diff --git a/.gitignore b/.gitignore index 22af9746b07a854159ce190cf70f35b692fe6fdc..57f16fb67c1b1589981416b323d7a9debc728665 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 ffb9c4edbc7019d9d5e9ec70735433afd19981f3..cfb970d2d52ef68ac54521fcc1b219cde62ea64d 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 79c94bd86dc865543a0df9af4f67298161fa3f1d..f28d23dc5ddc7dacef28f026b9a47ec42da1b9c6 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 c599990396de852a73c121c6d9ffd64ec16822e8..fa7e09e11519743ae6e438ea775e40940fe94e6e 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 3ba66ba75769c905851536afa8d2acf440ccb81a..604e12c1e7594332c371cfd34d31066aa885e9cb 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 + + '}'; + } }