Index: unk/ppStats/src/ppStatsSetup.c =================================================================== --- /trunk/ppStats/src/ppStatsSetup.c (revision 8399) +++ (revision ) @@ -1,343 +1,0 @@ -#include -#include -#include -#include - -#include "ppStats.h" -#include "ppStatsData.h" - -// Print usage information and die -static void usageAndDie(pmConfig *config // Configuration (contains the arguments list) - ) -{ - printf("Return headers, concepts and/or image statistics.\n\n" - "Usage:\n" - "\t%s INPUT.fits [OUTPUT_NAME]\n" - "\n", config->argv[0]); - psArgumentHelp(config->arguments); - psFree(config); - psLibFinalize(); - pmConceptsDone(); - pmConfigDone(); - exit(EXIT_FAILURE); -} - -// Generate a list from the arguments -static void listFromArguments(psMetadata *arguments, // Arguments to parse - const char *name, // Name of the item, for error message - const char *flag, // The flag for the argument of interest - psList *target // The target list - ) -{ - psString regex = NULL; // Regular expression for the flag - psStringAppend(®ex, "^%s$", flag); - psMetadataIterator *iterator = psMetadataIteratorAlloc(arguments, PS_LIST_HEAD, regex); // Iterator - psFree(regex); - psMetadataItem *item; // Item from iteration - while ((item = psMetadataGetAndIncrement(iterator))) { - if (item->type != PS_DATA_STRING) { - psLogMsg(__func__, PS_LOG_WARN, "%s name is not of type STRING (%x) --- ignored.\n", - name, item->type); - continue; - } - if (item->data.V && strlen(item->data.V) > 0) { - psListAdd(target, PS_LIST_TAIL, item->data.V); - } - } - psFree(iterator); - - return; -} - -// Strings in a recipe may be defined multiply (with MULTI) or listed on a single line -static void listFromRecipe(psMetadata *recipe, // Recipe to search - const char *name, // Name for item within recipe - psList *target // The target list - ) -{ - // If the list already has entries, don't read anything else - if (psListLength(target) > 0) { - return; - } - - // First check that at least one item of interest exists - psMetadataItem *checkItem = psMetadataLookup(recipe, name); - if (!checkItem) { - // Nothing to see here - return; - } - - psString regex = NULL; // Regular expression for the flag - psStringAppend(®ex, "^%s$", name); - psMetadataIterator *iterator = psMetadataIteratorAlloc(recipe, PS_LIST_HEAD, regex); - psFree(regex); - psMetadataItem *item; - int numItem = 0; // Occurrence of the item in the recipe; to help the user in case of trouble - while ((item = psMetadataGetAndIncrement(iterator))) { - numItem++; - if (item->type != PS_DATA_STRING) { - psLogMsg(__func__, PS_LOG_WARN, "Occurrence %d of %s in the recipe is " - "not of type STRING (%x) --- ignored.\n", numItem, name, item->type); - continue; - } - // Parse into a list of independent values - psList *values = psStringSplit(item->data.V, " ,;", false); - // Copy into the target - psListIterator *valuesIter = psListIteratorAlloc(values, PS_LIST_HEAD, false); - psString valueString; - while ((valueString = psListGetAndIncrement(valuesIter))) { - psListAdd(target, PS_LIST_TAIL, valueString); - } - psFree(valuesIter); - psFree(values); - } - psFree(iterator); - - return; -} - -// Set the statistics option; for arguments -static inline void statsOptionArguments(psMetadata *arguments, // Arguments to parse - const char *name, // Name for option - ppStatsData *data, // Configuration data - psStatsOptions option // Option to check for - ) -{ - if (psMetadataLookupBool(NULL, arguments, name)) { - data->stats->options |= option; - data->doStats = true; - } - return; -} - -// Print out what we're going to do, from the list -static void checkList(psList *list, // List - const char *name // Name of list - ) -{ - psString value; - psListIterator *iterator = psListIteratorAlloc(list, PS_LIST_HEAD, false); - while ((value = psListGetAndIncrement(iterator))) { - printf("%s: %s\n", name, value); - } - psFree(iterator); - return; -} - - -ppStatsData *ppStatsSetup(pmConfig *config // Configuration - ) -{ - // Setup and parse command-line arguments - psMetadata *arguments = config->arguments; // Arguments - psMetadataAddStr(arguments, PS_LIST_TAIL, "-chip", PS_META_DUPLICATE_OK, "Chip to inspect", NULL); - psMetadataAddStr(arguments, PS_LIST_TAIL, "-cell", PS_META_DUPLICATE_OK, "Cell to