Merge branch 'develop'

ObservationSim/Instrument/Chip/libCTI/src/add_CTI.c

+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "nrutil.h"
+#include <time.h>
+
+float poidev(float x, long *idum);
+void creattraps(long *seed,int ntrap,int ny,int nmax,float c,float beta,float **sp);
+void addCTI(int *a0,int ny,int noverscan,int nsp,float beta,float w, float c,float *t, float ***ntrap, int *acti, int release_seed,float *randv);
+//int read_fits_2D(const char *argv,float *galaxy,int imagesize);
+//int write_fits_2D(const char *argv,float **stars,int *dim);
+float ran1(long *idum);
+void CTI_simul(int **image, int nx, int ny, int noverscan, int nsp, float *rho_trap, float *t, float beta, float w, float c, int nmax, long *trap_seeds, int release_seed,int **imagecti){
+  int ntotal;
+  printf("image parameters: nx=%i ny=%i noverscan=%i\n",nx,ny,noverscan);
+  printf("input image: image[0][0]=%i image[50][60]=%i image[1000][20]=%i image[20][1000]=%i\n",image[0][0],image[50][60],image[1000][20],image[20][1000]);
+  printf("rho_trap rho1=%f rho2=%f rho3=%f\n",rho_trap[0],rho_trap[1],rho_trap[2]);
+  printf("t t1=%f t2=%f t3=%f\n",t[0],t[1],t[2]);
+  printf("volume parameter beta=%f,w=%f,c=%f\n",beta,w,c);
+  printf("nsp=%i,nmax=%i\n",nsp,nmax);
+  //printf("trap_seeds = %i,%i,%i\n",trap_seeds[0],trap_seeds[1],trap_seeds[2]);
+  printf("release_seed = %i\n",release_seed);
+  printf("begin CTI simulation\n");
+  float ***ntrap;
+  float *randv;
+  float tmp;
+  int ntrap_tmp,nrandv=100000;
+  int *a0,*acti,dim[2];
+  int i,j,k,l;
+  long iseed=-1;
+  ntotal=ny+noverscan;
+  ntrap = f3tensor(0,nsp-1,0,ny,0,nmax+1); 
+  a0=ivector(0,ny);
+  acti=ivector(0,ntotal);
+  randv=vector(0,nrandv);
+  for(i=0;i<nrandv;i++)randv[i]=ran1(&iseed);
+
+  printf("column k/%i, k=", nx);
+  for(k=0;k<nx;k++){
+    if(k % 8 == 0) fprintf(stdout, "%i  ",k); fflush(stdout);
+    for(l=0;l<nsp;l++){
+        tmp = rho_trap[l]*ny;
+        ntrap_tmp = poidev(tmp,&trap_seeds[l]);
+        creattraps(&trap_seeds[l],ntrap_tmp,ny,nmax,c,beta,ntrap[l]);
+       
+    }
+    
+    for(i=0;i<ny;i++){a0[i]=image[k][i];}
+
+    //for(i=0;i<ntotal;i++)acti[i]=0;
+    addCTI(a0,ny,noverscan,nsp,beta,w,c,t,ntrap,acti,release_seed,randv);
+    
+    for(i=0;i<ntotal;i++){
+      imagecti[k][i]=acti[i];
+    }
+  }
+  printf("\nCTI simulation finished!\n");
+  free_ivector(a0,0,ny);
+  free_ivector(acti,0,ntotal);
+  free_f3tensor(ntrap,0,nsp-1,0,ny,0,nmax+1);  
+  free_vector(randv,0,nrandv);
+  return;
+}
+
+void addCTI(int *a0,int ny,int noverscan, int nsp, float beta,float w, float c,float *t, float ***ntrap, int *acti, int release_seed,float *randv)
+{
+  
+  void trap_release(int *flow, int *traped,int ntraped,float *randv,int *ncumran,float f);
+  //float ran1(long *idum);
+  float *tmpntrap,*f,tmph[50];
+  float height,wre;
+  int flowt,ntraptot,ntraped,topoftrap,nrelease,ntraped0,tmptrapedt,ntrapsum;
+  int ntotal,i,j,k,nmove,isum,ntmp,isp,*tmptraped,**traped,*flow;
+  int ncumran,ncumran0,jc,*jcindx;
+  long hotseed=-1;
+  wre=1/w;
+  ntotal=ny+noverscan;
+  f=vector(0,nsp-1);
+  traped = imatrix(0,nsp-1,0,ntotal);
+  flow=ivector(0,ntotal); 
+  jcindx=ivector(0,ntotal);
+  
+  for(i=0;i<nsp;i++){f[i]=1-exp(-1./t[i]);}
+  
+  for(i=ny;i<ntotal;i++)flow[i]=0;
+  
+  for(i=0;i<nsp;i++){for(j=ny;j<ntotal;j++){traped[i][j] = 0;}}
+  
+ 
+  //initialize 
+  for(i=0;i<ny;i++){
+    flow[i]=a0[i];
+    for(j=0;j<nsp;j++){
+      ntraptot = ntrap[j][i][0];
+      height=flow[i]*wre;
+      if(ntraptot>0){
+	ntraped=0;
+	tmpntrap=ntrap[j][i];
+	while(tmpntrap[ntraped+1]<=height){ntraped++;}
+	if(flow[i]<ntraped)ntraped=flow[i];
+	flow[i]-=ntraped; 
