getArrayKeys(String path) throws IOException, FormatException {
- return getGroup(path).getArrayKeys();
+ private boolean isV2() {
+ return array instanceof dev.zarr.zarrjava.v2.Array;
}
public DataType getZarrPixelType(int pixType) {
DataType pixelType = null;
switch(pixType) {
case FormatTools.INT8:
- pixelType = DataType.i1;
+ pixelType = isV2() ? dev.zarr.zarrjava.v2.DataType.INT8 : dev.zarr.zarrjava.v3.DataType.INT8;
break;
case FormatTools.INT16:
- pixelType = DataType.i2;
+ pixelType = isV2() ? dev.zarr.zarrjava.v2.DataType.INT16 : dev.zarr.zarrjava.v3.DataType.INT16;
break;
case FormatTools.INT32:
- pixelType = DataType.i4;
+ pixelType = isV2() ? dev.zarr.zarrjava.v2.DataType.INT32 : dev.zarr.zarrjava.v3.DataType.INT32;
break;
case FormatTools.UINT8:
- pixelType = DataType.u1;
+ pixelType = isV2() ? dev.zarr.zarrjava.v2.DataType.UINT8 : dev.zarr.zarrjava.v3.DataType.UINT8;
break;
case FormatTools.UINT16:
- pixelType = DataType.u2;
+ pixelType = isV2() ? dev.zarr.zarrjava.v2.DataType.UINT16 : dev.zarr.zarrjava.v3.DataType.UINT16;
break;
case FormatTools.UINT32:
- pixelType = DataType.u4;
+ pixelType = isV2() ? dev.zarr.zarrjava.v2.DataType.UINT32 : dev.zarr.zarrjava.v3.DataType.UINT32;
break;
case FormatTools.FLOAT:
- pixelType = DataType.f4;
+ pixelType = isV2() ? dev.zarr.zarrjava.v2.DataType.FLOAT32 : dev.zarr.zarrjava.v3.DataType.FLOAT32;
break;
case FormatTools.DOUBLE:
- pixelType = DataType.f8;
+ pixelType = isV2() ? dev.zarr.zarrjava.v2.DataType.FLOAT64 : dev.zarr.zarrjava.v3.DataType.FLOAT64;
break;
}
return(pixelType);
}
public int getOMEPixelType(DataType pixType) {
-
int pixelType = -1;
- switch(pixType) {
- case i1:
+ if (isV2()) {
+ dev.zarr.zarrjava.v2.DataType dt = (dev.zarr.zarrjava.v2.DataType)pixType;
+ switch(dt) {
+ case INT8:
pixelType = FormatTools.INT8;
break;
- case i2:
+ case INT16:
pixelType = FormatTools.INT16;
break;
- case i4:
+ case INT32:
pixelType = FormatTools.INT32;
break;
- case u1:
+ case UINT8:
pixelType = FormatTools.UINT8;
break;
- case u2:
+ case UINT16:
pixelType = FormatTools.UINT16;
break;
- case u4:
+ case UINT32:
pixelType = FormatTools.UINT32;
break;
- case f4:
+ case FLOAT32:
pixelType = FormatTools.FLOAT;
break;
- case f8:
+ case FLOAT64:
pixelType = FormatTools.DOUBLE;
break;
- case i8:
+ default:
+ break;
+ }
+ }
+ else {
+ dev.zarr.zarrjava.v3.DataType dt = (dev.zarr.zarrjava.v3.DataType)pixType;
+ switch(dt) {
+ case INT8:
+ pixelType = FormatTools.INT8;
+ break;
+ case INT16:
+ pixelType = FormatTools.INT16;
+ break;
+ case INT32:
+ pixelType = FormatTools.INT32;
+ break;
+ case UINT8:
+ pixelType = FormatTools.UINT8;
+ break;
+ case UINT16:
+ pixelType = FormatTools.UINT16;
+ break;
+ case UINT32:
+ pixelType = FormatTools.UINT32;
+ break;
+ case FLOAT32:
+ pixelType = FormatTools.FLOAT;
+ break;
+ case FLOAT64:
pixelType = FormatTools.DOUBLE;
break;
default:
break;
}
+ }
return(pixelType);
}
@@ -193,179 +180,62 @@ public String getNoZarrMsg() {
@Override
public int[] getShape() {
- if (zarrArray != null) return zarrArray.getShape();
+ if (attr != null && attr.containsKey("shape")) {
+ long[] shape = (long[]) attr.get("shape");
