diff --git a/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java b/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
index 5dc328f05385264152873b68bf5578c26d3e0150..8719f7491f912ed682f8b41ac790270d53546d44 100644
--- a/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
+++ b/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
@@ -124,174 +124,171 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
public static < T extends RealType< T > & NativeType< T > > void run(String CSV_FILE)throws IOException, ParameterException
{
ImageJ ij = new ImageJ();
-// ij.launch( args );
setLogStatus();
- try ( Stream< String > lines = Files.lines( Paths.get( CSV_FILE ) ) )
+ try ( Stream< String > lines = Files.lines( Paths.get( CSV_FILE ) ) )//try-with-resources ensures the stream is closed properly.
{
List< List< String > > records = lines.map( line -> Arrays.asList( line.split( SEMI_COLON_DELIMITER ) ) )
.collect( Collectors.toList() );
LOGGER.debug( "the csv is loaded" );
for ( int i = 1; i < records.size(); i++ ) // skip the header
{
- List< String > line = records.get( i );
- // Input
- String inputPath = line.get( 0 );
- Dataset dataset = ArgumentCheck.input( ij.scifio().datasetIO().open( inputPath ) );
- String inputName = FilenameUtils.removeExtension(dataset.getName());
- String id = uniqueID();
- Path datasetLocation = Paths.get(inputPath).getParent();
-
- Path outputPath = Files.createDirectories(Paths.get(String.format("%s\\%s%s",datasetLocation.toString() , inputName, id)));
- setLogFilePath( String.format("%s\\log.txt", outputPath) );
-
- int nbChannel = ( int ) dataset.getChannels() > 0 ? ( int ) dataset.getChannels(): 1;
- ArrayList< ColorTable > colorTables = new ArrayList<>();
- for ( int channel = 0; channel < nbChannel ; channel++ )
+ try
{
- colorTables.add(dataset.getImgPlus().getColorTable( channel ));
- }
+ List< String > line = records.get( i );
+ // Input
+ String inputPath = line.get( 0 );
+ Dataset dataset = ArgumentCheck.input( ij.scifio().datasetIO().open( inputPath ) );
+ String inputName = FilenameUtils.removeExtension( dataset.getName() );
+ String id = uniqueID();
+ Path datasetLocation = Paths.get( inputPath ).getParent();
+
+ Path outputPath = Files.createDirectories( Paths.get( String.format( "%s\\%s%s", datasetLocation.toString(), inputName, id ) ) );
+ setLogFilePath( String.format( "%s\\log.txt", outputPath ) );
+
+ int nbChannel = ( int ) dataset.getChannels() > 0 ? ( int ) dataset.getChannels() : 1;
+ ArrayList< ColorTable > colorTables = new ArrayList<>();
+ for ( int channel = 0; channel < nbChannel; channel++ )
+ {
+ colorTables.add( dataset.getImgPlus().getColorTable( channel ) );
+ }
- // Preprocessing Parameters
- LOGGER.info( "Preprocessing parameters" );
- LOGGER.info( "------------------------" );
- int bin = ArgumentCheck.bin( line.get( 1 ) );
- int channel = ArgumentCheck.channel( line.get( 2 ), nbChannel );
-
-
- // Selection Parameters
- LOGGER.info( "Selection parameters" );
- LOGGER.info( "--------------------" );
- int amplitude = ArgumentCheck.amplitude( line.get( 3 ) );
- int otsu = ArgumentCheck.otsu( line.get( 4 ) );
- int islandSize = ArgumentCheck.islandSize( line.get( 5 ) );
- double sigmaXY = ArgumentCheck.sigmaXY( line.get( 6 ) );
- double sigmaZ = ArgumentCheck.sigmaZ( line.get( 7 ) );
-
- // Construction Parameters
