[yt-svn] commit/yt-3.0: 18 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Aug 14 07:19:22 PDT 2013
18 new commits in yt-3.0:
https://bitbucket.org/yt_analysis/yt-3.0/commits/70327960609d/
Changeset: 70327960609d
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 14:47:36
Summary: Instance of 'list' has no 'copy' member
Affected #: 1 file
diff -r 42a76b0f696070ca0179a633127f2a3c646925d6 -r 70327960609dbe05cea5974241bee4f5fff9297e yt/data_objects/field_info_container.py
--- a/yt/data_objects/field_info_container.py
+++ b/yt/data_objects/field_info_container.py
@@ -444,7 +444,7 @@
dd['units'] = self._units
dd['projected_units'] = self._projected_units,
dd['take_log'] = self.take_log
- dd['validators'] = self.validators.copy()
+ dd['validators'] = list(self.validators)
dd['particle_type'] = self.particle_type
dd['vector_field'] = self.vector_field
dd['display_field'] = True
https://bitbucket.org/yt_analysis/yt-3.0/commits/9d72bef9f9f5/
Changeset: 9d72bef9f9f5
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:03:08
Summary: Fix typo in YTRayBase
Affected #: 1 file
diff -r 70327960609dbe05cea5974241bee4f5fff9297e -r 9d72bef9f9f52fa4129191e797304d5d8f929602 yt/data_objects/selection_data_containers.py
--- a/yt/data_objects/selection_data_containers.py
+++ b/yt/data_objects/selection_data_containers.py
@@ -194,7 +194,7 @@
ts = np.abs(ts)
self._dts[grid.id] = dts
self._ts[grid.id] = ts
- self._masks[grid.id] = masks
+ self._masks[grid.id] = mask
return mask
https://bitbucket.org/yt_analysis/yt-3.0/commits/2a4fc1e2775a/
Changeset: 2a4fc1e2775a
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:11:59
Summary: use bin_profile2d instead of non existent Bin2DProfile in BinnedProfile2DInlineCut
Affected #: 1 file
diff -r 9d72bef9f9f52fa4129191e797304d5d8f929602 -r 2a4fc1e2775a9dc24afcd0680dd2841d1c107508 yt/data_objects/profiles.py
--- a/yt/data_objects/profiles.py
+++ b/yt/data_objects/profiles.py
@@ -545,6 +545,8 @@
self.total_stuff = source_data.sum()
binned_field = self._get_empty_field()
weight_field = self._get_empty_field()
+ m_field = self._get_empty_field()
+ q_field = self._get_empty_field()
used_field = self._get_empty_field()
mi = args[0]
bin_indices_x = args[1][self.indices].ravel().astype('int64')
@@ -553,8 +555,8 @@
weight_data = weight_data[mi][self.indices]
nx = bin_indices_x.size
#mylog.debug("Binning %s / %s times", source_data.size, nx)
- Bin2DProfile(bin_indices_x, bin_indices_y, weight_data, source_data,
- weight_field, binned_field, used_field)
+ bin_profile2d(bin_indices_x, bin_indices_y, weight_data, source_data,
+ weight_field, binned_field, m_field, q_field, used_field)
if accumulation: # Fix for laziness
if not iterable(accumulation):
raise SyntaxError("Accumulation needs to have length 2")
https://bitbucket.org/yt_analysis/yt-3.0/commits/4f9619414fd0/
Changeset: 4f9619414fd0
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:14:09
Summary: Fix typo in SlicePlotDataset.eval
Affected #: 1 file
diff -r 2a4fc1e2775a9dc24afcd0680dd2841d1c107508 -r 4f9619414fd07cf6b012d18ad8ff7cf13d6d3e6a yt/data_objects/analyzer_objects.py
--- a/yt/data_objects/analyzer_objects.py
+++ b/yt/data_objects/analyzer_objects.py
@@ -80,7 +80,7 @@
def eval(self, pf):
