[Yt-svn] yt: 3 new changesets
hg at spacepope.org
hg at spacepope.org
Tue Aug 24 18:52:29 PDT 2010
hg Repository: yt
details: yt/rev/c155ce023917
changeset: 1971:c155ce023917
user: mturk
date:
Tue Aug 24 13:38:14 2010 -0700
description:
[svn r1810] Cutting plane arguments were incorrect.
hg Repository: yt
details: yt/rev/49dd9b2bdcf4
changeset: 1972:49dd9b2bdcf4
user: Matthew Turk <matthewturk at gmail.com>
date:
Tue Aug 24 18:51:46 2010 -0700
description:
Merging from trunk
hg Repository: yt
details: yt/rev/6b820d6cc0a0
changeset: 1973:6b820d6cc0a0
user: Matthew Turk <matthewturk at gmail.com>
date:
Tue Aug 24 18:52:05 2010 -0700
description:
Merge
diffstat:
.hgignore | 3 +
yt/_amr_utils/DepthFirstOctree.pyx | 12 +-
yt/amr_utils.c | 2292 ++++++++++++++--------------
yt/arraytypes.py | 11 +
yt/command_line.py | 1 +
yt/extensions/enzo_simulation.py | 259 +-
yt/extensions/kdtree/fKD.f90 | 2 +-
yt/extensions/light_ray.py | 372 ++++
yt/extensions/merger_tree.py | 28 +
yt/extensions/volume_rendering/multi_texture.py | 302 +++
yt/fido/share_data.py | 83 +
yt/funcs.py | 25 +
yt/lagos/BaseDataTypes.py | 1 -
yt/lagos/BaseGridType.py | 16 +-
yt/lagos/Clump.py | 290 ---
yt/lagos/EnzoFields.py | 6 +
yt/lagos/FLASHFields.py | 26 +-
yt/lagos/GadgetFields.py | 89 +
yt/lagos/HaloFinding.py | 3 +
yt/lagos/HierarchyType.py | 119 +-
yt/lagos/OutputTypes.py | 20 +-
yt/lagos/TwoPointFunctions.py | 854 ----------
yt/lagos/UniversalFields.py | 9 +
yt/lagos/__init__.py | 3 +-
yt/lagos/two_point_functions.py | 854 ++++++++++
yt/math_utils.py | 327 ++++-
yt/ramses_reader.cpp | 574 +++---
yt/ramses_reader.pyx | 103 +-
yt/raven/plot_collection.py | 4 +-
yt/reason/plot_editors.py | 10 +-
yt/reason/reason_v2.py | 7 +-
yt/reason/tvtk_interface.py | 26 +-
32 files changed, 3950 insertions(+), 2781 deletions(-)
diffs (truncated from 17460 to 300 lines):
diff -r 8af6e82bef8c -r 6b820d6cc0a0 .hgignore
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.hgignore Tue Aug 24 18:52:05 2010 -0700
@@ -0,0 +1,3 @@
+syntax: glob
+*.pyc
+.*.swp
diff -r 8af6e82bef8c -r 6b820d6cc0a0 yt/_amr_utils/DepthFirstOctree.pyx
--- a/yt/_amr_utils/DepthFirstOctree.pyx Fri Aug 20 07:26:38 2010 -0700
+++ b/yt/_amr_utils/DepthFirstOctree.pyx Tue Aug 24 18:52:05 2010 -0700
@@ -77,15 +77,15 @@
cdef np.float64_t child_dx
cdef np.ndarray[np.float64_t, ndim=1] child_leftedges
cdef np.float64_t cx, cy, cz
- for k_off in range(k_f):
- k = k_off + k_i
- cz = (leftedges[2] + k*dx)
+ for i_off in range(i_f):
+ i = i_off + i_i
+ cx = (leftedges[0] + i*dx)
for j_off in range(j_f):
j = j_off + j_i
cy = (leftedges[1] + j*dx)
- for i_off in range(i_f):
- i = i_off + i_i
- cx = (leftedges[0] + i*dx)
+ for k_off in range(k_f):
+ k = k_off + k_i
+ cz = (leftedges[2] + k*dx)
ci = grid.child_indices[i,j,k]
if ci == -1:
for fi in range(fields.shape[0]):
diff -r 8af6e82bef8c -r 6b820d6cc0a0 yt/amr_utils.c
--- a/yt/amr_utils.c Fri Aug 20 07:26:38 2010 -0700
+++ b/yt/amr_utils.c Tue Aug 24 18:52:05 2010 -0700
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.13.beta0 on Tue Aug 10 16:02:46 2010 */
+/* Generated by Cython 0.13.beta0 on Mon Aug 2 07:18:26 2010 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -376,7 +376,7 @@
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":76
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":76
* cdef class VectorPlane
*
* cdef struct FieldInterpolationTable: # <<<<<<<<<<<<<<
@@ -396,7 +396,7 @@
int pass_through;
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":89
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":89
* int pass_through
*
* cdef void FIT_initialize_table(FieldInterpolationTable *fit, int nbins, # <<<<<<<<<<<<<<
@@ -411,7 +411,7 @@
int pass_through;
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/QuadTree.pyx":39
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/QuadTree.pyx":39
* void *alloca(int)
*
