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src/main/java/fr/pasteur/ida/zellige/gui/model/MainModel.java
View file @ e7432a54
......@@ -33,18 +33,26 @@ import net.imglib2.type.numeric.RealType;
public class MainModel< T extends RealType< T > & NativeType< T > >
{
private final PreprocessingModel< T > preprocessingModel;
private final SelectionModel selectionModel;
private final ConstructionModel< T > constructionModel;
private final ProjectionModel< T > projectionModel;
public MainModel( SelectionModel selectionModel, ConstructionModel< T > constructionModel, ProjectionModel< T > projectionModel )
public MainModel( PreprocessingModel< T > preprocessingModel, SelectionModel selectionModel, ConstructionModel< T > constructionModel, ProjectionModel< T > projectionModel )
{
this.preprocessingModel = preprocessingModel;
this.selectionModel = selectionModel;
this.constructionModel = constructionModel;
this.projectionModel = projectionModel;
}
public PreprocessingModel< T > getPreprocessingModel()
{
return preprocessingModel;
}
public SelectionModel getSelectionModel()
{
return selectionModel;
......
src/main/java/fr/pasteur/ida/zellige/gui/model/PreprocessingModel.java 0 → 100644
View file @ e7432a54
package fr.pasteur.ida.zellige.gui.model;
import javafx.beans.property.IntegerProperty;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.beans.property.SimpleIntegerProperty;
import javafx.beans.property.SimpleObjectProperty;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.display.ColorTable;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.real.FloatType;
import java.util.ArrayList;
public class PreprocessingModel< T extends RealType< T > & NativeType< T > >
{
private final IntegerProperty bin = new SimpleIntegerProperty();
private final IntegerProperty channel = new SimpleIntegerProperty();
private final IntegerProperty nbOfChannels = new SimpleIntegerProperty();
private final SimpleObjectProperty< RandomAccessibleInterval<T> > input = new SimpleObjectProperty<>();
private final SimpleObjectProperty< RandomAccessibleInterval<T> > input_channel = new SimpleObjectProperty<>();
private final SimpleObjectProperty< ImgFactory< T > > factory = new SimpleObjectProperty<>();
private final SimpleObjectProperty< Img< FloatType > > pretreatedImg = new SimpleObjectProperty<>();
private final SimpleBooleanProperty parameterChanged = new SimpleBooleanProperty(false);
private final SimpleObjectProperty< ArrayList< ColorTable > > colors = new SimpleObjectProperty<>(new ArrayList<>());
public IntegerProperty binProperty()
{
return bin;
}
public SimpleObjectProperty< Img< FloatType > > pretreatedImgProperty()
{
return pretreatedImg;
}
public IntegerProperty getChannel()
{
return channel;
}
public SimpleBooleanProperty getParameterChanged()
{
return parameterChanged;
}
public SimpleObjectProperty< ImgFactory< T > > getFactory()
{
return factory;
}
public SimpleObjectProperty< RandomAccessibleInterval< T > > getInput()
{
return input;
}
public IntegerProperty getNbOfChannels()
{
return nbOfChannels;
}
public SimpleObjectProperty< ArrayList<ColorTable > > getColors()
{
return colors;
}
public SimpleObjectProperty< RandomAccessibleInterval< T > > getInput_channel()
{
return input_channel;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/model/ProjectionModel.java
View file @ e7432a54
......@@ -28,311 +28,48 @@
*/
package fr.pasteur.ida.zellige.gui.model;
import fr.pasteur.ida.zellige.element.Projection;
import fr.pasteur.ida.zellige.element.ReferenceSurface;
import fr.pasteur.ida.zellige.steps.projection.ReferenceSurfaceProjection;
import fr.pasteur.ida.zellige.gui.ProjectionProperties;
import javafx.beans.property.*;
import net.imglib2.img.Img;
import net.imglib2.img.display.imagej.ImageJFunctions;
import javafx.scene.image.ImageView;
import net.imglib2.display.ColorTable;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.ArrayList;
public class ProjectionModel< T extends RealType< T > & NativeType< T > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( ProjectionModel.class );
private final SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfaces;
private final SimpleBooleanProperty delta1Functions;
private final SimpleBooleanProperty delta2Functions;
private final IntegerProperty delta1;
private final IntegerProperty delta2;
private final StringProperty method;
private final SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfaces = new SimpleObjectProperty<>( new ArrayList<>() );
private final SimpleObjectProperty< ArrayList< ProjectionProperties< T > > > projectionProperties = new SimpleObjectProperty<>( new ArrayList<>() );
private final SimpleObjectProperty< ImageView[] > imageViews = new SimpleObjectProperty<>();
private final SimpleIntegerProperty numberOfChannels = new SimpleIntegerProperty();
private final BooleanProperty rawHM;
private final BooleanProperty projection;
private final BooleanProperty extractedHM;
private final BooleanProperty reduced3Dspace;
private final BooleanProperty segmentedSurface;
private final BooleanProperty segmentedSurfaceMask;
private final BooleanProperty rawHMDisplay;
private final BooleanProperty projectionDisplay;
private final BooleanProperty extractedHMDisplay;
private final BooleanProperty reduced3DspaceDisplay;
private final BooleanProperty segmentedSurfaceDisplay;
private final BooleanProperty segmentedSurfaceMaskDisplay;
public ProjectionModel()
{
this.referenceSurfaces = new SimpleObjectProperty<>();
this.delta1Functions = new SimpleBooleanProperty( false );
this.delta2Functions = new SimpleBooleanProperty( false );
this.method = new SimpleStringProperty();
this.delta1 = new SimpleIntegerProperty();
this.delta2 = new SimpleIntegerProperty();
this.rawHM = new SimpleBooleanProperty();
