[Yt-svn] yt-commit r1408 - trunk/yt/lagos
jwise at wrangler.dreamhost.com
jwise at wrangler.dreamhost.com
Mon Aug 24 18:07:11 PDT 2009
Author: jwise
Date: Mon Aug 24 18:07:09 2009
New Revision: 1408
URL: http://yt.spacepope.org/changeset/1408
Log:
Added new data class, fixed resolution cutting planes, using trilinear
interpolation. There are grid boundary artifacts that need to be
fixed. I have experimented with vertex-centered data (currented used)
and (un)smoothed ghost zones. This data class will be useful in
creating volume renderings with slicing, completely contained in yt.
Added:
trunk/yt/lagos/PointsInVolume.c
trunk/yt/lagos/PointsInVolume.pyx
Modified:
trunk/yt/lagos/BaseDataTypes.py
trunk/yt/lagos/setup.py
Modified: trunk/yt/lagos/BaseDataTypes.py
==============================================================================
--- trunk/yt/lagos/BaseDataTypes.py (original)
+++ trunk/yt/lagos/BaseDataTypes.py Mon Aug 24 18:07:09 2009
@@ -28,6 +28,7 @@
data_object_registry = {}
from yt.lagos import *
+import PointsInVolume as PV
def restore_grid_state(func):
"""
@@ -71,6 +72,20 @@
return self._point_indices[grid.id]
return check_cache
+def cache_vc_data(func):
+ """
+ For computationally intensive operations, we can cache between
+ calls.
+ """
+ def check_cache(self, grid, field):
+ if isinstance(grid, FakeGridForParticles):
+ return func(self, grid, field)
+ elif grid.id not in self._vc_data[field]:
+ vc = func(self, grid, field)
+ self._vc_data[field][grid.id] = vc
+ return self._vc_data[field][grid.id]
+ return check_cache
+
class FakeGridForParticles(object):
"""
Mock up a grid to insert particle positions and radii
@@ -137,6 +152,7 @@
self.__set_default_field_parameters()
self._cut_masks = {}
self._point_indices = {}
+ self._vc_data = {}
for key, val in kwargs.items():
self.set_field_parameter(key, val)
@@ -930,6 +946,175 @@
return "%s/c%s_L%s" % \
(self._top_node, cen_name, L_name)
+class AMRFixedResCuttingPlaneBase(AMR2DData):
+ """
+ AMRFixedResCuttingPlaneBase is an oblique plane through the data,
+ defined by a normal vector and a coordinate. It trilinearly
+ interpolates the data to a fixed resolution slice. It differs from
+ the other data objects as it doesn't save the grid data, only the
+ interpolated data.
+ """
+ _top_node = "/FixedResCuttingPlanes"
+ _type_name = "fixed_res_cutting"
+ _con_args = ('normal', 'center', 'width', 'dims')
+ def __init__(self, normal, center, width, dims, fields = None,
+ node_name = None, **kwargs):
+ """
+ The fixed resolution Cutting Plane slices at an oblique angle,
+ where we use the *normal* vector at the *center* to define the
+ viewing plane. The plane is *width* units wide. The 'up'
+ direction is guessed at automatically if not given.
+ """
+ #
+ # Taken from Cutting Plane
+ #
+ AMR2DData.__init__(self, 4, fields, **kwargs)
+ self.center = center
+ self.width = width
+ self.dims = dims
+ self.dds = self.width / self.dims
+
+ self.set_field_parameter('center', center)
+ # Let's set up our plane equation
+ # ax + by + cz + d = 0
+ self._norm_vec = normal/na.sqrt(na.dot(normal,normal))
+ self._d = -1.0 * na.dot(self._norm_vec, self.center)
+ # First we try all three, see which has the best result:
+ vecs = na.identity(3)
+ _t = na.cross(self._norm_vec, vecs).sum(axis=1)
+ ax = _t.argmax()
+ self._x_vec = na.cross(vecs[ax,:], self._norm_vec).ravel()
+ self._x_vec /= na.sqrt(na.dot(self._x_vec, self._x_vec))
+ self._y_vec = na.cross(self._norm_vec, self._x_vec).ravel()
+ self._y_vec /= na.sqrt(na.dot(self._y_vec, self._y_vec))
+ self._rot_mat = na.array([self._x_vec,self._y_vec,self._norm_vec])
+ self._inv_mat = na.linalg.pinv(self._rot_mat)
+ self.set_field_parameter('cp_x_vec',self._x_vec)
+ self.set_field_parameter('cp_y_vec',self._y_vec)
+ self.set_field_parameter('cp_z_vec',self._norm_vec)
+
+ # Calculate coordinates of each pixel
+ _co = self.dds * \
+ (na.mgrid[-self.dims/2 : self.dims/2,
+ -self.dims/2 : self.dims/2] + 0.5)
+ self._coord = self.center + na.outer(_co[0,:,:], self._x_vec) + \
+ na.outer(_co[1,:,:], self._y_vec)
+ self._pixelmask = na.ones(self.dims*self.dims, dtype='int8')
+
+ if node_name is False:
+ self._refresh_data()
+ else:
+ if node_name is True: self._deserialize()
+ else: self._deserialize(node_name)
+
+ @property
+ def normal(self):
+ return self._norm_vec
+
+ def _get_list_of_grids(self):
+ # Just like the Cutting Plane but restrict the grids to be
+ # within width/2 of the center.
+ vertices = self.hierarchy.gridCorners
+ # Shape = (8,3,n_grid)
+ D = na.sum(self._norm_vec.reshape((1,3,1)) * vertices, axis=1) + self._d
+ valid_grids = na.where(na.logical_not(na.all(D<0,axis=0) |
+ na.all(D>0,axis=0) ))[0]
+ # Now restrict these grids to a rect. prism that bounds the slice
+ sliceCorners = na.array([ \
+ self.center + self.width * (+self._x_vec + self._y_vec),
+ self.center + self.width * (+self._x_vec - self._y_vec),
+ self.center + self.width * (-self._x_vec - self._y_vec),
+ self.center + self.width * (-self._x_vec + self._y_vec) ])
+ sliceLeftEdge = sliceCorners.min(axis=0)
+ sliceRightEdge = sliceCorners.max(axis=0)
+ # Check for bounding box and grid overlap
+ leftOverlap = na.less(self.hierarchy.gridLeftEdge[valid_grids],
+ sliceRightEdge).all(axis=1)
+ rightOverlap = na.greater(self.hierarchy.gridRightEdge[valid_grids],
+ sliceLeftEdge).all(axis=1)
+ self._grids = self.hierarchy.grids[valid_grids[
+ na.where(leftOverlap & rightOverlap)]]
+ self._grids = self._grids[::-1]
+
+
+ def _generate_coords(self):
+ self['px'] = self._coord[:,0].ravel()
+ self['py'] = self._coord[:,1].ravel()
+ self['pz'] = self._coord[:,2].ravel()
+ self['pdx'] = self.dds * 0.5
+ self['pdy'] = self.dds * 0.5
+ #self['pdz'] = self.dds * 0.5
+
+ def _get_data_from_grid(self, grid, field):
+ if not self.pf.field_info[field].particle_type:
+ pointI = self._get_point_indices(grid)
+ if len(pointI) == 0: return
+ vc = self._calc_vertex_centered_data(grid, field)
+ bds = na.array(zip(grid.LeftEdge,
+ grid.RightEdge)).ravel()
+ interp = TrilinearFieldInterpolator(vc, bds,
+ ['x', 'y', 'z'])
+ self[field][pointI] = interp( \
+ dict(x=self._coord[pointI,0],
+ y=self._coord[pointI,1],
+ z=self._coord[pointI,2])).ravel()
+
+ # Mark these pixels to speed things up
+ self._pixelmask[pointI] = 0
+
+ return
+ else:
+ raise SyntaxError("Making a fixed resolution slice with "
+ "particles isn't supported yet.")
