Changeset 5462

Timestamp:

Nov 2, 2005, 3:30:32 PM (21 years ago)

Author:

Paul Price

Message:

Working with release 8. Overscan, bias, flat-fielding all working.

Location:

trunk/archive/scripts/src/phase2

Files:

• papPhase2.c (modified) (14 diffs)
• phase2.config (modified) (2 diffs)
• pmConfig.c (modified) (3 diffs)
• pmFPA.c (modified) (1 diff)
• pmFPA.h (modified) (1 diff)
• pmFPAConceptsGet.c (modified) (21 diffs)
• pmFPAConceptsSet.c (modified) (7 diffs)
• pmFPAConstruct.c (modified) (6 diffs)
• pmFlatField.c (modified) (3 diffs)
• pmFlatField.h (modified) (2 diffs)
• pmFlatFieldErrors.h (modified) (1 diff)
• pmSubtractBias.c (modified) (10 diffs)
• pmSubtractBias.h (modified) (2 diffs)
• psAdditionals.c (modified) (11 diffs)

trunk/archive/scripts/src/phase2/papPhase2.c

@@ -250 +250 @@
             overscanFitType = PM_FIT_SPLINE;
             int order = psMetadataLookupS32(NULL, recipe, "OVERSCAN.ORDER"); // Order of polynomial fit
-//          overscanFit = psSpline1DAlloc(order, PS_POLYNOMIAL_ORD);
+            overscanFit = NULL;
+//          overscanFit = psSpline1DAlloc();
         } else if (strcasecmp(fit, "NONE") != 0) {
             psLogMsg("phase2", PS_LOG_WARN, "OVERSCAN.FIT (%s) is not one of NONE, POLYNOMIAL, or SPLINE:"
@@ -292 +293 @@
 
