ITK  5.0.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
itk::DCMTKSeriesFileNames Class Reference
Input and Output Filters | Module ITKIODCMTK

#include <itkDCMTKSeriesFileNames.h>

+ Inheritance diagram for itk::DCMTKSeriesFileNames:
+ Collaboration diagram for itk::DCMTKSeriesFileNames:

Detailed Description

Generate a sequence of filenames from a DICOM series.

This class generate a sequence of files whose filenames points to a DICOM file. The ordering is based on the following strategy: Read all images in the directory (assuming there is only one study/serie)

  1. Extract Image Orientation & Image Position from DICOM images, and then calculate the ordering based on the 3D coordinate of the slice
  2. If for some reason this information is not found or failed, another strategy is used: the ordering is based on 'Image Number'
  3. If this strategy also failed, then the filenames are ordered by lexicographical order.

If multiple volumes are being grouped as a single series for your dicom objects, you may want to try calling ->SetUseSeriesDetails(true) prior to calling SetDirectory().

Definition at line 51 of file itkDCMTKSeriesFileNames.h.

Public Types

using FilenamesContainer = FileNamesContainerType
 
using FileNamesContainerType = std::vector< std::string >
 
using Pointer = SmartPointer< Self >
 
using Self = DCMTKSeriesFileNames
 
using SeriesUIDContainer = SeriesUIDContainerType
 
using SeriesUIDContainerType = std::vector< std::string >
 
using Superclass = ProcessObject
 
- Public Types inherited from itk::ProcessObject
using ConstPointer = SmartPointer< const Self >
 
using DataObjectIdentifierType = DataObject::DataObjectIdentifierType
 
using DataObjectPointer = DataObject::Pointer
 
using DataObjectPointerArray = std::vector< DataObjectPointer >
 
using DataObjectPointerArraySizeType = DataObjectPointerArray::size_type
 
using MultiThreaderType = MultiThreaderBase
 
using NameArray = std::vector< DataObjectIdentifierType >
 
using Pointer = SmartPointer< Self >
 
using Self = ProcessObject
 
using Superclass = Object
 
- Public Types inherited from itk::Object
using ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = Object
 
using Superclass = LightObject
 
- Public Types inherited from itk::LightObject
using ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = LightObject
 

Public Member Functions

void AddSeriesRestriction (const std::string &)
 
virtual ::itk::LightObject::Pointer CreateAnother () const
 
const FileNamesContainerType & GetFileNames (const std::string serie)
 
const FileNamesContainerType & GetInputFileNames ()
 
virtual const char * GetNameOfClass () const
 
const FileNamesContainerType & GetOutputFileNames ()
 
const SeriesUIDContainerType & GetSeriesUIDs ()
 
bool GetUseSeriesDetails ()
 
void SetDirectory (std::string const &name)
 
void SetInputDirectory (const char *name)
 
void SetInputDirectory (std::string const &name)
 
void SetUseSeriesDetails (bool useSeriesDetails)
 
void SetOutputDirectory (std::string const &name)
 
virtual void SetRecursive (bool _arg)
 
virtual bool GetRecursive () const
 
virtual void RecursiveOn ()
 
virtual void RecursiveOff ()
 
virtual void SetLoadSequences (bool _arg)
 
virtual bool GetLoadSequences () const
 
virtual void LoadSequencesOn ()
 
virtual void LoadSequencesOff ()
 
- Public Member Functions inherited from itk::ProcessObject
virtual void AbortGenerateDataOff ()
 
virtual void AbortGenerateDataOn ()
 
virtual void EnlargeOutputRequestedRegion (DataObject *)
 
virtual const bool & GetAbortGenerateData () const
 
DataObjectPointerArray GetIndexedInputs ()
 
DataObjectPointerArray GetIndexedOutputs ()
 
NameArray GetInputNames () const
 
DataObjectPointerArray GetInputs ()
 
