int NI_FindObjects(PyArrayObject* input, npy_intp max_label,
npy_intp* regions)
{
int kk;
npy_intp size, jj;
NI_Iterator ii;
char *pi;
NPY_BEGIN_THREADS_DEF;
NPY_BEGIN_THREADS;
/* get input data, size and iterator: */
pi = (void *)PyArray_DATA(input);
size = 1;
for(kk = 0; kk < input->nd; kk++)
size *= input->dimensions[kk];
if (!NI_InitPointIterator(input, &ii))
goto exit;
if (input->nd > 0) {
for(jj = 0; jj < 2 * input->nd * max_label; jj++)
regions[jj] = -1;
} else {
for(jj = 0; jj < max_label; jj++)
regions[jj] = -1;
}
/* iterate over all points: */
for(jj = 0 ; jj < size; jj++) {
switch (NI_NormalizeType(input->descr->type_num)) {
CASE_FIND_OBJECT_POINT(pi, regions, input->nd, input->dimensions,
max_label, ii, Bool);
CASE_FIND_OBJECT_POINT(pi, regions, input->nd, input->dimensions,
max_label, ii, UInt8);
CASE_FIND_OBJECT_POINT(pi, regions, input->nd, input->dimensions,
max_label, ii, UInt16);
CASE_FIND_OBJECT_POINT(pi, regions, input->nd, input->dimensions,
max_label, ii, UInt32);
#if HAS_UINT64
CASE_FIND_OBJECT_POINT(pi, regions, input->nd, input->dimensions,
max_label, ii, UInt64);
#endif
CASE_FIND_OBJECT_POINT(pi, regions, input->nd, input->dimensions,
max_label, ii, Int8);
CASE_FIND_OBJECT_POINT(pi, regions, input->nd, input->dimensions,
max_label, ii, Int16);
CASE_FIND_OBJECT_POINT(pi, regions, input->nd, input->dimensions,
max_label, ii, Int32);
CASE_FIND_OBJECT_POINT(pi, regions, input->nd, input->dimensions,
max_label, ii, Int64);
break;
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
NI_ITERATOR_NEXT(ii, pi);
}
exit:
NPY_END_THREADS;
return PyErr_Occurred() ? 0 : 1;
}
/* Copy a line from an array to a buffer: */
int NI_ArrayToLineBuffer(NI_LineBuffer *buffer,
npy_intp *number_of_lines, int *more,
char * errmsg)
{
double *pb = buffer->buffer_data;
char *pa;
npy_intp length = buffer->line_length;
pb += buffer->size1;
*number_of_lines = 0;
/* fill until all lines in the array have been processed, or until
the buffer is full: */
while (buffer->next_line < buffer->array_lines &&
*number_of_lines < buffer->buffer_lines) {
pa = buffer->array_data;
/* copy the data from the array to the buffer: */
switch (buffer->array_type) {
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, Bool);
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, UInt8);
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, UInt16);
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, UInt32);
#if HAS_UINT64
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, UInt64);
#endif
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, Int8);
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, Int16);
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, Int32);
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, Int64);
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, Float32);
CASE_COPY_DATA_TO_LINE(pa, pb, length, buffer->line_stride, Float64);
default:
PyOS_snprintf(errmsg, NI_MAX_ERR_MSG, "array type %d not supported",
buffer->array_type);
return 0;
}
/* goto next line in the array: */
NI_ITERATOR_NEXT(buffer->iterator, buffer->array_data);
/* implement boundary conditions to the line: */
if (buffer->size1 + buffer->size2 > 0)
if (!NI_ExtendLine(pb - buffer->size1, length, buffer->size1,
buffer->size2, buffer->extend_mode,
buffer->extend_value,
errmsg))
return 0;
/* The number of the array lines copied: */
++(buffer->next_line);
/* keep track of (and return) the number of lines in the buffer: */
++(*number_of_lines);
pb += buffer->line_length + buffer->size1 + buffer->size2;
}
/* if not all array lines were processed, *more is set true: */
*more = buffer->next_line < buffer->array_lines;
return 1;
}
/* Copy a line from a buffer to an array: */
int NI_LineBufferToArray(NI_LineBuffer *buffer)
{
double *pb = buffer->buffer_data;
char *pa;
npy_intp jj, length = buffer->line_length;
pb += buffer->size1;
for(jj = 0; jj < buffer->buffer_lines; jj++) {
/* if all array lines are copied return: */
if (buffer->next_line == buffer->array_lines)
break;
pa = buffer->array_data;
/* copy data from the buffer to the array: */
switch (buffer->array_type) {
CASE_COPY_LINE_TO_DATA(NPY_BOOL, npy_bool,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_UBYTE, npy_ubyte,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_USHORT, npy_ushort,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_UINT, npy_uint,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_ULONG, npy_ulong,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_ULONGLONG, npy_ulonglong,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_BYTE, npy_byte,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_SHORT, npy_short,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_INT, npy_int,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_LONG, npy_long,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_LONGLONG, npy_longlong,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_FLOAT, npy_float,
pb, pa, length, buffer->line_stride);
CASE_COPY_LINE_TO_DATA(NPY_DOUBLE, npy_double,
pb, pa, length, buffer->line_stride);
default:
PyErr_Format(PyExc_RuntimeError, "array type %d not supported",
buffer->array_type);
return 0;
}
/* move to the next line in the array: */
NI_ITERATOR_NEXT(buffer->iterator, buffer->array_data);
/* number of lines copied: */
++(buffer->next_line);
/* move the buffer data pointer to the next line: */
pb += buffer->line_length + buffer->size1 + buffer->size2;
}
return 1;
}
/* Copy a line from a buffer to an array: */
int NI_LineBufferToArray(NI_LineBuffer *buffer)
{
double *pb = buffer->buffer_data;
char *pa;
maybelong jj, length = buffer->line_length;
pb += buffer->size1;
for(jj = 0; jj < buffer->buffer_lines; jj++) {
/* if all array lines are copied return: */
if (buffer->next_line == buffer->array_lines)
break;
pa = buffer->array_data;
/* copy data from the buffer to the array: */
switch (buffer->array_type) {
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, Bool);
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, UInt8);
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, UInt16);
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, UInt32);
#if HAS_UINT64
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, UInt64);
#endif
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, Int8);
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, Int16);
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, Int32);
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, Int64);
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, Float32);
CASE_COPY_LINE_TO_DATA(pb, pa, length, buffer->line_stride, Float64);
default:
PyErr_SetString(PyExc_RuntimeError, "array type not supported");
return 0;
}
/* move to the next line in the array: */
NI_ITERATOR_NEXT(buffer->iterator, buffer->array_data);
/* number of lines copied: */
++(buffer->next_line);
/* move the buffer data pointer to the next line: */
pb += buffer->line_length + buffer->size1 + buffer->size2;
}
return 1;
}
int NI_ZoomShift(PyArrayObject *input, PyArrayObject* zoom_ar,
PyArrayObject* shift_ar, PyArrayObject *output,
int order, int mode, double cval)
{
char *po, *pi;
npy_intp **zeros = NULL, **offsets = NULL, ***edge_offsets = NULL;
npy_intp ftmp[NPY_MAXDIMS], *fcoordinates = NULL, *foffsets = NULL;
npy_intp jj, hh, kk, filter_size, odimensions[NPY_MAXDIMS];
