diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index fccfa6a6aedbf02467344129fa2435fbd8ed4daa..0311a07b1dffbfdb28724b115a350640e0317230 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -27,11 +27,15 @@ release:
stage: versioning
when: manual
script:
- - curl --fail https://raw.githubusercontent.com/scijava/scijava-scripts/main/release-version.sh | bash -s -- --dry-run
-# script with dry-run option
-# - curl --fail https://raw.githubusercontent.com/scijava/scijava-scripts/main/release-version.sh | bash -s -- --dry-run
-
-
+ - git config user.name "$TECHUSER_NAME"
+ - git config user.email "$TECHUSER_MAIL"
+ - git remote set-url --push origin "https://oauth2:${TECHUSER_ACCESS_TOKEN}@gitlab.pasteur.fr/ctrebeau/zellige-core.git/"
+ - curl --fail https://raw.githubusercontent.com/scijava/scijava-scripts/main/valid-semver-bump.sh --output ../valid-semver-bump.sh
+ - curl --fail https://raw.githubusercontent.com/scijava/scijava-scripts/main/maven-helper.sh --output ../maven-helper.sh
+ - curl --fail https://raw.githubusercontent.com/scijava/scijava-scripts/main/release-version.sh --output ../release-version.sh
+ - "chmod +x ../release-version.sh"
+ - git checkout -f $CI_COMMIT_REF_NAME
+ - " ../release-version.sh --skip-version-check $MAJOR.$MINOR.$PATCH"
pages:
image: maven:3.6.3-jdk-11
@@ -47,7 +51,7 @@ pages:
- public
-ParamaterSweep_mouche:
+ParameterSweep_mouche:
image: maven:3.6.3-jdk-11
stage: test
when: manual
@@ -58,7 +62,7 @@ ParamaterSweep_mouche:
- target/*.csv
-ParamaterSweep_cochlée:
+ParameterSweep_cochlée:
image: maven:3.6.3-jdk-11
stage: test
when: manual
@@ -68,7 +72,7 @@ ParamaterSweep_cochlée:
paths:
- target/*.csv
-ParamaterSweep_culture:
+ParameterSweep_culture:
image: maven:3.6.3-jdk-11
stage: test
when: manual
@@ -78,7 +82,7 @@ ParamaterSweep_culture:
paths:
- target/*.csv
-ParamaterSweep_organoid:
+ParameterSweep_organoid:
image: maven:3.6.3-jdk-11
stage: test
when: manual
@@ -89,7 +93,7 @@ ParamaterSweep_organoid:
- target/*.csv
-ParamaterSweep_phantom:
+ParameterSweep_phantom:
image: maven:3.6.3-jdk-11
stage: test
when: manual
@@ -100,7 +104,7 @@ ParamaterSweep_phantom:
- target/*.csv
-doubleParamaterSweep:
+doubleParameterSweep:
image: maven:3.6.3-jdk-11
stage: test
when: manual
diff --git a/README.md b/README.md
index 44efd0aaa7eaddc402e0ccafc6d7c19b026ace38..c33bea00014184bbe8aa7c2dc4ce084149be9791 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-<img src="src/main/resources/icons/Zellige_logo.png" width="150" height="150" alt="drawing"/>
+<img src="src/main/resources/icons/Zellige_logo.png" width="408" height="408" alt="drawing"/>
# Zellige : 3D fluorescence microscopic images surface extraction tool.
diff --git a/pom.xml b/pom.xml
index eb5783f2674e69a1edef75d63991fb61b41d859c..6971106d8139ef14d19f7b469448d440cbd270a3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -39,12 +39,12 @@
<repository>
<id>jzy3d-snapshots</id>
<name>Jzy3d Snapshots</name>
- <url>http://maven.jzy3d.org/snapshots</url>
+ <url>https://maven.jzy3d.org/snapshots</url>
</repository>
<repository>
<id>jzy3d-releases</id>
<name>Jzy3d Releases</name>
- <url>http://maven.jzy3d.org/releases</url>
+ <url>https://maven.jzy3d.org/releases</url>
</repository>
</repositories>
@@ -156,19 +156,19 @@
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
- <version>1.2.3</version>
+ <version>1.2.11</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
- <version>5.7.0</version>
+ <version>5.9.0</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
- <version>5.7.0</version>
+ <version>5.9.0</version>
</dependency>
@@ -180,7 +180,7 @@
<dependency>
<groupId>org.assertj</groupId>
<artifactId>assertj-core</artifactId>
- <version>3.13.2</version>
+ <version>3.23.1</version>
<scope>test</scope>
</dependency>
<dependency>
@@ -203,17 +203,17 @@
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>javafx-controls</artifactId>
- <version>17.0.2</version>
+ <version>18.0.2</version>
</dependency>
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>javafx-fxml</artifactId>
- <version>17.0.2</version>
+ <version>18.0.2</version>
</dependency>
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>javafx-swing</artifactId>
- <version>18-ea+4</version>
+ <version>18.0.2</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
@@ -263,7 +263,7 @@
<url>https://research.pasteur.fr/fr/member/celine-trebeau/</url>
<email>celine.trebeau@pasteur.fr</email>
<organization>Institut Pasteur</organization>
- <organizationUrl>http://pasteur.fr/</organizationUrl>
+ <organizationUrl>https://pasteur.fr/</organizationUrl>
<roles>
<role>lead</role>
<role>developer</role>
@@ -277,7 +277,7 @@
<email>jean-yves.tinevez@pasteur.fr</email>
<url>https://research.pasteur.fr/en/member/jean-yves-tinevez/</url>
<organization>Institut Pasteur</organization>
- <organizationUrl>http://www.pasteur.fr/</organizationUrl>
+ <organizationUrl>https://www.pasteur.fr/</organizationUrl>
</contributor>
</contributors>
diff --git a/src/main/java/fr/pasteur/ida/zellige/Main.java b/src/main/java/fr/pasteur/ida/zellige/Main.java
index 59cc04cce15792eb0cf66c8bb8608dc811b60512..f685c19fe716e105a0b61623ab0a82ba775fd1fe 100644
--- a/src/main/java/fr/pasteur/ida/zellige/Main.java
+++ b/src/main/java/fr/pasteur/ida/zellige/Main.java
@@ -55,6 +55,8 @@ public class Main
{
private final static Logger LOGGER = LoggerFactory.getLogger( Main.class );
+
+ @SuppressWarnings( "unchecked" )
public static < T extends RealType< T > & NativeType< T > > void main( String[] args ) throws Exception
{
// Launch ImageJ.
@@ -66,7 +68,7 @@ public class Main
args[ 0 ]; /* The image path goes here !!!! */
LOGGER.debug( imagePath );
/* JY version for opening files. */
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
final Img< T > stackImage = ( Img< T > ) imgPlus.getImg();
@@ -138,11 +140,7 @@ public class Main
( stackImage, stackImage.factory() );
rse.select( pretreatmentParameters, classificationParameters, postTreatmentParameters );
rse.construct( constructionParameters );
-// for ( ReferenceSurface< T > referenceSurface : rse.getReferenceSurfaces() )
-// {
-// writeHeightMap( referenceSurface.getzMap(), imgPlus.getName(), referenceSurface.getIndex() );
-// }
-
+ rse.project( projectionParameters, displayParameters );
if ( ! GraphicsEnvironment.isHeadless() )
{
try
diff --git a/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java b/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
index eb5afa19cc8fbd3f5a1cbd3075003a2685ea78ed..c7c8071e15dc58377e685de773ac11ebb3b3caac 100644
--- a/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
+++ b/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
@@ -41,25 +41,15 @@ import fr.pasteur.ida.zellige.steps.projection.NoPossibleDisplayException;
import fr.pasteur.ida.zellige.steps.projection.ProjectionParameters;
import fr.pasteur.ida.zellige.steps.projection.ReferenceSurfaceProjection;
import fr.pasteur.ida.zellige.steps.selection.Selection;
-import fr.pasteur.ida.zellige.steps.selection.classification.AmplitudeClassification;
-import fr.pasteur.ida.zellige.steps.selection.classification.Classification;
import fr.pasteur.ida.zellige.steps.selection.classification.ClassificationParameters;
-import fr.pasteur.ida.zellige.steps.selection.classification.OtsuClassification;
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.PostTreatment;
import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatmentParameters;
-import fr.pasteur.ida.zellige.steps.selection.pretreatment.Pretreatment;
import fr.pasteur.ida.zellige.steps.selection.pretreatment.PretreatmentParameters;
import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
-import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.type.NativeType;
-import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.numeric.real.FloatType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -77,14 +67,6 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
private final RandomAccessibleInterval< T > input;
private final ImgFactory< T > factory;
- private final String filter = "GaussianBlur";
- private final double filterParameter = 2;
- private Img< FloatType > pretreatedImg;
- private Img< FloatType > amplitudeImg;
- private Img< FloatType > otsuImg;
- ArrayList< Surface > firstRoundSurfaces;
- private Img< BitType > ISImage;
- // private FloatType otsuValue;
private Pixels[][] maximums;
private final static double adequacy = 1;
@@ -102,10 +84,6 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
private int SS_smallSurfaces;
private int SS_goodSurfaces;
private static final String derivativeMethod = FORWARD;
- private Img< BitType > selectedAmplitude;
- private Img< BitType > selectedOtsu;
- private Img< BitType > selectionOutput;
-
public ReferenceSurfaceExtraction( RandomAccessibleInterval< T > input, ImgFactory< T > factory )
{
@@ -118,76 +96,15 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
return adequacy;
}
- public void computeClassificationImages() throws DataValidationException
- {
- pretreatedImg = Pretreatment.run( input, filterParameter );
- computeImages( pretreatedImg );
- }
- private void computeImages( RandomAccessibleInterval< FloatType > input ) throws DataValidationException
- {
- ImgFactory< FloatType > factory = new ArrayImgFactory<>( new FloatType() );
- amplitudeImg = AmplitudeClassification.computeAmplitudeImage( input, factory );
- otsuImg = OtsuClassification.computeOtsuImage( input, factory );
- }
- public void runAmplitudeClassification( int userThreshold )
- {
- LOGGER.debug( "Amplitude threshold value after user ={}", userThreshold );
- selectedAmplitude = AmplitudeClassification.applyThreshold( amplitudeImg, userThreshold );
- }
-
- public void runOtsuClassification( int userThreshold )
- {
- selectedOtsu = OtsuClassification.applyLocalThreshold( pretreatedImg, otsuImg, userThreshold );
- }
-
- public void runInterClassification()
- {
- selectionOutput = Classification.interClassification( selectedAmplitude, selectedAmplitude.factory(), selectedOtsu );
- LOGGER.debug( "The selected output has been changed" );
- }
-
- public void runIslandSearch( int islandSize )
- {
- ISImage = PostTreatment.runIslandSearch( selectionOutput, islandSize );
- }
-
- public void runSmoothing( int sigmaXY, int sigmaZ ) throws DataValidationException
- {
- maximums = PostTreatment.runSmoothing( ISImage, sigmaXY, sigmaZ );
- }
-
- public void runPostTreatment( double sigmaXY, double sigmaZ, int islandSize ) throws DataValidationException
- {
- runIslandSearch( islandSize );
- runSmoothing( ( int ) sigmaXY, ( int ) sigmaZ );
-// maximums = PostTreatment.run( selectionOutput, postTreatmentParameters );
- }
-
-
- public void select( PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters ) throws NoClassificationException, EmptyOutputException, DataValidationException
+ public void select( PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters ) throws NoClassificationException, DataValidationException
{
/* First step : Pixel selection */
LOGGER.debug( "Running selection..." );
maximums = Selection.run( input, pretreatmentParameters, classificationParameters, postTreatmentParameters );
}
- public void constructFirstRoundSurfaces( double startingSizeThreshold, int overlap, double connexityRate, double surfaceMinSizeFactor ) throws NoSurfaceFoundException
- {
- FirstRoundConstruction step1 = new FirstRoundConstruction( maximums, startingSizeThreshold, overlap, connexityRate, surfaceMinSizeFactor );
- step1.process();
- firstRoundSurfaces = step1.getSurfaces();
- }
-
- public void constructSecondRoundSurfacesAndCompletion( double startingSizeThreshold, int overlap, double connexityRate, double surfaceMinSizeFactor ) throws NoSurfaceFoundException
- {
- SecondRoundConstruction step2 = new SecondRoundConstruction( firstRoundSurfaces, startingSizeThreshold, overlap, connexityRate, surfaceMinSizeFactor );
- step2.process();
- ArrayList< Surface > finalSurfaces = step2.getSurfaces();
- referenceSurfaces.addAll( ConstructionCompletion.run( input, factory, finalSurfaces ) );
- }
-
public void construct( ConstructionParameters[] constructionParameters ) throws NoSurfaceFoundException
{
LOGGER.debug( "Running construction..." );
@@ -252,28 +169,11 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
}
}
-
- public boolean iSisDone()
- {
- return ISImage != null;
- }
-
- public void resetIS()
- {
- ISImage = null;
- }
-
-
public void setMaximums( Pixels[][] maximums )
{
this.maximums = maximums;
}
- public Img< BitType > getSelectionOutput()
- {
- return selectionOutput;
- }
-
public ArrayList< ReferenceSurface< T > > getReferenceSurfaces()
{
return referenceSurfaces;
@@ -355,15 +255,6 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
return SS_startingOS_count;
}
- public String getFilter()
- {
- return filter;
- }
-
- public double getFilterParameter()
- {
- return filterParameter;
- }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java b/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java
index a95697e6086a1575bf3019072aaf5f8238ddf98f..25b184117283cb0a1e904bddf2beb3a1320a3d78 100644
--- a/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java
+++ b/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java
@@ -33,6 +33,7 @@ import fr.pasteur.ida.zellige.gui.MainAppFrame;
import net.imagej.ImageJ;
import org.scijava.command.ContextCommand;
import org.scijava.plugin.Plugin;
+import org.scijava.util.VersionUtils;
import java.io.File;
import java.io.IOException;
@@ -58,11 +59,6 @@ public class Zellige extends ContextCommand
// Load the image.
Object obj = ij.io().open( new File( currentFolder, imageFilePath ).getAbsolutePath() );
- // for large images
-// final SCIFIOConfig config = new SCIFIOConfig();
-// config.imgOpenerSetImgModes( SCIFIOConfig.ImgMode.PLANAR );
-//
-// final Dataset obj = ij.scifio().datasetIO().open( imageFilePath, config );
// Display it.
ij.ui().show( obj );
@@ -76,7 +72,7 @@ public class Zellige extends ContextCommand
// Launch JavaFX interface
MainAppFrame app = new MainAppFrame( context() );
- app.setTitle( "Zellige v1.0.2" );
+ app.setTitle( "Version " + VersionUtils.getVersion( Zellige.class ) );
app.init();
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/Coordinate.java b/src/main/java/fr/pasteur/ida/zellige/element/Coordinate.java
index 43a74d8e9a4ceb5eb96dd6a89d6298c7f452663c..bb1afa8c90010c454e909abd05da5b9cf7ee20a2 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/Coordinate.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/Coordinate.java
@@ -93,9 +93,9 @@ public class Coordinate implements Comparable <Coordinate> //extends Pixel
/**
- * Computes the number of Coordinates which belong to the same surface than the current Pixel instance.
+ * Computes the number of Coordinates which belong to the same surface as the current Pixel instance.
*
- * @param pixels - the specified Pixel.
+ * @param pixels - the specified Pixel.
* @param distance - the distance constraint (0 or 1).
* @return the number of Coordinates next to the current Pixel.
*/
@@ -118,8 +118,8 @@ public class Coordinate implements Comparable <Coordinate> //extends Pixel
* Determines the Coordinate next to the current Coordinate instance.
*
* @param nextPixels - the next Pixel instance.
- * @param distance - the distance constraint.
- * @return a new Pixel containing the coordinates that respects the distance constraint,
+ * @param distance - the distance constraint.
+ * @return a new Pixel containing the coordinates that respect the distance constraint,
* null if no Coordinates are found.
*/
public Coordinate getNext( Pixels nextPixels, int distance )
diff --git a/src/main/java/fr/pasteur/ida/zellige/element/Pixels.java b/src/main/java/fr/pasteur/ida/zellige/element/Pixels.java
index 6237d12a9f34fb894bcb5cada2191e7ae7a040bb..788becc133b95254cee85fdbf8c1b334ee13136c 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/Pixels.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/Pixels.java
@@ -75,8 +75,7 @@ public class Pixels
/**
- *
- * @param pixels - the {@link Pixels} (list of Coordinates to add}
+ * @param pixels - the {@link Pixels} (list of Coordinates to add to.)
*/
public void addAll( Pixels pixels )
{
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 541781e997fb581c4ac3b59d4c69d6638002d6d6..6abf64d3dfa9d9290f855dc6cb3a3ff3c0100810 100644
--- a/src/main/java/fr/pasteur/ida/zellige/element/Surface.java
+++ b/src/main/java/fr/pasteur/ida/zellige/element/Surface.java
@@ -187,7 +187,7 @@ public class Surface
/**
- * Checks if this object shares a majority of {@link Pixels} with an other {@link Surface} object.
+ * Checks if this object shares a majority of {@link Pixels} with another {@link Surface} object.
*
* @param other the other {@link Surface} object.
* @return True if both {@link Surface} objects are similar, false otherwise.
@@ -211,7 +211,7 @@ public class Surface
}
/**
- * Combines the current instance with an other {@link Surface} instance.
+ * Combines the current instance with another {@link Surface} instance.
*
* @param otherSurface - the {@link Surface} to combine with.
*/
@@ -293,7 +293,7 @@ public class Surface
}
/**
- * Sets the specified {@link SurfaceLine} at the specified index position. If the Surfaline at the specified index
+ * Sets the specified {@link SurfaceLine} at the specified index position. If the SurfaceLine at the specified index
* not null, the both are merged.
*
* @param index the position of the SurfaceLine
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 e2720c4551502648ea890cad758794179927772d..cd0a7e51252015127a29e42dc18ff97abf2c9e49 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
@@ -195,7 +195,7 @@ public abstract class SurfaceLine
}
/**
- * Combines the current SurfaceLine instance to an other SurfaceLine instance.
+ * Combines the current SurfaceLine instance to another SurfaceLine instance.
*
* @param other - the other SurfaceLine.
*/
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 29fd5b6575f4ebddeea8f5eb4dda2a1665312f2c..67a5e1c7967c39cfc708397a78237c07b0820d1f 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
@@ -49,15 +49,6 @@ public class SurfaceLineX extends SurfaceLine
SurfaceLineX surfaceLineX = new SurfaceLineX( this.getLength(), this.getLine() + direction );
return this.match2( os, overlap, connexity, surfaceLineX );
}
- /**
- * 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 j - an integer witch indicates the line of the resulting SurfaceLine.
- * @param percent - the minimum percentage of match between the OS and the current instance.
- * @param matched - the minimum number of matching coordinates.
- * @return - a new SurfaceLine if there is a match, null otherwise.
- */
/**
* Constructor.
