Split inputs into blocks of equidistant slices (for use in DICOMITKSeriesGDCMReader). More...

#include <mitkEquiDistantBlocksSorter.h>

Inheritance diagram for mitk::EquiDistantBlocksSorter:

Collaboration diagram for mitk::EquiDistantBlocksSorter:

Classes
class	SliceGroupingAnalysisResult
	Return type of AnalyzeFileForITKImageSeriesReaderSpacingAssumption(). More...

Public Member Functions
	mitkClassMacro (EquiDistantBlocksSorter, DICOMDatasetSorter) static Pointer New()

virtual DICOMTagList	GetTagsOfInterest () override

virtual void	Sort () override
	Delegates work to AnalyzeFileForITKImageSeriesReaderSpacingAssumption(). AnalyzeFileForITKImageSeriesReaderSpacingAssumption() is called until it does not create multiple blocks anymore. More...

void	SetAcceptTilt (bool accept)
	Whether or not to accept images from a tilted acquisition in a single output group. More...

bool	GetAcceptTilt () const

void	SetToleratedOriginOffsetToAdaptive (double fractionOfInterSliceDistanct=0.3)
	See class description and SetToleratedOriginOffset(). More...

void	SetToleratedOriginOffset (double millimeters=0.005)
	See class description and SetToleratedOriginOffsetToAdaptive(). More...

double	GetToleratedOriginOffset () const

bool	IsToleratedOriginOffsetAbsolute () const

void	SetAcceptTwoSlicesGroups (bool accept)

bool	GetAcceptTwoSlicesGroups () const

virtual void	PrintConfiguration (std::ostream &os, const std::string &indent="") const override
	Print configuration details into stream. More...

virtual bool	operator== (const DICOMDatasetSorter &other) const override

Public Member Functions inherited from mitk::DICOMDatasetSorter
	mitkClassMacroItkParent (DICOMDatasetSorter, itk::LightObject) virtual DICOMTagList GetTagsOfInterest()=0
	Return the tags of interest (to facilitate scanning) More...

void	SetInput (DICOMDatasetList filenames)
	Input for sorting. More...

const DICOMDatasetList &	GetInput () const
	Input for sorting. More...

unsigned int	GetNumberOfOutputs () const
	Output of the sorting process. More...

const DICOMDatasetList &	GetOutput (unsigned int index) const
	Output of the sorting process. More...

DICOMDatasetList &	GetOutput (unsigned int index)
	Output of the sorting process. More...

Protected Types
typedef std::vector< SliceGroupingAnalysisResult >	ResultsList

Protected Member Functions
SliceGroupingAnalysisResult	AnalyzeFileForITKImageSeriesReaderSpacingAssumption (const DICOMDatasetList &files, bool groupsOfSimilarImages)
	Ensure an equal z-spacing for a group of files. More...

std::string	ConstCharStarToString (const char *s)
	Safely convert const char* to std::string. More...

	EquiDistantBlocksSorter ()

virtual	~EquiDistantBlocksSorter ()

	EquiDistantBlocksSorter (const EquiDistantBlocksSorter &other)

EquiDistantBlocksSorter &	operator= (const EquiDistantBlocksSorter &other)

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

virtual	~DICOMDatasetSorter ()

	DICOMDatasetSorter (const DICOMDatasetSorter &other)

DICOMDatasetSorter &	operator= (const DICOMDatasetSorter &other)

void	ClearOutputs ()

void	SetNumberOfOutputs (unsigned int numberOfOutputs)

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

Protected Attributes
bool	m_AcceptTilt

ResultsList	m_SliceGroupingResults

double	m_ToleratedOriginOffset

bool	m_ToleratedOriginOffsetIsAbsolute

bool	m_AcceptTwoSlicesGroups

Detailed Description

Split inputs into blocks of equidistant slices (for use in DICOMITKSeriesGDCMReader).

Since inter-slice distance is not recorded in DICOM tags, we must ensure that blocks are made up of slices that have equal distances between neighboring slices. This is especially necessary because itk::ImageSeriesReader is later used for the actual loading, and this class expects (and does nocht verify) equal inter-slice distance (see Forced Configuration).

To achieve such grouping, the inter-slice distance is calculated from the first two different slice positions of a block. Following slices are added to a block as long as they can be added by adding the calculated inter-slice distance to the last slice of the block. Slices that do not fit into the expected distance pattern, are set aside for further analysis. This grouping is done until each file has been assigned to a group.

Slices that share a position in space are also sorted into separate blocks during this step. So the result of this step is a set of blocks that contain only slices with equal z spacing and uniqe slices at each position.

During sorting, the origins (documented in tag image position patient) are compared against expected origins (from former origin plus moving direction). As there will be minor differences in numbers (from both calculations and unprecise tag values), we must be a bit tolerant here. The default behavior is to expect that an origin is not further away from the expected position than 30% of the inter-slice distance. To support a legacy behavior of a former loader (DicomSeriesReader), this default can be restricted to a constant number of millimeters by calling SetToleratedOriginOffset(mm).

Detailed implementation in AnalyzeFileForITKImageSeriesReaderSpacingAssumption().

Definition at line 57 of file mitkEquiDistantBlocksSorter.h.

Member Typedef Documentation

typedef std::vector<SliceGroupingAnalysisResult> mitk::EquiDistantBlocksSorter::ResultsList

protected

Definition at line 203 of file mitkEquiDistantBlocksSorter.h.