npy_intp idimensions[NPY_MAXDIMS], istrides[NPY_MAXDIMS];
npy_intp size;
double ***splvals = NULL;
NI_Iterator io;
npy_double *zooms = zoom_ar ? (npy_double*)PyArray_DATA(zoom_ar) : NULL;
npy_double *shifts = shift_ar ? (npy_double*)PyArray_DATA(shift_ar) : NULL;
int rank = 0;
NPY_BEGIN_THREADS_DEF;
NPY_BEGIN_THREADS;
for (kk = 0; kk < PyArray_NDIM(input); kk++) {
idimensions[kk] = PyArray_DIM(input, kk);
istrides[kk] = PyArray_STRIDE(input, kk);
odimensions[kk] = PyArray_DIM(output, kk);
}
rank = PyArray_NDIM(input);
/* if the mode is 'constant' we need some temps later: */
if (mode == NI_EXTEND_CONSTANT) {
zeros = malloc(rank * sizeof(npy_intp*));
if (NPY_UNLIKELY(!zeros)) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < rank; jj++)
zeros[jj] = NULL;
for(jj = 0; jj < rank; jj++) {
zeros[jj] = malloc(odimensions[jj] * sizeof(npy_intp));
if (NPY_UNLIKELY(!zeros[jj])) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
}
}
/* store offsets, along each axis: */
offsets = malloc(rank * sizeof(npy_intp*));
/* store spline coefficients, along each axis: */
splvals = malloc(rank * sizeof(double**));
/* store offsets at all edges: */
edge_offsets = malloc(rank * sizeof(npy_intp**));
if (NPY_UNLIKELY(!offsets || !splvals || !edge_offsets)) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < rank; jj++) {
offsets[jj] = NULL;
splvals[jj] = NULL;
edge_offsets[jj] = NULL;
}
for(jj = 0; jj < rank; jj++) {
offsets[jj] = malloc(odimensions[jj] * sizeof(npy_intp));
splvals[jj] = malloc(odimensions[jj] * sizeof(double*));
edge_offsets[jj] = malloc(odimensions[jj] * sizeof(npy_intp*));
if (NPY_UNLIKELY(!offsets[jj] || !splvals[jj] || !edge_offsets[jj])) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
for(hh = 0; hh < odimensions[jj]; hh++) {
splvals[jj][hh] = NULL;
edge_offsets[jj][hh] = NULL;
}
}
/* precalculate offsets, and offsets at the edge: */
for(jj = 0; jj < rank; jj++) {
double shift = 0.0, zoom = 0.0;
if (shifts)
shift = shifts[jj];
if (zooms)
zoom = zooms[jj];
for(kk = 0; kk < odimensions[jj]; kk++) {
double cc = (double)kk;
if (shifts)
cc += shift;
if (zooms)
cc *= zoom;
cc = map_coordinate(cc, idimensions[jj], mode);
if (cc > -1.0) {
npy_intp start;
if (zeros && zeros[jj])
zeros[jj][kk] = 0;
if (order & 1) {
start = (npy_intp)floor(cc) - order / 2;
} else {
start = (npy_intp)floor(cc + 0.5) - order / 2;
}
offsets[jj][kk] = istrides[jj] * start;
if (start < 0 || start + order >= idimensions[jj]) {
edge_offsets[jj][kk] = malloc((order + 1) * sizeof(npy_intp));
if (NPY_UNLIKELY(!edge_offsets[jj][kk])) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
for(hh = 0; hh <= order; hh++) {
npy_intp idx = start + hh;
npy_intp len = idimensions[jj];
if (len <= 1) {
idx = 0;
} else {
npy_intp s2 = 2 * len - 2;
if (idx < 0) {
idx = s2 * (npy_intp)(-idx / s2) + idx;
idx = idx <= 1 - len ? idx + s2 : -idx;
} else if (idx >= len) {
idx -= s2 * (npy_intp)(idx / s2);
if (idx >= len)
idx = s2 - idx;
}
}
edge_offsets[jj][kk][hh] = istrides[jj] * (idx - start);
}
}
if (order > 0) {
splvals[jj][kk] = malloc((order + 1) * sizeof(double));
if (NPY_UNLIKELY(!splvals[jj][kk])) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
spline_coefficients(cc, order, splvals[jj][kk]);
}
} else {
zeros[jj][kk] = 1;
}
}
}
filter_size = 1;
for(jj = 0; jj < rank; jj++)
filter_size *= order + 1;
if (!NI_InitPointIterator(output, &io))
goto exit;
pi = (void *)PyArray_DATA(input);
po = (void *)PyArray_DATA(output);
/* store all coordinates and offsets with filter: */
fcoordinates = malloc(rank * filter_size * sizeof(npy_intp));
foffsets = malloc(filter_size * sizeof(npy_intp));
if (NPY_UNLIKELY(!fcoordinates || !foffsets)) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < rank; jj++)
ftmp[jj] = 0;
kk = 0;
for(hh = 0; hh < filter_size; hh++) {
for(jj = 0; jj < rank; jj++)
fcoordinates[jj + hh * rank] = ftmp[jj];
foffsets[hh] = kk;
for(jj = rank - 1; jj >= 0; jj--) {
if (ftmp[jj] < order) {
ftmp[jj]++;
kk += istrides[jj];
break;
} else {
ftmp[jj] = 0;
kk -= istrides[jj] * order;
}
}
}
size = PyArray_SIZE(output);
for(kk = 0; kk < size; kk++) {
double t = 0.0;
npy_intp edge = 0, oo = 0, zero = 0;
for(hh = 0; hh < rank; hh++) {
if (zeros && zeros[hh][io.coordinates[hh]]) {
/* we use constant border condition */
zero = 1;
break;
}
oo += offsets[hh][io.coordinates[hh]];
if (edge_offsets[hh][io.coordinates[hh]])
edge = 1;
}
if (!zero) {
npy_intp *ff = fcoordinates;
const int type_num = PyArray_TYPE(input);
t = 0.0;
for(hh = 0; hh < filter_size; hh++) {
npy_intp idx = 0;
double coeff = 0.0;
if (NPY_UNLIKELY(edge)) {
/* use precalculated edge offsets: */
for(jj = 0; jj < rank; jj++) {
if (edge_offsets[jj][io.coordinates[jj]])
idx += edge_offsets[jj][io.coordinates[jj]][ff[jj]];
else
idx += ff[jj] * istrides[jj];
}
idx += oo;
} else {
/* use normal offsets: */
idx += oo + foffsets[hh];
}
switch (type_num) {
CASE_INTERP_COEFF(NPY_BOOL, npy_bool,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_UBYTE, npy_ubyte,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_USHORT, npy_ushort,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_UINT, npy_uint,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_ULONG, npy_ulong,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_ULONGLONG, npy_ulonglong,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_BYTE, npy_byte,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_SHORT, npy_short,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_INT, npy_int,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_LONG, npy_long,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_LONGLONG, npy_longlong,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_FLOAT, npy_float,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_DOUBLE, npy_double,
coeff, pi, idx);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError,
"data type not supported");
goto exit;
}
/* calculate interpolated value: */
for(jj = 0; jj < rank; jj++)
if (order > 0)
coeff *= splvals[jj][io.coordinates[jj]][ff[jj]];
t += coeff;
ff += rank;
}
} else {
t = cval;
}
/* store output: */
switch (PyArray_TYPE(output)) {
CASE_INTERP_OUT(NPY_BOOL, npy_bool, po, t);
CASE_INTERP_OUT_UINT(UBYTE, npy_ubyte, po, t);
CASE_INTERP_OUT_UINT(USHORT, npy_ushort, po, t);
CASE_INTERP_OUT_UINT(UINT, npy_uint, po, t);
CASE_INTERP_OUT_UINT(ULONG, npy_ulong, po, t);
CASE_INTERP_OUT_UINT(ULONGLONG, npy_ulonglong, po, t);
CASE_INTERP_OUT_INT(BYTE, npy_byte, po, t);
CASE_INTERP_OUT_INT(SHORT, npy_short, po, t);
CASE_INTERP_OUT_INT(INT, npy_int, po, t);
CASE_INTERP_OUT_INT(LONG, npy_long, po, t);
CASE_INTERP_OUT_INT(LONGLONG, npy_longlong, po, t);
CASE_INTERP_OUT(NPY_FLOAT, npy_float, po, t);
CASE_INTERP_OUT(NPY_DOUBLE, npy_double, po, t);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
NI_ITERATOR_NEXT(io, po);
}
exit:
NPY_END_THREADS;
if (zeros) {
for(jj = 0; jj < rank; jj++)
free(zeros[jj]);
free(zeros);
}
if (offsets) {
for(jj = 0; jj < rank; jj++)
free(offsets[jj]);
free(offsets);
}
if (splvals) {
for(jj = 0; jj < rank; jj++) {
if (splvals[jj]) {
for(hh = 0; hh < odimensions[jj]; hh++)
free(splvals[jj][hh]);
free(splvals[jj]);
}
}
free(splvals);
}
if (edge_offsets) {
for(jj = 0; jj < rank; jj++) {
if (edge_offsets[jj]) {
for(hh = 0; hh < odimensions[jj]; hh++)
free(edge_offsets[jj][hh]);
free(edge_offsets[jj]);
}
}
