Medical Imaging Interaction Toolkit  2018.4.99-6ca56567
Medical Imaging Interaction Toolkit
mitk::DataCollection Class Reference

#include <mitkDataCollection.h>

Inheritance diagram for mitk::DataCollection:
Collaboration diagram for mitk::DataCollection:

Public Member Functions

 mitkClassMacro (DataCollection, BaseData)
 
Pointer Clone () const
 
void UpdateOutputInformation () override
 
void SetRequestedRegionToLargestPossibleRegion () override
 Set the RequestedRegion to the LargestPossibleRegion. More...
 
bool RequestedRegionIsOutsideOfTheBufferedRegion () override
 Determine whether the RequestedRegion is outside of the BufferedRegion. More...
 
bool VerifyRequestedRegion () override
 Verify that the RequestedRegion is within the LargestPossibleRegion. More...
 
void SetRequestedRegion (const itk::DataObject *) override
 Set the requested region from this data object to match the requested region of the data object passed in as a parameter. More...
 
void Init (std::string name)
 
vcl_size_t AddData (DataObject::Pointer data, std::string name, std::string filePath="")
 AddData Add a data item. More...
 
void SetName (std::string name)
 SetName - Sets name of DataCollection. More...
 
std::string GetName () const
 
std::string GetDataFilePath (vcl_size_t index) const
 
vcl_size_t NameToIndex (std::string name)
 NameToIndex - Get index from data item name. More...
 
std::string IndexToName (vcl_size_t index) const
 IndexToName - Get name from index. More...
 
bool HasElement (std::string name)
 HasElement - check if element with this name exists in collection. More...
 
bool HasElement (vcl_size_t index)
 HasElement - check if element with this index exists in collection. More...
 
vcl_size_t Size () const
 Size - number of data items in collection. More...
 
void SetData (itk::DataObject::Pointer data, vcl_size_t index)
 SetData - set/update data item by index. More...
 
void SetData (itk::DataObject::Pointer data, std::string name)
 SetData - set/update data item by name. More...
 
itk::DataObject::Pointer GetData (vcl_size_t index)
 GetData Get original data by index. More...
 
itk::DataObject::Pointer GetData (std::string name)
 GetData Get original data by name. More...
 
mitk::Image::Pointer GetMitkImage (vcl_size_t index)
 GetMitkImage - casts data to mitk::Image and returns it. More...
 
mitk::Image::Pointer GetMitkImage (std::string name)
 GetMitkImage - casts data to mitk::Image and returns it. More...
 
template<class ImageType >
ImageType GetItkImage (vcl_size_t index, ImageType *itkImage)
 GetMitkImage - casts data to privided itk::Image pointer. More...
 
template<class ImageType >
ImageType GetItkImage (std::string name, ImageType *itkImage)
 GetMitkImage - casts data to privided itk::Image pointer. More...
 
itk::DataObject::Pointer & operator[] (vcl_size_t index)
 
itk::DataObject::Pointer & operator[] (std::string &name)
 
void SetNameForIndex (vcl_size_t index, std::string &name)
 SetNameForIndex - sets name for given data item by index. More...
 
void SetXMLFile (std::string absoluteXMlFile)
 SetXMLFile - sets xml file to which data collection is saved. More...
 
std::string GetXMLFile ()
 SetXMLFile - gets xml file to which data collection is supposed to be saved. More...
 
void SetParent (mitk::DataCollection *parent)
 SetParent - sets the parent collection. More...
 
mitk::DataCollectionGetParent ()
 GetParent - returns the parent collection if available else null is returned. More...
 
bool RemoveIndex (vcl_size_t index)
 RemoveIndex - removes element at index. More...
 
bool RemoveElement (std::string &name)
 RemoveElement - removes element with name. More...
 
void Clear () override
 Clear - clears the data collection. More...
 
mitk::DataNode::Pointer GetDataNode (vcl_size_t index)
 GetDataNode - returns data node containing data at index. More...
 
mitk::DataNode::Pointer GetDataNode (std::string name)
 GetDataNode - returns data node containing data with name. More...
 
mitk::Image::Pointer GetProbabilityMap (std::vector< std::string > probabilityNamesVector)
 GetProbabilityMap - returns vectorimage generated out of images with names in the probabilityNamesVector. More...
 
