#pragma once
/*=========================================================================

 medInria

 Copyright (c) INRIA 2013 All rights reserved.
 See LICENSE.txt for details in the root of the sources or:
 https://github.com/medInria/medInria-public/blob/master/LICENSE.txt

 This software is distributed WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  PURPOSE.

=========================================================================*/

/**
 * \file   medInrimageImageIO.h
 *         Much of the code for this file reader/writer was taken from
 *         the University of Iowa Imaging Group library with the
 *         permission of the authors, Milan Sonka, Joseph Reinhardt,
 *         Ryan Long, Hans Johnson, Gary Christensen, and others.
 *         The specification for this file format is taken from the
 *         web site http://www.mayo.edu/bir/PDF/ANALYZE75.pdf.
 * \author Gregoire Malandain
 *         INRIA 2003
 * \brief TO BE CAHNGED
 *        This file was written as a modification to the itkMetaImageIO
 *        as a new method for reading in files from the Inrimage 7.5 specification.
 *        An Inrimage 7.5 specification consists of 2 files.  The first file is has a .hdr extension
 *        that is the header information containing specific information about the
 *        image dimensions, and other information concerning the data.
 *        The second file has a .img file extenstion and it contains the raw image data.
 */

#include "itkImageIOBase.h"
#include <medImageIOExport.h>

#include <itkImageIOBase.h>
#include <itkMetaDataObject.h>
#include <itk_zlib.h>

/**
     * \author Gregoire Malandain
     * \brief Class that defines how to read Inrimage 4 file format.
     * */
class MEDIMAGEIO_EXPORT InrimageImageIO : public itk::ImageIOBase
{
public:
    /** Standard class typedefs. */
    using Self = InrimageImageIO;
    using Superclass = ImageIOBase;
    using Pointer = itk::SmartPointer<Self>;

    /** Method for creation through the object factory. */
    itkNewMacro(Self);

    /** Run-time type information (and related methods). */
    itkTypeMacro(InrimageImageIO, Superclass);

    /*-------- This part of the interfaces deals with reading data. ----- */

    /** Determine if the file can be read with this ImageIO implementation.
         * \author Gregoire Malandain
         * \param FileNameToRead The name of the file to test for reading.
         * \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
         * \return Returns true if this ImageIO can read the file specified.
         */
    bool CanReadFile(const char* FileNameToRead) override;

    /** Set the spacing and dimension information for the set filename. */
    virtual void ReadImageInformation();

    /** Convert to type_info */
    const std::type_info& ConvertToTypeInfo(itk::IOComponentEnum) const;

    /** Reads the data from disk into the memory buffer provided. */
    virtual void Read(void* buffer);

    /** Compute the size (in bytes) of the components of a pixel. For
         * example, and RGB pixel of unsigned char would have a
         * component size of 1 byte. NO MORE USEFUL FOR ITK > 1.8*/
    //virtual unsigned int GetComponentSize() const;

    /*-------- This part of the interfaces deals with writing data. ----- */

    /** Determine if the file can be written with this ImageIO implementation.
          * \param FileNameToWrite The name of the file to test for writing.
          * \author Gregoire Malandain
          * \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
          * \return Returns true if this ImageIO can write the file specified.
          */
    bool CanWriteFile(const char * FileNameToWrite) override;

    /** Set the spacing and dimension information for the set filename. */
    virtual void WriteImageInformation();

    /** Writes the data to disk from the memory buffer provided. Make sure
         * that the IORegions has been set properly. */
    void Write(const void* buffer) override;

protected:
    InrimageImageIO();
    ~InrimageImageIO();
    void PrintSelf(std::ostream& os, itk::Indent indent) const;

private:
    void SwapBytesIfNecessary(void * buffer, unsigned long numberOfPixels);

    void GetRotationMatrixFromAngles(double rx, double ry, double rz, vnl_matrix <double> &rotationMatrix);

    void GetRotationAnglesFromMatrix(const vnl_matrix <double> &rotationMatrix, std::vector <double> &r);

    gzFile m_file;

    /**  All of the information read in from the header file */
    unsigned int m_NumberBlocksInHeader;
    std::string m_header;
};