+
+ @time_execution
+ def get_data(self, fields = None):
+ """
+ Iterates over the list of fields and generates/reads them all.
+ """
+ self._get_list_of_grids()
+ if not self.has_key('pdx'):
+ self._generate_coords()
+ if fields == None:
+ fields_to_get = self.fields[:]
+ else:
+ fields_to_get = ensure_list(fields)
+ temp_data = {}
+ _size = self.dims * self.dims
+ for field in fields_to_get:
+ if self.data.has_key(field): continue
+ if field not in self.hierarchy.field_list:
+ if self._generate_field(field):
+ continue # A "True" return means we did it
+ if not self._vc_data.has_key(field):
+ self._vc_data[field] = {}
+ self[field] = na.zeros(_size, dtype='float64')
+ for grid in self._get_grids():
+ self._get_data_from_grid(grid, field)
+ self[field] = self._mpi_allsum(self[field]).reshape([self.dims]*2)#.transpose()
+
+ def interpolate_discretize(self, *args, **kwargs):
+ pass
+
+ @cache_vc_data
+ def _calc_vertex_centered_data(self, grid, field):
+ #return grid.retrieve_ghost_zones(1, field, smoothed=False)
+ return grid.get_vertex_centered_data(field)
+
+ def _get_point_indices(self, grid):
+ if self._pixelmask.max() == 0: return []
+ k = PV.PointsInVolume(self._coord, self._pixelmask,
+ grid.LeftEdge, grid.RightEdge,
+ grid.child_mask, just_one(grid['dx']))
+ return k
+
+ def _gen_node_name(self):
+ cen_name = ("%s" % (self.center,)).replace(" ","_")[1:-1]
+ L_name = ("%s" % self._norm_vec).replace(" ","_")[1:-1]
+ return "%s/c%s_L%s" % \
+ (self._top_node, cen_name, L_name)
+
+
class AMRProjBase(AMR2DData):
_top_node = "/Projections"
_key_fields = AMR2DData._key_fields + ['weight_field']
Added: trunk/yt/lagos/PointsInVolume.c
==============================================================================
--- (empty file)
+++ trunk/yt/lagos/PointsInVolume.c Mon Aug 24 18:07:09 2009
@@ -0,0 +1,4436 @@
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+static INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+
+static INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
+ PyObject *r;
+ if (!j) return NULL;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ return r;
+}
+
+
+#define __Pyx_GetItemInt_List(o, i, size, to_py_func) ((size <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_List_Fast(o, i, size <= sizeof(long)) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
+static INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, int fits_long) {
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ return __Pyx_GetItemInt_Generic(o, fits_long ? PyInt_FromLong(i) : PyLong_FromLongLong(i));
+}
+
+#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) ((size <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Tuple_Fast(o, i, size <= sizeof(long)) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
+static INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, int fits_long) {
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ return __Pyx_GetItemInt_Generic(o, fits_long ? PyInt_FromLong(i) : PyLong_FromLongLong(i));
+}
+
+
+#define __Pyx_GetItemInt(o, i, size, to_py_func) ((size <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Fast(o, i, size <= sizeof(long)) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
+static INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int fits_long) {
+ 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))) {
+ r = PySequence_GetItem(o, i);
+ }
+ else {
+ r = __Pyx_GetItemInt_Generic(o, fits_long ? PyInt_FromLong(i) : PyLong_FromLongLong(i));
+ }
+ return r;
+}
+
+static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
+ const char *name, int exact); /*proto*/
+#if PY_MAJOR_VERSION < 3
+static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags);
+static void __Pyx_ReleaseBuffer(Py_buffer *view);
+#else
+#define __Pyx_GetBuffer PyObject_GetBuffer
+#define __Pyx_ReleaseBuffer PyBuffer_Release
+#endif
+
+Py_ssize_t __Pyx_zeros[] = {0, 0, 0};
+Py_ssize_t __Pyx_minusones[] = {-1, -1, -1};
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+
+#if __PYX_USE_C99_COMPLEX
+ #define __Pyx_REAL_PART(z) __real__(z)
+ #define __Pyx_IMAG_PART(z) __imag__(z)
+#else
+ #define __Pyx_REAL_PART(z) ((z).real)
+ #define __Pyx_IMAG_PART(z) ((z).imag)
+#endif
+
+#define __pyx_PyObject_from_complex(z) PyComplex_FromDoubles((double)__Pyx_REAL_PART(z), (double)__Pyx_IMAG_PART(z))
+
+#if __PYX_USE_C99_COMPLEX
+
+ typedef float _Complex __pyx_t_float_complex;
+ static INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
+ return x + y*(__pyx_t_float_complex)_Complex_I;
+ }
+
+ #define __pyx_t_float_complex_is_zero(a) ((a) == 0)
+ #define __pyx_t_float_complex_eq(a, b) ((a) == (b))
+ #define __pyx_t_float_complex_add(a, b) ((a)+(b))
+ #define __pyx_t_float_complex_sub(a, b) ((a)-(b))
+ #define __pyx_t_float_complex_mul(a, b) ((a)*(b))
+ #define __pyx_t_float_complex_div(a, b) ((a)/(b))
+ #define __pyx_t_float_complex_neg(a) (-(a))
+
+#else
+
+ typedef struct { float real, imag; } __pyx_t_float_complex;
+ static INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
+ __pyx_t_float_complex c; c.real = x; c.imag = y; return c;
+ }
+
+ static INLINE int __pyx_t_float_complex_is_zero(__pyx_t_float_complex a) {
+ return (a.real == 0) & (a.imag == 0);
+ }
+
+ static INLINE int __pyx_t_float_complex_eq(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ return (a.real == b.real) & (a.imag == b.imag);
+ }
+
+ static INLINE __pyx_t_float_complex __pyx_t_float_complex_add(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ __pyx_t_float_complex z;
+ z.real = a.real + b.real;
+ z.imag = a.imag + b.imag;
+ return z;
+ }
+
+ static INLINE __pyx_t_float_complex __pyx_t_float_complex_sub(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ __pyx_t_float_complex z;
+ z.real = a.real - b.real;
+ z.imag = a.imag - b.imag;
+ return z;
+ }
+
+ static INLINE __pyx_t_float_complex __pyx_t_float_complex_mul(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ __pyx_t_float_complex z;
+ z.real = a.real * b.real - a.imag * b.imag;
+ z.imag = a.real * b.imag + a.imag * b.real;
+ return z;
+ }
+
+ static INLINE __pyx_t_float_complex __pyx_t_float_complex_div(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ __pyx_t_float_complex z;
+ float denom = b.real*b.real + b.imag*b.imag;
+ z.real = (a.real * b.real + a.imag * b.imag) / denom;
+ z.imag = (a.imag * b.real - a.real * b.imag) / denom;
+ return z;
+ }
+
+ static INLINE __pyx_t_float_complex __pyx_t_float_complex_neg(__pyx_t_float_complex a) {
+ __pyx_t_float_complex z;
+ z.real = -a.real;
+ z.imag = -a.imag;
+ return z;
+ }
+
+#endif
+
+#if __PYX_USE_C99_COMPLEX
+
+ typedef double _Complex __pyx_t_double_complex;
+ static INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
+ return x + y*(__pyx_t_double_complex)_Complex_I;
+ }
+
+ #define __pyx_t_double_complex_is_zero(a) ((a) == 0)
+ #define __pyx_t_double_complex_eq(a, b) ((a) == (b))
+ #define __pyx_t_double_complex_add(a, b) ((a)+(b))
+ #define __pyx_t_double_complex_sub(a, b) ((a)-(b))
+ #define __pyx_t_double_complex_mul(a, b) ((a)*(b))
+ #define __pyx_t_double_complex_div(a, b) ((a)/(b))
+ #define __pyx_t_double_complex_neg(a) (-(a))
+
+#else
+
+ typedef struct { double real, imag; } __pyx_t_double_complex;
+ static INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
