basic QA class

include/qa.h

@@ -0,0 +1,236 @@
+#ifndef _QA_H
+#define _QA_H
+
+#include "hdhC.h"
+#include "date.h"
+#include "annotation.h"
+#include "qa_data.h"
+#include "qa_time.h"
+#include "qa_PT.h"
+#include "qa_CORDEX.h"
+
+//! Quality Control Program Unit for CORDEX.
+/*! All the QA considerations are covered by this class.\n
+Features specific to an experiment are 'imported' by qa_EXPNAME.h,
+where EXPNAME indicates the experiment, e.g. CMIP5.\n
+The netCDF data-file is linked by a pointer to the InFile class
+instance. Results of the QA are written to a netCDF file
+(to the directory where the main program was started) with filename
+qa_<data-filename>.nc. Outlier test and such for replicated records
+are performed. Annotations are supplied via the Annotation class
+linked by a pointer.
+*/
+
+//! Struct containing dimensional properties to cross-check with table information.
+class QA : public IObj
+{
+  public:
+
+  //! Default constructor.
+  QA();
+  ~QA();
+
+  //! coresponding to virtual methods in IObj
+
+  //! Check field properties of the variable.
+  /*! Designed for multiple usage for sub-layers of a data block.
+      Each multiple-set must be invoked by calling method 'clearStatistics'.*/
+  bool   entry(void);
+
+  //! Initialisation of the QA object.
+  /*! Open the qa-result.nc file, when available or create
+   it from scratch. Meta data checks are performed.
+   Initialise time testing, time boundary testing, and cycles
+   within a time step. At the end  entry() is called to test
+   the data of fields.*/
+  bool   init(void) ;
+  void   linkObject(IObj *);
+
+  // special: from InFile with path and period stripped.
+  void   setFilename(hdhC::FileSplit&);
+  void   setTablePath(std::string p){tablePath=p;}
+
+  void   applyOptions(bool isPost=false);
+
+  //! Comparison of dimensions between file and standard table
+  /*! Cross-checks with the standard table are performed only once for
+   each variable at first time encounter in the CORDEX Project ensuring
+   conformance.*/
+
+  bool   checkDataBody(std::string vName="");
+
+  void   checkProjectTable(InFile &in);
+
+  /*! Close records for time and data.*/
+  void   closeEntry(void);
+
+  //! Make VarMetaData objects.
+  void   createVarMetaData(void);
+
+  //! Check the path to the tables;
+  void   defaultPrjTableName(void);
+
+  //! The final operations.
+  /*! An exit code is returned.*/
+  int    finally(int errCode=0);
+
+  //! The final qa data operations.
+  /*! Called from finall(). An exit code is returned.*/
+  int    finally_data(int errCode=0);
+
+  std::string
+         getAttValue(size_t v_ix, size_t a_ix);
+
+  int    getExitCode(void){return exitCode;}
+
+  //! Get path componenents.
+  /*! mode: "total": filename with total path, "file": filename,
+      "base": filename without extension, "ext": extension without '.',
+      "path": the path component without trailing '/'.*/
+  std::string
+         getPath(std::string& f, std::string mode="total");
+
+  //! Brief description of options
+  static void
+         help(void);
+
+  //! Initialisation of flushing gathered results to netCDF file.
+  /*! Parameter indicates the number of variables. */
+  void   initDataOutputBuffer(void);
+
+  //! Set default values.
+  void   initDefaults(void);
+
+  //! Global attributes of the qa-netCDF file.
+  /*! Partly reflecting global attributes from the sources. */
+  void   initGlobalAtts(InFile &);
+
+  //! Initialisiation of a resumed session.
+  /*! Happens for non-atomic data sets and those that are yet incomplete. */
+  void   initResumeSession(void);
+
+  bool   isProgress(void){ return ! qaTime.isNoProgress ; }
+
+  //! Get coordinates of grid-cells where an error occurred
+  /*! Does not work for tripolar coordinates */
+//  bool   locate( GeoMetaT<float>*, double *lat, double *lon, const char* );
+
+  //! Open a qa_result file for creation or appending data.
