Index: /trunk/psModules/src/camera/Makefile.am =================================================================== --- /trunk/psModules/src/camera/Makefile.am (revision 24835) +++ /trunk/psModules/src/camera/Makefile.am (revision 24836) @@ -23,4 +23,5 @@ pmFPAfileIO.c \ pmFPAfileFitsIO.c \ + pmFPAfileFringeIO.c \ pmFPAFlags.c \ pmFPALevel.c \ @@ -51,4 +52,5 @@ pmFPAfileIO.h \ pmFPAfileFitsIO.h \ + pmFPAfileFringeIO.h \ pmFPAFlags.h \ pmFPALevel.h \ Index: /trunk/psModules/src/camera/pmFPAfileFringeIO.c =================================================================== --- /trunk/psModules/src/camera/pmFPAfileFringeIO.c (revision 24836) +++ /trunk/psModules/src/camera/pmFPAfileFringeIO.c (revision 24836) @@ -0,0 +1,238 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include +#include + +#include "pmConfig.h" +//#include "pmConfigMask.h" +//#include "pmDetrendDB.h" + +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmFPALevel.h" +//#include "pmFPARead.h" +//#include "pmFPAWrite.h" +//#include "pmFPAMaskWeight.h" +#include "pmFPAview.h" +#include "pmFPAfile.h" +#include "pmFPAfileFringeIO.h" +#include "pmFPAfileFitsIO.h" +//#include "pmFPACopy.h" +//#include "pmFPAConstruct.h" +//#include "pmConceptsWrite.h" +#include "pmFringeStats.h" + +# define FRINGE_TABLE "FRINGE.MEASUREMENTS" + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Reading Fringe data +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// given an already-opened fits file, read the table corresponding to the specified view +bool pmFPAviewReadFringes(const pmFPAview *view, pmFPAfile *file) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(file, false); + + pmFPA *fpa = file->fpa; // FPA of interest + psFits *fits = file->fits; // FITS file + + if (view->chip == -1) { + return pmFPAReadFringes(fpa, fits) > 0; + } + + if (view->cell == -1) { + pmChip *chip = pmFPAviewThisChip(view, fpa); // Chip of interest + return pmChipReadFringes(chip, fits) > 0; + } + + pmCell *cell = pmFPAviewThisCell(view, fpa); // Cell of interest + return pmCellReadFringes(cell, fits) > 0; +} + +int pmFPAReadFringes(pmFPA *fpa, psFits *fits) +{ + PS_ASSERT_PTR_NON_NULL(fpa, 0); + PS_ASSERT_FITS_NON_NULL(fits, 0); + + int numRead = 0; // Number of reads + psArray *chips = fpa->chips; // Array of chips + for (int i = 0; i < chips->n; i++) { + pmChip *chip = chips->data[i]; // Chip of interest + numRead += pmChipReadFringes(chip, fits); + } + + return numRead; +} + +int pmChipReadFringes(pmChip *chip, psFits *fits) +{ + PS_ASSERT_PTR_NON_NULL(chip, 0); + PS_ASSERT_FITS_NON_NULL(fits, 0); + + int numRead = 0; // Number of reads + psArray *cells = chip->cells; // Array of cells + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; // Cell of interest + numRead += pmCellReadFringes(cell, fits); + } + + return numRead; +} + +int pmCellReadFringes(pmCell *cell, psFits *fits) +{ + PS_ASSERT_PTR_NON_NULL(cell, 0); + PS_ASSERT_FITS_NON_NULL(fits, 0); + + const char *chipName = psMetadataLookupStr(NULL, cell->parent->concepts, "CHIP.NAME"); // Name of chip + const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); // Name of cell + + // Fringe Table Extension name + psString extname = NULL; + psStringAppend(&extname, "FRINGE_%s_%s", chipName, cellName); + + if (!psFitsMoveExtName(fits, extname)) { + psError(PS_ERR_IO, false, "Unable to move to extension %s\n", extname); + psFree(extname); + return 0; + } + + psMetadata *header = psFitsReadHeader(NULL, fits); // The FITS header + if (!header) { + psError(PS_ERR_IO, false, "Unable to read header for extension %s\n", extname); + psFree(extname); + psFree(header); + return 