Interface for DICOM readers that produce mitk::Images. More...

#include <mitkDICOMFileReader.h>

Inheritance diagram for mitk::DICOMFileReader:

[legend]

Collaboration diagram for mitk::DICOMFileReader:

Public Types
typedef DICOMImageBlockDescriptor::AdditionalTagsMapType	AdditionalTagsMapType

Public Member Functions
	mitkClassMacroItkParent (DICOMFileReader, itk::Object)

virtual bool	CanHandleFile (const std::string &filename)=0
	Indicate whether this reader can handle given file. More...

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

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

virtual void	AnalyzeInputFiles ()=0
	Analyze 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...

virtual bool	LoadImages ()=0

virtual DICOMTagPathList	GetTagsOfInterest () const =0

virtual void	SetTagCache (const DICOMTagCache::Pointer &)=0
	A way to provide external knowledge about files and tag values is appreciated. 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 bool	operator== (const DICOMFileReader &other) const =0

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 bool	IsDICOM (const std::string &filename)
	Test whether a file is DICOM at all. More...

Protected Member Functions
	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 void	InternalPrintConfiguration (std::ostream &os) const =0
	Configuration description for human reader, to be implemented by sub-classes. More...

virtual AdditionalTagsMapType	GetAdditionalTagsOfInterest () const

mitk::DICOMImageBlockDescriptor::TagLookupTableToPropertyFunctor	GetTagLookupTableToPropertyFunctor () const

Detailed Description

Interface for DICOM readers that produce mitk::Images.

As described in The DICOMReader Module, this class structures the reader's part in the process of analyzing a set of DICOM files and selecting the most appropriate reader.

The overall loading process is as follows:

Define input files: a list of absolute filenames
Analyze the potential output: see what can be made of the input files, describe with DICOMImageBlockDescriptors
Load pixel data: an application will usually analyze files using multiple readers and only load with a single reader

Sub-classes are required to implement a number of methods that reflect above structure. See mitk::DICOMITKSeriesGDCMReader for an example.

To help applications in describing different readers to the user, each reader brings a number of methods that describe its configuration/specifics by means of a short label and a (longer) description.

Definition at line 55 of file mitkDICOMFileReader.h.

Member Typedef Documentation

◆ AdditionalTagsMapType

typedef DICOMImageBlockDescriptor::AdditionalTagsMapType mitk::DICOMFileReader::AdditionalTagsMapType

Type specifies additional tags of interest. Key is the tag path of interest. The value is an optional user defined name for the property that should be used to store the tag value(s). Empty value is default and will imply to use the found DICOMTagPath as property name.

Definition at line 108 of file mitkDICOMFileReader.h.

Constructor & Destructor Documentation

◆ DICOMFileReader() [1/2]

mitk::DICOMFileReader::DICOMFileReader ( )

protected

Definition at line 18 of file mitkDICOMFileReader.cpp.

References ~DICOMFileReader().

Referenced by ~DICOMFileReader().

◆ ~DICOMFileReader()

mitk::DICOMFileReader::~DICOMFileReader ( )

overrideprotected

Definition at line 24 of file mitkDICOMFileReader.cpp.

References DICOMFileReader().

Referenced by DICOMFileReader().

◆ DICOMFileReader() [2/2]

mitk::DICOMFileReader::DICOMFileReader ( const DICOMFileReader & other )

protected

Definition at line 29 of file mitkDICOMFileReader.cpp.

References operator=().

Member Function Documentation

◆ AnalyzeInputFiles()

virtual void mitk::DICOMFileReader::AnalyzeInputFiles ( )

pure virtual

Analyze input files.

Implemented in mitk::DICOMITKSeriesGDCMReader, and mitk::DICOMNullFileReader.

Referenced by mitk::DICOMFileReaderTestHelper::TestMitkImagesAreLoaded(), mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs(), and mitk::DICOMFileReaderTestHelper::TestSingleBlockIsRead().

◆ CanHandleFile()

virtual bool mitk::DICOMFileReader::CanHandleFile ( const std::string & filename )

pure virtual

Indicate whether this reader can handle given file.

Implemented in mitk::DICOMITKSeriesGDCMReader, and mitk::DICOMNullFileReader.

