Index: /trunk/ppNorm/.cvsignore
===================================================================
--- /trunk/ppNorm/.cvsignore	(revision 8031)
+++ /trunk/ppNorm/.cvsignore	(revision 8031)
@@ -0,0 +1,11 @@
+Makefile
+Makefile.in
+aclocal.m4
+autom4te.cache
+compile
+config.log
+config.status
+configure
+depcomp
+install-sh
+missing
Index: /trunk/ppNorm/Makefile.am
===================================================================
--- /trunk/ppNorm/Makefile.am	(revision 8031)
+++ /trunk/ppNorm/Makefile.am	(revision 8031)
@@ -0,0 +1,3 @@
+SUBDIRS = src
+
+CLEANFILES = *~ core core.*
Index: /trunk/ppNorm/autogen.sh
===================================================================
--- /trunk/ppNorm/autogen.sh	(revision 8031)
+++ /trunk/ppNorm/autogen.sh	(revision 8031)
@@ -0,0 +1,103 @@
+#!/bin/sh
+# Run this to generate all the initial makefiles, etc.
+
+srcdir=`dirname $0`
+test -z "$srcdir" && srcdir=.
+
+ORIGDIR=`pwd`
+cd $srcdir
+
+PROJECT=ppNorm
+TEST_TYPE=-f
+# change this to be a unique filename in the top level dir
+FILE=autogen.sh
+
+DIE=0
+
+LIBTOOLIZE=libtoolize
+ACLOCAL=aclocal
+AUTOHEADER=autoheader
+AUTOMAKE=automake
+AUTOCONF=autoconf
+
+#($LIBTOOLIZE --version) < /dev/null > /dev/null 2>&1 || {
+#        echo
+#        echo "You must have $LIBTOOlIZE installed to compile $PROJECT."
+#        echo "Download the appropriate package for your distribution,"
+#        echo "or get the source tarball at http://ftp.gnu.org/gnu/libtool/"
+#        DIE=1
+#}
+
+($ACLOCAL --version) < /dev/null > /dev/null 2>&1 || {
+        echo
+        echo "You must have $ACLOCAL installed to compile $PROJECT."
+        echo "Download the appropriate package for your distribution,"
+        echo "or get the source tarball at http://ftp.gnu.org/gnu/automake/"
+        DIE=1
+}
+
+#($AUTOHEADER --version) < /dev/null > /dev/null 2>&1 || {
+#        echo
+#        echo "You must have $AUTOHEADER installed to compile $PROJECT."
+#        echo "Download the appropriate package for your distribution,"
+#        echo "or get the source tarball at http://ftp.gnu.org/gnu/autoconf/"
+#        DIE=1
+#}
+
+($AUTOMAKE --version) < /dev/null > /dev/null 2>&1 || {
+        echo
+        echo "You must have $AUTOMAKE installed to compile $PROJECT."
+        echo "Download the appropriate package for your distribution,"
+        echo "or get the source tarball at http://ftp.gnu.org/gnu/automake/"
+        DIE=1
+}
+
+($AUTOCONF --version) < /dev/null > /dev/null 2>&1 || {
+        echo
+        echo "You must have $AUTOCONF installed to compile $PROJECT."
+        echo "Download the appropriate package for your distribution,"
+        echo "or get the source tarball at http://ftp.gnu.org/gnu/autoconf/"
+        DIE=1
+}
+
+if test "$DIE" -eq 1; then
+        exit 1
+fi
+
+test $TEST_TYPE $FILE || {
+        echo "You must run this script in the top-level $PROJECT directory"
+        exit 1
+}
+
+if test -z "$*"; then
+        echo "I am going to run ./configure with no arguments - if you wish "
+        echo "to pass any to it, please specify them on the $0 command line."
+fi
+
+#$LIBTOOLIZE --copy --force || echo "$LIBTOOlIZE failed"
+$ACLOCAL || echo "$ACLOCAL failed"
+#$AUTOHEADER || echo "$AUTOHEADER failed"
+$AUTOMAKE --add-missing --force-missing --copy || echo "$AUTOMAKE failed"
+$AUTOCONF || echo "$AUTOCONF failed"
+
+cd $ORIGDIR
+
+run_configure=true
+for arg in $*; do
+    case $arg in
+        --no-configure)
+            run_configure=false
+            ;;
+        *)
+            ;;
+    esac
+done
+
+if $run_configure; then
+    $srcdir/configure --enable-maintainer-mode "$@"
+    echo
+    echo "Now type 'make' to compile $PROJECT."
