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set plane coordinates #65

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merged 4 commits into from
Jul 6, 2023
Merged

set plane coordinates #65

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489242a
set plane coordinates
jburel Jul 4, 2023
1d05469
add null check for test
jburel Jul 5, 2023
12ccc40
Only adjust hyperstack coordinates if they're not already set and the…
ppouchin Jul 5, 2023
7ce4bfe
Add tests
ppouchin Jul 6, 2023
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41 changes: 38 additions & 3 deletions src/main/java/fr/igred/omero/roi/GenericShapeWrapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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);
Expand All @@ -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));
}


Expand Down
74 changes: 74 additions & 0 deletions src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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());
}

}