MultiThreaderType * GetMultiThreader () const
 
DataObjectPointerArraySizeType GetNumberOfIndexedInputs () const
 
DataObjectPointerArraySizeType GetNumberOfIndexedOutputs () const
 
DataObjectPointerArraySizeType GetNumberOfInputs () const
 
DataObjectPointerArraySizeType GetNumberOfOutputs () const
 
virtual
DataObjectPointerArraySizeType 		GetNumberOfValidRequiredInputs () const
 
NameArray GetOutputNames () const
 
DataObjectPointerArray GetOutputs ()
 
virtual const float & GetProgress () const
 
NameArray GetRequiredInputNames () const
 
bool HasInput (const DataObjectIdentifierType &key) const
 
bool HasOutput (const DataObjectIdentifierType &key) const
 
virtual DataObjectPointer MakeOutput (DataObjectPointerArraySizeType idx)
 
virtual DataObjectPointer MakeOutput (const DataObjectIdentifierType &)
 
virtual void PrepareOutputs ()
 
virtual void PropagateRequestedRegion (DataObject *output)
 
virtual void ResetPipeline ()
 
virtual void SetAbortGenerateData (bool _arg)
 
void SetMultiThreader (MultiThreaderType *threader)
 
virtual void Update ()
 
virtual void UpdateLargestPossibleRegion ()
 
virtual void UpdateOutputData (DataObject *output)
 
virtual void UpdateOutputInformation ()
 
void UpdateProgress (float progress)
 
virtual void SetReleaseDataFlag (bool flag)
 
virtual bool GetReleaseDataFlag () const
 
void ReleaseDataFlagOn ()
 
void ReleaseDataFlagOff ()
 
virtual void SetReleaseDataBeforeUpdateFlag (bool _arg)
 
virtual const bool & GetReleaseDataBeforeUpdateFlag () const
 
virtual void ReleaseDataBeforeUpdateFlagOn ()
 
virtual void ReleaseDataBeforeUpdateFlagOff ()
 
virtual void SetNumberOfWorkUnits (ThreadIdType _arg)
 
virtual const ThreadIdType & GetNumberOfWorkUnits () const
 
- Public Member Functions inherited from itk::Object
unsigned long AddObserver (const EventObject &event, Command *)
 
unsigned long AddObserver (const EventObject &event, Command *) const
 
virtual void DebugOff () const
 
virtual void DebugOn () const
 
Command * GetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionary & GetMetaDataDictionary ()
 
const MetaDataDictionary & GetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStamp & GetTimeStamp () const
 
bool HasObserver (const EventObject &event) const
 
void InvokeEvent (const EventObject &)
 
void InvokeEvent (const EventObject &) const
 
virtual void Modified () const
 
void Register () const override
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag)
 
void SetDebug (bool debugFlag) const
 
void SetReferenceCount (int) override
 
void UnRegister () const noexceptoverride
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
void SetMetaDataDictionary (MetaDataDictionary &&rrhs)
 
virtual void SetObjectName (std::string _arg)
 
virtual const std::string & GetObjectName () const
 
- Public Member Functions inherited from itk::LightObject
virtual void Delete ()
 
virtual int GetReferenceCount () const
 
 itkCloneMacro (Self)
 
void Print (std::ostream &os, Indent indent=0) const
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from itk::Object
static bool GetGlobalWarningDisplay ()
 
static void GlobalWarningDisplayOff ()
 
static void GlobalWarningDisplayOn ()
 
static Pointer New ()
 
static void SetGlobalWarningDisplay (bool flag)
 
- Static Public Member Functions inherited from itk::LightObject
static void BreakOnError ()
 
static Pointer New ()
 

Private Member Functions

void GetDicomData (const std::string &series, bool saveFileNames)
 

Private Attributes

std::string m_InputDirectory
 
FileNamesContainerType m_InputFileNames
 
bool m_LoadPrivateTags
 
bool m_LoadSequences
 
std::string m_OutputDirectory
 
FileNamesContainerType m_OutputFileNames
 
bool m_Recursive
 
SeriesUIDContainerType m_SeriesUIDs
 
bool m_UseSeriesDetails
 
virtual void SetLoadPrivateTags (bool _arg)
 
virtual bool GetLoadPrivateTags () const
 
virtual void LoadPrivateTagsOn ()
 
virtual void LoadPrivateTagsOff ()
 
 DCMTKSeriesFileNames ()
 
