Index: /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfile.c =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfile.c (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfile.c (revision 42371) @@ -539,4 +539,7 @@ if (!strcasecmp(type, "LINEARITY")) { return PM_FPA_FILE_LINEARITY; + } + if (!strcasecmp(type, "NEWNONLIN")) { + return PM_FPA_FILE_NEWNONLIN; } if (!strcasecmp(type, "ASTROM")) { Index: /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfile.h =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfile.h (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfile.h (revision 42371) @@ -55,4 +55,5 @@ PM_FPA_FILE_PATTERN_DEAD_CELLS, PM_FPA_FILE_LINEARITY, + PM_FPA_FILE_NEWNONLIN, PM_FPA_FILE_EXPNUM, } pmFPAfileType; Index: /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfileDefine.c =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfileDefine.c (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfileDefine.c (revision 42371) @@ -821,4 +821,8 @@ // find the file in the config list & generate a pmFPAfile for it based on the filerule +// return values (return, status): +// (not NULL, true) : file defined on RUN and can be loaded +// (NULL, true) : file not defined on RUN +// (NULL, false) : file defined on RUN, cannot be loaded pmFPAfile *pmFPAfileDefineFromRun(bool *success, pmFPAfile *bind, pmConfig *config, const char *filename) { Index: /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfileIO.c =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfileIO.c (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/camera/pmFPAfileIO.c (revision 42371) @@ -285,4 +285,5 @@ case PM_FPA_FILE_KAPA: case PM_FPA_FILE_LINEARITY: + case PM_FPA_FILE_NEWNONLIN: break; default: @@ -651,4 +652,5 @@ case PM_FPA_FILE_PATTERN_DEAD_CELLS: case PM_FPA_FILE_LINEARITY: + case PM_FPA_FILE_NEWNONLIN: case PM_FPA_FILE_EXPNUM: psTrace ("psModules.camera", 5, "closing %s (%s) (%d:%d:%d)\n", file->filename, file->name, view->chip, view->cell, view->readout); @@ -736,4 +738,5 @@ case PM_FPA_FILE_KAPA: case PM_FPA_FILE_LINEARITY: + case PM_FPA_FILE_NEWNONLIN: psTrace ("psModules.camera", 5, "nothing to free for %s (%s)\n", file->filename, file->name); return true; @@ -896,4 +899,5 @@ case PM_FPA_FILE_PATTERN_DEAD_CELLS: case PM_FPA_FILE_LINEARITY: + case PM_FPA_FILE_NEWNONLIN: case PM_FPA_FILE_EXPNUM: psTrace ("psModules.camera", 5, "opening %s (%s) (%d:%d:%d)\n", Index: /branches/eam_branches/ipp-20220316/psModules/src/concepts/pmConcepts.c =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/concepts/pmConcepts.c (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/concepts/pmConcepts.c (revision 42371) @@ -315,4 +315,6 @@ conceptRegisterStr("FPA.SHUTOUTC", "Time of exposure open", NULL,NULL,NULL,false, PM_FPA_LEVEL_FPA); conceptRegisterStr("FPA.SHUTCUTC", "Time of exposure close", NULL,NULL,NULL,false, PM_FPA_LEVEL_FPA); + conceptRegisterStr("FPA.SHMDOUTC", "Time of exposure open mid-focalplane", NULL,NULL,NULL,false, PM_FPA_LEVEL_FPA); + conceptRegisterStr("FPA.SHMDCUTC", "Time of exposure close mid-focalplane", NULL,NULL,NULL,false, PM_FPA_LEVEL_FPA); conceptRegisterF32("FPA.TEMP", "Temperature of focal plane", NULL, NULL, NULL, false, PM_FPA_LEVEL_FPA); Index: /branches/eam_branches/ipp-20220316/psModules/src/config/pmConfig.c =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/config/pmConfig.c (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/config/pmConfig.c (revision 42371) @@ -1304,6 +1304,5 @@ while ((camerasItem = psMetadataGetAndIncrement(camerasIter))) { // Open the camera information - psTrace("psModules.config.format", 3, "Inspecting camera %s (%s)\n", camerasItem->name, - camerasItem->comment); + psTrace("psModules.config.format", 3, "Inspecting camera %s (%s)\n", camerasItem->name, camerasItem->comment); assert(camerasItem->type == PS_DATA_METADATA); // It should be because we've read it in or deleted psMetadata *testCamera = camerasItem->data.md; // Camera to test against what we've got: Index: /branches/eam_branches/ipp-20220316/psModules/src/detrend/Makefile.am =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/detrend/Makefile.am (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/detrend/Makefile.am (revision 42371) @@ -10,4 +10,5 @@ pmMaskStats.c \ pmNonLinear.c \ + pmNewNonLinear.c \ pmBias.c \ pmOverscan.c \ @@ -30,4 +31,5 @@ pmMaskStats.h \ pmNonLinear.h \ + pmNewNonLinear.h \ pmBias.h \ pmOverscan.h \ Index: /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmDetrendDB.h =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmDetrendDB.h (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmDetrendDB.h (revision 42371) @@ -39,4 +39,5 @@ PM_DETREND_TYPE_VIDEODARK, PM_DETREND_TYPE_LINEARITY, + PM_DETREND_TYPE_NEWNONLIN, PM_DETREND_TYPE_AUXMASK, PM_DETREND_TYPE_KH_CORRECT, Index: /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmNewNonLinear.c =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmNewNonLinear.c (revision 42371) +++ /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmNewNonLinear.c (revision 42371) @@ -0,0 +1,56 @@ +#include +#include + +#include "pmHDU.h" +#include "pmFPA.h" +#include "pmNewNonLinear.h" + +// model is stored as a FITS table, read into an array +// each row is one knot, with (X, Y, dY2) +bool pmNewNonLinearityApply(pmReadout *inputReadout, psArray *table) +{ + PS_ASSERT_PTR_NON_NULL(table, false); + PS_ASSERT_PTR_NON_NULL(inputReadout, false); + PS_ASSERT_PTR_NON_NULL(inputReadout->image, false); + PS_ASSERT_IMAGE_TYPE(inputReadout->image, PS_TYPE_F32, false); + + psTimerStart ("nonlinear"); + + psImage *image = inputReadout->image; + + // create an empty 1D spline with table->n knots + psSpline1D *model = psSpline1DCreate(table->n); + + // parse the table entries + for (int i = 0; i < table->n; i++) { + psMetadata *row = table->data[i]; + + bool status; + model->xKnots[i] = psMetadataLookupF32(&status, row, "X_KNOT"); + model->yKnots[i] = psMetadataLookupF32(&status, row, "Y_KNOT"); + model->d2yKnots[i] = psMetadataLookupF32(&status, row, "DY2_DX"); + } + + // set equal spacing info? + // psSpline1DisEqualSpacing (model); + + for (int i = 0; i < image->numRows; i++) { // Loop over rows : note: problem with discontinuity here + for (int j = 0; j < image->numCols; j++) { // Loop over columns + // Calculate correction factor contribution for this pixel. + psF32 flux = image->data.F32[i][j]; + psF32 lFlux = log10(flux); + + psF32 factor = psSpline1DEval (model, lFlux); + + // Apply correction to image data + image->data.F32[i][j] = flux * factor; + + } + } + psLogMsg ("psModules", PS_LOG_MINUTIA, "apply correction: %f sec\n", psTimerMark ("nonlinear")); + + psFree (model); + + return(true); +} + Index: /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmNewNonLinear.h =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmNewNonLinear.h (revision 42371) +++ /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmNewNonLinear.h (revision 42371) @@ -0,0 +1,18 @@ +/* @file pmNewNonLinear.h + * @brief Perform new (2023) non-linear correction using spline fits + * + * @author Eugene Magnier, IfA + * Copyright 2023 Institute for Astronomy, University of Hawaii + */ + +#ifndef PM_NEW_NON_LINEAR_H +#define PM_NEW_NON_LINEAR_H + +/// @addtogroup detrend Detrend Creation and Application +/// @{ + +/// Correct non-linearity using spline +bool pmNewNonLinearityApply(pmReadout *inputReadout, psArray *table); + +/// @} +#endif Index: /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmOverscan.c =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmOverscan.c (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/detrend/pmOverscan.c (revision 42371) @@ -140,8 +140,12 @@ break; case PM_FIT_SPLINE: - // XXX I don't think psSpline1D is up to scratch yet --- it has no mask, and requires an - // input spline - overscanOpts->spline = psVectorFitSpline1D(reduced, ordinate); - fitted = psSpline1DEvalVector(overscanOpts->spline, ordinate); + + // XXX I don't think psSpline1D is up to scratch yet --- it has no mask, and it assumes + // a knot for every input point. it needs an argument like 'number of knots' for the + // output spline. EAM: still true 2023.01.22 + + // overscanOpts->spline = psVectorFitSpline1D(reduced, ordinate); + // fitted = psSpline1DEvalVector(overscanOpts->spline, ordinate); + psError(PS_ERR_UNKNOWN, true, "Spline overscan fitting is broken\n"); break; default: @@ -189,4 +193,5 @@ } case PM_FIT_SPLINE: { + /* psSpline1D *spline = overscanOpts->spline; // The spline for (int i = 0; i < spline->n; i++) { @@ -201,4 +206,5 @@ comment = NULL; } + */ // write metadata header value psMetadataAddF32(hdu->header, PS_LIST_TAIL, "OVER_VAL", PS_META_REPLACE, Index: /branches/eam_branches/ipp-20220316/psModules/src/objects/pmSourceMasks.h =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/objects/pmSourceMasks.h (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/objects/pmSourceMasks.h (revision 42371) @@ -72,4 +72,5 @@ PM_SOURCE_MODE2_ON_GHOST = 0x00800000, ///< > 25% of (PSF-weighted) pixels land on ghost PM_SOURCE_MODE2_ON_CROSSTALK = 0x01000000, ///< peaks land on electronic crostalk + PM_SOURCE_MODE2_ON_CTE = 0x02000000, ///< peaks land on CTE region Index: /branches/eam_branches/ipp-20220316/psModules/src/objects/pmSourcePhotometry.c =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/objects/pmSourcePhotometry.c (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/objects/pmSourcePhotometry.c (revision 42371) @@ -53,12 +53,13 @@ // make this a bit more clever and dynamic -static psImageMaskType maskSuspect = 0; -static psImageMaskType maskSpike = 0; -static psImageMaskType maskStarCore = 0; -static psImageMaskType maskBurntool = 0; -static psImageMaskType maskConvPoor = 0; -static psImageMaskType maskGhost = 0; -static psImageMaskType maskGlint = 0; -static psImageMaskType maskCrosstalk = 0; +static psImageMaskType maskSuspect = 0; +static psImageMaskType maskSpike = 0; +static psImageMaskType maskStarCore = 0; +static psImageMaskType maskBurntool = 0; +static psImageMaskType maskConvPoor = 0; +static psImageMaskType maskGhost = 0; +static psImageMaskType maskGlint = 0; +static psImageMaskType maskCrosstalk = 0; +static psImageMaskType maskCTE = 0; bool pmSourceMagnitudesInit (pmConfig *config, psMetadata *recipe) @@ -69,12 +70,13 @@ // we are going to test specially against these poor values if (config) { - maskSpike = pmConfigMaskGet("SPIKE", config); - maskStarCore = pmConfigMaskGet("STARCORE", config); - maskBurntool = pmConfigMaskGet("BURNTOOL", config); - maskConvPoor = pmConfigMaskGet("CONV.POOR", config); - maskGhost = pmConfigMaskGet("GHOST", config); - maskGlint = pmConfigMaskGet("GHOST", config); - maskCrosstalk = pmConfigMaskGet("CROSSTALK", config); - maskSuspect = maskSpike | maskStarCore | maskBurntool | maskConvPoor; + maskSpike = pmConfigMaskGet("SPIKE", config); + maskStarCore = pmConfigMaskGet("STARCORE", config); + maskBurntool = pmConfigMaskGet("BURNTOOL", config); + maskConvPoor = pmConfigMaskGet("CONV.POOR", config); + maskGhost = pmConfigMaskGet("GHOST", config); + maskGlint = pmConfigMaskGet("GHOST", config); + maskCrosstalk = pmConfigMaskGet("CROSSTALK", config); + maskCTE = pmConfigMaskGet("CTE", config); + maskSuspect = maskSpike | maskStarCore | maskBurntool | maskConvPoor; } @@ -440,4 +442,5 @@ float convpoorSum = 0; float ghostSum = 0; + float cteSum = 0; int Xo, Yo, dP; @@ -534,4 +537,9 @@ convpoorSum += value; } + // count pixels which are masked with an mask bit (bad or poor) + if (mask->data.PS_TYPE_IMAGE_MASK_DATA[my][mx] & maskCTE) { + cteSum += value; + } + } } @@ -555,4 +563,7 @@ if ((convpoorSum/modelSum) > 0.25) { source->mode2 |= PM_SOURCE_MODE2_ON_CONVPOOR; + } + if ((cteSum/modelSum) > 0.25) { + source->mode2 |= PM_SOURCE_MODE2_ON_CTE; } @@ -614,4 +625,5 @@ float convpoorSum = 0; float ghostSum = 0; + float cteSum = 0; int Xo, Yo, dP; @@ -683,4 +695,8 @@ convpoorSum += 1.; } + // count pixels which are masked with an mask bit (bad or poor) + if (mask->data.PS_TYPE_IMAGE_MASK_DATA[my][mx] & maskCTE) { + cteSum += 1.; + } } } @@ -701,4 +717,7 @@ if ((convpoorSum/modelSum) > 0.25) { source->mode2 |= PM_SOURCE_MODE2_ON_CONVPOOR; + } + if ((cteSum/modelSum) > 0.25) { + source->mode2 |= PM_SOURCE_MODE2_ON_CTE; } Index: /branches/eam_branches/ipp-20220316/psModules/src/psmodules.h =================================================================== --- /branches/eam_branches/ipp-20220316/psModules/src/psmodules.h (revision 42370) +++ /branches/eam_branches/ipp-20220316/psModules/src/psmodules.h (revision 42371) @@ -77,4 +77,5 @@ #include #include +#include #include #include