diff --git a/.gitignore b/.gitignore
index cfc34f0a3b795e77e26409b41458bf46078fe736..0500cccbbbaea66d4d8a83a6d8635c74f8b7902a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@ doc/
/**/*.plantuml
uml/
target/
+*.iml
diff --git a/src/main/java/StartingOSStats.java b/src/main/java/StartingOSStats.java
index 1217020f467ce7d90a2e76a27056c09b44bac865..11bf1a4fc718480b2f0b2de5c3708fd9d1bc9dda 100644
--- a/src/main/java/StartingOSStats.java
+++ b/src/main/java/StartingOSStats.java
@@ -97,8 +97,8 @@ public class StartingOSStats
if ( stackImage.numDimensions() == 3 )// Is it a stack ?
{
- ImageJFunctions.show( stackImage, "original" );
- ImageJFunctions.show( TestMIP.findMIP( stackImage, stackImage.factory() ), "MIP" );
+// ImageJFunctions.show( stackImage, "original" );
+// ImageJFunctions.show( TestMIP.findMIP( stackImage, stackImage.factory() ), "MIP" );
new ReferenceSurfaceExtraction<>( stackImage, stackImage.factory(),userParameters, advancedUserParameters );
}
else
diff --git a/src/main/java/fr/pasteur/ida/zellige/jzy3D/LocalExtremaDisplay.java b/src/main/java/fr/pasteur/ida/zellige/jzy3D/LocalExtremaDisplay.java
new file mode 100644
index 0000000000000000000000000000000000000000..1da3556f38abd52c3221e65fc447d1ede296999b
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/jzy3D/LocalExtremaDisplay.java
@@ -0,0 +1,87 @@
+package fr.pasteur.ida.zellige.jzy3D;
+
+
+import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
+import org.jzy3d.analysis.AbstractAnalysis;
+import org.jzy3d.chart.factories.AWTChartComponentFactory;
+import org.jzy3d.colors.Color;
+import org.jzy3d.maths.Coord3d;
+import org.jzy3d.plot3d.primitives.Scatter;
+import org.jzy3d.plot3d.rendering.canvas.Quality;
+
+
+public class LocalExtremaDisplay extends AbstractAnalysis
+{
+ private final Pixels[][] maximumCoordinates;
+ private final Color color;
+ private final String c;
+
+ public LocalExtremaDisplay( Pixels[][] localMaximums, Color color, String c )
+ {
+ this.maximumCoordinates = localMaximums;
+ this.color = color;
+ this.c = c;
+ init();
+ }
+
+ @Override
+ public void init( )
+ {
+ if ( maximumCoordinates != null )
+ {
+ int length = getNumberOfCoordinates();
+ System.out.println("number of coordinates for " + c + " : " + length);
+ Coord3d[] points = new Coord3d[ length ];
+ Color[] colors = new Color[ length ];
+
+ int x;
+ int y;
+ int z;
+ int index = 0;
+ for ( int i = 0; i <= this.maximumCoordinates.length - 1; i++ )
+ {
+ for ( int j = 0; j <= this.maximumCoordinates[ 0 ].length - 1; j++ )
+ {
+//
+ Pixels pixels = maximumCoordinates[ i ][ j ];
+ if ( pixels != null )
+ {
+ {
+ for ( Coordinate coordinate : pixels .get() )
+ {
+ z = coordinate.getZ();
+ points[ index ] = new Coord3d( coordinate.getX(), coordinate.getY(), z );
+ colors[ index ] = color;
+// System.out.println( points[index]);
+ index++;
+ }
+ }
+
+ }
+ }
+ }
+
+ Scatter scatter = new Scatter( points, colors );
+ scatter.setWidth( 1 );
+ chart = AWTChartComponentFactory.chart( Quality.Advanced, "awt" );
+ chart.getScene().add( scatter );
+ }
+ }
+
+ private int getNumberOfCoordinates()
+ {
+ int n = 0;
+ for ( int i = 0; i <= maximumCoordinates[0].length - 1; i++ )
+ {
+ for ( int j = 0; j <= maximumCoordinates.length - 1 ; j++ )
+ {
+ if( maximumCoordinates[j][i] != null)
+ {
+ n += maximumCoordinates[j][i].size();
+ }
+ }
+ }
+ return n;
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/main/Main.java b/src/main/java/fr/pasteur/ida/zellige/main/Main.java
index 0be1b5d25c4afe8e372632f074828b6f5cbc9675..aecee9f6a5ac04afc841ec8db7411048e798ca50 100644
--- a/src/main/java/fr/pasteur/ida/zellige/main/Main.java
+++ b/src/main/java/fr/pasteur/ida/zellige/main/Main.java
@@ -57,9 +57,9 @@ public class Main
// Input of the image.