- Public Member Functions inherited from mitk::BaseData
virtual std::vector< std::string > GetClassHierarchy () const
 
virtual const char * GetClassName () const
 
BaseProperty::ConstPointer GetConstProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=true) const override
 Get property by its key. More...
 
std::vector< std::string > GetPropertyKeys (const std::string &contextName="", bool includeDefaultContext=false) const override
 Query keys of existing properties. More...
 
std::vector< std::string > GetPropertyContextNames () const override
 Query names of existing contexts. More...
 
BasePropertyGetNonConstProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=true) override
 Get property by its key. More...
 
void SetProperty (const std::string &propertyKey, BaseProperty *property, const std::string &contextName="", bool fallBackOnDefaultContext=false) override
 Add new or change existent property. More...
 
void RemoveProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=false) override
 Removes a property. If the property does not exist, nothing will be done. More...
 
const mitk::TimeGeometryGetTimeGeometry () const
 Return the TimeGeometry of the data as const pointer. More...
 
const mitk::TimeGeometryGetTimeSlicedGeometry () const
 Return the TimeGeometry of the data as const pointer. More...
 
mitk::TimeGeometryGetTimeGeometry ()
 Return the TimeGeometry of the data as pointer. More...
 
const mitk::TimeGeometryGetUpdatedTimeGeometry ()
 Return the TimeGeometry of the data. More...
 
const mitk::TimeGeometryGetUpdatedTimeSliceGeometry ()
 Return the TimeGeometry of the data. More...
 
virtual void Expand (unsigned int timeSteps)
 Expands the TimeGeometry to a number of TimeSteps. More...
 
const mitk::BaseGeometryGetUpdatedGeometry (int t=0)
 Return the BaseGeometry of the data at time t. More...
 
mitk::BaseGeometryGetGeometry (int t=0) const
 Return the geometry, which is a TimeGeometry, of the data as non-const pointer. More...
 
void UpdateOutputInformation () override
 Update the information for this BaseData (the geometry in particular) so that it can be used as an output of a BaseProcess. More...
 
void CopyInformation (const itk::DataObject *data) override
 Copy information from the specified data set. More...
 
virtual bool IsInitialized () const
 Check whether the data has been initialized, i.e., at least the Geometry and other header data has been set. More...
 
virtual bool IsEmptyTimeStep (unsigned int t) const
 Check whether object contains data (at a specified time), e.g., a set of points may be empty. More...
 
virtual bool IsEmpty () const
 Check whether object contains data (at least at one point in time), e.g., a set of points may be empty. More...
 
void ExecuteOperation (Operation *operation) override
 overwrite if the Data can be called by an Interactor (StateMachine). More...
 
virtual void SetGeometry (BaseGeometry *aGeometry3D)
 Set the BaseGeometry of the data, which will be referenced (not copied!). Assumes the data object has only 1 time step ( is a 3D object ) and creates a new TimeGeometry which saves the given BaseGeometry. If an TimeGeometry has already been set for the object, it will be replaced after calling this function. More...
 
virtual void SetTimeGeometry (TimeGeometry *geometry)
 Set the TimeGeometry of the data, which will be referenced (not copied!). More...
 
virtual void SetClonedGeometry (const BaseGeometry *aGeometry3D)
 Set a clone of the provided Geometry as Geometry of the data. Assumes the data object has only 1 time step ( is a 3D object ) and creates a new TimeGeometry. If an TimeGeometry has already been set for the object, it will be replaced after calling this function. More...
 