free(edge_offsets);
}
free(foffsets);
free(fcoordinates);
return PyErr_Occurred() ? 0 : 1;
}
int
NI_GeometricTransform(PyArrayObject *input, int (*map)(npy_intp*, double*,
int, int, void*), void* map_data, PyArrayObject* matrix_ar,
PyArrayObject* shift_ar, PyArrayObject *coordinates,
PyArrayObject *output, int order, int mode, double cval)
{
char *po, *pi, *pc = NULL;
npy_intp **edge_offsets = NULL, **data_offsets = NULL, filter_size;
npy_intp ftmp[NPY_MAXDIMS], *fcoordinates = NULL, *foffsets = NULL;
npy_intp cstride = 0, kk, hh, ll, jj;
npy_intp size;
double **splvals = NULL, icoor[NPY_MAXDIMS];
npy_intp idimensions[NPY_MAXDIMS], istrides[NPY_MAXDIMS];
NI_Iterator io, ic;
npy_double *matrix = matrix_ar ? (npy_double*)PyArray_DATA(matrix_ar) : NULL;
npy_double *shift = shift_ar ? (npy_double*)PyArray_DATA(shift_ar) : NULL;
int irank = 0, orank;
NPY_BEGIN_THREADS_DEF;
NPY_BEGIN_THREADS;
for(kk = 0; kk < PyArray_NDIM(input); kk++) {
idimensions[kk] = PyArray_DIM(input, kk);
istrides[kk] = PyArray_STRIDE(input, kk);
}
irank = PyArray_NDIM(input);
orank = PyArray_NDIM(output);
/* if the mapping is from array coordinates: */
if (coordinates) {
/* initialize a line iterator along the first axis: */
if (!NI_InitPointIterator(coordinates, &ic))
goto exit;
cstride = ic.strides[0];
if (!NI_LineIterator(&ic, 0))
goto exit;
pc = (void *)(PyArray_DATA(coordinates));
}
/* offsets used at the borders: */
edge_offsets = malloc(irank * sizeof(npy_intp*));
data_offsets = malloc(irank * sizeof(npy_intp*));
if (NPY_UNLIKELY(!edge_offsets || !data_offsets)) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < irank; jj++)
data_offsets[jj] = NULL;
for(jj = 0; jj < irank; jj++) {
data_offsets[jj] = malloc((order + 1) * sizeof(npy_intp));
if (NPY_UNLIKELY(!data_offsets[jj])) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
}
/* will hold the spline coefficients: */
splvals = malloc(irank * sizeof(double*));
if (NPY_UNLIKELY(!splvals)) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < irank; jj++)
splvals[jj] = NULL;
for(jj = 0; jj < irank; jj++) {
splvals[jj] = malloc((order + 1) * sizeof(double));
if (NPY_UNLIKELY(!splvals[jj])) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
}
filter_size = 1;
for(jj = 0; jj < irank; jj++)
filter_size *= order + 1;
/* initialize output iterator: */
if (!NI_InitPointIterator(output, &io))
goto exit;
/* get data pointers: */
pi = (void *)PyArray_DATA(input);
po = (void *)PyArray_DATA(output);
/* make a table of all possible coordinates within the spline filter: */
fcoordinates = malloc(irank * filter_size * sizeof(npy_intp));
/* make a table of all offsets within the spline filter: */
foffsets = malloc(filter_size * sizeof(npy_intp));
if (NPY_UNLIKELY(!fcoordinates || !foffsets)) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < irank; jj++)
ftmp[jj] = 0;
kk = 0;
for(hh = 0; hh < filter_size; hh++) {
for(jj = 0; jj < irank; jj++)
fcoordinates[jj + hh * irank] = ftmp[jj];
foffsets[hh] = kk;
for(jj = irank - 1; jj >= 0; jj--) {
if (ftmp[jj] < order) {
ftmp[jj]++;
kk += istrides[jj];
break;
} else {
ftmp[jj] = 0;
kk -= istrides[jj] * order;
}
}
}
size = PyArray_SIZE(output);
for(kk = 0; kk < size; kk++) {
double t = 0.0;
int constant = 0, edge = 0;
npy_intp offset = 0;
if (map) {
NPY_END_THREADS;
/* call mappint functions: */
if (!map(io.coordinates, icoor, orank, irank, map_data)) {
if (!PyErr_Occurred())
PyErr_SetString(PyExc_RuntimeError,
"unknown error in mapping function");
goto exit;
}
NPY_BEGIN_THREADS;
} else if (matrix) {
/* do an affine transformation: */
npy_double *p = matrix;
for(hh = 0; hh < irank; hh++) {
icoor[hh] = 0.0;
for(ll = 0; ll < orank; ll++)
icoor[hh] += io.coordinates[ll] * *p++;
icoor[hh] += shift[hh];
}
} else if (coordinates) {
/* mapping is from an coordinates array: */
char *p = pc;
switch (PyArray_TYPE(coordinates)) {
CASE_MAP_COORDINATES(NPY_BOOL, npy_bool,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_UBYTE, npy_ubyte,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_USHORT, npy_ushort,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_UINT, npy_uint,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_ULONG, npy_ulong,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_ULONGLONG, npy_ulonglong,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_BYTE, npy_byte,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_SHORT, npy_short,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_INT, npy_int,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_LONG, npy_long,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_LONGLONG, npy_longlong,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_FLOAT, npy_float,
p, icoor, irank, cstride);
CASE_MAP_COORDINATES(NPY_DOUBLE, npy_double,
p, icoor, irank, cstride);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError,
"coordinate array data type not supported");
goto exit;
}
}
/* iterate over axes: */
for(hh = 0; hh < irank; hh++) {
/* if the input coordinate is outside the borders, map it: */
double cc = map_coordinate(icoor[hh], idimensions[hh], mode);
if (cc > -1.0) {
/* find the filter location along this axis: */
npy_intp start;
if (order & 1) {
start = (npy_intp)floor(cc) - order / 2;
} else {
start = (npy_intp)floor(cc + 0.5) - order / 2;
}
/* get the offset to the start of the filter: */
offset += istrides[hh] * start;
if (start < 0 || start + order >= idimensions[hh]) {
/* implement border mapping, if outside border: */
edge = 1;
edge_offsets[hh] = data_offsets[hh];
for(ll = 0; ll <= order; ll++) {
npy_intp idx = start + ll;
npy_intp len = idimensions[hh];
if (len <= 1) {
idx = 0;
} else {
npy_intp s2 = 2 * len - 2;
if (idx < 0) {
idx = s2 * (int)(-idx / s2) + idx;
idx = idx <= 1 - len ? idx + s2 : -idx;
} else if (idx >= len) {
idx -= s2 * (int)(idx / s2);
if (idx >= len)
idx = s2 - idx;
}
}
/* calculate and store the offests at this edge: */
edge_offsets[hh][ll] = istrides[hh] * (idx - start);
}
} else {
/* we are not at the border, use precalculated offsets: */
edge_offsets[hh] = NULL;
}
spline_coefficients(cc, order, splvals[hh]);
} else {
/* we use the constant border condition: */
constant = 1;
break;
}
}
if (!constant) {
npy_intp *ff = fcoordinates;
const int type_num = PyArray_TYPE(input);
t = 0.0;
for(hh = 0; hh < filter_size; hh++) {
double coeff = 0.0;
npy_intp idx = 0;
if (NPY_UNLIKELY(edge)) {
for(ll = 0; ll < irank; ll++) {
if (edge_offsets[ll])
idx += edge_offsets[ll][ff[ll]];
else
idx += ff[ll] * istrides[ll];
}
} else {
idx = foffsets[hh];
}
idx += offset;
switch (type_num) {
CASE_INTERP_COEFF(NPY_BOOL, npy_bool,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_UBYTE, npy_ubyte,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_USHORT, npy_ushort,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_UINT, npy_uint,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_ULONG, npy_ulong,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_ULONGLONG, npy_ulonglong,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_BYTE, npy_byte,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_SHORT, npy_short,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_INT, npy_int,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_LONG, npy_long,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_LONGLONG, npy_longlong,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_FLOAT, npy_float,
