From d7f60d3e95b1ecaec4def46ed3c20672534d2bac Mon Sep 17 00:00:00 2001
From: ctrebeau <ctrebeau@pasteur.fr>
Date: Mon, 31 Mar 2025 20:57:31 +0200
Subject: [PATCH] code cleanup
---
.../ida/zellige/element/Projection.java | 22 +----------
.../ida/zellige/element/ReferenceSurface.java | 7 ----
.../pasteur/ida/zellige/element/Surface.java | 37 -------------------
.../ida/zellige/element/ose/AbstractOSE.java | 6 +--
.../ida/zellige/element/ose/OSEList.java | 12 +++++-
.../element/surfaceLine/SurfaceLine.java | 15 ++++----
.../element/surfaceLine/SurfaceLineX.java | 17 +++++----
.../element/surfaceLine/SurfaceLineY.java | 2 -
.../pasteur/ida/zellige/gui/LogAppender.java | 2 +-
.../pasteur/ida/zellige/gui/MainAppFrame.java | 29 +++++++++------
.../controller/ConstructionController.java | 5 ++-
.../gui/controller/SelectionController.java | 3 +-
.../interactor/ConstructionInteractor.java | 5 ++-
.../zellige/gui/model/ConstructionModel.java | 10 +++--
.../gui/task/AmplitudeThresholdingTask.java | 6 ++-
.../ida/zellige/gui/task/BinningTask.java | 6 ++-
.../task/ComputeClassificationImagesTask.java | 6 ++-
.../gui/task/ConstructionCompletionTask.java | 8 ++--
.../gui/task/InterClassificationTask.java | 4 +-
.../zellige/gui/task/IslandSearchTask.java | 6 ++-
.../gui/task/OtsuThresholdingTask.java | 6 ++-
.../zellige/gui/task/PreprocessingTask.java | 6 ++-
.../gui/task/RunFirstConstructionTask.java | 6 ++-
.../gui/task/RunSecondConstructionTask.java | 8 ++--
.../ida/zellige/gui/task/SmoothingTask.java | 4 +-
.../fr/pasteur/ida/zellige/steps/Utils.java | 5 ---
.../steps/construction/Construction.java | 1 -
.../selection/util/ExtremaDetection.java | 1 -
.../selection/util/ExtremaDetection2D.java | 7 +---
29 files changed, 110 insertions(+), 142 deletions(-)
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/Projection.java b/src/main/java/fr/pasteur/ida/zellige/element/Projection.java
index 968f809..107f3ce 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/Projection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/Projection.java
@@ -30,14 +30,12 @@ package fr.pasteur.ida.zellige.element;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
-import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.numeric.integer.UnsignedShortType;
public class Projection< T extends RealType< T > & NativeType< T > >
{
- private int offset;
- private int deltaZ;
+ private final int offset;
+ private final int deltaZ;
private String method;
private final ReferenceSurface<T> referenceSurface;
private Img< T > projection;
@@ -52,13 +50,6 @@ public class Projection< T extends RealType< T > & NativeType< T > >
this.referenceSurface = referenceSurface;
}
- public Projection( ReferenceSurface< T > referenceSurface )
- {
- this.referenceSurface = referenceSurface;
- }
-
-
-
public Img< T > get()
{
return projection;
@@ -94,18 +85,9 @@ public class Projection< T extends RealType< T > & NativeType< T > >
this.subVolume = subVolume;
}
- public void setOffset( int offset )
- {
- this.offset = offset;
- }
-
public void setMethod( String method )
{
this.method = method;
}
- public void setDeltaZ( int deltaZ )
- {
- this.deltaZ = deltaZ;
- }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/ReferenceSurface.java b/src/main/java/fr/pasteur/ida/zellige/element/ReferenceSurface.java
index 0e586a6..b294169 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/ReferenceSurface.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/ReferenceSurface.java
@@ -86,13 +86,6 @@ public class ReferenceSurface< T extends RealType< T > & NativeType< T > >
}
}
-
- public Img< T > getRawProjection()
- {
- return rawProjection;
- }
-
-
public RandomAccessibleInterval< T > getInput()
{
return input;
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/Surface.java b/src/main/java/fr/pasteur/ida/zellige/element/Surface.java
index de4c54a..4269afa 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/Surface.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/Surface.java
@@ -149,43 +149,6 @@ public class Surface
return inCommon / ( double ) count;
}
- public boolean isTheSameSurfaceAs( Surface other )
- {
- for ( int i = 0; i <= this.getHeight() - 1; i++ )
- {
- SurfaceLine refLine = this.get( i );
- if ( refLine != null )
- {
- SurfaceLine toTest = other.get( i );
- if ( toTest != null )
- {
-
- for ( int j = 0; j < refLine.getLength(); j++ )
- {
- Pixels refPixels = refLine.get( j );
- if ( refPixels != null )
- {
- Pixels pixelsToTest = toTest.get( j );
- if ( pixelsToTest != null )
- {
-// return false;
-// }
- if ( ! refPixels.equals( pixelsToTest ) )
- {
- return false;
- }
- }
- }
- }
- }
-
- }
-
- }
- return true;
- }
-
-
/**
* Checks if this object shares a majority of {@link Pixels} with another {@link Surface} object.
