void apply_polyaffine(PyArrayObject* XYZ,
const PyArrayObject* Centers,
const PyArrayObject* Affines,
const PyArrayObject* Sigma)
{
PyArrayIterObject *iter_xyz, *iter_centers, *iter_affines;
int axis = 1;
double *xyz, *center, *affine, *sigma;
double w, W;
double mat[12], t_xyz[3];
size_t bytes_mat = 12*sizeof(double);
size_t bytes_xyz = 3*sizeof(double);
/* Initialize arrays and iterators */
sigma = PyArray_DATA(Sigma);
iter_xyz = (PyArrayIterObject*)PyArray_IterAllButAxis((PyObject*)XYZ, &axis);
iter_centers = (PyArrayIterObject*)PyArray_IterAllButAxis((PyObject*)Centers, &axis);
iter_affines = (PyArrayIterObject*)PyArray_IterAllButAxis((PyObject*)Affines, &axis);
/* Loop over input points */
while(iter_xyz->index < iter_xyz->size) {
xyz = PyArray_ITER_DATA(iter_xyz);
PyArray_ITER_RESET(iter_centers);
PyArray_ITER_RESET(iter_affines);
memset((void*)mat, 0, bytes_mat);
W = 0.0;
/* Loop over centers */
while(iter_centers->index < iter_centers->size) {
center = PyArray_ITER_DATA(iter_centers);
affine = PyArray_ITER_DATA(iter_affines);
w = _gaussian(xyz, center, sigma);
W += w;
_add_weighted_affine(mat, affine, w);
PyArray_ITER_NEXT(iter_centers);
PyArray_ITER_NEXT(iter_affines);
}
/* Apply matrix */
_apply_affine(t_xyz, mat, xyz, W);
memcpy((void*)xyz, (void*)t_xyz, bytes_xyz);
/* Update xyz iterator */
PyArray_ITER_NEXT(iter_xyz);
}
/* Free memory */
Py_XDECREF(iter_xyz);
Py_XDECREF(iter_centers);
Py_XDECREF(iter_affines);
return;
}
// the data should be FLOAT32 and should be ensured in the wrapper
static PyObject *interp3(PyObject *self, PyObject *args)
{
PyArrayObject *volume, *result, *C, *R, *S;
float *pr, *pc, *ps;
float *pvol, *pvc;
int xdim, ydim, zdim;
// We expect 4 arguments of the PyArray_Type
if(!PyArg_ParseTuple(args, "O!O!O!O!",
&PyArray_Type, &volume,
&PyArray_Type, &R,
&PyArray_Type, &C,
&PyArray_Type, &S)) return NULL;
if ( NULL == volume ) return NULL;
if ( NULL == C ) return NULL;
if ( NULL == R ) return NULL;
if ( NULL == S ) return NULL;
// result matrix is the same size as C and is float
result = (PyArrayObject*) PyArray_ZEROS(PyArray_NDIM(C), C->dimensions, NPY_FLOAT, 0);
// This is for reference counting ( I think )
PyArray_FLAGS(result) |= NPY_OWNDATA;
// massive use of iterators to progress through the data
PyArrayIterObject *itr_v, *itr_r, *itr_c, *itr_s;
itr_v = (PyArrayIterObject *) PyArray_IterNew(result);
itr_r = (PyArrayIterObject *) PyArray_IterNew(R);
itr_c = (PyArrayIterObject *) PyArray_IterNew(C);
itr_s = (PyArrayIterObject *) PyArray_IterNew(S);
pvol = (float *)PyArray_DATA(volume);
xdim = PyArray_DIM(volume, 0);
ydim = PyArray_DIM(volume, 1);
zdim = PyArray_DIM(volume, 2);
//printf("%f\n", pvol[4*20*30 + 11*30 + 15]);
while(PyArray_ITER_NOTDONE(itr_v))
{
pvc = (float *) PyArray_ITER_DATA(itr_v);
pr = (float *) PyArray_ITER_DATA(itr_r);
pc = (float *) PyArray_ITER_DATA(itr_c);
ps = (float *) PyArray_ITER_DATA(itr_s);
// The order is weird because the tricubic code below is
// for Fortran ordering. Note that the xdim changes fast in
// the code, whereas the rightmost dim should change fast
// in C multidimensional arrays.
*pvc = TriCubic(*ps, *pc, *pr, pvol, zdim, ydim, xdim);
PyArray_ITER_NEXT(itr_v);
PyArray_ITER_NEXT(itr_r);
PyArray_ITER_NEXT(itr_c);
PyArray_ITER_NEXT(itr_s);
}
return result;
}
/* wrapped cosine function */
static PyObject* cos_func_np(PyObject* self, PyObject* args)
{
PyArrayObject *in_array;
PyObject *out_array;
PyArrayIterObject *in_iter;
PyArrayIterObject *out_iter;
/* parse single numpy array argument */
if (!PyArg_ParseTuple(args, "O!", &PyArray_Type, &in_array))
return NULL;
/* construct the output array, like the input array */
out_array = PyArray_NewLikeArray(in_array, NPY_ANYORDER, NULL, 0);
if (out_array == NULL)
return NULL;
/* create the iterators */
/* TODO: this iterator API is deprecated since 1.6
* replace in favour of the new NpyIter API */
in_iter = (PyArrayIterObject *)PyArray_IterNew((PyObject*)in_array);
out_iter = (PyArrayIterObject *)PyArray_IterNew(out_array);
if (in_iter == NULL || out_iter == NULL)
goto fail;
/* iterate over the arrays */
while (in_iter->index < in_iter->size
&& out_iter->index < out_iter->size) {
/* get the datapointers */
double * in_dataptr = (double *)in_iter->dataptr;
double * out_dataptr = (double *)out_iter->dataptr;
/* cosine of input into output */
*out_dataptr = cos(*in_dataptr);
/* update the iterator */
PyArray_ITER_NEXT(in_iter);
PyArray_ITER_NEXT(out_iter);
}
/* clean up and return the result */
Py_DECREF(in_iter);
Py_DECREF(out_iter);
Py_INCREF(out_array);
return out_array;
/* in case bad things happen */
fail:
Py_XDECREF(out_array);
Py_XDECREF(in_iter);
Py_XDECREF(out_iter);
return NULL;
}
void histogram(double* H,
unsigned int clamp,
PyArrayIterObject* iter)
{
signed short *buf;
signed short i;
/* Reset the source image iterator */
PyArray_ITER_RESET(iter);
/* Re-initialize joint histogram */
memset((void*)H, 0, clamp*sizeof(double));
/* Loop over source voxels */
while(iter->index < iter->size) {
/* Source voxel intensity */
buf = (signed short*)PyArray_ITER_DATA(iter);
i = buf[0];
/* Update the histogram only if the current voxel is below the
intensity threshold */
if (i>=0)
H[i]++;
/* Update source index */
PyArray_ITER_NEXT(iter);
} /* End of loop over voxels */
return;
}
/*
Compute the interaction energy:
sum_i,j qi^T U qj
= sum_i qi^T sum_j U qj
*/
double interaction_energy(PyArrayObject* ppm,
const PyArrayObject* XYZ,
const PyArrayObject* U,
int ngb_size)
{
npy_intp k, x, y, z, pos;
double *p, *buf;
double res = 0.0, tmp;
PyArrayIterObject* iter;
int axis = 1;
double* ppm_data;
npy_intp K = ppm->dimensions[3];
npy_intp u2 = ppm->dimensions[2]*K;
npy_intp u1 = ppm->dimensions[1]*u2;
npy_intp* xyz;
const double* U_data = (double*)U->data;
int* ngb;
/* Neighborhood system */
ngb = _select_neighborhood_system(ngb_size);
/* Pointer to ppm array */
ppm_data = (double*)ppm->data;
/* Allocate auxiliary vector */
p = (double*)calloc(K, sizeof(double));
/* Loop over points */
iter = (PyArrayIterObject*)PyArray_IterAllButAxis((PyObject*)XYZ, &axis);
while(iter->index < iter->size) {
/* Compute the average ppm in the neighborhood */
xyz = PyArray_ITER_DATA(iter);
x = xyz[0];
y = xyz[1];
z = xyz[2];
_ngb_integrate(p, ppm, x, y, z, U_data, (const int*)ngb, ngb_size);
/* Calculate the dot product qi^T p where qi is the local
posterior */
tmp = 0.0;
pos = x*u1 + y*u2 + z*K;
for (k=0, buf=p; k<K; k++, pos++, buf++)
tmp += ppm_data[pos]*(*buf);
/* Update overall energy */
res += tmp;
/* Update iterator */
PyArray_ITER_NEXT(iter);
}
/* Free memory */
free(p);
Py_XDECREF(iter);
return res;
}
void allstats_ubyte(PyObject *inputarray, stats *result) {
PyObject *iter;
npy_ubyte *ptr;
iter = PyArray_IterNew(inputarray);
while (PyArray_ITER_NOTDONE(iter)) {
ptr = (npy_ubyte *)PyArray_ITER_DATA(iter);
updateStats(result, (double) (*ptr));
PyArray_ITER_NEXT(iter);
}
Py_XDECREF(iter);
}
static int
map_inc(PyArrayMapIterObject *mit, PyObject *op)
{
PyObject *arr = NULL;
PyArrayIterObject *it;
int index;
PyArray_Descr *descr;
/* Unbound Map Iterator */
if (mit->ait == NULL) {
return -1;
}
descr = mit->ait->ao->descr;
Py_INCREF(descr);
arr = PyArray_FromAny(op, descr, 0, 0, NPY_FORCECAST, NULL);
if (arr == NULL) {
return -1;
}
if ((mit->subspace != NULL) && (mit->consec)) {
if (mit->iteraxes[0] > 0) { /* then we need to swap */
_swap_axes(mit, (PyArrayObject **)&arr, 0);
if (arr == NULL) {
return -1;
}
}
}
/* Be sure values array is "broadcastable"
to shape of mit->dimensions, mit->nd */
if ((it = (PyArrayIterObject *)\
PyArray_BroadcastToShape(arr, mit->dimensions, mit->nd))==NULL) {
Py_DECREF(arr);
return -1;
}
index = mit->size;
PyArray_MapIterReset(mit);
while(index--) {
memmove(mit->dataptr, it->dataptr, PyArray_ITEMSIZE(arr));
*(double*)(mit->dataptr) = *(double*)(mit->dataptr) + *(double*)(it->dataptr);
PyArray_MapIterNext(mit);
PyArray_ITER_NEXT(it);
}
Py_DECREF(arr);
Py_DECREF(it);
return 0;
}
/*
Resample a 3d image submitted to an affine transformation.