slc = self.SlicePlot(pf, self.axis, self.field, center = self.center)
- return pc.save()
+ return slc.save()
class QuantityProxy(AnalysisTask):
_params = None
https://bitbucket.org/yt_analysis/yt-3.0/commits/c0e862a6488c/
Changeset: c0e862a6488c
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:19:55
Summary: add missing import ytcfg
Affected #: 1 file
diff -r 4f9619414fd07cf6b012d18ad8ff7cf13d6d3e6a -r c0e862a6488ced2348a78f3ce5e3b57d2394ed48 yt/data_objects/construction_data_containers.py
--- a/yt/data_objects/construction_data_containers.py
+++ b/yt/data_objects/construction_data_containers.py
@@ -36,6 +36,7 @@
import fileinput
from re import finditer
+from yt.config import ytcfg
from yt.funcs import *
from yt.utilities.logger import ytLogger
from .data_containers import \
https://bitbucket.org/yt_analysis/yt-3.0/commits/f03284539226/
Changeset: f03284539226
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:38:57
Summary: Raise NotImplementedError in StandardRadialAnalysis as it relies on undefined variable
Affected #: 1 file
diff -r c0e862a6488ced2348a78f3ce5e3b57d2394ed48 -r f03284539226dcae6b21976698aee171fc82fe4a yt/analysis_modules/halo_profiler/standard_analysis.py
--- a/yt/analysis_modules/halo_profiler/standard_analysis.py
+++ b/yt/analysis_modules/halo_profiler/standard_analysis.py
@@ -30,6 +30,7 @@
class StandardRadialAnalysis(object):
def __init__(self, pf, center, radius, n_bins = 128, inner_radius = None):
+ raise NotImplementedError # see TODO
self.pf = pf
# We actually don't want to replicate the handling of setting the
# center here, so we will pass it to the sphere creator.
@@ -53,6 +54,7 @@
prof = BinnedProfile1D(self.obj, self.n_bins, "Radius",
self.inner_radius, self.outer_radius)
by_weights = defaultdict(list)
+ # TODO: analysis_field_list is undefined
for fspec in analysis_field_list:
if isinstance(fspec, types.TupleType) and len(fspec) == 2:
field, weight = fspec
https://bitbucket.org/yt_analysis/yt-3.0/commits/47d4134be1c0/
Changeset: 47d4134be1c0
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:48:15
Summary: [coordinate_handler] use np rather than na, correct arctans to arctan2, correct item to field, fix import of _MPL
Affected #: 1 file
diff -r f03284539226dcae6b21976698aee171fc82fe4a -r 47d4134be1c007998436b90b8e51f5734d43301c yt/geometry/coordinate_handler.py
--- a/yt/geometry/coordinate_handler.py
+++ b/yt/geometry/coordinate_handler.py
@@ -36,7 +36,7 @@
ParallelAnalysisInterface, parallel_splitter
from yt.utilities.lib.misc_utilities import \
pixelize_cylinder
-import yt.visualization._MPL
+import yt.visualization._MPL as _MPL
from .cartesian_fields import CartesianFieldInfo
from .cylindrical_fields import CylindricalFieldInfo, PolarFieldInfo
@@ -103,7 +103,7 @@
c2[...,0] = ((coord[...,0] - center[0])**2.0
+ (coord[...,1] - center[1])**2.0)**0.5
c2[...,1] = coord[...,2] # rzt
- c2[...,2] = np.arctans(coord[...,1] - center[1],
+ c2[...,2] = np.arctan2(coord[...,1] - center[1],
coord[...,0] - center[0])
return c2
@@ -145,7 +145,7 @@
data_source['py'], data_source['pdx'],
data_source['pdy'], data_source['pdz'],
data_source.center, data_source._inv_mat, indices,
- data_source[item], size[0], size[1], bounds).transpose()