+	traped[j][i]=ntraped;
+      }
+      else{traped[j][i]=0;}
+    }
+  }
+
+  // rearrange trapes
+  jc=-1;
+  for(i=0;i<ny;i++){
+    ntrapsum=ntrap[0][i][0]+ntrap[1][i][0]+ntrap[2][i][0];
+    //if((ntrapsum!=0 || hotpixflag){ if there is none-zero trap or it is a hot pix
+    if(ntrapsum!=0){
+      jc++;
+      for(j=0;j<nsp;j++){
+	traped[j][jc]=traped[j][i];
+	ntraptot=ntrap[j][i][0];
+	for(k=0;k<=ntraptot+1;k++)ntrap[j][jc][k]=ntrap[j][i][k];
+      }      
+    }
+    jcindx[i+1]=jc;
+  }
+  for(i=ny;i<ntotal;i++)jcindx[i]=jc;
+
+  // add CTI effects
+  acti[0]=flow[0];
+  for(i=1;i<ntotal;i++){
+    nmove=jcindx[i];
+    for(j=nmove;j>=0;j--){    
+      //flow[i]+=poidev(0.01, &hotseed);
+      ncumran=randv[j+i]*10000;
+      height=flow[i]*wre;
+      
+      isp=0;    
+      tmpntrap=ntrap[isp][j];
+      ntraped=0; 
+      tmptraped=traped[isp];
+      while(tmpntrap[ntraped+1]<=height){ntraped++;}
+      topoftrap=tmptraped[j]-ntraped;	
+      if(topoftrap!=0){trap_release(&flow[i], &tmptraped[j],topoftrap,randv,&ncumran,f[isp]);}    
+      
+      isp=1;
+      tmpntrap=ntrap[isp][j];
+      ntraped=0; 
+      //height=flow[j]*wre; ;
+      tmptraped=traped[isp];
+      while(tmpntrap[ntraped+1]<=height){ntraped++;}
+      topoftrap=tmptraped[j]-ntraped;
+      if(topoftrap!=0){trap_release(&flow[i], &tmptraped[j],topoftrap,randv,&ncumran,f[isp]);}
+	
+      isp=2;
+      tmpntrap=ntrap[isp][j];
+      ntraped=0; 
+      //height=flow[j]*wre; 
+      tmptraped=traped[isp];
+      while(tmpntrap[ntraped+1]<=height){ntraped++;}
+      topoftrap=tmptraped[j]-ntraped;
+      if(topoftrap!=0){trap_release(&flow[i], &tmptraped[j],topoftrap,randv,&ncumran,f[isp]);}
+
+      //isp=3...
+      }
+    acti[i]=flow[i];
+  }
+  free_ivector(flow,0,ntotal);
+  free_ivector(jcindx,0,ntotal);
+  free_imatrix(traped,0,nsp-1,0,ntotal);
+  free_vector(f,0,nsp-1);
+  return;
+}
+
+
+void trap_release(int *flow, int *traped,int topoftrap,float *randv,int *ncumran,float f){
+  int ntmp,k;
+  if (topoftrap>0){  // release
+    for(k=0;k<topoftrap;k++){
+      *ncumran+=1;
+      if(randv[*ncumran]<f){
+	*flow+=1;
+	*traped-=1;
+      }	    
+    }
+    return;
+  }
+  else{     //trap
+    ntmp = -topoftrap;
+    if(*flow<ntmp)ntmp=*flow;
+    *flow-=ntmp; 
+    *traped += ntmp;
+  }
+  return;
+}
+
+/*int main(){
+  int read_fits_2D(const char *argv,float *galaxy,int imagesize);
+  int write_fits_2D(const char *argv,float **stars,int *dim);
+  int **image,nimg,kct,i,j;
+  float *image1,**imagecti;
+  int nx=4608,ny=4616,noverscan=84,nmax=12,nsp=3;
+  int ntotal;
+  float beta=0.478,w=84700,c=0;
+  float t[3] = {0.74,7.7,37};
+  float rho_trap[3] = {0.6,1.6,1.4};
+  char fname1[300];
+  int dim[2];
+  long trap_seeds[3] = {1,100,1000};
+  int release_seed = 10000;
+  clock_t start, end;
+  ntotal=ny+noverscan;
+  nimg=nx*ny;
+  image=imatrix(0,nx,0,ny);
+  image1=vector(0,nimg);
+  imagecti=matrix(0,nx,0,ntotal);
+  strcpy(fname1,"inputdata/image.fits");
+  read_fits_2D(fname1,image1,nimg);kct=0;    
+  for (j=0; j<ny; j++){
+    for(i=0;i<nx;i++){
+      image[i][j]=image1[kct];
+      kct++;
+    }}
+  
+  free_vector(image1,0,nimg);
+  start = clock();
+  CTI_simul(image, nx, ny, noverscan, nsp, rho_trap, t, beta, w, c, nmax, trap_seeds, release_seed, imagecti);
+  end = clock();
+  float time;
+  time = (end-start)/CLOCKS_PER_SEC;
+  printf("running time %f ms\n",time);
+  
+  // output final image
+  strcpy(fname1,"output/image_CTIfinal.fits");
+  dim[0]=nx;dim[1]=ntotal;
+  write_fits_2D(fname1,imagecti,dim);
+  free_matrix(imagecti,0,nx,0,ntotal);
+  free_imatrix(image,0,nx,0,ny);
+  return 0;
+  }*/