this.projection = new SimpleBooleanProperty();
this.extractedHM = new SimpleBooleanProperty();
this.reduced3Dspace = new SimpleBooleanProperty();
this.segmentedSurface = new SimpleBooleanProperty();
this.segmentedSurfaceMask = new SimpleBooleanProperty();
this.rawHMDisplay = new SimpleBooleanProperty( true );
this.projectionDisplay = new SimpleBooleanProperty( true );
this.extractedHMDisplay = new SimpleBooleanProperty( true );
this.reduced3DspaceDisplay = new SimpleBooleanProperty( true );
this.segmentedSurfaceDisplay = new SimpleBooleanProperty( true );
this.segmentedSurfaceMaskDisplay = new SimpleBooleanProperty( true );
}
public void showSegmentedSurfaceMask()
{
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
{
ImageJFunctions.show( referenceSurface.getProjection().getSegmentedSurfaceMask(), "Surface_mask_" + referenceSurface.getIndex() );
}
}
public void showSegmentedSurface()
{
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
{
ImageJFunctions.show( referenceSurface.getProjection().getSegmentedSurface(), "Segmented_surface_" + referenceSurface.getIndex() );
}
}
public void showReduced3DSpace()
{
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
{
ImageJFunctions.show( referenceSurface.getProjection().getReduced3DSpace(), "Reduced_3D_space_" + referenceSurface.getIndex() );
}
}
public void showExtractedHeightMaps()
{
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
{
ImageJFunctions.show( referenceSurface.getProjection().getExtractedHeightMap(), "Extracted_HM_" + referenceSurface.getIndex() );
}
}
public void showRawHeightMap()
{
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
{
ImageJFunctions.show( referenceSurface.getzMap(), "Raw_HM_" + referenceSurface.getIndex() );
}
}
public void showProjections()
{
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
{
ImageJFunctions.show( referenceSurface.getProjection().get(), "Projection_" + referenceSurface.getIndex() );
}
}
public void runProjection()
{
LOGGER.debug( "Starting projections ! " );
if ( ! delta1Functions.getValue() )
{
LOGGER.debug( "Output with delta1 " );
setOutputDelta1();
}
if ( ! delta2Functions.getValue() )
{
LOGGER.debug( "Output with delta2 " );
setOutputDelta2();
}
showOutput();
}
public void showOutput()
{
if ( rawHM.get() && rawHMDisplay.getValue() )
{
showRawHeightMap();
rawHMDisplay.setValue( false );
}
if ( projection.get() && projectionDisplay.get() )
{
showProjections();
projectionDisplay.setValue( false );
}
if ( extractedHM.get() && extractedHMDisplay.get() )
{
showExtractedHeightMaps();
extractedHMDisplay.setValue( false );
}
if ( segmentedSurface.get() && segmentedSurfaceDisplay.get() )
{
showSegmentedSurface();
segmentedSurface.setValue( false );
}
if ( reduced3Dspace.get() && reduced3DspaceDisplay.get() )
{
showReduced3DSpace();
reduced3DspaceDisplay.setValue( false );
}
if ( segmentedSurfaceMask.get() && segmentedSurfaceMaskDisplay.get() )
{
showSegmentedSurfaceMask();
segmentedSurfaceMask.setValue( false );
}
}
public void setOutputDelta1()
{
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
{
Projection< T > projection = referenceSurface.getProjection();
Img< UnsignedShortType > extractedHeightMap = ReferenceSurfaceProjection.getProjectionHeightMap( referenceSurface, method.get(), delta1.intValue() );
projection.setExtractedHeightMap( extractedHeightMap );
projection.setProjection( ReferenceSurfaceProjection.projection1( referenceSurface, this.method.get() ) );
projection.setSegmentedSurface( ReferenceSurfaceProjection.getSegmentedSurface( extractedHeightMap, referenceSurface.getInput(), referenceSurface.getFactory() ) );
projection.setReduced3DSpace( ReferenceSurfaceProjection.getExtractedHeightMapSubStack( referenceSurface, delta1.intValue() ) );
}
delta1Functions.setValue( true );
}
public void setOutputDelta2()
{
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
{
Projection< T > projection = referenceSurface.getProjection();
projection.setSegmentedSurfaceMask( ReferenceSurfaceProjection.getSegmentedSurfaceMask( projection.getSegmentedSurface(), delta2.intValue() ) );
}
delta2Functions.setValue( true );
}
public ArrayList< ReferenceSurface< T > > getReferenceSurfaces()
{
return referenceSurfaces.get();
}
public SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfacesProperty()
private final SimpleObjectProperty<ArrayList< ColorTable >> colors = new SimpleObjectProperty<>();
public SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > getReferenceSurfaces()
{
return referenceSurfaces;
}
public SimpleBooleanProperty delta1FunctionsProperty()
{
return delta1Functions;
}
public SimpleBooleanProperty delta2FunctionsProperty()
{
return delta2Functions;
}
public IntegerProperty delta1Property()
{
return delta1;
}
public IntegerProperty delta2Property()
{
return delta2;
}
public BooleanProperty rawHMProperty()
{
return rawHM;
}
public boolean isProjection()
{
return projection.get();
}
public BooleanProperty projectionProperty()
public SimpleObjectProperty< ImageView[] > getImageViews()
{
return projection;
return imageViews;
}
public BooleanProperty extractedHMProperty()
{
return extractedHM;
}
public BooleanProperty reduced3DspaceProperty()
{
return reduced3Dspace;
}
public BooleanProperty segmentedSurfaceProperty()
{
return segmentedSurface;
}
public BooleanProperty segmentedSurfaceMaskProperty()
{
return segmentedSurfaceMask;
}
public String getMethod()
{
return method.get();
}
public void setMethod( String method )
{
this.method.set( method );
}
public StringProperty methodProperty()
{
return method;
}
public BooleanProperty rawHMDisplayProperty()
{
return rawHMDisplay;
}
public BooleanProperty projectionDisplayProperty()
{
return projectionDisplay;
}
public BooleanProperty extractedHMDisplayProperty()
{
return extractedHMDisplay;
