libinsighttoolkit3-dev 3.20.1-1 / usr / include / InsightToolkit / IO / itkImageIOBase.h

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    itkImageIOBase.h
  Language:  C++
  Date:      $Date$
  Version:   $Revision$

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/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 notices for more information.

=========================================================================*/
#ifndef __itkImageIOBase_h
#define __itkImageIOBase_h

#include "itkLightProcessObject.h"
#include "itkObjectFactory.h"
#include "itkIndent.h"
#include "itkImageIORegion.h"
#include "vnl/vnl_vector.h"

#include <string>

namespace itk
{

/** \class ImageIOBase
 * \brief Abstract superclass defines image IO interface.
 *
 * ImageIOBase is a class that reads and/or writes image data
 * of a particular format (such as PNG or raw binary). The
 * ImageIOBase encapsulates both the reading and writing of data. The
 * ImageIOBase is used by the ImageFileReader class (to read data)
 * and the ImageFileWriter (to write data) into a single file. The
 * ImageSeriesReader and ImageSeriesWriter classes are used to read
 * and write data (in conjunction with ImageIOBase) when the data is
 * represented by a series of files. Normally the user does not directly
 * manipulate this class other than to instantiate it, set the FileName,
 * and assign it to a ImageFileReader/ImageFileWriter or
 * ImageSeriesReader/ImageSeriesWriter.
 *
 * A Pluggable factory pattern is used this allows different kinds of readers
 * to be registered (even at run time) without having to modify the
 * code in this class.
 *
 * \sa ImageFileWriter
 * \sa ImageFileReader
 * \sa ImageSeriesWriter
 * \sa ImageSeriesReader
 *
 * \ingroup IOFilters
 *
 */
class ITK_EXPORT ImageIOBase : public LightProcessObject
{
public:
  /** Standard class typedefs. */
  typedef ImageIOBase        Self;
  typedef LightProcessObject Superclass;
  typedef SmartPointer<Self> Pointer;

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

  /** Set/Get the name of the file to be read. */
  itkSetStringMacro(FileName);
  itkGetStringMacro(FileName);

  /** Types for managing image size and image index components. */
  typedef   long              IndexValueType;
  typedef   unsigned long     SizeValueType;

  /**
   * \class UnknownType
   * Used to return information when types are unknown.
   */
  class UnknownType {};

  /** Enums used to manipulate the pixel type. The pixel type provides
   * context for automatic data conversions (for instance, RGB to
   * SCALAR, VECTOR to SCALAR). */
  typedef  enum {UNKNOWNPIXELTYPE,SCALAR,RGB,RGBA,OFFSET,VECTOR,
                 POINT,COVARIANTVECTOR,SYMMETRICSECONDRANKTENSOR,
                 DIFFUSIONTENSOR3D,COMPLEX,FIXEDARRAY,MATRIX}  IOPixelType;

  /** Enums used to manipulate the component type. The component type
   * refers to the actual storage class associated with either a
   * SCALAR pixel type or elements of a compound pixel.
   */
  typedef  enum {UNKNOWNCOMPONENTTYPE,UCHAR,CHAR,USHORT,SHORT,UINT,INT,
                 ULONG,LONG, FLOAT,DOUBLE} IOComponentType;

  /** Set/Get the number of independent variables (dimensions) in the
   * image being read or written. Note this is not necessarily what
   * is written, rather the IORegion controls that. */
  void SetNumberOfDimensions(unsigned int);
  itkGetConstMacro(NumberOfDimensions, unsigned int);

  /** Set/Get the image dimensions in the x, y, z, etc. directions.
   * GetDimensions() is typically used after reading the data; the
   * SetDimensions() is used prior to writing the data. */
  virtual void SetDimensions(unsigned int i, unsigned int dim);
  virtual unsigned int GetDimensions(unsigned int i) const
  { return m_Dimensions[i]; }

  /** Set/Get the image origin on a axis-by-axis basis. The SetOrigin() method
   * is required when writing the image. */
  virtual void SetOrigin(unsigned int i, double origin);
  virtual double GetOrigin(unsigned int i) const
    {
    return m_Origin[i];
    }

