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A

actionApplyDisplay - Variable in class qupath.ext.biop.BIOPExtension.DisplayCommands
 
addMetadataToProject(Project<BufferedImage>, File) - Static method in class qupath.ext.biop.utils.Results
Conveniently add a bunch of metadata to each entry in the project
ApplyDisplaySettingsCommand - Class in qupath.ext.biop.commands
 
ApplyDisplaySettingsCommand(QuPathGUI) - Constructor for class qupath.ext.biop.commands.ApplyDisplaySettingsCommand
 

B

BIOPExtension - Class in qupath.ext.biop
 
BIOPExtension() - Constructor for class qupath.ext.biop.BIOPExtension
 
BIOPExtension.DisplayCommands - Class in qupath.ext.biop
Installs the "Apply Display Settings" command

E

expand(PathObject, double, boolean, boolean) - Static method in class qupath.ext.biop.utils.PathUtils
expand, taken from DilateAnnotationPlugin which returns an PathObject expanded or dilated by the given amount in pixels

G

getAllMeasurements() - Static method in class qupath.ext.biop.utils.Results
Returns all the measurements available in QuPath for the all pathObjects Then we can use things like getStringValue() and getDoubleValue()
getAllMeasurements(List<PathObject>) - Static method in class qupath.ext.biop.utils.Results
Creates an ObservableMeasurementTableData for the requested PathObjects
getAreaMicrons(PathObject) - Static method in class qupath.ext.biop.utils.PathUtils
returns the area of the current PathObject in calibrated units.
getDescription() - Method in class qupath.ext.biop.BIOPExtension
 
getFullImageAnnotation() - Static method in class qupath.ext.biop.utils.PathUtils
returns a rectangle with the whole dataset as an annotation.
getName() - Method in class qupath.ext.biop.BIOPExtension
 
getQuPathVersion() - Method in class qupath.ext.biop.BIOPExtension
 
getRepository() - Method in class qupath.ext.biop.BIOPExtension
 
getVersion() - Method in class qupath.ext.biop.BIOPExtension
 

I

installExtension(QuPathGUI) - Method in class qupath.ext.biop.BIOPExtension
 

M

makePieChart(String, Map<PathClass, Double>, PathObject) - Static method in class qupath.ext.biop.utils.PathUtils
Creates a series of detections as pie chart elements that are added to the provided parent object
merge(List<PathObject>) - Static method in class qupath.ext.biop.utils.PathUtils
Merge all PathObjects into a single PathObject

P

PathUtils - Class in qupath.ext.biop.utils
 
PathUtils() - Constructor for class qupath.ext.biop.utils.PathUtils
 

Q

qupath.ext.biop - package qupath.ext.biop
 
qupath.ext.biop.commands - package qupath.ext.biop.commands
 
qupath.ext.biop.utils - package qupath.ext.biop.utils
 

R

Results - Class in qupath.ext.biop.utils
Convenience class to export results only for the selected objects.
Results() - Constructor for class qupath.ext.biop.utils.Results
 
run() - Method in class qupath.ext.biop.commands.ApplyDisplaySettingsCommand
 

S

sendResultsToFile(ArrayList<String>, ArrayList<PathObject>) - Static method in class qupath.ext.biop.utils.Results
 
sendResultsToFile(ArrayList<String>, ArrayList<PathObject>, File) - Static method in class qupath.ext.biop.utils.Results
By making use of ObservableMeasurementTableData, we can query each result and get a string back Works, for area, PathClasses, parents, and of course any other measurement in the final table
sendResultsToFile(ArrayList<PathObject>) - Static method in class qupath.ext.biop.utils.Results
 

U

um - Static variable in class qupath.ext.biop.utils.Results
 
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