[Yt-svn] yt-commit r797 - trunk/yt/lagos
mturk at wrangler.dreamhost.com
mturk at wrangler.dreamhost.com
Mon Sep 22 08:35:21 PDT 2008
Author: mturk
Date: Mon Sep 22 08:35:20 2008
New Revision: 797
URL: http://yt.spacepope.org/changeset/797
Log:
Fixed multiple fields in the Octree
Added EnzoRay, which is an arbitrary ray caster, accepting start&end points.
This code sports a warning, because I've only tested it in the orthogonal case
(where it gives alrighty results) and also because I have recruited somebody
else to help out with that.
Additionally, I found that OrthoRay wasn't returning any points if it was on a
grid boundary, which I have fixed by giving the tie-breaker to the Left side.
I'm still learning Cython, so all these Cython routines end up being a lot
faster.
Modified:
trunk/yt/lagos/BaseDataTypes.py
trunk/yt/lagos/DepthFirstOctree.c
trunk/yt/lagos/DepthFirstOctree.pyx
trunk/yt/lagos/HierarchyType.py
trunk/yt/lagos/RTIntegrator.c
trunk/yt/lagos/RTIntegrator.pyx
trunk/yt/lagos/RayTracer.py
Modified: trunk/yt/lagos/BaseDataTypes.py
==============================================================================
--- trunk/yt/lagos/BaseDataTypes.py (original)
+++ trunk/yt/lagos/BaseDataTypes.py Mon Sep 22 08:35:20 2008
@@ -366,29 +366,90 @@
self._refresh_data()
def _get_list_of_grids(self):
- y = na.where( (self.px > self.pf.hierarchy.gridLeftEdge[:,self.px_ax])
+ # This bugs me, but we will give the tie to the LeftEdge
+ y = na.where( (self.px >= self.pf.hierarchy.gridLeftEdge[:,self.px_ax])
& (self.px < self.pf.hierarchy.gridRightEdge[:,self.px_ax])
- & (self.py > self.pf.hierarchy.gridLeftEdge[:,self.py_ax])
+ & (self.py >= self.pf.hierarchy.gridLeftEdge[:,self.py_ax])
& (self.py < self.pf.hierarchy.gridRightEdge[:,self.py_ax]))
self._grids = self.hierarchy.grids[y]
def _get_data_from_grid(self, grid, field):
# We are orthogonal, so we can feel free to make assumptions
# for the sake of speed.
- gdx = just_one(grid[self.px_dx])
- gdy = just_one(grid[self.py_dx])
- x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx)
- y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy)
- sl = [None,None,None]
- sl[self.px_ax] = slice(x_coord,x_coord+1,None)
- sl[self.py_ax] = slice(y_coord,y_coord+1,None)
- sl[self.axis] = slice(None)
+ if grid.id not in self._cut_masks:
+ gdx = just_one(grid[self.px_dx])
+ gdy = just_one(grid[self.py_dx])
+ x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx)
+ y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy)
+ sl = [None,None,None]
+ sl[self.px_ax] = slice(x_coord,x_coord+1,None)
+ sl[self.py_ax] = slice(y_coord,y_coord+1,None)
+ sl[self.axis] = slice(None)
+ self._cut_masks[grid.id] = sl
+ else:
+ sl = self._cut_masks[grid.id]
if not iterable(grid[field]):
gf = grid[field] * na.ones(grid.child_mask[sl].shape)
else:
gf = grid[field][sl]
return gf[na.where(grid.child_mask[sl])]
+class EnzoRayBase(Enzo1DData):
+ def __init__(self, start_point, end_point, fields=None, pf=None, **kwargs):
+ """
+ We accept a start point and an end point and then get all the data
+ between those two.
+ """
+ mylog.warning("This code is poorly tested. It may give bad data!")
+ Enzo1DData.__init__(self, pf, fields, **kwargs)
+ self.start_point = na.array(start_point)
+ self.end_point = na.array(end_point)
+ self.vec = self.end_point - self.start_point
+ self.center = self.start_point
+ self.set_field_parameter('center', self.start_point)
+ #self._refresh_data()
+
+ def _get_list_of_grids(self):
+ # Get the value of the line at each LeftEdge and RightEdge
+ LE = self.pf.h.gridLeftEdge
+ RE = self.pf.h.gridRightEdge
+ p = na.zeros(self.pf.h.num_grids, dtype='bool')
+ # Check left faces first
+ for i in range(3):
+ i1 = (i+1) % 3
+ i2 = (i+2) % 3
+ vs = self._get_line_at_coord(LE[:,i], i)
+ p = p | ( ( (LE[:,i1] < vs[:,i1]) & (RE[:,i1] > vs[:,i1]) ) \
+ & ( (LE[:,i2] < vs[:,i2]) & (RE[:,i2] > vs[:,i2]) ) )
+ vs = self._get_line_at_coord(RE[:,i], i)
+ p = p | ( ( (LE[:,i1] < vs[:,i1]) & (RE[:,i1] > vs[:,i1]) ) \
+ & ( (LE[:,i2] < vs[:,i2]) & (RE[:,i2] > vs[:,i2]) ) )
+ p = p | ( na.all( LE < self.start_point, axis=1 )
+ & na.all( RE > self.start_point, axis=1 ) )
+ p = p | ( na.all( LE < self.end_point, axis=1 )
+ & na.all( RE > self.end_point, axis=1 ) )
+ self._grids = self.hierarchy.grids.copy()#[p]
+
+ def _get_line_at_coord(self, v, index):
+ # t*self.vec + self.start_point = self.end_point
+ t = (v - self.start_point[index])/self.vec[index]
+ t = t.reshape((t.shape[0],1))
+ return self.start_point + t*self.vec
+
+ def _get_data_from_grid(self, grid, field):
+ mask = na.logical_and(self._get_cut_mask(grid),
+ grid.child_mask)
+ return grid[field][mask]
+
+ @cache_mask
+ def _get_cut_mask(self, grid):
+ mask = na.zeros(grid.ActiveDimensions, dtype='int')
+ import RTIntegrator as RT
+ RT.VoxelTraversal(mask, grid.LeftEdge, grid.RightEdge,
+ na.array([grid.dx, grid.dy, grid.dz]),
+ self.center, self.vec)
+ return mask
+
class Enzo2DData(EnzoData, GridPropertiesMixin):
_key_fields = ['px','py','pdx','pdy']
"""
Modified: trunk/yt/lagos/DepthFirstOctree.c
==============================================================================
--- trunk/yt/lagos/DepthFirstOctree.c (original)
+++ trunk/yt/lagos/DepthFirstOctree.c Mon Sep 22 08:35:20 2008
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.9.8.1.1 on Mon Sep 22 10:18:51 2008 */
+/* Generated by Cython 0.9.8.1.1 on Mon Sep 22 11:45:23 2008 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -189,6 +189,8 @@
static int __Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t(PyObject* obj, Py_buffer* buf, int flags, int nd); /*proto*/
#define __Pyx_BufPtrStrided1d(buf, i0, s0) ((char*)buf + i0 * s0)
#define __Pyx_BufPtrStrided3d(buf, i0, s0, i1, s1, i2, s2) ((char*)buf + i0 * s0 + i1 * s1 + i2 * s2)
+#define __Pyx_BufPtrStrided4d(buf, i0, s0, i1, s1, i2, s2, i3, s3) ((char*)buf + i0 * s0 + i1 * s1 + i2 * s2 + i3 * s3)
+#define __Pyx_BufPtrStrided2d(buf, i0, s0, i1, s1) ((char*)buf + i0 * s0 + i1 * s1)
static void __Pyx_RaiseBufferFallbackError(void); /*proto*/
@@ -203,8 +205,8 @@
#define __Pyx_ReleaseBuffer PyObject_ReleaseBuffer
#endif
-Py_ssize_t __Pyx_zeros[] = {0, 0, 0};
-Py_ssize_t __Pyx_minusones[] = {-1, -1, -1};
+Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0};
+Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1};
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
@@ -286,21 +288,45 @@
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
+/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":30
+ * cimport cython
+ *
+ * cdef class position: # <<<<<<<<<<<<<<
+ * cdef public int output_pos, refined_pos
+ *
+ */
+
struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_position {
PyObject_HEAD
int output_pos;
int refined_pos;
};
+/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":33
+ * cdef public int output_pos, refined_pos
+ *
+ * cdef class OctreeGrid: # <<<<<<<<<<<<<<
+ * cdef public object child_indices, fields, left_edges, dimensions, dx
+ * def __cinit__(self,
+ */
+
struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid {
PyObject_HEAD
PyObject *child_indices;
- PyObject *field;
+ PyObject *fields;
PyObject *left_edges;
PyObject *dimensions;
PyObject *dx;
};
+/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":47
+ * self.dx = dx
+ *
+ * cdef class OctreeGridList: # <<<<<<<<<<<<<<
+ * cdef public object grids
+ * def __cinit__(self, grids):
+ */
+
struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGridList {
PyObject_HEAD
PyObject *grids;
@@ -357,10 +383,18 @@
static char __pyx_k_15[] = "O";
static char __pyx_k_16[] = "only objects, int and float dtypes supported for ndarray buffer access so far (dtype is %d)";
+/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":35
+ * cdef class OctreeGrid:
+ * cdef public object child_indices, fields, left_edges, dimensions, dx
+ * def __cinit__(self, # <<<<<<<<<<<<<<
+ * np.ndarray[np.int_t, ndim=3] child_indices,
+ * np.ndarray[np.float64_t, ndim=4] fields,
+ */
+
static int __pyx_pf_2yt_5lagos_16DepthFirstOctree_10OctreeGrid___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pf_2yt_5lagos_16DepthFirstOctree_10OctreeGrid___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_child_indices = 0;
- PyArrayObject *__pyx_v_field = 0;
+ PyArrayObject *__pyx_v_fields = 0;
PyArrayObject *__pyx_v_left_edges = 0;
PyArrayObject *__pyx_v_dimensions = 0;
PyArrayObject *__pyx_v_dx = 0;
@@ -371,13 +405,15 @@
Py_ssize_t __pyx_bshape_0_child_indices = 0;
Py_ssize_t __pyx_bshape_1_child_indices = 0;
Py_ssize_t __pyx_bshape_2_child_indices = 0;
- Py_buffer __pyx_bstruct_field;
- Py_ssize_t __pyx_bstride_0_field = 0;
- Py_ssize_t __pyx_bstride_1_field = 0;
- Py_ssize_t __pyx_bstride_2_field = 0;
- Py_ssize_t __pyx_bshape_0_field = 0;
- Py_ssize_t __pyx_bshape_1_field = 0;
- Py_ssize_t __pyx_bshape_2_field = 0;
+ Py_buffer __pyx_bstruct_fields;
+ Py_ssize_t __pyx_bstride_0_fields = 0;
+ Py_ssize_t __pyx_bstride_1_fields = 0;
+ Py_ssize_t __pyx_bstride_2_fields = 0;
+ Py_ssize_t __pyx_bstride_3_fields = 0;
+ Py_ssize_t __pyx_bshape_0_fields = 0;
+ Py_ssize_t __pyx_bshape_1_fields = 0;
+ Py_ssize_t __pyx_bshape_2_fields = 0;
+ Py_ssize_t __pyx_bshape_3_fields = 0;
Py_buffer __pyx_bstruct_dx;
Py_ssize_t __pyx_bstride_0_dx = 0;
Py_ssize_t __pyx_bshape_0_dx = 0;
@@ -388,16 +424,16 @@
Py_ssize_t __pyx_bstride_0_dimensions = 0;
Py_ssize_t __pyx_bshape_0_dimensions = 0;
int __pyx_r;
- static char *__pyx_argnames[] = {"child_indices","field","left_edges","dimensions","dx",0};
+ static char *__pyx_argnames[] = {"child_indices","fields","left_edges","dimensions","dx",0};
if (likely(!__pyx_kwds) && likely(PyTuple_GET_SIZE(__pyx_args) == 5)) {
__pyx_v_child_indices = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 0));
- __pyx_v_field = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 1));
+ __pyx_v_fields = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 1));
__pyx_v_left_edges = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 2));
__pyx_v_dimensions = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 3));
__pyx_v_dx = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 4));
}
else {