ObservationSim/Instrument/Chip/libCTI/src/creattraps.c

+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "nrutil.h"
+void creattraps(long *seed,int ntrap,int ny,int nmax,float c,float beta,float **sp)
+{
+  //creat ntrap traps along one column
+  //sp[i][0] the number of trap in the ith pixle;
+  //sp[i][j] (c,1+c) the height of the jth trap in the ith pixle;
+  
+  float ran1(long *idum);
+  void sort(unsigned long n, float arr[]);
+  float tmp,betare,height;
+  int i,nyt,ntmp,j;
+  float *tmpv;
+  tmpv = vector(1,100);
+
+  if(nmax>50){printf(" the upper limite of trap in each pixe is too large, nmax=%d\n",nmax); getchar();}
+
+  
+  betare=1./beta;
+  for(i=0;i<ny;i++)sp[i][0]=0;
+  for(i=0;i<ntrap;i++){
+    nyt=ran1(seed)*ny;
+    sp[nyt][0]++;
+  }
+  for(i=0;i<ny;i++){
+    ntmp=sp[i][0];
+    if(ntmp==1){
+      height=ran1(seed)-c;
+      if(height<=0){sp[i][1]=0;}
+      else{
+        sp[i][1]=pow(height,betare);
+      }
+    }
+    if(ntmp>1){
+      if(ntmp>nmax)sp[i][0]=ntmp=nmax; // upper limite of trap in each pixel is nmax
+      for(j=1;j<=ntmp;j++)tmpv[j]=ran1(seed)-c;
+      
+      sort(ntmp, tmpv);
+      for(j=1;j<=ntmp;j++){
+	    height=tmpv[j];
+	    if(height<=0){sp[i][j]=0;}
+	    else{sp[i][j]=pow(height,betare);}
+      }
+    }
+    sp[i][ntmp+1]=999999;
+  }
+  free_vector(tmpv,1,100);
+}

ObservationSim/Instrument/Chip/libCTI/src/gammln.c

+#include <math.h>
+
+float gammln(float xx)
+{
+	double x,y,tmp,ser;
+	static double cof[6]={76.18009172947146,-86.50532032941677,
+		24.01409824083091,-1.231739572450155,
+		0.1208650973866179e-2,-0.5395239384953e-5};
+	int j;
+
+	y=x=xx;
+	tmp=x+5.5;
+	tmp -= (x+0.5)*log(tmp);
+	ser=1.000000000190015;
+	for (j=0;j<=5;j++) ser += cof[j]/++y;
+	return -tmp+log(2.5066282746310005*ser/x);
+}
+/* (C) Copr. 1986-92 Numerical Recipes Software )1!. */

