marRAW2Files Class Reference

#include <marDicomBase.h>

Inheritance diagram for marRAW2Files:

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Collaboration diagram for marRAW2Files:

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List of all members.

Public Member Functions
	marRAW2Files (marParameters *p=NULL)
	~marRAW2Files ()
virtual bool	loadImage (int i)
virtual void	loadActualSerie (wxGauge *gauge)
virtual void	saveVolume (std::string directory, std::string filename, vtkImageData *vtkimagedata, int voi[6], double slope, double intercept)
void	FlipY (vtkImageData *imagedata)
void	SetLittreEndianBigEndian (int value)
int	GetLittreEndianBigEndian ()
void	reset ()
void	copyFrom (const marObject &from)
virtual void	copyFrom (const marObject &from)=0
bool	save (std::ofstream &os)
bool	save (std::string &nw)
bool	load (std::ifstream &is)
bool	load (std::string &nr)
virtual wxString	GetPatientName ()
kVolume *	getVolume ()
void	SetVolume (kVolume *volume)
bool	volumeLoaded ()
void	freeVolume ()
std::vector< std::string * > *	GetListImages ()
void	CleanListImages ()
void	ResetLstFileNotReaded ()
std::string	GetMsgLstFile ()
void	setParameters (marParameters *p)
void	copyParameters (marParameters *p)
void	makeACopyParameters ()
marParameters *	getParameters ()
bool	parametersOwned ()
Protected Attributes
std::vector< std::string * >	_lstString
std::vector< char * >	_lstFileNotReaded

---

Detailed Description

Definition at line 76 of file marDicomBase.h.

---

Constructor & Destructor Documentation

marRAW2Files::marRAW2Files

(

marParameters *

p = NULL

)

Definition at line 410 of file marDicomBase.cpp.

:  marRAWFiles(p)
{
}

marRAW2Files::~marRAW2Files

(

)

Definition at line 415 of file marDicomBase.cpp.

{
}

---

Member Function Documentation

void marFilesBase::CleanListImages

(

)

[inherited]

Definition at line 45 of file marDicomBase.cpp.

References marFilesBase::_lstString.

Referenced by loadActualSerie(), marRAW2AsciiFiles::loadActualSerie(), and marRAWFiles::loadActualSerie().

{
        int i,size;
        size=this->_lstString.size();
        for(i=0;i<size;i++)
        {
                delete _lstString[i];
        }
        _lstString.clear();
}

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virtual void marObject::copyFrom

(

const marObject &

from

)

[pure virtual, inherited]

void marRAWFiles::copyFrom

(

const marObject &

from

)

[inherited]

Definition at line 269 of file marDicomBase.cpp.

{
}

void marObject::copyParameters

(

marParameters *

p

)

[inherited]

Definition at line 42 of file marObject.cpp.

References marObject::_parameters, and marObject::_parametersCopied.

{
    if( _parametersCopied && _parameters != NULL ) delete _parameters;
    _parameters = new marParameters( );
    *_parameters = *p;
    _parametersCopied = true;
}

void marRAW2Files::FlipY

(

vtkImageData *

imagedata

)

Definition at line 608 of file marDicomBase.cpp.

Referenced by loadActualSerie().

{
        vtkImageData *vtkimagedata = imagedata;
        vtkimagedata->Update();
        int dim[3];
        vtkimagedata->GetDimensions(dim);
        unsigned short tmp;
        unsigned short *pp=(unsigned short*)vtkimagedata->GetScalarPointer(0,0,0);
        int xx,yy,zz;
        int sizeX  = dim[0];
        int sizeY  = dim[1];
        int sizeY2 = sizeY/2;
        int sizeZ  = dim[2];
        long int deltaZ;
        long int deltaA;
        long int deltaB;

        for ( zz=0 ; zz<sizeZ ; zz++ )
        {
                deltaZ=zz*sizeX*sizeY;
                for ( xx=0 ; xx<sizeX ; xx++ )
                {
                for ( yy=0 ; yy<sizeY2 ; yy++ )
                        {
                                deltaA          = xx + yy*sizeX + deltaZ;
                                deltaB          = xx + (sizeY-yy-1)*sizeX + deltaZ;
                                tmp                     = pp[deltaA ];
                                pp[deltaA]      = pp[deltaB ];
                                pp[deltaB]      = tmp;
                                }
                        }
                }
   vtkimagedata->Update();

}

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void marFilesBase::freeVolume

(

)

[inherited]

Definition at line 31 of file marDicomBase.cpp.