- if (unlikely(!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "OOOOO", __pyx_argnames, &__pyx_v_child_indices, &__pyx_v_field, &__pyx_v_left_edges, &__pyx_v_dimensions, &__pyx_v_dx))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "OOOOO", __pyx_argnames, &__pyx_v_child_indices, &__pyx_v_fields, &__pyx_v_left_edges, &__pyx_v_dimensions, &__pyx_v_dx))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
goto __pyx_L4;
__pyx_L3_error:;
@@ -405,16 +441,16 @@
return -1;
__pyx_L4:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_child_indices), __pyx_ptype_5numpy_ndarray, 1, "child_indices", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_field), __pyx_ptype_5numpy_ndarray, 1, "field", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fields), __pyx_ptype_5numpy_ndarray, 1, "fields", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_left_edges), __pyx_ptype_5numpy_ndarray, 1, "left_edges", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dimensions), __pyx_ptype_5numpy_ndarray, 1, "dimensions", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dx), __pyx_ptype_5numpy_ndarray, 1, "dx", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_int_t((PyObject*)__pyx_v_child_indices, &__pyx_bstruct_child_indices, PyBUF_FORMAT| PyBUF_STRIDES, 3) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_child_indices = __pyx_bstruct_child_indices.strides[0]; __pyx_bstride_1_child_indices = __pyx_bstruct_child_indices.strides[1]; __pyx_bstride_2_child_indices = __pyx_bstruct_child_indices.strides[2];
__pyx_bshape_0_child_indices = __pyx_bstruct_child_indices.shape[0]; __pyx_bshape_1_child_indices = __pyx_bstruct_child_indices.shape[1]; __pyx_bshape_2_child_indices = __pyx_bstruct_child_indices.shape[2];
- if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t((PyObject*)__pyx_v_field, &__pyx_bstruct_field, PyBUF_FORMAT| PyBUF_STRIDES, 3) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_bstride_0_field = __pyx_bstruct_field.strides[0]; __pyx_bstride_1_field = __pyx_bstruct_field.strides[1]; __pyx_bstride_2_field = __pyx_bstruct_field.strides[2];
- __pyx_bshape_0_field = __pyx_bstruct_field.shape[0]; __pyx_bshape_1_field = __pyx_bstruct_field.shape[1]; __pyx_bshape_2_field = __pyx_bstruct_field.shape[2];
+ if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t((PyObject*)__pyx_v_fields, &__pyx_bstruct_fields, PyBUF_FORMAT| PyBUF_STRIDES, 4) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_bstride_0_fields = __pyx_bstruct_fields.strides[0]; __pyx_bstride_1_fields = __pyx_bstruct_fields.strides[1]; __pyx_bstride_2_fields = __pyx_bstruct_fields.strides[2]; __pyx_bstride_3_fields = __pyx_bstruct_fields.strides[3];
+ __pyx_bshape_0_fields = __pyx_bstruct_fields.shape[0]; __pyx_bshape_1_fields = __pyx_bstruct_fields.shape[1]; __pyx_bshape_2_fields = __pyx_bstruct_fields.shape[2]; __pyx_bshape_3_fields = __pyx_bstruct_fields.shape[3];
if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t((PyObject*)__pyx_v_left_edges, &__pyx_bstruct_left_edges, PyBUF_FORMAT| PyBUF_STRIDES, 1) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_left_edges = __pyx_bstruct_left_edges.strides[0];
__pyx_bshape_0_left_edges = __pyx_bstruct_left_edges.shape[0];
@@ -424,18 +460,58 @@
if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t((PyObject*)__pyx_v_dx, &__pyx_bstruct_dx, PyBUF_FORMAT| PyBUF_STRIDES, 1) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_dx = __pyx_bstruct_dx.strides[0];
__pyx_bshape_0_dx = __pyx_bstruct_dx.shape[0];
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":41
+ * np.ndarray[np.int_t, ndim=1] dimensions,
+ * np.ndarray[np.float64_t, ndim=1] dx):
+ * self.child_indices = child_indices # <<<<<<<<<<<<<<
+ * self.fields = fields
+ * self.left_edges = left_edges
+ */
Py_INCREF(((PyObject *)__pyx_v_child_indices));
Py_DECREF(((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->child_indices);
((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->child_indices = ((PyObject *)__pyx_v_child_indices);
- Py_INCREF(((PyObject *)__pyx_v_field));
- Py_DECREF(((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->field);
- ((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->field = ((PyObject *)__pyx_v_field);
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":42
+ * np.ndarray[np.float64_t, ndim=1] dx):
+ * self.child_indices = child_indices
+ * self.fields = fields # <<<<<<<<<<<<<<
+ * self.left_edges = left_edges
+ * self.dimensions = dimensions
+ */
+ Py_INCREF(((PyObject *)__pyx_v_fields));
+ Py_DECREF(((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->fields);
+ ((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->fields = ((PyObject *)__pyx_v_fields);
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":43
+ * self.child_indices = child_indices
+ * self.fields = fields
+ * self.left_edges = left_edges # <<<<<<<<<<<<<<
+ * self.dimensions = dimensions
+ * self.dx = dx
+ */
Py_INCREF(((PyObject *)__pyx_v_left_edges));
Py_DECREF(((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->left_edges);
((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->left_edges = ((PyObject *)__pyx_v_left_edges);
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":44
+ * self.fields = fields
+ * self.left_edges = left_edges
+ * self.dimensions = dimensions # <<<<<<<<<<<<<<
+ * self.dx = dx
+ *
+ */
Py_INCREF(((PyObject *)__pyx_v_dimensions));
Py_DECREF(((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->dimensions);
((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->dimensions = ((PyObject *)__pyx_v_dimensions);
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":45
+ * self.left_edges = left_edges
+ * self.dimensions = dimensions
+ * self.dx = dx # <<<<<<<<<<<<<<
+ *
+ * cdef class OctreeGridList:
+ */
Py_INCREF(((PyObject *)__pyx_v_dx));
Py_DECREF(((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->dx);
((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_v_self)->dx = ((PyObject *)__pyx_v_dx);
@@ -446,7 +522,7 @@
{ PyObject *__pyx_type, *__pyx_value, *__pyx_tb;
PyErr_Fetch(&__pyx_type, &__pyx_value, &__pyx_tb);
__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_child_indices, &__pyx_bstruct_child_indices);
- __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_field, &__pyx_bstruct_field);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_fields, &__pyx_bstruct_fields);
__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_dx, &__pyx_bstruct_dx);
__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_left_edges, &__pyx_bstruct_left_edges);
__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_dimensions, &__pyx_bstruct_dimensions);
@@ -456,7 +532,7 @@
goto __pyx_L2;
__pyx_L0:;
__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_child_indices, &__pyx_bstruct_child_indices);
- __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_field, &__pyx_bstruct_field);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_fields, &__pyx_bstruct_fields);
__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_dx, &__pyx_bstruct_dx);
__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_left_edges, &__pyx_bstruct_left_edges);
__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_dimensions, &__pyx_bstruct_dimensions);
@@ -464,6 +540,14 @@
return __pyx_r;
}
+/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":49
+ * cdef class OctreeGridList:
+ * cdef public object grids
+ * def __cinit__(self, grids): # <<<<<<<<<<<<<<
+ * self.grids = grids
+ *
+ */
+
static int __pyx_pf_2yt_5lagos_16DepthFirstOctree_14OctreeGridList___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pf_2yt_5lagos_16DepthFirstOctree_14OctreeGridList___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_grids = 0;
@@ -480,6 +564,14 @@
__Pyx_AddTraceback("yt.lagos.DepthFirstOctree.OctreeGridList.__cinit__");
return -1;
__pyx_L4:;
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":50
+ * cdef public object grids
+ * def __cinit__(self, grids):
+ * self.grids = grids # <<<<<<<<<<<<<<
+ *
+ * def __getitem__(self, int item):
+ */
Py_INCREF(__pyx_v_grids);
Py_DECREF(((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGridList *)__pyx_v_self)->grids);
((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGridList *)__pyx_v_self)->grids = __pyx_v_grids;
@@ -488,6 +580,14 @@
return __pyx_r;
}
+/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":52
+ * self.grids = grids
+ *
+ * def __getitem__(self, int item): # <<<<<<<<<<<<<<
+ * return self.grids[item]
+ *
+ */
+
static PyObject *__pyx_pf_2yt_5lagos_16DepthFirstOctree_14OctreeGridList___getitem__(PyObject *__pyx_v_self, PyObject *__pyx_arg_item); /*proto*/
static PyObject *__pyx_pf_2yt_5lagos_16DepthFirstOctree_14OctreeGridList___getitem__(PyObject *__pyx_v_self, PyObject *__pyx_arg_item) {
int __pyx_v_item;
@@ -501,6 +601,14 @@
__Pyx_AddTraceback("yt.lagos.DepthFirstOctree.OctreeGridList.__getitem__");
return NULL;
__pyx_L4:;
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":53
+ *
+ * def __getitem__(self, int item):
+ * return self.grids[item] # <<<<<<<<<<<<<<
+ *
+ * @cython.boundscheck(False)
+ */
__pyx_1 = __Pyx_GetItemInt(((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGridList *)__pyx_v_self)->grids, __pyx_v_item, 0); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_1;
__pyx_1 = 0;
@@ -516,6 +624,14 @@
return __pyx_r;
}
+/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":56
+ *
+ * @cython.boundscheck(False)
+ * def WalkRootgrid(np.ndarray[np.float64_t, ndim=2] output, # <<<<<<<<<<<<<<
+ * np.ndarray[np.int_t, ndim=1] refined,
+ * OctreeGridList grids, int pi, int s = 0, int r = 0):
+ */
+
static PyObject *__pyx_pf_2yt_5lagos_16DepthFirstOctree_WalkRootgrid(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_2yt_5lagos_16DepthFirstOctree_WalkRootgrid[] = "\n This function only gets called on a 'root grid' -- a base grid\n of the simulation we are converting. It will call a recursive walker.\n ";
static PyObject *__pyx_pf_2yt_5lagos_16DepthFirstOctree_WalkRootgrid(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
@@ -529,6 +645,7 @@
int __pyx_v_j;
int __pyx_v_k;
int __pyx_v_gi;
+ int __pyx_v_fi;
int __pyx_v_child_i;
int __pyx_v_child_j;
int __pyx_v_child_k;
@@ -536,7 +653,7 @@
struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *__pyx_v_grid = 0;
PyArrayObject *__pyx_v_child_indices = 0;
PyArrayObject *__pyx_v_dimensions = 0;
- PyArrayObject *__pyx_v_field = 0;
+ PyArrayObject *__pyx_v_fields = 0;
PyArrayObject *__pyx_v_leftedges = 0;
