Medical Imaging Interaction Toolkit
2016.11.0
Medical Imaging Interaction Toolkit
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Base Class for Fiber Bundles;. More...
#include <mitkFiberBundle.h>
Public Types | |
typedef itk::Image< unsigned char, 3 > | ItkUcharImgType |
Public Types inherited from mitk::BaseData | |
typedef BaseData | Self |
typedef itk::DataObject | Superclass |
typedef itk::SmartPointer< Self > | Pointer |
typedef itk::SmartPointer< const Self > | ConstPointer |
Public Member Functions | |
virtual void | UpdateOutputInformation () override |
virtual void | SetRequestedRegionToLargestPossibleRegion () override |
Set the RequestedRegion to the LargestPossibleRegion. More... | |
virtual bool | RequestedRegionIsOutsideOfTheBufferedRegion () override |
Determine whether the RequestedRegion is outside of the BufferedRegion. More... | |
virtual bool | VerifyRequestedRegion () override |
Verify that the RequestedRegion is within the LargestPossibleRegion. More... | |
virtual 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... | |
mitkClassMacro (FiberBundle, BaseData) static Pointer New() | |
Pointer | Clone () const |
mitkNewMacro1Param (Self, vtkSmartPointer< vtkPolyData >) void ColorFibersByCurvature(bool minMaxNorm | |
void | ColorFibersByScalarMap (mitk::Image::Pointer, bool opacity) |
template<typename TPixel > | |
void | ColorFibersByScalarMap (const mitk::PixelType pixelType, mitk::Image::Pointer, bool opacity) |
void | ColorFibersByOrientation () |
void | SetFiberOpacity (vtkDoubleArray *FAValArray) |
void | ResetFiberOpacity () |
void | SetFiberColors (vtkSmartPointer< vtkUnsignedCharArray > fiberColors) |
void | SetFiberColors (float r, float g, float b, float alpha=255) |
vtkSmartPointer< vtkUnsignedCharArray > | GetFiberColors () const |
void | Compress (float error=0.0) |
void | ResampleSpline (float pointDistance=1) |
void | ResampleSpline (float pointDistance, double tension, double continuity, double bias) |
bool | RemoveShortFibers (float lengthInMM) |
bool | RemoveLongFibers (float lengthInMM) |
bool | ApplyCurvatureThreshold (float minRadius, bool deleteFibers) |
void | MirrorFibers (unsigned int axis) |
void | RotateAroundAxis (double x, double y, double z) |
void | TranslateFibers (double x, double y, double z) |
void | ScaleFibers (double x, double y, double z, bool subtractCenter=true) |
void | TransformFibers (double rx, double ry, double rz, double tx, double ty, double tz) |
void | RemoveDir (vnl_vector_fixed< double, 3 > dir, double threshold) |
itk::Point< float, 3 > | TransformPoint (vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz) |
itk::Matrix< double, 3, 3 > | TransformMatrix (itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz) |
FiberBundle::Pointer | AddBundle (FiberBundle *fib) |
FiberBundle::Pointer | SubtractBundle (FiberBundle *fib) |
FiberBundle::Pointer | ExtractFiberSubset (DataNode *roi, DataStorage *storage) |
std::vector< long > | ExtractFiberIdSubset (DataNode *roi, DataStorage *storage) |
FiberBundle::Pointer | ExtractFiberSubset (ItkUcharImgType *mask, bool anyPoint, bool invert=false, bool bothEnds=true) |
FiberBundle::Pointer | RemoveFibersOutside (ItkUcharImgType *mask, bool invert=false) |
vtkSmartPointer< vtkPolyData > | GeneratePolyDataByIds (std::vector< long >) |
void | GenerateFiberIds () |
vtkSmartPointer< vtkFloatArray > | GetFiberWeights () const |
float | GetFiberWeight (unsigned int fiber) |
void | SetFiberWeights (float newWeight) |
void | SetFiberWeight (unsigned int fiber, float weight) |
void | SetFiberWeights (vtkSmartPointer< vtkFloatArray > weights) |
void | SetFiberPolyData (vtkSmartPointer< vtkPolyData >, bool updateGeometry=true) |
vtkSmartPointer< vtkPolyData > | GetFiberPolyData () const |
virtual int | GetNumFibers () |
int | GetNumFibers () const |
virtual float | GetMinFiberLength () |
virtual float | GetMaxFiberLength () |
virtual float | GetMeanFiberLength () |
virtual float | GetMedianFiberLength () |
virtual float | GetLengthStDev () |
virtual itk::TimeStamp | GetUpdateTime2D () |
virtual itk::TimeStamp | GetUpdateTime3D () |
void | RequestUpdate2D () |
void | RequestUpdate3D () |
void | RequestUpdate () |
unsigned long | GetNumberOfPoints () |
mitk::FiberBundle::Pointer | GetDeepCopy () |
bool | Equals (FiberBundle *fib, double eps=0.0001) |
virtual void | SetReferenceGeometry (mitk::BaseGeometry::Pointer _arg) |
virtual mitk::BaseGeometry::Pointer | GetReferenceGeometry () const |
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 void | Clear () |
Calls ClearData() and InitializeEmpty();. 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() | |
Static Public Attributes | |
static const char * | FIBER_ID_ARRAY |
Protected Member Functions | |
FiberBundle (vtkPolyData *fiberPolyData=nullptr) | |
virtual | ~FiberBundle () |
itk::Point< float, 3 > | GetItkPoint (double point[3]) |
void | UpdateFiberGeometry () |
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 | |
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 |
Base Class for Fiber Bundles;.
