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 3cf997f1182e0ef97699fc3b836cc2fbbe3429c5..2d26a67db57ad126ab29996dd79ccc98a11a772c 100644
--- a/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java
+++ b/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java
@@ -42,7 +42,7 @@ public class Zellige< T extends RealType< T > & NativeType< T > > implements Com
.getPath( "" )
.toAbsolutePath()
.toString();
- String imageFilePath = "doc/Mouche.tif";
+ String imageFilePath = "doc/Organoid.tif";
// Launch ImageJ.
ImageJ ij = new ImageJ();
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 72b06b6739b2e9ef4f1a0071d95624251bc381de..74ea63d827204c1ee8e6db4bd5ddefe1ab52dbbf 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
@@ -61,8 +61,8 @@ public class HMvsGT_Display< T extends RealType< T > & NativeType< T >, R extend
public static void main( String[] args )
{
- String pathGT = "C:\\Users\\ctrebeau\\Desktop\\Covid Zellige\\C2-MucilairB spike zo1 J4 Sars-3_Ground truth Height map.tif";
- String pathHM = "C:\\Users\\ctrebeau\\Desktop\\Covid Zellige\\C2-MucilairB spike zo1 J4 Sars-3_HM.tif";
+ 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 );
Img< FloatType > GT = ( Img< FloatType > ) imgPlusRef.getImg();
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 b92010221ea1481b03395d2570aa43656e9878ae..0808a25536d8fae62e6168eb3af3cd60e63904d8 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
@@ -47,11 +47,10 @@ public class HeightMapArrayWriter< T extends RealType< T > & NativeType< T > > e
public static < T extends RealType< T > & NativeType< T > > void main( String[] args )
{
- final String imagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\SNR\\snr_010\\multiSurface\\phantoms_snr10.mat_HM_02.tif"; /* The image path goes here !!!! */
+ final String imagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\Organoid\\Organoid_GT_HM1.tif"; /* The image path goes here !!!! */
System.out.println( imagePath );
/* JY version for opening files. */
final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
-
final Img< T > heightMap = ( Img< T > ) imgPlus.getImg();
writeHeightMap( heightMap, imgPlus.getName(), 2 );
System.out.println( "END" );
@@ -64,17 +63,20 @@ public class HeightMapArrayWriter< T extends RealType< T > & NativeType< T > > e
if ( surface != null )
{
CSVWriter csvWriter =
- new CSVWriter( originalInput + "_" + "HM" + "_" + surfaceNumber );
+ new CSVWriter( originalInput + "_" + "surface" );
Cursor< T > cursor = surface.cursor();
csvWriter.writeToFile( new String[]{ "x", "y", "z" } );
while ( cursor.hasNext() )
{
cursor.fwd();
{
- csvWriter.writeToFile(
- new String[]{ String.valueOf( cursor.getIntPosition( 0 ) ),
- String.valueOf( cursor.getIntPosition( 1 ) ),
- String.valueOf( cursor.get().getRealFloat() ) } );
+ if ( cursor.get().getRealFloat() != 0 )
+ {
+ csvWriter.writeToFile(
+ new String[]{ String.valueOf( cursor.getIntPosition( 0 ) ),
+ String.valueOf( cursor.getIntPosition( 1 ) ),
+ String.valueOf( cursor.get().getRealFloat() ) } );
+ }
}
}
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 05ea0151055ea954be640663d3cac27bacbf7f16..d5095dea73cb24daf9a498fc4ed832a8e9c0f3b1 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
@@ -23,7 +23,7 @@ public class DistanceImageWriter< T extends RealType< T > & NativeType< T >, R e
private final RandomAccessibleInterval< R > projection;
private final String fileName;
private final String[][] distances;
- private final int subtract = 0;
+ private final int subtract = - 1;
public DistanceImageWriter( RandomAccessibleInterval< T > groundTruth,
RandomAccessibleInterval< R > heightMap, String fileName )
@@ -45,8 +45,8 @@ public class DistanceImageWriter< T extends RealType< T > & NativeType< T >, R e
public static void main( String[] args ) throws IOException
{
- 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\\Downloads\\DatasetCulture_ParamSweepResults_LocalZProjector\\HeightMap_fs05_ms07_gauss2.00_binning4_deltaZ1.tif";
+ 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 );
Img< FloatType > GT = ( Img< FloatType > ) imgPlusRef.getImg();
new ImageJ();
@@ -55,7 +55,7 @@ public class DistanceImageWriter< T extends RealType< T > & NativeType< T >, R e
final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( pathHM ).get( 0 );
Img< FloatType > HM = ( Img< FloatType > ) imgPlus.getImg();
ImageJFunctions.show( HM );
- DistanceImageWriter.create( GT, HM, "Covid_LZP" );
+ DistanceImageWriter.create( GT, HM, "Mouche_distance4_crop" );
}
public void run() throws IOException
