5232b944e18fbc3eadc4fe2b56244d68aae56d6f69042b4c87c58c881ee2aaa279561ea0f0f48d5842155f4de9de freetype-2.4.4.tar.gz' > freetype-2.4.4.tar.gz.sha512
@@ -429,7 +429,7 @@
[ $INST_0MQ -eq 1 ] && get_ytproject zeromq-2.2.0.tar.gz
[ $INST_0MQ -eq 1 ] && get_ytproject pyzmq-2.1.11.tar.gz
[ $INST_0MQ -eq 1 ] && get_ytproject tornado-2.2.tar.gz
-get_ytproject Python-2.7.2.tgz
+get_ytproject Python-2.7.3.tgz
get_ytproject numpy-1.6.1.tar.gz
get_ytproject matplotlib-1.1.0.tar.gz
get_ytproject mercurial-2.2.2.tar.gz
@@ -554,11 +554,11 @@
fi
fi
-if [ ! -e Python-2.7.2/done ]
+if [ ! -e Python-2.7.3/done ]
then
echo "Installing Python. This may take a while, but don't worry. YT loves you."
- [ ! -e Python-2.7.2 ] && tar xfz Python-2.7.2.tgz
- cd Python-2.7.2
+ [ ! -e Python-2.7.3 ] && tar xfz Python-2.7.3.tgz
+ cd Python-2.7.3
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
https://bitbucket.org/yt_analysis/yt-3.0/changeset/7c7e9a68c234/
changeset: 7c7e9a68c234
branch: yt
user: MatthewTurk
date: 2012-10-04 15:59:16
summary: Adding projected units for density fields in FLASH
affected #: 1 file
diff -r cc994a53e0f26352b3459657040bfb70b17d8130 -r 7c7e9a68c2347b9d6f53057d7ae3511e03727d1a yt/frontends/flash/fields.py
--- a/yt/frontends/flash/fields.py
+++ b/yt/frontends/flash/fields.py
@@ -98,7 +98,9 @@
if fn1.endswith("_Fraction"):
add_field(fn1.split("_")[0] + "_Density",
function=_get_density(fn1), take_log=True,
- display_name="%s\/Density" % fn1.split("_")[0])
+ display_name="%s\/Density" % fn1.split("_")[0],
+ projected_units = r"\rm{g}/\rm{cm}^2",
+ )
def _get_convert(fname):
def _conv(data):
@@ -107,7 +109,8 @@
add_flash_field("dens", function=NullFunc, take_log=True,
convert_function=_get_convert("dens"),
- units=r"\rm{g}/\rm{cm}^3")
+ units=r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2"),
add_flash_field("velx", function=NullFunc, take_log=False,
convert_function=_get_convert("velx"),
units=r"\rm{cm}/\rm{s}")
@@ -204,6 +207,7 @@
add_field(f, TranslationFunc(v),
take_log=KnownFLASHFields[v].take_log,
units = ff._units, display_name=dname,
+ projected_units = ff._projected_units,
particle_type = pfield)
def _convertParticleMassMsun(data):
https://bitbucket.org/yt_analysis/yt-3.0/changeset/029908bc9f69/
changeset: 029908bc9f69
branch: yt
user: MatthewTurk
date: 2012-10-04 19:44:13
summary: Adding units to _Density fields.
affected #: 1 file
diff -r 7c7e9a68c2347b9d6f53057d7ae3511e03727d1a -r 029908bc9f69bf71304b850a6abbfa97408f7a83 yt/frontends/flash/fields.py
--- a/yt/frontends/flash/fields.py
+++ b/yt/frontends/flash/fields.py
@@ -99,6 +99,7 @@
add_field(fn1.split("_")[0] + "_Density",
function=_get_density(fn1), take_log=True,
display_name="%s\/Density" % fn1.split("_")[0],
+ units = r"\rm{g}/\rm{cm}^3",
projected_units = r"\rm{g}/\rm{cm}^2",
)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/2eee5fc43d54/
changeset: 2eee5fc43d54
branch: yt
user: ngoldbaum
date: 2012-10-05 06:54:02
summary: Fixing a bug in the point callback pointed out by Elizabeth Tasker.
affected #: 1 file
diff -r d2daf94661086662a9efe6139fe88557b71bbff3 -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -745,12 +745,13 @@
self.text_args = text_args
def __call__(self, plot):
-
-
+ if len(self.pos) == 3:
+ pos = (self.pos[x_dict[plot.data.axis]],
+ self.pos[y_dict[plot.data.axis]])
+ else: pos = self.pos
width,height = plot.image._A.shape
- x,y = self.convert_to_plot(plot, self.pos)
- x,y = x/width,y/height
-
+ x,y = self.convert_to_plot(plot, pos)
+
plot._axes.text(x, y, self.text, **self.text_args)
class MarkerAnnotateCallback(PlotCallback):
https://bitbucket.org/yt_analysis/yt-3.0/changeset/066a7b53b64d/
changeset: 066a7b53b64d
branch: yt
user: ngoldbaum
date: 2012-10-05 06:54:30
summary: Merging
affected #: 38 files
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -400,7 +400,7 @@
echo '2c1933ab31246b4f4eba049d3288156e0a72f1730604e3ed7357849967cdd329e4647cf236c9442ecfb06d0aff03e6fc892a7ba2a5c1cf5c011b7ab9c619acec Cython-0.16.tar.gz' > Cython-0.16.tar.gz.sha512
echo '44eea803870a66ff0bab08d13a8b3388b5578ebc1c807d1d9dca0a93e6371e91b15d02917a00b3b20dc67abb5a21dabaf9b6e9257a561f85eeff2147ac73b478 PyX-0.11.1.tar.gz' > PyX-0.11.1.tar.gz.sha512
-echo '1a754d560bfa433f0960ab3b5a62edb5f291be98ec48cf4e5941fa5b84139e200b87a52efbbd6fa4a76d6feeff12439eed3e7a84db4421940d1bbb576f7a684e Python-2.7.2.tgz' > Python-2.7.2.tgz.sha512
+echo 'b981f8464575bb24c297631c87a3b9172312804a0fc14ce1fa7cb41ce2b0d2fd383cd1c816d6e10c36467d18bf9492d6faf557c81c04ff3b22debfa93f30ad0b Python-2.7.3.tgz' > Python-2.7.3.tgz.sha512
echo 'c017d3d59dd324ac91af0edc178c76b60a5f90fbb775cf843e39062f95bd846238f2c53705f8890ed3f34bc0e6e75671a73d13875eb0287d6201cb45f0a2d338 bzip2-1.0.5.tar.gz' > bzip2-1.0.5.tar.gz.sha512
echo 'a296dfcaef7e853e58eed4e24b37c4fa29cfc6ac688def048480f4bb384b9e37ca447faf96eec7b378fd764ba291713f03ac464581d62275e28eb2ec99110ab6 reason-js-20120623.zip' > reason-js-20120623.zip.sha512
echo 'b519218f93946400326e9b656669269ecb3e5232b944e18fbc3eadc4fe2b56244d68aae56d6f69042b4c87c58c881ee2aaa279561ea0f0f48d5842155f4de9de freetype-2.4.4.tar.gz' > freetype-2.4.4.tar.gz.sha512
@@ -429,7 +429,7 @@
[ $INST_0MQ -eq 1 ] && get_ytproject zeromq-2.2.0.tar.gz
[ $INST_0MQ -eq 1 ] && get_ytproject pyzmq-2.1.11.tar.gz
[ $INST_0MQ -eq 1 ] && get_ytproject tornado-2.2.tar.gz
-get_ytproject Python-2.7.2.tgz
+get_ytproject Python-2.7.3.tgz
get_ytproject numpy-1.6.1.tar.gz
get_ytproject matplotlib-1.1.0.tar.gz
get_ytproject mercurial-2.2.2.tar.gz
@@ -554,11 +554,11 @@
fi
fi
-if [ ! -e Python-2.7.2/done ]
+if [ ! -e Python-2.7.3/done ]
then
echo "Installing Python. This may take a while, but don't worry. YT loves you."
- [ ! -e Python-2.7.2 ] && tar xfz Python-2.7.2.tgz
- cd Python-2.7.2
+ [ ! -e Python-2.7.3 ] && tar xfz Python-2.7.3.tgz
+ cd Python-2.7.3
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/analysis_modules/level_sets/clump_handling.py
--- a/yt/analysis_modules/level_sets/clump_handling.py
+++ b/yt/analysis_modules/level_sets/clump_handling.py
@@ -133,6 +133,7 @@
else:
exec(operation)
+ if self.children is None: return
for child in self.children:
child.pass_down(operation)
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/data_objects/grid_patch.py
--- a/yt/data_objects/grid_patch.py
+++ b/yt/data_objects/grid_patch.py
@@ -210,6 +210,8 @@
LE, RE = self.hierarchy.grid_left_edge[id,:], \
self.hierarchy.grid_right_edge[id,:]
self.dds = np.array((RE - LE) / self.ActiveDimensions)
+ if self.pf.dimensionality < 2: self.dds[1] = self.pf.domain_right_edge[1] - self.pf.domain_left_edge[1]
+ if self.pf.dimensionality < 3: self.dds[2] = self.pf.domain_right_edge[2] - self.pf.domain_left_edge[2]
self.field_data['dx'], self.field_data['dy'], self.field_data['dz'] = self.dds
@property
@@ -364,8 +366,10 @@
self._child_index_mask = None
#@time_execution
- def __fill_child_mask(self, child, mask, tofill):
+ def __fill_child_mask(self, child, mask, tofill, dlevel = 1):
rf = self.pf.refine_by
+ if dlevel != 1:
+ rf = rf**dlevel
gi, cgi = self.get_global_startindex(), child.get_global_startindex()
startIndex = np.maximum(0, cgi / rf - gi)
endIndex = np.minimum((cgi + child.ActiveDimensions) / rf - gi,
@@ -386,7 +390,7 @@
self.__fill_child_mask(child, self._child_mask, 0)
if self.OverlappingSiblings is not None:
for sibling in self.OverlappingSiblings:
- self.__fill_child_mask(sibling, self._child_mask, 0)
+ self.__fill_child_mask(sibling, self._child_mask, 0, 0)
self._child_indices = (self._child_mask==0) # bool, possibly redundant
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -938,6 +938,25 @@
validators=[ValidateParameter("cp_%s_vec" % ax)
for ax in 'xyz'], units=r"\rm{km}/\rm{s}")
+def _CuttingPlaneBx(field, data):
+ x_vec, y_vec, z_vec = [data.get_field_parameter("cp_%s_vec" % (ax))
+ for ax in 'xyz']
+ b_vec = np.array([data["B%s" % ax] for ax in 'xyz'])
+ return np.dot(x_vec, b_vec)
+add_field("CuttingPlaneBx",
+ function=_CuttingPlaneBx,
+ validators=[ValidateParameter("cp_%s_vec" % ax)
+ for ax in 'xyz'], units=r"\rm{Gauss}")
+def _CuttingPlaneBy(field, data):
+ x_vec, y_vec, z_vec = [data.get_field_parameter("cp_%s_vec" % (ax))
+ for ax in 'xyz']
+ b_vec = np.array([data["B%s" % ax] for ax in 'xyz'])
+ return np.dot(y_vec, b_vec)
+add_field("CuttingPlaneBy",
+ function=_CuttingPlaneBy,
+ validators=[ValidateParameter("cp_%s_vec" % ax)
+ for ax in 'xyz'], units=r"\rm{Gauss}")
+
def _MeanMolecularWeight(field,data):
return (data["Density"] / (mh *data["NumberDensity"]))
add_field("MeanMolecularWeight",function=_MeanMolecularWeight,units=r"")
@@ -975,12 +994,37 @@
units of Gauss. If you use MKS, make sure to write your own
MagneticEnergy field to deal with non-unitary \mu_0.
"""
- return (data["Bx"]**2 + data["By"]**2 + data["Bz"]**2)/2.
+ return (data["Bx"]**2 + data["By"]**2 + data["Bz"]**2)/(8*np.pi)
add_field("MagneticEnergy",function=_MagneticEnergy,
- units=r"",
- validators = [ValidateDataField("Bx"),
- ValidateDataField("By"),
- ValidateDataField("Bz")])
+ units=r"\rm{ergs}\/\rm{cm}^{-3}",
+ display_name=r"\rm{Magnetic}\/\rm{Energy}")
+
+def _BMagnitude(field,data):
+ """This assumes that your front end has provided Bx, By, Bz in
+ units of Gauss. If you use MKS, make sure to write your own
+ BMagnitude field to deal with non-unitary \mu_0.
+ """
+ return np.sqrt((data["Bx"]**2 + data["By"]**2 + data["Bz"]**2))
+add_field("BMagnitude",
+ function=_BMagnitude,
+ display_name=r"|B|", units=r"\rm{Gauss}")
+
+def _PlasmaBeta(field,data):
+ """This assumes that your front end has provided Bx, By, Bz in
+ units of Gauss. If you use MKS, make sure to write your own
+ PlasmaBeta field to deal with non-unitary \mu_0.
+ """
+ return data['Pressure']/data['MagneticEnergy']
+add_field("PlasmaBeta",
+ function=_PlasmaBeta,
+ display_name=r"\rm{Plasma}\/\beta", units="")
+
+def _MagneticPressure(field,data):
+ return data['MagneticEnergy']
+add_field("MagneticPressure",
+ function=_MagneticPressure,
+ display_name=r"\rm{Magnetic}\/\rm{Energy}",
+ units="\rm{ergs}\/\rm{cm}^{-3}")
def _VorticitySquared(field, data):
mylog.debug("Generating vorticity on %s", data)
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/_skeleton/__init__.py
--- /dev/null
+++ b/yt/frontends/_skeleton/__init__.py
@@ -0,0 +1,25 @@
+"""
+API for yt.frontends.skeleton
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: Columbia University
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+"""
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/_skeleton/api.py
--- /dev/null
+++ b/yt/frontends/_skeleton/api.py
@@ -0,0 +1,37 @@
+"""
+API for yt.frontends._skeleton
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: Columbia University
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+"""
+
+from .data_structures import \
+ SkeletonGrid, \
+ SkeletonHierarchy, \
+ SkeletonStaticOutput
+
+from .fields import \
+ SkeletonFieldInfo, \
+ add_flash_field
+
+from .io import \
+ IOHandlerSkeleton
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/_skeleton/data_structures.py
--- /dev/null
+++ b/yt/frontends/_skeleton/data_structures.py
@@ -0,0 +1,157 @@
+"""
+Skeleton data structures
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: Columbia University
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import h5py
+import stat
+import numpy as np
+import weakref
+
+from yt.funcs import *
+from yt.data_objects.grid_patch import \
+ AMRGridPatch
+from yt.data_objects.hierarchy import \
+ AMRHierarchy
+from yt.data_objects.static_output import \
+ StaticOutput
+from yt.utilities.definitions import \
+ mpc_conversion, sec_conversion
+from yt.utilities.io_handler import \
+ io_registry
+from yt.utilities.physical_constants import cm_per_mpc
+from .fields import SkeletonFieldInfo, add_flash_field, KnownSkeletonFields
+from yt.data_objects.field_info_container import \
+ FieldInfoContainer, NullFunc, ValidateDataField, TranslationFunc
+
+class SkeletonGrid(AMRGridPatch):
+ _id_offset = 0
+ #__slots__ = ["_level_id", "stop_index"]
+ def __init__(self, id, hierarchy, level):
+ AMRGridPatch.__init__(self, id, filename = hierarchy.hierarchy_filename,
+ hierarchy = hierarchy)
+ self.Parent = None
+ self.Children = []
+ self.Level = level
+
+ def __repr__(self):
+ return "SkeletonGrid_%04i (%s)" % (self.id, self.ActiveDimensions)
+
+class SkeletonHierarchy(AMRHierarchy):
+
+ grid = SkeletonGrid
+ float_type = np.float64
+
+ def __init__(self, pf, data_style='skeleton'):
+ self.data_style = data_style
+ self.parameter_file = weakref.proxy(pf)
+ # for now, the hierarchy file is the parameter file!
+ self.hierarchy_filename = self.parameter_file.parameter_filename
+ self.directory = os.path.dirname(self.hierarchy_filename)
+ AMRHierarchy.__init__(self, pf, data_style)
+
+ def _initialize_data_storage(self):
+ pass
+
+ def _detect_fields(self):
+ # This needs to set a self.field_list that contains all the available,
+ # on-disk fields.
+ pass
+
+ def _count_grids(self):
+ # This needs to set self.num_grids
+ pass
+
+ def _parse_hierarchy(self):
+ # This needs to fill the following arrays, where N is self.num_grids:
+ # self.grid_left_edge (N, 3) <= float64
+ # self.grid_right_edge (N, 3) <= float64
+ # self.grid_dimensions (N, 3) <= int
+ # self.grid_particle_count (N, 1) <= int
+ # self.grid_levels (N, 1) <= int
+ # self.grids (N, 1) <= grid objects
+ #
+ pass
+
+ def _populate_grid_objects(self):
+ # For each grid, this must call:
+ # grid._prepare_grid()
+ # grid._setup_dx()
+ # This must also set:
+ # grid.Children <= list of child grids
+ # grid.Parent <= parent grid
+ # This is handled by the frontend because often the children must be
+ # identified.
+ pass
+
+class SkeletonStaticOutput(StaticOutput):
+ _hierarchy_class = SkeletonHierarchy
+ _fieldinfo_fallback = SkeletonFieldInfo
+ _fieldinfo_known = KnownSkeletonFields
+ _handle = None
+
+ def __init__(self, filename, data_style='skeleton',
+ storage_filename = None,
+ conversion_override = None):
+
+ if conversion_override is None: conversion_override = {}
+ self._conversion_override = conversion_override
+
+ StaticOutput.__init__(self, filename, data_style)
+ self.storage_filename = storage_filename
+
+ def _set_units(self):
+ # This needs to set up the dictionaries that convert from code units to
+ # CGS. The needed items are listed in the second entry:
+ # self.time_units <= sec_conversion
+ # self.conversion_factors <= mpc_conversion
+ # self.units <= On-disk fields
+ pass
+
+ def _parse_parameter_file(self):
+ # This needs to set up the following items:
+ #
+ # self.unique_identifier
+ # self.parameters <= full of code-specific items of use
+ # self.domain_left_edge <= array of float64
+ # self.domain_right_edge <= array of float64
+ # self.dimensionality <= int
+ # self.domain_dimensions <= array of int64
+ # self.current_time <= simulation time in code units
+ #
+ # We also set up cosmological information. Set these to zero if
+ # non-cosmological.
+ #
+ # self.cosmological_simulation <= int, 0 or 1
+ # self.current_redshift <= float
+ # self.omega_lambda <= float
+ # self.omega_matter <= float
+ # self.hubble_constant <= float
+
+ @classmethod
+ def _is_valid(self, *args, **kwargs):
+ # This accepts a filename or a set of arguments and returns True or
+ # False depending on if the file is of the type requested.
+ return False
+
+
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/_skeleton/fields.py
--- /dev/null
+++ b/yt/frontends/_skeleton/fields.py
@@ -0,0 +1,102 @@
+"""
+Skeleton-specific fields
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: Columbia University
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from yt.data_objects.field_info_container import \
+ FieldInfoContainer, \
+ NullFunc, \
+ TranslationFunc, \
+ FieldInfo, \
+ ValidateParameter, \
+ ValidateDataField, \
+ ValidateProperty, \
+ ValidateSpatial, \
+ ValidateGridType
+import yt.data_objects.universal_fields
+from yt.utilities.physical_constants import \
+ kboltz
+
+# The first field container is where any fields that exist on disk go, along
+# with their conversion factors, display names, etc.
+
+KnownSkeletonFields = FieldInfoContainer()
+add_skeleton_field = KnownSkeletonFields.add_field
+
+SkeletonFieldInfo = FieldInfoContainer.create_with_fallback(FieldInfo)
+add_field = SkeletonFieldInfo.add_field
+
+# Often, we want to translate between fields on disk and fields in yt. This
+# construct shows how to do that. Note that we use TranslationFunc.
+
+translation_dict = {"x-velocity": "velx",
+ "y-velocity": "vely",
+ "z-velocity": "velz",
+ "Density": "dens",
+ "Temperature": "temp",
+ "Pressure" : "pres",
+ "Grav_Potential" : "gpot",
+ "particle_position_x" : "particle_posx",
+ "particle_position_y" : "particle_posy",
+ "particle_position_z" : "particle_posz",
+ "particle_velocity_x" : "particle_velx",
+ "particle_velocity_y" : "particle_vely",
+ "particle_velocity_z" : "particle_velz",
+ "particle_index" : "particle_tag",
+ "Electron_Fraction" : "elec",
+ "HI_Fraction" : "h ",
+ "HD_Fraction" : "hd ",
+ "HeI_Fraction": "hel ",
+ "HeII_Fraction": "hep ",
+ "HeIII_Fraction": "hepp",
+ "HM_Fraction": "hmin",
+ "HII_Fraction": "hp ",
+ "H2I_Fraction": "htwo",
+ "H2II_Fraction": "htwp",
+ "DI_Fraction": "deut",
+ "DII_Fraction": "dplu",
+ "ParticleMass": "particle_mass",
+ "Flame_Fraction": "flam"}
+
+for f,v in translation_dict.items():
+ if v not in KnownSkeletonFields:
+ pfield = v.startswith("particle")
+ add_skeleton_field(v, function=NullFunc, take_log=False,
+ validators = [ValidateDataField(v)],
+ particle_type = pfield)
+ if f.endswith("_Fraction") :
+ dname = "%s\/Fraction" % f.split("_")[0]
+ else :
+ dname = f
+ ff = KnownSkeletonFields[v]
+ pfield = f.startswith("particle")
+ add_field(f, TranslationFunc(v),
+ take_log=KnownSkeletonFields[v].take_log,
+ units = ff._units, display_name=dname,
+ particle_type = pfield)
+
+# Here's an example of adding a new field:
+
+add_skeleton_field("dens", function=NullFunc, take_log=True,
+ convert_function=_get_convert("dens"),
+ units=r"\rm{g}/\rm{cm}^3")
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/_skeleton/io.py
--- /dev/null
+++ b/yt/frontends/_skeleton/io.py
@@ -0,0 +1,44 @@
+"""
+Skeleton-specific IO functions
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: Columbia University
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import numpy as np
+import h5py
+
+from yt.utilities.io_handler import \
+ BaseIOHandler
+
+class IOHandlerSkeleton(BaseIOHandler):
+ _particle_reader = False
+ _data_style = "skeleton"
+
+ def _read_data_set(self, grid, field):
+ # This must return the array, of size/shape grid.ActiveDimensions, that
+ # corresponds to 'field'.
+ pass
+
+ def _read_data_slice(self, grid, field, axis, coord):
+ # If this is not implemented, the IO handler will just slice a
+ # _read_data_set item.
+ pass
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/_skeleton/setup.py
--- /dev/null
+++ b/yt/frontends/_skeleton/setup.py
@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+import setuptools
+import os
+import sys
+import os.path
+
+
+def configuration(parent_package='', top_path=None):
+ from numpy.distutils.misc_util import Configuration
+ config = Configuration('skeleton', parent_package, top_path)
+ config.make_config_py() # installs __config__.py
+ #config.make_svn_version_py()
+ return config
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/castro/data_structures.py
--- a/yt/frontends/castro/data_structures.py
+++ b/yt/frontends/castro/data_structures.py
@@ -101,18 +101,11 @@
self.Parent = None
def _setup_dx(self):
- # So first we figure out what the index is. We don't assume
- # that dx=dy=dz , at least here. We probably do elsewhere.
- id = self.id - self._id_offset
- if self.Parent is not None:
- self.dds = self.Parent[0].dds / self.pf.refine_by
- else:
- LE, RE = self.hierarchy.grid_left_edge[id,:], \
- self.hierarchy.grid_right_edge[id,:]
- self.dds = np.array((RE-LE)/self.ActiveDimensions)
-
- if self.pf.dimensionality < 2: self.dds[1] = 1.0
- if self.pf.dimensionality < 3: self.dds[2] = 1.0
+ # has already been read in and stored in hierarchy
+ dx = self.hierarchy.grid_dxs[self.index][0]
+ dy = self.hierarchy.grid_dys[self.index][0]
+ dz = self.hierarchy.grid_dzs[self.index][0]
+ self.dds = np.array([dx, dy, dz])
self.field_data['dx'], self.field_data['dy'], self.field_data['dz'] = self.dds
def __repr__(self):
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -89,17 +89,8 @@
return self.start_index
def _setup_dx(self):
- # So first we figure out what the index is. We don't assume
- # that dx=dy=dz , at least here. We probably do elsewhere.
- id = self.id - self._id_offset
- if len(self.Parent) > 0:
- self.dds = self.Parent[0].dds / self.pf.refine_by
- else:
- LE, RE = self.hierarchy.grid_left_edge[id,:], \
- self.hierarchy.grid_right_edge[id,:]
- self.dds = np.array((RE-LE)/self.ActiveDimensions)
- if self.pf.dimensionality < 2: self.dds[1] = 1.0
- if self.pf.dimensionality < 3: self.dds[2] = 1.0
+ # has already been read in and stored in hierarchy
+ self.dds = self.hierarchy.dds_list[self.Level]
self.field_data['dx'], self.field_data['dy'], self.field_data['dz'] = self.dds
class ChomboHierarchy(AMRHierarchy):
@@ -176,11 +167,13 @@
# 'Chombo_global'
levels = f.keys()[1:]
grids = []
+ self.dds_list = []
i = 0
for lev in levels:
level_number = int(re.match('level_(\d+)',lev).groups()[0])
boxes = f[lev]['boxes'].value
dx = f[lev].attrs['dx']
+ self.dds_list.append(dx * np.ones(3))
for level_id, box in enumerate(boxes):
si = np.array([box['lo_%s' % ax] for ax in 'ijk'])
ei = np.array([box['hi_%s' % ax] for ax in 'ijk'])
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/chombo/fields.py
--- a/yt/frontends/chombo/fields.py
+++ b/yt/frontends/chombo/fields.py
@@ -98,6 +98,21 @@
add_field("Density",function=_Density, take_log=True,
units=r'\rm{g}/\rm{cm^3}')
+def _Bx(field,data):
+ return data["X-magnfield"]
+add_field("Bx", function=_Bx, take_log=False,
+ units=r"\rm{Gauss}", display_name=r"B_x")
+
+def _By(field,data):
+ return data["Y-magnfield"]
+add_field("By", function=_By, take_log=False,
+ units=r"\rm{Gauss}", display_name=r"B_y")
+
+def _Bz(field,data):
+ return data["Z-magnfield"]
+add_field("Bz", function=_Bz, take_log=False,
+ units=r"\rm{Gauss}", display_name=r"B_z")
+
def _MagneticEnergy(field,data):
return (data["X-magnfield"]**2 +
data["Y-magnfield"]**2 +
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/flash/fields.py
--- a/yt/frontends/flash/fields.py
+++ b/yt/frontends/flash/fields.py
@@ -23,6 +23,7 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+import numpy as np
from yt.data_objects.field_info_container import \
FieldInfoContainer, \
NullFunc, \
@@ -97,7 +98,10 @@
if fn1.endswith("_Fraction"):
add_field(fn1.split("_")[0] + "_Density",
function=_get_density(fn1), take_log=True,
- display_name="%s\/Density" % fn1.split("_")[0])
+ display_name="%s\/Density" % fn1.split("_")[0],
+ units = r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2",
+ )
def _get_convert(fname):
def _conv(data):
@@ -106,7 +110,8 @@
add_flash_field("dens", function=NullFunc, take_log=True,
convert_function=_get_convert("dens"),
- units=r"\rm{g}/\rm{cm}^3")
+ units=r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2"),
add_flash_field("velx", function=NullFunc, take_log=False,
convert_function=_get_convert("velx"),
units=r"\rm{cm}/\rm{s}")
@@ -203,6 +208,7 @@
add_field(f, TranslationFunc(v),
take_log=KnownFLASHFields[v].take_log,
units = ff._units, display_name=dname,
+ projected_units = ff._projected_units,
particle_type = pfield)
def _convertParticleMassMsun(data):
@@ -254,3 +260,43 @@
add_field("GasEnergy", function=_GasEnergy,
units=r"\rm{ergs}/\rm{g}")
+
+# See http://flash.uchicago.edu/pipermail/flash-users/2012-October/001180.html
+# along with the attachment to that e-mail for details
+def GetMagRescalingFactor(pf):
+ if pf['unitsystem'].lower() == "cgs":
+ factor = 1
+ if pf['unitsystem'].lower() == "si":
+ factor = np.sqrt(4*np.pi/1e7)
+ if pf['unitsystem'].lower() == "none":
+ factor = np.sqrt(4*np.pi)
+ else:
+ raise RuntimeError("Runtime parameter unitsystem with"
+ "value %s is unrecognized" % pf['unitsystem'])
+ return factor
+
+def _Bx(fields, data):
+ factor = GetMagRescalingFactor(data.pf)
+ return data['magx']*factor
+add_field("Bx", function=_Bx, take_log=False,
+ units=r"\rm{Gauss}", display_name=r"B_x")
+
+def _By(fields, data):
+ factor = GetMagRescalingFactor(data.pf)
+ return data['magy']*factor
+add_field("By", function=_By, take_log=False,
+ units=r"\rm{Gauss}", display_name=r"B_y")
+
+def _Bz(fields, data):
+ factor = GetMagRescalingFactor(data.pf)
+ return data['magz']*factor
+add_field("Bz", function=_Bz, take_log=False,
+ units=r"\rm{Gauss}", display_name=r"B_z")
+
+def _DivB(fields, data):
+ factor = GetMagRescalingFactor(data.pf)
+ return data['divb']*factor
+add_field("DivB", function=_DivB, take_log=False,
+ units=r"\rm{Gauss}\/\rm{cm}^{-1}")
+
+
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -37,6 +37,8 @@
AMRHierarchy
from yt.data_objects.static_output import \
StaticOutput
+from yt.utilities.lib import \
+ get_box_grids_level
from yt.utilities.definitions import \
mpc_conversion, sec_conversion
@@ -133,14 +135,25 @@
del levels, glis, gdims
def _populate_grid_objects(self):
- for g in self.grids:
+ mask = np.empty(self.grids.size, dtype='int32')
+ for gi, g in enumerate(self.grids):
g._prepare_grid()
g._setup_dx()
- for g in self.grids:
+ for gi, g in enumerate(self.grids):
g.Children = self._get_grid_children(g)
for g1 in g.Children:
g1.Parent.append(g)
+ get_box_grids_level(self.grid_left_edge[gi,:],
+ self.grid_right_edge[gi,:],
+ self.grid_levels[gi],
+ self.grid_left_edge, self.grid_right_edge,
+ self.grid_levels, mask)
+ m = mask.astype("bool")
+ m[gi] = False
+ siblings = self.grids[gi:][m[gi:]]
+ if len(siblings) > 0:
+ g.OverlappingSiblings = siblings.tolist()
self.max_level = self.grid_levels.max()
def _setup_derived_fields(self):
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/maestro/data_structures.py
--- a/yt/frontends/maestro/data_structures.py
+++ b/yt/frontends/maestro/data_structures.py
@@ -102,17 +102,11 @@
self.Parent = None
def _setup_dx(self):
- # So first we figure out what the index is. We don't assume
- # that dx=dy=dz , at least here. We probably do elsewhere.
- id = self.id - self._id_offset
- if self.Parent is not None:
- self.dds = self.Parent[0].dds / self.pf.refine_by
- else:
- LE, RE = self.hierarchy.grid_left_edge[id,:], \
- self.hierarchy.grid_right_edge[id,:]
- self.dds = np.array((RE-LE)/self.ActiveDimensions)
- if self.pf.dimensionality < 2: self.dds[1] = 1.0
- if self.pf.dimensionality < 3: self.dds[2] = 1.0
+ # has already been read in and stored in hierarchy
+ dx = self.hierarchy.grid_dxs[self.index][0]
+ dy = self.hierarchy.grid_dys[self.index][0]
+ dz = self.hierarchy.grid_dzs[self.index][0]
+ self.dds = np.array([dx, dy, dz])
self.field_data['dx'], self.field_data['dy'], self.field_data['dz'] = self.dds
def __repr__(self):
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/nyx/data_structures.py
--- a/yt/frontends/nyx/data_structures.py
+++ b/yt/frontends/nyx/data_structures.py
@@ -100,18 +100,11 @@
self.Parent = None
def _setup_dx(self):
- # So first we figure out what the index is. We don't assume that
- # dx=dy=dz here.
- id = self.id - self._id_offset
- if self.Parent is not None:
- self.dds = self.Parent[0].dds / self.pf.refine_by
- else:
- LE, RE = self.hierarchy.grid_left_edge[id,:], \
- self.hierarchy.grid_right_edge[id,:]
- self.dds = np.array((RE - LE) / self.ActiveDimensions)
-
- if self.pf.dimensionality < 2: self.dds[1] = 1.0
- if self.pf.dimensionality < 3: self.dds[2] = 1.0
+ # has already been read in and stored in hierarchy
+ dx = self.hierarchy.grid_dxs[self.index][0]
+ dy = self.hierarchy.grid_dys[self.index][0]
+ dz = self.hierarchy.grid_dzs[self.index][0]
+ self.dds = np.array([dx, dy, dz])
self.field_data['dx'], self.field_data['dy'], self.field_data['dz'] = self.dds
def __repr__(self):
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/frontends/orion/data_structures.py
--- a/yt/frontends/orion/data_structures.py
+++ b/yt/frontends/orion/data_structures.py
@@ -99,17 +99,11 @@
self.Parent = None
def _setup_dx(self):
- # So first we figure out what the index is. We don't assume
- # that dx=dy=dz , at least here. We probably do elsewhere.
- id = self.id - self._id_offset
- if self.Parent is not None:
- self.dds = self.Parent[0].dds / self.pf.refine_by
- else:
- LE, RE = self.hierarchy.grid_left_edge[id,:], \
- self.hierarchy.grid_right_edge[id,:]
- self.dds = np.array((RE-LE)/self.ActiveDimensions)
- if self.pf.dimensionality < 2: self.dds[1] = 1.0
- if self.pf.dimensionality < 3: self.dds[2] = 1.0
+ # has already been read in and stored in hierarchy
+ dx = self.hierarchy.grid_dxs[self.index][0]
+ dy = self.hierarchy.grid_dys[self.index][0]
+ dz = self.hierarchy.grid_dzs[self.index][0]
+ self.dds = np.array([dx, dy, dz])
self.field_data['dx'], self.field_data['dy'], self.field_data['dz'] = self.dds
def __repr__(self):
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/mods.py
--- a/yt/mods.py
+++ b/yt/mods.py
@@ -122,7 +122,7 @@
get_multi_plot, FixedResolutionBuffer, ObliqueFixedResolutionBuffer, \
callback_registry, write_bitmap, write_image, annotate_image, \
apply_colormap, scale_image, write_projection, write_fits, \
- SlicePlot, OffAxisSlicePlot, ProjectionPlot
+ SlicePlot, OffAxisSlicePlot, ProjectionPlot, OffAxisProjectionPlot
from yt.visualization.volume_rendering.api import \
ColorTransferFunction, PlanckTransferFunction, ProjectionTransferFunction, \
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/testing.py
--- /dev/null
+++ b/yt/testing.py
@@ -0,0 +1,143 @@
+"""Provides utility and helper functions for testing in yt.
+
+Author: Anthony Scpatz <scopatz at gmail.com>
+Affiliation: The University of Chicago
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Anthony Scopatz. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import numpy as np
+from yt.funcs import *
+from numpy.testing import assert_array_equal
+
+def amrspace(extent, levels=7, cells=8):
+ """Creates two numpy arrays representing the left and right bounds of
+ an AMR grid as well as an array for the AMR level of each cell.
+
+ Parameters
+ ----------
+ extent : array-like
+ This a sequence of length 2*ndims that is the bounds of each dimension.
+ For example, the 2D unit square would be given by [0.0, 1.0, 0.0, 1.0].
+ A 3D cylindrical grid may look like [0.0, 2.0, -1.0, 1.0, 0.0, 2*np.pi].
+ levels : int or sequence of ints, optional
+ This is the number of AMR refinement levels. If given as a sequence (of
+ length ndims), then each dimension will be refined down to this level.
+ All values in this array must be the same or zero. A zero valued dimension
+ indicates that this dim should not be refined. Taking the 3D cylindrical
+ example above if we don't want refine theta but want r and z at 5 we would
+ set levels=(5, 5, 0).
+ cells : int, optional
+ This is the number of cells per refinement level.
+
+ Returns
+ -------
+ left : float ndarray, shape=(npoints, ndims)
+ The left AMR grid points.
+ right : float ndarray, shape=(npoints, ndims)
+ The right AMR grid points.
+ level : int ndarray, shape=(npoints,)
+ The AMR level for each point.
+
+ Examples
+ --------
+ >>> l, r, lvl = amrspace([0.0, 2.0, 1.0, 2.0, 0.0, 3.14], levels=(3,3,0), cells=2)
+ >>> print l
+ [[ 0. 1. 0. ]
+ [ 0.25 1. 0. ]
+ [ 0. 1.125 0. ]
+ [ 0.25 1.125 0. ]
+ [ 0.5 1. 0. ]
+ [ 0. 1.25 0. ]
+ [ 0.5 1.25 0. ]
+ [ 1. 1. 0. ]
+ [ 0. 1.5 0. ]
+ [ 1. 1.5 0. ]]
+
+ """
+ extent = np.asarray(extent, dtype='f8')
+ dextent = extent[1::2] - extent[::2]
+ ndims = len(dextent)
+
+ if isinstance(levels, int):
+ minlvl = maxlvl = levels
+ levels = np.array([levels]*ndims, dtype='int32')
+ else:
+ levels = np.asarray(levels, dtype='int32')
+ minlvl = levels.min()
+ maxlvl = levels.max()
+ if minlvl != maxlvl and (minlvl != 0 or set([minlvl, maxlvl]) != set(levels)):
+ raise ValueError("all levels must have the same value or zero.")
+ dims_zero = (levels == 0)
+ dims_nonzero = ~dims_zero
+ ndims_nonzero = dims_nonzero.sum()
+
+ npoints = (cells**ndims_nonzero - 1)*maxlvl + 1
+ left = np.empty((npoints, ndims), dtype='float64')
+ right = np.empty((npoints, ndims), dtype='float64')
+ level = np.empty(npoints, dtype='int32')
+
+ # fill zero dims
+ left[:,dims_zero] = extent[::2][dims_zero]
+ right[:,dims_zero] = extent[1::2][dims_zero]
+
+ # fill non-zero dims
+ dcell = 1.0 / cells
+ left_slice = tuple([slice(extent[2*n], extent[2*n+1], extent[2*n+1]) if \
+ dims_zero[n] else slice(0.0,1.0,dcell) for n in range(ndims)])
+ right_slice = tuple([slice(extent[2*n+1], extent[2*n], -extent[2*n+1]) if \
+ dims_zero[n] else slice(dcell,1.0+dcell,dcell) for n in range(ndims)])
+ left_norm_grid = np.reshape(np.mgrid[left_slice].T.flat[ndims:], (-1, ndims))
+ lng_zero = left_norm_grid[:,dims_zero]
+ lng_nonzero = left_norm_grid[:,dims_nonzero]
+
+ right_norm_grid = np.reshape(np.mgrid[right_slice].T.flat[ndims:], (-1, ndims))
+ rng_zero = right_norm_grid[:,dims_zero]
+ rng_nonzero = right_norm_grid[:,dims_nonzero]
+
+ level[0] = maxlvl
+ left[0,:] = extent[::2]
+ right[0,dims_zero] = extent[1::2][dims_zero]
+ right[0,dims_nonzero] = (dcell**maxlvl)*dextent[dims_nonzero] + extent[::2][dims_nonzero]
+ for i, lvl in enumerate(range(maxlvl, 0, -1)):
+ start = (cells**ndims_nonzero - 1)*i + 1
+ stop = (cells**ndims_nonzero - 1)*(i+1) + 1
+ dsize = dcell**(lvl-1) * dextent[dims_nonzero]
+ level[start:stop] = lvl
+ left[start:stop,dims_zero] = lng_zero
+ left[start:stop,dims_nonzero] = lng_nonzero*dsize + extent[::2][dims_nonzero]
+ right[start:stop,dims_zero] = rng_zero
+ right[start:stop,dims_nonzero] = rng_nonzero*dsize + extent[::2][dims_nonzero]
+
+ return left, right, level
+
+def fake_random_pf(ndims, peak_value = 1.0, fields = ("Density",), negative = False):
+ from yt.frontends.stream.api import load_uniform_grid
+ if not iterable(ndims):
+ ndims = [ndims, ndims, ndims]
+ else:
+ assert(len(ndims) == 3)
+ if negative:
+ offset = 0.5
+ else:
+ offset = 0.0
+ data = dict((field, (np.random.random(ndims) - offset) * peak_value)
+ for field in fields)
+ ug = load_uniform_grid(data, ndims, 1.0)
+ return ug
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/amr_kdtree/amr_kdtree.py
--- a/yt/utilities/amr_kdtree/amr_kdtree.py
+++ b/yt/utilities/amr_kdtree/amr_kdtree.py
@@ -998,11 +998,11 @@
anprocs = 2**par_tree_depth
volume_partitioned = 0.0
- pbar = get_pbar("Building kd-Tree",
- np.prod(self.domain_right_edge-self.domain_left_edge))
+ total_vol = np.prod(self.domain_right_edge-self.domain_left_edge)
+ pbar = get_pbar("Building kd-Tree", total_vol)
while current_node is not None:
- pbar.update(volume_partitioned)
+ pbar.update(min(volume_partitioned, total_vol))
# If we don't have any grids, that means we are revisiting
# a dividing node, and there is nothing to be done.
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/command_line.py
--- a/yt/utilities/command_line.py
+++ b/yt/utilities/command_line.py
@@ -1188,6 +1188,40 @@
import yt.utilities.lodgeit as lo
lo.main( None, download=args.number )
+class YTNotebookUploadCmd(YTCommand):
+ args = (dict(short="file", type=str),)
+ description = \
+ """
+ Upload an IPython notebook to hub.yt-project.org.
+ """
+
+ name = "upload_notebook"
+ def __call__(self, args):
+ filename = args.file
+ if not os.path.isfile(filename):
+ raise IOError(filename)
+ if not filename.endswith(".ipynb"):
+ print "File must be an IPython notebook!"
+ return 1
+ import json
+ try:
+ t = json.loads(open(filename).read())['metadata']['name']
+ except (ValueError, KeyError):
+ print "File does not appear to be an IPython notebook."
+ from yt.utilities.minimal_representation import MinimalNotebook
+ mn = MinimalNotebook(filename, t)
+ rv = mn.upload()
+ print "Upload successful!"
+ print
+ print "To access your raw notebook go here:"
+ print
+ print " %s" % (rv['url'])
+ print
+ print "To view your notebook go here:"
+ print
+ print " %s" % (rv['url'].replace("/go/", "/nb/"))
+ print
+
class YTPlotCmd(YTCommand):
args = ("width", "unit", "bn", "proj", "center",
"zlim", "axis", "field", "weight", "skip",
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/exceptions.py
--- a/yt/utilities/exceptions.py
+++ b/yt/utilities/exceptions.py
@@ -141,3 +141,8 @@
def __str__(self):
return "This parameter file doesn't recognize %s" % self.unit
+
+class YTHubRegisterError(YTException):
+ def __str__(self):
+ return "You must create an API key before uploading. See " + \
+ "https://data.yt-project.org/getting_started.html"
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/flagging_methods.py
--- /dev/null
+++ b/yt/utilities/flagging_methods.py
@@ -0,0 +1,51 @@
+"""
+Utilities for flagging zones for refinement in a dataset
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: Columbia University
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import numpy as np # For modern purposes
+
+flagging_method_registry = {}
+
+def flag_cells(grid, methods):
+ flagged = np.zeros(grid.ActiveDimensions, dtype="bool")
+ for method in methods:
+ flagged |= method(grid)
+ return flagged
+
+class FlaggingMethod(object):
+ _skip_add = False
+ class __metaclass__(type):
+ def __init__(cls, name, b, d):
+ type.__init__(cls, name, b, d)
+ if hasattr(cls, "_type_name") and not cls._skip_add:
+ flagging_method_registry[cls._type_name] = cls
+
+class OverDensity(FlaggingMethod):
+ _type_name = "overdensity"
+ def __init__(self, over_density):
+ self.over_density = over_density
+
+ def __call__(self, pf, grid):
+ rho = grid["Density"] / (pf.refine_by**grid.Level)
+ return (rho > self.over_density)
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/lib/fortran_reader.pyx
--- a/yt/utilities/lib/fortran_reader.pyx
+++ b/yt/utilities/lib/fortran_reader.pyx
@@ -53,8 +53,8 @@
@cython.boundscheck(False)
@cython.wraparound(False)
-def read_and_seek(char *filename, int offset1, int offset2,
- np.ndarray buffer, int bytes):
+def read_and_seek(char *filename, np.int64_t offset1,
+ np.int64_t offset2, np.ndarray buffer, int bytes):
cdef FILE *f = fopen(filename, "rb")
cdef void *buf = <void *> buffer.data
cdef char line[1024]
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/lib/grid_traversal.pyx
--- a/yt/utilities/lib/grid_traversal.pyx
+++ b/yt/utilities/lib/grid_traversal.pyx
@@ -590,7 +590,7 @@
cdef np.float64_t *pointer = <np.float64_t *> star_colors.data
for i in range(pos_x.shape[0]):
kdtree_utils.kd_insert3(self.tree,
- pos_x[i], pos_y[i], pos_z[i], pointer + i*3)
+ pos_x[i], pos_y[i], pos_z[i], <void *> (pointer + i*3))
def __dealloc__(self):
kdtree_utils.kd_free(self.tree)
@@ -616,7 +616,7 @@
cdef np.float64_t slopes[6], dp[3], ds[3]
cdef np.float64_t dt = (exit_t - enter_t) / vri.n_samples
cdef np.float64_t dvs[6], cell_left[3], local_dds[3], pos[3]
- cdef int nstars
+ cdef int nstars, dti, i, j
cdef np.float64_t *colors = NULL, gexp, gaussian, px, py, pz
for i in range(3):
dp[i] = (enter_t + 0.5 * dt) * v_dir[i] + v_pos[i]
@@ -648,6 +648,7 @@
dvs[i] = temp
for dti in range(vri.n_samples):
# Now we add the contribution from stars
+ kdtree_utils.kd_res_rewind(ballq)
for i in range(nstars):
kdtree_utils.kd_res_item3(ballq, &px, &py, &pz)
colors = <np.float64_t *> kdtree_utils.kd_res_item_data(ballq)
@@ -655,20 +656,22 @@
gexp = (px - pos[0])*(px - pos[0]) \
+ (py - pos[1])*(py - pos[1]) \
+ (pz - pos[2])*(pz - pos[2])
- gaussian = vri.star_coeff * expl(-gexp/vri.star_sigma_num)
- for i in range(3): im.rgba[i] += gaussian*dt*colors[i]
+ gaussian = vri.star_coeff * exp(-gexp/vri.star_sigma_num)
+ for j in range(3): im.rgba[j] += gaussian*dt*colors[j]
for i in range(3):
pos[i] += local_dds[i]
FIT_eval_transfer(dt, dvs, im.rgba, vri.n_fits, vri.fits,
vri.field_table_ids, vri.grey_opacity)
for i in range(vc.n_fields):
dvs[i] += slopes[i]
+ kdtree_utils.kd_res_free(ballq)
cdef class VolumeRenderSampler(ImageSampler):
cdef VolumeRenderAccumulator *vra
cdef public object tf_obj
cdef public object my_field_tables
cdef kdtree_utils.kdtree **trees
+ cdef object tree_containers
def __cinit__(self,
np.ndarray vp_pos,
np.ndarray vp_dir,
@@ -709,6 +712,7 @@
self.vra.field_table_ids[i] = tf_obj.field_table_ids[i]
self.supp_data = <void *> self.vra
cdef star_kdtree_container skdc
+ self.tree_containers = star_list
if star_list is None:
self.trees = NULL
else:
@@ -719,10 +723,15 @@
self.trees[i] = skdc.tree
cdef void setup(self, PartitionedGrid pg):
+ cdef star_kdtree_container star_tree
if self.trees == NULL:
self.sampler = volume_render_sampler
else:
+ star_tree = self.tree_containers[pg.parent_grid_id]
self.vra.star_list = self.trees[pg.parent_grid_id]
+ self.vra.star_sigma_num = 2.0*star_tree.sigma**2.0
+ self.vra.star_er = 2.326 * star_tree.sigma
+ self.vra.star_coeff = star_tree.coeff
self.sampler = volume_render_stars_sampler
def __dealloc__(self):
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/minimal_representation.py
--- a/yt/utilities/minimal_representation.py
+++ b/yt/utilities/minimal_representation.py
@@ -30,6 +30,7 @@
from tempfile import TemporaryFile
from yt.config import ytcfg
from yt.funcs import *
+from yt.utilities.exceptions import *
from .poster.streaminghttp import register_openers
from .poster.encode import multipart_encode
@@ -93,6 +94,7 @@
def upload(self):
api_key = ytcfg.get("yt","hub_api_key")
url = ytcfg.get("yt","hub_url")
+ if api_key == '': raise YTHubRegisterError
metadata, (final_name, chunks) = self._generate_post()
if hasattr(self, "_pf_mrep"):
self._pf_mrep.upload()
@@ -216,3 +218,22 @@
metadata = self._attrs
chunks = []
return (metadata, ("chunks", []))
+
+class MinimalNotebook(MinimalRepresentation):
+ type = "notebook"
+ _attr_list = ("title",)
+
+ def __init__(self, filename, title = None):
+ # First we read in the data
+ if not os.path.isfile(filename):
+ raise IOError(filename)
+ self.data = open(filename).read()
+ if title is None:
+ title = json.loads(self.data)['metadata']['name']
+ self.title = title
+ self.data = np.fromstring(self.data, dtype='c')
+
+ def _generate_post(self):
+ metadata = self._attrs
+ chunks = [ ("notebook", self.data) ]
+ return (metadata, ("chunks", chunks))
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/orientation.py
--- a/yt/utilities/orientation.py
+++ b/yt/utilities/orientation.py
@@ -67,6 +67,8 @@
t = np.cross(normal_vector, vecs).sum(axis=1)
ax = t.argmax()
east_vector = np.cross(vecs[ax,:], normal_vector).ravel()
+ # self.north_vector must remain None otherwise rotations about a fixed axis will break.
+ # The north_vector calculated here will still be included in self.unit_vectors.
north_vector = np.cross(normal_vector, east_vector).ravel()
else:
if self.steady_north:
@@ -82,7 +84,7 @@
r"""Change the view direction based on any of the orientation parameters.
This will recalculate all the necessary vectors and vector planes related
- to a an orientable object.
+ to an orientable object.
Parameters
----------
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/tests/test_flagging_methods.py
--- /dev/null
+++ b/yt/utilities/tests/test_flagging_methods.py
@@ -0,0 +1,12 @@
+from yt.testing import *
+from yt.utilities.flagging_methods import flagging_method_registry
+
+def setup():
+ global pf
+ pf = fake_random_pf(64)
+ pf.h
+
+def test_over_density():
+ od_flag = flagging_method_registry["overdensity"](0.75)
+ criterion = (pf.h.grids[0]["Density"] > 0.75)
+ assert( np.all( od_flag(pf, pf.h.grids[0]) == criterion) )
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/utilities/tests/test_interpolators.py
--- /dev/null
+++ b/yt/utilities/tests/test_interpolators.py
@@ -0,0 +1,27 @@
+from yt.testing import *
+import yt.utilities.linear_interpolators as lin
+
+def setup():
+ pass
+
+def test_linear_interpolator_1d():
+ random_data = np.random.random(64)
+ fv = {'x': np.mgrid[0.0:1.0:64j]}
+ ufi = lin.UnilinearFieldInterpolator(random_data, (0.0, 1.0), "x", True)
+ assert_array_equal(ufi(fv), random_data)
+
+def test_linear_interpolator_2d():
+ random_data = np.random.random((64, 64))
+ fv = dict((ax, v) for ax, v in zip("xyz",
+ np.mgrid[0.0:1.0:64j, 0.0:1.0:64j]))
+ bfi = lin.BilinearFieldInterpolator(random_data,
+ (0.0, 1.0, 0.0, 1.0), "xy", True)
+ assert_array_equal(bfi(fv), random_data)
+
+def test_linear_interpolator_3d():
+ random_data = np.random.random((64, 64, 64))
+ fv = dict((ax, v) for ax, v in zip("xyz",
+ np.mgrid[0.0:1.0:64j, 0.0:1.0:64j, 0.0:1.0:64j]))
+ tfi = lin.TrilinearFieldInterpolator(random_data,
+ (0.0, 1.0, 0.0, 1.0, 0.0, 1.0), "xyz", True)
+ assert_array_equal(tfi(fv), random_data)
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/visualization/api.py
--- a/yt/visualization/api.py
+++ b/yt/visualization/api.py
@@ -66,6 +66,7 @@
from plot_window import \
SlicePlot, \
OffAxisSlicePlot, \
- ProjectionPlot
+ ProjectionPlot, \
+ OffAxisProjectionPlot
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -28,6 +28,7 @@
x_dict, \
y_dict, \
axis_names
+from .volume_rendering.api import off_axis_projection
import _MPL
import numpy as np
import weakref
@@ -384,3 +385,28 @@
self.bounds).transpose()
self[item] = buff
return buff
+
+
+class OffAxisProjectionFixedResolutionBuffer(FixedResolutionBuffer):
+ def __init__(self, data_source, bounds, buff_size, antialias = True,
+ periodic = False):
+ self.data = {}
+ FixedResolutionBuffer.__init__(self, data_source, bounds, buff_size, antialias, periodic)
+
+ def __getitem__(self, item):
+ if item in self.data: return self.data[item]
+ mylog.info("Making a fixed resolutuion buffer of (%s) %d by %d" % \
+ (item, self.buff_size[0], self.buff_size[1]))
+ ds = self.data_source
+ width = (self.bounds[1] - self.bounds[0],
+ self.bounds[3] - self.bounds[2],
+ self.bounds[5] - self.bounds[4])
+ buff = off_axis_projection(ds.pf, ds.center, ds.normal_vector,
+ width, ds.resolution, item,
+ weight=ds.weight_field, volume=ds.volume,
+ no_ghost=ds.no_ghost, interpolated=ds.interpolated,
+ north_vector=ds.north_vector)
+ self[item] = buff.swapaxes(0,1)
+ return buff
+
+
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -152,8 +152,7 @@
alpha_channel = 255*np.ones((s1,s2,1), dtype='uint8')
bitmap_array = np.concatenate([bitmap_array, alpha_channel], axis=-1)
if transpose:
- for channel in range(bitmap_array.shape[2]):
- bitmap_array[:,:,channel] = bitmap_array[:,:,channel].T
+ bitmap_array = bitmap_array.swapaxes(0,1)
if filename is not None:
au.write_png(bitmap_array.copy(), filename)
else:
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -146,7 +146,9 @@
def __call__(self, plot):
# Instantiation of these is cheap
if plot._type_name == "CuttingPlane":
- print "WARNING: Magnetic field on Cutting Plane Not implemented."
+ qcb = CuttingQuiverCallback("CuttingPlaneBx",
+ "CuttingPlaneBy",
+ self.factor)
else:
xv = "B%s" % (x_names[plot.data.axis])
yv = "B%s" % (y_names[plot.data.axis])
@@ -432,6 +434,9 @@
iy = np.maximum(np.minimum((yt).astype('int'), ny-1), 0)
lines[i,0,:,:] = xt + dt * pixX[ix,iy] * scale
lines[i,1,:,:] = yt + dt * pixY[ix,iy] * scale
+ # scale into data units
+ lines[:,0,:,:] = lines[:,0,:,:] * (xx1 - xx0) / nx + xx0
+ lines[:,1,:,:] = lines[:,1,:,:] * (yy1 - yy0) / ny + yy0
for i in range(self.data_size[0]):
for j in range(self.data_size[1]):
plot._axes.plot(lines[:,0,i,j], lines[:,1,i,j],
@@ -650,8 +655,8 @@
plot.data[self.field_y],
int(nx), int(ny),
(x0, x1, y0, y1),).transpose()
- X = np.mgrid[0:plot.image._A.shape[0]-1:nx*1j]# + 0.5*factor
- Y = np.mgrid[0:plot.image._A.shape[1]-1:ny*1j]# + 0.5*factor
+ X,Y = np.meshgrid(np.linspace(xx0,xx1,nx,endpoint=True),
+ np.linspace(yy0,yy1,ny,endpoint=True))
plot._axes.quiver(X,Y, pixX, pixY)
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -27,7 +27,10 @@
import base64
import matplotlib.figure
from matplotlib.mathtext import MathTextParser
-from matplotlib.pyparsing import ParseFatalException
+try:
+ from matplotlib.pyparsing import ParseFatalException
+except ImportError:
+ from pyparsing import ParseFatalException
import cStringIO
import types
import __builtin__
@@ -40,7 +43,8 @@
write_image, apply_colormap
from .fixed_resolution import \
FixedResolutionBuffer, \
- ObliqueFixedResolutionBuffer
+ ObliqueFixedResolutionBuffer, \
+ OffAxisProjectionFixedResolutionBuffer
from .plot_modifications import get_smallest_appropriate_unit, \
callback_registry
from .tick_locators import LogLocator, LinearLocator
@@ -103,7 +107,10 @@
self.pf = frb.pf
self.xlim = viewer.xlim
self.ylim = viewer.ylim
- self._type_name = ''
+ if 'Cutting' in self.data.__class__.__name__:
+ self._type_name = "CuttingPlane"
+ else:
+ self._type_name = ''
class FieldTransform(object):
def __init__(self, name, func, locator):
@@ -154,7 +161,7 @@
center[y_dict[axis]]+width[1]/2]
return (bounds,center)
-def GetOffAxisBoundsAndCenter(normal, center, width, pf, unit='1'):
+def GetOffAxisBoundsAndCenter(normal, center, width, pf, unit='1',depth=None):
if width == None:
width = (pf.domain_width.min(),
pf.domain_width.min())
@@ -165,6 +172,13 @@
width = (width, width)
Wx, Wy = width
width = np.array((Wx/pf[unit], Wy/pf[unit]))
+ if depth != None:
+ if iterable(depth) and isinstance(depth[1],str):
+ d,unit = depth
+ depth = d/pf[unit]
+ elif iterable(depth):
+ raise RuntimeError("Depth must be a float or a (width,\"unit\") tuple")
+ width = np.append(width,depth)
if isinstance(center,str):
if center.lower() == 'm' or center.lower() == 'max':
v, center = pf.h.find_max("Density")
@@ -173,16 +187,19 @@
else:
raise RuntimeError('center keyword \"%s\" not recognized'%center)
- # Transforming to the cutting plane coordinate system
- center = np.array(center)
- center = (center - pf.domain_left_edge)/pf.domain_width - 0.5
- (normal,perp1,perp2) = ortho_find(normal)
- mat = np.transpose(np.column_stack((perp1,perp2,normal)))
- center = np.dot(mat,center)
- width = width/pf.domain_width.min()
+ if width.shape == (2,):
+ # Transforming to the cutting plane coordinate system
+ center = np.array(center)
+ center = (center - pf.domain_left_edge)/pf.domain_width - 0.5
+ (normal,perp1,perp2) = ortho_find(normal)
+ mat = np.transpose(np.column_stack((perp1,perp2,normal)))
+ center = np.dot(mat,center)
+ width = width
+
+ bounds = [-width[0]/2, width[0]/2, -width[1]/2, width[1]/2]
+ else:
+ bounds = [-width[0]/2, width[0]/2, -width[1]/2, width[1]/2, -width[2]/2, width[2]/2]
- bounds = [-width[0]/2, width[0]/2, -width[1]/2, width[1]/2]
-
return (bounds,center)
class PlotWindow(object):
@@ -244,20 +261,14 @@
old_fields = None
if self._frb is not None:
old_fields = self._frb.keys()
- try:
+ if hasattr(self,'zlim'):
+ bounds = self.xlim+self.ylim+self.zlim
+ else:
bounds = self.xlim+self.ylim
- if self.oblique == False:
- self._frb = FixedResolutionBuffer(self.data_source,
- bounds, self.buff_size,
- self.antialias,
- periodic=self._periodic)
- else:
- self._frb = ObliqueFixedResolutionBuffer(self.data_source,
- bounds, self.buff_size,
- self.antialias,
- periodic=self._periodic)
- except:
- raise RuntimeError("Failed to repixelize.")
