Changeset 28334 for branches/czw_branch/20100519/ppBackground

Timestamp:

Jun 15, 2010, 11:22:56 AM (16 years ago)

Author:

watersc1

Message:

association and jpegs look fine. random simtest errors are a bit worrying, though.

Location:

branches/czw_branch/20100519

Files:

• . (modified) (1 prop)
• ppBackground (modified) (1 prop)
• ppBackground/configure.ac (modified) (1 diff)
• ppBackground/src (modified) (1 prop)
• ppBackground/src/Makefile.am (modified) (4 diffs)
• ppBackground/src/ppBackground.c (modified) (3 diffs)
• ppBackground/src/ppBackground.h (modified) (2 diffs)
• ppBackground/src/ppBackgroundArguments.c (modified) (3 diffs)
• ppBackground/src/ppBackgroundCamera.c (modified) (3 diffs)
• ppBackground/src/ppBackgroundExit.c (modified) (1 diff)
• ppBackground/src/ppBackgroundLoop.c (modified) (9 diffs)
• ppBackground/src/ppBackgroundModel.c (deleted)
• ppBackground/src/ppBackgroundRestore.c (copied) (copied from trunk/ppBackground/src/ppBackgroundRestore.c )
• ppBackground/src/ppBackgroundVersionDefinitions.h.in (modified) (1 diff)

branches/czw_branch/20100519/ppBackground/configure.ac

@@ -20 +20 @@
 PKG_CHECK_MODULES([PSLIB], [pslib >= 1.0.0])
 PKG_CHECK_MODULES([PSMODULE], [psmodules >= 1.0.0])
-PKG_CHECK_MODULES([PSPHOT], [psphot >= 1.0.0])
+PKG_CHECK_MODULES([PPSTATS], [ppStats >= 1.0.0]) 
+PKG_CHECK_MODULES([PSPHOT], [psphot])
+
+AC_PATH_PROG([ERRORCODES], [psParseErrorCodes], [missing])
+if test "$ERRORCODES" = "missing" ; then
+  AC_MSG_ERROR([psParseErrorCodes is required])
+fi
 
 dnl Set CFLAGS for build

branches/czw_branch/20100519/ppBackground/src/Makefile.am

@@ -2 +2 @@
 
 if HAVE_SVNVERSION
-PPVIZPATTERN_VERSION=`$(SVNVERSION) ..`
+PPBACKGROUND_VERSION=`$(SVNVERSION) ..`
 else
-PPVIZPATTERN_VERSION="UNKNOWN"
+PPBACKGROUND_VERSION="UNKNOWN"
 endif
 
 if HAVE_SVN
-PPVIZPATTERN_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 }'`
-PPVIZPATTERN_SOURCE=`$(SVN) info | $(SED) -n -e 's/Repository UUID: // p'`
+PPBACKGROUND_BRANCH=`$(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 }'`
+PPBACKGROUND_SOURCE=`$(SVN) info | $(SED) -n -e 's/Repository UUID: // p'`
 else
-PPVIZPATTERN_BRANCH="UNKNOWN"
-PPVIZPATTERN_SOURCE="UNKNOWN"
+PPBACKGROUND_BRANCH="UNKNOWN"
+PPBACKGROUND_SOURCE="UNKNOWN"
 endif
 
@@ -19 +19 @@
 ppBackgroundVersionDefinitions.h: ppBackgroundVersionDefinitions.h.in FORCE
         -$(RM) ppBackgroundVersionDefinitions.h
-        $(SED) -e "s|@PPVIZPATTERN_VERSION@|\"$(PPVIZPATTERN_VERSION)\"|" -e "s|@PPVIZPATTERN_BRANCH@|\"$(PPVIZPATTERN_BRANCH)\"|" -e "s|@PPVIZPATTERN_SOURCE@|\"$(PPVIZPATTERN_SOURCE)\"|" ppBackgroundVersionDefinitions.h.in > ppBackgroundVersionDefinitions.h
+        $(SED) -e "s|@PPBACKGROUND_VERSION@|\"$(PPBACKGROUND_VERSION)\"|" -e "s|@PPBACKGROUND_BRANCH@|\"$(PPBACKGROUND_BRANCH)\"|" -e "s|@PPBACKGROUND_SOURCE@|\"$(PPBACKGROUND_SOURCE)\"|" ppBackgroundVersionDefinitions.h.in > ppBackgroundVersionDefinitions.h
 FORCE: ;
 
