[yt-svn] commit/yt: 3 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Fri Feb 28 15:13:18 PST 2014
3 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/3e71cde3f8c2/
Changeset: 3e71cde3f8c2
Branch: stable
User: MatthewTurk
Date: 2014-03-01 00:11:28
Summary: Merging from development stable.
Affected #: 22 files
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,5 +1,9 @@
-include distribute_setup.py README* CREDITS COPYING.txt CITATION
+include distribute_setup.py README* CREDITS COPYING.txt CITATION nose.cfg
recursive-include yt/gui/reason/html *.html *.png *.ico *.js
-recursive-include yt *.pyx *.pxd *.h README*
+recursive-include yt *.pyx *.pxd *.h README* *.glsl *.cu
recursive-include yt/utilities/kdtree *.f90 *.v Makefile LICENSE
-
+recursive-include yt/analysis_modules/halo_finding/rockstar *.py *.pyx
+prune yt/frontends/_skeleton
+prune tests
+graft yt/gui/reason/html/resources
+exclude clean.sh .hgchurn
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -503,10 +503,8 @@
cd $LIB
if [ ! -z `echo $LIB | grep h5py` ]
then
- shift
( ${DEST_DIR}/bin/python2.7 setup.py build --hdf5=${HDF5_DIR} $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
else
- shift
( ${DEST_DIR}/bin/python2.7 setup.py build $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
fi
( ${DEST_DIR}/bin/python2.7 setup.py install 2>&1 ) 1>> ${LOG_FILE} || do_exit
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/analysis_modules/halo_finding/setup.py
--- a/yt/analysis_modules/halo_finding/setup.py
+++ b/yt/analysis_modules/halo_finding/setup.py
@@ -1,9 +1,7 @@
#!/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('halo_finding', parent_package, top_path)
@@ -12,6 +10,5 @@
config.add_subpackage("parallel_hop")
if os.path.exists("rockstar.cfg"):
config.add_subpackage("rockstar")
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
+ config.make_config_py() # installs __config__.py
return config
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/analysis_modules/photon_simulator/photon_simulator.py
--- a/yt/analysis_modules/photon_simulator/photon_simulator.py
+++ b/yt/analysis_modules/photon_simulator/photon_simulator.py
@@ -27,6 +27,7 @@
cm_per_km, erg_per_keV
from yt.utilities.cosmology import Cosmology
from yt.utilities.orientation import Orientation
+from yt.utilities.definitions import mpc_conversion
from yt.utilities.parallel_tools.parallel_analysis_interface import \
communication_system, parallel_root_only, get_mpi_type, \
op_names, parallel_capable
@@ -415,7 +416,8 @@
def project_photons(self, L, area_new=None, exp_time_new=None,
redshift_new=None, dist_new=None,
absorb_model=None, psf_sigma=None,
- sky_center=None, responses=None):
+ sky_center=None, responses=None,
+ convolve_energies=False):
r"""
Projects photons onto an image plane given a line of sight.
@@ -443,8 +445,10 @@
sky_center : array_like, optional
Center RA, Dec of the events in degrees.
responses : list of strings, optional
- The names of the ARF and RMF files to convolve the photons with.
-
+ The names of the ARF and/or RMF files to convolve the photons with.
+ convolve_energies : boolean, optional
+ If this is set, the photon energies will be convolved with the RMF.
+
Examples
--------
>>> L = np.array([0.1,-0.2,0.3])
@@ -486,8 +490,10 @@
parameters = {}
if responses is not None:
+ responses = ensure_list(responses)
parameters["ARF"] = responses[0]
- parameters["RMF"] = responses[1]
+ if len(responses) == 2:
+ parameters["RMF"] = responses[1]
area_new = parameters["ARF"]
if (exp_time_new is None and area_new is None and
@@ -509,8 +515,13 @@
elo = f["SPECRESP"].data.field("ENERG_LO")
ehi = f["SPECRESP"].data.field("ENERG_HI")
eff_area = np.nan_to_num(f["SPECRESP"].data.field("SPECRESP"))
- weights = self._normalize_arf(parameters["RMF"])
- eff_area *= weights
+ if "RMF" in parameters:
+ weights = self._normalize_arf(parameters["RMF"])
+ eff_area *= weights
+ else:
+ mylog.warning("You specified an ARF but not an RMF. This is ok if the "+
+ "responses are normalized properly. If not, you may "+
+ "get inconsistent results.")
f.close()
Aratio = eff_area.max()/self.parameters["FiducialArea"]
else:
@@ -523,7 +534,11 @@
else:
if redshift_new is None:
zobs = 0.0
- D_A = dist[0]*self.pf.units["kpc"]/self.pf.units[dist[1]]
+ if dist_new[1] not in mpc_conversion:
+ mylog.error("Please specify dist_new in one of the following units: %s",
+ mpc_conversion.keys())
+ raise KeyError
+ D_A = dist_new[0]*mpc_conversion["kpc"]/mpc_conversion[dist_new[1]]
else:
zobs = redshift_new
D_A = self.cosmo.AngularDiameterDistance(0.0,zobs)*1000.
