Class to contain all the ITK/MITK logic for the MIDAS Morphological Segmentor pipeline, to separate from MorphologicalSegmentationView to make unit testing easier. More...
Public Member Functions | |
| mitkClassMacroItkParent (MorphologicalSegmentorPipelineManager, itk::Object) static Pointer New() | |
| void | SetDataStorage (mitk::DataStorage::Pointer dataStorage) |
| Sets the mitk::DataStorage on this object. More... | |
| mitk::DataStorage::Pointer | GetDataStorage () const |
| Gets the DataStorage pointer from this object. More... | |
| void | SetToolManager (mitk::ToolManager::Pointer toolManager) |
| Sets the mitk::ToolManager on this object. More... | |
| mitk::ToolManager::Pointer | GetToolManager () const |
| Gets the mitk::ToolManager from this object. More... | |
| void | OnThresholdingValuesChanged (double lowerThreshold, double upperThreshold, int axialSliceNumber) |
| Sets the thresholding parameters. More... | |
| void | OnErosionsValuesChanged (double upperThreshold, int numberOfErosions) |
| Sets the conditional erosion parameters. More... | |
| void | OnDilationsValuesChanged (double lowerPercentage, double upperPercentage, int numberOfDilations) |
| Sets the conditional dilation parameters. More... | |
| void | OnRethresholdingValuesChanged (int boxSize) |
| Sets the re-thresholding parameters. More... | |
| void | OnTabChanged (int tabIndex) |
| Called when we step to another stage of the pipeline, either fore or backwards. More... | |
| bool | HasSegmentationNode () const |
| Returns true if the segmentation node can be found which implicitly means we are "in progress". More... | |
| mitk::Image::ConstPointer | GetReferenceImage () const |
| Retrieves the reference image from the tool manager. More... | |
| mitk::Image::Pointer | GetWorkingImage (unsigned int dataIndex) const |
| Used to retrieve the working image from the tool manager. More... | |
| mitk::DataNode::Pointer | GetSegmentationNode () const |
| Used to retrieve the actual node of the image being segmented. More... | |
| mitk::Image::Pointer | GetSegmentationImage () const |
| Used to retrieve the segmentation image. More... | |
| void | GetPipelineParamsFromSegmentationNode (MorphologicalSegmentorPipelineParams ¶ms) const |
| Finds the segmentation node, and if present will populate params with the parameters found on the segmentation node. More... | |
| virtual bool | IsNodeASegmentationImage (const mitk::DataNode::Pointer node) const |
| For Morphological Editing, a Segmentation image should have a grey scale parent, and two binary children called SUBTRACTIONS_NAME and ADDITIONS_NAME. More... | |
| virtual bool | IsNodeAWorkingImage (const mitk::DataNode::Pointer node) const |
| For Morphological Editing, a Working image should be called either SUBTRACTIONS_NAME and ADDITIONS_NAME, and have a binary image parent. More... | |
| virtual bool | CanStartSegmentationForBinaryNode (const mitk::DataNode::Pointer node) const |
| For any binary image, we return true if the property midas.morph.stage is present, and false otherwise. More... | |
| virtual std::vector < mitk::DataNode * > | GetWorkingDataFromSegmentationNode (const mitk::DataNode::Pointer node) const |
| Assumes input is a valid segmentation node, then searches for the derived children of the node, looking for binary images called SUBTRACTIONS_NAME and ADDITIONS_NAME. Returns empty list if both not found. More... | |
| virtual mitk::DataNode * | GetSegmentationNodeFromWorkingData (const mitk::DataNode::Pointer node) const |
| Assumes input is a valid working node, then searches for a binary parent node, returns NULL if not found. More... | |
| void | SetSegmentationNodePropsFromReferenceImage () |
| Looks up the reference image, and sets default property values onto the segmentation node, which are later used to update GUI controls. More... | |
| void | UpdateSegmentation () |
| Calls update on the ITK pipeline using the MITK AccessByItk macros. More... | |
| void | FinalizeSegmentation () |
| Copies the final image out of the pipeline, and then disconnects the pipeline to stop it updating. More... | |
| void | ClearWorkingData () |
| Clears both images of the working data. More... | |
| void | RemoveWorkingData () |
