[Yt-svn] yt: 5 new changesets
hg at spacepope.org
hg at spacepope.org
Mon Jun 7 20:45:42 PDT 2010
hg Repository: yt
details: yt/rev/5bf24345615e
changeset: 1759:5bf24345615e
user: sskory
date:
Mon Jun 07 16:24:21 2010 -0400
description:
[svn r1744] Renaming and changing all mentions of MergerTree.py->merger_tree.py and HaloMassFcn.py->halo_mass_function.py.
hg Repository: yt
details: yt/rev/4924a31d95fb
changeset: 1760:4924a31d95fb
user: mturk
date:
Mon Jun 07 16:33:18 2010 -0400
description:
[svn r1745] Renaming clump.py to clump_handling.py.
hg Repository: yt
details: yt/rev/d803e02a89d8
changeset: 1761:d803e02a89d8
user: britton
date:
Mon Jun 07 16:34:06 2010 -0400
description:
[svn r1746] Caught one more file needing naming convention change.
hg Repository: yt
details: yt/rev/f4c03d6a485f
changeset: 1762:f4c03d6a485f
user: Matthew Turk <matthewturk at gmail.com>
date:
Mon Jun 07 23:43:07 2010 -0400
description:
Merging. Hopefully ... got rid of all case change problems.
hg Repository: yt
details: yt/rev/7e381df9ded8
changeset: 1763:7e381df9ded8
user: Matthew Turk <matthewturk at gmail.com>
date:
Mon Jun 07 23:45:30 2010 -0400
description:
Merge
diffstat:
.hgignore | 3 +
scripts/fbranch | 5 +-
scripts/fbury | 5 +-
scripts/fdigup | 5 +-
scripts/fido | 5 +-
scripts/fimport | 5 +-
yt/_amr_utils/FixedInterpolator.c | 26 +-
yt/_amr_utils/FixedInterpolator.h | 2 +
yt/_amr_utils/Octree.pyx | 280 +
yt/_amr_utils/QuadTree.pyx | 257 +
yt/_amr_utils/VolumeIntegrator.pyx | 43 +-
yt/_amr_utils/png_writer.pyx | 4 +-
yt/amr_utils.c | 5451 ++++++++++++++++------
yt/amr_utils.pyx | 1 +
yt/arraytypes.py | 11 +
yt/extensions/DualEPS.py | 699 ++
yt/extensions/HaloMassFcn.py | 726 ---
yt/extensions/MergerTree.py | 890 ---
yt/extensions/halo_mass_function.py | 736 +++
yt/extensions/kdtree/fKD.f90 | 173 +-
yt/extensions/kdtree/fKD.v | 42 +-
yt/extensions/kdtree/fKD_source.f90 | 10 +-
yt/extensions/lightcone/__init__.py | 2 +-
yt/extensions/merger_tree.py | 893 +++
yt/extensions/opengl_widgets/calculateRay.vertex.glsl | 63 +
yt/extensions/opengl_widgets/colormap.fragment.glsl | 12 +
yt/extensions/opengl_widgets/framebuffer.vertex.glsl | 12 +
yt/extensions/opengl_widgets/mip.fragment.glsl | 135 +
yt/extensions/opengl_widgets/mip_viewer.py | 450 +
yt/extensions/opengl_widgets/rendering_contexts.py | 88 +
yt/extensions/volume_rendering/multi_texture.py | 302 +
yt/fido/share_data.py | 83 +
yt/lagos/BaseDataTypes.py | 1 -
yt/lagos/Clump.py | 290 -
yt/lagos/HaloFinding.py | 137 +-
yt/lagos/OutputTypes.py | 19 +-