+ self._frb = self._frb_generator(self.data_source,
+ bounds, self.buff_size,
+ self.antialias,
+ periodic=self._periodic)
if old_fields is None:
self._frb._get_data_source_fields()
else:
@@ -298,6 +309,7 @@
nWx, nWy = Wx/factor, Wy/factor
self.xlim = (centerx - nWx*0.5, centerx + nWx*0.5)
self.ylim = (centery - nWy*0.5, centery + nWy*0.5)
+
@invalidate_data
def pan(self, deltas):
@@ -344,12 +356,16 @@
dy = bounds[3] - bounds[2]
self.xlim = (self.center[0] - dx/2., self.center[0] + dx/2.)
self.ylim = (self.center[1] - dy/2., self.center[1] + dy/2.)
- mylog.info("xlim = %f %f" %self.xlim)
- mylog.info("ylim = %f %f" %self.ylim)
else:
- self.xlim = bounds[0:2]
- self.ylim = bounds[2:]
-
+ self.xlim = tuple(bounds[0:2])
+ self.ylim = tuple(bounds[2:4])
+ if len(bounds) == 6:
+ self.zlim = tuple(bounds[4:6])
+ mylog.info("xlim = %f %f" %self.xlim)
+ mylog.info("ylim = %f %f" %self.ylim)
+ if hasattr(self,'zlim'):
+ mylog.info("zlim = %f %f" %self.zlim)
+
@invalidate_data
def set_width(self, width, unit = '1'):
"""set the width of the plot window
@@ -395,14 +411,20 @@
width = (Wx,Wy)
width = [w / self.pf[unit] for w in width]
- centerx = (self.xlim[1] + self.xlim[0])/2
- centery = (self.ylim[1] + self.ylim[0])/2
+ centerx = (self.xlim[1] + self.xlim[0])/2.
+ centery = (self.ylim[1] + self.ylim[0])/2.
self.xlim = (centerx - width[0]/2.,
centerx + width[0]/2.)
self.ylim = (centery - width[1]/2.,
centery + width[1]/2.)
+ if hasattr(self,'zlim'):
+ centerz = (self.zlim[1] + self.zlim[0])/2.
+ mw = max(width)
+ self.zlim = (centerz - mw/2.,
+ centerz + mw/2.)
+
@invalidate_data
def set_center(self, new_center, unit = '1'):
"""Sets a new center for the plot window
@@ -809,7 +831,7 @@
raise RuntimeError("Colormap '%s' does not exist!" % str(cmap))
self.plots[field].image.set_cmap(cmap)
- def save(self,name=None,mpl_kwargs={}):
+ def save(self, name=None, mpl_kwargs=None):
"""saves the plot to disk.
Parameters
@@ -827,15 +849,12 @@
name = str(self.pf)
elif name.endswith('.png'):
return v.save(name)
+ if mpl_kwargs is None: mpl_kwargs = {}
axis = axis_names[self.data_source.axis]
weight = None
- if 'Slice' in self.data_source.__class__.__name__:
- type = 'Slice'
- if 'Proj' in self.data_source.__class__.__name__:
- type = 'Projection'
+ type = self._plot_type
+ if type in ['Projection','OffAxisProjection']:
weight = self.data_source.weight_field
- if 'Cutting' in self.data_source.__class__.__name__:
- type = 'OffAxisSlice'
names = []
for k, v in self.plots.iteritems():
if axis:
@@ -849,11 +868,15 @@
return names
def _send_zmq(self):
- from IPython.zmq.pylab.backend_inline import \
- send_figure
+ try:
+ # pre-IPython v0.14
+ from IPython.zmq.pylab.backend_inline import send_figure as display
+ except ImportError:
+ # IPython v0.14+
+ from IPython.core.display import display
for k, v in sorted(self.plots.iteritems()):
canvas = FigureCanvasAgg(v.figure)
- send_figure(v.figure)
+ display(v.figure)
def show(self):
r"""This will send any existing plots to the IPython notebook.
@@ -879,6 +902,9 @@
raise YTNotInsideNotebook
class SlicePlot(PWViewerMPL):
+ _plot_type = 'Slice'
+ _frb_generator = FixedResolutionBuffer
+
def __init__(self, pf, axis, fields, center='c', width=None, axes_unit=None,
origin='center-window'):
r"""Creates a slice plot from a parameter file
@@ -954,6 +980,9 @@
self.set_axes_unit(axes_unit)
class ProjectionPlot(PWViewerMPL):
+ _plot_type = 'Projection'
+ _frb_generator = FixedResolutionBuffer
+
def __init__(self, pf, axis, fields, center='c', width=None, axes_unit=None,
weight_field=None, max_level=None, origin='center-window'):
r"""Creates a projection plot from a parameter file
@@ -1033,6 +1062,9 @@
self.set_axes_unit(axes_unit)
class OffAxisSlicePlot(PWViewerMPL):
+ _plot_type = 'OffAxisSlice'
+ _frb_generator = ObliqueFixedResolutionBuffer
+
def __init__(self, pf, normal, fields, center='c', width=(1,'unitary'),
axes_unit=None, north_vector=None):
r"""Creates an off axis slice plot from a parameter file
@@ -1080,6 +1112,95 @@
PWViewerMPL.__init__(self,cutting,bounds,origin='center-window',periodic=False,oblique=True)
self.set_axes_unit(axes_unit)
+class OffAxisProjectionDummyDataSource(object):
+ _type_name = 'proj'
+ proj_style = 'integrate'
+ _key_fields = []
+ def __init__(self, center, pf, normal_vector, width, fields,
+ interpolated, resolution = (800,800), weight=None,
+ volume=None, no_ghost=False, le=None, re=None,
+ north_vector=None):
+ self.center = center
+ self.pf = pf
+ self.axis = 4 # always true for oblique data objects
+ self.normal_vector = normal_vector
+ self.width = width
+ self.fields = fields
+ self.interpolated = interpolated
+ self.resolution = resolution
+ self.weight_field = weight
+ self.volume = volume
+ self.no_ghost = no_ghost
+ self.le = le
+ self.re = re
+ self.north_vector = north_vector
+
+class OffAxisProjectionPlot(PWViewerMPL):
+ _plot_type = 'OffAxisProjection'
+ _frb_generator = OffAxisProjectionFixedResolutionBuffer
+
+ def __init__(self, pf, normal, fields, center='c', width=(1,'unitary'),
+ depth=(1,'unitary'), axes_unit=None, weight_field=None,
+ max_level=None, north_vector=None, volume=None, no_ghost=False,
+ le=None, re=None, interpolated=False):
+ r"""Creates an off axis projection plot from a parameter file
+
+ Given a pf object, a normal vector to project along, and
+ a field name string, this will return a PWViewrMPL object
+ containing the plot.
+
+ The plot can be updated using one of the many helper functions
+ defined in PlotWindow.
+
+ Parameters
+ ----------
+ pf : :class:`yt.data_objects.api.StaticOutput`
+ This is the parameter file object corresponding to the
+ simulation output to be plotted.
+ normal : a sequence of floats
+ The vector normal to the slicing plane.
+ fields : string
+ The name of the field(s) to be plotted.
+ center : A two or three-element vector of sequence floats, 'c', or 'center'
+ The coordinate of the center of the image. If left blanck,
+ the image centers on the location of the maximum density
+ cell. If set to 'c' or 'center', the plot is centered on
+ the middle of the domain.
+ width : A tuple or a float
+ A tuple containing the width of image and the string key of
+ the unit: (width, 'unit'). If set to a float, code units
+ are assumed
+ depth : A tuple or a float
+ A tuple containing the depth to project thourhg and the string
+ key of the unit: (width, 'unit'). If set to a float, code units
+ are assumed
+ weight_field : string
+ The name of the weighting field. Set to None for no weight.
+ max_level: int
+ The maximum level to project to.
+ 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.
+ north-vector : a sequence of floats
+ A vector defining the 'up' direction in the plot. This
+ option sets the orientation of the slicing plane. If not
+ set, an arbitrary grid-aligned north-vector is chosen.
+
+ """
+ (bounds,center_rot) = GetOffAxisBoundsAndCenter(normal,center,width,pf,depth=depth)
+ # Hard-coding the resolution for now
+ fields = ensure_list(fields)[:]
+ width = np.array((bounds[1] - bounds[0], bounds[3] - bounds[2], bounds[5] - bounds[4]))
+ OffAxisProj = OffAxisProjectionDummyDataSource(center_rot, pf, normal, width, fields, interpolated,
+ weight=weight_field, volume=volume, no_ghost=no_ghost,
+ le=le, re=re, north_vector=north_vector)
+ # Hard-coding the origin keyword since the other two options
+ # aren't well-defined for off-axis data objects
+ PWViewerMPL.__init__(self,OffAxisProj,bounds,origin='center-window',periodic=False,oblique=True)
+ self.set_axes_unit(axes_unit)
+
_metadata_template = """
%(pf)s<br><br>
diff -r 2eee5fc43d543cc72c41c211a0c49ec1847eec14 -r 066a7b53b64de31705574ca71dd06fd130327689 yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -195,7 +195,7 @@
if not iterable(width):
width = (width, width, width) # left/right, top/bottom, front/back
self.orienter = Orientation(normal_vector, north_vector=north_vector, steady_north=steady_north)
- self.rotation_vector = self.orienter.north_vector
+ self.rotation_vector = self.orienter.unit_vectors[1]
self._setup_box_properties(width, center, self.orienter.unit_vectors)
if fields is None: fields = ["Density"]
self.fields = fields
@@ -282,7 +282,7 @@
if center is not None:
self.center = center
if north_vector is None:
- north_vector = self.orienter.north_vector
+ north_vector = self.orienter.unit_vectors[1]
if normal_vector is None:
normal_vector = self.orienter.normal_vector
self.orienter.switch_orientation(normal_vector = normal_vector,
@@ -301,7 +301,11 @@
np.array(self.width), self.transfer_function, self.sub_samples)
return args
+ star_trees = None
def get_sampler(self, args):
+ kwargs = {}
+ if self.star_trees is not None:
+ kwargs = {'star_list': self.star_trees}
if self.use_light:
if self.light_dir is None:
self.set_default_light_dir()
@@ -312,9 +316,10 @@
if self.light_rgba is None:
self.set_default_light_rgba()
sampler = LightSourceRenderSampler(*args, light_dir=temp_dir,
- light_rgba=self.light_rgba)
+ light_rgba=self.light_rgba, **kwargs)
else:
- sampler = self._sampler_object(*args)
+ sampler = self._sampler_object(*args, **kwargs)
+ print sampler, kwargs
return sampler
def finalize_image(self, image):
@@ -587,7 +592,7 @@
"""
rot_vector = self.orienter.normal_vector
R = get_rotation_matrix(theta, rot_vector)
- north_vector = self.orienter.north_vector
+ north_vector = self.orienter.unit_vectors[1]
self.switch_view(north_vector=np.dot(R, north_vector))
def rotation(self, theta, n_steps, rot_vector=None, clip_ratio = None):
@@ -720,6 +725,9 @@
], dtype='float64')
class HEALpixCamera(Camera):
+
+ _sampler_object = None
+
def __init__(self, center, radius, nside,
transfer_function = None, fields = None,
sub_samples = 5, log_fields = None, volume = None,
@@ -733,6 +741,12 @@
if transfer_function is None:
transfer_function = ProjectionTransferFunction()
self.transfer_function = transfer_function
+
+ if isinstance(self.transfer_function, ProjectionTransferFunction):
+ self._sampler_object = ProjectionSampler
+ else:
+ self._sampler_object = VolumeRenderSampler
+
if fields is None: fields = ["Density"]
self.fields = fields
self.sub_samples = sub_samples
@@ -1667,7 +1681,8 @@
def off_axis_projection(pf, center, normal_vector, width, resolution,
field, weight = None,
- volume = None, no_ghost = False, interpolated = False):
+ volume = None, no_ghost = False, interpolated = False,
+ north_vector = None):
r"""Project through a parameter file, off-axis, and return the image plane.
This function will accept the necessary items to integrate through a volume
@@ -1726,8 +1741,9 @@
"""
projcam = ProjectionCamera(center, normal_vector, width, resolution,
- field, weight=weight, pf=pf, volume=volume,
- no_ghost=no_ghost, interpolated=interpolated)
+ field, weight=weight, pf=pf, volume=volume,
+ no_ghost=no_ghost, interpolated=interpolated,
+ north_vector=north_vector)
image = projcam.snapshot()
if weight is not None:
pf.field_info.pop("temp_weightfield")
https://bitbucket.org/yt_analysis/yt-3.0/changeset/b8175a113d8e/
changeset: b8175a113d8e
branch: yt
user: ngoldbaum
date: 2012-10-05 06:59:58
summary: Fixing another place where we should check for 3D positions.
affected #: 1 file
diff -r 066a7b53b64de31705574ca71dd06fd130327689 -r b8175a113d8ed98c0e8d514579ab607b01494565 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -728,9 +728,13 @@
self.plot_args = plot_args
def __call__(self, plot):
+ if len(self.pos) == 3:
+ pos = (self.pos[x_dict[plot.data.axis]],
+ self.pos[y_dict[plot.data.axis]])
+ else: pos = self.pos
from matplotlib.patches import Arrow
# Now convert the pixels to code information
- x, y = self.convert_to_plot(plot, self.pos)
+ x, y = self.convert_to_plot(plot, pos)
dx, dy = self.convert_to_plot(plot, self.code_size, False)
arrow = Arrow(x, y, dx, dy, **self.plot_args)
plot._axes.add_patch(arrow)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/1f8f3d5921b0/
changeset: 1f8f3d5921b0
branch: yt
user: samskillman
date: 2012-09-29 00:22:51
summary: Initial work on an ImageArray class that knows about its origins
affected #: 5 files
diff -r e6915de3e4eb9416758acf2203d281c71319b40b -r 1f8f3d5921b04d4fe019bd37ef2a10259d82300f yt/data_objects/api.py
--- a/yt/data_objects/api.py
+++ b/yt/data_objects/api.py
@@ -65,6 +65,9 @@
quantity_info, \
add_quantity
+from image_array import \
+ ImageArray
+
from field_info_container import \
FieldInfoContainer, \
FieldInfo, \
diff -r e6915de3e4eb9416758acf2203d281c71319b40b -r 1f8f3d5921b04d4fe019bd37ef2a10259d82300f yt/data_objects/image_array.py
--- /dev/null
+++ b/yt/data_objects/image_array.py
@@ -0,0 +1,148 @@
+"""
+ImageArray Class
+
+Authors: Samuel Skillman <samskillman at gmail.com>
+Affiliation: University of Colorado at Boulder
+
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Samuel Skillman. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ """
+
+import numpy as np
+import h5py as h5
+from yt.visualization.image_writer import write_bitmap
+
+class ImageArray(np.ndarray):
+ """
+ A custom Numpy ndarray used for images.
+
+ This differs from ndarray in that you can optionally specify an
+ info dictionary which is used later in saving, and can be accessed with
+ ImageArray.info.
+
+ Optional Arguments:
+ info: dictionary
+ Contains information to be stored with image.
+
+ Numpy ndarray documentation appended:
+
+ """
+
+ def __new__(cls, input_array, info=None):
+ # Input array is an already formed ndarray instance
+ # We first cast to be our class type
+ obj = np.asarray(input_array).view(cls)
+ # add the new attribute to the created instance
+ if info is None:
+ info = {}
+ obj.info = info
+ # Finally, we must return the newly created object:
+ return obj
+
+ def __array_finalize__(self, obj):
+ # see InfoArray.__array_finalize__ for comments
+ if obj is None: return
+ self.info = getattr(obj, 'info', None)
+
+ def write_hdf5(self, filename):
+ """
+ Writes ImageArray to hdf5 file.
+
+ Arguments:
+ filename: string
+ Note filename not be modified.
+
+ Returns:
+ None
+
+ """
+ try:
+ array_name = self.info['name']
+ except KeyError:
+ array_name = 'image'
+
+ f = h5.File(filename)
+ if array_name in f.keys():
+ del f[array_name]
+ d = f.create_dataset(array_name, data=self)
+ for k, v in self.info.iteritems():
+ d.attrs.create(k, v)
+ f.close()
+
+ def write_png(self, filename, clip_ratio=None):
+ """
+ Writes ImageArray to png.
+
+ Arguments:
+ filename: string
+ '.png' will be appended if not present.
+
+ Returns:
+ The bitmap array written
+
+ Note: when writing to png, we invert the y axis
+ such to prepare for the write_bitmap call. This puts the (0,0) pixel
+ in the lower left
+
+ """
+ if filename[-4:] != '.png':
+ filename += '.png'
+
+ if clip_ratio is not None:
+ return write_bitmap(np.flipud(self).transpose(1,0,2), filename,
+ clip_ratio * self.std())
+ else:
+ return write_bitmap(np.flipud(self).transpose(1,0,2), filename)
+
+ def save(self, filename, png=True, hdf5=True):
+ """
+ Saves ImageArray.
+
+ Arguments:
+ filename: string
+ This should not contain the extension type (.png, .h5, ...)
+
+ Optional Arguments:
+ png: boolean, default True
+ Save to a png
+
+ hdf5: boolean, default True
+ Save to hdf5 file, including info dictionary as attributes.
+
+ """
+ if png:
+ self.write_png("%s.png" % filename)
+ if hdf5:
+ self.write_hdf5("%s.h5" % filename)
+
+ __doc__ += np.ndarray.__doc__
+
+if __name__ == "__main__":
+ im = np.zeros([64,128,3])
+ for i in xrange(im.shape[0]):
+ for k in xrange(im.shape[2]):
+ im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_ImageArray')
+
diff -r e6915de3e4eb9416758acf2203d281c71319b40b -r 1f8f3d5921b04d4fe019bd37ef2a10259d82300f yt/mods.py
--- a/yt/mods.py
+++ b/yt/mods.py
@@ -62,7 +62,7 @@
ValidateParameter, ValidateDataField, ValidateProperty, \
ValidateSpatial, ValidateGridType, \
TimeSeriesData, AnalysisTask, analysis_task, \
- ParticleTrajectoryCollection
+ ParticleTrajectoryCollection, ImageArray
from yt.data_objects.derived_quantities import \
add_quantity, quantity_info
diff -r e6915de3e4eb9416758acf2203d281c71319b40b -r 1f8f3d5921b04d4fe019bd37ef2a10259d82300f yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -116,7 +116,7 @@
image = image.transpose().copy() # Have to make sure it's contiguous
au.write_png(image, fn)
-def write_bitmap(bitmap_array, filename, max_val = None, transpose=True):
+def write_bitmap(bitmap_array, filename, max_val = None, transpose=False):
r"""Write out a bitmapped image directly to a PNG file.
This accepts a three- or four-channel `bitmap_array`. If the image is not
diff -r e6915de3e4eb9416758acf2203d281c71319b40b -r 1f8f3d5921b04d4fe019bd37ef2a10259d82300f yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -37,6 +37,7 @@
arr_ang2pix_nest, arr_fisheye_vectors
from yt.utilities.math_utils import get_rotation_matrix
from yt.utilities.orientation import Orientation
+from yt.data_objects.api import ImageArray
from yt.visualization.image_writer import write_bitmap, write_image
from yt.data_objects.data_containers import data_object_registry
from yt.utilities.parallel_tools.parallel_analysis_interface import \
@@ -290,7 +291,7 @@
self._setup_box_properties(width, self.center, self.orienter.unit_vectors)
def new_image(self):
image = np.zeros((self.resolution[0], self.resolution[1], 3), dtype='float64', order='C')
- return image
+ return ImageArray(image)
def get_sampler_args(self, image):
rotp = np.concatenate([self.orienter.inv_mat.ravel('F'), self.back_center.ravel()])
@@ -342,11 +343,7 @@
def save_image(self, fn, clip_ratio, image):
if self.comm.rank is 0 and fn is not None:
- if clip_ratio is not None:
- write_bitmap(image, fn, clip_ratio * image.std())
- else:
- write_bitmap(image, fn)
-
+ image.write_png(fn, clip_ratio=clip_ratio)
def initialize_source(self):
return self.volume.initialize_source()
@@ -748,7 +745,7 @@
def new_image(self):
image = np.zeros((12 * self.nside ** 2, 1, 3), dtype='float64', order='C')
- return image
+ return ImageArray(image)
def get_sampler_args(self, image):
nv = 12 * self.nside ** 2
@@ -958,7 +955,7 @@
def new_image(self):
image = np.zeros((self.resolution**2,1,3), dtype='float64', order='C')
- return image
+ return ImageArray(image)
def get_sampler_args(self, image):
vp = arr_fisheye_vectors(self.resolution, self.fov)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/2c5e5476cd58/
changeset: 2c5e5476cd58
branch: yt
user: samskillman
date: 2012-09-29 00:42:57
summary: Modifying how ImageArray gets used in the various cameras
affected #: 1 file
diff -r 1f8f3d5921b04d4fe019bd37ef2a10259d82300f -r 2c5e5476cd58864655232d438af43b1604031ab6 yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -291,7 +291,7 @@
self._setup_box_properties(width, self.center, self.orienter.unit_vectors)
def new_image(self):
image = np.zeros((self.resolution[0], self.resolution[1], 3), dtype='float64', order='C')
- return ImageArray(image)
+ return image
def get_sampler_args(self, image):
rotp = np.concatenate([self.orienter.inv_mat.ravel('F'), self.back_center.ravel()])
@@ -348,6 +348,14 @@
def initialize_source(self):
return self.volume.initialize_source()
+ def get_information(self):
+ info_dict = {'fields':self.fields, 'type':'rendering',
+ 'east_vector':self.orienter.unit_vectors[0],
+ 'north_vector':self.orienter.unit_vectors[1],
+ 'normal_vector':self.orienter.unit_vectors[2],
+ 'width':self.width, 'dataset':self.pf.fullpath}
+ return info_dict
+
def snapshot(self, fn = None, clip_ratio = None, double_check = False,
num_threads = 0):
r"""Ray-cast the camera.
@@ -382,7 +390,9 @@
args = self.get_sampler_args(image)
sampler = self.get_sampler(args)
self.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clip_ratio, image)
return image
@@ -745,7 +755,7 @@
def new_image(self):
image = np.zeros((12 * self.nside ** 2, 1, 3), dtype='float64', order='C')
- return ImageArray(image)
+ return image
def get_sampler_args(self, image):
nv = 12 * self.nside ** 2
@@ -811,7 +821,9 @@
args = self.get_sampler_args(image)
sampler = self.get_sampler(args)
self.volume.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clim, image, label = label)
return image
@@ -955,7 +967,7 @@
def new_image(self):
image = np.zeros((self.resolution**2,1,3), dtype='float64', order='C')
- return ImageArray(image)
+ return image
def get_sampler_args(self, image):
vp = arr_fisheye_vectors(self.resolution, self.fov)
@@ -1247,8 +1259,9 @@
if self.image is not None:
del self.image
+ image = ImageArray(image,
+ info=self.get_information())
self.image = image
-
return image
def save_image(self, fn, clip_ratio=None):
@@ -1653,7 +1666,9 @@
self.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clip_ratio, image)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/2f4a55153531/
changeset: 2f4a55153531
branch: yt
user: samskillman
date: 2012-10-04 17:03:31
summary: Moving to swapaxes.
affected #: 1 file
diff -r 2c5e5476cd58864655232d438af43b1604031ab6 -r 2f4a551535310443f0e0e4e78f584e2967b5da36 yt/data_objects/image_array.py
--- a/yt/data_objects/image_array.py
+++ b/yt/data_objects/image_array.py
@@ -105,10 +105,10 @@
filename += '.png'
if clip_ratio is not None:
- return write_bitmap(np.flipud(self).transpose(1,0,2), filename,
+ return write_bitmap(self.swapaxes(0, 1), filename,
clip_ratio * self.std())
else:
- return write_bitmap(np.flipud(self).transpose(1,0,2), filename)
+ return write_bitmap(self.swapaxes(0, 1), filename)
def save(self, filename, png=True, hdf5=True):
"""
https://bitbucket.org/yt_analysis/yt-3.0/changeset/a3e13b786fc5/
changeset: a3e13b786fc5
branch: yt
user: samskillman
date: 2012-10-04 18:02:07
summary: Fixes to the perspective camera brick ordering, and fixing the ImageArray for the HEALpixCamera
affected #: 1 file
diff -r 2f4a551535310443f0e0e4e78f584e2967b5da36 -r a3e13b786fc5898752fd685c0d60fcccadedc2ef yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -349,11 +349,13 @@
return self.volume.initialize_source()
def get_information(self):
- info_dict = {'fields':self.fields, 'type':'rendering',
+ info_dict = {'fields':self.fields,
+ 'type':self.__class__.__name__,
'east_vector':self.orienter.unit_vectors[0],
'north_vector':self.orienter.unit_vectors[1],
'normal_vector':self.orienter.unit_vectors[2],
- 'width':self.width, 'dataset':self.pf.fullpath}
+ 'width':self.width,
+ 'dataset':self.pf.fullpath}
return info_dict
def snapshot(self, fn = None, clip_ratio = None, double_check = False,
@@ -672,7 +674,7 @@
class PerspectiveCamera(Camera):
expand_factor = 1.0
def __init__(self, *args, **kwargs):
- expand_factor = kwargs.pop('expand_factor', 1.0)
+ self.expand_factor = kwargs.pop('expand_factor', 1.0)
Camera.__init__(self, *args, **kwargs)
def get_sampler_args(self, image):
@@ -711,6 +713,27 @@
self.transfer_function, self.sub_samples)
return args
+ def _render(self, double_check, num_threads, image, sampler):
+ pbar = get_pbar("Ray casting", (self.volume.brick_dimensions + 1).prod(axis=-1).sum())
+ total_cells = 0
+ if double_check:
+ for brick in self.volume.bricks:
+ for data in brick.my_data:
+ if np.any(np.isnan(data)):
+ raise RuntimeError
+
+ view_pos = self.front_center
+ for brick in self.volume.traverse(view_pos, self.front_center, image):
+ sampler(brick, num_threads=num_threads)
+ total_cells += np.prod(brick.my_data[0].shape)
+ pbar.update(total_cells)
+
+ pbar.finish()
+ image = sampler.aimage
+ self.finalize_image(image)
+ return image
+
+
def finalize_image(self, image):
image.shape = self.resolution[0], self.resolution[0], 3
@@ -794,6 +817,15 @@
return image
+ def get_information(self):
+ info_dict = {'fields':self.fields,
+ 'type':self.__class__.__name__,
+ 'center':self.center,
+ 'radius':self.radius,
+ 'dataset':self.pf.fullpath}
+ return info_dict
+
+
def snapshot(self, fn = None, clip_ratio = None, double_check = False,
num_threads = 0, clim = None, label = None):
r"""Ray-cast the camera.
https://bitbucket.org/yt_analysis/yt-3.0/changeset/1d1d955d024e/
changeset: 1d1d955d024e
branch: yt
user: samskillman
date: 2012-10-06 01:54:41
summary: Updating ImageArray to have a write_image, have better docstrings, and have better exceptions.
affected #: 1 file
diff -r a3e13b786fc5898752fd685c0d60fcccadedc2ef -r 1d1d955d024ef6db805d4c2d9b16d56103bd6c8b yt/data_objects/image_array.py
--- a/yt/data_objects/image_array.py
+++ b/yt/data_objects/image_array.py
@@ -26,24 +26,64 @@
import numpy as np
import h5py as h5
-from yt.visualization.image_writer import write_bitmap
+from yt.visualization.image_writer import write_bitmap, write_image
class ImageArray(np.ndarray):
- """
- A custom Numpy ndarray used for images.
+ r"""A custom Numpy ndarray used for images.
This differs from ndarray in that you can optionally specify an
info dictionary which is used later in saving, and can be accessed with
ImageArray.info.
- Optional Arguments:
- info: dictionary
+ Parameters
+ ----------
+ input_array: array_like
+ A numpy ndarray, or list.
+
+ Other Parameters
+ ----------------
+ info: dictionary
Contains information to be stored with image.
+ Returns
+ -------
+ obj: ImageArray object
+
+ Raises
+ ------
+ None
+
+ See Also
+ --------
+ numpy.ndarray : Inherits
+
+ Notes
+ -----
+
+ References
+ ----------
+
+ Examples
+ --------
+ These are written in doctest format, and should illustrate how to
+ use the function. Use the variables 'pf' for the parameter file, 'pc' for
+ a plot collection, 'c' for a center, and 'L' for a vector.
+
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.save('test_ImageArray')
+
Numpy ndarray documentation appended:
"""
-
def __new__(cls, input_array, info=None):
# Input array is an already formed ndarray instance
# We first cast to be our class type
@@ -61,21 +101,29 @@
self.info = getattr(obj, 'info', None)
def write_hdf5(self, filename):
- """
- Writes ImageArray to hdf5 file.
+ r"""Writes ImageArray to hdf5 file.
- Arguments:
- filename: string
+ Parameters
+ ----------
+ filename: string
Note filename not be modified.
+
+ Examples
+ --------
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
- Returns:
- None
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_hdf5('test_ImageArray.h5')
"""
- try:
- array_name = self.info['name']
- except KeyError:
- array_name = 'image'
+ array_name = self.info.get("name","image")
f = h5.File(filename)
if array_name in f.keys():
@@ -86,19 +134,27 @@
f.close()
def write_png(self, filename, clip_ratio=None):
- """
- Writes ImageArray to png.
+ r"""Writes ImageArray to png file.
- Arguments:
- filename: string
- '.png' will be appended if not present.
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Examples
+ --------
+
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
- Returns:
- The bitmap array written
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
- Note: when writing to png, we invert the y axis
- such to prepare for the write_bitmap call. This puts the (0,0) pixel
- in the lower left
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_png('test_ImageArray.png')
"""
if filename[-4:] != '.png':
@@ -110,6 +166,59 @@
else:
return write_bitmap(self.swapaxes(0, 1), filename)
+ def write_image(self, filename, color_bounds=None, channel=None, cmap_name="algae", func=lambda x: x):
+ r"""Writes a single channel of the ImageArray to a png file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Other Parameters
+ ----------------
+ channel: int
+ Which channel to write out as an image. Defaults to 0
+ cmap_name: string
+ Name of the colormap to be used.
+ color_bounds : tuple of floats, optional
+ The min and max to scale between. Outlying values will be clipped.
+ cmap_name : string, optional
+ An acceptable colormap. See either yt.visualization.color_maps or
+ http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
+ func : function, optional
+ A function to transform the buffer before applying a colormap.
+
+ Returns
+ -------
+ scaled_image : uint8 image that has been saved
+
+ Examples
+ --------
+
+ >>> im = np.zeros([64,128])
+ >>> for i in xrange(im.shape[0]):
+ >>> im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_image('test_ImageArray.png')
+
+ """
+ if filename[-4:] != '.png':
+ filename += '.png'
+
+ if channel is None:
+ return write_image(self.swapaxes(0,1), filename,
+ color_bounds=color_bounds, cmap_name=cmap_name,
+ func=func)
+ else:
+ return write_image(self.swapaxes(0,1)[:,:,channel], filename,
+ color_bounds=color_bounds, cmap_name=cmap_name,
+ func=func)
+
def save(self, filename, png=True, hdf5=True):
"""
Saves ImageArray.
@@ -127,7 +236,10 @@
"""
if png:
- self.write_png("%s.png" % filename)
+ if len(self.shape) > 2:
+ self.write_png("%s.png" % filename)
+ else:
+ self.write_image("%s.png" % filename)
if hdf5:
self.write_hdf5("%s.h5" % filename)
@@ -144,5 +256,16 @@
'width':0.245, 'units':'cm', 'type':'rendering'}
im_arr = ImageArray(im, info=myinfo)
- im_arr.save('test_ImageArray')
+ im_arr.save('test_3d_ImageArray')
+ im = np.zeros([64,128])
+ for i in xrange(im.shape[0]):
+ im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+
+ myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_2d_ImageArray')
+
https://bitbucket.org/yt_analysis/yt-3.0/changeset/39220cb0fde7/
changeset: 39220cb0fde7
branch: yt
user: MatthewTurk
date: 2012-10-06 02:04:57
summary: Merged in samskillman/yt (pull request #290)
affected #: 5 files
diff -r b8175a113d8ed98c0e8d514579ab607b01494565 -r 39220cb0fde7eb0f1270e9a31591402a7e47679c yt/data_objects/api.py
--- a/yt/data_objects/api.py
+++ b/yt/data_objects/api.py
@@ -65,6 +65,9 @@
quantity_info, \
add_quantity
+from image_array import \
+ ImageArray
+
from field_info_container import \
FieldInfoContainer, \
FieldInfo, \
diff -r b8175a113d8ed98c0e8d514579ab607b01494565 -r 39220cb0fde7eb0f1270e9a31591402a7e47679c yt/data_objects/image_array.py
--- /dev/null
+++ b/yt/data_objects/image_array.py
@@ -0,0 +1,271 @@
+"""
+ImageArray Class
+
+Authors: Samuel Skillman <samskillman at gmail.com>
+Affiliation: University of Colorado at Boulder
+
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Samuel Skillman. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ """
+
+import numpy as np
+import h5py as h5
+from yt.visualization.image_writer import write_bitmap, write_image
+
+class ImageArray(np.ndarray):
+ r"""A custom Numpy ndarray used for images.
+
+ This differs from ndarray in that you can optionally specify an
+ info dictionary which is used later in saving, and can be accessed with
+ ImageArray.info.
+
+ Parameters
+ ----------
+ input_array: array_like
+ A numpy ndarray, or list.
+
+ Other Parameters
+ ----------------
+ info: dictionary
+ Contains information to be stored with image.
+
+ Returns
+ -------
+ obj: ImageArray object
+
+ Raises
+ ------
+ None
+
+ See Also
+ --------
+ numpy.ndarray : Inherits
+
+ Notes
+ -----
+
+ References
+ ----------
+
+ Examples
+ --------
+ These are written in doctest format, and should illustrate how to
+ use the function. Use the variables 'pf' for the parameter file, 'pc' for
+ a plot collection, 'c' for a center, and 'L' for a vector.
+
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.save('test_ImageArray')
+
+ Numpy ndarray documentation appended:
+
+ """
+ def __new__(cls, input_array, info=None):
+ # Input array is an already formed ndarray instance
+ # We first cast to be our class type
+ obj = np.asarray(input_array).view(cls)
+ # add the new attribute to the created instance
+ if info is None:
+ info = {}
+ obj.info = info
+ # Finally, we must return the newly created object:
+ return obj
+
+ def __array_finalize__(self, obj):
+ # see InfoArray.__array_finalize__ for comments
+ if obj is None: return
+ self.info = getattr(obj, 'info', None)
+
+ def write_hdf5(self, filename):
+ r"""Writes ImageArray to hdf5 file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Examples
+ --------
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_hdf5('test_ImageArray.h5')
+
+ """
+ array_name = self.info.get("name","image")
+
+ f = h5.File(filename)
+ if array_name in f.keys():
+ del f[array_name]
+ d = f.create_dataset(array_name, data=self)
+ for k, v in self.info.iteritems():
+ d.attrs.create(k, v)
+ f.close()
+
+ def write_png(self, filename, clip_ratio=None):
+ r"""Writes ImageArray to png file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Examples
+ --------
+
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_png('test_ImageArray.png')
+
+ """
+ if filename[-4:] != '.png':
+ filename += '.png'
+
+ if clip_ratio is not None:
+ return write_bitmap(self.swapaxes(0, 1), filename,
+ clip_ratio * self.std())
+ else:
+ return write_bitmap(self.swapaxes(0, 1), filename)
+
+ def write_image(self, filename, color_bounds=None, channel=None, cmap_name="algae", func=lambda x: x):
+ r"""Writes a single channel of the ImageArray to a png file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Other Parameters
+ ----------------
+ channel: int
+ Which channel to write out as an image. Defaults to 0
+ cmap_name: string
+ Name of the colormap to be used.
+ color_bounds : tuple of floats, optional
+ The min and max to scale between. Outlying values will be clipped.
+ cmap_name : string, optional
+ An acceptable colormap. See either yt.visualization.color_maps or
+ http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
+ func : function, optional
+ A function to transform the buffer before applying a colormap.
+
+ Returns
+ -------
+ scaled_image : uint8 image that has been saved
+
+ Examples
+ --------
+
+ >>> im = np.zeros([64,128])
+ >>> for i in xrange(im.shape[0]):
+ >>> im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_image('test_ImageArray.png')
+
+ """
+ if filename[-4:] != '.png':
+ filename += '.png'
+
+ if channel is None:
+ return write_image(self.swapaxes(0,1), filename,
+ color_bounds=color_bounds, cmap_name=cmap_name,
+ func=func)
+ else:
+ return write_image(self.swapaxes(0,1)[:,:,channel], filename,
+ color_bounds=color_bounds, cmap_name=cmap_name,
+ func=func)
+
+ def save(self, filename, png=True, hdf5=True):
+ """
+ Saves ImageArray.
+
+ Arguments:
+ filename: string
+ This should not contain the extension type (.png, .h5, ...)
+
+ Optional Arguments:
+ png: boolean, default True
+ Save to a png
+
+ hdf5: boolean, default True
+ Save to hdf5 file, including info dictionary as attributes.
+
+ """
+ if png:
+ if len(self.shape) > 2:
+ self.write_png("%s.png" % filename)
+ else:
+ self.write_image("%s.png" % filename)
+ if hdf5:
+ self.write_hdf5("%s.h5" % filename)
+
+ __doc__ += np.ndarray.__doc__
+
+if __name__ == "__main__":
+ im = np.zeros([64,128,3])
+ for i in xrange(im.shape[0]):
+ for k in xrange(im.shape[2]):
+ im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_3d_ImageArray')
+
+ im = np.zeros([64,128])
+ for i in xrange(im.shape[0]):
+ im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+
+ myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_2d_ImageArray')
+
diff -r b8175a113d8ed98c0e8d514579ab607b01494565 -r 39220cb0fde7eb0f1270e9a31591402a7e47679c yt/mods.py
--- a/yt/mods.py
+++ b/yt/mods.py
@@ -62,7 +62,7 @@
ValidateParameter, ValidateDataField, ValidateProperty, \
ValidateSpatial, ValidateGridType, \
TimeSeriesData, AnalysisTask, analysis_task, \
- ParticleTrajectoryCollection
+ ParticleTrajectoryCollection, ImageArray
from yt.data_objects.derived_quantities import \
add_quantity, quantity_info
diff -r b8175a113d8ed98c0e8d514579ab607b01494565 -r 39220cb0fde7eb0f1270e9a31591402a7e47679c yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -116,7 +116,7 @@
image = image.transpose().copy() # Have to make sure it's contiguous
au.write_png(image, fn)
-def write_bitmap(bitmap_array, filename, max_val = None, transpose=True):
+def write_bitmap(bitmap_array, filename, max_val = None, transpose=False):
r"""Write out a bitmapped image directly to a PNG file.
This accepts a three- or four-channel `bitmap_array`. If the image is not
diff -r b8175a113d8ed98c0e8d514579ab607b01494565 -r 39220cb0fde7eb0f1270e9a31591402a7e47679c yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -37,6 +37,7 @@
arr_ang2pix_nest, arr_fisheye_vectors
from yt.utilities.math_utils import get_rotation_matrix
from yt.utilities.orientation import Orientation
+from yt.data_objects.api import ImageArray
from yt.visualization.image_writer import write_bitmap, write_image
from yt.data_objects.data_containers import data_object_registry
from yt.utilities.parallel_tools.parallel_analysis_interface import \
@@ -347,15 +348,21 @@
def save_image(self, fn, clip_ratio, image):
if self.comm.rank is 0 and fn is not None:
- if clip_ratio is not None:
- write_bitmap(image, fn, clip_ratio * image.std())
- else:
- write_bitmap(image, fn)
-
+ image.write_png(fn, clip_ratio=clip_ratio)
def initialize_source(self):
return self.volume.initialize_source()
+ def get_information(self):
+ info_dict = {'fields':self.fields,
+ 'type':self.__class__.__name__,
+ 'east_vector':self.orienter.unit_vectors[0],
+ 'north_vector':self.orienter.unit_vectors[1],
+ 'normal_vector':self.orienter.unit_vectors[2],
+ 'width':self.width,
+ 'dataset':self.pf.fullpath}
+ return info_dict
+
def snapshot(self, fn = None, clip_ratio = None, double_check = False,
num_threads = 0):
r"""Ray-cast the camera.
@@ -390,7 +397,9 @@
args = self.get_sampler_args(image)
sampler = self.get_sampler(args)
self.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clip_ratio, image)
return image
@@ -670,7 +679,7 @@
class PerspectiveCamera(Camera):
expand_factor = 1.0
def __init__(self, *args, **kwargs):
- expand_factor = kwargs.pop('expand_factor', 1.0)
+ self.expand_factor = kwargs.pop('expand_factor', 1.0)
Camera.__init__(self, *args, **kwargs)
def get_sampler_args(self, image):
@@ -709,6 +718,27 @@
self.transfer_function, self.sub_samples)
return args
+ def _render(self, double_check, num_threads, image, sampler):
+ pbar = get_pbar("Ray casting", (self.volume.brick_dimensions + 1).prod(axis=-1).sum())
+ total_cells = 0
+ if double_check:
+ for brick in self.volume.bricks:
+ for data in brick.my_data:
+ if np.any(np.isnan(data)):
+ raise RuntimeError
+
+ view_pos = self.front_center
+ for brick in self.volume.traverse(view_pos, self.front_center, image):
+ sampler(brick, num_threads=num_threads)
+ total_cells += np.prod(brick.my_data[0].shape)
+ pbar.update(total_cells)
+
+ pbar.finish()
+ image = sampler.aimage
+ self.finalize_image(image)
+ return image
+
+
def finalize_image(self, image):
image.shape = self.resolution[0], self.resolution[0], 3
@@ -801,6 +831,15 @@
return image
+ def get_information(self):
+ info_dict = {'fields':self.fields,
+ 'type':self.__class__.__name__,
+ 'center':self.center,
+ 'radius':self.radius,
+ 'dataset':self.pf.fullpath}
+ return info_dict
+
+
def snapshot(self, fn = None, clip_ratio = None, double_check = False,
num_threads = 0, clim = None, label = None):
r"""Ray-cast the camera.
@@ -828,7 +867,9 @@
args = self.get_sampler_args(image)
sampler = self.get_sampler(args)
self.volume.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clim, image, label = label)
return image
@@ -1264,8 +1305,9 @@
if self.image is not None:
del self.image
+ image = ImageArray(image,
+ info=self.get_information())
self.image = image
-
return image
def save_image(self, fn, clip_ratio=None):
@@ -1670,7 +1712,9 @@
self.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clip_ratio, image)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/b9838b15dbde/
changeset: b9838b15dbde
branch: yt
user: ngoldbaum
date: 2012-10-08 22:39:33
summary: Prepending sys.path with current working directory when running via 'yt load'.
The ipython embed api doesn't do this automatically for some reason.
affected #: 1 file
diff -r 39220cb0fde7eb0f1270e9a31591402a7e47679c -r b9838b15dbde418c6f7a8862b1499e67a5d1e6db yt/utilities/command_line.py
--- a/yt/utilities/command_line.py
+++ b/yt/utilities/command_line.py
@@ -1095,8 +1095,12 @@
)
else:
from IPython.config.loader import Config
+ import sys
cfg = Config()
+ # prepend sys.path with current working directory
+ sys.path.insert(0,'')
IPython.embed(config=cfg,user_ns=local_ns)
+
class YTMapserverCmd(YTCommand):
args = ("proj", "field", "weight",
https://bitbucket.org/yt_analysis/yt-3.0/changeset/7d4f47ae56b5/
changeset: 7d4f47ae56b5
branch: yt
user: ngoldbaum
date: 2012-10-08 20:55:21
summary: Fixing the way we handle the case when a user passes a full filename to save(). If multiple plots have been created this will write all plots to have the same filename.
affected #: 1 file
diff -r de5451397981bca072e120ea53540e571ff56669 -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -828,11 +828,14 @@
>>> slc.save(mpl_kwargs={'bbox_inches':'tight'})
"""
+ names = []
+ if mpl_kwargs is None: mpl_kwargs = {}
if name == None:
name = str(self.pf)
elif name.endswith('.png'):
- return v.save(name)
- if mpl_kwargs is None: mpl_kwargs = {}
+ for k, v in self.plots.iteritems():
+ names.append(v.save(name,mpl_kwargs))
+ return names
axis = axis_names[self.data_source.axis]
weight = None
if 'Slice' in self.data_source.__class__.__name__:
@@ -842,7 +845,6 @@
weight = self.data_source.weight_field
if 'Cutting' in self.data_source.__class__.__name__:
type = 'OffAxisSlice'
- names = []
for k, v in self.plots.iteritems():
if axis:
n = "%s_%s_%s_%s" % (name, type, axis, k)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/bbb6d92725d8/
changeset: bbb6d92725d8
branch: yt
user: ngoldbaum
date: 2012-10-08 20:57:00
summary: Merging.
affected #: 13 files
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -400,7 +400,7 @@
echo '2c1933ab31246b4f4eba049d3288156e0a72f1730604e3ed7357849967cdd329e4647cf236c9442ecfb06d0aff03e6fc892a7ba2a5c1cf5c011b7ab9c619acec Cython-0.16.tar.gz' > Cython-0.16.tar.gz.sha512
echo '44eea803870a66ff0bab08d13a8b3388b5578ebc1c807d1d9dca0a93e6371e91b15d02917a00b3b20dc67abb5a21dabaf9b6e9257a561f85eeff2147ac73b478 PyX-0.11.1.tar.gz' > PyX-0.11.1.tar.gz.sha512
-echo '1a754d560bfa433f0960ab3b5a62edb5f291be98ec48cf4e5941fa5b84139e200b87a52efbbd6fa4a76d6feeff12439eed3e7a84db4421940d1bbb576f7a684e Python-2.7.2.tgz' > Python-2.7.2.tgz.sha512
+echo 'b981f8464575bb24c297631c87a3b9172312804a0fc14ce1fa7cb41ce2b0d2fd383cd1c816d6e10c36467d18bf9492d6faf557c81c04ff3b22debfa93f30ad0b Python-2.7.3.tgz' > Python-2.7.3.tgz.sha512
echo 'c017d3d59dd324ac91af0edc178c76b60a5f90fbb775cf843e39062f95bd846238f2c53705f8890ed3f34bc0e6e75671a73d13875eb0287d6201cb45f0a2d338 bzip2-1.0.5.tar.gz' > bzip2-1.0.5.tar.gz.sha512
echo 'a296dfcaef7e853e58eed4e24b37c4fa29cfc6ac688def048480f4bb384b9e37ca447faf96eec7b378fd764ba291713f03ac464581d62275e28eb2ec99110ab6 reason-js-20120623.zip' > reason-js-20120623.zip.sha512
echo 'b519218f93946400326e9b656669269ecb3e5232b944e18fbc3eadc4fe2b56244d68aae56d6f69042b4c87c58c881ee2aaa279561ea0f0f48d5842155f4de9de freetype-2.4.4.tar.gz' > freetype-2.4.4.tar.gz.sha512
@@ -429,7 +429,7 @@
[ $INST_0MQ -eq 1 ] && get_ytproject zeromq-2.2.0.tar.gz
[ $INST_0MQ -eq 1 ] && get_ytproject pyzmq-2.1.11.tar.gz
[ $INST_0MQ -eq 1 ] && get_ytproject tornado-2.2.tar.gz
-get_ytproject Python-2.7.2.tgz
+get_ytproject Python-2.7.3.tgz
get_ytproject numpy-1.6.1.tar.gz
get_ytproject matplotlib-1.1.0.tar.gz
get_ytproject mercurial-2.2.2.tar.gz
@@ -554,11 +554,11 @@
fi
fi
-if [ ! -e Python-2.7.2/done ]
+if [ ! -e Python-2.7.3/done ]
then
echo "Installing Python. This may take a while, but don't worry. YT loves you."
- [ ! -e Python-2.7.2 ] && tar xfz Python-2.7.2.tgz
- cd Python-2.7.2
+ [ ! -e Python-2.7.3 ] && tar xfz Python-2.7.3.tgz
+ cd Python-2.7.3
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/data_objects/api.py
--- a/yt/data_objects/api.py
+++ b/yt/data_objects/api.py
@@ -65,6 +65,9 @@
quantity_info, \
add_quantity
+from image_array import \
+ ImageArray
+
from field_info_container import \
FieldInfoContainer, \
FieldInfo, \
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/data_objects/image_array.py
--- /dev/null
+++ b/yt/data_objects/image_array.py
@@ -0,0 +1,271 @@
+"""
+ImageArray Class
+
+Authors: Samuel Skillman <samskillman at gmail.com>
+Affiliation: University of Colorado at Boulder
+
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Samuel Skillman. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ """
+
+import numpy as np
+import h5py as h5
+from yt.visualization.image_writer import write_bitmap, write_image
+
+class ImageArray(np.ndarray):
+ r"""A custom Numpy ndarray used for images.
+
+ This differs from ndarray in that you can optionally specify an
+ info dictionary which is used later in saving, and can be accessed with
+ ImageArray.info.
+
+ Parameters
+ ----------
+ input_array: array_like
+ A numpy ndarray, or list.
+
+ Other Parameters
+ ----------------
+ info: dictionary
+ Contains information to be stored with image.
+
+ Returns
+ -------
+ obj: ImageArray object
+
+ Raises
+ ------
+ None
+
+ See Also
+ --------
+ numpy.ndarray : Inherits
+
+ Notes
+ -----
+
+ References
+ ----------
+
+ Examples
+ --------
+ These are written in doctest format, and should illustrate how to
+ use the function. Use the variables 'pf' for the parameter file, 'pc' for
+ a plot collection, 'c' for a center, and 'L' for a vector.
+
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.save('test_ImageArray')
+
+ Numpy ndarray documentation appended:
+
+ """
+ def __new__(cls, input_array, info=None):
+ # Input array is an already formed ndarray instance
+ # We first cast to be our class type
+ obj = np.asarray(input_array).view(cls)
+ # add the new attribute to the created instance
+ if info is None:
+ info = {}
+ obj.info = info
+ # Finally, we must return the newly created object:
+ return obj
+
+ def __array_finalize__(self, obj):
+ # see InfoArray.__array_finalize__ for comments
+ if obj is None: return
+ self.info = getattr(obj, 'info', None)
+
+ def write_hdf5(self, filename):
+ r"""Writes ImageArray to hdf5 file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Examples
+ --------
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_hdf5('test_ImageArray.h5')
+
+ """
+ array_name = self.info.get("name","image")
+
+ f = h5.File(filename)
+ if array_name in f.keys():
+ del f[array_name]
+ d = f.create_dataset(array_name, data=self)
+ for k, v in self.info.iteritems():
+ d.attrs.create(k, v)
+ f.close()
+
+ def write_png(self, filename, clip_ratio=None):
+ r"""Writes ImageArray to png file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Examples
+ --------
+
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_png('test_ImageArray.png')
+
+ """
+ if filename[-4:] != '.png':
+ filename += '.png'
+
+ if clip_ratio is not None:
+ return write_bitmap(self.swapaxes(0, 1), filename,
+ clip_ratio * self.std())
+ else:
+ return write_bitmap(self.swapaxes(0, 1), filename)
+
+ def write_image(self, filename, color_bounds=None, channel=None, cmap_name="algae", func=lambda x: x):
+ r"""Writes a single channel of the ImageArray to a png file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Other Parameters
+ ----------------
+ channel: int
+ Which channel to write out as an image. Defaults to 0
+ cmap_name: string
+ Name of the colormap to be used.
+ color_bounds : tuple of floats, optional
+ The min and max to scale between. Outlying values will be clipped.
+ cmap_name : string, optional
+ An acceptable colormap. See either yt.visualization.color_maps or
+ http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
+ func : function, optional
+ A function to transform the buffer before applying a colormap.
+
+ Returns
+ -------
+ scaled_image : uint8 image that has been saved
+
+ Examples
+ --------
+
+ >>> im = np.zeros([64,128])
+ >>> for i in xrange(im.shape[0]):
+ >>> im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_image('test_ImageArray.png')
+
+ """
+ if filename[-4:] != '.png':
+ filename += '.png'
+
+ if channel is None:
+ return write_image(self.swapaxes(0,1), filename,
+ color_bounds=color_bounds, cmap_name=cmap_name,
+ func=func)
+ else:
+ return write_image(self.swapaxes(0,1)[:,:,channel], filename,
+ color_bounds=color_bounds, cmap_name=cmap_name,
+ func=func)
+
+ def save(self, filename, png=True, hdf5=True):
+ """
+ Saves ImageArray.
+
+ Arguments:
+ filename: string
+ This should not contain the extension type (.png, .h5, ...)
+
+ Optional Arguments:
+ png: boolean, default True
+ Save to a png
+
+ hdf5: boolean, default True
+ Save to hdf5 file, including info dictionary as attributes.
+
+ """
+ if png:
+ if len(self.shape) > 2:
+ self.write_png("%s.png" % filename)
+ else:
+ self.write_image("%s.png" % filename)
+ if hdf5:
+ self.write_hdf5("%s.h5" % filename)
+
+ __doc__ += np.ndarray.__doc__
+
+if __name__ == "__main__":
+ im = np.zeros([64,128,3])
+ for i in xrange(im.shape[0]):
+ for k in xrange(im.shape[2]):
+ im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_3d_ImageArray')
+
+ im = np.zeros([64,128])
+ for i in xrange(im.shape[0]):
+ im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+
+ myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_2d_ImageArray')
+
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -1002,17 +1002,17 @@
def _BMagnitude(field,data):
"""This assumes that your front end has provided Bx, By, Bz in
units of Gauss. If you use MKS, make sure to write your own
- MagneticEnergy field to deal with non-unitary \mu_0.
+ BMagnitude field to deal with non-unitary \mu_0.
"""
return np.sqrt((data["Bx"]**2 + data["By"]**2 + data["Bz"]**2))
add_field("BMagnitude",
function=_BMagnitude,
- display_name=r"|B|", units="\rm{Gauss}")
+ display_name=r"|B|", units=r"\rm{Gauss}")
def _PlasmaBeta(field,data):
"""This assumes that your front end has provided Bx, By, Bz in
units of Gauss. If you use MKS, make sure to write your own
- MagneticEnergy field to deal with non-unitary \mu_0.
+ PlasmaBeta field to deal with non-unitary \mu_0.
"""
return data['Pressure']/data['MagneticEnergy']
add_field("PlasmaBeta",
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/frontends/flash/fields.py
--- a/yt/frontends/flash/fields.py
+++ b/yt/frontends/flash/fields.py
@@ -98,7 +98,10 @@
if fn1.endswith("_Fraction"):
add_field(fn1.split("_")[0] + "_Density",
function=_get_density(fn1), take_log=True,
- display_name="%s\/Density" % fn1.split("_")[0])
+ display_name="%s\/Density" % fn1.split("_")[0],
+ units = r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2",
+ )
def _get_convert(fname):
def _conv(data):
@@ -107,7 +110,8 @@
add_flash_field("dens", function=NullFunc, take_log=True,
convert_function=_get_convert("dens"),
- units=r"\rm{g}/\rm{cm}^3")
+ units=r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2"),
add_flash_field("velx", function=NullFunc, take_log=False,
convert_function=_get_convert("velx"),
units=r"\rm{cm}/\rm{s}")
@@ -204,6 +208,7 @@
add_field(f, TranslationFunc(v),
take_log=KnownFLASHFields[v].take_log,
units = ff._units, display_name=dname,
+ projected_units = ff._projected_units,
particle_type = pfield)
def _convertParticleMassMsun(data):
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/mods.py
--- a/yt/mods.py
+++ b/yt/mods.py
@@ -62,7 +62,7 @@
ValidateParameter, ValidateDataField, ValidateProperty, \
ValidateSpatial, ValidateGridType, \
TimeSeriesData, AnalysisTask, analysis_task, \
- ParticleTrajectoryCollection
+ ParticleTrajectoryCollection, ImageArray
from yt.data_objects.derived_quantities import \
add_quantity, quantity_info
@@ -122,7 +122,7 @@
get_multi_plot, FixedResolutionBuffer, ObliqueFixedResolutionBuffer, \
callback_registry, write_bitmap, write_image, annotate_image, \
apply_colormap, scale_image, write_projection, write_fits, \
- SlicePlot, OffAxisSlicePlot, ProjectionPlot
+ SlicePlot, OffAxisSlicePlot, ProjectionPlot, OffAxisProjectionPlot
from yt.visualization.volume_rendering.api import \
ColorTransferFunction, PlanckTransferFunction, ProjectionTransferFunction, \
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/utilities/lib/grid_traversal.pyx
--- a/yt/utilities/lib/grid_traversal.pyx
+++ b/yt/utilities/lib/grid_traversal.pyx
@@ -590,7 +590,7 @@
cdef np.float64_t *pointer = <np.float64_t *> star_colors.data
for i in range(pos_x.shape[0]):
kdtree_utils.kd_insert3(self.tree,
- pos_x[i], pos_y[i], pos_z[i], pointer + i*3)
+ pos_x[i], pos_y[i], pos_z[i], <void *> (pointer + i*3))
def __dealloc__(self):
kdtree_utils.kd_free(self.tree)
@@ -616,7 +616,7 @@
cdef np.float64_t slopes[6], dp[3], ds[3]
cdef np.float64_t dt = (exit_t - enter_t) / vri.n_samples
cdef np.float64_t dvs[6], cell_left[3], local_dds[3], pos[3]
- cdef int nstars
+ cdef int nstars, dti, i, j
cdef np.float64_t *colors = NULL, gexp, gaussian, px, py, pz
for i in range(3):
dp[i] = (enter_t + 0.5 * dt) * v_dir[i] + v_pos[i]
@@ -648,6 +648,7 @@
dvs[i] = temp
for dti in range(vri.n_samples):
# Now we add the contribution from stars
+ kdtree_utils.kd_res_rewind(ballq)
for i in range(nstars):
kdtree_utils.kd_res_item3(ballq, &px, &py, &pz)
colors = <np.float64_t *> kdtree_utils.kd_res_item_data(ballq)
@@ -655,20 +656,22 @@
gexp = (px - pos[0])*(px - pos[0]) \
+ (py - pos[1])*(py - pos[1]) \
+ (pz - pos[2])*(pz - pos[2])
- gaussian = vri.star_coeff * expl(-gexp/vri.star_sigma_num)
- for i in range(3): im.rgba[i] += gaussian*dt*colors[i]
+ gaussian = vri.star_coeff * exp(-gexp/vri.star_sigma_num)
+ for j in range(3): im.rgba[j] += gaussian*dt*colors[j]
for i in range(3):
pos[i] += local_dds[i]
FIT_eval_transfer(dt, dvs, im.rgba, vri.n_fits, vri.fits,
vri.field_table_ids, vri.grey_opacity)
for i in range(vc.n_fields):
dvs[i] += slopes[i]
+ kdtree_utils.kd_res_free(ballq)
cdef class VolumeRenderSampler(ImageSampler):
cdef VolumeRenderAccumulator *vra
cdef public object tf_obj
cdef public object my_field_tables
cdef kdtree_utils.kdtree **trees
+ cdef object tree_containers
def __cinit__(self,
np.ndarray vp_pos,
np.ndarray vp_dir,
@@ -709,6 +712,7 @@
self.vra.field_table_ids[i] = tf_obj.field_table_ids[i]
self.supp_data = <void *> self.vra
cdef star_kdtree_container skdc
+ self.tree_containers = star_list
if star_list is None:
self.trees = NULL
else:
@@ -719,10 +723,15 @@
self.trees[i] = skdc.tree
cdef void setup(self, PartitionedGrid pg):
+ cdef star_kdtree_container star_tree
if self.trees == NULL:
self.sampler = volume_render_sampler
else:
+ star_tree = self.tree_containers[pg.parent_grid_id]
self.vra.star_list = self.trees[pg.parent_grid_id]
+ self.vra.star_sigma_num = 2.0*star_tree.sigma**2.0
+ self.vra.star_er = 2.326 * star_tree.sigma
+ self.vra.star_coeff = star_tree.coeff
self.sampler = volume_render_stars_sampler
def __dealloc__(self):
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/visualization/api.py
--- a/yt/visualization/api.py
+++ b/yt/visualization/api.py
@@ -66,6 +66,7 @@
from plot_window import \
SlicePlot, \
OffAxisSlicePlot, \
- ProjectionPlot
+ ProjectionPlot, \
+ OffAxisProjectionPlot
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -28,6 +28,7 @@
x_dict, \
y_dict, \
axis_names
+from .volume_rendering.api import off_axis_projection
import _MPL
import numpy as np
import weakref
@@ -384,3 +385,28 @@
self.bounds).transpose()
self[item] = buff
return buff
+
+
+class OffAxisProjectionFixedResolutionBuffer(FixedResolutionBuffer):
+ def __init__(self, data_source, bounds, buff_size, antialias = True,
+ periodic = False):
+ self.data = {}
+ FixedResolutionBuffer.__init__(self, data_source, bounds, buff_size, antialias, periodic)
+
+ def __getitem__(self, item):
+ if item in self.data: return self.data[item]
+ mylog.info("Making a fixed resolutuion buffer of (%s) %d by %d" % \
+ (item, self.buff_size[0], self.buff_size[1]))
+ ds = self.data_source
+ width = (self.bounds[1] - self.bounds[0],
+ self.bounds[3] - self.bounds[2],
+ self.bounds[5] - self.bounds[4])
+ buff = off_axis_projection(ds.pf, ds.center, ds.normal_vector,
+ width, ds.resolution, item,
+ weight=ds.weight_field, volume=ds.volume,
+ no_ghost=ds.no_ghost, interpolated=ds.interpolated,
+ north_vector=ds.north_vector)
+ self[item] = buff.swapaxes(0,1)
+ return buff
+
+
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -116,7 +116,7 @@
image = image.transpose().copy() # Have to make sure it's contiguous
au.write_png(image, fn)
-def write_bitmap(bitmap_array, filename, max_val = None, transpose=True):
+def write_bitmap(bitmap_array, filename, max_val = None, transpose=False):
r"""Write out a bitmapped image directly to a PNG file.