References marFilesBase::_volume.

Referenced by InitExperiment_dll(), loadActualSerie(), marRAW2AsciiFiles::loadActualSerie(), marRAWFiles::loadActualSerie(), and marFilesBase::~marFilesBase().

                              {
        if( _volume ) delete _volume;
        _volume = NULL;
}

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std::vector< std::string * > * marFilesBase::GetListImages

(

)

[inherited]

Definition at line 39 of file marDicomBase.cpp.

References marFilesBase::_lstString.

{
        return &_lstString;
}

int marRAWFiles::GetLittreEndianBigEndian

(

)

[inherited]

Definition at line 260 of file marDicomBase.cpp.

References marRAWFiles::_littreEndianBigEndian.

{
        return _littreEndianBigEndian;
}

std::string marFilesBase::GetMsgLstFile

(

)

[inherited]

Definition at line 65 of file marDicomBase.cpp.

References marFilesBase::_lstFileNotReaded.

Referenced by LoadRangeImage::ForceToFinisReadActiveImages().

{
        int i,sizeLst;
//EEDx44
        std::string msgLstFile="";
        sizeLst=_lstFileNotReaded.size();
        for (i=0;i<sizeLst;i++)
        {
                msgLstFile = msgLstFile + *(_lstFileNotReaded[i]) ;
                msgLstFile = msgLstFile + "\n";
        }

        return msgLstFile;
}

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marParameters* marObject::getParameters

(

)

[inline, inherited]

Parameters analizers.

Definition at line 55 of file marObject.h.

Referenced by marAxisCT::adjustWall(), marAxis::calculateSignal(), marAxis::create2Dcontour(), marAxis::create2DDiameterMax(), marAxis::create2DDiameterMin(), marAxisCT::create2DDiametersMax(), marAxisCT::create2DDiametersMin(), marAxis::create3DSlice(), marAxis::createContour(), marAxisCT::createContours(), marAxis::createSlice(), marAxis::doSpline(), marAxisCT::extractLumen(), marExperiment::extractVascularTree(), marAxisCT::generatePoints(), marDynData::getActualVoxel(), marAxisCT::histogram(), marExperiment::initExperiment(), marExperiment::load(), marAxis::load(), loadActualSerie(), marRAW2AsciiFiles::loadActualSerie(), marRAWFiles::loadActualSerie(), marDynData::loadData(), marSimpleDicom::loadVolumeDXMM(), wxEmptyPanelWidget_2::OnBtnExtractTree_MH_JFC(), wxSurfaceWidget::OnManualAxis(), vtk3DQuantSurfaceWidget::Set3DSliceActor(), vtk3DSurfaceWidget::SetInitialPoint(), marAxisCT::setStartIndex(), marExperimentCT::updateCalcPercentage(), marAxisCT::updateCalcPercentage(), marExperimentCT::updateDiscontinuityThreshold(), marExperimentCT::updateLumenPercentage(), and marAxisCT::updateLumenPercentage().

{ return( _parameters ); };

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virtual wxString marFilesBase::GetPatientName

(

)

[inline, virtual, inherited]

Definition at line 26 of file marDicomBase.h.

{return _T(""); };

kVolume * marFilesBase::getVolume

(

)

[inherited]

Definition at line 19 of file marDicomBase.cpp.

References marFilesBase::_volume.

Referenced by PriorityLoadImageBar::Action_i(), CastVolume_dummy(), GetAreaValuesFromTotalVolume_dll(), GetImageIntensity_dll(), GetNumberOfImages_dll(), marInterfaceCT::initExperiment(), marInterface::initExperiment(), loadActualSerie(), marRAW2AsciiFiles::loadActualSerie(), marRAWFiles::loadImage(), LoadTkImages_dll(), wxMaracasFrame::OnStartExperiment(), and LoadRangeImage::Start().