PyArrayObject *__pyx_v_dx = 0;
PyArrayObject *__pyx_v_child_dx;
@@ -557,13 +674,6 @@
Py_buffer __pyx_bstruct_child_dx;
Py_ssize_t __pyx_bstride_0_child_dx = 0;
Py_ssize_t __pyx_bshape_0_child_dx = 0;
- Py_buffer __pyx_bstruct_field;
- Py_ssize_t __pyx_bstride_0_field = 0;
- Py_ssize_t __pyx_bstride_1_field = 0;
- Py_ssize_t __pyx_bstride_2_field = 0;
- Py_ssize_t __pyx_bshape_0_field = 0;
- Py_ssize_t __pyx_bshape_1_field = 0;
- Py_ssize_t __pyx_bshape_2_field = 0;
Py_buffer __pyx_bstruct_child_leftedges;
Py_ssize_t __pyx_bstride_0_child_leftedges = 0;
Py_ssize_t __pyx_bshape_0_child_leftedges = 0;
@@ -574,9 +684,20 @@
Py_ssize_t __pyx_bshape_0_child_indices = 0;
Py_ssize_t __pyx_bshape_1_child_indices = 0;
Py_ssize_t __pyx_bshape_2_child_indices = 0;
+ Py_buffer __pyx_bstruct_fields;
+ Py_ssize_t __pyx_bstride_0_fields = 0;
+ Py_ssize_t __pyx_bstride_1_fields = 0;
+ Py_ssize_t __pyx_bstride_2_fields = 0;
+ Py_ssize_t __pyx_bstride_3_fields = 0;
+ Py_ssize_t __pyx_bshape_0_fields = 0;
+ Py_ssize_t __pyx_bshape_1_fields = 0;
+ Py_ssize_t __pyx_bshape_2_fields = 0;
+ Py_ssize_t __pyx_bshape_3_fields = 0;
Py_buffer __pyx_bstruct_output;
Py_ssize_t __pyx_bstride_0_output = 0;
+ Py_ssize_t __pyx_bstride_1_output = 0;
Py_ssize_t __pyx_bshape_0_output = 0;
+ Py_ssize_t __pyx_bshape_1_output = 0;
PyObject *__pyx_r;
long __pyx_1;
PyObject *__pyx_2 = 0;
@@ -586,13 +707,14 @@
__pyx_t_5numpy_int_t __pyx_6;
__pyx_t_5numpy_int_t __pyx_7;
int __pyx_8;
- __pyx_t_5numpy_float64_t __pyx_9;
- PyObject *__pyx_10 = 0;
- int __pyx_11;
- PyObject *__pyx_12 = 0;
+ npy_intp __pyx_9;
+ __pyx_t_5numpy_float64_t __pyx_10;
+ PyObject *__pyx_11 = 0;
+ int __pyx_12;
PyObject *__pyx_13 = 0;
PyObject *__pyx_14 = 0;
PyObject *__pyx_15 = 0;
+ PyObject *__pyx_16 = 0;
PyArrayObject *__pyx_t_1 = NULL;
PyArrayObject *__pyx_t_2 = NULL;
PyArrayObject *__pyx_t_3 = NULL;
@@ -610,18 +732,20 @@
int __pyx_t_15;
int __pyx_t_16;
int __pyx_t_17;
- PyArrayObject *__pyx_t_18 = NULL;
+ int __pyx_t_18;
int __pyx_t_19;
- PyObject *__pyx_t_20 = NULL;
- PyObject *__pyx_t_21 = NULL;
+ PyArrayObject *__pyx_t_20 = NULL;
+ int __pyx_t_21;
PyObject *__pyx_t_22 = NULL;
- PyArrayObject *__pyx_t_23 = NULL;
- long __pyx_t_24;
- long __pyx_t_25;
+ PyObject *__pyx_t_23 = NULL;
+ PyObject *__pyx_t_24 = NULL;
+ PyArrayObject *__pyx_t_25 = NULL;
long __pyx_t_26;
long __pyx_t_27;
long __pyx_t_28;
long __pyx_t_29;
+ long __pyx_t_30;
+ long __pyx_t_31;
static char *__pyx_argnames[] = {"output","refined","grids","pi","s","r",0};
__pyx_self = __pyx_self;
__pyx_v_s = 0;
@@ -649,7 +773,7 @@
__pyx_v_child_grid = ((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)Py_None); Py_INCREF(Py_None);
__pyx_bstruct_child_indices.buf = NULL;
__pyx_bstruct_dimensions.buf = NULL;
- __pyx_bstruct_field.buf = NULL;
+ __pyx_bstruct_fields.buf = NULL;
__pyx_bstruct_leftedges.buf = NULL;
__pyx_bstruct_dx.buf = NULL;
__pyx_v_child_dx = ((PyArrayObject *)Py_None); Py_INCREF(Py_None);
@@ -660,17 +784,33 @@
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_output), __pyx_ptype_5numpy_ndarray, 1, "output", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_refined), __pyx_ptype_5numpy_ndarray, 1, "refined", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_grids), __pyx_ptype_2yt_5lagos_16DepthFirstOctree_OctreeGridList, 1, "grids", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t((PyObject*)__pyx_v_output, &__pyx_bstruct_output, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_bstride_0_output = __pyx_bstruct_output.strides[0];
- __pyx_bshape_0_output = __pyx_bstruct_output.shape[0];
+ if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t((PyObject*)__pyx_v_output, &__pyx_bstruct_output, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 2) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_bstride_0_output = __pyx_bstruct_output.strides[0]; __pyx_bstride_1_output = __pyx_bstruct_output.strides[1];
+ __pyx_bshape_0_output = __pyx_bstruct_output.shape[0]; __pyx_bshape_1_output = __pyx_bstruct_output.shape[1];
if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_int_t((PyObject*)__pyx_v_refined, &__pyx_bstruct_refined, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_refined = __pyx_bstruct_refined.strides[0];
__pyx_bshape_0_refined = __pyx_bstruct_refined.shape[0];
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":66
+ * cdef int child_i, child_j, child_k
+ * cdef OctreeGrid child_grid
+ * cdef OctreeGrid grid = grids[pi-1] # <<<<<<<<<<<<<<
+ * cdef np.ndarray[np.int_t, ndim=3] child_indices = grid.child_indices
+ * cdef np.ndarray[np.int_t, ndim=1] dimensions = grid.dimensions
+ */
__pyx_1 = (__pyx_v_pi - 1);
__pyx_2 = __Pyx_GetItemInt(((PyObject *)__pyx_v_grids), __pyx_1, 0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!(__Pyx_TypeTest(__pyx_2, __pyx_ptype_2yt_5lagos_16DepthFirstOctree_OctreeGrid))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_grid = ((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)__pyx_2);
__pyx_2 = 0;
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":67
+ * cdef OctreeGrid child_grid
+ * cdef OctreeGrid grid = grids[pi-1]
+ * cdef np.ndarray[np.int_t, ndim=3] child_indices = grid.child_indices # <<<<<<<<<<<<<<
+ * cdef np.ndarray[np.int_t, ndim=1] dimensions = grid.dimensions
+ * cdef np.ndarray[np.float64_t, ndim=4] fields = grid.fields
+ */
if (!(__Pyx_TypeTest(__pyx_v_grid->child_indices, __pyx_ptype_5numpy_ndarray))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = ((PyArrayObject *)__pyx_v_grid->child_indices);
if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_int_t((PyObject*)__pyx_t_1, &__pyx_bstruct_child_indices, PyBUF_FORMAT| PyBUF_STRIDES, 3) == -1)) {
@@ -682,6 +822,14 @@
__pyx_t_1 = 0;
Py_INCREF(__pyx_v_grid->child_indices);
__pyx_v_child_indices = ((PyArrayObject *)__pyx_v_grid->child_indices);
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":68
+ * cdef OctreeGrid grid = grids[pi-1]
+ * cdef np.ndarray[np.int_t, ndim=3] child_indices = grid.child_indices
+ * cdef np.ndarray[np.int_t, ndim=1] dimensions = grid.dimensions # <<<<<<<<<<<<<<
+ * cdef np.ndarray[np.float64_t, ndim=4] fields = grid.fields
+ * cdef np.ndarray[np.float64_t, ndim=1] leftedges = grid.left_edges
+ */
if (!(__Pyx_TypeTest(__pyx_v_grid->dimensions, __pyx_ptype_5numpy_ndarray))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = ((PyArrayObject *)__pyx_v_grid->dimensions);
if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_int_t((PyObject*)__pyx_t_2, &__pyx_bstruct_dimensions, PyBUF_FORMAT| PyBUF_STRIDES, 1) == -1)) {
@@ -693,17 +841,33 @@
__pyx_t_2 = 0;
Py_INCREF(__pyx_v_grid->dimensions);
__pyx_v_dimensions = ((PyArrayObject *)__pyx_v_grid->dimensions);
- if (!(__Pyx_TypeTest(__pyx_v_grid->field, __pyx_ptype_5numpy_ndarray))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = ((PyArrayObject *)__pyx_v_grid->field);
- if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t((PyObject*)__pyx_t_3, &__pyx_bstruct_field, PyBUF_FORMAT| PyBUF_STRIDES, 3) == -1)) {
- __pyx_v_field = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); __pyx_bstruct_field.buf = NULL;
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":69
+ * cdef np.ndarray[np.int_t, ndim=3] child_indices = grid.child_indices
+ * cdef np.ndarray[np.int_t, ndim=1] dimensions = grid.dimensions
+ * cdef np.ndarray[np.float64_t, ndim=4] fields = grid.fields # <<<<<<<<<<<<<<
+ * cdef np.ndarray[np.float64_t, ndim=1] leftedges = grid.left_edges
+ * cdef np.ndarray[np.float64_t, ndim=1] dx = grid.dx
+ */
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+ __pyx_t_3 = ((PyArrayObject *)__pyx_v_grid->fields);
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- } else {__pyx_bstride_0_field = __pyx_bstruct_field.strides[0]; __pyx_bstride_1_field = __pyx_bstruct_field.strides[1]; __pyx_bstride_2_field = __pyx_bstruct_field.strides[2];
- __pyx_bshape_0_field = __pyx_bstruct_field.shape[0]; __pyx_bshape_1_field = __pyx_bstruct_field.shape[1]; __pyx_bshape_2_field = __pyx_bstruct_field.shape[2];
+ } else {__pyx_bstride_0_fields = __pyx_bstruct_fields.strides[0]; __pyx_bstride_1_fields = __pyx_bstruct_fields.strides[1]; __pyx_bstride_2_fields = __pyx_bstruct_fields.strides[2]; __pyx_bstride_3_fields = __pyx_bstruct_fields.strides[3];
+ __pyx_bshape_0_fields = __pyx_bstruct_fields.shape[0]; __pyx_bshape_1_fields = __pyx_bstruct_fields.shape[1]; __pyx_bshape_2_fields = __pyx_bstruct_fields.shape[2]; __pyx_bshape_3_fields = __pyx_bstruct_fields.shape[3];
}
__pyx_t_3 = 0;
- Py_INCREF(__pyx_v_grid->field);
- __pyx_v_field = ((PyArrayObject *)__pyx_v_grid->field);
+ Py_INCREF(__pyx_v_grid->fields);
+ __pyx_v_fields = ((PyArrayObject *)__pyx_v_grid->fields);
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":70
+ * cdef np.ndarray[np.int_t, ndim=1] dimensions = grid.dimensions
+ * cdef np.ndarray[np.float64_t, ndim=4] fields = grid.fields
+ * cdef np.ndarray[np.float64_t, ndim=1] leftedges = grid.left_edges # <<<<<<<<<<<<<<
+ * cdef np.ndarray[np.float64_t, ndim=1] dx = grid.dx
+ * cdef np.ndarray[np.float64_t, ndim=1] child_dx
+ */
if (!(__Pyx_TypeTest(__pyx_v_grid->left_edges, __pyx_ptype_5numpy_ndarray))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = ((PyArrayObject *)__pyx_v_grid->left_edges);
if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t((PyObject*)__pyx_t_4, &__pyx_bstruct_leftedges, PyBUF_FORMAT| PyBUF_STRIDES, 1) == -1)) {
@@ -715,6 +879,14 @@
__pyx_t_4 = 0;
Py_INCREF(__pyx_v_grid->left_edges);
__pyx_v_leftedges = ((PyArrayObject *)__pyx_v_grid->left_edges);
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":71
+ * cdef np.ndarray[np.float64_t, ndim=4] fields = grid.fields
+ * cdef np.ndarray[np.float64_t, ndim=1] leftedges = grid.left_edges
+ * cdef np.ndarray[np.float64_t, ndim=1] dx = grid.dx # <<<<<<<<<<<<<<
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+ * cdef np.ndarray[np.float64_t, ndim=1] child_leftedges
+ */
if (!(__Pyx_TypeTest(__pyx_v_grid->dx, __pyx_ptype_5numpy_ndarray))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_v_grid->dx);
if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t((PyObject*)__pyx_t_5, &__pyx_bstruct_dx, PyBUF_FORMAT| PyBUF_STRIDES, 1) == -1)) {
@@ -726,26 +898,82 @@
__pyx_t_5 = 0;
Py_INCREF(__pyx_v_grid->dx);
__pyx_v_dx = ((PyArrayObject *)__pyx_v_grid->dx);
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":75
