Index: branches/eam_branches/ipp-20110213/ippToPsps/src/Batch.c =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/Batch.c (revision 30812) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/Batch.c (revision 31083) @@ -18,4 +18,5 @@ #include #include + #include "Batch.h" @@ -62,22 +63,9 @@ if (this->exitCode != PS_EXIT_SUCCESS) { - psError(PS_ERR_UNKNOWN, false, "Failed, so deleting %s", this->fitsOutPath); - - // if process failed, we need to delete that FITS file - if (remove(this->fitsOutPath) == -1) { - - psError(PS_ERR_UNKNOWN, false, "Unable to delete %s", this->fitsOutPath); - } + this->logger->print(this->logger, MSG_ERROR, "Batch", "Failed, so deleting fits file\n"); + this->fitsOut->delete(this->fitsOut); } - // ...otherwise, close file - else { - - int status = 0; - if (fits_close_file(this->fitsOut, &status)) { - - psError(PS_ERR_IO, false, "Unable to close FITS file %s", this->fitsOutPath); - fits_report_error(stderr, status); - } - } + + this->fitsOut->destroy(this->fitsOut); } @@ -99,5 +87,7 @@ if (this->dvoConfig != NULL) dvoConfigFree(this->dvoConfig); - ippToPspsConfig_Destructor(this->config); + // destroy objects + this->fitsGenerator->destroy(this->fitsGenerator); + this->initData->destroy(this->initData); pmConfigDone(); @@ -115,5 +105,5 @@ if (file == NULL) { - psError(PS_ERR_UNKNOWN, false, "Unable to open file at %s", this->fitsInPath); + this->logger->print(this->logger, MSG_ERROR, "Batch", "Unable to open file at %s\n", this->fitsInPath); return false; } @@ -123,5 +113,6 @@ while (fgets(line, 1000, file) != NULL) this->numOfInputFiles++; - printf ("Number of input files %d\n", this->numOfInputFiles); + this->logger->print(this->logger, MSG_INFO, "Batch", + "%d input file%s found\n", this->numOfInputFiles, (this->numOfInputFiles > 1) ? "s" : ""); if (this->numOfInputFiles < 1) return false; @@ -151,5 +142,5 @@ Sets-up and reads command-line arguments */ -static bool parseArguments(Batch* this, int argc, char **argv) { +static bool parseArguments(Batch* this, int argc, char **argv, char* configsDir, char* fitsOutFile) { // first deal with DVO database @@ -166,5 +157,5 @@ if (!this->pmconfig) { - psError(PS_ERR_UNKNOWN, false, "Unable to read configuration."); + this->logger->print(this->logger, MSG_ERROR, "Batch", "Unable to read configuration\n"); this->exitCode = PS_EXIT_CONFIG_ERROR; return false; @@ -178,4 +169,7 @@ haveSurveyType = false; + char fitsOutPath[1000]; + char configsBaseDir[1000]; + // decode arguments int32_t optind = 1; @@ -193,5 +187,5 @@ else if(strcmp(sw, "-output") == 0 ) { optind++; if( optind > ( argc-1 ) ) break; - strcpy(this->fitsOutPath, argv[optind]); + strcpy(fitsOutPath, argv[optind]); haveFitsOutPath = true; } @@ -203,5 +197,5 @@ else if(strcmp(sw, "-config") == 0 ) { optind++; if( optind > ( argc-1 ) ) break; - strcpy(this->configsDir, argv[optind]); + strcpy(configsBaseDir, argv[optind]); haveConfig = true; } @@ -211,4 +205,7 @@ haveSurveyType = true; } + else if(strcmp(sw, "-test") == 0 ) { + this->testMode = true; + } } @@ -216,19 +213,5 @@ } - - // setup command line arguments - //psMetadataAddStr(this->arguments, PS_LIST_TAIL, "-survey", 0, "Survey type", NULL); - - - // now check rest of arguments - //if (argc < 2 || !psArgumentParse(this->arguments, &argc, argv)) { - - // usage(this, argv[0]); - //this->exitCode = PS_EXIT_CONFIG_ERROR; - //return false; - // } - - //this->surveyType = psMemIncrRefCounter(psMetadataLookupStr(NULL, this->arguments, "-survey")); - + // check we have some input paths if (haveFitsInPath && !readInputFilePaths(this)) { @@ -237,15 +220,8 @@ } - return true; -} - -/** - Initialises file paths, creates FITS file etc - */ -bool init(Batch* this) { - - // create a config object - this->config = ippToPspsConfig_Constructor(this->configsDir); - if (this->config == NULL) { + // create an InitData object and get survey ID + this->initData = new_InitData(configsBaseDir, this->logger); + if (strlen(this->surveyType) > 0 && + !this->initData->getSurveyId(this->initData, this->surveyType, &this->surveyID)) { this->exitCode = PS_EXIT_CONFIG_ERROR; @@ -253,22 +229,14 @@ } - // get survey ID using config object - if (strlen(this->surveyType) > 0 && !ippToPspsConfig_getSurveyId(this->config, this->surveyType, &this->surveyID)) { - - this->exitCode = PS_EXIT_CONFIG_ERROR; - return false; - } + // create a FitsGenerator object + strcat(configsBaseDir, configsDir); + this->fitsGenerator = new_FitsGenerator(this->logger, configsBaseDir); + // create full FITS out path - sprintf (this->fitsOutPath, "%s/%s", this->fitsOutPath, this->fitsOutFile); + sprintf(fitsOutPath, "%s/%s", fitsOutPath, fitsOutFile); // create an output FITS file - int status=0; - if (fits_create_file(&this->fitsOut, this->fitsOutPath, &status)) { - fits_report_error(stderr, status); - psError(PS_ERR_IO, false, "Unable to create file at: '%s'", this->fitsOutPath); - this->exitCode = PS_EXIT_SYS_ERROR; - this->fitsOut = NULL; - return false; - } + this->fitsOut = new_Fits(fitsOutPath, this->logger); + if (this->fitsOut->getFilePtr(this->fitsOut) == NULL) return false; // create XML document for results @@ -278,5 +246,5 @@ xmlNodePtr rootNode = xmlNewNode(NULL, BAD_CAST "ippToPsps_Results"); xmlDocSetRootElement(this->resultsXmlDoc, rootNode); - xmlNewChild(rootNode, NULL, BAD_CAST "filename", BAD_CAST this->fitsOutFile); + xmlNewChild(rootNode, NULL, BAD_CAST "filename", BAD_CAST fitsOutFile); } @@ -289,13 +257,12 @@ static void print(Batch* this) { - printf("\n"); - printf("* surveyType : '%s'\n", this->surveyType); - printf("* surveyID : %d\n", this->surveyID); - printf("* resultsPath : '%s'\n", this->resultsPath); - printf("* numOfInputFiles : %d\n", this->numOfInputFiles); - printf("* fitsInPath : '%s'\n", this->fitsInPath); - printf("* fitsOutFile : '%s'\n", this->fitsOutFile); - printf("* fitsOutPath : '%s'\n", this->fitsOutPath); - printf("* configsDir : '%s'\n", this->configsDir); + this->logger->print(this->logger, MSG_INFO, "Batch", "\n"); + this->logger->print(this->logger, MSG_INFO, "Batch", " Class fields:\n"); + this->logger->print(this->logger, MSG_INFO, "Batch", "surveyType : %s\n", this->surveyType); + this->logger->print(this->logger, MSG_INFO, "Batch", "surveyID : %d\n", this->surveyID); + this->logger->print(this->logger, MSG_INFO, "Batch", "resultsPath : %s\n", this->resultsPath); + this->logger->print(this->logger, MSG_INFO, "Batch", "numOfInputFiles : %d\n", this->numOfInputFiles); + this->logger->print(this->logger, MSG_INFO, "Batch", "fitsInPath : %s\n", this->fitsInPath); + this->logger->print(this->logger, MSG_INFO, "Batch", "testMode : %s\n", this->testMode ? "yes" : "no"); } @@ -342,6 +309,7 @@ Constructor. Takes a Batch object and initialises it. */ -bool new_Batch(Batch *this) { - +bool new_Batch(Logger* logger, Batch *this) { + + this->logger = logger; this->surveyID = -1; this->resultsXmlDoc = NULL; @@ -349,13 +317,12 @@ this->inputFiles = NULL; this->fitsOut = NULL; - this->config = NULL; + this->fitsGenerator = NULL; this->pmconfig = NULL; this->exitCode = PS_EXIT_SUCCESS; - + this->testMode = false; + + // set up function pointers this->parseArguments = parseArguments; - this->init = init; this->print = print; - this->destroy = destroy; - this->gotResultsPath = gotResultsPath; this->gotFitsInPath = gotFitsInPath; @@ -363,4 +330,5 @@ this->gotConfig = gotConfig; this->gotSurveyType = gotSurveyType; + this->destroy = destroy; assert(this); Index: branches/eam_branches/ipp-20110213/ippToPsps/src/Batch.h =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/Batch.h (revision 30812) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/Batch.h (revision 31083) @@ -1,3 +1,3 @@ -/** @file ippToPsps.h +/** @file Batch.h * * @brief Batch @@ -6,5 +6,5 @@ * * @author IfA - * Copyright 2009 Institute for Astronomy, University of Hawaii + * Copyright 2011 Institute for Astronomy, University of Hawaii */ @@ -12,9 +12,14 @@ #define IPPTOPSPS_BATCH_H +#include +#include + #include #include -#include "Config.h" -#include -#include + +#include "FitsGenerator.h" +#include "Fits.h" +#include "InitData.h" +#include "Logger.h" /** @@ -25,29 +30,28 @@ - StackBatch - All subclasses need to implement the run() method and may need to implenent print() and/or init() + All subclasses need to implement the run() method and may need to implement print() */ typedef struct Batch { // fields - char surveyType[10]; // the survey type, eg 3PI, MD01, STS, SSS - int8_t surveyID; // survey ID - char fitsInPath[1000]; // path to FITS input - char resultsPath[1000]; // path to results file - xmlDocPtr resultsXmlDoc; // pointer to XML document for results - uint16_t numOfInputFiles; // number of input files - char** inputFiles; // array of input file names - char fitsOutFile[100]; // FITS output filename - char fitsOutPath[1000]; // path to FITS output - fitsfile *fitsOut; // output FITS file - char configsDir[500]; // path to IPP/PSPS mapping file - pmConfig* pmconfig; // pmConfig - dvoConfig* dvoConfig; // dvo database - IppToPspsConfig* config; // config structure - char todaysDate[20]; // today's date - int exitCode; // ps exit code + char surveyType[10]; // the survey type, eg 3PI, MD01, STS, SSS + int8_t surveyID; // survey ID + char fitsInPath[1000]; // path to FITS input + char resultsPath[1000]; // path to results file + xmlDocPtr resultsXmlDoc; // pointer to XML document for results + uint16_t numOfInputFiles; // number of input files + char** inputFiles; // array of input file names + Fits *fitsOut; // output FITS file + pmConfig* pmconfig; // pmConfig + dvoConfig* dvoConfig; // dvo database + FitsGenerator* fitsGenerator; // FitsGenerator object + InitData* initData; // InitData object + char todaysDate[20]; // today's date + int exitCode; // ps exit code + bool testMode; // test mode boolean + Logger* logger; // Logger object // methods bool (*parseArguments)(); - bool (*init)(); int (*run)(); void (*print)(); @@ -57,4 +61,6 @@ bool (*gotConfig)(); bool (*gotSurveyType)(); + + // destructor void (*destroy)(); @@ -62,5 +68,5 @@ // public functions -bool new_Batch(Batch *this); +bool new_Batch(Logger* logger, Batch *this); void ippToPsps_VersionPrint(void); Index: branches/eam_branches/ipp-20110213/ippToPsps/src/Config.c =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/Config.c (revision 30812) +++ (revision ) @@ -1,948 +1,0 @@ -/** @file ippToPspsConfig.c - * - * @ingroup ippToPsps - * - * @author IfA - * Copyright 2009 Institute for Astronomy, University of Hawaii - */ - -#include "ippToPspsConfig.h" -#include -#include -#include - -// Gets PS type from string -static int ippToPsps_GetDataType(char *typename) { - - if (!strncmp(typename, "TBYTE", 5)) return TBYTE; - if (!strncmp(typename, "TSHORT", 6)) return TSHORT; - if (!strncmp(typename, "TLONGLONG", 9)) return TLONGLONG; - if (!strncmp(typename, "TLONG", 5)) return TLONG; - if (!strncmp(typename, "TFLOAT", 6)) return TFLOAT; - if (!strncmp(typename, "TDOUBLE", 7)) return TDOUBLE; - if (!strncmp(typename, "TSTRING", 7)) return TSTRING; - - psError(PS_ERR_IO, false, "Don't understand type '%s'", typename); - - return 0; -} - -// finds a column within this table -static IppToPspsConfig_Column* ippToPspsConfig_findColumn(IppToPspsConfig_Table* table, const char* name) { - - IppToPspsConfig_Column* column = NULL; - - for (uint32_t i=0; inumOfColumns; i++) { - - if (strcmp(table->columns[i].pspsName, name) == 0) { - column = table->columns+i; - break; - } - } - - if (!column) psError(PS_ERR_IO, false, "Could not find column '%s' in table '%s'", name, table->name); - - return column; -} - -// finds a table from the array of tables -static IppToPspsConfig_Table* ippToPspsConfig_findTable(IppToPspsConfig* this, const char* name) { - - IppToPspsConfig_Table* table = NULL; - - for (uint32_t i=0; inumOfTables; i++) { - - if (strcmp(this->tables[i].name, name) == 0) { - table = this->tables+i; - break; - } - } - - if (!table) psError(PS_ERR_IO, false, "Could not find table '%s'", name); - - return table; -} - -// gets an attribute value from XML node -static bool ippToPspsConfig_getAttribute(xmlNode* node, const char* attName, char* _value) { - - xmlChar* value = xmlGetProp(node, (const xmlChar*)attName); - if (!value) return false; - sprintf(_value, "%s", value); - xmlFree(value); - - return true; -} - -// creates a FITS binary table and populates it with defaults based on definition in schema XML -static bool ippToPspsConfig_createTable(IppToPspsConfig_Table* table, fitsfile* fitsOut, const long nRows) { - - if (!table) return false; - if (nRows < 1) return false; - - long nCols = table->numOfColumns; - - char** colNames = (char**)calloc(nCols, sizeof(char*)); - char** colTypes = (char**)calloc(nCols, sizeof(char*)); - - uint32_t i = 0; - for (i=0;inumOfColumns; m++) { - - colNames[i] = table->columns[i].pspsName; - - // sprintf(colNames[i], table->columns[i].pspsName); - - switch (table->columns[i].pspsType) { - - case TBYTE: - sprintf(colTypes[i],"1B"); - break; - case TSHORT: - sprintf(colTypes[i],"1I"); - break; - case TLONG: - sprintf(colTypes[i],"1J"); // TODO - break; - case TLONGLONG: - sprintf(colTypes[i],"1K"); - break; - case TFLOAT: - sprintf(colTypes[i],"1E"); - break; - case TDOUBLE: - sprintf(colTypes[i],"1D"); - break; - case TSTRING: - sprintf(colTypes[i],"32A"); // TODO width? - break; - - default: - break; - } - - i++; - } - - int status = 0; - if (fits_create_tbl(fitsOut, BINARY_TBL, nRows, nCols, colNames, colTypes, NULL, table->name, &status)) { - - fits_report_error(stderr, status); - psError(PS_ERR_IO,"Unable to create table: %s", table->name); - } - - for (i=0;inumOfColumns; i++) { - - col = i+1; - - strcpy(tempStr,table->columns[i].defaultValue); - tempLong = atol(tempStr); - tempDouble = atof(tempStr); - - switch (table->columns[i].pspsType) { - - case TBYTE: - for(j=0;jchildren; node; node = node->next) { - - if (strcmp((const char*)node->name, name)==0) count++; - } - - return count; -} - -// searches through this table and finds attribute value for a provided key -static bool ippToPspsConfig_getRowAttribute(IppToPspsConfig* this, xmlNode* tableNode, - const char* keyName, const char* keyValue, - const char* attName, char* attValue) { - - xmlNode* node = NULL; - - char buffer[100]; - - // loop round all available rows for this table - for (node = tableNode->children; node; node = node->next) { - if (node->type == XML_ELEMENT_NODE) { - //psLogMsg("ippToPsps", PS_LOG_INFO, "Node name '%s'", (const char*)node->name ); - - if (strcmp((const char*)node->name, "row")==0) { - //psLogMsg("ippToPsps", PS_LOG_INFO, " Looking for key '%s'", keyName ); - - if (!ippToPspsConfig_getAttribute(node, keyName, buffer)) continue; - //psLogMsg("ippToPsps", PS_LOG_INFO, "Found key '%s' value '%s'", keyName, buffer ); - - if (strcmp(buffer, keyValue) != 0) continue; - ippToPspsConfig_getAttribute(node, attName, attValue); - //printf("FOUND %s %s %s %s \n", keyName, buffer, attName, attValue ); - return true; - - } - } - } - - psLogMsg("ippToPsps", PS_LOG_INFO, "Could not find value for '%s' for '%s' with value '%s'", attName, keyName, keyValue ); - return false; -} - -// opens an XML file and returns the document -static xmlDoc* ippToPspsConfig_openXmlFile(const char* path) { - - xmlDoc* doc = xmlReadFile(path, NULL, 0); - if (doc == NULL) psError(PS_ERR_IO, false, "Unable to open XML file at %s", path); - return doc; -} - -// closes an XML file -static bool ippToPspsConfig_closeXmlFile(xmlDoc* doc) { - - xmlFreeDoc(doc); - xmlCleanupParser(); - - return true; -} - -// gets filter ID for this filter name from 'init' data -static bool ippToPspsConfig_getInitValue( - IppToPspsConfig* this, - const char* tableName, - const char* keyName, const char* keyValue, - const char* attName, char* attValue) { - - bool ret = true; - - psString path = NULL; - psStringAppend(&path, "%s/../init/data.xml", this->configsPath); // TODO nasty - - xmlDoc* doc = ippToPspsConfig_openXmlFile(path); - - if (doc == NULL) { - psFree(path); - return false; - } - psFree(path); - - xmlNode* rootElement = xmlDocGetRootElement(doc); - - if (strcmp((const char*)rootElement->name, "tabledata")!