[yt-svn] commit/yt: 6 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Mon Mar 6 12:21:46 PST 2017
6 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/d0355d0c5caa/
Changeset: d0355d0c5caa
Branch: stable
User: atmyers
Date: 2017-02-07 00:25:21+00:00
Summary: Backporting PR #2517 https://bitbucket.org/yt_analysis/yt/pull-requests/2517
Affected #: 1 file
diff -r 6e21d872301261938bd87d6279be0bc99fe54711 -r d0355d0c5caaaade54f9edc9aea8bee3d9479dd1 yt/frontends/boxlib/data_structures.py
--- a/yt/frontends/boxlib/data_structures.py
+++ b/yt/frontends/boxlib/data_structures.py
@@ -374,8 +374,8 @@
periodicity = (True, True, True)
def __init__(self, output_dir,
- cparam_filename="inputs",
- fparam_filename="probin",
+ cparam_filename=None,
+ fparam_filename=None,
dataset_type='boxlib_native',
storage_filename=None,
units_override=None,
@@ -426,6 +426,8 @@
return False
args = inspect.getcallargs(cls.__init__, args, kwargs)
# This might need to be localized somehow
+ if args['cparam_filename'] is None:
+ return True # Treat as generic boxlib data
inputs_filename = os.path.join(
os.path.dirname(os.path.abspath(output_dir)),
args['cparam_filename'])
@@ -784,7 +786,7 @@
if any(("castro." in line for line in lines)): return False
if any(("nyx." in line for line in lines)): return False
if any(("maestro" in line.lower() for line in lines)): return False
- if any(("geometry.prob_lo" in line for line in lines)): return True
+ if any(("hyp." in line for line in lines)): return True
return False
@@ -792,6 +794,22 @@
_field_info_class = CastroFieldInfo
+ def __init__(self, output_dir,
+ cparam_filename='inputs',
+ fparam_filename='probin',
+ dataset_type='boxlib_native',
+ storage_filename=None,
+ units_override=None,
+ unit_system="cgs"):
+
+ super(CastroDataset, self).__init__(output_dir,
+ cparam_filename,
+ fparam_filename,
+ dataset_type,
+ storage_filename,
+ units_override,
+ unit_system)
+
@classmethod
def _is_valid(cls, *args, **kwargs):
# fill our args
@@ -854,6 +872,22 @@
_field_info_class = MaestroFieldInfo
+ def __init__(self, output_dir,
+ cparam_filename='inputs',
+ fparam_filename='probin',
+ dataset_type='boxlib_native',
+ storage_filename=None,
+ units_override=None,
+ unit_system="cgs"):
+
+ super(MaestroDataset, self).__init__(output_dir,
+ cparam_filename,
+ fparam_filename,
+ dataset_type,
+ storage_filename,
+ units_override,
+ unit_system)
+
@classmethod
def _is_valid(cls, *args, **kwargs):
# fill our args
@@ -954,6 +988,22 @@
_index_class = NyxHierarchy
+ def __init__(self, output_dir,
+ cparam_filename='inputs',
+ fparam_filename='probin',
+ dataset_type='boxlib_native',
+ storage_filename=None,
+ units_override=None,
+ unit_system="cgs"):
+
+ super(NyxDataset, self).__init__(output_dir,
+ cparam_filename,
+ fparam_filename,
+ dataset_type,
+ storage_filename,
+ units_override,
+ unit_system)
+
@classmethod
def _is_valid(cls, *args, **kwargs):
# fill our args
https://bitbucket.org/yt_analysis/yt/commits/3d2543dd132f/
Changeset: 3d2543dd132f
Branch: stable
User: xarthisius
Date: 2017-02-13 17:34:56+00:00
Summary: Backporting PR #2519 https://bitbucket.org/yt_analysis/yt/pull-requests/2519
Affected #: 6 files
diff -r d0355d0c5caaaade54f9edc9aea8bee3d9479dd1 -r 3d2543dd132f55358327de9e959a3ebcb5a5b79b yt/analysis_modules/halo_finding/hop/EnzoHop.c
--- a/yt/analysis_modules/halo_finding/hop/EnzoHop.c
+++ b/yt/analysis_modules/halo_finding/hop/EnzoHop.c
@@ -27,6 +27,9 @@
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
#endif
+void PrepareKD(KD kd);
+int kdMedianJst(KD kd, int d, int l, int u);
+void kdUpPass(KD kd, int iCell);
void initgrouplist(Grouplist *g);