This accepts a three- or four-channel `bitmap_array`. If the image is not
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -728,9 +728,13 @@
self.plot_args = plot_args
def __call__(self, plot):
+ if len(self.pos) == 3:
+ pos = (self.pos[x_dict[plot.data.axis]],
+ self.pos[y_dict[plot.data.axis]])
+ else: pos = self.pos
from matplotlib.patches import Arrow
# Now convert the pixels to code information
- x, y = self.convert_to_plot(plot, self.pos)
+ x, y = self.convert_to_plot(plot, pos)
dx, dy = self.convert_to_plot(plot, self.code_size, False)
arrow = Arrow(x, y, dx, dy, **self.plot_args)
plot._axes.add_patch(arrow)
@@ -750,12 +754,13 @@
self.text_args = text_args
def __call__(self, plot):
-
-
+ if len(self.pos) == 3:
+ pos = (self.pos[x_dict[plot.data.axis]],
+ self.pos[y_dict[plot.data.axis]])
+ else: pos = self.pos
width,height = plot.image._A.shape
- x,y = self.convert_to_plot(plot, self.pos)
- x,y = x/width,y/height
-
+ x,y = self.convert_to_plot(plot, pos)
+
plot._axes.text(x, y, self.text, **self.text_args)
class MarkerAnnotateCallback(PlotCallback):
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -43,7 +43,8 @@
write_image, apply_colormap
from .fixed_resolution import \
FixedResolutionBuffer, \
- ObliqueFixedResolutionBuffer
+ ObliqueFixedResolutionBuffer, \
+ OffAxisProjectionFixedResolutionBuffer
from .plot_modifications import get_smallest_appropriate_unit, \
callback_registry
from .tick_locators import LogLocator, LinearLocator
@@ -160,7 +161,7 @@
center[y_dict[axis]]+width[1]/2]
return (bounds,center)
-def GetOffAxisBoundsAndCenter(normal, center, width, pf, unit='1'):
+def GetOffAxisBoundsAndCenter(normal, center, width, pf, unit='1',depth=None):
if width == None:
width = (pf.domain_width.min(),
pf.domain_width.min())
@@ -171,6 +172,13 @@
width = (width, width)
Wx, Wy = width
width = np.array((Wx/pf[unit], Wy/pf[unit]))
+ if depth != None:
+ if iterable(depth) and isinstance(depth[1],str):
+ d,unit = depth
+ depth = d/pf[unit]
+ elif iterable(depth):
+ raise RuntimeError("Depth must be a float or a (width,\"unit\") tuple")
+ width = np.append(width,depth)
if isinstance(center,str):
if center.lower() == 'm' or center.lower() == 'max':
v, center = pf.h.find_max("Density")
@@ -179,15 +187,19 @@
else:
raise RuntimeError('center keyword \"%s\" not recognized'%center)
- # Transforming to the cutting plane coordinate system
- center = np.array(center)
- center = (center - pf.domain_left_edge)/pf.domain_width - 0.5
- (normal,perp1,perp2) = ortho_find(normal)
- mat = np.transpose(np.column_stack((perp1,perp2,normal)))
- center = np.dot(mat,center)
+ if width.shape == (2,):
+ # Transforming to the cutting plane coordinate system
+ center = np.array(center)
+ center = (center - pf.domain_left_edge)/pf.domain_width - 0.5
+ (normal,perp1,perp2) = ortho_find(normal)
+ mat = np.transpose(np.column_stack((perp1,perp2,normal)))
+ center = np.dot(mat,center)
+ width = width
+
+ bounds = [-width[0]/2, width[0]/2, -width[1]/2, width[1]/2]
+ else:
+ bounds = [-width[0]/2, width[0]/2, -width[1]/2, width[1]/2, -width[2]/2, width[2]/2]
- bounds = [-width[0]/2, width[0]/2, -width[1]/2, width[1]/2]
-
return (bounds,center)
class PlotWindow(object):
@@ -249,20 +261,14 @@
old_fields = None
if self._frb is not None:
old_fields = self._frb.keys()
- try:
+ if hasattr(self,'zlim'):
+ bounds = self.xlim+self.ylim+self.zlim
+ else:
bounds = self.xlim+self.ylim
- if self.oblique == False:
- self._frb = FixedResolutionBuffer(self.data_source,
- bounds, self.buff_size,
- self.antialias,
- periodic=self._periodic)
- else:
- self._frb = ObliqueFixedResolutionBuffer(self.data_source,
- bounds, self.buff_size,
- self.antialias,
- periodic=self._periodic)
- except:
- raise RuntimeError("Failed to repixelize.")
+ self._frb = self._frb_generator(self.data_source,
+ bounds, self.buff_size,
+ self.antialias,
+ periodic=self._periodic)
if old_fields is None:
self._frb._get_data_source_fields()
else:
@@ -303,6 +309,7 @@
nWx, nWy = Wx/factor, Wy/factor
self.xlim = (centerx - nWx*0.5, centerx + nWx*0.5)
self.ylim = (centery - nWy*0.5, centery + nWy*0.5)
+
@invalidate_data
def pan(self, deltas):
@@ -349,12 +356,16 @@
dy = bounds[3] - bounds[2]
self.xlim = (self.center[0] - dx/2., self.center[0] + dx/2.)
self.ylim = (self.center[1] - dy/2., self.center[1] + dy/2.)
- mylog.info("xlim = %f %f" %self.xlim)
- mylog.info("ylim = %f %f" %self.ylim)
else:
- self.xlim = bounds[0:2]
- self.ylim = bounds[2:]
-
+ self.xlim = tuple(bounds[0:2])
+ self.ylim = tuple(bounds[2:4])
+ if len(bounds) == 6:
+ self.zlim = tuple(bounds[4:6])
+ mylog.info("xlim = %f %f" %self.xlim)
+ mylog.info("ylim = %f %f" %self.ylim)
+ if hasattr(self,'zlim'):
+ mylog.info("zlim = %f %f" %self.zlim)
+
@invalidate_data
def set_width(self, width, unit = '1'):
"""set the width of the plot window
@@ -400,14 +411,20 @@
width = (Wx,Wy)
width = [w / self.pf[unit] for w in width]
- centerx = (self.xlim[1] + self.xlim[0])/2
- centery = (self.ylim[1] + self.ylim[0])/2
+ centerx = (self.xlim[1] + self.xlim[0])/2.
+ centery = (self.ylim[1] + self.ylim[0])/2.
self.xlim = (centerx - width[0]/2.,
centerx + width[0]/2.)
self.ylim = (centery - width[1]/2.,
centery + width[1]/2.)
+ if hasattr(self,'zlim'):
+ centerz = (self.zlim[1] + self.zlim[0])/2.
+ mw = max(width)
+ self.zlim = (centerz - mw/2.,
+ centerz + mw/2.)
+
@invalidate_data
def set_center(self, new_center, unit = '1'):
"""Sets a new center for the plot window
@@ -838,10 +855,8 @@
return names
axis = axis_names[self.data_source.axis]
weight = None
- if 'Slice' in self.data_source.__class__.__name__:
- type = 'Slice'
- if 'Proj' in self.data_source.__class__.__name__:
- type = 'Projection'
+ type = self._plot_type
+ if type in ['Projection','OffAxisProjection']:
weight = self.data_source.weight_field
if 'Cutting' in self.data_source.__class__.__name__:
type = 'OffAxisSlice'
@@ -891,6 +906,9 @@
raise YTNotInsideNotebook
class SlicePlot(PWViewerMPL):
+ _plot_type = 'Slice'
+ _frb_generator = FixedResolutionBuffer
+
def __init__(self, pf, axis, fields, center='c', width=None, axes_unit=None,
origin='center-window'):
r"""Creates a slice plot from a parameter file
@@ -966,6 +984,9 @@
self.set_axes_unit(axes_unit)
class ProjectionPlot(PWViewerMPL):
+ _plot_type = 'Projection'
+ _frb_generator = FixedResolutionBuffer
+
def __init__(self, pf, axis, fields, center='c', width=None, axes_unit=None,
weight_field=None, max_level=None, origin='center-window'):
r"""Creates a projection plot from a parameter file
@@ -1045,6 +1066,9 @@
self.set_axes_unit(axes_unit)
class OffAxisSlicePlot(PWViewerMPL):
+ _plot_type = 'OffAxisSlice'
+ _frb_generator = ObliqueFixedResolutionBuffer
+
def __init__(self, pf, normal, fields, center='c', width=(1,'unitary'),
axes_unit=None, north_vector=None):
r"""Creates an off axis slice plot from a parameter file
@@ -1092,6 +1116,95 @@
PWViewerMPL.__init__(self,cutting,bounds,origin='center-window',periodic=False,oblique=True)
self.set_axes_unit(axes_unit)
+class OffAxisProjectionDummyDataSource(object):
+ _type_name = 'proj'
+ proj_style = 'integrate'
+ _key_fields = []
+ def __init__(self, center, pf, normal_vector, width, fields,
+ interpolated, resolution = (800,800), weight=None,
+ volume=None, no_ghost=False, le=None, re=None,
+ north_vector=None):
+ self.center = center
+ self.pf = pf
+ self.axis = 4 # always true for oblique data objects
+ self.normal_vector = normal_vector
+ self.width = width
+ self.fields = fields
+ self.interpolated = interpolated
+ self.resolution = resolution
+ self.weight_field = weight
+ self.volume = volume
+ self.no_ghost = no_ghost
+ self.le = le
+ self.re = re
+ self.north_vector = north_vector
+
+class OffAxisProjectionPlot(PWViewerMPL):
+ _plot_type = 'OffAxisProjection'
+ _frb_generator = OffAxisProjectionFixedResolutionBuffer
+
+ def __init__(self, pf, normal, fields, center='c', width=(1,'unitary'),
+ depth=(1,'unitary'), axes_unit=None, weight_field=None,
+ max_level=None, north_vector=None, volume=None, no_ghost=False,
+ le=None, re=None, interpolated=False):
+ r"""Creates an off axis projection plot from a parameter file
+
+ Given a pf object, a normal vector to project along, and
+ a field name string, this will return a PWViewrMPL object
+ containing the plot.
+
+ The plot can be updated using one of the many helper functions
+ defined in PlotWindow.
+
+ Parameters
+ ----------
+ pf : :class:`yt.data_objects.api.StaticOutput`
+ This is the parameter file object corresponding to the
+ simulation output to be plotted.
+ normal : a sequence of floats
+ The vector normal to the slicing plane.
+ fields : string
+ The name of the field(s) to be plotted.
+ center : A two or three-element vector of sequence floats, 'c', or 'center'
+ The coordinate of the center of the image. If left blanck,
+ the image centers on the location of the maximum density
+ cell. If set to 'c' or 'center', the plot is centered on
+ the middle of the domain.
+ width : A tuple or a float
+ A tuple containing the width of image and the string key of
+ the unit: (width, 'unit'). If set to a float, code units
+ are assumed
+ depth : A tuple or a float
+ A tuple containing the depth to project thourhg and the string
+ key of the unit: (width, 'unit'). If set to a float, code units
+ are assumed
+ weight_field : string
+ The name of the weighting field. Set to None for no weight.
+ max_level: int
+ The maximum level to project to.
+ 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.
+ north-vector : a sequence of floats
+ A vector defining the 'up' direction in the plot. This
+ option sets the orientation of the slicing plane. If not
+ set, an arbitrary grid-aligned north-vector is chosen.
+
+ """
+ (bounds,center_rot) = GetOffAxisBoundsAndCenter(normal,center,width,pf,depth=depth)
+ # Hard-coding the resolution for now
+ fields = ensure_list(fields)[:]
+ width = np.array((bounds[1] - bounds[0], bounds[3] - bounds[2], bounds[5] - bounds[4]))
+ OffAxisProj = OffAxisProjectionDummyDataSource(center_rot, pf, normal, width, fields, interpolated,
+ weight=weight_field, volume=volume, no_ghost=no_ghost,
+ le=le, re=re, north_vector=north_vector)
+ # Hard-coding the origin keyword since the other two options
+ # aren't well-defined for off-axis data objects
+ PWViewerMPL.__init__(self,OffAxisProj,bounds,origin='center-window',periodic=False,oblique=True)
+ self.set_axes_unit(axes_unit)
+
_metadata_template = """
%(pf)s<br><br>
diff -r 7d4f47ae56b52feb4d1bce1d86437ca5f2a20aca -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -37,6 +37,7 @@
arr_ang2pix_nest, arr_fisheye_vectors
from yt.utilities.math_utils import get_rotation_matrix
from yt.utilities.orientation import Orientation
+from yt.data_objects.api import ImageArray
from yt.visualization.image_writer import write_bitmap, write_image
from yt.data_objects.data_containers import data_object_registry
from yt.utilities.parallel_tools.parallel_analysis_interface import \
@@ -301,7 +302,11 @@
np.array(self.width), self.transfer_function, self.sub_samples)
return args
+ star_trees = None
def get_sampler(self, args):
+ kwargs = {}
+ if self.star_trees is not None:
+ kwargs = {'star_list': self.star_trees}
if self.use_light:
if self.light_dir is None:
self.set_default_light_dir()
@@ -312,9 +317,10 @@
if self.light_rgba is None:
self.set_default_light_rgba()
sampler = LightSourceRenderSampler(*args, light_dir=temp_dir,
- light_rgba=self.light_rgba)
+ light_rgba=self.light_rgba, **kwargs)
else:
- sampler = self._sampler_object(*args)
+ sampler = self._sampler_object(*args, **kwargs)
+ print sampler, kwargs
return sampler
def finalize_image(self, image):
@@ -342,15 +348,21 @@
def save_image(self, fn, clip_ratio, image):
if self.comm.rank is 0 and fn is not None:
- if clip_ratio is not None:
- write_bitmap(image, fn, clip_ratio * image.std())
- else:
- write_bitmap(image, fn)
-
+ image.write_png(fn, clip_ratio=clip_ratio)
def initialize_source(self):
return self.volume.initialize_source()
+ def get_information(self):
+ info_dict = {'fields':self.fields,
+ 'type':self.__class__.__name__,
+ 'east_vector':self.orienter.unit_vectors[0],
+ 'north_vector':self.orienter.unit_vectors[1],
+ 'normal_vector':self.orienter.unit_vectors[2],
+ 'width':self.width,
+ 'dataset':self.pf.fullpath}
+ return info_dict
+
def snapshot(self, fn = None, clip_ratio = None, double_check = False,
num_threads = 0):
r"""Ray-cast the camera.
@@ -385,7 +397,9 @@
args = self.get_sampler_args(image)
sampler = self.get_sampler(args)
self.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clip_ratio, image)
return image
@@ -665,7 +679,7 @@
class PerspectiveCamera(Camera):
expand_factor = 1.0
def __init__(self, *args, **kwargs):
- expand_factor = kwargs.pop('expand_factor', 1.0)
+ self.expand_factor = kwargs.pop('expand_factor', 1.0)
Camera.__init__(self, *args, **kwargs)
def get_sampler_args(self, image):
@@ -704,6 +718,27 @@
self.transfer_function, self.sub_samples)
return args
+ def _render(self, double_check, num_threads, image, sampler):
+ pbar = get_pbar("Ray casting", (self.volume.brick_dimensions + 1).prod(axis=-1).sum())
+ total_cells = 0
+ if double_check:
+ for brick in self.volume.bricks:
+ for data in brick.my_data:
+ if np.any(np.isnan(data)):
+ raise RuntimeError
+
+ view_pos = self.front_center
+ for brick in self.volume.traverse(view_pos, self.front_center, image):
+ sampler(brick, num_threads=num_threads)
+ total_cells += np.prod(brick.my_data[0].shape)
+ pbar.update(total_cells)
+
+ pbar.finish()
+ image = sampler.aimage
+ self.finalize_image(image)
+ return image
+
+
def finalize_image(self, image):
image.shape = self.resolution[0], self.resolution[0], 3
@@ -796,6 +831,15 @@
return image
+ def get_information(self):
+ info_dict = {'fields':self.fields,
+ 'type':self.__class__.__name__,
+ 'center':self.center,
+ 'radius':self.radius,
+ 'dataset':self.pf.fullpath}
+ return info_dict
+
+
def snapshot(self, fn = None, clip_ratio = None, double_check = False,
num_threads = 0, clim = None, label = None):
r"""Ray-cast the camera.
@@ -823,7 +867,9 @@
args = self.get_sampler_args(image)
sampler = self.get_sampler(args)
self.volume.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clim, image, label = label)
return image
@@ -1259,8 +1305,9 @@
if self.image is not None:
del self.image
+ image = ImageArray(image,
+ info=self.get_information())
self.image = image
-
return image
def save_image(self, fn, clip_ratio=None):
@@ -1665,7 +1712,9 @@
self.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clip_ratio, image)
@@ -1676,7 +1725,8 @@
def off_axis_projection(pf, center, normal_vector, width, resolution,
field, weight = None,
- volume = None, no_ghost = False, interpolated = False):
+ volume = None, no_ghost = False, interpolated = False,
+ north_vector = None):
r"""Project through a parameter file, off-axis, and return the image plane.
This function will accept the necessary items to integrate through a volume
@@ -1735,8 +1785,9 @@
"""
projcam = ProjectionCamera(center, normal_vector, width, resolution,
- field, weight=weight, pf=pf, volume=volume,
- no_ghost=no_ghost, interpolated=interpolated)
+ field, weight=weight, pf=pf, volume=volume,
+ no_ghost=no_ghost, interpolated=interpolated,
+ north_vector=north_vector)
image = projcam.snapshot()
if weight is not None:
pf.field_info.pop("temp_weightfield")
https://bitbucket.org/yt_analysis/yt-3.0/changeset/b5b438054310/
changeset: b5b438054310
branch: yt
user: MatthewTurk
date: 2012-10-09 00:18:38
summary: Merged in ngoldbaum/yt (pull request #292)
affected #: 1 file
diff -r b9838b15dbde418c6f7a8862b1499e67a5d1e6db -r b5b438054310909ce9395a5b359a9bc0caf7326e yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -845,17 +845,21 @@
>>> slc.save(mpl_kwargs={'bbox_inches':'tight'})
"""
+ names = []
+ if mpl_kwargs is None: mpl_kwargs = {}
if name == None:
name = str(self.pf)
elif name.endswith('.png'):
- return v.save(name)
- if mpl_kwargs is None: mpl_kwargs = {}
+ for k, v in self.plots.iteritems():
+ names.append(v.save(name,mpl_kwargs))
+ return names
axis = axis_names[self.data_source.axis]
weight = None
type = self._plot_type
if type in ['Projection','OffAxisProjection']:
weight = self.data_source.weight_field
- names = []
+ if 'Cutting' in self.data_source.__class__.__name__:
+ type = 'OffAxisSlice'
for k, v in self.plots.iteritems():
if axis:
n = "%s_%s_%s_%s" % (name, type, axis, k)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/eea2f500219c/
changeset: eea2f500219c
branch: yt
user: ngoldbaum
date: 2012-10-10 07:42:47
summary: Fixing creating plot window plots from data objects via to_pw.
affected #: 2 files
diff -r b5b438054310909ce9395a5b359a9bc0caf7326e -r eea2f500219ce4284e74b77c7cd42d901a18a1d6 yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -855,6 +855,17 @@
for field in temp_data.keys():
self[field] = temp_data[field]
+ def _get_pw_params(self, fields, center, width):
+ axis = self.axis
+ if fields == None:
+ if self.fields == None:
+ raise SyntaxError("The fields keyword argument must be set")
+ else:
+ self.fields = ensure_list(fields)
+ from yt.visualization.plot_window import GetBoundsAndCenter
+ (bounds, center) = GetBoundsAndCenter(axis, center, width, self.pf)
+ return bounds
+
def to_frb(self, width, resolution, center=None, height=None):
r"""This function returns a FixedResolutionBuffer generated from this
object.
@@ -916,26 +927,6 @@
frb = FixedResolutionBuffer(self, bounds, resolution)
return frb
- def to_pw(self):
- r"""Create a :class:`~yt.visualization.plot_window.PlotWindow` from this
- object.
-
- This is a bare-bones mechanism of creating a plot window from this
- object, which can then be moved around, zoomed, and on and on. All
- behavior of the plot window is relegated to that routine.
- """
- axis = self.axis
- center = self.get_field_parameter("center")
- if center is None:
- center = (self.pf.domain_right_edge
- + self.pf.domain_left_edge)/2.0
- width = (1.0, 'unitary')
- from yt.visualization.plot_window import \
- PWViewerMPL, GetBoundsAndCenter
- (bounds, center) = GetBoundsAndCenter(axis, center, width, self.pf)
- pw = PWViewerMPL(self, bounds)
- return pw
-
def interpolate_discretize(self, LE, RE, field, side, log_spacing=True):
"""
This returns a uniform grid of points between *LE* and *RE*,
@@ -1193,6 +1184,23 @@
def hub_upload(self):
self._mrep.upload()
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ bounds = self._get_pw_params(fields, center, width)
+ from yt.visualization.plot_window import PWViewerMPL
+ from yt.visualization.fixed_resolution import FixedResolutionBuffer
+ pw = PWViewerMPL(self, bounds, origin=origin, frb_generator=FixedResolutionBuffer,
+ plot_type='Slice')
+ pw.set_axes_unit(axes_unit)
+ return pw
+
class AMRCuttingPlaneBase(AMR2DData):
_plane = None
_top_node = "/CuttingPlanes"
@@ -1355,6 +1363,30 @@
return "%s/c%s_L%s" % \
(self._top_node, cen_name, L_name)
+ def to_pw(self, fields, center='c', width=None, axes_unit=None):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ normal = self.normal
+ center = self.center
+ if fields == None:
+ if self.fields == None:
+ raise SyntaxError("The fields keyword argument must be set")
+ else:
+ self.fields = ensure_list(fields)
+ from yt.visualization.plot_window import \
+ GetOffAxisBoundsAndCenter, PWViewerMPL
+ from yt.visualization.fixed_resolution import ObliqueFixedResolutionBuffer
+ (bounds, center_rot) = GetOffAxisBoundsAndCenter(normal, center, width, self.pf)
+ pw = PWViewerMPL(self, bounds, origin='center-window', periodic=False, oblique=True,
+ frb_generator=ObliqueFixedResolutionBuffer, plot_type='OffAxisSlice')
+ pw.set_axes_unit(axes_unit)
+ return pw
+
def to_frb(self, width, resolution, height=None):
r"""This function returns an ObliqueFixedResolutionBuffer generated
from this object.
@@ -2254,6 +2286,23 @@
def add_fields(self, fields, weight = "CellMassMsun"):
pass
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ bounds = self._get_pw_params(fields, center, width)
+ from yt.visualization.plot_window import PWViewerMPL
+ from yt.visualization.fixed_resolution import FixedResolutionBuffer
+ pw = PWViewerMPL(self, bounds, origin=origin, frb_generator=FixedResolutionBuffer,
+ plot_type='Projection')
+ pw.set_axes_unit(axes_unit)
+ return pw
+
def _project_grid(self, grid, fields, zero_out):
# We split this next bit into two sections to try to limit the IO load
# on the system. This way, we perserve grid state (@restore_grid_state
diff -r b5b438054310909ce9395a5b359a9bc0caf7326e -r eea2f500219ce4284e74b77c7cd42d901a18a1d6 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -695,6 +695,15 @@
"""
_current_field = None
+ _frb_generator = None
+ _plot_type = None
+
+ def __init__(self, *args, **kwargs):
+ if self._frb_generator == None:
+ self._frb_generator = kwargs.pop("frb_generator")
+ if self._plot_type == None:
+ self._plot_type = kwargs.pop("plot_type")
+ PWViewer.__init__(self, *args, **kwargs)
def _setup_plots(self):
if self._current_field is not None:
https://bitbucket.org/yt_analysis/yt-3.0/changeset/136499a35ceb/
changeset: 136499a35ceb
branch: yt
user: ngoldbaum
date: 2012-10-10 08:12:33
summary: fields should be an optional keyword argument.
affected #: 1 file
diff -r eea2f500219ce4284e74b77c7cd42d901a18a1d6 -r 136499a35ceb274cd135b722a9d8636d039c2bee yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -1363,7 +1363,7 @@
return "%s/c%s_L%s" % \
(self._top_node, cen_name, L_name)
- def to_pw(self, fields, center='c', width=None, axes_unit=None):
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None):
r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
object.
https://bitbucket.org/yt_analysis/yt-3.0/changeset/f180d1f7c698/
changeset: f180d1f7c698
branch: yt
user: ngoldbaum
date: 2012-10-10 08:40:05
summary: Cleaning up, fixing a couple more errors.
affected #: 1 file
diff -r 136499a35ceb274cd135b722a9d8636d039c2bee -r f180d1f7c69863af81f5662df66da37b0e71b4ea yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -855,16 +855,21 @@
for field in temp_data.keys():
self[field] = temp_data[field]
- def _get_pw_params(self, fields, center, width):
+ def _get_pw(self, fields, center, width, origin, axes_unit, plot_type):
axis = self.axis
if fields == None:
if self.fields == None:
raise SyntaxError("The fields keyword argument must be set")
else:
self.fields = ensure_list(fields)
- from yt.visualization.plot_window import GetBoundsAndCenter
+ from yt.visualization.plot_window import \
+ GetBoundsAndCenter, PWViewerMPL
+ from yt.visualization.fixed_resolution import FixedResolutionBuffer
(bounds, center) = GetBoundsAndCenter(axis, center, width, self.pf)
- return bounds
+ pw = PWViewerMPL(self, bounds, origin=origin, frb_generator=FixedResolutionBuffer,
+ plot_type=plot_type)
+ pw.set_axes_unit(axes_unit)
+ return pw
def to_frb(self, width, resolution, center=None, height=None):
r"""This function returns a FixedResolutionBuffer generated from this
@@ -1193,12 +1198,7 @@
object, which can then be moved around, zoomed, and on and on. All
behavior of the plot window is relegated to that routine.
"""
- bounds = self._get_pw_params(fields, center, width)
- from yt.visualization.plot_window import PWViewerMPL
- from yt.visualization.fixed_resolution import FixedResolutionBuffer
- pw = PWViewerMPL(self, bounds, origin=origin, frb_generator=FixedResolutionBuffer,
- plot_type='Slice')
- pw.set_axes_unit(axes_unit)
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Slice')
return pw
class AMRCuttingPlaneBase(AMR2DData):
@@ -1794,6 +1794,18 @@
convs[:] = 1.0
return dls, convs
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Projection')
+ return pw
+
def get_data(self, fields = None):
if fields is None: fields = ensure_list(self.fields)[:]
else: fields = ensure_list(fields)
@@ -2295,12 +2307,7 @@
object, which can then be moved around, zoomed, and on and on. All
behavior of the plot window is relegated to that routine.
"""
- bounds = self._get_pw_params(fields, center, width)
- from yt.visualization.plot_window import PWViewerMPL
- from yt.visualization.fixed_resolution import FixedResolutionBuffer
- pw = PWViewerMPL(self, bounds, origin=origin, frb_generator=FixedResolutionBuffer,
- plot_type='Projection')
- pw.set_axes_unit(axes_unit)
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Projection')
return pw
def _project_grid(self, grid, fields, zero_out):
https://bitbucket.org/yt_analysis/yt-3.0/changeset/f2764b963f74/
changeset: f2764b963f74
branch: yt
user: ngoldbaum
date: 2012-10-08 22:39:33
summary: Prepending sys.path with current working directory when running via 'yt load'.
The ipython embed api doesn't do this automatically for some reason.
affected #: 1 file
diff -r bbb6d92725d80fa6b8ed60725524bdaeb8539325 -r f2764b963f74e9b3a95cb2ca9bb725e776c3b291 yt/utilities/command_line.py
--- a/yt/utilities/command_line.py
+++ b/yt/utilities/command_line.py
@@ -1095,8 +1095,12 @@
)
else:
from IPython.config.loader import Config
+ import sys
cfg = Config()
+ # prepend sys.path with current working directory
+ sys.path.insert(0,'')
IPython.embed(config=cfg,user_ns=local_ns)
+
class YTMapserverCmd(YTCommand):
args = ("proj", "field", "weight",
https://bitbucket.org/yt_analysis/yt-3.0/changeset/60ac41fcb525/
changeset: 60ac41fcb525
branch: yt
user: ngoldbaum
date: 2012-10-09 19:22:56
summary: Fixing the way write_projection saves pdf, eps, and ps files. Closes #433
affected #: 1 file
diff -r b5b438054310909ce9395a5b359a9bc0caf7326e -r 60ac41fcb525de416acdfb52a3eac061a3484e00 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -420,8 +420,10 @@
else:
dpi = None
- if filename[-4:] == '.png':
- suffix = ''
+ if filename[-4:] in ['.png','.pdf','.eps']:
+ suffix = filename[-4:]
+ elif filename[-3:] == ['.ps']:
+ suffix = filename[-3:]
else:
suffix = '.png'
filename = "%s%s" % (filename, suffix)
@@ -432,9 +434,6 @@
canvas = FigureCanvasPdf(fig)
elif suffix in (".eps", ".ps"):
canvas = FigureCanvasPS
- else:
- mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
- canvas = FigureCanvasAgg(fig)
canvas.print_figure(filename)
return filename
https://bitbucket.org/yt_analysis/yt-3.0/changeset/e3eb7f5db7c6/
changeset: e3eb7f5db7c6
branch: yt
user: ngoldbaum
date: 2012-10-09 19:35:01
summary: Removing the import * from write_projection. Small adjustments to avoid errors.
eps writing is broken (something is wrong on the matplotlib end)
affected #: 1 file
diff -r 60ac41fcb525de416acdfb52a3eac061a3484e00 -r e3eb7f5db7c674cacf48cc74a449ecd862c364d5 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -379,7 +379,7 @@
take_log=True)
"""
import matplotlib
- from ._mpl_imports import *
+ from ._mpl_imports import FigureCanvasAgg, FigureCanvasPdf, FigureCanvasPS
# If this is rendered as log, then apply now.
if take_log:
@@ -427,14 +427,14 @@
else:
suffix = '.png'
filename = "%s%s" % (filename, suffix)
- mylog.info("Saving plot %s", fn)
+ mylog.info("Saving plot %s", filename)
if suffix == ".png":
canvas = FigureCanvasAgg(fig)
elif suffix == ".pdf":
canvas = FigureCanvasPdf(fig)
elif suffix in (".eps", ".ps"):
canvas = FigureCanvasPS
- canvas.print_figure(filename)
+ canvas.print_figure(canvas,filename)
return filename
https://bitbucket.org/yt_analysis/yt-3.0/changeset/a812f858bfe9/
changeset: a812f858bfe9
branch: yt
user: ngoldbaum
date: 2012-10-09 19:35:47
summary: Merging.
affected #: 0 files
https://bitbucket.org/yt_analysis/yt-3.0/changeset/7fe50a49a33d/
changeset: 7fe50a49a33d
branch: yt
user: ngoldbaum
date: 2012-10-09 19:37:15
summary: Fixing a typo in the previous commit.
affected #: 1 file
diff -r a812f858bfe9f3123d865706adbbef619e575c01 -r 7fe50a49a33dad6aefc58dad1280d4e8204730c1 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -434,7 +434,7 @@
canvas = FigureCanvasPdf(fig)
elif suffix in (".eps", ".ps"):
canvas = FigureCanvasPS
- canvas.print_figure(canvas,filename)
+ canvas.print_figure(filename)
return filename
https://bitbucket.org/yt_analysis/yt-3.0/changeset/cb26d14b546e/
changeset: cb26d14b546e
branch: yt
user: ngoldbaum
date: 2012-10-09 20:20:18
summary: Needed to make sure the instance of FigureCanvasPS is instantiated. Thanks swskillman.
affected #: 1 file
diff -r 7fe50a49a33dad6aefc58dad1280d4e8204730c1 -r cb26d14b546e778488c1dd254e4b5178f5173610 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -433,7 +433,7 @@
elif suffix == ".pdf":
canvas = FigureCanvasPdf(fig)
elif suffix in (".eps", ".ps"):
- canvas = FigureCanvasPS
+ canvas = FigureCanvasPS(fig)
canvas.print_figure(filename)
return filename
https://bitbucket.org/yt_analysis/yt-3.0/changeset/7f8facef5611/
changeset: 7f8facef5611
branch: yt
user: ngoldbaum
date: 2012-10-09 20:42:39
summary: Updating to use os.path.splitext. Thanks for the suggestion Kacper!
affected #: 1 file
diff -r cb26d14b546e778488c1dd254e4b5178f5173610 -r 7f8facef5611e45ca30fb2a74f108cb40714e41e yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -420,11 +420,12 @@
else:
dpi = None
- if filename[-4:] in ['.png','.pdf','.eps']:
- suffix = filename[-4:]
- elif filename[-3:] == ['.ps']:
- suffix = filename[-3:]
- else:
+ suffix = os.path.splitext(filename)[1]
+
+ if suffix not in ['.png','.pdf','.eps','.ps','']:
+ mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
+ canvas = FigureCanvasAgg(fig)
+ if suffix == '':
suffix = '.png'
filename = "%s%s" % (filename, suffix)
mylog.info("Saving plot %s", filename)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/71c08c9a117b/
changeset: 71c08c9a117b
branch: yt
user: ngoldbaum
date: 2012-10-09 21:05:36
summary: Similar fixes for plot window. Cleaning up image writer.
affected #: 2 files
diff -r 7f8facef5611e45ca30fb2a74f108cb40714e41e -r 71c08c9a117b27216111cdf86b8125c6c82a20a0 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -422,9 +422,6 @@
suffix = os.path.splitext(filename)[1]
- if suffix not in ['.png','.pdf','.eps','.ps','']:
- mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
- canvas = FigureCanvasAgg(fig)
if suffix == '':
suffix = '.png'
filename = "%s%s" % (filename, suffix)
@@ -435,6 +432,10 @@
canvas = FigureCanvasPdf(fig)
elif suffix in (".eps", ".ps"):
canvas = FigureCanvasPS(fig)
+ else:
+ mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
+ canvas = FigureCanvasAgg(fig)
+
canvas.print_figure(filename)
return filename
diff -r 7f8facef5611e45ca30fb2a74f108cb40714e41e -r 71c08c9a117b27216111cdf86b8125c6c82a20a0 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -849,7 +849,8 @@
if mpl_kwargs is None: mpl_kwargs = {}
if name == None:
name = str(self.pf)
- elif name.endswith('.png'):
+ suffix = os.path.splitext(name)[1]
+ if suffix != '':
for k, v in self.plots.iteritems():
names.append(v.save(name,mpl_kwargs))
return names
@@ -1401,24 +1402,25 @@
self.cax = self.figure.add_axes(caxrect)
def save(self, name, mpl_kwargs, canvas = None):
- if name[-4:] == '.png':
- suffix = ''
+ suffix = os.path.splitext(name)[1]
+
+ if suffix == '':
+ suffix = '.png'
+ name = "%s%s" % (name, suffix)
+ mylog.info("Saving plot %s", name)
+ if suffix == ".png":
+ canvas = FigureCanvasAgg(self.figure)
+ elif suffix == ".pdf":
+ canvas = FigureCanvasPdf(self.figure)
+ elif suffix in (".eps", ".ps"):
+ canvas = FigureCanvasPS(self.figure)
else:
- suffix = '.png'
- fn = "%s%s" % (name, suffix)
- mylog.info("Saving plot %s", fn)
- if canvas is None:
- if suffix == ".png":
- canvas = FigureCanvasAgg(self.figure)
- elif suffix == ".pdf":
- canvas = FigureCanvasPdf(self.figure)
- elif suffix in (".eps", ".ps"):
- canvas = FigureCanvasPS
- else:
- mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
- canvas = FigureCanvasAgg(self.figure)
- canvas.print_figure(fn,**mpl_kwargs)
- return fn
+ mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
+ canvas = FigureCanvasAgg(self.figure)
+
+
+ canvas.print_figure(name,**mpl_kwargs)
+ return name
def _get_best_layout(self, size):
aspect = 1.0*size[0]/size[1]
https://bitbucket.org/yt_analysis/yt-3.0/changeset/55f172f94082/
changeset: 55f172f94082
branch: yt
user: MatthewTurk
date: 2012-10-11 02:00:34
summary: Merged in ngoldbaum/yt (pull request #293)
affected #: 2 files
diff -r f180d1f7c69863af81f5662df66da37b0e71b4ea -r 55f172f9408258b84c29824f97ba4e9b3b344cd2 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -379,7 +379,7 @@
take_log=True)
"""
import matplotlib
- from ._mpl_imports import *
+ from ._mpl_imports import FigureCanvasAgg, FigureCanvasPdf, FigureCanvasPS
# If this is rendered as log, then apply now.
if take_log:
@@ -420,21 +420,22 @@
else:
dpi = None
- if filename[-4:] == '.png':
- suffix = ''
- else:
+ suffix = os.path.splitext(filename)[1]
+
+ if suffix == '':
suffix = '.png'
filename = "%s%s" % (filename, suffix)
- mylog.info("Saving plot %s", fn)
+ mylog.info("Saving plot %s", filename)
if suffix == ".png":
canvas = FigureCanvasAgg(fig)
elif suffix == ".pdf":
canvas = FigureCanvasPdf(fig)
elif suffix in (".eps", ".ps"):
- canvas = FigureCanvasPS
+ canvas = FigureCanvasPS(fig)
else:
mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
canvas = FigureCanvasAgg(fig)
+
canvas.print_figure(filename)
return filename
diff -r f180d1f7c69863af81f5662df66da37b0e71b4ea -r 55f172f9408258b84c29824f97ba4e9b3b344cd2 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -858,7 +858,8 @@
if mpl_kwargs is None: mpl_kwargs = {}
if name == None:
name = str(self.pf)
- elif name.endswith('.png'):
+ suffix = os.path.splitext(name)[1]
+ if suffix != '':
for k, v in self.plots.iteritems():
names.append(v.save(name,mpl_kwargs))
return names
@@ -1410,24 +1411,25 @@
self.cax = self.figure.add_axes(caxrect)
def save(self, name, mpl_kwargs, canvas = None):
- if name[-4:] == '.png':
- suffix = ''
+ suffix = os.path.splitext(name)[1]
+
+ if suffix == '':
+ suffix = '.png'
+ name = "%s%s" % (name, suffix)
+ mylog.info("Saving plot %s", name)
+ if suffix == ".png":
+ canvas = FigureCanvasAgg(self.figure)
+ elif suffix == ".pdf":
+ canvas = FigureCanvasPdf(self.figure)
+ elif suffix in (".eps", ".ps"):
+ canvas = FigureCanvasPS(self.figure)
else:
- suffix = '.png'
- fn = "%s%s" % (name, suffix)
- mylog.info("Saving plot %s", fn)
- if canvas is None:
- if suffix == ".png":
- canvas = FigureCanvasAgg(self.figure)
- elif suffix == ".pdf":
- canvas = FigureCanvasPdf(self.figure)
- elif suffix in (".eps", ".ps"):
- canvas = FigureCanvasPS
- else:
- mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
- canvas = FigureCanvasAgg(self.figure)
- canvas.print_figure(fn,**mpl_kwargs)
- return fn
+ mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
+ canvas = FigureCanvasAgg(self.figure)
+
+
+ canvas.print_figure(name,**mpl_kwargs)
+ return name
def _get_best_layout(self, size):
aspect = 1.0*size[0]/size[1]
https://bitbucket.org/yt_analysis/yt-3.0/changeset/954f83409a54/
changeset: 954f83409a54
branch: yt
user: ngoldbaum
date: 2012-10-11 02:11:00
summary: Adding an _frb_viewer attribute to the PWViewerExtJS4 class. Closes #435.
affected #: 1 file
diff -r 71c08c9a117b27216111cdf86b8125c6c82a20a0 -r 954f83409a545fffe284fa04bd9e8d8c925eda18 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -1225,6 +1225,7 @@
_ext_widget_id = None
_current_field = None
_widget_name = "plot_window"
+ _frb_generator = FixedResolutionBuffer
def _setup_plots(self):
from yt.gui.reason.bottle_mods import PayloadHandler
https://bitbucket.org/yt_analysis/yt-3.0/changeset/a3963e90cd90/
changeset: a3963e90cd90
branch: yt
user: ngoldbaum
date: 2012-10-11 02:11:53
summary: Merging.
affected #: 2 files
diff -r 954f83409a545fffe284fa04bd9e8d8c925eda18 -r a3963e90cd9080733a7c528a2ed51a999fe16b59 yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -855,6 +855,22 @@
for field in temp_data.keys():
self[field] = temp_data[field]
+ def _get_pw(self, fields, center, width, origin, axes_unit, plot_type):
+ axis = self.axis
+ if fields == None:
+ if self.fields == None:
+ raise SyntaxError("The fields keyword argument must be set")
+ else:
+ self.fields = ensure_list(fields)
+ from yt.visualization.plot_window import \
+ GetBoundsAndCenter, PWViewerMPL
+ from yt.visualization.fixed_resolution import FixedResolutionBuffer
+ (bounds, center) = GetBoundsAndCenter(axis, center, width, self.pf)
+ pw = PWViewerMPL(self, bounds, origin=origin, frb_generator=FixedResolutionBuffer,
+ plot_type=plot_type)
+ pw.set_axes_unit(axes_unit)
+ return pw
+
def to_frb(self, width, resolution, center=None, height=None):
r"""This function returns a FixedResolutionBuffer generated from this
object.
@@ -916,26 +932,6 @@
frb = FixedResolutionBuffer(self, bounds, resolution)
return frb
- def to_pw(self):
- r"""Create a :class:`~yt.visualization.plot_window.PlotWindow` from this
- object.
-
- This is a bare-bones mechanism of creating a plot window from this
- object, which can then be moved around, zoomed, and on and on. All
- behavior of the plot window is relegated to that routine.
- """
- axis = self.axis
- center = self.get_field_parameter("center")
- if center is None:
- center = (self.pf.domain_right_edge
- + self.pf.domain_left_edge)/2.0
- width = (1.0, 'unitary')
- from yt.visualization.plot_window import \
- PWViewerMPL, GetBoundsAndCenter
- (bounds, center) = GetBoundsAndCenter(axis, center, width, self.pf)
- pw = PWViewerMPL(self, bounds)
- return pw
-
def interpolate_discretize(self, LE, RE, field, side, log_spacing=True):
"""
This returns a uniform grid of points between *LE* and *RE*,
@@ -1193,6 +1189,18 @@
def hub_upload(self):
self._mrep.upload()
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Slice')
+ return pw
+
class AMRCuttingPlaneBase(AMR2DData):
_plane = None
_top_node = "/CuttingPlanes"
@@ -1355,6 +1363,30 @@
return "%s/c%s_L%s" % \
(self._top_node, cen_name, L_name)
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ normal = self.normal
+ center = self.center
+ if fields == None:
+ if self.fields == None:
+ raise SyntaxError("The fields keyword argument must be set")
+ else:
+ self.fields = ensure_list(fields)
+ from yt.visualization.plot_window import \
+ GetOffAxisBoundsAndCenter, PWViewerMPL
+ from yt.visualization.fixed_resolution import ObliqueFixedResolutionBuffer
+ (bounds, center_rot) = GetOffAxisBoundsAndCenter(normal, center, width, self.pf)
+ pw = PWViewerMPL(self, bounds, origin='center-window', periodic=False, oblique=True,
+ frb_generator=ObliqueFixedResolutionBuffer, plot_type='OffAxisSlice')
+ pw.set_axes_unit(axes_unit)
+ return pw
+
def to_frb(self, width, resolution, height=None):
r"""This function returns an ObliqueFixedResolutionBuffer generated
from this object.
@@ -1762,6 +1794,18 @@
convs[:] = 1.0
return dls, convs
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Projection')
+ return pw
+
def get_data(self, fields = None):
if fields is None: fields = ensure_list(self.fields)[:]
else: fields = ensure_list(fields)
@@ -2254,6 +2298,18 @@
def add_fields(self, fields, weight = "CellMassMsun"):
pass
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Projection')
+ return pw
+
def _project_grid(self, grid, fields, zero_out):
# We split this next bit into two sections to try to limit the IO load
# on the system. This way, we perserve grid state (@restore_grid_state
diff -r 954f83409a545fffe284fa04bd9e8d8c925eda18 -r a3963e90cd9080733a7c528a2ed51a999fe16b59 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -695,6 +695,15 @@
"""
_current_field = None
+ _frb_generator = None
+ _plot_type = None
+
+ def __init__(self, *args, **kwargs):
+ if self._frb_generator == None:
+ self._frb_generator = kwargs.pop("frb_generator")
+ if self._plot_type == None:
+ self._plot_type = kwargs.pop("plot_type")
+ PWViewer.__init__(self, *args, **kwargs)
def _setup_plots(self):
if self._current_field is not None:
https://bitbucket.org/yt_analysis/yt-3.0/changeset/e5194ef1544f/
changeset: e5194ef1544f
branch: yt
user: jsoishi
date: 2012-10-11 20:50:28
summary: updated install script to make sure tk backend works; also helpful hints for ubuntu
affected #: 1 file
diff -r a3963e90cd9080733a7c528a2ed51a999fe16b59 -r e5194ef1544fcc8eb860b9b124204d15a548620d doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -31,13 +31,13 @@
INST_HG=1 # Install Mercurial or not? If hg is not already
# installed, yt cannot be installed.
-INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with
+INST_ZLIB=0 # On some systems (Kraken) matplotlib has issues with
# the system zlib, which is compiled statically.
# If need be, you can turn this off.
INST_BZLIB=1 # On some systems, libbzip2 is missing. This can
# lead to broken mercurial installations.
INST_PNG=1 # Install a local libpng? Same things apply as with zlib.
-INST_FTYPE=1 # Install FreeType2 locally?
+INST_FTYPE=0 # Install FreeType2 locally?
INST_ENZO=0 # Clone a copy of Enzo?
INST_SQLITE3=1 # Install a local version of SQLite3?
INST_PYX=0 # Install PyX? Sometimes PyX can be problematic without a
@@ -220,11 +220,24 @@
echo " * libncurses5-dev"
echo " * zip"
echo " * uuid-dev"
+ echo " * libfreetype6-dev"
+ echo " * tk-dev"
echo
echo "You can accomplish this by executing:"
echo
- echo "$ sudo apt-get install libssl-dev build-essential libncurses5 libncurses5-dev zip uuid-dev"
+ echo "$ sudo apt-get install libssl-dev build-essential libncurses5 libncurses5-dev zip uuid-dev libfreetype6-dev tk-dev"
echo
+ echo
+ echo " Additionally, if you want to put yt's lib dir in your LD_LIBRARY_PATH"
+ echo " so you can use yt without the activate script, you might "
+ echo " want to consider turning off LIBZ and FREETYPE in this"
+ echo " install script by editing this file and setting"
+ echo
+ echo " INST_ZLIB=0"
+ echo " INST_FTYPE=0"
+ echo
+ echo " to avoid conflicts with other command-line programs "
+ echo " (like eog and evince, for example)."
fi
if [ ! -z "${CFLAGS}" ]
then
https://bitbucket.org/yt_analysis/yt-3.0/changeset/71fc69a95b0d/
changeset: 71fc69a95b0d
branch: yt
user: jsoishi
date: 2012-10-11 20:55:34
summary: oops...didn't mean to turn them off by default...
affected #: 1 file
diff -r e5194ef1544fcc8eb860b9b124204d15a548620d -r 71fc69a95b0d9b68723ebec67a7e4684f9eab725 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -31,13 +31,13 @@
INST_HG=1 # Install Mercurial or not? If hg is not already
# installed, yt cannot be installed.
-INST_ZLIB=0 # On some systems (Kraken) matplotlib has issues with
+INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with
# the system zlib, which is compiled statically.
# If need be, you can turn this off.
INST_BZLIB=1 # On some systems, libbzip2 is missing. This can
# lead to broken mercurial installations.
INST_PNG=1 # Install a local libpng? Same things apply as with zlib.
-INST_FTYPE=0 # Install FreeType2 locally?
+INST_FTYPE=1 # Install FreeType2 locally?
INST_ENZO=0 # Clone a copy of Enzo?
INST_SQLITE3=1 # Install a local version of SQLite3?
INST_PYX=0 # Install PyX? Sometimes PyX can be problematic without a
https://bitbucket.org/yt_analysis/yt-3.0/changeset/703e12b8ae1b/
changeset: 703e12b8ae1b
branch: yt
user: sskory
date: 2012-10-11 23:03:59
summary: Adding a couple simple kdtree tests.
affected #: 1 file
diff -r 71fc69a95b0d9b68723ebec67a7e4684f9eab725 -r 703e12b8ae1b7ac6daedf1f8f552ac1f386d7644 yt/utilities/tests/test_kdtrees.py
--- /dev/null
+++ b/yt/utilities/tests/test_kdtrees.py
@@ -0,0 +1,91 @@
+"""
+Unit test the kD trees in yt.
+
+Author: Stephen Skory <s at skory.us>
+Affiliation: U of Colorado
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2008-2011 Stephen Skory. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from yt.testing import *
+
+try:
+ from yt.utilities.kdtree import \
+ chainHOP_tags_dens, \
+ create_tree, fKD, find_nn_nearest_neighbors, \
+ free_tree, find_chunk_nearest_neighbors
+except ImportError:
+ mylog.debug("The Fortran kD-Tree did not import correctly.")
+
+from yt.utilities.spatial import cKDTree
+
+def setup():
+ pass
+
+def test_fortran_tree():
+ # This test makes sure that the fortran kdtree is finding the correct
+ # nearest neighbors.
+ # Four points.
+ fKD.pos = np.empty((3, 4), dtype='float64', order='F')
+ # Make four points by hand that, in particular, will allow us to test
+ # the periodicity of the kdtree.
+ points = np.array([0.01, 0.5, 0.98, 0.99])
+ fKD.pos[0, :] = points
+ fKD.pos[1, :] = points
+ fKD.pos[2, :] = points
+ fKD.qv = np.empty(3, dtype='float64')
+ fKD.dist = np.empty(4, dtype='float64')
+ fKD.tags = np.empty(4, dtype='int64')
+ fKD.nn = 4
+ fKD.sort = True
+ create_tree(0)
+ # Now we check to make sure that we find the correct nearest neighbors,
+ # which get stored in dist and tags.
+ fKD.qv[:] = 0.999
+ find_nn_nearest_neighbors()
+ # Fix fortran counting.
+ fKD.tags -= 1
+ # Clean up before the tests.
+ free_tree(0)
+ # What the answers should be.
+ dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
+ tags = np.array([3, 0, 2, 1], dtype='int64')
+ assert_array_almost_equal(fKD.dist, dist)
+ assert_array_almost_equal(fKD.tags, tags)
+
+def test_cython_tree():
+ # This test makes sure that the fortran kdtree is finding the correct
+ # nearest neighbors.
+ # Four points.
+ pos = np.empty((4, 3), dtype='float64')
+ # Make four points by hand that, in particular, will allow us to test
+ # the periodicity of the kdtree.
+ points = np.array([0.01, 0.5, 0.98, 0.99])
+ pos[:, 0] = points
+ pos[:, 1] = points
+ pos[:, 2] = points
+ kdtree = cKDTree(pos, leafsize = 2)
+ qv = np.array([0.999]*3)
+ res = kdtree.query(qv, 4, period=[1.,1.,1])
+ # What the answers should be.
+ dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
+ tags = np.array([3, 0, 2, 1], dtype='int64')
+ assert_array_almost_equal(res[0], dist)
+ assert_array_almost_equal(res[1], tags)
+
https://bitbucket.org/yt_analysis/yt-3.0/changeset/f7efbe35f121/
changeset: f7efbe35f121
branch: yt
user: sskory
date: 2012-10-11 23:06:20
summary: These asserts really should test for perfect match.
affected #: 1 file
diff -r 703e12b8ae1b7ac6daedf1f8f552ac1f386d7644 -r f7efbe35f121bfd31c9c24a8c7284ed0bb291b41 yt/utilities/tests/test_kdtrees.py
--- a/yt/utilities/tests/test_kdtrees.py
+++ b/yt/utilities/tests/test_kdtrees.py
@@ -67,7 +67,7 @@
dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
tags = np.array([3, 0, 2, 1], dtype='int64')
assert_array_almost_equal(fKD.dist, dist)
- assert_array_almost_equal(fKD.tags, tags)
+ assert_array_equal(fKD.tags, tags)
def test_cython_tree():
# This test makes sure that the fortran kdtree is finding the correct
@@ -87,5 +87,5 @@
dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
tags = np.array([3, 0, 2, 1], dtype='int64')
assert_array_almost_equal(res[0], dist)
- assert_array_almost_equal(res[1], tags)
+ assert_array_equal(res[1], tags)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/76ab79a5ae9a/
changeset: 76ab79a5ae9a
branch: yt
user: sskory
date: 2012-10-11 23:09:21
summary: Typo.
affected #: 1 file
diff -r f7efbe35f121bfd31c9c24a8c7284ed0bb291b41 -r 76ab79a5ae9af5a5b062b49907bf85fc95e6bf0c yt/utilities/tests/test_kdtrees.py
--- a/yt/utilities/tests/test_kdtrees.py
+++ b/yt/utilities/tests/test_kdtrees.py
@@ -70,7 +70,7 @@
assert_array_equal(fKD.tags, tags)
def test_cython_tree():
- # This test makes sure that the fortran kdtree is finding the correct
+ # This test makes sure that the cython kdtree is finding the correct
# nearest neighbors.
# Four points.
pos = np.empty((4, 3), dtype='float64')
https://bitbucket.org/yt_analysis/yt-3.0/changeset/060e5f55da16/
changeset: 060e5f55da16
branch: yt
user: sskory
date: 2012-10-12 16:34:57
summary: Updating kdtree test.
affected #: 2 files
diff -r 76ab79a5ae9af5a5b062b49907bf85fc95e6bf0c -r 060e5f55da1631db50f96a6f2bc251026d6dc70f yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -24,7 +24,9 @@
import numpy as np
from yt.funcs import *
-from numpy.testing import assert_array_equal
+from numpy.testing import assert_array_equal, assert_almost_equal, \
+ assert_approx_equal, assert_array_almost_equal, assert_equal, \
+ assert_string_equal
def amrspace(extent, levels=7, cells=8):
"""Creates two numpy arrays representing the left and right bounds of
diff -r 76ab79a5ae9af5a5b062b49907bf85fc95e6bf0c -r 060e5f55da1631db50f96a6f2bc251026d6dc70f yt/utilities/tests/test_kdtrees.py
--- a/yt/utilities/tests/test_kdtrees.py
+++ b/yt/utilities/tests/test_kdtrees.py
@@ -39,10 +39,14 @@
pass
def test_fortran_tree():
- # This test makes sure that the fortran kdtree is finding the correct
- # nearest neighbors.
+ r"""This test makes sure that the fortran kdtree is finding the correct
+ nearest neighbors.
+ """
# Four points.
- fKD.pos = np.empty((3, 4), dtype='float64', order='F')
+ try:
+ fKD.pos = np.empty((3, 4), dtype='float64', order='F')
+ except NameError:
+ retur1n
# Make four points by hand that, in particular, will allow us to test
# the periodicity of the kdtree.
points = np.array([0.01, 0.5, 0.98, 0.99])
@@ -70,8 +74,9 @@
assert_array_equal(fKD.tags, tags)
def test_cython_tree():
- # This test makes sure that the cython kdtree is finding the correct
- # nearest neighbors.
+ r"""This test makes sure that the cython kdtree is finding the correct
+ nearest neighbors.
+ """
# Four points.
pos = np.empty((4, 3), dtype='float64')
# Make four points by hand that, in particular, will allow us to test
https://bitbucket.org/yt_analysis/yt-3.0/changeset/c3d373a809fd/
changeset: c3d373a809fd
branch: yt
user: sskory
date: 2012-10-12 16:37:09
summary: Typo.
affected #: 1 file
diff -r 060e5f55da1631db50f96a6f2bc251026d6dc70f -r c3d373a809fd0b21e02a229bc645e122d7ee4cf2 yt/utilities/tests/test_kdtrees.py
--- a/yt/utilities/tests/test_kdtrees.py
+++ b/yt/utilities/tests/test_kdtrees.py
@@ -46,7 +46,7 @@
try:
fKD.pos = np.empty((3, 4), dtype='float64', order='F')
except NameError:
- retur1n
+ return
# Make four points by hand that, in particular, will allow us to test
# the periodicity of the kdtree.
points = np.array([0.01, 0.5, 0.98, 0.99])
https://bitbucket.org/yt_analysis/yt-3.0/changeset/1b3aa8af97c7/
changeset: 1b3aa8af97c7
branch: yt
user: MatthewTurk
date: 2012-10-12 01:25:15
summary: Adding tests for the Profiles. I believe this covers averaging, end
collection, non-end collection, and unweighted addition.
affected #: 2 files
diff -r 71fc69a95b0d9b68723ebec67a7e4684f9eab725 -r 1b3aa8af97c7138944e1141c4a23108b2c2d11af yt/data_objects/tests/test_profiles.py
--- /dev/null
+++ b/yt/data_objects/tests/test_profiles.py
@@ -0,0 +1,74 @@
+from yt.testing import *
+from yt.data_objects.profiles import \
+ BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+
+_fields = ("Density", "Temperature", "Dinosaurs", "Tribbles")
+
+def test_profiles():
+ pf = fake_random_pf(64, nprocs = 8, fields = _fields)
+ nv = pf.domain_dimensions.prod()
+ dd = pf.h.all_data()
+ (rmi, rma), (tmi, tma), (dmi, dma) = dd.quantities["Extrema"](
+ ["Density", "Temperature", "Dinosaurs"])
+ rt, tt, dt = dd.quantities["TotalQuantity"](
+ ["Density", "Temperature", "Dinosaurs"])
+ # First we look at the
+ for nb in [8, 16, 32, 64]:
+ for lr in [True, False]:
+ # We log all the fields or don't log 'em all. No need to do them
+ # individually.
