void smf_flat_write( smf_flatmeth flatmeth, const char * flatname,
double refres, const smfData * bolval,
const smfData * powref, const smfData * bolref,
const smfData * polyfit, const Grp * prvgrp, int * status ) {
size_t colsize; /* number of columns */
double *dbuf = NULL; /* input double buffer for mean data */
double *dvar = NULL; /* input double buffer for variance of data */
char fitsrec[SC2STORE__MAXFITS*SZFITSCARD+1]; /* Store for FITS records */
int *ibuf = NULL; /* int buffer for mean data */
int indf = NDF__NOID; /* NDF identifier for output file */
size_t ncards; /* number of fits cards */
size_t numbols; /* number of bolometers */
double *outvar = NULL; /* buffer for variance of data */
int place = NDF__NOPL; /* Dummy placeholder for NDF */
size_t rowsize; /* number of rows */
JCMTState *state = NULL; /* State for this flatfield */
sc2ast_subarray_t subnum; /* subarray number */
AstFrameSet *result, *spacefset;
AstLutMap *heatmap;
AstFrame *heatfrm;
int *dksquid; /* pointer to dummy dark SQUID data */
size_t j; /* loop counter */
int jig_vert[1][2]; /* dummy jiggle vertices */
double jig_path[1][2]; /* dummy jiggle path */
size_t nframes = 0; /* Number of frames in bolval */
int npath = 0; /* size of jiggle path */
int nvert = 0; /* number of jiggle vertices */
char *xmlfile = NULL; /* dummy xmlfile name */
if (*status != SAI__OK) return;
if (!bolval->da) {
*status = SAI__ERROR;
errRep( "", "No flatfield solution provided for writing",
status );
return;
}
if (!bolval->da->heatval) {
*status = SAI__ERROR;
errRep( "", "Must provide heater values in DA struct to smf_flat_write"
" (possible programming error)", status );
return;
}
/* note that colsize is the number of rows and rowsize is the number of
columns */
colsize = (bolval->dims)[SC2STORE__ROW_INDEX];
rowsize = (bolval->dims)[SC2STORE__COL_INDEX];
numbols = colsize * rowsize;
nframes = (bolval->dims)[2];
/* Make sure we have a FLAT header that reflects this file
as the flatfield solution */
smf_fits_updateS( bolval->hdr, "FLAT", flatname, "Name of flat-field file",
status );
/* Create a FITS header for DA */
smf_fits_export2DA( bolval->hdr->fitshdr, &ncards, fitsrec, status );
/* Copy the data as integers so it can be written to data file. To
prevent overflow in the variance we store that as doubles */
ibuf = astMalloc( (numbols * nframes)*sizeof(*ibuf) );
outvar = astMalloc( (numbols * nframes)*sizeof(*outvar) );
dbuf = (bolval->pntr)[0];
dvar = (bolval->pntr)[1];
if (*status == SAI__OK) {
for (j = 0; j < (nframes * numbols); j++) {
/* These started off as integers so the mean value must fit in
an integer */
if ( dbuf[j] == VAL__BADD) {
ibuf[j] = VAL__BADI;
} else {
ibuf[j] = (int)dbuf[j];
}
/* Same data type so no need to convert bad values */
if (dvar) {
outvar[j] = dvar[j];
} else {
outvar[j] = VAL__BADD;
}
}
}
/* get subarray number */
smf_find_subarray( bolval->hdr, NULL, 0, &subnum, status );
/* Create dummy components for output file */
dksquid = astCalloc ( rowsize* nframes, sizeof(*dksquid) );
jig_vert[0][0] = 0;
jig_vert[0][1] = 0;
jig_path[0][0] = 0.0;
jig_path[0][1] = 0.0;
sc2store_setcompflag ( SC2STORE__NONE, status );
sc2store_wrtstream ( flatname, subnum, ncards,
fitsrec, colsize, rowsize, nframes,
(bolref->dims)[2], refres, 0, smf_flat_methstring( flatmeth, status ),
bolval->hdr->allState, NULL,
ibuf, dksquid, (bolref->pntr)[0], (powref->pntr)[0],
"FLATCAL", NULL, NULL, jig_vert,
nvert, jig_path, npath, xmlfile, status );
sc2store_free ( status );
/* To copy in the variance and modify fix up the WCS we need to reopen
the file */
ndfOpen( NULL, flatname, "UPDATE", "OLD", &indf, &place, status );
/* make sure that history is not written twice */
ndfHsmod( "SKIP", indf, status );
if (outvar) {
void *pntr[3];
int el;
ndfStype( "_DOUBLE", indf, "VARIANCE", status );
ndfMap( indf, "VARIANCE", "_DOUBLE", "WRITE", pntr, &el, status );
if (*status == SAI__OK) {