+ __pyx_t_double_complex c; c.real = x; c.imag = y; return c;
+ }
+
+ static INLINE int __pyx_t_double_complex_is_zero(__pyx_t_double_complex a) {
+ return (a.real == 0) & (a.imag == 0);
+ }
+
+ static INLINE int __pyx_t_double_complex_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ return (a.real == b.real) & (a.imag == b.imag);
+ }
+
+ static INLINE __pyx_t_double_complex __pyx_t_double_complex_add(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ __pyx_t_double_complex z;
+ z.real = a.real + b.real;
+ z.imag = a.imag + b.imag;
+ return z;
+ }
+
+ static INLINE __pyx_t_double_complex __pyx_t_double_complex_sub(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ __pyx_t_double_complex z;
+ z.real = a.real - b.real;
+ z.imag = a.imag - b.imag;
+ return z;
+ }
+
+ static INLINE __pyx_t_double_complex __pyx_t_double_complex_mul(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ __pyx_t_double_complex z;
+ z.real = a.real * b.real - a.imag * b.imag;
+ z.imag = a.real * b.imag + a.imag * b.real;
+ return z;
+ }
+
+ static INLINE __pyx_t_double_complex __pyx_t_double_complex_div(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ __pyx_t_double_complex z;
+ double denom = b.real*b.real + b.imag*b.imag;
+ z.real = (a.real * b.real + a.imag * b.imag) / denom;
+ z.imag = (a.imag * b.real - a.real * b.imag) / denom;
+ return z;
+ }
+
+ static INLINE __pyx_t_double_complex __pyx_t_double_complex_neg(__pyx_t_double_complex a) {
+ __pyx_t_double_complex z;
+ z.real = -a.real;
+ z.imag = -a.imag;
+ return z;
+ }
+
+#endif
+
+#if __PYX_USE_C99_COMPLEX
+
+ typedef long double _Complex __pyx_t_long__double_complex;
+ static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_from_parts(long double x, long double y) {
+ return x + y*(__pyx_t_long__double_complex)_Complex_I;
+ }
+
+ #define __pyx_t_long__double_complex_is_zero(a) ((a) == 0)
+ #define __pyx_t_long__double_complex_eq(a, b) ((a) == (b))
+ #define __pyx_t_long__double_complex_add(a, b) ((a)+(b))
+ #define __pyx_t_long__double_complex_sub(a, b) ((a)-(b))
+ #define __pyx_t_long__double_complex_mul(a, b) ((a)*(b))
+ #define __pyx_t_long__double_complex_div(a, b) ((a)/(b))
+ #define __pyx_t_long__double_complex_neg(a) (-(a))
+
+#else
+
+ typedef struct { long double real, imag; } __pyx_t_long__double_complex;
+ static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_from_parts(long double x, long double y) {
+ __pyx_t_long__double_complex c; c.real = x; c.imag = y; return c;
+ }
+
+ static INLINE int __pyx_t_long__double_complex_is_zero(__pyx_t_long__double_complex a) {
+ return (a.real == 0) & (a.imag == 0);
+ }
+
+ static INLINE int __pyx_t_long__double_complex_eq(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) {
+ return (a.real == b.real) & (a.imag == b.imag);
+ }
+
+ static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_add(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) {
+ __pyx_t_long__double_complex z;
+ z.real = a.real + b.real;
+ z.imag = a.imag + b.imag;
+ return z;
+ }
+
+ static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_sub(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) {
+ __pyx_t_long__double_complex z;
+ z.real = a.real - b.real;
+ z.imag = a.imag - b.imag;
+ return z;
+ }
+
+ static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_mul(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) {
+ __pyx_t_long__double_complex z;
+ z.real = a.real * b.real - a.imag * b.imag;
+ z.imag = a.real * b.imag + a.imag * b.real;
+ return z;
+ }
+
+ static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_div(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) {
+ __pyx_t_long__double_complex z;
+ long double denom = b.real*b.real + b.imag*b.imag;
+ z.real = (a.real * b.real + a.imag * b.imag) / denom;
+ z.imag = (a.imag * b.real - a.real * b.imag) / denom;
+ return z;
+ }
+
+ static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_neg(__pyx_t_long__double_complex a) {
+ __pyx_t_long__double_complex z;
+ z.real = -a.real;
+ z.imag = -a.imag;
+ return z;
+ }
+
+#endif
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
+static INLINE int __Pyx_StrEq(const char *, const char *); /*proto*/
+
+static INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
+
+static INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
+
+static INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
+
+static INLINE char __Pyx_PyInt_AsChar(PyObject *);
+
+static INLINE short __Pyx_PyInt_AsShort(PyObject *);
+
+static INLINE int __Pyx_PyInt_AsInt(PyObject *);
+
+static INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);
+
+static INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
+
+static INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
+
+static INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
+
+static INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
+
+static INLINE long __Pyx_PyInt_AsLong(PyObject *);
+
+static INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
+
+static INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
+
+static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
+
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size); /*proto*/
+
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
+static void __Pyx_AddTraceback(const char *funcname); /*proto*/
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+
+/* Type declarations */
+
+typedef npy_int8 __pyx_t_5numpy_int8_t;
+
+typedef npy_int16 __pyx_t_5numpy_int16_t;
+
+typedef npy_int32 __pyx_t_5numpy_int32_t;
+
+typedef npy_int64 __pyx_t_5numpy_int64_t;
+
+typedef npy_uint8 __pyx_t_5numpy_uint8_t;
+
+typedef npy_uint16 __pyx_t_5numpy_uint16_t;
+
+typedef npy_uint32 __pyx_t_5numpy_uint32_t;
+
+typedef npy_uint64 __pyx_t_5numpy_uint64_t;
+
+typedef npy_float32 __pyx_t_5numpy_float32_t;
+
+typedef npy_float64 __pyx_t_5numpy_float64_t;
+
+typedef npy_complex64 __pyx_t_5numpy_complex64_t;
+
+typedef npy_complex128 __pyx_t_5numpy_complex128_t;
+
+typedef npy_long __pyx_t_5numpy_int_t;
+
+typedef npy_longlong __pyx_t_5numpy_long_t;
+
+typedef npy_ulong __pyx_t_5numpy_uint_t;
+
+typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
+
+typedef npy_double __pyx_t_5numpy_float_t;
+
+typedef npy_double __pyx_t_5numpy_double_t;
+
+typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
+
+typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
+
+typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
+
+typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
+
+typedef npy_cdouble __pyx_t_5numpy_complex_t;
+/* Module declarations from python_buffer */
+
+/* Module declarations from stdlib */
+
+/* Module declarations from numpy */
+
+/* Module declarations from numpy */
+
+static PyTypeObject *__pyx_ptype_5numpy_dtype = 0;
+static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0;
+static INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/
+/* Module declarations from cython */
+
+/* Module declarations from yt.lagos.PointsInVolume */
+
+static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t = { "numpy.float64_t", NULL, sizeof(__pyx_t_5numpy_float64_t), 'R' };
+static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int8_t = { "numpy.int8_t", NULL, sizeof(__pyx_t_5numpy_int8_t), 'I' };
+static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int32_t = { "numpy.int32_t", NULL, sizeof(__pyx_t_5numpy_int32_t), 'I' };
