[yt-svn] commit/yt: 8 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Mon Nov 10 12:59:56 PST 2014
8 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/effba5d3bf1c/
Changeset: effba5d3bf1c
Branch: yt
User: hegan
Date: 2014-10-09 22:38:19+00:00
Summary: Allowing enzo to read in active particles that have array attributes
Affected #: 2 files
diff -r 047649b328179cc900ab38f3400390e440530ac1 -r effba5d3bf1c231dbedbe440d82572cd751fd180 yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -31,6 +31,7 @@
class IOHandlerPackedHDF5(BaseIOHandler):
_dataset_type = "enzo_packed_3d"
+ _array_fields = {}
_base = slice(None)
def _read_field_names(self, grid):
@@ -80,6 +81,11 @@
r"particle_position_%s")
x, y, z = (np.asarray(pds.get(pn % ax).value, dtype="=f8")
for ax in 'xyz')
+ for field in field_list:
+ if np.asarray(pds.get(field)).ndim > 1:
+ shape = pds.get(field).shape
+ self._array_fields[field] = shape
+
yield ptype, (x, y, z)
if f: f.close()
diff -r 047649b328179cc900ab38f3400390e440530ac1 -r effba5d3bf1c231dbedbe440d82572cd751fd180 yt/utilities/io_handler.py
--- a/yt/utilities/io_handler.py
+++ b/yt/utilities/io_handler.py
@@ -35,6 +35,7 @@
@add_metaclass(RegisteredIOHandler)
class BaseIOHandler(object):
_vector_fields = ()
+ _array_fields = ()
_dataset_type = None
_particle_reader = False
@@ -160,6 +161,8 @@
for field in fields:
if field[1] in self._vector_fields:
shape = (fsize[field], 3)
+ elif field[1] in self._array_fields:
+ shape = (fsize[field],)+self._array_fields[field[1]]
else:
shape = (fsize[field], )
rv[field] = np.empty(shape, dtype="float64")
https://bitbucket.org/yt_analysis/yt/commits/d0cd503cb324/
Changeset: d0cd503cb324
Branch: yt
User: hegan
Date: 2014-10-09 22:53:19+00:00
Summary: putting the check in read field names instead of particle coords, because it makes more sense there
Affected #: 1 file
diff -r effba5d3bf1c231dbedbe440d82572cd751fd180 -r d0cd503cb324398309c43b522b0636157db2f300 yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -35,6 +35,7 @@
_base = slice(None)
def _read_field_names(self, grid):
+ print grid.id
if grid.filename is None: return []
f = h5py.File(grid.filename, "r")
group = f["/Grid%08i" % grid.id]
@@ -51,6 +52,13 @@
fields.append( ("io", str(name)) )
else:
fields.append( ("enzo", str(name)) )
+ for ptype, field_list in sorted(group['Particles/'].items()):
+ pds = group['Particles/{0}'.format(ptype)]
+ for field in field_list:
+ if np.asarray(pds[field]).ndim > 1:
+ shape = pds[field].shape
+ self._array_fields[field] = shape
+
f.close()
return fields
@@ -81,10 +89,6 @@
r"particle_position_%s")
x, y, z = (np.asarray(pds.get(pn % ax).value, dtype="=f8")
for ax in 'xyz')
- for field in field_list:
- if np.asarray(pds.get(field)).ndim > 1:
- shape = pds.get(field).shape
- self._array_fields[field] = shape
yield ptype, (x, y, z)
if f: f.close()
https://bitbucket.org/yt_analysis/yt/commits/51ba99cbedc0/
Changeset: 51ba99cbedc0
Branch: yt
User: hegan
Date: 2014-10-09 22:54:37+00:00
Summary: forgot to delete print statement
Affected #: 1 file
diff -r d0cd503cb324398309c43b522b0636157db2f300 -r 51ba99cbedc0ad52ef5f49a8770f0a0187ab0968 yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -35,7 +35,6 @@
_base = slice(None)
def _read_field_names(self, grid):
- print grid.id
if grid.filename is None: return []
f = h5py.File(grid.filename, "r")
group = f["/Grid%08i" % grid.id]
https://bitbucket.org/yt_analysis/yt/commits/496866146692/
Changeset: 496866146692
Branch: yt
User: hegan
Date: 2014-10-09 22:55:27+00:00
Summary: removing accidentally added whitespace
Affected #: 1 file
diff -r 51ba99cbedc0ad52ef5f49a8770f0a0187ab0968 -r 496866146692ea88a09faade9affe75294724263 yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -88,7 +88,6 @@
r"particle_position_%s")
x, y, z = (np.asarray(pds.get(pn % ax).value, dtype="=f8")
for ax in 'xyz')
-
yield ptype, (x, y, z)
if f: f.close()
https://bitbucket.org/yt_analysis/yt/commits/4d2077532c89/
Changeset: 4d2077532c89
Branch: yt
User: hegan
Date: 2014-10-09 22:57:56+00:00
Summary: combining lines for clarity
Affected #: 1 file
diff -r 496866146692ea88a09faade9affe75294724263 -r 4d2077532c89c4b69fbbdc3588f5524017e045da yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -55,8 +55,7 @@
pds = group['Particles/{0}'.format(ptype)]
for field in field_list:
if np.asarray(pds[field]).ndim > 1:
- shape = pds[field].shape
- self._array_fields[field] = shape
