Changeset 9996

Timestamp:

Nov 14, 2006, 4:49:37 PM (19 years ago)

Author:

Paul Price

Message:

Reorganising shutter stuff to make it fit within the general framework in ppMergeCombine. Adding ppMergeMask to create a bad pixel mask.

Location:

trunk/ppMerge/src

Files:

• Makefile.am (modified) (2 diffs)
• ppMerge.c (modified) (2 diffs)
• ppMergeCombine.c (modified) (5 diffs)
• ppMergeMask.c (added)
• ppMergeMask.h (added)
• ppMergeOptions.c (modified) (10 diffs)
• ppMergeOptions.h (modified) (2 diffs)

trunk/ppMerge/src/Makefile.am

@@ -10 +10 @@
         ppMergeConfig.c         \
         ppMergeData.c           \
+        ppMergeMask.c           \
         ppMergeOptions.c        \
         ppMergeScaleZero.c
@@ -20 +21 @@
         ppMergeConfig.h         \
         ppMergeData.h           \
+        ppMergeMask.h           \
         ppMergeOptions.h        \
         ppMergeScaleZero.h

trunk/ppMerge/src/ppMerge.c

@@ -14 +14 @@
 #include "ppMergeCombine.h"
 #include "ppMergeScaleZero.h"
+#include "ppMergeMask.h"
 
 //#include "ppMem.h"
@@ -45 +46 @@
     }
 
-    // Measure the background in each image
     psImage *scale = NULL;              // The scalings
     psImage *zero = NULL;               // The zeros
-    ppMergeScaleZero(&scale, &zero, data, options, config);
 
-    // Do the combination and write
-    ppMergeCombine(scale, zero, data, options, config);
+    if (options->mask) {
+        // Generate a mask
+        ppMergeMask(data, options, config);
+    } else {
+        // Measure the background in each image
+        ppMergeScaleZero(&scale, &zero, data, options, config);
+
+        // Do the combination and write
+        ppMergeCombine(scale, zero, data, options, config);
+    }
 
     // Output the statistics

trunk/ppMerge/src/ppMergeCombine.c

@@ -78 +78 @@
 #endif
 
-#if 0
-// Write fringe extensions
-static void writeFringes(psMetadata *fringes, // Table of extensions with fringe statistics to write
-                         psFits *fits   // FITS file to which to write
-                         )
-{
-    assert(fringes);
-
-    // Write the fringe extensions
-    psMetadataIterator *fringesIter = psMetadataIteratorAlloc(fringes, PS_LIST_HEAD, false); // Iterator
-    psMetadataItem *fringeItem;         // Item from iteration
-    while ((fringeItem = psMetadataGetAndIncrement(fringesIter))) {
-        const char *extname = fringeItem->name; // Extension name
-        psArray *fringe = fringeItem->data.V; // Fringe data (array of fringe components)
-        if (!pmFringesWriteFits(fits, NULL, fringe, extname)) {
-            psWarning("Unable to write fringe data to extension %s\n", extname);
-        }
-    }
-
-    // Clear the list
-    while (psListLength(fringes->list) > 0) {
-        psMetadataRemoveIndex(fringes, PS_LIST_TAIL);
-    }
-
-    return;
-}
-#endif
 
 // Combine the inputs
@@ -133 +106 @@
     pmFPAWrite(data->out, data->outFile, config->database, true, false); // Write header only
     pmChip *chip;                       // Chip of interest
+    psRandom *rng = NULL;               // Random number generator; required for building a mask
+    if (options->mask) {
+        rng = psRandomAlloc(PS_RANDOM_TAUS, 0);
+    }
     while ((chip = pmFPAviewNextChip(view, fpa, 1))) {
         pmChipWrite(chip, data->outFile, config->database, true, false); // Write header only
@@ -150 +127 @@
             }
 
