Supplies a 3D surface from pre-processed segmentation. More...
#include <mitkManualSegmentationToSurfaceFilter.h>
Public Types | |
| typedef double | vtkDouble |
 Public Types inherited from mitk::ImageToSurfaceFilter | |
| enum | DecimationType { NoDecimation , DecimatePro , QuadricDecimation } |
| Enumeration of available polygon decimation strategies. More... | |
| Public Types inherited from mitk::SurfaceSource | |
| typedef Surface | OutputType |
| Public Types inherited from mitk::BaseDataSource | |
| typedef BaseData | OutputType |
| Output data type. More... | |
| typedef itk::DataObject::DataObjectIdentifierType | DataObjectIdentifierType |
| Identifier type for named data objects. More... | |
Public Member Functions | |
| mitkClassMacro (ManualSegmentationToSurfaceFilter, ImageToSurfaceFilter) | |
| void | GenerateData () override |
| Pointer | Clone () const |
| virtual void | SetMedianFilter3D (bool _arg) |
| virtual bool | GetMedianFilter3D () const |
| virtual void | MedianFilter3DOn () |
| virtual void | MedianFilter3DOff () |
| virtual void | SetInterpolation (bool _arg) |
| virtual bool | GetInterpolation () const |
| virtual void | InterpolationOn () |
| virtual void | InterpolationOff () |
| virtual void | SetUseGaussianImageSmooth (bool _arg) |
| virtual bool | GetUseGaussianImageSmooth () const |
| virtual void | UseGaussianImageSmoothOn () |
| virtual void | UseGaussianImageSmoothOff () |
| virtual void | SetGaussianStandardDeviation (double _arg) |
| virtual double | GetGaussianStandardDeviation () const |
| void | SetMedianKernelSize (int x, int y, int z) |
| virtual int | GetMedianKernelSizeX () const |
| virtual int | GetMedianKernelSizeY () const |
| virtual int | GetMedianKernelSizeZ () const |
| void | SetInterpolation (vtkDouble x, vtkDouble y, vtkDouble z) |
| Public Member Functions inherited from mitk::ImageToSurfaceFilter | |
| mitkClassMacro (ImageToSurfaceFilter, SurfaceSource) | |
| Pointer | Clone () const |
| void | GenerateData () override |
| void | GenerateOutputInformation () override |
| const mitk::Image * | GetInput (void) |
| virtual void | SetInput (const mitk::Image *image) |
| void | SetSmoothIteration (int smoothIteration) |
| Set the number of iterations used to smooth the surface. More... | |
| void | SetSmoothRelaxation (float smoothRelaxation) |
| Set the relaxation factor for Laplacian smoothing. More... | |
| virtual void | SetThreshold (ScalarType _arg) |
| Set the threshold used for surface extraction via vtkMarchingCubes. More... | |
| virtual ScalarType | GetThreshold () const |
| Get the threshold used for vtkMarchingCubes surface extraction. More... | |
| virtual void | SetSmooth (bool _arg) |
| Enable vtkSmoothPolyDataFilter for Laplacian smoothing. More... | |
| virtual void | SmoothOn () |
| Toggle surface smoothing on/off. More... | |
| virtual void | SmoothOff () |
| virtual bool | GetSmooth () const |
| Get whether surface smoothing is enabled. More... | |
| virtual DecimationType | GetDecimate () const |
| Get the current decimation mode. More... | |
| virtual void | SetDecimate (DecimationType _arg) |
| Set the decimation mode to reduce the number of triangles in the mesh. More... | |
| virtual void | SetTargetReduction (float _arg) |
| Set the desired target reduction of triangles in the range [0.0, 1.0]. More... | |
| virtual float | GetTargetReduction () const |
| Get the target reduction factor for the decimation filter. More... | |
| template<class T1 , class T2 , class T3 > | |
| void | mitkVtkLinearTransformPoint (T1 matrix[4][4], T2 in[3], T3 out[3]) |
| Transform a 3D point by a 4x4 matrix (affine transformation). More... | |
| Public Member Functions inherited from mitk::SurfaceSource | |
| mitkClassMacro (SurfaceSource, BaseDataSource) | |
| Pointer | Clone () const |
| mitkBaseDataSourceGetOutputDeclarations itk::DataObject::Pointer | MakeOutput (DataObjectPointerArraySizeType idx) override |
| Allocate a new output object and return it. More... | |
| itk::DataObject::Pointer | MakeOutput (const DataObjectIdentifierType &name) override |
| Allocate a new output object by name. More... | |
| Public Member Functions inherited from mitk::BaseDataSource | |
| mitkClassMacroItkParent (BaseDataSource, itk::ProcessObject) | |
| OutputType * | GetOutput () |
