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#include "cbf.h"
#include "cbf_simple.h"
#include "cbf_string.h"
#include "dps_peaksearch.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
void bin2x2(unsigned short *data, int width, int height, unsigned short *out);
int convertroi(char *roi, int fastdim, int slowdim,
int * fastlow, int * fasthigh, int * slowlow, int * slowhigh);
#define MAX_PEAKS 20000
DPS_Peak peaks[MAX_PEAKS];
int max_peaks = MAX_PEAKS;
void usage()
{
fprintf(stderr,"Usage: roi_peaksearch [--binagain] [--min-peak ioversig] \\\n"
" [--region_of_interest fastlow,fasthigh,slowlow,showhigh] \\\n"
" [--overlay overlay_file.cbf] [--mask mask_file.cbf] \\\n"
" [--min-spacing min_spacing] \\\n"
" [--min-value min_value] \\\n"
" file.cbf peaklist \n");
}
int main (int argc, char **argv)
{
unsigned short *out;
char * filename = NULL; /* The input file name */
char * maskname = NULL; /* An optional mask file (e.g. BKGINIT.cbf) */
char * overlayname = NULL; /* An optional peak/roi overlay file */
int min_spacing = 6; /* Minimum spacing in pixels between spots */
int min_value = 0; /* Minimum valid value */
double ioversig = 2.; /* Minimum peak height in I/sigma(I) */
int xsize, ysize;
char * roi = NULL;
char * strstrhit;
int n_peaks;
int i;
FILE *fp;
FILE *ovlp=NULL;
int nStat = 0;
cbf_handle hCBFile;
cbf_handle hCBFmask;
cbf_handle hCBFoverlay;
int nBinary_id, mask_nBinary_id;
unsigned int compression, mask_compression;
int binary_id, mask_binary_id;
size_t elsize, mask_elsize;
int elsigned, mask_elsigned;
int elunsigned, mask_elunsigned;
size_t elements, elements_read, mask_elements, mask_elements_read;
int minelement, mask_minelement;
int maxelement, mask_maxelement;
char* byteorder ="little_endian";
char* mask_byteorder;
size_t dim1, mask_dim1;
size_t dim2, mask_dim2;
size_t dim3, mask_dim3;
size_t padding, mask_padding;
int nDim0, nDim1;
int fastlow, fasthigh, slowlow, slowhigh;
unsigned short *ushort_data, *up;
int* pnData, *ip;
int* pmaskData=NULL;
int lastgood;
int error;
error = 0;
hCBFile = hCBFmask = hCBFoverlay = NULL;
if ( argc < 3 )
{
usage();
exit(-1);
}
while (argc > 3) {
if (argc > 4 && (0 == cbf_cistrcmp("--overlay-image",argv[1])
|| (0 == cbf_cistrcmp("--overlay",argv[1]))
|| (0 == cbf_cistrcmp("--ovl",argv[1])))) {
overlayname = argv[2];
argv+=2;
argc-=2;
ovlp = fopen(overlayname, "w+b");
if (!ovlp) {
fprintf(stderr,"roi_peaksearch: unable to open overlay cbf `%s'\n\n",overlayname);
usage();
exit(-1);
}
continue;
}
if (argc > 4 && (0 == cbf_cistrcmp("--mask",argv[1])
|| (0 == cbf_cistrcmp("--BKGINIT",argv[1])))) {
maskname = argv[2];
argv+=2;
argc-=2;
if ( ( fp = fopen(maskname, "rb" ) ) == NULL ) {
fprintf(stderr,"Error opening file\n");
return(1);
}
error |= cbf_make_handle(&hCBFmask);
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR in mask cbf_make_handle\n");
usage();
exit(-1);
}
error |= cbf_read_widefile(hCBFmask, fp, MSG_DIGEST);
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR in mask cbf_read_widefile\n");
usage();
exit(-1);
}
error |= cbf_find_tag(hCBFmask, "_array_data.data");
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR in cbf_find_tag\n");
usage();
exit(-1);
}
error |= cbf_find_column (hCBFmask, "data");
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR in cbf_find_column data\n");
usage();
exit(-1);
}
error|= cbf_get_integerarrayparameters_wdims (hCBFmask, &mask_compression,
