static void smf__calc_flatobskey( smfHead *hdr, char * keystr, size_t keylen,
int *status ) {
int curheat = 0;
int detbias = 0;
char subarray[10];
double shutter = 0.0;
size_t nwrite = 0;
int utdate = 0;
if (*status != SAI__OK) return;
if (!hdr) return;
/* get reference heater value, bias, shutter and subarray string */
/* PIXHEAT and DETBIAS are not written by the simulator so we default
those to 0 */
smf_getfitsi( hdr, "PIXHEAT", &curheat, status );
if (*status == SMF__NOKWRD) errAnnul(status);
/* As of September 1st we heater track after doing the flat ramp.
This means that the heater value will have changed slightly between
ramp and science. */
smf_getfitsi( hdr, "UTDATE", &utdate, status );
if (utdate >= 20110901 &&
(hdr->obstype == SMF__TYP_SCIENCE || hdr->obstype == SMF__TYP_POINTING)) {
curheat = 0;
}
smf_getfitsi( hdr, "DETBIAS", &detbias, status );
if (*status == SMF__NOKWRD) errAnnul(status);
smf_getfitsd( hdr, "SHUTTER", &shutter, status );
smf_find_subarray( hdr, subarray, sizeof(subarray), NULL,
status );
if (*status != SAI__OK) return;
nwrite = snprintf(keystr, keylen, "%s_%s_%.1f_%d_%d",
hdr->obsidss, subarray, shutter, detbias, curheat );
if (nwrite >= keylen) {
/* The string was truncated */
*status = SMF__STRUN;
errRep("", "String truncation forming flatfield key (Possible programming error)",
status );
}
}
static void
NDF_dealloc(NDF* self)
{
int status = SAI__OK;
errBegin(&status);
if (self->_ndfid != NDF__NOID) ndfAnnul( &self->_ndfid, &status);
if (status != SAI__OK) errAnnul(&status);
errEnd(&status);
PyObject_Del( self );
}
void smf_flatfield ( ThrWorkForce *wf, const smfData *idata, const smfArray * flats, AstKeyMap * heateffmap,
smfData **odata, const int flags, int *status ) {
if ( *status != SAI__OK ) return;
/* See if data are flatfielded */
smf_check_flat( idata, status );
/* Data are flatfielded if status set to SMF__FLATN */
if ( *status == SMF__FLATN ) {
errAnnul(status);
/* check *odata */
if ( *odata == NULL) {
msgOutif(MSG__DEBUG1," ",
"OK, data are flatfielded and output struct is NULL: cloning input",
status);
/* If NULL then we need to clone idata to odata i.e. copy the
pointer ONLY */
smf_clone_data( idata, odata, status );
} else {
msgOutif(MSG__DEBUG1," ",
"OK, data are flatfielded and odata exists", status);
/* Check and set */
smf_check_smfData( idata, *odata, flags, status );
}
} else if ( *status == SAI__OK ) {
/* OK data are not flatfielded: create smfData based on input and
apply flatfield */
/* Check if *odata exists */
if ( *odata == NULL) {
msgOutif(MSG__DEBUG1," ","Data not flatfielded, no output data file.", status);
/* If NULL then we need create odata not associated with a file
(i.e. leave smfFile NULL) */
/* Allocate space for *odata and all necessary cpts */
/* Set the rawconvert flag to return doubles in the DATA array */
*odata = smf_deepcopy_smfData( wf, idata, 1, flags, 0, 0, status );
} else {
/* OK, *odata exists */
msgOutif(MSG__DEBUG1," ","Data not flatfielded, output data file exists.", status);
/* Check and set */
smf_check_smfData( idata, *odata, flags, status );
}
/* Disable the check because we know that we have just checked */
smf_flatfield_smfData( *odata, flats, heateffmap, 1, status );
}
}
void smf_request_mask( ThrWorkForce *wf, const char *param, smfArray ** bbms, int *status) {
Grp * bbmgrp = NULL;
size_t nbbm;
/* initialise return value */
*bbms = NULL;
if (*status != SAI__OK) return;
kpg1Rgndf( param, 0, 1, "", &bbmgrp, &nbbm, status );
if (*status == PAR__NULL) {
bbms = NULL;
errAnnul( status );
} else {
smf_open_group( wf, bbmgrp, NULL, bbms, status );
}
if (bbmgrp) grpDelet( &bbmgrp, status );
}
void findback( int *status ){
/*
*+
* Name:
* FINDBACK
* Purpose:
* Estimate the background in an NDF by removing small scale structure.
* Language:
* C
* Type of Module:
* ADAM A-task
* Synopsis:
* void findback( int *status );
* Description:
* This application uses spatial filtering to remove structure with a
* scale size less than a specified size from a 1, 2, or 3 dimensional
* NDF, thus producing an estimate of the local background within the NDF.
*
* The algorithm proceeds as follows. A filtered form of the input data
* is first produced by replacing every input pixel by the minimum of
* the input values within a rectangular box centred on the pixel.
* This filtered data is then filtered again, using a filter that
* replaces every pixel value by the maximum value in a box centred on
* the pixel. This produces an estimate of the lower envelope of the data,
* but usually contains unacceptable sharp edges. In addition, this
* filtered data has a tendency to hug the lower envelope of the
* noise, thus under-estimating the true background of the noise-free
* data. The first problem is minimised by smoothing the background
* estimate using a filter that replaces every pixel value by the mean
* of the values in a box centred on the pixel. The second problem
* is minimised by estimating the difference between the input data
* and the background estimate within regions well removed from any
* bright areas. This difference is then extrapolated into the bright
* source regions and used as a correction to the background estimate.
* Specifically, the residuals between the input data and the initial
* background estimate are first formed, and residuals which are more
* than three times the RMS noise are set bad. The remaining residuals
* are smoothed with a mean filter. This smoothing will replace a lot
* of the bad values rejected above, but may not remove them all. Any
* remaining bad values are estimated by linear interpolation between
* the nearest good values along the first axis. The interpolated
* residuals are then smoothed again using a mean filter, to get a
* surface representing the bias in the initial background estimate.
* This surface is finally added onto the initial background estimate
* to obtain the output NDF.
* Usage:
* findback in out box
* ADAM Parameters:
* BOX() = _INTEGER (Read)
* The dimensions of each of the filters, in pixels. Each value
* should be odd (if an even value is supplied, the next higher odd
* value will be used). The number of values supplied should not
* exceed the number of significant (i.e. more than one element)
* pixel axes in the input array. If any trailing values of 1 are
* supplied, then each pixel value on the corresponding axes
* will be fitted independently of its neighbours. For instance,
* if the data array is 3-dimensional, and the third BOX value is 1,
* then each x-y plane will be fitted independently of the neighbouring
* planes. If the NDF has more than 1 pixel axis but only 1 value is
* supplied, then the same value will be used for the both the first
* and second pixel axes (a value of 1 will be assumed for the third
* axis if the input array is 3-dimensional).
* MSG_FILTER = _CHAR (Read)
* Controls the amount of diagnostic information reported. This is the
* standard messaging level. The default messaging level is NORM (2).
* A value of NONE or 0 will suppress all screen output. VERB (3) will
* indicate progress through the various stages of the algorithm. [NORM]
* IN = NDF (Read)
* The input NDF.
* RMS = _DOUBLE (Read)
* Specifies a value to use as the global RMS noise level in the
* supplied data array. The suggested default value is the square root
* of the mean of the values in the input NDF's Variance component.
* If the NDF has no Variance component, the suggested default
* is based on the differences between neighbouring pixel values,
* measured over the entire input NDF. If multiple slices within the
* NDF are to be processed independently (see parameter BOX), it
* may be more appropriate for a separate default RMS to be calculated
* for each slice. This will normally be the case if the noise could
* be different in each of the slices. In such cases a null (!) can
* be supplied for the RMS parameter, which forces a separate
* default RMS value to be found and used for each slice. Any
* pixel-to-pixel correlation in the noise can result in these
* defaults being too low.
* SUB = _LOGICAL (Read)
* If a TRUE value is supplied, the output NDF will contain the
* difference between the supplied input data and the estimated
* background. If a FALSE value is supplied, the output NDF will
* contain the estimated background itself. [FALSE]
* OUT = NDF (Write)
* The output NDF containing either the estimated background, or the
* background-subtracted input data, as specified by parameter SUB.
* Notes:
* - Smoothing cubes in 3 dimensions can be very slow.
* Copyright:
* Copyright (C) 2009 Science and Technology Facilities Council.
* Copyright (C) 2006, 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
* TIMJ: Tim Jenness (JAC, Hawaii)
* {enter_new_authors_here}
* History:
* 13-SEP-2006 (DSB):
* Original version.
* 19-MAR-2007 (DSB):
* - Added parameters SUB and RMS.
* - Fix bug that left the output NDF uninitialised if ILEVEL is set
* non-zero.
* - Use generic data type handling as in FINDCLUMPS.
* 14-JAN-2009 (TIMJ):
* Use MERS for message filtering.
* 29-JUL-2009 (TIMJ):
* Rename ILEVEL to MSG_FILTER
* 17-MAY-2011 (DSB):
* Use sqrt rather than sqrtf when calculating RMS.
* 12-SEP-2011 (DSB):
* Process slices in separate threads.
* {enter_further_changes_here}
*-
*/
/* Local Variables: */
CupidFindback0Data *job_data; /* Pointer to data for all jobs */
CupidFindback0Data *pdata; /* Pointer to data for current job */
Grp *grp; /* GRP identifier for configuration settings */
ThrWorkForce *wf = NULL; /* Pool of persistent worker threads */
char dtype[ 21 ]; /* HDS data type for output NDF */
char itype[ 21 ]; /* HDS data type to use when processing */
double *ipv; /* Pointer to Variance array */
double *pd1; /* Pointer to double precision input data */
double *pd2; /* Pointer to double precision output data */
double rms; /* Global rms error in data */
double sum; /* Sum of variances */
float *pf1; /* Pointer to single precision input data */
float *pf2; /* Pointer to single precision output data */
int *old_status; /* Pointer to original status value */
int box[ 3 ]; /* Dimensions of each cell in pixels */
int dim[ NDF__MXDIM ]; /* Dimensions of each NDF pixel axis */
int el; /* Number of elements mapped */
int i; /* Loop count */
int indf1; /* Identifier for input NDF */
int indf2; /* Identifier for output NDF */
int islice; /* Slice index */
int iystep; /* Index of slice in ydirection */
int izstep; /* Index of slice in z direction */
int lbnd[ NDF__MXDIM ]; /* Lower pixel bounds of slice */
int n; /* Number of values summed in "sum" */
int ndim; /* Total number of pixel axes in NDF */
int newalg; /* Use experimental algorithm variations? */
int nsdim; /* Number of significant pixel axes in NDF */
int nslice; /* Number of slices to process */
int nval; /* Number of values supplied */
int nystep; /* Number of independent y slices */
int nzstep; /* Number of slices in z direction */
int sdim[ 3 ]; /* Dimensions of each significant NDF axis */
int slice_dim[ 3 ]; /* Dimensions of each significant slice axis */
int slice_lbnd[ 3 ]; /* Lower bounds of each significant slice axis */
int slice_size; /* Number of pixels in each slice */
int state; /* Parameter state */
int sub; /* Output the background-subtracted input data? */
int type; /* Integer identifier for data type */
int ubnd[ NDF__MXDIM ]; /* Upper pixel bounds of slice */
int var; /* Does i/p NDF have a Variance component? */
size_t size; /* Size of GRP group */
void *ipd1; /* Pointer to input Data array */
void *ipd2; /* Pointer to output Data array */
void *ipdin; /* Pointer to input Data array */
void *ipdout; /* Pointer to output Data array */
/* Abort if an error has already occurred. */
if( *status != SAI__OK ) return;
/* Start an NDF context */
ndfBegin();
/* Record the existing AST status pointer, and ensure AST uses the supplied
status pointer instead. */
old_status = astWatch( status );
/* 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( "IN", 1, 1, "", &grp, &size, status );
ndgNdfas( grp, 1, "READ", &indf1, status );
grpDelet( &grp, status );
/* Get the pixel index bounds of the input NDF. */
ndfBound( indf1, NDF__MXDIM, lbnd, ubnd, &ndim, status );
/* Identify and count the number of significant axes (i.e. axes spanning
more than 1 pixel). Also record their dimensions. */
nsdim = 0;
for( i = 0; i < ndim; i++ ) {
dim[ i ] = ubnd[ i ] - lbnd[ i ] + 1;
if( dim[ i ] > 1 ) sdim[ nsdim++ ] = dim[ i ];
}
/* If there are too many significant axes, report an error. */
if( nsdim > 3 && *status == SAI__OK ) {
*status = SAI__ERROR;
ndfMsg( "N", indf1 );
msgSeti( "NS", nsdim );
errRep( "", "The NDF '^N' has ^NS significant pixel axes, but this"
"application requires 1, 2 or 3.", status );
}
/* Ensure we have 3 values in sdim (pad with trailings 1's if required). */
if( nsdim < 3 ) sdim[ 2 ] = 1;
if( nsdim < 2 ) sdim[ 1 ] = 1;
/* See if the output is to contain the background-subtracted data, or the
background estimate itself. */
parGet0l( "SUB", &sub, status );
/* Create the output by propagating everything except the Data and
(if we are outputting the background itself) Variance arrays. */
if( sub ) {
ndfProp( indf1, "UNITS,AXIS,WCS,QUALITY,VARIANCE", "OUT", &indf2,
status );
} else {
ndfProp( indf1, "UNITS,AXIS,WCS,QUALITY", "OUT", &indf2, status );
}
msgBlankif( MSG__VERB, status );
/* Get the dimensions of each of the filters, in pixels. If only one
value is supplied, duplicate it as the second value if the second axis
is significant. If fewer than 3 values were supplied, use 1 for the 3rd
value (whether or not it is significant). This results in each plane
being fitted independently of the adjacent planes by default. */
parGet1i( "BOX", nsdim, box, &nval, status );
if( *status != SAI__OK ) goto L999;
if( nval < 2 ) box[ 1 ] = ( nsdim > 1 ) ? box[ 0 ] : 1;
if( nval < 3 ) box[ 2 ] = 1;
/* Ensure box sizes are odd. */
box[ 0 ] = 2*( box[ 0 ] / 2 ) + 1;
box[ 1 ] = 2*( box[ 1 ] / 2 ) + 1;
box[ 2 ] = 2*( box[ 2 ] / 2 ) + 1;
msgOutiff( MSG__VERB, "", "Using box sizes [%d,%d,%d].", status,
box[0], box[1], box[2]);
/* If any trailing axes have a cell size of 1, then we apply the algorithm
independently to every pixel index on the trailing axes. First of all
set things up assuming that there are no trailing axes with cell size
of 1. */
nystep = 1;
nzstep = 1;
slice_dim[ 0 ] = sdim[ 0 ];
slice_dim[ 1 ] = sdim[ 1 ];
slice_dim[ 2 ] = sdim[ 2 ];
slice_lbnd[ 0 ] = lbnd[ 0 ];
slice_lbnd[ 1 ] = lbnd[ 1 ];
slice_lbnd[ 2 ] = lbnd[ 2 ];
/* If the 3rd pixel axis has a cell size of 1, arrange that each slice
contains a single plane. */
if( box[ 2 ] == 1 ) {
nzstep = sdim[ 2 ];
slice_dim[ 2 ] = 1;
/* If the 2nd pixel axis also has a cell size of 1, arrange that each slice
contains a single row. */
if( box[ 1 ] == 1 ) {
nystep = sdim[ 1 ];
slice_dim[ 1 ] = 1;
}
}
/* Determine the number of pixels in each independent slice. */
slice_size = slice_dim[ 0 ]*slice_dim[ 1 ]*slice_dim[ 2 ];
/* Decide what numeric data type to use, and set the output NDF data type. */
ndfMtype( "_REAL,_DOUBLE", indf1, indf1, "Data,Variance", itype,
20, dtype, 20, status );
if( !strcmp( itype, "_DOUBLE" ) ) {
type = CUPID__DOUBLE;
} else {
type = CUPID__FLOAT;
}
ndfStype( dtype, indf2, "Data,Variance", status );
/* Map the input and output arrays. */
ndfMap( indf1, "Data", itype, "READ", &ipdin, &el, status );
ndfMap( indf2, "Data", itype, "WRITE", &ipdout, &el, status );
/* If the rms value is supplied on the command, there is no need to
calculate a default value. */
parState( "RMS", &state, status );
if( state == PAR__GROUND ) {
/* Calculate the default RMS value. If the NDF has a Variance component
it is the square root of the mean Variance value. Otherwise, it is found
by looking at differences between adjacent pixel values in the Data
component. */
ndfState( indf1, "VARIANCE", &var, status );
if( *status == SAI__OK && var ) {
ndfMap( indf1, "VARIANCE", "_DOUBLE", "READ", (void *) &ipv, &el, status );
sum = 0.0;
n = 0;
for( i = 0; i < el; i++ ) {
if( ipv[ i ] != VAL__BADD ) {
sum += ipv[ i ];
n++;
}
}
if( n > 0 ) {
rms = sqrt( sum/n );
} else {
*status = SAI__ERROR;
errRep( "", "The supplied data contains insufficient "
"good Variance values to continue.", status );
}
} else {
ipv = NULL;
rms = cupidRms( type, ipdin, el, sdim[ 0 ], status );
}
/* Set the default RMS noise level. */
parDef0d( "RMS", rms, status );
}
/* Abort if an error has occurred. */
if( *status != SAI__OK ) goto L999;
/* Get the RMS noise level. */
parGet0d( "RMS", &rms, status );
/* Annul the error and use an RMS value of VAL__BAD if a null parameter
value was supplied. This causes an independent default noise estimate to
be used for each slice of the base NDF. */
if( *status == PAR__NULL ) {
errAnnul( status );
rms = VAL__BADD;
}
/* See if any experimental algorithm variations are to be used. */
parGet0l( "NEWALG", &newalg, status );
/* Create a pool of worker threads. */
wf = thrCreateWorkforce( thrGetNThread( "CUPID_THREADS", status ), status );
/* Get memory to hold a description of each job passed to a worker. There
is one job for each slice. */
nslice = nystep*nzstep;
job_data = astMalloc( nslice*sizeof( *job_data ) );
if( *status == SAI__OK ) {
/* Loop round all slices to be processed. */
ipd1 = ipdin;
ipd2 = ipdout;
islice = 0;
pdata = job_data;
for( izstep = 0; izstep < nzstep ; izstep++ ) {
slice_lbnd[ 1 ] = lbnd[ 1 ];
for( iystep = 0; iystep < nystep; iystep++, islice++,pdata++ ) {
/* Store the information needed by the function (cupidFindback0) that
does the work in a thread. */
pdata->islice = islice;
pdata->nslice = nslice;
pdata->type = type;
pdata->ndim = ndim;
pdata->box[ 0 ] = box[ 0 ];
pdata->box[ 1 ] = box[ 1 ];
pdata->box[ 2 ] = box[ 2 ];
pdata->rms = rms;
pdata->ipd1 = ipd1;
pdata->ipd2 = ipd2;
pdata->slice_dim[ 0 ] = slice_dim[ 0 ];
pdata->slice_lbnd[ 0 ] = slice_lbnd[ 0 ];
pdata->slice_dim[ 1 ] = slice_dim[ 1 ];
pdata->slice_lbnd[ 1 ] = slice_lbnd[ 1 ];
pdata->slice_dim[ 2 ] = slice_dim[ 2 ];
pdata->slice_lbnd[ 2 ] = slice_lbnd[ 2 ];
pdata->newalg = newalg;
pdata->slice_size = slice_size;
/* Submit a job to the workforce to process the current slice. */
thrAddJob( wf, 0, pdata, cupidFindback0, 0, NULL, status );
/* Update pointers to the start of the next slice in the input and output
arrays. */
if( type == CUPID__FLOAT ) {
ipd1 = ( (float *) ipd1 ) + slice_size;
ipd2 = ( (float *) ipd2 ) + slice_size;
} else {
ipd1 = ( (double *) ipd1 ) + slice_size;
ipd2 = ( (double *) ipd2 ) + slice_size;
}
/* Increment the lower bound on the 2nd pixel axis. */
slice_lbnd[ 1 ]++;
}
/* Increment the lower bound on the 3rd pixel axis. */
slice_lbnd[ 2 ]++;
}
/* Wait until all jobs have finished. */
thrWait( wf, status );
}
/* The output currently holds the background estimate. If the user has
requested that the output should hold the background-subtracted input
data, then do the arithmetic now. */
if( sub && *status == SAI__OK ) {
if( type == CUPID__FLOAT ) {
pf1 = (float *) ipdin;
pf2 = (float *) ipdout;
for( i = 0; i < el; i++, pf1++, pf2++ ) {
if( *pf1 != VAL__BADR && *pf2 != VAL__BADR ) {
*pf2 = *pf1 - *pf2;
} else {
*pf2 = VAL__BADR;
}
}
} else {
pd1 = (double *) ipdin;
pd2 = (double *) ipdout;
for( i = 0; i < el; i++, pd1++, pd2++ ) {
if( *pd1 != VAL__BADD && *pd2 != VAL__BADD ) {
*pd2 = *pd1 - *pd2;
} else {
*pd2 = VAL__BADD;
}
}
}
}
/* Tidy up */
L999:;
msgBlankif( MSG__VERB, status );
/* Free workspace. */
job_data = astFree( job_data );
wf = thrDestroyWorkforce( wf );
/* Reinstate the original AST inherited status value. */
astWatch( old_status );
/* End the NDF context */
ndfEnd( status );
/* If an error has occurred, issue another error report identifying the
program which has failed (i.e. this one). */
if( *status != SAI__OK ) {
errRep( "FINDBACK_ERR", "FINDBACK: Failed to find the background "
"of an NDF.", status );
}
}
void smf_find_science(const Grp * ingrp, Grp **outgrp, int reverttodark,
Grp **darkgrp, Grp **flatgrp, int reducedark,
int calcflat, smf_dtype darktype, smfArray ** darks,
smfArray **fflats, AstKeyMap ** heateffmap,
double * meanstep, int * status ) {
smfSortInfo *alldarks; /* array of sort structs for darks */
smfSortInfo *allfflats; /* array of fast flat info */
Grp * dgrp = NULL; /* Internal dark group */
double duration_darks = 0.0; /* total duration of all darks */
double duration_sci = 0.0; /* Duration of all science observations */
size_t dkcount = 0; /* Dark counter */
size_t ffcount = 0; /* Fast flat counter */
Grp * fgrp = NULL; /* Fast flat group */
size_t i; /* loop counter */
smfData *infile = NULL; /* input file */
size_t insize; /* number of input files */
size_t nsteps_dark = 0; /* Total number of steps for darks */
size_t nsteps_sci = 0; /* Total number of steps for science */
AstKeyMap * heatermap = NULL; /* Heater efficiency map */
AstKeyMap * obsmap = NULL; /* Info from all observations */
AstKeyMap * objmap = NULL; /* All the object names used */
AstKeyMap * scimap = NULL; /* All non-flat obs indexed by unique key */
Grp *ogrp = NULL; /* local copy of output group */
size_t sccount = 0; /* Number of accepted science files */
struct timeval tv1; /* Timer */
struct timeval tv2; /* Timer */
if (meanstep) *meanstep = VAL__BADD;
if (outgrp) *outgrp = NULL;
if (darkgrp) *darkgrp = NULL;
if (darks) *darks = NULL;
if (fflats) *fflats = NULL;
if (heateffmap) *heateffmap = NULL;
if (*status != SAI__OK) return;
/* Sanity check to make sure we return some information */
if ( outgrp == NULL && darkgrp == NULL && darks == NULL && fflats == NULL) {
*status = SAI__ERROR;
errRep( " ", FUNC_NAME ": Must have some non-NULL arguments"
" (possible programming error)", status);
return;
}
/* Start a timer to see how long this takes */
smf_timerinit( &tv1, &tv2, status );
/* Create new group for output files */
ogrp = smf_grp_new( ingrp, "Science", status );
/* and a new group for darks */
dgrp = smf_grp_new( ingrp, "DarkFiles", status );
/* and for fast flats */
fgrp = smf_grp_new( ingrp, "FastFlats", status );
/* and also create a keymap for the observation description */
obsmap = astKeyMap( "KeyError=1" );
/* and an object map */
objmap = astKeyMap( "KeyError=1" );
/* This keymap contains the sequence counters for each related
subarray/obsidss/heater/shutter combination and is used to decide
if a bad flat is relevant */
scimap = astKeyMap( "KeyError=1,KeyCase=0" );
/* This keymap is used to contain relevant heater efficiency data */
heatermap = astKeyMap( "KeyError=1,KeyCase=0" );
/* Work out how many input files we have and allocate sufficient sorting
space */
insize = grpGrpsz( ingrp, status );
alldarks = astCalloc( insize, sizeof(*alldarks) );
allfflats = astCalloc( insize, sizeof(*allfflats) );
/* check each file in turn */
for (i = 1; i <= insize; i++) {
int seqcount = 0;
char keystr[100]; /* Key for scimap entry */
/* open the file but just to get the header */
smf_open_file( ingrp, i, "READ", SMF__NOCREATE_DATA, &infile, status );
if (*status != SAI__OK) break;
/* Fill in the keymap with observation details */
smf_obsmap_fill( infile, obsmap, objmap, status );
/* Find the heater efficiency map if required */
if (*status == SAI__OK && heateffmap) {
char arrayidstr[32];
smf_fits_getS( infile->hdr, "ARRAYID", arrayidstr, sizeof(arrayidstr),
status );
if (!astMapHasKey( heatermap, arrayidstr ) ) {
smfData * heateff = NULL;
dim_t nbolos = 0;
smf_flat_params( infile, "RESIST", NULL, NULL, NULL, NULL, NULL,
NULL, NULL, NULL, NULL, NULL, &heateff, status );
smf_get_dims( heateff, NULL, NULL, &nbolos, NULL, NULL, NULL, NULL,
status );
if (heateff) astMapPut0P( heatermap, arrayidstr, heateff, NULL );
}
}
/* Get the sequence counter for the file. We do not worry about
duplicate sequence counters (at the moment) */
smf_find_seqcount( infile->hdr, &seqcount, status );
/* The key identifying this subarray/obsidss/heater/shutter combo */
smf__calc_flatobskey( infile->hdr, keystr, sizeof(keystr), status );
if (smf_isdark( infile, status )) {
/* Store the sorting information */
dkcount = smf__addto_sortinfo( infile, alldarks, i, dkcount, "Dark", status );
smf__addto_durations( infile, &duration_darks, &nsteps_dark, status );
astMapPutElemI( scimap, keystr, -1, seqcount );
} else {
/* compare sequence type with observation type and drop it (for now)
if they differ */
if ( infile->hdr->obstype == infile->hdr->seqtype ) {
/* Sanity check the header for corruption. Compare RTS_NUM with SEQSTART
and SEQEND. The first RTS_NUM must either be SEQSTART or else between
SEQSTART and SEQEND (if someone has giving us a section) */
int seqstart = 0;
int seqend = 0;
int firstnum = 0;
JCMTState *tmpState = NULL;
smf_getfitsi( infile->hdr, "SEQSTART", &seqstart, status );
smf_getfitsi( infile->hdr, "SEQEND", &seqend, status );
tmpState = infile->hdr->allState;
if( tmpState ) {
firstnum = (tmpState[0]).rts_num;
smf_smfFile_msg( infile->file, "F", 1, "<unknown file>");
if ( firstnum >= seqstart && firstnum <= seqend ) {
/* store the file in the output group */
ndgCpsup( ingrp, i, ogrp, status );
msgOutif(MSG__DEBUG, " ", "Non-dark file: ^F",status);
smf__addto_durations( infile, &duration_sci, &nsteps_sci, status );
astMapPutElemI( scimap, keystr, -1, seqcount );
sccount++;
} else {
msgOutif( MSG__QUIET, "",
"File ^F has a corrupt FITS header. Ignoring it.",
status );
}
} else {
smf_smfFile_msg( infile->file, "F", 1, "<unknown file>");
/* store the file in the output group */
ndgCpsup( ingrp, i, ogrp, status );
msgOutif( MSG__DEBUG, " ",
"File ^F lacks JCMTState: assuming it is non-dark",status);
smf__addto_durations( infile, &duration_sci, &nsteps_sci, status );
astMapPutElemI( scimap, keystr, -1, seqcount );
sccount++;
}
} else if (infile->hdr->seqtype == SMF__TYP_FASTFLAT ) {
ffcount = smf__addto_sortinfo( infile, allfflats, i, ffcount, "Fast flat", status );
} else {
smf_smfFile_msg( infile->file, "F", 1, "<unknown file>");
msgOutif(MSG__DEBUG, " ", "Sequence type mismatch with observation type: ^F",status);
}
}
/* close the file */
smf_close_file( &infile, status );
}
/* Store output group in return variable or else free it */
if (outgrp) {
*outgrp = ogrp;
} else {
grpDelet( &ogrp, status );
}
/* process flatfields if necessary */
if (ffcount > 0 && fflats ) {
smfArray * array = NULL;
/* sort flats into order */
qsort( allfflats, ffcount, sizeof(*allfflats), smf_sort_bydouble);
if (fflats) array = smf_create_smfArray( status );
/* now open the flats and store them if requested */
if (*status == SAI__OK && array && ffcount) {
size_t start_ffcount = ffcount;
AstKeyMap * flatmap = NULL;
if (calcflat) {
/* Use AgeUp so that we get the keys out in the sorted order
that allfflats used */
flatmap = astKeyMap( "KeyCase=0,KeyError=1,SortBy=AgeDown" );
}
/* Read each flatfield. Calculate a responsivity image and a flatfield
solution. Store these in a keymap along with related information
which is itself stored in a keymap indexed by a string made of
OBSIDSS, reference heater value, shutter and subarray.