virtual void SetClonedTimeGeometry (const TimeGeometry *geometry)
 Set a clone of the provided TimeGeometry as TimeGeometry of the data. More...
 
virtual void SetClonedGeometry (const BaseGeometry *aGeometry3D, unsigned int time)
 Set a clone of the provided geometry as BaseGeometry of a given time step. More...
 
mitk::PropertyList::Pointer GetPropertyList () const
 Get the data's property list. More...
 
void SetPropertyList (PropertyList *propertyList)
 Set the data's property list. More...
 
mitk::BaseProperty::Pointer GetProperty (const char *propertyKey) const
 Get the property (instance of BaseProperty) with key propertyKey from the PropertyList, and set it to this, respectively;. More...
 
void SetProperty (const char *propertyKey, BaseProperty *property)
 
virtual void SetOrigin (const Point3D &origin)
 Convenience method for setting the origin of the BaseGeometry instances of all time steps. More...
 
itk::SmartPointer< mitk::BaseDataSourceGetSource () const
 Get the process object that generated this data object. More...
 
unsigned int GetTimeSteps () const
 Get the number of time steps from the TimeGeometry As the base data has not a data vector given by itself, the number of time steps is defined over the time sliced geometry. In sub classes, a better implementation could be over the length of the data vector. More...
 
unsigned long GetMTime () const override
 Get the modified time of the last change of the contents this data object or its geometry. More...
 
void Graft (const DataObject *) override
 
- Public Member Functions inherited from mitk::OperationActor
 itkTypeMacroNoParent (OperationActor) virtual ~OperationActor()
 
- Public Member Functions inherited from mitk::Identifiable
 Identifiable ()
 
 Identifiable (const UIDType &uid)
 
 Identifiable (const Identifiable &)=delete
 
 Identifiable (Identifiable &&) noexcept
 
virtual ~Identifiable ()
 
Identifiableoperator= (const Identifiable &)=delete
 
Identifiableoperator= (Identifiable &&other) noexcept
 
virtual UIDType GetUID () const
 Get unique ID of an object. More...
 
- Public Member Functions inherited from mitk::IPropertyOwner
 ~IPropertyOwner () override
 
- Public Member Functions inherited from mitk::IPropertyProvider
virtual ~IPropertyProvider ()
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from mitk::BaseData
static const char * GetStaticNameOfClass ()
 

Protected Member Functions

 DataCollection ()
 
 ~DataCollection () override
 
- Protected Member Functions inherited from mitk::BaseData
 BaseData ()
 
 BaseData (const BaseData &other)
 
 ~BaseData () override
 
virtual void InitializeTimeGeometry (unsigned int timeSteps=1)
 Initialize the TimeGeometry for a number of time steps. The TimeGeometry is initialized empty and evenly timed. In many cases it will be necessary to overwrite this in sub-classes. More...
 
virtual void InitializeTimeSlicedGeometry (unsigned int timeSteps=1)
 Initialize the TimeGeometry for a number of time steps. The TimeGeometry is initialized empty and evenly timed. In many cases it will be necessary to overwrite this in sub-classes. More...
 
virtual void ClearData ()
 reset to non-initialized state, release memory More...
 
virtual void InitializeEmpty ()
 Pure virtual; Must be used in subclasses to get a data object to a valid state. Should at least create one empty object and call Superclass::InitializeTimeGeometry() to ensure an existing valid geometry. More...
 
void PrintSelf (std::ostream &os, itk::Indent indent) const override
 
- Protected Member Functions inherited from mitk::Identifiable
virtual void SetUID (const UIDType &uid)
 

Additional Inherited Members

- Public Types inherited from mitk::BaseData
typedef BaseData Self
 
typedef itk::DataObject Superclass
 
typedef itk::SmartPointer< SelfPointer
 
typedef itk::SmartPointer< const SelfConstPointer
 
- Public Types inherited from mitk::Identifiable
using UIDType = std::string
 
- Protected Attributes inherited from mitk::BaseData
bool m_LastRequestedRegionWasOutsideOfTheBufferedRegion
 
unsigned int m_SourceOutputIndexDuplicate
 
bool m_Initialized
 

Detailed Description

Definition at line 53 of file mitkDataCollection.h.

