Index: /branches/eam_branches/ipp-20130904/psphot/src/Makefile.am
===================================================================
--- /branches/eam_branches/ipp-20130904/psphot/src/Makefile.am	(revision 36270)
+++ /branches/eam_branches/ipp-20130904/psphot/src/Makefile.am	(revision 36271)
@@ -25,5 +25,5 @@
 libpsphot_la_LDFLAGS = $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
 
-bin_PROGRAMS = psphot psphotForced psphotFullForce psphotMinimal psphotMakePSF psphotStack psphotModelTest
+bin_PROGRAMS = psphot psphotForced psphotFullForce psphotMinimal psphotMakePSF psphotStack psphotModelTest psmakecff
 # bin_PROGRAMS = psphotPetrosianStudy psphotTest psphotMomentsStudy 
 
@@ -55,4 +55,9 @@
 psphotModelTest_LDFLAGS = $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
 psphotModelTest_LDADD = libpsphot.la
+
+psmakecff_CFLAGS = $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS)
+psmakecff_LDFLAGS = $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
+psmakecff_LDADD = libpsphot.la
+
 
 # psphotMomentsStudy_CFLAGS = $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS)
@@ -141,4 +146,8 @@
 	psphotMosaicChip.c	   \
 	psphotCleanup.c
+
+# a program that takes a cmf file and makes a cff file (input file for psphotFullForce
+psmakecff_SOURCES = \
+	psmakecff.c
 