@@ -609,7 +624,7 @@
if comm.rank == 0: mylog.info("Total number of observed photons: %d" % (num_events))
- if responses is not None:
+ if "RMF" in parameters and convolve_energies:
events, info = self._convolve_with_rmf(parameters["RMF"], events)
for k, v in info.items(): parameters[k] = v
@@ -733,8 +748,8 @@
self.wcs.wcs.cunit = ["deg"]*2
(self.events["xsky"],
self.events["ysky"]) = \
- self.wcs.wcs_pix2world(self.events["xpix"], self.events["ypix"],
- 1, ra_dec_order=True)
+ self.wcs.wcs_pix2world(self.events["xpix"],
+ self.events["ypix"], 1)
def keys(self):
return self.events.keys()
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/analysis_modules/photon_simulator/spectral_models.py
--- a/yt/analysis_modules/photon_simulator/spectral_models.py
+++ b/yt/analysis_modules/photon_simulator/spectral_models.py
@@ -15,9 +15,18 @@
import os
from yt.funcs import *
import h5py
+
+try:
+ import xspec
+except ImportError:
+ pass
+
try:
import astropy.io.fits as pyfits
- import xspec
+except ImportError:
+ pass
+
+try:
from scipy.integrate import cumtrapz
from scipy import stats
except ImportError:
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/analysis_modules/radmc3d_export/RadMC3DInterface.py
--- a/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py
+++ b/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py
@@ -182,10 +182,14 @@
LE = self.domain_left_edge
RE = self.domain_right_edge
+ # Radmc3D wants the cell wall positions in cgs. Convert here:
+ LE_cgs = LE * self.pf.units['cm']
+ RE_cgs = RE * self.pf.units['cm']
+
# calculate cell wall positions
- xs = [str(x) for x in np.linspace(LE[0], RE[0], dims[0]+1)]
- ys = [str(y) for y in np.linspace(LE[1], RE[1], dims[1]+1)]
- zs = [str(z) for z in np.linspace(LE[2], RE[2], dims[2]+1)]
+ xs = [str(x) for x in np.linspace(LE_cgs[0], RE_cgs[0], dims[0]+1)]
+ ys = [str(y) for y in np.linspace(LE_cgs[1], RE_cgs[1], dims[1]+1)]
+ zs = [str(z) for z in np.linspace(LE_cgs[2], RE_cgs[2], dims[2]+1)]
# writer file header
grid_file = open(self.grid_filename, 'w')
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/analysis_modules/setup.py
--- a/yt/analysis_modules/setup.py
+++ b/yt/analysis_modules/setup.py
@@ -1,12 +1,10 @@
#!/usr/bin/env python
-import setuptools
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('analysis_modules', parent_package, top_path)
config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
config.add_subpackage("absorption_spectrum")
config.add_subpackage("coordinate_transformation")
config.add_subpackage("cosmological_observation")
@@ -16,10 +14,15 @@
config.add_subpackage("halo_profiler")
config.add_subpackage("hierarchy_subset")
config.add_subpackage("level_sets")
+ config.add_subpackage("particle_trajectories")
+ config.add_subpackage("photon_simulator")
config.add_subpackage("radial_column_density")
config.add_subpackage("spectral_integrator")
config.add_subpackage("star_analysis")
config.add_subpackage("two_point_functions")
config.add_subpackage("radmc3d_export")
- config.add_subpackage("sunyaev_zeldovich")
+ config.add_subpackage("sunrise_export")
+ config.add_subpackage("sunyaev_zeldovich")
+ config.add_subpackage("particle_trajectories")
+ config.add_subpackage("photon_simulator")
return config
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/data_objects/hierarchy.py
--- a/yt/data_objects/hierarchy.py
+++ b/yt/data_objects/hierarchy.py
@@ -319,7 +319,11 @@
obj = self.get_data("/Objects", name)
if obj is None:
return
- obj = cPickle.loads(obj.value)
+ if isinstance(obj, np.ndarray):
+ obj = obj.tostring()
+ elif hasattr(obj, 'value'):
+ obj = obj.value
+ obj = cPickle.loads(obj)
if iterable(obj) and len(obj) == 2:
obj = obj[1] # Just the object, not the pf
if hasattr(obj, '_fix_pickle'): obj._fix_pickle()
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/data_objects/object_finding_mixin.py
--- a/yt/data_objects/object_finding_mixin.py
+++ b/yt/data_objects/object_finding_mixin.py
@@ -15,6 +15,7 @@
import numpy as np
+from yt.config import ytcfg
from yt.funcs import *
from yt.utilities.lib import \
get_box_grids_level, \
@@ -54,7 +55,19 @@
def find_max_cell_location(self, field, finest_levels = 3):
if finest_levels is not False:
- gi = (self.grid_levels >= self.max_level - finest_levels).ravel()
+ # This prevents bad values for the case that the number of grids to
+ # search is smaller than the number of processors being applied to
+ # the task, by
+ nproc = ytcfg.getint("yt", "__topcomm_parallel_size")
+ while 1:
+ gi = (self.grid_levels >= self.max_level - finest_levels).ravel()
+ if gi.sum() >= nproc:
+ break
+ elif finest_levels >= self.max_level:
+ raise YTTooParallel
+ else:
+ finest_levels += 1
+
source = self.grid_collection([0.0]*3, self.grids[gi])
else:
source = self.all_data()
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/frontends/athena/data_structures.py
--- a/yt/frontends/athena/data_structures.py
+++ b/yt/frontends/athena/data_structures.py
@@ -349,6 +349,8 @@
if len(self.parameters) == 0:
self._parse_parameter_file()
self.conversion_factors = defaultdict(lambda: 1.0)
+ if "EOSType" not in self.parameters:
+ self.parameters["EOSType"] = -1
if self.specified_parameters.has_key("LengthUnits") :
self._setup_getunits_units()
else :
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/frontends/athena/fields.py
--- a/yt/frontends/athena/fields.py
+++ b/yt/frontends/athena/fields.py
@@ -78,7 +78,7 @@
def _convertDensity(data) :
return data.convert("Density")
def _density(field, data) :
- return data["density"]
+ return data["density"].copy()
add_field("Density", function=_density, take_log=False,
units=r"\rm{g}/\rm{cm}^3", projected_units=r"\rm{g}/\rm{cm}^2",
convert_function=_convertDensity)
@@ -87,21 +87,21 @@
return data.convert("x-velocity")
def _xvelocity(field, data):
if "velocity_x" in data.pf.field_info:
- return data["velocity_x"]
+ return data["velocity_x"].copy()
else:
return data["momentum_x"]/data["density"]
add_field("x-velocity", function=_xvelocity, take_log=False,
units=r"\rm{cm}/\rm{s}", convert_function=_convertVelocity)
def _yvelocity(field, data):
if "velocity_y" in data.pf.field_info:
- return data["velocity_y"]
+ return data["velocity_y"].copy()
else:
return data["momentum_y"]/data["density"]
add_field("y-velocity", function=_yvelocity, take_log=False,
units=r"\rm{cm}/\rm{s}", convert_function=_convertVelocity)
def _zvelocity(field, data):
if "velocity_z" in data.pf.field_info:
- return data["velocity_z"]
+ return data["velocity_z"].copy()
else:
return data["momentum_z"]/data["density"]
add_field("z-velocity", function=_zvelocity, take_log=False,
@@ -128,7 +128,7 @@
return data.convert("Density")*data.convert("x-velocity")**2
def _pressure(field, data) :
if "pressure" in data.pf.field_info:
- return data["pressure"]
+ return data["pressure"].copy()
else:
eint = data["total_energy"] - 0.5*(data["momentum_x"]**2 +
data["momentum_y"]**2 +
@@ -154,17 +154,17 @@
def _convertBfield(data):
return np.sqrt(4*np.pi*data.convert("Density")*data.convert("x-velocity")**2)
def _Bx(field, data):
- return data['cell_centered_B_x']
+ return data['cell_centered_B_x'].copy()
add_field("Bx", function=_Bx, take_log=False,
units=r"\rm{Gauss}", display_name=r"B_x",
convert_function=_convertBfield)
def _By(field, data):
- return data['cell_centered_B_y']
+ return data['cell_centered_B_y'].copy()
add_field("By", function=_By, take_log=False,
units=r"\rm{Gauss}", display_name=r"B_y",
convert_function=_convertBfield)
def _Bz(field, data):
- return data['cell_centered_B_z']
+ return data['cell_centered_B_z'].copy()
add_field("Bz", function=_Bz, take_log=False,
units=r"\rm{Gauss}", display_name=r"B_z",
convert_function=_convertBfield)
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/frontends/enzo/fields.py
--- a/yt/frontends/enzo/fields.py
+++ b/yt/frontends/enzo/fields.py
@@ -355,7 +355,7 @@
amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(np.float64),
data["particle_position_y"][filter].astype(np.float64),
data["particle_position_z"][filter].astype(np.float64),
- data["particle_mass"][filter],
+ data["particle_mass"][filter].astype(np.float64),
np.int64(np.where(filter)[0].size),
blank, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
@@ -429,7 +429,7 @@
amr_utils.CICDeposit_3(data["particle_position_x"].astype(np.float64),
data["particle_position_y"].astype(np.float64),
data["particle_position_z"].astype(np.float64),
- particle_field_data,
+ particle_field_data.astype(np.float64),
data["particle_position_x"].size,
top, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
@@ -440,7 +440,7 @@
amr_utils.CICDeposit_3(data["particle_position_x"].astype(np.float64),
data["particle_position_y"].astype(np.float64),
data["particle_position_z"].astype(np.float64),
- data["particle_mass"],
+ data["particle_mass"].astype(np.float64),
data["particle_position_x"].size,
bottom, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
@@ -470,7 +470,7 @@
amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(np.float64),
data["particle_position_y"][filter].astype(np.float64),
data["particle_position_z"][filter].astype(np.float64),
- particle_field_data,
+ particle_field_data.astype(np.float64),
np.int64(np.where(filter)[0].size),
top, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
@@ -481,7 +481,7 @@
amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(np.float64),