+#define __Pyx_MODULE_NAME "yt.lagos.PointsInVolume"
+int __pyx_module_is_main_yt__lagos__PointsInVolume = 0;
+
+/* Implementation of yt.lagos.PointsInVolume */
+static PyObject *__pyx_int_3;
+static char __pyx_k___main__[] = "__main__";
+static PyObject *__pyx_kp___main__;
+static char __pyx_k_points[] = "points";
+static PyObject *__pyx_kp_points;
+static char __pyx_k_pmask[] = "pmask";
+static PyObject *__pyx_kp_pmask;
+static char __pyx_k_left_edge[] = "left_edge";
+static PyObject *__pyx_kp_left_edge;
+static char __pyx_k_right_edge[] = "right_edge";
+static PyObject *__pyx_kp_right_edge;
+static char __pyx_k_mask[] = "mask";
+static PyObject *__pyx_kp_mask;
+static char __pyx_k_dx[] = "dx";
+static PyObject *__pyx_kp_dx;
+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_31[] = "int8";
+static PyObject *__pyx_kp_31;
+static char __pyx_k_xrange[] = "xrange";
+static PyObject *__pyx_kp_xrange;
+static char __pyx_k_empty[] = "empty";
+static PyObject *__pyx_kp_empty;
+static char __pyx_k_32[] = "int32";
+static PyObject *__pyx_kp_32;
+static PyObject *__pyx_builtin_xrange;
+static PyObject *__pyx_int_15;
+static char __pyx_k___getbuffer__[] = "__getbuffer__";
+static PyObject *__pyx_kp___getbuffer__;
+static char __pyx_k___releasebuffer__[] = "__releasebuffer__";
+static PyObject *__pyx_kp___releasebuffer__;
+static char __pyx_k_info[] = "info";
+static PyObject *__pyx_kp_info;
+static char __pyx_k_flags[] = "flags";
+static PyObject *__pyx_kp_flags;
+static char __pyx_k_ValueError[] = "ValueError";
+static PyObject *__pyx_kp_ValueError;
+static char __pyx_k_range[] = "range";
+static PyObject *__pyx_kp_range;
+static char __pyx_k_itervalues[] = "itervalues";
+static PyObject *__pyx_kp_itervalues;
+static char __pyx_k_RuntimeError[] = "RuntimeError";
+static PyObject *__pyx_kp_RuntimeError;
+static PyObject *__pyx_kp_1;
+static PyObject *__pyx_kp_2;
+static PyObject *__pyx_kp_5;
+static PyObject *__pyx_kp_23;
+static PyObject *__pyx_builtin_ValueError;
+static PyObject *__pyx_builtin_range;
+static PyObject *__pyx_builtin_RuntimeError;
+static char __pyx_k_1[] = "ndarray is not C contiguous";
+static char __pyx_k_2[] = "ndarray is not Fortran contiguous";
+static char __pyx_k_3[] = ">";
+static char __pyx_k_4[] = "<";
+static char __pyx_k_5[] = "Non-native byte order not supported";
+static char __pyx_k_6[] = "b";
+static char __pyx_k_7[] = "B";
+static char __pyx_k_8[] = "h";
+static char __pyx_k_9[] = "H";
+static char __pyx_k_10[] = "i";
+static char __pyx_k_11[] = "I";
+static char __pyx_k_12[] = "l";
+static char __pyx_k_13[] = "L";
+static char __pyx_k_14[] = "q";
+static char __pyx_k_15[] = "Q";
+static char __pyx_k_16[] = "f";
+static char __pyx_k_17[] = "d";
+static char __pyx_k_18[] = "g";
+static char __pyx_k_19[] = "Zf";
+static char __pyx_k_20[] = "Zd";
+static char __pyx_k_21[] = "Zg";
+static char __pyx_k_22[] = "O";
+static char __pyx_k_23[] = "unknown dtype code in numpy.pxd (%d)";
+static char __pyx_k_24[] = "^";
+static PyObject *__pyx_kp_25;
+static PyObject *__pyx_kp_28;
+static PyObject *__pyx_kp_29;
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+ */
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+ PyArrayObject *__pyx_v_mask = 0;
+ float __pyx_v_dx;
+ PyArrayObject *__pyx_v_valid = 0;
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+ int __pyx_v_dim;
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+ Py_ssize_t __pyx_bshape_0_valid = 0;
+ Py_buffer __pyx_bstruct_right_edge;
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+ Py_ssize_t __pyx_bshape_0_right_edge = 0;
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+ PyArrayObject *__pyx_t_4 = NULL;
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+ int __pyx_t_6;
+ int __pyx_t_7;
+ int __pyx_t_8;
+ int __pyx_t_9;
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_t_15;
+ int __pyx_t_16;
+ int __pyx_t_17;
+ int __pyx_t_18;
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+ unsigned int __pyx_t_20;
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+ int __pyx_t_27;
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+ #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
+ #ifdef WITH_THREAD /* Python build with threading support? */
+ PyEval_InitThreads();
+ #endif
+ #endif
+ /*--- Initialize various global constants etc. ---*/
+ 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(__Pyx_NAMESTR("PointsInVolume"), __pyx_methods, __pyx_mdoc, 0, PYTHON_API_VERSION);
+ #else
+ __pyx_m = PyModule_Create(&__pyx_moduledef);
+ #endif
+ if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
+ #endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
+ if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ if (__pyx_module_is_main_yt__lagos__PointsInVolume) {
+ if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_kp___main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ }
+ /*--- Builtin init code ---*/
+ if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_skip_dispatch = 0;
+ /*--- Global init code ---*/
+ /*--- Function export code ---*/
+ /*--- Type init code ---*/
+ /*--- Type import code ---*/
+ __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr)); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject)); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Function import code ---*/
+ /*--- Execution code ---*/
+
+ /* "/Users/jwise/codes/yt/yt/lagos/PointsInVolume.pyx":27
+ *
+ *
+ * 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 = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_1);
+ if (PyObject_SetAttr(__pyx_m, __pyx_kp_np, __pyx_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_1); __pyx_1 = 0;
+
+ /* "/usr/local/python/lib/python2.6/site-packages/Cython/Includes/stdlib.pxd":2
+ *
+ * cdef extern from "stdlib.h" nogil: # <<<<<<<<<<<<<<
+ * void free(void *ptr)
+ * void *malloc(size_t size)
+ */
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_1);
+ __Pyx_AddTraceback("yt.lagos.PointsInVolume");
+ Py_DECREF(__pyx_m); __pyx_m = 0;
+ __pyx_L0:;
+ __Pyx_FinishRefcountContext();
+ #if PY_MAJOR_VERSION < 3
+ return;
+ #else
+ return __pyx_m;
+ #endif
+}
+
+static const char *__pyx_filenames[] = {
+ "PointsInVolume.pyx",
+ "numpy.pxd",
+};
+
+/* Runtime support code */
+
+static void __pyx_init_filenames(void) {
+ __pyx_f = __pyx_filenames;
+}
+
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name,
+ PyObject* kw_name)
+{
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION >= 3
+ "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
+ #else
+ "%s() got multiple values for keyword argument '%s'", func_name,
+ PyString_AS_STRING(kw_name));
+ #endif
+}
+
+static void __Pyx_RaiseArgtupleInvalid(
+ const char* func_name,
+ int exact,
+ Py_ssize_t num_min,
+ Py_ssize_t num_max,
+ Py_ssize_t num_found)
+{
+ Py_ssize_t num_expected;
+ const char *number, *more_or_less;
+
+ if (num_found < num_min) {
+ num_expected = num_min;
+ more_or_less = "at least";
+ } else {
+ num_expected = num_max;
+ more_or_less = "at most";
+ }
+ if (exact) {
+ more_or_less = "exactly";
+ }
+ number = (num_expected == 1) ? "" : "s";
+ PyErr_Format(PyExc_TypeError,
+ #if PY_VERSION_HEX < 0x02050000
+ "%s() takes %s %d positional argument%s (%d given)",
+ #else
