int smf_initial_sky( ThrWorkForce *wf, AstKeyMap *keymap, smfDIMMData *dat,
int *iters, int *status ) {
/* Local Variables: */
char refparam[ DAT__SZNAM ];/* Name for reference NDF parameter */
const char *cval; /* The IMPORTSKY string value */
double *ptr; /* Pointer to NDF Data array */
double *vptr; /* Pointer to NDF Variance array */
int indf1; /* Id. for supplied reference NDF */
int indf2; /* Id. for used section of reference NDF */
int nel; /* Number of mapped NDF pixels */
int result; /* Returned flag */
int there; /* Is there a smurf extension in the NDF? */
int update; /* Was NDF opened for UPDATE access? */
size_t i; /* Loop count */
size_t junk; /* Unused value */
/* Initialise the returned value to indicate no sky has been subtractred. */
result = 0;
/* Assume the sky map was not created by an interupted previous run of
makemap. */
*iters = -1;
/* Check inherited status. */
if( *status != SAI__OK ) return result;
/* Begin an AST context. */
astBegin;
/* The IMPORTSKY config parameter should have the name of the ADAM
parameter to use for acquiring the NDF that contains the initial sky
estimate. If IMPORTSKY is "1", use REF. */
cval = NULL;
astMapGet0C( keymap, "IMPORTSKY", &cval );
if( cval ) {
if( !astChrMatch( cval, "REF" ) &&
!astChrMatch( cval, "MASK2" ) &&
!astChrMatch( cval, "MASK3" ) ) {
astMapGet0I( keymap, "IMPORTSKY", &result );
cval = ( result > 0 ) ? "REF" : NULL;
}
if( cval ) {
result = 1;
strcpy( refparam, cval );
astChrCase( NULL, refparam, 1, 0 );
}
}
/* Do nothing more if we are not subtracting an initial sky from the data. */
if( result && *status == SAI__OK ) {
/* Begin an NDF context. */
ndfBegin();
/* Get an identifier for the NDF using the associated ADAM parameter.
First try UPDATE access. If this fails try READ access. */
ndfAssoc( refparam, "UPDATE", &indf1, status );
if( *status != SAI__OK ) {
errAnnul( status );
ndfAssoc( refparam, "READ", &indf1, status );
update = 0;
} else {
update = 1;
}
/* Tell the user what we are doing. */
ndfMsg( "N", indf1 );
msgOut( "", "Using ^N as the initial guess at the sky", status );
/* Get a section from this NDF that matches the bounds of the map. */
ndfSect( indf1, 2, dat->lbnd_out, dat->ubnd_out, &indf2, status );
/* Ensure masked values are not set bad in the mapped data array. */
ndfSbb( 0, indf2, status );
/* Map the data array section, and copy it into the map buffer. */
ndfMap( indf2, "DATA", "_DOUBLE", "READ", (void **) &ptr, &nel, status );
if( *status == SAI__OK ) {
memcpy( dat->map, ptr, dat->msize*sizeof(*ptr));
}
/* Map the variance array section, and copy it into the map buffer. */
ndfState( indf2, "VARIANCE", &there, status );
if( there ) {
ndfMap( indf2, "VARIANCE", "_DOUBLE", "READ", (void **) &vptr, &nel, status );
if( *status == SAI__OK ) {
memcpy( dat->mapvar, vptr, dat->msize*sizeof(*vptr));
}
}
/* If the NDF was created by a previous run of makemap that was interupted
using control-C, it will contain a NUMITER item in the smurf extension,
which gives the number of iterations that were completed before the
map was created. Obtain and return this value, if it exists. */
ndfXstat( indf1, SMURF__EXTNAME, &there, status );
if( there ) ndfXgt0i( indf1, SMURF__EXTNAME, "NUMITER", iters,
status );