 ~DCMTKSeriesFileNames () override
 
void PrintSelf (std::ostream &os, Indent indent) const override
 

Additional Inherited Members

- Protected Member Functions inherited from itk::ProcessObject
virtual void AddInput (DataObject *input)
 
void AddOptionalInputName (const DataObjectIdentifierType &)
 
void AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
 
virtual void AddOutput (DataObject *output)
 
bool AddRequiredInputName (const DataObjectIdentifierType &)
 
bool AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
 
virtual void CacheInputReleaseDataFlags ()
 
virtual void GenerateData ()
 
virtual void GenerateInputRequestedRegion ()
 
virtual void GenerateOutputInformation ()
 
virtual void GenerateOutputRequestedRegion (DataObject *output)
 
DataObject * GetInput (const DataObjectIdentifierType &key)
 
const DataObject * GetInput (const DataObjectIdentifierType &key) const
 
virtual const
DataObjectPointerArraySizeType & 		GetNumberOfRequiredInputs () const
 
virtual const
DataObjectPointerArraySizeType & 		GetNumberOfRequiredOutputs () const
 
bool IsIndexedInputName (const DataObjectIdentifierType &) const
 
bool IsIndexedOutputName (const DataObjectIdentifierType &) const
 
bool IsRequiredInputName (const DataObjectIdentifierType &) const
 
DataObjectPointerArraySizeType MakeIndexFromInputName (const DataObjectIdentifierType &name) const
 
DataObjectPointerArraySizeType MakeIndexFromOutputName (const DataObjectIdentifierType &name) const
 
DataObjectIdentifierType MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const
 
DataObjectIdentifierType MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const
 
virtual void PopBackInput ()
 
virtual void PopFrontInput ()
 
 ProcessObject ()
 
virtual void PropagateResetPipeline ()
 
virtual void PushBackInput (const DataObject *input)
 
virtual void PushFrontInput (const DataObject *input)
 
virtual void ReleaseInputs ()
 
virtual void RemoveInput (const DataObjectIdentifierType &key)
 
virtual void RemoveInput (DataObjectPointerArraySizeType)
 
virtual void RemoveOutput (const DataObjectIdentifierType &key)
 
virtual void RemoveOutput (DataObjectPointerArraySizeType idx)
 
bool RemoveRequiredInputName (const DataObjectIdentifierType &)
 
virtual void RestoreInputReleaseDataFlags ()
 
virtual void SetInput (const DataObjectIdentifierType &key, DataObject *input)
 
virtual void SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)
 
virtual void SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)
 
void SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
 
void SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
 
virtual void SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
 
virtual void SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
 
virtual void SetOutput (const DataObjectIdentifierType &key, DataObject *output)
 
virtual void SetPrimaryInput (DataObject *input)
 
virtual void SetPrimaryOutput (DataObject *output)
 
void SetRequiredInputNames (const NameArray &)
 
virtual void VerifyInputInformation () ITKv5_CONST
 
virtual void VerifyPreconditions () ITKv5_CONST
 
 ~ProcessObject () override
 
DataObject * GetInput (DataObjectPointerArraySizeType idx)
 
const DataObject * GetInput (DataObjectPointerArraySizeType idx) const
 
DataObject * GetPrimaryInput ()
 
const DataObject * GetPrimaryInput () const
 
virtual void SetPrimaryInputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryInputName () const
 
DataObject * GetOutput (const DataObjectIdentifierType &key)
 
const DataObject * GetOutput (const DataObjectIdentifierType &key) const
 
virtual void SetPrimaryOutputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryOutputName () const
 
DataObject * GetOutput (DataObjectPointerArraySizeType idx)
 
const DataObject * GetOutput (DataObjectPointerArraySizeType idx) const
 
DataObject * GetPrimaryOutput ()
 
const DataObject * GetPrimaryOutput () const
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &time)
 
 ~Object () override
 
- Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer InternalClone () const
 
 LightObject ()
 
virtual void PrintHeader (std::ostream &os, Indent indent) const
 
virtual void PrintTrailer (std::ostream &os, Indent indent) const
 
virtual ~LightObject ()
 
- Protected Attributes inherited from itk::ProcessObject
TimeStamp m_OutputInformationMTime
 
bool m_Updating
 
- Protected Attributes inherited from itk::LightObject
std::atomic< int > m_ReferenceCount
 

Member Typedef Documentation

using itk::DCMTKSeriesFileNames::FilenamesContainer = FileNamesContainerType

For backwards compatibility

Definition at line 71 of file itkDCMTKSeriesFileNames.h.

using itk::DCMTKSeriesFileNames::FileNamesContainerType = std::vector< std::string >

Type of the container that holds the file names in the series.

