Save multiple ROIs and fix fill color in ImageJ (#47)

ppouchin · web-flow · commit a956dabebf7d · 2023-02-08T18:08:02.000+01:00
* Add saveROIs method to ImageWrapper (speed)
* Update pom.xml, README and .editorconfig
* Make fill color null in ImageJ if transparent on OMERO
diff --git a/.editorconfig b/.editorconfig
@@ -71,7 +71,7 @@ ij_java_case_statement_on_separate_line = true
 ij_java_catch_on_new_line = false
 ij_java_class_annotation_wrap = split_into_lines
 ij_java_class_brace_style = end_of_line
-ij_java_class_count_to_use_import_on_demand = 10
+ij_java_class_count_to_use_import_on_demand = 20
 ij_java_class_names_in_javadoc = 1
 ij_java_do_not_indent_top_level_class_members = false
 ij_java_do_not_wrap_after_single_annotation = false
diff --git a/README.md b/README.md
@@ -1,4 +1,5 @@
 [![Java CI with Maven](https://github.com/GReD-Clermont/simple-omero-client/actions/workflows/maven.yml/badge.svg)](https://github.com/GReD-Clermont/simple-omero-client/actions/workflows/maven.yml)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=GReD-Clermont_simple-omero-client&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=GReD-Clermont_simple-omero-client)
 [![codecov](https://codecov.io/gh/GReD-Clermont/simple-omero-client/branch/main/graph/badge.svg)](https://codecov.io/gh/GReD-Clermont/simple-omero-client)
 [![DOI](https://img.shields.io/badge/DOI-10.12688%2Ff1000research.110385.2-GREEN)](https://doi.org/10.12688/f1000research.110385.2)
 
diff --git a/pom.xml b/pom.xml
@@ -9,7 +9,7 @@
 
     <groupId>fr.igred</groupId>
     <artifactId>simple-omero-client</artifactId>
-    <version>5.9.4</version>
+    <version>5.10.0</version>
     <packaging>jar</packaging>
 
     <name>Simple OMERO Client</name>
diff --git a/src/main/java/fr/igred/omero/repository/ImageWrapper.java b/src/main/java/fr/igred/omero/repository/ImageWrapper.java
@@ -364,6 +364,33 @@ public List<ImageWrapper> getFilesetImages(Client client)
     }
 
 
+    /**
+     * Links ROIs to the image in OMERO.
+     * <p> DO NOT USE IT IF A SHAPE WAS DELETED !!!
+     *
+     * @param client The client handling the connection.
+     * @param rois   ROIs to be added.
+     *
+     * @return The updated list of ROIs.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    public List<ROIWrapper> saveROIs(Client client, Collection<? extends ROIWrapper> rois)
+    throws ServiceException, AccessException, ExecutionException {
+        rois.forEach(r -> r.setImage(this));
+        List<ROIData>       roisData = rois.stream().map(ROIWrapper::asROIData).collect(Collectors.toList());
+        Collection<ROIData> results  = new ArrayList<>(0);
+        try {
+            results = client.getRoiFacility().saveROIs(client.getCtx(), data.getId(), roisData);
+        } catch (DSOutOfServiceException | DSAccessException e) {
+            handleServiceOrAccess(e, "Cannot link ROI to " + this);
+        }
+        return wrap(results, ROIWrapper::new);
+    }
+
+
     /**
      * Links a ROI to the image in OMERO
      * <p> DO NOT USE IT IF A SHAPE WAS DELETED !!!
diff --git a/src/main/java/fr/igred/omero/roi/EllipseWrapper.java b/src/main/java/fr/igred/omero/roi/EllipseWrapper.java
@@ -63,7 +63,7 @@ public EllipseWrapper(ij.gui.Roi ijRoi) {
              ijRoi.getBounds().getWidth() / 2,
              ijRoi.getBounds().getHeight() / 2);
         data.setText(ijRoi.getName());
-        super.copy(ijRoi);
+        super.copyFromIJRoi(ijRoi);
     }
 