+ "%s() takes %s %zd positional argument%s (%zd given)",
+ #endif
+ func_name, more_or_less, num_expected, number, num_found);
+}
+
+static int __Pyx_ParseOptionalKeywords(
+ PyObject *kwds,
+ PyObject **argnames[],
+ PyObject *kwds2,
+ PyObject *values[],
+ Py_ssize_t num_pos_args,
+ const char* function_name)
+{
+ PyObject *key = 0, *value = 0;
+ Py_ssize_t pos = 0;
+ PyObject*** name;
+ PyObject*** first_kw_arg = argnames + num_pos_args;
+
+ while (PyDict_Next(kwds, &pos, &key, &value)) {
+ name = first_kw_arg;
+ while (*name && (**name != key)) name++;
+ if (*name) {
+ values[name-argnames] = value;
+ } else {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+ #else
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
+ #endif
+ goto invalid_keyword_type;
+ } else {
+ for (name = first_kw_arg; *name; name++) {
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) break;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) break;
+ #endif
+ }
+ if (*name) {
+ values[name-argnames] = value;
+ } else {
+ /* unexpected keyword found */
+ for (name=argnames; name != first_kw_arg; name++) {
+ if (**name == key) goto arg_passed_twice;
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) goto arg_passed_twice;
+ #endif
+ }
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
+ }
+ }
+ }
+ }
+ return 0;
+arg_passed_twice:
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ goto bad;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%s() keywords must be strings", function_name);
+ goto bad;
+invalid_keyword:
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%s() got an unexpected keyword argument '%s'",
+ function_name, PyString_AsString(key));
+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+bad:
+ return -1;
+}
+
+static INLINE int __Pyx_IsLittleEndian(void) {
+ unsigned int n = 1;
+ return *(unsigned char*)(&n) != 0;
+}
+
+typedef struct {
+ __Pyx_StructField root;
+ __Pyx_BufFmt_StackElem* head;
+ size_t fmt_offset;
+ int new_count, enc_count;
+ int is_complex;
+ char enc_type;
+ char packmode;
+} __Pyx_BufFmt_Context;
+
+static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
+ __Pyx_BufFmt_StackElem* stack,
+ __Pyx_TypeInfo* type) {
+ stack[0].field = &ctx->root;
+ stack[0].parent_offset = 0;
+ ctx->root.type = type;
+ ctx->root.name = "buffer dtype";
+ ctx->root.offset = 0;
+ ctx->head = stack;
+ ctx->head->field = &ctx->root;
+ ctx->fmt_offset = 0;
+ ctx->head->parent_offset = 0;
+ ctx->packmode = '@';
+ ctx->new_count = 1;
+ ctx->enc_count = 0;
+ ctx->enc_type = 0;
+ ctx->is_complex = 0;
+ while (type->typegroup == 'S') {
+ ++ctx->head;
+ ctx->head->field = type->fields;
+ ctx->head->parent_offset = 0;
+ type = type->fields->type;
+ }
+}
+
+static int __Pyx_BufFmt_ParseNumber(const char** ts) {
+ int count;
+ const char* t = *ts;
+ if (*t < '0' || *t > '9') {
+ return -1;
+ } else {
+ count = *t++ - '0';
+ while (*t >= '0' && *t < '9') {
+ count *= 10;
+ count += *t++ - '0';
+ }
+ }
+ *ts = t;
+ return count;
+}
+
+static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) {
+ char msg[] = {ch, 0};
+ PyErr_Format(PyExc_ValueError, "Unexpected format string character: '%s'", msg);
+}
+
+static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) {
+ switch (ch) {
+ case 'b': return "'char'";
+ case 'B': return "'unsigned char'";
+ case 'h': return "'short'";
+ case 'H': return "'unsigned short'";
+ case 'i': return "'int'";
+ case 'I': return "'unsigned int'";
+ case 'l': return "'long'";
+ case 'L': return "'unsigned long'";
+ case 'q': return "'long long'";
+ case 'Q': return "'unsigned long long'";
+ case 'f': return (is_complex ? "'complex float'" : "'float'");
+ case 'd': return (is_complex ? "'complex double'" : "'double'");
+ case 'g': return (is_complex ? "'complex long double'" : "'long double'");
+ case 'T': return "a struct";
+ case 'O': return "Python object";
+ case 'P': return "a pointer";
+ case 0: return "end";
+ default: return "unparseable format string";
+ }
+}
+
+static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) {
+ switch (ch) {
+ case '?': case 'c': case 'b': case 'B': return 1;
+ case 'h': case 'H': return 2;
+ case 'i': case 'I': case 'l': case 'L': return 4;
+ case 'q': case 'Q': return 8;
+ case 'f': return (is_complex ? 8 : 4);
+ case 'd': return (is_complex ? 16 : 8);
+ case 'g': {
+ PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g')..");
+ return 0;
+ }
+ case 'O': case 'P': return sizeof(void*);
+ default:
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+}
+
+static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) {
+ switch (ch) {
+ case 'c': case 'b': case 'B': return 1;
+ case 'h': case 'H': return sizeof(short);
+ case 'i': case 'I': return sizeof(int);
+ case 'l': case 'L': return sizeof(long);
+ #ifdef HAVE_LONG_LONG
+ case 'q': case 'Q': return sizeof(PY_LONG_LONG);
+ #endif
+ case 'f': return sizeof(float) * (is_complex ? 2 : 1);
+ case 'd': return sizeof(double) * (is_complex ? 2 : 1);
+ case 'g': return sizeof(long double) * (is_complex ? 2 : 1);
+ case 'O': case 'P': return sizeof(void*);
+ default: {
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+ }
+}
+
+typedef struct { char c; short x; } __Pyx_st_short;
+typedef struct { char c; int x; } __Pyx_st_int;
+typedef struct { char c; long x; } __Pyx_st_long;
+typedef struct { char c; float x; } __Pyx_st_float;
+typedef struct { char c; double x; } __Pyx_st_double;
+typedef struct { char c; long double x; } __Pyx_st_longdouble;
+typedef struct { char c; void *x; } __Pyx_st_void_p;
+#ifdef HAVE_LONG_LONG
+typedef struct { char c; PY_LONG_LONG x; } __Pyx_s_long_long;
+#endif
+
+static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, int is_complex) {
+ switch (ch) {
+ case '?': case 'c': case 'b': case 'B': return 1;
+ case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short);
+ case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int);
+ case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long);
+#ifdef HAVE_LONG_LONG
+ case 'q': case 'Q': return sizeof(__Pyx_s_long_long) - sizeof(PY_LONG_LONG);
+#endif
+ case 'f': return sizeof(__Pyx_st_float) - sizeof(float);
+ case 'd': return sizeof(__Pyx_st_double) - sizeof(double);
+ case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double);
+ case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*);
+ default:
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+}
+
+static size_t __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) {
+ switch (ch) {
+ case 'c': case 'b': case 'h': case 'i': case 'l': case 'q': return 'I';
+ case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U';
+ case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R');
+ case 'O': return 'O';
+ case 'P': return 'P';
+ default: {
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+ }
+}
+
+static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) {
+ if (ctx->head == NULL || ctx->head->field == &ctx->root) {
+ const char* expected;
+ const char* quote;
+ if (ctx->head == NULL) {
+ expected = "end";
+ quote = "";
+ } else {
+ expected = ctx->head->field->type->name;
+ quote = "'";
+ }
+ PyErr_Format(PyExc_ValueError,
+ "Buffer dtype mismatch, expected %s%s%s but got %s",
+ quote, expected, quote,
+ __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex));
+ } else {
