svkFdfVolumeReader.h

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/*
 *  Copyright © 2009-2014 The Regents of the University of California.
 *  All Rights Reserved.
 *
 *  Redistribution and use in source and binary forms, with or without 
 *  modification, are permitted provided that the following conditions are met:
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 *      this list of conditions and the following disclaimer.
 *  •   Redistributions in binary form must reproduce the above copyright notice, 
 *      this list of conditions and the following disclaimer in the documentation 
 *      and/or other materials provided with the distribution.
 *  •   None of the names of any campus of the University of California, the name 
 *      "The Regents of the University of California," or the names of any of its 
 *      contributors may be used to endorse or promote products derived from this 
 *      software without specific prior written permission.
 *  
 *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
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 *  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
 *  IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
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/*
 *  $URL$
 *  $Rev$
 *  $Author$
 *  $Date$
 *
 *  Authors:
 *      Jason C. Crane, Ph.D.
 *      Beck Olson
 */


#ifndef SVK_FDF_VOLUME_READER_H
#define SVK_FDF_VOLUME_READER_H

#include <vtkInformation.h>
#include <vtkFloatArray.h>
#include <vtkStringArray.h>

#include <svkVarianReader.h>

#include <map>
#include <string>
#include <vector>


namespace svk {


class svkFdfVolumeReader : public svkVarianReader
{

    public:

        static svkFdfVolumeReader* New();
        vtkTypeMacro( svkFdfVolumeReader, svkVarianReader);

        // Description: 
        // A descriptive name for this format
        virtual const char* GetDescriptiveName() {
            return "Varian FDF File";
        }

        virtual svkImageReader2::ReaderType GetReaderType()
        {
            return svkImageReader2::VARIAN_FDF;
        }

        //  Methods:
        virtual int             CanReadFile(const char* fname);


    protected:

        svkFdfVolumeReader();
        ~svkFdfVolumeReader();

        virtual int                      FillOutputPortInformation(int port, vtkInformation* info);
        virtual void                     ExecuteInformation();
        virtual void                     ExecuteDataWithInformation(vtkDataObject *output, vtkInformation* outInfo);
        svkDcmHeader::DcmPixelDataFormat GetFileType();
        void                             ScaleTo16Bit( bool scaleTo16Bit, bool scaleToSignedShort, bool scaleToPositiveRange ); 


    private:

        //  Methods:
        virtual void                     InitDcmHeader();
        void                             InitPatientModule();
        void                             InitGeneralStudyModule();
        void                             InitGeneralSeriesModule();
        void                             InitGeneralEquipmentModule();
        void                             InitImagePixelModule();
        void                             InitMultiFrameFunctionalGroupsModule();
        void                             InitMultiFrameDimensionModule();
        void                             InitAcquisitionContextModule();
        void                             InitSharedFunctionalGroupMacros();
        void                             InitPerFrameFunctionalGroupMacros();
        //void                             InitFrameContentMacro();
        //void                             InitPlanePositionMacro();
        void                             InitPixelMeasuresMacro();
        void                             InitPlaneOrientationMacro();
        void                             InitMRReceiveCoilMacro();
        void                             ReadFdfFiles();
        string                           VarianToDicomDate(string* volumeDate);
        string                           GetDcmPatientPositionString();
        void                             GetTLCAndSliceSpacing(double* toplc, double* sliceSpacing); 
        void                             GetPixelSize( double* pixelSize);
        void                             ParseFdf();
        int                              GetFdfKeyValuePair( vtkStringArray* keySet = NULL);
        void                             SetKeysToSearch(vtkStringArray* fltArray, int fileIndex);
        int                              GetDataBufferSize();
        int                              GetHeaderValueAsInt(string keyString, int valueIndex = 0); 
        float                            GetHeaderValueAsFloat(string keyString, int valueIndex = 0); 
        string                           GetHeaderValueAsString(string keyString, int valueIndex = 0);
        bool                             IsKeyInHeader(string keyString); 
        void                             ParseAndSetStringElements(string key, string valueArrayString);
        void                             ConvertCmToMm();  
        void                             ConvertUserToMagnetFrame(); 
        string                           GetStringFromFloat(float floatValue); 
        void                             AddDimensionTo2DData();
        void                             PrintKeyValuePairs();
        void                             MapFloatValuesTo16Bit(
                                                vtkFloatArray* fltArray, 
                                                vtkDataArray* dataArray
                                         );

        //  Members:
        void*                                       pixelData; 
        ifstream*                                   fdfFile;
        map <string, vector<string> >       
                                                    fdfMap; 
        long                                        fileSize; 
        vtkStringArray*                             tmpFileNames;
        bool                                        scaleTo16Bit;
        bool                                        scaleToSignedShort;
        bool                                        scaleToPositiveRange;


};


}   //svk


#endif //SVK_FDF_VOLUME_READER_H