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/*=========================================================================
*
* Copyright NumFOCUS
*
* 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
*
* https://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 itkMetaImageIO_h
#define itkMetaImageIO_h
#include "ITKIOMetaExport.h"
#include <fstream>
#include "itkImageIOBase.h"
#include "itkSingletonMacro.h"
#include "itkMetaDataObject.h"
#include "metaObject.h"
#include "metaImage.h"
namespace itk
{
/**
* \class MetaImageIO
*
* \brief Read MetaImage file format.
*
* For a detailed description of using this format, please see
* https://www.itk.org/Wiki/ITK/MetaIO/Documentation
*
* \ingroup IOFilters
* \ingroup ITKIOMeta
*/
class ITKIOMeta_EXPORT MetaImageIO : public ImageIOBase
{
public:
ITK_DISALLOW_COPY_AND_MOVE(MetaImageIO);
/** Standard class type aliases. */
using Self = MetaImageIO;
using Superclass = ImageIOBase;
using Pointer = SmartPointer<Self>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(MetaImageIO);
/** 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. */
bool
SupportsDimension(unsigned long) override
{
return true;
}
/*-------- This part of the interfaces deals with reading data. ----- */
/** Determine the file type. Returns true if this ImageIO can read the
* file specified. */
bool
CanReadFile(const char *) override;
/** Set the spacing and dimension information for the set filename. */
void
ReadImageInformation() override;
/** Reads the data from disk into the memory buffer provided. */
void
Read(void * buffer) override;
MetaImage *
GetMetaImagePointer();
/*-------- This part of the interfaces deals with writing data. ----- */
/** Determine the file type. Returns true if this ImageIO can write the
* file specified. */
bool
CanWriteFile(const char *) override;
/** Set the spacing and dimension information for the set filename. */
void
WriteImageInformation() override;
/** Writes the data to disk from the memory buffer provided. Make sure
* that the IORegions has been set properly. */
void
Write(const void * buffer) override;
/** Set the filename for the Data file. Setting this will make the
Writer to use the non-Local mode and save header and data in
independent files */
virtual void
SetDataFileName(const char * filename);
/** set the precision in the MetaImage member
*/
virtual void
SetDoublePrecision(unsigned int precision)
{
m_MetaImage.SetDoublePrecision(precision);
}
/** Method for supporting streaming. Given a requested region, calculate what
* could be the region that we can read from the file. This is called the
* streamable region, which will be smaller than the LargestPossibleRegion and
* greater or equal to the RequestedRegion */
ImageIORegion
GenerateStreamableReadRegionFromRequestedRegion(const ImageIORegion & requestedRegion) const override;
unsigned int
GetActualNumberOfSplitsForWriting(unsigned int numberOfRequestedSplits,
const ImageIORegion & pasteRegion,
const ImageIORegion & largestPossibleRegion) override;
ImageIORegion
GetSplitRegionForWriting(unsigned int ithPiece,
unsigned int numberOfActualSplits,
const ImageIORegion & pasteRegion,
const ImageIORegion & largestPossibleRegion) override;
/** Determine if the ImageIO can stream reading from this
* file. Only time cannot stream read/write is if compression is used.
* CanRead must be called prior to this function. */
bool
CanStreamRead() override
{
if (m_MetaImage.CompressedData())
{
return false;
}
return true;
}
/** Determine if the ImageIO can stream writing to this
* file. Only time cannot stream read/write is if compression is used.
* Assumes file passes a CanRead call and its pixels are of the same
* type as the template of the writer. Can verify by first calling
* CanRead and then CanStreamRead prior to calling CanStreamWrite. */
bool
CanStreamWrite() override
{
if (this->GetUseCompression())
{
return false;
}
return true;
}
/** Determining the subsampling factor in case
* we want a coarse version of the image/
* \warning this is only used when streaming is on. */
itkSetMacro(SubSamplingFactor, unsigned int);
itkGetConstMacro(SubSamplingFactor, unsigned int);
/**
* Set the default precision when writing out the MetaImage header.
* MetaImage header contains values stored in memory as double,
* use this precision when writing out the value. The precision
* should only be defined in the range [0, 17] since a value of 17
* will make the conversion of a double floating-point to text and
* back exact.
* This function is not thread safe.
* Default value after static initialization is 17.
*/
static void
SetDefaultDoublePrecision(unsigned int precision);
static unsigned int
GetDefaultDoublePrecision();
protected:
MetaImageIO();
~MetaImageIO() override;
void
PrintSelf(std::ostream & os, Indent indent) const override;
template <unsigned int VNRows, unsigned int VNColumns = VNRows>
bool
WriteMatrixInMetaData(std::ostringstream & strs, const MetaDataDictionary & metaDict, const std::string & metaString);
private:
/** Only used to synchronize the global variable across static libraries.*/
itkGetGlobalDeclarationMacro(unsigned int, DefaultDoublePrecision);
MetaImage m_MetaImage{};
unsigned int m_SubSamplingFactor{};
static unsigned int * m_DefaultDoublePrecision;
};
template <unsigned int VNRows, unsigned int VNColumns>
bool
MetaImageIO::WriteMatrixInMetaData(std::ostringstream & strs,
const MetaDataDictionary & metaDict,
const std::string & metaString)
{
itk::Matrix<double, VNRows, VNColumns> mval;
if (ExposeMetaData<itk::Matrix<double, VNRows, VNColumns>>(metaDict, metaString, mval))
{
for (unsigned int i = 0; i < VNRows; ++i)
{
for (unsigned int j = 0; j < VNColumns; ++j)
{
strs << mval[i][j];
if (i != VNRows - 1 || j != VNColumns - 1)
{
strs << ' ';
}
}
}
return true;
}
return false;
}
} // end namespace itk
#endif // itkMetaImageIO_h
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