| const OutputType * | GetOutput () const |
| OutputType * | GetOutput (DataObjectPointerArraySizeType idx) |
| const OutputType * | GetOutput (DataObjectPointerArraySizeType idx) const |
| virtual void | GraftOutput (OutputType *output) |
| Graft the specified BaseData onto this BaseDataSource's output. More... | |
| virtual void | GraftOutput (const DataObjectIdentifierType &key, OutputType *output) |
| Graft the specified base data object onto a named output. More... | |
| virtual void | GraftNthOutput (unsigned int idx, OutputType *output) |
| Graft the specified base data object onto this BaseDataSource's idx'th output. More... | |
| bool | Updating () const |
| Check whether the pipeline is currently executing. More... | |
Static Public Member Functions | |
| static Pointer | New () |
| Static Public Member Functions inherited from mitk::ImageToSurfaceFilter | |
| static Pointer | New () |
| Static Public Member Functions inherited from mitk::SurfaceSource | |
| static Pointer | New () |
Protected Member Functions | |
| ManualSegmentationToSurfaceFilter () | |
| ~ManualSegmentationToSurfaceFilter () override | |
| Protected Member Functions inherited from mitk::ImageToSurfaceFilter | |
| ImageToSurfaceFilter () | |
| ~ImageToSurfaceFilter () override | |
| Destructor. More... | |
| void | CreateSurface (int time, vtkImageData *vtkimage, mitk::Surface *surface, const ScalarType threshold) |
| Create the surface for a single time step using vtkMarchingCubes. More... | |
| Protected Member Functions inherited from mitk::SurfaceSource | |
| SurfaceSource () | |
| ~SurfaceSource () override | |
| Protected Member Functions inherited from mitk::BaseDataSource | |
| BaseDataSource () | |
| Constructor. More... | |
| ~BaseDataSource () override | |
| Destructor. More... | |
Protected Attributes | |
| bool | m_MedianFilter3D |
| int | m_MedianKernelSizeX |
| int | m_MedianKernelSizeY |
| int | m_MedianKernelSizeZ |
| bool | m_UseGaussianImageSmooth |
| double | m_GaussianStandardDeviation |
| bool | m_Interpolation |
| vtkDouble | m_InterpolationX |
| vtkDouble | m_InterpolationY |
| vtkDouble | m_InterpolationZ |
| Protected Attributes inherited from mitk::ImageToSurfaceFilter | |
| bool | m_Smooth |
| Flag whether the created surface shall be smoothed (default is false). More... | |
| DecimationType | m_Decimate |
| Decimation mode. Default is NoDecimation. More... | |
| ScalarType | m_Threshold |
| Threshold for surface extraction. Default value is 1. More... | |
| float | m_TargetReduction |
| The reduction factor for the decimation filter. Range [0.0, 1.0]. More... | |
| int | m_SmoothIteration |
| The number of iterations for the smoothing filter. Default is 50. More... | |
| float | m_SmoothRelaxation |
| The relaxation factor for the smoothing filter. Default is 0.1. More... | |
Additional Inherited Members | |
| Static Protected Member Functions inherited from mitk::BaseDataSource | |
| static Pointer | New () |
Detailed Description
Supplies a 3D surface from pre-processed segmentation.
The resulting surface depends on a filter pipeline based on vtkMedian (1) and a Gaussian filter with vtkImageGaussianSmooth (2). All voxels can be changed to an isotropic representation of the image (note: the number of voxels in the image will change). The resulting isotropic image has 1mm isotropic voxels by default, but can be varied freely.
Definition at line 39 of file mitkManualSegmentationToSurfaceFilter.h.
Member Typedef Documentation
◆ vtkDouble
| typedef double mitk::ManualSegmentationToSurfaceFilter::vtkDouble |
Definition at line 44 of file mitkManualSegmentationToSurfaceFilter.h.
Constructor & Destructor Documentation
◆ ManualSegmentationToSurfaceFilter()
|
protected |
◆ ~ManualSegmentationToSurfaceFilter()
|
overrideprotected |
Member Function Documentation
◆ Clone()
| Pointer mitk::ManualSegmentationToSurfaceFilter::Clone | ( | ) | const |
◆ GenerateData()
|
override |
Will pre-process a segmentation voxelwise. The segmentation can use a hole fill relating a median filter and smooth by a Gaussian filter. The image can be interpolated to an isotropic image. By default every filter is disabled. This method calls CreateSurface from mitkImageToSurfaceFilter and does not need a manual call since we use Update().