*
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/ose/AbstractOSE.java b/src/main/java/fr/pasteur/ida/zellige/element/ose/AbstractOSE.java
index baa8e42..a3f584f 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/ose/AbstractOSE.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/ose/AbstractOSE.java
@@ -36,9 +36,7 @@ import java.util.ArrayList;
public abstract class AbstractOSE extends ArrayList< Coordinate >
{
- /* Not necessary for the program.*/
private final OSEStartingStatus startingStatus;
- /*-------------*/
/**
* The visited status for the 1D and 2D reconstructions.
@@ -62,10 +60,8 @@ public abstract class AbstractOSE extends ArrayList< Coordinate >
*/
public void set()
{
- Integer j = startingStatus.get( this.size() );
- startingStatus.put( this.size(), ( j == null ) ? 1 : j + 1 );
+ startingStatus.compute( this.size(), ( k, j ) -> ( j == null ) ? 1 : j + 1 );
startingStatus.setOSCount();
-
}
/**
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/ose/OSEList.java b/src/main/java/fr/pasteur/ida/zellige/element/ose/OSEList.java
index 60b1548..cc212f2 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/ose/OSEList.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/ose/OSEList.java
@@ -37,7 +37,6 @@ import java.util.Collection;
public class OSEList extends ArrayList< AbstractOSE >
{
-
public OSEList()
{
}
@@ -66,6 +65,10 @@ public class OSEList extends ArrayList< AbstractOSE >
return add;
}
+ /**
+ *
+ * @return the size of the OSE list
+ */
public int getSize()
{
int size = 0;
@@ -76,6 +79,9 @@ public class OSEList extends ArrayList< AbstractOSE >
return size;
}
+ /**
+ * Resets to false the visited status
+ */
public void reset()
{
for ( AbstractOSE os : this )
@@ -84,6 +90,10 @@ public class OSEList extends ArrayList< AbstractOSE >
}
}
+ /**
+ *
+ * @return true if the OSE list contains a starting OSE
+ */
public boolean containsAStart()
{
for ( AbstractOSE os : this )
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLine.java b/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLine.java
index 305afcd..1d9ddb0 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLine.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLine.java
@@ -74,14 +74,15 @@ public abstract class SurfaceLine
this.dimension = new Pixels[ length ] ;
set( os );
}
-
-
- public SurfaceLine( AbstractOSE os, int size )
- {
- this.dimension = new Pixels[ size] ;
- set( os );
- }
+ /**
+ *
+ * @param os
+ * @param overlap
+ * @param connexity
+ * @param surfaceLine
+ * @return
+ */
public SurfaceLine match2( AbstractOSE os, int overlap, double connexity, SurfaceLine surfaceLine )
{
int match = 0;
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineX.java b/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineX.java
index fded62f..6ba7479 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineX.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineX.java
@@ -44,6 +44,15 @@ public class SurfaceLineX extends SurfaceLine
this.setLine( os.get( 0 ).getY() );
}
+ /**
+ * Tests if the OS matches the SurfaceLine instance and creates a new SurfaceLine object if so.
+ *
+ * @param os - the OS to test against the SurfaceLine instance.
+ * @param direction - an integer witch indicates the line of the resulting SurfaceLine.