coeff, pi, idx);
CASE_INTERP_COEFF(NPY_DOUBLE, npy_double,
coeff, pi, idx);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError,
"data type not supported");
goto exit;
}
/* calculate the interpolated value: */
for(ll = 0; ll < irank; ll++)
if (order > 0)
coeff *= splvals[ll][ff[ll]];
t += coeff;
ff += irank;
}
} else {
t = cval;
}
/* store output value: */
switch (PyArray_TYPE(output)) {
CASE_INTERP_OUT(NPY_BOOL, npy_bool, po, t);
CASE_INTERP_OUT_UINT(UBYTE, npy_ubyte, po, t);
CASE_INTERP_OUT_UINT(USHORT, npy_ushort, po, t);
CASE_INTERP_OUT_UINT(UINT, npy_uint, po, t);
CASE_INTERP_OUT_UINT(ULONG, npy_ulong, po, t);
CASE_INTERP_OUT_UINT(ULONGLONG, npy_ulonglong, po, t);
CASE_INTERP_OUT_INT(BYTE, npy_byte, po, t);
CASE_INTERP_OUT_INT(SHORT, npy_short, po, t);
CASE_INTERP_OUT_INT(INT, npy_int, po, t);
CASE_INTERP_OUT_INT(LONG, npy_long, po, t);
CASE_INTERP_OUT_INT(LONGLONG, npy_longlong, po, t);
CASE_INTERP_OUT(NPY_FLOAT, npy_float, po, t);
CASE_INTERP_OUT(NPY_DOUBLE, npy_double, po, t);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
if (coordinates) {
NI_ITERATOR_NEXT2(io, ic, po, pc);
} else {
NI_ITERATOR_NEXT(io, po);
}
}
exit:
NPY_END_THREADS;
free(edge_offsets);
if (data_offsets) {
for(jj = 0; jj < irank; jj++)
free(data_offsets[jj]);
free(data_offsets);
}
if (splvals) {
for(jj = 0; jj < irank; jj++)
free(splvals[jj]);
free(splvals);
}
free(foffsets);
free(fcoordinates);
return PyErr_Occurred() ? 0 : 1;
}
int NI_ZoomShift(PyArrayObject *input, PyArrayObject* zoom_ar,
PyArrayObject* shift_ar, PyArrayObject *output,
int order, int mode, double cval)
{
char *po, *pi;
npy_intp **zeros = NULL, **offsets = NULL, ***edge_offsets = NULL;
npy_intp ftmp[MAXDIM], *fcoordinates = NULL, *foffsets = NULL;
npy_intp jj, hh, kk, filter_size, odimensions[MAXDIM];
npy_intp idimensions[MAXDIM], istrides[MAXDIM], *idxs = NULL;
npy_intp size;
double ***splvals = NULL;
NI_Iterator io;
Float64 *zooms = zoom_ar ? (Float64*)PyArray_DATA(zoom_ar) : NULL;
Float64 *shifts = shift_ar ? (Float64*)PyArray_DATA(shift_ar) : NULL;
int rank = 0, qq;
for(kk = 0; kk < input->nd; kk++) {
idimensions[kk] = input->dimensions[kk];
istrides[kk] = input->strides[kk];
odimensions[kk] = output->dimensions[kk];
}
rank = input->nd;
/* if the mode is 'constant' we need some temps later: */
if (mode == NI_EXTEND_CONSTANT) {
zeros = (npy_intp**)malloc(rank * sizeof(npy_intp*));
if (!zeros) {
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < rank; jj++)
zeros[jj] = NULL;
for(jj = 0; jj < rank; jj++) {
zeros[jj] = (npy_intp*)malloc(odimensions[jj] * sizeof(npy_intp));
if(!zeros[jj]) {
PyErr_NoMemory();
goto exit;
}
}
}
/* store offsets, along each axis: */
offsets = (npy_intp**)malloc(rank * sizeof(npy_intp*));
/* store spline coefficients, along each axis: */
splvals = (double***)malloc(rank * sizeof(double**));
/* store offsets at all edges: */
edge_offsets = (npy_intp***)malloc(rank * sizeof(npy_intp**));
if (!offsets || !splvals || !edge_offsets) {
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < rank; jj++) {
offsets[jj] = NULL;
splvals[jj] = NULL;
edge_offsets[jj] = NULL;
}
for(jj = 0; jj < rank; jj++) {
offsets[jj] = (npy_intp*)malloc(odimensions[jj] * sizeof(npy_intp));
splvals[jj] = (double**)malloc(odimensions[jj] * sizeof(double*));
edge_offsets[jj] = (npy_intp**)malloc(odimensions[jj] * sizeof(npy_intp*));
if (!offsets[jj] || !splvals[jj] || !edge_offsets[jj]) {
PyErr_NoMemory();
goto exit;
}
for(hh = 0; hh < odimensions[jj]; hh++) {
splvals[jj][hh] = NULL;
edge_offsets[jj][hh] = NULL;
}
}
/* precalculate offsets, and offsets at the edge: */
for(jj = 0; jj < rank; jj++) {
double shift = 0.0, zoom = 0.0;
if (shifts)
shift = shifts[jj];
if (zooms)
zoom = zooms[jj];
for(kk = 0; kk < odimensions[jj]; kk++) {
double cc = (double)kk;
if (shifts)
cc += shift;
if (zooms)
cc *= zoom;
cc = map_coordinate(cc, idimensions[jj], mode);
if (cc > -1.0) {
int start;
if (zeros && zeros[jj])
zeros[jj][kk] = 0;
if (order & 1) {
start = (int)floor(cc) - order / 2;
} else {
start = (int)floor(cc + 0.5) - order / 2;
}
offsets[jj][kk] = istrides[jj] * start;
if (start < 0 || start + order >= idimensions[jj]) {
edge_offsets[jj][kk] = (npy_intp*)malloc((order + 1) * sizeof(npy_intp));
if (!edge_offsets[jj][kk]) {
PyErr_NoMemory();
goto exit;
}
for(hh = 0; hh <= order; hh++) {
int idx = start + hh;
int len = idimensions[jj];
if (len <= 1) {
idx = 0;
} else {
int s2 = 2 * len - 2;
if (idx < 0) {
idx = s2 * (int)(-idx / s2) + idx;
idx = idx <= 1 - len ? idx + s2 : -idx;
} else if (idx >= len) {
idx -= s2 * (int)(idx / s2);
if (idx >= len)
idx = s2 - idx;
}
}
edge_offsets[jj][kk][hh] = istrides[jj] * (idx - start);
}
}
if (order > 0) {
splvals[jj][kk] = (double*)malloc((order + 1) * sizeof(double));
if (!splvals[jj][kk]) {
PyErr_NoMemory();
goto exit;
}
spline_coefficients(cc, order, splvals[jj][kk]);
}
} else {
zeros[jj][kk] = 1;
}
}
}
filter_size = 1;
for(jj = 0; jj < rank; jj++)
filter_size *= order + 1;
idxs = (npy_intp*)malloc(filter_size * sizeof(idxs));
if (!idxs) {
PyErr_NoMemory();
goto exit;
}
if (!NI_InitPointIterator(output, &io))
goto exit;
pi = (void *)PyArray_DATA(input);
po = (void *)PyArray_DATA(output);
/* store all coordinates and offsets with filter: */
fcoordinates = (npy_intp*)malloc(rank * filter_size * sizeof(npy_intp));
foffsets = (npy_intp*)malloc(filter_size * sizeof(npy_intp));
if (!fcoordinates || !foffsets) {
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < rank; jj++)
ftmp[jj] = 0;
kk = 0;
for(hh = 0; hh < filter_size; hh++) {
for(jj = 0; jj < rank; jj++)
fcoordinates[jj + hh * rank] = ftmp[jj];
foffsets[hh] = kk;
for(jj = rank - 1; jj >= 0; jj--) {
if (ftmp[jj] < order) {
ftmp[jj]++;
kk += istrides[jj];
break;
} else {
ftmp[jj] = 0;
kk -= istrides[jj] * order;
}
}
}
size = 1;
for(qq = 0; qq < output->nd; qq++)
size *= output->dimensions[qq];
for(kk = 0; kk < size; kk++) {
double t = 0.0;
int edge = 0, oo = 0, zero = 0;
for(hh = 0; hh < rank; hh++) {
if (zeros && zeros[hh][io.coordinates[hh]]) {
/* we use constant border condition */
zero = 1;
break;
}
oo += offsets[hh][io.coordinates[hh]];
if (edge_offsets[hh][io.coordinates[hh]])
edge = 1;
}
if (!zero) {
npy_intp *ff = fcoordinates;
for(hh = 0; hh < filter_size; hh++) {
int idx = 0;
if (edge) {
/* use precalculated edge offsets: */
for(jj = 0; jj < rank; jj++) {
if (edge_offsets[jj][io.coordinates[jj]])
idx += edge_offsets[jj][io.coordinates[jj]][ff[jj]];
else
idx += ff[jj] * istrides[jj];
}
idx += oo;
} else {
/* use normal offsets: */
idx += oo + foffsets[hh];
}
idxs[hh] = idx;
ff += rank;
}
}
if (!zero) {
npy_intp *ff = fcoordinates;
t = 0.0;
for(hh = 0; hh < filter_size; hh++) {
double coeff = 0.0;
switch(input->descr->type_num) {
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Bool);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], UInt8);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], UInt16);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], UInt32);
#if HAS_UINT64
CASE_INTERP_COEFF(coeff, pi, idxs[hh], UInt64);
#endif
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Int8);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Int16);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Int32);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Int64);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Float32);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Float64);