0; + } + + psArray *table = psFitsReadTable(fits); // The table + if (!table) { + psError(PS_ERR_UNKNOWN, false, "Unable to add read the fringe table data from the file"); + psFree (header); + psFree (extname); + return 0; + } + + psArray *fringes = pmFringesParseTable(table, header); + psFree(table); + psFree(header); + + if (!fringes) { + psError(PS_ERR_UNKNOWN, false, "Unable to add parse the fringe table data"); + psFree(extname); + return 0; + } + + if (!psMetadataAdd(cell->analysis, PS_LIST_TAIL, FRINGE_TABLE, PS_DATA_ARRAY, "Fringes", fringes)) { + psError(PS_ERR_UNKNOWN, false, "Unable to add fringe from extension %s to analysis metadata " + "for chip %s, cell %s\n", extname, chipName, cellName); + psFree(fringes); + psFree(extname); + return 0; + } + + psFree(fringes); // drop local reference + psFree(extname); + + return 1; +} + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// Writing fringe data +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +// given an already-opened fits file, write the table corresponding to the specified view +bool pmFPAviewWriteFringes(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(config, false); + + pmFPA *fpa = pmFPAfileSuitableFPA(file, view, config, false); // FPA of interest + psFits *fits = file->fits; // FITS file + + if (view->chip == -1) { + return pmFPAWriteFringes(fits, fpa) > 0; + } + + if (view->cell == -1) { + pmChip *chip = pmFPAviewThisChip(view, fpa); // Chip of interest + return pmChipWriteFringes(fits, chip) > 0; + } + + pmCell *cell = pmFPAviewThisCell(view, fpa); // Cell of interest + return pmCellWriteFringes(fits, cell) > 0; +} + +int pmFPAWriteFringes(psFits *fits, const pmFPA *fpa) +{ + PS_ASSERT_PTR_NON_NULL(fpa, 0); + PS_ASSERT_PTR_NON_NULL(fits, 0); + + int numWrite = 0; // Number of reads + psArray *chips = fpa->chips; // Array of chips + for (int i = 0; i < chips->n; i++) { + pmChip *chip = chips->data[i]; // Chip of interest + numWrite += pmChipWriteFringes(fits, chip); + } + + return numWrite; +} + +int pmChipWriteFringes(psFits *fits, const pmChip *chip) +{ + PS_ASSERT_PTR_NON_NULL(chip, 0); + PS_ASSERT_PTR_NON_NULL(fits, 0); + + int numWrite = 0; // Number of reads + psArray *cells = chip->cells; // Array of cells + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; // Cell of interest + numWrite += pmCellWriteFringes(fits, cell); + } + + return numWrite; +} + +int pmCellWriteFringes(psFits *fits, const pmCell *cell) +{ + PS_ASSERT_PTR_NON_NULL(cell, 0); + PS_ASSERT_PTR_NON_NULL(fits, 0); + + const char *chipName = psMetadataLookupStr(NULL, cell->parent->concepts, "CHIP.NAME"); // Name of chip + const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); // Name of cell + + psArray *fringes = psMetadataLookupPtr(NULL, cell->analysis, FRINGE_TABLE); // The FITS table + if (!fringes) { + // We wrote everything we could find + return 0; + } + + psMetadata *header = psMetadataAlloc(); + psArray *table = pmFringesFormatTable(header, fringes); + if (!table) { + // We wrote everything we could find + psFree(header); + return 0; + } + + psString extname = NULL; // Extension name + psStringAppend(&extname, "FRINGE_%s_%s", chipName, cellName); + + if (!psFitsWriteTable(fits, header, table, extname)) { + psError(PS_ERR_UNKNOWN, false, "Unable to write table from chip %s, cell %s to extension %s\n", + chipName, cellName, extname); + psFree(extname); + psFree(header); + return 0; + } + + psFree(extname); + psFree(header); + return 1; +} + + Index: /trunk/psModules/src/camera/pmFPAfileFringeIO.h =================================================================== --- /trunk/psModules/src/camera/pmFPAfileFringeIO.h (revision 24836) +++ /trunk/psModules/src/camera/pmFPAfileFringeIO.h (revision 24836) @@ -0,0 +1,30 @@ +/* @file pmFPAfileFringeIO.h + * @brief Read & Write Fringe tables + * + * @author EAM, IfA + * @author PAP, IfA + * + * @version $Revision: 1.16 $ + * @date $Date: 2009-02-06 02:31:24 $ + * Copyright 2004-2005 Institute for Astronomy, University of Hawaii + */ + +#ifndef PM_FPA_FILE_FRINGE_IO_H +#define PM_FPA_FILE_FRINGE_IO_H + +/// @addtogroup Camera Camera Layout +/// @{ + +/// Read an fringes into the current view +bool pmFPAviewReadFringes(const pmFPAview *view, pmFPAfile *file); +int pmFPAReadFringes(pmFPA *fpa, psFits *fits); +int pmChipReadFringes(pmChip *chip, psFits *fits); +int pmCellReadFringes(pmCell *cell, psFits *fits); +bool pmFPAviewWriteFringes(const pmFPAview *view, pmFPAfile *file, pmConfig *config); +int pmFPAWriteFringes(psFits *fits, const pmFPA *fpa); +int pmChipWriteFringes(psFits *fits, const pmChip *chip); +int pmCellWriteFringes(psFits *fits, const pmCell *cell); + +/// @} + +# endif Index: /trunk/psModules/src/camera/pmFPAfileIO.c =================================================================== --- /trunk/psModules/src/camera/pmFPAfileIO.c (revision 24835) +++ /trunk/psModules/src/camera/pmFPAfileIO.c (revision 24836) @@ -23,4 +23,5 @@ #include "pmFPAWrite.h" #include "pmFPAfileFitsIO.h" +#include "pmFPAfileFringeIO.h" #include "pmSpan.h" #include "pmFootprint.h" @@ -192,5 +193,5 @@ status = pmFPAviewReadFitsImage(view, file, config); if (status) { - if (!pmFPAviewReadFitsTable(view, file, "FRINGE")) { + if (!pmFPAviewReadFringes(view, file)) { psError(PS_ERR_UNKNOWN, false, "Unable to read fringe data from %s.\n", file->filename); return false; @@ -451,5 +452,5 @@ status = pmFPAviewWriteFitsImage (view, file, config); if (status) { - if (!pmFPAviewWriteFitsTable(view, file, "FRINGE", config)) { + if (!pmFPAviewWriteFringes(view, file, config)) { psError(PS_ERR_UNKNOWN, false, "Unable to write fringe data from %s.\n", file->filename); return false; Index: /trunk/psModules/src/detrend/pmFringeStats.c =================================================================== --- /trunk/psModules/src/detrend/pmFringeStats.c (revision 24835) +++ /trunk/psModules/src/detrend/pmFringeStats.c (revision 24836) @@ -464,4 +464,8 @@ for (long i = 0; i < fringes->n; i++) { pmFringeStats *fringe = fringes->data[i]; // The fringe of interest + if (!fringe) { + psWarning ("skipping empty fringe stats for entry %ld -- video cell?\n", i); + continue; + } pmFringeRegions *regions = fringe->regions; // The fringe regions if (numPoints == 0) { @@ -496,4 +500,8 @@ for (long i = 0; i < fringes->n; i++) { pmFringeStats *fringe = fringes->data[i]; // The fringe of interest + if (!fringe) { + psWarning ("skipping empty fringe stats for entry %ld -- video cell?\n", i); + continue; + } pmFringeRegions *regions = fringe->regions; // The fringe regions // Copy the data over @@ -520,7 +528,7 @@ ////////////////////////////////////////////////////////////////////////////////////////////////////////////// -bool pmFringesFormat(pmCell *cell, psMetadata *header, const psArray *fringes) -{ - PS_ASSERT_PTR_NON_NULL(cell, false); +psArray *pmFringesFormatTable(psMetadata *header, const psArray *fringes) +{ + PS_ASSERT_PTR_NON_NULL(header, false); PS_ASSERT_ARRAY_NON_NULL(fringes, false); @@ -531,5 +539,5 @@ if (stats->regions != regions) { psError(PS_ERR_BAD_PARAMETER_VALUE, true, "Regions for fringe statistics are not identical.