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NicoKiaruNicoKiaru
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removes wildcard imports
1 parent 4d2ed91 commit ddac2e1

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+315
-120
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59 files changed

+315
-120
lines changed

‎pom.xml

+8-7
Original file line numberDiff line numberDiff line change
@@ -120,9 +120,9 @@
120120
<!-- <scijava.app.directory>C:/Users/nicol/Desktop/fiji-win64-bdv-playground/Fiji.app/</scijava.app.directory> -->
121121

122122
<!-- package version below are not present in the parent pom. A version is needed -->
123-
<bigdataviewer-selector.version>0.2.1</bigdataviewer-selector.version>
123+
<bigdataviewer-selector.version>0.2.2</bigdataviewer-selector.version>
124124
<bigvolumeviewer.version>0.2.0</bigvolumeviewer.version>
125-
<reflections.version>0.9.11</reflections.version>
125+
<reflections.version>0.10.2</reflections.version> <!-- for test only -->
126126

127127
<!-- package version below are determined by the parent pom but need to be upgraded or temporarily fixed for bugs -->
128128
<scijava-ui-swing.version>0.16.1</scijava-ui-swing.version>
@@ -163,11 +163,6 @@
163163
<version>${bigvolumeviewer.version}</version>
164164
</dependency>
165165

166-
<dependency>
167-
<groupId>net.imglib2</groupId>
168-
<artifactId>imglib2-ij</artifactId>
169-
</dependency>
170-
171166
<dependency>
172167
<groupId>sc.fiji</groupId>
173168
<artifactId>bigwarp_fiji</artifactId>
@@ -192,6 +187,12 @@
192187
<scope>test</scope>
193188
</dependency>
194189

190+
<dependency>
191+
<groupId>net.imagej</groupId>
192+
<artifactId>imagej</artifactId>
193+
<scope>test</scope>
194+
</dependency>
195+
195196
</dependencies>
196197

197198
</project>

‎src/main/java/bdv/util/EmptySource.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,11 @@
3333
import bdv.viewer.Source;
3434
import mpicbg.spim.data.sequence.FinalVoxelDimensions;
3535
import mpicbg.spim.data.sequence.VoxelDimensions;
36-
import net.imglib2.*;
36+
import net.imglib2.FinalInterval;
37+
import net.imglib2.Localizable;
38+
import net.imglib2.RandomAccessible;
39+
import net.imglib2.RandomAccessibleInterval;
40+
import net.imglib2.RealRandomAccessible;
3741
import net.imglib2.position.FunctionRandomAccessible;
3842
import net.imglib2.realtransform.AffineTransform3D;
3943
import net.imglib2.type.numeric.integer.UnsignedShortType;

‎src/main/java/bdv/util/LUTConverterSetup.java

+1-1
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636
import java.util.List;
3737

3838
import net.imglib2.type.numeric.RealType;
39-
import org.scijava.listeners.*;
39+
import org.scijava.listeners.Listeners;
4040

4141
/**
4242
* {@link ConverterSetup} used to control a {@link RealLUTConverter} Note that

‎src/main/java/bdv/util/Procedural3DImageShort.java

+6-1
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,12 @@
3131

3232
import bdv.viewer.Source;
3333
import mpicbg.spim.data.sequence.VoxelDimensions;
34-
import net.imglib2.*;
34+
import net.imglib2.FinalInterval;
35+
import net.imglib2.Interval;
36+
import net.imglib2.RealInterval;
37+
import net.imglib2.RealPoint;
38+
import net.imglib2.RealRandomAccess;
39+
import net.imglib2.RealRandomAccessible;
3540
import net.imglib2.realtransform.AffineTransform3D;
3641
import net.imglib2.type.numeric.integer.UnsignedShortType;
3742
import java.util.function.ToIntFunction;

‎src/main/java/bdv/util/RAIHelper.java

+3-9
Original file line numberDiff line numberDiff line change
@@ -53,8 +53,6 @@
5353
import net.imglib2.view.Views;
5454
import org.slf4j.Logger;
5555
import org.slf4j.LoggerFactory;
56-
//import org.janelia.saalfeldlab.n5.imglib2.RandomAccessibleLoader;
57-
//import org.janelia.saalfeldlab.n5.imglib2.RandomAccessibleLoader;
5856

