Index: /trunk/ippToPsps/src/Batch.c =================================================================== --- /trunk/ippToPsps/src/Batch.c (revision 31010) +++ /trunk/ippToPsps/src/Batch.c (revision 31011) @@ -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); - } + psError(PS_ERR_UNKNOWN, false, "Failed, so deleting fits file"); + 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 +87,5 @@ if (this->dvoConfig != NULL) dvoConfigFree(this->dvoConfig); - ippToPspsConfig_Destructor(this->config); + this->config->destroy(this->config); pmConfigDone(); @@ -151,5 +139,5 @@ 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 @@ -178,4 +166,7 @@ haveSurveyType = false; + char fitsOutPath[1000]; + char configsBaseDir[1000]; + // decode arguments int32_t optind = 1; @@ -193,5 +184,5 @@ 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 +194,5 @@ else if(strcmp(sw, "-config") == 0 ) { optind++; if( optind > ( argc-1 ) ) break; - strcpy(this->configsDir, argv[optind]); + strcpy(configsBaseDir, argv[optind]); haveConfig = true; } @@ -220,17 +211,4 @@ - // 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")); if (haveFitsInPath && !readInputFilePaths(this)) { @@ -240,14 +218,7 @@ } - return true; -} - -/** - Initialises file paths, creates FITS file etc - */ -bool init(Batch* this) { - // create a config object - this->config = ippToPspsConfig_Constructor(this->configsDir); + strcat(configsBaseDir, configsDir); + this->config = new_Config(configsBaseDir); if (this->config == NULL) { @@ -257,5 +228,5 @@ // get survey ID using config object - if (strlen(this->surveyType) > 0 && !ippToPspsConfig_getSurveyId(this->config, this->surveyType, &this->surveyID)) { + if (strlen(this->surveyType) > 0 && !this->config->getSurveyId(this->config, this->surveyType, &this->surveyID)) { this->exitCode = PS_EXIT_CONFIG_ERROR; @@ -263,15 +234,9 @@ } // 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); + if (this->fitsOut->getFilePtr(this->fitsOut) == NULL) return false; // create XML document for results @@ -281,5 +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); } @@ -298,7 +263,4 @@ 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); } @@ -359,5 +321,5 @@ // set up function pointers this->parseArguments = parseArguments; - this->init = init; + //this->init = init; this->print = print; this->destroy = destroy; Index: /trunk/ippToPsps/src/Batch.h =================================================================== --- /trunk/ippToPsps/src/Batch.h (revision 31010) +++ /trunk/ippToPsps/src/Batch.h (revision 31011) @@ -18,4 +18,6 @@ #include +#include "Fits.h" + /** Abstract base class for all batches. Known subclasses are: @@ -25,5 +27,5 @@ - 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 implenent print() */ typedef struct Batch { @@ -37,11 +39,8 @@ 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 + Fits *fitsOut; // output FITS file pmConfig* pmconfig; // pmConfig dvoConfig* dvoConfig; // dvo database - IppToPspsConfig* config; // config structure + Config* config; // config structure char todaysDate[20]; // today's date int exitCode; // ps exit code @@ -50,5 +49,4 @@ // methods bool (*parseArguments)(); - bool (*init)(); int (*run)(); void (*print)(); @@ -58,4 +56,6 @@ bool (*gotConfig)(); bool (*gotSurveyType)(); + + // destructor void (*destroy)(); Index: /trunk/ippToPsps/src/Config.c =================================================================== --- /trunk/ippToPsps/src/Config.c (revision 31010) +++ /trunk/ippToPsps/src/Config.c (revision 31011) @@ -1,3 +1,3 @@ -/** @file ippToPspsConfig.c +/** @file Config.c * * @ingroup ippToPsps @@ -7,10 +7,14 @@ */ -#include "ippToPspsConfig.h" +#include "Config.h" #include #include #include -// Gets PS type from string +#include "Fits.h" + +/** + Gets PS type from string + */ static int ippToPsps_GetDataType(char *typename) { @@ -28,8 +32,10 @@ } -// finds a column within this table -static IppToPspsConfig_Column* ippToPspsConfig_findColumn(IppToPspsConfig_Table* table, const char* name) { - - IppToPspsConfig_Column* column = NULL; +/** + Finds a column within this table + */ +static Column* findColumn(Table* table, const