data["particle_position_y"][filter].astype(np.float64),
data["particle_position_z"][filter].astype(np.float64),
- data["particle_mass"][filter],
+ data["particle_mass"][filter].astype(np.float64),
np.int64(np.where(filter)[0].size),
bottom, np.array(data.LeftEdge).astype(np.float64),
np.array(data.ActiveDimensions).astype(np.int32),
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/frontends/flash/data_structures.py
--- a/yt/frontends/flash/data_structures.py
+++ b/yt/frontends/flash/data_structures.py
@@ -422,7 +422,7 @@
self.domain_right_edge = np.array(
[self.parameters["%smax" % ax] for ax in 'xyz']).astype("float64")
if self.dimensionality < 3:
- for d in (dimensionality)+range(3-dimensionality):
+ for d in [dimensionality]+range(3-dimensionality):
if self.domain_left_edge[d] == self.domain_right_edge[d]:
mylog.warning('Identical domain left edge and right edges '
'along dummy dimension (%i), attempting to read anyway' % d)
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/utilities/command_line.py
--- a/yt/utilities/command_line.py
+++ b/yt/utilities/command_line.py
@@ -1037,7 +1037,7 @@
mpd.upload()
class YTInstInfoCmd(YTCommand):
- name = "instinfo"
+ name = ["instinfo", "version"]
args = (
dict(short="-u", long="--update-source", action="store_true",
default = False,
@@ -1055,6 +1055,7 @@
def __call__(self, opts):
import pkg_resources
+ import yt
yt_provider = pkg_resources.get_provider("yt")
path = os.path.dirname(yt_provider.module_path)
print
@@ -1071,10 +1072,11 @@
vstring = get_yt_version()
if vstring is not None:
print
- print "The current version of the code is:"
+ print "The current version and changeset for the code is:"
print
print "---"
- print vstring.strip()
+ print "Version = %s" % yt.__version__
+ print "Changeset = %s" % vstring.strip()
print "---"
print
if "site-packages" not in path:
@@ -1614,6 +1616,7 @@
def __call__(self, opts):
import pkg_resources
+ import yt
yt_provider = pkg_resources.get_provider("yt")
path = os.path.dirname(yt_provider.module_path)
print
@@ -1631,10 +1634,11 @@
if "site-packages" not in path:
vstring = get_hg_version(path)
print
- print "The current version of the code is:"
+ print "The current version and changeset for the code is:"
print
print "---"
- print vstring.strip()
+ print "Version = %s" % yt.__version__
+ print "Changeset = %s" % vstring.strip()
print "---"
print
print "This installation CAN be automatically updated."
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/utilities/exceptions.py
--- a/yt/utilities/exceptions.py
+++ b/yt/utilities/exceptions.py
@@ -210,6 +210,10 @@
class YTEmptyProfileData(Exception):
pass
+class YTTooParallel(YTException):
+ def __str__(self):
+ return "You've used too many processors for this dataset."
+
class YTDuplicateFieldInProfile(Exception):
def __init__(self, field, new_spec, old_spec):
self.field = field
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/utilities/lib/marching_cubes.pyx
--- a/yt/utilities/lib/marching_cubes.pyx
+++ b/yt/utilities/lib/marching_cubes.pyx
@@ -535,6 +535,7 @@
vertices = np.zeros((triangles.count*3,3), dtype='float64')
if do_sample == 0:
FillAndWipeTriangles(vertices, triangles.first)
+ return vertices
cdef int nskip
if do_sample == 1:
nskip = 1
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/visualization/color_maps.py
--- a/yt/visualization/color_maps.py
+++ b/yt/visualization/color_maps.py
@@ -120,7 +120,7 @@
# Add colormaps in _colormap_data.py that weren't defined here
_vs = np.linspace(0,1,255)
for k,v in _cm.color_map_luts.iteritems():
- if k not in yt_colormaps:
+ if k not in yt_colormaps and k not in mcm.cmap_d:
cdict = { 'red': zip(_vs,v[0],v[0]),
'green': zip(_vs,v[1],v[1]),
'blue': zip(_vs,v[2],v[2]) }
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/visualization/eps_writer.py
--- a/yt/visualization/eps_writer.py
+++ b/yt/visualization/eps_writer.py
@@ -26,9 +26,12 @@
from .plot_types import \
VMPlot, \
ProfilePlot
+from .plot_collection import PlotCollection
from .plot_window import PlotWindow
+from .profile_plotter import PhasePlot
from .plot_modifications import get_smallest_appropriate_unit
+
class DualEPS(object):
def __init__(self, figsize=(12,12)):
r"""Initializes the DualEPS class to which we can progressively add layers
@@ -57,6 +60,14 @@
#=============================================================================
+ def return_field(self, plot):
+ if isinstance(plot, PlotWindow) or isinstance(plot, PhasePlot):
+ return plot.plots.keys()[0]
+ else:
+ return None
+
+#=============================================================================
+
