Index: branches/meh_branches/ppstack_test/psvideophot/src/Makefile.am =================================================================== --- branches/meh_branches/ppstack_test/psvideophot/src/Makefile.am (revision 32133) +++ branches/meh_branches/ppstack_test/psvideophot/src/Makefile.am (revision 33415) @@ -1,3 +1,4 @@ -bin_PROGRAMS = psvideophot +bin_PROGRAMS = psvideophot \ + dumpvideo noinst_HEADERS = \ @@ -40,4 +41,9 @@ psvideophotVersion.c +dumpvideo_CFLAGS = $(PSVIDEOPHOT_CFLAGS) $(PPSTATS_CFLAGS) $(PSASTRO_CFLAGS) $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS) +dumpvideo_LDFLAGS = $(PSVIDEOPHOT_LIBS) $(PSASTRO_LIBS) $(PPSTATS_LIBS) $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS) +dumpvideo_SOURCES = \ + dumpvideo.c + CLEANFILES = *~ Index: branches/meh_branches/ppstack_test/psvideophot/src/dumpvideo.c =================================================================== --- branches/meh_branches/ppstack_test/psvideophot/src/dumpvideo.c (revision 33415) +++ branches/meh_branches/ppstack_test/psvideophot/src/dumpvideo.c (revision 33415) @@ -0,0 +1,75 @@ +#include +#include +#include +#include + +int main (int argc, char **argv) { + + if (argc < 4) { + fprintf (stderr, "USAGE: dumpvideo (input) (extname) (output) [-includetable]\n"); + exit (2); + } + + pmConfig *config = pmConfigRead(&argc, argv, NULL); + if (config == NULL) { + psErrorStackPrint(stderr, "Can't find site configuration!\n"); + exit(EXIT_FAILURE); + } + + + + char *input = argv[1]; // Input file name + char *extname = argv[2]; // Extension of interest + char *output = argv[3]; // Output file name + + bool includetable = false; + if (argc > 4) { + includetable = true; + } + + psString inputResolved = pmConfigConvertFilename(input, config, false, false); + psFits *infile = psFitsOpen (inputResolved, "r"); // Input file + if (!infile) { + fprintf (stderr, "Unable to open input file %s", input); + exit (PS_EXIT_DATA_ERROR); + } + + psString outputResolved = pmConfigConvertFilename(output, config, true, true); + psFits *outfile = psFitsOpen (outputResolved, "w"); // Output file + if (!outfile) { + fprintf (stderr, "Unable to open output file %s", output); + exit(PS_EXIT_DATA_ERROR); + } + + if (!psFitsMoveExtName (infile, extname)) { + fprintf (stderr, "Unable to find extname %s\n", extname); + exit(PS_EXIT_DATA_ERROR); + } + + psMetadata *header = psFitsReadHeader (NULL, infile); + + psRegion region = {0, 0, 0, 0}; + psArray *cube = psFitsReadImageCube (infile, region); + + psFitsWriteImageCube (outfile, header, cube, extname); + + if (includetable) { + psString video_extname = NULL; + psStringAppend(&video_extname, "video_table_%s", extname); + if (!psFitsMoveExtName (infile, video_extname)) { + fprintf (stderr, "Unable to find extname %s\n", video_extname); + exit(PS_EXIT_DATA_ERROR); + } + psArray *table = psFitsReadTable(infile); + if (!psFitsWriteTable(outfile, NULL, table, video_extname)) { + fprintf (stderr, "Unable to write video table video_extname %s\n", video_extname); + exit(PS_EXIT_DATA_ERROR); + } + } + + psFitsClose(infile); + psFitsClose(outfile); + + return PS_EXIT_SUCCESS; +} + Index: branches/meh_branches/ppstack_test/psvideophot/src/psvideoLoop.c =================================================================== --- branches/meh_branches/ppstack_test/psvideophot/src/psvideoLoop.c (revision 32133) +++ branches/meh_branches/ppstack_test/psvideophot/src/psvideoLoop.c (revision 33415) @@ -44,4 +44,7 @@ } + psString class_id = psMetadataLookupStr(&status, config->arguments, "CLASS_ID"); + psString cell_id = psMetadataLookupStr(&status, config->arguments, "CELL_ID"); + pmConfigCamerasCull(config, NULL); @@ -56,13 +59,20 @@ } + psArray *output = NULL; + pmChip *chip; // Chip from FPA while ((chip = pmFPAviewNextChip(view, input->fpa, 1)) != NULL) { psLogMsg ("psvideophotLoop", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); + psString chipName = psMetadataLookupStr(&status, chip->concepts, "CHIP.NAME"); + if (strcmp(chipName, class_id)) { + continue; + } if (!chip->process || !chip->file_exists) { - continue; + ESCAPE("target chip has no data"); } if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { ESCAPE("load failure for Chip"); } + (void) class_id; double threshold = THRESHOLD; @@ -72,10 +82,16 @@ while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { psLogMsg ("psvideophotLoop", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); + psString cellName = psMetadataLookupStr(&status, cell->concepts, "CELL.NAME"); + if (strcmp(cellName, cell_id)) { + continue; + } if (!cell->process || !cell->file_exists) { - continue; + ESCAPE("target cell has no data"); } if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { ESCAPE("load failure for Cell"); } + + psLogMsg("psvideophotLoop", 1, "Found target cell %s %d. %ld readouts\n", cellName, view->cell, cell->readouts->n); // Put version information into the header @@ -87,9 +103,7 @@ if (cell->readouts->n <2) { - continue; + psLogMsg("psvideophotLoop", 1, "cell %s has only %ld readouts\n", cellName, cell->readouts->n); + ESCAPE("invalid video Cell"); } - - psString cellName = psMetadataLookupStr(&status, cell->concepts, "CELL.NAME"); - psLogMsg("psvideophotLoop", 1, "Found video cell %s %d\n", cellName, view->cell); // get the position of this cell on the chip @@ -114,6 +128,8 @@ // go find the video extension data - psString video_extension_name = NULL; - psStringAppend(&video_extension_name, "video_table_%s", cellName); + psString video_extension_name = psMetadataLookupStr(&status, config->arguments, "VIDEOEXTNAME"); + if (!video_extension_name) { + psStringAppend(&video_extension_name, "video_table_%s", cellName); + } psArray *video_table = readVideoTable(input, video_extension_name); if (!video_table) { @@ -121,5 +137,8 @@ ESCAPE("invalid image file"); } - psMetadataAddArray(cell->analysis, PS_LIST_TAIL, "VIDEO_DATA", 0, "", video_table); + psFree(video_extension_name); + // psMetadataAddArray(cell->analysis, PS_LIST_TAIL, "VIDEO_DATA", 0, "", video_table); + + output = (psArray *) psMemIncrRefCounter(video_table); if (cell->readouts->n != video_table->n) { @@ -180,4 +199,5 @@ double cnpix2 = psMetadataLookupS32(&status, row, "cnpix2"); + // avoid errors from unused variables (void) frame_start; (void) frame_complete; (void) rowpre; (void) cnpix1; (void) cnpix2; (void) fwhm_x; (void) fwhm_y; (void) fwhm; @@ -191,8 +211,9 @@ double star_readout_y = (centroid_y - cnpix2) / yBin; +#ifdef notdef printf("%4d %9.2f %9.2f %9.2f %.1f %.1f %9.6f %6.3f %6.3f %6.3f\n", frame, flux, snr, sky, star_readout_x, star_readout_y, frame_complete - frame_start, fwhm, fwhm_x, fwhm_y); - +#endif psStatsInit(stats); @@ -206,19 +227,34 @@ double stddev = stats->sampleStdev; double median = stats->sampleMedian; + double vpFlux = 0; + double vpSum = 0; + double xy[2] = {0, 0}; if (stddev > threshold) { - double sum = 0; - // XXX: use a point data type - double xy[2]; - Centering(readout->image, EDGE, &sum, xy, median); - double ourFlux; - ourFlux = SubSum(readout->image, xy, median); - - printf("%4d %9.2f %9.2f %9.2f %.1f %.1f %9.2f\n", - frame, ourFlux, ourFlux/stddev, median, xy[0], xy[1], stddev); + Centering(readout->image, EDGE, &vpSum, xy, median); + + if (isfinite(xy[0]) && isfinite(xy[1])) { + vpFlux = SubSum(readout->image, xy, median); + } + +// printf("%4d %9.2f %9.2f %9.2f %.1f %.1f %9.2f\n", +// frame, vpFlux, vpFlux/median, median, xy[0], xy[1], stddev); } else { - printf("%4d %9.2f %9.2f %8.2f\n", - frame, 0.0, stddev, median); - } +// printf("%4d %9.2f %9.2f %8.2f\n", +// frame, 0.0, stddev, median); + } + if (frame % 60 == 0) { + printf("frame flux sky snr X Y dt fwhm fwhm_x fwhm_y vp_flux vp_median vp_sum vp_stddev vp_x vp_y\n"); + } + printf("%4d %9.2f %9.2f %9.2f %.1f %.1f %9.6f %6.3f %6.3f %6.3f %9.2f %9.2f %9.2f %9.2f %.1f %.1f\n", + frame, flux, sky, snr, star_readout_x, star_readout_y, frame_complete - frame_start, + fwhm, fwhm_x, fwhm_y, + vpFlux, median, vpSum, stddev, xy[0], xy[1]); + psMetadataAddF32(row, PS_LIST_TAIL, "vp_flux", 0, "vp flux", vpFlux); + psMetadataAddF32(row, PS_LIST_TAIL, "vp_median", 0, "vp meidan", median); + psMetadataAddF32(row, PS_LIST_TAIL, "vp_stddev", 0, "vp meidan", stddev); + psMetadataAddF32(row, PS_LIST_TAIL, "vp_sum", 0, "vp sum of source", vpSum); + psMetadataAddF32(row, PS_LIST_TAIL, "vp_x", 0, "centroid x from vp", xy[0]); + psMetadataAddF32(row, PS_LIST_TAIL, "vp_y", 0, "centroid y from vp", xy[1]); } psLogMsg ("psvideophotLoop", 5, "Done processing video cell"); @@ -247,11 +283,22 @@ psFree(view); - // Dump configuration - psString dump_file = psMetadataLookupStr(&status, config->arguments, "DUMP_CONFIG"); - if (dump_file) { - if (!pmConfigDump(config, dump_file)) { - ESCAPE("Unable to dump configuration."); - } - } + psString outputName = psMetadataLookupStr(&status, config->arguments, "OUTPUT"); + psString realName = pmConfigConvertFilename(outputName, config, true, true); + if (!realName) { + psError(PS_ERR_UNKNOWN, false, "failed to convert filename for %s", outputName); + ESCAPE("cannot save output"); + } + psFits *outFits = psFitsOpen(realName, "w"); + if (!outFits) { + psError(PS_ERR_UNKNOWN, false, "failed to open output filename for %s", outputName); + ESCAPE(" "); + } + + psMetadata *outputHeader = lastHDU ? lastHDU->header : NULL; + if (!psFitsWriteTable(outFits, outputHeader, output, "videophotemetry")) { + psError(PS_ERR_UNKNOWN, false, "failed to write videophotometry table"); + ESCAPE("cannot write output"); + } + psFitsClose(outFits); return true; Index: branches/meh_branches/ppstack_test/psvideophot/src/psvideophotArguments.c =================================================================== --- branches/meh_branches/ppstack_test/psvideophot/src/psvideophotArguments.c (revision 32133) +++ branches/meh_branches/ppstack_test/psvideophot/src/psvideophotArguments.c (revision 33415) @@ -6,24 +6,10 @@ static void usage (void) { - fprintf(stderr, "USAGE: psvideophot [-file INPUT.fits] [-list INPUT.txt] OUTPUT\n\n"); + fprintf(stderr, "USAGE: psvideophot [-file INPUT.fits] [-list INPUT.txt] OUTPUT -class_id CLASS_ID -cell_id CELL_ID\n\n"); fprintf(stderr, "Optional arguments:\n"); fprintf(stderr, "\t-stats STATS.mdc: Output statistics into STATS.mdc\n"); - fprintf(stderr, "\t-isfringe: The input image contains fringe data.\n"); - fprintf(stderr, "\t-isdark: The input image contains dark data.\n"); - fprintf(stderr, "\t-usemask MASKVAL: Use this mask value (override recipe).\n"); - fprintf(stderr, "\t-chip CHIPNUM: Only process this chip number.\n"); - fprintf(stderr, "\t-norm VALUE: Divide through by this value when done.\n"); - fprintf(stderr, "\t-normlist file.mdc: normalizations by class_id.\n"); - fprintf(stderr, "\t-video: process video cells\n"); + fprintf(stderr, "\t-video_extname VIDEOEXTNAME: EXTNAME for video table\n"); fprintf(stderr, "\n"); fprintf(stderr, "Input options (single file / file list):\n"); - fprintf(stderr, "\t-noisemap/-noisemaplist: Noise Map image.\n"); - fprintf(stderr, "\t-bias/-biaslist: Bias image.\n"); - fprintf(stderr, "\t-dark/-darklist: Dark image.\n"); - fprintf(stderr, "\t-shutter/-shutterlist: Shutter image.\n"); - fprintf(stderr, "\t-flat/-flatlist: Flat image.\n"); - fprintf(stderr, "\t-mask/-masklist: Mask image.\n"); - fprintf(stderr, "\t-fringe/-fringelist: Fringe image and data.\n"); - fprintf(stderr, "\t-linearity/-linearlist: linearity correction file.