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

  Program:   Visualization Toolkit
  Module:    vtkNIFTIImageWriter.h

  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
  All rights reserved.
  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
/**
 * @class   vtkNIFTIImageWriter
 * @brief   Write NIfTI-1 and NIfTI-2 medical image files
 *
 * This class writes NIFTI files, either in .nii format or as separate
 * .img and .hdr files.  If told to write a file that ends in ".gz",
 * then the writer will automatically compress the file with zlib.
 * Images of type unsigned char that have 3 or 4 scalar components
 * will automatically be written as RGB or RGBA respectively.  Images
 * of type float or double that have 2 components will automatically be
 * written as complex values.
 * @par Thanks:
 * This class was contributed to VTK by the Calgary Image Processing and
 * Analysis Centre (CIPAC).
 * @sa
 * vtkNIFTIImageReader
*/

#ifndef vtkNIFTIImageWriter_h
#define vtkNIFTIImageWriter_h

#include "vtkIOImageModule.h" // For export macro
#include "vtkImageWriter.h"

class vtkMatrix4x4;
class vtkNIFTIImageHeader;

class VTKIOIMAGE_EXPORT vtkNIFTIImageWriter : public vtkImageWriter
{
public:
  //@{
  /**
   * Static method for construction.
   */
  static vtkNIFTIImageWriter *New();
  vtkTypeMacro(vtkNIFTIImageWriter, vtkImageWriter);
  //@}

  /**
   * Print information about this object.
   */
  void PrintSelf(ostream& os, vtkIndent indent) VTK_OVERRIDE;

  //@{
  /**
   * Set the version number for the NIfTI file format to use.
   * This can be 1, 2, or 0 (the default).  If set to zero, then it
   * will save as NIfTI version 1 unless SetNIFTIHeader() provided
   * header information from a NIfTI version 2 file.
   */
  vtkSetMacro(NIFTIVersion, int);
  vtkGetMacro(NIFTIVersion, int);
  //@}

  //@{
  /**
   * Set a short description (max 80 chars) of how the file was produced.
   * The default description is "VTKX.Y" where X.Y is the VTK version.
   */
  vtkSetStringMacro(Description);
  vtkGetStringMacro(Description);
  //@}

  //@{
  /**
   * Set the time dimension to use in the NIFTI file (or zero if none).
   * The number of components of the input data must be divisible by the time
   * dimension if the time dimension is not set to zero.  The vector dimension
   * will be set to the number of components divided by the time dimension.
   */
  vtkGetMacro(TimeDimension, int);
  vtkSetMacro(TimeDimension, int);
  vtkGetMacro(TimeSpacing, double);
  vtkSetMacro(TimeSpacing, double);
  //@}

   //@{
   /**
    * Set the slope and intercept for calibrating the scalar values.
    * Other programs that read the NIFTI file can use the equation
    * v = u*RescaleSlope + RescaleIntercept to rescale the data to
    * real values.  If both the slope and the intercept are zero,
    * then the SclSlope and SclIntercept in the header info provided
    * via SetNIFTIHeader() are used instead.
    */
   vtkSetMacro(RescaleSlope, double);
   vtkGetMacro(RescaleSlope, double);
   vtkSetMacro(RescaleIntercept, double);
   vtkGetMacro(RescaleIntercept, double);
   //@}

  //@{
  /**
   * Write planar RGB (separate R, G, and B planes), rather than packed RGB.
   * Use this option with extreme caution: the NIFTI standard requires RGB
   * pixels to be packed.  The Analyze format, however, was used to store
   * both planar RGB and packed RGB depending on the software, without any
   * indication in the header about which convention was being used.
   */
  vtkGetMacro(PlanarRGB, bool);
  vtkSetMacro(PlanarRGB, bool);
  vtkBooleanMacro(PlanarRGB, bool);
  //@}

  //@{
  /**
   * The QFac sets the ordering of the slices in the NIFTI file.
   * If QFac is -1, then the slice ordering in the file will be reversed
   * as compared to VTK. Use with caution.
   */
  vtkSetMacro(QFac, double);
  vtkGetMacro(QFac, double);
  //@}

  /**
   * Set the "qform" orientation and offset for the image data.
   * The 3x3 portion of the matrix must be orthonormal and have a
   * positive determinant, it will be used to compute the quaternion.
   * The last column of the matrix will be used for the offset.
   * In the NIFTI header, the qform_code will be set to 1.
   */
  void SetQFormMatrix(vtkMatrix4x4 *);
  vtkMatrix4x4 *GetQFormMatrix() { return this->QFormMatrix; }

  /**
   * Set a matrix for the "sform" transformation stored in the file.
   * Unlike the qform matrix, the sform matrix can contain scaling
   * information.  Before being stored in the NIFTI header, the
   * first three columns of the matrix will be multipled by the voxel
   * spacing. In the NIFTI header, the sform_code will be set to 2.
   */
  void SetSFormMatrix(vtkMatrix4x4 *);
  vtkMatrix4x4 *GetSFormMatrix() { return this->SFormMatrix; }

  //@{
  /**
   * Set the NIFTI header information to use when writing the file.
   * The data dimensions and pixdim from the supplied header will be
   * ignored.  Likewise, the QForm and SForm information in the supplied
   * header will be ignored if you have called SetQFormMatrix() or
   * SetSFormMatrix() to provide the orientation information for the file.
   */
  void SetNIFTIHeader(vtkNIFTIImageHeader *hdr);
  vtkNIFTIImageHeader *GetNIFTIHeader();
  //@}

protected:
  vtkNIFTIImageWriter();
  ~vtkNIFTIImageWriter();

  /**
   * Generate the header information for the file.
   */
  int GenerateHeader(vtkInformation *info, bool singleFile);

  /**
   * The main execution method, which writes the file.
   */
  virtual int RequestData(vtkInformation *request,
                          vtkInformationVector** inputVector,
                          vtkInformationVector* outputVector);

  /**
   * Make a new filename by replacing extension "ext1" with "ext2".
   * The extensions must include a period, must be three characters
   * long, and must be lower case.  A new string is returned that must
   * be deleted by the caller.
   */
  static char *ReplaceExtension(
    const char *fname, const char *ext1, const char *ext2);

  //@{
  /**
   * The size and spacing of the Time dimension to use in the file.
   */
  int TimeDimension;
  double TimeSpacing;
  //@}

  //@{
  /**
   * Information for rescaling data to quantitative units.
   */
  double RescaleIntercept;
  double RescaleSlope;
  //@}

  /**
   * Is -1 if VTK slice order is opposite to NIFTI slice order, +1 otherwise.
   */
  double QFac;

  //@{
  /**
   * The orientation matrices for the NIFTI file.
   */
  vtkMatrix4x4 *QFormMatrix;
  vtkMatrix4x4 *SFormMatrix;
  //@}

  /**
   * A description of how the file was produced.
   */
  char *Description;

  //@{
  /**
   * The header information.
   */
  vtkNIFTIImageHeader *NIFTIHeader;
  vtkNIFTIImageHeader *OwnHeader;
  int NIFTIVersion;
  //@}

  /**
   * Use planar RGB instead of the default (packed).
   */
  bool PlanarRGB;

private:
  vtkNIFTIImageWriter(const vtkNIFTIImageWriter&) VTK_DELETE_FUNCTION;
  void operator=(const vtkNIFTIImageWriter&) VTK_DELETE_FUNCTION;
};

#endif // vtkNIFTIImageWriter_h
