ITK  5.2.0
Insight Toolkit
Public Types | Public Member Functions | Static Public Member Functions | List of all members
itk::GDCMSeriesFileNames Class Reference

#include <itkGDCMSeriesFileNames.h>

+ Inheritance diagram for itk::GDCMSeriesFileNames:
+ Collaboration diagram for itk::GDCMSeriesFileNames:

Public Types

using FileNamesContainerType = FilenamesContainer
 
using Pointer = SmartPointer< Self >
 
using Self = GDCMSeriesFileNames
 
using SeriesUIDContainerType = SerieUIDContainer
 
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

virtual ::itk::LightObject::Pointer CreateAnother () const
 
const FileNamesContainerTypeGetInputFileNames ()
 
virtual const char * GetNameOfClass () const
 
void SetDirectory (std::string const &name)
 
void SetInputDirectory (const char *name)
 
void SetInputDirectory (std::string const &name)
 
- 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 ()
 
DataObjectPointerArraySizeType GetNumberOfIndexedInputs () const
 
DataObjectPointerArraySizeType GetNumberOfIndexedOutputs () const
 
DataObjectPointerArraySizeType GetNumberOfInputs () const
 
DataObjectPointerArraySizeType GetNumberOfOutputs () const
 
virtual DataObjectPointerArraySizeType GetNumberOfValidRequiredInputs () const
 
NameArray GetOutputNames () const
 
DataObjectPointerArray GetOutputs ()
 
virtual float GetProgress () const
 
NameArray GetRequiredInputNames () const
 
bool HasInput (const DataObjectIdentifierType &key) const
 
bool HasOutput (const DataObjectIdentifierType &key) const
 
void IncrementProgress (float increment)
 
virtual DataObjectPointer MakeOutput (const DataObjectIdentifierType &)
 
virtual DataObjectPointer MakeOutput (DataObjectPointerArraySizeType idx)
 
virtual void PropagateRequestedRegion (DataObject *output)
 
virtual void ResetPipeline ()
 
virtual void SetAbortGenerateData (bool _arg)
 
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 ThreadIdTypeGetNumberOfWorkUnits () const
 
MultiThreaderTypeGetMultiThreader () const
 
void SetMultiThreader (MultiThreaderType *threader)
 
virtual void PrepareOutputs ()
 
- Public Member Functions inherited from itk::Object
unsigned long AddObserver (const EventObject &event, Command *)
 
unsigned long AddObserver (const EventObject &event, Command *) const
 
unsigned long AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const
 
virtual void DebugOff () const
 
virtual void DebugOn () const
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary ()
 
const MetaDataDictionaryGetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStampGetTimeStamp () 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 noexcept override
 
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 ()
 
std::string m_InputDirectory = ""
 
std::string m_OutputDirectory = ""
 
FileNamesContainerType m_InputFileNames
 
FileNamesContainerType m_OutputFileNames
 
std::unique_ptr< gdcm::SerieHelper > m_SerieHelper
 
SeriesUIDContainerType m_SeriesUIDs
 
bool m_UseSeriesDetails = true
 
bool m_Recursive = false
 
bool m_LoadSequences = false
 
bool m_LoadPrivateTags = false
 
void SetOutputDirectory (std::string const &name)
 
const FileNamesContainerTypeGetOutputFileNames ()
 
const FileNamesContainerTypeGetFileNames (const std::string serie)
 
const SeriesUIDContainerTypeGetSeriesUIDs ()
 
virtual void SetRecursive (bool _arg)
 
virtual bool GetRecursive () const
 
virtual void RecursiveOn ()
 
virtual void RecursiveOff ()
 
void SetUseSeriesDetails (bool useSeriesDetails)
 
bool GetUseSeriesDetails () const
 
void AddSeriesRestriction (const std::string &tag)
 
virtual void SetLoadSequences (bool _arg)
 
virtual bool GetLoadSequences () const
 
virtual void LoadSequencesOn ()
 
virtual void LoadSequencesOff ()
 
virtual void SetLoadPrivateTags (bool _arg)
 
virtual bool GetLoadPrivateTags () const
 
virtual void LoadPrivateTagsOn ()
 
virtual void LoadPrivateTagsOff ()
 
