From be2675886104ea3540a4cd04b07a5997d93a1fc9 Mon Sep 17 00:00:00 2001
From: Amandine Tournay <amandine.tournay@pasteur.fr>
Date: Tue, 9 Mar 2021 19:07:46 +0100
Subject: [PATCH] Added project
---
.gitignore | 6 +
pom.xml | 92 ++++++++++
.../java/plugins/tprovoost/scale/Scale.java | 56 ++++++
.../plugins/tprovoost/scale/ScalePainter.java | 159 ++++++++++++++++++
.../tprovoost/scale/ScalePainterOld.java | 105 ++++++++++++
src/main/resources/Scale.png | Bin 0 -> 758 bytes
src/main/resources/Scale.xml | 78 +++++++++
src/main/resources/Scale_icon.png | Bin 0 -> 5132 bytes
8 files changed, 496 insertions(+)
create mode 100644 .gitignore
create mode 100644 pom.xml
create mode 100644 src/main/java/plugins/tprovoost/scale/Scale.java
create mode 100644 src/main/java/plugins/tprovoost/scale/ScalePainter.java
create mode 100644 src/main/java/plugins/tprovoost/scale/ScalePainterOld.java
create mode 100644 src/main/resources/Scale.png
create mode 100644 src/main/resources/Scale.xml
create mode 100644 src/main/resources/Scale_icon.png
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..3d47f98
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+.idea/
+target/
+.settings/
+*.iml
+.project
+.classpath
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..e61cd16
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,92 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <!-- Inherited Icy Parent POM -->
+ <parent>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>parent-pom-plugin</artifactId>
+ <version>1.0.3</version>
+ </parent>
+
+ <!-- Project Information -->
+ <artifactId>scale-bar</artifactId>
+ <version>3.1.6</version>
+
+ <packaging>jar</packaging>
+
+ <name>Scale Bar</name>
+ <description>
+ Displays a scale bar overlay on the sequence.
+ Warning: this plugin needs correct sequence metadata to be effective. Otherwise it will display wrong values.
+ </description>
+ <url>http://icy.bioimageanalysis.org/plugin/scale-bar/</url>
+ <inceptionYear>2020</inceptionYear>
+
+ <organization>
+ <name>Institut Pasteur</name>
+ <url>https://pasteur.fr</url>
+ </organization>
+
+ <licenses>
+ <license>
+ <name>GNU GPLv3</name>
+ <url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
+ <distribution>repo</distribution>
+ </license>
+ </licenses>
+
+ <developers>
+ <developer>
+ <id>sdallongeville</id>
+ <name>Stéphane Dallongeville</name>
+ <url>https://research.pasteur.fr/fr/member/stephane-dallongeville/</url>
+ <roles>
+ <role>founder</role>
+ <role>lead</role>
+ <role>architect</role>
+ <role>developer</role>
+ <role>debugger</role>
+ <role>tester</role>
+ <role>maintainer</role>
+ <role>support</role>
+ </roles>
+ </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>
+
+ <!-- The EzPlug library, simplifies writing UI for Icy plugins. -->
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>ezplug</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>
+ </repository>
+ </repositories>
+</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/scale/Scale.java b/src/main/java/plugins/tprovoost/scale/Scale.java
new file mode 100644
index 0000000..af5f315
--- /dev/null
+++ b/src/main/java/plugins/tprovoost/scale/Scale.java
@@ -0,0 +1,56 @@
+package plugins.tprovoost.scale;
+
+import icy.gui.main.GlobalSequenceListener;
+import icy.main.Icy;
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginDaemon;
+import icy.sequence.Sequence;
+
+public class Scale extends Plugin implements PluginDaemon
+{
+ ScalePainter sp;
+ GlobalSequenceListener globalSequenceListener;
+
+ @Override
+ public void run()
+ {
+ // nothing to do here
+ }
+
+ @Override
+ public void stop()
+ {
+ for (Sequence sequence : Icy.getMainInterface().getSequences())
+ sequence.removeOverlay(sp);
+
+ Icy.getMainInterface().removeGlobalSequenceListener(globalSequenceListener);
+ }
+
+ @Override
+ public void init()
+ {
+ // create painter