  /** Set/Get the image spacing on an axis-by-axis basis. The
   * SetSpacing() method is required when writing the image. */
  virtual void SetSpacing(unsigned int i, double spacing);
  virtual double GetSpacing(unsigned int i) const
    {
    return m_Spacing[i];
    }

  /** Set/Get the image direction on an axis-by-axis basis. The
   * SetDirection() method is required when writing the image. */
  virtual void SetDirection(unsigned int i, std::vector<double> &direction);
  virtual void SetDirection(unsigned int i, vnl_vector<double> &direction);
  virtual std::vector<double> GetDirection(unsigned int i) const
    {
    return m_Direction[i];
    }

  /** Return the directions to be assigned by default to recipient
   *  images whose dimension is smaller than the image dimension in file.  */
  virtual std::vector<double> GetDefaultDirection(unsigned int i) const;

  /** Specify the region of the image data to either read or
   * write. The IORegion specifies the part of the image to read or
   * write. Regions are defined with an index and a size vector. These
   * vectors define the start (lower-left corner) and length of the
   * region within the image. Make sure that the IORegion lies within
   * the image. */
  itkSetMacro(IORegion, ImageIORegion);
  itkGetConstReferenceMacro(IORegion, ImageIORegion);

  /** Set/Get the type of the pixel. The PixelTypes provides context
   * to the IO mechanisms for data conversions.  PixelTypes can be
   * SCALAR, RGB, RGBA, VECTOR, COVARIANTVECTOR, POINT, INDEX. If
   * the PIXELTYPE is SCALAR, then the NumberOfComponents should be 1.
   * Anyother of PIXELTYPE will have more than one component. */
  itkSetEnumMacro(PixelType, IOPixelType);
  itkGetEnumMacro(PixelType, IOPixelType);

  /** SetPixelTypeInfo is used by writers to convert from an ITK
   * strongly typed pixel to a ImageIO (weaker) typed pixel. This
   * function sets these PixelType, ComponentType, and
   * NumberOfComponents based on RTTI type_info structure passed
   * in. The function returns false if the pixel type is not
   * supported. */
  virtual bool SetPixelTypeInfo(const std::type_info& ptype);

  /** Set/Get the component type of the image. This is always a native
   * type. */
  itkSetEnumMacro(ComponentType,IOComponentType);
  itkGetEnumMacro(ComponentType,IOComponentType);
  virtual const std::type_info& GetComponentTypeInfo() const;

  /** Set/Get the number of components per pixel in the image. This may
   * be set by the reading process. For SCALAR pixel types,
   * NumberOfComponents will be 1.  For other pixel types,
   * NumberOfComponents will be greater than or equal to one. */
  itkSetMacro(NumberOfComponents,unsigned int);
  itkGetConstReferenceMacro(NumberOfComponents,unsigned int);

  /** Set/Get a boolean to use the compression or not. */
  itkSetMacro(UseCompression,bool);
  itkGetConstMacro(UseCompression,bool);
  itkBooleanMacro(UseCompression);

  /** Set/Get a boolean to use streaming while reading or not. */
  itkSetMacro(UseStreamedReading,bool);
  itkGetConstMacro(UseStreamedReading,bool);
  itkBooleanMacro(UseStreamedReading);

  /** Set/Get a boolean to use streaming while writing or not. */
  itkSetMacro(UseStreamedWriting,bool);
  itkGetConstMacro(UseStreamedWriting,bool);
  itkBooleanMacro(UseStreamedWriting);


  /** Convenience method returns the IOComponentType as a string. This can be
   * used for writing output files. */
  std::string GetComponentTypeAsString(IOComponentType) const;

  /** Convenience method returns the IOPixelType as a string. This can be
   * used for writing output files. */
  std::string GetPixelTypeAsString(IOPixelType) const;

  /** Enums used to specify write style: whether binary or ASCII. Some
   * subclasses use this, some ignore it. */
  typedef  enum {ASCII,Binary,TypeNotApplicable} FileType;