 GDCMSeriesFileNames ()
 
 ~GDCMSeriesFileNames () override
 
void PrintSelf (std::ostream &os, Indent indent) const override
 

Additional Inherited Members

- Protected Member Functions inherited from itk::ProcessObject
 ProcessObject ()
 
 ~ProcessObject () override
 
DataObjectGetInput (const DataObjectIdentifierType &key)
 
const DataObjectGetInput (const DataObjectIdentifierType &key) const
 
DataObjectGetInput (DataObjectPointerArraySizeType idx)
 
const DataObjectGetInput (DataObjectPointerArraySizeType idx) const
 
virtual void SetInput (const DataObjectIdentifierType &key, DataObject *input)
 
virtual void SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)
 
virtual void AddInput (DataObject *input)
 
virtual void PushBackInput (const DataObject *input)
 
virtual void PopBackInput ()
 
virtual void PushFrontInput (const DataObject *input)
 
virtual void PopFrontInput ()
 
virtual void RemoveInput (const DataObjectIdentifierType &key)
 
virtual void RemoveInput (DataObjectPointerArraySizeType)
 
DataObjectGetPrimaryInput ()
 
const DataObjectGetPrimaryInput () const
 
virtual void SetPrimaryInputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryInputName () const
 
virtual void SetPrimaryInput (DataObject *input)
 
void SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
 
virtual void SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
 
virtual const DataObjectPointerArraySizeTypeGetNumberOfRequiredInputs () const
 
bool RemoveRequiredInputName (const DataObjectIdentifierType &)
 
bool IsRequiredInputName (const DataObjectIdentifierType &) const
 
void SetRequiredInputNames (const NameArray &)
 
bool AddRequiredInputName (const DataObjectIdentifierType &)
 
bool AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
 
void AddOptionalInputName (const DataObjectIdentifierType &)
 
void AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
 
DataObjectGetOutput (const DataObjectIdentifierType &key)
 
const DataObjectGetOutput (const DataObjectIdentifierType &key) const
 
virtual void SetPrimaryOutputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryOutputName () const
 
DataObjectGetOutput (DataObjectPointerArraySizeType idx)
 
const DataObjectGetOutput (DataObjectPointerArraySizeType idx) const
 
virtual void SetOutput (const DataObjectIdentifierType &key, DataObject *output)
 
virtual void RemoveOutput (const DataObjectIdentifierType &key)
 
DataObjectGetPrimaryOutput ()
 
const DataObjectGetPrimaryOutput () const
 
virtual void SetPrimaryOutput (DataObject *output)
 
virtual void SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)
 
virtual void AddOutput (DataObject *output)
 
virtual void RemoveOutput (DataObjectPointerArraySizeType idx)
 
virtual void SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
 
virtual const DataObjectPointerArraySizeTypeGetNumberOfRequiredOutputs () const
 
void SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
 
DataObjectIdentifierType MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const
 
DataObjectIdentifierType MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const
 
DataObjectPointerArraySizeType MakeIndexFromInputName (const DataObjectIdentifierType &name) const
 
DataObjectPointerArraySizeType MakeIndexFromOutputName (const DataObjectIdentifierType &name) const
 
bool IsIndexedInputName (const DataObjectIdentifierType &) const
 
bool IsIndexedOutputName (const DataObjectIdentifierType &) const
 
virtual void VerifyPreconditions () ITKv5_CONST
 
virtual void VerifyInputInformation () ITKv5_CONST
 
virtual void GenerateInputRequestedRegion ()
 
virtual void GenerateOutputRequestedRegion (DataObject *output)
 
virtual void GenerateOutputInformation ()
 
virtual void GenerateData ()
 
virtual void PropagateResetPipeline ()
 
virtual void ReleaseInputs ()
 
virtual void CacheInputReleaseDataFlags ()
 
virtual void RestoreInputReleaseDataFlags ()
 
virtual bool GetThreaderUpdateProgress () const
 
virtual void ThreaderUpdateProgressOn ()
 
virtual void ThreaderUpdateProgressOff ()
 
virtual void SetThreaderUpdateProgress (bool arg)
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
 ~Object () override
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &time)
 