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/CheckBoxDisplay.java b/src/main/java/fr/pasteur/ida/zellige/gui/CheckBoxDisplay.java
index 8c21045e1d5e3a76c6b5aa34ce1b72f03d1a73a7..4765406574f0eb1893a291ec19f898fce4b803fa 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/CheckBoxDisplay.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/CheckBoxDisplay.java
@@ -34,7 +34,7 @@ import javafx.scene.control.CheckBox;
public class CheckBoxDisplay extends CheckBox
{
- private SimpleBooleanProperty notDisplayed = new SimpleBooleanProperty( true );
+ private final SimpleBooleanProperty notDisplayed = new SimpleBooleanProperty( true );
// private boolean notDisplayed = true;
@@ -43,11 +43,6 @@ public class CheckBoxDisplay extends CheckBox
return notDisplayed.getValue();
}
- public void disable()
- {
- notDisplayed.setValue( false );
- }
-
public void enable()
{
notDisplayed.setValue( true );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/DisplayController.java b/src/main/java/fr/pasteur/ida/zellige/gui/DisplayController.java
deleted file mode 100644
index d239a7d56bf955a4177d1e712dec1bd43b33a4c9..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/gui/DisplayController.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.gui;
-
-import javafx.fxml.FXML;
-import javafx.fxml.Initializable;
-import javafx.scene.control.CheckBox;
-
-import java.net.URL;
-import java.util.ResourceBundle;
-
-public class DisplayController implements Initializable
-{
-
- @FXML
- private CheckBox extractedSurface;
-
- @FXML
- private CheckBox heightMapStack;
-
- @FXML
- private CheckBox heightMapStackMask;
-
- @FXML
- private CheckBox heightmap;
-
- @FXML
- private CheckBox projection;
-
- @Override
- public void initialize( URL url, ResourceBundle resourceBundle )
- {
-
- }
-}
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 e1803dd3cb0165420b5e977111c0fc433f2488e0..66e1c752f7836b0ebab8887604ceaa2515c91e91 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/MainAppFrame.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/MainAppFrame.java
@@ -30,7 +30,7 @@ package fr.pasteur.ida.zellige.gui;
import ch.qos.logback.classic.LoggerContext;
import ch.qos.logback.classic.encoder.PatternLayoutEncoder;
-import fr.pasteur.ida.zellige.steps.selection.exception.DataValidationException;
+import fr.pasteur.ida.zellige.gui.controller.MainController;
import javafx.application.Platform;
import javafx.embed.swing.JFXPanel;
import javafx.fxml.FXMLLoader;
@@ -104,13 +104,11 @@ public class MainAppFrame extends JFrame
{
// this.ij = context.;
this.image = context.getService( ImageDisplayService.class );
- ;
this.logService = context.getService( LogService.class );
- ;
this.setIconImages( ICONS );
}
- public static final ImageIcon scaleImage( final ImageIcon icon, final int w, final int h )
+ public static ImageIcon scaleImage( final ImageIcon icon, final int w, final int h )
{
int nw = icon.getIconWidth();
int nh = icon.getIconHeight();
@@ -129,15 +127,6 @@ public class MainAppFrame extends JFrame
return new ImageIcon( icon.getImage().getScaledInstance( nw, nh, Image.SCALE_SMOOTH ) );
}
- public LogService getLogService()
- {
- return logService;
- }
-
- public ImageJ getIj()
- {
- return ij;
- }
public ImageDisplayService getImage()
{
@@ -187,7 +176,7 @@ public class MainAppFrame extends JFrame
this.setSize( ( int ) scene.getWidth() + 20, ( int ) scene.getHeight() + 50 );
controller.initExtraction();
}
- catch ( IOException | DataValidationException e )
+ catch ( IOException e )
{
e.printStackTrace();
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ParameterSlider.java b/src/main/java/fr/pasteur/ida/zellige/gui/ParameterSlider.java
index 3b59faad38020e3c758e1730deeddd50b864bea5..e030ed336304da7d21670e30cebe29c4abc8b300 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ParameterSlider.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/ParameterSlider.java
@@ -44,7 +44,6 @@ import java.io.IOException;
public abstract class ParameterSlider extends GridPane
{
- public static String INTERVAL1 = "[0-9]|[1-4][0-9]|[5][0]";
private final String name;
private final int minorTickUnit;
private final double majorTickUnit, increment, defaultValue, min, max;
@@ -55,7 +54,6 @@ public abstract class ParameterSlider extends GridPane
@FXML
private TextField textField;
private StringProperty userValue;
- private DoubleProperty sliderProperty;
private Number previousValue = 1;
private final String interval;
private final PseudoClass errorClass = PseudoClass.getPseudoClass( "error" );
@@ -103,7 +101,7 @@ public abstract class ParameterSlider extends GridPane
slider.setShowTickLabels( true );
slider.setMajorTickUnit( majorTickUnit );
slider.setMinorTickCount( minorTickUnit );
- slider.setSnapToTicks( false );
+ slider.setSnapToTicks( true );
userValue = textFieldProperty();
textField.getStyleClass().add( "error" );
bindProperties();
@@ -117,11 +115,9 @@ public abstract class ParameterSlider extends GridPane
public void listenerSetting()
{
this.userValueProperty().addListener( event ->
- {
- this.getTextField().pseudoClassStateChanged(
- this.getErrorClass(), ! this.getTextField().getText().matches( this.getInterval() )
- );
- } );
+ this.getTextField().pseudoClassStateChanged(
+ this.getErrorClass(), ! this.getTextField().getText().matches( this.getInterval() )
+ ) );
}
public abstract void bindProperties();
@@ -155,16 +151,6 @@ public abstract class ParameterSlider extends GridPane
return textField.textProperty();
}
- public String getLabelText()
- {
- return labelProperty().get();
- }
-
- public StringProperty labelProperty()
- {
- return label.textProperty();
-
- }
public PseudoClass getErrorClass()
{
@@ -181,32 +167,11 @@ public abstract class ParameterSlider extends GridPane
return slider;
}
- public double getSliderProperty()
- {
- return sliderProperty.get();
- }
-
public DoubleProperty sliderProperty()
{
return getSlider().valueProperty();
}
-
- public void setSlider( Slider slider )
- {
- this.slider = slider;
- }
-
- public String getUserValue()
- {
- return userValue.get();
- }
-
- public void setUserValue( String userValue )
- {
- this.userValue.set( userValue );
- }
-
public StringProperty userValueProperty()
{
return userValue;
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ParameterSliderDouble.java b/src/main/java/fr/pasteur/ida/zellige/gui/ParameterSliderDouble.java
index 33be7c2c1bbd71446c3ab4266110dde9598a12f0..5d9e81e7c51d651c87a0aeff46743463fde8c9da 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ParameterSliderDouble.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/ParameterSliderDouble.java
@@ -67,6 +67,8 @@ public class ParameterSliderDouble extends ParameterSlider
@Override
public Number fromString( String s )
{
+ LOGGER.debug( "String value is {}", s );
+ LOGGER.debug( "Number value is {}", Double.parseDouble( s ) );
try
{
return Double.parseDouble( s );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ZDoubleProperty.java b/src/main/java/fr/pasteur/ida/zellige/gui/ZDoubleProperty.java
new file mode 100644
index 0000000000000000000000000000000000000000..a9245da5083e4ae0f07a04953a5914e1afd1bd4a
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/ZDoubleProperty.java
@@ -0,0 +1,13 @@
+package fr.pasteur.ida.zellige.gui;
+
+import javafx.beans.property.SimpleDoubleProperty;
+import org.apache.commons.math3.util.Precision;
+
+public class ZDoubleProperty extends SimpleDoubleProperty
+{
+ public double value()
+ {
+ return Precision.round( doubleValue(), 1 );
+
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ZSlicesSlider.java b/src/main/java/fr/pasteur/ida/zellige/gui/ZSlicesSlider.java
index 80e66f279474426e1e55867d9fa991c1405632f2..425f3113c509d7b2696b5d9d9a3ae1fc87465fb6 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ZSlicesSlider.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/ZSlicesSlider.java
@@ -41,7 +41,7 @@ public class ZSlicesSlider extends FlowPane
@FXML
Slider slider;
- int userValue;
+ private int userValue;
public ZSlicesSlider()
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ConstructionController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/ConstructionController.java
similarity index 94%
rename from src/main/java/fr/pasteur/ida/zellige/gui/ConstructionController.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/controller/ConstructionController.java
index 36598971132047dae4bb9734e52693052a19476a..e8e514f51a33a0eb1190f6b0c9809f02845fb5ae 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ConstructionController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/ConstructionController.java
@@ -26,8 +26,12 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package fr.pasteur.ida.zellige.gui;
+package fr.pasteur.ida.zellige.gui.controller;
+import fr.pasteur.ida.zellige.gui.ParameterSliderDouble;
+import fr.pasteur.ida.zellige.gui.ParameterSliderInteger;
+import fr.pasteur.ida.zellige.gui.model.ConstructionModel;
+import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.beans.value.ChangeListener;
import javafx.fxml.FXML;
@@ -59,7 +63,7 @@ public class ConstructionController< T extends RealType< T > & NativeType< T > >
@FXML
private ParameterSliderDouble st2;
@FXML
- private ParameterSliderDouble surfaceSize;
+ private ParameterSliderInteger surfaceSize;
@Override
@@ -138,12 +142,6 @@ public class ConstructionController< T extends RealType< T > & NativeType< T > >
}
-
- public double getSurfaceSize()
- {
- return surfaceSize.getSlider().getValue();
- }
-
public ConstructionModel< T > getConstructionModel()
{
return constructionModel;
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/MainController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java
similarity index 66%
rename from src/main/java/fr/pasteur/ida/zellige/gui/MainController.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java
index c6d5d2c3b61e89e0249baa6af39d8cb4ab825050..da59a7a492cb327655edfb319c1ad9fb2a35ff77 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/MainController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java
@@ -26,19 +26,25 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package fr.pasteur.ida.zellige.gui;
+package fr.pasteur.ida.zellige.gui.controller;
+import fr.pasteur.ida.zellige.gui.ClassifiedImages;
+import fr.pasteur.ida.zellige.gui.LogAppender;
+import fr.pasteur.ida.zellige.gui.MainAppFrame;
import fr.pasteur.ida.zellige.gui.exception.NoA3DStackException;
import fr.pasteur.ida.zellige.gui.exception.NoInputException;
+import fr.pasteur.ida.zellige.gui.model.ConstructionModel;
+import fr.pasteur.ida.zellige.gui.model.MainModel;
+import fr.pasteur.ida.zellige.gui.model.ProjectionModel;
+import fr.pasteur.ida.zellige.gui.model.SelectionModel;
+import fr.pasteur.ida.zellige.gui.parameter.ConstructionParameter;
+import fr.pasteur.ida.zellige.gui.parameter.ProjectionParameter;
+import fr.pasteur.ida.zellige.gui.parameter.SelectionParameter;
+import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
import fr.pasteur.ida.zellige.gui.task.AbstractTask;
import fr.pasteur.ida.zellige.gui.task.ComputeClassificationImagesTask;
import fr.pasteur.ida.zellige.gui.task.DisplayDatasetChoicesTask;
import fr.pasteur.ida.zellige.gui.task.PretreatmentTask;
-import fr.pasteur.ida.zellige.steps.construction.exception.NoSurfaceFoundException;
-import fr.pasteur.ida.zellige.steps.projection.NoPossibleDisplayException;
-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 javafx.application.Platform;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.beans.property.SimpleObjectProperty;
@@ -89,7 +95,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
@FXML
private ProjectionController< T > projectionController;
@FXML
- private SelectionController selectionController;
+ private SelectionController< T > selectionController;
MainModel< T > model;
@@ -154,16 +160,9 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
// run button initialization
runButton.setOnAction( actionEvent ->
{
- try
- {
- disableGUI.setValue( true );
- changedParameters.setValue( false );
- run2();
- }
- catch ( DataValidationException | EmptyOutputException | NoClassificationException | NoSurfaceFoundException | NoPossibleDisplayException e )
- {
- showError( e );
- }
+ disableGUI.setValue( true );
+ changedParameters.setValue( false );
+ run2();
} );
/* Binding properties*/
@@ -195,101 +194,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
logInfo.setText( LogAppender.getLogMessage() ) ) );
}
- // public void run() throws DataValidationException, EmptyOutputException, NoClassificationException, NoSurfaceFoundException, NoPossibleDisplayException
-// {
-// long[] dims = new long[ currentDataset.numDimensions() ];
-// currentDataset.dimensions( dims );
-// mainAppFrame.getLogService().info( "Zellige received the image: " + currentDataset.getName() );
-// mainAppFrame.getLogService().info( "Size: " + Util.printInterval( currentDataset ) );
-// mainAppFrame.getLogService().info( "Type: " + currentDataset.firstElement().getClass().toGenericString() );
-// mainAppFrame.getLogService().info( "Dimensionality: " + currentDataset.numDimensions() + "D" );
-// for ( int d = 0; d < currentDataset.numDimensions(); d++ )
-// {
-// mainAppFrame.getLogService().info( " - dimension " + d + ": [" + currentDataset.axis( d ).type() + "], 1 unit = " + currentDataset.averageScale( d ) + " " + currentDataset.axis( d ).unit() );
-// }
-// // Fixed parameters
-// String filter = "GaussianBlur";
-// double filterParameter = 2;
-// // End of fixed parameters
-// int connexity = 4;
-//
-// double startingOsSize1 = constructionController.getSt1();
-// int overlap1 = constructionController.getR1();
-// double connexityRate1 = constructionController.getC1();
-// double startingOsSize2 = constructionController.getSt2();
-// int overlap2 = constructionController.getR2();
-// double connexityRate2 = constructionController.getC2();
-// double surfaceMinSizeFactor = constructionController.getSurfaceSize();
-// int delta = projectionController.getDelta();
-// String method = projectionController.getMethod();
-// /* Print parameters.*/
-// mainAppFrame.getLogService().info( "Input : " + currentDataset.getName() );
-// mainAppFrame.getLogService().info( "filter : " + filter );
-// mainAppFrame.getLogService().info( "filterParameter : " + filterParameter );
-// mainAppFrame.getLogService().info( "amplitude : " + getAmplitude() );
-// mainAppFrame.getLogService().info( "threshold : " + getOtsu() );
-// mainAppFrame.getLogService().info( "connexity : " + connexity );
-// mainAppFrame.getLogService().info( "islandSize : " + getIsland() );
-// mainAppFrame.getLogService().info( "sigmaXY : " + getSigmaXY() );
-// mainAppFrame.getLogService().info( "sigmaZ : " + getSigmaZ() );
-// mainAppFrame.getLogService().info( "startingOsSize1 : " + startingOsSize1 );
-// mainAppFrame.getLogService().info( "overlap1 : " + overlap1 );
-// mainAppFrame.getLogService().info( "connexityRate1 : " + connexityRate1 );
-// mainAppFrame.getLogService().info( "startingOsSize2 : " + startingOsSize2 );
-// mainAppFrame.getLogService().info( "overlap2 : " + overlap2 );
-// mainAppFrame.getLogService().info( "connexityRate2 : " + connexityRate2 );
-// mainAppFrame.getLogService().info( "surfaceMinimumSizeFactor : " + surfaceMinSizeFactor );
-// mainAppFrame.getLogService().info( "delta : " + delta + "\n" );
-// /* End of Print parameters.*/
-//
-// SimpleObjectProperty<Pixels[][]> pixelsProperty = new SimpleObjectProperty<>();
-// fromIslandSearch();
-//// AbstractTask< Pixels[][] > runPostTreatmentTask = new RunPostTreatmentTask<>( extraction, getSigmaXY(), getSigmaZ(), getIsland(), connexity );
-//// runPostTreatmentTask.setOnSucceeded( workerStateEvent ->
-//// {
-//// AbstractTask< ArrayList< Surface > > runFirstConstructionTask = new RunFirstConstructionTask(
-//// runPostTreatmentTask.getValue(),
-//// startingOsSize1,
-//// overlap1,
-//// connexityRate1,
-//// surfaceMinSizeFactor );
-//// runFirstConstructionTask.setOnSucceeded( workerStateEvent2 ->
-//// {
-//// AbstractTask< ArrayList< Surface > > runSecondConstructionTask = new RunSecondConstructionTask(
-//// runFirstConstructionTask.getValue(),
-//// startingOsSize2,
-//// overlap2,
-//// connexityRate2,
-//// surfaceMinSizeFactor );
-//// runSecondConstructionTask.setOnSucceeded( workerStateEvent3 ->
-//// {
-//// ImgPlus< T > input = ( ImgPlus< T > ) currentDataset.getImgPlus();
-//// AbstractTask< ArrayList< ReferenceSurface< T > > > constructionCompletionTask = new ConstructionCompletionTask<>( input, input.factory(), runSecondConstructionTask.getValue() );
-//// constructionCompletionTask.setOnSucceeded( workerStateEvent4 ->
-//// {
-//// extraction.getReferenceSurfaces().addAll( constructionCompletionTask.getValue() );
-//// AbstractTask< Void > projectionTask = new ProjectionTask<>( constructionCompletionTask.getValue(), delta, method,
-//// projectionController.getProjection(),
-//// projectionController.getRawHeightmap(),
-//// projectionController.getExtractedHeightMap(),
-//// projectionController.getReduced3DSpace(),
-//// projectionController.getSegmentedSurface(),
-//// projectionController.getSegmentedSurfaceMask(),
-//// projectionController.getDelta2() );
-//// projectionTask.start();
-//// } );
-//// constructionCompletionTask.start();
-//// } );
-//// runSecondConstructionTask.start();
-////
-//// } );
-//// runFirstConstructionTask.start();
-//// } );
-//// runPostTreatmentTask.start();
-//
-// }
-
- public void initExtraction() throws DataValidationException
+ public void initExtraction()
{
LOGGER.debug( "Init Extraction" );
@@ -350,7 +255,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
// mainAppFrame.getLogService().info( "delta : " + delta + "\n" );
// /* End of Print parameters.*/
- public void run2() throws DataValidationException, EmptyOutputException, NoClassificationException, NoSurfaceFoundException, NoPossibleDisplayException
+ public void run2()
{
if ( selectionController.getSelectionModel().selectedPixelsProperty().getValue() != null )
@@ -399,6 +304,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
displayTask.start();
}
+ @SuppressWarnings( "unchecked" )
public void setCurrentDataset( Dataset dataset )
{
if ( dataset != currentDataset.getValue() )
@@ -445,30 +351,40 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
return ( int ) selectionController.getIsland().getSlider().getValue();
}
- public int getSigmaXY()
- {
- return ( int ) selectionController.getXyBlur().getSlider().getValue();
- }
-
- public int getSigmaZ()
- {
- return ( int ) selectionController.getzBlur().getSlider().getValue();
- }
-
@FXML
public void saveParameters() throws IOException
{
SimpleDateFormat dtf = new SimpleDateFormat( "yyyyMMdd_HHmmss" );
- FileChooser fileChooser = chooseAFile( dtf.format( new Date() ) + "_zellige_param", "Sava Parameters...", "ZelligeParameters", "*.json" );
+ FileChooser fileChooser = chooseAFile( dtf.format( new Date() ) + "_zellige_param", "Sava Parameters..." );
File file = fileChooser.showSaveDialog( null );
if ( file != null )
{
- ZelligeParameters.serialize( new ZelligeParameters( model ), file );
+ SelectionParameter sp = build( model.getSelectionModel() );
+ ConstructionParameter cp = build( model.getConstructionModel() );
+ ProjectionParameter pp = build( model.getProjectionModel() );
+
+ ZelligeParameters.serialize( new ZelligeParameters( sp, cp, pp ), file );
}
}
+
+ private SelectionParameter build( SelectionModel model )
+ {
+ return new SelectionParameter( model.amplitudeProperty(), model.otsuProperty(), model.islandProperty(), model.xyBlurProperty(), model.zBlurProperty() );
+ }
+
+ private ConstructionParameter build( ConstructionModel< T > model )
+ {
+ return new ConstructionParameter( model.c1Property(), model.r1Property(), model.st1Property(), model.c2Property(), model.r2Property(), model.st2Property(), model.surfaceSizeProperty() );
+ }
+
+ private ProjectionParameter build( ProjectionModel< T > model )
+ {
+ return new ProjectionParameter( model.delta1Property(), model.delta2Property(), model.methodProperty() );
+ }
+
@FXML
- public void loadParameters() throws IOException, ClassNotFoundException
+ public void loadParameters() throws IOException
{
File f = chooseFile();
LOGGER.debug( "The file has been choose" );
@@ -481,17 +397,17 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
private File chooseFile()
{
- FileChooser fileChooser = chooseAFile( null, "Select a Zellige parameter file",
- "ZelligeParameters", "*.json" );
+ FileChooser fileChooser = chooseAFile( null, "Select a Zellige parameter file"
+ );
return fileChooser.showOpenDialog( null );
}
- private FileChooser chooseAFile( String initialFileNme, String title, String description, String extension )
+ private FileChooser chooseAFile( String initialFileNme, String title )
{
FileChooser fileChooser = new FileChooser();
fileChooser.setTitle( title );
fileChooser.setInitialFileName( initialFileNme );
- FileChooser.ExtensionFilter extFilter = new FileChooser.ExtensionFilter( description, extension );
+ FileChooser.ExtensionFilter extFilter = new FileChooser.ExtensionFilter( "ZelligeParameters", "*.json" );
fileChooser.getExtensionFilters().add( extFilter );
return fileChooser;
}
@@ -500,6 +416,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
{
selectionController.setParameters( parameters );
constructionController.setParameters( parameters );
+ projectionController.setParameters( parameters );
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ProjectionController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/ProjectionController.java
similarity index 94%
rename from src/main/java/fr/pasteur/ida/zellige/gui/ProjectionController.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/controller/ProjectionController.java
index 267a05cc319f66f653f74642700309f7a4c03649..2e312d5fae1a68f5fe6675a81910929c06f4c8e0 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ProjectionController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/ProjectionController.java
@@ -26,8 +26,11 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package fr.pasteur.ida.zellige.gui;
+package fr.pasteur.ida.zellige.gui.controller;
+import fr.pasteur.ida.zellige.gui.CheckBoxDisplay;
+import fr.pasteur.ida.zellige.gui.model.ProjectionModel;
+import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
import javafx.beans.property.BooleanProperty;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.collections.FXCollections;
@@ -240,4 +243,11 @@ public class ProjectionController< T extends RealType< T > & NativeType< T > > i
selected.bind( checkBox.selectedProperty() );
notDisplayed.bindBidirectional( checkBox.notDisplayedProperty() );
}
+
+ public void setParameters( ZelligeParameters parameters )
+ {
+ delta1.getValueFactory().setValue( parameters.getDelta1() );
+ delta2.getValueFactory().setValue( parameters.getDelta2() );
+ methodComboBox.getSelectionModel().select( parameters.getMethod() );
+ }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/SelectionController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java
similarity index 95%
rename from src/main/java/fr/pasteur/ida/zellige/gui/SelectionController.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java
index 9c83aca5bebdd08d497e1b55d004e2f1a10bae0f..92576a425b56a41737b522a5459f4138c18f31f3 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/SelectionController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java
@@ -26,8 +26,12 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package fr.pasteur.ida.zellige.gui;
+package fr.pasteur.ida.zellige.gui.controller;
+import fr.pasteur.ida.zellige.gui.ParameterSliderInteger;
+import fr.pasteur.ida.zellige.gui.ZSlicesSlider;
+import fr.pasteur.ida.zellige.gui.model.SelectionModel;
+import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
import fr.pasteur.ida.zellige.gui.task.ImageFXDisplayTask;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.beans.value.ChangeListener;
@@ -37,14 +41,16 @@ import javafx.geometry.Pos;
import javafx.scene.image.ImageView;
import javafx.scene.layout.FlowPane;
import net.imglib2.img.Img;
+import net.imglib2.type.NativeType;
import net.imglib2.type.logic.BitType;
+import net.imglib2.type.numeric.RealType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.net.URL;
import java.util.ResourceBundle;
-public class SelectionController implements Initializable
+public class SelectionController< T extends RealType< T > & NativeType< T > > implements Initializable
{
private final static Logger LOGGER = LoggerFactory.getLogger( SelectionController.class );
@@ -231,7 +237,7 @@ public class SelectionController implements Initializable
public void setDisplay()
{
stack.getChildren().clear();
- ImageView i = selectionModel.imageViewsProperty().getValue()[ zSlices.userValue ];
+ ImageView i = selectionModel.imageViewsProperty().getValue()[ zSlices.getUserValue() ];
stack.getChildren().add( i );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/exception/NotANumberException.java b/src/main/java/fr/pasteur/ida/zellige/gui/exception/NotANumberException.java
index c434df0f0b69b45340efb3ba4c2a71ccfdf6416b..62acf2a112ca169ed5a6a2cfb7d527e6ec8873a8 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/exception/NotANumberException.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/exception/NotANumberException.java
@@ -31,12 +31,10 @@ package fr.pasteur.ida.zellige.gui.exception;
public class NotANumberException extends Exception
{
- private final String message = "Please enter a number !";
-
@Override
public String getMessage()
{
- return message;
+ return "Please enter a number !";
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ConstructionModel.java b/src/main/java/fr/pasteur/ida/zellige/gui/model/ConstructionModel.java
similarity index 76%
rename from src/main/java/fr/pasteur/ida/zellige/gui/ConstructionModel.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/model/ConstructionModel.java
index 7f87307dece15d5f745142ea6d2e4475135028d7..d54f6b6a881ca2c3dc92f48d429736429e748d86 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ConstructionModel.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/model/ConstructionModel.java
@@ -26,19 +26,21 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package fr.pasteur.ida.zellige.gui;
+package fr.pasteur.ida.zellige.gui.model;
import fr.pasteur.ida.zellige.element.Pixels;
import fr.pasteur.ida.zellige.element.ReferenceSurface;
import fr.pasteur.ida.zellige.element.Surface;
+import fr.pasteur.ida.zellige.gui.ZDoubleProperty;
+import fr.pasteur.ida.zellige.gui.controller.MainController;
import fr.pasteur.ida.zellige.gui.task.AbstractTask;
import fr.pasteur.ida.zellige.gui.task.ConstructionCompletionTask;
import fr.pasteur.ida.zellige.gui.task.RunFirstConstructionTask;
import fr.pasteur.ida.zellige.gui.task.RunSecondConstructionTask;
import fr.pasteur.ida.zellige.steps.construction.exception.FirstRoundConstructionException;