 
@@ -288,12 +288,7 @@ public Roi toImageJ() {
             double y2 = shape2.getY();
             roi = new EllipseRoi(x1, y1, x2, y2, ratio);
         }
-        roi.setStrokeColor(getStroke());
-        roi.setFillColor(getFill());
-        int c = Math.max(0, getC() + 1);
-        int z = Math.max(0, getZ() + 1);
-        int t = Math.max(0, getT() + 1);
-        roi.setPosition(c, z, t);
+        copyToIJRoi(roi);
         return roi;
     }
 
diff --git a/src/main/java/fr/igred/omero/roi/GenericShapeWrapper.java b/src/main/java/fr/igred/omero/roi/GenericShapeWrapper.java
@@ -95,7 +95,7 @@ static ShapeList fromImageJ(ij.gui.Roi ijRoi) {
                     points.add(new PointWrapper(x[i], y[i]));
                 }
                 points.forEach(p -> p.setText(ijRoi.getName()));
-                points.forEach(p -> p.copy(ijRoi));
+                points.forEach(p -> p.copyFromIJRoi(ijRoi));
                 list.addAll(points);
                 break;
             case Roi.COMPOSITE:
@@ -122,7 +122,7 @@ static ShapeList fromImageJ(ij.gui.Roi ijRoi) {
      *
      * @param ijRoi An ImageJ Roi.
      */
-    protected void copy(ij.gui.Roi ijRoi) {
+    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));
@@ -137,6 +137,23 @@ protected void copy(ij.gui.Roi ijRoi) {
     }
 
 
+    /**
+     * Copies details to an ImageJ ROI (name, position, stroke color, fill color, stroke width).
+     *
+     * @param ijRoi An ImageJ Roi.
+     */
+    protected void copyToIJRoi(ij.gui.Roi ijRoi) {
+        ijRoi.setName(getText());
+        ijRoi.setStrokeColor(getStroke());
+        Color fill = getFill();
+        if(!TRANSPARENT.equals(fill)) ijRoi.setFillColor(getFill());
+        int c = Math.max(0, getC() + 1);
+        int z = Math.max(0, getZ() + 1);
+        int t = Math.max(0, getT() + 1);
+        ijRoi.setPosition(c, z, t);
+    }
+
+
     /**
      * Gets the ShapeData object contained.
      *
@@ -420,13 +437,7 @@ public RectangleWrapper getBoundingBox() {
      */
     public Roi toImageJ() {
         Roi roi = new ij.gui.ShapeRoi(createTransformedAWTShape()).trySimplify();
-        roi.setName(getText());
-        roi.setStrokeColor(getStroke());
-        roi.setFillColor(getFill());
-        int c = Math.max(0, getC() + 1);
-        int z = Math.max(0, getZ() + 1);
-        int t = Math.max(0, getT() + 1);
-        roi.setPosition(c, z, t);
+        copyToIJRoi(roi);
         return roi;
     }
 
diff --git a/src/main/java/fr/igred/omero/roi/LineWrapper.java b/src/main/java/fr/igred/omero/roi/LineWrapper.java
@@ -70,7 +70,7 @@ public LineWrapper(Line line) {
                 data.getShapeSettings().setMarkerStart(ARROW);
             }
         }
-        super.copy(line);
+        super.copyFromIJRoi(line);
     }
 
 
@@ -295,12 +295,7 @@ public Roi toImageJ() {
             default:
                 roi = new Line(x1, y1, x2, y2);
         }
-        roi.setStrokeColor(getStroke());
-        roi.setFillColor(getFill());
-        int c = Math.max(0, getC() + 1);
-        int z = Math.max(0, getZ() + 1);
-        int t = Math.max(0, getT() + 1);
-        roi.setPosition(c, z, t);
+        copyToIJRoi(roi);
         return roi;
     }
 
diff --git a/src/main/java/fr/igred/omero/roi/MaskWrapper.java b/src/main/java/fr/igred/omero/roi/MaskWrapper.java
@@ -305,12 +305,7 @@ public Roi toImageJ() {
 
             roi = new ij.gui.RotatedRectRoi(x1, y1, x2, y2, getWidth());
         }
-        roi.setStrokeColor(getStroke());
-        roi.setFillColor(getFill());
-        int c = Math.max(0, getC() + 1);
-        int z = Math.max(0, getZ() + 1);
-        int t = Math.max(0, getT() + 1);
-        roi.setPosition(c, z, t);
+        copyToIJRoi(roi);
         return roi;
     }
 
diff --git a/src/main/java/fr/igred/omero/roi/PointWrapper.java b/src/main/java/fr/igred/omero/roi/PointWrapper.java
@@ -190,13 +190,7 @@ public ij.gui.Roi toImageJ() {
         double y = awtShape.getBounds2D().getY();
 