Tvox is the voxel transformation from the image to the destination grid.
*/
void cubic_spline_resample3d(PyArrayObject* im_resampled, const PyArrayObject* im,
const double* Tvox, int cast_integer,
int mode_x, int mode_y, int mode_z)
{
double i1;
PyObject* py_i1;
PyArrayObject* im_spline_coeff;
PyArrayIterObject* imIter = (PyArrayIterObject*)PyArray_IterNew((PyObject*)im_resampled);
unsigned int x, y, z;
unsigned dimX = PyArray_DIM(im, 0);
unsigned dimY = PyArray_DIM(im, 1);
unsigned dimZ = PyArray_DIM(im, 2);
npy_intp dims[3] = {dimX, dimY, dimZ};
double Tx, Ty, Tz;
/* Compute the spline coefficient image */
im_spline_coeff = (PyArrayObject*)PyArray_SimpleNew(3, dims, NPY_DOUBLE);
cubic_spline_transform(im_spline_coeff, im);
/* Force iterator coordinates to be updated */
UPDATE_ITERATOR_COORDS(imIter);
/* Resampling loop */
while(imIter->index < imIter->size) {
x = imIter->coordinates[0];
y = imIter->coordinates[1];
z = imIter->coordinates[2];
_apply_affine_transform(&Tx, &Ty, &Tz, Tvox, x, y, z);
i1 = cubic_spline_sample3d(Tx, Ty, Tz, im_spline_coeff, mode_x, mode_y, mode_z);
if (cast_integer)
i1 = ROUND(i1);
/* Copy interpolated value into numpy array */
py_i1 = PyFloat_FromDouble(i1);
PyArray_SETITEM(im_resampled, PyArray_ITER_DATA(imIter), py_i1);
Py_DECREF(py_i1);
/* Increment iterator */
PyArray_ITER_NEXT(imIter);
}
/* Free memory */
Py_DECREF(imIter);
Py_DECREF(im_spline_coeff);
return;
}
static int copy_int(PyArrayIterObject *itx, PyArrayNeighborhoodIterObject *niterx,
npy_intp *bounds,
PyObject **out)
{
npy_intp i, j;
npy_int *ptr;
npy_intp odims[NPY_MAXDIMS];
PyArrayObject *aout;
/*
* For each point in itx, copy the current neighborhood into an array which
* is appended at the output list
*/
for (i = 0; i < itx->size; ++i) {
PyArrayNeighborhoodIter_Reset(niterx);
for (j = 0; j < PyArray_NDIM(itx->ao); ++j) {
odims[j] = bounds[2 * j + 1] - bounds[2 * j] + 1;
}
aout = (PyArrayObject*)PyArray_SimpleNew(
PyArray_NDIM(itx->ao), odims, NPY_INT);
if (aout == NULL) {
return -1;
}
ptr = (npy_int*)PyArray_DATA(aout);
for (j = 0; j < niterx->size; ++j) {
*ptr = *((npy_int*)niterx->dataptr);
PyArrayNeighborhoodIter_Next(niterx);
ptr += 1;
}
PyList_Append(*out, (PyObject*)aout);
Py_DECREF(aout);
PyArray_ITER_NEXT(itx);
}
return 0;
}
/* Array evaluates as "TRUE" if any of the elements are non-zero*/
static int
array_any_nonzero(PyArrayObject *arr)
{
npy_intp counter;
PyArrayIterObject *it;
npy_bool anyTRUE = NPY_FALSE;
it = (PyArrayIterObject *)PyArray_IterNew((PyObject *)arr);
if (it == NULL) {
return anyTRUE;
}
counter = it->size;
while (counter--) {
if (PyArray_DESCR(arr)->f->nonzero(it->dataptr, arr)) {
anyTRUE = NPY_TRUE;
break;
}
PyArray_ITER_NEXT(it);
}
Py_DECREF(it);
return anyTRUE;
}
static void _cubic_spline_transform(PyArrayObject* res, int axis, double* work)
{
PyArrayIterObject* iter;
unsigned int dim, stride;
/* Instantiate iterator and views */
iter = (PyArrayIterObject*)PyArray_IterAllButAxis((PyObject*)res, &axis);
dim = PyArray_DIM((PyArrayObject*)iter->ao, axis);
stride = PyArray_STRIDE((PyArrayObject*)iter->ao, axis)/sizeof(double);
/* Apply the cubic spline transform along given axis */
while(iter->index < iter->size) {
_copy_double_buffer(work, PyArray_ITER_DATA(iter), dim, stride);
_cubic_spline_transform1d(PyArray_ITER_DATA(iter), work, dim, stride, 1);
PyArray_ITER_NEXT(iter);
}
/* Free local structures */
Py_DECREF(iter);
return;
}
static int copy_object(PyArrayIterObject *itx, PyArrayNeighborhoodIterObject *niterx,
npy_intp *bounds,
PyObject **out)
{
npy_intp i, j;
npy_intp odims[NPY_MAXDIMS];
PyArrayObject *aout;
PyArray_CopySwapFunc *copyswap = PyArray_DESCR(itx->ao)->f->copyswap;
npy_int itemsize = PyArray_ITEMSIZE(itx->ao);
/*
* For each point in itx, copy the current neighborhood into an array which
* is appended at the output list
*/
for (i = 0; i < itx->size; ++i) {
PyArrayNeighborhoodIter_Reset(niterx);
for (j = 0; j < PyArray_NDIM(itx->ao); ++j) {
odims[j] = bounds[2 * j + 1] - bounds[2 * j] + 1;
}
aout = (PyArrayObject*)PyArray_SimpleNew(PyArray_NDIM(itx->ao), odims, NPY_OBJECT);
if (aout == NULL) {
return -1;
}
for (j = 0; j < niterx->size; ++j) {
copyswap(PyArray_BYTES(aout) + j * itemsize, niterx->dataptr, 0, NULL);
PyArrayNeighborhoodIter_Next(niterx);
}
PyList_Append(*out, (PyObject*)aout);
Py_DECREF(aout);
PyArray_ITER_NEXT(itx);
}
return 0;
}
//query the ball tree. Arguments are the array of search points
// and the number of nearest neighbors, k (optional)
static PyObject *
BallTree_query(BallTreeObject *self, PyObject *args, PyObject *kwds){
//we use goto statements : all variables should be declared up front
int return_distance = 1;
long int k = 1;
PyObject *arg = NULL;
PyObject *arr = NULL;
PyObject *nbrs = NULL;
PyObject *dist = NULL;
PyArrayIterObject *arr_iter = NULL;
PyArrayIterObject *nbrs_iter = NULL;
PyArrayIterObject *dist_iter = NULL;
long int* nbrs_data;
double* dist_data;
static char *kwlist[] = {"x", "k", "return_distance", NULL};
int nd, pt_size, pt_inc;
npy_intp* dim;
//parse arguments. If k is not provided, the default is 1
if(!PyArg_ParseTupleAndKeywords(args,kwds,"O|li",kwlist,
&arg,&k,&return_distance)){
goto fail;
}
//check value of k
if(k < 1){
PyErr_SetString(PyExc_ValueError,
"k must be positive");
goto fail;
}
if(k > self->size){
PyErr_SetString(PyExc_ValueError,
"k must not be greater than number of points");
goto fail;
}
//get the array object from the first argument
arr = PyArray_FROM_OTF(arg,NPY_DOUBLE,NPY_ALIGNED);
//check that the array was properly constructed
if(arr==NULL){
PyErr_SetString(PyExc_ValueError,
"pt must be convertable to array");
goto fail;
}
nd = PyArray_NDIM(arr);
if(nd == 0){
PyErr_SetString(PyExc_ValueError,
"pt cannot be zero-sized array");
goto fail;
}
pt_size = PyArray_DIM(arr,nd-1);
if( pt_size != self->tree->PointSize() ){
PyErr_SetString(PyExc_ValueError,
"points are incorrect dimension");
goto fail;
}
//create a neighbors array and distance array
dim = new npy_intp[nd];
for(int i=0; i<nd-1;i++)
dim[i] = PyArray_DIM(arr,i);
dim[nd-1] = k;
nbrs = (PyObject*)PyArray_SimpleNew(nd,dim,PyArray_LONG);
if(return_distance)
dist = (PyObject*)PyArray_SimpleNew(nd,dim,PyArray_DOUBLE);
delete[] dim;
if(nbrs==NULL)
goto fail;
//create iterators to cycle through points
nd-=1;
arr_iter = (PyArrayIterObject*)PyArray_IterAllButAxis(arr,&nd);
nbrs_iter = (PyArrayIterObject*)PyArray_IterAllButAxis(nbrs,&nd);
if(return_distance)
dist_iter = (PyArrayIterObject*)PyArray_IterAllButAxis(dist,&nd);
nd+=1;
if( arr_iter==NULL || nbrs_iter==NULL ||
(arr_iter->size != nbrs_iter->size) ||
(return_distance &&
(dist_iter==NULL || (arr_iter->size != dist_iter->size))) ){
PyErr_SetString(PyExc_ValueError,
"failure constructing iterators");
goto fail;
}
pt_inc = PyArray_STRIDES(arr)[nd-1] / PyArray_DESCR(arr)->elsize;
if( (PyArray_STRIDES(nbrs)[nd-1] != PyArray_DESCR(nbrs)->elsize ) ||
(return_distance &&
(PyArray_STRIDES(dist)[nd-1] != PyArray_DESCR(dist)->elsize )) ){
PyErr_SetString(PyExc_ValueError,
"nbrs & dist not allocated as a C-array");
goto fail;
}
//iterate through points and determine neighbors
//warning: if nbrs is not a C-array, or if we're not iterating
// over the last dimension, this may cause a seg fault.
if(return_distance){
while(arr_iter->index < arr_iter->size){
BallTree_Point pt(arr,
(double*)PyArray_ITER_DATA(arr_iter),
pt_inc,pt_size);
nbrs_data = (long int*)(PyArray_ITER_DATA(nbrs_iter));
dist_data = (double*)(PyArray_ITER_DATA(dist_iter));
self->tree->query(pt,k,nbrs_data,dist_data);
PyArray_ITER_NEXT(arr_iter);
PyArray_ITER_NEXT(nbrs_iter);
PyArray_ITER_NEXT(dist_iter);
}
}else{
while(arr_iter->index < arr_iter->size){
BallTree_Point pt(arr,
(double*)PyArray_ITER_DATA(arr_iter),
pt_inc,pt_size);
nbrs_data = (long int*)(PyArray_ITER_DATA(nbrs_iter));
self->tree->query(pt,k,nbrs_data);
PyArray_ITER_NEXT(arr_iter);
PyArray_ITER_NEXT(nbrs_iter);
}
}
//if only one neighbor is requested, then resize the neighbors array
if(k==1){
PyArray_Dims dims;
dims.ptr = PyArray_DIMS(arr);
dims.len = PyArray_NDIM(arr)-1;
//PyArray_Resize returns None - this needs to be picked
// up and dereferenced.
