diff --git a/.gitignore b/.gitignore
index bf678dd154daf5cd3c5fdf5b9c22738fed75066a..57f16fb67c1b1589981416b323d7a9debc728665 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,8 +1,41 @@
-.idea/
+/build*
+/workspace
+setting.xml
+release/
target/
-bin/
-.settings/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
-.project
+*.ipr
+
+### Eclipse ###
+.apt_generated
.classpath
-SpotDetectorBlock.jar
+.factorypath
+.project
+.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 09473f6e1f70e7f03bcff948afb091559ba4754e..09d18711bba5f10926e702873342253475421082 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,13 +7,11 @@
<parent>
<artifactId>pom-icy</artifactId>
<groupId>org.bioimageanalysis.icy</groupId>
- <version>2.1.2</version>
+ <version>3.0.0-a.1</version>
</parent>
<artifactId>spot-detector-block</artifactId>
- <version>1.0.0</version>
-
- <packaging>jar</packaging>
+ <version>2.0.0-a.1</version>
<name>Spot Detector block</name>
<description>
@@ -21,6 +19,14 @@
</description>
<dependencies>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>ezplug</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>protocols</artifactId>
+ </dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>spot-detector</artifactId>
@@ -30,7 +36,7 @@
<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/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java b/src/main/java/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java
index 2b51f70b230e50d5f823e484c5df8c594f33178a..fb6d307f01ae622b20b42f8b91050a14e0201f57 100644
--- a/src/main/java/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java
+++ b/src/main/java/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java
@@ -1,70 +1,91 @@
-package plugins.fab.waveletspotdetectorblock;
+/*
+ * 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/>.
+ */
-import java.util.ArrayList;
+package plugins.fab.waveletspotdetectorblock;
-import icy.plugin.abstract_.Plugin;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceUtil;
-import icy.system.thread.ThreadUtil;
+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.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROI2D;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceUtil;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.util.VarList;
-import plugins.adufour.vars.lang.VarBoolean;
-import plugins.adufour.vars.lang.VarEnum;
-import plugins.adufour.vars.lang.VarInteger;
-import plugins.adufour.vars.lang.VarROIArray;
-import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.lang.*;
import plugins.adufour.vars.util.VarException;
import plugins.fab.spotDetector.DetectionSpot;
import plugins.fab.spotDetector.detector.DetectionToROI;
import plugins.fab.spotDetector.detector.UDWTScale;
import plugins.fab.spotDetector.detector.UDWTWaveletCore;
-public class WaveletSpotDetectorBlock extends Plugin implements Block
-{
+import java.util.ArrayList;
- enum detectionMethodEnum
- {
+@IcyPluginName("Wavelet Spot Detector")
+@IcyPluginIcon(path = "/spot-detector-block.png")
+public class WaveletSpotDetectorBlock extends Plugin implements Block {
+ enum detectionMethodEnum {
BRIGHT_SPOT, DARK_SPOT
}
- VarSequence inputSequenceVar = new VarSequence("input Sequence", null);
- VarEnum<detectionMethodEnum> detectionMethod = new VarEnum<detectionMethodEnum>("Spot to detect",
- detectionMethodEnum.BRIGHT_SPOT);
+ VarSequence inputSequenceVar = new VarSequence("Input Sequence", null);
+ VarEnum<detectionMethodEnum> detectionMethod = new VarEnum<>("Spot to detect", detectionMethodEnum.BRIGHT_SPOT);
VarBoolean computeWATConsideringROIBoolean = new VarBoolean("Compute WAT considering ROI", false);
VarSequence inputSequenceROIVar = new VarSequence("ROIs from sequence for WAT", null);
VarBoolean force2DWaveletVar = new VarBoolean("Force 2D Wavelets", false);
VarROIArray inputROIForMask = new VarROIArray("ROIs for detection mask", null);
- VarBoolean[] useScaleBoolean = {new VarBoolean("Scale 1", false), new VarBoolean("Scale 2", true),
- new VarBoolean("Scale 3", false), new VarBoolean("Scale 4", false), new VarBoolean("Scale 5", false)};
-
- VarInteger[] scaleParameter = {new VarInteger("Th. scale 1:", 100), new VarInteger("Th. scale 2:", 100),
- new VarInteger("Th. scale 3:", 100), new VarInteger("Th. scale 4:", 100), new VarInteger("Th. scale 5:", 100)};
-
- VarSequence outSequence = new VarSequence("output Sequence", null);
- VarSequence denoisedSequence = new VarSequence("denoised Sequence", null);
+ VarBoolean[] useScaleBoolean = {
+ new VarBoolean("Scale 1", false),
+ new VarBoolean("Scale 2", true),
+ new VarBoolean("Scale 3", false),
+ new VarBoolean("Scale 4", false),
+ new VarBoolean("Scale 5", false)
+ };
+
+ VarInteger[] scaleParameter = {
+ new VarInteger("Th. scale 1:", 100),
+ new VarInteger("Th. scale 2:", 100),
+ new VarInteger("Th. scale 3:", 100),
+ new VarInteger("Th. scale 4:", 100),
+ new VarInteger("Th. scale 5:", 100)
+ };
+
+ //VarSequence outSequence = new VarSequence("output Sequence", null);
+ //VarSequence denoisedSequence = new VarSequence("denoised Sequence", null);
VarSequence binarySpotSequence = new VarSequence("binary Spot Sequence", null);
VarROIArray detectionAsROIOut = new VarROIArray("detection as ROIs", null);
@Override
- public void run()
- {
-
+ public void run() {
// test if input sequence has only 1 channel.
