diff --git a/.gitignore b/.gitignore
index 3d47f986c41db29ec6dc0d5036bf760b3a1cf366..57f16fb67c1b1589981416b323d7a9debc728665 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,41 @@
-.idea/
+/build*
+/workspace
+setting.xml
+release/
target/
-.settings/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
+*.ipr
+
+### Eclipse ###
+.apt_generated
+.classpath
+.factorypath
.project
-.classpath
\ No newline at end of file
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 1f12d2d6e7f7957625c0aea07e2ed3ee4d53333b..ddb0adaae907a4be27a49400509f735d23121dab 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,15 +7,13 @@
<!-- Inherited Icy Parent POM -->
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>parent-pom-plugin</artifactId>
- <version>1.0.3</version>
+ <artifactId>pom-icy</artifactId>
+ <version>3.0.0-a.1</version>
</parent>
<!-- Project Information -->
<artifactId>roi-tooltip</artifactId>
- <version>1.1.4</version>
-
- <packaging>jar</packaging>
+ <version>2.0.0-a.1</version>
<name>ROI Tooltip</name>
<description>
@@ -23,7 +21,7 @@
position and size. - number of interior points and contour points. - perimeter, area, surface area, volume. - min, max, mean
intensity. This plugin is a daemon plugin, that means plugin is automatically loaded when Icy starts.
</description>
- <url>http://icy.bioimageanalysis.org/plugin/roi-tooltip/</url>
+ <url>https://icy.bioimageanalysis.org/plugin/roi-tooltip/</url>
<inceptionYear>2020</inceptionYear>
<organization>
@@ -57,31 +55,11 @@
</developer>
</developers>
- <!-- Project properties -->
- <properties>
-
- </properties>
-
- <!-- Project build configuration -->
- <build>
-
- </build>
-
- <!-- List of project's dependencies -->
- <dependencies>
- <!-- The core of Icy -->
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-kernel</artifactId>
- </dependency>
- </dependencies>
-
<!-- Icy Maven repository (to find parent POM) -->
<repositories>
<repository>
<id>icy</id>
- <name>Icy's Nexus</name>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/stef/roi/ROIToolTip.java b/src/main/java/plugins/stef/roi/ROIToolTip.java
index 808c80c06974ce0555ad7cc50306b667f7be7a15..aa405f4e4eec44922fe077f4a29a17aec1d54c62 100644
--- a/src/main/java/plugins/stef/roi/ROIToolTip.java
+++ b/src/main/java/plugins/stef/roi/ROIToolTip.java
@@ -1,36 +1,51 @@
+/*
+ * Copyright (c) 2010-2024. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy 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 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.stef.roi;
-import icy.canvas.IcyCanvas;
-import icy.canvas.IcyCanvas2D;
-import icy.canvas.Layer;
-import icy.gui.main.ActiveViewerListener;
-import icy.gui.viewer.Viewer;
-import icy.gui.viewer.ViewerEvent;
-import icy.image.IntensityInfo;
-import icy.main.Icy;
-import icy.math.MathUtil;
-import icy.painter.Overlay;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginDaemon;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.roi.ROI3D;
-import icy.roi.ROIEvent;
-import icy.roi.ROIEvent.ROIEventType;
-import icy.roi.ROIListener;
-import icy.roi.ROIUtil;
-import icy.sequence.Sequence;
-import icy.system.thread.SingleProcessor;
-import icy.util.GraphicsUtil;
-import icy.util.StringUtil;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.Point;
-import java.awt.Rectangle;
-import java.awt.RenderingHints;
+import org.bioimageanalysis.extension.kernel.roi.descriptor.measure.ROIAreaDescriptor;
+import org.bioimageanalysis.extension.kernel.roi.descriptor.measure.ROIPerimeterDescriptor;
+import org.bioimageanalysis.extension.kernel.roi.descriptor.measure.ROISurfaceAreaDescriptor;
+import org.bioimageanalysis.extension.kernel.roi.descriptor.measure.ROIVolumeDescriptor;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.math.MathUtil;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginDaemon;
+import org.bioimageanalysis.icy.gui.GraphicsUtil;
+import org.bioimageanalysis.icy.gui.canvas.IcyCanvas;
+import org.bioimageanalysis.icy.gui.canvas.IcyCanvas2D;
+import org.bioimageanalysis.icy.gui.canvas.Layer;
+import org.bioimageanalysis.icy.gui.listener.ActiveViewerListener;
+import org.bioimageanalysis.icy.gui.viewer.Viewer;
+import org.bioimageanalysis.icy.gui.viewer.ViewerEvent;
+import org.bioimageanalysis.icy.model.overlay.Overlay;
+import org.bioimageanalysis.icy.model.roi.*;
+import org.bioimageanalysis.icy.model.roi.descriptor.IntensityDescriptorInfos;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.thread.SingleProcessor;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
+
+import java.awt.*;
import java.awt.geom.Rectangle2D;
import java.util.ArrayList;
import java.util.List;
@@ -38,39 +53,40 @@ import java.util.List;
/**
* ROI Tooltip plugin.<br>
* Display a tool tip with extras informations on focused ROI in Canvas2D.