inspect", NULL); - psMetadataAddStr(arguments, PS_LIST_TAIL, "-header", PS_META_DUPLICATE_OK, "Header to look up", NULL); - psMetadataAddStr(arguments, PS_LIST_TAIL, "-concept", PS_META_DUPLICATE_OK, "Concept to look up", NULL); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-mean", 0, "Calculate sample mean", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-stdev", 0, "Calculate sample standard deviation", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-median", 0, "Calculate sample median", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-quartile", 0, "Calculate sample quartiles", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-robust-median", 0, "Calculate robust median", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-robust-stdev", 0, "Calculate robust standard deviation", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-robust-quartile", 0, "Calculate robust quartile range", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-fitted-mean", 0, "Calculate fitted mean", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-fitted-stdev", 0, "Calculate fitted standard deviation", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-clipped-mean", 0, "Calculate clipped median", false); - psMetadataAddBool(arguments, PS_LIST_TAIL, "-clipped-stdev", 0, "Calculate clipped standard deviation", false); - psMetadataAddS32(arguments, PS_LIST_TAIL, "-iter", 0, "Clipping iterations", 0); - psMetadataAddF32(arguments, PS_LIST_TAIL, "-rej", 0, "Clipping level", 0.0); - psMetadataAddF32(arguments, PS_LIST_TAIL, "-sample", 0, "Sampling fraction", 0.0); - - if (*config->argc == 1) { - // No command-line arguments: print the help - usageAndDie(config); - } - if (!psArgumentParse(arguments, config->argc, config->argv) || - (*config->argc != 2 && *config->argc != 3)) { - printf("Unable to parse command-line arguments.\n\n"); - usageAndDie(config); - } - - // Parse the command-line options - ppStatsData *data = ppStatsDataAlloc(); // The data - data->inName = config->argv[1]; - // Output filename is optional - if (*config->argc == 3) { - data->outName = config->argv[2]; - } - - listFromArguments(arguments, "Chip", "-chip", data->chips); - listFromArguments(arguments, "Cell", "-cell", data->cells); - listFromArguments(arguments, "Header", "-header", data->headers); - listFromArguments(arguments, "Concept", "-concept", data->concepts); - - // Set the statistics options - statsOptionArguments(arguments, "-mean", data, PS_STAT_SAMPLE_MEAN); - statsOptionArguments(arguments, "-stdev", data, PS_STAT_SAMPLE_STDEV); - statsOptionArguments(arguments, "-median", data, PS_STAT_SAMPLE_MEDIAN); - statsOptionArguments(arguments, "-quartile", data, PS_STAT_SAMPLE_QUARTILE); - statsOptionArguments(arguments, "-robust-median", data, PS_STAT_ROBUST_MEDIAN); - statsOptionArguments(arguments, "-robust-stdev", data, PS_STAT_ROBUST_STDEV); - statsOptionArguments(arguments, "-robust-quartile", data, PS_STAT_ROBUST_QUARTILE); - statsOptionArguments(arguments, "-fitted-mean", data, PS_STAT_FITTED_MEAN); - statsOptionArguments(arguments, "-fitted-stdev", data, PS_STAT_FITTED_STDEV); - statsOptionArguments(arguments, "-clipped-mean", data, PS_STAT_CLIPPED_MEAN); - statsOptionArguments(arguments, "-clipped-stdev", data, PS_STAT_CLIPPED_STDEV); - data->stats->clipSigma = psMetadataLookupF32(NULL, arguments, "-rej"); - data->stats->clipIter = psMetadataLookupS32(NULL, arguments, "-iter"); - data->sample = psMetadataLookupF32(NULL, arguments, "-sample"); - - - // Open the input file, determine the camera - { - data->inFile = psFitsOpen(data->inName, "r"); - if (!data->inFile) { - psError(PS_ERR_IO, false, "Unable to open input file %s\n", data->inName); - goto die; - } - psMetadata *header = psFitsReadHeader(NULL, data->inFile); // The FITS (primary) header - psMetadata *format = pmConfigCameraFormatFromHeader(config, header); - if (!format) { - psError(PS_ERR_UNKNOWN, false, "Unable to determine camera format for %s\n", data->inName); - psFree(header); - goto die; - } - data->inFPA = pmFPAConstruct(config->camera); - if (!data->inFPA) { - psError(PS_ERR_UNKNOWN, false, "Unable to construct FPA for %s\n", data->inName); - psFree(header); - psFree(format); - goto die; - } - pmFPAview *view = pmFPAAddSourceFromHeader(data->inFPA, header, format); - psFree(header); - psFree(format); - if (!view) { - psError(PS_ERR_UNKNOWN, false, "Unable to add input file %s to FPA.