int SinkDetect(WF3Info *wf3, SingleGroup *x){
extern int status;
int i,j, jj;
short dqval=0;
float scipix; /*to save the value of the science pixel*/
float refdate=50000.;
int keep_going=1;
sprintf(MsgText,"\nPerforming SINK pixel detection for imset %i",x->group_num);
trlmessage(MsgText);
/*THE SCIENCE IMAGE*/
SingleGroup raz; /*quad rotated image to work with*/
/* INIT THE SCIENCE INPUT */
initSingleGroup (&raz);
allocSingleGroup (&raz,RAZ_COLS/2, RAZ_ROWS);
/*CONVERT DQ DATA TO RAZ FORMAT FOR SCIENCE FILE*/
makedqRAZ(x, &raz);
makeSciSingleRAZ(x, &raz);
/* GET THE SINK FILE REFERENCE IMAGE FROM SINKFILE AND INITIALIZE */
FloatHdrData sinkref;
initFloatHdrData(&sinkref);
getFloatHD(wf3->sink.name,"SCI",x->group_num,&sinkref);
/*NOW TURN THE SINK REFERENCE IMAGES INTO RAZ FORMAT*/
FloatTwoDArray sinkraz;
initFloatData(&sinkraz); /*float 2d arrays*/
allocFloatData(&sinkraz,RAZ_COLS/2, RAZ_ROWS);
makeFloatRaz(&sinkref.data,&sinkraz,x->group_num);
/*THE MJD OF THE SCIENCE EXPOSURE IS THE COMPARISON DATE
THE FOLLOWING TRANSLATION TAKEN FROM ISR WFC3-2014-22.PDF */
scipix=0.;
for (i=0;i<(RAZ_COLS/2);i++){
for (j=0; j<RAZ_ROWS; j++){
if ( (PPix(&sinkraz,i,j) > refdate) && ( wf3->expstart > PPix(&sinkraz,i,j)) ){
keep_going=1;
/*FLAG THE PRIMARY SINK PIXEL*/
dqval = TRAP | DQPix (raz.dq.data, i, j);
DQSetPix (raz.dq.data, i, j, dqval);
scipix = Pix(raz.sci.data,i,j);
/*FLAG THE DOWNSTREAM PIXEL*/
if (PPix(&sinkraz,i,j-1) < 0 ){
dqval = TRAP | DQPix (raz.dq.data, i, j-1);
DQSetPix (raz.dq.data, i, j-1, dqval);
}
/*FLAG THE UPSTREAM PIXELS*/
for (jj=j+1; jj<RAZ_ROWS; jj++){
if ((int) PPix(&sinkraz,i,jj) == 0)
keep_going=0;
if ( PPix(&sinkraz,i,jj) > refdate)
keep_going=0;
if ( 0. < PPix(&sinkraz,i,jj) && PPix(&sinkraz,i,jj) < 1000. && keep_going){
if (scipix <= PPix(&sinkraz,i,jj) ){
dqval = TRAP | DQPix (raz.dq.data, i, jj);
DQSetPix (raz.dq.data, i, jj, dqval);
}
} else {
keep_going=0;
}
}
} /*end if*/
} /*end j*/
}/*end i*/
/*format the dq data back to expected orientation*/
undodqRAZ(x,&raz);
freeSingleGroup(&raz);
freeFloatData(&sinkraz);
freeFloatHdrData(&sinkref);
trlmessage("Sink pixel flagging complete");
return(status);
}
int loadPCTETAB (char *filename, CTEParamsFast *pars) {
/* Read the cte parameters from the reference table PCTETAB
These are taken from the PCTETAB global header:
CTE_NAME - name of cte algorithm
CTE_VER - version number of cte algorithm
CTEDATE0 - date of instrument installation in HST, in fractional years
CTEDATE1 - reference date of CTE model pinning, in fractional years
PCTETLEN - max length of CTE trail
PCTERNOI - readnoise amplitude and clipping level
PCTESMIT - number of iterations used in CTE forward modeling
PCTESHFT - number of iterations used in the parallel transfer
PCTENSMD - readnoise mitigation algorithm
PCTETRSH - over-subtraction threshold
The table has 4 extensions:
Filename: wfc3_cte.fits
No. Name Type Cards Dimensions Format
0 PRIMARY PrimaryHDU 21 ()
1 QPROF BinTableHDU 16 <pars->nTraps>R x 3C ['i', 'i', 'i']