default:
PyErr_SetString(PyExc_RuntimeError,
"data type not supported");
goto exit;
}
/* calculate interpolated value: */
for(jj = 0; jj < rank; jj++)
if (order > 0)
coeff *= splvals[jj][io.coordinates[jj]][ff[jj]];
t += coeff;
ff += rank;
}
} else {
t = cval;
}
/* store output: */
switch (output->descr->type_num) {
CASE_INTERP_OUT(po, t, Bool);
CASE_INTERP_OUT_UINT(po, t, UInt8, 0, MAX_UINT8);
CASE_INTERP_OUT_UINT(po, t, UInt16, 0, MAX_UINT16);
CASE_INTERP_OUT_UINT(po, t, UInt32, 0, MAX_UINT32);
#if HAS_UINT64
/* FIXME */
CASE_INTERP_OUT_UINT(po, t, UInt64, 0, MAX_UINT32);
#endif
CASE_INTERP_OUT_INT(po, t, Int8, MIN_INT8, MAX_INT8);
CASE_INTERP_OUT_INT(po, t, Int16, MIN_INT16, MAX_INT16);
CASE_INTERP_OUT_INT(po, t, Int32, MIN_INT32, MAX_INT32);
CASE_INTERP_OUT_INT(po, t, Int64, MIN_INT64, MAX_INT64);
CASE_INTERP_OUT(po, t, Float32);
CASE_INTERP_OUT(po, t, Float64);
default:
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
NI_ITERATOR_NEXT(io, po);
}
exit:
if (zeros) {
for(jj = 0; jj < rank; jj++)
if (zeros[jj])
free(zeros[jj]);
free(zeros);
}
if (offsets) {
for(jj = 0; jj < rank; jj++)
if (offsets[jj])
free(offsets[jj]);
free(offsets);
}
if (splvals) {
for(jj = 0; jj < rank; jj++) {
if (splvals[jj]) {
for(hh = 0; hh < odimensions[jj]; hh++)
if (splvals[jj][hh])
free(splvals[jj][hh]);
free(splvals[jj]);
}
}
free(splvals);
}
if (edge_offsets) {
for(jj = 0; jj < rank; jj++) {
if (edge_offsets[jj]) {
for(hh = 0; hh < odimensions[jj]; hh++)
if (edge_offsets[jj][hh])
free(edge_offsets[jj][hh]);
free(edge_offsets[jj]);
}
}
free(edge_offsets);
}
if (foffsets)
free(foffsets);
if (fcoordinates)
free(fcoordinates);
if (idxs)
free(idxs);
return PyErr_Occurred() ? 0 : 1;
}
int
NI_GeometricTransform(PyArrayObject *input, int (*map)(npy_intp*, double*,
int, int, void*), void* map_data, PyArrayObject* matrix_ar,
PyArrayObject* shift_ar, PyArrayObject *coordinates,
PyArrayObject *output, int order, int mode, double cval)
{
char *po, *pi, *pc = NULL;
npy_intp **edge_offsets = NULL, **data_offsets = NULL, filter_size;
npy_intp ftmp[MAXDIM], *fcoordinates = NULL, *foffsets = NULL;
npy_intp cstride = 0, kk, hh, ll, jj, *idxs = NULL;
npy_intp size;
double **splvals = NULL, icoor[MAXDIM];
npy_intp idimensions[MAXDIM], istrides[MAXDIM];
NI_Iterator io, ic;
Float64 *matrix = matrix_ar ? (Float64*)PyArray_DATA(matrix_ar) : NULL;
Float64 *shift = shift_ar ? (Float64*)PyArray_DATA(shift_ar) : NULL;
int irank = 0, orank, qq;
for(kk = 0; kk < input->nd; kk++) {
idimensions[kk] = input->dimensions[kk];
istrides[kk] = input->strides[kk];
}
irank = input->nd;
orank = output->nd;
/* if the mapping is from array coordinates: */
if (coordinates) {
/* initialze a line iterator along the first axis: */
if (!NI_InitPointIterator(coordinates, &ic))
goto exit;
cstride = ic.strides[0];
if (!NI_LineIterator(&ic, 0))
goto exit;
pc = (void *)(PyArray_DATA(coordinates));
}
/* offsets used at the borders: */
edge_offsets = (npy_intp**)malloc(irank * sizeof(npy_intp*));
data_offsets = (npy_intp**)malloc(irank * sizeof(npy_intp*));
if (!edge_offsets || !data_offsets) {
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < irank; jj++)
data_offsets[jj] = NULL;
for(jj = 0; jj < irank; jj++) {
data_offsets[jj] = (npy_intp*)malloc((order + 1) * sizeof(npy_intp));
if (!data_offsets[jj]) {
PyErr_NoMemory();
goto exit;
}
}
/* will hold the spline coefficients: */
splvals = (double**)malloc(irank * sizeof(double*));
if (!splvals) {
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < irank; jj++)
splvals[jj] = NULL;
for(jj = 0; jj < irank; jj++) {
splvals[jj] = (double*)malloc((order + 1) * sizeof(double));
if (!splvals[jj]) {
PyErr_NoMemory();
goto exit;
}
}
filter_size = 1;
for(jj = 0; jj < irank; jj++)
filter_size *= order + 1;
idxs = (npy_intp*)malloc(filter_size * sizeof(idxs));
if (!idxs) {
PyErr_NoMemory();
goto exit;
}
/* initialize output iterator: */
if (!NI_InitPointIterator(output, &io))
goto exit;
/* get data pointers: */
pi = (void *)PyArray_DATA(input);
po = (void *)PyArray_DATA(output);
/* make a table of all possible coordinates within the spline filter: */
fcoordinates = (npy_intp*)malloc(irank * filter_size * sizeof(npy_intp));
/* make a table of all offsets within the spline filter: */
foffsets = (npy_intp*)malloc(filter_size * sizeof(npy_intp));
if (!fcoordinates || !foffsets) {
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < irank; jj++)
ftmp[jj] = 0;
kk = 0;
for(hh = 0; hh < filter_size; hh++) {
for(jj = 0; jj < irank; jj++)
fcoordinates[jj + hh * irank] = ftmp[jj];
foffsets[hh] = kk;
for(jj = irank - 1; jj >= 0; jj--) {
if (ftmp[jj] < order) {
ftmp[jj]++;
kk += istrides[jj];
break;
} else {
ftmp[jj] = 0;
kk -= istrides[jj] * order;
}
}
}
size = 1;
for(qq = 0; qq < output->nd; qq++)
size *= output->dimensions[qq];
for(kk = 0; kk < size; kk++) {
double t = 0.0;
int constant = 0, edge = 0, offset = 0;
if (map) {
/* call mappint functions: */
if (!map(io.coordinates, icoor, orank, irank, map_data)) {
if (!PyErr_Occurred())
PyErr_SetString(PyExc_RuntimeError,
"unknown error in mapping function");
goto exit;
}
} else if (matrix) {
/* do an affine transformation: */
Float64 *p = matrix;
for(hh = 0; hh < irank; hh++) {
icoor[hh] = 0.0;
for(ll = 0; ll < orank; ll++)
icoor[hh] += io.coordinates[ll] * *p++;
icoor[hh] += shift[hh];
}
} else if (coordinates) {
/* mapping is from an coordinates array: */
char *p = pc;
switch(coordinates->descr->type_num) {
CASE_MAP_COORDINATES(p, icoor, irank, cstride, Bool);
CASE_MAP_COORDINATES(p, icoor, irank, cstride, UInt8);
CASE_MAP_COORDINATES(p, icoor, irank, cstride, UInt16);
CASE_MAP_COORDINATES(p, icoor, irank, cstride, UInt32);
#if HAS_UINT64
CASE_MAP_COORDINATES(p, icoor, irank, cstride, UInt64);
#endif
CASE_MAP_COORDINATES(p, icoor, irank, cstride, Int8);
CASE_MAP_COORDINATES(p, icoor, irank, cstride, Int16);
CASE_MAP_COORDINATES(p, icoor, irank, cstride, Int32);
CASE_MAP_COORDINATES(p, icoor, irank, cstride, Int64);
CASE_MAP_COORDINATES(p, icoor, irank, cstride, Float32);
CASE_MAP_COORDINATES(p, icoor, irank, cstride, Float64);
default:
PyErr_SetString(PyExc_RuntimeError,
"coordinate array data type not supported");
goto exit;
}
}
/* iterate over axes: */
for(hh = 0; hh < irank; hh++) {
/* if the input coordinate is outside the borders, map it: */
double cc = map_coordinate(icoor[hh], idimensions[hh], mode);
if (cc > -1.0) {
/* find the filter location along this axis: */
int start;
if (order & 1) {
start = (int)floor(cc) - order / 2;
} else {
start = (int)floor(cc + 0.5) - order / 2;
}
/* get the offset to the start of the filter: */
offset += istrides[hh] * start;
if (start < 0 || start + order >= idimensions[hh]) {
/* implement border mapping, if outside border: */
edge = 1;
edge_offsets[hh] = data_offsets[hh];
for(ll = 0; ll <= order; ll++) {
int idx = start + ll;
int len = idimensions[hh];
if (len <= 1) {
idx = 0;
} else {
int s2 = 2 * len - 2;
if (idx < 0) {
idx = s2 * (int)(-idx / s2) + idx;
idx = idx <= 1 - len ? idx + s2 : -idx;
} else if (idx >= len) {
idx -= s2 * (int)(idx / s2);
if (idx >= len)
idx = s2 - idx;
}
}
/* calculate and store the offests at this edge: */
edge_offsets[hh][ll] = istrides[hh] * (idx - start);
}
} else {
/* we are not at the border, use precalculated offsets: */