*/
for (i = 0; i < start_ffcount; i++ ) {
size_t ori_index = (allfflats[i]).index;
smfData * outfile = NULL;
char keystr[100];
AstKeyMap * infomap = astKeyMap( "KeyError=1" );
int oplen = 0;
char thisfile[MSG__SZMSG];
int seqcount = 0;
/* read filename from group */
infile = NULL;
smf_open_file( ingrp, ori_index, "READ", 0, &infile, status );
if ( *status != SAI__OK ) {
/* This should not happen because we have already opened
the file. If it does happen we abort with error. */
if (infile) smf_close_file( &infile, status );
break;
}
/* Calculate the key for this observation */
smf__calc_flatobskey( infile->hdr, keystr, sizeof(keystr), status );
/* Get the file name for error messages */
smf_smfFile_msg( infile->file, "F", 1, "<unknown file>" );
msgLoad( "", "^F", thisfile, sizeof(thisfile), &oplen, status );
/* And the sequence counter to link against science observations */
smf_find_seqcount( infile->hdr, &seqcount, status );
/* Prefill infomap */
astMapPut0C( infomap, "FILENAME", thisfile, "");
astMapPut0I( infomap, "SEQCOUNT", seqcount, "");
/* Collapse it */
if (*status == SAI__OK) {
smf_flat_fastflat( infile, &outfile, status );
if (*status == SMF__BADFLAT) {
errFlush( status );
if (calcflat) {
/* Need to generate an outfile like smf_flat_fastflat
and one heater setting will force smf_flat_calcflat to fail */
smf_flat_malloc( 1, infile, NULL, &outfile, status );
} else {
if (outfile) smf_close_file( &outfile, status );
if (infile) smf_close_file( &infile, status );
infomap = astAnnul( infomap );
ffcount--;
continue;
}
}
}
if (outfile && *status == SAI__OK) {
smf_close_file( &infile, status );
infile = outfile;
if (calcflat) {
size_t ngood = 0;
smfData * curresp = NULL;
int utdate;
if (*status == SAI__OK) {
ngood = smf_flat_calcflat( MSG__VERB, NULL, "RESIST",
"FLATMETH", "FLATORDER", NULL, "RESPMASK",
"FLATSNR", NULL, infile, &curresp, status );
if (*status != SAI__OK) {
/* if we failed to calculate a flatfield we continue but force the
flatfield to be completely bad. This will force the science data associated
with the flatfield to be correctly blanked. We do not annul though
if we have a SUBPAR error telling us that we have failed to define
our parameters properly. */
if (*status != SUBPAR__NOPAR) errAnnul(status);
/* parameters of flatfield */
ngood = 0;
/* Generate a blank flatfield and blank responsivity image */
smf_flat_badflat( infile, &curresp, status );
}
/* Retrieve the UT date so we can decide whether to compare
flatfields */
smf_getfitsi( infile->hdr, "UTDATE", &utdate, status );
/* Store the responsivity data for later on and the processed
flatfield until we have vetted it */
astMapPut0P( infomap, "CALCFLAT", infile, "" );
astMapPut0P( infomap, "RESP", curresp, "" );
astMapPut0I( infomap, "UTDATE", utdate, "" );
astMapPut0I( infomap, "ISGOOD", 1, "" );
astMapPut0I( infomap, "NGOOD", ngood, "" );
astMapPut0I( infomap, "GRPINDEX", ori_index, "" );
astMapPut0I( infomap, "SMFTYP", infile->hdr->obstype, "" );
astMapPutElemA( flatmap, keystr, -1, infomap );
}
} else { /* if (calcflat) */
/* Store the collapsed flatfield - the processed flat is not stored here yet */
smf_addto_smfArray( array, infile, status );
/* Copy the group info */
ndgCpsup( ingrp, ori_index, fgrp, status );
}
} /* if (outfile) */
/* Annul the keymap (will be fine if it is has been stored in another keymap) */
infomap = astAnnul( infomap );
} /* End loop over flatfields */
/* Now we have to loop over the related flatfields to disable
bolometers that are not good and also decide whether we
need to set status to bad. */
if (*status == SAI__OK && calcflat ) {
size_t nkeys = astMapSize( flatmap );
for (i = 0; i < nkeys; i++ ) {
const char *key = astMapKey( flatmap, i );
int nf = 0;
AstKeyMap ** kmaps = NULL;
int nelem = astMapLength( flatmap, key );
kmaps = astMalloc( sizeof(*kmaps) * nelem );
astMapGet1A( flatmap, key, nelem, &nelem, kmaps );
for ( nf = 0; nf < nelem && *status == SAI__OK; nf++ ) {
AstKeyMap * infomap = kmaps[nf];
int isgood = 0;
astMapGet0I( infomap, "ISGOOD", &isgood );
if (isgood) {
/* The flatfield worked */
size_t ngood = 0;
int itemp;
int utdate = 0;
int ratioFlats = 0;
/* Get the UT date - we do not compare flatfields after
the time we enabled heater tracking at each sequence. */
astMapGet0I( infomap, "UTDATE", &utdate );
/* Get the number of good bolometers at this point */
astMapGet0I( infomap, "NGOOD", &itemp );
ngood = itemp;
/* Decide if we want to do the ratio test. We default to
not doing it between 20110901 and 20120827 which is
the period when we did mini-heater tracks before each
flat. ! indicates that we choose based on date. */
if (*status == SAI__OK) {
parGet0l( "FLATUSENEXT", &ratioFlats, status );
if ( *status == PAR__NULL ) {
errAnnul( status );
if (utdate >= 20110901 || utdate <= 20120827 ) {
ratioFlats = 0;
} else {
ratioFlats = 1;
}
}
}
/* Can we compare with the next flatfield? */
if (ngood < SMF__MINSTATSAMP || !ratioFlats ) {
/* no point doing all the ratio checking for this */
} else if ( nelem - nf >= 2 ) {
AstKeyMap * nextmap = kmaps[nf+1];
const char *nextfname = NULL;
const char *fname = NULL;
smfData * curresp = NULL;
smfData * nextresp = NULL;
smfData * curflat = NULL;
void *tmpvar = NULL;
size_t bol = 0;
smfData * ratio = NULL;
double *in1 = NULL;
double *in2 = NULL;
double mean = VAL__BADD;
size_t nbolo;
double *out = NULL;
double sigma = VAL__BADD;
float clips[] = { 5.0, 5.0 }; /* 5.0 sigma iterative clip */
size_t ngoodz = 0;
astMapGet0C( nextmap, "FILENAME", &nextfname );
astMapGet0C( infomap, "FILENAME", &fname );
/* Retrieve the responsivity images from the keymap */
astMapGet0P( infomap, "RESP", &tmpvar );
curresp = tmpvar;
astMapGet0P( nextmap, "RESP", &tmpvar );
nextresp = tmpvar;
astMapGet0P( infomap, "CALCFLAT", &tmpvar );
curflat = tmpvar;
nbolo = (curresp->dims)[0] * (curresp->dims)[1];
/* get some memory for the ratio if we have not already.
We could get some memory once assuming each flat has the
same number of bolometers... */
ratio = smf_deepcopy_smfData( curresp, 0, 0, 0, 0, status );
if( *status == SAI__OK ) {
/* divide: smf_divide_smfData ? */
in1 = (curresp->pntr)[0];
in2 = (nextresp->pntr)[0];
out = (ratio->pntr)[0];
for (bol=0; bol<nbolo;bol++) {
if ( in1[bol] != VAL__BADD && in1[bol] != 0.0 &&
in2[bol] != VAL__BADD && in2[bol] != 0.0 ) {
out[bol] = in1[bol] / in2[bol];
} else {
out[bol] = VAL__BADD;
}
}
}
/* find some statistics */
smf_clipped_stats1D( out, 2, clips, 1, nbolo, NULL, 0, 0, &mean,
&sigma, NULL, 0, &ngoodz, status );
if (*status == SMF__INSMP) {
errAnnul(status);
msgOutiff( MSG__QUIET, "",
"Flatfield ramp ratio of %s with %s had too few bolometers (%zu < %d).",
status, fname, nextfname, ngoodz, SMF__MINSTATSAMP );
ngood = ngoodz; /* Must be lower or equal to original ngood */
} else if (*status == SAI__OK && mean != VAL__BADD && sigma != VAL__BADD && curflat->da) {
/* Now flag the flatfield as bad for bolometers that have changed
more than n%. We expect the variation to be 1+/-a small bit */
const double pmrange = 0.10;
double thrlo = 1.0 - pmrange;
double thrhi = 1.0 + pmrange;
size_t nmasked = 0;
double *flatcal = curflat->da->flatcal;
msgOutiff( MSG__DEBUG, "", "Flatfield fast ramp ratio mean = %g +/- %g (%zu bolometers)",
status, mean, sigma, ngood);
/* we can just set the first slice of the flatcal to bad. That should
be enough to disable the entire bolometer. We have just read these
data so they should be in ICD order. */
for (bol=0; bol<nbolo;bol++) {
if ( out[bol] != VAL__BADD &&
(out[bol] < thrlo || out[bol] > thrhi ) ) {
flatcal[bol] = VAL__BADD;
nmasked++;
} else if ( in1[bol] != VAL__BADD && in2[bol] == VAL__BADD ) {
/* A bolometer is bad next time but good now so we must set it bad now */
flatcal[bol] = VAL__BADD;
nmasked++;
}
}
if ( nmasked > 0 ) {
msgOutiff( MSG__NORM, "", "Masked %zu bolometers in %s from unstable flatfield",
status, nmasked, fname );
/* update ngood to take into account the masking */
ngood -= nmasked;
}
}
smf_close_file( &ratio, status );
} /* End of flatfield responsivity comparison */
/* if we only have a few bolometers left we now consider this
a bad flat unless it is actually an engineering measurement
where expect some configurations to give zero bolometers */
if (ngood < SMF__MINSTATSAMP) {
const char *fname = NULL;
void * tmpvar = NULL;
int smftyp = 0;
smfData * curflat = NULL;
astMapGet0I( infomap, "SMFTYP", &smftyp );
astMapGet0C( infomap, "FILENAME", &fname );
if (smftyp != SMF__TYP_NEP) {
msgOutiff( MSG__QUIET, "",
"Flatfield %s has %zu good bolometer%s.%s",
status, fname, ngood, (ngood == 1 ? "" : "s"),
( ngood == 0 ? "" : " Keeping none.") );
isgood = 0;
/* Make sure that everything is blanked. */
if (ngood > 0) {
astMapGet0P( infomap, "CALCFLAT", &tmpvar );
curflat = tmpvar;
if (curflat && curflat->da) {
size_t bol;
size_t nbolo = (curflat->dims)[0] * (curflat->dims)[1];
double *flatcal = curflat->da->flatcal;
for (bol=0; bol<nbolo; bol++) {
/* Just need to set the first element to bad */
flatcal[bol] = VAL__BADD;
}
}
}
} else {
msgOutiff( MSG__NORM, "",
"Flatfield ramp file %s has %zu good bolometer%s. Eng mode.",
status, fname, ngood, (ngood == 1 ? "" : "s") );
}
}
/* We do not need the responsivity image again */
{
void *tmpvar = NULL;
smfData * resp = NULL;
astMapGet0P( infomap, "RESP", &tmpvar );
resp = tmpvar;
if (resp) smf_close_file( &resp, status );
astMapRemove( infomap, "RESP" );
}
} /* End of isgood comparison */
/* We are storing flats even if they failed. Let the downstream
software worry about it */
{
int ori_index;
smfData * flatfile = NULL;
void *tmpvar = NULL;
/* Store in the output group */
astMapGet0I( infomap, "GRPINDEX", &ori_index );
ndgCpsup( ingrp, ori_index, fgrp, status );
/* And store in the smfArray */
astMapGet0P( infomap, "CALCFLAT", &tmpvar );
astMapRemove( infomap, "CALCFLAT" );
flatfile = tmpvar;
smf_addto_smfArray( array, flatfile, status );
}
/* Free the object as we go */
kmaps[nf] = astAnnul( kmaps[nf] );
} /* End of loop over this obsidss/subarray/heater */
kmaps = astFree( kmaps );
}
}
if (array->ndat) {
if (fflats) *fflats = array;
} else {
smf_close_related(&array, status );
if (fflats) *fflats = NULL;
}
}
}
/* no need to do any more if neither darks nor darkgrp are defined or we might
be wanting to revert to darks. */
if (dkcount > 0 && (darks || darkgrp || reverttodark ) ) {
smfArray * array = NULL;
/* sort darks into order */
qsort( alldarks, dkcount, sizeof(*alldarks), smf_sort_bydouble);
if (darks) array = smf_create_smfArray( status );
/* now open the darks and store them if requested */
if (*status == SAI__OK) {
for (i = 0; i < dkcount; i++ ) {
size_t ori_index = (alldarks[i]).index;
/* Store the entry in the output group */
ndgCpsup( ingrp, ori_index, dgrp, status );
if (darks) {
/* read the value from the new group */
smf_open_file( dgrp, i+1, "READ", 0, &infile, status );
/* do we have to process these darks? */
if (reducedark) {
smfData *outfile = NULL;
smf_reduce_dark( infile, darktype, &outfile, status );
if (outfile) {
smf_close_file( &infile, status );
infile = outfile;
}
}
smf_addto_smfArray( array, infile, status );
}
}
if (darks) *darks = array;
}
}
/* free memory */
alldarks = astFree( alldarks );
allfflats = astFree( allfflats );
if( reverttodark && outgrp && (grpGrpsz(*outgrp,status)==0) &&
(grpGrpsz(dgrp,status)>0) ) {
/* If outgrp requested but no science observations were found, and
dark observations were found, return darks in outgrp and set
flatgrp and darkgrp to NULL. This is to handle cases where we
want to process data taken in the dark like normal science
data. To activate this behaviour set reverttodark */
msgOutiff( MSG__NORM, "", "Treating the dark%s as science data",
status, ( dkcount > 1 ? "s" : "" ) );
*outgrp = dgrp;
if( darkgrp ){
*darkgrp = NULL;
}
if( flatgrp ) {
*flatgrp = NULL;
}
grpDelet( &ogrp, status);
grpDelet( &fgrp, status);
if (meanstep && nsteps_dark > 0) *meanstep = duration_darks / nsteps_dark;
/* Have to clear the darks smfArray as well */
if (darks) smf_close_related( darks, status );
} else {
/* Store the output groups in the return variable or free it */
if (darkgrp) {
*darkgrp = dgrp;
} else {
grpDelet( &dgrp, status);
}
if (flatgrp) {
*flatgrp = fgrp;
} else {
grpDelet( &fgrp, status);
}
if (meanstep && nsteps_sci > 0) *meanstep = duration_sci / nsteps_sci;
}
msgSeti( "ND", sccount );
msgSeti( "DK", dkcount );
msgSeti( "FF", ffcount );
msgSeti( "TOT", insize );
if ( insize == 1 ) {
if (dkcount == 1) {
msgOutif( MSG__VERB, " ", "Single input file was a dark",
status);
} else if (ffcount == 1) {
msgOutif( MSG__VERB, " ", "Single input file was a fast flatfield",
status);
} else if (sccount == 1) {
msgOutif( MSG__VERB, " ", "Single input file was accepted (observation type same as sequence type)",
status);
} else {
msgOutif( MSG__VERB, " ", "Single input file was not accepted.",
status);
}
} else {
if (dkcount == 1) {
msgSetc( "DKTXT", "was a dark");
} else {
msgSetc( "DKTXT", "were darks");
}
if (ffcount == 1) {
msgSetc( "FFTXT", "was a fast flat");
} else {
msgSetc( "FFTXT", "were fast flats");
}
if (sccount == 1) {
msgSetc( "NDTXT", "was science");
} else {
msgSetc( "NDTXT", "were science");
}
/* This might be a useful message */
msgOutif( MSG__NORM, " ", "Out of ^TOT input files, ^DK ^DKTXT, ^FF ^FFTXT "
"and ^ND ^NDTXT", status );
}
if (meanstep && *meanstep != VAL__BADD) {
msgOutiff( MSG__VERB, "", "Mean step time for input files = %g sec",
status, *meanstep );
}
/* Store the heater efficiency map */
if (*status != SAI__OK) heatermap = smf_free_effmap( heatermap, status );
if (heateffmap) *heateffmap = heatermap;
/* Now report the details of the observation */
smf_obsmap_report( MSG__NORM, obsmap, objmap, status );
obsmap = astAnnul( obsmap );
objmap = astAnnul( objmap );
scimap = astAnnul( scimap );
msgOutiff( SMF__TIMER_MSG, "",
"Took %.3f s to find science observations",
status, smf_timerupdate( &tv1, &tv2, status ) );
return;
}
void smf_calc_mode ( smfHead * hdr, int * status ) {
char sam_mode[SZFITSTR]; /* Value of SAM_MODE header */
char obs_type[SZFITSTR]; /* value of OBS_TYPE header */
char sw_mode[SZFITSTR]; /* value of SW_MODE header */
char seq_type[SZFITSTR]; /* value of SEQ_TYPE header */
char inbeamstr[SZFITSTR]; /* value of INBEAM header */
smf_obstype type = SMF__TYP_NULL; /* temporary type */
smf_obstype stype = SMF__TYP_NULL; /* temporary seq type */
smf_obsmode mode = SMF__OBS_NULL; /* temporary mode */
smf_swmode swmode = SMF__SWM_NULL; /* Switching mode */
smf_inbeam_t inbeam = SMF__INBEAM_NOTHING; /* what is in beam? */
if (*status != SAI__OK) return;
if (hdr == NULL) {
*status = SAI__ERROR;
errRep( " ", "Null pointer supplied to " FUNC_NAME, status );
return;
}
/* Proceed if we're using a valid instrument */
if( hdr->instrument != INST__NONE ) {
/* Read the relevant headers */
smf_fits_getS( hdr, "SAM_MODE", sam_mode, sizeof(sam_mode), status );
smf_fits_getS( hdr, "SW_MODE", sw_mode, sizeof(sw_mode), status );
smf_fits_getS( hdr, "OBS_TYPE", obs_type, sizeof(obs_type), status );
/* INBEAM can be undef */
inbeamstr[0] = '\0';
smf_getfitss( hdr, "INBEAM", inbeamstr, sizeof(inbeamstr), status );
/* SEQ_TYPE is "new" */
if ( *status == SAI__OK ) {
smf_fits_getS( hdr, "SEQ_TYPE", seq_type, sizeof(seq_type), status );
if (*status == SMF__NOKWRD ) {
errAnnul( status );
one_strlcpy( seq_type, obs_type, sizeof(seq_type), status );
}
}
/* start with sample type */
if (strcasecmp( sam_mode, "SCAN" ) == 0 ||
strcasecmp( sam_mode, "RASTER") == 0 ) {
mode = SMF__OBS_SCAN;
} else if (strcasecmp( sam_mode, "STARE" ) == 0) {
mode = SMF__OBS_STARE;
} else if (strcasecmp( sam_mode, "DREAM" ) == 0) {
mode = SMF__OBS_DREAM;
} else if (strcasecmp( sam_mode, "JIGGLE" ) == 0) {
mode = SMF__OBS_JIGGLE;
} else if (strcasecmp( sam_mode, "GRID" ) == 0) {
mode = SMF__OBS_GRID;
} else {
if (*status != SAI__OK) {
*status = SAI__ERROR;
msgSetc( "MOD", sam_mode );
errRep( " ", "Unrecognized observing mode '^MOD'", status );
}
}
/* switching mode: options are "none", "pssw", "chop", "freqsw", "self" */
if (strcasecmp( sw_mode, "NONE" ) == 0 ) {
swmode = SMF__SWM_NULL;
} else if (strcasecmp( sw_mode, "PSSW" ) == 0) {
swmode = SMF__SWM_PSSW;
} else if (strcasecmp( sw_mode, "CHOP" ) == 0) {
swmode = SMF__SWM_CHOP;
} else if (strcasecmp( sw_mode, "SELF" ) == 0) {
swmode = SMF__SWM_SELF;
} else if (strcasecmp( sw_mode, "FREQSW" ) == 0) {
swmode = SMF__SWM_FREQSW;
} else {
if (*status != SAI__OK) {
*status = SAI__ERROR;
msgSetc( "MOD", sw_mode );
errRep( " ", "Unrecognized switching mode '^MOD'", status );
}
}
/* obs type */
type = smf__parse_obstype( obs_type, status );
stype = smf__parse_obstype( seq_type, status );
/* in beam (convert to upper case to make it case insensitive) */
astChrCase( NULL, inbeamstr, 1, 0 );
if ( smf_pattern_extract( inbeamstr, "(POL)", NULL, NULL, 0, status ) ) {
inbeam |= SMF__INBEAM_POL;
}
if ( smf_pattern_extract( inbeamstr, "(FTS)", NULL, NULL, 0, status ) ) {
inbeam |= SMF__INBEAM_FTS;
}
if ( smf_pattern_extract( inbeamstr, "(BODY)", NULL, NULL, 0, status ) ) {
inbeam |= SMF__INBEAM_BLACKBODY;
/* We could consider ensuring FTS is not set in this case */
}
}
hdr->obstype = type;
hdr->seqtype = stype;
hdr->obsmode = mode;
hdr->swmode = swmode;
hdr->inbeam = inbeam;
}
void smf_write_bolomap( ThrWorkForce *wf, smfArray *res, smfArray *lut,
smfArray *qua, smfDIMMData *dat, dim_t msize,
const Grp *bolrootgrp, int varmapmethod,
const int *lbnd_out, const int *ubnd_out,
AstFrameSet *outfset, int *status ) {
int addtomap=0; /* Set if adding to existing map */
size_t bstride; /* Bolometer stride */
double *curmap=NULL; /* Pointer to current map being rebinned */
double *curvar=NULL; /* Pointer to variance associate with curmap */
dim_t dsize; /* Size of data arrays in containers */
size_t idx=0; /* index within subgroup */
size_t k; /* loop counter */
int *lut_data=NULL; /* Pointer to DATA component of lut */
char name[GRP__SZNAM+1]; /* Buffer for storing names */
dim_t nbolo; /* Number of bolometers */
size_t nbolomaps = 0; /* Number of bolomaps written */
char *pname=NULL; /* Poiner to name */
smf_qual_t *qua_data=NULL; /* Pointer to DATA component of qua */
double *res_data=NULL; /* Pointer to DATA component of res */
if( *status != SAI__OK ) return;
if( !res || !lut || !qua || !dat || !bolrootgrp ||
!lbnd_out || !ubnd_out || !outfset ) {
*status = SAI__ERROR;
errRep( "", FUNC_NAME ": NULL inputs supplied", status );
return;
}
/* Loop over subgroup index (subarray) */
for( idx=0; idx<res->ndat; idx++ ) {
smf_qual_t *bolomask = NULL;
double *bmapweight = NULL;
double *bmapweightsq = NULL;
int *bhitsmap = NULL;
/* Pointers to everything we need */
res_data = res->sdata[idx]->pntr[0];
lut_data = lut->sdata[idx]->pntr[0];
qua_data = qua->sdata[idx]->pntr[0];
smf_get_dims( res->sdata[idx], NULL, NULL, &nbolo, NULL,
&dsize, &bstride, NULL, status );
/* Make a copy of the quality at first time slice as a good
bolo mask, and then set quality to SMF__Q_BADB. Later we
will unset BADB for one bolo at a time to make individual
maps. */
bolomask = astMalloc( nbolo*sizeof(*bolomask) );
bmapweight = astMalloc( msize*sizeof(*bmapweight) );
bmapweightsq = astMalloc( msize*sizeof(*bmapweightsq) );
bhitsmap = astMalloc( msize*sizeof(*bhitsmap) );
if( *status == SAI__OK ) {
for( k=0; k<nbolo; k++ ) {
bolomask[k] = qua_data[k*bstride];
qua_data[k*bstride] = SMF__Q_BADB;
}
/* Identify good bolos in the copied mask and produce a map */
for( k=0; (k<nbolo)&&(*status==SAI__OK); k++ ) {
if( !(bolomask[k]&SMF__Q_BADB) ) {
Grp *mgrp=NULL; /* Temporary group to hold map names */
smfData *mapdata=NULL;/* smfData for new map */
char tmpname[GRP__SZNAM+1]; /* temp name buffer */
char thisbol[20]; /* name particular to this bolometer */
size_t col, row;
char subarray[10];
nbolomaps++;
/* Set the quality back to good for this single bolometer */
qua_data[k*bstride] = bolomask[k];
/* Create a name for the new map, take into account the
chunk number and subarray. Only required if we are using a single
output container. */
pname = tmpname;
grpGet( bolrootgrp, 1, 1, &pname, sizeof(tmpname), status );
one_strlcpy( name, tmpname, sizeof(name), status );
one_strlcat( name, ".", sizeof(name), status );
/* Subarray, column and row. HDS does not care about case but we
convert to upper case anyhow. */
smf_find_subarray( res->sdata[idx]->hdr, subarray, sizeof(subarray),
NULL, status );
if (*status == SAI__OK) {
size_t len = strlen(subarray);
size_t n = 0;
for (n=0; n<len; n++) {
subarray[n] = toupper(subarray[n]);
}
}
col = (k % res->sdata[idx]->dims[1])+1;
row = (k / res->sdata[idx]->dims[1])+1;
sprintf( thisbol, "%3sC%02zuR%02zu",
subarray,
col, /* x-coord */
row ); /* y-coord */
one_strlcat( name, thisbol, sizeof(name), status );
mgrp = grpNew( "bolomap", status );
grpPut1( mgrp, name, 0, status );
msgOutf( "", "*** Writing single bolo map %s", status,
name );
/* Try to open an existing extention first. Create a new map
array, and then later we'll add it to the existing
one. If it isn't there, create it. */
smf_open_file( mgrp, 1, "UPDATE", 0, &mapdata, status );
if( *status == SAI__OK ) {
/* Allocate memory for the new rebinned data */
curmap = astCalloc( msize, sizeof(*curmap) );
curvar = astCalloc( msize, sizeof(*curvar) );
addtomap = 1;
} else if( *status == DAT__NAMIN ) {
/* Create a new extension */
errAnnul( status );
smf_open_newfile ( mgrp, 1, SMF__DOUBLE, 2, lbnd_out,
ubnd_out, SMF__MAP_VAR, &mapdata, status);
/* Rebin directly into the newly mapped space */
if( *status == SAI__OK ) {
curmap = mapdata->pntr[0];
curvar = mapdata->pntr[1];
addtomap = 0;
}
}
/* Rebin the data for this single bolometer. Don't care
about variance weighting because all samples from
same detector are about the same. */
smf_rebinmap1( wf, res->sdata[idx],
dat->noi ? dat->noi[0]->sdata[idx] : NULL,
lut_data, 0, 0, 0, NULL, 0,
SMF__Q_GOOD, varmapmethod,
AST__REBININIT | AST__REBINEND,
curmap, bmapweight, bmapweightsq, bhitsmap,
curvar, msize, NULL, status );
/* If required, add this new map to the existing one */
if( addtomap ) {
size_t i;
double *oldmap=NULL;
double *oldvar=NULL;
double weight;
if( *status == SAI__OK ) {
oldmap = mapdata->pntr[0];
oldvar = mapdata->pntr[1];
for( i=0; i<msize; i++ ) {
if( oldmap[i]==VAL__BADD ) {
/* No data in this pixel in the old map, just copy */
oldmap[i] = curmap[i];
oldvar[i] = curvar[i];
} else if( curmap[i]!=VAL__BADD &&
oldvar[i]!=VAL__BADD && oldvar[i]!=0 &&
curvar[i]!=VAL__BADD && curvar[i]!=0 ) {
/* Both old and new values available */
weight = 1/oldvar[i] + 1/curvar[i];
oldmap[i] = (oldmap[i]/oldvar[i] + curmap[i]/curvar[i]) /
weight;
oldvar[i] = 1/weight;
}
}
}
/* Free up temporary arrays */
curmap = astFree( curmap );
curvar = astFree( curvar );
}
/* Write out COLNUM and ROWNUM to FITS header */
if( *status == SAI__OK ) {
AstFitsChan *fitschan=NULL;
fitschan = astFitsChan ( NULL, NULL, " " );
atlPtfti( fitschan, "COLNUM", col, "bolometer column", status);
atlPtfti( fitschan, "ROWNUM", row, "bolometer row", status );
atlPtfts( fitschan, "SUBARRAY", subarray, "Subarray identifier",
status );
kpgPtfts( mapdata->file->ndfid, fitschan, status );
if( fitschan ) fitschan = astAnnul( fitschan );
/* Set the bolo to bad quality again */
qua_data[k*bstride] = SMF__Q_BADB;
/* Write WCS */
smf_set_moving(outfset,NULL,status);
ndfPtwcs( outfset, mapdata->file->ndfid, status );
}
/* Clean up */
if( mgrp ) grpDelet( &mgrp, status );
if( mapdata ) smf_close_file( &mapdata, status );
}
}
/* Set quality back to its original state */
for( k=0; k<nbolo; k++ ) {
qua_data[k*bstride] = bolomask[k];
}
}
/* Free up memory */
bolomask = astFree( bolomask );
bmapweight = astFree( bmapweight );
bmapweightsq = astFree( bmapweightsq );
bhitsmap = astFree( bhitsmap );
}
msgOutf( "", "*** Wrote %zu bolo maps", status, nbolomaps );
}
void smurf_sc2clean( int *status ) {
smfArray *array = NULL; /* Data to be cleaned */
Grp *basegrp=NULL; /* Grp containing first file each chunk */
size_t basesize; /* Number of files in base group */
smfArray *bbms = NULL; /* Bad bolometer masks */
smfArray *concat=NULL; /* Pointer to a smfArray */
size_t contchunk; /* Continuous chunk counter */
smfArray *darks = NULL; /* Dark data */
int ensureflat; /* Flag for flatfielding data */
smfArray *flatramps = NULL;/* Flatfield ramps */
AstKeyMap *heateffmap = NULL; /* Heater efficiency data */
smfData *odata = NULL; /* Pointer to output data struct */
Grp *fgrp = NULL; /* Filtered group, no darks */
size_t gcount=0; /* Grp index counter */
size_t idx; /* Subarray counter */
Grp *igrp = NULL; /* Input group of files */
smfGroup *igroup=NULL; /* smfGroup corresponding to igrp */
dim_t maxconcat=0; /* Longest continuous chunk length in samples */
double maxlen=0; /* Constrain maxconcat to this many seconds */
size_t ncontchunks=0; /* Number continuous chunks outside iter loop */
Grp *ogrp = NULL; /* Output group of files */
size_t osize; /* Total number of NDF names in the output group */
dim_t padStart=0; /* How many samples padding at start */
dim_t padEnd=0; /* How many samples padding at end */
size_t size; /* Number of files in input group */
int temp; /* Temporary signed integer */
int usedarks; /* flag for using darks */
ThrWorkForce *wf = NULL; /* Pointer to a pool of worker threads */
int writecom; /* Write COMmon mode to NDF if calculated? */
int writegai; /* Write GAIns to NDF if calculated? */
/* Main routine */
ndfBegin();
/* Find the number of cores/processors available and create a pool of
threads of the same size. */
wf = thrGetWorkforce( thrGetNThread( SMF__THREADS, status ), status );
/* Read the input file */
kpg1Rgndf( "IN", 0, 1, "", &igrp, &size, status );
/* Filter out darks */
smf_find_science( wf, igrp, &fgrp, 1, NULL, NULL, 1, 1, SMF__NULL, &darks,
&flatramps, &heateffmap, NULL, status );
/* input group is now the filtered group so we can use that and
free the old input group */
size = grpGrpsz( fgrp, status );
grpDelet( &igrp, status);
igrp = fgrp;
fgrp = NULL;
if (size == 0) {
msgOutif(MSG__NORM, " ","All supplied input frames were filtered,"
" nothing to do", status );
goto CLEANUP;
}
/* --- Parse ADAM parameters ---------------------------------------------- */
/* Maximum length of a continuous chunk */
parGdr0d( "MAXLEN", 0, 0, VAL__MAXD, 1, &maxlen, status );
/* Padding */
parGdr0i( "PADSTART", 0, 0, VAL__MAXI, 1, &temp, status );
padStart = (dim_t) temp;
parGdr0i( "PADEND", 0, 0, VAL__MAXI, 1, &temp, status );
padEnd = (dim_t) temp;
/* Are we using darks? */
parGet0l( "USEDARKS", &usedarks, status );
/* Are we flatfielding? */
parGet0l( "FLAT", &ensureflat, status );
/* Write COM/GAI to NDFs if calculated? */
parGet0l( "COM", &writecom, status );
parGet0l( "GAI", &writegai, status );
/* Get group of bolometer masks and read them into a smfArray */
smf_request_mask( wf, "BBM", &bbms, status );
/* Group the input files by subarray and continuity ----------------------- */
smf_grp_related( igrp, size, 1, 0, maxlen-padStart-padEnd, NULL, NULL,
&maxconcat, NULL, &igroup, &basegrp, NULL, status );
/* Obtain the number of continuous chunks and subarrays */
if( *status == SAI__OK ) {
ncontchunks = igroup->chunk[igroup->ngroups-1]+1;
}
basesize = grpGrpsz( basegrp, status );
/* Get output file(s) */
kpg1Wgndf( "OUT", basegrp, basesize, basesize,
"More output files required...",
&ogrp, &osize, status );
/* Loop over continuous chunks and clean -----------------------------------*/
gcount = 1;
for( contchunk=0;(*status==SAI__OK)&&contchunk<ncontchunks; contchunk++ ) {
AstKeyMap *keymap=NULL;
int dkclean;
AstKeyMap *sub_instruments=NULL;
/* Place cleaning parameters into a keymap and set defaults. Do
this inside the loop in case we are cleaning files with
differing sub-instruments. Note that we use the map-maker
defaults file here (which loads the sc2clean defaults) so that
we populate the locked keymap with all the parameters that
people may come across to allow them to load their map-maker
config directly into sc2clean.