yt/lagos/StructureFunctionGenerator.py | 750 ---
yt/lagos/TwoPointFunctions.py | 796 +++
yt/lagos/__init__.py | 4 +-
yt/lagos/clump.py | 290 -
yt/lagos/clump_handling.py | 290 +
yt/lagos/parallelHOP/parallelHOP.py | 9 +-
yt/mods.py | 2 +-
yt/raven/PlotTypes.py | 6 +-
yt/raven/plot_collection.py | 1133 ++++-
yt/reason/plot_editors.py | 10 +-
yt/reason/reason_v2.py | 5 +-
yt/reason/tvtk_interface.py | 5 +-
48 files changed, 10438 insertions(+), 4728 deletions(-)
diffs (truncated from 24019 to 300 lines):
diff -r ea258e3dfc95 -r 7e381df9ded8 .hgignore
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.hgignore Mon Jun 07 23:45:30 2010 -0400
@@ -0,0 +1,3 @@
+syntax: glob
+*.pyc
+.*.swp
diff -r ea258e3dfc95 -r 7e381df9ded8 scripts/fbranch
--- a/scripts/fbranch Mon Jun 07 14:38:23 2010 -0400
+++ b/scripts/fbranch Mon Jun 07 23:45:30 2010 -0400
@@ -1,1 +1,4 @@
-basic.py
\ No newline at end of file
+#!python2.5
+import yt.fido
+
+yt.fido.runAction()
diff -r ea258e3dfc95 -r 7e381df9ded8 scripts/fbury
--- a/scripts/fbury Mon Jun 07 14:38:23 2010 -0400
+++ b/scripts/fbury Mon Jun 07 23:45:30 2010 -0400
@@ -1,1 +1,4 @@
-basic.py
\ No newline at end of file
+#!python2.5
+import yt.fido
+
+yt.fido.runAction()
diff -r ea258e3dfc95 -r 7e381df9ded8 scripts/fdigup
--- a/scripts/fdigup Mon Jun 07 14:38:23 2010 -0400
+++ b/scripts/fdigup Mon Jun 07 23:45:30 2010 -0400
@@ -1,1 +1,4 @@
-basic.py
\ No newline at end of file
+#!python2.5
+import yt.fido
+
+yt.fido.runAction()
diff -r ea258e3dfc95 -r 7e381df9ded8 scripts/fido
--- a/scripts/fido Mon Jun 07 14:38:23 2010 -0400
+++ b/scripts/fido Mon Jun 07 23:45:30 2010 -0400
@@ -1,1 +1,4 @@
-basic.py
\ No newline at end of file
+#!python2.5
+from yt.mods import *
+
+fido.runAction()
diff -r ea258e3dfc95 -r 7e381df9ded8 scripts/fimport
--- a/scripts/fimport Mon Jun 07 14:38:23 2010 -0400
+++ b/scripts/fimport Mon Jun 07 23:45:30 2010 -0400
@@ -1,1 +1,4 @@
-basic.py
\ No newline at end of file
+#!python2.5
+from yt.mods import *
+
+fido.runAction()
diff -r ea258e3dfc95 -r 7e381df9ded8 yt/_amr_utils/FixedInterpolator.c
--- a/yt/_amr_utils/FixedInterpolator.c Mon Jun 07 14:38:23 2010 -0400
+++ b/yt/_amr_utils/FixedInterpolator.c Mon Jun 07 23:45:30 2010 -0400
@@ -28,8 +28,9 @@
#define VINDEX(A,B,C) data[((((A)+ci[0])*(ds[1]+1)+((B)+ci[1]))*(ds[2]+1)+ci[2]+(C))]
// (((C*ds[1])+B)*ds[0]+A)
+#define OINDEX(A,B,C) data[(A)*(ds[1]+1)*(ds[2]+1)+(B)*ds[2]+(B)+(C)]
-npy_float64 fast_interpolate(int *ds, int *ci, npy_float64 *dp,
+npy_float64 fast_interpolate(int ds[3], int ci[3], npy_float64 dp[3],
npy_float64 *data)
