From 5a11be25f354b42b267dd507e3cf00aa12185a7f Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Thu, 27 Jun 2024 17:11:48 +0200
Subject: [PATCH] updated pom to v2.0.0-a.1, fix classes accordingly to new
architecture, updated .gitignore
---
.gitignore | 42 ++++++++++++++++---
pom.xml | 8 ++--
.../plugins/nchenouard/spot/Detection.java | 10 ++---
.../nchenouard/spot/DetectionResult.java | 7 ++--
.../java/plugins/nchenouard/spot/Spot.java | 14 ++++++-
5 files changed, 62 insertions(+), 19 deletions(-)
diff --git a/.gitignore b/.gitignore
index 22af974..57f16fb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,9 +1,41 @@
-.idea/
-.settings/
-build/
+/build*
+/workspace
+setting.xml
+release/
target/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
-*.eml
+*.ipr
+
+### Eclipse ###
+.apt_generated
.classpath
+.factorypath
.project
-**/.DS_Store
\ 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 ffb9c4e..cfb970d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,20 +7,18 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>2.2.0</version>
+ <version>3.0.0-a.1</version>
</parent>
<artifactId>spot-detection-utilities</artifactId>
- <version>2.0.0</version>
-
- <packaging>jar</packaging>
+ <version>2.0.0-a.1</version>
<name>Detection Utilities</name>
<repositories>
<repository>
<id>icy</id>
- <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/nchenouard/spot/Detection.java b/src/main/java/plugins/nchenouard/spot/Detection.java
index 79c94bd..f28d23d 100644
--- a/src/main/java/plugins/nchenouard/spot/Detection.java
+++ b/src/main/java/plugins/nchenouard/spot/Detection.java
@@ -18,11 +18,11 @@
package plugins.nchenouard.spot;
-import icy.file.xml.XMLPersistent;
-import icy.painter.Overlay;
-import icy.system.IcyExceptionHandler;
-import icy.util.ClassUtil;
-import icy.util.XMLUtil;
+import org.bioimageanalysis.icy.common.reflect.ClassUtil;
+import org.bioimageanalysis.icy.io.xml.XMLPersistent;
+import org.bioimageanalysis.icy.io.xml.XMLUtil;
+import org.bioimageanalysis.icy.model.overlay.Overlay;
+import org.bioimageanalysis.icy.system.IcyExceptionHandler;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
diff --git a/src/main/java/plugins/nchenouard/spot/DetectionResult.java b/src/main/java/plugins/nchenouard/spot/DetectionResult.java
index c599990..fa7e09e 100644
--- a/src/main/java/plugins/nchenouard/spot/DetectionResult.java
+++ b/src/main/java/plugins/nchenouard/spot/DetectionResult.java
@@ -18,8 +18,9 @@
package plugins.nchenouard.spot;
-import icy.plugin.abstract_.Plugin;
-import icy.sequence.Sequence;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
import java.util.TreeMap;
import java.util.Vector;
@@ -30,7 +31,7 @@ import java.util.Vector;
*
* @author nicolas chenouard and Fabrice de Chaumont
*/
-
+@IcyPluginName("Detection Result")
public class DetectionResult extends Plugin {
private final TreeMap<Integer, Vector<Spot>> results;
private Sequence sourceSequence;
diff --git a/src/main/java/plugins/nchenouard/spot/Spot.java b/src/main/java/plugins/nchenouard/spot/Spot.java
index 3ba66ba..604e12c 100644
--- a/src/main/java/plugins/nchenouard/spot/Spot.java
+++ b/src/main/java/plugins/nchenouard/spot/Spot.java
@@ -18,6 +18,8 @@
package plugins.nchenouard.spot;
+import org.bioimageanalysis.icy.system.IcyExceptionHandler;
+
import java.io.PrintStream;
import java.text.NumberFormat;
import java.text.ParseException;
@@ -73,7 +75,7 @@ public class Spot {
s.mass_center.z = nf.parse(coordinates[2]).intValue();
}
catch (final ParseException e) {
- e.printStackTrace();
+ IcyExceptionHandler.showErrorMessage(e, true);
return null;
}
return s;
@@ -88,4 +90,14 @@ public class Spot {
printOut.print(mass_center.y + ",");
printOut.print(mass_center.z + "];");
}
+
+ @Override
+ public String toString() {
+ return "Spot{" + "mass_center=" + mass_center +
+ ", minIntensity=" + minIntensity +
+ ", maxIntensity=" + maxIntensity +
+ ", meanIntensity=" + meanIntensity +
+ ", point3DList=" + point3DList +
+ '}';
+ }
}
--
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