+ self._array_fields[field] = pds[field].shape
f.close()
return fields
https://bitbucket.org/yt_analysis/yt/commits/94fd67265ef3/
Changeset: 94fd67265ef3
Branch: yt
User: hegan
Date: 2014-10-09 23:07:07+00:00
Summary: added check to make this work even if Particles field doesnt exist
Affected #: 1 file
diff -r 4d2077532c89c4b69fbbdc3588f5524017e045da -r 94fd67265ef3e6fcb8441fbcf56bc911074a313b yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -51,11 +51,13 @@
fields.append( ("io", str(name)) )
else:
fields.append( ("enzo", str(name)) )
- for ptype, field_list in sorted(group['Particles/'].items()):
- pds = group['Particles/{0}'.format(ptype)]
- for field in field_list:
- if np.asarray(pds[field]).ndim > 1:
- self._array_fields[field] = pds[field].shape
+
+ if 'Particles' in group.keys():
+ for ptype, field_list in sorted(group['Particles/'].items()):
+ pds = group['Particles/{0}'.format(ptype)]
+ for field in field_list:
+ if np.asarray(pds[field]).ndim > 1:
+ self._array_fields[field] = pds[field].shape
f.close()
return fields
https://bitbucket.org/yt_analysis/yt/commits/313696c644b8/
Changeset: 313696c644b8
Branch: yt
User: hegan
Date: 2014-10-09 23:34:26+00:00
Summary: removing class level dictionary declaration and moving particle array field check from read_fields to read_particle_coords
Affected #: 2 files
diff -r 94fd67265ef3e6fcb8441fbcf56bc911074a313b -r 313696c644b8c2583f2ec76d4347511daad3cfe2 yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -31,7 +31,6 @@
class IOHandlerPackedHDF5(BaseIOHandler):
_dataset_type = "enzo_packed_3d"
- _array_fields = {}
_base = slice(None)
def _read_field_names(self, grid):
@@ -51,14 +50,6 @@
fields.append( ("io", str(name)) )
else:
fields.append( ("enzo", str(name)) )
-
- if 'Particles' in group.keys():
- for ptype, field_list in sorted(group['Particles/'].items()):
- pds = group['Particles/{0}'.format(ptype)]
- for field in field_list:
- if np.asarray(pds[field]).ndim > 1:
- self._array_fields[field] = pds[field].shape
-
f.close()
return fields
@@ -89,6 +80,9 @@
r"particle_position_%s")
x, y, z = (np.asarray(pds.get(pn % ax).value, dtype="=f8")
for ax in 'xyz')
+ for field in field_list:
+ if np.asarray(pds[field]).ndim > 1:
+ self._array_fields[field] = pds[field].shape
yield ptype, (x, y, z)
if f: f.close()
diff -r 94fd67265ef3e6fcb8441fbcf56bc911074a313b -r 313696c644b8c2583f2ec76d4347511daad3cfe2 yt/utilities/io_handler.py
--- a/yt/utilities/io_handler.py
+++ b/yt/utilities/io_handler.py
@@ -35,7 +35,6 @@
@add_metaclass(RegisteredIOHandler)
class BaseIOHandler(object):
_vector_fields = ()
- _array_fields = ()
_dataset_type = None
_particle_reader = False
@@ -44,6 +43,7 @@
self.ds = ds
self._last_selector_id = None
self._last_selector_counts = None
+ self._array_fields = {}
# We need a function for reading a list of sets
# and a function for *popping* from a queue all the appropriate sets
https://bitbucket.org/yt_analysis/yt/commits/feba284df7fe/
Changeset: feba284df7fe
Branch: yt
User: MatthewTurk
Date: 2014-11-10 20:59:45+00:00
Summary: Merged in hegan/yt (pull request #1248)
[Minor Enhancement] Allowing enzo frontend to read in active particles that have array attributes
Affected #: 2 files
diff -r 9153a5a32dce19164cc66f8073a26d460aa74cbe -r feba284df7fea6ac46d0329b9ed2a0bfde6487a2 yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -83,6 +83,9 @@
r"particle_position_%s")
x, y, z = (np.asarray(pds.get(pn % ax).value, dtype="=f8")
for ax in 'xyz')
+ for field in field_list:
+ if np.asarray(pds[field]).ndim > 1:
+ self._array_fields[field] = pds[field].shape
yield ptype, (x, y, z)
if f: f.close()
diff -r 9153a5a32dce19164cc66f8073a26d460aa74cbe -r feba284df7fea6ac46d0329b9ed2a0bfde6487a2 yt/utilities/io_handler.py
--- a/yt/utilities/io_handler.py
+++ b/yt/utilities/io_handler.py
@@ -43,6 +43,7 @@
self.ds = ds
self._last_selector_id = None
self._last_selector_counts = None
+ self._array_fields = {}
# We need a function for reading a list of sets
# and a function for *popping* from a queue all the appropriate sets
@@ -160,6 +161,8 @@
for field in fields:
if field[1] in self._vector_fields:
shape = (fsize[field], 3)
+ elif field[1] in self._array_fields:
+ shape = (fsize[field],)+self._array_fields[field[1]]
else:
shape = (fsize[field], )
rv[field] = np.empty(shape, dtype="float64")
Repository URL: https://bitbucket.org/yt_analysis/yt/
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