[yt-svn] commit/yt: 5 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Mon Sep 29 07:33:41 PDT 2014
5 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/f634a10ec30f/
Changeset: f634a10ec30f
Branch: yt
User: xarthisius
Date: 2014-09-22 21:05:57+00:00
Summary: [gdf] handle geometry keyword
Affected #: 2 files
diff -r ea3ba359275aadaa72aeb5543bef652a6e364b16 -r f634a10ec30f9c8493604d79d44820b4c8e05923 yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -5,13 +5,13 @@
"""
-#-----------------------------------------------------------------------------
+# ----------------------------------------------------------------------------
# Copyright (c) 2013, yt Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
+# ----------------------------------------------------------------------------
import h5py
import types
@@ -26,12 +26,20 @@
GridIndex
from yt.data_objects.static_output import \
Dataset
+from yt.utilities.exceptions import \
+ YTGDFUnknownGeometry
from yt.utilities.lib.misc_utilities import \
get_box_grids_level
-from yt.units.yt_array import \
- uconcatenate, YTArray
+from .fields import GDFFieldInfo
-from .fields import GDFFieldInfo
+
+GEOMETRY_TRANS = {
+ 0: "cartesian",
+ 1: "polar",
+ 2: "cylindrical",
+ 3: "spherical",
+}
+
class GDFGrid(AMRGridPatch):
_id_offset = 0
@@ -65,6 +73,7 @@
self.dds
self.dds = self.ds.arr(self.dds, "code_length")
+
class GDFHierarchy(GridIndex):
grid = GDFGrid
@@ -145,8 +154,9 @@
Gets back all the grids between a left edge and right edge
"""
eps = np.finfo(np.float64).eps
- grid_i = np.where(np.all((self.grid_right_edge - left_edge) > eps, axis=1) &
- np.all((right_edge - self.grid_left_edge) > eps, axis=1))
+ grid_i = np.where(
+ np.all((self.grid_right_edge - left_edge) > eps, axis=1) &
+ np.all((right_edge - self.grid_left_edge) > eps, axis=1))
return self.grids[grid_i], grid_i
@@ -162,7 +172,7 @@
_field_info_class = GDFFieldInfo
def __init__(self, filename, dataset_type='grid_data_format',
- storage_filename=None, geometry = 'cartesian'):
+ storage_filename=None, geometry=None):
self.geometry = geometry
self.fluid_types += ("gdf",)
Dataset.__init__(self, filename, dataset_type)
@@ -198,7 +208,7 @@
current_unit = h5f["/dataset_units/%s" % unit_name]
value = current_unit.value
unit = current_unit.attrs["unit"]
- setattr(self, unit_name, self.quan(value,unit))
+ setattr(self, unit_name, self.quan(value, unit))
else:
self.length_unit = self.quan(1.0, "cm")
self.mass_unit = self.quan(1.0, "g")
@@ -214,6 +224,14 @@
else:
self.data_software = "unknown"
sp = self._handle["/simulation_parameters"].attrs
+ if self.geometry is None:
+ if "geometry" in sp:
+ try:
+ self.geometry = GEOMETRY_TRANS[sp["geometry"]]
+ except KeyError:
+ raise YTGDFUnknownGeometry(sp["geometry"])
+ else:
+ self.geometry = "cartesian"
self.parameters.update(sp)
self.domain_left_edge = sp["domain_left_edge"][:]
self.domain_right_edge = sp["domain_right_edge"][:]
diff -r ea3ba359275aadaa72aeb5543bef652a6e364b16 -r f634a10ec30f9c8493604d79d44820b4c8e05923 yt/utilities/exceptions.py
--- a/yt/utilities/exceptions.py
+++ b/yt/utilities/exceptions.py
@@ -94,7 +94,7 @@
def __str__(self):
return ("The display name \"%s\" "
- "of the derived field %s "
+ "of the derived field %s "
"contains the following LaTeX parser errors:\n" ) \
% (self.display_name, self.field_name) + self.mathtext_error
@@ -106,7 +106,7 @@
def __str__(self):
