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extractkernOnes.c
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extractkernOnes.c
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#include<stdio.h>
#include<string.h>
#include<strings.h>
#include<math.h>
#include<malloc.h>
#include<stdlib.h>
#include<fitsio.h>
#define max(x,y) x>y?x:y
#define min(x,y) x<y?x:y
/* globals */
int ngauss=3, *deg_fixe=NULL, dofullImage=0;
float *sigma_gauss=NULL;
int fwKernel,nCompKer,nComp,nBGVectors,nCompTotal,kerOrder,bgOrder,nR;
double *filter_x,*filter_y,**kernel_vec,*kernel_coeffs,*kernel,kSumIm;
char *inConv = NULL;
long oNaxes[2];
char **regions = NULL;
float xConv=1e10, yConv=1e10;
int rPixX, rPixY;
/* funcs */
void getKernelInfo(char *);
void getKernel(char *, double **, int, int);
void fits_get_kernel_btbl(fitsfile *, double **, int);
void getKernelVec();
double *kernel_vector(int, int, int, int, int *);
double make_kernel(int, int, double *);
void spatial_convolve(float *, int, int, float, float, double *, float *);
double get_background(int, int, double *);
void printError(int);
int main(int argc, char **argv)
{
int iarg, i, j, xsize, ysize, ndelta;
int status=0;
float numKerFW=2;
double kSum;
char *diffim = NULL, *outConv = NULL;
float *delta = NULL, *dconv = NULL;
double *kernelSol = NULL;
long cNaxes[2];
char scrStr[256], help[4096];
fitsfile *fPtr;
sprintf(help, "Usage : extractkern [options] diffimage outimage\n");
sprintf(help, "%sOptions:\n", help);
sprintf(help, "%s [-xy x y] : convolve kernel with delta function at x,y\n", help);
sprintf(help, "%s [-nkw numkwidth] : # kernel widths for outimage size (%.1f)\n", help, numKerFW);
sprintf(help, "%s [-a] : sample entire diffimage size with delta functions\n", help);
sprintf(help, "%s [-im image] : convolve fitsfile instead of delta function\n\n", help);
sprintf(help, "%s To be used in conjuntion with the diffimage produced by hotpants\n", help);
sprintf(help, "%s using the -hki option. [-xy] convolves a delta function at\n", help);
sprintf(help, "%s the image position x, y with the spatially varying kernel\n", help);
sprintf(help, "%s used in the hotpants convolution. Provides a visual realization \n", help);
sprintf(help, "%s of the kernel at that position, and can be useful for cosmic ray\n", help);
sprintf(help, "%s discrimination. Also, if used with the [-im] option, one may\n", help);
sprintf(help, "%s reconstruct the entire convolved image to avoid storing it on disk.\n", help);
/* read in command options. j counts # of required args given */
for (iarg=1, j=0; iarg < argc; iarg++) {
if (argv[iarg][0]=='-') {
if (strcasecmp(argv[iarg]+1,"xy")==0) {
sscanf(argv[++iarg], "%f", &xConv);
sscanf(argv[++iarg], "%f", &yConv);
} else if (strcasecmp(argv[iarg]+1,"nkw")==0) {
sscanf(argv[++iarg], "%f", &numKerFW);
} else if (strcasecmp(argv[iarg]+1,"a")==0) {
dofullImage = 1;
xConv = 0;
yConv = 0;
} else if (strcasecmp(argv[iarg]+1,"im")==0) {
inConv = argv[++iarg];
xConv = 0;
yConv = 0;
} else {
fprintf(stderr, "Unknown option %s\n", argv[iarg]);
exit(1);
}
} else {
diffim = argv[iarg++];
outConv = argv[iarg++];
}
}
if (iarg < 2) {
/* not enough command line images...*/
fprintf(stderr, "%s\n", help);
exit(1);
}
/* insanity checking */
if ( ((xConv == 1e10) || (yConv == 1e10)) && !(dofullImage) && !(inConv) ) {
fprintf(stderr, "Sorry, I do not know what to do, exiting...\n");
exit(1);
}
deg_fixe = (int *)calloc(ngauss, sizeof(int));