+ * @param overlap - the minimum number of matching coordinates.
+ * @param connexity - the minimum percentage of match between the OS and the current instance.
+ * @return - a new SurfaceLine if there is a match, null otherwise.
+ */
public SurfaceLine match( AbstractOSE os, int direction, int overlap, double connexity )
{
SurfaceLineX surfaceLineX = new SurfaceLineX( this.getLength(), this.getLine() + direction );
@@ -61,12 +70,4 @@ public class SurfaceLineX extends SurfaceLine
super(length, line );
}
- public SurfaceLineX( AbstractOSE os, int size )
- {
- super( os , size);
- this.setLine( os.get( 0 ).getY() );
- }
-
-
-
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineY.java b/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineY.java
index 9b30ebd..5b064f6 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineY.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineY.java
@@ -66,8 +66,6 @@ public class SurfaceLineY extends SurfaceLine
* @param connexity - the minimum percentage of match between the OS and the current instance.
* @return - a new SurfaceLine if there is a match, null otherwise.
*/
-
-
public SurfaceLine match( AbstractOSE os, int direction, int overlap, double connexity )
{
SurfaceLineY surfaceLineY = new SurfaceLineY( this.getLength(), this.getLine() + direction );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/LogAppender.java b/src/main/java/fr/pasteur/ida/zellige/gui/LogAppender.java
index b5f865a..f378ff4 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/LogAppender.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/LogAppender.java
@@ -51,7 +51,7 @@ public class LogAppender extends AppenderBase< ILoggingEvent >
protected void append( ILoggingEvent iLoggingEvent )
{
String level = iLoggingEvent.getLevel().toString();
- if ( level.equals( Level.INFO.toString() ) )
+ if ( level.equals( Level.INFO.toString()) && iLoggingEvent.getMarker().contains( "GUI" ))
{
logMessage.setValue( iLoggingEvent.getFormattedMessage() );
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/MainAppFrame.java b/src/main/java/fr/pasteur/ida/zellige/gui/MainAppFrame.java
index 9c77c3f..2959530 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/MainAppFrame.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/MainAppFrame.java
@@ -45,6 +45,8 @@ import org.scijava.log.LogService;
import org.scijava.plugin.Parameter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.slf4j.Marker;
+import org.slf4j.MarkerFactory;
import javax.swing.*;
import java.awt.*;
@@ -57,7 +59,7 @@ import java.util.ResourceBundle;
public class MainAppFrame extends JFrame
{
- private final static Logger LOGGER = LoggerFactory.getLogger( MainAppFrame.class );
+ public static final Marker GUI_MARKER = MarkerFactory.getMarker("GUI");
private ImageJ ij;
private final ImageDisplayService image;
@Parameter
@@ -86,15 +88,21 @@ public class MainAppFrame extends JFrame
*/
public void setLogStatus()
{
- LoggerContext lc = ( LoggerContext ) LoggerFactory.getILoggerFactory();
- PatternLayoutEncoder ple = new PatternLayoutEncoder();
- ple.setPattern( "%msg%n" );
- ple.setContext( lc );
- ple.start();
- LogAppender appender = new LogAppender();
+ // Get the logger context
+ LoggerContext context = ( LoggerContext ) LoggerFactory.getILoggerFactory();
+
+ // Configure the log pattern
+ PatternLayoutEncoder layout = new PatternLayoutEncoder();
+ layout.setPattern( "%msg%n" );
+ layout.setContext( context );
+ layout.start();
- appender.setContext( lc );
+ // Create and start the custom LogAppender
+ LogAppender appender = new LogAppender();
+ appender.setContext( context );
appender.start();
+
+ // Get the root logger and add the appender
ch.qos.logback.classic.Logger logbackLogger =
( ch.qos.logback.classic.Logger ) LoggerFactory.getLogger( Logger.ROOT_LOGGER_NAME );
logbackLogger.addAppender( appender );
@@ -102,7 +110,6 @@ public class MainAppFrame extends JFrame
public MainAppFrame( Context context )
{
-// this.ij = context.;
this.image = context.getService( ImageDisplayService.class );
this.logService = context.getService( LogService.class );
this.setIconImages( ICONS );
@@ -160,14 +167,12 @@ public class MainAppFrame extends JFrame
{
ResourceBundle bundle = ResourceBundle.getBundle( "gui" );// access to properties f
FXMLLoader loader = new FXMLLoader( MainAppFrame.class.getClassLoader().getResource( "fr.pasteur.ida.zellige.gui.view/Main.fxml" ), bundle );
-
VBox rootLayout = loader.load();
// Get the controller and add an ImageJ context to it.
