; $Id: $SSW/proba2/swap/idl/prep/p2sw_pixrep.pro#1 $ ; ; Copyright (c) Trinity College Dublin. All rights reserved. ;+ ; NAME: ; P2SW_PIXREP ; ; PURPOSE: ; This function reinstates onboard cosmic ray replaced pixels and ; saturated pixels in PROBA2/SWAP images. ; ; CATEGORY: ; PROBA2/SWAP calibration. ; ; CALLING SEQUENCE: ; ; Result = P2SW_PIXREP( Index, Image, Fname [, CALDIR=caldir, $ ; VERSION=version, RUNID=runid, /NO_PIXLIST, $ ; /NO_SATREP, /VERBOSE, /LMAT, _EXTRA=ex ] ) ; ; INPUTS: ; Index: FITS header in structure format for PROBA2/SWAP image ; to be processed. ; ; Image: PROBA2/SWAP image to be processed. ; ; Fname: FITS Filename of PROBA2/SWAP image to be processed. ; ; OPTIONAL INPUTS: ; CALDIR: File system pathway to PROBA2/SWAP calibration files. ; DEFAULT: local SSWIDL folder ('$SSW/proba2/swap/caldb') ; ; VERSION: Master P2SW_PREP code version number for LMAT logging ; and HISTORY tag entries. ; ; RUNID: Unique processing run identifier for P2SC pipeline ; operations. Used only if LMAT is set. ; ; KEYWORD PARAMETERS: ; NO_PIXLIST: Set this keyword to skip possible application of ; pixel replacement from FITS extension table. ; ; NO_SATREP: Set this keyword to skip replacement of pixels above ; predetermined saturation levels. ; ; VERBOSE: Set this keyword to print run-status information to ; standard output ; ; LMAT: Set this keyword to enable default reporting mode for ; P2SC pipeline operations. Not for use via SSW. ; ; OUTPUTS: ; This function returns the input image with the missing pixels ; contained in the input image FITS extension replaced by their ; local 3x3 pixel median value. Pixels identified as saturated ; are replaced with 4400 using the closest-in-time saturation ; map correction FITS file supplied in the SSW-distributed caldb ; directory. Correction is not applied if image was binned 2x2 ; onboard. Input Index structure is updated during processing ; - e.g., HISTORY appended. ; ; PROCEDURE: ; Input images have their FITS file checked for the existence ; of an extension containing a list of missing pixels which are ; replaced by their local 3x3 pixel median values. A further ; saturated pixel replacement is carried out using the ; closest-in-time observing mode specific saturation FITS file ; supplied in the SSW-distributed caldb directory or a ; user-defined directory (optional input CALDIR). Pixels are ; identified as being within the saturation regime if their ; values lie above 0.95 x (saturation frame value) with these ; pixels being replaced by 4400. ; ; MODIFICATION HISTORY: ; Written by: D. Shaun Bloomfield, 24-Jan-2009. ; Apr 2009 Added IDL-format description. ; Jun 2009 Added ROB calls to send2lmat.pro for logging. ; Moved FITS history updating into sub-routines. ; Added option to supply calibration file dir. ; Jul 2009 Added handling of sub-fielded images. ; Aug 2009 Added rebinning of native resolution ; calibration files for rebinned images. ; Added optional call to check for missing pixel ; list in FITS extension. ; Oct 2009 Changed handling of pixel list FITS extension. ; Mar 2010 Fixed filename call for FITS extension reading. ; Fixed handling of NO_PIXLIST keyword. ; May 2010 Finalized IDL-format description. ; Apr 2013 Added optional call to skip saturation replacement (dbs) ;- FUNCTION p2sw_pixrep, index, image, fname, $ caldir=caldir, version=version, runid=runid, $ no_pixlist=no_pixlist, verbose=verbose, $ no_satrep = no_satrep, lmat=lmat, _extra=ex prognam = 'p2sw_pixrep.pro' delim = get_delim() ;--- Check keyword inputs and set keyword-dependencies IF KEYWORD_SET(caldir) THEN caldir = caldir ELSE caldir = STRCOMPRESS(GETENV('SSW'), /remove_all) + '/proba2/swap/caldb' IF KEYWORD_SET(version) THEN version = version ELSE version = '' IF KEYWORD_SET(runid) THEN runid = LONG(runid) ELSE runid = 0 no_pixlist = KEYWORD_SET(no_pixlist) no_satrep = KEYWORD_SET(no_satrep) verbose = KEYWORD_SET(verbose) lmat = KEYWORD_SET(lmat) ;--- Get filename for LMAT messaging IF KEYWORD_SET(lmat) THEN fn = index[0].filename image1 = image ;--- Check whether to attempt check for missing pixel list IF ~(no_pixlist) THEN BEGIN ;--- Check for FITS extension IF ( index.extend NE 0 ) THEN BEGIN ;--- Re-read FITS file to extract FITS extension #1 img_ext = READFITS( fname, himg_ext, /EXTEN, /SILENT ) ;--- If extension information exists then process IF ( img_ext[0] NE -1 ) THEN BEGIN ;--- img_ext is a 3xN element array