+ data_source[field], size[0], size[1], bounds).transpose()
return buff
def convert_from_cartesian(self, coord):
@@ -258,7 +258,7 @@
@property
def period(self):
- return na.array([0.0, 0.0, 2.0*np.pi])
+ return np.array([0.0, 0.0, 2.0*np.pi])
class CylindricalCoordinateHandler(CoordinateHandler):
@@ -331,5 +331,5 @@
@property
def period(self):
- return na.array([0.0, 0.0, 2.0*np.pi])
+ return np.array([0.0, 0.0, 2.0*np.pi])
https://bitbucket.org/yt_analysis/yt-3.0/commits/dc24dc3ba01b/
Changeset: dc24dc3ba01b
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:49:36
Summary: Import missing YTCoordinateNotImplemented
Affected #: 1 file
diff -r 47d4134be1c007998436b90b8e51f5734d43301c -r dc24dc3ba01bd91dd7c791bdfc344fe4dc4b8ab5 yt/geometry/cylindrical_fields.py
--- a/yt/geometry/cylindrical_fields.py
+++ b/yt/geometry/cylindrical_fields.py
@@ -35,6 +35,8 @@
NeedsDataField, \
NeedsProperty, \
NeedsParameter
+from yt.utilities.exceptions import \
+ YTCoordinateNotImplemented
CylindricalFieldInfo = FieldInfoContainer()
CylindricalFieldInfo.name = id(CylindricalFieldInfo)
https://bitbucket.org/yt_analysis/yt-3.0/commits/aeaf685eea86/
Changeset: aeaf685eea86
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:53:30
Summary: Fix numpy functions invocation
Affected #: 1 file
diff -r dc24dc3ba01bd91dd7c791bdfc344fe4dc4b8ab5 -r aeaf685eea8634b5adbae6af0ce605796cc689d9 yt/utilities/cosmology.py
--- a/yt/utilities/cosmology.py
+++ b/yt/utilities/cosmology.py
@@ -61,7 +61,7 @@
self.HubbleDistance()))
elif (self.OmegaCurvatureNow < 0):
return (self.HubbleDistance() / np.sqrt(np.fabs(self.OmegaCurvatureNow)) *
- sin(np.sqrt(np.fabs(self.OmegaCurvatureNow)) *
+ np.sin(np.sqrt(np.fabs(self.OmegaCurvatureNow)) *
self.ComovingRadialDistance(z_i,z_f) / self.HubbleDistance()))
else:
return self.ComovingRadialDistance(z_i,z_f)
@@ -73,7 +73,7 @@
np.sqrt(1 + self.OmegaCurvatureNow *
sqr(self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance())) -
- anp.sinh(np.fabs(self.OmegaCurvatureNow) *
+ np.sinh(np.fabs(self.OmegaCurvatureNow) *
self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance()) / np.sqrt(self.OmegaCurvatureNow)) / 1e9)
elif (self.OmegaCurvatureNow < 0):
@@ -83,7 +83,7 @@
np.sqrt(1 + self.OmegaCurvatureNow *
sqr(self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance())) -
- asin(np.fabs(self.OmegaCurvatureNow) *
+ np.asin(np.fabs(self.OmegaCurvatureNow) *
self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance()) /
np.sqrt(np.fabs(self.OmegaCurvatureNow))) / 1e9)
https://bitbucket.org/yt_analysis/yt-3.0/commits/8dff5d1142a2/
Changeset: 8dff5d1142a2
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:55:26
Summary: Fix numpy functions invocation
Affected #: 1 file
diff -r aeaf685eea8634b5adbae6af0ce605796cc689d9 -r 8dff5d1142a248cca4f42f860b8e82a9a75aceb3 yt/utilities/cosmology.py
--- a/yt/utilities/cosmology.py
+++ b/yt/utilities/cosmology.py
@@ -83,7 +83,7 @@
np.sqrt(1 + self.OmegaCurvatureNow *
sqr(self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance())) -
- np.asin(np.fabs(self.OmegaCurvatureNow) *
+ np.arcsin(np.fabs(self.OmegaCurvatureNow) *
self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance()) /
np.sqrt(np.fabs(self.OmegaCurvatureNow))) / 1e9)