import fr.pasteur.ida.zellige.steps.construction.exception.SecondRoundConstructionException;
-import javafx.beans.property.DoubleProperty;
-import javafx.beans.property.SimpleDoubleProperty;
+import javafx.beans.property.IntegerProperty;
+import javafx.beans.property.SimpleIntegerProperty;
import javafx.beans.property.SimpleObjectProperty;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.ImgFactory;
@@ -54,35 +56,35 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >
private final static Logger LOGGER = LoggerFactory.getLogger( ConstructionModel.class );
- private final DoubleProperty c1;
- private final DoubleProperty c2;
- private final DoubleProperty r1;
- private final DoubleProperty r2;
- private final DoubleProperty st1;
- private final DoubleProperty st2;
- private final DoubleProperty surfaceSize;
+ private final ZDoubleProperty c1;
+ private final ZDoubleProperty c2;
+ private final IntegerProperty r1;
+ private final IntegerProperty r2;
+ private final ZDoubleProperty st1;
+ private final ZDoubleProperty st2;
+ private final ZDoubleProperty surfaceSize;
private final SimpleObjectProperty< ArrayList< Surface > > firstRoundSurfaces = new SimpleObjectProperty<>();
private final SimpleObjectProperty< ArrayList< Surface > > secondRoundSurfaces = new SimpleObjectProperty<>();
private final SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfaces = new SimpleObjectProperty<>();
- SimpleObjectProperty< Pixels[][] > maximums = new SimpleObjectProperty<>();
+ private final SimpleObjectProperty< Pixels[][] > maximums = new SimpleObjectProperty<>();
private RandomAccessibleInterval< T > input;
private ImgFactory< T > factory;
public ConstructionModel()
{
- c1 = new SimpleDoubleProperty();
- c2 = new SimpleDoubleProperty();
- r1 = new SimpleDoubleProperty();
- r2 = new SimpleDoubleProperty();
- st1 = new SimpleDoubleProperty();
- st2 = new SimpleDoubleProperty();
- surfaceSize = new SimpleDoubleProperty();
+ c1 = new ZDoubleProperty();
+ c2 = new ZDoubleProperty();
+ r1 = new SimpleIntegerProperty();
+ r2 = new SimpleIntegerProperty();
+ st1 = new ZDoubleProperty();
+ st2 = new ZDoubleProperty();
+ surfaceSize = new ZDoubleProperty();
}
public void firstRound()
{
LOGGER.info( "Computing first round construction..." );
- AbstractTask< ArrayList< Surface > > firstRoundTask = new RunFirstConstructionTask( maximums.getValue(), st1.doubleValue(), r1.intValue(), c1.doubleValue(), surfaceSize.doubleValue() );
+ AbstractTask< ArrayList< Surface > > firstRoundTask = new RunFirstConstructionTask( maximums.getValue(), st1.doubleValue(), r1.intValue(), c1.doubleValue(), surfaceSize.doubleValue() / 100.0 );
firstRoundTask.setOnSucceeded( workerStateEvent ->
{
firstRoundSurfaces.setValue( firstRoundTask.getValue() );
@@ -100,7 +102,7 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >
public void secondRound()
{
LOGGER.info( "Computing second round construction..." );
- AbstractTask< ArrayList< Surface > > secondRoundTask = new RunSecondConstructionTask( firstRoundSurfacesProperty().getValue(), st2.getValue(), r2.intValue(), c2.doubleValue(), surfaceSize.doubleValue() );
+ AbstractTask< ArrayList< Surface > > secondRoundTask = new RunSecondConstructionTask( firstRoundSurfacesProperty().getValue(), st2.getValue(), r2.intValue(), c2.doubleValue(), surfaceSize.doubleValue() / 100.0 );
secondRoundTask.setOnSucceeded( workerStateEvent ->
{
secondRoundSurfacesProperty().setValue( secondRoundTask.getValue() );
@@ -136,129 +138,81 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >
constructionCompletionTask.start();
}
- public double getC1()
- {
- return c1.get();
- }
- public DoubleProperty c1Property()
+ public ZDoubleProperty c1Property()
{
return c1;
}
- public double getC2()
- {
- return c2.get();
- }
-
- public DoubleProperty c2Property()
+ public ZDoubleProperty c2Property()
{
return c2;
}
- public double getR1()
- {
- return r1.get();
- }
-
- public DoubleProperty r1Property()
+ public IntegerProperty r1Property()
{
return r1;
}
- public double getR2()
- {
- return r2.get();
- }
-
- public DoubleProperty r2Property()
+ public IntegerProperty r2Property()
{
return r2;
}
- public double getSt1()
- {
- return st1.get();
- }
-
- public DoubleProperty st1Property()
+ public ZDoubleProperty st1Property()
{
return st1;
}
- public double getSt2()
- {
- return st2.get();
- }
-
- public DoubleProperty st2Property()
+ public ZDoubleProperty st2Property()
{
return st2;
}
- public double getSurfaceSize()
- {
- return surfaceSize.get();
- }
-
- public DoubleProperty surfaceSizeProperty()
+ public ZDoubleProperty surfaceSizeProperty()
{
return surfaceSize;
}
- public ArrayList< Surface > getFirstRoundSurfaces()
- {
- return firstRoundSurfaces.get();
- }
-
public SimpleObjectProperty< ArrayList< Surface > > firstRoundSurfacesProperty()
{
return firstRoundSurfaces;
}
- public ArrayList< Surface > getSecondRoundSurfaces()
- {
- return secondRoundSurfaces.get();
- }
-
public SimpleObjectProperty< ArrayList< Surface > > secondRoundSurfacesProperty()
{
return secondRoundSurfaces;
}
- public ArrayList< ReferenceSurface< T > > getReferenceSurfaces()
- {
- return referenceSurfaces.get();
- }
-
public SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfacesProperty()
{
return referenceSurfaces;
}
- public RandomAccessibleInterval< T > getInput()
+ public void setInput( RandomAccessibleInterval< T > input )
{
- return input;
+ this.input = input;
}
- public void setInput( RandomAccessibleInterval< T > input )
+
+ public void setFactory( ImgFactory< T > factory )
{
- this.input = input;
+ this.factory = factory;
}
- public ImgFactory< T > getFactory()
+ public double getC1()
{
- return factory;
+ return c1.get();
}
- public void setFactory( ImgFactory< T > factory )
+ public RandomAccessibleInterval< T > getInput()
{
- this.factory = factory;
+ return input;
}
- public Pixels[][] getMaximums()
+ public ImgFactory< T > getFactory()
{
- return maximums.get();
+ return factory;
}
public SimpleObjectProperty< Pixels[][] > maximumsProperty()
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/MainModel.java b/src/main/java/fr/pasteur/ida/zellige/gui/model/MainModel.java
similarity index 98%
rename from src/main/java/fr/pasteur/ida/zellige/gui/MainModel.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/model/MainModel.java
index 57762809ebb881c56746c300c3c536dd04b0dcfd..3d0934940b8f40b1afd27cc19004f8a41f7ef727 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/MainModel.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/model/MainModel.java
@@ -26,7 +26,7 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package fr.pasteur.ida.zellige.gui;
+package fr.pasteur.ida.zellige.gui.model;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ProjectionModel.java b/src/main/java/fr/pasteur/ida/zellige/gui/model/ProjectionModel.java
similarity index 99%
rename from src/main/java/fr/pasteur/ida/zellige/gui/ProjectionModel.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/model/ProjectionModel.java
index 4b3e6d90fd2b7f78c38f68541bc1885f6d8335bb..1c48ffe29728f4cf8dc458daddaa6edcbefbf7df 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ProjectionModel.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/model/ProjectionModel.java
@@ -26,7 +26,7 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package fr.pasteur.ida.zellige.gui;
+package fr.pasteur.ida.zellige.gui.model;
import fr.pasteur.ida.zellige.element.Projection;
import fr.pasteur.ida.zellige.element.ReferenceSurface;
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/SelectionModel.java b/src/main/java/fr/pasteur/ida/zellige/gui/model/SelectionModel.java
similarity index 99%
rename from src/main/java/fr/pasteur/ida/zellige/gui/SelectionModel.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/model/SelectionModel.java
index a86aca3f7fd07aa2fb0486c2d7fecffd3b852819..4b1d8d341d4bc8fb020e1d7385782beb48b2dd9d 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/SelectionModel.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/model/SelectionModel.java
@@ -26,9 +26,10 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package fr.pasteur.ida.zellige.gui;
+package fr.pasteur.ida.zellige.gui.model;
import fr.pasteur.ida.zellige.element.Pixels;
+import fr.pasteur.ida.zellige.gui.ClassifiedImages;
import fr.pasteur.ida.zellige.gui.task.*;
import javafx.beans.property.DoubleProperty;
import javafx.beans.property.SimpleBooleanProperty;
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ConstructionParameter.java b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ConstructionParameter.java
new file mode 100644
index 0000000000000000000000000000000000000000..d665ebdcc0097642917c6e5735b5b1498f638222
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ConstructionParameter.java
@@ -0,0 +1,62 @@
+package fr.pasteur.ida.zellige.gui.parameter;
+
+import fr.pasteur.ida.zellige.gui.ZDoubleProperty;
+import javafx.beans.property.IntegerProperty;
+
+public class ConstructionParameter
+{
+
+ private final double c1;
+ private final int r1;
+ private final double st1;
+ private final double c2;
+ private final int r2;
+ private final double st2;
+ private final int surfaceSize;
+
+ public ConstructionParameter( ZDoubleProperty c1, IntegerProperty r1, ZDoubleProperty st1, ZDoubleProperty c2, IntegerProperty r2, ZDoubleProperty st2, ZDoubleProperty surfaceSize )
+ {
+ this.c1 = c1.value();
+ this.r1 = r1.intValue();
+ this.st1 = st1.value();
+ this.c2 = c2.value();
+ this.r2 = r2.intValue();
+ this.st2 = st2.value();
+ this.surfaceSize = surfaceSize.intValue();
+ }
+
+ public double getC1()
+ {
+ return c1;
+ }
+
+ public int getR1()
+ {
+ return r1;
+ }
+
+ public double getSt1()
+ {
+ return st1;
+ }
+
+ public double getC2()
+ {
+ return c2;
+ }
+
+ public int getR2()
+ {
+ return r2;
+ }
+
+ public double getSt2()
+ {
+ return st2;
+ }
+
+ public int getSurfaceSize()
+ {
+ return surfaceSize;
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ProjectionParameter.java b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ProjectionParameter.java
new file mode 100644
index 0000000000000000000000000000000000000000..a9fd199bdd1d159eec908966c5128d7ccdac4055
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ProjectionParameter.java
@@ -0,0 +1,34 @@
+package fr.pasteur.ida.zellige.gui.parameter;
+
+import javafx.beans.property.IntegerProperty;
+import javafx.beans.property.StringProperty;
+
+public class ProjectionParameter
+{
+
+ private final int delta1;
+ private final int delta2;
+ private final String method;
+
+ public ProjectionParameter( IntegerProperty delta1, IntegerProperty delta2, StringProperty method )
+ {
+ this.delta1 = delta1.intValue();
+ this.delta2 = delta2.intValue();
+ this.method = method.get();
+ }
+
+ public int getDelta1()
+ {
+ return delta1;
+ }
+
+ public int getDelta2()
+ {
+ return delta2;
+ }
+
+ public String getMethod()
+ {
+ return method;
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/parameter/SelectionParameter.java b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/SelectionParameter.java
new file mode 100644
index 0000000000000000000000000000000000000000..1af00ac5cc7ad7ae8d140f087ebfbb023e37bdb3
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/SelectionParameter.java
@@ -0,0 +1,46 @@
+package fr.pasteur.ida.zellige.gui.parameter;
+
+import javafx.beans.property.DoubleProperty;
+
+public class SelectionParameter
+{
+ private final int amplitude;
+ private final int otsu;
+ private final int island;
+ private final int xyBlur;
+ private final int zBlur;
+
+ public SelectionParameter( DoubleProperty amplitude, DoubleProperty otsu, DoubleProperty island, DoubleProperty xyBlur, DoubleProperty zBlur )
+ {
+ this.amplitude = amplitude.intValue();
+ this.otsu = otsu.intValue();
+ this.island = island.intValue();
+ this.xyBlur = xyBlur.intValue();
+ this.zBlur = zBlur.intValue();
+ }
+
+ public int getAmplitude()
+ {
+ return amplitude;
+ }
+
+ public int getOtsu()
+ {
+ return otsu;
+ }
+
+ public int getIsland()
+ {
+ return island;
+ }
+
+ public int getXyBlur()
+ {
+ return xyBlur;
+ }
+
+ public int getzBlur()
+ {
+ return zBlur;
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ZelligeParameters.java b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ZelligeParameters.java
similarity index 66%
rename from src/main/java/fr/pasteur/ida/zellige/gui/ZelligeParameters.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/parameter/ZelligeParameters.java
index a7cb76be31cea74cebf964fc53d7aba2d46f9264..23fb31197cd66e3dfed658bedc75c1528f754477 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ZelligeParameters.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ZelligeParameters.java
@@ -6,13 +6,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
- *
+ *
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
- *
+ *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -26,15 +26,18 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package fr.pasteur.ida.zellige.gui;
+package fr.pasteur.ida.zellige.gui.parameter;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
-import java.io.*;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.stream.Collectors;
+import java.util.stream.Stream;
public class ZelligeParameters
{
@@ -52,39 +55,36 @@ public class ZelligeParameters
private final double c2;
private final int r2;
private final double st2;
- private final double surfaceSize;
+ private final int surfaceSize;
//projection
private final int delta1;
private final int delta2;
private final String method;
- public ZelligeParameters( MainModel model )
+ public ZelligeParameters( SelectionParameter sp, ConstructionParameter cp, ProjectionParameter pp )
{
-
- SelectionModel selectionModel = model.getSelectionModel();
- ConstructionModel constructionModel = model.getConstructionModel();
- ProjectionModel projectionModel = model.getProjectionModel();
// selection
- amplitude = selectionModel.amplitudeProperty().intValue();
- otsu = selectionModel.otsuProperty().intValue();
- island = selectionModel.islandProperty().intValue();
- xyBlur = selectionModel.xyBlurProperty().intValue();
- zBlur = selectionModel.zBlurProperty().intValue();
+ amplitude = sp.getAmplitude();
+ otsu = sp.getOtsu();
+ island = sp.getIsland();
+ xyBlur = sp.getXyBlur();
+ zBlur = sp.getzBlur();
// construction
- c1 = constructionModel.c1Property().doubleValue();
- r1 = constructionModel.r1Property().intValue();
- st1 = constructionModel.st1Property().doubleValue();
- c2 = constructionModel.c2Property().doubleValue();
- r2 = constructionModel.r2Property().intValue();
- st2 = constructionModel.st2Property().doubleValue();
- surfaceSize = constructionModel.surfaceSizeProperty().doubleValue();
+ c1 = cp.getC1();
+ r1 = cp.getR1();
+ st1 = cp.getSt1();
+ c2 = cp.getC2();
+ r2 = cp.getR2();
+ st2 = cp.getSt2();
+ surfaceSize = cp.getSurfaceSize();
// projection
- delta1 = projectionModel.delta1Property().intValue();
- delta2 = projectionModel.delta2Property().intValue();
- method = projectionModel.methodProperty().get();
+ delta1 = pp.getDelta1();
+ delta2 = pp.getDelta2();
+ method = pp.getMethod();
}
+
public static void serialize( final ZelligeParameters parameters, final File file ) throws IOException
{
final Gson gson = new GsonBuilder().setPrettyPrinting().create();
@@ -94,22 +94,24 @@ public class ZelligeParameters
{
writer.append( str );
}
-
}
-
- public static ZelligeParameters deserialize( final File file ) throws FileNotFoundException, IOException, ClassNotFoundException
+ public static ZelligeParameters deserialize( final File file
+ ) throws IOException, SecurityException
{
- try ( FileReader ignored = new FileReader( file ) )
+ try ( Stream< String > streams = Files.lines( Paths.get( file.getAbsolutePath() ) ) )
{
- final String str = Files.lines( Paths.get( file.getAbsolutePath() ) )
- .collect( Collectors.joining( System.lineSeparator() ) );
+ if ( streams != null )
+ {
+ String s = streams.collect( Collectors.joining( System.lineSeparator() ) );
+ final Gson gson = new GsonBuilder().setPrettyPrinting().create();
- final Gson gson = new GsonBuilder().setPrettyPrinting().create();
+ return ( s.isEmpty() )
+ ? null
+ : gson.fromJson( s, ZelligeParameters.class );
+ }
- return ( str == null || str.isEmpty() )
- ? null
- : gson.fromJson( str, ZelligeParameters.class );
+ return null;
}
}
@@ -173,6 +175,11 @@ public class ZelligeParameters
return surfaceSize;
}
+ public String getMethod()
+ {
+ return method;
+ }
+
public int getDelta1()
{
return delta1;
@@ -182,9 +189,4 @@ public class ZelligeParameters
{
return delta2;
}
-
- public String getMethod()
- {
- return method;
- }
}
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 5e68372ca03bda790d4e31c520f7228e9e2667f3..50494dd4d2ec16cbadaf36db0709dd374cbdcee9 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
@@ -52,7 +52,7 @@ public class AmplitudeThresholdingTask extends AbstractTask< Img< BitType > >
}
@Override
- protected Img< BitType > call() throws Exception
+ protected Img< BitType > call()
{
LOGGER.info( "Computing amplitude thresholding..." );
return AmplitudeClassification.applyThreshold( images.getValue().getAmplitudeImg(), amplitudeThreshold );
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 0181077e2d9bf66e0fe9433ebd3e46407882fc2c..3ff1d90bd3beb502d4900dbc86f24c50936f6f7e 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
@@ -56,7 +56,7 @@ public class ConstructionCompletionTask< T extends RealType< T > & NativeType< T
}
@Override
- protected ArrayList< ReferenceSurface< T > > call() throws Exception
+ protected ArrayList< ReferenceSurface< T > > call()
{
LOGGER.info( "Processing construction completion..." );
return ConstructionCompletion.run( input, factory, finalSurfaces );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/DisplayDatasetChoicesTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/DisplayDatasetChoicesTask.java
index b3826bd0bb3af32b7f6a457551c42ea9ce084039..074f3d916b72613bde83ca1c83bcd03d983fcd92 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/DisplayDatasetChoicesTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/DisplayDatasetChoicesTask.java
@@ -47,7 +47,7 @@ public class DisplayDatasetChoicesTask extends AbstractTask< ArrayList< Dataset
}
@Override
- protected ArrayList< Dataset > call() throws Exception
+ protected ArrayList< Dataset > call()
{
ArrayList< ImageDisplay > imageDisplays = ( ArrayList< ImageDisplay > ) imageDisplayService.getImageDisplays();
ArrayList< Dataset > tempDatasets = new ArrayList<>( imageDisplays.size() );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/ImageFXDisplayTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/ImageFXDisplayTask.java
index 1a92c8479ec842b7f822129d70cd3739486d052a..5c8feb3ba78cb082e25eb82ab2b1ad6f1560e5a7 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/ImageFXDisplayTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/ImageFXDisplayTask.java
@@ -48,7 +48,7 @@ public class ImageFXDisplayTask extends AbstractTask< ImageView[] >
@Override
- protected ImageView[] call() throws Exception
+ protected ImageView[] call()
{
ImageFXDisplay display = new ImageFXDisplay( input.getValue() );
display.set();
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 7fbe48400d1cbf89f54f82d8b24954c6516e44fe..cb86733367484a1abd8393ce161c737caadb1925 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
@@ -50,7 +50,7 @@ public class InterClassificationTask extends AbstractTask< Img< BitType > >
@Override
- protected Img< BitType > call() throws Exception
+ protected Img< BitType > call()
{
LOGGER.info( "Computing inter-classification..." );
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 2f5d8d41e2517557e879f8a6edf7cb6750f8acda..7e71fac25ece610fbfa4a4514d229779fc4671a4 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
@@ -50,7 +50,7 @@ public class IslandSearchTask extends AbstractTask< Img< BitType > >
}
@Override
- protected Img< BitType > call() throws Exception
+ protected Img< BitType > call()
{
LOGGER.info( "Computing Island Search..." );
Img< BitType > img = PostTreatment.runIslandSearch( image.getValue(), islandSize.intValue() );
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 32e3fb20f780deb6c60ca77bf4028d1d5b4476e8..4fafcd4a2d39094c48caedeb68a498170e31d63c 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
@@ -54,7 +54,7 @@ public class OtsuThresholdingTask extends AbstractTask< Img< BitType > >
}
@Override
- protected Img< BitType > call() throws Exception
+ protected Img< BitType > call()
{
LOGGER.info( "Computing otsu thresholding..." );
return OtsuClassification.applyLocalThreshold( pretreatedImage.getValue(), images.getValue().getOtsuImg(), otsuThreshold );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/PretreatmentTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/PretreatmentTask.java
index f23053a020d010a1899fbf0ab8ce08ea54244bf9..7cc65fb66123a301189914773b30025a9b40a754 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/PretreatmentTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/PretreatmentTask.java
@@ -50,7 +50,8 @@ public class PretreatmentTask< T extends RealType< T > & NativeType< T > > exten
}
@Override
- protected Img< FloatType > call() throws Exception
+ @SuppressWarnings( "unchecked" )
+ protected Img< FloatType > call()
{
LOGGER.info( "Computing pretreatment..." );
ImgPlus< T > input = ( ImgPlus< T > ) dataset.getImgPlus();
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 f4572b2a2c9a5227d11d0c18ddbc2cd00b28d5c5..429746ab65b52ab3a1c549dd9b10cd84034ad656 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
@@ -56,7 +56,7 @@ public class RunFirstConstructionTask extends AbstractTask< ArrayList< Surface >
}
@Override
- protected ArrayList< Surface > call() throws Exception
+ protected ArrayList< Surface > call()
{
LOGGER.info( "Computing first round construction..." );
FirstRoundConstruction step1 = new FirstRoundConstruction( maximums, startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor );
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 c30b4800fbf4ecaa0ef1c3e67f94ddfcbe7d1ecf..b32f7a9b0b53100fe0db027c90aec769b8ac3b27 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
@@ -56,7 +56,7 @@ public class RunSecondConstructionTask extends AbstractTask< ArrayList< Surface
}
@Override
- protected ArrayList< Surface > call() throws Exception
+ protected ArrayList< Surface > call()
{
LOGGER.info( "Computing second round construction..." );
SecondRoundConstruction step2 = new SecondRoundConstruction( surfaces, startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor );
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/SetCurrentDatasetTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/SetCurrentDatasetTask.java
deleted file mode 100644
index 7a83c081b7c73b94c3d8fa50d857930eb70cac74..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/SetCurrentDatasetTask.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.gui.task;
-
-
-import net.imagej.Dataset;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class SetCurrentDatasetTask extends AbstractTask< Dataset >
-
-{
- private final Logger LOGGER = LoggerFactory.getLogger( SetCurrentDatasetTask.class );
- private final Dataset dataset;
-
-
- public SetCurrentDatasetTask( Dataset dataset )
- {
- this.dataset = dataset;
- LOGGER.debug( " constructor" );
- }
-
- @Override
- protected Dataset call() throws Exception
- {
- LOGGER.debug( "Task's start." );
- if ( dataset.numDimensions() != 3 )
- {
- LOGGER.debug( "This input is not a z-stack" );
- return null;
- }
- return dataset;
- }
-
-
- //
- @Override
- protected void succeeded()
- {
- super.succeeded();
- LOGGER.debug( "Task successful" );
- }
-
-
-}
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 fc8cb4befa639d97bb2d56d963566c69a819d2a1..6845b02527ac58e1857c43ebb014bcaa09fe1e2c 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/Utils.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/Utils.java
@@ -52,7 +52,7 @@ public class Utils
* @param <T> - source and output type
* @param input - the source image as a {@link RandomAccessibleInterval}
* @param output - the filtered image as a {@link RandomAccessibleInterval}
- * @param sigma - a array containing the standard deviations for each dimension.
+ * @param sigma - an array containing the standard deviations for each dimension.
*/
public static < T extends RealType< T > & NativeType< T > > void
gaussianConvolution( RandomAccessibleInterval< T > input, RandomAccessibleInterval< T > output,
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/ConstructionCompletion.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/ConstructionCompletion.java
index 7bcfadfdf0062beff482ba6daa728a3d66eaf5cd..9ae18abbfa5bfb29702ef2346bbb947279174947 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/ConstructionCompletion.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/ConstructionCompletion.java
@@ -47,7 +47,7 @@ import java.util.ArrayList;
/**
- * This class allows to get a height map from a {@link Surface} by averaging the Z values or discarding them if not possible (gteZmap())
+ * This class allows to get a height map from a {@link Surface} by averaging the Z values or discarding them if not possible (getZMap())
* and by interpolating when possible if there is any missing internal values (processZMap()).
*
* @param <T> the input type
@@ -123,13 +123,6 @@ public class ConstructionCompletion< T extends RealType< T > & NativeType< T > >
randomAccess.get().set( new UnsignedShortType( z + 1 ) );
}
}
- else
- {
- if ( pixel != null )
- {
-// LOGGER.debug( "more than two : " + pixel );
- }
- }
}
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/Interpolation.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/Interpolation.java
index 3c624ad6740fb4d92fa0c9787fe220d84fce7340..23a9daee943b4c4dd6f9210167cecc17500ee80f 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/Interpolation.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/Interpolation.java
@@ -114,9 +114,9 @@ public class Interpolation
}
/**
- * Determines the constant b of the linear equation y = ax + b given one point P1(x1, y1) and the slope a.
+ * Determines the constant b of the linear equation y = ax + b given one point P1(x1, y1) and the slope 'a'.
*
- * @param a - the slope a of the linear equation y = ax + b.
+ * @param a - the slope 'a' of the linear equation y = ax + b.
* @param x1 - x coordinates for the first point.
* @param z1 - z coordinates for the first point.
* @return the b constant of the linear equation y = ax + b.
@@ -131,7 +131,7 @@ public class Interpolation
* Determines the unknown z coordinate of a point P given its x coordinate,
* the slope and the constant of the linear equation y = ax + b.
*
- * @param a - the slope a of the linear equation y = ax + b.
+ * @param a - the slope 'a' of the linear equation y = ax + b.
* @param b - the b constant of the linear equation y = ax + b.
* @param x - the x coordinate of a point with unknown z coordinate.
* @return - the z coordinate corresponding to the x coordinate.