◆ ClearOutputs()

void mitk::DICOMFileReader::ClearOutputs ( )

protected

Definition at line 106 of file mitkDICOMFileReader.cpp.

References SetNumberOfOutputs().

Referenced by mitk::DICOMNullFileReader::AnalyzeInputFiles(), mitk::DICOMITKSeriesGDCMReader::AnalyzeInputFiles(), and GetNumberOfOutputs().

◆ GetAdditionalTagsOfInterest()

mitk::DICOMFileReader::AdditionalTagsMapType mitk::DICOMFileReader::GetAdditionalTagsOfInterest ( ) const

protectedvirtual

Definition at line 200 of file mitkDICOMFileReader.cpp.

Referenced by mitk::DICOMITKSeriesGDCMReader::AnalyzeInputFiles(), mitk::ThreeDnTDICOMSeriesReader::Condense3DBlocks(), and mitk::DICOMITKSeriesGDCMReader::GetTagsOfInterest().

◆ GetConfigurationDescription()

std::string mitk::DICOMFileReader::GetConfigurationDescription ( ) const

One-sentence description of the reader's loading "strategy".

Definition at line 77 of file mitkDICOMFileReader.cpp.

References SetInputFiles().

Referenced by mitk::DICOMReaderConfigurator::CreateConfigStringFromReader(), and SetConfigurationDescription().

◆ GetConfigurationLabel()

std::string mitk::DICOMFileReader::GetConfigurationLabel ( ) const

Short label/name to describe this reader.

Definition at line 62 of file mitkDICOMFileReader.cpp.

References SetConfigurationDescription().

Referenced by mitk::DICOMReaderConfigurator::CreateConfigStringFromReader(), and SetConfigurationLabel().

◆ GetInputFiles()

const mitk::StringList & mitk::DICOMFileReader::GetInputFiles ( ) const

This input files.

Definition at line 92 of file mitkDICOMFileReader.cpp.

References GetNumberOfOutputs().

Referenced by mitk::DICOMNullFileReader::AnalyzeInputFiles(), mitk::DICOMITKSeriesGDCMReader::AnalyzeInputFiles(), SetInputFiles(), and mitk::DICOMFileReaderTestHelper::TestInputFilenames().

◆ GetNumberOfOutputs()

unsigned int mitk::DICOMFileReader::GetNumberOfOutputs ( ) const

Number of outputs, only meaningful after calling AnalyzeInputFiles()

Definition at line 99 of file mitkDICOMFileReader.cpp.

References ClearOutputs().

Referenced by mitk::DICOMITKSeriesGDCMReader::AnalyzeInputFiles(), GetInputFiles(), mitk::ThreeDnTDICOMSeriesReader::LoadImages(), mitk::DICOMITKSeriesGDCMReader::LoadImages(), mitk::DICOMFileReaderTestHelper::TestInputFilenames(), mitk::DICOMFileReaderTestHelper::TestMitkImagesAreLoaded(), mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs(), and mitk::DICOMFileReaderTestHelper::TestSingleBlockIsRead().

◆ GetOutput()

const mitk::DICOMImageBlockDescriptor & mitk::DICOMFileReader::GetOutput ( unsigned int index ) const

Individual outputs, only meaningful after calling AnalyzeInputFiles().

Exceptions

std::invalid_argument

Definition at line 162 of file mitkDICOMFileReader.cpp.

References InternalGetOutput().

Referenced by PrintOutputs(), mitk::DICOMFileReaderTestHelper::TestMitkImagesAreLoaded(), and mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs().

◆ GetTagLookupTableToPropertyFunctor()

mitk::DICOMImageBlockDescriptor::TagLookupTableToPropertyFunctor mitk::DICOMFileReader::GetTagLookupTableToPropertyFunctor ( ) const

protected

Definition at line 222 of file mitkDICOMFileReader.cpp.

Referenced by mitk::DICOMITKSeriesGDCMReader::AnalyzeInputFiles(), and mitk::ThreeDnTDICOMSeriesReader::Condense3DBlocks().

◆ GetTagsOfInterest()

virtual DICOMTagPathList mitk::DICOMFileReader::GetTagsOfInterest ( ) const

pure virtual

Implemented in mitk::DICOMITKSeriesGDCMReader, and mitk::DICOMNullFileReader.