*/
sub_instruments = smf_subinst_keymap( SMF__SUBINST_NONE,
NULL, igrp,
igroup->subgroups[contchunk][0],
status );
keymap = kpg1Config( "CONFIG", "$SMURF_DIR/smurf_makemap.def",
sub_instruments, 1, status );
if( sub_instruments ) sub_instruments = astAnnul( sub_instruments );
/* Now rerun smf_grp_related to figure out how long each downsampled
chunk of data will be. */
if( basegrp ) grpDelet( &basegrp, status );
if( igroup ) smf_close_smfGroup( &igroup, status );
smf_grp_related( igrp, size, 1, 0, maxlen-padStart-padEnd, NULL, keymap,
&maxconcat, NULL, &igroup, &basegrp, NULL, status );
/* Concatenate this continuous chunk */
smf_concat_smfGroup( wf, NULL, igroup, usedarks ? darks:NULL, bbms, flatramps,
heateffmap, contchunk, ensureflat, 1, NULL, 0, NULL,
NULL, NO_FTS, padStart, padEnd, 0, &concat, NULL, status );
if( *status == SAI__OK) {
/* clean the dark squids now since we might need to use them
to clean the bolometer data */
smf_get_cleanpar( keymap, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL,
&dkclean, NULL, NULL, NULL, NULL, NULL, NULL, NULL,
NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL,
NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL,
NULL, NULL, NULL, status );
for( idx=0; dkclean&&(*status==SAI__OK)&&idx<concat->ndat; idx++ ) {
odata = concat->sdata[idx];
if( odata && odata->da && odata->da->dksquid ) {
smfData *dksquid = odata->da->dksquid;
AstKeyMap *kmap=NULL;
msgOut("", TASK_NAME ": cleaning dark squids", status);
/* fudge the header so that we can get at JCMTState */
dksquid->hdr = odata->hdr;
/* clean darks using cleandk.* parameters */
astMapGet0A( keymap, "CLEANDK", &kmap );
array = smf_create_smfArray( status );
smf_addto_smfArray( array, dksquid, status );
smf_clean_smfArray( wf, array, NULL, NULL, NULL, kmap, status );
if( array ) {
array->owndata = 0;
smf_close_related( wf, &array, status );
}
if( kmap ) kmap = astAnnul( kmap );
/* Unset hdr pointer so that we don't accidentally close it */
dksquid->hdr = NULL;
}
}
/* Then the main data arrays */
if( *status == SAI__OK ) {
smfArray *com = NULL;
smfArray *gai = NULL;
char filename[GRP__SZNAM+1];
msgOut("", TASK_NAME ": cleaning bolometer data", status );
smf_clean_smfArray( wf, concat, NULL, &com, &gai, keymap, status );
/* If ADAM parameters for COM or GAI were specified, and the
common-mode was calculated, export to files here */
if( writecom && com ) {
for( idx=0; (*status==SAI__OK)&&(idx<com->ndat); idx++ ) {
smf_model_createHdr( com->sdata[idx], SMF__COM, concat->sdata[idx],
status );
smf_stripsuffix( com->sdata[idx]->file->name,
SMF__DIMM_SUFFIX, filename, status );
smf_dataOrder( wf, com->sdata[idx], 1, status );
smf_write_smfData( wf, com->sdata[idx], NULL, filename, NULL, 0,
NDF__NOID, MSG__NORM, 0, NULL, NULL, status );
}
}
if( writegai && gai ) {
for( idx=0; (*status==SAI__OK)&&(idx<gai->ndat); idx++ ) {
smf_model_createHdr( gai->sdata[idx], SMF__GAI, concat->sdata[idx],
status );
smf_stripsuffix( gai->sdata[idx]->file->name,
SMF__DIMM_SUFFIX, filename, status );
smf_dataOrder( wf, gai->sdata[idx], 1, status );
smf_write_smfData( wf, gai->sdata[idx], NULL, filename, NULL, 0,
NDF__NOID, MSG__NORM, 0, NULL, NULL, status );
}
}
/* Close com and gai */
if( com ) smf_close_related( wf, &com, status );
if( gai ) smf_close_related( wf, &gai, status );
}
/* Report statistics (currently need a smfArray for that) */
if (*status == SAI__OK) {
size_t last_qcount[SMF__NQBITS];
size_t last_nmap = 0;
smf_qualstats_report( wf, MSG__VERB, SMF__QFAM_TSERIES, 1, concat,
last_qcount, &last_nmap, 1, NULL, NULL, status );
}
/* Clean up for contchunk loop */
if( keymap ) keymap = astAnnul( keymap );
}
/* Export concatenated/cleaned data for each subarray to NDF file */
for( idx=0; (*status==SAI__OK)&&idx<concat->ndat; idx++ ) {
odata = concat->sdata[idx];
/* Complete the history information in the output NDF so that it
includes group parameters accessed since the default history
information was written to the NDF (in smf_open_and_flatfield). */
smf_puthistory( odata, "SMURF:SC2CLEAN", status );
/* Ensure ICD data order */
smf_dataOrder( wf, odata, 1, status );
if( odata->file && odata->file->name ) {
smf_write_smfData( wf, odata, NULL, NULL, ogrp, gcount, NDF__NOID,
MSG__VERB, 0, NULL, NULL, status );
} else {
*status = SAI__ERROR;
errRep( FUNC_NAME,
"Unable to determine file name for concatenated data.",
status );
}
/* Increment the group index counter */
gcount++;
}
/* Close the smfArray */
smf_close_related( wf, &concat, status );
}
/* Write out the list of output NDF names, annulling the error if a null
parameter value is supplied. */
if( *status == SAI__OK && ogrp ) {
grpList( "OUTFILES", 0, 0, NULL, ogrp, status );
if( *status == PAR__NULL ) errAnnul( status );
}
CLEANUP:
/* Tidy up after ourselves: release the resources used by the grp routines */
if( darks ) smf_close_related( wf, &darks, status );
if( flatramps ) smf_close_related( wf, &flatramps, status );
if (heateffmap) heateffmap = smf_free_effmap( heateffmap, status );
if( bbms ) smf_close_related( wf, &bbms, status );
if( igrp ) grpDelet( &igrp, status);
if( ogrp ) grpDelet( &ogrp, status);
if( basegrp ) grpDelet( &basegrp, status );
if( igroup ) smf_close_smfGroup( &igroup, status );
fftw_cleanup();
ndfEnd( status );
}
void smurf_dreamweights ( int *status ) {
/* Local Variables */
Grp *confgrp = NULL; /* Group containing configuration file */
smfData *data = NULL; /* Input data */
const int defgridminmax[] = { -4, 4, -4, 4 }; /* Default extent xmin,xmax,ymin,ymax */
int gridminmax[4]; /* Extent of grid points array */
int gridpts[DREAM__MXGRID][2]; /* Array of points for reconstruction grid */
double gridstep; /* Size of reconstruction grid in arcsec */
size_t i; /* Loop counter */
Grp *igrp = NULL; /* Input group of NDFs */
size_t size; /* Size of input Grp of files */
AstKeyMap *keymap = NULL; /* Pointer to keymap of config settings */
size_t ksize; /* Size of group containing CONFIG file */
int ngrid; /* Number of points in reconstruction grid */
Grp *ogrp = NULL; /* Group of output weights files */
size_t outsize; /* Size of output Grp of files */
/* Main routine */
ndfBegin();
/* Get group of input raw data NDFs */
kpg1Rgndf( "NDF", 0, 1, "", &igrp, &size, status );
/* Get group of output files from user: assume 1 output file for
every input file */
kpg1Wgndf( "OUT", igrp, size, size, "More output files required...",
&ogrp, &outsize, status );
/* Read configuration settings into keymap */
if (*status == SAI__OK) {
kpg1Gtgrp( "CONFIG", &confgrp, &ksize, status );
if (*status == PAR__NULL) {
/* NULL value so provide defaults */
errAnnul( status );
msgOutif(MSG__VERB, " ", "No config file specified - assuming default configuration parameters", status);
keymap = astKeyMap(" " );
astMapPut1I( keymap, "GRIDMINMAX", 4, (int*)defgridminmax, " " );
astMapPut0D( keymap, "GRIDSTEP", 6.28, " " );
} else {
kpg1Kymap( confgrp, &keymap, status );
}
if( confgrp ) grpDelet( &confgrp, status );
}
/* Determine grid parameters from inputs given above */
smf_dream_getgrid( keymap, &gridstep, &ngrid, gridminmax, gridpts, status);
/* Annul keymap immediately as it is no longer required */
if (keymap) keymap = astAnnul( keymap );
/* Loop over number of files */
for ( i=1; (i<= size) && (*status == SAI__OK); i++) {
/* Open file */
smf_open_file( NULL, igrp, i, "READ", 0, &data, status );
/* Calculate weights based on this file */
smf_dream_calcweights( data, ogrp, i, gridstep, ngrid, gridminmax,
&(gridpts[0]), status);
/* Immediately check status on return and abort if an error occured */
if ( *status != SAI__OK ) {
msgSeti("I",i);
msgSeti("N",size);
errRep(FUNC_NAME, "Unable to determine DREAM weights for file ^I of ^N",
status);
}
smf_close_file( NULL, &data, status );
}
/* Free up resources */
if ( ogrp != NULL ) {
grpDelet( &ogrp, status);
}
if ( igrp != NULL ) {
grpDelet( &igrp, status);
}
ndfEnd( status );
msgOutif(MSG__VERB," ", "DREAM weights calculation completed successfully",
status);
}
void smurf_extinction( int * status ) {
/* Local Variables */
smfArray *bbms = NULL; /* Bad bolometer masks */
smfArray *darks = NULL; /* Dark data */
AstKeyMap *extpars = NULL; /* Tau relation keymap */
Grp *fgrp = NULL; /* Filtered group, no darks */
smfArray *flatramps = NULL;/* Flatfield ramps */
int has_been_sky_removed = 0;/* Data are sky-removed */
AstKeyMap *heateffmap = NULL; /* Heater efficiency data */
size_t i; /* Loop counter */
Grp *igrp = NULL; /* Input group */
AstKeyMap *keymap=NULL; /* Keymap for storing parameters */
smf_tausrc tausrc; /* enum value of optical depth source */
smf_extmeth extmeth; /* Extinction correction method */
char tausource[LEN__METHOD]; /* String for optical depth source */
char method[LEN__METHOD]; /* String for extinction airmass method */
smfData *odata = NULL; /* Output data struct */
Grp *ogrp = NULL; /* Output group */
size_t outsize; /* Total number of NDF names in the output group */
size_t size; /* Number of files in input group */
double tau = 0.0; /* Zenith tau at this wavelength */
ThrWorkForce *wf = NULL; /* Pointer to a pool of worker threads */
if (*status != SAI__OK) return;
/* Main routine */
ndfBegin();
/* Find the number of cores/processors available and create a pool of
threads of the same size. */
wf = thrGetWorkforce( thrGetNThread( SMF__THREADS, status ), status );
/* Read the input file */
kpg1Rgndf( "IN", 0, 1, "", &igrp, &size, status );
/* Filter out darks */
smf_find_science( igrp, &fgrp, 0, NULL, NULL, 1, 1, SMF__NULL, &darks,
&flatramps, &heateffmap, NULL, status );
/* input group is now the filtered group so we can use that and
free the old input group */
size = grpGrpsz( fgrp, status );
grpDelet( &igrp, status);
igrp = fgrp;
fgrp = NULL;
if (size > 0) {
/* Get output file(s) */
kpg1Wgndf( "OUT", igrp, size, size, "More output files required...",
&ogrp, &outsize, status );
} else {
msgOutif(MSG__NORM, " ","All supplied input frames were DARK,"
" nothing to extinction correct", status );
}
/* Get group of pixel masks and read them into a smfArray */
smf_request_mask( "BBM", &bbms, status );
/* Read the tau relations from config file or group. We do not
allow sub instrument overloading because these are all values
based on filter name. */
keymap = kpg1Config( "TAUREL", "$SMURF_DIR/smurf_extinction.def", NULL,
1, status );
/* and we need to use the EXT entry */
astMapGet0A( keymap, "EXT", &extpars );
keymap = astAnnul( keymap );
/* Get tau source */
parChoic( "TAUSRC", "Auto",
"Auto,CSOtau,CSOFit, Filtertau, WVMraw", 1,
tausource, sizeof(tausource), status);
/* Decide how the correction is to be applied - convert to flag */
parChoic( "METHOD", "ADAPTIVE",
"Adaptive,Quick,Full,", 1, method, sizeof(method), status);
/* Place parameters into a keymap and extract values */
if( *status == SAI__OK ) {
keymap = astKeyMap( " " );
if( astOK ) {
astMapPut0C( keymap, "TAUSRC", tausource, NULL );
astMapPut0C( keymap, "TAUMETHOD", method, NULL );
smf_get_extpar( keymap, &tausrc, &extmeth, NULL, status );
}
}
for (i=1; i<=size && ( *status == SAI__OK ); i++) {
/* Flatfield - if necessary */
smf_open_and_flatfield( igrp, ogrp, i, darks, flatramps, heateffmap,
&odata, status );
if (*status != SAI__OK) {
/* Error flatfielding: tell the user which file it was */
msgSeti("I",i);
errRep(TASK_NAME, "Unable to open the ^I th file", status);
}
/* Mask out bad pixels - mask data array not quality array */
smf_apply_mask( odata, bbms, SMF__BBM_DATA, 0, status );
/* Now check that the data are sky-subtracted */
if ( !smf_history_check( odata, "smf_subtract_plane", status ) ) {
/* Should we override remsky check? */
parGet0l("HASSKYREM", &has_been_sky_removed, status);
if ( !has_been_sky_removed && *status == SAI__OK ) {
*status = SAI__ERROR;
msgSeti("I",i);
errRep("", "Input data from file ^I are not sky-subtracted", status);
}
}
/* If status is OK, make decisions on source keywords the first
time through. */
if ( *status == SAI__OK && i == 1 ) {
if (tausrc == SMF__TAUSRC_CSOTAU ||
tausrc == SMF__TAUSRC_AUTO ||
tausrc == SMF__TAUSRC_TAU) {
double deftau;
const char * param = NULL;
smfHead *ohdr = odata->hdr;
/* get default CSO tau -- this could be calculated from CSO fits */
deftau = smf_calc_meantau( ohdr, status );
/* Now ask for desired CSO tau */
if ( tausrc == SMF__TAUSRC_CSOTAU || tausrc == SMF__TAUSRC_AUTO) {
param = "CSOTAU";
} else if (tausrc == SMF__TAUSRC_TAU) {
param = "FILTERTAU";
deftau = smf_cso2filt_tau( ohdr, deftau, extpars, status );
}
parGdr0d( param, deftau, 0.0,1.0, 1, &tau, status );
} else if ( tausrc == SMF__TAUSRC_CSOFIT || tausrc == SMF__TAUSRC_WVMRAW ) {
/* Defer a message until after extinction correction */
} else {
*status = SAI__ERROR;
errRep("", "Unsupported opacity source. Possible programming error.",
status);
}
}
/* Apply extinction correction - note that a check is made to
determine whether the data have already been extinction
corrected */
smf_correct_extinction( wf, odata, &tausrc, extmeth, extpars, tau, NULL, NULL, status );
if ( tausrc == SMF__TAUSRC_WVMRAW ) {
msgOutif(MSG__VERB," ", "Used Raw WVM data for extinction correction", status);
} else if ( tausrc == SMF__TAUSRC_CSOFIT ) {
msgOutif(MSG__VERB," ", "Used fit to CSO data for extinction correction", status);
} else if ( tausrc == SMF__TAUSRC_CSOTAU ) {
msgOutif(MSG__VERB," ", "Used an explicit CSO tau value for extinction correction", status);
} else if ( tausrc == SMF__TAUSRC_TAU ) {
msgOutif(MSG__VERB," ", "Used an explicit filter tau value for extinction correction", status);
} else {
if (*status == SAI__OK) {
const char * taustr = smf_tausrc_str( tausrc, status );
*status = SAI__ERROR;
errRepf( "", "Unexpected opacity source used for extinction correction of %s."
" Possible programming error.", status, taustr );
}
}
/* Set character labels */
smf_set_clabels( "Extinction corrected",NULL, NULL, odata->hdr, status);
smf_write_clabels( odata, status );
/* Free resources for output data */
smf_close_file( &odata, status );
}
/* Write out the list of output NDF names, annulling the error if a null
parameter value is supplied. */
if( *status == SAI__OK && ogrp ) {
grpList( "OUTFILES", 0, 0, NULL, ogrp, status );
if( *status == PAR__NULL ) errAnnul( status );
}
/* Tidy up after ourselves: release the resources used by the grp routines */
if (darks) smf_close_related( &darks, status );
if (bbms) smf_close_related( &bbms, status );
if( flatramps ) smf_close_related( &flatramps, status );
if (heateffmap) heateffmap = smf_free_effmap( heateffmap, status );
grpDelet( &igrp, status);
grpDelet( &ogrp, status);
if( keymap ) keymap = astAnnul( keymap );
if (extpars) extpars = astAnnul( extpars );
ndfEnd( status );
}
int smf_fix_data ( msglev_t msglev, smfData * data, int * status ) {
int have_fixed = 0; /* Did we fix anything? */
smfHead *hdr = NULL; /* Data header struct */
size_t i; /* Loop counter */
size_t j; /* Loop counter */
size_t k; /* Loop counter */
size_t l; /* Loop counter */
sc2ast_subarray_t subnum; /* subarray number */
int was_fixed = 0; /* Were these data fixed before? */
if (*status != SAI__OK) return have_fixed;
/* Validate arguments - need smfData with smfHead including FITS
and state */
smf_validate_smfData( data, 1, 0, status );
if (*status != SAI__OK) return have_fixed;
hdr = data->hdr;
smf_validate_smfHead( hdr, 1, 1, status );
if (*status != SAI__OK) return have_fixed;
/* Only works on SCUBA-2 time-series data */
if( (hdr->instrument != INST__SCUBA2) ||
(data->ndims != 3) ) {
return have_fixed;
}
/* Need to at least have a DATA component. It might be a good idea
to check if there is a file associated with the data, and check
to see whether the caller mapped the DATA, VARIANCE, QUALITY. If
they only mapped a subset of those, we could generate a warning that
this routine may be introducing an inconsistency */
if( !data->pntr[0] ) {
return have_fixed;
}
/* Check to see if a FIXDATA FITS keyword exists -- if so, smf_fix_data
has already been run on the data and we return. */
smf_getfitsi( hdr, SMFFIXDATA, &was_fixed, status );
if( *status == SMF__NOKWRD ) {
errAnnul( status );
} else {
return have_fixed;
}
/* Fix the May/June 2011 s4a row readout order error. Check the
subarray first, then get the MJD for the start of the observation
to decide if we need to proceed. */
smf_find_subarray( hdr, NULL, 0, &subnum, status );
if( (*status == SAI__OK) && (subnum == S4A) ) {
double dateendfix; /* UTC MJD end date when fix needed */
double dateobs; /* UTC MJD observation start */
double datestartfix; /* UTS MJD start date when fix needed */
AstTimeFrame *tf = NULL; /* time frame for date conversion */
/* Get the MJD for start of the observation */
smf_find_dateobs( hdr, &dateobs, NULL, status );
/* Get the MJD for the first and last dates bracketing the period
during which the row order fix needs to be done */
tf = astTimeFrame( " " );
astSet( tf, "TimeScale=UTC" );
/* From Mike Macintosh Thu, 7 Jul 2011 15:07:51 +0000:
"I did a scan of the engineering MCE status files and it looks
the 'missing' row on s4a originated between 09:30 and 10:30 HST
on 26 May 2011. I haven't checked in detail whether the
'missing' row was consistently missing after that date but the
assumption is that it was."
*/
astSet( tf, "TimeOrigin=%s", "2011-05-26T19:00:00" );
datestartfix = astGetD( tf, "TimeOrigin" );
/* From Dan Bintley Wed, 06 Jul 2011 00:23:18 -1000:
"I have changed the source code in
/jac_sw/itsroot/scuba2_src/scuba2Da/setup/SG450_M1004D1000/mce_zero.txt"
*/
astSet( tf, "TimeOrigin=%s", "2011-07-06T10:23:00" );
dateendfix = astGetD( tf, "TimeOrigin" );
tf = astAnnul( tf );
/* Proceed with fix if within date range */
if( (*status == SAI__OK) && (dateobs >= datestartfix) &&
(dateobs <= dateendfix) ) {
size_t targetbolo;
size_t sourcebolo;
size_t bstride;
dim_t ncols;
dim_t nrows;
dim_t ntslice;
size_t tstride;
msgOutif( msglev, "", INDENT "Reparing row order readout error", status );
smf_get_dims( data, &nrows, &ncols, NULL, &ntslice, NULL, &bstride,
&tstride, status );
if( (*status==SAI__OK) && (nrows != 40) ) {
*status = SAI__ERROR;
errRep( "", FUNC_NAME ": looks like we need to fix the data, but we "
"don't have 40 rows.", status );
}
/* Rows 0--13 are OK, row 14 was not read out
(FIXDATA_S4A_MISSROW), so we need to move all of rows 14--38
up to the range 15--39. After doing the shift, overwrite the
missing row 14 with 0 (or should this be VAL__BAD? in some
situations?) */
if( *status==SAI__OK ) {
/* Row counter */
for( i=nrows-1; (*status==SAI__OK)&&(i>=(FIXDATA_S4A_MISSROW+1)); i-- ){
for( j=0; (*status==SAI__OK)&&(j<ncols); j++ ) {
smf_qual_t *qual = data->qual;
/* Calculate the bolo index */
if( SC2STORE__ROW_INDEX ) {
/* Fastest changing index is column number */
sourcebolo = (i-1)*ncols + j;
targetbolo = i*ncols + j;
} else {
/* Fastest changing index is row number */
sourcebolo = (i-1) + j*nrows;
targetbolo = i + j*nrows;
}
/* Loop for DATA / VARIANCE components */
for( l=0; (*status==SAI__OK)&&(l<2); l++ ) {
void *buf = data->pntr[l];
if( buf ) {
switch( data->dtype ) {
case SMF__INTEGER:
for( k=0; k<ntslice; k++ ) {
((int *)buf)[targetbolo*bstride + k*tstride] =
((int *)buf)[sourcebolo*bstride + k*tstride];
}
if( i==(FIXDATA_S4A_MISSROW+1) ) {
for( k=0; k<ntslice; k++ ) {
((int *)buf)[sourcebolo*bstride + k*tstride] = 0;
}
}
break;
case SMF__USHORT:
for( k=0; k<ntslice; k++ ) {
((unsigned short *)buf)[targetbolo*bstride + k*tstride] =
((unsigned short *)buf)[sourcebolo*bstride + k*tstride];
}
if( i==(FIXDATA_S4A_MISSROW+1) ) {
for( k=0; k<ntslice; k++ ) {
((unsigned short *)buf)[sourcebolo*bstride + k*tstride] =
0;
}
}
break;
case SMF__DOUBLE:
for( k=0; k<ntslice; k++ ) {
((double *)buf)[targetbolo*bstride + k*tstride] =
((double *)buf)[sourcebolo*bstride + k*tstride];
}
if( i==(FIXDATA_S4A_MISSROW+1) ) {
for( k=0; k<ntslice; k++ ) {
((double *)buf)[sourcebolo*bstride + k*tstride] =
0;
}
}
break;
default:
*status = SAI__ERROR;
errRepf( "", FUNC_NAME
": Don't know how to handle %s type.", status,
smf_dtype_str(data->dtype,status) );
}
}
}
/* Now do quality: Just set SMF__Q_BADDA for the dead
row. Not sure if I should do something with sidecar
quality as well? */
if( qual ) {
for( k=0; k<ntslice; k++ ) {
qual[targetbolo*bstride + k*tstride] =
qual[sourcebolo*bstride + k*tstride];
}
if( i==(FIXDATA_S4A_MISSROW+1) ) {
for( k=0; k<ntslice; k++ ) {
qual[sourcebolo*bstride + k*tstride] = SMF__Q_BADDA;
}
}
}
}
}
}
/* If we get here and status is OK, set return value */
if( *status == SAI__OK ) {
have_fixed |= SMF__FIXED_ROWORDER;
}
}
}
/* Set FITS header so that we know smf_fix_data was run */
smf_fits_updateL( hdr, SMFFIXDATA, have_fixed,
(have_fixed ? "Data have been fixed" : "Data do not require fixing"),
status );
return have_fixed;
}
void smf_subip( ThrWorkForce *wf, smfArray *res, smfArray *lut, int *lbnd_out,
int *ubnd_out, AstKeyMap *keymap, AstFrameSet *outfs, int *status ) {
/* Local Variables: */
HDSLoc *loc = NULL;
HDSLoc *sloc = NULL;
SmfSubIPData *job_data = NULL;
SmfSubIPData *pdata;
char ipref[200];
char subname[10];
const char *ipdata;
const char *qu;
dim_t bolostep;
dim_t nbolo;
dim_t ntslice;
double *angcdata;
double *c0data;
double *imapdata;
double *ipang;
double *p0data;
double *p1data;
int angcndf;
int c0ndf;
int imapndf;
int iw;
int nmap;
int nw;
int p0ndf;
int p1ndf;
size_t bstride;
size_t idx;
size_t tstride;
smfData *data;
smf_qual_t *qua_data;
/* Check inherited status */
if( *status != SAI__OK ) return;
/* Check if we have pol2 data, and see if it is Q or U. */
qu = NULL;
for( idx = 0; idx < res->ndat; idx++ ) {
data = res->sdata[idx];
if( !strcmp( data->hdr->dlabel, "Q" ) ){
if( !qu ) {
qu = "Q";
} else if( strcmp( qu, "Q" ) ) {
*status = SAI__ERROR;
break;
}
} else if( !strcmp( data->hdr->dlabel, "U" ) ) {
if( !qu ) {
qu = "U";
} else if( strcmp( qu, "U" ) ) {
*status = SAI__ERROR;
break;
}
} else if( qu ) {
*status = SAI__ERROR;
qu = NULL;
break;
}
}
/* Report an error if there is a mix of pol2 and non-pol2, or a mix of Q
and U. */
if( *status != SAI__OK ) {
if( qu ) {
errRep( "", "smf_subip: Input data contains mix of Q and U "
"data", status );
} else {
errRep( "", "smf_subip: Input data contains mix of POL2 and "
"non-POL2 data", status );
}
/* If we have pol2 data, get the path to the total intensity image that
is to be used to define the level of IP correction required. If no
value is supplied, annul the error and set "qu" NULL to indicate we should
leave immediately. */
} else if( qu && *status == SAI__OK ) {
parGet0c( "IPREF", ipref, sizeof(ipref), status );
if( *status == PAR__NULL ) {
errAnnul( status );
qu = NULL;
}
}
/* If we are applying IP correction... */
if( qu && *status == SAI__OK ) {
msgOutf( "", "smf_subip: applying instrumental polarisation %s "
"correction based on total intensity map `%s'", status,
qu, ipref );
/* Get an identifier for the IPREF NDF. */
ndfFind( NULL, ipref, &imapndf, status );
/* Resample the NDFs data values onto the output map grid. */
imapdata = smf_alignndf( imapndf, outfs, lbnd_out, ubnd_out,
status );
/* Annul the NDF identifier. */
ndfAnnul( &imapndf, status );
/* Create structures used to pass information to the worker threads. */
nw = wf ? wf->nworker : 1;
job_data = astMalloc( nw*sizeof( *job_data ) );
/* Get the path to the container file holding the IP model parameters. */
ipdata = "$STARLINK_DIR/share/smurf/ipdata.sdf";
astMapGet0C( keymap, "IPDATA", &ipdata );
/* Open the container file. */
hdsOpen( ipdata, "READ", &loc, status );
/* Do the IP correction for each subarray (s8a, s8b, etc) in turn. */
for( idx = 0; idx < res->ndat && *status == SAI__OK; idx++ ) {
data = res->sdata[idx];
/* Get an array holding the angle (rad.s) from north to focal plane Y,
measured positive in the sense of rotation from focal plane Y to focal
plane X, for every bolometer sample in the smfData. The values are bolo
ordered so that "bstride" is 1 and "tstsride" is nbolo. */
ipang = smf1_calcang( data, status );
/* Get the number of bolometers and time slices for the current subarray,
together with the strides between adjacent bolometers and adjacent
time slices. */
smf_get_dims( data, NULL, NULL, &nbolo, &ntslice, NULL, &bstride,
&tstride, status );
/* Get a locator for the structure holding the IP parameters for the
current subarray */
smf_find_subarray( data->hdr, subname, sizeof( subname ), NULL,
status );
datFind( loc, subname, &sloc, status );
/* Begin an NDF context. */
ndfBegin();
/* Get identifiers for the NDFs holding the individual parameters. Each
NDF holds a parameter value for each bolometer. */
ndfFind( sloc, "P0", &p0ndf, status );
ndfFind( sloc, "P1", &p1ndf, status );
ndfFind( sloc, "C0", &c0ndf, status );
ndfFind( sloc, "ANGC", &angcndf, status );
/* Map them. Check each one has the expected number of elements. */
ndfMap( p0ndf, "DATA", "_DOUBLE", "READ", (void **) &p0data,
&nmap, status );
if( nmap != (int) nbolo && *status == SAI__OK ) {
*status = SAI__ERROR;
ndfMsg( "N", p0ndf );
errRep( "", "smf_subip: Bad dimensions for ^N - should be 32x40.", status );
}
ndfMap( p1ndf, "DATA", "_DOUBLE", "READ", (void **) &p1data,
&nmap, status );
if( nmap != (int) nbolo && *status == SAI__OK ) {
*status = SAI__ERROR;
ndfMsg( "N", p1ndf );
errRep( "", "smf_subip: Bad dimensions for ^N - should be 32x40.", status );
}
ndfMap( c0ndf, "DATA", "_DOUBLE", "READ", (void **) &c0data,
&nmap, status );
if( nmap != (int) nbolo && *status == SAI__OK ) {
*status = SAI__ERROR;
ndfMsg( "N", c0ndf );
errRep( "", "smf_subip: Bad dimensions for ^N - should be 32x40.", status );
}
ndfMap( angcndf, "DATA", "_DOUBLE", "READ", (void **) &angcdata,
&nmap, status );
if( nmap != (int) nbolo && *status == SAI__OK ) {
*status = SAI__ERROR;
ndfMsg( "N", angcndf );
errRep( "", "smf_subip: Bad dimensions for ^N - should be 32x40.", status );
}
/* Get a pointer to the quality array for the residuals. */
qua_data = smf_select_qualpntr( data, NULL, status );
/* See how many bolometers to process in each thread. */
bolostep = nbolo/nw;
if( bolostep == 0 ) bolostep = 1;
/* Create jobs to apply the IP correction to a range of bolometers. */
for( iw = 0; iw < nw; iw++ ) {
pdata = job_data + iw;
/* Set the range of bolometers (b1 to b2) to be processed by the current
job. */
pdata->b1 = iw*bolostep;
if( iw < nw - 1 ) {
pdata->b2 = pdata->b1 + bolostep - 1;
} else {
pdata->b2 = nbolo - 1 ;
}
/* Store the other info needed by the worker thread. */
pdata->ntslice = ntslice;
pdata->nbolo = nbolo;
pdata->res_data = res->sdata[idx]->pntr[0];
pdata->lut_data = lut->sdata[idx]->pntr[0];
pdata->qua_data = qua_data;
pdata->ipang = ipang;
pdata->bstride = bstride;
pdata->tstride = tstride;
pdata->imapdata = imapdata;
pdata->qu = qu;
pdata->p0data = p0data;
pdata->p1data = p1data;
pdata->c0data = c0data;
pdata->angcdata = angcdata;
pdata->allstate = data->hdr->allState;
/* Submit the job for execution by the next available thread. */
thrAddJob( wf, 0, pdata, smf1_subip, 0, NULL, status );
}
/* Wait for all jobs to complete. */
thrWait( wf, status );
/* End the NDF context, thus unmapping and freeing all NDF identifiers
created since the context was started. */
ndfEnd( status );
/* Free locator for subarray IP parameters. */
datAnnul( &sloc, status );
ipang = astFree( ipang );
}
/* Free resources. */
datAnnul( &loc, status );
imapdata = astFree( imapdata );
job_data = astFree( job_data );
}
}
void smf_fits_outhdr( AstFitsChan * inhdr, AstFitsChan ** outhdr,
int * status ) {
/* Local Variables: */
AstFitsChan *temphdr = NULL; /* FitsChan holding temporary FITS headers */
/* List of BEGIN headers that are retained even if different */
const char * begin_items[] = {
"DATE-OBS",
"DUT1",
"LOFREQS",
"AMSTART",
"AZSTART",
"ELSTART",
"HSTSTART",
"LSTSTART",
"TSPSTART",
"ATSTART",
"HUMSTART",
"BPSTART",
"WNDSPDST",
"WNDDIRST",
"TAU225ST",
"TAUDATST",
"WVMTAUST",
"WVMDATST",
"SEEINGST",
"FRLEGTST",
"BKLEGTST",
"SEQSTART",
NULL
};
const char * end_items[] = {
"DATE-END",
"LOFREQE",
"AMEND",
"AZEND",
"ELEND",
"HSTEND",
"LSTEND",
"TSPEND",
"ATEND",
"HUMEND",
"BPEND",
"WNDSPDEN",
"WNDDIREN",
"TAU225EN",
"TAUDATEN",
"WVMTAUEN",
"WVMDATEN",
"SEEINGEN",
"FRLEGTEN",
"BKLEGTEN",
"SEQEND",
"OBSGEO-X",
"OBSGEO-Y",
"OBSGEO-Z",
NULL
};
/* Check inherited status. */
if ( *status != SAI__OK ) return;
/* If this is the first file, get a copy of the input NDFs FITS extension
(held in a FitsChan). This FitsChan will be used to hold the FITS
header for the output NDF. Also remove contiguous blank lines. */
if( *outhdr == NULL ) {
*outhdr = astCopy( inhdr );
atlRmblft( *outhdr, status );
/* If this is not the first file, merge the input NDF's FITS extension
into the output NDF's FITS extension by removing any headers from the
output FITS extension that do not have identical values in the input
FITS extension. */
} else {
smfHead hdr;
double mjdnew = 0.0;
double mjdref = 0.0;
AstFitsChan * begfits = NULL;
AstFitsChan * endfits = NULL;
/* need to make sure that the merging will not remove headers that need
to be retained covering start and end state. This means that we take a copy
of the input header and manually synchronize END/START headers before calling
the ATL merge routine. */
/* Do not have access to smfData so need to set one up or duplicate code
in smf_find_dateobs */
if (*status == SAI__OK) {
hdr.allState = NULL;
hdr.fitshdr = inhdr;
smf_find_dateobs( &hdr, &mjdnew, NULL, status );
hdr.fitshdr = *outhdr;
smf_find_dateobs( &hdr, &mjdref, NULL, status );
if (*status == SMF__NOKWRD) {
/* if there is no date information we just do what we can */
errAnnul( status );
mjdnew = 0.0;
mjdref = 0.0;
}
}
if (mjdnew < mjdref) {
/* input header is older than merged header:
Copy beginfits from INPUT to MERGE
Copy endfits from MERGE to INPUT
*/
begfits = astCopy( inhdr );
endfits = astCopy( *outhdr );
} else {
/* input header is newer than merged header:
Copy beginfits from MERGE to INPUT
Copy endfits from INPUT to MERGE
Do this even if dates are identical or if we could not read a date.