\n"); - return false; + return NULL; } } @@ -557,20 +565,8 @@ // Vectors: x, y, mask, f, df - psMetadata *scalars = psMemIncrRefCounter(header); // Metadata to hold the scalars; will be the header - if (!scalars) { - scalars = psMetadataAlloc(); - } - psMetadataAddS32(scalars, PS_LIST_TAIL, "PSFRNGDX", PS_META_REPLACE, "Median box half-width", - regions->dX); - psMetadataAddS32(scalars, PS_LIST_TAIL, "PSFRNGDY", PS_META_REPLACE, "Median box half-height", - regions->dY); - psMetadataAddS32(scalars, PS_LIST_TAIL, "PSFRNGNX", PS_META_REPLACE, "Large-scale smoothing in x", - regions->nX); - psMetadataAddS32(scalars, PS_LIST_TAIL, "PSFRNGNY", PS_META_REPLACE, "Large-scale smoothing in y", - regions->nY); - psMetadataAdd(cell->analysis, PS_LIST_TAIL, "FRINGE.HEADER", PS_DATA_METADATA, - "Header for fringe data", scalars); - psFree(scalars); - + psMetadataAddS32(header, PS_LIST_TAIL, "PSFRNGDX", PS_META_REPLACE, "Median box half-width", regions->dX); + psMetadataAddS32(header, PS_LIST_TAIL, "PSFRNGDY", PS_META_REPLACE, "Median box half-height", regions->dY); + psMetadataAddS32(header, PS_LIST_TAIL, "PSFRNGNX", PS_META_REPLACE, "Large-scale smoothing in x", regions->nX); + psMetadataAddS32(header, PS_LIST_TAIL, "PSFRNGNY", PS_META_REPLACE, "Large-scale smoothing in y", regions->nY); psArray *table = psArrayAlloc(numRows); // The table @@ -605,27 +601,13 @@ } - psMetadataAdd(cell->analysis, PS_LIST_TAIL, "FRINGE", PS_DATA_ARRAY, "Fringe data", table); - - return true; -} - - -psArray *pmFringesParse(pmCell *cell) -{ - PS_ASSERT_PTR_NON_NULL(cell, NULL); + return table; +} + +psArray *pmFringesParseTable(psArray *table, psMetadata *header) +{ + PS_ASSERT_PTR_NON_NULL(table, NULL); + PS_ASSERT_PTR_NON_NULL(header, NULL); bool mdok; // Status of MD lookup - psMetadata *header = psMetadataLookupMetadata(&mdok, cell->analysis, "FRINGE.HEADER"); // Header - if (!mdok || !header) { - psError(PS_ERR_UNKNOWN, false, "Unable to find header for fringe data.\n"); - return NULL; - } - - psArray *table = psMetadataLookupPtr(NULL, cell->analysis, "FRINGE"); // FITS table - if (!table) { - psError(PS_ERR_UNKNOWN, false, "Unable to find table for fringe data.\n"); - return NULL; - } - // Read the scalars from the header @@ -722,4 +704,55 @@ } +bool pmFringesFormat(pmCell *cell, psMetadata *inHeader, const psArray *fringes) +{ + PS_ASSERT_PTR_NON_NULL(cell, false); + PS_ASSERT_ARRAY_NON_NULL(fringes, false); + + psMetadata *header = psMemIncrRefCounter(inHeader); // Metadata to hold the scalars; will be the header + if (!inHeader) { + inHeader = psMetadataAlloc(); + } + + psArray *table = pmFringesFormatTable(header, fringes); + if (!table) { + psError (PS_ERR_UNKNOWN, false, "unable to generate table from fringes"); + psFree(header); + return NULL; + } + + psMetadataAdd(cell->analysis, PS_LIST_TAIL, "FRINGE.HEADER", PS_DATA_METADATA, "Header for fringe data", header); + psFree(header); + + psMetadataAdd(cell->analysis, PS_LIST_TAIL, "FRINGE.TABLE", PS_DATA_ARRAY, "Fringe data", table); + psFree(table); + + return true; +} + +psArray *pmFringesParse(pmCell *cell) +{ + PS_ASSERT_PTR_NON_NULL(cell, NULL); + + bool mdok; // Status of MD lookup + psMetadata *header = psMetadataLookupMetadata(&mdok, cell->analysis, "FRINGE.HEADER"); // Header + if (!mdok || !header) { + psError(PS_ERR_UNKNOWN, false, "Unable to find header for fringe data.\n"); + return NULL; + } + + psArray *table = psMetadataLookupPtr(NULL, cell->analysis, "FRINGE.TABLE"); // FITS table + if (!table) { + psError(PS_ERR_UNKNOWN, false, "Unable to find table for fringe data.