+else
+    echo
+    echo "Now run 'configure' and 'make' to compile $PROJECT."
+fi
Index: /trunk/ppNorm/configure.ac
===================================================================
--- /trunk/ppNorm/configure.ac	(revision 8031)
+++ /trunk/ppNorm/configure.ac	(revision 8031)
@@ -0,0 +1,62 @@
+AC_PREREQ(2.59)
+
+AC_INIT([ppNorm], [0.0.1], [price@ifa.hawaii.edu])
+AC_CONFIG_SRCDIR([src])
+
+AM_INIT_AUTOMAKE([1.6 foreign dist-bzip2])
+dnl AM_CONFIG_HEADER([config.h])
+AM_MAINTAINER_MODE
+
+AC_LANG(C)
+AC_GNU_SOURCE
+AC_PROG_CC
+AC_PROG_INSTALL
+dnl AC_PROG_LIBTOOL
+
+dnl handle debug building
+AC_ARG_ENABLE(optimize,
+  [AS_HELP_STRING(--enable-optimize,enable compiler optimization)],
+  [AC_MSG_RESULT(compile optimization enabled)
+   CFLAGS="${CFLAGS=} -O2"],
+  [AC_MSG_RESULT([compile optimization disabled])
+   CFLAGS="${CFLAGS=} -O0 -g"]
+)
+
+ppNorm_CFLAGS="-Wall -Werror -std=c99"
+ppNorm_LDFLAGS=""
+                                                                                
+dnl handle debug building
+AC_ARG_ENABLE(optimize,
+  [AS_HELP_STRING(--enable-optimize,enable compiler optimization)],
+  [AC_MSG_RESULT(compile optimization enabled)
+   CFLAGS="${CFLAGS=} -O2"],
+  [AC_MSG_RESULT([compile optimization disabled])
+   CFLAGS="${CFLAGS=} -O0 -g"]
+)
+ 
+dnl handle path coverage checking
+AC_ARG_ENABLE(coverage,
+  [AS_HELP_STRING(--enable-coverage,enable path coverage checking)],
+  [AC_MSG_RESULT(path coverage enabled)
+   CFLAGS="${CFLAGS=} -fprofile-arcs -ftest-coverage -pg"]
+)
+ 
+PKG_CHECK_MODULES([PSLIB], [pslib >= 0.9.0])
+PKG_CHECK_MODULES([PSMODULE], [psmodule >= 0.0.0])
+
+dnl handle profiler building
+AC_ARG_ENABLE(profile,
+  [AS_HELP_STRING(--enable-profile,enable compiler profiler information inclusion)],
+  [AC_MSG_RESULT(compile optimization enabled)
+  ppNorm_CFLAGS="${ppNorm_CFLAGS} -g -pg"
+  ppNorm_LDFLAGS="${ppNorm_LDFLAGS} -pg -Wl,--start-group -Wl,-Bstatic"]
+  )
+   
+AC_SUBST([ppNorm_CFLAGS])
+AC_SUBST([ppNorm_LDFLAGS])
+
+AC_CONFIG_FILES([
+  Makefile
+  src/Makefile
+])
+AC_OUTPUT
Index: /trunk/ppNorm/src/.cvsignore
===================================================================
--- /trunk/ppNorm/src/.cvsignore	(revision 8031)
+++ /trunk/ppNorm/src/.cvsignore	(revision 8031)
@@ -0,0 +1,4 @@
+Makefile
+Makefile.in
+ppNorm
+.deps
Index: /trunk/ppNorm/src/Makefile.am
===================================================================
--- /trunk/ppNorm/src/Makefile.am	(revision 8031)
+++ /trunk/ppNorm/src/Makefile.am	(revision 8031)
@@ -0,0 +1,22 @@
+bin_PROGRAMS = ppNorm
+
+ppNorm_CFLAGS += $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS)
+ppNorm_LDFLAGS += $(PSMODULE_LIBS) $(PSLIB_LIBS) -Wl,-Bdynamic
+
+ppNorm_SOURCES =		\
+	ppNorm.c		\
+	ppNormData.c		\
+	ppNormLoop.c		\
+	ppNormSetup.c
+
+noinst_HEADERS =		\
+	ppNormData.h		\
+	ppNorm.h
+
+CLEANFILES = *~
+
+clean-local:
+	-rm -f TAGS
+# Tags for emacs
+tags:
+	etags `find . -name \*.[ch] -print`
Index: /trunk/ppNorm/src/ppNorm.c
===================================================================
--- /trunk/ppNorm/src/ppNorm.c	(revision 8031)
+++ /trunk/ppNorm/src/ppNorm.c	(revision 8031)
@@ -0,0 +1,29 @@
+#include <stdio.h>
+#include <pslib.h>
+#include <psmodules.h>
+
+#include "ppNorm.h"
+
+int main(int argc, char *argv[])
+{
+
+    psLibInit(NULL);
+    psTimerStart(TIMERNAME);
+
+    // Parse the configuration and arguments
+    pmConfig *config = pmConfigRead(&argc, argv);
+
+    // Get the options, open the files
+    ppNormData *data = ppNormSetup(config);
+
+    // Go through the FPA and do the hard work
+    ppNormLoop(data, config);
+
+    psFree(data);
+    psFree(config);
+    pmConceptsDone();
+    pmConfigDone();
+    psLibFinalize();
+
+    return EXIT_SUCCESS;