*/
begfits = astCopy( *outhdr );
endfits = astCopy( inhdr );
}
/* oldfits gets the END items from newfits.
newfits gets the BEGIN items from oldfits*/
smf__fits_copy_items( begfits, endfits, begin_items, status );
smf__fits_copy_items( endfits, begfits, end_items, status );
/* now we can merge oldfits and newfits */
atlMgfts( 3, begfits, endfits, &temphdr, status );
(void) astAnnul( begfits );
(void) astAnnul( endfits );
(void) astAnnul( *outhdr );
*outhdr = temphdr;
}
/* Remove any ASTWARN cards from the output header, but retain them
within the input header. Any such warnings in the input header will
be displayed when the input NDF is closed using smf_close_file. This
helps to track down bugs caused by keywords unintentionally having
undefined values in an input NDF. */
astClear( *outhdr, "Card" );
while( astFindFits( *outhdr, "ASTWARN", NULL, 0 ) ){
astDelFits( *outhdr );
}
}
/* Fill a single gap in a single bolometer time-stream. */
static void smf1_fillgap( double *data, int pstart, int pend, size_t tstride,
int jstart, int jend, gsl_rng *r, int *status ){
/* Local Variables: */
double *pd;
double fillval;
double grad;
double offset;
double s1;
double sigma;
double sigmal;
double sigmar;
double vl;
double vr;
double x[ BOX ];
double y[ BOX ];
int jhi;
int jlo;
int k;
int s2;
int jj;
/* Check inherited status */
if( *status != SAI__OK ) return;
/* If the gap is only a single sample, use the mean of the adjacent
samples. These are sure to be good, since they would be part of the
gap if they were bad. */
if( jstart == jend ) {
if( jstart > pstart ) {
s1 = data[ ( jstart - 1 )*tstride ];
s2 = 1;
} else {
s1 = 0.0;
s2 = 0;
}
if( jend < pend ) {
s1 += data[ ( jend + 1 )*tstride ];
s2++;
}
data[ jstart*tstride ] = s2 ? s1/s2 : 0.0;
/* For larger gaps, we fill it with a straight line plus noise. */
} else {
/* Find an estimate of the mean value and noise level at the start of the
gap. We do this by fitting a straight line to the good data immediately
before the start of the gap. Indicate we do not yet know the value or
noise at the start of the gap. */
vl = VAL__BADD;
sigmal = VAL__BADD;
/* The last sample in the box is the first sample before the gap. The first
sample in the box is BOX samples before that. */
jhi = jstart - 1;
jlo = jstart - BOX;
/* If the lower end of the box is off the start of the array, set it to
the start of the array. */
if( jlo < pstart ) jlo = pstart;
/* Check the box is large enough to fit. */
if( jhi - jlo + 1 >= MINBOX ) {
/* Copy the box data values into two arrays suitable for kpg1Fit1d. */
k = 0;
pd = data + jlo*tstride;
for( jj = jlo; jj <= jhi; jj++,k++ ) {
x[ k ] = jj;
y[ k ] = *pd;
pd += tstride;
}
/* Attempt to do the fit, annulling any error (e.g. caused by too few
good values in the box - i.e. if there are other gaps very close to
the one we are filling). */
if( *status == SAI__OK ) {
kpg1Fit1d( 1, k, y, x, &grad, &offset, &sigmal, status );
if( *status != SAI__OK ) {
errAnnul( status );
sigmal = VAL__BADD;
/* If the fit succeeded, find the data value which the line has at the
start of the gap. */
} else {
vl = grad*jstart + offset;
}
}
}
/* If we cannot do the fit, use the mean of the (up to) 3 good values
immediately prior to the gap, and use zero noise. */
if( sigmal == VAL__BADD ) {
s1 = 0.0;
s2 = 0;
jlo = jstart - 3;
if( jlo < pstart ) jlo = pstart;
pd = data + jlo*tstride;
for( jj = jlo; jj <= jhi; jj++ ) {
if( *pd != VAL__BADD ) {
s1 += *pd;
s2++;
}
pd += tstride;
}
if( s2 > 0 ) vl = s1/s2;
}
/* Now find an estimate of the mean value and noise level at the end of the
gap in the same way. Indicate we do not yet know the value or noise at the
end of the gap. */
vr = VAL__BADD;
sigmar = VAL__BADD;
/* The first sample in the box is the first sample after the gap. The last
sample in the box is BOX samples after that. */
jlo = jend + 1;
jhi = jend + BOX;
/* If the upper end of the box is off the end of the array, set it to
the end of the array. */
if( jhi > pend ) jhi = pend;
/* Check the box is large enough to fit. */
if( jhi - jlo + 1 >= MINBOX ) {
/* Copy the box data values into two arrays suitable for kpg1Fit1d. */
k = 0;
pd = data + jlo*tstride;
for( jj = jlo; jj <= jhi; jj++,k++ ) {
x[ k ] = jj;
y[ k ] = *pd;
pd += tstride;
}
/* Attempt to do the fit, annulling any error (e.g. caused by too few
good values in the box - i.e. if there are other gaps very close to
the one we are filling). */
if( *status == SAI__OK ) {
kpg1Fit1d( 1, k, y, x, &grad, &offset, &sigmar, status );
if( *status != SAI__OK ) {
errAnnul( status );
sigmar = VAL__BADD;
/* If the fit succeeded, find the data value which the line has at the
end of the gap. */
} else {
vr = grad*jend + offset;
}
}
}
/* If we cannot do the fit, use the mean of the (up to) 3 good values
immediately after the gap, and use zero noise. */
if( sigmar == VAL__BADD ) {
s1 = 0.0;
s2 = 0;
jhi = jend + 3;
if( jhi > pend ) jhi = pend;
pd = data + jlo*tstride;
for( jj = jlo; jj <= jhi; jj++ ) {
if( *pd != VAL__BADD ) {
s1 += *pd;
s2++;
}
pd += tstride;
}
if( s2 > 0 ) vr = s1/s2;
}
/* If we have the mean value at start and end of the box, we fill it with
a straight line that interpolates these values, with added noise if
possible. */
if( vl != VAL__BADD && vr != VAL__BADD ) {
/* Find the noise level to use. */
if( sigmal != VAL__BADD && sigmar != VAL__BADD ) {
sigma = 0.5*( sigmal + sigmar );
} else if( sigmal != VAL__BADD ) {
sigma = sigmal;
} else if( sigmar != VAL__BADD ) {
sigma = sigmar;
} else {
sigma = 0.0;
}
/* Find the gradient and offset for the straight line used to create the
replacement values for the gap. */
grad = ( vr - vl )/ ( jend - jstart );
offset = vl - grad*jstart;
/* Replace the gap values with the straight line values, plus noise. */
pd = data + jstart*tstride;
if( sigma > 0.0 ) {
for( jj = jstart; jj <= jend; jj++ ) {
*pd = grad*jj + offset + gsl_ran_gaussian( r, sigma );
pd += tstride;
}
} else {
for( jj = jstart; jj <= jend; jj++ ) {
*pd = grad*jj + offset;
pd += tstride;
}
}
/* If we do not have the mean value at start or end of the box, we fill it
with a constant value. */
} else {
if( vl != VAL__BADD ) {
fillval = vl;
} else if( vr != VAL__BADD ) {
fillval = vr;
} else {
fillval = 0.0;
}
pd = data + jstart*tstride;
for( jj = jstart; jj <= jend; jj++ ) {
*pd = fillval;
pd += tstride;
}
}
}
}
double cupidConfigD( AstKeyMap *config, const char *name, double def,
int *status ){
/*
*+
* Name:
* cupidConfigD
* Purpose:
* Get the value of a configuration parameter.
* Language:
* Starlink C
* Synopsis:
* double cupidConfigD( AstKeyMap *config, const char *name, double def,
* int *status )
* Description:
* This function returns a named value from the supplied KeyMap. If
* the KeyMap does not contain the named value, an attempt is made to
* obtain a value from a secondary KeyMap which should be stored
* within the supplied KeyMap, using a key equal to the constant
* string CUPID__CONFIG. If the secondary KeyMap does not contain a
* value, then the supplied default value is returned. In either case,
* the returned value is stored in the KeyMap.
* Parameters:
* config
* An AST KeyMap holding the configuration parameters. If NULL is
* supplied, the default value is returned without error.
* name
* The name of the value to extract from the KeyMap.
* def
* The default value to use.
* status
* Pointer to the inherited status value.
* Returned Value:
* The required value. The supplied default value is returned if an
* error occurs.
* Copyright:
* Copyright (C) 2005 Particle Physics & Astronomy Research Council.
* Copyright (C) 2008 Science & Technology Facilities 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:
* 5-OCT-2005 (DSB):
* Original version.
* 26-MAR-2008 (DSB):
* Re-report a more friendly message iof the supplied text could
* not be interpreted as a numerical value.
* {enter_further_changes_here}
* Bugs:
* {note_any_bugs_here}
*-
*/
/* Local Variables: */
AstObject *sconfig; /* Object pointer obtained from KeyMap */
const char *text; /* Pointer to uninterprted text value */
double ret; /* The returned value */
/* Initialise */
ret = def;
/* Abort if an error has already occurred, or if no KeyMap was supplied. */
if( *status != SAI__OK || !config ) return ret;
/* Attempt to extract the named value from the supplied KeyMap. */
if( !astMapGet0D( config, name, &ret ) ) {
/* If the value was not found in the KeyMap, see if the KeyMap contains a
secondary KeyMap. */
if( astMapGet0A( config, CUPID__CONFIG, &sconfig ) ) {
/* If it does, see if the secondary KayMap contains a value for the named
entry. If it does, remove the value from the KeyMap so it does not
appear in the CUPID NDF extension. */
if( astMapGet0D( (AstKeyMap *) sconfig, name, &ret ) ) {
astMapRemove( (AstKeyMap *) sconfig, name );
/* If the text supplied by the user could not be interpreted as a
floating point value, re-report the error. */
} else if( *status == AST__MPGER ) {
ret = def;
errAnnul( status );
if( astMapGet0C( config, name, &text ) ) {
*status = SAI__ERROR;
msgSetc( "T", text );
msgSetc( "N", name );
errRep( "", "Illegal value \"^T\" supplied for configuration "
"parameter ^N.", status );
}
/* If the value was not found in either KeyMap, return the default value. */
} else {
ret = def;
}
/* Free the pointer to the secondary KeyMap. */
sconfig = astAnnul( sconfig );
/* If no secondary KeyMap was found, return the default value. */
} else {
ret = def;
}
/* Store the returned value in the supplied KeyMap if it is good. */
if( ret != VAL__BADD ) astMapPut0D( config, name, ret, NULL );
/* If the text supplied by the user could not be interpreted as a
floating point value, re-report the error. */
} else if( *status == AST__MPGER ) {
ret = def;
errAnnul( status );
if( astMapGet0C( config, name, &text ) ) {
*status = SAI__ERROR;
msgSetc( "T", text );
msgSetc( "N", name );
errRep( "", "Illegal value \"^T\" supplied for configuration "
"parameter ^N.", status );
}
}
/* Return the result. */
return ret;
}
void smurf_unmakecube( int *status ) {
/* Local Variables */
AstFrame *tfrm = NULL; /* Current Frame from input WCS */
AstFrameSet *wcsin = NULL; /* WCS Frameset for input cube */
AstMapping *tmap = NULL; /* Base->current Mapping from input WCS */
AstSkyFrame *iskyfrm = NULL; /* SkyFrame from the input WCS Frameset */
Grp *detgrp = NULL; /* Group of detector names */
Grp *igrp1 = NULL; /* Group of input sky cube files */
Grp *igrp2 = NULL; /* Group of input template files */
Grp *ogrp = NULL; /* Group containing output file */
NdgProvenance *oprov = NULL;/* Provenance for the output NDF */
SkyCube *sky_cubes = NULL; /* Pointer to array of sky cube descriptions */
SkyCube *skycube = NULL; /* Pointer to next sky cube description */
char pabuf[ 10 ]; /* Text buffer for parameter value */
double params[ 4 ]; /* astResample parameters */
int axes[ 2 ]; /* Indices of selected axes */
int blank; /* Was a blank line just output? */
int flag; /* Was the group expression flagged? */
int ifile; /* Input file index */
int interp = 0; /* Pixel interpolation method */
int iskycube; /* Index of current sky cube */
int nel; /* Number of elements in 3D array */
int nparam = 0; /* No. of parameters required for interpolation scheme */
int ondf; /* Output time series NDF identifier */
int outax[ 2 ]; /* Indices of corresponding output axes */
int overlap; /* Does time series overlap sky cube? */
int sdim[3]; /* Array of significant pixel axes */
int usedetpos; /* Should the detpos array be used? */
size_t ndet; /* Number of detectors supplied for "DETECTORS" */
size_t nskycube; /* Number of supplied sky cubes */
size_t outsize; /* Number of files in output group */
size_t size; /* Number of files in input group */
smfData *data = NULL; /* Pointer to data struct */
void *in_data = NULL; /* Pointer to the input cube data array */
void *out_data = NULL; /* Pointer to the output cube data array */
#if defined(FPTRAP)
feenableexcept(FE_DIVBYZERO|FE_INVALID|FE_OVERFLOW);
#endif
/* Check inherited status */
if( *status != SAI__OK ) return;
/* We have not yet displayed a blank line on stdout. */
blank = 0;
/* Begin an AST context */
astBegin;
/* Begin an NDF context. */
ndfBegin();
/* Get a group holding the input sky cubes. */
kpg1Rgndf( "IN", 0, 1, "", &igrp1, &nskycube, status );
/* Create an array of structures to hold information about each input sky
cube. */
sky_cubes = astMalloc( sizeof( SkyCube )*(size_t) nskycube );
/* Store a description of each sky cube. */
if( sky_cubes ) {
for( iskycube = 0; iskycube < nskycube; iskycube++ ) {
skycube = sky_cubes + iskycube;
/* Get an NDF identifier for the next sky cube. */
ndgNdfas( igrp1, iskycube + 1, "READ", &(skycube->indf), status );
/* Get the WCS FrameSet from the sky cube, together with its pixel index
bounds. */
kpg1Asget( skycube->indf, 3, 0, 1, 1, sdim, skycube->slbnd,
skycube->subnd, &wcsin, status );
/* Get the base->current Mapping from the input WCS FrameSet, and split it
into two Mappings; one (iskymap) that maps the first 2 GRID axes into
celestial sky coordinates, and one (ispecmap) that maps the third GRID
axis into a spectral coordinate. Also extract the SpecFrame and
SkyFrame from the current Frame. */
tmap = astGetMapping( wcsin, AST__BASE, AST__CURRENT );
tfrm = astGetFrame( wcsin, AST__CURRENT );
axes[ 0 ] = 1;
axes[ 1 ] = 2;
astMapSplit( tmap, 2, axes, outax, &(skycube->iskymap) );
iskyfrm = astPickAxes( tfrm, 2, outax, NULL );
axes[ 0 ] = 3;
astMapSplit( tmap, 1, axes, outax, &(skycube->ispecmap) );
skycube->ispecfrm = astPickAxes( tfrm, 1, outax, NULL );
/* Create a copy of "iskyfrm" representing absolute coords rather than
offsets. We assume the target is moving if the cube represents offsets. */
skycube->abskyfrm = astCopy( iskyfrm );
astClear( skycube->abskyfrm, "SkyRefIs" );
skycube->moving = ( *status == SAI__OK &&
!strcmp( astGetC( iskyfrm, "SkyRefIs" ),
"Origin" ) ) ? 1 : 0;
/* Invert the Mappings (for the convenience of smf_resamplecube), so
that they go from current Frame to grid axis. */
astInvert( skycube->ispecmap );
astInvert( skycube->iskymap );
/* For efficiency, annul manually the unneeded AST objects created in
this loop. */
wcsin = astAnnul( wcsin );
tmap = astAnnul( tmap );
tfrm = astAnnul( tfrm );
iskyfrm = astAnnul( iskyfrm );
}
}
/* See if the detector positions are to be read from the RECEPPOS array
in the template NDFs. Otherwise, they are calculated on the basis of
the FPLANEX/Y arrays. */
parGet0l( "USEDETPOS", &usedetpos, status );
/* Get the detectors to use. If a null value is supplied, annull the
error. Otherwise, make the group case insensitive. */
detgrp = NULL;
if( *status == SAI__OK ) {
kpg1Gtgrp( "DETECTORS", &detgrp, &ndet, status );
if( *status == PAR__NULL ) {
errAnnul( status );
if (detgrp) {
grpDelet( &detgrp, status );
}
} else {
grpSetcs( detgrp, 0, status );
}
}
/* Get the pixel interpolation scheme to use. */
parChoic( "INTERP", "NEAREST", "NEAREST,LINEAR,SINC,"
"SINCSINC,SINCCOS,SINCGAUSS,SOMB,SOMBCOS",
1, pabuf, 10, status );
if( !strcmp( pabuf, "NEAREST" ) ) {
interp = AST__NEAREST;
nparam = 0;
} else if( !strcmp( pabuf, "LINEAR" ) ) {
interp = AST__LINEAR;
nparam = 0;
} else if( !strcmp( pabuf, "SINC" ) ) {
interp = AST__SINC;
nparam = 1;
} else if( !strcmp( pabuf, "SINCSINC" ) ) {
interp = AST__SINCSINC;
nparam = 2;
} else if( !strcmp( pabuf, "SINCCOS" ) ) {
interp = AST__SINCCOS;
nparam = 2;
} else if( !strcmp( pabuf, "SINCGAUSS" ) ) {
interp = AST__SINCGAUSS;
nparam = 2;
} else if( !strcmp( pabuf, "SOMB" ) ) {
interp = AST__SOMB;
nparam = 1;
} else if( !strcmp( pabuf, "SOMBCOS" ) ) {
interp = AST__SOMBCOS;
nparam = 2;
} else if( *status == SAI__OK ) {
nparam = 0;
*status = SAI__ERROR;
msgSetc( "V", pabuf );
errRep( "", "Support not available for INTERP = ^V (programming "
"error)", status );
}
/* Get an additional parameter vector if required. */
if( nparam > 0 ) parExacd( "PARAMS", nparam, params, status );
/* Get a group of reference time series files to use as templates for
the output time series files.*/
ndgAssoc( "REF", 1, &igrp2, &size, &flag, status );
/* Create a group holding the names of the corresponding output NDFs. */
ndgCreat ( "OUT", igrp2, &ogrp, &outsize, &flag, status );
if( outsize != size && *status == SAI__OK ) {
*status = SAI__ERROR;
msgSeti( "O", outsize );
msgSeti( "I", size );
errRep( "", "Numbers of input reference cubes (^I) and output "
"cubes (^O) differ.", status );
}
/* Loop round all the template time series files. */
for( ifile = 1; ifile <= size && *status == SAI__OK; ifile++ ) {
/* Start a new NDF context. */
ndfBegin();
/* Obtain information about the current template NDF, but do not map the
arrays. */
smf_open_file( igrp2, ifile, "READ", SMF__NOCREATE_DATA, &data, status );
/* Issue a suitable message and abort if anything went wrong. */
if( *status != SAI__OK ) {
errRep( FUNC_NAME, "Could not open input template file.", status );
break;
} else {
if( data->file == NULL ) {
*status = SAI__ERROR;
errRep( FUNC_NAME, "No smfFile associated with smfData.",
status );
break;
} else if( data->hdr == NULL ) {
*status = SAI__ERROR;
errRep( FUNC_NAME, "No smfHead associated with smfData.",
status );
break;
}
}
/* Report the name of the input template. */
smf_smfFile_msg( data->file, "FILE", 1, "<unknown>" );
msgSeti( "THISFILE", ifile );
msgSeti( "NUMFILES", size );
msgOutif( MSG__NORM, " ", "Simulating ^THISFILE/^NUMFILES ^FILE",
status );
/* Create the output NDF by propagation from the input template NDF.
Everything is copied except for the array components and any PROVENANCE
extension. */
ndgNdfpr( data->file->ndfid, "TITLE,LABEL,UNITS,AXIS,WCS,HISTORY,"
"NOEXTENSION(PROVENANCE)", ogrp, ifile, &ondf, status );
/* Ensure the output NDF has a history component. */
ndfHcre( ondf, status );
/* Get a pointer to the mapped output data array. Set all values bad. */
ndfMap( ondf, "DATA", "_REAL", "WRITE/BAD", &out_data, &nel, status );
/* If the detector positions are to calculated on the basis of FPLANEX/Y
rather than detpos, then free the detpos array in the templates smfHead
structure. This will cause smf_tslice_ast to use the fplanex/y values. */
if( !usedetpos && data->hdr->detpos ) {
astFree( (double *) data->hdr->detpos );
data->hdr->detpos = NULL;
}
/* Get a pointer to a structure holding provenance information for the
output time series. */
oprov = ndgReadProv( ondf, "SMURF:UNMAKECUBE", status );
/* Record details of the template in the provenance structure for the
output time series. */
ndgPutProv( oprov, data->file->ndfid, NULL, 0, status );
/* Loop round all input sky cubes. */
for( iskycube = 0; iskycube < nskycube; iskycube++ ) {
skycube = sky_cubes + iskycube;
/* Record details of the input cube in the provenance extension of the
output time series. */
ndgPutProv( oprov, skycube->indf, NULL, 0, status );
/* See if the current time series overlaps the current sky cube. */
smf_resampcube( data, skycube->abskyfrm,
skycube->iskymap, skycube->ispecfrm,
skycube->ispecmap, detgrp, skycube->moving,
skycube->slbnd, skycube->subnd, interp,
params, NULL, NULL, &overlap, status );
/* If not, pass on to the next sky cube. */
if( overlap ) {
/* Report the name of the sky cube. */
ndfMsg( "NDF", skycube->indf );
msgOutif( MSG__NORM, " ", " Re-sampling ^NDF", status );
/* Map the data array in the current sky cube. */
ndfMap( skycube->indf, "DATA", "_REAL", "READ", &in_data, &nel,
status );
/* Resample the cube data into the output time series. */
smf_resampcube( data, skycube->abskyfrm,
skycube->iskymap, skycube->ispecfrm,
skycube->ispecmap, detgrp, skycube->moving,
skycube->slbnd, skycube->subnd, interp,
params, in_data, out_data, &overlap, status );
/* Unmap the data array. */
ndfUnmap( skycube->indf, "DATA", status );
}
}
/* Write the provenance structure to the output NDF, and then free it. */
ndgWriteProv( oprov, ondf, 1, status );
oprov =ndgFreeProv( oprov, status );
/* Close the input time series file. */
if( data != NULL ) {
smf_close_file( &data, status );
data = NULL;
}
/* End the NDF context. */
ndfEnd( status );
}
/* Close any input data file that is still open due to an early exit from
the above loop. */
if( data != NULL ) {
smf_close_file( &data, status );
data = NULL;
}
/* Free remaining resources. */
if( detgrp != NULL) grpDelet( &detgrp, status);
if( igrp1 != NULL) grpDelet( &igrp1, status);
if( igrp2 != NULL) grpDelet( &igrp2, status);
if( ogrp != NULL) grpDelet( &ogrp, status);
sky_cubes = astFree( sky_cubes );
/* End the NDF context. */
ndfEnd( status );
/* End the tile's AST context. */
astEnd;
/* Issue a status indication.*/
if( *status == SAI__OK ) {
msgOutif(MSG__VERB," ",TASK_NAME " succeeded, time series written.", status);
} else {
msgOutif(MSG__VERB," ",TASK_NAME " failed.", status);
}
}
void smurf_sc2concat( int *status ) {
/* Local Variables */
Grp *basegrp=NULL; /* Grp containing first file each chunk */
size_t basesize; /* Number of files in base group */
smfArray *concat=NULL; /* Pointer to a smfArray */
size_t contchunk; /* Continuous chunk counter */
smfArray *darks = NULL; /* dark frames */
int ensureflat; /* Flag for flatfielding data */
Grp *fgrp = NULL; /* Filtered group, no darks */
smfArray * flatramps = NULL; /* Flatfield ramps */
AstKeyMap *heateffmap = NULL; /* Heater efficiency data */
size_t gcount=0; /* Grp index counter */
size_t idx; /* Subarray counter */
int usedarks; /* flag for using darks */
Grp *igrp = NULL; /* Group of input files */
smfGroup *igroup=NULL; /* smfGroup corresponding to igrp */
size_t isize; /* Number of files in input group */
dim_t maxconcat=0; /* Longest continuous chunk length in samples */
double maxlen; /* Constrain maxconcat to this many seconds */
size_t ncontchunks=0; /* Number continuous chunks outside iter loop */
Grp *ogrp = NULL; /* Output files */
size_t osize; /* Number of files in input group */
dim_t padStart=0; /* How many samples padding at start */
dim_t padEnd=0; /* How many samples padding at end */
int temp; /* Temporary signed integer */
ThrWorkForce *wf = NULL; /* Pointer to a pool of worker threads */
if (*status != SAI__OK) return;
/* Main routine */
ndfBegin();
/* Find the number of cores/processors available and create a pool of
threads of the same size. */
wf = thrGetWorkforce( thrGetNThread( SMF__THREADS, status ), status );
/* Read the input file */
kpg1Rgndf( "IN", 0, 1, "", &igrp, &isize, status );
/* Filter out darks */
smf_find_science( igrp, &fgrp, 1, NULL, NULL, 1, 1, SMF__NULL, &darks,
&flatramps, &heateffmap, NULL, status );
/* input group is now the filtered group so we can use that and
free the old input group */
isize = grpGrpsz( fgrp, status );
grpDelet( &igrp, status);
igrp = fgrp;
fgrp = NULL;
if (isize == 0) {
msgOutif(MSG__NORM, " ","All supplied input frames were filtered,"
" nothing to do", status );
goto CLEANUP;
}
/* --- Parse ADAM parameters ------------------------ */
/* Maximum length of a continuous chunk */
parGdr0d( "MAXLEN", 0, 0, VAL__MAXD, 1, &maxlen, status );
/* Padding */
parGdr0i( "PADSTART", 0, 0, VAL__MAXI, 1, &temp, status );
padStart = (dim_t) temp;
parGdr0i( "PADEND", 0, 0, VAL__MAXI, 1, &temp, status );
padEnd = (dim_t) temp;
/* Are we using darks? */
parGet0l( "USEDARKS", &usedarks, status );
/* Are we flatfielding? */
parGet0l( "FLAT", &ensureflat, status );
/* Group the input files by subarray and continuity */
smf_grp_related( igrp, isize, 1, 0, maxlen-padStart-padEnd, NULL, NULL,
&maxconcat, NULL, &igroup, &basegrp, NULL, status );
/* Obtain the number of continuous chunks and subarrays */
if( *status == SAI__OK ) {
ncontchunks = igroup->chunk[igroup->ngroups-1]+1;
}
basesize = grpGrpsz( basegrp, status );
/* Get output file(s) */
kpg1Wgndf( "OUT", basegrp, basesize, basesize,
"More output files required...",
&ogrp, &osize, status );
/* Loop over continuous chunks */
gcount = 1;
for( contchunk=0;(*status==SAI__OK)&&contchunk<ncontchunks; contchunk++ ) {
/* Concatenate this continuous chunk */
smf_concat_smfGroup( wf, NULL, igroup, usedarks ? darks:NULL, NULL, flatramps,
heateffmap, contchunk, ensureflat, 1, NULL, 0, NULL, NULL,
NO_FTS, padStart, padEnd, 0, &concat, NULL, status );
/* Export concatenated data for each subarray to NDF file */
for( idx=0; (*status==SAI__OK)&&idx<concat->ndat; idx++ ) {
if( concat->sdata[idx]->file && concat->sdata[idx]->file->name ) {
smf_write_smfData( concat->sdata[idx], NULL, NULL, ogrp, gcount,
NDF__NOID, MSG__VERB, 0, status );
} else {
*status = SAI__ERROR;
errRep( FUNC_NAME,
"Unable to determine file name for concatenated data.",
status );
}
/* Increment the group index counter */
gcount++;
}
/* Close the smfArray */
smf_close_related( &concat, status );
}
/* Write out the list of output NDF names, annulling the error if a null
parameter value is supplied. */
if( *status == SAI__OK && ogrp ) {
grpList( "OUTFILES", 0, 0, NULL, ogrp, status );
if( *status == PAR__NULL ) errAnnul( status );
}
CLEANUP:
if( darks ) smf_close_related( &darks, status );
if( flatramps ) smf_close_related( &flatramps, status );
if (heateffmap) heateffmap = smf_free_effmap( heateffmap, status );
if( igrp ) grpDelet( &igrp, status);
if( basegrp ) grpDelet( &basegrp, status );
if( ogrp ) grpDelet( &ogrp, status );
if( igroup ) smf_close_smfGroup( &igroup, status );
ndfEnd( status );
if( *status == SAI__OK ) {
msgOutif(MSG__VERB," ","SC2CONCAT succeeded.", status);
} else {
msgOutif(MSG__VERB," ","SC2CONCAT failed.", status);
}
}
void smf_bolonoise( ThrWorkForce *wf, smfData *data, double gfrac,
size_t window, double f_low,
double f_white1, double f_white2,
int nep, size_t len, double *whitenoise, double *fratio,
smfData **fftpow,int *status ) {
double *base=NULL; /* Pointer to base coordinates of array */
size_t bstride; /* bolometer index stride */
double df=1; /* Frequency step size in Hz */
size_t i; /* Loop counter */
size_t i_low; /* Index in power spectrum to f_low */
size_t i_w1; /* Index in power spectrum to f_white1 */
size_t i_w2; /* Index in power spectrum to f_white2 */
size_t j; /* Loop counter */
size_t mingood; /* Min. required no. of good values in bolometer */
dim_t nbolo; /* Number of bolometers */
dim_t ndata; /* Number of data points */
dim_t nf=0; /* Number of frequencies */
size_t ngood; /* Number of good samples */
dim_t ntslice; /* Number of time slices */
double p_low; /* Power at f_low */
double p_white; /* Average power from f_white1 to f_white2 */
smfData *pow=NULL; /* Pointer to power spectrum data */
smf_qual_t *qua=NULL; /* Pointer to quality component */
double steptime=1; /* Length of a sample in seconds */
size_t tstride; /* time index stride */
if (*status != SAI__OK) return;
/* Check inputs */
if (!smf_dtype_check_fatal( data, NULL, SMF__DOUBLE, status )) return;
if( !data->hdr ) {
*status = SAI__ERROR;
errRep( "", FUNC_NAME ": smfData has no header", status );
return;
}
/* Obtain dimensions */
smf_get_dims( data, NULL, NULL, &nbolo, &ntslice, &ndata, &bstride, &tstride,
status );
if( *status==SAI__OK ) {
steptime = data->hdr->steptime;
if( steptime < VAL__SMLD ) {
*status = SAI__ERROR;
errRep("", FUNC_NAME ": FITS header error, STEPTIME must be > 0",
status);
} else {
/* Frequency steps in the FFT */
df = 1. / (steptime * (double) ntslice );
}
}
/* Initialize arrays */
if( whitenoise ) for(i=0; i<nbolo; i++) whitenoise[i] = VAL__BADD;
if( fratio ) for(i=0; i<nbolo; i++) fratio[i] = VAL__BADD;
/* FFT the data and convert to polar power spectral density form */
pow = smf_fft_data( wf, data, NULL, 0, len, status );
smf_convert_bad( wf, pow, status );
smf_fft_cart2pol( wf, pow, 0, 1, status );
{
dim_t fdims[2];
smf_isfft( pow, NULL, NULL, fdims, NULL, NULL, status );
if( *status == SAI__OK ) nf=fdims[0];
}
/* Check for reasonble frequencies, and integer offsets in the array */
i_low = smf_get_findex( f_low, df, nf, status );
i_w1 = smf_get_findex( f_white1, df, nf, status );
i_w2 = smf_get_findex( f_white2, df, nf, status );
/* Get the quality pointer from the smfData so that we can mask known
bad bolometer. */
qua = smf_select_qualpntr( data, NULL, status );
/* The minimum required number of good values in a bolometer. */
mingood = ( gfrac > 0.0 ) ? ntslice*gfrac : 0;
/* Loop over detectors */
for( i=0; (*status==SAI__OK)&&(i<nbolo); i++ )
if( !qua || !(qua[i*bstride]&SMF__Q_BADB) ) {
/* Pointer to start of power spectrum */
base = pow->pntr[0];
base += nf*i;
/* Smooth the power spectrum */
smf_boxcar1D( base, nf, 1, window, NULL, 0, 1, NULL, status );
/* Measure the power */
if( *status == SAI__OK ) {
p_low = base[i_low];
smf_stats1D( base+i_w1, 1, i_w2-i_w1+1, NULL, 0, 0, &p_white, NULL, NULL,
&ngood, status );
/* It's OK if bad status was generated as long as a mean was calculated */
if( *status==SMF__INSMP ) {
errAnnul( status );
/* if we had no good data there was probably a problem with SMF__Q_BADB
so we simply go to the next bolometer */
if (ngood == 0) continue;
}
/* Count the number of initially good values for the current
bolometer. */
if( (*status==SAI__OK) && qua ) {
ngood = 0;
for( j=0; j<ntslice; j++ ) {
if( qua[i*bstride + j*tstride] == 0 ) ngood++;
}
/* Set bolometer to bad if no power detected, or the number of good
values is too low. */
if( (p_low <= 0) || (p_white <= 0) || (ngood < mingood) ) {
for( j=0; j<ntslice; j++ ) {
qua[i*bstride + j*tstride] |= SMF__Q_BADB;
}
}
}
}
if( (*status==SAI__OK) && (!qua || !(qua[i*bstride]&SMF__Q_BADB)) ) {
/* Power ratio requested */
if ( fratio ) {
fratio[i] = p_low/p_white;
}
/* Store values */
if( whitenoise ) {
/* Integrate the PSD by multiplying the average white noise
level by total number of samples and the frequency spacing:
this calculates the time-domain variance (in 200 Hz SCUBA-2
samples for example) assuming this level holds at all
frequencies. */
whitenoise[i] = p_white * ntslice * df;
/* If NEP set, scale this to variance in a 1-second average by
dividing by the sampling frequency (equivalent to
multiplying by sample length). */
if( nep ) {
whitenoise[i] *= steptime;
}
}
}
}
/* Clean up if the caller does not want to take over the power spectrum */
if( pow ) {
if (fftpow) {
*fftpow = pow;
} else {
smf_close_file( &pow, status );
}
}
}
void smurf_calcqu( int *status ) {
/* Local Variables: */
AstFitsChan *fc; /* Holds FITS headers for output NDFs */
AstKeyMap *config; /* Holds all cleaning parameters */
AstKeyMap *dkpars; /* Holds dark squid cleaning parameters */
AstKeyMap *heateffmap = NULL; /* Heater efficiency data */
AstKeyMap *sub_instruments;/* Indicates which instrument is being used */
Grp *bgrp = NULL; /* Group of base names for each chunk */
Grp *igrp = NULL; /* Group of input files */
Grp *ogrp = NULL; /* Group of output files */
Grp *sgrp = NULL; /* Group of science files */
HDSLoc *loci = NULL; /* Locator for output I container file */
HDSLoc *locq = NULL; /* Locator for output Q container file */
HDSLoc *locu = NULL; /* Locator for output U container file */
NdgProvenance *oprov; /* Provenance to store in each output NDF */
ThrWorkForce *wf; /* Pointer to a pool of worker threads */
char headval[ 81 ]; /* FITS header value */
char ndfname[ 30 ]; /* Name of output Q or U NDF */
char polcrd[ 81 ]; /* FITS 'POL_CRD' header value */
char subarray[ 10 ]; /* Subarray name (e.g. "s4a", etc) */
double angrot; /* Angle from focal plane X axis to fixed analyser */
double paoff; /* WPLATE value corresponding to POL_ANG=0.0 */
float arcerror; /* Max acceptable error (arcsec) in one block */
int block_end; /* Index of last time slice in block */
int block_start; /* Index of first time slice in block */
int dkclean; /* Clean dark squids? */
int fix; /* Fix the POL-2 triggering issue? */
int iblock; /* Index of current block */
int iplace; /* NDF placeholder for current block's I image */
int ipolcrd; /* Reference direction for waveplate angles */
int maxsize; /* Max no. of time slices in a block */
int minsize; /* Min no. of time slices in a block */
int nc; /* Number of characters written to a string */
int pasign; /* +1 or -1 indicating sense of POL_ANG value */
int qplace; /* NDF placeholder for current block's Q image */
int submean; /* Subtract mean value from each time slice? */
int uplace; /* NDF placeholder for current block's U image */
size_t ichunk; /* Continuous chunk counter */
size_t idx; /* Subarray counter */
size_t igroup; /* Index for group of related input NDFs */
size_t inidx; /* Index into group of science input NDFs */
size_t nchunk; /* Number continuous chunks outside iter loop */
size_t ssize; /* Number of science files in input group */
smfArray *concat = NULL; /* Pointer to smfArray holding bolometer data */
smfArray *darks = NULL; /* dark frames */
smfArray *dkarray = NULL; /* Pointer to smfArray holding dark squid data */
smfArray *flatramps = NULL;/* Flatfield ramps */
smfData *data = NULL; /* Concatenated data for one subarray */
smfData *dkdata = NULL; /* Concatenated dark squid data for one subarray */
smfGroup *sgroup = NULL; /* smfGroup corresponding to sgrp */
/* Check inhereited status */
if( *status != SAI__OK ) return;
/* Start new AST and NDF contexts. */
astBegin;
ndfBegin();
/* Find the number of cores/processors available and create a work force
holding the same number of threads. */
wf = thrGetWorkforce( thrGetNThread( SMF__THREADS, status ), status );
/* Get a group of input files */
kpg1Rgndf( "IN", 0, 1, " Give more NDFs...", &igrp, &ssize, status );
/* Get a group containing just the files holding science data. */
smf_find_science( igrp, &sgrp, 0, NULL, NULL, 1, 1, SMF__NULL, &darks,
&flatramps, &heateffmap, NULL, status );
/* Check we have at least once science file. */
ssize = grpGrpsz( sgrp, status );
if( ssize == 0 ) {
msgOutif( MSG__NORM, " ", "All supplied input frames were DARK.",
status );
} else {
/* See if a correction should be made for the POL2 triggering issue. */
parGet0l( "FIX", &fix, status );
/* Create HDS container files to hold the output NDFs. */
datCreat( "OUTQ", "CALCQU", 0, 0, status );
datCreat( "OUTU", "CALCQU", 0, 0, status );
/* Associate the locators with the structures. */
datAssoc( "OUTQ", "WRITE", &locq, status );
datAssoc( "OUTU", "WRITE", &locu, status );
/* The I images are optional. */
if( *status == SAI__OK ) {
datCreat( "OUTI", "CALCQU", 0, 0, status );
datAssoc( "OUTI", "WRITE", &loci, status );
if( *status == PAR__NULL ) {
errAnnul( status );
loci = NULL;
}
}
/* Group the input files so that all files within a single group have the
same wavelength and belong to the same subscan of the same observation.