final String imagePath =
- "doc/STK.tif";
+// "doc/STK.tif";
// "C:\\Users\\ctrebeau\\Desktop\\MoucheAile\\STK\\STK_Mouche_c01_f0001_p005.tif";
-// "C:\\Users\\ctrebeau\\Downloads\\phantom3b_combined.tif";
+ "C:\\Users\\ctrebeau\\Downloads\\phantom3b_combined.tif";
// "C:\\Users\\ctrebeau\\Desktop\\HighRes\\STK_170706_Vangl2-Lp-wt_E14.5_Phall_cochlea_01bHighRes_c01_f0001_p005.tif";
System.out.println(imagePath);
// Creation of the image : version with unsigned type. */
@@ -95,8 +95,8 @@ public class Main
if ( stackImage.numDimensions() == 3 )// Is it a stack ?
{
- ImageJFunctions.show( stackImage, "original" );
- ImageJFunctions.show( TestMIP.findMIP( stackImage, stackImage.factory() ), "MIP" );
+// ImageJFunctions.show( stackImage, "original" );
+// ImageJFunctions.show( TestMIP.findMIP( stackImage, stackImage.factory() ), "MIP" );
ReferenceSurfaceExtraction rse = new ReferenceSurfaceExtraction<>( stackImage, stackImage.factory(),userParameters, advancedUserParameters );
rse.extract();
rse.project();
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/ReferenceSurfaceExtraction.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/ReferenceSurfaceExtraction.java
index 3bd58de8119623e4ad034cd4a17295ae0c9cc090..366344fd78f3ffc975a7d55c6551e63574d4e85d 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/ReferenceSurfaceExtraction.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/ReferenceSurfaceExtraction.java
@@ -22,6 +22,7 @@ import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import org.jzy3d.analysis.AnalysisLauncher;
+import org.jzy3d.colors.Color;
import java.util.ArrayList;
@@ -116,7 +117,7 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
}
}
}
- displayMaximums( tempCoordinates );
+// displayMaximums( tempCoordinates );
return tempCoordinates;
}
@@ -162,7 +163,7 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
// First step : fill in the holes with linear interpolation. */
Img< UnsignedShortType > interpolated = Interpolation.run( surface.getZMap() );
Img< UnsignedShortType > smoothed = interpolated.copy();
- ImageJFunctions.show( smoothed, "smoothed" );
+// ImageJFunctions.show( smoothed, "smoothed" );
// Second step: smooth the elevation map with gaussian blur
Utils.gaussConvolution( interpolated, smoothed, new double[]{ 1.0, 1.0 } );
return smoothed;
@@ -221,7 +222,7 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
int index = 0;
for( Surface surface : surfaces )
{
- displaySurface( surface );
+// displaySurface( surface );
Img< UnsignedShortType > processedZMap = processedZMap( surface );
ReferenceSurface< T > referenceSurface = new ReferenceSurface<>( input, factory, processedZMap, index++ );
referenceSurfaces.add( referenceSurface );
@@ -233,8 +234,8 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
for(ReferenceSurface<T> referenceSurface : referenceSurfaces)
{
referenceSurface.setProjection( userParameters.getProjectionType(), userParameters.getDelta() );
- DisplayParameter displayParameter = new DisplayParameter( userParameters.getDelta(), true,
- true, true, true );
+ DisplayParameter displayParameter = new DisplayParameter( userParameters.getDelta(), false,
+ false, false, true );
referenceSurface.display( displayParameter );
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacePixelSelection.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacePixelSelection.java
index aa34c762171b31e780f748682c82a7d96833466b..217c89b22ee7a70522712ba19bac32669dad9f13 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacePixelSelection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacePixelSelection.java
@@ -1,5 +1,6 @@
package fr.pasteur.ida.zellige.surfaceConstruction.construction;
+import fr.pasteur.ida.zellige.jzy3D.LocalExtremaDisplay;
import fr.pasteur.ida.zellige.jzy3D.LocalMaximumsDisplay;