=0) { - psError(PS_ERR_IO, false, "Root node of XML is not 'tabledata', as it should be"); - return false; - } - - xmlNode* node = NULL; - char tempStr[100]; - - // loop round all available tables - for (node = rootElement->children; node; node = node->next) { - if (node->type == XML_ELEMENT_NODE) { - - if (strcmp((const char*)node->name, "table")!=0) continue; - if (!ippToPspsConfig_getAttribute(node, "name", tempStr)) continue; - if (strcmp(tempStr, tableName)!=0) continue; - - ret = ippToPspsConfig_getRowAttribute(this, node, keyName, keyValue, attName, attValue); - break; - } - - } - - ippToPspsConfig_closeXmlFile(doc); - - return ret; -} - -// gets survey ID from survey name -bool ippToPspsConfig_getSurveyId(IppToPspsConfig* this, const char* surveyType, int8_t* surveyId) { - - char buffer[10]; - if (!ippToPspsConfig_getInitValue(this, "Survey", "name", surveyType, "surveyID", buffer)) { - - *surveyId = -1; - return false; - } - - *surveyId = atoi(buffer); - return true; -} - -// gets filter ID from filter type -bool ippToPspsConfig_getFilterId(IppToPspsConfig* this, const char* filterType, int8_t* filterId) { - - char tmp[2]; - strncpy(tmp,filterType,1); - tmp[1] = '\0'; - char buffer[10]; - if (!ippToPspsConfig_getInitValue(this, "Filter", "filterType", tmp, "filterID", buffer)) { - - *filterId = -1; - return false; - } - - *filterId = atoi(buffer); - return true; -} - -// populate the provided table with data from XML -static bool ippToPspsConfig_populateTable(IppToPspsConfig_Table* table, xmlNode* rootElement, fitsfile *fitsOut) { - - char tempStr[100]; - xmlNode* node = NULL; - xmlNode* tableNode = NULL; - - // first check we have data for this table in XML file - for (node = rootElement->children; node; node = node->next) { - if (node->type == XML_ELEMENT_NODE) { - - if (strcmp((const char*)node->name, "table")!=0) continue; - if (!ippToPspsConfig_getAttribute(node, "name", tempStr)) continue; - if (strcmp(tempStr, table->name)==0) {tableNode = node; break;} - } - } - - if(!tableNode) { - - psError(PS_ERR_IO,"Could not find table: %s", table->name); - return false; - } - - // now count the number of rows - int nRows = ippToPspsConfig_countChildren(tableNode, "row"); - if (nRows < 1) return false; - if (!ippToPspsConfig_createTable(table, fitsOut, nRows)) return false; - - int rows=0; - int status; - char** strcol = (char**)calloc(1, sizeof(char**)); - strcol[0] = (char*)calloc(32,sizeof(char)); // TODO 20? size issue - - int8_t* bytecol = calloc(1, sizeof(uint8_t)); - int16_t* shortcol = calloc(1, sizeof(uint16_t)); - long* longcol = calloc(1, sizeof(long)); - double* doublecol = calloc(1, sizeof(double)); - float* floatcol = calloc(1, sizeof(float)); - - int col; - - // now get rows - for (node = tableNode->children; node; node = node->next) { - - if (strcmp((const char*)node->name, "row")!=0) continue; - - rows++; - - // get column data for this row - for (int i=0;inumOfColumns;i++) { - - col = i+1; - - if (!ippToPspsConfig_getAttribute(node, table->columns[i].pspsName, tempStr)) continue; - - strncpy(strcol[0], tempStr, 32); - status=0; - //psLogMsg("ippToPsps", PS_LOG_INFO, "Values %s - %ld - %f - %d", strcol[0], longcol[0], doublecol[0], bytecol[0]); - switch (table->columns[i].pspsType) { - - case TBYTE: - bytecol[0] = atoi(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, bytecol, &status); - break; - case TSHORT: - shortcol[0] = atoi(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, shortcol, &status); - break; - case TLONG: - case TLONGLONG: - longcol[0] = atol(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, longcol, &status); - break; - case TFLOAT: - floatcol[0] = atof(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, floatcol, &status); - break; - case TDOUBLE: - doublecol[0] = atof(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, doublecol, &status); - break; - case TSTRING: - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, strcol, &status); - break; - - } - if (status) psError(PS_ERR_IO, false, "Unable to write value of %s to column %s in table %s", - tempStr, table->columns[i].pspsName, table->name); - } - } - - free(bytecol); - free(shortcol); - free(longcol); - free(floatcol); - free(doublecol); - free(strcol[0]); - free(strcol); - - return true; -} - -// loads a table description from XML -static bool ippToPspsConfig_loadTableDescription(IppToPspsConfig_Table* table, xmlNode* tableNode) { - - bool ret = true; - char tableName[100]; - ippToPspsConfig_getAttribute(tableNode, "name", tableName); - strcpy(table->name, tableName); - - // count how many columns we have coming in and allocate memory for them - table->numOfColumns = ippToPspsConfig_countChildren(tableNode, "column"); - table->columns = calloc(table->numOfColumns, sizeof(IppToPspsConfig_Column)); - // psLogMsg("ippToPsps", PS_LOG_INFO, " Found '%d' columns", table->numOfColumns); - - char buffer[200]; - xmlNode* node; - int columnNum = 0; - - for (node = tableNode->children; node; node = node->next) { - - if (strcmp((const char*)node->name, "column") != 0) continue; - - table->columns[columnNum].usingDefault = true; - - // column name - ippToPspsConfig_getAttribute(node, "name", buffer); - sprintf(table->columns[columnNum].pspsName, buffer); - - // column type - ippToPspsConfig_getAttribute(node, "type", buffer); - table->columns[columnNum].pspsType = ippToPsps_GetDataType(buffer); - - // default value - ippToPspsConfig_getAttribute(node, "default", buffer); - sprintf(table->columns[columnNum].defaultValue, buffer); - - // comment - ippToPspsConfig_getAttribute(node, "comment", buffer); - sprintf(table->columns[columnNum].comment, buffer); - - # if 0 - psLogMsg("ippToPsps", PS_LOG_INFO, "'%s' name='%s' type='%d' default='%s' comment='%s'", - table->name, - table->columns[columnNum].pspsName, - table->columns[columnNum].pspsType, - table->columns[columnNum].defaultValue, - table->columns[columnNum].comment); -# endif - columnNum++; - } - - - if (columnNum < 1) { - - psError(PS_ERR_IO, false, "Found no columns for table '%s'", tableName); - ret = false; - } - - if (columnNum != table->numOfColumns) - psError(PS_ERR_IO, false, "Mismatch between number of columns expected (%d) and those found (%d)", table->numOfColumns, columnNum); - - return ret; -} - -// read table shapes from XML file -bool ippToPspsConfig_loadTableDescriptions(IppToPspsConfig* this) { - - bool ret = true; - - psString path = NULL; - psStringAppend(&path, "%s/tables.xml", this->configsPath); - - xmlDoc* doc = ippToPspsConfig_openXmlFile(path); - - if (doc == NULL) { - - psFree(path); - return false; - } - psFree(path); - - xmlNode* rootElement = xmlDocGetRootElement(doc); - - if (strcmp((const char*)rootElement->name, "tableDescriptions")!=0) { - - psError(PS_ERR_IO, false, "Root node of XML is not 'tableDescriptions', as it should be"); - return false; - } - - // count how many tables we have coming in and allocate memory for them - this->numOfTables = ippToPspsConfig_countChildren(rootElement, "table"); - this->tables = calloc(this->numOfTables, sizeof(IppToPspsConfig_Table)); - // psLogMsg("ippToPsps", PS_LOG_INFO, " Found '%d' tables", this->numOfTables); - - xmlNode* node = NULL; - IppToPspsConfig_Table* table = NULL; - - int tableNum = 0; - // loop round all available table descriptions - for (node = rootElement->children; node; node = node->next) { - if (node->type == XML_ELEMENT_NODE) { - - if (strcmp((const char*)node->name, "table")==0) { - - table = this->tables+tableNum; - - if (!ippToPspsConfig_loadTableDescription(table, node)) ret = false; - else tableNum++; - } - } - } - - if (tableNum != this->numOfTables) - psError(PS_ERR_IO, false, "Mismatch between number of tables expected (%d) and those found (%d)", this->numOfTables, tableNum); - - ippToPspsConfig_closeXmlFile(doc); - - return ret; -} - -// loads mappings from XML for a particular table -static bool ippToPspsConfig_loadTableMappings(IppToPspsConfig* this, xmlNode* tableNode) { - - bool ret = false; - - xmlNode* node = NULL; - - char tableName[100]; - ippToPspsConfig_getAttribute(tableNode, "name", tableName); - - IppToPspsConfig_Table* table = ippToPspsConfig_findTable(this, tableName); - IppToPspsConfig_Column* column = NULL; - if (!table) return false; - - char buffer[100]; - //psLogMsg("ippToPsps", PS_LOG_INFO, "Table '%s'", tableName); - - // loop round all available mappings for this table - for (node = tableNode->children; node; node = node->next) { - if (node->type == XML_ELEMENT_NODE) { - - if (strcmp((const char*)node->name, "map")==0) { - - // column type - ippToPspsConfig_getAttribute(node, "pspsName", buffer); - column = ippToPspsConfig_findColumn(table, buffer); - - if (!column) continue; - - // IPP name - ippToPspsConfig_getAttribute(node, "ippName", buffer); - strcpy(column->ippName, buffer); - - // IPP type - ippToPspsConfig_getAttribute(node, "ippType", buffer); - column->ippType = ippToPsps_GetDataType(buffer); - - column->usingDefault = false; - - //psLogMsg("ippToPsps", PS_LOG_INFO, "...mapping PSPS:'%s' to '%s' '%d'", column->pspsName, column->ippName, column->ippColNum ); - } - } - } - - return ret; -} - -// reads table mappings from XML file -static bool ippToPspsConfig_loadMappings(IppToPspsConfig* this) { - - bool ret = true; - - psString path = NULL; - psStringAppend(&path, "%s/map.xml", this->configsPath); - - xmlDoc* doc = ippToPspsConfig_openXmlFile(path); - - if (doc == NULL) { - psFree(path); - return false; - } - psFree(path); - - xmlNode* rootElement = xmlDocGetRootElement(doc); - - if (strcmp((const char*)rootElement->name, "tabledata")!=0) { - psError(PS_ERR_IO, false, "Root node of XML is not 'tabledata', as it should be"); - return false; - } - - xmlNode* node = NULL; - - // loop round all available tables - for (node = rootElement->children; node; node = node->next) { - if (node->type == XML_ELEMENT_NODE) { - - if (strcmp((const char*)node->name, "table")==0) { - - if (!ippToPspsConfig_loadTableMappings(this, node)) ret = false; - } - } - } - - ippToPspsConfig_closeXmlFile(doc); - - return ret; -} - -// populate the provided table with data from XML -bool ippToPspsConfig_populateFromFile(IppToPspsConfig* this, fitsfile *fitsOut) { - - bool ret = true; - psString path = NULL; - psStringAppend(&path, "%s/data.xml", this->configsPath); - - xmlDoc* doc = ippToPspsConfig_openXmlFile(path); - - if (doc == NULL) { - psFree(path); - return false; - } - psFree(path); - - xmlNode* rootElement = xmlDocGetRootElement(doc); - - if (strcmp((const char*)rootElement->name, "tabledata")!=0) { - psError(PS_ERR_IO, false, "Root node of XML is not 'tabledata', as it should be"); - return false; - } - - for (uint32_t i=0; inumOfTables; i++) { - if (!ippToPspsConfig_populateTable(this->tables+i, rootElement, fitsOut)) { - ret = false; - } - } - - ippToPspsConfig_closeXmlFile(doc); - - return ret; -} - -// gets the contents of a FITS column vector -bool ippToPspsConfig_getColumnVector( - int col, - long row, - int type, - int repeat, - float* vector, - fitsfile *fitsIn) { - - int status = 0; - int anynull = 0; - - fits_read_col(fitsIn, type, col, row, 1, repeat, NULL, vector, &anynull, &status); - - if (status) { - psError(PS_ERR_IO, false, "Failed to read vector column %d row %ld", col, row); - return false; - } - - int i; - for(i=0; inumOfColumns; i++) { - - if (strlen(table->columns[i].ippName) < 1) continue; - -int dummy; - - if (!ippToPspsConfig_getFitsColumnMeta( - table->columns[i].ippName, - &table->columns[i].ippColNum, - // &table->columns[i].ippType, TODO getting wrong type for some reason - &dummy, - &table->columns[i].ippRepeat, - fitsIn)) {return false;} - } - } - - int col; - for (uint32_t i=0; inumOfColumns; i++) { - - readStatus = 0; - writeStatus = 0; - - if (!table->columns[i].usingDefault) { - - col = i+1; - - switch (table->columns[i].ippType) { - - case TBYTE: - if (fromHeader) { - fits_read_key(fitsIn, TBYTE, table->columns[i].ippName, &int8col[0], NULL, &readStatus); - if (!isfinite(int8col[0])) int8col[0] = int8null; - } - else fits_read_col(fitsIn, TBYTE, table->columns[i].ippColNum, 1, 1, nRows, &int8null, int8col, &anynull, &readStatus); - fits_write_col(fitsOut, TBYTE, col, 1, 1, nRows, int8col, &writeStatus); - break; - case TSHORT: - if (fromHeader) { - fits_read_key(fitsIn, TSHORT, table->columns[i].ippName, &int16col[0], NULL, &readStatus); - if (!isfinite(int16col[0])) int16col[0] = int16null; - } - else fits_read_col(fitsIn, TSHORT, table->columns[i].ippColNum, 1, 1, nRows, &int16null, int16col, &anynull, &readStatus); - fits_write_col(fitsOut, TSHORT, col, 1, 1, nRows, int16col, &writeStatus); - break; - case TLONG: - if (fromHeader) { - fits_read_key(fitsIn, TLONG, table->columns[i].ippName, &longcol[0], NULL, &readStatus); - if (!isfinite(longcol[0])) longcol[0] = longnull; - } - else fits_read_col(fitsIn, TLONG, table->columns[i].ippColNum, 1, 1, nRows, &longnull, longcol, &anynull, &readStatus); - fits_write_col(fitsOut, TLONG, col, 1, 1, nRows, longcol, &writeStatus); - break; - case TLONGLONG: - if (fromHeader) { - fits_read_key(fitsIn, TLONGLONG, table->columns[i].ippName, &longcol[0], NULL, &readStatus); - if (!isfinite(longcol[0])) longcol[0] = longnull; - } - else fits_read_col(fitsIn, TLONGLONG, table->columns[i].ippColNum, 1, 1, nRows, &longnull, longcol, &anynull, &readStatus); - fits_write_col(fitsOut, TLONGLONG, col, 1, 1, nRows, longcol, &writeStatus); - break; - case TFLOAT: - if (fromHeader) { - fits_read_key(fitsIn, TFLOAT, table->columns[i].ippName,&floatcol[0], NULL, &readStatus); - if (!isfinite(floatcol[0])) floatcol[0] = floatnull; - } - else fits_read_col(fitsIn, TFLOAT, table->columns[i].ippColNum, 1, 1, nRows, &floatnull, floatcol, &anynull, &readStatus); - fits_write_col(fitsOut, TFLOAT, col, 1, 1, nRows, floatcol, &writeStatus); - break; - case TDOUBLE: - if (fromHeader) { - fits_read_key(fitsIn, TDOUBLE, table->columns[i].ippName, &doublecol[0], NULL, &readStatus); - if (!isfinite(doublecol[0])) doublecol[0] = doublenull; - } - else fits_read_col(fitsIn, TDOUBLE, table->columns[i].ippColNum, 1, 1, nRows, &doublenull, doublecol, &anynull, &readStatus); - fits_write_col(fitsOut, TDOUBLE, col, 1, 1, nRows, doublecol, &writeStatus); - break; - case TSTRING: - if (fromHeader) fits_read_key(fitsIn, TSTRING, table->columns[i].ippName, strcol[0], NULL, &readStatus); - else fits_read_col(fitsIn, TSTRING, table->columns[i].ippColNum, 1, 1, nRows, " ", strcol, &anynull, &readStatus); - fits_write_col(fitsOut, TSTRING, col, 1, 1, nRows, strcol, &writeStatus); - break; - - default: - psError(PS_ERR_IO, false, "Don't know IPP type (%d) for mapping from '%d' '%s' to '%s'", table->columns[i].ippType, - table->columns[i].ippColNum, table->columns[i].ippName, table->columns[i].pspsName); - break; - } - - // TODO need these errors, but strange error handling runs out of memory - //if (readStatus) { - // psError(PS_ERR_IO, false, "Unable to read col num '%d' col name '%s', type %d", - // table->columns[i].ippColNum, table->columns[i].ippName, table->columns[i].ippType); - // fits_report_error(stderr, readStatus); - //} - //if (writeStatus) { - // psError(PS_ERR_IO, false, "Unable to write col '%s'", table->columns[i].pspsName ); - // fits_report_error(stderr, writeStatus); - //} - } - } - - free(int8col); - free(int16col); - free(longcol); - free(floatcol); - free(doublecol); - for (uint32_t i=0; inumOfTables;i++) - free(this->tables[i].columns); - - free(this->tables); - psFree(this->configsPath); - free(this); - } -} - -// Constructor. Loads IPP -> PSPS mappings from a csv -IppToPspsConfig* ippToPspsConfig_Constructor(const char* path) { - - IppToPspsConfig* this = NULL; - - this = malloc(sizeof(IppToPspsConfig)); - - this->configsPath = NULL; - psStringAppend(&this->configsPath, path); - - // load tables descriptions from XML - if (ippToPspsConfig_loadTableDescriptions(this)) { - - // load any mappings we may have from