[yt-svn] commit/yt: 5 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Feb 24 11:33:28 PST 2016
5 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/6b93609ba222/
Changeset: 6b93609ba222
Branch: yt
User: brittonsmith
Date: 2016-01-30 12:27:16+00:00
Summary: Adding cython port of FindBindingEnergy.
Affected #: 1 file
diff -r 34ed15d98fe48c75d824fbf6246d8ab89c4e2398 -r 6b93609ba222f817ab6d6b0748ee5960008f7ee9 yt/utilities/lib/misc_utilities.pyx
--- a/yt/utilities/lib/misc_utilities.pyx
+++ b/yt/utilities/lib/misc_utilities.pyx
@@ -13,12 +13,13 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
+from yt.funcs import get_pbar
import numpy as np
from yt.units.yt_array import YTArray
cimport numpy as np
cimport cython
cimport libc.math as math
-from libc.math cimport abs
+from libc.math cimport abs, sqrt
from fp_utils cimport fmin, fmax, i64min, i64max
from yt.geometry.selection_routines cimport _ensure_code
@@ -966,3 +967,48 @@
dest[i,j,k] += dsp * (overlap[0]*overlap[1]*overlap[2])
else:
dest[i,j,k] = dsp
+
+ at cython.cdivision(True)
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+def gravitational_binding_energy(
+ np.float64_t[:] mass,
+ np.float64_t[:] x,
+ np.float64_t[:] y,
+ np.float64_t[:] z,
+ int truncate,
+ np.float64_t kinetic):
+
+ cdef int q_outer, q_inner, n_q, i
+ cdef np.float64_t mass_o, x_o, y_o, z_o
+ cdef np.float64_t mass_i, x_i, y_i, z_i
+ cdef np.float64_t this_potential, total_potential
+ total_potential = 0.
+
+ i = 0
+ n_q = mass.size
+ pbar = get_pbar("Calculating potential for %d cells" % n_q,
+ 0.5 * (n_q**2 - n_q))
+ for q_outer in range(n_q - 1):
+ this_potential = 0.
+ mass_o = mass[q_outer]
+ x_o = x[q_outer]
+ y_o = y[q_outer]
+ z_o = z[q_outer]
+ for q_inner in range(q_outer + 1, n_q):
+ mass_i = mass[q_inner]
+ x_i = x[q_inner]
+ y_i = y[q_inner]
+ z_i = z[q_inner]
+ this_potential += mass_o * mass_i / \
+ sqrt((x_i - x_o) * (x_i - x_o) +
+ (y_i - y_o) * (y_i - y_o) +
+ (z_i - z_o) * (z_i - z_o))
+ i += n_q - q_outer
+ pbar.update(i)
+ total_potential += this_potential
+ if truncate and total_potential / kinetic:
+ break
+ pbar.finish()
+
+ return total_potential
https://bitbucket.org/yt_analysis/yt/commits/9701c1c6fd0c/
Changeset: 9701c1c6fd0c
Branch: yt
User: brittonsmith
Date: 2016-01-30 12:29:22+00:00
Summary: Replacing call to c function with cython version.
Affected #: 1 file
diff -r 6b93609ba222f817ab6d6b0748ee5960008f7ee9 -r 9701c1c6fd0c43a54800413b47394b123262fcb9 yt/analysis_modules/level_sets/clump_validators.py
--- a/yt/analysis_modules/level_sets/clump_validators.py
+++ b/yt/analysis_modules/level_sets/clump_validators.py
@@ -13,7 +13,8 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-from yt.utilities.data_point_utilities import FindBindingEnergy
+from yt.utilities.lib.misc_utilities import \
+ gravitational_binding_energy
from yt.utilities.operator_registry import \
OperatorRegistry
from yt.utilities.physical_constants import \
@@ -64,11 +65,12 @@
(bulk_velocity[2] - clump["all", "particle_velocity_z"])**2)).sum()
potential = clump.data.ds.quan(G *
- FindBindingEnergy(clump["gas", "cell_mass"].in_cgs(),
- clump["index", "x"].in_cgs(),
- clump["index", "y"].in_cgs(),
- clump["index", "z"].in_cgs(),
- truncate, (kinetic / G).in_cgs()),
+ gravitational_binding_energy(
+ clump["gas", "cell_mass"].in_cgs(),
+ clump["index", "x"].in_cgs(),
+ clump["index", "y"].in_cgs(),
+ clump["index", "z"].in_cgs(),
+ truncate, (kinetic / G).in_cgs()),
kinetic.in_cgs().units)
if truncate and potential >= kinetic:
@@ -76,7 +78,7 @@
if use_particles:
potential += clump.data.ds.quan(G *
- FindBindingEnergy(
+ gravitational_binding_energy(
clump["all", "particle_mass"].in_cgs(),
clump["all", "particle_position_x"].in_cgs(),
clump["all", "particle_position_y"].in_cgs(),
https://bitbucket.org/yt_analysis/yt/commits/f45f7851fbd3/
Changeset: f45f7851fbd3
Branch: yt
User: brittonsmith
Date: 2016-01-30 17:15:36+00:00
Summary: Add extra bit to if statement.
Affected #: 1 file
diff -r 9701c1c6fd0c43a54800413b47394b123262fcb9 -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 yt/utilities/lib/misc_utilities.pyx
--- a/yt/utilities/lib/misc_utilities.pyx
+++ b/yt/utilities/lib/misc_utilities.pyx
@@ -1007,7 +1007,7 @@
i += n_q - q_outer
pbar.update(i)
total_potential += this_potential
- if truncate and total_potential / kinetic:
+ if truncate and total_potential / kinetic > 1.:
break
pbar.finish()
https://bitbucket.org/yt_analysis/yt/commits/2ef50ab5517d/
Changeset: 2ef50ab5517d
Branch: yt
User: brittonsmith
Date: 2016-02-17 18:01:18+00:00
Summary: Merging.
Affected #: 122 files
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -28,40 +28,37 @@
yt/utilities/spatial/ckdtree.c
yt/utilities/lib/alt_ray_tracers.c
yt/utilities/lib/amr_kdtools.c
+yt/utilities/lib/basic_octree.c
yt/utilities/lib/bitarray.c
-yt/utilities/lib/CICDeposit.c
-yt/utilities/lib/ContourFinding.c
-yt/utilities/lib/DepthFirstOctree.c
+yt/utilities/lib/contour_finding.c
+yt/utilities/lib/depth_first_octree.c
yt/utilities/lib/element_mappings.c
-yt/utilities/lib/FixedInterpolator.c
yt/utilities/lib/fortran_reader.c
yt/utilities/lib/freetype_writer.c
yt/utilities/lib/geometry_utils.c
yt/utilities/lib/image_utilities.c
-yt/utilities/lib/Interpolators.c
+yt/utilities/lib/interpolators.c
yt/utilities/lib/kdtree.c
yt/utilities/lib/line_integral_convolution.c
+yt/utilities/lib/mesh_construction.cpp
+yt/utilities/lib/mesh_intersection.cpp
+yt/utilities/lib/mesh_samplers.cpp
+yt/utilities/lib/mesh_traversal.cpp
yt/utilities/lib/mesh_utilities.c
yt/utilities/lib/misc_utilities.c
-yt/utilities/lib/Octree.c
-yt/utilities/lib/GridTree.c
+yt/utilities/lib/particle_mesh_operations.c
yt/utilities/lib/origami.c
+yt/utilities/lib/particle_mesh_operations.c
yt/utilities/lib/pixelization_routines.c
yt/utilities/lib/png_writer.c
-yt/utilities/lib/PointsInVolume.c
-yt/utilities/lib/QuadTree.c
-yt/utilities/lib/RayIntegrators.c
+yt/utilities/lib/points_in_volume.c
+yt/utilities/lib/quad_tree.c
+yt/utilities/lib/ray_integrators.c
yt/utilities/lib/ragged_arrays.c
-yt/utilities/lib/VolumeIntegrator.c
yt/utilities/lib/grid_traversal.c
yt/utilities/lib/marching_cubes.c
yt/utilities/lib/png_writer.h
yt/utilities/lib/write_array.c
-yt/utilities/lib/element_mappings.c
-yt/utilities/lib/mesh_construction.cpp
-yt/utilities/lib/mesh_samplers.cpp
-yt/utilities/lib/mesh_traversal.cpp
-yt/utilities/lib/mesh_intersection.cpp
syntax: glob
*.pyc
.*.swp
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 clean.sh
--- a/clean.sh
+++ b/clean.sh
@@ -1,4 +1,1 @@
-find . -name "*.so" -exec rm -v {} \;
-find . -name "*.pyc" -exec rm -v {} \;
-find . -name "__config__.py" -exec rm -v {} \;
-rm -rvf build dist
+hg --config extensions.purge= purge --all yt
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 doc/source/examining/loading_data.rst
--- a/doc/source/examining/loading_data.rst
+++ b/doc/source/examining/loading_data.rst
@@ -330,12 +330,17 @@
Exodus II Data
--------------
+.. note::
+ To load Exodus II data, you need to have the `netcdf4 <http://unidata.github.io/
+ netcdf4-python/>`_ python interface installed.
+
Exodus II is a file format for Finite Element datasets that is used by the MOOSE
framework for file IO. Support for this format (and for unstructured mesh data in
-general) is a new feature as of yt 3.3, so while we aim to fully support it, we also expect
-there to be some buggy features at present. Currently, yt can visualize first-order
-mesh types only (4-node quads, 8-node hexes, 3-node triangles, and 4-node tetrahedra).
-Development of higher-order visualization capability is a work in progress.
+general) is a new feature as of yt 3.3, so while we aim to fully support it, we
+also expect there to be some buggy features at present. Currently, yt can visualize
+quads, hexes, triangles, and tetrahedral element types at first order. Additionally,
+there is experimental support for the high-order visualization of 20-node hex elements.