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionParameters.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionParameters.java
index 9607bec078e5734335b29c5fedbd04ffc2e091cd..ed44fc6b818b982ab595cdfe0e38ae03eef0998c 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionParameters.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionParameters.java
@@ -34,7 +34,7 @@ public class ConstructionParameters
private final double startingSizeThreshold;
private final int overlap;
private final double connexityRate;
- private double surfaceMinSizeFactor;
+ private final double surfaceMinSizeFactor;
public ConstructionParameters( double startingSizeThreshold, int overlap, double connexityRate, double surfaceMinSizeFactor )
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionRound.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionRound.java
index e43a6282511b69195f5285a8917d3731ab13e8ac..fd54a703876d58f3cdff2e7550377000a94d69be 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionRound.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionRound.java
@@ -202,8 +202,4 @@ public abstract class ConstructionRound
return startingOSCount;
}
- public void setStartingOSCount( int startingOSCount )
- {
- this.startingOSCount = startingOSCount;
- }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstruction.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstruction.java
index 7f22314c37d86cbfd260ca2c6ee2fa14eba8c3f6..f393d0f897441fbd2578943f4be100a18b8c2f59 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstruction.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstruction.java
@@ -71,7 +71,7 @@ public abstract class OseConstruction
/**
* This method finds all the possible 2D surfaces that can be created from the coordinates detected as
- * local maximums on a array of {@link }.
+ * local maximums on an array of {@link }.
*
* @param rawCoordinates - the raw Coordinates from the projection.
* @return all the orthogonal surfaces for the projection as an {@link ArrayList <AbstractOSE>}.
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstructionYZ.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstructionYZ.java
index 9e124fdc5441904daf36907923825446464b75f7..c3fe75f9ea04cb34b2267d146e5b5247151fa48e 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstructionYZ.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstructionYZ.java
@@ -86,10 +86,12 @@ public class OseConstructionYZ extends OseConstruction
for ( Pixels [] pixelLine : this.getMaximums() )
{
- for (Pixels pixels : pixelLine)
- if ( pixels != null )
+ for ( Pixels pixels : pixelLine )
{
- pixels.resetSideCoordinate();
+ if ( pixels != null )
+ {
+ pixels.resetSideCoordinate();
+ }
}
}
LOGGER.debug( "Ose reset" );
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java b/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java
index 60b33a7021f8fdbda3628600646dcaaa2ebdd312..1645246f2dc4f4c34518926acb814b6f786d8c6a 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java
@@ -50,21 +50,15 @@ import static fr.pasteur.ida.zellige.steps.Utils.setPosition;
* @author ctrebeau
* Methods to extract the reference surface from a stack with the height map obtained with the program.
*/
+@SuppressWarnings( "Duplicates" )
public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T > >
{
- private final int delta;
-
- public ReferenceSurfaceProjection( int delta )
- {
- this.delta = delta;
- }
-
public static < T extends RealType< T > & NativeType< T > > void run( ReferenceSurface< T > referenceSurface,
ProjectionParameters projectionParameters,
DisplayParameters displayParameters ) throws NoPossibleDisplayException
{
- ReferenceSurfaceProjection< T > referenceSurfaceProjection = new ReferenceSurfaceProjection<>( projectionParameters.getDelta() );
+ ReferenceSurfaceProjection< T > referenceSurfaceProjection = new ReferenceSurfaceProjection<>();
referenceSurfaceProjection.set( referenceSurface, projectionParameters );
referenceSurfaceProjection.display( referenceSurface, projectionParameters, displayParameters );
}
@@ -79,7 +73,7 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
boolean segmentedSurfaceMaskDisplay,
int delta2 ) throws NoPossibleDisplayException
{
- ReferenceSurfaceProjection< T > referenceSurfaceProjection = new ReferenceSurfaceProjection<>( delta );
+ ReferenceSurfaceProjection< T > referenceSurfaceProjection = new ReferenceSurfaceProjection<>();
referenceSurfaceProjection.set( referenceSurface, delta, projectionType, delta2 );
referenceSurfaceProjection.display( referenceSurface, delta, projectionType,
projectionDisplay,
@@ -137,7 +131,7 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
/**
* @param referenceSurface the considered reference surface
* @param delta the desired user volume value
- * @param <T> the type of the referece surface
+ * @param <T> the type of the reference surface
* @return the extracted height map subStack
*/
public static < T extends RealType< T > & NativeType< T > > Img< T > getExtractedHeightMapSubStack
@@ -323,7 +317,7 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
*
* @param stackAccess - the {@link RandomAccess} of original stack
* @param stop - the maximum value that z can take.
- * @param delta - the delta to which the search will occurred.
+ * @param delta - the delta to which the search will occur.
* @param <T> - the type of the {@link RandomAccess}
* @return - the z value for which the pixel intensity is maximal.
*/
@@ -404,7 +398,6 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
referenceSurface.getProjection().setExtractedHeightMap( getProjectionHeightMap( referenceSurface, projectionType, delta ) );
referenceSurface.getProjection().setReduced3DSpace( getExtractedHeightMapSubStack( referenceSurface, delta ) );
referenceSurface.getProjection().setProjection( projection1( referenceSurface, projectionType ) );
-// referenceSurface.getProjection().setSegmentedSurface( getSegmentedSurface( referenceSurface, delta ) );
referenceSurface.getProjection().setSegmentedSurface( getSegmentedSurface( referenceSurface.getProjection().getExtractedHeightMap(),
referenceSurface.getInput(),
referenceSurface.getFactory() ) );
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/Selection.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/Selection.java
index 5f96d0769d0d0e44b901ba861c7674d4c3a7267a..67adf573f422ad9a28e3c97ed1b4fb4cc42b2b77 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/Selection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/Selection.java
@@ -34,7 +34,6 @@ import fr.pasteur.ida.zellige.steps.selection.classification.Classification;
import fr.pasteur.ida.zellige.steps.selection.classification.ClassificationParameters;
import fr.pasteur.ida.zellige.steps.selection.classification.OtsuClassification;
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.PostTreatment;
import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatmentParameters;
@@ -77,7 +76,7 @@ public class Selection< T extends RealType< T > & NativeType< T > >
}
public static < T extends RealType< T > & NativeType< T > > Pixels[][]
- run( RandomAccessibleInterval< T > input, PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters ) throws EmptyOutputException, NoClassificationException, DataValidationException
+ run( RandomAccessibleInterval< T > input, PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters ) throws NoClassificationException, DataValidationException
{
LOGGER.debug( "Starting process..." );
Selection< T > selection = new Selection<>( pretreatmentParameters, classificationParameters, postTreatmentParameters, input );
@@ -108,11 +107,10 @@ public class Selection< T extends RealType< T > & NativeType< T > >
}
/**
- * @throws EmptyOutputException if the input image is empty
* @throws NoClassificationException if the no classification was performed
* @throws DataValidationException if one of the input parameters is not valid
*/
- public void run() throws EmptyOutputException, NoClassificationException, DataValidationException
+ public void run() throws NoClassificationException, DataValidationException
{
/* Pretreatment of the image.*/
Img< FloatType > pretreatedImage = Pretreatment.run( input, radius );
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/AmplitudeClassification.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/AmplitudeClassification.java
index 37c2ace40228a29a75e84d182686d5ffaebff3ea..e5c10449f285d3b05f337a5090589d7d549ce4bf 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/AmplitudeClassification.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/AmplitudeClassification.java
@@ -57,7 +57,6 @@ public class AmplitudeClassification< T extends RealType< T > & NativeType< T >
private double userThreshold;
private Img< BitType > output;
private static long processingTime;
- private static double firstMaxValue;
private final static Logger LOGGER = LoggerFactory.getLogger( AmplitudeClassification.class );
@@ -92,13 +91,6 @@ public class AmplitudeClassification< T extends RealType< T > & NativeType< T >
return classification.getOutput();
}
- public static < T extends RealType< T > & NativeType< T > > Img< BitType >
- applyThreshold( Img< T > input, T value, double userThreshold )
- {
- value.mul( userThreshold );
- return Thresholder.threshold( input, value, true, 5 );
- }
-
public static < T extends RealType< T > & NativeType< T > > Img< BitType >
applyThreshold( Img< T > input, int userThreshold )
{
@@ -228,11 +220,6 @@ public class AmplitudeClassification< T extends RealType< T > & NativeType< T >
return maxValue;
}
- public static double getFirstMaxValue()
- {
- return firstMaxValue;
- }
-
//
public void run() throws DataValidationException
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/Classification.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/Classification.java
index 678409ca69099c2944b2195d4709d65fb05d4c44..daf19da0c8bfc4363fe45be718024f3007095cd5 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/Classification.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/Classification.java
@@ -68,8 +68,6 @@ public class Classification< T extends RealType< T > & NativeType< T > >
this.factory = factory;
}
-
-
/**
* Static method to provide a 2-part classification on a 3D image
*
@@ -79,23 +77,22 @@ public class Classification< T extends RealType< T > & NativeType< T > >
* @param parameters - the parameters for the 2-parts classification
* @return a binary image
* @throws NoClassificationException if the binary image is empty.
- * @throws DataValidationException} if the value of parameter amplitudeThreshold is not valid.
+ * @throws DataValidationException if the value of parameter amplitudeThreshold is not valid.
*/
public static < T extends RealType< T > & NativeType< T > > Img< BitType >
run( RandomAccessibleInterval< T > input, ImgFactory< T > factory, ClassificationParameters parameters ) throws NoClassificationException, DataValidationException
{
Classification< T > classification = new Classification<>( input, factory );
- classification.process( factory, parameters );
+ classification.process( parameters );
return classification.output;
}
/**
- * @param factory - the input {@link ImgFactory}
* @param parameters - the user parameters to set the classifications
* @throws NoClassificationException if both classifications are set to Zero
* @throws DataValidationException if one of the user thresholds is incorrect
*/
- void process( ImgFactory< T > factory, ClassificationParameters parameters ) throws NoClassificationException, DataValidationException
+ void process( ClassificationParameters parameters ) throws NoClassificationException, DataValidationException
{
LOGGER.debug( "Starting classification..." );
int amplitudeThreshold = parameters.getAmplitudeThreshold();
@@ -177,37 +174,4 @@ public class Classification< T extends RealType< T > & NativeType< T > >
return output;
}
-
- /**
- * @param amplitude an {@link BitType}{@link Img}
- * @param factory the same {@link BitType} {@link ImgFactory} as amplitude
- * @param thresholds another {@link BitType}{@link Img}
- * @return the intersection of both image
- */
- public static Img< BitType > runInterClassification( IterableInterval< BitType > amplitude,
- ImgFactory< BitType > factory,
- RandomAccessibleInterval< BitType > thresholds )
- {
- Img< BitType > output = factory.create( thresholds );
- Cursor< BitType > amplitudeCursor = amplitude.localizingCursor();
- RandomAccess< BitType > thresholdAccess
- = thresholds.randomAccess();
- RandomAccess< BitType > outputAccess = output.randomAccess();
- while ( amplitudeCursor.hasNext() )
- {
- amplitudeCursor.fwd();
- if ( amplitudeCursor.get().getRealDouble() != 0 )
- {
- thresholdAccess.setPosition( amplitudeCursor );
- if ( thresholdAccess.get().get() )
- {
- outputAccess.setPosition( amplitudeCursor );
- outputAccess.get().setOne();
- }
- }
- }
- return output;
- }
-
-
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/HistogramZ.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/HistogramZ.java
index b6e4419910e97cef4b6facc06bee5a45cc0300d8..89ab05e12ac43ebb850844dd31b29731e0d76c0d 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/HistogramZ.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/HistogramZ.java
@@ -147,11 +147,11 @@ public class HistogramZ< T > implements Algorithm, Benchmark
}
/**
- * Creates and returns the a Type whose value corresponds to the center of
- * the bin indexed by i.
+ * Creates and returns the {@link Type} whose value corresponds to the center of
+ * the bin indexed by the value i.
*
* @param i the requested bin index.
- * @return a Type whose value corresponds to the requested bin center.
+ * @return a {@link Type} whose value corresponds to the requested bin center.
*/
public T getBinCenter( final int i )
{
@@ -167,7 +167,7 @@ public class HistogramZ< T > implements Algorithm, Benchmark
*/
public ArrayList< T > getBinCenters()
{
- final ArrayList< T > binCenters = new ArrayList< T >( histogram.length );
+ final ArrayList< T > binCenters = new ArrayList<>( histogram.length );
for ( int i = 0; i < histogram.length; ++ i )
{
binCenters.add( i, getBinMapper().invMap( i ) );
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/OtsuClassification.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/OtsuClassification.java
index ce5ee18af7e89876119c390b66567b13c7544c45..3aa5c5a16109a561316ce88e1db379e4d1bec75d 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/OtsuClassification.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/OtsuClassification.java
@@ -57,7 +57,7 @@ public class OtsuClassification< T extends RealType< T > & NativeType< T > >
* @param input the input image as a {@link RandomAccessibleInterval}
* @param factory the input factory
* @param output the resulting binary image as a {@link Img<BitType> }
- * @param userThreshold the the user's intensity threshold
+ * @param userThreshold the user's intensity threshold
*/
private OtsuClassification( final RandomAccessibleInterval< T > input, final ImgFactory< T > factory, final Img< BitType > output, int userThreshold )
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/PostTreatment.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/PostTreatment.java
index 2e53cd32f4aa95ddc0aa4c33e52c85c4b6425567..ee89938b1dd90e69acfd0ec8a8f3e8852159fe2f 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/PostTreatment.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/PostTreatment.java
@@ -163,7 +163,7 @@ public class PostTreatment
public static Pixels[][] runSmoothing( Img< BitType > ISImage, int sigmaXY, int sigmaZ ) throws DataValidationException
{
Img< FloatType > converted = convertBitTypeIntoFloatType( ISImage );
- // Use of Converter.convert() not possible because classifiedPixel type do not extends RealType
+ // Use of Converter.convert() not possible because classifiedPixel type do not extend RealType
/* Dilatation of the resulting image*/
runDilatation( converted, sigmaXY, sigmaZ );
@@ -185,7 +185,7 @@ public class PostTreatment
}
/* Conversion into FloatType before dilatation */
Img< FloatType > converted = convertBitTypeIntoFloatType( temp );
- // Use of Converter.convert() not possible because classifiedPixel type do not extends RealType
+ // Use of Converter.convert() not possible because classifiedPixel type do not extend RealType
/* Dilatation of the resulting image*/
runDilatation( converted, parameters );
@@ -207,7 +207,7 @@ public class PostTreatment
}
/* Conversion into FloatType before dilatation */
Img< FloatType > converted = convertBitTypeIntoFloatType( temp );
- // Use of Converter.convert() not possible because classifiedPixel type do not extends RealType
+ // Use of Converter.convert() not possible because classifiedPixel type do not extend RealType
/* Dilatation of the resulting image*/
runDilatation( converted, sigmaXY, sigmaZ );
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/islandSearch/IslandSearch.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/islandSearch/IslandSearch.java
index 7ef954790535ac7c203997059e90edce924c09c5..8528599d4ac438ec957f38a204f424d82a20b6dd 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/islandSearch/IslandSearch.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/islandSearch/IslandSearch.java
@@ -87,15 +87,6 @@ public class IslandSearch
return output;
}
- public static int getInputCount()
- {
- return inputCount;
- }
-
- public static int getPixelRemovedCount()
- {
- return pixelRemovedCount;
- }
/**
* Computes the island search
@@ -105,6 +96,8 @@ public class IslandSearch
World world = convertImgIntoWorld();
world.run();
convertWorldIntoImg( world, output );
+ LOGGER.debug( "Input count : {}.", inputCount );
+ LOGGER.debug( "Number of pixels removed : {}.", pixelRemovedCount );
}
/**
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java
index b8fcda26ebc0c7988f26b6df5b00800f134ed0af..b1e897c994954207a62d32f5bd42a5c55a0988b6 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java
@@ -88,7 +88,7 @@ public class Pretreatment< T extends RealType< T > & NativeType< T > >
*
* @param <T> - the type of the input Img.
* @param image - the input Img.
- * @param factory
+ * @param factory - the image factory.
* @return a new Img with normalize pixel intensity values.
*/
private static < T extends RealType< T > & NativeType< T > > Img< T > normalizeImage(
@@ -123,7 +123,7 @@ public class Pretreatment< T extends RealType< T > & NativeType< T > >
/**
* @param input - the source image as a {@link RandomAccessibleInterval}
* @param factory - the source and output factory
- * @param sigma - a array containing the standard deviations for each dimension.
+ * @param sigma - an array containing the standard deviations for each dimension.
* @param <T> - source and output type
* @return - the filtered image as a {@link RandomAccessibleInterval}
*/
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/PretreatmentParameters.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/PretreatmentParameters.java
index 7b78c63564b9023ec0be88e88f5de8f2df8f2e45..c48493a782b4245894d31df6c68b9ad0eacf6fc0 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/PretreatmentParameters.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/PretreatmentParameters.java
@@ -62,7 +62,7 @@ public class PretreatmentParameters
* Checks the length of the parameters according to the method choose
*
* @param parameter the method arguments
- * @throws DataValidationException if at the pramaters legnth (the number of arguments) is not valid according to the method choose
+ * @throws DataValidationException if at the parameters' length (the number of arguments) is not valid according to the method choose
*/
private void checkParametersLength( double parameter ) throws DataValidationException
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/Util.java b/src/main/java/fr/pasteur/ida/zellige/utils/Util.java
new file mode 100644
index 0000000000000000000000000000000000000000..44f41014b0deb393eaf9e0db7fadbee0dd3e6d76
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/Util.java
@@ -0,0 +1,30 @@
+package fr.pasteur.ida.zellige.utils;
+
+import net.imglib2.RandomAccess;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+
+import static fr.pasteur.ida.zellige.steps.Utils.setPositionAndGet;
+
+public class Util
+{
+
+ public static < S extends RealType< S > & NativeType< S > > float[][] convert( RandomAccessibleInterval< S > input, int subtract )
+ {
+ float[][] array = new float[ ( int ) input.dimension( 1 ) ][ ( int ) input.dimension( 0 ) ];
+ RandomAccess< S > access = input.randomAccess();
+ for ( int x = 0; x < ( int ) input.dimension( 0 ); x++ )
+ {
+ for ( int y = 0; y < ( int ) input.dimension( 1 ); y++ )
+ {
+ float value = setPositionAndGet( access, x, y ).getRealFloat();
+ if ( value + subtract != 0 )
+ {
+ array[ y ][ x ] = value;
+ }
+ }
+ }
+ return array;
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/All_GT_Display.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/All_GT_Display.java
index 45a937baa1eab953e1225d3f6b85a2a76213af72..a108c4c646774c8874cffcdf3fcc768a22b01957 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/All_GT_Display.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/All_GT_Display.java
@@ -28,14 +28,13 @@
*/
package fr.pasteur.ida.zellige.utils.jzy3D;
+import fr.pasteur.ida.zellige.utils.Util;
import io.scif.img.IO;
import io.scif.img.SCIFIOImgPlus;
-import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.numeric.real.FloatType;
import org.jzy3d.analysis.AbstractAnalysis;
import org.jzy3d.analysis.AnalysisLauncher;
import org.jzy3d.chart.factories.AWTChartComponentFactory;
@@ -48,13 +47,11 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList;
-import static fr.pasteur.ida.zellige.steps.Utils.setPositionAndGet;
-
public class All_GT_Display< T extends RealType< T > & NativeType< T > > extends AbstractAnalysis
{
private final static Logger LOGGER = LoggerFactory.getLogger( All_GT_Display.class );
private final ArrayList< RandomAccessibleInterval< T > > groundTruths;
- private String[] gtColors = { "#283D66", "#A1B9EA", "#5A88E6", "#465166", "#466AB3", "", "", "" };
+ private final String[] gtColors = { "#283D66", "#A1B9EA", "#5A88E6", "#465166", "#466AB3", "", "", "" };
public All_GT_Display( ArrayList< RandomAccessibleInterval< T > > groundTruths )
{
@@ -62,7 +59,8 @@ public class All_GT_Display< T extends RealType< T > & NativeType< T > > extends
init();
}
- public static void main( String[] args )
+ @SuppressWarnings( "unchecked" )
+ public static < T extends RealType< T > & NativeType< T > > void main( String[] args )
{
final String[] refImagePath = new String[]{
@@ -73,12 +71,14 @@ public class All_GT_Display< T extends RealType< T > & NativeType< T > > extends
"C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\GT\\Ground truth Height map_4.tif"
};
- ArrayList< RandomAccessibleInterval< FloatType > > GTs = new ArrayList<>();
+
+ ArrayList< RandomAccessibleInterval< T > > GTs = new ArrayList<>();
+
for ( String path : refImagePath )
{
LOGGER.debug( path );
- SCIFIOImgPlus< ? > refImgPlus = IO.openImgs( path ).get( 0 );
- GTs.add( ( Img< FloatType > ) refImgPlus.getImg() );
+ SCIFIOImgPlus< ? > refImgPlus = IO.openAll( path ).get( 0 );
+ GTs.add( ( Img< T > ) refImgPlus.getImg() );
}
All_GT_Display.display( GTs );
}
@@ -94,7 +94,7 @@ public class All_GT_Display< T extends RealType< T > & NativeType< T > > extends
{
try
{
- All_GT_Display display = new All_GT_Display( groundTruths );
+ All_GT_Display< T > display = new All_GT_Display<>( groundTruths );
AnalysisLauncher.open( display );
}
catch ( Exception e )
@@ -110,7 +110,7 @@ public class All_GT_Display< T extends RealType< T > & NativeType< T > > extends
ArrayList< float[][] > GTs = new ArrayList<>();
for ( RandomAccessibleInterval< T > GT : groundTruths )
{
- GTs.add( convert( GT, 0 ) );
+ GTs.add( Util.convert( GT, 0 ) );
}
int count = 0;
for ( float[][] gt : GTs )
@@ -144,32 +144,14 @@ public class All_GT_Display< T extends RealType< T > & NativeType< T > > extends
chart.getScene().add( scatter );
}
- public < S extends RealType< S > & NativeType< S > > float[][] convert( RandomAccessibleInterval< S > input, int subtract )
- {
- float[][] array = new float[ ( int ) input.dimension( 1 ) ][ ( int ) input.dimension( 0 ) ];
- RandomAccess< S > access = input.randomAccess();
- for ( int x = 0; x < ( int ) input.dimension( 0 ); x++ )
- {
- for ( int y = 0; y < ( int ) input.dimension( 0 ); y++ )
- {
- float value = setPositionAndGet( access, x, y ).getRealFloat();
- if ( value + subtract != 0 )
- {
- array[ y ][ x ] = value;
- }
- }
- }
- return array;
- }
-
public int getCount( float[][] map )
{
int count = 0;
for ( int x = 0; x < map[ 0 ].length; x++ )
{
- for ( int y = 0; y < map.length; y++ )
+ for ( float[] floats : map )
{
- float mapValue = map[ y ][ x ];
+ float mapValue = floats[ x ];
if ( mapValue != 0 )
{
count++;
@@ -197,21 +179,11 @@ public class All_GT_Display< T extends RealType< T > & NativeType< T > > extends
return new Color( RGB[ 0 ], RGB[ 1 ], RGB[ 2 ] );
}
- public Color getColor( int[] RGB, float alpha )
- {
- return new Color( RGB[ 0 ], RGB[ 1 ], RGB[ 2 ], alpha );
- }
-
public Color getColor( String hex )
{
return getColor( hexToRGB( hex ) );
}
- public Color getColor( String hex, float alpha )
- {
- return getColor( hexToRGB( hex ), alpha );
-
- }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_GT_DifferenceDisplay.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_GT_DifferenceDisplay.java
index 842b7268d20396202adf8bcce2d35572b8547b95..f926bc267e73ee80662ee37b10b219c08d32d196 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_GT_DifferenceDisplay.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_GT_DifferenceDisplay.java
@@ -28,9 +28,9 @@
*/
package fr.pasteur.ida.zellige.utils.jzy3D;
+import fr.pasteur.ida.zellige.utils.Util;
import io.scif.img.IO;
import io.scif.img.SCIFIOImgPlus;
-import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
@@ -44,8 +44,6 @@ import org.jzy3d.maths.Coord3d;
import org.jzy3d.plot3d.primitives.Scatter;
import org.jzy3d.plot3d.rendering.canvas.Quality;
-import static fr.pasteur.ida.zellige.steps.Utils.setPositionAndGet;
-
public class HM_GT_DifferenceDisplay< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > > extends AbstractAnalysis
{
private final RandomAccessibleInterval< T > groundTruth;
@@ -73,7 +71,7 @@ public class HM_GT_DifferenceDisplay< T extends RealType< T > & NativeType< T >,
{
try
{
- HM_GT_DifferenceDisplay display = new HM_GT_DifferenceDisplay( groundTruth, heightMap );
+ HM_GT_DifferenceDisplay< T, R > display = new HM_GT_DifferenceDisplay<>( groundTruth, heightMap );
AnalysisLauncher.open( display );
}
catch ( Exception e )
@@ -83,18 +81,17 @@ public class HM_GT_DifferenceDisplay< T extends RealType< T > & NativeType< T >,
}
}
+ @SuppressWarnings( { "unchecked", "DuplicatedCode" } )
public static void main( String[] args )
{
String refImagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige Analysis\\files\\Curv\\curv_100\\phantoms_curvtest_zmap100_gt.tif";
String imagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige Analysis\\files\\Curv\\curv_100\\phantoms_curv100_HM_centralDerivative_noSmooth.tif";
- final SCIFIOImgPlus< ? > imgPlusRef = IO.openImgs( refImagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlusRef = IO.openAll( refImagePath ).get( 0 );
Img< FloatType > GT = ( Img< FloatType > ) imgPlusRef.getImg();
/* The raw image to test*/
-// final String imagePath = "doc/Cochlée1.tif";
-// final String imagePath = "C:\\Users\\ctrebeau\\Desktop\\phantom_tests_snr_1surf\\phantoms_1surf_snr0.mat.tif";
