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 0061e6ebb7fab96c083fd0737ce85b8b3c59c3dc..4fd9c0e17538bfe8246475c41cb992ba132804ee 100644 --- a/src/main/java/fr/pasteur/ida/zellige/main/Main.java +++ b/src/main/java/fr/pasteur/ida/zellige/main/Main.java @@ -63,9 +63,9 @@ public class Main // Input of the image. final String imagePath = - "doc/STK_060.tif"; +// "doc/STK_060.tif"; // "C:\\Users\\ctrebeau\\Desktop\\MoucheAile\\STK\\STK_Mouche_c01_f0001_p005.tif"; -// "C:\\Users\\ctrebeau\\Downloads\\phantom3_combined.tif"; + "C:\\Users\\ctrebeau\\Downloads\\phantom3_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. */ 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 65243e2ef15eaa654c5b2542a93c3b721847d115..99f07e41c91d40f58876e200714f4915269f18bb 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsuClassification.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsuClassification.java @@ -129,8 +129,8 @@ public class LocalOtsuClassification { sourceCursor.fwd(); outputCursor.fwd(); - final float s = sourceCursor.get().getRealFloat(); - final float o = outputCursor.get().getRealFloat(); + final double s = sourceCursor.get().getRealDouble(); + final double o = outputCursor.get().getRealDouble(); { if (s >= Math.max( o, threshold))// background subtraction { 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 3cf8992d79ccdd458d12023ccef04a18ee17d0c2..74e9bc4941cf457a3435b4043d4b202b3686e0da 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java @@ -91,7 +91,7 @@ public class MaximumAmplitudeClassification { maxAccess.setPosition( z, 2 ); - float maxValue = maxAccess.get().getRealFloat(); + double maxValue = maxAccess.get().getRealDouble(); if ( maxValue != 0 ) { minAccess.setPosition( maxAccess ); @@ -112,7 +112,7 @@ public class MaximumAmplitudeClassification * @param <T> the type of the {@link RandomAccess} * @return the chosen amplitude value of the local maximum positioned at minAccess location */ - private static < T extends RealType< T > & NativeType< T > > double getAmplitude( float maxValue, RandomAccess< T > minAccess , int depth) + private static < T extends RealType< T > & NativeType< T > > double getAmplitude( double maxValue, RandomAccess< T > minAccess , int depth) { double up = findValueUp( minAccess, maxValue ); double down = findValueDown( minAccess, maxValue , depth); @@ -133,7 +133,7 @@ public class MaximumAmplitudeClassification * @return the amplitude value above the local maximum location in the Z dimension */ private static < T extends RealType< T > & NativeType< T > > double findValueUp( - RandomAccess< T > minAccess, float maxValue ) + RandomAccess< T > minAccess, double maxValue ) { int start = minAccess.getIntPosition( 2 ); for ( int z = start - 1; z >= 0; z-- ) @@ -156,7 +156,7 @@ public class MaximumAmplitudeClassification * @return the amplitude value below the local maximum location in the Z dimension */ private static < T extends RealType< T > & NativeType< T > > double findValueDown( - RandomAccess< T > minAccess, float maxValue, int depth ) + RandomAccess< T > minAccess, double maxValue, int depth ) { int start = minAccess.getIntPosition( 2 ); for ( int z = start + 1; z <= depth - 1; z++ ) diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/StackProjection.java b/src/main/java/fr/pasteur/ida/zellige/utils/StackProjection.java index ed9343d324f7aedf68e2be71653a230d889711e6..373a2bd749143bb4da63ceb476a0b888f35acf8e 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/StackProjection.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/StackProjection.java @@ -342,7 +342,7 @@ public class StackProjection for ( int y = 0; y <= input.dimension( 1 ) - 1; y++ ) { inputAccess.setPosition( y, 1 ); - float[] column = new float[ ( int ) input.dimension( 2 ) ]; + double[] column = new double[ ( int ) input.dimension( 2 ) ]; for ( int z = 0; z <= input.dimension( 2 ) - 1; z++ ) { inputAccess.setPosition( z, 2 ); @@ -357,9 +357,9 @@ public class StackProjection - static float median( float[] a ) + static double median( double[] a ) { - float[] sorted = a.clone(); + double[] sorted = a.clone(); Arrays.sort( sorted ); int middle = a.length / 2; diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/SurfacePixelSelection.java b/src/main/java/fr/pasteur/ida/zellige/utils/SurfacePixelSelection.java index f06bc1c863bcd4611c996216f271fa64ea6b7507..02ab175c03657975001d6eecac671c7e5c7197e5 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/SurfacePixelSelection.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/SurfacePixelSelection.java @@ -104,7 +104,7 @@ public class SurfacePixelSelection { for ( int z = 0; z <= stack.dimension( 2 ) - 1; z++ ) { - float value = Utils.setPositionAndGet( access, x, y, z ).getRealFloat(); + double value = Utils.setPositionAndGet( access, x, y, z ).getRealDouble(); if ( value > 0 ) { if ( pixels[ y ][ x ] == null )