Also identify chunks of data that are contiguous in time, and
determine to which such chunk each group belongs. All this information
is returned in a smfGroup structure ("*sgroup"). */
smf_grp_related( sgrp, ssize, 1, 1, 0, NULL, NULL, NULL,
NULL, &sgroup, &bgrp, NULL, status );
/* Obtain the number of contiguous chunks. */
if( *status == SAI__OK ) {
nchunk = sgroup->chunk[ sgroup->ngroups - 1 ] + 1;
} else {
nchunk = 0;
}
/* Indicate we have not yet found a value for the ARCERROR parameter. */
arcerror = 0.0;
/* Loop over all contiguous chunks */
for( ichunk = 0; ichunk < nchunk && *status == SAI__OK; ichunk++ ) {
/* Display the chunk number. */
if( nchunk > 1 ) {
msgOutiff( MSG__VERB, "", " Doing chunk %d of %d.",
status, (int) ichunk + 1, (int) nchunk );
}
/* Concatenate the data within this contiguous chunk. This produces a
smfArray ("concat") containing a smfData for each subarray present in
the chunk. Each smfData holds the concatenated data for a single
subarray. */
smf_concat_smfGroup( wf, NULL, sgroup, darks, NULL, flatramps,
heateffmap, ichunk, 1, 1, NULL, 0, NULL, NULL,
0, 0, 0, &concat, NULL, status );
/* Get a KeyMap holding values for the configuration parameters. Since we
sorted by wavelength when calling smf_grp_related, we know that all
smfDatas in the current smfArray (i.e. chunk) will relate to the same
wavelength. Therefore we can use the same parameters for all smfDatas in
the current smfArray. */
sub_instruments = smf_subinst_keymap( SMF__SUBINST_NONE,
concat->sdata[ 0 ], NULL,
0, status );
config = kpg1Config( "CONFIG", "$SMURF_DIR/smurf_calcqu.def",
sub_instruments, status );
sub_instruments = astAnnul( sub_instruments );
/* Get the CALCQU specific parameters. */
if( !astMapGet0I( config, "PASIGN", &pasign ) ) pasign = 1;
msgOutiff( MSG__VERB, "", "PASIGN=%d", status, pasign );
if( !astMapGet0D( config, "PAOFF", &paoff ) ) paoff = 0.0;
msgOutiff( MSG__VERB, "", "PAOFF=%g", status, paoff );
if( !astMapGet0D( config, "ANGROT", &angrot ) ) angrot = 90.0;
msgOutiff( MSG__VERB, "", "ANGROT=%g", status, angrot );
if( !astMapGet0I( config, "SUBMEAN", &submean ) ) submean = 0;
msgOutiff( MSG__VERB, "", "SUBMEAN=%d", status, submean );
/* See if the dark squids should be cleaned. */
if( !astMapGet0I( config, "DKCLEAN", &dkclean ) ) dkclean = 0;
/* If required, clean the dark squids now since we might need to use them to
clean the bolometer data. */
if( dkclean ) {
/* Create a smfArray containing the dark squid data. For each one, store
a pointer to the main header so that smf_clean_smfArray can get at the
JCMTState information. */
dkarray = smf_create_smfArray( status );
for( idx = 0; idx < concat->ndat && *status == SAI__OK; idx++ ) {
data = concat->sdata[ idx ];
if( data && data->da && data->da->dksquid ) {
dkdata = data->da->dksquid;
dkdata->hdr = data->hdr;
smf_addto_smfArray( dkarray, dkdata, status );
}
}
/* Clean the smfArray containing the dark squid data. Use the "CLEANDK.*"
parameters. */
(void) astMapGet0A( config, "CLEANDK", &dkpars );
smf_clean_smfArray( wf, dkarray, NULL, NULL, NULL, dkpars, status );
dkpars = astAnnul( dkpars );
/* Nullify the header pointers so that we don't accidentally close any. */
if( dkarray ) {
for( idx = 0; idx < dkarray->ndat; idx++ ) {
dkdata = dkarray->sdata[ idx ];
dkdata->hdr = NULL;
}
/* Free the smfArray holding the dark squid data, but do not free the
individual smfDatas within it. */
dkarray->owndata = 0;
smf_close_related( &dkarray, status );
}
}
/* Now clean the bolometer data */
smf_clean_smfArray( wf, concat, NULL, NULL, NULL, config, status );
/* If required correct for the POL2 triggering issue. */
if( fix ) smf_fix_pol2( wf, concat, status );
/* Loop round each sub-array in the current contiguous chunk of data. */
for( idx = 0; idx < concat->ndat && *status == SAI__OK; idx++ ) {
data = concat->sdata[ idx ];
/* Find the name of the subarray that generated the data. */
smf_find_subarray( data->hdr, subarray, sizeof(subarray), NULL,
status );
/* Display the sub-array. */
if( concat->ndat > 1 ) {
msgOutiff( MSG__VERB, "", " Doing sub-array %s.",
status, subarray );
}
/* Create an empty provenance structure. Each input NDF that contributes
to the current chunk and array will be added as an ancestor to this
structure, which will later be stored in each output NDF created for
this chunk and array. */
oprov = ndgReadProv( NDF__NOID, "SMURF:CALCQU", status );
/* Indicate we do not yet have any FITS headers for the output NDFs */
fc = NULL;
/* Indicate we do not yet know the coordinate reference frame for the
half-waveplate angle. */
polcrd[ 0 ] = 0;
ipolcrd = 0;
/* Go through the smfGroup looking for groups of related input NDFs that
contribute to the current chunk. */
for( igroup = 0; igroup < sgroup->ngroups; igroup++ ) {
if( sgroup->chunk[ igroup ] == ichunk ) {
/* Get the integer index into the GRP group (sgrp) that holds the input NDFs.
This index identifies the input NDF that provides the data for the current
chunk and subarray. This assumes that the order in which smf_concat_smfGroup
stores arrays in the "concat" smfArray matches the order in which
smf_grp_related stores arrays within the sgroup->subgroups. */
inidx = sgroup->subgroups[ igroup ][ idx ];
/* Add this input NDF as an ancestor into the output provenance structure. */
smf_accumulate_prov( NULL, sgrp, inidx, NDF__NOID,
"SMURF:CALCQU", &oprov, status );
/* Merge the FITS headers from the current input NDF into the FitsChan
that holds headers for the output NDFs. The merging retains only those
headers which have the same value in all input NDFs. */
smf_fits_outhdr( data->hdr->fitshdr, &fc, status );
/* Get the polarimetry related FITS headers and check that all input NDFs
have usabie values. */
headval[ 0 ] = 0;
smf_getfitss( data->hdr, "POL_MODE", headval,
sizeof(headval), status );
if( strcmp( headval, "CONSTANT" ) && *status == SAI__OK ) {
*status = SAI__ERROR;
grpMsg( "N", sgrp, inidx );
errRep( " ", "Input NDF ^N does not contain "
"polarimetry data obtained with a spinning "
"half-waveplate.", status );
}
headval[ 0 ] = 0;
smf_getfitss( data->hdr, "POLWAVIN", headval,
sizeof(headval), status );
if( strcmp( headval, "Y" ) && *status == SAI__OK ) {
*status = SAI__ERROR;
grpMsg( "N", sgrp, inidx );
errRep( " ", "Half-waveplate was not in the beam for "
"input NDF ^N.", status );
}
headval[ 0 ] = 0;
smf_getfitss( data->hdr, "POLANLIN", headval,
sizeof(headval), status );
if( strcmp( headval, "Y" ) && *status == SAI__OK ) {
*status = SAI__ERROR;
grpMsg( "N", sgrp, inidx );
errRep( " ", "Analyser was not in the beam for input "
"NDF ^N.", status );
}
if( polcrd[ 0 ] ) {
headval[ 0 ] = 0;
smf_getfitss( data->hdr, "POL_CRD", headval,
sizeof(headval), status );
if( strcmp( headval, polcrd ) && *status == SAI__OK ) {
*status = SAI__ERROR;
errRep( " ", "Input NDFs have differing values for "
"FITS header 'POL_CRD'.", status );
}
} else {
smf_getfitss( data->hdr, "POL_CRD", polcrd,
sizeof(polcrd), status );
if( !strcmp( polcrd, "FPLANE" ) ) {
ipolcrd = 0;
} else if( !strcmp( polcrd, "AZEL" ) ) {
ipolcrd = 1;
} else if( !strcmp( polcrd, "TRACKING" ) ) {
ipolcrd = 2;
} else if( *status == SAI__OK ) {
*status = SAI__ERROR;
msgSetc( "N", data->file->name );
msgSetc( "V", polcrd );
errRep( " ", "Input NDF ^N contains unknown value "
"'^V' for FITS header 'POL_CRD'.", status );
}
}
}
}
/* If not already done, get the maximum spatial drift (in arc-seconds) that
can be tolerated whilst creating a single I/Q/U image. The default value is
half the makemap default pixel size. Also get limits on the number of
time slices in any block. */
if( arcerror == 0.0 ) {
parDef0d( "ARCERROR", 0.5*smf_calc_telres( data->hdr->fitshdr,
status ), status );
parGet0r( "ARCERROR", &arcerror, status );
parGet0i( "MAXSIZE", &maxsize, status );
parGet0i( "MINSIZE", &minsize, status );
if( maxsize > 0 && maxsize < minsize && *status == SAI__OK ) {
*status = SAI__ERROR;
errRepf( "", "Value of parameter MAXSIZE (%d) is less "
"than value of parameter MINSIZE (%d)", status,
maxsize, minsize );
}
}
/* The algorithm that calculates I, Q and U assumes that all samples for a
single bolometer measure flux from the same point on the sky. Due to
sky rotation, this will not be the case - each bolometer will drift
slowly across the sky. However, since the drift is (or should be)
slow we can apply the I/Q/U algorithm to blocks of contiguous data over
which the bolometers do not move significantly. We produce a separate
I, Q and U image for each such block. The first block starts at the first
time slice in the smfData. */
block_start = 0;
/* Find the time slice at which the corner bolometers have moved
a critical distance (given by parameter ARCERROR) from their
positions at the start of the block. Then back off some time slices
to ensure that the block holds an integral number of half-waveplate
rotations. */
block_end = smf_block_end( data, block_start, ipolcrd, arcerror,
maxsize, status );
/* Loop round creating I/Q/U images for each block. Count them. */
iblock = 0;
while( block_end >= 0 && *status == SAI__OK ) {
/* Skip very short blocks. */
if( block_end - block_start > minsize ) {
/* Display the start and end of the block. */
msgOutiff( MSG__VERB, "", " Doing time slice block %d "
"-> %d", status, (int) block_start,
(int) block_end );
/* Get the name for the Q NDF for this block. Start of with "Q" followed by
the block index. */
iblock++;
nc = sprintf( ndfname, "Q%d", iblock );
/* Append the subarray name to the NDF name. */
nc += sprintf( ndfname + nc, "_%s", subarray );
/* Append the chunk index to the NDF name. */
nc += sprintf( ndfname + nc, "_%d", (int) ichunk );
/* Get NDF placeholder for the Q NDF. The NDFs are created inside the
output container file. */
ndfPlace( locq, ndfname, &qplace, status );
/* The name of the U NDF is the same except the initial "Q" is changed to
"U". */
ndfname[ 0 ] = 'U';
ndfPlace( locu, ndfname, &uplace, status );
/* The name of the I NDF is the same except the initial "Q" is changed to
"I". */
if( loci ) {
ndfname[ 0 ] = 'I';
ndfPlace( loci, ndfname, &iplace, status );
} else {
iplace = NDF__NOPL;
}
/* Store the chunk and block numbers as FITS headers. */
atlPtfti( fc, "POLCHUNK", (int) ichunk, "Chunk index used by CALCQU", status );
atlPtfti( fc, "POLBLOCK", iblock, "Block index used by CALCQU", status );
/* Create the Q and U images for the current block of time slices from
the subarray given by "idx", storing them in the output container
file. */
smf_calc_iqu( wf, data, block_start, block_end, ipolcrd,
qplace, uplace, iplace, oprov, fc,
pasign, AST__DD2R*paoff, AST__DD2R*angrot,
submean, status );
/* Warn about short blocks. */
} else {
msgOutiff( MSG__VERB, "", " Skipping short block of %d "
"time slices (parameter MINSIZE=%d).", status,
block_end - block_start - 1, minsize );
}
/* The next block starts at the first time slice following the previous
block. */
block_start = block_end + 1;
/* Find the time slice at which the corner bolometers have moved
a critical distance (given by parameter ARCERROR) from their
positions at the start of the block. Then back off some time slices
to ensure that the block holds an integral number of half-waveplate
rotations. This returns -1 if all time slices have been used. */
block_end = smf_block_end( data, block_start, ipolcrd,
arcerror, maxsize, status );
}
/* Free resources */
oprov = ndgFreeProv( oprov, status );
fc = astAnnul( fc );
}
config = astAnnul( config );
/* Close the smfArray. */
smf_close_related( &concat, status );
}
/* Annul the locators for the output container files. */
datAnnul( &locq, status );
datAnnul( &locu, status );
if( loci ) datAnnul( &loci, status );
/* The parameter system hangs onto a primary locator for each container
file, so cancel the parameters to annul these locators. */
datCancl( "OUTQ", status );
datCancl( "OUTU", status );
datCancl( "OUTI", status );
}
/* Free resources. */
smf_close_related( &darks, status );
smf_close_related( &flatramps, status );
if( igrp ) grpDelet( &igrp, status);
if( sgrp ) grpDelet( &sgrp, status);
if( bgrp ) grpDelet( &bgrp, status );
if( ogrp ) grpDelet( &ogrp, status );
if( sgroup ) smf_close_smfGroup( &sgroup, status );
if (heateffmap) heateffmap = smf_free_effmap( heateffmap, status );
/* End the NDF and AST contexts. */
ndfEnd( status );
astEnd;
/* Issue a status indication.*/
if( *status == SAI__OK ) {
msgOutif( MSG__VERB, " ", "CALCQU succeeded.", status);
} else {
msgOutif( MSG__VERB, " ", "CALCQU failed.", status);
}
}
/* Main entry */
void smf_jsadicer( int indf, const char *base, int trim, smf_inst_t instrument,
smf_jsaproj_t proj, size_t *ntile, Grp *grp, int *status ){
/* Local Variables: */
AstBox *box;
AstFitsChan *fc;
AstFrame *specfrm = NULL;
AstFrame *tile_frm = NULL;
AstFrameSet *iwcs;
AstFrameSet *tfs = NULL;
AstFrameSet *tile_wcs;
AstMapping *ndf_map = NULL;
AstMapping *p2pmap = NULL;
AstMapping *specmap = NULL;
AstMapping *tile_map = NULL;
AstRegion *region;
Grp *grpt = NULL;
char *path;
char dtype[ NDF__SZFTP + 1 ];
char jsatile_comment[45];
char type[ NDF__SZTYP + 1 ];
const char *dom = NULL;
const char *keyword;
const char *latsys = NULL;
const char *lonsys = NULL;
double *pd;
double dlbnd[3];
double dubnd[3];
double gcen[3];
double lbnd_in[3];
double lbnd_out[3];
double ubnd_in[3];
double ubnd_out[3];
float *pf;
int *created_tiles = NULL;
int *tiles;
int axlat;
int axlon;
int axspec;
int bbox[ 6 ];
int i;
int ifrm;
int igrid;
int indfo;
int indfs;
int indfx;
int inperm[3];
int ipixel;
int ishpx;
int isxph;
int itile;
int ix;
int iy;
int iz;
int junk;
int latax = -1;
int lbnd[3];
int lbnd_tile[ 3 ];
int lbndx[ NDF__MXDIM ];
int lonax = -1;
int nbase;
int ndim;
int ndimx;
int nfrm;
int nsig;
int ntiles;
int olbnd[ 3 ];
int oubnd[ 3 ];
int outperm[ 3 ];
int place;
int qual;
int tile_index;
int tile_lbnd[2];
int tile_ubnd[2];
int ubnd[3];
int ubnd_tile[ 3 ];
int ubndx[ NDF__MXDIM ];
int var;
size_t iext;
size_t size;
smfJSATiling tiling;
unsigned char *ipq = NULL;
void *ipd = NULL;
void *ipv = NULL;
/* Initialise */
*ntile = 0;
/* Check inherited status */
if( *status != SAI__OK ) return;
/* Begin an AST context. */
astBegin;
/* Begin an NDF context. */
ndfBegin();
/* Note the used length of the supplied base string. If it ends with
".sdf", reduce it by 4. */
nbase = astChrLen( base );
if( !strcmp( base + nbase - 4, ".sdf" ) ) nbase -= 4;
/* Allocate a buffer large enough to hold the full path for an output NDF. */
path = astMalloc( nbase + 25 );
/* Get the WCS from the NDF. */
kpg1Gtwcs( indf, &iwcs, status );
/* Note if the NDF projection is HPX or XPH. */
ishpx = astChrMatch( astGetC( iwcs, "Projection" ), "HEALPix" );
isxph = astChrMatch( astGetC( iwcs, "Projection" ), "polar HEALPix" );
/* Report an error if the NDFs projection is neither of these. */
if( !ishpx && !isxph && *status == SAI__OK ) {
ndfMsg( "N", indf );
*status = SAI__ERROR;
errRep( "", "The input NDF (^N) does not appear to be gridded "
"on the JSA all-sky pixel grid.", status );
}
/* Get the bounds of the NDF in pixel indices and the the corresponding
double precision GRID bounds (reduce the size of the grid by a small
amount to avoid problems with tiles that are on the edge of the valid sky
regions - astMapRegion can report an error for such tiles). Also store
the GRID coords of the centre. Also count the number of significant
pixel axes. */
ndfBound( indf, 3, lbnd, ubnd, &ndim, status );
nsig = 0;
for( i = 0; i < ndim; i++ ) {
dlbnd[ i ] = 0.5 + 0.1;
dubnd[ i ] = ubnd[ i ] - lbnd[ i ] + 1.5 - 0.1;
gcen[ i ] = 0.5*( dlbnd[ i ] + dubnd[ i ] );
if( ubnd[ i ] > lbnd[ i ] ) nsig++;
}
/* Find the one-based indices of the RA, Dec and spectral axes in the
current Frame of the NDF. */
axlon = 0;
if( astGetI( iwcs, "IsLonAxis(1)" ) ) {
axlon = 1;
lonsys = astGetC( iwcs, "System(1)" );
} else if( astGetI( iwcs, "IsLonAxis(2)" ) ) {
axlon = 2;
lonsys = astGetC( iwcs, "System(2)" );
} else if( ndim == 3 && astGetI( iwcs, "IsLonAxis(3)" ) ) {
axlon = 3;
lonsys = astGetC( iwcs, "System(3)" );
} else if( *status == SAI__OK ) {
*status = SAI__ERROR;
errRep( "", "smf_jsadicer: Cannot find the longitude axis in the "
"input NDF.", status );
}
axlat = 0;
if( astGetI( iwcs, "IsLatAxis(1)" ) ) {
axlat = 1;
latsys = astGetC( iwcs, "System(1)" );
} else if( astGetI( iwcs, "IsLatAxis(2)" ) ) {
axlat = 2;
latsys = astGetC( iwcs, "System(2)" );
} else if( ndim == 3 && astGetI( iwcs, "IsLatAxis(3)" ) ) {
axlat = 3;
latsys = astGetC( iwcs, "System(3)" );
} else if( *status == SAI__OK ) {
*status = SAI__ERROR;
errRep( "", "smf_jsadicer: Cannot find the latitude axis in the "
"input NDF.", status );
}
axspec = 6 - axlon - axlat;
/* Report an error if the spatial axes are not ICRS RA and Dec. */
if( ( lonsys && strcmp( lonsys, "ICRS" ) ) ||
( latsys && strcmp( latsys, "ICRS" ) ) ) {
if( *status == SAI__OK ) {
*status = SAI__ERROR;
ndfMsg( "N", indf );
errRep( "", "smf_jsadicer: The spatial axes in '^N' are not "
"ICRS RA and Dec.", status );
}
}
/* Create a Box describing the region covered by the NDF pixel grid in
GRID coords. */
box = astBox( astGetFrame( iwcs, AST__BASE ), 1, dlbnd, dubnd,
AST__NULL, " " );
/* Map this Box into the current WCS Frame of the NDF. */
region = astMapRegion( box, iwcs, iwcs );
/* If no instrument was specified, we will determine the instrument from
the contexts of the FITS extension. Copy the NDF FITS extension to a
FitsChan. Annul the error if the NDF no FITS extension. */
if( instrument == SMF__INST_NONE && *status == SAI__OK ) {
kpgGtfts( indf, &fc, status );
if( *status == KPG__NOFTS ) {
errAnnul( status );
fc = NULL;
}
} else {
fc = NULL;
}
/* Get the parameters of the required tiling scheme. */
smf_jsainstrument( NULL, fc, instrument, &tiling, status );
/* Get a list of the JSA tiles touched by the supplied NDF. */
tiles = smf_jsatiles_region( region, &tiling, &ntiles, status );
if( ntiles == 0 && *status == SAI__OK ) {
*status = SAI__ERROR;
errRep( "", "smf_jsadicer: No JSA tiles found touching supplied NDF "
"(programming error).", status );
}
/* Does the input NDF have a Variance component? */
ndfState( indf, "Variance", &var, status );
/* Does the input NDF have a Quality component? */
ndfState( indf, "Quality", &qual, status );
/* Decide on the data type to use: _REAL or _DOUBLE. */
ndfMtype( "_REAL,_DOUBLE", indf, indf, "Data", type, sizeof(type), dtype,
sizeof(dtype), status );
/* Tell the user what is happening. */
msgBlank( status );
msgOutf( "", "Dicing %s into JSA tiles:", status,
( nsig == 2 ) ? "map" : "cube" );
/* Loop round all tiles that overlap the supplied NDF. */
for( itile = 0; itile < ntiles && *status == SAI__OK; itile++ ) {
tile_index = tiles[ itile ];
/* Get the spatial pixel bounds of the current tile within the requested
JSA all-sky projection. Also get the (2D) WCS FrameSet for the tile. */
smf_jsatile( tile_index, &tiling, 0, proj, NULL, &tile_wcs, NULL,
tile_lbnd, tile_ubnd, status );
/* Extract the tile pixel->WCS mapping and WCS Frame. We know the indices
of the required Frames because they are hard-wired in smf_jsatile. */
tile_map = astGetMapping( tile_wcs, 3, 2 );
tile_frm = astGetFrame( tile_wcs, 2 );
/* Find the indices of the grid and pixel frames in the input NDF. */
ipixel = -1;
igrid = astGetI( iwcs, "Base" );
nfrm = astGetI( iwcs, "NFrame" );
for( ifrm = 0; ifrm < nfrm; ifrm++ ) {
dom = astGetC( astGetFrame( iwcs, ifrm + 1 ), "Domain" );
