Changeset 21085

Timestamp:

Jan 4, 2009, 12:32:32 PM (17 years ago)

Author:

bills

Message:

When destreaking chip stage images, use replace the mask from the chip
stage with the mask from the camera stage, destreaking them both.
Added program to prepare images for release by insuring that all masked
pixels are set to NAN

Location:

trunk

Files:

• ippScripts/scripts/magic_destreak.pl (modified) (2 diffs)
• magic/remove/src/Makefile.simple (modified) (2 diffs)
• magic/remove/src/streaksio.c (modified) (5 diffs)
• magic/remove/src/streaksrelease.c (added)
• magic/remove/src/streaksremove.c (modified) (8 diffs)
• magic/remove/src/streaksremove.h (modified) (1 diff)

trunk/ippScripts/scripts/magic_destreak.pl

@@ -176 +176 @@
 my $image = $uri;
 
-my ($mask, $weight, $astrom);
+my ($mask, $ch_mask, $weight, $astrom);
 
 if ($stage eq "raw") {
     $astrom = $ipprc->filename("PSASTRO.OUTPUT", $cam_path_base);
 } elsif ($stage eq "chip") {
-    $mask   = $ipprc->filename("PPIMAGE.CHIP.MASK", $path_base, $class_id);
+    # we use the mask output from the camera stage for input and replace
+    # the output of the chip stage with that mask as well.
+    $mask   = $ipprc->filename("PSASTRO.OUTPUT.MASK", $cam_path_base, $class_id);
+    $ch_mask= $ipprc->filename("PPIMAGE.CHIP.MASK", $path_base, $class_id);
     $weight = $ipprc->filename("PPIMAGE.CHIP.WEIGHT", $path_base, $class_id);
     $astrom = $ipprc->filename("PSASTRO.OUTPUT", $cam_path_base);
@@ -198 +201 @@
     $command .= " -astrom $astrom" if defined $astrom;
     $command .= " -mask $mask" if defined $mask;
+    $command .= " -chip_mask $ch_mask" if defined $ch_mask;
     $command .= " -weight $weight" if defined $weight;
     $command .= " -skycelllist $skycell_list" if defined $skycell_list;

trunk/magic/remove/src/Makefile.simple

@@ -16 +16 @@
     Line.o
 
-REPLACE_OBJECTS=    \
+REPLACE_OBJECTS=      \
     ${COMMON_OBJECTS} \
     streaksreplace.o
 
-COMPARE_OBJECTS=    \
+COMPARE_OBJECTS=      \
     ${COMMON_OBJECTS} \
     streakscompare.o
 
+RELEASE_OBJECTS=      \
+    ${COMMON_OBJECTS} \
+    streaksrelease.o
+
 STREAKSFLAGS=-DSTREAKS_COMPRESS_OUTPUT=1
 OPTFLAGS= -g
+#CFLAGS=`psmodules-config --cflags` -std=gnu99 ${OPTFLAGS} ${STREAKSFLAGS}
 CFLAGS=`psmodules-config --cflags` -std=gnu99 ${OPTFLAGS}
 LDFLAGS=`psmodules-config --libs`
 
-PROGRAMS= streaksremove streaksreplace streakscompare
+PROGRAMS= streaksremove streaksreplace streakscompare streaksrelease
 
 all:    ${PROGRAMS}
@@ -39 +44 @@
 streakscompare:  ${COMPARE_OBJECTS}
 
+streaksrelease:  ${RELEASE_OBJECTS}
+
 install:        ${PROGRAMS}
         install -t  $(PSCONFDIR)/$(PSCONFIG)/bin streaksremove
         install -t  $(PSCONFDIR)/$(PSCONFIG)/bin streaksreplace
         install -t  $(PSCONFDIR)/$(PSCONFIG)/bin streakscompare
+        install -t  $(PSCONFDIR)/$(PSCONFIG)/bin streaksrelease
 
 clean:

trunk/magic/remove/src/streaksio.c

@@ -5 +5 @@
 static nebServer *ourNebServer = NULL;
 
+// open the files required for streaks procesing.
+// if remove is true the calling program is streaksremove and the recovery files are outputs
+// if false the recovery files are inputs
 streakFiles *openFiles(pmConfig *config, bool remove)
 {
@@ -30 +33 @@
 
     if (remove) {
+        // XXX: the recovery file should be required if stage is raw and the replace flag is set
+        // that is if the input raw image is to be destroyed
         sf->recImage = sFileOpen(config, stage, "RECOVERY", inputBasename, false);
     } else {
@@ -45 +50 @@
         }
     }
+    // If we're in streaksremove and operating on a chip stage image
+    // if we are passed a mask it is camera stage mask and we also
+    // need to destreak the chip level mask file as well
+    if (remove && sf->inMask && (stage == IPP_STAGE_CHIP)) {
+        sf->inChMask = sFileOpen(config, stage, "INPUT.CHMASK", NULL, true);
+        inputBasename = basename(sf->inChMask->name);
+        sf->outChMask = sFileOpen(config, stage, "OUTPUT", inputBasename, true);
+        sf->recChMask = sFileOpen(config, stage, "RECOVERY", inputBasename, false);
+    }
+
     sf->inWeight = sFileOpen(config, stage, "INPUT.WEIGHT", NULL, false);
     if (sf->inWeight) {
@@ -421 +436 @@
     // XXX: This function assumes that it is only used for a single
     // chip single cell FPA (i.e. a skycell)
+    assert(sf->inImage->pmfile->fpa->chips->n == 1);
+
     pmFPAview *view = sf->view;
-    assert(view->chip == 0);
+    if (view) {
+        // The view was allocated and the chip set by setupAstrometry()
+        assert(view->chip == 0);
+    } else {
+        sf->view = pmFPAviewAlloc(0);
+        view = sf->view;
+        sf->chip = pmFPAviewNextChip(view, sf->inImage->pmfile->fpa, 1);
+        assert(sf->chip != NULL);
+    }
     view->cell = 0;
     sf->cell =  pmFPAviewThisCell(view, sf->inImage->pmfile->fpa);
@@ -747 +772 @@
         closeImage(sf->recMask);
     }
+    if (sf->inChMask) {
+        closeImage(sf->inChMask);
+        closeImage(sf->outChMask);
+        closeImage(sf->recChMask);
+    }
     if (sf->inWeight) {
         closeImage(sf->inWeight);

trunk/magic/remove/src/streaksremove.c

@@ -85 +85 @@
     int totalStreakPixels = 0;
 