+  /*! CopY time variable from input-nc file.
+   Collect some properties of the in-netcdf-file in
+   struct varMeDa. Also check properties against tables.
+  */
+  void   openQA_Nc(InFile&);
+
+  //! Perform only post-processing
+  bool   postProc(void);
+  bool   postProc_outlierTest(void);
+
+  void   resumeSession(void);
+
+  //! Connect this with the object to be checked
+  void   setInFilePointer(InFile *p) { pIn = p; }
+
+  //! Unused.
+  /*! Needed to be conform to a specific Base class functionality */
+  void   setSrcStr(std::string s)
+             {srcStr.push_back(s); return;}
+
+  //! Store results in the internal buffer
+  /*! The buffer is flushed to file every 'flushCountMax' time steps.*/
+  void   store(std::vector<hdhC::FieldData> &fA);
+  void   storeData(VariableMetaData&, hdhC::FieldData& );
+  void   storeTime(void);
+
+  //! Name of the netCDF file with results of the quality control
+  std::string tablePath;
+  struct hdhC::FileSplit qaFile;
+  struct hdhC::FileSplit projectTableFile;
+
+  std::string qaNcfileFlags;
+
+  int exitCode;
+  bool isExit;
+
+  Annotation* notes;
+  NcAPI*      nc;
+  QA_Exp      qaExp;
+  QA_Time     qaTime;
+
+  int thisId;
+
+  size_t currQARec;
+  size_t importedRecFromPrevQA; // initial num of recs in the write-to-nc-file
+  MtrxArr<double> tmp_mv;
+
+  // the same buf-size for all buffer is required for testing replicated records
+  size_t bufferSize;
+
+  // init for test about times
+  bool enablePostProc;
+  bool enableVersionInHistory;
+  bool isClearBits;
+  bool isFileComplete;
+  bool isFirstFile;
+  bool isNotFirstRecord;
+  bool isPrintTimeBoundDates;
+  bool isResumeSession;
+
+  size_t nextRecords;
+
+  bool isCheckMeta;
+  bool isCheckTime;
+  bool isCheckData;
+
+  std::vector<std::string> excludedAttribute;
+  std::vector<std::string> overruleAllFlagsOption;
+
+  std::vector<std::string> constValueOption;
+  std::vector<std::string> fillValueOption;
+  std::vector<std::string> outlierOpts;
+  std::vector<std::string> replicationOpts;
+  std::vector<std::string> requiredAttributesOption;
+
+  int identNum;
+  char        fileSequenceState;
+  std::string prevVersionFile;
+  std::vector<std::string> srcStr;
+  std::string revision;
+
+  std::string fail;
+  std::string fileStr;
+  std::string notAvailable;
+  std::string blank;
+  std::string no_blank;
+  std::string s_colon;
+  std::string s_empty;
+  std::string s_mismatch;
+  std::string s_upper;
+  std::string s_lower;
+
+  std::string n_axis;
+  std::string n_cell_methods;
+  std::string n_long_name;
+  std::string n_outputVarName;
+  std::string n_positive;
+  std::string n_standard_name;
+  std::string n_units;
+
+  std::string getCaptIntroDim(VariableMetaData &vMD,
+                   struct DimensionMetaData &nc_entry,
+                   struct DimensionMetaData &tbl_entry, std::string att="");
+  void        appendToHistory();
+  bool        getExit(void);
+  std::string getSubjectsIntroDim(VariableMetaData &vMD,
+                   struct DimensionMetaData &nc_entry,
+                   struct DimensionMetaData &tbl_entry, bool isColon=true);
+  std::string getVarnameFromFilename(std::string str);
+  bool        not_equal(double x1, double x2, double epsilon);
+  void        pushBackVarMeDa(Variable*);
+  void        setExit(int);
+  void        setCheckMode(std::string);
+  void        setProcessing(void);
+  void        setTable(std::string, std::string acronym="");
+};
+
+#endif