ObservationSim/Instrument/Chip/libCTI/src/gasdev.c

+#include <math.h>
+
+float gasdev(long *idum)
+{
+	float ran1(long *idum);
+	static int iset=0;
+	static float gset;
+	float fac,rsq,v1,v2;
+
+	if  (iset == 0) {
+		do {
+			v1=2.0*ran1(idum)-1.0;
+			v2=2.0*ran1(idum)-1.0;
+			rsq=v1*v1+v2*v2;
+		} while (rsq >= 1.0 || rsq == 0.0);
+		fac=sqrt(-2.0*log(rsq)/rsq);
+		gset=v1*fac;
+		iset=1;
+		return v2*fac;
+	} else {
+		iset=0;
+		return gset;
+	}
+}
+/* (C) Copr. 1986-92 Numerical Recipes Software )1!. */

ObservationSim/Instrument/Chip/libCTI/src/nrutil.h

+/* CAUTION: This is the ANSI C (only) version of the Numerical Recipes
+   utility file nrutil.h.  Do not confuse this file with the same-named
+   file nrutil.h that may be supplied in a 'misc' subdirectory.
+   *That* file is the one from the book, and contains both ANSI and
+   traditional K&R versions, along with #ifdef macros to select the
+   correct version.  *This* file contains only ANSI C.               */
+
+#ifndef _NR_UTILS_H_
+#define _NR_UTILS_H_
+
+static float sqrarg;
+#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 : sqrarg*sqrarg)
+
+static double dsqrarg;
+#define DSQR(a) ((dsqrarg=(a)) == 0.0 ? 0.0 : dsqrarg*dsqrarg)
+
+static double dmaxarg1,dmaxarg2;
+#define DMAX(a,b) (dmaxarg1=(a),dmaxarg2=(b),(dmaxarg1) > (dmaxarg2) ?\
+        (dmaxarg1) : (dmaxarg2))
+
+static double dminarg1,dminarg2;
+#define DMIN(a,b) (dminarg1=(a),dminarg2=(b),(dminarg1) < (dminarg2) ?\
+        (dminarg1) : (dminarg2))
+
+static float maxarg1,maxarg2;
+#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1) > (maxarg2) ?\
+        (maxarg1) : (maxarg2))
+
+static float minarg1,minarg2;
+#define FMIN(a,b) (minarg1=(a),minarg2=(b),(minarg1) < (minarg2) ?\
+        (minarg1) : (minarg2))
+
+static long lmaxarg1,lmaxarg2;
+#define LMAX(a,b) (lmaxarg1=(a),lmaxarg2=(b),(lmaxarg1) > (lmaxarg2) ?\
+        (lmaxarg1) : (lmaxarg2))
+
+static long lminarg1,lminarg2;
+#define LMIN(a,b) (lminarg1=(a),lminarg2=(b),(lminarg1) < (lminarg2) ?\
+        (lminarg1) : (lminarg2))
+
+static int imaxarg1,imaxarg2;
+#define IMAX(a,b) (imaxarg1=(a),imaxarg2=(b),(imaxarg1) > (imaxarg2) ?\
+        (imaxarg1) : (imaxarg2))
+
+static int iminarg1,iminarg2;
+#define IMIN(a,b) (iminarg1=(a),iminarg2=(b),(iminarg1) < (iminarg2) ?\
+        (iminarg1) : (iminarg2))
+
+#define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
+
+void nrerror(char error_text[]);
+float *vector(long nl, long nh);
+int *ivector(long nl, long nh);
+unsigned char *cvector(long nl, long nh);
+long *lvector(long nl, long nh);
+double *dvector(long nl, long nh);
+float **matrix(long nrl, long nrh, long ncl, long nch);
+double **dmatrix(long nrl, long nrh, long ncl, long nch);
+int **imatrix(long nrl, long nrh, long ncl, long nch);
+float **submatrix(float **a, long oldrl, long oldrh, long oldcl, long oldch,
+	long newrl, long newcl);
+float **convert_matrix(float *a, long nrl, long nrh, long ncl, long nch);
+float ***f3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
+void free_vector(float *v, long nl, long nh);
+void free_ivector(int *v, long nl, long nh);
+void free_cvector(unsigned char *v, long nl, long nh);
+void free_lvector(long *v, long nl, long nh);
+void free_dvector(double *v, long nl, long nh);
+void free_matrix(float **m, long nrl, long nrh, long ncl, long nch);
+void free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch);
+void free_imatrix(int **m, long nrl, long nrh, long ncl, long nch);
+void free_submatrix(float **b, long nrl, long nrh, long ncl, long nch);
+void free_convert_matrix(float **b, long nrl, long nrh, long ncl, long nch);
+void free_f3tensor(float ***t, long nrl, long nrh, long ncl, long nch,
+	long ndl, long ndh);
+
+
+int  ***i3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
+void free_i3tensor(int ***t, long nrl, long nrh, long ncl, long nch,     
+	long ndl, long ndh);
+
+unsigned char  ***b3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
+void free_b3tensor(unsigned char ***t, long nrl, long nrh, long ncl, long nch,     
+	long ndl, long ndh);
+
+double ***d3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
+void free_d3tensor(double ***t, long nrl, long nrh, long ncl, long nch,
+	long ndl, long ndh);
+
+
+char **cmatrix(long nrl, long nrh, long ncl, long nch);
+void free_cmatrix(char **m, long nrl, long nrh, long ncl, long nch);
+
+#endif /* _NR_UTILS_H_ */