5957
import static net.imglib2.img.basictypeaccess.AccessFlags.VOLATILE;
6058
import static net.imglib2.type.PrimitiveType.BYTE;
@@ -87,14 +85,10 @@ public class RAIHelper {
8785

8886
final T type = Util.getTypeFromInterval(source);
8987

90-
final long costPerValue = getBitsPerBlock(blockSize, type);
91-
9288
final CachedCellImg<T, ?> img;
93-
final Cache<Long, Cell<?>> cache =
94-
// new BoundedSoftRefLoaderCache(100)
95-
new GlobalLoaderCache(objectSource, timepoint, level).withLoader(
96-
LoadedCellCacheLoader.get(grid, loader, type, AccessFlags.setOf(
97-
VOLATILE)));
89+
final Cache<Long, Cell<?>> cache = new GlobalLoaderCache(objectSource,
90+
timepoint, level).withLoader(LoadedCellCacheLoader.get(grid, loader, type,
91+
AccessFlags.setOf(VOLATILE)));
9892

9993
if (GenericByteType.class.isInstance(type)) {
10094
img = new CachedCellImg(grid, type, cache, ArrayDataAccessFactory.get(

‎src/main/java/bdv/util/ResampledSource.java

+1-2
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,6 @@
4545
import net.imglib2.view.Views;
4646
import org.slf4j.Logger;
4747
import org.slf4j.LoggerFactory;
48-
import sc.fiji.bdvpg.services.SourceAndConverterServices;
4948
import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
5049

5150
import java.util.ArrayList;
@@ -137,7 +136,7 @@ public class ResampledSource<T extends NumericType<T> & NativeType<T>>
137136
* @param originInterpolation specifies whether the origin source should be
138137
* interpolated of not in the resampling process
139138
* @param defaultMipMapLevel mipmap level chosen to resample the origin source
140-
* if reuseMipMaps is false
139+
* if reuseMipMaps is false
141140
*/
142141
public ResampledSource(Source<T> source, Source<?> resamplingModel,
143142
String name, boolean reuseMipMaps, boolean cache,

‎src/main/java/bdv/util/VolatileSource.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -44,7 +44,11 @@
4444
import net.imglib2.type.numeric.integer.UnsignedIntType;
4545
import net.imglib2.type.numeric.integer.UnsignedShortType;
4646
import net.imglib2.type.numeric.real.FloatType;
47-
import net.imglib2.type.volatiles.*;
47+
import net.imglib2.type.volatiles.VolatileARGBType;
48+
import net.imglib2.type.volatiles.VolatileFloatType;
49+
import net.imglib2.type.volatiles.VolatileUnsignedByteType;
50+
import net.imglib2.type.volatiles.VolatileUnsignedIntType;
51+
import net.imglib2.type.volatiles.VolatileUnsignedShortType;
4852
import net.imglib2.view.ExtendedRandomAccessibleInterval;
4953
import net.imglib2.view.Views;
5054

‎src/main/java/net/imglib2/realtransform/AffineTransform3DAdapter.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,11 @@
2929

3030
package net.imglib2.realtransform;
3131

32-
import com.google.gson.*;
32+
import com.google.gson.JsonDeserializationContext;
33+
import com.google.gson.JsonElement;
34+
import com.google.gson.JsonObject;
35+
import com.google.gson.JsonParseException;
36+
import com.google.gson.JsonSerializationContext;
3337
import org.scijava.plugin.Plugin;
3438
import sc.fiji.persist.IClassAdapter;
3539
import java.lang.reflect.Type;

‎src/main/java/net/imglib2/realtransform/InvertibleRealTransformSequenceAdapter.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,11 @@
2929

3030
package net.imglib2.realtransform;
3131

32-
import com.google.gson.*;
32+
import com.google.gson.JsonDeserializationContext;
33+
import com.google.gson.JsonElement;
34+
import com.google.gson.JsonObject;
35+
import com.google.gson.JsonParseException;
36+
import com.google.gson.JsonSerializationContext;
3337
import org.scijava.plugin.Plugin;
3438
import org.slf4j.Logger;
3539
import org.slf4j.LoggerFactory;

