Changeset 14000

Timestamp:

Jul 3, 2007, 10:01:23 AM (19 years ago)

Author:

eugene

Message:

consolidating includes in ppImage.h; adding ppImageMetadataStats and ppImagePixelStats

Location:

trunk/ppImage/src

Files:

• Makefile.am (modified) (3 diffs)
• ppImage.c (modified) (1 diff)
• ppImage.h (modified) (3 diffs)
• ppImageArguments.c (modified) (1 diff)
• ppImageDetrend.h (deleted)
• ppImageDetrendFringe.c (modified) (1 diff)
• ppImageDetrendFringe.h (deleted)
• ppImageDetrendReadout.c (modified) (1 diff)
• ppImageLoop.c (modified) (5 diffs)
• ppImageMetadataStats.c (added)
• ppImageOptions.h (deleted)
• ppImagePixelStats.c (added)
• ppImageStats.c (modified) (4 diffs)
• ppImageStatsOutput.c (added)
• ppImageVersion.c (modified) (1 diff)
• ppImageVersion.h (deleted)

trunk/ppImage/src/Makefile.am

@@ -4 +4 @@
 
 noinst_HEADERS = \
-        ppImage.h \
-        ppImageOptions.h \
-        ppImageDetrendFringe.h \
-        ppImageVersion.h
+        ppImage.h 
 
 ppImage_CPPFLAGS = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(PSPHOT_CFLAGS) $(PSASTRO_CFLAGS) $(PPSTATS_CFLAGS) $(ppImage_CFLAGS)
@@ -27 +24 @@
         ppImageAddstar.c \
         ppImageStats.c \
+        ppImageStatsOutput.c \
+        ppImagePixelStats.c \
+        ppImageMetadataStats.c \
         ppImageDefineFile.c \
+        ppImageFileCheck.c \
         ppImageVersion.c
 
@@ -50 +51 @@
         ppImageAddstar.c \
         ppImageStats.c \
+        ppImageStatsOutput.c \
+        ppImagePixelStats.c \
+        ppImageMetadataStats.c \
         ppImageDefineFile.c \
+        ppImageFileCheck.c \
         ppImageVersion.c
 

trunk/ppImage/src/ppImage.c

@@ -45 +45 @@
     return PS_EXIT_SUCCESS;
 }
-
-void ppImageFileCheck (pmConfig *config) {
-
-    // add the output names to the output-type files
-    psMetadataItem *item = NULL;
-    psMetadataIterator *iter = psMetadataIteratorAlloc (config->files, PS_LIST_HEAD, NULL);
-    while ((item = psMetadataGetAndIncrement (iter)) != NULL) {
-        pmFPAfile *file = item->data.V;
-        pmFPA *fpa = file->fpa;
-        fprintf (stderr, "file %s\n", file->name);
-        if (!fpa) {
-            fprintf (stderr, "  has no FPA\n");
-            continue;
-        }
-        if (fpa->hdu) {
-            if (fpa->hdu->images) fprintf (stderr, "  (%d,%d) images\n", -1, -1);
-            if (fpa->hdu->weights) fprintf (stderr, "  (%d,%d) weights\n", -1, -1);
-            if (fpa->hdu->masks) fprintf (stderr, "  (%d,%d) masks\n", -1, -1);
-            if (fpa->hdu->header) fprintf (stderr, "  (%d,%d) header\n", -1, -1);
-        } else {
-            // fprintf (stderr, "  has no fpa data (%d,%d)\n", -1, -1);
-        }
-        for (int i = 0; i < fpa->chips->n; i++) {
-            pmChip *chip = fpa->chips->data[i];
-            if (chip->hdu) {
-                if (chip->hdu->images) fprintf (stderr, "  (%d,%d) images\n", i, -1);
-                if (chip->hdu->weights) fprintf (stderr, "  (%d,%d) weights\n", i, -1);
-                if (chip->hdu->masks) fprintf (stderr, "  (%d,%d) masks\n", i, -1);
-                if (chip->hdu->header) fprintf (stderr, "  (%d,%d) header\n", i, -1);
-            } else {
-                // fprintf (stderr, "  has no chip data (%d,%d)\n", i, -1);
-            }
-            for (int j = 0; j < chip->cells->n; j++) {
-                pmCell *cell = chip->cells->data[j];
-                if (cell->hdu) {
-                    if (cell->hdu->images) fprintf (stderr, "  (%d,%d) images\n", i, j);
-                    if (cell->hdu->weights) fprintf (stderr, "  (%d,%d) weights\n", i, j);
-                    if (cell->hdu->masks) fprintf (stderr, "  (%d,%d) masks\n", i, j);
-                    if (cell->hdu->header) fprintf (stderr, "  (%d,%d) header\n", i, j);
-                } else {
-                    // fprintf (stderr, "  has no cell data (%d,%d)\n", i, j);
-                }
-                for (int k = 0; k < cell->readouts->n; k++) {
-                    pmReadout *readout = cell->readouts->data[k];
-                    if (readout) {
-                        if (readout->image) fprintf (stderr, "  (%d,%d,%d) image\n", i, j, k);
-                        if (readout->weight) fprintf (stderr, "  (%d,%d,%d) weight\n", i, j, k);
-                        if (readout->mask) fprintf (stderr, "  (%d,%d,%d) masks\n", i, j, k);
-                    }
-                }
-            }
-        }
-    }
-    psFree (iter);
-}

