diff --git a/pom.xml b/pom.xml index bfb4a61..bdaf1ce 100644 --- a/pom.xml +++ b/pom.xml @@ -134,15 +134,17 @@ de.embl.cba imagej-utils - 0.5.0 + 0.5.1 de.embl.cba fiji-slurm + 0.6.2 de.embl.cba imaris-writer + 0.2.1 diff --git a/src/main/java/de/embl/cba/cats/CATS.java b/src/main/java/de/embl/cba/cats/CATS.java index c190108..be21318 100644 --- 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 index 3eeb63b..78eefab 100644 --- 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 index 3a5b1cd..ad0bf76 100644 --- 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 index bd7f8e0..504f75d 100644 --- 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 index 9678d4c..2819603 100644 --- 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 index 5b868a0..b3ee668 100644 --- 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 index 020b63f..91c84b8 100644 --- 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 index d08d4a2..8d42645 100644 --- 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 index 5b46527..1895599 100644 --- 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 index bde4a6f..1d93a1b 100644 --- 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 index 317b21c..fd5ea4e 100644 --- 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 index b6ac54b..9e524d7 100644 --- 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 index f5440c3..c17f99b 100644 --- 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 index 4064e4a..dda783f 100644 --- 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 index 0fe4364..e6dd025 100644 --- 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 index 0638d84..2f1fcb8 100644 --- 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 index d5793fd..88c9e7d 100644 --- 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 index 906e530..1da3ee3 100644 --- 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 index a5a825a..fea5159 100644 --- 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 index 17fb2f7..198257f 100644 --- 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;