[yt-svn] commit/yt: 2 new changesets
Bitbucket
commits-noreply at bitbucket.org
Thu Jan 10 07:20:36 PST 2013
2 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/71056b6a6ce1/
changeset: 71056b6a6ce1
branch: yt
user: xarthisius
date: 2013-01-10 16:14:03
summary: [chombo] close all hdf5 file handles once they're no longer necessary
affected #: 1 file
diff -r ad241a5772fc214f75370fae5ba3da7f457e13c0 -r 71056b6a6ce1bf89c361a8f3874f22579d65aea0 yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -42,7 +42,7 @@
pluto2enzoDict, \
yt2plutoFieldsDict, \
parameterDict \
-
+
from yt.funcs import *
from yt.data_objects.grid_patch import \
AMRGridPatch
@@ -74,7 +74,7 @@
"""
Return the integer starting index for each dimension at the current
level.
-
+
"""
if self.start_index != None:
return self.start_index
@@ -96,7 +96,7 @@
class ChomboHierarchy(AMRHierarchy):
grid = ChomboGrid
-
+
def __init__(self,pf,data_style='chombo_hdf5'):
self.domain_left_edge = pf.domain_left_edge
self.domain_right_edge = pf.domain_right_edge
@@ -127,7 +127,7 @@
particle_position_z = float(line.split(' ')[3])
coord = [particle_position_x, particle_position_y, particle_position_z]
# for each particle, determine which grids contain it
- # copied from object_finding_mixin.py
+ # copied from object_finding_mixin.py
mask=np.ones(self.num_grids)
for i in xrange(len(coord)):
np.choose(np.greater(self.grid_left_edge[:,i],coord[i]), (mask,0), mask)
@@ -146,7 +146,7 @@
def _detect_fields(self):
ncomp = int(self._fhandle['/'].attrs['num_components'])
self.field_list = [c[1] for c in self._fhandle['/'].attrs.items()[-ncomp:]]
-
+
def _setup_classes(self):
dd = self._get_data_reader_dict()
AMRHierarchy._setup_classes(self, dd)
@@ -156,10 +156,10 @@
self.num_grids = 0
for lev in self._levels:
self.num_grids += self._fhandle[lev]['Processors'].len()
-
+
def _parse_hierarchy(self):
f = self._fhandle # shortcut
-
+
# this relies on the first Group in the H5 file being
# 'Chombo_global'
levels = f.keys()[1:]
@@ -211,7 +211,7 @@
_hierarchy_class = ChomboHierarchy
_fieldinfo_fallback = ChomboFieldInfo
_fieldinfo_known = KnownChomboFields
-
+
def __init__(self, filename, data_style='chombo_hdf5',
storage_filename = None, ini_filename = None):
fileh = h5py.File(filename,'r')
@@ -220,7 +220,8 @@
self.fullplotdir = os.path.abspath(filename)
StaticOutput.__init__(self,filename,data_style)
self.storage_filename = storage_filename
-
+ fileh.close()
+
def _set_units(self):
"""
Generates the conversion to various physical _units based on the parameter file
@@ -274,6 +275,7 @@
self.dimensionality = 3
fileh = h5py.File(self.parameter_filename,'r')
self.refine_by = fileh['/level_0'].attrs['ref_ratio']
+ fileh.close()
def _parse_pluto_file(self, ini_filename):
"""
@@ -288,7 +290,7 @@
lines = open(self.ini_filename).readlines()
# read the file line by line, storing important parameters
for lineI, line in enumerate(lines):
- try:
+ try:
param, sep, vals = map(rstrip,line.partition(' '))
except ValueError:
mylog.error("ValueError: '%s'", line)
@@ -316,13 +318,14 @@
RE = dx0*((np.array(list(fileh['/level_0'].attrs['prob_domain'])))[3:] + 1)
fileh.close()
return RE
-
+
def __calc_domain_dimensions(self):
fileh = h5py.File(self.parameter_filename,'r')
L_index = ((np.array(list(fileh['/level_0'].attrs['prob_domain'])))[0:3])
R_index = ((np.array(list(fileh['/level_0'].attrs['prob_domain'])))[3:] + 1)
+ fileh.close()
return R_index - L_index
-
+
@classmethod
def _is_valid(self, *args, **kwargs):
try:
https://bitbucket.org/yt_analysis/yt/commits/213e04419915/
changeset: 213e04419915
branch: yt
user: MatthewTurk
date: 2013-01-10 16:20:32
summary: Merged in xarthisius/yt (pull request #395: [chombo] close all hdf5 file handles once they're no longer necessary)
affected #: 1 file
diff -r c5e0f2a0ac7a143690f17f9cf48e2ebc41c683c8 -r 213e0441991554ca0392e7e8a7905114cf06842b yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -42,7 +42,7 @@
pluto2enzoDict, \
yt2plutoFieldsDict, \
parameterDict \
-
+
from yt.funcs import *
from yt.data_objects.grid_patch import \
AMRGridPatch
@@ -74,7 +74,7 @@
"""
Return the integer starting index for each dimension at the current
level.