+Development of more high-order visualization capability is a work in progress.
To load an Exodus II dataset, you can use the ``yt.load`` command on the Exodus II
file:
@@ -348,14 +353,15 @@
Because Exodus II datasets can have multiple steps (which can correspond to time steps,
picard iterations, non-linear solve iterations, etc...), you can also specify a step
argument when you load an Exodus II data that defines the index at which to look when
-you read data from the file.
+you read data from the file. Omitting this argument is the same as passing in 0, and
+setting ``step=-1`` selects the last time output in the file.
You can access the connectivity information directly by doing:
.. code-block:: python
import yt
- ds = yt.load("MOOSE_sample_data/out.e-s010", step=0)
+ ds = yt.load("MOOSE_sample_data/out.e-s010", step=-1)
print(ds.index.meshes[0].connectivity_coords)
print(ds.index.meshes[0].connectivity_indices)
print(ds.index.meshes[1].connectivity_coords)
@@ -368,7 +374,7 @@
.. code-block:: python
import yt
- ds = yt.load("MOOSE_sample_data/out.e-s010", step=0)
+ ds = yt.load("MOOSE_sample_data/out.e-s010")
print(ds.field_list)
This will give you a list of field names like ``('connect1', 'diffused')`` and
@@ -380,7 +386,7 @@
.. code-block:: python
import yt
- ds = yt.load("MOOSE_sample_data/out.e-s010", step=0)
+ ds = yt.load("MOOSE_sample_data/out.e-s010")
ad = ds.all_data() # geometric selection, this just grabs everything
print(ad['connect1', 'convected'])
@@ -390,7 +396,7 @@
.. code-block:: python
import yt
- ds = yt.load("MOOSE_sample_data/out.e-s010", step=0)
+ ds = yt.load("MOOSE_sample_data/out.e-s010")
ad = ds.all_data()
print(ad['connect1', 'convected'].shape)
@@ -401,7 +407,7 @@
.. code-block:: python
import yt
- ds = yt.load("MOOSE_sample_data/out.e-s010", step=0)
+ ds = yt.load("MOOSE_sample_data/out.e-s010")
ad = ds.all_data()
print(ad['connect1', 'vertex_x'])
@@ -411,7 +417,7 @@
.. code-block:: python
import yt
- ds = yt.load("MOOSE_sample_data/out.e-s010", step=0)
+ ds = yt.load("MOOSE_sample_data/out.e-s010")
ad = ds.all_data()
print(ad['connect1', 'conv_indicator'].shape)
@@ -420,6 +426,61 @@
For information about visualizing unstructured mesh data, including Exodus II datasets,
please see :ref:`unstructured-mesh-slices` and :ref:`unstructured_mesh_rendering`.
+Displacement Fields
+^^^^^^^^^^^^^^^^^^^
+
+Finite element codes often solve for the displacement of each vertex from its
+original position as a node variable, rather than updating the actual vertex
+positions with time. For analysis and visualization, it is often useful to turn
+these displacements on or off, and to be able to scale them arbitrarily to
+emphasize certain features of the solution. To allow this, if ``yt`` detects
+displacement fields in an Exodus II dataset (using the convention that they will
+ be named ``disp_x``, ``disp_y``, etc...), it will add optionally add these to
+the mesh vertex positions for the purposes of visualization. Displacement fields
+can be controlled when a dataset is loaded by passing in an optional dictionary
+to the ``yt.load`` command. This feature is turned off by default, meaning that
+a dataset loaded as
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("MOOSE_sample_data/mps_out.e")
+
+will not include the displacements in the vertex positions. The displacements can
+be turned on separately for each mesh in the file by passing in a a tuple of
+(scale, offset) pairs for the meshes you want to enable displacements for.
+For example, the following code snippet turns displacements on for the second
+mesh, but not the first:
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("MOOSE_sample_data/mps_out.e", step=10,
+ displacements={'connect2': (1.0, [0.0, 0.0, 0.0])})
+
+The displacements can also be scaled by an arbitrary factor before they are
+added in to the vertex positions. The following code turns on displacements
+for both ``connect1`` and ``connect2``, scaling the former by a factor of 5.0
+and the later by a factor of 10.0:
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("MOOSE_sample_data/mps_out.e", step=10,
+ displacements={'connect1': (5.0, [0.0, 0.0, 0.0]),
+ 'connect2': (10.0, [0.0, 0.0, 0.0])})
+
+Finally, we can also apply an arbitrary offset to the mesh vertices after
+the scale factor is applied. For example, the following code scales all
+displacements in the second mesh by a factor of 5.0, and then shifts
+each vertex in the mesh by 1.0 unit in the z-direction:
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("MOOSE_sample_data/mps_out.e", step=10,
+ displacements={'connect2': (5.0, [0.0, 0.0, 1.0])})
+
FITS Data
---------
@@ -1232,10 +1293,9 @@
yt has support for reading halo catalogs produced by Rockstar and the inline
FOF/SUBFIND halo finders of Gadget and OWLS. The halo catalogs are treated as
-particle datasets where each particle represents a single halo. At this time,
-yt does not have the ability to load the member particles for a given halo.
-However, once loaded, further halo analysis can be performed using
-:ref:`halo_catalog`.
+particle datasets where each particle represents a single halo. Member particles
+for individual halos can be accessed through halo data containers. Further halo
+analysis can be performed using :ref:`halo_catalog`.
In the case where halo catalogs are written to multiple files, one must only
give the path to one of them.
@@ -1269,11 +1329,39 @@
# x component of the spin
print(ad["Subhalo", "SubhaloSpin_0"])
+Halo member particles are accessed by creating halo data containers with the
+type of halo ("Group" or "Subhalo") and the halo id. Scalar values for halos
+can be accessed in the same way. Halos also have mass, position, and velocity
+attributes.
+
+.. code-block:: python
+
+ halo = ds.halo("Group", 0)
+ # member particles for this halo
+ print halo["member_ids"]
+ # halo virial radius
+ print halo["Group_R_Crit200"]
+ # halo mass
+ print halo.mass
+
+Subhalos containers can be created using either their absolute ids or their
+subhalo ids.
+
+.. code-block:: python
+
+ # first subhalo of the first halo
+ subhalo = ds.halo("Subhalo", (0, 0))
+ # this subhalo's absolute id
+ print subhalo.group_identifier
+ # member particles
+ print subhalo["member_ids"]
+
OWLS FOF/SUBFIND
^^^^^^^^^^^^^^^^
OWLS halo catalogs have a very similar structure to regular Gadget halo catalogs.
-The two field types are "FOF" and "SUBFIND".
+The two field types are "FOF" and "SUBFIND". At this time, halo member particles
+cannot be loaded.
.. code-block:: python
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 doc/source/visualizing/unstructured_mesh_rendering.rst
--- a/doc/source/visualizing/unstructured_mesh_rendering.rst
+++ b/doc/source/visualizing/unstructured_mesh_rendering.rst
@@ -14,7 +14,7 @@
.. code-block:: bash
- conda install -c http://use.yt/with_conda/ yt
+ conda install -c http://use.yt/with_conda/ yt=3.3_dev
If you want to install from source, you can use the ``get_yt.sh`` script.
