Index: trunk/psModules/src/camera/pmFPAMaskWeight.c =================================================================== --- trunk/psModules/src/camera/pmFPAMaskWeight.c (revision 13567) +++ trunk/psModules/src/camera/pmFPAMaskWeight.c (revision 13591) @@ -93,5 +93,5 @@ ////////////////////////////////////////////////////////////////////////////////////////////////////////////// -bool pmReadoutSetMask(pmReadout *readout) +bool pmReadoutSetMask(pmReadout *readout, psMaskType satMask, psMaskType badMask) { PS_ASSERT_PTR_NON_NULL(readout, false); @@ -131,8 +131,8 @@ for (int j = 0; j < image->numCols; j++) { if (imageData[i][j] >= saturation) { - maskData[i][j] |= PM_MASK_SAT; + maskData[i][j] |= satMask; } if (imageData[i][j] <= bad) { - maskData[i][j] |= PM_MASK_BAD; + maskData[i][j] |= badMask; } } @@ -145,5 +145,5 @@ // pixels. currently, it will set mask bits if (value <= BAD) or (value >= SATURATION) // should we optionally ignore these tests? -bool pmReadoutGenerateMask(pmReadout *readout) +bool pmReadoutGenerateMask(pmReadout *readout, psMaskType satMask, psMaskType badMask) { PS_ASSERT_PTR_NON_NULL(readout, false); @@ -188,5 +188,5 @@ } - return pmReadoutSetMask(readout); + return pmReadoutSetMask(readout, satMask, badMask); } @@ -282,5 +282,5 @@ } -bool pmReadoutGenerateMaskWeight(pmReadout *readout, bool poisson) +bool pmReadoutGenerateMaskWeight(pmReadout *readout, psMaskType satMask, psMaskType badMask, bool poisson) { PS_ASSERT_PTR_NON_NULL(readout, false); @@ -288,5 +288,5 @@ bool success = true; // Was everything successful? - success &= pmReadoutGenerateMask(readout); + success &= pmReadoutGenerateMask(readout, satMask, badMask); success &= pmReadoutGenerateWeight(readout, poisson); @@ -294,5 +294,5 @@ } -bool pmCellGenerateMaskWeight(pmCell *cell, bool poisson) +bool pmCellGenerateMaskWeight(pmCell *cell, psMaskType satMask, psMaskType badMask, bool poisson) { PS_ASSERT_PTR_NON_NULL(cell, false); @@ -302,5 +302,5 @@ for (int i = 0; i < readouts->n; i++) { pmReadout *readout = readouts->data[i]; // The readout - pmReadoutGenerateMaskWeight(readout, poisson); + pmReadoutGenerateMaskWeight(readout, poisson, satMask, badMask); } Index: trunk/psModules/src/camera/pmFPAMaskWeight.h =================================================================== --- trunk/psModules/src/camera/pmFPAMaskWeight.h (revision 13567) +++ trunk/psModules/src/camera/pmFPAMaskWeight.h (revision 13591) @@ -5,6 +5,6 @@ * @author Eugene Magnier, IfA * - * @version $Revision: 1.8 $ $Name: not supported by cvs2svn $ - * @date $Date: 2007-03-30 21:12:56 $ + * @version $Revision: 1.9 $ $Name: not supported by cvs2svn $ + * @date $Date: 2007-06-02 03:51:03 $ * Copyright 2005-2006 Institute for Astronomy, University of Hawaii */ @@ -16,17 +16,24 @@ /// @{ +#if 0 /// Pixel mask values typedef enum { - PM_MASK_CLEAR = 0x00, ///< The pixel is not masked - PM_MASK_TRAP = 0x01, ///< The pixel is a charge trap. - PM_MASK_BADCOL = 0x02, ///< The pixel is a bad column. - PM_MASK_SAT = 0x04, ///< The pixel is saturated. - PM_MASK_BAD = 0x08, ///< The pixel is low - PM_MASK_FLAT = 0x10, ///< The pixel is non-positive in the flat-field. - PM_MASK_MARK = 0x20, ///< The pixel is marked as temporarily ignored - PM_MASK_EXT1 = 0x40, ///< This mask value is not used - PM_MASK_EXT2 = 0x80, ///< This mask value is not used + PM_MASK_CLEAR = 0x00, ///< The pixel is not masked + PM_MASK_BLANK = 0x01, ///< The pixel is blank or has no (valid) data + PM_MASK_FLAT = 0x02, ///< The pixel is non-positive in the flat-field + PM_MASK_DETECTOR = 0x02, ///< The detector pixel is bad (e.g., bad column, charge trap) + PM_MASK_SAT = 0x04, ///< The pixel is saturated in the image of interest + PM_MASK_BAD = 0x04, ///< The pixel is low in the image of interest + PM_MASK_RANGE = 0x04, ///< The pixel is out of range in the image of interest + PM_MASK_CR = 0x08, ///< The pixel is probably a CR + PM_MASK_SPARE1 = 0x10, ///< Spare mask value + PM_MASK_SPARE2 = 0x20, ///< Spare mask value + PM_MASK_SUSPECT = 0x40, ///< The pixel is suspected of being bad, but may not be + PM_MASK_MARK = 0x80, ///< The pixel is marked as temporarily ignored } pmMaskValue; - +#else +#define PM_MASK_MARK 0x80 ///< The pixel is marked as temporarily ignored +#define PM_MASK_SAT 0x04 ///< The pixel is saturated in the image of interest +#endif /// Set a temporary readout mask using CELL.SATURATION and CELL.BAD @@ -35,6 +42,8 @@ /// within the readout is temporary --- it is not added to the HDU. This is intended for when the user is /// iterating using pmReadoutReadNext, in which case the HDU can't be generated. -bool pmReadoutSetMask(pmReadout *readout ///< Readout for which to set mask - ); +bool pmReadoutSetMask(pmReadout *readout, ///< Readout for which to set mask + psMaskType sat, ///< Mask value to give saturated pixels + psMaskType bad ///< Mask value to give bad (low) pixels + ); @@ -53,6 +62,8 @@ /// Identifies pixels that are saturated (>= CELL.SATURATION) or bad (<= CELL.BAD). The mask that is produced /// is suitable for output (complete with HDU entry). This is intended for most operations. -bool pmReadoutGenerateMask(pmReadout *readout ///< Readout for which to generate mask - ); +bool pmReadoutGenerateMask(pmReadout *readout, ///< Readout for which to generate mask + psMaskType sat, ///< Mask value to give saturated pixels + psMaskType bad ///< Mask value to give bad (low) pixels + ); /// Generate a weight map (suitable for output) using CELL.GAIN and CELL.READNOISE @@ -69,5 +80,7 @@ /// Calls pmReadoutGenerateMask and pmReadoutGenerateWeight for the readout bool pmReadoutGenerateMaskWeight(pmReadout *readout, ///< Readout for which to generate mask and weights - bool poisson ///< Use poisson weights (in addition to read noise)? + psMaskType sat, ///< Mask value to give saturated pixels + psMaskType bad, ///< Mask value to give bad (low) pixels + bool poisson ///< Use poisson weights (in addition to read noise)? ); @@ -76,5 +89,7 @@ /// Calls pmReadoutGenerateMaskWeight for each readout within the cell. bool pmCellGenerateMaskWeight(pmCell *cell, ///< Cell for which to generate mask and weights - bool poisson ///< Use poisson weights (in addition to read noise)? + psMaskType sat, ///< Mask value to give saturated pixels + psMaskType bad, ///< Mask value to give bad (low) pixels + bool poisson ///< Use poisson weights (in addition to read noise)? ); /// @} Index: trunk/psModules/src/config/Makefile.am =================================================================== --- trunk/psModules/src/config/Makefile.am (revision 13567) +++ trunk/psModules/src/config/Makefile.am (revision 13591) @@ -8,4 +8,5 @@ pmConfigCamera.c \ pmConfigCommand.c \ + pmConfigMask.c \ pmVersion.c \ pmErrorCodes.c @@ -16,4 +17,5 @@ pmConfigCamera.h \ pmConfigCommand.h \ + pmConfigMask.h \ pmVersion.h \ pmErrorCodes.h Index: trunk/psModules/src/config/pmConfigMask.c =================================================================== --- trunk/psModules/src/config/pmConfigMask.c (revision 13591) +++ trunk/psModules/src/config/pmConfigMask.c (revision 13591) @@ -0,0 +1,40 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include +#include +#include + +#include "pmConfigMask.h" + + +psMaskType pmConfigMask(const char *masks, const pmConfig *config) +{ + PS_ASSERT_STRING_NON_EMPTY(masks, 0); + + psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, "MASKS"); // The recipe + if (!recipe) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find MASKS recipe."); + return 0; + } + + psMaskType mask = 0; // Mask value, to return + + psArray *names = psStringSplitArray(masks, " ,;", false); // Array of symbolic names + for (int i = 0; i < names->n; i++) { + const char *name = names->data[i]; // Symbolic name of interest + bool mdok; // Status of MD lookup + psMaskType value = psMetadataLookupU8(&mdok, recipe, name); + if (!mdok) { + psError(PS_ERR_BAD_PARAMETER_VALUE, false, + "Unable to find mask value for %s in MASK recipe", name); + psFree(names); + return 0; + } + mask |= value; + } + psFree(names); + + return mask; +} Index: trunk/psModules/src/config/pmConfigMask.h =================================================================== --- trunk/psModules/src/config/pmConfigMask.h (revision 13591) +++ trunk/psModules/src/config/pmConfigMask.h (revision 13591) @@ -0,0 +1,30 @@ +/* @file pmConfigMask.h + * @brief Mask configuration functions + * + * @author Paul Price, IfA + * + * @version $Revision: 1.1 $ $Name: not supported by cvs2svn $ + * @date $Date: 2007-06-02 03:51:03 $ + * Copyright 2007 Institute for Astronomy, University of Hawaii + */ + +#ifndef PM_CONFIG_MASK_H +#define PM_CONFIG_MASK_H + +#include +#include + +#define PM_MASKS_RECIPE "MASKS" + +/// @addtogroup Config Configuration System +/// @{ + +/// Return a mask value given a list of symbolic names +/// +/// The mask values are derived from the MASKS recipe +psMaskType pmConfigMask(const char *masks, ///< List of symbolic names, space/comma delimited + const pmConfig *config ///< Configuration + ); + + +#endif Index: trunk/psModules/src/detrend/pmFlatField.c =================================================================== --- trunk/psModules/src/detrend/pmFlatField.c (revision 13567) +++ trunk/psModules/src/detrend/pmFlatField.c (revision 13591) @@ -12,5 +12,5 @@ #include "pmFlatField.h" -bool pmFlatField(pmReadout *in, const pmReadout *flat) +bool pmFlatField(pmReadout *in, const pmReadout *flat, psMaskType badFlat) { PS_ASSERT_PTR_NON_NULL(in, false); @@ -79,5 +79,5 @@ if (flatValue <= 0.0 || (flatMask && flatMask->data.U8[j + yOffset][i + xOffset])) { \ if (inMask) { \ - inMask->data.U8[j][i] |= PM_MASK_FLAT; \ + inMask->data.PS_TYPE_MASK_DATA[j][i] |= badFlat; \ } \ inImage->data.TYPE[j][i] = SPECIAL; \ Index: trunk/psModules/src/detrend/pmFlatField.h =================================================================== --- trunk/psModules/src/detrend/pmFlatField.h (revision 13567) +++ trunk/psModules/src/detrend/pmFlatField.h (revision 13591) @@ -5,6 +5,6 @@ * @author Paul Price, IfA * - * @version $Revision: 1.9 $ $Name: not supported by cvs2svn $ - * @date $Date: 2007-03-30 21:12:56 $ + * @version $Revision: 1.10 $ $Name: not supported by cvs2svn $ + * @date $Date: 2007-06-02 03:51:03 $ * Copyright 2004-2006 Institute for Astronomy, University of Hawaii */ @@ -24,5 +24,6 @@ /// are masked, if there is a mask present in the input readout. bool pmFlatField(pmReadout *in, ///< Readout with input image - const pmReadout *flat ///< Readout with flat image + const pmReadout *flat, ///< Readout with flat image + psMaskType badFlat ///< Mask value to give bad flat pixels ); /// @} Index: trunk/psModules/src/detrend/pmMaskBadPixels.c =================================================================== --- trunk/psModules/src/detrend/pmMaskBadPixels.c (revision 13567) +++ trunk/psModules/src/detrend/pmMaskBadPixels.c (revision 13591) @@ -66,15 +66,4 @@ } } - } else { - // set raised pixels in exMask which are selected by maskVal - for (int j = 0; j < inMask->numRows; j++) { - int xJ = j - offRow; - for (int i = 0; i < inMask->numCols; i++) { - int xI = i - offCol; - if (exVal[xJ][xI] == 0) { - inVal[j][i] |= PM_MASK_BAD; - } - } - } } @@ -82,5 +71,5 @@ psString timeString = psTimeToISO(time); // String with time psFree(time); - psStringPrepend(&timeString, "Static mask applied at "); + psStringPrepend(&timeString, "Static mask (selecting %x) applied at ", maskVal); psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, timeString, ""); Index: trunk/psModules/src/imcombine/pmReadoutCombine.c =================================================================== --- trunk/psModules/src/imcombine/pmReadoutCombine.c (revision 13567) +++ trunk/psModules/src/imcombine/pmReadoutCombine.c (revision 13591) @@ -29,4 +29,5 @@ params->combine = combine; params->maskVal = 0; + params->blank = 0; params->nKeep = 0; params->fracHigh = 0.0; @@ -335,5 +336,5 @@ if (numValid == 0) { - outputMask[yOut][xOut] = PM_MASK_FLAT; + outputMask[yOut][xOut] = params->blank; outputImage[yOut][xOut] = NAN; continue; Index: trunk/psModules/src/imcombine/pmReadoutCombine.h =================================================================== --- trunk/psModules/src/imcombine/pmReadoutCombine.h (revision 13567) +++ trunk/psModules/src/imcombine/pmReadoutCombine.h (revision 13591) @@ -1,10 +1,10 @@ /* @file pmReadoutCombine.h * @brief Combine multiple readouts - * + * * @author George Gusciora, MHPCC * @author Paul Price, IfA - * - * @version $Revision: 1.11 $ $Name: not supported by cvs2svn $ - * @date $Date: 2007-03-30 21:12:56 $ + * + * @version $Revision: 1.12 $ $Name: not supported by cvs2svn $ + * @date $Date: 2007-06-02 03:51:03 $ * Copyright 2004-2006 Institute for Astronomy, University of Hawaii */ @@ -24,4 +24,5 @@ psStatsOptions combine; ///< Statistic to use when performing the combination psMaskType maskVal; ///< Mask value + psMaskType blank; ///< Mask value to give blank (i.e., no data) pixels int nKeep; ///< Mimimum number of pixels to keep float fracHigh; ///< Fraction of high pixels to immediately throw Index: trunk/psModules/src/psmodules.h =================================================================== --- trunk/psModules/src/psmodules.h (revision 13567) +++ trunk/psModules/src/psmodules.h (revision 13591) @@ -24,4 +24,5 @@ #include #include +#include #include