int main (int argc, char **argv) {
char *inlist; /* input file name */
char *outlist; /* output blev file name */
/*int switch_on = 0;*/ /* was any switch specified? */
int printtime = NO; /* print time after each step? */
int verbose = NO; /* print additional info? */
int quiet = NO; /* print additional info? */
int too_many = 0; /* too many command-line arguments? */
int i, j; /* loop indexes */
int k;
IRAFPointer i_imt, o_imt; /* imt list pointers */
char *input; /* name of input science file */
char *output; /* name of output file */
int n_in, n_out; /* number of files in each list */
int n;
/* Input and output suffixes. */
char isuffix[] = "_raw";
char osuffix[] = "_blv_tmp";
/* A structure to pass the calibration switches to ACSCCD */
CalSwitch ccd_sw;
/* reference file keywords and names */
RefFileInfo refnames;
void InitRefFile (RefFileInfo *);
void FreeRefFile (RefFileInfo *);
void initSwitch (CalSwitch *);
int ACSccd (char *, char *, CalSwitch *, RefFileInfo *, int, int);
int DefSwitch (char *);
int MkName (char *, char *, char *, char *, char *, int);
void WhichError (int);
int CompareNumbers (int, int, char *);
/* For image header access */
Hdr phdr;
int LoadHdr (char *, Hdr *);
int GetSwitch (Hdr *, char *, int *);
c_irafinit (argc, argv);
/* Allocate space for file names. */
inlist = calloc (ACS_LINE+1, sizeof (char));
outlist = calloc (ACS_LINE+1, sizeof (char));
input = calloc (ACS_LINE+1, sizeof (char));
output = calloc (ACS_LINE+1, sizeof (char));
if (inlist == NULL || outlist == NULL ||
input == NULL || output == NULL) {
printf ("Can't even begin; out of memory.\n");
exit (ERROR_RETURN);
}
inlist[0] = '\0';
outlist[0] = '\0';
input[0] = '\0';
output[0] = '\0';
/* Initialize the lists of reference file keywords and names. */
InitRefFile (&refnames);
/* Initial values. */
initSwitch (&ccd_sw);
for (i = 1; i < argc; i++) {
/**********
if (strcmp (argv[i], "-dqi") == 0) {
ccd_sw.dqicorr = PERFORM;
switch_on = 1;
} else if (strcmp (argv[i], "-atod") == 0) {
ccd_sw.atodcorr = PERFORM;
switch_on = 1;
} else if (strcmp (argv[i], "-blev") == 0) {
ccd_sw.blevcorr = PERFORM;
switch_on = 1;
} else if (strcmp (argv[i], "-bias") == 0) {
ccd_sw.biascorr = PERFORM;
switch_on = 1;
} else if (argv[i][0] == '-') {
**********/
if (argv[i][0] == '-') {
for (j = 1; argv[i][j] != '\0'; j++) {
if (argv[i][j] == 't') {
printtime = YES;
} else if (argv[i][j] == 'v') {
verbose = YES;
} else if (argv[i][j] == 'q') {
quiet = YES;
} else {
printf (MsgText, "Unrecognized option %s\n", argv[i]);
FreeNames (inlist, outlist, input, output);
exit (1);
}
}
} else if (inlist[0] == '\0') {
strcpy (inlist, argv[i]);
} else if (outlist[0] == '\0') {
strcpy (outlist, argv[i]);
} else {
too_many = 1;
}
}
if (inlist[0] == '\0' || too_many) {
printf ("syntax: acsccd [-t] [-v] [-q] input output\n");
/*
printf (" command-line switches:\n");
printf (" -dqi -atod -blev -bias\n");
*/
FreeNames (inlist, outlist, input, output);
exit (ERROR_RETURN);
}
/* Initialize the structure for managing trailer file comments */
InitTrlBuf ();
/* Copy command-line value for QUIET to structure */
SetTrlQuietMode(quiet);
/* Was no calibration switch specified on command line?