- LOGGER.info( "Construction parameters" );
- LOGGER.info( "-----------------------" );
- int FIRST_ROUND = 1;
- double startingOsSize1 = ArgumentCheck.startingOsSize( line.get( 8 ), FIRST_ROUND );
- int overlap1 = ArgumentCheck.overlap( line.get( 9 ), FIRST_ROUND );
- double connexityRate1 = ArgumentCheck.connexity( line.get( 10 ), FIRST_ROUND );
- int SECOND_ROUND = 2;
- double startingOsSize2 = ArgumentCheck.startingOsSize( line.get( 11 ), SECOND_ROUND );
- int overlap2 = ArgumentCheck.overlap( line.get( 12 ), SECOND_ROUND );
- double connexityRate2 = ArgumentCheck.connexity( line.get( 13 ), SECOND_ROUND );
- double surfaceMinSizeFactor = Double.parseDouble( line.get( 14 ) );
-
- // Projection Parameters
- LOGGER.info( "\nProjection parameters" );
- LOGGER.info( "--------------------" );
- ArrayList< ChannelProjectionParameter > pp = new ArrayList<>();
- for ( int n = 0; n < nbChannel; n++ )
- {
- LOGGER.info( " Channel {}", (n+1 ));
+ // Preprocessing Parameters
+ LOGGER.info( "Preprocessing parameters" );
+ LOGGER.info( "------------------------" );
+ int bin = ArgumentCheck.bin( line.get( 1 ) );
+ int channel = ArgumentCheck.channel( line.get( 2 ), nbChannel );
+
+
+ // Selection Parameters
+ LOGGER.info( "Selection parameters" );
+ LOGGER.info( "--------------------" );
+ int amplitude = ArgumentCheck.amplitude( line.get( 3 ) );
+ int otsu = ArgumentCheck.otsu( line.get( 4 ) );
+ int islandSize = ArgumentCheck.islandSize( line.get( 5 ) );
+ double sigmaXY = ArgumentCheck.sigmaXY( line.get( 6 ) );
+ double sigmaZ = ArgumentCheck.sigmaZ( line.get( 7 ) );
+
+ // Construction Parameters
+ LOGGER.info( "Construction parameters" );
+ LOGGER.info( "-----------------------" );
+ int FIRST_ROUND = 1;
+ double startingOsSize1 = ArgumentCheck.startingOsSize( line.get( 8 ), FIRST_ROUND );
+ int overlap1 = ArgumentCheck.overlap( line.get( 9 ), FIRST_ROUND );
+ double connexityRate1 = ArgumentCheck.connexity( line.get( 10 ), FIRST_ROUND );
+ int SECOND_ROUND = 2;
+ double startingOsSize2 = ArgumentCheck.startingOsSize( line.get( 11 ), SECOND_ROUND );
+ int overlap2 = ArgumentCheck.overlap( line.get( 12 ), SECOND_ROUND );
+ double connexityRate2 = ArgumentCheck.connexity( line.get( 13 ), SECOND_ROUND );
+ double surfaceMinSizeFactor = Double.parseDouble( line.get( 14 ) );
+
+ // Projection Parameters
+ LOGGER.info( "\nProjection parameters" );
+ LOGGER.info( "--------------------" );
+ ArrayList< ChannelProjectionParameter > pp = new ArrayList<>();
+ for ( int n = 0; n < nbChannel; n++ )
+ {
+ LOGGER.info( " Channel {}", ( n + 1 ) );
// int channelNb = n * 1;
- int delta = ArgumentCheck.delta( line.get( 15 + (3 * n) ), n );
- int offset = ArgumentCheck.offset( line.get( 16 + (3 * n) ), n );
- String method = ArgumentCheck.method( line.get( 17 +(3 * n) ), n );
- ChannelProjectionParameter parameters = new ChannelProjectionParameter( delta, offset, method );
- pp.add( parameters );
- }
- ProjectionParameters projectionParameters =new ProjectionParameters( pp );
- LOGGER.debug( "All argument are checked." );
+ int delta = ArgumentCheck.delta( line.get( 15 + ( 3 * n ) ), n );
+ int offset = ArgumentCheck.offset( line.get( 16 + ( 3 * n ) ), n );
+ String method = ArgumentCheck.method( line.get( 17 + ( 3 * n ) ), n );
+ ChannelProjectionParameter parameters = new ChannelProjectionParameter( delta, offset, method );