2 SCLBYCOL BinTableHDU 20 <pars->nScaleTableColumns> x 5C ['i', 'e', 'e', 'e', 'e']
3 RPROF ImageHDU 12 (<pars->nTraps>, 100) float32
4 CPROF ImageHDU 12 (<pars->nTraps>, 100) float32
*/
extern int status; /* variable for return status */
/* VARIABLE FOR FILENAME + EXTENSION NUMBER. */
char filename_wext[strlen(filename) + 4];
/* NAMES OF DATA COLUMNS WE WANT FROM THE FILE, DATA WILL BE STORED IN THE PARS STRUCTURE */
const char wcol[] = "W";
const char qlevq[] = "QLEV_Q";
const char dpdew[] = "DPDE_W";
const char iz[] = "IZ";
const char sens512[]= "SENS_0512";
const char sens1024[] = "SENS_1024";
const char sens1536[] = "SENS_1536";
const char sens2048[] = "SENS_2048";
/* HSTIO VARIABLES */
Hdr hdr_ptr;
initHdr(&hdr_ptr);
/* LOAD PRIMARY HEADER */
if (LoadHdr(filename, &hdr_ptr)) {
sprintf(MsgText,"(pctecorr) Error loading header from %s",filename);
cteerror(MsgText);
status = OPEN_FAILED;
return status;
}
/* GET CTE_NAME KEYWORD */
if (GetKeyStr (&hdr_ptr, "CTE_NAME", NO_DEFAULT, "", pars->cte_name, SZ_CBUF)) {
cteerror("(pctecorr) Error reading CTE_NAME keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"\nCTE_NAME: %s",pars->cte_name);
trlmessage(MsgText);
/* GET VERSION NUMBER */
if (GetKeyStr(&hdr_ptr, "CTE_VER", NO_DEFAULT, "", pars->cte_ver, SZ_CBUF)) {
cteerror("(pctecorr) Error reading CTE_VER keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"CTE_VER: %s",pars->cte_ver);
trlmessage(MsgText);
/* GET DATE OF INSTRUMENT INSTALLATION IN HST */
if (GetKeyDbl(&hdr_ptr, "CTEDATE0", NO_DEFAULT, -999, &pars->cte_date0)) {
cteerror("(pctecorr) Error reading CTEDATE0 keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"CTEDATE0: %g",pars->cte_date0);
trlmessage(MsgText);
/* GET REFRENCE DATE OF CTE MODEL PINNING */
if (GetKeyDbl(&hdr_ptr, "CTEDATE1", NO_DEFAULT, -999, &pars->cte_date1)) {
cteerror("(pctecorr) Error reading CTEDATE1 keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"CTEDATE1: %g",pars->cte_date1);
trlmessage(MsgText);
/* READ MAX LENGTH OF CTE TRAIL */
if (GetKeyInt(&hdr_ptr, "PCTETLEN", NO_DEFAULT, -999, &pars->cte_len)) {
cteerror("(pctecorr) Error reading PCTETLEN keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"PCTETLEN: %d",pars->cte_len);
trlmessage(MsgText);
/* GET READ NOISE CLIPPING LEVEL */
if (GetKeyDbl(&hdr_ptr, "PCTERNOI", NO_DEFAULT, -999, &pars->rn_amp)) {
cteerror("(pctecorr) Error reading PCTERNOI keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"PCTERNOI: %f",pars->rn_amp);
trlmessage(MsgText);
/* GET NUMBER OF ITERATIONS USED IN FORWARD MODEL */
if (GetKeyInt(&hdr_ptr, "PCTENFOR", NO_DEFAULT, -999, &pars->n_forward)) {
cteerror("(pctecorr) Error reading PCTENFOR keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"PCTERNFOR: %d",pars->n_forward);
trlmessage(MsgText);
/* GET NUMBER OF ITERATIONS USED IN PARALLEL TRANSFER*/
if (GetKeyInt(&hdr_ptr, "PCTENPAR", NO_DEFAULT, -999, &pars->n_par)) {
