Medical Imaging Interaction Toolkit
2018.4.99-389bf124
Medical Imaging Interaction Toolkit
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#include <mitkDataCollection.h>
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::DataCollection * | GetParent () |
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... | |
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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... | |
BaseProperty * | GetNonConstProperty (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::TimeGeometry * | GetTimeGeometry () const |
Return the TimeGeometry of the data as const pointer. More... | |
const mitk::TimeGeometry * | GetTimeSlicedGeometry () const |
Return the TimeGeometry of the data as const pointer. More... | |
mitk::TimeGeometry * | GetTimeGeometry () |
Return the TimeGeometry of the data as pointer. More... | |
const mitk::TimeGeometry * | GetUpdatedTimeGeometry () |
Return the TimeGeometry of the data. More... | |
const mitk::TimeGeometry * | GetUpdatedTimeSliceGeometry () |
Return the TimeGeometry of the data. More... | |
virtual void | Expand (unsigned int timeSteps) |
Expands the TimeGeometry to a number of TimeSteps. More... | |
const mitk::BaseGeometry * | GetUpdatedGeometry (int t=0) |
Return the BaseGeometry of the data at time t. More... | |
mitk::BaseGeometry * | GetGeometry (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::BaseDataSource > | GetSource () 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 |
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itkTypeMacroNoParent (OperationActor) virtual ~OperationActor() | |
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Identifiable () | |
Identifiable (const UIDType &uid) | |
Identifiable (const Identifiable &)=delete | |
Identifiable (Identifiable &&) noexcept | |
virtual | ~Identifiable () |
Identifiable & | operator= (const Identifiable &)=delete |
Identifiable & | operator= (Identifiable &&other) noexcept |
UIDType | GetUID () const |
Get unique ID of an object. More... | |
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~IPropertyOwner () override | |
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virtual | ~IPropertyProvider () |
Static Public Member Functions | |
static Pointer | New () |
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static const char * | GetStaticNameOfClass () |
Protected Member Functions | |
DataCollection () | |
~DataCollection () override | |
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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 |
Additional Inherited Members | |
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typedef BaseData | Self |
typedef itk::DataObject | Superclass |
typedef itk::SmartPointer< Self > | Pointer |
typedef itk::SmartPointer< const Self > | ConstPointer |
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using | UIDType = std::string |
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bool | m_LastRequestedRegionWasOutsideOfTheBufferedRegion |
unsigned int | m_SourceOutputIndexDuplicate |
bool | m_Initialized |
Definition at line 53 of file mitkDataCollection.h.
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protected |
Definition at line 21 of file mitkDataCollection.cpp.
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overrideprotected |
Definition at line 26 of file mitkDataCollection.cpp.
vcl_size_t mitk::DataCollection::AddData | ( | DataObject::Pointer | data, |
std::string | name, | ||
std::string | filePath = "" |
||
) |
AddData Add a data item.
data | Images/Fibers/DataCollections |
name | name that allows identifying this data (e.g. a category T2, Segmentation , etc ...) |
description |
Definition at line 37 of file mitkDataCollection.cpp.
References SetParent().
Referenced by mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::AddImage().
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overridevirtual |
Clear - clears the data collection.
Reimplemented from mitk::BaseData.
Definition at line 294 of file mitkDataCollection.cpp.
References Clear().
Referenced by Clear().
Pointer mitk::DataCollection::Clone | ( | ) | const |
itk::DataObject::Pointer mitk::DataCollection::GetData | ( | vcl_size_t | index | ) |
GetData Get original data by index.
To ensure a mitk::Image is returned use mitk::GetMitkImage
index |
Definition at line 137 of file mitkDataCollection.cpp.
References HasElement(), and mitkThrow.
Referenced by mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::AddImage(), mitk::CollectionWriter::ExportCollectionToFolder(), GetData(), GetDataNode(), GetItkImage(), GetMitkImage(), GetProbabilityMap(), mitk::CollectionWriter::SaveCollection(), and mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::ToBegin().
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
name |
Definition at line 146 of file mitkDataCollection.cpp.
References GetData(), and NameToIndex().
std::string mitk::DataCollection::GetDataFilePath | ( | vcl_size_t | index | ) | const |
Definition at line 62 of file mitkDataCollection.cpp.
References mitkThrow.
Referenced by mitk::CollectionWriter::ExportCollectionToFolder(), and mitk::CollectionWriter::SaveCollection().
mitk::DataNode::Pointer mitk::DataCollection::GetDataNode | ( | vcl_size_t | index | ) |
GetDataNode - returns data node containing data at index.
index |
Definition at line 333 of file mitkDataCollection.cpp.
References GetData(), GetMitkImage(), IndexToName(), and mitk::DataNode::New().
Referenced by GetDataNode().
mitk::DataNode::Pointer mitk::DataCollection::GetDataNode | ( | std::string | name | ) |
GetDataNode - returns data node containing data with name.
name |
Definition at line 348 of file mitkDataCollection.cpp.
References GetDataNode(), and NameToIndex().
ImageType mitk::DataCollection::GetItkImage | ( | vcl_size_t | index, |
ImageType * | itkImage | ||
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GetMitkImage - casts data to privided itk::Image pointer.
Definition at line 203 of file mitkDataCollection.cpp.
References mitk::CastToItkImage(), GetData(), and image.
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().
mitk::Image::Pointer mitk::DataCollection::GetMitkImage | ( | vcl_size_t | index | ) |
GetMitkImage - casts data to mitk::Image and returns it.
index |
Definition at line 176 of file mitkDataCollection.cpp.