+ __Pyx_StructField* field = ctx->head->field;
+ __Pyx_StructField* parent = (ctx->head - 1)->field;
+ PyErr_Format(PyExc_ValueError,
+ "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'",
+ field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex),
+ parent->type->name, field->name);
+ }
+}
+
+static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
+ char group;
+ size_t size, offset;
+ if (ctx->enc_type == 0) return 0;
+ group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex);
+ do {
+ __Pyx_StructField* field = ctx->head->field;
+ __Pyx_TypeInfo* type = field->type;
+
+ if (ctx->packmode == '@' || ctx->packmode == '^') {
+ size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex);
+ } else {
+ size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex);
+ }
+ if (ctx->packmode == '@') {
+ int align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex);
+ int align_mod_offset;
+ if (align_at == 0) return -1;
+ align_mod_offset = ctx->fmt_offset % align_at;
+ if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset;
+ }
+
+ if (type->size != size || type->typegroup != group) {
+ if (type->typegroup == 'C' && type->fields != NULL) {
+ /* special case -- treat as struct rather than complex number */
+ size_t parent_offset = ctx->head->parent_offset + field->offset;
+ ++ctx->head;
+ ctx->head->field = type->fields;
+ ctx->head->parent_offset = parent_offset;
+ continue;
+ }
+
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return -1;
+ }
+
+ offset = ctx->head->parent_offset + field->offset;
+ if (ctx->fmt_offset != offset) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer dtype mismatch; next field is at offset %"PY_FORMAT_SIZE_T"d "
+ "but %"PY_FORMAT_SIZE_T"d expected", ctx->fmt_offset, offset);
+ return -1;
+ }
+
+ ctx->fmt_offset += size;
+
+ --ctx->enc_count; /* Consume from buffer string */
+
+ /* Done checking, move to next field, pushing or popping struct stack if needed */
+ while (1) {
+ if (field == &ctx->root) {
+ ctx->head = NULL;
+ if (ctx->enc_count != 0) {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return -1;
+ }
+ break; /* breaks both loops as ctx->enc_count == 0 */
+ }
+ ctx->head->field = ++field;
+ if (field->type == NULL) {
+ --ctx->head;
+ field = ctx->head->field;
+ continue;
+ } else if (field->type->typegroup == 'S') {
+ size_t parent_offset = ctx->head->parent_offset + field->offset;
+ if (field->type->fields->type == NULL) continue; /* empty struct */
+ field = field->type->fields;
+ ++ctx->head;
+ ctx->head->field = field;
+ ctx->head->parent_offset = parent_offset;
+ break;
+ } else {
+ break;
+ }
+ }
+ } while (ctx->enc_count);
+ ctx->enc_type = 0;
+ ctx->is_complex = 0;
+ return 0;
+}
+
+static int __Pyx_BufFmt_FirstPack(__Pyx_BufFmt_Context* ctx) {
+ if (ctx->enc_type != 0 || ctx->packmode != '@') {
+ PyErr_SetString(PyExc_ValueError, "Buffer packing mode currently only allowed at beginning of format string (this is a defect)");
+ return -1;
+ }
+ return 0;
+}
+
+static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) {
+ int got_Z = 0;
+ while (1) {
+ switch(*ts) {
+ case 0:
+ if (ctx->enc_type != 0 && ctx->head == NULL) {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return NULL;
+ }
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ if (ctx->head != NULL) {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return NULL;
+ }
+ return ts;
+ case ' ':
+ case 10:
+ case 13:
+ ++ts;
+ break;
+ case '<':
+ if (!__Pyx_IsLittleEndian()) {
+ PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler");
+ return NULL;
+ }
+ if (__Pyx_BufFmt_FirstPack(ctx) == -1) return NULL;
+ ctx->packmode = '=';
+ ++ts;
+ break;
+ case '>':
+ case '!':
+ if (__Pyx_IsLittleEndian()) {
+ PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler");
+ return NULL;
+ }
+ if (__Pyx_BufFmt_FirstPack(ctx) == -1) return NULL;
+ ctx->packmode = '=';
+ ++ts;
+ break;
+ case '=':
+ case '@':
+ case '^':
+ if (__Pyx_BufFmt_FirstPack(ctx) == -1) return NULL;
+ ctx->packmode = *ts++;
+ break;
+ case 'T': /* substruct */
+ {
+ int i;
+ const char* ts_after_sub;
+ int struct_count = ctx->new_count;
+ ctx->new_count = 1;
+ ++ts;
+ if (*ts != '{') {
+ PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'");
+ return NULL;
+ }
+ ++ts;
+ ts_after_sub = ts;
+ for (i = 0; i != struct_count; ++i) {
+ ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts);
+ if (!ts_after_sub) return NULL;
+ }
+ ts = ts_after_sub;
+ }
+ break;
+ case '}': /* end of substruct; either repeat or move on */
+ ++ts;
+ return ts;
+ case 'x':
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->fmt_offset += ctx->new_count;
+ ctx->new_count = 1;
+ ctx->enc_count = 0;
+ ctx->enc_type = 0;
+ ++ts;
+ break;
+ case 'Z':
+ got_Z = 1;
+ ++ts;
+ if (*ts != 'f' && *ts != 'd' && *ts != 'g') {
+ __Pyx_BufFmt_RaiseUnexpectedChar('Z');
+ return NULL;
+ } /* fall through */
+ case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
+ case 'l': case 'L': case 'q': case 'Q':
+ case 'f': case 'd': case 'g':
+ case 'O':
+ if (ctx->enc_type == *ts && got_Z == ctx->is_complex) {
+ /* Continue pooling same type */
+ ctx->enc_count += ctx->new_count;
+ } else {
+ /* New type */
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_count = ctx->new_count;
+ ctx->enc_type = *ts;
+ ctx->is_complex = got_Z;
+ }
+ ++ts;
+ ctx->new_count = 1;
+ got_Z = 0;
+ break;
+ default:
+ {
+ ctx->new_count = __Pyx_BufFmt_ParseNumber(&ts);
+ if (ctx->new_count == -1) { /* First char was not a digit */
+ char msg[2] = { *ts, 0 };
+ PyErr_Format(PyExc_ValueError,
+ "Does not understand character buffer dtype format string ('%s')", msg);
+ return NULL;
+ }
+ }
+
+ }
+ }
+}
+
+static INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
+ buf->buf = NULL;
+ buf->obj = NULL;
+ buf->strides = __Pyx_zeros;
+ buf->shape = __Pyx_zeros;
+ buf->suboffsets = __Pyx_minusones;
+}
+
+static int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack) {
+ 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) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer has wrong number of dimensions (expected %d, got %d)",
+ nd, buf->ndim);
+ goto fail;
+ }
+ if (!cast) {
+ __Pyx_BufFmt_Context ctx;
+ __Pyx_BufFmt_Init(&ctx, stack, dtype);
+ if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
+ }
+ if ((unsigned)buf->itemsize != dtype->size) {
+ PyErr_Format(PyExc_ValueError,
+ "Item size of buffer (%"PY_FORMAT_SIZE_T"d byte%s) does not match size of '%s' (%"PY_FORMAT_SIZE_T"d byte%s)",
+ buf->itemsize, (buf->itemsize > 1) ? "s" : "",
+ dtype->name,
+ dtype->size, (dtype->size > 1) ? "s" : "");
+ goto fail;
+ }
+ if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
+ return 0;
+fail:;
+ __Pyx_ZeroBuffer(buf);
+ return -1;
+}
+
+static INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
+ if (info->buf == NULL) return;
+ if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
+ __Pyx_ReleaseBuffer(info);
+}
+
+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 INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+#if PY_MAJOR_VERSION >= 3
+ /* Note: this is a temporary work-around to prevent crashes in Python 3.0 */
+ if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) {
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ PyErr_NormalizeException(&type, &value, &tb);