def axis_box(self, xrange=(0,1), yrange=(0,1), xlabel="", ylabel="",
xlog=False, ylog=False, xdata=None, ydata=None,
tickcolor=None, bare_axes=False,
@@ -275,18 +286,17 @@
>>> d.axis_box_yt(p)
>>> d.save_fig()
"""
- if isinstance(plot, PlotWindow):
+ if isinstance(plot, (PlotWindow, PhasePlot)):
plot.refresh()
- width = plot.width[0]
else:
plot._redraw_image()
- if isinstance(plot, VMPlot):
- width = plot.width
- if isinstance(plot, VMPlot) or isinstance(plot, PlotWindow):
+ if isinstance(plot, (VMPlot, PlotWindow)):
if isinstance(plot, PlotWindow):
data = plot._frb
+ width = plot.width[0]
else:
data = plot.data
+ width = plot.width
if units == None:
units = get_smallest_appropriate_unit(width, plot.pf)
_xrange = (0, width * plot.pf[units])
@@ -314,6 +324,26 @@
_ylabel = 'Image y (%s)' % (units)
if tickcolor == None:
_tickcolor = pyx.color.cmyk.white
+ elif isinstance(plot, PhasePlot):
+ k = plot.plots.keys()[0]
+ _xrange = plot[k].axes.get_xlim()
+ _yrange = plot[k].axes.get_ylim()
+ _xlog = plot.profile.x_log
+ _ylog = plot.profile.y_log
+ if bare_axes:
+ _xlabel = ""
+ _ylabel = ""
+ else:
+ if xlabel != None:
+ _xlabel = xlabel
+ else:
+ _xlabel = plot[k].axes.get_xlabel()
+ if ylabel != None:
+ _ylabel = ylabel
+ else:
+ _ylabel = plot[k].axes.get_ylabel()
+ if tickcolor == None:
+ _tickcolor = None
else:
_xrange = plot._axes.get_xlim()
_yrange = plot._axes.get_ylim()
@@ -412,7 +442,7 @@
plot.colorbar = None
plot._redraw_image()
_p1 = plot._figure
- elif isinstance(plot, PlotWindow):
+ elif isinstance(plot, (PlotWindow, PhasePlot)):
self.field = field
if self.field == None:
self.field = plot.plots.keys()[0]
@@ -424,18 +454,22 @@
plot.refresh()
_p1 = plot.plots[self.field].figure
# hack to account for non-square display ratios (not sure why)
- shift = 12.0 / 340
+ if isinstance(plot, PlotWindow):
+ shift = 12.0 / 340
elif isinstance(plot, ProfilePlot):
plot._redraw_image()
# Remove colorbar
_p1 = plot._figure
_p1.delaxes(_p1.axes[1])
+ else:
+ raise RuntimeError("Unknown plot type")
+
_p1.axes[0].set_axis_off() # remove axes
_p1.axes[0].set_position([-shift,0,1,1]) # rescale figure
_p1.set_facecolor('w') # set background color
figure_canvas = FigureCanvasAgg(_p1)
figure_canvas.draw()
- size = _p1.get_size_inches() * _p1.dpi
+ size = (_p1.get_size_inches() * _p1.dpi).astype('int')
image = pyx.bitmap.image(size[0], size[1], "RGB",
figure_canvas.tostring_rgb())
#figure_canvas.print_png('test.png')
@@ -507,6 +541,12 @@
# Scale the colorbar
shift = (0.5*(1.0-shrink[0])*size[0], 0.5*(1.0-shrink[1])*size[1])
+ # To facilitate strething rather than shrinking
+ # If stretched in both directions (makes no sense?) then y dominates.
+ if(shrink[0] > 1.0):
+ shift = (0.05*self.figsize[0], 0.5*(1.0-shrink[1])*size[1])
+ if(shrink[1] > 1.0):
+ shift = (0.5*(1.0-shrink[0])*size[0], 0.05*self.figsize[1])
size = (size[0] * shrink[0], size[1] * shrink[1])
origin = (origin[0] + shift[0], origin[1] + shift[1])
@@ -567,7 +607,7 @@
#=============================================================================
- def colorbar_yt(self, plot, **kwargs):
+ def colorbar_yt(self, plot, field=None, **kwargs):
r"""Wrapper around DualEPS.colorbar to take information from a yt plot.
Accepts all parameters that DualEPS.colorbar takes.
@@ -587,7 +627,9 @@
>>> d.save_fig()
"""
_cmap = None
- if isinstance(plot, PlotWindow):
+ if field != None:
+ self.field = field
+ if isinstance(plot, (PlotWindow, PhasePlot)):
_cmap = plot._colormaps[self.field]
else:
if plot.cmap != None:
@@ -601,10 +643,13 @@
_zlabel = _zlabel.replace("_","\;")
_zlog = plot.log_field
_zrange = (plot.norm.vmin, plot.norm.vmax)
- elif isinstance(plot, PlotWindow):
+ elif isinstance(plot, (PlotWindow, PhasePlot)):
proj = plot._plot_type.endswith("Projection") and \
plot.data_source.weight_field == None
- _zlabel = plot.pf.field_info[self.field].get_label(proj)
+ if isinstance(plot, PlotWindow):
+ _zlabel = plot.pf.field_info[self.field].get_label(proj)
+ else:
+ _zlabel = plot.data_source.pf.field_info[self.field].get_label(proj)
_zlabel = _zlabel.replace("_","\;")
_zlog = plot.get_log(self.field)[self.field]
if plot.plots[self.field].zmin == None:
@@ -656,6 +701,59 @@
#=============================================================================
+ def arrow(self, size=0.2, label="", loc=(0.05,0.08), labelloc="top",
+ color=pyx.color.cmyk.white,
+ linewidth=pyx.style.linewidth.normal):
+ r"""Draws an arrow in the current figure
+
+ Parameters
+ ----------
+ size : float
+ Length of arrow (base to tip) in units of the figure size.
+ label : string
+ Annotation label of the arrow.
+ loc : tuple of floats
+ Location of the left hand side of the arrow in units of
+ the figure size.