return ("The unit display name \"%s\" "
- "of the derived field %s "
+ "of the derived field %s "
"contains the following LaTeX parser errors:\n" ) \
% (self.unit_name, self.field_name) + self.mathtext_error
@@ -116,7 +116,7 @@
def __str__(self):
return self.message
-
+
class MissingParameter(YTException):
def __init__(self, ds, parameter):
YTException.__init__(self, ds=ds)
@@ -425,3 +425,14 @@
def __str__(self):
return "A file already exists at %s and clobber=False." % self.filename
+
+
+class YTGDFUnknownGeometry(Exception):
+ def __init__(self, geometry):
+ self.geometry = geometry
+
+ def __str__(self):
+ return '''Unknown geometry %i. Please refer to GDF standard
+ for more information''' % self.geometry
+
+
https://bitbucket.org/yt_analysis/yt/commits/df52f47f6d7b/
Changeset: df52f47f6d7b
Branch: yt
User: xarthisius
Date: 2014-09-22 21:36:26+00:00
Summary: Allow one-element arrays for geometry attribute
Affected #: 1 file
diff -r f634a10ec30f9c8493604d79d44820b4c8e05923 -r df52f47f6d7b6db06fdb57c4f0c7dae9604a83bd yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -227,9 +227,9 @@
if self.geometry is None:
if "geometry" in sp:
try:
- self.geometry = GEOMETRY_TRANS[sp["geometry"]]
+ self.geometry = GEOMETRY_TRANS[just_one(sp["geometry"])]
except KeyError:
- raise YTGDFUnknownGeometry(sp["geometry"])
+ raise YTGDFUnknownGeometry(just_one(sp["geometry"]))
else:
self.geometry = "cartesian"
self.parameters.update(sp)
https://bitbucket.org/yt_analysis/yt/commits/bfa80d9d9286/
Changeset: bfa80d9d9286
Branch: yt
User: xarthisius
Date: 2014-09-24 18:42:00+00:00
Summary: revert autopep8 changes
Affected #: 1 file
diff -r df52f47f6d7b6db06fdb57c4f0c7dae9604a83bd -r bfa80d9d92869d6c30034e5a4978db77d08106cd yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -5,13 +5,13 @@
"""
-# ----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
# Copyright (c) 2013, yt Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
-# ----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
import h5py
import types
https://bitbucket.org/yt_analysis/yt/commits/666cf0bc995d/
Changeset: 666cf0bc995d
Branch: yt
User: xarthisius
Date: 2014-09-24 18:47:47+00:00
Summary: Simplify the logic behind geometry setting. Thanks to Matt for the suggestion
Affected #: 1 file
diff -r bfa80d9d92869d6c30034e5a4978db77d08106cd -r 666cf0bc995de720af90b98c0a25bd0f12bdba1e yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -225,13 +225,11 @@
self.data_software = "unknown"
sp = self._handle["/simulation_parameters"].attrs
if self.geometry is None:
- if "geometry" in sp:
- try:
- self.geometry = GEOMETRY_TRANS[just_one(sp["geometry"])]
- except KeyError:
- raise YTGDFUnknownGeometry(just_one(sp["geometry"]))
- else:
- self.geometry = "cartesian"
+ geometry = just_one(sp.get("geometry", 0))
+ try:
+ self.geometry = GEOMETRY_TRANS[geometry]
+ except KeyError:
+ raise YTGDFUnknownGeometry(geometry)
self.parameters.update(sp)
self.domain_left_edge = sp["domain_left_edge"][:]
self.domain_right_edge = sp["domain_right_edge"][:]
https://bitbucket.org/yt_analysis/yt/commits/ed713bccf4b8/
Changeset: ed713bccf4b8
Branch: yt
User: MatthewTurk
Date: 2014-09-29 14:33:33+00:00
Summary: Merged in xarthisius/yt (pull request #1219)
[gdf] handle geometry keyword
Affected #: 2 files
diff -r 3d43afd7ca4b56d679f8744bedc554c8b5f5b3a7 -r ed713bccf4b8d6bf0b45f6f3e1bbd6f1308187ca yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -26,12 +26,20 @@