@@ -25 +25 @@
 
 
-ppBackground_CPPFLAGS = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(PSPHOT_CFLAGS) $(PPBACKGROUND_CFLAGS)
-ppBackground_LDFLAGS  = $(PSLIB_LIBS)   $(PSMODULE_LIBS)   $(PSPHOT_LIBS)   $(PPBACKGROUND_LIBS)
+ppBackground_CPPFLAGS = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(PPSTATS_CFLAGS) $(PSPHOT_CFLAGS) $(PPBACKGROUND_CFLAGS)
+ppBackground_LDFLAGS  = $(PSLIB_LIBS)   $(PSMODULE_LIBS)   $(PPSTATS_LIBS)   $(PSPHOT_LIBS)   $(PPBACKGROUND_LIBS)
 
 ppBackground_SOURCES =          \
@@ -35 +35 @@
         ppBackgroundLoop.c      \
         ppBackgroundVersion.c   \
-        ppBackgroundModel.c     \
-        ppBackgroundErrorCodes.c
+        ppBackgroundRestore.c   \
+        ppBackgroundErrorCodes.c        \
+        ppBackgroundExit.c
 
 noinst_HEADERS = \

branches/czw_branch/20100519/ppBackground/src/ppBackground.c

@@ -6 +6 @@
 #include <pslib.h>
 #include <psmodules.h>
+#include <psphot.h>
 
 #include "ppBackground.h"
@@ -12 +13 @@
 {
     ppBackgroundVersionPrint();
+
+    pmErrorRegister();
+    psphotErrorRegister();
+    ppBackgroundErrorRegister();
 
     ppBackgroundData *data = ppBackgroundDataInit(&argc, argv);
@@ -46 +51 @@
         }
         data->statsFile = NULL;
-        pmConfigRunFilenameAddWrite(data->config, "STATS", data->statsName);
         exitValue = ppBackgroundExitCode(exitValue);
     }

branches/czw_branch/20100519/ppBackground/src/ppBackground.h

@@ -5 +5 @@
 #include <psmodules.h>
 
-#include <ppBackgroundErrorCodes.h>
+#include "ppBackgroundErrorCodes.h"
 
 #define PPBACKGROUND_RECIPE "PPBACKGROUND"      // Recipe name
@@ -37 +37 @@
     );
 
+/// Restore the background to an image
+bool ppBackgroundRestore(
+    pmChip *chip,                       // Chip to correct
+    const pmChip *background,           // Chip with background model
+    const pmChip *pattern,              // Chip with pattern
+    const pmFPAview *view,              // View to data
+    pmConfig *config                    // Configuration
+    );
+
 /// Determine exit code
 psExit ppBackgroundExitCode(

branches/czw_branch/20100519/ppBackground/src/ppBackgroundArguments.c

@@ -45 +45 @@
     assert(data->config);
 
-    psMetadata *arguments = psMetadataAlloc(); // Command-line arguments
+    psMetadata *arguments = data->config->arguments;
     psMetadataAddStr(arguments, PS_LIST_TAIL, "-pattern", 0, "Filename of pattern correction", NULL);
     psMetadataAddStr(arguments, PS_LIST_TAIL, "-background", 0, "Filename of background model", NULL);
-    psMetadataAddStr(arguments, PS_LIST_TAIL, "-image", 0, "Filename of image", NULL);
+    psMetadataAddStr(arguments, PS_LIST_TAIL, "-image", 0, "Filename of image (required)", NULL);
     psMetadataAddStr(arguments, PS_LIST_TAIL, "-mask", 0, "Filename of mask", NULL);
+    psMetadataAddStr(arguments, PS_LIST_TAIL, "-stats", 0, "Output statistics file", NULL);
+    psMetadataAddStr(arguments, PS_LIST_TAIL, "-dumpconfig", 0, "Output configuration file", NULL);
     if (argc == 1 || !psArgumentParse(arguments, &argc, argv) || argc != 2) {
         usage(argv[0], arguments, data);
@@ -59 +61 @@
     data->maskName = psMemIncrRefCounter(psMetadataLookupStr(NULL, arguments, "-mask"));
     data->outRoot = psStringCopy(argv[1]);
-    psMetadataAddStr(data->config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "Output root name", data->outRoot);
+    psMetadataAddStr(arguments, PS_LIST_TAIL, "OUTPUT", 0, "Output root name", data->outRoot);
 
     psTrace("ppBackground", 1, "Done reading command-line arguments\n");
-    psFree(arguments);
 
     if (!data->patternName && !data->backgroundName) {
@@ -68 +69 @@
         return false;
     }
+    if (!data->imageName) {
+        psError(PPBACKGROUND_ERR_CONFIG, true, "Must specify -image");
+        return false;
+    }
 