/* If the NDF has a Quality component, import it and create initial AST,
FLT, PCA, SSN and COM masks from it. These will often be over-ridden by
new masks calculated with smf_calcmodel_ast below, but will not be
over-written if the masks have been frozen by xxx.zero_freeze. */
ndfState( indf2, "Quality", &there, status );
if( there && dat->mapqual ) {
smf_qual_t *qarray = smf_qual_map( wf, indf2, "Read", NULL, &junk,
status );
if( *status == SAI__OK ) {
smf_qual_t *pq = qarray;
for( i = 0; i < dat->msize; i++,pq++ ) {
if( *pq & SMF__MAPQ_AST ) {
if( !dat->ast_mask ) dat->ast_mask = astCalloc( dat->msize,
sizeof( *(dat->ast_mask) ) );
(dat->ast_mask)[ i ] = 1;
}
if( *pq & SMF__MAPQ_FLT ) {
if( !dat->flt_mask ) dat->flt_mask = astCalloc( dat->msize,
sizeof( *(dat->flt_mask) ) );
(dat->flt_mask)[ i ] = 1;
}
if( *pq & SMF__MAPQ_COM ) {
if( !dat->com_mask ) dat->com_mask = astCalloc( dat->msize,
sizeof( *(dat->com_mask) ) );
(dat->com_mask)[ i ] = 1;
}
if( *pq & SMF__MAPQ_SSN ) {
if( !dat->ssn_mask ) dat->ssn_mask = astCalloc( dat->msize,
sizeof( *(dat->ssn_mask) ) );
(dat->ssn_mask)[ i ] = 1;
}
if( *pq & SMF__MAPQ_PCA ) {
if( !dat->pca_mask ) dat->pca_mask = astCalloc( dat->msize,
sizeof( *(dat->pca_mask) ) );
(dat->pca_mask)[ i ] = 1;
}
}
}
qarray = astFree( qarray );
}
/* Indicate the map arrays within the supplied smfDIMMData structure now
contain usable values. We need to do this before calling
smf_calcmodel_ast below so that the right mask gets used in
smf_calcmodel_ast. */
dat->mapok = 1;
/* Apply any existinction correction to the cleaned bolometer data. */
if( dat->ext ) smf_calcmodel_ext( wf, dat, 0, keymap, dat->ext, 0,
status);
/* Sample the above map at the position of each bolometer sample and
subtract the sampled value from the cleaned bolometer value. */
smf_calcmodel_ast( wf, dat, 0, keymap, NULL, SMF__DIMM_PREITER, status);
/* Remove any existinction correction to the modifed bolometer data. */
if( dat->ext ) smf_calcmodel_ext( wf, dat, 0, keymap, dat->ext,
SMF__DIMM_INVERT, status);
/* If the NDF was opened with UPDATE access, update the quality array in
the NDF to reflect the AST mask created by smf_calcmodel_ast above. */
if( update ) {
smf_qual_t *qarray = astStore( NULL, dat->mapqual, dat->msize*sizeof(*qarray) );
qarray = smf_qual_unmap( wf, indf2, SMF__QFAM_MAP, qarray, status );
}
/* End the NDF context. */
ndfEnd( status );
}
/* End the AST context. */
astEnd;
/* Return the pointer to the boolean mask. */
return result;
}
smf_qual_t * smf_qual_unmap( ThrWorkForce *wf, int indf, smf_qfam_t family,
smf_qual_t * qual, smf_qual_t mask, int * status ) {
int canwrite = 0; /* can we write to the file? */
size_t nqbits = 0; /* Number of quality bits in this family */
SmfQualUnmapData *job_data = NULL;
SmfQualUnmapData *pdata;
int nw;
size_t step;
int iw;
if (*status != SAI__OK) goto CLEANUP;
/* do nothing if there is no quality */
if (!qual) return NULL;
/* if we do not have an NDF identifier we just free the memory */
if (indf == NDF__NOID) goto CLEANUP;
/* See if we have WRITE access to the file */
ndfIsacc( indf, "WRITE", &canwrite, status );
/* if we have WRITE access and the data were not mapped we have
to copy to the file. Also check we have a non-NULL input pointer.