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
Img< FloatType > HM = ( Img< FloatType > ) imgPlus.getImg();
HM_GT_DifferenceDisplay.displayDiff( GT, HM );
@@ -103,8 +100,8 @@ public class HM_GT_DifferenceDisplay< T extends RealType< T > & NativeType< T >,
@Override
public void init()
{
- float[][] GT = convert( groundTruth, 0 );
- float[][] HM = convert( projection, 0 );
+ float[][] GT = Util.convert( groundTruth, 0 );
+ float[][] HM = Util.convert( projection, 0 );
int count = getCount( GT );
Coord3d[] points = new Coord3d[ count ];
Color[] colors = new Color[ count ];
@@ -168,33 +165,14 @@ public class HM_GT_DifferenceDisplay< T extends RealType< T > & NativeType< T >,
chart = AWTChartComponentFactory.chart( Quality.Advanced, "newt" );
chart.getScene().add( scatter );
}
-
- public < S extends RealType< S > & NativeType< S > > float[][] convert( RandomAccessibleInterval< S > input, int subtract )
- {
- float[][] array = new float[ ( int ) input.dimension( 1 ) ][ ( int ) input.dimension( 0 ) ];
- RandomAccess< S > access = input.randomAccess();
- for ( int x = 0; x < ( int ) input.dimension( 0 ); x++ )
- {
- for ( int y = 0; y < ( int ) input.dimension( 0 ); y++ )
- {
- float value = setPositionAndGet( access, x, y ).getRealFloat();
- if ( value + subtract != 0 )
- {
- array[ y ][ x ] = value;
- }
- }
- }
- return array;
- }
-
public int getCount( float[][] map )
{
int count = 0;
for ( int x = 0; x < map[ 0 ].length; x++ )
{
- for ( int y = 0; y < map.length; y++ )
+ for ( float[] floats : map )
{
- float mapValue = map[ y ][ x ];
+ float mapValue = floats[ x ];
if ( mapValue != 0 )
{
count++;
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_GT_Display.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_GT_Display.java
index 3548086a2b5715000612503e92958a9d194de981..a7f3e2bf61d87c06798ed9d5a1f9595e15c09c58 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_GT_Display.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_GT_Display.java
@@ -28,6 +28,7 @@
*/
package fr.pasteur.ida.zellige.utils.jzy3D;
+import fr.pasteur.ida.zellige.utils.Util;
import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.type.NativeType;
@@ -69,7 +70,7 @@ public class HM_GT_Display< T extends RealType< T > & NativeType< T >, R extends
{
try
{
- HM_GT_Display display = new HM_GT_Display( groundTruth, heightMap );
+ HM_GT_Display< T, R > display = new HM_GT_Display<>( groundTruth, heightMap );
AnalysisLauncher.open( display );
}
catch ( Exception e )
@@ -82,8 +83,8 @@ public class HM_GT_Display< T extends RealType< T > & NativeType< T >, R extends
@Override
public void init()
{
- float[][] GT = convert( groundTruth, 0 );
- float[][] HM = convert( projection, 0 );
+ float[][] GT = Util.convert( groundTruth, 0 );
+ float[][] HM = Util.convert( projection, 0 );
int count = getCount( GT, HM );
Coord3d[] points = new Coord3d[ count ];
Color[] colors = new Color[ count ];
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages.java
index ce43c76d8e8865830aa758d2c6a70df24061efb4..20e432b6809f65d98d6e8a8a0b01e31493346a93 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages.java
@@ -28,9 +28,9 @@
*/
package fr.pasteur.ida.zellige.utils.jzy3D;
+import fr.pasteur.ida.zellige.utils.Util;
import io.scif.img.IO;
import io.scif.img.SCIFIOImgPlus;
-import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
@@ -46,8 +46,6 @@ import org.jzy3d.plot3d.rendering.canvas.Quality;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import static fr.pasteur.ida.zellige.steps.Utils.setPositionAndGet;
-
public class HM_black_GT_distanceDisplay_realImages< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > > extends AbstractAnalysis
{
private final static Logger LOGGER = LoggerFactory.getLogger( HM_black_GT_distanceDisplay_realImages.class );
@@ -76,7 +74,7 @@ public class HM_black_GT_distanceDisplay_realImages< T extends RealType< T > & N
{
try
{
- HM_black_GT_distanceDisplay_realImages display = new HM_black_GT_distanceDisplay_realImages( groundTruth, heightMap );
+ HM_black_GT_distanceDisplay_realImages< T, R > display = new HM_black_GT_distanceDisplay_realImages<>( groundTruth, heightMap );
AnalysisLauncher.open( display );
}
catch ( Exception e )
@@ -86,18 +84,18 @@ public class HM_black_GT_distanceDisplay_realImages< T extends RealType< T > & N
}
}
+
+ @SuppressWarnings( { "unchecked", "DuplicatedCode" } )
public static void main( String[] args )
{
String refImagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige Analysis\\files\\Curv\\curv_100\\phantoms_curvtest_zmap100_gt.tif";
String imagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige Analysis\\files\\Curv\\curv_100\\phantoms_curv100_HM_centralDerivative_noSmooth.tif";
- final SCIFIOImgPlus< ? > imgPlusRef = IO.openImgs( refImagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlusRef = IO.openAll( refImagePath ).get( 0 );
Img< FloatType > GT = ( Img< FloatType > ) imgPlusRef.getImg();
/* The raw image to test*/
-// final String imagePath = "doc/Cochlée1.tif";
-// final String imagePath = "C:\\Users\\ctrebeau\\Desktop\\phantom_tests_snr_1surf\\phantoms_1surf_snr0.mat.tif";
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
Img< FloatType > HM = ( Img< FloatType > ) imgPlus.getImg();
HM_black_GT_distanceDisplay_realImages.displayDiff( GT, HM );
@@ -106,8 +104,8 @@ public class HM_black_GT_distanceDisplay_realImages< T extends RealType< T > & N
@Override
public void init()
{
- float[][] GT = convert( groundTruth, 0 );
- float[][] HM = convert( projection, 0 );
+ float[][] GT = Util.convert( groundTruth, 0 );
+ float[][] HM = Util.convert( projection, 0 );
int count = getCount( GT ) + getCount( HM );
Coord3d[] points = new Coord3d[ count ];
Color[] colors = new Color[ count ];
@@ -177,32 +175,15 @@ public class HM_black_GT_distanceDisplay_realImages< T extends RealType< T > & N
chart.getScene().add( scatter );
}
- public < S extends RealType< S > & NativeType< S > > float[][] convert( RandomAccessibleInterval< S > input, int subtract )
- {
- float[][] array = new float[ ( int ) input.dimension( 1 ) ][ ( int ) input.dimension( 0 ) ];
- RandomAccess< S > access = input.randomAccess();
- for ( int x = 0; x < ( int ) input.dimension( 0 ); x++ )
- {
- for ( int y = 0; y < ( int ) input.dimension( 0 ); y++ )
- {
- float value = setPositionAndGet( access, x, y ).getRealFloat();
- if ( value + subtract != 0 )
- {
- array[ y ][ x ] = value;
- }
- }
- }
- return array;
- }
public int getCount( float[][] map )
{
int count = 0;
for ( int x = 0; x < map[ 0 ].length; x++ )
{
- for ( int y = 0; y < map.length; y++ )
+ for ( float[] floats : map )
{
- float mapValue = map[ y ][ x ];
+ float mapValue = floats[ x ];
if ( mapValue != 0 )
{
count++;
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages_2D.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages_2D.java
index d70d85e4a8d7ef7fa7cb3b50906e5bc6de99fa35..cca852ffde11cd327c0dff71c40f1100aa92a46b 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages_2D.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages_2D.java
@@ -28,9 +28,9 @@
*/
package fr.pasteur.ida.zellige.utils.jzy3D;
+import fr.pasteur.ida.zellige.utils.Util;
import io.scif.img.IO;
import io.scif.img.SCIFIOImgPlus;
-import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
@@ -46,8 +46,6 @@ import org.jzy3d.plot3d.rendering.canvas.Quality;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import static fr.pasteur.ida.zellige.steps.Utils.setPositionAndGet;
-
public class HM_black_GT_distanceDisplay_realImages_2D< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > > extends AbstractAnalysis
{
private final static Logger LOGGER = LoggerFactory.getLogger( HM_black_GT_distanceDisplay_realImages_2D.class );
@@ -76,7 +74,7 @@ public class HM_black_GT_distanceDisplay_realImages_2D< T extends RealType< T >
{
try
{
- HM_black_GT_distanceDisplay_realImages_2D display = new HM_black_GT_distanceDisplay_realImages_2D( groundTruth, heightMap );
+ HM_black_GT_distanceDisplay_realImages_2D< T, R > display = new HM_black_GT_distanceDisplay_realImages_2D<>( groundTruth, heightMap );
AnalysisLauncher.open( display );
}
catch ( Exception e )
@@ -86,18 +84,17 @@ public class HM_black_GT_distanceDisplay_realImages_2D< T extends RealType< T >
}
}
+ @SuppressWarnings( "unchecked" )
public static void main( String[] args )
{
String refImagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\SNR\\snr_010\\multiSurface\\phantoms_snr10.mat_HM_02.tif";
String imagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\SNR\\snr_010\\multiSurface\\phantoms_snrtest_zmap3_gt.tif";
- final SCIFIOImgPlus< ? > imgPlusRef = IO.openImgs( refImagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlusRef = IO.openAll( refImagePath ).get( 0 );
Img< FloatType > GT = ( Img< FloatType > ) imgPlusRef.getImg();
/* The raw image to test*/
-// final String imagePath = "doc/Cochlée1.tif";
-// final String imagePath = "C:\\Users\\ctrebeau\\Desktop\\phantom_tests_snr_1surf\\phantoms_1surf_snr0.mat.tif";
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
Img< FloatType > HM = ( Img< FloatType > ) imgPlus.getImg();
HM_black_GT_distanceDisplay_realImages_2D.displayDiff( GT, HM );
@@ -106,8 +103,8 @@ public class HM_black_GT_distanceDisplay_realImages_2D< T extends RealType< T >
@Override
public void init()
{
- float[][] GT = convert( groundTruth, 0 );
- float[][] HM = convert( projection, 0 );
+ float[][] GT = Util.convert( groundTruth, 0 );
+ float[][] HM = Util.convert( projection, 0 );
int count = getCount( GT ) + getCount( HM );
Coord3d[] points = new Coord3d[ count ];
Color[] colors = new Color[ count ];
@@ -177,32 +174,14 @@ public class HM_black_GT_distanceDisplay_realImages_2D< T extends RealType< T >
chart.getScene().add( scatter );
}
- public < S extends RealType< S > & NativeType< S > > float[][] convert( RandomAccessibleInterval< S > input, int subtract )
- {
- float[][] array = new float[ ( int ) input.dimension( 1 ) ][ ( int ) input.dimension( 0 ) ];
- RandomAccess< S > access = input.randomAccess();
- for ( int x = 0; x < ( int ) input.dimension( 0 ); x++ )
- {
- for ( int y = 0; y < ( int ) input.dimension( 0 ); y++ )
- {
- float value = setPositionAndGet( access, x, y ).getRealFloat();
- if ( value + subtract != 0 )
- {
- array[ y ][ x ] = value;
- }
- }
- }
- return array;
- }
-
public int getCount( float[][] map )
{
int count = 0;
for ( int x = 0; x < map[ 0 ].length; x++ )
{
- for ( int y = 0; y < map.length; y++ )
+ for ( float[] floats : map )
{
- float mapValue = map[ y ][ x ];
+ float mapValue = floats[ x ];
if ( mapValue != 0 )
{
count++;
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HMvsGT_Display.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HMvsGT_Display.java
index f18d3d6c0cce1eb6afd7c6543712f513be814781..2e05e87feb58d8b91d80d591ec317c6a1c87092d 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HMvsGT_Display.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HMvsGT_Display.java
@@ -28,9 +28,9 @@
*/
package fr.pasteur.ida.zellige.utils.jzy3D;
+import fr.pasteur.ida.zellige.utils.Util;
import io.scif.img.IO;
import io.scif.img.SCIFIOImgPlus;
-import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
@@ -46,20 +46,19 @@ import org.jzy3d.plot3d.rendering.canvas.Quality;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import static fr.pasteur.ida.zellige.steps.Utils.setPositionAndGet;
-
public class HMvsGT_Display< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > > extends AbstractAnalysis
{
private final static Logger LOGGER = LoggerFactory.getLogger( HMvsGT_Display.class );
private final RandomAccessibleInterval< T > groundTruth;
private final RandomAccessibleInterval< R > projection;
- private final int subtract = - 1;
+ private final int subtract;
public HMvsGT_Display( RandomAccessibleInterval< T > groundTruth,
- RandomAccessibleInterval< R > heightMap )
+ RandomAccessibleInterval< R > heightMap, int subtract )
{
this.groundTruth = groundTruth;
this.projection = heightMap;
+ this.subtract = subtract;
init();
}
@@ -72,12 +71,12 @@ public class HMvsGT_Display< T extends RealType< T > & NativeType< T >, R extend
* @param <R> the ground truth type
*/
public static < T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > > void displayDiff( RandomAccessibleInterval< T > groundTruth,
- RandomAccessibleInterval< R > heightMap )
+ RandomAccessibleInterval< R > heightMap, int subtract )
{
{
try
{
- HMvsGT_Display display = new HMvsGT_Display( groundTruth, heightMap );
+ HMvsGT_Display< T, R > display = new HMvsGT_Display<>( groundTruth, heightMap, subtract );
AnalysisLauncher.open( display );
}
catch ( Exception e )
@@ -87,28 +86,27 @@ public class HMvsGT_Display< T extends RealType< T > & NativeType< T >, R extend
}
}
+ @SuppressWarnings( "unchecked" )
public static void main( String[] args )
{
String pathGT = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Organoid\\Organoid_GT_HM2.tif";
String pathHM = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\Organoid\\Organoid_HM_0.tif";
- final SCIFIOImgPlus< ? > imgPlusRef = IO.openImgs( pathGT ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlusRef = IO.openAll( pathGT ).get( 0 );
Img< FloatType > GT = ( Img< FloatType > ) imgPlusRef.getImg();
/* The raw image to test*/
-// final String imagePath = "doc/Cochlée1.tif";
-// final String imagePath = "C:\\Users\\ctrebeau\\Desktop\\phantom_tests_snr_1surf\\phantoms_1surf_snr0.mat.tif";
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( pathHM ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( pathHM ).get( 0 );
Img< FloatType > HM = ( Img< FloatType > ) imgPlus.getImg();
- HMvsGT_Display.displayDiff( GT, HM );
+ HMvsGT_Display.displayDiff( GT, HM, - 1 );
}
@Override
public void init()
{
- float[][] GT = convert( groundTruth, 0 );
- float[][] HM = convert( projection, 0 );
+ float[][] GT = Util.convert( groundTruth, 0 );
+ float[][] HM = Util.convert( projection, 0 );
int count = getCount( GT ) + getCount( HM ) + 2;
Coord3d[] points = new Coord3d[ count ];
Color[] colors = new Color[ count ];
@@ -147,32 +145,14 @@ public class HMvsGT_Display< T extends RealType< T > & NativeType< T >, R extend
chart.getScene().add( scatter );
}
- public < S extends RealType< S > & NativeType< S > > float[][] convert( RandomAccessibleInterval< S > input, int subtract )
- {
- float[][] array = new float[ ( int ) input.dimension( 1 ) ][ ( int ) input.dimension( 0 ) ];
- RandomAccess< S > access = input.randomAccess();
- for ( int x = 0; x < ( int ) input.dimension( 0 ); x++ )
- {
- for ( int y = 0; y < ( int ) input.dimension( 1 ); y++ )
- {
- float value = setPositionAndGet( access, x, y ).getRealFloat();
- if ( value + subtract != 0 )
- {
- array[ y ][ x ] = value;
- }
- }
- }
- return array;
- }
-
public int getCount( float[][] map )
{
int count = 0;
for ( int x = 0; x < map[ 0 ].length; x++ )
{
- for ( int y = 0; y < map.length; y++ )
+ for ( float[] floats : map )
{
- float mapValue = map[ y ][ x ];
+ float mapValue = floats[ x ];
if ( mapValue != 0 )
{
count++;
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HeightMapArrayWriter.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HeightMapArrayWriter.java
index ceabd5a8431e32a596f3c11a946a84d1cbb9f167..70559880d74c654cc5dd529ada63f2ee49da8bfb 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HeightMapArrayWriter.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HeightMapArrayWriter.java
@@ -61,7 +61,7 @@ public class HeightMapArrayWriter< T extends RealType< T > & NativeType< T > > e
{
try
{
- new HeightMapArrayWriter( surface, originalInput, surfaceNumber );
+ new HeightMapArrayWriter<>( surface, originalInput, surfaceNumber );
}
catch ( Exception e )
{
@@ -69,12 +69,14 @@ public class HeightMapArrayWriter< T extends RealType< T > & NativeType< T > > e
}
}
+
+ @SuppressWarnings( "unchecked" )
public static < T extends RealType< T > & NativeType< T > > void main( String[] args )
{
final String imagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\Organoid\\Organoid_GT_HM1.tif"; /* The image path goes here !!!! */
LOGGER.debug( imagePath );
/* JY version for opening files. */
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
final Img< T > heightMap = ( Img< T > ) imgPlus.getImg();
writeHeightMap( heightMap, imgPlus.getName(), 2 );
@@ -87,7 +89,7 @@ public class HeightMapArrayWriter< T extends RealType< T > & NativeType< T > > e
if ( surface != null )
{
CSVWriter csvWriter =
- new CSVWriter( originalInput + "_" + "surface" );
+ new CSVWriter( originalInput + "_" + "surface " + surfaceNumber );
Cursor< T > cursor = surface.cursor();
csvWriter.writeToFile( new String[]{ "x", "y", "z" } );
while ( cursor.hasNext() )
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/LocalMaximumsDisplay.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/LocalMaximumsDisplay.java
index 98c5acd7e539acb4f3631d05cbd3b7bfe19580dc..31bd8bab4ebefe73a71951c2200e9cede2e7ec08 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/LocalMaximumsDisplay.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/LocalMaximumsDisplay.java
@@ -74,9 +74,6 @@ public class LocalMaximumsDisplay extends AbstractAnalysis
}
}
// else
-// {
-// LOGGER.warn( "No Graphics Environment detected" );
-// }
}
@Override
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/DistanceImageWriter.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/DistanceImageWriter.java
index 3d458fae73e9d65aacf741f3458ac071936ecefd..4f6d5ef13069d13a46518a49b75ef804872c795d 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/test/DistanceImageWriter.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/DistanceImageWriter.java
@@ -28,10 +28,10 @@
*/
package fr.pasteur.ida.zellige.utils.test;
+import fr.pasteur.ida.zellige.utils.Util;
import ij.ImageJ;
import io.scif.img.IO;
import io.scif.img.SCIFIOImgPlus;
-import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.img.display.imagej.ImageJFunctions;
@@ -43,8 +43,6 @@ import org.slf4j.LoggerFactory;
import java.io.IOException;
-import static fr.pasteur.ida.zellige.steps.Utils.setPositionAndGet;
-
public class DistanceImageWriter< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
{
@@ -52,40 +50,39 @@ public class DistanceImageWriter< T extends RealType< T > & NativeType< T >, R e
private final RandomAccessibleInterval< T > groundTruth;
private final RandomAccessibleInterval< R > projection;
private final String fileName;
- private final String[][] distances;
- private final int subtract = - 1;
+ private final int subtract;
public DistanceImageWriter( RandomAccessibleInterval< T > groundTruth,
- RandomAccessibleInterval< R > heightMap, String fileName )
+ RandomAccessibleInterval< R > heightMap, String fileName, int subtract )
{
this.groundTruth = groundTruth;
this.projection = heightMap;
this.fileName = fileName;
- distances = new String[ ( int ) groundTruth.dimension( 1 ) ][ ( int ) groundTruth.dimension( 0 ) ];
+ this.subtract = subtract;
}
public static < T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
void create( RandomAccessibleInterval< T > groundTruth,
- RandomAccessibleInterval< R > heightMap, String fileName ) throws IOException
+ RandomAccessibleInterval< R > heightMap, String fileName, int subtract ) throws IOException
{
- DistanceImageWriter writer = new DistanceImageWriter( groundTruth, heightMap, fileName );
+ DistanceImageWriter< T, R > writer = new DistanceImageWriter<>( groundTruth, heightMap, fileName, subtract );
writer.run();
-// writer.writeInfile();
}
+ @SuppressWarnings( { "unchecked", "DuplicatedCode" } )
public static void main( String[] args ) throws IOException
{
String pathGT = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\GT\\Ground truth Height map_4_crop.tif";
String pathHM = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\Mouche\\Mouche_HM_3.tif";
- final SCIFIOImgPlus< ? > imgPlusRef = IO.openImgs( pathGT ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlusRef = IO.openAll( pathGT ).get( 0 );
Img< FloatType > GT = ( Img< FloatType > ) imgPlusRef.getImg();
new ImageJ();
ImageJFunctions.show( GT );
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( pathHM ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( pathHM ).get( 0 );
Img< FloatType > HM = ( Img< FloatType > ) imgPlus.getImg();
ImageJFunctions.show( HM );
- DistanceImageWriter.create( GT, HM, "Mouche_distance4_crop" );
+ DistanceImageWriter.create( GT, HM, "Mouche_distance4_crop", - 1 );
}
public void run() throws IOException
@@ -93,8 +90,8 @@ public class DistanceImageWriter< T extends RealType< T > & NativeType< T >, R e
CSVWriter writer = new CSVWriter( fileName );
String[] header = { "x", "y", "distance" };
writer.writeToFile( header );
- float[][] GT = convert( groundTruth, 0 );
- float[][] HM = convert( projection, 0 );
+ float[][] GT = Util.convert( groundTruth, 0 );
+ float[][] HM = Util.convert( projection, 0 );
double mse = 0;
int count = 0;
for ( int x = 0; x < GT[ 0 ].length; x++ )
@@ -107,7 +104,6 @@ public class DistanceImageWriter< T extends RealType< T > & NativeType< T >, R e
{
double distance = Math.abs( GTValue - ( HMValue + subtract ) );
writer.writeToFile( new String[]{ String.valueOf( x ), String.valueOf( y ), String.valueOf( distance ) } );
- distances[ y ][ x ] = String.valueOf( distance );
mse += Math.pow( distance, 2 );
count++;
}
@@ -122,22 +118,4 @@ public class DistanceImageWriter< T extends RealType< T > & NativeType< T >, R e
writer.close();
}
-
- public < S extends RealType< S > & NativeType< S > > float[][] convert( RandomAccessibleInterval< S > input, int subtract )
- {
- float[][] array = new float[ ( int ) input.dimension( 1 ) ][ ( int ) input.dimension( 0 ) ];
- RandomAccess< S > access = input.randomAccess();
- for ( int x = 0; x < ( int ) input.dimension( 0 ); x++ )
- {
- for ( int y = 0; y < ( int ) input.dimension( 1 ); y++ )
- {
- float value = setPositionAndGet( access, x, y ).getRealFloat();
- if ( value + subtract != 0 )
- {
- array[ y ][ x ] = value;
- }
- }
- }
- return array;
- }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/GroundTruthConversion.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/GroundTruthConversion.java
index 510c1ada9ec740047f397afa0bc73a783098b7ac..4427c1f19320c6f1bb288848ae62ef03df01d810 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/test/GroundTruthConversion.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/GroundTruthConversion.java
@@ -40,15 +40,16 @@ import net.imglib2.type.numeric.real.FloatType;
public class GroundTruthConversion
{
+ @SuppressWarnings( "unchecked" )
public static void main( String[] args )
{
- ImageJ ij = new ImageJ();
+ new ImageJ();
final String refImagePath = "doc/Ground truth Height map.tif";
- final SCIFIOImgPlus< ? > refImgPlus = IO.openImgs( refImagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > refImgPlus = IO.openAll( refImagePath ).get( 0 );
Img< FloatType > img = ( Img< FloatType > ) refImgPlus.getImg();
ImageJFunctions.show( img, "Ground truth" );
final String maskPath = "doc/STK_BG_ROI.tif";
- final SCIFIOImgPlus< ? > maskImgPlus = IO.openImgs( maskPath ).get( 0 );
+ final SCIFIOImgPlus< ? > maskImgPlus = IO.openAll( maskPath ).get( 0 );
Img< UnsignedByteType > mask = ( Img< UnsignedByteType > ) maskImgPlus.getImg();
ImageJFunctions.show( mask, "BG mask" );
Cursor< UnsignedByteType > cursor = mask.localizingCursor();
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/ParameterSweepFiles.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/ParameterSweepFiles.java
index 9d5fab1b420f93f6ae127e277cabb7385eaf4bc8..f7f95cfd4e723e2f6692c31ffbe20008217d4b20 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/test/ParameterSweepFiles.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/ParameterSweepFiles.java
@@ -45,6 +45,7 @@ public class ParameterSweepFiles< T extends RealType< T > & NativeType< T >, R e
private final Img< R > tested;
private final String path;
+ @SuppressWarnings( "unchecked" )
public ParameterSweepFiles( final String[] refImagePath, final String imagePath, String destinationPath )
{
/* The reference height maps*/
@@ -52,12 +53,12 @@ public class ParameterSweepFiles< T extends RealType< T > & NativeType< T >, R e
for ( String path : refImagePath )
{
LOGGER.debug( path );
- SCIFIOImgPlus< ? > refImgPlus = IO.openImgs( path ).get( 0 );
+ SCIFIOImgPlus< ? > refImgPlus = IO.openAll( path ).get( 0 );
refs.add( ( Img< T > ) refImgPlus.getImg() );
}
/* The raw image to test*/
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
tested = ( Img< R > ) imgPlus.getImg();
this.path = destinationPath;
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/RMSEAndCoverageComputation.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/RMSEAndCoverageComputation.java
index 0399011f2ab3aeb166d6594b3f1e642ad962c2a8..b8b01fe35d81a20af3bd52e3e7101265591d476a 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/test/RMSEAndCoverageComputation.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/RMSEAndCoverageComputation.java
@@ -202,19 +202,20 @@ public class RMSEAndCoverageComputation< T extends RealType< T > & NativeType< T
return projection;
}
+ @SuppressWarnings( { "unchecked", "DuplicatedCode" } )
public static void main( String[] args ) throws NotAnHeightMapException, DifferentReferenceTestedSizeException
{
- String pathGT = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Covid Zellige\\C2-MucilairB spike zo1 J4 Sars-3_Ground truth Height map.tif";
- String pathHM = "C:\\Users\\ctrebeau\\Nextcloud\\Zellige\\ResultatsJYT\\C2-MucilairB_spike_zo1_J4_Sars-3_SME_ZMAP_ref1_nCH1_CF.tif";
- final SCIFIOImgPlus< ? > imgPlusRef = IO.openImgs( pathGT ).get( 0 );
+ String pathGT = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\GT\\Ground truth Height map_4_crop.tif";
+ String pathHM = "C:\\Users\\ctrebeau\\Desktop\\Figures mouche dif values\\blurxy10\\Raw_HM_7.tif";
+ final SCIFIOImgPlus< ? > imgPlusRef = IO.openAll( pathGT ).get( 0 );
Img< FloatType > GT = ( Img< FloatType > ) imgPlusRef.getImg();
new ImageJ();
ImageJFunctions.show( GT );
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( pathHM ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( pathHM ).get( 0 );
Img< FloatType > HM = ( Img< FloatType > ) imgPlus.getImg();
ImageJFunctions.show( HM );
- RMSEAndCoverageComputation computation = new RMSEAndCoverageComputation( GT, 0, HM );
+ RMSEAndCoverageComputation< FloatType, FloatType > computation = new RMSEAndCoverageComputation<>( GT, 0, HM );
computation.compute();
LOGGER.debug( "RMSE = " + computation.RMSE );
LOGGER.debug( "Coverage = " + computation.coverage );
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/ZelligePipelineAnalyse.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/ZelligePipelineAnalyse.java
index 96700df097e147f3f749d92ad5086803957d6c65..d56bd7abaeff302adfa8ddedf1f51189f233afe0 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/test/ZelligePipelineAnalyse.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/ZelligePipelineAnalyse.java
@@ -59,6 +59,7 @@ public class ZelligePipelineAnalyse< T extends RealType< T > & NativeType< T >,
errorList = new ArrayList<>();
}
+ @SuppressWarnings( { "unchecked", "rawtypes" } )
public void run( final ZParameters parameters, final Img< R > tested, final ArrayList< Img > GT ) throws Exception
{
long startTime = System.currentTimeMillis();
@@ -83,13 +84,12 @@ public class ZelligePipelineAnalyse< T extends RealType< T > & NativeType< T >,
LOGGER.debug( "Construction processing time : {} ms", constructionProcessingTime );
ArrayList< ReferenceSurface< R > > surfaces = extraction.getReferenceSurfaces();
- for ( Img< T > refImage : GT )// Parsing of GT list.
