Index: branches/pap/ippconfig/recipes/ppMerge.config =================================================================== --- branches/pap/ippconfig/recipes/ppMerge.config (revision 23948) +++ branches/pap/ippconfig/recipes/ppMerge.config (revision 25027) @@ -1,50 +1,61 @@ # Recipe configuration for ppMerge -ROWS S32 128 # Number of rows to read at once -ELECTRONS F32 100.0 # Minimum number of electrons for useful signal -SAMPLE S32 100000 # Sampling factor for measuring the background -REJ F32 3.0 # Rejection threshold (sigma) -ITER S32 2 # Number of rejection iterations -FRACHIGH F32 0.0 # Fraction of high pixels to reject immediately -FRACLOW F32 0.0 # Fraction of low pixels to reject immediately -NKEEP S32 5 # Minimum number of pixels in stack to keep -VARIANCES BOOL FALSE # Use image variances in combination? -FRINGE.NUM S32 10000 # Number of fringe regions -FRINGE.SIZE S32 5 # Half-size of fringe regions -FRINGE.XSMOOTH S32 5 # Number of smoothing regions in x -FRINGE.YSMOOTH S32 11 # Number of smoothing regions in y -CTE.MIN F32 0.2 # regions lower than this in the CTE image are masked -SHUTTER.SIZE S32 128 # Size for shutter measurement regions -MASK.SUSPECT F32 5.0 # Threshold for suspect pixels (sigma) -MASK.BAD F32 0.2 # Threshold for bad pixels -MASK.MODE STR FRACTION # Mode for identifying bad pixels in the suspect map -MASK.CHIPSTATS BOOL TRUE # Measure stats for masking by chip (otherwise by readout)? -MASK.GROW S32 0 # Grow bad pixels by this radius -MASK.SET.VALUE STR FLAT # set this bit in the output mask +ROWS S32 128 # Number of rows to read at once +ELECTRONS F32 100.0 # Minimum number of electrons for useful signal +SAMPLE S32 100000 # Sampling factor for measuring the background +REJ F32 3.0 # Rejection threshold (sigma) +ITER S32 2 # Number of rejection iterations +FRACHIGH F32 0.0 # Fraction of high pixels to reject immediately +FRACLOW F32 0.0 # Fraction of low pixels to reject immediately +NKEEP S32 5 # Minimum number of pixels in stack to keep +VARIANCES BOOL FALSE # Use image variances in combination? -COMBINE STR CLIPPED # Statistic to use for combination -MEAN STR ROBUST_MEDIAN # Statistic to use to measure the mean -STDEV STR ROBUST_STDEV # Statistic to use to measure the stdev +FRINGE.NUM S32 10000 # Number of fringe regions +FRINGE.SIZE S32 5 # Half-size of fringe regions +FRINGE.XSMOOTH S32 5 # Number of smoothing regions in x +FRINGE.YSMOOTH S32 11 # Number of smoothing regions in y +FRINGE.SMOOTH BOOL FALSE # Smooth the output image? +FRINGE.SMOOTH.SIGMA F32 2.0 # Sigma of smoothing Gaussian -MASK.SMOOTH.SUSPECT BOOL TRUE # smooth the suspect-pixel image before making mask -MASK.SMOOTH.SCALE F32 3.0 # sigma (pixels) of smoothing kernel +CTE.MIN F32 0.5 # regions lower than this in the CTE image are masked +SHUTTER.SIZE S32 128 # Size for shutter measurement regions -STATS.BY.CHIP BOOL TRUE # measure stats for masking by chip (or by readout) -MASK.GROW.NPIX S32 3 # measure stats for masking by chip (or by readout) +INPUT.MASKS.USE BOOL TRUE # respect the input mask data? + +COMBINE STR CLIPPED # Statistic to use for combination +MEAN STR ROBUST_MEDIAN # Statistic to use to measure the mean +STDEV STR ROBUST_STDEV # Statistic to use to measure the stdev + +MASK.SUSPECT.MODE STR SIGMA # how to identify suspect pixels: SIGMA, VALUE +MASK.SUSPECT.MIN F32 -100.0 # for MASK.SUSPECT.MODE == VALUE, below this is suspect +MASK.SUSPECT.MAX F32 +100.0 # for MASK.SUSPECT.MODE == VALUE, above this is suspect +MASK.SUSPECT.SIGMA F32 5.0 # Threshold for suspect pixels (sigma) + +MASK.SMOOTH.SUSPECT BOOL TRUE # smooth the suspect-pixel image before making mask +MASK.SMOOTH.SCALE F32 3.0 # sigma (pixels) of smoothing kernel + +MASK.BAD F32 0.2 # Threshold for bad pixels +MASK.MODE STR FRACTION # Mode for identifying bad pixels in the suspect map +MASK.CHIPSTATS BOOL TRUE # Measure stats for masking by chip (otherwise by readout)? +MASK.GROW S32 0 # Grow bad pixels by this radius +MASK.SET.VALUE STR FLAT # set this bit in the output mask + +STATS.BY.CHIP BOOL TRUE # measure stats for masking by chip (or by readout) +MASK.GROW.NPIX S32 3 # measure stats for masking by chip (or by readout) # Ordinates for fitting dark current -DARK.ORDINATES METADATA - CELL.DARKTIME S32 1 # Traditional dark current term +DARK.ORDINATES METADATA + CELL.DARKTIME S32 1 # Traditional dark current term END -DARK.NORM STR NONE # Dark normalisation concept +DARK.NORM STR NONE # Dark normalisation concept # Bias combination --- don't want min/max rejection -PPMERGE_BIAS METADATA - REJ F32 3.0 # Rejection threshold (sigma) - ITER S32 2 # Number of rejection iterations - FRACHIGH F32 0.0 # Fraction of high pixels to reject immediately - FRACLOW F32 0.0 # Fraction of low pixels to reject immediately - VARIANCES BOOL FALSE # Use image variances? - COMBINE STR CLIPPED # Statistic to use for combination: +PPMERGE_BIAS METADATA + REJ F32 3.0 # Rejection threshold (sigma) + ITER S32 2 # Number of rejection iterations + FRACHIGH F32 0.0 # Fraction of high pixels to reject immediately + FRACLOW F32 0.0 # Fraction of low pixels to reject immediately + VARIANCES BOOL FALSE # Use image variances? + COMBINE STR CLIPPED # Statistic to use for combination: END @@ -52,45 +63,45 @@ # Dark combination --- don't want min/max rejection # More aggressive clipping than bias, so as to remove CRs -PPMERGE_DARK METADATA - REJ F32 3.0 # Rejection threshold (sigma) - ITER S32 2 # Number of rejection iterations - FRACHIGH F32 0.0 # Fraction of high pixels to reject immediately - FRACLOW F32 0.0 # Fraction of low pixels to reject immediately - VARIANCES BOOL TRUE # Use image variances? - COMBINE STR CLIPPED # Statistic to use for combination: +PPMERGE_DARK METADATA + REJ F32 3.0 # Rejection threshold (sigma) + ITER S32 2 # Number of rejection iterations + FRACHIGH F32 0.0 # Fraction of high pixels to reject immediately + FRACLOW F32 0.0 # Fraction of low pixels to reject immediately + VARIANCES BOOL TRUE # Use image variances? + COMBINE STR CLIPPED # Statistic to use for combination: END # Flat combination --- use min/max rejection -PPMERGE_FLAT METADATA - REJ F32 3.0 # Rejection threshold (sigma) - ITER S32 1 # Number of rejection iterations - FRACHIGH F32 0.3 # Fraction of high pixels to reject immediately - FRACLOW F32 0.1 # Fraction of low pixels to reject immediately - NKEEP S32 5 # Minimum number of pixels in stack to keep - VARIANCES BOOL TRUE # Use image variances? - COMBINE STR MEAN # Statistic to