memcpy( pntr[0], outvar, sizeof(*outvar)*el );
}
}
/* For the WCS a time frame is less relevant than heater settings */
astBegin;
/* Create frame for focal plane coordinates */
sc2ast_createwcs( subnum, NULL, NULL, NULL, NO_FTS, &spacefset, status );
/* Copy it to make sure we do not mess with the cache */
result = astCopy( spacefset );
/* and switch to BOLO frame which is best for bolometer analysis */
{
int frnum = AST__NOFRAME;
kpg1Asffr( result, "BOLO", &frnum, status );
if (frnum != AST__NOFRAME) astSetI( result, "CURRENT", frnum );
}
/* Create a simple frame for heater settings */
heatfrm = astFrame( 1, "Domain=HEATER,Label(1)=Heater Setting" );
heatmap = astLutMap( nframes, bolval->da->heatval, 1.0, 1.0, " " );
/* Append the heater axis to the spatial frameset */
atlAddWcsAxis( result, (AstMapping *)heatmap, (AstFrame *) heatfrm,
NULL, NULL, status );
/* write it to the NDF */
ndfPtwcs( result, indf, status );
/* Write provenance information */
if (prvgrp) {
size_t size = grpGrpsz( prvgrp, status );
char prvname[ 2 * PAR__SZNAM + 1];
smf_get_taskname( NULL, prvname, status );
for (j=1; j<=size; j++) {
smf_accumulate_prov( NULL, prvgrp, j, indf, prvname, NULL, status );
}
}
/* Write the polynomial expansion into an extension */
if (polyfit) {
char fitfile[GRP__SZNAM+1];
int fndf = NDF__NOID;
place = NDF__NOPL;
one_strlcpy( fitfile, flatname, sizeof(fitfile), status );
one_strlcat( fitfile, ".MORE.SMURF.FLATFIT", sizeof(fitfile), status );
/* create the file */
smf_write_smfData( polyfit, NULL, fitfile, NULL, 0, NDF__NOID,
MSG__VERB, 0, status );
/* Same WCS as the main file */
ndfOpen( NULL, fitfile, "UPDATE", "OLD", &fndf, &place, status );
ndfPtwcs( result, fndf, status );
ndfAnnul( &fndf, status );
}
astEnd;
ndfAnnul( &indf, status);
if (ibuf) ibuf = astFree( ibuf );
if (outvar) outvar = astFree( outvar );
if (dksquid) dksquid = astFree( dksquid );
if (state) state = astFree( state );
}
void clumpinfo( int *status ) {
/*
*+
* Name:
* CLUMPINFO
* Purpose:
* Obtain information about one or more previously identified clumps.
* Language:
* C
* Type of Module:
* ADAM A-task
* Description:
* This application returns various items of information about a
* single clump, or a collection of clumps, previously identified
* using FINDCLUMPS or EXTRACTCLUMPS.
* Usage:
* clumpinfo ndf clumps quiet
* ADAM Parameters:
* CLUMPS = LITERAL (Read)
* Specifies the indices of the clumps to be included in the
* returned information. It can take any of the following values:
*
* - "ALL" or "*" -- All clumps.
*
* - "xx,yy,zz" -- A list of clump indices.
*
* - "xx:yy" -- Clump indices between xx and yy inclusively. When
* xx is omitted the range begins from one; when yy is omitted the
* range ends with the final clump index.
*
* - Any reasonable combination of above values separated by
* commas.
* FLBND( ) = _DOUBLE (Write)
* The lower bounds of the bounding box enclosing the selected
* clumps in the current WCS Frame of the input NDF. Celestial axis
* values are always in units of radians, but spectral axis units
* will be in the spectral units used by the current WCS Frame.
* FUBND( ) = _DOUBLE (Write)
* The upper bounds of the bounding box enclosing the selected
* clumps. See parameter FLBND for more details.
* LBOUND( ) = _INTEGER (Write)
* The lower pixel bounds of bounding box enclosing the selected
* clumps.
* NCLUMPS = _INTEGER (Write)
* The total number of clumps descrriptions stored within the supplied
* NDF.
* NDF = NDF (Read)
* The NDF defining the previously identified clumps. This
* should contain a CUPID extension describing all the identified
* clumps, in the format produced by FINDCLUMPS or EXTRACTCLUMPS.
* QUIET = _LOGICAL (Read)
* If TRUE, then no information is written out to the screen,
* although the output parameters are still assigned values. [FALSE]
* UBOUND( ) = _INTEGER (Write)
* The upper pixel bounds of bounding box enclosing the selected
* clumps.