Be sure to set the INST_YT_SOURCE and INST_UNSTRUCTURED flags to 1 at the
@@ -114,7 +114,7 @@
cam = sc.camera
cam.focus = ds.arr([0.0, 0.0, 0.0], 'code_length')
cam_pos = ds.arr([-3.0, 3.0, -3.0], 'code_length')
- north_vector = ds.arr([0.0, 1.0, 1.0], 'dimensionless')
+ north_vector = ds.arr([0.0, -1.0, -1.0], 'dimensionless')
cam.set_position(cam_pos, north_vector)
# increase the default resolution
@@ -142,7 +142,7 @@
cam = sc.camera
cam.focus = ds.arr([0.0, 0.0, 0.0], 'code_length')
cam_pos = ds.arr([-3.0, 3.0, -3.0], 'code_length')
- north_vector = ds.arr([0.0, 1.0, 1.0], 'dimensionless')
+ north_vector = ds.arr([0.0, -1.0, -1.0], 'dimensionless')
cam.set_position(cam_pos, north_vector)
# increase the default resolution
@@ -174,7 +174,7 @@
cam = sc.camera
cam.focus = ds.arr([0.0, 0.0, 0.0], 'code_length')
cam_pos = ds.arr([-3.0, 3.0, -3.0], 'code_length')
- north_vector = ds.arr([0.0, 1.0, 1.0], 'dimensionless')
+ north_vector = ds.arr([0.0, -1.0, -1.0], 'dimensionless')
cam.set_position(cam_pos, north_vector)
# increase the default resolution
@@ -205,7 +205,7 @@
cam = sc.camera
camera_position = ds.arr([3.0, 3.0, 3.0], 'code_length')
cam.set_width(ds.arr([2.0, 2.0, 2.0], 'code_length'))
- north_vector = ds.arr([0.0, 1.0, 0.0], 'dimensionless')
+ north_vector = ds.arr([0.0, -1.0, 0.0], 'dimensionless')
cam.set_position(camera_position, north_vector)
# increase the default resolution
@@ -236,7 +236,7 @@
# adjust the camera position and orientation
cam = sc.camera
camera_position = ds.arr([-1.0, 1.0, -0.5], 'code_length')
- north_vector = ds.arr([0.0, 1.0, 1.0], 'dimensionless')
+ north_vector = ds.arr([0.0, -1.0, -1.0], 'dimensionless')
cam.width = ds.arr([0.04, 0.04, 0.04], 'code_length')
cam.set_position(camera_position, north_vector)
@@ -248,6 +248,43 @@
sc.annotate_mesh_lines()
sc.save()
+The dataset in the above example contains displacement fields, so this is a good
+opportunity to demonstrate their use. The following example is exactly like the
+above, except we scale the displacements by a factor of a 10.0, and additionally
+add an offset to the mesh by 1.0 unit in the x-direction:
+
+.. python-script::
+
+ import yt
+
+ # We load the last time frame
+ ds = yt.load("MOOSE_sample_data/mps_out.e", step=-1,
+ displacements={'connect2': (10.0, [0.01, 0.0, 0.0])})
+
+ # create a default scene
+ sc = yt.create_scene(ds, ("connect2", "temp"))
+
+ # override the default colormap. This time we also override
+ # the default color bounds
+ ms = sc.get_source(0)
+ ms.cmap = 'hot'
+ ms.color_bounds = (500.0, 1700.0)
+
+ # adjust the camera position and orientation
+ cam = sc.camera
+ camera_position = ds.arr([-1.0, 1.0, -0.5], 'code_length')
+ north_vector = ds.arr([0.0, 1.0, 1.0], 'dimensionless')
+ cam.width = ds.arr([0.05, 0.05, 0.05], 'code_length')
+ cam.set_position(camera_position, north_vector)
+
+ # increase the default resolution
+ cam.resolution = (800, 800)
+
+ # render, draw the element boundaries, and save
+ sc.render()
+ sc.annotate_mesh_lines()
+ sc.save()
+
As with other volume renderings in yt, you can swap out different lenses. Here is
an example that uses a "perspective" lens, for which the rays diverge from the
camera position according to some opening angle:
@@ -270,7 +307,7 @@
cam = Camera(ds, lens_type='perspective')
cam.focus = ds.arr([0.0, 0.0, 0.0], 'code_length')
cam_pos = ds.arr([-4.5, 4.5, -4.5], 'code_length')
- north_vector = ds.arr([0.0, 1.0, 1.0], 'dimensionless')
+ north_vector = ds.arr([0.0, -1.0, -1.0], 'dimensionless')
cam.set_position(cam_pos, north_vector)
# tell our scene to use it
@@ -303,7 +340,7 @@
cam = Camera(ds)
cam.focus = ds.arr([0.0, 0.0, 0.0], 'code_length')
cam.set_position(ds.arr([-3.0, 3.0, -3.0], 'code_length'),
- ds.arr([0.0, 1.0, 0.0], 'dimensionless'))
+ ds.arr([0.0, -1.0, 0.0], 'dimensionless'))
cam.set_width = ds.arr([8.0, 8.0, 8.0], 'code_length')
cam.resolution = (800, 800)
@@ -348,7 +385,7 @@
cam = sc.camera
cam.focus = ds.arr([0.0, 0.0, 0.0], 'code_length')
cam_pos = ds.arr([-3.0, 3.0, -3.0], 'code_length')
- north_vector = ds.arr([0.0, 1.0, 1.0], 'dimensionless')
+ north_vector = ds.arr([0.0, -1.0, -1.0], 'dimensionless')
cam.set_position(cam_pos, north_vector)
# increase the default resolution
@@ -398,7 +435,7 @@
cam = Camera(ds)
camera_position = ds.arr([0.1, 0.0, 0.1], 'code_length')
cam.focus = ds.domain_center
- north_vector = ds.arr([0.3032476, 0.71782557, -0.62671153], 'dimensionless')
+ north_vector = ds.arr([-0.3032476, -0.71782557, 0.62671153], 'dimensionless')
cam.width = ds.arr([ 0.04, 0.04, 0.04], 'code_length')
cam.resolution = (800, 800)
cam.set_position(camera_position, north_vector)
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 setup.py
--- a/setup.py
+++ b/setup.py
@@ -1,27 +1,20 @@
import os
-import os.path
import glob
import sys
-import time
-import subprocess
-import shutil
-import glob
+from sys import platform as _platform
+from setuptools import setup, find_packages
+from setuptools.extension import Extension
+from setuptools.command.build_ext import build_ext as _build_ext
+from setuptools.command.build_py import build_py as _build_py
+from setupext import \
+ check_for_openmp, check_for_pyembree, read_embree_location, \
+ get_mercurial_changeset_id
if sys.version_info < (2, 7):
print("yt currently requires Python version 2.7")
print("certain features may fail unexpectedly and silently with older versions.")
sys.exit(1)
-import setuptools
-from distutils.command.build_py import build_py
-from numpy.distutils.misc_util import appendpath
-from numpy.distutils.command import install_data as np_install_data
-from numpy.distutils import log
-from distutils import version
-
-from distutils.core import Command
-from distutils.spawn import find_executable
-
MAPSERVER_FILES = []
MAPSERVER_DIRS = [
"",
@@ -36,109 +29,277 @@
files += glob.glob("%s/*.%s" % (dir_name, ext))
MAPSERVER_FILES.append((dir_name, files))
-# Verify that we have Cython installed
-REQ_CYTHON = '0.22'
-try:
- import Cython
- needs_cython = \
- version.LooseVersion(Cython.__version__) < version.LooseVersion(REQ_CYTHON)
-except ImportError as e:
- needs_cython = True
-
-if needs_cython:
- print("Cython is a build-time requirement for the source tree of yt.")
- print("Please either install yt from a provided, release tarball,")
- print("or install Cython (version %s or higher)." % REQ_CYTHON)
- print("You may be able to accomplish this by typing:")
- print(" pip install -U Cython")
- sys.exit(1)
-
-######
-# This next bit comes from Matthew Brett, to get Cython working with NumPy
-# distutils. I added a bit to get C++ Cython working.
-from os.path import join as pjoin, dirname
-from distutils.dep_util import newer_group
-from distutils.errors import DistutilsError
-
-
-def generate_a_pyrex_source(self, base, ext_name, source, extension):
- ''' Monkey patch for numpy build_src.build_src method
-
- Uses Cython instead of Pyrex.
-
- Assumes Cython is present
- '''
- if self.inplace:
- target_dir = dirname(base)
- else:
- target_dir = appendpath(self.build_src, dirname(base))
- if extension.language == "c++":
- cplus = True
- file_ext = ".cpp"
- else:
- cplus = False
- file_ext = ".c"
- target_file = pjoin(target_dir, ext_name + file_ext)
- depends = [source] + extension.depends
- if self.force or newer_group(depends, target_file, 'newer'):
- import Cython.Compiler.Main
- log.info("cythonc:> %s" % (target_file))
- self.mkpath(target_dir)
- options = Cython.Compiler.Main.CompilationOptions(
- defaults=Cython.Compiler.Main.default_options,
- include_path=extension.include_dirs,
- cplus=cplus,
- output_file=target_file)
- cython_result = Cython.Compiler.Main.compile(source,
- options=options)
- if cython_result.num_errors != 0:
- raise DistutilsError("%d errors while compiling %r with Cython"
- % (cython_result.num_errors, source))
- return target_file
-
-
-from numpy.distutils.command import build_src
-build_src.build_src.generate_a_pyrex_source = generate_a_pyrex_source
-# End snippet
-######
-
VERSION = "3.3.dev0"
if os.path.exists('MANIFEST'):
os.remove('MANIFEST')
-def get_mercurial_changeset_id(target_dir):
- """adapted from a script by Jason F. Harris, published at
+if check_for_openmp() is True:
+ omp_args = ['-fopenmp']
+else:
+ omp_args = None
- http://jasonfharris.com/blog/2010/05/versioning-your-application-with-the-mercurial-changeset-hash/
- """
- import subprocess
- import re
- get_changeset = subprocess.Popen('hg identify -b -i',
- stdout=subprocess.PIPE,
- stderr=subprocess.PIPE,
- shell=True)
+cython_extensions = [
+ Extension("yt.analysis_modules.photon_simulator.utils",
+ ["yt/analysis_modules/photon_simulator/utils.pyx"]),
+ Extension("yt.analysis_modules.ppv_cube.ppv_utils",