sigma_gauss = (float *)calloc(ngauss, sizeof(float));
/* fill up global kernel info */
getKernelInfo(diffim);
/* set array and comp sizes */
nCompKer = 0;
for (i = 0; i < ngauss; i++)
nCompKer += ((deg_fixe[i] + 1) * (deg_fixe[i] + 2)) / 2;
nComp = ((kerOrder + 1) * (kerOrder + 2)) / 2;
nBGVectors = ((bgOrder + 1) * (bgOrder + 2)) / 2;
nCompTotal = nCompKer * nComp + nBGVectors;
kernelSol = (double *)realloc(kernelSol, (nCompTotal+1)*sizeof(double));
/* allocate more kernel vectors */
if ( !( filter_x = (double *)malloc(nCompKer*fwKernel*sizeof(double))) ||
!( filter_y = (double *)malloc(nCompKer*fwKernel*sizeof(double))) ||
!( kernel = (double *)malloc(fwKernel*fwKernel*sizeof(double))) ||
!( kernel_vec = (double **)malloc(nCompKer*sizeof(double *))) ||
!( kernel_coeffs = (double *)malloc(nCompKer*sizeof(double))) )
exit(3);
/* Set output image size */
if (! (dofullImage) ) {
xsize = numKerFW * fwKernel;
ysize = numKerFW * fwKernel;
oNaxes[0] = xsize;
oNaxes[1] = ysize;
}
else {
xsize = oNaxes[0];
ysize = oNaxes[1];
}
/* you can input a shape to be convolved, theoretically... */
if (inConv) {
if ( fits_open_file(&fPtr, inConv, 0, &status) ||
fits_get_img_param(fPtr, 2, NULL, NULL, cNaxes, &status) )
printError(status);
delta = (float *)realloc(delta, cNaxes[0]*cNaxes[1]*sizeof(float));
if ( fits_read_img_flt(fPtr, 1, 1, cNaxes[0]*cNaxes[1], 0, delta, 0, &status) ||
fits_close_file(fPtr, &status) )
printError(status);
xsize = cNaxes[0];
ysize = cNaxes[1];
oNaxes[0] = cNaxes[0];
oNaxes[1] = cNaxes[1];
}
else {
delta = (float *)realloc(delta, xsize*ysize*sizeof(float));
memset(delta, 0, xsize*ysize*sizeof(float));
ndelta = 0;
for (j = fwKernel-1; j < (ysize-1); j += fwKernel) {
for (i = fwKernel-1; i < (xsize-1); i += fwKernel) {
/* delta function in middle */
delta[i + xsize*j] = 1.;
ndelta += 1;
}
}
}
/* output convolved image */
dconv = (float *)realloc(dconv, xsize*ysize*sizeof(float));
memset(dconv, 0, xsize*ysize*sizeof(float));
/* fill weight matrices kernel_vec, calls kernel_vector */
getKernelVec();
/* read kernel solution */
getKernel(diffim, &kernelSol, xsize, ysize);
/* do the convolution, fills kernel and calls make_kernel */
spatial_convolve(delta, xsize, ysize, xConv, yConv, kernelSol, dconv);
/* clobber output image */
sprintf(scrStr, "!%s", outConv);
/* create and open new empty output FITS file, using input image as template.*/
if ( fits_create_file(&fPtr, scrStr, &status) ||
fits_create_img(fPtr, FLOAT_IMG, 2, oNaxes, &status) ||
fits_write_img_flt(fPtr, 1, 1, xsize*ysize, dconv, &status) ||
fits_close_file(fPtr, &status) )
printError(status);
/* sanity check - add up all pixels in the image */
kSum = 0;
for (i = 0; i < xsize*ysize; i++) {
kSum += dconv[i];
}
fprintf(stderr, " Actual sum of pixels in convolved image : %.6f\n", kSum);
fprintf(stderr, " Kernel Sum from input image : %.6f\n", kSumIm);
for (i = 0; i < 10; i++)
if (regions[i]) free(regions[i]);
if (regions) free(regions);
if (kernelSol) free(kernelSol);
if (delta) free(delta);
if (dconv) free(dconv);
if (filter_x) free(filter_x);
if (filter_y) free(filter_y);
if (kernel) free(kernel);
if (kernel_vec) free(kernel_vec);
if (kernel_coeffs) free(kernel_coeffs);
return 1;
}
/* ********************************** */
/* from functions.c */
/* ********************************** */
void getKernelInfo(char *kimage) {
/*****************************************************
Get all 1-time info from kernel fits header, overriding defaults
and command line options.
