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|
/* Copyright (C) 2003-2005 Peter J. Verveer
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
*
* 3. The name of the author may not be used to endorse or promote
* products derived from this software without specific prior
* written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
* OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
* GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
* WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include "ni_support.h"
#include "ni_measure.h"
#include <stdlib.h>
#include <math.h>
#include <float.h>
#include <assert.h>
typedef struct {
Int32 index1, index2;
void* next;
} _index_pair;
#define CASE_LABEL(_p, _pi, _type) \
case t ## _type: \
*_p = *(_type*)_pi ? -1 : 0; \
break
int NI_Label(PyArrayObject* input, PyArrayObject* strct,
maybelong *max_label, PyArrayObject* output)
{
int kk;
maybelong jj, ll, ssize, size, filter_size, *offsets = NULL;
maybelong mask_value, *oo;
Bool *ps, *footprint = NULL;
char *pi, *po;
Int32 index = 0, *index_map = NULL;
NI_FilterIterator fi;
NI_Iterator ii, io;
_index_pair *pairs = NULL;
/* structure size */
ssize = 1;
for(kk = 0; kk < strct->nd; kk++)
ssize *= strct->dimensions[kk];
/* we only use the first half of the structure data, so we make a
temporary structure for use with the filter functions: */
footprint = (Bool*)malloc(ssize * sizeof(Bool));
if (!footprint) {
PyErr_NoMemory();
goto exit;
}
ps = (Bool*)NA_OFFSETDATA(strct);
filter_size = 0;
for(jj = 0; jj < ssize / 2; jj++) {
footprint[jj] = ps[jj];
if (ps[jj])
++filter_size;
}
for(jj = ssize / 2; jj < ssize; jj++)
footprint[jj] = 0;
/* get data and size */
pi = NA_OFFSETDATA(input);
po = NA_OFFSETDATA(output);
size = 1;
for(kk = 0; kk < output->nd; kk++)
size *= output->dimensions[kk];
if (!NI_InitPointIterator(input, &ii))
goto exit;
if (!NI_InitPointIterator(output, &io))
goto exit;
/* set all elements in the output corresponding to non-zero elements
in input to -1: */
for(jj = 0; jj < size; jj++) {
Int32 *p = (Int32*)po;
switch (input->descr->type_num) {
CASE_LABEL(p, pi, Bool);
CASE_LABEL(p, pi, UInt8);
CASE_LABEL(p, pi, UInt16);
CASE_LABEL(p, pi, UInt32);
#if HAS_UINT64
CASE_LABEL(p, pi, UInt64);
#endif
CASE_LABEL(p, pi, Int8);
CASE_LABEL(p, pi, Int16);
CASE_LABEL(p, pi, Int32);
CASE_LABEL(p, pi, Int64);
CASE_LABEL(p, pi, Float32);
CASE_LABEL(p, pi, Float64);
default:
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
NI_ITERATOR_NEXT2(ii, io, pi, po);
}
/* calculate the filter offsets: */
if (!NI_InitFilterOffsets(output, footprint, strct->dimensions, NULL,
NI_EXTEND_CONSTANT, &offsets, &mask_value, NULL))
goto exit;
/* initialize filter iterator: */
if (!NI_InitFilterIterator(input->nd, strct->dimensions, filter_size,
input->dimensions, NULL, &fi))
goto exit;
/* reset output iterator: */
NI_ITERATOR_RESET(io);
po = NA_OFFSETDATA(output);
/* iterator over the elements: */
oo = offsets;
for(jj = 0; jj < size; jj++) {
if (*(Int32*)po < 0) {
Int32 neighbor = 0;
/* iterate over structuring element: */
for(ll = 0; ll < filter_size; ll++) {
int offset = oo[ll];
if (offset != mask_value) {
Int32 tt = *(Int32*)(po + offset);
if (tt > 0) {
/* this element is next to an already found object: */
if (neighbor && neighbor != tt) {
/* we have two objects that must be merged later: */
_index_pair* tp = (_index_pair*)malloc(sizeof(_index_pair));
