From 9fa488b95f4fde1543f1318231a53cad80c55a36 Mon Sep 17 00:00:00 2001
From: jean-marie burel <j.burel@dundee.ac.uk>
Date: Thu, 6 Jul 2023 06:47:57 +0100
Subject: [PATCH] Set ROI plane coordinates (#65)

* set plane coordinates
* add null check for test
* Only adjust hyperstack coordinates if they're not already set and the corresponding image can be retrieved
* Add tests
---
 .../igred/omero/roi/GenericShapeWrapper.java  | 41 +++++++++-
 .../fr/igred/omero/roi/ROI2ImageJTest.java    | 74 +++++++++++++++++++
 2 files changed, 112 insertions(+), 3 deletions(-)

diff --git a/src/main/java/fr/igred/omero/roi/GenericShapeWrapper.java b/src/main/java/fr/igred/omero/roi/GenericShapeWrapper.java
index 5c9a4e97..f66d1d5f 100644
--- a/src/main/java/fr/igred/omero/roi/GenericShapeWrapper.java
+++ b/src/main/java/fr/igred/omero/roi/GenericShapeWrapper.java
@@ -22,6 +22,7 @@
 import fr.igred.omero.Client;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
+import ij.ImagePlus;
 import ij.gui.Line;
 import ij.gui.Roi;
 import ij.gui.ShapeRoi;
@@ -136,9 +137,6 @@ static ShapeList fromImageJ(ij.gui.Roi ijRoi) {
      * @param ijRoi An ImageJ Roi.
      */
     protected void copyFromIJRoi(ij.gui.Roi ijRoi) {
-        data.setC(Math.max(-1, ijRoi.getCPosition() - 1));
-        data.setZ(Math.max(-1, ijRoi.getZPosition() - 1));
-        data.setT(Math.max(-1, ijRoi.getTPosition() - 1));
         LengthI size          = new LengthI(ijRoi.getStrokeWidth(), UnitsLength.POINT);
         Color   defaultStroke = Optional.ofNullable(Roi.getColor()).orElse(Color.YELLOW);
         Color   defaultFill   = Optional.ofNullable(Roi.getDefaultFillColor()).orElse(TRANSPARENT);
@@ -147,6 +145,43 @@ protected void copyFromIJRoi(ij.gui.Roi ijRoi) {
         data.getShapeSettings().setStrokeWidth(size);
         data.getShapeSettings().setStroke(stroke);
         data.getShapeSettings().setFill(fill);
+
+        // Set the plane
+        int c = ijRoi.getCPosition();
+        int z = ijRoi.getZPosition();
+        int t = ijRoi.getTPosition();
+
+        // Adjust coordinates if ROI does not have hyperstack positions
+        if (!ijRoi.hasHyperStackPosition()) {
+            ImagePlus imp = ijRoi.getImage();
+            if (imp == null) {
+                imp = ij.WindowManager.getImage(ijRoi.getImageID());
+            }
+            if (imp != null) {
+                int stackSize = imp.getStackSize();
+                int imageC    = imp.getNChannels();
+                int imageZ    = imp.getNSlices();
+                int imageT    = imp.getNFrames();
+                int pos       = ijRoi.getPosition();
+
+                // Reset values
+                c = 1;
+                z = 1;
+                t = 1;
+
+                if (stackSize == imageZ) {
+                    z = pos;
+                } else if (stackSize == imageC) {
+                    c = pos;
+                } else if (stackSize == imageT) {
+                    t = pos;
+                }
+            }
+        }
+
+        data.setC(Math.max(-1, c - 1));
+        data.setZ(Math.max(-1, z - 1));
+        data.setT(Math.max(-1, t - 1));
     }
 
 
diff --git a/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java b/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java
index a8b453a1..36c148e7 100644
--- a/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java
+++ b/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java
@@ -19,6 +19,8 @@
 
 
 import fr.igred.omero.BasicTest;
+import ij.IJ;
+import ij.ImagePlus;
 import ij.gui.Arrow;
 import ij.gui.EllipseRoi;
 import ij.gui.Line;
@@ -457,4 +459,76 @@ void convertPolyline() {
         assertEquals(polyline.getT(), newPolyline.getT());
     }
 
+
+    @Test
+    void convertRectangleWithCStack() {
+        ImagePlus img = IJ.createImage("test", "grayscale", 1000, 1000, 10, 1, 1);
+        int pos = 4;
+        img.setPosition(pos);
+
+        Roi ijRoi = new Roi(10, 10, 10, 10);
+        ijRoi.setPosition(img);
+        ijRoi.setImage(img);
+
+        assertEquals(pos, ijRoi.getPosition());
+
+        List<Roi> roiList = new ArrayList<>(1);
+        roiList.add(ijRoi);
+        ROIWrapper roi = ROIWrapper.fromImageJ(roiList, null).get(0);
+
+        RectangleWrapper newRectangle = roi.getShapes().getElementsOf(RectangleWrapper.class).get(0);
+
+        assertEquals(pos - 1, newRectangle.getC());
+        assertEquals(0, newRectangle.getZ());
+        assertEquals(0, newRectangle.getT());
+    }
+
+
+    @Test
+    void convertRectangleWithZStack() {
+        ImagePlus img = IJ.createImage("test", "grayscale", 1000, 1000, 1, 10, 1);
+        int pos = 5;
+        img.setPosition(pos);
+
+        Roi ijRoi = new Roi(10, 10, 10, 10);
+        ijRoi.setPosition(img);
+        ijRoi.setImage(img);
+
+        assertEquals(pos, ijRoi.getPosition());
+
+        List<Roi> roiList = new ArrayList<>(1);
+        roiList.add(ijRoi);
+        ROIWrapper roi = ROIWrapper.fromImageJ(roiList, null).get(0);
+
+        RectangleWrapper newRectangle = roi.getShapes().getElementsOf(RectangleWrapper.class).get(0);
+
+        assertEquals(0, newRectangle.getC());
+        assertEquals(pos - 1, newRectangle.getZ());
+        assertEquals(0, newRectangle.getT());
+    }
+
+
+    @Test
+    void convertRectangleWithTStack() {
+        ImagePlus img = IJ.createImage("test", "grayscale", 1000, 1000, 1, 1, 10);
+        int pos = 6;
+        img.setPosition(pos);
+
+        Roi ijRoi = new Roi(10, 10, 10, 10);
+        ijRoi.setPosition(img);
+        ijRoi.setImage(img);
+
+        assertEquals(pos, ijRoi.getPosition());
+
+        List<Roi> roiList = new ArrayList<>(1);
+        roiList.add(ijRoi);
+        ROIWrapper roi = ROIWrapper.fromImageJ(roiList, null).get(0);
+
+        RectangleWrapper newRectangle = roi.getShapes().getElementsOf(RectangleWrapper.class).get(0);
+
+        assertEquals(0, newRectangle.getC());
+        assertEquals(0, newRectangle.getZ());
+        assertEquals(pos - 1, newRectangle.getT());
+    }
+
 }