From 1b20330e54e2e1cc7e88d4ffc2bca5d73f0a2bb6 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Thu, 18 May 2017 13:42:38 -0400
Subject: [PATCH] ENH: Try using Python instead of Groovy

---
 src/imagej_open.groovy | 54 -----------------------------------------
 src/imagej_open.py     | 55 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 55 insertions(+), 54 deletions(-)
 delete mode 100644 src/imagej_open.groovy
 create mode 100644 src/imagej_open.py

diff --git a/src/imagej_open.groovy b/src/imagej_open.groovy
deleted file mode 100644
index f5c09e4..0000000
--- a/src/imagej_open.groovy
+++ /dev/null
@@ -1,54 +0,0 @@
-/**
- * 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")
diff --git a/src/imagej_open.py b/src/imagej_open.py
new file mode 100644
index 0000000..9c41b69
--- /dev/null
+++ b/src/imagej_open.py
@@ -0,0 +1,55 @@
+# @DatasetIOService ds
+# @UIService ui
+# @File(label="Raw images directory", description="Images path", style="directory", value="/share/Pariksheet/consultations/rnai-screen-tf/results/z_projection") path
+# @String(label="Plate name", choices={"160415_015529-V", "501B102", "502B98", "503B99", "507B99"}) plate
+# @String(label="Well", value="C03") well
+# @OUTPUT Dataset image
+
+# It looks like the only "ImageJ2" way of opening a single-TIFF
+# image series is using the big data viewer:
+# http://forum.imagej.net/t/wrap-imageplus-virtualstack-into-imglib2/4154/10
+# The big data viewer VirtualStackImageLoader requires an ImagePlus as input.
+
+# Open the image stack and convert to hyperstack
+import glob
+import os.path
+
+files = glob.glob(os.path.join(str(path), "{}_{}*".format(plate, well)))
+files.sort()
+# There doesn't seem to be a trivial way to read multiple files.
+#ims = [ds.open(filename) for filename in files]
+#print(type(ims[0]))
+from io.scif.config import SCIFIOConfig
+from io.scif.img import ImgOpener
+#from io.scif import SCIFIO
+import net.imagej.ImageJ as ij
+
+config = (
+    SCIFIOConfig()
+    .groupableSetGroupFiles(True)
+)
+im = ds.open(files[0], config)
+print(im)
+#ds = ij.scifio()#.datasetIO().open(files[0], config);
+#im = ImgOpener().openImg(files[0], config)
+#print(dir(im))
+#print(im.metadata.getImageCount())
+
+#scifio = SCIFIO()
+#reader = scifio.initializer().initializeReader(files[0])
+#print(reader.getMetadata().getImageCount())
+
+#from ij import IJ, WindowManager
+#IJ.run("Image Sequence...",
+#       "open={path} file={pattern} sort".format(
+#       path=path, pattern="{}_{}".format(plate, well)))
+#im = WindowManager.getCurrentImage()
+#IJ.run("Stack to Hyperstack...",
+#       "order=xyctz channels=3 slices=1 frames={frames} display=Composite".format(
+#       frames=im.getNSlices() / 3))
+#IJ.Stack.setActiveChannels("011");
+#IJ.run("Blue");
+#IJ.Stack.setActiveChannels("101");
+#IJ.run("Red");
+#IJ.Stack.setActiveChannels("110");
+#IJ.run("Green");