* cdef struct QuadTreeNode: # <<<<<<<<<<<<<<
@@ -428,7 +428,7 @@
struct __pyx_t_2yt_9amr_utils_QuadTreeNode *children[2][2];
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":118
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":118
* return (bv + dd*dy*fit.idbin)
*
* cdef class TransferFunctionProxy: # <<<<<<<<<<<<<<
@@ -449,7 +449,7 @@
PyObject *my_field_tables;
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":36
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":36
* self.refined_pos = 0
*
* cdef class OctreeGrid: # <<<<<<<<<<<<<<
@@ -467,7 +467,7 @@
int level;
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":53
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":53
* self.level = level
*
* cdef class OctreeGridList: # <<<<<<<<<<<<<<
@@ -480,7 +480,7 @@
PyObject *grids;
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":575
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":575
* return 1
*
* cdef class ProtoPrism: # <<<<<<<<<<<<<<
@@ -499,7 +499,7 @@
int parent_grid_id;
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":30
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":30
* cimport cython
*
* cdef class position: # <<<<<<<<<<<<<<
@@ -513,7 +513,7 @@
int refined_pos;
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":543
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":543
* tf.eval_transfer(dt, self.dvs, rgba, grad)
*
* cdef class GridFace: # <<<<<<<<<<<<<<
@@ -530,7 +530,7 @@
__pyx_t_5numpy_float64_t right_edge[3];
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/QuadTree.pyx":99
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/QuadTree.pyx":99
* free(node)
*
* cdef class QuadTree: # <<<<<<<<<<<<<<
@@ -547,7 +547,7 @@
__pyx_t_5numpy_int64_t top_grid_dims[2];
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":74
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":74
* np.float64_t *data, np.float64_t *grad)
*
* cdef class VectorPlane # <<<<<<<<<<<<<<
@@ -579,7 +579,7 @@
__pyx_t_5numpy_float64_t *y_vec;
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":299
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":299
* tv[offset + k] = fv[k]
*
* cdef class PartitionedGrid: # <<<<<<<<<<<<<<
@@ -605,7 +605,7 @@
};
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":543
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":543
* tf.eval_transfer(dt, self.dvs, rgba, grad)
*
* cdef class GridFace: # <<<<<<<<<<<<<<
@@ -619,7 +619,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_GridFace *__pyx_vtabptr_2yt_9amr_utils_GridFace;
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":118
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":118
* return (bv + dd*dy*fit.idbin)
*
* cdef class TransferFunctionProxy: # <<<<<<<<<<<<<<
@@ -633,7 +633,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_TransferFunctionProxy *__pyx_vtabptr_2yt_9amr_utils_TransferFunctionProxy;
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":575
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":575
* return 1
*
* cdef class ProtoPrism: # <<<<<<<<<<<<<<
@@ -647,7 +647,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_ProtoPrism *__pyx_vtabptr_2yt_9amr_utils_ProtoPrism;
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/QuadTree.pyx":99
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/QuadTree.pyx":99
* free(node)
*
* cdef class QuadTree: # <<<<<<<<<<<<<<
@@ -664,7 +664,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_QuadTree *__pyx_vtabptr_2yt_9amr_utils_QuadTree;
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":222
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":222
* #rgba[i+3] += trgba[i] * (1.0 - rgba[i+3])*dt*trgba[i+3]
*
* cdef class VectorPlane: # <<<<<<<<<<<<<<
@@ -680,7 +680,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_VectorPlane *__pyx_vtabptr_2yt_9amr_utils_VectorPlane;