cteerror("(pctecorr) Error reading PCTENPAR keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"PCTERNPAR: %d",pars->n_par);
trlmessage(MsgText);
/* GET READ NOISE MITIGATION ALGORITHM*/
if (GetKeyInt(&hdr_ptr, "PCTENSMD", NO_DEFAULT, -999, &pars->noise_mit)) {
cteerror("(pctecorr) Error reading PCTENSMD keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"PCTENSMD: %d",pars->noise_mit);
trlmessage(MsgText);
/* GET OVER SUBTRACTION THRESHOLD */
if (GetKeyDbl(&hdr_ptr, "PCTETRSH", NO_DEFAULT, -999, &pars->thresh)) {
cteerror("(pctecorr) Error reading PCTETRSH keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"PCTETRSH: %g",pars->thresh);
trlmessage(MsgText);
/*FIX THE READOUT CR'S? */
if (GetKeyInt(&hdr_ptr, "FIXROCR", NO_DEFAULT, -999, &pars->fix_rocr)){
cteerror("(pctecorr) Error reading FIXROCR keyword from PCTETAB");
status = KEYWORD_MISSING;
return status;
}
sprintf(MsgText,"FIXROCR: %d",pars->fix_rocr);
trlmessage(MsgText);
/* DONE READING STUFF FROM THE PRIMARY HEADER */
freeHdr(&hdr_ptr);
/****************************************************************************/
/* READ DATA FROM FIRST TABLE EXTENSIONS */
sprintf(filename_wext, "%s[%i]", filename, 1);
/* OPEN PARAMETERS FILE TO EXTENSION NUMBER 1 */
IRAFPointer tbl_ptr = c_tbtopn(filename_wext, IRAF_READ_ONLY, 0); // xtables table pointer
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error opening %s with xtables",filename_wext);
cteerror(MsgText);
status = OPEN_FAILED;
c_tbtclo(tbl_ptr);
return status;
}
/* READ DATA FROM TABLE */
/* get column pointer for w */
IRAFPointer w_ptr = c_tbcfnd1_retPtr(tbl_ptr, wcol);
if (c_iraferr() || !w_ptr) {
sprintf(MsgText,"(pctecorr) Error getting column %s of PCTETAB",wcol);
cteerror(MsgText);
status = COLUMN_NOT_FOUND;
return status;
}
/* GET COLUMN POINTER FOR QLEVQ */
IRAFPointer qlevq_ptr = c_tbcfnd1_retPtr(tbl_ptr, qlevq);
if (c_iraferr() || !qlevq_ptr) {
sprintf(MsgText,"(pctecorr) Error getting column %s of PCTETAB",qlevq);
cteerror(MsgText);
status = COLUMN_NOT_FOUND;
return status;
}
/* GET COLUMN POINTER FOR DPDEW */
IRAFPointer dpdew_ptr = c_tbcfnd1_retPtr(tbl_ptr, dpdew);
if (c_iraferr() || !dpdew_ptr) {
sprintf(MsgText,"(pctecorr) Error getting column %s of PCTETAB",dpdew);
cteerror(MsgText);
status = COLUMN_NOT_FOUND;
return status;
}
// LOOP OVER TABLE ROWS UP TO SIZE TRAPS
int ctraps = 0; // actual usable traps, i.e. see if more traps were added to reference file
{unsigned j;
for (j = 0; j < pars->nTraps; ++j) {
/* GET W FROM THIS ROW */
pars->wcol_data[j] = c_tbeGetInt(tbl_ptr, w_ptr, j+1);
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error reading row %d of column %s in PCTETAB",j+1, wcol);
cteerror(MsgText);
status = TABLE_ERROR;
return status;
}
/* GET QLEVQ FROM THIS ROW */
pars->qlevq_data[j] = c_tbeGetDouble(tbl_ptr, qlevq_ptr, j+1);
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error reading row %d of column %s in PCTETAB",j+1, qlevq);
cteerror(MsgText);
status = TABLE_ERROR;
return status;
}
if (pars->qlevq_data[j] < 999999.)