ObservationSim/Instrument/Chip/libCTI/src/poidev.c

+#include <math.h>
+#define PI 3.141592654
+
+float poidev(float xm, int *idum)
+{
+	float gammln(float xx);
+	float ran1(int *idum);
+	static float sq,alxm,g,oldm=(-1.0);
+	float em,t,y;
+
+	if (xm < 12.0) {
+		if (xm != oldm) {
+			oldm=xm;
+			g=exp(-xm);
+		}
+		em = -1;
+		t=1.0;
+		do {
+			++em;
+			t *= ran1(idum);
+		} while (t > g);
+	} else {
+		if (xm != oldm) {
+			oldm=xm;
+			sq=sqrt(2.0*xm);
+			alxm=log(xm);
+			g=xm*alxm-gammln(xm+1.0);
+		}
+		do {
+			do {
+				y=tan(PI*ran1(idum));
+				em=sq*y+xm;
+			} while (em < 0.0);
+			em=floor(em);
+			t=0.9*(1.0+y*y)*exp(em*alxm-gammln(em+1.0)-g);
+		} while (ran1(idum) > t);
+	}
+	return em;
+}
+
+float poidev_copy(float xm, int *idum)
+{
+	float gammln(float xx);
+	float ran1_copy(int *idum);
+	static float sq1,alxm1,g1,oldm1=(-1.0);
+	float em,t,y;
+
+	if (xm < 12.0) {
+		if (xm != oldm1) {
+			oldm1=xm;
+			g1=exp(-xm);
+		}
+		em = -1;
+		t=1.0;
+		do {
+			++em;
+			t *= ran1_copy(idum);
+		} while (t > g1);
+	} else {
+		if (xm != oldm1) {
+			oldm1=xm;
+			sq1=sqrt(2.0*xm);
+			alxm1=log(xm);
+			g1=xm*alxm1-gammln(xm+1.0);
+		}
+		do {
+			do {
+				y=tan(PI*ran1_copy(idum));
+				em=sq1*y+xm;
+			} while (em < 0.0);
+			em=floor(em);
+			t=0.9*(1.0+y*y)*exp(em*alxm1-gammln(em+1.0)-g1);
+		} while (ran1_copy(idum) > t);
+	}
+	return em;
+}
+
+#undef PI
+/* (C) Copr. 1986-92 Numerical Recipes Software )1!. */

ObservationSim/Instrument/FocalPlane.py

@@ -2,17 +2,24 @@ import galsim
 import numpy as np
 
 class FocalPlane(object):
-    def __init__(self, config=None, survey_type='Photometric', bad_chips=None):
+    def __init__(self, config=None, chip_list=None, survey_type='Photometric', bad_chips=None):
         """Get the focal plane layout
         """
         self.nchips = 42
+        self.ignore_chips = []
+
         if bad_chips == None:
             self.bad_chips = []
         else:
             self.bad_chips = bad_chips
+            for chip_id in bad_chips:
+                self.ignore_chips.append(chip_id)
         
-        self.ignore_chips = []
-        if survey_type == 'Photometric':
+        if chip_list is not None:
+            for i in range(42):
+                if not (i+1 in chip_list):
+                    self.ignore_chips.append(i+1)
+        elif survey_type == 'Photometric':
             for i in range(5):
                 self.ignore_chips.append(i+1)
                 self.ignore_chips.append(i+26)