default values (mostly PERFORM) except ATODCORR
if (!switch_on) {*/
ccd_sw.dqicorr = DefSwitch ("dqicorr");
ccd_sw.atodcorr = DefSwitch ("atodcorr");
ccd_sw.blevcorr = DefSwitch ("blevcorr");
ccd_sw.biascorr = DefSwitch ("biascorr");
/*}*/
/* Expand the templates. */
i_imt = c_imtopen (inlist);
o_imt = c_imtopen (outlist);
n_in = c_imtlen (i_imt);
n_out = c_imtlen (o_imt);
/* The number of input and output files must be the same. */
if (CompareNumbers (n_in, n_out, "output"))
status = 1;
if (status) {
FreeNames (inlist, outlist, input, output);
CloseTrlBuf();
exit (ERROR_RETURN);
}
/* Loop over the list of input files. */
for (n = 0; n < n_in; n++) {
k = c_imtgetim (i_imt, input, ACS_LINE);
if (n_out > 0)
k = c_imtgetim (o_imt, output, ACS_LINE);
else
output[0] = '\0';
/* Open input image in order to read its primary header. */
if (LoadHdr (input, &phdr)) {
WhichError (status);
sprintf (MsgText, "Skipping %s", input);
trlmessage (MsgText);
continue;
}
/* Determine osuffix. */
strcpy(osuffix, "_blv_tmp");
if (MkName (input, isuffix, osuffix, "", output, ACS_LINE)) {
WhichError (status);
sprintf (MsgText, "Skipping %s", input);
trlmessage (MsgText);
continue;
}
/* Calibrate the current input file. */
if (ACSccd (input, output, &ccd_sw, &refnames, printtime, verbose)) {
sprintf (MsgText, "Error processing %s.", input);
trlerror (MsgText);
WhichError (status);
}
}
/* Close lists of file names, and free name buffers. */
c_imtclose (i_imt);
c_imtclose (o_imt);
CloseTrlBuf();
FreeRefFile (&refnames);
FreeNames (inlist, outlist, input, output);
if (status)
exit (ERROR_RETURN);
else
exit (0);
}
int ProcessACSCCD (AsnInfo *asn, ACSInfo *acshdr, int *save_tmp, int printtime, const unsigned nThreads, const unsigned cteAlgorithmGen, const char * pcteTabNameFromCmd) {
extern int status;
RefFileInfo sciref; /* ref file keywords and names */
CalSwitch sci_sw; /* all cal switches for science file */
CalSwitch acsccd_sci_sw; /* ACSCCD switches for science file */
CalSwitch acscte_sci_sw; /* ACSCTE switches for science file */
CalSwitch acs2d_sci_sw; /* ACS2D switches for science file */
int save_crj; /* don't delete crj_tmp file? */
int prod; /* which CR-split/Rptobs product? */
int posid; /* counter for input products */
int expid; /* counter for input exposures */
int newpreface = NO; /* switch for keeping previous comments for
all remaining trailer files */
char *acsrej_input; /* list of input names for ACSREJ */
char *acsrejc_input; /* list of CTE corrected input names for ACSREJ */
char *acsrej_msgtext; /* str for list of input filenames */
char *acsrejc_msgtext; /* str for list of CTE corrected input filenames */
int nchars; /* Number of chars for input string to ACSREJ */
void ACSDefaults (ACSInfo *);
void InitRefFile (RefFileInfo *);
void FreeRefFile (RefFileInfo *);
int ACSRefInit (ACSInfo *, CalSwitch *, RefFileInfo *);
int ACSccd (char *, char *, CalSwitch *, RefFileInfo *, int, int);
int ACScte (char *, char *, CalSwitch *, RefFileInfo *, int, int, int, const unsigned cteAlgorithmGen, const char * pcteTabNameFromCmd, const bool forwardModelOnly);
int ACS2d (char *, char *,CalSwitch *, RefFileInfo *, int, int);
int GetAsnMember (AsnInfo *, int, int, int, ACSInfo *);
int GetSingle (AsnInfo *, ACSInfo *);
int CheckCorr (AsnInfo *, ACSInfo *);
int InsertACSSuffix (ACSInfo *);
save_crj = *save_tmp; /* initial value; */
/* Loop over the products/positions for each CR-split/Repeat-Obs set. */
for (prod = 0; prod < asn->numprod; prod++) {
if (asn->verbose){
sprintf (MsgText, "CALACS: processing CCD product %d", prod);
trlmessage (MsgText);
}
/* Process this PARTIAL/SINGLE/FULL product... */
for (posid = 1; posid <= asn->numsp; posid++) {
if (asn->verbose) {
sprintf (MsgText,"CALACS: processing posid = %d", posid);
trlmessage (MsgText);
}
/* Allocate space for ACSREJ input image list */
if ( (asn->crcorr == PERFORM) || (asn->rptcorr == PERFORM) ) {
nchars = asn->spmems[posid] * CHAR_FNAME_LENGTH;
acsrej_input = (char *) calloc( nchars + 1, sizeof(char));
/* Initialize this string to NULL */
acsrej_input[0] = '\0';
acsrejc_input = (char *) calloc( nchars + 1, sizeof(char));
/* Initialize this string to NULL */
acsrejc_input[0] = '\0';
}
/* Run ACSCCD on individual EXPosures. */
for (expid = 1; expid <= asn->spmems[posid]; expid++) {
/* From this point on, we are working with ONE image at a time */
/* Read in Member keyword info from --FIRST-- EXP image header */
/*if(prod == 0 && posid == 1 && expid == 1) { */
if(expid == 1) {
/* (Re-)Initialize the lists of reference file keywords
and names. */
InitRefFile (&sciref);
/* Assign default values in acs. */
ACSDefaults (acshdr);
if (asn->process == SINGLE ) {
if (GetSingle (asn, acshdr) )
return (status);
} else {
if( GetAsnMember(asn, prod, posid, expid, acshdr))
return (status);
}
/* Initialize variables, and get info (cal switches and
reference file names) from primary headers.
