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Medical Imaging Interaction Toolkit
2016.11.0
Medical Imaging Interaction Toolkit
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Medical Imaging Interaction Toolkit
2016.11.0
Medical Imaging Interaction Toolkit
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#include <mitkDataCollection.h>
Public Member Functions | |
| mitkClassMacro (DataCollection, BaseData) static Pointer New() | |
| Pointer | Clone () const |
| virtual void | UpdateOutputInformation () |
| virtual void | SetRequestedRegionToLargestPossibleRegion () |
| Set the RequestedRegion to the LargestPossibleRegion. More... | |
| virtual bool | RequestedRegionIsOutsideOfTheBufferedRegion () |
| Determine whether the RequestedRegion is outside of the BufferedRegion. More... | |
| virtual bool | VerifyRequestedRegion () |
| Verify that the RequestedRegion is within the LargestPossibleRegion. More... | |
| virtual void | SetRequestedRegion (const itk::DataObject *) |
| 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 () |
| 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 |
| 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 TimeGeometry as TimeGeometry 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... | |
| virtual unsigned long | GetMTime () const override |
| Get the modified time of the last change of the contents this data object or its geometry. More... | |
| virtual void | Graft (const DataObject *) override |
| Public Member Functions inherited from mitk::OperationActor | |
| itkTypeMacroNoParent (OperationActor) virtual ~OperationActor() | |
Protected Member Functions | |
| DataCollection () | |
| virtual | ~DataCollection () |
| Protected Member Functions inherited from mitk::BaseData | |
| BaseData () | |
| BaseData (const BaseData &other) | |
| ~BaseData () | |
| 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... | |
| virtual void | PrintSelf (std::ostream &os, itk::Indent indent) const override |
Additional Inherited Members | |
| Public Types inherited from mitk::BaseData | |
| typedef BaseData | Self |
| typedef itk::DataObject | Superclass |
| typedef itk::SmartPointer< Self > | Pointer |
| typedef itk::SmartPointer< const Self > | ConstPointer |
| Static Public Member Functions inherited from mitk::BaseData | |
| static const char * | GetStaticNameOfClass () |
| Protected Attributes inherited from mitk::BaseData | |
| bool | m_LastRequestedRegionWasOutsideOfTheBufferedRegion |
| unsigned int | m_SourceOutputIndexDuplicate |
| bool | m_Initialized |
Definition at line 55 of file mitkDataCollection.h.
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protected |
Definition at line 25 of file mitkDataCollection.cpp.
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protectedvirtual |
Definition at line 30 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 41 of file mitkDataCollection.cpp.
References SetParent().
Referenced by mitk::CollectionDilation::DilateBinaryByName(), mitk::CollectionDilation::ErodeBinaryByName(), and mitk::CollectionGrayOpening::PerformGrayOpening().
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virtual |
Clear - clears the data collection.
Reimplemented from mitk::BaseData.
Definition at line 298 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 141 of file mitkDataCollection.cpp.
References mitkThrow.
Referenced by mitk::TumorInvasionClassification::DescriptionToLogFile(), mitk::CollectionDilation::DilateBinaryByName(), mitk::CollectionDilation::ErodeBinaryByName(), mitk::CollectionWriter::ExportCollectionToFolder(), mitk::CollectionGrayOpening::PerformGrayOpening(), and mitk::CollectionWriter::SaveCollection().
| 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 150 of file mitkDataCollection.cpp.
References GetData().
| std::string mitk::DataCollection::GetDataFilePath | ( | vcl_size_t | index | ) | const |
Definition at line 66 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 337 of file mitkDataCollection.cpp.
References GetData(), and mitk::DataNode::New().
| mitk::DataNode::Pointer mitk::DataCollection::GetDataNode | ( | std::string | name | ) |
GetDataNode - returns data node containing data with name.
| name |
Definition at line 352 of file mitkDataCollection.cpp.
| ImageType mitk::DataCollection::GetItkImage | ( | vcl_size_t | index, |
| ImageType * | itkImage | ||
| ) |
GetMitkImage - casts data to privided itk::Image pointer.
Definition at line 207 of file mitkDataCollection.cpp.
References mitk::CastToItkImage(), and GetData().
| ImageType mitk::DataCollection::GetItkImage | ( | std::string | name, |
| ImageType * | itkImage | ||
| ) |
GetMitkImage - casts data to privided itk::Image pointer.
