From de4f6e7227dcaa04d6017273a01799e2f227fd58 Mon Sep 17 00:00:00 2001
From: Amandine Tournay <amandine.tournay@pasteur.fr>
Date: Tue, 9 Mar 2021 17:17:09 +0100
Subject: [PATCH] Added project
---
.gitignore | 6 +
pom.xml | 104 ++++++++++++
.../trackprocessors/DistanceProfiler.java | 157 ++++++++++++++++++
3 files changed, 267 insertions(+)
create mode 100644 .gitignore
create mode 100644 pom.xml
create mode 100644 src/main/java/plugins/adufour/trackprocessors/DistanceProfiler.java
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..16a016f
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,104 @@
+<?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>distance-profiler</artifactId>
+ <version>1.0.0</version>
+
+ <packaging>jar</packaging>
+
+ <name>Distance Profiler</name>
+ <description>
+ rack Processor plugin that computes the relative distance between detections and their evolution over time, with possibility to
+ export to Excel for further analysis
+ </description>
+ <url>http://icy.bioimageanalysis.org/plugin/distance-profiler-track-processor/</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>
+
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>track-manager</artifactId>
+ <version>1.4.6</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>workbooks</artifactId>
+ <version>3.4.10</version>
+ </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/adufour/trackprocessors/DistanceProfiler.java b/src/main/java/plugins/adufour/trackprocessors/DistanceProfiler.java
new file mode 100644
index 0000000..ef189ea
--- /dev/null
+++ b/src/main/java/plugins/adufour/trackprocessors/DistanceProfiler.java
@@ -0,0 +1,157 @@
+package plugins.adufour.trackprocessors;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+
+import javax.swing.JButton;
+import javax.swing.JFileChooser;
+import javax.swing.JPanel;
+import javax.vecmath.Point3d;
+
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+
+import icy.gui.dialog.ConfirmDialog;
+import plugins.adufour.vars.gui.swing.SwingVarEditor;
+import plugins.adufour.vars.lang.VarWorkbook;
+import plugins.fab.trackmanager.PluginTrackManagerProcessor;
+import plugins.fab.trackmanager.TrackGroup;
+import plugins.fab.trackmanager.TrackSegment;
+import plugins.nchenouard.spot.Detection;
+
+public class DistanceProfiler extends PluginTrackManagerProcessor
+{
+ public DistanceProfiler()
+ {
+ setName("Relative distance between detections");
+ }
+
+ @Override
+ public void Close()
+ {
+
+ }
+
+ @Override
+ public void Compute()
+ {
+ panel.setVisible(false);
+ panel.removeAll();
+ panel.setLayout(new BorderLayout());
+
+ final VarWorkbook wb = new VarWorkbook("Distance profile", "Distance profile");
+ SwingVarEditor<Workbook> viewer = (SwingVarEditor<Workbook>) wb.createVarViewer();
+ panel.add(viewer.getEditorComponent(), BorderLayout.CENTER);
+
+ Sheet sheet = wb.getValue().getSheetAt(0);
+ int rowIndex = 0;
+
+ Row headerRow = sheet.createRow(rowIndex++);
+ headerRow.createCell(0).setCellValue("Group (A)");
+ headerRow.createCell(1).setCellValue("Track (A)");
+ headerRow.createCell(2).setCellValue("Group (B)");
+ headerRow.createCell(3).setCellValue("Track (B)");
+ headerRow.createCell(4).setCellValue("Frame");
+ headerRow.createCell(5).setCellValue("Distance (pixels)");
+
+ // System.out.println("Track Group (A)\tTrack ID (A)\tTrack Group (B)\tTrack ID (B)\tFrame\tDistance (pixels)");
+
+ ArrayList<TrackGroup> trackGroups = trackPool.getTrackGroupList();
+
+ for (int trackGroupIndexA = 0; trackGroupIndexA < trackGroups.size(); trackGroupIndexA++)
+ {
+ TrackGroup tgA = trackGroups.get(trackGroupIndexA);
+ ArrayList<TrackSegment> trackSegmentsA = tgA.getTrackSegmentList();
+
+ for (int trackGroupIndexB = trackGroupIndexA; trackGroupIndexB < trackGroups.size(); trackGroupIndexB++)
+ {
+ TrackGroup tgB = trackGroups.get(trackGroupIndexB);
+ ArrayList<TrackSegment> trackSegmentsB = tgB.getTrackSegmentList();
+
+ for (int trackSegmentIndexA = 0; trackSegmentIndexA < trackSegmentsA.size(); trackSegmentIndexA++)
+ {
+ TrackSegment tsA = trackSegmentsA.get(trackSegmentIndexA);
+ int trackIDA = tgA.getTrackSegmentList().indexOf(tsA);
+
+ for (int trackSegmentIndexB = trackSegmentIndexA; trackSegmentIndexB < trackSegmentsB.size(); trackSegmentIndexB++)
+ {
+ TrackSegment tsB = trackSegmentsB.get(trackSegmentIndexB);
+
+ if (tsA == tsB) continue;
+
+ int trackIDB = tgB.getTrackSegmentList().indexOf(tsB);
+
+ // measure the distance between each detection set
+ for (Detection dA : tsA.getDetectionList())
+ {
+ Point3d pA = new Point3d(dA.getX(), dA.getY(), dA.getZ());
+
+ for (Detection dB : tsB.getDetectionList())
+ {
+ if (dA.getT() != dB.getT()) continue;
+
+ Point3d pB = new Point3d(dB.getX(), dB.getY(), dB.getZ());
+
+ Row row = sheet.createRow(rowIndex++);
+ row.createCell(0).setCellValue(tgA.getDescription());
+ row.createCell(1).setCellValue("" + trackIDA);
+ row.createCell(2).setCellValue(tgB.getDescription());
+ row.createCell(3).setCellValue("" + trackIDB);
+ row.createCell(4).setCellValue("" + dA.getT());
+ row.createCell(5).setCellValue(pA.distance(pB));
+ // System.out.println(tgA.getDescription() + "\t" + trackIDA + "\t"
+ // + tgB.getDescription() + "\t" + trackIDB + "\t" + dA.getT() +
+ // "\t" + pA.distance(pB));
+ }
+ }
+ }
+ }
+ }
+ }
+ // notify the viewer that the value has changed
+ viewer.valueChanged(wb, null, wb.getValue());
+
+ JPanel options = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ JButton bExport = new JButton("Export to Excel");
+ bExport.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ JFileChooser f = new JFileChooser();
+ if (f.showOpenDialog(getPanel().getParent()) != JFileChooser.APPROVE_OPTION) return;
+
+ File file = f.getSelectedFile();
+ if (!file.getPath().endsWith(".xls") && !file.getPath().endsWith(".xlsx")) file = new File(file.getPath() + ".xls");
+
+ if (!file.exists() || ConfirmDialog.confirm("Overwrite " + file.getPath() + "?"))
+ {
+ try
+ {
+ wb.getValue().write(new FileOutputStream(file, false));
+ }
+ catch (Exception e1)
+ {
+ throw new RuntimeException(e1);
+ }
+ }
+ }
+ });
+ options.add(bExport);
+
+ panel.add(options, BorderLayout.NORTH);
+
+ panel.setVisible(true);
+ }
+
+ @Override
+ public void displaySequenceChanged()
+ {
+ }
+}
--
GitLab