if( astChrMatch( dom, "PIXEL" ) ) ipixel = ifrm + 1;
}
/* If required, extract the pixel->spectral mapping and spectral frame in
the input NDF, and add it in parallel with the above tile mapping. */
if( ndim == 3 ) {
astSetI( iwcs, "Base", ipixel );
tfs = atlFrameSetSplit( iwcs, "DSBSPECTRUM SPECTRUM", NULL,
NULL, status );
astSetI( iwcs, "Base", igrid );
if( tfs ) {
specmap = astGetMapping( tfs, AST__BASE, AST__CURRENT );
specfrm = astGetFrame( tfs, AST__CURRENT );
} else if( *status == SAI__OK ) {
*status = SAI__ERROR;
ndfMsg( "N", indf );
errRep( "", "smf_jsadicer: Cannot find the spectral axis "
"in '^N'.", status );
}
tile_map = (AstMapping *) astCmpMap( tile_map, specmap, 0, " " );
tile_frm = (AstFrame *) astCmpFrame( tile_frm, specfrm, " " );
}
/* Ensure the Epoch is inherited form the input NDF. */
astSetD( tile_frm, "Epoch", astGetD( iwcs, "Epoch" ) );
/* Currently tile axis 1 is RA, axis 2 is Dec and axis 3 (if present) is
spectral. Append a PermMap that re-orders these tile WCS axes to match
those of the NDF. */
outperm[ axlon - 1 ] = 1;
outperm[ axlat - 1 ] = 2;
outperm[ axspec - 1 ] = 3;
inperm[ 0 ] = axlon;
inperm[ 1 ] = axlat;
inperm[ 2 ] = axspec;
tile_map = (AstMapping *) astCmpMap( tile_map, astPermMap( ndim, inperm,
ndim, outperm,
NULL, " " ),
1, " " );
tile_map = astSimplify( tile_map );
/* Also re-order the WCS axes in the tile frame. */
astPermAxes( tile_frm, outperm );
/* We want the zero-based indicies of the input pixel axes corresponding
to ra, dec and spectral. So find the indicies of the pixel axes in the
supplied NDF that are most closely aligned with each WCS axis. */
atlPairAxes( iwcs, NULL, gcen, NULL, inperm, status );
if( inperm[ 0 ] == axlon ) {
lonax = 0;
} else if( inperm[ 1 ] == axlon ) {
lonax = 1;
} else {
lonax = 2;
}
if( inperm[ 0 ] == axlat ) {
latax = 0;
} else if( inperm[ 1 ] == axlat ) {
latax = 1;
} else {
latax = 2;
}
/* To get the mapping from pixel coords in the input NDF to pixel coords
in the output NDF, we invert the above mapping so that it goes from WCS
to pixel, and append it to the end of the NDF pixel->WCS mapping. */
ndf_map = astGetMapping( iwcs, ipixel, AST__CURRENT );
astInvert( tile_map );
p2pmap = (AstMapping *) astCmpMap( ndf_map, tile_map, 1, " " );
p2pmap = astSimplify( p2pmap );
astInvert( tile_map );
/* Show the bounds of the tile within the input NDF. */
msgOutiff( MSG__DEBUG, "", " tile %d has bounds (%d:%d,%d:%d) "
"within the output NDF.", status, tile_index,
tile_lbnd[ 0 ], tile_ubnd[ 0 ], tile_lbnd[ 1 ],
tile_ubnd[ 1 ] );
/* Next job is to find the pixel bounds of the output NDF to create
which will hold data for the current tile. First map the pixel bounds
of the whole tile from output to input. */
lbnd_in[ 0 ] = tile_lbnd[ 0 ] - 0.5;
lbnd_in[ 1 ] = tile_lbnd[ 1 ] - 0.5;
lbnd_in[ 2 ] = lbnd[ 2 ] - 0.5;
ubnd_in[ 0 ] = tile_ubnd[ 0 ] - 0.5;
ubnd_in[ 1 ] = tile_ubnd[ 1 ] - 0.5;
ubnd_in[ 2 ] = ubnd[ 2 ] - 0.5;
astMapBox( p2pmap, lbnd_in, ubnd_in, 0, 1, lbnd_out + 0,
ubnd_out + 0, NULL, NULL );
astMapBox( p2pmap, lbnd_in, ubnd_in, 0, 2, lbnd_out + 1,
ubnd_out + 1, NULL, NULL );
if( ndim == 3 ) astMapBox( p2pmap, lbnd_in, ubnd_in, 0, 3,
lbnd_out + 2, ubnd_out + 2, NULL,
NULL );
lbnd_tile[ 0 ] = floor( lbnd_out[ 0 ] ) + 1;
lbnd_tile[ 1 ] = floor( lbnd_out[ 1 ] ) + 1;
lbnd_tile[ 2 ] = floor( lbnd_out[ 2 ] ) + 1;
ubnd_tile[ 0 ] = floor( ubnd_out[ 0 ] ) + 1;
ubnd_tile[ 1 ] = floor( ubnd_out[ 1 ] ) + 1;
ubnd_tile[ 2 ] = floor( ubnd_out[ 2 ] ) + 1;
/* Show the bounds of the tile within the input NDF. */
msgOutiff( MSG__DEBUG, "", " tile %d has bounds (%d:%d,%d:%d) "
"within the input NDF.", status, tile_index,
lbnd_tile[ 0 ], ubnd_tile[ 0 ], lbnd_tile[ 1 ],
ubnd_tile[ 1 ] );
/* If required, trim the bounds to the extent of the input NDF. */
if( trim ) {
if( lbnd_tile[ 0 ] < lbnd[ 0 ] ) lbnd_tile[ 0 ] = lbnd[ 0 ];
if( lbnd_tile[ 1 ] < lbnd[ 1 ] ) lbnd_tile[ 1 ] = lbnd[ 1 ];
if( lbnd_tile[ 2 ] < lbnd[ 2 ] ) lbnd_tile[ 2 ] = lbnd[ 2 ];
if( ubnd_tile[ 0 ] > ubnd[ 0 ] ) ubnd_tile[ 0 ] = ubnd[ 0 ];
if( ubnd_tile[ 1 ] > ubnd[ 1 ] ) ubnd_tile[ 1 ] = ubnd[ 1 ];
if( ubnd_tile[ 2 ] > ubnd[ 2 ] ) ubnd_tile[ 2 ] = ubnd[ 2 ];
}
/* Check there is some overlap. */
if( lbnd_tile[ 0 ] <= ubnd_tile[ 0 ] &&
lbnd_tile[ 1 ] <= ubnd_tile[ 1 ] &&
lbnd_tile[ 2 ] <= ubnd_tile[ 2 ] ){
/* Now need to check if this section of the input NDF contains any good
values. We also find the bounding box of the good values (within the
input pixel coordinate system). So first obtain and map the required
section of the input NDF. */
ndfSect( indf, ndim, lbnd_tile, ubnd_tile, &indfs, status );
ndfMap( indfs, "Data", type, "Read", &ipd, &junk, status );
if( var ) ndfMap( indfs, "Variance", type, "Read", &ipv, &junk, status );
if( qual ) ndfMap( indfs, "Quality", "_UBYTE", "Read", (void **) &ipq,
&junk, status );
/* Initialise the pixel bounds (within the input NDF) of the box holding
good data values for the current tile. */
bbox[ 0 ] = INT_MAX;
bbox[ 1 ] = INT_MAX;
bbox[ 2 ] = INT_MAX;
bbox[ 3 ] = -INT_MAX;
bbox[ 4 ] = -INT_MAX;
bbox[ 5 ] = -INT_MAX;
/* Loop round all pixels in the section. */
if( *status == SAI__OK ) {
if( !strcmp( type, "_REAL" ) ) {
pf = (float *) ipd;
for( iz = lbnd_tile[ 2 ]; iz <= ubnd_tile[ 2 ]; iz++ ) {
for( iy = lbnd_tile[ 1 ]; iy <= ubnd_tile[ 1 ]; iy++ ) {
for( ix = lbnd_tile[ 0 ]; ix <= ubnd_tile[ 0 ]; ix++ ) {
if( *(pf++) != VAL__BADR ) {
if( ix < bbox[ 0 ] ) bbox[ 0 ] = ix;
if( iy < bbox[ 1 ] ) bbox[ 1 ] = iy;
if( iz < bbox[ 2 ] ) bbox[ 2 ] = iz;
if( ix > bbox[ 3 ] ) bbox[ 3 ] = ix;
if( iy > bbox[ 4 ] ) bbox[ 4 ] = iy;
if( iz > bbox[ 5 ] ) bbox[ 5 ] = iz;
}
}
}
}
} else {
pd = (double *) ipd;
for( iz = lbnd_tile[ 2 ]; iz <= ubnd_tile[ 2 ]; iz++ ) {
for( iy = lbnd_tile[ 1 ]; iy <= ubnd_tile[ 1 ]; iy++ ) {
for( ix = lbnd_tile[ 0 ]; ix <= ubnd_tile[ 0 ]; ix++ ) {
if( *(pd++) != VAL__BADD ) {
if( ix < bbox[ 0 ] ) bbox[ 0 ] = ix;
if( iy < bbox[ 1 ] ) bbox[ 1 ] = iy;
if( iz < bbox[ 2 ] ) bbox[ 2 ] = iz;
if( ix > bbox[ 3 ] ) bbox[ 3 ] = ix;
if( iy > bbox[ 4 ] ) bbox[ 4 ] = iy;
if( iz > bbox[ 5 ] ) bbox[ 5 ] = iz;
}
}
}
}
}
/* Skip empty tiles. */
if( bbox[ 0 ] != INT_MAX ) {
msgOutf( "", " tile %d", status, tile_index );
/* If required, trim the bounds to the edges of the bounding box. */
if( trim >= 2 ) {
olbnd[ 0 ] = bbox[ 0 ];
olbnd[ 1 ] = bbox[ 1 ];
olbnd[ 2 ] = bbox[ 2 ];
oubnd[ 0 ] = bbox[ 3 ];
oubnd[ 1 ] = bbox[ 4 ];
oubnd[ 2 ] = bbox[ 5 ];
} else {
olbnd[ 0 ] = lbnd_tile[ 0 ];
olbnd[ 1 ] = lbnd_tile[ 1 ];
olbnd[ 2 ] = lbnd_tile[ 2 ];
oubnd[ 0 ] = ubnd_tile[ 0 ];
oubnd[ 1 ] = ubnd_tile[ 1 ];
oubnd[ 2 ] = ubnd_tile[ 2 ];
}
/* Modify these pixel bounds so that they refer to the output NDF. */
lbnd_in[ 0 ] = olbnd[ 0 ] - 0.5;
lbnd_in[ 1 ] = olbnd[ 1 ] - 0.5;
lbnd_in[ 2 ] = olbnd[ 2 ] - 0.5;
ubnd_in[ 0 ] = oubnd[ 0 ] - 0.5;
ubnd_in[ 1 ] = oubnd[ 1 ] - 0.5;
ubnd_in[ 2 ] = oubnd[ 2 ] - 0.5;
astMapBox( p2pmap, lbnd_in, ubnd_in, 1, 1, lbnd_out + 0,
ubnd_out + 0, NULL, NULL );
astMapBox( p2pmap, lbnd_in, ubnd_in, 1, 2, lbnd_out + 1,
ubnd_out + 1, NULL, NULL );
if( ndim == 3 ) astMapBox( p2pmap, lbnd_in, ubnd_in, 1, 3,
lbnd_out + 2, ubnd_out + 2, NULL,
NULL );
olbnd[ 0 ] = floor( lbnd_out[ 0 ] ) + 1;
olbnd[ 1 ] = floor( lbnd_out[ 1 ] ) + 1;
olbnd[ 2 ] = floor( lbnd_out[ 2 ] ) + 1;
oubnd[ 0 ] = floor( ubnd_out[ 0 ] ) + 1;
oubnd[ 1 ] = floor( ubnd_out[ 1 ] ) + 1;
oubnd[ 2 ] = floor( ubnd_out[ 2 ] ) + 1;
/* Get the full path to the output NDF for the current tile, and create an
NDF placeholder for it. */
sprintf( path, "%.*s_%d", nbase, base, tile_index );
ndfPlace( NULL, path, &place, status );
/* Create a new output NDF by copying the meta-data from the input NDF
section. */
ndfScopy( indfs, "Units", &place, &indfo, status );
/* Set the pixel bounds of the output NDF to the values found above and copy
the input data for the current tile into it. */
smf1_jsadicer( indfo, olbnd, oubnd, tile_map, tile_frm, p2pmap,
ipd, ipv, ipq, status );
/* Add the name of this output NDF to the group holding the names of the
output NDFs that have actually been created. */
if( grp ) grpPut1( grp, path, 0, status );
/* Add a TILENUM header to the output FITS extension. */
kpgGtfts( indfo, &fc, status );
if( *status == KPG__NOFTS ) {
errAnnul( status );
fc = astFitsChan( NULL, NULL, " " );
/* If the last card is "END", remove it. */
} else {
astSetI( fc, "Card", astGetI( fc, "NCARD" ) );
keyword = astGetC( fc, "CardName" );
if( keyword && !strcmp( keyword, "END" ) ) astDelFits( fc );
}
one_snprintf(jsatile_comment, 45, "JSA all-sky tile index (Nside=%i)",
status, tiling.ntpf);
atlPtfti( fc, "TILENUM", tile_index, jsatile_comment, status );
kpgPtfts( indfo, fc, status );
fc = astAnnul( fc );
/* Now store an STC-S polygon that describes the shortest boundary
enclosing the good data in the output NDF, and store it as an NDF extension. */
kpgPutOutline( indfo, 0.5, 1, status );
/* We now reshape any extension NDFs contained within the output NDF to
have the same spatial bounds as the main NDF (but only for extension
NDFs that originally have the same spatial bounds as the supplied NDF).
Get a group containing paths to all extension NDFs in the output NDF. */
ndgMoreg( indfo, &grpt, &size, status );
/* Loop round each output extension NDF. */
for( iext = 1; iext <= size && *status == SAI__OK; iext++ ) {
ndgNdfas( grpt, iext, "Update", &indfx, status );
/* Get its bounds. */
ndfBound( indfx, NDF__MXDIM, lbndx, ubndx, &ndimx, status );
/* See if this extension NDF has the same bounds on the spatial axes as
the supplied NDF. */
if( ndimx > 1 && lbndx[ lonax ] == lbnd[ lonax ] &&
lbndx[ latax ] == lbnd[ latax ] &&
ubndx[ lonax ] == ubnd[ lonax ] &&
ubndx[ latax ] == ubnd[ latax ] ) {
/* If so, change the bounds of the output extension NDF so that they are
the same as the main NDF on the spatial axes, and map the original
contents of the NDF onto the new pixel grid. */
smf1_jsadicer( indfx, olbnd, oubnd, tile_map, tile_frm, p2pmap,
NULL, NULL, NULL, status );
}
/* Annul the extension NDF identifier. */
ndfAnnul( &indfx, status );
}
/* Free resources associated with the current tile. */
grpDelet( &grpt, status );
ndfAnnul( &indfo, status );
/* Issue warnings about empty tiles. */
} else {
msgOutiff( MSG__VERB, "", " tile %d is empty and so will not be "
"created", status, tile_index );
}
}
/* Free the section of the input NDF. */
ndfAnnul( &indfs, status );
/* Append the index of this tile in the list of tiles to be created. */
created_tiles = astGrow( created_tiles, ++(*ntile),
sizeof( *created_tiles ) );
if( *status == SAI__OK ) created_tiles[ *ntile - 1 ] = tile_index;
} else {
msgOutiff( MSG__DEBUG, "", " Tile %d does not overlap the input "
"NDF after trimming.", status, tile_index );
}
}
msgBlank( status );
/* Write the indicies of the created tiles out to a parameter. */
if( *ntile ) parPut1i( "JSATILELIST", *ntile, created_tiles, status );
/* Free resources. */
created_tiles = astFree( created_tiles );
tiles = astFree( tiles );
path = astFree( path );
/* End the NDF context. */
ndfEnd( status );
/* End the AST context. */
astEnd;
}
void smurf_jsatileinfo( int *status ) {
/* Local Variables */
AstCmpRegion *overlap;
AstFitsChan *fc;
AstFrameSet *fs;
AstObject *obj;
AstRegion *region;
AstRegion *target;
HDSLoc *cloc = NULL;
HDSLoc *xloc = NULL;
char *jcmt_tiles;
char *tilendf = NULL;
char text[ 200 ];
double dec[ 8 ];
double dist;
double dlbnd[ 2 ];
double dubnd[ 2 ];
double gx[ 8 ];
double gy[ 8 ];
double maxdist;
double norm_radec[2];
double point1[ 2 ];
double point2[ 2 ];
double ra[ 8 ];
double ra0;
double dec0;
int *ipntr;
int axes[ 2 ];
int create;
int dirlen;
int el;
int exists;
int flag;
int i;
int indf1;
int indf2;
int indf3;
int itile;
int iv;
int jtile;
int lbnd[ 2 ];
int local_origin;
int nc;
int place;
int tlbnd[ 2 ];
int tubnd[ 2 ];
int ubnd[ 2 ];
smf_jsaproj_t proj;
int xt;
int yt;
smfJSATiling skytiling;
void *pntr;
/* Check inherited status */
if( *status != SAI__OK ) return;
/* Start a new AST context. */
astBegin;
/* Get the instrument to use abnd get the parameters describing the
layout of its JSA tiles. */
smf_jsainstrument( "INSTRUMENT", NULL, SMF__INST_NONE, &skytiling,
status );
/* Return the maximum tile index. */
parPut0i( "MAXTILE", skytiling.ntiles - 1, status );
/* Abort if an error has occurred. */
if( *status != SAI__OK ) goto L999;
/* Decide what sort of projection to use. */
parChoic( "PROJ", "HPX", "HPX,HPX12,XPHN,XPHS", 1, text, sizeof(text),
status );
proj = smf_jsaproj_fromstr( text, 1, status );
/* If required, create an all-sky NDF in which each pixel covers the area
of a single tile, and holds the integer tile index. The NDF has an
initial size of 1x1 pixels, but is expanded later to the required size. */
lbnd[ 0 ] = ubnd[ 0 ] = lbnd[ 1 ] = ubnd[ 1 ] = 1;
ndfCreat( "ALLSKY", "_INTEGER", 2, lbnd, ubnd, &indf3, status );
/* If a null (!) value was supplied for parameter ALLSKY, annull the
error and pass on. */
if( *status == PAR__NULL ) {
errAnnul( status );
/* Otherwise, create a FrameSet describing the whole sky in which each
pixel corresponds to a single tile. */
} else {
smf_jsatile( -1, &skytiling, 0, proj, NULL, &fs, NULL, lbnd, ubnd,
status );
/* Change the bounds of the output NDF. */
ndfSbnd( 2, lbnd, ubnd, indf3, status );
/* Store the FrameSet in the NDF. */
ndfPtwcs( fs, indf3, status );
/* Map the data array. */
ndfMap( indf3, "Data", "_INTEGER", "WRITE/BAD", (void **) &ipntr, &el,
status );
/* Create all-sky map using XPH projection. */
if( *status == SAI__OK ) {
/* Loop round every tile index. */
for( jtile = 0; jtile < skytiling.ntiles; jtile++ ) {
/* Get the zero-based (x,y) indices of the tile within an HPX projection.
This flips the bottom left half-facet up to the top right. */
smf_jsatilei2xy( jtile, &skytiling, &xt, &yt, NULL, status );
/* Convert these HPX indices to the corresponding indices within the
required projection. Note, the lower left facet is split by the above
call to smf_jsatilei2xy tile (i.e. (xt,yt) indices are *not* in the
"raw" mode). For instance, (0,0) is not a valid tile. */
smf_jsatilexyconv( &skytiling, proj, xt, yt, 0, &xt, &yt, status );
/* Get the vector index of the corresponding element of the all-sky NDF. */
if( proj == SMF__JSA_HPX || proj == SMF__JSA_HPX12 ) {
iv = xt + 5*skytiling.ntpf*yt;
} else {
iv = xt + 4*skytiling.ntpf*yt;
}
/* Report an error if this element has already been assigned a tile
index. Otherwise, store the tile index. */
if( ipntr[ iv ] == VAL__BADI ) {
ipntr[ iv ] = jtile;
} else if( *status == SAI__OK ) {
*status = SAI__ERROR;
errRepf( "", "%s projection assigns multiple tiles to "
"pixel (%d,%d).", status, text, xt, yt );
break;
}
}
}
/* Store NDF title. */
sprintf( text, "JSA tile indices for %s data", skytiling.name );
ndfCput( text, indf3, "TITLE", status );
/* Store the instrument as a component in the SMURF extension. */
ndfXnew( indf3, "SMURF", "INSTRUMENT", 0, 0, &xloc, status );
ndfXpt0c( skytiling.name, indf3, "SMURF", "INSTRUMENT", status );
datAnnul( &xloc, status );
/* Close the NDF. */
ndfAnnul( &indf3, status );
}
/* Abort if an error has occurred. */
if( *status != SAI__OK ) goto L999;
/* Get the zero-based index of the required tile. If a null value is
supplied, annull the error and skip to the end. */
parGdr0i( "ITILE", 0, 0, skytiling.ntiles - 1, 0, &itile, status );
if( *status == PAR__NULL ) {
errAnnul( status );
goto L999;
}
/* See if the pixel origin is to be at the centre of the tile. */
parGet0l( "LOCAL", &local_origin, status );
/* Display the tile number. */
msgBlank( status );
msgSeti( "ITILE", itile );
msgSeti( "MAXTILE", skytiling.ntiles - 1);
msgOut( " ", " Tile ^ITILE (from 0 to ^MAXTILE):", status );
/* Get the FITS header, FrameSet and Region defining the tile, and the tile
bounds in pixel indices. */
smf_jsatile( itile, &skytiling, local_origin, proj, &fc, &fs, ®ion,
lbnd, ubnd, status );
/* Write the FITS headers out to a file, annulling the error if the
header is not required. */
if( *status == SAI__OK ) {
atlDumpFits( "HEADER", fc, status );
if( *status == PAR__NULL ) errAnnul( status );
}
/* If required, write the Region out to a text file. */
if( *status == SAI__OK ) {
atlCreat( "REGION", (AstObject *) region, status );
if( *status == PAR__NULL ) errAnnul( status );
}
/* Store the lower and upper pixel bounds of the tile. */
parPut1i( "LBND", 2, lbnd, status );
parPut1i( "UBND", 2, ubnd, status );
/* Display pixel bounds on the screen. */
msgSeti( "XL", lbnd[ 0 ] );
msgSeti( "XU", ubnd[ 0 ] );
msgSeti( "YL", lbnd[ 1 ] );
msgSeti( "YU", ubnd[ 1 ] );
msgOut( " ", " Pixel bounds: (^XL:^XU,^YL:^YU)", status );
/* Get the RA,Dec at the tile centre. */
if( astTest( fs, "SkyRef" ) ) {
ra0 = astGetD( fs, "SkyRef(1)" );
dec0 = astGetD( fs, "SkyRef(2)" );
/* Format the central RA and Dec. and display. Call astNorm on the
coordinates provided that the frame set has the correct number of
axes (which it should as it comes from smf_jsatile). */
norm_radec[0] = ra0;
norm_radec[1] = dec0;
if (astGetI(fs, "Naxes") == 2) astNorm(fs, norm_radec);
msgSetc( "RACEN", astFormat( fs, 1, norm_radec[ 0 ] ));
msgSetc( "DECCEN", astFormat( fs, 2, norm_radec[ 1 ] ));
msgOut( " ", " Centre (ICRS): RA=^RACEN DEC=^DECCEN", status );
/* Transform a collection of points on the edge of the region (corners and
side mid-points) from GRID coords to RA,Dec. */
point1[ 0 ] = 0.5;
point1[ 1 ] = 0.5;
point2[ 0 ] = ubnd[ 0 ] - lbnd[ 0 ] + 1;
point2[ 1 ] = ubnd[ 1 ] - lbnd[ 1 ] + 1;
gx[ 0 ] = point1[ 0 ]; /* Bottom left */
gy[ 0 ] = point1[ 1 ];
gx[ 1 ] = point1[ 0 ]; /* Centre left */
gy[ 1 ] = gy[ 0 ];
gx[ 2 ] = point1[ 0 ]; /* Top left */
gy[ 2 ] = point2[ 1 ];
gx[ 3 ] = gx[ 0 ]; /* Top centre */
gy[ 3 ] = point2[ 1 ];
gx[ 4 ] = point2[ 0 ]; /* Top right */
gy[ 4 ] = point2[ 1 ];
gx[ 5 ] = point2[ 0 ]; /* Centre right */
gy[ 5 ] = gy[ 0 ];
gx[ 6 ] = point2[ 0 ]; /* Bottom right */
gy[ 6 ] = point1[ 1 ];
gx[ 7 ] = gx[ 0 ]; /* Bottom centre */
gy[ 7 ] = point1[ 1 ];
astTran2( fs, 8, gx, gy, 1, ra, dec );
/* Find the arc-distance from the centre to the furthest point from the
centre. */
point1[ 0 ] = ra0;
point1[ 1 ] = dec0;
maxdist = -1.0;
for( i = 1; i < 8; i++ ) {
if( ra[ i ] != AST__BAD && dec[ i ] != AST__BAD ) {
point2[ 0 ] = ra[ i ];
point2[ 1 ] = dec[ i ];
dist = astDistance( fs, point1, point2 );
if( dist > maxdist ) maxdist = dist;
}
}
/* Convert from radius to diameter. */
maxdist *= 2.0;
/* Format this size as a dec value (i.e. arc-distance) and display it. */
if( maxdist > 0.0 ) {
msgSetc( "SIZE", astFormat( fs, 2, maxdist ) );
msgOut( " ", " Size: ^SIZE", status );
} else {
maxdist = AST__BAD;
msgOut( " ", " Size: <unknown>", status );
}
/* If a discontinuity passes through the tile, the centre and size may be
unknown. */
} else {
ra0 = AST__BAD;
dec0 = AST__BAD;
maxdist = AST__BAD;
msgOut( " ", " Centre (ICRS): RA=<unknown> DEC=<unknown>", status );
msgOut( " ", " Size: <unknown>", status );
}
/* Write the tile centre ra and dec in radians to the output parameters. */
parPut0d( "RACEN", norm_radec[ 0 ], status );
parPut0d( "DECCEN", norm_radec[ 1 ], status );
/* Write the size to the output parameter as radians. */
parPut0d( "SIZE", maxdist, status );
/* Get the translation of the environment variable JSA_TILE_DIR. */
jcmt_tiles = getenv( "JSA_TILE_DIR" );
/* Initialise the path to the tile's NDF to hold the root directory.