If the data were mapped we still have to make sure the quality names
are stored. */
if ( canwrite && qual ) {
int highbit = -1; /* highest bit used */
size_t i;
int itemp;
int lowbit = -1; /* Lowest bit used */
size_t nout;
int nqual = 0;
void *qpntr[1];
size_t qcount[SMF__NQBITS]; /* statically allocate the largest array */
IRQLocs *qlocs;
unsigned char * qmap;
int there;
ndfMsg( "FILE", indf );
msgOutif( MSG__DEBUG, "", "Finalising quality for file ^FILE", status);
if (family == SMF__QFAM_TCOMP ) {
/* note that TCOMP is not an allowed quality because SMURF should not be
using it anywhere in a permanent way. */
*status = SAI__ERROR;
ndfMsg( "NDF", indf );
errRepf( "", "Unsupported quality family '%s' for quality unmapping of "
"file ^NDF", status, smf_qfamily_str(family,status) );
goto CLEANUP;
} else if (family == SMF__QFAM_NULL) {
/* In this case we have to assume that we just cast the quality
to UBYTE and copy it without changing anything or naming the
entries. Use a simple type conversion. */
ndfMap( indf, "QUALITY", "_UBYTE", "WRITE", &qpntr[0], &itemp, status );
qmap = qpntr[0];
nout = itemp;
for (i = 0; i<nout; i++) {
qmap[i] = qual[i];
}
ndfUnmap( indf, "QUALITY", status );
/* Turn on all quality */
ndfSbb( 255, indf, status );
/* we are finished so jump to tidy up */
goto CLEANUP;
}
/* work out how many quality items are in this family */
nqbits = smf_qfamily_count( family, status );
/* initialize qcount */
for (i=0; i<SMF__NQBITS; i++) {
qcount[i] = 0;
}
/* how many pixels in NDF (assumed to be number in quality) */
ndfSize( indf, &itemp, status );
nout = itemp;
/* How many threads do we get to play with */
nw = wf ? wf->nworker : 1;
/* Find how many elements to process in each worker thread. */
step = nout/nw;
if( step == 0 ) step = 1;
/* Allocate job data for threads, and store common values. Ensure that the
last thread picks up any left-over elements. */
job_data = astCalloc( nw, sizeof(*job_data) );
if( *status == SAI__OK ) {
for( iw = 0; iw < nw; iw++ ) {
pdata = job_data + iw;
pdata->i1 = iw*step;
if( iw < nw - 1 ) {
pdata->i2 = pdata->i1 + step - 1;
} else {
pdata->i2 = nout - 1 ;
}
pdata->nqbits = nqbits;
pdata->qual = qual;
pdata->nout = nout;
}
}
/* Work out which bits are actually used */
if (*status == SAI__OK) {
size_t k;
/* now we try to be a bit clever. It may be a mistake since we have to
do multiple passes through "qual". First determine how many quality
bits are actually set. */
for( iw = 0; iw < nw; iw++ ) {
pdata = job_data + iw;
pdata->operation = 1;
thrAddJob( wf, 0, pdata, smf1_qual_unmap, 0, NULL, status );
}
thrWait( wf, status );
for( iw = 0; iw < nw; iw++ ) {
pdata = job_data + iw;
for( k=0; k<nqbits; k++ ) {
qcount[k] += pdata->qcount[k];
}
}
/* Reset the counts to zero for any bits that are not required
(i.e. are not set in "mask"). */
for( k=0; k<nqbits; k++ ) {
if( ! (mask & (1<<k)) ) qcount[k] = 0;
}
/* see how many we got */
for (k=0; k<nqbits; k++) {
if ( qcount[k] ) {
nqual++;
highbit = k;
if (lowbit < 0) lowbit = k;
}
}
}
/* for IRQ we need to ensure the SMURF extension exists so open and annul it if it is missing.