+ int[] res = new int[shape.length];
+ for (int i = 0; i < shape.length; i++) {
+ res[i] = (int) shape[i];
+ }
+ return res;
+ }
return null;
}
@Override
public int[] getChunkSize() {
- if (zarrArray != null) return zarrArray.getChunks();
+ if (attr != null && attr.containsKey("chunkShape"))
+ return (int[]) attr.get("chunkShape");
return null;
}
@Override
public int getPixelType() {
- if (zarrArray != null) return getOMEPixelType(zarrArray.getDataType());
+ if (attr != null && attr.containsKey("dataType"))
+ return getOMEPixelType((DataType) attr.get("dataType"));
return 0;
}
@Override
public boolean isLittleEndian() {
- if (zarrArray != null) return (zarrArray.getByteOrder().equals(ByteOrder.LITTLE_ENDIAN));
+ if (attr != null && attr.containsKey("littleEndian"))
+ return (boolean) attr.get("littleEndian");
return false;
}
@Override
public void close() throws IOException {
- zarrArray = null;
- currentId = null;
- if (s3fs != null) {
- s3fs.close();
- }
+ array = null;
+ attr = null;
}
@Override
public boolean isOpen() {
- return (zarrArray != null && currentId != null);
+ return (array != null);
}
-
- @Override
- public String getID() {
- return currentId;
- }
-
+
@Override
public Object readBytes(int[] shape, int[] offset) throws FormatException, IOException {
- if (zarrArray != null) {
+ if (array != null) {
try {
- return zarrArray.read(shape, offset);
- } catch (InvalidRangeException e) {
- throw new FormatException(e);
- }
- }
- else throw new IOException("No Zarr file opened");
- }
-
- @Override
- public void saveBytes(Object data, int[] shape, int[] offset) throws FormatException, IOException {
- if (zarrArray != null) {
- try {
- zarrArray.write(data, shape, offset);
- } catch (InvalidRangeException e) {
+ long[] offsetLong = new long[offset.length];
+ for (int i = 0; i < offset.length; i++) {
+ offsetLong[i] = offset[i];
+ }
+ return array.read(offsetLong, shape).getDataAsByteBuffer().array();
+ } catch (ZarrException e) {
throw new FormatException(e);
}
}
else throw new IOException("No Zarr file opened");
}
-
- @Override
- public void create(String file, MetadataRetrieve meta, int[] chunks, Compression compression) throws IOException {
- int seriesCount = meta.getImageCount();
- int resolutionCount = 1;
-
- ArrayParams params = new ArrayParams();
- params.chunks(chunks);
- params.compressor(nullComp);
-
- boolean isLittleEndian = !meta.getPixelsBigEndian(0);
- if (isLittleEndian) {
- params.byteOrder(ByteOrder.LITTLE_ENDIAN);
- }
-
- int x = meta.getPixelsSizeX(0).getValue().intValue();
- int y = meta.getPixelsSizeY(0).getValue().intValue();
- int z = meta.getPixelsSizeZ(0).getValue().intValue();
- int c = meta.getPixelsSizeC(0).getValue().intValue();
- int t = meta.getPixelsSizeT(0).getValue().intValue();
- // c /= meta.getChannelSamplesPerPixel(0, 0).getValue().intValue();
- int [] shape = {x, y, z, c, t};
- params.shape(shape);
-
- int pixelType = FormatTools.pixelTypeFromString(meta.getPixelsType(0).toString());
- DataType zarrPixelType = getZarrPixelType(pixelType);
- int bytes = FormatTools.getBytesPerPixel(pixelType);