char* name) { + + Column* column = NULL; for (uint32_t i=0; inumOfColumns; i++) { @@ -46,8 +52,10 @@ } -// finds a table from the array of tables -static IppToPspsConfig_Table* ippToPspsConfig_findTable(IppToPspsConfig* this, const char* name) { - - IppToPspsConfig_Table* table = NULL; +/** + Finds a table from the array of tables + */ +static Table* findTable(Config* this, const char* name) { + + Table* table = NULL; for (uint32_t i=0; inumOfTables; i++) { @@ -64,6 +72,8 @@ } -// gets an attribute value from XML node -static bool ippToPspsConfig_getAttribute(xmlNode* node, const char* attName, char* _value) { +/** + Gets an attribute value from XML node + */ +static bool getAttribute(xmlNode* node, const char* attName, char* _value) { xmlChar* value = xmlGetProp(node, (const xmlChar*)attName); @@ -75,6 +85,8 @@ } -// 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) { +/** + 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; @@ -98,28 +110,21 @@ 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; + 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; + break; } @@ -127,10 +132,5 @@ } - 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); - } + fitsOut->createBinaryTable(fitsOut, nRows, nCols, colNames, colTypes, table->name); for (i=0;iwriteColumn(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; @@ -214,6 +214,8 @@ } -// count number of children with the provided name -static int ippToPspsConfig_countChildren(xmlNode* rootNode, const char* name) { +/* + Counts number of children with the provided name + */ +static int countChildren(xmlNode* rootNode, const char* name) { int count = 0; @@ -228,6 +230,8 @@ } -// searches through this table and finds attribute value for a provided key -static bool ippToPspsConfig_getRowAttribute(IppToPspsConfig* this, xmlNode* tableNode, +/** + Searches through this table and finds attribute value for a provided key + */ +static bool getRowAttribute(Config* this, xmlNode* tableNode, const char* keyName, const char* keyValue, const char* attName, char* attValue) { @@ -243,11 +247,11 @@ 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 ); + //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; - ippToPspsConfig_getAttribute(node, attName, attValue); + getAttribute(node, attName, attValue); //printf("FOUND %s %s %s %s \n", keyName, buffer, attName, attValue ); return true; @@ -261,6 +265,8 @@ } -// opens an XML file and returns the document -static xmlDoc* ippToPspsConfig_openXmlFile(const char* path) { +/* + opens an XML file and returns the document + */ +static xmlDoc* openXmlFile(const char* path) { xmlDoc* doc = xmlReadFile(path, NULL, 0); @@ -269,6 +275,8 @@ } -// closes an XML file -static bool ippToPspsConfig_closeXmlFile(xmlDoc* doc) { +/* + closes an XML file + */ +static bool closeXmlFile(xmlDoc* doc) { xmlFreeDoc(doc); @@ -278,7 +286,9 @@ } -// gets filter ID for this filter name from 'init' data -static bool ippToPspsConfig_getInitValue( - IppToPspsConfig* this, +/** + Gets a value from the 'init' data + */ +static bool getInitValue( + Config* this, const char* tableName, const char* keyName, const char* keyValue, @@ -290,5 +300,5 @@ psStringAppend(&path, "%s/../init/data.xml", this->configsPath); // TODO nasty - xmlDoc* doc = ippToPspsConfig_openXmlFile(path); + xmlDoc* doc = openXmlFile(path); if (doc == NULL) { @@ -313,8 +323,8 @@ if (strcmp((const char*)node->name, "table")!=0) continue; - if (!ippToPspsConfig_getAttribute(node, "name", tempStr)) continue; + if (!getAttribute(node, "name", tempStr)) continue; if (strcmp(tempStr, tableName)!