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Separate classes for basic and project-wide purpose
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@h-dh
h-dh committed Oct 15, 2015
1 parent 77a27a9 commit 27645a8
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Showing 16 changed files with 568 additions and 1,892 deletions.
4 changes: 2 additions & 2 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@ BASE_HEADER = annotation.h base.h brace_op.h data_statistics.h date.h \
time_control.h variable.h

QA_SOURCE = CF.cpp CellStatistics.cpp FD_interface.cpp Oper.cpp OutFile.cpp Parse.cpp \
QA_data.cpp QA_time.cpp QA_PT.cpp QA_main.cpp
QA.cpp QA_data.cpp QA_time.cpp QA_PT.cpp QA_main.cpp
QA_HEADER = cell_statistics.h cf.h fd_interface.h oper.h out_file.h parse.h \
qa_data.h qa_PT.h qa_main.h qa_time.h
qa.h qa_data.h qa_PT.h qa_main.h qa_time.h

#vpath %.c $(QA_PATH)/src
#vpath %.cpp $(QA_PATH)/src
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12 changes: 6 additions & 6 deletions include/qa_CMIP5.h
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@@ -1,9 +1,10 @@
#ifndef _QA_H
#define _QA_H
#ifndef _QA_CMIP5_H
#define _QA_CMIP5_H

#include "hdhC.h"
#include "date.h"
#include "annotation.h"
#include "qa.h"
#include "qa_data.h"
#include "qa_time.h"
#include "qa_PT.h"
Expand Down Expand Up @@ -283,9 +284,6 @@ class QA : public IObj
void findVarReqTableSheetSub(std::string &str0,
VariableMetaData &vMD, std::vector<std::string> &);

std::string
getCurrentTable(void){ return currTable ; }

//! Store properties of a dimension in the struct.
/*! Note: the name of the dimension is passed by the struct.*/
void getDimMetaData(InFile &in,
Expand Down Expand Up @@ -324,6 +322,9 @@ class QA : public IObj
std::string
getVarnameFromFilename(std::string str);

std::string
getVarnameInPrjTable(std::string vN="");

//! Brief description of options
static void
help(void);
Expand Down Expand Up @@ -456,7 +457,6 @@ class QA : public IObj
std::string maxDateRange;

std::string cfStndNames;
std::string currTable;
std::string MIP_tableName;
std::string frequency;
std::string totalPeriod;
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184 changes: 17 additions & 167 deletions include/qa_CORDEX.h
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Original file line number Diff line number Diff line change
@@ -1,22 +1,20 @@
#ifndef _QA_H
#define _QA_H
#ifndef _QA_CORDEX_H
#define _QA_CORDEX_H

#include "hdhC.h"
#include "date.h"
#include "annotation.h"
#include "qa.h"
#include "qa_data.h"
#include "qa_time.h"
#include "qa_PT.h"

//! Quality Control Program Unit for CORDEX.
/*! All the QA considerations are covered by this class.\n
The QA_CORDEX.cpp and qa_CORDEX.h files have to be linked to
QA.cpp and qa.h, respectively.\n
/*! All the QA considerations specific to CORDEX are covered by this class.\n
Requested properties from the cordex_archive_specifications.pdf
from http://cordex.dmi.dk/joomla/images/CORDEX are checked as well
as specifications in CORDEX_variables_requirement_table.pdf.\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
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
Expand Down Expand Up @@ -79,42 +77,14 @@ class VariableMetaData
void setParent(QA *p){pQA=p;}
};

class QA : public IObj
class QA_Exp
{
public:

//! Default constructor.
QA();
~QA();
QA_Exp();

//! 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 applyOptions(std::vector<std::string>&);

void checkDimStandardTable(ReadLine &tbl, InFile &in,
VariableMetaData &var,
Expand Down Expand Up @@ -193,8 +163,6 @@ class QA : public IObj
/*! For variables defined for a specific pressure level, eg.ta850*/
void checkPressureCoord(InFile&);

void checkProjectTable(InFile &in);

void checkVarTableEntry(
VariableMetaData &,
VariableMetaData &tbl_entry);
Expand Down Expand Up @@ -225,9 +193,6 @@ class QA : public IObj
VariableMetaData &,
VariableMetaData &tbl_entry);