- *
- * @author Stephane
+ *
+ * @author Stephane Dallongeville
*/
-public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerListener, ROIListener
-{
- private class ROICalculator implements Runnable
- {
- public ROICalculator()
- {
+@IcyPluginName("ROI Tooltip")
+@IcyPluginIcon(path = "/roi-tooltip.png")
+public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerListener, ROIListener {
+ private class ROICalculator implements Runnable {
+ @Contract(pure = true)
+ public ROICalculator() {
super();
}
@Override
- public void run()
- {
+ public void run() {
final Sequence seq = activeSequence;
final ROI roi = focusedROI;
- try
- {
- if ((seq != null) && (roi != null))
- {
- intensityInfo = ROIUtil.getIntensityInfo(activeSequence, focusedROI);
+ try {
+ if ((seq != null) && (roi != null)) {
+ //intensityInfo = ROIUtil.getIntensityInfo(activeSequence, focusedROI);
+ intensityInfo = ROIUtil.computeIntensityDescriptors(focusedROI, activeSequence, true);
points = MathUtil.roundSignificant(roi.getNumberOfPoints(), 2, true);
contourPoints = MathUtil.roundSignificant(roi.getNumberOfContourPoints(), 2, true);
- perimeter = ROIUtil.getPerimeter(activeSequence, roi);
- area = ROIUtil.getArea(activeSequence, roi);
- surfaceArea = ROIUtil.getSurfaceArea(activeSequence, roi);
- volume = ROIUtil.getVolume(activeSequence, roi);
+ //perimeter = ROIUtil.getPerimeter(activeSequence, roi);
+ perimeter = (Double) ROIUtil.computeDescriptor(ROIPerimeterDescriptor.ID, roi, activeSequence);
+ //area = ROIUtil.getArea(activeSequence, roi);
+ area = (Double) ROIUtil.computeDescriptor(ROIAreaDescriptor.ID, roi, activeSequence);
+ //surfaceArea = ROIUtil.getSurfaceArea(activeSequence, roi);
+ surfaceArea = (Double) ROIUtil.computeDescriptor(ROISurfaceAreaDescriptor.ID, roi, activeSequence);
+ //volume = ROIUtil.getVolume(activeSequence, roi);
+ volume = (Double) ROIUtil.computeDescriptor(ROIVolumeDescriptor.ID, roi, activeSequence);
}
}
- catch (Exception e)
- {
+ catch (final Exception e) {
// async process, ROI can change in the meantime
}
@@ -78,31 +94,25 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
}
}
- private class HintOverlay extends Overlay
- {
- public HintOverlay()
- {
+ private class HintOverlay extends Overlay {
+ public HintOverlay() {
super("ROI tip", OverlayPriority.TOOLTIP_LOW);
}
- private String enlarge(String text, int len)
- {
- String result = text;
+ @Contract(pure = true)
+ private @NotNull String enlarge(final String text, final int len) {
+ final StringBuilder result = new StringBuilder(text);
while (result.length() < len)
- result += ' ';
- return result;
+ result.append(' ');
+ return result.toString();
}
@Override
- public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas)
- {
- if (canvas instanceof IcyCanvas2D)
- {
- final IcyCanvas2D cnv2d = (IcyCanvas2D) canvas;
+ public void paint(final Graphics2D g, final Sequence sequence, final IcyCanvas canvas) {
+ if (canvas instanceof final IcyCanvas2D cnv2d) {
ROI roi = sequence.getFocusedROI();
- if (roi == null)
- {
+ if (roi == null) {
// search in selected ROI
final ROI2D selectedRoi = sequence.getSelectedROI2D();
@@ -111,16 +121,16 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
roi = selectedRoi;
}
- if (roi != null)
