Index: /trunk/archive/scripts/src/phase2/Makefile.am
===================================================================
--- /trunk/archive/scripts/src/phase2/Makefile.am	(revision 5797)
+++ /trunk/archive/scripts/src/phase2/Makefile.am	(revision 5798)
@@ -1,40 +1,40 @@
 bin_PROGRAMS = phase2
 
-phase2_CPPFLAGS = $(PSLIB_CFLAGS) $(phase2_CFLAGS)
-phase2_LDADD = $(PSLIB_LIBS)
+phase2_CPPFLAGS = $(PSLIB_CFLAGS) $(PSMODULE_CFLAGS) $(phase2_CFLAGS)
+phase2_LDADD = $(PSLIB_LIBS) $(PSMODULE_LIBS)
 phase2_SOURCES = \
-	papPhase2.c \
-	papStuff.c \
-	pmChipMosaic.c \
-	pmConfig.c \
-	pmFPA.c \
-	pmFPAConceptsGet.c \
-	pmFPAConceptsSet.c \
-	pmFPAConstruct.c \
-	pmFPARead.c \
-	pmFPAWrite.c \
-	pmFlatField.c \
-	pmMaskBadPixels.c \
-	pmNonLinear.c \
-	pmSubtractBias.c \
-	psAdditionals.c
+	papPhase2.c
+#	papStuff.c \
+#	pmChipMosaic.c \
+#	pmConfig.c \
+#	pmFPA.c \
+#	pmFPAConceptsGet.c \
+#	pmFPAConceptsSet.c \
+#	pmFPAConstruct.c \
+#	pmFPARead.c \
+#	pmFPAWrite.c \
+#	pmFlatField.c \
+#	pmMaskBadPixels.c \
+#	pmNonLinear.c \
+#	pmSubtractBias.c \
+#	psAdditionals.c
 
-noinst_HEADERS = \
-	papStuff.h \
-	pmChipMosaic.h \
-	pmConfig.h \
-	pmFPA.h \
-	pmFPAConceptsGet.h \
-	pmFPAConceptsSet.h \
-	pmFPAConstruct.h \
-	pmFPARead.h \
-	pmFPAWrite.h \
-	pmFlatField.h \
-	pmFlatFieldErrors.h \
-	pmMaskBadPixels.h \
-	pmMaskBadPixelsErrors.h \
-	pmNonLinear.h \
-	pmSubtractBias.h \
-	psAdditionals.h
+noinst_HEADERS =
+#	papStuff.h \
+#	pmChipMosaic.h \
+#	pmConfig.h \
+#	pmFPA.h \
+#	pmFPAConceptsGet.h \
+#	pmFPAConceptsSet.h \
+#	pmFPAConstruct.h \
+#	pmFPARead.h \
+#	pmFPAWrite.h \
+#	pmFlatField.h \
+#	pmFlatFieldErrors.h \
+#	pmMaskBadPixels.h \
+#	pmMaskBadPixelsErrors.h \
+#	pmNonLinear.h \
+#	pmSubtractBias.h \
+#	psAdditionals.h
 
 EXTRA_DIST = \
Index: /trunk/archive/scripts/src/phase2/configure.ac
===================================================================
--- /trunk/archive/scripts/src/phase2/configure.ac	(revision 5797)
+++ /trunk/archive/scripts/src/phase2/configure.ac	(revision 5798)
@@ -15,4 +15,5 @@
 
 PKG_CHECK_MODULES([PSLIB], [pslib >= 0.9.0]) 
+PKG_CHECK_MODULES([PSMODULE], [psmodule >= 0.0.0]) 
 
 CFLAGS="${CFLAGS} -DTESTING"
Index: /trunk/archive/scripts/src/phase2/papPhase2.c
===================================================================
--- /trunk/archive/scripts/src/phase2/papPhase2.c	(revision 5797)
+++ /trunk/archive/scripts/src/phase2/papPhase2.c	(revision 5798)
@@ -3,7 +3,9 @@
 
 #include "pslib.h"
+
 #include "psAdditionals.h"
 
-#include "pmFPA.h"
+#include "pmAstrometry.h"
+#include "pmReadout.h"
 #include "pmConfig.h"
 #include "pmFPAConstruct.h"
@@ -110,8 +112,8 @@
     const char *inputName = argv[1];    // Name of input image
     const char *outputName = argv[2];   // Name of output image
-    const char *biasName = psMetadataLookupString(NULL, arguments, "-bias"); // Name of bias image
-    const char *darkName = psMetadataLookupString(NULL, arguments, "-dark"); // Name of dark image
-    const char *flatName = psMetadataLookupString(NULL, arguments, "-flat"); // Name of flat-field image
-    const char *maskName = psMetadataLookupString(NULL, arguments, "-mask"); // Name of mask image
+    const char *biasName = psMetadataLookupStr(NULL, arguments, "-bias"); // Name of bias image
+    const char *darkName = psMetadataLookupStr(NULL, arguments, "-dark"); // Name of dark image
+    const char *flatName = psMetadataLookupStr(NULL, arguments, "-flat"); // Name of flat-field image
+    const char *maskName = psMetadataLookupStr(NULL, arguments, "-mask"); // Name of mask image
     const int chipNum = psMetadataLookupS32(NULL, arguments, "-chip"); // Chip number to work on
     printf("Input: %s\nOutput: %s\n", inputName, outputName);
@@ -211,5 +213,5 @@
     if (psMetadataLookupBool(NULL, recipe, "OVERSCAN")) {
         doOverscan = true;
-        psString mode = psMetadataLookupString(NULL, recipe, "OVERSCAN.MODE");
+        psString mode = psMetadataLookupStr(NULL, recipe, "OVERSCAN.MODE");
         if (strcasecmp(mode, "INDIVIDUAL") == 0) {
             overscanMode = PM_OVERSCAN_ROWS;
@@ -221,5 +223,5 @@
                      " assuming NONE.\n", mode);
         }
-        psString fit = psMetadataLookupString(NULL, recipe, "OVERSCAN.FIT");
+        psString fit = psMetadataLookupStr(NULL, recipe, "OVERSCAN.FIT");
         if (strcasecmp(fit, "POLYNOMIAL") == 0) {
             overscanFitType = PM_FIT_POLYNOMIAL;
@@ -240,5 +242,5 @@
             overscanBins = 1;
         }
-        psString stat = psMetadataLookupString(NULL, recipe, "OVERSCAN.STAT");
+        psString stat = psMetadataLookupStr(NULL, recipe, "OVERSCAN.STAT");
         if (strcasecmp(stat, "MEAN")) {
             overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEAN);
@@ -552,5 +554,5 @@
                                 psMetadata *options = dataItem->data.V; // Options with concept values as keys
                                 bool mdok = false; // Success of MD lookup
-                                psString concept = psMetadataLookupString(&mdok, recipe, "NONLIN.SOURCE");
+                                psString concept = psMetadataLookupStr(&mdok, recipe, "NONLIN.SOURCE");
                                 if (! mdok || ! concept) {
                                     psLogMsg("phase2", PS_LOG_WARN, "Non-linearity correction desired, but "
@@ -750,5 +752,6 @@
                                                        inputReadout->image->numRows,
                                                        PS_TYPE_U8);
-                    pmReadout *dummyMask = pmReadoutAlloc(NULL, dummyImage, NULL, 0, 0, 1, 1);
+                    pmReadout *dummyMask = pmReadoutAlloc(NULL);
+                    dummyMask->image = dummyImage;
                     (void)pmFlatField(inputReadout, dummyMask, flatReadout);
                     psFree(dummyMask);