&mask_nBinary_id,
&mask_elsize,
&mask_elsigned,
&mask_elunsigned,
&mask_elements,
&mask_minelement,
&mask_maxelement,
(const char **) &mask_byteorder,
&mask_dim1, &mask_dim2, &mask_dim3, &mask_padding);
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR in cbf_get_integerarrayparameters_wdims\n");
usage();
exit(-1);
}
if (mask_dim3 == 0) mask_dim3 = 1;
if (mask_dim2 == 0) mask_dim2 = 1;
if (mask_dim1 == 0) mask_dim1 = mask_elements;
continue;
}
if (argc > 4 && (0 == cbf_cistrcmp("--min-i-over-sigma",argv[1])
|| (0 == cbf_cistrcmp("--min-peak",argv[1])))) {
ioversig = atof(argv[2]);
argv+=2;
argc-=2;
continue;
}
if (argc > 4 && (0 == cbf_cistrcmp("--min-spacing",argv[1]))) {
min_spacing = (int)(0.5+atof(argv[2]));
if (min_spacing < 1) min_spacing = 1;
argv+=2;
argc-=2;
continue;
}
if (argc > 4 && (0 == cbf_cistrcmp("--min-value",argv[1]))) {
min_value = (int)(atof(argv[2]));
argv+=2;
argc-=2;
continue;
}
if(0 == cbf_cistrcmp("--binagain", argv[1])
|| 0 == cbf_cistrcmp("-binagain",argv[1]))
{
argv++;
argc--;
continue;
}
if(argc > 4 && (0 == cbf_cistrcmp("--region-of-interest", argv[1])
|| 0==cbf_cistrcmp("roi",argv[1]))) {
if (roi) {
fprintf(stderr,"roi_peaksearch: only one roi supported\n\n");
usage();
exit(-1);
}
roi = argv[2];
argv += 2;
argc -= 2;
continue;
}
strstrhit = strstr(argv[1], "--region_of_interest");
if(NULL != strstrhit && strstrhit==argv[1] ) {
roi = argv[1]+strlen("--region_of_interest")+1;
if (*(roi-1)!='='||strlen(roi)<3){
fprintf(stderr,"roi_peaksearch: %s should be --region_of_interest=fastlow,fasthigh,slowlow,slowhigh\n\n", argv[1]);
usage();
exit(-1);
}
argv++;
argc--;
continue;
}
usage();
exit(-1);
}
filename=argv[1];
if ( ( fp = fopen(filename, "rb" ) ) == NULL ) {
fprintf(stderr,"Error opening file\n");
exit(-1);
}
error |= cbf_make_handle(&hCBFile);
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR %x in cbf_make_handle\n", error);
exit(-1);
}
error |= cbf_read_widefile(hCBFile, fp, MSG_DIGEST);
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR %x in cbf_read_widefile\n", error);
exit(-1);
}
error |= cbf_find_tag(hCBFile, "_array_data.data");
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR %x in cbf_find_tag\n", error);
exit(-1);
}
error |= cbf_find_column (hCBFile, "data");
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR %x in cbf_find_column data\n", error);
exit(-1);
}
error |= cbf_get_integerarrayparameters_wdims (hCBFile, &compression,
&nBinary_id,
&elsize,
&elsigned,
&elunsigned,
&elements,
&minelement,
&maxelement,
(const char **) &byteorder,
&dim1, &dim2, &dim3, &padding);
if (dim1 == 0) dim1 = elements;
if (dim2 == 0) dim2 = 1;
if (dim3 == 0) dim3 = 1;
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR %x in cbf_get_integerarrayparameters_wdims\n", error);
exit(-1);
}
nDim0 = (int)dim1;
nDim1 = (int)dim2;
xsize = nDim0;
ysize = nDim1;
if (convertroi ( roi, xsize, ysize, &fastlow, &fasthigh, &slowlow, &slowhigh) ) {
fprintf(stderr,"roi_peaksearch: invalid region of interest '%s'\n", roi);
usage();
exit(-1);
}
out = (unsigned short *)malloc ((fasthigh-fastlow+1)*(slowhigh-slowlow+1)*sizeof( unsigned short ));
if (out == NULL) {
fprintf(stderr,"roi_peaksearch: ERROR can not allocate %ld bytes\n",(long unsigned int) (fasthigh-fastlow+1)*(slowhigh-slowlow+1)*sizeof( unsigned short ));
fflush(stderr); exit(-1);
}
if(NULL == (pnData = (int *) malloc(dim1 * dim2 * dim2 * elsize)))
{