=0) continue; - ret = ippToPspsConfig_getRowAttribute(this, node, keyName, keyValue, attName, attValue); + ret = getRowAttribute(this, node, keyName, keyValue, attName, attValue); break; } @@ -322,14 +332,16 @@ } - ippToPspsConfig_closeXmlFile(doc); + closeXmlFile(doc); return ret; } -// gets survey ID from survey name -bool ippToPspsConfig_getSurveyId(IppToPspsConfig* this, const char* surveyType, int8_t* surveyId) { +/* + Gets survey ID from survey name + */ +static bool getSurveyId(Config* this, const char* surveyType, int8_t* surveyId) { char buffer[10]; - if (!ippToPspsConfig_getInitValue(this, "Survey", "name", surveyType, "surveyID", buffer)) { + if (!getInitValue(this, "Survey", "name", surveyType, "surveyID", buffer)) { *surveyId = -1; @@ -341,6 +353,8 @@ } -// gets filter ID from filter type -bool ippToPspsConfig_getFilterId(IppToPspsConfig* this, const char* filterType, int8_t* filterId) { +/* + Gets filter ID from filter type + */ +static bool getFilterId(Config* this, const char* filterType, int8_t* filterId) { char tmp[2]; @@ -348,5 +362,5 @@ tmp[1] = '\0'; char buffer[10]; - if (!ippToPspsConfig_getInitValue(this, "Filter", "filterType", tmp, "filterID", buffer)) { + if (!getInitValue(this, "Filter", "filterType", tmp, "filterID", buffer)) { *filterId = -1; @@ -358,6 +372,8 @@ } -// populate the provided table with data from XML -static bool ippToPspsConfig_populateTable(IppToPspsConfig_Table* table, xmlNode* rootElement, fitsfile *fitsOut) { +/** + Populates the provided table with data from XML + */ +static bool populateTable(Table* table, xmlNode* rootElement, Fits *fitsOut) { char tempStr[100]; @@ -370,5 +386,5 @@ if (strcmp((const char*)node->name, "table")!=0) continue; - if (!ippToPspsConfig_getAttribute(node, "name", tempStr)) continue; + if (!getAttribute(node, "name", tempStr)) continue; if (strcmp(tempStr, table->name)==0) {tableNode = node; break;} } @@ -382,7 +398,7 @@ // now count the number of rows - int nRows = ippToPspsConfig_countChildren(tableNode, "row"); + int nRows = countChildren(tableNode, "row"); if (nRows < 1) return false; - if (!ippToPspsConfig_createTable(table, fitsOut, nRows)) return false; + if (!createTable(table, fitsOut, nRows)) return false; int rows=0; @@ -411,5 +427,5 @@ col = i+1; - if (!ippToPspsConfig_getAttribute(node, table->columns[i].pspsName, tempStr)) continue; + if (!getAttribute(node, table->columns[i].pspsName, tempStr)) continue; strncpy(strcol[0], tempStr, 32); @@ -420,25 +436,25 @@ case TBYTE: bytecol[0] = atoi(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, bytecol, &status); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, bytecol); break; case TSHORT: shortcol[0] = atoi(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, shortcol, &status); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, shortcol); break; case TLONG: case TLONGLONG: longcol[0] = atol(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, longcol, &status); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, longcol); break; case TFLOAT: floatcol[0] = atof(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, floatcol, &status); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, floatcol); break; case TDOUBLE: doublecol[0] = atof(tempStr); - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, doublecol, &status); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, doublecol); break; case TSTRING: - fits_write_col(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, strcol, &status); + fitsOut->writeColumn(fitsOut, table->columns[i].pspsType, col, rows, 1, 1, strcol); break; @@ -460,15 +476,17 @@ } -// loads a table description from XML -static bool ippToPspsConfig_loadTableDescription(IppToPspsConfig_Table* table, xmlNode* tableNode) { +/** + Loads a table description from XML + */ +static bool loadTableDescription(Table* table, xmlNode* tableNode) { bool ret = true; char tableName[100]; - ippToPspsConfig_getAttribute(tableNode, "name", tableName); + 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)); + table->numOfColumns = countChildren(tableNode, "column"); + table->columns = calloc(table->numOfColumns, sizeof(Column)); // psLogMsg("ippToPsps", PS_LOG_INFO, " Found '%d' columns", table->numOfColumns); @@ -484,17 +502,17 @@ // column name - ippToPspsConfig_getAttribute(node, "name", buffer); + getAttribute(node, "name", buffer); sprintf(table->columns[columnNum].pspsName, buffer); // column type - ippToPspsConfig_getAttribute(node, "type", buffer); + getAttribute(node, "type", buffer); table->columns[columnNum].pspsType = ippToPsps_GetDataType(buffer); // default value - ippToPspsConfig_getAttribute(node, "default", buffer); + getAttribute(node, "default", buffer); sprintf(table->columns[columnNum].defaultValue, buffer); // comment - ippToPspsConfig_getAttribute(node, "comment", buffer); + getAttribute(node, "comment", buffer); sprintf(table->columns[columnNum].comment, buffer); @@ -523,6 +541,8 @@ } -// read table shapes from XML file -bool ippToPspsConfig_loadTableDescriptions(IppToPspsConfig* this) { +/** + Reads table shapes from XML file + */ +static bool loadTableDescriptions(Config* this) { bool ret = true; @@ -531,5 +551,5 @@ psStringAppend(&path, "%s/tables.xml", this->configsPath); - xmlDoc* doc = ippToPspsConfig_openXmlFile(path); + xmlDoc* doc = openXmlFile(path); if (doc == NULL) { @@ -549,10 +569,10 @@ // 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)); + 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; - IppToPspsConfig_Table* table = NULL; + Table* table = NULL; int tableNum = 0; @@ -565,5 +585,5 @@ table = this->tables+tableNum; - if (!ippToPspsConfig_loadTableDescription(table, node)) ret = false; + if (!loadTableDescription(table, node)) ret = false; else tableNum++; } @@ -574,11 +594,13 @@ psError(PS_ERR_IO, false, "Mismatch between number of tables expected (%d) and those found (%d)", this->numOfTables, tableNum); - ippToPspsConfig_closeXmlFile(doc); + closeXmlFile(doc); return ret; } -// loads mappings from XML for a particular table -static bool ippToPspsConfig_loadTableMappings(IppToPspsConfig* this, xmlNode* tableNode) { +/** + Loads mappings from XML for a particular table + */ +static bool loadTableMappings(Config* this, xmlNode* tableNode) { bool ret = false; @@ -587,8 +609,8 @@ char tableName[100]; - ippToPspsConfig_getAttribute(tableNode, "name", tableName); - - IppToPspsConfig_Table* table = ippToPspsConfig_findTable(this, tableName); - IppToPspsConfig_Column* column = NULL; + getAttribute(tableNode, "name", tableName); + + Table* table = findTable(this, tableName); + Column* column = NULL; if (!table) return false; @@ -603,15 +625,15 @@ // column type - ippToPspsConfig_getAttribute(node, "pspsName", buffer); - column = ippToPspsConfig_findColumn(table, buffer); + getAttribute(node, "pspsName", buffer); + column = findColumn(table, buffer); if (!column) continue; // IPP name - ippToPspsConfig_getAttribute(node, "ippName", buffer); + getAttribute(node, "ippName", buffer); strcpy(column->ippName, buffer); // IPP type - ippToPspsConfig_getAttribute(node, "ippType", buffer); + getAttribute(node, "ippType", buffer); column->ippType = ippToPsps_GetDataType(buffer); @@ -626,6 +648,8 @@ } -// reads table mappings from XML file -static bool ippToPspsConfig_loadMappings(IppToPspsConfig* this) { +/** + Reads table mappings from XML file + */ +static bool loadMappings(Config* this) { bool ret = true; @@ -634,5 +658,5 @@ psStringAppend(&path, "%s/map.xml", this->configsPath); - xmlDoc* doc = ippToPspsConfig_openXmlFile(path); + xmlDoc* doc = openXmlFile(path); if (doc == NULL) { @@ -657,16 +681,18 @@ if (strcmp((const char*)node->name, "table")==0) { - if (!ippToPspsConfig_loadTableMappings(this, node)) ret = false; + if (!loadTableMappings(this, node)) ret = false; } } } - ippToPspsConfig_closeXmlFile(doc); + closeXmlFile(doc); return ret; } -// populate the provided table with data from XML -bool ippToPspsConfig_populateFromFile(IppToPspsConfig* this, fitsfile *fitsOut) { +/** + Populate the provided table with data from XML + */ +static bool populateFromFile(Config* this, Fits *fitsOut) { bool ret = true; @@ -674,5 +700,5 @@ psStringAppend(&path, "%s/data.xml", this->configsPath); - xmlDoc* doc = ippToPspsConfig_openXmlFile(path); + xmlDoc* doc = openXmlFile(path); if (doc == NULL) { @@ -690,69 +716,21 @@ for (uint32_t i=0; inumOfTables; i++) { - if (!ippToPspsConfig_populateTable(this->tables+i, rootElement, fitsOut)) { + if (!populateTable(this->tables+i, rootElement, fitsOut)) { ret = false; } } - ippToPspsConfig_closeXmlFile(doc); + 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; icolumns[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 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; } } @@ -802,7 +763,4 @@ for (uint32_t i=0; inumOfColumns; i++) { - readStatus = 0; - writeStatus = 0; - if (!table->columns[i].usingDefault) { @@ -813,54 +771,48 @@ case TBYTE: if (fromHeader) { - fits_read_key(fitsIn, TBYTE, table->columns[i].ippName, &int8col[0], NULL, &readStatus); - if (!isfinite(int8col[0])) int8col[0] = int8null; + fitsIn->getHeaderKeyValue(fitsIn, TBYTE, table->columns[i].ippName, &int8col[0]); } - 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); + 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) { - fits_read_key(fitsIn, TSHORT, table->columns[i].ippName, &int16col[0], NULL, &readStatus); - if (!isfinite(int16col[0])) int16col[0] = int16null; + fitsIn->getHeaderKeyValue(fitsIn, TSHORT, table->columns[i].ippName, &int16col[0]); } - 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); + 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) { - fits_read_key(fitsIn, TLONG, table->columns[i].ippName, &longcol[0], NULL, &readStatus); - if (!isfinite(longcol[0])) longcol[0] = longnull; + fitsIn->getHeaderKeyValue(fitsIn, TLONG, table->columns[i].ippName, &longcol[0]); } - 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); + 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) { - fits_read_key(fitsIn, TLONGLONG, table->columns[i].ippName, &longcol[0], NULL, &readStatus); - if (!isfinite(longcol[0])) longcol[0] = longnull; + fitsIn->getHeaderKeyValue(fitsIn, TLONGLONG, table->columns[i].ippName, &longcol[0]); } - 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); + 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) { - fits_read_key(fitsIn, TFLOAT, table->columns[i].ippName,&floatcol[0], NULL, &readStatus); - if (!isfinite(floatcol[0])) floatcol[0] = floatnull; + fitsIn->getHeaderKeyValue(fitsIn, TFLOAT, table->columns[i].ippName,&floatcol[0]); } - 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); + 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) { - fits_read_key(fitsIn, TDOUBLE, table->columns[i].ippName, &doublecol[0], NULL, &readStatus); - if (!isfinite(doublecol[0])) doublecol[0] = doublenull; + fitsIn->getHeaderKeyValue(fitsIn, TDOUBLE, table->columns[i].ippName, &doublecol[0]); } - 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); + 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) 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); + 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; @@ -870,15 +822,4 @@ 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); - //} } } @@ -895,23 +836,26 @@ } -// creates and populates a table -bool ippToPspsConfig_writeTable( - IppToPspsConfig* this, - fitsfile* fitsIn, - fitsfile* fitsOut, +/** + Creates and populates a table + */ +static bool createAndPopulateTable( + Config* this, + Fits* fitsIn, + Fits* fitsOut, const long nRows, const char* tableName, - const bool fromHeader) { - - - IppToPspsConfig_Table* table = ippToPspsConfig_findTable(this, tableName); + const int fromHeader) { + + Table* table = findTable(this, tableName); if (!table) return false; - if(!ippToPspsConfig_createTable(table, fitsOut, nRows)) return false; - return ippToPspsConfig_populateTableFromFits(table, fitsIn, fitsOut, nRows, fromHeader); -} - -// Destructor. -void ippToPspsConfig_Destructor(IppToPspsConfig* this) { + if(!createTable(table, fitsOut, nRows)) return false; + return populateTableFromFits(table, fitsIn, fitsOut, nRows, fromHeader); +} + +/** + Destructor. + */ +static void destroy(Config* this) { if (this != NULL ) { @@ -927,19 +871,26 @@ } -// Constructor. Loads IPP -> PSPS mappings from a csv -IppToPspsConfig* ippToPspsConfig_Constructor(const char* path) { - - IppToPspsConfig* this = NULL; - - this = malloc(sizeof(IppToPspsConfig)); +/** + Constructor. Loads IPP -> PSPS mappings from an XML file + */ +Config* new_Config(const char* path) { + + Config* this = (Config*)calloc(1, sizeof(Config)); this->configsPath = NULL; psStringAppend(&this->configsPath, path); + // method pointers + this->getFilterId = getFilterId; + this->getSurveyId = getSurveyId; + this->createAndPopulateTable = createAndPopulateTable; + this->populateFromFile = populateFromFile; + this->destroy = destroy; + // load tables descriptions from XML - if (ippToPspsConfig_loadTableDescriptions(this)) { + if (loadTableDescriptions(this)) { // load any mappings we may have from XML - ippToPspsConfig_loadMappings(this); + loadMappings(this); } Index: /trunk/ippToPsps/src/Config.h =================================================================== --- /trunk/ippToPsps/src/Config.h (revision 31010) +++ /trunk/ippToPsps/src/Config.h (revision 31011) @@ -1,3 +1,3 @@ -/** @file ippToPspsConfig.h +/** @file Config.h * * @brief ippToPsps @@ -9,11 +9,11 @@ */ -#ifndef IPPTOPSPSCONFIG_H -#define IPPTOPSPSCONFIG_H +#ifndef IPPTOPSPS_CONFIG_H +#define IPPTOPSPS_CONFIG_H #include // column class -typedef struct { +typedef struct Column { int ippColNum; @@ -27,56 +27,41 @@ char comment[300]; -} IppToPspsConfig_Column; +} Column; // table class -typedef struct { +typedef struct Table { char name[32]; - IppToPspsConfig_Column* columns; + Column* columns; int numOfColumns; -} IppToPspsConfig_Table; +} Table; -// -typedef struct { +/** + Class encapsulating ... TODO + +*/ +typedef struct Config { + + // fields psString configsPath; - IppToPspsConfig_Table* tables; + Table* tables; int numOfTables; -} IppToPspsConfig; + // methods + bool (*getFilterId)(); + bool (*getSurveyId)(); + bool (*createAndPopulateTable)(); + bool (*populateFromFile)(); -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); + // destructor + void (*destroy)(); -// 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); +} Config; -bool ippToPspsConfig_getColumnVector( - int col, - long row, - int type, - int repeat, - float* vector, - fitsfile *fitsIn); +// constructor +Config* new_Config(const char* path); +#endif // IPPTOPSPS_CONFIG_H - - -#endif // IPPTOPSPSCONFIG_H - Index: /trunk/ippToPsps/src/DetectionBatch.c =================================================================== --- /trunk/ippToPsps/src/DetectionBatch.c (revision 31010) +++ /trunk/ippToPsps/src/DetectionBatch.c (revision 31011) @@ -1,4 +1,7 @@ #include "DetectionBatch.h" #include "DetectionBatchEnums.h" + +#include "Fits.h" + /** @@ -43,53 +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]); + 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.config->createAndPopulateTable(this->base.config, 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.config->getFilterId(this->base.config, 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 @@ -107,10 +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)); @@ -129,5 +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)); @@ -186,21 +169,22 @@ sprintf(ccdNumber, "%d%d", x, y); - // check we can move to detections table in smf + // check we CAN move to detections table in smf sprintf(extensionName, "XY%s.psf", ccdNumber); - if (!ippToPspsConfig_moveToExtensionTable(fitsIn, extensionName)) continue; + if (!fitsIn->moveToBinaryTable(fitsIn, extensionName)) continue; // move to header extension sprintf(extensionName, "XY%s.hdr", ccdNumber); - if (!ippToPspsConfig_moveToExtensionHeader(fitsIn, 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); @@ -221,6 +205,5 @@ if (numDvoDetections > this->MAXDETECT ) { - psError(PS_ERR_IO, false, - " Number of detections (%d) exceeds max limit (%ld)\n", + psError(PS_ERR_IO, false, " Number of detections (%d) exceeds max limit (%ld)\n", numDvoDetections, this->MAXDETECT); error = true; @@ -229,54 +212,46 @@ // create ImageMeta - ippToPspsConfig_writeTable(this->base.config, fitsIn, this->base.fitsOut, 1, "ImageMeta", true); + this->base.config->createAndPopulateTable(this->base.config, 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); - if (!ippToPspsConfig_moveToExtensionTable(fitsIn, 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 @@ -288,4 +263,5 @@ // 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) @@ -355,5 +331,5 @@ // 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; @@ -363,36 +339,33 @@ // 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.config->createAndPopulateTable(this->base.config, 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.config->createAndPopulateTable(this->base.config, 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.config->createAndPopulateTable(this->base.config, 