Definition at line 219 of file mitkDataCollection.cpp.
References mitk::CastToItkImage(), and GetData().
| mitk::Image::Pointer mitk::DataCollection::GetMitkImage | ( | vcl_size_t | index | ) |
GetMitkImage - casts data to mitk::Image and returns it.
| index |
Definition at line 180 of file mitkDataCollection.cpp.
References GetData().
Referenced by mitk::CollectionDilation::DilateBinaryByName(), mitk::CollectionDilation::ErodeBinaryByName(), mitk::CollectionWriter::ExportCollectionToFolder(), mitk::CollectionGrayOpening::PerformGrayOpening(), 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 201 of file mitkDataCollection.cpp.
| std::string mitk::DataCollection::GetName | ( | ) | const |
Definition at line 61 of file mitkDataCollection.cpp.
Referenced by mitk::TumorInvasionClassification::DescriptionToLogFile(), 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 258 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 357 of file mitkDataCollection.cpp.
References GetData(), mitk::New(), 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 247 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 101 of file mitkDataCollection.cpp.
| bool mitk::DataCollection::HasElement | ( | vcl_size_t | index | ) |
HasElement - check if element with this index exists in collection.
| index |
Definition at line 108 of file mitkDataCollection.cpp.
| std::string mitk::DataCollection::IndexToName | ( | vcl_size_t | index | ) | const |
IndexToName - Get name from index.
| index |
Definition at line 90 of file mitkDataCollection.cpp.
References MITK_ERROR, and mitkThrow.
Referenced by mitk::TumorInvasionClassification::DescriptionToLogFile(), mitk::CollectionWriter::ExportCollectionToFolder(), and mitk::CollectionWriter::SaveCollection().
| void mitk::DataCollection::Init | ( | std::string | name | ) |
Definition at line 35 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 75 of file mitkDataCollection.cpp.
References mitkThrow.
| itk::DataObject::Pointer & mitk::DataCollection::operator[] | ( | vcl_size_t | index | ) |
Definition at line 231 of file mitkDataCollection.cpp.
| itk::DataObject::Pointer & mitk::DataCollection::operator[] | ( | std::string & | name | ) |
Definition at line 237 of file mitkDataCollection.cpp.
| bool mitk::DataCollection::RemoveElement | ( | std::string & | name | ) |
RemoveElement - removes element with name.
| name |
Definition at line 290 of file mitkDataCollection.cpp.
| bool mitk::DataCollection::RemoveIndex | ( | vcl_size_t | index | ) |
RemoveIndex - removes element at index.
| index |
Definition at line 272 of file mitkDataCollection.cpp.
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virtual |
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 322 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 122 of file mitkDataCollection.cpp.
References mitkThrow.
| void mitk::DataCollection::SetData | ( | itk::DataObject::Pointer | data, |
| std::string | name | ||
| ) |
SetData - set/update data item by name.
| data | |
| name |
Definition at line 135 of file mitkDataCollection.cpp.
| void mitk::DataCollection::SetName | ( | std::string | name | ) |
SetName - Sets name of DataCollection.
| name |
Definition at line 55 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 263 of file mitkDataCollection.cpp.
| void mitk::DataCollection::SetParent | ( | mitk::DataCollection * | parent | ) |
SetParent - sets the parent collection.
| parent |
Definition at line 252 of file mitkDataCollection.cpp.
Referenced by AddData().
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virtual |
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 332 of file mitkDataCollection.cpp.
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virtual |
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 318 of file mitkDataCollection.cpp.
| void mitk::DataCollection::SetXMLFile | ( | std::string | absoluteXMlFile | ) |
SetXMLFile - sets xml file to which data collection is saved.
Definition at line 242 of file mitkDataCollection.cpp.
| vcl_size_t mitk::DataCollection::Size | ( | ) | const |
Size - number of data items in collection.
Definition at line 116 of file mitkDataCollection.cpp.
Referenced by mitk::TumorInvasionClassification::DescriptionToLogFile(), mitk::CollectionDilation::DilateBinaryByName(), mitk::CollectionDilation::ErodeBinaryByName(), mitk::CollectionWriter::ExportCollectionToFolder(), mitk::CollectionGrayOpening::PerformGrayOpening(), and mitk::CollectionWriter::SaveCollection().
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virtual |
Definition at line 313 of file mitkDataCollection.cpp.
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virtual |
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 327 of file mitkDataCollection.cpp.
1.8.9.1 
