Index: unk/ppFringe/.cvsignore =================================================================== --- /trunk/ppFringe/.cvsignore (revision 10003) +++ (revision ) @@ -1,11 +1,0 @@ -Makefile.in -aclocal.m4 -autom4te.cache -compile -configure -depcomp -install-sh -missing -Makefile -config.log -config.status Index: unk/ppFringe/Makefile.am =================================================================== --- /trunk/ppFringe/Makefile.am (revision 10003) +++ (revision ) @@ -1,3 +1,0 @@ -SUBDIRS = src - -CLEANFILES = *~ core core.* Index: unk/ppFringe/autogen.sh =================================================================== --- /trunk/ppFringe/autogen.sh (revision 10003) +++ (revision ) @@ -1,103 +1,0 @@ -#!/bin/sh -# Run this to generate all the initial makefiles, etc. - -srcdir=`dirname $0` -test -z "$srcdir" && srcdir=. - -ORIGDIR=`pwd` -cd $srcdir - -PROJECT=ppFringe -TEST_TYPE=-f -# change this to be a unique filename in the top level dir -FILE=autogen.sh - -DIE=0 - -LIBTOOLIZE=libtoolize -ACLOCAL=aclocal -AUTOHEADER=autoheader -AUTOMAKE=automake -AUTOCONF=autoconf - -#($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 $PROJECT." -fi Index: unk/ppFringe/configure.ac =================================================================== --- /trunk/ppFringe/configure.ac (revision 10003) +++ (revision ) @@ -1,38 +1,0 @@ -AC_PREREQ(2.59) - -AC_INIT([ppFringe], [0.0.1], [price@ifa.hawaii.edu]) -AC_CONFIG_SRCDIR([src]) - -AM_INIT_AUTOMAKE([1.6 foreign dist-bzip2]) -AM_CONFIG_HEADER([src/config.h]) -AM_MAINTAINER_MODE - -AC_LANG(C) -AC_GNU_SOURCE -AC_PROG_CC -AC_PROG_INSTALL -dnl AC_PROG_LIBTOOL - -dnl enable largefile supports -AC_SYS_LARGEFILE - -dnl handle debug building -AC_ARG_ENABLE(optimize, - [AS_HELP_STRING(--enable-optimize,enable compiler optimization)], - [AC_MSG_RESULT(compile optimization enabled) - CFLAGS="${CFLAGS=} -O2"], - [AC_MSG_RESULT([compile optimization disabled]) - CFLAGS="${CFLAGS=} -O0 -g"] -) - -PKG_CHECK_MODULES([PSLIB], [pslib >= 0.12.99]) -PKG_CHECK_MODULES([PSMODULE], [psmodules >= 0.12.99]) - -ppFringe_CFLAGS="-Wall -Werror -std=c99" -AC_SUBST([ppFringe_CFLAGS]) - -AC_CONFIG_FILES([ - Makefile - src/Makefile -]) -AC_OUTPUT Index: unk/ppFringe/src/.cvsignore =================================================================== --- /trunk/ppFringe/src/.cvsignore (revision 10003) +++ (revision ) @@ -1,7 +1,0 @@ -Makefile.in -ppFringe -Makefile -.deps -config.h -config.h.in -stamp-h1 Index: unk/ppFringe/src/Makefile.am =================================================================== --- /trunk/ppFringe/src/Makefile.am (revision 10003) +++ (revision ) @@ -1,26 +1,0 @@ -bin_PROGRAMS = ppFringe - -ppFringe_CFLAGS += $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS) -ppFringe_LDFLAGS = $(PSMODULE_LIBS) $(PSLIB_LIBS) -### For profiling: -#ppMerge_CFLAGS += -g -pg -fprofile-arcs $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS) -#ppMerge_LDFLAGS = -pg -Wl,--start-group -Wl,-Bstatic $(PSMODULE_LIBS) $(PSLIB_LIBS) -Wl,-Bdynamic - -ppFringe_SOURCES = \ - ppFringe.c \ - ppFringeData.c \ - ppFringeLoop.c \ - ppFringeSetup.c - -noinst_HEADERS = \ - ppFringeData.h \ - ppFringe.h \ - ppFringeSetup.h - -CLEANFILES = *~ - -clean-local: - -rm -f TAGS -# Tags for emacs -tags: - etags `find . -name \*.[ch] -print` Index: unk/ppFringe/src/ppFringe.c =================================================================== --- /trunk/ppFringe/src/ppFringe.c (revision 10003) +++ (revision ) @@ -1,33 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include -#include -#include - -#include "ppFringe.