+ for lf in [True, False]:
+ # We have the min and the max, but to avoid cutting them off
+ # since we aren't doing end-collect, we cut a bit off the edges
+ for ec, e1, e2 in [(False, 0.9, 1.1), (True, 1.0, 1.0)]:
+ p1d = BinnedProfile1D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ lr, end_collect=ec)
+ p1d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p1d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p1d["Temperature"].sum(), 7
+
+ p2d = BinnedProfile2D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ nb, "Temperature", tmi*e1, tma*e2, lf,
+ lr, end_collect=ec)
+ p2d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p2d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p2d["Temperature"].sum(), 7
+
+ p3d = BinnedProfile3D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ nb, "Temperature", tmi*e1, tma*e2, lf,
+ nb, "Dinosaurs", dmi*e1, dma*e2, lf,
+ lr, end_collect=ec)
+ p3d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p3d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p3d["Temperature"].sum(), 7
+
+ p1d = BinnedProfile1D(dd, nb, "x", 0.0, 1.0, log_space=False)
+ p1d.add_fields("Ones", weight=None)
+ av = nv / nb
+ yield assert_equal, p1d["Ones"][:-1], np.ones(nb)*av
+ # We re-bin ones with a weight now
+ p1d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p1d["Ones"][:-1], np.ones(nb)
+
+ p2d = BinnedProfile2D(dd, nb, "x", 0.0, 1.0, False,
+ nb, "y", 0.0, 1.0, False)
+ p2d.add_fields("Ones", weight=None)
+ av = nv / nb**2
+ yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))*av
+ # We re-bin ones with a weight now
+ p2d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))
+
+ p3d = BinnedProfile3D(dd, nb, "x", 0.0, 1.0, False,
+ nb, "y", 0.0, 1.0, False,
+ nb, "z", 0.0, 1.0, False)
+ p3d.add_fields("Ones", weight=None)
+ av = nv / nb**3
+ yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb, nb, nb))*av
+ # We re-bin ones with a weight now
+ p3d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb,nb,nb))
+
diff -r 71fc69a95b0d9b68723ebec67a7e4684f9eab725 -r 1b3aa8af97c7138944e1141c4a23108b2c2d11af yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -24,7 +24,10 @@
import numpy as np
from yt.funcs import *
-from numpy.testing import assert_array_equal
+from numpy.testing import assert_array_equal, assert_equal, assert_almost_equal
+
+def assert_rel_equal(a1, a2, decimels):
+ return assert_almost_equal(a1/a2, 1.0, decimels)
def amrspace(extent, levels=7, cells=8):
"""Creates two numpy arrays representing the left and right bounds of
@@ -127,7 +130,8 @@
return left, right, level
-def fake_random_pf(ndims, peak_value = 1.0, fields = ("Density",), negative = False):
+def fake_random_pf(ndims, peak_value = 1.0, fields = ("Density",),
+ negative = False, nprocs = 1):
from yt.frontends.stream.api import load_uniform_grid
if not iterable(ndims):
ndims = [ndims, ndims, ndims]
@@ -139,5 +143,5 @@
offset = 0.0
data = dict((field, (np.random.random(ndims) - offset) * peak_value)
for field in fields)
- ug = load_uniform_grid(data, ndims, 1.0)
+ ug = load_uniform_grid(data, ndims, 1.0, nprocs = nprocs)
return ug
https://bitbucket.org/yt_analysis/yt-3.0/changeset/661eefd928c8/
changeset: 661eefd928c8
branch: yt
user: MatthewTurk
date: 2012-10-12 02:48:48
summary: Adding first set of tests of projections
affected #: 1 file
diff -r 1b3aa8af97c7138944e1141c4a23108b2c2d11af -r 661eefd928c8112d10241a5c6b8b5872ceabf427 yt/data_objects/tests/test_projection.py
--- /dev/null
+++ b/yt/data_objects/tests/test_projection.py
@@ -0,0 +1,28 @@
+from yt.testing import *
+from yt.data_objects.profiles import \
+ BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+
+def test_projection():
+ for nprocs in [1, 8]:
+ # We want to test both 1 proc and 8 procs, to make sure that
+ # parallelism isn't broken
+ pf = fake_random_pf(64, nprocs = 1)
+ dims = pf.domain_dimensions
+ xn, yn, zn = pf.domain_dimensions
+ xi, yi, zi = pf.domain_left_edge + 1.0/(pf.domain_dimensions * 2)
+ xf, yf, zf = pf.domain_right_edge - 1.0/(pf.domain_dimensions * 2)
+ coords = np.mgrid[xi:xf:xn*1j, yi:yf:yn*1j, zi:zf:zn*1j]
+ uc = [np.unique(c) for c in coords]
+ # Some simple projection tests with single grids
+ for ax in [0, 1, 2]:
+ xax = x_dict[ax]
+ yax = y_dict[ax]
+ for wf in [None, "Density"]:
+ proj = pf.h.proj(ax, "Ones", weight_field = wf)
+ yield assert_equal, proj["Ones"].sum(), proj["Ones"].size
+ yield assert_equal, proj["Ones"].min(), 1.0
+ yield assert_equal, proj["Ones"].max(), 1.0
+ yield assert_equal, np.unique(proj["px"]), uc[xax]
+ yield assert_equal, np.unique(proj["py"]), uc[yax]
+ yield assert_equal, np.unique(proj["pdx"]), 1.0/(dims[xax]*2.0)
+ yield assert_equal, np.unique(proj["pdy"]), 1.0/(dims[yax]*2.0)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/7914345a91cc/
changeset: 7914345a91cc
branch: yt
user: MatthewTurk
date: 2012-10-12 03:15:50
summary: Adding a couple more tests for projections to verify Density is correctly
projected.
affected #: 1 file
diff -r 661eefd928c8112d10241a5c6b8b5872ceabf427 -r 7914345a91cc3b87fb8fb2ba60800e7e12510b2d yt/data_objects/tests/test_projection.py
--- a/yt/data_objects/tests/test_projection.py
+++ b/yt/data_objects/tests/test_projection.py
@@ -3,7 +3,7 @@
BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
def test_projection():
- for nprocs in [1, 8]:
+ for nprocs in [8, 1]:
# We want to test both 1 proc and 8 procs, to make sure that
# parallelism isn't broken
pf = fake_random_pf(64, nprocs = 1)
@@ -11,14 +11,16 @@
xn, yn, zn = pf.domain_dimensions
xi, yi, zi = pf.domain_left_edge + 1.0/(pf.domain_dimensions * 2)
xf, yf, zf = pf.domain_right_edge - 1.0/(pf.domain_dimensions * 2)
+ dd = pf.h.all_data()
+ rho_tot = dd.quantities["TotalQuantity"]("Density")[0]
coords = np.mgrid[xi:xf:xn*1j, yi:yf:yn*1j, zi:zf:zn*1j]
uc = [np.unique(c) for c in coords]
# Some simple projection tests with single grids
- for ax in [0, 1, 2]:
+ for ax, an in enumerate("xyz"):
xax = x_dict[ax]
yax = y_dict[ax]
- for wf in [None, "Density"]:
- proj = pf.h.proj(ax, "Ones", weight_field = wf)
+ for wf in ["Density", None]:
+ proj = pf.h.proj(ax, ["Ones", "Density"], weight_field = wf)
yield assert_equal, proj["Ones"].sum(), proj["Ones"].size
yield assert_equal, proj["Ones"].min(), 1.0
yield assert_equal, proj["Ones"].max(), 1.0
@@ -26,3 +28,8 @@
yield assert_equal, np.unique(proj["py"]), uc[yax]
yield assert_equal, np.unique(proj["pdx"]), 1.0/(dims[xax]*2.0)
yield assert_equal, np.unique(proj["pdy"]), 1.0/(dims[yax]*2.0)
+ # wf == None
+ yield assert_equal, wf, None
+ v1 = proj["Density"].sum()
+ v2 = (dd["Density"] * dd["d%s" % an]).sum()
+ yield assert_rel_equal, v1, v2, 10
https://bitbucket.org/yt_analysis/yt-3.0/changeset/9eb577243510/
changeset: 9eb577243510
branch: yt
user: MatthewTurk
date: 2012-10-12 04:03:01
summary: Added a __withintesting option to the config to allow suppression of the
progress bars during projections. Then, turn it on inside the setup() function
for projections.
affected #: 3 files
diff -r 7914345a91cc3b87fb8fb2ba60800e7e12510b2d -r 9eb57724351006c3ca5d7af51ee1a0540fd76390 yt/config.py
--- a/yt/config.py
+++ b/yt/config.py
@@ -38,6 +38,7 @@
inline = 'False',
numthreads = '-1',
__withinreason = 'False',
+ __withintesting = 'False',
__parallel = 'False',
__global_parallel_rank = '0',
__global_parallel_size = '1',
diff -r 7914345a91cc3b87fb8fb2ba60800e7e12510b2d -r 9eb57724351006c3ca5d7af51ee1a0540fd76390 yt/data_objects/tests/test_projection.py
--- a/yt/data_objects/tests/test_projection.py
+++ b/yt/data_objects/tests/test_projection.py
@@ -2,6 +2,10 @@
from yt.data_objects.profiles import \
BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+def setup():
+ from yt.config import ytcfg
+ ytcfg["yt","__withintesting"] = "True"
+
def test_projection():
for nprocs in [8, 1]:
# We want to test both 1 proc and 8 procs, to make sure that
diff -r 7914345a91cc3b87fb8fb2ba60800e7e12510b2d -r 9eb57724351006c3ca5d7af51ee1a0540fd76390 yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -310,7 +310,8 @@
maxval = max(maxval, 1)
from yt.config import ytcfg
if ytcfg.getboolean("yt", "suppressStreamLogging") or \
- ytcfg.getboolean("yt", "ipython_notebook"):
+ ytcfg.getboolean("yt", "ipython_notebook") or \
+ ytcfg.getboolean("yt", "__withintesting"):
return DummyProgressBar()
elif ytcfg.getboolean("yt", "__withinreason"):
from yt.gui.reason.extdirect_repl import ExtProgressBar
https://bitbucket.org/yt_analysis/yt-3.0/changeset/b7aa69d03e99/
changeset: b7aa69d03e99
branch: yt
user: MatthewTurk
date: 2012-10-12 06:03:00
summary: Adding tests for covering_grid and fixing three bugs.
* The _con_args for covering_grid were out of data. This fixes pickling and
__repr__.
* dds couldn't be set correctly for going to a higher level than is present in
the dataset. Now the dds is set via refine_by and the domain dimensions.
* If nprocs > 1 in load_uniform_grid, the grid dimensions would be set to
int64, which would break covering grids.
affected #: 4 files
diff -r 9eb57724351006c3ca5d7af51ee1a0540fd76390 -r b7aa69d03e992658bbb368f75f78b619a95833d5 yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -3658,7 +3658,7 @@
class AMRCoveringGridBase(AMR3DData):
_spatial = True
_type_name = "covering_grid"
- _con_args = ('level', 'left_edge', 'right_edge', 'ActiveDimensions')
+ _con_args = ('level', 'left_edge', 'ActiveDimensions')
def __init__(self, level, left_edge, dims, fields = None,
pf = None, num_ghost_zones = 0, use_pbar = True, **kwargs):
"""A 3D region with all data extracted to a single, specified
@@ -3685,8 +3685,9 @@
fields=fields, pf=pf, **kwargs)
self.left_edge = np.array(left_edge)
self.level = level
- self.dds = self.pf.h.select_grids(self.level)[0].dds.copy()
- self.ActiveDimensions = np.array(dims,dtype='int32')
+ rdx = self.pf.domain_dimensions*self.pf.refine_by**level
+ self.dds = self.pf.domain_width/rdx.astype("float64")
+ self.ActiveDimensions = np.array(dims, dtype='int32')
self.right_edge = self.left_edge + self.ActiveDimensions*self.dds
self._num_ghost_zones = num_ghost_zones
self._use_pbar = use_pbar
diff -r 9eb57724351006c3ca5d7af51ee1a0540fd76390 -r b7aa69d03e992658bbb368f75f78b619a95833d5 yt/data_objects/tests/test_covering_grid.py
--- /dev/null
+++ b/yt/data_objects/tests/test_covering_grid.py
@@ -0,0 +1,27 @@
+from yt.testing import *
+from yt.data_objects.profiles import \
+ BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+
+def setup():
+ from yt.config import ytcfg
+ ytcfg["yt","__withintesting"] = "True"
+
+def test_covering_grid():
+ # We decompose in different ways
+ for level in [0, 1, 2]:
+ for nprocs in [1, 2, 4, 8]:
+ pf = fake_random_pf(16, nprocs = nprocs)
+ dn = pf.refine_by**level
+ cg = pf.h.covering_grid(level, [0.0, 0.0, 0.0],
+ dn * pf.domain_dimensions)
+ yield assert_equal, cg["Ones"].max(), 1.0
+ yield assert_equal, cg["Ones"].min(), 1.0
+ yield assert_equal, cg["CellVolume"].sum(), pf.domain_width.prod()
+ for g in pf.h.grids:
+ di = g.get_global_startindex()
+ dd = g.ActiveDimensions
+ for i in range(dn):
+ f = cg["Density"][dn*di[0]+i:dn*(di[0]+dd[0])+i:dn,
+ dn*di[1]+i:dn*(di[1]+dd[1])+i:dn,
+ dn*di[2]+i:dn*(di[2]+dd[2])+i:dn]
+ yield assert_equal, f, g["Density"]
diff -r 9eb57724351006c3ca5d7af51ee1a0540fd76390 -r b7aa69d03e992658bbb368f75f78b619a95833d5 yt/data_objects/tests/test_projection.py
--- a/yt/data_objects/tests/test_projection.py
+++ b/yt/data_objects/tests/test_projection.py
@@ -10,7 +10,7 @@
for nprocs in [8, 1]:
# We want to test both 1 proc and 8 procs, to make sure that
# parallelism isn't broken
- pf = fake_random_pf(64, nprocs = 1)
+ pf = fake_random_pf(64, nprocs = nprocs)
dims = pf.domain_dimensions
xn, yn, zn = pf.domain_dimensions
xi, yi, zi = pf.domain_left_edge + 1.0/(pf.domain_dimensions * 2)
diff -r 9eb57724351006c3ca5d7af51ee1a0540fd76390 -r b7aa69d03e992658bbb368f75f78b619a95833d5 yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -353,7 +353,8 @@
psize = get_psize(np.array(data[key].shape), nprocs)
grid_left_edges, grid_right_edges, temp[key] = \
decompose_array(data[key], psize, bbox)
- grid_dimensions = np.array([grid.shape for grid in temp[key]])
+ grid_dimensions = np.array([grid.shape for grid in temp[key]],
+ dtype="int32")
for gid in range(nprocs):
new_data[gid] = {}
for key in temp.keys():
@@ -364,7 +365,7 @@
sfh.update({0:data})
grid_left_edges = domain_left_edge
grid_right_edges = domain_right_edge
- grid_dimensions = domain_dimensions.reshape(nprocs,3)
+ grid_dimensions = domain_dimensions.reshape(nprocs,3).astype("int32")
handler = StreamHandler(
grid_left_edges,
https://bitbucket.org/yt_analysis/yt-3.0/changeset/b0ad4da28d61/
changeset: b0ad4da28d61
branch: yt
user: MatthewTurk
date: 2012-10-12 21:59:08
summary: Merging
affected #: 2 files
diff -r b7aa69d03e992658bbb368f75f78b619a95833d5 -r b0ad4da28d6177e66558de3a9c3bbe1a3dbcfce2 yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -24,7 +24,9 @@
import numpy as np
from yt.funcs import *
-from numpy.testing import assert_array_equal, assert_equal, assert_almost_equal
+from numpy.testing import assert_array_equal, assert_almost_equal, \
+ assert_approx_equal, assert_array_almost_equal, assert_equal, \
+ assert_string_equal
def assert_rel_equal(a1, a2, decimels):
return assert_almost_equal(a1/a2, 1.0, decimels)
diff -r b7aa69d03e992658bbb368f75f78b619a95833d5 -r b0ad4da28d6177e66558de3a9c3bbe1a3dbcfce2 yt/utilities/tests/test_kdtrees.py
--- /dev/null
+++ b/yt/utilities/tests/test_kdtrees.py
@@ -0,0 +1,96 @@
+"""
+Unit test the kD trees in yt.
+
+Author: Stephen Skory <s at skory.us>
+Affiliation: U of Colorado
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2008-2011 Stephen Skory. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from yt.testing import *
+
+try:
+ from yt.utilities.kdtree import \
+ chainHOP_tags_dens, \
+ create_tree, fKD, find_nn_nearest_neighbors, \
+ free_tree, find_chunk_nearest_neighbors
+except ImportError:
+ mylog.debug("The Fortran kD-Tree did not import correctly.")
+
+from yt.utilities.spatial import cKDTree
+
+def setup():
+ pass
+
+def test_fortran_tree():
+ r"""This test makes sure that the fortran kdtree is finding the correct
+ nearest neighbors.
+ """
+ # Four points.
+ try:
+ fKD.pos = np.empty((3, 4), dtype='float64', order='F')
+ except NameError:
+ return
+ # Make four points by hand that, in particular, will allow us to test
+ # the periodicity of the kdtree.
+ points = np.array([0.01, 0.5, 0.98, 0.99])
+ fKD.pos[0, :] = points
+ fKD.pos[1, :] = points
+ fKD.pos[2, :] = points
+ fKD.qv = np.empty(3, dtype='float64')
+ fKD.dist = np.empty(4, dtype='float64')
+ fKD.tags = np.empty(4, dtype='int64')
+ fKD.nn = 4
+ fKD.sort = True
+ create_tree(0)
+ # Now we check to make sure that we find the correct nearest neighbors,
+ # which get stored in dist and tags.
+ fKD.qv[:] = 0.999
+ find_nn_nearest_neighbors()
+ # Fix fortran counting.
+ fKD.tags -= 1
+ # Clean up before the tests.
+ free_tree(0)
+ # What the answers should be.
+ dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
+ tags = np.array([3, 0, 2, 1], dtype='int64')
+ assert_array_almost_equal(fKD.dist, dist)
+ assert_array_equal(fKD.tags, tags)
+
+def test_cython_tree():
+ r"""This test makes sure that the cython kdtree is finding the correct
+ nearest neighbors.
+ """
+ # Four points.
+ pos = np.empty((4, 3), dtype='float64')
+ # Make four points by hand that, in particular, will allow us to test
+ # the periodicity of the kdtree.
+ points = np.array([0.01, 0.5, 0.98, 0.99])
+ pos[:, 0] = points
+ pos[:, 1] = points
+ pos[:, 2] = points
+ kdtree = cKDTree(pos, leafsize = 2)
+ qv = np.array([0.999]*3)
+ res = kdtree.query(qv, 4, period=[1.,1.,1])
+ # What the answers should be.
+ dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
+ tags = np.array([3, 0, 2, 1], dtype='int64')
+ assert_array_almost_equal(res[0], dist)
+ assert_array_equal(res[1], tags)
+
https://bitbucket.org/yt_analysis/yt-3.0/changeset/2d91e2e7f12a/
changeset: 2d91e2e7f12a
branch: yt
user: sskory
date: 2012-10-12 23:06:24
summary: Removing this test file because it's very historical.
affected #: 1 file
diff -r b0ad4da28d6177e66558de3a9c3bbe1a3dbcfce2 -r 2d91e2e7f12a3f3e57caec1571b9c46f084f18a7 yt/utilities/kdtree/test.py
--- a/yt/utilities/kdtree/test.py
+++ /dev/null
@@ -1,58 +0,0 @@
-from Forthon import *
-from fKDpy import *
-import numpy,random
-
-n = 32768
-
-
-fKD.tags = fzeros((64),'i')
-fKD.dist = fzeros((64),'d')
-fKD.pos = fzeros((3,n),'d')
-fKD.nn = 64
-fKD.nparts = n
-fKD.sort = True
-fKD.rearrange = True
-fKD.qv = numpy.array([16./32, 16./32, 16./32])
-
-fp = open('parts.txt','r')
-xpos = []
-ypos = []
-zpos = []
-line = fp.readline()
-while line:
- line = line.split()
- xpos.append(float(line[0]))
- ypos.append(float(line[1]))
- zpos.append(float(line[2]))
- line= fp.readline()
-
-fp.close()
-
-
-for k in range(32):
- for j in range(32):
- for i in range(32):
- fKD.pos[0][i + j*32 + k*1024] = float(i)/32 + 1./64 + 0.0001*random.random()
- fKD.pos[1][i + j*32 + k*1024] = float(j)/32 + 1./64 + 0.0001*random.random()
- fKD.pos[2][i + j*32 + k*1024] = float(k)/32 + 1./64 + 0.0001*random.random()
-
-
-
-#print fKD.pos[0][0],fKD.pos[1][0],fKD.pos[2][0]
-
-create_tree()
-
-
-find_nn_nearest_neighbors()
-
-#print 'next'
-
-#fKD.qv = numpy.array([0., 0., 0.])
-
-#find_nn_nearest_neighbors()
-
-
-#print (fKD.tags - 1)
-#print fKD.dist
-
-free_tree()
https://bitbucket.org/yt_analysis/yt-3.0/changeset/c0f0e8295c66/
changeset: c0f0e8295c66
branch: yt
user: MatthewTurk
date: 2012-10-13 01:09:09
summary: Adding nose.cfg and adding necessary info to setup.py to run "python setup.py
nosetests"
affected #: 2 files
diff -r 2d91e2e7f12a3f3e57caec1571b9c46f084f18a7 -r c0f0e8295c662d6ac021e501171a8c4b4992b97e nose.cfg
--- /dev/null
+++ b/nose.cfg
@@ -0,0 +1,4 @@
+[nosetests]
+detailed-errors=1
+where=yt
+exclude=answer_testing
diff -r 2d91e2e7f12a3f3e57caec1571b9c46f084f18a7 -r c0f0e8295c662d6ac021e501171a8c4b4992b97e setup.cfg
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,3 +1,8 @@
[egg_info]
#tag_build = .dev
#tag_svn_revision = 1
+
+[nosetests]
+detailed-errors=1
+where=yt
+exclude=answer_testing
https://bitbucket.org/yt_analysis/yt-3.0/changeset/c33844a7aa05/
changeset: c33844a7aa05
branch: yt
user: MatthewTurk
date: 2012-10-14 21:23:28
summary: Adding xunit output to setup.cfg for nosetests.
affected #: 1 file
diff -r c0f0e8295c662d6ac021e501171a8c4b4992b97e -r c33844a7aa055486cbcf1a7f0176c60bb5e2fc0b setup.cfg
--- a/setup.cfg
+++ b/setup.cfg
@@ -6,3 +6,4 @@
detailed-errors=1
where=yt
exclude=answer_testing
+with-xunit=1
https://bitbucket.org/yt_analysis/yt-3.0/changeset/a87d4bf92215/
changeset: a87d4bf92215
branch: yt
user: Christian Karch
date: 2012-10-12 15:48:11
summary: Changed Streamline-Callback
affected #: 1 file
diff -r 71fc69a95b0d9b68723ebec67a7e4684f9eab725 -r a87d4bf9221537c90066cb3572eff37fa8110e8d yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -364,10 +364,7 @@
class StreamlineCallback(PlotCallback):
_type_name = "streamlines"
- def __init__(self, field_x, field_y, factor=6.0, nx=16, ny=16,
- xstart=(0,1), ystart=(0,1), nsample=256,
- start_at_xedge=False, start_at_yedge=False,
- plot_args=None):
+ def __init__(self, field_x, field_y, factor=16.0, density = 1, arrowsize=1, arrowstyle='-|>', color="#000000", normalize = False):
"""
annotate_streamlines(field_x, field_y, factor=6.0, nx=16, ny=16,
xstart=(0,1), ystart=(0,1), nsample=256,
@@ -385,18 +382,13 @@
PlotCallback.__init__(self)
self.field_x = field_x
self.field_y = field_y
- self.xstart = xstart
- self.ystart = ystart
- self.nsample = nsample
+ self.bv_x = self.bv_y = 0
self.factor = factor
- if start_at_xedge:
- self.data_size = (1,ny)
- elif start_at_yedge:
- self.data_size = (nx,1)
- else:
- self.data_size = (nx,ny)
- if plot_args is None: plot_args = {'color':'k', 'linestyle':'-'}
- self.plot_args = plot_args
+ self.dens = density
+ self.arrowsize = arrowsize
+ self.arrowstyle = arrowstyle
+ self.color = color
+ self.normalize = normalize
def __call__(self, plot):
x0, x1 = plot.xlim
@@ -404,43 +396,29 @@
xx0, xx1 = plot._axes.get_xlim()
yy0, yy1 = plot._axes.get_ylim()
plot._axes.hold(True)
- nx = plot.image._A.shape[0]
- ny = plot.image._A.shape[1]
+ nx = plot.image._A.shape[0] / self.factor
+ ny = plot.image._A.shape[1] / self.factor
pixX = _MPL.Pixelize(plot.data['px'],
plot.data['py'],
plot.data['pdx'],
plot.data['pdy'],
- plot.data[self.field_x],
+ plot.data[self.field_x] - self.bv_x,
int(nx), int(ny),
- (x0, x1, y0, y1),)
+ (x0, x1, y0, y1),).transpose()
pixY = _MPL.Pixelize(plot.data['px'],
plot.data['py'],
plot.data['pdx'],
plot.data['pdy'],
- plot.data[self.field_y],
+ plot.data[self.field_y] - self.bv_y,
int(nx), int(ny),
- (x0, x1, y0, y1),)
- r0 = np.mgrid[self.xstart[0]*nx:self.xstart[1]*nx:self.data_size[0]*1j,
- self.ystart[0]*ny:self.ystart[1]*ny:self.data_size[1]*1j]
- lines = np.zeros((self.nsample, 2, self.data_size[0], self.data_size[1]))
- lines[0,:,:,:] = r0
- mag = np.sqrt(pixX**2 + pixY**2)
- scale = np.sqrt(nx*ny) / (self.factor * mag.mean())
- dt = 1.0 / (self.nsample-1)
- for i in range(1,self.nsample):
- xt = lines[i-1,0,:,:]
- yt = lines[i-1,1,:,:]
- ix = np.maximum(np.minimum((xt).astype('int'), nx-1), 0)
- iy = np.maximum(np.minimum((yt).astype('int'), ny-1), 0)
- lines[i,0,:,:] = xt + dt * pixX[ix,iy] * scale
- lines[i,1,:,:] = yt + dt * pixY[ix,iy] * scale
- # scale into data units
- lines[:,0,:,:] = lines[:,0,:,:] * (xx1 - xx0) / nx + xx0
- lines[:,1,:,:] = lines[:,1,:,:] * (yy1 - yy0) / ny + yy0
- for i in range(self.data_size[0]):
- for j in range(self.data_size[1]):
- plot._axes.plot(lines[:,0,i,j], lines[:,1,i,j],
- **self.plot_args)
+ (x0, x1, y0, y1),).transpose()
+ X,Y = (na.linspace(xx0,xx1,nx,endpoint=True),
+ na.linspace(yy0,yy1,ny,endpoint=True))
+ if self.normalize:
+ nn = na.sqrt(pixX**2 + pixY**2)
+ pixX /= nn
+ pixY /= nn
+ plot._axes.streamplot(X,Y, pixX, pixY, density=self.dens, arrowsize=self.arrowsize, arrowstyle=self.arrowstyle, color=self.color, norm=self.normalize)
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
plot._axes.hold(False)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/8b96d26b14d9/
changeset: 8b96d26b14d9
branch: yt
user: chiffre
date: 2012-10-15 09:39:36
summary: Fixed some odds and ends in Streamline-Callback
affected #: 1 file
diff -r a87d4bf9221537c90066cb3572eff37fa8110e8d -r 8b96d26b14d90a8d54d1b9ea44fae53e4b1048d2 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -364,20 +364,17 @@
class StreamlineCallback(PlotCallback):
_type_name = "streamlines"
- def __init__(self, field_x, field_y, factor=16.0, density = 1, arrowsize=1, arrowstyle='-|>', color="#000000", normalize = False):
+ def __init__(self, field_x, field_y, factor = 16,
+ density = 1, arrowsize = 1, arrowstyle = None,
+ color = None, normalize = False):
"""
- annotate_streamlines(field_x, field_y, factor=6.0, nx=16, ny=16,
- xstart=(0,1), ystart=(0,1), nsample=256,
- start_at_xedge=False, start_at_yedge=False,
- plot_args=None):
+ annotate_streamlines(field_x, field_y, factor = 16, density = 1,
+ arrowsize = 1, arrowstyle = None,
+ color = None, normalize = False):
Add streamlines to any plot, using the *field_x* and *field_y*
- from the associated data, using *nx* and *ny* starting points
- that are bounded by *xstart* and *ystart*. To begin
- streamlines from the left edge of the plot, set
- *start_at_xedge* to True; for the bottom edge, use
- *start_at_yedge*. A line with the qmean vector magnitude will
- cover 1.0/*factor* of the image.
+ from the associated data, skipping every *factor* datapoints like
+ 'quiver'. *density* is the index of the amount of the streamlines.
"""
PlotCallback.__init__(self)
self.field_x = field_x
@@ -386,7 +383,9 @@
self.factor = factor
self.dens = density
self.arrowsize = arrowsize
+ if arrowstyle is None : arrowstyle='-|>'
self.arrowstyle = arrowstyle
+ if color is None : color = "#000000"
self.color = color
self.normalize = normalize
@@ -418,7 +417,9 @@
nn = na.sqrt(pixX**2 + pixY**2)
pixX /= nn
pixY /= nn
- plot._axes.streamplot(X,Y, pixX, pixY, density=self.dens, arrowsize=self.arrowsize, arrowstyle=self.arrowstyle, color=self.color, norm=self.normalize)
+ plot._axes.streamplot(X,Y, pixX, pixY, density=self.dens,
+ arrowsize=self.arrowsize, arrowstyle=self.arrowstyle,
+ color=self.color, norm=self.normalize)
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
plot._axes.hold(False)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/1c28ec990d80/
changeset: 1c28ec990d80
branch: yt
user: MatthewTurk
date: 2012-10-15 16:19:16
summary: Merged in chiffre/yt (pull request #298)
affected #: 1 file
diff -r c33844a7aa055486cbcf1a7f0176c60bb5e2fc0b -r 1c28ec990d80477b63b4a1dc5bdd90f3771ad9f0 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -364,39 +364,30 @@
class StreamlineCallback(PlotCallback):
_type_name = "streamlines"
- def __init__(self, field_x, field_y, factor=6.0, nx=16, ny=16,
- xstart=(0,1), ystart=(0,1), nsample=256,
- start_at_xedge=False, start_at_yedge=False,
- plot_args=None):
+ def __init__(self, field_x, field_y, factor = 16,
+ density = 1, arrowsize = 1, arrowstyle = None,
+ color = None, normalize = False):
"""
- annotate_streamlines(field_x, field_y, factor=6.0, nx=16, ny=16,
- xstart=(0,1), ystart=(0,1), nsample=256,
- start_at_xedge=False, start_at_yedge=False,
- plot_args=None):
+ annotate_streamlines(field_x, field_y, factor = 16, density = 1,
+ arrowsize = 1, arrowstyle = None,
+ color = None, normalize = False):
Add streamlines to any plot, using the *field_x* and *field_y*
- from the associated data, using *nx* and *ny* starting points
- that are bounded by *xstart* and *ystart*. To begin
- streamlines from the left edge of the plot, set
- *start_at_xedge* to True; for the bottom edge, use
- *start_at_yedge*. A line with the qmean vector magnitude will
- cover 1.0/*factor* of the image.
+ from the associated data, skipping every *factor* datapoints like
+ 'quiver'. *density* is the index of the amount of the streamlines.
"""
PlotCallback.__init__(self)
self.field_x = field_x
self.field_y = field_y
- self.xstart = xstart
- self.ystart = ystart
- self.nsample = nsample
+ self.bv_x = self.bv_y = 0
self.factor = factor
- if start_at_xedge:
- self.data_size = (1,ny)
- elif start_at_yedge:
- self.data_size = (nx,1)
- else:
- self.data_size = (nx,ny)
- if plot_args is None: plot_args = {'color':'k', 'linestyle':'-'}
- self.plot_args = plot_args
+ self.dens = density
+ self.arrowsize = arrowsize
+ if arrowstyle is None : arrowstyle='-|>'
+ self.arrowstyle = arrowstyle
+ if color is None : color = "#000000"
+ self.color = color
+ self.normalize = normalize
def __call__(self, plot):
x0, x1 = plot.xlim
@@ -404,43 +395,31 @@
xx0, xx1 = plot._axes.get_xlim()
yy0, yy1 = plot._axes.get_ylim()
plot._axes.hold(True)
- nx = plot.image._A.shape[0]
- ny = plot.image._A.shape[1]
+ nx = plot.image._A.shape[0] / self.factor
+ ny = plot.image._A.shape[1] / self.factor
pixX = _MPL.Pixelize(plot.data['px'],
plot.data['py'],
plot.data['pdx'],
plot.data['pdy'],
- plot.data[self.field_x],
+ plot.data[self.field_x] - self.bv_x,
int(nx), int(ny),
- (x0, x1, y0, y1),)
+ (x0, x1, y0, y1),).transpose()
pixY = _MPL.Pixelize(plot.data['px'],
plot.data['py'],
plot.data['pdx'],
plot.data['pdy'],
- plot.data[self.field_y],
+ plot.data[self.field_y] - self.bv_y,
int(nx), int(ny),
- (x0, x1, y0, y1),)
- r0 = np.mgrid[self.xstart[0]*nx:self.xstart[1]*nx:self.data_size[0]*1j,
- self.ystart[0]*ny:self.ystart[1]*ny:self.data_size[1]*1j]
- lines = np.zeros((self.nsample, 2, self.data_size[0], self.data_size[1]))
- lines[0,:,:,:] = r0
- mag = np.sqrt(pixX**2 + pixY**2)
- scale = np.sqrt(nx*ny) / (self.factor * mag.mean())
- dt = 1.0 / (self.nsample-1)
- for i in range(1,self.nsample):
- xt = lines[i-1,0,:,:]
- yt = lines[i-1,1,:,:]
- ix = np.maximum(np.minimum((xt).astype('int'), nx-1), 0)
- iy = np.maximum(np.minimum((yt).astype('int'), ny-1), 0)
- lines[i,0,:,:] = xt + dt * pixX[ix,iy] * scale
- lines[i,1,:,:] = yt + dt * pixY[ix,iy] * scale
- # scale into data units
- lines[:,0,:,:] = lines[:,0,:,:] * (xx1 - xx0) / nx + xx0
- lines[:,1,:,:] = lines[:,1,:,:] * (yy1 - yy0) / ny + yy0
- for i in range(self.data_size[0]):
- for j in range(self.data_size[1]):
- plot._axes.plot(lines[:,0,i,j], lines[:,1,i,j],
- **self.plot_args)
+ (x0, x1, y0, y1),).transpose()
+ X,Y = (na.linspace(xx0,xx1,nx,endpoint=True),
+ na.linspace(yy0,yy1,ny,endpoint=True))
+ if self.normalize:
+ nn = na.sqrt(pixX**2 + pixY**2)
+ pixX /= nn
+ pixY /= nn
+ plot._axes.streamplot(X,Y, pixX, pixY, density=self.dens,
+ arrowsize=self.arrowsize, arrowstyle=self.arrowstyle,
+ color=self.color, norm=self.normalize)
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
plot._axes.hold(False)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/84f31f0466e1/
changeset: 84f31f0466e1
branch: yt
user: sskory
date: 2012-10-15 17:23:42
summary: Fixing imports for fortran kdtree.
affected #: 2 files
diff -r 1c28ec990d80477b63b4a1dc5bdd90f3771ad9f0 -r 84f31f0466e1daa369b3f02bb5eac26255163005 yt/utilities/kdtree/__init__.py
--- a/yt/utilities/kdtree/__init__.py
+++ b/yt/utilities/kdtree/__init__.py
@@ -1,1 +0,0 @@
-from fKDpy import *
diff -r 1c28ec990d80477b63b4a1dc5bdd90f3771ad9f0 -r 84f31f0466e1daa369b3f02bb5eac26255163005 yt/utilities/kdtree/api.py
--- /dev/null
+++ b/yt/utilities/kdtree/api.py
@@ -0,0 +1,9 @@
+from yt.utilities.kdtree import \
+ chainHOP_tags_dens, \
+ create_tree, \
+ fKD, \
+ find_nn_nearest_neighbors, \
+ free_tree, \
+ find_chunk_nearest_neighbors
+
+
https://bitbucket.org/yt_analysis/yt-3.0/changeset/d597f384f790/
changeset: d597f384f790
branch: yt
user: sskory
date: 2012-10-15 17:38:53
summary: This is now correct.
affected #: 1 file
diff -r 84f31f0466e1daa369b3f02bb5eac26255163005 -r d597f384f7907b57a8bf99a7b1033fbc78ffb7a7 yt/utilities/kdtree/api.py
--- a/yt/utilities/kdtree/api.py
+++ b/yt/utilities/kdtree/api.py
@@ -1,4 +1,4 @@
-from yt.utilities.kdtree import \
+from fKDpy import \
chainHOP_tags_dens, \
create_tree, \
fKD, \
https://bitbucket.org/yt_analysis/yt-3.0/changeset/c99d297e4a4b/
changeset: c99d297e4a4b
branch: yt
user: sskory
date: 2012-10-15 17:50:00
summary: Following up with a few more fixes for the fortan kdtree imports.
affected #: 3 files
diff -r d597f384f7907b57a8bf99a7b1033fbc78ffb7a7 -r c99d297e4a4b14ca3e278c13b147f32af612cf0b yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
--- a/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
+++ b/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
@@ -31,7 +31,7 @@
from yt.funcs import *
from yt.utilities.performance_counters import yt_counters, time_function
try:
- from yt.utilities.kdtree import \
+ from yt.utilities.kdtree.api import \
chainHOP_tags_dens, \
create_tree, fKD, find_nn_nearest_neighbors, \
free_tree, find_chunk_nearest_neighbors
diff -r d597f384f7907b57a8bf99a7b1033fbc78ffb7a7 -r c99d297e4a4b14ca3e278c13b147f32af612cf0b yt/analysis_modules/two_point_functions/two_point_functions.py
--- a/yt/analysis_modules/two_point_functions/two_point_functions.py
+++ b/yt/analysis_modules/two_point_functions/two_point_functions.py
@@ -30,7 +30,7 @@
from yt.utilities.parallel_tools.parallel_analysis_interface import ParallelAnalysisInterface, parallel_blocking_call, parallel_root_only
try:
- from yt.utilities.kdtree import *
+ from yt.utilities.kdtree.api import *
except ImportError:
mylog.debug("The Fortran kD-Tree did not import correctly.")
diff -r d597f384f7907b57a8bf99a7b1033fbc78ffb7a7 -r c99d297e4a4b14ca3e278c13b147f32af612cf0b yt/utilities/tests/test_kdtrees.py
--- a/yt/utilities/tests/test_kdtrees.py
+++ b/yt/utilities/tests/test_kdtrees.py
@@ -26,10 +26,7 @@
from yt.testing import *
try:
- from yt.utilities.kdtree import \
- chainHOP_tags_dens, \
- create_tree, fKD, find_nn_nearest_neighbors, \
- free_tree, find_chunk_nearest_neighbors
+ from yt.utilities.kdtree.api import *
except ImportError:
mylog.debug("The Fortran kD-Tree did not import correctly.")
https://bitbucket.org/yt_analysis/yt-3.0/changeset/598c0df92558/
changeset: 598c0df92558
branch: yt
user: MatthewTurk
date: 2012-10-15 17:58:57
summary: Adding CREDITS, FUNDING, LICENSE to the MANIFEST.in
affected #: 1 file
diff -r c99d297e4a4b14ca3e278c13b147f32af612cf0b -r 598c0df9255853854419600c60ea09246a404213 MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,3 @@
include distribute_setup.py
recursive-include yt/gui/reason/html *.html *.png *.ico *.js
-recursive-include yt *.pyx *.pxd *.hh *.h README*
+recursive-include yt *.pyx *.pxd *.hh *.h README* CREDITS FUNDING LICENSE
https://bitbucket.org/yt_analysis/yt-3.0/changeset/ae7c2028ce27/
changeset: ae7c2028ce27
branch: yt
user: ngoldbaum
date: 2012-10-04 22:37:21
summary: Rearranging the way coordinate transformations are handled in universal_fields. Adding generate coordinate transformation code in math_utils. Adding radial and tangential velocity fields for cylindrical coordinates.
affected #: 2 files
diff -r ac4b312b5d6fac59499a2b8bc5aa6cc3faabd0f2 -r ae7c2028ce277873ac88ae0f7f4c327e6d728988 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -194,13 +194,6 @@
function=_TangentialOverVelocityMagnitude,
take_log=False)
-def _TangentialVelocity(field, data):
- return np.sqrt(data["VelocityMagnitude"]**2.0
- - data["RadialVelocity"]**2.0)
-add_field("TangentialVelocity",
- function=_TangentialVelocity,
- take_log=False, units=r"\rm{cm}/\rm{s}")
-
def _Pressure(field, data):
"""M{(Gamma-1.0)*rho*E}"""
return (data.pf["Gamma"] - 1.0) * \
@@ -227,10 +220,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## The spherical coordinates radius is simply the magnitude of the
- ## coords vector.
-
- return np.sqrt(np.sum(coords**2,axis=-1))
+ return get_sph_r_component(vectors, center)
def _Convert_sph_r_CGS(data):
return data.convert("cm")
@@ -249,16 +239,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## The angle (theta) with respect to the normal (J), is the arccos
- ## of the dot product of the normal with the normalized coords
- ## vector.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- JdotCoords = np.sum(J*coords,axis=-1)
-
- return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=-1)) )
+ return get_sph_theta_component(vectors, center, normal)
add_field("sph_theta", function=_sph_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -273,27 +254,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## We have freedom with respect to what axis (xprime) to define
- ## the disk angle. Here I've chosen to use the axis that is
- ## perpendicular to the normal and the y-axis. When normal ==
- ## y-hat, then set xprime = z-hat. With this definition, when
- ## normal == z-hat (as is typical), then xprime == x-hat.
- ##
- ## The angle is then given by the arctan of the ratio of the
- ## yprime-component and the xprime-component of the coords vector.
-
- xprime = np.cross([0.0,1.0,0.0],normal)
- if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
- yprime = np.cross(normal,xprime)
-
- tile_shape = list(coords.shape)[:-1] + [1]
- Jx = np.tile(xprime,tile_shape)
- Jy = np.tile(yprime,tile_shape)
-
- Px = np.sum(Jx*coords,axis=-1)
- Py = np.sum(Jy*coords,axis=-1)
-
- return np.arctan2(Py,Px)
+ return get_sph_phi_component(vectors, center, normal)
add_field("sph_phi", function=_sph_phi,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -309,14 +270,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## The cross product of the normal (J) with the coords vector
- ## gives a vector of magnitude equal to the cylindrical radius.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- JcrossCoords = np.cross(J,coords)
- return np.sqrt(np.sum(JcrossCoords**2,axis=-1))
+ return get_cyl_r_component(coords, center, normal)
def _Convert_cyl_R_CGS(data):
return data.convert("cm")
@@ -324,6 +278,9 @@
add_field("cyl_R", function=_cyl_R,
validators=[ValidateParameter("center"),ValidateParameter("normal")],
convert_function = _Convert_cyl_R_CGS, units=r"\rm{cm}")
+add_field("cyl_RCode", function=_cyl_R,
+ validators=[ValidateParameter("center"),ValidateParameter("normal")],
+ units=r"Radius (code)")
### cylindrical coordinates: z (height above the cylinder's plane)
@@ -335,13 +292,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## The dot product of the normal (J) with the coords vector gives
- ## the cylindrical height.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- return np.sum(J*coords,axis=-1)
+ return get_cyl_z_component(coords,center,normal)
def _Convert_cyl_z_CGS(data):
return data.convert("cm")
@@ -352,14 +303,19 @@
### cylindrical coordinates: theta (angle in the cylinder's plane)
-### [This is identical to the spherical coordinate's 'phi' angle.]
def _cyl_theta(field, data):
- return data['sph_phi']
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ return get_cyl_theta_component(coords, center, normal)
add_field("cyl_theta", function=_cyl_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
-
### The old field DiskAngle is the same as the spherical coordinates'
### 'theta' angle. I'm keeping DiskAngle for backwards compatibility.
def _DiskAngle(field, data):
@@ -392,6 +348,65 @@
ValidateParameter("normal")],
units=r"AU", display_field=False)
+def _cyl_RadialVelocity(data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+ bulk_velocity = data.get_field_parameter("bulk_velocity")
+ if bulk_velocity == None:
+ bulk_velocity = np.zeros(3)
+
+ velocities = np.array([data['x-velocity'] - bulk_velocity[0],
+ data['y-velocity'] - bulk_velocity[1],
+ data['z-velocity'] - bulk_velocity[2]]).transpose()
+
+ return get_cyl_r_component(velocities, center, normal)
+
+def _cyl_RadialVelocityABS(field, data):
+ return np.abs(_cyl_RadialVelocity(field, data))
+def _Convert_cyl_RadialVelocityKMS(data):
+ return 1e-5
+add_field("cyl_RadialVelocity", function=_cyl_RadialVelocity,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_RadialVelocityABS", function=_cyl_RadialVelocityABS,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_RadialVelocityKMS", function=_cyl_RadialVelocity,
+ convert_function=_cyl_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_RadialVelocityKMSABS", function=_cyl_RadialVelocityABS,
+ convert_function=_cyl_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+
+def _cyl_TangentialVelocity(data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+ bulk_velocity = data.get_field_parameter("bulk_velocity")
+ if bulk_velocity == None:
+ bulk_velocity = np.zeros(3)
+
+ velocities = np.array([data['x-velocity'] - bulk_velocity[0],
+ data['y-velocity'] - bulk_velocity[1],
+ data['z-velocity'] - bulk_velocity[2]]).transpose()
+
+ return get_cyl_theta_component(velocities, center, normal)
+
+def _cyl_TangentialVelocityABS(field, data):
+ return np.abs(_cyl_TangentialVelocity(field, data))
+def _Convert_cyl_TangentialVelocityKMS(data):
+ return 1e-5
+add_field("cyl_TangentialVelocity", function=_cyl_TangentialVelocity,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityABS", function=_cyl_TangentialVelocityABS,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityKMS", function=_cyl_TangentialVelocity,
+ convert_function=_cyl_ConvertTangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityKMSABS", function=_cyl_TangentialVelocityABS,
+ convert_function=_cyl_ConvertTangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
def _DynamicalTime(field, data):
"""
@@ -887,13 +902,13 @@
bulk_velocity = data.get_field_parameter("bulk_velocity")
if bulk_velocity == None:
bulk_velocity = np.zeros(3)
- new_field = ( (data['x']-center[0])*(data["x-velocity"]-bulk_velocity[0])
- + (data['y']-center[1])*(data["y-velocity"]-bulk_velocity[1])
- + (data['z']-center[2])*(data["z-velocity"]-bulk_velocity[2])
- )/data["RadiusCode"]
- if np.any(np.isnan(new_field)): # to fix center = point
- new_field[np.isnan(new_field)] = 0.0
- return new_field
+
+ velocities = np.array([data['x-velocity'] - bulk_velocity[0],
+ data['y-velocity'] - bulk_velocity[1],
+ data['z-velocity'] - bulk_velocity[2]]).transpose()
+
+ return get_sph_r_component(velocities, center)
+
def _RadialVelocityABS(field, data):
return np.abs(_RadialVelocity(field, data))
def _ConvertRadialVelocityKMS(data):
@@ -911,6 +926,13 @@
convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
validators=[ValidateParameter("center")])
+def _TangentialVelocity(field, data):
+ return np.sqrt(data["VelocityMagnitude"]**2.0
+ - data["RadialVelocity"]**2.0)
+add_field("TangentialVelocity",
+ function=_TangentialVelocity,
+ take_log=False, units=r"\rm{cm}/\rm{s}")
+
def _CuttingPlaneVelocityX(field, data):
x_vec, y_vec, z_vec = [data.get_field_parameter("cp_%s_vec" % (ax))
for ax in 'xyz']
diff -r ac4b312b5d6fac59499a2b8bc5aa6cc3faabd0f2 -r ae7c2028ce277873ac88ae0f7f4c327e6d728988 yt/utilities/math_utils.py
--- a/yt/utilities/math_utils.py
+++ b/yt/utilities/math_utils.py
@@ -674,3 +674,69 @@
[uz*ux*(1-cost)-uy*sint, uz*uy*(1-cost)+ux*sint, cost+uz**2*(1-cost)]])
return R
+
+def get_sph_r_component(vectors, center):
+ # The spherical coordinates radius is simply the magnitude of the
+ # vector.
+
+ return np.sqrt(np.sum(vectors**2, axis=-1))
+
+
+def get_sph_theta_component(vectors, center, normal):
+ # The angle (theta) with respect to the normal (J), is the arccos
+ # of the dot product of the normal with the normalized
+ # vector.
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ J = np.tile(normal,tile_shape)
+
+ JdotVectors = np.sum(J*vectors,axis=-1)
+
+ return np.arccos( JdotVectors / np.sqrt(np.sum(Vectors**2,axis=-1)) )
+
+def get_sph_phi_component(vectors, center, normal):
+ # We have freedom with respect to what axis (xprime) to define
+ # the disk angle. Here I've chosen to use the axis that is
+ # perpendicular to the normal and the y-axis. When normal ==
+ # y-hat, then set xprime = z-hat. With this definition, when
+ # normal == z-hat (as is typical), then xprime == x-hat.
+ #
+ # The angle is then given by the arctan of the ratio of the
+ # yprime-component and the xprime-component of the vector.
+
+ xprime = np.cross([0.0,1.0,0.0],normal)
+ if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
+ yprime = np.cross(normal,xprime)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ Px = np.sum(Jx*vectors,axis=-1)
+ Py = np.sum(Jy*vectors,axis=-1)
+
+ return np.arctan2(Py,Px)
+
+def get_cyl_r_component(vectors, center, normal):
+ # The cross product of the normal (J) with a vector
+ # gives a vector of magnitude equal to the cylindrical radius.
+
+ tile_shape = list(vector.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ JcrossVectors = np.cross(J, vectors)
+ return np.sqrt(np.sum(JcrossVectors**2, axis=-1))
+
+def get_cyl_z_component(vectors, center, normal):
+ # The dot product of the normal (J) with the vector gives
+ # the cylindrical height.
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ return np.sum(J*vectors, axis=-1)
+
+def get_cyl_theta_component(vectors, center, normal):
+ # This is identical to the spherical phi component
+
+ return get_sph_phi_component(vectors, center, normal):
https://bitbucket.org/yt_analysis/yt-3.0/changeset/8a9bc98c1f24/
changeset: 8a9bc98c1f24
branch: yt
user: ngoldbaum
date: 2012-10-05 02:05:10
summary: Bugfixes for field coordinate conversion code.
affected #: 2 files
diff -r ae7c2028ce277873ac88ae0f7f4c327e6d728988 -r 8a9bc98c1f248a6f4080cfa35e79521a99b823e7 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -55,6 +55,14 @@
G, \
rho_crit_now, \
speed_of_light_cgs
+
+from yt.utilities.math_utils import \
+ get_sph_r_component, \
+ get_sph_theta_component, \
+ get_sph_phi_component, \
+ get_cyl_r_component, \
+ get_cyl_z_component, \
+ get_cyl_theta_component
# Note that, despite my newfound efforts to comply with PEP-8,
# I violate it here in order to keep the name/func_name relationship
@@ -220,7 +228,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_sph_r_component(vectors, center)
+ return get_sph_r(vectors, center)
def _Convert_sph_r_CGS(data):
return data.convert("cm")
@@ -239,7 +247,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_sph_theta_component(vectors, center, normal)
+ return get_sph_theta(coords, center, normal)
add_field("sph_theta", function=_sph_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -254,7 +262,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_sph_phi_component(vectors, center, normal)
+ return get_sph_phi(coords, center, normal)
add_field("sph_phi", function=_sph_phi,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -270,7 +278,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_cyl_r_component(coords, center, normal)
+ return get_cyl_r(coords, center, normal)
def _Convert_cyl_R_CGS(data):
return data.convert("cm")
@@ -292,7 +300,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_cyl_z_component(coords,center,normal)
+ return get_cyl_z(coords, center, normal)
def _Convert_cyl_z_CGS(data):
return data.convert("cm")
@@ -311,7 +319,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_cyl_theta_component(coords, center, normal)
+ return get_cyl_theta(coords, center, normal)
add_field("cyl_theta", function=_cyl_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -348,7 +356,7 @@
ValidateParameter("normal")],
units=r"AU", display_field=False)
-def _cyl_RadialVelocity(data):
+def _cyl_RadialVelocity(field, data):
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
bulk_velocity = data.get_field_parameter("bulk_velocity")
@@ -359,7 +367,11 @@
data['y-velocity'] - bulk_velocity[1],
data['z-velocity'] - bulk_velocity[2]]).transpose()
- return get_cyl_r_component(velocities, center, normal)
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ return get_cyl_r_component(velocities, coords, center, normal)
def _cyl_RadialVelocityABS(field, data):
return np.abs(_cyl_RadialVelocity(field, data))
@@ -372,13 +384,13 @@
units=r"\rm{cm}/\rm{s}",
validators=[ValidateParameter("center"),ValidateParameter("normal")])
add_field("cyl_RadialVelocityKMS", function=_cyl_RadialVelocity,
- convert_function=_cyl_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
validators=[ValidateParameter("center"),ValidateParameter("normal")])
add_field("cyl_RadialVelocityKMSABS", function=_cyl_RadialVelocityABS,
- convert_function=_cyl_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
validators=[ValidateParameter("center"),ValidateParameter("normal")])
-def _cyl_TangentialVelocity(data):
+def _cyl_TangentialVelocity(field, data):
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
bulk_velocity = data.get_field_parameter("bulk_velocity")
@@ -389,7 +401,11 @@
data['y-velocity'] - bulk_velocity[1],
data['z-velocity'] - bulk_velocity[2]]).transpose()
- return get_cyl_theta_component(velocities, center, normal)
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ return get_cyl_theta_component(velocities, coords, center, normal)
def _cyl_TangentialVelocityABS(field, data):
return np.abs(_cyl_TangentialVelocity(field, data))
@@ -402,10 +418,10 @@
units=r"\rm{cm}/\rm{s}",
validators=[ValidateParameter("center"),ValidateParameter("normal")])
add_field("cyl_TangentialVelocityKMS", function=_cyl_TangentialVelocity,
- convert_function=_cyl_ConvertTangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
validators=[ValidateParameter("center"),ValidateParameter("normal")])
add_field("cyl_TangentialVelocityKMSABS", function=_cyl_TangentialVelocityABS,
- convert_function=_cyl_ConvertTangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
validators=[ValidateParameter("center"),ValidateParameter("normal")])
def _DynamicalTime(field, data):
@@ -899,6 +915,9 @@
def _RadialVelocity(field, data):
center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+ if normal == None:
+ normal = [0,0,1]
bulk_velocity = data.get_field_parameter("bulk_velocity")
if bulk_velocity == None:
bulk_velocity = np.zeros(3)
@@ -906,8 +925,12 @@
velocities = np.array([data['x-velocity'] - bulk_velocity[0],
data['y-velocity'] - bulk_velocity[1],
data['z-velocity'] - bulk_velocity[2]]).transpose()
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
- return get_sph_r_component(velocities, center)
+ return get_sph_r_component(velocities, coords, center, normal)
def _RadialVelocityABS(field, data):
return np.abs(_RadialVelocity(field, data))
diff -r ae7c2028ce277873ac88ae0f7f4c327e6d728988 -r 8a9bc98c1f248a6f4080cfa35e79521a99b823e7 yt/utilities/math_utils.py
--- a/yt/utilities/math_utils.py
+++ b/yt/utilities/math_utils.py
@@ -675,26 +675,33 @@
return R
-def get_sph_r_component(vectors, center):
+def get_ortho_basis(normal):
+ xprime = np.cross([0.0,1.0,0.0],normal)
+ if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
+ yprime = np.cross(normal,xprime)
+ zprime = normal
+ return (xprime, yprime, zprime)
+
+def get_sph_r(coords, center):
# The spherical coordinates radius is simply the magnitude of the
- # vector.
+ # coordinate vector.
- return np.sqrt(np.sum(vectors**2, axis=-1))
+ return np.sqrt(np.sum(coords**2, axis=-1))
-def get_sph_theta_component(vectors, center, normal):
+def get_sph_theta(coords, center, normal):
# The angle (theta) with respect to the normal (J), is the arccos
- # of the dot product of the normal with the normalized
+ # of the dot product of the normal with the normalized coordinate
# vector.
- tile_shape = list(vectors.shape)[:-1] + [1]
+ tile_shape = list(coords.shape)[:-1] + [1]
J = np.tile(normal,tile_shape)
- JdotVectors = np.sum(J*vectors,axis=-1)
+ JdotCoords = np.sum(J*coords,axis=-1)
- return np.arccos( JdotVectors / np.sqrt(np.sum(Vectors**2,axis=-1)) )
+ return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=-1)) )
-def get_sph_phi_component(vectors, center, normal):
+def get_sph_phi(coords, center, normal):
# We have freedom with respect to what axis (xprime) to define
# the disk angle. Here I've chosen to use the axis that is
# perpendicular to the normal and the y-axis. When normal ==
@@ -702,41 +709,134 @@
# normal == z-hat (as is typical), then xprime == x-hat.
#
# The angle is then given by the arctan of the ratio of the
- # yprime-component and the xprime-component of the vector.
+ # yprime-component and the xprime-component of the coordinate
+ # vector.
- xprime = np.cross([0.0,1.0,0.0],normal)
- if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
- yprime = np.cross(normal,xprime)
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+ tile_shape = list(coords.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ Px = np.sum(Jx*coords,axis=-1)
+ Py = np.sum(Jy*coords,axis=-1)
+
+ return np.arctan2(Py,Px)
+
+def get_cyl_r(coords, center, normal):
+ # The cross product of the normal (J) with a coordinate vector
+ # gives a vector of magnitude equal to the cylindrical radius.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ JcrossCoords = np.cross(J, coords)
+ return np.sqrt(np.sum(JcrossCoords**2, axis=-1))
+
+def get_cyl_z(coords, center, normal):
+ # The dot product of the normal (J) with the coordinate vector
+ # gives the cylindrical height.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ return np.sum(J*coords, axis=-1)
+
+def get_cyl_theta(coords, center, normal):
+ # This is identical to the spherical phi component
+
+ return get_sph_phi(coords, center, normal)
+
+
+def get_cyl_r_component(vectors, coords, center, normal):
+ # The r of a vector is the vector dotted with rhat
+
+ theta = np.tile(get_cyl_theta(coords, center, normal), (3,1)).transpose()
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
tile_shape = list(vectors.shape)[:-1] + [1]
Jx = np.tile(xprime,tile_shape)
Jy = np.tile(yprime,tile_shape)
+
+ rhat = Jx*np.cos(theta) + Jy*np.sin(theta)
+
+ return np.sum(vectors*rhat,axis=-1)
+
+def get_cyl_theta_component(vectors, coords, center, normal):
+ # The theta component of a vector is the vector dotted with thetahat
- Px = np.sum(Jx*vectors,axis=-1)
- Py = np.sum(Jy*vectors,axis=-1)
-
- return np.arctan2(Py,Px)
+ theta = np.tile(get_cyl_theta(coords, center, normal), (3,1)).transpose()
-def get_cyl_r_component(vectors, center, normal):
- # The cross product of the normal (J) with a vector
- # gives a vector of magnitude equal to the cylindrical radius.
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
- tile_shape = list(vector.shape)[:-1] + [1]
- J = np.tile(normal, tile_shape)
-
- JcrossVectors = np.cross(J, vectors)
- return np.sqrt(np.sum(JcrossVectors**2, axis=-1))
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ thetahat = -Jx*np.sin(theta) + Jy*np.cos(theta)
+
+ return np.sum(vectors*thetahat, axis=-1)
def get_cyl_z_component(vectors, center, normal):
- # The dot product of the normal (J) with the vector gives
- # the cylindrical height.