+ ["yt/analysis_modules/ppv_cube/ppv_utils.pyx"],
+ libraries=["m"]),
+ Extension("yt.geometry.grid_visitors",
+ ["yt/geometry/grid_visitors.pyx"],
+ include_dirs=["yt/utilities/lib"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/geometry/grid_visitors.pxd"]),
+ Extension("yt.geometry.grid_container",
+ ["yt/geometry/grid_container.pyx"],
+ include_dirs=["yt/utilities/lib/"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/geometry/grid_container.pxd",
+ "yt/geometry/grid_visitors.pxd"]),
+ Extension("yt.geometry.oct_container",
+ ["yt/geometry/oct_container.pyx"],
+ include_dirs=["yt/utilities/lib"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/geometry/oct_container.pxd",
+ "yt/geometry/selection_routines.pxd"]),
+ Extension("yt.geometry.oct_visitors",
+ ["yt/geometry/oct_visitors.pyx"],
+ include_dirs=["yt/utilities/lib/"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/geometry/oct_container.pxd",
+ "yt/geometry/selection_routines.pxd"]),
+ Extension("yt.geometry.particle_oct_container",
+ ["yt/geometry/particle_oct_container.pyx"],
+ include_dirs=["yt/utilities/lib/"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/geometry/oct_container.pxd",
+ "yt/geometry/selection_routines.pxd"]),
+ Extension("yt.geometry.selection_routines",
+ ["yt/geometry/selection_routines.pyx"],
+ include_dirs=["yt/utilities/lib/"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/utilities/lib/grid_traversal.pxd",
+ "yt/geometry/oct_container.pxd",
+ "yt/geometry/oct_visitors.pxd",
+ "yt/geometry/grid_container.pxd",
+ "yt/geometry/grid_visitors.pxd",
+ "yt/geometry/selection_routines.pxd"]),
+ Extension("yt.geometry.particle_deposit",
+ ["yt/geometry/particle_deposit.pyx"],
+ include_dirs=["yt/utilities/lib/"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/geometry/oct_container.pxd",
+ "yt/geometry/selection_routines.pxd",
+ "yt/geometry/particle_deposit.pxd"]),
+ Extension("yt.geometry.particle_smooth",
+ ["yt/geometry/particle_smooth.pyx"],
+ include_dirs=["yt/utilities/lib/"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/geometry/oct_container.pxd",
+ "yt/geometry/selection_routines.pxd",
+ "yt/geometry/particle_deposit.pxd",
+ "yt/geometry/particle_smooth.pxd"]),
+ Extension("yt.geometry.fake_octree",
+ ["yt/geometry/fake_octree.pyx"],
+ include_dirs=["yt/utilities/lib/"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/geometry/oct_container.pxd",
+ "yt/geometry/selection_routines.pxd"]),
+ Extension("yt.utilities.spatial.ckdtree",
+ ["yt/utilities/spatial/ckdtree.pyx"],
+ libraries=["m"]),
+ Extension("yt.utilities.lib.bitarray",
+ ["yt/utilities/lib/bitarray.pyx"],
+ libraries=["m"], depends=["yt/utilities/lib/bitarray.pxd"]),
+ Extension("yt.utilities.lib.contour_finding",
+ ["yt/utilities/lib/contour_finding.pyx"],
+ include_dirs=["yt/utilities/lib/",
+ "yt/geometry/"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/utilities/lib/amr_kdtools.pxd",
+ "yt/utilities/lib/grid_traversal.pxd",
+ "yt/utilities/lib/contour_finding.pxd",
+ "yt/geometry/oct_container.pxd"]),
+ Extension("yt.utilities.lib.geometry_utils",
+ ["yt/utilities/lib/geometry_utils.pyx"],
+ extra_compile_args=omp_args,
+ extra_link_args=omp_args,
+ libraries=["m"], depends=["yt/utilities/lib/fp_utils.pxd"]),
+ Extension("yt.utilities.lib.marching_cubes",
+ ["yt/utilities/lib/marching_cubes.pyx",
+ "yt/utilities/lib/fixed_interpolator.c"],
+ include_dirs=["yt/utilities/lib/"],
+ libraries=["m"],
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/utilities/lib/fixed_interpolator.pxd",
+ "yt/utilities/lib/fixed_interpolator.h",
+ ]),
+ Extension("yt.utilities.lib.pixelization_routines",
+ ["yt/utilities/lib/pixelization_routines.pyx",
+ "yt/utilities/lib/pixelization_constants.c"],
+ include_dirs=["yt/utilities/lib/"],
+ language="c++",
+ libraries=["m"], depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/utilities/lib/pixelization_constants.h",
+ "yt/utilities/lib/element_mappings.pxd"]),
+ Extension("yt.utilities.lib.origami",
+ ["yt/utilities/lib/origami.pyx",
+ "yt/utilities/lib/origami_tags.c"],
+ include_dirs=["yt/utilities/lib/"],
+ depends=["yt/utilities/lib/origami_tags.h"]),
+ Extension("yt.utilities.lib.grid_traversal",
+ ["yt/utilities/lib/grid_traversal.pyx",
+ "yt/utilities/lib/fixed_interpolator.c",
+ "yt/utilities/lib/kdtree.c"],
+ include_dirs=["yt/utilities/lib/"],
+ libraries=["m"],
+ extra_compile_args=omp_args,
+ extra_link_args=omp_args,
+ depends=["yt/utilities/lib/fp_utils.pxd",
+ "yt/utilities/lib/kdtree.h",
+ "yt/utilities/lib/fixed_interpolator.h",
+ "yt/utilities/lib/fixed_interpolator.pxd",
+ "yt/utilities/lib/field_interpolation_tables.pxd"]),
+ Extension("yt.utilities.lib.element_mappings",
+ ["yt/utilities/lib/element_mappings.pyx"],
+ libraries=["m"], depends=["yt/utilities/lib/element_mappings.pxd"]),
+ Extension("yt.utilities.lib.alt_ray_tracers",
+ ["yt/utilities/lib/alt_ray_tracers.pyx"],
+ libraries=["m"]),
+]
- if (get_changeset.stderr.read() != ""):
- print("Error in obtaining current changeset of the Mercurial repository")
- changeset = None
+lib_exts = [
+ "particle_mesh_operations", "depth_first_octree", "fortran_reader",
+ "interpolators", "misc_utilities", "basic_octree", "image_utilities",
+ "points_in_volume", "quad_tree", "ray_integrators", "mesh_utilities",
+ "amr_kdtools"
+]
+for ext_name in lib_exts:
+ cython_extensions.append(
+ Extension("yt.utilities.lib.{}".format(ext_name),
+ ["yt/utilities/lib/{}.pyx".format(ext_name)],
+ libraries=["m"], depends=["yt/utilities/lib/fp_utils.pxd"]))
- changeset = get_changeset.stdout.read().strip().decode("UTF-8")
- if (not re.search("^[0-9a-f]{12}", changeset)):
- print("Current changeset of the Mercurial repository is malformed")
- changeset = None
+lib_exts = ["write_array", "ragged_arrays", "line_integral_convolution"]
+for ext_name in lib_exts:
+ cython_extensions.append(
+ Extension("yt.utilities.lib.{}".format(ext_name),
+ ["yt/utilities/lib/{}.pyx".format(ext_name)]))
- return changeset
+extensions = [
+ Extension("yt.analysis_modules.halo_finding.fof.EnzoFOF",
+ ["yt/analysis_modules/halo_finding/fof/EnzoFOF.c",
+ "yt/analysis_modules/halo_finding/fof/kd.c"],
+ libraries=["m"]),
+ Extension("yt.analysis_modules.halo_finding.hop.EnzoHop",
+ glob.glob("yt/analysis_modules/halo_finding/hop/*.c")),
+ Extension("yt.frontends.artio._artio_caller",
+ ["yt/frontends/artio/_artio_caller.pyx"] +
+ glob.glob("yt/frontends/artio/artio_headers/*.c"),
+ include_dirs=["yt/frontends/artio/artio_headers/",
+ "yt/geometry/",
+ "yt/utilities/lib/"],
+ depends=glob.glob("yt/frontends/artio/artio_headers/*.c") +
+ ["yt/utilities/lib/fp_utils.pxd",
+ "yt/geometry/oct_container.pxd",
+ "yt/geometry/selection_routines.pxd",
+ "yt/geometry/particle_deposit.pxd"]),
+ Extension("yt.utilities.spatial._distance_wrap",
+ glob.glob("yt/utilities/spatial/src/*.c")),
+ Extension("yt.visualization._MPL",
+ ["yt/visualization/_MPL.c"],
+ libraries=["m"]),
+ Extension("yt.utilities.data_point_utilities",
+ ["yt/utilities/data_point_utilities.c"],
+ libraries=["m"]),
+]
+# EMBREE
+if check_for_pyembree() is not None:
+ embree_extensions = [
+ Extension("yt.utilities.lib.mesh_construction",
+ ["yt/utilities/lib/mesh_construction.pyx"],
+ depends=["yt/utilities/lib/mesh_construction.pxd"]),
+ Extension("yt.utilities.lib.mesh_traversal",
+ ["yt/utilities/lib/mesh_traversal.pyx"],
+ depends=["yt/utilities/lib/mesh_traversal.pxd",
+ "yt/utilities/lib/grid_traversal.pxd"]),
+ Extension("yt.utilities.lib.mesh_samplers",
+ ["yt/utilities/lib/mesh_samplers.pyx"],
+ depends=["yt/utilities/lib/mesh_samplers.pxd",
+ "yt/utilities/lib/element_mappings.pxd",
+ "yt/utilities/lib/mesh_construction.pxd"]),
+ Extension("yt.utilities.lib.mesh_intersection",
+ ["yt/utilities/lib/mesh_intersection.pyx"],
+ depends=["yt/utilities/lib/mesh_intersection.pxd",
+ "yt/utilities/lib/mesh_construction.pxd"]),
+ ]
-class my_build_src(build_src.build_src):
- def run(self):
- build_src.build_src.run(self)
+ embree_prefix = os.path.abspath(read_embree_location())
+ if _platform == "darwin":
+ embree_lib_name = "embree.2"
+ else:
+ embree_lib_name = "embree"
+ for ext in embree_extensions:
+ ext.include_dirs.append(os.path.join(embree_prefix, 'include'))
+ ext.library_dirs.append(os.path.join(embree_prefix, 'lib'))
+ ext.language = "c++"
+ ext.libraries += ["m", embree_lib_name]
-class my_build_py(build_py):
+ cython_extensions += embree_extensions
+
+# ROCKSTAR
+if os.path.exists("rockstar.cfg"):
+ try:
+ rd = open("rockstar.cfg").read().strip()
+ except IOError:
+ print("Reading Rockstar location from rockstar.cfg failed.")
+ print("Please place the base directory of your")
+ print("Rockstar install in rockstar.cfg and restart.")
