getElementsOf(Class clazz) {
- return stream().filter(clazz::isInstance)
- .map(clazz::cast)
- .collect(Collectors.toList());
- }
-
-
- /**
- * Wraps the specified AnnotationData object and add it to the end of this list.
- *
- * @param shape element to be wrapped and appended to this list
- *
- * @return {@code true} (as specified by {@link ArrayList#add(Object)})
- */
- public boolean add(AnnotationData shape) {
- boolean added;
-
- try {
- added = add(wrap(shape));
- } catch (IllegalArgumentException e) {
- added = false;
- }
-
- return added;
- }
-
-}
diff --git a/src/main/java/fr/igred/omero/core/PlaneInfoWrapper.java b/src/main/java/fr/igred/omero/core/PlaneInfoWrapper.java
index 91b921db..05f4bf37 100644
--- a/src/main/java/fr/igred/omero/core/PlaneInfoWrapper.java
+++ b/src/main/java/fr/igred/omero/core/PlaneInfoWrapper.java
@@ -24,6 +24,10 @@
import omero.model.Time;
+/**
+ * Class containing a PlaneInfoData object.
+ * Wraps function calls to the PlaneInfoData contained.
+ */
public class PlaneInfoWrapper extends ObjectWrapper implements PlaneInfo {
/**
diff --git a/src/main/java/fr/igred/omero/roi/ROI.java b/src/main/java/fr/igred/omero/roi/ROI.java
index 371e1fd9..42e8932e 100644
--- a/src/main/java/fr/igred/omero/roi/ROI.java
+++ b/src/main/java/fr/igred/omero/roi/ROI.java
@@ -261,7 +261,7 @@ default void addShapes(Iterable shapes) {
*
* @return list of shape contained in the ROIData.
*/
- ShapeList getShapes();
+ List getShapes();
/**
diff --git a/src/main/java/fr/igred/omero/roi/ROIWrapper.java b/src/main/java/fr/igred/omero/roi/ROIWrapper.java
index d7521908..bb37f834 100644
--- a/src/main/java/fr/igred/omero/roi/ROIWrapper.java
+++ b/src/main/java/fr/igred/omero/roi/ROIWrapper.java
@@ -23,6 +23,7 @@
import fr.igred.omero.core.Image;
import fr.igred.omero.exception.AccessException;
import fr.igred.omero.exception.ServiceException;
+import fr.igred.omero.util.Wrapper;
import ij.gui.PointRoi;
import ij.gui.ShapeRoi;
import omero.RString;
@@ -33,7 +34,6 @@
import java.util.ArrayList;
import java.util.Collection;
-import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
@@ -222,13 +222,8 @@ public void addShape(Shape shape) {
* @return list of shape contained in the ROIData.
*/
@Override
- public ShapeList getShapes() {
- List shapeData = data.getShapes();
- ShapeList shapes = new ShapeList(shapeData.size());
- shapeData.stream()
- .sorted(Comparator.comparing(ShapeData::getId))
- .forEachOrdered(shapes::add);
- return shapes;
+ public List getShapes() {
+ return wrap(data.getShapes(), Wrapper::wrap);
}
@@ -298,7 +293,7 @@ public List toImageJ(String property) {
String ijNameProperty = ROI.ijNameProperty(property);
String roiID = String.valueOf(getId());
- ShapeList shapes = getShapes();
+ List shapes = getShapes();
Map> sameSlice = shapes.stream()
.collect(groupingBy(Shape::getCZT,
diff --git a/src/main/java/fr/igred/omero/roi/ShapeList.java b/src/main/java/fr/igred/omero/roi/ShapeList.java
deleted file mode 100644
index 2cdb4a21..00000000
--- a/src/main/java/fr/igred/omero/roi/ShapeList.java
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
- * Copyright (C) 2020-2024 GReD
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU General Public License as published by the Free Software
- * Foundation; either version 2 of the License, or (at your option) any later
- * version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with
- * this program; if not, write to the Free Software Foundation, Inc., 51 Franklin
- * Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-package fr.igred.omero.roi;
-
-
-import omero.gateway.model.ShapeData;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.stream.Collectors;
-
-import static fr.igred.omero.util.Wrapper.wrap;
-
-
-/** List of ShapeWrapper objects */
-public class ShapeList extends ArrayList {
-
-
- private static final long serialVersionUID = -5942132062803749727L;
-
-
- /**
- * Constructs an empty list with an initial capacity of ten.
- */
- public ShapeList() {
- }
-
-
- /**
- * Constructs an empty list with the specified initial capacity.