- {
+ if (roi != null) {
roiFocused(roi);
- if (roi instanceof ROI2D)
- {
+ if (roi instanceof ROI2D) {
final Rectangle2D bounds = ((ROI2D) roi).getBounds2D();
- final List<String> text = new ArrayList<String>();
- final String perim = perimeter;
- final String surfArea = surfaceArea;
+ final List<String> text = new ArrayList<>();
+ //final String perim = perimeter;
+ final double perim = perimeter;
+ //final String surfArea = surfaceArea;
+ final double surfArea = surfaceArea;
// if (processor.isProcessing())
// updatingMark = "*";
@@ -131,17 +141,19 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
text.add("Position X " + StringUtil.toString(bounds.getX(), 1));
text.add("Size X " + StringUtil.toString(bounds.getWidth(), 1));
text.add("Interior " + StringUtil.toString(points) + " px");
- if (!StringUtil.isEmpty(perim))
- text.add("Perimeter " + perim);
- if (!StringUtil.isEmpty(surfArea))
- text.add("Surf. area " + surfArea);
+ //if (!StringUtil.isEmpty(perim))
+ if (perim > 0)
+ text.add("Perimeter " + String.format("%.2f", perim));
+ //if (!StringUtil.isEmpty(surfArea))
+ if (surfArea > 0)
+ text.add("Surf. area " + String.format("%.2f", surfArea));
int maxLength = 0;
- for (String t : text)
+ for (final String t : text)
maxLength = Math.max(maxLength, t.length());
maxLength += 2;
- String tooltipText = "";
+ String tooltipText; // = "";
int ind = 0;
tooltipText = enlarge(text.get(ind++), maxLength);
@@ -151,23 +163,22 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
tooltipText += enlarge(text.get(ind++), maxLength);
tooltipText += "Contour " + StringUtil.toString(contourPoints) + " px" + "\n";
- if (!StringUtil.isEmpty(perim))
- {
+ //if (!StringUtil.isEmpty(perim)) {
+ if (perim > 0) {
tooltipText += enlarge(text.get(ind++), maxLength);
- tooltipText += "Area " + area + "\n";
+ tooltipText += "Area " + String.format("%.2f", area) + "\n";
}
- if (!StringUtil.isEmpty(surfArea))
- {
+ //if (!StringUtil.isEmpty(surfArea)) {
+ if (surfArea > 0) {
tooltipText += enlarge(text.get(ind++), maxLength);
- tooltipText += "Volume " + volume + "\n";
+ tooltipText += "Volume " + String.format("%.2f", volume) + "\n";
}
- if (intensityInfo != null)
- {
+ if (intensityInfo != null) {
tooltipText += "Intensity ";
- tooltipText += "min: " + StringUtil.toString(intensityInfo.minIntensity, 1) + " ";
- tooltipText += "max: " + StringUtil.toString(intensityInfo.maxIntensity, 1) + " ";
- tooltipText += "mean: " + StringUtil.toString(intensityInfo.meanIntensity, 1);
+ tooltipText += "min: " + StringUtil.toString(intensityInfo.min, 1) + " ";
+ tooltipText += "max: " + StringUtil.toString(intensityInfo.max, 1) + " ";
+ tooltipText += "mean: " + StringUtil.toString(intensityInfo.mean, 1);
}
final Graphics2D g2 = (Graphics2D) g.create();
@@ -194,10 +205,9 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
g2.dispose();
}
- else if (roi instanceof ROI3D)
- {
+ else if (roi instanceof ROI3D) {
// not yet supported
-
+ IcyLogger.warn(this.getClass(), "ROI3D not supported yet.");
}
}
}
@@ -214,31 +224,33 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
/**
* ROI calculated infos
*/
- IntensityInfo intensityInfo;
+ //IntensityInfo intensityInfo;
+ IntensityDescriptorInfos intensityInfo;
