From 9f58dbbc6d618f08805570cbd30004f5805b3061 Mon Sep 17 00:00:00 2001
From: Amandine Tournay <amandine.tournay@pasteur.fr>
Date: Tue, 9 Mar 2021 19:09:47 +0100
Subject: [PATCH] Added project
---
.gitignore | 6 +
SpotDetectorBlock.jar | Bin 0 -> 8596 bytes
bin/META-INF/MANIFEST.MF | 2 +
bin/SpotDetectorBlock.jar | Bin 0 -> 8596 bytes
bin/export.jardesc | 16 ++
.../WaveletSpotDetectorBlock$1.class | Bin 0 -> 1589 bytes
...potDetectorBlock$detectionMethodEnum.class | Bin 0 -> 1476 bytes
.../WaveletSpotDetectorBlock.class | Bin 0 -> 7761 bytes
export.jardesc | 16 ++
.../WaveletSpotDetectorBlock$1.class | Bin 0 -> 1593 bytes
...potDetectorBlock$detectionMethodEnum.class | Bin 0 -> 1476 bytes
.../WaveletSpotDetectorBlock.class | Bin 0 -> 7769 bytes
.../WaveletSpotDetectorBlock.java | 272 ++++++++++++++++++
13 files changed, 312 insertions(+)
create mode 100644 .gitignore
create mode 100644 SpotDetectorBlock.jar
create mode 100644 bin/META-INF/MANIFEST.MF
create mode 100644 bin/SpotDetectorBlock.jar
create mode 100644 bin/export.jardesc
create mode 100644 bin/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$1.class
create mode 100644 bin/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$detectionMethodEnum.class
create mode 100644 bin/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.class
create mode 100644 export.jardesc
create mode 100644 src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$1.class
create mode 100644 src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$detectionMethodEnum.class
create mode 100644 src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.class
create mode 100644 src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.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/SpotDetectorBlock.jar b/SpotDetectorBlock.jar
new file mode 100644
index 0000000000000000000000000000000000000000..539289c9d1d969b9060a79531a676bad1798603b
GIT binary patch
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diff --git a/bin/META-INF/MANIFEST.MF b/bin/META-INF/MANIFEST.MF
new file mode 100644
index 0000000..59499bc
--- /dev/null
+++ b/bin/META-INF/MANIFEST.MF
@@ -0,0 +1,2 @@
+Manifest-Version: 1.0
+
diff --git a/bin/SpotDetectorBlock.jar b/bin/SpotDetectorBlock.jar
new file mode 100644
index 0000000000000000000000000000000000000000..539289c9d1d969b9060a79531a676bad1798603b
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diff --git a/bin/export.jardesc b/bin/export.jardesc
new file mode 100644
index 0000000..d048986
--- /dev/null
+++ b/bin/export.jardesc
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="WINDOWS-1252" standalone="no"?>
+<jardesc>
+ <jar path="Spot Detector Block/SpotDetectorBlock.jar"/>
+ <options buildIfNeeded="true" compress="true" descriptionLocation="/Spot Detector Block/export.jardesc" exportErrors="false" exportWarnings="true" includeDirectoryEntries="true" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
+ <storedRefactorings deprecationInfo="true" structuralOnly="false"/>
+ <selectedProjects/>
+ <manifest generateManifest="true" manifestLocation="/Icy-Kernel/META-INF/MANIFEST.MF" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
+ <sealing sealJar="false">
+ <packagesToSeal/>
+ <packagesToUnSeal/>
+ </sealing>
+ </manifest>
+ <selectedElements exportClassFiles="true" exportJavaFiles="true" exportOutputFolder="false">
+ <javaElement handleIdentifier="=Spot Detector Block/src"/>
+ </selectedElements>
+</jardesc>
diff --git a/bin/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$1.class b/bin/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$1.class
new file mode 100644
index 0000000000000000000000000000000000000000..78f5baa5a3e3033f8603fd5038459ef0c1aaa04d
GIT binary patch
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HcmV?d00001
diff --git a/bin/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$detectionMethodEnum.class b/bin/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$detectionMethodEnum.class
new file mode 100644
index 0000000000000000000000000000000000000000..4cb76999790403d420aae245c0c06b27112b62bf
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diff --git a/bin/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.class b/bin/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.class
new file mode 100644
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HcmV?d00001
diff --git a/export.jardesc b/export.jardesc
new file mode 100644
index 0000000..d048986
--- /dev/null
+++ b/export.jardesc
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="WINDOWS-1252" standalone="no"?>
+<jardesc>
+ <jar path="Spot Detector Block/SpotDetectorBlock.jar"/>
+ <options buildIfNeeded="true" compress="true" descriptionLocation="/Spot Detector Block/export.jardesc" exportErrors="false" exportWarnings="true" includeDirectoryEntries="true" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
+ <storedRefactorings deprecationInfo="true" structuralOnly="false"/>
+ <selectedProjects/>
+ <manifest generateManifest="true" manifestLocation="/Icy-Kernel/META-INF/MANIFEST.MF" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
+ <sealing sealJar="false">
+ <packagesToSeal/>
+ <packagesToUnSeal/>
+ </sealing>
+ </manifest>
+ <selectedElements exportClassFiles="true" exportJavaFiles="true" exportOutputFolder="false">
+ <javaElement handleIdentifier="=Spot Detector Block/src"/>
+ </selectedElements>
+</jardesc>
diff --git a/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$1.class b/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$1.class
new file mode 100644
index 0000000000000000000000000000000000000000..21a2c8cbbc3885ff46fd45e056396a28fa6c1b92
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diff --git a/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$detectionMethodEnum.class b/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock$detectionMethodEnum.class
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diff --git a/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java b/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java
new file mode 100644
index 0000000..cf32d9a
--- /dev/null
+++ b/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java
@@ -0,0 +1,272 @@
+package plugins.fab.waveletspotdetectorblock;
+
+import icy.plugin.abstract_.Plugin;
+import icy.roi.ROI;
+import icy.roi.ROI2D;
+import icy.sequence.Sequence;
+import icy.system.thread.ThreadUtil;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import javax.xml.bind.JAXBContext;
+
+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.VarGenericArray;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.lang.VarSequence;
+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 {
+
+ 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 );
+ 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);
+ VarSequence binarySpotSequence = new VarSequence("binary Spot Sequence", null);
+ VarROIArray detectionAsROIOut = new VarROIArray("detection as ROIs", null);
+
+ @Override
+ 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.getSizeC() != 1 )
+ {
+ throw new VarException("The input sequence must contain only 1 channel. Please use 'Extract Channel' prior to the WaveletBlock");
+ }
+
+// inputChannelVar
+
+ // init detection.