\n"); fprintf(stderr, "\n"); exit (2); @@ -63,4 +49,29 @@ // psMetadata *options = psMetadataAlloc (); // psMetadataAddPtr (config->arguments, PS_LIST_TAIL, "PSVIDEOPHOT.OPTIONS", PS_DATA_METADATA, "", options); + + if ((argnum = psArgumentGet(argc, argv, "-class_id"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "CLASS_ID", PS_META_REPLACE, + "Chip to process", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + fprintf(stderr, "-class_id is required\n"); + usage(); + } + if ((argnum = psArgumentGet(argc, argv, "-cell_id"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "CELL_ID", PS_META_REPLACE, + "Cell to process", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + fprintf(stderr, "-cell_id is required\n"); + usage(); + } + if ((argnum = psArgumentGet(argc, argv, "-video_extname"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "VIDEOEXTNAME", PS_META_REPLACE, + "EXTNAME of video table", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } if ((argnum = psArgumentGet(argc, argv, "-stats"))) { @@ -117,4 +128,5 @@ // the input file is a required argument; if not found, we will exit pmConfigFileSetsMD (config->arguments, &argc, argv, "INPUT", "-file", "-list"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "ASTROM", "-astrom", "-astromlist"); // if these command-line options are supplied, load the file name lists into config->arguments @@ -168,5 +180,5 @@ // Add the input and output images (which remain on the command-line) to the arguments list - psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "Name of the output image", argv[1]); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "Name of the output table", argv[1]); return config; Index: branches/meh_branches/ppstack_test/psvideophot/src/psvideophotParseCamera.c =================================================================== --- branches/meh_branches/ppstack_test/psvideophot/src/psvideophotParseCamera.c (revision 32133) +++ branches/meh_branches/ppstack_test/psvideophot/src/psvideophotParseCamera.c (revision 33415) @@ -7,6 +7,4 @@ psvideophotOptions *psvideophotParseCamera(pmConfig *config) { - bool status = false; - if (!psvideophotDefineFile(config, NULL, "PSVIDEOPHOT.INPUT", "INPUT", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_NONE)) { psError(PS_ERR_IO, false, "Can't find an input image source"); @@ -16,155 +14,13 @@ psAssert(input, "We just put it there!"); +#ifdef notyet // add recipe options supplied on command line + bool status = false; psMetadata *recipe = psMetadataLookupPtr(&status, config->recipes, RECIPE_NAME); +#endif // parse the options from the metadata format to the psvideophotOptions structure psvideophotOptions *options = psvideophotOptionsParse(config); - // the following are defined from the argument list, if given, - // otherwise they revert to the config information - // not all input or output images are used in a given recipe - - int nThreads = psMetadataLookupS32(&status, config->arguments, "NTHREADS"); - if (nThreads > 0) { - int nScanRows = psMetadataLookupS32(&status, recipe, "SCAN.ROWS"); - pmDetrendSetThreadTasks(nScanRows); - } - - // the following files are output targets - pmFPAfile *outImage = pmFPAfileDefineOutput(config, input->fpa, "PSVIDEOPHOT.OUTPUT"); - if (!outImage) { - psError(PS_ERR_IO, false, _("Unable to generate output file from PSVIDEOPHOT.OUTPUT")); - psFree(options); - return NULL; - } - if (outImage->type != PM_FPA_FILE_OBJ) { - psError(PS_ERR_IO, true, "PSVIDEOPHOT.OUTPUT is not of type OBJ"); - psFree(options); - return NULL; - } - - // XXX should these be bound explicitly to the outImage->fpa rather than the input->fpa? - pmFPAfile *chipImage = pmFPAfileDefineChipMosaic(config, input->fpa, "PSVIDEOPHOT.CHIP"); - if (!chipImage) { - psError(PS_ERR_IO, false, _("Unable to generate new file from PSVIDEOPHOT.CHIP")); - psFree(options); - return NULL; - } - if (chipImage->type != PM_FPA_FILE_OBJ) { - psError(PS_ERR_IO, true, "PSVIDEOPHOT.CHIP is not of type OBJ"); - psFree(options); - return NULL; - } - - - // chipImage -> psphotInput (pmFPAfileDefineFromFile) : fpa is constructed - // psphotInput -> psphotOutput (pmFPAfileDefineOutputFromFile) : fpa is equated - // psphotOutput -> psastroInput (pmFPAfileDefineInput) : fpa is ref-copied - // psastroInput -> psastroModel (pmFPAfileDefineFromArgs : fpa is ref-copied - // psastroInput -> psastroModel (pmFPAfileDefineFromConf : fpa is constructed - // psastroInput -> psastroModel (pmFPAfileDefineFromDetDB : fpa is constructed (pmDetrendSelect uses input concepts ) - - // For photometry, we operate on the chip-mosaicked image - // we create a copy of the mosaicked image for psphot so we can write out a clean image - - - // this file is just used as a carrier; output files (eg, PSPHOT.RESID) are defined by - // psphotDefineFiles - pmFPAfile *psphotInput = pmFPAfileDefineFromFile (config, chipImage, 1, 1, "PSPHOT.INPUT"); - PS_ASSERT (psphotInput, false); - - // specify the number of psphot input images - psMetadataAddS32 (config->arguments, PS_LIST_TAIL, "PSPHOT.INPUT.NUM", PS_META_REPLACE, "number of inputs", 1); - - // define associated psphot input/output files - if (!psphotDefineFiles (config, psphotInput)) { - psError(PSPHOT_ERR_CONFIG, false, - "Trouble defining the additional input/output files for psphot"); - return false; - } - - - // For photometry, we operate on the chip-mosaicked image - - - // save any of these files? - outImage->save = options->BaseFITS; - - - chipImage->save = options->ChipFITS; - - - - // outImage is used as a carrier: input to chipImage -> require the data to remain at the CHIP level - outImage->freeLevel = PS_MIN(outImage->freeLevel, PM_FPA_LEVEL_CHIP); - outImage->dataLevel = outImage->freeLevel; - outImage->fileLevel = PS_MIN(outImage->fileLevel, outImage->dataLevel); - - // outMask and outVariance must be freed at the same level as outImage (all freed by pmFPAFreeData) - - - // the input data is the same as the outImage data : force the free levels to match - input->freeLevel = PS_MIN(outImage->freeLevel, input->freeLevel); - - // define the binned target files (which may just be carriers for some camera configurations) - - // Chip selection: turn on only the chips specified (pass status to suppress missing-key log msg) - char *chipLine = psMetadataLookupStr(&status, config->arguments, "CHIP_SELECTIONS"); - psArray *chips = psStringSplitArray(chipLine, ",", false); - if (chips->n > 0) { - pmFPASelectChip (input->fpa, -1, true); // deselect all chips - for (int i = 0; i < chips->n; i++) { - int chipNum = atoi(chips->data[i]); - if (! pmFPASelectChip(input->fpa, chipNum, false)) { - psError(PS_ERR_IO, false, "Chip number %d doesn't exist in camera.\n", chipNum); - psFree(options); - return false; - } - } - } - psFree (chips); - - if (psMetadataLookupBool(NULL, config->arguments, "INPUT_IS_FRINGE")) { - // It's a fringe file, so change the file type - input->type = PM_FPA_FILE_FRINGE; - outImage->type = PM_FPA_FILE_FRINGE; - } - if (psMetadataLookupBool(NULL, config->arguments, "INPUT_IS_DARK")) { - // It's a dark file, so change the file type - input->type = PM_FPA_FILE_DARK; - outImage->type = PM_FPA_FILE_DARK; - // Turn off compression --- there are just too many nasties that can happen - psFree(outImage->compression); - outImage->compression = NULL; - psFree(outImage->options); - outImage->options = NULL; - } - - // Turn off mask and variance output if we're not doing anything interesting - - if (psTraceGetLevel("psvideophot.config") > 0) { - // Get a look inside all the files. - psMetadataIterator *filesIter = psMetadataIteratorAlloc(config->files, PS_LIST_HEAD, NULL); - psMetadataItem *item; // Item from iteration - fprintf(stderr, "Files:\n"); - while ((item = psMetadataGetAndIncrement(filesIter))) { - pmFPAfile *file = item->data.V; // File of interest - fprintf(stderr, "%s: %p %p %p (%p) %p\n", file->name, - file->src, file->fpa, - file->camera, file->fpa->camera, file->format); - } - psFree(filesIter); - } - - // Change the input dark type between the old (IMAGE) and new (multi-DARK). - // Hopefully this is a temporary change until we all move over to using the new dark types - bool mdok; // Status of MD lookup - if (options->doDark && psMetadataLookupBool(&mdok, recipe, "OLDDARK")) { - pmFPAfile *dark = psMetadataLookupPtr(NULL, config->files, "PSVIDEOPHOT.DARK"); - assert(dark); - dark->type = PM_FPA_FILE_IMAGE; - } - return (options); }