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+ */
__pyx_v_curpos->output_pos = __pyx_v_s;
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":76
+ * cdef position curpos
+ * curpos.output_pos = s
+ * curpos.refined_pos = r # <<<<<<<<<<<<<<
+ * for k in range(dimensions[2]):
+ * print k
+ */
__pyx_v_curpos->refined_pos = __pyx_v_r;
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":77
+ * curpos.output_pos = s
+ * curpos.refined_pos = r
+ * for k in range(dimensions[2]): # <<<<<<<<<<<<<<
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+ * for j in range(dimensions[1]):
+ */
__pyx_t_6 = 2;
if (__pyx_t_6 < 0) __pyx_t_6 += __pyx_bshape_0_dimensions;
__pyx_3 = *((__pyx_t_5numpy_int_t *)((__pyx_t_5numpy_int_t *)__Pyx_BufPtrStrided1d(__pyx_bstruct_dimensions.buf, __pyx_t_6, __pyx_bstride_0_dimensions)));
for (__pyx_v_k = 0; __pyx_v_k < __pyx_3; __pyx_v_k+=1) {
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__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_child_indices, &__pyx_bstruct_child_indices);
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__Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_child_indices, &__pyx_bstruct_child_indices);
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Py_XDECREF(__pyx_v_grid);
Py_XDECREF(__pyx_v_child_indices);
Py_XDECREF(__pyx_v_dimensions);
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Py_XDECREF(__pyx_v_leftedges);
Py_XDECREF(__pyx_v_dx);
Py_DECREF(__pyx_v_child_dx);
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return __pyx_r;
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static PyObject *__pyx_pf_2yt_5lagos_16DepthFirstOctree_RecurseOctree(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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int __pyx_v_i_i;
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int __pyx_v_k;
int __pyx_v_k_off;
int __pyx_v_ci;
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PyObject *__pyx_v_child_i;
PyObject *__pyx_v_child_j;
PyObject *__pyx_v_child_k;
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PyArrayObject *__pyx_v_dimensions = 0;
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PyArrayObject *__pyx_v_leftedges = 0;
PyArrayObject *__pyx_v_dx = 0;
PyArrayObject *__pyx_v_child_dx;
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Py_ssize_t __pyx_bshape_1_child_indices = 0;
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Py_ssize_t __pyx_bstride_0_output = 0;
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Py_ssize_t __pyx_bshape_0_output = 0;
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int __pyx_7;
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int __pyx_t_7;
int __pyx_t_8;
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long __pyx_t_20;
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+ long __pyx_t_22;
+ long __pyx_t_23;
+ long __pyx_t_24;
+ long __pyx_t_25;
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__pyx_v_curpos = ((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_position *)PyTuple_GET_ITEM(__pyx_args, 3));
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+ __pyx_v_pi = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 5)); if (unlikely((__pyx_v_pi == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ if (unlikely(!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "iiiOiiOOO", __pyx_argnames, &__pyx_v_i_i, &__pyx_v_j_i, &__pyx_v_k_i, &__pyx_v_curpos, &__pyx_v_gi, &__pyx_v_pi, &__pyx_v_output, &__pyx_v_refined, &__pyx_v_grids))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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goto __pyx_L4;
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@@ -1098,7 +1472,7 @@
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__pyx_bstruct_child_indices.buf = NULL;
__pyx_bstruct_dimensions.buf = NULL;
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__pyx_bstruct_leftedges.buf = NULL;
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__pyx_v_child_dx = ((PyArrayObject *)Py_None); Py_INCREF(Py_None);
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case NPY_ULONG:
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":64
+ * elif t == NPY_UINT: f = "I"
+ * elif t == NPY_LONG: f = "l"
+ * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<<
+ * elif t == NPY_LONGLONG: f = "q"
+ * elif t == NPY_ULONGLONG: f = "Q"
+ */
__pyx_v_f = __pyx_k_9;
break;
case NPY_LONGLONG:
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":65
+ * elif t == NPY_LONG: f = "l"
+ * elif t == NPY_ULONG: f = "L"
+ * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<<
+ * elif t == NPY_ULONGLONG: f = "Q"
+ * elif t == NPY_FLOAT: f = "f"
+ */
__pyx_v_f = __pyx_k_10;
break;
case NPY_ULONGLONG:
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":66
+ * elif t == NPY_ULONG: f = "L"
+ * elif t == NPY_LONGLONG: f = "q"
+ * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<<
+ * elif t == NPY_FLOAT: f = "f"
+ * elif t == NPY_DOUBLE: f = "d"
+ */
__pyx_v_f = __pyx_k_11;
break;
case NPY_FLOAT:
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":67
+ * elif t == NPY_LONGLONG: f = "q"
+ * elif t == NPY_ULONGLONG: f = "Q"
+ * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<<
+ * elif t == NPY_DOUBLE: f = "d"
+ * elif t == NPY_LONGDOUBLE: f = "g"
+ */
__pyx_v_f = __pyx_k_12;
break;
case NPY_DOUBLE:
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":68
+ * elif t == NPY_ULONGLONG: f = "Q"
+ * elif t == NPY_FLOAT: f = "f"
+ * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<<
+ * elif t == NPY_LONGDOUBLE: f = "g"
+ * elif t == NPY_OBJECT: f = "O"
+ */
__pyx_v_f = __pyx_k_13;
break;
case NPY_LONGDOUBLE:
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":69
+ * elif t == NPY_FLOAT: f = "f"
+ * elif t == NPY_DOUBLE: f = "d"
+ * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<<
+ * elif t == NPY_OBJECT: f = "O"
+ *
+ */
__pyx_v_f = __pyx_k_14;
break;
case NPY_OBJECT:
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":70
+ * elif t == NPY_DOUBLE: f = "d"
+ * elif t == NPY_LONGDOUBLE: f = "g"
+ * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<<
+ *
+ * if f == NULL:
+ */
__pyx_v_f = __pyx_k_15;
break;
}
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":72
+ * elif t == NPY_OBJECT: f = "O"
+ *
+ * if f == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError("only objects, int and float dtypes supported for ndarray buffer access so far (dtype is %d)" % t)
+ * info.format = f
+ */
__pyx_1 = (__pyx_v_f == NULL);
if (__pyx_1) {
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":73
+ *
+ * if f == NULL:
+ * raise ValueError("only objects, int and float dtypes supported for ndarray buffer access so far (dtype is %d)" % t) # <<<<<<<<<<<<<<
+ * info.format = f
+ *
+ */
__pyx_2 = PyInt_FromLong(__pyx_v_t); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_3 = PyNumber_Remainder(__pyx_kp_16, __pyx_2); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
Py_DECREF(__pyx_2); __pyx_2 = 0;
@@ -1518,6 +2345,14 @@
goto __pyx_L6;
}
__pyx_L6:;
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":74
+ * if f == NULL:
+ * raise ValueError("only objects, int and float dtypes supported for ndarray buffer access so far (dtype is %d)" % t)
+ * info.format = f # <<<<<<<<<<<<<<
+ *
+ *
+ */
__pyx_v_info->format = __pyx_v_f;
__pyx_r = 0;
@@ -1699,7 +2534,7 @@
if (!o) return 0;
p = ((struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)o);
p->child_indices = Py_None; Py_INCREF(Py_None);
- p->field = Py_None; Py_INCREF(Py_None);
+ p->fields = Py_None; Py_INCREF(Py_None);
p->left_edges = Py_None; Py_INCREF(Py_None);
p->dimensions = Py_None; Py_INCREF(Py_None);
p->dx = Py_None; Py_INCREF(Py_None);
@@ -1712,7 +2547,7 @@
static void __pyx_tp_dealloc_2yt_5lagos_16DepthFirstOctree_OctreeGrid(PyObject *o) {
struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *p = (struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid *)o;
Py_XDECREF(p->child_indices);
- Py_XDECREF(p->field);
+ Py_XDECREF(p->fields);
Py_XDECREF(p->left_edges);
Py_XDECREF(p->dimensions);
Py_XDECREF(p->dx);
@@ -1725,8 +2560,8 @@
if (p->child_indices) {
e = (*v)(p->child_indices, a); if (e) return e;
}
- if (p->field) {
- e = (*v)(p->field, a); if (e) return e;
+ if (p->fields) {
+ e = (*v)(p->fields, a); if (e) return e;
}
if (p->left_edges) {
e = (*v)(p->left_edges, a); if (e) return e;
@@ -1746,8 +2581,8 @@
tmp = ((PyObject*)p->child_indices);
p->child_indices = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
- tmp = ((PyObject*)p->field);
- p->field = Py_None; Py_INCREF(Py_None);
+ tmp = ((PyObject*)p->fields);
+ p->fields = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->left_edges);
p->left_edges = Py_None; Py_INCREF(Py_None);
@@ -1767,7 +2602,7 @@
static struct PyMemberDef __pyx_members_2yt_5lagos_16DepthFirstOctree_OctreeGrid[] = {
{"child_indices", T_OBJECT, offsetof(struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid, child_indices), 0, 0},
- {"field", T_OBJECT, offsetof(struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid, field), 0, 0},
+ {"fields", T_OBJECT, offsetof(struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid, fields), 0, 0},
{"left_edges", T_OBJECT, offsetof(struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid, left_edges), 0, 0},
{"dimensions", T_OBJECT, offsetof(struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid, dimensions), 0, 0},
{"dx", T_OBJECT, offsetof(struct __pyx_obj_2yt_5lagos_16DepthFirstOctree_OctreeGrid, dx), 0, 0},
@@ -2207,9 +3042,25 @@
__pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject)); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Function import code ---*/
/*--- Execution code ---*/
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/DepthFirstOctree.pyx":26
+ * """
+ *
+ * import numpy as np # <<<<<<<<<<<<<<
+ * cimport numpy as np
+ * cimport cython
+ */
__pyx_1 = __Pyx_Import(__pyx_kp_numpy, 0); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyObject_SetAttr(__pyx_m, __pyx_kp_np, __pyx_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
Py_DECREF(__pyx_1); __pyx_1 = 0;
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":36
+ * # experimental exception made for __getbuffer__ and __releasebuffer__
+ * # -- the details of this may change.
+ * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
+ * # This implementation of getbuffer is geared towards Cython
+ * # requirements, and does not yet fullfill the PEP (specifically,
+ */
#if PY_MAJOR_VERSION < 3
return;
#else
Modified: trunk/yt/lagos/DepthFirstOctree.pyx
==============================================================================
--- trunk/yt/lagos/DepthFirstOctree.pyx (original)
+++ trunk/yt/lagos/DepthFirstOctree.pyx Mon Sep 22 08:35:20 2008
@@ -31,15 +31,15 @@
cdef public int output_pos, refined_pos
cdef class OctreeGrid:
- cdef public object child_indices, field, left_edges, dimensions, dx
+ cdef public object child_indices, fields, left_edges, dimensions, dx
def __cinit__(self,
np.ndarray[np.int_t, ndim=3] child_indices,
- np.ndarray[np.float64_t, ndim=3] field,
+ np.ndarray[np.float64_t, ndim=4] fields,
np.ndarray[np.float64_t, ndim=1] left_edges,
np.ndarray[np.int_t, ndim=1] dimensions,
np.ndarray[np.float64_t, ndim=1] dx):
self.child_indices = child_indices
- self.field = field
+ self.fields = fields
self.left_edges = left_edges
self.dimensions = dimensions
self.dx = dx
@@ -53,20 +53,20 @@
return self.grids[item]
@cython.boundscheck(False)
-def WalkRootgrid(np.ndarray[np.float64_t, ndim=1] output,
+def WalkRootgrid(np.ndarray[np.float64_t, ndim=2] output,
np.ndarray[np.int_t, ndim=1] refined,
OctreeGridList grids, int pi, int s = 0, int r = 0):
"""
This function only gets called on a 'root grid' -- a base grid
of the simulation we are converting. It will call a recursive walker.
"""
- cdef int i, j, k, gi
+ cdef int i, j, k, gi, fi
cdef int child_i, child_j, child_k
cdef OctreeGrid child_grid
cdef OctreeGrid grid = grids[pi-1]
cdef np.ndarray[np.int_t, ndim=3] child_indices = grid.child_indices
cdef np.ndarray[np.int_t, ndim=1] dimensions = grid.dimensions
- cdef np.ndarray[np.float64_t, ndim=3] field = grid.field
+ cdef np.ndarray[np.float64_t, ndim=4] fields = grid.fields
cdef np.ndarray[np.float64_t, ndim=1] leftedges = grid.left_edges
cdef np.ndarray[np.float64_t, ndim=1] dx = grid.dx
cdef np.ndarray[np.float64_t, ndim=1] child_dx
@@ -80,7 +80,8 @@
for i in range(dimensions[0]):
gi = child_indices[i,j,k]
if gi == -1:
- output[curpos.output_pos] = field[i,j,k]
+ for fi in range(fields.shape[0]):
+ output[curpos.output_pos,fi] = fields[fi,i,j,k]
refined[curpos.refined_pos] = 0
curpos.output_pos += 1
curpos.refined_pos += 1
@@ -98,16 +99,16 @@
@cython.boundscheck(False)
def RecurseOctree(int i_i, int j_i, int k_i,
position curpos, int gi, int pi,
- np.ndarray[np.float64_t, ndim=1] output,
+ np.ndarray[np.float64_t, ndim=2] output,
np.ndarray[np.int_t, ndim=1] refined,
OctreeGridList grids):
- cdef int i, i_off, j, j_off, k, k_off, ci
+ cdef int i, i_off, j, j_off, k, k_off, ci, fi
cdef child_i, child_j, child_k
cdef OctreeGrid child_grid
cdef OctreeGrid grid = grids[gi-1]
cdef np.ndarray[np.int_t, ndim=3] child_indices = grid.child_indices
cdef np.ndarray[np.int_t, ndim=1] dimensions = grid.dimensions
- cdef np.ndarray[np.float64_t, ndim=3] field = grid.field
+ cdef np.ndarray[np.float64_t, ndim=4] fields = grid.fields
cdef np.ndarray[np.float64_t, ndim=1] leftedges = grid.left_edges
cdef np.ndarray[np.float64_t, ndim=1] dx = grid.dx
cdef np.ndarray[np.float64_t, ndim=1] child_dx
@@ -121,7 +122,8 @@
i = i_off + i_i
ci = grid.child_indices[i,j,k]
if ci == -1:
- output[curpos.output_pos] = grid.field[i,j,k]
+ for fi in range(fields.shape[0]):
+ output[curpos.output_pos,fi] = fields[fi,i,j,k]
refined[curpos.refined_pos] = 0
curpos.output_pos += 1
curpos.refined_pos += 1
Modified: trunk/yt/lagos/HierarchyType.py
==============================================================================
--- trunk/yt/lagos/HierarchyType.py (original)
+++ trunk/yt/lagos/HierarchyType.py Mon Sep 22 08:35:20 2008
@@ -179,7 +179,8 @@
self.smoothed_covering_grid = classobj("EnzoSmoothedCoveringGrid",(EnzoSmoothedCoveringGrid,), dd)
self.sphere = classobj("EnzoSphere",(EnzoSphereBase,), dd)
self.cutting = classobj("EnzoCuttingPlane",(EnzoCuttingPlaneBase,), dd)
- self.ray = classobj("EnzoOrthoRay",(EnzoOrthoRayBase,), dd)
+ self.ray = classobj("EnzoRay",(EnzoRayBase,), dd)
+ self.ortho_ray = classobj("EnzoOrthoRay",(EnzoOrthoRayBase,), dd)
self.disk = classobj("EnzoCylinder",(EnzoCylinderBase,), dd)
self.grid_collection = classobj("EnzoGridCollection",(EnzoGridCollection,), dd)
@@ -752,7 +753,7 @@
f.close()
mylog.info("Wrote %s particles to %s", tot, filename)
- def _generate_flat_octree(self, field):
+ def _generate_flat_octree(self, fields):
"""
Generates two arrays, one of the actual values in a depth-first flat
octree array, and the other of the values describing the refinement.
@@ -760,18 +761,21 @@
field used in the data array.
