[yt-svn] commit/yt: 5 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Apr 2 11:02:38 PDT 2014
5 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/9d5cf6adfdad/
Changeset: 9d5cf6adfdad
Branch: yt-3.0
User: BW Keller
Date: 2014-04-01 21:13:23
Summary: Fixed a bug I introduced when I changed the default tipsy left/right edges
to None from 0.
Affected #: 1 file
diff -r 4d587415567c90f92d13aa5742a80b61ede1fcae -r 9d5cf6adfdad2e15fd4f3ac418fc0961e2f4a9de yt/frontends/sph/io.py
--- a/yt/frontends/sph/io.py
+++ b/yt/frontends/sph/io.py
@@ -542,6 +542,8 @@
if pf.domain_left_edge is not None and pf.domain_right_edge is not None:
return
with open(data_file.filename, "rb") as f:
+ pf.domain_left_edge = 0
+ pf.domain_right_edge = 0
f.seek(pf._header_offset)
for iptype, ptype in enumerate(self._ptypes):
# We'll just add the individual types separately
https://bitbucket.org/yt_analysis/yt/commits/f1647954e99b/
Changeset: f1647954e99b
Branch: yt-3.0
User: BW Keller
Date: 2014-04-01 21:22:00
Summary: Merged.
Affected #: 1 file
diff -r 6b95f2a269c34bcbdff3ca212b67ddce1401d9e9 -r f1647954e99b344be0fe547243b72b7f34abd73d yt/frontends/sph/io.py
--- a/yt/frontends/sph/io.py
+++ b/yt/frontends/sph/io.py
@@ -542,6 +542,8 @@
if pf.domain_left_edge is not None and pf.domain_right_edge is not None:
return
with open(data_file.filename, "rb") as f:
+ pf.domain_left_edge = 0
+ pf.domain_right_edge = 0
f.seek(pf._header_offset)
for iptype, ptype in enumerate(self._ptypes):
# We'll just add the individual types separately
https://bitbucket.org/yt_analysis/yt/commits/a6f1a21e46da/
Changeset: a6f1a21e46da
Branch: yt-3.0
User: BW Keller
Date: 2014-04-01 22:21:07
Summary: I needed to make a good handful of changes to ensure that domain_left_edge and
domain_right_edge being set to None doesn't cause crashes in various areas of
the code.
Affected #: 3 files
diff -r f1647954e99b344be0fe547243b72b7f34abd73d -r a6f1a21e46da7b18f7c8e55f45a891864bbf1527 yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -186,8 +186,12 @@
self._setup_classes()
def _set_derived_attrs(self):
- self.domain_center = 0.5 * (self.domain_right_edge + self.domain_left_edge)
- self.domain_width = self.domain_right_edge - self.domain_left_edge
+ if self.domain_left_edge is None or self.domain_right_edge is None:
+ self.domain_center = np.zeros(3)
+ self.domain_width = np.zeros(3)
+ else:
+ self.domain_center = 0.5 * (self.domain_right_edge + self.domain_left_edge)
+ self.domain_width = self.domain_right_edge - self.domain_left_edge
if not isinstance(self.current_time, YTQuantity):
self.current_time = self.quan(self.current_time, "code_time")
# need to do this if current_time was set before units were set
@@ -616,7 +620,10 @@
self.length_unit / self.time_unit)
self.unit_registry.modify("code_velocity", vel_unit)
# domain_width does not yet exist
- DW = self.arr(self.domain_right_edge - self.domain_left_edge, "code_length")
+ if self.domain_left_edge is None or self.domain_right_edge is None:
+ DW = np.zeros(3)
+ else:
+ DW = self.arr(self.domain_right_edge - self.domain_left_edge, "code_length")
self.unit_registry.modify("unitary", DW.max())
_arr = None