+}
Index: /trunk/ppNorm/src/ppNorm.h
===================================================================
--- /trunk/ppNorm/src/ppNorm.h	(revision 8031)
+++ /trunk/ppNorm/src/ppNorm.h	(revision 8031)
@@ -0,0 +1,21 @@
+#ifndef PP_NORM_H
+#define PP_NORM_H
+
+#define RECIPENAME "PPNORM"
+#define TIMERNAME "PPNORM"
+#define INPUTNAME "PPNORM.INPUT"
+#define OUTPUTNAME "PPNORM.OUTPUT"
+
+#include <psmodules.h>
+#include "ppNormData.h"
+
+// Set up the options and input/output files
+ppNormData *ppNormSetup(pmConfig *config // Configuration
+    );
+
+// Loop over the input image and do all the hard work
+void ppNormLoop(ppNormData *data,       // The data
+                pmConfig *config        // Configuration
+    );
+
+#endif
Index: /trunk/ppNorm/src/ppNormData.c
===================================================================
--- /trunk/ppNorm/src/ppNormData.c	(revision 8031)
+++ /trunk/ppNorm/src/ppNormData.c	(revision 8031)
@@ -0,0 +1,27 @@
+#include <stdio.h>
+#include <pslib.h>
+
+#include "ppNormData.h"
+
+static void normDataFree(ppNormData *data // Data to free
+    )
+{
+    // Nothing to free; this function is just for identification purposes
+    return;
+}
+
+
+ppNormData *ppNormDataAlloc(void)
+{
+    ppNormData *data = psAlloc(sizeof(ppNormData)); // Newly allocated data
+    psMemSetDeallocator(data, (psFreeFunc)normDataFree);
+
+    data->sample = 0;
+    data->maskVal = 0;
+    data->stat = 0;
+    data->rej = 0.0;
+    data->iter = 0;
+
+    return data;
+}
+
Index: /trunk/ppNorm/src/ppNormData.h
===================================================================
--- /trunk/ppNorm/src/ppNormData.h	(revision 8031)
+++ /trunk/ppNorm/src/ppNormData.h	(revision 8031)
@@ -0,0 +1,19 @@
+#ifndef PP_NORM_DATA_H
+#define PP_NORM_DATA_H
+
+#include <pslib.h>
+#include <psmodules.h>
+
+// Options for processing
+typedef struct {
+    float sample;                       // Fraction of cell to sample for statistics
+    psMaskType maskVal;                 // Mask value for images
+    psStatsOptions stat;                // Statistic to use
+    float rej;                          // Rejection limit
+    int iter;                           // Rejection iterations
+} ppNormData;
+
+// Allocator
+ppNormData *ppNormDataAlloc(void);
+
+#endif
Index: /trunk/ppNorm/src/ppNormLoop.c
===================================================================
--- /trunk/ppNorm/src/ppNormLoop.c	(revision 8031)
+++ /trunk/ppNorm/src/ppNormLoop.c	(revision 8031)
@@ -0,0 +1,245 @@
+#include <stdio.h>
+#include <assert.h>
+#include <string.h>
+#include <pslib.h>
+#include <psmodules.h>
+
+#include "ppNorm.h"
+
+#define MAX_ITER 10                     // Maximum number of iterations for pmFlatNormalize
+#define TOLERANCE 1e-3                  // Tolerance to reach for pmFlatNormalize
+
+
+// Count the number of cells in an FPA
+static int countCells(pmFPAfile *file,  // The FPA file for which to count cells
+                      pmConfig *config  // Configuration
+    )
+{
+    pmFPAview *view = pmFPAviewAlloc(0);// View of FPA
+    long numCells = 0;                  // Number of cells
+
+    pmChip *chip;                       // Chip, from iteration
+    while ((chip = pmFPAviewNextChip(view, file->fpa, 1))) {
+        if (!chip->file_exists) {
+            continue;
+        }
+
+        pmCell *cell;                   // Cell, from iteration
+        while ((cell = pmFPAviewNextCell(view, file->fpa, 1))) {
+            if (!cell->file_exists) {
+                continue;
+            }
+
+            numCells++;
+        }
+    }
+
+    psFree(view);
+    return numCells;
+}
+
+
+
+
+
+void ppNormLoop(ppNormData *data,       // The data
+                pmConfig *config        // Configuration