XML - ippToPspsConfig_loadMappings(this); - } - - return this; -} - Index: branches/eam_branches/ipp-20110213/ippToPsps/src/Config.h =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/Config.h (revision 30812) +++ (revision ) @@ -1,82 +1,0 @@ -/** @file ippToPspsConfig.h - * - * @brief ippToPsps - * - * @ingroup ippToPsps - * - * @author IfA - * Copyright 2009 Institute for Astronomy, University of Hawaii - */ - -#ifndef IPPTOPSPSCONFIG_H -#define IPPTOPSPSCONFIG_H - -#include - -// column class -typedef struct { - - int ippColNum; - char ippName[100]; - int ippType; - long ippRepeat; - char pspsName[100]; // TODO change to 'name' - int pspsType; - bool usingDefault; - char defaultValue[100]; - char comment[300]; - -} IppToPspsConfig_Column; - -// table class -typedef struct { - - char name[32]; - IppToPspsConfig_Column* columns; - int numOfColumns; - -} IppToPspsConfig_Table; - -// -typedef struct { - - psString configsPath; - IppToPspsConfig_Table* tables; - int numOfTables; - -} IppToPspsConfig; - -IppToPspsConfig* ippToPspsConfig_Constructor(const char* filePath); -bool ippToPspsConfig_populateFromFile(IppToPspsConfig* this, fitsfile *fitsOut); // TODO remove -void ippToPspsConfig_Destructor(); -bool ippToPspsConfig_writeTable( - IppToPspsConfig* this, - fitsfile* fitsIn, - fitsfile* fitsOut, - const long nRows, - const char* tableName, - const bool fromHeader); - -// getters -bool ippToPspsConfig_getFilterId(IppToPspsConfig* this, const char* filterType, int8_t* filterId); -bool ippToPspsConfig_getSurveyId(IppToPspsConfig* this, const char* surveyType, int8_t* surveyId); -bool ippToPspsConfig_getFitsColumnMeta( - char* name, - int* colNum, - int* type, - long* repeat, - fitsfile *fitsIn); - -bool ippToPspsConfig_getColumnVector( - int col, - long row, - int type, - int repeat, - float* vector, - fitsfile *fitsIn); - - - - -#endif // IPPTOPSPSCONFIG_H - Index: branches/eam_branches/ipp-20110213/ippToPsps/src/DetectionBatch.c =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/DetectionBatch.c (revision 30812) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/DetectionBatch.c (revision 31083) @@ -1,4 +1,7 @@ #include "DetectionBatch.h" #include "DetectionBatchEnums.h" + +#include "Fits.h" + /** @@ -18,4 +21,23 @@ /** + Writes results to XML file + */ +static bool writeResults(DetectionBatch* this, long minObjID, long maxObjID, long totalDetectionsOut) { + + if (!this->base.resultsXmlDoc) return false; + + xmlNodePtr rootNode = xmlDocGetRootElement(this->base.resultsXmlDoc); + char tmp[100]; + sprintf(tmp, "%ld", minObjID); + xmlNewChild(rootNode, NULL, BAD_CAST "minObjID", BAD_CAST tmp); + sprintf(tmp, "%ld", maxObjID); + xmlNewChild(rootNode, NULL, BAD_CAST "maxObjID", BAD_CAST tmp); + sprintf(tmp, "%ld", totalDetectionsOut); + xmlNewChild(rootNode, NULL, BAD_CAST "totalDetections", BAD_CAST tmp); + + return true; +} + +/** Does the work. Loops through the provided smf files, tallies the contents with the DVO database already connected to and generates a new FITS file of the fomat required by PSPS (i.e. a binary table per PSPS database table) */ @@ -24,53 +46,38 @@ if (this->base.exitCode != PS_EXIT_SUCCESS) return this->base.exitCode; - int status = 0; - fitsfile *fitsIn; - - if (fits_open_file(&fitsIn, this->base.inputFiles[0], READONLY, &status)) { - - fits_report_error(stderr, status); - return PS_EXIT_SYS_ERROR; - } - - // get primary header and pull stuff out for later - int nKeys; - fits_get_hdrspace(fitsIn, &nKeys, NULL, &status); - - float zptObs, exposureTime; - char filterType[20]; - double obsTime; - double expStart; - double expTime; - status=0; fits_read_key(fitsIn, TFLOAT, "ZPT_OBS", &zptObs, NULL, &status); - status=0; fits_read_key(fitsIn, TFLOAT, "EXPREQ", &exposureTime, NULL, &status); - status=0; fits_read_key(fitsIn, TSTRING, "FILTERID", filterType, NULL, &status); - status=0; fits_read_key(fitsIn, TDOUBLE, "MJD-OBS", &expStart, NULL, &status); - status=0; fits_read_key(fitsIn, TDOUBLE, "EXPTIME", &expTime, NULL, &status); - obsTime = expStart + (expTime/172800.0); // exp start plus half exp time (converted from secs to days) - - ippToPspsConfig_writeTable(this->base.config, fitsIn, this->base.fitsOut, 1, "FrameMeta", true); + // open input FITS file + Fits* fitsIn = existing_Fits(this->base.inputFiles[0], this->base.logger); + if (fitsIn->getFilePtr(fitsIn) == NULL) return PS_EXIT_SYS_ERROR; + + // read some header values + float zptObs; fitsIn->getHeaderKeyValue(fitsIn, TFLOAT, "ZPT_OBS", &zptObs); + float exposureTime; fitsIn->getHeaderKeyValue(fitsIn, TFLOAT, "EXPREQ", &exposureTime); + char filterType[20]; fitsIn->getHeaderKeyValue(fitsIn, TSTRING, "FILTERID", filterType); + double expStart; fitsIn->getHeaderKeyValue(fitsIn, TDOUBLE, "MJD-OBS", &expStart); + double expTime; fitsIn->getHeaderKeyValue(fitsIn, TDOUBLE, "EXPTIME", &expTime); + double obsTime = expStart + (expTime/172800.0); // exp start plus half exp time (converted from secs to days) + + + this->base.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, 1, "FrameMeta", true); // FrameMeta values - fits_write_col(this->base.fitsOut, TLONG, FRAMEMETA_FRAMEID, 1, 1, 1, &this->expId, &status); - fits_write_col(this->base.fitsOut, TSTRING, FRAMEMETA_FRAMENAME, 1, 1, 1, &(this->expName), &status); - fits_write_col(this->base.fitsOut, TBYTE, FRAMEMETA_SURVEYID, 1, 1, 1, &this->base.surveyID, &status); - int8_t filterID = -1; - if (!ippToPspsConfig_getFilterId(this->base.config, filterType, &filterID)) { + if (!this->base.initData->getFilterId(this->base.initData, filterType, &filterID)) { this->base.exitCode = PS_EXIT_DATA_ERROR; return this->base.exitCode; } - - fits_write_col(this->base.fitsOut, TBYTE, FRAMEMETA_FILTERID, 1, 1, 1, &filterID, &status); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, FRAMEMETA_FILTERID, 1, 1, 1, &filterID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONG, FRAMEMETA_FRAMEID, 1, 1, 1, &this->expId); + this->base.fitsOut->writeColumn(this->base.fitsOut, TSTRING, FRAMEMETA_FRAMENAME, 1, 1, 1, &(this->expName)); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, FRAMEMETA_SURVEYID, 1, 1, 1, &this->base.surveyID); + int16_t cameraID = 1; // TODO - fits_write_col(this->base.fitsOut, TSHORT, FRAMEMETA_CAMERAID, 1, 1, 1, &cameraID, &status); - int16_t cameraConfigID = 1; // TODO - fits_write_col(this->base.fitsOut, TSHORT, FRAMEMETA_CAMERACONFIGID, 1, 1, 1, &cameraConfigID, &status); - int16_t telescopeID = 1; // TODO - fits_write_col(this->base.fitsOut, TSHORT, FRAMEMETA_TELESCOPEID, 1, 1, 1, &telescopeID, &status); + this->base.fitsOut->writeColumn(this->base.fitsOut, TSHORT, FRAMEMETA_CAMERAID, 1, 1, 1, &cameraID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TSHORT, FRAMEMETA_CAMERACONFIGID, 1, 1, 1, &cameraConfigID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TSHORT, FRAMEMETA_TELESCOPEID, 1, 1, 1, &telescopeID); // stuff to keep from psf.hdr header @@ -88,10 +95,6 @@ uint32_t s,d, invalidDvoRows, nChipDetectionsOut = 0; - long longnull = -999; - float floatnull = -999.0; - int anynull = 0; - char ccdNumber[3], extensionName[15]; - // for storing FITS column data + // for storing FITS column data - do this once, to avoid expension free/calloc for each chip long* ippIDet = (long*)calloc(this->MAXDETECT, sizeof(long)); float* instMag = (float*)calloc(this->MAXDETECT, sizeof(float)); @@ -110,5 +113,4 @@ int8_t* filterIDs = (int8_t*)calloc(this->MAXDETECT, sizeof(int8_t)); int8_t* surveyIDs = (int8_t*)calloc(this->MAXDETECT, sizeof(int8_t)); - char** assocDate = (char**)calloc(this->MAXDETECT, sizeof(char*)); for (uint32_t i=0; iMAXDETECT;i++) assocDate[i] = (char*)malloc(20*sizeof(char)); @@ -119,5 +121,8 @@ filterIDs[s] = filterID; surveyIDs[s] = this->base.surveyID; - strcpy(assocDate[s], this->base.todaysDate); + + // if running in test mode, don't use today's date + if (this->base.testMode) strcpy(assocDate[s], "2010-01-01"); + else strcpy(assocDate[s], this->base.todaysDate); } @@ -133,8 +138,31 @@ int ippIDetNum, instMagNum, instMagErrNum, peakMagNum; bool error = false; - - // loop round all 60 chips - for (int x=0; x<8; x++) { - for (int y=0; y<8; y++) { + int startX, stopX, startY, stopY; + + // in test mode, only run for chip 33 + if (this->base.testMode) { + + startX = 3; + stopX = 4; + startY = 3; + stopY = 4; + } + // in 'normal' mode, run for all chips + else { + + startX = 0; + stopX = 8; + startY = 0; + stopY = 8; + } + + this->base.logger->print(this->base.logger, MSG_INFO, "DetectionBatch", + "+-----------+---------+----------+----------------+--------------+--------------+\n"); + this->base.logger->print(this->base.logger, MSG_INFO, "DetectionBatch", + "| Extension | Rows in | Rows out | Duplicate IDs | Invalid Flux | Bogus det ID |\n"); + + // loop round chips + for (int x=startX; xmoveToBinaryTable(fitsIn, extensionName)) continue; // move to header extension sprintf(extensionName, "XY%s.hdr", ccdNumber); - status=0; - if (fits_movnam_hdu(fitsIn, IMAGE_HDU, extensionName, 0, &status)) { - psError(PS_ERR_IO, false, "Can't move to extension: %s skipping this chip\n", extensionName); - continue; - } + if (!fitsIn->moveToHeader(fitsIn, extensionName)) continue; // stuff to save from psf.hdr - status=0; fits_read_key(fitsIn, TFLOAT, "FWHM_MAJ", &fwhmMaj, NULL, &status); - status=0; fits_read_key(fitsIn, TFLOAT, "FWHM_MIN", &fwhmMin, NULL, &status); - status=0; fits_read_key(fitsIn, TFLOAT, "IQ_FW1", &momentMaj, NULL, &status); - status=0; fits_read_key(fitsIn, TFLOAT, "IQ_FW2", &momentMin, NULL, &status); - status=0; fits_read_key(fitsIn, TLONG, "IMAGEID", &imageId, NULL, &status); - status=0; fits_read_key(fitsIn, TLONG, "SOURCEID", &sourceId, NULL, &status); - status=0; fits_read_key(fitsIn, TLONG, "NASTRO", &numPhotoRef, NULL, &status); + fitsIn->getHeaderKeyValue(fitsIn, TFLOAT, "FWHM_MAJ", &fwhmMaj); + fitsIn->getHeaderKeyValue(fitsIn, TFLOAT, "FWHM_MIN", &fwhmMin); + fitsIn->getHeaderKeyValue(fitsIn, TFLOAT, "IQ_FW1", &momentMaj); + fitsIn->getHeaderKeyValue(fitsIn, TFLOAT, "IQ_FW2", &momentMin); + fitsIn->getHeaderKeyValue(fitsIn, TLONG, "IMAGEID", &imageId); + fitsIn->getHeaderKeyValue(fitsIn, TLONG, "SOURCEID", &sourceId); + fitsIn->getHeaderKeyValue(fitsIn, TLONG, "NASTRO", &numPhotoRef); totalNumPhotoRef += numPhotoRef; // total up for storing in FrameMeta + // access DVO database skylist = dvoSkyListByExternID(this->base.dvoConfig, sourceId, imageId, &image); if (skylist == NULL) { - psError(PS_ERR_IO, false, + this->base.logger->print(this->base.logger, MSG_ERROR, "DetectionBatch", "DVO: can't find SkyList for sourceId='%d' imageId='%d' (CCD = XY%s): skipping this chip\n", sourceId, imageId, ccdNumber); @@ -189,6 +210,5 @@ if (numDvoDetections > this->MAXDETECT ) { - psError(PS_ERR_IO, false, - " Number of detections (%d) exceeds max limit (%ld)\n", + this->base.logger->print(this->base.logger, MSG_ERROR, "DetectionBatch", "Number of detections (%d) exceeds max limit (%ld)\n", numDvoDetections, this->MAXDETECT); error = true; @@ -197,58 +217,46 @@ // create ImageMeta - ippToPspsConfig_writeTable(this->base.config, fitsIn, this->base.fitsOut, 1, "ImageMeta", true); + this->base.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, 1, "ImageMeta", true); psfFwhm = (fwhmMaj+fwhmMin)/2; momentFwhm = (momentMaj+momentMin)/2; imageFlags = (uint64_t)image->flags; - fits_write_col(this->base.fitsOut, TLONGLONG, IMAGEMETA_IMAGEID, 1, 1, 1, &pspsImageId, &status); - fits_write_col(this->base.fitsOut, TLONG, IMAGEMETA_FRAMEID, 1, 1, 1, &this->expId, &status); - fits_write_col(this->base.fitsOut, TSHORT, IMAGEMETA_CCDID, 1, 1, 1, &image->ccdnum, &status); - fits_write_col(this->base.fitsOut, TLONG, IMAGEMETA_PHOTOCALID, 1, 1, 1, &image->photcode, &status); - fits_write_col(this->base.fitsOut, TBYTE, IMAGEMETA_FILTERID, 1, 1, 1, &filterID, &status); - fits_write_col(this->base.fitsOut, TFLOAT, IMAGEMETA_PHOTOSCAT, 1, 1, 1, &zptObs, &status); - fits_write_col(this->base.fitsOut, TFLOAT, IMAGEMETA_PSFFWHM, 1, 1, 1, &psfFwhm, &status); - fits_write_col(this->base.fitsOut, TFLOAT, IMAGEMETA_MOMENTFWHM, 1, 1, 1, &momentFwhm, &status); - fits_write_col(this->base.fitsOut, TFLOAT, IMAGEMETA_PHOTOZERO, 1, 1, 1, &zptObs, &status); - fits_write_col(this->base.fitsOut, TLONGLONG, IMAGEMETA_QAFLAGS, 1, 1, 1, &imageFlags, &status); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, IMAGEMETA_IMAGEID, 1, 1, 1, &pspsImageId); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONG, IMAGEMETA_FRAMEID, 1, 1, 1, &this->expId); + this->base.fitsOut->writeColumn(this->base.fitsOut, TSHORT, IMAGEMETA_CCDID, 1, 1, 1, &image->ccdnum); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONG, IMAGEMETA_PHOTOCALID, 1, 1, 1, &image->photcode); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, IMAGEMETA_FILTERID, 1, 1, 1, &filterID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, IMAGEMETA_PHOTOSCAT, 1, 1, 1, &zptObs); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, IMAGEMETA_PSFFWHM, 1, 1, 1, &psfFwhm); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, IMAGEMETA_MOMENTFWHM, 1, 1, 1, &momentFwhm); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, IMAGEMETA_PHOTOZERO, 1, 1, 1, &zptObs); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, IMAGEMETA_QAFLAGS, 1, 1, 1, &imageFlags); // now move BACK to detections table in smf sprintf(extensionName, "XY%s.psf", ccdNumber); - status=0; - if (fits_movnam_hdu(fitsIn, BINARY_TBL, extensionName, 0, &status)) { - psError(PS_ERR_IO, false, "Can't move to extension: %s skipping\n", extensionName); - continue; - } - - // keep a running count of 'images' we find in order to write total to FrameMeta at the end + long nChipDetectionsIn = 0; + if (!fitsIn->moveToBinaryTableAndCountRows(fitsIn, extensionName, &nChipDetectionsIn)) continue; + + // keep a running count of 'images' we find in order to write total into FrameMeta at the end nOta++; - - long nChipDetectionsIn = 0; - if (fits_get_num_rows(fitsIn, &nChipDetectionsIn, &status)) { - fits_report_error(stderr, status); - } // loop round detections to populate some extra stuff s = d = nChipDetectionsOut = invalidDvoRows = 0; - // determine column numbers for certain IPP detection columns + // determine column numbers for certain IPP detection columns - do this only once to save time if (firstTimeIn) { - status=0;fits_get_colnum(fitsIn, CASESEN, "IPP_IDET", &ippIDetNum, &status); - if (status) psError(PS_ERR_IO, false, "Unable to read col num for IPP_IDET"); - status=0;fits_get_colnum(fitsIn, CASESEN, "PSF_INST_MAG", &instMagNum, &status); - if (status) psError(PS_ERR_IO, false, "Unable to read col num for PSF_INST_MAG"); - status=0;fits_get_colnum(fitsIn, CASESEN, "PSF_INST_MAG_SIG", &instMagErrNum, &status); - if (status) psError(PS_ERR_IO, false, "Unable to read col num for PSF_INST_MAG_SIG"); - status=0;fits_get_colnum(fitsIn, CASESEN, "PEAK_FLUX_AS_MAG", &peakMagNum, &status); - if (status) psError(PS_ERR_IO, false, "Unable to read col num for PEAK_FLUX_AS_MAG"); + fitsIn->getColumnNumber(fitsIn, "IPP_IDET", &ippIDetNum); + fitsIn->getColumnNumber(fitsIn, "PSF_INST_MAG", &instMagNum); + fitsIn->getColumnNumber(fitsIn, "PSF_INST_MAG_SIG", &instMagErrNum); + fitsIn->getColumnNumber(fitsIn, "PEAK_FLUX_AS_MAG", &peakMagNum); firstTimeIn=false; } - anynull = 0; - fits_read_col(fitsIn, TLONG, ippIDetNum, 1, 1, nChipDetectionsIn, &longnull, ippIDet, &anynull, &status); - fits_read_col(fitsIn, TFLOAT, instMagNum, 1, 1, nChipDetectionsIn, &floatnull, instMag, &anynull, &status); - fits_read_col(fitsIn, TFLOAT, instMagErrNum, 1, 1, nChipDetectionsIn, &floatnull, instMagErr, &anynull, &status); - fits_read_col(fitsIn, TFLOAT, peakMagNum, 1, 1, nChipDetectionsIn, &floatnull, peakMag, &anynull, &status); + //anynull = 0; + fitsIn->readColumn(fitsIn, TLONG, ippIDetNum, 1, 1, nChipDetectionsIn, ippIDet); + fitsIn->readColumn(fitsIn, TFLOAT, instMagNum, 1, 1, nChipDetectionsIn, instMag); + fitsIn->readColumn(fitsIn, TFLOAT, instMagErrNum, 1, 1, nChipDetectionsIn, instMagErr); + fitsIn->readColumn(fitsIn, TFLOAT, peakMagNum, 