- *
- * @param initialCapacity the initial capacity of the list
- *
- * @throws IllegalArgumentException if the specified initial capacity is negative
- */
- public ShapeList(int initialCapacity) {
- super(initialCapacity);
- }
-
-
- /**
- * Gets a list of elements from this list whose class is specified.
- *
- * @param clazz Class of the wanted elements.
- * @param Subclass of ShapeWrapper.
- *
- * @return See above.
- */
- public List getElementsOf(Class clazz) {
- return stream().filter(clazz::isInstance)
- .map(clazz::cast)
- .collect(Collectors.toList());
- }
-
-
- /**
- * Wraps the specified ShapeData object and add it to the end of this list.
- *
- * @param shape element to be wrapped and appended to this list
- *
- * @return {@code true} (as specified by {@link ArrayList#add(Object)})
- */
- public boolean add(ShapeData shape) {
- boolean added;
-
- try {
- added = add(wrap(shape));
- } catch (IllegalArgumentException e) {
- added = false;
- }
-
- return added;
- }
-
-}
diff --git a/src/main/java/fr/igred/omero/roi/ShapeWrapper.java b/src/main/java/fr/igred/omero/roi/ShapeWrapper.java
index 18e165f6..9c63111e 100644
--- a/src/main/java/fr/igred/omero/roi/ShapeWrapper.java
+++ b/src/main/java/fr/igred/omero/roi/ShapeWrapper.java
@@ -35,6 +35,7 @@
import java.awt.Font;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.LinkedList;
@@ -81,9 +82,9 @@ protected ShapeWrapper(T s) {
*
* @return A list of shapes.
*/
- static ShapeList fromImageJ(ij.gui.Roi ijRoi) {
- ShapeList list = new ShapeList();
- int type = ijRoi.getType();
+ static List fromImageJ(ij.gui.Roi ijRoi) {
+ List list = new ArrayList<>(ijRoi.size());
+ int type = ijRoi.getType();
switch (type) {
case Roi.FREEROI:
case Roi.TRACED_ROI:
diff --git a/src/test/java/fr/igred/omero/annotations/RatingAnnotationTest.java b/src/test/java/fr/igred/omero/annotations/RatingAnnotationTest.java
index c106403d..1eb0368d 100644
--- a/src/test/java/fr/igred/omero/annotations/RatingAnnotationTest.java
+++ b/src/test/java/fr/igred/omero/annotations/RatingAnnotationTest.java
@@ -26,6 +26,7 @@
import java.util.List;
+import static fr.igred.omero.RemoteObject.getElementsOf;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
@@ -41,8 +42,7 @@ void testAddRating1() throws Exception {
RatingAnnotation rating = new RatingAnnotationWrapper(score);
image.link(client, rating);
- List ratings = image.getAnnotations(client)
- .getElementsOf(RatingAnnotation.class);
+ List ratings = getElementsOf(image.getAnnotations(client), RatingAnnotation.class);
client.delete(ratings);
assertEquals(1, ratings.size());
@@ -59,8 +59,7 @@ void testAddRating2() throws Exception {
rating.setRating(score);
image.link(client, rating);
- List ratings = image.getAnnotations(client)
- .getElementsOf(RatingAnnotation.class);
+ List ratings = getElementsOf(image.getAnnotations(client), RatingAnnotation.class);
client.delete(ratings);
assertEquals(1, ratings.size());
@@ -72,15 +71,14 @@ void testAddRating2() throws Exception {
void testRate1() throws Exception {
Image image = client.getImage(IMAGE1.id);
int score1 = 4;
- int score2 = 3;
+ int score2 = 3;
image.rate(client, score1);
int rating1 = image.getMyRating(client);
image.rate(client, score2);
int rating2 = image.getMyRating(client);
- List ratings = image.getAnnotations(client)
- .getElementsOf(RatingAnnotation.class);
+ List ratings = getElementsOf(image.getAnnotations(client), RatingAnnotation.class);
client.delete(ratings);
assertEquals(1, ratings.size());
@@ -93,8 +91,8 @@ void testRate1() throws Exception {
void testRate2() throws Exception {
Image image = client.getImage(IMAGE1.id);
int score0 = 1;
- int score1 = 2;
- int score2 = 3;
+ int score1 = 2;
+ int score2 = 3;
RatingAnnotation rating1 = new RatingAnnotationWrapper(new RatingAnnotationData());
