Extends DICOMITKSeriesGDCMReader by sorting/grouping into 3D+t image blocks. More...

#include <mitkThreeDnTDICOMSeriesReader.h>

Inheritance diagram for mitk::ThreeDnTDICOMSeriesReader:

Collaboration diagram for mitk::ThreeDnTDICOMSeriesReader:

Public Member Functions
	mitkClassMacro (ThreeDnTDICOMSeriesReader, DICOMITKSeriesGDCMReader)

	mitkCloneMacro (ThreeDnTDICOMSeriesReader)

	mitkNewMacro1Param (ThreeDnTDICOMSeriesReader, unsigned int)

void	SetGroup3DandT (bool on)
	Control whether 3D+t grouping shall actually be attempted. More...

bool	GetGroup3DandT () const

bool	LoadImages () override
	Load via multiple calls to itk::ImageSeriesReader. More...

bool	operator== (const DICOMFileReader &other) const override

Public Member Functions inherited from mitk::DICOMITKSeriesGDCMReader
	mitkClassMacro (DICOMITKSeriesGDCMReader, DICOMFileReader)

	mitkCloneMacro (DICOMITKSeriesGDCMReader)

	mitkNewMacro1Param (DICOMITKSeriesGDCMReader, unsigned int)

	mitkNewMacro2Param (DICOMITKSeriesGDCMReader, unsigned int, bool)

void	AnalyzeInputFiles () override
	Runs the sorting / splitting process described in Loading strategy. Method required by DICOMFileReader. More...

bool	CanHandleFile (const std::string &filename) override
	Indicate whether this reader can handle given file. More...

virtual void	AddSortingElement (DICOMDatasetSorter *sorter, bool atFront=false)
	Add an element to the sorting procedure described in Loading strategy. More...

ConstSorterList	GetFreelyConfiguredSortingElements () const

void	SetFixTiltByShearing (bool on)
	Controls whether to "fix" tilted acquisitions by shearing the output (see Gantry tilt handling). More...

bool	GetFixTiltByShearing () const

void	SetAcceptTwoSlicesGroups (bool accept) const
	Controls whether groups of only two images are accepted when ensuring consecutive slices via EquiDistantBlocksSorter. More...

bool	GetAcceptTwoSlicesGroups () const

void	SetToleratedOriginOffsetToAdaptive (double fractionOfInterSliceDistanct=0.3) const
	See Forced Configuration. More...

void	SetToleratedOriginOffset (double millimeters=0.005) const
	See Forced Configuration. More...

void	SetSimpleVolumeReading (bool read)
	Ignore all dicom tags that are non-essential for simple 3D volume import. More...

bool	GetSimpleVolumeReading ()
	Ignore all dicom tags that are non-essential for simple 3D volume import. More...

double	GetToleratedOriginError () const

bool	IsToleratedOriginOffsetAbsolute () const

double	GetDecimalPlacesForOrientation () const

DICOMTagPathList	GetTagsOfInterest () const override

Public Member Functions inherited from mitk::DICOMFileReader
	mitkClassMacroItkParent (DICOMFileReader, itk::Object)

void	SetInputFiles (const StringList &filenames)
	This input files. More...

const StringList &	GetInputFiles () const
	This input files. More...

unsigned int	GetNumberOfOutputs () const
	Number of outputs, only meaningful after calling AnalyzeInputFiles() More...

const DICOMImageBlockDescriptor &	GetOutput (unsigned int index) const
	Individual outputs, only meaningful after calling AnalyzeInputFiles(). More...

void	SetConfigurationLabel (const std::string &)
	Short label/name to describe this reader. More...

std::string	GetConfigurationLabel () const
	Short label/name to describe this reader. More...

void	SetConfigurationDescription (const std::string &)
	One-sentence description of the reader's loading "strategy". More...

std::string	GetConfigurationDescription () const
	One-sentence description of the reader's loading "strategy". More...

void	PrintConfiguration (std::ostream &os) const
	Print configuration description to given stream, for human reader. More...

void	PrintOutputs (std::ostream &os, bool filenameDetails=false) const
	Print output description to given stream, for human reader. More...

virtual void	SetAdditionalTagsOfInterest (const AdditionalTagsMapType &tagList)
	Set a list of DICOMTagPaths that specifiy all DICOM-Tags that will be copied into the property of the mitk::Image. More...

virtual void	SetTagLookupTableToPropertyFunctor (mitk::DICOMImageBlockDescriptor::TagLookupTableToPropertyFunctor functor)
	Set a functor that defines how the slice-specific tag-values are stored in a Property. More...