PyObject *NoneObj = PyArray_Resize( (PyArrayObject*)nbrs, &dims,
0, NPY_ANYORDER );
if (NoneObj == NULL){
goto fail;
}
Py_DECREF(NoneObj);
if(return_distance){
NoneObj = PyArray_Resize( (PyArrayObject*)dist, &dims,
0, NPY_ANYORDER );
if (NoneObj == NULL){
goto fail;
}
Py_DECREF(NoneObj);
}
}
if(return_distance){
Py_DECREF(arr_iter);
Py_DECREF(nbrs_iter);
Py_DECREF(dist_iter);
Py_DECREF(arr);
arr = Py_BuildValue("(OO)",dist,nbrs);
Py_DECREF(nbrs);
Py_DECREF(dist);
return arr;
}else{
Py_DECREF(arr_iter);
Py_DECREF(nbrs_iter);
Py_DECREF(arr);
return nbrs;
}
fail:
Py_XDECREF(arr);
Py_XDECREF(nbrs);
Py_XDECREF(dist);
Py_XDECREF(arr_iter);
Py_XDECREF(nbrs_iter);
Py_XDECREF(dist_iter);
return NULL;
}
PyArrayObject* make_edges(const PyArrayObject* idx,
int ngb_size)
{
int* ngb = _select_neighborhood_system(ngb_size);
PyArrayIterObject* iter = (PyArrayIterObject*)PyArray_IterNew((PyObject*)idx);
int* buf_ngb;
npy_intp xi, yi, zi, xj, yj, zj;
npy_intp u2 = idx->dimensions[2];
npy_intp u1 = idx->dimensions[1]*u2;
npy_intp u0 = idx->dimensions[0]*u1;
npy_intp mask_size = 0, n_edges = 0;
npy_intp idx_i;
npy_intp *buf_idx;
npy_intp *edges_data, *buf_edges;
npy_intp ngb_idx;
npy_intp pos;
PyArrayObject* edges;
npy_intp dim[2] = {0, 2};
/* First loop over the input array to determine the mask size */
while(iter->index < iter->size) {
buf_idx = (npy_intp*)PyArray_ITER_DATA(iter);
if (*buf_idx >= 0)
mask_size ++;
PyArray_ITER_NEXT(iter);
}
/* Allocate the array of edges using an upper bound of the required
memory space */
edges_data = (npy_intp*)malloc(2 * ngb_size * mask_size * sizeof(npy_intp));
/* Second loop over the input array */
PyArray_ITER_RESET(iter);
iter->contiguous = 0; /* To force coordinates to be updated */
buf_edges = edges_data;
while(iter->index < iter->size) {
xi = iter->coordinates[0];
yi = iter->coordinates[1];
zi = iter->coordinates[2];
buf_idx = (npy_intp*)PyArray_ITER_DATA(iter);
idx_i = *buf_idx;
/* Loop over neighbors if current point is within the mask */
if (idx_i >= 0) {
buf_ngb = ngb;
for (ngb_idx=0; ngb_idx<ngb_size; ngb_idx++) {
/* Get neighbor coordinates */
xj = xi + *buf_ngb; buf_ngb++;
yj = yi + *buf_ngb; buf_ngb++;
zj = zi + *buf_ngb; buf_ngb++;
pos = xj*u1 + yj*u2 + zj;
/* Store edge if neighbor is within the mask */
if ((pos < 0) || (pos >= u0))
continue;
buf_idx = (npy_intp*)idx->data + pos;
if (*buf_idx < 0)
continue;
buf_edges[0] = idx_i;
buf_edges[1] = *buf_idx;
n_edges ++;
buf_edges += 2;
}
}
/* Increment iterator */
PyArray_ITER_NEXT(iter);
}
/* Reallocate edges array to account for connections suppressed due to masking */
edges_data = realloc((void *)edges_data, 2 * n_edges * sizeof(npy_intp));
dim[0] = n_edges;
edges = (PyArrayObject*) PyArray_SimpleNewFromData(2, dim, NPY_INTP, (void*)edges_data);
/* Transfer ownership to python (to avoid memory leaks!) */
edges->flags = (edges->flags) | NPY_OWNDATA;
/* Free memory */
Py_XDECREF(iter);
return edges;
}
void ve_step(PyArrayObject* ppm,
const PyArrayObject* ref,
const PyArrayObject* XYZ,
const PyArrayObject* U,
int ngb_size,
double beta)
{
npy_intp k, x, y, z, pos;
double *p, *buf, *ppm_data;
double psum, tmp;
PyArrayIterObject* iter;
int axis = 1;
npy_intp K = ppm->dimensions[3];
npy_intp u2 = ppm->dimensions[2]*K;
npy_intp u1 = ppm->dimensions[1]*u2;
const double* ref_data = (double*)ref->data;
const double* U_data = (double*)U->data;
npy_intp* xyz;
int* ngb;
/* Neighborhood system */
ngb = _select_neighborhood_system(ngb_size);
/* Pointer to the data array */
ppm_data = (double*)ppm->data;
/* Allocate auxiliary vectors */
p = (double*)calloc(K, sizeof(double));
/* Loop over points */
iter = (PyArrayIterObject*)PyArray_IterAllButAxis((PyObject*)XYZ, &axis);
while(iter->index < iter->size) {
/* Integrate the energy over the neighborhood */
xyz = PyArray_ITER_DATA(iter);
x = xyz[0];
y = xyz[1];
z = xyz[2];
_ngb_integrate(p, ppm, x, y, z, U_data, (const int*)ngb, ngb_size);
/* Apply exponential transform, multiply with reference and
compute normalization constant */
psum = 0.0;
for (k=0, pos=(iter->index)*K, buf=p; k<K; k++, pos++, buf++) {
tmp = exp(-2 * beta * (*buf)) * ref_data[pos];
psum += tmp;
*buf = tmp;
}
/* Normalize to unitary sum */
pos = x*u1 + y*u2 + z*K;
if (psum > TINY)
for (k=0, buf=p; k<K; k++, pos++, buf++)
ppm_data[pos] = *buf/psum;
else
for (k=0, buf=p; k<K; k++, pos++, buf++)
ppm_data[pos] = (*buf+TINY/(double)K)/(psum+TINY);
/* Update iterator */
PyArray_ITER_NEXT(iter);
}
/* Free memory */
free(p);
Py_XDECREF(iter);
return;
}
static PyObject *AscanfCall( ascanf_Function *af, PyObject *arglist, long repeats, int asarray, int deref,
PAO_Options *opts, char *caller )
{ int fargs= 0, aargc= 0, volatile_args= 0;
double result= 0, *aresult=NULL;
static double *AARGS= NULL;
static char *ATYPE= NULL;
static ascanf_Function *LAF= NULL;
static size_t LAFN= 0;
double *aargs= NULL;
char *atype= NULL;
ascanf_Function *laf= NULL, *af_array= NULL;
size_t lafN= 0;
PyObject *ret= NULL;
static ascanf_Function *nDindex= NULL;
int aV = ascanf_verbose;
if( arglist ){
if( PyList_Check(arglist) ){
if( !(arglist= PyList_AsTuple(arglist)) ){
PyErr_SetString( XG_PythonError, "unexpected failure converting argument list to tuple" );
// PyErr_SetString( PyExc_RuntimeError, "unexpected failure converting argument list to tuple" );
return(NULL);
}
}
if( !PyTuple_Check(arglist) ){
PyErr_SetString(
XG_PythonError,
// PyExc_SyntaxError,
"arguments to the ascanf method should be passed as a tuple or list\n"
" NB: a 1-element tuple is specified as (value , ) !!\n"
);
return(NULL);
}
aargc= PyTuple_Size(arglist);
}
else{
aargc= 0;
}
if( !af ){
goto PAC_ESCAPE;
}
if( af->type!= _ascanf_procedure && af->Nargs> 0 ){
/* procedures can have as many arguments as MaxArguments, which is probably too much to allocate here.
\ However, we know how many arguments a function can get (if all's well...), and we can assure that
\ it will have space for those arguments
\ 20061015: unless it also has MaxArguments, i.e. Nargs<0 ...