* Notes:
* - It is hoped to extend the range of information reported by this
* application as new requirements arise.
* Synopsis:
* void clumpinfo( int *status );
* Copyright:
* Copyright (C) 2007 Particle Physics & Astronomy Research Council.
* All Rights Reserved.
* Licence:
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License as
* published by the Free Software Foundation; either version 2 of
* the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be
* useful, but WITHOUT ANY WARRANTY; without even the implied
* warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street,Fifth Floor, Boston, MA
* 02110-1301, USA
* Authors:
* DSB: David S. Berry
* {enter_new_authors_here}
* History:
* 22-MAR-2007 (DSB):
* Original version.
* {enter_further_changes_here}
* Bugs:
* {note_any_bugs_here}
*-
*/
/* Local Variables: */
AstFrame *cfrm; /* Pointer to current WCS Frame */
AstMapping *cmap; /* Pointer to PIXEL->current Frame Mapping */
CupidClumpInfo info; /* Structure holding returned information */
Grp *grp = NULL; /* GRP group holding input NDF name */
HDSLoc *aloc = NULL; /* Locator for CLUMPS array in CUPID extension */
HDSLoc *cloc = NULL; /* Locator for a single CLUMP structure */
HDSLoc *xloc = NULL; /* Locator for CUPID extension */
char *p; /* Pointer into tmpstr string */
char tmpstr[ 100 ]; /* Buffer for temporary strings */
const char *dom; /* Pointer to axis Domain name */
double flbnd[ NDF__MXDIM ]; /* Lower bounds of WCS bounding box */
double fubnd[ NDF__MXDIM ]; /* Upper bounds of WCS bounding box */
double plbnd[ NDF__MXDIM ]; /* Lower bounds of PIXEL bounding box */
double pubnd[ NDF__MXDIM ]; /* Upper bounds of PIXEL bounding box */
int *clump_flags = NULL; /* Flags indicating if each clump is to be used */
int *clump_indices = NULL;/* List of indices of clumps to be used */
int i; /* Loop count */
int iclump; /* One-based clump index */
int indf; /* NDF identifier for input NDF */
int ipix; /* Index of PIXEL Frame */
size_t nclumps; /* No. of clump descriptions within the supplied NDF */
int nuse; /* Number of clumps to be used */
int primary; /* Value for locator primary flag */
int quiet; /* Supress screen output? */
size_t size; /* Number of values in group "*grp" */
int there; /* Does the enquired object exist? */
/* Abort if an error has already occurred. */
if( *status != SAI__OK ) return;
/* Begin an AST context */
astBegin;
/* Start an NDF context */
ndfBegin();
/* Obtain the input NDF and get a locator for the array of clump
descriptions within it.
----------------------------------------------------------------- */
/* Get an identifier for the input NDF. We use NDG (via kpg1_Rgndf)
instead of calling ndfAssoc directly since NDF/HDS has problems with
file names containing spaces, which NDG does not have. */
kpg1Rgndf( "NDF", 1, 1, "", &grp, &size, status );
ndgNdfas( grp, 1, "READ", &indf, status );
grpDelet( &grp, status );
/* Check the NDF has a suitable CUPID extension containing an array of
clump cut-outs. Get an HDS locator for the array. */
ndfXstat( indf, "CUPID", &there, status );
if( !there ) {
if( *status == SAI__OK ) {
*status = SAI__ERROR;
ndfMsg( "NDF", indf );
errRep( "", "The NDF \"^NDF\" does not contain a CUPID extension "
"such as created by FINDCLUMPS or EXTRACTCLUMPS.", status );
}
} else {
ndfXloc( indf, "CUPID", "READ", &xloc, status );
datThere( xloc, "CLUMPS", &there, status );
if( !there ) {
if( *status == SAI__OK ) {
*status = SAI__ERROR;
ndfMsg( "NDF", indf );
errRep( "", "The CUPID extension within NDF \"^NDF\" does not "
"contain an array of clumps such as created by "
"FINDCLUMPS or EXTRACTCLUMPS.", status );
}
} else {
datFind( xloc, "CLUMPS", &aloc, status );
primary = 1;
datPrmry( 1, &aloc, &primary, status );
}
datAnnul( &xloc, status );
}
/* Abort if we have no clumps array locator, or if an error occurred. */
if( !aloc || *status != SAI__OK ) goto L999;
/* Calculate the required clump information, and store it in the "info"
structure.