- 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 ()
 
- Static Protected Member Functions inherited from itk::ProcessObject
static constexpr float progressFixedToFloat (uint32_t fixed)
 
static uint32_t progressFloatToFixed (float f)
 
- Protected Attributes inherited from itk::ProcessObject
bool m_Updating
 
TimeStamp m_OutputInformationMTime
 
- Protected Attributes inherited from itk::LightObject
std::atomic< int > m_ReferenceCount
 

Detailed Description

Generate a sequence of filenames from a DICOM series.

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

  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 'Instance 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().

Examples
Examples/IO/DicomSeriesReadGaussianImageWrite.cxx, Examples/IO/DicomSeriesReadImageWrite2.cxx, Examples/IO/DicomSeriesReadPrintTags.cxx, Examples/IO/DicomSeriesReadSeriesWrite.cxx, SphinxExamples/src/IO/GDCM/ReadAndPrintDICOMTags/Code.cxx, SphinxExamples/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Code.cxx, and SphinxExamples/src/IO/GDCM/ResampleDICOMSeries/Code.cxx.

Definition at line 63 of file itkGDCMSeriesFileNames.h.

Member Typedef Documentation

◆ FileNamesContainerType

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

Definition at line 74 of file itkGDCMSeriesFileNames.h.

◆ Pointer

Definition at line 71 of file itkGDCMSeriesFileNames.h.

◆ Self

Standard class type aliases.

Definition at line 69 of file itkGDCMSeriesFileNames.h.

◆ SeriesUIDContainerType

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

Definition at line 77 of file itkGDCMSeriesFileNames.h.

◆ Superclass

Definition at line 70 of file itkGDCMSeriesFileNames.h.

Constructor & Destructor Documentation

◆ GDCMSeriesFileNames()

itk::GDCMSeriesFileNames::GDCMSeriesFileNames ( )
protected

Contains the input directory where the DICOM serie is found

◆ ~GDCMSeriesFileNames()

itk::GDCMSeriesFileNames::~GDCMSeriesFileNames ( )
overrideprotected

Contains the input directory where the DICOM serie is found

Member Function Documentation

◆ AddSeriesRestriction()

void itk::GDCMSeriesFileNames::AddSeriesRestriction ( const std::string &  tag)

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)

◆ CreateAnother()

virtual::itk::LightObject::Pointer itk::GDCMSeriesFileNames::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.

◆ GetFileNames()

const FileNamesContainerType& itk::GDCMSeriesFileNames::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.

◆ GetInputFileNames()

const FileNamesContainerType& itk::GDCMSeriesFileNames::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

◆ GetLoadPrivateTags()

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

Contains the input directory where the DICOM serie is found

◆ GetLoadSequences()

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

Contains the input directory where the DICOM serie is found

◆ GetNameOfClass()

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

Run-time type information (and related methods).

Reimplemented from itk::ProcessObject.

◆ GetOutputFileNames()

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

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

◆ GetRecursive()

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

Contains the input directory where the DICOM serie is found

◆ GetSeriesUIDs()

const SeriesUIDContainerType& itk::GDCMSeriesFileNames::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.

◆ GetUseSeriesDetails()

bool itk::GDCMSeriesFileNames::GetUseSeriesDetails ( ) const
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 161 of file itkGDCMSeriesFileNames.h.

◆ LoadPrivateTagsOff()

virtual void itk::GDCMSeriesFileNames::LoadPrivateTagsOff ( )
virtual

Contains the input directory where the DICOM serie is found

◆ LoadPrivateTagsOn()

virtual void itk::GDCMSeriesFileNames::LoadPrivateTagsOn ( )
virtual

Contains the input directory where the DICOM serie is found

◆ LoadSequencesOff()

virtual void itk::GDCMSeriesFileNames::LoadSequencesOff ( )
virtual

Contains the input directory where the DICOM serie is found

◆ LoadSequencesOn()

virtual void itk::GDCMSeriesFileNames::LoadSequencesOn ( )
virtual

Contains the input directory where the DICOM serie is found

◆ New()

static Pointer itk::GDCMSeriesFileNames::New ( )
static

Method for creation through the object factory.