Definition at line 44 of file mitkFiberBundle.h.
typedef itk::Image<unsigned char, 3> mitk::FiberBundle::ItkUcharImgType |
Definition at line 48 of file mitkFiberBundle.h.
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Definition at line 53 of file mitkFiberBundle.cpp.
References ColorFibersByOrientation(), GenerateFiberIds(), mitk::New(), and UpdateFiberGeometry().
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protectedvirtual |
Definition at line 71 of file mitkFiberBundle.cpp.
mitk::FiberBundle::Pointer mitk::FiberBundle::AddBundle | ( | mitk::FiberBundle * | fib | ) |
Definition at line 119 of file mitkFiberBundle.cpp.
References GetFiberPolyData(), GetFiberWeight(), GetNumFibers(), MITK_INFO, MITK_WARN, and mitk::New().
bool mitk::FiberBundle::ApplyCurvatureThreshold | ( | float | minRadius, |
bool | deleteFibers | ||
) |
Definition at line 1583 of file mitkFiberBundle.cpp.
References MITK_INFO, and mitk::New().
Pointer mitk::FiberBundle::Clone | ( | ) | const |
void mitk::FiberBundle::ColorFibersByOrientation | ( | ) |
Definition at line 297 of file mitkFiberBundle.cpp.
References MITK_DEBUG, and mitk::New().
Referenced by FiberBundle().
void mitk::FiberBundle::ColorFibersByScalarMap | ( | mitk::Image::Pointer | FAimage, |
bool | opacity | ||
) |
Definition at line 557 of file mitkFiberBundle.cpp.
References mitkPixelTypeMultiplex2.
void mitk::FiberBundle::ColorFibersByScalarMap | ( | const mitk::PixelType | pixelType, |
mitk::Image::Pointer | image, | ||
bool | opacity | ||
) |
Definition at line 565 of file mitkFiberBundle.cpp.
References mitk::LookupTable::JET, mitk::New(), and mitk::LookupTable::New().
void mitk::FiberBundle::Compress | ( | float | error = 0.0 | ) |
Definition at line 1843 of file mitkFiberBundle.cpp.
References MITK_INFO, and mitk::New().
bool mitk::FiberBundle::Equals | ( | mitk::FiberBundle * | fib, |
double | eps = 0.0001 |
||
) |
Definition at line 1954 of file mitkFiberBundle.cpp.
References GetFiberPolyData(), GetNumFibers(), and MITK_INFO.
std::vector< long > mitk::FiberBundle::ExtractFiberIdSubset | ( | DataNode * | roi, |
DataStorage * | storage | ||
) |
Definition at line 906 of file mitkFiberBundle.cpp.
References mitk::DataNode::GetData(), mitk::DataStorage::GetDerivations(), min(), MITK_INFO, and mitk::New().
mitk::FiberBundle::Pointer mitk::FiberBundle::ExtractFiberSubset | ( | DataNode * | roi, |
DataStorage * | storage | ||
) |
Definition at line 893 of file mitkFiberBundle.cpp.
References mitk::DataNode::GetData(), and mitk::New().