}
public BooleanProperty reduced3DspaceDisplayProperty()
public SimpleIntegerProperty getNumberOfChannels()
{
return reduced3DspaceDisplay;
return numberOfChannels;
}
public BooleanProperty segmentedSurfaceDisplayProperty()
public SimpleObjectProperty< ArrayList< ProjectionProperties< T > > > getProjectionProperties()
{
return segmentedSurfaceDisplay;
return projectionProperties;
}
public BooleanProperty segmentedSurfaceMaskDisplayProperty()
public SimpleObjectProperty< ArrayList< ColorTable > > getColors()
{
return segmentedSurfaceMaskDisplay;
return colors;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/model/SelectionModel.java
View file @ e7432a54
......@@ -28,28 +28,20 @@
*/
package fr.pasteur.ida.zellige.gui.model;
import fr.pasteur.ida.zellige.element.Pixels;
import fr.pasteur.ida.zellige.gui.ClassifiedImages;
import fr.pasteur.ida.zellige.gui.task.*;
import javafx.beans.property.DoubleProperty;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.beans.property.SimpleDoubleProperty;
import javafx.beans.property.SimpleObjectProperty;
import javafx.beans.property.*;
import javafx.scene.image.ImageView;
import net.imglib2.img.Img;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.real.FloatType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class SelectionModel
{
private final static Logger LOGGER = LoggerFactory.getLogger( SelectionModel.class );
private final DoubleProperty amplitude;
private final DoubleProperty otsu;
private final DoubleProperty island;
private final DoubleProperty xyBlur;
private final DoubleProperty zBlur;
private final IntegerProperty amplitude;
private final IntegerProperty otsu;
private final IntegerProperty island;
private final IntegerProperty xyBlur;
private final IntegerProperty zBlur;
private final SimpleBooleanProperty disableGUI = new SimpleBooleanProperty();
private final SimpleObjectProperty< Img< BitType > > islandSearchImage = new SimpleObjectProperty<>();
private final SimpleObjectProperty< ClassifiedImages< FloatType > > images = new SimpleObjectProperty<>();
......@@ -57,80 +49,18 @@ public class SelectionModel
private final SimpleObjectProperty< Img< BitType > > selectedAmplitude = new SimpleObjectProperty<>();
private final SimpleObjectProperty< Img< BitType > > selectedOtsu = new SimpleObjectProperty<>();
private final SimpleObjectProperty< Img< BitType > > interClassifiedImage = new SimpleObjectProperty<>();
private final SimpleObjectProperty< Pixels[][] > selectedPixels = new SimpleObjectProperty<>();
private final SimpleObjectProperty< Img<FloatType> > selectedPixels = new SimpleObjectProperty<>();
private final SimpleObjectProperty< ImageView[] > imageViews = new SimpleObjectProperty<>();
private final SimpleBooleanProperty parameterChanged = new SimpleBooleanProperty(false);
public SelectionModel()
{
amplitude = new SimpleDoubleProperty();
otsu = new SimpleDoubleProperty();
island = new SimpleDoubleProperty();
xyBlur = new SimpleDoubleProperty();
zBlur = new SimpleDoubleProperty();
}
public void runAmplitudeTask()
{
AmplitudeThresholdingTask amplitudeTask = new AmplitudeThresholdingTask( images, amplitude.getValue().intValue() );
amplitudeTask.setOnSucceeded( workerStateEvent ->
{
selectedAmplitude.setValue( amplitudeTask.getValue() );
disableGUI.setValue( false );
} );
amplitudeTask.start();
}
public void runOtsuTask()
{
OtsuThresholdingTask otsuTask = new OtsuThresholdingTask( pretreatedImg, images, otsu.getValue().intValue() );
otsuTask.setOnSucceeded( workerStateEvent ->
{
selectedOtsu.setValue( otsuTask.getValue() );
disableGUI.setValue( false );
} );
otsuTask.start();
}
public void runInterClassification()
{
InterClassificationTask interClassificationTask = new InterClassificationTask( selectedAmplitude, selectedOtsu );
interClassificationTask.setOnSucceeded( event -> interClassifiedImage.setValue( interClassificationTask.getValue() ) );
interClassificationTask.start();
}
public void runIslandSearch()
{
IslandSearchTask islandSearchTask = new IslandSearchTask( interClassifiedImage, island );
islandSearchTask.setOnSucceeded( workerStateEvent ->
islandSearchImage.setValue( islandSearchTask.getValue() ) );
islandSearchTask.setOnFailed( workerStateEvent -> LOGGER.debug( "FAILED" ) );
islandSearchTask.start();
}
public void runSmoothing()
{
SmoothingTask smoothingTask = new SmoothingTask( islandSearchImage, xyBlur, zBlur );
smoothingTask.setOnSucceeded( event ->
{
selectedPixels.setValue( smoothingTask.getValue() );
LOGGER.debug( "max is set" );
} );
smoothingTask.start();
}
public void runPixelSelection()
{
if ( islandSearchImage.getValue() == null )
{
LOGGER.debug( "Island search image is NULL" );
runIslandSearch();
}
else if ( selectedPixelsProperty().getValue() == null )
public SelectionModel()
{
LOGGER.debug( "Island search image is not NULL" );
runSmoothing();
}
amplitude = new SimpleIntegerProperty();
otsu = new SimpleIntegerProperty();
island = new SimpleIntegerProperty();
xyBlur = new SimpleIntegerProperty();
zBlur = new SimpleIntegerProperty();
}
public double getAmplitude()
......@@ -138,12 +68,12 @@ public class SelectionModel
return amplitude.get();
}
public void setAmplitude( double amplitude )
public void setAmplitude( int amplitude )
{
this.amplitude.set( amplitude );
}
public DoubleProperty amplitudeProperty()
public IntegerProperty amplitudeProperty()
{
return amplitude;
}
......@@ -153,12 +83,12 @@ public class SelectionModel
return otsu.get();
}
public void setOtsu( double otsu )
public void setOtsu( int otsu )
{
this.otsu.set( otsu );
}
public DoubleProperty otsuProperty()
public IntegerProperty otsuProperty()
{
return otsu;
}
......@@ -168,161 +98,73 @@ public class SelectionModel
return island.get();
}
public void setIsland( double island )