     // Read in the input pixels
+    psLogMsg("phase2", PS_LOG_INFO, "Opening input image: %s\n", inputName);
     if (! pmFPARead(input, inputFile, header, database)) {
         psErrorStackPrint(stderr, "Unable to populate camera from FITS file: %s\n", inputName);
@@ -316 +318 @@
             exit(EXIT_FAILURE);
         }
+        psLogMsg("phase2", PS_LOG_INFO, "Opening bias image: %s\n", biasName);
+        if (! pmFPARead(bias, biasFile, biasHeader, database)) {
+            psErrorStackPrint(stderr, "Unable to populate bias camera from fits FITS: %s\n", biasName);
+            exit(EXIT_FAILURE);
+        }
         psFree(biasHeader);
-        if (! pmFPARead(bias, biasFile, NULL, database)) {
-            psErrorStackPrint(stderr, "Unable to populate bias camera from fits FITS: %s\n", biasName);
-            exit(EXIT_FAILURE);
-        }
 #ifdef PRODUCTION
         psFitsClose(biasFile);
@@ -339 +342 @@
             exit(EXIT_FAILURE);
         }
+        psLogMsg("phase2", PS_LOG_INFO, "Opening dark image: %s\n", darkName);
+        if (! pmFPARead(dark, darkFile, darkHeader, database)) {
+            psErrorStackPrint(stderr, "Unable to populate dark camera from fits FITS: %s\n", darkName);
+            exit(EXIT_FAILURE);
+        }
         psFree(darkHeader);
-        if (! pmFPARead(dark, darkFile, NULL, database)) {
-            psErrorStackPrint(stderr, "Unable to populate dark camera from fits FITS: %s\n", darkName);
-            exit(EXIT_FAILURE);
-        }
 #ifdef PRODUCTION
         psFitsClose(darkFile);
@@ -362 +366 @@
             exit(EXIT_FAILURE);
         }
+        psLogMsg("phase2", PS_LOG_INFO, "Opening mask image: %s\n", maskName);
+        if (! pmFPARead(mask, maskFile, maskHeader, database)) {
+            psErrorStackPrint(stderr, "Unable to populate mask camera from fits FITS: %s\n", maskName);
+            exit(EXIT_FAILURE);
+        }
         psFree(maskHeader);
-        if (! pmFPARead(mask, maskFile, NULL, database)) {
-            psErrorStackPrint(stderr, "Unable to populate mask camera from fits FITS: %s\n", maskName);
-            exit(EXIT_FAILURE);
-        }
+
 #ifdef PRODUCTION
         psFitsClose(maskFile);
@@ -380 +386 @@
         psFits *flatFile = psFitsAlloc(flatName);
 #endif
+        if (! flatFile) {
+            psErrorStackPrint(stderr, "Can't open flat image: %s\n", flatName);
+            exit(EXIT_FAILURE);
+        }
         psMetadata *flatHeader = psFitsReadHeader(NULL, flatFile); // FITS header for flat
         if (! pmConfigValidateCamera(camera, flatHeader)) {
@@ -385 +395 @@
             exit(EXIT_FAILURE);
         }
+        psLogMsg("phase2", PS_LOG_INFO, "Opening flat image: %s\n", flatName);
+        if (! pmFPARead(flat, flatFile, flatHeader, database)) {
+            psErrorStackPrint(stderr, "Unable to populate flat camera from fits FITS: %s\n", flatName);
+            exit(EXIT_FAILURE);
+        }
         psFree(flatHeader);
-        if (! pmFPARead(flat, flatFile, NULL, database)) {
-            psErrorStackPrint(stderr, "Unable to populate flat camera from fits FITS: %s\n", flatName);
-            exit(EXIT_FAILURE);
-        }
 #ifdef PRODUCTION
         psFitsClose(flatFile);
@@ -499 +510 @@
                     } else {
                         switch (dataItem->type) {
-                          case PS_META_VEC:
+                          case PS_DATA_VECTOR:
                             {
                                 // These are the polynomial coefficients
@@ -518 +529 @@
                             }
                             break;
-                          case PS_META_STR:
+                          case PS_DATA_STRING:
                             {
                                 // This is a filename
@@ -536 +547 @@
                             }
                             break;
-                          case PS_META_META:
+                          case PS_DATA_METADATA:
                             {
                                 // This is a menu
@@ -550 +561 @@
                                         psLogMsg("phase2", PS_LOG_WARN, "Unable to find value of concept %s "
                                                  "for non-linearity correction --- ignored.\n", concept);
-                                    } else if (conceptValueItem->type != PS_META_STR) {
+                                    } else if (conceptValueItem->type != PS_DATA_STRING) {
                                         psLogMsg("phase2", PS_LOG_WARN, "Type for concept %s isn't STRING, as"
                                                  " expected for non-linearity correction --- ignored.\n",
@@ -561 +572 @@
                                             psLogMsg("phase2", PS_LOG_WARN, "Unable to find %s in NONLIN.DATA"
                                                      " --- ignored.\n", conceptValue);
-                                        } else if (optionItem->type == PS_META_VEC) {
+                                        } else if (optionItem->type == PS_DATA_VECTOR) {
                                             // These are the polynomial coefficients
                                             psVector *coeff = optionItem->data.V; // The coefficient vector
@@ -578 +589 @@
                                             psFree(coeff);
                                             psFree(correction);
-                                        } else if (optionItem->type == PS_META_STR) {
+                                        } else if (optionItem->type == PS_DATA_STRING) {
                                             // This is a filename
                                             psString tableName = optionItem->data.V; // The filename
@@ -673 +684 @@
                     // Output overscan fit results, if required
                     if (doOverscan) {
-                        switch (overscanFitType) {
-                          case PM_FIT_POLYNOMIAL:
-                            {
-                                psPolynomial1D *poly = (psPolynomial1D*)overscanFit;    // The polynomial
-                                psString coeffs = NULL; // String containing the coefficients
-                                for (int i = 0; i < poly->n; i++) {
-                                    psStringAppend(&coeffs, "%e ", poly->coeff[i]);
-                                }
-                                psLogMsg("phase2", PS_LOG_INFO, "Overscan polynomial coefficients:\n%s\n",
-                                         coeffs);
-                                psFree(coeffs);
-                            }
-                            break;
-                          case PM_FIT_SPLINE:
-                            {
-                                psSpline1D *spline = (psSpline1D*)overscanFit; // The spline
-                                psString coeffs = NULL; // String containing the coefficients
-                                for (int i = 0; i < spline->n; i++) {
-                                    psPolynomial1D *poly = spline->spline[i]; // i-th polynomial
-                                    psStringAppend(&coeffs, "%d: ", i);
-                                    for (int j = 0; j < poly->n; j++) {
+                        if (! overscanFit) {
+                            psLogMsg("phase2", PS_LOG_WARN, "No fit generated!\n");
+                        } else {
+                            switch (overscanFitType) {
+                              case PM_FIT_POLYNOMIAL:
+                                {
+                                    psPolynomial1D *poly = (psPolynomial1D*)overscanFit; // The polynomial
+                                    psString coeffs = NULL;     // String containing the coefficients
+                                    for (int i = 0; i < poly->nX; i++) {
                                         psStringAppend(&coeffs, "%e ", poly->coeff[i]);
                                     }
-                                    psStringAppend(&coeffs, "\n");
+                                    psLogMsg("phase2", PS_LOG_INFO, "Overscan polynomial coefficients:\n%s\n",
+                                             coeffs);
+                                    psFree(coeffs);
                                 }
-                                psLogMsg("phase2", PS_LOG_INFO, "Overscan spline coefficients:\n%s\n",
-                                         coeffs);
-                                psFree(coeffs);
+                                break;
+                              case PM_FIT_SPLINE:
+                                {
+                                    psSpline1D *spline = (psSpline1D*)overscanFit; // The spline
+                                    psString coeffs = NULL;     // String containing the coefficients
+                                    for (int i = 0; i < spline->n; i++) {
+                                        psPolynomial1D *poly = spline->spline[i]; // i-th polynomial
+                                        psStringAppend(&coeffs, "%d: ", i);
+                                        for (int j = 0; j < poly->nX; j++) {
+                                            psStringAppend(&coeffs, "%e ", poly->coeff[i]);
+                                        }
+                                        psStringAppend(&coeffs, "\n");
+                                    }
+                                    psLogMsg("phase2", PS_LOG_INFO, "Overscan spline coefficients:\n%s\n",
+                                             coeffs);
+                                    psFree(coeffs);
+                                }
+                                break;
+                              case PM_FIT_NONE:
+                                break;
+                              default:
+                                psAbort(__func__, "Should never get here!!!\n");
                             }
-                            break;
-                          case PM_FIT_NONE:
-                            break;
-                          default:
-                            psAbort(__func__, "Should never get here!!!\n");
                         }
                     }
                 }
 