+
+ UDWTWaveletCore waveletCore = new UDWTWaveletCore();
+
+ boolean detectNegative ;
+
+ if ( detectionMethod.getValue() == detectionMethodEnum.BRIGHT_SPOT )
+ {
+ detectNegative = false;
+ }else
+ {
+ detectNegative = true;
+ }
+
+ boolean computeWATwithROI = computeWATConsideringROIBoolean.getValue();
+
+ // copy ROI from input sequence to the computation sequence
+
+ Sequence inputComputationSequence = inputSequence.getCopy();
+
+ if ( inputSequenceROIVar.getValue() !=null )
+ {
+ for ( ROI2D roi : inputSequenceROIVar.getValue().getROI2Ds() )
+ {
+ ROI2D roiCopy = (ROI2D) roi.getCopy();
+
+ if( roiCopy != null )
+ {
+ inputComputationSequence.addROI( roiCopy );
+ }
+ }
+ }
+
+ //Icy.addSequence( inputComputationSequence );
+
+ // create UDWTScale Parameter list.
+
+ final ArrayList<UDWTScale> UDWTScaleArrayList = new ArrayList<UDWTScale>();
+
+// 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 );
+ }
+ }
+
+ });
+
+
+ // Perform detection.
+
+ ArrayList<DetectionSpot> detectionResult;
+ detectionResult = waveletCore.computeDetection(
+ true,
+ UDWTScaleArrayList ,
+ inputComputationSequence ,
+ detectNegative ,
+ computeWATwithROI , force2DWaveletVar.getValue() );
+
+// System.out.println( "ROI Mask : " + inputROIForMask.getValue() );
+
+ // Filter spot with ROIs.
+
+ if ( inputROIForMask.getValue().length != 0 )
+ {
+ ArrayList<DetectionSpot> detectionResultCopy = new ArrayList<DetectionSpot>( detectionResult );
+
+ detectionList:
+ 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>( );
+ detectionList.add( spot );
+ detectionAsROI = DetectionToROI.convertDetectionToROI( detectionList ).get( 0 );
+ } catch ( NullPointerException e )
+ {
+ System.err.println("Error in spot to ROI conversion");
+ }
+
+ if ( detectionAsROI == null )
+ {
+ System.err.println("Can't convert spot to ROI. spot=" + spot );
+ continue;
+ }
+
+// System.out.println( "spot as ROI to test: " + detectionAsROI.getBounds5D() );
+
+ for ( ROI roi : inputROIForMask.getValue() )
+ {
+// System.out.println( "roi contenant: " + roi.getBounds5D() );
+
+ if ( roi.contains( detectionAsROI ) )
+ {
+// System.out.println("contains");
+ continue detectionList;
+ }
+ }
+// System.out.println("don't contains");
+
+ detectionResult.remove( spot );
+
+ }
+ }
+
+
+ // set outputs.
+
+ // binary output: propagate ROIs.
+ {
+ Sequence binarySequence = waveletCore.getBinarySequence();
+
+ if ( inputSequenceROIVar.getValue() !=null )
+ {
+ for ( ROI2D roi : inputSequenceROIVar.getValue().getROI2Ds() )
+ {
+ //System.out.println("roi:"+roi);
+ String name = roi.getName();
+
+ ROI2D roiCopy = (ROI2D) roi.getCopy();
+ roi.setName( name ); // because of the bug when coppying roi.
+ roiCopy.setName( name ); // else the name has " copy" in the end of it.
+
+ binarySequence.addROI( roiCopy );
+ }
+ }
+
+ binarySpotSequence.setValue( binarySequence );
+ }
+
+ // output detection as ROI
+ {
+ ArrayList<ROI> roiList = DetectionToROI.convertDetectionToROI( detectionResult );
+ ROI roi[] = new ROI[ roiList.size() ];
+ int i = 0;
+ for ( ROI roiCandidate : roiList )
+ {
+ roi[i] = roiCandidate;
+ i++;
+ }
+ detectionAsROIOut.setValue( roi );
+ }
+
+
+ }
+
+ @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] );
+ }
+ for (int i = 0 ; i<5 ; i++)
+ {
+ inputMap.add( scaleParameter[i] );
+ }
+ inputMap.add( force2DWaveletVar );
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap) {
+
+// outputMap.add( outSequence );
+// outputMap.add( denoisedSequence );
+ outputMap.add( binarySpotSequence );
+ outputMap.add( detectionAsROIOut );
+
+ }
+
+}
--
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