Use the current working directory if JSA_TILE_DIR is undefined. */
if( jcmt_tiles ) {
nc = 0;
tilendf = astAppendString( tilendf, &nc, jcmt_tiles );
} else {
nc = 512;
jcmt_tiles = astMalloc( nc );
while( !getcwd( jcmt_tiles, nc ) ) {
nc *= 2;
jcmt_tiles = astRealloc( jcmt_tiles, nc );
}
nc = 0;
tilendf = astAppendString( tilendf, &nc, jcmt_tiles );
jcmt_tiles = astFree( jcmt_tiles );
}
/* Complete the path to the tile's NDF. */
tilendf = astAppendString( tilendf, &nc, "/" );
tilendf = astAppendString( tilendf, &nc, skytiling.subdir );
dirlen = nc;
sprintf( text, "/tile_%d.sdf", itile );
tilendf = astAppendString( tilendf, &nc, text );
/* Write it to the output parameter. */
parPut0c( "TILENDF", tilendf, status );
/* See if the NDF exists, and store the flag in the output parameter. */
exists = access( tilendf, F_OK ) ? 0 : 1;
parPut0l( "EXISTS", exists, status );
/* If the NDF does not exist, create it if required. */
parGet0l( "CREATE", &create, status );
if( !exists && create && *status == SAI__OK ) {
/* Write the NDF info to the screen. */
msgSetc( "NDF", tilendf );
msgOutif( MSG__NORM, " ", " NDF: ^NDF (created)", status );
/* Temporarily terminate the NDF path at the end of the subdirectory. */
tilendf[ dirlen ] = 0;
/* Create the required directory (does nothing if the directory
already exists). It is given read/write/search permissions for owner
and group, and read/search permissions for others. */
(void) mkdir( tilendf, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH );
/* Replace the character temporarily overwritten above. */
tilendf[ dirlen ] = '/';
/* Now create the tile's NDF. */
ndfPlace( NULL, tilendf, &place, status );
ndfNew( skytiling.type, 2, lbnd, ubnd, &place, &indf1, status );
/* Fill its data array with zeros. */
ndfMap( indf1, "Data", skytiling.type, "WRITE/ZERO", &pntr, &el,
status );
/* Store the WCS FrameSet. */
ndfPtwcs( fs, indf1, status );
/* If the instrument jsatiles.have variance, fill the variance array with zeros. */
if( skytiling.var ) {
ndfMap( indf1, "Variance", skytiling.type, "WRITE/ZERO", &pntr,
&el, status );
}
/* Create a SMURF extension. */
ndfXnew( indf1, SMURF__EXTNAME, SMURF__EXTTYPE, 0, NULL, &xloc, status );
/* Store the tile number and instrument name in the extension. */
datNew0I( xloc, "TILE", status );
datFind( xloc, "TILE", &cloc, status );
datPut0I( cloc, itile, status );
datAnnul( &cloc, status );
datNew0C( xloc, "INSTRUMENT", strlen( skytiling.name ), status );
datFind( xloc, "INSTRUMENT", &cloc, status );
datPut0C( cloc, skytiling.name, status );
datAnnul( &cloc, status );
/* Create a weights NDF within the SMURF extension, and fill its data
array with zeros. */
ndfPlace( xloc, "WEIGHTS", &place, status );
ndfNew( skytiling.type, 2, lbnd, ubnd, &place, &indf2, status );
ndfMap( indf2, "Data", skytiling.type, "WRITE/ZERO", &pntr, &el,
status );
ndfPtwcs( fs, indf2, status );
ndfAnnul( &indf2, status );
/* Annul the extension locator and the main NDF identifier. */
datAnnul( &xloc, status );
ndfAnnul( &indf1, status );
/* Write the NDF info to the screen. */
} else {
msgSetc( "NDF", tilendf );
msgSetc( "E", exists ? "exists" : "does not exist" );
msgOut( " ", " NDF: ^NDF (^E)", status );
}
/* Initialise TBND and TLBND to indicate no overlap. */
tlbnd[ 0 ] = 1;
tlbnd[ 1 ] = 1;
tubnd[ 0 ] = 0;
tubnd[ 1 ] = 0;
/* Attempt to to get an AST Region (assumed to be in some 2D sky coordinate
system) using parameter "TARGET". */
if( *status == SAI__OK ) {
kpg1Gtobj( "TARGET", "Region",
(void (*)( void )) F77_EXTERNAL_NAME(ast_isaregion),
&obj, status );
/* Annul the error if none was obtained. */
if( *status == PAR__NULL ) {
errAnnul( status );
/* Otherwise, use the supplied object. */
} else {
target = (AstRegion *) obj;
/* If the target Region is 3-dimensional, remove the third axis, which
is assumed to be a spectral axis. */
if( astGetI( target, "Naxes" ) == 3 ) {
axes[ 0 ] = 1;
axes[ 1 ] = 2;
target = astPickAxes( target, 2, axes, NULL );
}
/* See if there is any overlap between the target and the tile. */
overlap = NULL;
flag = astOverlap( region, target );
if( flag == 0 ) {
msgOut( "", " Cannot convert between the coordinate system of the "
"supplied target and the tile.", status );
} else if( flag == 1 || flag == 6 ) {
msgOut( "", " There is no overlap between the target and the tile.",
status );
} else if( flag == 2 ) {
msgOut( "", " The tile is contained within the target.",
status );
tlbnd[ 0 ] = lbnd[ 0 ];
tlbnd[ 1 ] = lbnd[ 1 ];
tubnd[ 0 ] = ubnd[ 0 ];
tubnd[ 1 ] = ubnd[ 1 ];
} else if( flag == 3 ) {
overlap = astCmpRegion( region, target, AST__AND, " " );
} else if( flag == 4 ) {
overlap = astCmpRegion( region, target, AST__AND, " " );
} else if( flag == 5 ) {
msgOut( "", " The target and tile are identical.",
status );
tlbnd[ 0 ] = lbnd[ 0 ];
tlbnd[ 1 ] = lbnd[ 1 ];
tubnd[ 0 ] = ubnd[ 0 ];
tubnd[ 1 ] = ubnd[ 1 ];
} else if( *status == SAI__OK ) {
*status = SAI__OK;
errRepf( "", "Unexpected value %d returned by astOverlap "
"(programming error).", status, flag );
}
/* If a region containing the intersection of the tile and target was
created above, map it into the grid coordinate system of the tile. */
if( overlap ) {
overlap = astMapRegion( overlap, astGetMapping( fs, AST__CURRENT,
AST__BASE ),
astGetFrame( fs, AST__BASE ) );
/* Get its GRID bounds. */
astGetRegionBounds( overlap, dlbnd, dubnd );
/* Convert to integer. */
tlbnd[ 0 ] = ceil( dlbnd[ 0 ] - 0.5 );
tlbnd[ 1 ] = ceil( dlbnd[ 1 ] - 0.5 );
tubnd[ 0 ] = ceil( dubnd[ 0 ] - 0.5 );
tubnd[ 1 ] = ceil( dubnd[ 1 ] - 0.5 );
/* Convert to PIXEL indices within the tile. */
tlbnd[ 0 ] += lbnd[ 0 ] - 1;
tlbnd[ 1 ] += lbnd[ 1 ] - 1;
tubnd[ 0 ] += lbnd[ 0 ] - 1;
tubnd[ 1 ] += lbnd[ 1 ] - 1;
msgOutf( "", " The target overlaps section (%d:%d,%d:%d).",
status, tlbnd[ 0 ], tubnd[ 0 ], tlbnd[ 1 ], tubnd[ 1 ] );
}
}
}
/* Store the pixel index bounds of the tiles overlap with the target. */
parPut1i( "TLBND", 2, tlbnd, status );
parPut1i( "TUBND", 2, tubnd, status );
/* Arrive here if an error occurs. */
L999:;
/* Free resources. */
tilendf = astFree( tilendf );
/* End the AST context. */
astEnd;
/* Issue a status indication.*/
msgBlank( status );
if( *status == SAI__OK ) {
msgOutif( MSG__VERB, "", "JSATILEINFO succeeded.", status);
} else {
msgOutif( MSG__VERB, "", "JSATILEINFO failed.", status);
}
}
void smf_calc_mapcoord( ThrWorkForce *wf, AstKeyMap *config, smfData *data,
AstFrameSet *outfset, int moving, int *lbnd_out,
int *ubnd_out, fts2Port fts_port, int flags,
int *status ) {
/* Local Variables */
AstSkyFrame *abskyfrm = NULL;/* Output SkyFrame (always absolute) */
AstMapping *bolo2map=NULL; /* Combined mapping bolo->map coordinates */
int bndndf=NDF__NOID; /* NDF identifier for map bounds */
void *data_pntr[1]; /* Array of pointers to mapped arrays in ndf */
int *data_index; /* Mapped DATA_ARRAY part of NDF */
int docalc=1; /* If set calculate the LUT */
int doextension=0; /* Try to write LUT to MAPCOORD extension */
smfFile *file=NULL; /* smfFile pointer */
AstObject *fstemp = NULL; /* AstObject version of outfset */
int ii; /* loop counter */
int indf_lat = NDF__NOID; /* Identifier for NDF to receive lat values */
int indf_lon = NDF__NOID; /* Identifier for NDF to receive lon values */
smfCalcMapcoordData *job_data=NULL; /* Array of job */
int lbnd[1]; /* Pixel bounds for 1d pointing array */
int lbnd_old[2]; /* Pixel bounds for existing LUT */
int lbnd_temp[1]; /* Bounds for bounds NDF component */
int lutndf=NDF__NOID; /* NDF identifier for coordinates */
AstMapping *map2sky_old=NULL;/* Existing mapping map->celestial coord. */
HDSLoc *mapcoordloc=NULL; /* HDS locator to the MAPCOORD extension */
int nw; /* Number of worker threads */
AstFrameSet *oldfset=NULL; /* Pointer to existing WCS info */
AstSkyFrame *oskyfrm = NULL; /* SkyFrame from the output WCS Frameset */
smfCalcMapcoordData *pdata=NULL; /* Pointer to job data */
double *lat_ptr = NULL; /* Pointer to array to receive lat values */
double *lon_ptr = NULL; /* Pointer to array to receive lon values */
int ubnd[1]; /* Pixel bounds for 1d pointing array */
int ubnd_old[2]; /* Pixel bounds for existing LUT */
int ubnd_temp[1]; /* Bounds for bounds NDF component */
int *lut = NULL; /* The lookup table */
dim_t nbolo=0; /* Number of bolometers */
dim_t ntslice=0; /* Number of time slices */
int nmap; /* Number of mapped elements */
AstMapping *sky2map=NULL; /* Mapping celestial->map coordinates */
size_t step; /* step size for dividing up work */
AstCmpMap *testcmpmap=NULL; /* Combined forward/inverse mapping */
AstMapping *testsimpmap=NULL;/* Simplified testcmpmap */
double *theta = NULL; /* Scan direction at each time slice */
int tstep; /* Time slices between full Mapping calculations */
int exportlonlat; /* Dump longitude and latitude values? */
/* Main routine */
if (*status != SAI__OK) return;
/* How many threads do we get to play with */
nw = wf ? wf->nworker : 1;
/* Initialize bounds to avoid compiler warnings */
lbnd_old[0] = 0;
lbnd_old[1] = 0;
ubnd_old[0] = 0;
ubnd_old[1] = 0;
/* Check for pre-existing LUT and de-allocate it. This will only waste
time if the MAPCOORD extension is found to be valid and it has
to be re-loaded from disk. */
smf_close_mapcoord( data, status );
/* Assert ICD data order */
smf_dataOrder( data, 1, status );
/* Get the data dimensions */
smf_get_dims( data, NULL, NULL, &nbolo, &ntslice, NULL, NULL, NULL, status );
/* If SMF__NOCREATE_FILE is not set, and file associated with an NDF,
map a new MAPCOORD extension (or verify an existing one) */
if( !(flags & SMF__NOCREATE_FILE) && data->file ) {
doextension = 1;
} else {
doextension = 0;
docalc = 1;
}
/* Create / check for existing MAPCOORD extension */
if( doextension ) {
file = data->file;
/* Check type of file before proceeding */
if( file->isSc2store ) {
*status = SAI__ERROR;
errRep(FUNC_NAME,
"File was opened by sc2store library (raw data?)",
status);
}
if( !file->isTstream ) {
*status = SAI__ERROR;
errRep(FUNC_NAME, "File does not contain time stream data",status);
}
/* Get HDS locator to the MAPCOORD extension */
mapcoordloc = smf_get_xloc( data, "MAPCOORD", "MAP_PROJECTION", "UPDATE",
0, 0, status );
/* Obtain NDF identifier/placeholder for LUT in MAPCOORD extension*/
lbnd[0] = 0;
ubnd[0] = nbolo*ntslice-1;
lutndf = smf_get_ndfid( mapcoordloc, "LUT", "UPDATE", "UNKNOWN",
"_INTEGER", 1, lbnd, ubnd, status );
if( *status == SAI__OK ) {
/* store the NDF identifier */
file->mapcoordid = lutndf;
/* Create sky to output grid mapping using the base coordinates to
get the coordinates of the tangent point if it hasn't been done
yet. */
sky2map = astGetMapping( outfset, AST__CURRENT, AST__BASE );
}
/* Before mapping the LUT, first check for existing WCS information
and LBND/UBND for the output map. If they are already correct don't
bother re-calculating the LUT! */
if( *status == SAI__OK ) {
/* Try reading in the WCS information */
kpg1Wread( mapcoordloc, "WCS", &fstemp, status );
oldfset = (AstFrameSet*)fstemp;
if( *status == SAI__OK ) {
/* Check that the old and new mappings are the same by
checking that combining one with the inverse of the other
reduces to a UnitMap. */
map2sky_old = astGetMapping( oldfset, AST__BASE, AST__CURRENT );
testcmpmap = astCmpMap( map2sky_old, sky2map, 1, " " );
testsimpmap = astSimplify( testcmpmap );
if( astIsAUnitMap( testsimpmap ) ) {
/* The mappings are the same, now just check the pixel
bounds in the output map */
lbnd_temp[0] = 1;
ubnd_temp[0] = 2;
bndndf = smf_get_ndfid( mapcoordloc, "LBND", "READ", "UNKNOWN",
"_INTEGER", 1, lbnd_temp, ubnd_temp,
status );
if( *status == SAI__OK ) {
ndfMap( bndndf, "DATA", "_INTEGER", "READ", data_pntr, &nmap,
status );
data_index = data_pntr[0];
if( *status == SAI__OK ) {
lbnd_old[0] = data_index[0];
lbnd_old[1] = data_index[1];
}
ndfAnnul( &bndndf, status );
}
bndndf = smf_get_ndfid( mapcoordloc, "UBND", "READ", "UNKNOWN",
"_INTEGER", 1, lbnd_temp, ubnd_temp,
status );
if( *status == SAI__OK ) {
ndfMap( bndndf, "DATA", "_INTEGER", "READ", data_pntr, &nmap,
status );
data_index = data_pntr[0];
if( *status == SAI__OK ) {
ubnd_old[0] = data_index[0];
ubnd_old[1] = data_index[1];
}
ndfAnnul( &bndndf, status );
}
if( *status == SAI__OK ) {
/* If we get this far finally do the bounds check! */
if( (lbnd_old[0] == lbnd_out[0]) &&
(lbnd_old[1] == lbnd_out[1]) &&
(ubnd_old[0] == ubnd_out[0]) &&
(ubnd_old[1] == ubnd_out[1]) ) {
docalc = 0; /* We don't have to re-calculate the LUT */
msgOutif(MSG__VERB," ",FUNC_NAME ": Existing LUT OK",
status);
}
}
}
/* Bad status / AST errors at this point due to problems with
MAPCOORD. Annul and continue calculating new MAPCOORD extension. */
astClearStatus;
errAnnul(status);
} else {
/* Bad status due to non-existence of MAPCOORD. Annul and continue */
errAnnul(status);
}
}
}
/* If we need to calculate the LUT do it here */
if( docalc && (*status == SAI__OK) ) {
msgOutif(MSG__VERB," ", FUNC_NAME ": Calculate new LUT",
status);
/* Get the increment in time slices between full Mapping calculations.
The Mapping for intermediate time slices will be approximated. */
dim_t dimval;
smf_get_nsamp( config, "TSTEP", data, &dimval, status );
tstep = dimval;
/* Get space for the LUT */
if( doextension ) {
/* Map the LUT array */
ndfMap( lutndf, "DATA", "_INTEGER", "WRITE", data_pntr, &nmap,
status );
data_index = data_pntr[0];
if( *status == SAI__OK ) {
lut = data_index;
} else {
errRep( FUNC_NAME, "Unable to map LUT in MAPCOORD extension",
status);
}
} else {
/* alloc the LUT and THETA arrays */
lut = astMalloc( (nbolo*ntslice)*sizeof(*(data->lut)) );
theta = astMalloc( ntslice*sizeof(*(data->theta)) );
}
/* Retrieve the sky2map mapping from the output frameset (actually
map2sky) */
oskyfrm = astGetFrame( outfset, AST__CURRENT );
sky2map = astGetMapping( outfset, AST__BASE, AST__CURRENT );
/* If the longitude and latitude is being dumped, create new NDFs to
hold them, and map them. */
if( config ) {
astMapGet0I( config, "EXPORTLONLAT", &exportlonlat );
if( exportlonlat ) {
lon_ptr = smf1_calc_mapcoord1( data, nbolo, ntslice, oskyfrm,
&indf_lon, 1, status );
lat_ptr = smf1_calc_mapcoord1( data, nbolo, ntslice, oskyfrm,
&indf_lat, 2, status );
}
}
/* Invert the mapping to get Output SKY to output map coordinates */
astInvert( sky2map );
/* Create a SkyFrame in absolute coordinates */
abskyfrm = astCopy( oskyfrm );
astClear( abskyfrm, "SkyRefIs" );
astClear( abskyfrm, "SkyRef(1)" );
astClear( abskyfrm, "SkyRef(2)" );
if( *status == SAI__OK ) {
/* --- Begin parellelized portion ------------------------------------ */
/* Start a new job context. Each call to thrWait within this
context will wait until all jobs created within the context have
completed. Jobs created in higher contexts are ignored by thrWait. */
thrBeginJobContext( wf, status );
/* Allocate job data for threads */
job_data = astCalloc( nw, sizeof(*job_data) );
if( *status == SAI__OK ) {
/* Set up job data, and start calculating pointing for blocks of
time slices in different threads */
if( nw > (int) ntslice ) {
step = 1;
} else {
step = ntslice/nw;
}
for( ii=0; (*status==SAI__OK)&&(ii<nw); ii++ ) {
pdata = job_data + ii;
/* Blocks of time slices */
pdata->t1 = ii*step;
pdata->t2 = (ii+1)*step-1;
/* Ensure that the last thread picks up any left-over tslices */
if( (ii==(nw-1)) && (pdata->t1<(ntslice-1)) ) {
pdata->t2=ntslice-1;
}
pdata->ijob = -1;
pdata->lut = lut;
pdata->theta = theta;
pdata->lbnd_out = lbnd_out;
pdata->moving = moving;
pdata->ubnd_out = ubnd_out;
pdata->tstep = tstep;
pdata->lat_ptr = lat_ptr;
pdata->lon_ptr = lon_ptr;
pdata->fts_port = fts_port;
/* Make deep copies of AST objects and unlock them so that each
thread can then lock them for their own exclusive use */
pdata->abskyfrm = astCopy( abskyfrm );
astUnlock( pdata->abskyfrm, 1 );
pdata->sky2map = astCopy( sky2map );
astUnlock( pdata->sky2map, 1 );
/* Similarly, make a copy of the smfData, including only the header
information which each thread will need in order to make calls to
smf_rebin_totmap */
pdata->data = smf_deepcopy_smfData( data, 0, SMF__NOCREATE_FILE |
SMF__NOCREATE_DA |
SMF__NOCREATE_FTS |
SMF__NOCREATE_DATA |
SMF__NOCREATE_VARIANCE |
SMF__NOCREATE_QUALITY, 0, 0,
status );
smf_lock_data( pdata->data, 0, status );
}
for( ii=0; ii<nw; ii++ ) {
/* Submit the job */
pdata = job_data + ii;
pdata->ijob = thrAddJob( wf, THR__REPORT_JOB, pdata,
smfCalcMapcoordPar, 0, NULL, status );
}
/* Wait until all of the jobs submitted within the current job
context have completed */
thrWait( wf, status );
}
/* End the current job context. */
thrEndJobContext( wf, status );
/* --- End parellelized portion -------------------------------------- */
/* Set the lut pointer in data to the buffer */
data->lut = lut;
data->theta = theta;
/* Write the WCS for the projection to the extension */
if( doextension ) {
kpg1Wwrt( (AstObject*)outfset, "WCS", mapcoordloc, status );
/* Write the pixel bounds for the map to the extension */
lbnd_temp[0] = 1; /* Don't get confused! Bounds for NDF that will */
ubnd_temp[0] = 2; /* contain the bounds for the output 2d map! */
bndndf = smf_get_ndfid( mapcoordloc, "LBND", "UPDATE", "UNKNOWN",
"_INTEGER", 1, lbnd_temp, ubnd_temp, status );
ndfMap( bndndf, "DATA", "_INTEGER", "WRITE", data_pntr, &nmap,
status );
data_index = data_pntr[0];
if( *status == SAI__OK ) {
data_index[0] = lbnd_out[0];
data_index[1] = lbnd_out[1];
} else {
errRep( FUNC_NAME, "Unable to map LBND in MAPCOORD extension",
status);
}
ndfAnnul( &bndndf, status );
bndndf = smf_get_ndfid( mapcoordloc, "UBND", "UPDATE", "UNKNOWN",
"_INTEGER", 1, lbnd_temp, ubnd_temp, status );
ndfMap( bndndf, "DATA", "_INTEGER", "WRITE", data_pntr, &nmap,
status );
data_index = data_pntr[0];
if( *status == SAI__OK ) {
data_index[0] = ubnd_out[0];
data_index[1] = ubnd_out[1];
} else {
errRep( FUNC_NAME, "Unable to map UBND in MAPCOORD extension",
status);
}
ndfAnnul( &bndndf, status );
}
}
}
/* Clean Up */
if( testsimpmap ) testsimpmap = astAnnul( testsimpmap );
if( testcmpmap ) testcmpmap = astAnnul( testcmpmap );
if( map2sky_old ) map2sky_old = astAnnul( map2sky_old );
if( oldfset ) oldfset = astAnnul( oldfset );
if (sky2map) sky2map = astAnnul( sky2map );
if (bolo2map) bolo2map = astAnnul( bolo2map );
if( abskyfrm ) abskyfrm = astAnnul( abskyfrm );
if( oskyfrm ) oskyfrm = astAnnul( oskyfrm );
if( mapcoordloc ) datAnnul( &mapcoordloc, status );
if( indf_lat != NDF__NOID ) ndfAnnul( &indf_lat, status );
if( indf_lon != NDF__NOID ) ndfAnnul( &indf_lon, status );
/* If we get this far, docalc=0, and status is OK, there must be
a good LUT in there already. Map it so that it is accessible to
the caller; "UPDATE" so that the caller can modify it if desired. */
if( (*status == SAI__OK) && (docalc == 0) ) {
smf_open_mapcoord( data, "UPDATE", status );
}
/* Clean up job data */
if( job_data ) {
for( ii=0; (*status==SAI__OK)&&(ii<nw); ii++ ) {
pdata = job_data + ii;
if( pdata->data ) {
smf_lock_data( pdata->data, 1, status );
smf_close_file( &(pdata->data), status );
}
astLock( pdata->abskyfrm, 0 );
pdata->abskyfrm = astAnnul( pdata->abskyfrm );
astLock( pdata->sky2map, 0 );
pdata->sky2map = astAnnul( pdata->sky2map );
}
job_data = astFree( job_data );
}
}
F77_SUBROUTINE(err_annul)( INTEGER(STATUS) ) {
int status;
F77_IMPORT_INTEGER( *STATUS, status );
errAnnul( &status );
F77_EXPORT_INTEGER( status, *STATUS );
}
void smf_pread( Grp *igrp, const char *param, int *status ){
/* Local Variables: */
AstMapping *dlatmap;
AstMapping *dlonmap;
AstMapping *taimap;
AstTable *table;
char file[ GRP__SZNAM + 1 ];
char pbuf[ GRP__SZNAM + 1 ];
const char *system;
void *p;
/* Before we check the error status, see if we are annulling previously
created Mappings. If so, get each formatted pointer from the group
metadata, get an Object pointer form it, lock it for use by the
current thread, and then annul it. Remove the metadata item from the
group. */
if( !param ) {
pbuf[ 0 ] = 0;
smf_get_grp_metadata( igrp, "DLONMAP", pbuf, status );
if( pbuf[ 0 ] ) {
sscanf( pbuf, "%p", &p );
dlonmap = (AstMapping *) p;
astLock( dlonmap, 0 );
dlonmap = astAnnul( dlonmap );
smf_remove_grp_metadata( igrp, "DLONMAP", status );
}
pbuf[ 0 ] = 0;
smf_get_grp_metadata( igrp, "DLATMAP", pbuf, status );
if( pbuf[ 0 ] ) {
sscanf( pbuf, "%p", &p );
dlatmap = (AstMapping *) p;
astLock( dlatmap, 0 );
dlatmap = astAnnul( dlatmap );
smf_remove_grp_metadata( igrp, "DLATMAP", status );
}
return;
}
/* Check the inherited status. */
if( *status != SAI__OK ) return;
/* Use the specified parameter to get the name of the text file containing
the table of pointing corrections. */
parGet0c( param, file, sizeof( file ) - 1, status );
/* If no file was specified, annul the error. */
if( *status == PAR__NULL ) {
errAnnul( status );
/* If a file was obtained sccuesfully, read it. */
} else if( *status == SAI__OK ) {
/* Start an AST context. */
astBegin;
/* Attempt to read an AST Table from the text file. */
table = atlReadTable( file, status );
/* Create a LutMap from each of the three columns. */
taimap = (AstMapping *) atlTablelutMap( table, "TAI", status );
dlonmap = (AstMapping *) atlTablelutMap( table, "DLON", status );
dlatmap = (AstMapping *) atlTablelutMap( table, "DLAT", status );
/* Create Mappings that transforms TAI into a DLON and DLAT. These use
linear interpolation for non-tabulated TAI values. */
astInvert( taimap );
dlonmap = (AstMapping *) astCmpMap( taimap, dlonmap, 1, " " );
dlatmap = (AstMapping *) astCmpMap( taimap, dlatmap, 1, " " );
/* Format the pointers to these two Mappings and store them in the
supplied group using names "DLONMAP" and "DLATMAP". */
sprintf( pbuf, "%p", (void *) dlonmap );
smf_add_grp_metadata( igrp, "DLONMAP", pbuf, status );
sprintf( pbuf, "%p", (void *) dlatmap );
smf_add_grp_metadata( igrp, "DLATMAP", pbuf, status );
/* See what system the DLON/DLAT values refer to (default to AZEL). Store
it in the group. */
if( !astMapGet0C( table, "SYSTEM", &system ) ) system = "AZEL";
smf_add_grp_metadata( igrp, "PSYSTEM", system, status );
/* Unlock the pointers to the Mappings so that they can be used by a
different thread. This also exempts the pointers from AST context
handling (until they are re-locked) so the following call to astEnd
will not annull them. */
astUnlock( dlonmap, 1 );
astUnlock( dlatmap, 1 );
/* End the AST context. This annuls all Objects created during the
context, except for the unlocked Mappings. */
astEnd;
/* Debug message. */
msgSetc( "F", file );
msgSetc( "S", system );
msgOutif( MSG__DEBUG, " ", "^S pointing corrections read from file ^F",
status );
/* Issue a context message if anything went wrong. */
if( *status != SAI__OK ) {
msgSetc( "F", file );
errRep( " ", "Failed to read pointing corrections from text file ^F.",
status );
}
}
}
void smf_clipnoise( double *clipdata, size_t ndata, int cliplog,
double cliplow, double cliphigh, size_t *nclipped,
int *status ) {
const float clips[] = {5,3,1};
const size_t nclips = sizeof(clips)/sizeof(*clips);
size_t i;
size_t nlow=0;
size_t nhigh=0;
double *work=NULL;
double median, mean, sigma;
if( *status != SAI__OK ) return;
if( cliplog ) msgOutif( MSG__DEBUG, "", FUNC_NAME
": taking log10 of the data", status );
if( (cliphigh > 0) || (cliplow > 0 ) ) {
work = astCalloc( ndata, sizeof(*work) );
/* Copy the data, or its log, into a buffer */
if( *status == SAI__OK ) {
for( i=0; i<ndata; i++ ) {
if( (clipdata[i] != VAL__BADD) && (clipdata[i] > 0) ) {
work[i] = cliplog ? log10(clipdata[i]) : clipdata[i];
} else {
work[i] = VAL__BADD;
}
}
}
/* Measure the clipped median, mean and standard deviation. We
step down from 5- to 1-sigma, using the median rather than the
mean as our central measure to ensure robustness against large
outliers. This should end up near the mode of the distribution,
although the RMS of the sample will under-estimate, by nearly a
factor of 2, the standard deviation for a Gaussian distribution
since we've clipped so much of the wings. We scale it back up
so that it would give the right answer for a Gaussian. */
smf_clipped_stats1D( work, nclips, clips, 1, ndata, NULL, 0, 0,
&mean, &sigma, &median, 1, NULL, status );
/* Assume that we do not need to clip if we can not get good
statistics */
if (*status == SMF__INSMP) {
errAnnul( status );
msgOutif(MSG__NORM, "",
"Noise clipping disabled as there are too few bolometers",
status );
goto CLEANUP;
}
sigma *= 1.85;
msgOutiff( MSG__DEBUG, "", FUNC_NAME
": mean=%lg median=%lg standard dev=%lg",
status, mean, median, sigma );
/* Then clip the high/low outliers relative to the median */
if( *status==SAI__OK ) {
for( i=0; i<ndata; i++ ) {
if( work[i] != VAL__BADD ) {
double d = work[i] - median;
if( (cliphigh>0) &&
(d >= sigma*cliphigh) ) {
clipdata[i] = VAL__BADD;
nhigh++;
}
if( (cliplow>0) &&
(-d >= sigma*cliplow) ) {
clipdata[i] = VAL__BADD;
nlow++;
}
}
}
}
if( nhigh ) msgOutiff( MSG__VERB, "", FUNC_NAME
": clipped %zu values >= %lg",
status, nhigh,
cliplog ? pow(10,median + sigma*cliphigh) :
median + sigma*cliphigh );
if( nlow ) msgOutiff( MSG__VERB, "", FUNC_NAME
": clipped %zu values <= %lg",
status, nlow,
cliplog ? pow(10,median - sigma*cliplow) :
median - sigma*cliplow );
/* Return number of clipped values */
if( nclipped ) *nclipped = nhigh+nlow;
CLEANUP:
/* Free temporary buffer */
if( work ) work = astFree( work );
}
}
void smurf_sc2pca( int *status ) {
smfData *amplitudes=NULL; /* Amplitudes of each component */
smfArray *bbms=NULL; /* Bad bolometer masks */
smfData *components=NULL; /* Components */
smfArray *darks=NULL ; /* Dark data */
int ensureflat; /* Flag for flatfielding data */
smfData *data=NULL; /* Pointer to input smfData */
Grp *fgrp=NULL; /* Filtered group, no darks */
smfArray *flatramps=NULL; /* Flatfield ramps */
AstKeyMap *heateffmap = NULL; /* Heater efficiency data */
size_t i=0; /* Counter, index */
Grp *igrp=NULL; /* Input group of files */
Grp *outampgrp=NULL; /* Output amplitude group of files */
Grp *outcompgrp=NULL; /* Output component group of files */
size_t outampsize; /* Total number of NDF names in ocompgrp */
size_t outcompsize; /* Total number of NDF names in ocompgrp */
size_t size; /* Number of files in input group */
ThrWorkForce *wf=NULL; /* Pointer to a pool of worker threads */
/* Main routine */
ndfBegin();
/* Find the number of cores/processors available and create a pool of
threads of the same size. */
wf = thrGetWorkforce( thrGetNThread( SMF__THREADS, status ), status );
/* Get input file(s) */
kpg1Rgndf( "IN", 0, 1, "", &igrp, &size, status );
/* Are we flatfielding? */
parGet0l( "FLAT", &ensureflat, status );
/* Filter out useful data (revert to darks if no science data) */
smf_find_science( wf, igrp, &fgrp, 1, NULL, NULL, 1, 1, SMF__NULL, &darks,
&flatramps, &heateffmap, NULL, status );
/* input group is now the filtered group so we can use that and
free the old input group */
size = grpGrpsz( fgrp, status );
grpDelet( &igrp, status);
igrp = fgrp;
fgrp = NULL;
if( size > 0 ) {
/* Get output file(s) */
kpg1Wgndf( "OUTAMP", igrp, size, size, "More output files required...",
&outampgrp, &outampsize, status );
kpg1Wgndf( "OUTCOMP", igrp, size, size, "More output files required...",
&outcompgrp, &outcompsize, status );
} else {
msgOutif(MSG__NORM, " ","All supplied input frames were DARK,"
" nothing to flatfield", status );
}
/* Get group of bolometer masks and read them into a smfArray */
smf_request_mask( wf, "BBM", &bbms, status );
for( i=1; i<=size; i++ ) {
if( *status != SAI__OK ) break;
/* Load data, flatfielding and/or opening raw as double as necessary */
smf_open_asdouble( wf, igrp, i, darks, flatramps, heateffmap, ensureflat, &data, status );
/* Mask out bad bolometers */
smf_apply_mask( wf, data, bbms, SMF__BBM_DATA|SMF__BBM_QUAL, 0, status );
/* Sync quality with bad values */
smf_update_quality( wf, data, 1, NULL, 0, 0.05, status );
/* Calculate the PCA */
smf_clean_pca( wf, data, 0, 0, 0, &components, &litudes, 0, 1, NULL,
status );
/* Write out to the new files */
smf_write_smfData( wf, amplitudes, NULL, NULL, outampgrp, i, 0, MSG__VERB,
0, status );
smf_write_smfData( wf, components, NULL, NULL, outcompgrp, i, 0, MSG__VERB,
0, status );
/* Free resources for output data */
smf_close_file( wf, &data, status );
smf_close_file( wf, &litudes, status );
smf_close_file( wf, &components, status );
}
/* Write out the list of output NDF names, annulling the error if a null
parameter value is supplied. */
if( *status == SAI__OK && outampgrp ) {
grpList( "OUTAMPFILES", 0, 0, NULL, outampgrp, status );
if( *status == PAR__NULL ) errAnnul( status );
}
if( *status == SAI__OK && outcompgrp ) {
grpList( "OUTCOMPFILES", 0, 0, NULL, outcompgrp, status );
if( *status == PAR__NULL ) errAnnul( status );
}
/* Tidy up after ourselves: release the resources used by the grp routines */
if( igrp ) grpDelet( &igrp, status);
if( outampgrp ) grpDelet( &outampgrp, status);
if( outcompgrp ) grpDelet( &outcompgrp, status);
if( darks ) smf_close_related( wf, &darks, status );
if( bbms ) smf_close_related( wf, &bbms, status );
if( flatramps ) smf_close_related( wf, &flatramps, status );
if (heateffmap) heateffmap = smf_free_effmap( heateffmap, status );
ndfEnd( status );
}