void hop_main(KD kd, HC *my_comm, float densthres);
void regroup_main(float dens_outer, HC *my_comm);
diff -r d0355d0c5caaaade54f9edc9aea8bee3d9479dd1 -r 3d2543dd132f55358327de9e959a3ebcb5a5b79b yt/geometry/oct_container.pyx
--- a/yt/geometry/oct_container.pyx
+++ b/yt/geometry/oct_container.pyx
@@ -821,7 +821,7 @@
self.visit_all_octs(selector, visitor)
assert ((visitor.global_index+1)*visitor.nz == visitor.index)
-cdef int root_node_compare(void *a, void *b) nogil:
+cdef int root_node_compare(const void *a, const void *b) nogil:
cdef OctKey *ao
cdef OctKey *bo
ao = <OctKey *>a
diff -r d0355d0c5caaaade54f9edc9aea8bee3d9479dd1 -r 3d2543dd132f55358327de9e959a3ebcb5a5b79b yt/utilities/lib/fixed_interpolator.h
--- a/yt/utilities/lib/fixed_interpolator.h
+++ b/yt/utilities/lib/fixed_interpolator.h
@@ -29,6 +29,8 @@
void eval_gradient(int ds[3], npy_float64 dp[3], npy_float64 *data, npy_float64 *grad);
+void offset_fill(int *ds, npy_float64 *data, npy_float64 *gridval);
+
void vertex_interp(npy_float64 v1, npy_float64 v2, npy_float64 isovalue,
npy_float64 vl[3], npy_float64 dds[3],
npy_float64 x, npy_float64 y, npy_float64 z,
diff -r d0355d0c5caaaade54f9edc9aea8bee3d9479dd1 -r 3d2543dd132f55358327de9e959a3ebcb5a5b79b yt/utilities/lib/marching_cubes.pyx
--- a/yt/utilities/lib/marching_cubes.pyx
+++ b/yt/utilities/lib/marching_cubes.pyx
@@ -18,7 +18,11 @@
import numpy as np
from yt.utilities.lib.fp_utils cimport imax, fmax, imin, fmin, iclip, fclip
from libc.stdlib cimport malloc, free, abs
-from fixed_interpolator cimport *
+from fixed_interpolator cimport \
+ eval_gradient, \
+ offset_fill, \
+ offset_interpolate, \
+ vertex_interp
cdef extern from "marching_cubes.h":
int tri_table[256][16]
diff -r d0355d0c5caaaade54f9edc9aea8bee3d9479dd1 -r 3d2543dd132f55358327de9e959a3ebcb5a5b79b yt/utilities/spatial/ckdtree.pyx
--- a/yt/utilities/spatial/ckdtree.pyx
+++ b/yt/utilities/spatial/ckdtree.pyx
@@ -369,7 +369,7 @@
stdlib.free(node)
def __dealloc__(cKDTree self):
- if <int>(self.tree) == 0:
+ if self.tree == NULL:
# should happen only if __init__ was never called
return
self.__free_tree(self.tree)
diff -r d0355d0c5caaaade54f9edc9aea8bee3d9479dd1 -r 3d2543dd132f55358327de9e959a3ebcb5a5b79b yt/utilities/spatial/src/distance_wrap.c
--- a/yt/utilities/spatial/src/distance_wrap.c
+++ b/yt/utilities/spatial/src/distance_wrap.c
@@ -863,7 +863,7 @@
else {
X = (double*)X_->data;
dm = (double*)dm_->data;
- w = (const double*)w_->data;
+ w = (double*)w_->data;
m = X_->dimensions[0];
n = X_->dimensions[1];
https://bitbucket.org/yt_analysis/yt/commits/d8bb338885a3/
Changeset: d8bb338885a3
Branch: stable
User: ngoldbaum
Date: 2017-02-16 20:45:57+00:00
Summary: Backporting PR #2521 https://bitbucket.org/yt_analysis/yt/pull-requests/2521
Affected #: 2 files
diff -r 3d2543dd132f55358327de9e959a3ebcb5a5b79b -r d8bb338885a39db3db0ec483bd615c0b66778d18 yt/visualization/volume_rendering/scene.py
--- a/yt/visualization/volume_rendering/scene.py
+++ b/yt/visualization/volume_rendering/scene.py
@@ -501,6 +501,7 @@
for k, source in self.transparent_sources:
im = source.render(camera, zbuffer=opaque)
+ opaque.rgba = im
return im
diff -r 3d2543dd132f55358327de9e959a3ebcb5a5b79b -r d8bb338885a39db3db0ec483bd615c0b66778d18 yt/visualization/volume_rendering/tests/test_vr_orientation.py
--- a/yt/visualization/volume_rendering/tests/test_vr_orientation.py
+++ b/yt/visualization/volume_rendering/tests/test_vr_orientation.py
@@ -31,6 +31,7 @@
sc = Scene()
vol = VolumeSource(ds, field=('gas', 'density'))
+ sc.add_source(vol)
tf = vol.transfer_function
tf = ColorTransferFunction((0.1, 1.0))
@@ -53,7 +54,6 @@
north_vector=[0., 0., 1.])
cam.set_width(ds.domain_width*2.)