Constructor & Destructor Documentation

◆ DataCollection()

mitk::DataCollection::DataCollection ( )
protected

Definition at line 21 of file mitkDataCollection.cpp.

◆ ~DataCollection()

mitk::DataCollection::~DataCollection ( )
overrideprotected

Definition at line 26 of file mitkDataCollection.cpp.

Member Function Documentation

◆ AddData()

vcl_size_t mitk::DataCollection::AddData ( DataObject::Pointer  data,
std::string  name,
std::string  filePath = "" 
)

AddData Add a data item.

Parameters
dataImages/Fibers/DataCollections
namename that allows identifying this data (e.g. a category T2, Segmentation , etc ...)
description
Returns

Definition at line 37 of file mitkDataCollection.cpp.

References SetParent().

Referenced by mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::AddImage().

◆ Clear()

void mitk::DataCollection::Clear ( )
overridevirtual

Clear - clears the data collection.

Reimplemented from mitk::BaseData.

Definition at line 294 of file mitkDataCollection.cpp.

References Clear().

Referenced by Clear().

◆ Clone()

Pointer mitk::DataCollection::Clone ( ) const

◆ GetData() [1/2]

itk::DataObject::Pointer mitk::DataCollection::GetData ( vcl_size_t  index)

◆ GetData() [2/2]

itk::DataObject::Pointer mitk::DataCollection::GetData ( std::string  name)

GetData Get original data by name.

To ensure a mitk::Image is returned use mitk::GetMitkImage

Parameters
name
Returns

Definition at line 146 of file mitkDataCollection.cpp.

References GetData(), and NameToIndex().

◆ GetDataFilePath()

std::string mitk::DataCollection::GetDataFilePath ( vcl_size_t  index) const

◆ GetDataNode() [1/2]

mitk::DataNode::Pointer mitk::DataCollection::GetDataNode ( vcl_size_t  index)

GetDataNode - returns data node containing data at index.

Parameters
index
Returns

Definition at line 333 of file mitkDataCollection.cpp.

References GetData(), GetMitkImage(), IndexToName(), and mitk::DataNode::New().

Referenced by GetDataNode().

◆ GetDataNode() [2/2]

mitk::DataNode::Pointer mitk::DataCollection::GetDataNode ( std::string  name)

GetDataNode - returns data node containing data with name.

Parameters
name
Returns

Definition at line 348 of file mitkDataCollection.cpp.

References GetDataNode(), and NameToIndex().

◆ GetItkImage() [1/2]

template<class ImageType >
ImageType mitk::DataCollection::GetItkImage ( vcl_size_t  index,
ImageType itkImage 
)

GetMitkImage - casts data to privided itk::Image pointer.

Definition at line 203 of file mitkDataCollection.cpp.

References mitk::CastToItkImage(), GetData(), and image.

◆ GetItkImage() [2/2]

template<class ImageType >
ImageType mitk::DataCollection::GetItkImage ( std::string  name,
ImageType itkImage 
)

GetMitkImage - casts data to privided itk::Image pointer.

Definition at line 215 of file mitkDataCollection.cpp.

References mitk::CastToItkImage(), GetData(), image, and NameToIndex().

◆ GetMitkImage() [1/2]

mitk::Image::Pointer mitk::DataCollection::GetMitkImage ( vcl_size_t  index)

GetMitkImage - casts data to mitk::Image and returns it.

Note
returns nullptr is object is no mitk::Image or itk::Image
Parameters
index
Returns

Definition at line 176 of file mitkDataCollection.cpp.

References GetData().

Referenced by mitk::CollectionWriter::ExportCollectionToFolder(), GetDataNode(), GetMitkImage(), and mitk::CollectionWriter::SaveCollection().