public void setIsland( int island )
{
this.island.set( island );
}
public DoubleProperty islandProperty()
public IntegerProperty islandProperty()
{
return island;
}
public DoubleProperty xyBlurProperty()
public IntegerProperty xyBlurProperty()
{
return xyBlur;
}
public double getzBlur()
{
return zBlur.get();
}
public DoubleProperty zBlurProperty()
public IntegerProperty zBlurProperty()
{
return zBlur;
}
public boolean isDisableGUI()
{
return disableGUI.get();
}
public void setDisableGUI( boolean disableGUI )
{
this.disableGUI.set( disableGUI );
}
public SimpleBooleanProperty disableGUIProperty()
{
return disableGUI;
}
public Pixels[][] getSelectedPixels()
{
return selectedPixels.get();
}
public void setSelectedPixels( Pixels[][] selectedPixels )
{
this.selectedPixels.set( selectedPixels );
}
public SimpleObjectProperty< Pixels[][] > selectedPixelsProperty()
public SimpleObjectProperty< Img<FloatType> > selectedPixelsProperty()
{
return selectedPixels;
}
public ClassifiedImages< FloatType > getImages()
{
return images.get();
}
public void setImages( ClassifiedImages< FloatType > images )
{
this.images.set( images );
}
public SimpleObjectProperty< ClassifiedImages< FloatType > > imagesProperty()
{
return images;
}
public Img< BitType > getIslandSearchImage()
{
return islandSearchImage.get();
}
public void setIslandSearchImage( Img< BitType > islandSearchImage )
{
this.islandSearchImage.set( islandSearchImage );
}
public SimpleObjectProperty< Img< BitType > > islandSearchImageProperty()
{
return islandSearchImage;
}
public Img< FloatType > getPretreatedImg()
{
return pretreatedImg.get();
}
public void setPretreatedImg( Img< FloatType > pretreatedImg )
{
this.pretreatedImg.set( pretreatedImg );
}
public SimpleObjectProperty< Img< FloatType > > pretreatedImgProperty()
{
return pretreatedImg;
}
public Img< BitType > getSelectedAmplitude()
{
return selectedAmplitude.get();
}
public void setSelectedAmplitude( Img< BitType > selectedAmplitude )
{
this.selectedAmplitude.set( selectedAmplitude );
}
public SimpleObjectProperty< Img< BitType > > selectedAmplitudeProperty()
{
return selectedAmplitude;
}
public Img< BitType > getSelectedOtsu()
{
return selectedOtsu.get();
}
public void setSelectedOtsu( Img< BitType > selectedOtsu )
{
this.selectedOtsu.set( selectedOtsu );
}
public SimpleObjectProperty< Img< BitType > > selectedOtsuProperty()
{
return selectedOtsu;
}
public Img< BitType > getInterClassifiedImage()
{
return interClassifiedImage.get();
}
public void setInterClassifiedImage( Img< BitType > interClassifiedImage )
{
this.interClassifiedImage.set( interClassifiedImage );
}
public SimpleObjectProperty< Img< BitType > > interClassifiedImageProperty()
{
return interClassifiedImage;
}
public ImageView[] getImageViews()
{
return imageViews.get();
}
public SimpleObjectProperty< ImageView[] > imageViewsProperty()
{
return imageViews;
}
public SimpleBooleanProperty getParameterChanged()
{
return parameterChanged;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/parameter/ConstructionParameter.java deleted 100644 → 0
View file @ dc73e7b1
/*-
* #%L
* Zellige
* %%
* Copyright (C) 2020 - 2023 Institut Pasteur
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package fr.pasteur.ida.zellige.gui.parameter;
import fr.pasteur.ida.zellige.gui.ZDoubleProperty;
import javafx.beans.property.IntegerProperty;
public class ConstructionParameter
{
private final double c1;
private final int r1;
private final double st1;
private final double c2;
private final int r2;
private final double st2;
private final int surfaceSize;
public ConstructionParameter( ZDoubleProperty c1, IntegerProperty r1, ZDoubleProperty st1, ZDoubleProperty c2, IntegerProperty r2, ZDoubleProperty st2, ZDoubleProperty surfaceSize )
{
this.c1 = c1.value();
this.r1 = r1.intValue();
this.st1 = st1.value();
this.c2 = c2.value();
this.r2 = r2.intValue();
this.st2 = st2.value();
this.surfaceSize = surfaceSize.intValue();
}
public double getC1()
{
return c1;
}
public int getR1()
{
return r1;
}
public double getSt1()
{
return st1;
}
public double getC2()
{
return c2;
}
public int getR2()
{
return r2;
}
public double getSt2()
{
return st2;
}
public int getSurfaceSize()
{
return surfaceSize;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/parameter/ProjectionParameter.java deleted 100644 → 0
View file @ dc73e7b1
/*-
* #%L
* Zellige
* %%
* Copyright (C) 2020 - 2023 Institut Pasteur
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package fr.pasteur.ida.zellige.gui.parameter;
import javafx.beans.property.IntegerProperty;
import javafx.beans.property.StringProperty;
public class ProjectionParameter
{
private final int delta1;
private final int delta2;
private final String method;
public ProjectionParameter( IntegerProperty delta1, IntegerProperty delta2, StringProperty method )
{
this.delta1 = delta1.intValue();
this.delta2 = delta2.intValue();
this.method = method.get();
}
public int getDelta1()
{
return delta1;
}
public int getDelta2()
{
return delta2;
}
public String getMethod()
{
return method;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/parameter/SelectionParameter.java deleted 100644 → 0
View file @ dc73e7b1
/*-
* #%L
* Zellige
* %%
* Copyright (C) 2020 - 2023 Institut Pasteur
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package fr.pasteur.ida.zellige.gui.parameter;
import javafx.beans.property.DoubleProperty;
public class SelectionParameter
{
private final int amplitude;
private final int otsu;
private final int island;
private final int xyBlur;
private final int zBlur;
public SelectionParameter( DoubleProperty amplitude, DoubleProperty otsu, DoubleProperty island, DoubleProperty xyBlur, DoubleProperty zBlur )
{
this.amplitude = amplitude.intValue();
this.otsu = otsu.intValue();