rating1.setRating(score0);
@@ -106,8 +104,7 @@ void testRate2() throws Exception {
image.rate(client, score2);
int myRating2 = image.getMyRating(client);
- List ratings = image.getAnnotations(client)
- .getElementsOf(RatingAnnotation.class);
+ List ratings = getElementsOf(image.getAnnotations(client), RatingAnnotation.class);
client.delete(ratings);
assertEquals(1, ratings.size());
@@ -120,15 +117,14 @@ void testRate2() throws Exception {
void testRate3() throws Exception {
Dataset dataset = client.getDataset(DATASET1.id);
int score1 = 4;
- int score2 = 3;
+ int score2 = 3;
dataset.rate(client, score1);
int rating1 = dataset.getMyRating(client);
dataset.rate(client, score2);
int rating2 = dataset.getMyRating(client);
- List ratings = dataset.getAnnotations(client)
- .getElementsOf(RatingAnnotation.class);
+ List ratings = getElementsOf(dataset.getAnnotations(client), RatingAnnotation.class);
client.delete(ratings);
assertEquals(1, ratings.size());
diff --git a/src/test/java/fr/igred/omero/annotations/TextualAnnotationTest.java b/src/test/java/fr/igred/omero/annotations/TextualAnnotationTest.java
index b4e00a8c..ccf894b6 100644
--- a/src/test/java/fr/igred/omero/annotations/TextualAnnotationTest.java
+++ b/src/test/java/fr/igred/omero/annotations/TextualAnnotationTest.java
@@ -24,6 +24,7 @@
import java.util.List;
+import static fr.igred.omero.RemoteObject.getElementsOf;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -39,9 +40,9 @@ void testAddTextualAnnotation1() throws Exception {
TextualAnnotation text = new TextualAnnotationWrapper(test);
image.link(client, text);
- AnnotationList annotations = image.getAnnotations(client);
+ List annotations = image.getAnnotations(client);
- List texts = annotations.getElementsOf(TextualAnnotation.class);
+ List texts = getElementsOf(annotations, TextualAnnotation.class);
client.delete(texts);
assertEquals(1, texts.size());
@@ -58,9 +59,9 @@ void testAddTextualAnnotation2() throws Exception {
TextualAnnotation text = new TextualAnnotationWrapper("New");
text.setText(test);
image.link(client, text);
- AnnotationList annotations = image.getAnnotations(client);
+ List annotations = image.getAnnotations(client);
- List texts = annotations.getElementsOf(TextualAnnotation.class);
+ List texts = getElementsOf(annotations, TextualAnnotation.class);
client.delete(texts);
assertEquals(1, texts.size());
diff --git a/src/test/java/fr/igred/omero/core/ImageTest.java b/src/test/java/fr/igred/omero/core/ImageTest.java
index 15a88225..84f7ba5a 100644
--- a/src/test/java/fr/igred/omero/core/ImageTest.java
+++ b/src/test/java/fr/igred/omero/core/ImageTest.java
@@ -19,7 +19,7 @@
import fr.igred.omero.UserTest;
-import fr.igred.omero.annotations.AnnotationList;
+import fr.igred.omero.annotations.Annotation;
import fr.igred.omero.annotations.FileAnnotation;
import fr.igred.omero.annotations.MapAnnotation;
import fr.igred.omero.annotations.MapAnnotationWrapper;
@@ -153,7 +153,7 @@ void testGetWellSamples() throws Exception {
@Test
void testGetAnnotations() throws Exception {
- AnnotationList annotations = client.getImage(IMAGE1.id).getAnnotations(client);
+ List annotations = client.getImage(IMAGE1.id).getAnnotations(client);
assertEquals(3, annotations.size());
}
diff --git a/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java b/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java
index b72a9b9d..0e6f6f74 100644
--- a/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java
+++ b/src/test/java/fr/igred/omero/roi/ROI2ImageJTest.java
@@ -44,6 +44,7 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import static fr.igred.omero.RemoteObject.getElementsOf;