fprintf(stderr,"roi_peaksearch: ERROR can not allocate %ld bytes for data\n",(long unsigned int) (fasthigh-fastlow+1)*(slowhigh-slowlow+1)*sizeof( unsigned short ));
fflush(stderr);
exit(-1);
}
if(NULL == (ushort_data = (unsigned short *) malloc(nDim0 * nDim1 * sizeof (unsigned short))))
{
return(1);
}
if (hCBFmask) {
if(NULL == (pmaskData = (int *) malloc(mask_dim1 * mask_dim2 * mask_dim3 * elsize)))
{
fprintf(stderr,"roi_peaksearch: ERROR unable to allocate %ld bytes for mask\n",
(unsigned long)(mask_dim1 * mask_dim2 * mask_dim3 * elsize));
fflush(stderr); exit(-1);
}
error |= cbf_get_integerarray (hCBFmask,
&mask_binary_id, (void *)pmaskData,
mask_elsize, mask_elsigned,
mask_elements, &mask_elements_read);
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR %x in mask cbf_get_integerarray\n", error);
fflush(stderr); exit(-1);
}
}
error |= cbf_get_integerarray (hCBFile,
&binary_id, (void *)pnData,
elsize, elsigned,
elements, &elements_read);
if (0 != error) {
fprintf(stderr,"roi_peaksearch: ERROR in cbf_get_integerarray\n");
fflush(stderr); exit(-1);
}
int k;
up = ushort_data;
ip = pnData;
k = nDim0*nDim1;
for(i = 0; i < k; i++) {
if ((0xFFFF0000 &*ip) != 0) {
*up++ = 0xFFFD;
ip++; }
else {
lastgood = *ip++;
if ((0xFFF0 & lastgood) == 0xFFF0) lastgood = 0xFFFF;
*up++ = (unsigned short) (lastgood &0xFFFF);
}
}
// *data = ushort_data;
if ( !overlayname ) free(pnData);
// istat = cbf2adscimg_sub(filename, &header, &raw);
// istat = rdfile ( filename, &hp, &lhead, (char**) &raw, &dim, size, &type );
{
unsigned short * ip = out;
int i, j;
for(j = slowlow; j <= slowhigh; j++) {
for(i = fastlow; i <= fasthigh; i++) {
*ip = 0x0000ffff &
(int)ushort_data[j*xsize +i];
if (hCBFmask && i < mask_dim1 && j < mask_dim2 && (pmaskData[j*mask_dim1+i]&0xFFFC)==0xFFFC)
*ip = 0xFFFF;
ip++;
}
}
}
n_peaks = dps_peaksearch(out,
fasthigh-fastlow+1, slowhigh-slowlow+1,
max_peaks, ioversig,
min_spacing,
peaks,
min_value);
// n_peaks = dps_peaksearch_cn(raw, xsize, ysize, max_peaks, ioversig, min_spacing, peaks);
fprintf(stdout, "Number of peaks found with I/sigma > %.2f is %d\n", ioversig, n_peaks);
fprintf(stdout, "PeaksCount : %d\n", n_peaks);
fprintf(stdout, "Top 10 peaks:\n");
fprintf(stdout, " x y I/sigma\n");
for(i = 0; i < 10; i++)
fprintf(stdout, "%7.2f %7.2f %9.2f\n", peaks[i].x+fastlow, peaks[i].y+slowlow, peaks[i].isigma);
if(NULL == (fp = fopen(argv[2], "w")))
{
fprintf(stderr, "roi_peaksearch: Cannot create %s as output peaklist file\n", argv[2]);
exit(0);
}
for(i = 0; i < n_peaks; i++) {
int xlow, xhigh, ylow, yhigh, xcen, ycen, ix, iy;
int heat, min_crossw, min_crossh;
fprintf(fp, "%7.2f %7.2f %9.2f\n", peaks[i].x+fastlow, peaks[i].y+slowlow, peaks[i].isigma);
if (overlayname) {
int tempx, tempy=0;
min_crossw = (peaks[i].peakfw+1)/2-1;
min_crossh = (peaks[i].peakfh+1)/2-1;
if (min_crossw<1) min_crossw=1;
if (min_crossh<1) min_crossh=1;
xcen = peaks[i].x+fastlow+0.5;
ycen = peaks[i].y+slowlow+0.5;
xlow = xcen - peaks[i].peakfw;
if (xlow < 0) xlow = 0;
xhigh = xcen + peaks[i].peakfw;
if (xhigh >= nDim0) xhigh = nDim0-1;
ylow = ycen - peaks[i].peakfh;
if (ylow < 0) ylow = 0;
yhigh = ycen + peaks[i].peakfh;
if (yhigh >= nDim1) yhigh = nDim1-1;
heat = (int)(peaks[i].isigma/10.0+0.5);
if (heat < 7) heat = 7;
if (heat > 65520) heat = 65520;
for (ix = xlow; ix <=xhigh; ix++) {
tempy = ylow+rint((double)(ix-xlow)/((double)(xhigh-xlow))*(double)(yhigh-ylow));