+ print("(ex: \"echo '/path/to/Rockstar-0.99' > rockstar.cfg\" )")
+ sys.exit(1)
+
+ rockstar_extdir = "yt/analysis_modules/halo_finding/rockstar"
+ rockstar_extensions = [
+ Extension("yt.analysis_modules.halo_finding.rockstar.rockstar_interface",
+ sources=[os.path.join(rockstar_extdir, "rockstar_interface.pyx")]),
+ Extension("yt.analysis_modules.halo_finding.rockstar.rockstar_groupies",
+ sources=[os.path.join(rockstar_extdir, "rockstar_groupies.pyx")])
+ ]
+ for ext in rockstar_extensions:
+ ext.library_dirs.append(rd)
+ ext.libraries.append("rockstar")
+ ext.define_macros.append(("THREADSAFE", ""))
+ ext.include_dirs += [rd,
+ os.path.join(rd, "io"), os.path.join(rd, "util")]
+ extensions += rockstar_extensions
+
+if os.environ.get("GPERFTOOLS", "no").upper() != "NO":
+ gpd = os.environ["GPERFTOOLS"]
+ idir = os.path.join(gpd, "include")
+ ldir = os.path.join(gpd, "lib")
+ print(("INCLUDE AND LIB DIRS", idir, ldir))
+ cython_extensions.append(
+ Extension("yt.utilities.lib.perftools_wrap",
+ ["yt/utilities/lib/perftools_wrap.pyx"],
+ libraries=["profiler"],
+ library_dirs=[ldir],
+ include_dirs=[idir]))
+
+class build_py(_build_py):
def run(self):
# honor the --dry-run flag
if not self.dry_run:
@@ -148,68 +309,74 @@
self.mkpath(target_dir)
with open(os.path.join(target_dir, '__hg_version__.py'), 'w') as fobj:
fobj.write("hg_version = '%s'\n" % changeset)
+ _build_py.run(self)
- build_py.run(self)
+class build_ext(_build_ext):
+ # subclass setuptools extension builder to avoid importing numpy
+ # at top level in setup.py. See http://stackoverflow.com/a/21621689/1382869
+ def finalize_options(self):
+ _build_ext.finalize_options(self)
+ # Prevent numpy from thinking it is still in its setup process
+ # see http://stackoverflow.com/a/21621493/1382869
+ __builtins__.__NUMPY_SETUP__ = False
+ import numpy
+ self.include_dirs.append(numpy.get_include())
+setup(
+ name="yt",
+ version=VERSION,
+ description="An analysis and visualization toolkit for Astrophysical "
+ + "simulations, focusing on Adaptive Mesh Refinement data "
+ "from Enzo, Orion, FLASH, and others.",
+ classifiers=["Development Status :: 5 - Production/Stable",
+ "Environment :: Console",
+ "Intended Audience :: Science/Research",
+ "License :: OSI Approved :: BSD License",
+ "Operating System :: MacOS :: MacOS X",
+ "Operating System :: POSIX :: AIX",
+ "Operating System :: POSIX :: Linux",
+ "Programming Language :: C",
+ "Programming Language :: Python",
+ "Topic :: Scientific/Engineering :: Astronomy",
+ "Topic :: Scientific/Engineering :: Physics",
+ "Topic :: Scientific/Engineering :: Visualization"],
+ keywords='astronomy astrophysics visualization ' +
+ 'amr adaptivemeshrefinement',
+ entry_points={'console_scripts': [
+ 'yt = yt.utilities.command_line:run_main',
+ ],
+ 'nose.plugins.0.10': [
+ 'answer-testing = yt.utilities.answer_testing.framework:AnswerTesting'
+ ]
+ },
+ packages=find_packages(),
+ setup_requires=[
+ 'numpy',
+ 'cython>=0.22'
+ ],
+ install_requires=[
+ # 'matplotlib', # messes up nosetests will be fixed in future PRs
+ 'sympy',
+ 'numpy',
+ 'IPython',
+ ],
+ cmdclass={'build_ext': build_ext, 'build_py': build_py},
+ author="The yt project",
+ author_email="yt-dev at lists.spacepope.org",
+ url="http://yt-project.org/",
+ license="BSD",
+ zip_safe=False,
+ scripts=["scripts/iyt"],
+ data_files=MAPSERVER_FILES,
+ ext_modules=cython_extensions + extensions
+)
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
-
- config = Configuration(None, parent_package, top_path)
- config.set_options(ignore_setup_xxx_py=True,
- assume_default_configuration=True,
- delegate_options_to_subpackages=True,
- quiet=True)
-
- config.make_config_py()
- # config.make_svn_version_py()
- config.add_subpackage('yt', 'yt')
- config.add_scripts("scripts/iyt")
-
- return config
-
-
-def setup_package():
-
- from numpy.distutils.core import setup
-
- setup(
- name="yt",
- version=VERSION,
- description="An analysis and visualization toolkit for Astrophysical "
- + "simulations, focusing on Adaptive Mesh Refinement data "
- "from Enzo, Orion, FLASH, and others.",
- classifiers=["Development Status :: 5 - Production/Stable",
- "Environment :: Console",
- "Intended Audience :: Science/Research",
- "License :: OSI Approved :: BSD License",
- "Operating System :: MacOS :: MacOS X",
- "Operating System :: POSIX :: AIX",
- "Operating System :: POSIX :: Linux",
- "Programming Language :: C",
- "Programming Language :: Python",
- "Topic :: Scientific/Engineering :: Astronomy",
- "Topic :: Scientific/Engineering :: Physics",
- "Topic :: Scientific/Engineering :: Visualization"],
- keywords='astronomy astrophysics visualization ' +
- 'amr adaptivemeshrefinement',
- entry_points={'console_scripts': [
- 'yt = yt.utilities.command_line:run_main',
- ],
- 'nose.plugins.0.10': [
- 'answer-testing = yt.utilities.answer_testing.framework:AnswerTesting'
- ]
- },
- author="The yt project",
- author_email="yt-dev at lists.spacepope.org",
- url="http://yt-project.org/",
- license="BSD",
- configuration=configuration,
- zip_safe=False,
- data_files=MAPSERVER_FILES,
- cmdclass={'build_py': my_build_py, 'build_src': my_build_src},
- )
- return
-
-if __name__ == '__main__':
- setup_package()
+# This info about 'ckdtree' should be incorporated somehow...
+# setup(maintainer="SciPy Developers",
+# author="Anne Archibald",
+# maintainer_email="scipy-dev at scipy.org",
+# description="Spatial algorithms and data structures",
+# url="http://www.scipy.org",
+# license="SciPy License (BSD Style)",
+# **configuration(top_path='').todict()
+# )
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 setupext.py
--- /dev/null
+++ b/setupext.py
@@ -0,0 +1,100 @@
+import os
+from pkg_resources import resource_filename
+import shutil
+import subprocess
+import sys
+import tempfile
+
+def check_for_openmp():
+ """Returns True if local setup supports OpenMP, False otherwise"""
+
+ # See https://bugs.python.org/issue25150
+ if sys.version_info[:3] == (3, 5, 0) or os.name == 'nt':
+ return False
+
+ # Create a temporary directory
+ tmpdir = tempfile.mkdtemp()
+ curdir = os.getcwd()
+ exit_code = 1
+
+ try:
+ os.chdir(tmpdir)
+
+ # Get compiler invocation
+ compiler = os.getenv('CC', 'cc')
+ compiler = compiler.split(' ')
+
+ # Attempt to compile a test script.
+ # See http://openmp.org/wp/openmp-compilers/
+ filename = r'test.c'
+ file = open(filename, 'wt', 1)
+ file.write(
+ "#include <omp.h>\n"
+ "#include <stdio.h>\n"
+ "int main() {\n"
+ "#pragma omp parallel\n"
+ "printf(\"Hello from thread %d, nthreads %d\\n\", omp_get_thread_num(), omp_get_num_threads());\n"
+ "}"
+ )
+ file.flush()
+ with open(os.devnull, 'w') as fnull:
+ exit_code = subprocess.call(compiler + ['-fopenmp', filename],
+ stdout=fnull, stderr=fnull)
+
+ # Clean up
+ file.close()
+ except OSError:
+ return False
+ finally:
+ os.chdir(curdir)
+ shutil.rmtree(tmpdir)
+
+ return exit_code == 0
+
+
+def check_for_pyembree():
+ try:
+ fn = resource_filename("pyembree", "rtcore.pxd")
+ except ImportError:
+ return None
+ return os.path.dirname(fn)
+
+
+def read_embree_location():
+ '''
+
+ Attempts to locate the embree installation. First, we check for an
+ EMBREE_DIR environment variable. If one is not defined, we look for
+ an embree.cfg file in the root yt source directory. Finally, if that
+ is not present, we default to /usr/local. If embree is installed in a
+ non-standard location and none of the above are set, the compile will
+ not succeed. This only gets called if check_for_pyembree() returns
+ something other than None.
+
+ '''
+
+ rd = os.environ.get('EMBREE_DIR')
+ if rd is not None:
+ return rd
+ print("EMBREE_DIR not set. Attempting to read embree.cfg")
+ try:
+ rd = open("embree.cfg").read().strip()
+ return rd
+ except IOError:
+ print("Reading Embree location from embree.cfg failed.")
+ print("If compilation fails, please place the base directory")
+ print("of your Embree install in embree.cfg and restart.")
+ return '/usr/local'
+
+
+def get_mercurial_changeset_id(target_dir):
+ '''
+ Returns changeset and branch using hglib
+ '''
+ try:
+ import hglib
+ except ImportError:
+ return None
+ with hglib.open(target_dir) as repo:
+ changeset = repo.identify(id=True, branch=True).strip().decode('utf8')
+ return changeset
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/cosmological_observation/light_cone/setup.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('light_cone', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/cosmological_observation/light_ray/setup.py
--- a/yt/analysis_modules/cosmological_observation/light_ray/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('light_ray', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/cosmological_observation/setup.py
--- a/yt/analysis_modules/cosmological_observation/setup.py
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('cosmological_observation', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- config.add_subpackage("light_cone")
- config.add_subpackage("light_ray")
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/halo_finding/fof/setup.py
--- a/yt/analysis_modules/halo_finding/fof/setup.py
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('fof', parent_package, top_path)
- config.add_extension("EnzoFOF", sources=["EnzoFOF.c",
- "kd.c"],
- libraries=["m"])
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/halo_finding/hop/setup.py
--- a/yt/analysis_modules/halo_finding/hop/setup.py
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('hop', parent_package, top_path)
- config.add_extension("EnzoHop", sources=["EnzoHop.c",
- "hop_hop.c",
- "hop_kd.c",
- "hop_regroup.c",
- "hop_slice.c",
- "hop_smooth.c"])
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/halo_finding/rockstar/setup.py
--- a/yt/analysis_modules/halo_finding/rockstar/setup.py
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-import os.path
-import sys
-
-def configuration(parent_package='',top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('rockstar',parent_package,top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- try:
- rd = open("rockstar.cfg").read().strip()
- except IOError:
- print("Reading Rockstar location from rockstar.cfg failed.")