import static org.junit.jupiter.api.Assertions.assertArrayEquals;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertInstanceOf;
@@ -228,7 +229,7 @@ void convertEllipse() {
ROI roi = ROIWrapper.fromImageJ(roiList).get(0);
- Ellipse newEllipse = roi.getShapes().getElementsOf(Ellipse.class).get(0);
+ Ellipse newEllipse = getElementsOf(roi.getShapes(), Ellipse.class).get(0);
assertEquals(ellipse.getX(), newEllipse.getX(), Double.MIN_VALUE);
assertEquals(ellipse.getY(), newEllipse.getY(), Double.MIN_VALUE);
@@ -252,7 +253,7 @@ void convertRectangle() {
roiList.add(ijRectangle);
ROI roi = ROIWrapper.fromImageJ(roiList, null).get(0);
- Rectangle newRectangle = roi.getShapes().getElementsOf(Rectangle.class).get(0);
+ Rectangle newRectangle = getElementsOf(roi.getShapes(), Rectangle.class).get(0);
assertEquals(rectangle.getX(), newRectangle.getX(), Double.MIN_VALUE);
assertEquals(rectangle.getY(), newRectangle.getY(), Double.MIN_VALUE);
@@ -282,7 +283,7 @@ void convertArrow() {
roiList.add(ijArrow);
ROI roi = ROIWrapper.fromImageJ(roiList, "").get(0);
- fr.igred.omero.roi.Line newArrow = roi.getShapes().getElementsOf(Line.class).get(0);
+ fr.igred.omero.roi.Line newArrow = getElementsOf(roi.getShapes(), Line.class).get(0);
assertEquals(arrow.getX1(), newArrow.getX2(), Double.MIN_VALUE);
assertEquals(arrow.getY1(), newArrow.getY2(), Double.MIN_VALUE);
@@ -313,7 +314,7 @@ void convertLine() {
roiList.add(ijLine);
ROI roi = ROIWrapper.fromImageJ(roiList, ROI.IJ_PROPERTY).get(0);
- fr.igred.omero.roi.Line newLine = roi.getShapes().getElementsOf(Line.class).get(0);
+ Line newLine = getElementsOf(roi.getShapes(), Line.class).get(0);
assertEquals(line.getX1(), newLine.getX1(), Double.MIN_VALUE);
assertEquals(line.getY1(), newLine.getY1(), Double.MIN_VALUE);
@@ -349,7 +350,7 @@ void convertMask() {
roiList.add(imgRoi);
ROI roi = ROIWrapper.fromImageJ(roiList).get(0);
- Mask newMask = roi.getShapes().getElementsOf(Mask.class).get(0);
+ Mask newMask = getElementsOf(roi.getShapes(), Mask.class).get(0);
int[][] checkMask = newMask.getMaskAsBinaryArray();
assertEquals(mask.getX(), newMask.getX(), Double.MIN_VALUE);
@@ -381,7 +382,7 @@ void convertPoint() {
roiList.add(ijPoint);
ROI roi = ROIWrapper.fromImageJ(roiList).get(0);
- Point newPoint = roi.getShapes().getElementsOf(Point.class).get(0);
+ Point newPoint = getElementsOf(roi.getShapes(), Point.class).get(0);
assertEquals(point.getX(), newPoint.getX(), Double.MIN_VALUE);
assertEquals(point.getY(), newPoint.getY(), Double.MIN_VALUE);
@@ -410,7 +411,7 @@ void convertText() {
roiList.add(ijPoint);
ROI roi = ROIWrapper.fromImageJ(roiList).get(0);
- Text newText = roi.getShapes().getElementsOf(Text.class).get(0);
+ Text newText = getElementsOf(roi.getShapes(), Text.class).get(0);
assertEquals(text.getX(), newText.getX(), Double.MIN_VALUE);
assertEquals(text.getY(), newText.getY(), Double.MIN_VALUE);
@@ -469,7 +470,7 @@ void convertPolygon() {
roiList.add(ijPolygon);
ROI roi = ROIWrapper.fromImageJ(roiList).get(0);
- Polygon newPolygon = roi.getShapes().getElementsOf(Polygon.class).get(0);
+ Polygon newPolygon = getElementsOf(roi.getShapes(), Polygon.class).get(0);
assertEquals(polygon.getPoints(), newPolygon.getPoints());
assertEquals(polygon.getC(), newPolygon.getC());
@@ -500,7 +501,7 @@ void convertPolyline() {
roiList.add(ijPolyline);
ROI roi = ROIWrapper.fromImageJ(roiList).get(0);
- Polyline newPolyline = roi.getShapes().getElementsOf(Polyline.class).get(0);
+ Polyline newPolyline = getElementsOf(roi.getShapes(), Polyline.class).get(0);
assertEquals(polyline.getPoints(), newPolyline.getPoints());
assertEquals(polyline.getC(), newPolyline.getC());
@@ -525,7 +526,7 @@ void convertRectangleWithCStack() {
roiList.add(ijRoi);
ROI roi = ROIWrapper.fromImageJ(roiList, null).get(0);