+ PyErr_NormalizeException(&tmp_type, &tmp_value, &tmp_tb);
+ tstate->exc_type = 0;
+ tstate->exc_value = 0;
+ tstate->exc_traceback = 0;
+ PyException_SetContext(value, tmp_value);
+ Py_DECREF(tmp_type);
+ Py_XDECREF(tmp_tb);
+ }
+#endif
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+
+
+
+static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
+ const char *name, int exact)
+{
+ if (!type) {
+ PyErr_Format(PyExc_SystemError, "Missing type object");
+ return 0;
+ }
+ if (none_allowed && obj == Py_None) return 1;
+ else if (exact) {
+ if (Py_TYPE(obj) == type) return 1;
+ }
+ else {
+ if (PyObject_TypeCheck(obj, type)) return 1;
+ }
+ PyErr_Format(PyExc_TypeError,
+ "Argument '%s' has incorrect type (expected %s, got %s)",
+ name, type->tp_name, Py_TYPE(obj)->tp_name);
+ return 0;
+}
+
+#if PY_MAJOR_VERSION < 3
+static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
+ #if PY_VERSION_HEX >= 0x02060000
+ if (Py_TYPE(obj)->tp_flags & Py_TPFLAGS_HAVE_NEWBUFFER)
+ return PyObject_GetBuffer(obj, view, flags);
+ #endif
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pf_5numpy_7ndarray___getbuffer__(obj, view, flags);
+ else {
+ PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
+ return -1;
+ }
+}
+
+static void __Pyx_ReleaseBuffer(Py_buffer *view) {
+ PyObject* obj = view->obj;
+ if (obj) {
+if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) __pyx_pf_5numpy_7ndarray___releasebuffer__(obj, view);
+ Py_DECREF(obj);
+ view->obj = NULL;
+ }
+}
+
+#endif
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
+ PyObject *__import__ = 0;
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ __import__ = __Pyx_GetAttrString(__pyx_b, "__import__");
+ if (!__import__)
+ goto bad;
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(__import__,
+ name, global_dict, empty_dict, list, NULL);
+bad:
+ Py_XDECREF(empty_list);
+ Py_XDECREF(__import__);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
+ PyObject *result;
+ result = PyObject_GetAttr(dict, name);
+ if (!result)
+ PyErr_SetObject(PyExc_NameError, name);
+ return result;
+}
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+static INLINE int __Pyx_StrEq(const char *s1, const char *s2) {
+ while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
+ return *s1 == *s2;
+}
+
+static INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
+ if (sizeof(unsigned char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned char)val)) {
+ if (unlikely(val == -1 && PyErr_Occurred()))
+ return (unsigned char)-1;
+ if (unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned char");
+ return (unsigned char)-1;
+ }
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to unsigned char");
+ return (unsigned char)-1;
+ }
+ return (unsigned char)val;
+ }
+ return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
+ if (sizeof(unsigned short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned short)val)) {
+ if (unlikely(val == -1 && PyErr_Occurred()))
+ return (unsigned short)-1;
+ if (unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned short");
+ return (unsigned short)-1;
+ }
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to unsigned short");
+ return (unsigned short)-1;
+ }
+ return (unsigned short)val;
+ }
+ return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
+ if (sizeof(unsigned int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned int)val)) {
+ if (unlikely(val == -1 && PyErr_Occurred()))
+ return (unsigned int)-1;
+ if (unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned int");
+ return (unsigned int)-1;
+ }
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to unsigned int");
+ return (unsigned int)-1;
+ }
+ return (unsigned int)val;
+ }
+ return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
+ if (sizeof(char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(char)val)) {
+ if (unlikely(val == -1 && PyErr_Occurred()))
+ return (char)-1;
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to char");
+ return (char)-1;
+ }
+ return (char)val;
+ }
+ return (char)__Pyx_PyInt_AsLong(x);
+}
+
+static INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
+ if (sizeof(short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(short)val)) {
+ if (unlikely(val == -1 && PyErr_Occurred()))
+ return (short)-1;
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to short");
+ return (short)-1;
+ }
+ return (short)val;
+ }
+ return (short)__Pyx_PyInt_AsLong(x);
+}
+
+static INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (unlikely(val == -1 && PyErr_Occurred()))
+ return (int)-1;
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to int");
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
+ if (sizeof(signed char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed char)val)) {
+ if (unlikely(val == -1 && PyErr_Occurred()))
+ return (signed char)-1;
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to signed char");
+ return (signed char)-1;
+ }
+ return (signed char)val;
+ }
+ return (signed char)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
+ if (sizeof(signed short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed short)val)) {
+ if (unlikely(val == -1 && PyErr_Occurred()))
+ return (signed short)-1;
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to signed short");
+ return (signed short)-1;
+ }
+ return (signed short)val;
+ }
+ return (signed short)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
+ if (sizeof(signed int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed int)val)) {
+ if (unlikely(val == -1 && PyErr_Occurred()))
+ return (signed int)-1;
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to signed int");
+ return (signed int)-1;
+ }
+ return (signed int)val;
+ }
+ return (signed int)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)val;
+ } else
+#endif
+ if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ unsigned long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned long)-1;
+ val = __Pyx_PyInt_AsUnsignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ unsigned PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ return (long)val;
+ } else
+#endif
+ if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) {
+ return PyLong_AsLong(x);
+ } else {
+ long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (long)-1;
+ val = __Pyx_PyInt_AsLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ return (PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) {
+ return PyLong_AsLongLong(x);
+ } else {
+ PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ return (signed long)val;
+ } else
+#endif
+ if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) {
+ return PyLong_AsLong(x);
+ } else {
+ signed long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed long)-1;
+ val = __Pyx_PyInt_AsSignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ return (signed PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) {
+ return PyLong_AsLongLong(x);
+ } else {
+ signed PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsSignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+#ifndef __PYX_HAVE_RT_ImportType
+#define __PYX_HAVE_RT_ImportType
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
+ long size)
+{
+ PyObject *py_module = 0;
+ PyObject *result = 0;