+ pp.add( parameters );
+ }
+ ProjectionParameters projectionParameters = new ProjectionParameters( pp );
+ LOGGER.debug( "All argument are checked." );
- //Parameters
- SelectionParameters selectionParameters = new SelectionParameters( amplitude, otsu, sigmaZ, sigmaXY, islandSize );
- PretreatmentParameters pretreatmentParameters = new PretreatmentParameters( channel, bin );
+ //Parameters
+ SelectionParameters selectionParameters = new SelectionParameters( amplitude, otsu, sigmaZ, sigmaXY, islandSize );
+ PretreatmentParameters pretreatmentParameters = new PretreatmentParameters( channel, bin );
// ClassificationParameters classificationParameters = new ClassificationParameters( amplitude, otsu );
// PostTreatmentParameters postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, islandSize, CONNEXITY );
- ConstructionParameters[] constructionParameters = new ConstructionParameters[2];
- constructionParameters [0] = new ConstructionParameters( startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor );
- constructionParameters [1] = new ConstructionParameters( startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor );
+ ConstructionParameters[] constructionParameters = new ConstructionParameters[ 2 ];
+ constructionParameters[ 0 ] = new ConstructionParameters( startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor );
+ constructionParameters[ 1 ] = new ConstructionParameters( startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor );
- //set the input
- Img<T> input ;
- if ( nbChannel == 1 )
- {
- try
+ //set the input
+ Img< T > input;
+ if ( nbChannel == 1 )
{
- input = ( create4dimImage( dataset ) );
+ try
+ {
+ input = ( create4dimImage( dataset ) );
+ }
+ catch ( Exception e )
+ {
+ throw new RuntimeException( e );
+ }
}
- catch ( Exception e )
+ else
{
- throw new RuntimeException( e );
+ input = ( ( Img< T > ) dataset.getImgPlus() );
}
- }
- else
- {
- input = ( ( Img< T > ) dataset.getImgPlus() );
- }
- // Set the target channel
- RandomAccessibleInterval<T> inputChannel = Views.hyperSlice( input, 2, (channel -1) );
+ // Set the target channel
+ RandomAccessibleInterval< T > inputChannel = Views.hyperSlice( input, 2, ( channel - 1 ) );
- // Preprocessing and selection steps
- ImageJFunctions.show(input, "input");
- Img <FloatType > selectedPixels = Selection.run(inputChannel, pretreatmentParameters, selectionParameters );
+ // Preprocessing and selection steps
+ ImageJFunctions.show( input, "input" );
+ Img< FloatType > selectedPixels = Selection.run( inputChannel, pretreatmentParameters, selectionParameters );
- // Construction step
- ArrayList< ReferenceSurface< T > > referenceSurfaces = Construction.run(constructionParameters, input, input.factory(), selectedPixels, bin);
+ // Construction step
+ ArrayList< ReferenceSurface< T > > referenceSurfaces = Construction.run( constructionParameters, input, input.factory(), selectedPixels, bin );
- // Projection step
- ArrayList< ImgPlus<T> > finalProjections = new ArrayList<>();
+ // Projection step
+ ArrayList< ImgPlus< T > > finalProjections = new ArrayList<>();
- for ( int j = 0; j < referenceSurfaces.size(); j++ )
- {
- ArrayList<Img<T>> channelProjections = new ArrayList<>();
- Img< UnsignedShortType > zMap = referenceSurfaces.get(j).getzMap();
- for ( int k = 0; k < nbChannel; k++ )
+ for ( int j = 0; j < referenceSurfaces.size(); j++ )
{
- ChannelProjectionParameter cpp = projectionParameters.getChannelProjectionParameters().get( k );
- RandomAccessibleInterval<T> channelImg = Views.hyperSlice( input, 2, k );
- Img<T> subVolume = ReferenceSurfaceProjection.getSubStack( channelImg, input.factory(),zMap, cpp.getDelta(), cpp.getOffset());
-
- Img<T> p = ReferenceSurfaceProjection.run( subVolume, cpp.getMethod());
- channelProjections.add(k, p );
+ ArrayList< Img< T > > channelProjections = new ArrayList<>();
+ Img< UnsignedShortType > zMap = referenceSurfaces.get( j ).getzMap();
+ for ( int k = 0; k < nbChannel; k++ )
+ {
+ ChannelProjectionParameter cpp = projectionParameters.getChannelProjectionParameters().get( k );
+ RandomAccessibleInterval< T > channelImg = Views.hyperSlice( input, 2, k );
+ Img< T > subVolume = ReferenceSurfaceProjection.getSubStack( channelImg, input.factory(), zMap, cpp.getDelta(), cpp.getOffset() );
+
+ Img< T > p = ReferenceSurfaceProjection.run( subVolume, cpp.getMethod() );
+ channelProjections.add( k, p );
+ }
+ Img< T > temp = ReferenceSurfaceProjection.regroupChannels( channelProjections );
+ String projectionName = String.format( "%s_proj_%d", inputName, ( j + 1 ) );
+ ImgPlus< T > finalProjection = ReferenceSurfaceProjection.setColorsAndName( temp, colorTables, projectionName );
+ finalProjections.add( finalProjection );
}
- Img<T> temp = ReferenceSurfaceProjection.regroupChannels( channelProjections );
- String projectionName = String.format( "%s_proj_%d", inputName, (j+1) );
- ImgPlus< T > finalProjection = ReferenceSurfaceProjection.setColorsAndName( temp, colorTables, projectionName );
- finalProjections.add( finalProjection );
+ ImgSaver saver = new ImgSaver();
+ for ( int j = 0; j < referenceSurfaces.size(); j++ )
+ {
+ ImgPlus< T > projection = finalProjections.get( j );
+ String imgLocation = String.format( "%s\\%s%s", outputPath, projection.getName(), ".tif" );
+ saver.saveImg( imgLocation, projection );
+ }
+ LOGGER.debug( "End of process" );
+ fileAppender.stop();
+ }
+ catch (DataValidationException | TimeLapseException | NoA3DStackException e )
+ {
+ LOGGER.info( "Error processing line {} : {}", i, e.getMessage() );
+ fileAppender.stop();
}
- ImgSaver saver = new ImgSaver();
- for ( int j = 0; j < referenceSurfaces.size(); j++ )
+ catch(ImageTooLargeException | NoClassificationException | NoSurfaceFoundException e)
{
- ImgPlus<T> projection = finalProjections.get(j);
- String imgLocation = String.format( "%s\\%s%s",outputPath , projection.getName(), ".tif");
- saver.saveImg(imgLocation, projection ) ;
+ LOGGER.info( "" );
+ fileAppender.stop();
}
- LOGGER.debug("End of process");
- fileAppender.stop();
+
}
}
- catch ( TimeLapseException e )
- {
- throw new RuntimeException( e );
- }
- catch ( DataValidationException e )
- {
- throw new RuntimeException( e );
- }
- catch ( NoSurfaceFoundException e )
- {
- throw new RuntimeException( e );
- }
- catch ( NoClassificationException e )
- {
- throw new RuntimeException( e );
- }
- catch ( ImageTooLargeException e )
- {
- throw new RuntimeException( e );
- }
- catch ( NoA3DStackException e )
+ catch ( IOException e )
{
+ LOGGER.info( "Failed to open file: {}", CSV_FILE );
throw new RuntimeException( e );
}
+
+
+
}
/**
* Creates a new LogAppender to display the program state in the GUI.
