Package qupath.imagej.detect.cells
Class SubcellularDetection
java.lang.Object
qupath.lib.plugins.AbstractPlugin<BufferedImage>
qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>
qupath.imagej.detect.cells.SubcellularDetection
- All Implemented Interfaces:
PathInteractivePlugin<BufferedImage>
,PathPlugin<BufferedImage>
Experimental plugin to help with the quantification of subcellular structures.
- Author:
- Pete Bankhead
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Field Summary
Fields inherited from class qupath.lib.plugins.AbstractInteractivePlugin
params
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
addRunnableTasks
(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
<PathObject> getParentObjects
(ImageData<BufferedImage> imageData) Get a collection of objects to process, based on the contents of the PluginRunner.Collection
<Class<? extends PathObject>> Get a collection of possible parent objects that the plugin could have.boolean
runPlugin
(TaskRunner taskRunner, ImageData<BufferedImage> imageData, String arg) Run the plugin.Methods inherited from class qupath.lib.plugins.AbstractInteractivePlugin
alwaysPromptForObjects, getLoggableParameters, getParameterList, parseArgument
Methods inherited from class qupath.lib.plugins.AbstractPlugin
addWorkflowStep, getTasks, postprocess, preprocess, rearrangeByStride, requestHierarchyUpdate
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Constructor Details
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SubcellularDetection
public SubcellularDetection()
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Method Details
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runPlugin
Description copied from interface:PathPlugin
Run the plugin. A PluginRunner may be provided that this plugin can use to update the user on its progress.Note: This command should block until it has completed processing.
- Specified by:
runPlugin
in interfacePathPlugin<BufferedImage>
- Overrides:
runPlugin
in classAbstractPlugin<BufferedImage>
- Parameters:
taskRunner
-arg
-- Returns:
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addRunnableTasks
protected void addRunnableTasks(ImageData<BufferedImage> imageData, PathObject parentObject, List<Runnable> tasks) Description copied from class:AbstractPlugin
For 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:
addRunnableTasks
in classAbstractPlugin<BufferedImage>
- Parameters:
imageData
-parentObject
-tasks
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getDefaultParameterList
Description copied from class:AbstractInteractivePlugin
This should return a default ParameterList containing any information that is needed to repeat the task exactly.- Specified by:
getDefaultParameterList
in interfacePathInteractivePlugin<BufferedImage>
- Specified by:
getDefaultParameterList
in classAbstractInteractivePlugin<BufferedImage>
- Parameters:
imageData
-- Returns:
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getName
Description copied from interface:PathPlugin
Get 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.
- Returns:
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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:PathPlugin
Get a brief description of the plugin's purpose & operation.If no description is provided, this may return null.
- Returns:
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getParentObjects
Description copied from class:AbstractPlugin
Get a collection of objects to process, based on the contents of the PluginRunner. This could (for example) return the selected object, the root object, all detection objects... depending upon what the plugin does. Each object this returns will be passed to addRunnableTasks to create a task to run. In practice, this method can be overridden to return anything/nothing if getTasks is overridden instead.- Specified by:
getParentObjects
in classAbstractPlugin<BufferedImage>
- Parameters:
imageData
-- Returns:
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getSupportedParentObjectClasses
Description copied from interface:PathInteractivePlugin
Get 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.- Returns:
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