◆ PrintSelf()

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

Contains the input directory where the DICOM serie is found

Reimplemented from itk::ProcessObject.

◆ RecursiveOff()

virtual void itk::GDCMSeriesFileNames::RecursiveOff ( )
virtual

Contains the input directory where the DICOM serie is found

◆ RecursiveOn()

virtual void itk::GDCMSeriesFileNames::RecursiveOn ( )
virtual

Contains the input directory where the DICOM serie is found

◆ SetDirectory()

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

Set the directory that contains the DICOM series.

Definition at line 97 of file itkGDCMSeriesFileNames.h.

◆ SetInputDirectory() [1/2]

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

Set the directory that contains the DICOM series.

◆ SetInputDirectory() [2/2]

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

Set the directory that contains the DICOM series.

◆ SetLoadPrivateTags()

virtual void itk::GDCMSeriesFileNames::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.

◆ SetLoadSequences()

virtual void itk::GDCMSeriesFileNames::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.

◆ SetOutputDirectory()

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

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

Definition at line 110 of file itkGDCMSeriesFileNames.h.

◆ SetRecursive()

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

Recursively parse the input directory. Must be set before the call to SetInputDirectory().

◆ SetUseSeriesDetails()

void itk::GDCMSeriesFileNames::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

◆ m_InputDirectory

std::string itk::GDCMSeriesFileNames::m_InputDirectory = ""
private

Contains the input directory where the DICOM serie is found

Definition at line 201 of file itkGDCMSeriesFileNames.h.

◆ m_InputFileNames

FileNamesContainerType itk::GDCMSeriesFileNames::m_InputFileNames
private

Internal structure to keep the list of input/output filenames

Definition at line 207 of file itkGDCMSeriesFileNames.h.

◆ m_LoadPrivateTags

bool itk::GDCMSeriesFileNames::m_LoadPrivateTags = false
private

Contains the input directory where the DICOM serie is found

Definition at line 219 of file itkGDCMSeriesFileNames.h.

◆ m_LoadSequences

bool itk::GDCMSeriesFileNames::m_LoadSequences = false
private

Contains the input directory where the DICOM serie is found

Definition at line 218 of file itkGDCMSeriesFileNames.h.

◆ m_OutputDirectory

std::string itk::GDCMSeriesFileNames::m_OutputDirectory = ""
private

Contains the output directory where the DICOM serie should be written

Definition at line 204 of file itkGDCMSeriesFileNames.h.

◆ m_OutputFileNames

FileNamesContainerType itk::GDCMSeriesFileNames::m_OutputFileNames
private

Contains the input directory where the DICOM serie is found

Definition at line 208 of file itkGDCMSeriesFileNames.h.

◆ m_Recursive

bool itk::GDCMSeriesFileNames::m_Recursive = false
private

Contains the input directory where the DICOM serie is found

Definition at line 217 of file itkGDCMSeriesFileNames.h.

◆ m_SerieHelper

std::unique_ptr<gdcm::SerieHelper> itk::GDCMSeriesFileNames::m_SerieHelper
private

Internal structure to order serie from one directory

Definition at line 211 of file itkGDCMSeriesFileNames.h.

◆ m_SeriesUIDs

SeriesUIDContainerType itk::GDCMSeriesFileNames::m_SeriesUIDs
private

Internal structure to keep the list of series UIDs

Definition at line 214 of file itkGDCMSeriesFileNames.h.

◆ m_UseSeriesDetails

bool itk::GDCMSeriesFileNames::m_UseSeriesDetails = true
private

Contains the input directory where the DICOM serie is found

Definition at line 216 of file itkGDCMSeriesFileNames.h.


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