+                // Trim, so that flat, fringe etc computations are faster.
+                psRegion *trimRegion = psMetadataLookupPtr(NULL, inputCell->concepts, "CELL.TRIMSEC");
+                psImage *trimmed = psImageSubset(inputReadout->image, *trimRegion);
+                psFree(inputReadout->image);
+                inputReadout->image = trimmed;
+
                 // Flat-field correction
                 if (doFlat) {
-                    (void)pmFlatField(inputReadout, flatReadout);
+                    psLogMsg("phase2", PS_LOG_INFO, "Performing flat field.\n");
+#ifndef PRODUCTION
+                    psImage *dummyImage = psImageAlloc(inputReadout->image->numCols,
+                                                       inputReadout->image->numRows,
+                                                       PS_TYPE_U8);
+                    pmReadout *dummyMask = pmReadoutAlloc(NULL, dummyImage, NULL, 0, 0, 1, 1, 1, 1);
+                    (void)pmFlatField(inputReadout, dummyMask, flatReadout);
+                    psFree(dummyMask);
+                    psFree(dummyImage);
+#endif
                 }
 

trunk/archive/scripts/src/phase2/phase2.config

@@ -3 +3 @@
 # List of tasks to perform
 MASK            BOOL    FALSE           # Mask bad pixels
-NONLIN          BOOL    FALSE           # Non-linearity correction
+NONLIN          BOOL    TRUE            # Non-linearity correction
 BIAS            BOOL    FALSE           # Bias subtraction
 DARK            BOOL    FALSE           # Dark subtraction
-OVERSCAN        BOOL    TRUE            # Overscan subtraction
+OVERSCAN        BOOL    FALSE           # Overscan subtraction
 FLAT            BOOL    FALSE           # Flat-field normalisation
 FRINGE          BOOL    FALSE           # Fringe subtraction
@@ -58 +58 @@
 # Overscan subtraction
 OVERSCAN.MODE           STR     INDIVIDUAL      # NONE | INDIVIDUAL | ALL
-OVERSCAN.FIT            STR     SPLINE          # NONE | POLYNOMIAL | SPLINE
-OVERSCAN.ORDER          S32     10              # Order of polynomial fit
+#OVERSCAN.FIT           STR     SPLINE          # NONE | POLYNOMIAL | SPLINE
+OVERSCAN.FIT            STR     POLYNOMIAL      # NONE | POLYNOMIAL | SPLINE
+OVERSCAN.ORDER          S32     5               # Order of polynomial fit
 OVERSCAN.BIN            S32     0               # Number of pixels per bin
 OVERSCAN.STAT           STR     MEAN            # MEAN | MEDIAN

trunk/archive/scripts/src/phase2/pmConfig.c

@@ -141 +141 @@
         psMetadataItem *traceItem = NULL; // Item from MD iteration
         while (traceItem = psMetadataGetAndIncrement(traceIter)) {
-            if (traceItem->type != PS_META_S32) {
+            if (traceItem->type != PS_DATA_S32) {
                 psLogMsg(__func__, PS_LOG_WARN, "The level for trace component %s is not of type S32 (%x)\n",
                          traceItem->name, traceItem->type);
@@ -181 +181 @@
         // Check to see if the rule works
         switch (ruleItem->type) {
-          case PS_META_STR:
+          case PS_DATA_STRING:
             psTrace(__func__, 8, "Matching %s: '%s' vs '%s'\n", ruleItem->name,
                     ruleItem->data.V, headerItem->data.V);
@@ -247 +247 @@
                 cameraItem->comment);
         psMetadata *camera = NULL;      // The camera metadata
-        if (cameraItem->type == PS_META_META) {
+        if (cameraItem->type == PS_DATA_METADATA) {
             camera = psMemIncrRefCounter(cameraItem->data.md);
-        } else if (cameraItem->type == PS_META_STR) {
+        } else if (cameraItem->type == PS_DATA_STRING) {
             psTrace(__func__, 5, "Reading camera configuration for %s...\n", cameraItem->name);
             int badLines = 0;           // Number of bad lines in reading camera configuration

trunk/archive/scripts/src/phase2/pmFPA.c

@@ -202 +202 @@
     pmReadout *readout = psAlloc(sizeof(pmReadout));
     psMemSetDeallocator(readout, (psFreeFunc)p_pmReadoutFree);
-    cell->readouts = psArrayAdd(cell->readouts, 0, readout);
+    if (cell) {
+        cell->readouts = psArrayAdd(cell->readouts, 0, readout);
+    }
     
     // Set the components

trunk/archive/scripts/src/phase2/pmFPA.h

@@ -6 +6 @@
 
 // Temporary metadata types
-#define PS_META_CHIP PS_META_UNKNOWN
-#define PS_META_CELL PS_META_UNKNOWN
+//#define PS_META_CHIP PS_DATA_UNKNOWN
+//#define PS_META_CELL PS_DATA_UNKNOWN
 
 typedef struct {

trunk/archive/scripts/src/phase2/pmFPAConceptsGet.c

@@ -100 +100 @@
     psMetadataItem *defItem = psMetadataLookup(defaults, concept);
     if (defItem) {
-        if (defItem->type == PS_META_META) {
+        if (defItem->type == PS_DATA_METADATA) {
             // A dependent default
             psTrace(__func__, 7, "Evaluating dependent default....\n");
@@ -122 +122 @@
                 return NULL;
             }
-            if (depItem->type != PS_META_STR) {
+            if (depItem->type != PS_DATA_STRING) {
                 psError(PS_ERR_IO, true, "Value of %s is not of type string, as required for dependency"
                         " --- ignored.\n", dependsOn);
@@ -270 +270 @@
     if (item) {
         switch (item->type) {
-          case PS_META_F32:
+          case PS_DATA_F32:
             value = item->data.F32;
             break;
-          case PS_META_F64:
+          case PS_DATA_F64:
             // Assume it's OK to truncate to floating point from double
             value = (float)item->data.F64;
             break;
-          case PS_META_S32:
+          case PS_DATA_S32:
             // Promote to float
             value = (float)item->data.S32;
@@ -370 +370 @@
     if (item) {
         switch (item->type) {
-          case PS_META_STR:
+          case PS_DATA_STRING:
             value = item->data.V;
             break;
@@ -383 +383 @@
     psTrace(__func__, 7, "Adding %s (%s): %s\n", name, comment, value);
 