{
int i;
@@ -48,7 +49,28 @@
return dv;
}
-npy_float64 trilinear_interpolate(int *ds, int *ci, npy_float64 *dp,
+npy_float64 offset_interpolate(int ds[3], npy_float64 dp[3], npy_float64 *data)
+{
+ int i;
+ npy_float64 dv, vz[4];
+
+ dv = 1.0 - dp[2];
+ vz[0] = dv*OINDEX(0,0,0) + dp[2]*OINDEX(0,0,1);
+ vz[1] = dv*OINDEX(0,1,0) + dp[2]*OINDEX(0,1,1);
+ vz[2] = dv*OINDEX(1,0,0) + dp[2]*OINDEX(1,0,1);
+ vz[3] = dv*OINDEX(1,1,0) + dp[2]*OINDEX(1,1,1);
+
+ dv = 1.0 - dp[1];
+ vz[0] = dv*vz[0] + dp[1]*vz[1];
+ vz[1] = dv*vz[2] + dp[1]*vz[3];
+
+ dv = 1.0 - dp[0];
+ vz[0] = dv*vz[0] + dp[0]*vz[1];
+
+ return vz[0];
+}
+
+npy_float64 trilinear_interpolate(int ds[3], int ci[3], npy_float64 dp[3],
npy_float64 *data)
{
/* dims is one less than the dimensions of the array */
diff -r ea258e3dfc95 -r 7e381df9ded8 yt/_amr_utils/FixedInterpolator.h
--- a/yt/_amr_utils/FixedInterpolator.h Mon Jun 07 14:38:23 2010 -0400
+++ b/yt/_amr_utils/FixedInterpolator.h Mon Jun 07 23:45:30 2010 -0400
@@ -36,6 +36,8 @@
npy_float64 fast_interpolate(int ds[3], int ci[3], npy_float64 dp[3],
npy_float64 *data);
+npy_float64 offset_interpolate(int ds[3], npy_float64 dp[3], npy_float64 *data);
+
npy_float64 trilinear_interpolate(int ds[3], int ci[3], npy_float64 dp[3],
npy_float64 *data);
diff -r ea258e3dfc95 -r 7e381df9ded8 yt/_amr_utils/Octree.pyx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/yt/_amr_utils/Octree.pyx Mon Jun 07 23:45:30 2010 -0400
@@ -0,0 +1,280 @@
+"""
+A refine-by-two AMR-specific octree
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: UCSD
+Homepage: http://yt.enzotools.org/
+License:
+ Copyright (C) 2010 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+
+import numpy as np
+cimport numpy as np
+# Double up here for def'd functions
+cimport numpy as cnp
+cimport cython
+
+from stdlib cimport malloc, free, abs
+
+cdef extern from "stdlib.h":
+ # NOTE that size_t might not be int
+ void *alloca(int)
+
+cdef struct OctreeNode:
+ np.float64_t *val
+ np.float64_t weight_val
+ np.int64_t pos[3]
+ int level
+ int nvals
+ OctreeNode *children[2][2][2]
+
+cdef void OTN_add_value(OctreeNode *self,
+ np.float64_t *val, np.float64_t weight_val):
+ cdef int i
+ for i in range(self.nvals):
+ self.val[i] += val[i]
+ self.weight_val += weight_val
+
+cdef void OTN_refine(OctreeNode *self):
+ cdef int i, j, i1, j1
+ cdef np.int64_t npos[3]
+ cdef OctreeNode *node
+ for i in range(2):
+ npos[0] = self.pos[0] * 2 + i
+ for j in range(2):
+ npos[1] = self.pos[1] * 2 + j
+ # We have to be careful with allocation...