double points;
double contourPoints;
- String perimeter;
- String area;
- String surfaceArea;
- String volume;
-
- public ROIToolTip()
- {
+ //String perimeter;
+ double perimeter;
+ //String area;
+ double area;
+ //String surfaceArea;
+ double surfaceArea;
+ //String volume;
+ double volume;
+
+ public ROIToolTip() {
super();
overlay = new HintOverlay();
- intensityInfo = new IntensityInfo();
+ intensityInfo = new IntensityDescriptorInfos();
processor = new SingleProcessor(true);
}
- void updateInfos()
- {
+ void updateInfos() {
processor.submit(new ROICalculator());
}
@Override
- public void init()
- {
+ public void init() {
activeViewer = null;
activeSequence = null;
focusedROI = null;
@@ -250,24 +262,20 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
}
@Override
- public void run()
- {
+ public void run() {
// nothing to do here
}
@Override
- public void stop()
- {
+ public void stop() {
Icy.getMainInterface().removeActiveViewerListener(this);
viewerActivated(null);
roiFocused(null);
}
- public void sequenceActivated(Sequence sequence)
- {
- if (activeSequence != sequence)
- {
+ public void sequenceActivated(final Sequence sequence) {
+ if (activeSequence != sequence) {
if (activeSequence != null)
activeSequence.removeOverlay(overlay);
@@ -279,10 +287,8 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
}
}
- public void roiFocused(ROI roi)
- {
- if (focusedROI != roi)
- {
+ public void roiFocused(final ROI roi) {
+ if (focusedROI != roi) {
if (focusedROI != null)
focusedROI.removeListener(this);
@@ -296,27 +302,22 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
}
@Override
- public void roiChanged(ROIEvent event)
- {
- if (event.getType() == ROIEventType.ROI_CHANGED)
+ public void roiChanged(final @NotNull ROIEvent event) {
+ if (event.getType() == ROIEvent.ROIEventType.ROI_CHANGED)
updateInfos();
}
@Override
- public void viewerActivated(Viewer viewer)
- {
- if (activeViewer != viewer)
- {
+ public void viewerActivated(final Viewer viewer) {
+ if (activeViewer != viewer) {
float alpha = 1f;
- if (activeViewer != null)
- {
+ if (activeViewer != null) {
final IcyCanvas canvas = activeViewer.getCanvas();
- if (canvas != null)
- {
+ if (canvas != null) {
final Layer layer = canvas.getLayer(overlay);
if (layer != null)
- alpha = layer.getAlpha();
+ alpha = layer.getOpacity();
}
}
@@ -330,28 +331,24 @@ public class ROIToolTip extends Plugin implements PluginDaemon, ActiveViewerList
sequenceActivated(sequence);
- if (activeViewer != null)
- {
+ if (activeViewer != null) {
final IcyCanvas canvas = activeViewer.getCanvas();
- if (canvas != null)
- {
+ if (canvas != null) {
final Layer layer = canvas.getLayer(overlay);
if (layer != null)
- layer.setAlpha(alpha);
+ layer.setOpacity(alpha);
}
}
}
}
@Override
- public void viewerDeactivated(Viewer viewer)
- {
+ public void viewerDeactivated(final Viewer viewer) {
// nothing here
}
@Override
- public void activeViewerChanged(ViewerEvent event)
- {
+ public void activeViewerChanged(final ViewerEvent event) {
// nothing here
}
}
\ No newline at end of file
diff --git a/src/main/resources/icon.png b/src/main/resources/roi-tooltip.png
similarity index 100%
rename from src/main/resources/icon.png
rename to src/main/resources/roi-tooltip.png