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/VolumeIntegrator.pyx":299
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":299
* tv[offset + k] = fv[k]
*
* cdef class PartitionedGrid: # <<<<<<<<<<<<<<
@@ -1761,7 +1761,7 @@
static PyObject *__pyx_int_3;
static PyObject *__pyx_int_15;
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":31
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":31
*
* cdef class position:
* cdef public int output_pos, refined_pos # <<<<<<<<<<<<<<
@@ -1853,7 +1853,7 @@
return __pyx_r;
}
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":32
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":32
* cdef class position:
* cdef public int output_pos, refined_pos
* def __cinit__(self): # <<<<<<<<<<<<<<
@@ -1869,7 +1869,7 @@
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
- /* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":33
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":33
* cdef public int output_pos, refined_pos
* def __cinit__(self):
* self.output_pos = 0 # <<<<<<<<<<<<<<
@@ -1878,7 +1878,7 @@
*/
((struct __pyx_obj_2yt_9amr_utils_position *)__pyx_v_self)->output_pos = 0;
- /* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":34
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":34
* def __cinit__(self):
* self.output_pos = 0
* self.refined_pos = 0 # <<<<<<<<<<<<<<
@@ -1892,7 +1892,7 @@
return __pyx_r;
}
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":37
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":37
*
* cdef class OctreeGrid:
* cdef public object child_indices, fields, left_edges, dimensions, dx # <<<<<<<<<<<<<<
@@ -2130,7 +2130,7 @@
return __pyx_r;
}
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":38
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":38
* cdef class OctreeGrid:
* cdef public object child_indices, fields, left_edges, dimensions, dx
* cdef public int level # <<<<<<<<<<<<<<
@@ -2180,7 +2180,7 @@
return __pyx_r;
}
-/* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":39
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":39
* cdef public object child_indices, fields, left_edges, dimensions, dx
* cdef public int level
* def __cinit__(self, # <<<<<<<<<<<<<<
@@ -2341,7 +2341,7 @@
__pyx_bstride_0_dx = __pyx_bstruct_dx.strides[0];
__pyx_bshape_0_dx = __pyx_bstruct_dx.shape[0];
- /* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":46
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":46
* np.ndarray[np.float64_t, ndim=1] dx,
* int level):
* self.child_indices = child_indices # <<<<<<<<<<<<<<
@@ -2354,7 +2354,7 @@
__Pyx_DECREF(((struct __pyx_obj_2yt_9amr_utils_OctreeGrid *)__pyx_v_self)->child_indices);
((struct __pyx_obj_2yt_9amr_utils_OctreeGrid *)__pyx_v_self)->child_indices = ((PyObject *)__pyx_v_child_indices);
- /* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":47
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":47
* int level):
* self.child_indices = child_indices
* self.fields = fields # <<<<<<<<<<<<<<
@@ -2367,7 +2367,7 @@
__Pyx_DECREF(((struct __pyx_obj_2yt_9amr_utils_OctreeGrid *)__pyx_v_self)->fields);
((struct __pyx_obj_2yt_9amr_utils_OctreeGrid *)__pyx_v_self)->fields = ((PyObject *)__pyx_v_fields);
- /* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":48
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":48
* self.child_indices = child_indices
* self.fields = fields
* self.left_edges = left_edges # <<<<<<<<<<<<<<
@@ -2380,7 +2380,7 @@
__Pyx_DECREF(((struct __pyx_obj_2yt_9amr_utils_OctreeGrid *)__pyx_v_self)->left_edges);
((struct __pyx_obj_2yt_9amr_utils_OctreeGrid *)__pyx_v_self)->left_edges = ((PyObject *)__pyx_v_left_edges);
- /* "/Users/matthewturk/Development/yt/trunk/yt/_amr_utils/DepthFirstOctree.pyx":49
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/DepthFirstOctree.pyx":49
* self.fields = fields
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