Definition at line 68 of file itkDCMTKSeriesFileNames.h.

using itk::DCMTKSeriesFileNames::Pointer = SmartPointer< Self >

Definition at line 59 of file itkDCMTKSeriesFileNames.h.

using itk::DCMTKSeriesFileNames::Self = DCMTKSeriesFileNames

Standard class type aliases.

Definition at line 57 of file itkDCMTKSeriesFileNames.h.

using itk::DCMTKSeriesFileNames::SeriesUIDContainer = SeriesUIDContainerType

For backwards compatibility.

Definition at line 65 of file itkDCMTKSeriesFileNames.h.

using itk::DCMTKSeriesFileNames::SeriesUIDContainerType = std::vector< std::string >

Type of the container that holds the UID's for the series.

Definition at line 62 of file itkDCMTKSeriesFileNames.h.

using itk::DCMTKSeriesFileNames::Superclass = ProcessObject

Definition at line 58 of file itkDCMTKSeriesFileNames.h.

Constructor & Destructor Documentation

itk::DCMTKSeriesFileNames::DCMTKSeriesFileNames ( )
protected

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

itk::DCMTKSeriesFileNames::~DCMTKSeriesFileNames ( )
overrideprotected

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

Member Function Documentation

void itk::DCMTKSeriesFileNames::AddSeriesRestriction ( const std::string &  )
inline

Add more restriction on the selection of a Series. This follow the same approach as SetUseSeriesDetails, but allow a user to add even more DICOM tags to take into account for subrefining a set of DICOM files into multiple series. Format for tag is "group|element" of a DICOM tag.

Warning
User need to set SetUseSeriesDetails(true)

Definition at line 155 of file itkDCMTKSeriesFileNames.h.

virtual::itk::LightObject::Pointer itk::DCMTKSeriesFileNames::CreateAnother ( ) const
virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

void itk::DCMTKSeriesFileNames::GetDicomData ( const std::string &  series,
bool  saveFileNames 
)
private

internal method for reading out filenames and UID lists

const FileNamesContainerType& itk::DCMTKSeriesFileNames::GetFileNames ( const std::string  serie)

Returns a vector containing the series' file names. The file names are ordered by the strategy define in header. All DICOM files have the same exact UID equal to the one user's specified. An extended UID may be returned/used if SetUseSeriesDetails(true) has been called.

const FileNamesContainerType& itk::DCMTKSeriesFileNames::GetInputFileNames ( )

Returns a vector containing the series' file names. The file names are ordered by the strategy define in header. No sorting is done based on UID

virtual bool itk::DCMTKSeriesFileNames::GetLoadPrivateTags ( ) const
virtual

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

virtual bool itk::DCMTKSeriesFileNames::GetLoadSequences ( ) const
virtual

Parse any sequences in the DICOM file. Defaults to false to skip sequences. This makes loading DICOM files faster when sequences are not needed.

virtual const char* itk::DCMTKSeriesFileNames::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from itk::ProcessObject.

const FileNamesContainerType& itk::DCMTKSeriesFileNames::GetOutputFileNames ( )

Returns a vector containing the series' file names. The file names are ordered in the same extact order as the input one. This could be dangerous if the writing has changed 3rd position or some other DICOM tag in the header

virtual bool itk::DCMTKSeriesFileNames::GetRecursive ( ) const
virtual

Recursively parse the input directory

const SeriesUIDContainerType& itk::DCMTKSeriesFileNames::GetSeriesUIDs ( )

Returns a vector containing all the UIDs found when parsing the direcory specified via SetDirectory. If no direcory is specified return an empty vector. An extended UID may be returned/used if SetUseSeriesDetails(true) has been called.

bool itk::DCMTKSeriesFileNames::GetUseSeriesDetails ( )
inline

Returns true if using additional series information such as ProtocolName and SeriesName to identify when a single SeriesUID contains multiple 3D volumes - as can occur with perfusion and DTI imaging

Definition at line 144 of file itkDCMTKSeriesFileNames.h.