We are completely rewriting any IRQ information so we have to delete any previously existing
IRQ extension. */
irqDelet( indf, status );
ndfXstat( indf, SMURF__EXTNAME, &there, status );
if (!there) {
HDSLoc * smurfloc = NULL;
/* Create SMURF extension if it does not already exist */
ndfXnew( indf, SMURF__EXTNAME, SMURF__EXTTYPE, 0, NULL, &smurfloc, status );
if (smurfloc) datAnnul( &smurfloc, status );
}
irqNew( indf, SMURF__EXTNAME, &qlocs, status );
/* malloced so we need to map and copy over the values. IRQ
names need to be set BEFORE we copy. */
/* Map the quality component with WRITE access */
ndfMap( indf, "QUALITY", "_UBYTE", "WRITE", &qpntr[0], &itemp, status );
qmap = qpntr[0];
/* we assume the number of elements in "qual" is the same as in "qmap" */
if (*status == SAI__OK) {
size_t k;
/* if we only have 8 or fewer bits active we can just compress
by mapping them to the lower 8 bits. This will work if we also
set the IRQ quality names in the NDF. */
if (nqual == 0 ) {
/* easy */
memset( qmap, 0, nout * smf_dtype_sz( SMF__UBYTE, status ) );
} else if ( nqual <= 8 ) {
size_t curbit = 0;
/* and the quality names. Start at lowbit and go to highbit
knowing that we have shifted them down so that lowbit in qual
is bit 0 in NDF. */
for (k=lowbit; k<=(size_t)highbit; k++) {
if (qcount[k]) {
int fixed = 0; /* is bit fixed? */
const char * qdesc = NULL; /* Description of quality */
const char * qstr = NULL; /* Quality string identifier */
curbit++;
qstr = smf_qual_str( family, 1, k, &qdesc, status );
irqAddqn( qlocs, qstr, 0, qdesc, status );
irqFxbit( qlocs, qstr, curbit, &fixed, status );
}
}
/* shift them down */
for( iw = 0; iw < nw; iw++ ) {
pdata = job_data + iw;
pdata->operation = 2;
pdata->qmap = qmap;
pdata->highbit = highbit;
pdata->lowbit = lowbit;
for( k=0; k<nqbits; k++ ) {
pdata->qcount[k] = qcount[k];
}
thrAddJob( wf, 0, pdata, smf1_qual_unmap, 0, NULL, status );
}
thrWait( wf, status );
} else {
size_t curbit = 0;
/* Quality names are now needed and we have to write them
all out because we have not compressed the bits in the
output quality array we've only compressed the input.
To limit the number of active bits we'd have to copy the
compressed bits to the output and then set the quality
names but IRQ does not let you do that so you would need
to run through the entire array first counting which bits
were used. */
for (k=0; k<SMF__NQBITS_TCOMP; k++) {
int fixed = 0;
const char * qdesc = NULL; /* Description of quality */
const char * qstr = NULL; /* Quality string identifier */
qstr = smf_qual_str( SMF__QFAM_TCOMP, 1, k, &qdesc, status );
/* Set the quality name */
irqAddqn( qlocs, qstr, 0, qdesc, status );
curbit++;
irqFxbit( qlocs, qstr, curbit, &fixed, status );
}
/* compress them */
for( iw = 0; iw < nw; iw++ ) {
pdata = job_data + iw;
pdata->operation = 3;
pdata->qmap = qmap;
thrAddJob( wf, 0, pdata, smf1_qual_unmap, 0, NULL, status );
}
thrWait( wf, status );
}
}
/* Unmap quality */
ndfUnmap( indf, "QUALITY", status );
/* Set the badbits mask to enable all quality by default.
Do not do this for MAP quality at the moment. */
if (family != SMF__QFAM_MAP) ndfSbb( 255, indf, status );
/* release IRQ resources */
irqRlse( &qlocs, status );
}
CLEANUP:
/* Tidy up */
qual = astFree( qual );
job_data = astFree( job_data );
return NULL;
}
smf_qual_t * smf_qual_unmap( int indf, smf_qfam_t family, smf_qual_t * qual, int * status ) {
int canwrite = 0; /* can we write to the file? */
size_t nqbits = 0; /* Number of quality bits in this family */
if (*status != SAI__OK) goto CLEANUP;
/* do nothing if there is no quality */
if (!qual) return NULL;
/* if we do not have an NDF identifier we just free the memory */
if (indf == NDF__NOID) goto CLEANUP;
/* See if we have WRITE access to the file */
ndfIsacc( indf, "WRITE", &canwrite, status );
/* if we have WRITE access and the data were not mapped we have
to copy to the file. Also check we have a non-NULL input pointer.
