Commit 051ef73b authored by Wei Chengliang's avatar Wei Chengliang
Browse files

update add_CTI.c << add_CTIfinal.c

parent 848d0846

ObservationSim/Instrument/Chip/libBF/libmoduleBF.so

deleted100755 → 0
−20.8 KiB

File deleted.

View file

ObservationSim/Instrument/Chip/libCTI/CTI_modeling.py

+2 −1
Original line number Diff line number Diff line
@@ -16,7 +16,7 @@ lib = CDLL(lib_path) 
CTI_simul = lib.__getattr__('CTI_simul')

CTI_simul.argtypes = [POINTER(POINTER(c_int)),c_int,c_int,c_int,c_int,POINTER(c_float),POINTER(c_float),\

                    c_float,c_float,c_float,c_int,POINTER(c_int),c_int,POINTER(POINTER(c_int))]



'''

get_trap_h = lib.__getattr__('save_trap_map')

get_trap_h.argtypes = [POINTER(c_int), c_int, c_int, c_int, c_int, POINTER(c_float), c_float, c_float, c_char_p]
@@ -44,6 +44,7 @@ def bin2fits(bin_file,fits_dir,nsp,nx,ny,nmax): 
            h[np.where(ntrap<j+1)] = 0

            datai[j+1,:,:] = h

        fits.writeto(fits_dir+"/trap_"+str(i+1)+".fits",datai,overwrite=True)

'''

        

def numpy_matrix_to_int_pointer(arr):

    int_pointer_array = (POINTER(c_int)*arr.shape[0])()

ObservationSim/Instrument/Chip/libCTI/libmoduleCTI.so

deleted100755 → 0
−38.3 KiB

File deleted.

View file

ObservationSim/Instrument/Chip/libCTI/readme

+1 −1
Original line number Diff line number Diff line 
CTI_lgl_v0.3/



add_CTI3.c >> add_CTI.c
 
add_CTIfinal.c >> add_CTI.c

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

+129 −209
Original line number Diff line number Diff line
@@ -5,11 +5,13 @@ 
#include "nrutil.h"

#include <time.h>



float poidev(float x, int *idum);

void creattraps(int *seed,int ntrap,int ny,int nmax,float c,float beta,float **sp);

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);

float ran1(int *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, int *trap_seeds, int release_seed,int **imagecti){

//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]);
@@ -17,14 +19,16 @@ void CTI_simul(int **image, int nx, int ny, int noverscan, int nsp, float *rho_t 
  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("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 tmp,*randv;

  float *randv;

  float tmp;

  int ntrap_tmp,nrandv=100000;

  int *a0,*acti,dim[2];

  int i,j,k,l,iseed=-1;

  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);
@@ -32,17 +36,19 @@ void CTI_simul(int **image, int nx, int ny, int noverscan, int nsp, float *rho_t 
  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++){

    printf("column k=%i/%i\r",k,nx);

    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++){
@@ -59,256 +65,170 @@ void CTI_simul(int **image, int nx, int ny, int noverscan, int nsp, float *rho_t 


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)

{

  float ran1(int *idum);

  float *f,*tmpntrap;

  

  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 *flow,**traped,flowt,ntraptot,ntraped,topoftrap,nrelease;

  int ntotal,i,j,k,nmove,isum,ntmp,isp,*tmptraped,ncumran;

  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); 

  for(i=0;i<nsp;i++){

    f[i] = 1-exp(-1/t[i]);

  }

  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(j=0;j<ntotal;j++){traped[0][j]=traped[1][j]=traped[2][j]=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++){

    for(j=0;j<nsp;j++){

      ntraptot = ntrap[j][i][0];

      height=flow[i]*wre;

      //sp0

      ntraptot = ntrap[0][i][0];

      if(ntraptot>0){

	ntraped=0;

	tmpntrap=ntrap[0][i];

	tmpntrap=ntrap[j][i];

	while(tmpntrap[ntraped+1]<=height){ntraped++;}

	if(flow[i]<ntraped)ntraped=flow[i];

	flow[i]-=ntraped; 

	traped[0][i]=ntraped;

	traped[j][i]=ntraped;

      }

      //sp1;

      ntraptot = ntrap[1][i][0];

      if(ntraptot>0){

	ntraped=0;

	tmpntrap=ntrap[1][i];

	while(tmpntrap[ntraped+1]<=height){ntraped++;}

	if(flow[i]<ntraped)ntraped=flow[i];

	flow[i]-=ntraped; 

	traped[1][i]=ntraped;

      }

      //sp2;

      ntraptot = ntrap[2][i][0];

      if(ntraptot>0){

	ntraped=0;

	tmpntrap=ntrap[2][i];

	while(tmpntrap[ntraped+1]<=height){ntraped++;}

	if(flow[i]<ntraped)ntraped=flow[i];

	flow[i]-=ntraped; 

	traped[2][i]=ntraped;

      else{traped[j][i]=0;}

    }

  }



  // add CTI effects

  for(i=0;i<ntotal;i++){

    acti[i] = flow[0];

    nmove=ny;

     ncumran=randv[i]*10000;

    if(i>noverscan)nmove=ntotal-i;  

    for(j=0;j<nmove;j++){

      flow[j]=flow[j+1];

      height=flow[j]*wre;

      //sp0

      ntraptot=ntrap[0][j][0];

      if(ntraptot>0){

	ntraped=0; 

	//height=flow[j]*wre; 

	tmpntrap=ntrap[0][j];

	tmptraped=traped[0];

	while(tmpntrap[ntraped+1]<=height){ntraped++;}

	topoftrap=tmptraped[j]-ntraped;

	if(topoftrap==0){} //do nothing

	else if (topoftrap>0){  // release

	  for(k=0;k<topoftrap;k++){

	    ncumran++;

	    if(randv[ncumran]<f[0]){

	      flow[j]++;

	      tmptraped[j]--;

