Update to zarr-java 0.1.0 and bioformats2raw 0.12.0-rc2

Requires updating the minimum Java version to 11, see glencoesoftware/bioformats2raw#294

Author: melissalinkert

build.gradle

@@ -8,9 +8,14 @@ plugins {
 group = 'com.glencoesoftware'
 version = '0.10.0-SNAPSHOT'
 
-mainClassName = 'com.glencoesoftware.pyramid.PyramidFromDirectoryWriter'
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
+application {
+  mainClass = 'com.glencoesoftware.pyramid.PyramidFromDirectoryWriter'
+}
+java {
+  toolchain {
+    languageVersion = JavaLanguageVersion.of(11)
+  }
+}
 
 repositories {
     mavenCentral()
@@ -30,11 +35,11 @@ repositories {
 
 dependencies {
     implementation 'net.java.dev.jna:jna:5.10.0'
-    implementation 'dev.zarr:zarr-java:0.0.10'
+    implementation 'dev.zarr:zarr-java:0.1.0'
     implementation 'info.picocli:picocli:4.7.5'
     implementation 'me.tongfei:progressbar:0.9.0'
     implementation 'ome:formats-bsd:8.3.0'
-    implementation 'com.glencoesoftware:bioformats2raw:0.12.0-rc1'
+    implementation 'com.glencoesoftware:bioformats2raw:0.12.0-rc2'
     implementation group: 'ch.qos.logback', name: 'logback-classic', version: '1.3.15'
     implementation group: 'ch.qos.logback', name: 'logback-core', version: '1.3.15'
 
@@ -61,7 +66,7 @@ jar {
             "Implementation-Title": "raw2ometiff converter",
             "Implementation-Version": archiveVersion,
             "Implementation-Vendor": "Glencoe Software Inc.",
-            "Main-Class": mainClassName
+            "Main-Class": application.mainClass
         )
     }
 }

src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java

@@ -718,7 +718,9 @@ private byte[] readTile(PyramidSeries s, ResolutionDescriptor descriptor,
         ", position = [" + pos[0] + ", " + pos[1] + ", " + pos[2] + "]");
     }
     try {
-      ucar.ma2.Array tile = block.read(Utils.toLongArray(gridPosition), shape);
+      ucar.ma2.Array tile = block.read(
+        Utils.toLongArray(gridPosition),
+        Utils.toLongArray(shape));
       ByteBuffer buf = tile.getDataAsByteBuffer(
         s.littleEndian ? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN);
       byte[] bytes = new byte[buf.remaining()];