+    )
+{
+    assert(psStatsSingleOption(data->stat));
+    psStats *bgStats = psStatsAlloc(data->stat); // Statistics for the background
+    bgStats->clipIter = data->iter;
+    bgStats->clipSigma = data->rej;
+
+    bool mdok;                          // Status of MD lookup
+    pmFPAfile *input = psMetadataLookupPtr(&mdok, config->files, INPUTNAME); // Input FPA file
+    if (!input || !mdok) {
+        psAbort(__func__, "Should never get here: I'm sure I saved it.\n");
+    }
+
+    long numCells = countCells(input, config); // Number cells
+
+    psImage *backgrounds = psImageAlloc(numCells, 1, PS_TYPE_F32); // Matrix of backgrounds.  Only single exp.
+    psVector *gains = psVectorAlloc(numCells, PS_TYPE_F32); // Vector of gains for the cells
+    gains->n = numCells;
+
+    // Iterate through the FPA, getting the background
+    pmFPAview *view = pmFPAviewAlloc(0);// View of FPA
+    long cellNum = -1;                   // Cell number, for indexing
+    if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
+        psError(PS_ERR_IO, false, "Unable to check file I/O.\n");
+        goto done;
+    }
+    pmChip *chip;                       // Chip, from iteration
+    while ((chip = pmFPAviewNextChip(view, input->fpa, 1))) {
+        if (!chip->file_exists) {
+            continue;
+        }
+        const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); // Name of chip
+        if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) {
+            psError(PS_ERR_IO, false, "Unable to check file I/O at chip %s.\n", chipName);
+            goto done;
+        }
+        pmCell *cell;                   // Cell, from iteration
+        while ((cell = pmFPAviewNextCell(view, input->fpa, 1))) {
+            if (!cell->file_exists) {
+                continue;
+            }
+            cellNum++;
+            const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); // Name of cell
+            if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
+                psError(PS_ERR_IO, false, "Unable to check file I/O at chip %s, cell %s.\n",
+                        chipName, cellName);
+                goto done;
+            }
+
+            if (cell->readouts->n > 1) {
+                psLogMsg(__func__, PS_LOG_WARN, "Chip %s, cell %s contains %d readouts --- "
+                         "only the first will be used.\n", chipName, cellName, cell->readouts->n);
+            }
+            pmReadout *readout = cell->readouts->data[0];
+
+            if (data->sample <= 0.0) {
+                psImageStats(bgStats, readout->image, readout->mask, data->maskVal);
+            } else {
+                // Apply sampling
+                psImage *image = readout->image; // The image of interest
+                psImage *mask = readout->mask; // The mask image
+                int numSamples = data->sample * image->numCols * image->numRows; // Number of samples
+                int sampleSpace = 1.0 / data->sample; // Space between samples
+                psVector *sampleValues = psVectorAlloc(numSamples, PS_TYPE_F32); // Vector of samples
+                sampleValues->n = numSamples;
+                psVector *sampleMask = NULL;  // Corresponding mask
+                if (mask) {
+                    sampleMask = psVectorAlloc(numSamples, PS_TYPE_U8);
+                    sampleMask->n = numSamples;
+                }
+                for (int i = 0; i < numSamples; i++) {
+                    int j = i * sampleSpace;
+                    int y = j / image->numRows;
+                    int x = j % image->numRows;
+                    sampleValues->data.F32[i] = image->data.F32[y][x];
+                    if (mask) {
+                        sampleMask->data.U8[i] = mask->data.U8[y][x];