trunk/ppImage/src/ppImage.h

@@ -14 +14 @@
 #include "psphot.h"
 #include "psastro.h"
-#include "ppImageOptions.h"
+#include "ppStats.h"
 
 #define RECIPE_NAME "PPIMAGE"           // Name of the recipe to use
 #define TIMERNAME "ppImage"             // Name of timer
+
+// Options for ppImage processing
+typedef struct {
+    bool doMask;                        // Mask bad pixels
+    psMaskType maskValue;               // apply this bit-mask to choose masked bits
+    psMaskType satMask;                 // Mask value to give saturated pixels
+    psMaskType badMask;                 // Mask value to give bad pixels
+    psMaskType flatMask;                // Mask value to give bad flat pixels
+    psMaskType blankMask;               // Mask value to give blank pixels
+
+    bool doBias;                        // Bias subtraction
+    bool doDark;                        // Dark subtraction
+    bool doShutter;                     // Shutter correction
+    bool doFlat;                        // Flat-field normalisation
+    bool doFringe;                      // Fringe subtraction
+    bool doPhotom;                      // Source identification and photometry
+    bool doAstromChip;                  // per-chip Astrometry
+    bool doAstromMosaic;                // full-mosaic Astrometry
+    bool doAddstar;                     // add results to object database?
+
+    bool doOverscan;                    // Overscan subtraction
+    pmOverscanOptions *overscan;        // Overscan options
+
+    bool doNonLin;                      // Non-linearity correction
+    psDataType nonLinearType;
+    psMetadataItem *nonLinearData;
+    void *nonLinearSource;
+
+    bool doStats;
+
+    bool BaseFITS;
+    bool ChipFITS;
+    bool FPA1FITS;
+    bool FPA2FITS;
+
+    bool Bin1FITS;
+    bool Bin1JPEG;
+    int xBin1, yBin1;
+
+    bool Bin2FITS;
+    bool Bin2JPEG;
+    int xBin2, yBin2;
+
+    float fringeRej;                    // Fringe rejection limit
+    int fringeIter;                     // Fringe iterations
+    float fringeKeep;                   // Fringe keep fraction
+} ppImageOptions;
+
+// Cells to be used in the detrend
+typedef struct {
+    pmCell *input;                      // The input cell, to be operated upon
+    pmCell *mask;                       // The bad pixel mask
+    pmCell *bias;                       // The bias correction
+    pmCell *dark;                       // The dark correction
+    pmCell *flat;                       // The flat-field correction
+} ppImageDetrend;
+
+ppImageOptions *ppImageOptionsAlloc(void);
+
+// Determine the processing options
+ppImageOptions *ppImageOptionsParse(pmConfig *config);
 
 // Get the configuration
@@ -35 +96 @@
 
 bool ppImageDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, ppImageOptions *options);
-bool ppImageDetrendMask(pmReadout *input, pmReadout *mask);
 
 bool ppImageDetrendNonLinear(pmReadout *input, ppImageOptions *options);
 bool ppImageDetrendNonLinearLookup(pmReadout *input, psMetadataItem *dataItem);
 bool ppImageDetrendNonLinearPolynomial(pmReadout *input, psMetadataItem *dataItem);
+
+bool ppImageDetrendCell(ppImageDetrend *detrend, ppImageOptions *options, pmConfig *config);
+bool ppImageDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, ppImageOptions *options);
+pmReadout* ppImageDetrendSelectFirst(pmCell *cell, char *name, bool doThis);
 
 bool ppImageRebinChip (pmConfig *config, pmFPAview *view, char *outName);
@@ -69 +133 @@
 