◆ InternalGetOutput()

mitk::DICOMImageBlockDescriptor & mitk::DICOMFileReader::InternalGetOutput ( unsigned int index )

protected

non-const access to the DICOMImageBlockDescriptor

Definition at line 177 of file mitkDICOMFileReader.cpp.

References IsDICOM().

Referenced by GetOutput(), mitk::ThreeDnTDICOMSeriesReader::LoadImages(), and mitk::DICOMITKSeriesGDCMReader::LoadMitkImageForOutput().

◆ InternalPrintConfiguration()

virtual void mitk::DICOMFileReader::InternalPrintConfiguration ( std::ostream & os ) const

protectedpure virtual

Configuration description for human reader, to be implemented by sub-classes.

Implemented in mitk::DICOMITKSeriesGDCMReader, and mitk::DICOMNullFileReader.

Referenced by PrintConfiguration().

◆ IsDICOM()

bool mitk::DICOMFileReader::IsDICOM ( const std::string & filename )

static

Test whether a file is DICOM at all.

Definition at line 193 of file mitkDICOMFileReader.cpp.

Referenced by InternalGetOutput(), mitkDICOMPreloadedVolumeTest(), and mitkDICOMTestingSanityTest().

◆ LoadImages()

virtual bool mitk::DICOMFileReader::LoadImages ( )

pure virtual

Load the mitk::Images in our outputs, the DICOMImageBlockDescriptor. To be called only after AnalyzeInputFiles(). Take care of potential exceptions!

Implemented in mitk::DICOMITKSeriesGDCMReader, mitk::ThreeDnTDICOMSeriesReader, and mitk::DICOMNullFileReader.

Referenced by mitk::DICOMFileReaderTestHelper::TestMitkImagesAreLoaded(), and mitk::DICOMFileReaderTestHelper::TestSingleBlockIsRead().

◆ mitkClassMacroItkParent()

mitk::DICOMFileReader::mitkClassMacroItkParent	(	DICOMFileReader	,
		itk::Object
	)

◆ operator=()

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

protected

Definition at line 40 of file mitkDICOMFileReader.cpp.

References SetConfigurationLabel().

Referenced by DICOMFileReader(), mitk::DICOMNullFileReader::operator=(), and mitk::DICOMITKSeriesGDCMReader::operator=().

◆ operator==()

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

pure virtual

Implemented in mitk::DICOMITKSeriesGDCMReader, mitk::ClassicDICOMSeriesReader, mitk::ThreeDnTDICOMSeriesReader, and mitk::DICOMNullFileReader.

◆ PrintConfiguration()

void mitk::DICOMFileReader::PrintConfiguration ( std::ostream & os ) const

Print configuration description to given stream, for human reader.

Definition at line 136 of file mitkDICOMFileReader.cpp.

References InternalPrintConfiguration(), and PrintOutputs().

Referenced by SetOutput().

◆ PrintOutputs()

void mitk::DICOMFileReader::PrintOutputs	(	std::ostream &	os,
		bool	filenameDetails = `false`
	)		const

Print output description to given stream, for human reader.

Definition at line 146 of file mitkDICOMFileReader.cpp.

References GetOutput(), and mitk::DICOMImageBlockDescriptor::Print().

Referenced by PrintConfiguration(), and mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs().

◆ SetAdditionalTagsOfInterest()

void mitk::DICOMFileReader::SetAdditionalTagsOfInterest ( const AdditionalTagsMapType & tagList )

virtual

Set a list of DICOMTagPaths that specifiy all DICOM-Tags that will be copied into the property of the mitk::Image.

This method can be used to specify a list of DICOM-tags that shall be available after the loading. The value in the tagMap is an optional user defined name for the property key that should be used when storing the property). Empty value is default and will imply to use the found DICOMTagPath as property key. By default the content of the DICOM tags will be stored in a StringLookupTable on the mitk::Image. This behaviour can be changed by setting a different TagLookupTableToPropertyFunctor via SetTagLookupTableToPropertyFunctor().

Definition at line 206 of file mitkDICOMFileReader.cpp.

◆ SetConfigurationDescription()

void mitk::DICOMFileReader::SetConfigurationDescription ( const std::string & desc )

One-sentence description of the reader's loading "strategy".