◆ GetMitkImage() [2/2]

mitk::Image::Pointer mitk::DataCollection::GetMitkImage ( std::string  name)

GetMitkImage - casts data to mitk::Image and returns it.

Note
returns nullptr is object is no mitk::Image or itk::Image
Parameters
name
Returns

Definition at line 197 of file mitkDataCollection.cpp.

References GetMitkImage(), and NameToIndex().

◆ GetName()

std::string mitk::DataCollection::GetName ( ) const

◆ GetParent()

mitk::DataCollection * mitk::DataCollection::GetParent ( )

GetParent - returns the parent collection if available else null is returned.

Returns

Definition at line 254 of file mitkDataCollection.cpp.

◆ GetProbabilityMap()

mitk::Image::Pointer mitk::DataCollection::GetProbabilityMap ( std::vector< std::string >  probabilityNamesVector)

GetProbabilityMap - returns vectorimage generated out of images with names in the probabilityNamesVector.

Parameters
probabilityNamesVector
Returns

Definition at line 353 of file mitkDataCollection.cpp.

References GetData(), and mitk::Image::New().

◆ GetXMLFile()

std::string mitk::DataCollection::GetXMLFile ( )

SetXMLFile - gets xml file to which data collection is supposed to be saved.

Definition at line 243 of file mitkDataCollection.cpp.

Referenced by mitk::CollectionWriter::SaveCollection().

◆ HasElement() [1/2]

bool mitk::DataCollection::HasElement ( std::string  name)

◆ HasElement() [2/2]

bool mitk::DataCollection::HasElement ( vcl_size_t  index)

HasElement - check if element with this index exists in collection.

Parameters
index
Returns

Definition at line 104 of file mitkDataCollection.cpp.

◆ IndexToName()

std::string mitk::DataCollection::IndexToName ( vcl_size_t  index) const

◆ Init()

void mitk::DataCollection::Init ( std::string  name)

Definition at line 31 of file mitkDataCollection.cpp.

◆ mitkClassMacro()

mitk::DataCollection::mitkClassMacro ( DataCollection  ,
BaseData   
)

◆ NameToIndex()

vcl_size_t mitk::DataCollection::NameToIndex ( std::string  name)

NameToIndex - Get index from data item name.

Parameters
name
Returns

Definition at line 71 of file mitkDataCollection.cpp.

References mitkThrow.

Referenced by GetData(), GetDataNode(), GetItkImage(), GetMitkImage(), operator[](), RemoveElement(), and SetData().

◆ New()

◆ operator[]() [1/2]

itk::DataObject::Pointer & mitk::DataCollection::operator[] ( vcl_size_t  index)

Definition at line 227 of file mitkDataCollection.cpp.

Referenced by operator[]().

◆ operator[]() [2/2]

itk::DataObject::Pointer & mitk::DataCollection::operator[] ( std::string &  name)

Definition at line 233 of file mitkDataCollection.cpp.

References NameToIndex(), and operator[]().

◆ RemoveElement()

bool mitk::DataCollection::RemoveElement ( std::string &  name)

RemoveElement - removes element with name.

Parameters
name
Returns

Definition at line 286 of file mitkDataCollection.cpp.

References HasElement(), NameToIndex(), and RemoveIndex().

◆ RemoveIndex()

bool mitk::DataCollection::RemoveIndex ( vcl_size_t  index)

RemoveIndex - removes element at index.

Parameters
index
Returns

Definition at line 268 of file mitkDataCollection.cpp.

References HasElement().

Referenced by RemoveElement().

◆ RequestedRegionIsOutsideOfTheBufferedRegion()

bool mitk::DataCollection::RequestedRegionIsOutsideOfTheBufferedRegion ( )
overridevirtual

Determine whether the RequestedRegion is outside of the BufferedRegion.