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ChannelPanel.java b/src/main/java/fr/pasteur/ida/zellige/gui/ChannelPanel.java
index 5c17c399025d728e39eb97a3687b5a3f77f2b702..ef5d7239533c855c31cb2033c974e9c0582024c5 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ChannelPanel.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/ChannelPanel.java
@@ -51,8 +51,9 @@ public class ChannelPanel extends Pane implements Initializable
ObservableList< String > list = FXCollections.observableArrayList( "MIP", "Mean" );
method.setItems( list );
method.getSelectionModel().selectFirst();
+
SpinnerValueFactory< Integer > valueFactory2 =
- new SpinnerValueFactory.IntegerSpinnerValueFactory( 0, 30, 0, 1 );
+ new SpinnerValueFactory.IntegerSpinnerValueFactory( -3, 3, 0, 1 );
offset.setValueFactory( valueFactory2 );
}
@@ -76,4 +77,13 @@ public class ChannelPanel extends Pane implements Initializable
{
return view;
}
+
+
+ public void setSpinners (int nbSlices)
+ {
+ deltaZ.setValueFactory( new SpinnerValueFactory.IntegerSpinnerValueFactory( 0, nbSlices - 1, 1, 1 ));
+
+ offset.setValueFactory( new SpinnerValueFactory.IntegerSpinnerValueFactory( - (nbSlices - 1), nbSlices - 1, 1, 1 ));
+
+ }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ReferenceSurfacePanel.java b/src/main/java/fr/pasteur/ida/zellige/gui/ReferenceSurfacePanel.java
index d1ab05ec00eccd6ee59d35cab3bd7e4f9b4793f4..1b75b4e89512fbeca86001370587023a82be8c0b 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ReferenceSurfacePanel.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/ReferenceSurfacePanel.java
@@ -18,14 +18,13 @@ public class ReferenceSurfacePanel < T extends RealType< T > & NativeType< T > >
private TabPane channelTools;
-
@FXML
private Button run;
private final ProjectionProperties<T> projectionProperties;
- public ReferenceSurfacePanel( int channels)
+ public ReferenceSurfacePanel( int channels, int nbSlices)
{
FXMLLoader fxmlLoader = new FXMLLoader( ReferenceSurfacePanel.class.getClassLoader().
getResource( "fr.pasteur.ida.zellige.gui.view/ReferenceSurfacePanel.fxml" ) );
@@ -43,6 +42,7 @@ public class ReferenceSurfacePanel < T extends RealType< T > & NativeType< T > >
{
Tab tab = new Tab( "C" + i );
ChannelPanel pane = new ChannelPanel();
+ pane.setSpinners( nbSlices );
tab.setContent( pane );
getChannelTools().getTabs().add( tab );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/controller/PreprocessingController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/PreprocessingController.java
index d5753bff91f63594baacb161302dbeac7f76631c..073f0781e2c9d7c3f28d57c3e5c29281f3dc6b4c 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/controller/PreprocessingController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/PreprocessingController.java
@@ -132,7 +132,7 @@ public class PreprocessingController< T extends RealType< T > & NativeType< T >
StackPane stackPane = parentController.getProjectionController().getStackPane();
stackPane.getChildren().clear();
parentController.getProjectionController().getModel().getNumberOfChannels().set( getModel().getNbOfChannels().get() );
- ReferenceSurfacePanel<T> panel = new ReferenceSurfacePanel<>( getModel().getNbOfChannels().get() );
+ ReferenceSurfacePanel<T> panel = new ReferenceSurfacePanel<>( getModel().getNbOfChannels().get(), (int) getModel().getInput().getValue().dimension( 3 ) );
stackPane.getChildren().add( panel );
}
else
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/controller/ProjectionController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/ProjectionController.java
index 4521dec90b4abceb22c3b576a9866238ef1e29c2..d9f019567c21064a490f4eb1ef45cae994e462ec 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/controller/ProjectionController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/ProjectionController.java
@@ -121,7 +121,7 @@ public class ProjectionController< T extends RealType< T > & NativeType< T > > i
for ( int i = 0; i < getModel().getReferenceSurfaces().get().size(); i++ )
{
// sets a new projection panel according to the input channel number.
- ReferenceSurfacePanel< T > panel = new ReferenceSurfacePanel<>( channels );
+ ReferenceSurfacePanel< T > panel = new ReferenceSurfacePanel<>( channels, (int) parentController.getPreprocessingController().getModel().getInput().getValue().dimension( 3 ) );
// Adding properties to each reference surfaces
getModel().getProjectionProperties().get().add( panel.getProjectionProperties() );
stackPane.getChildren().add( panel );