Index: /trunk/psModules/src/camera/pmFPAfile.c =================================================================== --- /trunk/psModules/src/camera/pmFPAfile.c (revision 16840) +++ /trunk/psModules/src/camera/pmFPAfile.c (revision 16841) @@ -435,4 +435,7 @@ if (!strcasecmp (type, "FRINGE")) { return PM_FPA_FILE_FRINGE; + } + if (!strcasecmp (type, "DARK")) { + return PM_FPA_FILE_DARK; } if (!strcasecmp (type, "HEADER")) { @@ -473,4 +476,6 @@ case PM_FPA_FILE_FRINGE: return ("FRINGE"); + case PM_FPA_FILE_DARK: + return("DARK"); case PM_FPA_FILE_HEADER: return ("HEADER"); Index: /trunk/psModules/src/camera/pmFPAfile.h =================================================================== --- /trunk/psModules/src/camera/pmFPAfile.h (revision 16840) +++ /trunk/psModules/src/camera/pmFPAfile.h (revision 16841) @@ -4,6 +4,6 @@ * @author EAM, IfA * - * @version $Revision: 1.28 $ $Name: not supported by cvs2svn $ - * @date $Date: 2008-02-07 23:45:56 $ + * @version $Revision: 1.29 $ $Name: not supported by cvs2svn $ + * @date $Date: 2008-03-06 20:47:50 $ * Copyright 2004-2005 Institute for Astronomy, University of Hawaii */ @@ -28,10 +28,11 @@ PM_FPA_FILE_RAW, PM_FPA_FILE_IMAGE, + PM_FPA_FILE_MASK, + PM_FPA_FILE_WEIGHT, + PM_FPA_FILE_FRINGE, + PM_FPA_FILE_DARK, PM_FPA_FILE_PSF, PM_FPA_FILE_JPEG, PM_FPA_FILE_KAPA, - PM_FPA_FILE_MASK, - PM_FPA_FILE_WEIGHT, - PM_FPA_FILE_FRINGE, PM_FPA_FILE_HEADER, PM_FPA_FILE_ASTROM, Index: /trunk/psModules/src/camera/pmFPAfileFitsIO.c =================================================================== --- /trunk/psModules/src/camera/pmFPAfileFitsIO.c (revision 16840) +++ /trunk/psModules/src/camera/pmFPAfileFitsIO.c (revision 16841) @@ -20,4 +20,5 @@ #include "pmFPACopy.h" #include "pmFPAConstruct.h" +#include "pmDark.h" pmFPA *pmFPAfileSuitableFPA(const pmFPAfile *file, const pmFPAview *view, const pmConfig *config) @@ -243,4 +244,11 @@ } +bool pmFPAviewReadFitsDark(const pmFPAview *view, pmFPAfile *file) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(file, false); + return fpaViewReadFitsImage(view, file, pmFPAReadDark, pmChipReadDark, pmCellReadDark); +} + bool pmFPAviewReadFitsHeaderSet(const pmFPAview *view, pmFPAfile *file) { @@ -337,4 +345,11 @@ PS_ASSERT_PTR_NON_NULL(file, false); return fpaViewWriteFitsImage(view, file, config, pmFPAWriteWeight, pmChipWriteWeight, pmCellWriteWeight); +} + +bool pmFPAviewWriteFitsDark(const pmFPAview *view, pmFPAfile *file, const pmConfig *config) +{ + PS_ASSERT_PTR_NON_NULL(view, false); + PS_ASSERT_PTR_NON_NULL(file, false); + return fpaViewWriteFitsImage(view, file, config, pmFPAWriteDark, pmChipWriteDark, pmCellWriteDark); } Index: /trunk/psModules/src/camera/pmFPAfileFitsIO.h =================================================================== --- /trunk/psModules/src/camera/pmFPAfileFitsIO.h (revision 16840) +++ /trunk/psModules/src/camera/pmFPAfileFitsIO.h (revision 16841) @@ -5,6 +5,6 @@ * @author PAP, IfA * - * @version $Revision: 1.9 $ $Name: not supported by cvs2svn $ - * @date $Date: 2007-07-14 03:19:01 $ + * @version $Revision: 1.10 $ $Name: not supported by cvs2svn $ + * @date $Date: 2008-03-06 20:47:50 $ * Copyright 2004-2005 Institute for Astronomy, University of Hawaii */ @@ -30,4 +30,9 @@ ); +/// Read a dark into the current view +bool pmFPAviewReadFitsDark(const pmFPAview *view, ///< View specifying level of interest + pmFPAfile *file ///< FPA file into which to read + ); + /// Read an image header into the current view bool pmFPAviewReadFitsHeaderSet(const pmFPAview *view, ///< View specifying level of interest @@ -52,4 +57,10 @@ const pmConfig *config ///< Configuration ); + +/// Write the dark for the specified view +bool pmFPAviewWriteFitsDark(const pmFPAview *view, ///< View specifying level of interest + pmFPAfile *file, ///< FPA file to write + const pmConfig *config ///< Configuration + ); /// Write a PHU for a fits image if needed Index: /trunk/psModules/src/camera/pmFPAfileIO.c =================================================================== --- /trunk/psModules/src/camera/pmFPAfileIO.c (revision 16840) +++ /trunk/psModules/src/camera/pmFPAfileIO.c (revision 16841) @@ -174,6 +174,9 @@ status = pmFPAviewReadFitsHeaderSet(view, file); break; + case PM_FPA_FILE_DARK: + status = pmFPAviewReadFitsDark(view, file); + break; case PM_FPA_FILE_FRINGE: - status = pmFPAviewReadFitsImage (view, file); + status = pmFPAviewReadFitsImage(view, file); if (status) { if (!pmFPAviewReadFitsTable(view, file, "FRINGE")) { @@ -247,8 +250,9 @@ switch (file->type) { - case PM_FPA_FILE_IMAGE: - case PM_FPA_FILE_MASK: - case PM_FPA_FILE_WEIGHT: - case PM_FPA_FILE_FRINGE: { + case PM_FPA_FILE_IMAGE: + case PM_FPA_FILE_MASK: + case PM_FPA_FILE_WEIGHT: + case PM_FPA_FILE_FRINGE: + case PM_FPA_FILE_DARK: { // create FPA structure component based on view psMetadata *format = file->format; // Camera format configuration @@ -397,4 +401,5 @@ fitsType |= (file->type == PM_FPA_FILE_HEADER); fitsType |= (file->type == PM_FPA_FILE_FRINGE); + fitsType |= (file->type == PM_FPA_FILE_DARK); fitsType |= (file->type == PM_FPA_FILE_CMP); fitsType |= (file->type == PM_FPA_FILE_CMF); @@ -451,4 +456,7 @@ case PM_FPA_FILE_HEADER: psAbort ("no HEADER write functions defined"); + break; + case PM_FPA_FILE_DARK: + status = pmFPAviewWriteFitsDark(view, file, config); break; case PM_FPA_FILE_FRINGE: @@ -532,4 +540,5 @@ case PM_FPA_FILE_HEADER: case PM_FPA_FILE_FRINGE: + case PM_FPA_FILE_DARK: case PM_FPA_FILE_CMF: case PM_FPA_FILE_PSF: @@ -593,4 +602,5 @@ case PM_FPA_FILE_HEADER: case PM_FPA_FILE_FRINGE: + case PM_FPA_FILE_DARK: status = pmFPAviewFreeData(view, file); break; @@ -736,4 +746,5 @@ case PM_FPA_FILE_HEADER: case PM_FPA_FILE_FRINGE: + case PM_FPA_FILE_DARK: case PM_FPA_FILE_CMF: case PM_FPA_FILE_PSF: @@ -882,4 +893,5 @@ case PM_FPA_FILE_MASK: case PM_FPA_FILE_WEIGHT: + case PM_FPA_FILE_DARK: case PM_FPA_FILE_FRINGE: status = pmFPAviewFitsWritePHU (view, file, config); Index: /trunk/psModules/src/detrend/Makefile.am =================================================================== --- /trunk/psModules/src/detrend/Makefile.am (revision 16840) +++ /trunk/psModules/src/detrend/Makefile.am (revision 16841) @@ -13,5 +13,6 @@ pmDetrendDB.c \ pmShutterCorrection.c \ - pmShifts.c + pmShifts.c \ + pmDark.c # pmSkySubtract.c @@ -27,5 +28,6 @@ pmDetrendDB.h \ pmShutterCorrection.h \ - pmShifts.h + pmShifts.h \ + pmDark.h # pmSkySubtract.h Index: /trunk/psModules/src/detrend/pmBias.c =================================================================== --- /trunk/psModules/src/detrend/pmBias.c (revision 16840) +++ /trunk/psModules/src/detrend/pmBias.c (revision 16841) @@ -113,4 +113,5 @@ } if (dark) { + psWarning("Dark processing is now available using pmDark --- perhaps you should use that instead?"); PS_ASSERT_PTR_NON_NULL(view, false); PS_ASSERT_IMAGE_NON_NULL(dark->image, false); @@ -121,5 +122,5 @@ if (!pmOverscanSubtract (in, overscanOpts)) { - return false; + return false; } @@ -148,16 +149,16 @@ } - float darkNorm = 1.0; + float darkNorm = 1.0; float inNorm = pmFPADarkNorm(in->parent->parent->parent, view, inTime); - // if we have a normalized dark exposure, we simply multiply the master by inNorm. if - // we do not have a normalized exposure, we have to scale the master as well. XXX do - // we need to explicitly identify the master as normalized? + // if we have a normalized dark exposure, we simply multiply the master by inNorm. if + // we do not have a normalized exposure, we have to scale the master as well. XXX do + // we need to explicitly identify the master as normalized? - if (darkTime != 1.0) { - darkNorm = pmFPADarkNorm(dark->parent->parent->parent, view, darkTime); - } + if (darkTime != 1.0) { + darkNorm = pmFPADarkNorm(dark->parent->parent->parent, view, darkTime); + } - if (isnan(inNorm) || isnan(darkNorm)) { + if (isnan(inNorm) || isnan(darkNorm)) { psError(PS_ERR_UNKNOWN, false, "Unable to determine dark normalisations."); return false; Index: /trunk/psModules/src/detrend/pmDark.c =================================================================== --- /trunk/psModules/src/detrend/pmDark.c (revision 16840) +++ /trunk/psModules/src/detrend/pmDark.c (revision 16841) @@ -25,4 +25,6 @@ static bool ordinateLookup(float *value, // Value of ordinate, to return const char *name, // Name of ordinate (concept name) + bool scale, // Scale the value? + float min, float max, // Minimum and maximum values for scaling const pmReadout *ro // Readout of interest ) @@ -60,4 +62,11 @@ psWarning("Non-finite value (%f) of concept %s in readout", *value, name); return false; + } + if (scale) { + if (*value < min || *value > max) { + psWarning("Value of concept %s (%f) outside range (%f:%f)", name, *value, min, max); + return false; + } + *value = 2.0 * (*value - min) / (max - min) - 1.0; } @@ -130,12 +139,9 @@ float value = NAN; // Value of ordinate - if (!ordinateLookup(&value, ord->name, ro)) { + if (!ordinateLookup(&value, ord->name, ord->scale, ord->min, ord->max, ro)) { roMask->data.U8[j] = 0xff; val->data.F32[i] = NAN; numBadInputs++; continue; - } - if (ord->scale) { - value = 2.0 * (value - ord->min) / (ord->max - ord->min) - 1.0; } val->data.F32[i] = value; @@ -280,5 +286,4 @@ return false; } - PS_ASSERT_ARRAYS_SIZE_EQUAL(dark->readouts, ordinates, false); int numOrdinates = ordinates->n; // Number of ordinates @@ -287,5 +292,5 @@ pmDarkOrdinate *ord = ordinates->data[i]; // Ordinate of interest float value = NAN; // Value for ordinate - if (!ordinateLookup(&value, ord->name, readout)) { + if (!ordinateLookup(&value, ord->name, ord->scale, ord->min, ord->max, readout)) { psError(PS_ERR_UNKNOWN, true, "Unable to find value for %s", ord->name); psFree(values); @@ -317,5 +322,5 @@ } float value = psPolynomialMDEval(poly, values); // Value of dark current - readout->image->data.F32[y][x] = value; + readout->image->data.F32[y][x] -= value; if (readout->mask && !isfinite(value)) { readout->mask->data.PS_TYPE_MASK_DATA[y][x] = bad; Index: /trunk/psModules/src/detrend/pmDark.h =================================================================== --- /trunk/psModules/src/detrend/pmDark.h (revision 16841) +++ /trunk/psModules/src/detrend/pmDark.h (revision 16841) @@ -0,0 +1,93 @@ +#ifndef PM_DARK_H +#define PM_DARK_H + +#include +#include +#include + +#define PM_DARK_ANALYSIS_ORDINATES "DARK.ORDINATES" // Name for dark ordinates in the cell analysis metadata + +// An ordinate for fitting darks +typedef struct { + psString name; // Name of concept to fit + int order; // Polynomial order to fit + bool scale; // Rescale values? + float min, max; // Minimum and maximum values for rescaling +} pmDarkOrdinate; + +// Allocator +pmDarkOrdinate *pmDarkOrdinateAlloc(const char *name, // Name for ordinate + int order // Order for ordinate + ); + + +// Combine darks +bool pmDarkCombine(pmCell *output, // Output cell; readouts will be attached + const psArray *inputs, // Input readouts for combination + psArray *ordinates, // Ordinates for fitting + int iter, // Number of rejection iterations + float rej, // Rejection threshold (standard deviations) + psMaskType maskVal // Value to mask + ); + +// Apply dark +bool pmDarkApply(pmReadout *readout, // Readout to which to apply dark + const pmCell *dark, // Dark to apply + psMaskType bad // Mask value to give bad pixels + ); + +// I/O functions for darks + +// Write all darks within an FPA +bool pmFPAWriteDark(pmFPA *fpa, // FPA to write + psFits *fits, // FITS file to which to write + psDB *db, // Database, for concepts + bool blank, // Write a blank only? + bool recurse // Recurse to lower levels? + ); + +// Write all darks within a chip +bool pmChipWriteDark(pmChip *chip, // Chip to write + psFits *fits, // FITS file to which to write + psDB *db, // Database, for concepts + bool blank, // Write a blank only? + bool recurse // Recurse to lower levels? + ); + +// Write a dark to a FITS file +bool pmCellWriteDark(pmCell *cell, // Cell containing dark information + psFits *fits, // FITS file to which to write + psDB *db, // Database, for concepts + bool blank // Write a blank only? + ); + +// Read dark for all FPA from a FITS file +bool pmFPAReadDark(pmFPA *fpa, // FPA for which to read + psFits *fits, // FITS file to read + psDB *db // Database, for concepts + ); + +// Read dark for all chip from a FITS file +bool pmChipReadDark(pmChip *chip, // Chip for which to read + psFits *fits, // FITS file to read + psDB *db // Database, for concepts + ); + +// Read dark for a cell from a FITS file +bool pmCellReadDark(pmCell *cell, // Cell for which to read + psFits *fits, // FITS file to read + psDB *db // Database, for concepts + ); + +// Write dark table to FITS file +bool pmDarkWrite(psFits *fits, // FITS file to which to write + const psMetadata *header, // Header to write + const psArray *ordinates // Dark ordinates to write + ); + +// Read dark table from FITS file +psArray *pmDarkRead(psFits *fits // FITS file to read + ); + + +#endif Index: /trunk/psModules/src/psmodules.h =================================================================== --- /trunk/psModules/src/psmodules.h (revision 16840) +++ /trunk/psModules/src/psmodules.h (revision 16841) @@ -68,4 +68,5 @@ #include // #include +#include // the following headers are from psModule:astrom