this.island = island.intValue();
this.xyBlur = xyBlur.intValue();
this.zBlur = zBlur.intValue();
}
public int getAmplitude()
{
return amplitude;
}
public int getOtsu()
{
return otsu;
}
public int getIsland()
{
return island;
}
public int getXyBlur()
{
return xyBlur;
}
public int getzBlur()
{
return zBlur;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/parameter/ZelligeParameters.java
View file @ e7432a54
......@@ -30,61 +30,39 @@ package fr.pasteur.ida.zellige.gui.parameter;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import fr.pasteur.ida.zellige.steps.construction.rounds.ConstructionParameters;
import fr.pasteur.ida.zellige.steps.projection.ProjectionParameters;
import fr.pasteur.ida.zellige.steps.selection.SelectionParameters;
import fr.pasteur.ida.zellige.steps.selection.pretreatment.PretreatmentParameters;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.stream.Collectors;
import java.util.stream.Stream;
public class ZelligeParameters
{
private final PretreatmentParameters pretreatmentParameters;
//selection
private final int amplitude;
private final int otsu;
private final int island;
private final int xyBlur;
private final int zBlur;
//construction
private final double c1;
private final int r1;
private final double st1;
private final double c2;
private final int r2;
private final double st2;
private final int surfaceSize;
//projection
private final int delta1;
private final int delta2;
private final String method;
private final SelectionParameters selectionParameters;
private final ConstructionParameters[] constructionParameters;
private final ArrayList<ProjectionParameters> projectionParameters;
public ZelligeParameters( SelectionParameter sp, ConstructionParameter cp, ProjectionParameter pp )
public ZelligeParameters( PretreatmentParameters pretreatmentParameters, SelectionParameters selectionParameters, ConstructionParameters[] constructionParameters, ArrayList< ProjectionParameters > projectionParameters )
{
// selection
amplitude = sp.getAmplitude();
otsu = sp.getOtsu();
island = sp.getIsland();
xyBlur = sp.getXyBlur();
zBlur = sp.getzBlur();
// construction
c1 = cp.getC1();
r1 = cp.getR1();
st1 = cp.getSt1();
c2 = cp.getC2();
r2 = cp.getR2();
st2 = cp.getSt2();
surfaceSize = cp.getSurfaceSize();
// projection
delta1 = pp.getDelta1();
delta2 = pp.getDelta2();
method = pp.getMethod();
this.pretreatmentParameters = pretreatmentParameters;
this.selectionParameters = selectionParameters;
this.constructionParameters = constructionParameters;
this.projectionParameters = projectionParameters;
}
public static void serialize( final ZelligeParameters parameters, final File file ) throws IOException
{
final Gson gson = new GsonBuilder().setPrettyPrinting().create();
......@@ -115,78 +93,23 @@ public class ZelligeParameters
}
}
public int getAmplitude()
{
return amplitude;
}
public int getOtsu()
{
return otsu;
}
public int getIsland()
{
return island;
}
public int getXyBlur()
{
return xyBlur;
}
public int getzBlur()
{
return zBlur;
}
public double getC1()
{
return c1;
}
public int getR1()
{
return r1;
}
public double getSt1()
{
return st1;
}
public double getC2()
{
return c2;
}
public int getR2()
{
return r2;
}
public double getSt2()
{
return st2;
}
public double getSurfaceSize()
public PretreatmentParameters getPretreatmentParameters()
{
return surfaceSize;
return pretreatmentParameters;
}
public String getMethod()
public SelectionParameters getSelectionParameters()
{
return method;
return selectionParameters;
}
public int getDelta1()
public ConstructionParameters[] getConstructionParameters()
{
return delta1;
return constructionParameters;
}
public int getDelta2()
public ArrayList< ProjectionParameters > getProjectionParameters()
{
return delta2;
return projectionParameters;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/task/AmplitudeThresholdingTask.java
View file @ e7432a54
......@@ -28,33 +28,35 @@
*/
package fr.pasteur.ida.zellige.gui.task;
import fr.pasteur.ida.zellige.gui.ClassifiedImages;
import fr.pasteur.ida.zellige.steps.selection.classification.AmplitudeClassification;
import javafx.beans.property.SimpleObjectProperty;
import net.imglib2.img.Img;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.real.FloatType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class AmplitudeThresholdingTask extends AbstractTask< Img< BitType > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( AmplitudeThresholdingTask.class );
private final SimpleObjectProperty< ClassifiedImages< FloatType > > images;
private final Img<FloatType> input;
private final int amplitudeThreshold;
public AmplitudeThresholdingTask( SimpleObjectProperty< ClassifiedImages< FloatType > > images, int amplitudeThreshold )
public AmplitudeThresholdingTask( Img<FloatType> input, int amplitudeThreshold )
{
this.images = images;
this.input = input;
this.amplitudeThreshold = amplitudeThreshold;
}
@Override
protected Img< BitType > call()
{
LOGGER.info( "Computing amplitude thresholding..." );
return AmplitudeClassification.applyThreshold( images.getValue().getAmplitudeImg(), amplitudeThreshold );
LOGGER.info(GUI_MARKER, "Computing amplitude thresholding..." );
Img< BitType > output = AmplitudeClassification.applyThreshold( input, amplitudeThreshold );
LOGGER.info( GUI_MARKER,"Amplitude thresholds computed..." );
return output;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/task/BinningTask.java 0 → 100644
View file @ e7432a54
package fr.pasteur.ida.zellige.gui.task;
import fr.pasteur.ida.zellige.steps.selection.util.Binning;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class BinningTask < T extends RealType< T > & NativeType< T > > extends AbstractTask<Img<T>>
{
private final static Logger LOGGER = LoggerFactory.getLogger( BinningTask.class );