-    psMetadataAdd(concepts, PS_LIST_TAIL, name, PS_META_STR, comment, value);
+    psMetadataAdd(concepts, PS_LIST_TAIL, name, PS_DATA_STRING, comment, value);
 }
 
@@ -428 +428 @@
                 ra = raItem->data.F64;
                 break;
-              case PS_META_STR:
+              case PS_DATA_STRING:
                 // Sexagesimal format
                 {
@@ -480 +480 @@
         }
 
-        psMetadataAdd(fpa->concepts, PS_LIST_TAIL, "FPA.RA", PS_META_F64, 
+        psMetadataAdd(fpa->concepts, PS_LIST_TAIL, "FPA.RA", PS_DATA_F64, 
                       "Right Ascension of the boresight (radians)", ra);
 
@@ -497 +497 @@
                 dec = decItem->data.F64;
                 break;
-              case PS_META_STR:
+              case PS_DATA_STRING:
                 // Sexagesimal format
                 {
@@ -549 +549 @@
         }
 
-        psMetadataAdd(fpa->concepts, PS_LIST_TAIL, "FPA.DEC", PS_META_F64, 
+        psMetadataAdd(fpa->concepts, PS_LIST_TAIL, "FPA.DEC", PS_DATA_F64, 
                       "Declination of the boresight (radians)", dec);
 
@@ -633 +633 @@
             psError(PS_ERR_IO, false, "Couldn't find CELL.TRIMSEC.\n");
             *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0);
-        } else if (secItem->type != PS_META_STR) {
+        } else if (secItem->type != PS_DATA_STRING) {
             psError(PS_ERR_IO, true, "CELL.TRIMSEC is not of type STR (%x)\n", secItem->type);
             *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0);
@@ -643 +643 @@
                 psError(PS_ERR_IO, false, "Couldn't find CELL.TRIMSEC.SOURCE.\n");
                 *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0);
-            } else if (sourceItem->type != PS_META_STR) {
+            } else if (sourceItem->type != PS_DATA_STRING) {
                 psError(PS_ERR_IO, true, "CELL.TRIMSEC.SOURCE is not of type STR (%x)\n", sourceItem->type);
                 *trimsec = psRegionSet(0.0, 0.0, 0.0, 0.0);
@@ -681 +681 @@
         } // Looking up CELL.TRIMSEC
 
-        psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.TRIMSEC", PS_META_UNKNOWN,
+        psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.TRIMSEC", PS_DATA_UNKNOWN,
                       "Trim section", trimsec);
         psFree(trimsec);
@@ -693 +693 @@
         if (! secItem) {
             psError(PS_ERR_IO, false, "Couldn't find CELL.BIASSEC.\n");
-        } else if (secItem->type != PS_META_STR) {
+        } else if (secItem->type != PS_DATA_STRING) {
             psError(PS_ERR_IO, true, "CELL.BIASSEC is not of type STR (%x)\n", secItem->type);
         } else {
@@ -701 +701 @@
             if (! sourceItem) {
                 psError(PS_ERR_IO, false, "Couldn't find CELL.BIASSEC.SOURCE.\n");
-            } else if (sourceItem->type != PS_META_STR) {
+            } else if (sourceItem->type != PS_DATA_STRING) {
                 psError(PS_ERR_IO, true, "CELL.BIASSEC.SOURCE is not of type STR (%x)\n", sourceItem->type);
             } else {
@@ -752 +752 @@
         } // Looking up CELL.BIASSEC
 
-        psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.BIASSEC", PS_META_LIST, "Bias sections", biassecs);
+        psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.BIASSEC", PS_DATA_LIST, "Bias sections", biassecs);
         psFree(biassecs);
     }
@@ -762 +762 @@
         if (! binItem) {
             psError(PS_ERR_IO, false, "Couldn't find CELL.XBIN.\n");
-        } else if (binItem->type == PS_META_STR) {
+        } else if (binItem->type == PS_DATA_STRING) {
             psString binString = binItem->data.V; // The string containing the binning
             if (sscanf(binString, "%d %*d", &xBin) != 1 &&
@@ -784 +784 @@
         if (! binItem) {
             psError(PS_ERR_IO, false, "Couldn't find CELL.YBIN.\n");
-        } else if (binItem->type == PS_META_STR) {
+        } else if (binItem->type == PS_DATA_STRING) {
             psString binString = binItem->data.V; // The string containing the binning
             if (sscanf(binString, "%*d %d", &yBin) != 1 &&
@@ -809 +809 @@
         if (! sysItem) {
             psError(PS_ERR_IO, true, "Couldn't find CELL.TIMESYS --- assuming UTC.\n");
-        } else if (sysItem->type != PS_META_STR) {
+        } else if (sysItem->type != PS_DATA_STRING) {
             psError(PS_ERR_IO, true, "CELL.TIMESYS isn't of type STRING --- assuming UTC.\n");
         } else {
@@ -839 +839 @@
                 if (mdok && strlen(timeFormat) > 0) {
                     switch (timeItem->type) {
-                      case PS_META_STR:
+                      case PS_DATA_STRING:
                         {
                             psString timeString = timeItem->data.V;     // String with the time
@@ -887 +887 @@
                                             psError(PS_ERR_IO, false, "Unable to find time header: %s\n",
                                                     timeName);
-                                        } else if (timeItem->type == PS_META_STR) {
+                                        } else if (timeItem->type == PS_DATA_STRING) {
                                             // Time is a string, in the usual way:
                                             psStringAppend(&dateString, "T%s", timeItem->data.V);
@@ -965 +965 @@
         } // Getting CELL.TIME
 