 # psphotTest_SOURCES = \
Index: /branches/eam_branches/ipp-20130904/psphot/src/psmakecff.c
===================================================================
--- /branches/eam_branches/ipp-20130904/psphot/src/psmakecff.c	(revision 36271)
+++ /branches/eam_branches/ipp-20130904/psphot/src/psmakecff.c	(revision 36271)
@@ -0,0 +1,171 @@
+# ifdef HAVE_CONFIG_H
+# include <config.h>
+# endif
+
+#include <stdio.h>
+#include <pslib.h>
+#include <psmodules.h>
+#include "psphot.h"
+
+static pmConfig* psmakecffArguments(int, char**);
+static bool psmakecffParseCamera(pmConfig *);
+static bool psmakecffImageLoop(pmConfig*);
+
+int main (int argc, char **argv) {
+
+    psMemInit();
+    psTimerStart ("complete");
+    pmErrorRegister();                  // register psModule's error codes/messages
+    psphotInit();
+
+    // load command-line arguments, options, and system config data
+    pmConfig *config = psmakecffArguments (argc, argv);
+    assert(config);
+
+//    psphotVersionPrint();
+
+    // load input data (config and images (signal, noise, mask)
+    if (!psmakecffParseCamera (config)) {
+        psErrorStackPrint(stderr, "Error setting up the camera\n");
+        exit (1);
+    }
+
+    // call psphot for each readout
+    if (!psmakecffImageLoop (config)) {
+        psErrorStackPrint(stderr, "Error in the psphot image loop\n");
+        exit(1);
+    }
+
+//    psLogMsg ("psphot", PS_LOG_WARN, "complete psphot run: %f sec\n", psTimerMark ("complete"));
+
+//    psErrorCode exit_status = psphotGetExitStatus();
+//    psphotCleanup (config);
+    exit (0);
+}
+
+// all functions which return to this level must raise one of the top-level error codes if they
+// exit with an error.  these error codes are used to specify the program exit status
+
+void usage() {
+    fprintf(stderr, "usage: psmakecff -sources <input cmf> <output>\n");
+    exit (1);
+}
+
+static pmConfig* psmakecffArguments(int argc, char **argv) {
+
+    pmConfig *config =  pmConfigRead(&argc, argv, PSPHOT_RECIPE);
+    int N;
+
+    if (config == NULL) {
+      psErrorStackPrint(stderr, "Can't read site configuration");
+	exit(PS_EXIT_CONFIG_ERROR);
+    }
+    if ((N = psArgumentGet (argc, argv, "-sources"))) {
+        pmConfigFileSetsMD(config->arguments, &argc, argv, "SOURCES", "-sources", "-sourceslist");
+    } else {
+        usage();
+    }
+    if (argc < 2) {
+        usage();
+    }
+    psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", PS_DATA_STRING, "", argv[1]);
+
+    return config;
+}
+static bool psmakecffParseCamera(pmConfig *config) {
+    bool status = false;
+
+    pmFPAfile *sources = pmFPAfileDefineFromArgs(&status, config, "PSPHOT.INPUT.CMF", "SOURCES");
+    if (!status) {
+        psError(PS_ERR_UNKNOWN, false, "failed to build FPA from sources file");
+        return false;
+    }
+
+    pmFPAfile *output = pmFPAfileDefineOutputFromFile (config, sources, "PSMAKECFF.OUTPUT.CFF");
+    if (!output) {
+        psError(PS_ERR_UNKNOWN, false, "failed to build output FPA");
+        return false;
+    }
+    output->save = true;
+
+    return true;
+}
+
+# define ESCAPE(MESSAGE) {				\
+	psError(PSPHOT_ERR_DATA, false, MESSAGE);	        \
+	psFree (view);					\
+	return false;					\
+    }
+
+bool psmakecffImageLoop (pmConfig *config) {
+
+    bool status;
+    pmChip *chip;
+    pmCell *cell;
+    pmReadout *readout;
+
+    pmFPAfile *input = psMetadataLookupPtr (&status, config->files, "PSPHOT.INPUT.CMF");
+    if (!status) {
+        psError(PSPHOT_ERR_PROG, false, "Can't find input data!");
+        return false;
+    }
+
+    pmFPAfile *output = psMetadataLookupPtr (&status, config->files, "PSMAKECFF.OUTPUT.CFF");
+    if (!output) {
+        psError(PSPHOT_ERR_PROG, false, "Can't find output data!");
+        return false;
+    }
+
+    pmFPAview *view = pmFPAviewAlloc (0);
+    pmHDU *lastHDU = NULL;              // Last HDU updated
+
+    // files associated with the science image
+    if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE ("failed input for fpa in psphot.");
+
+    // select the appropriate recipe information
+    psMetadata *recipe  = psMetadataLookupPtr (&status, config->recipes, PSPHOT_RECIPE);
+    psAssert (recipe, "missing recipe?");
+
+//    psImageMaskType maskTest = psMetadataLookupImageMask(&status, recipe, "MASK.PSPHOT");
+
+    // for psphot, we force data to be read at the chip level
+    while ((chip = pmFPAviewNextChip (view, input->fpa, 1)) != NULL) {
+        psLogMsg ("psmakecmf", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process);
+        if (! chip->process || ! chip->file_exists) { continue; }
+
+#ifdef notdef
+        pmFPAfileActivate (config->files, false, NULL);
+        pmFPAfileActivate (config->files, true, "PSPHOT.LOAD");
+#endif
+        if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE ("failed input for Chip in psmakecff.");
+
+        // there is now only a single chip (multiple readouts?). loop over it and process
+        while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) {
+            psLogMsg ("psmakecmf", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process);
+
+            // process each of the readouts
+            while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) {
+                psLogMsg ("psmakecmf", 6, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process);
+                if (! readout->data_exists) { continue; }
+
+		pmHDU *hdu = pmHDUGetHighest(input->fpa, chip, cell);
+		if (hdu && hdu != lastHDU) {
+		    // psphotVersionHeaderFull(hdu->header);
+		    lastHDU = hdu;
+                }
+            }
+
+        }
+        // Defer output and closing of files until we've (possibly) done the NFrames analysis below
+//        pmFPAfileActivate (config->files, false, NULL);
+
+        if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE ("failed pmFPAfileIOChecks for Chip in psmakecff.");
+    }
+    if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE ("failed pmFPAfileIOChecks for FPA in psphot.");
+
+    // fail if we failed to handle an error
+    if (psErrorCodeLast() != PS_ERR_NONE) psAbort ("failed to handle an error!");
+
+    psFree (view);
+    return true;
+}