- sc.add_source(vol)
yield VRImageComparisonTest(
sc, ds, '%s_%04d' % (lens_type, frame), decimals)
https://bitbucket.org/yt_analysis/yt/commits/ba3aeb491856/
Changeset: ba3aeb491856
Branch: stable
User: jzuhone
Date: 2017-02-17 19:30:06+00:00
Summary: Backporting PR #2523 https://bitbucket.org/yt_analysis/yt/pull-requests/2523
Affected #: 1 file
diff -r d8bb338885a39db3db0ec483bd615c0b66778d18 -r ba3aeb49185628741502f265d24407513aa8c034 yt/frontends/gadget/fields.py
--- a/yt/frontends/gadget/fields.py
+++ b/yt/frontends/gadget/fields.py
@@ -83,8 +83,11 @@
# Assume cosmic abundances
x_H = 0.76
gamma = 5.0/3.0
- # Assume zero ionization
- mu = 4.0 / (3.0 * x_H + 1.0)
+ if data.has_field_parameter("mean_molecular_weight"):
+ mu = data.get_field_parameter("mean_molecular_weight")
+ else:
+ # Assume zero ionization
+ mu = 4.0 / (3.0 * x_H + 1.0)
ret = data[ptype, "InternalEnergy"]*(gamma-1)*mu*mp/kb
return ret.in_units(self.ds.unit_system["temperature"])
https://bitbucket.org/yt_analysis/yt/commits/d50cc29f67ce/
Changeset: d50cc29f67ce
Branch: stable
User: ngoldbaum
Date: 2017-02-17 20:23:14+00:00
Summary: fix syntax error in units_override example
Affected #: 1 file
diff -r ba3aeb49185628741502f265d24407513aa8c034 -r d50cc29f67ce10e313269ec37b3cd381cb2c0073 doc/source/examining/loading_data.rst
--- a/doc/source/examining/loading_data.rst
+++ b/doc/source/examining/loading_data.rst
@@ -147,9 +147,9 @@
import yt
- units_override = {"length_unit":(1.0,"Mpc"),
- "time_unit"(1.0,"Myr"),
- "mass_unit":(1.0e14,"Msun")}
+ units_override = {"length_unit": (1.0, "Mpc"),
+ "time_unit": (1.0, "Myr"),
+ "mass_unit": (1.0e14, "Msun")}
ds = yt.load("id0/cluster_merger.0250.vtk", units_override=units_override)
https://bitbucket.org/yt_analysis/yt/commits/490ac254e4e1/
Changeset: 490ac254e4e1
Branch: stable
User: jzuhone
Date: 2017-01-26 03:55:37+00:00
Summary: Backporting PR #2502 https://bitbucket.org/yt_analysis/yt/pull-requests/2502
Affected #: 1 file
diff -r d50cc29f67ce10e313269ec37b3cd381cb2c0073 -r 490ac254e4e1c90183698b4fac698912fa343dd8 yt/visualization/volume_rendering/off_axis_projection.py
--- a/yt/visualization/volume_rendering/off_axis_projection.py
+++ b/yt/visualization/volume_rendering/off_axis_projection.py
@@ -136,7 +136,6 @@
def temp_weightfield(a, b):
tr = b[f].astype("float64") * b[w]
return b.apply_units(tr, a.units)
- return tr
return temp_weightfield
data_source.ds.field_info.add_field(weightfield,
function=_make_wf(item, weight))
@@ -144,7 +143,6 @@
# its dependencies..
deps, _ = data_source.ds.field_info.check_derived_fields([weightfield])
data_source.ds.field_dependencies.update(deps)
- fields = [weightfield, weight]
vol.set_field(weightfield)
vol.set_weight_field(weight)
ptf = ProjectionTransferFunction()
@@ -200,6 +198,9 @@
image = vol.finalize_image(camera, vol.sampler.aimage)
image = ImageArray(image, funits, registry=data_source.ds.unit_registry, info=image.info)
+ if weight is not None:
+ data_source.ds.field_info.pop(("index", "temp_weightfield"))
+
if method == "integrate":
if weight is None:
dl = width[2].in_units(data_source.ds.unit_system["length"])
Repository URL: https://bitbucket.org/yt_analysis/yt/
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