Single LICENSE.md file, disable and remove license file headers

pom.xml

@@ -124,7 +124,11 @@
 		<license.projectName>N5 Viewer</license.projectName>
 		<license.organizationName>Saalfeld Lab</license.organizationName>
 		<license.copyrightOwners>Igor Pisarev, Stephan Saalfeld</license.copyrightOwners>
-		<license.excludes>**/resources/**</license.excludes>
+		<!-- managed by `copy-resources` plugin  -->
+		<license.skipUpdateLicense>true</license.skipUpdateLicense>
+		<license.skipUpdateProjectLicense>true</license.skipUpdateProjectLicense>
+
+		<scijava.jvm.version>8</scijava.jvm.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
@@ -134,16 +138,17 @@
 		<bigdataviewer-core.version>10.6.1</bigdataviewer-core.version>
 		<bigdataviewer-vistools.version>1.0.0-beta-36</bigdataviewer-vistools.version>
 
-		<n5.version>4.0.0-alpha-12</n5.version>
-		<n5-aws-s3.version>4.4.0-alpha-9</n5-aws-s3.version>
-		<n5-blosc.version>2.0.0-alpha-4</n5-blosc.version>
-		<n5-google-cloud.version>5.2.0-alpha-7</n5-google-cloud.version>
-		<n5-hdf5.version>2.3.0-alpha-7</n5-hdf5.version>
-		<n5-ij.version>4.5.0-alpha-7</n5-ij.version>
-		<n5-imglib2.version>7.1.0-alpha-8</n5-imglib2.version>
-		<n5-universe.version>2.4.0-alpha-9</n5-universe.version>
-		<n5-zarr.version>2.0.0-alpha-8</n5-zarr.version>
-		<n5-zstandard.version>2.0.0-alpha-4</n5-zstandard.version>
+		<n5.version>4.0.0</n5.version>
+		<n5-aws-s3.version>5.0.0</n5-aws-s3.version>
+		<n5-blosc.version>2.0.0</n5-blosc.version>
+		<n5-google-cloud.version>6.0.0</n5-google-cloud.version>
+		<n5-hdf5.version>3.0.0</n5-hdf5.version>
+		<n5-ij.version>5.0.0-alpha-8-SNAPSHOT</n5-ij.version>
+		<n5-imglib2.version>8.0.0</n5-imglib2.version>
+		<n5-universe.version>3.0.0</n5-universe.version>
+		<n5-zarr.version>2.0.0</n5-zarr.version>
+		<n5-zstandard.version>2.0.0</n5-zstandard.version>
+
 	</properties>
 
 	<dependencies>
@@ -227,4 +232,63 @@
 			<url>https://maven.scijava.org/content/groups/public</url>
 		</repository>
 	</repositories>
+
+	<build>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.codehaus.mojo</groupId>
+					<artifactId>license-maven-plugin</artifactId>
+					<configuration>
+						<excludes>
+							<exclude>**/*.json</exclude>
+							<exclude>**/resources/**</exclude>
+						</excludes>
+					</configuration>
+				</plugin>
+				<plugin>
+					<groupId>org.codehaus.mojo</groupId>
+					<artifactId>build-helper-maven-plugin</artifactId>
+					<executions>
+						<execution>
+							<id>timestamp-property</id>
+							<goals>
+								<goal>timestamp-property</goal>
+							</goals>
+							<phase>validate</phase>
+							<configuration>
+								<name>current.year</name>
+								<pattern>yyyy</pattern>
+							</configuration>
+						</execution>
+					</executions>
+				</plugin>
+				<plugin>
+					<artifactId>maven-resources-plugin</artifactId>
+					<executions>
+						<execution>
+							<id>copy</id>
+							<phase>compile</phase>
+							<goals>
+								<goal>copy-resources</goal>
+							</goals>
+							<configuration>
+								<outputDirectory>${basedir}</outputDirectory>
+								<resources>
+									<resource>
+										<directory>doc</directory>
+										<includes>
+											<include>*.md</include>
+										</includes>
+										<filtering>true</filtering>
+									</resource>
+								</resources>
+							</configuration>
+						</execution>
+					</executions>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+	</build>
+
 </project>

src/main/java/org/janelia/saalfeldlab/control/AdjustableClippingIntControl.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control;
 