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); } @@ -436,12 +409,11 @@ // write number of images we have found into FrameMeta table - if (ippToPspsConfig_moveToExtensionTable(this->base.fitsOut, "FrameMeta")) { - - 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); + 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); @@ -496,5 +468,7 @@ } - 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 ( @@ -532,4 +506,5 @@ this->MAXDETECT = 200000; + // method pointers this->print = print; this->destroy = destroy; @@ -538,10 +513,5 @@ 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); return this; @@ -565,5 +535,5 @@ detectionBatch->destroy(detectionBatch); - double secs = psTimerMark("ippToPsps"); + double secs = psTimerMark("detectionbatch"); psLogMsg("detectionbatch", 3, "detectionbatch completed %ssuccessfully, with exit code %d, in %.1f %s\n", Index: /trunk/ippToPsps/src/InitBatch.c =================================================================== --- /trunk/ippToPsps/src/InitBatch.c (revision 31010) +++ /trunk/ippToPsps/src/InitBatch.c (revision 31011) @@ -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.config->populateFromFile(this->base.config, 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 ( @@ -68,14 +68,10 @@ } + // method pointers this->print = print; this->destroy = destroy; this->base.run = run; - if (!parseArguments(this, *argc, argv)) { return this; } - - strcat(this->base.configsDir, "/init"); - sprintf(this->base.fitsOutFile, "00000000.FITS"); - - this->base.init(&this->base); + parseArguments(this, *argc, argv); return this; Index: /trunk/ippToPsps/src/InitBatch.h =================================================================== --- /trunk/ippToPsps/src/InitBatch.h (revision 31010) +++ /trunk/ippToPsps/src/InitBatch.h (revision 31011) @@ -24,8 +24,11 @@ // methods void (*print)(); + + // destructor void (*destroy)(); } InitBatch; +// constructor InitBatch *new_InitBatch(int *argc, char **argv); Index: /trunk/ippToPsps/src/StackBatch.c =================================================================== --- /trunk/ippToPsps/src/StackBatch.c (revision 31010) +++ /trunk/ippToPsps/src/StackBatch.c (revision 31011) @@ -1,4 +1,6 @@ #include "StackBatch.h" #include "StackBatchEnums.h" + +#include "Fits.h" /** @@ -13,181 +15,96 @@ /** - 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); + + printf("Looping through %ld psf detections\n", nDet); + float mag; + long unmatched = 0, totalDetections = 0, numOfDuplicates = 0, numInvalidFlux = 0, numDetectionsOut = 0; + + 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.config->createAndPopulateTable(this->base.config, 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); + + } + 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); @@ -195,14 +112,258 @@ 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; + if (!fitsIn->moveToBinaryTableAndCountRows(fitsIn, "SkyChip.xrad", &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)); + } + + printf("Looping through %ld extended source detections\n", nDet); + 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.config->createAndPopulateTable(this->base.config, 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; + if (!fitsIn->moveToBinaryTableAndCountRows(fitsIn, "SkyChip.xfit", &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); + + printf("Looping through %ld model fit rows\n", nDet); + for (long i = 0; ibase.config->createAndPopulateTable(this->base.config, 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.config->createAndPopulateTable(this->base.config, 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]); + 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.config->getFilterId(this->base.config, 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.config->createAndPopulateTable(this->base.config, 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); + printf("dsdsdddds\n\n"); + 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; } - /** @@ -240,5 +401,7 @@ } - 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 ( @@ -275,14 +438,10 @@ 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); return this; @@ -321,4 +480,2 @@ } - -