◆ GetGaussianStandardDeviation()
|
virtual |
Returns the standard deviation of the Gaussian filter which will be used when filter is enabled.
◆ GetInterpolation()
|
virtual |
Returns activation state of interpolation filter.
◆ GetMedianFilter3D()
|
virtual |
Return state if median filter is enabled.
◆ GetMedianKernelSizeX()
|
virtual |
Returns the kernel size in the first direction.
◆ GetMedianKernelSizeY()
|
virtual |
Returns the kernel size in the second direction.
◆ GetMedianKernelSizeZ()
|
virtual |
Returns the kernel size in the third direction.
◆ GetUseGaussianImageSmooth()
|
virtual |
Returns activation state of standard deviation filter.
◆ InterpolationOff()
|
virtual |
◆ InterpolationOn()
|
virtual |
Enable the interpolation filter (second filter in pipeline) for isotropic voxel.
◆ MedianFilter3DOff()
|
virtual |
◆ MedianFilter3DOn()
|
virtual |
Enable the median filter (first filter in pipeline).
◆ mitkClassMacro()
| mitk::ManualSegmentationToSurfaceFilter::mitkClassMacro | ( | ManualSegmentationToSurfaceFilter | , |
| ImageToSurfaceFilter | |||
| ) |
◆ New()
|
static |
◆ SetGaussianStandardDeviation()
|
virtual |
Set standard deviation for Gaussian Filter.
- Parameters
-
_arg by default 1.5
◆ SetInterpolation() [1/2]
|
virtual |
Supplies a method to enable Interpolation.
◆ SetInterpolation() [2/2]
| void mitk::ManualSegmentationToSurfaceFilter::SetInterpolation | ( | vtkDouble | x, |
| vtkDouble | y, | ||
| vtkDouble | z | ||
| ) |
Set the values for Spacing in X, Y and Z-Dimension
◆ SetMedianFilter3D()
|
virtual |
Supplies a method for setting median filter by a bool value.
◆ SetMedianKernelSize()
| void mitk::ManualSegmentationToSurfaceFilter::SetMedianKernelSize | ( | int | x, |
| int | y, | ||
| int | z | ||
| ) |
Set the Kernel for Median3DFilter. By default kernel is set to 3x3x3. If you choose '1' nothing will be processed in this direction.
◆ SetUseGaussianImageSmooth()
|
virtual |
Supplies a method for Gaussian filter (third filter in pipeline).
◆ UseGaussianImageSmoothOff()
|
virtual |
◆ UseGaussianImageSmoothOn()
|
virtual |
Enables Gaussian image smooth. As well the threshold for the CreateSurface() method will raise the threshold to 49 and changes the image range set from 0 to 100. It is made for reasons in binary images to prevent conflicts with the used filter. There are better results for dividing fore- and background.
Member Data Documentation
◆ m_GaussianStandardDeviation
|
protected |
Definition at line 154 of file mitkManualSegmentationToSurfaceFilter.h.
◆ m_Interpolation
|
protected |
Definition at line 155 of file mitkManualSegmentationToSurfaceFilter.h.
◆ m_InterpolationX
|
protected |
Definition at line 157 of file mitkManualSegmentationToSurfaceFilter.h.
◆ m_InterpolationY
|
protected |
Definition at line 158 of file mitkManualSegmentationToSurfaceFilter.h.
◆ m_InterpolationZ
|
protected |
Definition at line 159 of file mitkManualSegmentationToSurfaceFilter.h.
◆ m_MedianFilter3D
|
protected |
Definition at line 151 of file mitkManualSegmentationToSurfaceFilter.h.
◆ m_MedianKernelSizeX
|
protected |
Definition at line 152 of file mitkManualSegmentationToSurfaceFilter.h.
◆ m_MedianKernelSizeY
|
protected |
Definition at line 152 of file mitkManualSegmentationToSurfaceFilter.h.
◆ m_MedianKernelSizeZ
|
protected |
Definition at line 152 of file mitkManualSegmentationToSurfaceFilter.h.
◆ m_UseGaussianImageSmooth
|
protected |
Definition at line 153 of file mitkManualSegmentationToSurfaceFilter.h.
The documentation for this class was generated from the following file:
