Changeset 24244 for branches/cnb_branches/cnb_branch_20090301/ppStack/src

Timestamp:

May 26, 2009, 1:59:32 PM (17 years ago)

Author:

beaumont

Message:

merged with trunk

Location:

branches/cnb_branches/cnb_branch_20090301

Files:

• . (modified) (1 prop)
• ppStack (modified) (1 prop)
• ppStack/src (modified) (1 prop)
• ppStack/src/Makefile.am (modified) (1 diff)
• ppStack/src/ppStackArguments.c (modified) (1 diff)
• ppStack/src/ppStackCombineFinal.c (modified) (1 diff)
• ppStack/src/ppStackCombineInitial.c (modified) (1 diff)
• ppStack/src/ppStackConvolve.c (modified) (1 diff)
• ppStack/src/ppStackFinish.c (modified) (2 diffs)
• ppStack/src/ppStackMatch.c (modified) (5 diffs)
• ppStack/src/ppStackPhotometry.c (modified) (2 diffs)
• ppStack/src/ppStackSetup.c (modified) (3 diffs)
• ppStack/src/ppStackVersion.c (modified) (3 diffs)
• ppStack/src/ppStackVersionDefinitions.h.in (copied) (copied from trunk/ppStack/src/ppStackVersionDefinitions.h.in )

branches/cnb_branches/cnb_branch_20090301/ppStack/src

@@ -9 +9 @@
 config.h.in
 stamp-h1
+ppStackVersionDefinitions.h

@@ -9 +9 @@
 config.h.in
 stamp-h1
+ppStackVersionDefinitions.h

branches/cnb_branches/cnb_branch_20090301/ppStack/src/Makefile.am

@@ -1 +1 @@
 bin_PROGRAMS = ppStack
 
-# PPSTACK_VERSION=`if [ -e ../../VERSION ]; then cat ../../VERSION; else svnversion; fi`
-# PPSTACK_BRANCH=`if [ -e ../../BRANCH ]; then cat ../../BRANCH; else svn info | sed -n -e '/URL:/ h' -e '/Repository Root:/ { x; H; x; s|Repository Root: \(.*\)\nURL: \1\(.*\)|\2| ; s|^/|| ; s|/[a-zA-Z]*/src.*|| ; p }'; fi`
-# PPSTACK_SOURCE=`if [ -e ../../SOURCE ]; then cat ../../SOURCE; else svn info | sed -n -e 's/Repository UUID: // p'; fi`
-# 
-# # Force recompilation of ppStackVersion.c, since it gets the version information
-# ppStackVersion.c: FORCE
-#       touch ppStackVersion.c
-# FORCE: ;
+if HAVE_SVNVERSION
+PPSTACK_VERSION=`$(SVNVERSION) ..`
+else
+PPSTACK_VERSION="UNKNOWN"
+endif
 
-ppStack_CFLAGS  = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(PSPHOT_CFLAGS) $(PPSTATS_CFLAGS) $(PPSTACK_CFLAGS) -DPPSTACK_VERSION=$(SVN_VERSION) -DPPSTACK_BRANCH=$(SVN_BRANCH) -DPPSTACK_SOURCE=$(SVN_SOURCE)
+if HAVE_SVN
+PPSTACK_BRANCH=`$(SVN) info .. | $(SED) -n -e '/URL:/ h' -e '/Repository Root:/ { x; H; x; s|Repository Root: \(.*\)\nURL: \1\(.*\)|\2| ; s|^/|| ; s|/[a-zA-Z]*/src.*|| ; p }'`
+PPSTACK_SOURCE=`$(SVN) info | $(SED) -n -e 's/Repository UUID: // p'`
+else
+PPSTACK_BRANCH="UNKNOWN"
+PPSTACK_SOURCE="UNKNOWN"
+endif
+
+# Force recompilation of ppStackVersion.c, since it gets the version information
+ppStackVersion.c: ppStackVersionDefinitions.h
+ppStackVersionDefinitions.h: ppStackVersionDefinitions.h.in FORCE
+        -$(RM) ppStackVersionDefinitions.h
+        $(SED) -e "s|@PPSTACK_VERSION@|\"$(PPSTACK_VERSION)\"|" -e "s|@PPSTACK_BRANCH@|\"$(PPSTACK_BRANCH)\"|" -e "s|@PPSTACK_SOURCE@|\"$(PPSTACK_SOURCE)\"|" ppStackVersionDefinitions.h.in > ppStackVersionDefinitions.h
+FORCE: ;
+
+ppStack_CFLAGS  = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(PSPHOT_CFLAGS) $(PPSTATS_CFLAGS) $(PPSTACK_CFLAGS)
 ppStack_LDFLAGS = $(PSLIB_LIBS)   $(PSMODULE_LIBS)   $(PSPHOT_LIBS)   $(PPSTATS_LIBS)   $(PPSTACK_LIBS)
 

branches/cnb_branches/cnb_branch_20090301/ppStack/src/ppStackArguments.c

@@ -119 +119 @@
 {
     assert(config);
+
+    {
+        int argNum = psArgumentGet(argc, argv, "-debug"); // Debugging argument number
+        if (argNum) {
+            psArgumentRemove(argNum, &argc, argv);
+            pmSubtractionRegions(true);
+        }
+    }
 
     // This capability makes things much faster when debugging

branches/cnb_branches/cnb_branch_20090301/ppStack/src/ppStackCombineFinal.c

@@ -47 +47 @@
     }
 
+    // Sum covariance matrices
+    double sumWeights = 0.0;            // Sum of weights
+    for (int i = 0; i < options->num; i++) {
+        if (options->inputMask->data.U8[i]) {
+            psFree(options->covariances->data[i]);
+            options->covariances->data[i] = NULL;
+            continue;
+        }
+        psKernel *covar = options->covariances->data[i]; // Covariance matrix
+        float weight = options->weightings->data.F32[i]; // Weight to apply
+        psBinaryOp(covar->image, covar->image, "*", psScalarAlloc(weight, PS_TYPE_F32));
+        sumWeights += weight;
+    }
+    pmReadout *outRO = options->outRO;  // Output readout
+    outRO->covariance = psImageCovarianceSum(options->covariances);
+    psBinaryOp(outRO->covariance->image, outRO->covariance->image, "/",
+               psScalarAlloc(sumWeights, PS_TYPE_F32));
+    psFree(options->covariances); options->covariances = NULL;
+    psImageCovarianceTransfer(outRO->variance, outRO->covariance);
+
 #ifdef TESTING
     pmStackVisualPlotTestImage(outRO->image, "combined_initial.fits");

branches/cnb_branches/cnb_branch_20090301/ppStack/src/ppStackCombineInitial.c

@@ -87 +87 @@
 #endif
 
-    // Sum covariance matrices
-    for (int i = 0; i < options->num; i++) {
-        if (options->inputMask->data.U8[i]) {
-            psFree(options->covariances->data[i]);
-            options->covariances->data[i] = NULL;
-        }
-    }
-    options->outRO->covariance = psImageCovarianceSum(options->covariances);
-    psFree(options->covariances); options->covariances = NULL;
     psFree(options->matchChi2); options->matchChi2 = NULL;
 

branches/cnb_branches/cnb_branch_20090301/ppStack/src/ppStackConvolve.c

@@ -112 +112 @@
 
         // Write the temporary convolved files
-        if (options->convolve) {
-            pmHDU *hdu = readout->parent->parent->parent->hdu; // HDU for convolved image
-            assert(hdu);
-            ppStackWriteImage(options->imageNames->data[i], hdu->header, readout->image, config);
-            psMetadata *maskHeader = psMetadataCopy(NULL, hdu->header); // Copy of header, for mask
-            pmConfigMaskWriteHeader(config, maskHeader);
-            ppStackWriteImage(options->maskNames->data[i], maskHeader, readout->mask, config);
-            psFree(maskHeader);
-            psImageCovarianceTransfer(readout->variance, readout->covariance);
-            ppStackWriteImage(options->varianceNames->data[i], hdu->header, readout->variance, config);
+        pmHDU *hdu = readout->parent->parent->parent->hdu; // HDU for convolved image
+        assert(hdu);
+        ppStackWriteImage(options->imageNames->data[i], hdu->header, readout->image, config);
+        psMetadata *maskHeader = psMetadataCopy(NULL, hdu->header); // Copy of header, for mask
+        pmConfigMaskWriteHeader(config, maskHeader);
+        ppStackWriteImage(options->maskNames->data[i], maskHeader, readout->mask, config);
+        psFree(maskHeader);
+        psImageCovarianceTransfer(readout->variance, readout->covariance);
+        ppStackWriteImage(options->varianceNames->data[i], hdu->header, readout->variance, config);
 #ifdef TESTING
-            {
-                psString name = NULL;
-                psStringAppend(&name, "covariance_%d.fits", i);
-                ppStackWriteImage(name, hdu->header, readout->covariance->image, config);
-                pmStackVisualPlotTestImage(readout->covariance->image, name);
-                psFree(name);
-            }
+        {
+            psString name = NULL;
+            psStringAppend(&name, "covariance_%d.fits", i);
+            ppStackWriteImage(name, hdu->header, readout->covariance->image, config);
+            pmStackVisualPlotTestImage(readout->covariance->image, name);
+            psFree(name);
+        }
 #endif
-        }
 
         pmCell *inCell = readout->parent; // Input cell

branches/cnb_branches/cnb_branch_20090301/ppStack/src/ppStackFinish.c

@@ -58 +58 @@
         psFree((void *)statsMDC);
         fclose(options->statsFile); options->statsFile = NULL;
+        pmConfigRunFilenameAddWrite(config, "STATS", psMetadataLookupStr(NULL, config->arguments, "STATS"));
     }
 
@@ -65 +66 @@
     psString dump = psMetadataLookupStr(&mdok, config->arguments, "DUMP_CONFIG"); // File for config
     if (dump) {
-        pmFPAfile *input = psMetadataLookupPtr(NULL, config->files, "PPSTACK.INPUT"); // Input file
-        pmConfigDump(config, input->fpa, dump);
+        pmConfigDump(config, dump);
     }
 

branches/cnb_branches/cnb_branch_20090301/ppStack/src/ppStackMatch.c

@@ -209 +209 @@
             pmFPAview *view = pmFPAviewAlloc(0); // View to readout of interest
             view->chip = view->cell = view->readout = 0;
-            psString filename = pmFPAfileNameFromRule(filerule->rule, file, view); // Filename of interest
+            psString filename = pmFPAfileNameFromRule(file->filerule, file, view); // Filename of interest
 
             // Read convolution kernel
@@ -241 +241 @@
                 !readImage(&readout->variance, options->varianceNames->data[index], config)) {
                 psError(PS_ERR_IO, false, "Unable to read previously produced image.");
-                psFree(imageName);
-                psFree(maskName);
-                psFree(varianceName);
                 return false;
             }
-            psFree(imageName);
-            psFree(maskName);
-            psFree(varianceName);
 
             psRegion *region = psMetadataLookupPtr(NULL, conv->analysis,
@@ -317 +311 @@
             }
 
+            fake->mask = psImageCopy(NULL, readout->mask, PS_TYPE_IMAGE_MASK);
+
             // Add the background into the target image
             psImage *bgImage = stackBackgroundModel(readout, config); // Image of background
@@ -361 +357 @@
                     psFree(stampSources);
                     psFree(conv);
+                    if (threads > 0) {
+                        pmSubtractionThreadsFinalize(readout, fake);
+                    }
                     return false;
                 }
@@ -375 +374 @@
                     psFree(stampSources);
                     psFree(conv);
+                    if (threads > 0) {
+                        pmSubtractionThreadsFinalize(readout, fake);
+                    }
                     return false;
                 }

branches/cnb_branches/cnb_branch_20090301/ppStack/src/ppStackPhotometry.c

@@ -69 +69 @@
 
     if (!psphotReadoutKnownSources(config, photView, inSources)) {
-        // Clear the error, so that the output files are written.
-        psError(PS_ERR_UNKNOWN, false, "Unable to perform photometry on stacked image.");
-        psFree(photView);
-        return false;
+        // This is likely a data quality issue
+        // XXX Split into multiple cases using error codes?
+        psErrorStackPrint(stderr, "Unable to perform photometry on image");
+        psWarning("Unable to perform photometry on image --- suspect bad data quality.");
+        if (options->stats && psMetadataLookupS32(NULL, options->stats, "QUALITY") == 0) {
+            psMetadataAddS32(options->stats, PS_LIST_TAIL, "QUALITY", PS_META_REPLACE,
+                             "Unable to perform photometry on image", psErrorCodeLast());
+        }
+        psErrorClear();
+        psphotFilesActivate(config, false);
     }
 