Sequence inputSequence = inputSequenceVar.getValue();
- if (inputSequence == null)
- {
- throw new VarException("The input sequence must be set");
+ if (inputSequence == null) {
+ throw new VarException(inputSequenceVar, "The input sequence must be set");
}
- if (inputSequence.getSizeC() != 1)
- {
- throw new VarException(
- "The input sequence must contain only 1 channel. Please use 'Extract Channel' prior to the WaveletBlock");
+ if (inputSequence.getSizeC() != 1) {
+ throw new VarException(inputSequenceVar, "The input sequence must contain only 1 channel. Please use 'Extract Channel' prior to the WaveletBlock");
}
// inputChannelVar
@@ -75,38 +96,26 @@ public class WaveletSpotDetectorBlock extends Plugin implements Block
boolean detectNegative;
- if (detectionMethod.getValue() == detectionMethodEnum.BRIGHT_SPOT)
- {
- detectNegative = false;
- }
- else
- {
- detectNegative = true;
- }
+ detectNegative = detectionMethod.getValue() != detectionMethodEnum.BRIGHT_SPOT;
boolean computeWATwithROI = computeWATConsideringROIBoolean.getValue();
// copy ROI from input sequence to the computation sequence
Sequence inputComputationSequence;
- try
- {
+ try {
inputComputationSequence = SequenceUtil.getCopy(inputSequence);
}
- catch (InterruptedException ex)
- {
+ catch (InterruptedException ex) {
// interrupt process
return;
}
- if (inputSequenceROIVar.getValue() != null)
- {
- for (ROI2D roi : inputSequenceROIVar.getValue().getROI2Ds())
- {
+ if (inputSequenceROIVar.getValue() != null) {
+ for (ROI2D roi : inputSequenceROIVar.getValue().getROI2Ds()) {
ROI2D roiCopy = (ROI2D) roi.getCopy();
- if (roiCopy != null)
- {
+ if (roiCopy != null) {
inputComputationSequence.addROI(roiCopy);
}
}
@@ -116,73 +125,63 @@ public class WaveletSpotDetectorBlock extends Plugin implements Block
// create UDWTScale Parameter list.
- final ArrayList<UDWTScale> UDWTScaleArrayList = new ArrayList<UDWTScale>();
+ final ArrayList<UDWTScale> UDWTScaleArrayList = new ArrayList<>();
// System.out.println("Block debug.");
- ThreadUtil.invokeNow(new Runnable()
- {
-
- @Override
- public void run()
- {
-
- for (int i = 0; i < 5; i++)
- {
- // System.out.println( "Scale enabled #" +i +" : " + useScaleBoolean[i].getValue() );
- UDWTScale scale = new UDWTScale(i + 1, useScaleBoolean[i].getValue(), scaleParameter[i].getValue());
- UDWTScaleArrayList.add(scale);
- }
+ ThreadUtil.invokeNow(() -> {
+ for (int i = 0; i < 5; i++) {
+ // System.out.println( "Scale enabled #" +i +" : " + useScaleBoolean[i].getValue() );
+ UDWTScale scale = new UDWTScale(i + 1, useScaleBoolean[i].getValue(), scaleParameter[i].getValue());
+ UDWTScaleArrayList.add(scale);
}
});
// Perform detection.
- try
- {
- ArrayList<DetectionSpot> detectionResult = waveletCore.computeDetection(true, UDWTScaleArrayList, inputComputationSequence,
- detectNegative, computeWATwithROI, force2DWaveletVar.getValue());
+ try {
+ ArrayList<DetectionSpot> detectionResult = waveletCore.computeDetection(
+ true,
+ UDWTScaleArrayList,
+ inputComputationSequence,
+ detectNegative,
+ computeWATwithROI,
+ force2DWaveletVar.getValue()
+ );
- // System.out.println( "ROI Mask : " + inputROIForMask.getValue() );
+ // System.out.println( "ROI Mask : " + inputROIForMask.getValue() );
- // Filter spot with ROIs.
- if (inputROIForMask.getValue().length != 0)
- {
- ArrayList<DetectionSpot> detectionResultCopy = new ArrayList<DetectionSpot>(detectionResult);
+ // Filter spot with ROIs.