If the data were mapped we still have to make sure the quality names
are stored. */
if ( canwrite && qual ) {
int highbit = -1; /* highest bit used */
size_t i;
int itemp;
int lowbit = -1; /* Lowest bit used */
size_t nout;
int nqual = 0;
void *qpntr[1];
size_t qcount[SMF__NQBITS]; /* statically allocate the largest array */
IRQLocs *qlocs;
unsigned char * qmap;
int there;
ndfMsg( "FILE", indf );
msgOutif( MSG__DEBUG, "", "Finalising quality for file ^FILE", status);
if (family == SMF__QFAM_TCOMP ) {
/* note that TCOMP is not an allowed quality because SMURF should not be
using it anywhere in a permanent way. */
*status = SAI__ERROR;
ndfMsg( "NDF", indf );
errRepf( "", "Unsupported quality family '%s' for quality unmapping of "
"file ^NDF", status, smf_qfamily_str(family,status) );
goto CLEANUP;
} else if (family == SMF__QFAM_NULL) {
/* In this case we have to assume that we just cast the quality
to UBYTE and copy it without changing anything or naming the
entries. Use a simple type conversion. */
ndfMap( indf, "QUALITY", "_UBYTE", "WRITE", &qpntr[0], &itemp, status );
qmap = qpntr[0];
nout = itemp;
for (i = 0; i<nout; i++) {
qmap[i] = qual[i];
}
ndfUnmap( indf, "QUALITY", status );
/* Turn on all quality */
ndfSbb( 255, indf, status );
/* we are finished so jump to tidy up */
goto CLEANUP;
}
/* work out how many quality items are in this family */
nqbits = smf_qfamily_count( family, status );
/* initialize qcount */
for (i=0; i<SMF__NQBITS; i++) {
qcount[i] = 0;
}
/* how many pixels in NDF (assumed to be number in quality) */
ndfSize( indf, &itemp, status );
nout = itemp;
/* Work out which bits are actually used */
if (*status == SAI__OK) {
size_t k;
/* now we try to be a bit clever. It may be a mistake since we have to
do multiple passes through "qual". First determine how many quality
bits are actually set. */
for (i = 0; i<nout; i++) {
/* try all the bits */
for( k=0; k<nqbits; k++ ) {
if( qual[i] & BIT_TO_VAL(k) ) {
qcount[k]++;
}
}
}
/* see how many we got */
for (k=0; k<nqbits; k++) {
if ( qcount[k] ) {
nqual++;
highbit = k;
if (lowbit < 0) lowbit = k;
}
}
}
/* for IRQ we need to ensure the SMURF extension exists so open and annul it if it is missing.