*****************************************************/
fitsfile *kPtr;
int i, existsTable, status = 0;
char hKeyword[1024];
/* open the input kernel image */
if ( fits_open_file(&kPtr, kimage, 0, &status) )
printError(status);
/* required keyword in primary HDU */
if ( fits_read_key_log(kPtr, "KERINFO", &existsTable, NULL, &status) )
printError(status);
if (!(existsTable)) {
fits_close_file(kPtr, &status);
fprintf(stderr, "This image does not appear to contain a kernel table, exiting...\n");
exit(1);
}
/* move to binary kernel table... */
if ( fits_get_num_hdus(kPtr, &existsTable, &status) ||
fits_movabs_hdu(kPtr, existsTable, NULL, &status) ||
fits_read_key(kPtr, TINT, "NGAUSS", &ngauss, NULL, &status) ||
fits_read_key(kPtr, TINT, "FWKERN", &fwKernel, NULL, &status) ||
fits_read_key(kPtr, TINT, "CKORDER", &kerOrder, NULL, &status) ||
fits_read_key(kPtr, TINT, "BGORDER", &bgOrder, NULL, &status) )
printError(status);
deg_fixe = (int *)realloc(deg_fixe, ngauss*sizeof(int));
sigma_gauss = (float *)realloc(sigma_gauss, ngauss*sizeof(float));
/* read kernel gaussian info */
for (i = 0; i < ngauss; i++) {
sprintf(hKeyword, "DGAUSS%d", i+1);
if (fits_read_key(kPtr, TINT, hKeyword, °_fixe[i], NULL, &status))
printError(status);
sprintf(hKeyword, "SGAUSS%d", i+1);
if (fits_read_key(kPtr, TFLOAT, hKeyword, &sigma_gauss[i], NULL, &status))
printError(status);
}
if (fits_close_file(kPtr, &status) )
printError(status);
return;
}
void getKernel(char *kimage, double **kerSol, int xsize, int ysize) {
/* read in kernel image for region */
fitsfile *fPtr;
int status = 0, i;
char hKeyword[1024];
int rXMin, rXMax, rYMin, rYMax;
int rXBMin, rXBMax, rYBMin, rYBMax;
int hwKernel = fwKernel/2;
/* open the input kernel image */
if ( fits_open_file(&fPtr, kimage, 0, &status) )
printError(status);
/* get its size if needed */
if ( dofullImage || inConv )
if ( fits_get_img_param(fPtr, 2, NULL, NULL, oNaxes, &status) )
printError(status);
/* grab all regions in the primary image header, up to 10 in number */
regions = (char **)malloc(10*sizeof(char *));
for (i = 0; i < 10; i++)
regions[i] = (char *)malloc(80*sizeof(char));
if ( fits_read_keys_str(fPtr, "REGION", 0, 9, regions, &nR, &status ) )
printError(status);
for (i = 0; i < nR; i++) {
if (sscanf(regions[i], "[%d:%d,%d:%d]", &rXMin, &rXMax, &rYMin, &rYMax) != 4) {
fprintf(stderr, "Problem with region %d (%s), exiting...\n", i, regions[i]);
exit(1);
}
if ( ((xConv>-1) && (yConv>-1)) && ((xConv+1) >= rXMin &&
(xConv+1) <= rXMax &&
(yConv+1) >= rYMin &&
(yConv+1) <= rYMax)) {
/* we got our guy, lets roll! */
sprintf(hKeyword, "KSUM%02d", i);
if (fits_read_key(fPtr, TDOUBLE, hKeyword, &kSumIm, NULL, &status))
printError(status);
/* set region sizes */
rXBMin = max(0, rXMin - hwKernel);
rYBMin = max(0, rYMin - hwKernel);
rXBMax = min(xsize, rXMax + hwKernel);
rYBMax = min(ysize, rYMax + hwKernel);
rPixX = rXBMax - rXBMin + 1;
rPixY = rYBMax - rYBMin + 1;
break;
}
else {
rXMin = rXMax = rYMin = rYMax = 0;