+                    }
+                }
+                psVectorStats(bgStats, sampleValues, sampleMask, NULL, data->maskVal);
+                psFree(sampleValues);
+                psFree(sampleMask);
+            }
+
+            backgrounds->data.F32[0][cellNum] = psStatsGetValue(bgStats, data->stat);
+            psTrace(__func__, 3, "Background for chip %s, cell %s (%d) is %f\n", chipName, cellName,
+                    cellNum, backgrounds->data.F32[0][cellNum]);
+
+            gains->data.F32[cellNum] = psMetadataLookupF32(&mdok, cell->concepts, "CELL.GAIN");
+            if (!mdok || isnan(gains->data.F32[cellNum])) {
+                psLogMsg(__func__, PS_LOG_WARN, "Unable to access CELL.GAIN for cell --- ignored.\n");
+            }
+
+            if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) {
+                psError(PS_ERR_IO, false, "Unable to check file I/O at chip %s, cell %s.\n",
+                        chipName, cellName);
+                goto done;
+            }
+            pmCellFreeData(cell);
+        }
+        if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) {
+            psError(PS_ERR_IO, false, "Unable to check file I/O at chip %s.\n", chipName);
+            goto done;
+        }
+        pmChipFreeData(chip);
+    }
+    if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) {
+        psError(PS_ERR_IO, false, "Unable to check file I/O.\n");
+        goto done;
+    }
+    pmFPAFreeData(input->fpa);
+
+    bool converge = false;              // Did the normalisation converge?
+    psVector *fluxes = pmFlatNormalize(&converge, gains, backgrounds, MAX_ITER, TOLERANCE);
+    if (!converge || !fluxes) {
+        psError(PS_ERR_UNKNOWN, false, "Normalisation failed to converge.\n");
+        goto done;
+    }
+
+    assert(fluxes->n == 1);             // Only a single integration
+    if (fluxes->data.F32[0] <= 0.0) {
+        psError(PS_ERR_UNKNOWN, false, "Non-positive value (%f) returned for normalisation.\n",
+                fluxes->data.F32[0]);
+        goto done;
+    }
+    float invFlux = 1.0 / fluxes->data.F32[0]; // The inverse flux; multiply by this to normalise
+
+    // Go through the image, normalising the fluxes
+    pmFPAfileActivate(config->files, true, OUTPUTNAME);
+    pmFPAviewReset(view);
+
+    {
+        long cellNum = -1;                   // Cell number, for indexing
+        if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
+            psError(PS_ERR_IO, false, "Unable to check file I/O.\n");
+            goto done;
+        }
+        pmChip *chip;                       // Chip, from iteration
+        while ((chip = pmFPAviewNextChip(view, input->fpa, 1))) {
+            if (!chip->file_exists) {
+                continue;
+            }
+            const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); // Name of chip
+            if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) {
+                psError(PS_ERR_IO, false, "Unable to check file I/O at chip %s.\n", chipName);
+                goto done;
+            }
+            pmCell *cell;                   // Cell, from iteration
+            while ((cell = pmFPAviewNextCell(view, input->fpa, 1))) {
+                if (!cell->file_exists) {
+                    continue;
+                }
+                cellNum++;
+                const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); // Name of cell
+                if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
+                    psError(PS_ERR_IO, false, "Unable to check file I/O at chip %s, cell %s.\n",
+                            chipName, cellName);
+                    goto done;
+                }
+