@@ -88 +94 @@
         psArray *sources = psMetadataLookupPtr(NULL, photRO->analysis, "PSPHOT.SOURCES"); // Sources
         psMetadataAddS32(options->stats, PS_LIST_TAIL, "NUM_SOURCES", 0,
-                         "Number of sources detected", sources->n);
+                         "Number of sources detected", sources ? sources->n : 0);
         psMetadataAddF32(options->stats, PS_LIST_TAIL, "TIME_PHOT", 0,
                          "Time to do photometry", psTimerMark("PPSTACK_PHOT"));

branches/cnb_branches/cnb_branch_20090301/ppStack/src/ppStackSetup.c

@@ -13 +13 @@
 #define BUFFER 16                       // Buffer for name array
 
-// Generate an array of input filenames
-static psArray *stackNameArray(const ppStackOptions *options, // Stack options
-                               pmConfig *config, // Configuration
-                               const char *name // Name of file
-    )
-{
-    psAssert(config, "Require configuration");
-    psAssert(config, "Require file name");
-
-    psArray *array = psArrayAllocEmpty(options->num); // Array with filenames
-    pmFPAview *view = pmFPAviewAlloc(0);// View to readout
-    view->chip = view->cell = view->readout = -1;
-
-    for (int i = 0; i < options->num; i++) {
-        pmFPAfile *file = pmFPAfileSelectSingle(config->files, name, i); // File of interest
-
-        psString filename = pmFPAfileName(file, view, config); // Filename of interest
-        psAssert(filename, "Can't determine filename");
-        psArrayAdd(array, array->n, filename);
-        psFree(filename);               // Drop reference
-    }
-
-    return array;
-}
-
 
 bool ppStackSetup(ppStackOptions *options, pmConfig *config)
@@ -47 +22 @@
     psAssert(recipe, "We've thrown an error on this before.");
 
-    options->convolve = psMetadataLookupBool(NULL, config->arguments, "CONVOLVE"); // Convolve images?
+    options->convolve = psMetadataLookupBool(NULL, recipe, "CONVOLVE"); // Convolve images?
     if (!psMetadataLookupBool(NULL, config->arguments, "HAVE.PSF")) {
         psWarning("No PSFs provided --- unable to convolve to common PSF.");
@@ -68 +43 @@
         psFree(resolved);
         options->stats = psMetadataAlloc();
+        psMetadataAddS32(options->stats, PS_LIST_TAIL, "QUALITY", 0, "No problems", 0);
     }
 
     // Generate temporary names for convolved images
-    if (options->convolve) {
-        const char *tempDir = psMetadataLookupStr(NULL, recipe, "TEMP.DIR"); // Directory for temporary images
-        if (!tempDir) {
-            psError(PS_ERR_BAD_PARAMETER_VALUE, false, "Unable to find TEMP.DIR in recipe");
-            return false;
-        }
+    const char *tempDir = psMetadataLookupStr(NULL, recipe, "TEMP.DIR"); // Directory for temporary images
+    if (!tempDir) {
+        psError(PS_ERR_BAD_PARAMETER_VALUE, false, "Unable to find TEMP.DIR in recipe");
+        return false;
+    }
 
-        psString outputName = psStringCopy(psMetadataLookupStr(NULL, config->arguments,
-                                                               "OUTPUT")); // Name for temporary files
-        const char *tempName = basename(outputName);
-        if (!tempName) {
-            psError(PS_ERR_BAD_PARAMETER_VALUE, false, "Unable to construct basename for temporary files.");
-            psFree(outputName);
-            return false;
-        }
+    psString outputName = psStringCopy(psMetadataLookupStr(NULL, config->arguments,
+                                                           "OUTPUT")); // Name for temporary files
+    const char *tempName = basename(outputName);
+    if (!tempName) {
+        psError(PS_ERR_BAD_PARAMETER_VALUE, false, "Unable to construct basename for temporary files.");
+        psFree(outputName);
+        return false;
+    }
 