+ if (inputROIForMask.getValue().length != 0) {
+ ArrayList<DetectionSpot> detectionResultCopy = new ArrayList<>(detectionResult);
detectionList:
- for (DetectionSpot spot : detectionResultCopy)
- {
+ for (DetectionSpot spot : detectionResultCopy) {
// Point2D spotCoordinates = new Point2D.Double( spot.getMassCenter().x , spot.getMassCenter().y );
// spot.getMassCenter()
ROI detectionAsROI = null;
- try
- {
- ArrayList<DetectionSpot> detectionList = new ArrayList<DetectionSpot>();
+ try {
+ ArrayList<DetectionSpot> detectionList = new ArrayList<>();
detectionList.add(spot);
- detectionAsROI = DetectionToROI.convertDetectionToROI(detectionList).get(0);
+ detectionAsROI = DetectionToROI.convertDetectionToROI(detectionList).getFirst();
}
- catch (NullPointerException e)
- {
- System.err.println("Error in spot to ROI conversion");
+ catch (NullPointerException e) {
+ IcyLogger.error(this.getClass(), "Error in spot to ROI conversion.");
}
- if (detectionAsROI == null)
- {
- System.err.println("Can't convert spot to ROI. spot=" + spot);
+ if (detectionAsROI == null) {
+ IcyLogger.error(this.getClass(), "Can't convert spot to ROI. spot=" + spot);
continue;
}
// System.out.println( "spot as ROI to test: " + detectionAsROI.getBounds5D() );
- for (ROI roi : inputROIForMask.getValue())
- {
+ for (ROI roi : inputROIForMask.getValue()) {
// System.out.println( "roi contenant: " + roi.getBounds5D() );
- if (roi.contains(detectionAsROI))
- {
+ if (roi.contains(detectionAsROI)) {
// System.out.println("contains");
continue detectionList;
}
@@ -200,10 +199,8 @@ public class WaveletSpotDetectorBlock extends Plugin implements Block
{
Sequence binarySequence = waveletCore.getBinarySequence();
- if (inputSequenceROIVar.getValue() != null)
- {
- for (ROI2D roi : inputSequenceROIVar.getValue().getROI2Ds())
- {
+ if (inputSequenceROIVar.getValue() != null) {
+ for (ROI2D roi : inputSequenceROIVar.getValue().getROI2Ds()) {
// System.out.println("roi:"+roi);
String name = roi.getName();
@@ -221,52 +218,44 @@ public class WaveletSpotDetectorBlock extends Plugin implements Block
// output detection as ROI
{
ArrayList<ROI> roiList = DetectionToROI.convertDetectionToROI(detectionResult);
- ROI roi[] = new ROI[roiList.size()];
+ ROI[] roi = new ROI[roiList.size()];
int i = 0;
- for (ROI roiCandidate : roiList)
- {
+ for (ROI roiCandidate : roiList) {
roi[i] = roiCandidate;
i++;
}
detectionAsROIOut.setValue(roi);
}
}
- catch (InterruptedException e)
- {
+ catch (InterruptedException e) {
// protocols process interrupted
Thread.currentThread().interrupt();
}
}
@Override
- public void declareInput(VarList inputMap)
- {
-
- inputMap.add(inputSequenceVar);
- inputMap.add(detectionMethod);
- inputMap.add("input Sequence ROIs", inputSequenceROIVar);
- inputMap.add(computeWATConsideringROIBoolean);
- inputMap.add(inputROIForMask);
-
- for (int i = 0; i < 5; i++)
- {
- inputMap.add(useScaleBoolean[i]);
+ public void declareInput(@NotNull VarList inputMap) {
+ inputMap.add("input-sequence", inputSequenceVar);
+ inputMap.add("detection-method", detectionMethod);
+ inputMap.add("input-sequence-rois", inputSequenceROIVar);
+ inputMap.add("compute-wat-considering-roi", computeWATConsideringROIBoolean);
+ inputMap.add("input-roi-for-mask", inputROIForMask);
+
+ for (int i = 0; i < 5; i++) {
+ inputMap.add("use-scale-" + i, useScaleBoolean[i]);
}
- for (int i = 0; i < 5; i++)
- {
- inputMap.add(scaleParameter[i]);
+ for (int i = 0; i < 5; i++) {
+ inputMap.add("scale-value-" + i, scaleParameter[i]);
}
- inputMap.add(force2DWaveletVar);
+ inputMap.add("force-2d-wavelet", force2DWaveletVar);
}
@Override
- public void declareOutput(VarList outputMap)
- {
-
+ public void declareOutput(@NotNull VarList outputMap) {
// outputMap.add( outSequence );
// outputMap.add( denoisedSequence );
- outputMap.add(binarySpotSequence);
- outputMap.add(detectionAsROIOut);
+ outputMap.add("Binary Spot Sequence", binarySpotSequence);
+ outputMap.add("Detection as ROI", detectionAsROIOut);
}
diff --git a/src/main/resources/spot-detector-block.png b/src/main/resources/spot-detector-block.png
new file mode 100644
index 0000000000000000000000000000000000000000..fc0a7455a4c58ab68ab497d0e1ad058e45c28cc4
Binary files /dev/null and b/src/main/resources/spot-detector-block.png differ