+ labelloc : string
+ Location of the label with respect to the line. Can be
+ "top" or "bottom"
+ color : `pyx.color.*.*`
+ Color of the arrow. Example: pyx.color.cymk.white
+ linewidth : `pyx.style.linewidth.*`
+ Width of the arrow. Example: pyx.style.linewidth.normal
+
+ Examples
+ --------
+ >>> d = DualEPS()
+ >>> d.axis_box(xrange=(0,100), yrange=(1e-3,1), ylog=True)
+ >>> d.insert_image("arrow_image.jpg")
+ >>> d.arrow(size=0.2, label="Black Hole!", loc=(0.05, 0.1))
+ >>> d.save_fig()
+ """
+ line = pyx.path.line(self.figsize[0]*loc[0],
+ self.figsize[1]*loc[1],
+ self.figsize[0]*(loc[0]+size),
+ self.figsize[1]*loc[1])
+ self.canvas.stroke(line, [linewidth, color, pyx.deco.earrow()])
+
+
+ if labelloc == "bottom":
+ yoff = -0.1*size
+ valign = pyx.text.valign.top
+ else:
+ yoff = +0.1*size
+ valign = pyx.text.valign.bottom
+ if label != "":
+ self.canvas.text(self.figsize[0]*(loc[0]+0.5*size),
+ self.figsize[1]*(loc[1]+yoff), label,
+ [color, valign, pyx.text.halign.center])
+
+
+
+
+#=============================================================================
+
def scale_line(self, size=0.2, label="", loc=(0.05,0.08), labelloc="top",
color=pyx.color.cmyk.white,
linewidth=pyx.style.linewidth.normal):
@@ -686,6 +784,7 @@
>>> d.scale_line(size=0.2, label="1 kpc", loc=(0.05, 0.1))
>>> d.save_fig()
"""
+
line = pyx.path.line(self.figsize[0]*loc[0],
self.figsize[1]*loc[1],
self.figsize[0]*(loc[0]+size),
@@ -783,13 +882,13 @@
#=============================================================================
#=============================================================================
-def multiplot(ncol, nrow, yt_plots=None, images=None, xranges=None,
- yranges=None, xlabels=None, ylabels=None,
+def multiplot(ncol, nrow, yt_plots=None, fields=None, images=None,
+ xranges=None, yranges=None, xlabels=None, ylabels=None,
xdata=None, ydata=None, colorbars=None,
shrink_cb=0.95, figsize=(8,8), margins=(0,0), titles=None,
savefig=None, format="eps", yt_nocbar=False, bare_axes=False,
xaxis_flags=None, yaxis_flags=None,
- cb_flags=None):
+ cb_flags=None, cb_location=None, plot_collection=False):
r"""Convenience routine to create a multi-panel figure from yt plots or
JPEGs. The images are first placed from the origin, and then
bottom-to-top and left-to-right.
@@ -834,6 +933,11 @@
axes.
cb_flags : list of booleans
Flags for each plot to have a colorbar or not.
+ cb_location : list of strings
+ Strings to control the location of the colorbar (left, right,
+ top, bottom)
+ plot_collection : boolean
+ Set to true to yt_plots is a PlotCollection
Examples
--------
@@ -858,8 +962,9 @@
yt plots.
"""
# Error check
+ npanels = ncol*nrow
if images != None:
- if len(images) != ncol*nrow:
+ if len(images) != npanels:
raise RuntimeError("Number of images (%d) doesn't match nrow(%d)"\
" x ncol(%d)." % (len(images), nrow, ncol))
return
@@ -872,26 +977,29 @@
_yt = True
else:
_yt = False
+ if fields == None:
+ fields = [None] * npanels
# If no ranges or labels given and given only images, fill them in.
if not _yt:
if xranges is None:
xranges = []
- for i in range(nrow*ncol): xranges.append((0,1))
+ for i in range(npanels): xranges.append((0,1))
if yranges is None:
yranges = []
- for i in range(nrow*ncol): yranges.append((0,1))
+ for i in range(npanels): yranges.append((0,1))
if xlabels is None:
xlabels = []
- for i in range(nrow*ncol): xlabels.append("")
+ for i in range(npanels): xlabels.append("")
if ylabels is None:
ylabels = []
- for i in range(nrow*ncol): ylabels.append("")
+ for i in range(npanels): ylabels.append("")
d = DualEPS(figsize=figsize)
count = 0
for j in range(nrow):
- ypos = j*(figsize[1] + margins[1])
+ invj = nrow - j - 1
+ ypos = invj*(figsize[1] + margins[1])
for i in range(ncol):
xpos = i*(figsize[0] + margins[0])
index = j*ncol + i
@@ -930,7 +1038,8 @@
ylabel = ylabels[j]
else:
ylabel = None
- d.insert_image_yt(yt_plots[index], pos=(xpos, ypos))
+ d.insert_image_yt(yt_plots[index], pos=(xpos, ypos),
+ field=fields[index])
d.axis_box_yt(yt_plots[index], pos=(xpos, ypos),
bare_axes=bare_axes, xaxis_side=xaxis,
yaxis_side=yaxis,
@@ -956,7 +1065,8 @@
100.0 * d.canvas.bbox().bottom().t,
100.0 * d.canvas.bbox().top().t - d.figsize[1])
for j in range(nrow):
- ypos0 = j*(figsize[1] + margins[1])
+ invj = nrow - j - 1
+ ypos0 = invj*(figsize[1] + margins[1])
for i in range(ncol):
xpos0 = i*(figsize[0] + margins[0])
index = j*ncol + i
@@ -964,32 +1074,49 @@
if cb_flags != None:
if cb_flags[index] == False:
continue
- if ncol == 1:
- orientation = "right"
+ if cb_location == None:
+ if ncol == 1:
+ orientation = "right"
+ elif i == 0:
+ orientation = "left"
+ elif i+1 == ncol:
+ orientation = "right"
+ elif j == 0:
+ orientation = "bottom"
+ elif j+1 == nrow:
+ orientation = "top"
+ else:
+ orientation = None # Marker for interior plot
+ else:
+ if fields[index] not in cb_location.keys():
+ raise RuntimeError("%s not found in cb_location dict" %
+ fields[index])
+ return
+ orientation = cb_location[fields[index]]
+ if orientation == "right":
xpos = bbox[1]
ypos = ypos0
- elif j == 0:
- orientation = "bottom"
+ elif orientation == "left":
+ xpos = bbox[0]
+ ypos = ypos0
+ elif orientation == "bottom":
ypos = bbox[2]
xpos = xpos0
- elif i == 0:
- orientation = "left"
- xpos = bbox[0]
- ypos = ypos0
- elif i+1 == ncol:
- orientation = "right"
- xpos = bbox[1]
- ypos = ypos0
- elif j+1 == nrow:
- orientation = "top"
+ elif orientation == "top":
ypos = bbox[3]
xpos = xpos0
else:
+ mylog.warning("Unknown colorbar location %s. "
+ "No colorbar displayed." % orientation)
orientation = None # Marker for interior plot
if orientation != None:
if _yt:
+ # Set field if undefined
+ if fields[index] == None:
+ fields[index] = d.return_field(yt_plots[index])
d.colorbar_yt(yt_plots[index],
+ field=fields[index],
pos=[xpos,ypos],
shrink=shrink_cb,
orientation=orientation)
@@ -1009,8 +1136,8 @@
#=============================================================================
-def multiplot_yt(ncol, nrow, plot_col, **kwargs):
- r"""Wrapper for multiplot that takes a yt PlotCollection.