1, 1, nChipDetectionsIn, peakMag); // DVO detections are ordered by IPP_IDET, which increments from 0 in SMF table @@ -260,4 +268,5 @@ // loop through all detections in smf file extension for this chip. // there are three ways for a detection to be ommitted from the final FITS output: + // // 1. it has a duplicate obj ID to a previous detection // 2. it has an invalid detection ID (< 0 or > max DVO det ID) @@ -312,5 +321,5 @@ // check for invalid flux values, and skip them - if ( !peakFluxOk || !instFluxOk) { + if (!peakFluxOk || !instFluxOk) { removeList[numOfDuplicates+numInvalidFlux+numOfInvalidIppIDet] = s+1; numInvalidFlux++; @@ -327,5 +336,5 @@ // write number of rows (detections) to ImageMeta - fits_write_col(this->base.fitsOut, TLONG, IMAGEMETA_NDETECT, 1, 1, 1, &nChipDetectionsOut, &status); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONG, IMAGEMETA_NDETECT, 1, 1, 1, &nChipDetectionsOut); int totalRemove = numOfDuplicates+numInvalidFlux+numOfInvalidIppIDet; @@ -335,41 +344,36 @@ // detections - ippToPspsConfig_writeTable(this->base.config, fitsIn, this->base.fitsOut, nChipDetectionsIn, "Detection", false); - fits_write_col(this->base.fitsOut, TLONGLONG, DETECTION_OBJID, 1, 1, nChipDetectionsIn, objID, &status); - fits_write_col(this->base.fitsOut, TLONGLONG, DETECTION_DETECTID, 1, 1, nChipDetectionsIn, detectID, &status); - fits_write_col(this->base.fitsOut, TLONGLONG, DETECTION_IPPOBJID, 1, 1, nChipDetectionsIn, ippObjID, &status); - fits_write_col(this->base.fitsOut, TLONGLONG, DETECTION_IPPDETECTID, 1, 1, nChipDetectionsIn, ippDetectID, &status); - fits_write_col(this->base.fitsOut, TBYTE, DETECTION_FILTERID, 1, 1, nChipDetectionsIn, filterIDs, &status); - fits_write_col(this->base.fitsOut, TBYTE, DETECTION_SURVEYID, 1, 1, nChipDetectionsIn, surveyIDs, &status); - fits_write_col(this->base.fitsOut, TLONGLONG, DETECTION_IMAGEID, 1, 1, nChipDetectionsIn, imageID, &status); - fits_write_col(this->base.fitsOut, TDOUBLE, DETECTION_OBSTIME, 1, 1, nChipDetectionsIn, obsTimes, &status); - fits_write_col(this->base.fitsOut, TFLOAT, DETECTION_INSTFLUX, 1, 1, nChipDetectionsIn, instFlux, &status); - fits_write_col(this->base.fitsOut, TFLOAT, DETECTION_INSTFLUXERR, 1, 1, nChipDetectionsIn, instFluxErr, &status); - fits_write_col(this->base.fitsOut, TFLOAT, DETECTION_PEAKADU, 1, 1, nChipDetectionsIn, peakFlux, &status); - fits_write_col(this->base.fitsOut, TSTRING, DETECTION_ASSOCDATE, 1, 1, nChipDetectionsIn, assocDate, &status); - fits_write_col(this->base.fitsOut, TLONGLONG, DETECTION_INFOFLAG, 1, 1, nChipDetectionsIn, flags, &status); - if (numOfDuplicates||numInvalidFlux||numOfInvalidIppIDet) - fits_delete_rowlist(this->base.fitsOut, removeList, totalRemove, &status); + this->base.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, nChipDetectionsIn, "Detection", false); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, DETECTION_OBJID, 1, 1, nChipDetectionsIn, objID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, DETECTION_DETECTID, 1, 1, nChipDetectionsIn, detectID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, DETECTION_IPPOBJID, 1, 1, nChipDetectionsIn, ippObjID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, DETECTION_IPPDETECTID, 1, 1, nChipDetectionsIn, ippDetectID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, DETECTION_FILTERID, 1, 1, nChipDetectionsIn, filterIDs); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, DETECTION_SURVEYID, 1, 1, nChipDetectionsIn, surveyIDs); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, DETECTION_IMAGEID, 1, 1, nChipDetectionsIn, imageID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TDOUBLE, DETECTION_OBSTIME, 1, 1, nChipDetectionsIn, obsTimes); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, DETECTION_INSTFLUX, 1, 1, nChipDetectionsIn, instFlux); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, DETECTION_INSTFLUXERR, 1, 1, nChipDetectionsIn, instFluxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, DETECTION_PEAKADU, 1, 1, nChipDetectionsIn, peakFlux); + this->base.fitsOut->writeColumn(this->base.fitsOut, TSTRING, DETECTION_ASSOCDATE, 1, 1, nChipDetectionsIn, assocDate); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, DETECTION_INFOFLAG, 1, 1, nChipDetectionsIn, flags); + if (numOfDuplicates||numInvalidFlux||numOfInvalidIppIDet) this->base.fitsOut->deleteRows(this->base.fitsOut, removeList, totalRemove); // skinny object - ippToPspsConfig_writeTable(this->base.config, fitsIn, this->base.fitsOut, nChipDetectionsIn, "SkinnyObject", false); - fits_write_col(this->base.fitsOut, TLONGLONG, SKINNYOBJECT_OBJID, 1, 1, nChipDetectionsIn, objID, &status); - fits_write_col(this->base.fitsOut, TLONGLONG, SKINNYOBJECT_IPPOBJID, 1, 1, nChipDetectionsIn, ippObjID, &status); - fits_write_col(this->base.fitsOut, TBYTE, SKINNYOBJECT_SURVEYID, 1, 1, nChipDetectionsIn, surveyIDs, &status); - if (numOfDuplicates||numInvalidFlux||numOfInvalidIppIDet) - fits_delete_rowlist(this->base.fitsOut, removeList, totalRemove, &status); + this->base.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, nChipDetectionsIn, "SkinnyObject", false); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, SKINNYOBJECT_OBJID, 1, 1, nChipDetectionsIn, objID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, SKINNYOBJECT_IPPOBJID, 1, 1, nChipDetectionsIn, ippObjID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, SKINNYOBJECT_SURVEYID, 1, 1, nChipDetectionsIn, surveyIDs); + if (numOfDuplicates||numInvalidFlux||numOfInvalidIppIDet) this->base.fitsOut->deleteRows(this->base.fitsOut, removeList, totalRemove); // object calibration color - ippToPspsConfig_writeTable(this->base.config, fitsIn, this->base.fitsOut, nChipDetectionsIn, "ObjectCalColor", false); - fits_write_col(this->base.fitsOut, TLONGLONG, OBJECTCALCOLOR_OBJID, 1, 1, nChipDetectionsIn, objID, &status); - fits_write_col(this->base.fitsOut, TLONGLONG, OBJECTCALCOLOR_IPPOBJID, 1, 1, nChipDetectionsIn, ippObjID, &status); - fits_write_col(this->base.fitsOut, TBYTE, OBJECTCALCOLOR_FILTERID, 1, 1, nChipDetectionsIn, filterIDs, &status); - if (numOfDuplicates||numInvalidFlux||numOfInvalidIppIDet) - fits_delete_rowlist(this->base.fitsOut, removeList, totalRemove, &status); + this->base.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, nChipDetectionsIn, "ObjectCalColor", false); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, OBJECTCALCOLOR_OBJID, 1, 1, nChipDetectionsIn, objID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, OBJECTCALCOLOR_IPPOBJID, 1, 1, nChipDetectionsIn, ippObjID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, OBJECTCALCOLOR_FILTERID, 1, 1, nChipDetectionsIn, filterIDs); + if (numOfDuplicates||numInvalidFlux||numOfInvalidIppIDet) this->base.fitsOut->deleteRows(this->base.fitsOut, removeList, totalRemove); } - psLogMsg("ippToPsps", PS_LOG_INFO, - "+-----------+---------+----------+----------------+--------------+--------------+\n" - "| Extension | Rows in | Rows out | Duplicate IDs | Invalid Flux | Bogus det ID |\n" + this->base.logger->print(this->base.logger, MSG_INFO, "DetectionBatch", "| %s | %5ld | %5d | %5d | %5d | %5d |\n", extensionName, nChipDetectionsIn, nChipDetectionsOut, numOfDuplicates, numInvalidFlux, numOfInvalidIppIDet); @@ -384,5 +388,8 @@ } - psLogMsg("ippToPsps", PS_LOG_INFO, "Total detections for this exposure = %ld\n", totalDetectionsOut); + this->base.logger->print(this->base.logger, MSG_INFO, "DetectionBatch", + "+-----------+---------+----------+----------------+--------------+--------------+\n"); + + this->base.logger->print(this->base.logger, MSG_INFO, "DetectionBatch", "Total detections for this exposure = %ld\n", totalDetectionsOut); // free-up memory @@ -408,27 +415,15 @@ // write number of images we have found into FrameMeta table - status=0; - if (fits_movnam_hdu(this->base.fitsOut, BINARY_TBL, "FrameMeta", 0, &status)) - psError(PS_ERR_IO, false, "Can't move back to FrameMeta extension to write number of OTAs\n"); - else { - fits_write_col(this->base.fitsOut, TSHORT, FRAMEMETA_NOTA, 1, 1, 1, &nOta, &status); - fits_write_col(this->base.fitsOut, TSHORT, FRAMEMETA_NUMPHOTOREF, 1, 1, 1, &totalNumPhotoRef, &status); - } - status=0; - if (fits_close_file(fitsIn, &status)) fits_report_error(stderr, status); - // write results - if (this->base.resultsXmlDoc) { - - xmlNodePtr rootNode = xmlDocGetRootElement(this->base.resultsXmlDoc); - char tmp[100]; - sprintf(tmp, "%ld", minObjID); - xmlNewChild(rootNode, NULL, BAD_CAST "minObjID", BAD_CAST tmp); - sprintf(tmp, "%ld", maxObjID); - xmlNewChild(rootNode, NULL, BAD_CAST "maxObjID", BAD_CAST tmp); - sprintf(tmp, "%ld", totalDetectionsOut); - xmlNewChild(rootNode, NULL, BAD_CAST "totalDetections", BAD_CAST tmp); - } - - psLogMsg("ippToPsps", PS_LOG_INFO, "Data written for a total of %d chips/OTAs", nOta); + if (this->base.fitsOut->moveToBinaryTable(this->base.fitsOut, "FrameMeta")) { + + this->base.fitsOut->writeColumn(this->base.fitsOut, TSHORT, FRAMEMETA_NOTA, 1, 1, 1, &nOta); + this->base.fitsOut->writeColumn(this->base.fitsOut, TSHORT, FRAMEMETA_NUMPHOTOREF, 1, 1, 1, &totalNumPhotoRef); + } + + fitsIn->destroy(fitsIn); + + writeResults(this, minObjID, maxObjID, totalDetectionsOut); + + this->base.logger->print(this->base.logger, MSG_INFO, "DetectionBatch", "Data written for a total of %d chips/OTAs\n", nOta); if (error || nOta < 1) this->base.exitCode = PS_EXIT_DATA_ERROR; @@ -438,5 +433,4 @@ } - /** Print-out this class. Calls base-calls print method first. @@ -446,7 +440,7 @@ this->base.print(&this->base); - printf("* exp ID : %d\n", this->expId); - printf("* exp name : '%s'\n", this->expName ? this->expName : "undef"); - printf("\n"); + this->base.logger->print(this->base.logger, MSG_INFO, "DetectionBatch", "exp ID : %d\n", this->expId); + this->base.logger->print(this->base.logger, MSG_INFO, "DetectionBatch", "exp name : %s\n", this->expName ? this->expName : "undef"); + this->base.logger->print(this->base.logger, MSG_INFO, "DetectionBatch", "\n"); } @@ -480,5 +474,7 @@ } - this->base.parseArguments(&this->base, argc, argv); + char fitsOutFile[40]; + sprintf(fitsOutFile, "%08d.FITS", this->expId); + this->base.parseArguments(&this->base, argc, argv, "/detection", fitsOutFile); if ( @@ -491,5 +487,5 @@ !haveExpName) { - printf("\n* ERROR with supplied arguments:"); + this->base.logger->print(this->base.logger, MSG_ERROR, "DetectionBatch", "Problem with supplied arguments\n"); this->print(this); this->base.exitCode = PS_EXIT_CONFIG_ERROR; @@ -503,17 +499,15 @@ Constructor. Returns a new DetectionBatch object. */ -DetectionBatch* new_DetectionBatch(int *argc, char **argv) { - +DetectionBatch* new_DetectionBatch(Logger* logger, int *argc, char **argv) { + + logger->print(logger, MSG_DEBUG, "DetectionBatch", "Constructor\n"); DetectionBatch *this = (DetectionBatch*)calloc(1, sizeof(DetectionBatch)); // call base-class constructor - if (!new_Batch(&this->base)) { - - psError(PS_ERR_IO, false, "Unable to create Batch base-class object"); - return this; - } + new_Batch(logger, &this->base); this->MAXDETECT = 200000; + // method pointers this->print = print; this->destroy = destroy; @@ -522,10 +516,7 @@ this->expName = (char*)calloc(100, sizeof(char)); - if (!parseArguments(this, *argc, argv)) { return this; } - - strcat(this->base.configsDir, "/detection"); - sprintf(this->base.fitsOutFile, "%08d.FITS", this->expId); - - this->base.init(&this->base); + parseArguments(this, *argc, argv); + + this->print(this); return this; @@ -537,27 +528,19 @@ int main(int argc, char **argv) { - psTimerStart("detectionbatch"); - - ippToPsps_VersionPrint(); - - int exitCode; - - DetectionBatch* detectionBatch = new_DetectionBatch(&argc, argv); +// ippToPsps_VersionPrint(); + + Logger* logger = new_Logger(NULL, false); +// Logger* logger = new_Logger("./detBatchLog.txt", false); + logger->print(logger, MSG_INFO, "main", "Creating new detection batch\n"); + + DetectionBatch* detectionBatch = new_DetectionBatch(logger, &argc, argv); detectionBatch->base.run(detectionBatch); - exitCode = detectionBatch->base.exitCode; + int exitCode = detectionBatch->base.exitCode; detectionBatch->destroy(detectionBatch); - double secs = psTimerMark("ippToPsps"); - - psLogMsg("detectionbatch", 3, "detectionbatch completed %ssuccessfully, with exit code %d, in %.1f %s\n", - (exitCode == PS_EXIT_SUCCESS) ? "" : "un", - exitCode, - (secs<60.0) ? secs : (secs/60.0), - (secs<60.0) ? "sec(s)" : "min(s)"); - // tidy up - psTimerStop(); psLibFinalize(); + logger->destroy(logger); return exitCode; Index: branches/eam_branches/ipp-20110213/ippToPsps/src/DetectionBatch.h =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/DetectionBatch.h (revision 30812) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/DetectionBatch.h (revision 31083) @@ -31,5 +31,5 @@ } DetectionBatch; -DetectionBatch *new_DetectionBatch(int *argc, char **argv); +DetectionBatch *new_DetectionBatch(Logger* logger, int *argc, char **argv); # endif // IPPTOPSPS_DETECTIONBATCH_H Index: branches/eam_branches/ipp-20110213/ippToPsps/src/Fits.c =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/Fits.c (revision 31083) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/Fits.c (revision 31083) @@ -0,0 +1,450 @@ +/** @file Fits.c + * + * @ingroup ippToPsps + * + * Source for all methods in the Fits class + * + * @author IfA + * Copyright 2011 Institute for Astronomy, University of Hawaii + */ + +#include "Fits.h" + +/** + Non-class method + + Gets cfitsio type from string + */ +int Fits_getDataType(char *typename) { + + if (!strncmp(typename, "TBYTE", 5)) return TBYTE; + if (!strncmp(typename, "TSHORT", 6)) return TSHORT; + if (!strncmp(typename, "TLONGLONG", 9)) return TLONGLONG; + if (!strncmp(typename, "TLONG", 5)) return TLONG; + if (!strncmp(typename, "TFLOAT", 6)) return TFLOAT; + if (!strncmp(typename, "TDOUBLE", 7)) return TDOUBLE; + if (!strncmp(typename, "TSTRING", 7)) return TSTRING; + +// this->logger->print(this->logger, MSG_ERROR, "Fits", "Don't understand data type '%s'", typename); + + return 0; +} + +/** + Destructor + */ +static void destroy(Fits* this) { + + this->logger->print(this->logger, MSG_DEBUG, "Fits", "Destructor\n"); + + int status = 0; + if (fits_close_file(this->file, &status)) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to close FITS file '%s'\n", this->path); + fits_report_error(stderr, status); + } + else + this->logger->print(this->logger, MSG_DEBUG, "Fits", "Closed FITS file '%s'\n", this->path); + + free(this); +} + +/** + Gets a header key value + */ +static bool getHeaderKeyValue(Fits* this, int type, char* name, void* value) { + + int status = 0; + fits_read_key(this->file, type, name, value, NULL, &status); + + if (status) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Could not get value for header key '%s' from file at '%s'\n", name, this->path); + return false; + } + + return true; +} + +/* + Gets the contents of a column vector + */ +static bool getColumnVector( + Fits* this, + int col, + long row, + int type, + int repeat, + float* vector) { + + int status = 0; + int anynull = 0; + + // remember to add 1 to row number since cfitsio is the stupidest libary ever written + fits_read_col(this->file, type, col, row+1, 1, repeat, NULL, vector, &anynull, &status); + + if (status) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Failed to read vector column %d row %ld\n", col, row); + return false; + } + + return true; +} + +/** + Gets the column number for the provided column name + */ +static bool getColumnNumber(Fits* this, char* name, int* number) { + + int status = 0; + fits_get_colnum(this->file, CASESEN, name, number, &status); + if (status) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Could not get column number for '%s'\n", name); + return false; + } + + return true; +} + +/* + Gets metadata about a column + */ +bool getColumnMeta( + Fits* this, + char* name, + int* colNum, + int* type, + long* repeat) { + + int status = 0; + fits_get_colnum(this->file, CASESEN, name, colNum, &status); + if (status) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to read col '%s'\n", name); + return false; + } + + status = 0; + fits_get_eqcoltype(this->file, *colNum, type, repeat, NULL, &status); + if (status) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to read type info for '%s'\n", name); + return false; + } + + return true; +} + + +/** + Moves to a certain extension of provided name and type + */ +bool moveToExtension(Fits* this, char* name, int type) { + + int status = 0; + if (fits_movnam_hdu(this->file, type, name, 0, &status)) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Can't move to table extension named '%s'\n", name); + return false; + } + + return true; +} + +/** + Moves to a certain header extension + */ +static bool moveToHeader(Fits* this, char* name) { + + return moveToExtension(this, name, IMAGE_HDU); +} + +/** + Moves to a certain binary table extension + */ +static bool moveToBinaryTable(Fits* this, char* name) { + + return moveToExtension(this, name, BINARY_TBL); +} + +/** + Counts the rows in the current table extension + */ +static bool countRows(Fits* this, long* count) { + + int status = 0; + if (fits_get_num_rows(this->file, count, &status)) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Count not count rows in this table\n"); + return false; + } + + return true; +} + +/** + Moves to a certain binary table extension and counts rows within + */ +static bool moveToBinaryTableAndCountRows(Fits* this, char* name, long* count) { + + if (!moveToExtension(this, name, BINARY_TBL)) return false; + return countRows(this, count); +} + +/** + Deletes this file. + */ +static bool delete(Fits* this) { + + if (remove(this->path) == -1) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to delete '%s'\n", this->path); + return false; + } + + this->logger->print(this->logger, MSG_INFO, "Fits", "Deleted FITS file at '%s'\n", this->path); + + return true; +} + +/** + Returns the file path. + */ +static char* getPath(Fits* this) { + + return this->path; +} + +/** + Returns the file pointer. + */ +static fitsfile* getFilePtr(Fits* this) { + + return this->file; +} + +/** + Deletes a bunch of rows from the current binary table + */ +static bool deleteRows(Fits* this, long *rowlist, long nrows) { + + int status = 0; + fits_delete_rowlist(this->file, rowlist, nrows, &status); + if (status) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to delete rows using rowlist\n"); + return false; + } + + return true; +} + +/** + Reads a column from the current binary table + */ +static bool readColumn( + Fits* this, + int datatype, + int colnum, + LONGLONG firstrow, + LONGLONG firstelem, + LONGLONG nelements, + void* coldata) { + + int anynull = 0; + int status = 0; + + if (datatype == TBYTE) { + + int8_t nullval = -99; + fits_read_col(this->file, datatype, colnum, firstrow, firstelem, nelements, &nullval, coldata, &anynull, &status); + } + else if (datatype == TSHORT) { + + int16_t nullval = -999; + fits_read_col(this->file, datatype, colnum, firstrow, firstelem, nelements, &nullval, coldata, &anynull, &status); + } + else if (datatype == TLONG || datatype == TLONGLONG) { + + long nullval = -999; + fits_read_col(this->file, datatype, colnum, firstrow, firstelem, nelements, &nullval, coldata, &anynull, &status); + } + else if (datatype == TFLOAT) { + + float nullval = -999.0; + fits_read_col(this->file, datatype, colnum, firstrow, firstelem, nelements, &nullval, coldata, &anynull, &status); + } + else if (datatype == TDOUBLE) { + + double nullval = -999.0; + fits_read_col(this->file, datatype, colnum, firstrow, firstelem, nelements, &nullval, coldata, &anynull, &status); + } + else if (datatype == TSTRING) { + + char nullval[20]; + strcpy(nullval, "null"); + fits_read_col(this->file, datatype, colnum, firstrow, firstelem, nelements, &nullval, coldata, &anynull, &status); + } + else { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Don't understand datatype '%d'\n", datatype); + return false; + } + + if (status) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to read column data from column %d\n", colnum); + return false; + + } + + return true; +} + +/** + Reads a column from the current binary table providing column name + */ +static bool readColumnUsingName( + Fits* this, + int datatype, + char* colname, + LONGLONG firstrow, + LONGLONG firstelem, + LONGLONG nelements, + void* coldata) { + + int colnum; + if (!getColumnNumber(this, colname, &colnum)) return false; + + return readColumn(this, datatype, colnum, firstrow, firstelem, nelements, coldata); +} + +/** + Writes a column to the current binary table + */ +static bool writeColumn( + Fits* this, + int datatype, + int colnum, + LONGLONG firstrow, + LONGLONG firstelem, + LONGLONG nelements, + void* coldata) { + + int status = 0; + fits_write_col(this->file, datatype, colnum, firstrow, firstelem, nelements, coldata, &status); + if (status) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to write column data for column %d\n", colnum); + return false; + + } + + return true; +} + +/** + Creates a new binary table + */ +static bool createBinaryTable( + Fits* this, + LONGLONG nRows, + int nCols, + char *names[], + char *types[], + char *name) { + + int status = 0; + fits_create_tbl(this->file, BINARY_TBL, nRows, nCols, names, types, NULL, name, &status); + + if (status) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to create table: '%s'\n", name); + return false; + } + + + return true; +} + +/** + Initilization common to all constructors + */ +static Fits* init(const char* path, Logger* logger) { + + Fits* this = (Fits*)calloc(1, sizeof(Fits)); + + // fields + strcpy(this->path, path); + this->logger = logger; + + // method pointers + this->getFilePtr = getFilePtr; + this->getPath = getPath; + this->countRows = countRows; + this->getColumnMeta = getColumnMeta; + this->getColumnNumber = getColumnNumber; + this->getColumnVector = getColumnVector; + this->readColumn = readColumn; + this->readColumnUsingName = readColumnUsingName; + this->getHeaderKeyValue = getHeaderKeyValue; + this->moveToExtension = moveToExtension; + this->moveToHeader = moveToHeader; + this->moveToBinaryTable = moveToBinaryTable; + this->moveToBinaryTableAndCountRows = moveToBinaryTableAndCountRows; + this->deleteRows = deleteRows; + this->createBinaryTable = createBinaryTable; + this->writeColumn = writeColumn; + this->delete = delete; + this->destroy = destroy; + + assert(this); + + return this; +} + +/** + Constructor. + + Returns a new Fits object representing an existing FITS file. + +*/ +Fits* existing_Fits(const char* path, Logger* logger) { + + Fits* this = init(path, logger); + this->logger->print(this->logger, MSG_DEBUG, "Fits", "Constructor for existing file at '%s'\n", path); + + int status = 0; + if (fits_open_file(&this->file, path, READONLY, &status)) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to open FITS file here %s\n", path); + this->file = NULL; + } + + + return this; +} + +/** + Constructor. + + Returns a new Fits object representing a new FITS file. + */ +Fits* new_Fits(const char* path, Logger* logger) { + + Fits* this = init(path, logger); + this->logger->print(this->logger, MSG_DEBUG, "Fits", "Constructor for new file at '%s'\n", path); + + int status = 0; + if (fits_create_file(&this->file, path, &status)) { + + this->logger->print(this->logger, MSG_ERROR, "Fits", "Unable to create FITS file here '%s'\n", path); + this->file = NULL; + } + + return this; +} + + Index: branches/eam_branches/ipp-20110213/ippToPsps/src/Fits.h =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/Fits.h (revision 31083) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/Fits.h (revision 31083) @@ -0,0 +1,64 @@ +/** @file Fits.h + * + * @brief An encapsulation of necessary cfitsio functions + * + * @ingroup ippToPsps + * + * @author IfA + * Copyright 2011 Institute for Astronomy, University of Hawaii + */ + +#ifndef IPPTOPSPS_FITS_H +#define IPPTOPSPS_FITS_H + +#include + +#include "Logger.h" + +/** + + Class that encapsulates a FITS file, making an OO interface to the dreaded cfitsio + + */ +typedef struct Fits { + + // fields + fitsfile* file; // cfitsio file pointer + char path[1000]; // FITS path + Logger* logger; // logger object + + // accessor methods + fitsfile* (*getFilePtr)(); + int (*getDataType)(); + char* (*getPath)(); + bool (*countRows)(); + bool (*getColumnMeta)(); + bool (*getColumnNumber)(); + bool (*getColumnVector)(); + bool (*readColumn)(); + bool (*readColumnUsingName)(); + bool (*getHeaderKeyValue)(); + + // mutators + bool (*moveToExtension)(); + bool (*moveToHeader)(); + bool (*moveToBinaryTable)(); + bool (*moveToBinaryTableAndCountRows)(); + bool (*createBinaryTable)(); + bool (*writeColumn)(); + bool (*deleteRows)(); + bool (*delete)(); + + // destructor + void (*destroy)(); + +} Fits; + +// constructors +Fits* existing_Fits(const char* path, Logger* logger); +Fits* new_Fits(const char* path, Logger* logger); + +// non-class methods +int Fits_getDataType(char *typename); + +# endif // IPPTOPSPS_FITS_H Index: branches/eam_branches/ipp-20110213/ippToPsps/src/FitsGenerator.c =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/FitsGenerator.c (revision 31083) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/FitsGenerator.c (revision 31083) @@ -0,0 +1,781 @@ +/** @file FitsGenerator.c + * + * @ingroup ippToPsps + * + * @author IfA + * Copyright 2011 Institute for Astronomy, University of Hawaii + */ + +#include "FitsGenerator.h" +#include +#include +#include + +#include "Fits.h" + +/** + Finds a column within this table + */ +static Column* findColumn(FitsGenerator* this, Table* table, const char* name) { + + Column* column = NULL; + + for (uint32_t i=0; inumOfColumns; i++) { + + if (strcmp(table->columns[i].pspsName, name) == 0) { + column = table->columns+i; + break; + } + } + + if (!column) this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Could not find column '%s' in table '%s'\n", name, table->name); + + return column; +} + +/** + Finds a table from the array of tables + */ +static Table* findTable(FitsGenerator* this, const char* name) { + + Table* table = NULL; + + for (uint32_t i=0; inumOfTables; i++) { + + if (strcmp(this->tables[i].name, name) == 0) { + table = this->tables+i; + break; + } + } + + if (!table) this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Could not find table '%s'\n", name); + + return table; +} + +/** + Gets an attribute value from XML node + */ +static bool getAttribute(xmlNode* node, const char* attName, char* _value) { + + xmlChar* value = xmlGetProp(node, (const xmlChar*)attName); + if (!value) return false; + sprintf(_value, "%s", value); + xmlFree(value); + + return true; +} + +/** + Creates a FITS binary table and populates it with defaults based on definition in schema XML + */ +static bool createTable(Table* table, Fits* fitsOut, const long nRows) { + + if (!table) return false; + if (nRows < 1) return false; + + long nCols = table->numOfColumns; + + char** colNames = (char**)calloc(nCols, sizeof(char*)); + char** colTypes = (char**)calloc(nCols, sizeof(char*)); + + uint32_t i = 0; + for (i=0;inumOfColumns; m++) { + + colNames[i] = table->columns[i].pspsName; + + // sprintf(colNames[i], table->columns[i].pspsName); + + switch (table->columns[i].pspsType) { + + case TBYTE: sprintf(colTypes[i],"1B"); + break; + case TSHORT: sprintf(colTypes[i],"1I"); + break; + case TLONG: sprintf(colTypes[i],"1J"); // TODO + break; + case TLONGLONG: sprintf(colTypes[i],"1K"); + break; + case TFLOAT: sprintf(colTypes[i],"1E"); + break; + case TDOUBLE: sprintf(colTypes[i],"1D"); + break; + case TSTRING: sprintf(colTypes[i],"32A"); // TODO width? + break; + + default: + break; + } + + i++; + } + + fitsOut->createBinaryTable(fitsOut, nRows, nCols, colNames, colTypes, table->name); + + for (i=0;inumOfColumns; i++) { + + col = i+1; + + strcpy(tempStr,table->columns[i].defaultValue); + tempLong = atol(tempStr); + tempDouble = atof(tempStr); + + switch (table->columns[i].pspsType) { + + case TBYTE: + for(j=0;jwriteColumn(fitsOut, TBYTE, col, 1, 1, nRows, int8col); + break; + case TSHORT: + for(j=0;jwriteColumn(fitsOut, TSHORT, col, 1, 1, nRows, int16col); + break; + case TLONG: + for(j=0;jwriteColumn(fitsOut, TLONG, col, 1, 1, nRows, longcol); + break; + + case TLONGLONG: + for(j=0;jwriteColumn(fitsOut, TLONGLONG, col, 1, 1, nRows, longcol); + break; + + case TFLOAT: + for(j=0;jwriteColumn(fitsOut, TFLOAT, col, 1, 1, nRows, floatcol); + break; + + case TDOUBLE: + for(j=0;jwriteColumn(fitsOut, TDOUBLE, col, 1, 1, nRows, doublecol); + break; + + case TSTRING: + for(j=0;jwriteColumn(fitsOut, TSTRING, col, 1, 1, nRows, strcol); + break; + + default: + break; + } + } + + free(int8col); + free(int16col); + free(longcol); + free(floatcol); + free(doublecol); + for (uint32_t i=0; ichildren; node; node = node->next) { + + if (strcmp((const char*)node->name, name)==0) count++; + } + + return count; +} + +/* + opens an XML file and returns the document + */ +static xmlDoc* openXmlFile(FitsGenerator* this, const char* path) { + + xmlDoc* doc = xmlReadFile(path, NULL, 0); + if (doc == NULL) this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Unable to open XML file at %s\n", path); + return doc; +} + +/* + closes an XML file + */ +static bool closeXmlFile(xmlDoc* doc) { + + xmlFreeDoc(doc); + xmlCleanupParser(); + + return true; +} + +/** + Populates the provided table with data from XML + */ +static bool populateTable(FitsGenerator* this, Table* table, xmlNode* rootElement, Fits *fitsOut) { + + char tempStr[100]; + xmlNode* node = NULL; + xmlNode* tableNode = NULL; + + // first check we have data for this table in XML file + for (node = rootElement->children; node; node = node->next) { + if (node->type == XML_ELEMENT_NODE) { + + if (strcmp((const char*)node->name, "table")!=0) continue; + if (!getAttribute(node, "name", tempStr)) continue; + if (strcmp(tempStr, table->name)==0) {tableNode = node; break;} + } + } + + if(!tableNode) { + + this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Could not find table: %s\n", table->name); + return false; + } + + // now count the number of rows + int nRows = countChildren(tableNode, "row"); + if (nRows < 1) return false; + if (!createTable(table, fitsOut, nRows)) return false; + + int rows=0; + int status; + char** strcol = (char**)calloc(1, sizeof(char**)); + strcol[0] = (char*)calloc(32,sizeof(char)); // TODO 20? size issue + + int8_t* bytecol = calloc(1, sizeof(uint8_t)); + int16_t* shortcol = calloc(1, sizeof(uint16_t)); + long* longcol = calloc(1, sizeof(long)); + double* doublecol = calloc(1, sizeof(double)); + float* floatcol = calloc(1, sizeof(float)); + + int col; + + // now get rows + for (node = tableNode->children; node; node = node->next) { + + if (strcmp((const char*)node->name, "row")!