 /**

src/main/java/org/janelia/saalfeldlab/control/ButtonControl.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control;
 
 /**

src/main/java/org/janelia/saalfeldlab/control/ClippingIntControl.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control;
 
 /**

src/main/java/org/janelia/saalfeldlab/control/Control.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control;
 
 import java.util.Set;

src/main/java/org/janelia/saalfeldlab/control/IntControl.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control;
 
 import java.util.Set;

src/main/java/org/janelia/saalfeldlab/control/VPotControl.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control;
 
 /**

src/main/java/org/janelia/saalfeldlab/control/mcu/MCUBDVControls.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control.mcu;
 
 import java.util.function.IntConsumer;

src/main/java/org/janelia/saalfeldlab/control/mcu/MCUButtonControl.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control.mcu;
 
 import java.util.function.IntConsumer;

src/main/java/org/janelia/saalfeldlab/control/mcu/MCUControl.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control.mcu;
 
 import java.util.HashSet;

src/main/java/org/janelia/saalfeldlab/control/mcu/MCUControlPanel.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control.mcu;
 
 import javax.sound.midi.InvalidMidiDataException;

src/main/java/org/janelia/saalfeldlab/control/mcu/MCUFaderControl.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control.mcu;
 
 import java.util.function.IntConsumer;

src/main/java/org/janelia/saalfeldlab/control/mcu/MCUVPotControl.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control.mcu;
 
 import java.util.concurrent.Future;

src/main/java/org/janelia/saalfeldlab/control/mcu/XTouchMiniMCUControlPanel.java

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.janelia.saalfeldlab.control.mcu;
 
 import javax.sound.midi.InvalidMidiDataException;

src/main/java/org/janelia/saalfeldlab/n5/bdv/ColorGenerator.java

@@ -1,24 +1,3 @@
-/*-
- * #%L
- * N5 Viewer
- * %%
- * Copyright (C) 2017 - 2022 Igor Pisarev, Stephan Saalfeld
- * %%
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public
- * License along with this program.  If not, see
- * <http://www.gnu.org/licenses/gpl-3.0.html>.
- * #L%
- */
 package org.janelia.saalfeldlab.n5.bdv;
 
 import java.util.Random;

src/main/java/org/janelia/saalfeldlab/n5/bdv/CropController.java

@@ -1,24 +1,3 @@
-/*-
- * #%L
- * N5 Viewer
- * %%
- * Copyright (C) 2017 - 2022 Igor Pisarev, Stephan Saalfeld
- * %%
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public
- * License along with this program.  If not, see
- * <http://www.gnu.org/licenses/gpl-3.0.html>.
- * #L%
- */
 package org.janelia.saalfeldlab.n5.bdv;
 
 import java.awt.Checkbox;

src/main/java/org/janelia/saalfeldlab/n5/bdv/MultiscaleDatasets.java

@@ -1,24 +1,3 @@
-/*-
- * #%L
- * N5 Viewer
- * %%
- * Copyright (C) 2017 - 2022 Igor Pisarev, Stephan Saalfeld
- * %%
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public
- * License along with this program.  If not, see
- * <http://www.gnu.org/licenses/gpl-3.0.html>.
- * #L%
- */
 package org.janelia.saalfeldlab.n5.bdv;
 
 import java.util.Arrays;

src/main/java/org/janelia/saalfeldlab/n5/bdv/N5Viewer.java

@@ -1,24 +1,3 @@
-/*-
- * #%L
- * N5 Viewer
- * %%
- * Copyright (C) 2017 - 2022 Igor Pisarev, Stephan Saalfeld
- * %%
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public
- * License along with this program.  If not, see
- * <http://www.gnu.org/licenses/gpl-3.0.html>.
- * #L%
- */
 package org.janelia.saalfeldlab.n5.bdv;
 