+                if (cell->readouts->n > 1) {
+                    psLogMsg(__func__, PS_LOG_WARN, "Chip %s, cell %s contains %d readouts --- "
+                             "only the first will be used.\n", chipName, cellName, cell->readouts->n);
+                }
+                pmReadout *readout = cell->readouts->data[0];
+
+                psTrace(__func__, 3, "Dividing chip %s, cell %s (%d) by %f\n", chipName, cellName,
+                        cellNum, fluxes->data.F32[0]);
+
+                psBinaryOp(readout->image, readout->image, "*", psScalarAlloc(invFlux, PS_TYPE_F32));
+
+                if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) {
+                    psError(PS_ERR_IO, false, "Unable to check file I/O at chip %s, cell %s.\n",
+                            chipName, cellName);
+                    goto done;
+                }
+                pmCellFreeData(cell);
+            }
+            if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) {
+                psError(PS_ERR_IO, false, "Unable to check file I/O at chip %s.\n", chipName);
+                goto done;
+            }
+            pmChipFreeData(chip);
+        }
+        if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) {
+            psError(PS_ERR_IO, false, "Unable to check file I/O.\n");
+            goto done;
+        }
+        pmFPAFreeData(input->fpa);
+    }
+
+done:
+    psFree(view);
+    psFree(bgStats);
+    psFree(backgrounds);
+    psFree(gains);
+
+    return;
+}
Index: /trunk/ppNorm/src/ppNormSetup.c
===================================================================
--- /trunk/ppNorm/src/ppNormSetup.c	(revision 8031)
+++ /trunk/ppNorm/src/ppNormSetup.c	(revision 8031)
@@ -0,0 +1,157 @@
+#include <stdio.h>
+#include <pslib.h>
+#include <psmodules.h>
+#include <string.h>
+
+#include "ppNorm.h"
+#include "ppNormData.h"
+
+// Print usage information and die
+static void usageAndDie(pmConfig *config      // Configuration (contains the arguments list)
+    )
+{
+    printf("Normalize the input FPA.\n\n"
+           "Usage:\n"
+           "\t%s [-file INPUT.fits] [-list LIST] OUTPUT\n"
+           "\n", config->argv[0]);
+    psArgumentHelp(config->arguments);
+    psFree(config);
+    psLibFinalize();
+    pmConceptsDone();
+    pmConfigDone();
+    exit(EXIT_FAILURE);
+}
+
+ppNormData *ppNormSetup(pmConfig *config // Configuration
+    )
+{
+    // Setup and parse command-line arguments
+    psMetadata *arguments = config->arguments; // Arguments
+    psMetadataAddStr(arguments, PS_LIST_TAIL, "-stat", 0, "Statistic to use", NULL);
+    psMetadataAddF32(arguments, PS_LIST_TAIL, "-sample", 0, "Sampling fraction", 0.0);
+    psMetadataAddF32(arguments, PS_LIST_TAIL, "-rej", 0, "Rejection level", 0.0);
+    psMetadataAddS32(arguments, PS_LIST_TAIL, "-iter", 0, "Rejection iterations", 0);
+
+    // No command-line arguments: print the help
+    if (*config->argc == 1) {
+        usageAndDie(config);
+    }
+
+    // Get input files
+    if (!pmConfigFileSetsMD(config->arguments, config, "INPUT", "-file", "-list")) {
+        psError(PS_ERR_IO, false, "Unable to open input files.\n");
+        usageAndDie(config);
+    }
+
+    if (!psArgumentParse(arguments, config->argc, config->argv)) {
+        printf("Unable to parse command-line arguments.\n\n");
+        usageAndDie(config);
+    }
+
+    // The output (root) name is the final thing left on the command-line
+    if (*config->argc != 2) {
+        usageAndDie(config);
+    }
+    // Parse the command-line options
+    ppNormData *data = ppNormDataAlloc(); // The data
+    psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", 0,
+                     "Name of the output image", config->argv[1]);
+
+    // Read the camera
