From 231559b97cb761f0a16dd6113d0dc447d5b8e904 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Thu, 18 May 2017 13:41:54 -0400
Subject: [PATCH] ENH: Play around with ImageJ groovy opener

---
 src/imagej_open.groovy | 47 +++++++++++++++++++++++++++++++++++-------
 1 file changed, 40 insertions(+), 7 deletions(-)

diff --git a/src/imagej_open.groovy b/src/imagej_open.groovy
index 5315bfc..f5c09e4 100644
--- a/src/imagej_open.groovy
+++ b/src/imagej_open.groovy
@@ -1,7 +1,21 @@
+/**
+ * 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 = "/share/Pariksheet/consultations/rnai-screen-tf"
+def prefix_project = "/share/Pariksheet/consultations/rnai-screen-tf"
 
 /**
  * Read a stack of raw images.
@@ -9,13 +23,32 @@ def prefix = "/share/Pariksheet/consultations/rnai-screen-tf"
  * @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 dirBg = new File("$prefix/results/z_projection")
-	def found = []
-	dirBg.eachFileMatch(FileType.FILES, ~/${plate}_${well}_.+/) {
-		found << it.name
+def open = { String plate, String well ->
+	def opener = new FolderOpener()
+	opener.run()
+
+	// Build a list of the relevant image files.
+	def dirBg = new File( "${prefix_project}/results/z_projection" )
+	def files = []
+	dirBg.eachFileMatch( FileType.FILES, ~/${plate}_${well}_.+/ ) {
+		files << it.name
 	}
-	println found
+	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")