Improve Logger dependencies

embl-cba · Jul 16, 2020 · b030933 · b030933
1 parent e1fd67c
commit b030933
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Showing 21 changed files with 27 additions and 29 deletions.
diff --git a/pom.xml b/pom.xml
@@ -134,15 +134,17 @@
 		<dependency>
 			<groupId>de.embl.cba</groupId>
 			<artifactId>imagej-utils</artifactId>
-			<version>0.5.0</version>
+			<version>0.5.1</version>
 		</dependency>
 		<dependency>
 			<groupId>de.embl.cba</groupId>
 			<artifactId>fiji-slurm</artifactId>
+			<version>0.6.2</version>
 		</dependency>
 		<dependency>
 			<groupId>de.embl.cba</groupId>
 			<artifactId>imaris-writer</artifactId>
+			<version>0.2.1</version>
 		</dependency>
 <!--		<dependency>-->
 <!--			<groupId>de.embl.cba</groupId>-->

diff --git a/src/main/java/de/embl/cba/cats/CATS.java b/src/main/java/de/embl/cba/cats/CATS.java
@@ -28,8 +28,8 @@
 import de.embl.cba.cats.ui.ApplyClassifierOnSlurmCommand;
 import de.embl.cba.cats.utils.*;
 import de.embl.cba.classifiers.weka.FastRandomForest;
-import de.embl.cba.utils.logging.IJLazySwingLogger;
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.IJLazySwingLogger;
+import de.embl.cba.log.Logger;
 import fiji.util.gui.GenericDialogPlus;
 import ij.*;
 import ij.gui.GenericDialog;

diff --git a/src/main/java/de/embl/cba/cats/classification/AttributeSelector.java b/src/main/java/de/embl/cba/cats/classification/AttributeSelector.java
@@ -1,7 +1,7 @@
 package de.embl.cba.cats.classification;
 
 import de.embl.cba.classifiers.weka.FastRandomForest;
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 import weka.core.Instances;
 
 import java.util.ArrayList;

diff --git a/src/main/java/de/embl/cba/cats/classification/ClassificationRangeUtils.java b/src/main/java/de/embl/cba/cats/classification/ClassificationRangeUtils.java
@@ -2,7 +2,7 @@
 
 import de.embl.cba.cats.CATS;
 import de.embl.cba.cats.utils.IntervalUtils;
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 import ij.IJ;
 import ij.ImagePlus;
 import ij.gui.Roi;

diff --git a/src/main/java/de/embl/cba/cats/features/FeatureProvider.java b/src/main/java/de/embl/cba/cats/features/FeatureProvider.java
@@ -22,7 +22,7 @@
  */
 
 import de.embl.cba.cats.features.settings.FeatureSettings;
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 import de.embl.cba.cats.CATS;
 import ij.IJ;
 import ij.ImagePlus;

diff --git a/src/main/java/de/embl/cba/cats/instances/InstancesUtils.java b/src/main/java/de/embl/cba/cats/instances/InstancesUtils.java
@@ -2,7 +2,7 @@
 
 import de.embl.cba.cats.labels.Label;
 import de.embl.cba.cats.features.settings.FeatureSettings;
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 import ij.ImagePlus;
 import ij.process.ImageProcessor;
 import net.imglib2.FinalInterval;

diff --git a/src/main/java/de/embl/cba/cats/labelimagetraining/AccuracyEvaluation.java b/src/main/java/de/embl/cba/cats/labelimagetraining/AccuracyEvaluation.java
@@ -3,7 +3,7 @@
 import de.embl.cba.cats.CATS;
 import de.embl.cba.cats.results.ResultImage;
 import de.embl.cba.cats.utils.ThreadUtils;
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 import ij.ImagePlus;
 import ij.Prefs;
 import ij.process.ImageProcessor;
@@ -15,9 +15,7 @@
 import java.util.concurrent.Future;
 
 import static de.embl.cba.cats.CATS.logger;
-import static de.embl.cba.cats.utils.IntervalUtils.X;
-import static de.embl.cba.cats.utils.IntervalUtils.Y;
-import static de.embl.cba.cats.utils.IntervalUtils.Z;
+import static de.embl.cba.cats.utils.IntervalUtils.*;
 
 public class AccuracyEvaluation
 {

diff --git a/src/main/java/de/embl/cba/cats/labels/LabelUtils.java b/src/main/java/de/embl/cba/cats/labels/LabelUtils.java
@@ -1,8 +1,7 @@
 package de.embl.cba.cats.labels;
 
-import de.embl.cba.cats.labels.Label;
-import de.embl.cba.utils.logging.Logger;
 import de.embl.cba.cats.instances.InstancesAndMetadata;
+import de.embl.cba.log.Logger;
 import weka.core.Instances;
 
 import java.awt.*;
@@ -11,7 +10,6 @@
 import java.util.Set;
 
 import static de.embl.cba.cats.instances.InstancesAndMetadata.Metadata.*;
-import static de.embl.cba.cats.instances.InstancesAndMetadata.Metadata.Metadata_Label_Id;
 
 public abstract class LabelUtils
 {

diff --git a/src/main/java/de/embl/cba/cats/results/CallableResultImageBinner.java b/src/main/java/de/embl/cba/cats/results/CallableResultImageBinner.java
@@ -1,7 +1,7 @@
 package de.embl.cba.cats.results;
 
 import de.embl.cba.bigdataprocessor.utils.Utils;
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 import ij.ImagePlus;
 import ij.ImageStack;
 import ij.plugin.Binner;

diff --git a/src/main/java/de/embl/cba/cats/results/ResultExport.java b/src/main/java/de/embl/cba/cats/results/ResultExport.java
@@ -6,6 +6,7 @@
 import de.embl.cba.imaris.ImarisDataSet;
 import de.embl.cba.imaris.ImarisUtils;
 import de.embl.cba.imaris.ImarisWriter;
+import de.embl.cba.log.Logger;
 import ij.IJ;
 import ij.ImagePlus;
 import ij.ImageStack;
@@ -144,7 +145,7 @@ public static ImagePlus getBinnedClassImage(
 
     public static ImagePlus getBinnedClassImageMemoryEfficient(
             int classId, ResultExportSettings settings, int t,
-            de.embl.cba.utils.logging.Logger logger, int numThreads )
+            Logger logger, int numThreads )
     {
         logger.info( "Computing probability image for " + settings.classNames.get( classId ) + ", using " + numThreads + " threads." );
 

diff --git a/src/main/java/de/embl/cba/cats/results/ResultExportSettings.java b/src/main/java/de/embl/cba/cats/results/ResultExportSettings.java
@@ -1,6 +1,6 @@
 package de.embl.cba.cats.results;
 
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 import ij.ImagePlus;
 
 import java.awt.*;

diff --git a/src/main/java/de/embl/cba/cats/results/ResultImageDisk.java b/src/main/java/de/embl/cba/cats/results/ResultImageDisk.java
@@ -5,7 +5,7 @@
 import de.embl.cba.bigdataprocessor.virtualstack2.VirtualStack2;
 import de.embl.cba.cats.CATS;
 import de.embl.cba.cats.utils.IntervalUtils;
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 import ij.ImagePlus;
 import ij.ImageStack;
 import ij.io.FileSaver;
@@ -48,7 +48,6 @@ public ArrayList< ImagePlus > exportResults( ResultExportSettings resultExportSe
         return ResultExport.exportResults( resultExportSettings );
     }
 
-
     @Override
     public ImageProcessor getSlice( int slice, int frame )
     {

diff --git a/src/main/java/de/embl/cba/cats/results/ResultImageRAM.java b/src/main/java/de/embl/cba/cats/results/ResultImageRAM.java
@@ -2,7 +2,7 @@
 
 import de.embl.cba.bigdataprocessor.utils.Utils;
 import de.embl.cba.cats.CATS;
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 
 import ij.ImagePlus;
 import ij.ImageStack;

diff --git a/src/main/java/de/embl/cba/cats/ui/ApplyClassifierCommand.java b/src/main/java/de/embl/cba/cats/ui/ApplyClassifierCommand.java
@@ -3,7 +3,7 @@
 import de.embl.cba.cats.CATS;
 import de.embl.cba.cats.results.ResultExportSettings;
 import de.embl.cba.cats.results.ResultImage;
-import de.embl.cba.utils.logging.IJLazySwingLogger;
+import de.embl.cba.log.IJLazySwingLogger;
 import ij.IJ;
 import org.scijava.command.Command;
 import org.scijava.log.LogService;

diff --git a/src/main/java/de/embl/cba/cats/ui/ApplyClassifierOnSlurmCommand.java b/src/main/java/de/embl/cba/cats/ui/ApplyClassifierOnSlurmCommand.java
@@ -6,7 +6,7 @@
 import de.embl.cba.cluster.SlurmJobMonitor;
 import de.embl.cba.cats.utils.IOUtils;
 import de.embl.cba.cats.utils.IntervalUtils;
-import de.embl.cba.utils.fileutils.PathMapper;
+import de.embl.cba.util.PathMapper;
 import net.imagej.ImageJ;
 import net.imglib2.FinalInterval;
 import org.scijava.command.Command;

diff --git a/src/main/java/de/embl/cba/cats/ui/BatchClassificationCommand.java b/src/main/java/de/embl/cba/cats/ui/BatchClassificationCommand.java
@@ -5,7 +5,7 @@
 import de.embl.cba.cats.results.ResultImage;
 import de.embl.cba.cats.utils.IOUtils;
 import de.embl.cba.cats.utils.Utils;
-import de.embl.cba.utils.logging.IJLazySwingLogger;
+import de.embl.cba.log.IJLazySwingLogger;
 import ij.IJ;
 import net.imagej.ImageJ;
 import org.scijava.command.Command;

diff --git a/src/main/java/de/embl/cba/cats/ui/BatchClassificationOnSlurmCommand.java b/src/main/java/de/embl/cba/cats/ui/BatchClassificationOnSlurmCommand.java
@@ -5,8 +5,8 @@
 import de.embl.cba.cluster.JobSettings;
 import de.embl.cba.cluster.SlurmJobMonitor;
 import de.embl.cba.cats.utils.IOUtils;
-import de.embl.cba.utils.fileutils.PathMapper;
-import de.embl.cba.utils.logging.IJLazySwingLogger;
+import de.embl.cba.util.PathMapper;
+import de.embl.cba.log.IJLazySwingLogger;
 import org.scijava.command.Command;
 import org.scijava.log.LogService;
 import org.scijava.plugin.Parameter;

diff --git a/src/main/java/de/embl/cba/cats/ui/ClassificationCommand.txt b/src/main/java/de/embl/cba/cats/ui/ClassificationCommand.txt
@@ -4,7 +4,7 @@ import de.embl.cba.cats.CATS;
 import de.embl.cba.cats.results.ResultExportSettings;
 import de.embl.cba.cats.results.ResultImage;
 import de.embl.cba.cats.utils.IOUtils;
-import de.embl.cba.utils.logging.IJLazySwingLogger;
+import de.embl.cba.log.IJLazySwingLogger;
 import ij.IJ;
 import org.scijava.command.Command;
 import org.scijava.log.LogService;

diff --git a/src/main/java/de/embl/cba/cats/utils/CommandUtils.java b/src/main/java/de/embl/cba/cats/utils/CommandUtils.java
@@ -2,7 +2,7 @@
 
 import de.embl.cba.cluster.ImageJCommandsSubmitter;
 import de.embl.cba.cats.ui.ApplyClassifierOnSlurmCommand;
-import de.embl.cba.utils.fileutils.PathMapper;
+import de.embl.cba.util.PathMapper;
 import ij.IJ;
 import org.scijava.Context;
 import org.scijava.command.CommandService;

diff --git a/src/main/java/de/embl/cba/cats/utils/IOUtils.java b/src/main/java/de/embl/cba/cats/utils/IOUtils.java
@@ -1,7 +1,7 @@
 package de.embl.cba.cats.utils;
 
 import de.embl.cba.bigdataprocessor.BigDataProcessor;
-import de.embl.cba.utils.fileutils.FileRegMatcher;
+import de.embl.cba.util.FileRegMatcher;
 import ij.IJ;
 import ij.ImagePlus;
 import ij.io.OpenDialog;

diff --git a/src/main/java/de/embl/cba/cats/utils/ThreadUtils.java b/src/main/java/de/embl/cba/cats/utils/ThreadUtils.java
@@ -1,6 +1,6 @@
 package de.embl.cba.cats.utils;
 
-import de.embl.cba.utils.logging.Logger;
+import de.embl.cba.log.Logger;
 
 import java.util.ArrayList;
 import java.util.concurrent.ExecutionException;