}
}
if ( (rXMin == 0) && (rXMax == 0) && (rYMin == 0) && (rYMax == 0) ) {
/* we did not get our guy, shucks... */
fprintf(stderr, "Unable to locate appropriate region for %.2f, %.2f, exiting...\n", xConv, yConv);
exit(2);
}
fits_get_kernel_btbl(fPtr, &(*kerSol), i);
return;
}
void fits_get_kernel_btbl(fitsfile *kPtr, double **kernelSol, int nRegion) {
int status=0, existsTable;
/* move to binary kernel table... */
if ( fits_get_num_hdus(kPtr, &existsTable, &status) ||
fits_movabs_hdu(kPtr, existsTable, NULL, &status) )
printError(status);
memset(*kernelSol, 0, (nCompTotal+1)*sizeof(double));
if (fits_read_col(kPtr, TDOUBLE, nRegion+1, 1, 1, (nCompTotal+1), 0, *kernelSol, 0, &status))
printError(status);
return;
}
/* ********************************** */
/* from alard.c */
/* ********************************** */
void getKernelVec() {
/*****************************************************
* Fills kernel_vec with kernel weight filter, called only once
*****************************************************/
int ig, idegx, idegy, nvec;
int ren;
nvec = 0;
for (ig = 0; ig < ngauss; ig++) {
for (idegx = 0; idegx <= deg_fixe[ig]; idegx++) {
for (idegy = 0; idegy <= deg_fixe[ig]-idegx; idegy++) {
/* stores kernel weight mask for each order */
kernel_vec[nvec] = kernel_vector(nvec, idegx, idegy, ig, &ren);
nvec++;
}
}
}
}
double *kernel_vector(int n, int deg_x, int deg_y, int ig, int *ren) {
/*****************************************************
* Creates kernel sized entry for kernel_vec for each kernel degree
* Mask of filter_x * filter_y, filter = exp(-x**2 sig) * x^deg
* Subtract off kernel_vec[0] if n > 0
* NOTE: this does not use any image
******************************************************/
double *vector=NULL,*kernel0=NULL;
int i,j,k,dx,dy,ix;
double sum_x,sum_y,x,qe;
vector = (double *)malloc(fwKernel*fwKernel*sizeof(double));
dx = (deg_x / 2) * 2 - deg_x;
dy = (deg_y / 2) * 2 - deg_y;
sum_x = sum_y = 0.0;
*ren = 0;
for (ix = 0; ix < fwKernel; ix++) {
x = (double)(ix - fwKernel/2);
k = ix+n*fwKernel;
qe = exp(-x * x * sigma_gauss[ig]);
filter_x[k] = qe * pow(x, deg_x);
filter_y[k] = qe * pow(x, deg_y);
sum_x += filter_x[k];
sum_y += filter_y[k];
}
if (n > 0)
kernel0 = kernel_vec[0];
sum_x = 1. / sum_x;
sum_y = 1. / sum_y;
if (dx == 0 && dy == 0) {
for (ix = 0; ix < fwKernel; ix++) {
filter_x[ix+n*fwKernel] *= sum_x;
filter_y[ix+n*fwKernel] *= sum_y;
}
for (i = 0; i < fwKernel; i++) {
for (j = 0; j < fwKernel; j++) {
vector[i+fwKernel*j] = filter_x[i+n*fwKernel] * filter_y[j+n*fwKernel];
}
}
if (n > 0) {
for (i = 0; i < fwKernel * fwKernel; i++) {
vector[i] -= kernel0[i];
}
*ren = 1;
}
} else {
for (i = 0; i < fwKernel; i++) {
for (j = 0; j < fwKernel; j++) {
vector[i+fwKernel*j] = filter_x[i+n*fwKernel] * filter_y[j+n*fwKernel];
}
}
}
return vector;
}
double make_kernel(int xi, int yi, double *kernelSol) {
/*****************************************************
* Create the appropriate kernel at xi, yi, return sum