                                 {
        return( _volume );
}

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bool marObject::load

(

std::string &

nr

)

[inherited]

Definition at line 67 of file marObject.cpp.

References marObject::load().

Referenced by marObject::load().

{
    std::ifstream is( nr.c_str( ) );

    if( is ) {

        load( is );
        is.close( );
        return( true );

    } // fi

    return( false );
}

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bool marRAWFiles::load

(

std::ifstream &

is

)

[virtual, inherited]

Implements marObject.

Definition at line 278 of file marDicomBase.cpp.

{
        return true;
}

void marRAW2Files::loadActualSerie

(

wxGauge *

gauge

)

[virtual]

Reimplemented from marRAWFiles.

Definition at line 427 of file marDicomBase.cpp.

References marFilesBase::_lstString, marFilesBase::CleanListImages(), marParameters::e_RescaleIntercept, marParameters::e_RescaleSlope, marParameters::e_voxel_x_dimension, marParameters::e_voxel_y_dimension, marParameters::e_voxel_z_dimension, FlipY(), marFilesBase::freeVolume(), marObject::getParameters(), marFilesBase::getVolume(), marParameters::setDoubleParam(), and marFilesBase::SetVolume().

{

        // Read File List
        FILE *ff;
        ff = fopen( _lstString[0] -> c_str() , "r"); 
        char tmp[255];

        // type
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        //int type =    atoi(tmp);  // 200  // JPRx

        //size x,y,z
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        int wx  =       atoi(tmp);
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        int wy  =       atoi(tmp);
//      fscanf(ff,"%s",tmp);
//      fscanf(ff,"%s",tmp);
//      int wz  =       atoi(tmp);

        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        int wz1 =       atoi(tmp);
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        int wz2 =       atoi(tmp);

        int wz = wz2-wz1;
        
        // spacing x,y,z
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        double spx      =       atof(tmp);
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        double spy      =       atof(tmp);
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        double spz      =       atof(tmp);

        // Intercept Slope
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        double intercept        =       atof(tmp);
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        double slope            =       atof(tmp);

        // L/B
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        int littleBig   =       atoi(tmp);

        // bits
        fscanf(ff,"%s",tmp);
        fscanf(ff,"%s",tmp);
        int bits        =       atoi(tmp);

        if ((bits!=8) && (bits!=16)){
                bits=16;
        }
        
        fscanf(ff,"%s",tmp);
        std::string file(tmp);
        std::string namefile( *_lstString[1] );  // directory
        namefile=namefile+"/";                   // +  
        namefile=namefile+file;                  // file

        fclose(ff);


        this->CleanListImages();

        // Create Free Memory block image
        freeVolume();

        if (wz==0)
        {
                wz=1;
        }


        kVolume *vol =new kVolume( kVolume::USHORT, wx, wy, wz,spx, spy, spz, malloc(sizeof(unsigned short)*wx*wy*wz ) );
        SetVolume( vol );


        // Define Spacing
        getParameters( )->setDoubleParam( marParameters::e_voxel_x_dimension, spx );
        getParameters( )->setDoubleParam( marParameters::e_voxel_y_dimension, spy );
        getParameters( )->setDoubleParam( marParameters::e_voxel_z_dimension, spz );

        // Define Intercept Slope
        getParameters( )->setDoubleParam( marParameters::e_RescaleIntercept , 0 );
        getParameters( )->setDoubleParam( marParameters::e_RescaleSlope     , 1 );

        void *p_vol=(void*)getVolume( )->castVtk()->GetScalarPointer(0,0,0);
        FILE *fff=fopen( (char*)namefile.c_str() , "r+" );
    if (bits==16)
    {
                fseek( fff , wx*wy*wz1*2 , SEEK_CUR );
        fread( (char*)p_vol , wx*wy*wz*2,1, fff);
            fclose(fff);


        // littleBigEndien
                if (littleBig==1){
                        long int                ii;
                        char                    tmpB;
                        char                    *pp = (char*)p_vol;
                        unsigned short   *valueA;
                        long int dataSize       = wx*wy*wz;
                        for (ii=0;ii<dataSize;ii++)
                        {
                                tmpB            = *pp;
                                *pp                     = *(pp+1);
                                *(pp+1)         = tmpB;
                                
