imagej_open.groovy

/**
 * Overlay CellProfiler ROIs.
 *
 * Uses ImageJ2 libraries whereever possible.
 */

import groovy.io.FileType // Recurse directories per http://stackoverflow.com/a/3954639
//import ij.io.Opener
//import io.scif.SCIFIO

import ij.plugin.FolderOpener

import io.scif.img.ImgOpener

import net.imglib2.img.display.imagej.ImageJFunctions

/** Path to project Git repo */
def prefix_project = "/share/Pariksheet/consultations/rnai-screen-tf"

/**
 * Read a stack of raw images.
 * 
 * @param plate name of the plate to match
 * @param well name of the well in [A-P][01-24] format
 */
def open = { String plate, String well ->
	def opener = new FolderOpener()
	opener.run()

	// Build a list of the relevant image files.
	def dirBg = new File( "${prefix_project}/results/z_projection" )
	def files = []
	dirBg.eachFileMatch( FileType.FILES, ~/${plate}_${well}_.+/ ) {
		files << it.name
	}
	paths = files.collect { "${dirBg}/${it}" }

	//def imp = new Opener().openImage("${prefix}")

	// Open the images as a stack per the scifio tutorial
	// https://github.com/scifio/scifio-tutorials
	//def scifio = new SCIFIO()
	//def reader = scifio.initializer().initializeReader(paths[0])
	//reader.getClass().getMethods().each {println it}

	// Open using imglib2 ImgOpener() as described in wiki examples
	// http://imagej.net/ImgLib2_Examples
	def imgOpener = new ImgOpener()
	def im = imgOpener.openImg( paths[0] )
	//ImageJFunctions.show( im )
	//println im
}

open("160415_015529-V", "C03")