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Commit 9bf9ed92 authored by Stéphane DALLONGEVILLE's avatar Stéphane DALLONGEVILLE
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updated for interruptible tasks (Icy 2.4.0)

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src/plugins/fab/waveletspotdetectorblock/WaveletSpotDetectorBlock.java
+ 243
− 241
View file @ 9bf9ed92
package plugins.fab.waveletspotdetectorblock; package plugins.fab.waveletspotdetectorblock;
import java.util.ArrayList;
import icy.plugin.abstract_.Plugin; import icy.plugin.abstract_.Plugin;
import icy.roi.ROI; import icy.roi.ROI;
import icy.roi.ROI2D; import icy.roi.ROI2D;
import icy.sequence.Sequence; import icy.sequence.Sequence;
import icy.sequence.SequenceUtil;
import icy.system.thread.ThreadUtil; 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.lang.Block;
import plugins.adufour.blocks.util.VarList; import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarBoolean; import plugins.adufour.vars.lang.VarBoolean;
import plugins.adufour.vars.lang.VarEnum; import plugins.adufour.vars.lang.VarEnum;
import plugins.adufour.vars.lang.VarGenericArray;
import plugins.adufour.vars.lang.VarInteger; import plugins.adufour.vars.lang.VarInteger;
import plugins.adufour.vars.lang.VarROIArray; import plugins.adufour.vars.lang.VarROIArray;
import plugins.adufour.vars.lang.VarSequence; import plugins.adufour.vars.lang.VarSequence;
...@@ -25,248 +21,254 @@ import plugins.fab.spotDetector.detector.DetectionToROI; ...@@ -25,248 +21,254 @@ import plugins.fab.spotDetector.detector.DetectionToROI;
import plugins.fab.spotDetector.detector.UDWTScale; import plugins.fab.spotDetector.detector.UDWTScale;
import plugins.fab.spotDetector.detector.UDWTWaveletCore; import plugins.fab.spotDetector.detector.UDWTWaveletCore;
public class WaveletSpotDetectorBlock extends Plugin implements Block { 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; enum detectionMethodEnum
{
BRIGHT_SPOT, DARK_SPOT
}
try VarSequence inputSequenceVar = new VarSequence("input Sequence", null);
{ VarEnum<detectionMethodEnum> detectionMethod = new VarEnum<detectionMethodEnum>("Spot to detect",
ArrayList<DetectionSpot> detectionList = new ArrayList<DetectionSpot>( ); detectionMethodEnum.BRIGHT_SPOT);
detectionList.add( spot ); VarBoolean computeWATConsideringROIBoolean = new VarBoolean("Compute WAT considering ROI", false);
detectionAsROI = DetectionToROI.convertDetectionToROI( detectionList ).get( 0 ); VarSequence inputSequenceROIVar = new VarSequence("ROIs from sequence for WAT", null);
} catch ( NullPointerException e ) VarBoolean force2DWaveletVar = new VarBoolean("Force 2D Wavelets", false);
{ VarROIArray inputROIForMask = new VarROIArray("ROIs for detection mask", null);
System.err.println("Error in spot to ROI conversion");
}
if ( detectionAsROI == 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)};
System.err.println("Can't convert spot to ROI. spot=" + spot );
continue;
}
// 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() ) VarSequence outSequence = new VarSequence("output Sequence", null);
{ VarSequence denoisedSequence = new VarSequence("denoised Sequence", null);
// System.out.println( "roi contenant: " + roi.getBounds5D() ); VarSequence binarySpotSequence = new VarSequence("binary Spot Sequence", null);
VarROIArray detectionAsROIOut = new VarROIArray("detection as ROIs", null);
if ( roi.contains( detectionAsROI ) )
{
// System.out.println("contains");
continue detectionList;
}
}
// System.out.println("don't contains");
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. if (inputSequence.getSizeC() != 1)
{
// binary output: propagate ROIs. throw new VarException(
{ "The input sequence must contain only 1 channel. Please use 'Extract Channel' prior to the WaveletBlock");
Sequence binarySequence = waveletCore.getBinarySequence(); }
if ( inputSequenceROIVar.getValue() !=null ) // inputChannelVar
{
for ( ROI2D roi : inputSequenceROIVar.getValue().getROI2Ds() ) // init detection.
{
//System.out.println("roi:"+roi); UDWTWaveletCore waveletCore = new UDWTWaveletCore();
String name = roi.getName();
boolean detectNegative;
ROI2D roiCopy = (ROI2D) roi.getCopy();
roi.setName( name ); // because of the bug when coppying roi. if (detectionMethod.getValue() == detectionMethodEnum.BRIGHT_SPOT)
roiCopy.setName( name ); // else the name has " copy" in the end of it. {
detectNegative = false;
binarySequence.addROI( roiCopy ); }
} else
} {
detectNegative = true;
binarySpotSequence.setValue( binarySequence ); }
}
boolean computeWATwithROI = computeWATConsideringROIBoolean.getValue();
// output detection as ROI
{ // copy ROI from input sequence to the computation sequence
ArrayList<ROI> roiList = DetectionToROI.convertDetectionToROI( detectionResult ); Sequence inputComputationSequence;
ROI roi[] = new ROI[ roiList.size() ];
int i = 0; try
for ( ROI roiCandidate : roiList ) {
{ inputComputationSequence = SequenceUtil.getCopy(inputSequence);
roi[i] = roiCandidate; }
i++; catch (InterruptedException ex)
} {
detectionAsROIOut.setValue( roi ); // interrupt process
} return;
}
} if (inputSequenceROIVar.getValue() != null)
{
@Override for (ROI2D roi : inputSequenceROIVar.getValue().getROI2Ds())
public void declareInput(VarList inputMap) { {
ROI2D roiCopy = (ROI2D) roi.getCopy();
inputMap.add( inputSequenceVar );
inputMap.add( detectionMethod ); if (roiCopy != null)
inputMap.add( "input Sequence ROIs" , inputSequenceROIVar ); {
inputMap.add( computeWATConsideringROIBoolean ); inputComputationSequence.addROI(roiCopy);
inputMap.add( inputROIForMask ); }
}
for (int i = 0 ; i<5 ; i++) }
{
inputMap.add( useScaleBoolean[i] ); // Icy.addSequence( inputComputationSequence );
}
for (int i = 0 ; i<5 ; i++) // create UDWTScale Parameter list.
{
inputMap.add( scaleParameter[i] ); final ArrayList<UDWTScale> UDWTScaleArrayList = new ArrayList<UDWTScale>();
}
inputMap.add( force2DWaveletVar ); // System.out.println("Block debug.");
}
ThreadUtil.invokeNow(new Runnable()
@Override {
public void declareOutput(VarList outputMap) {
@Override
// outputMap.add( outSequence ); public void run()
// outputMap.add( denoisedSequence ); {
outputMap.add( binarySpotSequence );
outputMap.add( detectionAsROIOut ); 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);
}
} }
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