diff --git a/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java b/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java
index cf32d9a11718ca62862bdc5acc2ac7a5d36c3d74..c63f413db53f6ad34c9d8501ece12ce206bf139e 100644
--- a/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java
+++ b/src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java
@@ -1,21 +1,17 @@
package plugins.fab.waveletspotdetectorblock;
+import java.util.ArrayList;
+
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 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;
@@ -25,248 +21,254 @@ 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()
+public class WaveletSpotDetectorBlock extends Plugin implements Block
+{
- ROI detectionAsROI = null;
+ enum detectionMethodEnum
+ {
+ BRIGHT_SPOT, DARK_SPOT
+ }
- 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");
- }
+ 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);
- if ( detectionAsROI == null )
- {
- System.err.println("Can't convert spot to ROI. spot=" + spot );
- continue;
- }
+ 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)};
-// System.out.println( "spot as ROI to test: " + detectionAsROI.getBounds5D() );
+ 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)};
- 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");
+ 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);
- detectionResult.remove( spot );
+ @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");
+ }
- // 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 );
-
- }
+ 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;
+
+ try
+ {
+ inputComputationSequence = SequenceUtil.getCopy(inputSequence);
+ }
+ catch (InterruptedException ex)
+ {
+ // interrupt process
+ return;
+ }
+
+ 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.
+ try
+ {
+ 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);
+ }
+ }
+ 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]);
+ }
+ 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);
+
+ }
}