if (!tp) {
PyErr_NoMemory();
goto exit;
}
tp->next = pairs;
/* the pairs must be ordered: */
if (neighbor < tt) {
tp->index1 = neighbor;
tp->index2 = tt;
} else {
tp->index1 = tt;
tp->index2 = neighbor;
}
pairs = tp;
} else {
neighbor = tt;
}
}
}
}
if (neighbor) {
/* this point belongs to an existing object */
*(Int32*)po = neighbor;
} else {
/* this may be a new object: */
*(Int32*)po = ++index;
}
}
NI_FILTER_NEXT(fi, io, oo, po);
}
*max_label = index;
/* merge any touching objects: */
if (pairs) {
Int32 counter;
index_map = (Int32*)malloc(index * sizeof(Int32));
if (!index_map) {
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < index; jj++)
index_map[jj] = (Int32)jj;
while (pairs) {
Int32 idx1 = pairs->index1 - 1;
Int32 idx2 = pairs->index2 - 1;
if (index_map[idx2] == idx1 || index_map[idx2] == idx2) {
/* if this pair was already processed, or if idx2 was not
mapped yet, we delete this pair and map idx2 to idx1: */
_index_pair *tp = pairs;
pairs = tp->next;
free(tp);
index_map[idx2] = idx1;
} else {
/* idx2 was already mapped, therefore we find what it was
mapped to and change the current pair to the result of that
and idx1. Since the pair is not destroyed, it will be
re-processed with the adapted values. */
idx2 = index_map[idx2];
/* keep the pairs ordered: */
if (idx1 < idx2) {
pairs->index1 = idx1 + 1;
pairs->index2 = idx2 + 1;
} else {
pairs->index1 = idx2 + 1;
pairs->index2 = idx1 + 1;
}
}
}
for(jj = 0; jj < index; jj++) {
/* if the current index maps to a index that is also mapped,
change it to map to that index. Since an index always maps to
a lower index or to itself, this will make sure that at the
end all indices map to an unmapped index. */
if (index_map[index_map[jj]] < index_map[jj])
index_map[jj] = index_map[index_map[jj]];
}
/* renumber the indices that are not mapped: */
counter = 0;
for(jj = 0; jj < index; jj++)
if (index_map[jj] == jj)
index_map[jj] = ++counter;
else
index_map[jj] = index_map[index_map[jj]];
}
/* relabel the output if we merged some objects: */
if (index_map) {
*max_label = 0;
NI_ITERATOR_RESET(io);
po = NA_OFFSETDATA(output);
for(jj = 0; jj < size; jj++) {
Int32 p = *(Int32*)po;
if (p > 0 )
*(Int32*)po = index_map[p - 1];
if (*(Int32*)po > *max_label)
*max_label = *(Int32*)po;
NI_ITERATOR_NEXT(io, po);
}
}
exit:
if (offsets) free(offsets);
if (index_map) free(index_map);
while (pairs) {
_index_pair *tp = pairs;
pairs = (_index_pair*)pairs->next;
free(tp);
}
if (footprint)
free(footprint);
return PyErr_Occurred() ? 0 : 1;
}
#define CASE_FIND_OBJECT_POINT(_pi, _regions, _rank, _dimensions, \
_max_label, _ii, _type) \
case t ## _type: \
{ \
int _kk; \
maybelong _sindex = *(_type*)_pi - 1; \
if (_sindex >= 0 && _sindex < _max_label) { \
if (_rank > 0) { \
_sindex *= 2 * _rank; \
if (_regions[_sindex] < 0) { \
for(_kk = 0; _kk < _rank; _kk++) { \
maybelong _cc = _ii.coordinates[_kk]; \
_regions[_sindex + _kk] = _cc; \
_regions[_sindex + _kk + _rank] = _cc + 1; \
} \
} else { \
for(_kk = 0; _kk < _rank; _kk++) { \
maybelong _cc = _ii.coordinates[_kk]; \
if (_cc < _regions[_sindex + _kk]) \
_regions[_sindex + _kk] = _cc; \
if (_cc + 1 > _regions[_sindex + _kk + _rank]) \
_regions[_sindex + _kk + _rank] = _cc + 1; \
} \
} \
} else { \
_regions[_sindex] = 1; \
} \
} \
} \
break
int NI_FindObjects(PyArrayObject* input, maybelong max_label,
maybelong* regions)
{
int kk;
maybelong size, jj;