virtual void itk::DCMTKSeriesFileNames::LoadPrivateTagsOff ( )
virtual

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

virtual void itk::DCMTKSeriesFileNames::LoadPrivateTagsOn ( )
virtual

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

virtual void itk::DCMTKSeriesFileNames::LoadSequencesOff ( )
virtual

Parse any sequences in the DICOM file. Defaults to false to skip sequences. This makes loading DICOM files faster when sequences are not needed.

virtual void itk::DCMTKSeriesFileNames::LoadSequencesOn ( )
virtual

Parse any sequences in the DICOM file. Defaults to false to skip sequences. This makes loading DICOM files faster when sequences are not needed.

static Pointer itk::DCMTKSeriesFileNames::New ( )
static

Method for creation through the object factory.

void itk::DCMTKSeriesFileNames::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
overrideprotectedvirtual

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

Reimplemented from itk::ProcessObject.

virtual void itk::DCMTKSeriesFileNames::RecursiveOff ( )
virtual

Recursively parse the input directory

virtual void itk::DCMTKSeriesFileNames::RecursiveOn ( )
virtual

Recursively parse the input directory

void itk::DCMTKSeriesFileNames::SetDirectory ( std::string const &  name)
inline

Set the directory that contains the DICOM series.

Definition at line 88 of file itkDCMTKSeriesFileNames.h.

void itk::DCMTKSeriesFileNames::SetInputDirectory ( const char *  name)

Set the directory that contains the DICOM series.

void itk::DCMTKSeriesFileNames::SetInputDirectory ( std::string const &  name)

Set the directory that contains the DICOM series.

virtual void itk::DCMTKSeriesFileNames::SetLoadPrivateTags ( bool  _arg)
virtual

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

virtual void itk::DCMTKSeriesFileNames::SetLoadSequences ( bool  _arg)
virtual

Parse any sequences in the DICOM file. Defaults to false to skip sequences. This makes loading DICOM files faster when sequences are not needed.

void itk::DCMTKSeriesFileNames::SetOutputDirectory ( std::string const &  name)
inline

Set the directory where the output DICOM serie should be written.

Definition at line 99 of file itkDCMTKSeriesFileNames.h.

virtual void itk::DCMTKSeriesFileNames::SetRecursive ( bool  _arg)
virtual

Recursively parse the input directory

void itk::DCMTKSeriesFileNames::SetUseSeriesDetails ( bool  useSeriesDetails)

Use additional series information such as ProtocolName and SeriesName to identify when a single SeriesUID contains multiple 3D volumes - as can occur with perfusion and DTI imaging

Member Data Documentation

std::string itk::DCMTKSeriesFileNames::m_InputDirectory
private

Contains the input directory where the DICOM serie is found

Definition at line 187 of file itkDCMTKSeriesFileNames.h.

FileNamesContainerType itk::DCMTKSeriesFileNames::m_InputFileNames
private

Internal structure to keep the list of input/output filenames

Definition at line 193 of file itkDCMTKSeriesFileNames.h.

bool itk::DCMTKSeriesFileNames::m_LoadPrivateTags
private

Definition at line 204 of file itkDCMTKSeriesFileNames.h.

bool itk::DCMTKSeriesFileNames::m_LoadSequences
private

Definition at line 203 of file itkDCMTKSeriesFileNames.h.

std::string itk::DCMTKSeriesFileNames::m_OutputDirectory
private

Contains the output directory where the DICOM serie should be written

Definition at line 190 of file itkDCMTKSeriesFileNames.h.

FileNamesContainerType itk::DCMTKSeriesFileNames::m_OutputFileNames
private

Definition at line 194 of file itkDCMTKSeriesFileNames.h.

bool itk::DCMTKSeriesFileNames::m_Recursive
private

Definition at line 202 of file itkDCMTKSeriesFileNames.h.

SeriesUIDContainerType itk::DCMTKSeriesFileNames::m_SeriesUIDs
private

Internal structure to order serie from one directory Internal structure to keep the list of series UIDs

Definition at line 199 of file itkDCMTKSeriesFileNames.h.

bool itk::DCMTKSeriesFileNames::m_UseSeriesDetails
private

Definition at line 201 of file itkDCMTKSeriesFileNames.h.

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