=0) continue; + + rows++; + + // get column data for this row + for (int i=0;inumOfColumns;i++) { + + col = i+1; + + if (!getAttribute(node, table->columns[i].pspsName, tempStr)) continue; + + strncpy(strcol[0], tempStr, 32); + status=0; + //psLogMsg("ippToPsps", PS_LOG_INFO, "Values %s - %ld - %f - %d", strcol[0], longcol[0], doublecol[0], bytecol[0]); + switch (table->columns[i].pspsType) { + + case TBYTE: + bytecol[0] = atoi(tempStr); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, bytecol); + break; + case TSHORT: + shortcol[0] = atoi(tempStr); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, shortcol); + break; + case TLONG: + case TLONGLONG: + longcol[0] = atol(tempStr); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, longcol); + break; + case TFLOAT: + floatcol[0] = atof(tempStr); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, floatcol); + break; + case TDOUBLE: + doublecol[0] = atof(tempStr); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, doublecol); + break; + case TSTRING: + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, strcol); + break; + + } + if (status) this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Unable to write value of %s to column %s in table %s\n", + tempStr, table->columns[i].pspsName, table->name); + } + } + + free(bytecol); + free(shortcol); + free(longcol); + free(floatcol); + free(doublecol); + free(strcol[0]); + free(strcol); + + return true; +} + +/** + Loads a table description from XML + */ +static bool loadTableDescription(FitsGenerator* this, Table* table, xmlNode* tableNode) { + + bool ret = true; + char tableName[100]; + getAttribute(tableNode, "name", tableName); + strcpy(table->name, tableName); + + // count how many columns we have coming in and allocate memory for them + table->numOfColumns = countChildren(tableNode, "column"); + table->columns = calloc(table->numOfColumns, sizeof(Column)); + // psLogMsg("ippToPsps", PS_LOG_INFO, " Found '%d' columns", table->numOfColumns); + + char buffer[200]; + xmlNode* node; + int columnNum = 0; + + for (node = tableNode->children; node; node = node->next) { + + if (strcmp((const char*)node->name, "column") != 0) continue; + + table->columns[columnNum].usingDefault = true; + + // column name + getAttribute(node, "name", buffer); + sprintf(table->columns[columnNum].pspsName, buffer); + + // column type + getAttribute(node, "type", buffer); + table->columns[columnNum].pspsType = Fits_getDataType(buffer); + + // default value + getAttribute(node, "default", buffer); + sprintf(table->columns[columnNum].defaultValue, buffer); + + // comment + getAttribute(node, "comment", buffer); + sprintf(table->columns[columnNum].comment, buffer); + + # if 0 + psLogMsg("ippToPsps", PS_LOG_INFO, "'%s' name='%s' type='%d' default='%s' comment='%s'", + table->name, + table->columns[columnNum].pspsName, + table->columns[columnNum].pspsType, + table->columns[columnNum].defaultValue, + table->columns[columnNum].comment); +# endif + columnNum++; + } + + + if (columnNum < 1) { + + this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Found no columns for table '%s'\n", tableName); + ret = false; + } + + if (columnNum != table->numOfColumns) + this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Mismatch between number of columns expected (%d) and those found (%d)\n", + table->numOfColumns, columnNum); + + return ret; +} + +/** + Reads table shapes from XML file + */ +static bool loadTableDescriptions(FitsGenerator* this) { + + bool ret = true; + + psString path = NULL; + psStringAppend(&path, "%s/tables.xml", this->configsPath); + + xmlDoc* doc = openXmlFile(this, path); + + if (doc == NULL) { + + psFree(path); + return false; + } + psFree(path); + + xmlNode* rootElement = xmlDocGetRootElement(doc); + + if (strcmp((const char*)rootElement->name, "tableDescriptions")!=0) { + + this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Root node of XML is not 'tableDescriptions', as it should be\n"); + return false; + } + + // count how many tables we have coming in and allocate memory for them + this->numOfTables = countChildren(rootElement, "table"); + this->tables = calloc(this->numOfTables, sizeof(Table)); + // psLogMsg("ippToPsps", PS_LOG_INFO, " Found '%d' tables", this->numOfTables); + + xmlNode* node = NULL; + Table* table = NULL; + + int tableNum = 0; + // loop round all available table descriptions + for (node = rootElement->children; node; node = node->next) { + if (node->type == XML_ELEMENT_NODE) { + + if (strcmp((const char*)node->name, "table")==0) { + + table = this->tables+tableNum; + + if (!loadTableDescription(this, table, node)) ret = false; + else tableNum++; + } + } + } + + if (tableNum != this->numOfTables) + this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Mismatch between number of tables expected (%d) and those found (%d)\n", + this->numOfTables, tableNum); + + closeXmlFile(doc); + + return ret; +} + +/** + Loads mappings from XML for a particular table + */ +static bool loadTableMappings(FitsGenerator* this, xmlNode* tableNode) { + + bool ret = false; + + xmlNode* node = NULL; + + char tableName[100]; + getAttribute(tableNode, "name", tableName); + + Table* table = findTable(this, tableName); + Column* column = NULL; + if (!table) return false; + + char buffer[100]; + //psLogMsg("ippToPsps", PS_LOG_INFO, "Table '%s'", tableName); + + // loop round all available mappings for this table + for (node = tableNode->children; node; node = node->next) { + if (node->type == XML_ELEMENT_NODE) { + + if (strcmp((const char*)node->name, "map")==0) { + + // column type + getAttribute(node, "pspsName", buffer); + column = findColumn(this, table, buffer); + + if (!column) continue; + + // IPP name + getAttribute(node, "ippName", buffer); + strcpy(column->ippName, buffer); + + // IPP type + getAttribute(node, "ippType", buffer); + column->ippType = Fits_getDataType(buffer); + + column->usingDefault = false; + + //psLogMsg("ippToPsps", PS_LOG_INFO, "...mapping PSPS:'%s' to '%s' '%d'", column->pspsName, column->ippName, column->ippColNum ); + } + } + } + + return ret; +} + +/** + Reads table mappings from XML file + */ +static bool loadMappings(FitsGenerator* this) { + + bool ret = true; + + char path[1000]; + sprintf(path, "%s/map.xml", this->configsPath); + + struct stat sts; + if ((stat(path, &sts)) == -1) { + this->logger->print(this->logger, MSG_INFO, "FitsGenerator", + "No map file found at '%s'\n", path); + return false; + } + + xmlDoc* doc = openXmlFile(this, path); + + if (doc == NULL) { + + this->logger->print(this->logger, MSG_ERROR,"FitsGenerator", + "Could not create XML document from '%s'\n", path); + return false; + } + + this->logger->print(this->logger, MSG_INFO, "FitsGenerator", + "Using map file at '%s'\n", path); + xmlNode* rootElement = xmlDocGetRootElement(doc); + + if (strcmp((const char*)rootElement->name, "tabledata")!=0) { + this->logger->print(this->logger, MSG_ERROR,"FitsGenerator", + "Root node of XML is not 'tabledata', as it should be\n"); + return false; + } + + xmlNode* node = NULL; + + // loop round all available tables + for (node = rootElement->children; node; node = node->next) { + if (node->type == XML_ELEMENT_NODE) { + + if (strcmp((const char*)node->name, "table")==0) { + + if (!loadTableMappings(this, node)) ret = false; + } + } + } + + closeXmlFile(doc); + + return ret; +} + +/** + Populate the provided table with data from XML + */ +static bool populateFromFile(FitsGenerator* this, Fits *fitsOut) { + + bool ret = true; + psString path = NULL; + psStringAppend(&path, "%s/data.xml", this->configsPath); + + xmlDoc* doc = openXmlFile(this, path); + + if (doc == NULL) { + psFree(path); + return false; + } + psFree(path); + + xmlNode* rootElement = xmlDocGetRootElement(doc); + + if (strcmp((const char*)rootElement->name, "tabledata")!=0) { + this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", + "Root node of XML is not 'tabledata', as it should be\n"); + return false; + } + + for (uint32_t i=0; inumOfTables; i++) { + if (!populateTable(this, this->tables+i, rootElement, fitsOut)) { + ret = false; + } + } + + closeXmlFile(doc); + + return ret; +} + +/** + Populate with data from another FITS table into this one + */ +static bool populateTableFromFits( + FitsGenerator* this, + Table* table, + Fits *fitsIn, + Fits *fitsOut, + const long nRows, + const bool fromHeader) { + + if (!table) return false; + if (!fitsIn) return false; + + int8_t* int8col = (int8_t*)calloc(nRows, sizeof(int8_t)); + int16_t* int16col = (int16_t*)calloc(nRows, sizeof(int16_t)); + long* longcol = (long*)calloc(nRows, sizeof(long)); + float* floatcol = (float*)calloc(nRows, sizeof(float)); + double* doublecol = (double*)calloc(nRows, sizeof(double)); + char** strcol = (char**)calloc(nRows, sizeof(char**)); + for (uint32_t i=0; inumOfColumns; i++) { + + if (strlen(table->columns[i].ippName) < 1) continue; + + int dummy; // TODO getting wrong type for some reason + if (!fitsIn->getColumnMeta(fitsIn, table->columns[i].ippName, &table->columns[i].ippColNum, &dummy, &table->columns[i].ippRepeat)) return false; + } + } + + int col; + for (uint32_t i=0; inumOfColumns; i++) { + + if (!table->columns[i].usingDefault) { + + col = i+1; + + switch (table->columns[i].ippType) { + + case TBYTE: + if (fromHeader) { + fitsIn->getHeaderKeyValue(fitsIn, TBYTE, table->columns[i].ippName, &int8col[0]); + } + else fitsIn->readColumn(fitsIn, TBYTE, table->columns[i].ippColNum, 1, 1, nRows, int8col); + fitsOut->writeColumn(fitsOut, TBYTE, col, 1, 1, nRows, int8col); + break; + case TSHORT: + if (fromHeader) { + fitsIn->getHeaderKeyValue(fitsIn, TSHORT, table->columns[i].ippName, &int16col[0]); + } + else fitsIn->readColumn(fitsIn, TSHORT, table->columns[i].ippColNum, 1, 1, nRows, int16col); + fitsOut->writeColumn(fitsOut, TSHORT, col, 1, 1, nRows, int16col); + break; + case TLONG: + if (fromHeader) { + fitsIn->getHeaderKeyValue(fitsIn, TLONG, table->columns[i].ippName, &longcol[0]); + } + else fitsIn->readColumn(fitsIn, TLONG, table->columns[i].ippColNum, 1, 1, nRows, longcol); + fitsOut->writeColumn(fitsOut, TLONG, col, 1, 1, nRows, longcol); + break; + case TLONGLONG: + if (fromHeader) { + fitsIn->getHeaderKeyValue(fitsIn, TLONGLONG, table->columns[i].ippName, &longcol[0]); + } + else fitsIn->readColumn(fitsIn, TLONGLONG, table->columns[i].ippColNum, 1, 1, nRows, longcol); + fitsOut->writeColumn(fitsOut, TLONGLONG, col, 1, 1, nRows, longcol); + break; + case TFLOAT: + if (fromHeader) { + fitsIn->getHeaderKeyValue(fitsIn, TFLOAT, table->columns[i].ippName,&floatcol[0]); + } + else fitsIn->readColumn(fitsIn, TFLOAT, table->columns[i].ippColNum, 1, 1, nRows, floatcol); + fitsOut->writeColumn(fitsOut, TFLOAT, col, 1, 1, nRows, floatcol); + break; + case TDOUBLE: + if (fromHeader) { + fitsIn->getHeaderKeyValue(fitsIn, TDOUBLE, table->columns[i].ippName, &doublecol[0]); + } + else fitsIn->readColumn(fitsIn, TDOUBLE, table->columns[i].ippColNum, 1, 1, nRows, doublecol); + fitsOut->writeColumn(fitsOut, TDOUBLE, col, 1, 1, nRows, doublecol); + break; + case TSTRING: + if (fromHeader) fitsIn->getHeaderKeyValue(fitsIn, TSTRING, table->columns[i].ippName, strcol[0]); + else fitsIn->readColumn(fitsIn, TSTRING, table->columns[i].ippColNum, 1, 1, nRows, strcol); + fitsOut->writeColumn(fitsOut, TSTRING, col, 1, 1, nRows, strcol); + break; + + default: + this->logger->print(this->logger, MSG_ERROR, "FitsGenerator", "Don't know IPP type (%d) for mapping from '%d' '%s' to '%s'\n", table->columns[i].ippType, + table->columns[i].ippColNum, table->columns[i].ippName, table->columns[i].pspsName); + break; + } + } + } + + free(int8col); + free(int16col); + free(longcol); + free(floatcol); + free(doublecol); + for (uint32_t i=0; inumOfTables;i++) + free(this->tables[i].columns); + + free(this->tables); + psFree(this->configsPath); + free(this); +} + +/** + Constructor. + */ +FitsGenerator* new_FitsGenerator(Logger* logger, const char* path) { + + FitsGenerator* this = (FitsGenerator*)calloc(1, sizeof(FitsGenerator)); + + this->configsPath = NULL; + psStringAppend(&this->configsPath, path); + this->logger = logger; + + // method pointers + this->createAndPopulateTable = createAndPopulateTable; + this->populateFromFile = populateFromFile; + this->destroy = destroy; + + // load tables descriptions from XML + if (loadTableDescriptions(this)) { + + // load any mappings we may have from XML + loadMappings(this); + } + + return this; +} + Index: branches/eam_branches/ipp-20110213/ippToPsps/src/FitsGenerator.h =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/FitsGenerator.h (revision 31083) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/FitsGenerator.h (revision 31083) @@ -0,0 +1,72 @@ +/** @file FitsGenerator.h + * + * @brief ippToPsps + * + * @ingroup ippToPsps + * + * @author IfA + * Copyright 2011 Institute for Astronomy, University of Hawaii + */ + +#ifndef IPPTOPSPS_FITSGENERATOR_H +#define IPPTOPSPS_FITSGENERATOR_H + +#include + +#include "Logger.h" + +// column class +typedef struct Column { + + int ippColNum; + char ippName[100]; + int ippType; + long ippRepeat; + char pspsName[100]; // TODO change to 'name' + int pspsType; + bool usingDefault; + char defaultValue[100]; + char comment[300]; + +} Column; + +// table class +typedef struct Table { + + char name[32]; + Column* columns; + int numOfColumns; + +} Table; + +/** + + Class used for generating FITS files. + + - Uses XML table definitions to create table shapes + - Uses XML map files to populate tables from another FITS files + - Uses XML data files to populate tables with set values + +*/ +typedef struct FitsGenerator { + + // fields + psString configsPath; + Table* tables; + int numOfTables; + Logger* logger; + + // methods + bool (*createAndPopulateTable)(); + bool (*populateFromFile)(); + + // destructor + void (*destroy)(); + +} FitsGenerator; + +// constructor +FitsGenerator* new_FitsGenerator(Logger* logger, const char* path); + +#endif // IPPTOPSPS_FITSGENERATOR_H + Index: branches/eam_branches/ipp-20110213/ippToPsps/src/InitBatch.c =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/InitBatch.c (revision 30812) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/InitBatch.c (revision 31083) @@ -18,5 +18,5 @@ if (this->base.exitCode != PS_EXIT_SUCCESS) return this->base.exitCode; - if (!ippToPspsConfig_populateFromFile(this->base.config, this->base.fitsOut)) + if (!this->base.fitsGenerator->populateFromFile(this->base.fitsGenerator, this->base.fitsOut)) this->base.exitCode = PS_EXIT_CONFIG_ERROR; else this->base.exitCode = PS_EXIT_SUCCESS; @@ -34,9 +34,9 @@ /** - Reads command-line arguments. Calls base-calls print method first. + Reads command-line arguments. */ static bool parseArguments(InitBatch* this, int argc, char **argv) { - this->base.parseArguments(&this->base, argc, argv); + this->base.parseArguments(&this->base, argc, argv, "/init", "00000000.FITS"); if ( @@ -44,10 +44,8 @@ !this->base.gotConfig() ) { - printf("\n* ERROR with supplied arguments:"); - this->print(this); + this->base.logger->print(this->base.logger, MSG_ERROR, "InitBatch", "Problem with supplied arguments\n"); this->base.exitCode = PS_EXIT_CONFIG_ERROR; return false; } - return true; @@ -57,25 +55,20 @@ Constructor */ -InitBatch* new_InitBatch(int *argc, char **argv) { +InitBatch* new_InitBatch(Logger* logger, int *argc, char **argv) { + logger->print(logger, MSG_DEBUG, "InitBatch", "Constructor\n"); InitBatch *this = (InitBatch*)calloc(1, sizeof(InitBatch)); // call base-class constructor - if (!new_Batch(&this->base)) { + new_Batch(logger, &this->base); - psError(PS_ERR_IO, false, "Unable to create Batch base-class object"); - return this; - } - + // method pointers this->print = print; this->destroy = destroy; this->base.run = run; - if (!parseArguments(this, *argc, argv)) { return this; } + parseArguments(this, *argc, argv); - strcat(this->base.configsDir, "/init"); - sprintf(this->base.fitsOutFile, "00000000.FITS"); - - this->base.init(&this->base); + this->print(this); return this; @@ -87,27 +80,18 @@ int main(int argc, char **argv) { - psTimerStart("initbatch"); +// ippToPsps_VersionPrint(); - ippToPsps_VersionPrint(); + Logger* logger = new_Logger(NULL, false); + logger->print(logger, MSG_INFO, "main", "Creating new initialization batch\n"); - int exitCode; - - InitBatch* initBatch = new_InitBatch(&argc, argv); + InitBatch* initBatch = new_InitBatch(logger, &argc, argv); initBatch->base.run(initBatch); - exitCode = initBatch->base.exitCode; + int exitCode = initBatch->base.exitCode; initBatch->destroy(initBatch); - double secs = psTimerMark("initbatch"); - - psLogMsg("initbatch", 3, "initbatch completed %ssuccessfully, with exit code %d, in %.1f %s\n", - (exitCode == PS_EXIT_SUCCESS) ? "" : "un", - exitCode, - (secs<60.0) ? secs : (secs/60.0), - (secs<60.0) ? "sec(s)" : "min(s)"); - // tidy up - psTimerStop(); psLibFinalize(); + logger->destroy(logger); return exitCode; Index: branches/eam_branches/ipp-20110213/ippToPsps/src/InitBatch.h =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/InitBatch.h (revision 30812) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/InitBatch.h (revision 31083) @@ -24,9 +24,12 @@ // methods void (*print)(); + + // destructor void (*destroy)(); } InitBatch; -InitBatch *new_InitBatch(int *argc, char **argv); +// constructor +InitBatch *new_InitBatch(Logger *logger, int *argc, char **argv); # endif // IPPTOPSPS_INITBATCH_H Index: branches/eam_branches/ipp-20110213/ippToPsps/src/InitData.c =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/InitData.c (revision 31083) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/InitData.c (revision 31083) @@ -0,0 +1,225 @@ +/** @file InitData.c + * + * @ingroup ippToPsps + * + * @author IfA + * Copyright 2011 Institute for Astronomy, University of Hawaii + */ + +#include "InitData.h" +#include "Fits.h" + + +/** + Gets an attribute value from XML node + */ +static bool getAttribute(xmlNode* node, const char* attName, char* _value) { + + xmlChar* value = xmlGetProp(node, (const xmlChar*)attName); + if (!value) return false; + sprintf(_value, "%s", value); + xmlFree(value); + + return true; +} + +/** + Searches through this table and finds attribute value for a provided key + */ +static bool getRowAttribute( + InitData* this, + xmlNode* tableNode, + const char* keyName, + const char* keyValue, + const char* attName, + char* attValue) { + + xmlNode* node = NULL; + + char buffer[100]; + + // loop round all available rows for this table + for (node = tableNode->children; node; node = node->next) { + if (node->type == XML_ELEMENT_NODE) { + //psLogMsg("ippToPsps", PS_LOG_INFO, "Node name '%s'", (const char*)node->name ); + + if (strcmp((const char*)node->name, "row")==0) { + //psLogMsg("ippToPsps", PS_LOG_INFO, " Looking for key '%s'", keyName ); + + if (!getAttribute(node, keyName, buffer)) continue; + //psLogMsg("ippToPsps", PS_LOG_INFO, "Found key '%s' value '%s'", keyName, buffer ); + + if (strcmp(buffer, keyValue) != 0) continue; + getAttribute(node, attName, attValue); + //printf("FOUND %s %s %s %s \n", keyName, buffer, attName, attValue ); + return true; + + } + } + } + + this->logger->print(this->logger, MSG_ERROR, + "InitData", "Could not find value for '%s' for '%s' with value '%s'\n", + attName, keyName, keyValue); + + return false; +} + +/** + Gets a value from the 'init' data + */ +static bool getInitValue( + InitData* this, + const char* tableName, + const char* keyName, + const char* keyValue, + const char* attName, + char* attValue) { + + bool ret = true; + + xmlNode* rootElement = xmlDocGetRootElement(this->doc); + + if (strcmp((const char*)rootElement->name, "tabledata")!