Index: trunk/psModules/src/imcombine/pmSubtractionIO.c
===================================================================
--- trunk/psModules/src/imcombine/pmSubtractionIO.c	(revision 18146)
+++ trunk/psModules/src/imcombine/pmSubtractionIO.c	(revision 19189)
@@ -1,7 +1,12 @@
 #include <stdio.h>
 #include <pslib.h>
+#include <strings.h>
 
 #include "pmHDU.h"
 #include "pmFPA.h"
+#include "pmFPAview.h"
+#include "pmFPAfile.h"
+#include "pmFPAfileFitsIO.h"
+#include "pmConcepts.h"
 
 #include "pmSubtraction.h"
@@ -62,9 +67,10 @@
 }
 
+//////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
 bool pmReadoutWriteSubtractionKernels(pmReadout *ro, psFits *fits)
 {
     PM_ASSERT_READOUT_NON_NULL(ro, false);
     PS_ASSERT_FITS_NON_NULL(fits, false);
-
 
     // Extract the regions and solutions used in the image matching
@@ -159,6 +165,6 @@
     // CVS tags, used to identify the version of this file (in case incompatibilities are introduced)
     psString cvsFile = psStringCopy("$RCSfile: pmSubtractionIO.c,v $");
-    psString cvsRev  = psStringCopy("$Revision: 1.1 $");
-    psString cvsDate = psStringCopy("$Date: 2008-06-16 21:59:43 $");
+    psString cvsRev  = psStringCopy("$Revision: 1.2 $");
+    psString cvsDate = psStringCopy("$Date: 2008-08-25 22:14:04 $");
     psStringSubstitute(&cvsFile, NULL, "RCSfile: ");
     psStringSubstitute(&cvsRev,  NULL, "Revision: ");
@@ -190,4 +196,75 @@
     return true;
 }
+
+static bool pmCellWriteSubtractionKernels(pmCell *cell, const pmFPAview *view,
+                                          pmFPAfile *file, pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(cell, false);
+    PS_ASSERT_PTR_NON_NULL(cell->readouts, false);
+    PS_ASSERT_PTR_NON_NULL(view, false);
+
+    pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view
+    *thisView = *view;
+
+    for (int i = 0; i < cell->readouts->n; i++) {
+        pmReadout *readout = cell->readouts->data[i];
+        thisView->readout = i;
+        if (!pmReadoutWriteSubtractionKernels(readout, file->fits)) {
+            psError(PS_ERR_IO, false, "Failed to write %dth readout", i);
+            psFree(thisView);
+            return false;
+        }
+    }
+    psFree(thisView);
+    return true;
+}
+
+static bool pmChipWriteSubtractionKernels(pmChip *chip, const pmFPAview *view,
+                                          pmFPAfile *file, pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(chip, false);
+    PS_ASSERT_PTR_NON_NULL(chip->cells, false);
+    PS_ASSERT_PTR_NON_NULL(view, false);
+
+    pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view
+    *thisView = *view;
+
+    for (int i = 0; i < chip->cells->n; i++) {
+        pmCell *cell = chip->cells->data[i];
+        thisView->cell = i;
+        if (!pmCellWriteSubtractionKernels(cell, thisView, file, config)) {
+            psError(PS_ERR_IO, false, "Failed to write %dth cell", i);
+            psFree(thisView);
+            return false;
+        }
+    }
+    psFree(thisView);
+    return true;
+}
+
+static bool pmFPAWriteSubtractionKernels(pmFPA *fpa, const pmFPAview *view,
+                                         pmFPAfile *file, pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(view, false);
+    PS_ASSERT_PTR_NON_NULL(fpa, false);
+    PS_ASSERT_PTR_NON_NULL(fpa->chips, false);
+
+    pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view
+    *thisView = *view;
+
+    for (int i = 0; i < fpa->chips->n; i++) {
+        pmChip *chip = fpa->chips->data[i];
+        thisView->chip = i;
+        if (!pmChipWriteSubtractionKernels(chip, thisView, file, config)) {
+            psError(PS_ERR_IO, false, "Failed to write %dth chip", i);
+            psFree(thisView);
+            return false;
+        }
+    }
+    psFree(thisView);
+    return true;
+}
+
+//////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
 