NI_Iterator ii;
char *pi;
/* get input data, size and iterator: */
pi = NA_OFFSETDATA(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 (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:
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
NI_ITERATOR_NEXT(ii, pi);
}
exit:
return PyErr_Occurred() ? 0 : 1;
}
/* macro to get input value: */
#if HAS_UINT64
#define NI_GET_VALUE(_pi, _v, _type) \
{ \
switch(_type) { \
case tBool: \
_v = (*(Bool*)_pi) != 0; \
break; \
case tUInt8: \
_v = *(UInt8*)_pi; \
break; \
case tUInt16: \
_v = *(UInt16*)_pi; \
break; \
case tUInt32: \
_v = *(UInt32*)_pi; \
break; \
case tInt8: \
_v = *(Int8*)_pi; \
break; \
case tInt16: \
_v = *(Int16*)_pi; \
break; \
case tInt32: \
_v = *(Int32*)_pi; \
break; \
case tInt64: \
_v = *(Int64*)_pi; \
break; \
case tUInt64: \
_v = *(UInt64*)_pi; \
break; \
case tFloat32: \
_v = *(Float32*)_pi; \
break; \
case tFloat64: \
_v = *(Float64*)_pi; \
break; \
default: \
PyErr_SetString(PyExc_RuntimeError, "data type not supported"); \
return 0; \
} \
}
#else
#define NI_GET_VALUE(_pi, _v, _type) \
{ \
switch(_type) { \
case tBool: \
_v = (*(Bool*)_pi) != 0; \
break; \
case tUInt8: \
_v = *(UInt8*)_pi; \
break; \
case tUInt16: \
_v = *(UInt16*)_pi; \
break; \
case tUInt32: \
_v = *(UInt32*)_pi; \
break; \
case tInt8: \
_v = *(Int8*)_pi; \
break; \
case tInt16: \
_v = *(Int16*)_pi; \
break; \
case tInt32: \
_v = *(Int32*)_pi; \
break; \
case tInt64: \
_v = *(Int64*)_pi; \
break; \
case tFloat32: \
_v = *(Float32*)_pi; \
break; \
case tFloat64: \
_v = *(Float64*)_pi; \
break; \
default: \
PyErr_SetString(PyExc_RuntimeError, "data type not supported"); \
return 0; \
} \
}
#endif
/* macro to get label value: */
#if HAS_UINT64
#define NI_GET_LABEL(_pm, _label, _type) \
{ \
if (_pm) { \
switch(_type) { \
case tBool: \
_label = *(Bool*)_pm; \
break; \
case tUInt8: \
_label = *(UInt8*)_pm; \
break; \
case tUInt16: \
_label = *(UInt16*)_pm; \
break; \
case tUInt32: \
_label = *(UInt32*)_pm; \
break; \
case tUInt64: \
_label = *(UInt64*)_pm; \
break; \
case tInt8: \
_label = *(Int8*)_pm; \
break; \
case tInt16: \
_label = *(Int16*)_pm; \
break; \
case tInt32: \
_label = *(Int32*)_pm; \
break; \
case tInt64: \
_label = *(Int64*)_pm; \
break; \
case tFloat32: \
_label = *(Float32*)_pm; \
break; \
case tFloat64: \
_label = *(Float64*)_pm; \
break; \
default: \
PyErr_SetString(PyExc_RuntimeError, "data type not supported"); \
return 0; \
} \
} \
}
#else
#define NI_GET_LABEL(_pm, _label, _type) \
{ \
if (_pm) { \
switch(_type) { \
case tBool: \
_label = *(Bool*)_pm; \
break; \
case tUInt8: \
_label = *(UInt8*)_pm; \
break; \
case tUInt16: \
_label = *(UInt16*)_pm; \
break; \
case tUInt32: \
_label = *(UInt32*)_pm; \
break; \
case tInt8: \
_label = *(Int8*)_pm; \
break; \
case tInt16: \
_label = *(Int16*)_pm; \
break; \
case tInt32: \
_label = *(Int32*)_pm; \
break; \
case tInt64: \
_label = *(Int64*)_pm; \
break; \
case tFloat32: \
_label = *(Float32*)_pm; \
break; \
case tFloat64: \
_label = *(Float64*)_pm; \
break; \
default: \
PyErr_SetString(PyExc_RuntimeError, "data type not supported"); \
return 0; \
} \
} \
}
#endif
int NI_Statistics(PyArrayObject *input, PyArrayObject *labels,
maybelong min_label, maybelong max_label, maybelong *indices,
maybelong n_results, double *sum, maybelong *total, double *variance,
double *minimum, double *maximum, maybelong* min_pos, maybelong* max_pos)