-            // Building a shutter correction
-            if (options->shutter) {
-                // Read in the pixels
-                int numRead = 0;  // Number of inputs read
-                psVector *exptimes = psVectorAlloc(filenames->n, PS_TYPE_F32);  // Reference measurements
-                psVectorInit(exptimes, 0);
-                psArray *images = psArrayAlloc(filenames->n); // Array of images
-                psArray *weights = psArrayAlloc(filenames->n); // Array of weights
-                psArray *masks = psArrayAlloc(filenames->n); // Array of masks
+            // Read bit by bit
+            int numRead;  // Number of inputs read
+            int numScan = 0;
+
+            do {
+                numRead = 0;
                 for (int i = 0; i < filenames->n; i++) {
                     if (! filenames->data[i] || strlen(filenames->data[i]) == 0) {
@@ -167 +141 @@
                         continue;
                     }
-                    pmFPA *fpaIn = data->in->data[i]; // Input FPA
-                    pmChip *chipIn = fpaIn->chips->data[view->chip]; // Input chip
-                    pmCell *cellIn = chipIn->cells->data[view->cell]; // Input cell
-                    if (!cellIn->file_exists) {
-                        // || !cellIn->data_exists) {
-                        continue;
-                    }
-                    if (!pmCellRead(cellIn, fits, config->database) || cellIn->readouts->n == 0) {
-                        continue;
-                    }
-                    if (cellIn->readouts->n > 1) {
-                        psWarning("Multiple readouts in file %d, chip %d, cell %d --- "
-                                  "only the first will be used.\n", i, view->chip, view->cell);
-                    }
-                    float exptime = psMetadataLookupF32(NULL, cellIn->concepts, "CELL.EXPOSURE");
-                    if (!isfinite(exptime)) {
-                        psWarning("File %d, chip %d, cell %d has bad exposure time.\n",
-                                  i, view->chip, view->cell);
-                    }
-                    exptimes->data.F32[i] = exptime;
-                    pmReadout *readoutIn = cellIn->readouts->data[0];
-                    pmReadoutSetWeight(readoutIn);
-                    images->data[i] = psMemIncrRefCounter(readoutIn->image);
-                    weights->data[i] = psMemIncrRefCounter(readoutIn->weight);
-                    masks->data[i] = psMemIncrRefCounter(readoutIn->mask);
-                    numRead++;
+
+                    if (!stack->data[i]) {
+                        pmFPA *fpaIn = data->in->data[i]; // Input FPA
+                        pmChip *chipIn = fpaIn->chips->data[view->chip]; // Input chip
+                        pmCell *cellIn = chipIn->cells->data[view->cell]; // Input cell
+                        stack->data[i] = pmReadoutAlloc(cellIn); // Input readout
+                    }
+
+                    // Only reading and writing the first readout in each cell (plane 0)
+                    if (pmReadoutReadNext(stack->data[i], fits, 0, options->rows)) {
+                        // For anything except BIAS and DARK, we want a mask
+                        if (options->scale || options->zero || options->shutter) {
+                            pmReadoutSetMask(stack->data[i]);
+                        }
+                        if (options->shutter) {
+                            pmReadoutSetWeight(stack->data[i]);
+                        }
+
+                        numRead++;
+                    } else {
+                        psTrace("ppMerge", 3, "Unable to read from file %d for chip %d, "
+                                "cell %d, scan %d\n", i, view->chip, view->cell, numScan);
+                    }
+
                 }
-                if (numRead > 1) {
-                    readout->image = pmShutterCorrectionMeasure(exptimes, images, weights, masks,
-                                                                options->shutterSize, options->mean,
-                                                                options->stdev, options->shutterIter,
-                                                                options->shutterRej,
-                                                                options->combine->maskVal);
-                    psTrace("ppMerge", 5, "Chip %d, cell %d\n", view->chip, view->cell);
-                } else {
-                    psError(PS_ERR_UNKNOWN, true, "Not enough images to combine: %d\n", numRead);
-                    psFree(images);
-                    psFree(exptimes);
-                    return false;
+
+                psTrace("ppMerge", 5, "Chip %d, cell %d, scan %d\n", view->chip, view->cell, numScan);
+                if (numRead > 0) {
+
+                    if (options->shutter) {
+                        readout->image = pmShutterCorrectionMeasure(stack, options->shutterSize,
+                                                                    options->mean, options->stdev,
+                                                                    options->shutterIter,
+                                                                    options->shutterRej,
+                                                                    options->combine->maskVal);
+                    } else {
+                        pmReadoutCombine(readout, stack, cellZeros, cellScales, options->combine);
+                    }
                 }
-                psFree(images);
-                psFree(masks);
-                psFree(weights);
-                psFree(exptimes);
-            } else {
-#if 1
-                // Read bit by bit
-
-                int numRead;  // Number of inputs read
-                int numScan = 0;
-                do {
-                    numRead = 0;
-                    for (int i = 0; i < filenames->n; i++) {
-                        if (! filenames->data[i] || strlen(filenames->data[i]) == 0) {
-                            continue;
-                        }
-                        psFits *fits = data->files->data[i]; // FITS file handle
-                        if (!fits) {
-                            continue;
-                        }
-
-                        if (!stack->data[i]) {
-                            pmFPA *fpaIn = data->in->data[i]; // Input FPA
-                            pmChip *chipIn = fpaIn->chips->data[view->chip]; // Input chip
-                            pmCell *cellIn = chipIn->cells->data[view->cell]; // Input cell
-                            stack->data[i] = pmReadoutAlloc(cellIn); // Input readout
-                        }
-
-                        // Only reading and writing the first readout in each cell (plane 0)
-                        if (pmReadoutReadNext(stack->data[i], fits, 0, options->rows)) {
-                            // For anything except BIAS and DARK, we want a mask
-                            if (options->scale || options->zero) {
-                                pmReadoutSetMask(stack->data[i]);
-                            }
-                            numRead++;
-                        } else {
-                            psTrace("ppMerge", 3, "Unable to read from file %d for chip %d, "
-                                    "cell %d, scan %d\n", i, view->chip, view->cell, numScan);
-                        }
-                    }
-
-                    psTrace("ppMerge", 5, "Chip %d, cell %d, scan %d\n", view->chip, view->cell, numScan);
-                    if (numRead > 0) {
-                        pmReadoutCombine(readout, stack, cellZeros, cellScales, options->combine);
-                    }
-                    numScan++;
-
-                } while (numRead > 0);
-
-#else
-            // Read whole cells at a time
-
-                printf("Chip %d, cell %d\n", view->chip, view->cell);
-                int numRead = 0;  // Number of inputs read
-                for (int i = 0; i < filenames->n; i++) {
-                    if (! filenames->data[i] || strlen(filenames->data[i]) == 0) {
-                        continue;
-                    }
-                    psFits *fits = data->files->data[i]; // FITS file handle
-                    if (!fits) {
-                        continue;
-                    }
-                    pmFPA *fpaIn = data->in->data[i]; // Input FPA
-                    pmChip *chipIn = fpaIn->chips->data[view->chip]; // Input chip
-                    pmCell *cellIn = chipIn->cells->data[view->cell]; // Input cell
-                    if (!cellIn->file_exists || !cellIn->data_exists) {
-                        continue;
-                    }
-                    if (!pmCellRead(cellIn, fits, config->database) || cellIn->readouts->n == 0) {
-                        continue;
-                    }
-                    stack->data[i] = cellIn->readouts->data[0];
-                    numRead++;
-                }
-                if (numRead > 0) {
-                    pmReadoutCombine(readout, stack, cellZeros, cellScales, options->combine);
-                    psTrace("ppMerge", 5, "Chip %d, cell %d\n", view->chip, view->cell);
-                }
-
-                memCheck();
-#endif
-            }
+                numScan++;
+
+            } while (numRead > 0);
 
