Index: trunk/ppNoiseMap/src/ppNoiseMap.h =================================================================== --- trunk/ppNoiseMap/src/ppNoiseMap.h (revision 24453) +++ trunk/ppNoiseMap/src/ppNoiseMap.h (revision 24458) @@ -12,236 +12,37 @@ #include "pslib.h" #include "psmodules.h" -#include "psphot.h" -#include "psastro.h" -#include "ppStats.h" -#define RECIPE_NAME "PPNOISEMAP" // Name of the recipe to use -#define TIMER_TOTAL "PPNOISE.TOTAL" // Name of timer for total time -#define TIMER_DETREND "PPNOISE.DETREND" // Name of timer for detrend time -#define TIMER_PHOT "PPNOISE.PHOT" // Name of timer for photometry time +#define RECIPE_NAME "PPNOISEMAP" // Name of the recipe to use +#define TIMER_TOTAL "PPNOISEMAP.TOTAL" // Name of timer for total time -// Options for ppImage processing -typedef struct { - // actions which ppImage should perform - bool doMaskBuild; // Build internal mask - bool doVarianceBuild; // Build internal variance map - bool doMask; // Mask bad pixels - bool doNonLin; // Non-linearity correction - bool doOverscan; // Overscan subtraction - bool doBias; // Bias subtraction - bool doDark; // Dark subtraction - bool doRemnance; // Remnance masking - bool doShutter; // Shutter correction - bool doFlat; // Flat-field normalisation - bool doFringe; // Fringe subtraction - bool doPhotom; // Source identification and photometry - bool doBG; // Background subtraction - bool doAstromChip; // per-chip Astrometry - bool doAstromMosaic; // full-mosaic Astrometry - bool doStats; // call ppStats on the image - bool checkCTE; // measure pixel-based variance +/// Get the configuration +pmConfig *ppNoiseMapArguments(int argc, char **argv); - // output files requested - bool BaseFITS; - bool BaseMaskFITS; - bool BaseVarianceFITS; +/// Determine what type of camera, and initialise +bool ppNoiseMapParseCamera(pmConfig *config); - bool ChipFITS; - bool ChipMaskFITS; - bool ChipVarianceFITS; +/// Loop over the input +bool ppNoiseMapLoop(pmConfig *config); - bool FPA1FITS; - bool FPA2FITS; - bool Bin1FITS; - bool Bin1JPEG; - bool Bin2FITS; - bool Bin2JPEG; +/// free memory, check for leaks +void ppNoiseMapCleanup (pmConfig *config); - // make values for abstract concepts of masking - psImageMaskType maskValue; // apply this bit-mask to choose masked bits - psImageMaskType markValue; // apply this bit-mask to choose masked bits - psImageMaskType satMask; // Mask value to give saturated pixels - psImageMaskType badMask; // Mask value to give bad pixels - psImageMaskType flatMask; // Mask value to give bad flat pixels - psImageMaskType blankMask; // Mask value to give blank pixels - - // non-linear correction parameters - psDataType nonLinearType; - psMetadataItem *nonLinearData; - void *nonLinearSource; - - // options for the analysis - pmOverscanOptions *overscan; // Overscan options - - // binning parameters - int xBin1; // x-binning, scale 1 - int yBin1; // y-binning, scale 1 - int xBin2; // x-binning, scale 2 - int yBin2; // y-binning, scale 2 - - // parameters used by the fringe analysis - float fringeRej; // Fringe rejection limit - int fringeIter; // Fringe iterations - float fringeKeep; // Fringe keep fraction - - int remnanceSize; // Size for remnance detection - float remnanceThresh; // Threshold for remnance detection - - char *normClass; // class to use for per-class normalization -} ppImageOptions; - -// Cells to be used in the detrend -typedef struct { - pmCell *input; // The input cell, to be operated upon - pmCell *mask; // The bad pixel mask - pmCell *bias; // The bias correction - pmCell *dark; // The dark correction - pmCell *flat; // The flat-field correction -} ppImageDetrend; - -ppImageOptions *ppImageOptionsAlloc(void); - -// Determine the processing options -ppImageOptions *ppImageOptionsParse(pmConfig *config); - -// Get the configuration -pmConfig *ppImageArguments(int argc, char **argv); - -// Determine what type of camera, and initialise -ppImageOptions *ppImageParseCamera(pmConfig *config); -bool ppImageSetMaskBits (pmConfig *config, ppImageOptions *options); - -// Loop over the input -bool ppImageLoop(pmConfig *config, ppImageOptions *options); - -// free memory, check for leaks -void ppImageCleanup (pmConfig *config, ppImageOptions *options); - -// perform the detrend analysis on the current readout -bool ppImageDetrendReadout (pmConfig *config, ppImageOptions *options, pmFPAview *view); - -bool ppImageDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, ppImageOptions *options); - -bool ppImageDetrendNonLinear(pmReadout *input, ppImageOptions *options); -bool ppImageDetrendNonLinearLookup(pmReadout *input, psMetadataItem *dataItem); -bool ppImageDetrendNonLinearPolynomial(pmReadout *input, psMetadataItem *dataItem); - -bool ppImageDetrendCell(ppImageDetrend *detrend, ppImageOptions *options, pmConfig *config); -bool ppImageDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, ppImageOptions *options); -pmReadout* ppImageDetrendSelectFirst(pmCell *cell, char *name, bool doThis); - -bool ppImageDetrendFree(pmConfig *config, pmFPAview *view); -bool ppImageFringeFree(pmConfig *config, pmFPAview *view); - -bool ppImageCheckCTE(pmConfig *config, ppImageOptions *options, pmFPAview *view); - -// Record which detrend file was used for the detrending -bool ppImageDetrendRecord( - pmCell *cell, // Cell of interest - const pmConfig *config, // Configuration - const ppImageOptions *options, // Processing options - const pmFPAview *view // View to cell - ); - -bool ppImageRebinChip (pmConfig *config, pmFPAview *view, ppImageOptions *options, char *outName); - -bool ppImagePhotom (pmConfig *config, pmFPAview *view); -bool ppImageAstrom (pmConfig *config); -bool ppImageAddstar (pmConfig *config); - -// Subtract background from the chip-mosaicked image -bool ppImageSubtractBackground( - pmConfig *config, // Configuration - const pmFPAview *view, // View to chip of interest - const ppImageOptions *options // Processing options - ); - -bool ppImageMosaicChip (pmConfig *config, const ppImageOptions *options, const pmFPAview *view, - const char *outFile, const char *inFile); -bool ppImageMosaicFPA (pmConfig *config, const ppImageOptions *options, - const char *outFile, const char *inFile); - -bool ppImageSetMaskBits (pmConfig *config, ppImageOptions *options); - -void ppImageFileCheck (pmConfig *config); - -// functions used by ppFocus -pmConfig *ppFocusArguments(int argc, char **argv); -ppImageOptions *ppFocusParseCamera (pmConfig *config, int entry); -bool ppFocusGetFWHM (pmConfig *config, psVector *focus, psVector *fwhm); -bool ppFocusFitFWHM (pmConfig *config, psVector *focus, psVector *fwhm); - -void ppFocusDropCamera (pmConfig *config); - -bool ppImageDefineFile (pmConfig *config, pmFPA *input, char *filerule, char *argname, pmFPAfileType fileType, pmDetrendType detrendType); - -// write stats to output file -bool ppImageStatsOutput(pmConfig *config, // Configuration - psMetadata *stats, // Statistics output - const ppImageOptions *options // Options - ); - - -// Measure fringes -bool ppImageDetrendFringeMeasure(pmReadout *readout, // Readout to measure - pmCell *fringe, // Fringe cell (each readout is a different component) - const bool isResidual, - const ppImageOptions *options // Options - ); - -// Solve the fringe system -bool ppImageDetrendFringeSolve(pmChip *scienceChip, // Chip with science - const pmChip *refChip, // Chip with reference fringes - const bool isResidual, - const ppImageOptions *options // Options - ); - -// Generate fringe frame -bool ppImageDetrendFringeGenerate(pmCell *science, // Science cell - pmCell *fringes, // Fringe cell, one readout per fringe component - const ppImageOptions *options // Options - ); - - -bool ppImageDetrendFringeApply (pmConfig *config, // config - pmChip *chip, // science chip - const pmFPAview *inputView, // current view - const ppImageOptions *options // options - ); +/// define the input files +bool ppNoiseMapDefineFile (pmConfig *config, pmFPA *input, char *filerule, char *argname, pmFPAfileType fileType); /// Return short version information -psString ppImageVersion(void); +psString ppNoiseMapVersion(void); /// Return software source -psString ppImageSource(void); +psString ppNoiseMapSource(void); /// Return long version information -psString ppImageVersionLong(void); +psString ppNoiseMapVersionLong(void); /// Populate the header with version information for all dependencies -bool ppImageVersionHeader(psMetadata *metadata ///< Header to populate - ); +bool ppNoiseMapVersionHeader(psMetadata *header); /// Print version information -void ppImageVersionPrint(void); - - -// calculate stats, including MD5 -bool ppImagePixelStats(pmConfig *config,// Configuration - psMetadata *stats, // Statistics output - const ppImageOptions *options, // Options - const pmFPAview *inputView // View to data - ); - -// calculate stats from headers and concepts -bool ppImageMetadataStats(pmConfig *config, // Configuration - psMetadata *stats, // Statistics output - const ppImageOptions *options // Options - ); - -void ppImageFileCheck(pmConfig *config); - -/// Dump memory summary to text file -void ppImageMemoryDump(const char *description); +void ppNoiseMapVersionPrint(void); #endif