{
char *pi = NULL, *pm = NULL;
NI_Iterator ii, mi;
maybelong jj, size, idx = 0, label = 1, doit = 1;
int qq;
/* input iterator: */
if (!NI_InitPointIterator(input, &ii))
return 0;
/* input data: */
pi = NA_OFFSETDATA(input);
if (labels) {
if (!NI_InitPointIterator(labels, &mi))
return 0;
pm = NA_OFFSETDATA(labels);
}
/* 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_MIN;
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, 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, 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_MIN))
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 = NA_OFFSETDATA(input);
if (labels) {
/* reset label iterator: */
NI_ITERATOR_RESET(mi);
pm = NA_OFFSETDATA(labels);
}
for(jj = 0; jj < size; jj++) {
NI_GET_LABEL(pm, label, 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, 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);
}
}
return 1;
}
int NI_CenterOfMass(PyArrayObject *input, PyArrayObject *labels,
maybelong min_label, maybelong max_label, maybelong *indices,
maybelong n_results, double *center_of_mass)
{
char *pi = NULL, *pm = NULL;
NI_Iterator ii, mi;
maybelong jj, kk, size, idx = 0, label = 1, doit = 1;
double *sum = NULL;
int qq;
/* input iterator: */
if (!NI_InitPointIterator(input, &ii))
goto exit;
/* input data: */
pi = NA_OFFSETDATA(input);
if (labels) {
if (!NI_InitPointIterator(labels, &mi))
goto exit;
pm = NA_OFFSETDATA(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;
}
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, 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, 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:
if (sum)
free(sum);
return PyErr_Occurred() == NULL;
}
int NI_Histogram(PyArrayObject *input, PyArrayObject *labels,
maybelong min_label, maybelong max_label, maybelong *indices,
maybelong n_results, PyArrayObject **histograms,
double min, double max, maybelong nbins)
{
char *pi = NULL, *pm = NULL;
NI_Iterator ii, mi;
maybelong jj, kk, size, idx = 0, label = 1, doit = 1;
Int32 **ph = NULL;
double bsize;
int qq;
/* input iterator: */
if (!NI_InitPointIterator(input, &ii))
goto exit;
/* input data: */
pi = NA_OFFSETDATA(input);
if (labels) {
if (!NI_InitPointIterator(labels, &mi))
goto exit;
pm = NA_OFFSETDATA(labels);
}
ph = (Int32**)malloc(n_results * sizeof(Int32*));
if (!ph) {
PyErr_NoMemory();
goto exit;
}
for(jj = 0; jj < n_results; jj++) {
ph[jj] = (Int32*)NA_OFFSETDATA(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, 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) {
int bin;
double val;
NI_GET_VALUE(pi, val, input->descr->type_num);
if (val >= min && val < max) {
bin = (int)((val - min) / bsize);
++(ph[idx][bin]);
}
}
if (labels) {
NI_ITERATOR_NEXT2(ii, mi, pi, pm);
} else {
NI_ITERATOR_NEXT(ii, pi);
}
}
exit:
if (ph)
free(ph);
return PyErr_Occurred() == NULL;
}
#define WS_GET_INDEX(_index, _c_strides, _b_strides, _rank, _out, \
_contiguous, _type) \
do { \
if (_contiguous) { \
_out = _index * sizeof(_type); \
} else { \
int _qq; \
maybelong _cc, _idx = _index; \
_out = 0; \
for (_qq = 0; _qq < _rank; _qq++) { \
_cc = _idx / _c_strides[_qq]; \
_idx -= _cc * _c_strides[_qq]; \
_out += _b_strides[_qq] * _cc; \
} \
} \
} while(0)
#define CASE_GET_INPUT(_ival, _pi, _type) \
case t ## _type: \
_ival = *((_type*)_pi); \
break
#define CASE_GET_LABEL(_label, _pm, _type) \
case t ## _type: \
_label = *(_type*)_pm; \
