ScriptWriter.h

#ifndef DEF_SCRIPTWRITER
#define DEF_SCRIPTWRITER

/*std classes*/
#include <iostream>
#include <string>
#include <vector>
#include <math.h>// for the absolute value
#include <string>
#include <iostream>
#include <iomanip>

// QT 
#include <QString>
#include <QStringList>

/*json classes*/
#include <iostream>
#include "nlohmann/json.hpp"

/*itk classes*/
#include "itkImage.h"
#include "itkImageFileReader.h"

/* Namespace */
using json = nlohmann::json;


class ScriptWriter
{
  public:
    ScriptWriter();

/* SUB  WRITING FUNCTIONS */
    std::string pyExecuteCommandPreprocessCase ( std::string NameOfFileVarToTest, std::string NameOfCmdVarToExec, std::string ErrorTxtToDisplay, std::string SpacesBeforeFirstIf );

/*WRITING FUNCTIONS*/
    void WriteScript();
    void Preprocess();
    void AtlasBuilding();
    void MainScript();
    // New code with template python code
    void WriteScriptFromTemplate(QStringList);
    void PreprocessFromTemplate(std::string);
    void AtlasBuildingFromTemplate(std::string);
    void MainScriptFromTemplate(std::string);
    void UtilitiesScriptFromTemplate(std::string);

/*SCRIPT ACCESSORS*/
    void setExecutableDir(std::string);
    std::string getScript_Preprocess();
    std::string getScript_AtlasBuilding();
    std::string getScript_Main();
    std::string getScript_Utilities();

/*CHECK DATASET*/
    int setCroppingSize( bool SafetyMargin ); // returns 0 if no cropping , 1 if cropping needed
    int CheckVoxelSize(QStringList); // returns 0 if voxel size OK , otherwise 1

/*SET THE VALUES*/
    /* Script Configuration */
    void SaveScriptConfiguration(void);

    /* */
    void setHierarchy(json);

    /* */
    void setCasesPath(std::vector < std::string > CasesPath);
    void clearCasesPath();
    void setOutputPath(std::string OutputPath);
    void setRegType(int RegType);
    void setnbLoops(int nbLoops);
    void setnbLoopsDTIReg(int nbLoopsDTIReg);
    void setTemplatePath(std::string FAAtlasrefPath);
    void setOverwrite(int Overwrite);
    void setInterpolType(std::string Type);
    void setInterpolOption(std::string Option);
    void setTensInterpol(std::string TensInterpol);
    void setInterpolLogOption(std::string InterpolLogOption);
    void setTensorTfm(std::string TensTfm);
    void setSoftPath(std::vector < std::string > SoftPath);
    void setDTIRegOptions(std::vector < std::string > DTIRegOptions);
    void setDTIRegExtraPath(std::string DTIRegExtraPath);
    void setBFAffineTfmMode(std::string BFAffineTfmMode);
    void setGridProcess(bool useGridProcess);
    void setGridGeneralCommand(std::string GridCommand);
    void setGridAtlasCommand(std::string GridCommand);
    std::string setGridCommand(std::string GridCommand);
    void setPythonPath(std::string PythonPath);
    void setNbThreads(int NbThreads);
    int setScalarMeasurement( std::string scalarMeasurement ) ;

  private:
/* Environment */
    std::string m_ExecutableDir;

/* Hierarchical Build */
    json m_HierarchyBuild;

/* VALUES */
    std::vector < std::string > m_CasesPath;
    std::vector < std::string > m_CasesIDs;
    std::string m_OutputPath;
    int m_RegType; //=0 for using template and =1 for using existing first case
    int m_nbLoops;
    int m_nbLoopsDTIReg; // default 1. Number of iteration over final resampling.
    std::string m_TemplatePath;
    std::string m_CropSize [3]; //x,y,z
    int m_NeedToBeCropped; //=0 if not and =1 if need to be cropped
    int m_Overwrite; //=0 if not and =1 if overwrite on existing files
    std::string m_InterpolType;
    std::string m_InterpolOption;
    std::string m_TensInterpol;
    std::string m_InterpolLogOption;
    std::string m_TensTfm;
    std::vector < std::string > m_SoftPath; // contains the path to the softwares: 1=ImageMath, 2=ResampleDTIlogEuclidean, 3=CropDTI, 4=dtiprocess, 5=BRAINSFit, 6=AtlasWerks, 7=dtiaverage, 8=DTI-Reg, 9=unu
    std::vector < std::string > m_DTIRegOptions;
    std::string m_DTIRegExtraPath;
    std::string m_BFAffineTfmMode;
    bool m_useGridProcess;
    std::string m_GridGeneralCommand;
    std::string m_GridAtlasCommand;
    std::string m_PythonPath;
    std::string m_NbThreadsString;
    std::string m_ScalarMeasurement;

/* SCRIPTS */
    std::string m_Script_Preprocess; //contains the whole Script for Pre processing
    std::string m_Script_AtlasBuilding; //contains the whole Script for Atlas Building
    std::string m_Script_Main;//contains the whole Main Script
    std::string m_Script_Utilities;//contains utilities script
};
#endif