Static Public Member Functions
static Pointer	New ()

static bool	GetDefaultGroup3DandT ()

Static Public Member Functions inherited from mitk::DICOMITKSeriesGDCMReader
static Pointer	New ()

static int	GetDefaultDecimalPlacesForOrientation ()

static bool	GetDefaultSimpleVolumeImport ()

static bool	GetDefaultFixTiltByShearing ()

Static Public Member Functions inherited from mitk::DICOMFileReader
static bool	IsDICOM (const std::string &filename)
	Test whether a file is DICOM at all. More...

Protected Member Functions
	ThreeDnTDICOMSeriesReader (unsigned int decimalPlacesForOrientation=Superclass::m_DefaultDecimalPlacesForOrientation)

	~ThreeDnTDICOMSeriesReader () override

	ThreeDnTDICOMSeriesReader (const ThreeDnTDICOMSeriesReader &other)

ThreeDnTDICOMSeriesReader &	operator= (const ThreeDnTDICOMSeriesReader &other)

SortingBlockList	Condense3DBlocks (SortingBlockList &) override
	Analyze the groups produced by DICOMITKSeriesGDCMReader for 3D+t properties. This method tests whether some blocks are at the same spatial position and groups them into single blocks. More...

bool	LoadMitkImageForImageBlockDescriptor (DICOMImageBlockDescriptor &block) const override

Protected Member Functions inherited from mitk::DICOMITKSeriesGDCMReader
void	InternalPrintConfiguration (std::ostream &os) const override
	Configuration description for human reader, to be implemented by sub-classes. More...

void	PushLocale () const
	Remember current locale on stack, activate "C" locale. "C" locale is required for correct parsing of numbers by itk::ImageSeriesReader. More...

void	PopLocale () const
	Activate last remembered locale from locale stack "C" locale is required for correct parsing of numbers by itk::ImageSeriesReader. More...

	DICOMITKSeriesGDCMReader (unsigned int decimalPlacesForOrientation=m_DefaultDecimalPlacesForOrientation, bool simpleVolumeImport=m_DefaultSimpleVolumeImport)

	~DICOMITKSeriesGDCMReader () override

	DICOMITKSeriesGDCMReader (const DICOMITKSeriesGDCMReader &other)

DICOMITKSeriesGDCMReader &	operator= (const DICOMITKSeriesGDCMReader &other)

virtual DICOMTagCache::Pointer	GetTagCache () const

void	SetTagCache (const DICOMTagCache::Pointer &) override
	A way to provide external knowledge about files and tag values is appreciated. More...

virtual bool	LoadMitkImageForOutput (unsigned int o)
	Loads the mitk::Image by means of an itk::ImageSeriesReader. More...

Protected Member Functions inherited from mitk::DICOMFileReader
	DICOMFileReader ()

	~DICOMFileReader () override

	DICOMFileReader (const DICOMFileReader &other)

DICOMFileReader &	operator= (const DICOMFileReader &other)

void	ClearOutputs ()

void	SetNumberOfOutputs (unsigned int numberOfOutputs)

void	SetOutput (unsigned int index, const DICOMImageBlockDescriptor &output)

DICOMImageBlockDescriptor &	InternalGetOutput (unsigned int index)
	non-const access to the DICOMImageBlockDescriptor More...

virtual AdditionalTagsMapType	GetAdditionalTagsOfInterest () const

mitk::DICOMImageBlockDescriptor::TagLookupTableToPropertyFunctor	GetTagLookupTableToPropertyFunctor () const

Protected Attributes
bool	m_Group3DandT

Protected Attributes inherited from mitk::DICOMITKSeriesGDCMReader
bool	m_FixTiltByShearing

bool	m_SimpleVolumeReading

mitk::EquiDistantBlocksSorter::Pointer	m_EquiDistantBlocksSorter

mitk::NormalDirectionConsistencySorter::Pointer	m_NormalDirectionConsistencySorter

Static Protected Attributes
static const bool	m_DefaultGroup3DandT

Static Protected Attributes inherited from mitk::DICOMITKSeriesGDCMReader
static const int	m_DefaultDecimalPlacesForOrientation

static const bool	m_DefaultSimpleVolumeImport

static const bool	m_DefaultFixTiltByShearing

Additional Inherited Members
Public Types inherited from mitk::DICOMITKSeriesGDCMReader
typedef const std::list< DICOMDatasetSorter::ConstPointer >	ConstSorterList