	    }

	  }

  // 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];

      }      

	else{     //trap

	  ntmp = -topoftrap;

	  if(flow[j]<ntmp)ntmp=flow[j];

	  flow[j]-=ntmp; 

	  tmptraped[j] += ntmp;

    }

    jcindx[i+1]=jc;

  }

      //sp1

      ntraptot=ntrap[1][j][0];

      if(ntraptot>0){

  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; 

	//height=flow[j]*wre; 

	tmpntrap=ntrap[1][j];

	tmptraped=traped[1];

      tmptraped=traped[isp];

      while(tmpntrap[ntraped+1]<=height){ntraped++;}

      topoftrap=tmptraped[j]-ntraped;	

	if(topoftrap==0){} //do nothing

	else if (topoftrap>0){  // release

	  for(k=0;k<topoftrap;k++){

	    ncumran++;

	    if(randv[ncumran]<f[1]){

	      flow[j]++;

	      tmptraped[j]--;

	    }

	  }

	}

	else{     //trap

	  ntmp = -topoftrap;

	  if(flow[j]<ntmp)ntmp=flow[j];

	  flow[j]-=ntmp; 

	  tmptraped[j] += ntmp;

	}

      }

      if(topoftrap!=0){trap_release(&flow[i], &tmptraped[j],topoftrap,randv,&ncumran,f[isp]);}    

      

      //sp2

      ntraptot=ntrap[2][j][0];

      if(ntraptot>0){

      isp=1;

      tmpntrap=ntrap[isp][j];

      ntraped=0; 

	//height=flow[j]*wre; 

	tmpntrap=ntrap[2][j];

	tmptraped=traped[2];

      //height=flow[j]*wre; ;

      tmptraped=traped[isp];

      while(tmpntrap[ntraped+1]<=height){ntraped++;}

      topoftrap=tmptraped[j]-ntraped;

	if(topoftrap==0){} //do nothing

	else if (topoftrap>0){  // release

	  for(k=0;k<topoftrap;k++){

	    ncumran++;

	    if(randv[ncumran]<f[2]){

	      flow[j]++;

	      tmptraped[j]--;

	    }

	  }

	}

	else{     //trap

	  ntmp = -topoftrap;

	  if(flow[j]<ntmp)ntmp=flow[j];

	  flow[j]-=ntmp; 

	  tmptraped[j] += ntmp;

	}

      }

      

      //if(nsp==3)continue;

      if(topoftrap!=0){trap_release(&flow[i], &tmptraped[j],topoftrap,randv,&ncumran,f[isp]);}

	

      /*isp=3;

	ntraptot=ntrap[isp][j][0];

	if(ntraptot>0){

      isp=2;

      tmpntrap=ntrap[isp][j];

      ntraped=0; 

      //height=flow[j]*wre; 

	tmpntrap=ntrap[isp][j];

      tmptraped=traped[isp];

      while(tmpntrap[ntraped+1]<=height){ntraped++;}

      topoftrap=tmptraped[j]-ntraped;

	if(topoftrap==0){} //do nothing

	else if (topoftrap>0){  // release

	for(k=0;k<topoftrap;k++){

	if(ran1(&release_seed)<f[isp]){

	flow[j]++;

	tmptraped[j]--;

	}

	}

	}

	else{     //trap

	ntmp = -topoftrap;

	if(flow[j]<ntmp)ntmp=flow[j];

	flow[j]-=ntmp; 

	tmptraped[j] += ntmp;

	}

	}*/

      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_vector(f,0,nsp-1);

  free_ivector(jcindx,0,ntotal);

  free_imatrix(traped,0,nsp-1,0,ntotal);

  free_vector(f,0,nsp-1);

  return;

}



void save_trap_map(int *trap_seeds, int nsp, int nx, int ny, int nmax, float *rho_trap, float beta, float c, char *filename){

    printf("saving trap map rho_trap = %f,%f,%f, c = %f, beta = %f, nmax = %i, trap_seed = %i,%i,%i\n",rho_trap[0],rho_trap[1],rho_trap[2],c,beta,nmax,trap_seeds[0],trap_seeds[1],trap_seeds[2]);

    float tmp;

    int ntrap_tmp;

    float **sp;

    float hsp;

    sp = matrix(0,ny,0,nmax);

    FILE *file = fopen(filename,"wb");

    for(int j=0;j<nx;j++){

        for(int 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,sp);

            for(int i=0;i<ny;i++){

                for(int k=0;k<nmax;k++){

                    hsp = sp[i][k];

                    unsigned char *hsp_char = (unsigned char *)&hsp;

                    unsigned char bytes[4];

                    bytes[0] = hsp_char[0];

                    bytes[1] = hsp_char[1];

                    bytes[2] = hsp_char[2];

                    bytes[3] = hsp_char[3];

                    fwrite(bytes,sizeof(unsigned char),4,file);



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;

  }

    fclose(file);

    free_matrix(sp,0,ny,0,nmax);

  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;

  int **image,nimg,kct,i,j;

  float *image1,**imagecti;

  int nx=4608,ny=4616,noverscan=84,nmax=10,nsp=3;

  int ntotal = ny+noverscan;

  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],i,j;

  int trap_seeds[3] = {1,100,1000};

  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);

  

  imagecti=matrix(0,nx,0,ntotal);

  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++){

  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\n",time);

  printf("running time %f ms\n",time);

  

  // output final image

  strcpy(fname1,"output/image_CTI.fits");

  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);