 // write stats to output file 
-bool ppImageStatsOutput (pmConfig *config, pmFPA *fpa, const ppImageOptions *options);
+bool ppImageStatsOutput (pmConfig *config, const ppImageOptions *options);
+
+
+// Measure fringes
+bool ppImageDetrendFringeMeasure(pmReadout *readout, // Readout to measure
+                                 pmCell *fringe, // Fringe cell (each readout is a different component)
+                                 const bool isResidual,
+                                 const ppImageOptions *options // Options
+    );
+
+// Solve the fringe system
+bool ppImageDetrendFringeSolve(pmChip *scienceChip, // Chip with science
+                               const pmChip *refChip, // Chip with reference fringes
+                               const bool isResidual,
+                               const ppImageOptions *options // Options
+    );
+
+// Generate fringe frame
+bool ppImageDetrendFringeGenerate(pmCell *science, // Science cell
+                                  pmCell *fringes, // Fringe cell, one readout per fringe component
+                                  const ppImageOptions *options // Options
+    );
+
+
+bool ppImageDetrendFringeApply (pmConfig *config, // config
+                                pmChip *chip, // science chip
+                                const pmFPAview *inputView, // current view
+                                const ppImageOptions *options // options
+    );
+
+/// Return short version information
+psString ppImageVersion(void);
+
+/// Return long version information
+psString ppImageVersionLong(void);
+
+/// Update the metadata with version information for all dependencies
+void ppImageVersionMetadata(psMetadata *metadata ///< Metadata to update with version information
+    );
+
+
+// calculate stats, including MD5
+bool ppImagePixelStats (pmConfig *config, const ppImageOptions *options, const pmFPAview *inputView);
+
+// calculate stats from headers and concepts
+bool ppImageMetadataStats (pmConfig *config, const ppImageOptions *options);
+
+void ppImageFileCheck (pmConfig *config);
 
 #endif

trunk/ppImage/src/ppImageArguments.c

@@ -4 +4 @@
 
 #include "ppImage.h"
-#include "ppImageVersion.h"
-#include "ppStatsVersion.h"
 
 static void usage (void) {

trunk/ppImage/src/ppImageDetrendFringe.c

@@ -3 +3 @@
 #endif
 
-#include <stdio.h>
-#include <pslib.h>
-#include <psmodules.h>
-
-#include "ppImageOptions.h"
-#include "ppImageDetrendFringe.h"
+#include "ppImage.h"
 
 bool ppImageDetrendFringeMeasure(pmReadout *readout, pmCell *fringe, const bool isResidual, const ppImageOptions *options)

trunk/ppImage/src/ppImageDetrendReadout.c

@@ -4 +4 @@
 
 #include "ppImage.h"
-#include "ppImageDetrendFringe.h"
 
 bool ppImageDetrendReadout(pmConfig *config, ppImageOptions *options, pmFPAview *view)

trunk/ppImage/src/ppImageLoop.c

@@ -4 +4 @@
 
 #include "ppImage.h"
-#include "ppImageDetrendFringe.h"
-#include "ppImageVersion.h"
 
 bool ppImageLoop (pmConfig *config, ppImageOptions *options) {
@@ -88 +86 @@
         
         // measure various statistics for this image
-        if (!ppImageStats (config, chip, view, options)) {
+        if (!ppImagePixelStats (config, options, view)) {
             psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to measures stats for image");
             psFree (view);
@@ -119 +117 @@
         }
 
-        // Close cells
+        // Close cells (XXX shouldn't pmFPAfileClose iterate down as needed?)
         view->cell = -1;
         while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) {
@@ -139 +137 @@
     }
 
-    // Write out summary statistics
-    if (!ppImageStatsOutput (config, input->fpa, options)) {
-        psError(PS_ERR_UNKNOWN, false, "Unable to write statistics file.\n");
-        psFree (view);
-        return false;
-    }
-
     // XXX an optional full-scale FPA mosaic could happen here
     // it would require us to NOT free PPIMAGE.CHIP until here
@@ -161 +152 @@
     }
 
