Harmonize jzarr

pom.xml

@@ -32,6 +32,20 @@
     </scm>
 
     <developers>
+        <developer>
+            <id>SabineEmbacher</id>
+            <name>Sabine Embacher</name>
+            <roles>
+                <role>maintainer</role>
+            </roles>
+        </developer>
+        <developer>
+            <id>TonioF</id>
+            <name>Tonio Fincke</name>
+            <roles>
+                <role>maintainer</role>
+            </roles>
+        </developer>
         <developer>
             <id>joshmoore</id>
             <name>Josh Moore</name>
@@ -119,23 +133,7 @@
         <dependency>
             <groupId>org.assertj</groupId>
             <artifactId>assertj-core</artifactId>
-            <version>3.19.0</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.lasersonlab</groupId>
-            <artifactId>s3fs</artifactId>
-            <version>2.2.3</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.dataformat</groupId>
-                    <artifactId>jackson-dataformat-cbor</artifactId>
-                </exclusion>
-            </exclusions>
+            <version>3.27.7</version>
             <scope>test</scope>
         </dependency>
     </dependencies>
@@ -154,7 +152,7 @@
     <repositories>
         <repository>
             <id>unidata.releases</id>
-            <url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases</url>
+            <url>https://artifacts.unidata.ucar.edu/repository/unidata-all/</url>
             <snapshots><enabled>false</enabled></snapshots>
         </repository>
     </repositories>
@@ -265,14 +263,6 @@
                     </excludes>
                 </configuration>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-surefire-plugin</artifactId>
-                    <version>3.0.0-M5</version>
-                    <configuration>
-                        <includes>**/*.java</includes>
-                    </configuration>
-             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-gpg-plugin</artifactId>
@@ -332,4 +322,4 @@
         </profile>
     </profiles>
 
-</project>
+</project>

src/main/java/com/bc/zarr/ArrayParams.java

@@ -36,7 +36,6 @@
  * The class ArrayParams implements the Builder pattern. It is used on java side to imitate the pythonic default
  * value feature for function arguments. So the recognition factor for users who are familiar with the python zarr
  * framework should be high. E.g.:
- *
  * Python example:
  * <pre>
  *    za = zarr.create(
@@ -58,7 +57,6 @@
  *    );
  * </pre>
  * Shape must be given!
- *
  * If not given ... parameter default values are:
  * <pre>
  *   boolean chunked = true;
@@ -92,7 +90,6 @@ public ArrayParams shape(int... shape) {
 
     /**
      * Sets the optional {@code chunks} and returns a reference to this Builder so that the methods can be chained together.
-     *
      * The number of dimensions must be equal to the number of dimensions of the shape.
      *
      * @param chunks the {@code chunks} to set.

src/main/java/com/bc/zarr/CompressorFactory.java

@@ -40,7 +40,6 @@
 import java.io.OutputStream;
 import java.nio.ByteBuffer;
 import java.util.Arrays;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.zip.Deflater;

src/main/java/com/bc/zarr/ZarrArray.java

@@ -321,7 +321,14 @@ private boolean isBufferShapeEqualChunkShape(int[] bufferShape) {
     }
 
     private boolean isZeroOffset(int[] offset) {
-        return Arrays.equals(offset, new int[offset.length]);
+        //return Arrays.equals(offset, new int[offset.length]);
+        // avoid new for a test
+        for (int i : offset) {
+            if (i != 0) {
+                return false;
+            }
+        }
+        return true;
     }
 
     public void writeAttributes(Map<String, Object> attributes) throws IOException {

src/main/java/com/bc/zarr/chunk/ChunkReaderWriterImpl_Byte.java

@@ -29,6 +29,7 @@
 import com.bc.zarr.storage.Store;
 import ucar.ma2.Array;
 import ucar.ma2.DataType;
+import ucar.ma2.IndexIterator;
 
 import java.io.*;
 
@@ -57,14 +58,31 @@ public Array read(String storeKey) throws IOException {
         }
     }
 
