mitk::ClassicDICOMSeriesReader Class Reference

Sorting and grouping like mitk::DicomSeriesReader until 2013. More...

#include <mitkClassicDICOMSeriesReader.h>

Inheritance diagram for mitk::ClassicDICOMSeriesReader:

Collaboration diagram for mitk::ClassicDICOMSeriesReader:

Public Member Functions
	mitkClassMacro (ClassicDICOMSeriesReader, DICOMITKSeriesGDCMReader)
	mitkCloneMacro (ClassicDICOMSeriesReader)
bool	operator== (const DICOMFileReader &other) const override
Public Member Functions inherited from mitk::ThreeDnTDICOMSeriesReader
	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
virtual void	OnlyCondenseSameSeriesOn ()
virtual void	OnlyCondenseSameSeriesOff ()
virtual void	SetOnlyCondenseSameSeries (bool _arg)
virtual bool	GetOnlyCondenseSameSeries () 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 specify 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 Public Member Functions inherited from mitk::ThreeDnTDICOMSeriesReader
static Pointer	New ()
static bool	GetDefaultGroup3DandT ()
static bool	GetDefaultOnlyCondenseSameSeries ()
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
	ClassicDICOMSeriesReader ()
	~ClassicDICOMSeriesReader () override
	ClassicDICOMSeriesReader (const ClassicDICOMSeriesReader &other)
ClassicDICOMSeriesReader &	operator= (const ClassicDICOMSeriesReader &other)
Protected Member Functions inherited from mitk::ThreeDnTDICOMSeriesReader
	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

Additional Inherited Members
Public Types inherited from mitk::DICOMFileReader
typedef DICOMImageBlockDescriptor::AdditionalTagsMapType	AdditionalTagsMapType
Public Attributes inherited from mitk::DICOMITKSeriesGDCMReader
const typedef std::list< DICOMDatasetSorter::ConstPointer >	ConstSorterList
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...
Protected Attributes inherited from mitk::ThreeDnTDICOMSeriesReader
bool	m_Group3DandT
bool	m_OnlyCondenseSameSeries
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 inherited from mitk::ThreeDnTDICOMSeriesReader
const static bool	m_DefaultGroup3DandT
const static bool	m_DefaultOnlyCondenseSameSeries
Static Protected Attributes inherited from mitk::DICOMITKSeriesGDCMReader
const static int	m_DefaultDecimalPlacesForOrientation
const static bool	m_DefaultSimpleVolumeImport
const static bool	m_DefaultFixTiltByShearing

Detailed Description

Sorting and grouping like mitk::DicomSeriesReader until 2013.

This class implements the same functionality as the legacy class DicomSeriesReader, except that it is 75 lines instead of 2500 lines.

Warning

Since the old class is known to have problems with some series, it is advised to use a good configuration of DICOMITKSeriesGDCMReader, which can be obtained by using DICOMFileReaderSelector.

The following text documents the actual sorting logic of this reader.

The class groups datasets that have different values in any of the following tags:

• (0028,0010) Number of Rows
• (0028,0011) Number of Columns
• (0028,0030) Pixel Spacing
• (0018,1164) Imager Pixel Spacing
• (0020,0037) Image Orientation (Patient)
• (0018,0050) Slice Thickness
• (0028,0008) Number of Frames
• (0020,000e) Series Instance UID

Within each of the groups, datasets are sorted by the value of the following tags (primary sorting first):

• (0020,0032) Image Position (Patient) (distance from zero along normal of (0020,0037) Image Orientation (Patient))
• (0020,0012) Acquisition Number
• (0008,0032) Acquisition Time
• (0018,1060) Trigger Time
• (0008,0018) SOP Instance UID (last resort, not really meaningful but decides clearly)

If the series was acquired using a tilted gantry, this will be "fixed" by applying a shear transformation.

If multiple images occupy the same position in space, it is assumed that this indicated a 3D+t image.

Definition at line 57 of file mitkClassicDICOMSeriesReader.h.

Constructor & Destructor Documentation

ClassicDICOMSeriesReader() [1/2]

mitk::ClassicDICOMSeriesReader::ClassicDICOMSeriesReader ( )

protected

~ClassicDICOMSeriesReader()

mitk::ClassicDICOMSeriesReader::~ClassicDICOMSeriesReader ( )

overrideprotected

ClassicDICOMSeriesReader() [2/2]

mitk::ClassicDICOMSeriesReader::ClassicDICOMSeriesReader ( const ClassicDICOMSeriesReader &  other )

protected

Member Function Documentation

mitkClassMacro()

mitk::ClassicDICOMSeriesReader::mitkClassMacro	(	ClassicDICOMSeriesReader	,
		DICOMITKSeriesGDCMReader
	)

mitkCloneMacro()

mitk::ClassicDICOMSeriesReader::mitkCloneMacro

(

ClassicDICOMSeriesReader

)

New()

static Pointer mitk::ClassicDICOMSeriesReader::New ( )

static

operator=()

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

protected

operator==()

bool mitk::ClassicDICOMSeriesReader::operator== ( const DICOMFileReader &  other ) const

overridevirtual

Implements mitk::DICOMFileReader.

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The documentation for this class was generated from the following file:

• mitkClassicDICOMSeriesReader.h