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 81f98f3b2e4f8a989afd378c3afb629f58e3b345..3bf7ba8f94042f00a9fb919330540380c15fade1 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
@@ -192,6 +192,7 @@ public class ZelligePipelineAnalyse< T extends RealType< T > & NativeType< T >,
}
else
{
+
return new String[]{
String.valueOf( error.getIndex() ),
String.valueOf( getSelectedPixelNumber() ),
@@ -217,6 +218,7 @@ public class ZelligePipelineAnalyse< T extends RealType< T > & NativeType< T >,
String.valueOf( extraction.getSS_goodSurfaces() ),
String.valueOf( extraction.getSS_smallSurfaces() ),
String.valueOf( extraction.getReferenceSurfaces().size() ) };
+
}
}
return null;
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 19762f91104a62c3a4af63afa69c3e7d722dbe21..71c61933cf38db75ca049e8ba97bfee8d1ab9b5a 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java
@@ -1,24 +1,29 @@
package fr.pasteur.ida.zellige.behavior;
-import fr.pasteur.ida.zellige.utils.jzy3D.HM_GT_DifferenceDisplay;
import fr.pasteur.ida.zellige.utils.test.*;
-import net.imagej.ImageJ;
-import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
-import net.imglib2.img.display.imagej.ImageJFunctions;
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.Disabled;
+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 > >
@@ -30,13 +35,42 @@ public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extend
static Img tested;
private final int delta = 0;
private double surfaceMinSizeFactor = 0.05;
- private final 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" };
+ 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
@@ -50,7 +84,7 @@ public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extend
"src/test/resources/Mouche/Ground truth Height map_4.tif"
};
- ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "Mouche" );
+ ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "Timeout" );
ref = files.getRefs();
tested = files.getTested();
writer = new CSVWriter( files.getPath() );
@@ -65,10 +99,10 @@ public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extend
RMSEAndCoverageComputation.setSubtract( - 1 );
}
- @AfterAll
- static void closeBw() throws IOException
+ // The test times out and is skipped
+ public void givesTimeout() throws InterruptedException
{
- writer.close();
+ Thread.sleep( 1000 );
}
// @Ignore
@@ -82,42 +116,35 @@ public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extend
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, surfaceMinSizeFactor, delta );
-
- parameters.print();
- ZelligePipelineAnalyse< T, R > analyse = new ZelligePipelineAnalyse();
- analyse.run( parameters, tested, ref );
- for ( RMSEAndCoverageComputation r : analyse.getErrorList() )
+ try
{
- String[] line = buildStringLine( testedParameter, testedParameterValue, analyse.getErrorAnalysis( r ), optimalSet );
- writer.writeToFile( line );
+ 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 );
+ }
}
- }
-
- 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 )
+ catch ( Exception exception )
{
- line[ index ] = s;
- index++;
+ for ( int i = 0; i < ref.size(); i++ )
+ {
+ writer.writeToFile( errorLine );
+ }
}
- line[ line.length - 1 ] = optimalSet;
- return line;
}
- @Disabled( "Ignored" )
- @CsvSource( value = "Amplitude;0.9;GaussianBlur;2;0.9;0.1;4;10;2;3;0.7;10;0.7;0.1;10;0.8;YES",
+ // @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,
@@ -127,35 +154,60 @@ public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extend
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 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 )
+ try
{
- 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++;
+ 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 );
+ }
}
- while ( true )
+ 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/ParameterSweepCochlee2.java
index 2063fbf5096be0758af78c6594b9e6d44a5c4e27..b8f285c4be28a3a3a49cb1f37d7cc3e798d7ef8a 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCochlee2.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCochlee2.java
@@ -42,7 +42,7 @@ public class ParameterSweepCochlee2< T extends RealType< T > & NativeType< T >,
static Img tested;
private static CSVWriter writer;
private final int delta = 0;
- private final String parameterSweepCSVFile = "src/test/resources/Cochlée2/PS_Cochlée2.csv";
+ 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 =
new String[]{
@@ -51,12 +51,12 @@ public class ParameterSweepCochlee2< T extends RealType< T > & NativeType< T >,
@Rule
- public Timeout globalTimeout = new Timeout( 10, SECONDS );
+ public Timeout globalTimeout = new Timeout( 10000, SECONDS );
@BeforeAll
static void init() throws IOException
{
- ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, sample );
+ ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "PT_" + sample );
ref = files.getRefs();
tested = files.getTested();
writer = new CSVWriter( files.getPath() );
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCulture.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCulture.java
index 23e1d953ea599675c3507b4ed29d58ac0b176280..cc6c8b1189a3b834e955232da8b02d053bb1e1a9 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCulture.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepCulture.java
@@ -39,7 +39,7 @@ 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 = "src/test/resources/Culture/PS_Culture.csv";
+ private final String parameterSweepCSVFile = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\ProcessingTime\\Cuture_PT.csv";
private final double surfaceMinSizeFactor = 0.3;
public String[] errorLine =
new String[]{
@@ -50,7 +50,7 @@ public class ParameterSweepCulture< T extends RealType< T > & NativeType< T >, R
@BeforeAll
static void init() throws IOException
{
- ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, sample );
+ ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "PT_" + sample );
ref = files.getRefs();
tested = files.getTested();
writer = new CSVWriter( files.getPath() );
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMouche.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMouche.java
index b6aab8f0914c8ca4f1aab0da72a3f4657259a23a..555e356f8403de4b664fb718790689d83a861931 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMouche.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepMouche.java
@@ -47,14 +47,14 @@ public class ParameterSweepMouche< T extends RealType< T > & NativeType< T >, R
static Img tested;
private static CSVWriter writer;
private final int delta = 0;
- private final String parameterSweepCSVFile = "src/test/resources/Mouche/Mouche_PS.csv";
+ 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
{
- ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, sample );
+ ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "PT_" + sample );
ref = files.getRefs();
tested = files.getTested();
writer = new CSVWriter( files.getPath() );
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoid.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoid.java
index 988c277f49a9e3593844522e643a60557f6084a9..723c6d144b940b2f32268cd9c037c28edadb23db 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoid.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepOrganoid.java
@@ -44,14 +44,14 @@ public class ParameterSweepOrganoid< T extends RealType< T > & NativeType< T >,
static Img tested;
private static CSVWriter writer;
private final int delta = 0;
- private final String parameterSweepCSVFile = "src/test/resources/Organoid/Organoid_PS.csv";
+ private final String parameterSweepCSVFile = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\ProcessingTime\\Organoid_PT.csv";
private final double surfaceMinSizeFactor = 0.1;
// @Ignore
@BeforeAll
static void init() throws IOException
{
- ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, sample );
+ ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "PT_" + sample );
ref = files.getRefs();
tested = files.getTested();
writer = new CSVWriter( files.getPath() );
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantom.java b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantom.java
index 1604e4c43f86b2f049f7186d9d380f5721e6e2dc..019eb98df43d9a8e2141d8bae7ad060652681479 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantom.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweepPhantom.java
@@ -45,14 +45,14 @@ public class ParameterSweepPhantom< T extends RealType< T > & NativeType< T >, R
static Img tested;
private static CSVWriter writer;
private final int delta = 0;
- private final String parameterSweepCSVFile = "src/test/resources/Phantom/Phantom_PS.csv";
+ private final String parameterSweepCSVFile = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\Paper_012022\\ProcessingTime\\Phantom_PT.csv";
private final double surfaceMinSizeFactor = 0.8;
// @Ignore
@BeforeAll
static void init() throws IOException
{
- ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, sample );
+ ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "PT_" + sample );
ref = files.getRefs();
tested = files.getTested();
writer = new CSVWriter( files.getPath() );