import fr.pasteur.ida.zellige.surfaceConstruction.parameters.UserParameters;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
@@ -18,6 +19,7 @@ import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.real.FloatType;
import org.jzy3d.analysis.AnalysisLauncher;
+import org.jzy3d.colors.Color;
public class SurfacePixelSelection
{
@@ -46,7 +48,7 @@ public class SurfacePixelSelection
maximums = maximumSearch( normalized, factory );
/* Output */
- displayMaximums( maximums );
+ displayExtrema( maximums, Color.BLACK, "Black total maximums");
}
/**
@@ -79,18 +81,18 @@ public class SurfacePixelSelection
{
/* Grid of amplitude thresholds */
Img< FloatType > amplitudeImg = MaximumAmplitudeClassification.find(input,factory,userParameters.getAmplitude() , 0.10);
- ImageJFunctions.show( amplitudeImg," amplitude" );
-
+// ImageJFunctions.show( amplitudeImg," amplitude" );
+ displayExtrema( amplitudeImg, Color.GRAY, "Gray maxima amplitude" );
/* Grid of local thresholds*/
Img< BitType > thresholds = LocalOtsuClassification.find( input, factory, userParameters.getThreshold());
-
+ displayExtrema( thresholds, Color.BLUE , " Blue Otsu threshold");
/* Pixel selection */
Img<FloatType> finalList = Threshold.classification( amplitudeImg, amplitudeImg.factory(), thresholds );
-
+ displayExtrema( finalList, Color.RED, " Red otsu and amplitude intersection " );
/* Dilatation of the resulting image*/
double sigma = userParameters.getSigmas();
Utils.gaussConvolution( finalList.copy(), finalList, new double[]{ sigma, sigma, 1 } );
- ImageJFunctions.show(finalList, "blurred maximums" );
+// ImageJFunctions.show(finalList, "blurred maximums" );
/* Local maximum detection due to previous smoothing*/
finalList = LocalExtremaDetection.findMaxima( finalList.copy(), finalList.factory() );
@@ -102,7 +104,7 @@ public class SurfacePixelSelection
* @param <T>
* @return
*/
- public < T extends RealType< T > & NativeType< T > > Pixels[][] buildPixelArray(
+ public static < T extends RealType< T > & NativeType< T > > Pixels[][] buildPixelArray(
final RandomAccessibleInterval< T > stack )
{
RandomAccess< T > access = stack.randomAccess();
@@ -151,4 +153,24 @@ public class SurfacePixelSelection
{
return maximums;
}
+
+
+ public static void displayExtrema(Pixels[][] extrema , Color color, String c)
+ {
+ try
+ {
+ LocalExtremaDisplay localExtremaDisplay = new LocalExtremaDisplay( extrema, color, c );
+ AnalysisLauncher.open( localExtremaDisplay );
+ }
+ catch ( Exception e )
+ {
+ e.printStackTrace();
+ }
+ }
+
+ public static < T extends RealType< T > & NativeType< T > > void displayExtrema(Img<T> img , Color color, String c)
+ {
+ Pixels[][] extrema = buildPixelArray( img );
+ displayExtrema( extrema, color, c );
+ }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ReferenceSurface.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ReferenceSurface.java
index 0ab013ec3ae2e4f4b2526dd83bdb68afc13c165c..d2462d8b0646e05210f2e09c3e742db314a27bf8 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ReferenceSurface.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ReferenceSurface.java
@@ -37,7 +37,7 @@ public class ReferenceSurface< T extends RealType< T > & NativeType< T > >
{
this.delta = delta;
this.projectionType = projectionType;
- ImageJFunctions.show( zMap, "input zMap" );
+// ImageJFunctions.show( zMap, "input zMap" );
extractedStack = StackProjection.getExtractedStack( input, factory, zMap, delta );
if ( projectionType.equals( "MIP" ) ||
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/Surface.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/Surface.java
index 9d460f5c639350e4d0552a7f9487f018e553c614..3c82ae97ce7279c05f922cf20ff59b6689f69cb3 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/Surface.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/Surface.java