MainController< T > controller = loader.getController();
controller.setMainApp( this );
-
// Show the scene containing the root layout.
scene = new Scene( rootLayout );
this.fxPanel.setScene( scene );
@@ -183,4 +188,6 @@ public class MainAppFrame extends JFrame
}
+
+
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/controller/ConstructionController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/ConstructionController.java
index 8a4ec17..1ce2e79 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/controller/ConstructionController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/ConstructionController.java
@@ -51,6 +51,7 @@ import org.slf4j.LoggerFactory;
import java.net.URL;
import java.util.ResourceBundle;
+import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
import static fr.pasteur.ida.zellige.gui.controller.MainController.showError;
import static fr.pasteur.ida.zellige.gui.controller.MainController.showInfo;
import static fr.pasteur.ida.zellige.gui.controller.SelectionController.setNextOutputToNull;
@@ -199,7 +200,7 @@ public class ConstructionController< T extends RealType< T > & NativeType< T > >
{
disableGUI( true );
- LOGGER.info( "Running construction" );
+ LOGGER.info(GUI_MARKER, "Running construction" );
if ( getModel().maximumsProperty().getValue() != null )
{
if ( getModel().firstRoundSurfacesProperty().getValue() == null )
@@ -220,7 +221,7 @@ public class ConstructionController< T extends RealType< T > & NativeType< T > >
ConstructionDisplayTask< T > task = new ConstructionDisplayTask<>( getModel().referenceSurfacesProperty().getValue() );
task.setOnSucceeded( workerStateEvent ->
{
- LOGGER.info( "Construction display completed." );
+ LOGGER.info(GUI_MARKER, "Construction display completed." );
getModel().getImageViews().setValue( task.getValue() );
parentController.getProjectionController().getModel().getImageViews().set( task.getValue() );
// parentController.getProjectionController().getModel().getReferenceSurfaces().
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java
index 034c83b..66059bc 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java
@@ -53,6 +53,7 @@ import org.slf4j.LoggerFactory;
import java.net.URL;
import java.util.ResourceBundle;
+import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
import static fr.pasteur.ida.zellige.gui.controller.MainController.showInfo;
@@ -283,7 +284,7 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
SelectionDisplayTask selectionDisplayTask = new SelectionDisplayTask( getModel().selectedPixelsProperty().getValue() );
selectionDisplayTask.setOnSucceeded( workerStateEvent ->
{
- LOGGER.info( "Double classification done." );
+ LOGGER.info( GUI_MARKER,"Double classification done!!!!!." );
getModel().imageViewsProperty().setValue( selectionDisplayTask.getValue() );
setDisplay();
} );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/interactor/ConstructionInteractor.java b/src/main/java/fr/pasteur/ida/zellige/gui/interactor/ConstructionInteractor.java
index d6482ce..d6aa533 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/interactor/ConstructionInteractor.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/interactor/ConstructionInteractor.java
@@ -16,6 +16,7 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList;
+import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
import static fr.pasteur.ida.zellige.gui.controller.MainController.showError;
public class ConstructionInteractor< T extends RealType< T > & NativeType< T > >
@@ -54,7 +55,7 @@ public class ConstructionInteractor< T extends RealType< T > & NativeType< T > >
public void secondRound()
{
- LOGGER.info( "Computing second round construction..." );
+ LOGGER.info( GUI_MARKER,"Computing second round construction..." );
if ( model.firstRoundSurfacesProperty().getValue() != null )
{
AbstractTask< ArrayList< Surface > > secondRoundTask = new RunSecondConstructionTask(
@@ -73,7 +74,7 @@ public class ConstructionInteractor< T extends RealType< T > & NativeType< T > >
}
else
{
- LOGGER.info( "Second round construction done." );
+ LOGGER.info(GUI_MARKER, "Second round construction done." );
}
} );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/model/ConstructionModel.java b/src/main/java/fr/pasteur/ida/zellige/gui/model/ConstructionModel.java
index efa62a2..0a2c2b1 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/model/ConstructionModel.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/model/ConstructionModel.java
@@ -53,6 +53,8 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList;
+import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
+
public class ConstructionModel< T extends RealType< T > & NativeType< T > >