+def multiplot_yt(ncol, nrow, plots, fields=None, **kwargs):
+ r"""Wrapper for multiplot that takes a yt PlotWindow or PlotCollection.
Accepts all parameters used in multiplot.
@@ -1020,8 +1147,8 @@
Number of columns in the figure.
nrow : integer
Number of rows in the figure.
- plot_col : `PlotCollection`
- yt PlotCollection that has the plots to be used.
+ plots : `PlotCollection` or `PlotWindow`
+ yt PlotCollection or PlotWindow that has the plots to be used.
Examples
--------
@@ -1040,18 +1167,42 @@
>>> mp = multiplot_yt(2,2,pc,savefig="yt",shrink_cb=0.9, bare_axes=False,
>>> yt_nocbar=False, margins=(0.5,0.5))
"""
- if len(plot_col.plots) < nrow*ncol:
- raise RuntimeError("Number of plots in PlotCollection is less "\
- "than nrow(%d) x ncol(%d)." % \
- (len(plot_col.plots), nrow, ncol))
+ # Determine whether the plots are organized in a PlotCollection,
+ # PlotWindow, or list of PlotWindows
+ if isinstance(plots, PlotCollection):
+ if len(plots.plots) < nrow*ncol:
+ raise RuntimeError("Number of plots in PlotCollection is less "\
+ "than nrow(%d) x ncol(%d)." % \
+ (len(plots.plots), nrow, ncol))
+ return
+ figure = multiplot(ncol, nrow, yt_plots=plots.plots,
+ plot_collection=True, **kwargs)
+ elif isinstance(plots, PlotWindow):
+ if fields == None:
+ fields = plots.fields
+ if len(fields) < nrow*ncol:
+ raise RuntimeError("Number of plots is less "\
+ "than nrow(%d) x ncol(%d)." % \
+ (len(fields), nrow, ncol))
+ return
+ figure = multiplot(ncol, nrow, yt_plots=plots, fields=fields, **kwargs)
+ elif isinstance(plots, list) and isinstance(plots[0], PlotWindow):
+ if len(plots) < nrow*ncol:
+ raise RuntimeError("Number of plots is less "\
+ "than nrow(%d) x ncol(%d)." % \
+ (len(fields), nrow, ncol))
+ return
+ figure = multiplot(ncol, nrow, yt_plots=plots, fields=fields, **kwargs)
+ else:
+ raise RuntimeError("Unknown plot type in multiplot_yt")
return
- figure = multiplot(ncol, nrow, yt_plots=plot_col.plots, **kwargs)
return figure
#=============================================================================
-def single_plot(plot, figsize=(12,12), cb_orient="right", bare_axes=False,
- savefig=None, colorbar=True, file_format='eps', **kwargs):
+def single_plot(plot, field=None, figsize=(12,12), cb_orient="right",
+ bare_axes=False, savefig=None, colorbar=True,
+ file_format='eps', **kwargs):
r"""Wrapper for DualEPS routines to create a figure directy from a yt
plot. Calls insert_image_yt, axis_box_yt, and colorbar_yt.
@@ -1080,7 +1231,7 @@
>>> single_plot(p, savefig="figure1")
"""
d = DualEPS(figsize=figsize)
- d.insert_image_yt(plot)
+ d.insert_image_yt(plot, field=field)
d.axis_box_yt(plot, bare_axes=bare_axes, **kwargs)
if colorbar:
d.colorbar_yt(plot, orientation=cb_orient)
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -885,6 +885,7 @@
If set to 'c', 'center' or left blank, the plot is centered on the
middle of the domain. If set to 'max' or 'm', the center will be at
the point of highest density.
+ width : tuple or a float.
