Index: trunk/psModules/src/detrend/Makefile.am =================================================================== --- trunk/psModules/src/detrend/Makefile.am (revision 16824) +++ 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 16824) +++ 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 16824) +++ 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