"""
import DepthFirstOctree as dfo
+ fields = ensure_list(fields)
o_length = r_length = 0
grids = []
for g in self.grids:
+ ff = na.array([g[f] for f in fields])
grids.append(dfo.OctreeGrid(
g.child_index_mask,
- g[field].astype("float64"),
+ ff.astype("float64"),
g.LeftEdge.astype('float64'),
g.ActiveDimensions.astype('int'),
na.ones(1,dtype='float64') * g.dx))
o_length += g.child_mask.ravel().sum()
r_length += g.ActiveDimensions.prod()
- output = na.zeros(o_length, dtype='float64')
+ g.clear_data()
+ output = na.zeros((o_length,len(fields)), dtype='float64')
refined = na.zeros(r_length, dtype='int')
ogl = dfo.OctreeGridList(grids)
dfo.WalkRootgrid(output, refined, ogl, 1, 0)
Modified: trunk/yt/lagos/RTIntegrator.c
==============================================================================
--- trunk/yt/lagos/RTIntegrator.c (original)
+++ trunk/yt/lagos/RTIntegrator.c Mon Sep 22 08:35:20 2008
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.9.8.1.1 on Thu Sep 4 08:25:13 2008 */
+/* Generated by Cython 0.9.8.1.1 on Mon Sep 22 17:29:14 2008 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -174,6 +174,8 @@
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;
static const char **__pyx_f;
+
+static char __pyx_mdoc[] = "\nSimle integrators for the radiative transfer equation\n\nAuthor: Matthew Turk <matthewturk at gmail.com>\nAffiliation: KIPAC/SLAC/Stanford\nHomepage: http://yt.enzotools.org/\nLicense:\n Copyright (C) 2008 Matthew Turk. All Rights Reserved.\n\n This file is part of yt.\n\n yt is free software; you can redistribute it and/or modify\n it under the terms of the GNU General Public License as published by\n the Free Software Foundation; either version 3 of the License, or\n (at your option) any later version.\n\n This program is distributed in the hope that it will be useful,\n but WITHOUT ANY WARRANTY; without even the implied warranty of\n MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n GNU General Public License for more details.\n\n You should have received a copy of the GNU General Public License\n along with this program. If not, see <http://www.gnu.org/licenses/>.\n";
static INLINE void __Pyx_SafeReleaseBuffer(PyObject* obj, Py_buffer* info);
static INLINE void __Pyx_ZeroBuffer(Py_buffer* buf); /*proto*/
static INLINE const char* __Pyx_ConsumeWhitespace(const char* ts); /*proto*/
@@ -185,6 +187,12 @@
#define __Pyx_BufPtrStrided2d(buf, i0, s0, i1, s1) ((char*)buf + i0 * s0 + i1 * s1)
#define __Pyx_BufPtrStrided3d(buf, i0, s0, i1, s1, i2, s2) ((char*)buf + i0 * s0 + i1 * s1 + i2 * s2)
#define __Pyx_BufPtrStrided1d(buf, i0, s0) ((char*)buf + i0 * s0)
+static const char* __Pyx_BufferTypestringCheck_item_nn___pyx_t_5numpy_int_t(const char* ts); /*proto*/
+
+static int __Pyx_GetBuffer_nn___pyx_t_5numpy_int_t(PyObject* obj, Py_buffer* buf, int flags, int nd); /*proto*/
+static const char* __Pyx_BufferTypestringCheck_item_nn___pyx_t_5numpy_float64_t(const char* ts); /*proto*/
+
+static int __Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t(PyObject* obj, Py_buffer* buf, int flags, int nd); /*proto*/
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, char *name, int exact); /*proto*/
@@ -204,6 +212,50 @@
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+static int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
+
+static INLINE int __Pyx_SetItemInt(PyObject *o, Py_ssize_t i, PyObject *v, int is_unsigned) {
+ int r;
+ if (PyList_CheckExact(o) && 0 <= i && i < PyList_GET_SIZE(o)) {
+ Py_DECREF(PyList_GET_ITEM(o, i));
+ Py_INCREF(v);
+ PyList_SET_ITEM(o, i, v);
+ return 1;
+ }
+ else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_ass_item && (likely(i >= 0) || !is_unsigned))
+ r = PySequence_SetItem(o, i, v);
+ else {
+ PyObject *j = (likely(i >= 0) || !is_unsigned) ? PyInt_FromLong(i) : PyLong_FromUnsignedLongLong((sizeof(unsigned long long) > sizeof(Py_ssize_t) ? (1ULL << (sizeof(Py_ssize_t)*8)) : 0) + i);
+ if (!j)
+ return -1;
+ r = PyObject_SetItem(o, j, v);
+ Py_DECREF(j);
+ }
+ return r;
+}
+
+static INLINE PyObject *__Pyx_GetItemInt(PyObject *o, Py_ssize_t i, int is_unsigned) {
+ PyObject *r;
+ if (PyList_CheckExact(o) && 0 <= i && i < PyList_GET_SIZE(o)) {
+ r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ }
+ else if (PyTuple_CheckExact(o) && 0 <= i && i < PyTuple_GET_SIZE(o)) {
+ r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ }
+ else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0) || !is_unsigned))
+ r = PySequence_GetItem(o, i);
+ else {
+ PyObject *j = (likely(i >= 0) || !is_unsigned) ? PyInt_FromLong(i) : PyLong_FromUnsignedLongLong((sizeof(unsigned long long) > sizeof(Py_ssize_t) ? (1ULL << (sizeof(Py_ssize_t)*8)) : 0) + i);
+ if (!j)
+ return 0;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ }
+ return r;
+}
+
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static PyTypeObject *__Pyx_ImportType(char *module_name, char *class_name, long size); /*proto*/
@@ -261,10 +313,26 @@
/* Implementation of yt.lagos.RTIntegrator */
+static PyObject *__pyx_int_3;
+static PyObject *__pyx_int_neg_1;
+static PyObject *__pyx_int_0;
+static PyObject *__pyx_int_1;
static char __pyx_k_numpy[] = "numpy";
static PyObject *__pyx_kp_numpy;
static char __pyx_k_np[] = "np";
static PyObject *__pyx_kp_np;
+static char __pyx_k_ones[] = "ones";
+static PyObject *__pyx_kp_ones;
+static char __pyx_k_dtype[] = "dtype";
+static PyObject *__pyx_kp_dtype;
+static char __pyx_k_17[] = "float64";
+static PyObject *__pyx_kp_17;
+static char __pyx_k_zeros[] = "zeros";
+static PyObject *__pyx_kp_zeros;
+static char __pyx_k_18[] = "int64";
+static PyObject *__pyx_kp_18;
+static char __pyx_k_floor[] = "floor";
+static PyObject *__pyx_kp_floor;
static char __pyx_k___getbuffer__[] = "__getbuffer__";
static PyObject *__pyx_kp___getbuffer__;
static char __pyx_k_RuntimeError[] = "RuntimeError";
@@ -292,7 +360,7 @@
static char __pyx_k_15[] = "O";
static char __pyx_k_16[] = "only objects, int and float dtypes supported for ndarray buffer access so far (dtype is %d)";
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+/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":31
*
* @cython.boundscheck(False)
* def Transfer3D(np.ndarray[np.float_t, ndim=2] i_s, # <<<<<<<<<<<<<<
@@ -377,42 +445,42 @@
__pyx_v_o_s = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 1));
__pyx_v_e = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 2));
__pyx_v_a = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 3));
- __pyx_v_imin = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 4)); if (unlikely((__pyx_v_imin == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_imax = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 5)); if (unlikely((__pyx_v_imax == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_jmin = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 6)); if (unlikely((__pyx_v_jmin == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_jmax = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 7)); if (unlikely((__pyx_v_jmax == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_kmin = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 8)); if (unlikely((__pyx_v_kmin == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_kmax = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 9)); if (unlikely((__pyx_v_kmax == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_istride = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 10)); if (unlikely((__pyx_v_istride == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_jstride = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 11)); if (unlikely((__pyx_v_jstride == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_dx = __pyx_PyFloat_AsDouble(PyTuple_GET_ITEM(__pyx_args, 12)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_imin = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 4)); if (unlikely((__pyx_v_imin == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_imax = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 5)); if (unlikely((__pyx_v_imax == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_jmin = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 6)); if (unlikely((__pyx_v_jmin == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_jmax = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 7)); if (unlikely((__pyx_v_jmax == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_kmin = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 8)); if (unlikely((__pyx_v_kmin == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_kmax = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 9)); if (unlikely((__pyx_v_kmax == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_istride = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 10)); if (unlikely((__pyx_v_istride == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_jstride = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 11)); if (unlikely((__pyx_v_jstride == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_dx = __pyx_PyFloat_AsDouble(PyTuple_GET_ITEM(__pyx_args, 12)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
else {
- if (unlikely(!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "OOOOiiiiiiiif", __pyx_argnames, &__pyx_v_i_s, &__pyx_v_o_s, &__pyx_v_e, &__pyx_v_a, &__pyx_v_imin, &__pyx_v_imax, &__pyx_v_jmin, &__pyx_v_jmax, &__pyx_v_kmin, &__pyx_v_kmax, &__pyx_v_istride, &__pyx_v_jstride, &__pyx_v_dx))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "OOOOiiiiiiiif", __pyx_argnames, &__pyx_v_i_s, &__pyx_v_o_s, &__pyx_v_e, &__pyx_v_a, &__pyx_v_imin, &__pyx_v_imax, &__pyx_v_jmin, &__pyx_v_jmax, &__pyx_v_kmin, &__pyx_v_kmax, &__pyx_v_istride, &__pyx_v_jstride, &__pyx_v_dx))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
goto __pyx_L4;
__pyx_L3_error:;
__Pyx_AddTraceback("yt.lagos.RTIntegrator.Transfer3D");
return NULL;
__pyx_L4:;
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- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_o_s), __pyx_ptype_5numpy_ndarray, 1, "o_s", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_e), __pyx_ptype_5numpy_ndarray, 1, "e", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_a), __pyx_ptype_5numpy_ndarray, 1, "a", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_i_s, &__pyx_bstruct_i_s, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 2) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_i_s), __pyx_ptype_5numpy_ndarray, 1, "i_s", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_o_s), __pyx_ptype_5numpy_ndarray, 1, "o_s", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_e), __pyx_ptype_5numpy_ndarray, 1, "e", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_a), __pyx_ptype_5numpy_ndarray, 1, "a", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_i_s, &__pyx_bstruct_i_s, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 2) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_i_s = __pyx_bstruct_i_s.strides[0]; __pyx_bstride_1_i_s = __pyx_bstruct_i_s.strides[1];
__pyx_bshape_0_i_s = __pyx_bstruct_i_s.shape[0]; __pyx_bshape_1_i_s = __pyx_bstruct_i_s.shape[1];
- if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_o_s, &__pyx_bstruct_o_s, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 3) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_o_s, &__pyx_bstruct_o_s, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 3) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_o_s = __pyx_bstruct_o_s.strides[0]; __pyx_bstride_1_o_s = __pyx_bstruct_o_s.strides[1]; __pyx_bstride_2_o_s = __pyx_bstruct_o_s.strides[2];
__pyx_bshape_0_o_s = __pyx_bstruct_o_s.shape[0]; __pyx_bshape_1_o_s = __pyx_bstruct_o_s.shape[1]; __pyx_bshape_2_o_s = __pyx_bstruct_o_s.shape[2];
- if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_e, &__pyx_bstruct_e, PyBUF_FORMAT| PyBUF_STRIDES, 3) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_e, &__pyx_bstruct_e, PyBUF_FORMAT| PyBUF_STRIDES, 3) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_e = __pyx_bstruct_e.strides[0]; __pyx_bstride_1_e = __pyx_bstruct_e.strides[1]; __pyx_bstride_2_e = __pyx_bstruct_e.strides[2];