{
@@ -91,7 +93,7 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >
public void firstRound()
{
- LOGGER.info( "Computing first round construction..." );
+ LOGGER.info(GUI_MARKER, "Computing first round construction..." );
AbstractTask< ArrayList< Surface > > firstRoundTask = new RunFirstConstructionTask( maximums.getValue(), st1.doubleValue(), r1.intValue(), c1.doubleValue(), surfaceSize.doubleValue() / 100.0 );
firstRoundTask.setOnSucceeded( workerStateEvent ->
{
@@ -102,14 +104,14 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >
MainController.showError( new FirstRoundConstructionException() );
}
} );
- LOGGER.info( "First round construction done." );
+ LOGGER.info( GUI_MARKER,"First round construction done." );
firstRoundTask.start();
}
public void secondRound()
{
- LOGGER.info( "Computing second round construction..." );
+ LOGGER.info( GUI_MARKER,"Computing second round construction..." );
AbstractTask< ArrayList< Surface > > secondRoundTask = new RunSecondConstructionTask( firstRoundSurfacesProperty().getValue(), st2.getValue(), r2.intValue(), c2.doubleValue(), surfaceSize.doubleValue() / 100.0 );
secondRoundTask.setOnSucceeded( workerStateEvent ->
{
@@ -120,7 +122,7 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >
MainController.showError( new SecondRoundConstructionException() );
}
} );
- LOGGER.info( "Second round construction done." );
+ LOGGER.info( GUI_MARKER,"Second round construction done." );
secondRoundTask.start();
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/AmplitudeThresholdingTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/AmplitudeThresholdingTask.java
index 3077ef1..52601f9 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/AmplitudeThresholdingTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/AmplitudeThresholdingTask.java
@@ -35,6 +35,8 @@ 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 AmplitudeThresholdingTask extends AbstractTask< Img< BitType > >
{
@@ -52,9 +54,9 @@ public class AmplitudeThresholdingTask extends AbstractTask< Img< BitType > >
@Override
protected Img< BitType > call()
{
- LOGGER.info( "Computing amplitude thresholding..." );
+ LOGGER.info(GUI_MARKER, "Computing amplitude thresholding..." );
Img< BitType > output = AmplitudeClassification.applyThreshold( input, amplitudeThreshold );
- LOGGER.info( "Amplitude thresholds computed..." );
+ LOGGER.info( GUI_MARKER,"Amplitude thresholds computed..." );
return output;
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/BinningTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/BinningTask.java
index df35175..f017dec 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/BinningTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/BinningTask.java
@@ -8,6 +8,8 @@ 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 );
@@ -22,9 +24,9 @@ public class BinningTask < T extends RealType< T > & NativeType< T > > extends A
@Override
protected Img<T> call() {
- LOGGER.info( "Binning" );
+ LOGGER.info( GUI_MARKER,"Binning" );
Img<T> binnedImage = Binning.run( input, bin );
- LOGGER.info( "Image binned !" );
+ LOGGER.info( GUI_MARKER,"Image binned !" );
return binnedImage;
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/ComputeClassificationImagesTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/ComputeClassificationImagesTask.java
index e5e69db..e6abffa 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/ComputeClassificationImagesTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/ComputeClassificationImagesTask.java
@@ -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;
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionCompletionTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionCompletionTask.java
index 2e11661..6a3400b 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionCompletionTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionCompletionTask.java
@@ -40,6 +40,8 @@ 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( ConstructionCompletionTask.class );
@@ -60,12 +62,12 @@ public class ConstructionCompletionTask< T extends RealType< T > & NativeType< T
@Override
protected ArrayList< ReferenceSurface< T > > call()
{
- LOGGER.info( "Processing construction completion..." );
+ LOGGER.info( GUI_MARKER,"Processing construction completion..." );
ArrayList< ReferenceSurface< T > > list = ConstructionCompletion.run( input, factory, finalSurfaces , bin);
- LOGGER.info( "construction completed..." );
+ LOGGER.info(GUI_MARKER, "construction completed..." );
if ( list.isEmpty() )
{
- LOGGER.info( "no surfaces..." );
+ LOGGER.info( GUI_MARKER,"no surfaces..." );
}