+ sp = new ScalePainter();
+ globalSequenceListener = new GlobalSequenceListener()
+ {
+ @Override
+ public void sequenceOpened(Sequence sequence)
+ {
+ sequence.addOverlay(sp);
+ }
+
+ @Override
+ public void sequenceClosed(Sequence sequence)
+ {
+ sequence.removeOverlay(sp);
+ }
+ };
+
+ // add the Scale Bar overlay on opened sequences
+ for (Sequence sequence : Icy.getMainInterface().getSequences())
+ sequence.addOverlay(sp);
+
+ // listen new opened sequence
+ Icy.getMainInterface().addGlobalSequenceListener(globalSequenceListener);
+ }
+}
diff --git a/src/main/java/plugins/tprovoost/scale/ScalePainter.java b/src/main/java/plugins/tprovoost/scale/ScalePainter.java
new file mode 100644
index 0000000..af4f9ce
--- /dev/null
+++ b/src/main/java/plugins/tprovoost/scale/ScalePainter.java
@@ -0,0 +1,159 @@
+package plugins.tprovoost.scale;
+
+import icy.canvas.IcyCanvas;
+import icy.canvas.IcyCanvas2D;
+import icy.math.MathUtil;
+import icy.math.UnitUtil;
+import icy.math.UnitUtil.UnitPrefix;
+import icy.painter.Overlay;
+import icy.sequence.Sequence;
+import icy.util.GraphicsUtil;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+
+public class ScalePainter extends Overlay
+{
+ /**
+ * Possible rounded scale factors : 1 --> 900
+ */
+ final static double[] scaleRoundedFactors = new double[] {1d, 2d, 3d, 4d, 5d, 6d, 7d, 8d, 9d, 10d, 20d, 30d, 40d,
+ 50d, 60d, 70d, 80d, 90d, 100d, 200d, 300d, 400d, 500d, 600d, 700d, 800d, 900d};
+
+ public ScalePainter()
+ {
+ super("Scale Bar");
+ }
+
+ @Override
+ public void paint(Graphics2D g2, Sequence sequence, IcyCanvas canvas)
+ {
+ if (g2 == null)
+ return;
+ if (!(canvas instanceof IcyCanvas2D))
+ return;
+
+ final IcyCanvas2D c2d = (IcyCanvas2D) canvas;
+ final Graphics2D g = (Graphics2D) g2.create();
+
+ double scaleFactor = c2d.getScaleX();
+ g.transform(c2d.getInverseTransform());
+
+ BasicStroke[] stroke = new BasicStroke[4];
+ stroke[0] = new BasicStroke(2f);
+ stroke[1] = new BasicStroke(3f);
+ stroke[2] = new BasicStroke(4f);
+ stroke[3] = new BasicStroke(5f);
+ int w = canvas.getCanvasSizeX();
+ int h = canvas.getCanvasSizeY();
+ double pxSize = sequence.getPixelSizeX();
+ int space = 20; // spacing from borders
+
+ int sizeW = w / 8;
+ // get the value with the best display possible
+ double valueReal = sizeW * pxSize / scaleFactor / 10;
+ UnitPrefix bestUnit = UnitUtil.getBestUnit(valueReal, UnitPrefix.MICRO, 1);
+ double valueRealBestUnit = UnitUtil.getValueInUnit(valueReal * 10, UnitPrefix.MICRO, bestUnit);
+
+ double closestScale = MathUtil.closest(valueRealBestUnit, scaleRoundedFactors);
+
+ // closest scale in px
+ int closestScPx = (int) (UnitUtil.getValueInUnit(closestScale, bestUnit, UnitPrefix.MICRO) / pxSize * scaleFactor);
+ // int closestScPx = closestScale;
+
+ g.setColor(Color.BLACK);
+ g.setStroke(stroke[3]);
+ // g.drawLine(w - space - closestScPx, h - space, w - space, h - space);
+ g.drawLine(space, h - space, space + closestScPx, h - space);
+
+ g.setColor(Color.WHITE);
+ g.setStroke(stroke[2]);
+ g.drawLine(space, h - space, space + closestScPx, h - space);
+
+ int fontSize = 14;
+ Font font = new Font("Arial", Font.PLAIN, fontSize);
+ g.setFont(font);
+ String pixelString = "" + closestScale + " " + bestUnit + "m";
+ int txW = g.getFontMetrics().charsWidth(pixelString.toCharArray(), 0, pixelString.length());
+ int txH = g.getFontMetrics().getHeight();
+
+ g.setColor(Color.black);
+ // GraphicsUtil.drawString(g, pixelString, w - space - closestScPx / 2 -
+ // txW / 2, h - space - txH, true);
+ GraphicsUtil.drawString(g, pixelString, space + closestScPx / 2 - txW / 2, h - space - txH, true);
+
+ g.dispose();
+ }
+
+ double convertScale(IcyCanvas canvas, double value)
+ {
+ return canvas.canvasToImageLogDeltaX((int) value);
+ }
+
+ public class CompositeStroke implements Stroke
+ {
+ private Stroke stroke1, stroke2;
+
