Changeset 27840 for branches/simtest_nebulous_branches/magic/remove/src/streaksio.c

Timestamp:

May 3, 2010, 8:50:52 AM (16 years ago)

Author:

eugene

Message:

updates from trunk

Location:

branches/simtest_nebulous_branches

Files:

• . (modified) (1 prop)
• magic (modified) (1 prop)
• magic/remove (modified) (1 prop)
• magic/remove/src (modified) (1 prop)
• magic/remove/src/streaksio.c (modified) (23 diffs)

branches/simtest_nebulous_branches/magic

@@ -1 +1 @@
 magic
 ssa-core-cpp
-Makefile
 Makefile.bak

@@ -1 +1 @@
 magic
 ssa-core-cpp
-Makefile
 Makefile.bak

branches/simtest_nebulous_branches/magic/remove/src

@@ -4 +4 @@
 streakscompare
 streaksrelease
-makefile
+Makefile
+Makefile.in
+config.h
+.deps
+streaksVersionDefinitions.h
+config.h.in
+stamp-h1

@@ -4 +4 @@
 streakscompare
 streaksrelease
-makefile
+Makefile
+Makefile.in
+config.h
+.deps
+streaksVersionDefinitions.h
+config.h.in
+stamp-h1

branches/simtest_nebulous_branches/magic/remove/src/streaksio.c

@@ -12 +12 @@
 // Assumptions about the file structure of non-raw files
 // The 'image' for each file (image, mask weight) is contained in the first
-// extension. 
+// extension.
 
 
@@ -121 +121 @@
     sf->transparentStreaks = psMetadataLookupF64(&status, config->arguments, "TRANSPARENT_STREAKS");
 
+    sf->stats = psMetadataAlloc();
+    psString statsFileName= psMetadataLookupStr(&status, config->arguments, "STATS");
+    if (statsFileName) {
+        sf->statsFile = fopen(statsFileName, "w");
+        if (!sf->statsFile) {
+            psError(PS_ERR_IO, true, "failed to open stats file %s", statsFileName);
+            streaksExit("", PS_EXIT_CONFIG_ERROR);
+        }
+    }
+
     return sf;
 }
@@ -128 +138 @@
 {
     freeImages(sf);
-    psFree(sf->warpedPixels);
+    psFree(sf->diffedPixels);
     psFree(sf->tiles);
     psFree(sf->view);
@@ -288 +298 @@
         sfile->resolved_name = psStringCopy(sfile->pmfile->filename);
 
+        sfile->nHDU = psFitsGetSize(sfile->pmfile->fits);
+
         // copy header from fpu
         sfile->header = (psMetadata*) psMemIncrRefCounter(sfile->pmfile->fpa->hdu->header);
-
-        sfile->nHDU = psFitsGetSize(sfile->pmfile->fits);
 
         return sfile;
@@ -625 +635 @@
         streaksExit("", PS_EXIT_DATA_ERROR);
     }
- 
+
     bool status;
     in->extname = psMetadataLookupStr(&status, in->header, "EXTNAME");
@@ -654 +664 @@
             streaksExit("", PS_EXIT_DATA_ERROR);
         }
-        psImage *image = (psImage *) (in->imagecube->data[0]);
+
+        // Ensure input is of the expected type
+        psDataType expected = isMask ? PS_TYPE_IMAGE_MASK : PS_TYPE_F32; // Expected type for image
+        for (int i = 0; i < in->imagecube->n; i++) {
+            psImage *image = in->imagecube->data[i]; // Image of interest
+            if (image->type.type != expected) {
+                psImage *temp = psImageCopy(NULL, image, expected);
+                psFree(image);
+                in->imagecube->data[i] = temp;
+            }
+        }
     }
     setDataExtent(stage, in, (stage == IPP_STAGE_RAW) && !isMask);
@@ -671 +691 @@
     sfile->fits->options = psFitsOptionsAlloc();
     sfile->fits->options->scaling = PS_FITS_SCALE_MANUAL;
+    sfile->fits->options->fuzz = false;
     sfile->fits->options->bitpix = bitpix;
     sfile->fits->options->bscale = bscale;
@@ -789 +810 @@
         return;
     }
+    streaksVersionHeaderFull(sfile->header);
+
     if (!psFitsWriteImage(sfile->fits, sfile->header, sfile->image, 0, extname)) {
         psError(PS_ERR_IO, false, "failed to write image to %s extnum: %d",
@@ -806 +829 @@
         return;
     }
+    streaksVersionHeaderFull(sfile->header);
     if (!psFitsWriteImageCube(sfile->fits, sfile->header, imagecube, extname)) {
         psError(PS_ERR_IO, false, "failed to write image to %s extnum: %d",
@@ -840 +864 @@
     sfile->header = NULL;
     psFree(sfile->image);
-    sfile->header = NULL;
+    sfile->image = NULL;
     psFree(sfile->imagecube);
-    sfile->header = NULL;
+    sfile->imagecube = NULL;
 }
 