diff -r f1647954e99b344be0fe547243b72b7f34abd73d -r a6f1a21e46da7b18f7c8e55f45a891864bbf1527 yt/frontends/sph/data_structures.py
--- a/yt/frontends/sph/data_structures.py
+++ b/yt/frontends/sph/data_structures.py
@@ -456,6 +456,7 @@
continue
# parse parameters according to tipsy parameter type
param, val = (i.strip() for i in line.split('=', 1))
+ val = val.split()[0]
if param.startswith('n') or param.startswith('i'):
val = long(val)
elif param.startswith('d'):
diff -r f1647954e99b344be0fe547243b72b7f34abd73d -r a6f1a21e46da7b18f7c8e55f45a891864bbf1527 yt/frontends/sph/io.py
--- a/yt/frontends/sph/io.py
+++ b/yt/frontends/sph/io.py
@@ -539,7 +539,7 @@
ind = 0
# Check to make sure that the domain hasn't already been set
# by the parameter file
- if pf.domain_left_edge is not None and pf.domain_right_edge is not None:
+ if np.all(np.isfinite(pf.domain_left_edge)) and np.all(np.isfinite(pf.domain_right_edge)):
return
with open(data_file.filename, "rb") as f:
pf.domain_left_edge = 0
@@ -558,9 +558,9 @@
mi = pp["Coordinates"][ax].min()
ma = pp["Coordinates"][ax].max()
outlier = YTArray(np.max(np.abs((mi,ma))), 'code_length')
- if outlier > pf.domain_right_edge or -outlier < pf.domain_left_edge:
- pf.domain_left_edge = -outlier
- pf.domain_right_edge = outlier
+ if outlier > pf.domain_right_edge or -outlier < pf.domain_left_edge:
+ pf.domain_left_edge = -1.01*outlier
+ pf.domain_right_edge = 1.01*outlier
ind += c
pf.domain_left_edge = np.ones(3)*pf.domain_left_edge
pf.domain_right_edge = np.ones(3)*pf.domain_right_edge
https://bitbucket.org/yt_analysis/yt/commits/f5b3f25f15ba/
Changeset: f5b3f25f15ba
Branch: yt-3.0
User: BW Keller
Date: 2014-04-02 18:58:58
Summary: Made some quick fixes as per PR #783 comments from Matt Turk.
Affected #: 2 files
diff -r a6f1a21e46da7b18f7c8e55f45a891864bbf1527 -r f5b3f25f15ba8ea72db4f35809cbc367743644c1 yt/frontends/sph/data_structures.py
--- a/yt/frontends/sph/data_structures.py
+++ b/yt/frontends/sph/data_structures.py
@@ -456,7 +456,7 @@
continue
# parse parameters according to tipsy parameter type
param, val = (i.strip() for i in line.split('=', 1))
- val = val.split()[0]
+ val = val.split('#')[0]
if param.startswith('n') or param.startswith('i'):
val = long(val)
elif param.startswith('d'):
diff -r a6f1a21e46da7b18f7c8e55f45a891864bbf1527 -r f5b3f25f15ba8ea72db4f35809cbc367743644c1 yt/frontends/sph/io.py
--- a/yt/frontends/sph/io.py
+++ b/yt/frontends/sph/io.py
@@ -559,8 +559,8 @@
ma = pp["Coordinates"][ax].max()
outlier = YTArray(np.max(np.abs((mi,ma))), 'code_length')
if outlier > pf.domain_right_edge or -outlier < pf.domain_left_edge:
- pf.domain_left_edge = -1.01*outlier
- pf.domain_right_edge = 1.01*outlier
+ pf.domain_left_edge = -1.01*outlier # scale these up so the domain is slightly
+ pf.domain_right_edge = 1.01*outlier # larger than the most distant particle position
ind += c
pf.domain_left_edge = np.ones(3)*pf.domain_left_edge
pf.domain_right_edge = np.ones(3)*pf.domain_right_edge
https://bitbucket.org/yt_analysis/yt/commits/9f6ad437aa6f/
Changeset: 9f6ad437aa6f
Branch: yt-3.0
User: MatthewTurk
Date: 2014-04-02 20:02:28
Summary: Merged in bwkeller/yt/yt-3.0 (pull request #783)
Bug fixes from last pull request
Affected #: 3 files