| Removes the images we are using for editing during connection breaker from the DataStorage. More... | |
| void | DestroyPipeline (mitk::Image::Pointer segmentation) |
| Completely removes the current pipeline. More... | |
Static Public Attributes | |
| static const std::string | PROPERTY_MIDAS_MORPH_SEGMENTATION_FINISHED = "midas.morph.finished" |
| A static string, (to avoid code duplication), to hold the name of the property that determines if a morphological segmentation is finished. More... | |
| static const std::string | SEGMENTATION_OF_LAST_STAGE_NAME = "MORPHO_SEGMENTATION_OF_LAST_STAGE" |
| The output of the previous stage of the segmentation pipeline. More... | |
Protected Member Functions | |
| MorphologicalSegmentorPipelineManager () | |
| virtual | ~MorphologicalSegmentorPipelineManager () |
| MorphologicalSegmentorPipelineManager (const MorphologicalSegmentorPipelineManager &) | |
| MorphologicalSegmentorPipelineManager & | operator= (const MorphologicalSegmentorPipelineManager &) |
Detailed Description
Class to contain all the ITK/MITK logic for the MIDAS Morphological Segmentor pipeline, to separate from MorphologicalSegmentationView to make unit testing easier.
This pipeline implements the paper:
"Interactive algorithms for the segmentation and quantification of 3-D MRI brain scans" by P. A. Freeborough, N. C. Fox and R. I. Kitney, published in Computer Methods and Programs in Biomedicine 53 (1997) 15-25.
- See also
- niftkBaseSegmentorController
- MorphologicalSegmentationView
- MorphologicalSegmentorPipeline
- MorphologicalSegmentorPipelineInterface
- MorphologicalSegmentorPipelineParams
Constructor & Destructor Documentation
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Member Function Documentation
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For any binary image, we return true if the property midas.morph.stage is present, and false otherwise.
| void niftk::MorphologicalSegmentorPipelineManager::ClearWorkingData | ( | ) |
Clears both images of the working data.
| void niftk::MorphologicalSegmentorPipelineManager::DestroyPipeline | ( | mitk::Image::Pointer | segmentation | ) |
Completely removes the current pipeline.
| void niftk::MorphologicalSegmentorPipelineManager::FinalizeSegmentation | ( | ) |
Copies the final image out of the pipeline, and then disconnects the pipeline to stop it updating.
| mitk::DataStorage::Pointer niftk::MorphologicalSegmentorPipelineManager::GetDataStorage | ( | ) | const |
Gets the DataStorage pointer from this object.
| void niftk::MorphologicalSegmentorPipelineManager::GetPipelineParamsFromSegmentationNode | ( | MorphologicalSegmentorPipelineParams & | params | ) | const |
Finds the segmentation node, and if present will populate params with the parameters found on the segmentation node.
| mitk::Image::ConstPointer niftk::MorphologicalSegmentorPipelineManager::GetReferenceImage | ( | ) | const |
Retrieves the reference image from the tool manager.
| mitk::Image::Pointer niftk::MorphologicalSegmentorPipelineManager::GetSegmentationImage | ( | ) | const |
Used to retrieve the segmentation image.
| mitk::DataNode::Pointer niftk::MorphologicalSegmentorPipelineManager::GetSegmentationNode | ( | ) | const |
Used to retrieve the actual node of the image being segmented.
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Assumes input is a valid working node, then searches for a binary parent node, returns NULL if not found.
| mitk::ToolManager::Pointer niftk::MorphologicalSegmentorPipelineManager::GetToolManager | ( | ) | const |
Gets the mitk::ToolManager from this object.
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Assumes input is a valid segmentation node, then searches for the derived children of the node, looking for binary images called SUBTRACTIONS_NAME and ADDITIONS_NAME. Returns empty list if both not found.
| mitk::Image::Pointer niftk::MorphologicalSegmentorPipelineManager::GetWorkingImage | ( | unsigned int | dataIndex | ) | const |
Used to retrieve the working image from the tool manager.
| bool niftk::MorphologicalSegmentorPipelineManager::HasSegmentationNode | ( | ) | const |
Returns true if the segmentation node can be found which implicitly means we are "in progress".