@@ -269,7 +269,7 @@
# 3) For OmegaMatterNow > 1 and OmegaLambdaNow == 0, use sin/cos.
if ((self.OmegaMatterNow > 1) and (self.OmegaLambdaNow == 0)):
- eta = np.acos(1 - 2*(1-self.OmegaMatterNow)/self.OmegaMatterNow/(1+z))
+ eta = np.arccos(1 - 2*(1-self.OmegaMatterNow)/self.OmegaMatterNow/(1+z))
TimeHubble0 = self.OmegaMatterNow/(2*np.power(1.0-self.OmegaMatterNow, 1.5))*\
(eta - np.sin(eta))
https://bitbucket.org/yt_analysis/yt-3.0/commits/c9c5a19f8378/
Changeset: c9c5a19f8378
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 15:57:11
Summary: Add missing import
Affected #: 1 file
diff -r 8dff5d1142a248cca4f42f860b8e82a9a75aceb3 -r c9c5a19f837899d026c05f3f9a20973f92d77569 yt/utilities/rpdb.py
--- a/yt/utilities/rpdb.py
+++ b/yt/utilities/rpdb.py
@@ -25,6 +25,7 @@
import cmd, pdb, cStringIO, xmlrpclib, socket, sys
import traceback
+import signal
from SimpleXMLRPCServer import SimpleXMLRPCServer
from yt.config import ytcfg
https://bitbucket.org/yt_analysis/yt-3.0/commits/6bb777879a23/
Changeset: 6bb777879a23
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 16:00:49
Summary: Fix YTCannotParseUnitDisplayName constructor
Affected #: 1 file
diff -r c9c5a19f837899d026c05f3f9a20973f92d77569 -r 6bb777879a2325d710337bbdcebe1680b76b8ade yt/utilities/exceptions.py
--- a/yt/utilities/exceptions.py
+++ b/yt/utilities/exceptions.py
@@ -109,7 +109,7 @@
% (self.display_name, self.field_name) + self.mathtext_error
class YTCannotParseUnitDisplayName(YTException):
- def __init__(self, field_name, display_unit, mathtext_error):
+ def __init__(self, field_name, unit_name, mathtext_error):
self.field_name = field_name
self.unit_name = unit_name
self.mathtext_error = mathtext_error
https://bitbucket.org/yt_analysis/yt-3.0/commits/f2b331ca1bea/
Changeset: f2b331ca1bea
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 16:07:05
Summary: Add remark about code that needs to be fixed
Affected #: 1 file
diff -r 6bb777879a2325d710337bbdcebe1680b76b8ade -r f2b331ca1beae82ba519b1c108052ce7b738fd1a yt/utilities/flagging_methods.py
--- a/yt/utilities/flagging_methods.py
+++ b/yt/utilities/flagging_methods.py
@@ -162,6 +162,9 @@
# Note that sd is offset by one
if sd[i-1] * sd[i] < 0:
strength = np.abs(sd[i-1] - sd[i])
+ # TODO this differs from what I could find in ENZO
+ # there's |center - i| < |center - zero_cross| instead
+ # additionally zero_cross is undefined in first pass
if strength > zero_strength or \
(strength == zero_strength and np.abs(center - i) < np.abs(zero_cross -i )):
zero_strength = strength
https://bitbucket.org/yt_analysis/yt-3.0/commits/e1b0663331a3/
Changeset: e1b0663331a3
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 16:08:21
Summary: Fix variable names
Affected #: 1 file
diff -r f2b331ca1beae82ba519b1c108052ce7b738fd1a -r e1b0663331a3e3bfdf0c086e2a4e77a395ca6774 yt/utilities/fortran_utils.py
--- a/yt/utilities/fortran_utils.py
+++ b/yt/utilities/fortran_utils.py
@@ -121,7 +121,8 @@
vec_fmt = "%s%s" % (endian, d)
vec_size = struct.calcsize(vec_fmt)
if vec_len % vec_size != 0:
- print "fmt = '%s' ; length = %s ; size= %s" % (fmt, length, size)
+ print("fmt = '%s' ; length = %s ; size= %s"
+ % (vec_fmt, vec_len, vec_size))
raise RuntimeError
vec_num = vec_len / vec_size
if isinstance(f, file): # Needs to be explicitly a file
https://bitbucket.org/yt_analysis/yt-3.0/commits/064221095e72/
Changeset: 064221095e72
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 16:12:39
Summary: Add missing scipy import
Affected #: 1 file
diff -r e1b0663331a3e3bfdf0c086e2a4e77a395ca6774 -r 064221095e72d944372686481365a570217a178a yt/utilities/pykdtree.py
--- a/yt/utilities/pykdtree.py