=0) { + this->logger->print(this->logger, MSG_ERROR, + "InitData", "Root node of XML is not 'tabledata', as it should be\n"); + return false; + } + + xmlNode* node = NULL; + char tempStr[100]; + + // loop round all available tables + for (node = rootElement->children; node; node = node->next) { + if (node->type == XML_ELEMENT_NODE) { + + if (strcmp((const char*)node->name, "table")!=0) continue; + if (!getAttribute(node, "name", tempStr)) continue; + if (strcmp(tempStr, tableName)!=0) continue; + + ret = getRowAttribute(this, node, keyName, keyValue, attName, attValue); + break; + } + + } + + return ret; +} + +/** + Gets model fit ID from name + */ +static bool getModelFitId(InitData* this, const char* name, int8_t* id) { + + char buffer[10]; + if (!getInitValue(this, "FitModel", "name", name, "fitModelID", buffer)) { + + *id = -1; + return false; + } + + *id = atoi(buffer); + return true; +} + +/** + Gets survey ID from survey name + */ +static bool getSurveyId(InitData* this, const char* name, int8_t* id) { + + char buffer[10]; + if (!getInitValue(this, "Survey", "name", name, "surveyID", buffer)) { + + *id = -1; + return false; + } + + *id = atoi(buffer); + return true; +} + +/** + Gets stack type ID from stack type string + */ +static bool getStackTypeId(InitData* this, const char* type, int8_t* id) { + + char buffer[20]; + if (!getInitValue(this, "StackType", "stackType", type, "stackTypeID", buffer)) { + + *id = -1; + return false; + } + + *id = atoi(buffer); + return true; +} + +/** + Gets filter ID from filter type string + */ +static bool getFilterId(InitData* this, const char* type, int8_t* id) { + + char tmp[2]; + strncpy(tmp, type,1); + tmp[1] = '\0'; + char buffer[10]; + if (!getInitValue(this, "Filter", "filterType", tmp, "filterID", buffer)) { + + *id = -1; + return false; + } + + *id = atoi(buffer); + return true; +} + +/** + Destructor. + */ +static void destroy(InitData* this) { + + if (this == NULL) return; + + if (this->doc != NULL) { + + xmlFreeDoc(this->doc); + xmlCleanupParser(); + } + + this->logger->print(this->logger, MSG_DEBUG, "InitData", "Destructor\n"); + + free(this); +} + +/** + Constructor. + */ +InitData* new_InitData(const char* path, Logger* logger) { + + InitData* this = (InitData*)calloc(1, sizeof(InitData)); + this->logger = logger; + + this->logger->print(this->logger, MSG_DEBUG, "InitData", "Constructor\n"); + + sprintf(this->path, "%s/init/data.xml", path); + + this->doc = xmlReadFile(this->path, NULL, 0); + + if (this->doc == NULL) + this->logger->print(this->logger, MSG_ERROR, + "InitData", "Unable to open init data file at '%s'\n", this->path); + else + this->logger->print(this->logger, MSG_INFO, + "InitData", "Using init data file at '%s'\n", this->path); + + + // method pointers + this->getFilterId = getFilterId; + this->getSurveyId = getSurveyId; + this->getStackTypeId = getStackTypeId; + this->getModelFitId = getModelFitId; + this->destroy = destroy; + + return this; +} + Index: branches/eam_branches/ipp-20110213/ippToPsps/src/InitData.h =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/InitData.h (revision 31083) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/InitData.h (revision 31083) @@ -0,0 +1,48 @@ +/** @file InitData.h + * + * @brief ippToPsps + * + * @ingroup ippToPsps + * + * @author IfA + * Copyright 2011 Institute for Astronomy, University of Hawaii + */ + +#ifndef IPPTOPSPS_INITDATA_H +#define IPPTOPSPS_INITDATA_H + +#include +#include + +#include + +#include "Logger.h" + +/** + + Class encapsulating the initialization data + +*/ +typedef struct InitData { + + // fields + char path[1000]; + xmlDoc* doc; + Logger* logger; + + // methods + bool (*getFilterId)(); + bool (*getSurveyId)(); + bool (*getStackTypeId)(); + bool (*getModelFitId)(); + + // destructor + void (*destroy)(); + +} InitData; + +// constructor +InitData* new_InitData(const char* path, Logger* logger); + +#endif // IPPTOPSPS_INITDATA_H + Index: branches/eam_branches/ipp-20110213/ippToPsps/src/Logger.c =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/Logger.c (revision 31083) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/Logger.c (revision 31083) @@ -0,0 +1,119 @@ +/** @file Logger.c + * + * @ingroup ippToPsps + * + * Source for all methods in the Logger class + * + * @author IfA + * Copyright 2011 Institute for Astronomy, University of Hawaii + */ + +#include +#include +#include +#include + #include + +#include "Logger.h" + +/** + Destructor + */ +static void destroy(Logger* this) { + + struct timeval stopTime; + gettimeofday(&stopTime, 0); + double secs = (double)(stopTime.tv_sec-this->startTime.tv_sec); + + this->print(this, MSG_INFO, "Logger", + "Completed in %.1f %s\n", + (secs<60.0) ? secs : (secs/60.0), + (secs<60.0) ? "sec(s)" : "min(s)"); + + this->print(this, MSG_DEBUG, "Logger", "Destructor\n"); + free(this); +} + +/** + Prints a message + */ +static void print(void* this, const int8_t typeInt, const char* class, const char* fmt, ...) { + + Logger* logger = (Logger*)this; + + va_list args; + va_start(args, fmt); + char msg_fmt[1000]; + + // get message-type string + char typeStr[20]; + switch(typeInt) { + + case MSG_INFO: + sprintf(typeStr, "INFO"); + break; + case MSG_ERROR: + sprintf(typeStr, "ERROR"); + break; + case MSG_DEBUG: + if (!logger->showDebug) return; + sprintf(typeStr, "DEBUG"); + break; + default: + break; + } + + // get time string + char timeStr[30]; + time_t now = time(NULL); + struct tm tim = *(localtime(&now)); + strftime(timeStr, 30, "%Y/%m/%d %H:%M:%S",&tim); + + if (typeInt == MSG_NONE) + sprintf(msg_fmt, "%s", fmt); + else + sprintf(msg_fmt, "%18s | %6s | %15s | %s ", timeStr, typeStr, class, fmt); + + + // write either to file or stdout + if(logger->file == NULL) vprintf(msg_fmt, args); + else vfprintf(logger->file, msg_fmt, args); +} + +/** + Constructor. + + Returns a new Logger object. + + path - path to file where log should be saved, otherwise stdout is used + showDebug - show debug messages or not + */ +Logger* new_Logger(const char* path, const int8_t showDebug) { + + Logger* this = (Logger*)calloc(1, sizeof(Logger)); + + this->file = NULL; + this->showDebug = showDebug; + gettimeofday(&this->startTime, 0); + + // open a file to write to + if (path != NULL) this->file = fopen(path, "w+"); + + print(this, MSG_DEBUG, "Logger", "Constructor\n"); + print(this, MSG_INFO, "Logger", "Starting timer\n"); + + if (path != NULL) { + + if (this->file == NULL) + print(this, MSG_ERROR, "Logger", "Cannot open file for writing here '%s'\n", path); + else + printf("**** Saving log to '%s'\n", path); + } + + // method pointers + this->print = print; + this->destroy = destroy; + + return this; +} + Index: branches/eam_branches/ipp-20110213/ippToPsps/src/Logger.h =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/Logger.h (revision 31083) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/Logger.h (revision 31083) @@ -0,0 +1,49 @@ +/** @file logger.h + * + * @brief Batch + * + * @ingroup ippToPsps + * + * @author IfA + * Copyright 2011 Institute for Astronomy, University of Hawaii + */ + +#ifndef IPPTOPSPS_LOGGER_H +#define IPPTOPSPS_LOGGER_H + +// message types +typedef enum { + + MSG_INFO, + MSG_ERROR, + MSG_DEBUG, + MSG_NONE + +} MessageTypes; + + +/** + Logger class. + + Prints either to stdout or a file + */ +typedef struct Logger { + + // fields + FILE* file; + struct timeval startTime; + int8_t showDebug; + + // methods + void (*print)(void* logger, const int8_t typeInt, const char* class, const char* fmt, ...); + + // destructor + void (*destroy)(); + +} Logger; + +// constructor +Logger* new_Logger(const char* path, const int8_t showDebug); + +# endif // IPPTOPSPS_LOGGER_H + Index: branches/eam_branches/ipp-20110213/ippToPsps/src/Makefile.am =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/Makefile.am (revision 30812) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/Makefile.am (revision 31083) @@ -31,5 +31,8 @@ Batch.c \ Version.c \ - Config.c + Fits.c \ + InitData.c \ + Logger.c \ + FitsGenerator.c # detectionbatch @@ -40,5 +43,8 @@ Batch.c \ Version.c \ - Config.c + Fits.c \ + InitData.c \ + Logger.c \ + FitsGenerator.c # stackbatch @@ -49,5 +55,8 @@ Batch.c \ Version.c \ - Config.c + Fits.c \ + InitData.c \ + Logger.c \ + FitsGenerator.c clean-local: Index: branches/eam_branches/ipp-20110213/ippToPsps/src/StackBatch.c =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/StackBatch.c (revision 30812) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/StackBatch.c (revision 31083) @@ -1,4 +1,6 @@ #include "StackBatch.h" #include "StackBatchEnums.h" + +#include "Fits.h" /** @@ -13,181 +15,103 @@ /** - Does the work. - */ -static int run(StackBatch* this) { - - if (this->base.exitCode != PS_EXIT_SUCCESS) return this->base.exitCode; - - int status = 0; - fitsfile *fitsIn; - - if (fits_open_file(&fitsIn, this->base.inputFiles[0], READONLY, &status)) { - - fits_report_error(stderr, status); - return PS_EXIT_SYS_ERROR; - } - - - // get primary header and pull stuff out for later - int nKeys = 0; - fits_get_hdrspace(fitsIn, &nKeys, NULL, &status); - float exposureTime; status=0; fits_read_key(fitsIn, TFLOAT, "EXPTIME", &exposureTime, NULL, &status); - char filterType[20]; status=0; fits_read_key(fitsIn, TSTRING, "FILTER", filterType, NULL, &status); - - + Creates the StackDetection table + */ +static bool createStackDetectionTable( + StackBatch* this, + Fits* fitsIn, + int8_t* filterIDs, + int8_t* surveyIDs, + long* skycellIDs, + float exposureTime + ) { + + char extensionName[25]; + sprintf(extensionName, "SkyChip.psf"); + long nDet = 0; + if (!fitsIn->moveToBinaryTableAndCountRows(fitsIn, extensionName, &nDet)) return false; + + + // allocate stuff char** assocDate = (char**)calloc(this->MAXDETECT, sizeof(char**)); for (uint32_t i=0; iMAXDETECT;i++) assocDate[i] = (char*)calloc(20,sizeof(char)); - - - - // write StackMeta - ippToPspsConfig_writeTable(this->base.config, fitsIn, this->base.fitsOut, 1, "StackMeta", true); - fits_write_col(this->base.fitsOut, TLONG, STACKMETA_SKYCELLID, 1, 1, 1, &this->skycellId, &status); - - int8_t filterID = -1; - if (!ippToPspsConfig_getFilterId(this->base.config, filterType, &filterID)) { - -// this->base.exitCode = PS_EXIT_DATA_ERROR; - // return this->base.exitCode; TODO - } - long* removeList = (long*)calloc(this->MAXDETECT, sizeof(long)); float* instMag = (float*)calloc(this->MAXDETECT, sizeof(float)); - int8_t* filterIDs = (int8_t*)calloc(this->MAXDETECT, sizeof(int8_t)); - int8_t* surveyIDs = (int8_t*)calloc(this->MAXDETECT, sizeof(int8_t)); - float floatnull = -999.0; - int anynull = 0; - - fits_write_col(this->base.fitsOut, TBYTE, STACKMETA_FILTERID, 1, 1, 1, &filterID, &status); - - fits_write_col(this->base.fitsOut, TBYTE, STACKMETA_SURVEYID, 1, 1, 1, &this->base.surveyID, &status); - - - // psf detections - char extensionName[15]; - sprintf(extensionName, "Chip.psf"); - if (fits_movnam_hdu(fitsIn, BINARY_TBL, extensionName, 0, &status)) { - psError(PS_ERR_IO, false, "Can't move to extension: %s\n", extensionName); - - } - else { - - // some stuff is the same for all detections so we can populate here - for (long s = 0; sMAXDETECT; s++) { - - filterIDs[s] = filterID; - surveyIDs[s] = this->base.surveyID; - strcpy(assocDate[s], this->base.todaysDate); + float* peakMag = (float*)calloc(this->MAXDETECT, sizeof(float)); + float* peakFlux = (float*)calloc(this->MAXDETECT, sizeof(float)); + int* flags1 = (int*)calloc(this->MAXDETECT, sizeof(int)); + int* flags2 = (int*)calloc(this->MAXDETECT, sizeof(int)); + uint64_t* infoFlags = (uint64_t*)calloc(this->MAXDETECT, sizeof(uint64_t)); + + bool peakFluxOk; + + // some stuff is the same for all detections so we can populate here + for (long s = 0; sMAXDETECT; s++) { + + // if running in test mode, don't use today's date + if (this->base.testMode) strcpy(assocDate[s], "2010-01-01"); + else strcpy(assocDate[s], this->base.todaysDate); + } + + fitsIn->readColumnUsingName(fitsIn, TFLOAT, "PSF_INST_MAG", 1, 1, nDet, instMag); + fitsIn->readColumnUsingName(fitsIn, TFLOAT, "PEAK_FLUX_AS_MAG", 1, 1, nDet, peakMag); + fitsIn->readColumnUsingName(fitsIn, TLONG, "FLAGS", 1, 1, nDet, flags1); + fitsIn->readColumnUsingName(fitsIn, TLONG, "FLAGS2", 1, 1, nDet, flags2); + + this->base.logger->print(this->base.logger, MSG_INFO, "StackBatch", + "Looping through %ld psf detection rows from '%s'\n", nDet, extensionName); + float mag; + long unmatched = 0, totalDetections = 0, numOfDuplicates = 0, numInvalidFlux = 0, numDetectionsOut = 0; + + this->base.logger->print(this->base.logger, MSG_INFO, "StackBatch", + "+---------------+---------+----------+------------------+---------------+--------------+\n"); + this->base.logger->print(this->base.logger, MSG_INFO, "StackBatch", + "| Extension | Rows in | Rows out | Missing from DVO | Duplicate IDs | Invalid Flux |\n"); + + for (long s=0; s 0) { - - ippToPspsConfig_writeTable(this->base.config, fitsIn, this->base.fitsOut, nDet, "StackDetection", false); - fits_write_col(this->base.fitsOut, TLONG, STACKDETECTION_SKYCELLID, 1, 1, 1, &this->skycellId, &status); - fits_write_col(this->base.fitsOut, TBYTE, STACKDETECTION_FILTERID, 1, 1, nDet, filterIDs, &status); - fits_write_col(this->base.fitsOut, TBYTE, STACKDETECTION_SURVEYID, 1, 1, nDet, surveyIDs, &status); - fits_write_col(this->base.fitsOut, TSTRING, STACKDETECTION_ASSOCDATE, 1, 1, nDet, assocDate, &status); - - if (numInvalidFlux) fits_delete_rowlist(this->base.fitsOut, removeList, numInvalidFlux, &status); - - } - psLogMsg("ippToPsps", PS_LOG_INFO, - "+---------------+---------+----------+------------------+---------------+--------------+\n" - "| Extension | Rows in | Rows out | Missing from DVO | Duplicate IDs | Invalid Flux |\n" - "| %12s | %5ld | %5ld | %5ld | %5ld | %5ld |\n", - extensionName, nDet, numDetectionsOut, unmatched, numOfDuplicates, numInvalidFlux); - - } - - - - // extended source - sprintf(extensionName, "Chip.xsrc"); - if (fits_movnam_hdu(fitsIn, BINARY_TBL, extensionName, 0, &status)) { - psError(PS_ERR_IO, false, "Can't move to extension: %s\n", extensionName); - - } - else { - - int colNum; - int type; - long repeat; - - ippToPspsConfig_getFitsColumnMeta( - "PROF_FLUX", - &colNum, - &type, - &repeat, - fitsIn); - printf("PROF_FILL = %d %d %ld\n", colNum, type, repeat); - float* vector = calloc(repeat, sizeof(float)); - - ippToPspsConfig_getColumnVector( - colNum, - 1, - type, - repeat, - vector, - fitsIn); - - - - free(vector); - - long nDet = 0; - if (fits_get_num_rows(fitsIn, &nDet, &status)) { - fits_report_error(stderr, status); - } - - printf("Looping through %ld extended source detections\n", nDet); - for (long s = 0; sbase.config, fitsIn, this->base.fitsOut, nDet, "StackApFlx", false); - fits_write_col(this->base.fitsOut, TBYTE, STACKAPFLX_FILTERID, 1, 1, nDet, filterIDs, &status); - fits_write_col(this->base.fitsOut, TBYTE, STACKAPFLX_SURVEYID, 1, 1, nDet, surveyIDs, &status); - } + } + + numDetectionsOut = totalDetections - numInvalidFlux; + if (numDetectionsOut > 0) { + + this->base.