         PointRoi roi = new PointRoi(x, y);
-
-        roi.setStrokeColor(getStroke());
-        roi.setFillColor(getFill());
-        int c = Math.max(0, getC() + 1);
-        int z = Math.max(0, getZ() + 1);
-        int t = Math.max(0, getT() + 1);
-        roi.setPosition(c, z, t);
+        copyToIJRoi(roi);
 
         return roi;
     }
diff --git a/src/main/java/fr/igred/omero/roi/PolygonWrapper.java b/src/main/java/fr/igred/omero/roi/PolygonWrapper.java
@@ -69,7 +69,7 @@ public PolygonWrapper(Roi ijRoi) {
 
         data.setPoints(points);
         data.setText(ijRoi.getName());
-        super.copy(ijRoi);
+        super.copyFromIJRoi(ijRoi);
     }
 
 
diff --git a/src/main/java/fr/igred/omero/roi/PolylineWrapper.java b/src/main/java/fr/igred/omero/roi/PolylineWrapper.java
@@ -68,7 +68,7 @@ public PolylineWrapper(Roi ijRoi) {
 
         data.setPoints(points);
         data.setText(ijRoi.getName());
-        super.copy(ijRoi);
+        super.copyFromIJRoi(ijRoi);
     }
 
 
diff --git a/src/main/java/fr/igred/omero/roi/RectangleWrapper.java b/src/main/java/fr/igred/omero/roi/RectangleWrapper.java
@@ -62,7 +62,7 @@ public RectangleWrapper(ij.gui.Roi ijRoi) {
              ijRoi.getBounds().getHeight());
 
         data.setText(ijRoi.getName());
-        super.copy(ijRoi);
+        super.copyFromIJRoi(ijRoi);
     }
 
 
@@ -270,12 +270,7 @@ public Roi toImageJ() {
 
             roi = new ij.gui.RotatedRectRoi(x1, y1, x2, y2, getWidth());
         }
-        roi.setStrokeColor(getStroke());
-        roi.setFillColor(getFill());
-        int c = Math.max(0, getC() + 1);
-        int z = Math.max(0, getZ() + 1);
-        int t = Math.max(0, getT() + 1);
-        roi.setPosition(c, z, t);
+        copyToIJRoi(roi);
         return roi;
     }
 
diff --git a/src/main/java/fr/igred/omero/roi/TextWrapper.java b/src/main/java/fr/igred/omero/roi/TextWrapper.java
@@ -56,7 +56,7 @@ public TextWrapper() {
      */
     public TextWrapper(TextRoi text) {
         this(text.getText(), text.getBounds().getX(), text.getBounds().getY());
-        super.copy(text);
+        super.copyFromIJRoi(text);
     }
 
 
@@ -198,17 +198,11 @@ public void setCoordinates(double[] coordinates) {
     public ij.gui.Roi toImageJ() {
         java.awt.Shape awtShape = createTransformedAWTShape();
 
-        String text = getText();
-        double x    = awtShape.getBounds2D().getX();
-        double y    = awtShape.getBounds2D().getY();
-
-        TextRoi roi = new TextRoi(x, y, text);
-        roi.setStrokeColor(getStroke());
-        roi.setFillColor(getFill());
-        int c = Math.max(0, getC() + 1);
-        int z = Math.max(0, getZ() + 1);
-        int t = Math.max(0, getT() + 1);
-        roi.setPosition(c, z, t);
+        double x = awtShape.getBounds2D().getX();
+        double y = awtShape.getBounds2D().getY();
+
+        TextRoi roi = new TextRoi(x, y, getText());
+        copyToIJRoi(roi);
 
         return roi;
     }
diff --git a/src/test/java/fr/igred/omero/annotations/ImageJTableTest.java b/src/test/java/fr/igred/omero/annotations/ImageJTableTest.java
@@ -439,11 +439,12 @@ void testCreateTableWithLocalROIFromIJResults2() throws Exception {
 
     @Test
     void testCreateTableWithROINamesFromIJResults1() throws Exception {
-        ROIWrapper roi1 = new ROIWrapper();
-        ROIWrapper roi2 = new ROIWrapper();
+        List<ROIWrapper> rois = new ArrayList<>(2);
+        rois.add(new ROIWrapper());
+        rois.add(new ROIWrapper());
 
-        roi1.setImage(image);
-        roi2.setImage(image);
+        rois.get(0).setImage(image);
+        rois.get(1).setImage(image);
 
         for (int i = 0; i < 4; i++) {
             RectangleWrapper rectangle = new RectangleWrapper();
@@ -453,18 +454,15 @@ void testCreateTableWithROINamesFromIJResults1() throws Exception {
             rectangle.setT(0);
             rectangle.setC(0);
 