+ for k in range(2):
+ npos[2] = self.pos[2] * 2 + k
+ self.children[i][j][k] = OTN_initialize(
+ npos,
+ self.nvals, self.val, self.weight_val,
+ self.level + 1)
+ for i in range(self.nvals): self.val[i] = 0.0
+ self.weight_val = 0.0
+
+cdef OctreeNode *OTN_initialize(np.int64_t pos[3], int nvals,
+ np.float64_t *val, np.float64_t weight_val,
+ int level):
+ cdef OctreeNode *node
+ cdef int i, j
+ node = <OctreeNode *> malloc(sizeof(OctreeNode))
+ node.pos[0] = pos[0]
+ node.pos[1] = pos[1]
+ node.pos[2] = pos[2]
+ node.nvals = nvals
+ node.val = <np.float64_t *> malloc(
+ nvals * sizeof(np.float64_t))
+ for i in range(nvals):
+ node.val[i] = val[i]
+ node.weight_val = weight_val
+ for i in range(2):
+ for j in range(2):
+ for k in range(2):
+ node.children[i][j][k] = NULL
+ node.level = level
+ return node
+
+cdef void OTN_free(OctreeNode *node):
+ cdef int i, j
+ for i in range(2):
+ for j in range(2):
+ for k in range(2):
+ if node.children[i][j][k] == NULL: continue
+ OTN_free(node.children[i][j][k])
+ free(node.val)
+ free(node)
+
+cdef class Octree:
+ cdef int nvals
+ cdef np.int64_t po2[80]
+ cdef OctreeNode ****root_nodes
+ cdef np.int64_t top_grid_dims[3]
+
+ def __cinit__(self, np.ndarray[np.int64_t, ndim=1] top_grid_dims,
+ int nvals):
+ cdef int i, j
+ cdef OctreeNode *node
+ cdef np.int64_t pos[3]
+ cdef np.float64_t *vals = <np.float64_t *> alloca(
+ sizeof(np.float64_t)*nvals)
+ cdef np.float64_t weight_val = 0.0
+ self.nvals = nvals
+ for i in range(nvals): vals[i] = 0.0
+
+ self.top_grid_dims[0] = top_grid_dims[0]
+ self.top_grid_dims[1] = top_grid_dims[1]
+ self.top_grid_dims[2] = top_grid_dims[2]
+
+ # This wouldn't be necessary if we did bitshifting...
+ for i in range(80):
+ self.po2[i] = 2**i
+ # Cython doesn't seem to like sizeof(OctreeNode ***)
+ self.root_nodes = <OctreeNode ****> \
+ malloc(sizeof(void*) * top_grid_dims[0])
+
+ # We initialize our root values to 0.0.
+ for i in range(top_grid_dims[0]):
+ pos[0] = i
+ self.root_nodes[i] = <OctreeNode ***> \
+ malloc(sizeof(OctreeNode **) * top_grid_dims[1])
+ for j in range(top_grid_dims[1]):
+ pos[1] = j
+ self.root_nodes[i][j] = <OctreeNode **> \
+ malloc(sizeof(OctreeNode *) * top_grid_dims[1])
+ for k in range(top_grid_dims[2]):
+ pos[2] = k
+ self.root_nodes[i][j][k] = OTN_initialize(
+ pos, nvals, vals, weight_val, 0)
+
+ cdef void add_to_position(self,
+ int level, np.int64_t pos[3],
+ np.float64_t *val,
+ np.float64_t weight_val):
+ cdef int i, j
+ cdef OctreeNode *node
+ node = self.find_on_root_level(pos, level)
+ cdef np.int64_t fac
+ for L in range(level):
+ if node.children[0][0][0] == NULL:
+ OTN_refine(node)
+ # Maybe we should use bitwise operators?
+ fac = self.po2[level - L - 1]
+ i = (pos[0] >= fac*(2*node.pos[0]+1))
+ j = (pos[1] >= fac*(2*node.pos[1]+1))
+ k = (pos[2] >= fac*(2*node.pos[2]+1))
+ node = node.children[i][j][k]
+ OTN_add_value(node, val, weight_val)
+
+ cdef OctreeNode *find_on_root_level(self, np.int64_t pos[3], int level):
+ # We need this because the root level won't just have four children
+ # So we find on the root level, then we traverse the tree.
+ cdef np.int64_t i, j
+ i = <np.int64_t> (pos[0] / self.po2[level])
+ j = <np.int64_t> (pos[1] / self.po2[level])
+ k = <np.int64_t> (pos[2] / self.po2[level])
+ return self.root_nodes[i][j][k]
+
+
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ def add_array_to_tree(self, int level,
+ np.ndarray[np.int64_t, ndim=1] pxs,
+ np.ndarray[np.int64_t, ndim=1] pys,
+ np.ndarray[np.int64_t, ndim=1] pzs,
+ np.ndarray[np.float64_t, ndim=2] pvals,
+ np.ndarray[np.float64_t, ndim=1] pweight_vals):
+ cdef int np = pxs.shape[0]
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