// SPDX-FileCopyrightText: Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
// SPDX-FileCopyrightText: Copyright (c) 2006 Atamai, Inc.
// SPDX-License-Identifier: BSD-3-Clause
/**
 * @class   vtkMINCImageWriter
 * @brief   A writer for MINC files.
 *
 * MINC is a NetCDF-based medical image file format that was developed
 * at the Montreal Neurological Institute in 1992.
 * The data is written slice-by-slice, and this writer is therefore
 * suitable for streaming MINC data that is larger than the memory
 * size through VTK.  This writer can also produce files with up to
 * 4 dimensions, where the fourth dimension is provided by using
 * AddInput() to specify multiple input data sets.  If you want to
 * set header information for the file, you must supply a
 * vtkMINCImageAttributes
 * @sa
 * vtkMINCImageReader vtkMINCImageAttributes
 * @par Thanks:
 * Thanks to David Gobbi for writing this class and Atamai Inc. for
 * contributing it to VTK.
 */

#ifndef vtkMINCImageWriter_h
#define vtkMINCImageWriter_h

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

VTK_ABI_NAMESPACE_BEGIN
class vtkStringArray;
class vtkIdTypeArray;
class vtkDoubleArray;
class vtkMatrix4x4;

// A special class that holds the attributes
class vtkMINCImageAttributes;

class VTKIOMINC_EXPORT vtkMINCImageWriter : public vtkImageWriter
{
public:
  vtkTypeMacro(vtkMINCImageWriter, vtkImageWriter);

  static vtkMINCImageWriter* New();
  void PrintSelf(ostream& os, vtkIndent indent) override;

  /**
   * Get the extension for this file format.
   */
  virtual const char* GetFileExtensions() { return ".mnc"; }

  /**
   * Get the name of this file format.
   */
  virtual const char* GetDescriptiveName() { return "MINC"; }

  /**
   * Set the file name.
   */
  void SetFileName(VTK_FILEPATH const char* name) override;

  /**
   * Write the data.  This will attempt to stream the data
   * slice-by-slice through the pipeline and out to the file,
   * unless the whole extent of the input has already been
   * updated.
   */
  void Write() override;

  ///@{
  /**
   * Set a matrix that describes the orientation of the data.  The
   * three columns of this matrix should give the unit-vector
   * directions for the VTK x, y and z dimensions respectively.
   * The writer will use this information to determine how to map
   * the VTK dimensions to the canonical MINC dimensions, and if
   * necessary, the writer will re-order one or more dimensions
   * back-to-front to ensure that no MINC dimension ends up with
   * a direction cosines vector whose dot product with the canonical
   * unit vector for that dimension is negative.
   */
  virtual void SetDirectionCosines(vtkMatrix4x4* matrix);
  vtkGetObjectMacro(DirectionCosines, vtkMatrix4x4);
  ///@}

  ///@{
  /**
   * Set the slope and intercept for rescaling the intensities.  The
   * default values are zero, which indicates to the reader that no
   * rescaling is to be performed.
   */
  vtkSetMacro(RescaleSlope, double);
  vtkGetMacro(RescaleSlope, double);
  vtkSetMacro(RescaleIntercept, double);
  vtkGetMacro(RescaleIntercept, double);
  ///@}

  ///@{
  /**
   * Set the image attributes, which contain patient information and
   * other useful metadata.
   */
  virtual void SetImageAttributes(vtkMINCImageAttributes* attributes);
  virtual vtkMINCImageAttributes* GetImageAttributes() { return this->ImageAttributes; }
  ///@}

  ///@{
  /**
   * Set whether to validate that all variable attributes that
   * have been set are ones that are listed in the MINC standard.
   */
  vtkSetMacro(StrictValidation, vtkTypeBool);
  vtkBooleanMacro(StrictValidation, vtkTypeBool);
  vtkGetMacro(StrictValidation, vtkTypeBool);
  ///@}

  ///@{
  /**
   * Set a string value to append to the history of the file.  This
   * string should describe, briefly, how the file was processed.
   */
  vtkSetStringMacro(HistoryAddition);
  vtkGetStringMacro(HistoryAddition);
  ///@}

protected:
  vtkMINCImageWriter();
  ~vtkMINCImageWriter() override;

  int MINCImageType;
  int MINCImageTypeSigned;
  int MINCImageMinMaxDims;

  vtkMatrix4x4* DirectionCosines;
  double RescaleSlope;
  double RescaleIntercept;
  vtkTypeBool StrictValidation;
  int DataUpdateExtent[6];

  int FileDataType;
  double FileValidRange[2];
  double InternalRescaleSlope;
  double InternalRescaleIntercept;

  int ComputeValidRangeFromScalarRange;

  vtkStringArray* FileDimensionNames;

  vtkMINCImageAttributes* ImageAttributes;

  int Permutation[3];
  int Flip[3];

  int MismatchedInputs;
  int MINCFileId;

  char* HistoryAddition;

  virtual int OpenNetCDFFile(const char* filename, int& ncid);
  virtual int CloseNetCDFFile(int ncid);

  virtual int IndexFromDimensionName(const char* dimName);
  virtual void ComputePermutationFromOrientation(int permutation[3], int flip[3]);
  virtual int CreateMINCDimensions(vtkImageData* input, int timeStep, int* dimids);
  virtual int CreateMINCVariables(vtkImageData* input, int timeStep, int* dimids);
  virtual int WriteMINCFileAttributes(vtkImageData* input, int timeStep);
  virtual int WriteMINCData(vtkImageData* input, int frameNumber, int wholeExt[6], int upExt[6]);
  virtual void FindRescale(double& rescaleSlope, double& rescaleIntercept);
  virtual void FindMINCValidRange(double range[2]);

  int FillInputPortInformation(int port, vtkInformation* info) override;

  int RequestInformation(vtkInformation* request, vtkInformationVector** inputVector,
    vtkInformationVector* outputVector) override;

  int RequestUpdateExtent(vtkInformation* request, vtkInformationVector** inputVector,
    vtkInformationVector* outputVector) override;

  int RequestData(vtkInformation* request, vtkInformationVector** inputVector,
    vtkInformationVector* outputVector) override;

private:
  vtkMINCImageWriter(const vtkMINCImageWriter&) = delete;
  void operator=(const vtkMINCImageWriter&) = delete;
};

VTK_ABI_NAMESPACE_END
#endif