             psFree(stack);
@@ -392 +286 @@
 
     psFree(view);
+    psFree(rng);
 
     return true;

trunk/ppMerge/src/ppMergeOptions.c

@@ -37 +37 @@
     options->fringe = false;
     options->shutter = false;
+    options->mask = false;
     options->sample = 1;
     options->mean = PS_STAT_SAMPLE_MEDIAN;
@@ -47 +48 @@
     options->shutterIter = 2;
     options->shutterRej = 3.0;
+    options->maskSuspect = 5.0;
+    options->maskBad = 10.0;
     options->onOff = 0;
     options->combine = pmCombineParamsAlloc(PS_STAT_SAMPLE_MEAN);
@@ -143 +146 @@
     OPTION_PARSE(options->shutterIter,       recipe, "SHUTTER.ITER",   S32);
     OPTION_PARSE(options->shutterRej,        recipe, "SHUTTER.REJECT", F32);
+    OPTION_PARSE(options->maskSuspect,       recipe, "MASK.SUSPECT",   F32);
+    OPTION_PARSE(options->maskBad,           recipe, "MASK.BAD",       F32);
 
     options->combine->combine = parseStat(recipe, "COMBINE");
@@ -159 +164 @@
             options->fringe = false;
             options->shutter = false;
+            options->mask = false;
         } else if (strcasecmp(type, "DARK") == 0) {
             options->zero = false;
@@ -165 +171 @@
             options->fringe = false;
             options->shutter = false;
+            options->mask = false;
         } else if (strcasecmp(type, "FLAT") == 0) {
             options->zero = false;
@@ -171 +178 @@
             options->fringe = false;
             options->shutter = false;
+            options->mask = false;
         } else if (strcasecmp(type, "FRINGE") == 0) {
             options->zero = true;
@@ -177 +185 @@
             options->fringe = true;
             options->shutter = false;
+            options->mask = false;
         } else if (strcasecmp(type, "SHUTTER") == 0) {
             options->zero = false;
@@ -183 +192 @@
             options->fringe = false;
             options->shutter = true;
+            options->mask = false;
+            options->rows = 0;          // Read the whole image at once
+        } else if (strcasecmp(type, "MASK") == 0) {
+            options->zero = false;
+            options->scale = false;
+            options->darktime = false;
+            options->fringe = false;
+            options->shutter = false;
+            options->mask = true;
         } else {
             psLogMsg(__func__, PS_LOG_WARN, "Unrecognised image type: %s --- assuming BIAS.\n", type);
@@ -190 +208 @@
             options->fringe = false;
             options->shutter = false;
+            options->mask = false;
         }
     } else {
@@ -198 +217 @@
         options->fringe = false;
         options->shutter = false;
+        options->mask = false;
     }
 

trunk/ppMerge/src/ppMergeOptions.h

@@ -24 +24 @@
     bool fringe;                        // Make fringe measurements?
     bool shutter;                       // Generate shutter correction?
+    bool mask;                          // Generate bad pixel mask?
     unsigned int sample;                // Sampling factor for measuring the background
     psStatsOptions mean;                // Statistic to use to measure the mean
@@ -34 +35 @@
     int shutterIter;                    // Number of iterations for shutter measurement
     float shutterRej;                   // Rejection limit for shutter measurement
+    float maskSuspect;                  // Threshold for identifying suspect pixels
+    float maskBad;                      // Threshold for identifying bad pixels
     ppOnOff onOff;                      // On/off pairs?
     pmCombineParams *combine;           // Combination parameters