break
#define CASE_PUT_LABEL(_label, _pl, _type) \
case t ## _type: \
*((_type*)_pl) = _label; \
break
#define CASE_WINDEX1(_v_index, _p_index, _strides, _istrides, _irank, \
_icont, _p_idx, _v_idx, _pi, _vval, _pval, _type) \
case t ## _type: \
WS_GET_INDEX(_v_index, _strides, _istrides, _irank, _p_idx, _icont, \
_type); \
WS_GET_INDEX(_p_index, _strides, _istrides, _irank, _v_idx, _icont, \
_type); \
_vval = *(_type*)(_pi + _v_idx); \
_pval = *(_type*)(_pi + _p_idx); \
break
#define CASE_WINDEX2(_v_index, _strides, _ostrides, _irank, _idx, \
_ocont, _label, _pl, _type) \
case t ## _type: \
WS_GET_INDEX(_v_index, _strides, _ostrides, _irank, _idx, \
_ocont, _type); \
_label = *(_type*)(_pl + _idx); \
break
#define CASE_WINDEX3(_p_index, _strides, _ostrides, _irank, _idx, \
_ocont, _label, _pl, _type) \
case t ## _type: \
WS_GET_INDEX(_p_index, _strides, _ostrides, _irank, _idx, \
_ocont, _type); \
*(_type*)(_pl + _idx) = _label; \
break
#define DONE_TYPE UInt8
#define COST_TYPE UInt16
#define WS_MAXDIM 7
typedef struct {
maybelong index;
COST_TYPE cost;
void *next, *prev;
DONE_TYPE done;
} NI_WatershedElement;
int NI_WatershedIFT(PyArrayObject* input, PyArrayObject* markers,
PyArrayObject* strct, PyArrayObject* output)
{
char *pl, *pm, *pi;
int ll;
maybelong size, jj, hh, kk, maxval;
maybelong strides[WS_MAXDIM], coordinates[WS_MAXDIM];
maybelong *nstrides = NULL, nneigh, ssize;
int i_contiguous, o_contiguous;
NI_WatershedElement *temp = NULL, **first = NULL, **last = NULL;
Bool *ps = NULL;
NI_Iterator mi, ii, li;
i_contiguous = PyArray_ISCONTIGUOUS(input);
o_contiguous = PyArray_ISCONTIGUOUS(output);
ssize = 1;
for(ll = 0; ll < strct->nd; ll++)
ssize *= strct->dimensions[ll];
if (input->nd > WS_MAXDIM) {
PyErr_SetString(PyExc_RuntimeError, "too many dimensions");
goto exit;
}
size = 1;
for(ll = 0; ll < input->nd; ll++)
size *= input->dimensions[ll];
/* Storage for the temporary queue data. */
temp = (NI_WatershedElement*)malloc(size * sizeof(NI_WatershedElement));
if (!temp) {
PyErr_NoMemory();
goto exit;
}
pi = NA_OFFSETDATA(input);
if (!NI_InitPointIterator(input, &ii))
goto exit;
/* Initialization and find the maximum of the input. */
maxval = 0;
for(jj = 0; jj < size; jj++) {
int ival = 0;
switch(input->descr->type_num) {
CASE_GET_INPUT(ival, pi, UInt8);
CASE_GET_INPUT(ival, pi, UInt16);
default:
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 = NA_OFFSETDATA(input);
/* Allocate and initialize the storage for the queue. */
first = (NI_WatershedElement**)malloc((maxval + 1) *
sizeof(NI_WatershedElement*));
last = (NI_WatershedElement**)malloc((maxval + 1) *
sizeof(NI_WatershedElement*));
if (!first || !last) {
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 = NA_OFFSETDATA(markers);
pl = NA_OFFSETDATA(output);
/* initialize all nodes */
for(ll = 0; ll < input->nd; ll++)
coordinates[ll] = 0;
for(jj = 0; jj < size; jj++) {
/* get marker */
int label = 0;
switch(markers->descr->type_num) {
CASE_GET_LABEL(label, pm, UInt8);
CASE_GET_LABEL(label, pm, UInt16);
CASE_GET_LABEL(label, pm, UInt32);
#if HAS_UINT64
CASE_GET_LABEL(label, pm, UInt64);
#endif
CASE_GET_LABEL(label, pm, Int8);
CASE_GET_LABEL(label, pm, Int16);
CASE_GET_LABEL(label, pm, Int32);
CASE_GET_LABEL(label, pm, Int64);
default:
PyErr_SetString(PyExc_RuntimeError, "data type not supported");
goto exit;
}
switch(output->descr->type_num) {
