Index (qupath-extension-biop 1.1.0 API)

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

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

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

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

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.
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
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

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

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.

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