Changeset 18365

Timestamp:

Jun 29, 2008, 2:55:44 PM (18 years ago)

Author:

eugene

Message:

add smoothing of suspect pixels; chip and cell options; skip unused chips and cells as needed

Location:

trunk/ppMerge/src

Files:

• ppMergeArguments.c (modified) (2 diffs)
• ppMergeCamera.c (modified) (2 diffs)
• ppMergeMask.c (modified) (10 diffs)

trunk/ppMerge/src/ppMergeArguments.c

@@ -162 +162 @@
     psMetadataAddBool(arguments, PS_LIST_TAIL, "-mask-chip",    0, "Measure mask statistics by chip?", false);
 
+    psMetadataAddBool(arguments, PS_LIST_TAIL, "-mask-smooth-suspect",  0, "smooth suspect pixels?", false);
+    psMetadataAddF32(arguments, PS_LIST_TAIL, "-mask-smooth-scale",  0, "smoothing sigma for suspect pixels", NAN);
+
+    // chip & cell selections are used to limit chips to be processed
+    int argnum;
+    if ((argnum = psArgumentGet (argc, argv, "-chip"))) {
+        psArgumentRemove (argnum, &argc, argv);
+        psMetadataAddStr (config->arguments, PS_LIST_TAIL, "CHIP_SELECTIONS", PS_DATA_STRING, "", argv[argnum]);
+        psArgumentRemove (argnum, &argc, argv);
+    }
+    if ((argnum = psArgumentGet (argc, argv, "-cell"))) {
+        psArgumentRemove (argnum, &argc, argv);
+        psMetadataAddStr (config->arguments, PS_LIST_TAIL, "CELL_SELECTIONS", PS_DATA_STRING, "", argv[argnum]);
+        psArgumentRemove (argnum, &argc, argv);
+    }
+
     if (argc == 1 || !psArgumentParse(arguments, &argc, argv) || argc != 3) {
         usage(argv[0], arguments);
@@ -269 +285 @@
     VALUE_ARG_RECIPE_BOOL("-mask-chip",     "MASK.CHIPSTATS");
 
+    VALUE_ARG_RECIPE_BOOL("-mask-smooth-suspect", "MASK.SMOOTH.SUSPECT");
+    VALUE_ARG_RECIPE_FLOAT("-mask-smooth-scale", "MASK.SMOOTH.SCALE", F32);
 
     const char *maskModeStr = psMetadataLookupStr(NULL, arguments, "-mask-mode"); // Mode to identify bad pix

trunk/ppMerge/src/ppMergeCamera.c

@@ -30 +30 @@
         return false;
     }
+
+    // Chip selection: turn on only the chips specified.
+    bool status;
+    char *chipLine = psMetadataLookupStr(&status, config->arguments, "CHIP_SELECTIONS");
+    psArray *chips = psStringSplitArray (chipLine, ",", false);
+    if (chips->n > 0) {
+        pmFPASelectChip (fpa, -1, true); // deselect all chips
+        for (int i = 0; i < chips->n; i++) {
+            int chipNum = atoi(chips->data[i]);
+            if (! pmFPASelectChip(fpa, chipNum, false)) {
+                psError(PS_ERR_IO, false, "Chip number %d doesn't exist in camera.\n", chipNum);
+                psFree (chips);
+                return false;
+            }
+        }
+    }
+    psFree (chips);
+
+    // Cell selection: turn on only the cells specified.  Note that this affects the same cell
+    // for all chips
+    char *cellLine = psMetadataLookupStr(&status, config->arguments, "CELL_SELECTIONS");
+    psArray *cells = psStringSplitArray (cellLine, ",", false);
+    if (cells->n > 0) {
+        for (int i = 0; i < fpa->chips->n; i++) {
+            pmChip *chip = fpa->chips->data[i];
+            pmChipSelectCell (chip, -1, true); // deselect all cells
+            for (int j = 0; j < cells->n; j++) {
+                int cellNum = atoi(cells->data[j]);
+                if (! pmChipSelectCell(chip, cellNum, false)) {
+                    psError(PS_ERR_IO, false, "Cell number %d doesn't exist in camera.\n", cellNum);
+                    psFree (cells);
+                    return false;
+                }
+            }
+        }
+    }
+    psFree (cells);
 
     pmFPAfile *output = pmFPAfileDefineOutput(config, fpa, name);
@@ -229 +266 @@
                 pmHDU *hdu = pmHDUGetLowest(fpa, chip, cell); // HDU for cell
                 if (!hdu || hdu->blankPHU) {
-                    psFree(cell->concepts);
-                    cell->concepts = NULL;
                     cell->data_exists = false;
                     cell->file_exists = false;
                     culled++;
+                    if (cell->concepts) {
+                        psFree(cell->concepts);
+                        cell->concepts = NULL;
+                    }
                 }
             }
             if (culled == cells->n) {
-                psFree(chip->concepts);
-                chip->concepts = NULL;
                 chip->data_exists = false;
                 chip->file_exists = false;
+                if (chip->concepts) {
+                    psFree(chip->concepts);
+                    chip->concepts = NULL;
+                }
             }
         }

trunk/ppMerge/src/ppMergeMask.c

@@ -37 +37 @@
     psMaskType maskGrowVal = psMetadataLookupU8(NULL, config->arguments, "MASK.GROWVAL"); // Value for grown mask
 