+++ b/yt/utilities/pykdtree.py
@@ -2,6 +2,7 @@
# Released under the scipy license
import sys
import numpy as np
+import scipy
from heapq import heappush, heappop
def minkowski_distance_p(x,y,p=2):
https://bitbucket.org/yt_analysis/yt-3.0/commits/439dd6935784/
Changeset: 439dd6935784
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 16:13:20
Summary: Fix truncated RuntimeError
Affected #: 1 file
diff -r 064221095e72d944372686481365a570217a178a -r 439dd693578491d07f66e2446bc8fe24a7a606e9 yt/utilities/parameter_file_storage.py
--- a/yt/utilities/parameter_file_storage.py
+++ b/yt/utilities/parameter_file_storage.py
@@ -221,7 +221,8 @@
def __init__(self, path = None):
if path is None:
path = ytcfg.get("yt", "enzo_db")
- if len(path) == 0: raise Runtime
+ if len(path) == 0:
+ raise RuntimeError
import sqlite3
self.conn = sqlite3.connect(path)
https://bitbucket.org/yt_analysis/yt-3.0/commits/a87641d47168/
Changeset: a87641d47168
Branch: yt-3.0
User: xarthisius
Date: 2013-07-19 16:25:36
Summary: Add missing imports, flag one code path in partition_region_3d with NotImplemented error as number of return arguments is different than in the other places in the method and one variable is undefined
Affected #: 3 files
diff -r 439dd693578491d07f66e2446bc8fe24a7a606e9 -r a87641d4716822efc34c2444387bc7cc8ac9fb5f yt/utilities/parallel_tools/controller_system.py
--- a/yt/utilities/parallel_tools/controller_system.py
+++ b/yt/utilities/parallel_tools/controller_system.py
@@ -27,6 +27,8 @@
from .parallel_analysis_interface import MPI
except ImportError:
pass
+from .parallel_analysis_interface import \
+ ProcessorPool
from contextmanager import contextlib
from abc import ABCMeta, abstractmethod, abstractproperty
diff -r 439dd693578491d07f66e2446bc8fe24a7a606e9 -r a87641d4716822efc34c2444387bc7cc8ac9fb5f yt/utilities/parallel_tools/io_runner.py
--- a/yt/utilities/parallel_tools/io_runner.py
+++ b/yt/utilities/parallel_tools/io_runner.py
@@ -24,7 +24,10 @@
"""
import os
-from .parallel_analysis_interface import ProcessorPool
+import np
+from yt.utilities.logger import ytLogger as mylog
+from .parallel_analysis_interface import \
+ ProcessorPool, parallel_objects
from yt.utilities.io_handler import BaseIOHandler
from contextlib import contextmanager
import time
@@ -168,6 +171,7 @@
pf.h.io = original_io
def io_nodes(fn, n_io, n_work, func, *args, **kwargs):
+ from yt.mods import load
pool, wg = ProcessorPool.from_sizes([(n_io, "io"), (n_work, "work")])
rv = None
if wg.name == "work":
diff -r 439dd693578491d07f66e2446bc8fe24a7a606e9 -r a87641d4716822efc34c2444387bc7cc8ac9fb5f yt/utilities/parallel_tools/parallel_analysis_interface.py
--- a/yt/utilities/parallel_tools/parallel_analysis_interface.py
+++ b/yt/utilities/parallel_tools/parallel_analysis_interface.py
@@ -1115,8 +1115,9 @@
"""
LE, RE = left_edge[:], right_edge[:]
if not self._distributed:
+ raise NotImplemented
return LE, RE, re
-
+
cc = MPI.Compute_dims(self.comm.size / rank_ratio, 3)
mi = self.comm.rank % (self.comm.size / rank_ratio)
cx, cy, cz = np.unravel_index(mi, cc)
https://bitbucket.org/yt_analysis/yt-3.0/commits/e2fc6f0ed6b6/
Changeset: e2fc6f0ed6b6
Branch: yt-3.0
User: MatthewTurk
Date: 2013-08-14 16:19:16
Summary: Merged in xarthisius/yt-3.0 (pull request #72)
Small bugfixes
Affected #: 18 files
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/analysis_modules/halo_profiler/standard_analysis.py
--- a/yt/analysis_modules/halo_profiler/standard_analysis.py
+++ b/yt/analysis_modules/halo_profiler/standard_analysis.py
@@ -30,6 +30,7 @@
class StandardRadialAnalysis(object):
def __init__(self, pf, center, radius, n_bins = 128, inner_radius = None):
