[yt-svn] commit/yt: 31 new changesets
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Thu Feb 14 10:45:59 PST 2013
31 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/31361cabdc34/
changeset: 31361cabdc34
branch: yt
user: atmyers
date: 2013-02-06 21:34:24
summary: setting the 'cosmological simulation' parameter in the Chombo frontend to False by default
affected #: 1 file
diff -r 5a379eb6dc53e51731a82be30308812d8676d68c -r 31361cabdc3488e4fb692afd40ab013771d13c8b yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -220,6 +220,7 @@
self.fullplotdir = os.path.abspath(filename)
StaticOutput.__init__(self,filename,data_style)
self.storage_filename = storage_filename
+ self.cosmological_simulation = False
fileh.close()
def _set_units(self):
https://bitbucket.org/yt_analysis/yt/commits/adc5ab9dc397/
changeset: adc5ab9dc397
branch: yt
user: atmyers
date: 2013-02-06 22:44:19
summary: refactoring the gdf writer a bit and adding the option to write to single fields to backup files
affected #: 1 file
diff -r 31361cabdc3488e4fb692afd40ab013771d13c8b -r adc5ab9dc397ffedad5d56b683b46d8c339ee35d yt/utilities/grid_data_format/writer.py
--- a/yt/utilities/grid_data_format/writer.py
+++ b/yt/utilities/grid_data_format/writer.py
@@ -46,6 +46,74 @@
The path of the file to output.
"""
+
+ f = _create_new_gdf(pf, gdf_path, data_author, data_comment,
+ particle_type_name)
+
+ # now add the fields one-by-one
+ for field_name in pf.h.field_list:
+ _write_field_to_gdf(pf, f, field_name, particle_type_name)
+
+ # don't forget to close the file.
+ f.close()
+
+def save_field(pf, field_name):
+ backup_filename = pf.backup_filename
+ if os.path.exists(backup_filename):
+ # backup file already exists, open it
+ f = h5py.File(backup_filename, "a")
+ else:
+ # backup file does not exist, create it
+ f = _create_new_gdf(pf, backup_filename, data_author=None, data_comment=None,
+ particle_type_name="dark_matter")
+
+ # now save the field
+ _write_field_to_gdf(pf, f, field_name, particle_type_name="dark_matter")
+
+ # don't forget to close the file.
+ f.close()
+
+def _write_field_to_gdf(pf, fhandle, field_name, particle_type_name):
+
+ # add field info to field_types group
+ g = fhandle["field_types"]
+ # create the subgroup with the field's name
+ sg = g.create_group(field_name)
+
+ # grab the display name and units from the field info container.
+ display_name = pf.field_info[field_name].display_name
+ units = pf.field_info[field_name].get_units()
+
+ # check that they actually contain something...
+ if display_name:
+ sg.attrs["field_name"] = display_name
+ else:
+ sg.attrs["field_name"] = field_name
+ if units:
+ sg.attrs["field_units"] = units
+ else:
+ sg.attrs["field_units"] = "None"
+ # @todo: the values must be in CGS already right?
+ sg.attrs["field_to_cgs"] = 1.0
+ # @todo: is this always true?
+ sg.attrs["staggering"] = 0
+
+ # now add actual data, grid by grid
+ g = fhandle["data"]
+ for grid in pf.h.grids:
+ grid_group = g["grid_%010i" % grid.id]
+ particles_group = grid_group["particles"]
+ pt_group = particles_group[particle_type_name]
+ # add the field data to the grid group
+ # Check if this is a real field or particle data.
+ field_obj = pf.field_info[field_name]
+ if field_obj.particle_type: # particle data
+ pt_group[field_name] = grid.get_data(field_name)
+ else: # a field
+ grid_group[field_name] = grid.get_data(field_name)
+
+def _create_new_gdf(pf, gdf_path, data_author=None, data_comment=None,
+ particle_type_name="dark_matter"):
# Make sure we have the absolute path to the file first
gdf_path = os.path.abspath(gdf_path)
@@ -100,29 +168,6 @@
###
g = f.create_group("field_types")
- # Which field list should we iterate over?
- for field_name in pf.h.field_list:
- # create the subgroup with the field's name
- sg = g.create_group(field_name)
-
- # grab the display name and units from the field info container.
- display_name = pf.field_info[field_name].display_name
- units = pf.field_info[field_name].get_units()
-
- # check that they actually contain something...
- if display_name:
- sg.attrs["field_name"] = display_name
- else:
- sg.attrs["field_name"] = field_name
- if units:
- sg.attrs["field_units"] = units
- else:
- sg.attrs["field_units"] = "None"
- # @todo: the values must be in CGS already right?