 import static bdv.BigDataViewer.createConverterToARGB;
@@ -77,10 +56,9 @@
 import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultichannelMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultiscaleMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata;
-import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.NgffSingleScaleAxesMetadata;
-import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadata;
-import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata;
-import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.OmeNgffV05Metadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata;
 import org.scijava.ui.behaviour.io.InputTriggerConfig;
 import org.scijava.ui.behaviour.util.Actions;
 import org.scijava.ui.behaviour.util.InputActionBindings;
@@ -513,8 +491,10 @@ public static <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> &
 			AffineTransform3D[] transforms = null;
 
 			final N5Metadata metadata = selectedMetadata.get(i);
-			final String srcName = metadata.getName();
-
+			String srcName = metadata.getName();
+			if( srcName == null || srcName.isEmpty()) {
+				srcName = n5.getURI().toString().replaceFirst("/$", "").replaceFirst(".*/", "");
+			}
 
 			// TODO: simplify this if/elseif block: much of these ifwall cases can be combined
 			if (metadata instanceof N5SingleScaleMetadata) {
@@ -544,12 +524,6 @@ public static <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> &
 						.sort(multiScaleDataset.getPaths(), multiScaleDataset.spatialTransforms3d());
 				datasetsToOpen = msd.getPaths();
 				transforms = msd.getTransforms();
-			} else if (metadata instanceof OmeNgffV05Metadata) {
-				final OmeNgffV05Metadata multiScaleDataset = (OmeNgffV05Metadata)metadata;
-				final MultiscaleDatasets msd = MultiscaleDatasets
-						.sort(multiScaleDataset.getPaths(), multiScaleDataset.spatialTransforms3d());
-				datasetsToOpen = msd.getPaths();
-				transforms = msd.getTransforms();
 			} else if (metadata instanceof N5CosemMultiScaleMetadata) {
 				final N5CosemMultiScaleMetadata multiScaleDataset = (N5CosemMultiScaleMetadata)metadata;
 				final MultiscaleDatasets msd = MultiscaleDatasets
@@ -844,27 +818,6 @@ private static NgffSingleScaleAxesMetadata isNgffMultiscale(final N5Metadata met
 				if( children[0] instanceof NgffSingleScaleAxesMetadata)
 					return children[0];
 
-		}
-		else if (metadata instanceof OmeNgffV05Metadata) {
-
-			final OmeNgffV05Metadata ngff = (OmeNgffV05Metadata)metadata;
-			final OmeNgffMultiScaleMetadata[] ms = ngff.multiscales;
-
-			// TODO when do we not just take the first one?
-			final NgffSingleScaleAxesMetadata[] children = ms[0].getChildrenMetadata();
-			if( children.length > 0 )
-				if( children[0] instanceof NgffSingleScaleAxesMetadata)
-					return children[0];
-
-		}
-		else if(metadata instanceof OmeNgffMultiScaleMetadata )
-		{
-			final OmeNgffMultiScaleMetadata ms = (OmeNgffMultiScaleMetadata)metadata;
-			final NgffSingleScaleAxesMetadata[] children = ms.getChildrenMetadata();
-			if( children.length > 0 )
-				if( children[0] instanceof NgffSingleScaleAxesMetadata)
-					return children[0];
-
 		}
 
 		return null;
@@ -888,8 +841,9 @@ private static <T extends NumericType<T> & NativeType<T>, V extends NumericType<
 			for (int level = 0; level < images.length; ++level)
 				channels[level] = Views.hyperSlice(images[level], 2, c);
 
+			final String channelName = nChannels > 1 ? srcName + "_ch" + c : srcName;
 			final RandomAccessibleIntervalMipmapSource4D<T> source = new RandomAccessibleIntervalMipmapSource4D<>(
-					channels, type, transforms, vd, srcName, true);
+					channels, type, transforms, vd, channelName, true);
 
 			// TODO fix generics
 			final ValuePair<Source<T>, Source<V>> pair = new ValuePair(