Package qupath.imagej.detect.tissue
Class SimpleTissueDetection2
java.lang.Object
qupath.lib.plugins.AbstractPlugin<T>
qupath.lib.plugins.AbstractInteractivePlugin<T>
qupath.lib.plugins.AbstractDetectionPlugin<BufferedImage>
qupath.imagej.detect.tissue.SimpleTissueDetection2
- All Implemented Interfaces:
PathInteractivePlugin<BufferedImage>,PathPlugin<BufferedImage>
Very basic global thresholding command to identify tissue regions.
Uses fixed approach to downsampling images & global threshold applied to RGB images only.
TODO: Provide choice of channels to threshold
TODO: Support 16-bit data
- Author:
- Pete Bankhead
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected voidaddRunnableTasks(ImageData<BufferedImage> imageData, PathObject parentObject, List<Runnable> tasks) For a specified parent object, generate a task to run.getDefaultParameterList(ImageData<BufferedImage> imageData) This should return a default ParameterList containing any information that is needed to repeat the task exactly.Get a brief description of the plugin's purpose & operation.(Optional) short one-line description of the results, e.g.getName()Get the name of the plugin for display.protected Collection<? extends PathObject>getParentObjects(ImageData<BufferedImage> imageData) Get all selected objects that are instances of a supported class.Collection<Class<? extends PathObject>>Get a collection of possible parent objects that the plugin could have.Methods inherited from class qupath.lib.plugins.AbstractInteractivePlugin
alwaysPromptForObjects, getLoggableParameters, getParameterList, parseArgumentMethods inherited from class qupath.lib.plugins.AbstractPlugin
addWorkflowStep, getTasks, postprocess, preprocess, rearrangeByStride, requestHierarchyUpdate, runPluginMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface qupath.lib.plugins.PathPlugin
runPlugin
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Constructor Details
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SimpleTissueDetection2
public SimpleTissueDetection2()Constructor.
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Method Details
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getDefaultParameterList
Description copied from class:AbstractInteractivePluginThis should return a default ParameterList containing any information that is needed to repeat the task exactly.- Specified by:
getDefaultParameterListin interfacePathInteractivePlugin<BufferedImage>- Specified by:
getDefaultParameterListin classAbstractInteractivePlugin<BufferedImage>- Returns:
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getName
Description copied from interface:PathPluginGet the name of the plugin for display.This should be descriptive and, above all, short - as it may be used for menu item names & dialog box titles.
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getLastResultsDescription
Description copied from interface:PathPlugin(Optional) short one-line description of the results, e.g. to say how many objects detected. GUIs may choose to display this on a label during interactive processing.- Returns:
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getDescription
Description copied from interface:PathPluginGet a brief description of the plugin's purpose & operation.If no description is provided, this may return null.
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addRunnableTasks
protected void addRunnableTasks(ImageData<BufferedImage> imageData, PathObject parentObject, List<Runnable> tasks) Description copied from class:AbstractPluginFor a specified parent object, generate a task to run. In practice, this method can be overridden to return anything/nothing if getTasks is overridden instead.- Specified by:
addRunnableTasksin classAbstractPlugin<BufferedImage>
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getParentObjects
Description copied from class:AbstractDetectionPluginGet all selected objects that are instances of a supported class.- Overrides:
getParentObjectsin classAbstractDetectionPlugin<BufferedImage>- Returns:
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getSupportedParentObjectClasses
Description copied from interface:PathInteractivePluginGet a collection of possible parent objects that the plugin could have. This may be used, for example, to specified that analysis may be applied to any/all TMA cores or annotations. If no parent objects are required, PathRootObject.class should be returned in the list.- Specified by:
getSupportedParentObjectClassesin interfacePathInteractivePlugin<BufferedImage>- Overrides:
getSupportedParentObjectClassesin classAbstractDetectionPlugin<BufferedImage>- Returns:
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