-        psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.TIME", PS_META_UNKNOWN, "Time of exposure", time);
+        psMetadataAdd(cell->concepts, PS_LIST_TAIL, "CELL.TIME", PS_DATA_UNKNOWN, "Time of exposure", time);
         psFree(time);
     }

trunk/archive/scripts/src/phase2/pmFPAConceptsSet.c

@@ -68 +68 @@
         }
         return (item1->data.F64 == item2->data.F64) ? true : false;
-      case PS_META_STR:
-        if (item2->type != PS_META_STR) {
+      case PS_DATA_STRING:
+        if (item2->type != PS_DATA_STRING) {
             return false;
         }
@@ -112 +112 @@
         // XXX: Need to expand range of types
         switch (concept->type) {
-          case PS_META_STR:
+          case PS_DATA_STRING:
             headerItem = psMetadataItemAllocStr(keyword, concept->comment, concept->data.V);
             break;
-          case PS_META_S32:
+          case PS_DATA_S32:
             headerItem = psMetadataItemAllocS32(keyword, concept->comment, concept->data.S32);
             break;
-          case PS_META_F32:
+          case PS_DATA_F32:
             headerItem = psMetadataItemAllocF32(keyword, concept->comment, concept->data.F32);
             break;
-          case PS_META_F64:
+          case PS_DATA_F64:
             headerItem = psMetadataItemAllocF64(keyword, concept->comment, concept->data.F64);
             break;
@@ -183 +183 @@
     psMetadataItem *defItem = psMetadataLookup(defaults, concept->name);
     if (defItem) {
-        if (defItem->type == PS_META_META) {
+        if (defItem->type == PS_DATA_METADATA) {
             // A dependent default
             psTrace(__func__, 7, "Evaluating dependent default....\n");
@@ -205 +205 @@
                 return false;
             }
-            if (depItem->type != PS_META_STR) {
+            if (depItem->type != PS_DATA_STRING) {
                 psError(PS_ERR_IO, true, "Value of %s is not of type string, as required for dependency"
                         " --- ignored.\n", dependsOn);
@@ -555 +555 @@
         if (! sourceItem) {
             psError(PS_ERR_IO, false, "Couldn't find CELL.TRIMSEC.SOURCE.\n");
-        } else if (sourceItem->type != PS_META_STR) {
+        } else if (sourceItem->type != PS_DATA_STRING) {
             psError(PS_ERR_IO, true, "CELL.TRIMSEC.SOURCE is not of type STR (%x)\n", sourceItem->type);
         } else {
@@ -596 +596 @@
         if (! sourceItem) {
             psError(PS_ERR_IO, false, "Couldn't find CELL.BIASSEC.SOURCE.\n");
-        } else if (sourceItem->type != PS_META_STR) {
+        } else if (sourceItem->type != PS_DATA_STRING) {
             psError(PS_ERR_IO, true, "CELL.BIASSEC.SOURCE is not of type STR (%x)\n", sourceItem->type);
         } else {
@@ -668 +668 @@
                             psRegion *biassec = psListGetAndIncrement(biassecsIter);
                             psString biassecString = psRegionToString(*biassec);
-                            psMetadataAdd(header, PS_LIST_TAIL, keyword, PS_META_STR | PS_META_REPLACE,
+                            psMetadataAdd(header, PS_LIST_TAIL, keyword, PS_DATA_STRING | PS_META_REPLACE,
                                           "Bias section", biassecString);
                             psFree(biassecString);

trunk/archive/scripts/src/phase2/pmFPAConstruct.c

@@ -37 +37 @@
     psMetadataItem *item = NULL;        // Item from iteration
     while (item = psMetadataGetAndIncrement(iter)) {
-        if (item->type == PS_META_MULTI || item->type == PS_META_META) {
-            psLogMsg(__func__, PS_LOG_WARN, "PS_META_MULTI and PS_META_META are not supported in a cell "
-                     "definition --- %s ignored.\n", item->name);
+        if (item->type == PS_DATA_METADATA_MULTI || item->type == PS_DATA_METADATA) {
+            psLogMsg(__func__, PS_LOG_WARN, "PS_DATA_METADATA_MULTI and PS_DATA_METADATA are not supported "
+                     "in a cell definition --- %s ignored.\n", item->name);
             continue;
         }
@@ -89 +89 @@
                 pmChip *chip = pmChipAlloc(fpa, extName); // The chip
                 chip->data = pmPixelDataAlloc(extName); // Prepare chip to receive FITS data
-                if (contentItem->type != PS_META_STR) {
+                if (contentItem->type != PS_DATA_STRING) {
                     psLogMsg(__func__, PS_LOG_WARN, "Type of content item (%x) is not string: ignored\n",
                              contentItem->type);
@@ -117 +117 @@
                 psTrace(__func__, 1, "Getting %s....\n", extName);
 
-                if (contentItem->type != PS_META_STR) {
+                if (contentItem->type != PS_DATA_STRING) {
                     psLogMsg(__func__, PS_LOG_WARN, "Type of content item (%x) is not string: ignored\n",
                              contentItem->type);
@@ -136 +136 @@
                     if (! chipItem) {
                         chip = pmChipAlloc(fpa, chipName);
-                        psMetadataAdd(chips, PS_LIST_TAIL, chipName, PS_META_CHIP, "", chip);
+                        psMetadataAdd(chips, PS_LIST_TAIL, chipName, PS_DATA_UNKNOWN, "", chip);
                     } else {
                         chip = psMemIncrRefCounter(chipItem->data.V);
@@ -161 +161 @@
                 psString chipName = contentItem->name; // The name of the chip
 