@@ -283,2 +360,248 @@
     return true;
 }
+
+static bool pmCellReadSubtractionKernels(pmCell *cell, const pmFPAview *view,
+                                         pmFPAfile *file, pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(view, false);
+    PS_ASSERT_PTR_NON_NULL(cell, false);
+    PS_ASSERT_PTR_NON_NULL(cell->readouts, false);
+
+    pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view
+    *thisView = *view;
+
+    // Create a readout if none exists
+    if (!cell->readouts || cell->readouts->n == 0) {
+        pmReadout *readout = pmReadoutAlloc(cell); // New readout
+        psFree(readout);                // Drop reference
+    }
+
+    cell->data_exists = false;
+    for (int i = 0; i < cell->readouts->n; i++) {
+        pmReadout *readout = cell->readouts->data[i];
+        thisView->readout = i;
+        pmReadoutReadSubtractionKernels(readout, file->fits);
+        if (!readout->data_exists) {
+            continue;
+        }
+
+        // load in the concept information for this cell
+        if (!pmConceptsReadCell(cell, PM_CONCEPT_SOURCE_HEADER, true, NULL)) {
+            psErrorClear();
+            psWarning("Difficulty reading concepts for cell; attempting to proceed.");
+        }
+        cell->data_exists = true;
+    }
+    psFree(thisView);
+
+    return true;
+}
+
+static bool pmChipReadSubtractionKernels(pmChip *chip, const pmFPAview *view,
+                                         pmFPAfile *file, pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(view, false);
+    PS_ASSERT_PTR_NON_NULL(chip, false);
+    PS_ASSERT_PTR_NON_NULL(chip->cells, false);
+
+    pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view
+    *thisView = *view;
+
+    chip->data_exists = false;
+    for (int i = 0; i < chip->cells->n; i++) {
+        pmCell *cell = chip->cells->data[i];
+        thisView->cell = i;
+        pmCellReadSubtractionKernels(cell, thisView, file, config);
+        if (!cell->data_exists) {
+            continue;
+        }
+        chip->data_exists = true;
+    }
+    psFree(thisView);
+
+    if (!pmConceptsReadChip(chip, PM_CONCEPT_SOURCE_HEADER, true, true, NULL)) {
+        psError(PS_ERR_IO, false, "Failed to read concepts for chip.\n");
+        return false;
+    }
+
+    return true;
+}
+
+static bool pmFPAReadSubtractionKernels(pmFPA *fpa, const pmFPAview *view,
+                                        pmFPAfile *file, pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(view, false);
+    PS_ASSERT_PTR_NON_NULL(file, false);
+    PS_ASSERT_PTR_NON_NULL(file->fpa, false);
+    PS_ASSERT_PTR_NON_NULL(file->fpa->chips, false);
+
+    pmFPAview *thisView = pmFPAviewAlloc(view->nRows); // Copy of input view
+    *thisView = *view;
+
+    for (int i = 0; i < fpa->chips->n; i++) {
+        pmChip *chip = fpa->chips->data[i];
+        thisView->chip = i;
+        pmChipReadSubtractionKernels(chip, thisView, file, config);
+    }
+    psFree(thisView);
+
+    if (!pmConceptsReadFPA(fpa, PM_CONCEPT_SOURCE_HEADER, true, NULL)) {
+        psError(PS_ERR_IO, false, "Failed to read concepts for fpa.\n");
+        return false;
+    }
+
+    return true;
+}
+
+//////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+bool pmSubtractionWriteKernels(const pmFPAview *view, pmFPAfile *file, pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(view, false);
+    PS_ASSERT_PTR_NON_NULL(file, false);
+    PS_ASSERT_PTR_NON_NULL(file->fpa, false);
+
+    pmFPA *fpa = pmFPAfileSuitableFPA(file, view, config, false); // Suitable FPA for writing
+
+    if (view->chip == -1) {
+        if (!pmFPAWriteSubtractionKernels(fpa, view, file, config)) {
+            psError(PS_ERR_IO, false, "Failed to write subtraction kernels from fpa");
+            psFree(fpa);
+            return false;
+        }
+        psFree(fpa);
+        return true;
+    }
+
+    if (view->chip >= fpa->chips->n) {