Constructor & Destructor Documentation

mitk::EquiDistantBlocksSorter::EquiDistantBlocksSorter ( )

protected

Definition at line 122 of file mitkEquiDistantBlocksSorter.cpp.

mitk::EquiDistantBlocksSorter::~EquiDistantBlocksSorter ( )

protectedvirtual

Definition at line 142 of file mitkEquiDistantBlocksSorter.cpp.

mitk::EquiDistantBlocksSorter::EquiDistantBlocksSorter ( const EquiDistantBlocksSorter & other )

protected

Definition at line 132 of file mitkEquiDistantBlocksSorter.cpp.

Member Function Documentation

mitk::EquiDistantBlocksSorter::SliceGroupingAnalysisResult mitk::EquiDistantBlocksSorter::AnalyzeFileForITKImageSeriesReaderSpacingAssumption	(	const DICOMDatasetList &	files,
		bool	groupsOfSimilarImages
	)

protected

Ensure an equal z-spacing for a group of files.

Takes as input a number of images, which are all equally oriented and spatially sorted along their normal direction.

Internally used by GetSeries. Returns two lists: the first one contins slices of equal inter-slice spacing. The second list contains remaining files, which need to be run through AnalyzeFileForITKImageSeriesReaderSpacingAssumption again.

Relevant code that is matched here is in itkImageSeriesReader.txx (ImageSeriesReader<TOutputImage>::GenerateOutputInformation(void)), lines 176 to 245 (as of ITK 3.20)

Definition at line 337 of file mitkEquiDistantBlocksSorter.cpp.

std::string mitk::EquiDistantBlocksSorter::ConstCharStarToString ( const char * s )

protected

Safely convert const char* to std::string.

Definition at line 330 of file mitkEquiDistantBlocksSorter.cpp.

bool mitk::EquiDistantBlocksSorter::GetAcceptTilt ( ) const

Definition at line 194 of file mitkEquiDistantBlocksSorter.cpp.

bool mitk::EquiDistantBlocksSorter::GetAcceptTwoSlicesGroups ( ) const

Definition at line 208 of file mitkEquiDistantBlocksSorter.cpp.

mitk::DICOMTagList mitk::EquiDistantBlocksSorter::GetTagsOfInterest ( )

overridevirtual

Definition at line 231 of file mitkEquiDistantBlocksSorter.cpp.

double mitk::EquiDistantBlocksSorter::GetToleratedOriginOffset ( ) const

Definition at line 315 of file mitkEquiDistantBlocksSorter.cpp.

bool mitk::EquiDistantBlocksSorter::IsToleratedOriginOffsetAbsolute ( ) const

Definition at line 322 of file mitkEquiDistantBlocksSorter.cpp.

mitk::EquiDistantBlocksSorter::mitkClassMacro	(	EquiDistantBlocksSorter	,
		DICOMDatasetSorter
	)

mitk::EquiDistantBlocksSorter & mitk::EquiDistantBlocksSorter::operator= ( const EquiDistantBlocksSorter & other )

protected

Definition at line 216 of file mitkEquiDistantBlocksSorter.cpp.

References m_AcceptTilt, m_AcceptTwoSlicesGroups, m_ToleratedOriginOffset, m_ToleratedOriginOffsetIsAbsolute, and mitk::DICOMDatasetSorter::operator=().

bool mitk::EquiDistantBlocksSorter::operator== ( const DICOMDatasetSorter & other ) const

overridevirtual

Implements mitk::DICOMDatasetSorter.

Definition at line 148 of file mitkEquiDistantBlocksSorter.cpp.

References mitk::eps.

void mitk::EquiDistantBlocksSorter::PrintConfiguration	(	std::ostream &	os,
		const std::string &	indent = `""`
	)		const

overridevirtual

Print configuration details into stream.

Implements mitk::DICOMDatasetSorter.

Definition at line 165 of file mitkEquiDistantBlocksSorter.cpp.

void mitk::EquiDistantBlocksSorter::SetAcceptTilt ( bool accept )

Whether or not to accept images from a tilted acquisition in a single output group.

Definition at line 186 of file mitkEquiDistantBlocksSorter.cpp.

void mitk::EquiDistantBlocksSorter::SetAcceptTwoSlicesGroups ( bool accept )

Definition at line 201 of file mitkEquiDistantBlocksSorter.cpp.

void mitk::EquiDistantBlocksSorter::SetToleratedOriginOffset ( double millimeters = 0.005 )

See class description and SetToleratedOriginOffsetToAdaptive().

Default value of 0.005 is calculated so that we get a maximum of 1/10mm error when having a measurement crosses 20 slices in z direction (too strict? we don't know better..).

Definition at line 303 of file mitkEquiDistantBlocksSorter.cpp.

References MITK_WARN.

void mitk::EquiDistantBlocksSorter::SetToleratedOriginOffsetToAdaptive ( double fractionOfInterSliceDistanct = 0.3 )

See class description and SetToleratedOriginOffset().

Definition at line 285 of file mitkEquiDistantBlocksSorter.cpp.

References MITK_WARN.

void mitk::EquiDistantBlocksSorter::Sort ( )

overridevirtual

Delegates work to AnalyzeFileForITKImageSeriesReaderSpacingAssumption(). AnalyzeFileForITKImageSeriesReaderSpacingAssumption() is called until it does not create multiple blocks anymore.

Implements mitk::DICOMDatasetSorter.

Definition at line 243 of file mitkEquiDistantBlocksSorter.cpp.

References mitk::EquiDistantBlocksSorter::SliceGroupingAnalysisResult::GetBlockDatasets(), mitk::EquiDistantBlocksSorter::SliceGroupingAnalysisResult::GetUnsortedDatasets(), and MITK_DEBUG.