if (ix < xcen-min_crossw || ix > xcen+min_crossw) {
pnData[ix+nDim0*tempy] ^= heat;
}
if (ix <= xlow+1 || ix >= xhigh-1) {
pnData[ix+nDim0*tempy] ^= 0xFF00;
}
}
for (iy = ylow; iy <=yhigh; iy++) {
tempx = xhigh-rint((double)(iy-ylow)/((double)(yhigh-ylow))*(double)(xhigh-xlow));
if (iy < ycen-min_crossh || iy > ycen+min_crossh) {
pnData[tempx+nDim0*iy] ^= heat;
}
if (iy <= ylow+1 || iy >= yhigh-1) {
pnData[tempy+nDim0*iy] ^= 0xFF00;
}
}
}
}
fclose(fp);
if (overlayname) {
if (roi) {
int xlow, xhigh, ylow, yhigh, ix, iy;
if (fastlow > 0){
xlow = fastlow-1;
for (iy = slowlow; iy < slowhigh; iy+=2){
pnData[xlow+nDim0*iy] ^= 0xFF00;
}
}
if (fasthigh < nDim0-1){
xhigh = fasthigh+1;
for (iy = slowlow; iy < slowhigh; iy+=2){
pnData[xhigh+nDim0*iy] ^= 0xFF00;
}
}
if (slowlow > 0){
ylow = slowlow-1;
for (ix = fastlow; ix < fasthigh; ix+=2){
pnData[ix+nDim0*ylow] ^= 0xFF00;
}
}
if (slowhigh < nDim1-1){
yhigh = slowhigh+1;
for (ix = fastlow; ix < fasthigh; ix+=2){
pnData[ix+nDim0*yhigh] ^= 0xFF00;
}
}
}
if (hCBFmask) {
int i, j;
for(j = slowlow; j <= slowhigh; j++) {
for(i = fastlow; i <= fasthigh; i++) {
if (i < mask_dim1 && j < mask_dim2 && (pmaskData[j*mask_dim1+i]&0xFFFC)==0xFFFC)
pnData[i+nDim0*j] = -3;
ip++;
}
}
}
nStat = cbf_set_integerarray_wdims_fs(hCBFile,
compression,
binary_id,
(void *)pnData,
elsize,
elsigned,
elements,
byteorder,
dim1,dim2,dim3,padding);
if (0 != nStat) fprintf(stderr,"roi_peaksearch: ERROR %x in cbf_set_integerarray_wdims_fs\n", nStat);
else {
nStat = cbf_write_widefile (hCBFile, ovlp, 1, CBF, MIME_HEADERS | MSG_DIGEST, ENC_NONE|ENC_CRTERM | ENC_LFTERM);
if (0 != nStat) fprintf(stderr,"roi_peaksearch: ERROR %x in cbf_write_widefile\n", nStat);
}
free(pnData);
}
// cbf_free_handle hopefully closes the file?
nStat = cbf_free_handle (hCBFile);
exit(0);
}
int convertroi(char *roi, int fastdim, int slowdim,
int * fastlow, int * fasthigh, int * slowlow, int * slowhigh) {
char * endptr;
char * str;
if (!fastlow || !fasthigh || !slowlow || !slowhigh) return CBF_ARGUMENT;
*fastlow = *slowlow = 0;
*fasthigh = fastdim-1;
*slowhigh = slowdim-1;
if (!roi) {
return CBF_SUCCESS;
}
str = roi;
*fastlow = (int)strtol(str,&endptr,0);
if (*fastlow < 0) *fastlow = 0;
if (*fastlow > fastdim-1) *fastlow = fastdim-1;
if (*endptr == '\0') return CBF_SUCCESS;
if (*endptr != ',') return CBF_FORMAT;
str = endptr+1;
*fasthigh = (int)strtol(str,&endptr,0);
if (*fasthigh < *fastlow) *fasthigh = *fastlow;
if (*fasthigh > fastdim-1) *fasthigh = fastdim-1;
if (*endptr == '\0') return CBF_SUCCESS;
if (*endptr != ',') return CBF_FORMAT;
str = endptr+1;
*slowlow = (int)strtol(str,&endptr,0);
if (*slowlow < 0) *slowlow = 0;
if (*slowlow > slowdim-1) *slowlow = slowdim-1;
if (*endptr == '\0') return CBF_SUCCESS;
if (*endptr != ',') return CBF_FORMAT;
str = endptr+1;
*slowhigh = (int)strtol(str,&endptr,0);
if (*slowhigh < *slowlow) *slowhigh = *slowlow;
if (*slowhigh > slowdim-1) *slowhigh = slowdim-1;
if (*endptr == '\0') return CBF_SUCCESS;
return CBF_FORMAT;
}
/*
* bin an image 2x2
*/
void bin2x2(unsigned short *data, int width, int height, unsigned short *out)
{
register int j, i;
int pixel;
for(j=0;j<(height-1);j+=2)
for(i=0;i<(width-1);i+=2) {
pixel = data[j*width + i] +
data[j*width + i + 1] +
data[(j+1)*width + i] +
data[(j+1)*width + i + 1] ;
if(pixel > 65535)
*out++ = 65535;
else
*out++ = (pixel + 2)/4;
}
}
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