/*! Close records for time and data.*/
void closeEntry(void);

//! Make VarMetaData objects.
void createVarMetaData(void);

Expand All @@ -247,14 +212,6 @@ class QA : public IObj
std::vector<std::vector<std::string> > &T2,
int &table_id, size_t &row );

//! 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);

//! Find entry of a requested variable in the standard table.
bool findTableEntry(ReadLine &, std::string &,
VariableMetaData &tble_entry);
Expand All @@ -269,24 +226,12 @@ class QA : public IObj
std::string
getAttValue(size_t v_ix, size_t a_ix);

std::string
getCurrentTable(void){ return currTable ; }

//! Store properties of a dimension in the struct.
/*! Note: the name of the dimension is passed by the struct.*/
bool getDimMetaData(InFile &in,
VariableMetaData &,
struct DimensionMetaData &, std::string &);

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");

std::string
getFrequency(void);

Expand All @@ -296,12 +241,10 @@ class QA : public IObj
//! Get the Standard table name from the global attributes
void getSubTable(void);

// std::string
// getTablePath(void){ return tablePath; }
std::string
getTableEntryID(std::string vN="");

//! Brief description of options
static void
help(void);
void init(QA*, std::vector<std::string>&);

//! Initialisation of flushing gathered results to netCDF file.
/*! Parameter indicates the number of variables. */
Expand All @@ -310,33 +253,12 @@ class QA : public IObj
//! 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);

//! Check the path to the tables;
void inqTables(void);

bool isProgress(void){ return ! qaTime.isNoProgress ; }
/*! For non-atomic data sets and such being incomplete, yet. */
void initResumeSession(std::vector<std::string>& prevTargets);

//! 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);
//! Check existence of tables
bool inqTables(void);

//! Read the headlines for dimensions and variable.
/*! Read from the standard table; used to identify columns.*/
Expand All @@ -354,16 +276,6 @@ class QA : public IObj
std::vector<std::string> &,
std::vector<std::vector<std::string> > &);

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;}

//! Cross-check with standard table.
/*! Prepare the check for dimensions and variable.*/
void varReqTableCheck(InFile &in,
Expand All @@ -389,12 +301,6 @@ class QA : public IObj
std::map<std::string, size_t> &col) ;
*/

//! 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);

//! Test the time-period of the input file.
/*! If the end-date in the filename and the last time value
match within the uncertainty of 0.75% of the time-step, then
Expand All @@ -409,112 +315,56 @@ class QA : public IObj
bool testPeriodFormat(std::vector<std::string> &sd) ;

//! Name of the netCDF file with results of the quality control
std::string tablePath;
struct hdhC::FileSplit qaFile;
struct hdhC::FileSplit archiveDesignTable;
struct hdhC::FileSplit GCM_ModelnameTable;
struct hdhC::FileSplit projectTableFile;
struct hdhC::FileSplit RCM_ModelnameTable;
struct hdhC::FileSplit varReqTable;

std::string qaNcfileFlags;

int exitCode;
bool isExit;

std::vector<VariableMetaData> varMeDa;

NcAPI *nc;
QA_Time qaTime;
QA* pQA;

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 enabledCompletenessCheck;
bool isUseStrict;
bool isCaseInsensitiveVarName;
bool isCheckParentExpID;
bool isCheckParentExpRIP;
bool isClearBits;
bool isFileComplete;
bool isFirstFile;
bool isNotFirstRecord;
bool isPrintTimeBoundDates;
bool isResumeSession;
bool isRotated;

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;

std::string cfStndNames;
std::string currTable;

std::string frequency;
std::string parentExpID;
std::string parentExpRIP;
std::string experiment_id;
std::string subTable ;

int identNum;
std::string fVarname;
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 setTable(std::string, std::string acronym="");
};

#endif

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