CASE_PUT_LABEL(label, pl, UInt8);
CASE_PUT_LABEL(label, pl, UInt16);
CASE_PUT_LABEL(label, pl, UInt32);
#if HAS_UINT64
CASE_PUT_LABEL(label, pl, UInt64);
#endif
CASE_PUT_LABEL(label, pl, Int8);
CASE_PUT_LABEL(label, pl, Int16);
CASE_PUT_LABEL(label, pl, Int32);
CASE_PUT_LABEL(label, pl, Int64);
default:
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 = input->nd - 1; ll >= 0; ll--)
if (coordinates[ll] < input->dimensions[ll] - 1) {
coordinates[ll]++;
break;
} else {
coordinates[ll] = 0;
}
}
pl = NA_OFFSETDATA(output);
ps = (Bool*)NA_OFFSETDATA(strct);
nneigh = 0;
for (kk = 0; kk < ssize; kk++)
if (ps[kk] && kk != (ssize / 2))
++nneigh;
nstrides = (maybelong*)malloc(nneigh * sizeof(maybelong));
if (!nstrides) {
PyErr_NoMemory();
goto exit;
}
strides[input->nd - 1] = 1;
for(ll = input->nd - 2; ll >= 0; ll--)
strides[ll] = input->dimensions[ll + 1] * strides[ll + 1];
for(ll = 0; ll < input->nd; 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 < input->nd; ll++)
offset += coordinates[ll] * strides[ll];
if (offset != 0)
nstrides[jj++] += offset;
}
for(ll = input->nd - 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++) {
maybelong 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 < input->nd; qq++) {
cc = idx / strides[qq];
if (cc < 0 || cc >= input->dimensions[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(input->descr->type_num) {
CASE_WINDEX1(v_index, p_index, strides, input->strides,
input->nd, i_contiguous, p_idx, v_idx, pi,
vval, pval, UInt8);
CASE_WINDEX1(v_index, p_index, strides, input->strides,
input->nd, i_contiguous, p_idx, v_idx, pi,
vval, pval, UInt16);
default:
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(output->descr->type_num) {
CASE_WINDEX2(v_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, UInt8);
CASE_WINDEX2(v_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, UInt16);
CASE_WINDEX2(v_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, UInt32);
#if HAS_UINT64
CASE_WINDEX2(v_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, UInt64);
#endif
CASE_WINDEX2(v_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, Int8);
CASE_WINDEX2(v_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, Int16);
CASE_WINDEX2(v_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, Int32);
CASE_WINDEX2(v_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, Int64);
default:
PyErr_SetString(PyExc_RuntimeError,
"data type not supported");
goto exit;
}
switch(output->descr->type_num) {
CASE_WINDEX3(p_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, UInt8);
CASE_WINDEX3(p_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, UInt16);
CASE_WINDEX3(p_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, UInt32);
#if HAS_UINT64
CASE_WINDEX3(p_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, UInt64);
#endif
CASE_WINDEX3(p_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, Int8);
CASE_WINDEX3(p_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, Int16);
CASE_WINDEX3(p_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, Int32);
CASE_WINDEX3(p_index, strides, output->strides, input->nd,
idx, o_contiguous, label, pl, Int64);
default:
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 appropiate 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:
if (temp)
free(temp);
if (first)
free(first);
if (last)
free(last);
if (nstrides)
free(nstrides);
return PyErr_Occurred() ? 0 : 1;
}
|