Referenced by QmitkTbssRoiAnalysisWidget::CreateTracts().
mitk::FiberBundle::Pointer mitk::FiberBundle::ExtractFiberSubset | ( | ItkUcharImgType * | mask, |
bool | anyPoint, | ||
bool | invert = false , |
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bool | bothEnds = true |
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) |
Definition at line 645 of file mitkFiberBundle.cpp.
References MITK_INFO, and mitk::New().
void mitk::FiberBundle::GenerateFiberIds | ( | ) |
Definition at line 628 of file mitkFiberBundle.cpp.
References mitk::New().
Referenced by FiberBundle().
vtkSmartPointer< vtkPolyData > mitk::FiberBundle::GeneratePolyDataByIds | ( | std::vector< long > | fiberIds | ) |
Definition at line 84 of file mitkFiberBundle.cpp.
References MITK_INFO, and mitk::New().
mitk::FiberBundle::Pointer mitk::FiberBundle::GetDeepCopy | ( | ) |
Definition at line 76 of file mitkFiberBundle.cpp.
References mitk::New().
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Definition at line 74 of file mitkFiberBundle.h.
Referenced by mitk::FiberBundleMapper2D::GenerateDataForRenderer(), and mitk::FiberBundleMapper3D::InternalGenerateData().
vtkSmartPointer< vtkPolyData > mitk::FiberBundle::GetFiberPolyData | ( | ) | const |
Definition at line 292 of file mitkFiberBundle.cpp.
Referenced by AddBundle(), TrackVisFiberReader::append(), Equals(), mitk::FiberBundleMapper2D::GenerateDataForRenderer(), mitk::FiberBundleMapper3D::InternalGenerateData(), and SubtractBundle().
float mitk::FiberBundle::GetFiberWeight | ( | unsigned int | fiber | ) |
Definition at line 1169 of file mitkFiberBundle.cpp.
Referenced by AddBundle().
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inline |
Definition at line 109 of file mitkFiberBundle.h.
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protected |
Definition at line 260 of file mitkFiberBundle.cpp.
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virtual |
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virtual |
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unsigned long mitk::FiberBundle::GetNumberOfPoints | ( | ) |
Definition at line 1832 of file mitkFiberBundle.cpp.
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Referenced by AddBundle(), TrackVisFiberReader::append(), Equals(), and SubtractBundle().
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inline |
Definition at line 118 of file mitkFiberBundle.h.
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virtual |
Referenced by TrackVisFiberReader::create().
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Referenced by mitk::FiberBundleMapper2D::Update().
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Referenced by mitk::FiberBundleMapper3D::GenerateDataForRenderer().
void mitk::FiberBundle::MirrorFibers | ( | unsigned int | axis | ) |
Definition at line 1485 of file mitkFiberBundle.cpp.
References MITK_INFO, and mitk::New().
mitk::FiberBundle::mitkClassMacro | ( | FiberBundle | , |
BaseData | |||
) |
mitk::FiberBundle::mitkNewMacro1Param | ( | Self | , |
vtkSmartPointer< vtkPolyData > | |||
) |
void mitk::FiberBundle::RemoveDir | ( | vnl_vector_fixed< double, 3 > | dir, |
double | threshold | ||
) |
Definition at line 1520 of file mitkFiberBundle.cpp.
References mitk::New().
mitk::FiberBundle::Pointer mitk::FiberBundle::RemoveFibersOutside | ( | ItkUcharImgType * | mask, |
bool | invert = false |
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) |
Definition at line 815 of file mitkFiberBundle.cpp.
References MITK_INFO, and mitk::New().
bool mitk::FiberBundle::RemoveLongFibers | ( | float | lengthInMM | ) |
Definition at line 1715 of file mitkFiberBundle.cpp.
References MITK_INFO, and mitk::New().
bool mitk::FiberBundle::RemoveShortFibers | ( | float | lengthInMM | ) |
Definition at line 1663 of file mitkFiberBundle.cpp.
References min(), MITK_INFO, MITK_WARN, and mitk::New().
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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 2012 of file mitkFiberBundle.cpp.
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Definition at line 128 of file mitkFiberBundle.h.
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inline |
Definition at line 126 of file mitkFiberBundle.h.
Referenced by mitk::FiberBundleMapper2D::Update().
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Definition at line 127 of file mitkFiberBundle.h.
Referenced by mitk::FiberBundleMapper3D::GenerateDataForRenderer().
void mitk::FiberBundle::ResampleSpline | ( | float | pointDistance = 1 | ) |
Definition at line 1827 of file mitkFiberBundle.cpp.
void mitk::FiberBundle::ResampleSpline | ( | float | pointDistance, |
double | tension, | ||
double | continuity, | ||
double | bias | ||
) |
Definition at line 1758 of file mitkFiberBundle.cpp.