*/
if (ACSRefInit (acshdr, &sci_sw, &sciref))
return (status);
/* Make sure 'save_tmp' and 'save_crj' are no
longer set to 'DUMMY'.
If save_tmp was set from the command-line, then
ignore what is set in the header keyword
EXPSCORR.
*/
if (*save_tmp == DUMMY) {
*save_tmp = NO;
save_crj = *save_tmp;
}
if (asn->verbose) {
trlmessage ("CALACS: Got reference file information");
}
/* Store the trailer file comments into preface */
newpreface = YES;
} else {
if (asn->process == SINGLE ) {
if (GetSingle (asn, acshdr))
return (status);
} else {
if( GetAsnMember(asn, prod, posid, expid, acshdr))
return (status);
}
/* Construct output and temporary file names. */
if (InsertACSSuffix (acshdr))
return (status);
}
/* Check ASN table settings for CRCORR/RPTCORR
against image header values. If they are not
consistent, print out a ERROR message and quit.
Only need to perform this check on the first image
in the association. WJH 21 May 1999
*/
if (prod == 0 && posid == 1 && expid == 1) {
if (CheckCorr(asn, acshdr))
return (status);
}
/* Copy switch values for ACSCCD, ACSCTE, and ACS2D
argument lists. */
SetACSSw(&sci_sw, &acsccd_sci_sw, &acscte_sci_sw, &acs2d_sci_sw);
if (asn->verbose) {
trlmessage ("CALACS: Processing switches set... ");
}
/* Ready to process input image now... */
/* Do we have anything to do with this image? */
if (acshdr->sci_basic_2d != PERFORM &&
acshdr->sci_basic_ccd != PERFORM &&
acshdr->sci_basic_cte != PERFORM &&
acshdr->sci_crcorr != PERFORM &&
acshdr->sci_rptcorr != PERFORM ){
trlwarn ("No calibration switch was set to PERFORM.");
FreeRefFile (&sciref);
return (status = NOTHING_TO_DO);
}
/* First, initialize the Input CCD image with ACSCCD.
Then, perform PCTECORR if needed.
Then, either do cosmic ray rejection followed by ACS2D,
or just run ACS2D. */
/* First do atodcorr, dqicorr, and blevcorr
(or copy the name). */
if (acshdr->sci_basic_ccd == PERFORM) {
/* This is acsccd; note that we use acsccd_sci_sw. */
/* Copy all messages up to here into preface buffer
to be prepended to all input file trailer files */
if (newpreface == YES) {
InitTrlPreface();
}
SetTrlPrefaceMode (YES);
if (ACSccd (acshdr->rawfile, acshdr->blv_tmp,
&acsccd_sci_sw, &sciref, printtime,
asn->verbose))
return (status);
/* Reset switches */
ResetACSSw (&acsccd_sci_sw, &acs2d_sci_sw);
} else {
/* Copy the input file to blv_tmp. We need to do this
because acsrej may (depending on the crmask column
in the crrejtab) modify the DQ flags in its input file.
*/
if (CopyFFile (acshdr->rawfile, acshdr->blv_tmp))
return (status);
}
/* Do PCTECORR now. */
if (acshdr->sci_basic_cte == PERFORM) {
// ``forwardModelOnly = false`` because it is not part of the pipeline processing.