‎src/main/java/net/imglib2/realtransform/ThinPlateSplineTransformAdapter.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,11 @@
2929

3030
package net.imglib2.realtransform;
3131

32-
import com.google.gson.*;
32+
import com.google.gson.JsonDeserializationContext;
33+
import com.google.gson.JsonElement;
34+
import com.google.gson.JsonObject;
35+
import com.google.gson.JsonParseException;
36+
import com.google.gson.JsonSerializationContext;
3337
import jitk.spline.ThinPlateR2LogRSplineKernelTransform;
3438
import org.scijava.plugin.Plugin;
3539
import org.slf4j.Logger;

‎src/main/java/net/imglib2/realtransform/ThinPlateSplineTransformRunTimeAdapter.java

-2
Original file line numberDiff line numberDiff line change
@@ -30,8 +30,6 @@
3030
package net.imglib2.realtransform;
3131

3232
import org.scijava.plugin.Plugin;
33-
import org.slf4j.Logger;
34-
import org.slf4j.LoggerFactory;
3533
import sc.fiji.persist.IClassRuntimeAdapter;
3634

3735
/**

‎src/main/java/net/imglib2/realtransform/Wrapped2DTransformAs3DRealTransformAdapter.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,11 @@
2929

3030
package net.imglib2.realtransform;
3131

32-
import com.google.gson.*;
32+
import com.google.gson.JsonDeserializationContext;
33+
import com.google.gson.JsonElement;
34+
import com.google.gson.JsonObject;
35+
import com.google.gson.JsonParseException;
36+
import com.google.gson.JsonSerializationContext;
3337
import org.scijava.plugin.Plugin;
3438
import org.slf4j.Logger;
3539
import org.slf4j.LoggerFactory;

‎src/main/java/net/imglib2/realtransform/Wrapped2DTransformAs3DRealTransformRunTimeAdapter.java

-2
Original file line numberDiff line numberDiff line change
@@ -30,8 +30,6 @@
3030
package net.imglib2.realtransform;
3131

3232
import org.scijava.plugin.Plugin;
33-
import org.slf4j.Logger;
34-
import org.slf4j.LoggerFactory;
3533
import sc.fiji.persist.IClassRuntimeAdapter;
3634

3735
/**

‎src/main/java/net/imglib2/realtransform/WrappedIterativeInvertibleRealTransformAdapter.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,11 @@
2929

3030
package net.imglib2.realtransform;
3131

32-
import com.google.gson.*;
32+
import com.google.gson.JsonDeserializationContext;
33+
import com.google.gson.JsonElement;
34+
import com.google.gson.JsonObject;
35+
import com.google.gson.JsonParseException;
36+
import com.google.gson.JsonSerializationContext;
3337
import net.imglib2.realtransform.inverse.WrappedIterativeInvertibleRealTransform;
3438
import org.scijava.plugin.Plugin;
3539
import sc.fiji.persist.IClassAdapter;

‎src/main/java/sc/fiji/bdvpg/bdv/BdvHandleHelper.java

+9-3
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,10 @@
3535
import bdv.util.BdvOptions;
3636
import bdv.util.BdvOverlay;
3737
import bdv.viewer.Source;
38-
import net.imglib2.*;
38+
import net.imglib2.FinalInterval;
39+
import net.imglib2.FinalRealInterval;
40+
import net.imglib2.Interval;
41+
import net.imglib2.RandomAccessibleInterval;
3942
import net.imglib2.realtransform.AffineTransform3D;
4043
import net.imglib2.type.numeric.ARGBType;
4144
import net.imglib2.util.Intervals;
@@ -51,8 +54,11 @@
5154
import sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService;
5255
import sc.fiji.bdvpg.viewers.ViewerAdapter;
5356

54-
import javax.swing.*;
55-
import java.awt.*;
57+
import javax.swing.JFrame;
58+
import javax.swing.KeyStroke;
59+
import javax.swing.SwingUtilities;
60+
import java.awt.Color;
61+
import java.awt.Graphics2D;
5662
import java.awt.event.WindowAdapter;
5763
import java.awt.event.WindowEvent;
5864
import java.io.File;

‎src/main/java/sc/fiji/bdvpg/bdv/MenuAdder.java

+3-1
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,9 @@
3232
import bdv.util.BdvHandle;
3333
import bdv.util.BdvHandleFrame;
3434