References GetData().
Referenced by mitk::CollectionWriter::ExportCollectionToFolder(), GetDataNode(), GetMitkImage(), and mitk::CollectionWriter::SaveCollection().
mitk::Image::Pointer mitk::DataCollection::GetMitkImage | ( | std::string | name | ) |
GetMitkImage - casts data to mitk::Image and returns it.
name |
Definition at line 197 of file mitkDataCollection.cpp.
References GetMitkImage(), and NameToIndex().
std::string mitk::DataCollection::GetName | ( | ) | const |
Definition at line 57 of file mitkDataCollection.cpp.
Referenced by mitk::CollectionWriter::ExportCollectionToFolder(), and mitk::CollectionWriter::SaveCollection().
mitk::DataCollection * mitk::DataCollection::GetParent | ( | ) |
GetParent - returns the parent collection if available else null is returned.
Definition at line 254 of file mitkDataCollection.cpp.
mitk::Image::Pointer mitk::DataCollection::GetProbabilityMap | ( | std::vector< std::string > | probabilityNamesVector | ) |
GetProbabilityMap - returns vectorimage generated out of images with names in the probabilityNamesVector.
probabilityNamesVector |
Definition at line 353 of file mitkDataCollection.cpp.
References GetData(), and mitk::Image::New().
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().
bool mitk::DataCollection::HasElement | ( | std::string | name | ) |
HasElement - check if element with this name exists in collection.
name |
Definition at line 97 of file mitkDataCollection.cpp.
Referenced by mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::AddImage(), GetData(), mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::NextObject(), RemoveElement(), RemoveIndex(), SetData(), and mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::ToBegin().
bool mitk::DataCollection::HasElement | ( | vcl_size_t | index | ) |
HasElement - check if element with this index exists in collection.
index |
Definition at line 104 of file mitkDataCollection.cpp.
std::string mitk::DataCollection::IndexToName | ( | vcl_size_t | index | ) | const |
IndexToName - Get name from index.
index |
Definition at line 86 of file mitkDataCollection.cpp.
References MITK_ERROR, and mitkThrow.
Referenced by mitk::CollectionWriter::ExportCollectionToFolder(), GetDataNode(), mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::GetFilePrefix(), and mitk::CollectionWriter::SaveCollection().
void mitk::DataCollection::Init | ( | std::string | name | ) |
Definition at line 31 of file mitkDataCollection.cpp.
mitk::DataCollection::mitkClassMacro | ( | DataCollection | , |
BaseData | |||
) |
vcl_size_t mitk::DataCollection::NameToIndex | ( | std::string | name | ) |
NameToIndex - Get index from data item name.
name |
Definition at line 71 of file mitkDataCollection.cpp.
References mitkThrow.
Referenced by GetData(), GetDataNode(), GetItkImage(), GetMitkImage(), operator[](), RemoveElement(), and SetData().
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static |
itk::DataObject::Pointer & mitk::DataCollection::operator[] | ( | vcl_size_t | index | ) |
Definition at line 227 of file mitkDataCollection.cpp.
Referenced by operator[]().
itk::DataObject::Pointer & mitk::DataCollection::operator[] | ( | std::string & | name | ) |
Definition at line 233 of file mitkDataCollection.cpp.
References NameToIndex(), and operator[]().
bool mitk::DataCollection::RemoveElement | ( | std::string & | name | ) |
RemoveElement - removes element with name.
name |
Definition at line 286 of file mitkDataCollection.cpp.
References HasElement(), NameToIndex(), and RemoveIndex().
bool mitk::DataCollection::RemoveIndex | ( | vcl_size_t | index | ) |
RemoveIndex - removes element at index.
index |
Definition at line 268 of file mitkDataCollection.cpp.
References HasElement().
Referenced by RemoveElement().
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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.
void mitk::DataCollection::SetData | ( | itk::DataObject::Pointer | data, |
vcl_size_t | index | ||
) |
SetData - set/update data item by index.
data | |
index |
Definition at line 118 of file mitkDataCollection.cpp.
References HasElement(), and mitkThrow.
Referenced by SetData(), and mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::ToBegin().
void mitk::DataCollection::SetData | ( | itk::DataObject::Pointer | data, |
std::string | name | ||
) |
SetData - set/update data item by name.
data | |
name |
Definition at line 131 of file mitkDataCollection.cpp.
References NameToIndex(), and SetData().
void mitk::DataCollection::SetName | ( | std::string | name | ) |
SetName - Sets name of DataCollection.
name |
Definition at line 51 of file mitkDataCollection.cpp.
void mitk::DataCollection::SetNameForIndex | ( | vcl_size_t | index, |
std::string & | name | ||
) |
SetNameForIndex - sets name for given data item by index.
index | |
name |
Definition at line 259 of file mitkDataCollection.cpp.
void mitk::DataCollection::SetParent | ( | mitk::DataCollection * | parent | ) |
SetParent - sets the parent collection.
parent |
Definition at line 248 of file mitkDataCollection.cpp.
Referenced by AddData().
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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.
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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.
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.
vcl_size_t mitk::DataCollection::Size | ( | ) | const |
Size - number of data items in collection.
Definition at line 112 of file mitkDataCollection.cpp.
Referenced by mitk::CollectionWriter::ExportCollectionToFolder(), and mitk::CollectionWriter::SaveCollection().
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override |
Definition at line 309 of file mitkDataCollection.cpp.
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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.