@@ -848 +872 @@
 closeImages(streakFiles *sf)
 {
+    if (sf->stage == IPP_STAGE_RAW) {
+        if (sf->view) {
+            sf->view->readout = -1;
+            pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_AFTER);
+            sf->view->cell = -1;
+            pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_AFTER);
+            sf->view->chip = -1;
+            pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_AFTER);
+        }
+    }
     closeImage(sf->inImage);
     closeImage(sf->outImage);
@@ -902 +936 @@
     bool free_user_copies = true;
     if (user_copies == NULL) {
-        user_copies = "2";
-        free_user_copies = false;
+        // input does not have replication requested
+        return true;
     }
     if (!nebSetXattr(server, outFile->name, "user.copies", user_copies,  NEB_REPLACE)) {
@@ -909 +943 @@
         return false;
     }
-    if (!nebReplicate(server, outFile->name, "any", NULL)) {
+    if (!nebReplicate(server, outFile->name, NULL, NULL)) {
         psError(PM_ERR_UNKNOWN, true, "nebReplicate failed for %s\n%s", outFile->name, nebErr(server));
         return false;
@@ -925 +959 @@
 replicateOutputs(streakFiles *sfiles)
 {
-    bool status = false;
-
     if (!replicate(sfiles->outImage, sfiles->inImage)) {
         psError(PM_ERR_SYS, false, "failed to replicate outImage.");
@@ -973 +1005 @@
 
         if (!nebSwap(server, in->name, out->name)) {
-            psError(PM_ERR_SYS, true, "failed to swap files for: %s.",
+            psError(PM_ERR_SYS, true, "failed to swap files for %s: %s.",
                 in->name, nebErr(server));
             return false;
@@ -1097 +1129 @@
 setMaskedToNAN(streakFiles *sfiles, psU32 maskMask, bool printCounts)
 {
-        int maskedPixels = 0;
-        int nandPixels = 0;
-        int nandWeights = 0;
+        long maskedPixels = 0;
+        long nandPixels = 0;
+        long nandWeights = 0;
 
         psImage *image = sfiles->outImage->image;
+        int imageType = image->type.type;
+        double exciseValue = sfiles->inImage->exciseValue;
+
         psImage *mask = sfiles->inMask->image;
         psImage *weight = NULL;
+        int weightType = 0;
+        double weightExciseValue = NAN;
         if (sfiles->outWeight) {
             weight = sfiles->outWeight->image;
-        }
-        double exciseValue = sfiles->inImage->exciseValue;
+            weightType = weight->type.type;
+            weightExciseValue = sfiles->inWeight->exciseValue;
+        }
 