+ public CompositeStroke(Stroke stroke1, Stroke stroke2)
+ {
+ this.stroke1 = stroke1;
+ this.stroke2 = stroke2;
+ }
+
+ @Override
+ public Shape createStrokedShape(Shape shape)
+ {
+ return stroke2.createStrokedShape(stroke1.createStrokedShape(shape));
+ }
+ }
+
+// private int findBestScale(IcyCanvas2D canvas, Sequence s)
+// {
+// int w = s.getWidth();
+// int minSize = w / 8;
+// int maxSize = w / 4;
+// double pxSize = s.getPixelSizeX();
+// double tab[] = new double[maxSize - minSize];
+// double scaleFactor = canvas.getScaleX();
+//
+// // generate all values
+// for (int i = minSize; i < maxSize; ++i)
+// {
+//
+// // get the value with the best display possible
+// double valueReal = i * pxSize / scaleFactor;
+// UnitPrefix bestUnit = UnitUtil.getBestUnit(valueReal, UnitPrefix.MICRO, 1);
+// double bestValue = UnitUtil.getValueInUnit(valueReal, UnitPrefix.MICRO, bestUnit);
+// bestValue = ((int) (bestValue * 100)) / 100d;
+//
+// tab[i - minSize] = bestValue;
+// }
+//
+// // return the first value with a round value
+// for (int i = 0; i < maxSize - minSize; ++i)
+// {
+// double bestValue = tab[i];
+// if (bestValue == (int) bestValue)
+// {
+// return i + minSize;
+// }
+// }
+//
+// // otherwise, return first value with only one decimal
+// for (int i = 0; i < maxSize - minSize; ++i)
+// {
+// double bestValue = tab[i];
+// if (bestValue == ((int) (bestValue * 10)) / 10d)
+// {
+// return i + minSize;
+// }
+// }
+//
+// // otherwise, return w / 4
+// return w / 4;
+// }
+}
diff --git a/src/main/java/plugins/tprovoost/scale/ScalePainterOld.java b/src/main/java/plugins/tprovoost/scale/ScalePainterOld.java
new file mode 100644
index 0000000..caf0c37
--- /dev/null
+++ b/src/main/java/plugins/tprovoost/scale/ScalePainterOld.java
@@ -0,0 +1,105 @@
+package plugins.tprovoost.scale;
+
+import icy.canvas.IcyCanvas;
+import icy.canvas.IcyCanvas2D;
+import icy.math.UnitUtil;
+import icy.math.UnitUtil.UnitPrefix;
+import icy.painter.Overlay;
+import icy.roi.ROI2D;
+import icy.sequence.Sequence;
+import icy.util.GraphicsUtil;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+
+public class ScalePainterOld extends Overlay
+{
+ public ScalePainterOld()
+ {
+ super("Scale Bar");
+ }
+
+ @Override
+ public void paint(Graphics2D g2, Sequence sequence, IcyCanvas canvas)
+ {
+ if (g2 == null)
+ return;
+ Graphics2D g = (Graphics2D) g2.create();
+ // g.transform(((IcyCanvas2D) canvas).getInverseTransform());
+ int w = sequence.getWidth();
+ int h = sequence.getHeight();
+ int sizeW = w / 10;
+ double pxSize = sequence.getPixelSizeX();
+ int spaceFBords = 20; // spacing from borders
+
+ BasicStroke[] stroke = new BasicStroke[4];
+ stroke[0] = new BasicStroke((float) canvas.canvasToImageLogDeltaX(2));
+ stroke[1] = new BasicStroke((float) canvas.canvasToImageLogDeltaX(3));
+ stroke[2] = new BasicStroke((float) canvas.canvasToImageLogDeltaX(4));
+ stroke[3] = new BasicStroke((float) canvas.canvasToImageLogDeltaX(5));
+
+ // get the value with the best display possible
+ double valueReal = sizeW * pxSize / 10;
+ UnitPrefix bestUnit = UnitUtil.getBestUnit(valueReal, UnitPrefix.MICRO, 1);
+ double bestValue = UnitUtil.getValueInUnit(valueReal * 10, UnitPrefix.MICRO, bestUnit);
+
+ // get the best scale possible
+ int closestScale = 0;
+ if (bestValue < 10)
+ {
+ closestScale = (int) bestValue;
+ } else
+ closestScale = (int) (bestValue / 10) * 10;
+
+ // closest scale in px
+ int closestScPx = (int) (UnitUtil.getValueInUnit(closestScale, bestUnit, UnitPrefix.MICRO) / pxSize);
+
+ g.setColor(Color.BLACK);
+ g.setStroke(stroke[3]);
+ g.drawLine(w - spaceFBords - closestScPx, h - spaceFBords, w - spaceFBords, h - spaceFBords);
+
+ g.setColor(Color.WHITE);
+ g.setStroke(stroke[2]);
+ g.drawLine(w - spaceFBords - closestScPx, h - spaceFBords, w - spaceFBords, h - spaceFBords);
+
+ int fontSize = (int) canvas.canvasToImageLogDeltaX(14);