+    protected boolean isFillOnly(Array array) {
+        if (fill == null) {
+            return false;
+        }
+        final IndexIterator iter = array.getIndexIterator();
+        while (iter.hasNext()) {
+            if (iter.getByteNext() != fill.byteValue()) {
+                return false;
+            }
+        }
+        return true;
+    }
+
     @Override
     public void write(String storeKey, Array array) throws IOException {
-        final byte[] bytes = (byte[]) array.get1DJavaArray(DataType.BYTE);
-        try (
-                final ByteArrayInputStream is = new ByteArrayInputStream(bytes);
-                final OutputStream os = store.getOutputStream(storeKey)
-        ) {
-            compressor.compress(is, os);
+        if (isFillOnly(array)) {
+            store.delete(storeKey);
+        } else {
+            final byte[] bytes = (byte[]) array.get1DJavaArray(DataType.BYTE);
+            try (
+                    final ByteArrayInputStream is = new ByteArrayInputStream(bytes);
+                    final OutputStream os = store.getOutputStream(storeKey)
+            ) {
+                compressor.compress(is, os);
+            }
         }
     }
 }

src/main/java/com/bc/zarr/chunk/ChunkReaderWriterImpl_Double.java

@@ -29,6 +29,7 @@
 import com.bc.zarr.storage.Store;
 import ucar.ma2.Array;
 import ucar.ma2.DataType;
+import ucar.ma2.IndexIterator;
 
 import javax.imageio.stream.ImageInputStream;
 import javax.imageio.stream.ImageOutputStream;
@@ -69,18 +70,44 @@ public Array read(String storeKey) throws IOException {
         }
     }
 
+    protected boolean isFillOnly(Array array) {
+        if (fill == null) {
+            return false;
+        }
+        final IndexIterator iter = array.getIndexIterator();
+        final double fillValue = fill.doubleValue();
+        if (Double.isNaN(fillValue)) {
+            while (iter.hasNext()) {
+                if (! Double.isNaN(iter.getDoubleNext())) {
+                    return false;
+                }
+            }
+        } else {
+            while (iter.hasNext()) {
+                if (iter.getDoubleNext() != fillValue) {
+                    return false;
+                }
+            }
+        }
+        return true;
+    }
+
     @Override
     public void write(String storeKey, Array array) throws IOException {
-        try (
-                final ImageOutputStream iis = new MemoryCacheImageOutputStream(new ByteArrayOutputStream());
-                final InputStream is = new ZarrInputStreamAdapter(iis);
-                final OutputStream os = store.getOutputStream(storeKey)
-        ) {
-            final double[] doubles = (double[]) array.get1DJavaArray(DataType.DOUBLE);
-            iis.setByteOrder(order);
-            iis.writeDoubles(doubles, 0, doubles.length);
-            iis.seek(0);
-            compressor.compress(is, os);
+        if (isFillOnly(array)) {
+            store.delete(storeKey);
+        } else {
+            try (
+                    final ImageOutputStream iis = new MemoryCacheImageOutputStream(new ByteArrayOutputStream());
+                    final InputStream is = new ZarrInputStreamAdapter(iis);
+                    final OutputStream os = store.getOutputStream(storeKey)
+            ) {
+                final double[] doubles = (double[]) array.get1DJavaArray(DataType.DOUBLE);
+                iis.setByteOrder(order);
+                iis.writeDoubles(doubles, 0, doubles.length);
+                iis.seek(0);
+                compressor.compress(is, os);
+            }
         }
     }
 }

src/main/java/com/bc/zarr/chunk/ChunkReaderWriterImpl_Float.java

@@ -29,6 +29,7 @@
 import com.bc.zarr.storage.Store;
 import ucar.ma2.Array;
 import ucar.ma2.DataType;
+import ucar.ma2.IndexIterator;
 
 import javax.imageio.stream.ImageInputStream;
 import javax.imageio.stream.ImageOutputStream;
@@ -69,18 +70,44 @@ public Array read(String storeKey) throws IOException {
         }
     }
 