return list;
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/InterClassificationTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/InterClassificationTask.java
index 129f208..20b064b 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/InterClassificationTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/InterClassificationTask.java
@@ -35,6 +35,8 @@ 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 > >
{
@@ -53,7 +55,7 @@ public class InterClassificationTask extends AbstractTask< Img< BitType > >
protected Img< BitType > call()
{
- LOGGER.info( "Computing inter-classification..." );
+ LOGGER.info(GUI_MARKER, "Computing inter-classification..." );
return Classification.interClassification( selectedAmplitude.getValue(), selectedAmplitude.getValue().factory(), selectedOtsu.getValue() );
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/IslandSearchTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/IslandSearchTask.java
index def2e08..66a8a4c 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/IslandSearchTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/IslandSearchTask.java
@@ -36,6 +36,8 @@ 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 > >
{
@@ -52,9 +54,9 @@ public class IslandSearchTask extends AbstractTask< Img< BitType > >
@Override
protected Img< BitType > call()
{
- LOGGER.info( "Computing Island Search..." );
+ LOGGER.info( GUI_MARKER,"Computing Island Search..." );
Img< BitType > img = PostTreatment.runIslandSearch( image.getValue(), islandSize.intValue() );
- LOGGER.debug( "Task's end." );
+ LOGGER.info( GUI_MARKER,"Task's end." );
return img;
// return iSImage;
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java
index 982b552..0c47372 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java
@@ -36,6 +36,8 @@ 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 OtsuThresholdingTask extends AbstractTask< Img< BitType > >
{
@@ -55,9 +57,9 @@ public class OtsuThresholdingTask extends AbstractTask< Img< BitType > >
@Override
protected Img< BitType > call()
{
- LOGGER.info( "Computing otsu thresholding..." );
+ LOGGER.info( GUI_MARKER,"Computing otsu thresholding..." );
Img< BitType > output = OtsuClassification.applyLocalThreshold( pretreatedImage.getValue(), input, otsuThreshold );
- LOGGER.info( "Amplitude thresholds computed..." );
+ LOGGER.info( GUI_MARKER,"Amplitude thresholds computed..." );
return output;
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/PreprocessingTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/PreprocessingTask.java
index 8952281..a88b965 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/PreprocessingTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/PreprocessingTask.java
@@ -37,6 +37,8 @@ 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 PreprocessingTask< T extends RealType< T > & NativeType< T > > extends AbstractTask< Img< FloatType > >
{
@@ -55,10 +57,10 @@ public class PreprocessingTask< T extends RealType< T > & NativeType< T > > exte
@Override
protected Img< FloatType > call()
{
- LOGGER.info( "Computing pretreatment..." );
+ LOGGER.info(GUI_MARKER, "Computing pretreatment..." );
Img< FloatType > pretreatedImg = Pretreatment.run( input, radius, bin );
- LOGGER.debug( "Done." );
+ LOGGER.info( GUI_MARKER,"Done." );
return pretreatedImg;
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/RunFirstConstructionTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/RunFirstConstructionTask.java
index 6b08062..967f50e 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/RunFirstConstructionTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/RunFirstConstructionTask.java
@@ -38,6 +38,8 @@ 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 );
@@ -59,7 +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
{
@@ -67,7 +69,7 @@ public class RunFirstConstructionTask extends AbstractTask< ArrayList< Surface >
}
catch ( NoSurfaceFoundException e )
{
- LOGGER.info( "First round : No surfaces found..." );
+ LOGGER.info( GUI_MARKER,"First round : No surfaces found..." );
return null;
}
return step1.getSurfaces();
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/RunSecondConstructionTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/RunSecondConstructionTask.java
index eb4f672..c9dcd4e 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/RunSecondConstructionTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/RunSecondConstructionTask.java
@@ -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 );
@@ -58,16 +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( "Second round : {} surface(s) found", step2.getSurfaces().size() );