+ PyObject *py_name = 0;
+
+ py_module = __Pyx_ImportModule(module_name);
+ if (!py_module)
+ goto bad;
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(class_name);
+ #else
+ py_name = PyUnicode_FromString(class_name);
+ #endif
+ if (!py_name)
+ goto bad;
+ result = PyObject_GetAttr(py_module, py_name);
+ Py_DECREF(py_name);
+ py_name = 0;
+ Py_DECREF(py_module);
+ py_module = 0;
+ if (!result)
+ goto bad;
+ if (!PyType_Check(result)) {
+ PyErr_Format(PyExc_TypeError,
+ "%s.%s is not a type object",
+ module_name, class_name);
+ goto bad;
+ }
+ if (((PyTypeObject *)result)->tp_basicsize != size) {
+ PyErr_Format(PyExc_ValueError,
+ "%s.%s does not appear to be the correct type object",
+ module_name, class_name);
+ goto bad;
+ }
+ return (PyTypeObject *)result;
+bad:
+ Py_XDECREF(py_module);
+ Py_XDECREF(result);
+ return 0;
+}
+#endif
+
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+
+static void __Pyx_AddTraceback(const char *funcname) {
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ PyObject *py_globals = 0;
+ PyObject *empty_string = 0;
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(__pyx_filename);
+ #else
+ py_srcfile = PyUnicode_FromString(__pyx_filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (__pyx_clineno) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ #if PY_MAJOR_VERSION < 3
+ empty_string = PyString_FromStringAndSize("", 0);
+ #else
+ empty_string = PyBytes_FromStringAndSize("", 0);
+ #endif
+ if (!empty_string) goto bad;
+ py_code = PyCode_New(
+ 0, /*int argcount,*/
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*int kwonlyargcount,*/
+ #endif
+ 0, /*int nlocals,*/
+ 0, /*int stacksize,*/
+ 0, /*int flags,*/
+ empty_string, /*PyObject *code,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ __pyx_lineno, /*int firstlineno,*/
+ empty_string /*PyObject *lnotab*/
+ );
+ if (!py_code) goto bad;
+ py_frame = PyFrame_New(
+ PyThreadState_GET(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ py_globals, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ py_frame->f_lineno = __pyx_lineno;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ Py_XDECREF(empty_string);
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+ while (t->p) {
+ #if PY_MAJOR_VERSION < 3
+ if (t->is_unicode && (!t->is_identifier)) {
+ *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
+ } else if (t->intern) {
+ *t->p = PyString_InternFromString(t->s);
+ } else {
+ *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
+ }
+ #else /* Python 3+ has unicode identifiers */
+ if (t->is_identifier || (t->is_unicode && t->intern)) {
+ *t->p = PyUnicode_InternFromString(t->s);
+ } else if (t->is_unicode) {
+ *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
+ } else {
+ *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
+ }
+ #endif
+ if (!*t->p)
+ return -1;
+ ++t;
+ }
+ return 0;
+}
+
+/* Type Conversion Functions */
+
+static INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
+ if (x == Py_True) return 1;
+ else if ((x == Py_False) | (x == Py_None)) return 0;
+ else return PyObject_IsTrue(x);
+}
+
+static INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
+ PyNumberMethods *m;
+ const char *name = NULL;
+ PyObject *res = NULL;
+#if PY_VERSION_HEX < 0x03000000
+ if (PyInt_Check(x) || PyLong_Check(x))
+#else
+ if (PyLong_Check(x))
+#endif
+ return Py_INCREF(x), x;
+ m = Py_TYPE(x)->tp_as_number;
+#if PY_VERSION_HEX < 0x03000000
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Int(x);
+ }
+ else if (m && m->nb_long) {
+ name = "long";
+ res = PyNumber_Long(x);
+ }
+#else
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Long(x);
+ }
+#endif
+ if (res) {
+#if PY_VERSION_HEX < 0x03000000
+ if (!PyInt_Check(res) && !PyLong_Check(res)) {
+#else
+ if (!PyLong_Check(res)) {
+#endif
+ PyErr_Format(PyExc_TypeError,
+ "__%s__ returned non-%s (type %.200s)",
+ name, name, Py_TYPE(res)->tp_name);
+ Py_DECREF(res);
+ return NULL;
+ }
+ }
+ else if (!PyErr_Occurred()) {
+ PyErr_SetString(PyExc_TypeError,
+ "an integer is required");
+ }
+ return res;
+}
+
+static INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
+ Py_ssize_t ival;
+ PyObject* x = PyNumber_Index(b);
+ if (!x) return -1;
+ ival = PyInt_AsSsize_t(x);
+ Py_DECREF(x);
+ return ival;
+}
+
+static INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
+#if PY_VERSION_HEX < 0x02050000
+ if (ival <= LONG_MAX)
+ return PyInt_FromLong((long)ival);
+ else {
+ unsigned char *bytes = (unsigned char *) &ival;
+ int one = 1; int little = (int)*(unsigned char*)&one;
+ return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
+ }
+#else
+ return PyInt_FromSize_t(ival);
+#endif
+}
+
+static INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
+ unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
+ if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
+ return (size_t)-1;
+ } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to size_t");
+ return (size_t)-1;
+ }
+ return (size_t)val;
+}
+
+
Added: trunk/yt/lagos/PointsInVolume.pyx
==============================================================================
--- (empty file)
+++ trunk/yt/lagos/PointsInVolume.pyx Mon Aug 24 18:07:09 2009
@@ -0,0 +1,71 @@
+"""
+Checks for points contained in a volume
+
+Author: John Wise <jwise77 at gmail.com>
+Affiliation: Princeton
+Homepage: http://yt.enzotools.org/
+License:
+ Copyright (C) 2009 John. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+
+import numpy as np
+cimport numpy as np
+cimport cython
+
+ at cython.wraparound(False)
+ at cython.boundscheck(False)
+def PointsInVolume(np.ndarray[np.float64_t, ndim=2] points,
+ np.ndarray[np.int8_t, ndim=1] pmask, # pixel mask
+ np.ndarray[np.float64_t, ndim=1] left_edge,
+ np.ndarray[np.float64_t, ndim=1] right_edge,
+ np.ndarray[np.int32_t, ndim=3] mask,
+ float dx):
+ cdef np.ndarray[np.int8_t, ndim=1] \
+ valid = np.zeros(points.shape[0], dtype='int8')
+ cdef int i, dim, count
+ cdef double dx_inv
+ cdef unsigned int idx[3]
+ count = 0
+ dx_inv = 1.0 / dx
+ for i in xrange(points.shape[0]):
+ if pmask[i] == 0:
+ continue
+ for dim in xrange(3):
+ if points[i,dim] < left_edge[dim] or points[i,dim] > right_edge[dim]:
+ valid[i] = 0
+ break
+ if valid[i] == 1:
+ for dim in xrange(3):
+ idx[dim] = <unsigned int> \
+ ((points[i,dim] - left_edge[dim]) * dx_inv)
+ if mask[idx[0], idx[1], idx[2]] == 1:
+ valid[i] = 1
+ count += 1
+
+ cdef np.ndarray[np.int32_t, ndim=1] result = np.empty(count, dtype='int32')
+ count = 0
+ for i in xrange(points.shape[0]):
+ if valid[i] == 1 and pmask[i] == 1:
+ result[count] = i
+ count += 1
+
+ return result
+
+
+
Modified: trunk/yt/lagos/setup.py
==============================================================================
--- trunk/yt/lagos/setup.py (original)
+++ trunk/yt/lagos/setup.py Mon Aug 24 18:07:09 2009
@@ -22,6 +22,7 @@
config.add_extension("PointCombine", "yt/lagos/PointCombine.c", libraries=["m"])
config.add_extension("RTIntegrator", "yt/lagos/RTIntegrator.c")
config.add_extension("Interpolators", "yt/lagos/Interpolators.c")
+ config.add_extension("PointsInVolume", "yt/lagos/PointsInVolume.c")
#config.add_extension("DepthFirstOctree", "yt/lagos/DepthFirstOctree.c")
config.add_subpackage("hop")
config.add_subpackage("fof")
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