ctraps+=1;
/* GET DPDEW FROM THIS ROW */
pars->dpdew_data[j] = c_tbeGetDouble(tbl_ptr, dpdew_ptr, j+1);
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error reading row %d of column %s in PCTETAB",j+1, dpdew);
cteerror(MsgText);
status = TABLE_ERROR;
return status;
}
if (ctraps > pars->nTraps){
sprintf(MsgText,"More TRAPS in reference file than available, update TRAPS: %i -> %i",pars->nTraps,(int)ctraps);
trlmessage(MsgText);
}
}}
/*IF CTRAPS EVER OVERFLOWS INT THIS NEEDS TO BE CHANGED*/
pars->cte_traps = ctraps;
/*
sprintf(MsgText,"(pctecorr) data check for PCTETAB QPROF, row %i, %i\t%g\t%g\ttraps=%i\n",20,
pars->wcol_data[19],pars->qlevq_data[19], pars->dpdew_data[19], pars->cte_traps);
trlmessage(MsgText);
*/
/* CLOSE CTE PARAMETERS FILE FOR EXTENSION 1*/
c_tbtClose((void*)&tbl_ptr);
assert(!tbl_ptr);
/****************************************************************************/
/****************************************************************************/
/* READ CTE SCALING DATA FROM SECOND TABLE EXTENSION */
sprintf(filename_wext, "%s[%i]", filename, 2);
tbl_ptr = c_tbtopn(filename_wext, IRAF_READ_ONLY, 0);
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error opening %s with xtables",filename_wext);
cteerror(MsgText);
status = OPEN_FAILED;
c_tbtclo(tbl_ptr);
return status;
}
/*get column pointer for iz column*/
IRAFPointer iz_ptr = c_tbcfnd1_retPtr(tbl_ptr, iz);
if (c_iraferr() || iz_ptr == 0) {
sprintf(MsgText,"(pctecorr) Error getting column %s of PCTETAB",iz);
cteerror(MsgText);
status = COLUMN_NOT_FOUND;
return status;
}
/* get column pointer for sens512 */
IRAFPointer sens512_ptr = c_tbcfnd1_retPtr(tbl_ptr, sens512);
if (c_iraferr() || w_ptr == 0) {
sprintf(MsgText,"(pctecorr) Error getting column %s of PCTETAB",sens512);
cteerror(MsgText);
status = COLUMN_NOT_FOUND;
return status;
}
/* get column pointer for sens1024 */
IRAFPointer sens1024_ptr = c_tbcfnd1_retPtr(tbl_ptr, sens1024);
if (c_iraferr() || w_ptr == 0) {
sprintf(MsgText,"(pctecorr) Error getting column %s of PCTETAB",sens1024);
cteerror(MsgText);
status = COLUMN_NOT_FOUND;
return status;
}
/* get column pointer for sens1536 */
IRAFPointer sens1536_ptr = c_tbcfnd1_retPtr(tbl_ptr, sens1536);
if (c_iraferr() || w_ptr == 0) {
sprintf(MsgText,"(pctecorr) Error getting column %s of PCTETAB",sens1536);
cteerror(MsgText);
status = COLUMN_NOT_FOUND;
return status;
}
/* get column pointer for sens2048 */
IRAFPointer sens2048_ptr = c_tbcfnd1_retPtr(tbl_ptr, sens2048);
if (c_iraferr() || w_ptr == 0) {
sprintf(MsgText,"(pctecorr) Error getting column %s of PCTETAB",sens2048);
cteerror(MsgText);
status = COLUMN_NOT_FOUND;
return status;
}
/* read data from table */
/* loop over table rows */
{unsigned j;