edge_offsets[hh] = NULL;
}
spline_coefficients(cc, order, splvals[hh]);
} else {
/* we use the constant border condition: */
constant = 1;
break;
}
}
if (!constant) {
npy_intp *ff = fcoordinates;
for(hh = 0; hh < filter_size; hh++) {
int idx = 0;
if (edge) {
for(ll = 0; ll < irank; ll++) {
if (edge_offsets[ll])
idx += edge_offsets[ll][ff[ll]];
else
idx += ff[ll] * istrides[ll];
}
} else {
idx = foffsets[hh];
}
idx += offset;
idxs[hh] = idx;
ff += irank;
}
}
if (!constant) {
npy_intp *ff = fcoordinates;
t = 0.0;
for(hh = 0; hh < filter_size; hh++) {
double coeff = 0.0;
switch(input->descr->type_num) {
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Bool);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], UInt8);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], UInt16);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], UInt32);
#if HAS_UINT64
CASE_INTERP_COEFF(coeff, pi, idxs[hh], UInt64);
#endif
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Int8);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Int16);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Int32);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Int64);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Float32);
CASE_INTERP_COEFF(coeff, pi, idxs[hh], Float64);
default:
PyErr_SetString(PyExc_RuntimeError,
"data type not supported");
goto exit;
}
/* calculate the interpolated value: */
for(ll = 0; ll < irank; ll++)
if (order > 0)
coeff *= splvals[ll][ff[ll]];
t += coeff;
ff += irank;
}
} else {
t = cval;
}
/* store output value: */
switch (output->descr->type_num) {
CASE_INTERP_OUT(po, t, Bool);
CASE_INTERP_OUT_UINT(po, t, UInt8, 0, MAX_UINT8);
CASE_INTERP_OUT_UINT(po, t, UInt16, 0, MAX_UINT16);
CASE_INTERP_OUT_UINT(po, t, UInt32, 0, MAX_UINT32);
#if HAS_UINT64
/* FIXME */
CASE_INTERP_OUT_UINT(po, t, UInt64, 0, MAX_UINT32);
#endif
CASE_INTERP_OUT_INT(po, t, Int8, MIN_INT8, MAX_INT8);
CASE_INTERP_OUT_INT(po, t, Int16, MIN_INT16, MAX_INT16);
CASE_INTERP_OUT_INT(po, t, Int32, MIN_INT32, MAX_INT32);
CASE_INTERP_OUT_INT(po, t, Int64, MIN_INT64, MAX_INT64);
CASE_INTERP_OUT(po, t, Float32);
CASE_INTERP_OUT(po, t, Float64);
default:
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
if (coordinates) {
NI_ITERATOR_NEXT2(io, ic, po, pc);
} else {
NI_ITERATOR_NEXT(io, po);
}
}
exit:
if (edge_offsets)
free(edge_offsets);
if (data_offsets) {
for(jj = 0; jj < irank; jj++)
free(data_offsets[jj]);
free(data_offsets);
}
if (splvals) {
for(jj = 0; jj < irank; jj++)
free(splvals[jj]);
free(splvals);
}
if (foffsets)
free(foffsets);
if (fcoordinates)
free(fcoordinates);
if (idxs)
free(idxs);
return PyErr_Occurred() ? 0 : 1;
}
int NI_FindObjects(PyArrayObject* input, npy_intp max_label,
npy_intp* regions)
{
npy_intp size, jj;
NI_Iterator ii;
char *pi;
NPY_BEGIN_THREADS_DEF;
NPY_BEGIN_THREADS;
/* get input data, size and iterator: */
pi = (void *)PyArray_DATA(input);
size = PyArray_SIZE(input);
if (!NI_InitPointIterator(input, &ii))
goto exit;
if (PyArray_NDIM(input) > 0) {
for (jj = 0; jj < 2 * PyArray_NDIM(input) * max_label; jj++) {
regions[jj] = -1;
}
} else {
for(jj = 0; jj < max_label; jj++)
regions[jj] = -1;
}
/* iterate over all points: */
for(jj = 0 ; jj < size; jj++) {
switch (PyArray_TYPE(input)) {
CASE_FIND_OBJECT_POINT(NPY_BOOL, npy_bool,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_UBYTE, npy_ubyte,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_USHORT, npy_ushort,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_UINT, npy_uint,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_ULONG, npy_ulong,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_ULONGLONG, npy_ulonglong,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_BYTE, npy_byte,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_SHORT, npy_short,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_INT, npy_int,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_LONG, npy_long,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_LONGLONG, npy_longlong,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_FLOAT, npy_float,
pi, regions, input, max_label, ii);
CASE_FIND_OBJECT_POINT(NPY_DOUBLE, npy_double,
pi, regions, input, max_label, ii);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
NI_ITERATOR_NEXT(ii, pi);
}
exit:
NPY_END_THREADS;
return PyErr_Occurred() ? 0 : 1;
}
int NI_WatershedIFT(PyArrayObject* input, PyArrayObject* markers,
PyArrayObject* strct, PyArrayObject* output)
{
char *pl, *pm, *pi;
int ll;
npy_intp size, jj, hh, kk, maxval;
npy_intp strides[WS_MAXDIM], coordinates[WS_MAXDIM];
npy_intp *nstrides = NULL, nneigh, ssize;
int i_contiguous, o_contiguous;
NI_WatershedElement *temp = NULL, **first = NULL, **last = NULL;
npy_bool *ps = NULL;
NI_Iterator mi, ii, li;
NPY_BEGIN_THREADS_DEF;
i_contiguous = PyArray_ISCONTIGUOUS(input);
o_contiguous = PyArray_ISCONTIGUOUS(output);
ssize = PyArray_SIZE(strct);
if (PyArray_NDIM(input) > WS_MAXDIM) {
PyErr_SetString(PyExc_RuntimeError, "too many dimensions");
goto exit;
}
size = PyArray_SIZE(input);
/* Storage for the temporary queue data. */
temp = malloc(size * sizeof(NI_WatershedElement));
if (!temp) {
PyErr_NoMemory();
goto exit;
}
NPY_BEGIN_THREADS;
pi = (void *)PyArray_DATA(input);
if (!NI_InitPointIterator(input, &ii))
goto exit;
/* Initialization and find the maximum of the input. */
maxval = 0;
for(jj = 0; jj < size; jj++) {
npy_intp ival = 0;
switch (PyArray_TYPE(input)) {
CASE_GET_INPUT(NPY_UINT8, npy_uint8, ival, pi);
CASE_GET_INPUT(NPY_UINT16, npy_uint16, ival, pi);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
temp[jj].index = jj;
temp[jj].done = 0;
if (ival > maxval)
maxval = ival;
NI_ITERATOR_NEXT(ii, pi);
}
pi = (void *)PyArray_DATA(input);
/* Allocate and initialize the storage for the queue. */
first = malloc((maxval + 1) * sizeof(NI_WatershedElement*));
last = malloc((maxval + 1) * sizeof(NI_WatershedElement*));
if (NPY_UNLIKELY(!first || !last)) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
for(hh = 0; hh <= maxval; hh++) {
first[hh] = NULL;
last[hh] = NULL;
}
if (!NI_InitPointIterator(markers, &mi))
goto exit;
if (!NI_InitPointIterator(output, &li))
goto exit;
pm = (void *)PyArray_DATA(markers);
pl = (void *)PyArray_DATA(output);
/* initialize all nodes */
for (ll = 0; ll < PyArray_NDIM(input); ll++) {
coordinates[ll] = 0;
}
for(jj = 0; jj < size; jj++) {
/* get marker */
int label = 0;
switch (PyArray_TYPE(markers)) {
CASE_GET_LABEL(NPY_UBYTE, npy_ubyte, label, pm);
CASE_GET_LABEL(NPY_USHORT, npy_ushort, label, pm);
CASE_GET_LABEL(NPY_UINT, npy_uint, label, pm);
CASE_GET_LABEL(NPY_ULONG, npy_ulong, label, pm);
CASE_GET_LABEL(NPY_ULONGLONG, npy_ulonglong, label, pm);
CASE_GET_LABEL(NPY_BYTE, npy_byte, label, pm);
CASE_GET_LABEL(NPY_SHORT, npy_short, label, pm);
CASE_GET_LABEL(NPY_INT, npy_int, label, pm);
CASE_GET_LABEL(NPY_LONG, npy_long, label, pm);
CASE_GET_LABEL(NPY_LONGLONG, npy_longlong, label, pm);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
switch (PyArray_TYPE(output)) {
CASE_PUT_LABEL(NPY_UBYTE, npy_ubyte, label, pl);
CASE_PUT_LABEL(NPY_USHORT, npy_ushort, label, pl);
CASE_PUT_LABEL(NPY_UINT, npy_uint, label, pl);
CASE_PUT_LABEL(NPY_ULONG, npy_ulong, label, pl);
CASE_PUT_LABEL(NPY_ULONGLONG, npy_ulonglong, label, pl);
CASE_PUT_LABEL(NPY_BYTE, npy_byte, label, pl);
CASE_PUT_LABEL(NPY_SHORT, npy_short, label, pl);