-
+
"""
if self.start_index != None:
return self.start_index
@@ -96,7 +96,7 @@
class ChomboHierarchy(AMRHierarchy):
grid = ChomboGrid
-
+
def __init__(self,pf,data_style='chombo_hdf5'):
self.domain_left_edge = pf.domain_left_edge
self.domain_right_edge = pf.domain_right_edge
@@ -127,7 +127,7 @@
particle_position_z = float(line.split(' ')[3])
coord = [particle_position_x, particle_position_y, particle_position_z]
# for each particle, determine which grids contain it
- # copied from object_finding_mixin.py
+ # copied from object_finding_mixin.py
mask=np.ones(self.num_grids)
for i in xrange(len(coord)):
np.choose(np.greater(self.grid_left_edge[:,i],coord[i]), (mask,0), mask)
@@ -146,7 +146,7 @@
def _detect_fields(self):
ncomp = int(self._fhandle['/'].attrs['num_components'])
self.field_list = [c[1] for c in self._fhandle['/'].attrs.items()[-ncomp:]]
-
+
def _setup_classes(self):
dd = self._get_data_reader_dict()
AMRHierarchy._setup_classes(self, dd)
@@ -156,10 +156,10 @@
self.num_grids = 0
for lev in self._levels:
self.num_grids += self._fhandle[lev]['Processors'].len()
-
+
def _parse_hierarchy(self):
f = self._fhandle # shortcut
-
+
# this relies on the first Group in the H5 file being
# 'Chombo_global'
levels = f.keys()[1:]
@@ -211,7 +211,7 @@
_hierarchy_class = ChomboHierarchy
_fieldinfo_fallback = ChomboFieldInfo
_fieldinfo_known = KnownChomboFields
-
+
def __init__(self, filename, data_style='chombo_hdf5',
storage_filename = None, ini_filename = None):
fileh = h5py.File(filename,'r')
@@ -220,7 +220,8 @@
self.fullplotdir = os.path.abspath(filename)
StaticOutput.__init__(self,filename,data_style)
self.storage_filename = storage_filename
-
+ fileh.close()
+
def _set_units(self):
"""
Generates the conversion to various physical _units based on the parameter file
@@ -274,6 +275,7 @@
self.dimensionality = 3
fileh = h5py.File(self.parameter_filename,'r')
self.refine_by = fileh['/level_0'].attrs['ref_ratio']
+ fileh.close()
def _parse_pluto_file(self, ini_filename):
"""
@@ -288,7 +290,7 @@
lines = open(self.ini_filename).readlines()
# read the file line by line, storing important parameters
for lineI, line in enumerate(lines):
- try:
+ try:
param, sep, vals = map(rstrip,line.partition(' '))
except ValueError:
mylog.error("ValueError: '%s'", line)
@@ -316,13 +318,14 @@
RE = dx0*((np.array(list(fileh['/level_0'].attrs['prob_domain'])))[3:] + 1)
fileh.close()
return RE
-
+
def __calc_domain_dimensions(self):
fileh = h5py.File(self.parameter_filename,'r')
L_index = ((np.array(list(fileh['/level_0'].attrs['prob_domain'])))[0:3])
R_index = ((np.array(list(fileh['/level_0'].attrs['prob_domain'])))[3:] + 1)
+ fileh.close()
return R_index - L_index
-
+
@classmethod
def _is_valid(self, *args, **kwargs):
try:
Repository URL: https://bitbucket.org/yt_analysis/yt/
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