-    // Iterate through each component of the input (only one except for raw stage)
+    // Iterate through each component of the input (there is only one except for raw images)
     do {
         bool exciseImageCube = false;
@@ -223 +223 @@
     fprintf(stderr, "\t-remove: remove the original image after processing (requires -replace)\n");
     fprintf(stderr, "\t-keepnonwarped: do not exise pixels that were not part of difference processing\n");
-    fprintf(stderr, "\t-transparent val: instead of setting exicsed pixel to NAN add val\n");
+    fprintf(stderr, "\t-transparent val: instead of setting excicsed pixel to NAN add val\n");
+    fprintf(stderr, "\t-chip_mask MASK.fits: name of mask for chip stage (camera stage mask is passed tih -mask)\n");
 
     exit(2);
@@ -333 +334 @@
         psArgumentRemove(argnum, &argc, argv);
         bool nebulousMask = IN_NEBULOUS(argv[argnum]);
+        // This isn't a strict requirement if stage == IPP_STAGE_CHIP
         if (nebulousMask != nebulousImage) {
             psError(PS_ERR_UNKNOWN, true, "mask image must be %snebulous path with %s image path\n",
@@ -340 +342 @@
         psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.MASK", 0,
                 "name of input mask image", argv[argnum]);
+        psArgumentRemove(argnum, &argc, argv);
+    }
+
+    if ((argnum = psArgumentGet(argc, argv, "-chip_mask"))) {
+        if (stage != IPP_STAGE_CHIP) {
+            psError(PS_ERR_UNKNOWN, true, "-chip_mask only allowed at chip stage");
+            usage();
+        }
+        psArgumentRemove(argnum, &argc, argv);
+        bool nebulousMask = IN_NEBULOUS(argv[argnum]);
+        if (nebulousMask != nebulousImage) {
+            psError(PS_ERR_UNKNOWN, true, "chip mask image must be %snebulous path with %s image path\n",
+                nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular");
+            usage();
+        }
+        psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.CHMASK", 0,
+                "name of input chip mask image", argv[argnum]);
         psArgumentRemove(argnum, &argc, argv);
     }
@@ -429 +448 @@
         streaksExit("", PS_EXIT_UNKNOWN_ERROR);
     }
+    // For the chip level files, copy the WCS from the astrometry file to the header
+    // XXX: do we want to do this for raw images as well?
     if (sf->stage == IPP_STAGE_CHIP) {
-        // For the chip level files, copy the WCS from the astrometry file to the header
         if (!sf->bilevelAstrometry) {
             updateAstrometry = true;
@@ -481 +501 @@
             pmAstromWriteWCS(sf->outMask->header, sf->inAstrom->fpa, sf->chip, 0.001);
         }
-
         setupImageRefs(sf->outMask, sf->recMask, sf->inMask, sf->extnum, exciseAll);
+        if (sf->outChMask) {
+            sf->outChMask->header = (psMetadata *) psMemIncrRefCounter(sf->outMask->header);
+            sf->outChMask->image = (psImage *) psMemIncrRefCounter(sf->outMask->image);
+            if (sf->recChMask) {
+                sf->recChMask->header = (psMetadata *) psMemIncrRefCounter(sf->recMask->header);
+                sf->recChMask->image = (psImage *) psMemIncrRefCounter(sf->recMask->image);
+            }
+        }
 
 #ifdef STREAKS_COMPRESS_OUTPUT
@@ -490 +517 @@
         if (sf->recMask) {
             psFitsSetCompression(sf->recMask->fits, PS_FITS_COMPRESS_PLIO, sf->tiles, 8, 0, 0);
+        }
+        if (sf->outChMask) {
+            copyFitsOptions(sf->outChMask, sf->recChMask, sf->inMask);
+            psFitsSetCompression(sf->outChMask->fits, PS_FITS_COMPRESS_PLIO, sf->tiles, 8, 0, 0);
+            if (sf->recChMask) {
+                psFitsSetCompression(sf->recChMask->fits, PS_FITS_COMPRESS_PLIO, sf->tiles, 8, 0, 0);
+            }
         }
 #endif
@@ -567 +601 @@
         writeImage(sf->outMask, extname, sf->extnum);
         writeImage(sf->recMask, extname, sf->extnum);
+        if (sf->stage == IPP_STAGE_CHIP) {
+            writeImage(sf->outChMask, extname, sf->extnum);
+            writeImage(sf->recChMask, extname, sf->extnum);
+        }
     }
     if (sf->outWeight) {

trunk/magic/remove/src/streaksremove.h

@@ -54 +54 @@
     sFile *recMask;
     sFile *recWeight;
+    sFile *inChMask;    // for chip stage input mask is camera mask and output goes to both chip and cam masks
+    sFile *outChMask;
+    sFile *recChMask;
     psString class_id;
     pmFPAfile  *inAstrom;