                                valueA= ((unsigned short*)pp);
                                if (*valueA>=32000)
                                {
                                        *valueA=0;
                                } 
                                pp              = pp+2;

                        }
                }

                unsigned short                  *pp = (unsigned short*)p_vol;
                int tmpInt;
                int ii, dataSize        = wx*wy*wz;
                for (ii=0;ii<dataSize;ii++)
                {
                        tmpInt = (int) (*pp);
                        tmpInt  = (int)  ( tmpInt*slope+intercept );
                        if (tmpInt<0)
                        {
                                tmpInt=0;
                        } 
                        if (tmpInt>65535) 
                        {
                                tmpInt=65535;
                        }
                        (*pp) = (unsigned short)tmpInt;
                        pp              = pp+1;
                }

    } else {
        unsigned short *pShort=(unsigned short*)p_vol;
        int i8bitImage,size8bitImage = wx*wy*wz;
        unsigned char *pChar=(unsigned char*)malloc( size8bitImage );
                fseek( fff , wx*wy*wz1 , SEEK_CUR );
        fread( (unsigned char*)pChar , size8bitImage,1, fff);
            fclose(fff);
                double tmpDouble;
        for ( i8bitImage=0 ; i8bitImage < size8bitImage ; i8bitImage++ )
        {
                        
                        tmpDouble=(float)pChar[ i8bitImage ];
                        tmpDouble=tmpDouble*slope+intercept;
                        if (tmpDouble<0)
                        {
                                tmpDouble=0;
                        } 
                pShort[ i8bitImage ] = (unsigned short)tmpDouble;
        }
        free (pChar);
    }

// Y- Flip
        FlipY( getVolume( )->castVtk() );
        
}

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bool marRAW2Files::loadImage

(

int

i

)

[virtual]

Reimplemented from marRAWFiles.

Definition at line 419 of file marDicomBase.cpp.

{
        return true;
}

void marObject::makeACopyParameters

(

)

[inline, inherited]

Definition at line 48 of file marObject.h.

    {
            copyParameters( _parameters );
    }

bool marObject::parametersOwned

(

)

[inline, inherited]

Definition at line 56 of file marObject.h.

{ return( _parametersCopied ); };

void marRAWFiles::reset

(

)

[virtual, inherited]

Virtual general methods (must be defined in each sub-class).

Implements marObject.

Definition at line 265 of file marDicomBase.cpp.

{
}

void marFilesBase::ResetLstFileNotReaded

(

)

[inherited]

Definition at line 58 of file marDicomBase.cpp.

References marFilesBase::_lstFileNotReaded.

Referenced by LoadRangeImage::Start().

{
        _lstFileNotReaded.clear();
}

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bool marObject::save

(

std::string &

nw

)

[inherited]

Persistence methods

Definition at line 51 of file marObject.cpp.

References marObject::save().

{
    std::ofstream os( nw.c_str( ) );

    if( os ) {

        save( os );
        os.close( );
        return( true );

    } // fi

    return( false );
}

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bool marRAWFiles::save

(

std::ofstream &

os

)

[virtual, inherited]

Virtual persistence methods (must be defined in each sub-class).

Implements marObject.

Definition at line 273 of file marDicomBase.cpp.

{
        return true;
}

void marRAW2Files::saveVolume	(	std::string	directory,
		std::string	filename,
		vtkImageData *	vtkimagedata,
		int	voi[6],
		double	slope,
		double	intercept
	)			[virtual]

Definition at line 646 of file marDicomBase.cpp.

Referenced by marAxisCT::generateFile(), wxVtkClipping3DViewCntrlPanel::OnBtnSaveRawVolume(), and wxMaracasImageBrowser02::OnBtSaveVOIData().