+ LOGGER.info(GUI_MARKER, "Second round : {} surface(s) found", step2.getSurfaces().size() );
}
catch ( NoSurfaceFoundException e )
{
- LOGGER.info( "No surface found" );
+ LOGGER.info( GUI_MARKER,"No surface found" );
return null;
}
return step2.getSurfaces();
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/SmoothingTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/SmoothingTask.java
index 51535b5..6466287 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/SmoothingTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/SmoothingTask.java
@@ -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 SmoothingTask extends AbstractTask<Img < FloatType >>
{
@@ -56,7 +58,7 @@ public class SmoothingTask extends AbstractTask<Img < FloatType >>
@Override
protected Img<FloatType> call() throws Exception
{
- LOGGER.info( "Computing first smoothing..." );
+ LOGGER.info( GUI_MARKER,"Computing first smoothing..." );
return PostTreatment.runSmoothing( islandSearchImage.getValue(), sigmaXY.intValue(), sigmaZ.intValue() );
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/Utils.java b/src/main/java/fr/pasteur/ida/zellige/steps/Utils.java
index 29c0929..c527c80 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/Utils.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/Utils.java
@@ -34,12 +34,8 @@ import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.real.FloatType;
-import net.imglib2.view.IterableRandomAccessibleInterval;
-import net.imglib2.view.RandomAccessibleIntervalCursor;
import net.imglib2.view.Views;
-
-
/**
* Some "utils" methods.
*/
@@ -85,7 +81,6 @@ public class Utils
randomAccess.setPosition( z, 2 );
}
-
public static < T extends RealType< T > & NativeType< T > > T setPositionAndGet( RandomAccess< T > randomAccess, int u, int v )
{
setPosition( randomAccess, u, v );
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/Construction.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/Construction.java
index f52b373..f1c8a0b 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/Construction.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/Construction.java
@@ -1,6 +1,5 @@
package fr.pasteur.ida.zellige.steps.construction;
-import fr.pasteur.ida.zellige.ReferenceSurfaceExtraction;
import fr.pasteur.ida.zellige.element.ReferenceSurface;
import fr.pasteur.ida.zellige.element.Surface;
import fr.pasteur.ida.zellige.steps.construction.exception.NoSurfaceFoundException;
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection.java
index 6d1cd56..dcdf665 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection.java
@@ -43,7 +43,6 @@ import org.slf4j.LoggerFactory;
public class ExtremaDetection< T extends RealType< T > & NativeType< T > >
{
-
public static final String MAX = "max";
public static final String MIN = "min";
private final static Logger LOGGER = LoggerFactory.getLogger( ExtremaDetection.class );
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection2D.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection2D.java
index e4507dc..a2a5495 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection2D.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection2D.java
@@ -40,7 +40,6 @@ import static fr.pasteur.ida.zellige.steps.selection.util.ExtremaDetection.MAX;
public class ExtremaDetection2D< T extends RealType< T > & NativeType< T > >
{
-
private final RandomAccessibleInterval< T > inputSection;
private final ImgFactory< T > factory;
private final RandomAccessibleInterval< T > extrema;
@@ -86,15 +85,13 @@ public class ExtremaDetection2D< T extends RealType< T > & NativeType< T > >
}
}
-
/**
* @param section the section considered
* @param sectionDerivative the corresponding partial derivative section of the input image as a {@link RandomAccessibleInterval}
*/
private void
computeExtrema
- ( RandomAccessibleInterval< T > section, RandomAccessibleInterval< T > sectionDerivative
- )
+ ( RandomAccessibleInterval< T > section, RandomAccessibleInterval< T > sectionDerivative )
{
RandomAccess< T > derivativeAccess = Views.extendMirrorSingle( sectionDerivative ).randomAccess();
RandomAccess< T > extremaAccess = extrema.randomAccess();
@@ -125,7 +122,7 @@ public class ExtremaDetection2D< T extends RealType< T > & NativeType< T > >
* @param z - the index of the Z dimension
* @return - true if the position (v, z) is a local maximum false otherwise.
*/
- private boolean isALocalExtrema( RandomAccess< T > derivative, int z ) //throws Exception
+ private boolean isALocalExtrema( RandomAccess< T > derivative, int z )
{
derivative.setPosition( z, 1 );
final double tZero = derivative.get().getRealDouble();
--
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