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 - ppFringeData *data = ppFringeSetup(config); - - // Go through the FPA and measure the fringes - ppFringeLoop(data, config); - - psFree(data); - psFree(config); - pmConceptsDone(); - pmConfigDone(); - psLibFinalize(); - - return EXIT_SUCCESS; -} Index: unk/ppFringe/src/ppFringe.h =================================================================== --- /trunk/ppFringe/src/ppFringe.h (revision 10003) +++ (revision ) @@ -1,19 +1,0 @@ -#ifndef PP_FRINGE_H -#define PP_FRINGE_H - -#define RECIPE "PPFRINGE" -#define TIMERNAME "PPFRINGE" - -#include -#include "ppFringeData.h" - -// Set up the options and input/output files -ppFringeData *ppFringeSetup(pmConfig *config // Configuration - ); - -// Loop over the input image and do all the hard work -void ppFringeLoop(ppFringeData *data, // The data - const pmConfig *config// Configuration - ); - -#endif Index: unk/ppFringe/src/ppFringeData.c =================================================================== --- /trunk/ppFringe/src/ppFringeData.c (revision 10003) +++ (revision ) @@ -1,49 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include -#include - -#include "ppFringeData.h" - -static void fringeDataFree(ppFringeData *data // Data to free - ) -{ - // inName, outName and templateName are not on the psLib memory system (they are from argv). - psFree(data->inFPA); - - if (data->inFile) { - psFitsClose(data->inFile); - data->inFile = NULL; - } - if (data->outFile) { - psFitsClose(data->outFile); - data->outFile = NULL; - } - return; -} - - -ppFringeData *ppFringeDataAlloc(void) -{ - ppFringeData *data = psAlloc(sizeof(ppFringeData)); // Newly allocated data - psMemSetDeallocator(data, (psFreeFunc)fringeDataFree); - - data->inName = NULL; - data->outName = NULL; - data->numPoints = 0; - data->xWidth = 0; - data->yWidth = 0; - data->xSmooth = 0; - data->ySmooth = 0; - data->maskVal = 0; - - data->inFile = NULL; - data->outFile = NULL; - data->inFPA = NULL; - - return data; -} - - Index: unk/ppFringe/src/ppFringeData.h =================================================================== --- /trunk/ppFringe/src/ppFringeData.h (revision 10003) +++ (revision ) @@ -1,24 +1,0 @@ -#ifndef PP_FRINGE_DATA_H -#define PP_FRINGE_DATA_H - -#include -#include - -typedef struct { - // Options - const char *inName; // Input FITS image file - const char *outName; // Output FITS table file - int numPoints; // Number of fringe points - int xWidth, yWidth; // Width of fringe points in x and y - int xSmooth, ySmooth; // Large-scale smoothing in x and y - psMaskType maskVal; // Mask value - // Data - psFits *inFile; // Input file handle - psFits *outFile; // Output file handle - pmFPA *inFPA; // Input FPA -} ppFringeData; - -// Allocator -ppFringeData *ppFringeDataAlloc(void); - -#endif Index: unk/ppFringe/src/ppFringeLoop.c =================================================================== --- /trunk/ppFringe/src/ppFringeLoop.c (revision 10003) +++ (revision ) @@ -1,172 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include -#include -#include -#include - -#include "ppFringe.h" - -void ppFringeLoop(ppFringeData *data, // The data - const pmConfig *config// Configuration - ) -{ - psRandom *rng = NULL; // Random number generator - - // Set up output header - const char *detId = psMetadataLookupStr(NULL, config->arguments, "-detid"); // Detector ID, for header - const char *classId = psMetadataLookupStr(NULL, config->arguments, "-classid"); // Class ID, for header - psMetadata *outHeader = psMetadataAlloc(); // Header for output - if (detId && strlen(detId) > 0) { - psMetadataAddStr(outHeader, PS_LIST_TAIL, "DETID", 0, "Detector ID for this image.", detId); - } - if (classId && strlen(classId) > 0) { - psMetadataAddStr(outHeader, PS_LIST_TAIL, "CLASSID", 0, "Class ID for this image.", classId); - } - - // Get table of contents for the output FITS file - // XXX what is the EXTNAME?? - psMetadata *contents = psFitsReadHeaderSet(NULL, data->outFile); - if (!contents || contents->list->n == 0) { - psFitsWriteBlank(data->outFile, NULL, ""); - } - - // Iterate through the FPA - pmFPA *fpa = data->inFPA; // The FPA of interest - psArray *chips = fpa->chips; // Array of component chips - for (long i = 0; i < chips->n; i++) { - pmChip *chip = chips->data[i]; // The chip of interest - if (!chip) { - continue; - } - const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); // Name of chip - psArray *cells = chip->cells; // Array of component cells - for (long j = 0; j < cells->n; j++) { - pmCell *cell = cells->data[j]; // The cell of interest - if (!cell) { - continue; - } - const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); // Name of cell - - if (!pmCellRead(cell, data->inFile, config->database)) { - psLogMsg(__func__, PS_LOG_WARN, "Unable to read chip %s cell %s\n", chipName, cellName); - pmCellFreeData(cell); - continue; - } - - psArray *readouts = cell->readouts; // Array of component readouts - if (readouts->n == 0) { - pmCellFreeData(cell); - continue; - } - if (readouts->n > 1) { - psLogMsg(__func__, PS_LOG_WARN, "Multiple readouts (%ld) present in chip %s cell %s --- " - "using only the first.\n", readouts->n, chipName, cellName); - } - pmReadout *readout = readouts->data[0]; // The readout of interest - if (!readout->image) { - psLogMsg(__func__, PS_LOG_WARN, "No image associated with readout in chip %s cell %s --- " - "ignored.\n", chipName, cellName); - pmCellFreeData(cell); - continue; - } - - // Look for this chip/cell in the output file - pmFringeRegions *regions = NULL; // Points at which to measure fringes - bool preDefined = false; // Are the regions defined in the output file? - psString extname = NULL; - psStringAppend(&extname, "%s_%s", chipName, cellName); - if (contents && contents->list->n > 0) { - bool mdok; // Status of MD lookup - psMetadata *header = psMetadataLookupMetadata(&mdok, contents, extname); // Header - if (mdok && header) { - regions = pmFringeRegionsReadFits(NULL, data->outFile, extname); - if (regions) { - preDefined = true; - } else { - psLogMsg(__func__, PS_LOG_WARN, "Unable to read fringe regions for chip %s cell %s " - " --- will generate new regions.\n", chipName, cellName); - } - } - } - - // Otherwise, generate one ourselves - if (!regions) { - if (!rng) { - rng = psRandomAlloc(PS_RANDOM_TAUS, 0); - } - // Create points to measure fringes - regions = pmFringeRegionsAlloc(data->numPoints, data->xWidth, data->yWidth, - data->xSmooth, data->ySmooth); - if (!pmFringeRegionsCreatePoints(regions, readout->image, rng)) { - psLogMsg(__func__, PS_LOG_WARN, "Unable to create fringe regions for chip %s cell %s --- " - "ignored.\n", chipName, cellName); - psFree(extname); - psFree(regions); - pmCellFreeData(cell); - continue; - } - } - - // Measure fringes - pmFringeStats *fringeStats = pmFringeStatsMeasure(regions, readout, data->maskVal); - psFree(regions); // Drop reference - if (!fringeStats) { - psLogMsg(__func__, PS_LOG_WARN, "Unable to measure fringes for chip %s cell %s --- " - "ignored.\n", chipName, cellName); - pmCellFreeData(cell); - continue; - } - - // Write fringe regions - if (!preDefined && - !pmFringeRegionsWriteFits(data->outFile, NULL, fringeStats->regions, extname)) { - psLogMsg(__func__, PS_LOG_WARN, "Unable to write fringe regions for chip %s cell %s --- " - "ignored.\n", chipName, cellName); - psFree(fringeStats); - psFree(extname); - pmCellFreeData(cell); - continue; - } - - int version = 0; // Version number - if (preDefined) { - // Find the lowest possible version number that isn't already taken - psMetadata *header = NULL; // Header from the table of contents - bool mdok = true; // Status of MD lookup - do { - version++; - psString checkName = NULL; // Extension name to check - psStringAppend(&checkName, "%s:%d", extname, version); - header = psMetadataLookupMetadata(&mdok, contents, checkName); - psFree(checkName); - } while (mdok && header); - } - - // Write fringe measurements - psStringAppend(&extname, ":%d", version); - if (!pmFringeStatsWriteFits(data->outFile, outHeader, fringeStats, extname)) { - psLogMsg(__func__, PS_LOG_WARN, "Unable to write fringe measurements for chip %s cell %s --- " - "ignored.