{

        std::string filename             = directory+"/"+name;

                // Crop
        vtkExtractVOI *crop = vtkExtractVOI::New();
        crop->SetInput( imagedata );
        crop->SetVOI( voi );
        crop->Update();

        int dim[3];
        int ext[6];
        double spc[3];
        crop->GetOutput()->GetDimensions(dim);
        crop->GetOutput()->GetSpacing(spc);
        crop->GetOutput()->GetExtent(ext);


        vtkImageChangeInformation* change = vtkImageChangeInformation::New();
        change->SetInput( crop->GetOutput() );


//      change->SetExtentTranslation( -ext[0], -ext[2], -ext[4] );
   

        change->SetOutputSpacing ( spc[0] , spc[1] , spc[2] );
        change->Update();    //important

//   change->SetExtentTranslation( ext[0], ext[2], ext[4] );
//      change->Update();


        // write mdh file
   std::string nameMW            = filename+".mhd";

        vtkMetaImageWriter *writer = vtkMetaImageWriter::New( );
        writer->SetInput( change->GetOutput() );
        writer->SetFileName( nameMW.c_str() );
        writer->SetFileDimensionality( 3 );
        writer->Write( );

                // write maracas file
        std::string nameM=filename+".maracas";


        FILE *ff;
        ff=fopen(nameM.c_str(),"w");
                fprintf(ff,"MaracasType 200\n" );
                fprintf(ff,"sizeX %d\n",dim[0] );
                fprintf(ff,"sizeY %d\n",dim[1] );
                fprintf(ff,"sizeZ1 %d\n",0 );
                fprintf(ff,"sizeZ2 %d\n",dim[2] );
                fprintf(ff,"spcX %f\n",spc[0]  );
                fprintf(ff,"spcY %f\n",spc[1]  );
                fprintf(ff,"spcZ %f\n",spc[2]  );
                fprintf(ff,"intercept %f\n",intercept );
                fprintf(ff,"slope %f\n",slope );
                fprintf(ff,"LB %d\n",0 );
                fprintf(ff,"bits %d\n",16 );
                fprintf(ff,"%s.raw\n", name.c_str() );
        fclose(ff);

        writer  -> Delete();
        change  -> Delete();
        crop    -> Delete();
}

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void marRAWFiles::SetLittreEndianBigEndian

(

int

value

)

[inherited]

Definition at line 255 of file marDicomBase.cpp.

References marRAWFiles::_littreEndianBigEndian.

Referenced by marRAWFiles::loadActualSerie().

{
        _littreEndianBigEndian = value;
}

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void marObject::setParameters

(

marParameters *

p

)

[inherited]

Parameters assignation methods.

You can assign a marParameters object by reference (setParameters) or by value (copyParameters). Besides, if you want to make your actual reference to be by value, call makeACopyParameters.

Definition at line 34 of file marObject.cpp.

References marObject::_parameters, and marObject::_parametersCopied.

{
    if( _parametersCopied && _parameters != NULL ) delete _parameters;
    _parameters = p;
    _parametersCopied = false;
}

void marFilesBase::SetVolume

(

kVolume *

volume

)

[inherited]

Definition at line 23 of file marDicomBase.cpp.

References marFilesBase::_volume.

Referenced by loadActualSerie(), marRAW2AsciiFiles::loadActualSerie(), marRAWFiles::loadActualSerie(), marSimpleDicom::loadVolumeDXMM(), and wxMaracasFrame::OnStartExperiment().

                                              {
        _volume=volume;
}

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bool marFilesBase::volumeLoaded

(

)

[inherited]

Definition at line 27 of file marDicomBase.cpp.

References marFilesBase::_volume.

                                {
        return( _volume != NULL );
}

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Member Data Documentation

std::vector< char*> marFilesBase::_lstFileNotReaded [protected, inherited]

Definition at line 45 of file marDicomBase.h.

Referenced by marFilesBase::GetMsgLstFile(), marRAWFiles::loadImage(), and marFilesBase::ResetLstFileNotReaded().

std::vector< std::string*> marFilesBase::_lstString [protected, inherited]

Definition at line 44 of file marDicomBase.h.

Referenced by marFilesBase::CleanListImages(), marFilesBase::GetListImages(), loadActualSerie(), marRAW2AsciiFiles::loadActualSerie(), marRAWFiles::loadActualSerie(), and marRAWFiles::loadImage().

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The documentation for this class was generated from the following files:

• /home/davila/Creatis/creaMaracasVisu/lib/maracasVisuLib/src/kernel/marDicomBase.h
• /home/davila/Creatis/creaMaracasVisu/lib/maracasVisuLib/src/kernel/marDicomBase.cpp