Groovy - How to access area value for an annotation?

[Carlos Moro]

Hello,

When trying .getArea() in a ROI object for an annotation, I can't see the method, even in (https://github.com/qupath/qupath/blob/master/qupath-core/src/main/java/qupath/lib/roi/interfaces/ROI.java).

This is the snippet I'm trying:

def detectedRegions = QP.getAnnotationObjects()  

println "Number of detected regions $detectecRegions.size"

def regionAreas = []

for (aRegion in detectedRegions) {

regionsAreas << aRegion.getROI().getArea() // Doesn't work

}

Best wishes,

Carlos

[micros...@gmail.com]

I am not exactly sure about this but... I used the following to get close to what I think you want.

First, this quick script from Pete helps me a lot when looking at these kinds of problems 

// Get an object... any object

def myObject = getSelectedROI()

// An alternative below; this would show what's available with Ctrl+space in the script editor

// def myObject = new qupath.lib.scripting.QPEx()

// Print the methods you can have access to

for (m in myObject.getClass().getMethods()){

    println(m)

}

The following also seems to work for a single selected AWT Area in my project

def selected = getSelectedObject()

def area = selected.getROI().getArea()

println(area)

Finally, changing the code to the following works for me, so I think the problem is in the list you are creating, or writing to the list.  Unfortunately I am not all that good at Groovy so I cannot nail down how to actually make it work.

import qupath.lib.scripting.QP

def regionAreas = 0

for (def aRegion : QP.getAnnotationObjects()) {

regionsAreas = aRegion.getROI().getArea() 

println(regionsAreas)

}

That script should go through all of your areas and print them...  I did have to include the imported library for this to work.

[micros...@gmail.com]

Oh, actually I think the problem was just that you have regionsAreas in one place and regionAreas in another!

[Carlos Moro]

Thanks a lot! Yes, it worked  :)

Problem was not the typo but I couldn't see the method getArea() recognized by the IDE (Eclipse). I shall give a try IntellliJ as recommended O:)

Running the handy script to see the methods made it clear: 

"INFO: public double qupath.lib.roi.PolygonROI.getArea()"

This method is not defined in interface ROI returned by (getROI) but in class PolygonROI. 

I wasn't aware of differences between Java and Groovy, the latter finds methods defined for an object without need to be specified in every interface  ;)

Best wishes,

Carlos

[micros...@gmail.com]

Oh nice!  I am still trying to get Eclipse set up so that I can tinker, but have not been very successful with it yet.  I will keep that in mind once I do.

[Carlos Moro]

Works very well!  I have collected a series of screenshots illustrating how to set up Eclipse for QuPath (groovy) scripting, I'll upload in a thread very soon!  ;)

Best wishes,

Carlos

[Pete]

Hi,

To explain a bit: the ROI interface doesn’t include getArea(), but the PathArea interface does.  PolygonROI implements the both.

The idea was that some ROIs might not have an area… i.e. a LineROI.  So if you wanted to be extra careful, you could check

if (roi instanceof PathArea)

before requesting the area…. or else just assume that it will probably work and carry on without the cast (Groovy doesn’t insist on it).

However, one warning: getArea() is defined in terms of pixels!  It is a property of the ROI, which doesn’t know anything at all about the image it is part of.  The aim was to keep the ROI class as simple as possible.

With that in mind you might actually want to use the

getScaledArea(double pixelWidth, double pixelHeight)

method.

It's a bit more effort; you could hard-code the pixel sizes if you know them to be constant, or query them in the script.

Here’s a demonstration to show it in action:

def imageData = getCurrentImageData()

def server = imageData.getServer()

def pixelWidthMicrons = server.getPixelWidthMicrons()

def pixelHeightMicrons = server.getPixelHeightMicrons()

def roi = getSelectedROI()

def areaPixels = roi.getArea()

def areaPixels2 = roi.getScaledArea(1, 1)

def areaMicrons = roi.getScaledArea(pixelWidthMicrons, pixelHeightMicrons)

def areaMM = roi.getScaledArea(pixelWidthMicrons/1000, pixelHeightMicrons/1000)

println "Area in pixels: " + areaPixels

println "Scaled area in pixels: " + areaPixels2

println "Area in microns: " + areaMicrons

println "Area in mm: " + areaMM

[Pete]

Oh, and this link could be useful:

http://groovy-lang.org/differences.html

It describes some of the differences between Groovy and Java.  Number 2 (Multi-Methods) is especially relevant.  I remember that Java's behavior in this surprised me in the past... and Groovy handles things a bit differently.

[Carlos Moro]

Hi Pete,

Thanks a lot, very useful and interesting!

Best wishes,

Carlos