\n"); + return NULL; + } + + psArray *fringes = pmFringesParseTable(table, header); + if (!fringes) { + psError(PS_ERR_UNKNOWN, false, "Unable to add parse the fringe table data"); + return NULL; + } + + return fringes; +} ////////////////////////////////////////////////////////////////////////////////////////////////////////////// Index: /trunk/psModules/src/detrend/pmFringeStats.h =================================================================== --- /trunk/psModules/src/detrend/pmFringeStats.h (revision 24835) +++ /trunk/psModules/src/detrend/pmFringeStats.h (revision 24836) @@ -142,11 +142,27 @@ ////////////////////////////////////////////////////////////////////////////////////////////////////////////// -/// Write an array of fringes measurements to a FITS table. -/// -/// Writes an array of fringe measurements for a cell as a FITS table in the analysis metadata. The array of -/// fringe statistics must all use the same fringe regions (or there is no point in storing them all -/// together). The header is supplemented with scalar values dX, dY, nX and nY (as PSFRNGDX, PSFRNGDY, -/// PSFRNGNX, PSFRNGNY) from the fringe regions, while the fringe coordinates and mask are written as a FITS -/// table (as x, y, mask, f, df; f and df are vectors). +/// Convert an array of fringes measurements to a psArray suitable for writing as a FITS table. +/// +/// Converts an array of fringe measurements for a cell into the corresponding rows of a FITS +/// table (array of psMetadata). The array of fringe statistics must all use the same fringe +/// regions (or there is no point in storing them all together). The header is supplemented +/// with scalar values dX, dY, nX and nY (as PSFRNGDX, PSFRNGDY, PSFRNGNX, PSFRNGNY) from the +/// fringe regions, while the fringe coordinates and mask are written as a FITS table rows (as +/// x, y, mask, f, df; f and df are vectors). Use psFitsTableWrite to save the resulting rows +/// to disk. +psArray *pmFringesFormatTable(psMetadata *header, const psArray *fringes); + + +/// Parses an array of fringes measurements from a FITS table. +/// +/// The fringes for the cell are read from the FITS table (array of psMetadata rows). The +/// table provides the region and the (possibly multiple) fringe statistics for that region. +/// The supplied header defines the scalar values dX, dY, nX and nY (as PSFRNGDX, PSFRNGDY, +/// PSFRNGNX, PSFRNGNY) +psArray *pmFringesParseTable(psArray *table, psMetadata *header); + +/// Deprecated Function: converts the fringes to a FITS table (array of psMetadata) and saves +/// them on the cell->analysis; scalar values are dX, dY, nX and nY are written to the header +/// (as PSFRNGDX, PSFRNGDY, PSFRNGNX, PSFRNGNY) bool pmFringesFormat(pmCell *cell, ///< Cell for which to write psMetadata *header, ///< Header, or NULL @@ -154,12 +170,8 @@ ); -/// Parses an array of fringes measurements from a FITS table. -/// -/// The fringes for the cell are read from the FITS table in the analysis metadata. The table provides the -/// region and the (possibly multiple) fringe statistics for that region. The current extension is used if -/// the extension name is not provided. +/// Deprecated Function: pulls a the header and FITS table (array of psMetadata) representing +/// the fringes from the cell->analysis and converts to fringe measurements psArray *pmFringesParse(pmCell *cell ///< Cell for which to read fringes ); - ////////////////////////////////////////////////////////////////////////////////////////////////////////////// Index: /trunk/psModules/src/psmodules.h =================================================================== --- /trunk/psModules/src/psmodules.h (revision 24835) +++ /trunk/psModules/src/psmodules.h (revision 24836) @@ -47,4 +47,5 @@ #include #include +#include #include #include