\n", chipName, cellName); - psFree(fringeStats); - psFree(extname); - pmCellFreeData(cell); - continue; - } - - psFree(fringeStats); - psFree(extname); - pmCellFreeData(cell); - } - pmChipFreeData(chip); - } - pmFPAFreeData(fpa); - - psFree(rng); - psFree(contents); - psFree(outHeader); - - return; -} Index: unk/ppFringe/src/ppFringeSetup.c =================================================================== --- /trunk/ppFringe/src/ppFringeSetup.c (revision 10003) +++ (revision ) @@ -1,120 +1,0 @@ -#ifdef HAVE_CONFIG_H -#include -#endif - -#include -#include -#include -#include - -#include "ppFringe.h" - -// Print usage information and die -static void usageAndDie(pmConfig *config // Configuration (contains the arguments list) - ) -{ - printf("Generate fringe points for a FITS image file.\n\n" - "Usage:\n" - "\t%s INPUT.fits OUTPUT.fits\n" - "\n", config->argv[0]); - psArgumentHelp(config->arguments); - psFree(config); - psLibFinalize(); - pmConceptsDone(); - pmConfigDone(); - exit(EXIT_FAILURE); -} - -ppFringeData *ppFringeSetup(pmConfig *config // Configuration - ) -{ - // Setup and parse command-line arguments - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-detid", 0, "Detrend identifier", NULL); - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-classid", 0, "Class identifier", NULL); - - if (*config->argc == 1) { - // No command-line arguments: print the help - usageAndDie(config); - } - if (!psArgumentParse(config->arguments, config->argc, config->argv) || *config->argc < 2) { - printf("Unable to parse command-line arguments.\n\n"); - usageAndDie(config); - } - - ppFringeData *data = ppFringeDataAlloc(); // The data - data->inName = config->argv[1]; - data->outName = config->argv[2]; - - // Open the input file, determine the camera - data->inFile = psFitsOpen(data->inName, "r"); - if (!data->inFile) { - psError(PS_ERR_IO, false, "Unable to open input file %s\n", data->inName); - goto die; - } - psMetadata *header = psFitsReadHeader(NULL, data->inFile); // The FITS (primary) header - psMetadata *format = pmConfigCameraFormatFromHeader(config, header); - if (!format) { - psError(PS_ERR_UNKNOWN, false, "Unable to determine camera format for %s\n", data->inName); - psFree(header); - goto die; - } - data->inFPA = pmFPAConstruct(config->camera); - if (!data->inFPA) { - psError(PS_ERR_UNKNOWN, false, "Unable to construct FPA for %s\n", data->inName); - psFree(header); - psFree(format); - goto die; - } - pmFPAview *view = pmFPAAddSourceFromHeader(data->inFPA, header, format); - psFree(header); - psFree(format); - if (!view) { - psError(PS_ERR_UNKNOWN, false, "Unable to add input file %s to FPA.\n", data->inName); - goto die; - } - psFree(view); - - // Now we have a camera format, we can read the recipe - bool mdok; // Status of MD lookup - psMetadata *recipe = psMetadataLookupMetadata(&mdok, config->recipes, RECIPE); // The recipe - if (!recipe) { - psError(PS_ERR_IO, true, "Unable to find recipe %s.\n", RECIPE); - goto die; - } - - #define READ_RECIPE_ITEM(NAME, RECIPE, TARGET, TYPE) \ - { \ - bool mdok; \ - TARGET = psMetadataLookup##TYPE(&mdok, RECIPE, NAME); \ - if (!mdok || TARGET <= 0) { \ - psError(PS_ERR_BAD_PARAMETER_VALUE, true, "%s in the recipe is not valid: %d.\n", NAME, \ - TARGET); \ - goto die; \ - } \ - } - - READ_RECIPE_ITEM("NUMPOINTS", recipe, data->numPoints, S32); - READ_RECIPE_ITEM("XWIDTH", recipe, data->xWidth, S32); - READ_RECIPE_ITEM("YWIDTH", recipe, data->yWidth, S32); - READ_RECIPE_ITEM("XSMOOTH", recipe, data->xSmooth, S32); - READ_RECIPE_ITEM("YSMOOTH", recipe, data->ySmooth, S32); - READ_RECIPE_ITEM("MASKVAL", recipe, data->maskVal, U8); - - // Open the output file - data->outFile = psFitsOpen(data->outName, "a+"); - if (!data->outFile) { - psError(PS_ERR_IO, false, "Unable to open output file %s\n", data->outName); - goto die; - } - - return data; - - // Common path for error conditions: clean up and exit. -die: - psFree(config); - psFree(data); - pmConceptsDone(); - pmConfigDone(); - psLibFinalize(); - exit(EXIT_FAILURE); -} Index: unk/ppFringe/src/ppFringeSetup.h =================================================================== --- /trunk/ppFringe/src/ppFringeSetup.h (revision 10003) +++ (revision ) @@ -1,5 +1,0 @@ -#ifndef PP_FRINGE_SETUP_H -#define PP_FRINGE_SETUP_H - - -#endif