*****************************************************/
int i1,k,ix,iy,i;
double ax,ay,sum_kernel;
double xf, yf;
k = 2;
/* RANGE FROM -1 to 1 */
xf = (xi - 0.5 * rPixX) / (0.5 * rPixX);
yf = (yi - 0.5 * rPixY) / (0.5 * rPixY);
for (i1 = 1; i1 < nCompKer; i1++) {
kernel_coeffs[i1] = 0.0;
ax = 1.0;
for (ix = 0; ix <= kerOrder; ix++) {
ay = 1.0;
for (iy = 0; iy <= kerOrder - ix; iy++) {
kernel_coeffs[i1] += kernelSol[k++] * ax * ay;
ay *= yf;
}
ax *= xf;
}
}
kernel_coeffs[0] = kernelSol[1];
for (i = 0; i < fwKernel * fwKernel; i++)
kernel[i] = 0.0;
sum_kernel = 0.0;
for (i = 0; i < fwKernel * fwKernel; i++) {
for (i1 = 0; i1 < nCompKer; i1++) {
kernel[i] += kernel_coeffs[i1] * kernel_vec[i1][i];
}
sum_kernel += kernel[i];
}
return sum_kernel;
}
void spatial_convolve(float *image, int xSize, int ySize, float xConv, float yConv, double *kernelSol, float *outim) {
/*****************************************************
* Take image and convolve it using the kernelSol every kernel width
*****************************************************/
int i1,j1,i2,j2,nsteps_x,nsteps_y,i,j,i0,j0,ic,jc,ik,jk;
double q;
int x0, y0, hwKernel = fwKernel/2;
nsteps_x = ceil((double)(xSize)/(double)fwKernel);
nsteps_y = ceil((double)(ySize)/(double)fwKernel);
x0 = max(0, (int)(xConv - xSize/2));
y0 = max(0, (int)(yConv - ySize/2));
for (j1 = 0; j1 < nsteps_y; j1++) {
j0 = j1 * fwKernel + hwKernel;
for(i1 = 0; i1 < nsteps_x; i1++) {
i0 = i1 * fwKernel + hwKernel;
make_kernel(x0 + i0 + hwKernel, y0 + j0 + hwKernel, kernelSol);
for (j2 = 0; j2 < fwKernel; j2++) {
j = j0 + j2;
if (j >= (ySize - hwKernel)) break;
for (i2 = 0; i2 < fwKernel; i2++) {
i = i0 + i2;
if (i >= (xSize - hwKernel)) break;
q = 0;
for (jc = j - hwKernel; jc <= j + hwKernel; jc++) {
jk = j - jc + hwKernel;
for (ic = i - hwKernel; ic <= i + hwKernel; ic++) {
ik = i - ic + hwKernel;
q += image[ic+xSize*jc] * kernel[ik+jk*fwKernel];
}
}
outim[i+xSize*j] = q;
}
}
}
}
return;
}
double get_background(int xi, int yi, double *kernelSol) {
/*****************************************************
* Return background value at xi, yi
*****************************************************/
double background,ax,ay,xf,yf;
int i,j,k;
int ncompBG;
ncompBG = (nCompKer - 1) * ( ((kerOrder + 1) * (kerOrder + 2)) / 2 ) + 1;
background = 0.0;
k = 1;
/* RANGE FROM -1 to 1 */
xf = (xi - 0.5 * rPixX) / (0.5 * rPixX);
yf = (yi - 0.5 * rPixY) / (0.5 * rPixY);
ax=1.0;
for (i = 0; i <= bgOrder; i++) {
ay = 1.0;
for (j = 0; j <= bgOrder - i; j++) {
background += kernelSol[ncompBG+k++] * ax * ay;
ay *= yf;
}
ax *= xf;
}
return background;
}
void printError(int status) {
/*****************************************************/
/* Print out cfitsio error messages and exit program */
/*****************************************************/
if (status) {
fits_report_error(stderr, status); /* print error report */
exit( status ); /* terminate the program, returning error status */
}
return;
}