+ # The z component of a vector is the vector dotted with zhat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ zhat = np.tile(zprime, tile_shape)
+
+ return np.sum(vectors*zhat, axis=-1)
+
+def get_sph_r_component(vectors, coords, center, normal):
+ # The r component of a vector is the vector dotted with rhat
+ theta = get_sph_theta(coords, center, normal)
+ phi = get_sph_phi(coords, center, normal)
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
tile_shape = list(vectors.shape)[:-1] + [1]
- J = np.tile(normal, tile_shape)
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+ Jz = np.tile(zprime,tile_shape)
- return np.sum(J*vectors, axis=-1)
+ rhat = Jx*np.sin(theta)*np.cos(phi) + \
+ Jy*np.sin(theta)*np.sin(phi) + \
+ Jz*np.cos(theta)
-def get_cyl_theta_component(vectors, center, normal):
- # This is identical to the spherical phi component
+ return np.sum(vectors*rhat, axis=-1)
- return get_sph_phi_component(vectors, center, normal):
+def get_sph_phi_component(vectors, coords, center, normal):
+ # The phi component of a vector is the vector dotted with phihat
+
+ phi = get_sph_phi(coords, center, normal)
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ phihat = -Jx*np.sin(phi) + Jy*np.cos(phi)
+
+ return np.sum(vectors*phihat, axis=-1)
+
+def get_sph_theta_component(vectors, coords, center, normal):
+ # The theta component of a vector is the vector dotted with thetahat
+
+ theta = get_sph_theta(coords, center, normal)
+ phi = get_sph_phi(coords, center, normal)
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+ Jz = np.tile(zprime,tile_shape)
+
+ thetahat = Jx*np.cos(theta)*np.cos(phi) + \
+ Jy*np.cos(theta)*np.sin(theta) - \
+ Jz*np.sin(theta)
+
+ return np.sum(vectors*thetahat, axis=-1)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/5d49ffb0208e/
changeset: 5d49ffb0208e
branch: yt
user: ngoldbaum
date: 2012-10-05 02:24:24
summary: Adding fields that grab the magnetic field in spherical coordinates.
affected #: 1 file
diff -r 8a9bc98c1f248a6f4080cfa35e79521a99b823e7 -r 5d49ffb0208ea4c4eafd593b38880d0dadd542d4 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -267,8 +267,6 @@
add_field("sph_phi", function=_sph_phi,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
-
-
### cylindrical coordinates: R (radius in the cylinder's plane)
def _cyl_R(field, data):
center = data.get_field_parameter("center")
@@ -1071,6 +1069,51 @@
display_name=r"\rm{Magnetic}\/\rm{Energy}",
units="\rm{ergs}\/\rm{cm}^{-3}")
+def _BPoloidal(field,data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ return get_sph_theta_component(Bfields, coords, center, normal)
+add_field("BPoloidal", function=_BPoloidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+
+def _BToroidal(field,data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ return get_sph_phi_component(Bfields, coords, center, normal)
+add_field("BToroidal", function=_BToroidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+
+def _BRadial(field,data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ return get_sph_r_component(Bfields, coords, center, normal)
+add_field("BRadial", function=_BPoloidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+
def _VorticitySquared(field, data):
mylog.debug("Generating vorticity on %s", data)
# We need to set up stencils
https://bitbucket.org/yt_analysis/yt-3.0/changeset/3bd4fe744fa7/
changeset: 3bd4fe744fa7
branch: yt
user: ngoldbaum
date: 2012-10-06 11:32:22
summary: Merging
affected #: 2 files
diff -r b8175a113d8ed98c0e8d514579ab607b01494565 -r 3bd4fe744fa7b1e36f6cbe86289405028ab2c149 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -55,6 +55,14 @@
G, \
rho_crit_now, \
speed_of_light_cgs
+
+from yt.utilities.math_utils import \
+ get_sph_r_component, \
+ get_sph_theta_component, \
+ get_sph_phi_component, \
+ get_cyl_r_component, \
+ get_cyl_z_component, \
+ get_cyl_theta_component
# Note that, despite my newfound efforts to comply with PEP-8,
# I violate it here in order to keep the name/func_name relationship
@@ -194,13 +202,6 @@
function=_TangentialOverVelocityMagnitude,
take_log=False)
-def _TangentialVelocity(field, data):
- return np.sqrt(data["VelocityMagnitude"]**2.0
- - data["RadialVelocity"]**2.0)
-add_field("TangentialVelocity",
- function=_TangentialVelocity,
- take_log=False, units=r"\rm{cm}/\rm{s}")
-
def _Pressure(field, data):
"""M{(Gamma-1.0)*rho*E}"""
return (data.pf["Gamma"] - 1.0) * \
@@ -227,10 +228,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## The spherical coordinates radius is simply the magnitude of the
- ## coords vector.
-
- return np.sqrt(np.sum(coords**2,axis=-1))
+ return get_sph_r(vectors, center)
def _Convert_sph_r_CGS(data):
return data.convert("cm")
@@ -249,16 +247,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## The angle (theta) with respect to the normal (J), is the arccos
- ## of the dot product of the normal with the normalized coords
- ## vector.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- JdotCoords = np.sum(J*coords,axis=-1)
-
- return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=-1)) )
+ return get_sph_theta(coords, center, normal)
add_field("sph_theta", function=_sph_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -273,33 +262,11 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## We have freedom with respect to what axis (xprime) to define
- ## the disk angle. Here I've chosen to use the axis that is
- ## perpendicular to the normal and the y-axis. When normal ==
- ## y-hat, then set xprime = z-hat. With this definition, when
- ## normal == z-hat (as is typical), then xprime == x-hat.
- ##
- ## The angle is then given by the arctan of the ratio of the
- ## yprime-component and the xprime-component of the coords vector.
-
- xprime = np.cross([0.0,1.0,0.0],normal)
- if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
- yprime = np.cross(normal,xprime)
-
- tile_shape = list(coords.shape)[:-1] + [1]
- Jx = np.tile(xprime,tile_shape)
- Jy = np.tile(yprime,tile_shape)
-
- Px = np.sum(Jx*coords,axis=-1)
- Py = np.sum(Jy*coords,axis=-1)
-
- return np.arctan2(Py,Px)
+ return get_sph_phi(coords, center, normal)
add_field("sph_phi", function=_sph_phi,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
-
-
### cylindrical coordinates: R (radius in the cylinder's plane)
def _cyl_R(field, data):
center = data.get_field_parameter("center")
@@ -309,14 +276,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## The cross product of the normal (J) with the coords vector
- ## gives a vector of magnitude equal to the cylindrical radius.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- JcrossCoords = np.cross(J,coords)
- return np.sqrt(np.sum(JcrossCoords**2,axis=-1))
+ return get_cyl_r(coords, center, normal)
def _Convert_cyl_R_CGS(data):
return data.convert("cm")
@@ -324,6 +284,9 @@
add_field("cyl_R", function=_cyl_R,
validators=[ValidateParameter("center"),ValidateParameter("normal")],
convert_function = _Convert_cyl_R_CGS, units=r"\rm{cm}")
+add_field("cyl_RCode", function=_cyl_R,
+ validators=[ValidateParameter("center"),ValidateParameter("normal")],
+ units=r"Radius (code)")
### cylindrical coordinates: z (height above the cylinder's plane)
@@ -335,13 +298,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- ## The dot product of the normal (J) with the coords vector gives
- ## the cylindrical height.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- return np.sum(J*coords,axis=-1)
+ return get_cyl_z(coords, center, normal)
def _Convert_cyl_z_CGS(data):
return data.convert("cm")
@@ -352,14 +309,19 @@
### cylindrical coordinates: theta (angle in the cylinder's plane)
-### [This is identical to the spherical coordinate's 'phi' angle.]
def _cyl_theta(field, data):
- return data['sph_phi']
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ return get_cyl_theta(coords, center, normal)
add_field("cyl_theta", function=_cyl_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
-
### The old field DiskAngle is the same as the spherical coordinates'
### 'theta' angle. I'm keeping DiskAngle for backwards compatibility.
def _DiskAngle(field, data):
@@ -392,6 +354,73 @@
ValidateParameter("normal")],
units=r"AU", display_field=False)
+def _cyl_RadialVelocity(field, data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+ bulk_velocity = data.get_field_parameter("bulk_velocity")
+ if bulk_velocity == None:
+ bulk_velocity = np.zeros(3)
+
+ velocities = np.array([data['x-velocity'] - bulk_velocity[0],
+ data['y-velocity'] - bulk_velocity[1],
+ data['z-velocity'] - bulk_velocity[2]]).transpose()
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ return get_cyl_r_component(velocities, coords, center, normal)
+
+def _cyl_RadialVelocityABS(field, data):
+ return np.abs(_cyl_RadialVelocity(field, data))
+def _Convert_cyl_RadialVelocityKMS(data):
+ return 1e-5
+add_field("cyl_RadialVelocity", function=_cyl_RadialVelocity,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_RadialVelocityABS", function=_cyl_RadialVelocityABS,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_RadialVelocityKMS", function=_cyl_RadialVelocity,
+ convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_RadialVelocityKMSABS", function=_cyl_RadialVelocityABS,
+ convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+
+def _cyl_TangentialVelocity(field, data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+ bulk_velocity = data.get_field_parameter("bulk_velocity")
+ if bulk_velocity == None:
+ bulk_velocity = np.zeros(3)
+
+ velocities = np.array([data['x-velocity'] - bulk_velocity[0],
+ data['y-velocity'] - bulk_velocity[1],
+ data['z-velocity'] - bulk_velocity[2]]).transpose()
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ return get_cyl_theta_component(velocities, coords, center, normal)
+
+def _cyl_TangentialVelocityABS(field, data):
+ return np.abs(_cyl_TangentialVelocity(field, data))
+def _Convert_cyl_TangentialVelocityKMS(data):
+ return 1e-5
+add_field("cyl_TangentialVelocity", function=_cyl_TangentialVelocity,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityABS", function=_cyl_TangentialVelocityABS,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityKMS", function=_cyl_TangentialVelocity,
+ convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityKMSABS", function=_cyl_TangentialVelocityABS,
+ convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
def _DynamicalTime(field, data):
"""
@@ -884,16 +913,23 @@
def _RadialVelocity(field, data):
center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+ if normal == None:
+ normal = [0,0,1]
bulk_velocity = data.get_field_parameter("bulk_velocity")
if bulk_velocity == None:
bulk_velocity = np.zeros(3)
- new_field = ( (data['x']-center[0])*(data["x-velocity"]-bulk_velocity[0])
- + (data['y']-center[1])*(data["y-velocity"]-bulk_velocity[1])
- + (data['z']-center[2])*(data["z-velocity"]-bulk_velocity[2])
- )/data["RadiusCode"]
- if np.any(np.isnan(new_field)): # to fix center = point
- new_field[np.isnan(new_field)] = 0.0
- return new_field
+
+ velocities = np.array([data['x-velocity'] - bulk_velocity[0],
+ data['y-velocity'] - bulk_velocity[1],
+ data['z-velocity'] - bulk_velocity[2]]).transpose()
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ return get_sph_r_component(velocities, coords, center, normal)
+
def _RadialVelocityABS(field, data):
return np.abs(_RadialVelocity(field, data))
def _ConvertRadialVelocityKMS(data):
@@ -911,6 +947,13 @@
convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
validators=[ValidateParameter("center")])
+def _TangentialVelocity(field, data):
+ return np.sqrt(data["VelocityMagnitude"]**2.0
+ - data["RadialVelocity"]**2.0)
+add_field("TangentialVelocity",
+ function=_TangentialVelocity,
+ take_log=False, units=r"\rm{cm}/\rm{s}")
+
def _CuttingPlaneVelocityX(field, data):
x_vec, y_vec, z_vec = [data.get_field_parameter("cp_%s_vec" % (ax))
for ax in 'xyz']
@@ -1026,6 +1069,51 @@
display_name=r"\rm{Magnetic}\/\rm{Energy}",
units="\rm{ergs}\/\rm{cm}^{-3}")
+def _BPoloidal(field,data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ return get_sph_theta_component(Bfields, coords, center, normal)
+add_field("BPoloidal", function=_BPoloidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+
+def _BToroidal(field,data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ return get_sph_phi_component(Bfields, coords, center, normal)
+add_field("BToroidal", function=_BToroidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+
+def _BRadial(field,data):
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = np.array([data['x'] - center[0],
+ data['y'] - center[1],
+ data['z'] - center[2]]).transpose()
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ return get_sph_r_component(Bfields, coords, center, normal)
+add_field("BRadial", function=_BPoloidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("center"),ValidateParameter("normal")])
+
def _VorticitySquared(field, data):
mylog.debug("Generating vorticity on %s", data)
# We need to set up stencils
diff -r b8175a113d8ed98c0e8d514579ab607b01494565 -r 3bd4fe744fa7b1e36f6cbe86289405028ab2c149 yt/utilities/math_utils.py
--- a/yt/utilities/math_utils.py
+++ b/yt/utilities/math_utils.py
@@ -674,3 +674,169 @@
[uz*ux*(1-cost)-uy*sint, uz*uy*(1-cost)+ux*sint, cost+uz**2*(1-cost)]])
return R
+
+def get_ortho_basis(normal):
+ xprime = np.cross([0.0,1.0,0.0],normal)
+ if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
+ yprime = np.cross(normal,xprime)
+ zprime = normal
+ return (xprime, yprime, zprime)
+
+def get_sph_r(coords, center):
+ # The spherical coordinates radius is simply the magnitude of the
+ # coordinate vector.
+
+ return np.sqrt(np.sum(coords**2, axis=-1))
+
+
+def get_sph_theta(coords, center, normal):
+ # The angle (theta) with respect to the normal (J), is the arccos
+ # of the dot product of the normal with the normalized coordinate
+ # vector.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal,tile_shape)
+
+ JdotCoords = np.sum(J*coords,axis=-1)
+
+ return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=-1)) )
+
+def get_sph_phi(coords, center, normal):
+ # We have freedom with respect to what axis (xprime) to define
+ # the disk angle. Here I've chosen to use the axis that is
+ # perpendicular to the normal and the y-axis. When normal ==
+ # y-hat, then set xprime = z-hat. With this definition, when
+ # normal == z-hat (as is typical), then xprime == x-hat.
+ #
+ # The angle is then given by the arctan of the ratio of the
+ # yprime-component and the xprime-component of the coordinate
+ # vector.
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ Px = np.sum(Jx*coords,axis=-1)
+ Py = np.sum(Jy*coords,axis=-1)
+
+ return np.arctan2(Py,Px)
+
+def get_cyl_r(coords, center, normal):
+ # The cross product of the normal (J) with a coordinate vector
+ # gives a vector of magnitude equal to the cylindrical radius.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ JcrossCoords = np.cross(J, coords)
+ return np.sqrt(np.sum(JcrossCoords**2, axis=-1))
+
+def get_cyl_z(coords, center, normal):
+ # The dot product of the normal (J) with the coordinate vector
+ # gives the cylindrical height.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ return np.sum(J*coords, axis=-1)
+
+def get_cyl_theta(coords, center, normal):
+ # This is identical to the spherical phi component
+
+ return get_sph_phi(coords, center, normal)
+
+
+def get_cyl_r_component(vectors, coords, center, normal):
+ # The r of a vector is the vector dotted with rhat
+
+ theta = np.tile(get_cyl_theta(coords, center, normal), (3,1)).transpose()
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ rhat = Jx*np.cos(theta) + Jy*np.sin(theta)
+
+ return np.sum(vectors*rhat,axis=-1)
+
+def get_cyl_theta_component(vectors, coords, center, normal):
+ # The theta component of a vector is the vector dotted with thetahat
+
+ theta = np.tile(get_cyl_theta(coords, center, normal), (3,1)).transpose()
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ thetahat = -Jx*np.sin(theta) + Jy*np.cos(theta)
+
+ return np.sum(vectors*thetahat, axis=-1)
+
+def get_cyl_z_component(vectors, center, normal):
+ # The z component of a vector is the vector dotted with zhat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ zhat = np.tile(zprime, tile_shape)
+
+ return np.sum(vectors*zhat, axis=-1)
+
+def get_sph_r_component(vectors, coords, center, normal):
+ # The r component of a vector is the vector dotted with rhat
+
+ theta = get_sph_theta(coords, center, normal)
+ phi = get_sph_phi(coords, center, normal)
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+ Jz = np.tile(zprime,tile_shape)
+
+ rhat = Jx*np.sin(theta)*np.cos(phi) + \
+ Jy*np.sin(theta)*np.sin(phi) + \
+ Jz*np.cos(theta)
+
+ return np.sum(vectors*rhat, axis=-1)
+
+def get_sph_phi_component(vectors, coords, center, normal):
+ # The phi component of a vector is the vector dotted with phihat
+
+ phi = get_sph_phi(coords, center, normal)
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ phihat = -Jx*np.sin(phi) + Jy*np.cos(phi)
+
+ return np.sum(vectors*phihat, axis=-1)
+
+def get_sph_theta_component(vectors, coords, center, normal):
+ # The theta component of a vector is the vector dotted with thetahat
+
+ theta = get_sph_theta(coords, center, normal)
+ phi = get_sph_phi(coords, center, normal)
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+ Jz = np.tile(zprime,tile_shape)
+
+ thetahat = Jx*np.cos(theta)*np.cos(phi) + \
+ Jy*np.cos(theta)*np.sin(theta) - \
+ Jz*np.sin(theta)
+
+ return np.sum(vectors*thetahat, axis=-1)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/809bff333e8b/
changeset: 809bff333e8b
branch: yt
user: ngoldbaum
date: 2012-10-06 12:20:53
summary: Rearranging things. Fixing the imports so that the cylindrical and spherical coordinate fields don't break. Fixing some typos.
This still reads x, y, z, vx, vy, and vz multiple times for my test script.
affected #: 2 files
diff -r 3bd4fe744fa7b1e36f6cbe86289405028ab2c149 -r 809bff333e8b5022ed54799209c3e69a668a78f1 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -62,7 +62,10 @@
get_sph_phi_component, \
get_cyl_r_component, \
get_cyl_z_component, \
- get_cyl_theta_component
+ get_cyl_theta_component, \
+ get_cyl_r, get_cyl_theta, \
+ get_cyl_z, get_sph_r, \
+ get_sph_theta, get_sph_phi
# Note that, despite my newfound efforts to comply with PEP-8,
# I violate it here in order to keep the name/func_name relationship
@@ -247,7 +250,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_sph_theta(coords, center, normal)
+ return get_sph_theta(coords, normal)
add_field("sph_theta", function=_sph_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -262,7 +265,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_sph_phi(coords, center, normal)
+ return get_sph_phi(coords, normal)
add_field("sph_phi", function=_sph_phi,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -276,7 +279,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_cyl_r(coords, center, normal)
+ return get_cyl_r(coords, normal)
def _Convert_cyl_R_CGS(data):
return data.convert("cm")
@@ -298,7 +301,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_cyl_z(coords, center, normal)
+ return get_cyl_z(coords, normal)
def _Convert_cyl_z_CGS(data):
return data.convert("cm")
@@ -317,7 +320,7 @@
data['y'] - center[1],
data['z'] - center[2]]).transpose()
- return get_cyl_theta(coords, center, normal)
+ return get_cyl_theta(coords, normal)
add_field("cyl_theta", function=_cyl_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -355,7 +358,6 @@
units=r"AU", display_field=False)
def _cyl_RadialVelocity(field, data):
- center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
bulk_velocity = data.get_field_parameter("bulk_velocity")
if bulk_velocity == None:
@@ -365,11 +367,9 @@
data['y-velocity'] - bulk_velocity[1],
data['z-velocity'] - bulk_velocity[2]]).transpose()
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ theta = np.tile(data['cyl_theta'], (3, 1)).transpose()
- return get_cyl_r_component(velocities, coords, center, normal)
+ return get_cyl_r_component(velocities, theta, normal)
def _cyl_RadialVelocityABS(field, data):
return np.abs(_cyl_RadialVelocity(field, data))
@@ -377,19 +377,18 @@
return 1e-5
add_field("cyl_RadialVelocity", function=_cyl_RadialVelocity,
units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
add_field("cyl_RadialVelocityABS", function=_cyl_RadialVelocityABS,
units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
add_field("cyl_RadialVelocityKMS", function=_cyl_RadialVelocity,
convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
add_field("cyl_RadialVelocityKMSABS", function=_cyl_RadialVelocityABS,
convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
def _cyl_TangentialVelocity(field, data):
- center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
bulk_velocity = data.get_field_parameter("bulk_velocity")
if bulk_velocity == None:
@@ -399,11 +398,9 @@
data['y-velocity'] - bulk_velocity[1],
data['z-velocity'] - bulk_velocity[2]]).transpose()
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
-
- return get_cyl_theta_component(velocities, coords, center, normal)
+ theta = np.tile(data['cyl_theta'], (3, 1)).transpose()
+
+ return get_cyl_theta_component(velocities, theta, normal)
def _cyl_TangentialVelocityABS(field, data):
return np.abs(_cyl_TangentialVelocity(field, data))
@@ -411,16 +408,16 @@
return 1e-5
add_field("cyl_TangentialVelocity", function=_cyl_TangentialVelocity,
units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
add_field("cyl_TangentialVelocityABS", function=_cyl_TangentialVelocityABS,
units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
add_field("cyl_TangentialVelocityKMS", function=_cyl_TangentialVelocity,
convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
add_field("cyl_TangentialVelocityKMSABS", function=_cyl_TangentialVelocityABS,
convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
def _DynamicalTime(field, data):
"""
@@ -912,7 +909,6 @@
display_name = "Radius (code)")
def _RadialVelocity(field, data):
- center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
if normal == None:
normal = [0,0,1]
@@ -924,28 +920,23 @@
data['y-velocity'] - bulk_velocity[1],
data['z-velocity'] - bulk_velocity[2]]).transpose()
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ theta = np.tile(data['sph_theta'], (3, 1)).transpose()
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
- return get_sph_r_component(velocities, coords, center, normal)
+ return get_sph_r_component(velocities, theta, phi, normal)
def _RadialVelocityABS(field, data):
return np.abs(_RadialVelocity(field, data))
def _ConvertRadialVelocityKMS(data):
return 1e-5
add_field("RadialVelocity", function=_RadialVelocity,
- units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center")])
+ units=r"\rm{cm}/\rm{s}")
add_field("RadialVelocityABS", function=_RadialVelocityABS,
- units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center")])
+ units=r"\rm{cm}/\rm{s}")
add_field("RadialVelocityKMS", function=_RadialVelocity,
- convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center")])
+ convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}")
add_field("RadialVelocityKMSABS", function=_RadialVelocityABS,
- convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center")])
+ convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}")
def _TangentialVelocity(field, data):
return np.sqrt(data["VelocityMagnitude"]**2.0
@@ -1070,49 +1061,45 @@
units="\rm{ergs}\/\rm{cm}^{-3}")
def _BPoloidal(field,data):
- center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
-
Bfields = np.array([data['Bx'], data['By'], data['Bz']])
- return get_sph_theta_component(Bfields, coords, center, normal)
+ theta = np.tile(data['sph_theta'], (3, 1)).transpose()
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_theta_component(Bfields, theta, phi, normal)
+
add_field("BPoloidal", function=_BPoloidal,
units=r"\rm{Gauss}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
def _BToroidal(field,data):
- center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
-
Bfields = np.array([data['Bx'], data['By'], data['Bz']])
- return get_sph_phi_component(Bfields, coords, center, normal)
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_phi_component(Bfields, phi, normal)
+
add_field("BToroidal", function=_BToroidal,
units=r"\rm{Gauss}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
def _BRadial(field,data):
- center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
-
Bfields = np.array([data['Bx'], data['By'], data['Bz']])
- return get_sph_r_component(Bfields, coords, center, normal)
+ theta = np.tile(data['sph_theta'], (3, 1)).transpose()
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_r_component(Bfields, theta, phi, normal)
+
add_field("BRadial", function=_BPoloidal,
units=r"\rm{Gauss}",
- validators=[ValidateParameter("center"),ValidateParameter("normal")])
+ validators=[ValidateParameter("normal")])
def _VorticitySquared(field, data):
mylog.debug("Generating vorticity on %s", data)
diff -r 3bd4fe744fa7b1e36f6cbe86289405028ab2c149 -r 809bff333e8b5022ed54799209c3e69a668a78f1 yt/utilities/math_utils.py
--- a/yt/utilities/math_utils.py
+++ b/yt/utilities/math_utils.py
@@ -682,14 +682,14 @@
zprime = normal
return (xprime, yprime, zprime)
-def get_sph_r(coords, center):
+def get_sph_r(coords):
# The spherical coordinates radius is simply the magnitude of the
# coordinate vector.
return np.sqrt(np.sum(coords**2, axis=-1))
-def get_sph_theta(coords, center, normal):
+def get_sph_theta(coords, normal):
# The angle (theta) with respect to the normal (J), is the arccos
# of the dot product of the normal with the normalized coordinate
# vector.
@@ -701,7 +701,7 @@
return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=-1)) )
-def get_sph_phi(coords, center, normal):
+def get_sph_phi(coords, normal):
# We have freedom with respect to what axis (xprime) to define
# the disk angle. Here I've chosen to use the axis that is
# perpendicular to the normal and the y-axis. When normal ==
@@ -723,7 +723,7 @@
return np.arctan2(Py,Px)
-def get_cyl_r(coords, center, normal):
+def get_cyl_r(coords, normal):
# The cross product of the normal (J) with a coordinate vector
# gives a vector of magnitude equal to the cylindrical radius.
@@ -733,7 +733,7 @@
JcrossCoords = np.cross(J, coords)
return np.sqrt(np.sum(JcrossCoords**2, axis=-1))
-def get_cyl_z(coords, center, normal):
+def get_cyl_z(coords, normal):
# The dot product of the normal (J) with the coordinate vector
# gives the cylindrical height.
@@ -742,17 +742,15 @@
return np.sum(J*coords, axis=-1)
-def get_cyl_theta(coords, center, normal):
+def get_cyl_theta(coords, normal):
# This is identical to the spherical phi component
- return get_sph_phi(coords, center, normal)
+ return get_sph_phi(coords, normal)
-def get_cyl_r_component(vectors, coords, center, normal):
+def get_cyl_r_component(vectors, theta, normal):
# The r of a vector is the vector dotted with rhat
- theta = np.tile(get_cyl_theta(coords, center, normal), (3,1)).transpose()
-
(xprime, yprime, zprime) = get_ortho_basis(normal)
tile_shape = list(vectors.shape)[:-1] + [1]
@@ -763,11 +761,9 @@
return np.sum(vectors*rhat,axis=-1)
-def get_cyl_theta_component(vectors, coords, center, normal):
+def get_cyl_theta_component(vectors, theta, normal):
# The theta component of a vector is the vector dotted with thetahat
- theta = np.tile(get_cyl_theta(coords, center, normal), (3,1)).transpose()
-
(xprime, yprime, zprime) = get_ortho_basis(normal)
tile_shape = list(vectors.shape)[:-1] + [1]
@@ -778,9 +774,8 @@
return np.sum(vectors*thetahat, axis=-1)
-def get_cyl_z_component(vectors, center, normal):
+def get_cyl_z_component(vectors, normal):
# The z component of a vector is the vector dotted with zhat
-
(xprime, yprime, zprime) = get_ortho_basis(normal)
tile_shape = list(vectors.shape)[:-1] + [1]
@@ -788,12 +783,9 @@
return np.sum(vectors*zhat, axis=-1)
-def get_sph_r_component(vectors, coords, center, normal):
+def get_sph_r_component(vectors, theta, phi, normal):
# The r component of a vector is the vector dotted with rhat
- theta = get_sph_theta(coords, center, normal)
- phi = get_sph_phi(coords, center, normal)
-
(xprime, yprime, zprime) = get_ortho_basis(normal)
tile_shape = list(vectors.shape)[:-1] + [1]
@@ -807,10 +799,10 @@
return np.sum(vectors*rhat, axis=-1)
-def get_sph_phi_component(vectors, coords, center, normal):
+def get_sph_phi_component(vectors, phi, normal):
# The phi component of a vector is the vector dotted with phihat
- phi = get_sph_phi(coords, center, normal)
+ phi = get_sph_phi(coords, normal)
(xprime, yprime, zprime) = get_ortho_basis(normal)
@@ -822,11 +814,11 @@
return np.sum(vectors*phihat, axis=-1)
-def get_sph_theta_component(vectors, coords, center, normal):
+def get_sph_theta_component(vectors, theta, phi, normal):
# The theta component of a vector is the vector dotted with thetahat
- theta = get_sph_theta(coords, center, normal)
- phi = get_sph_phi(coords, center, normal)
+ theta = get_sph_theta(coords, normal)
+ phi = get_sph_phi(coords, normal)
(xprime, yprime, zprime) = get_ortho_basis(normal)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/28ee8407e8ac/
changeset: 28ee8407e8ac
branch: yt
user: ngoldbaum
date: 2012-10-06 21:42:52
summary: Moving the code that obtains relative velocities to cython. Refactoring the coordinate transformation code. Using the appropriate unit converstion constants from physical_constants.py. Thanks for the suggestions Kacper!
affected #: 3 files
diff -r 809bff333e8b5022ed54799209c3e69a668a78f1 -r 28ee8407e8ac563031468f9a1f535e52b3f4eaae yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -32,7 +32,7 @@
from yt.funcs import *
-from yt.utilities.lib import CICDeposit_3, obtain_rvec
+from yt.utilities.lib import CICDeposit_3, obtain_rvec, obtain_rv_vec
from yt.utilities.cosmology import Cosmology
from field_info_container import \
add_field, \
@@ -54,7 +54,8 @@
kboltz, \
G, \
rho_crit_now, \
- speed_of_light_cgs
+ speed_of_light_cgs, \
+ km_per_cm
from yt.utilities.math_utils import \
get_sph_r_component, \
@@ -190,12 +191,8 @@
def _VelocityMagnitude(field, data):
"""M{|v|}"""
- bulk_velocity = data.get_field_parameter("bulk_velocity")
- if bulk_velocity == None:
- bulk_velocity = np.zeros(3)
- return ( (data["x-velocity"]-bulk_velocity[0])**2.0 + \
- (data["y-velocity"]-bulk_velocity[1])**2.0 + \
- (data["z-velocity"]-bulk_velocity[2])**2.0 )**(1.0/2.0)
+ velocities = obtain_rv_vec(data)
+ return np.sqrt(np.sum(velocities**2,axis=-1))
add_field("VelocityMagnitude", function=_VelocityMagnitude,
take_log=False, units=r"\rm{cm}/\rm{s}")
@@ -227,9 +224,7 @@
def _sph_r(field, data):
center = data.get_field_parameter("center")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
return get_sph_r(vectors, center)
@@ -246,9 +241,7 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transepose()
return get_sph_theta(coords, normal)
@@ -261,10 +254,8 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
-
+ coords = obtain_rvec(data).transpose()
+
return get_sph_phi(coords, normal)
add_field("sph_phi", function=_sph_phi,
@@ -275,9 +266,7 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
return get_cyl_r(coords, normal)
@@ -297,9 +286,7 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
return get_cyl_z(coords, normal)
@@ -316,9 +303,7 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
return get_cyl_theta(coords, normal)
@@ -359,13 +344,7 @@
def _cyl_RadialVelocity(field, data):
normal = data.get_field_parameter("normal")
- bulk_velocity = data.get_field_parameter("bulk_velocity")
- if bulk_velocity == None:
- bulk_velocity = np.zeros(3)
-
- velocities = np.array([data['x-velocity'] - bulk_velocity[0],
- data['y-velocity'] - bulk_velocity[1],
- data['z-velocity'] - bulk_velocity[2]]).transpose()
+ velocities = obtain_rv_vec(data).transpose()
theta = np.tile(data['cyl_theta'], (3, 1)).transpose()
@@ -374,7 +353,7 @@
def _cyl_RadialVelocityABS(field, data):
return np.abs(_cyl_RadialVelocity(field, data))
def _Convert_cyl_RadialVelocityKMS(data):
- return 1e-5
+ return km_per_cm
add_field("cyl_RadialVelocity", function=_cyl_RadialVelocity,
units=r"\rm{cm}/\rm{s}",
validators=[ValidateParameter("normal")])
@@ -390,14 +369,7 @@
def _cyl_TangentialVelocity(field, data):
normal = data.get_field_parameter("normal")
- bulk_velocity = data.get_field_parameter("bulk_velocity")
- if bulk_velocity == None:
- bulk_velocity = np.zeros(3)
-
- velocities = np.array([data['x-velocity'] - bulk_velocity[0],
- data['y-velocity'] - bulk_velocity[1],
- data['z-velocity'] - bulk_velocity[2]]).transpose()
-
+ velocities = obtain_rv_vec(data).transpose()
theta = np.tile(data['cyl_theta'], (3, 1)).transpose()
return get_cyl_theta_component(velocities, theta, normal)
@@ -405,7 +377,7 @@
def _cyl_TangentialVelocityABS(field, data):
return np.abs(_cyl_TangentialVelocity(field, data))
def _Convert_cyl_TangentialVelocityKMS(data):
- return 1e-5
+ return km_per_cm
add_field("cyl_TangentialVelocity", function=_cyl_TangentialVelocity,
units=r"\rm{cm}/\rm{s}",
validators=[ValidateParameter("normal")])
@@ -666,13 +638,7 @@
take_log=False, display_field=False)
def obtain_velocities(data):
- if data.has_field_parameter("bulk_velocity"):
- bv = data.get_field_parameter("bulk_velocity")
- else: bv = np.zeros(3, dtype='float64')
- xv = data["x-velocity"] - bv[0]
- yv = data["y-velocity"] - bv[1]
- zv = data["z-velocity"] - bv[2]
- return xv, yv, zv
+ return obtain_rv_vec(data)
def _convertSpecificAngularMomentum(data):
return data.convert("cm")
@@ -737,7 +703,7 @@
# convert_function=_convertSpecificAngularMomentum, vector_field=True,
# units=r"\rm{cm}^2/\rm{s}", validators=[ValidateParameter('center')])
def _convertSpecificAngularMomentumKMSMPC(data):
- return data.convert("mpc")/1e5
+ return km_per_cm*data.convert("mpc")
#add_field("ParticleSpecificAngularMomentumKMSMPC",
# function=_ParticleSpecificAngularMomentum, particle_type=True,
# convert_function=_convertSpecificAngularMomentumKMSMPC, vector_field=True,
@@ -912,14 +878,7 @@
normal = data.get_field_parameter("normal")
if normal == None:
normal = [0,0,1]
- bulk_velocity = data.get_field_parameter("bulk_velocity")
- if bulk_velocity == None:
- bulk_velocity = np.zeros(3)
-
- velocities = np.array([data['x-velocity'] - bulk_velocity[0],
- data['y-velocity'] - bulk_velocity[1],
- data['z-velocity'] - bulk_velocity[2]]).transpose()
-
+ velocities = obtain_rv_vec(data).transpose()
theta = np.tile(data['sph_theta'], (3, 1)).transpose()
phi = np.tile(data['sph_phi'], (3, 1)).transpose()
@@ -928,7 +887,7 @@
def _RadialVelocityABS(field, data):
return np.abs(_RadialVelocity(field, data))
def _ConvertRadialVelocityKMS(data):
- return 1e-5
+ return km_per_cm
add_field("RadialVelocity", function=_RadialVelocity,
units=r"\rm{cm}/\rm{s}")
add_field("RadialVelocityABS", function=_RadialVelocityABS,
diff -r 809bff333e8b5022ed54799209c3e69a668a78f1 -r 28ee8407e8ac563031468f9a1f535e52b3f4eaae yt/utilities/lib/geometry_utils.pyx
--- a/yt/utilities/lib/geometry_utils.pyx
+++ b/yt/utilities/lib/geometry_utils.pyx
@@ -338,3 +338,45 @@
rg[2,i,j,k] = zg[i,j,k] - c[2]
return rg
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+ at cython.cdivision(True)
+def obtain_rv_vec(data):
+ # This is just to let the pointers exist and whatnot. We can't cdef them
+ # inside conditionals.
+ cdef np.ndarray[np.float64_t, ndim=1] vxf
+ cdef np.ndarray[np.float64_t, ndim=1] vyf
+ cdef np.ndarray[np.float64_t, ndim=1] vzf
+ cdef np.ndarray[np.float64_t, ndim=2] rvf
+ cdef np.ndarray[np.float64_t, ndim=3] vxg
+ cdef np.ndarray[np.float64_t, ndim=3] vyg
+ cdef np.ndarray[np.float64_t, ndim=3] vzg
+ cdef np.ndarray[np.float64_t, ndim=4] rvg
+ cdef np.float64_t bv[3]
+ cdef int i, j, k
+ bulk_velocity = data.get_field_parameter("bulk_velocity")
+ bv[0] = bulk_velocity[0]; bv[1] = bulk_velocity[1]; bv[2] = bulk_velocity[2]
+ if len(data['x-velocity'].shape) == 1:
+ # One dimensional data
+ vxf = data['x-velocity']
+ vyf = data['y-velocity']
+ vzf = data['z-velocity']
+ rvf = np.empty((3, vxf.shape[0]), 'float64')
+ for i in range(vxf.shape[0]):
+ rvf[0, i] = vxf[i] - bv[0]
+ rvf[1, i] = vyf[i] - bv[1]
+ rvf[2, i] = vzf[i] - bv[2]
+ return rvf
+ else:
+ # Three dimensional data
+ vxg = data['x']
+ vyg = data['y']
+ vzg = data['z']
+ rvg = np.empty((3, vxg.shape[0], vxg.shape[1], vxg.shape[2]), 'float64')
+ for i in range(vxg.shape[0]):
+ for j in range(vxg.shape[1]):
+ for k in range(vxg.shape[2]):
+ rvg[0,i,j,k] = vxg[i,j,k] - bv[0]
+ rvg[1,i,j,k] = vyg[i,j,k] - bv[1]
+ rvg[2,i,j,k] = vzg[i,j,k] - bv[2]
+ return rvg
diff -r 809bff333e8b5022ed54799209c3e69a668a78f1 -r 28ee8407e8ac563031468f9a1f535e52b3f4eaae yt/utilities/lib/misc_utilities.pyx
--- a/yt/utilities/lib/misc_utilities.pyx
+++ b/yt/utilities/lib/misc_utilities.pyx
@@ -233,49 +233,6 @@
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
-def obtain_rvec(data):
- # This is just to let the pointers exist and whatnot. We can't cdef them
- # inside conditionals.
- cdef np.ndarray[np.float64_t, ndim=1] xf
- cdef np.ndarray[np.float64_t, ndim=1] yf
- cdef np.ndarray[np.float64_t, ndim=1] zf
- cdef np.ndarray[np.float64_t, ndim=2] rf
- cdef np.ndarray[np.float64_t, ndim=3] xg
- cdef np.ndarray[np.float64_t, ndim=3] yg
- cdef np.ndarray[np.float64_t, ndim=3] zg
- cdef np.ndarray[np.float64_t, ndim=4] rg
- cdef np.float64_t c[3]
- cdef int i, j, k
- center = data.get_field_parameter("center")
- c[0] = center[0]; c[1] = center[1]; c[2] = center[2]
- if len(data['x'].shape) == 1:
- # One dimensional data
- xf = data['x']
- yf = data['y']
- zf = data['z']
- rf = np.empty((3, xf.shape[0]), 'float64')
- for i in range(xf.shape[0]):
- rf[0, i] = xf[i] - c[0]
- rf[1, i] = yf[i] - c[1]
- rf[2, i] = zf[i] - c[2]
- return rf
- else:
- # Three dimensional data
- xg = data['x']
- yg = data['y']
- zg = data['z']
- rg = np.empty((3, xg.shape[0], xg.shape[1], xg.shape[2]), 'float64')
- for i in range(xg.shape[0]):
- for j in range(xg.shape[1]):
- for k in range(xg.shape[2]):
- rg[0,i,j,k] = xg[i,j,k] - c[0]
- rg[1,i,j,k] = yg[i,j,k] - c[1]
- rg[2,i,j,k] = zg[i,j,k] - c[2]
- return rg
-
- at cython.boundscheck(False)
- at cython.wraparound(False)
- at cython.cdivision(True)
def kdtree_get_choices(np.ndarray[np.float64_t, ndim=3] data,
np.ndarray[np.float64_t, ndim=1] l_corner,
np.ndarray[np.float64_t, ndim=1] r_corner):
https://bitbucket.org/yt_analysis/yt-3.0/changeset/c9edc60694ed/
changeset: c9edc60694ed
branch: yt
user: ngoldbaum
date: 2012-10-06 21:47:32
summary: Forgot a stray tranpose()
affected #: 1 file
diff -r 28ee8407e8ac563031468f9a1f535e52b3f4eaae -r c9edc60694edef326a39c43080831dd472de5583 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -191,7 +191,7 @@
def _VelocityMagnitude(field, data):
"""M{|v|}"""
- velocities = obtain_rv_vec(data)
+ velocities = obtain_rv_vec(data).transpose()
return np.sqrt(np.sum(velocities**2,axis=-1))
add_field("VelocityMagnitude", function=_VelocityMagnitude,
take_log=False, units=r"\rm{cm}/\rm{s}")
https://bitbucket.org/yt_analysis/yt-3.0/changeset/3b427b92d9da/
changeset: 3b427b92d9da
branch: yt
user: ngoldbaum
date: 2012-10-09 03:53:45
summary: Merging.
affected #: 4 files
diff -r b9838b15dbde418c6f7a8862b1499e67a5d1e6db -r 3b427b92d9dab845eff0d6bd6a3105c90735c014 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -32,7 +32,7 @@
from yt.funcs import *
-from yt.utilities.lib import CICDeposit_3, obtain_rvec
+from yt.utilities.lib import CICDeposit_3, obtain_rvec, obtain_rv_vec
from yt.utilities.cosmology import Cosmology
from field_info_container import \
add_field, \
@@ -54,7 +54,19 @@
kboltz, \
G, \
rho_crit_now, \
- speed_of_light_cgs
+ speed_of_light_cgs, \
+ km_per_cm
+
+from yt.utilities.math_utils import \
+ get_sph_r_component, \
+ get_sph_theta_component, \
+ get_sph_phi_component, \
+ get_cyl_r_component, \
+ get_cyl_z_component, \
+ get_cyl_theta_component, \
+ get_cyl_r, get_cyl_theta, \
+ get_cyl_z, get_sph_r, \
+ get_sph_theta, get_sph_phi
# Note that, despite my newfound efforts to comply with PEP-8,
# I violate it here in order to keep the name/func_name relationship
@@ -179,12 +191,8 @@
def _VelocityMagnitude(field, data):
"""M{|v|}"""
- bulk_velocity = data.get_field_parameter("bulk_velocity")
- if bulk_velocity == None:
- bulk_velocity = np.zeros(3)
- return ( (data["x-velocity"]-bulk_velocity[0])**2.0 + \
- (data["y-velocity"]-bulk_velocity[1])**2.0 + \
- (data["z-velocity"]-bulk_velocity[2])**2.0 )**(1.0/2.0)
+ velocities = obtain_rv_vec(data).transpose()
+ return np.sqrt(np.sum(velocities**2,axis=-1))
add_field("VelocityMagnitude", function=_VelocityMagnitude,
take_log=False, units=r"\rm{cm}/\rm{s}")
@@ -194,13 +202,6 @@
function=_TangentialOverVelocityMagnitude,
take_log=False)
-def _TangentialVelocity(field, data):
- return np.sqrt(data["VelocityMagnitude"]**2.0
- - data["RadialVelocity"]**2.0)
-add_field("TangentialVelocity",
- function=_TangentialVelocity,
- take_log=False, units=r"\rm{cm}/\rm{s}")
-
def _Pressure(field, data):
"""M{(Gamma-1.0)*rho*E}"""
return (data.pf["Gamma"] - 1.0) * \
@@ -223,14 +224,9 @@
def _sph_r(field, data):
center = data.get_field_parameter("center")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
- ## The spherical coordinates radius is simply the magnitude of the
- ## coords vector.
-
- return np.sqrt(np.sum(coords**2,axis=-1))
+ return get_sph_r(vectors, center)
def _Convert_sph_r_CGS(data):
return data.convert("cm")
@@ -245,20 +241,9 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transepose()
- ## The angle (theta) with respect to the normal (J), is the arccos
- ## of the dot product of the normal with the normalized coords
- ## vector.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- JdotCoords = np.sum(J*coords,axis=-1)
-
- return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=-1)) )
+ return get_sph_theta(coords, normal)
add_field("sph_theta", function=_sph_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -269,54 +254,21 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
-
- ## We have freedom with respect to what axis (xprime) to define
- ## the disk angle. Here I've chosen to use the axis that is
- ## perpendicular to the normal and the y-axis. When normal ==
- ## y-hat, then set xprime = z-hat. With this definition, when
- ## normal == z-hat (as is typical), then xprime == x-hat.
- ##
- ## The angle is then given by the arctan of the ratio of the
- ## yprime-component and the xprime-component of the coords vector.
+ coords = obtain_rvec(data).transpose()
- xprime = np.cross([0.0,1.0,0.0],normal)
- if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
- yprime = np.cross(normal,xprime)
-
- tile_shape = list(coords.shape)[:-1] + [1]
- Jx = np.tile(xprime,tile_shape)
- Jy = np.tile(yprime,tile_shape)
-
- Px = np.sum(Jx*coords,axis=-1)
- Py = np.sum(Jy*coords,axis=-1)
-
- return np.arctan2(Py,Px)
+ return get_sph_phi(coords, normal)
add_field("sph_phi", function=_sph_phi,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
-
-
### cylindrical coordinates: R (radius in the cylinder's plane)
def _cyl_R(field, data):
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
- ## The cross product of the normal (J) with the coords vector
- ## gives a vector of magnitude equal to the cylindrical radius.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- JcrossCoords = np.cross(J,coords)
- return np.sqrt(np.sum(JcrossCoords**2,axis=-1))
+ return get_cyl_r(coords, normal)
def _Convert_cyl_R_CGS(data):
return data.convert("cm")
@@ -324,6 +276,9 @@
add_field("cyl_R", function=_cyl_R,
validators=[ValidateParameter("center"),ValidateParameter("normal")],
convert_function = _Convert_cyl_R_CGS, units=r"\rm{cm}")
+add_field("cyl_RCode", function=_cyl_R,
+ validators=[ValidateParameter("center"),ValidateParameter("normal")],
+ units=r"Radius (code)")
### cylindrical coordinates: z (height above the cylinder's plane)
@@ -331,17 +286,9 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
- ## The dot product of the normal (J) with the coords vector gives
- ## the cylindrical height.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- return np.sum(J*coords,axis=-1)
+ return get_cyl_z(coords, normal)
def _Convert_cyl_z_CGS(data):
return data.convert("cm")
@@ -352,14 +299,17 @@
### cylindrical coordinates: theta (angle in the cylinder's plane)
-### [This is identical to the spherical coordinate's 'phi' angle.]
def _cyl_theta(field, data):
- return data['sph_phi']
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = obtain_rvec(data).transpose()
+
+ return get_cyl_theta(coords, normal)
add_field("cyl_theta", function=_cyl_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
-
### The old field DiskAngle is the same as the spherical coordinates'
### 'theta' angle. I'm keeping DiskAngle for backwards compatibility.
def _DiskAngle(field, data):
@@ -392,6 +342,54 @@
ValidateParameter("normal")],
units=r"AU", display_field=False)
+def _cyl_RadialVelocity(field, data):
+ normal = data.get_field_parameter("normal")
+ velocities = obtain_rv_vec(data).transpose()
+
+ theta = np.tile(data['cyl_theta'], (3, 1)).transpose()
+
+ return get_cyl_r_component(velocities, theta, normal)
+
+def _cyl_RadialVelocityABS(field, data):
+ return np.abs(_cyl_RadialVelocity(field, data))
+def _Convert_cyl_RadialVelocityKMS(data):
+ return km_per_cm
+add_field("cyl_RadialVelocity", function=_cyl_RadialVelocity,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_RadialVelocityABS", function=_cyl_RadialVelocityABS,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_RadialVelocityKMS", function=_cyl_RadialVelocity,
+ convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_RadialVelocityKMSABS", function=_cyl_RadialVelocityABS,
+ convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+
+def _cyl_TangentialVelocity(field, data):
+ normal = data.get_field_parameter("normal")
+ velocities = obtain_rv_vec(data).transpose()
+ theta = np.tile(data['cyl_theta'], (3, 1)).transpose()
+
+ return get_cyl_theta_component(velocities, theta, normal)
+
+def _cyl_TangentialVelocityABS(field, data):
+ return np.abs(_cyl_TangentialVelocity(field, data))
+def _Convert_cyl_TangentialVelocityKMS(data):
+ return km_per_cm
+add_field("cyl_TangentialVelocity", function=_cyl_TangentialVelocity,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityABS", function=_cyl_TangentialVelocityABS,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityKMS", function=_cyl_TangentialVelocity,
+ convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityKMSABS", function=_cyl_TangentialVelocityABS,
+ convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("normal")])
def _DynamicalTime(field, data):
"""
@@ -640,13 +638,7 @@
take_log=False, display_field=False)
def obtain_velocities(data):
- if data.has_field_parameter("bulk_velocity"):
- bv = data.get_field_parameter("bulk_velocity")
- else: bv = np.zeros(3, dtype='float64')
- xv = data["x-velocity"] - bv[0]
- yv = data["y-velocity"] - bv[1]
- zv = data["z-velocity"] - bv[2]
- return xv, yv, zv
+ return obtain_rv_vec(data)
def _convertSpecificAngularMomentum(data):
return data.convert("cm")
@@ -711,7 +703,7 @@
# convert_function=_convertSpecificAngularMomentum, vector_field=True,
# units=r"\rm{cm}^2/\rm{s}", validators=[ValidateParameter('center')])
def _convertSpecificAngularMomentumKMSMPC(data):
- return data.convert("mpc")/1e5
+ return km_per_cm*data.convert("mpc")
#add_field("ParticleSpecificAngularMomentumKMSMPC",
# function=_ParticleSpecificAngularMomentum, particle_type=True,
# convert_function=_convertSpecificAngularMomentumKMSMPC, vector_field=True,
@@ -883,33 +875,34 @@
display_name = "Radius (code)")
def _RadialVelocity(field, data):
- center = data.get_field_parameter("center")
- bulk_velocity = data.get_field_parameter("bulk_velocity")
- if bulk_velocity == None:
- bulk_velocity = np.zeros(3)
- new_field = ( (data['x']-center[0])*(data["x-velocity"]-bulk_velocity[0])
- + (data['y']-center[1])*(data["y-velocity"]-bulk_velocity[1])
- + (data['z']-center[2])*(data["z-velocity"]-bulk_velocity[2])
- )/data["RadiusCode"]
- if np.any(np.isnan(new_field)): # to fix center = point
- new_field[np.isnan(new_field)] = 0.0
- return new_field
+ normal = data.get_field_parameter("normal")
+ if normal == None:
+ normal = [0,0,1]
+ velocities = obtain_rv_vec(data).transpose()
+ theta = np.tile(data['sph_theta'], (3, 1)).transpose()
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_r_component(velocities, theta, phi, normal)
+
def _RadialVelocityABS(field, data):
return np.abs(_RadialVelocity(field, data))
def _ConvertRadialVelocityKMS(data):
- return 1e-5
+ return km_per_cm
add_field("RadialVelocity", function=_RadialVelocity,
- units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center")])
+ units=r"\rm{cm}/\rm{s}")
add_field("RadialVelocityABS", function=_RadialVelocityABS,
- units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center")])
+ units=r"\rm{cm}/\rm{s}")
add_field("RadialVelocityKMS", function=_RadialVelocity,
- convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center")])
+ convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}")
add_field("RadialVelocityKMSABS", function=_RadialVelocityABS,
- convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center")])
+ convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}")
+
+def _TangentialVelocity(field, data):
+ return np.sqrt(data["VelocityMagnitude"]**2.0
+ - data["RadialVelocity"]**2.0)
+add_field("TangentialVelocity",
+ function=_TangentialVelocity,
+ take_log=False, units=r"\rm{cm}/\rm{s}")
def _CuttingPlaneVelocityX(field, data):
x_vec, y_vec, z_vec = [data.get_field_parameter("cp_%s_vec" % (ax))
@@ -1026,6 +1019,47 @@
display_name=r"\rm{Magnetic}\/\rm{Energy}",
units="\rm{ergs}\/\rm{cm}^{-3}")
+def _BPoloidal(field,data):
+ normal = data.get_field_parameter("normal")
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ theta = np.tile(data['sph_theta'], (3, 1)).transpose()
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_theta_component(Bfields, theta, phi, normal)
+
+add_field("BPoloidal", function=_BPoloidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("normal")])
+
+def _BToroidal(field,data):
+ normal = data.get_field_parameter("normal")
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_phi_component(Bfields, phi, normal)
+
+add_field("BToroidal", function=_BToroidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("normal")])
+
+def _BRadial(field,data):
+ normal = data.get_field_parameter("normal")
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ theta = np.tile(data['sph_theta'], (3, 1)).transpose()
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_r_component(Bfields, theta, phi, normal)
+
+add_field("BRadial", function=_BPoloidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("normal")])
+
def _VorticitySquared(field, data):
mylog.debug("Generating vorticity on %s", data)
# We need to set up stencils
diff -r b9838b15dbde418c6f7a8862b1499e67a5d1e6db -r 3b427b92d9dab845eff0d6bd6a3105c90735c014 yt/utilities/lib/geometry_utils.pyx
--- a/yt/utilities/lib/geometry_utils.pyx
+++ b/yt/utilities/lib/geometry_utils.pyx
@@ -338,3 +338,45 @@
rg[2,i,j,k] = zg[i,j,k] - c[2]
return rg
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+ at cython.cdivision(True)
+def obtain_rv_vec(data):
+ # This is just to let the pointers exist and whatnot. We can't cdef them
+ # inside conditionals.
+ cdef np.ndarray[np.float64_t, ndim=1] vxf
+ cdef np.ndarray[np.float64_t, ndim=1] vyf
+ cdef np.ndarray[np.float64_t, ndim=1] vzf
+ cdef np.ndarray[np.float64_t, ndim=2] rvf
+ cdef np.ndarray[np.float64_t, ndim=3] vxg
+ cdef np.ndarray[np.float64_t, ndim=3] vyg
+ cdef np.ndarray[np.float64_t, ndim=3] vzg
+ cdef np.ndarray[np.float64_t, ndim=4] rvg
+ cdef np.float64_t bv[3]
+ cdef int i, j, k
+ bulk_velocity = data.get_field_parameter("bulk_velocity")
+ bv[0] = bulk_velocity[0]; bv[1] = bulk_velocity[1]; bv[2] = bulk_velocity[2]
+ if len(data['x-velocity'].shape) == 1:
+ # One dimensional data
+ vxf = data['x-velocity']
+ vyf = data['y-velocity']
+ vzf = data['z-velocity']
+ rvf = np.empty((3, vxf.shape[0]), 'float64')
+ for i in range(vxf.shape[0]):
+ rvf[0, i] = vxf[i] - bv[0]
+ rvf[1, i] = vyf[i] - bv[1]
+ rvf[2, i] = vzf[i] - bv[2]
+ return rvf
+ else:
+ # Three dimensional data
+ vxg = data['x']
+ vyg = data['y']
+ vzg = data['z']
+ rvg = np.empty((3, vxg.shape[0], vxg.shape[1], vxg.shape[2]), 'float64')
+ for i in range(vxg.shape[0]):
+ for j in range(vxg.shape[1]):
+ for k in range(vxg.shape[2]):
+ rvg[0,i,j,k] = vxg[i,j,k] - bv[0]
+ rvg[1,i,j,k] = vyg[i,j,k] - bv[1]
+ rvg[2,i,j,k] = vzg[i,j,k] - bv[2]
+ return rvg
diff -r b9838b15dbde418c6f7a8862b1499e67a5d1e6db -r 3b427b92d9dab845eff0d6bd6a3105c90735c014 yt/utilities/lib/misc_utilities.pyx
--- a/yt/utilities/lib/misc_utilities.pyx
+++ b/yt/utilities/lib/misc_utilities.pyx
@@ -233,49 +233,6 @@
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
-def obtain_rvec(data):
- # This is just to let the pointers exist and whatnot. We can't cdef them
- # inside conditionals.
- cdef np.ndarray[np.float64_t, ndim=1] xf
- cdef np.ndarray[np.float64_t, ndim=1] yf
- cdef np.ndarray[np.float64_t, ndim=1] zf
- cdef np.ndarray[np.float64_t, ndim=2] rf
- cdef np.ndarray[np.float64_t, ndim=3] xg
- cdef np.ndarray[np.float64_t, ndim=3] yg
- cdef np.ndarray[np.float64_t, ndim=3] zg
- cdef np.ndarray[np.float64_t, ndim=4] rg
- cdef np.float64_t c[3]
- cdef int i, j, k
- center = data.get_field_parameter("center")
- c[0] = center[0]; c[1] = center[1]; c[2] = center[2]
- if len(data['x'].shape) == 1:
- # One dimensional data
- xf = data['x']
- yf = data['y']
- zf = data['z']
- rf = np.empty((3, xf.shape[0]), 'float64')
- for i in range(xf.shape[0]):
- rf[0, i] = xf[i] - c[0]
- rf[1, i] = yf[i] - c[1]
- rf[2, i] = zf[i] - c[2]
- return rf
- else:
- # Three dimensional data
- xg = data['x']
- yg = data['y']
- zg = data['z']
- rg = np.empty((3, xg.shape[0], xg.shape[1], xg.shape[2]), 'float64')
- for i in range(xg.shape[0]):
- for j in range(xg.shape[1]):
- for k in range(xg.shape[2]):
- rg[0,i,j,k] = xg[i,j,k] - c[0]
- rg[1,i,j,k] = yg[i,j,k] - c[1]
- rg[2,i,j,k] = zg[i,j,k] - c[2]
- return rg
-
- at cython.boundscheck(False)
- at cython.wraparound(False)
- at cython.cdivision(True)
def kdtree_get_choices(np.ndarray[np.float64_t, ndim=3] data,
np.ndarray[np.float64_t, ndim=1] l_corner,
np.ndarray[np.float64_t, ndim=1] r_corner):
diff -r b9838b15dbde418c6f7a8862b1499e67a5d1e6db -r 3b427b92d9dab845eff0d6bd6a3105c90735c014 yt/utilities/math_utils.py
--- a/yt/utilities/math_utils.py
+++ b/yt/utilities/math_utils.py
@@ -674,3 +674,161 @@
[uz*ux*(1-cost)-uy*sint, uz*uy*(1-cost)+ux*sint, cost+uz**2*(1-cost)]])
return R
+
+def get_ortho_basis(normal):
+ xprime = np.cross([0.0,1.0,0.0],normal)
+ if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
+ yprime = np.cross(normal,xprime)
+ zprime = normal
+ return (xprime, yprime, zprime)
+
+def get_sph_r(coords):
+ # The spherical coordinates radius is simply the magnitude of the
+ # coordinate vector.
+
+ return np.sqrt(np.sum(coords**2, axis=-1))
+
+
+def get_sph_theta(coords, normal):
+ # The angle (theta) with respect to the normal (J), is the arccos
+ # of the dot product of the normal with the normalized coordinate
+ # vector.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal,tile_shape)
+
+ JdotCoords = np.sum(J*coords,axis=-1)
+
+ return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=-1)) )
+
+def get_sph_phi(coords, normal):
+ # We have freedom with respect to what axis (xprime) to define
+ # the disk angle. Here I've chosen to use the axis that is
+ # perpendicular to the normal and the y-axis. When normal ==
+ # y-hat, then set xprime = z-hat. With this definition, when
+ # normal == z-hat (as is typical), then xprime == x-hat.
+ #
+ # The angle is then given by the arctan of the ratio of the
+ # yprime-component and the xprime-component of the coordinate
+ # vector.