containing: ;--- img_ext[0, *] - the pixel x coordinates, ;--- img_ext[1, *] - the pixel y coordinates, ;--- img_ext[2, *] - the pixel original values err_num = 2202L err_msg = 'Expected FITS extension exists in Level-0 file' IF ~(lmat) THEN BEGIN IF (verbose) THEN MESSAGE, '** '+err_msg+' **', /CONTINUE ENDIF ELSE SEND2LMAT, 'SWBSDG', version, runid, err_msg + ' for file: ' + fn, err_num, prognam+', line: ', '/p2sc/temp/swbsdg' ;--- Convert image extension header into structured index ind_ext = FITSHEAD2STRUCT( himg_ext ) ;--- Determine number of missing pixel indices n_mis_pix = ind_ext.naxis2 ;--- Replace each onboard-corrected pixel with its original value FOR i = 0, n_mis_pix-1 DO image1[ img_ext[0, i], img_ext[1, i] ] = img_ext[2, i] ;--- Set HISTORY update text ; tagval_a = STRING('Replaced ', n_mis_pix, ' onboard-corrected pixels with original values', FORMAT='(a,i7,a)') tagval_a = STRING('Replaced ', n_mis_pix, ' pixels with preprocessed values', FORMAT='(a,i4,a)') ;--- Report if requested IF (verbose) THEN MESSAGE, 'HISTORY record updated: '+tagval_a, /CONTINUE ;--- Add update text into HISTORY field of index structure UPDATE_HISTORY, index, tagval_a, CALLER='P2SW_PIXREP '+version ;--- If no missing pixel indices in extension then report ERROR ENDIF ELSE BEGIN err_num = 3201L err_msg = 'No missing pixel indices in expected FITS extension' IF ~(lmat) THEN BEGIN IF (verbose) THEN MESSAGE, '** '+err_msg+' **', /CONTINUE ENDIF ELSE SEND2LMAT, 'SWBSDG', version, runid, err_msg + ' for file: ' + fn, err_num, prognam+', line: ', '/p2sc/temp/swbsdg' ENDELSE ENDIF ENDIF ELSE IF (verbose) THEN PRINT, '** No onboard cosmic ray list correction applied. **' image2 = image1 IF ~(no_satrep) THEN BEGIN ;--- Check whether or not 2x2 binning was applied onboard IF ( STRMID( STRUPCASE( index.rebin ), 0, 2 ) NE 'ON' ) THEN BEGIN ;--- Check for APS-CMOS detector capture mode mode = STRLOWCASE( index.cap_mode ) ;--- Check for most recent saturation level map sat_files = FILE_SEARCH( caldir+'/swap_sat'+mode+'_????????_??????.fits', COUNT=sat_cnt ) IF (sat_cnt GT 0) THEN BEGIN sat_tdiff = ANYTIM( index.DATE_OBS ) - $ ANYTIM( FILE2TIME( sat_files ) ) sat_older = WHERE( sat_tdiff GT 0., n_sat_older ) IF (n_sat_older GT 0) THEN BEGIN sat_valid = sat_files[ ( REVERSE(sat_older) )[0] ] sat_used = ( REVERSE( STRSPLIT( sat_valid, delim, /EXTRACT ) ) )[0] ENDIF ELSE BEGIN sat_valid = sat_files[0] sat_used = ( REVERSE( STRSPLIT( sat_valid, delim, /EXTRACT ) ) )[0] err_num = 4210L err_msg = 'No '+STRUPCASE(mode)+' saturation level FITS files older than image - using '+sat_used IF ~(lmat) THEN BEGIN IF (verbose) THEN MESSAGE, '** '+err_msg+' **', /CONTINUE ENDIF ELSE SEND2LMAT, 'SWBSDG', version, runid, err_msg, err_num, prognam+', line: ', '/p2sc/temp/swbsdg' ENDELSE ;--- Read in saturation level image MREADFITS, sat_valid, sat_ind, sat_tmp, /SILENT, _EXTRA=ex ;--- Embed detector sub-field region of interest in array of 5500's ;--- Ensures that no out-of-sub-field pixels can have a value above 0.95*5500 sat_img = INTARR( index.naxis1, index.naxis2 )+5500 sat_img[ index.firstcol-1:index.last_col-1, index.firstrow-1:index.last_row-1 ] = $ sat_tmp[ index.firstcol-1:index.last_col-1, index.firstrow-1:index.last_row-1 ] sat_pix = WHERE( image2 GE (0.95*sat_img), n_sat_pix ) IF (n_sat_pix GT 0) THEN image2[sat_pix] = 4400 ;--- Set HISTORY update text ; tagval_c = STRING('Replaced ', n_sat_pix, ' saturated pixels (values above those in '+sat_used+') with 4400', FORMAT='(a,i7,a)') tagval_c = 'Replaced wrt '+sat_used ;--- Report if requested IF (verbose) THEN MESSAGE, 'HISTORY record updated: '+tagval_c, /CONTINUE ;--- Add update text into HISTORY field of index structure UPDATE_HISTORY, index, tagval_c, CALLER='P2SW_PIXREP '+version ;--- If no saturation level map files then report ERROR ENDIF ELSE BEGIN err_num = 4209L err_msg = 'No '+STRUPCASE(mode)+' saturation level FITS files found in '+caldir IF ~(lmat) THEN BEGIN MESSAGE, '** '+err_msg+' **', /CONTINUE ENDIF ELSE SEND2LMAT, 'SWBSDG', version, runid, err_msg, err_num, prognam+', line: ', '/p2sc/temp/swbsdg' RETURN, err_msg ENDELSE ;--- If 2x2 binning was applied onboard then skip saturation map correction ENDIF ELSE BEGIN IF (verbose) THEN MESSAGE, '** No saturation correction applied due to onboard binning **', /CONTINUE ENDELSE ENDIF ELSE IF (verbose) THEN PRINT, '** No saturation correction applied. **' RETURN, image2 END