+ Font font = new Font("Arial", Font.PLAIN, fontSize);
+ g.setFont(font);
+ String pixelString = "" + closestScale + " " + bestUnit + "m";
+ int txW = g.getFontMetrics().charsWidth(pixelString.toCharArray(), 0, pixelString.length());
+ int txH = g.getFontMetrics().getHeight();
+
+ // g.fillRect(w - spaceFBords - closestScPx / 2 - txW / 2, h -
+ // spaceFBords - txH, txW, txH);
+
+ g.setColor(Color.black);
+ GraphicsUtil.drawString(g, pixelString, w - spaceFBords - closestScPx / 2 - txW / 2, h - spaceFBords - txH, true);
+
+ g.dispose();
+ }
+
+ double convertScale(IcyCanvas canvas, double value)
+ {
+ return canvas.canvasToImageLogDeltaX((int) value);
+ }
+
+ public class CompositeStroke implements Stroke
+ {
+ private Stroke stroke1, stroke2;
+
+ public CompositeStroke(Stroke stroke1, Stroke stroke2)
+ {
+ this.stroke1 = stroke1;
+ this.stroke2 = stroke2;
+ }
+
+ public Shape createStrokedShape(Shape shape)
+ {
+ return stroke2.createStrokedShape(stroke1.createStrokedShape(shape));
+ }
+ }
+}
diff --git a/src/main/resources/Scale.png b/src/main/resources/Scale.png
new file mode 100644
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diff --git a/src/main/resources/Scale.xml b/src/main/resources/Scale.xml
new file mode 100644
index 0000000..9a16e0b
--- /dev/null
+++ b/src/main/resources/Scale.xml
@@ -0,0 +1,78 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<root>
+<url><![CDATA[http://icy.bioimageanalysis.org/repository/getXMLPluginFile.php?pluginId=179&beta=0]]></url><name>Scale Bar</name><version>2.0.0.0</version><required_kernel_version>1.3.6.0</required_kernel_version><kernel_ver>1.3.6.0</kernel_ver><jar_url><![CDATA[http://icy.bioimageanalysis.org/repository/getJarFile.php?pluginId=179&beta=0]]></jar_url><icon_url><![CDATA[http://bioimageanalysis.org/icy/image.php?idAttach=1229]]></icon_url><image_url><![CDATA[http://bioimageanalysis.org/icy/image.php?idAttach=2020]]></image_url><description><![CDATA[Displays a scale bar overlay on the sequence. Be advised, this plugin needs correct Metadata on the sequence to be effective or it will display wrong values.]]></description><classname><![CDATA[plugins.tprovoost.scale.Scale]]></classname><author><![CDATA[tprovoost - Thomas Provoost]]></author><changelog><![CDATA[-
+Version 2.0.0.0
+Date 2013-07-03 12:15:38
+
+* Bottom left now. This will make it avoid being invisible because of the zoom factor is displayed at the same time
+* the scale bar now fully works
+
+-
+Version 1.6.0.0
+Date 2013-07-03 12:02:48
+
+* Uses orders of magnitude instead of precise values.
+* size of scale bar never changes now: will always be : size of the canvas / 8.
+
+-
+Version 1.5.0.0
+Date 2013-06-26 16:52:26
+
+* Now only updates text while zooming, and change the size and value after the zoom
+
+-
+Version 1.4.0.0
+Date 2013-06-26 11:20:13
+
+* fixed bar location issue
+
+-
+Version 1.3.1.0
+Date 2013-06-17 15:18:23
+
+* removed debug information
+
+-
+Version 1.3.0.0
+Date 2013-06-17 15:17:46
+
+* now scales with images zoom
+
+-
+Version 1.2.0.0
+Date 2013-06-17 14:15:50
+
+* removed white rectangle
+* now shadow on text
+
+-
+Version 1.1.0.0
+Date 2013-01-11 16:30:30
+
+Updated to 1.3.0.0
+
+-
+Version 1.0.0.2
+Date 2012-10-22 17:10:43
+
+* corrected 3D issue.
+
+-
+Version 1.0.0.1
+Date 2012-07-03 09:23:11
+
+Corrected issue with compilation.
+
+-
+Version 1.0.0.0
+Date 2012-07-02 21:17:10
+
+Updated to Icy last version.
+
+-
+Version 0.0.1.0
+Date 2012-06-20 14:33:49
+
+
+
+]]></changelog><web><![CDATA[http://icy.bioimageanalysis.org/plugin/Scale_Bar]]></web><dependencies></dependencies></root>
\ No newline at end of file
diff --git a/src/main/resources/Scale_icon.png b/src/main/resources/Scale_icon.png
new file mode 100644
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--
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