  /** Enums used to specify byte order; whether Big Endian or Little Endian.
   * Some subclasses use this, some ignore it. */
  typedef  enum {BigEndian,LittleEndian,OrderNotApplicable} ByteOrder;

  /** These methods control whether the file is written binary or ASCII.
   * Many file formats (i.e., subclasses) ignore this flag. */
  itkSetEnumMacro(FileType,FileType);
  itkGetEnumMacro(FileType,FileType);
  void SetFileTypeToASCII()
    {
    this->SetFileType(ASCII);
    }
  void SetFileTypeToBinary()
    {
    this->SetFileType(Binary);
    }

  /** These methods indicate the byte ordering of the file you are
   * trying to read in. These methods will then either swap or not
   * swap the bytes depending on the byte ordering of the machine it
   * is being run on. For example, reading in a BigEndian file on a
   * BigEndian machine will result in no swapping. Trying to read the
   * same file on a LittleEndian machine will result in swapping.
   * Note: most UNIX machines are BigEndian while PC's and VAX's are
   * LittleEndian. So if the file you are reading in was generated on
   * a VAX or PC, SetByteOrderToLittleEndian() otherwise
   * SetByteOrderToBigEndian().  Some ImageIOBase subclasses
   * ignore these methods. */
  itkSetEnumMacro(ByteOrder,ByteOrder);
  itkGetEnumMacro(ByteOrder,ByteOrder);
  void SetByteOrderToBigEndian()
    {
    this->SetByteOrder(BigEndian);
    }
  void SetByteOrderToLittleEndian()
    {
    this->SetByteOrder(LittleEndian);
    }

  /** Convenience method returns the FileType as a string. This can be
   * used for writing output files. */
  std::string GetFileTypeAsString(FileType) const;

  /** Convenience method returns the ByteOrder as a string. This can be
   * used for writing output files. */
  std::string GetByteOrderAsString(ByteOrder) const;

  /** Type for representing size of bytes, and or positions along a file */
  typedef std::streamoff SizeType;

  /** Type for representing size of bytes, and or positions along a memory buffer */
  typedef size_t    BufferSizeType;

  /** Convenient method for accessing the number of bytes to get to
   * the next pixel. Returns m_Strides[1]; 
   * 
   * Please note that this methods depends the private methods
   * ComputeStrides being called, otherwise this is the incorrect value.
   */
  virtual SizeType GetPixelStride () const;

  /** Return the number of pixels in the image. */
  SizeType GetImageSizeInPixels() const;

  /** Return the number of bytes in the image. */
  SizeType GetImageSizeInBytes() const;

  /** Return the number of pixels times the number
   * of components in the image. */
  SizeType GetImageSizeInComponents() const;


  /** 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. This method can be invoked only after
   * the component type is set. */
  virtual unsigned int GetComponentSize() const;


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

  /** Determine the file type. Returns true if this ImageIO can read the
   * file specified. */
  virtual bool CanReadFile(const char*) = 0;

  /** Determine if the ImageIO can stream reading from this
      file. Default is false. */
  virtual bool CanStreamRead()
    {
    return false;
    }

  /** Determine if the ImageIO method uses an internal buffer to read
   *   the file, and if that buffer can be exported and used in 
   *   the pipeline. Default is false. */
  virtual bool CanUseOwnBuffer()
    {
    return false;
    }

  virtual void ReadUsingOwnBuffer()
    {
    return;
    }

  virtual void * GetOwnBuffer()
    {
    return static_cast<void *>( 0 );
    }

  /** Read the spacing and dimentions of the image.
   * Assumes SetFileName has been called with a valid file name. */
  virtual void ReadImageInformation() = 0;

  /** Reads the data from disk into the memory buffer provided. */
  virtual void Read(void* buffer) = 0;


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

  /** Determine the file type. Returns true if this ImageIO can read the
   * file specified. */
  virtual bool CanWriteFile(const char*)  = 0;

  /** Determine if the ImageIO can stream writing to this file. Default is false. 
   *
   * There are two types of non exclusive streaming: pasteing subregions, and iterative
   * If true then 
   */
  virtual bool CanStreamWrite()
    {
    return false;
    }