- print("Please place the base directory of your")
- print("Rockstar install in rockstar.cfg and restart.")
- print("(ex: \"echo '/path/to/Rockstar-0.99' > rockstar.cfg\" )")
- sys.exit(1)
- config.add_extension("rockstar_interface",
- "yt/analysis_modules/halo_finding/rockstar/rockstar_interface.pyx",
- library_dirs=[rd],
- libraries=["rockstar"],
- #define_macros = [("THREADSAFE", "__thread")],
- define_macros = [("THREADSAFE", "")],
- include_dirs=[rd,
- os.path.join(rd, "io"),
- os.path.join(rd, "util")])
- config.add_extension("rockstar_groupies",
- "yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.pyx",
- library_dirs=[rd],
- libraries=["rockstar"],
- #define_macros = [("THREADSAFE", "__thread")],
- define_macros = [("THREADSAFE", "")],
- include_dirs=[rd,
- os.path.join(rd, "io"),
- os.path.join(rd, "util")])
- return config
-
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/halo_finding/setup.py
--- a/yt/analysis_modules/halo_finding/setup.py
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python
-import os.path
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('halo_finding', parent_package, top_path)
- config.add_subpackage("fof")
- config.add_subpackage("hop")
- if os.path.exists("rockstar.cfg"):
- config.add_subpackage("rockstar")
- config.make_config_py() # installs __config__.py
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/halo_mass_function/setup.py
--- a/yt/analysis_modules/halo_mass_function/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('halo_mass_function', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/level_sets/setup.py
--- a/yt/analysis_modules/level_sets/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('level_sets', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/particle_trajectories/setup.py
--- a/yt/analysis_modules/particle_trajectories/setup.py
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('particle_trajectories', parent_package, top_path)
- #config.add_subpackage("tests")
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/photon_simulator/setup.py
--- a/yt/analysis_modules/photon_simulator/setup.py
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('photon_simulator', parent_package, top_path)
- config.add_extension("utils",
- ["yt/analysis_modules/photon_simulator/utils.pyx"])
- config.add_subpackage("tests")
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/ppv_cube/setup.py
--- a/yt/analysis_modules/ppv_cube/setup.py
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('ppv_cube', parent_package, top_path)
- config.add_extension("ppv_utils",
- ["yt/analysis_modules/ppv_cube/ppv_utils.pyx"],
- libraries=["m"])
- config.add_subpackage("tests")
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/setup.py
--- a/yt/analysis_modules/setup.py
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('analysis_modules', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- config.add_subpackage("absorption_spectrum")
- config.add_subpackage("cosmological_observation")
- config.add_subpackage("halo_analysis")
- config.add_subpackage("halo_finding")
- config.add_subpackage("halo_mass_function")
- config.add_subpackage("level_sets")
- config.add_subpackage("particle_trajectories")
- config.add_subpackage("photon_simulator")
- config.add_subpackage("spectral_integrator")
- config.add_subpackage("star_analysis")
- config.add_subpackage("two_point_functions")
- config.add_subpackage("radmc3d_export")
- config.add_subpackage("sunrise_export")
- config.add_subpackage("sunyaev_zeldovich")
- config.add_subpackage("particle_trajectories")
- config.add_subpackage("photon_simulator")
- config.add_subpackage("ppv_cube")
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/spectral_integrator/setup.py
--- a/yt/analysis_modules/spectral_integrator/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('spectral_integrator', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/star_analysis/setup.py
--- a/yt/analysis_modules/star_analysis/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('star_analysis', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/sunyaev_zeldovich/setup.py
--- a/yt/analysis_modules/sunyaev_zeldovich/setup.py
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('sunyaev_zeldovich', parent_package, top_path)
- config.add_subpackage("tests")
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/analysis_modules/two_point_functions/setup.py
--- a/yt/analysis_modules/two_point_functions/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('two_point_functions', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/config.py
--- a/yt/config.py
+++ b/yt/config.py
@@ -39,7 +39,7 @@
storeparameterfiles = 'False',
parameterfilestore = 'parameter_files.csv',
maximumstoreddatasets = '500',
- skip_dataset_cache = 'False',
+ skip_dataset_cache = 'True',
loadfieldplugins = 'True',
pluginfilename = 'my_plugins.py',
parallel_traceback = 'False',
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/data_objects/construction_data_containers.py
--- a/yt/data_objects/construction_data_containers.py
+++ b/yt/data_objects/construction_data_containers.py
@@ -702,11 +702,11 @@
if cls is None:
raise YTParticleDepositionNotImplemented(method)
# We allocate number of zones, not number of octs
- op = cls(self.ActiveDimensions.prod(), kernel_name)
+ op = cls(self.ActiveDimensions, kernel_name)
op.initialize()
op.process_grid(self, positions, fields)
vals = op.finalize()
- return vals.reshape(self.ActiveDimensions, order="C")
+ return vals.copy(order="C")
def write_to_gdf(self, gdf_path, fields, nprocs=1, field_units=None,
**kwargs):
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/data_objects/derived_quantities.py
--- a/yt/data_objects/derived_quantities.py
+++ b/yt/data_objects/derived_quantities.py
@@ -436,22 +436,26 @@
"""
def count_values(self, use_gas=True, use_particles=True):
num_vals = 0
- if use_gas: num_vals += 4
- if use_particles: num_vals += 4
+ # create the index if it doesn't exist yet
+ self.data_source.ds.index
+ self.use_gas = use_gas & \
+ (("gas", "cell_mass") in self.data_source.ds.field_info)
+ self.use_particles = use_particles & \
+ (("all", "particle_mass") in self.data_source.ds.field_info)
+ if self.use_gas:
+ num_vals += 4
+ if self.use_particles:
+ num_vals += 4
self.num_vals = num_vals
- def process_chunk(self, data, use_gas=True, use_particles=True):
- use_gas &= \
- (("gas", "cell_mass") in self.data_source.ds.field_info)
- use_particles &= \
- (("all", "particle_mass") in self.data_source.ds.field_info)
+ def process_chunk(self, data, **kwargs):
rvals = []
- if use_gas:
+ if self.use_gas:
rvals.extend([(data["gas", "specific_angular_momentum_%s" % axis] *
data["gas", "cell_mass"]).sum(dtype=np.float64) \
for axis in "xyz"])
rvals.append(data["gas", "cell_mass"].sum(dtype=np.float64))
- if use_particles:
+ if self.use_particles:
rvals.extend([(data["all", "particle_specific_angular_momentum_%s" % axis] *
data["all", "particle_mass"]).sum(dtype=np.float64) \
for axis in "xyz"])
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/data_objects/grid_patch.py
--- a/yt/data_objects/grid_patch.py
+++ b/yt/data_objects/grid_patch.py
@@ -327,12 +327,13 @@
if cls is None:
raise YTParticleDepositionNotImplemented(method)
# We allocate number of zones, not number of octs
- op = cls(self.ActiveDimensions.prod(), kernel_name)
+ # Everything inside this is fortran ordered, so we reverse it here.
+ op = cls(tuple(self.ActiveDimensions)[::-1], kernel_name)
op.initialize()
op.process_grid(self, positions, fields)
vals = op.finalize()
if vals is None: return
- return vals.reshape(self.ActiveDimensions, order="C")
+ return vals.transpose() # Fortran-ordered, so transpose.
def select_blocks(self, selector):
mask = self._get_selector_mask(selector)
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/data_objects/octree_subset.py
--- a/yt/data_objects/octree_subset.py
+++ b/yt/data_objects/octree_subset.py
@@ -90,10 +90,11 @@
return self._num_zones + 2*self._num_ghost_zones
def _reshape_vals(self, arr):
- if len(arr.shape) == 4 and arr.flags["F_CONTIGUOUS"]:
- return arr
nz = self.nz
- n_oct = arr.shape[0] / (nz**3.0)
+ if len(arr.shape) <= 2:
+ n_oct = arr.shape[0] / (nz**3)
+ else:
+ n_oct = max(arr.shape)
if arr.size == nz*nz*nz*n_oct:
new_shape = (nz, nz, nz, n_oct)
elif arr.size == nz*nz*nz*n_oct * 3:
@@ -115,10 +116,9 @@
def select_blocks(self, selector):
mask = self.oct_handler.mask(selector, domain_id = self.domain_id)
- mask = self._reshape_vals(mask)
slicer = OctreeSubsetBlockSlice(self)
for i, sl in slicer:
- yield sl, mask[:,:,:,i]
+ yield sl, mask[i,...]
def select_tcoords(self, dobj):
# These will not be pre-allocated, which can be a problem for speed and
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/data_objects/selection_data_containers.py
--- a/yt/data_objects/selection_data_containers.py
+++ b/yt/data_objects/selection_data_containers.py
@@ -69,7 +69,11 @@
_con_args = ('p',)
def __init__(self, p, ds=None, field_parameters=None, data_source=None):
super(YTPoint, self).__init__(ds, field_parameters, data_source)
- self.p = p
+ if isinstance(p, YTArray):
+ # we pass p through ds.arr to ensure code units are attached
+ self.p = self.ds.arr(p)
+ else:
+ self.p = self.ds.arr(p, 'code_length')
class YTOrthoRay(YTSelectionContainer1D):
"""
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/data_objects/setup.py
--- a/yt/data_objects/setup.py
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('data_objects', parent_package, top_path)
- config.add_subpackage("tests")
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -988,7 +988,8 @@
deps, _ = self.field_info.check_derived_fields([name])
self.field_dependencies.update(deps)
- def add_deposited_particle_field(self, deposit_field, method, kernel_name='cubic'):
+ def add_deposited_particle_field(self, deposit_field, method, kernel_name='cubic',
+ weight_field='particle_mass'):
"""Add a new deposited particle field
Creates a new deposited field based on the particle *deposit_field*.
