How can I draw a ROI using groovy script?

[Murali S]

I am new to QuPath. I found that its a great tool.

I am having list of xy coordinates like [(x1, y1), (x2, y2), ...]. Now I want to draw a ROI (polygon) for those points through scripting. I am not able to find the correct method to draw it. Please help me to fix this.

Also if possible try to give me an example here. It will be great for me.

Thank you,

Murali S.

[Pete]

There currently isn't a 'helper' method to create the polygon regions of interest very concisely in a script, but there is some information about the steps you need at https://github.com/qupath/qupath/issues/61 

You'll need to import the corresponding Java classes, create your region of interest, create an object to display, and then add the object.

Your script might look something like this:

import qupath.lib.objects.*

import qupath.lib.roi.*

// Any vertices

def x = [100, 200, 300] as float[]

def y = [150, 350, 250] as float[]

// Create object

def roi = new PolygonROI(x, y, -1, 0, 0)

def pathObject = new PathAnnotationObject(roi)

// Add object to hierarchy

addObject(pathObject)

[Murali S]

Thank you Pete. It is the solution for my issue.

[Murali S]

Can we add annotations class for the region while drawing it?

[Pete]

Does the 'Auto set' button (under list of classifications in the Annotations tab) do what you want?

This enables all new annotations to automatically have a specified classification.

[Murali S]

I was on the vacation. I achieved my requirement by using following code.

def r = 255
def g = 0
def b = 0
def className = "Benign"
QP.addObject(new PathAnnotationObject(new PolygonROI(x,y, -1, 0, 0), new PathClass(className,qupath.lib.common.ColorTools.makeRGB(r, g, b))))

Thank you Pete.

Thanks & Regards,

Murali S.

[Pete]

Good that you solved the problem.  Just one thing: the constructor for PathClass is not public, and shouldn't really be used directly (even if Groovy allows it).

Rather, you can obtain PathClass objects using PathClassFactory.getPathClass(String name, Integer color).

This ensures that classifications with the same name are represented by the same object - which is required for some commands to work as expected (e.g. when checking if classifications are equal).