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ Px = np.sum(Jx*coords,axis=-1)
+ Py = np.sum(Jy*coords,axis=-1)
+
+ return np.arctan2(Py,Px)
+
+def get_cyl_r(coords, normal):
+ # The cross product of the normal (J) with a coordinate vector
+ # gives a vector of magnitude equal to the cylindrical radius.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ JcrossCoords = np.cross(J, coords)
+ return np.sqrt(np.sum(JcrossCoords**2, axis=-1))
+
+def get_cyl_z(coords, normal):
+ # The dot product of the normal (J) with the coordinate vector
+ # gives the cylindrical height.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ return np.sum(J*coords, axis=-1)
+
+def get_cyl_theta(coords, normal):
+ # This is identical to the spherical phi component
+
+ return get_sph_phi(coords, normal)
+
+
+def get_cyl_r_component(vectors, theta, normal):
+ # The r of a vector is the vector dotted with rhat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ rhat = Jx*np.cos(theta) + Jy*np.sin(theta)
+
+ return np.sum(vectors*rhat,axis=-1)
+
+def get_cyl_theta_component(vectors, theta, normal):
+ # The theta component of a vector is the vector dotted with thetahat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ thetahat = -Jx*np.sin(theta) + Jy*np.cos(theta)
+
+ return np.sum(vectors*thetahat, axis=-1)
+
+def get_cyl_z_component(vectors, normal):
+ # The z component of a vector is the vector dotted with zhat
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ zhat = np.tile(zprime, tile_shape)
+
+ return np.sum(vectors*zhat, axis=-1)
+
+def get_sph_r_component(vectors, theta, phi, normal):
+ # The r component of a vector is the vector dotted with rhat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+ Jz = np.tile(zprime,tile_shape)
+
+ rhat = Jx*np.sin(theta)*np.cos(phi) + \
+ Jy*np.sin(theta)*np.sin(phi) + \
+ Jz*np.cos(theta)
+
+ return np.sum(vectors*rhat, axis=-1)
+
+def get_sph_phi_component(vectors, phi, normal):
+ # The phi component of a vector is the vector dotted with phihat
+
+ phi = get_sph_phi(coords, normal)
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ phihat = -Jx*np.sin(phi) + Jy*np.cos(phi)
+
+ return np.sum(vectors*phihat, axis=-1)
+
+def get_sph_theta_component(vectors, theta, phi, normal):
+ # The theta component of a vector is the vector dotted with thetahat
+
+ theta = get_sph_theta(coords, normal)
+ phi = get_sph_phi(coords, normal)
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+ Jz = np.tile(zprime,tile_shape)
+
+ thetahat = Jx*np.cos(theta)*np.cos(phi) + \
+ Jy*np.cos(theta)*np.sin(theta) - \
+ Jz*np.sin(theta)
+
+ return np.sum(vectors*thetahat, axis=-1)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/10a6246dd7cd/
changeset: 10a6246dd7cd
branch: yt
user: ngoldbaum
date: 2012-10-09 03:54:00
summary: Merging.
affected #: 1 file
diff -r 3b427b92d9dab845eff0d6bd6a3105c90735c014 -r 10a6246dd7cd27f2fadcff8ec92a3c93a5ffc6d0 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -845,17 +845,21 @@
>>> slc.save(mpl_kwargs={'bbox_inches':'tight'})
"""
+ names = []
+ if mpl_kwargs is None: mpl_kwargs = {}
if name == None:
name = str(self.pf)
elif name.endswith('.png'):
- return v.save(name)
- if mpl_kwargs is None: mpl_kwargs = {}
+ for k, v in self.plots.iteritems():
+ names.append(v.save(name,mpl_kwargs))
+ return names
axis = axis_names[self.data_source.axis]
weight = None
type = self._plot_type
if type in ['Projection','OffAxisProjection']:
weight = self.data_source.weight_field
- names = []
+ if 'Cutting' in self.data_source.__class__.__name__:
+ type = 'OffAxisSlice'
for k, v in self.plots.iteritems():
if axis:
n = "%s_%s_%s_%s" % (name, type, axis, k)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/d32d3d12f91e/
changeset: d32d3d12f91e
branch: yt
user: ngoldbaum
date: 2012-10-11 21:37:14
summary: Merging.
affected #: 4 files
diff -r 10a6246dd7cd27f2fadcff8ec92a3c93a5ffc6d0 -r d32d3d12f91ef1c0c5450317a269d0480d2ccdeb doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -220,11 +220,24 @@
echo " * libncurses5-dev"
echo " * zip"
echo " * uuid-dev"
+ echo " * libfreetype6-dev"
+ echo " * tk-dev"
echo
echo "You can accomplish this by executing:"
echo
- echo "$ sudo apt-get install libssl-dev build-essential libncurses5 libncurses5-dev zip uuid-dev"
+ echo "$ sudo apt-get install libssl-dev build-essential libncurses5 libncurses5-dev zip uuid-dev libfreetype6-dev tk-dev"
echo
+ echo
+ echo " Additionally, if you want to put yt's lib dir in your LD_LIBRARY_PATH"
+ echo " so you can use yt without the activate script, you might "
+ echo " want to consider turning off LIBZ and FREETYPE in this"
+ echo " install script by editing this file and setting"
+ echo
+ echo " INST_ZLIB=0"
+ echo " INST_FTYPE=0"
+ echo
+ echo " to avoid conflicts with other command-line programs "
+ echo " (like eog and evince, for example)."
fi
if [ ! -z "${CFLAGS}" ]
then
diff -r 10a6246dd7cd27f2fadcff8ec92a3c93a5ffc6d0 -r d32d3d12f91ef1c0c5450317a269d0480d2ccdeb yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -855,6 +855,22 @@
for field in temp_data.keys():
self[field] = temp_data[field]
+ def _get_pw(self, fields, center, width, origin, axes_unit, plot_type):
+ axis = self.axis
+ if fields == None:
+ if self.fields == None:
+ raise SyntaxError("The fields keyword argument must be set")
+ else:
+ self.fields = ensure_list(fields)
+ from yt.visualization.plot_window import \
+ GetBoundsAndCenter, PWViewerMPL
+ from yt.visualization.fixed_resolution import FixedResolutionBuffer
+ (bounds, center) = GetBoundsAndCenter(axis, center, width, self.pf)
+ pw = PWViewerMPL(self, bounds, origin=origin, frb_generator=FixedResolutionBuffer,
+ plot_type=plot_type)
+ pw.set_axes_unit(axes_unit)
+ return pw
+
def to_frb(self, width, resolution, center=None, height=None):
r"""This function returns a FixedResolutionBuffer generated from this
object.
@@ -916,26 +932,6 @@
frb = FixedResolutionBuffer(self, bounds, resolution)
return frb
- def to_pw(self):
- r"""Create a :class:`~yt.visualization.plot_window.PlotWindow` from this
- object.
-
- This is a bare-bones mechanism of creating a plot window from this
- object, which can then be moved around, zoomed, and on and on. All
- behavior of the plot window is relegated to that routine.
- """
- axis = self.axis
- center = self.get_field_parameter("center")
- if center is None:
- center = (self.pf.domain_right_edge
- + self.pf.domain_left_edge)/2.0
- width = (1.0, 'unitary')
- from yt.visualization.plot_window import \
- PWViewerMPL, GetBoundsAndCenter
- (bounds, center) = GetBoundsAndCenter(axis, center, width, self.pf)
- pw = PWViewerMPL(self, bounds)
- return pw
-
def interpolate_discretize(self, LE, RE, field, side, log_spacing=True):
"""
This returns a uniform grid of points between *LE* and *RE*,
@@ -1193,6 +1189,18 @@
def hub_upload(self):
self._mrep.upload()
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Slice')
+ return pw
+
class AMRCuttingPlaneBase(AMR2DData):
_plane = None
_top_node = "/CuttingPlanes"
@@ -1355,6 +1363,30 @@
return "%s/c%s_L%s" % \
(self._top_node, cen_name, L_name)
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ normal = self.normal
+ center = self.center
+ if fields == None:
+ if self.fields == None:
+ raise SyntaxError("The fields keyword argument must be set")
+ else:
+ self.fields = ensure_list(fields)
+ from yt.visualization.plot_window import \
+ GetOffAxisBoundsAndCenter, PWViewerMPL
+ from yt.visualization.fixed_resolution import ObliqueFixedResolutionBuffer
+ (bounds, center_rot) = GetOffAxisBoundsAndCenter(normal, center, width, self.pf)
+ pw = PWViewerMPL(self, bounds, origin='center-window', periodic=False, oblique=True,
+ frb_generator=ObliqueFixedResolutionBuffer, plot_type='OffAxisSlice')
+ pw.set_axes_unit(axes_unit)
+ return pw
+
def to_frb(self, width, resolution, height=None):
r"""This function returns an ObliqueFixedResolutionBuffer generated
from this object.
@@ -1762,6 +1794,18 @@
convs[:] = 1.0
return dls, convs
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Projection')
+ return pw
+
def get_data(self, fields = None):
if fields is None: fields = ensure_list(self.fields)[:]
else: fields = ensure_list(fields)
@@ -2254,6 +2298,18 @@
def add_fields(self, fields, weight = "CellMassMsun"):
pass
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Projection')
+ return pw
+
def _project_grid(self, grid, fields, zero_out):
# We split this next bit into two sections to try to limit the IO load
# on the system. This way, we perserve grid state (@restore_grid_state
diff -r 10a6246dd7cd27f2fadcff8ec92a3c93a5ffc6d0 -r d32d3d12f91ef1c0c5450317a269d0480d2ccdeb yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -379,7 +379,7 @@
take_log=True)
"""
import matplotlib
- from ._mpl_imports import *
+ from ._mpl_imports import FigureCanvasAgg, FigureCanvasPdf, FigureCanvasPS
# If this is rendered as log, then apply now.
if take_log:
@@ -420,21 +420,22 @@
else:
dpi = None
- if filename[-4:] == '.png':
- suffix = ''
- else:
+ suffix = os.path.splitext(filename)[1]
+
+ if suffix == '':
suffix = '.png'
filename = "%s%s" % (filename, suffix)
- mylog.info("Saving plot %s", fn)
+ mylog.info("Saving plot %s", filename)
if suffix == ".png":
canvas = FigureCanvasAgg(fig)
elif suffix == ".pdf":
canvas = FigureCanvasPdf(fig)
elif suffix in (".eps", ".ps"):
- canvas = FigureCanvasPS
+ canvas = FigureCanvasPS(fig)
else:
mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
canvas = FigureCanvasAgg(fig)
+
canvas.print_figure(filename)
return filename
diff -r 10a6246dd7cd27f2fadcff8ec92a3c93a5ffc6d0 -r d32d3d12f91ef1c0c5450317a269d0480d2ccdeb yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -695,6 +695,15 @@
"""
_current_field = None
+ _frb_generator = None
+ _plot_type = None
+
+ def __init__(self, *args, **kwargs):
+ if self._frb_generator == None:
+ self._frb_generator = kwargs.pop("frb_generator")
+ if self._plot_type == None:
+ self._plot_type = kwargs.pop("plot_type")
+ PWViewer.__init__(self, *args, **kwargs)
def _setup_plots(self):
if self._current_field is not None:
@@ -849,7 +858,8 @@
if mpl_kwargs is None: mpl_kwargs = {}
if name == None:
name = str(self.pf)
- elif name.endswith('.png'):
+ suffix = os.path.splitext(name)[1]
+ if suffix != '':
for k, v in self.plots.iteritems():
names.append(v.save(name,mpl_kwargs))
return names
@@ -1224,6 +1234,7 @@
_ext_widget_id = None
_current_field = None
_widget_name = "plot_window"
+ _frb_generator = FixedResolutionBuffer
def _setup_plots(self):
from yt.gui.reason.bottle_mods import PayloadHandler
@@ -1401,24 +1412,25 @@
self.cax = self.figure.add_axes(caxrect)
def save(self, name, mpl_kwargs, canvas = None):
- if name[-4:] == '.png':
- suffix = ''
+ suffix = os.path.splitext(name)[1]
+
+ if suffix == '':
+ suffix = '.png'
+ name = "%s%s" % (name, suffix)
+ mylog.info("Saving plot %s", name)
+ if suffix == ".png":
+ canvas = FigureCanvasAgg(self.figure)
+ elif suffix == ".pdf":
+ canvas = FigureCanvasPdf(self.figure)
+ elif suffix in (".eps", ".ps"):
+ canvas = FigureCanvasPS(self.figure)
else:
- suffix = '.png'
- fn = "%s%s" % (name, suffix)
- mylog.info("Saving plot %s", fn)
- if canvas is None:
- if suffix == ".png":
- canvas = FigureCanvasAgg(self.figure)
- elif suffix == ".pdf":
- canvas = FigureCanvasPdf(self.figure)
- elif suffix in (".eps", ".ps"):
- canvas = FigureCanvasPS
- else:
- mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
- canvas = FigureCanvasAgg(self.figure)
- canvas.print_figure(fn,**mpl_kwargs)
- return fn
+ mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
+ canvas = FigureCanvasAgg(self.figure)
+
+
+ canvas.print_figure(name,**mpl_kwargs)
+ return name
def _get_best_layout(self, size):
aspect = 1.0*size[0]/size[1]
https://bitbucket.org/yt_analysis/yt-3.0/changeset/6b249ecbf0e6/
changeset: 6b249ecbf0e6
branch: yt
user: ngoldbaum
date: 2012-10-11 21:53:06
summary: Need to check to see if bulk_velocity is defined.
affected #: 1 file
diff -r d32d3d12f91ef1c0c5450317a269d0480d2ccdeb -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 yt/utilities/lib/geometry_utils.pyx
--- a/yt/utilities/lib/geometry_utils.pyx
+++ b/yt/utilities/lib/geometry_utils.pyx
@@ -355,6 +355,8 @@
cdef np.float64_t bv[3]
cdef int i, j, k
bulk_velocity = data.get_field_parameter("bulk_velocity")
+ if bulk_velocity == None:
+ bulk_velocity = np.zeros(3)
bv[0] = bulk_velocity[0]; bv[1] = bulk_velocity[1]; bv[2] = bulk_velocity[2]
if len(data['x-velocity'].shape) == 1:
# One dimensional data
https://bitbucket.org/yt_analysis/yt-3.0/changeset/ab186e76a23a/
changeset: ab186e76a23a
branch: yt
user: ngoldbaum
date: 2012-10-15 20:55:46
summary: Merging.
affected #: 18 files
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,3 @@
include distribute_setup.py
recursive-include yt/gui/reason/html *.html *.png *.ico *.js
-recursive-include yt *.pyx *.pxd *.hh *.h README*
+recursive-include yt *.pyx *.pxd *.hh *.h README* CREDITS FUNDING LICENSE
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e nose.cfg
--- /dev/null
+++ b/nose.cfg
@@ -0,0 +1,4 @@
+[nosetests]
+detailed-errors=1
+where=yt
+exclude=answer_testing
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e setup.cfg
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,3 +1,9 @@
[egg_info]
#tag_build = .dev
#tag_svn_revision = 1
+
+[nosetests]
+detailed-errors=1
+where=yt
+exclude=answer_testing
+with-xunit=1
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
--- a/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
+++ b/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
@@ -31,7 +31,7 @@
from yt.funcs import *
from yt.utilities.performance_counters import yt_counters, time_function
try:
- from yt.utilities.kdtree import \
+ from yt.utilities.kdtree.api import \
chainHOP_tags_dens, \
create_tree, fKD, find_nn_nearest_neighbors, \
free_tree, find_chunk_nearest_neighbors
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/analysis_modules/two_point_functions/two_point_functions.py
--- a/yt/analysis_modules/two_point_functions/two_point_functions.py
+++ b/yt/analysis_modules/two_point_functions/two_point_functions.py
@@ -30,7 +30,7 @@
from yt.utilities.parallel_tools.parallel_analysis_interface import ParallelAnalysisInterface, parallel_blocking_call, parallel_root_only
try:
- from yt.utilities.kdtree import *
+ from yt.utilities.kdtree.api import *
except ImportError:
mylog.debug("The Fortran kD-Tree did not import correctly.")
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/config.py
--- a/yt/config.py
+++ b/yt/config.py
@@ -38,6 +38,7 @@
inline = 'False',
numthreads = '-1',
__withinreason = 'False',
+ __withintesting = 'False',
__parallel = 'False',
__global_parallel_rank = '0',
__global_parallel_size = '1',
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -3658,7 +3658,7 @@
class AMRCoveringGridBase(AMR3DData):
_spatial = True
_type_name = "covering_grid"
- _con_args = ('level', 'left_edge', 'right_edge', 'ActiveDimensions')
+ _con_args = ('level', 'left_edge', 'ActiveDimensions')
def __init__(self, level, left_edge, dims, fields = None,
pf = None, num_ghost_zones = 0, use_pbar = True, **kwargs):
"""A 3D region with all data extracted to a single, specified
@@ -3685,8 +3685,9 @@
fields=fields, pf=pf, **kwargs)
self.left_edge = np.array(left_edge)
self.level = level
- self.dds = self.pf.h.select_grids(self.level)[0].dds.copy()
- self.ActiveDimensions = np.array(dims,dtype='int32')
+ rdx = self.pf.domain_dimensions*self.pf.refine_by**level
+ self.dds = self.pf.domain_width/rdx.astype("float64")
+ self.ActiveDimensions = np.array(dims, dtype='int32')
self.right_edge = self.left_edge + self.ActiveDimensions*self.dds
self._num_ghost_zones = num_ghost_zones
self._use_pbar = use_pbar
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/data_objects/tests/test_covering_grid.py
--- /dev/null
+++ b/yt/data_objects/tests/test_covering_grid.py
@@ -0,0 +1,27 @@
+from yt.testing import *
+from yt.data_objects.profiles import \
+ BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+
+def setup():
+ from yt.config import ytcfg
+ ytcfg["yt","__withintesting"] = "True"
+
+def test_covering_grid():
+ # We decompose in different ways
+ for level in [0, 1, 2]:
+ for nprocs in [1, 2, 4, 8]:
+ pf = fake_random_pf(16, nprocs = nprocs)
+ dn = pf.refine_by**level
+ cg = pf.h.covering_grid(level, [0.0, 0.0, 0.0],
+ dn * pf.domain_dimensions)
+ yield assert_equal, cg["Ones"].max(), 1.0
+ yield assert_equal, cg["Ones"].min(), 1.0
+ yield assert_equal, cg["CellVolume"].sum(), pf.domain_width.prod()
+ for g in pf.h.grids:
+ di = g.get_global_startindex()
+ dd = g.ActiveDimensions
+ for i in range(dn):
+ f = cg["Density"][dn*di[0]+i:dn*(di[0]+dd[0])+i:dn,
+ dn*di[1]+i:dn*(di[1]+dd[1])+i:dn,
+ dn*di[2]+i:dn*(di[2]+dd[2])+i:dn]
+ yield assert_equal, f, g["Density"]
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/data_objects/tests/test_profiles.py
--- /dev/null
+++ b/yt/data_objects/tests/test_profiles.py
@@ -0,0 +1,74 @@
+from yt.testing import *
+from yt.data_objects.profiles import \
+ BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+
+_fields = ("Density", "Temperature", "Dinosaurs", "Tribbles")
+
+def test_profiles():
+ pf = fake_random_pf(64, nprocs = 8, fields = _fields)
+ nv = pf.domain_dimensions.prod()
+ dd = pf.h.all_data()
+ (rmi, rma), (tmi, tma), (dmi, dma) = dd.quantities["Extrema"](
+ ["Density", "Temperature", "Dinosaurs"])
+ rt, tt, dt = dd.quantities["TotalQuantity"](
+ ["Density", "Temperature", "Dinosaurs"])
+ # First we look at the
+ for nb in [8, 16, 32, 64]:
+ for lr in [True, False]:
+ # We log all the fields or don't log 'em all. No need to do them
+ # individually.
+ for lf in [True, False]:
+ # We have the min and the max, but to avoid cutting them off
+ # since we aren't doing end-collect, we cut a bit off the edges
+ for ec, e1, e2 in [(False, 0.9, 1.1), (True, 1.0, 1.0)]:
+ p1d = BinnedProfile1D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ lr, end_collect=ec)
+ p1d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p1d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p1d["Temperature"].sum(), 7
+
+ p2d = BinnedProfile2D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ nb, "Temperature", tmi*e1, tma*e2, lf,
+ lr, end_collect=ec)
+ p2d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p2d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p2d["Temperature"].sum(), 7
+
+ p3d = BinnedProfile3D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ nb, "Temperature", tmi*e1, tma*e2, lf,
+ nb, "Dinosaurs", dmi*e1, dma*e2, lf,
+ lr, end_collect=ec)
+ p3d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p3d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p3d["Temperature"].sum(), 7
+
+ p1d = BinnedProfile1D(dd, nb, "x", 0.0, 1.0, log_space=False)
+ p1d.add_fields("Ones", weight=None)
+ av = nv / nb
+ yield assert_equal, p1d["Ones"][:-1], np.ones(nb)*av
+ # We re-bin ones with a weight now
+ p1d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p1d["Ones"][:-1], np.ones(nb)
+
+ p2d = BinnedProfile2D(dd, nb, "x", 0.0, 1.0, False,
+ nb, "y", 0.0, 1.0, False)
+ p2d.add_fields("Ones", weight=None)
+ av = nv / nb**2
+ yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))*av
+ # We re-bin ones with a weight now
+ p2d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))
+
+ p3d = BinnedProfile3D(dd, nb, "x", 0.0, 1.0, False,
+ nb, "y", 0.0, 1.0, False,
+ nb, "z", 0.0, 1.0, False)
+ p3d.add_fields("Ones", weight=None)
+ av = nv / nb**3
+ yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb, nb, nb))*av
+ # We re-bin ones with a weight now
+ p3d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb,nb,nb))
+
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/data_objects/tests/test_projection.py
--- /dev/null
+++ b/yt/data_objects/tests/test_projection.py
@@ -0,0 +1,39 @@
+from yt.testing import *
+from yt.data_objects.profiles import \
+ BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+
+def setup():
+ from yt.config import ytcfg
+ ytcfg["yt","__withintesting"] = "True"
+
+def test_projection():
+ for nprocs in [8, 1]:
+ # We want to test both 1 proc and 8 procs, to make sure that
+ # parallelism isn't broken
+ pf = fake_random_pf(64, nprocs = nprocs)
+ dims = pf.domain_dimensions
+ xn, yn, zn = pf.domain_dimensions
+ xi, yi, zi = pf.domain_left_edge + 1.0/(pf.domain_dimensions * 2)
+ xf, yf, zf = pf.domain_right_edge - 1.0/(pf.domain_dimensions * 2)
+ dd = pf.h.all_data()
+ rho_tot = dd.quantities["TotalQuantity"]("Density")[0]
+ coords = np.mgrid[xi:xf:xn*1j, yi:yf:yn*1j, zi:zf:zn*1j]
+ uc = [np.unique(c) for c in coords]
+ # Some simple projection tests with single grids
+ for ax, an in enumerate("xyz"):
+ xax = x_dict[ax]
+ yax = y_dict[ax]
+ for wf in ["Density", None]:
+ proj = pf.h.proj(ax, ["Ones", "Density"], weight_field = wf)
+ yield assert_equal, proj["Ones"].sum(), proj["Ones"].size
+ yield assert_equal, proj["Ones"].min(), 1.0
+ yield assert_equal, proj["Ones"].max(), 1.0
+ yield assert_equal, np.unique(proj["px"]), uc[xax]
+ yield assert_equal, np.unique(proj["py"]), uc[yax]
+ yield assert_equal, np.unique(proj["pdx"]), 1.0/(dims[xax]*2.0)
+ yield assert_equal, np.unique(proj["pdy"]), 1.0/(dims[yax]*2.0)
+ # wf == None
+ yield assert_equal, wf, None
+ v1 = proj["Density"].sum()
+ v2 = (dd["Density"] * dd["d%s" % an]).sum()
+ yield assert_rel_equal, v1, v2, 10
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -353,7 +353,8 @@
psize = get_psize(np.array(data[key].shape), nprocs)
grid_left_edges, grid_right_edges, temp[key] = \
decompose_array(data[key], psize, bbox)
- grid_dimensions = np.array([grid.shape for grid in temp[key]])
+ grid_dimensions = np.array([grid.shape for grid in temp[key]],
+ dtype="int32")
for gid in range(nprocs):
new_data[gid] = {}
for key in temp.keys():
@@ -364,7 +365,7 @@
sfh.update({0:data})
grid_left_edges = domain_left_edge
grid_right_edges = domain_right_edge
- grid_dimensions = domain_dimensions.reshape(nprocs,3)
+ grid_dimensions = domain_dimensions.reshape(nprocs,3).astype("int32")
handler = StreamHandler(
grid_left_edges,
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -310,7 +310,8 @@
maxval = max(maxval, 1)
from yt.config import ytcfg
if ytcfg.getboolean("yt", "suppressStreamLogging") or \
- ytcfg.getboolean("yt", "ipython_notebook"):
+ ytcfg.getboolean("yt", "ipython_notebook") or \
+ ytcfg.getboolean("yt", "__withintesting"):
return DummyProgressBar()
elif ytcfg.getboolean("yt", "__withinreason"):
from yt.gui.reason.extdirect_repl import ExtProgressBar
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -24,7 +24,12 @@
import numpy as np
from yt.funcs import *
-from numpy.testing import assert_array_equal
+from numpy.testing import assert_array_equal, assert_almost_equal, \
+ assert_approx_equal, assert_array_almost_equal, assert_equal, \
+ assert_string_equal
+
+def assert_rel_equal(a1, a2, decimels):
+ return assert_almost_equal(a1/a2, 1.0, decimels)
def amrspace(extent, levels=7, cells=8):
"""Creates two numpy arrays representing the left and right bounds of
@@ -127,7 +132,8 @@
return left, right, level
-def fake_random_pf(ndims, peak_value = 1.0, fields = ("Density",), negative = False):
+def fake_random_pf(ndims, peak_value = 1.0, fields = ("Density",),
+ negative = False, nprocs = 1):
from yt.frontends.stream.api import load_uniform_grid
if not iterable(ndims):
ndims = [ndims, ndims, ndims]
@@ -139,5 +145,5 @@
offset = 0.0
data = dict((field, (np.random.random(ndims) - offset) * peak_value)
for field in fields)
- ug = load_uniform_grid(data, ndims, 1.0)
+ ug = load_uniform_grid(data, ndims, 1.0, nprocs = nprocs)
return ug
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/utilities/kdtree/__init__.py
--- a/yt/utilities/kdtree/__init__.py
+++ b/yt/utilities/kdtree/__init__.py
@@ -1,1 +0,0 @@
-from fKDpy import *
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/utilities/kdtree/api.py
--- /dev/null
+++ b/yt/utilities/kdtree/api.py
@@ -0,0 +1,9 @@
+from fKDpy import \
+ chainHOP_tags_dens, \
+ create_tree, \
+ fKD, \
+ find_nn_nearest_neighbors, \
+ free_tree, \
+ find_chunk_nearest_neighbors
+
+
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/utilities/kdtree/test.py
--- a/yt/utilities/kdtree/test.py
+++ /dev/null
@@ -1,58 +0,0 @@
-from Forthon import *
-from fKDpy import *
-import numpy,random
-
-n = 32768
-
-
-fKD.tags = fzeros((64),'i')
-fKD.dist = fzeros((64),'d')
-fKD.pos = fzeros((3,n),'d')
-fKD.nn = 64
-fKD.nparts = n
-fKD.sort = True
-fKD.rearrange = True
-fKD.qv = numpy.array([16./32, 16./32, 16./32])
-
-fp = open('parts.txt','r')
-xpos = []
-ypos = []
-zpos = []
-line = fp.readline()
-while line:
- line = line.split()
- xpos.append(float(line[0]))
- ypos.append(float(line[1]))
- zpos.append(float(line[2]))
- line= fp.readline()
-
-fp.close()
-
-
-for k in range(32):
- for j in range(32):
- for i in range(32):
- fKD.pos[0][i + j*32 + k*1024] = float(i)/32 + 1./64 + 0.0001*random.random()
- fKD.pos[1][i + j*32 + k*1024] = float(j)/32 + 1./64 + 0.0001*random.random()
- fKD.pos[2][i + j*32 + k*1024] = float(k)/32 + 1./64 + 0.0001*random.random()
-
-
-
-#print fKD.pos[0][0],fKD.pos[1][0],fKD.pos[2][0]
-
-create_tree()
-
-
-find_nn_nearest_neighbors()
-
-#print 'next'
-
-#fKD.qv = numpy.array([0., 0., 0.])
-
-#find_nn_nearest_neighbors()
-
-
-#print (fKD.tags - 1)
-#print fKD.dist
-
-free_tree()
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/utilities/tests/test_kdtrees.py
--- /dev/null
+++ b/yt/utilities/tests/test_kdtrees.py
@@ -0,0 +1,93 @@
+"""
+Unit test the kD trees in yt.
+
+Author: Stephen Skory <s at skory.us>
+Affiliation: U of Colorado
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2008-2011 Stephen Skory. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from yt.testing import *
+
+try:
+ from yt.utilities.kdtree.api import *
+except ImportError:
+ mylog.debug("The Fortran kD-Tree did not import correctly.")
+
+from yt.utilities.spatial import cKDTree
+
+def setup():
+ pass
+
+def test_fortran_tree():
+ r"""This test makes sure that the fortran kdtree is finding the correct
+ nearest neighbors.
+ """
+ # Four points.
+ try:
+ fKD.pos = np.empty((3, 4), dtype='float64', order='F')
+ except NameError:
+ return
+ # Make four points by hand that, in particular, will allow us to test
+ # the periodicity of the kdtree.
+ points = np.array([0.01, 0.5, 0.98, 0.99])
+ fKD.pos[0, :] = points
+ fKD.pos[1, :] = points
+ fKD.pos[2, :] = points
+ fKD.qv = np.empty(3, dtype='float64')
+ fKD.dist = np.empty(4, dtype='float64')
+ fKD.tags = np.empty(4, dtype='int64')
+ fKD.nn = 4
+ fKD.sort = True
+ create_tree(0)
+ # Now we check to make sure that we find the correct nearest neighbors,
+ # which get stored in dist and tags.
+ fKD.qv[:] = 0.999
+ find_nn_nearest_neighbors()
+ # Fix fortran counting.
+ fKD.tags -= 1
+ # Clean up before the tests.
+ free_tree(0)
+ # What the answers should be.
+ dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
+ tags = np.array([3, 0, 2, 1], dtype='int64')
+ assert_array_almost_equal(fKD.dist, dist)
+ assert_array_equal(fKD.tags, tags)
+
+def test_cython_tree():
+ r"""This test makes sure that the cython kdtree is finding the correct
+ nearest neighbors.
+ """
+ # Four points.
+ pos = np.empty((4, 3), dtype='float64')
+ # Make four points by hand that, in particular, will allow us to test
+ # the periodicity of the kdtree.
+ points = np.array([0.01, 0.5, 0.98, 0.99])
+ pos[:, 0] = points
+ pos[:, 1] = points
+ pos[:, 2] = points
+ kdtree = cKDTree(pos, leafsize = 2)
+ qv = np.array([0.999]*3)
+ res = kdtree.query(qv, 4, period=[1.,1.,1])
+ # What the answers should be.
+ dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
+ tags = np.array([3, 0, 2, 1], dtype='int64')
+ assert_array_almost_equal(res[0], dist)
+ assert_array_equal(res[1], tags)
+
diff -r 6b249ecbf0e6c643d2054fef8cf5c6657c740b55 -r ab186e76a23ad019537af4b9b3e05bac62c3284e yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -364,39 +364,30 @@
class StreamlineCallback(PlotCallback):
_type_name = "streamlines"
- def __init__(self, field_x, field_y, factor=6.0, nx=16, ny=16,
- xstart=(0,1), ystart=(0,1), nsample=256,
- start_at_xedge=False, start_at_yedge=False,
- plot_args=None):
+ def __init__(self, field_x, field_y, factor = 16,
+ density = 1, arrowsize = 1, arrowstyle = None,
+ color = None, normalize = False):
"""
- annotate_streamlines(field_x, field_y, factor=6.0, nx=16, ny=16,
- xstart=(0,1), ystart=(0,1), nsample=256,
- start_at_xedge=False, start_at_yedge=False,
- plot_args=None):
+ annotate_streamlines(field_x, field_y, factor = 16, density = 1,
+ arrowsize = 1, arrowstyle = None,
+ color = None, normalize = False):
Add streamlines to any plot, using the *field_x* and *field_y*
- from the associated data, using *nx* and *ny* starting points
- that are bounded by *xstart* and *ystart*. To begin
- streamlines from the left edge of the plot, set
- *start_at_xedge* to True; for the bottom edge, use
- *start_at_yedge*. A line with the qmean vector magnitude will
- cover 1.0/*factor* of the image.
+ from the associated data, skipping every *factor* datapoints like
+ 'quiver'. *density* is the index of the amount of the streamlines.
"""
PlotCallback.__init__(self)
self.field_x = field_x
self.field_y = field_y
- self.xstart = xstart
- self.ystart = ystart
- self.nsample = nsample
+ self.bv_x = self.bv_y = 0
self.factor = factor
- if start_at_xedge:
- self.data_size = (1,ny)
- elif start_at_yedge:
- self.data_size = (nx,1)
- else:
- self.data_size = (nx,ny)
- if plot_args is None: plot_args = {'color':'k', 'linestyle':'-'}
- self.plot_args = plot_args
+ self.dens = density
+ self.arrowsize = arrowsize
+ if arrowstyle is None : arrowstyle='-|>'
+ self.arrowstyle = arrowstyle
+ if color is None : color = "#000000"
+ self.color = color
+ self.normalize = normalize
def __call__(self, plot):
x0, x1 = plot.xlim
@@ -404,43 +395,31 @@
xx0, xx1 = plot._axes.get_xlim()
yy0, yy1 = plot._axes.get_ylim()
plot._axes.hold(True)
- nx = plot.image._A.shape[0]
- ny = plot.image._A.shape[1]
+ nx = plot.image._A.shape[0] / self.factor
+ ny = plot.image._A.shape[1] / self.factor
pixX = _MPL.Pixelize(plot.data['px'],
plot.data['py'],
plot.data['pdx'],
plot.data['pdy'],
- plot.data[self.field_x],
+ plot.data[self.field_x] - self.bv_x,
int(nx), int(ny),
- (x0, x1, y0, y1),)
+ (x0, x1, y0, y1),).transpose()
pixY = _MPL.Pixelize(plot.data['px'],
plot.data['py'],
plot.data['pdx'],
plot.data['pdy'],
- plot.data[self.field_y],
+ plot.data[self.field_y] - self.bv_y,
int(nx), int(ny),
- (x0, x1, y0, y1),)
- r0 = np.mgrid[self.xstart[0]*nx:self.xstart[1]*nx:self.data_size[0]*1j,
- self.ystart[0]*ny:self.ystart[1]*ny:self.data_size[1]*1j]
- lines = np.zeros((self.nsample, 2, self.data_size[0], self.data_size[1]))
- lines[0,:,:,:] = r0
- mag = np.sqrt(pixX**2 + pixY**2)
- scale = np.sqrt(nx*ny) / (self.factor * mag.mean())
- dt = 1.0 / (self.nsample-1)
- for i in range(1,self.nsample):
- xt = lines[i-1,0,:,:]
- yt = lines[i-1,1,:,:]
- ix = np.maximum(np.minimum((xt).astype('int'), nx-1), 0)
- iy = np.maximum(np.minimum((yt).astype('int'), ny-1), 0)
- lines[i,0,:,:] = xt + dt * pixX[ix,iy] * scale
- lines[i,1,:,:] = yt + dt * pixY[ix,iy] * scale
- # scale into data units
- lines[:,0,:,:] = lines[:,0,:,:] * (xx1 - xx0) / nx + xx0
- lines[:,1,:,:] = lines[:,1,:,:] * (yy1 - yy0) / ny + yy0
- for i in range(self.data_size[0]):
- for j in range(self.data_size[1]):
- plot._axes.plot(lines[:,0,i,j], lines[:,1,i,j],
- **self.plot_args)
+ (x0, x1, y0, y1),).transpose()
+ X,Y = (na.linspace(xx0,xx1,nx,endpoint=True),
+ na.linspace(yy0,yy1,ny,endpoint=True))
+ if self.normalize:
+ nn = na.sqrt(pixX**2 + pixY**2)
+ pixX /= nn
+ pixY /= nn
+ plot._axes.streamplot(X,Y, pixX, pixY, density=self.dens,
+ arrowsize=self.arrowsize, arrowstyle=self.arrowstyle,
+ color=self.color, norm=self.normalize)
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
plot._axes.hold(False)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/91ffdf886339/
changeset: 91ffdf886339
branch: yt
user: ngoldbaum
date: 2012-10-16 01:06:32
summary: Adding tests for the coordinate conversion code.
affected #: 2 files
diff -r ab186e76a23ad019537af4b9b3e05bac62c3284e -r 91ffdf8863397a75a1b01134f689ce36e139af03 yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -26,7 +26,7 @@
from yt.funcs import *
from numpy.testing import assert_array_equal, assert_almost_equal, \
assert_approx_equal, assert_array_almost_equal, assert_equal, \
- assert_string_equal
+ assert_array_less, assert_string_equal
def assert_rel_equal(a1, a2, decimels):
return assert_almost_equal(a1/a2, 1.0, decimels)
@@ -139,11 +139,16 @@
ndims = [ndims, ndims, ndims]
else:
assert(len(ndims) == 3)
- if negative:
- offset = 0.5
- else:
- offset = 0.0
+ if not iterable(negative):
+ negative = [negative for f in fields]
+ assert(len(fields) == len(negative))
+ offsets = []
+ for n in negative:
+ if n:
+ offsets.append(0.5)
+ else:
+ offsets.append(0.0)
data = dict((field, (np.random.random(ndims) - offset) * peak_value)
- for field in fields)
+ for field,offset in zip(fields,offsets))
ug = load_uniform_grid(data, ndims, 1.0, nprocs = nprocs)
return ug
diff -r ab186e76a23ad019537af4b9b3e05bac62c3284e -r 91ffdf8863397a75a1b01134f689ce36e139af03 yt/utilities/math_utils.py
--- a/yt/utilities/math_utils.py
+++ b/yt/utilities/math_utils.py
@@ -717,7 +717,7 @@
tile_shape = list(coords.shape)[:-1] + [1]
Jx = np.tile(xprime,tile_shape)
Jy = np.tile(yprime,tile_shape)
-
+
Px = np.sum(Jx*coords,axis=-1)
Py = np.sum(Jy*coords,axis=-1)
@@ -802,8 +802,6 @@
def get_sph_phi_component(vectors, phi, normal):
# The phi component of a vector is the vector dotted with phihat
- phi = get_sph_phi(coords, normal)
-
(xprime, yprime, zprime) = get_ortho_basis(normal)
tile_shape = list(vectors.shape)[:-1] + [1]
@@ -817,18 +815,15 @@
def get_sph_theta_component(vectors, theta, phi, normal):
# The theta component of a vector is the vector dotted with thetahat
- theta = get_sph_theta(coords, normal)
- phi = get_sph_phi(coords, normal)
-
(xprime, yprime, zprime) = get_ortho_basis(normal)
tile_shape = list(vectors.shape)[:-1] + [1]
Jx = np.tile(xprime,tile_shape)
Jy = np.tile(yprime,tile_shape)
Jz = np.tile(zprime,tile_shape)
-
+
thetahat = Jx*np.cos(theta)*np.cos(phi) + \
- Jy*np.cos(theta)*np.sin(theta) - \
+ Jy*np.cos(theta)*np.sin(phi) - \
Jz*np.sin(theta)
return np.sum(vectors*thetahat, axis=-1)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/018cc61ee15a/
changeset: 018cc61ee15a
branch: yt
user: ngoldbaum
date: 2012-10-16 01:07:48
summary: Forgot to hg add.
affected #: 2 files
diff -r 91ffdf8863397a75a1b01134f689ce36e139af03 -r 018cc61ee15ac835460585283838f1a06461ca60 yt/utilities/lib/tests/test_geometry_utils.py
--- /dev/null
+++ b/yt/utilities/lib/tests/test_geometry_utils.py
@@ -0,0 +1,30 @@
+from yt.testing import *
+from yt.utilities.lib import obtain_rvec, obtain_rv_vec
+
+_fields = ("Density", "x-velocity", "y-velocity", "z-velocity")
+
+def test_obtain_rvec():
+ pf = fake_random_pf(64, nprocs=8, fields=_fields,
+ negative = [False, True, True, True])
+
+ dd = pf.h.sphere((0.5,0.5,0.5), 0.2)
+
+ coords = obtain_rvec(dd)
+
+ r = np.sqrt(np.sum(coords*coords,axis=0))
+
+ assert_array_less(r.max(), 0.2)
+
+ assert_array_less(0.0, r.min())
+
+def test_obtain_rv_vec():
+ pf = fake_random_pf(64, nprocs=8, fields=_fields,
+ negative = [False, True, True, True])
+
+ dd = pf.h.all_data()
+
+ vels = obtain_rv_vec(dd)
+
+ assert_array_equal(vels[0,:], dd['x-velocity'])
+ assert_array_equal(vels[1,:], dd['y-velocity'])
+ assert_array_equal(vels[2,:], dd['z-velocity'])
diff -r 91ffdf8863397a75a1b01134f689ce36e139af03 -r 018cc61ee15ac835460585283838f1a06461ca60 yt/utilities/tests/test_coordinate_conversions.py
--- /dev/null
+++ b/yt/utilities/tests/test_coordinate_conversions.py
@@ -0,0 +1,128 @@
+from yt.testing import *
+from yt.utilities.math_utils import \
+ get_sph_r_component, \
+ get_sph_theta_component, \
+ get_sph_phi_component, \
+ get_cyl_r_component, \
+ get_cyl_z_component, \
+ get_cyl_theta_component, \
+ get_cyl_r, get_cyl_theta, \
+ get_cyl_z, get_sph_r, \
+ get_sph_theta, get_sph_phi
+
+# Randomly generated coordinates in the domain [[-1,1],[-1,1],-1,1]]
+coords = np.array([[-0.41503037, -0.22102472, -0.55774212],
+ [ 0.73828247, -0.17913899, 0.64076921],
+ [ 0.08922066, -0.94254844, -0.61774511],
+ [ 0.10173242, -0.95789145, 0.16294352],
+ [ 0.73186508, -0.3109153 , 0.75728738],
+ [ 0.8757989 , -0.41475119, -0.57039201],
+ [ 0.58040762, 0.81969082, 0.46759728],
+ [-0.89983356, -0.9853683 , -0.38355343]])
+
+def test_spherical_coordinate_conversion():
+ normal = [0, 0, 1]
+ real_r = [ 0.72950559, 0.99384957, 1.13047198, 0.97696269,
+ 1.09807968, 1.12445067, 1.10788685, 1.38843954]
+ real_theta = [ 2.44113629, 0.87012028, 2.14891444, 1.4032274 ,
+ 0.80979483, 2.10280198, 1.13507735, 1.85068416]
+ real_phi = [-2.65224483, -0.23804243, -1.47641858, -1.46498842,
+ -0.40172325, -0.4422801 , 0.95466734, -2.31085392]
+
+ calc_r = get_sph_r(coords)
+ calc_theta = get_sph_theta(coords, normal)
+ calc_phi = get_sph_phi(coords, normal)
+
+ assert_array_almost_equal(calc_r, real_r)
+ assert_array_almost_equal(calc_theta, real_theta)
+ assert_array_almost_equal(calc_phi, real_phi)
+
+ normal = [1, 0, 0]
+ real_theta = [ 2.17598842, 0.73347681, 1.49179079, 1.46647589,
+ 0.8412984 , 0.67793705, 1.0193883 , 2.27586987]
+ real_phi = [-0.37729951, -2.86898397, -0.99063518, -1.73928995,
+ -2.75201227,-0.62870527, 2.08920872, -1.19959244]
+
+ calc_theta = get_sph_theta(coords, normal)
+ calc_phi = get_sph_phi(coords, normal)
+
+ assert_array_almost_equal(calc_theta, real_theta)
+ assert_array_almost_equal(calc_phi, real_phi)
+
+def test_cylindrical_coordiante_conversion():
+ normal = [0, 0, 1]
+ real_r = [ 0.47021498, 0.75970506, 0.94676179, 0.96327853,
+ 0.79516968, 0.96904193, 1.00437346, 1.3344104 ]
+ real_theta = [-2.65224483, -0.23804243, -1.47641858, -1.46498842,
+ -0.40172325, -0.4422801 , 0.95466734, -2.31085392]
+ real_z = [-0.55774212, 0.64076921, -0.61774511, 0.16294352,
+ 0.75728738, -0.57039201, 0.46759728, -0.38355343]
+
+ calc_r = get_cyl_r(coords, normal)
+ calc_theta = get_cyl_theta(coords, normal)
+ calc_z = get_cyl_z(coords, normal)
+
+ assert_array_almost_equal(calc_r, real_r)
+ assert_array_almost_equal(calc_theta, real_theta)
+ assert_array_almost_equal(calc_z, real_z)
+
+ normal = [1, 0, 0]
+ real_r = [ 0.59994016, 0.66533898, 1.12694569, 0.97165149,
+ 0.81862843, 0.70524152, 0.94368441, 1.05738542]
+ real_theta = [-0.37729951, -2.86898397, -0.99063518, -1.73928995,
+ -2.75201227, -0.62870527, 2.08920872, -1.19959244]
+ real_z = [-0.41503037, 0.73828247, 0.08922066, 0.10173242,
+ 0.73186508, 0.8757989 , 0.58040762, -0.89983356]
+
+ calc_r = get_cyl_r(coords, normal)
+ calc_theta = get_cyl_theta(coords, normal)
+ calc_z = get_cyl_z(coords, normal)
+
+ assert_array_almost_equal(calc_r, real_r)
+ assert_array_almost_equal(calc_theta, real_theta)
+ assert_array_almost_equal(calc_z, real_z)
+
+def test_spherical_coordinate_projections():
+ normal = [0, 0, 1]
+ theta = get_sph_theta(coords, normal)
+ theta_pass = np.tile(theta, (3, 1)).T
+ phi = get_sph_phi(coords, normal)
+ phi_pass = np.tile(phi, (3, 1)).T
+ zero = np.tile(0,coords.shape[0])
+
+ # Purely radial field
+ vecs = np.array([np.sin(theta)*np.cos(phi), np.sin(theta)*np.sin(phi), np.cos(theta)]).T
+ assert_array_almost_equal(zero, get_sph_theta_component(vecs, theta_pass, phi_pass, normal))
+ assert_array_almost_equal(zero, get_sph_phi_component(vecs, phi_pass, normal))
+
+ # Purely toroidal field
+ vecs = np.array([-np.sin(phi), np.cos(phi), zero]).T
+ assert_array_almost_equal(zero, get_sph_theta_component(vecs, theta_pass, phi_pass, normal))
+ assert_array_almost_equal(zero, get_sph_r_component(vecs, theta_pass, phi_pass, normal))
+
+ # Purely poloidal field
+ vecs = np.array([np.cos(theta)*np.cos(phi), np.cos(theta)*np.sin(phi), -np.sin(theta)]).T
+ assert_array_almost_equal(zero, get_sph_phi_component(vecs, phi_pass, normal))
+ assert_array_almost_equal(zero, get_sph_r_component(vecs, theta_pass, phi_pass, normal))
+
+def test_cylindrical_coordinate_projections():
+ normal = [0, 0, 1]
+ theta = get_cyl_theta(coords, normal)
+ theta_pass = np.tile(theta, (3, 1)).T
+ z = get_cyl_z(coords, normal)
+ zero = np.tile(0, coords.shape[0])
+
+ # Purely radial field
+ vecs = np.array([np.cos(theta), np.sin(theta), zero]).T
+ assert_array_almost_equal(zero, get_cyl_theta_component(vecs, theta_pass, normal))
+ assert_array_almost_equal(zero, get_cyl_z_component(vecs, normal))
+
+ # Purely toroidal field
+ vecs = np.array([-np.sin(theta), np.cos(theta), zero]).T
+ assert_array_almost_equal(zero, get_cyl_z_component(vecs, normal))
+ assert_array_almost_equal(zero, get_cyl_r_component(vecs, theta_pass, normal))
+
+ # Purely z field
+ vecs = np.array([zero, zero, z]).T
+ assert_array_almost_equal(zero, get_cyl_theta_component(vecs, theta_pass, normal))
+ assert_array_almost_equal(zero, get_cyl_r_component(vecs, theta_pass, normal))
https://bitbucket.org/yt_analysis/yt-3.0/changeset/fbb264f8e6e8/
changeset: fbb264f8e6e8
branch: yt
user: brittonsmith
date: 2012-08-03 19:59:35
summary: Made sure bad halo profiler output files are removed instead of trying to
append to them.
affected #: 1 file
diff -r 018cc61ee15ac835460585283838f1a06461ca60 -r fbb264f8e6e827f47fc2f865908b4a5877d41816 yt/analysis_modules/halo_profiler/multi_halo_profiler.py
--- a/yt/analysis_modules/halo_profiler/multi_halo_profiler.py
+++ b/yt/analysis_modules/halo_profiler/multi_halo_profiler.py
@@ -606,6 +606,7 @@
if newProfile:
mylog.info("Writing halo %d" % halo['id'])
+ if os.path.exists(filename): os.remove(filename)
if filename.endswith('.h5'):
profile.write_out_h5(filename)
else:
https://bitbucket.org/yt_analysis/yt-3.0/changeset/075253179b15/
changeset: 075253179b15
branch: yt
user: MatthewTurk
date: 2012-10-16 03:03:42
summary: Adding fixes for field datatypes in the geometry_utils
affected #: 1 file
diff -r fbb264f8e6e827f47fc2f865908b4a5877d41816 -r 075253179b15993fbc59c1ee05c4fbe6dce1e615 yt/utilities/lib/geometry_utils.pyx
--- a/yt/utilities/lib/geometry_utils.pyx
+++ b/yt/utilities/lib/geometry_utils.pyx
@@ -360,9 +360,9 @@
bv[0] = bulk_velocity[0]; bv[1] = bulk_velocity[1]; bv[2] = bulk_velocity[2]
if len(data['x-velocity'].shape) == 1:
# One dimensional data
- vxf = data['x-velocity']
- vyf = data['y-velocity']
- vzf = data['z-velocity']
+ vxf = data['x-velocity'].astype("float64")
+ vyf = data['y-velocity'].astype("float64")
+ vzf = data['z-velocity'].astype("float64")
rvf = np.empty((3, vxf.shape[0]), 'float64')
for i in range(vxf.shape[0]):
rvf[0, i] = vxf[i] - bv[0]
@@ -371,9 +371,9 @@
return rvf
else:
# Three dimensional data
- vxg = data['x']
- vyg = data['y']
- vzg = data['z']
+ vxg = data['x-velocity'].astype("float64")
+ vyg = data['y-velocity'].astype("float64")
+ vzg = data['z-velocity'].astype("float64")
rvg = np.empty((3, vxg.shape[0], vxg.shape[1], vxg.shape[2]), 'float64')
for i in range(vxg.shape[0]):
for j in range(vxg.shape[1]):
https://bitbucket.org/yt_analysis/yt-3.0/changeset/36a7c57aa39c/
changeset: 36a7c57aa39c
branch: yt
user: ngoldbaum
date: 2012-10-16 03:15:52
summary: Bugfix for VelocityMagnitude
affected #: 1 file
diff -r 075253179b15993fbc59c1ee05c4fbe6dce1e615 -r 36a7c57aa39c8202c9df7f4deab897890ad5d736 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -191,8 +191,8 @@
def _VelocityMagnitude(field, data):
"""M{|v|}"""
- velocities = obtain_rv_vec(data).transpose()
- return np.sqrt(np.sum(velocities**2,axis=-1))
+ velocities = obtain_rv_vec(data)
+ return np.sqrt(np.sum(velocities**2,axis=0))
add_field("VelocityMagnitude", function=_VelocityMagnitude,
take_log=False, units=r"\rm{cm}/\rm{s}")
https://bitbucket.org/yt_analysis/yt-3.0/changeset/529288f3186b/
changeset: 529288f3186b
branch: yt
user: ngoldbaum
date: 2012-10-16 03:24:13
summary: Fixing a bug in the definition of VelocityMagnitude.
affected #: 1 file
diff -r 36a7c57aa39c8202c9df7f4deab897890ad5d736 -r 529288f3186b70dc06a2f1360e9b2e94d7a09fe9 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -241,7 +241,7 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = obtain_rvec(data).transepose()
+ coords = obtain_rvec(data).transpose()
return get_sph_theta(coords, normal)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/d23fa50f9c18/
changeset: d23fa50f9c18
branch: yt
user: xarthisius
date: 2012-10-16 17:45:30
summary: [decompose] don't rely on numpy's array_split, explicitly calculate array chunks instead
affected #: 1 file
diff -r 529288f3186b70dc06a2f1360e9b2e94d7a09fe9 -r d23fa50f9c18c1aceee3f2eb64d74cdbfaf1a1cb yt/utilities/decompose.py
--- a/yt/utilities/decompose.py
+++ b/yt/utilities/decompose.py
@@ -134,13 +134,17 @@
def split_array(tab, psize):
- """ Split array into px*py*pz subarrays using internal numpy routine. """
- temp = [np.array_split(array, psize[1], axis=1)
- for array in np.array_split(tab, psize[2], axis=2)]
- temp = [item for sublist in temp for item in sublist]
- temp = [np.array_split(array, psize[0], axis=0) for array in temp]
- temp = [item for sublist in temp for item in sublist]
- return temp
+ """ Split array into px*py*pz subarrays. """
+ n_d = np.array(tab.shape, dtype=np.int64)
+ slices = []
+ for i in range(psize[0]):
+ for j in range(psize[1]):
+ for k in range(psize[2]):
+ pc = np.array((i, j, k), dtype=np.int64)
+ le = n_d * pc / psize
+ re = n_d * (pc + np.ones(3, dtype=np.int64)) / psize
+ slices.append(np.s_[le[0]:re[0], le[1]:re[1], le[2]:re[2]] )
+ return [tab[sl] for sl in slices]
if __name__ == "__main__":
https://bitbucket.org/yt_analysis/yt-3.0/changeset/caca310b61f1/
changeset: caca310b61f1
branch: yt
user: xarthisius
date: 2012-10-16 17:46:29
summary: [decompose] improve evaluation of domain decomposition for non 3d case
affected #: 1 file
diff -r d23fa50f9c18c1aceee3f2eb64d74cdbfaf1a1cb -r caca310b61f1983fe888bd24a5f4041ffe111318 yt/utilities/decompose.py
--- a/yt/utilities/decompose.py
+++ b/yt/utilities/decompose.py
@@ -68,9 +68,11 @@
def evaluate_domain_decomposition(n_d, pieces, ldom):
""" Evaluate longest to shortest edge ratio
BEWARE: lot's of magic here """
- ideal_bsize = 3.0 * (pieces * np.product(n_d) ** 2) ** (1.0 / 3.0)
- bsize = int(np.sum(
- ldom / np.array(n_d, dtype=np.float64) * np.product(n_d)))
+ eff_dim = (n_d > 1).sum()
+ ideal_bsize = eff_dim * (pieces * np.product(n_d) ** (eff_dim-1)) ** (1.0 / eff_dim)
+ mask = np.where(n_d > 1)
+ nd = np.array(n_d, dtype=np.float64)[mask]
+ bsize = int(np.sum(ldom[mask] / nd * np.product(nd)))
load_balance = float(np.product(n_d)) / \
(float(pieces) * np.product((n_d - 1) / ldom + 1))
https://bitbucket.org/yt_analysis/yt-3.0/changeset/d32225d2d84c/
changeset: d32225d2d84c
branch: yt
user: xarthisius
date: 2012-10-16 18:48:37
summary: [decompose] add unit tests, pep8
affected #: 2 files
diff -r caca310b61f1983fe888bd24a5f4041ffe111318 -r d32225d2d84cbb00ee3948e9c117f57ba4d73171 yt/utilities/decompose.py
--- a/yt/utilities/decompose.py
+++ b/yt/utilities/decompose.py
@@ -69,7 +69,8 @@
""" Evaluate longest to shortest edge ratio
BEWARE: lot's of magic here """
eff_dim = (n_d > 1).sum()
- ideal_bsize = eff_dim * (pieces * np.product(n_d) ** (eff_dim-1)) ** (1.0 / eff_dim)
+ ideal_bsize = eff_dim * (pieces * np.product(n_d) ** (eff_dim - 1)
+ ) ** (1.0 / eff_dim)
mask = np.where(n_d > 1)
nd = np.array(n_d, dtype=np.float64)[mask]
bsize = int(np.sum(ldom[mask] / nd * np.product(nd)))
@@ -143,20 +144,7 @@
for j in range(psize[1]):
for k in range(psize[2]):
pc = np.array((i, j, k), dtype=np.int64)
- le = n_d * pc / psize
+ le = n_d * pc / psize
re = n_d * (pc + np.ones(3, dtype=np.int64)) / psize
- slices.append(np.s_[le[0]:re[0], le[1]:re[1], le[2]:re[2]] )
+ slices.append(np.s_[le[0]:re[0], le[1]:re[1], le[2]:re[2]])
return [tab[sl] for sl in slices]
-
-
-if __name__ == "__main__":
-
- NPROC = 12
- ARRAY = np.zeros((128, 128, 129))
- BBOX = np.array([[0., 1.0], [-1.5, 1.5], [1.0, 2.5]])
-
- PROCS = get_psize(np.array(ARRAY.shape), NPROC)
- LE, RE, DATA = decompose_array(ARRAY, PROCS, BBOX)
-
- for idx in range(NPROC):
- print LE[idx, :], RE[idx, :], DATA[idx].shape
diff -r caca310b61f1983fe888bd24a5f4041ffe111318 -r d32225d2d84cbb00ee3948e9c117f57ba4d73171 yt/utilities/tests/test_decompose.py
--- /dev/null
+++ b/yt/utilities/tests/test_decompose.py
@@ -0,0 +1,93 @@
+"""
+Test suite for cartesian domain decomposition.