References MITK_INFO, and mitk::New().
void mitk::FiberBundle::ResetFiberOpacity | ( | ) |
Definition at line 549 of file mitkFiberBundle.cpp.
void mitk::FiberBundle::RotateAroundAxis | ( | double | x, |
double | y, | ||
double | z | ||
) |
Definition at line 1350 of file mitkFiberBundle.cpp.
References M_PI, and mitk::New().
void mitk::FiberBundle::ScaleFibers | ( | double | x, |
double | y, | ||
double | z, | ||
bool | subtractCenter = true |
||
) |
Definition at line 1410 of file mitkFiberBundle.cpp.
References mitk::BaseGeometry::GetCenter(), MITK_INFO, and mitk::New().
void mitk::FiberBundle::SetFiberColors | ( | vtkSmartPointer< vtkUnsignedCharArray > | fiberColors | ) |
Definition at line 1199 of file mitkFiberBundle.cpp.
void mitk::FiberBundle::SetFiberColors | ( | float | r, |
float | g, | ||
float | b, | ||
float | alpha = 255 |
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) |
Definition at line 608 of file mitkFiberBundle.cpp.
References mitk::New().
void mitk::FiberBundle::SetFiberOpacity | ( | vtkDoubleArray * | FAValArray | ) |
Definition at line 537 of file mitkFiberBundle.cpp.
void mitk::FiberBundle::SetFiberPolyData | ( | vtkSmartPointer< vtkPolyData > | fiberPD, |
bool | updateGeometry = true |
||
) |
Definition at line 272 of file mitkFiberBundle.cpp.
References mitk::New().
Referenced by TrackVisFiberReader::read().
void mitk::FiberBundle::SetFiberWeight | ( | unsigned int | fiber, |
float | weight | ||
) |
Definition at line 1194 of file mitkFiberBundle.cpp.
void mitk::FiberBundle::SetFiberWeights | ( | float | newWeight | ) |
Definition at line 1174 of file mitkFiberBundle.cpp.
void mitk::FiberBundle::SetFiberWeights | ( | vtkSmartPointer< vtkFloatArray > | weights | ) |
Definition at line 1180 of file mitkFiberBundle.cpp.
References MITK_INFO.
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Referenced by TrackVisFiberReader::read().
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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 2020 of file mitkFiberBundle.cpp.
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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 2008 of file mitkFiberBundle.cpp.
mitk::FiberBundle::Pointer mitk::FiberBundle::SubtractBundle | ( | mitk::FiberBundle * | fib | ) |
Definition at line 189 of file mitkFiberBundle.cpp.
References mitk::eps, GetFiberPolyData(), GetNumFibers(), MITK_INFO, and mitk::New().
void mitk::FiberBundle::TransformFibers | ( | double | rx, |
double | ry, | ||
double | rz, | ||
double | tx, | ||
double | ty, | ||
double | tz | ||
) |
Definition at line 1288 of file mitkFiberBundle.cpp.
References M_PI, and mitk::New().
itk::Matrix< double, 3, 3 > mitk::FiberBundle::TransformMatrix | ( | itk::Matrix< double, 3, 3 > | m, |
double | rx, | ||
double | ry, | ||
double | rz | ||
) |
Definition at line 1217 of file mitkFiberBundle.cpp.
References M_PI.
itk::Point< float, 3 > mitk::FiberBundle::TransformPoint | ( | vnl_vector_fixed< double, 3 > | point, |
double | rx, | ||
double | ry, | ||
double | rz, | ||
double | tx, | ||
double | ty, | ||
double | tz | ||
) |
Definition at line 1248 of file mitkFiberBundle.cpp.
References M_PI.
void mitk::FiberBundle::TranslateFibers | ( | double | x, |
double | y, | ||
double | z | ||
) |
Definition at line 1455 of file mitkFiberBundle.cpp.
References mitk::New().
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protected |
Definition at line 1077 of file mitkFiberBundle.cpp.
References mitk::New(), and mitk::Geometry3D::New().
Referenced by FiberBundle().
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Definition at line 2004 of file mitkFiberBundle.cpp.
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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 2016 of file mitkFiberBundle.cpp.
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Definition at line 51 of file mitkFiberBundle.h.