+ raise NotImplementedError # see TODO
self.pf = pf
# We actually don't want to replicate the handling of setting the
# center here, so we will pass it to the sphere creator.
@@ -53,6 +54,7 @@
prof = BinnedProfile1D(self.obj, self.n_bins, "Radius",
self.inner_radius, self.outer_radius)
by_weights = defaultdict(list)
+ # TODO: analysis_field_list is undefined
for fspec in analysis_field_list:
if isinstance(fspec, types.TupleType) and len(fspec) == 2:
field, weight = fspec
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/data_objects/analyzer_objects.py
--- a/yt/data_objects/analyzer_objects.py
+++ b/yt/data_objects/analyzer_objects.py
@@ -80,7 +80,7 @@
def eval(self, pf):
slc = self.SlicePlot(pf, self.axis, self.field, center = self.center)
- return pc.save()
+ return slc.save()
class QuantityProxy(AnalysisTask):
_params = None
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/data_objects/construction_data_containers.py
--- a/yt/data_objects/construction_data_containers.py
+++ b/yt/data_objects/construction_data_containers.py
@@ -36,6 +36,7 @@
import fileinput
from re import finditer
+from yt.config import ytcfg
from yt.funcs import *
from yt.utilities.logger import ytLogger
from .data_containers import \
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/data_objects/field_info_container.py
--- a/yt/data_objects/field_info_container.py
+++ b/yt/data_objects/field_info_container.py
@@ -444,7 +444,7 @@
dd['units'] = self._units
dd['projected_units'] = self._projected_units,
dd['take_log'] = self.take_log
- dd['validators'] = self.validators.copy()
+ dd['validators'] = list(self.validators)
dd['particle_type'] = self.particle_type
dd['vector_field'] = self.vector_field
dd['display_field'] = True
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/data_objects/profiles.py
--- a/yt/data_objects/profiles.py
+++ b/yt/data_objects/profiles.py
@@ -545,6 +545,8 @@
self.total_stuff = source_data.sum()
binned_field = self._get_empty_field()
weight_field = self._get_empty_field()
+ m_field = self._get_empty_field()
+ q_field = self._get_empty_field()
used_field = self._get_empty_field()
mi = args[0]
bin_indices_x = args[1][self.indices].ravel().astype('int64')
@@ -553,8 +555,8 @@
weight_data = weight_data[mi][self.indices]
nx = bin_indices_x.size
#mylog.debug("Binning %s / %s times", source_data.size, nx)
- Bin2DProfile(bin_indices_x, bin_indices_y, weight_data, source_data,
- weight_field, binned_field, used_field)
+ bin_profile2d(bin_indices_x, bin_indices_y, weight_data, source_data,
+ weight_field, binned_field, m_field, q_field, used_field)
if accumulation: # Fix for laziness
if not iterable(accumulation):
raise SyntaxError("Accumulation needs to have length 2")
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/data_objects/selection_data_containers.py
--- a/yt/data_objects/selection_data_containers.py
+++ b/yt/data_objects/selection_data_containers.py
@@ -194,7 +194,7 @@
ts = np.abs(ts)
self._dts[grid.id] = dts
self._ts[grid.id] = ts
- self._masks[grid.id] = masks