  /** Writes the spacing and dimentions of the image.
   * Assumes SetFileName has been called with a valid file name. */
  virtual void WriteImageInformation() = 0;

  /** Writes the data to disk from the memory buffer provided. Make sure
   * that the IORegions has been set properly. The buffer is cast to a
   * pointer to the beginning of the image data. */
  virtual void Write( const void* buffer) = 0;

  /* --- Support reading and writing data as a series of files. --- */

  /** The different types of ImageIO's can support data of varying
   * dimensionality. For example, some file formats are strictly 2D
   * while others can support 2D, 3D, or even n-D. This method returns
   * true/false as to whether the ImageIO can support the dimension
   * indicated. */
  virtual bool SupportsDimension(unsigned long dim)
    {
    return (dim == 2);
    }

  /** Method for supporting streaming.  Given a requested region, determine what
   * could be the region that we can read from the file. This is called the
   * streamable region, which will be equal or smaller than the
   * LargestPossibleRegion (unless it was dimensionaly clipped) and
   * greater or equal to the RequestedRegion
   *
   * the resulting IORegion may be a greater dimensions the the
   * requested IORegion, if the the derived class is unable to read
   * the requested region. For example if the file has a size of [ 10,
   * 10, 10] but the requested region is [10, 10] the return may be 3 dimensions.
   */
  virtual ImageIORegion 
  GenerateStreamableReadRegionFromRequestedRegion( const ImageIORegion & requested ) const;

  
  
  /** Before this method is called all the configuration will be done,
   * that is Streaming/PasteRegion/Compression/Filename etc
   * If pasting is being used the number of requested splits is for that 
   * region not the largest. The derived ImageIO class should verify that 
   * the file is capable of being writen with this configuration.
   * If pasted is enabled and is not support or does not work with the file, 
   * then an excepetion should be thrown. 
   *
   * The default implementation depends on CanStreamWrite.
   * If false then 1 is returned (unless pasting is indicated), so that the whole file will be updated in one region.
   * If true then its assumed that any arbitrary region can be writen
   * to any file. So the users request will be respected. If a derived
   * class has more restictive conditions then they should be checked
   */
  virtual unsigned int GetActualNumberOfSplitsForWriting(unsigned int numberOfRequestedSplits,
                                                         const ImageIORegion &pasteRegion,
                                                         const ImageIORegion &largestPossibleRegion);
             
  /** returns the ith IORegion 
   * 
   * numberOfActualSplits should be the value returned from GetActualNumberOfSplitsForWriting with the same parameters
   *
   * Derieved classes should overload this method to return a compatible region
   */
  virtual ImageIORegion GetSplitRegionForWriting(unsigned int ithPiece, 
                                                 unsigned int numberOfActualSplits,
                                                 const ImageIORegion &pasteRegion,
                                                 const ImageIORegion &largestPossibleRegion);

  /** Type for the list of strings to be used for extensions.  */
  typedef  std::vector< std::string >    ArrayOfExtensionsType;

  /** This method returns an array with the list of filename extensions
   * supported for reading by this ImageIO class. This is intended to
   * facilitate GUI and application level integration. 
   */
  const ArrayOfExtensionsType & GetSupportedReadExtensions() const;

  /** This method returns an array with the list of filename extensions
   * supported for writing by this ImageIO class. This is intended to
   * facilitate GUI and application level integration. 
   */
  const ArrayOfExtensionsType & GetSupportedWriteExtensions() const;


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

  /** Used internally to keep track of the type of the pixel. */
  IOPixelType m_PixelType;

  /** Used internally to keep track of the type of the component. It is set
   * when ComputeStrides() is invoked. */
  IOComponentType m_ComponentType;

  /** Big or Little Endian, and the type of the file. (May be ignored.) */
  ByteOrder      m_ByteOrder;
  FileType       m_FileType;

  /** Does the ImageIOBase object have enough info to be of use? */
  bool m_Initialized;

  /** Filename to read */
  std::string m_FileName;

  /** Stores the number of components per pixel. This will be 1 for 
   * grayscale images, 3 for RGBPixel images, and 4 for RGBPixelA images. */
  unsigned int m_NumberOfComponents;