+    bool status = false;                // Status of function calls
+    pmFPAfile *input = pmFPAfileDefineFromArgs(&status, config, INPUTNAME, "INPUT");
+    if (!status) {
+        psError(PS_ERR_IO, false, "Failed to build FPA from %s.INPUT.\n", INPUTNAME);
+        goto die;
+    }
+
+    pmFPAfile *output = pmFPAfileDefineOutput(config, input->fpa, OUTPUTNAME);
+    if (!output) {
+        psError(PS_ERR_UNKNOWN, false, "Failed to build output from %s.OUTPUT.\n", OUTPUTNAME);
+        goto die;
+    }
+    pmFPAfileActivate(config->files, false, OUTPUTNAME); // We don't want to use this until later
+
+#if 0
+    psFree(input);                      // Drop reference
+    psFree(output);                     // Drop reference
+#endif
+
+    // Get the command-line arguments
+    const char *statString = psMetadataLookupStr(NULL, arguments, "-stat"); // Statistic of choice
+    if (statString && strlen(statString) > 0) {
+        data->stat = psStatsOptionFromString(statString);
+        if (data->stat == 0) {
+            psError(PS_ERR_BAD_PARAMETER_VALUE, false, "Unable to interpret statistic: %s\n", statString);
+            goto die;
+        }
+    }
+    data->sample = psMetadataLookupF32(NULL, arguments, "-sample");
+
+    // Determine recipe parameters
+    bool mdok;                          // Status of MD lookup
+    psMetadata *recipe = psMetadataLookupMD(&mdok, config->recipes, RECIPENAME);
+    if (!mdok || !recipe) {
+        psLogMsg(__func__, PS_LOG_WARN, "Unable to find recipe %s --- attempting to proceed.\n", RECIPENAME);
+        return data;
+    }
+
+    if (data->sample == 0) {
+        float sample = psMetadataLookupF32(&mdok, recipe, "SAMPLE"); // Sample fraction
+        if (mdok && sample > 0) {
+            data->sample = sample;
+        } else {
+            psLogMsg(__func__, PS_LOG_WARN, "SAMPLE in recipe is not of type F32 and positive --- "
+                     "retaining default.\n");
+        }
+    }
+
+    psMaskType maskVal = psMetadataLookupU8(&mdok, recipe, "MASKVAL"); // Mask value
+    if (mdok) {
+        data->maskVal = maskVal;
+    } else {
+        psLogMsg(__func__, PS_LOG_WARN, "ITER in recipe is not of type U8 --- retaining default.\n");
+    }
+
+    if (data->stat == 0) {
+        const char *statName = psMetadataLookupStr(&mdok, recipe, "STAT"); // Statistics name
+        if (!mdok || !statName || strlen(statName) == 0) {
+            psError(PS_ERR_UNKNOWN, true, "Unable to find STAT of type STR in the recipe.\n");
+            goto die;
+        }
+        data->stat = psStatsOptionFromString(statName);
+        if (data->stat == 0) {
+            psError(PS_ERR_BAD_PARAMETER_VALUE, false, "Unable to parse STAT in recipe: %s\n", statName);
+            goto die;
+        }
+    }
+
+    // Clipping options
+    if (data->stat == PS_STAT_CLIPPED_MEAN && data->iter == 0 && isnan(data->rej)) {
+        int iter = psMetadataLookupS32(&mdok, recipe, "ITER"); // Number of rejection iterations
+        if (mdok && iter > 0) {
+            data->iter = iter;
+        } else {
+            psError(PS_ERR_BAD_PARAMETER_VALUE, true, "ITER in recipe is not of type S32 and positive.\n");
+            goto die;
+        }
+        float rej = psMetadataLookupF32(&mdok, recipe, "REJ"); // Rejection level
+        if (mdok && rej > 0) {
+            data->rej = rej;
+        } else {
+            psError(PS_ERR_BAD_PARAMETER_VALUE, true, "REJ in recipe is not of type F32 and positive.\n");
+            goto die;
+        }
+    }
+
+    return data;
+
+    // Common path for error conditions: clean up and exit.
+die:
+    psFree(config);
+    psFree(data);
+    pmConceptsDone();
+    pmConfigDone();
+    psLibFinalize();
+    exit(EXIT_FAILURE);
+}