From bdf5f0d6f1aa566360ec09c2784a49d1d52bea85 Mon Sep 17 00:00:00 2001
From: ctrebeau <ctrebeau@pasteur.fr>
Date: Mon, 18 Oct 2021 09:22:34 +0200
Subject: [PATCH] feature - add minimum surface size factor as a user parameter
(variable surfaceMinSizeFactor) This factor set the minimum size that a
surface has to be to be kept as a surface of interest.
---
src/main/java/fr/pasteur/ida/zellige/Main.java | 8 +++++---
.../fr/pasteur/ida/zellige/command/ZelligeCommand.java | 8 ++++++--
.../construction/rounds/ConstructionParameters.java | 9 ++++++++-
.../steps/construction/rounds/ConstructionRound.java | 4 +++-
.../rounds/surface/SurfacesConstruction.java | 10 ++++++----
.../fr/pasteur/ida/zellige/utils/test/ZParameters.java | 6 +++---
.../pasteur/ida/zellige/behavior/ParameterSweep.java | 5 +++--
7 files changed, 34 insertions(+), 16 deletions(-)
diff --git a/src/main/java/fr/pasteur/ida/zellige/Main.java b/src/main/java/fr/pasteur/ida/zellige/Main.java
index 44b2963b..0e66c540 100644
--- a/src/main/java/fr/pasteur/ida/zellige/Main.java
+++ b/src/main/java/fr/pasteur/ida/zellige/Main.java
@@ -53,7 +53,8 @@ public class Main
double startingOsSize2 = Double.parseDouble( args[ 10 ] );
int overlap2 = Integer.parseInt( args[ 11 ] );
double connexityRate2 = Double.parseDouble( args[ 12 ] );
- int delta = Integer.parseInt( args[ 13 ] );
+ double surfaceMinSizeFactor = Double.parseDouble( args[ 13 ] );
+ int delta = Integer.parseInt( args[ 14 ] );
/* End of parameters. */
@@ -78,6 +79,7 @@ public class Main
System.out.println( "starting os size2 : " + startingOsSize2 );
System.out.println( "overlap2 :" + overlap2 );
System.out.println( "connexityRate2 :" + connexityRate2 );
+ System.out.println( "surface Minimum size factor : " + surfaceMinSizeFactor );
System.out.println( "delta : " + delta );
System.out.println( System.lineSeparator() );
/* End of Print parameters.*/
@@ -87,8 +89,8 @@ public class Main
PostTreatmentParameters postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, islandSize, connexity );
ProjectionParameters projectionParameters = new ProjectionParameters( delta, "MIP" );// no other method implemented yet.
ConstructionParameters[] constructionParameters = new ConstructionParameters[]{
- new ConstructionParameters( startingOsSize1, overlap1, connexityRate1 ),
- new ConstructionParameters( startingOsSize2, overlap2, connexityRate2 ) };
+ new ConstructionParameters( startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor ),
+ new ConstructionParameters( startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor ) };
DisplayParameters displayParameters = new DisplayParameters(
diff --git a/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand.java b/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand.java
index a672b19c..020b895d 100644
--- a/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand.java
+++ b/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand.java
@@ -76,9 +76,13 @@ public class ZelligeCommand< T extends RealType< T > & NativeType< T > > extends
@Parameter
private double connexityRate2;
+ @Parameter
+ private double surfaceMinSizeFactor;
+
@Parameter
private int delta;
+
public static void main( String[] args ) throws IOException
{
String currentFolder = FileSystems.getDefault()
@@ -173,8 +177,8 @@ public class ZelligeCommand< T extends RealType< T > & NativeType< T > > extends
e.printStackTrace();
}
ConstructionParameters[] constructionParameters = new ConstructionParameters[]{
- new ConstructionParameters( startingOsSize1, overlap1, connexityRate1 ),
- new ConstructionParameters( startingOsSize2, overlap2, connexityRate2 ) };
+ new ConstructionParameters( startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor ),
+ new ConstructionParameters( startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor ) };
DisplayParameters displayParameters = new DisplayParameters(
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 72df91af..ff750967 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
@@ -6,12 +6,14 @@ public class ConstructionParameters
private final double startingSizeThreshold;
private final int overlap;
private final double connexityRate;
+ private double surfaceMinSizeFactor;
- public ConstructionParameters( double startingSizeThreshold, int overlap, double connexityRate )
+ public ConstructionParameters( double startingSizeThreshold, int overlap, double connexityRate, double surfaceMinSizeFactor )
{
this.startingSizeThreshold = startingSizeThreshold;
this.overlap = overlap;
this.connexityRate = connexityRate;
+ this.surfaceMinSizeFactor = surfaceMinSizeFactor;
}
@@ -29,4 +31,9 @@ public class ConstructionParameters
{
return connexityRate;
}
+
+ public double getSurfaceMinSizeFactor()
+ {
+ return 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 2e387c23..8c013192 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
@@ -18,6 +18,7 @@ public abstract class ConstructionRound
private final double startingSizeThreshold;
private final int overlap;
private final double connexityRate;
+ private final double surfaceMinSizeFactor;
private final ArrayList< Surface > surfaces;
private long OSConstructionProcessingTime;
private long ConstructionProcessingTime;
@@ -32,6 +33,7 @@ public abstract class ConstructionRound
this.overlap = constructionParameters.getOverlap();
this.connexityRate = constructionParameters.getConnexityRate();
this.surfaces = new ArrayList<>();
+ this.surfaceMinSizeFactor = constructionParameters.getSurfaceMinSizeFactor();
}
void finalizeSurface( ArrayList< Surface > surfaces ) throws NoSurfaceFoundException
@@ -106,7 +108,7 @@ public abstract class ConstructionRound
protected ArrayList< Surface > constructSurfaces( OSEListArray oseLists, int lineLength )
{
SurfacesConstruction construction =
- new SurfacesConstruction( oseLists, lineLength, overlap, connexityRate );
+ new SurfacesConstruction( oseLists, lineLength, overlap, connexityRate, surfaceMinSizeFactor );
construction.buildAllSurfaces();
int tempSmallSurfaceCount = construction.getSmallSurfaceCount();
smallSurfacesCount += tempSmallSurfaceCount;
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/surface/SurfacesConstruction.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/surface/SurfacesConstruction.java
index 2b9ac2e4..c0780093 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/surface/SurfacesConstruction.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/surface/SurfacesConstruction.java
@@ -24,18 +24,20 @@ public class SurfacesConstruction
private final double connexity;
private final int overlap;
private int smallSurfaceCount;
+ private final double surfaceMinSizeFactor;
- public SurfacesConstruction( OSEListArray oseLists, int width, int overlap, double connexity )
+ public SurfacesConstruction( OSEListArray oseLists, int width, int overlap, double connexity, double surfaceMinSizeFactor )
{
this.oseListArray = oseLists;
this.width = width;
this.connexity = connexity;
this.overlap = overlap;
+ this.surfaceMinSizeFactor = surfaceMinSizeFactor;
}
- public static ArrayList< Surface > run( OSEListArray oseListArray, int surfaceLineLength, int overlap, double connexity )
+ public static ArrayList< Surface > run( OSEListArray oseListArray, int surfaceLineLength, int overlap, double connexity, double surfaceMinSizeFactor )
{
- SurfacesConstruction reconstruction = new SurfacesConstruction( oseListArray, surfaceLineLength, overlap, connexity );
+ SurfacesConstruction reconstruction = new SurfacesConstruction( oseListArray, surfaceLineLength, overlap, connexity, surfaceMinSizeFactor );
reconstruction.buildAllSurfaces();
return reconstruction.constructedSurfaces;
}
@@ -68,7 +70,7 @@ public class SurfacesConstruction
*/
private void checkSurface( Surface surface )
{
- if ( surface.getSize() >= width * oseListArray.getLength() * 0.2 )
+ if ( surface.getSize() >= width * oseListArray.getLength() * surfaceMinSizeFactor )
{
constructedSurfaces.add( surface );
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/ZParameters.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/ZParameters.java
index 7a9fb62e..702c1a3d 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/test/ZParameters.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/ZParameters.java
@@ -25,15 +25,15 @@ public class ZParameters
double XYSmoothing, double ZSmoothing,
double startingThreshold1, int overlap1, double connexityRate1,
double startingThreshold2, int overlap2, double connexityRate2,
- int delta ) throws DataValidationException
+ double surfaceMinSizeFactor, int delta ) throws DataValidationException
{
pretreatmentParameters = new PretreatmentParameters( filter, filterParameter );
classificationParameters = new ClassificationParameters( amplitudeThreshold, otsuThreshold );
postTreatmentParameters = new PostTreatmentParameters( XYSmoothing, ZSmoothing, ISSize, ISConnexity );
constructionParameters = new ConstructionParameters[]{
- new ConstructionParameters( startingThreshold1, overlap1, connexityRate1 ),
- new ConstructionParameters( startingThreshold2, overlap2, connexityRate2 ) };
+ new ConstructionParameters( startingThreshold1, overlap1, connexityRate1, surfaceMinSizeFactor ),
+ new ConstructionParameters( startingThreshold2, overlap2, connexityRate2, surfaceMinSizeFactor ) };
projectionParameters = new ProjectionParameters( delta, "MIP" );
}
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java
index 11c5aa4f..87c077ca 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java
@@ -28,6 +28,7 @@ public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extend
static ArrayList< Img > ref;
static Img tested;
private final int delta = 0;
+ private double surfaceMinSizeFactor;
// @Ignore
@BeforeAll
@@ -74,7 +75,7 @@ public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extend
ZParameters parameters = new ZParameters( filter, filterParameter,
amplitudeThreshold, otsuThreshold, ISConnexity, ISSize, XYSmoothing, ZSmoothing,
startingThreshold1, overlap1, connexityRate1,
- startingThreshold2, overlap2, connexityRate2, delta );
+ startingThreshold2, overlap2, connexityRate2, surfaceMinSizeFactor, delta );
parameters.print();
ZelligePipelineAnalyse< T, R > analyse = new ZelligePipelineAnalyse();
@@ -121,7 +122,7 @@ public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extend
ZParameters parameters = new ZParameters( filter, filterParameter,
amplitudeThreshold, otsuThreshold, ISConnexity, ISSize, XYSmoothing, ZSmoothing,
startingThreshold1, overlap1, connexityRate1,
- startingThreshold2, overlap2, connexityRate2, delta );
+ startingThreshold2, overlap2, connexityRate2, surfaceMinSizeFactor, delta );
parameters.print();
ZelligePipelineAnalyse< T, R > analyse = new ZelligePipelineAnalyse();
--
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