+    ppImageFileCheck (config);
+
+    // Write out summary statistics
+    if (!ppImageMetadataStats (config, options)) {
+        psError(PS_ERR_UNKNOWN, false, "Unable to write statistics file.\n");
+        psFree (view);
+        return false;
+    }
+
+
+    // Write out summary statistics
+    if (!ppImageStatsOutput (config, options)) {
+        psError(PS_ERR_UNKNOWN, false, "Unable to write statistics file.\n");
+        psFree (view);
+        return false;
+    }
+
     // Close FPA
     if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) {

trunk/ppImage/src/ppImageStats.c

@@ -3 +3 @@
 #endif
 
-#include <stdio.h>
-#include <pslib.h>
-#include <psmodules.h>
-
 #include "ppImage.h"
-#include "ppStats.h"
 
 // calculate stats, including MD5
@@ -42 +37 @@
         if (options->doStats) {
 
-            pmFPAfile *output = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.OUTPUT");
-            if (!mdok || !output) {
-                psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find file PPIMAGE.OUTPUT.");
+            pmFPAfile *outImage = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.OUTPUT");
+            pmFPAfile *outPhotom = psMetadataLookupPtr(&mdok, config->files, "PSPHOT.OUTPUT");
+            pmFPAfile *outAstrom = psMetadataLookupPtr(&mdok, config->files, "PSASTRO.OUTPUT");
+
+            if (!outImage && !outPhotom && !outAstrom) {
+                psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find any output file (PPIMAGE.OUTPUT, PSPHOT.OUTPUT, PSASTRO.OUTPUT).");
                 psFree (view);
                 psFree(stats);
@@ -50 +48 @@
             }
 
-            if (!ppStats(stats, output->fpa, view,
+            // get the latest output product available
+            pmFPAfile *output = outAstrom;
+            if (!output) {
+                output = outPhotom;
+            }
+            if (!output) {
+                output = outImage;
+            }
+
+            if (!ppStatsFPA(stats, output->fpa, view,
                          options->satMask | options->badMask | options->maskValue,
                          config)) {
@@ -98 +105 @@
     return true;
 }
-
-// write stats to output file 
-bool ppImageStatsOutput (pmConfig *config, pmFPA *fpa, const ppImageOptions *options) {
-
-    bool mdok;
-
-    // measure statistics, or ignore?
-    if (!options->doStats) return true;
-        
-    // get the output stats filename
-    const char *statsName = psMetadataLookupStr(&mdok, config->arguments, "STATS"); // Filename for statistics
-    if (!statsName && !strlen(statsName)) {
-        psError (PS_ERR_UNEXPECTED_NULL, false, "missing STATS entry in arguments list.");
-        return false;
-    }
-
-    // convert to a real UNIX filename
-    psString resolved = pmConfigConvertFilename(statsName, config, true); // Resolved filename
-    FILE *statsFile = fopen (resolved, "w");
-    if (!statsFile) {
-        psError(PS_ERR_IO, true, "Unable to open statistics file %s for writing.\n", resolved);
-        psFree(resolved);
-        return false;
-    }
-    psFree(resolved);
-
-    // select the fpa-level analysis stats metadata:
-    psMetadata *stats = psMetadataLookupPtr (&mdok, fpa->analysis, "PPIMAGE.STATS");
-    if (!stats) {
-        psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find PPIMAGE.STATS entry in fpa analysis.\n");
-        return false;
-    }
-
-    // convert the stats MDC to a string
-    char *statsMDC = psMetadataConfigFormat(stats);
-    if (!statsMDC || strlen(statsMDC) == 0) {
-        psError(PS_ERR_IO, false, "Unable to serialize stats metadata.\n");
-        return false;
-    } 
-
-    // write the stats MDC to a file
-    // XXX why does this not call psMetadataConfigPrint?
-    fprintf(statsFile, "%s", statsMDC);
-
-    psFree(statsMDC);
-    fclose(statsFile);
-    return true;
-}

trunk/ppImage/src/ppImageVersion.c

@@ -3 +3 @@
 #endif
 
-#include <stdio.h>
-#include <pslib.h>
-#include <psmodules.h>
-#include <psphot.h>
-#include <psastro.h>
-#include <ppStats.h>
-
-#include "ppImageVersion.h"
+#include "ppImage.h"
 
 static const char *cvsTag = "$Name: not supported by cvs2svn $";// CVS tag name