Zarrv3 quick czireader and other fixes

.gitignore

@@ -17,3 +17,5 @@
 # IntelliJ  #
 .idea/
 SPIM_Registration.iml
+
+.claude

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>net.preibisch</groupId>
 	<artifactId>multiview-reconstruction</artifactId>
-	<version>9.0.0-SNAPSHOT</version>
+	<version>9.0.1-SNAPSHOT</version>
 
 	<name>Multiview Reconstruction</name>
 	<description>Software for the reconstruction of multi-view microscopic acquisitions
@@ -98,6 +98,10 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 
 		<license.licenseName>gpl_v2</license.licenseName>
 		<license.copyrightOwners>Multiview Reconstruction developers.</license.copyrightOwners>
+		<scijava.jvm.version>17</scijava.jvm.version>
+		<scijava.javadoc.url.java>https://javadoc.scijava.org/Java11/</scijava.javadoc.url.java>
+		<scijava.javadoc.url.javafx>https://javadoc.scijava.org/JavaFX11/</scijava.javadoc.url.javafx>
+		<legacyMode>true</legacyMode> <!-- NB: Make javadoc less strict about Java module system. -->
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
@@ -119,6 +123,8 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 		<imglib2-cache.version>1.0.0-beta-20</imglib2-cache.version>
 		<imglib2-realtransform.version>4.0.5</imglib2-realtransform.version>
 		<imglib2-algorithm.version>0.18.3</imglib2-algorithm.version>
+		<bigdataviewer-core.version>10.6.11</bigdataviewer-core.version>
+		<javafx.version>19.0.2.1</javafx.version>
 		<multiview-simulation.version>0.3.1</multiview-simulation.version>
 
 		<mpicbg.version>1.6.6</mpicbg.version>
@@ -318,6 +324,11 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 			<artifactId>ijp-kheops</artifactId>
 			<version>${ijp-kheops.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>ch.epfl.biop</groupId>
+			<artifactId>quick-start-czi-reader</artifactId>
+			<version>0.3.0</version>
+		</dependency>
 		<dependency>
 			<groupId>com.google.code.gson</groupId>
 			<artifactId>gson</artifactId>
@@ -361,6 +372,23 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 			<artifactId>slf4j-api</artifactId>
 		</dependency>
 
+		<!-- JavaFX dependencies -->
+		<dependency>
+			<groupId>org.openjfx</groupId>
+			<artifactId>javafx-base</artifactId>
+			<classifier>${scijava.natives.classifier.javafx}</classifier>
+		</dependency>
+		<dependency>
+			<groupId>org.openjfx</groupId>
+			<artifactId>javafx-controls</artifactId>
+			<classifier>${scijava.natives.classifier.javafx}</classifier>
+		</dependency>
+		<dependency>
+			<groupId>org.openjfx</groupId>
+			<artifactId>javafx-swing</artifactId>
+			<classifier>${scijava.natives.classifier.javafx}</classifier>
+		</dependency>
+
 		<!-- Test dependencies -->
 		<dependency>
 			<groupId>org.junit.jupiter</groupId>
@@ -405,7 +433,7 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 	</build>
 
 	<profiles>
-	<profile>
+		<profile>
 			<id>fatjar</id>
 			<build>
 				<plugins>
@@ -455,6 +483,28 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 				</plugins>
 			</build>
 		</profile>
+		<profile>
+			<id>with-deps</id>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-dependency-plugin</artifactId>
+						<executions>
+							<execution>
+								<id>copy-dependencies</id>
+								<phase>package</phase>
+								<goals><goal>copy-dependencies</goal></goals>
+								<configuration>
+									<outputDirectory>${project.build.directory}/deps</outputDirectory>
+									<includeScope>runtime</includeScope>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
 	</profiles>
 
 </project>

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/SmartSPIM.java

@@ -227,7 +227,7 @@ public static boolean populateImageSize( final SmartSPIMMetaData metadata, final
 						IOFunctions.println( "file names are not equal. Stopping." );
 						return false;
 					}
-					
+
 				}
 
 		return true;

src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5Api.java

@@ -39,6 +39,7 @@
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 
+import mpicbg.spim.data.sequence.VoxelDimensions;
 import org.bigdataviewer.n5.N5CloudImageLoader;
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.DataType;
@@ -192,13 +193,15 @@ else if ( n5Params.format == StorageFormat.HDF5 )
 							}
 							else
 							{
+								VoxelDimensions vx = data.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getVoxelSize();
 								// 5d OME-ZARR with dimension=1 in c and t
 								mrInfo = N5ApiTools.setupBdvDatasetsOMEZARR_ResaveRaw(
 										n5Writer,
 										viewId,
 										dataTypes.get( viewId.getViewSetupId() ),
 										dimensions.get( viewId.getViewSetupId() ),
-										//data.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getVoxelSize().dimensionsAsDoubleArray(),
+										vx.dimensionsAsDoubleArray(), // resolutionS0
+										vx.unit(),
 										compression,
 										blockSize,
 										downsamplings,

src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayRawImagesPopup.java

@@ -29,7 +29,6 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
-import java.util.stream.Collectors;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;