private final int bin;
private final RandomAccessibleInterval<T> input;
public BinningTask( int bin, RandomAccessibleInterval< T > input )
{
this.bin = bin;
this.input = input;
}
@Override
protected Img<T> call() {
LOGGER.info( GUI_MARKER,"Binning" );
Img<T> binnedImage = Binning.run( input, bin );
LOGGER.info( GUI_MARKER,"Image binned !" );
return binnedImage;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/task/ComputeClassificationImagesTask.java
View file @ e7432a54
......@@ -38,6 +38,8 @@ import net.imglib2.type.numeric.real.FloatType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class ComputeClassificationImagesTask extends AbstractTask< ClassifiedImages< FloatType > >
{
......@@ -53,12 +55,12 @@ public class ComputeClassificationImagesTask extends AbstractTask< ClassifiedIma
@Override
protected ClassifiedImages< FloatType > call() throws Exception
{
LOGGER.info( "Computing classified images..." );
LOGGER.info( GUI_MARKER,"Computing classified images..." );
ImgFactory< FloatType > factory = new ArrayImgFactory<>( new FloatType() );
ClassifiedImages< FloatType > images = new ClassifiedImages<>();
images.setAmplitudeImg( AmplitudeClassification.computeAmplitudeImage( pretreatedImg, factory ) );
images.setOtsuImg( OtsuClassification.computeOtsuImage( pretreatedImg, factory ) );
LOGGER.debug( "Classification images computed" );
LOGGER.debug( GUI_MARKER,"Classification images computed" );
return images;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionCompletionTask.java
View file @ e7432a54
......@@ -40,26 +40,36 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class ConstructionCompletionTask< T extends RealType< T > & NativeType< T > > extends AbstractTask< ArrayList< ReferenceSurface< T > > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( ConstructionCompletion.class );
private final static Logger LOGGER = LoggerFactory.getLogger( ConstructionCompletionTask.class );
private final RandomAccessibleInterval< T > input;
private final ImgFactory< T > factory;
private final ArrayList< Surface > finalSurfaces;
private final int bin;
public ConstructionCompletionTask( RandomAccessibleInterval< T > input, ImgFactory< T > factory, ArrayList< Surface > finalSurfaces )
public ConstructionCompletionTask( RandomAccessibleInterval< T > input, ImgFactory< T > factory, ArrayList< Surface > finalSurfaces, int bin )
{
this.input = input;
this.factory = factory;
this.finalSurfaces = finalSurfaces;
this.bin = bin;
}
@Override
protected ArrayList< ReferenceSurface< T > > call()
{
LOGGER.info( "Processing construction completion..." );
return ConstructionCompletion.run( input, factory, finalSurfaces );
LOGGER.info( GUI_MARKER,"Processing construction completion..." );
ArrayList< ReferenceSurface< T > > list = ConstructionCompletion.run( input, factory, finalSurfaces , bin);
LOGGER.info(GUI_MARKER, "construction completed..." );
if ( list.isEmpty() )
{
LOGGER.info( GUI_MARKER,"no surfaces..." );
}
return list;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionDisplayTask.java 0 → 100644
View file @ e7432a54
package fr.pasteur.ida.zellige.gui.task;
import fr.pasteur.ida.zellige.element.ReferenceSurface;
import fr.pasteur.ida.zellige.gui.ImageFXDisplay;
import javafx.scene.image.ImageView;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.ArrayList;
public class ConstructionDisplayTask< T extends RealType< T > & NativeType< T > > extends AbstractTask< ImageView[] >
{
private final static Logger LOGGER = LoggerFactory.getLogger( ConstructionDisplayTask.class );
private final ArrayList< ReferenceSurface< T > > referenceSurfaces;
public ConstructionDisplayTask( ArrayList< ReferenceSurface< T > > referenceSurfaces )
{
this.referenceSurfaces = referenceSurfaces;
}
@Override
protected ImageView[] call() throws IOException
{
ImageView[] imageViews = new ImageView[ referenceSurfaces.size() ];
int index = 0;
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces )
{
ImageFXDisplay.setHM( referenceSurface.getzMap(), imageViews, index++ );
}
LOGGER.debug( "Task done. Display of {} height map(s).", referenceSurfaces.size() );
return imageViews;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/task/InterClassificationTask.java
View file @ e7432a54
......@@ -29,20 +29,21 @@
package fr.pasteur.ida.zellige.gui.task;
import fr.pasteur.ida.zellige.steps.selection.classification.Classification;
import javafx.beans.property.SimpleObjectProperty;
import net.imglib2.img.Img;
import net.imglib2.type.logic.BitType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class InterClassificationTask extends AbstractTask< Img< BitType > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( InterClassificationTask.class );
private final SimpleObjectProperty< Img< BitType > > selectedAmplitude;
private final SimpleObjectProperty< Img< BitType > > selectedOtsu;
private final Img< BitType >selectedAmplitude;
private final Img< BitType >selectedOtsu;
public InterClassificationTask( SimpleObjectProperty< Img< BitType > > selectedAmplitude, SimpleObjectProperty< Img< BitType > > selectedOtsu )
public InterClassificationTask( Img< BitType > selectedAmplitude, Img< BitType > selectedOtsu )
{
this.selectedAmplitude = selectedAmplitude;
this.selectedOtsu = selectedOtsu;
......@@ -53,8 +54,8 @@ public class InterClassificationTask extends AbstractTask< Img< BitType > >
protected Img< BitType > call()
{
LOGGER.info( "Computing inter-classification..." );
return Classification.interClassification( selectedAmplitude.getValue(), selectedAmplitude.getValue().factory(), selectedOtsu.getValue() );
LOGGER.info(GUI_MARKER, "Computing inter-classification..." );
return Classification.interClassification( selectedAmplitude, selectedAmplitude.factory(), selectedOtsu );
}
......