__pyx_bshape_0_e = __pyx_bstruct_e.shape[0]; __pyx_bshape_1_e = __pyx_bstruct_e.shape[1]; __pyx_bshape_2_e = __pyx_bstruct_e.shape[2];
- if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_a, &__pyx_bstruct_a, PyBUF_FORMAT| PyBUF_STRIDES, 3) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_a, &__pyx_bstruct_a, PyBUF_FORMAT| PyBUF_STRIDES, 3) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_a = __pyx_bstruct_a.strides[0]; __pyx_bstride_1_a = __pyx_bstruct_a.strides[1]; __pyx_bstride_2_a = __pyx_bstruct_a.strides[2];
__pyx_bshape_0_a = __pyx_bstruct_a.shape[0]; __pyx_bshape_1_a = __pyx_bstruct_a.shape[1]; __pyx_bshape_2_a = __pyx_bstruct_a.shape[2];
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":25
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":50
* cdef int k, kk
* cdef float temp
* for i in range((imax-imin)*istride): # <<<<<<<<<<<<<<
@@ -422,7 +490,7 @@
__pyx_1 = ((__pyx_v_imax - __pyx_v_imin) * __pyx_v_istride);
for (__pyx_v_i = 0; __pyx_v_i < __pyx_1; __pyx_v_i+=1) {
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":26
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":51
* cdef float temp
* for i in range((imax-imin)*istride):
* ii = i + imin*istride # <<<<<<<<<<<<<<
@@ -431,7 +499,7 @@
*/
__pyx_v_ii = (__pyx_v_i + (__pyx_v_imin * __pyx_v_istride));
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":27
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":52
* for i in range((imax-imin)*istride):
* ii = i + imin*istride
* for j in range((jmax-jmin)*jstride): # <<<<<<<<<<<<<<
@@ -441,7 +509,7 @@
__pyx_2 = ((__pyx_v_jmax - __pyx_v_jmin) * __pyx_v_jstride);
for (__pyx_v_j = 0; __pyx_v_j < __pyx_2; __pyx_v_j+=1) {
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":28
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":53
* ii = i + imin*istride
* for j in range((jmax-jmin)*jstride):
* jj = j + jmin*jstride # <<<<<<<<<<<<<<
@@ -450,7 +518,7 @@
*/
__pyx_v_jj = (__pyx_v_j + (__pyx_v_jmin * __pyx_v_jstride));
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":29
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":54
* for j in range((jmax-jmin)*jstride):
* jj = j + jmin*jstride
* temp = i_s[ii,jj] # <<<<<<<<<<<<<<
@@ -464,7 +532,7 @@
__pyx_3 = *((__pyx_t_5numpy_float_t *)((__pyx_t_5numpy_float_t *)__Pyx_BufPtrStrided2d(__pyx_bstruct_i_s.buf, __pyx_t_1, __pyx_bstride_0_i_s, __pyx_t_2, __pyx_bstride_1_i_s)));
__pyx_v_temp = __pyx_3;
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":30
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":55
* jj = j + jmin*jstride
* temp = i_s[ii,jj]
* for k in range(kmax-kmin): # <<<<<<<<<<<<<<
@@ -474,7 +542,7 @@
__pyx_4 = (__pyx_v_kmax - __pyx_v_kmin);
for (__pyx_v_k = 0; __pyx_v_k < __pyx_4; __pyx_v_k+=1) {
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":31
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":56
* temp = i_s[ii,jj]
* for k in range(kmax-kmin):
* o_s[i,j,k] = temp + dx*(e[i,j,k] - temp*a[i,j,k]) # <<<<<<<<<<<<<<
@@ -503,7 +571,7 @@
if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_bshape_2_o_s;
*((__pyx_t_5numpy_float_t *)__Pyx_BufPtrStrided3d(__pyx_bstruct_o_s.buf, __pyx_t_9, __pyx_bstride_0_o_s, __pyx_t_10, __pyx_bstride_1_o_s, __pyx_t_11, __pyx_bstride_2_o_s)) = (__pyx_v_temp + (__pyx_v_dx * (__pyx_3 - (__pyx_v_temp * __pyx_5))));
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":32
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":57
* for k in range(kmax-kmin):
* o_s[i,j,k] = temp + dx*(e[i,j,k] - temp*a[i,j,k])
* temp = o_s[i,j,k] # <<<<<<<<<<<<<<
@@ -520,7 +588,7 @@
__pyx_v_temp = __pyx_3;
}
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":33
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":58
* o_s[i,j,k] = temp + dx*(e[i,j,k] - temp*a[i,j,k])
* temp = o_s[i,j,k]
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@@ -557,7 +625,7 @@
return __pyx_r;
}
-/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":36
+/* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":61
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* def Transfer1D(float i_s, # <<<<<<<<<<<<<<
@@ -600,40 +668,40 @@
static char *__pyx_argnames[] = {"i_s","o_s","e","a","dx","imin","imax",0};
__pyx_self = __pyx_self;
if (likely(!__pyx_kwds) && likely(PyTuple_GET_SIZE(__pyx_args) == 7)) {
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+ __pyx_v_i_s = __pyx_PyFloat_AsDouble(PyTuple_GET_ITEM(__pyx_args, 0)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_v_o_s = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 1));
__pyx_v_e = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 2));
__pyx_v_a = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 3));
__pyx_v_dx = ((PyArrayObject *)PyTuple_GET_ITEM(__pyx_args, 4));
- __pyx_v_imin = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 5)); if (unlikely((__pyx_v_imin == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_imax = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 6)); if (unlikely((__pyx_v_imax == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_imin = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 5)); if (unlikely((__pyx_v_imin == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_imax = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 6)); if (unlikely((__pyx_v_imax == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
else {
- if (unlikely(!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "fOOOOii", __pyx_argnames, &__pyx_v_i_s, &__pyx_v_o_s, &__pyx_v_e, &__pyx_v_a, &__pyx_v_dx, &__pyx_v_imin, &__pyx_v_imax))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "fOOOOii", __pyx_argnames, &__pyx_v_i_s, &__pyx_v_o_s, &__pyx_v_e, &__pyx_v_a, &__pyx_v_dx, &__pyx_v_imin, &__pyx_v_imax))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
goto __pyx_L4;
__pyx_L3_error:;
__Pyx_AddTraceback("yt.lagos.RTIntegrator.Transfer1D");
return NULL;
__pyx_L4:;
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_o_s), __pyx_ptype_5numpy_ndarray, 1, "o_s", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_e), __pyx_ptype_5numpy_ndarray, 1, "e", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_a), __pyx_ptype_5numpy_ndarray, 1, "a", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_bstride_0_o_s = __pyx_bstruct_o_s.strides[0];
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+ if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_e, &__pyx_bstruct_e, PyBUF_FORMAT| PyBUF_STRIDES, 1) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_e = __pyx_bstruct_e.strides[0];
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+ if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_a, &__pyx_bstruct_a, PyBUF_FORMAT| PyBUF_STRIDES, 1) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_bstride_0_a = __pyx_bstruct_a.strides[0];
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+ if (unlikely(__Pyx_GetBuffer_nn___pyx_t_5numpy_float_t((PyObject*)__pyx_v_dx, &__pyx_bstruct_dx, PyBUF_FORMAT| PyBUF_STRIDES, 1) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_bshape_0_dx = __pyx_bstruct_dx.shape[0];
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+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":68
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*/
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- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":44
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":69
* cdef int i
* for i in range(imin, imax):
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@@ -662,11 +730,12 @@
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+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":70
* for i in range(imin, imax):
* o_s[i] = i_s + dx[i]*(e[i] - i_s*a[i])
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*/
__pyx_t_5 = __pyx_v_i;
if (__pyx_t_5 < 0) __pyx_t_5 += __pyx_bshape_0_o_s;
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__pyx_v_i_s = __pyx_1;
}
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":46
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*/
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__pyx_r = __pyx_4;
__pyx_4 = 0;
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+ if (__Pyx_SetItemInt(((PyObject *)__pyx_v_tmax), 1, __pyx_2, 0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_2); __pyx_2 = 0;
+ goto __pyx_L21;
+ }
+ /*else*/ {
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":138
+ * tmax[1] += tdelta[1]
+ * else:
+ * cur_ind[2] += step[2] # <<<<<<<<<<<<<<
+ * tmax[2] += tdelta[2]
+ * return
+ */
+ __pyx_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_step), 2, 0); if (!__pyx_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_4 = __Pyx_GetItemInt(((PyObject *)__pyx_v_cur_ind), 2, 0); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_3 = PyNumber_InPlaceAdd(__pyx_4, __pyx_5); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_5); __pyx_5 = 0;
+ Py_DECREF(__pyx_4); __pyx_4 = 0;
+ if (__Pyx_SetItemInt(((PyObject *)__pyx_v_cur_ind), 2, __pyx_3, 0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_3); __pyx_3 = 0;
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":139
+ * else:
+ * cur_ind[2] += step[2]
+ * tmax[2] += tdelta[2] # <<<<<<<<<<<<<<
+ * return
+ */
+ __pyx_2 = __Pyx_GetItemInt(((PyObject *)__pyx_v_tdelta), 2, 0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_tmax), 2, 0); if (!__pyx_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_1 = PyNumber_InPlaceAdd(__pyx_5, __pyx_2); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_2); __pyx_2 = 0;
+ Py_DECREF(__pyx_5); __pyx_5 = 0;
+ if (__Pyx_SetItemInt(((PyObject *)__pyx_v_tmax), 2, __pyx_1, 0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_1); __pyx_1 = 0;
+ }
+ __pyx_L21:;
+ }
+ __pyx_L19:;
+ }
+ __pyx_L17:;
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":140
+ * cur_ind[2] += step[2]
+ * tmax[2] += tdelta[2]
+ * return # <<<<<<<<<<<<<<
+ */
+ __pyx_r = Py_None; Py_INCREF(Py_None);
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; Py_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ Py_XDECREF(__pyx_1);
+ Py_XDECREF(__pyx_2);
+ Py_XDECREF(__pyx_3);
+ Py_XDECREF(__pyx_4);
+ Py_XDECREF(__pyx_5);
+ { PyObject *__pyx_type, *__pyx_value, *__pyx_tb;
+ PyErr_Fetch(&__pyx_type, &__pyx_value, &__pyx_tb);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_right_edge, &__pyx_bstruct_right_edge);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_grid_mask, &__pyx_bstruct_grid_mask);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_u, &__pyx_bstruct_u);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_dx, &__pyx_bstruct_dx);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_v, &__pyx_bstruct_v);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_left_edge, &__pyx_bstruct_left_edge);
+ PyErr_Restore(__pyx_type, __pyx_value, __pyx_tb);}
+ __Pyx_AddTraceback("yt.lagos.RTIntegrator.VoxelTraversal");
+ __pyx_r = NULL;
+ goto __pyx_L2;
+ __pyx_L0:;
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_right_edge, &__pyx_bstruct_right_edge);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_grid_mask, &__pyx_bstruct_grid_mask);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_u, &__pyx_bstruct_u);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_dx, &__pyx_bstruct_dx);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_v, &__pyx_bstruct_v);
+ __Pyx_SafeReleaseBuffer((PyObject*)__pyx_v_left_edge, &__pyx_bstruct_left_edge);
+ __pyx_L2:;
+ Py_XDECREF(__pyx_v_step);
+ Py_XDECREF(__pyx_v_cur_ind);
+ Py_XDECREF(__pyx_v_tdelta);
+ Py_XDECREF(__pyx_v_tmax);
+ return __pyx_r;
+}
+
/* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":36
* # experimental exception made for __getbuffer__ and __releasebuffer__
* # -- the details of this may change.
