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#6 closed - Display of program state

Closed #6 closed - Display of program state
feature_gui into dev
Closed Céline TREBEAU requested to merge feature_gui into dev
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src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand.java deleted 100644 → 0
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package fr.pasteur.ida.zellige.command;
import fr.pasteur.ida.zellige.ReferenceSurfaceExtraction;
import fr.pasteur.ida.zellige.steps.construction.exception.NoSurfaceFoundException;
import fr.pasteur.ida.zellige.steps.construction.rounds.ConstructionParameters;
import fr.pasteur.ida.zellige.steps.projection.DisplayParameters;
import fr.pasteur.ida.zellige.steps.projection.NoPossibleDisplayException;
import fr.pasteur.ida.zellige.steps.projection.ProjectionParameters;
import fr.pasteur.ida.zellige.steps.selection.classification.ClassificationParameters;
import fr.pasteur.ida.zellige.steps.selection.exception.DataValidationException;
import fr.pasteur.ida.zellige.steps.selection.exception.EmptyOutputException;
import fr.pasteur.ida.zellige.steps.selection.exception.NoClassificationException;
import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatmentParameters;
import fr.pasteur.ida.zellige.steps.selection.pretreatment.PretreatmentParameters;
import ij.IJ;
import net.imagej.Dataset;
import net.imagej.ImageJ;
import net.imagej.ImgPlus;
import net.imagej.display.ImageDisplayService;
import net.imagej.ops.OpService;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.util.Util;
import org.scijava.command.ContextCommand;
import org.scijava.log.LogService;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import java.io.File;
import java.io.IOException;
import java.nio.file.FileSystems;
@Plugin( type = ZelligeCommand.class, name = "Zellige", menuPath = "Plugins > Process > Zellige" )
public class ZelligeCommand< T extends RealType< T > & NativeType< T > > extends ContextCommand
{
@Parameter
protected OpService ops;
@Parameter
private ImageDisplayService imageDisplayService;
@Parameter
private LogService logService;
@Parameter( label = "Amplitude threshold", min = "0", max = "255", stepSize = "1" )
private int amplitude = 5;
@Parameter( label = "Otsu threshold", min = "0", max = "255", stepSize = "1" )
private int otsu = 5;
@Parameter( label = "XY blur radius", min = "0", max = "10" )
private int sigmaXY = 1;
@Parameter( label = "Z blur radius", min = "0", max = "10" )
private int sigmaZ = 1;
@Parameter( label = "Min Island size", min = "0", max = "50", stepSize = "5" )
private int islandSize = 5;
@Parameter( label = "Island connectivity", min = "4", max = "8", stepSize = "4" )
private int connexity = 4;
@Parameter( label = "1st round Starting OSE size", min = "0", max = "1", stepSize = "0.1" )
private double startingOsSize1 = 0.8;
@Parameter( label = "1st round overlap ", min = "0", max = "50" )
private int overlap1 = 10;
@Parameter( label = "1st round matching rate", min = "0.5", max = "1", stepSize = "0.05" )
private double connexityRate1 = 0.8;
@Parameter( label = "2nd round Starting OSE size", min = "0", max = "1", stepSize = "0.1" )
private double startingOsSize2 = 0.1;
@Parameter( label = "2nd round overlap", min = "0", max = "50", stepSize = "5" )
private int overlap2 = 10;
@Parameter( label = "2nd round matching rate", min = "0.5", max = "1", stepSize = "0.05" )
private double connexityRate2 = 0.9;
@Parameter( label = "Min surface size (rel to XY image size)", min = "0.05", max = "1", stepSize = "0.1" )
private double surfaceMinSizeFactor;
@Parameter( label = "Projection width (deltaZ)", min = "0" )
private int delta;
public static void main( String[] args ) throws IOException
{
String currentFolder = FileSystems.getDefault()
.getPath( "" )
.toAbsolutePath()
.toString();
String imageFilePath = "doc/Cochlée1.tif";
// Launch ImageJ.
ImageJ ij = new ImageJ();
ij.launch( args );
// Load the image.
Object obj = ij.io().open( new File( currentFolder, imageFilePath ).getAbsolutePath() );
// Display it.
ij.ui().show( obj );
ij.command().run( ZelligeCommand.class, true );
}
@Override
public void run()
{
/*
* Get current dataset.
*/
Dataset dataset = imageDisplayService.getActiveDataset();
if ( null == dataset )
{
logService.error( "Please open an image before running Zellige." );
return;
}
/*
* Wrap it into an ImgLib2 'Plus' image.
*/
@SuppressWarnings( "unchecked" )
ImgPlus< T > img = ( ImgPlus< T > ) dataset.getImgPlus();
long[] dims = new long[ dataset.numDimensions() ];
dataset.dimensions( dims );
IJ.log( "Zellige received the image: " + img.getName() );
IJ.log( "Size: " + Util.printInterval( img ) );
IJ.log( "Type: " + img.firstElement().getClass().toGenericString() );
IJ.log( "Dimensionality: " + img.numDimensions() + "D" );
for ( int d = 0; d < img.numDimensions(); d++ )
{
IJ.log( " - dimension " + d + ": [" + img.axis( d ).type() + "], 1 unit = " + img.averageScale( d ) + " " + img.axis( d ).unit() );
}
// Fixed parameters for now...
String filter = "GaussianBlur";
double filterParameter = 2;
IJ.log( "Input image : " + dataset.getName() );
IJ.log( "filter : " + filter );
IJ.log( "filter parameter : " + filterParameter );
IJ.log( "amplitude : " + amplitude );
IJ.log( "threshold : " + otsu );
IJ.log( "connexity : " + connexity );
IJ.log( "island size : " + islandSize );
IJ.log( "sigmaXY : " + sigmaXY );
IJ.log( "sigmaZ : " + sigmaZ );
IJ.log( "starting os size1 : " + startingOsSize1 );
IJ.log( "overlap1 :" + overlap1 );
IJ.log( "connexityRate1 :" + connexityRate1 );
IJ.log( "starting os size2 : " + startingOsSize2 );
IJ.log( "overlap2 :" + overlap2 );
IJ.log( "connexityRate2 :" + connexityRate2 );
IJ.log( "surface Minimum size factor : " + surfaceMinSizeFactor );
IJ.log( "delta : " + delta );
PretreatmentParameters pretreatmentParameters = null;
try
{
pretreatmentParameters = new PretreatmentParameters( filter, filterParameter );
}
catch ( DataValidationException e )
{
e.printStackTrace();
}
ClassificationParameters classificationParameters = null;
try
{
classificationParameters = new ClassificationParameters( amplitude, otsu );
}
catch ( DataValidationException e )
{
e.printStackTrace();
}
PostTreatmentParameters postTreatmentParameters = null;
try
{
postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, islandSize, connexity );
}
catch ( DataValidationException e )
{
e.printStackTrace();
}
ProjectionParameters projectionParameters = null;// no other method implemented yet.
try
{
projectionParameters = new ProjectionParameters( delta, "MIP" );
}
catch ( DataValidationException e )
{
e.printStackTrace();
}
ConstructionParameters[] constructionParameters = new ConstructionParameters[]{
new ConstructionParameters( startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor ),
new ConstructionParameters( startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor ) };
DisplayParameters displayParameters = new DisplayParameters(
true,
false,
false,
true,
false, true );
if ( img.numDimensions() == 3 )// Is it a stack ?
{
ReferenceSurfaceExtraction< T > rse = new ReferenceSurfaceExtraction<>
( img, img.factory() );
try
{
rse.select( pretreatmentParameters, classificationParameters, postTreatmentParameters );
}
catch ( NoClassificationException | EmptyOutputException | DataValidationException e )
{
e.printStackTrace();
}
try
{
rse.construct( constructionParameters );
}
catch ( NoSurfaceFoundException e )
{
e.printStackTrace();
}
try
{
rse.project( projectionParameters, displayParameters );
IJ.log( " Number of surfaces found : " + rse.getReferenceSurfaces().size() );
}
catch ( NoPossibleDisplayException e )
{
e.printStackTrace();
}
}
else
{
System.out.println( " This image has to be a z-stack ! " );
}
}
}