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, nDet, "StackDetection", false); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONG, STACKDETECTION_SKYCELLID, 1, 1, nDet, skycellIDs); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, STACKDETECTION_FILTERID, 1, 1, nDet, filterIDs); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKDETECTION_PEAKFLUX, 1, 1, nDet, peakFlux); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, STACKDETECTION_SURVEYID, 1, 1, nDet, surveyIDs); + this->base.fitsOut->writeColumn(this->base.fitsOut, TSTRING, STACKDETECTION_ASSOCDATE, 1, 1, nDet, assocDate); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONGLONG, STACKDETECTION_INFOFLAG, 1, 1, nDet, flags1); + + if (numInvalidFlux) this->base.fitsOut->deleteRows(this->base.fitsOut, removeList, numInvalidFlux); + + } + + this->base.logger->print(this->base.logger, MSG_INFO, "StackBatch", + "| %12s | %5ld | %5ld | %5ld | %5ld | %5ld |\n", + extensionName, nDet, numDetectionsOut, unmatched, numOfDuplicates, numInvalidFlux); + this->base.logger->print(this->base.logger, MSG_INFO, "StackBatch", + "+---------------+---------+----------+------------------+---------------+--------------+\n"); @@ -195,15 +119,264 @@ free(removeList); free(instMag); + free(flags1); + free(flags2); + free(infoFlags); + for (uint32_t i=0; iMAXDETECT;i++) free(assocDate[i]); + free(assocDate); + + return true; +} +/** + Structure to encapsulate block of flux values for StackApFlx table + */ +typedef struct { + + float* flx; + float* flxErr; + float* flxStd; + float* flxFill; + +} StackApFlxFluxes; + +/** + Creates the StackApFlx table for extended source attributes + */ +static bool createStackApFlxTable( + StackBatch* this, + Fits* fitsIn, + int8_t* filterIDs, + int8_t* surveyIDs + ) { + + long nDet = 0; + char extensionName[15]; + sprintf(extensionName, "SkyChip.xrad"); + if (!fitsIn->moveToBinaryTableAndCountRows(fitsIn, extensionName, &nDet)) return false; + + + int aperFluxColNum, aperFluxErrColNum, aperFluxStDevColNum, aperFluxFillColNum; + int type; // all the same type + long repeat; + + fitsIn->getColumnMeta(fitsIn, "APER_FLUX", &aperFluxColNum, &type, &repeat); + fitsIn->getColumnMeta(fitsIn, "APER_FLUX_ERR", &aperFluxErrColNum, &type, &repeat); + fitsIn->getColumnMeta(fitsIn, "APER_FLUX_STDEV", &aperFluxStDevColNum, &type, &repeat); + fitsIn->getColumnMeta(fitsIn, "APER_FILL", &aperFluxFillColNum, &type, &repeat); + float* vector = calloc(repeat, sizeof(float)); + + // we store 10 different flux values + StackApFlxFluxes* stackApFlxFluxes = (StackApFlxFluxes*)calloc(11, sizeof(StackApFlxFluxes)); + for (long i=0; i<11; i++) { + + stackApFlxFluxes[i].flx = (float*)calloc(nDet, sizeof(float)); + stackApFlxFluxes[i].flxErr = (float*)calloc(nDet, sizeof(float)); + stackApFlxFluxes[i].flxStd = (float*)calloc(nDet, sizeof(float)); + stackApFlxFluxes[i].flxFill = (float*)calloc(nDet, sizeof(float)); + } + + this->base.logger->print(this->base.logger, MSG_INFO, "StackBatch", + "Looping through %ld extended source detections from extension '%s'\n", nDet, extensionName); + for (long s=0; sgetColumnVector(fitsIn, aperFluxColNum,s, type, repeat, vector); + for (int i=0; igetColumnVector(fitsIn, aperFluxErrColNum,s, type, repeat, vector); + for (int i=0; igetColumnVector(fitsIn, aperFluxStDevColNum,s, type, repeat, vector); + for (int i=0; igetColumnVector(fitsIn, aperFluxFillColNum,s, type, repeat, vector); + for (int i=0; ibase.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, nDet, "StackApFlx", false); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, STACKAPFLX_FILTERID, 1, 1, nDet, filterIDs); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, STACKAPFLX_SURVEYID, 1, 1, nDet, surveyIDs); + + // R1->r10 flux values + // 1 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR1, 1, 1, nDet, stackApFlxFluxes[0].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR1ERR, 1, 1, nDet, stackApFlxFluxes[0].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR1STD, 1, 1, nDet, stackApFlxFluxes[0].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR1FILL, 1, 1, nDet, stackApFlxFluxes[0].flxFill); + // 2 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR2, 1, 1, nDet, stackApFlxFluxes[1].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR2ERR, 1, 1, nDet, stackApFlxFluxes[1].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR2STD, 1, 1, nDet, stackApFlxFluxes[1].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR2FILL, 1, 1, nDet, stackApFlxFluxes[1].flxFill); + // 3 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR3, 1, 1, nDet, stackApFlxFluxes[2].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR3ERR, 1, 1, nDet, stackApFlxFluxes[2].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR3STD, 1, 1, nDet, stackApFlxFluxes[2].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR3FILL, 1, 1, nDet, stackApFlxFluxes[2].flxFill); + // 4 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR4, 1, 1, nDet, stackApFlxFluxes[3].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR4ERR, 1, 1, nDet, stackApFlxFluxes[3].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR4STD, 1, 1, nDet, stackApFlxFluxes[3].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR4FILL, 1, 1, nDet, stackApFlxFluxes[3].flxFill); + // 5 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR5, 1, 1, nDet, stackApFlxFluxes[4].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR5ERR, 1, 1, nDet, stackApFlxFluxes[4].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR5STD, 1, 1, nDet, stackApFlxFluxes[4].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR5FILL, 1, 1, nDet, stackApFlxFluxes[4].flxFill); + // 6 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR6, 1, 1, nDet, stackApFlxFluxes[5].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR6ERR, 1, 1, nDet, stackApFlxFluxes[5].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR6STD, 1, 1, nDet, stackApFlxFluxes[5].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR6FILL, 1, 1, nDet, stackApFlxFluxes[5].flxFill); + // 7 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR7, 1, 1, nDet, stackApFlxFluxes[6].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR7ERR, 1, 1, nDet, stackApFlxFluxes[6].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR7STD, 1, 1, nDet, stackApFlxFluxes[6].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR7FILL, 1, 1, nDet, stackApFlxFluxes[6].flxFill); + // 8 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR8, 1, 1, nDet, stackApFlxFluxes[7].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR8ERR, 1, 1, nDet, stackApFlxFluxes[7].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR8STD, 1, 1, nDet, stackApFlxFluxes[7].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR8FILL, 1, 1, nDet, stackApFlxFluxes[7].flxFill); + // 9 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR9, 1, 1, nDet, stackApFlxFluxes[8].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR9ERR, 1, 1, nDet, stackApFlxFluxes[8].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR9STD, 1, 1, nDet, stackApFlxFluxes[8].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR9FILL, 1, 1, nDet, stackApFlxFluxes[8].flxFill); + // 10 + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR10, 1, 1, nDet, stackApFlxFluxes[9].flx); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR10ERR, 1, 1, nDet, stackApFlxFluxes[9].flxErr); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR10STD, 1, 1, nDet, stackApFlxFluxes[9].flxStd); + this->base.fitsOut->writeColumn(this->base.fitsOut, TFLOAT, STACKAPFLX_FLXR10FILL, 1, 1, nDet, stackApFlxFluxes[9].flxFill); + + for (long i=0; i<11; i++) { + + free(stackApFlxFluxes[i].flx); + free(stackApFlxFluxes[i].flxErr); + free(stackApFlxFluxes[i].flxStd); + free(stackApFlxFluxes[i].flxFill); + } + + free(stackApFlxFluxes); + + return true; +} + +/** + Creates the StackModelFit table + */ +static bool createStackModelFitTable( + StackBatch* this, + Fits *fitsIn, + int8_t* filterIDs, + int8_t* surveyIDs) { + + long nDet = 0; + char extensionName[40]; + sprintf(extensionName, "SkyChip.xfit"); + if (!fitsIn->moveToBinaryTableAndCountRows(fitsIn, extensionName, &nDet)) return false; + + long* ippIdets = (long*)calloc(this->MAXDETECT, sizeof(long)); + char** modelTypes = (char**)calloc(this->MAXDETECT, sizeof(char**)); + for (uint32_t i=0; iMAXDETECT;i++) modelTypes[i] = (char*)calloc(20,sizeof(char)); + + // read whole columns + fitsIn->readColumnUsingName(fitsIn, TLONG, "IPP_IDET", 1, 1, nDet, ippIdets); + fitsIn->readColumnUsingName(fitsIn, TSTRING, "MODEL_TYPE", 1, 1, nDet, modelTypes); + + this->base.logger->print(this->base.logger, MSG_INFO, "StackBatch", + "Looping through %ld model fit rows from '%s'\n", nDet, extensionName); + for (long i = 0; ibase.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, nDet, "StackModelFit", false); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, STACKMODELFIT_FILTERID, 1, 1, nDet, filterIDs); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, STACKMODELFIT_SURVEYID, 1, 1, nDet, surveyIDs); + + // free up + free(ippIdets); + for (uint32_t i=0; iMAXDETECT;i++) free(modelTypes[i]); + free(modelTypes); + + return true; +} + +/** + Creates the StackToImage table + */ +static bool createStackToImageTable( + StackBatch* this, + Fits* fitsIn + ) { + + this->base.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, 3/*TODO*/, "StackToImage", false); + + return true; +} + +/** + Does the work. Writes all extensions to new FITS file. + */ +static int run(StackBatch* this) { + + if (this->base.exitCode != PS_EXIT_SUCCESS) return this->base.exitCode; + + // open input FITS file + Fits* fitsIn = existing_Fits(this->base.inputFiles[0], this->base.logger); + if (fitsIn->getFilePtr(fitsIn) == NULL) return PS_EXIT_SYS_ERROR; + + // get primary header and pull stuff out for later + float exposureTime; fitsIn->getHeaderKeyValue(fitsIn, TFLOAT, "EXPTIME", &exposureTime); + char filterType[20]; fitsIn->getHeaderKeyValue(fitsIn, TSTRING, "FILTER", filterType); + + int8_t filterID = -1; + if (!this->base.initData->getFilterId(this->base.initData, filterType, &filterID)) { + + // this->base.exitCode = PS_EXIT_DATA_ERROR; + // return this->base.exitCode; TODO + } + + exposureTime = 60.0;// TODO + filterID = 3; // TODO + + // write StackMeta + this->base.fitsGenerator->createAndPopulateTable(this->base.fitsGenerator, fitsIn, this->base.fitsOut, 1, "StackMeta", true); + this->base.fitsOut->writeColumn(this->base.fitsOut, TLONG, STACKMETA_SKYCELLID, 1, 1, 1, &this->skycellId); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, STACKMETA_FILTERID, 1, 1, 1, &filterID); + this->base.fitsOut->writeColumn(this->base.fitsOut, TBYTE, STACKMETA_SURVEYID, 1, 1, 1, &this->base.surveyID); + + // allocate stuff for other extensions + int8_t* filterIDs = (int8_t*)calloc(this->MAXDETECT, sizeof(int8_t)); + int8_t* surveyIDs = (int8_t*)calloc(this->MAXDETECT, sizeof(int8_t)); + long* skycellIDs = (long*)calloc(this->MAXDETECT, sizeof(long)); + + // some stuff is the same for all detections so we can populate here + for (long s = 0; sMAXDETECT; s++) { + + skycellIDs[s] = this->skycellId; + filterIDs[s] = filterID; + surveyIDs[s] = this->base.surveyID; + } + + // create all extensions + createStackDetectionTable(this, fitsIn, filterIDs, surveyIDs, skycellIDs, exposureTime); + createStackApFlxTable(this, fitsIn, filterIDs, surveyIDs); + createStackModelFitTable(this, fitsIn, filterIDs, surveyIDs); + createStackToImageTable(this, fitsIn); + + // free stuff up free(filterIDs); free(surveyIDs); - - status=0; - if (fits_close_file(fitsIn, &status)) fits_report_error(stderr, status); - + free(skycellIDs); + fitsIn->destroy(fitsIn); return this->base.exitCode; } - /** Print-out this class. Calls base-calls print method first. @@ -213,6 +386,6 @@ this->base.print(&this->base); - printf("* skycell ID : %d\n", this->skycellId); - printf("\n"); + this->base.logger->print(this->base.logger, MSG_INFO, "StackBatch", "skycell ID : %d\n", this->skycellId); + this->base.logger->print(this->base.logger, MSG_INFO, "StackBatch", "\n"); } @@ -240,5 +413,7 @@ } - this->base.parseArguments(&this->base, argc, argv); + char fitsOutFile[40]; + sprintf(fitsOutFile, "%08d.FITS", this->skycellId); + this->base.parseArguments(&this->base, argc, argv, "/stack", fitsOutFile); if ( @@ -262,27 +437,22 @@ Constructor */ -StackBatch* new_StackBatch(int *argc, char **argv) { - +StackBatch* new_StackBatch(Logger* logger, int *argc, char **argv) { + + logger->print(logger, MSG_DEBUG, "StackBatch", "Constructor\n"); StackBatch *this = (StackBatch*)calloc(1, sizeof(StackBatch)); // call base-class constructor - if (!new_Batch(&this->base)) { - - psError(PS_ERR_IO, false, "Unable to create Batch base-class object"); - return this; - } + new_Batch(logger, &this->base); this->MAXDETECT = 150000; + // method pointers this->print = print; this->destroy = destroy; this->base.run = run; - if (!parseArguments(this, *argc, argv)) { return this; } - - strcat(this->base.configsDir, "/stack"); - sprintf(this->base.fitsOutFile, "%08d.FITS", this->skycellId); - - this->base.init(&this->base); + parseArguments(this, *argc, argv); + + this->print(this); return this; @@ -294,26 +464,17 @@ int main(int argc, char **argv) { - psTimerStart("stackbatch"); - - ippToPsps_VersionPrint(); - - int exitCode; - - StackBatch* stackBatch = new_StackBatch(&argc, argv); +// ippToPsps_VersionPrint(); + + Logger* logger = new_Logger(NULL, false); + logger->print(logger, MSG_INFO, "main", "Creating new stack batch\n"); + + StackBatch* stackBatch = new_StackBatch(logger, &argc, argv); stackBatch->base.run(stackBatch); - exitCode = stackBatch->base.exitCode; + int exitCode = stackBatch->base.exitCode; stackBatch->destroy(stackBatch); - double secs = psTimerMark("stackbatch"); - - psLogMsg("stackbatch", 3, "stackbatch completed %ssuccessfully, with exit code %d, in %.1f %s\n", - (exitCode == PS_EXIT_SUCCESS) ? "" : "un", - exitCode, - (secs<60.0) ? secs : (secs/60.0), - (secs<60.0) ? "sec(s)" : "min(s)"); - // tidy up - psTimerStop(); + logger->destroy(logger); psLibFinalize(); @@ -321,4 +482,2 @@ } - - Index: branches/eam_branches/ipp-20110213/ippToPsps/src/StackBatch.h =================================================================== --- branches/eam_branches/ipp-20110213/ippToPsps/src/StackBatch.h (revision 30812) +++ branches/eam_branches/ipp-20110213/ippToPsps/src/StackBatch.h (revision 31083) @@ -30,5 +30,5 @@ } StackBatch; -StackBatch *new_StackBatch(int *argc, char **argv); +StackBatch *new_StackBatch(Logger* logger, int *argc, char **argv); # endif // IPPTOPSPS_STACKBATCH_H