*/
fargs= af->Nargs;
}
{ long n= (aargc+fargs+1)*2;
if( opts->call_reentrant ){
lafN= n;
aargs= (double*) calloc( lafN, sizeof(double) );
atype= (char*) calloc( lafN, sizeof(char) );
if( !aargs || !atype || !(laf= (ascanf_Function*) calloc( lafN, sizeof(ascanf_Function) )) ){
PyErr_NoMemory();
return(NULL);
}
}
else{
if( !LAF ){
LAFN= n;
AARGS= (double*) calloc( LAFN, sizeof(double) );
ATYPE= (char*) calloc( LAFN, sizeof(char) );
if( !AARGS || !ATYPE || !(LAF= (ascanf_Function*) calloc( LAFN, sizeof(ascanf_Function) )) ){
PyErr_NoMemory();
return(NULL);
}
}
else if( n> LAFN ){
AARGS= (double*) realloc( AARGS, n * sizeof(double) );
ATYPE= (char*) realloc( ATYPE, n * sizeof(char) );
if( !AARGS || !ATYPE || !(LAF= (ascanf_Function*) realloc( LAF, n * sizeof(ascanf_Function) )) ){
PyErr_NoMemory();
return(NULL);
}
else{
for( ; LAFN< n; LAFN++ ){
AARGS[LAFN]= 0;
memset( &LAF[LAFN], 0, sizeof(ascanf_Function) );
}
}
LAFN= n;
}
aargs= AARGS;
atype= ATYPE;
laf= LAF;
lafN= LAFN;
}
}
{ int a= 0, i;
if( opts->verbose > 1 ){
ascanf_verbose = 1;
}
if( af->type== _ascanf_array ){
if( !nDindex ){
nDindex= Py_getNamedAscanfVariable("nDindex");
}
if( nDindex ){
af_array= af;
aargs[a]= (af->own_address)? af->own_address : take_ascanf_address(af);
af= nDindex;
a+= 1;
}
}
for( i= 0; i< aargc; i++, a++ ){
PyObject *arg= PyTuple_GetItem(arglist, i);
ascanf_Function *aaf;
if( PyFloat_Check(arg) ){
aargs[a]= PyFloat_AsDouble(arg);
atype[a]= 1;
}
#ifdef USE_COBJ
else if( PyCObject_Check(arg) ){
if( (aaf= PyCObject_AsVoidPtr(arg)) && (PyCObject_GetDesc(arg)== aaf->function) ){
aargs[a]= (aaf->own_address)? aaf->own_address : take_ascanf_address(aaf);
atype[a]= 2;
}
else{
PyErr_SetString( XG_PythonError, "unsupported PyCObject type does not contain ascanf pointer" );
// PyErr_SetString( PyExc_TypeError, "unsupported PyCObject type does not contain ascanf pointer" );
goto PAC_ESCAPE;
}
}
#else
else if( PyAscanfObject_Check(arg) ){
if( (aaf= PyAscanfObject_AsAscanfFunction(arg)) ){
aargs[a]= (aaf->own_address)? aaf->own_address : take_ascanf_address(aaf);
atype[a]= 2;
}
else{
PyErr_SetString( XG_PythonError, "invalid PyAscanfObject type does not contain ascanf pointer" );
// PyErr_SetString( PyExc_TypeError, "invalid PyAscanfObject type does not contain ascanf pointer" );
goto PAC_ESCAPE;
}
}
#endif
else if( PyInt_Check(arg) || PyLong_Check(arg) ){
aargs[a]= PyInt_AsLong(arg);
atype[a]= 3;
}
else if( PyBytes_Check(arg)
#ifdef IS_PY3K
|| PyUnicode_Check(arg)
#endif
){
static char *AFname= "AscanfCall-Static-StringPointer";
ascanf_Function *saf= &laf[a];
memset( saf, 0, sizeof(ascanf_Function) );
saf->type= _ascanf_variable;
saf->function= ascanf_Variable;
if( !(saf->name= PyObject_Name(arg)) ){
saf->name= XGstrdup(AFname);
}
saf->is_address= saf->take_address= True;
saf->is_usage= saf->take_usage= True;
saf->internal= True;
#ifdef IS_PY3K
if( PyUnicode_Check(arg) ){
PyObject *bytes = NULL;
char *str = NULL;
PYUNIC_TOSTRING( arg, bytes, str );
if( !str ){
if( bytes ){
Py_XDECREF(bytes);
}
goto PAC_ESCAPE;
}
saf->usage= parse_codes( XGstrdup(str) );
Py_XDECREF(bytes);
}
else
#endif
{
saf->usage= parse_codes( XGstrdup( PyBytes_AsString(arg) ) );
}
aargs[a]= take_ascanf_address(saf);
atype[a]= 4;
if( i && af_array ){
volatile_args+= 1;
}
}
else if( PyArray_Check(arg)
|| PyTuple_Check(arg)
|| PyList_Check(arg)
){
static char *AFname= "AscanfCall-Static-ArrayPointer";
ascanf_Function *saf= &laf[a];
PyArrayObject *parray;
atype[a]= 6;
if( PyList_Check(arg) ){
if( !(arg= PyList_AsTuple(arg)) ){
PyErr_SetString( XG_PythonError, "unexpected failure converting argument to tuple" );
// PyErr_SetString( PyExc_RuntimeError, "unexpected failure converting argument to tuple" );
goto PAC_ESCAPE;
/* return(NULL); */
}
else{
atype[a]= 5;
}
}
memset( saf, 0, sizeof(ascanf_Function) );
saf->type= _ascanf_array;
saf->function= ascanf_Variable;
if( !(saf->name= PyObject_Name(arg)) ){
saf->name= XGstrdup(AFname);
}
saf->is_address= saf->take_address= True;
saf->internal= True;
if( a ){
saf->car= &laf[a-1];
}
else{
saf->car= &laf[lafN-1];
}
if( PyTuple_Check(arg) ){
saf->N= PyTuple_Size(arg);
parray= NULL;
}
else{
saf->N= PyArray_Size(arg);
parray= (PyArrayObject*) arg;
atype[a]= 7;
}
if( (saf->array= (double*) malloc( saf->N * sizeof(double) )) ){
int j;
if( parray ){
PyArrayObject* xd= NULL;
double *PyArrayBuf= NULL;
PyArrayIterObject *it;
if( (xd = (PyArrayObject*) PyArray_ContiguousFromObject( (PyObject*) arg, PyArray_DOUBLE, 0, 0 )) ){
PyArrayBuf= (double*)PyArray_DATA(xd); /* size would be N*sizeof(double) */
}
else{
it= (PyArrayIterObject*) PyArray_IterNew(arg);
}
if( PyArrayBuf ){
// for( j= 0; j< saf->N; j++ ){
// /* 20061016: indices used to be i?!?! */
// saf->array[j]= PyArrayBuf[j];
// }
if( saf->array != PyArrayBuf ){
memcpy( saf->array, PyArrayBuf, saf->N * sizeof(double) );
}
}
else{
for( j= 0; j< saf->N; j++ ){
saf->array[j]= PyFloat_AsDouble( PyArray_DESCR(parray)->f->getitem( it->dataptr, arg) );
PyArray_ITER_NEXT(it);
}
}
if( xd ){
Py_XDECREF(xd);
}
else{
Py_DECREF(it);
}
}
else{
for( j= 0; j< saf->N; j++ ){
saf->array[j]= PyFloat_AsDouble( PyTuple_GetItem(arg,j) );
}
}
aargs[a]= take_ascanf_address(saf);
if( i && af_array ){
volatile_args+= 1;
}
}
else{
PyErr_NoMemory();
goto PAC_ESCAPE;
}
}
#if 0
else{
PyErr_SetString( XG_PythonError, "arguments should be scalars, strings, arrays or ascanf pointers" );
// PyErr_SetString( PyExc_SyntaxError, "arguments should be scalars, strings, arrays or ascanf pointers" );
goto PAC_ESCAPE;
}
#else
else{
static char *AFname= "AscanfCall-Static-PyObject";
ascanf_Function *saf= &laf[a];
memset( saf, 0, sizeof(ascanf_Function) );
saf->function= ascanf_Variable;
saf->internal= True;
saf= make_ascanf_python_object( saf, arg, "AscanfCall" );
if( !saf->name ){
if( saf->PyObject_Name ){
saf->name= XGstrdup(saf->PyObject_Name);
}
else{
saf->name= XGstrdup(AFname);
}
}
aargs[a]= take_ascanf_address(saf);
atype[a]= 4;
if( i && af_array ){
volatile_args+= 1;
}
}
#endif
}
if( a> aargc ){
aargc= a;
}
}
static PyObject* py_fitexpsin(PyObject *obj, PyObject *args, PyObject *kwds)
{
PyArrayObject *data = NULL;
PyArrayObject *fitt = NULL;
PyArrayObject *rslt = NULL;
PyArrayIterObject *data_it = NULL;
PyArrayIterObject *fitt_it = NULL;
PyArrayIterObject *rslt_it = NULL;
Py_ssize_t newshape[NPY_MAXDIMS];
double *poly = NULL;
double *coef = NULL;
double *buff = NULL;
int i, j, error, lastaxis, numdata;
int startcoef = -1;
int numcoef = MAXCOEF;
int axis = NPY_MAXDIMS;
double deltat = 1.0;
static char *kwlist[] = {"data", "numcoef",
"deltat", "axis", NULL};
if (!PyArg_ParseTupleAndKeywords(args, kwds, "O&|idO&", kwlist,
PyConverter_AnyDoubleArray, &data, &numcoef, &deltat,
PyArray_AxisConverter, &axis)) return NULL;
if (axis < 0) {
axis += PyArray_NDIM(data);
}
if ((axis < 0) || (axis >= NPY_MAXDIMS)) {
PyErr_Format(PyExc_ValueError, "invalid axis");
goto _fail;
}
lastaxis = PyArray_NDIM(data) - 1;
if ((numcoef < 1) || (numcoef > MAXCOEF)) {
PyErr_Format(PyExc_ValueError, "numcoef out of bounds");
goto _fail;
}
if (startcoef < 0) { /* start regression away from zero coefficients */
startcoef = 4;
}
if (startcoef > numcoef - 2) {
PyErr_Format(PyExc_ValueError, "startcoef out of bounds");
goto _fail;
}
numdata = (int)PyArray_DIM(data, axis);
if (numcoef > numdata)
numcoef = numdata;
if ((numcoef - startcoef - 1) < 3) {
PyErr_Format(PyExc_ValueError,
"number of coefficients insufficient to fit data");
goto _fail;
}
/* fitted data */
fitt = (PyArrayObject *)PyArray_SimpleNew(PyArray_NDIM(data),
PyArray_DIMS(data), NPY_DOUBLE);
if (fitt == NULL) {
PyErr_Format(PyExc_MemoryError, "unable to allocate fitt array");
goto _fail;
}
/* fitted parameters */
j = 0;
for (i = 0; i < PyArray_NDIM(data); i++) {
if (i != axis)
newshape[j++] = PyArray_DIM(data, i);
}
newshape[j] = 5;
rslt = (PyArrayObject *)PyArray_SimpleNew(PyArray_NDIM(data),
newshape, NPY_DOUBLE);
if (rslt == NULL) {
PyErr_Format(PyExc_MemoryError, "unable to allocate rslt array");
goto _fail;
}
/* working buffer */
buff = (double *)PyMem_Malloc(3*numdata * sizeof(double));
if (buff == NULL) {
PyErr_Format(PyExc_MemoryError, "unable to allocate buff array");
goto _fail;
}
/* buffer for differential coefficients */