+ self._masks[grid.id] = mask
return mask
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/geometry/coordinate_handler.py
--- a/yt/geometry/coordinate_handler.py
+++ b/yt/geometry/coordinate_handler.py
@@ -36,7 +36,7 @@
ParallelAnalysisInterface, parallel_splitter
from yt.utilities.lib.misc_utilities import \
pixelize_cylinder
-import yt.visualization._MPL
+import yt.visualization._MPL as _MPL
from .cartesian_fields import CartesianFieldInfo
from .cylindrical_fields import CylindricalFieldInfo, PolarFieldInfo
@@ -103,7 +103,7 @@
c2[...,0] = ((coord[...,0] - center[0])**2.0
+ (coord[...,1] - center[1])**2.0)**0.5
c2[...,1] = coord[...,2] # rzt
- c2[...,2] = np.arctans(coord[...,1] - center[1],
+ c2[...,2] = np.arctan2(coord[...,1] - center[1],
coord[...,0] - center[0])
return c2
@@ -145,7 +145,7 @@
data_source['py'], data_source['pdx'],
data_source['pdy'], data_source['pdz'],
data_source.center, data_source._inv_mat, indices,
- data_source[item], size[0], size[1], bounds).transpose()
+ data_source[field], size[0], size[1], bounds).transpose()
return buff
def convert_from_cartesian(self, coord):
@@ -258,7 +258,7 @@
@property
def period(self):
- return na.array([0.0, 0.0, 2.0*np.pi])
+ return np.array([0.0, 0.0, 2.0*np.pi])
class CylindricalCoordinateHandler(CoordinateHandler):
@@ -331,5 +331,5 @@
@property
def period(self):
- return na.array([0.0, 0.0, 2.0*np.pi])
+ return np.array([0.0, 0.0, 2.0*np.pi])
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/geometry/cylindrical_fields.py
--- a/yt/geometry/cylindrical_fields.py
+++ b/yt/geometry/cylindrical_fields.py
@@ -35,6 +35,8 @@
NeedsDataField, \
NeedsProperty, \
NeedsParameter
+from yt.utilities.exceptions import \
+ YTCoordinateNotImplemented
CylindricalFieldInfo = FieldInfoContainer()
CylindricalFieldInfo.name = id(CylindricalFieldInfo)
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/cosmology.py
--- a/yt/utilities/cosmology.py
+++ b/yt/utilities/cosmology.py
@@ -61,7 +61,7 @@
self.HubbleDistance()))
elif (self.OmegaCurvatureNow < 0):
return (self.HubbleDistance() / np.sqrt(np.fabs(self.OmegaCurvatureNow)) *
- sin(np.sqrt(np.fabs(self.OmegaCurvatureNow)) *
+ np.sin(np.sqrt(np.fabs(self.OmegaCurvatureNow)) *
self.ComovingRadialDistance(z_i,z_f) / self.HubbleDistance()))
else:
return self.ComovingRadialDistance(z_i,z_f)
@@ -73,7 +73,7 @@
np.sqrt(1 + self.OmegaCurvatureNow *
sqr(self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance())) -
- anp.sinh(np.fabs(self.OmegaCurvatureNow) *
+ np.sinh(np.fabs(self.OmegaCurvatureNow) *
self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance()) / np.sqrt(self.OmegaCurvatureNow)) / 1e9)
elif (self.OmegaCurvatureNow < 0):
@@ -83,7 +83,7 @@
np.sqrt(1 + self.OmegaCurvatureNow *
sqr(self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance())) -
- asin(np.fabs(self.OmegaCurvatureNow) *
+ np.arcsin(np.fabs(self.OmegaCurvatureNow) *
self.ComovingTransverseDistance(z_i,z_f) /
self.HubbleDistance()) /
np.sqrt(np.fabs(self.OmegaCurvatureNow))) / 1e9)