     PS_ASSERT_STRING_NON_EMPTY(data->outRoot, false);
+
+    const char *statsName = psMetadataLookupStr(NULL, arguments, "-stats");
+    if (statsName) {
+        data->statsFile = fopen(statsName, "w");
+        if (!data->statsFile) {
+            psError(PPBACKGROUND_ERR_IO, true, "Unable to open statistics file %s", statsName);
+            return false;
+        }
+        data->stats = psMetadataAlloc();
+        pmConfigRunFilenameAddWrite(data->config, "STATS", statsName);
+    }
 
     return true;

branches/czw_branch/20100519/ppBackground/src/ppBackgroundCamera.c

@@ -32 +32 @@
     bool status;                        // Status of file definition
 
-    fileArguments("PATTERN", data->patternName, "Input pattern", data->config);
-    pmFPAfile *pattern = pmFPAfileDefineFromArgs(&status, data->config, "PPBACKGROUND.PATTERN",
-                                                 "PATTERN"); // File
-    if (!status) {
-        psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.PATTERN");
-        return false;
+    if (data->patternName) {
+        fileArguments("PATTERN", data->patternName, "Input pattern", data->config);
+        pmFPAfileDefineFromArgs(&status, data->config, "PPBACKGROUND.PATTERN", "PATTERN"); // File
+        if (!status) {
+            psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.PATTERN");
+            return false;
+        }
     }
 
-    fileArguments("BACKGROUND", data->backgroundName, "Input background model", data->config);
-    pmFPAfile *background = pmFPAfileBindFromArgs(&status, data->config, "PPBACKGROUND.BACKGROUND",
-                                                  "BACKGROUND"); // File
-    if (!status) {
-        psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.BACKGROUND");
-        return false;
+    if (data->backgroundName) {
+        fileArguments("BACKGROUND", data->backgroundName, "Input background model", data->config);
+        pmFPAfileDefineFromArgs(&status, data->config, "PPBACKGROUND.BACKGROUND", "BACKGROUND"); // File
+        if (!status) {
+            psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.BACKGROUND");
+            return false;
+        }
     }
 
-    fileArguments("IMAGE", data->backgroundName, "Input uncorrected image", data->config);
-    pmFPAfile *image = pmFPAfileBindFromArgs(&status, background, data->config, "PPBACKGROUND.IMAGE",
-                                             "IMAGE"); // File
-    if (!status) {
+    fileArguments("IMAGE", data->imageName, "Input uncorrected image", data->config);
+    pmFPAfile *image = pmFPAfileDefineFromArgs(&status, data->config, "PPBACKGROUND.IMAGE",
+                                               "IMAGE"); // File
+    if (!status || !image) {
         psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.IMAGE");
         return false;
     }
 
-    fileArguments("MASK", data->backgroundName, "Input uncorrected mask", data->config);
-    pmFPAfile *mask = pmFPAfileBindFromArgs(&status, image, data->config, "PPBACKGROUND.MASK",
-                                              "MASK"); // File
+    fileArguments("MASK", data->maskName, "Input uncorrected mask", data->config);
+    pmFPAfileBindFromArgs(&status, image, data->config, "PPBACKGROUND.MASK", "MASK"); // File
     if (!status) {
         psError(psErrorCodeLast(), false, "Failed to build file from PPBACKGROUND.MASK");
@@ -64 +65 @@
     }
 
-    pmFPAfile *output = pmFPAfileDefineOutput(data->config, file->fpa, "PPBACKGROUND.OUTPUT");
+    pmFPAfile *output = pmFPAfileDefineOutput(data->config, image->fpa, "PPBACKGROUND.OUTPUT");
     if (!output) {
         psError(psErrorCodeLast(), false, "Unable to define output.");
@@ -70 +71 @@
     }
     output->save = true;
+
+    pmFPAfile *outMask = pmFPAfileDefineOutput(data->config, output->fpa, "PPBACKGROUND.OUTPUT.MASK");
+    if (!outMask) {
+        psError(psErrorCodeLast(), false, "Unable to define output.");
+        return false;
+    }
+    outMask->save = true;
 