if (ACScte(acshdr->blv_tmp, acshdr->blc_tmp,
&acscte_sci_sw, &sciref, printtime,
asn->verbose, nThreads, cteAlgorithmGen, pcteTabNameFromCmd, false)) {
return (status);
}
}
/* We now are working with blv_tmp here... */
/* Copy (cat) blv_tmp name to acsrej_input string */
if ( (acshdr->sci_crcorr == PERFORM) ||
(acshdr->sci_rptcorr == PERFORM) ) {
strcat(acsrej_input, acshdr->blv_tmp);
if (expid < asn->spmems[posid]) {
/* Don't add a comma to the end of the last filename*/
strcat(acsrej_input, ",");
}
/* Also, add blv_tmp to list of files to be deleted */
strcpy(asn->product[prod].subprod[posid].exp[expid].blv_tmp,
acshdr->blv_tmp);
/* do this again for CTE corrected exposures */
if (acscte_sci_sw.pctecorr == PERFORM) {
strcat(acsrejc_input, acshdr->blc_tmp);
if (expid < asn->spmems[posid]) {
/* Don't add a comma to the end of the last filename*/
strcat(acsrejc_input, ",");
}
/* Also, add blc_tmp to list of files to be deleted */
strcpy(asn->product[prod].subprod[posid].exp[expid].blc_tmp, acshdr->blc_tmp);
}
}
} /* end loop of individual EXPosures for running ACSCCD */
/* Cosmic ray rejection, followed by basic 2-D processing
of _crj_tmp. */
if ( (acshdr->sci_crcorr == PERFORM) ||
(acshdr->sci_rptcorr == PERFORM) ) {
if (asn->verbose) {
sprintf (MsgText,"CALACS: Now process position %d from product %d", posid, prod);
trlmessage (MsgText);
}
/* Commented out, not sure why these need to be reset.
Everything should have correct settings after ACSCCD.
MRD 17-May-2011 */
/* Copy switch values for ACSCCD, ACSCTE, and ACS2D
argument lists. */
/*SetACSSw (&sci_sw, &acsccd_sci_sw, &acscte_sci_sw, &acs2d_sci_sw); */
/* Reset DQICORR, since it will already have been done...
WJH 23-Apr-2002 */
/*acs2d_sci_sw.dqicorr = COMPLETE; */
if (asn->debug){
sprintf(MsgText,"Non-CTE corrected Input to ACSREJ is:");
trlmessage(MsgText);
/* Need to allocate memory for a separate string to be
long enough to hold all the input names when printing
it out. Caused pipeline problems otherwise.
WJH 19-Mar-04 */
acsrej_msgtext = calloc(strlen(acsrej_input)+25,
sizeof(char));
sprintf (acsrej_msgtext, "%s", acsrej_input);
trlmessage(acsrej_msgtext);
free(acsrej_msgtext);
sprintf(MsgText,"Non-CTE corrected Output to ACSREJ is: %s", acshdr->crj_tmp);
trlmessage(MsgText);
if (acscte_sci_sw.pctecorr == PERFORM) {
sprintf(MsgText,"CTE corrected Input to ACSREJ is:");
trlmessage(MsgText);
/* Need to allocate memory for a separate string to be
long enough to hold all the input names when printing
it out. Caused pipeline problems otherwise.
WJH 19-Mar-04 */
acsrejc_msgtext = calloc(strlen(acsrejc_input)+25, sizeof(char));
sprintf (acsrejc_msgtext, "%s",acsrejc_input);
trlmessage(acsrejc_msgtext);
free(acsrejc_msgtext);
sprintf(MsgText,"CTE corrected Output to ACSREJ is: %s", acshdr->crc_tmp);
trlmessage(MsgText);
}
}
/* Set up the correct value of ASN_MTYP for ACSREJ
output image. */
if ( strncmp(acshdr->asn_table, acshdr->crj_tmp, 9) ) {
/* crj_tmp is a sub-product */
strcpy (acshdr->mtype, asn->product[prod].subprod[posid].mtype);
} else {
/* crj_tmp leads to a product with same rootname as asn_table */
strcpy (acshdr->mtype, asn->product[prod].mtype);
}
// Reject cosmic rays.
int pctecorrSwitchState = acscte_sci_sw.pctecorr;
if (!OmitStep(pctecorrSwitchState))
{
// Temporarily set this to OMIT so that ACS2d, called within
// the ACSRej_oWrapper call stack, uses the non-CTE darks.