@@ -1003,13 +1004,15 @@
method : string
This is the "method name" which will be looked up in the
`particle_deposit` namespace as `methodname_deposit`. Current
- methods include `count`, `simple_smooth`, `sum`, `std`, `cic`,
- `weighted_mean`, `mesh_id`, and `nearest`.
+ methods include `simple_smooth`, `sum`, `std`, `cic`, `weighted_mean`,
+ `mesh_id`, and `nearest`.
kernel_name : string, default 'cubic'
This is the name of the smoothing kernel to use. It is only used for
the `simple_smooth` method and is otherwise ignored. Current
supported kernel names include `cubic`, `quartic`, `quintic`,
`wendland2`, `wendland4`, and `wendland6`.
+ weight_field : string, default 'particle_mass'
+ Weighting field name for deposition method `weighted_mean`.
Returns
-------
@@ -1021,38 +1024,45 @@
ptype, deposit_field = deposit_field[0], deposit_field[1]
else:
raise RuntimeError
+
units = self.field_info[ptype, deposit_field].units
+ take_log = self.field_info[ptype, deposit_field].take_log
+ name_map = {"sum": "sum", "std":"std", "cic": "cic", "weighted_mean": "avg",
+ "nearest": "nn", "simple_smooth": "ss", "count": "count"}
+ field_name = "%s_" + name_map[method] + "_%s"
+ field_name = field_name % (ptype, deposit_field.replace('particle_', ''))
+
+ if method == "count":
+ field_name = "%s_count" % ptype
+ if ("deposit", field_name) in self.field_info:
+ mylog.warning("The deposited field %s already exists" % field_name)
+ return ("deposit", field_name)
+ else:
+ units = "dimensionless"
+ take_log = False
def _deposit_field(field, data):
"""
- Create a grid field for particle wuantities weighted by particle
- mass, using cloud-in-cell deposition.
+ Create a grid field for particle quantities using given method.
"""
pos = data[ptype, "particle_position"]
- # get back into density
- if method != 'count':
- pden = data[ptype, "particle_mass"]
- top = data.deposit(pos, [data[(ptype, deposit_field)]*pden],
- method=method, kernel_name=kernel_name)
- bottom = data.deposit(pos, [pden], method=method,
- kernel_name=kernel_name)
- top[bottom == 0] = 0.0
- bnz = bottom.nonzero()
- top[bnz] /= bottom[bnz]
- d = data.ds.arr(top, input_units=units)
+ if method == 'weighted_mean':
+ d = data.ds.arr(data.deposit(pos, [data[ptype, deposit_field],
+ data[ptype, weight_field]],
+ method=method, kernel_name=kernel_name),
+ input_units=units)
+ d[np.isnan(d)] = 0.0
else:
d = data.ds.arr(data.deposit(pos, [data[ptype, deposit_field]],
- method=method,
- kernel_name=kernel_name))
+ method=method, kernel_name=kernel_name),
+ input_units=units)
return d
- name_map = {"cic": "cic", "sum": "nn", "count": "count"}
- field_name = "%s_" + name_map[method] + "_%s"
- field_name = field_name % (ptype, deposit_field.replace('particle_', ''))
+
self.add_field(
("deposit", field_name),
function=_deposit_field,
units=units,
- take_log=False,
+ take_log=take_log,
validators=[ValidateSpatial()])
return ("deposit", field_name)
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/data_objects/tests/test_points.py
--- a/yt/data_objects/tests/test_points.py
+++ b/yt/data_objects/tests/test_points.py
@@ -10,6 +10,17 @@
from yt.config import ytcfg
ytcfg["yt","__withintesting"] = "True"
+def test_point_creation():
+ ds = fake_random_ds(16)
+ p1 = ds.point(ds.domain_center)
+ p2 = ds.point([0.5, 0.5, 0.5])
+ p3 = ds.point([0.5, 0.5, 0.5]*yt.units.cm)
+
+ # ensure all three points are really at the same position
+ for fname in 'xyz':
+ assert_equal(p1[fname], p2[fname])
+ assert_equal(p1[fname], p3[fname])
+
def test_domain_point():
nparticles = 3
ds = fake_random_ds(16, particles=nparticles)
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/extern/setup.py
--- a/yt/extern/setup.py
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env python
-#----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('extern', parent_package, top_path)
- config.add_subpackage("tqdm")
- config.make_config_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/fields/setup.py
--- a/yt/fields/setup.py
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('fields', parent_package, top_path)
- config.add_subpackage("tests")
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/fields/tests/test_fields.py
--- a/yt/fields/tests/test_fields.py
+++ b/yt/fields/tests/test_fields.py
@@ -33,7 +33,7 @@
fields.append(("gas", fname))
units.append(code_units)
- base_ds = fake_random_ds(4, fields=fields, units=units, particles=10)
+ base_ds = fake_random_ds(4, fields=fields, units=units, particles=20)
base_ds.index
base_ds.cosmological_simulation = 1
@@ -195,12 +195,28 @@
yield TestFieldAccess(field, nproc)
def test_add_deposited_particle_field():
+ # NOT tested: "std", "mesh_id", "nearest" and "simple_smooth"
global base_ds
- fn = base_ds.add_deposited_particle_field(('io', 'particle_ones'), 'count')
- assert_equal(fn, ('deposit', 'io_count_ones'))
ad = base_ds.all_data()
+
+ # Test "count", "sum" and "cic" method
+ for method in ["count", "sum", "cic"]:
+ fn = base_ds.add_deposited_particle_field(('io', 'particle_mass'), method)
+ expected_fn = 'io_%s' if method == "count" else 'io_%s_mass'
+ assert_equal(fn, ('deposit', expected_fn % method))
+ ret = ad[fn]
+ if method == "count":
+ assert_equal(ret.sum(), ad['particle_ones'].sum())
+ else:
+ assert_almost_equal(ret.sum(), ad['particle_mass'].sum())
+
+ # Test "weighted_mean" method
+ fn = base_ds.add_deposited_particle_field(('io', 'particle_ones'), 'weighted_mean',
+ weight_field='particle_ones')
+ assert_equal(fn, ('deposit', 'io_avg_ones'))
ret = ad[fn]
- assert_equal(ret.sum(), ad['particle_ones'].sum())
+ # The sum should equal the number of cells that have particles
+ assert_equal(ret.sum(), np.count_nonzero(ad[("deposit", "io_count")]))
@requires_file('GadgetDiskGalaxy/snapshot_200.hdf5')
def test_add_smoothed_particle_field():
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/_skeleton/setup.py
--- a/yt/frontends/_skeleton/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('skeleton', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/art/setup.py
--- a/yt/frontends/art/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='',top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('art',parent_package,top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/artio/_artio_caller.pyx
--- a/yt/frontends/artio/_artio_caller.pyx
+++ b/yt/frontends/artio/_artio_caller.pyx
@@ -8,15 +8,14 @@
from yt.utilities.lib.fp_utils cimport imax
from yt.geometry.oct_container cimport \
SparseOctreeContainer
-from yt.geometry.oct_visitors cimport \
- OctVisitorData, oct_visitor_function, Oct, \
- fill_file_indices_oind, fill_file_indices_rind
+from yt.geometry.oct_visitors cimport Oct
from yt.geometry.particle_deposit cimport \
ParticleDepositOperation
from libc.stdint cimport int32_t, int64_t
from libc.stdlib cimport malloc, free
from libc.string cimport memcpy
import data_structures
+from yt.utilities.lib.misc_utilities import OnceIndirect
cdef extern from "platform_dep.h":
void *alloca(int)
@@ -1556,6 +1555,9 @@
if fields is None:
fields = []
nf = len(fields)
+ cdef np.float64_t[::cython.view.indirect, ::1] field_pointers
+ if nf > 0: field_pointers = OnceIndirect(fields)
+ cdef np.float64_t[:] field_vals = np.empty(nf, dtype="float64")
cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector, -1)
cdef np.ndarray[np.int64_t, ndim=1] domain_ind
@@ -1570,17 +1572,9 @@
continue
domain_ind[sfc - self.sfc_start] = j
j += 1
- cdef np.float64_t **field_pointers
- cdef np.float64_t *field_vals
cdef np.float64_t pos[3]
cdef np.float64_t left_edge[3]
cdef int coords[3]
- cdef np.ndarray[np.float64_t, ndim=1] tarr
- field_pointers = <np.float64_t**> alloca(sizeof(np.float64_t *) * nf)
- field_vals = <np.float64_t*>alloca(sizeof(np.float64_t) * nf)
- for i in range(nf):
- tarr = fields[i]
- field_pointers[i] = <np.float64_t *> tarr.data
cdef int dims[3]
dims[0] = dims[1] = dims[2] = 1
cdef np.int64_t offset, moff
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/artio/artio_headers/cosmology.c
--- a/yt/frontends/artio/artio_headers/cosmology.c
+++ b/yt/frontends/artio/artio_headers/cosmology.c
@@ -443,9 +443,18 @@
double cosmology_get_value_from_table(CosmologyParameters *c, double a, double table[])
{
- int idx = (int)(c->ndex*(log10(a)-c->la[0]));
+ // This is special case code for boundary conditions
+ double la = log10(a);
+ if (fabs(la - c->la[c->size-1]) < 1.0e-14) {
+ return table[c->size-1];
+ } else if (fabs(la - c->la[0]) < 1.0e-14) {
+ return table[0];
+ }
- ASSERT(idx>=0 && idx<c->size);
+ int idx = (int)(c->ndex*(la-c->la[0]));
+
+ // Note that because we do idx+1 below, we need -1 here.
