Package ch.epfl.biop.qupath.utils

Class GUIUtils

  • public class GUIUtils
extends qupath.lib.gui.scripting.QPEx
    Here we store a bunch of utility functions that are relevant to QuPath's User interface Like setting colors, lookup tables and such

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String PROJECT_BASE_DIR  

      • Fields inherited from class qupath.lib.scripting.QP

        BRIGHTFIELD_H_DAB, BRIGHTFIELD_H_E, BRIGHTFIELD_OTHER, FLUORESCENCE, OTHER

    • Constructor Summary

      Constructors 
      Constructor Description
      GUIUtils()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static ij.ImagePlus getImagePlus​(qupath.lib.objects.PathObject pathObject, int downsample)  
      static ij.ImagePlus getImagePlus​(qupath.lib.objects.PathObject pathObject, int downsample, boolean includeROI, boolean includeOverlay)  
      static ij.ImagePlus getImagePlus​(qupath.lib.objects.PathObject pathObject, int downsample, boolean includeROI, boolean includeOverlay, boolean doZ, boolean doT)  
      static qupath.lib.images.servers.ImageServer getSelectedChannelsServer​(qupath.lib.images.servers.ImageServer currentServer, java.util.List<java.lang.String> channelNames)  

      • Methods inherited from class qupath.lib.gui.scripting.QPEx

        copyToClipboard, exportTMAData, exportTMAData, getCoreClasses, getCurrentViewer, getQuPath, getWindow, promptForFile, runPlugin, runPlugin, saveAnnotationMeasurements, saveAnnotationMeasurements, saveDetectionMeasurements, saveDetectionMeasurements, saveImageMeasurements, saveImageMeasurements, saveMeasurements, saveMeasurements, saveTMAMeasurements, saveTMAMeasurements, setChannelDisplayRange, setChannelDisplayRange, setChannelDisplayRange, setChannelDisplayRange, writeImage, writeRenderedImage, writeRenderedImage, writeRenderedImageRegion, writeRenderedImageRegion

      • Methods inherited from class qupath.lib.scripting.QP

        addObject, addObjects, addObjects, addPixelClassifierMeasurements, addPixelClassifierMeasurements, addShapeMeasurements, addShapeMeasurements, addShapeMeasurements, buildFilePath, buildServer, buildServer, classifyDetectionsByCentroid, classifyDetectionsByCentroid, classifySelected, classifySelected, clearAllObjects, clearAllObjects, clearAnnotationMeasurements, clearAnnotationMeasurements, clearAnnotations, clearCellMeasurements, clearCellMeasurements, clearDetectionMeasurements, clearDetectionMeasurements, clearDetections, clearMeasurements, clearMeasurements, clearMeasurements, clearMeasurements, clearMeasurements, clearRootMeasurements, clearRootMeasurements, clearSelectedObjects, clearSelectedObjects, clearTileMeasurements, clearTileMeasurements, clearTMACoreMeasurements, clearTMACoreMeasurements, clearTMAGrid, createAnnotationsFromPixelClassifier, createAnnotationsFromPixelClassifier, createDetectionsFromPixelClassifier, createDetectionsFromPixelClassifier, createSelectAllObject, createSelectAllObject, describe, describe, deselectAll, deselectAll, detectionCentroidDistances, detectionCentroidDistances, detectionCentroidDistances, detectionToAnnotationDistances, detectionToAnnotationDistances, detectionToAnnotationDistances, duplicateSelectedAnnotations, fileExists, fireHierarchyUpdate, fireHierarchyUpdate, getAllObjects, getAnnotationObjects, getAnnotationObjectsAsArray, getBasePathClass, getCellObjects, getColorRGB, getCurrentHierarchy, getCurrentImageData, getCurrentServer, getCurrentServerPath, getDerivedPathClass, getDerivedPathClass, getDetectionObjects, getDetectionObjectsAsArray, getNonIntensityAncestorPathClass, getObjects, getObjects, getPathClass, getPathClass, getProject, getProjectEntry, getProjectEntryMetadataValue, getSelectedObject, getSelectedObjects, getSelectedROI, getTMACoreList, hasMeasurement, insertObjects, insertObjects, isDirectory, isTMADearrayed, loadImageData, loadObjectClassifier, loadPixelClassifier, makeInverseAnnotation, makeInverseAnnotation, makeInverseAnnotation, makeInverseAnnotation, makeInverseAnnotation, measurement, mergeAnnotations, mergeAnnotations, mergePointsForAllClasses, mergePointsForSelectedObjectClasses, mergeSelectedAnnotations, mergeSelectedAnnotations, mkdirs, nObjects, relabelTMAGrid, relabelTMAGrid, removeMeasurements, removeMeasurements, removeObject, removeObjects, removeObjects, replaceClassification, replaceClassification, replaceClassification, replaceClassification, resetBatchProjectAndImage, resetClassifications, resetClassifications, resetDetectionClassifications, resetIntensityClassifications, resetIntensityClassifications, resetIntensityClassifications, resetSelection, resetTMAMetadata, resetTMAMetadata, resolveHierarchy, resolveHierarchy, resolvePath, runClassifier, runClassifier, runClassifier, runObjectClassifier, runObjectClassifier, selectAnnotations, selectAnnotations, selectCells, selectCells, selectDetections, selectDetections, selectObjects, selectObjects, selectObjects, selectObjects, selectObjects, selectObjects, selectObjectsByClass, selectObjectsByClass, selectObjectsByClassification, selectObjectsByClassification, selectObjectsByMeasurement, selectObjectsByPathClass, selectObjectsByPathClass, selectTiles, selectTiles, selectTMACores, selectTMACores, selectTMACores, selectTMACores, setBatchProjectAndImage, setCellIntensityClassifications, setCellIntensityClassifications, setChannelColors, setChannelColors, setChannelNames, setChannelNames, setChannels, setChannels, setColorDeconvolutionStains, setDetectionIntensityClassifications, setDetectionIntensityClassifications, setImageType, setImageType, setIntensityClassifications, setIntensityClassifications, setIntensityClassifications, setIntensityClassificationsForSelected, setPixelSizeMicrons, setPixelSizeMicrons, setPixelSizeMicrons, setSelectedObject, writeImage, writeImage, writeImageRegion, writePredictionImage, writePredictionImage

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • PROJECT_BASE_DIR

        public static final java.lang.String PROJECT_BASE_DIR
        See Also:
        Constant Field Values

    • Constructor Detail

      • GUIUtils

        public GUIUtils()

    • Method Detail

      • getImagePlus

        public static ij.ImagePlus getImagePlus​(qupath.lib.objects.PathObject pathObject,
                                        int downsample,
                                        boolean includeROI,
                                        boolean includeOverlay)

      • getImagePlus

        public static ij.ImagePlus getImagePlus​(qupath.lib.objects.PathObject pathObject,
                                        int downsample)

      • getImagePlus

        public static ij.ImagePlus getImagePlus​(qupath.lib.objects.PathObject pathObject,
                                        int downsample,
                                        boolean includeROI,
                                        boolean includeOverlay,
                                        boolean doZ,
                                        boolean doT)

      • getSelectedChannelsServer

        public static qupath.lib.images.servers.ImageServer getSelectedChannelsServer​(qupath.lib.images.servers.ImageServer currentServer,
                                                                              java.util.List<java.lang.String> channelNames)