 #if 0

branches/czw_branch/20100519/ppBackground/src/ppBackgroundExit.c

@@ -13 +13 @@
     if (errorCode != PS_ERR_NONE) {
         pmFPAfileFreeSetStrict(false);
-        psErrorStackPrint(stderr, "Error in subtraction:");
+        psErrorStackPrint(stderr, "Error in background restoration:");
         switch (errorCode) {
           case PS_ERR_UNKNOWN:

branches/czw_branch/20100519/ppBackground/src/ppBackgroundLoop.c

@@ -6 +6 @@
 #include <pslib.h>
 #include <psmodules.h>
+#include <ppStats.h>
 
 #include "ppBackground.h"
@@ -13 +14 @@
 {
     pmConfig *config = data->config;                                        // Configuration data
-    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPBACKGROUND.BACKGROUND", 0);
+    pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPBACKGROUND.IMAGE", 0);
     pmFPAfile *patternFile = pmFPAfileSelectSingle(config->files, "PPBACKGROUND.PATTERN", 0); // File with data
+    pmFPAfile *bgFile = pmFPAfileSelectSingle(config->files, "PPBACKGROUND.BACKGROUND", 0);   // File with bg
     pmFPA *patternMosaic = pmFPAConstruct(file->camera, file->cameraName); // Mosaicked FPA for pattern
 
-    psImageMaskType maskBad = pmConfigMaskGet("BLANK", config); // Mask value to set
+    psImageMaskType maskBad = pmConfigMaskGet("DETECTOR", config); // Mask value to set
 
     pmFPAview *view = pmFPAviewAlloc(0); // Pointer into FPA hierarchy
@@ -34 +36 @@
         }
 
-        if (chip->cell->n > 1) {
+        if (chip->cells->n > 1) {
             psError(PPBACKGROUND_ERR_CONFIG, true,
                     "Input image and background model should be chip-mosaicked");
@@ -44 +46 @@
             pmFPAfileActivate(config->files, true, "PPBACKGROUND.PATTERN");
 
-            pmCell *cell;               // Cell with pattern data
+            pmCell *patternCell;               // Cell with pattern data
             while ((patternCell = pmFPAviewNextCell(view, patternFile->fpa, 1))) {
-                if (!cell->process || !cell->file_exists) {
+                if (!patternCell->process || !patternCell->file_exists) {
                     continue;
                 }
@@ -68 +70 @@
                     // Get size of image from concepts
                     if (numCols == 0 || numRows == 0) {
-                        numCols = psMetadataLookupS32(NULL, cell->concepts, "CELL.XSIZE");
-                        numRows = psMetadataLookupS32(NULL, cell->concepts, "CELL.YSIZE");
+                        numCols = psMetadataLookupS32(NULL, patternCell->concepts, "CELL.XSIZE");
+                        numRows = psMetadataLookupS32(NULL, patternCell->concepts, "CELL.YSIZE");
                     }
                     // Get size of image from TRIMSEC
                     if (numCols == 0 || numRows == 0) {
-                        psRegion *trimsec = psMetadataLookupPtr(NULL, cell->concepts, "CELL.TRIMSEC");
+                        psRegion *trimsec = psMetadataLookupPtr(NULL, patternCell->concepts, "CELL.TRIMSEC");
                         numCols = trimsec->x1 - trimsec->x0;
                         numRows = trimsec->y1 - trimsec->y0;
@@ -84 +86 @@
                     readout->image = psImageAlloc(numCols, numRows, PS_TYPE_F32);
                     psImageInit(readout->image, 0.0);
+                    readout->mask = psImageAlloc(numCols, numRows, PS_TYPE_IMAGE_MASK);
+                    psImageInit(readout->mask, 0);
 
                     if (!pmPatternRowApply(readout, maskBad) || !pmPatternCellApply(readout, maskBad)) {
@@ -91 +95 @@
 
                     // Remove bias sections to avoid warnings
-                    psMetadataItem *biassec = psMetadataLookup(patternRO->parent->concepts, "CELL.BIASSEC");
+                    psMetadataItem *biassec = psMetadataLookup(patternCell->concepts, "CELL.BIASSEC");
                     if (psListLength(biassec->data.V)) {
                         psFree(biassec->data.V);
@@ -114 +118 @@
             }
 