-            if (i % 2 == 1) roi1.addShape(rectangle);
-            else roi2.addShape(rectangle);
+            if (i % 2 == 1) rois.get(0).addShape(rectangle);
+            else rois.get(1).addShape(rectangle);
         }
 
-        image.saveROI(client, roi1);
-        image.saveROI(client, roi2);
-
-        List<ROIWrapper> rois   = image.getROIs(client);
-        List<Roi>        ijRois = ROIWrapper.toImageJ(rois);
+        List<ROIWrapper> newROIs = image.saveROIs(client, rois);
+        List<Roi>        ijRois  = ROIWrapper.toImageJ(newROIs);
 
-        String label1 = image.getName() + ":" + rois.get(0).getShapes().get(0).getText() + ":4";
-        String label2 = image.getName() + ":" + rois.get(1).getShapes().get(0).getText() + ":10";
+        String label1 = image.getName() + ":" + newROIs.get(0).getShapes().get(0).getText() + ":4";
+        String label2 = image.getName() + ":" + newROIs.get(1).getShapes().get(0).getText() + ":10";
 
         ResultsTable results1 = createOneRowResultsTable(label1, volume1, unit1);
         ResultsTable results2 = createOneRowResultsTable(label2, volume2, unit2);
@@ -481,12 +479,12 @@ void testCreateTableWithROINamesFromIJResults1() throws Exception {
 
         assertEquals(2, rowCount);
         assertEquals(imageId, ((DataObject) data[0][0]).getId());
-        assertEquals(rois.get(0).getId(), ((DataObject) data[1][0]).getId());
+        assertEquals(newROIs.get(0).getId(), ((DataObject) data[1][0]).getId());
         assertEquals(label1, data[2][0]);
         assertEquals(volume1, (Double) data[3][0], Double.MIN_VALUE);
         assertEquals(unit1, data[4][0]);
         assertEquals(imageId, ((DataObject) data[0][1]).getId());
-        assertEquals(rois.get(1).getId(), ((DataObject) data[1][1]).getId());
+        assertEquals(newROIs.get(1).getId(), ((DataObject) data[1][1]).getId());
         assertEquals(label2, data[2][1]);
         assertEquals(volume2, (Double) data[3][1], Double.MIN_VALUE);
         assertEquals(unit2, data[4][1]);
diff --git a/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java b/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java
@@ -28,6 +28,7 @@
 import ij.gui.TextRoi;
 import org.junit.jupiter.api.Test;
 
+import java.awt.Color;
 import java.awt.geom.AffineTransform;
 import java.awt.geom.Ellipse2D;
 import java.awt.geom.Point2D;
@@ -37,6 +38,7 @@
 import java.util.regex.Pattern;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
 
 
 class ROI2ImageJTest extends BasicTest {
@@ -252,12 +254,14 @@ void convertArrow() {
         LineWrapper arrow = new LineWrapper(3, 3, 10, 10);
         arrow.setCZT(0, 0, 2);
         arrow.asShapeData().getShapeSettings().setMarkerStart(LineWrapper.ARROW);
+        arrow.setFill(new Color(0, 0, 0, 0));
 
         Arrow ijArrow = (Arrow) arrow.toImageJ();
         assertEquals(arrow.getX1(), ijArrow.x2d, Double.MIN_VALUE);
         assertEquals(arrow.getY1(), ijArrow.y2d, Double.MIN_VALUE);
         assertEquals(arrow.getX2(), ijArrow.x1d, Double.MIN_VALUE);
         assertEquals(arrow.getY2(), ijArrow.y1d, Double.MIN_VALUE);
+        assertNull(ijArrow.getFillColor());
 
         List<Roi> roiList = new ArrayList<>(1);
         roiList.add(ijArrow);
@@ -281,12 +285,14 @@ void convertArrow() {
     void convertLine() {
         LineWrapper line = new LineWrapper(3, 3, 10, 10);
         line.setCZT(0, 0, 2);
+        line.setFill(Color.BLUE);
 
         Line ijLine = (Line) line.toImageJ();
         assertEquals(line.getX1(), ijLine.x1d, Double.MIN_VALUE);
         assertEquals(line.getY1(), ijLine.y1d, Double.MIN_VALUE);
         assertEquals(line.getX2(), ijLine.x2d, Double.MIN_VALUE);
         assertEquals(line.getY2(), ijLine.y2d, Double.MIN_VALUE);
+        assertEquals(Color.BLUE, line.getFill());
 
         List<Roi> roiList = new ArrayList<>(1);
         roiList.add(ijLine);