for (j = 0; j < pars->nScaleTableColumns; ++j)
{
/* get trap from this row */
pars->iz_data[j] = c_tbeGetInt(tbl_ptr, iz_ptr, j+1);
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error reading row %d of column %s in PCTETAB",j+1, iz);
cteerror(MsgText);
return (status = TABLE_ERROR);
}
pars->scale512[j] = c_tbeGetDouble(tbl_ptr, sens512_ptr, j+1);
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error reading row %d of column %s in PCTETAB",j+1, sens512);
cteerror(MsgText);
return (status = TABLE_ERROR);
}
pars->scale1024[j] = c_tbeGetDouble(tbl_ptr, sens1024_ptr, j+1);
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error reading row %d of column %s in PCTETAB",j+1, sens1024);
cteerror(MsgText);
return (status = TABLE_ERROR);
}
pars->scale1536[j] = c_tbeGetDouble(tbl_ptr, sens1536_ptr, j+1);
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error reading row %d of column %s in PCTETAB",j+1, sens1536);
cteerror(MsgText);
return (status = TABLE_ERROR);
}
pars->scale2048[j] = c_tbeGetDouble(tbl_ptr, sens2048_ptr, j+1);
if (c_iraferr()) {
sprintf(MsgText,"(pctecorr) Error reading row %d of column %s in PCTETAB",j+1, sens2048);
cteerror(MsgText);
return (status = TABLE_ERROR);
}
}}
// for testing
/*{
unsigned j = pars->nColumns;
sprintf(MsgText,"(pctecorr) data check for PCTETAB SCLBYCOL row %d, %d %g\t%g\t%g\t%g\ntotal traps = %i",
j,pars->iz_data[j-1],pars->scale512[j-1],pars->scale1024[j-1],pars->scale1536[j-1],pars->scale2048[j-1],pars->cte_traps);
trlmessage(MsgText);
}
*/
/* close CTE parameters file for extension 2*/
c_tbtClose((void*)&tbl_ptr);
assert(!tbl_ptr);
/****************************************************************************/
/* extension 3: differential trail profile as image */
ctemessage("Reading in image from extension 3");
/* Get the coefficient images from the PCTETAB */
pars->rprof = malloc(sizeof(*pars->rprof));
if (pars->rprof == NULL){
sprintf (MsgText, "Can't allocate memory for RPROF ref data");
trlerror (MsgText);
return (status = 1);
}
initFloatHdrData(pars->rprof);
pars->rprof->data.storageOrder = COLUMNMAJOR;
if (getFloatHD (filename, "RPROF", 1, pars->rprof)){
return (status=1);
}
/****************************************************************************/
/* ext number 4 : cummulative trail profile as image */
ctemessage("Reading in image from extension 4");
pars->cprof = malloc(sizeof(*pars->cprof));
if (pars->cprof == NULL){
sprintf (MsgText, "Can't allocate memory for CPROF ref data");
trlerror (MsgText);
return (status = 1);
}
/* Get the coefficient images from the PCTETAB */
initFloatHdrData (pars->cprof);
pars->cprof->data.storageOrder = COLUMNMAJOR;
if (getFloatHD (filename, "CPROF", 1, pars->cprof)){
return (status=1);
}
return(status);
}