petebankhead

/**
 * Groovy script to convert a binary image into one in which every foreground pixel
 * has a value equal to the area of the (8-connected) region containing it.
 *
 * Why?
 *
 * Well, this gives a way to apply an area-based threshold quickly and intuitively.
 * Simply set a threshold on the area map, and apply it to create a new binary image.
 *
 * Created by Pete on 22/11/2016.

petebankhead

/**
 * Testing different methods of accessing pixel values from
 * an ImageProcessor within ImageJ1.
 *
 * (Personally, I prefer getf(x, y)....)
 *
 * Created by Pete on 23/11/2016.
 */

import ij.process.*

petebankhead

/**
 * Export a thumbnail image, with and without an overlay, using QuPath.
 *
 * For tissue microarrays, the scripting code written by the 'File -> Export TMA data'
 * command is probably more appropriate.
 *
 * However, for all other kinds of images where batch export is needed this script can be used.
 *
 * @author Pete Bankhead
 */

petebankhead

/*
 * Sample script to run a GUI command from QuPath v0.1.1
 *
 * @author Pete Bankhead
 */
 

// Specify command to run
// Note: Only the simple name is required if the menu item has a unique name
//       Otherwise, the full path to the menu item should be give, separated by >

petebankhead

/**
 * Simple script to assign metadata values to TMA cores according to row.
 *
 * @author Pete Bankhead
 */


import qupath.lib.scripting.QP

petebankhead

/*
 * Assign a selected annotation to be a child of whichever TMA core contains its centroid.
 * 
 * This can be useful whenever an annotation is drawn *slightly* overlapping the core, 
 * and so is not automatically assigned to be a child of the core - but it should be.
 *
 * @author Pete Bankhead
 */

// Ensure annotation is selected!

petebankhead

// Change this to reflect the path to QuPath!
// Here, I'm using a Mac.
// Note: I copied all native libraries (*.dylib, *.jnilib) into Fiji.app/lib/macos so that they could be found.
def pathQuPath = "/Users/pete/Desktop/QuPath.app/Contents/Java/"

// Get the Groovy classloader
def cl = this.class.classLoader

// Figure out where the main QuPath Jars are to be found
def dirBase = new File(pathQuPath)

petebankhead

// Prompt to get sigma values for the Difference of Gaussians filtering
Dialog.create("Choose filter sizes for DoG filtering");
Dialog.addNumber("Gaussian sigma 1", 1);
Dialog.addNumber("Gaussian sigma 2", 2);
Dialog.show();
sigma1 = Dialog.getNumber();
sigma2 = Dialog.getNumber();

// Get the current image
idOrig = getImageID();

petebankhead

// guiscript=true
def qupath = getQuPath()
def menuItem = qupath.getMenuItem("Automate>Show workflow command history")
menuItem.fire()

/* If guiscript=true is missing from the first line,
 * then menuItem.fire() will fail because it is called on the wrong thread.
 * 
 * In this case, the required syntax would be:
 * 

petebankhead

// Note: This sets the class according to spot/cluster location,
// but does not try to set meaningful colors at this point

// Get all spots/clusters
def clusters = getObjects({p -> p.class == qupath.imagej.detect.cells.SubcellularDetection.SubcellularObject.class})

// Loop through all clusters
for (c in clusters) {
    // Find the containing cell
    def cell = c.getParent()