@@ -265,7 +265,7 @@ public class Surface
}
}
}
- ImageJFunctions.show( zMap, "after getzmap" );
+// ImageJFunctions.show( zMap, "after getzmap" );
System.out.println(" Thre count = " + count);
return zMap;
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/Interpolation.java b/src/main/java/fr/pasteur/ida/zellige/utils/Interpolation.java
index 76a1a0a6bcb10d75ee0f9d30a1abda5701cf368b..7e06b1c62f9e3b31238f7006a177d89eb55baf5b 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/Interpolation.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/Interpolation.java
@@ -21,7 +21,7 @@ public class Interpolation
public static Img<UnsignedShortType> run( RandomAccessibleInterval< UnsignedShortType > input )
{
InterpolationOperator operator = new InterpolationOperator( input );
- ImageJFunctions.show( operator.getOutput() );
+// ImageJFunctions.show( operator.getOutput() );
return operator.getOutput();
}
@@ -43,11 +43,11 @@ public class Interpolation
*/
private void execute()
{
- ImageJFunctions.show( input, "zMap" );
+// ImageJFunctions.show( input, "zMap" );
Img< UnsignedShortType > interpolated0 = execute( input, 0 );
- ImageJFunctions.show( interpolated0, "interpolated 0" );
+// ImageJFunctions.show( interpolated0, "interpolated 0" );
Img< UnsignedShortType > interpolated1 = execute( input, 1 );
- ImageJFunctions.show( interpolated1, "interpolated 1" );
+// ImageJFunctions.show( interpolated1, "interpolated 1" );
Cursor< UnsignedShortType > cursor0 = interpolated0.cursor();
Cursor< UnsignedShortType > cursor1 = interpolated1.cursor();
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsuClassification.java b/src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsuClassification.java
index c7a4ecb329d9af6847222aaf45bad4fac5673e09..23d6fd1eba8cc4124e0239fe49f509e4d7cce0af 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsuClassification.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsuClassification.java
@@ -130,7 +130,7 @@ public class LocalOtsuClassification
}
}
}
- ImageJFunctions.show( binary, "binary" );
+// ImageJFunctions.show( binary, "binary" );
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java b/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java
index 88314c5a9b614b19cfbde095b8204463d0c1b1e8..78d30ea53b89b81aaea08f78c9779d10dcd817c0 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java
@@ -1,5 +1,6 @@
package fr.pasteur.ida.zellige.utils;
+import fr.pasteur.ida.zellige.surfaceConstruction.construction.SurfacePixelSelection;
import net.imglib2.Cursor;
import net.imglib2.Interval;
import net.imglib2.RandomAccess;
@@ -17,6 +18,7 @@ import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.Util;
import net.imglib2.view.IntervalView;
import net.imglib2.view.Views;
+import org.jzy3d.colors.Color;
import java.util.List;
@@ -45,7 +47,7 @@ public class MaximumAmplitudeClassification
Img< FloatType > output = floatTypeImgFactory.create( input );
new BackgroundForegroundGrid( maximumAmplitude.getAmplitude(), output, sizePercent );
Utils.gaussConvolution( output.copy(), output, new double[]{ 0, 0, 0.5 } );
- ImageJFunctions.show( output, "new class amplitude" );
+// ImageJFunctions.show( output, "new class amplitude" );
return output;
}
@@ -172,9 +174,8 @@ public class MaximumAmplitudeClassification
public void run()
{
-// Img< T > maximums = LocalMaximumDetection.findMaximums( input, factory );
Img< T > maximums = LocalExtremaDetection.findMaxima( input, factory );
-// Img< T > minimums = LocalMinimumDetection.findMinimums( input, factory );
+ SurfacePixelSelection.displayExtrema( maximums, Color.MAGENTA, "Magenta total maximums" );
Img< T > minimums = LocalExtremaDetection.findMinima( input, factory );
Img< T > amp = getAmplitude( maximums, factory, minimums );
T TMax = Threshold.getFirstMaxValue( maximums, false );