-                if (contentItem->type != PS_META_STR) {
+                if (contentItem->type != PS_DATA_STRING) {
                     psLogMsg(__func__, PS_LOG_WARN, "Type of content item (%x) is not string: ignored\n",
                              contentItem->type);
@@ -234 +234 @@
                 psString extName = contentItem->name; // The name of the extension
                 // Content is a cell type
-                if (contentItem->type != PS_META_STR) {
+                if (contentItem->type != PS_DATA_STRING) {
                     psLogMsg(__func__, PS_LOG_WARN,
                              "CONTENT metadata for extension %s is not of type string, but %x --- ignored\n",

trunk/archive/scripts/src/phase2/pmFlatField.c

@@ -18 +18 @@
  *  @author Ross Harman, MHPCC
  *
- *  @version $Revision: 1.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2005-09-23 02:58:30 $
+ *  @version $Revision: 1.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2005-11-03 01:30:32 $
  *
  *  Copyright 2004 Maui High Performance Computing Center, University of Hawaii
  */
 
-#include <stdio.h>
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include<stdio.h>
+#include<math.h>
 #include <string.h>
+
 #include "pslib.h"
-
-#include "pmFPA.h"
 #include "pmFlatField.h"
 #include "pmMaskBadPixels.h"
@@ -34 +38 @@
 
 
-bool pmFlatField(pmReadout *in, const pmReadout *flat)
+bool pmFlatField(pmReadout *in, pmReadout *mask, const pmReadout *flat)
 {
+    // XXX: Not sure if this is correct.  Must consult with IfA.
+    PS_ASSERT_PTR_NON_NULL(mask, false);
     int i = 0;
     int j = 0;
@@ -67 +73 @@
                  PS_ERRORTEXT_pmFlatField_NULL_FLAT_IMAGE);
         return false;
-    } else if(in->mask == NULL) {
-        in->mask = psImageAlloc(inImage->numCols, inImage->numRows, PS_TYPE_MASK);
-        memset(in->mask->data.V[0], 0, inImage->numCols*inImage->numRows*PSELEMTYPE_SIZEOF(PS_TYPE_MASK));
     }
-    inMask = in->mask;
+    inMask = mask->image;
 
     // Check input image and its mask are not larger than flat image
-    if(inImage->numRows>flatImage->numRows || inImage->numCols>flatImage->numCols) {
+
+    if (inImage->numRows>flatImage->numRows || inImage->numCols>flatImage->numCols) {
         psError( PS_ERR_BAD_PARAMETER_SIZE, true,
                  PS_ERRORTEXT_pmFlatField_SIZE_INPUT_IMAGE,
                  inImage->numRows, inImage->numCols, flatImage->numRows, flatImage->numCols);
         return false;
-    } else if(inMask->numRows>flatImage->numRows || inMask->numCols > flatImage->numCols) {
+    }
+    if (inMask->numRows > flatImage->numRows || inMask->numCols > flatImage->numCols) {
         psError( PS_ERR_BAD_PARAMETER_SIZE, true,
                  PS_ERRORTEXT_pmFlatField_SIZE_MASK_IMAGE,

trunk/archive/scripts/src/phase2/pmFlatField.h

@@ -18 +18 @@
  *  @author Ross Harman, MHPCC
  *
- *  @version $Revision: 1.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2005-09-23 02:58:30 $
+ *  @version $Revision: 1.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2005-11-03 01:30:32 $
  *
  *  Copyright 2004 Maui High Performance Computing Center, University of Hawaii
  */
+
+#include "pslib.h"
+#include "pmFPA.h" // #include "pmAstrometry.h"
+
 
 /** Execute flat field module.
@@ -31 +35 @@
  *  @return  bool: True or false for success or failure
  */
-
-#include "pmFPA.h"
-
 bool pmFlatField(
-    pmReadout *in,          ///< Redout with input image and mask
+    pmReadout *in,          ///< Readout with input image
+    pmReadout *mask,        ///< Input image mask
     const pmReadout *flat   ///< Readout with flat image
 );

trunk/archive/scripts/src/phase2/pmFlatFieldErrors.h

@@ -7 +7 @@
  *  @author Ross Harman, MHPCC
  *
- *  @version $Revision: 1.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2005-09-23 02:59:05 $
+ *  @version $Revision: 1.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2005-11-03 01:30:32 $
  *
  *  Copyright 2004 Maui High Performance Computing Center, University of Hawaii

trunk/archive/scripts/src/phase2/pmSubtractBias.c

@@ -6 +6 @@
  *  @author GLG, MHPCC
  *
- *  @version $Revision: 1.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2005-09-23 02:58:30 $
+ *  @version $Revision: 1.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2005-11-03 01:30:32 $
  *
  *  Copyright 2004 Maui High Performance Computing Center, University of Hawaii
@@ -22 +22 @@
 #define PM_SUBTRACT_BIAS_SPLINE_ORDER 3
 