----------------------------------------------------------------- */
/* Indicate that the structure holding the returned information has not
yet been initialised. */
info.init = 0;
/* Get the WCS FrameSet from the input NDF, and store a pointer to it in
the "info" structure. */
kpg1Gtwcs( indf, &(info.iwcs), status );
/* Get the number of clumps defined within the input NDF. */
datSize( aloc, &nclumps, status );
/* Get the list of clump indices to iclude in the returned information. */
clump_flags = astMalloc( sizeof( int )*nclumps );
clump_indices = astMalloc( sizeof( int )*nclumps );
kpg1Gilst( 1, (int) nclumps, (int) nclumps, "CLUMPS", clump_flags, clump_indices,
&nuse, status );
/* Loop round all clumps that are to be used. */
for( i = 0; i < nuse && *status == SAI__OK; i++ ) {
iclump = clump_indices[ i ];
/* Get a locator for this clump. */
datCell( aloc, 1, &iclump, &cloc, status );
/* Update the returned information to include this clump. */
cupidClumpInfo1( cloc, &info, status );
/* Annul the clump structure locator. */
datAnnul( &cloc, status );
}
/* Write out the information to the screen and to appropriate output
parameters.
----------------------------------------------------------------- */
/* See if screen output is required. */
parGet0l( "QUIET", &quiet, status );
if( !quiet ) msgBlank( status );
/* The number of clumps defined within the input NDF... */
parPut0i( "NCLUMPS", (int) nclumps, status );
if( ! quiet ) {
msgSeti( "NCLUMPS", (int) nclumps );
msgOut( "", " Total no. of clumps: ^NCLUMPS", status );
}
/* Pixel index bounding box... */
parPut1i( "LBOUND", info.npix, info.lbnd, status );
parPut1i( "UBOUND", info.npix, info.ubnd, status );
if( !quiet ) {
p = tmpstr + sprintf( tmpstr, "( " );
for( i = 0; i < info.npix; i++) {
p += sprintf( p, "%d:%d", info.lbnd[ i ], info.ubnd[ i ] );
if( i < info.npix - 1 ) p += sprintf( p, ", " );
}
p += sprintf( p, " )" );
msgSetc( "SECTION", tmpstr );
msgOut( "", " Pixel index bounding box: ^SECTION", status );
}
/* WCS bounding box (first convert the pixel index bounding box into WCS
coords)... */
cfrm = astGetFrame( info.iwcs, AST__CURRENT );
kpg1Asffr( info.iwcs, "PIXEL", &ipix, status );
cmap = astGetMapping( info.iwcs, ipix, AST__CURRENT );
for( i = 0; i < info.npix; i++ ) {
plbnd[ i ] = info.lbnd[ i ] - 1.0;
pubnd[ i ] = info.ubnd[ i ];
}
for( i = 0; i < info.nwcs; i++ ) {
astMapBox( cmap, plbnd, pubnd, 1, i + 1, flbnd + i, fubnd + i,
NULL, NULL);
}
astNorm( cfrm, flbnd );
astNorm( cfrm, fubnd );
parPut1d( "FLBND", info.nwcs, flbnd, status );
parPut1d( "FUBND", info.nwcs, fubnd, status );
if( !quiet ) {
msgOut( "", " WCS bounding box:", status );
for( i = 0; i < info.nwcs; i++) {
msgSetc( "L", astFormat( cfrm, i + 1, flbnd[ i ] ) );
msgSetc( "U", astFormat( cfrm, i + 1, fubnd[ i ] ) );
sprintf( tmpstr, "Domain(%d)", i + 1 );
dom = astGetC( cfrm, tmpstr );
if( dom && strcmp( dom, "SKY" ) ) {
sprintf( tmpstr, "Unit(%d)", i + 1 );
msgSetc( "UNT", astGetC( cfrm, tmpstr ) );
} else {
msgSetc( "UNT", "" );
}
sprintf( tmpstr, "Label(%d)", i + 1 );
msgSetc( "LAB", astGetC( cfrm, tmpstr ) );
msgOut( "", " ^LAB: ^L -> ^U ^UNT", status );
}
}
if( !quiet ) msgBlank( status );
/* Tidy up.
-------- */
L999:
;
/* Free resources. */
clump_flags = astFree( clump_flags );
clump_indices = astFree( clump_indices );
if( aloc ) datAnnul( &aloc, status );
/* End the NDF context */
ndfEnd( status );
/* End the AST context */
astEnd;
/* If an error has occurred, issue another error report identifying the
program which has failed (i.e. this one). */
if( *status != SAI__OK ) {
errRep( "CLUMPINFO_ERR", "CLUMPINFO: Failed to obtain information "
"about one or more previously identified clumps.", status );
}
}