\n", data->inName); - goto die; - } - psFree(view); - } - - // Open the output file - if (data->outName && strlen(data->outName) > 0) { - data->outFile = fopen(data->outName, "w"); - if (!data->outFile) { - psError(PS_ERR_IO, false, "Unable to open output file %s\n", data->outName); - goto die; - } - } else { - data->outFile = stdout; - } - - // Determine recipe parameters - bool mdok; // Status of MD lookup - psMetadata *recipe = psMetadataLookupMD(&mdok, config->recipes, RECIPENAME); - if (!mdok || !recipe) { - psLogMsg(__func__, PS_LOG_WARN, "Unable to find recipe %s.\n", RECIPENAME); - return data; - } - - listFromRecipe(recipe, "CHIP", data->chips); - listFromRecipe(recipe, "CELL", data->cells); - listFromRecipe(recipe, "HEADER", data->headers); - listFromRecipe(recipe, "CONCEPT", data->concepts); - - // Parse the statistics options - psList *recipeStats = psListAlloc(NULL); - listFromRecipe(recipe, "STAT", recipeStats); - if (psListLength(recipeStats) > 0) { - psListIterator *iterator = psListIteratorAlloc(recipeStats, PS_LIST_HEAD, false); - psString stat; - - - #define CHECK_STAT(NAME, SYMBOL) \ - if (strcasecmp(stat, NAME) == 0) { \ - data->stats->options |= SYMBOL; \ - data->doStats = true; \ - } - - while ((stat = psListGetAndIncrement(iterator))) { - // This might look a little weird if automatically formated, - // but it's legal C once the pre-processing has been done, and - // it reads a lot better than a whole heap of "if-then-else" statements. - CHECK_STAT("MEAN", PS_STAT_SAMPLE_MEAN) else - CHECK_STAT("STDEV", PS_STAT_SAMPLE_STDEV) else - CHECK_STAT("MEDIAN", PS_STAT_SAMPLE_MEDIAN) else - CHECK_STAT("QUARTILE", PS_STAT_SAMPLE_QUARTILE) else - CHECK_STAT("SAMPLE_MEAN", PS_STAT_SAMPLE_MEAN) else - CHECK_STAT("SAMPLE_STDEV", PS_STAT_SAMPLE_STDEV) else - CHECK_STAT("SAMPLE_MEDIAN", PS_STAT_SAMPLE_MEDIAN) else - CHECK_STAT("SAMPLE_QUARTILE", PS_STAT_SAMPLE_QUARTILE) else - CHECK_STAT("ROBUST", PS_STAT_ROBUST_MEDIAN) else - CHECK_STAT("ROBUST_MEDIAN", PS_STAT_ROBUST_MEDIAN) else - CHECK_STAT("ROBUST_STDEV", PS_STAT_ROBUST_STDEV) else - CHECK_STAT("ROBUST_QUARTILE", PS_STAT_ROBUST_QUARTILE) else - CHECK_STAT("FITTED", PS_STAT_FITTED_MEAN) else - CHECK_STAT("FITTED_MEAN", PS_STAT_FITTED_MEAN) else - CHECK_STAT("FITTED_STDEV", PS_STAT_ROBUST_STDEV) else - CHECK_STAT("CLIPPED", PS_STAT_CLIPPED_MEAN) else - CHECK_STAT("CLIPPED_MEAN", PS_STAT_CLIPPED_MEAN) else - CHECK_STAT("CLIPPED_STDEV", PS_STAT_CLIPPED_STDEV) else { - psLogMsg(__func__, PS_LOG_WARN, "Can't interpret STATS entry in recipe: " - "%s --- ignored.\n", stat); - } - } - } - psFree(recipeStats); - - // Clipping options - if (data->stats->clipIter == 0 && isnan(data->stats->clipSigma)) { - int iter = psMetadataLookupS32(&mdok, recipe, "ITER"); // Number of clipping iterations - if (mdok && iter > 0) { - data->stats->clipIter = iter; - } else { - psLogMsg(__func__, PS_LOG_WARN, "ITER in recipe is not of type S32 and positive --- " - "retaining default.\n"); - } - float rej = psMetadataLookupF32(&mdok, recipe, "REJ"); // Clipping level - if (mdok && rej > 0) { - data->stats->clipSigma = rej; - } else { - psLogMsg(__func__, PS_LOG_WARN, "REJ in recipe is not of type F32 and positive --- " - "retaining default.\n"); - } - } - - if (data->sample == 0) { - float sample = psMetadataLookupF32(&mdok, recipe, "SAMPLE"); // Sample fraction - if (mdok && sample > 0) { - data->sample = sample; - } else { - psLogMsg(__func__, PS_LOG_WARN, "SAMPLE in recipe is not of type F32 and positive --- " - "retaining default.\n"); - } - } - - psMaskType maskVal = psMetadataLookupU8(&mdok, recipe, "MASKVAL"); // Mask value - if (mdok) { - data->maskVal = maskVal; - } else { - psLogMsg(__func__, PS_LOG_WARN, "ITER in recipe is not of type U8 --- retaining default.\n"); - } - - // Print out what we're going to do - if (psTraceGetLevel(__func__) > 9) { - checkList(data->chips, "CHIP"); - checkList(data->cells, "CELL"); - checkList(data->headers, "HEADER"); - checkList(data->concepts, "CONCEPT"); - } - - return data; - - // Common path for error conditions: clean up and exit. -die: - psFree(config); - psFree(data); - pmConceptsDone(); - pmConfigDone(); - psLibFinalize(); - exit(EXIT_FAILURE); -}