+// XXX: put these in psConstants.h
+void PS_POLY1D_PRINT(psPolynomial1D *poly)
+{
+    printf("-------------- PS_POLY1D_PRINT() --------------\n");
+    printf("poly->nX is %d\n", poly->nX);
+    for (psS32 i = 0 ; i < (1 + poly->nX) ; i++) {
+        printf("poly->coeff[%d] is %f\n", i, poly->coeff[i]);
+    }
+}
+
+void PS_PRINT_SPLINE(psSpline1D *mySpline)
+{
+    printf("-------------- PS_PRINT_SPLINE() --------------\n");
+    printf("mySpline->n is %d\n", mySpline->n);
+    for (psS32 i = 0 ; i < mySpline->n ; i++) {
+        PS_POLY1D_PRINT(mySpline->spline[i]);
+    }
+    PS_VECTOR_PRINT_F32(mySpline->knots);
+}
+
+#define PS_IMAGE_PRINT_F32_HIDEF(NAME) \
+printf("======== printing %s ========\n", #NAME); \
+for (int i = 0 ; i < (NAME)->numRows ; i++) { \
+    for (int j = 0 ; j < (NAME)->numCols ; j++) { \
+        printf("%.5f ", (NAME)->data.F32[i][j]); \
+    } \
+    printf("\n"); \
+}\
+
 /******************************************************************************
 psSubtractFrame(): this routine will take as input a readout for the input
 image and a readout for the bias image.  The bias image is subtracted in
 place from the input image.
- *****************************************************************************/
+*****************************************************************************/
 static pmReadout *SubtractFrame(pmReadout *in,
                                 const pmReadout *bias)
@@ -143 +172 @@
     return(opt);
 }
+
+
 
 /******************************************************************************
@@ -161 +192 @@
     psTrace(".psModule.pmSubtracBias.ScaleOverscanVector", 4,
             "---- ScaleOverscanVector() begin (%d -> %d) ----\n", overscanVector->n, n);
+    //    PS_VECTOR_PRINT_F32(overscanVector);
 
     if (NULL == overscanVector) {
@@ -182 +214 @@
     psF32 x;
     psS32 i;
-
+    printf("Got here\n");
     if (fit == PM_FIT_POLYNOMIAL) {
         // Fit a polynomial to the old overscan vector.
@@ -204 +236 @@
         // Fit a spline to the old overscan vector.
         mySpline = (psSpline1D *) fitSpec;
+        // XXX: Does it make any sense to have a psSpline argument?
         if (mySpline == NULL) {
             mustFreeSpline = 1;
@@ -210 +243 @@
         //
         // NOTE: Since the X arg in the psVectorFitSpline1D() function is NULL,
-        // splines enpoints will be from 0.0 to overscanVector->n-1.  Must scale
+        // splines endpoints will be from 0.0 to overscanVector->n-1.  Must scale
         // properly when doing the spline eval.
         //
-        mySpline = psVectorFitSpline1D(mySpline, NULL, overscanVector, NULL);
+        //        mySpline = psVectorFitSpline1D(mySpline, NULL, overscanVector, NULL);
+        mySpline = psVectorFitSpline1D(NULL, overscanVector);
         if (mySpline == NULL) {
             psError(PS_ERR_UNKNOWN, false, "ScaleOverscanVector()(2): Could not fit a spline to the psVector.\n");
             return(NULL);
         }
+        //        PS_PRINT_SPLINE(mySpline);
 
         // For each element of the new vector, convert the x-ordinate to that
@@ -230 +265 @@
             psFree(mySpline);
         }
+        //        PS_VECTOR_PRINT_F32(newVec);
+
 
     } else {
@@ -376 +413 @@
     tmpOverscan = (psListElem *) overscans->head;
     while (NULL != tmpOverscan) {
+        //        PS_IMAGE_PRINT_F32_HIDEF(in->image);
         myOverscanImage = (psImage *) tmpOverscan->data;
 
@@ -557 +595 @@
                 }
             } else if (fit == PM_FIT_SPLINE) {
+                // XXX: This makes no sense
+                // XXX: must free mySpline?
                 mySpline = (psSpline1D *) fitSpec;
-                mySpline = psVectorFitSpline1D(mySpline, NULL, overscanVector, NULL);
+                mySpline = psVectorFitSpline1D(NULL, overscanVector);
                 if (mySpline == NULL) {
                     psError(PS_ERR_UNKNOWN, false, "Could not fit a spline to overscan vector.  Returning in image.\n");

trunk/archive/scripts/src/phase2/pmSubtractBias.h

@@ -6 +6 @@
  *  @author GLG, MHPCC
  *
- *  @version $Revision: 1.1 $ $Name: not supported by cvs2svn $
- *  @date $Date: 2005-09-23 02:58:30 $
+ *  @version $Revision: 1.2 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2005-11-03 01:30:32 $
  *
  *  Copyright 2004 Maui High Performance Computing Center, University of Hawaii
@@ -23 +23 @@
 #include<math.h>
 #include "pslib.h"
-#include "pmFPA.h"
+
+#include "pmFPA.h"   //#include "pmAstrometry.h"
 