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`[![Java CI with Maven](https://github.com/GReD-Clermont/simple-omero-client/actions/workflows/maven.yml/badge.svg)](https://github.com/GReD-Clermont/simple-omero-client/actions/workflows/maven.yml)`
	`2`	`+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=GReD-Clermont_simple-omero-client&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=GReD-Clermont_simple-omero-client)`
`2`	`3`	`[![codecov](https://codecov.io/gh/GReD-Clermont/simple-omero-client/branch/main/graph/badge.svg)](https://codecov.io/gh/GReD-Clermont/simple-omero-client)`
`3`	`4`	`[![DOI](https://img.shields.io/badge/DOI-10.12688%2Ff1000research.110385.2-GREEN)](https://doi.org/10.12688/f1000research.110385.2)`
`4`	`5`
Original file line number	Diff line number	Diff line change
`@@ -63,7 +63,7 @@ public EllipseWrapper(ij.gui.Roi ijRoi) {`
`63`	`63`	`ijRoi.getBounds().getWidth() / 2,`
`64`	`64`	`ijRoi.getBounds().getHeight() / 2);`
`65`	`65`	`data.setText(ijRoi.getName());`
`66`		`- super.copy(ijRoi);`
	`66`	`+ super.copyFromIJRoi(ijRoi);`
`67`	`67`	`}`
`68`	`68`
`69`	`69`
`@@ -288,12 +288,7 @@ public Roi toImageJ() {`
`288`	`288`	`double y2 = shape2.getY();`
`289`	`289`	`roi = new EllipseRoi(x1, y1, x2, y2, ratio);`
`290`	`290`	`}`
`291`		`- roi.setStrokeColor(getStroke());`
`292`		`- roi.setFillColor(getFill());`
`293`		`- int c = Math.max(0, getC() + 1);`
`294`		`- int z = Math.max(0, getZ() + 1);`
`295`		`- int t = Math.max(0, getT() + 1);`
`296`		`- roi.setPosition(c, z, t);`
	`291`	`+ copyToIJRoi(roi);`
`297`	`292`	`return roi;`
`298`	`293`	`}`
`299`	`294`
Original file line number	Diff line number	Diff line change
`@@ -70,7 +70,7 @@ public LineWrapper(Line line) {`
`70`	`70`	`data.getShapeSettings().setMarkerStart(ARROW);`
`71`	`71`	`}`
`72`	`72`	`}`
`73`		`- super.copy(line);`
	`73`	`+ super.copyFromIJRoi(line);`
`74`	`74`	`}`
`75`	`75`
`76`	`76`
`@@ -295,12 +295,7 @@ public Roi toImageJ() {`
`295`	`295`	`default:`
`296`	`296`	`roi = new Line(x1, y1, x2, y2);`
`297`	`297`	`}`
`298`		`- roi.setStrokeColor(getStroke());`
`299`		`- roi.setFillColor(getFill());`
`300`		`- int c = Math.max(0, getC() + 1);`
`301`		`- int z = Math.max(0, getZ() + 1);`
`302`		`- int t = Math.max(0, getT() + 1);`
`303`		`- roi.setPosition(c, z, t);`
	`298`	`+ copyToIJRoi(roi);`
`304`	`299`	`return roi;`
`305`	`300`	`}`
`306`	`301`
Original file line number	Diff line number	Diff line change
`@@ -305,12 +305,7 @@ public Roi toImageJ() {`
`305`	`305`
`306`	`306`	`roi = new ij.gui.RotatedRectRoi(x1, y1, x2, y2, getWidth());`
`307`	`307`	`}`
`308`		`- roi.setStrokeColor(getStroke());`
`309`		`- roi.setFillColor(getFill());`
`310`		`- int c = Math.max(0, getC() + 1);`
`311`		`- int z = Math.max(0, getZ() + 1);`
`312`		`- int t = Math.max(0, getT() + 1);`
`313`		`- roi.setPosition(c, z, t);`
	`308`	`+ copyToIJRoi(roi);`
`314`	`309`	`return roi;`
`315`	`310`	`}`
`316`	`311`
Original file line number	Diff line number	Diff line change
`@@ -69,7 +69,7 @@ public PolygonWrapper(Roi ijRoi) {`
`69`	`69`
`70`	`70`	`data.setPoints(points);`
`71`	`71`	`data.setText(ijRoi.getName());`
`72`		`- super.copy(ijRoi);`
	`72`	`+ super.copyFromIJRoi(ijRoi);`
`73`	`73`	`}`
`74`	`74`
`75`	`75`