Definition at line 69 of file mitkDICOMFileReader.cpp.

References GetConfigurationDescription().

Referenced by mitk::ClassicDICOMSeriesReader::ClassicDICOMSeriesReader(), and GetConfigurationLabel().

◆ SetConfigurationLabel()

void mitk::DICOMFileReader::SetConfigurationLabel ( const std::string & label )

Short label/name to describe this reader.

Definition at line 54 of file mitkDICOMFileReader.cpp.

References GetConfigurationLabel().

Referenced by mitk::ClassicDICOMSeriesReader::ClassicDICOMSeriesReader(), and operator=().

◆ SetInputFiles()

void mitk::DICOMFileReader::SetInputFiles ( const StringList & filenames )

This input files.

Definition at line 84 of file mitkDICOMFileReader.cpp.

References GetInputFiles().

Referenced by GetConfigurationDescription(), mitk::DICOMFileReaderTestHelper::TestInputFilenames(), mitk::DICOMFileReaderTestHelper::TestMitkImagesAreLoaded(), mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs(), and mitk::DICOMFileReaderTestHelper::TestSingleBlockIsRead().

◆ SetNumberOfOutputs()

void mitk::DICOMFileReader::SetNumberOfOutputs ( unsigned int numberOfOutputs )

protected

Definition at line 113 of file mitkDICOMFileReader.cpp.

References SetOutput().

Referenced by mitk::DICOMNullFileReader::AnalyzeInputFiles(), mitk::DICOMITKSeriesGDCMReader::AnalyzeInputFiles(), ClearOutputs(), and mitk::ThreeDnTDICOMSeriesReader::Condense3DBlocks().

◆ SetOutput()

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

protected

Definition at line 120 of file mitkDICOMFileReader.cpp.

References PrintConfiguration().

Referenced by mitk::DICOMNullFileReader::AnalyzeInputFiles(), mitk::DICOMITKSeriesGDCMReader::AnalyzeInputFiles(), mitk::ThreeDnTDICOMSeriesReader::Condense3DBlocks(), and SetNumberOfOutputs().

◆ SetTagCache()

virtual void mitk::DICOMFileReader::SetTagCache ( const DICOMTagCache::Pointer & )

pure virtual

A way to provide external knowledge about files and tag values is appreciated.

Implemented in mitk::DICOMITKSeriesGDCMReader, and mitk::DICOMNullFileReader.

◆ SetTagLookupTableToPropertyFunctor()

void mitk::DICOMFileReader::SetTagLookupTableToPropertyFunctor ( mitk::DICOMImageBlockDescriptor::TagLookupTableToPropertyFunctor functor )

virtual

Set a functor that defines how the slice-specific tag-values are stored in a Property.

This method sets a functor that is given a StringLookupTable that contains the values of one DICOM tag mapped to the slice index. The functor is supposed to store these values in an mitk Property.

By default, the StringLookupTable is stored in a StringLookupTableProperty except if all values are identical. In this case, the unique value is stored only once in a StringProperty.

Definition at line 214 of file mitkDICOMFileReader.cpp.

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ AdditionalTagsMapType

Constructor & Destructor Documentation

◆ DICOMFileReader() [1/2]

◆ ~DICOMFileReader()

◆ DICOMFileReader() [2/2]

Member Function Documentation

◆ AnalyzeInputFiles()

◆ CanHandleFile()

◆ ClearOutputs()

◆ GetAdditionalTagsOfInterest()

◆ GetConfigurationDescription()

◆ GetConfigurationLabel()

◆ GetInputFiles()

◆ GetNumberOfOutputs()

◆ GetOutput()

◆ GetTagLookupTableToPropertyFunctor()

◆ GetTagsOfInterest()

◆ InternalGetOutput()

◆ InternalPrintConfiguration()

◆ IsDICOM()

◆ LoadImages()

◆ mitkClassMacroItkParent()

◆ operator=()

◆ operator==()

◆ PrintConfiguration()

◆ PrintOutputs()

◆ SetAdditionalTagsOfInterest()

◆ SetConfigurationDescription()

◆ SetConfigurationLabel()

◆ SetInputFiles()

◆ SetNumberOfOutputs()

◆ SetOutput()

◆ SetTagCache()

◆ SetTagLookupTableToPropertyFunctor()