Width can have four different formats to support windows with variable
x and y widths. They are:
@@ -1149,8 +1150,6 @@
self.set_axes_unit(axes_unit)
def _recreate_frb(self):
- if self._frb is not None:
- raise NotImplementedError
super(OffAxisProjectionPlot, self)._recreate_frb()
_metadata_template = """
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/visualization/profile_plotter.py
--- a/yt/visualization/profile_plotter.py
+++ b/yt/visualization/profile_plotter.py
@@ -28,7 +28,9 @@
from .plot_window import WindowPlotMPL
from .base_plot_types import ImagePlotMPL
-from .plot_container import ImagePlotContainer
+from .plot_container import \
+ ImagePlotContainer, \
+ log_transform, linear_transform
from .image_writer import \
write_image, apply_colormap
from yt.data_objects.profiles import \
@@ -532,6 +534,7 @@
self.plot_title = {}
self.z_log = {}
self.z_title = {}
+ self._initfinished = False
if profile is None:
profile = create_profile(data_source,
@@ -545,6 +548,7 @@
figure_size, fontsize)
# This is a fallback, in case we forget.
self._setup_plots()
+ self._initfinished = True
def _get_field_title(self, field_z, profile):
pf = profile.data_source.pf
@@ -621,6 +625,10 @@
self.plots[f].axes.xaxis.set_label_text(x_title)
self.plots[f].axes.yaxis.set_label_text(y_title)
self.plots[f].cax.yaxis.set_label_text(z_title)
+ if z_scale == "log":
+ self._field_transform[f] = log_transform
+ else:
+ self._field_transform[f] = linear_transform
if f in self.plot_title:
self.plots[f].axes.set_title(self.plot_title[f])
@@ -633,6 +641,7 @@
[ax.xaxis.label, ax.yaxis.label, cbax.yaxis.label]
for label in labels:
label.set_color(self._font_color)
+ self._plot_valid = True
def save(self, name=None, mpl_kwargs=None):
r"""
@@ -702,6 +711,7 @@
def __init__(self, x_data, y_data, data,
x_scale, y_scale, z_scale, cmap,
zlim, size, fontsize, figure, axes, cax):
+ self._initfinished = False
self._draw_colorbar = True
self._draw_axes = True
self._cache_layout(size, fontsize)
@@ -723,6 +733,7 @@
figure, axes, cax)
self._init_image(x_data, y_data, data, x_scale, y_scale, z_scale,
zlim, cmap)
+ self._initfinished = True
def _init_image(self, x_data, y_data, image_data,
x_scale, y_scale, z_scale, zlim, cmap):
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -239,8 +239,7 @@
else:
self.use_kd = isinstance(volume, AMRKDTree)
self.volume = volume
- self.center = (self.re + self.le) / 2.0
- self.region = self.pf.h.region(self.center, self.le, self.re)
+ self.region = None
def _setup_box_properties(self, width, center, unit_vectors):
self.width = width
@@ -299,6 +298,9 @@
>>> write_bitmap(im, 'render_with_grids.png')
"""
+ if self.region is None:
+ self.region = self.pf.h.region((self.re + self.le) / 2.0,
+ self.le, self.re)
corners = self.region.grid_corners
levels = self.region.grid_levels[:,0]
diff -r ec9a5117fc0817ccd1f668c22933c18b036e642a -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a yt/visualization/volume_rendering/transfer_functions.py
--- a/yt/visualization/volume_rendering/transfer_functions.py
+++ b/yt/visualization/volume_rendering/transfer_functions.py
@@ -620,7 +620,7 @@
--------
>>> tf = ColorTransferFunction( (-10.0, -5.0) )
- >>> tf.sample_colormap(-7.0, 0.01, 'algae')
+ >>> tf.sample_colormap(-7.0, 0.01, colormap='algae')
"""
if col_bounds is None:
rel = (v - self.x_bounds[0])/(self.x_bounds[1] - self.x_bounds[0])
https://bitbucket.org/yt_analysis/yt/commits/f1e22ef9f3a2/
Changeset: f1e22ef9f3a2
Branch: stable
User: MatthewTurk
Date: 2014-03-01 00:11:47
Summary: Updating to 2.6.2
Affected #: 1 file
diff -r 3e71cde3f8c291f39eabc2b3796fc390cb836d9a -r f1e22ef9f3a225f818c43262e6ce9644e05ffa21 setup.py
--- a/setup.py
+++ b/setup.py
@@ -156,7 +156,7 @@
# End snippet
######
-VERSION = "2.6.1"
+VERSION = "2.6.2"
if os.path.exists('MANIFEST'):
os.remove('MANIFEST')
https://bitbucket.org/yt_analysis/yt/commits/f7c69809dbd0/
Changeset: f7c69809dbd0
Branch: stable
User: MatthewTurk
Date: 2014-03-01 00:11:57
Summary: Added tag yt-2.6.2 for changeset f1e22ef9f3a2
Affected #: 1 file
diff -r f1e22ef9f3a225f818c43262e6ce9644e05ffa21 -r f7c69809dbd06518c3f023de475ac8d607a9ca76 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -5171,3 +5171,4 @@
21c0314cee16242b6685e42a74d16f7a993c9a88 yt-2.5.5
053487f48672b8fd5c43af992e92bc2f2499f31f yt-2.6
d43ff9d8e20f2d2b8f31f4189141d2521deb341b yt-2.6.1
+f1e22ef9f3a225f818c43262e6ce9644e05ffa21 yt-2.6.2
Repository URL: https://bitbucket.org/yt_analysis/yt/
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