+ for ( Img refImage : GT )// Parsing of GT list.
{
index++;
ArrayList< RMSEAndCoverageComputation< T, UnsignedShortType > > tempList = new ArrayList<>();
for ( ReferenceSurface< R > rf : surfaces )// Test of each reconstructed surface
{
-// ImageJFunctions.show(rf.getZMap(), "Zmap");
RMSEAndCoverageComputation< T, UnsignedShortType > errors =
new RMSEAndCoverageComputation<>( refImage, index, rf.getzMap() );
errors.compute();
@@ -109,7 +109,7 @@ public class ZelligePipelineAnalyse< T extends RealType< T > & NativeType< T >,
stopTime = System.currentTimeMillis();
LOGGER.debug( "An NoSurfaceFoundException was raised" );
constructionProcessingTime = stopTime - extractionStartTime;
- for ( Img< T > refImage : GT )// Parsing of GT list.
+ for ( int i = 0; i < GT.size(); i++ )
{
index++;
RMSEAndCoverageComputation< T, UnsignedShortType > errors =
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Construction.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Construction.fxml
index 9ffbca1aa051bae8449da9de52ba6ba9731e6372..557e68b8b480d3675b68e2527a19fdd560aaced4 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Construction.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Construction.fxml
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--suppress JavaFxDefaultTag -->
<?import fr.pasteur.ida.zellige.gui.*?>
<?import javafx.geometry.Insets?>
<?import javafx.scene.control.Label?>
@@ -7,7 +8,7 @@
<StepPanel xmlns:fx="http://javafx.com/fxml" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
minHeight="-Infinity" minWidth="-Infinity" name="Construction" prefHeight="369.0" prefWidth="405.0"
stylesheets="@theme2.css" xmlns="http://javafx.com/javafx"
- fx:controller="fr.pasteur.ida.zellige.gui.ConstructionController">
+ fx:controller="fr.pasteur.ida.zellige.gui.controller.ConstructionController">
<children>
<GridPane alignment="CENTER" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
minWidth="-Infinity" prefHeight="333.0" prefWidth="405.0" vgap="15.0">
@@ -69,8 +70,8 @@
prefHeight="36.0" prefWidth="340.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS"
GridPane.rowIndex="2" GridPane.vgrow="ALWAYS">
- <ParameterSliderDouble fx:id="surfaceSize" default="0.7" increment="0.05" interval="%INTERVAL3"
- major="0.2" max="1" min="0" minor="1" name="Surface min size"/>
+ <ParameterSliderInteger fx:id="surfaceSize" default="50" increment="1" interval="%INTERVAL4"
+ major="20" max="100" min="0" minor="3" name="Surface min size"/>
</VBox>
<Label alignment="CENTER" minWidth="-Infinity" prefHeight="14.0" prefWidth="100.0" rotate="-90.0"
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Display.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Display.fxml
index 6daef4a3cf2b317049f9d10bd6564adfb80fb010..511fbddd9357da31ac8c1d72515bc4db553f2881 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Display.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Display.fxml
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--suppress JavaFxDefaultTag -->
<?import fr.pasteur.ida.zellige.gui.*?>
<?import javafx.geometry.Insets?>
<?import javafx.scene.control.Label?>
@@ -37,7 +38,6 @@
</Label>
</top>
<styleClass>
- <String fx:value="step_border"/>
<String fx:value="step-title"/>
</styleClass>
</BorderPane>
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml
index 901d9de2731a4063bcc0ae22bb6ee525330e111c..b22f97166fbc38cef4cce29a62376af30f8fe166 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--suppress JavaFxDefaultTag, JavaFxUnresolvedFxIdReference -->
<?import javafx.geometry.Insets?>
<?import javafx.scene.control.*?>
<?import javafx.scene.image.Image?>
@@ -9,7 +10,7 @@
<VBox xmlns:fx="http://javafx.com/fxml" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
minHeight="-Infinity" minWidth="-Infinity" prefHeight="786.0" prefWidth="866.0" spacing="5.0"
stylesheets="@theme2.css" xmlns="http://javafx.com/javafx"
- fx:controller="fr.pasteur.ida.zellige.gui.MainController">
+ fx:controller="fr.pasteur.ida.zellige.gui.controller.MainController">
<padding>
<Insets left="10.0" right="10.0" top="5.0"/>
</padding>
@@ -30,7 +31,7 @@
</HBox>
<HBox alignment="CENTER_RIGHT" prefHeight="45.0" prefWidth="333.0" spacing="10.0">
<children>
- <Button fx:id="load" mnemonicParsing="false" onAction="#loadParameters" text="Load parameters">
+ <Button mnemonicParsing="false" onAction="#loadParameters" text="Load parameters">
<graphic>
<ImageView fitHeight="15.0" fitWidth="22.0" pickOnBounds="true" preserveRatio="true">
<image>
@@ -39,7 +40,7 @@
</ImageView>
</graphic>
</Button>
- <Button fx:id="save" mnemonicParsing="false" onAction="#saveParameters" text="Save Parameters">
+ <Button mnemonicParsing="false" onAction="#saveParameters" text="Save Parameters">
<graphic>
<ImageView fitHeight="15.0" fitWidth="26.0" pickOnBounds="true" preserveRatio="true">
<image>
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Projection.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Projection.fxml
index f96f29fd022265a0f2a639bcb5cb51143c7887bc..db6ff07a78a7dac75d7d3a88d6592d14f3d5ab90 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Projection.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Projection.fxml
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--suppress JavaFxDefaultTag -->
<?import fr.pasteur.ida.zellige.gui.*?>
<?import javafx.geometry.*?>
<?import javafx.scene.control.*?>
@@ -7,7 +8,7 @@
<StepPanel xmlns:fx="http://javafx.com/fxml" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
minHeight="-Infinity" minWidth="-Infinity" name="Projection" prefHeight="342.0" prefWidth="400.0"
stylesheets="@theme2.css" xmlns="http://javafx.com/javafx"
- fx:controller="fr.pasteur.ida.zellige.gui.ProjectionController">
+ fx:controller="fr.pasteur.ida.zellige.gui.controller.ProjectionController">
<children>
<VBox alignment="CENTER" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
minHeight="-Infinity" prefHeight="312.0" prefWidth="389.0">
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Selection.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Selection.fxml
index 13dfafd8bde5896ba08219f9b018e50183b28128..08e23d88d8158eb75380a12fda16204f4cac4b9b 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Selection.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Selection.fxml
@@ -1,13 +1,14 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--suppress JavaFxDefaultTag -->
<?import fr.pasteur.ida.zellige.gui.*?>
<?import javafx.geometry.Insets?>
<?import javafx.scene.control.Label?>
<?import javafx.scene.layout.*?>
-<StepPanel xmlns:fx="http://javafx.com/fxml" fillWidth="true" maxHeight="-Infinity" maxWidth="-Infinity"
+<StepPanel xmlns:fx="http://javafx.com/fxml" maxHeight="-Infinity" maxWidth="-Infinity"
minHeight="-Infinity" minWidth="-Infinity" name="Selection" prefHeight="336.0" prefWidth="815.0"
spacing="5.0" stylesheets="@theme2.css" xmlns="http://javafx.com/javafx"
- fx:controller="fr.pasteur.ida.zellige.gui.SelectionController">
+ fx:controller="fr.pasteur.ida.zellige.gui.controller.SelectionController">
<children>
<HBox alignment="CENTER" minHeight="-Infinity" minWidth="-Infinity" prefHeight="293.0" prefWidth="815.0">
<children>
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/StepPanel.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/StepPanel.fxml
index 1260545552c3b9ca2643961b5b6f467fa5f4bf14..b49b698657c34246376cdc01c912fcea90b2cca6 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/StepPanel.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/StepPanel.fxml
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--suppress JavaFxDefaultTag -->
<?import javafx.geometry.Insets?>
<?import javafx.scene.control.Label?>
<?import javafx.scene.control.Separator?>
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/ZSlicesSlider.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/ZSlicesSlider.fxml
index 7207d188abdcaf802102f1714048d39a62b577a2..988c4996e1390cd5c0b99e852144befdfff02adc 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/ZSlicesSlider.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/ZSlicesSlider.fxml
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--suppress JavaFxDefaultTag -->
<?import javafx.scene.control.Slider?>
<?import javafx.scene.layout.FlowPane?>
<fx:root xmlns:fx="http://javafx.com/fxml" alignment="CENTER" columnHalignment="CENTER" prefHeight="47.0"
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/theme2.css b/src/main/resources/fr.pasteur.ida.zellige.gui.view/theme2.css
index d1808955d3b4492bdefe1779ae476b5a84223b54..24b3e969eba0a59cc15557d7a3aadb5e98e005cf 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/theme2.css
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/theme2.css
@@ -27,6 +27,7 @@
* #L%
*/
+/*noinspection CssInvalidFunction*/
.root {
-fx-base: #ececec;
-fx-color: -fx-base;
@@ -92,6 +93,7 @@ parameter-slider-integer.label {
}
+/*noinspection ALL*/
.slider .thumb {
-fx-background-color: linear-gradient(to bottom, derive(-fx-text-box-border, -20%), derive(-fx-text-box-border, -30%)),
-fx-inner-border,
@@ -112,6 +114,7 @@ parameter-slider-integer.label {
-fx-background-radius: 1.0em; /* makes sure this remains circular */
}
+/*noinspection CssInvalidFunction*/
.slider .track {
-fx-background-color: #484c54A3,
linear-gradient(to bottom, derive(-fx-text-box-border, -10%), -fx-text-box-border),
@@ -144,6 +147,7 @@ parameter-slider-integer.label {
-fx-alignment: center;
}
+/*noinspection CssInvalidPseudoSelector*/
.text-input:error {
-fx-text-fill: black;
-fx-border-insets: 0;
@@ -153,6 +157,7 @@ parameter-slider-integer.label {
-fx-background-color: derive(red, 99%);
}
+/*noinspection CssInvalidFunction*/
.text-input:focused {
-fx-highlight-fill: -fx-accent;
-fx-highlight-text-fill: white;
diff --git a/src/main/resources/gui.properties b/src/main/resources/gui.properties
index b559d6b7142be08fb7f9350fe826b80d9e48cb7f..d6c80ea2c53cd339622ae413785fc02cb351ab6e 100644
--- a/src/main/resources/gui.properties
+++ b/src/main/resources/gui.properties
@@ -32,4 +32,5 @@ INTERVAL1=[0-9]|[1-4][0-9]|[5][0]
INTERVAL2=[0-9]|[1][0]
#[0.0 - 1.0]
INTERVAL3=0?\\.[0-9]|[1]\\.[0]?|[0]|[1]
-#
+#[0 - 100]
+INTERVAL4=[0-9]|[1-9][0-9]|[1][0][0]
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/DoubleParameterSweep.java b/src/test/java/fr/pasteur/ida/zellige/behavior/DoubleParameterSweep.java
deleted file mode 100644
index dba9cef9a6cda36abedcba346b1c835b0275e2f4..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/DoubleParameterSweep.java
+++ /dev/null
@@ -1,137 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-//package fr.pasteur.ida.zellige.behavior;
-//
-//import fr.pasteur.ida.zellige.ReferenceSurfaceExtraction;
-//import fr.pasteur.ida.zellige.utils.test.ZParameters;
-//import fr.pasteur.ida.zellige.utils.test.CSVWriter;
-//import fr.pasteur.ida.zellige.utils.test.ParameterSweepFiles;
-//import fr.pasteur.ida.zellige.utils.test.RMSEAndCoverageComputation;
-//import fr.pasteur.ida.zellige.utils.test.ZelligePipelineAnalyse;
-//import net.imglib2.img.Img;
-//import net.imglib2.type.numeric.real.FloatType;
-//import org.junit.jupiter.api.AfterAll;
-//import org.junit.jupiter.api.BeforeAll;
-//import org.junit.jupiter.params.ParameterizedTest;
-//import org.junit.jupiter.params.provider.CsvFileSource;
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
-//
-//import java.io.IOException;
-//import java.util.ArrayList;
-//
-//
-//public class DoubleParameterSweep
-//{
-//
-// private final static Logger LOGGER = LoggerFactory.getLogger( DoubleParameterSweep.class );
-// static ArrayList< Img< FloatType > > ref;
-// static Img< FloatType > tested;
-// private static CSVWriter writer;
-//
-// @BeforeAll
-// static void init() throws IOException
-// {
-// String imagePath = "src/test/resources/Mouche_c01_f0001_p013/STK_Mouche_c01_f0001_p013.tif";
-// final String[] refImagePath = new String[]{
-// "src/test/resources/Mouche_c01_f0001_p013/Ground truth Height map_1.tif",
-// "src/test/resources/Mouche_c01_f0001_p013/Ground truth Height map_2.tif",
-// "src/test/resources/Mouche_c01_f0001_p013/Ground truth Height map_3.tif",
-// "src/test/resources/Mouche_c01_f0001_p013/Ground truth Height map_4.tif" };
-// ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "Mouche_c01_f0001_p013_doubleSweep" );
-// ref = files.getRefs();
-// tested = files.getTested();
-// writer = new CSVWriter( files.getPath() );
-// String[] header = { "Parameter1", "Parameter1Value", "Parameter2", "Parameter2Value",
-// "GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT", "ConstructionPT",
-// "FS_OS_PT", "FS_surface_PT", "SS_OS_PT", "SS_surface_PT", "Total_PT",
-// "FS_OS_count", "FS_startingOS_count", "SS_OS_count", "SS_startingOS_count",
-// "FS_good", "FS_small", "FS_finalised",
-// "SS_good", "SS_small", "SS_finalised", "OptimizedSet" };
-// writer.writeToFile( header );
-// }
-//
-// @AfterAll
-// static void closeBw() throws IOException
-// {
-// writer.close();
-// }
-//
-// @ParameterizedTest
-// @CsvFileSource( files = "src/test/resources/Mouche_c01_f0001_p013/Mouche_c01_f0001_p013_SweepThreshold.csv",
-// numLinesToSkip = 1, delimiterString = ";" )
-// void parameterSweep3( String testedParameter1, String testedParameterValue1,
-// String testedParameter2, String testedParameterValue2,
-// String filter, int filterParameter,
-// double amplitudeThreshold, double otsuThreshold,
-// int ISConnexity, int ISSize,
-// double XYSmoothing, double ZSmoothing,
-// double startingThreshold1, int overlap1, double connexityRate1,
-// double startingThreshold2, int overlap2, double connexityRate2,
-// String optimalSet ) throws Exception
-// {
-// LOGGER.info( "Parameter sweep " );
-// LOGGER.debug( " The parameter sweep is done for a total of {} ground truths", ref.size() );
-// ZParameters parameters = new ZParameters( filter, filterParameter,
-// amplitudeThreshold, otsuThreshold, ISConnexity, ISSize, XYSmoothing, ZSmoothing,
-// startingThreshold1, overlap1, connexityRate1,
-// startingThreshold2, overlap2, connexityRate2 );
-// double adequacy = 1;
-// ReferenceSurfaceExtraction.setAdequacy( adequacy );
-// parameters.print();
-// ZelligePipelineAnalyse analyse = new ZelligePipelineAnalyse();
-// analyse.run( parameters, tested, ref );
-// for ( RMSEAndCoverageComputation r : analyse.getErrorList() )
-// {
-// String[] line = buildStringLine(
-// testedParameter1, testedParameterValue1,
-// testedParameter2, testedParameterValue2,
-// analyse.getErrorAnalysis( r ), optimalSet );
-// writer.writeToFile( line );
-// }
-// }
-//
-// public String[] buildStringLine( String testedParameter1, String testedParameterValue1, String testedParameter2, String testedParameterValue2,
-// String[] error, String optimalSet )
-// {
-// String[] line = new String[ 5 + error.length ];
-// line[ 0 ] = testedParameter1;
-// line[ 1 ] = testedParameterValue1;
-// line[ 2 ] = testedParameter2;
-// line[ 3 ] = testedParameterValue2;
-// int index = 4;
-// for ( String s : error )
-// {
-// line[ index ] = s;
-// index++;
-// }
-// line[ line.length - 1 ] = optimalSet;
-// return line;
-// }
-//}
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/OneSurfaceConstructionTest.java b/src/test/java/fr/pasteur/ida/zellige/behavior/OneSurfaceConstructionTest.java
deleted file mode 100644
index b076b1a9ad1d475c5c4fa020f7267fa855e4c048..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/OneSurfaceConstructionTest.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.behavior;
-
-class OneSurfaceConstructionTest
-{
-
-
-
-}
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java
deleted file mode 100644
index 622deaee639baea4e5d5ae380b6cb3a96e5dbba3..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java
+++ /dev/null
@@ -1,241 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.behavior;
-
-import fr.pasteur.ida.zellige.utils.test.*;
-import net.imglib2.img.Img;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.numeric.integer.UnsignedShortType;
-import org.junit.Rule;
-import org.junit.internal.runners.statements.FailOnTimeout;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.CsvFileSource;
-import org.junit.jupiter.params.provider.CsvSource;
-import org.junit.rules.Timeout;
-import org.junit.runner.Description;
-import org.junit.runners.model.Statement;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.concurrent.TimeoutException;
-
-import static fr.pasteur.ida.zellige.behavior.Utils.buildStringLine;
-
-//@Ignore
-public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
-{
-
- private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweep.class );
- private static CSVWriter writer;
- static ArrayList< Img > ref;
- static Img tested;
- private final int delta = 0;
- private final double surfaceMinSizeFactor = 0.05;
- private static final int MIN_TIMEOUT = 200;
- public String[] errorLine =
- new String[]{
- "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN",
- "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN" };
-
- @AfterAll
- static void closeBw() throws IOException
- {
- writer.close();
- }
-
- @Rule
- public Timeout timeout = new Timeout( MIN_TIMEOUT )
- {
- public Statement apply( Statement base, Description description )
- {
- return new FailOnTimeout( base, MIN_TIMEOUT )
- {
- @Override
- public void evaluate() throws Throwable
- {
- try
- {
- super.evaluate();
- throw new TimeoutException();
- }
- catch ( Exception e )
- {
- }
- }
- };
- }
-
-
- };
-
- // @Ignore
- @BeforeAll
- static void init() throws IOException
- {
- String imagePath = "doc/Mouche.tif";
- final String[] refImagePath = new String[]{
- "src/test/resources/Mouche/Ground truth Height map_1.tif",
- "src/test/resources/Mouche/Ground truth Height map_2.tif",
- "src/test/resources/Mouche/Ground truth Height map_3.tif",
- "src/test/resources/Mouche/Ground truth Height map_4.tif"
-
- };
- ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "Timeout" );
- ref = files.getRefs();
- tested = files.getTested();
- writer = new CSVWriter( files.getPath() );
- String[] header = { "Parameter1", "Parameter1Value",
- "GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT",
- "AmplitudePT", "OtsuPT", "IslandSearchPT",
- "ConstructionPT", "FS_OS_PT", "FS_surface_PT", "SS_OS_PT", "SS_surface_PT", "Total_PT",
- "FS_OS_count", "FS_startingOS_count", "SS_OS_count", "SS_startingOS_count",
- "FS_good", "FS_small", "FS_finalised",
- "SS_good", "SS_small", "SS_finalised", "OptimizedSet" };
- writer.writeToFile( header );
- RMSEAndCoverageComputation.setSubtract( - 1 );
- }
-
- // The test times out and is skipped
- public void givesTimeout() throws InterruptedException
- {
- Thread.sleep( 1000 );
- }
-
- // @Ignore
- @ParameterizedTest
- @CsvFileSource( files = "src/test/resources/Mouche/Mouche_ParameterSweep.csv", numLinesToSkip = 1, delimiterString = ";" )
- void parameterSweep( String testedParameter, String testedParameterValue, String filter, int filterParameter,
- int amplitudeThreshold, int otsuThreshold,
- int ISConnexity, int ISSize,
- double XYSmoothing, double ZSmoothing,
- double startingThreshold1, int overlap1, double connexityRate1,
- double startingThreshold2, int overlap2, double connexityRate2,
- String optimalSet ) throws Exception
- {
- try
- {
- ZParameters parameters = new ZParameters( filter, filterParameter,
- amplitudeThreshold, otsuThreshold, ISConnexity, ISSize, XYSmoothing, ZSmoothing,
- startingThreshold1, overlap1, connexityRate1,
- startingThreshold2, overlap2, connexityRate2, surfaceMinSizeFactor, delta );
-
- parameters.print();
- ZelligePipelineAnalyse< T, R > analyse = new ZelligePipelineAnalyse<>();
- analyse.run( parameters, tested, ref );
- for ( RMSEAndCoverageComputation< T, UnsignedShortType > r : analyse.getErrorList() )
- {
- String[] line = buildStringLine( testedParameter, testedParameterValue, analyse.getErrorAnalysis( r ), optimalSet );
- writer.writeToFile( line );
- }
- }
- catch ( Exception exception )
- {
- for ( int i = 0; i < ref.size(); i++ )
- {
- writer.writeToFile( errorLine );
- }
- }
- }
-
-
- // @Disabled( "Ignored" )
- @Test
- @CsvSource( value = "Amplitude;0;GaussianBlur;2;0;1;4;5;5;1;0.7;10;0.8;0.1;5;0.9;NO",
- delimiterString = ";" )
- void parameterSweepSingle( String testedParameter, String testedParameterValue, String filter, int filterParameter,
- int amplitudeThreshold, int otsuThreshold,
- int ISConnexity, int ISSize,
- double XYSmoothing, double ZSmoothing,
- double startingThreshold1, int overlap1, double connexityRate1,
- double startingThreshold2, int overlap2, double connexityRate2,
- String optimalSet ) throws Exception
- {
-
- try
- {
- ZParameters parameters = new ZParameters( filter, filterParameter,
- amplitudeThreshold, otsuThreshold, ISConnexity, ISSize, XYSmoothing, ZSmoothing,
- startingThreshold1, overlap1, connexityRate1,
- startingThreshold2, overlap2, connexityRate2, surfaceMinSizeFactor, delta );
-
- parameters.print();
- ZelligePipelineAnalyse< T, R > analyse = new ZelligePipelineAnalyse<>();
- analyse.run( parameters, tested, ref );
- for ( RMSEAndCoverageComputation< T, UnsignedShortType > r : analyse.getErrorList() )
- {
- String[] line = buildStringLine( testedParameter, testedParameterValue, analyse.getErrorAnalysis( r ), optimalSet );
- writer.writeToFile( line );
- }
- }
- catch ( InterruptedException exception )
- {
- for ( int i = 0; i < ref.size(); i++ )
- {
- writer.writeToFile( errorLine );