diff -r 2ef55a7a3a8b8ba66fd8f68c31b744b91ff361ee -r 9f6ad437aa6f9b677dd83ad1979d49edb923c69c yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -186,8 +186,12 @@
self._setup_classes()
def _set_derived_attrs(self):
- self.domain_center = 0.5 * (self.domain_right_edge + self.domain_left_edge)
- self.domain_width = self.domain_right_edge - self.domain_left_edge
+ if self.domain_left_edge is None or self.domain_right_edge is None:
+ self.domain_center = np.zeros(3)
+ self.domain_width = np.zeros(3)
+ else:
+ self.domain_center = 0.5 * (self.domain_right_edge + self.domain_left_edge)
+ self.domain_width = self.domain_right_edge - self.domain_left_edge
if not isinstance(self.current_time, YTQuantity):
self.current_time = self.quan(self.current_time, "code_time")
# need to do this if current_time was set before units were set
@@ -616,7 +620,10 @@
self.length_unit / self.time_unit)
self.unit_registry.modify("code_velocity", vel_unit)
# domain_width does not yet exist
- DW = self.arr(self.domain_right_edge - self.domain_left_edge, "code_length")
+ if self.domain_left_edge is None or self.domain_right_edge is None:
+ DW = np.zeros(3)
+ else:
+ DW = self.arr(self.domain_right_edge - self.domain_left_edge, "code_length")
self.unit_registry.modify("unitary", DW.max())
_arr = None
diff -r 2ef55a7a3a8b8ba66fd8f68c31b744b91ff361ee -r 9f6ad437aa6f9b677dd83ad1979d49edb923c69c yt/frontends/sph/data_structures.py
--- a/yt/frontends/sph/data_structures.py
+++ b/yt/frontends/sph/data_structures.py
@@ -456,6 +456,7 @@
continue
# parse parameters according to tipsy parameter type
param, val = (i.strip() for i in line.split('=', 1))
+ val = val.split('#')[0]
if param.startswith('n') or param.startswith('i'):
val = long(val)
elif param.startswith('d'):
diff -r 2ef55a7a3a8b8ba66fd8f68c31b744b91ff361ee -r 9f6ad437aa6f9b677dd83ad1979d49edb923c69c yt/frontends/sph/io.py
--- a/yt/frontends/sph/io.py
+++ b/yt/frontends/sph/io.py
@@ -539,9 +539,11 @@
ind = 0
# Check to make sure that the domain hasn't already been set
# by the parameter file
- if pf.domain_left_edge is not None and pf.domain_right_edge is not None:
+ if np.all(np.isfinite(pf.domain_left_edge)) and np.all(np.isfinite(pf.domain_right_edge)):
return
with open(data_file.filename, "rb") as f:
+ pf.domain_left_edge = 0
+ pf.domain_right_edge = 0
f.seek(pf._header_offset)
for iptype, ptype in enumerate(self._ptypes):
# We'll just add the individual types separately
@@ -556,9 +558,9 @@
mi = pp["Coordinates"][ax].min()
ma = pp["Coordinates"][ax].max()
outlier = YTArray(np.max(np.abs((mi,ma))), 'code_length')
- if outlier > pf.domain_right_edge or -outlier < pf.domain_left_edge:
- pf.domain_left_edge = -outlier
- pf.domain_right_edge = outlier
+ if outlier > pf.domain_right_edge or -outlier < pf.domain_left_edge:
+ pf.domain_left_edge = -1.01*outlier # scale these up so the domain is slightly
+ pf.domain_right_edge = 1.01*outlier # larger than the most distant particle position
ind += c
pf.domain_left_edge = np.ones(3)*pf.domain_left_edge
pf.domain_right_edge = np.ones(3)*pf.domain_right_edge
Repository URL: https://bitbucket.org/yt_analysis/yt/
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