Index (qupath-extension-biop 3.2.0 API)

A

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
applySettings() - Method in class qupath.ext.biop.commands.ApplyDisplaySettingsCommand

Channels - Class in qupath.ext.biop.utils: Channels class to handle loading and saving channel settings It can modify channels based on either a simple text file or a string of the type position, name, color, minDisplay, maxDisplay eg.
Channels() - Constructor for class qupath.ext.biop.utils.Channels
computeValidation(ObjectClassifier<BufferedImage>, String, String) - Method in class qupath.ext.biop.ml.ObjectClassifierValidation

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
getCurrentChannelSettings() - Static method in class qupath.ext.biop.utils.Channels: Return the current channel names, colors and minMax displays to a list NOTE: Channels that are not currently selected will not be sent
getDescription() - Method in class qupath.ext.biop.BIOPExtension
getName() - Method in class qupath.ext.biop.BIOPExtension
getQuPathVersion() - Method in class qupath.ext.biop.BIOPExtension
getRepository() - Method in class qupath.ext.biop.BIOPExtension

ObjectClassifierValidation - Class in qupath.ext.biop.ml
ObjectClassifierValidation(Project<BufferedImage>) - Constructor for class qupath.ext.biop.ml.ObjectClassifierValidation

readChannelSettings(File) - Static method in class qupath.ext.biop.utils.Channels: Read the settings from a simple text file, generally made using Channels.writeChannelSettings(List, File) but could also be made manually
readChannelSettings(String) - Static method in class qupath.ext.biop.utils.Channels: Read the parameters of a simple string with each line formatted as: position, name, color, minDisplay, maxDisplay eg.
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

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
setChannelSettings(File) - Static method in class qupath.ext.biop.utils.Channels: Set the channels directly from a text file
setChannelSettings(List<Channels.Channel>) - Static method in class qupath.ext.biop.utils.Channels: This method actually sets the channel displays based on the channels list.
show() - Method in class qupath.ext.biop.ml.ObjectClassifierValidation
showAndSave(String) - Method in class qupath.ext.biop.ml.ObjectClassifierValidation

writeChannelSettings(List<Channels.Channel>, File) - Static method in class qupath.ext.biop.utils.Channels: Write the provided Channels to a file