- sg.attrs["field_to_cgs"] = 1.0
- # @todo: is this always true?
- sg.attrs["staggering"] = 0
-
###
# "particle_types" group
###
@@ -147,25 +192,14 @@
###
# "data" group -- where we should spend the most time
###
+
g = f.create_group("data")
-
for grid in pf.h.grids:
# add group for this grid
-
grid_group = g.create_group("grid_%010i" % grid.id)
# add group for the particles on this grid
particles_group = grid_group.create_group("particles")
pt_group = particles_group.create_group(particle_type_name)
- # add the field data to the grid group
- for field_name in pf.h.field_list:
- # Check if this is a real field or particle data.
- field_obj = pf.field_info[field_name]
+ return f
- if field_obj.particle_type: # particle data
- pt_group[field_name] = grid.get_data(field_name)
- else: # a field
- grid_group[field_name] = grid.get_data(field_name)
-
- # don't forget to close the file.
- f.close()
https://bitbucket.org/yt_analysis/yt/commits/2124bcf32368/
changeset: 2124bcf32368
branch: yt
user: atmyers
date: 2013-02-06 22:45:08
summary: adding a backup_filename parameter to the chombo frontend
affected #: 1 file
diff -r adc5ab9dc397ffedad5d56b683b46d8c339ee35d -r 2124bcf3236800b20ce10a21e3b11aa232e957e3 yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -220,6 +220,7 @@
self.fullplotdir = os.path.abspath(filename)
StaticOutput.__init__(self,filename,data_style)
self.storage_filename = storage_filename
+ self.backup_filename = self.fullplotdir + '_backup.gdf'
self.cosmological_simulation = False
fileh.close()
https://bitbucket.org/yt_analysis/yt/commits/2b305e8d52e1/
changeset: 2b305e8d52e1
branch: yt
user: atmyers
date: 2013-02-07 00:57:45
summary: modifying the io routines for the Chombo frontend to check the backup file
affected #: 1 file
diff -r 2124bcf3236800b20ce10a21e3b11aa232e957e3 -r 2b305e8d52e1c2e5725901bcd47a38b8ce8ba892 yt/frontends/chombo/io.py
--- a/yt/frontends/chombo/io.py
+++ b/yt/frontends/chombo/io.py
@@ -50,20 +50,30 @@
fhandle.close()
def _read_data_set(self,grid,field):
- fhandle = h5py.File(grid.hierarchy.hierarchy_filename,'r')
+ # try to read from backup file first
+ try:
+ backup_filename = grid.pf.backup_filename
+ fhandle = h5py.File(backup_filename, 'r')
+ g = fhandle["data"]
+ grid_group = g["grid_%010i" % grid.id]
+ data = grid_group[field][:]
+ fhandle.close()
+ return data
+ except:
+ fhandle = h5py.File(grid.hierarchy.hierarchy_filename,'r')
- field_dict = self._field_dict(fhandle)
- lstring = 'level_%i' % grid.Level
- lev = fhandle[lstring]
- dims = grid.ActiveDimensions
- boxsize = dims.prod()
+ field_dict = self._field_dict(fhandle)
+ lstring = 'level_%i' % grid.Level
+ lev = fhandle[lstring]
+ dims = grid.ActiveDimensions
+ boxsize = dims.prod()
- grid_offset = lev[self._offset_string][grid._level_id]
- start = grid_offset+field_dict[field]*boxsize
- stop = start + boxsize
- data = lev[self._data_string][start:stop]
+ grid_offset = lev[self._offset_string][grid._level_id]
+ start = grid_offset+field_dict[field]*boxsize
+ stop = start + boxsize
+ data = lev[self._data_string][start:stop]
- fhandle.close()
+ fhandle.close()
return data.reshape(dims, order='F')
def _read_data_slice(self, grid, field, axis, coord):
https://bitbucket.org/yt_analysis/yt/commits/cd792f88aca4/
changeset: cd792f88aca4
branch: yt
user: atmyers
date: 2013-02-07 00:58:50
summary: detecting fields in the backup as well for the Chombo frontend
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/ec04e80b9ece/
changeset: ec04e80b9ece
branch: yt
user: atmyers
date: 2013-02-07 02:23:20
summary: adding a docstring to the save_field function
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/84f10af3293d/
changeset: 84f10af3293d
branch: yt
user: atmyers
date: 2013-02-08 02:07:27
summary: some refactoring of the io functions to support saving of derived fields accross all frontends
affected #: 2 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/600e45161059/
changeset: 600e45161059
branch: yt
user: atmyers
date: 2013-02-08 02:33:38
summary: catching an exception for when you try to write a field with a name that already exits
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/14efec3bd683/
changeset: 14efec3bd683
branch: yt
user: atmyers
date: 2013-02-08 02:34:50
summary: Merged yt_analysis/yt into yt
affected #: 21 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/4b71796d20a0/
changeset: 4b71796d20a0
branch: yt
user: atmyers
date: 2013-02-08 02:41:00
summary: don't need this import anymore
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/50d895cf7cb2/
changeset: 50d895cf7cb2
branch: yt
user: atmyers
date: 2013-02-08 02:45:22
summary: merging
affected #: 21 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/df9196aa7996/
changeset: df9196aa7996
branch: yt
user: atmyers
date: 2013-02-08 07:18:56
summary: further refactoring of the derived field saving mechanism. Supports the Enzo frontend now
affected #: 4 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/00407b021b37/
changeset: 00407b021b37
branch: yt
user: atmyers
date: 2013-02-08 08:13:55
summary: adding support for orion data
affected #: 2 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/4ada4f91eaf5/
changeset: 4ada4f91eaf5
branch: yt
user: atmyers
date: 2013-02-08 09:21:01
summary: flash
affected #: 2 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/73eeba46c80b/
changeset: 73eeba46c80b
branch: yt
user: atmyers
date: 2013-02-08 21:12:07
summary: replacing clunky function name '_read_data_set_from_pf' with '_read_data'
affected #: 5 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/43cd92f9d706/
changeset: 43cd92f9d706
branch: yt
user: atmyers
date: 2013-02-08 21:16:00
summary: forgot one place
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/c00f33f71331/
changeset: c00f33f71331
branch: yt
user: atmyers
date: 2013-02-08 21:25:13
summary: making _read_data_set --> _read_data change in all of the other frontends
affected #: 11 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/ce9625180cfe/
changeset: ce9625180cfe
branch: yt
user: atmyers
date: 2013-02-08 21:41:40
summary: set the backup_filename in the base StaticOutput class rather than in the individual frontends
affected #: 5 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/da27899e8fd7/
changeset: da27899e8fd7
branch: yt
user: atmyers
date: 2013-02-08 21:57:52
summary: catching a couple of exceptions and changing the default backup file location
affected #: 2 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/5cd51067274f/
changeset: 5cd51067274f
branch: yt
user: atmyers
date: 2013-02-08 23:05:57
summary: fixing some changes I somehow accidently made to the periodicity checking in the flash, orion, and enzo frontents
affected #: 3 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/47caf837151a/
changeset: 47caf837151a
branch: yt
user: atmyers
date: 2013-02-08 23:08:28
summary: missed this one
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/4dc9fe209517/
changeset: 4dc9fe209517
branch: yt
user: atmyers
date: 2013-02-08 23:09:57
summary: maybe this time
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/84d25f6ceac9/
changeset: 84d25f6ceac9
branch: yt
user: atmyers
date: 2013-02-10 03:45:20
summary: fixing grid offset bug in this version too
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/fa56e6874158/
changeset: fa56e6874158
branch: yt
user: atmyers
date: 2013-02-10 07:34:10
summary: resolving conflict
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/15cc336494aa/
changeset: 15cc336494aa
branch: yt
user: atmyers
date: 2013-02-10 09:14:21
summary: fixing a couple of bugs
affected #: 2 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/5e7383e0ce54/
changeset: 5e7383e0ce54
branch: yt
user: atmyers
date: 2013-02-14 03:08:41
summary: Merged yt_analysis/yt into yt
affected #: 9 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/043815a1ec25/
changeset: 043815a1ec25
branch: yt
user: atmyers
date: 2013-02-14 06:56:34
summary: only check disk for presence of data file once
affected #: 2 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/4ff66fe9aa72/
changeset: 4ff66fe9aa72
branch: yt
user: atmyers
date: 2013-02-14 18:28:39
summary: simplfying the detect fields code somewhat
affected #: 1 file
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/c237cc8de828/
changeset: c237cc8de828
branch: yt
user: atmyers
date: 2013-02-14 19:03:35
summary: warn people if they try to save particle fields
affected #: 2 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/e1b7792e6807/
changeset: e1b7792e6807
branch: yt
user: MatthewTurk
date: 2013-02-14 19:25:39
summary: Adjusting IO frontends for the new sidecar file.
affected #: 15 files
Diff not available.
https://bitbucket.org/yt_analysis/yt/commits/5027f592349e/
changeset: 5027f592349e
branch: yt
user: MatthewTurk
date: 2013-02-14 19:45:49
summary: Merged in atmyers/yt (pull request #416)
Saving derived fields to disk
affected #: 24 files
Diff not available.
Repository URL: https://bitbucket.org/yt_analysis/yt/
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