-        const char *tempImage = psMetadataLookupStr(NULL, recipe, "TEMP.IMAGE"); // Suffix for images
-        const char *tempMask = psMetadataLookupStr(NULL, recipe, "TEMP.MASK"); // Suffix for masks
-        const char *tempVariance = psMetadataLookupStr(NULL, recipe, "TEMP.VARIANCE"); // Suffix for var maps
-        if (!tempImage || !tempMask || !tempVariance) {
-            psError(PS_ERR_BAD_PARAMETER_VALUE, false,
-                    "Unable to find TEMP.IMAGE, TEMP.MASK and TEMP.VARIANCE in recipe");
-            psFree(outputName);
-            return false;
-        }
+    const char *tempImage = psMetadataLookupStr(NULL, recipe, "TEMP.IMAGE"); // Suffix for images
+    const char *tempMask = psMetadataLookupStr(NULL, recipe, "TEMP.MASK"); // Suffix for masks
+    const char *tempVariance = psMetadataLookupStr(NULL, recipe, "TEMP.VARIANCE"); // Suffix for var maps
+    if (!tempImage || !tempMask || !tempVariance) {
+        psError(PS_ERR_BAD_PARAMETER_VALUE, false,
+                "Unable to find TEMP.IMAGE, TEMP.MASK and TEMP.VARIANCE in recipe");
+        psFree(outputName);
+        return false;
+    }
 
-        options->imageNames = psArrayAlloc(num);
-        options->maskNames = psArrayAlloc(num);
-        options->varianceNames = psArrayAlloc(num);
-        for (int i = 0; i < num; i++) {
-            psString imageName = NULL, maskName = NULL, varianceName = NULL; // Names for convolved images
-            psStringAppend(&imageName, "%s/%s.%d.%s", tempDir, tempName, i, tempImage);
-            psStringAppend(&maskName, "%s/%s.%d.%s", tempDir, tempName, i, tempMask);
-            psStringAppend(&varianceName, "%s/%s.%d.%s", tempDir, tempName, i, tempVariance);
-            psTrace("ppStack", 5, "Temporary files: %s %s %s\n", imageName, maskName, varianceName);
-            options->imageNames->data[i] = imageName;
-            options->maskNames->data[i] = maskName;
-            options->varianceNames->data[i] = varianceName;
-        }
-        psFree(outputName);
-    } else {
-        options->imageNames = stackNameArray(options, config, "PPSTACK.INPUT");
-        options->maskNames = stackNameArray(options, config, "PPSTACK.INPUT.MASK");
-        options->varianceNames = stackNameArray(options, config, "PPSTACK.INPUT.VARIANCE");
+    options->imageNames = psArrayAlloc(num);
+    options->maskNames = psArrayAlloc(num);
+    options->varianceNames = psArrayAlloc(num);
+    for (int i = 0; i < num; i++) {
+        psString imageName = NULL, maskName = NULL, varianceName = NULL; // Names for convolved images
+        psStringAppend(&imageName, "%s/%s.%d.%s", tempDir, tempName, i, tempImage);
+        psStringAppend(&maskName, "%s/%s.%d.%s", tempDir, tempName, i, tempMask);
+        psStringAppend(&varianceName, "%s/%s.%d.%s", tempDir, tempName, i, tempVariance);
+        psTrace("ppStack", 5, "Temporary files: %s %s %s\n", imageName, maskName, varianceName);
+        options->imageNames->data[i] = imageName;
+        options->maskNames->data[i] = maskName;
+        options->varianceNames->data[i] = varianceName;
     }
+    psFree(outputName);
 
     if (!pmConfigMaskSetBits(NULL, NULL, config)) {

branches/cnb_branches/cnb_branch_20090301/ppStack/src/ppStackVersion.c

@@ -10 +10 @@
 
 #include "ppStack.h"
+#include "ppStackVersionDefinitions.h"
 
 #ifndef PPSTACK_VERSION
@@ -21 +22 @@
 #endif
 
-#define xstr(s) str(s)
-#define str(s) #s
-
 psString ppStackVersion(void)
 {
     char *value = NULL;
-    psStringAppend(&value, "%s@%s", xstr(PPSTACK_BRANCH), xstr(PPSTACK_VERSION));
+    psStringAppend(&value, "%s@%s", PPSTACK_BRANCH, PPSTACK_VERSION);
     return value;
 }
@@ -33 +31 @@
 psString ppStackSource(void)
 {
-    return psStringCopy(xstr(PPSTACK_SOURCE));
+    return psStringCopy(PPSTACK_SOURCE);
 }
 

@@ -9 +9 @@
 config.h.in
 stamp-h1
+ppStackVersionDefinitions.h