Public Types inherited from mitk::DICOMFileReader
typedef DICOMImageBlockDescriptor::AdditionalTagsMapType	AdditionalTagsMapType

Protected Types inherited from mitk::DICOMITKSeriesGDCMReader
typedef std::vector< DICOMDatasetAccessingImageFrameList >	SortingBlockList

Static Protected Member Functions inherited from mitk::DICOMITKSeriesGDCMReader
static std::string	GetActiveLocale ()
	Return active C locale. More...

static SortingBlockList	InternalExecuteSortingStep (unsigned int sortingStepIndex, const DICOMDatasetSorter::Pointer &sorter, const SortingBlockList &input)
	Sorting step as described in Loading strategy. More...

static ReaderImplementationLevel	GetReaderImplementationLevel (const std::string sopClassUID)
	Describe this reader's confidence for given SOP class UID. More...

Detailed Description

Extends DICOMITKSeriesGDCMReader by sorting/grouping into 3D+t image blocks.

This class reuses the DICOMITKSeriesGDCMReader class and adds the option of grouping 3D blocks at the same spatial position into a single block, which is loaded as a 3D+t mitk::Image (compare to Sub-classes can condense multiple blocks into a single larger block).

To group two output blocks into a single 3D+t block, this class tests a number of requirements that the two blocks must fulfill:

the origin of the first slice must be identical
the origin of the last slice must be identical
the number of slices must be identical

The output blocks described by DICOMImageBlockDescriptor will contains the following properties:

"3D+t": true if the image is 3D+t
"timesteps": number of timesteps of an image (only defined if "3D+t" is true)

Definition at line 41 of file mitkThreeDnTDICOMSeriesReader.h.

Constructor & Destructor Documentation

◆ ThreeDnTDICOMSeriesReader() [1/2]

mitk::ThreeDnTDICOMSeriesReader::ThreeDnTDICOMSeriesReader ( unsigned int decimalPlacesForOrientation = Superclass::m_DefaultDecimalPlacesForOrientation )

protected

Definition at line 17 of file mitkThreeDnTDICOMSeriesReader.cpp.

◆ ~ThreeDnTDICOMSeriesReader()

mitk::ThreeDnTDICOMSeriesReader::~ThreeDnTDICOMSeriesReader ( )

overrideprotected

Definition at line 31 of file mitkThreeDnTDICOMSeriesReader.cpp.

References operator=().

Referenced by ThreeDnTDICOMSeriesReader().

◆ ThreeDnTDICOMSeriesReader() [2/2]

mitk::ThreeDnTDICOMSeriesReader::ThreeDnTDICOMSeriesReader ( const ThreeDnTDICOMSeriesReader & other )

protected

Definition at line 24 of file mitkThreeDnTDICOMSeriesReader.cpp.

References ~ThreeDnTDICOMSeriesReader().

Member Function Documentation

◆ Condense3DBlocks()

mitk::DICOMITKSeriesGDCMReader::SortingBlockList mitk::ThreeDnTDICOMSeriesReader::Condense3DBlocks ( SortingBlockList & resultOf3DGrouping )

overrideprotectedvirtual

Analyze the groups produced by DICOMITKSeriesGDCMReader for 3D+t properties. This method tests whether some blocks are at the same spatial position and groups them into single blocks.

Reimplemented from mitk::DICOMITKSeriesGDCMReader.

Definition at line 79 of file mitkThreeDnTDICOMSeriesReader.cpp.

References mitk::ConvertToDICOMDatasetAccessingImageFrameList(), mitk::ConvertToDICOMDatasetList(), mitk::ConvertToDICOMImageFrameList(), mitk::DICOMFileReader::GetAdditionalTagsOfInterest(), mitk::DICOMITKSeriesGDCMReader::GetTagCache(), mitk::DICOMFileReader::GetTagLookupTableToPropertyFunctor(), LoadImages(), m_Group3DandT, mitk::DICOMITKSeriesGDCMReader::m_NormalDirectionConsistencySorter, MITK_DEBUG, mitk::DICOMFileReader::SetNumberOfOutputs(), mitk::DICOMFileReader::SetOutput(), and mitk::DICOMImageBlockDescriptor::SetTagCache().