This method returns true if the RequestedRegion is outside the BufferedRegion (true if at least one pixel is outside). This is used by the pipeline mechanism to determine whether a filter needs to re-execute in order to satisfy the current request. If the current RequestedRegion is already inside the BufferedRegion from the previous execution (and the current filter is up to date), then a given filter does not need to re-execute

Implements mitk::BaseData.

Definition at line 318 of file mitkDataCollection.cpp.

◆ SetData() [1/2]

void mitk::DataCollection::SetData ( itk::DataObject::Pointer  data,
vcl_size_t  index 
)

SetData - set/update data item by index.

Parameters
data
index

Definition at line 118 of file mitkDataCollection.cpp.

References HasElement(), and mitkThrow.

Referenced by SetData(), and mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::ToBegin().

◆ SetData() [2/2]

void mitk::DataCollection::SetData ( itk::DataObject::Pointer  data,
std::string  name 
)

SetData - set/update data item by name.

Parameters
data
name

Definition at line 131 of file mitkDataCollection.cpp.

References NameToIndex(), and SetData().

◆ SetName()

void mitk::DataCollection::SetName ( std::string  name)

SetName - Sets name of DataCollection.

Parameters
name

Definition at line 51 of file mitkDataCollection.cpp.

◆ SetNameForIndex()

void mitk::DataCollection::SetNameForIndex ( vcl_size_t  index,
std::string &  name 
)

SetNameForIndex - sets name for given data item by index.

Parameters
index
name

Definition at line 259 of file mitkDataCollection.cpp.

◆ SetParent()

void mitk::DataCollection::SetParent ( mitk::DataCollection parent)

SetParent - sets the parent collection.

Parameters
parent

Definition at line 248 of file mitkDataCollection.cpp.

Referenced by AddData().

◆ SetRequestedRegion()

void mitk::DataCollection::SetRequestedRegion ( const itk::DataObject *  data)
overridevirtual

Set the requested region from this data object to match the requested region of the data object passed in as a parameter.

This method is implemented in the concrete subclasses of BaseData.

Implements mitk::BaseData.

Definition at line 328 of file mitkDataCollection.cpp.

◆ SetRequestedRegionToLargestPossibleRegion()

void mitk::DataCollection::SetRequestedRegionToLargestPossibleRegion ( )
overridevirtual

Set the RequestedRegion to the LargestPossibleRegion.

This forces a filter to produce all of the output in one execution (i.e. not streaming) on the next call to Update().

Implements mitk::BaseData.

Definition at line 314 of file mitkDataCollection.cpp.

◆ SetXMLFile()

void mitk::DataCollection::SetXMLFile ( std::string  absoluteXMlFile)

SetXMLFile - sets xml file to which data collection is saved.

Definition at line 238 of file mitkDataCollection.cpp.

◆ Size()

vcl_size_t mitk::DataCollection::Size ( ) const

Size - number of data items in collection.

Returns

Definition at line 112 of file mitkDataCollection.cpp.

Referenced by mitk::CollectionWriter::ExportCollectionToFolder(), and mitk::CollectionWriter::SaveCollection().

◆ UpdateOutputInformation()

void mitk::DataCollection::UpdateOutputInformation ( )
override

Definition at line 309 of file mitkDataCollection.cpp.

◆ VerifyRequestedRegion()

bool mitk::DataCollection::VerifyRequestedRegion ( )
overridevirtual

Verify that the RequestedRegion is within the LargestPossibleRegion.

If the RequestedRegion is not within the LargestPossibleRegion, then the filter cannot possibly satisfy the request. This method returns true if the request can be satisfied (even if it will be necessary to process the entire LargestPossibleRegion) and returns false otherwise. This method is used by PropagateRequestedRegion(). PropagateRequestedRegion() throws a InvalidRequestedRegionError exception if the requested region is not within the LargestPossibleRegion.

Implements mitk::BaseData.

Definition at line 323 of file mitkDataCollection.cpp.


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