libinsighttoolkit4-dev 4.9.0-4ubuntu1 / usr / include / ITK-4.9 / itkImageSeriesReader.h

/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkImageSeriesReader_h
#define itkImageSeriesReader_h
#include "ITKIOImageBaseExport.h"

#include "itkSize.h"
#include <vector>
#include <string>
#include "itkMetaDataDictionary.h"
#include "itkImageFileReader.h"

namespace itk
{
/** \brief Data source that reads image data from a series of disk files.
 *
 * This class builds an n-dimension image from multiple n-1
 * dimension image files. The files stored in a vector of strings
 * are read using the ImageFileReader. File format may vary between
 * the files, but the image data must have the same Size for all
 * dimensions.
 *
 * \sa GDCMSeriesFileNames
 * \sa NumericSeriesFileNames
 * \ingroup IOFilters
 *
 */

template< typename TOutputImage >
class ITKIOImageBase_HIDDEN ImageSeriesReader:public ImageSource< TOutputImage >
{
public:
  /** Standard class typedefs. */
  typedef ImageSeriesReader           Self;
  typedef ImageSource< TOutputImage > Superclass;
  typedef SmartPointer< Self >        Pointer;

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

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

  /** The size of the output image. */
  typedef typename TOutputImage::SizeType SizeType;

  /** The index of the output image. */
  typedef typename TOutputImage::IndexType IndexType;

  /** The region of the output image. */
  typedef typename TOutputImage::RegionType ImageRegionType;

  /** The pixel type of the output image. */
  typedef typename TOutputImage::PixelType OutputImagePixelType;

  /** The pixel type of the output image. */
  typedef MetaDataDictionary                  DictionaryType;
  typedef MetaDataDictionary *                DictionaryRawPointer;
  typedef std::vector< DictionaryRawPointer > DictionaryArrayType;
  typedef const DictionaryArrayType *         DictionaryArrayRawPointer;

  typedef  std::vector< std::string > FileNamesContainer;

  /** Set the vector of strings that contains the file names. Files
   * are processed in sequential order. */
  void SetFileNames(const FileNamesContainer & name)
  {
    if ( m_FileNames != name )
      {
      m_FileNames = name;
      this->Modified();
      }
  }

  const FileNamesContainer & GetFileNames() const
  {
    return m_FileNames;
  }

  /** Set the first file name to be processed. This deletes previous
   * filenames. */
  void SetFileName(std::string const & name)
  {
    m_FileNames.clear();
    m_FileNames.push_back(name);
    this->Modified();
  }

  /** Add a single filename to the list of files. */
  void AddFileName(std::string const & name)
  {
    m_FileNames.push_back(name);
    this->Modified();
  }

  /** ReverseOrderOn changes the order of travesal of the file names
   * from last to first */
  itkSetMacro(ReverseOrder, bool);
  itkGetConstMacro(ReverseOrder, bool);
  itkBooleanMacro(ReverseOrder);

  /** Set/Get the ImageIO helper class. By default, the
   * ImageSeriesReader uses the factory mechanism of the
   * ImageFileReader to determine the file type. This method can be
   * used to specify which IO to use. */
  itkSetObjectMacro(ImageIO, ImageIOBase);
  itkGetModifiableObjectMacro(ImageIO, ImageIOBase);

  /** \brief Set/Get MetaDataDictionaryArrayUpdate enables the updating of
   * the MetaDataDictionaryArray.
   *
   * By default this is enabled. It may be advantageous to disable
   * this feature when streaming, if this array is not need, as it may
   * redure the number of times each file is read.
   *
   * /sa GetMetaDataDictionaryArray()
   */
  itkSetMacro(MetaDataDictionaryArrayUpdate, bool);
  itkGetConstMacro(MetaDataDictionaryArrayUpdate, bool);
  itkBooleanMacro(MetaDataDictionaryArrayUpdate);

  /** Prepare the allocation of the output image during the first back
   * propagation of the pipeline. */
  virtual void GenerateOutputInformation(void) ITK_OVERRIDE;

  /** Give the reader a chance to indicate that it will produce more
   * output than it was requested to produce. ImageSeriesReader cannot
   * currently read a portion of an image (since the ImageIO objects
   * cannot read a portion of an image), so the ImageSeriesReader must
   * enlarge the RequestedRegion to the size of the image on disk. */
  virtual void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;

  /** Get access to the Array of MetaDataDictionaries which are
* updated in the GenerateData methods */
  DictionaryArrayRawPointer GetMetaDataDictionaryArray() const;

  /** Set the stream On or Off */
  itkSetMacro(UseStreaming, bool);
  itkGetConstReferenceMacro(UseStreaming, bool);
  itkBooleanMacro(UseStreaming);

protected:
  ImageSeriesReader() :
    m_ImageIO(ITK_NULLPTR),
    m_ReverseOrder(false),
    m_NumberOfDimensionsInImage(0),
    m_UseStreaming(true),
    m_MetaDataDictionaryArrayUpdate(true)
      {}
  ~ImageSeriesReader();
  void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;

  /** Does the real work. */
  virtual void GenerateData() ITK_OVERRIDE;

  /** The image format, 0 will use the factory mechnism. */
  ImageIOBase::Pointer m_ImageIO;

  /** Select the traversal order. */
  bool m_ReverseOrder;

  /** A list of filenames to be processed. */
  FileNamesContainer m_FileNames;

  /** The number of independent variables in the images that comprise
   *  the series. This is also used as the slice moving dimension
   *  index for the output image. That is for reading a series of 2D
   *  images into  a 3D image, the moving dimension index is 2.
   */
  unsigned int m_NumberOfDimensionsInImage;

  /** Array of MetaDataDictionaries. This allows to hold information from the
   * ImageIO objects after reading every sub image in the series */
  DictionaryArrayType m_MetaDataDictionaryArray;

  bool m_UseStreaming;

private:
  ImageSeriesReader(const Self &) ITK_DELETE_FUNCTION;
  void operator=(const Self &) ITK_DELETE_FUNCTION;

  typedef ImageFileReader< TOutputImage > ReaderType;

  int ComputeMovingDimensionIndex(ReaderType *reader);

  /** Modified time of the MetaDataDictionaryArray */
  TimeStamp m_MetaDataDictionaryArrayMTime;

  /** Indicated if the MMDA should be updated */
  bool m_MetaDataDictionaryArrayUpdate;
};
} //namespace ITK

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkImageSeriesReader.hxx"
#endif

#endif // itkImageSeriesReader_h