public class SegmentWithMarkedPointProcess extends SegmentIntoMarks
Different operations occur on a set of marks (a configuration), with each operation termed a kernel. These operations can, for example:
Each set of marks has an associated energy, a score determining how desirable it is for the optimization routine. Certain scores are retained according to an optimization-scheme, either deterministically or stochastically, either greedily or with some non-greedy steps.
Constructor and Description |
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SegmentWithMarkedPointProcess() |
Modifier and Type | Method and Description |
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SegmentMarksState |
createExperimentState() |
OutputEnabledMutable |
defaultOutputs()
If specified, default rules for determine which outputs are enabled or not.
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DefineOutputterWithEnergy |
getDefine()
Adds definitions of stacks/objects etc.
|
StackDisplayer |
getDisplayer()
How to convert an image to be displayed to the user.
|
EnergySchemeCreator |
getEnergySchemeCreator()
Creates an energy scheme that assigns an energy score to each collection of marks.
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FeedbackReceiverBean<VoxelizedMarksWithEnergy> |
getFeedbackReceiver()
Processes feedback from the segmentation algorithm for outputting / debugging.
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KernelProposer<VoxelizedMarksWithEnergy,UpdatableMarksList> |
getKernelProposer()
Proposes kernel-changes during iterations of hte marked-point-processes.
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MarkWithIdentifierFactory |
getMarkFactory()
Creates a new mark, before perhaps further manipulations by a kernel.
|
OptimizationScheme<VoxelizedMarksWithEnergy,VoxelizedMarksWithEnergy,UpdatableMarksList> |
getOptimization()
The optimization-scheme that determines which configurations are accepted/rejected from one
iteration to the next.
|
boolean |
isExitBeforeOptimization()
Iff true the algorithm exits before optimization begins (useful for debugging).
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boolean |
isFixRandomSeed()
Iff true uses a constant seed for the random-number-generator (useful for debugging).
|
MarkCollection |
segment(SharedObjects sharedObjects,
Optional<Dictionary> dictionary,
InputOutputContext context) |
void |
setDefine(DefineOutputterWithEnergy define)
Adds definitions of stacks/objects etc.
|
void |
setDisplayer(StackDisplayer displayer)
How to convert an image to be displayed to the user.
|
void |
setEnergySchemeCreator(EnergySchemeCreator energySchemeCreator)
Creates an energy scheme that assigns an energy score to each collection of marks.
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void |
setExitBeforeOptimization(boolean exitBeforeOptimization)
Iff true the algorithm exits before optimization begins (useful for debugging).
|
void |
setFeedbackReceiver(FeedbackReceiverBean<VoxelizedMarksWithEnergy> feedbackReceiver)
Processes feedback from the segmentation algorithm for outputting / debugging.
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void |
setFixRandomSeed(boolean fixRandomSeed)
Iff true uses a constant seed for the random-number-generator (useful for debugging).
|
void |
setKernelProposer(KernelProposer<VoxelizedMarksWithEnergy,UpdatableMarksList> kernelProposer)
Proposes kernel-changes during iterations of hte marked-point-processes.
|
void |
setMarkFactory(MarkWithIdentifierFactory markFactory)
Creates a new mark, before perhaps further manipulations by a kernel.
|
void |
setOptimization(OptimizationScheme<VoxelizedMarksWithEnergy,VoxelizedMarksWithEnergy,UpdatableMarksList> optimization)
The optimization-scheme that determines which configurations are accepted/rejected from one
iteration to the next.
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getBackgroundStackName, setBackgroundStackName
checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString
public SegmentMarksState createExperimentState()
createExperimentState
in class SegmentIntoMarks
public MarkCollection segment(SharedObjects sharedObjects, Optional<Dictionary> dictionary, InputOutputContext context) throws SegmentationFailedException
segment
in class SegmentIntoMarks
SegmentationFailedException
public OutputEnabledMutable defaultOutputs()
SegmentIntoMarks
defaultOutputs
in class SegmentIntoMarks
public OptimizationScheme<VoxelizedMarksWithEnergy,VoxelizedMarksWithEnergy,UpdatableMarksList> getOptimization()
public void setOptimization(OptimizationScheme<VoxelizedMarksWithEnergy,VoxelizedMarksWithEnergy,UpdatableMarksList> optimization)
public MarkWithIdentifierFactory getMarkFactory()
public void setMarkFactory(MarkWithIdentifierFactory markFactory)
public EnergySchemeCreator getEnergySchemeCreator()
public void setEnergySchemeCreator(EnergySchemeCreator energySchemeCreator)
public KernelProposer<VoxelizedMarksWithEnergy,UpdatableMarksList> getKernelProposer()
public void setKernelProposer(KernelProposer<VoxelizedMarksWithEnergy,UpdatableMarksList> kernelProposer)
public FeedbackReceiverBean<VoxelizedMarksWithEnergy> getFeedbackReceiver()
public void setFeedbackReceiver(FeedbackReceiverBean<VoxelizedMarksWithEnergy> feedbackReceiver)
public DefineOutputterWithEnergy getDefine()
public void setDefine(DefineOutputterWithEnergy define)
public boolean isExitBeforeOptimization()
public void setExitBeforeOptimization(boolean exitBeforeOptimization)
public boolean isFixRandomSeed()
Otherwise, the random-number-generator seeds from the system clock.
public void setFixRandomSeed(boolean fixRandomSeed)
Otherwise, the random-number-generator seeds from the system clock.
public StackDisplayer getDisplayer()
public void setDisplayer(StackDisplayer displayer)
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.