coef = (double *)PyMem_Malloc((3+1)*(numcoef+1) * sizeof(double));
if (coef == NULL) {
PyErr_Format(PyExc_MemoryError, "unable to allocate coef array");
goto _fail;
}
/* precalculate normalized Chebyshev polynomial */
poly = (double *)PyMem_Malloc(numdata * (numcoef+1) * sizeof(double));
if (poly == NULL) {
PyErr_Format(PyExc_MemoryError, "unable to allocate poly");
goto _fail;
}
error = chebypoly(numdata, numcoef, poly, 1);
if (error != 0) {
PyErr_Format(PyExc_ValueError,
"chebypoly() failed with error code %i", error);
goto _fail;
}
/* iterate over all but specified axis */
data_it = (PyArrayIterObject *)PyArray_IterAllButAxis(
(PyObject *)data, &axis);
fitt_it = (PyArrayIterObject *)PyArray_IterAllButAxis(
(PyObject *)fitt, &axis);
rslt_it = (PyArrayIterObject *)PyArray_IterAllButAxis(
(PyObject *)rslt, &lastaxis);
while (data_it->index < data_it->size) {
error = fitexpsin(
(char *)data_it->dataptr,
(int)PyArray_STRIDE(data, axis),
numdata,
poly,
coef,
numcoef,
deltat,
startcoef,
buff,
(double *)rslt_it->dataptr,
(char *)fitt_it->dataptr,
(int)PyArray_STRIDE(fitt, axis));
if (error != 0) {
PyErr_Format(PyExc_ValueError,
"fitexpsin() failed with error code %i", error);
goto _fail;
}
PyArray_ITER_NEXT(data_it);
PyArray_ITER_NEXT(fitt_it);
PyArray_ITER_NEXT(rslt_it);
}
Py_XDECREF(data_it);
Py_XDECREF(fitt_it);
Py_XDECREF(rslt_it);
Py_XDECREF(data);
PyMem_Free(poly);
PyMem_Free(coef);
PyMem_Free(buff);
return Py_BuildValue("(N, N)", rslt, fitt);
_fail:
Py_XDECREF(data_it);
Py_XDECREF(fitt_it);
Py_XDECREF(rslt_it);
Py_XDECREF(data);
Py_XDECREF(fitt);
Py_XDECREF(rslt);
PyMem_Free(poly);
PyMem_Free(coef);
PyMem_Free(buff);
return NULL;
}
static PyObject*
PyUnits_convert(
PyUnits* self,
PyObject* args,
PyObject* kwds) {
int status = 1;
PyObject* input = NULL;
PyArrayObject* input_arr = NULL;
PyArrayObject* output_arr = NULL;
PyObject* input_iter = NULL;
PyObject* output_iter = NULL;
double input_val;
double output_val;
if (!PyArg_ParseTuple(args, "O:UnitConverter.convert", &input)) {
goto exit;
}
input_arr = (PyArrayObject*)PyArray_FromObject(
input, NPY_DOUBLE, 0, NPY_MAXDIMS);
if (input_arr == NULL) {
goto exit;
}
output_arr = (PyArrayObject*)PyArray_SimpleNew(
PyArray_NDIM(input_arr), PyArray_DIMS(input_arr), PyArray_DOUBLE);
if (output_arr == NULL) {
goto exit;
}
input_iter = PyArray_IterNew((PyObject*)input_arr);
if (input_iter == NULL) {
goto exit;
}
output_iter = PyArray_IterNew((PyObject*)output_arr);
if (output_iter == NULL) {
goto exit;
}
if (self->power != 1.0) {
while (PyArray_ITER_NOTDONE(input_iter)) {
input_val = *(double *)PyArray_ITER_DATA(input_iter);
output_val = pow(self->scale*input_val + self->offset, self->power);
if (errno) {
PyErr_SetFromErrno(PyExc_ValueError);
goto exit;
}
*(double *)PyArray_ITER_DATA(output_iter) = output_val;
PyArray_ITER_NEXT(input_iter);
PyArray_ITER_NEXT(output_iter);
}
} else {
while (PyArray_ITER_NOTDONE(input_iter)) {
input_val = *(double *)PyArray_ITER_DATA(input_iter);
output_val = self->scale*input_val + self->offset;
*(double *)PyArray_ITER_DATA(output_iter) = output_val;
PyArray_ITER_NEXT(input_iter);
PyArray_ITER_NEXT(output_iter);
}
}
status = 0;
exit:
Py_XDECREF((PyObject*)input_arr);
Py_XDECREF(input_iter);
Py_XDECREF(output_iter);
if (status) {
Py_XDECREF((PyObject*)output_arr);
return NULL;
}
return (PyObject*)output_arr;
}
//Wrapper for Brute-Force neighbor search
static PyObject*
BallTree_knn_brute(PyObject *self, PyObject *args, PyObject *kwds){
long int k = 1;
std::vector<BallTree_Point*> Points;
PyObject *arg1 = NULL;
PyObject *arg2 = NULL;
PyObject *arr1 = NULL;
PyObject *arr2 = NULL;
PyObject *nbrs = NULL;
long int* nbrs_data;
PyArrayIterObject *arr2_iter = NULL;
PyArrayIterObject *nbrs_iter = NULL;
static char *kwlist[] = {"x", "pt", "k", NULL};
npy_intp* dim;
int nd, pt_size, pt_inc;
long int N;
long int D;
//parse arguments. If k is not provided, the default is 1
if(!PyArg_ParseTupleAndKeywords(args,kwds,"OO|l",kwlist,
&arg1,&arg2,&k))
goto fail;
//First array should be a 2D array of doubles
arr1 = PyArray_FROM_OTF(arg1,NPY_DOUBLE,0);
if(arr1==NULL)
goto fail;
if( PyArray_NDIM(arr1) != 2){
PyErr_SetString(PyExc_ValueError,
"x must be two dimensions");
goto fail;
}
//Second array should be a 1D array of doubles
arr2 = PyArray_FROM_OTF(arg2,NPY_DOUBLE,0);
if(arr2==NULL)
goto fail;
nd = PyArray_NDIM(arr2);
if(nd == 0){
PyErr_SetString(PyExc_ValueError,
"pt cannot be zero-sized array");
goto fail;
}
pt_size = PyArray_DIM(arr2,nd-1);
//Check that dimensions match
N = PyArray_DIMS(arr1)[0];
D = PyArray_DIMS(arr1)[1];
if( pt_size != D ){
PyErr_SetString(PyExc_ValueError,
"pt must be same dimension as x");
goto fail;
}
//check the value of k
if(k<1){
PyErr_SetString(PyExc_ValueError,
"k must be a positive integer");
goto fail;
}
if(k>N){
PyErr_SetString(PyExc_ValueError,
"k must be less than the number of points");
goto fail;
}
//create a neighbors array and distance array
dim = new npy_intp[nd];
for(int i=0; i<nd-1;i++)
dim[i] = PyArray_DIM(arr2,i);
dim[nd-1] = k;
nbrs = (PyObject*)PyArray_SimpleNew(nd,dim,PyArray_LONG);
delete[] dim;
if(nbrs==NULL)
goto fail;
//create iterators to cycle through points
nd-=1;
arr2_iter = (PyArrayIterObject*)PyArray_IterAllButAxis(arr2,&nd);
nbrs_iter = (PyArrayIterObject*)PyArray_IterAllButAxis(nbrs,&nd);
nd+=1;
if( arr2_iter==NULL ||
nbrs_iter==NULL ||
(arr2_iter->size != nbrs_iter->size) ){
PyErr_SetString(PyExc_ValueError,
"failure constructing iterators");
goto fail;
}
pt_inc = PyArray_STRIDES(arr2)[nd-1] / PyArray_DESCR(arr2)->elsize;
if(PyArray_STRIDES(nbrs)[nd-1] != PyArray_DESCR(nbrs)->elsize ){
PyErr_SetString(PyExc_ValueError,
"nbrs not allocated as a C-array");
goto fail;
}
//create the list of points
pt_inc = PyArray_STRIDES(arr1)[1]/PyArray_DESCR(arr1)->elsize;
Points.resize(N);
for(int i=0;i<N;i++)
Points[i] = new BallTree_Point(arr1,
(double*)PyArray_GETPTR2(arr1,i,0),
pt_inc, PyArray_DIM(arr1,1));
//iterate through points and determine neighbors
//warning: if nbrs is not a C-array, or if we're not iterating
// over the last dimension, this may cause a seg fault.
while(arr2_iter->index < arr2_iter->size){
BallTree_Point Query_Point(arr2,
(double*)PyArray_ITER_DATA(arr2_iter),
pt_inc,pt_size);
nbrs_data = (long int*)(PyArray_ITER_DATA(nbrs_iter));
BruteForceNeighbors(Points, Query_Point,
k, nbrs_data );
PyArray_ITER_NEXT(arr2_iter);
PyArray_ITER_NEXT(nbrs_iter);
}
for(int i=0;i<N;i++)
delete Points[i];
//if only one neighbor is requested, then resize the neighbors array
if(k==1){
PyArray_Dims dims;
dims.ptr = PyArray_DIMS(arr2);
dims.len = PyArray_NDIM(arr2)-1;
//PyArray_Resize returns None - this needs to be picked
// up and dereferenced.
PyObject *NoneObj = PyArray_Resize( (PyArrayObject*)nbrs, &dims,
0, NPY_ANYORDER );
if (NoneObj == NULL){
goto fail;
}
Py_DECREF(NoneObj);
}
return nbrs;
fail:
Py_XDECREF(arr1);
Py_XDECREF(arr2);
Py_XDECREF(nbrs);
Py_XDECREF(arr2_iter);
Py_XDECREF(nbrs_iter);
return NULL;
}
int joint_histogram(PyArrayObject* JH,
unsigned int clampI,
unsigned int clampJ,
PyArrayIterObject* iterI,
const PyArrayObject* imJ_padded,
const PyArrayObject* Tvox,
long interp)
{
const signed short* J=(signed short*)imJ_padded->data;
size_t dimJX=imJ_padded->dimensions[0]-2;
size_t dimJY=imJ_padded->dimensions[1]-2;
size_t dimJZ=imJ_padded->dimensions[2]-2;
signed short Jnn[8];
double W[8];
signed short *bufI, *bufJnn;
double *bufW;
signed short i, j;
size_t off;
size_t u2 = imJ_padded->dimensions[2];
size_t u3 = u2+1;
size_t u4 = imJ_padded->dimensions[1]*u2;
size_t u5 = u4+1;
size_t u6 = u4+u2;
size_t u7 = u6+1;
double wx, wy, wz, wxwy, wxwz, wywz;
double W0, W2, W3, W4;
int nn, nx, ny, nz;
double *H = (double*)PyArray_DATA(JH);
double Tx, Ty, Tz;
double *tvox = (double*)PyArray_DATA(Tvox);
void (*interpolate)(unsigned int, double*, unsigned int, const signed short*, const double*, int, void*);
void* interp_params = NULL;
prng_state rng;
/*
Check assumptions regarding input arrays. If it fails, the
function will return -1 without doing anything else.
iterI : assumed to iterate over a signed short encoded, possibly
non-contiguous array.
imJ_padded : assumed C-contiguous (last index varies faster) & signed
short encoded.
H : assumed C-contiguous.
Tvox : assumed C-contiguous:
either a 3x4=12-sized array (or bigger) for an affine transformation
or a 3xN array for a pre-computed transformation, with N equal
to the size of the array corresponding to iterI (no checking
done)
*/
if (PyArray_TYPE(iterI->ao) != NPY_SHORT) {
fprintf(stderr, "Invalid type for the array iterator\n");
return -1;
}
if ( (!PyArray_ISCONTIGUOUS(imJ_padded)) ||
(!PyArray_ISCONTIGUOUS(JH)) ||
(!PyArray_ISCONTIGUOUS(Tvox)) ) {
fprintf(stderr, "Some non-contiguous arrays\n");
return -1;
}
/* Reset the source image iterator */
PyArray_ITER_RESET(iterI);
/* Set interpolation method */
if (interp==0)
interpolate = &_pv_interpolation;
else if (interp>0)
interpolate = &_tri_interpolation;
else { /* interp < 0 */
interpolate = &_rand_interpolation;
prng_seed(-interp, &rng);
interp_params = (void*)(&rng);
}
/* Re-initialize joint histogram */
memset((void*)H, 0, clampI*clampJ*sizeof(double));
/* Looop over source voxels */
while(iterI->index < iterI->size) {
/* Source voxel intensity */
bufI = (signed short*)PyArray_ITER_DATA(iterI);
i = bufI[0];
/* Compute the transformed grid coordinates of current voxel */
Tx = *tvox; tvox++;
Ty = *tvox; tvox++;
Tz = *tvox; tvox++;
/* Test whether the current voxel is below the intensity
threshold, or the transformed point is completly outside
the reference grid */
if ((i>=0) &&
(Tx>-1) && (Tx<dimJX) &&
(Ty>-1) && (Ty<dimJY) &&
(Tz>-1) && (Tz<dimJZ)) {
/*
Nearest neighbor (floor coordinates in the padded
image, hence +1).
Notice that using the floor function doubles excetution time.
FIXME: see if we can replace this with assembler instructions.
*/
nx = FLOOR(Tx) + 1;
ny = FLOOR(Ty) + 1;
nz = FLOOR(Tz) + 1;
/* The convention for neighbor indexing is as follows:
*
* Floor slice Ceil slice
*
* 2----6 3----7 y
* | | | | ^
* | | | | |
* 0----4 1----5 ---> x
*/
/*** Trilinear interpolation weights.
Note: wx = nnx + 1 - Tx, where nnx is the location in
the NON-PADDED grid */
wx = nx - Tx;
wy = ny - Ty;
wz = nz - Tz;
wxwy = wx*wy;
wxwz = wx*wz;
wywz = wy*wz;
/*** Prepare buffers */
bufJnn = Jnn;
bufW = W;
/*** Initialize neighbor list */
off = nx*u4 + ny*u2 + nz;
nn = 0;
/*** Neighbor 0: (0,0,0) */
W0 = wxwy*wz;
APPEND_NEIGHBOR(off, W0);
/*** Neighbor 1: (0,0,1) */
APPEND_NEIGHBOR(off+1, wxwy-W0);
/*** Neighbor 2: (0,1,0) */
W2 = wxwz-W0;
APPEND_NEIGHBOR(off+u2, W2);
/*** Neightbor 3: (0,1,1) */
W3 = wx-wxwy-W2;
APPEND_NEIGHBOR(off+u3, W3);
/*** Neighbor 4: (1,0,0) */
W4 = wywz-W0;
APPEND_NEIGHBOR(off+u4, W4);
/*** Neighbor 5: (1,0,1) */
APPEND_NEIGHBOR(off+u5, wy-wxwy-W4);
/*** Neighbor 6: (1,1,0) */
APPEND_NEIGHBOR(off+u6, wz-wxwz-W4);
/*** Neighbor 7: (1,1,1) */
APPEND_NEIGHBOR(off+u7, 1-W3-wy-wz+wywz);
/* Update the joint histogram using the desired interpolation technique */
interpolate(i, H, clampJ, Jnn, W, nn, interp_params);
} /* End of IF TRANSFORMS INSIDE */
/* Update source index */
PyArray_ITER_NEXT(iterI);
} /* End of loop over voxels */
return 0;
}
static PyObject *
py_interpolate(
PyObject *obj,
PyObject *args,
PyObject *kwds)
{
PyArrayObject *xdata = NULL;
PyArrayObject *data = NULL;
PyArrayObject *xout = NULL;
PyArrayObject *out = NULL;
PyArrayObject *oout = NULL;
PyArrayIterObject *dit = NULL;
PyArrayIterObject *oit = NULL;
npy_intp dstride, ostride, xdstride, xostride, size, outsize;
Py_ssize_t newshape[NPY_MAXDIMS];
int axis = NPY_MAXDIMS;
int i, ndim, error;
double *buffer = NULL;
static char *kwlist[] = {"x", "y", "x_new", "axis", "out", NULL};
if (!PyArg_ParseTupleAndKeywords(args, kwds, "O&O&O&|O&O&", kwlist,
PyConverter_AnyDoubleArray, &xdata,
PyConverter_AnyDoubleArray, &data,
PyConverter_AnyDoubleArray, &xout,
PyArray_AxisConverter, &axis,
PyOutputConverter_AnyDoubleArrayOrNone, &oout))
goto _fail;
/* check axis */
ndim = PyArray_NDIM(data);
if ((axis == NPY_MAXDIMS) || (axis == -1)) {
axis = ndim - 1;
} else if ((axis < 0) || (axis > NPY_MAXDIMS)) {
PyErr_Format(PyExc_ValueError, "invalid axis");
goto _fail;
}
if ((PyArray_NDIM(xdata) != 1) || (PyArray_NDIM(xout) != 1)) {
PyErr_Format(PyExc_ValueError,
"x-arrays must be one dimensional");
goto _fail;
}
size = PyArray_DIM(data, axis);
outsize = PyArray_DIM(xout, 0);
if (size < 3) {
PyErr_Format(PyExc_ValueError, "size along axis is too small");
goto _fail;
}
if (size != PyArray_DIM(xdata, 0)) {
PyErr_Format(PyExc_ValueError,
"size of x-array must match data shape at axis");
goto _fail;
}
for (i = 0; i < ndim; i++) {
newshape[i] = (i == axis) ? outsize : PyArray_DIM(data, i);
}
if (oout == NULL) {
/* create a new output array */
out = (PyArrayObject*)PyArray_SimpleNew(ndim, newshape, NPY_DOUBLE);
if (out == NULL) {
PyErr_Format(PyExc_ValueError, "failed to allocate output array");
goto _fail;
}
} else if (ndim != PyArray_NDIM(oout)) {
PyErr_Format(PyExc_ValueError,
"output and data array dimension mismatch");
goto _fail;
} else {
for (i = 0; i < ndim; i++) {
if (newshape[i] != PyArray_DIM(oout, i)) {
PyErr_Format(PyExc_ValueError, "wrong output shape");
goto _fail;
}
}
out = oout;
}
/* iterate over all but specified axis */
dit = (PyArrayIterObject *)PyArray_IterAllButAxis((PyObject *)data, &axis);
oit = (PyArrayIterObject *)PyArray_IterAllButAxis((PyObject *)out, &axis);
dstride = PyArray_STRIDE(data, axis);
ostride = PyArray_STRIDE(out, axis);
xdstride = PyArray_STRIDE(xdata, 0);
xostride = PyArray_STRIDE(xout, 0);
buffer = (double *)PyMem_Malloc((size * 4 + 4) * sizeof(double));
if (buffer == NULL) {
PyErr_Format(PyExc_ValueError, "failed to allocate output buffer");
goto _fail;
}
while (dit->index < dit->size) {
error = interpolate(
size,
PyArray_DATA(xdata), xdstride,
dit->dataptr, dstride,
outsize,
PyArray_DATA(xout), xostride,
oit->dataptr, ostride,
buffer);
if (error != 0) {
PyErr_Format(PyExc_ValueError, "interpolate() failed");
goto _fail;
}
PyArray_ITER_NEXT(oit);
PyArray_ITER_NEXT(dit);
}
PyMem_Free(buffer);
Py_DECREF(oit);
Py_DECREF(dit);
Py_DECREF(data);
Py_DECREF(xout);
Py_DECREF(xdata);
/* Return output vector if not provided as argument */
if (oout == NULL) {
return PyArray_Return(out);
} else {
Py_INCREF(Py_None);
return Py_None;
}
_fail:
Py_XDECREF(xdata);
Py_XDECREF(xout);
Py_XDECREF(data);
Py_XDECREF(oit);
Py_XDECREF(dit);
if (buffer != NULL)
PyMem_Free(buffer);
if (oout == NULL)
Py_XDECREF(out);
else
Py_XDECREF(oout);
return NULL;
}
void joint_histogram(double* H,
unsigned int clampI,
unsigned int clampJ,
PyArrayIterObject* iterI,
const PyArrayObject* imJ_padded,
const double* Tvox,
int affine,
int interp)
{
const signed short* J=(signed short*)imJ_padded->data;
size_t dimJX=imJ_padded->dimensions[0]-2;
size_t dimJY=imJ_padded->dimensions[1]-2;
size_t dimJZ=imJ_padded->dimensions[2]-2;
signed short Jnn[8];
double W[8];
signed short *bufI, *bufJnn;
double *bufW;
signed short i, j;
size_t off;
size_t u2 = imJ_padded->dimensions[2];
size_t u3 = u2+1;
size_t u4 = imJ_padded->dimensions[1]*u2;
size_t u5 = u4+1;
size_t u6 = u4+u2;
size_t u7 = u6+1;
double wx, wy, wz, wxwy, wxwz, wywz;
double W0, W2, W3, W4;
size_t x, y, z;
int nn, nx, ny, nz;
double Tx, Ty, Tz;
double *bufTvox = (double*)Tvox;
void (*interpolate)(unsigned int, double*, unsigned int, const signed short*, const double*, int, void*);
void* interp_params = NULL;
rk_state rng;
/* Reset the source image iterator */
PyArray_ITER_RESET(iterI);
/* Make sure the iterator the iterator will update coordinate values */
UPDATE_ITERATOR_COORDS(iterI);
/* Set interpolation method */
if (interp==0)
interpolate = &_pv_interpolation;
else if (interp>0)
interpolate = &_tri_interpolation;
else { /* interp < 0 */
interpolate = &_rand_interpolation;
rk_seed(-interp, &rng);
interp_params = (void*)(&rng);
}
/* Re-initialize joint histogram */
memset((void*)H, 0, clampI*clampJ*sizeof(double));
/* Looop over source voxels */
while(iterI->index < iterI->size) {
/* Source voxel intensity */
bufI = (signed short*)PyArray_ITER_DATA(iterI);
i = bufI[0];
/* Compute the transformed grid coordinates of current voxel */
if (affine) {
/* Get voxel coordinates and apply transformation on-the-fly*/
x = iterI->coordinates[0];
y = iterI->coordinates[1];
z = iterI->coordinates[2];
_affine_transform(&Tx, &Ty, &Tz, Tvox, x, y, z);
}
else
/* Use precomputed transformed coordinates */
bufTvox = _precomputed_transform(&Tx, &Ty, &Tz, (const double*)bufTvox);
/* Test whether the current voxel is below the intensity
threshold, or the transformed point is completly outside
the reference grid */
if ((i>=0) &&
(Tx>-1) && (Tx<dimJX) &&
(Ty>-1) && (Ty<dimJY) &&
(Tz>-1) && (Tz<dimJZ)) {
/*
Nearest neighbor (floor coordinates in the padded
image, hence +1).
Notice that using the floor function doubles excetution time.
FIXME: see if we can replace this with assembler instructions.
*/
nx = FLOOR(Tx) + 1;
ny = FLOOR(Ty) + 1;
nz = FLOOR(Tz) + 1;
/* The convention for neighbor indexing is as follows:
*
* Floor slice Ceil slice
*
* 2----6 3----7 y
* | | | | ^
* | | | | |
* 0----4 1----5 ---> x
*/
/*** Trilinear interpolation weights.
Note: wx = nnx + 1 - Tx, where nnx is the location in
the NON-PADDED grid */
wx = nx - Tx;
wy = ny - Ty;
wz = nz - Tz;
wxwy = wx*wy;
wxwz = wx*wz;
wywz = wy*wz;
/*** Prepare buffers */
bufJnn = Jnn;
bufW = W;
/*** Initialize neighbor list */
off = nx*u4 + ny*u2 + nz;
nn = 0;
/*** Neighbor 0: (0,0,0) */
W0 = wxwy*wz;
APPEND_NEIGHBOR(off, W0);
/*** Neighbor 1: (0,0,1) */
APPEND_NEIGHBOR(off+1, wxwy-W0);
/*** Neighbor 2: (0,1,0) */
W2 = wxwz-W0;
APPEND_NEIGHBOR(off+u2, W2);
/*** Neightbor 3: (0,1,1) */
W3 = wx-wxwy-W2;
APPEND_NEIGHBOR(off+u3, W3);
/*** Neighbor 4: (1,0,0) */
W4 = wywz-W0;
APPEND_NEIGHBOR(off+u4, W4);
/*** Neighbor 5: (1,0,1) */
APPEND_NEIGHBOR(off+u5, wy-wxwy-W4);
/*** Neighbor 6: (1,1,0) */
APPEND_NEIGHBOR(off+u6, wz-wxwz-W4);
/*** Neighbor 7: (1,1,1) */
APPEND_NEIGHBOR(off+u7, 1-W3-wy-wz+wywz);
/* Update the joint histogram using the desired interpolation technique */
interpolate(i, H, clampJ, Jnn, W, nn, interp_params);
} /* End of IF TRANSFORMS INSIDE */
/* Update source index */
PyArray_ITER_NEXT(iterI);
} /* End of loop over voxels */
return;
}
//query the ball tree. Arguments are the array of search points
// and the radius around each point to search
static PyObject *
BallTree_queryball(BallTreeObject *self, PyObject *args, PyObject *kwds){
//we use goto statements : all variables should be declared up front
int count_only = 0;
double r;
PyObject *arg = NULL;
PyObject *arr = NULL;
PyObject *nbrs = NULL;
PyArrayIterObject* arr_iter = NULL;
PyArrayIterObject* nbrs_iter = NULL;
int nd, pt_size, pt_inc;
static char *kwlist[] = {"x", "r", "count_only", NULL};
//parse arguments. If kmax is not provided, the default is 20
if(!PyArg_ParseTupleAndKeywords(args,kwds,"Od|i",
kwlist,&arg,&r,&count_only)){
goto fail;
}
//check value of r
if(r < 0){
PyErr_SetString(PyExc_ValueError,
"r must not be negative");
goto fail;
}
//get the array object from the first argument
arr = PyArray_FROM_OTF(arg,NPY_DOUBLE,NPY_ALIGNED);
//check that the array was properly constructed
if(arr==NULL){
PyErr_SetString(PyExc_ValueError,
"pt must be convertable to array");
goto fail;
}
nd = PyArray_NDIM(arr);
if(nd == 0){
PyErr_SetString(PyExc_ValueError,
"pt cannot be zero-sized array");
goto fail;
}
pt_size = PyArray_DIM(arr,nd-1);
if( pt_size != self->tree->PointSize() ){
PyErr_SetString(PyExc_ValueError,
"points are incorrect dimension");
goto fail;
}
// Case 1: return arrays of all neighbors for each point
//
if(!count_only){
//create a neighbors array. This is an array of python objects.
// each of which will be a numpy array of neighbors
nbrs = (PyObject*)PyArray_SimpleNew(nd-1,PyArray_DIMS(arr),
PyArray_OBJECT);
if(nbrs==NULL){
goto fail;
}
//create iterators to cycle through points
--nd;
arr_iter = (PyArrayIterObject*)PyArray_IterAllButAxis(arr,&nd);
nbrs_iter = (PyArrayIterObject*)PyArray_IterNew(nbrs);
++nd;
if( arr_iter==NULL || nbrs_iter==NULL ||
(arr_iter->size != nbrs_iter->size)){
PyErr_SetString(PyExc_ValueError,
"unable to construct iterator");
goto fail;
}
pt_inc = PyArray_STRIDES(arr)[nd-1] / PyArray_DESCR(arr)->elsize;
if(PyArray_NDIM(nbrs)==0){
BallTree_Point pt(arr,
(double*)PyArray_ITER_DATA(arr_iter),
pt_inc,pt_size);
std::vector<long int> nbrs_vec;
self->tree->query_ball(pt,r,nbrs_vec);
npy_intp N_nbrs = nbrs_vec.size();
PyObject* nbrs_obj = PyArray_SimpleNew(1, &N_nbrs, PyArray_LONG);
long int* data = (long int*)PyArray_DATA(nbrs_obj);
for(int i=0; i<N_nbrs; i++)
data[i] = nbrs_vec[i];
PyObject* tmp = nbrs;
nbrs = nbrs_obj;
Py_DECREF(tmp);
}else{
while(arr_iter->index < arr_iter->size){
BallTree_Point pt(arr,
(double*)PyArray_ITER_DATA(arr_iter),
pt_inc,pt_size);
std::vector<long int> nbrs_vec;
self->tree->query_ball(pt,r,nbrs_vec);
npy_intp N_nbrs = nbrs_vec.size();
PyObject* nbrs_obj = PyArray_SimpleNew(1, &N_nbrs,
PyArray_LONG);
long int* data = (long int*)PyArray_DATA(nbrs_obj);
for(int i=0; i<N_nbrs; i++)
data[i] = nbrs_vec[i];
PyObject** nbrs_data = (PyObject**)PyArray_ITER_DATA(nbrs_iter);
PyObject* tmp = nbrs_data[0];
nbrs_data[0] = nbrs_obj;
Py_XDECREF(tmp);
PyArray_ITER_NEXT(arr_iter);
PyArray_ITER_NEXT(nbrs_iter);
}
}
}
// Case 2 : return number of neighbors for each point
else{
//create an array to keep track of the count
nbrs = (PyObject*)PyArray_SimpleNew(nd-1,PyArray_DIMS(arr),
PyArray_LONG);
if(nbrs==NULL){
goto fail;
}
//create iterators to cycle through points
--nd;
arr_iter = (PyArrayIterObject*)PyArray_IterAllButAxis(arr,&nd);
nbrs_iter = (PyArrayIterObject*)PyArray_IterNew(nbrs);
++nd;
if( arr_iter==NULL || nbrs_iter==NULL ||
(arr_iter->size != nbrs_iter->size)){
PyErr_SetString(PyExc_ValueError,
"unable to construct iterator");
goto fail;
}
//go through points and call BallTree::query_ball to count neighbors
pt_inc = PyArray_STRIDES(arr)[nd-1] / PyArray_DESCR(arr)->elsize;
while(arr_iter->index < arr_iter->size){
BallTree_Point pt(arr,
(double*)PyArray_ITER_DATA(arr_iter),
pt_inc,pt_size);
long int* nbrs_count = (long int*)PyArray_ITER_DATA(nbrs_iter);
*nbrs_count = self->tree->query_ball(pt,r);
PyArray_ITER_NEXT(arr_iter);
PyArray_ITER_NEXT(nbrs_iter);
}
}
Py_DECREF(nbrs_iter);
Py_DECREF(arr_iter);
Py_DECREF(arr);
return nbrs;
fail:
Py_XDECREF(nbrs_iter);
Py_XDECREF(arr_iter);
Py_XDECREF(arr);
Py_XDECREF(nbrs);
return NULL;
}
static PyObject *frputvect(PyObject *self, PyObject *args, PyObject *keywds) {
FrFile *oFile;
FrameH *frame;
FrProcData *proc;
FrAdcData *adc;
FrSimData *sim;
FrVect *vect;
int verbose=0, nData, nBits, type, subType, arrayType;
double dx, sampleRate, start;
char blank[] = "";
char *filename=NULL, *history=NULL;
char channel[MAX_STR_LEN], x_unit[MAX_STR_LEN], y_unit[MAX_STR_LEN], kind[MAX_STR_LEN];
PyObject *temp;
char msg[MAX_STR_LEN];
PyObject *channellist, *channellist_iter, *framedict, *array;
PyArrayIterObject *arrayIter;
PyArray_Descr *temp_descr;
static char *kwlist[] = {"filename", "channellist", "history", "verbose",
NULL};
/*--------------- unpack arguments --------------------*/
verbose = 0;
/* The | in the format string indicates the next arguments are
optional. They are simply not assigned anything. */
if (!PyArg_ParseTupleAndKeywords(args, keywds, "sO|si", kwlist,
&filename, &channellist, &history, &verbose)) {
Py_RETURN_NONE;
}
FrLibSetLvl(verbose);
if (history == NULL) {
history = blank;
}
/*-------- create frames, create vectors, and fill them. ------*/
// Channel-list must be any type of sequence
if (!PySequence_Check(channellist)) {
PyErr_SetNone(PyExc_TypeError);
return NULL;
}
// Get channel name from first dictionary
framedict = PySequence_GetItem(channellist, (Py_ssize_t)0);
if (framedict == NULL) {
PyErr_SetString(PyExc_ValueError, "channellist is empty!");
return NULL;
}
PyDict_ExtractString(channel, framedict, "name");
Py_XDECREF(framedict);
if (PyErr_Occurred()) {return NULL;}
if (verbose > 0) {
printf("Creating frame %s...\n", channel);
}
frame = FrameNew(channel);
if (frame == NULL) {
snprintf(msg, MAX_STR_LEN, "FrameNew failed (%s)", FrErrorGetHistory());
PyErr_SetString(PyExc_FrError, msg);
return NULL;