We are completely rewriting any IRQ information so we have to delete any previously existing
IRQ extension. */
irqDelet( indf, status );
ndfXstat( indf, SMURF__EXTNAME, &there, status );
if (!there) {
HDSLoc * smurfloc = NULL;
/* Create SMURF extension if it does not already exist */
ndfXnew( indf, SMURF__EXTNAME, SMURF__EXTTYPE, 0, NULL, &smurfloc, status );
if (smurfloc) datAnnul( &smurfloc, status );
}
irqNew( indf, SMURF__EXTNAME, &qlocs, status );
/* malloced so we need to map and copy over the values. IRQ
names need to be set BEFORE we copy. */
/* Map the quality component with WRITE access */
ndfMap( indf, "QUALITY", "_UBYTE", "WRITE", &qpntr[0], &itemp, status );
qmap = qpntr[0];
/* we assume the number of elements in "qual" is the same as in "qmap" */
if (*status == SAI__OK) {
size_t k;
/* if we only have 8 or fewer bits active we can just compress
by mapping them to the lower 8 bits. This will work if we also
set the IRQ quality names in the NDF. */
if (nqual == 0 ) {
/* easy */
memset( qmap, 0, nout * smf_dtype_sz( SMF__UBYTE, status ) );
} else if ( nqual <= 8 ) {
size_t curbit = 0;
/* and the quality names. Start at lowbit and go to highbit
knowing that we have shifted them down so that lowbit in qual
is bit 0 in NDF. */
for (k=lowbit; k<=(size_t)highbit; k++) {
if (qcount[k]) {
int fixed = 0; /* is bit fixed? */
const char * qdesc = NULL; /* Description of quality */
const char * qstr = NULL; /* Quality string identifier */
curbit++;
qstr = smf_qual_str( family, 1, k, &qdesc, status );
irqAddqn( qlocs, qstr, 0, qdesc, status );
irqFxbit( qlocs, qstr, curbit, &fixed, status );
}
}
/* shift them down */
for (i=0; i<nout; i++) {
curbit = 0;
qmap[i] = 0;
for (k=lowbit; k<=(size_t)highbit; k++) {
/* was this bit used by this data array? */
if (qcount[k]) {
/* was the bit set for this location? */
if ( qual[i]&BIT_TO_VAL(k)) {
qmap[i] |= BIT_TO_VAL(curbit);
}
curbit++;
}
}
}
} else {
size_t curbit = 0;
/* Quality names are now needed and we have to write them
all out because we have not compressed the bits in the
output quality array we've only compressed the input.
To limit the number of active bits we'd have to copy the
compressed bits to the output and then set the quality
names but IRQ does not let you do that so you would need
to run through the entire array first counting which bits
were used. */
for (k=0; k<SMF__NQBITS_TCOMP; k++) {
int fixed = 0;
const char * qdesc = NULL; /* Description of quality */
const char * qstr = NULL; /* Quality string identifier */
qstr = smf_qual_str( SMF__QFAM_TCOMP, 1, k, &qdesc, status );
/* Set the quality name */
irqAddqn( qlocs, qstr, 0, qdesc, status );
curbit++;
irqFxbit( qlocs, qstr, curbit, &fixed, status );
}
/* compress them */
for (i = 0; i<nout; i++) {
qmap[i] = 0;
if (qual[i]) {
if ( qual[i] & (SMF__Q_BADDA|SMF__Q_BADB|SMF__Q_NOISE) ) {
qmap[i] |= SMF__TCOMPQ_BAD;
}
if ( qual[i] & (SMF__Q_APOD|SMF__Q_PAD) ) {
qmap[i] |= SMF__TCOMPQ_ENDS;
}
if ( qual[i] & (SMF__Q_JUMP|SMF__Q_SPIKE|SMF__Q_FILT|SMF__Q_EXT|SMF__Q_LOWAP|SMF__Q_BADEF) ) {
qmap[i] |= SMF__TCOMPQ_BLIP;
}
if ( qual[i] & (SMF__Q_COM) ) {
qmap[i] |= SMF__TCOMPQ_MATCH;
}
if ( qual[i] & (SMF__Q_STAT) ) {
qmap[i] |= SMF__TCOMPQ_TEL;
}
if (qmap[i] == 0 ) {
/* something went wrong. We missed a quality bit somewhere */
msgOutiff(MSG__QUIET, "", FUNC_NAME ": Untested quality bit found"
" in position %zu with value %u", status,
i, (unsigned int)qual[i]);
}
}
}
}
}
/* Unmap quality */
ndfUnmap( indf, "QUALITY", status );
/* Set the badbits mask to enable all quality by default.
Do not do this for MAP quality at the moment. */
if (family != SMF__QFAM_MAP) ndfSbb( 255, indf, status );
/* release IRQ resources */
irqRlse( &qlocs, status );
}
CLEANUP:
/* Tidy up */
if (qual) qual = astFree( qual );
return NULL;
}