- }
- }
-
-// ImageJ ij = new ImageJ();
-// LOGGER.info( "Parameter sweep " );
-// LOGGER.debug( " The parameter sweep is done for a total of {} ground truths", ref.size() );
-// ZParameters parameters = new ZParameters( filter, filterParameter,
-// amplitudeThreshold, otsuThreshold, ISConnexity, ISSize, XYSmoothing, ZSmoothing,
-// startingThreshold1, overlap1, connexityRate1,
-// startingThreshold2, overlap2, connexityRate2, surfaceMinSizeFactor, delta );
-//
-// parameters.print();
-// ZelligePipelineAnalyse< T, R > analyse = new ZelligePipelineAnalyse();
-// analyse.run( parameters, tested, ref );
-// for ( RMSEAndCoverageComputation r : analyse.getErrorList() )
-// {
-// String[] line = buildStringLine( testedParameter, testedParameterValue, analyse.getErrorAnalysis( r ), optimalSet );
-// writer.writeToFile( line );
-// }
-
- int index = 0;
-// for ( RandomAccessibleInterval rai : ref )
-// {
-// HM_GT_DifferenceDisplay.displayDiff( ref.get( index ), analyse.getErrorList().get( index ).getProjection() );
-// ImageJFunctions.show( ref.get( index ), "GT" );
-// ImageJFunctions.show( analyse.getErrorList().get( index ).getProjection(), "HM" );
-// index++;
-// }
-// while ( true )
-// {
-//
-// }
- }
-
-}
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCochlee2.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCochlee2Test.java
similarity index 95%
rename from src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCochlee2.java
rename to src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCochlee2Test.java
index 833947d9c82ae6e32c84e8f481b66fe814d94fba..8ad2baa3fee4772dc6738523adb287014492b30c 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCochlee2.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCochlee2Test.java
@@ -6,13 +6,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
- *
+ *
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
- *
+ *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -49,10 +49,11 @@ import static fr.pasteur.ida.zellige.behavior.Utils.buildStringLine;
import static java.util.concurrent.TimeUnit.SECONDS;
-public class ParameterSweepCochlee2< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
+@SuppressWarnings( { "unchecked", "rawtypes" } )
+public class ParameterSweepCochlee2Test< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
{
- private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepCochlee2.class );
+ private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepCochlee2Test.class );
private static final String[] header = { "Parameter1", "Parameter1Value",
"GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT",
"AmplitudePT", "OtsuPT", "IslandSearchPT",
@@ -66,13 +67,14 @@ public class ParameterSweepCochlee2< T extends RealType< T > & NativeType< T >,
private static final String[] refImagePath = new String[]{
"src/test/resources/Cochlée2/Ground truth Height map.tif"
};
+ @SuppressWarnings( "rawtype" )
static ArrayList< Img > ref;
static Img tested;
private static CSVWriter writer;
private final int delta = 0;
private final String parameterSweepCSVFile = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\ProcessingTime\\Cochlée2_PT.csv";
private final double surfaceMinSizeFactor = 0.8;
- public String[] errorLine =
+ public final String[] errorLine =
new String[]{
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN",
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN" };
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCulture.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCultureTest.java
similarity index 95%
rename from src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCulture.java
rename to src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCultureTest.java
index 085ad523558a280adc6a74f093435917e531ba6a..40483ca1ea03bb6c0d61b8a7784c91397799ead0 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCulture.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCultureTest.java
@@ -6,13 +6,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
- *
+ *
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
- *
+ *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -46,10 +46,11 @@ import java.util.ArrayList;
import static fr.pasteur.ida.zellige.behavior.Utils.buildStringLine;
-public class ParameterSweepCulture< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
+@SuppressWarnings( { "unchecked", "rawtypes" } )
+public class ParameterSweepCultureTest< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
{
- private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepCulture.class );
+ private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepCultureTest.class );
private static final String[] header = { "Parameter1", "Parameter1Value",
"GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT",
"AmplitudePT", "OtsuPT", "IslandSearchPT",
@@ -67,9 +68,9 @@ public class ParameterSweepCulture< T extends RealType< T > & NativeType< T >, R
static Img tested;
private static CSVWriter writer;
private final int delta = 0;
- private final String parameterSweepCSVFile = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\ProcessingTime\\Cuture_PT.csv";
+ private final String parameterSweepCSVFile = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\ProcessingTime\\Culture_PT.csv";
private final double surfaceMinSizeFactor = 0.3;
- public String[] errorLine =
+ public final String[] errorLine =
new String[]{
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN",
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN" };
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMouche.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMoucheTest.java
similarity index 95%
rename from src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMouche.java
rename to src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMoucheTest.java
index 41822cff07bf9e08df1b1b3a58d2aada4e09de06..df529f17e5559330dd8b46ebea25b280ce34a1ba 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMouche.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMoucheTest.java
@@ -6,13 +6,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
- *
+ *
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
- *
+ *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -46,10 +46,11 @@ import java.util.ArrayList;
import static fr.pasteur.ida.zellige.behavior.Utils.buildStringLine;
-public class ParameterSweepMouche< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
+@SuppressWarnings( { "unchecked", "rawtypes" } )
+public class ParameterSweepMoucheTest< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
{
- private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepMouche.class );
+ private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepMoucheTest.class );
private static final String[] header = { "Parameter1", "Parameter1Value",
"GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT",
"AmplitudePT", "OtsuPT", "IslandSearchPT",
@@ -57,7 +58,7 @@ public class ParameterSweepMouche< T extends RealType< T > & NativeType< T >, R
"FS_OS_count", "FS_startingOS_count", "SS_OS_count", "SS_startingOS_count",
"FS_good", "FS_small", "FS_finalised",
"SS_good", "SS_small", "SS_finalised", "OptimizedSet" };
- public String[] errorLine =
+ public final String[] errorLine =
new String[]{
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN",
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN" };
@@ -78,7 +79,6 @@ public class ParameterSweepMouche< T extends RealType< T > & NativeType< T >, R
private final String parameterSweepCSVFile = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\ProcessingTime\\Mouche_PT.csv";
private final double surfaceMinSizeFactor = 0.05;
- // @Ignore
@BeforeAll
static void init() throws IOException
{
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoid.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoidTest.java
similarity index 95%
rename from src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoid.java
rename to src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoidTest.java
index 719db557eb490e74c849f888a302cda4ed2455f8..246dd51f00ed4de1e5c849c45f9dac9daae68f55 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoid.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoidTest.java
@@ -46,10 +46,11 @@ import java.util.ArrayList;
import static fr.pasteur.ida.zellige.behavior.Utils.buildStringLine;
-public class ParameterSweepOrganoid< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
+@SuppressWarnings( { "unchecked", "rawtypes" } )
+public class ParameterSweepOrganoidTest< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
{
- private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepOrganoid.class );
+ private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepOrganoidTest.class );
private static final String[] header = { "Parameter1", "Parameter1Value",
"GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT",
"AmplitudePT", "OtsuPT", "IslandSearchPT",
@@ -57,7 +58,7 @@ public class ParameterSweepOrganoid< T extends RealType< T > & NativeType< T >,
"FS_OS_count", "FS_startingOS_count", "SS_OS_count", "SS_startingOS_count",
"FS_good", "FS_small", "FS_finalised",
"SS_good", "SS_small", "SS_finalised", "OptimizedSet" };
- public String[] errorLine =
+ public final String[] errorLine =
new String[]{
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN",
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN" };
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantom.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantomTest.java
similarity index 93%
rename from src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantom.java
rename to src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantomTest.java
index 5e8dd59ecc7411e7e8828b0891953f86f64e9386..4c673606b8c72bb079802a3ac8c27346e6269599 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantom.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantomTest.java
@@ -46,10 +46,10 @@ import java.util.ArrayList;
import static fr.pasteur.ida.zellige.behavior.Utils.buildStringLine;
-public class ParameterSweepPhantom< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
+@SuppressWarnings( { "unchecked", "rawtypes" } )
+public class ParameterSweepPhantomTest< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
{
-
- private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepPhantom.class );
+ private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweepPhantomTest.class );
private static final String[] header = { "Parameter1", "Parameter1Value",
"GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT",
"AmplitudePT", "OtsuPT", "IslandSearchPT",
@@ -57,7 +57,7 @@ public class ParameterSweepPhantom< T extends RealType< T > & NativeType< T >, R
"FS_OS_count", "FS_startingOS_count", "SS_OS_count", "SS_startingOS_count",
"FS_good", "FS_small", "FS_finalised",
"SS_good", "SS_small", "SS_finalised", "OptimizedSet" };
- public String[] errorLine =
+ public final String[] errorLine =
new String[]{
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN",
"NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN", "NaN" };
@@ -78,7 +78,7 @@ public class ParameterSweepPhantom< T extends RealType< T > & NativeType< T >, R
// @Ignore
@BeforeAll
- static void init() throws IOException
+ static < T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > > void init() throws IOException
{
ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "PT_" + sample );
ref = files.getRefs();
@@ -131,6 +131,4 @@ public class ParameterSweepPhantom< T extends RealType< T > & NativeType< T >, R
}
}
}
-
-
}
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/PipelineTest.java b/src/test/java/fr/pasteur/ida/zellige/behavior/PipelineTest.java
deleted file mode 100644
index 2014e845c5228ac9fc036d9419bc1f2c073579f1..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/PipelineTest.java
+++ /dev/null
@@ -1,253 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-//package fr.pasteur.ida.zellige.behavior;
-//
-//import fr.pasteur.ida.zellige.ReferenceSurfaceExtraction;
-//import fr.pasteur.ida.zellige.utils.jzy3D.HM_GT_Display;
-//import fr.pasteur.ida.zellige.utils.test.ZParameters;
-//import fr.pasteur.ida.zellige.utils.test.CSVWriter;
-//import fr.pasteur.ida.zellige.utils.test.ParameterSweepFiles;
-//import fr.pasteur.ida.zellige.utils.test.RMSEAndCoverageComputation;
-//import fr.pasteur.ida.zellige.utils.test.ZelligePipelineAnalyse;
-//import ij.ImageJ;
-//import net.imglib2.img.Img;
-//import net.imglib2.type.NativeType;
-//import net.imglib2.type.numeric.RealType;
-//import net.imglib2.type.numeric.real.FloatType;
-//import org.junit.jupiter.api.AfterAll;
-//import org.junit.jupiter.api.BeforeAll;
-//import org.junit.jupiter.params.ParameterizedTest;
-//import org.junit.jupiter.params.provider.CsvFileSource;
-//import org.junit.jupiter.params.provider.CsvSource;
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
-//
-//import java.io.IOException;
-//import java.util.ArrayList;
-//
-//
-//public class PipelineTest < T extends RealType< T > & NativeType< T >, R extends RealType < R > & NativeType < R > >
-//{
-//
-// private final static Logger LOGGER = LoggerFactory.getLogger( PipelineTest.class );
-// ArrayList< Img< T > > ref;
-// Img< R > tested;
-// private static CSVWriter writer;
-//
-// @BeforeAll
-// void init()
-// {
-// String imagePath = "C:\\Users\\ctrebeau\\Desktop\\STK_Mouche_c01_f0001_p013\\STK_Mouche_c01_f0001_p013.tif";
-// final String[] refImagePath = new String[]{
-// "C:\\Users\\ctrebeau\\Desktop\\STK_Mouche_c01_f0001_p013\\GT\\Ground truth Height map_1.tif",
-// "C:\\Users\\ctrebeau\\Desktop\\STK_Mouche_c01_f0001_p013\\GT\\Ground truth Height map_2.tif",
-// "C:\\Users\\ctrebeau\\Desktop\\STK_Mouche_c01_f0001_p013\\GT\\Ground truth Height map_3.tif",
-// "C:\\Users\\ctrebeau\\Desktop\\STK_Mouche_c01_f0001_p013\\GT\\Ground truth Height map_4.tif" };
-// ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "Mouche_c01_f0001_p013_08" );
-// ref = files.getRefs();
-// tested = files.getTested();
-// writer = new CSVWriter( files.getPath() );
-// }
-//
-// @AfterAll
-// static void closeBw() throws IOException
-// {
-// writer.close();
-// }
-//
-// @ParameterizedTest
-// @CsvFileSource( files = "C:\\Users\\ctrebeau\\Desktop\\STK_Mouche_c01_f0001_p013\\Mouche_c01_f0001_p013_SweepSelection.csv", numLinesToSkip = 2, delimiterString = ";" )
-// void parameterSweep( String testedParameter, String testedParameterValue, String filter, int filterParameter,
-// double amplitudeThreshold, double otsuThreshold,
-// int ISConnexity, int ISSize,
-// double XYSmoothing, double ZSmoothing,
-// double startingThreshold1, int overlap1, double connexityRate1,
-// double startingThreshold2, int overlap2, double connexityRate2,
-// String optimalSet ) throws Exception
-// {
-// LOGGER.info( "Parameter sweep " );
-// LOGGER.debug( " The parameter sweep is done for a total of {} ground truths", ref.size() );
-// ZParameters parameters = new ZParameters( filter, filterParameter,
-// amplitudeThreshold, otsuThreshold, ISConnexity, ISSize, XYSmoothing, ZSmoothing,
-// startingThreshold1, overlap1, connexityRate1,
-// startingThreshold2, overlap2, connexityRate2 );
-// double adequacy = 1;
-// ReferenceSurfaceExtraction.setAdequacy( adequacy );
-// parameters.print();
-// ZelligePipelineAnalyse analyse = new ZelligePipelineAnalyse();
-// analyse.run( parameters, tested, ref );
-// for ( RMSEAndCoverageComputation r : analyse.getErrorList() )
-// {
-// String[] line = buildStringLine( testedParameter, testedParameterValue, analyse.getErrorAnalysis( r ), optimalSet );
-// writer.writeToFile( line );
-// }
-// }
-//
-// @ParameterizedTest
-// @CsvFileSource( files = "C:\\Users\\ctrebeau\\Desktop\\STK_Mouche_c01_f0001_p013\\Mouche_c01_f0001_p013_SweepThreshold.csv",
-// numLinesToSkip = 12, delimiterString = ";" )
-// void parameterSweep3( String testedParameter1, String testedParameterValue1,
-// String testedParameter2, String testedParameterValue2,
-// String filter, int filterParameter,
-// double amplitudeThreshold, double otsuThreshold,
-// int ISConnexity, int ISSize,
-// double XYSmoothing, double ZSmoothing,
-// double startingThreshold1, int overlap1, double connexityRate1,
-// double startingThreshold2, int overlap2, double connexityRate2,
-// String optimalSet ) throws Exception
-// {
-// LOGGER.info( "Parameter sweep " );
-// LOGGER.debug( " The parameter sweep is done for a total of {} ground truths", ref.size() );
-// ZParameters parameters = new ZParameters( filter, filterParameter,
-// amplitudeThreshold, otsuThreshold, ISConnexity, ISSize, XYSmoothing, ZSmoothing,
-// startingThreshold1, overlap1, connexityRate1,
-// startingThreshold2, overlap2, connexityRate2 );
-// double adequacy = 1;
-// ReferenceSurfaceExtraction.setAdequacy( adequacy );
-// parameters.print();
-// ZelligePipelineAnalyse analyse = new ZelligePipelineAnalyse();
-// analyse.run( parameters, tested, ref );
-// String[] header = { "Parameter1", "Parameter1Value", "Parameter2", "Parameter2Value",
-// "GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT", "ConstructionPT",
-// "FS_OS_PT", "FS_surface_PT", "SS_OS_PT", "SS_surface_PT", "Total_PT",
-// "FS_OS_count", "FS_startingOS_count", "SS_OS_count", "SS_startingOS_count", "FS_good", "FS_small", "FS_finalised",
-// "SS_good", "SS_small", "SS_finalised", "OptimizedSet" };
-// writer.writeToFile( header );
-// for ( RMSEAndCoverageComputation r : analyse.getErrorList() )
-// {
-// String[] line = buildStringLine(
-// testedParameter1, testedParameterValue1,
-// testedParameter2, testedParameterValue2,
-// analyse.getErrorAnalysis( r ), optimalSet );
-// writer.writeToFile( line );
-// }
-// }
-//
-// @ParameterizedTest
-// @CsvSource( value = "AmplitudeThreshold;0.8;GaussianBlur;2;0.8;0.1;4;5;4;1;0.75;10;0.8;0.1;10;0.9;YES",
-// delimiterString = ";" )
-// void parameterSweep2( String testedParameter, String testedParameterValue, String filter, int filterParameter,
-// double amplitudeThreshold, double otsuThreshold,
-// int ISConnexity, int ISSize,
-// double XYSmoothing, double ZSmoothing,
-// double startingThreshold1, int overlap1, double connexityRate1,
-// double startingThreshold2, int overlap2, double connexityRate2,
-// String optimalSet ) throws Exception
-// {
-// ImageJ ij = new ImageJ();
-// LOGGER.info( "Parameter sweep " );
-// LOGGER.debug( " The parameter sweep is done for a total of {} ground truth", ref.size() );
-// ZParameters parameters = new ZParameters( filter, filterParameter,
-// amplitudeThreshold, otsuThreshold, ISConnexity, ISSize, XYSmoothing, ZSmoothing,
-// startingThreshold1, overlap1, connexityRate1,
-// startingThreshold2, overlap2, connexityRate2 );
-// double adequacy = 1;
-// ReferenceSurfaceExtraction.setAdequacy( adequacy );
-// parameters.print();
-//
-// ZelligePipelineAnalyse analyse = new ZelligePipelineAnalyse();
-// analyse.run( parameters, tested, ref );
-// String[] header = { "Parameter1", "Parameter1Value",
-// "GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT", "ConstructionPT",
-// "FS_OS_PT", "FS_surface_PT", "SS_OS_PT", "SS_surface_PT", "Total_PT",
-// "FS_OS_count", "FS_startingOS_count", "SS_OS_count", "SS_startingOS_count",
-// "FS_good", "FS_small", "FS_finalised",
-// "SS_good", "SS_small", "SS_finalised", "OptimizedSet" };
-// writer.writeToFile( header );
-// if ( ! analyse.getErrorList().isEmpty() )
-// {
-// for ( RMSEAndCoverageComputation r : analyse.getErrorList() )
-// {
-// String[] line = buildStringLine( testedParameter, testedParameterValue, analyse.getErrorAnalysis( r ), optimalSet );
-// writer.writeToFile( line );
-// HM_GT_Display.displayDiff( r.getGroundTruth(), r.getProjection() );
-//
-// }
-// }
-// else
-// {
-// for ( Img< FloatType > i : ref )
-// {
-// String[] line = buildStringLine( testedParameter, testedParameterValue, analyse.getErrorAnalysis( null ), optimalSet );
-// writer.writeToFile( line );
-// }
-// }
-// while ( true )
-// {
-//
-// }
-// }
-//
-// public String[] buildStringLine( String testedParameter1, String testedParameterValue1,
-// String[] error, String optimalSet )
-// {
-// String[] line = new String[ 3 + error.length ];
-// line[ 0 ] = testedParameter1;
-// line[ 1 ] = testedParameterValue1;
-// int index = 2;
-// for ( String s : error )
-// {
-// line[ index ] = s;
-// index++;
-// }
-// line[ line.length - 1 ] = optimalSet;
-// return line;
-// }
-//
-// public String[] buildStringLine( String testedParameter1, String testedParameterValue1, String testedParameter2, String testedParameterValue2,
-// String[] error, String optimalSet )
-// {
-// String[] line = new String[ 5 + error.length ];
-// line[ 0 ] = testedParameter1;
-// line[ 1 ] = testedParameterValue1;
-// line[ 2 ] = testedParameter2;
-// line[ 3 ] = testedParameterValue2;
-// int index = 4;
-// for ( String s : error )
-// {
-// line[ index ] = s;
-// index++;
-// }
-// line[ line.length - 1 ] = optimalSet;
-// return line;
-// }
-//
-// public String[] buildStringLine( String[] error, String optimalSet )
-// {
-// String[] line = new String[ 1 + error.length ];
-// int index = 0;
-// for ( String s : error )
-// {
-// line[ index ] = s;
-// index++;
-// }
-// line[ line.length - 1 ] = optimalSet;
-// return line;
-// }
-//}
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSE_SameSurfaceTest.java b/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java
similarity index 90%
rename from src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSE_SameSurfaceTest.java
rename to src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java
index 29003a125b59e020d2a1a1595f908101521bd4bd..c32e9d8818a24b4b8ab4ce88374c113d69e84c34 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSE_SameSurfaceTest.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java
@@ -39,7 +39,6 @@ import fr.pasteur.ida.zellige.steps.construction.rounds.surface.SurfaceConstruct
import fr.pasteur.ida.zellige.steps.selection.Selection;
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;
@@ -49,6 +48,7 @@ import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import org.junit.Ignore;
+import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
@@ -57,15 +57,14 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.TreeMap;
-import static org.assertj.core.api.Assertions.assertThat;
-
-public class StartingOSE_SameSurfaceTest
+public class StartingOSESameSurfaceTest
{
- private final static Logger LOGGER = LoggerFactory.getLogger( StartingOSE_SameSurfaceTest.class );
+ private final static Logger LOGGER = LoggerFactory.getLogger( StartingOSESameSurfaceTest.class );
+
@Ignore
@DisplayName( "Two starting OSE from the same surface don't necessarily produce the exact same surface" )
@Test
- < T extends RealType< T > & NativeType< T > > void TwoStartingOSEFromTheSameSurface_whenUseForStartASurface_DonTProduceTheExactSameSurface() throws DataValidationException, EmptyOutputException, NoClassificationException
+ < T extends RealType< T > & NativeType< T > > void TwoStartingOSEFromTheSameSurface_whenUseForStartASurface_DonTProduceTheExactSameSurface() throws DataValidationException, NoClassificationException
{
/* Parameters*/
int amplitude = 5;
@@ -80,21 +79,19 @@ public class StartingOSE_SameSurfaceTest
PostTreatmentParameters postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, 5, 8 );
final String imagePath = "doc/Phantom.tif";
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
-
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
+ @SuppressWarnings( "unchecked" )
final Img< T > source = ( Img< T > ) imgPlus.getImg();
Pixels[][] maximums = Selection.run( source, pretreatmentParameters, classificationParameters, postTreatmentParameters );
OSEListArray oseLists = OseConstructionXZ.run( maximums, startingSizeThreshold );
int width = maximums[ 0 ].length;
- ArrayList< AbstractOSE > list1 = findAllStartingOSE( oseLists );
+ ArrayList< AbstractOSE > osePartOfSurface = findAllStartingOSE( oseLists );
AbstractOSE ose1 = oseLists.getAStartingOse();
Surface reference = SurfaceConstruction.run( oseLists, ose1, width, overlap, connexity );
ArrayList< AbstractOSE > list2 = findAllStartingOSE( oseLists );
-
- ArrayList< AbstractOSE > osePartOfSurface = list1;
osePartOfSurface.removeAll( list2 );
LOGGER.debug( "surface starting ose : " + osePartOfSurface.size() );
TreeMap< Double, Integer > uniqueSurface = new TreeMap<>();
@@ -108,7 +105,7 @@ public class StartingOSE_SameSurfaceTest
uniqueSurface.put( overlappingRate, ( j == null ) ? 1 : j + 1 );
}
LOGGER.debug( String.valueOf( uniqueSurface ) );
- assertThat( uniqueSurface.size() > 1 );
+ Assertions.assertTrue( uniqueSurface.size() > 1 );
}
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/SurfaceConstructionBehaviorTest.java b/src/test/java/fr/pasteur/ida/zellige/behavior/SurfaceConstructionBehaviorTest.java
deleted file mode 100644
index 9be2483db031cc37d57a42e50a012ad292b350fd..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/SurfaceConstructionBehaviorTest.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.behavior;
-
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-
-public class SurfaceConstructionBehaviorTest< T extends RealType< T > & NativeType< T > >
-{
-
-// @Test
-// void testIt() throws DataValidationException, NoClassificationException, EmptyOutputException
-// {
-// /* Parameters*/
-// double amplitude = 0;
-// double otsu = 1;
-// double sigmaXY = 2;
-// double sigmaZ = 0;
-// double startingSizeThreshold = 0.9;
-// int overlap = 10;
-// double connexity = 0.7;
-// int overlap1 = 30;
-// double connexity1 = 0.9;
-//
-// PretreatmentParameters pretreatmentParameters = new PretreatmentParameters( "Median", 2 );
-// PixelClassificationParameters classificationParameters = new PixelClassificationParameters( amplitude, otsu );
-// PostTreatmentParameters postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, 5, 8 );
-// PixelSelectionParameters pixelSelectionParameters = new PixelSelectionParameters( pretreatmentParameters, classificationParameters, postTreatmentParameters );
-// ConstructionParameters[] constructionParameters = new ConstructionParameters[]{
-// new ConstructionParameters( 0.75, overlap, connexity ),
-// new ConstructionParameters( 0.1, overlap1, connexity1 )};
-// ij.ImageJ ij = new ImageJ();
-// final String imagePath = "doc/STK_08.tif";
-// final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
-//
-// final Img< T > source = ( Img< T > ) imgPlus.getImg();
-//
-// Pixels[][] maximums = PixelSelection.run( source, pixelSelectionParameters );
-// OSEListArray oseLists = OseConstructionXZ.runConstruction( maximums, startingSizeThreshold );
-//
-//// displayMaximums( maximums );
-//
-// Construction rounds = new Construction();
-// rounds.process( maximums, constructionParameters );
-// ArrayList<Surface> surfaces = rounds.getReferenceSurfaces();
-// for(Surface surface : surfaces)
-// {
-//// displaySurface( surface );
-// }
-//
-// while(true);
-// }
-}
diff --git a/src/test/java/fr/pasteur/ida/zellige/element/PixelsTest.java b/src/test/java/fr/pasteur/ida/zellige/element/PixelsTest.java
index 867573f6621f930310ff1bff14e0ad1f3f2a1c26..95410785710982ec4f862bc2cfc018f9fd61dbd5 100644
--- a/src/test/java/fr/pasteur/ida/zellige/element/PixelsTest.java
+++ b/src/test/java/fr/pasteur/ida/zellige/element/PixelsTest.java
@@ -50,40 +50,6 @@ class PixelsTest
}
- @Test
- void add()
- {
- }
-
- @Test
- void addAll()
- {
- }
-
- @Test
- void get()
- {
- }
-
- @Test
- void resetSideCoordinate()
- {
- }
-
- @Test
- void size()
- {
- }
-
- @Test
- void testGet()
- {
- }
-
- @Test
- void containsAll()
- {
- }
@Test
void testEquals()
@@ -99,8 +65,5 @@ class PixelsTest
assertThat( pixels ).isEqualTo( pixels2 );
}
- @Test
- void testToString()
- {
- }
+
}
diff --git a/src/test/java/fr/pasteur/ida/zellige/element/SurfaceTest.java b/src/test/java/fr/pasteur/ida/zellige/element/SurfaceTest.java
deleted file mode 100644
index fe78a7532a94d5b0a217073841f73ab03f837065..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/element/SurfaceTest.java
+++ /dev/null
@@ -1,96 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.element;
-
-import org.junit.jupiter.api.Test;
-
-class SurfaceTest
-{
-
- @Test
- void hasDuplicate()
- {
- }
-
- @Test
- void sameSurface()
- {
- }
-
- @Test
- void merge()
- {
- }
-
- @Test
- void transpose()
- {
- }
-
- @Test
- void get()
- {
- }
-
- @Test
- void testGet()
- {
- }
-
- @Test
- void set()
- {
- }
-
- @Test
- void set1()
- {
-
- }
-
- @Test
- void getZMap()
- {
- }
-
- @Test
- void getSize()
- {
- }
-
- @Test
- void getWidth()
- {
- }
-
- @Test
- void getHeight()
- {
- }
-}
diff --git a/src/test/java/fr/pasteur/ida/zellige/parameters/PixelSelectionParametersTest.java b/src/test/java/fr/pasteur/ida/zellige/parameters/PixelSelectionParametersTest.java
deleted file mode 100644
index 31fd7d439805ac12f393152aa9d880ec922ebdb1..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/parameters/PixelSelectionParametersTest.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.parameters;
-
-public class PixelSelectionParametersTest
-{
-
-// @Test
-// void rightPixelSelectionParameters_whenCreatingANewInstance_DonTRaiseAValidationDataException()
-// {
-// double amplitudeThreshold = 1.0;
-// double otsuThreshold = 1.5;
-// double sigmaXY = 2.0;
-// double sigmaZ = 3.0;
-// assertDoesNotThrow( () -> new PixelSelectionParameters(amplitudeThreshold, otsuThreshold, sigmaXY, sigmaZ) );
-// }
-//
-//
-// @Test
-// void amplitudeThresholdUnderZero_WhenCreatingANewInstance_raisesAValidationDataException()
-// {
-// double amplitudeThreshold = -1;
-// double otsuThreshold = 1.5;
-// double sigmaXY = 2.0;
-// double sigmaZ = 3.0;
-// DataValidationException exception = assertThrows(DataValidationException.class, () -> new PixelSelectionParameters(amplitudeThreshold, otsuThreshold, sigmaXY, sigmaZ) );
-// assertThat(exception).hasMessageContaining( "Amplitude" );
-// }
-//
-// @Test
-// void otsuThresholdUnderZero_WhenCreatingANewInstance_raisesAValidationDataException()
-// {
-// double amplitudeThreshold = 1;
-// double otsuThreshold = -1;
-// double sigmaXY = 2.0;
-// double sigmaZ = 3.0;
-// DataValidationException exception = assertThrows(DataValidationException.class, () -> new PixelSelectionParameters(amplitudeThreshold, otsuThreshold, sigmaXY, sigmaZ) );
-// assertThat(exception).hasMessageContaining( "Otsu" );
-// }
-//
-// @Test
-// void sigmaXYThresholdUnderZero_WhenCreatingANewInstance_raisesAValidationDataException()
-// {
-// double amplitudeThreshold = 1;
-// double otsuThreshold = 1;
-// double sigmaXY = -1;
-// double sigmaZ = 3.0;
-// DataValidationException exception = assertThrows(DataValidationException.class, () -> new PixelSelectionParameters(amplitudeThreshold, otsuThreshold, sigmaXY, sigmaZ) );
-// assertThat(exception).hasMessageContaining( "XY" );
-// }
-//
-// @Test
-// void sigmaZThresholdUnderZero_WhenCreatingANewInstance_raisesAValidationDataException()
-// {
-// double amplitudeThreshold = 1;
-// double otsuThreshold = 1;
-// double sigmaXY = 1;
-// double sigmaZ = -1;
-// DataValidationException exception = assertThrows(DataValidationException.class, () -> new PixelSelectionParameters(amplitudeThreshold, otsuThreshold, sigmaXY, sigmaZ) );
-// assertThat(exception).hasMessageContaining( "Z" );
-// }
-
-}
diff --git a/src/test/java/fr/pasteur/ida/zellige/parameters/PretreatmentParametersTest.java b/src/test/java/fr/pasteur/ida/zellige/parameters/PretreatmentParametersTest.java
index 479fbb424b3d5125ec32688897001071414816c8..362cf1b5c2ae44358039cd8b360b8fe8e70d6119 100644
--- a/src/test/java/fr/pasteur/ida/zellige/parameters/PretreatmentParametersTest.java
+++ b/src/test/java/fr/pasteur/ida/zellige/parameters/PretreatmentParametersTest.java
@@ -48,7 +48,7 @@ public class PretreatmentParametersTest
@DisplayName( "Any method associated with the right number of parameters should not raise any exception" )
@ParameterizedTest
@CsvSource( { GAUSSIAN_BLUR + ", 1" } )
- void rightMethodWithRightParameterValue_whenChecked_doesnTRaiseAnyException( String method, double value )
+ void rightMethodWithRightParameterValue_whenChecked_doesntRaiseAnyException( String method, double value )
{
assertDoesNotThrow( () -> new PretreatmentParameters( method, value ) );
}
diff --git a/src/test/java/fr/pasteur/ida/zellige/pixelSelection/PixelClassificationTest.java b/src/test/java/fr/pasteur/ida/zellige/pixelSelection/PixelClassificationTest.java
deleted file mode 100644
index 8ac5107482c236d9cbf002349c267faefe2a969a..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/pixelSelection/PixelClassificationTest.java
+++ /dev/null
@@ -1,97 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.pixelSelection;
-
-class PixelClassificationTest
-{
-
-// @DisplayName( "When neither of the two thresholds is equals to Zero both classifications are done" )
-// @Test
-// void NoneZeroThresholdValue_usesBothClassifications() throws DataValidationException, NoClassificationException, EmptyOutputException
-// {
-// // Given
-// PixelClassificationParameters parameters = new PixelClassificationParameters( 1, 1 );
-// ImgFactory< FloatType > factory = new ArrayImgFactory<>( new FloatType() );
-// RandomAccessibleInterval< FloatType > rai = factory.create( 5, 5, 5 );
-// PixelClassification< FloatType > classificationSpy = spy( new PixelClassification<>() );
-// double amplitudeThreshold = parameters.getAmplitudeThreshold();
-// double otsuThreshold = parameters.getOtsuThreshold();
-// // When
-// classificationSpy.process( rai, factory, parameters );
-// // Then
-// Mockito.verify( classificationSpy, Mockito.times( 1 ) ).processBothClassification( rai, factory, amplitudeThreshold,otsuThreshold );
-// }
-//
-// @DisplayName( "When both thresholds equal Zero a DataValidationException is raised" )
-// @Test
-// void ZeroThresholdValues_raisesAnException() throws DataValidationException
-// {
-// // Given
-// PixelClassificationParameters parameters = new PixelClassificationParameters( 0, 0 );
-// ImgFactory< FloatType > factory = new ArrayImgFactory<>( new FloatType() );
-// RandomAccessibleInterval< FloatType > rai = factory.create( 5, 5, 5 );
-// PixelClassification< FloatType > classification = new PixelClassification<>();
-//
-// // When
-// assertThrows(NoClassificationException.class, () -> classification.process( rai, factory, parameters ));
-// }
-//
-// @DisplayName( "When Amplitude Threshold equals Zero only the Otsu classification is done" )
-// @Test
-// void AnAmplitudeThresholdSetToZero_usesOnlyOtsuClassification() throws DataValidationException, NoClassificationException, EmptyOutputException
-// {
-// // Given
-// PixelClassificationParameters parameters = new PixelClassificationParameters( 0, 0.1 );
-// ImgFactory< FloatType > factory = new ArrayImgFactory<>( new FloatType() );
-// RandomAccessibleInterval< FloatType > rai = factory.create( 5, 5, 5 );
-// PixelClassification< FloatType > classificationSpy = spy( new PixelClassification<>() );
-// double otsuThreshold = parameters.getOtsuThreshold();
-// // When
-// classificationSpy.process( rai, factory, parameters );
-// // Then
-// Mockito.verify( classificationSpy, Mockito.times( 1 ) ).processOtsuClassification( rai, factory, otsuThreshold );
-// }
-//
-// @DisplayName( "When Otsu Threshold equals Zero only the Amplitude classification is done" )
-// @Test
-// void AnOtsuThresholdSetToZero_usesOnlyAmplitudeClassification() throws DataValidationException, NoClassificationException, EmptyOutputException
-// {
-// // Given
-// PixelClassificationParameters parameters = new PixelClassificationParameters( 1, 0 );
-// ImgFactory< FloatType > factory = new ArrayImgFactory<>( new FloatType() );
-// RandomAccessibleInterval< FloatType > rai = factory.create( 5, 5, 5 );
-// PixelClassification< FloatType > classificationSpy = spy( new PixelClassification<>() );
-// double amplitudeThreshold = parameters.getAmplitudeThreshold();
-// // When
-// classificationSpy.process( rai, factory, parameters );
-// // Then
-// Mockito.verify( classificationSpy, Mockito.times( 1 ) ).processAmplitudeClassification( rai, factory, amplitudeThreshold );
-// }
-
-}
diff --git a/src/test/java/fr/pasteur/ida/zellige/pixelSelection/islandSearch/SandTest.java b/src/test/java/fr/pasteur/ida/zellige/pixelSelection/islandSearch/SandTest.java
index 003149f6c2ee1cc5ade3d146ef334dbb9e7b6429..3497d2462d84d25ea6cd0208581f631d208f8228 100644
--- a/src/test/java/fr/pasteur/ida/zellige/pixelSelection/islandSearch/SandTest.java
+++ b/src/test/java/fr/pasteur/ida/zellige/pixelSelection/islandSearch/SandTest.java
@@ -86,6 +86,6 @@ class SandTest
{
Sand sand = new Sand( 0, 0, 0 );
Sand sand2 = new Sand( 0, 0, 0 );
- assertTrue( sand.equals( sand2 ) );
+ assertEquals( sand, sand2 );
}
}
diff --git a/src/test/java/fr/pasteur/ida/zellige/pixelSelection/pretreatment/PreTreatmentTest.java b/src/test/java/fr/pasteur/ida/zellige/pixelSelection/pretreatment/PreTreatmentTest.java
deleted file mode 100644
index 8ff4d20b92a22b11ef479a965527526fa2824e8d..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/pixelSelection/pretreatment/PreTreatmentTest.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.pixelSelection.pretreatment;
-
-public class PreTreatmentTest
-{
-
- public static final String GAUSSIAN_BLUR = "GaussianBlur";
- public static final String MEDIAN = "Median";
-
-
-//@DisplayName("When MEDIAN is selected as method in PretreatmentParameters the medianFilterDenoising method is used" )
-// @Test
-// void aMedianFilterAsParameter_whenTreated_usesTheMedianFilterDenoisingMethod() throws DataValidationException
-// {
-//
-// PretreatmentParameters parameters = new PretreatmentParameters( MEDIAN, 2 );
-// RandomAccessibleInterval< FloatType > rai = new ArrayImgFactory<>( new FloatType() ).create( 5, 5, 5 );
-// Pretreatment<FloatType> pretreatment = new Pretreatment<>(rai, parameters);
-// Pretreatment<FloatType> pretreatmentSpy = Mockito.spy( pretreatment );
-// pretreatmentSpy.run();
-// Mockito.verify(pretreatmentSpy, Mockito.times( 1 )).medianFilterDenoising(any(RandomAccessibleInterval.class));
-// }
-//
-//
-// @DisplayName("When GAUSSIAN_BLUR is selected as method in PretreatmentParameters the gaussianBlurFilterDenoising method is used" )
-// @Test
-// void aGaussianBlurFilterAsParameter_whenTreated_usesTheMedianFilterDenoisingMethod() throws DataValidationException
-// {
-// PretreatmentParameters parameters = new PretreatmentParameters( GAUSSIAN_BLUR, 1 );
-// RandomAccessibleInterval< FloatType > rai = new ArrayImgFactory<>( new FloatType() ).create( 5, 5, 5 );
-// Pretreatment<FloatType> pretreatment = new Pretreatment<>(rai, parameters);
-// Pretreatment<FloatType> pretreatmentSpy = Mockito.spy( pretreatment );
-// pretreatmentSpy.run();
-// Mockito.verify(pretreatmentSpy, Mockito.times( 1 )).gaussianBlurFilterDenoising(any(RandomAccessibleInterval.class));
-// }
-}
diff --git a/src/test/java/fr/pasteur/ida/zellige/pixelSelection/util/ExtremaDetectionTest.java b/src/test/java/fr/pasteur/ida/zellige/pixelSelection/util/ExtremaDetectionTest.java
index 53dd58b78ff65116fe5631fe653180909eba9843..1cdb31be7f6127a37e35cd251212e489fc262de7 100644
--- a/src/test/java/fr/pasteur/ida/zellige/pixelSelection/util/ExtremaDetectionTest.java
+++ b/src/test/java/fr/pasteur/ida/zellige/pixelSelection/util/ExtremaDetectionTest.java
@@ -46,6 +46,7 @@ import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.spy;
+@SuppressWarnings( { "unchecked", "rawtypes" } )
public class ExtremaDetectionTest
{
@@ -62,6 +63,7 @@ public class ExtremaDetectionTest
assertThat( exception ).hasMessageContaining( "3D image" );
}
+
@DisplayName( "The input and the factory are the same type" )
@Test
void differentTypeBetweenInputAndFactoryWhenProvidedRaisesAnException()
diff --git a/src/test/java/fr/pasteur/ida/zellige/utils/LocalExtremaDetectionTest.java b/src/test/java/fr/pasteur/ida/zellige/utils/LocalExtremaDetectionTest.java
deleted file mode 100644
index 52b895b755aa0d7ac2007e0db595c3c8df22ac0a..0000000000000000000000000000000000000000
--- a/src/test/java/fr/pasteur/ida/zellige/utils/LocalExtremaDetectionTest.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*-
- * #%L
- * Zellige
- * %%
- * Copyright (C) 2020 - 2022 Institut Pasteur
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-package fr.pasteur.ida.zellige.utils;
-
-import org.junit.jupiter.api.Test;
-
-import static org.junit.jupiter.api.Assertions.*;
-
-class LocalExtremaDetectionTest
-{
-
- @Test
- void findMinima()
- {
- }
-
- @Test
- void findMaxima()
- {
- }
-}
diff --git a/src/test/java/fr/pasteur/ida/zellige/utils/RMSEAndCoverageComputationTest.java b/src/test/java/fr/pasteur/ida/zellige/utils/RMSEAndCoverageComputationTest.java
index 73e48eb8c7c83de0c46cd3063bf42b26422a708e..dadd908c34fa8214faacd112fa3b0905095659cf 100644
--- a/src/test/java/fr/pasteur/ida/zellige/utils/RMSEAndCoverageComputationTest.java
+++ b/src/test/java/fr/pasteur/ida/zellige/utils/RMSEAndCoverageComputationTest.java
@@ -40,6 +40,7 @@ import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.IntType;
+import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
@@ -101,36 +102,37 @@ public class RMSEAndCoverageComputationTest
}
+ @SuppressWarnings( "unchecked" )
@DisplayName( "Two identical image has an RMSE equals to 0 " )
@Test
< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
void whenTheRefHMAndTheTestedHMAreIdenticalTheRMSEEqualsZero() throws Exception
{
final String imagePath = "doc/fakeHeightMap.tif";
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
final Img< T > ref = ( Img< T > ) imgPlus.getImg();
final Img< R > tested = ( Img< R > ) imgPlus.getImg();
RMSEAndCoverageComputation< T, R > determination = new RMSEAndCoverageComputation<>( ref, 0, tested );
- determination.setSubtract( 0 );
+ RMSEAndCoverageComputation.setSubtract( 0 );
determination.compute();
assertThat( determination.getRMSE() == 0 ).isTrue();
}
+ @SuppressWarnings( "unchecked" )
@DisplayName( "Two identical image has an reconstruction proportion equals to 1 " )
@Test
< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
void whenTheRefHMAndTheTestedHMAreIdenticalTheReconstructionProportionEqualsOne() throws Exception
{
final String imagePath = "doc/fakeHeightMap.tif";
- final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
+ final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
final Img< T > ref = ( Img< T > ) imgPlus.getImg();
final Img< R > tested = ( Img< R > ) imgPlus.getImg();
RMSEAndCoverageComputation< T, R > determination = new RMSEAndCoverageComputation<>( ref, 0, tested );
determination.compute();
- assertThat( determination.getCoverage() == 1 );
-
+ Assertions.assertEquals( determination.getCoverage(), 1 );
}
}