 typedef enum {

trunk/archive/scripts/src/phase2/psAdditionals.c

@@ -15 +15 @@
             psError(PS_ERR_IO, true, "Couldn't find %s in the metadata.\n");
         }
-    } else if (item->type != PS_META_META) {
+    } else if (item->type != PS_DATA_METADATA) {
         // The value at the key isn't metadata
         if (status) {
             *status = false;
         } else {
-            psLogMsg(__func__, PS_LOG_WARN, "%s isn't of type PS_META_META, as expected.\n");
+            psLogMsg(__func__, PS_LOG_WARN, "%s isn't of type PS_DATA_METADATA, as expected.\n");
         }
         value = NULL;
@@ -45 +45 @@
             psError(PS_ERR_IO, true, "Couldn't find %s in the metadata.\n");
         }
-    } else if (item->type != PS_META_STR) {
+    } else if (item->type != PS_DATA_STRING) {
         // The value at the key isn't of the desired type
         if (status) {
             *status = false;
         } else {
-            psLogMsg(__func__, PS_LOG_WARN, "%s isn't of type PS_META_STR, as expected.\n");
+            psLogMsg(__func__, PS_LOG_WARN, "%s isn't of type PS_DATA_STRING, as expected.\n");
         }
         value = NULL;
@@ -79 +79 @@
         printf(": ");
         switch (item->type) {
-          case PS_META_STR:
+          case PS_DATA_STRING:
             printf("%s", item->data.V);
             break;
-          case PS_META_BOOL:
+          case PS_DATA_BOOL:
             if (item->data.B) {
                 printf("True");
@@ -89 +89 @@
             }
             break;
-          case PS_META_S32:
+          case PS_DATA_S32:
             printf("%d", item->data.S32);
             break;
-          case PS_META_F32:
+          case PS_DATA_F32:
             printf("%f", item->data.F32);
             break;
-          case PS_META_F64:
+          case PS_DATA_F64:
             printf("%f", item->data.F64);
             break;
-          case PS_META_META:
+          case PS_DATA_METADATA:
             printf("\n");
             psMetadataPrint(item->data.V, level + 1);
@@ -200 +200 @@
     switch(item->type) {
         // Only doing a representative set of types
-      case PS_META_S32:
+      case PS_DATA_S32:
         newItem = psMetadataItemAlloc(item->name, item->type, item->comment, atoi(argv[argnum]));
         psArgumentRemove(argnum, argc, argv);
         break;
-      case PS_META_F32:
+      case PS_DATA_F32:
         newItem = psMetadataItemAlloc(item->name, item->type, item->comment, atof(argv[argnum]));
         psArgumentRemove(argnum, argc, argv);
         break;
-      case PS_META_BOOL:
+      case PS_DATA_BOOL:
         // Turn option on; no optional argument to remove
         newItem = psMetadataItemAlloc(item->name, item->type, item->comment, true);
         break;
         // XXX: Include the other numerical types
-      case PS_META_STR:
+      case PS_DATA_STRING:
         {
             //psString string = psStringCopy(argv[argnum]);     // Get the argument into PS memory management
@@ -250 +250 @@
         if (argItem) {
             psArgumentRemove(i, argc, argv); // Remove the switch
-            if (argItem->type != PS_META_MULTI) {
-                if (argItem->type != PS_META_BOOL && *argc < i + 1) {
+            if (argItem->type != PS_DATA_METADATA_MULTI) {
+                if (argItem->type != PS_DATA_BOOL && *argc < i + 1) {
                     psError(PS_ERR_IO, true, "Required argument for %s is missing.\n", argItem->name);
                     // XXX: Cleanup before returning
@@ -318 +318 @@
         switch (oldItem->type) {
             // Only doing a representative set of types
-          case PS_META_S32:
+          case PS_DATA_S32:
             oldItem->data.S32 = newItem->data.S32;
             break;
-          case PS_META_F32:
+          case PS_DATA_F32:
             oldItem->data.F32 = newItem->data.F32;
             break;
-          case PS_META_BOOL:
+          case PS_DATA_BOOL:
             oldItem->data.B = newItem->data.B;
             break;
             // XXX: Include the other numerical types
-          case PS_META_STR:
+          case PS_DATA_STRING:
             psFree(oldItem->data.V);
             oldItem->data.V = psMemIncrRefCounter(newItem->data.V);
             break;
-          case PS_META_MULTI:
+          case PS_DATA_METADATA_MULTI:
             {
                 psList *newMulti = psMemIncrRefCounter(newItem->data.V);        // The new list of MULTI
@@ -347 +347 @@
                     switch (oldMultiItem->type) {
                         // Only doing a representative set of types
-                      case PS_META_S32:
+                      case PS_DATA_S32:
                         oldItem->data.S32 = newItem->data.S32;
                         break;
-                      case PS_META_F32:
+                      case PS_DATA_F32:
                         oldItem->data.F32 = newItem->data.F32;
                         break;
                         // XXX: Include the other numerical types
-                      case PS_META_STR:
+                      case PS_DATA_STRING:
                         psFree(oldItem->data.V);
                         oldItem->data.V = psMemIncrRefCounter(newItem->data.V);
@@ -385 +385 @@
     switch (arg->type) {
         // Only doing a representative set of types
-      case PS_META_S32:
+      case PS_DATA_S32:
         return arg->data.S32 >= 0 ? (int)log10f((float)arg->data.S32) + 1 :
             (int)log10f(-(float)arg->data.S32) + 2;
         // XXX: Other numerical types
-      case PS_META_F32:
+      case PS_DATA_F32:
         return arg->data.F32 >= 0 ? 12 : 13; // -d.dddddde?dd
-      case PS_META_F64:
+      case PS_DATA_F64:
         return arg->data.F64 >= 0 ? 12 : 13; // -d.dddddde?dd
-      case PS_META_BOOL:
+      case PS_DATA_BOOL:
         return arg->data.B ? 4 : 5;
-      case PS_META_STR:
+      case PS_DATA_STRING:
         return strlen(arg->data.V);
       default:
@@ -450 +450 @@
         switch (argItem->type) {
             // Only doing a representative set of types
-          case PS_META_S32:
+          case PS_DATA_S32:
             printf("%d", argItem->data.S32);
             break;
             // XXX: Other numerical types
-          case PS_META_F32:
+          case PS_DATA_F32:
             printf("%.6e", argItem->data.F32);
             break;
-          case PS_META_F64:
+          case PS_DATA_F64:
             printf("%.6e", argItem->data.F64);
             break;
-          case PS_META_BOOL:
+          case PS_DATA_BOOL:
             if (argItem->data.B) {
                 printf("TRUE");
@@ -467 +467 @@
             }
             break;
-          case PS_META_STR:
+          case PS_DATA_STRING:
             printf("%s", argItem->data.V);
             break;