Useful simple commands

describe(aThing)  //to find functions that can be done with/to this object

//Get the name of the current image without its extension. Great for naming export files
name = getCurrentImageNameWithoutExtension() #In earlier versions name = GeneralTools.getNameWithoutExtension(getCurrentImageData().getServer().getMetadata().getName())
fullNameWithExtension = getProjectEntry().getImageName()

//Other methods to get image names - with extension
nameOfImageInViewer = getCurrentViewer().getServer().getFile().getName()
nameOfActiveImage = getProjectEntry().getImageName()

getCurrentHierarchy()
getCurrentViewer()
getCurrentImageData()
getCurrentServer()

//Combine describe and the getCurrent functions to get a better idea of what each represents

//Find the current average pixel size of the image - assumes square sized pixels which is not always the case
double pixelSize = imageData.getServer().getPixelCalibration().getAveragedPixelSize()

//Other useful pixel functions via getPixelCalibration() include
.getAveragedPixelSizeMicrons()
.getPixelHeight()
.getPixelWidth()
.getPixelWidthUnit()
//find even more using describe()

//Generate a list of all classes of detection objects that exist in the current image
classes = PathObjectTools.getRepresentedPathClasses(getCurrentHierarchy(), qupath.lib.objects.PathDetectionObject)

resetSelection()
selectAnnotations()
selectObjectsByClassification("Necrosis", "Tumor");
selectDetections()
selectCells()
selectAllObjects()
selectTMACores()

getCurrentHierarchy().getSelectionModel().setSelectedObject(objectToSelect, true);
getCurrentHierarchy().getSelectionModel().selectObjects(listToSelect);

PathClassifierTools.getAvailableFeatures(getDetectionObjects()).each { println(it) }

removeObject(pathObject) #updated from removeObject(object, true) after 0.6.0rc3
removeObjectAndDescendants(pathObject) # as of 0.6.0
removeSelectedObjects(); #Was clearSelectedObjects();
removeObjects(listOfObjects,true)

addObject(object)
addObjects(listOfObjects)
createFullImageAnnotation(true) #was createSelectAllObject(true), true makes it selected upon creation, false not selected

resolveHierarchy() //try to naturally resolve all objects

//Let the interface know when something has changed, sometimes reclassifications by script will only show up when you zoom in and out, or similar
fireHierarchyUpdate()

//All together:
import qupath.lib.gui.commands.Commands
imageData = getCurrentImageData();
//Select something, see selection macros above, then
Commands.insertSelectedObjectsInHierarchy(imageData)

//Alternatively
someHierarchy.insertPathObjects(collectionOfObjects);
//or
insertObjects(collectionOfObjects)


//Another option for a new set of objects in the variable outsideCells, for example
getCurrentHierarchy().insertPathObjects(outsideCells)


//Add some objects to a particular hierarchy, maybe in another image
otherHierarchy.addPathObjects(objects) //allows you to move objects between images

//Adding detections below other detections - REINSERT SUBCELLULAR DETECTION!!!
getCellObjects().each{

    subcells = getCurrentHierarchy().getObjectsForROI(qupath.lib.objects.PathDetectionObject, it.getROI()).findAll{s->!s.isCell()}
    it.addPathObjects(subcells);
}
fireHierarchyUpdate()

notAString.toString()
string = "50"
double number = string as double
//"number" is now 50.0, a double

object.measurements.put("measurement name", doubleValue)
double cellArea = measurement(cell, "Cell: Area")
cellAreaPixels = cell.getROI().getArea()
nuclearAreaPixels = cell.getNucleusROI().getArea()
//Multiply the above value by the pixel area (pixel height*pixel width) to get the area in microns)

String name = object.getName()
object.setName("SomeString")
def roi = object.getROI()
object.setPathClass(getPathClass("Tumor"))

detections = getDetectionObjects()
annotations = getAnnotationObjects()
cells = getCellObjects()
// example of list.collect{some code that returns something}
listOfAreasFromEachCell = cells.collect{measurement(it, "Nucleus: Area")}
//Returning a single object
selected = getSelectedObject()
//Return children of a selected object - based on hierarchy
children = getSelectedObject().getChildObjects()
//Return all selected objects - this will return a list even if it is a list of 1 object!
selected = getSelectedObjects()

//get ALL objects, excluding the IMAGE ITSELF, which you do get if you use getAllObjects()
everythingAndTheImage=getAllObjectsWithoutRoot()

//all Detections within another object’s ROI (note the getROI() at the end)

objectsInside = getCurrentHierarchy().getObjectsForROI(qupath.lib.objects.PathDetectionObject, objectIWantThingsInsideOf.getROI())

//All child objects of a single selected annotation (in this case) - what you get here can be tricky depending on whether resolveHierarchy() has been run or not

childObjects = getSelectedObject().getChildObjects()

def roi = ROIs.createRectangleROI((x,y,sizeX,sizeY, ImagePlane.getDefaultPlane())
newTiles << PathObjects.createDetectionObject(roi, getPathClass(c))
//
//Some time later
addObjects(newTiles)

//Saving data in an image
getProject().getEntry(getCurrentImageData()).saveImageData(getCurrentImageData())
//Use imageData from a different image
entry = getProject().getImageList().find{it.getImageName() == "CMU-1.svs"}
entryImageData = entry.readImageData()

//do some things to the hierarchy of that image
//e.g. entryImageData().getHierarchy().getAnnotationObjects()
//more code
entry.saveImageData(entryImageData)

def server = getCurrentServer()
def uris = server.getURIs()
def file = new File(uris[0])
println file.getAbsolutePath()

def classifier = loadObjectClassifier(name)
classifier.classifyObjects(imageData, cells, false)