+ ASSERT(idx>=0 && (idx<c->size-1));
/*
// Do it as a function of aUni rather than la to ensure exact inversion
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/artio/setup.py
--- a/yt/frontends/artio/setup.py
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env python
-import glob
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- artio_sources = glob.glob("yt/frontends/artio/artio_headers/*.c")
- config = Configuration('artio', parent_package, top_path)
- config.add_extension("_artio_caller",
- ["yt/frontends/artio/_artio_caller.pyx"] +
- artio_sources,
- include_dirs=["yt/frontends/artio/artio_headers/",
- "yt/geometry/",
- "yt/utilities/lib/"],
- depends=artio_sources +
- ["yt/utilities/lib/fp_utils.pxd",
- "yt/geometry/oct_container.pxd",
- "yt/geometry/selection_routines.pxd",
- "yt/geometry/particle_deposit.pxd"])
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/athena/setup.py
--- a/yt/frontends/athena/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('athena', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/boxlib/data_structures.py
--- a/yt/frontends/boxlib/data_structures.py
+++ b/yt/frontends/boxlib/data_structures.py
@@ -178,8 +178,15 @@
raise RuntimeError("yt needs cylindrical to be 2D")
self.level_dds[:,2] = 2*np.pi
default_zbounds = (0.0, 2*np.pi)
+ elif self.ds.geometry == "spherical":
+ # BoxLib only supports 1D spherical, so ensure
+ # the other dimensions have the right extent.
+ self.level_dds[:,1] = np.pi
+ self.level_dds[:,2] = 2*np.pi
+ default_ybounds = (0.0, np.pi)
+ default_zbounds = (0.0, 2*np.pi)
else:
- raise RuntimeError("yt only supports cartesian and cylindrical coordinates.")
+ raise RuntimeError("Unknown BoxLib coordinate system.")
if int(next(header_file)) != 0:
raise RuntimeError("INTERNAL ERROR! This should be a zero.")
@@ -586,8 +593,10 @@
self.geometry = "cartesian"
elif coordinate_type == 1:
self.geometry = "cylindrical"
+ elif coordinate_type == 2:
+ self.geometry = "spherical"
else:
- raise RuntimeError("yt does not yet support spherical geometry")
+ raise RuntimeError("Unknown BoxLib coord_type")
# overrides for 1/2-dimensional data
if self.dimensionality == 1:
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/boxlib/setup.py
--- a/yt/frontends/boxlib/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('boxlib', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/chombo/setup.py
--- a/yt/frontends/chombo/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('chombo', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/eagle/setup.py
--- a/yt/frontends/eagle/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('eagle', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/enzo/data_structures.py
--- a/yt/frontends/enzo/data_structures.py
+++ b/yt/frontends/enzo/data_structures.py
@@ -277,14 +277,14 @@
active_particles = True
nap = dict((ap_type, []) for ap_type in
params["Physics"]["ActiveParticles"]["ActiveParticlesEnabled"])
- elif version == 2.2:
- active_particles = True
+ else:
nap = {}
- for type in self.parameters.get("AppendActiveParticleType", []):
- nap[type] = []
- else:
- active_particles = False
- nap = None
+ if "AppendActiveParticleType" in self.parameters:
+ active_particles = True
+ for type in self.parameters.get("AppendActiveParticleType", []):
+ nap[type] = []
+ else:
+ active_particles = False
for grid_id in range(self.num_grids):
pbar.update(grid_id)
# We will unroll this list
@@ -394,7 +394,7 @@
fields = []
for ptype in self.dataset["AppendActiveParticleType"]:
select_grids = self.grid_active_particle_count[ptype].flat
- if np.any(select_grids) is False:
+ if not np.any(select_grids):
current_ptypes = self.dataset.particle_types
new_ptypes = [p for p in current_ptypes if p != ptype]
self.dataset.particle_types = new_ptypes
diff -r f45f7851fbd329f397e4f865ab5f249ba16d77a8 -r 2ef50ab5517d0d772ff1484fa559596cca7546b6 yt/frontends/enzo/setup.py
--- a/yt/frontends/enzo/setup.py
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env python
-
-
-def configuration(parent_package='', top_path=None):
- from numpy.distutils.misc_util import Configuration
- config = Configuration('enzo', parent_package, top_path)
- config.make_config_py() # installs __config__.py
- #config.make_svn_version_py()
- return config
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt/commits/dda193582d6c/
Changeset: dda193582d6c
Branch: yt
User: ngoldbaum
Date: 2016-02-24 19:33:14+00:00
Summary: Merged in brittonsmith/yt (pull request #1972)
Porting c function, FindBindingEnergy, to Cython
Affected #: 2 files
diff -r cef8aa8a3bb23ecdc6cd8f91d3bdf1701fb1608e -r dda193582d6c210518df5d127cef1a7294dca692 yt/analysis_modules/level_sets/clump_validators.py
--- a/yt/analysis_modules/level_sets/clump_validators.py
+++ b/yt/analysis_modules/level_sets/clump_validators.py
@@ -13,7 +13,8 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-from yt.utilities.data_point_utilities import FindBindingEnergy
+from yt.utilities.lib.misc_utilities import \
+ gravitational_binding_energy
from yt.utilities.operator_registry import \
OperatorRegistry
from yt.utilities.physical_constants import \
@@ -64,11 +65,12 @@
(bulk_velocity[2] - clump["all", "particle_velocity_z"])**2)).sum()
potential = clump.data.ds.quan(G *
- FindBindingEnergy(clump["gas", "cell_mass"].in_cgs(),
- clump["index", "x"].in_cgs(),
- clump["index", "y"].in_cgs(),
- clump["index", "z"].in_cgs(),
- truncate, (kinetic / G).in_cgs()),
+ gravitational_binding_energy(
+ clump["gas", "cell_mass"].in_cgs(),
+ clump["index", "x"].in_cgs(),
+ clump["index", "y"].in_cgs(),
+ clump["index", "z"].in_cgs(),
+ truncate, (kinetic / G).in_cgs()),
kinetic.in_cgs().units)
if truncate and potential >= kinetic:
@@ -76,7 +78,7 @@
if use_particles:
potential += clump.data.ds.quan(G *
- FindBindingEnergy(
+ gravitational_binding_energy(
clump["all", "particle_mass"].in_cgs(),
clump["all", "particle_position_x"].in_cgs(),
clump["all", "particle_position_y"].in_cgs(),
diff -r cef8aa8a3bb23ecdc6cd8f91d3bdf1701fb1608e -r dda193582d6c210518df5d127cef1a7294dca692 yt/utilities/lib/misc_utilities.pyx
--- a/yt/utilities/lib/misc_utilities.pyx
+++ b/yt/utilities/lib/misc_utilities.pyx
@@ -13,12 +13,13 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
+from yt.funcs import get_pbar
import numpy as np
from yt.units.yt_array import YTArray
cimport numpy as np
cimport cython
cimport libc.math as math
-from libc.math cimport abs
+from libc.math cimport abs, sqrt
from yt.utilities.lib.fp_utils cimport fmin, fmax, i64min, i64max
from yt.geometry.selection_routines cimport _ensure_code
@@ -974,6 +975,51 @@
else:
dest[i,j,k] = dsp
+ at cython.cdivision(True)
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+def gravitational_binding_energy(
+ np.float64_t[:] mass,
+ np.float64_t[:] x,
+ np.float64_t[:] y,
+ np.float64_t[:] z,
+ int truncate,
+ np.float64_t kinetic):
+
+ cdef int q_outer, q_inner, n_q, i
+ cdef np.float64_t mass_o, x_o, y_o, z_o
+ cdef np.float64_t mass_i, x_i, y_i, z_i
+ cdef np.float64_t this_potential, total_potential
+ total_potential = 0.
+
+ i = 0
+ n_q = mass.size
+ pbar = get_pbar("Calculating potential for %d cells" % n_q,
+ 0.5 * (n_q**2 - n_q))
+ for q_outer in range(n_q - 1):
+ this_potential = 0.
+ mass_o = mass[q_outer]
+ x_o = x[q_outer]
+ y_o = y[q_outer]
+ z_o = z[q_outer]
+ for q_inner in range(q_outer + 1, n_q):
+ mass_i = mass[q_inner]
+ x_i = x[q_inner]
+ y_i = y[q_inner]
+ z_i = z[q_inner]
+ this_potential += mass_o * mass_i / \
+ sqrt((x_i - x_o) * (x_i - x_o) +
+ (y_i - y_o) * (y_i - y_o) +
+ (z_i - z_o) * (z_i - z_o))
+ i += n_q - q_outer
+ pbar.update(i)
+ total_potential += this_potential
+ if truncate and total_potential / kinetic > 1.:
+ break
+ pbar.finish()
+
+ return total_potential
+
# The OnceIndirect code is from:
# http://stackoverflow.com/questions/10465091/assembling-a-cython-memoryview-from-numpy-arrays/12991519#12991519
# This is under the CC-BY-SA license.
Repository URL: https://bitbucket.org/yt_analysis/yt/
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