@@ -269,7 +269,7 @@
# 3) For OmegaMatterNow > 1 and OmegaLambdaNow == 0, use sin/cos.
if ((self.OmegaMatterNow > 1) and (self.OmegaLambdaNow == 0)):
- eta = np.acos(1 - 2*(1-self.OmegaMatterNow)/self.OmegaMatterNow/(1+z))
+ eta = np.arccos(1 - 2*(1-self.OmegaMatterNow)/self.OmegaMatterNow/(1+z))
TimeHubble0 = self.OmegaMatterNow/(2*np.power(1.0-self.OmegaMatterNow, 1.5))*\
(eta - np.sin(eta))
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/exceptions.py
--- a/yt/utilities/exceptions.py
+++ b/yt/utilities/exceptions.py
@@ -109,7 +109,7 @@
% (self.display_name, self.field_name) + self.mathtext_error
class YTCannotParseUnitDisplayName(YTException):
- def __init__(self, field_name, display_unit, mathtext_error):
+ def __init__(self, field_name, unit_name, mathtext_error):
self.field_name = field_name
self.unit_name = unit_name
self.mathtext_error = mathtext_error
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/flagging_methods.py
--- a/yt/utilities/flagging_methods.py
+++ b/yt/utilities/flagging_methods.py
@@ -162,6 +162,9 @@
# Note that sd is offset by one
if sd[i-1] * sd[i] < 0:
strength = np.abs(sd[i-1] - sd[i])
+ # TODO this differs from what I could find in ENZO
+ # there's |center - i| < |center - zero_cross| instead
+ # additionally zero_cross is undefined in first pass
if strength > zero_strength or \
(strength == zero_strength and np.abs(center - i) < np.abs(zero_cross -i )):
zero_strength = strength
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/fortran_utils.py
--- a/yt/utilities/fortran_utils.py
+++ b/yt/utilities/fortran_utils.py
@@ -121,7 +121,8 @@
vec_fmt = "%s%s" % (endian, d)
vec_size = struct.calcsize(vec_fmt)
if vec_len % vec_size != 0:
- print "fmt = '%s' ; length = %s ; size= %s" % (fmt, length, size)
+ print("fmt = '%s' ; length = %s ; size= %s"
+ % (vec_fmt, vec_len, vec_size))
raise RuntimeError
vec_num = vec_len / vec_size
if isinstance(f, file): # Needs to be explicitly a file
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/parallel_tools/controller_system.py
--- a/yt/utilities/parallel_tools/controller_system.py
+++ b/yt/utilities/parallel_tools/controller_system.py
@@ -27,6 +27,8 @@
from .parallel_analysis_interface import MPI
except ImportError:
pass
+from .parallel_analysis_interface import \
+ ProcessorPool
from contextmanager import contextlib
from abc import ABCMeta, abstractmethod, abstractproperty
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/parallel_tools/io_runner.py
--- a/yt/utilities/parallel_tools/io_runner.py
+++ b/yt/utilities/parallel_tools/io_runner.py
@@ -24,7 +24,10 @@
"""
import os
-from .parallel_analysis_interface import ProcessorPool
+import np
+from yt.utilities.logger import ytLogger as mylog
+from .parallel_analysis_interface import \
+ ProcessorPool, parallel_objects
from yt.utilities.io_handler import BaseIOHandler
from contextlib import contextmanager
import time
@@ -168,6 +171,7 @@
pf.h.io = original_io
def io_nodes(fn, n_io, n_work, func, *args, **kwargs):
+ from yt.mods import load
pool, wg = ProcessorPool.from_sizes([(n_io, "io"), (n_work, "work")])
rv = None
if wg.name == "work":
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/parallel_tools/parallel_analysis_interface.py
--- a/yt/utilities/parallel_tools/parallel_analysis_interface.py
+++ b/yt/utilities/parallel_tools/parallel_analysis_interface.py
@@ -1115,8 +1115,9 @@
"""
LE, RE = left_edge[:], right_edge[:]
if not self._distributed:
+ raise NotImplemented
return LE, RE, re
-
+
cc = MPI.Compute_dims(self.comm.size / rank_ratio, 3)
mi = self.comm.rank % (self.comm.size / rank_ratio)
cx, cy, cz = np.unravel_index(mi, cc)
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/parameter_file_storage.py
--- a/yt/utilities/parameter_file_storage.py
+++ b/yt/utilities/parameter_file_storage.py
@@ -221,7 +221,8 @@
def __init__(self, path = None):
if path is None:
path = ytcfg.get("yt", "enzo_db")
- if len(path) == 0: raise Runtime
+ if len(path) == 0:
+ raise RuntimeError
import sqlite3
self.conn = sqlite3.connect(path)
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/pykdtree.py
--- a/yt/utilities/pykdtree.py
+++ b/yt/utilities/pykdtree.py
@@ -2,6 +2,7 @@
# Released under the scipy license
import sys
import numpy as np
+import scipy
from heapq import heappush, heappop
def minkowski_distance_p(x,y,p=2):
diff -r dddd65254a02e9fde765ac4e9cc91311ccb56b1d -r e2fc6f0ed6b6e5d3bfc40175a84c37f8df08bff9 yt/utilities/rpdb.py
--- a/yt/utilities/rpdb.py
+++ b/yt/utilities/rpdb.py
@@ -25,6 +25,7 @@
import cmd, pdb, cStringIO, xmlrpclib, socket, sys
import traceback
+import signal
from SimpleXMLRPCServer import SimpleXMLRPCServer
from yt.config import ytcfg
Repository URL: https://bitbucket.org/yt_analysis/yt-3.0/
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