  /** The number of independent dimensions in the image. */
  unsigned int m_NumberOfDimensions;

  /** Should we compress the data? */
  bool m_UseCompression;

  /** Should we use streaming for reading */
  bool m_UseStreamedReading;
  
  /** Should we use streaming for writing */
  bool m_UseStreamedWriting;

  /** The region to read or write. The region contains information about the
   * data within the region to read or write. */
  ImageIORegion m_IORegion;

  /** The array which stores the number of pixels in the x, y, z directions. */
  std::vector< SizeValueType > m_Dimensions;

  /** The array which stores the spacing of pixels in the 
   * x, y, z directions. */
  std::vector<double> m_Spacing;

  /** The array which stores the origin of the image. */
  std::vector<double> m_Origin;

  /** The arrays which store the direction cosines of the image. */
  std::vector<std::vector<double> > m_Direction;

  /** Stores the number of bytes it takes to get to the next 'thing'
   * e.g. component, pixel, row, slice, etc. */
  std::vector< SizeType > m_Strides;

  /** Return the object to an initialized state, ready to be used */
  virtual void Reset(const bool freeDynamic = true);

  /** Resize the ImageIOBase object to new dimensions. */
  void Resize(const unsigned int numDimensions, 
              const unsigned int* dimensions);

  /** Compute the size (in bytes) of the pixel. For
   * example, and RGB pixel of unsigned char would have size 3 bytes. */
  virtual unsigned int GetPixelSize() const;

  /** Calculates the different strides (distance from one thing to the next).
   * Upon return,
   * strides[0] = bytes to get to the next component of a pixel,
   * strides[1] = bytes to get to the next pixel in x direction,
   * strides[2] = bytes to get to the next row in y direction,
   * strides[3] = bytes to get to the next slice in z direction, etc. */
  void ComputeStrides();

  /** Convenient method for accessing number of bytes to get to the next pixel 
   * component. Returns m_Strides[0]. */
  SizeType GetComponentStride() const;

  /** Convenient method for accessing the number of bytes to get to the 
   * next row. Returns m_Strides[2]. */
  SizeType GetRowStride () const;

  /** Convenient method for accessing the number of bytes to get to the 
   * next slice. Returns m_Strides[3]. */
  SizeType GetSliceStride () const;

  /** Convenient method to write a buffer as ASCII text. */
  void WriteBufferAsASCII(std::ostream& os, const void *buffer,
                          IOComponentType ctype,
                          SizeType numberOfBytesToWrite);

  /** Convenient method to read a buffer as ASCII text. */
  void ReadBufferAsASCII(std::istream& os, void *buffer,
                         IOComponentType ctype,
                         SizeType numberOfBytesToBeRead);

  /** Convenient method to read a buffer as binary. Return true on success. */
  bool ReadBufferAsBinary(std::istream& os, void *buffer, SizeType numberOfBytesToBeRead);

  
  /** Insert an extension to the list of supported extensions for reading. */
  void AddSupportedReadExtension( const char * extension );

  /** Insert an extension to the list of supported extensions for writing. */
  void AddSupportedWriteExtension( const char * extension );

  /** an implementation of ImageRegionSplitter:GetNumberOfSplits 
   */
  virtual unsigned int GetActualNumberOfSplitsForWritingCanStreamWrite(unsigned int numberOfRequestedSplits,
                                                                       const ImageIORegion &pasteRegion) const;

  /** an implementation of  ImageRegionSplitter:GetSplit
   */
  virtual ImageIORegion GetSplitRegionForWritingCanStreamWrite(unsigned int ithPiece, 
                                                               unsigned int numberOfActualSplits,
                                                               const ImageIORegion &pasteRegion) const;

private:
  ImageIOBase(const Self&); //purposely not implemented
  void operator=(const Self&); //purposely not implemented

  ArrayOfExtensionsType    m_SupportedReadExtensions;
  ArrayOfExtensionsType    m_SupportedWriteExtensions;

};

} // end namespace itk

#endif // __itkImageIOBase_h