+    protected boolean isFillOnly(Array array) {
+        if (fill == null) {
+            return false;
+        }
+        final IndexIterator iter = array.getIndexIterator();
+        final float fillValue = fill.floatValue();
+        if (Float.isNaN(fillValue)) {
+            while (iter.hasNext()) {
+                if (! Float.isNaN(iter.getFloatNext())) {
+                    return false;
+                }
+            }
+        } else {
+            while (iter.hasNext()) {
+                if (iter.getFloatNext() != fillValue) {
+                    return false;
+                }
+            }
+        }
+        return true;
+    }
+
     @Override
     public void write(String storeKey, Array array) throws IOException {
-        try (
-                final ImageOutputStream iis = new MemoryCacheImageOutputStream(new ByteArrayOutputStream());
-                final InputStream is = new ZarrInputStreamAdapter(iis);
-                final OutputStream os = store.getOutputStream(storeKey)
-        ) {
-            final float[] floats = (float[]) array.get1DJavaArray(DataType.FLOAT);
-            iis.setByteOrder(order);
-            iis.writeFloats(floats, 0, floats.length);
-            iis.seek(0);
-            compressor.compress(is, os);
+        if (isFillOnly(array)) {
+            store.delete(storeKey);
+        } else {
+            try (
+                    final ImageOutputStream iis = new MemoryCacheImageOutputStream(new ByteArrayOutputStream());
+                    final InputStream is = new ZarrInputStreamAdapter(iis);
+                    final OutputStream os = store.getOutputStream(storeKey)
+            ) {
+                final float[] floats = (float[]) array.get1DJavaArray(DataType.FLOAT);
+                iis.setByteOrder(order);
+                iis.writeFloats(floats, 0, floats.length);
+                iis.seek(0);
+                compressor.compress(is, os);
+            }
         }
     }
 }

src/main/java/com/bc/zarr/chunk/ChunkReaderWriterImpl_Integer.java

@@ -29,6 +29,7 @@
 import com.bc.zarr.storage.Store;
 import ucar.ma2.Array;
 import ucar.ma2.DataType;
+import ucar.ma2.IndexIterator;
 
 import javax.imageio.stream.ImageInputStream;
 import javax.imageio.stream.ImageOutputStream;
@@ -69,18 +70,35 @@ public Array read(String storeKey) throws IOException {
         }
     }
 
+    protected boolean isFillOnly(Array array) {
+        if (fill == null) {
+            return false;
+        }
+        final IndexIterator iter = array.getIndexIterator();
+        while (iter.hasNext()) {
+            if (iter.getIntNext() != fill.intValue()) {
+                return false;
+            }
+        }
+        return true;
+    }
+
     @Override
     public void write(String storeKey, Array array) throws IOException {
-        try (
-                final ImageOutputStream iis = new MemoryCacheImageOutputStream(new ByteArrayOutputStream());
-                final InputStream is = new ZarrInputStreamAdapter(iis);
-                final OutputStream os = store.getOutputStream(storeKey)
-        ) {
-            final int[] ints = (int[]) array.get1DJavaArray(DataType.INT);
-            iis.setByteOrder(order);
-            iis.writeInts(ints, 0, ints.length);
-            iis.seek(0);
-            compressor.compress(is, os);
+        if (isFillOnly(array)) {
+            store.delete(storeKey);
+        } else {
+            try (
+                    final ImageOutputStream iis = new MemoryCacheImageOutputStream(new ByteArrayOutputStream());
+                    final InputStream is = new ZarrInputStreamAdapter(iis);
+                    final OutputStream os = store.getOutputStream(storeKey)
+            ) {
+                final int[] ints = (int[]) array.get1DJavaArray(DataType.INT);
+                iis.setByteOrder(order);
+                iis.writeInts(ints, 0, ints.length);
+                iis.seek(0);
+                compressor.compress(is, os);
+            }
         }
     }
 }