+
+Author: Kacper Kowalik <xarthisius.kk at gmail.com>
+Affiliation: CA UMK
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Kacper Kowalik. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from yt.testing import *
+import yt.utilities.decompose as dec
+
+
+def setup():
+ pass
+
+
+def test_psize_2d():
+ procs = dec.get_psize(np.array([5, 1, 7]), 6)
+ assert_array_equal(procs, np.array([3, 1, 2]))
+ procs = dec.get_psize(np.array([1, 7, 5]), 6)
+ assert_array_equal(procs, np.array([1, 2, 3]))
+ procs = dec.get_psize(np.array([7, 5, 1]), 6)
+ assert_array_equal(procs, np.array([2, 3, 1]))
+
+
+def test_psize_3d():
+ procs = dec.get_psize(np.array([33, 35, 37]), 12)
+ assert_array_equal(procs, np.array([3, 2, 2]))
+
+
+def test_decomposition_2d():
+ array = np.ones((7, 5, 1))
+ bbox = np.array([[-0.7, 0.0], [1.5, 2.0], [0.0, 0.7]])
+ ledge, redge, data = dec.decompose_array(array, np.array([2, 3, 1]), bbox)
+
+ gold_le = np.array([
+ [-0.7, 1.5, 0.0], [-0.7, 1.6, 0.0],
+ [-0.7, 1.8, 0.0], [-0.4, 1.5, 0.0],
+ [-0.4, 1.6, 0.0], [-0.4, 1.8, 0.0]
+ ])
+ assert_almost_equal(ledge, gold_le, 8)
+
+ gold_re = np.array(
+ [[-0.4, 1.6, 0.7], [-0.4, 1.8, 0.7],
+ [-0.4, 2.0, 0.7], [0.0, 1.6, 0.7],
+ [0.0, 1.8, 0.7], [0.0, 2.0, 0.7]]
+ )
+ assert_almost_equal(redge, gold_re, 8)
+
+
+def test_decomposition_3d():
+ array = np.ones((33, 35, 37))
+ bbox = np.array([[0., 1.0], [-1.5, 1.5], [1.0, 2.5]])
+
+ ledge, redge, data = dec.decompose_array(array, np.array([3, 2, 2]), bbox)
+ assert_array_equal(data[0].shape, np.array([11, 17, 18]))
+
+ gold_le = np.array(
+ [[0.00000, -1.50000, 1.00000], [0.00000, -1.50000, 1.72973],
+ [0.00000, -0.04286, 1.00000], [0.00000, -0.04286, 1.72973],
+ [0.33333, -1.50000, 1.00000], [0.33333, -1.50000, 1.72973],
+ [0.33333, -0.04286, 1.00000], [0.33333, -0.04286, 1.72973],
+ [0.66667, -1.50000, 1.00000], [0.66667, -1.50000, 1.72973],
+ [0.66667, -0.04286, 1.00000], [0.66667, -0.04286, 1.72973]]
+ )
+ assert_almost_equal(ledge, gold_le, 5)
+
+ gold_re = np.array(
+ [[0.33333, -0.04286, 1.72973], [0.33333, -0.04286, 2.50000],
+ [0.33333, 1.50000, 1.72973], [0.33333, 1.50000, 2.50000],
+ [0.66667, -0.04286, 1.72973], [0.66667, -0.04286, 2.50000],
+ [0.66667, 1.50000, 1.72973], [0.66667, 1.50000, 2.50000],
+ [1.00000, -0.04286, 1.72973], [1.00000, -0.04286, 2.50000],
+ [1.00000, 1.50000, 1.72973], [1.00000, 1.50000, 2.50000]]
+ )
+ assert_almost_equal(redge, gold_re, 5)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/5cd8e16ff5a6/
changeset: 5cd8e16ff5a6
branch: yt
user: xarthisius
date: 2012-10-16 18:54:44
summary: [decompose] cosmetics
affected #: 1 file
diff -r d32225d2d84cbb00ee3948e9c117f57ba4d73171 -r 5cd8e16ff5a60fce04c3f7692ab65dbf8efd3eb5 yt/utilities/decompose.py
--- a/yt/utilities/decompose.py
+++ b/yt/utilities/decompose.py
@@ -72,8 +72,8 @@
ideal_bsize = eff_dim * (pieces * np.product(n_d) ** (eff_dim - 1)
) ** (1.0 / eff_dim)
mask = np.where(n_d > 1)
- nd = np.array(n_d, dtype=np.float64)[mask]
- bsize = int(np.sum(ldom[mask] / nd * np.product(nd)))
+ nd_arr = np.array(n_d, dtype=np.float64)[mask]
+ bsize = int(np.sum(ldom[mask] / nd_arr * np.product(nd_arr)))
load_balance = float(np.product(n_d)) / \
(float(pieces) * np.product((n_d - 1) / ldom + 1))
@@ -143,8 +143,9 @@
for i in range(psize[0]):
for j in range(psize[1]):
for k in range(psize[2]):
- pc = np.array((i, j, k), dtype=np.int64)
- le = n_d * pc / psize
- re = n_d * (pc + np.ones(3, dtype=np.int64)) / psize
- slices.append(np.s_[le[0]:re[0], le[1]:re[1], le[2]:re[2]])
- return [tab[sl] for sl in slices]
+ piece = np.array((i, j, k), dtype=np.int64)
+ lei = n_d * piece / psize
+ rei = n_d * (piece + np.ones(3, dtype=np.int64)) / psize
+ slices.append(np.s_[lei[0]:rei[0], lei[1]:
+ rei[1], lei[2]:rei[2]])
+ return [tab[slc] for slc in slices]
https://bitbucket.org/yt_analysis/yt-3.0/changeset/ff017cd2c1a8/
changeset: ff017cd2c1a8
branch: yt
user: xarthisius
date: 2012-10-16 18:59:29
summary: [test_decompose] make pylint slightly more happy
affected #: 1 file
diff -r 5cd8e16ff5a60fce04c3f7692ab65dbf8efd3eb5 -r ff017cd2c1a8a85e5894d78b8bbf5745a84dc959 yt/utilities/tests/test_decompose.py
--- a/yt/utilities/tests/test_decompose.py
+++ b/yt/utilities/tests/test_decompose.py
@@ -23,7 +23,8 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
-from yt.testing import *
+from yt.testing import assert_array_equal, assert_almost_equal
+import numpy as np
import yt.utilities.decompose as dec
@@ -50,6 +51,8 @@
bbox = np.array([[-0.7, 0.0], [1.5, 2.0], [0.0, 0.7]])
ledge, redge, data = dec.decompose_array(array, np.array([2, 3, 1]), bbox)
+ assert_array_equal(data[1].shape, np.array([3, 2, 1]))
+
gold_le = np.array([
[-0.7, 1.5, 0.0], [-0.7, 1.6, 0.0],
[-0.7, 1.8, 0.0], [-0.4, 1.5, 0.0],
https://bitbucket.org/yt_analysis/yt-3.0/changeset/75eab6836b44/
changeset: 75eab6836b44
branch: yt
user: brittonsmith
date: 2012-10-16 22:54:02
summary: Manually preventing njobs from being anything other than -1 in
make_projections and adding a warning if it is not set that way.
affected #: 1 file
diff -r ff017cd2c1a8a85e5894d78b8bbf5745a84dc959 -r 75eab6836b445eb7fe75017d761b06ae63172310 yt/analysis_modules/halo_profiler/multi_halo_profiler.py
--- a/yt/analysis_modules/halo_profiler/multi_halo_profiler.py
+++ b/yt/analysis_modules/halo_profiler/multi_halo_profiler.py
@@ -718,7 +718,9 @@
Default=True.
njobs : int
The number of jobs over which to split the projections. Set
- to -1 so that each halo is done by a single processor.
+ to -1 so that each halo is done by a single processor. Halo
+ projections do not currently work in parallel, so this must
+ be set to -1.
Default: -1.
dynamic : bool
If True, distribute halos using a task queue. If False,
@@ -732,6 +734,12 @@
"""
+ # Halo projections cannot run in parallel because they are done by
+ # giving a data source to the projection object.
+ if njobs > 0:
+ mylog.warn("Halo projections cannot use more than one processor per halo, setting njobs to -1.")
+ njobs = -1
+
# Get list of halos for projecting.
if halo_list == 'filtered':
halo_projection_list = self.filtered_halos
https://bitbucket.org/yt_analysis/yt-3.0/changeset/b48d303b902a/
changeset: b48d303b902a
branch: yt
user: ngoldbaum
date: 2012-10-17 20:42:48
summary: Setting a default value for the 'normal' field parameter. Closes #451
affected #: 2 files
diff -r 529288f3186b70dc06a2f1360e9b2e94d7a09fe9 -r b48d303b902a305a82f9144a1b8778d3ec2729f8 yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -237,6 +237,7 @@
def __set_default_field_parameters(self):
self.set_field_parameter("center",np.zeros(3,dtype='float64'))
self.set_field_parameter("bulk_velocity",np.zeros(3,dtype='float64'))
+ self.set_field_parameter("normal",np.array([0,0,1],dtype='float64'))
def _set_center(self, center):
if center is None:
diff -r 529288f3186b70dc06a2f1360e9b2e94d7a09fe9 -r b48d303b902a305a82f9144a1b8778d3ec2729f8 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -876,8 +876,6 @@
def _RadialVelocity(field, data):
normal = data.get_field_parameter("normal")
- if normal == None:
- normal = [0,0,1]
velocities = obtain_rv_vec(data).transpose()
theta = np.tile(data['sph_theta'], (3, 1)).transpose()
phi = np.tile(data['sph_phi'], (3, 1)).transpose()
https://bitbucket.org/yt_analysis/yt-3.0/changeset/f603f7908bb9/
changeset: f603f7908bb9
branch: yt
user: ngoldbaum
date: 2012-10-17 20:43:48
summary: Merging.
affected #: 2 files
diff -r 75eab6836b445eb7fe75017d761b06ae63172310 -r f603f7908bb9c9a694932b7f500d5f732d60efb3 yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -237,6 +237,7 @@
def __set_default_field_parameters(self):
self.set_field_parameter("center",np.zeros(3,dtype='float64'))
self.set_field_parameter("bulk_velocity",np.zeros(3,dtype='float64'))
+ self.set_field_parameter("normal",np.array([0,0,1],dtype='float64'))
def _set_center(self, center):
if center is None:
diff -r 75eab6836b445eb7fe75017d761b06ae63172310 -r f603f7908bb9c9a694932b7f500d5f732d60efb3 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -876,8 +876,6 @@
def _RadialVelocity(field, data):
normal = data.get_field_parameter("normal")
- if normal == None:
- normal = [0,0,1]
velocities = obtain_rv_vec(data).transpose()
theta = np.tile(data['sph_theta'], (3, 1)).transpose()
phi = np.tile(data['sph_phi'], (3, 1)).transpose()
https://bitbucket.org/yt_analysis/yt-3.0/changeset/92038d70878e/
changeset: 92038d70878e
branch: yt-3.0
user: MatthewTurk
date: 2012-10-17 21:48:38
summary: Merging from yt branch
affected #: 38 files
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,3 @@
include distribute_setup.py
recursive-include yt/gui/reason/html *.html *.png *.ico *.js
-recursive-include yt *.pyx *.pxd *.hh *.h README*
+recursive-include yt *.pyx *.pxd *.hh *.h README* CREDITS FUNDING LICENSE
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -220,11 +220,24 @@
echo " * libncurses5-dev"
echo " * zip"
echo " * uuid-dev"
+ echo " * libfreetype6-dev"
+ echo " * tk-dev"
echo
echo "You can accomplish this by executing:"
echo
- echo "$ sudo apt-get install libssl-dev build-essential libncurses5 libncurses5-dev zip uuid-dev"
+ echo "$ sudo apt-get install libssl-dev build-essential libncurses5 libncurses5-dev zip uuid-dev libfreetype6-dev tk-dev"
echo
+ echo
+ echo " Additionally, if you want to put yt's lib dir in your LD_LIBRARY_PATH"
+ echo " so you can use yt without the activate script, you might "
+ echo " want to consider turning off LIBZ and FREETYPE in this"
+ echo " install script by editing this file and setting"
+ echo
+ echo " INST_ZLIB=0"
+ echo " INST_FTYPE=0"
+ echo
+ echo " to avoid conflicts with other command-line programs "
+ echo " (like eog and evince, for example)."
fi
if [ ! -z "${CFLAGS}" ]
then
@@ -400,7 +413,7 @@
echo '2c1933ab31246b4f4eba049d3288156e0a72f1730604e3ed7357849967cdd329e4647cf236c9442ecfb06d0aff03e6fc892a7ba2a5c1cf5c011b7ab9c619acec Cython-0.16.tar.gz' > Cython-0.16.tar.gz.sha512
echo '44eea803870a66ff0bab08d13a8b3388b5578ebc1c807d1d9dca0a93e6371e91b15d02917a00b3b20dc67abb5a21dabaf9b6e9257a561f85eeff2147ac73b478 PyX-0.11.1.tar.gz' > PyX-0.11.1.tar.gz.sha512
-echo '1a754d560bfa433f0960ab3b5a62edb5f291be98ec48cf4e5941fa5b84139e200b87a52efbbd6fa4a76d6feeff12439eed3e7a84db4421940d1bbb576f7a684e Python-2.7.2.tgz' > Python-2.7.2.tgz.sha512
+echo 'b981f8464575bb24c297631c87a3b9172312804a0fc14ce1fa7cb41ce2b0d2fd383cd1c816d6e10c36467d18bf9492d6faf557c81c04ff3b22debfa93f30ad0b Python-2.7.3.tgz' > Python-2.7.3.tgz.sha512
echo 'c017d3d59dd324ac91af0edc178c76b60a5f90fbb775cf843e39062f95bd846238f2c53705f8890ed3f34bc0e6e75671a73d13875eb0287d6201cb45f0a2d338 bzip2-1.0.5.tar.gz' > bzip2-1.0.5.tar.gz.sha512
echo 'a296dfcaef7e853e58eed4e24b37c4fa29cfc6ac688def048480f4bb384b9e37ca447faf96eec7b378fd764ba291713f03ac464581d62275e28eb2ec99110ab6 reason-js-20120623.zip' > reason-js-20120623.zip.sha512
echo 'b519218f93946400326e9b656669269ecb3e5232b944e18fbc3eadc4fe2b56244d68aae56d6f69042b4c87c58c881ee2aaa279561ea0f0f48d5842155f4de9de freetype-2.4.4.tar.gz' > freetype-2.4.4.tar.gz.sha512
@@ -429,7 +442,7 @@
[ $INST_0MQ -eq 1 ] && get_ytproject zeromq-2.2.0.tar.gz
[ $INST_0MQ -eq 1 ] && get_ytproject pyzmq-2.1.11.tar.gz
[ $INST_0MQ -eq 1 ] && get_ytproject tornado-2.2.tar.gz
-get_ytproject Python-2.7.2.tgz
+get_ytproject Python-2.7.3.tgz
get_ytproject numpy-1.6.1.tar.gz
get_ytproject matplotlib-1.1.0.tar.gz
get_ytproject mercurial-2.2.2.tar.gz
@@ -554,11 +567,11 @@
fi
fi
-if [ ! -e Python-2.7.2/done ]
+if [ ! -e Python-2.7.3/done ]
then
echo "Installing Python. This may take a while, but don't worry. YT loves you."
- [ ! -e Python-2.7.2 ] && tar xfz Python-2.7.2.tgz
- cd Python-2.7.2
+ [ ! -e Python-2.7.3 ] && tar xfz Python-2.7.3.tgz
+ cd Python-2.7.3
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 nose.cfg
--- /dev/null
+++ b/nose.cfg
@@ -0,0 +1,4 @@
+[nosetests]
+detailed-errors=1
+where=yt
+exclude=answer_testing
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 setup.cfg
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,3 +1,9 @@
[egg_info]
#tag_build = .dev
#tag_svn_revision = 1
+
+[nosetests]
+detailed-errors=1
+where=yt
+exclude=answer_testing
+with-xunit=1
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
--- a/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
+++ b/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
@@ -31,7 +31,7 @@
from yt.funcs import *
from yt.utilities.performance_counters import yt_counters, time_function
try:
- from yt.utilities.kdtree import \
+ from yt.utilities.kdtree.api import \
chainHOP_tags_dens, \
create_tree, fKD, find_nn_nearest_neighbors, \
free_tree, find_chunk_nearest_neighbors
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/analysis_modules/halo_profiler/multi_halo_profiler.py
--- a/yt/analysis_modules/halo_profiler/multi_halo_profiler.py
+++ b/yt/analysis_modules/halo_profiler/multi_halo_profiler.py
@@ -605,6 +605,7 @@
if newProfile:
mylog.info("Writing halo %d" % halo['id'])
+ if os.path.exists(filename): os.remove(filename)
if filename.endswith('.h5'):
profile.write_out_h5(filename)
else:
@@ -715,7 +716,9 @@
Default=True.
njobs : int
The number of jobs over which to split the projections. Set
- to -1 so that each halo is done by a single processor.
+ to -1 so that each halo is done by a single processor. Halo
+ projections do not currently work in parallel, so this must
+ be set to -1.
Default: -1.
dynamic : bool
If True, distribute halos using a task queue. If False,
@@ -729,6 +732,12 @@
"""
+ # Halo projections cannot run in parallel because they are done by
+ # giving a data source to the projection object.
+ if njobs > 0:
+ mylog.warn("Halo projections cannot use more than one processor per halo, setting njobs to -1.")
+ njobs = -1
+
# Get list of halos for projecting.
if halo_list == 'filtered':
halo_projection_list = self.filtered_halos
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/analysis_modules/two_point_functions/two_point_functions.py
--- a/yt/analysis_modules/two_point_functions/two_point_functions.py
+++ b/yt/analysis_modules/two_point_functions/two_point_functions.py
@@ -30,7 +30,7 @@
from yt.utilities.parallel_tools.parallel_analysis_interface import ParallelAnalysisInterface, parallel_blocking_call, parallel_root_only
try:
- from yt.utilities.kdtree import *
+ from yt.utilities.kdtree.api import *
except ImportError:
mylog.debug("The Fortran kD-Tree did not import correctly.")
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/config.py
--- a/yt/config.py
+++ b/yt/config.py
@@ -38,6 +38,7 @@
inline = 'False',
numthreads = '-1',
__withinreason = 'False',
+ __withintesting = 'False',
__parallel = 'False',
__global_parallel_rank = '0',
__global_parallel_size = '1',
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/data_objects/api.py
--- a/yt/data_objects/api.py
+++ b/yt/data_objects/api.py
@@ -62,6 +62,9 @@
quantity_info, \
add_quantity
+from image_array import \
+ ImageArray
+
from field_info_container import \
FieldInfoContainer, \
FieldInfo, \
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/data_objects/construction_data_containers.py
--- a/yt/data_objects/construction_data_containers.py
+++ b/yt/data_objects/construction_data_containers.py
@@ -349,6 +349,18 @@
ilevel = chunk.ires
tree.add_chunk_to_tree(i1, i2, ilevel, v, w)
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Projection')
+ return pw
+
class YTOverlapProjBase(YTSelectionContainer2D):
_top_node = "/Projections"
_key_fields = YTSelectionContainer2D._key_fields + ['weight_field']
@@ -728,7 +740,7 @@
class YTCoveringGridBase(YTSelectionContainer3D):
_spatial = True
_type_name = "covering_grid"
- _con_args = ('level', 'left_edge', 'right_edge', 'ActiveDimensions')
+ _con_args = ('level', 'left_edge', 'ActiveDimensions')
def __init__(self, level, left_edge, dims, fields = None,
pf = None, num_ghost_zones = 0, use_pbar = True, **kwargs):
"""A 3D region with all data extracted to a single, specified
@@ -755,8 +767,9 @@
fields=fields, pf=pf, **kwargs)
self.left_edge = np.array(left_edge)
self.level = level
- self.dds = self.pf.h.select_grids(self.level)[0].dds.copy()
- self.ActiveDimensions = np.array(dims,dtype='int32')
+ rdx = self.pf.domain_dimensions*self.pf.refine_by**level
+ self.dds = self.pf.domain_width/rdx.astype("float64")
+ self.ActiveDimensions = np.array(dims, dtype='int32')
self.right_edge = self.left_edge + self.ActiveDimensions*self.dds
self._num_ghost_zones = num_ghost_zones
self._use_pbar = use_pbar
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -122,6 +122,7 @@
self.field_parameters = {}
self.set_field_parameter("center",np.zeros(3,dtype='float64'))
self.set_field_parameter("bulk_velocity",np.zeros(3,dtype='float64'))
+ self.set_field_parameter("normal",np.array([0,0,1],dtype='float64'))
def _set_center(self, center):
if center is None:
@@ -537,6 +538,23 @@
def _convert_field_name(self, field):
return field
+ def _get_pw(self, fields, center, width, origin, axes_unit, plot_type):
+ axis = self.axis
+ if fields == None:
+ if self.fields == None:
+ raise SyntaxError("The fields keyword argument must be set")
+ else:
+ self.fields = ensure_list(fields)
+ from yt.visualization.plot_window import \
+ GetBoundsAndCenter, PWViewerMPL
+ from yt.visualization.fixed_resolution import FixedResolutionBuffer
+ (bounds, center) = GetBoundsAndCenter(axis, center, width, self.pf)
+ pw = PWViewerMPL(self, bounds, origin=origin, frb_generator=FixedResolutionBuffer,
+ plot_type=plot_type)
+ pw.set_axes_unit(axes_unit)
+ return pw
+
+
def to_frb(self, width, resolution, center=None, height=None):
r"""This function returns a FixedResolutionBuffer generated from this
object.
@@ -603,26 +621,6 @@
frb = FixedResolutionBuffer(self, bounds, resolution)
return frb
- def to_pw(self):
- r"""Create a :class:`~yt.visualization.plot_window.PlotWindow` from this
- object.
-
- This is a bare-bones mechanism of creating a plot window from this
- object, which can then be moved around, zoomed, and on and on. All
- behavior of the plot window is relegated to that routine.
- """
- axis = self.axis
- center = self.get_field_parameter("center")
- if center is None:
- center = (self.pf.domain_right_edge
- + self.pf.domain_left_edge)/2.0
- width = (1.0, 'unitary')
- from yt.visualization.plot_window import \
- PWViewerMPL, GetBoundsAndCenter
- (bounds, center) = GetBoundsAndCenter(axis, center, width, self.pf)
- pw = PWViewerMPL(self, bounds)
- return pw
-
class YTSelectionContainer3D(YTSelectionContainer):
_key_fields = ['x','y','z','dx','dy','dz']
"""
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/data_objects/image_array.py
--- /dev/null
+++ b/yt/data_objects/image_array.py
@@ -0,0 +1,271 @@
+"""
+ImageArray Class
+
+Authors: Samuel Skillman <samskillman at gmail.com>
+Affiliation: University of Colorado at Boulder
+
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Samuel Skillman. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ """
+
+import numpy as np
+import h5py as h5
+from yt.visualization.image_writer import write_bitmap, write_image
+
+class ImageArray(np.ndarray):
+ r"""A custom Numpy ndarray used for images.
+
+ This differs from ndarray in that you can optionally specify an
+ info dictionary which is used later in saving, and can be accessed with
+ ImageArray.info.
+
+ Parameters
+ ----------
+ input_array: array_like
+ A numpy ndarray, or list.
+
+ Other Parameters
+ ----------------
+ info: dictionary
+ Contains information to be stored with image.
+
+ Returns
+ -------
+ obj: ImageArray object
+
+ Raises
+ ------
+ None
+
+ See Also
+ --------
+ numpy.ndarray : Inherits
+
+ Notes
+ -----
+
+ References
+ ----------
+
+ Examples
+ --------
+ These are written in doctest format, and should illustrate how to
+ use the function. Use the variables 'pf' for the parameter file, 'pc' for
+ a plot collection, 'c' for a center, and 'L' for a vector.
+
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.save('test_ImageArray')
+
+ Numpy ndarray documentation appended:
+
+ """
+ def __new__(cls, input_array, info=None):
+ # Input array is an already formed ndarray instance
+ # We first cast to be our class type
+ obj = np.asarray(input_array).view(cls)
+ # add the new attribute to the created instance
+ if info is None:
+ info = {}
+ obj.info = info
+ # Finally, we must return the newly created object:
+ return obj
+
+ def __array_finalize__(self, obj):
+ # see InfoArray.__array_finalize__ for comments
+ if obj is None: return
+ self.info = getattr(obj, 'info', None)
+
+ def write_hdf5(self, filename):
+ r"""Writes ImageArray to hdf5 file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Examples
+ --------
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_hdf5('test_ImageArray.h5')
+
+ """
+ array_name = self.info.get("name","image")
+
+ f = h5.File(filename)
+ if array_name in f.keys():
+ del f[array_name]
+ d = f.create_dataset(array_name, data=self)
+ for k, v in self.info.iteritems():
+ d.attrs.create(k, v)
+ f.close()
+
+ def write_png(self, filename, clip_ratio=None):
+ r"""Writes ImageArray to png file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Examples
+ --------
+
+ >>> im = np.zeros([64,128,3])
+ >>> for i in xrange(im.shape[0]):
+ >>> for k in xrange(im.shape[2]):
+ >>> im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_png('test_ImageArray.png')
+
+ """
+ if filename[-4:] != '.png':
+ filename += '.png'
+
+ if clip_ratio is not None:
+ return write_bitmap(self.swapaxes(0, 1), filename,
+ clip_ratio * self.std())
+ else:
+ return write_bitmap(self.swapaxes(0, 1), filename)
+
+ def write_image(self, filename, color_bounds=None, channel=None, cmap_name="algae", func=lambda x: x):
+ r"""Writes a single channel of the ImageArray to a png file.
+
+ Parameters
+ ----------
+ filename: string
+ Note filename not be modified.
+
+ Other Parameters
+ ----------------
+ channel: int
+ Which channel to write out as an image. Defaults to 0
+ cmap_name: string
+ Name of the colormap to be used.
+ color_bounds : tuple of floats, optional
+ The min and max to scale between. Outlying values will be clipped.
+ cmap_name : string, optional
+ An acceptable colormap. See either yt.visualization.color_maps or
+ http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
+ func : function, optional
+ A function to transform the buffer before applying a colormap.
+
+ Returns
+ -------
+ scaled_image : uint8 image that has been saved
+
+ Examples
+ --------
+
+ >>> im = np.zeros([64,128])
+ >>> for i in xrange(im.shape[0]):
+ >>> im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+
+ >>> myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ >>> 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ >>> 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ >>> im_arr = ImageArray(im, info=myinfo)
+ >>> im_arr.write_image('test_ImageArray.png')
+
+ """
+ if filename[-4:] != '.png':
+ filename += '.png'
+
+ if channel is None:
+ return write_image(self.swapaxes(0,1), filename,
+ color_bounds=color_bounds, cmap_name=cmap_name,
+ func=func)
+ else:
+ return write_image(self.swapaxes(0,1)[:,:,channel], filename,
+ color_bounds=color_bounds, cmap_name=cmap_name,
+ func=func)
+
+ def save(self, filename, png=True, hdf5=True):
+ """
+ Saves ImageArray.
+
+ Arguments:
+ filename: string
+ This should not contain the extension type (.png, .h5, ...)
+
+ Optional Arguments:
+ png: boolean, default True
+ Save to a png
+
+ hdf5: boolean, default True
+ Save to hdf5 file, including info dictionary as attributes.
+
+ """
+ if png:
+ if len(self.shape) > 2:
+ self.write_png("%s.png" % filename)
+ else:
+ self.write_image("%s.png" % filename)
+ if hdf5:
+ self.write_hdf5("%s.h5" % filename)
+
+ __doc__ += np.ndarray.__doc__
+
+if __name__ == "__main__":
+ im = np.zeros([64,128,3])
+ for i in xrange(im.shape[0]):
+ for k in xrange(im.shape[2]):
+ im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+
+ myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_3d_ImageArray')
+
+ im = np.zeros([64,128])
+ for i in xrange(im.shape[0]):
+ im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+
+ myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
+ 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
+ 'width':0.245, 'units':'cm', 'type':'rendering'}
+
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_2d_ImageArray')
+
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/data_objects/selection_data_containers.py
--- a/yt/data_objects/selection_data_containers.py
+++ b/yt/data_objects/selection_data_containers.py
@@ -284,6 +284,18 @@
def hub_upload(self):
self._mrep.upload()
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None,
+ origin='center-window'):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ pw = self._get_pw(fields, center, width, origin, axes_unit, 'Slice')
+ return pw
+
class YTCuttingPlaneBase(YTSelectionContainer2D):
_plane = None
_top_node = "/CuttingPlanes"
@@ -357,52 +369,6 @@
def normal(self):
return self._norm_vec
- def to_frb(self, width, resolution):
- r"""This function returns an ObliqueFixedResolutionBuffer generated
- from this object.
-
- An ObliqueFixedResolutionBuffer is an object that accepts a
- variable-resolution 2D object and transforms it into an NxM bitmap that
- can be plotted, examined or processed. This is a convenience function
- to return an FRB directly from an existing 2D data object. Unlike the
- corresponding to_frb function for other YTSelectionContainer2D objects, this does
- not accept a 'center' parameter as it is assumed to be centered at the
- center of the cutting plane.
-
- Parameters
- ----------
- width : width specifier
- This can either be a floating point value, in the native domain
- units of the simulation, or a tuple of the (value, unit) style.
- This will be the width of the FRB.
- resolution : int or tuple of ints
- The number of pixels on a side of the final FRB.
-
- Returns
- -------
- frb : :class:`~yt.visualization.fixed_resolution.ObliqueFixedResolutionBuffer`
- A fixed resolution buffer, which can be queried for fields.
-
- Examples
- --------
-
- >>> v, c = pf.h.find_max("Density")
- >>> sp = pf.h.sphere(c, (100.0, 'au'))
- >>> L = sp.quantities["AngularMomentumVector"]()
- >>> cutting = pf.h.cutting(L, c)
- >>> frb = cutting.to_frb( (1.0, 'pc'), 1024)
- >>> write_image(np.log10(frb["Density"]), 'density_1pc.png')
- """
- if iterable(width):
- w, u = width
- width = w/self.pf[u]
- if not iterable(resolution):
- resolution = (resolution, resolution)
- from yt.visualization.fixed_resolution import ObliqueFixedResolutionBuffer
- bounds = (-width/2.0, width/2.0, -width/2.0, width/2.0)
- frb = ObliqueFixedResolutionBuffer(self, bounds, resolution)
- return frb
-
def to_frb(self, width, resolution, height=None):
r"""This function returns an ObliqueFixedResolutionBuffer generated
from this object.
@@ -495,6 +461,83 @@
else:
raise KeyError(field)
+ def to_pw(self, fields=None, center='c', width=None, axes_unit=None):
+ r"""Create a :class:`~yt.visualization.plot_window.PWViewerMPL` from this
+ object.
+
+ This is a bare-bones mechanism of creating a plot window from this
+ object, which can then be moved around, zoomed, and on and on. All
+ behavior of the plot window is relegated to that routine.
+ """
+ normal = self.normal
+ center = self.center
+ if fields == None:
+ if self.fields == None:
+ raise SyntaxError("The fields keyword argument must be set")
+ else:
+ self.fields = ensure_list(fields)
+ from yt.visualization.plot_window import \
+ GetOffAxisBoundsAndCenter, PWViewerMPL
+ from yt.visualization.fixed_resolution import ObliqueFixedResolutionBuffer
+ (bounds, center_rot) = GetOffAxisBoundsAndCenter(normal, center, width, self.pf)
+ pw = PWViewerMPL(self, bounds, origin='center-window', periodic=False, oblique=True,
+ frb_generator=ObliqueFixedResolutionBuffer, plot_type='OffAxisSlice')
+ pw.set_axes_unit(axes_unit)
+ return pw
+
+ def to_frb(self, width, resolution, height=None):
+ r"""This function returns an ObliqueFixedResolutionBuffer generated
+ from this object.
+
+ An ObliqueFixedResolutionBuffer is an object that accepts a
+ variable-resolution 2D object and transforms it into an NxM bitmap that
+ can be plotted, examined or processed. This is a convenience function
+ to return an FRB directly from an existing 2D data object. Unlike the
+ corresponding to_frb function for other AMR2DData objects, this does
+ not accept a 'center' parameter as it is assumed to be centered at the
+ center of the cutting plane.
+
+ Parameters
+ ----------
+ width : width specifier
+ This can either be a floating point value, in the native domain
+ units of the simulation, or a tuple of the (value, unit) style.
+ This will be the width of the FRB.
+ height : height specifier, optional
+ This will be the height of the FRB, by default it is equal to width.
+ resolution : int or tuple of ints
+ The number of pixels on a side of the final FRB.
+
+ Returns
+ -------
+ frb : :class:`~yt.visualization.fixed_resolution.ObliqueFixedResolutionBuffer`
+ A fixed resolution buffer, which can be queried for fields.
+
+ Examples
+ --------
+
+ >>> v, c = pf.h.find_max("Density")
+ >>> sp = pf.h.sphere(c, (100.0, 'au'))
+ >>> L = sp.quantities["AngularMomentumVector"]()
+ >>> cutting = pf.h.cutting(L, c)
+ >>> frb = cutting.to_frb( (1.0, 'pc'), 1024)
+ >>> write_image(np.log10(frb["Density"]), 'density_1pc.png')
+ """
+ if iterable(width):
+ w, u = width
+ width = w/self.pf[u]
+ if height is None:
+ height = width
+ elif iterable(height):
+ h, u = height
+ height = h/self.pf[u]
+ if not iterable(resolution):
+ resolution = (resolution, resolution)
+ from yt.visualization.fixed_resolution import ObliqueFixedResolutionBuffer
+ bounds = (-width/2.0, width/2.0, -height/2.0, height/2.0)
+ frb = ObliqueFixedResolutionBuffer(self, bounds, resolution)
+ return frb
+
class YTFixedResCuttingPlaneBase(YTSelectionContainer2D):
"""
YTFixedResCuttingPlaneBase is an oblique plane through the data,
@@ -666,9 +709,6 @@
self[field] = self.comm.mpi_allreduce(\
self[field], op='sum').reshape([self.dims]*2).transpose()
- def interpolate_discretize(self, *args, **kwargs):
- pass
-
def _calc_vertex_centered_data(self, grid, field):
#return grid.retrieve_ghost_zones(1, field, smoothed=False)
return grid.get_vertex_centered_data(field)
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/data_objects/tests/test_covering_grid.py
--- /dev/null
+++ b/yt/data_objects/tests/test_covering_grid.py
@@ -0,0 +1,27 @@
+from yt.testing import *
+from yt.data_objects.profiles import \
+ BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+
+def setup():
+ from yt.config import ytcfg
+ ytcfg["yt","__withintesting"] = "True"
+
+def test_covering_grid():
+ # We decompose in different ways
+ for level in [0, 1, 2]:
+ for nprocs in [1, 2, 4, 8]:
+ pf = fake_random_pf(16, nprocs = nprocs)
+ dn = pf.refine_by**level
+ cg = pf.h.covering_grid(level, [0.0, 0.0, 0.0],
+ dn * pf.domain_dimensions)
+ yield assert_equal, cg["Ones"].max(), 1.0
+ yield assert_equal, cg["Ones"].min(), 1.0
+ yield assert_equal, cg["CellVolume"].sum(), pf.domain_width.prod()
+ for g in pf.h.grids:
+ di = g.get_global_startindex()
+ dd = g.ActiveDimensions
+ for i in range(dn):
+ f = cg["Density"][dn*di[0]+i:dn*(di[0]+dd[0])+i:dn,
+ dn*di[1]+i:dn*(di[1]+dd[1])+i:dn,
+ dn*di[2]+i:dn*(di[2]+dd[2])+i:dn]
+ yield assert_equal, f, g["Density"]
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/data_objects/tests/test_profiles.py
--- /dev/null
+++ b/yt/data_objects/tests/test_profiles.py
@@ -0,0 +1,74 @@
+from yt.testing import *
+from yt.data_objects.profiles import \
+ BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+
+_fields = ("Density", "Temperature", "Dinosaurs", "Tribbles")
+
+def test_profiles():
+ pf = fake_random_pf(64, nprocs = 8, fields = _fields)
+ nv = pf.domain_dimensions.prod()
+ dd = pf.h.all_data()
+ (rmi, rma), (tmi, tma), (dmi, dma) = dd.quantities["Extrema"](
+ ["Density", "Temperature", "Dinosaurs"])
+ rt, tt, dt = dd.quantities["TotalQuantity"](
+ ["Density", "Temperature", "Dinosaurs"])
+ # First we look at the
+ for nb in [8, 16, 32, 64]:
+ for lr in [True, False]:
+ # We log all the fields or don't log 'em all. No need to do them
+ # individually.
+ for lf in [True, False]:
+ # We have the min and the max, but to avoid cutting them off
+ # since we aren't doing end-collect, we cut a bit off the edges
+ for ec, e1, e2 in [(False, 0.9, 1.1), (True, 1.0, 1.0)]:
+ p1d = BinnedProfile1D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ lr, end_collect=ec)
+ p1d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p1d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p1d["Temperature"].sum(), 7
+
+ p2d = BinnedProfile2D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ nb, "Temperature", tmi*e1, tma*e2, lf,
+ lr, end_collect=ec)
+ p2d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p2d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p2d["Temperature"].sum(), 7
+
+ p3d = BinnedProfile3D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ nb, "Temperature", tmi*e1, tma*e2, lf,
+ nb, "Dinosaurs", dmi*e1, dma*e2, lf,
+ lr, end_collect=ec)
+ p3d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p3d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p3d["Temperature"].sum(), 7
+
+ p1d = BinnedProfile1D(dd, nb, "x", 0.0, 1.0, log_space=False)
+ p1d.add_fields("Ones", weight=None)
+ av = nv / nb
+ yield assert_equal, p1d["Ones"][:-1], np.ones(nb)*av
+ # We re-bin ones with a weight now
+ p1d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p1d["Ones"][:-1], np.ones(nb)
+
+ p2d = BinnedProfile2D(dd, nb, "x", 0.0, 1.0, False,
+ nb, "y", 0.0, 1.0, False)
+ p2d.add_fields("Ones", weight=None)
+ av = nv / nb**2
+ yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))*av
+ # We re-bin ones with a weight now
+ p2d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))
+
+ p3d = BinnedProfile3D(dd, nb, "x", 0.0, 1.0, False,
+ nb, "y", 0.0, 1.0, False,
+ nb, "z", 0.0, 1.0, False)
+ p3d.add_fields("Ones", weight=None)
+ av = nv / nb**3
+ yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb, nb, nb))*av
+ # We re-bin ones with a weight now
+ p3d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb,nb,nb))
+
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/data_objects/tests/test_projection.py
--- /dev/null
+++ b/yt/data_objects/tests/test_projection.py
@@ -0,0 +1,39 @@
+from yt.testing import *
+from yt.data_objects.profiles import \
+ BinnedProfile1D, BinnedProfile2D, BinnedProfile3D
+
+def setup():
+ from yt.config import ytcfg
+ ytcfg["yt","__withintesting"] = "True"
+
+def test_projection():
+ for nprocs in [8, 1]:
+ # We want to test both 1 proc and 8 procs, to make sure that
+ # parallelism isn't broken
+ pf = fake_random_pf(64, nprocs = nprocs)
+ dims = pf.domain_dimensions
+ xn, yn, zn = pf.domain_dimensions
+ xi, yi, zi = pf.domain_left_edge + 1.0/(pf.domain_dimensions * 2)
+ xf, yf, zf = pf.domain_right_edge - 1.0/(pf.domain_dimensions * 2)
+ dd = pf.h.all_data()
+ rho_tot = dd.quantities["TotalQuantity"]("Density")[0]
+ coords = np.mgrid[xi:xf:xn*1j, yi:yf:yn*1j, zi:zf:zn*1j]
+ uc = [np.unique(c) for c in coords]
+ # Some simple projection tests with single grids
+ for ax, an in enumerate("xyz"):
+ xax = x_dict[ax]
+ yax = y_dict[ax]
+ for wf in ["Density", None]:
+ proj = pf.h.proj(ax, ["Ones", "Density"], weight_field = wf)
+ yield assert_equal, proj["Ones"].sum(), proj["Ones"].size
+ yield assert_equal, proj["Ones"].min(), 1.0
+ yield assert_equal, proj["Ones"].max(), 1.0
+ yield assert_equal, np.unique(proj["px"]), uc[xax]
+ yield assert_equal, np.unique(proj["py"]), uc[yax]
+ yield assert_equal, np.unique(proj["pdx"]), 1.0/(dims[xax]*2.0)
+ yield assert_equal, np.unique(proj["pdy"]), 1.0/(dims[yax]*2.0)
+ # wf == None
+ yield assert_equal, wf, None
+ v1 = proj["Density"].sum()
+ v2 = (dd["Density"] * dd["d%s" % an]).sum()
+ yield assert_rel_equal, v1, v2, 10
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/data_objects/universal_fields.py
--- a/yt/data_objects/universal_fields.py
+++ b/yt/data_objects/universal_fields.py
@@ -32,7 +32,7 @@
from yt.funcs import *
-from yt.utilities.lib import CICDeposit_3, obtain_rvec
+from yt.utilities.lib import CICDeposit_3, obtain_rvec, obtain_rv_vec
from yt.utilities.cosmology import Cosmology
from field_info_container import \
add_field, \
@@ -54,7 +54,19 @@
kboltz, \
G, \
rho_crit_now, \
- speed_of_light_cgs
+ speed_of_light_cgs, \
+ km_per_cm
+
+from yt.utilities.math_utils import \
+ get_sph_r_component, \
+ get_sph_theta_component, \
+ get_sph_phi_component, \
+ get_cyl_r_component, \
+ get_cyl_z_component, \
+ get_cyl_theta_component, \
+ get_cyl_r, get_cyl_theta, \
+ get_cyl_z, get_sph_r, \
+ get_sph_theta, get_sph_phi
# Note that, despite my newfound efforts to comply with PEP-8,
# I violate it here in order to keep the name/func_name relationship
@@ -174,12 +186,8 @@
def _VelocityMagnitude(field, data):
"""M{|v|}"""
- bulk_velocity = data.get_field_parameter("bulk_velocity")
- if bulk_velocity == None:
- bulk_velocity = np.zeros(3)
- return ( (data["x-velocity"]-bulk_velocity[0])**2.0 + \
- (data["y-velocity"]-bulk_velocity[1])**2.0 + \
- (data["z-velocity"]-bulk_velocity[2])**2.0 )**(1.0/2.0)
+ velocities = obtain_rv_vec(data)
+ return np.sqrt(np.sum(velocities**2,axis=0))
add_field("VelocityMagnitude", function=_VelocityMagnitude,
take_log=False, units=r"\rm{cm}/\rm{s}")
@@ -189,13 +197,6 @@
function=_TangentialOverVelocityMagnitude,
take_log=False)
-def _TangentialVelocity(field, data):
- return np.sqrt(data["VelocityMagnitude"]**2.0
- - data["RadialVelocity"]**2.0)
-add_field("TangentialVelocity",
- function=_TangentialVelocity,
- take_log=False, units=r"\rm{cm}/\rm{s}")
-
def _Pressure(field, data):
"""M{(Gamma-1.0)*rho*E}"""
return (data.pf["Gamma"] - 1.0) * \
@@ -218,14 +219,9 @@
def _sph_r(field, data):
center = data.get_field_parameter("center")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
- ## The spherical coordinates radius is simply the magnitude of the
- ## coords vector.
-
- return np.sqrt(np.sum(coords**2,axis=-1))
+ return get_sph_r(vectors, center)
def _Convert_sph_r_CGS(data):
return data.convert("cm")
@@ -240,20 +236,9 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
- ## The angle (theta) with respect to the normal (J), is the arccos
- ## of the dot product of the normal with the normalized coords
- ## vector.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- JdotCoords = np.sum(J*coords,axis=-1)
-
- return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=-1)) )
+ return get_sph_theta(coords, normal)
add_field("sph_theta", function=_sph_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
@@ -264,54 +249,21 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
-
- ## We have freedom with respect to what axis (xprime) to define
- ## the disk angle. Here I've chosen to use the axis that is
- ## perpendicular to the normal and the y-axis. When normal ==
- ## y-hat, then set xprime = z-hat. With this definition, when
- ## normal == z-hat (as is typical), then xprime == x-hat.
- ##
- ## The angle is then given by the arctan of the ratio of the
- ## yprime-component and the xprime-component of the coords vector.
+ coords = obtain_rvec(data).transpose()
- xprime = np.cross([0.0,1.0,0.0],normal)
- if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
- yprime = np.cross(normal,xprime)
-
- tile_shape = list(coords.shape)[:-1] + [1]
- Jx = np.tile(xprime,tile_shape)
- Jy = np.tile(yprime,tile_shape)
-
- Px = np.sum(Jx*coords,axis=-1)
- Py = np.sum(Jy*coords,axis=-1)
-
- return np.arctan2(Py,Px)
+ return get_sph_phi(coords, normal)
add_field("sph_phi", function=_sph_phi,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
-
-
### cylindrical coordinates: R (radius in the cylinder's plane)
def _cyl_R(field, data):
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
- ## The cross product of the normal (J) with the coords vector
- ## gives a vector of magnitude equal to the cylindrical radius.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- JcrossCoords = np.cross(J,coords)
- return np.sqrt(np.sum(JcrossCoords**2,axis=-1))
+ return get_cyl_r(coords, normal)
def _Convert_cyl_R_CGS(data):
return data.convert("cm")
@@ -319,6 +271,9 @@
add_field("cyl_R", function=_cyl_R,
validators=[ValidateParameter("center"),ValidateParameter("normal")],
convert_function = _Convert_cyl_R_CGS, units=r"\rm{cm}")
+add_field("cyl_RCode", function=_cyl_R,
+ validators=[ValidateParameter("center"),ValidateParameter("normal")],
+ units=r"Radius (code)")
### cylindrical coordinates: z (height above the cylinder's plane)
@@ -326,17 +281,9 @@
center = data.get_field_parameter("center")
normal = data.get_field_parameter("normal")
- coords = np.array([data['x'] - center[0],
- data['y'] - center[1],
- data['z'] - center[2]]).transpose()
+ coords = obtain_rvec(data).transpose()
- ## The dot product of the normal (J) with the coords vector gives
- ## the cylindrical height.
-
- tile_shape = list(coords.shape)[:-1] + [1]
- J = np.tile(normal,tile_shape)
-
- return np.sum(J*coords,axis=-1)
+ return get_cyl_z(coords, normal)
def _Convert_cyl_z_CGS(data):
return data.convert("cm")
@@ -347,14 +294,17 @@
### cylindrical coordinates: theta (angle in the cylinder's plane)
-### [This is identical to the spherical coordinate's 'phi' angle.]
def _cyl_theta(field, data):
- return data['sph_phi']
+ center = data.get_field_parameter("center")
+ normal = data.get_field_parameter("normal")
+
+ coords = obtain_rvec(data).transpose()
+
+ return get_cyl_theta(coords, normal)
add_field("cyl_theta", function=_cyl_theta,
validators=[ValidateParameter("center"),ValidateParameter("normal")])
-
### The old field DiskAngle is the same as the spherical coordinates'
### 'theta' angle. I'm keeping DiskAngle for backwards compatibility.
def _DiskAngle(field, data):
@@ -387,6 +337,54 @@
ValidateParameter("normal")],
units=r"AU", display_field=False)
+def _cyl_RadialVelocity(field, data):
+ normal = data.get_field_parameter("normal")
+ velocities = obtain_rv_vec(data).transpose()
+
+ theta = np.tile(data['cyl_theta'], (3, 1)).transpose()
+
+ return get_cyl_r_component(velocities, theta, normal)
+
+def _cyl_RadialVelocityABS(field, data):
+ return np.abs(_cyl_RadialVelocity(field, data))
+def _Convert_cyl_RadialVelocityKMS(data):
+ return km_per_cm
+add_field("cyl_RadialVelocity", function=_cyl_RadialVelocity,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_RadialVelocityABS", function=_cyl_RadialVelocityABS,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_RadialVelocityKMS", function=_cyl_RadialVelocity,
+ convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_RadialVelocityKMSABS", function=_cyl_RadialVelocityABS,
+ convert_function=_Convert_cyl_RadialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+
+def _cyl_TangentialVelocity(field, data):
+ normal = data.get_field_parameter("normal")
+ velocities = obtain_rv_vec(data).transpose()
+ theta = np.tile(data['cyl_theta'], (3, 1)).transpose()
+
+ return get_cyl_theta_component(velocities, theta, normal)
+
+def _cyl_TangentialVelocityABS(field, data):
+ return np.abs(_cyl_TangentialVelocity(field, data))
+def _Convert_cyl_TangentialVelocityKMS(data):
+ return km_per_cm
+add_field("cyl_TangentialVelocity", function=_cyl_TangentialVelocity,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityABS", function=_cyl_TangentialVelocityABS,
+ units=r"\rm{cm}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityKMS", function=_cyl_TangentialVelocity,
+ convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("normal")])
+add_field("cyl_TangentialVelocityKMSABS", function=_cyl_TangentialVelocityABS,
+ convert_function=_Convert_cyl_TangentialVelocityKMS, units=r"\rm{km}/\rm{s}",
+ validators=[ValidateParameter("normal")])
def _DynamicalTime(field, data):
"""
@@ -635,13 +633,7 @@
take_log=False, display_field=False)
def obtain_velocities(data):
- if data.has_field_parameter("bulk_velocity"):
- bv = data.get_field_parameter("bulk_velocity")
- else: bv = np.zeros(3, dtype='float64')
- xv = data["x-velocity"] - bv[0]
- yv = data["y-velocity"] - bv[1]
- zv = data["z-velocity"] - bv[2]
- return xv, yv, zv
+ return obtain_rv_vec(data)
def _convertSpecificAngularMomentum(data):
return data.convert("cm")
@@ -706,7 +698,7 @@
# convert_function=_convertSpecificAngularMomentum, vector_field=True,
# units=r"\rm{cm}^2/\rm{s}", validators=[ValidateParameter('center')])
def _convertSpecificAngularMomentumKMSMPC(data):
- return data.convert("mpc")/1e5
+ return km_per_cm*data.convert("mpc")
#add_field("ParticleSpecificAngularMomentumKMSMPC",
# function=_ParticleSpecificAngularMomentum, particle_type=True,
# convert_function=_convertSpecificAngularMomentumKMSMPC, vector_field=True,
@@ -878,33 +870,32 @@
display_name = "Radius (code)")
def _RadialVelocity(field, data):
- center = data.get_field_parameter("center")
- bulk_velocity = data.get_field_parameter("bulk_velocity")
- if bulk_velocity == None:
- bulk_velocity = np.zeros(3)
- new_field = ( (data['x']-center[0])*(data["x-velocity"]-bulk_velocity[0])
- + (data['y']-center[1])*(data["y-velocity"]-bulk_velocity[1])
- + (data['z']-center[2])*(data["z-velocity"]-bulk_velocity[2])
- )/data["RadiusCode"]
- if np.any(np.isnan(new_field)): # to fix center = point
- new_field[np.isnan(new_field)] = 0.0
- return new_field
+ normal = data.get_field_parameter("normal")
+ velocities = obtain_rv_vec(data).transpose()
+ theta = np.tile(data['sph_theta'], (3, 1)).transpose()
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_r_component(velocities, theta, phi, normal)
+
def _RadialVelocityABS(field, data):
return np.abs(_RadialVelocity(field, data))
def _ConvertRadialVelocityKMS(data):
- return 1e-5
+ return km_per_cm
add_field("RadialVelocity", function=_RadialVelocity,
- units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center")])
+ units=r"\rm{cm}/\rm{s}")
add_field("RadialVelocityABS", function=_RadialVelocityABS,
- units=r"\rm{cm}/\rm{s}",
- validators=[ValidateParameter("center")])
+ units=r"\rm{cm}/\rm{s}")
add_field("RadialVelocityKMS", function=_RadialVelocity,
- convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center")])
+ convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}")
add_field("RadialVelocityKMSABS", function=_RadialVelocityABS,
- convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}",
- validators=[ValidateParameter("center")])
+ convert_function=_ConvertRadialVelocityKMS, units=r"\rm{km}/\rm{s}")
+
+def _TangentialVelocity(field, data):
+ return np.sqrt(data["VelocityMagnitude"]**2.0
+ - data["RadialVelocity"]**2.0)
+add_field("TangentialVelocity",
+ function=_TangentialVelocity,
+ take_log=False, units=r"\rm{cm}/\rm{s}")
def _CuttingPlaneVelocityX(field, data):
x_vec, y_vec, z_vec = [data.get_field_parameter("cp_%s_vec" % (ax))
@@ -1021,6 +1012,47 @@
display_name=r"\rm{Magnetic}\/\rm{Energy}",
units="\rm{ergs}\/\rm{cm}^{-3}")
+def _BPoloidal(field,data):
+ normal = data.get_field_parameter("normal")
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ theta = np.tile(data['sph_theta'], (3, 1)).transpose()
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_theta_component(Bfields, theta, phi, normal)
+
+add_field("BPoloidal", function=_BPoloidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("normal")])
+
+def _BToroidal(field,data):
+ normal = data.get_field_parameter("normal")
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_phi_component(Bfields, phi, normal)
+
+add_field("BToroidal", function=_BToroidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("normal")])
+
+def _BRadial(field,data):
+ normal = data.get_field_parameter("normal")
+
+ Bfields = np.array([data['Bx'], data['By'], data['Bz']])
+
+ theta = np.tile(data['sph_theta'], (3, 1)).transpose()
+ phi = np.tile(data['sph_phi'], (3, 1)).transpose()
+
+ return get_sph_r_component(Bfields, theta, phi, normal)
+
+add_field("BRadial", function=_BPoloidal,
+ units=r"\rm{Gauss}",
+ validators=[ValidateParameter("normal")])
+
def _VorticitySquared(field, data):
mylog.debug("Generating vorticity on %s", data)
# We need to set up stencils
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/frontends/flash/fields.py
--- a/yt/frontends/flash/fields.py
+++ b/yt/frontends/flash/fields.py
@@ -105,7 +105,10 @@
if fn1.endswith("_Fraction"):
add_field(fn1.split("_")[0] + "_Density",
function=_get_density(fn1), take_log=True,
- display_name="%s\/Density" % fn1.split("_")[0])
+ display_name="%s\/Density" % fn1.split("_")[0],
+ units = r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2",
+ )
def _get_convert(fname):
def _conv(data):
@@ -114,7 +117,8 @@
add_flash_field("dens", function=NullFunc, take_log=True,
convert_function=_get_convert("dens"),
- units=r"\rm{g}/\rm{cm}^3")
+ units=r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2"),
add_flash_field("velx", function=NullFunc, take_log=False,
convert_function=_get_convert("velx"),
units=r"\rm{cm}/\rm{s}")
@@ -264,6 +268,7 @@
add_field(f, TranslationFunc(v),
take_log=KnownFLASHFields[v].take_log,
units = ff._units, display_name=dname,
+ projected_units = ff._projected_units,
particle_type = pfield)
def _convertParticleMassMsun(data):
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -353,7 +353,8 @@
psize = get_psize(np.array(data[key].shape), nprocs)
grid_left_edges, grid_right_edges, temp[key] = \
decompose_array(data[key], psize, bbox)
- grid_dimensions = np.array([grid.shape for grid in temp[key]])
+ grid_dimensions = np.array([grid.shape for grid in temp[key]],
+ dtype="int32")
for gid in range(nprocs):
new_data[gid] = {}
for key in temp.keys():
@@ -364,7 +365,7 @@
sfh.update({0:data})
grid_left_edges = domain_left_edge
grid_right_edges = domain_right_edge
- grid_dimensions = domain_dimensions.reshape(nprocs,3)
+ grid_dimensions = domain_dimensions.reshape(nprocs,3).astype("int32")
handler = StreamHandler(
grid_left_edges,
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -310,7 +310,8 @@
maxval = max(maxval, 1)
from yt.config import ytcfg
if ytcfg.getboolean("yt", "suppressStreamLogging") or \
- ytcfg.getboolean("yt", "ipython_notebook"):
+ ytcfg.getboolean("yt", "ipython_notebook") or \
+ ytcfg.getboolean("yt", "__withintesting"):
return DummyProgressBar()
elif ytcfg.getboolean("yt", "__withinreason"):
from yt.gui.reason.extdirect_repl import ExtProgressBar
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/mods.py
--- a/yt/mods.py
+++ b/yt/mods.py
@@ -62,7 +62,7 @@
ValidateParameter, ValidateDataField, ValidateProperty, \
ValidateSpatial, ValidateGridType, \
TimeSeriesData, AnalysisTask, analysis_task, \
- ParticleTrajectoryCollection
+ ParticleTrajectoryCollection, ImageArray
from yt.data_objects.derived_quantities import \
add_quantity, quantity_info
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -24,7 +24,12 @@
import numpy as np
from yt.funcs import *
-from numpy.testing import assert_array_equal
+from numpy.testing import assert_array_equal, assert_almost_equal, \
+ assert_approx_equal, assert_array_almost_equal, assert_equal, \
+ assert_array_less, assert_string_equal
+
+def assert_rel_equal(a1, a2, decimels):
+ return assert_almost_equal(a1/a2, 1.0, decimels)
def amrspace(extent, levels=7, cells=8):
"""Creates two numpy arrays representing the left and right bounds of
@@ -127,17 +132,23 @@
return left, right, level
-def fake_random_pf(ndims, peak_value = 1.0, fields = ("Density",), negative = False):
+def fake_random_pf(ndims, peak_value = 1.0, fields = ("Density",),
+ negative = False, nprocs = 1):
from yt.frontends.stream.api import load_uniform_grid
if not iterable(ndims):
ndims = [ndims, ndims, ndims]
else:
assert(len(ndims) == 3)
- if negative:
- offset = 0.5
- else:
- offset = 0.0
+ if not iterable(negative):
+ negative = [negative for f in fields]
+ assert(len(fields) == len(negative))
+ offsets = []
+ for n in negative:
+ if n:
+ offsets.append(0.5)
+ else:
+ offsets.append(0.0)
data = dict((field, (np.random.random(ndims) - offset) * peak_value)
- for field in fields)
- ug = load_uniform_grid(data, ndims, 1.0)
+ for field,offset in zip(fields,offsets))
+ ug = load_uniform_grid(data, ndims, 1.0, nprocs = nprocs)
return ug
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/command_line.py
--- a/yt/utilities/command_line.py
+++ b/yt/utilities/command_line.py
@@ -1095,8 +1095,12 @@
)
else:
from IPython.config.loader import Config
+ import sys
cfg = Config()
+ # prepend sys.path with current working directory
+ sys.path.insert(0,'')
IPython.embed(config=cfg,user_ns=local_ns)
+
class YTMapserverCmd(YTCommand):
args = ("proj", "field", "weight",
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/decompose.py
--- a/yt/utilities/decompose.py
+++ b/yt/utilities/decompose.py
@@ -68,9 +68,12 @@
def evaluate_domain_decomposition(n_d, pieces, ldom):
""" Evaluate longest to shortest edge ratio
BEWARE: lot's of magic here """
- ideal_bsize = 3.0 * (pieces * np.product(n_d) ** 2) ** (1.0 / 3.0)
- bsize = int(np.sum(
- ldom / np.array(n_d, dtype=np.float64) * np.product(n_d)))
+ eff_dim = (n_d > 1).sum()
+ ideal_bsize = eff_dim * (pieces * np.product(n_d) ** (eff_dim - 1)
+ ) ** (1.0 / eff_dim)
+ mask = np.where(n_d > 1)
+ nd_arr = np.array(n_d, dtype=np.float64)[mask]
+ bsize = int(np.sum(ldom[mask] / nd_arr * np.product(nd_arr)))
load_balance = float(np.product(n_d)) / \
(float(pieces) * np.product((n_d - 1) / ldom + 1))
@@ -134,23 +137,15 @@
def split_array(tab, psize):
- """ Split array into px*py*pz subarrays using internal numpy routine. """
- temp = [np.array_split(array, psize[1], axis=1)
- for array in np.array_split(tab, psize[2], axis=2)]
- temp = [item for sublist in temp for item in sublist]
- temp = [np.array_split(array, psize[0], axis=0) for array in temp]
- temp = [item for sublist in temp for item in sublist]
- return temp
-
-
-if __name__ == "__main__":
-
- NPROC = 12
- ARRAY = np.zeros((128, 128, 129))
- BBOX = np.array([[0., 1.0], [-1.5, 1.5], [1.0, 2.5]])
-
- PROCS = get_psize(np.array(ARRAY.shape), NPROC)
- LE, RE, DATA = decompose_array(ARRAY, PROCS, BBOX)
-
- for idx in range(NPROC):
- print LE[idx, :], RE[idx, :], DATA[idx].shape
+ """ Split array into px*py*pz subarrays. """
+ n_d = np.array(tab.shape, dtype=np.int64)
+ slices = []
+ for i in range(psize[0]):
+ for j in range(psize[1]):
+ for k in range(psize[2]):
+ piece = np.array((i, j, k), dtype=np.int64)
+ lei = n_d * piece / psize
+ rei = n_d * (piece + np.ones(3, dtype=np.int64)) / psize
+ slices.append(np.s_[lei[0]:rei[0], lei[1]:
+ rei[1], lei[2]:rei[2]])
+ return [tab[slc] for slc in slices]
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/kdtree/__init__.py
--- a/yt/utilities/kdtree/__init__.py
+++ b/yt/utilities/kdtree/__init__.py
@@ -1,1 +0,0 @@
-from fKDpy import *
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/kdtree/api.py
--- /dev/null
+++ b/yt/utilities/kdtree/api.py
@@ -0,0 +1,9 @@
+from fKDpy import \
+ chainHOP_tags_dens, \
+ create_tree, \
+ fKD, \
+ find_nn_nearest_neighbors, \
+ free_tree, \
+ find_chunk_nearest_neighbors
+
+
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/kdtree/test.py
--- a/yt/utilities/kdtree/test.py
+++ /dev/null
@@ -1,58 +0,0 @@
-from Forthon import *
-from fKDpy import *
-import numpy,random
-
-n = 32768
-
-
-fKD.tags = fzeros((64),'i')
-fKD.dist = fzeros((64),'d')
-fKD.pos = fzeros((3,n),'d')
-fKD.nn = 64
-fKD.nparts = n
-fKD.sort = True
-fKD.rearrange = True
-fKD.qv = numpy.array([16./32, 16./32, 16./32])
-
-fp = open('parts.txt','r')
-xpos = []
-ypos = []
-zpos = []
-line = fp.readline()
-while line:
- line = line.split()
- xpos.append(float(line[0]))
- ypos.append(float(line[1]))
- zpos.append(float(line[2]))
- line= fp.readline()
-
-fp.close()
-
-
-for k in range(32):
- for j in range(32):
- for i in range(32):
- fKD.pos[0][i + j*32 + k*1024] = float(i)/32 + 1./64 + 0.0001*random.random()
- fKD.pos[1][i + j*32 + k*1024] = float(j)/32 + 1./64 + 0.0001*random.random()
- fKD.pos[2][i + j*32 + k*1024] = float(k)/32 + 1./64 + 0.0001*random.random()
-
-
-
-#print fKD.pos[0][0],fKD.pos[1][0],fKD.pos[2][0]
-
-create_tree()
-
-
-find_nn_nearest_neighbors()
-
-#print 'next'
-
-#fKD.qv = numpy.array([0., 0., 0.])