35-
import javax.swing.*;
35+
import javax.swing.JMenu;
36+
import javax.swing.JMenuBar;
37+
import javax.swing.JMenuItem;
3638
import java.awt.event.ActionListener;
3739

3840
/**

‎src/main/java/sc/fiji/bdvpg/bdv/navigate/RayCastPositionerSliderAdder.java

+2-2
Original file line numberDiff line numberDiff line change
@@ -39,8 +39,8 @@
3939
import sc.fiji.bdvpg.bdv.BdvHandleHelper;
4040
import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
4141

42-
import javax.swing.*;
43-
import java.awt.*;
42+
import javax.swing.JSlider;
43+
import java.awt.BorderLayout;
4444
import java.util.ArrayList;
4545
import java.util.List;
4646
import java.util.stream.Collectors;

‎src/main/java/sc/fiji/bdvpg/bdv/navigate/ViewerTransformAdjuster.java

+4-1
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,10 @@
3333
import bdv.util.BdvHandle;
3434
import bdv.viewer.SourceAndConverter;
3535
import bdv.viewer.ViewerState;
36-
import net.imglib2.*;
36+
import net.imglib2.FinalRealInterval;
37+
import net.imglib2.Interval;
38+
import net.imglib2.RealInterval;
39+
import net.imglib2.RealPoint;
3740
import net.imglib2.realtransform.AffineTransform3D;
3841
import net.imglib2.util.Intervals;
3942
import net.imglib2.util.LinAlgHelpers;

‎src/main/java/sc/fiji/bdvpg/behaviour/EditorBehaviourInstaller.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,11 @@
4141
import sc.fiji.bdvpg.bdv.config.BdvSettingsGUISetter;
4242
import sc.fiji.bdvpg.scijava.command.bdv.BdvSourcesRemoverCommand;
4343
import sc.fiji.bdvpg.scijava.command.bdv.BdvSourcesShowCommand;
44-
import sc.fiji.bdvpg.scijava.command.source.*;
44+
import sc.fiji.bdvpg.scijava.command.source.BasicTransformerCommand;
45+
import sc.fiji.bdvpg.scijava.command.source.InteractiveBrightnessAdjusterCommand;
46+
import sc.fiji.bdvpg.scijava.command.source.SourceColorChangerCommand;
47+
import sc.fiji.bdvpg.scijava.command.source.SourcesInvisibleMakerCommand;
48+
import sc.fiji.bdvpg.scijava.command.source.SourcesRemoverCommand;
4549
import sc.fiji.bdvpg.services.SourceAndConverterServices;
4650

4751
import java.io.File;

‎src/main/java/sc/fiji/bdvpg/bvv/BvvHandleHelper.java

+2-1
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,8 @@
3333
import org.scijava.cache.CacheService;
3434
import org.scijava.object.ObjectService;
3535

36-
import javax.swing.*;
36+
import javax.swing.JFrame;
37+
import javax.swing.SwingUtilities;
3738
import java.awt.event.WindowAdapter;
3839
import java.awt.event.WindowEvent;
3940
import java.lang.ref.WeakReference;