+        psError(PS_ERR_UNKNOWN, false, "Writing chip == %d (>= chips->n == %ld)", view->chip, fpa->chips->n);
+        psFree(fpa);
+        return false;
+    }
+    pmChip *chip = fpa->chips->data[view->chip];
+
+    if (view->cell == -1) {
+        if (!pmChipWriteSubtractionKernels(chip, view, file, config)) {
+            psError(PS_ERR_IO, false, "Failed to write objects from chip");
+            psFree(fpa);
+            return false;
+        }
+        psFree(fpa);
+        return true;
+    }
+
+    if (view->cell >= chip->cells->n) {
+        psError(PS_ERR_UNKNOWN, false, "Writing cell == %d (>= cells->n == %ld)",
+                view->cell, chip->cells->n);
+        psFree(fpa);
+        return false;
+    }
+    pmCell *cell = chip->cells->data[view->cell];
+
+    if (view->readout == -1) {
+        if (!pmCellWriteSubtractionKernels(cell, view, file, config)) {
+            psError(PS_ERR_IO, false, "Failed to write objects from cell");
+            psFree(fpa);
+            return false;
+        }
+        psFree(fpa);
+        return true;
+    }
+
+    if (view->readout >= cell->readouts->n) {
+        psError(PS_ERR_UNKNOWN, false, "Writing readout == %d (>= readouts->n == %ld)",
+                view->readout, cell->readouts->n);
+        psFree(fpa);
+        return false;
+    }
+    pmReadout *readout = cell->readouts->data[view->readout];
+
+    if (!pmReadoutWriteSubtractionKernels(readout, file->fits)) {
+        psError(PS_ERR_IO, false, "Failed to write objects from readout %d", view->readout);
+        psFree(fpa);
+        return false;
+    }
+
+    psFree(fpa);
+    return true;
+}
+
+bool pmSubtractionWritePHU(const pmFPAview *view, pmFPAfile *file, pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(view, false);
+    PS_ASSERT_PTR_NON_NULL(file, false);
+
+    if (file->wrote_phu) {
+        return true;
+    }
+    if (file->fileLevel != PM_FPA_LEVEL_FPA) {
+        return true;
+    }
+    if (file->fpa->chips->n == 1) {
+        return true;
+    }
+
+    // find the FPA phu
+    pmFPA *fpa = pmFPAfileSuitableFPA(file, view, config, false); // Suitable FPA for writing
+    pmHDU *phu = psMemIncrRefCounter(pmFPAviewThisPHU(view, fpa));
+    psFree(fpa);
+
+    // if there is no PHU, this is a single header+image (extension-less) file. This could be the case for an
+    // input SPLIT set of files being written out as a MEF.  if there is a PHU, write it out as a 'blank'
+    psMetadata *outhead = psMetadataAlloc();
+    if (phu) {
+        psMetadataCopy (outhead, phu->header);
+    }
+    psFree(phu);
+
+    pmConfigConformHeader(outhead, file->format);
+
+    psFitsWriteBlank(file->fits, outhead, "");
+    file->wrote_phu = true;
+
+    psTrace("pmFPAfile", 5, "wrote phu %s (type: %d)\n", file->filename, file->type);
+    psFree(outhead);
+
+    return true;
+}
+
+bool pmSubtractionReadKernels(const pmFPAview *view, pmFPAfile *file, pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(view, false);
+    PS_ASSERT_PTR_NON_NULL(file, false);
+    PS_ASSERT_PTR_NON_NULL(file->fpa, false);
+
+    pmFPA *fpa = file->fpa;
+
+    if (view->chip == -1) {
+        pmFPAReadSubtractionKernels(fpa, view, file, config);
+        return true;
+    }
+
+    if (view->chip >= fpa->chips->n) {
+        return false;
+    }
+    pmChip *chip = fpa->chips->data[view->chip];
+
+    if (view->cell == -1) {
+        pmChipReadSubtractionKernels(chip, view, file, config);
+        return true;
+    }
+
+    if (view->cell >= chip->cells->n) {
+        return false;
+    }
+    pmCell *cell = chip->cells->data[view->cell];
+
+    if (view->readout == -1) {
+        pmCellReadSubtractionKernels(cell, view, file, config);
+        return true;
+    }
+
+    if (view->readout >= cell->readouts->n) {
+        return false;
+    }
+    pmReadout *readout = cell->readouts->data[view->readout];
+
+    return pmReadoutReadSubtractionKernels(readout, file->fits);
+}