+    bool smoothSuspect = psMetadataLookupBool(&mdok, config->arguments, "MASK.SMOOTH.SUSPECT"); // Radius to grow mask
+    float smoothScale = psMetadataLookupF32(&mdok, config->arguments, "MASK.SMOOTH.SCALE"); // Radius to grow mask
+
     psStats *statistics = psStatsAlloc(meanStat | stdevStat); // Statistics for background
 
@@ -42 +45 @@
     pmChip *outChip = pmFPAfileThisChip(config->files, view, outName); // Output chip
     psFree(outName);
+    
+    int numCells = 1;
+    if (chipStats) {
+        // count the number of active cells for this chip:
+        numCells = 0;
+        for (int i = 0; i < outChip->cells->n; i++) {
+            pmCell *cell = outChip->cells->data[i];
+            if (!cell->process) continue;
+            numCells ++;
+        }
+    }
 
     // For each input file, get the statistics, which can be calculated at the chip or cell levels
@@ -58 +72 @@
         pmCell *inCell;                 // Input cell
         while ((inCell = pmFPAviewNextCell(inView, inFPA, 1))) {
+
+            // the output FPA structure carries the information about which cells to process
+            pmCell *outCell = pmFPAfileThisCell(config->files, inView, "PPMERGE.OUTPUT.MASK"); // Output cell
+            if (!outCell->process) continue;
+
             pmHDU *hdu = pmHDUFromCell(inCell); // HDU for cell
             if (!hdu || hdu->blankPHU) {
@@ -99 +118 @@
             }
 
-            pmCell *outCell = pmFPAfileThisCell(config->files, inView, "PPMERGE.OUTPUT.MASK"); // Output cell
             pmReadout *outRO = NULL;    // Output readout
             if (outCell->readouts && outCell->readouts->n == 1) {
@@ -111 +129 @@
             int numCols = readout->image->numCols, numRows = readout->image->numRows; // Image size
             int numPix = numCols * numRows; // Number of pixels
-            int numCells = chipStats ? readout->parent->parent->cells->n : 1; // Number of cells
             int num = PS_MIN(numPix, sample / numCells); // Number of values to add
             if (!chipStats) {
@@ -166 +183 @@
             inView->cell = -1;
             while ((inCell = pmFPAviewNextCell(inView, inFPA, 1))) {
+
+                // the output FPA structure carries the information about which cells to process
+                pmCell *outCell = pmFPAfileThisCell(config->files, inView, "PPMERGE.OUTPUT.MASK"); // Output cell
+                if (!outCell->process) continue;
+
                 pmHDU *hdu = pmHDUFromCell(inCell); // HDU for cell
                 if (!hdu || hdu->blankPHU) {
@@ -206 +228 @@
     *outView = *view;
     while ((outCell = pmFPAviewNextCell(outView, outFPA, 1))) {
+
+        // skipp inactive cells
+        if (!outCell->process) continue;
+
         pmHDU *hdu = pmHDUFromCell(outCell); // HDU for cell
         if (!hdu || hdu->blankPHU) {
@@ -216 +242 @@
         assert(outCell->readouts && outCell->readouts->n == 1);
         pmReadout *outRO = outCell->readouts->data[0]; // Output readout
+
+        if (smoothSuspect) {
+            // XXX test output of suspect pixel image
+            psImage *suspects = psMetadataLookupPtr(NULL, outRO->analysis, PM_MASK_ANALYSIS_SUSPECT); // Suspect img
+            assert (suspects);
+            psImageSmooth (suspects, smoothScale, 3); // extend smoothing region to 3-sigma
+        }
+
         if (!pmMaskIdentifyBadPixels(outRO, maskVal, maskBad, maskMode)) {
             psError(PS_ERR_UNKNOWN, false, "Unable to mask bad pixels");
@@ -359 +393 @@
     pmChip *outChip;                    // Chip of interest
     while ((outChip = pmFPAviewNextChip(view, outFPA, 1))) {
+
+        if (!outChip->process) continue;
+
         if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
             goto PPMERGE_MASK_ERROR;
@@ -370 +407 @@
         }
 
-        psList *inChips = psListAlloc(NULL);
-        for (int i=0; i < numFiles; i++) {
-            pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT", i); // Input file
-            pmChip *chip = pmFPAviewThisChip(view, file->fpa);
-            psListAdd(inChips, PS_LIST_TAIL, chip);
-        }
-        if (!pmConceptsAverageChips(outChip, inChips, true)) {
-            psError(PS_ERR_UNKNOWN, false, "Unable to average Chip concepts.");
-            psFree(inChips);
-            goto PPMERGE_MASK_ERROR;
-        }
-        psFree(inChips);
+        if (outChip->data_exists) {
+            psList *inChips = psListAlloc(NULL);
+            for (int i=0; i < numFiles; i++) {
+                pmFPAfile *file = pmFPAfileSelectSingle(config->files, "PPMERGE.INPUT", i); // Input file
+                pmChip *chip = pmFPAviewThisChip(view, file->fpa);
+                psListAdd(inChips, PS_LIST_TAIL, chip);
+            }
+            if (!pmConceptsAverageChips(outChip, inChips, true)) {
+                psError(PS_ERR_UNKNOWN, false, "Unable to average Chip concepts.");
+                psFree(inChips);
+                goto PPMERGE_MASK_ERROR;
+            }
+            psFree(inChips);
+        }
         if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) {
             goto PPMERGE_MASK_ERROR;