}
if (verbose > 0) {
printf("Now iterating...\n");
}
// Iterators allow one to deal with non-contiguous arrays
channellist_iter = PyObject_GetIter(channellist);
arrayIter = NULL;
while ((framedict = PyIter_Next(channellist_iter))) {
if (verbose > 0) {
printf("In loop...\n");
}
// Extract quantities from dict -- all borrowed references
PyDict_ExtractString(channel, framedict, "name");
CHECK_ERROR;
start = PyDict_ExtractDouble(framedict, "start");
CHECK_ERROR;
dx = PyDict_ExtractDouble(framedict, "dx");
CHECK_ERROR;
array = PyDict_GetItemString(framedict, "data");
if (!PyArray_Check(array)) {
snprintf(msg, MAX_STR_LEN, "data is not an array");
PyErr_SetString(PyExc_TypeError, msg);
}
CHECK_ERROR;
nData = PyArray_SIZE(array);
nBits = PyArray_ITEMSIZE(array)*8;
arrayType = PyArray_TYPE(array);
// kind, x_unit, y_unit, type, and subType have default values
temp = PyDict_GetItemString(framedict, "kind");
if (temp != NULL) {strncpy(kind, PyString_AsString(temp), MAX_STR_LEN);}
else {snprintf(kind, MAX_STR_LEN, "PROC");}
temp = PyDict_GetItemString(framedict, "x_unit");
if (temp != NULL) {strncpy(x_unit, PyString_AsString(temp), MAX_STR_LEN);}
else {strncpy(x_unit, blank, MAX_STR_LEN);}
temp = PyDict_GetItemString(framedict, "y_unit");
if (temp != NULL) {strncpy(y_unit, PyString_AsString(temp), MAX_STR_LEN);}
else {strncpy(y_unit, blank, MAX_STR_LEN);}
temp = PyDict_GetItemString(framedict, "type");
if (temp != NULL) {type = (int)PyInt_AsLong(temp);}
else {type = 1;}
temp = PyDict_GetItemString(framedict, "subType");
if (temp != NULL) {subType = (int)PyInt_AsLong(temp);}
else {subType = 0;}
// check for errors
CHECK_ERROR;
if (dx <= 0 || array == NULL || nData==0) {
temp = PyObject_Str(framedict);
snprintf(msg, MAX_STR_LEN, "Input dictionary contents: %s", PyString_AsString(temp));
Py_XDECREF(temp);
FrameFree(frame);
Py_XDECREF(framedict);
Py_XDECREF(channellist_iter);
PyErr_SetString(PyExc_ValueError, msg);
return NULL;
}
if (verbose > 0) {
printf("type = %d, subType = %d, start = %f, dx = %f\n",
type, subType, start, dx);
}
sampleRate = 1./dx;
if (verbose > 0) {
printf("Now copying data to vector...\n");
}
// Create empty vector (-typecode ==> empty) with metadata,
// then copy data to vector
vect = NULL;
arrayIter = (PyArrayIterObject *)PyArray_IterNew(array);
if(arrayType == NPY_INT16) {
vect = FrVectNew1D(channel,-FR_VECT_2S,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataS[arrayIter->index] = *((npy_int16 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_INT32) {
vect = FrVectNew1D(channel,-FR_VECT_4S,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataI[arrayIter->index] = *((npy_int32 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_INT64) {
vect = FrVectNew1D(channel,-FR_VECT_8S,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataL[arrayIter->index] = *((npy_int64 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_UINT8) {
vect = FrVectNew1D(channel,-FR_VECT_1U,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataU[arrayIter->index] = *((npy_uint8 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_UINT16) {
vect = FrVectNew1D(channel,-FR_VECT_2U,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataUS[arrayIter->index] = *((npy_uint16 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_UINT32) {
vect = FrVectNew1D(channel,-FR_VECT_4U,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataUI[arrayIter->index] = *((npy_uint32 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_UINT64) {
vect = FrVectNew1D(channel,-FR_VECT_8U,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataUL[arrayIter->index] = *((npy_uint64 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_FLOAT32) {
vect = FrVectNew1D(channel,-FR_VECT_4R,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataF[arrayIter->index] = *((npy_float32 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_FLOAT64) {
vect = FrVectNew1D(channel,-FR_VECT_8R,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataD[arrayIter->index] = *((npy_float64 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
/* FrVects don't have complex pointers. Numpy stores complex
numbers in the same way, but we have to trick it into giving
us a (real) float pointer. */
else if(arrayType == NPY_COMPLEX64) {
vect = FrVectNew1D(channel,-FR_VECT_8C,nData,dx,x_unit,y_unit);
temp_descr = PyArray_DescrFromType(NPY_FLOAT32);
temp = PyArray_View((PyArrayObject *)array, temp_descr, NULL);
Py_XDECREF(temp_descr);
Py_XDECREF(arrayIter);
arrayIter = (PyArrayIterObject *)PyArray_IterNew(temp);
while (arrayIter->index < arrayIter->size) {
vect->dataF[arrayIter->index] = *((npy_float32 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}
Py_XDECREF(temp);}
else if(arrayType == NPY_COMPLEX128) {
vect = FrVectNew1D(channel,-FR_VECT_16C,nData,dx,x_unit,y_unit);
temp_descr = PyArray_DescrFromType(NPY_FLOAT64);
temp = PyArray_View((PyArrayObject *)array, temp_descr, NULL);
Py_XDECREF(temp_descr);
Py_XDECREF(arrayIter);
arrayIter = (PyArrayIterObject *)PyArray_IterNew(temp);
while (arrayIter->index < arrayIter->size) {
vect->dataD[arrayIter->index] = *((npy_float64 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}
Py_XDECREF(temp);}
else PyErr_SetString(PyExc_TypeError, msg);
if (PyErr_Occurred()) {
if (vect != NULL) FrVectFree(vect);
FrameFree(frame);
Py_XDECREF(framedict);
Py_XDECREF(channellist_iter);
Py_XDECREF(arrayIter);
return NULL;
}
if (verbose > 0) {
printf("Done copying...\n");
FrameDump(frame, stdout, 6);
}
// Add Fr*Data to frame and attach vector to Fr*Data
if (strncmp(kind, "PROC", MAX_STR_LEN)==0) {
proc = FrProcDataNew(frame, channel, sampleRate, 1, nBits);
FrVectFree(proc->data);
proc->data = vect;
proc->type = type;
proc->subType = subType;
frame->GTimeS = (npy_uint32)start;
frame->GTimeN = (npy_uint32)((start-(frame->GTimeS))*1e9);
if (type==1) { // time series
proc->tRange = nData*dx;
frame->dt = nData*dx;
} else if (type==2) { // frequency series
proc->fRange = nData*dx;
}
} else if (strncmp(kind, "ADC", MAX_STR_LEN)==0) {
adc = FrAdcDataNew(frame, channel, sampleRate, 1, nBits);
FrVectFree(adc->data);
adc->data = vect;
frame->dt = nData*dx;
frame->GTimeS = (npy_uint32)start;
frame->GTimeN = (npy_uint32)((start-(frame->GTimeS))*1e9);
} else {// Already tested that kind is one of these strings above
sim = FrSimDataNew(frame, channel, sampleRate, 1, nBits);
FrVectFree(sim->data);
sim->data = vect;
frame->dt = nData*dx;
frame->GTimeS = (npy_uint32)start;
frame->GTimeN = (npy_uint32)((start-(frame->GTimeS))*1e9);
}
if (verbose > 0) {
printf("Attached vect to frame.\n");
}
// Clean up (all python objects in loop should be borrowed references)
Py_XDECREF(framedict);
Py_XDECREF(arrayIter);
} // end iteration over channellist
Py_XDECREF(channellist_iter);
// At this point, there should be no Python references left!
/*------------- Write file -----------------------------*/
oFile = FrFileONewH(filename, 1, history); // 1 ==> gzip contents
if (oFile == NULL) {
snprintf(msg, MAX_STR_LEN, "%s\n", FrErrorGetHistory());
PyErr_SetString(PyExc_FrError, msg);
FrFileOEnd(oFile);
return NULL;
}
if (FrameWrite(frame, oFile) != FR_OK) {
snprintf(msg, MAX_STR_LEN, "%s\n", FrErrorGetHistory());
PyErr_SetString(PyExc_FrError, msg);
FrFileOEnd(oFile);
return NULL;
}
/* The FrFile owns data and vector memory. Do not free them separately. */
FrFileOEnd(oFile);
FrameFree(frame);
Py_RETURN_NONE;
};