Package ch.epfl.biop.qupath.utils

Class Utils

java.lang.Object

qupath.lib.scripting.QP

ch.epfl.biop.qupath.utils.Utils

public class Utils
extends qupath.lib.scripting.QP

Utilities for QuPath scripting that make no use of the GUI

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	um

Fields inherited from class qupath.lib.scripting.QP

BRIGHTFIELD_H_DAB, BRIGHTFIELD_H_E, BRIGHTFIELD_OTHER, FLUORESCENCE, OTHER, PROJECT_BASE_DIR

Constructor Summary

Constructors

Constructor	Description
Utils()

Method Summary

Modifier and Type	Method	Description
static qupath.lib.gui.measure.ObservableMeasurementTableData	getAllMeasurements()	Returns all the measurements available in QuPath for the all pathObjects Then we can use things like getStringValue() and getDoubleValue()
static qupath.lib.gui.measure.ObservableMeasurementTableData	getAllMeasurements(java.util.List<qupath.lib.objects.PathObject> pathObjects)	Creates an ObservableMeasurementTableData for the requested PathObjects
static double	getPixelSize()	Returns the current pixel size of the active image in microns
static void	sendResultsToFile(java.util.ArrayList<java.lang.String> resultColumns, java.util.ArrayList<qupath.lib.objects.PathObject> objects)
static void	sendResultsToFile(java.util.ArrayList<java.lang.String> resultColumns, java.util.ArrayList<qupath.lib.objects.PathObject> objects, java.io.File resultsFile)	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
static void	sendResultsToFile(java.util.ArrayList<qupath.lib.objects.PathObject> objects)

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, getCoreClasses, 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, runPlugin, runPlugin, 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

um

public static final java.lang.String um

See Also:

Constant Field Values

Constructor Detail

Utils

public Utils()

Method Detail

sendResultsToFile

public static void sendResultsToFile(java.util.ArrayList<java.lang.String> resultColumns,
                                     java.util.ArrayList<qupath.lib.objects.PathObject> objects,
                                     java.io.File resultsFile)

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

Parameters:

resultColumns - a list of all the results we want to have, exactly the same names as in teh Measurement Results tables

objects - the pathObjects we want to get the measurements from

resultsFile - the file where this tool should write to. Note that if the file exists, it will be appended

See Also:

ObservableMeasurementTableData

sendResultsToFile

public static void sendResultsToFile(java.util.ArrayList<java.lang.String> resultColumns,
                                     java.util.ArrayList<qupath.lib.objects.PathObject> objects)

sendResultsToFile

public static void sendResultsToFile(java.util.ArrayList<qupath.lib.objects.PathObject> objects)

getAllMeasurements

public static qupath.lib.gui.measure.ObservableMeasurementTableData getAllMeasurements()

Returns all the measurements available in QuPath for the all pathObjects Then we can use things like getStringValue() and getDoubleValue()

Returns:

a class that you can use to access the results

See Also:

ObservableMeasurementTableData

getAllMeasurements

public static qupath.lib.gui.measure.ObservableMeasurementTableData getAllMeasurements(java.util.List<qupath.lib.objects.PathObject> pathObjects)

Creates an ObservableMeasurementTableData for the requested PathObjects

Parameters:

pathObjects - a list of PathObjects to compute measurements from

Returns:

an object you can access the results getStringValue() and getDoubleValue()

See Also:

ObservableMeasurementTableData

getPixelSize

public static double getPixelSize()

Returns the current pixel size of the active image in microns

Returns:

the pixel size in um/px