-            pmChip *mosaic = pmFPAviewThisChip(view, patternMosaic); // Chip for mosaicked pattern
-            if (!pmChipMosaic(mosaic, chip, true, maskBad)) {
-                psError(psErrorCodeLast(), false, "Unable to mosaic pattern correction");
-                return false;
+            if (data->patternName) {
+                pmChip *patternChip = pmFPAviewThisChip(view, patternFile->fpa); // Chip for pattern
+                pmChip *mosaic = pmFPAviewThisChip(view, patternMosaic); // Chip for mosaicked pattern
+                if (!mosaic->hdu && !mosaic->parent->hdu) {
+                    pmFPAAddSourceFromView(patternMosaic, view, file->format);
+                }
+                if (!pmChipMosaic(mosaic, patternChip, true, maskBad)) {
+                    psError(psErrorCodeLast(), false, "Unable to mosaic pattern correction");
+                    return false;
+                }
+                pmFPAfileActivate(config->files, true, NULL);
+            //            pmFPAfileActivate(config->files, false, "PPBACKGROUND.PATTERN");
             }
-            pmFPAfileActivate(config->files, true, NULL);
-            pmFPAfileActivate(config->files, false, "PPBACKGROUND.PATTERN");
         }
 
+        pmChip *patternChip = patternFile ? pmFPAviewThisChip(view, patternMosaic) : NULL; // Chip with pattern
+        pmChip *bgChip = bgFile ? pmFPAviewThisChip(view, bgFile->fpa) : NULL; // Chip with background model
+        if (!ppBackgroundRestore(chip, bgChip, patternChip, view, config)) {
+            psError(psErrorCodeLast(), false, "Unable to replace background");
+            return false;
+        }
+        pmChipFreeData(patternChip);
 
-
-
-
-
-
-                pmHDU *hdu = pmHDUGetLowest(file->fpa, chip, cell); // HDU for readout
-                if (!hdu) {
-                    psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find HDU for data.");
-                    return false;
-                }
-                if (!hdu->header) {
-                    hdu->header = psMetadataAlloc();
-                }
-                ppBackgroundVersionHeader(hdu->header);
-
-
-
-
-
-
-
+        pmHDU *hdu = pmHDUGetLowest(file->fpa, chip, NULL); // HDU for chip
+        if (!hdu) {
+            psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find HDU for data.");
+            return false;
+        }
+        if (!hdu->header) {
+            hdu->header = psMetadataAlloc();
+        }
+        ppBackgroundVersionHeader(hdu->header);
 
         // Chip
@@ -158 +163 @@
     }
 
+    psFree(patternMosaic);
+
+    if (data->stats) {
+        psImageMaskType maskVal = 0;    // Bits to mask
+        if (!pmConfigMaskSetBits(&maskVal, NULL, config)) {
+            psError(psErrorCodeLast(), false, "Unable to find bits to mask");
+            return false;
+        }
+        ppStatsFPA(data->stats, file->fpa, view, maskVal, config);
+    }
+
+    psFree(view);
+
     return true;
 }

branches/czw_branch/20100519/ppBackground/src/ppBackgroundVersionDefinitions.h.in

@@ -1 @@
-#ifndef PPVIZPATTERN_VERSION_DEFINITIONS_H
-#define PPVIZPATTERN_VERSION_DEFINITIONS_H
+#ifndef PPBACKGROUND_VERSION_DEFINITIONS_H
+#define PPBACKGROUND_VERSION_DEFINITIONS_H
 
-#define PPVIZPATTERN_VERSION @PPVIZPATTERN_VERSION@ // SVN version
-#define PPVIZPATTERN_BRANCH  @PPVIZPATTERN_BRANCH@  // SVN branch
-#define PPVIZPATTERN_SOURCE  @PPVIZPATTERN_SOURCE@  // SVN source
+#define PPBACKGROUND_VERSION @PPBACKGROUND_VERSION@ // SVN version
+#define PPBACKGROUND_BRANCH  @PPBACKGROUND_BRANCH@  // SVN branch
+#define PPBACKGROUND_SOURCE  @PPBACKGROUND_SOURCE@  // SVN source
 
 #endif