src/main/java/fr/pasteur/ida/zellige/gui/task/IslandSearchTask.java
View file @ e7432a54
......@@ -29,21 +29,21 @@
package fr.pasteur.ida.zellige.gui.task;
import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatment;
import javafx.beans.property.DoubleProperty;
import javafx.beans.property.SimpleObjectProperty;
import net.imglib2.img.Img;
import net.imglib2.type.logic.BitType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class IslandSearchTask extends AbstractTask< Img< BitType > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( IslandSearchTask.class );
private final SimpleObjectProperty< Img< BitType > > image;
private final DoubleProperty islandSize;
private final Img< BitType > image;
private final int islandSize;
public IslandSearchTask( SimpleObjectProperty< Img< BitType > > image, DoubleProperty islandSize )
public IslandSearchTask( Img< BitType > image, int islandSize )
{
this.image = image;
this.islandSize = islandSize;
......@@ -52,9 +52,9 @@ public class IslandSearchTask extends AbstractTask< Img< BitType > >
@Override
protected Img< BitType > call()
{
LOGGER.info( "Computing Island Search..." );
Img< BitType > img = PostTreatment.runIslandSearch( image.getValue(), islandSize.intValue() );
LOGGER.debug( "Task's end." );
LOGGER.info( GUI_MARKER,"Computing Island Search..." );
Img< BitType > img = PostTreatment.runIslandSearch( image, islandSize );
LOGGER.info( GUI_MARKER,"Task's end." );
return img;
// return iSImage;
}
......
src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java
View file @ e7432a54
......@@ -28,35 +28,37 @@
*/
package fr.pasteur.ida.zellige.gui.task;
import fr.pasteur.ida.zellige.gui.ClassifiedImages;
import fr.pasteur.ida.zellige.steps.selection.classification.OtsuClassification;
import javafx.beans.property.SimpleObjectProperty;
import net.imglib2.img.Img;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.real.FloatType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class OtsuThresholdingTask extends AbstractTask< Img< BitType > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( OtsuThresholdingTask.class );
private final SimpleObjectProperty< Img< FloatType > > pretreatedImage;
private final SimpleObjectProperty< ClassifiedImages< FloatType > > images;
private final Img< FloatType > pretreatedImage;
private final Img<FloatType> input;
private final int otsuThreshold;
public OtsuThresholdingTask( SimpleObjectProperty< Img< FloatType > > pretreatedImage, SimpleObjectProperty< ClassifiedImages< FloatType > > images, int otsuThreshold )
public OtsuThresholdingTask( Img< FloatType > pretreatedImage, Img<FloatType> input, int otsuThreshold )
{
this.pretreatedImage = pretreatedImage;
this.images = images;
this.input = input;
this.otsuThreshold = otsuThreshold;
}
@Override
protected Img< BitType > call()
{
LOGGER.info( "Computing otsu thresholding..." );
return OtsuClassification.applyLocalThreshold( pretreatedImage.getValue(), images.getValue().getOtsuImg(), otsuThreshold );
LOGGER.info( GUI_MARKER,"Computing otsu thresholding..." );
Img< BitType > output = OtsuClassification.applyLocalThreshold( pretreatedImage, input, otsuThreshold );
LOGGER.info( GUI_MARKER,"Amplitude thresholds computed..." );
return output;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/task/PretreatmentTask.java → src/main/java/fr/pasteur/ida/zellige/gui/task/PreprocessingTask.java
View file @ e7432a54
......@@ -29,8 +29,7 @@
package fr.pasteur.ida.zellige.gui.task;
import fr.pasteur.ida.zellige.steps.selection.pretreatment.Pretreatment;
import net.imagej.Dataset;
import net.imagej.ImgPlus;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
......@@ -38,25 +37,30 @@ import net.imglib2.type.numeric.real.FloatType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class PretreatmentTask< T extends RealType< T > & NativeType< T > > extends AbstractTask< Img< FloatType > >
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class PreprocessingTask< T extends RealType< T > & NativeType< T > > extends AbstractTask< Img< FloatType > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( PretreatmentTask.class );
private final Dataset dataset;
private final static Logger LOGGER = LoggerFactory.getLogger( PreprocessingTask.class );
private final RandomAccessibleInterval<T> input;
private final double radius;
private final int bin;
public PretreatmentTask( Dataset dataset )
public PreprocessingTask( RandomAccessibleInterval<T> input, double radius, int bin)
{
this.dataset = dataset;
this.input = input;
this.radius = radius;
this.bin = bin;
}
@Override
@SuppressWarnings( "unchecked" )
protected Img< FloatType > call()
{
LOGGER.info( "Computing pretreatment..." );
ImgPlus< T > input = ( ImgPlus< T > ) dataset.getImgPlus();
Img< FloatType > pretreatedImg = Pretreatment.run( input );
LOGGER.debug( "Done." );
LOGGER.info(GUI_MARKER, "Computing pretreatment..." );
Img< FloatType > pretreatedImg = Pretreatment.run( input, radius, bin );