CASE_PUT_LABEL(NPY_INT, npy_int, label, pl);
CASE_PUT_LABEL(NPY_LONG, npy_long, label, pl);
CASE_PUT_LABEL(NPY_LONGLONG, npy_longlong, label, pl);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
NI_ITERATOR_NEXT2(mi, li, pm, pl);
if (label != 0) {
/* This node is a marker */
temp[jj].cost = 0;
if (!first[0]) {
first[0] = &(temp[jj]);
first[0]->next = NULL;
first[0]->prev = NULL;
last[0] = first[0];
} else {
if (label > 0) {
/* object markers are enqueued at the beginning, so they
are processed first. */
temp[jj].next = first[0];
temp[jj].prev = NULL;
first[0]->prev = &(temp[jj]);
first[0] = &(temp[jj]);
} else {
/* background markers are enqueued at the end, so they are
processed after the object markers. */
temp[jj].next = NULL;
temp[jj].prev = last[0];
last[0]->next = &(temp[jj]);
last[0] = &(temp[jj]);
}
}
} else {
/* This node is not a marker */
temp[jj].cost = maxval + 1;
temp[jj].next = NULL;
temp[jj].prev = NULL;
}
for (ll = PyArray_NDIM(input) - 1; ll >= 0; ll--) {
if (coordinates[ll] < PyArray_DIMS(input)[ll] - 1) {
coordinates[ll]++;
break;
} else {
coordinates[ll] = 0;
}
}
}
pl = (void *)PyArray_DATA(output);
ps = (npy_bool*)PyArray_DATA(strct);
nneigh = 0;
for (kk = 0; kk < ssize; kk++)
if (ps[kk] && kk != (ssize / 2))
++nneigh;
nstrides = malloc(nneigh * sizeof(npy_intp));
if (NPY_UNLIKELY(!nstrides)) {
NPY_END_THREADS;
PyErr_NoMemory();
goto exit;
}
strides[PyArray_NDIM(input) - 1] = 1;
for (ll = PyArray_NDIM(input) - 2; ll >= 0; ll--) {
strides[ll] = PyArray_DIM(input, ll + 1) * strides[ll + 1];
}
for (ll = 0; ll < PyArray_NDIM(input); ll++) {
coordinates[ll] = -1;
}
for(kk = 0; kk < nneigh; kk++)
nstrides[kk] = 0;
jj = 0;
for(kk = 0; kk < ssize; kk++) {
if (ps[kk]) {
int offset = 0;
for (ll = 0; ll < PyArray_NDIM(input); ll++) {
offset += coordinates[ll] * strides[ll];
}
if (offset != 0)
nstrides[jj++] += offset;
}
for (ll = PyArray_NDIM(input) - 1; ll >= 0; ll--) {
if (coordinates[ll] < 1) {
coordinates[ll]++;
break;
} else {
coordinates[ll] = -1;
}
}
}
/* Propagation phase: */
for(jj = 0; jj <= maxval; jj++) {
while (first[jj]) {
/* dequeue first element: */
NI_WatershedElement *v = first[jj];
first[jj] = first[jj]->next;
if (first[jj])
first[jj]->prev = NULL;
v->prev = NULL;
v->next = NULL;
/* Mark element as done: */
v->done = 1;
/* Iterate over the neighbors of the element: */
for(hh = 0; hh < nneigh; hh++) {
npy_intp v_index = v->index, p_index = v->index, idx, cc;
int qq, outside = 0;
p_index += nstrides[hh];
/* check if the neighbor is within the extent of the array: */
idx = p_index;
for (qq = 0; qq < PyArray_NDIM(input); qq++) {
cc = idx / strides[qq];
if (cc < 0 || cc >= PyArray_DIM(input, qq)) {
outside = 1;
break;
}
idx -= cc * strides[qq];
}
if (!outside) {
NI_WatershedElement *p = &(temp[p_index]);
if (!(p->done)) {
/* If the neighbor was not processed yet: */
int max, pval, vval, wvp, pcost, label, p_idx, v_idx;
switch (PyArray_TYPE(input)) {
CASE_WINDEX1(NPY_UBYTE, npy_ubyte,
v_index, p_index, strides,
PyArray_STRIDES(input), PyArray_NDIM(input),
i_contiguous, p_idx, v_idx, pi, vval, pval);
CASE_WINDEX1(NPY_USHORT, npy_ushort,
v_index, p_index, strides,
PyArray_STRIDES(input), PyArray_NDIM(input),
i_contiguous, p_idx, v_idx, pi, vval, pval);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError,
"data type not supported");
goto exit;
}
/* Calculate cost: */
wvp = pval - vval;
if (wvp < 0)
wvp = -wvp;
/* Find the maximum of this cost and the current
element cost: */
pcost = p->cost;
max = v->cost > wvp ? v->cost : wvp;
if (max < pcost) {
/* If this maximum is less than the neighbors cost,
adapt the cost and the label of the neighbor: */
int idx;
p->cost = max;
switch (PyArray_TYPE(output)) {
CASE_WINDEX2(NPY_UBYTE, npy_ubyte,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX2(NPY_USHORT, npy_ushort,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX2(NPY_UINT, npy_uint,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX2(NPY_ULONG, npy_ulong,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX2(NPY_ULONGLONG, npy_ulonglong,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX2(NPY_BYTE, npy_byte,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX2(NPY_SHORT, npy_short,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX2(NPY_INT, npy_int,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX2(NPY_LONG, npy_long,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX2(NPY_LONGLONG, npy_longlong,
v_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError,
"data type not supported");
goto exit;
}
switch (PyArray_TYPE(output)) {
CASE_WINDEX3(NPY_UBYTE, npy_ubyte,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX3(NPY_USHORT, npy_ushort,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX3(NPY_UINT, npy_uint,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX3(NPY_ULONG, npy_ulong,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX3(NPY_ULONGLONG, npy_ulonglong,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX3(NPY_BYTE, npy_byte,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX3(NPY_SHORT, npy_short,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX3(NPY_INT, npy_int,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX3(NPY_LONG, npy_long,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
CASE_WINDEX3(NPY_LONGLONG, npy_longlong,
p_index, strides,
PyArray_STRIDES(output),
PyArray_NDIM(input),
idx, o_contiguous, label, pl);
default:
NPY_END_THREADS;
PyErr_SetString(PyExc_RuntimeError,
"data type not supported");
goto exit;
}
/* If the neighbor is in a queue, remove it: */
if (p->next || p->prev) {
NI_WatershedElement *prev = p->prev, *next = p->next;
if (first[pcost] == p)
first[pcost] = next;
if (last[pcost] == p)
last[pcost] = prev;
if (prev)
prev->next = next;
if (next)
next->prev = prev;
}
/* Insert the neighbor in the appropriate queue: */
if (label < 0) {
p->prev = last[max];
p->next = NULL;
if (last[max])
last[max]->next = p;
last[max] = p;
if (!first[max])
first[max] = p;
} else {
p->next = first[max];
p->prev = NULL;
if (first[max])
first[max]->prev = p;
first[max] = p;
if (!last[max])
last[max] = p;
}
}
}
}
}
}
}
exit:
NPY_END_THREADS;
free(temp);
free(first);
free(last);
free(nstrides);
return PyErr_Occurred() ? 0 : 1;
}
int NI_Histogram(PyArrayObject *input, PyArrayObject *labels,
npy_intp min_label, npy_intp max_label, npy_intp *indices,
npy_intp n_results, PyArrayObject **histograms,
double min, double max, npy_intp nbins)
{
char *pi = NULL, *pm = NULL;
NI_Iterator ii, mi;
npy_intp jj, kk, size, idx = 0, label = 1, doit = 1;
Int32 **ph = NULL;
double bsize;
int qq;
NPY_BEGIN_THREADS_DEF;
/* input iterator: */
if (!NI_InitPointIterator(input, &ii))
goto exit;
/* input data: */
pi = (void *)PyArray_DATA(input);
if (labels) {
if (!NI_InitPointIterator(labels, &mi))
goto exit;
pm = (void *)PyArray_DATA(labels);
}
ph = (Int32**)malloc(n_results * sizeof(Int32*));
if (!ph) {
PyErr_NoMemory();
goto exit;
}
NPY_BEGIN_THREADS;
for(jj = 0; jj < n_results; jj++) {
ph[jj] = (Int32*)PyArray_DATA(histograms[jj]);
for(kk = 0; kk < nbins; kk++)
ph[jj][kk] = 0;
}
bsize = (max - min) / (double)nbins;
/* input size: */
size = 1;
for(qq = 0; qq < input->nd; qq++)
size *= input->dimensions[qq];
/* iterate over array: */
for(jj = 0; jj < size; jj++) {
NI_GET_LABEL(pm, label, NI_NormalizeType(labels->descr->type_num));