void smurf_fts2_split(int* status)
{
if( *status != SAI__OK ) { return; }
const double STAGE_LENGTH = 450.0; /* mm */
int LR = 0; /* Treat as Low Resolution scan */
Grp* gIn = NULL; /* Input group */
Grp* gOut = NULL; /* Output group */
Grp* gTmp = NULL; /* Temporary group */
smfData* inData = NULL; /* Pointer to input data */
smfData* outData = NULL; /* Pointer to output data */
double* outData_pntr = NULL; /* Pointer to output data values array */
int nMirPos = 0; /* Number of frames where the mirror actually moves */
int nStart = 0; /* Frame index where the mirror starts moving */
int nStartNext = 0; /* Frame index where the mirror starts moving in the next scan */
int nStop = 0; /* Frame index where the mirror stops */
int lrStart = 0; /* Frame index where low resolution mirror limit starts */
int hrStop = 0; /* Frame index where high resolution mirror limit stops */
int hrStart = 0; /* Frame index where high resolution mirror limit starts */
int lrStop = 0; /* Frame index where low resolution mirror limit stops */
int lrCentre = 0; /* Frame index at centre of low resolution mirror positions */
int i = 0; /* Counter */
int j = 0; /* Counter */
int k = 0; /* Counter */
int n = 0; /* Counter */
double fNyquist = 0.0; /* Nyquist frequency */
double dz = 0.0; /* Step size in evenly spaced OPD grid */
double* MIRPOS = NULL; /* Mirror positions */
size_t nFiles = 0; /* Size of the input group */
size_t nOutFiles = 0; /* Size of the output group */
size_t fIndex = 0; /* File index */
size_t nWidth = 0; /* Data cube width */
size_t nHeight = 0; /* Data cube height */
size_t nFrames = 0; /* Data cube depth in input file */
size_t nFramesOut = 0; /* Data cube depth in output file */
size_t nFramesOutPrev = 0; /* Data cube depth in previous output file */
size_t hrFramesOut = 0; /* Data cube depth in high res output file */
size_t hrFramesOutPrev = 0; /* Data cube depth in previous high res output file */
size_t lrFramesOut = 0; /* Data cube depth in low res output file */
size_t lrFramesOutPrev = 0; /* Data cube depth in previous low res output file */
size_t nPixels = 0; /* Number of bolometers in the subarray */
char object[SZFITSTR];
char subarray[SZFITSTR];
char obsID[SZFITSTR];
char scanMode[SZFITSTR];
double scanVel = 0.0; /* Mirror speed in mm/sec */
double stepTime = 0.0; /* RTS step time, average sample rate */
double minOPD = 0; /* OPD minimum */
double maxOPD = 0; /* OPD maximum */
double ZPD = 0;
double lrmmBandPass = 0.0; /* low res mm +/- offset from centre */
int lrBandPassFrames = 0; /* Number of low res band pass frames from centre +/- length of lrmmBandPass */
int nTmp = 0;
int nMax = 0;
int nOPD = 0;
int bolIndex = 0;
int index = 0;
int indexIn = 0;
int indexOut = 0;
int badPixel = 0;
int k0 = 0;
int indexZPD = 0;
int done = 0; /* Track completion of extracting multiple scans */
int outDataCount = 0; /* The number of output data files being written */
double lenLeft,
lenRight,
minLenLeft,
minLenRight,
minLen,
minZPD,
maxZPD,
midZPD = 0.0; /* Mirror position half side measures */
int midZPDPos = 0; /* Middle ZPD position in mirror position array */
double EPSILON = 0.0;
char fileName[SMF_PATH_MAX+1];
char scanNumStr[5+1]; /* String form of scan number of the input file */
int scanNum = 0; /* Scan number of the input file */
int conNum = 0; /* Concatenation number of the input file (left shifted scanNum) */
int scanDir = 0; /* Scan direction: 1 -> back to front (positive), -1 -> front to back (negative) */
JCMTState *allState = NULL; /* Temporary buffer for reduced header allState array data */
/* Get Input, Output groups */
kpg1Rgndf("IN", 0, 1, "", &gIn, &nFiles, status);
kpg1Wgndf("OUT", gOut, nFiles, nFiles, "More output files expected!", &gOut, &nOutFiles, status);
/* Read in ADAM parameters */
parGet0d("BANDPASS", &lrmmBandPass, status); /* Low res mm band +/- offset from centre */
/* Treat as Low Resolution scan? */
if(lrmmBandPass > 0) {
LR = 1;
}
/* Eliminate the first record in the output group, since it will be replaced later */
gTmp = grpCopy(gOut, 1, 1, 1, status);
grpDelet(&gOut, status);
gOut = gTmp;
/* BEGIN NDF */
ndfBegin();
/* Loop through each input file */
for(fIndex = 1; fIndex <= nFiles; fIndex++) {
/* Open Observation file */
smf_open_file(gIn, fIndex, "READ", 0, &inData, status);
if(*status != SAI__OK) {
*status = SAI__ERROR;
errRep(FUNC_NAME, "Unable to open the source file!", status);
goto CLEANUP;
}
smf_fits_getS(inData->hdr, "OBJECT", object, sizeof(object), status);
smf_fits_getS(inData->hdr, "SUBARRAY", subarray, sizeof(subarray), status);
smf_fits_getS(inData->hdr, "OBSID", obsID, sizeof(obsID), status);
smf_fits_getS(inData->hdr, "FTS_MODE", scanMode, sizeof(scanMode), status);
smf_fits_getD(inData->hdr, "SCANVEL", &scanVel, status);
smf_fits_getD(inData->hdr, "STEPTIME", &stepTime, status);
/* Nyquist frequency */
fNyquist = 10.0 / (8.0 * scanVel * stepTime);
dz = 1.0 / (2.0 * fNyquist);
EPSILON = scanVel * stepTime / 2;
/* Extract the scan number from the input file to be incremented in the output files */
one_strlcpy(scanNumStr, &(inData->file->name[strlen(inData->file->name) - 8]),
astMIN(SMF_PATH_MAX + 1, 5), status);
if (*status == ONE__TRUNC) {
errRep(FUNC_NAME, "Error extracting scanNumStr!", status);
errAnnul(status);
}
/* Create a temporary base file name from input file name */
one_strlcpy(fileName, inData->file->name,
astMIN(SMF_PATH_MAX + 1, strlen(inData->file->name) - 7), status);
if (*status == ONE__TRUNC) {
errRep(FUNC_NAME, "Error extracting base fileName!", status);
errAnnul(status);
}
scanNum = (int) one_strtod(scanNumStr, status);
if (*status != SAI__OK) {
errRep(FUNC_NAME, "Error extracting scanNum!", status);
errAnnul(status);
}
/* Left shift scanNum to conNum as a prefix to make output scan number unique */
if(scanNum < 100) {
conNum = scanNum * 100;
} else if(scanNum < 1000) {
conNum = scanNum * 10;
}
/*printf("%s: Processing file: %s, having basename: %s and scanNumStr: %s, scanNum: %04d\n",
TASK_NAME, inData->file->name, fileName, scanNumStr, scanNum);*/
/* Data cube dimensions */
nWidth = inData->dims[0];
nHeight = inData->dims[1];
nFrames = inData->dims[2];
nPixels = nWidth * nHeight;
/* Mirror positions in mm */
nTmp = nFrames;
MIRPOS = astCalloc(nFrames, sizeof(*MIRPOS));
fts2_getmirrorpositions(inData, MIRPOS, &nTmp, status); // (mm)
if(*status != SAI__OK) {
*status = SAI__ERROR;
errRep( FUNC_NAME, "Unable to get the mirror positions!", status);
goto CLEANUP;
}
nStart = -1;
nStop = -1;
nStartNext = 0;
hrStart = -1;
hrStop = -1;
lrStart = -1;
lrStop = -1;
outDataCount = 0;
done = 0;
do {
/* Find the next range of single scan mirror positions for which to extract corresponding NDF data */
for(n=nStartNext; n<nFrames-1; n++){
if(hrStart < 0 && fabs(MIRPOS[n+1] - MIRPOS[n]) >= EPSILON) {
nStart = n;
hrStart = n;
/*printf("%s: Split nStart=%d\n", TASK_NAME, nStart);*/
}
if(hrStart >= 0 && hrStop < 0 && (fabs(MIRPOS[n+1] - MIRPOS[n]) < EPSILON || n+1 == nFrames-1)) {
hrStop = n+1;
hrFramesOutPrev = hrFramesOut;
hrFramesOut = abs(hrStop - hrStart) + 1;
outDataCount++;
nStop = hrStop;
nFramesOutPrev = hrFramesOutPrev;
nFramesOut = hrFramesOut;
/*printf("%s: Split: %d of %d frames found at hrStart=%d, hrStop=%d\n",
TASK_NAME, outDataCount, hrFramesOut, hrStart, hrStop);*/
break;
}
}
/* Determine scan direction */
if(MIRPOS[hrStart] < MIRPOS[hrStop]) {
scanDir = 1; /* Positive */
} else {
scanDir = -1; /* Negative */
}
/* Limit to specified mirror position range */
if(LR) {
/* Calculate how many frames correspond to the given +/- mm of LR bandpass */
lrBandPassFrames = lrmmBandPass / dz;
/* Find the centre of the current scan */
lrCentre = floor((abs(hrStop-hrStart)+1)/2);
/* Set low res start and stop values at corresponding frame offsets from centre */
lrStart = lrCentre - lrBandPassFrames;
lrStop = lrCentre + lrBandPassFrames;
lrFramesOutPrev = lrFramesOut;
lrFramesOut = abs(lrStop - lrStart) + 1;
nStart = lrStart;
nStop = lrStop;
nFramesOutPrev = lrFramesOutPrev;
nFramesOut = lrFramesOut;
/*printf("%s: LR Split: %d of %d frames found at lrStart=%d, lrStop=%d\n",
TASK_NAME, outDataCount, lrFramesOut, lrStart, lrStop);*/
}
/* Check for end of data condition */
if(hrStop < hrStart || hrStop >= nFrames-1) {
hrStop = nFrames-1;
done = 1;
}
/* Output scan if there is a start and stop position found,
and for the last scan if it's the only one
and if it's not too short (compared to the previous one) */
/*printf("%s: nStart=%d, nStop=%d, nFramesOutPrev=%d, nFramesOut=%d\n", TASK_NAME, nStart, nStop, nFramesOutPrev, nFramesOut);*/
if(nStart >=0 && nStop > 0 &&
(nFramesOutPrev == 0 ||
(nFramesOutPrev > 0 && nFramesOut > 0 && (double)hrFramesOut/(double)hrFramesOutPrev >= 0.5))) {
/* Copy single scan NDF data from input to output */
outData = smf_deepcopy_smfData(inData, 0, SMF__NOCREATE_DATA | SMF__NOCREATE_FTS, 0, 0, status);
outData->dtype = SMF__DOUBLE;
outData->ndims = 3;
outData->dims[0] = nWidth;
outData->dims[1] = nHeight;
outData->dims[2] = nFramesOut;
outData_pntr = (double*) astMalloc((nPixels * nFramesOut) * sizeof(*outData_pntr));
outData->pntr[0] = outData_pntr;
outData->hdr->nframes = nFramesOut;
for(i=0; i<nWidth; i++) {
for(j=0; j<nHeight; j++) {
bolIndex = i + j * nWidth;
for(k=nStart; k<=nStop; k++) {
indexIn = bolIndex + k * nPixels;
indexOut = bolIndex + (k-nStart) * nPixels;
*((double*)(outData->pntr[0]) + indexOut) = *((double*)(inData->pntr[0]) + indexIn);
}
}
}
/* Update the FITS headers */
outData->fts = smf_create_smfFts(status);
/* Update FITS component */
smf_fits_updateD(outData->hdr, "FNYQUIST", fNyquist, "Nyquist frequency (cm^-1)", status);
smf_fits_updateI(outData->hdr, "MIRSTART", 1, "Frame index in which the mirror starts moving", status);
smf_fits_updateI(outData->hdr, "MIRSTOP", nFramesOut, "Frame index in which the mirror stops moving", status);
smf_fits_updateI(outData->hdr, "SCANDIR", scanDir, "Scan direction", status);
smf_fits_updateD(outData->hdr, "OPDMIN", 0.0, "Minimum OPD", status);
smf_fits_updateD(outData->hdr, "OPDSTEP", 0.0, "OPD step size", status);
/* Update the JCMTSTATE header */
/* Reallocate outData header array memory to reduced size */
allState = (JCMTState*) astRealloc(outData->hdr->allState, nFramesOut * sizeof(*(outData->hdr->allState)));
if(*status == SAI__OK && allState) {
outData->hdr->allState = allState;
} else {
errRepf(TASK_NAME, "Error reallocating allState JCMTState header", status);
goto CLEANUP;
}
for(k=nStart; k<=nStop; k++) {
/* Copy over JCMTstate */
/*printf("%s: memcpy allState: %d to: %p from: %p size: %d\n",TASK_NAME, k,
(void *) &(outData->hdr->allState[k-nStart]), (void *) &(inData->hdr->allState[k]), sizeof(*(outData->hdr->allState)) );*/
memcpy( (void *) &(outData->hdr->allState[k-nStart]), (void *) &(inData->hdr->allState[k]), sizeof(*(outData->hdr->allState)) );
/*printf("%s: Scan: %d index: %d rts_num: %d\n", TASK_NAME, outDataCount, k-nStart, outData->hdr->allState[k-nStart].rts_num);*/
/*printf("%s: Scan: %d index: %d fts_pos: %f\n", TASK_NAME, outDataCount, k-nStart, outData->hdr->allState[k-nStart].fts_pos);*/
}
/* Write output */
/* Append unique suffix to fileName */
/* This must be modified by the concatenation file scan number to improve uniqueness */
n = one_snprintf(outData->file->name, SMF_PATH_MAX, "%s%04d_scn.sdf", status, fileName, conNum+outDataCount);
/*printf("%s: Writing outData->file->name: %s\n", TASK_NAME, outData->file->name);*/
if(n < 0 || n >= SMF_PATH_MAX) {
errRepf(TASK_NAME, "Error creating outData->file->name", status);
goto CLEANUP;
}
/* Update the list of output _scn file names */
grpPut1(gOut, outData->file->name, 0, status);
if(*status != SAI__OK) {
errRepf(TASK_NAME, "Error saving outData file name", status);
goto CLEANUP;
}
smf_write_smfData(outData, NULL, outData->file->name, gOut, fIndex, 0, MSG__VERB, 0, status);
if(*status != SAI__OK) {
errRepf(TASK_NAME, "Error writing outData file", status);
goto CLEANUP;
}
smf_close_file(&outData, status);
if(*status != SAI__OK) {
errRepf(TASK_NAME, "Error closing outData file", status);
goto CLEANUP;
}
if(*status != SAI__OK) {
errRepf(TASK_NAME, "Error closing outData file", status);
goto CLEANUP;
}
}/* else {
if(!(nStart >=0 && nStop)) printf("%s: Output scan condition failed: nStart(%d) >= nStop(%d) is FALSE\n",TASK_NAME, nStart, nStop);
if(!(nFramesOutPrev == 0 ||
(nFramesOutPrev > 0 && nFramesOut > 0 && (double)nFramesOut/(double)nFramesOutPrev >= 0.5))) printf("%s: Output scan condition failed: nFramesOutPrev(%d) == 0 || (nFramesOutPrev(%d) > 0 && nFramesOut(%d) > 0 && nFramesOut/nFramesOutPrev (%f) >= 0.5) is FALSE\n", TASK_NAME, nFramesOutPrev, nFramesOutPrev, nFramesOut, (double)nFramesOut/(double)nFramesOutPrev);
}*/
/* Prepare for next iteration */
nStartNext = hrStop + 1;
hrStart = -1;
hrStop = -1;
} while (!done);
/* Deallocate memory used by arrays */
if(MIRPOS) { MIRPOS = astFree(MIRPOS); }
/* Close the file */
smf_close_file(&inData, status);
}
CLEANUP:
/* Deallocate memory used by arrays */
if(inData) { smf_close_file(&inData, status); }
if(outData) { smf_close_file(&outData, status); }
/* END NDF */
ndfEnd(status);
/* Write out the list of output NDF names, annulling the error if a null
parameter value is supplied. */
if( *status == SAI__OK && gOut ) {
grpList( "OUTFILES", 0, 0, NULL, gOut, status );
if( *status == PAR__NULL ) {
errRep(FUNC_NAME, "Error writing OUTFILES!", status);
errAnnul( status );
}
}
/* Delete groups */
if(gIn) { grpDelet(&gIn, status); }
if(gOut) { grpDelet(&gOut, status); }
}
void smurf_sc2fft( int *status ) {
int avpspec=0; /* Flag for doing average power spectrum */
double avpspecthresh=0; /* Threshold noise for detectors in avpspec */
Grp * basegrp = NULL; /* Basis group for output filenames */
smfArray *bbms = NULL; /* Bad bolometer masks */
smfArray *concat=NULL; /* Pointer to a smfArray */
size_t contchunk; /* Continuous chunk counter */
smfArray *darks = NULL; /* dark frames */
int ensureflat; /* Flag for flatfielding data */
Grp *fgrp = NULL; /* Filtered group, no darks */
smfArray *flatramps = NULL;/* Flatfield ramps */
AstKeyMap *heateffmap = NULL; /* Heater efficiency data */
size_t gcount=0; /* Grp index counter */
size_t i; /* Loop counter */
smfGroup *igroup=NULL; /* smfGroup corresponding to igrp */
Grp *igrp = NULL; /* Input group of files */
int inverse=0; /* If set perform inverse transform */
int isfft=0; /* Are data fft or real space? */
dim_t maxconcat=0; /* Longest continuous chunk length in samples */
size_t ncontchunks=0; /* Number continuous chunks outside iter loop */
smfData *odata=NULL; /* Pointer to output smfData to be exported */
Grp *ogrp = NULL; /* Output group of files */
size_t outsize; /* Total number of NDF names in the output group */
int polar=0; /* Flag for FFT in polar coordinates */
int power=0; /* Flag for squaring amplitude coeffs */
size_t size; /* Number of files in input group */
smfData *tempdata=NULL; /* Temporary smfData pointer */
int weightavpspec=0; /* Flag for 1/noise^2 weighting */
ThrWorkForce *wf = NULL; /* Pointer to a pool of worker threads */
int zerobad; /* Zero VAL__BADD before taking FFT? */
/* Main routine */
ndfBegin();
/* Find the number of cores/processors available and create a pool of
threads of the same size. */
wf = thrGetWorkforce( thrGetNThread( SMF__THREADS, status ), status );
/* Get input file(s) */
kpg1Rgndf( "IN", 0, 1, "", &igrp, &size, status );
/* Filter out darks */
smf_find_science( igrp, &fgrp, 1, NULL, NULL, 1, 1, SMF__NULL, &darks,
&flatramps, &heateffmap, NULL, status );
/* input group is now the filtered group so we can use that and
free the old input group */
size = grpGrpsz( fgrp, status );
grpDelet( &igrp, status);
igrp = fgrp;
fgrp = NULL;
/* We now need to combine files from the same subarray and same sequence
to form a continuous time series */
smf_grp_related( igrp, size, 1, 0, 0, NULL, NULL, &maxconcat, NULL, &igroup,
&basegrp, NULL, status );
/* Get output file(s) */
size = grpGrpsz( basegrp, status );
if( size > 0 ) {
kpg1Wgndf( "OUT", basegrp, size, size, "More output files required...",
&ogrp, &outsize, status );
} else {
msgOutif(MSG__NORM, " ", TASK_NAME ": All supplied input frames were DARK,"
" nothing to do", status );
}
/* Get group of bolometer masks and read them into a smfArray */
smf_request_mask( "BBM", &bbms, status );
/* Obtain the number of continuous chunks and subarrays */
if( *status == SAI__OK ) {
ncontchunks = igroup->chunk[igroup->ngroups-1]+1;
}
msgOutiff( MSG__NORM, "", "Found %zu continuous chunk%s", status, ncontchunks,
(ncontchunks > 1 ? "s" : "") );
/* Are we flatfielding? */
parGet0l( "FLAT", &ensureflat, status );
/* Are we doing an inverse transform? */
parGet0l( "INVERSE", &inverse, status );
/* Are we using polar coordinates instead of cartesian for the FFT? */
parGet0l( "POLAR", &polar, status );
/* Are we going to assume amplitudes are squared? */
parGet0l( "POWER", &power, status );
/* Are we going to zero bad values first? */
parGet0l( "ZEROBAD", &zerobad, status );
/* Are we calculating the average power spectrum? */
parGet0l( "AVPSPEC", &avpspec, status );
if( avpspec ) {
power = 1;
parGet0d( "AVPSPECTHRESH", &avpspecthresh, status );
parGet0l( "WEIGHTAVPSPEC", &weightavpspec, status );
}
/* If power is true, we must be in polar form */
if( power && !polar) {
msgOutif( MSG__NORM, " ", TASK_NAME
": power spectrum requested so setting POLAR=TRUE", status );
polar = 1;
}
gcount = 1;
for( contchunk=0;(*status==SAI__OK)&&contchunk<ncontchunks; contchunk++ ) {
size_t idx;
/* Concatenate this continuous chunk but forcing a raw data read.
We will need quality. */
smf_concat_smfGroup( wf, NULL, igroup, darks, NULL, flatramps, heateffmap,
contchunk, ensureflat, 1, NULL, 0, NULL, NULL, 0, 0, 0,
&concat, NULL, status );
/* Now loop over each subarray */
/* Export concatenated data for each subarray to NDF file */
for( idx=0; (*status==SAI__OK)&&idx<concat->ndat; idx++ ) {
if( concat->sdata[idx] ) {
smfData * idata = concat->sdata[idx];
int provid = NDF__NOID;
dim_t nbolo; /* Number of detectors */
dim_t ndata; /* Number of data points */
/* Apply a mask to the quality array and data array */
smf_apply_mask( idata, bbms, SMF__BBM_QUAL|SMF__BBM_DATA, 0, status );
smf_get_dims( idata, NULL, NULL, &nbolo, NULL, &ndata, NULL, NULL,
status );
/* Check for double precision data */
if( idata->dtype != SMF__DOUBLE ) {
*status = SAI__ERROR;
errRep( "", FUNC_NAME ": data are not double precision.", status );
}
/* Are we zeroing VAL__BADD? */
if( (*status==SAI__OK) && zerobad ) {
double *data= (double *) idata->pntr[0];
for( i=0; i<ndata; i++ ) {
if( data[i] == VAL__BADD ) {
data[i] = 0;
}
}
}
/* Check whether we need to transform the data at all */
isfft = smf_isfft(idata,NULL,NULL,NULL,NULL,NULL,status);
if( isfft && avpspec && (*status == SAI__OK) ) {
*status = SAI__ERROR;
errRep( "", FUNC_NAME
": to calculate average power spectrum input data cannot "
"be FFT", status );
}
if( (*status == SAI__OK) && (isfft == inverse) ) {
if( avpspec ) {
/* If calculating average power spectrum do the transforms with
smf_bolonoise so that we can also measure the noise of
each detector */
double *whitenoise=NULL;
smf_qual_t *bolomask=NULL;
double mean, sig, freqlo;
size_t ngood, newgood;
whitenoise = astCalloc( nbolo, sizeof(*whitenoise) );
bolomask = astCalloc( nbolo, sizeof(*bolomask) );
freqlo = 1. / (idata->hdr->steptime * idata->hdr->nframes);
smf_bolonoise( wf, idata, 1, freqlo, SMF__F_WHITELO,
SMF__F_WHITEHI, 1, 0, whitenoise, NULL, &odata,
status );
/* Initialize quality */
for( i=0; i<nbolo; i++ ) {
if( whitenoise[i] == VAL__BADD ) {
bolomask[i] = SMF__Q_BADB;
} else {
/* smf_bolonoise returns a variance, so take sqrt */
whitenoise[i] = sqrt(whitenoise[i]);
}
}
ngood=-1;
newgood=0;
/* Iteratively cut n-sigma noisy outlier detectors */
while( ngood != newgood ) {
ngood = newgood;
smf_stats1D( whitenoise, 1, nbolo, bolomask, 1, SMF__Q_BADB,
&mean, &sig, NULL, NULL, status );
msgOutiff( MSG__DEBUG, "", TASK_NAME
": mean=%lf sig=%lf ngood=%li\n", status,
mean, sig, ngood);
newgood=0;
for( i=0; i<nbolo; i++ ) {
if( whitenoise[i] != VAL__BADD ){
if( (whitenoise[i] - mean) > avpspecthresh *sig ) {
whitenoise[i] = VAL__BADD;
bolomask[i] = SMF__Q_BADB;
} else {
newgood++;
}
}
}
}
msgOutf( "", TASK_NAME
": Calculating average power spectrum of best %li "
" bolometers.", status, newgood);
/* If using 1/noise^2 weights, calculate 1/whitenoise^2 in-place
to avoid allocating another array */
if( weightavpspec ) {
msgOutif( MSG__VERB, "", TASK_NAME ": using 1/noise^2 weights",
status );
for( i=0; i<nbolo; i++ ) {
if( whitenoise[i] && (whitenoise[i] != VAL__BADD) ) {
whitenoise[i] = 1/(whitenoise[i]*whitenoise[i]);
}
}
}
/* Calculate the average power spectrum of good detectors */
tempdata = smf_fft_avpspec( odata, bolomask, 1, SMF__Q_BADB,
weightavpspec ? whitenoise : NULL,
status );
smf_close_file( &odata, status );
whitenoise = astFree( whitenoise );
bolomask = astFree( bolomask );
odata = tempdata;
tempdata = NULL;
/* Store the number of good bolometers */
parPut0i( "NGOOD", newgood, status );
} else {
/* Otherwise do forward/inverse transforms here as needed */
/* If inverse transform convert to cartesian representation first */
if( inverse && polar ) {
smf_fft_cart2pol( wf, idata, 1, power, status );
}
/* Tranform the data */
odata = smf_fft_data( wf, idata, NULL, inverse, 0, status );
smf_convert_bad( wf, odata, status );
if( inverse ) {
/* If output is time-domain, ensure that it is ICD bolo-ordered */
smf_dataOrder( odata, 1, status );
} else if( polar ) {
/* Store FFT of data in polar form */
smf_fft_cart2pol( wf, odata, 0, power, status );
}
}
/* open a reference input file for provenance propagation */
ndgNdfas( basegrp, gcount, "READ", &provid, status );
/* Export the data to a new file */
smf_write_smfData( odata, NULL, NULL, ogrp, gcount, provid,
MSG__VERB, 0, status );
/* Free resources */
ndfAnnul( &provid, status );
smf_close_file( &odata, status );
} else {
msgOutif( MSG__NORM, " ",
"Data are already transformed. No output will be produced",
status );
}
}
/* Update index into group */
gcount++;
}
/* Close the smfArray */
smf_close_related( &concat, status );
}
/* Write out the list of output NDF names, annulling the error if a null
parameter value is supplied. */
if( *status == SAI__OK ) {
grpList( "OUTFILES", 0, 0, NULL, ogrp, status );
if( *status == PAR__NULL ) errAnnul( status );
}
/* Tidy up after ourselves: release the resources used by the grp routines */
grpDelet( &igrp, status);
grpDelet( &ogrp, status);
if (basegrp) grpDelet( &basegrp, status );
if( igroup ) smf_close_smfGroup( &igroup, status );
if( flatramps ) smf_close_related( &flatramps, status );
if (heateffmap) heateffmap = smf_free_effmap( heateffmap, status );
if (bbms) smf_close_related( &bbms, status );
ndfEnd( status );
/* Ensure that FFTW doesn't have any used memory kicking around */
fftw_cleanup();
}
void
smf_flat_params( const smfData * refdata, const char resistpar[],
const char methpar[], const char orderpar[], const char snrminpar[],
double * refohms, double **resistance, int * outrows,
int * outcols, smf_flatmeth *flatmeth,
int * order, double * snrmin, smfData ** heateff,
int * status ) {
dim_t datarows = 0; /* Number of rows in refdata */
dim_t datacols = 0; /* Number of columns in refdata */
size_t j = 0; /* Counter, index */
char method[SC2STORE_FLATLEN]; /* flatfield method string */
size_t nbols; /* Number of bolometers */
double refohmsval = 0.0; /* Internal version of refohms */
AstKeyMap * resmap = NULL; /* Resistor map */
AstKeyMap * subarrays = NULL; /* Subarray lookup table */
char thissub[32]; /* This sub-instrument string */
if (resistance) *resistance = NULL;
if (*status != SAI__OK) return;
if (!refdata) {
*status = SAI__ERROR;
errRep( "", "Must provide reference data file to calculate flatfield parameters"
" (possible programming error)", status );
return;
}
/* Based on refdata we now need to calculate the default reference
resistance and retrieve the correct heater efficiency file for each array.
We need the unique subarray string so that we can set up a look up keymap.
There is no code in SMURF to return all the known subarrays but
we need to know all the options in order to use kpg1Config. */
subarrays = astKeyMap( " " );
astMapPut0I( subarrays, "CG450MK2_M0907D0501", 0, NULL );
astMapPut0I( subarrays, "CG850MK2_M0904D0503", 0, NULL );
astMapPut0I( subarrays, "SG850_M0906D1005", 0, NULL );
astMapPut0I( subarrays, "SG850_M1002D1006", 0, NULL );
astMapPut0I( subarrays, "SG850_M1005D1007", 0, NULL );
astMapPut0I( subarrays, "SG850_M1003D1004", 0, NULL );
astMapPut0I( subarrays, "SG450_M1004D1000", 0, NULL );
astMapPut0I( subarrays, "SG450_M1007D1002", 0, NULL );
astMapPut0I( subarrays, "SG450_M1006D1003", 0, NULL );
astMapPut0I( subarrays, "SG450_M1009D1008", 0, NULL );
/* and indicate which subarray we are interested in (uppercased) */
smf_fits_getS( refdata->hdr, "ARRAYID", thissub, sizeof(thissub), status );
{ /* need to uppercase */
size_t l = strlen(thissub);
for (j=0;j<l;j++) {
thissub[j] = toupper(thissub[j]);
}
}
astMapPut0I( subarrays, thissub, 1, NULL );
/* Read the config file */
resmap = kpg1Config( resistpar, "$SMURF_DIR/smurf_calcflat.def",
subarrays, 1, status );
subarrays = astAnnul( subarrays );
if (*status != SAI__OK) goto CLEANUP;
/* Read the reference resistance */
astMapGet0D( resmap, "REFRES", &refohmsval );
if (refohms && *status == SAI__OK) {
*refohms = refohmsval;
msgOutiff(MSG__VERB, "",
"Read reference resistance for subarray %s of %g ohms\n",
status, thissub, *refohms );
}
/* We no longer want to read per-bolometer resistor values from the
config file. To retain backwards compatibility with the current
implementation of smf_flat_standardpow we simply fill the
per-bol resistance array with the reference resistance which
effectively disables smf_flat_standardpow */
smf_get_dims( refdata, &datarows, &datacols, NULL, NULL, NULL, NULL, NULL, status );
nbols = datacols * datarows;
if (*status == SAI__OK && resistance ) {
*resistance = astMalloc( nbols*sizeof(**resistance) );
for (j = 0; j < (size_t)nbols; j++) {
(*resistance)[j] = refohmsval;
}
}
/* Get the heater efficiency file */
if (heateff && astMapHasKey( resmap, "HEATEFF" ) ) {
const char * heateffstr = NULL;
if (astMapGet0C( resmap, "HEATEFF", &heateffstr )) {
Grp * heateffgrp = NULL;
smfData * heatefftmp = NULL;
heateffgrp = grpNew( "heateff", status );
grpPut1( heateffgrp, heateffstr, 0, status );
smf_open_file( NULL, heateffgrp, 1, "READ", SMF__NOTTSERIES|SMF__NOFIX_METADATA, &heatefftmp, status );
/* Divorce the smfData from the underlying file. This file stays open for the entire
duration of the data processing and can some times lead to issues when we attempt
to close it an hour after we opened it (it's usually on an NFS disk) */
if (*status == SAI__OK) {
*heateff = smf_deepcopy_smfData( NULL, heatefftmp, 0,
SMF__NOCREATE_FILE | SMF__NOCREATE_FTS |
SMF__NOCREATE_DA,
0, 0, status );
smf_close_file(NULL, &heatefftmp, status);
}
/* Check the dimensions */
if (*status == SAI__OK) {
dim_t heatrows = 0;
dim_t heatcols = 0;
smf_get_dims( *heateff, &heatrows, &heatcols, NULL, NULL, NULL, NULL, NULL, status );
if (*status == SAI__OK) {
if ( datarows != heatrows || datacols != heatcols ) {
*status = SAI__ERROR;
errRepf( "", "Dimensions of heater efficiency file %s are (%zu, %zu)"
" but flatfield has dimensions (%zu, %zu)",
status, heateffstr, (size_t)heatrows, (size_t)heatcols,
(size_t)datarows, (size_t)datacols);
}
}
if (*status == SAI__OK) {
smf_dtype_check_fatal( *heateff, NULL, SMF__DOUBLE, status );
if (*status == SMF__BDTYP) {
errRepf("", "Heater efficiency data in %s should be double precision",
status, heateffstr);
}
}
if (*status == SAI__OK) {
char heateffarrid[32];
smf_fits_getS( refdata->hdr, "ARRAYID", heateffarrid, sizeof(heateffarrid), status );
if (*status != SAI__OK) errAnnul( status );
if (strcasecmp( thissub, heateffarrid ) != 0 ) {
if (*status == SAI__OK) {
*status = SAI__ERROR;
errRepf("", "Subarray associated with heater efficiency image (%s)"
" does not match that of the data to be flatfielded (%s)",
status, heateffarrid, thissub );
}
}
}
}
if (heateffgrp) grpDelet( &heateffgrp, status );
}
}
if (methpar && flatmeth) {
/* See if we want to use TABLE or POLYNOMIAL mode */
parChoic( methpar, "POLYNOMIAL", "POLYNOMIAL, TABLE", 1,
method, sizeof(method), status );
*flatmeth = smf_flat_methcode( method, status );
if (*flatmeth == SMF__FLATMETH_POLY) {
/* need an order for the polynomial */
if (order && orderpar) {
parGdr0i( orderpar, 1, 1, 3, 1, order, status );
/* and if the order is 1 then we can ask for the snr min */
if (snrminpar && *order == 1) {
parGet0d( snrminpar, snrmin, status );
}
}
} else {
/* need an snr min for table mode responsivities */
if (snrminpar) parGet0d( snrminpar, snrmin, status );
}
}
if (outrows) *outrows = datarows;
if (outcols) *outcols = datacols;
CLEANUP:
resmap = astAnnul( resmap );
if (*status != SAI__OK) {
if (resistance && *resistance) *resistance = astFree( *resistance );
if (heateff && *heateff) smf_close_file( NULL, heateff, status );
}
return;
}