‎src/main/java/sc/fiji/bdvpg/cache/AbstractGlobalCache.java

+12-12
Original file line numberDiff line numberDiff line change
@@ -50,18 +50,18 @@
5050
* {@link bdv.ViewerImgLoader} in order to use the bigdataviewer playground
5151
* global cache. Two implementations are provided: - a Caffeine backed cache
5252
* {@link CaffeineGlobalCache} - and a LinkedHashMap cache
53-
* {@link BoundedLinkedHashMapGlobalCache} The
54-
* {@link GlobalCacheBuilder} object can be serialized to store the
55-
* cache configuration The global caching allows to bound the memory used when
56-
* many sources are potentially accessed in a random manner by the program. The
57-
* reason to use many sources is if the user wants to work on different spim
58-
* data objects at the same time, work with resampled sources, etc Global
59-
* caching allow to bound the memory used at the JVM level, instead of a per
60-
* source level or per spimdata level. Each value of the value is weighted by
61-
* its memory footprint, assuming it is a {@link Cell} object. If the value is
62-
* not a Cell object, an error is logged. This allows to bound memory correctly
63-
* even when sources have very different block size (setting a fixed number of
64-
* items maintained in cache would not be precise enough).
53+
* {@link BoundedLinkedHashMapGlobalCache} The {@link GlobalCacheBuilder} object
54+
* can be serialized to store the cache configuration The global caching allows
55+
* to bound the memory used when many sources are potentially accessed in a
56+
* random manner by the program. The reason to use many sources is if the user
57+
* wants to work on different spim data objects at the same time, work with
58+
* resampled sources, etc Global caching allow to bound the memory used at the
59+
* JVM level, instead of a per source level or per spimdata level. Each value of
60+
* the value is weighted by its memory footprint, assuming it is a {@link Cell}
61+
* object. If the value is not a Cell object, an error is logged. This allows to
62+
* bound memory correctly even when sources have very different block size
63+
* (setting a fixed number of items maintained in cache would not be precise
64+
* enough).
6565
*
6666
* @author Nicolas Chiaruttini
6767
*/

‎src/main/java/sc/fiji/bdvpg/scijava/BdvScijavaHelper.java

+3-1
Original file line numberDiff line numberDiff line change
@@ -38,7 +38,9 @@
3838
import org.slf4j.Logger;
3939
import org.slf4j.LoggerFactory;
4040

41-
import javax.swing.*;
41+
import javax.swing.JMenu;
42+
import javax.swing.JMenuBar;
43+
import javax.swing.JMenuItem;
4244
import java.util.Arrays;
4345
import java.util.List;
4446
import java.util.stream.Collectors;

‎src/main/java/sc/fiji/bdvpg/scijava/ScijavaSwingUI.java

+1-1
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@
4242
import org.scijava.widget.InputHarvester;
4343
import org.scijava.widget.InputPanel;
4444

45-
import javax.swing.*;
45+
import javax.swing.JPanel;
4646
import java.util.Collections;
4747
import java.util.List;
4848

‎src/main/java/sc/fiji/bdvpg/scijava/adapter/AbstractSpimdataAdapter.java

+7-1
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,13 @@
2929

3030
package sc.fiji.bdvpg.scijava.adapter;
3131

32-
import com.google.gson.*;
32+
import com.google.gson.JsonDeserializationContext;
33+
import com.google.gson.JsonDeserializer;
34+
import com.google.gson.JsonElement;
35+
import com.google.gson.JsonObject;
36+
import com.google.gson.JsonParseException;
37+
import com.google.gson.JsonSerializationContext;
38+
import com.google.gson.JsonSerializer;
3339
import mpicbg.spim.data.generic.AbstractSpimData;
3440
import org.slf4j.Logger;
3541
import org.slf4j.LoggerFactory;

‎src/main/java/sc/fiji/bdvpg/scijava/adapter/SourceAndConverterAdapter.java

+7-1
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,13 @@
3131

3232
import bdv.viewer.Source;
3333
import bdv.viewer.SourceAndConverter;
34-
import com.google.gson.*;
34+
import com.google.gson.JsonDeserializationContext;
35+
import com.google.gson.JsonDeserializer;
36+
import com.google.gson.JsonElement;
37+
import com.google.gson.JsonObject;
38+
import com.google.gson.JsonParseException;
39+
import com.google.gson.JsonSerializationContext;
40+
import com.google.gson.JsonSerializer;
3541
import net.imglib2.display.ColorConverter;
3642
import net.imglib2.type.numeric.ARGBType;
3743
import org.scijava.InstantiableException;

‎src/main/java/sc/fiji/bdvpg/scijava/adapter/source/EmptySourceAdapter.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,11 @@
3131

3232
import bdv.util.EmptySource;
3333
import bdv.viewer.SourceAndConverter;
34-
import com.google.gson.*;
34+
import com.google.gson.JsonDeserializationContext;
35+
import com.google.gson.JsonElement;
36+
import com.google.gson.JsonObject;
37+
import com.google.gson.JsonParseException;
38+
import com.google.gson.JsonSerializationContext;
3539
import org.scijava.plugin.Plugin;
3640
import sc.fiji.bdvpg.services.SourceAndConverterAdapter;
3741
import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;

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