LOGGER.info( GUI_MARKER,"Done." );
return pretreatedImg;
}
}
src/main/java/fr/pasteur/ida/zellige/gui/task/ProjectionTask.java 0 → 100644
View file @ e7432a54
package fr.pasteur.ida.zellige.gui.task;
import fr.pasteur.ida.zellige.element.ReferenceSurface;
import fr.pasteur.ida.zellige.gui.ChannelToolProperty;
import fr.pasteur.ida.zellige.gui.ProjectionProperties;
import fr.pasteur.ida.zellige.steps.projection.ReferenceSurfaceProjection;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;
import java.util.ArrayList;
public class ProjectionTask< T extends RealType< T > & NativeType< T > > extends AbstractTask< Img< T > >
{
private final ReferenceSurface< T > referenceSurface;
private final ProjectionProperties< T > properties;
public ProjectionTask( ReferenceSurface< T > referenceSurface, ProjectionProperties< T > properties )
{
this.referenceSurface = referenceSurface;
this.properties = properties;
}
@Override
protected Img< T > call()
{
ArrayList< Img< T > > projections = new ArrayList<>();
for ( int channel = 0; channel < properties.getProperties().get().size(); channel++ )
{
RandomAccessibleInterval< T > input = Views.hyperSlice( referenceSurface.getInput(), 2, channel );
ChannelToolProperty< T > channelToolProperty = properties.getProperties().get().get( channel );
String method = channelToolProperty.getMethod().get();
if ( channelToolProperty.getSubVolume().get() == null )
{
int delta = channelToolProperty.getDeltaZ().get();
int offset = channelToolProperty.getOffset().get();
Img< T > subVolume = ReferenceSurfaceProjection.getSubStack(
input,
referenceSurface.getFactory(),
referenceSurface.getzMap(),
delta,
offset );
channelToolProperty.getSubVolume().set( subVolume );
}
Img< T > projection = ReferenceSurfaceProjection.run( channelToolProperty.getSubVolume().get(), method );
projections.add( projection );
}
return ReferenceSurfaceProjection.regroupChannels( projections );
}
}
src/main/java/fr/pasteur/ida/zellige/gui/task/RunFirstConstructionTask.java
View file @ e7432a54
......@@ -28,25 +28,28 @@
*/
package fr.pasteur.ida.zellige.gui.task;
import fr.pasteur.ida.zellige.element.Pixels;
import fr.pasteur.ida.zellige.element.Surface;
import fr.pasteur.ida.zellige.steps.construction.exception.NoSurfaceFoundException;
import fr.pasteur.ida.zellige.steps.construction.rounds.FirstRoundConstruction;
import net.imglib2.img.Img;
import net.imglib2.type.numeric.real.FloatType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class RunFirstConstructionTask extends AbstractTask< ArrayList< Surface > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( RunFirstConstructionTask.class );
private final Pixels[][] maximums;
private final Img< FloatType > maximums;
private final double startingOsSize1;
private final int overlap1;
private final double connexityRate1;
private final double surfaceMinSizeFactor;
public RunFirstConstructionTask( Pixels[][] maximums, double startingOsSize1, int overlap1, double connexityRate1, double surfaceMinSizeFactor )
public RunFirstConstructionTask(Img<FloatType> maximums, double startingOsSize1, int overlap1, double connexityRate1, double surfaceMinSizeFactor )
{
this.maximums = maximums;
this.startingOsSize1 = startingOsSize1;
......@@ -58,7 +61,7 @@ public class RunFirstConstructionTask extends AbstractTask< ArrayList< Surface >
@Override
protected ArrayList< Surface > call()
{
LOGGER.info( "Computing first round construction..." );
LOGGER.info( GUI_MARKER,"Computing first round construction..." );
FirstRoundConstruction step1 = new FirstRoundConstruction( maximums, startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor );
try
{
......@@ -66,7 +69,7 @@ public class RunFirstConstructionTask extends AbstractTask< ArrayList< Surface >
}
catch ( NoSurfaceFoundException e )
{
LOGGER.info( GUI_MARKER,"First round : No surfaces found..." );
return null;
}
return step1.getSurfaces();
......
src/main/java/fr/pasteur/ida/zellige/gui/task/RunSecondConstructionTask.java
View file @ e7432a54
......@@ -36,6 +36,8 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
public class RunSecondConstructionTask extends AbstractTask< ArrayList< Surface > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( RunSecondConstructionTask.class );
......@@ -58,15 +60,16 @@ public class RunSecondConstructionTask extends AbstractTask< ArrayList< Surface
@Override
protected ArrayList< Surface > call()
{
LOGGER.info( "Computing second round construction..." );
LOGGER.info( GUI_MARKER,"Computing second round construction..." );
SecondRoundConstruction step2 = new SecondRoundConstruction( surfaces, startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor );
try
{
step2.process();
LOGGER.info(GUI_MARKER, "Second round : {} surface(s) found", step2.getSurfaces().size() );
}
catch ( NoSurfaceFoundException e )
{
LOGGER.info( GUI_MARKER,"No surface found" );
return null;
}
return step2.getSurfaces();
......