@@ -1045,6 +2175,7 @@
static struct PyMethodDef __pyx_methods[] = {
{"Transfer3D", (PyCFunction)__pyx_pf_2yt_5lagos_12RTIntegrator_Transfer3D, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2yt_5lagos_12RTIntegrator_Transfer3D},
{"Transfer1D", (PyCFunction)__pyx_pf_2yt_5lagos_12RTIntegrator_Transfer1D, METH_VARARGS|METH_KEYWORDS, 0},
+ {"VoxelTraversal", (PyCFunction)__pyx_pf_2yt_5lagos_12RTIntegrator_VoxelTraversal, METH_VARARGS|METH_KEYWORDS, 0},
{0, 0, 0, 0}
};
@@ -1054,7 +2185,7 @@
static struct PyModuleDef __pyx_moduledef = {
PyModuleDef_HEAD_INIT,
"RTIntegrator",
- 0, /* m_doc */
+ __pyx_mdoc, /* m_doc */
-1, /* m_size */
__pyx_methods /* m_methods */,
NULL, /* m_reload */
@@ -1067,6 +2198,12 @@
static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 1, 1, 1},
{&__pyx_kp_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 1, 1},
+ {&__pyx_kp_ones, __pyx_k_ones, sizeof(__pyx_k_ones), 1, 1, 1},
+ {&__pyx_kp_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 1, 1, 1},
+ {&__pyx_kp_17, __pyx_k_17, sizeof(__pyx_k_17), 1, 1, 1},
+ {&__pyx_kp_zeros, __pyx_k_zeros, sizeof(__pyx_k_zeros), 1, 1, 1},
+ {&__pyx_kp_18, __pyx_k_18, sizeof(__pyx_k_18), 1, 1, 1},
+ {&__pyx_kp_floor, __pyx_k_floor, sizeof(__pyx_k_floor), 1, 1, 1},
{&__pyx_kp___getbuffer__, __pyx_k___getbuffer__, sizeof(__pyx_k___getbuffer__), 0, 1, 1},
{&__pyx_kp_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 1, 1, 1},
{&__pyx_kp_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 1, 1, 1},
@@ -1083,6 +2220,10 @@
}
static int __Pyx_InitGlobals(void) {
+ __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
return 0;
__pyx_L1_error:;
@@ -1105,7 +2246,7 @@
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4("RTIntegrator", __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ __pyx_m = Py_InitModule4("RTIntegrator", __pyx_methods, __pyx_mdoc, 0, PYTHON_API_VERSION);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
@@ -1127,13 +2268,15 @@
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":1
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":26
+ * """
+ *
* import numpy as np # <<<<<<<<<<<<<<
* cimport numpy as np
* cimport cython
*/
- __pyx_1 = __Pyx_Import(__pyx_kp_numpy, 0); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttr(__pyx_m, __pyx_kp_np, __pyx_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_1 = __Pyx_Import(__pyx_kp_numpy, 0); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_kp_np, __pyx_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
Py_DECREF(__pyx_1); __pyx_1 = 0;
/* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":36
@@ -1271,6 +2414,100 @@
__Pyx_ZeroBuffer(buf);
return -1;
}
+static const char* __Pyx_BufferTypestringCheck_item_nn___pyx_t_5numpy_int_t(const char* ts) {
+ int ok;
+ if (*ts == '1') ++ts;
+ switch (*ts) {
+ case 'b': ok = (sizeof(__pyx_t_5numpy_int_t) == sizeof(char) && (__pyx_t_5numpy_int_t)-1 < 0); break;
+ case 'h': ok = (sizeof(__pyx_t_5numpy_int_t) == sizeof(short) && (__pyx_t_5numpy_int_t)-1 < 0); break;
+ case 'i': ok = (sizeof(__pyx_t_5numpy_int_t) == sizeof(int) && (__pyx_t_5numpy_int_t)-1 < 0); break;
+ case 'l': ok = (sizeof(__pyx_t_5numpy_int_t) == sizeof(long) && (__pyx_t_5numpy_int_t)-1 < 0); break;
+ case 'q': ok = (sizeof(__pyx_t_5numpy_int_t) == sizeof(long long) && (__pyx_t_5numpy_int_t)-1 < 0); break; default: ok = 0;
+ }
+ if (!ok) {
+ PyErr_Format(PyExc_ValueError, "Buffer datatype mismatch (rejecting on '%s')", ts);
+ return NULL;
+ } else return ts + 1;
+
+}
+
+static int __Pyx_GetBuffer_nn___pyx_t_5numpy_int_t(PyObject* obj, Py_buffer* buf, int flags, int nd) {
+ const char* ts;
+ if (obj == Py_None) {
+ __Pyx_ZeroBuffer(buf);
+ return 0;
+ }
+ buf->buf = NULL;
+ if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail;
+ if (buf->ndim != nd) {
+ __Pyx_BufferNdimError(buf, nd);
+ goto fail;
+ }
+ ts = buf->format;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheckEndian(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheck_item_nn___pyx_t_5numpy_int_t(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ if (*ts != 0) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected non-struct buffer data type (expected end, got '%s')", ts);
+ goto fail;
+ }
+ if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
+ return 0;
+fail:;
+ __Pyx_ZeroBuffer(buf);
+ return -1;
+}
+static const char* __Pyx_BufferTypestringCheck_item_nn___pyx_t_5numpy_float64_t(const char* ts) {
+ int ok;
+ if (*ts == '1') ++ts;
+ switch (*ts) {
+ case 'f': ok = (sizeof(__pyx_t_5numpy_float64_t) == sizeof(float) && (__pyx_t_5numpy_float64_t)-1 < 0); break;
+ case 'd': ok = (sizeof(__pyx_t_5numpy_float64_t) == sizeof(double) && (__pyx_t_5numpy_float64_t)-1 < 0); break;
+ case 'g': ok = (sizeof(__pyx_t_5numpy_float64_t) == sizeof(long double) && (__pyx_t_5numpy_float64_t)-1 < 0); break; default: ok = 0;
+ }
+ if (!ok) {
+ PyErr_Format(PyExc_ValueError, "Buffer datatype mismatch (rejecting on '%s')", ts);
+ return NULL;
+ } else return ts + 1;
+
+}
+
+static int __Pyx_GetBuffer_nn___pyx_t_5numpy_float64_t(PyObject* obj, Py_buffer* buf, int flags, int nd) {
+ const char* ts;
+ if (obj == Py_None) {
+ __Pyx_ZeroBuffer(buf);
+ return 0;
+ }
+ buf->buf = NULL;
+ if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail;
+ if (buf->ndim != nd) {
+ __Pyx_BufferNdimError(buf, nd);
+ goto fail;
+ }
+ ts = buf->format;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheckEndian(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheck_item_nn___pyx_t_5numpy_float64_t(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ if (*ts != 0) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected non-struct buffer data type (expected end, got '%s')", ts);
+ goto fail;
+ }
+ if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
+ return 0;
+fail:;
+ __Pyx_ZeroBuffer(buf);
+ return -1;
+}
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, char *name, int exact) {
if (!type) {
PyErr_Format(PyExc_SystemError, "Missing type object");
@@ -1358,6 +2595,20 @@
return result;
}
+static int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
+ if (!type) {
+ PyErr_Format(PyExc_SystemError, "Missing type object");
+ return 0;
+ }
+ if (obj == Py_None || PyObject_TypeCheck(obj, type))
+ return 1;
+ PyErr_Format(PyExc_TypeError, "Cannot convert %s to %s",
+ Py_TYPE(obj)->tp_name, type->tp_name);
+ return 0;
+}
+
+
+
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
Py_XINCREF(type);
Py_XINCREF(value);
Modified: trunk/yt/lagos/RTIntegrator.pyx
==============================================================================
--- trunk/yt/lagos/RTIntegrator.pyx (original)
+++ trunk/yt/lagos/RTIntegrator.pyx Mon Sep 22 08:35:20 2008
@@ -69,3 +69,72 @@
o_s[i] = i_s + dx[i]*(e[i] - i_s*a[i])
i_s = o_s[i]
return i_s
+
+ at cython.boundscheck(False)
+def VoxelTraversal(np.ndarray[np.int_t, ndim=3] grid_mask,
+ np.ndarray[np.float64_t, ndim=1] left_edge,
+ np.ndarray[np.float64_t, ndim=1] right_edge,
+ np.ndarray[np.float64_t, ndim=1] dx,
+ np.ndarray[np.float64_t, ndim=1] u,
+ np.ndarray[np.float64_t, ndim=1] v):
+ # We're roughly following Amanatides & Woo
+ # Find the first place the ray hits the grid on its path
+ # Do left edge then right edge in each dim
+ cdef int i, x, y
+ cdef double tl, tr, intersect_t, intersect
+ cdef np.ndarray step = np.ones(3, dtype=np.float64) # maybe just ints?
+ cdef np.ndarray cur_ind = np.zeros(3, dtype=np.int64) # maybe just ints?
+ cdef np.ndarray tdelta = np.zeros(3, dtype=np.float64)
+ cdef np.ndarray tmax = np.zeros(3, dtype=np.float64)
+ intersect_t = 1e30
+ for i in range(3):
+ # As long as we're iterating, set some other stuff, too
+ if (v[i] < 0): step[i] = -1
+ x = (i+1)%3
+ y = (i+2)%3
+ tl = (left_edge[i] - u[i])/v[i]
+ tr = (right_edge[i] - u[i])/v[i]
+ if (left_edge[x] <= (u[x] + tl*v[x]) < right_edge[x]) and \
+ (left_edge[y] <= (u[y] + tl*v[y]) < right_edge[y]) and \
+ (0 <= tl < intersect_t):
+ intersect_t = tl
+ if (left_edge[x] <= (u[x] + tr*v[x]) < right_edge[x]) and \
+ (left_edge[y] <= (u[y] + tr*v[y]) < right_edge[y]) and \
+ (0 <= tr < intersect_t):
+ intersect_t = tr
+ if (left_edge[0] <= u[0] <= right_edge[0]) and \
+ (left_edge[1] <= u[1] <= right_edge[1]) and \
+ (left_edge[2] <= u[2] <= right_edge[2]):
+ intersect_t = 0
+ if intersect_t > 1e29: return
+ # Now get the indices of the intersection
+ for i in range(3):
+ intersect = u[i] + intersect_t * v[i]
+ cur_ind[i] = np.floor((intersect - left_edge[i])/dx[i])
+ if step[i] > 0: tdelta[i] = intersect - ((cur_ind[i]+1) * dx[i])
+ if step[i] < 0: tdelta[i] = intersect - (cur_ind[i] * dx[i])
+ tmax[i] = dx[i]/v[i]
+ # We now know where we have pierced the grid initially.
+ cdef int in_cells = 1
+ while 1:
+ if cur_ind[0] >= grid_mask.shape[0] or \
+ cur_ind[1] >= grid_mask.shape[1] or \
+ cur_ind[2] >= grid_mask.shape[2]:
+ break
+ else:
+ grid_mask[cur_ind[0], cur_ind[1], cur_ind[2]] = 1
+ if tmax[0] < tmax[1]:
+ if tmax[0] < tmax[2]:
+ cur_ind[0] += step[0]
+ tmax[0] += tdelta[0]
+ else:
+ cur_ind[2] += step[2]
+ tmax[2] += tdelta[2]
+ else:
+ if tmax[1] < tmax[2]:
+ cur_ind[1] += step[1]
+ tmax[1] += tdelta[1]
+ else:
+ cur_ind[2] += step[2]
+ tmax[2] += tdelta[2]
+ return
Modified: trunk/yt/lagos/RayTracer.py
==============================================================================
--- trunk/yt/lagos/RayTracer.py (original)
+++ trunk/yt/lagos/RayTracer.py Mon Sep 22 08:35:20 2008
@@ -37,7 +37,7 @@
self.fill_buff()
def _trace_single_ray(self, x, y):
- ray = self.pf.h.ray(self.axis, (x, y))
+ ray = self.pf.h.ortho_ray(self.axis, (x, y))
order = ray[axis_names[self.axis]].argsort()
if self.reverse: order = order[::-1]
return self.func(ray, order)
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