         if (printCounts) {
@@ -1117 +1155 @@
                 // these gets are not necessary, we could just set the pixels to nan
                 // but I want to get the counts
-                double imageVal  = psImageGet(image, x, y);
-                psU32 maskVal;
+                double imageVal = 0; // avoid compiler warning
+                if (imageType == PS_TYPE_F32) {
+                    imageVal  = image->data.F32[y][x];
+                } else if (imageType == PS_TYPE_S16) {
+                    imageVal = image->data.S16[y][x];
+                } else if (imageType == PS_TYPE_U16) {
+                    imageVal = image->data.U16[y][x];
+                } else {
+                    psError(PS_ERR_PROGRAMMING, true, "unexpected image type found: %d\n",
+                                imageType);
+                    streaksExit("", PS_EXIT_PROG_ERROR);
+                }
+                psU32 maskVal = 0;
                 if (sfiles->stage == IPP_STAGE_RAW) {
-                    int xChip, yChip;
+                    unsigned int xChip, yChip;
                     cellToChipInt(&xChip, &yChip, sfiles->astrom, x, y);
-                    maskVal = psImageGet(mask, xChip, yChip);
+                    maskVal = mask->data.PS_TYPE_IMAGE_MASK_DATA[yChip][xChip];
                 } else {
-                    maskVal = psImageGet(mask, x, y);
+                    maskVal = mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x];
                 }
                 if (maskVal & maskMask) {
                     ++maskedPixels;
-                    if (!isExciseValue(imageVal, sfiles->inImage->exciseValue)) {
+                    if (!isExciseValue(imageVal, exciseValue)) {
                         ++nandPixels;
-                        psImageSet(image, x, y, exciseValue);
+                        if (imageType == PS_TYPE_F32) {
+                            image->data.F32[y][x] = exciseValue;
+                        } else if (imageType == PS_TYPE_S16) {
+                            image->data.S16[y][x] = exciseValue;
+                        } else if (imageType == PS_TYPE_U16) {
+                            image->data.U16[y][x] = exciseValue;
+                        } else {
+                            psError(PS_ERR_PROGRAMMING, true, "unexpected image type found: %d\n",
+                                imageType);
+                            streaksExit("", PS_EXIT_PROG_ERROR);
+                        }
                     }
                     if (weight) {
-                        double weightVal = weight ? psImageGet(weight, x, y) : 0;
-                        if (!isnan(weightVal)) {
-                            ++nandWeights;
-                            psImageSet(weight, x, y, NAN);
+                        if (weightType == PS_TYPE_F32) {
+                            double weightVal = weight->data.F32[y][x];
+                            if (!isnan(weightVal)) {
+                                ++nandWeights;
+                                weight->data.F32[y][x] = NAN;
+                            }
+                        } else if(weightType == PS_TYPE_S16) {
+                            double weightVal = weight->data.S16[y][x];
+                            if (!isExciseValue(weightVal, weightExciseValue)) {
+                                ++nandWeights;
+                                image->data.S16[y][x] = weightExciseValue;
+                            }
+                        } else if (weightType == PS_TYPE_U16) {
+                            double weightVal = weight->data.U16[y][x];
+                            if (!isExciseValue(weightVal, weightExciseValue)) {
+                                ++nandWeights;
+                                image->data.U16[y][x] = weightExciseValue;
+                            }
+                        } else {
+                            psError(PS_ERR_PROGRAMMING, true, "unexpected image type found: %d\n",
+                                    weightType);
+                                streaksExit("", PS_EXIT_PROG_ERROR);
                         }
                     }
@@ -1144 +1221 @@
         if (printCounts) {
             psLogMsg(sfiles->program_name, PS_LOG_INFO, "time to NAN mask pixels: %f\n", psTimerClear("NAN_MASKED"));
-            int totalPixels = image->numRows * image->numCols;
+            long totalPixels = image->numRows * image->numCols;
             psLogMsg(sfiles->program_name, PS_LOG_INFO, "pixels:        %10ld\n", totalPixels);
             psLogMsg(sfiles->program_name, PS_LOG_INFO, "masked pixels: %10ld %4.2f%%\n", maskedPixels, 100. * maskedPixels / totalPixels);
@@ -1167 +1244 @@
         psMetadataAddU16(in->header, PS_LIST_TAIL, "BLANK", 0, "", 65535);
         psMetadataAddU16(in->header, PS_LIST_TAIL, "ZBLANK", 0, "", 65535);
-    } else {
+    } else if (in->image->type.type == PS_TYPE_S16) {
+        in->exciseValue = 32767;
+        psMetadataAddU16(in->header, PS_LIST_TAIL, "BLANK", 0, "", 32767);
+        psMetadataAddU16(in->header, PS_LIST_TAIL, "ZBLANK", 0, "", 32767);
+    } else if (in->image->type.type == PS_TYPE_F32) {
         in->exciseValue = NAN;
-    }
-}
-
-void
-strkGetMaskValues(streakFiles *sfiles, psU32 *maskStreak, psU32 *maskMask)
-{
+    } else {
+        psError(PS_ERR_PROGRAMMING, true, "unexpected image type found: %d\n", in->image->type.type);
+        streaksExit("", PS_EXIT_PROG_ERROR);
+    }
+}
+
+// Get the mask values that we need.
+// If an input mask file is provided get them from there.
+// Otherwise get them from the recipe MASKS
+void
+strkGetMaskValues(streakFiles *sfiles)
+{
+    if (sfiles->maskStreak) {
+        // already done
+        return;
+    }
     if (sfiles->inMask && sfiles->inMask->header) {
         if (!pmConfigMaskReadHeader(sfiles->config, sfiles->inMask->header)) {
@@ -1187 +1278 @@
         streaksExit("", PS_EXIT_CONFIG_ERROR);
     }
-    *maskStreak = psMetadataLookupU32(&status, masks, "STREAK");
+    sfiles->maskStreak = psMetadataLookupU32(&status, masks, "STREAK");
     if (!status) {
         psError(PM_ERR_CONFIG, false, "failed to lookup mask value for STREAK in recipes\n");
@@ -1203 +1294 @@
         }
     }
-    *maskMask = ~convPoor;
+    sfiles->maskMask = ~convPoor;
 }
 
@@ -1215 +1306 @@
         if (SFILE_IS_IMAGE(in)) {
             // Turn off compression (code adapted from pmFPAWrite)
-#ifdef SAVE_AND_RESTORE_COMPRESSION
             int bitpix = out->fits->options ? out->fits->options->bitpix : 0; // Desired bits per pixel
             psFitsCompression *compress = psFitsCompressionGet(out->fits); // Current compression options
-#endif
             if (!psFitsSetCompression(out->fits, PS_FITS_COMPRESS_NONE, NULL, 0, 0, 0)) {
                 psError(PM_ERR_UNKNOWN, false, "failed to turn off compression for extension %d\n", extnum);
                 streaksExit("", PS_EXIT_UNKNOWN_ERROR);
             }
-#ifdef SAVE_AND_RESTORE_COMPRESSION
             if (out->fits->options) {
                 out->fits->options->bitpix = 0;
@@ -1238 +1326 @@
                 streaksExit("", PS_EXIT_UNKNOWN_ERROR);
             }
-#endif
         } else {
             copyTable(out, in, extnum);

@@ -1 +1 @@
 magic
 ssa-core-cpp
-Makefile
 Makefile.bak

@@ -4 +4 @@
 streakscompare
 streaksrelease
-makefile
+Makefile
+Makefile.in
+config.h
+.deps
+streaksVersionDefinitions.h
+config.h.in
+stamp-h1