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For Morphological Editing, a Segmentation image should have a grey scale parent, and two binary children called SUBTRACTIONS_NAME and ADDITIONS_NAME.
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virtual |
For Morphological Editing, a Working image should be called either SUBTRACTIONS_NAME and ADDITIONS_NAME, and have a binary image parent.
| niftk::MorphologicalSegmentorPipelineManager::mitkClassMacroItkParent | ( | MorphologicalSegmentorPipelineManager | , |
| itk::Object | |||
| ) |
| void niftk::MorphologicalSegmentorPipelineManager::OnDilationsValuesChanged | ( | double | lowerPercentage, |
| double | upperPercentage, | ||
| int | numberOfDilations | ||
| ) |
Sets the conditional dilation parameters.
- Parameters
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lowerPercentage the lower percentage of the mean intensity value within the current region of interest, below which voxels are not dilated. upperPercentage the upper percentage of the mean intensity value within the current region of interest, below which voxels are not dilated. numberOfDilations the number of dilation iterations to perform
| void niftk::MorphologicalSegmentorPipelineManager::OnErosionsValuesChanged | ( | double | upperThreshold, |
| int | numberOfErosions | ||
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Sets the conditional erosion parameters.
- Parameters
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upperThreshold the highest greyscale intensity value, above which the binary volume is not eroded numberOfErosions the number of erosion iterations to perform
Sets the re-thresholding parameters.
- Parameters
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boxSize the size of the re-thresholding box (see paper).
Called when we step to another stage of the pipeline, either fore or backwards.
- Parameters
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stage the new stage where we stepped to
| void niftk::MorphologicalSegmentorPipelineManager::OnThresholdingValuesChanged | ( | double | lowerThreshold, |
| double | upperThreshold, | ||
| int | axialSliceNumber | ||
| ) |
Sets the thresholding parameters.
- Parameters
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lowerThreshold the lowest intensity value included in the segmentation upperThreshold the upper intensity value included in the segmentation axialSliceNumber the number of the first slice, counting from the inferior end of the imaging volume to include in the imaging volume.
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| void niftk::MorphologicalSegmentorPipelineManager::RemoveWorkingData | ( | ) |
Removes the images we are using for editing during connection breaker from the DataStorage.
| void niftk::MorphologicalSegmentorPipelineManager::SetDataStorage | ( | mitk::DataStorage::Pointer | dataStorage | ) |
Sets the mitk::DataStorage on this object.
| void niftk::MorphologicalSegmentorPipelineManager::SetSegmentationNodePropsFromReferenceImage | ( | ) |
Looks up the reference image, and sets default property values onto the segmentation node, which are later used to update GUI controls.
| void niftk::MorphologicalSegmentorPipelineManager::SetToolManager | ( | mitk::ToolManager::Pointer | toolManager | ) |
Sets the mitk::ToolManager on this object.
| void niftk::MorphologicalSegmentorPipelineManager::UpdateSegmentation | ( | ) |
Calls update on the ITK pipeline using the MITK AccessByItk macros.
Note: We pass NULLs to the pipeline for the inputs that have not been changed. This is to avoid unnecessary conversions.
Note:
We have to set the IgnoreLock option on the read accessors here, so that the paintbrush tool can apply its write lock on the same images. Here, we keep smart pointers to these images throughout the life of the pipeline. Releasing the smart pointers would result in releasing the read lock (and therefore no conflict with the paintbrush tool) but it would also mean that we need to re-connect the pipeline over and over again and we would need to re-execute filters even if their input images have not changed. (The whole pipeline approach would become senseless.)
As we are bypassing the locking mechanism, we must ensure it by the GUI logic that the paintbrush interactor and the pipeline update are not working at the same time.
Member Data Documentation
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A static string, (to avoid code duplication), to hold the name of the property that determines if a morphological segmentation is finished.
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The output of the previous stage of the segmentation pipeline.
The documentation for this class was generated from the following files:
