Rename package net.imglib2.atlas to net.imglib2.labkit

src/main/java/net/imglib2/atlas/ActionsAndBehaviours.java → src/main/java/net/imglib2/labkit/ActionsAndBehaviours.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import bdv.util.BdvHandle;
 import org.scijava.ui.behaviour.Behaviour;

src/main/java/net/imglib2/atlas/AtlasUtils.java → src/main/java/net/imglib2/labkit/AtlasUtils.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessible;
@@ -13,7 +13,6 @@
 import net.imglib2.type.numeric.IntegerType;
 import net.imglib2.type.numeric.NumericType;
 import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.numeric.integer.ShortType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.type.numeric.real.FloatType;

src/main/java/net/imglib2/atlas/BatchSegmenter.java → src/main/java/net/imglib2/labkit/BatchSegmenter.java

@@ -1,13 +1,13 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import ij.ImagePlus;
 import io.scif.img.ImgIOException;
 import io.scif.img.ImgSaver;
 import net.imagej.ops.OpEnvironment;
 import net.imagej.ops.OpService;
 import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.atlas.classification.Classifier;
-import net.imglib2.atlas.classification.weka.TrainableSegmentationClassifier;
+import net.imglib2.labkit.classification.Classifier;
+import net.imglib2.labkit.classification.weka.TrainableSegmentationClassifier;
 import net.imglib2.exception.IncompatibleTypeException;
 import net.imglib2.img.Img;
 import net.imglib2.img.array.ArrayImgs;

src/main/java/net/imglib2/atlas/BrushOverlay.java → src/main/java/net/imglib2/labkit/BrushOverlay.java

@@ -1,7 +1,7 @@
 /**
  *
  */
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import java.awt.AlphaComposite;
 import java.awt.BasicStroke;
@@ -14,8 +14,7 @@
 
 import bdv.util.Affine3DHelpers;
 import bdv.viewer.ViewerPanel;
-import net.imglib2.atlas.color.ColorMap;
-import net.imglib2.atlas.color.ColorMapProvider;
+import net.imglib2.labkit.color.ColorMapProvider;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.ui.OverlayRenderer;
 

src/main/java/net/imglib2/atlas/DefaultHolder.java → src/main/java/net/imglib2/labkit/DefaultHolder.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import java.util.function.Consumer;
 

src/main/java/net/imglib2/atlas/Extensible.java → src/main/java/net/imglib2/labkit/Extensible.java

@@ -1,9 +1,9 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import bdv.util.BdvStackSource;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.Volatile;
-import net.imglib2.atlas.labeling.Labeling;
+import net.imglib2.labkit.labeling.Labeling;
 import net.imglib2.type.numeric.NumericType;
 import net.imglib2.ui.OverlayRenderer;
 import org.scijava.Context;

src/main/java/net/imglib2/atlas/FeatureStack.java → src/main/java/net/imglib2/labkit/FeatureStack.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import net.imglib2.FinalInterval;
 import net.imglib2.Interval;

src/main/java/net/imglib2/atlas/Holder.java → src/main/java/net/imglib2/labkit/Holder.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import java.util.function.Consumer;
 

src/main/java/net/imglib2/atlas/ImgLabelingTest.java → src/main/java/net/imglib2/labkit/ImgLabelingTest.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import net.imglib2.Cursor;
 import net.imglib2.Localizable;

src/main/java/net/imglib2/atlas/LabelingComponent.java → src/main/java/net/imglib2/labkit/LabelingComponent.java

@@ -1,14 +1,14 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import bdv.util.*;
 import bdv.viewer.DisplayMode;
 import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.atlas.actions.ToggleVisibility;
-import net.imglib2.atlas.color.ColorMapProvider;
-import net.imglib2.atlas.color.UpdateColormap;
-import net.imglib2.atlas.control.brush.*;
-import net.imglib2.atlas.labeling.Labeling;
-import net.imglib2.atlas.labeling.LabelsLayer;
+import net.imglib2.labkit.actions.ToggleVisibility;
+import net.imglib2.labkit.color.ColorMapProvider;
+import net.imglib2.labkit.color.UpdateColormap;
+import net.imglib2.labkit.control.brush.*;
+import net.imglib2.labkit.labeling.Labeling;
+import net.imglib2.labkit.labeling.LabelsLayer;
 import net.imglib2.img.cell.CellGrid;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.trainable_segmention.RevampUtils;

src/main/java/net/imglib2/atlas/Main.java → src/main/java/net/imglib2/labkit/Main.java

@@ -1,6 +1,6 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
-import net.imglib2.atlas.actions.AbstractFileIoAcion;
+import net.imglib2.labkit.actions.AbstractFileIoAcion;
 
 import javax.swing.*;
 import javax.swing.filechooser.FileFilter;

src/main/java/net/imglib2/atlas/MainFrame.java → src/main/java/net/imglib2/labkit/MainFrame.java

@@ -1,11 +1,11 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import io.scif.services.DatasetIOService;
 import net.imagej.Dataset;
-import net.imglib2.atlas.actions.SetLabelsAction;
-import net.imglib2.atlas.inputimage.DatasetInputImage;
-import net.imglib2.atlas.labeling.Labeling;
-import net.imglib2.atlas.labeling.LabelingSerializer;
+import net.imglib2.labkit.actions.SetLabelsAction;
+import net.imglib2.labkit.inputimage.DatasetInputImage;
+import net.imglib2.labkit.labeling.Labeling;
+import net.imglib2.labkit.labeling.LabelingSerializer;
 import net.imglib2.trainable_segmention.RevampUtils;
 import org.scijava.Context;
 

src/main/java/net/imglib2/atlas/MenuBar.java → src/main/java/net/imglib2/labkit/MenuBar.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import org.scijava.ui.behaviour.util.RunnableAction;
 

src/main/java/net/imglib2/atlas/Notifier.java → src/main/java/net/imglib2/labkit/Notifier.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import java.util.List;
 import java.util.concurrent.CopyOnWriteArrayList;

src/main/java/net/imglib2/atlas/PaintLabelsAndTrain.java → src/main/java/net/imglib2/labkit/PaintLabelsAndTrain.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 public class PaintLabelsAndTrain
 {

src/main/java/net/imglib2/atlas/ParallelUtils.java → src/main/java/net/imglib2/labkit/ParallelUtils.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import net.imglib2.FinalInterval;
 import net.imglib2.Interval;

src/main/java/net/imglib2/atlas/Preferences.java → src/main/java/net/imglib2/labkit/Preferences.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import org.scijava.Context;
 import org.scijava.prefs.PrefService;

src/main/java/net/imglib2/atlas/RandomAccessibleContainer.java → src/main/java/net/imglib2/labkit/RandomAccessibleContainer.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import java.util.HashSet;
 

src/main/java/net/imglib2/atlas/RealRandomAccessibleContainer.java → src/main/java/net/imglib2/labkit/RealRandomAccessibleContainer.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import java.util.HashSet;
 

src/main/java/net/imglib2/atlas/SegmentationComponent.java → src/main/java/net/imglib2/labkit/SegmentationComponent.java

@@ -1,4 +1,4 @@
-package net.imglib2.atlas;
+package net.imglib2.labkit;
 
 import bdv.util.BdvStackSource;
 import bdv.util.volatiles.SharedQueue;
@@ -7,27 +7,27 @@
 import net.imagej.ops.OpService;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.Volatile;
-import net.imglib2.atlas.actions.AddLabelingIoAction;
-import net.imglib2.atlas.actions.BatchSegmentAction;
-import net.imglib2.atlas.actions.ChangeFeatureSettingsAction;
-import net.imglib2.atlas.actions.ClassifierIoAction;
-import net.imglib2.atlas.actions.LabelingIoAction;
-import net.imglib2.atlas.actions.OpenImageAction;
-import net.imglib2.atlas.actions.OrthogonalView;
-import net.imglib2.atlas.actions.SegmentationAsLabelAction;
-import net.imglib2.atlas.actions.SegmentationSave;
-import net.imglib2.atlas.actions.SelectClassifier;
-import net.imglib2.atlas.actions.ZAxisScaling;
-import net.imglib2.atlas.classification.Classifier;
-import net.imglib2.atlas.classification.PredictionLayer;
-import net.imglib2.atlas.classification.TrainClassifier;
-import net.imglib2.atlas.classification.weka.TimeSeriesClassifier;
-import net.imglib2.atlas.classification.weka.TrainableSegmentationClassifier;
-import net.imglib2.atlas.inputimage.DefaultInputImage;
-import net.imglib2.atlas.inputimage.InputImage;
-import net.imglib2.atlas.labeling.Labeling;
-import net.imglib2.atlas.panel.LabelPanel;
-import net.imglib2.atlas.plugin.MeasureConnectedComponents;
+import net.imglib2.labkit.actions.AddLabelingIoAction;
+import net.imglib2.labkit.actions.BatchSegmentAction;
+import net.imglib2.labkit.actions.ChangeFeatureSettingsAction;
+import net.imglib2.labkit.actions.ClassifierIoAction;
+import net.imglib2.labkit.actions.LabelingIoAction;
+import net.imglib2.labkit.actions.OpenImageAction;
+import net.imglib2.labkit.actions.OrthogonalView;
+import net.imglib2.labkit.actions.SegmentationAsLabelAction;
+import net.imglib2.labkit.actions.SegmentationSave;
+import net.imglib2.labkit.actions.SelectClassifier;
+import net.imglib2.labkit.actions.ZAxisScaling;
+import net.imglib2.labkit.classification.Classifier;
+import net.imglib2.labkit.classification.PredictionLayer;
+import net.imglib2.labkit.classification.TrainClassifier;
+import net.imglib2.labkit.classification.weka.TimeSeriesClassifier;
+import net.imglib2.labkit.classification.weka.TrainableSegmentationClassifier;
+import net.imglib2.labkit.inputimage.DefaultInputImage;
+import net.imglib2.labkit.inputimage.InputImage;
+import net.imglib2.labkit.labeling.Labeling;
+import net.imglib2.labkit.panel.LabelPanel;
+import net.imglib2.labkit.plugin.MeasureConnectedComponents;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.trainable_segmention.RevampUtils;
 import net.imglib2.trainable_segmention.pixel_feature.filter.GroupedFeatures;

src/main/java/net/imglib2/atlas/actions/AbstractFileIoAcion.java → src/main/java/net/imglib2/labkit/actions/AbstractFileIoAcion.java

@@ -1,13 +1,11 @@
-package net.imglib2.atlas.actions;
+package net.imglib2.labkit.actions;
 
-import net.imglib2.atlas.Extensible;
-import net.imglib2.atlas.MainFrame;
+import net.imglib2.labkit.Extensible;
 
 import javax.swing.*;
 import javax.swing.filechooser.FileFilter;
 import javax.swing.filechooser.FileNameExtensionFilter;
 import java.io.File;
-import java.util.function.Consumer;
 
 /**
  * @author Matthias Arzt

src/main/java/net/imglib2/atlas/actions/AddLabelingIoAction.java → src/main/java/net/imglib2/labkit/actions/AddLabelingIoAction.java

@@ -1,18 +1,13 @@
-package net.imglib2.atlas.actions;
+package net.imglib2.labkit.actions;
 
 import net.imglib2.Cursor;
 import net.imglib2.RandomAccess;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.atlas.AtlasUtils;
-import net.imglib2.atlas.Extensible;
-import net.imglib2.atlas.Holder;
-import net.imglib2.atlas.inputimage.InputImage;
-import net.imglib2.atlas.labeling.Labeling;
-import net.imglib2.atlas.labeling.LabelingSerializer;
-import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.labkit.Extensible;
+import net.imglib2.labkit.Holder;
+import net.imglib2.labkit.labeling.Labeling;
+import net.imglib2.labkit.labeling.LabelingSerializer;
 import net.imglib2.roi.IterableRegion;
 import net.imglib2.type.logic.BitType;
-import net.imglib2.type.numeric.IntegerType;
 
 import javax.swing.filechooser.FileNameExtensionFilter;
 import java.io.IOException;

src/main/java/net/imglib2/atlas/actions/BatchSegmentAction.java → src/main/java/net/imglib2/labkit/actions/BatchSegmentAction.java

@@ -1,9 +1,8 @@
-package net.imglib2.atlas.actions;
+package net.imglib2.labkit.actions;
 
-import net.imglib2.atlas.BatchSegmenter;
-import net.imglib2.atlas.Extensible;
-import net.imglib2.atlas.MainFrame;
-import net.imglib2.atlas.classification.Classifier;
+import net.imglib2.labkit.BatchSegmenter;
+import net.imglib2.labkit.Extensible;
+import net.imglib2.labkit.classification.Classifier;
 import net.imglib2.trainable_segmention.RevampUtils;
 import org.scijava.Cancelable;
 import org.scijava.Context;
@@ -14,7 +13,6 @@
 import org.scijava.module.process.PreprocessorPlugin;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.PluginService;
-import org.scijava.ui.behaviour.util.RunnableAction;
 import org.scijava.ui.swing.widget.SwingInputHarvester;
 import org.scijava.widget.FileWidget;
 import org.scijava.widget.InputHarvester;

src/main/java/net/imglib2/atlas/actions/ChangeFeatureSettingsAction.java → src/main/java/net/imglib2/labkit/actions/ChangeFeatureSettingsAction.java

@@ -1,7 +1,7 @@
-package net.imglib2.atlas.actions;
+package net.imglib2.labkit.actions;
 
-import net.imglib2.atlas.Extensible;
-import net.imglib2.atlas.classification.Classifier;
+import net.imglib2.labkit.Extensible;
+import net.imglib2.labkit.classification.Classifier;
 import net.imglib2.trainable_segmention.gui.FeatureSettingsGui;
 import net.imglib2.trainable_segmention.pixel_feature.settings.FeatureSettings;
 

src/main/java/net/imglib2/atlas/actions/ClassifierIoAction.java → src/main/java/net/imglib2/labkit/actions/ClassifierIoAction.java

@@ -1,8 +1,7 @@
-package net.imglib2.atlas.actions;
+package net.imglib2.labkit.actions;
 
-import net.imglib2.atlas.Extensible;
-import net.imglib2.atlas.MainFrame;
-import net.imglib2.atlas.classification.Classifier;
+import net.imglib2.labkit.Extensible;
+import net.imglib2.labkit.classification.Classifier;
 
 import javax.swing.filechooser.FileNameExtensionFilter;
 

src/main/java/net/imglib2/atlas/actions/LabelingIoAction.java → src/main/java/net/imglib2/labkit/actions/LabelingIoAction.java

@@ -1,12 +1,12 @@
-package net.imglib2.atlas.actions;
+package net.imglib2.labkit.actions;
 
 import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.atlas.AtlasUtils;
-import net.imglib2.atlas.Extensible;
-import net.imglib2.atlas.Holder;
-import net.imglib2.atlas.inputimage.InputImage;
-import net.imglib2.atlas.labeling.Labeling;
-import net.imglib2.atlas.labeling.LabelingSerializer;
+import net.imglib2.labkit.AtlasUtils;
+import net.imglib2.labkit.Extensible;
+import net.imglib2.labkit.Holder;
+import net.imglib2.labkit.inputimage.InputImage;
+import net.imglib2.labkit.labeling.Labeling;
+import net.imglib2.labkit.labeling.LabelingSerializer;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.type.numeric.IntegerType;
 

src/main/java/net/imglib2/atlas/actions/OpenImageAction.java → src/main/java/net/imglib2/labkit/actions/OpenImageAction.java

@@ -1,7 +1,7 @@
-package net.imglib2.atlas.actions;
+package net.imglib2.labkit.actions;
 
-import net.imglib2.atlas.Extensible;
-import net.imglib2.atlas.MainFrame;
+import net.imglib2.labkit.Extensible;
+import net.imglib2.labkit.MainFrame;
 
 /**
  * @author Matthias Arzt

src/main/java/net/imglib2/atlas/actions/OrthogonalView.java → src/main/java/net/imglib2/labkit/actions/OrthogonalView.java

@@ -1,12 +1,8 @@
-package net.imglib2.atlas.actions;
+package net.imglib2.labkit.actions;
 
 import bdv.viewer.ViewerPanel;
-import net.imglib2.atlas.Extensible;
-import net.imglib2.atlas.MainFrame;
+import net.imglib2.labkit.Extensible;
 import net.imglib2.realtransform.AffineTransform3D;
-import org.scijava.ui.behaviour.util.RunnableAction;
-
-import javax.swing.*;
 
 /**
  * @author Matthias Arzt

src/main/java/net/imglib2/atlas/actions/SegmentationAsLabelAction.java → src/main/java/net/imglib2/labkit/actions/SegmentationAsLabelAction.java

@@ -1,13 +1,12 @@
-package net.imglib2.atlas.actions;
+package net.imglib2.labkit.actions;
 
-import io.scif.img.ImgSaver;
 import net.imglib2.Cursor;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccess;
-import net.imglib2.atlas.Extensible;
-import net.imglib2.atlas.Holder;
-import net.imglib2.atlas.classification.PredictionLayer;
-import net.imglib2.atlas.labeling.Labeling;
+import net.imglib2.labkit.Extensible;
+import net.imglib2.labkit.Holder;
+import net.imglib2.labkit.classification.PredictionLayer;
+import net.imglib2.labkit.labeling.Labeling;
 import net.imglib2.converter.Converter;
 import net.imglib2.converter.Converters;
 import net.imglib2.img.Img;