use for combination: +PPMERGE_FLAT METADATA + REJ F32 3.0 # Rejection threshold (sigma) + ITER S32 1 # Number of rejection iterations + FRACHIGH F32 0.3 # Fraction of high pixels to reject immediately + FRACLOW F32 0.1 # Fraction of low pixels to reject immediately + NKEEP S32 5 # Minimum number of pixels in stack to keep + VARIANCES BOOL TRUE # Use image variances? + COMBINE STR MEAN # Statistic to use for combination: END # Fringe combination --- already included in default, above -PPMERGE_FRINGE METADATA - FRACHIGH F32 0.1 # Fraction of high pixels to reject immediately - VARIANCES BOOL TRUE # Use image variances? +PPMERGE_FRINGE METADATA + FRACHIGH F32 0.1 # Fraction of high pixels to reject immediately + VARIANCES BOOL TRUE # Use image variances? END # Mask generation --- already included in default, above PPMERGE_DARKMASK METADATA - ITER S32 2 # Number of iterations - MASK.BAD F32 0.2 # Threshold for bad pixels (sigma) - MASK.MODE STR FRACTION # Mode for identifying bad pixels in the suspect map - MASK.SET.VALUE STR DARK # set this bit in the output mask + ITER S32 2 # Number of iterations + MASK.BAD F32 0.2 # Threshold for bad pixels (sigma) + MASK.MODE STR FRACTION # Mode for identifying bad pixels in the suspect map + MASK.SET.VALUE STR DARK # set this bit in the output mask END # Mask generation --- already included in default, above PPMERGE_FLATMASK METADATA - ITER S32 2 # Number of iterations - MASK.BAD F32 0.2 # Threshold for bad pixels (sigma) - MASK.MODE STR FRACTION # Mode for identifying bad pixels in the suspect map - MASK.SET.VALUE STR FLAT # set this bit in the output mask + ITER S32 2 # Number of iterations + MASK.BAD F32 0.2 # Threshold for bad pixels (sigma) + MASK.MODE STR FRACTION # Mode for identifying bad pixels in the suspect map + MASK.SET.VALUE STR FLAT # set this bit in the output mask END @@ -98,17 +109,18 @@ # but it then sets a mask based on the resulting data values (using CTE.MIN) PPMERGE_CTEMASK METADATA - REJ F32 3.0 # Rejection threshold (sigma) - ITER S32 2 # Number of rejection iterations - FRACHIGH F32 0.0 # Fraction of high pixels to reject immediately - FRACLOW F32 0.0 # Fraction of low pixels to reject immediately - VARIANCES BOOL FALSE # Use image variances? - COMBINE STR CLIPPED # Statistic to use for combination: - CTE.MIN F32 0.2 # regions lower than this in the CTE image are masked - MASK.SET.VALUE STR CTE # set this bit in the output mask + REJ F32 3.0 # Rejection threshold (sigma) + ITER S32 2 # Number of rejection iterations + FRACHIGH F32 0.0 # Fraction of high pixels to reject immediately + FRACLOW F32 0.0 # Fraction of low pixels to reject immediately + VARIANCES BOOL FALSE # Use image variances? + COMBINE STR CLIPPED # Statistic to use for combination: + CTE.MIN F32 0.5 # regions lower than this in the CTE image are masked + MASK.SET.VALUE STR CTE # set this bit in the output mask + INPUT.MASKS.USE BOOL FALSE # respect the input mask data? END # Shutter generation --- already included in default, above -PPMERGE_SHUTTER METADATA - REJ F32 2.0 # Rejection threshold (sigma) - ITER S32 1 # Number of rejection iterations +PPMERGE_SHUTTER METADATA + REJ F32 2.0 # Rejection threshold (sigma) + ITER S32 1 # Number of rejection iterations END