GridIndex
from yt.data_objects.static_output import \
Dataset
+from yt.utilities.exceptions import \
+ YTGDFUnknownGeometry
from yt.utilities.lib.misc_utilities import \
get_box_grids_level
-from yt.units.yt_array import \
- uconcatenate, YTArray
+from .fields import GDFFieldInfo
-from .fields import GDFFieldInfo
+
+GEOMETRY_TRANS = {
+ 0: "cartesian",
+ 1: "polar",
+ 2: "cylindrical",
+ 3: "spherical",
+}
+
class GDFGrid(AMRGridPatch):
_id_offset = 0
@@ -65,6 +73,7 @@
self.dds
self.dds = self.ds.arr(self.dds, "code_length")
+
class GDFHierarchy(GridIndex):
grid = GDFGrid
@@ -145,8 +154,9 @@
Gets back all the grids between a left edge and right edge
"""
eps = np.finfo(np.float64).eps
- grid_i = np.where(np.all((self.grid_right_edge - left_edge) > eps, axis=1) &
- np.all((right_edge - self.grid_left_edge) > eps, axis=1))
+ grid_i = np.where(
+ np.all((self.grid_right_edge - left_edge) > eps, axis=1) &
+ np.all((right_edge - self.grid_left_edge) > eps, axis=1))
return self.grids[grid_i], grid_i
@@ -162,7 +172,7 @@
_field_info_class = GDFFieldInfo
def __init__(self, filename, dataset_type='grid_data_format',
- storage_filename=None, geometry = 'cartesian'):
+ storage_filename=None, geometry=None):
self.geometry = geometry
self.fluid_types += ("gdf",)
Dataset.__init__(self, filename, dataset_type)
@@ -198,7 +208,7 @@
current_unit = h5f["/dataset_units/%s" % unit_name]
value = current_unit.value
unit = current_unit.attrs["unit"]
- setattr(self, unit_name, self.quan(value,unit))
+ setattr(self, unit_name, self.quan(value, unit))
else:
self.length_unit = self.quan(1.0, "cm")
self.mass_unit = self.quan(1.0, "g")
@@ -214,6 +224,12 @@
else:
self.data_software = "unknown"
sp = self._handle["/simulation_parameters"].attrs
+ if self.geometry is None:
+ geometry = just_one(sp.get("geometry", 0))
+ try:
+ self.geometry = GEOMETRY_TRANS[geometry]
+ except KeyError:
+ raise YTGDFUnknownGeometry(geometry)
self.parameters.update(sp)
self.domain_left_edge = sp["domain_left_edge"][:]
self.domain_right_edge = sp["domain_right_edge"][:]
diff -r 3d43afd7ca4b56d679f8744bedc554c8b5f5b3a7 -r ed713bccf4b8d6bf0b45f6f3e1bbd6f1308187ca yt/utilities/exceptions.py
--- a/yt/utilities/exceptions.py
+++ b/yt/utilities/exceptions.py
@@ -94,7 +94,7 @@
def __str__(self):
return ("The display name \"%s\" "
- "of the derived field %s "
+ "of the derived field %s "
"contains the following LaTeX parser errors:\n" ) \
% (self.display_name, self.field_name) + self.mathtext_error
@@ -106,7 +106,7 @@
def __str__(self):
return ("The unit display name \"%s\" "
- "of the derived field %s "
+ "of the derived field %s "
"contains the following LaTeX parser errors:\n" ) \
% (self.unit_name, self.field_name) + self.mathtext_error
@@ -116,7 +116,7 @@
def __str__(self):
return self.message
-
+
class MissingParameter(YTException):
def __init__(self, ds, parameter):
YTException.__init__(self, ds=ds)
@@ -425,3 +425,14 @@
def __str__(self):
return "A file already exists at %s and clobber=False." % self.filename
+
+
+class YTGDFUnknownGeometry(Exception):
+ def __init__(self, geometry):
+ self.geometry = geometry
+
+ def __str__(self):
+ return '''Unknown geometry %i. Please refer to GDF standard
+ for more information''' % self.geometry
+
+
Repository URL: https://bitbucket.org/yt_analysis/yt/
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