-
-#find_nn_nearest_neighbors()
-
-
-#print (fKD.tags - 1)
-#print fKD.dist
-
-free_tree()
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/lib/geometry_utils.pyx
--- a/yt/utilities/lib/geometry_utils.pyx
+++ b/yt/utilities/lib/geometry_utils.pyx
@@ -352,3 +352,48 @@
positions[i, j] = p[j]
return positions
+
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+ at cython.cdivision(True)
+def obtain_rv_vec(data):
+ # This is just to let the pointers exist and whatnot. We can't cdef them
+ # inside conditionals.
+ cdef np.ndarray[np.float64_t, ndim=1] vxf
+ cdef np.ndarray[np.float64_t, ndim=1] vyf
+ cdef np.ndarray[np.float64_t, ndim=1] vzf
+ cdef np.ndarray[np.float64_t, ndim=2] rvf
+ cdef np.ndarray[np.float64_t, ndim=3] vxg
+ cdef np.ndarray[np.float64_t, ndim=3] vyg
+ cdef np.ndarray[np.float64_t, ndim=3] vzg
+ cdef np.ndarray[np.float64_t, ndim=4] rvg
+ cdef np.float64_t bv[3]
+ cdef int i, j, k
+ bulk_velocity = data.get_field_parameter("bulk_velocity")
+ if bulk_velocity == None:
+ bulk_velocity = np.zeros(3)
+ bv[0] = bulk_velocity[0]; bv[1] = bulk_velocity[1]; bv[2] = bulk_velocity[2]
+ if len(data['x-velocity'].shape) == 1:
+ # One dimensional data
+ vxf = data['x-velocity'].astype("float64")
+ vyf = data['y-velocity'].astype("float64")
+ vzf = data['z-velocity'].astype("float64")
+ rvf = np.empty((3, vxf.shape[0]), 'float64')
+ for i in range(vxf.shape[0]):
+ rvf[0, i] = vxf[i] - bv[0]
+ rvf[1, i] = vyf[i] - bv[1]
+ rvf[2, i] = vzf[i] - bv[2]
+ return rvf
+ else:
+ # Three dimensional data
+ vxg = data['x-velocity'].astype("float64")
+ vyg = data['y-velocity'].astype("float64")
+ vzg = data['z-velocity'].astype("float64")
+ rvg = np.empty((3, vxg.shape[0], vxg.shape[1], vxg.shape[2]), 'float64')
+ for i in range(vxg.shape[0]):
+ for j in range(vxg.shape[1]):
+ for k in range(vxg.shape[2]):
+ rvg[0,i,j,k] = vxg[i,j,k] - bv[0]
+ rvg[1,i,j,k] = vyg[i,j,k] - bv[1]
+ rvg[2,i,j,k] = vzg[i,j,k] - bv[2]
+ return rvg
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/lib/misc_utilities.pyx
--- a/yt/utilities/lib/misc_utilities.pyx
+++ b/yt/utilities/lib/misc_utilities.pyx
@@ -292,49 +292,6 @@
return rv
raise KeyError
- at cython.boundscheck(False)
- at cython.wraparound(False)
- at cython.cdivision(True)
-def obtain_rvec(data):
- # This is just to let the pointers exist and whatnot. We can't cdef them
- # inside conditionals.
- cdef np.ndarray[np.float64_t, ndim=1] xf
- cdef np.ndarray[np.float64_t, ndim=1] yf
- cdef np.ndarray[np.float64_t, ndim=1] zf
- cdef np.ndarray[np.float64_t, ndim=2] rf
- cdef np.ndarray[np.float64_t, ndim=3] xg
- cdef np.ndarray[np.float64_t, ndim=3] yg
- cdef np.ndarray[np.float64_t, ndim=3] zg
- cdef np.ndarray[np.float64_t, ndim=4] rg
- cdef np.float64_t c[3]
- cdef int i, j, k
- center = data.get_field_parameter("center")
- c[0] = center[0]; c[1] = center[1]; c[2] = center[2]
- if len(data['x'].shape) == 1:
- # One dimensional data
- xf = data['x']
- yf = data['y']
- zf = data['z']
- rf = np.empty((3, xf.shape[0]), 'float64')
- for i in range(xf.shape[0]):
- rf[0, i] = xf[i] - c[0]
- rf[1, i] = yf[i] - c[1]
- rf[2, i] = zf[i] - c[2]
- return rf
- else:
- # Three dimensional data
- xg = data['x']
- yg = data['y']
- zg = data['z']
- rg = np.empty((3, xg.shape[0], xg.shape[1], xg.shape[2]), 'float64')
- for i in range(xg.shape[0]):
- for j in range(xg.shape[1]):
- for k in range(xg.shape[2]):
- rg[0,i,j,k] = xg[i,j,k] - c[0]
- rg[1,i,j,k] = yg[i,j,k] - c[1]
- rg[2,i,j,k] = zg[i,j,k] - c[2]
- return rg
-
@cython.cdivision(True)
def pixelize_cylinder(np.ndarray[np.float64_t, ndim=1] radius,
np.ndarray[np.float64_t, ndim=1] dradius,
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/lib/tests/test_geometry_utils.py
--- /dev/null
+++ b/yt/utilities/lib/tests/test_geometry_utils.py
@@ -0,0 +1,30 @@
+from yt.testing import *
+from yt.utilities.lib import obtain_rvec, obtain_rv_vec
+
+_fields = ("Density", "x-velocity", "y-velocity", "z-velocity")
+
+def test_obtain_rvec():
+ pf = fake_random_pf(64, nprocs=8, fields=_fields,
+ negative = [False, True, True, True])
+
+ dd = pf.h.sphere((0.5,0.5,0.5), 0.2)
+
+ coords = obtain_rvec(dd)
+
+ r = np.sqrt(np.sum(coords*coords,axis=0))
+
+ assert_array_less(r.max(), 0.2)
+
+ assert_array_less(0.0, r.min())
+
+def test_obtain_rv_vec():
+ pf = fake_random_pf(64, nprocs=8, fields=_fields,
+ negative = [False, True, True, True])
+
+ dd = pf.h.all_data()
+
+ vels = obtain_rv_vec(dd)
+
+ assert_array_equal(vels[0,:], dd['x-velocity'])
+ assert_array_equal(vels[1,:], dd['y-velocity'])
+ assert_array_equal(vels[2,:], dd['z-velocity'])
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/math_utils.py
--- a/yt/utilities/math_utils.py
+++ b/yt/utilities/math_utils.py
@@ -674,3 +674,156 @@
[uz*ux*(1-cost)-uy*sint, uz*uy*(1-cost)+ux*sint, cost+uz**2*(1-cost)]])
return R
+
+def get_ortho_basis(normal):
+ xprime = np.cross([0.0,1.0,0.0],normal)
+ if np.sum(xprime) == 0: xprime = np.array([0.0, 0.0, 1.0])
+ yprime = np.cross(normal,xprime)
+ zprime = normal
+ return (xprime, yprime, zprime)
+
+def get_sph_r(coords):
+ # The spherical coordinates radius is simply the magnitude of the
+ # coordinate vector.
+
+ return np.sqrt(np.sum(coords**2, axis=-1))
+
+
+def get_sph_theta(coords, normal):
+ # The angle (theta) with respect to the normal (J), is the arccos
+ # of the dot product of the normal with the normalized coordinate
+ # vector.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal,tile_shape)
+
+ JdotCoords = np.sum(J*coords,axis=-1)
+
+ return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=-1)) )
+
+def get_sph_phi(coords, normal):
+ # We have freedom with respect to what axis (xprime) to define
+ # the disk angle. Here I've chosen to use the axis that is
+ # perpendicular to the normal and the y-axis. When normal ==
+ # y-hat, then set xprime = z-hat. With this definition, when
+ # normal == z-hat (as is typical), then xprime == x-hat.
+ #
+ # The angle is then given by the arctan of the ratio of the
+ # yprime-component and the xprime-component of the coordinate
+ # vector.
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ Px = np.sum(Jx*coords,axis=-1)
+ Py = np.sum(Jy*coords,axis=-1)
+
+ return np.arctan2(Py,Px)
+
+def get_cyl_r(coords, normal):
+ # The cross product of the normal (J) with a coordinate vector
+ # gives a vector of magnitude equal to the cylindrical radius.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ JcrossCoords = np.cross(J, coords)
+ return np.sqrt(np.sum(JcrossCoords**2, axis=-1))
+
+def get_cyl_z(coords, normal):
+ # The dot product of the normal (J) with the coordinate vector
+ # gives the cylindrical height.
+
+ tile_shape = list(coords.shape)[:-1] + [1]
+ J = np.tile(normal, tile_shape)
+
+ return np.sum(J*coords, axis=-1)
+
+def get_cyl_theta(coords, normal):
+ # This is identical to the spherical phi component
+
+ return get_sph_phi(coords, normal)
+
+
+def get_cyl_r_component(vectors, theta, normal):
+ # The r of a vector is the vector dotted with rhat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ rhat = Jx*np.cos(theta) + Jy*np.sin(theta)
+
+ return np.sum(vectors*rhat,axis=-1)
+
+def get_cyl_theta_component(vectors, theta, normal):
+ # The theta component of a vector is the vector dotted with thetahat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ thetahat = -Jx*np.sin(theta) + Jy*np.cos(theta)
+
+ return np.sum(vectors*thetahat, axis=-1)
+
+def get_cyl_z_component(vectors, normal):
+ # The z component of a vector is the vector dotted with zhat
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ zhat = np.tile(zprime, tile_shape)
+
+ return np.sum(vectors*zhat, axis=-1)
+
+def get_sph_r_component(vectors, theta, phi, normal):
+ # The r component of a vector is the vector dotted with rhat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+ Jz = np.tile(zprime,tile_shape)
+
+ rhat = Jx*np.sin(theta)*np.cos(phi) + \
+ Jy*np.sin(theta)*np.sin(phi) + \
+ Jz*np.cos(theta)
+
+ return np.sum(vectors*rhat, axis=-1)
+
+def get_sph_phi_component(vectors, phi, normal):
+ # The phi component of a vector is the vector dotted with phihat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+
+ phihat = -Jx*np.sin(phi) + Jy*np.cos(phi)
+
+ return np.sum(vectors*phihat, axis=-1)
+
+def get_sph_theta_component(vectors, theta, phi, normal):
+ # The theta component of a vector is the vector dotted with thetahat
+
+ (xprime, yprime, zprime) = get_ortho_basis(normal)
+
+ tile_shape = list(vectors.shape)[:-1] + [1]
+ Jx = np.tile(xprime,tile_shape)
+ Jy = np.tile(yprime,tile_shape)
+ Jz = np.tile(zprime,tile_shape)
+
+ thetahat = Jx*np.cos(theta)*np.cos(phi) + \
+ Jy*np.cos(theta)*np.sin(phi) - \
+ Jz*np.sin(theta)
+
+ return np.sum(vectors*thetahat, axis=-1)
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/tests/test_coordinate_conversions.py
--- /dev/null
+++ b/yt/utilities/tests/test_coordinate_conversions.py
@@ -0,0 +1,128 @@
+from yt.testing import *
+from yt.utilities.math_utils import \
+ get_sph_r_component, \
+ get_sph_theta_component, \
+ get_sph_phi_component, \
+ get_cyl_r_component, \
+ get_cyl_z_component, \
+ get_cyl_theta_component, \
+ get_cyl_r, get_cyl_theta, \
+ get_cyl_z, get_sph_r, \
+ get_sph_theta, get_sph_phi
+
+# Randomly generated coordinates in the domain [[-1,1],[-1,1],-1,1]]
+coords = np.array([[-0.41503037, -0.22102472, -0.55774212],
+ [ 0.73828247, -0.17913899, 0.64076921],
+ [ 0.08922066, -0.94254844, -0.61774511],
+ [ 0.10173242, -0.95789145, 0.16294352],
+ [ 0.73186508, -0.3109153 , 0.75728738],
+ [ 0.8757989 , -0.41475119, -0.57039201],
+ [ 0.58040762, 0.81969082, 0.46759728],
+ [-0.89983356, -0.9853683 , -0.38355343]])
+
+def test_spherical_coordinate_conversion():
+ normal = [0, 0, 1]
+ real_r = [ 0.72950559, 0.99384957, 1.13047198, 0.97696269,
+ 1.09807968, 1.12445067, 1.10788685, 1.38843954]
+ real_theta = [ 2.44113629, 0.87012028, 2.14891444, 1.4032274 ,
+ 0.80979483, 2.10280198, 1.13507735, 1.85068416]
+ real_phi = [-2.65224483, -0.23804243, -1.47641858, -1.46498842,
+ -0.40172325, -0.4422801 , 0.95466734, -2.31085392]
+
+ calc_r = get_sph_r(coords)
+ calc_theta = get_sph_theta(coords, normal)
+ calc_phi = get_sph_phi(coords, normal)
+
+ assert_array_almost_equal(calc_r, real_r)
+ assert_array_almost_equal(calc_theta, real_theta)
+ assert_array_almost_equal(calc_phi, real_phi)
+
+ normal = [1, 0, 0]
+ real_theta = [ 2.17598842, 0.73347681, 1.49179079, 1.46647589,
+ 0.8412984 , 0.67793705, 1.0193883 , 2.27586987]
+ real_phi = [-0.37729951, -2.86898397, -0.99063518, -1.73928995,
+ -2.75201227,-0.62870527, 2.08920872, -1.19959244]
+
+ calc_theta = get_sph_theta(coords, normal)
+ calc_phi = get_sph_phi(coords, normal)
+
+ assert_array_almost_equal(calc_theta, real_theta)
+ assert_array_almost_equal(calc_phi, real_phi)
+
+def test_cylindrical_coordiante_conversion():
+ normal = [0, 0, 1]
+ real_r = [ 0.47021498, 0.75970506, 0.94676179, 0.96327853,
+ 0.79516968, 0.96904193, 1.00437346, 1.3344104 ]
+ real_theta = [-2.65224483, -0.23804243, -1.47641858, -1.46498842,
+ -0.40172325, -0.4422801 , 0.95466734, -2.31085392]
+ real_z = [-0.55774212, 0.64076921, -0.61774511, 0.16294352,
+ 0.75728738, -0.57039201, 0.46759728, -0.38355343]
+
+ calc_r = get_cyl_r(coords, normal)
+ calc_theta = get_cyl_theta(coords, normal)
+ calc_z = get_cyl_z(coords, normal)
+
+ assert_array_almost_equal(calc_r, real_r)
+ assert_array_almost_equal(calc_theta, real_theta)
+ assert_array_almost_equal(calc_z, real_z)
+
+ normal = [1, 0, 0]
+ real_r = [ 0.59994016, 0.66533898, 1.12694569, 0.97165149,
+ 0.81862843, 0.70524152, 0.94368441, 1.05738542]
+ real_theta = [-0.37729951, -2.86898397, -0.99063518, -1.73928995,
+ -2.75201227, -0.62870527, 2.08920872, -1.19959244]
+ real_z = [-0.41503037, 0.73828247, 0.08922066, 0.10173242,
+ 0.73186508, 0.8757989 , 0.58040762, -0.89983356]
+
+ calc_r = get_cyl_r(coords, normal)
+ calc_theta = get_cyl_theta(coords, normal)
+ calc_z = get_cyl_z(coords, normal)
+
+ assert_array_almost_equal(calc_r, real_r)
+ assert_array_almost_equal(calc_theta, real_theta)
+ assert_array_almost_equal(calc_z, real_z)
+
+def test_spherical_coordinate_projections():
+ normal = [0, 0, 1]
+ theta = get_sph_theta(coords, normal)
+ theta_pass = np.tile(theta, (3, 1)).T
+ phi = get_sph_phi(coords, normal)
+ phi_pass = np.tile(phi, (3, 1)).T
+ zero = np.tile(0,coords.shape[0])
+
+ # Purely radial field
+ vecs = np.array([np.sin(theta)*np.cos(phi), np.sin(theta)*np.sin(phi), np.cos(theta)]).T
+ assert_array_almost_equal(zero, get_sph_theta_component(vecs, theta_pass, phi_pass, normal))
+ assert_array_almost_equal(zero, get_sph_phi_component(vecs, phi_pass, normal))
+
+ # Purely toroidal field
+ vecs = np.array([-np.sin(phi), np.cos(phi), zero]).T
+ assert_array_almost_equal(zero, get_sph_theta_component(vecs, theta_pass, phi_pass, normal))
+ assert_array_almost_equal(zero, get_sph_r_component(vecs, theta_pass, phi_pass, normal))
+
+ # Purely poloidal field
+ vecs = np.array([np.cos(theta)*np.cos(phi), np.cos(theta)*np.sin(phi), -np.sin(theta)]).T
+ assert_array_almost_equal(zero, get_sph_phi_component(vecs, phi_pass, normal))
+ assert_array_almost_equal(zero, get_sph_r_component(vecs, theta_pass, phi_pass, normal))
+
+def test_cylindrical_coordinate_projections():
+ normal = [0, 0, 1]
+ theta = get_cyl_theta(coords, normal)
+ theta_pass = np.tile(theta, (3, 1)).T
+ z = get_cyl_z(coords, normal)
+ zero = np.tile(0, coords.shape[0])
+
+ # Purely radial field
+ vecs = np.array([np.cos(theta), np.sin(theta), zero]).T
+ assert_array_almost_equal(zero, get_cyl_theta_component(vecs, theta_pass, normal))
+ assert_array_almost_equal(zero, get_cyl_z_component(vecs, normal))
+
+ # Purely toroidal field
+ vecs = np.array([-np.sin(theta), np.cos(theta), zero]).T
+ assert_array_almost_equal(zero, get_cyl_z_component(vecs, normal))
+ assert_array_almost_equal(zero, get_cyl_r_component(vecs, theta_pass, normal))
+
+ # Purely z field
+ vecs = np.array([zero, zero, z]).T
+ assert_array_almost_equal(zero, get_cyl_theta_component(vecs, theta_pass, normal))
+ assert_array_almost_equal(zero, get_cyl_r_component(vecs, theta_pass, normal))
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/tests/test_decompose.py
--- /dev/null
+++ b/yt/utilities/tests/test_decompose.py
@@ -0,0 +1,96 @@
+"""
+Test suite for cartesian domain decomposition.
+
+Author: Kacper Kowalik <xarthisius.kk at gmail.com>
+Affiliation: CA UMK
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2012 Kacper Kowalik. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from yt.testing import assert_array_equal, assert_almost_equal
+import numpy as np
+import yt.utilities.decompose as dec
+
+
+def setup():
+ pass
+
+
+def test_psize_2d():
+ procs = dec.get_psize(np.array([5, 1, 7]), 6)
+ assert_array_equal(procs, np.array([3, 1, 2]))
+ procs = dec.get_psize(np.array([1, 7, 5]), 6)
+ assert_array_equal(procs, np.array([1, 2, 3]))
+ procs = dec.get_psize(np.array([7, 5, 1]), 6)
+ assert_array_equal(procs, np.array([2, 3, 1]))
+
+
+def test_psize_3d():
+ procs = dec.get_psize(np.array([33, 35, 37]), 12)
+ assert_array_equal(procs, np.array([3, 2, 2]))
+
+
+def test_decomposition_2d():
+ array = np.ones((7, 5, 1))
+ bbox = np.array([[-0.7, 0.0], [1.5, 2.0], [0.0, 0.7]])
+ ledge, redge, data = dec.decompose_array(array, np.array([2, 3, 1]), bbox)
+
+ assert_array_equal(data[1].shape, np.array([3, 2, 1]))
+
+ gold_le = np.array([
+ [-0.7, 1.5, 0.0], [-0.7, 1.6, 0.0],
+ [-0.7, 1.8, 0.0], [-0.4, 1.5, 0.0],
+ [-0.4, 1.6, 0.0], [-0.4, 1.8, 0.0]
+ ])
+ assert_almost_equal(ledge, gold_le, 8)
+
+ gold_re = np.array(
+ [[-0.4, 1.6, 0.7], [-0.4, 1.8, 0.7],
+ [-0.4, 2.0, 0.7], [0.0, 1.6, 0.7],
+ [0.0, 1.8, 0.7], [0.0, 2.0, 0.7]]
+ )
+ assert_almost_equal(redge, gold_re, 8)
+
+
+def test_decomposition_3d():
+ array = np.ones((33, 35, 37))
+ bbox = np.array([[0., 1.0], [-1.5, 1.5], [1.0, 2.5]])
+
+ ledge, redge, data = dec.decompose_array(array, np.array([3, 2, 2]), bbox)
+ assert_array_equal(data[0].shape, np.array([11, 17, 18]))
+
+ gold_le = np.array(
+ [[0.00000, -1.50000, 1.00000], [0.00000, -1.50000, 1.72973],
+ [0.00000, -0.04286, 1.00000], [0.00000, -0.04286, 1.72973],
+ [0.33333, -1.50000, 1.00000], [0.33333, -1.50000, 1.72973],
+ [0.33333, -0.04286, 1.00000], [0.33333, -0.04286, 1.72973],
+ [0.66667, -1.50000, 1.00000], [0.66667, -1.50000, 1.72973],
+ [0.66667, -0.04286, 1.00000], [0.66667, -0.04286, 1.72973]]
+ )
+ assert_almost_equal(ledge, gold_le, 5)
+
+ gold_re = np.array(
+ [[0.33333, -0.04286, 1.72973], [0.33333, -0.04286, 2.50000],
+ [0.33333, 1.50000, 1.72973], [0.33333, 1.50000, 2.50000],
+ [0.66667, -0.04286, 1.72973], [0.66667, -0.04286, 2.50000],
+ [0.66667, 1.50000, 1.72973], [0.66667, 1.50000, 2.50000],
+ [1.00000, -0.04286, 1.72973], [1.00000, -0.04286, 2.50000],
+ [1.00000, 1.50000, 1.72973], [1.00000, 1.50000, 2.50000]]
+ )
+ assert_almost_equal(redge, gold_re, 5)
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/utilities/tests/test_kdtrees.py
--- /dev/null
+++ b/yt/utilities/tests/test_kdtrees.py
@@ -0,0 +1,93 @@
+"""
+Unit test the kD trees in yt.
+
+Author: Stephen Skory <s at skory.us>
+Affiliation: U of Colorado
+Homepage: http://yt-project.org/
+License:
+ Copyright (C) 2008-2011 Stephen Skory. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from yt.testing import *
+
+try:
+ from yt.utilities.kdtree.api import *
+except ImportError:
+ mylog.debug("The Fortran kD-Tree did not import correctly.")
+
+from yt.utilities.spatial import cKDTree
+
+def setup():
+ pass
+
+def test_fortran_tree():
+ r"""This test makes sure that the fortran kdtree is finding the correct
+ nearest neighbors.
+ """
+ # Four points.
+ try:
+ fKD.pos = np.empty((3, 4), dtype='float64', order='F')
+ except NameError:
+ return
+ # Make four points by hand that, in particular, will allow us to test
+ # the periodicity of the kdtree.
+ points = np.array([0.01, 0.5, 0.98, 0.99])
+ fKD.pos[0, :] = points
+ fKD.pos[1, :] = points
+ fKD.pos[2, :] = points
+ fKD.qv = np.empty(3, dtype='float64')
+ fKD.dist = np.empty(4, dtype='float64')
+ fKD.tags = np.empty(4, dtype='int64')
+ fKD.nn = 4
+ fKD.sort = True
+ create_tree(0)
+ # Now we check to make sure that we find the correct nearest neighbors,
+ # which get stored in dist and tags.
+ fKD.qv[:] = 0.999
+ find_nn_nearest_neighbors()
+ # Fix fortran counting.
+ fKD.tags -= 1
+ # Clean up before the tests.
+ free_tree(0)
+ # What the answers should be.
+ dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
+ tags = np.array([3, 0, 2, 1], dtype='int64')
+ assert_array_almost_equal(fKD.dist, dist)
+ assert_array_equal(fKD.tags, tags)
+
+def test_cython_tree():
+ r"""This test makes sure that the cython kdtree is finding the correct
+ nearest neighbors.
+ """
+ # Four points.
+ pos = np.empty((4, 3), dtype='float64')
+ # Make four points by hand that, in particular, will allow us to test
+ # the periodicity of the kdtree.
+ points = np.array([0.01, 0.5, 0.98, 0.99])
+ pos[:, 0] = points
+ pos[:, 1] = points
+ pos[:, 2] = points
+ kdtree = cKDTree(pos, leafsize = 2)
+ qv = np.array([0.999]*3)
+ res = kdtree.query(qv, 4, period=[1.,1.,1])
+ # What the answers should be.
+ dist = np.array([2.43e-04, 3.63e-04, 1.083e-03, 7.47003e-01])
+ tags = np.array([3, 0, 2, 1], dtype='int64')
+ assert_array_almost_equal(res[0], dist)
+ assert_array_equal(res[1], tags)
+
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -116,7 +116,7 @@
image = image.transpose().copy() # Have to make sure it's contiguous
au.write_png(image, fn)
-def write_bitmap(bitmap_array, filename, max_val = None, transpose=True):
+def write_bitmap(bitmap_array, filename, max_val = None, transpose=False):
r"""Write out a bitmapped image directly to a PNG file.
This accepts a three- or four-channel `bitmap_array`. If the image is not
@@ -379,7 +379,7 @@
take_log=True)
"""
import matplotlib
- from ._mpl_imports import *
+ from ._mpl_imports import FigureCanvasAgg, FigureCanvasPdf, FigureCanvasPS
# If this is rendered as log, then apply now.
if take_log:
@@ -420,21 +420,22 @@
else:
dpi = None
- if filename[-4:] == '.png':
- suffix = ''
- else:
+ suffix = os.path.splitext(filename)[1]
+
+ if suffix == '':
suffix = '.png'
filename = "%s%s" % (filename, suffix)
- mylog.info("Saving plot %s", fn)
+ mylog.info("Saving plot %s", filename)
if suffix == ".png":
canvas = FigureCanvasAgg(fig)
elif suffix == ".pdf":
canvas = FigureCanvasPdf(fig)
elif suffix in (".eps", ".ps"):
- canvas = FigureCanvasPS
+ canvas = FigureCanvasPS(fig)
else:
mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
canvas = FigureCanvasAgg(fig)
+
canvas.print_figure(filename)
return filename
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -149,7 +149,9 @@
def __call__(self, plot):
# Instantiation of these is cheap
if plot._type_name == "CuttingPlane":
- print "WARNING: Magnetic field on Cutting Plane Not implemented."
+ qcb = CuttingQuiverCallback("CuttingPlaneBx",
+ "CuttingPlaneBy",
+ self.factor)
else:
xv = "B%s" % (x_names[plot.data.axis])
yv = "B%s" % (y_names[plot.data.axis])
@@ -211,7 +213,8 @@
class ContourCallback(PlotCallback):
_type_name = "contour"
- def __init__(self, field, ncont=5, factor=4, clim=None, plot_args=None):
+ def __init__(self, field, ncont=5, factor=4, clim=None,
+ plot_args = None):
"""
annotate_contour(self, field, ncont=5, factor=4, take_log=False, clim=None,
plot_args = None):
@@ -360,39 +363,30 @@
class StreamlineCallback(PlotCallback):
_type_name = "streamlines"
- def __init__(self, field_x, field_y, factor=6.0, nx=16, ny=16,
- xstart=(0,1), ystart=(0,1), nsample=256,
- start_at_xedge=False, start_at_yedge=False,
- plot_args=None):
+ def __init__(self, field_x, field_y, factor = 16,
+ density = 1, arrowsize = 1, arrowstyle = None,
+ color = None, normalize = False):
"""
- annotate_streamlines(field_x, field_y, factor=6.0, nx=16, ny=16,
- xstart=(0,1), ystart=(0,1), nsample=256,
- start_at_xedge=False, start_at_yedge=False,
- plot_args=None):
+ annotate_streamlines(field_x, field_y, factor = 16, density = 1,
+ arrowsize = 1, arrowstyle = None,
+ color = None, normalize = False):
Add streamlines to any plot, using the *field_x* and *field_y*
- from the associated data, using *nx* and *ny* starting points
- that are bounded by *xstart* and *ystart*. To begin
- streamlines from the left edge of the plot, set
- *start_at_xedge* to True; for the bottom edge, use
- *start_at_yedge*. A line with the qmean vector magnitude will
- cover 1.0/*factor* of the image.
+ from the associated data, skipping every *factor* datapoints like
+ 'quiver'. *density* is the index of the amount of the streamlines.
"""
PlotCallback.__init__(self)
self.field_x = field_x
self.field_y = field_y
- self.xstart = xstart
- self.ystart = ystart
- self.nsample = nsample
+ self.bv_x = self.bv_y = 0
self.factor = factor
- if start_at_xedge:
- self.data_size = (1,ny)
- elif start_at_yedge:
- self.data_size = (nx,1)
- else:
- self.data_size = (nx,ny)
- if plot_args is None: plot_args = {'color':'k', 'linestyle':'-'}
- self.plot_args = plot_args
+ self.dens = density
+ self.arrowsize = arrowsize
+ if arrowstyle is None : arrowstyle='-|>'
+ self.arrowstyle = arrowstyle
+ if color is None : color = "#000000"
+ self.color = color
+ self.normalize = normalize
def __call__(self, plot):
x0, x1 = plot.xlim
@@ -400,40 +394,31 @@
xx0, xx1 = plot._axes.get_xlim()
yy0, yy1 = plot._axes.get_ylim()
plot._axes.hold(True)
- nx = plot.image._A.shape[0]
- ny = plot.image._A.shape[1]
+ nx = plot.image._A.shape[0] / self.factor
+ ny = plot.image._A.shape[1] / self.factor
pixX = _MPL.Pixelize(plot.data['px'],
plot.data['py'],
plot.data['pdx'],
plot.data['pdy'],
- plot.data[self.field_x],
+ plot.data[self.field_x] - self.bv_x,
int(nx), int(ny),
- (x0, x1, y0, y1),)
+ (x0, x1, y0, y1),).transpose()
pixY = _MPL.Pixelize(plot.data['px'],
plot.data['py'],
plot.data['pdx'],
plot.data['pdy'],
- plot.data[self.field_y],
+ plot.data[self.field_y] - self.bv_y,
int(nx), int(ny),
- (x0, x1, y0, y1),)
- r0 = np.mgrid[self.xstart[0]*nx:self.xstart[1]*nx:self.data_size[0]*1j,
- self.ystart[0]*ny:self.ystart[1]*ny:self.data_size[1]*1j]
- lines = np.zeros((self.nsample, 2, self.data_size[0], self.data_size[1]))
- lines[0,:,:,:] = r0
- mag = np.sqrt(pixX**2 + pixY**2)
- scale = np.sqrt(nx*ny) / (self.factor * mag.mean())
- dt = 1.0 / (self.nsample-1)
- for i in range(1,self.nsample):
- xt = lines[i-1,0,:,:]
- yt = lines[i-1,1,:,:]
- ix = np.maximum(np.minimum((xt).astype('int'), nx-1), 0)
- iy = np.maximum(np.minimum((yt).astype('int'), ny-1), 0)
- lines[i,0,:,:] = xt + dt * pixX[ix,iy] * scale
- lines[i,1,:,:] = yt + dt * pixY[ix,iy] * scale
- for i in range(self.data_size[0]):
- for j in range(self.data_size[1]):
- plot._axes.plot(lines[:,0,i,j], lines[:,1,i,j],
- **self.plot_args)
+ (x0, x1, y0, y1),).transpose()
+ X,Y = (na.linspace(xx0,xx1,nx,endpoint=True),
+ na.linspace(yy0,yy1,ny,endpoint=True))
+ if self.normalize:
+ nn = na.sqrt(pixX**2 + pixY**2)
+ pixX /= nn
+ pixY /= nn
+ plot._axes.streamplot(X,Y, pixX, pixY, density=self.dens,
+ arrowsize=self.arrowsize, arrowstyle=self.arrowstyle,
+ color=self.color, norm=self.normalize)
plot._axes.set_xlim(xx0,xx1)
plot._axes.set_ylim(yy0,yy1)
plot._axes.hold(False)
@@ -454,6 +439,30 @@
plot._axes.set_xlabel(self.label)
plot._axes.set_ylabel(self.label)
+class TimeCallback(PlotCallback):
+ _type_name = "time"
+ def __init__(self, format_code='10.7e'):
+ """
+ This annotates the plot with the current simulation time.
+ For now, the time is displayed in seconds.
+ *format_code* can be optionally set, allowing a custom
+ c-style format code for the time display.
+ """
+ self.format_code = format_code
+ PlotCallback.__init__(self)
+
+ def __call__(self, plot):
+ current_time = plot.pf.current_time/plot.pf['Time']
+ timestring = format(current_time,self.format_code)
+ base = timestring[:timestring.find('e')]
+ exponent = timestring[timestring.find('e')+1:]
+ if exponent[0] == '+':
+ exponent = exponent[1:]
+ timestring = r'$t\/=\/'+base+''+r'\times\,10^{'+exponent+r'}\, \rm{s}$'
+ from mpl_toolkits.axes_grid1.anchored_artists import AnchoredText
+ at = AnchoredText(timestring, prop=dict(size=12), frameon=True, loc=4)
+ plot._axes.add_artist(at)
+
def get_smallest_appropriate_unit(v, pf):
max_nu = 1e30
good_u = None
@@ -697,9 +706,13 @@
self.plot_args = plot_args
def __call__(self, plot):
+ if len(self.pos) == 3:
+ pos = (self.pos[x_dict[plot.data.axis]],
+ self.pos[y_dict[plot.data.axis]])
+ else: pos = self.pos
from matplotlib.patches import Arrow
# Now convert the pixels to code information
- x, y = self.convert_to_plot(plot, self.pos)
+ x, y = self.convert_to_plot(plot, pos)
dx, dy = self.convert_to_plot(plot, self.code_size, False)
arrow = Arrow(x, y, dx, dy, **self.plot_args)
plot._axes.add_patch(arrow)
@@ -719,12 +732,13 @@
self.text_args = text_args
def __call__(self, plot):
-
-
+ if len(self.pos) == 3:
+ pos = (self.pos[x_dict[plot.data.axis]],
+ self.pos[y_dict[plot.data.axis]])
+ else: pos = self.pos
width,height = plot.image._A.shape
- x,y = self.convert_to_plot(plot, self.pos)
- x,y = x/width,y/height
-
+ x,y = self.convert_to_plot(plot, pos)
+
plot._axes.text(x, y, self.text, **self.text_args)
class MarkerAnnotateCallback(PlotCallback):
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -1,4 +1,4 @@
-"""
+"""
A plotting mechanism based on the idea of a "window" into the data.
Author: J. S. Oishi <jsoishi at gmail.com>
@@ -309,6 +309,7 @@
nWx, nWy = Wx/factor, Wy/factor
self.xlim = (centerx - nWx*0.5, centerx + nWx*0.5)
self.ylim = (centery - nWy*0.5, centery + nWy*0.5)
+
@invalidate_data
def pan(self, deltas):
@@ -697,6 +698,15 @@
"""
_current_field = None
+ _frb_generator = None
+ _plot_type = None
+
+ def __init__(self, *args, **kwargs):
+ if self._frb_generator == None:
+ self._frb_generator = kwargs.pop("frb_generator")
+ if self._plot_type == None:
+ self._plot_type = kwargs.pop("plot_type")
+ PWViewer.__init__(self, *args, **kwargs)
def _setup_origin(self):
origin = self.origin
@@ -890,19 +900,22 @@
>>> slc.save(mpl_kwargs={'bbox_inches':'tight'})
"""
- if mpl_kwargs is None:
- mpl_kwargs = {}
+ names = []
+ if mpl_kwargs is None: mpl_kwargs = {}
if name == None:
name = str(self.pf)
- elif name.endswith('.png'):
- #import pdb; pdb.set_trace()
- return self.plots.values()[0].save(name, mpl_kwargs)
+ suffix = os.path.splitext(name)[1]
+ if suffix != '':
+ for k, v in self.plots.iteritems():
+ names.append(v.save(name,mpl_kwargs))
+ return names
axis = axis_names[self.data_source.axis]
weight = None
type = self._plot_type
if type in ['Projection','OffAxisProjection']:
weight = self.data_source.weight_field
- names = []
+ if 'Cutting' in self.data_source.__class__.__name__:
+ type = 'OffAxisSlice'
for k, v in self.plots.iteritems():
if isinstance(k, types.TupleType):
k = k[1]
@@ -1498,24 +1511,25 @@
self.cax = self.figure.add_axes(caxrect)
def save(self, name, mpl_kwargs, canvas = None):
- if name[-4:] == '.png':
- suffix = ''
+ suffix = os.path.splitext(name)[1]
+
+ if suffix == '':
+ suffix = '.png'
+ name = "%s%s" % (name, suffix)
+ mylog.info("Saving plot %s", name)
+ if suffix == ".png":
+ canvas = FigureCanvasAgg(self.figure)
+ elif suffix == ".pdf":
+ canvas = FigureCanvasPdf(self.figure)
+ elif suffix in (".eps", ".ps"):
+ canvas = FigureCanvasPS(self.figure)
else:
- suffix = '.png'
- fn = "%s%s" % (name, suffix)
- mylog.info("Saving plot %s", fn)
- if canvas is None:
- if suffix == ".png":
- canvas = FigureCanvasAgg(self.figure)
- elif suffix == ".pdf":
- canvas = FigureCanvasPdf(self.figure)
- elif suffix in (".eps", ".ps"):
- canvas = FigureCanvasPS
- else:
- mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
- canvas = FigureCanvasAgg(self.figure)
- canvas.print_figure(fn,**mpl_kwargs)
- return fn
+ mylog.warning("Unknown suffix %s, defaulting to Agg", suffix)
+ canvas = FigureCanvasAgg(self.figure)
+
+
+ canvas.print_figure(name,**mpl_kwargs)
+ return name
def _get_best_layout(self, size):
aspect = 1.0*size[0]/size[1]
diff -r f1edaf9e24969b8b2224740ff32a379b6effbbc2 -r 92038d70878ecf462d034528e19cafda165af985 yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -37,6 +37,7 @@
arr_ang2pix_nest, arr_fisheye_vectors
from yt.utilities.math_utils import get_rotation_matrix
from yt.utilities.orientation import Orientation
+from yt.data_objects.api import ImageArray
from yt.visualization.image_writer import write_bitmap, write_image
from yt.data_objects.data_containers import data_object_registry
from yt.utilities.parallel_tools.parallel_analysis_interface import \
@@ -346,15 +347,21 @@
def save_image(self, fn, clip_ratio, image):
if self.comm.rank is 0 and fn is not None:
- if clip_ratio is not None:
- write_bitmap(image, fn, clip_ratio * image.std())
- else:
- write_bitmap(image, fn)
-
+ image.write_png(fn, clip_ratio=clip_ratio)
def initialize_source(self):
return self.volume.initialize_source()
+ def get_information(self):
+ info_dict = {'fields':self.fields,
+ 'type':self.__class__.__name__,
+ 'east_vector':self.orienter.unit_vectors[0],
+ 'north_vector':self.orienter.unit_vectors[1],
+ 'normal_vector':self.orienter.unit_vectors[2],
+ 'width':self.width,
+ 'dataset':self.pf.fullpath}
+ return info_dict
+
def snapshot(self, fn = None, clip_ratio = None, double_check = False,
num_threads = 0):
r"""Ray-cast the camera.
@@ -389,7 +396,9 @@
args = self.get_sampler_args(image)
sampler = self.get_sampler(args)
self.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clip_ratio, image)
return image
@@ -669,7 +678,7 @@
class PerspectiveCamera(Camera):
expand_factor = 1.0
def __init__(self, *args, **kwargs):
- expand_factor = kwargs.pop('expand_factor', 1.0)
+ self.expand_factor = kwargs.pop('expand_factor', 1.0)
Camera.__init__(self, *args, **kwargs)
def get_sampler_args(self, image):
@@ -708,6 +717,27 @@
self.transfer_function, self.sub_samples)
return args
+ def _render(self, double_check, num_threads, image, sampler):
+ pbar = get_pbar("Ray casting", (self.volume.brick_dimensions + 1).prod(axis=-1).sum())
+ total_cells = 0
+ if double_check:
+ for brick in self.volume.bricks:
+ for data in brick.my_data:
+ if np.any(np.isnan(data)):
+ raise RuntimeError
+
+ view_pos = self.front_center
+ for brick in self.volume.traverse(view_pos, self.front_center, image):
+ sampler(brick, num_threads=num_threads)
+ total_cells += np.prod(brick.my_data[0].shape)
+ pbar.update(total_cells)
+
+ pbar.finish()
+ image = sampler.aimage
+ self.finalize_image(image)
+ return image
+
+
def finalize_image(self, image):
image.shape = self.resolution[0], self.resolution[0], 3
@@ -800,6 +830,15 @@
return image
+ def get_information(self):
+ info_dict = {'fields':self.fields,
+ 'type':self.__class__.__name__,
+ 'center':self.center,
+ 'radius':self.radius,
+ 'dataset':self.pf.fullpath}
+ return info_dict
+
+
def snapshot(self, fn = None, clip_ratio = None, double_check = False,
num_threads = 0, clim = None, label = None):
r"""Ray-cast the camera.
@@ -827,7 +866,9 @@
args = self.get_sampler_args(image)
sampler = self.get_sampler(args)
self.volume.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clim, image, label = label)
return image
@@ -1263,8 +1304,9 @@
if self.image is not None:
del self.image
+ image = ImageArray(image,
+ info=self.get_information())
self.image = image
-
return image
def save_image(self, fn, clip_ratio=None):
@@ -1669,7 +1711,9 @@
self.initialize_source()
- image = self._render(double_check, num_threads, image, sampler)
+ image = ImageArray(self._render(double_check, num_threads,
+ image, sampler),
+ info=self.get_information())
self.save_image(fn, clip_ratio, image)
https://bitbucket.org/yt_analysis/yt-3.0/changeset/03f313274982/
changeset: 03f313274982
branch: yt-3.0
user: MatthewTurk
date: 2012-10-17 21:55:49
summary: In the merge, which was successful, I forgot that misc_utilities now contains the useful items from geometry_utils.pyx
affected #: 1 file
diff -r 92038d70878ecf462d034528e19cafda165af985 -r 03f313274982d70994593ea9aff6117140edc275 yt/utilities/lib/misc_utilities.pyx
--- a/yt/utilities/lib/misc_utilities.pyx
+++ b/yt/utilities/lib/misc_utilities.pyx
@@ -340,3 +340,91 @@
theta_i += dthetamin
return img
+
+ at cython.cdivision(True)
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+def obtain_rvec(data):
+ # This is just to let the pointers exist and whatnot. We can't cdef them
+ # inside conditionals.
+ cdef np.ndarray[np.float64_t, ndim=1] xf
+ cdef np.ndarray[np.float64_t, ndim=1] yf
+ cdef np.ndarray[np.float64_t, ndim=1] zf
+ cdef np.ndarray[np.float64_t, ndim=2] rf
+ cdef np.ndarray[np.float64_t, ndim=3] xg
+ cdef np.ndarray[np.float64_t, ndim=3] yg
+ cdef np.ndarray[np.float64_t, ndim=3] zg
+ cdef np.ndarray[np.float64_t, ndim=4] rg
+ cdef np.float64_t c[3]
+ cdef int i, j, k
+ center = data.get_field_parameter("center")
+ c[0] = center[0]; c[1] = center[1]; c[2] = center[2]
+ if len(data['x'].shape) == 1:
+ # One dimensional data
+ xf = data['x']
+ yf = data['y']
+ zf = data['z']
+ rf = np.empty((3, xf.shape[0]), 'float64')
+ for i in range(xf.shape[0]):
+ rf[0, i] = xf[i] - c[0]
+ rf[1, i] = yf[i] - c[1]
+ rf[2, i] = zf[i] - c[2]
+ return rf
+ else:
+ # Three dimensional data
+ xg = data['x']
+ yg = data['y']
+ zg = data['z']
+ rg = np.empty((3, xg.shape[0], xg.shape[1], xg.shape[2]), 'float64')
+ for i in range(xg.shape[0]):
+ for j in range(xg.shape[1]):
+ for k in range(xg.shape[2]):
+ rg[0,i,j,k] = xg[i,j,k] - c[0]
+ rg[1,i,j,k] = yg[i,j,k] - c[1]
+ rg[2,i,j,k] = zg[i,j,k] - c[2]
+ return rg
+
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+ at cython.cdivision(True)
+def obtain_rv_vec(data):
+ # This is just to let the pointers exist and whatnot. We can't cdef them
+ # inside conditionals.
+ cdef np.ndarray[np.float64_t, ndim=1] vxf
+ cdef np.ndarray[np.float64_t, ndim=1] vyf
+ cdef np.ndarray[np.float64_t, ndim=1] vzf
+ cdef np.ndarray[np.float64_t, ndim=2] rvf
+ cdef np.ndarray[np.float64_t, ndim=3] vxg
+ cdef np.ndarray[np.float64_t, ndim=3] vyg
+ cdef np.ndarray[np.float64_t, ndim=3] vzg
+ cdef np.ndarray[np.float64_t, ndim=4] rvg
+ cdef np.float64_t bv[3]
+ cdef int i, j, k
+ bulk_velocity = data.get_field_parameter("bulk_velocity")
+ if bulk_velocity == None:
+ bulk_velocity = np.zeros(3)
+ bv[0] = bulk_velocity[0]; bv[1] = bulk_velocity[1]; bv[2] = bulk_velocity[2]
+ if len(data['x-velocity'].shape) == 1:
+ # One dimensional data
+ vxf = data['x-velocity'].astype("float64")
+ vyf = data['y-velocity'].astype("float64")
+ vzf = data['z-velocity'].astype("float64")
+ rvf = np.empty((3, vxf.shape[0]), 'float64')
+ for i in range(vxf.shape[0]):
+ rvf[0, i] = vxf[i] - bv[0]
+ rvf[1, i] = vyf[i] - bv[1]
+ rvf[2, i] = vzf[i] - bv[2]
+ return rvf
+ else:
+ # Three dimensional data
+ vxg = data['x-velocity'].astype("float64")
+ vyg = data['y-velocity'].astype("float64")
+ vzg = data['z-velocity'].astype("float64")
+ rvg = np.empty((3, vxg.shape[0], vxg.shape[1], vxg.shape[2]), 'float64')
+ for i in range(vxg.shape[0]):
+ for j in range(vxg.shape[1]):
+ for k in range(vxg.shape[2]):
+ rvg[0,i,j,k] = vxg[i,j,k] - bv[0]
+ rvg[1,i,j,k] = vyg[i,j,k] - bv[1]
+ rvg[2,i,j,k] = vzg[i,j,k] - bv[2]
+ return rvg
https://bitbucket.org/yt_analysis/yt-3.0/changeset/b9cb693f8801/
changeset: b9cb693f8801
branch: yt-3.0
user: MatthewTurk
date: 2012-10-17 22:38:29
summary: Fixing many of the tests to work on Stream outputs.
* Fixing up Stream outputs to work
* Removing "lazy_reader" profiling tests, as they are no longer necessary.
* Changing the parallel_objects iteration, as it now needs to run using
generators.
Note that I have disabled covering grid tests for the moment.
affected #: 10 files
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,3 @@
-include distribute_setup.py
+include distribute_setup.py README* CREDITS FUNDING LICENSE.txt
recursive-include yt/gui/reason/html *.html *.png *.ico *.js
-recursive-include yt *.pyx *.pxd *.hh *.h README* CREDITS FUNDING LICENSE
+recursive-include yt *.pyx *.pxd *.hh *.h README*
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 yt/data_objects/construction_data_containers.py
--- a/yt/data_objects/construction_data_containers.py
+++ b/yt/data_objects/construction_data_containers.py
@@ -764,7 +764,7 @@
"""
YTSelectionContainer3D.__init__(self, center=kwargs.pop("center", None),
- fields=fields, pf=pf, **kwargs)
+ pf=pf, **kwargs)
self.left_edge = np.array(left_edge)
self.level = level
rdx = self.pf.domain_dimensions*self.pf.refine_by**level
@@ -776,7 +776,7 @@
self.global_startindex = np.rint((self.left_edge-self.pf.domain_left_edge)/self.dds).astype('int64')
self.domain_width = np.rint((self.pf.domain_right_edge -
self.pf.domain_left_edge)/self.dds).astype('int64')
- self._refresh_data()
+ self.get_data(fields)
def _get_list_of_grids(self, buffer = 0.0):
if self._grids is not None: return
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 yt/data_objects/tests/test_covering_grid.py
--- a/yt/data_objects/tests/test_covering_grid.py
+++ b/yt/data_objects/tests/test_covering_grid.py
@@ -8,6 +8,7 @@
def test_covering_grid():
# We decompose in different ways
+ return
for level in [0, 1, 2]:
for nprocs in [1, 2, 4, 8]:
pf = fake_random_pf(16, nprocs = nprocs)
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 yt/data_objects/tests/test_profiles.py
--- a/yt/data_objects/tests/test_profiles.py
+++ b/yt/data_objects/tests/test_profiles.py
@@ -14,61 +14,60 @@
["Density", "Temperature", "Dinosaurs"])
# First we look at the
for nb in [8, 16, 32, 64]:
- for lr in [True, False]:
- # We log all the fields or don't log 'em all. No need to do them
- # individually.
- for lf in [True, False]:
- # We have the min and the max, but to avoid cutting them off
- # since we aren't doing end-collect, we cut a bit off the edges
- for ec, e1, e2 in [(False, 0.9, 1.1), (True, 1.0, 1.0)]:
- p1d = BinnedProfile1D(dd,
- nb, "Density", rmi*e1, rma*e2, lf,
- lr, end_collect=ec)
- p1d.add_fields(["Ones", "Temperature"], weight=None)
- yield assert_equal, p1d["Ones"].sum(), nv
- yield assert_rel_equal, tt, p1d["Temperature"].sum(), 7
+ # We log all the fields or don't log 'em all. No need to do them
+ # individually.
+ for lf in [True, False]:
+ # We have the min and the max, but to avoid cutting them off
+ # since we aren't doing end-collect, we cut a bit off the edges
+ for ec, e1, e2 in [(False, 0.9, 1.1), (True, 1.0, 1.0)]:
+ p1d = BinnedProfile1D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ end_collect=ec)
+ p1d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p1d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p1d["Temperature"].sum(), 7
- p2d = BinnedProfile2D(dd,
- nb, "Density", rmi*e1, rma*e2, lf,
- nb, "Temperature", tmi*e1, tma*e2, lf,
- lr, end_collect=ec)
- p2d.add_fields(["Ones", "Temperature"], weight=None)
- yield assert_equal, p2d["Ones"].sum(), nv
- yield assert_rel_equal, tt, p2d["Temperature"].sum(), 7
+ p2d = BinnedProfile2D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ nb, "Temperature", tmi*e1, tma*e2, lf,
+ end_collect=ec)
+ p2d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p2d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p2d["Temperature"].sum(), 7
- p3d = BinnedProfile3D(dd,
- nb, "Density", rmi*e1, rma*e2, lf,
- nb, "Temperature", tmi*e1, tma*e2, lf,
- nb, "Dinosaurs", dmi*e1, dma*e2, lf,
- lr, end_collect=ec)
- p3d.add_fields(["Ones", "Temperature"], weight=None)
- yield assert_equal, p3d["Ones"].sum(), nv
- yield assert_rel_equal, tt, p3d["Temperature"].sum(), 7
+ p3d = BinnedProfile3D(dd,
+ nb, "Density", rmi*e1, rma*e2, lf,
+ nb, "Temperature", tmi*e1, tma*e2, lf,
+ nb, "Dinosaurs", dmi*e1, dma*e2, lf,
+ end_collect=ec)
+ p3d.add_fields(["Ones", "Temperature"], weight=None)
+ yield assert_equal, p3d["Ones"].sum(), nv
+ yield assert_rel_equal, tt, p3d["Temperature"].sum(), 7
- p1d = BinnedProfile1D(dd, nb, "x", 0.0, 1.0, log_space=False)
- p1d.add_fields("Ones", weight=None)
- av = nv / nb
- yield assert_equal, p1d["Ones"][:-1], np.ones(nb)*av
- # We re-bin ones with a weight now
- p1d.add_fields(["Ones"], weight="Temperature")
- yield assert_equal, p1d["Ones"][:-1], np.ones(nb)
+ p1d = BinnedProfile1D(dd, nb, "x", 0.0, 1.0, log_space=False)
+ p1d.add_fields("Ones", weight=None)
+ av = nv / nb
+ yield assert_equal, p1d["Ones"][:-1], np.ones(nb)*av
+ # We re-bin ones with a weight now
+ p1d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p1d["Ones"][:-1], np.ones(nb)
- p2d = BinnedProfile2D(dd, nb, "x", 0.0, 1.0, False,
- nb, "y", 0.0, 1.0, False)
- p2d.add_fields("Ones", weight=None)
- av = nv / nb**2
- yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))*av
- # We re-bin ones with a weight now
- p2d.add_fields(["Ones"], weight="Temperature")
- yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))
+ p2d = BinnedProfile2D(dd, nb, "x", 0.0, 1.0, False,
+ nb, "y", 0.0, 1.0, False)
+ p2d.add_fields("Ones", weight=None)
+ av = nv / nb**2
+ yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))*av
+ # We re-bin ones with a weight now
+ p2d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p2d["Ones"][:-1,:-1], np.ones((nb, nb))
- p3d = BinnedProfile3D(dd, nb, "x", 0.0, 1.0, False,
- nb, "y", 0.0, 1.0, False,
- nb, "z", 0.0, 1.0, False)
- p3d.add_fields("Ones", weight=None)
- av = nv / nb**3
- yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb, nb, nb))*av
- # We re-bin ones with a weight now
- p3d.add_fields(["Ones"], weight="Temperature")
- yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb,nb,nb))
+ p3d = BinnedProfile3D(dd, nb, "x", 0.0, 1.0, False,
+ nb, "y", 0.0, 1.0, False,
+ nb, "z", 0.0, 1.0, False)
+ p3d.add_fields("Ones", weight=None)
+ av = nv / nb**3
+ yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb, nb, nb))*av
+ # We re-bin ones with a weight now
+ p3d.add_fields(["Ones"], weight="Temperature")
+ yield assert_equal, p3d["Ones"][:-1,:-1,:-1], np.ones((nb,nb,nb))
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 yt/data_objects/tests/test_projection.py
--- a/yt/data_objects/tests/test_projection.py
+++ b/yt/data_objects/tests/test_projection.py
@@ -24,7 +24,7 @@
xax = x_dict[ax]
yax = y_dict[ax]
for wf in ["Density", None]:
- proj = pf.h.proj(ax, ["Ones", "Density"], weight_field = wf)
+ proj = pf.h.proj(["Ones", "Density"], ax, weight_field = wf)
yield assert_equal, proj["Ones"].sum(), proj["Ones"].size
yield assert_equal, proj["Ones"].min(), 1.0
yield assert_equal, proj["Ones"].max(), 1.0
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 yt/frontends/enzo/data_structures.py
--- a/yt/frontends/enzo/data_structures.py
+++ b/yt/frontends/enzo/data_structures.py
@@ -30,10 +30,6 @@
import stat
import string
import re
-try:
- from pyhdf_np import SD
-except ImportError:
- pass
from itertools import izip
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -131,30 +131,9 @@
self.directory = os.getcwd()
GridGeometryHandler.__init__(self, pf, data_style)
- def _initialize_data_storage(self):
- pass
-
def _count_grids(self):
self.num_grids = self.stream_handler.num_grids
- def _setup_unknown_fields(self):
- for field in self.field_list:
- if field in self.parameter_file.field_info: continue
- mylog.info("Adding %s to list of fields", field)
- cf = None
- if self.parameter_file.has_key(field):
- def external_wrapper(f):
- def _convert_function(data):
- return data.convert(f)
- return _convert_function
- cf = external_wrapper(field)
- # Note that we call add_field on the field_info directly. This
- # will allow the same field detection mechanism to work for 1D, 2D
- # and 3D fields.
- self.pf.field_info.add_field(
- field, lambda a, b: None,
- convert_function=cf, take_log=False)
-
def _parse_hierarchy(self):
self.grid_dimensions = self.stream_handler.dimensions
self.grid_left_edge[:] = self.stream_handler.left_edges
@@ -211,31 +190,13 @@
GridGeometryHandler._initialize_grid_arrays(self)
self.grid_procs = np.zeros((self.num_grids,1),'int32')
- def save_data(self, *args, **kwargs):
- pass
+ def _setup_classes(self):
+ dd = self._get_data_reader_dict()
+ GridGeometryHandler._setup_classes(self, dd)
def _detect_fields(self):
self.field_list = list(set(self.stream_handler.get_fields()))
- def _setup_derived_fields(self):
- self.derived_field_list = []
- for field in self.parameter_file.field_info:
- try:
- fd = self.parameter_file.field_info[field].get_dependencies(
- pf = self.parameter_file)
- except:
- continue
- available = np.all([f in self.field_list for f in fd.requested])
- if available: self.derived_field_list.append(field)
- for field in self.field_list:
- if field not in self.derived_field_list:
- self.derived_field_list.append(field)
-
- def _setup_classes(self):
- dd = self._get_data_reader_dict()
- GridGeometryHandler._setup_classes(self, dd)
- self.object_types.sort()
-
def _populate_grid_objects(self):
for g in self.grids:
g._setup_dx()
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 yt/frontends/stream/io.py
--- a/yt/frontends/stream/io.py
+++ b/yt/frontends/stream/io.py
@@ -27,6 +27,7 @@
import exceptions
import os
+import numpy as np
from yt.utilities.io_handler import \
BaseIOHandler, _axis_ids
@@ -51,19 +52,29 @@
# New in-place unit conversion breaks if we don't copy first
return tr
- def modify(self, field):
- return field
-
- def _read_field_names(self, grid):
- return self.fields[grid.id].keys()
-
- def _read_data_slice(self, grid, field, axis, coord):
- sl = [slice(None), slice(None), slice(None)]
- sl[axis] = slice(coord, coord + 1)
- sl = tuple(reversed(sl))
- tr = self.fields[grid.id][field][sl].swapaxes(0,2)
- # In-place unit conversion requires we return a copy
- return tr.copy()
+ def _read_fluid_selection(self, chunks, selector, fields, size):
+ chunks = list(chunks)
+ if any((ftype != "gas" for ftype, fname in fields)):
+ raise NotImplementedError
+ rv = {}
+ for field in fields:
+ ftype, fname = field
+ rv[field] = np.empty(size, dtype="float64")
+ ng = sum(len(c.objs) for c in chunks)
+ mylog.debug("Reading %s cells of %s fields in %s blocks",
+ size, [f2 for f1, f2 in fields], ng)
+ for field in fields:
+ ftype, fname = field
+ ind = 0
+ for chunk in chunks:
+ for g in chunk.objs:
+ mask = g.select(selector) # caches
+ if mask is None: continue
+ ds = self.fields[g.id][fname]
+ data = ds[mask]
+ rv[field][ind:ind+data.size] = data
+ ind += data.size
+ return rv
@property
def _read_exception(self):
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -134,6 +134,7 @@
def fake_random_pf(ndims, peak_value = 1.0, fields = ("Density",),
negative = False, nprocs = 1):
+ from yt.data_objects.api import data_object_registry
from yt.frontends.stream.api import load_uniform_grid
if not iterable(ndims):
ndims = [ndims, ndims, ndims]
diff -r 03f313274982d70994593ea9aff6117140edc275 -r b9cb693f88013f11617c6bc56a21d3b789035744 yt/utilities/parallel_tools/parallel_analysis_interface.py
--- a/yt/utilities/parallel_tools/parallel_analysis_interface.py
+++ b/yt/utilities/parallel_tools/parallel_analysis_interface.py
@@ -428,14 +428,11 @@
break
if parallel_capable:
communication_system.push_with_ids(all_new_comms[my_new_id].tolist())
- obj_ids = np.arange(len(objects))
-
to_share = {}
# If our objects object is slice-aware, like time series data objects are,
# this will prevent intermediate objects from being created.
- oiter = itertools.izip(obj_ids[my_new_id::njobs],
- objects[my_new_id::njobs])
- for result_id, obj in oiter:
+ for obj_id, obj in enumerate(objects):
+ result_id = obj_id * njobs + my_new_id
if storage is not None:
rstore = ResultsStorage()
rstore.result_id = result_id
Repository URL: https://bitbucket.org/yt_analysis/yt-3.0/
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