// This is not thread safe.
acs2d_sci_sw.pctecorr = OMIT;
}
if ((status = ACSRej_0Wrapper(acsrej_input,
acshdr->crj_tmp,
acshdr->crjfile,
asn->product[prod].subprod[posid].crj_tmp,
acshdr,
asn,
prod,
posid,
&acs2d_sci_sw,
&sciref,
printtime,
save_crj,
True)))
{
//freeStuff
delete((void**)&acsrej_input);
return status;
}
if (!OmitStep(pctecorrSwitchState))
acs2d_sci_sw.pctecorr = pctecorrSwitchState;
delete((void**)&acsrej_input);
/* now repeat the same thing with CTE corrected products */
if (!OmitStep(acscte_sci_sw.pctecorr))
{
if ((status = ACSRej_0Wrapper(acsrejc_input,
acshdr->crc_tmp,
acshdr->crcfile,
asn->product[prod].subprod[posid].crc_tmp,
acshdr,
asn,
prod,
posid,
&acs2d_sci_sw,
&sciref,
printtime,
save_crj,
False)))
{
//freeStuff
delete((void**)&acsrejc_input);
return status;
}
}
delete((void**)&acsrejc_input);
} /* End of CRCORR processing */
if (asn->debug){
trlmessage("Run ACS2D for CCD next...");
}
/* Run ACS2D on individual EXPosures. */
for (expid = 1; expid <= asn->spmems[posid]; expid++) {
/* From this point on, we are working with ONE image
at a time... */
/* load acs file info */
if (asn->process == SINGLE ) {
if (GetSingle (asn, acshdr) )
return (status);
} else {
if( GetAsnMember(asn, prod, posid, expid, acshdr))
return (status);
}
/* Construct output and temporary file names. */
if (InsertACSSuffix (acshdr))
return (status);
/* If we are not performing CRCORR or RPTCORR or
EXPSCORR is set to PERFORM, then finish
processing individual EXP files with ACS2D...
*/
if ( (acshdr->sci_crcorr != PERFORM) ||
(acshdr->sci_rptcorr != PERFORM) ||
(sci_sw.expscorr == PERFORM) ) {
if (asn->debug) {
trlmessage("CRCORR not set to Perform or EXPSCORR turned on...");
}
if (acshdr->sci_basic_2d == PERFORM) {
SetTrlPrefaceMode (NO);
if (asn->copy_input == PERFORM) {
if (CopyFFile (acshdr->fltfile, acshdr->blv_tmp))
return (status);
remove (acshdr->fltfile);
}
/* Basic 2-D processing (flat field, etc). */
/* temporarily set acs2d_sci_sw.pctecorr to omit so the
correct acs2d processing is done */
if (acs2d_sci_sw.pctecorr == PERFORM) {
acs2d_sci_sw.pctecorr = OMIT;
if (ACS2d (acshdr->blv_tmp, acshdr->fltfile,
&acs2d_sci_sw, &sciref, printtime,
asn->verbose))
return (status);
acs2d_sci_sw.pctecorr = PERFORM;
} else {
if (ACS2d (acshdr->blv_tmp, acshdr->fltfile,
&acs2d_sci_sw, &sciref, printtime,
asn->verbose))
return (status);
}
} else {
/* If we are not performing CRCORR, then copy
blv_tmp file into a final _flt file. */
if (acshdr->sci_crcorr != PERFORM ||
acshdr->sci_rptcorr != PERFORM) {
if (CopyFFile (acshdr->blv_tmp, acshdr->fltfile))
return (status);
}
}
/* now repeat ACS2D processing for CTE products */
if (acshdr->sci_basic_2d == PERFORM &&
acscte_sci_sw.pctecorr == PERFORM) {
if (asn->copy_input == PERFORM) {
if (CopyFFile (acshdr->flcfile, acshdr->blc_tmp))
return (status);
remove (acshdr->flcfile);
}
/* Basic 2-D processing (flat field, etc). */
if (ACS2d (acshdr->blc_tmp, acshdr->flcfile,
&acs2d_sci_sw, &sciref, printtime,
asn->verbose))
return (status);
} else if (acscte_sci_sw.pctecorr == PERFORM) {
/* If we are not performing CRCORR, then copy
blc_tmp file into a final _flc file. */
if (acshdr->sci_crcorr != PERFORM ||
acshdr->sci_rptcorr != PERFORM) {
if (CopyFFile (acshdr->blc_tmp, acshdr->flcfile))
return (status);
}
}
} /* Finished processing blv_tmp file through ACS2D */
/* Now, delete _blv_tmp and _blc_tmp files */
if (*save_tmp != YES) {
remove (acshdr->blv_tmp);
if (acscte_sci_sw.pctecorr == PERFORM) {
remove (acshdr->blc_tmp);
}
}
} /* End loop over ind EXP for making _flt and _flc files. */
/* Reset the trailer file preface to NULL since
it has already been copied into trailer files */
ResetTrlPreface();
} /* End of processing for SINGLE/PARTIAL product */
} /* End loop over CCD products here... */
/* Done with lists of reference file keywords and names. */
FreeRefFile (&sciref);
return (status);
}