- Rectangle newRectangle = roi.getShapes().getElementsOf(Rectangle.class).get(0);
+ Rectangle newRectangle = getElementsOf(roi.getShapes(), Rectangle.class).get(0);
assertEquals(pos - 1, newRectangle.getC());
assertEquals(0, newRectangle.getZ());
@@ -549,7 +550,7 @@ void convertRectangleWithZStack() {
roiList.add(ijRoi);
ROI roi = ROIWrapper.fromImageJ(roiList, null).get(0);
- Rectangle newRectangle = roi.getShapes().getElementsOf(Rectangle.class).get(0);
+ Rectangle newRectangle = getElementsOf(roi.getShapes(), Rectangle.class).get(0);
assertEquals(0, newRectangle.getC());
assertEquals(pos - 1, newRectangle.getZ());
@@ -573,7 +574,7 @@ void convertRectangleWithTStack() {
roiList.add(ijRoi);
ROI roi = ROIWrapper.fromImageJ(roiList, null).get(0);
- Rectangle newRectangle = roi.getShapes().getElementsOf(Rectangle.class).get(0);
+ Rectangle newRectangle = getElementsOf(roi.getShapes(), Rectangle.class).get(0);
assertEquals(0, newRectangle.getC());
assertEquals(0, newRectangle.getZ());
diff --git a/src/test/java/fr/igred/omero/roi/ROITest.java b/src/test/java/fr/igred/omero/roi/ROITest.java
index e795b14d..6665c523 100644
--- a/src/test/java/fr/igred/omero/roi/ROITest.java
+++ b/src/test/java/fr/igred/omero/roi/ROITest.java
@@ -28,6 +28,7 @@
import java.util.Collection;
import java.util.List;
+import static fr.igred.omero.RemoteObject.getElementsOf;
import static java.util.Collections.singletonList;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -264,15 +265,15 @@ void testROIAllShapes() throws Exception {
image.saveROIs(client, roiWrapper);
List rois = image.getROIs(client);
- ShapeList shapes = rois.get(0).getShapes();
- List points = shapes.getElementsOf(Point.class);
- List texts = shapes.getElementsOf(Text.class);
- List rectangles = shapes.getElementsOf(Rectangle.class);
- List masks = shapes.getElementsOf(Mask.class);
- List ellipses = shapes.getElementsOf(Ellipse.class);
- List lines = shapes.getElementsOf(Line.class);
- List polylines = shapes.getElementsOf(Polyline.class);
- List polygons = shapes.getElementsOf(Polygon.class);
+ List shapes = rois.get(0).getShapes();
+ List points = getElementsOf(shapes, Point.class);
+ List texts = getElementsOf(shapes, Text.class);
+ List rectangles = getElementsOf(shapes, Rectangle.class);
+ List masks = getElementsOf(shapes, Mask.class);
+ List ellipses = getElementsOf(shapes, Ellipse.class);
+ List lines = getElementsOf(shapes, Line.class);
+ List polylines = getElementsOf(shapes, Polyline.class);
+ List polygons = getElementsOf(shapes, Polygon.class);
assertEquals(1, rois.size());
assertEquals(8, shapes.size());
diff --git a/src/test/java/fr/igred/omero/util/WrapperTest.java b/src/test/java/fr/igred/omero/util/WrapperTest.java
index 47ccd230..bd8d4ef2 100644
--- a/src/test/java/fr/igred/omero/util/WrapperTest.java
+++ b/src/test/java/fr/igred/omero/util/WrapperTest.java
@@ -20,7 +20,6 @@
import fr.igred.omero.BasicTest;
import fr.igred.omero.ObjectWrapper;
-import fr.igred.omero.annotations.AnnotationList;
import fr.igred.omero.annotations.FileAnnotationWrapper;
import fr.igred.omero.annotations.MapAnnotationWrapper;
import fr.igred.omero.annotations.RatingAnnotationWrapper;
@@ -92,8 +91,6 @@
import java.util.stream.Stream;
import static fr.igred.omero.util.Wrapper.wrap;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertSame;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Named.named;
@@ -199,16 +196,6 @@ void testWrapWrongAnnotationData() {
}
- @Test
- void testAddWrongAnnotationDataToAnnotationList() {
- AnnotationList annotations = new AnnotationList();
-
- boolean added = annotations.add(new WrongAnnotationData());
- assertFalse(added);
- assertEquals(0, annotations.size());
- }
-
-
private static class WrongDataObject extends DataObject {
WrongDataObject() {