if (min_label >= 0) {
if (label >= min_label && label <= max_label) {
idx = indices[label - min_label];
doit = idx >= 0;
} else {
doit = 0;
}
} else {
doit = label != 0;
}
if (doit) {
npy_intp bin;
double val;
NI_GET_VALUE(pi, val, NI_NormalizeType(input->descr->type_num));
if (val >= min && val < max) {
bin = (npy_intp)((val - min) / bsize);
++(ph[idx][bin]);
}
}
if (labels) {
NI_ITERATOR_NEXT2(ii, mi, pi, pm);
} else {
NI_ITERATOR_NEXT(ii, pi);
}
}
exit:
NPY_END_THREADS;
free(ph);
return PyErr_Occurred() == NULL;
}
int NI_CenterOfMass(PyArrayObject *input, PyArrayObject *labels,
npy_intp min_label, npy_intp max_label, npy_intp *indices,
npy_intp n_results, double *center_of_mass)
{
char *pi = NULL, *pm = NULL;
NI_Iterator ii, mi;
npy_intp jj, kk, size, idx = 0, label = 1, doit = 1;
double *sum = NULL;
int qq;
NPY_BEGIN_THREADS_DEF;
/* input iterator: */
if (!NI_InitPointIterator(input, &ii))
goto exit;
/* input data: */
pi = (void *)PyArray_DATA(input);
if (labels) {
if (!NI_InitPointIterator(labels, &mi))
goto exit;
pm = (void *)PyArray_DATA(labels);
}
/* input size: */
size = 1;
for(qq = 0; qq < input->nd; qq++)
size *= input->dimensions[qq];
sum = (double*)malloc(n_results * sizeof(double));
if (!sum) {
PyErr_NoMemory();
goto exit;
}
NPY_BEGIN_THREADS;
for(jj = 0; jj < n_results; jj++) {
sum[jj] = 0.0;
for(kk = 0; kk < input->nd; kk++)
center_of_mass[jj * input->nd + kk] = 0.0;
}
/* iterate over array: */
for(jj = 0; jj < size; jj++) {
NI_GET_LABEL(pm, label, NI_NormalizeType(labels->descr->type_num));
if (min_label >= 0) {
if (label >= min_label && label <= max_label) {
idx = indices[label - min_label];
doit = idx >= 0;
} else {
doit = 0;
}
} else {
doit = label != 0;
}
if (doit) {
double val;
NI_GET_VALUE(pi, val, NI_NormalizeType(input->descr->type_num));
sum[idx] += val;
for(kk = 0; kk < input->nd; kk++)
center_of_mass[idx * input->nd + kk] += val * ii.coordinates[kk];
}
if (labels) {
NI_ITERATOR_NEXT2(ii, mi, pi, pm);
} else {
NI_ITERATOR_NEXT(ii, pi);
}
}
for(jj = 0; jj < n_results; jj++)
for(kk = 0; kk < input->nd; kk++)
center_of_mass[jj * input->nd + kk] /= sum[jj];
exit:
NPY_END_THREADS;
free(sum);
return PyErr_Occurred() == NULL;
}
int NI_Statistics(PyArrayObject *input, PyArrayObject *labels,
npy_intp min_label, npy_intp max_label, npy_intp *indices,
npy_intp n_results, double *sum, npy_intp *total, double *variance,
double *minimum, double *maximum, npy_intp* min_pos, npy_intp* max_pos)
{
char *pi = NULL, *pm = NULL;
NI_Iterator ii, mi;
npy_intp jj, size, idx = 0, label = 1, doit = 1;
int qq;
NPY_BEGIN_THREADS_DEF;
/* input iterator: */
if (!NI_InitPointIterator(input, &ii))
return 0;
/* input data: */
pi = (void *)PyArray_DATA(input);
if (labels) {
if (!NI_InitPointIterator(labels, &mi))
return 0;
pm = (void *)PyArray_DATA(labels);
}
NPY_BEGIN_THREADS;
/* input size: */
size = 1;
for(qq = 0; qq < input->nd; qq++)
size *= input->dimensions[qq];
for(jj = 0; jj < n_results; jj++) {
if (sum)
sum[jj] = 0.0;
if (total)
total[jj] = 0;
if (variance)
variance[jj] = 0;
if (minimum)
minimum[jj] = DBL_MAX;
if (maximum)
maximum[jj] = -DBL_MAX;
if (min_pos)
min_pos[jj] = 0;
if (max_pos)
max_pos[jj] = 0;
}
/* iterate over array: */
for(jj = 0; jj < size; jj++) {
NI_GET_LABEL(pm, label, NI_NormalizeType(labels->descr->type_num));
if (min_label >= 0) {
if (label >= min_label && label <= max_label) {
idx = indices[label - min_label];
doit = idx >= 0;
} else {
doit = 0;
}
} else {
doit = label != 0;
}
if (doit) {
double val;
NI_GET_VALUE(pi, val, NI_NormalizeType(input->descr->type_num));
if (sum)
sum[idx] += val;
if (total)
total[idx]++;
if (minimum && val < minimum[idx]) {
minimum[idx] = val;
if (min_pos)
min_pos[idx] = jj;
}
if (maximum && (val > maximum[idx])) {
maximum[idx] = val;
if (max_pos)
max_pos[idx] = jj;
}
}
if (labels) {
NI_ITERATOR_NEXT2(ii, mi, pi, pm);
} else {
NI_ITERATOR_NEXT(ii, pi);
}
}
if (minimum) {
for(jj = 0; jj < n_results; jj++) {
if (!(minimum[jj] < DBL_MAX))
minimum[jj] = 0.0;
}
}
if (maximum) {
for(jj = 0; jj < n_results; jj++) {
if (!(maximum[jj] > -DBL_MAX))
maximum[jj] = 0.0;
}
}
if (variance) {
int do_var = 0;
for(jj = 0; jj < n_results; jj++)
if (total[jj] > 1) {
do_var = 1;
break;
}
if (do_var) {
/* reset input iterator: */
NI_ITERATOR_RESET(ii);
pi = (void *)PyArray_DATA(input);
if (labels) {
/* reset label iterator: */
NI_ITERATOR_RESET(mi);
pm = (void *)PyArray_DATA(labels);
}
for(jj = 0; jj < size; jj++) {
NI_GET_LABEL(pm, label, NI_NormalizeType(labels->descr->type_num));
if (min_label >= 0) {
if (label >= min_label && label <= max_label) {
idx = indices[label - min_label];
doit = idx >= 0;
} else {
doit = 0;
}
} else {
doit = label != 0;
}
if (doit) {
double val;
NI_GET_VALUE(pi, val, NI_NormalizeType(input->descr->type_num));
val = val - sum[idx] / total[idx];
variance[idx] += val * val;
}
if (labels) {
NI_ITERATOR_NEXT2(ii, mi, pi, pm);
} else {
NI_ITERATOR_NEXT(ii, pi);
}
}
for(jj = 0; jj < n_results; jj++)
variance[jj] = (total[jj] > 1 ?
variance[jj] / (total[jj] - 1) : 0.0);
}
}
NPY_END_THREADS;
return 1;
}
/* Copy a line from an array to a buffer: */
int NI_ArrayToLineBuffer(NI_LineBuffer *buffer,
npy_intp *number_of_lines, int *more)
{
double *pb = buffer->buffer_data;
char *pa;
npy_intp length = buffer->line_length;
pb += buffer->size1;
*number_of_lines = 0;
/* fill until all lines in the array have been processed, or until
the buffer is full: */
while (buffer->next_line < buffer->array_lines &&
*number_of_lines < buffer->buffer_lines) {
pa = buffer->array_data;
/* copy the data from the array to the buffer: */
switch (buffer->array_type) {
CASE_COPY_DATA_TO_LINE(NPY_BOOL, npy_bool,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_UBYTE, npy_ubyte,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_USHORT, npy_ushort,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_UINT, npy_uint,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_ULONG, npy_ulong,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_ULONGLONG, npy_ulonglong,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_BYTE, npy_byte,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_SHORT, npy_short,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_INT, npy_int,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_LONG, npy_long,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_LONGLONG, npy_longlong,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_FLOAT, npy_float,
pa, pb, length, buffer->line_stride);
CASE_COPY_DATA_TO_LINE(NPY_DOUBLE, npy_double,
pa, pb, length, buffer->line_stride);
default:
PyErr_Format(PyExc_RuntimeError, "array type %d not supported",
buffer->array_type);
return 0;
}
/* goto next line in the array: */
NI_ITERATOR_NEXT(buffer->iterator, buffer->array_data);
/* implement boundary conditions to the line: */
if (buffer->size1 + buffer->size2 > 0) {
if (!NI_ExtendLine(pb - buffer->size1, length, buffer->size1,
buffer->size2, buffer->extend_mode,
buffer->extend_value)) {
return 0;
}
}
/* The number of the array lines copied: */
++(buffer->next_line);
/* keep track of (and return) the number of lines in the buffer: */
++(*number_of_lines);
pb += buffer->line_length + buffer->size1 + buffer->size2;
}
/* if not all array lines were processed, *more is set true: */
*more = buffer->next_line < buffer->array_lines;
return 1;
}