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/*=========================================================================
*
* 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 itkBruker2dseqImageIO_h
#define itkBruker2dseqImageIO_h
#include "ITKIOBrukerExport.h"
#include "itkImageIOBase.h"
#include "itkVectorContainer.h"
namespace itk
{
/** \class Bruker2dseqImageIO
* \brief Class that defines how to read Bruker file format.
*
* The following is a brief description of the Bruker file format.
*
* Within the directory representing a 'session' on the scanner, data is laid
* out thus:
*
* session/
* 1/ <- Series/Acquisition number
* method <- An important header file
* acqp <- Another important header
* fid <- Raw data
* **other unimportant files**
* pdata/
* 1/ <- Reconstruction number (may be multiple)
* 2dseq <- Reconstructed data
* visu_pars <- Most important header
* reco <- Mostly duplicated in visu_pars
* procs <- Unimportant header
* id <- Unimportant header
* 2/
* ...
*
* The minimum required data to read the image is the '2dseq' and 'visu_pars'
* file. To use this reader, specify the 2dseq file as the filename. It will
* check for the existence of the visu_pars file. If both these exist, the file
* is opened. If the other header files exist (method, acqp, etc.) in the
* correct locations then they will be read and added to the meta-data
* dictionary, but they are not used to read the image data itself.
*
* This class supports reading only.
*
* This file reader has been updated for ParaVision 6 2dseq files. The original
* code was written by Don C. Bigler at Penn State in 2004. It has been
* significantly changed, as Bruker also changed the format for ParaVision 6.
* In particular a new header file, 'visu_pars' was introduced that means that
* multiple headers no longer need to be read in order to read the '2dseq'
* file. However, if the other Bruker headers are still present they are read
* and added to the meta-data in case users wish to extract data from them.
*
* The original implementation was contributed as a paper to the Insight Journal
* https://hdl.handle.net/1926/1381
*
* \ingroup ITKIOBruker
*
* \author Tobias C Wood, King's College London 2017
*/
class ITKIOBruker_EXPORT Bruker2dseqImageIO : public ImageIOBase
{
public:
/* Standard class typedefs. */
typedef Bruker2dseqImageIO Self;
typedef ImageIOBase Superclass;
typedef SmartPointer< Self > Pointer;
typedef SmartPointer< const Self > ConstPointer;
/** New macro for creation of through a SmartPointer. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(Bruker2dseqImageIO, ImageIOBase);
/** Determine if the necessary files exist to read the specified 2dseq file.
* Returns true if all required files exist. */
virtual bool CanReadFile(const char *FileNameToRead) ITK_OVERRIDE;
/** Set the spacing and dimension information for the set filename. */
virtual void ReadImageInformation() ITK_OVERRIDE;
/** Reads the data from disk into the memory buffer provided. */
virtual void Read(void *buffer) ITK_OVERRIDE;
/** Writing files has not been implemented for Bruker 2dseq.
* This function will always return false. */
virtual bool CanWriteFile( const char *itkNotUsed(FileNameToWrite) ) ITK_OVERRIDE
{
return false;
}
/** Not implemented. */
virtual void WriteImageInformation() ITK_OVERRIDE
{
return;
}
/** Not implemented - does nothing */
virtual void Write( const void *itkNotUsed(buffer) ) ITK_OVERRIDE
{
return;
}
protected:
Bruker2dseqImageIO();
~Bruker2dseqImageIO() ITK_OVERRIDE;
virtual void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
private:
ITK_DISALLOW_COPY_AND_ASSIGN(Bruker2dseqImageIO);
void SwapBytesIfNecessary(void *buffer, SizeValueType numberOfPixels);
ImageIOBase::IOComponentType m_OnDiskComponentType;
ImageIOBase::ByteOrder m_MachineByteOrder;
};
} // end namespace itk
#endif // itkBruker2dseqImageIO_h
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