- params.dataType(zarrPixelType);
-
- if (seriesCount > 1) {
- ZarrGroup root = ZarrGroup.create(file);
- ZarrGroup currentGroup = root;
- for (int i = 0; i < seriesCount; i++) {
- x = meta.getPixelsSizeX(i).getValue().intValue();
- y = meta.getPixelsSizeY(i).getValue().intValue();
- z = meta.getPixelsSizeZ(i).getValue().intValue();
- c = meta.getPixelsSizeC(i).getValue().intValue();
- t = meta.getPixelsSizeT(i).getValue().intValue();
- // c /= meta.getChannelSamplesPerPixel(i, 0).getValue().intValue();
- shape = new int[]{x, y, z, c, t};
- params.shape(shape);
-
- pixelType = FormatTools.pixelTypeFromString(meta.getPixelsType(i).toString());
- zarrPixelType = getZarrPixelType(pixelType);
- params.dataType(zarrPixelType);
-
- isLittleEndian = !meta.getPixelsBigEndian(i);
- if (isLittleEndian) {
- params.byteOrder(ByteOrder.LITTLE_ENDIAN);
- }
-
- if (meta instanceof IPyramidStore) {
- resolutionCount = ((IPyramidStore) meta).getResolutionCount(i);
- }
- if (resolutionCount > 1) {
- currentGroup = root.createSubGroup("Series"+i);
- for (int j = 0; j < resolutionCount; j++) {
- zarrArray = currentGroup.createArray("Resolution"+j, params);
- }
- }
- else {
- zarrArray = currentGroup.createArray("Series"+i, params);
- }
- }
- }
- else {
- zarrArray = ZarrArray.create(file, params);
- }
- currentId = file;
- }
-
- @Override
- public void create(String id, MetadataRetrieve meta, int[] chunks) throws IOException {
- create(id, meta, chunks, Compression.NONE);
- }
-
- private String stripZarrRoot(String path) {
- return path.substring(path.indexOf(".zarr")+5);
- }
-
- private String getZarrRoot(String path) {
- return path.substring(0, path.indexOf(".zarr")+5);
- }
-
- private ZarrGroup getGroup(String path) throws IOException {
- ZarrGroup group = null;
- if (s3fs == null) {
- group = ZarrGroup.open(path);
- }
- else {
- s3fs.updateRoot(getZarrRoot(s3fs.getRoot()) + stripZarrRoot(path));
- group = ZarrGroup.open(s3fs);
- }
- return group;
- }
-
- private ZarrArray getArray(String path) throws IOException {
- ZarrArray array = null;
- if (s3fs == null) {
- array = ZarrArray.open(path);
- }
- else {
- s3fs.updateRoot(getZarrRoot(s3fs.getRoot()) + stripZarrRoot(path));
- array = ZarrArray.open(s3fs);
- }
- return array;
- }
-
- public boolean usingS3FileSystemStore() {
- return s3fs != null;
- }
}
diff --git a/src/loci/formats/services/ZarrLocation.java b/src/loci/formats/services/ZarrLocation.java
new file mode 100644
index 0000000..adefa4b
--- /dev/null
+++ b/src/loci/formats/services/ZarrLocation.java
@@ -0,0 +1,289 @@
+package loci.formats.services;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+
+import dev.zarr.zarrjava.core.Array;
+import dev.zarr.zarrjava.core.ArrayMetadata;
+import dev.zarr.zarrjava.core.Group;
+import dev.zarr.zarrjava.core.Node;
+import dev.zarr.zarrjava.store.FilesystemStore;
+import dev.zarr.zarrjava.store.HttpStore;
+import dev.zarr.zarrjava.store.S3Store;
+import dev.zarr.zarrjava.store.StoreHandle;
+import dev.zarr.zarrjava.v2.Endianness;
+import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider;
+import software.amazon.awssdk.auth.credentials.AwsBasicCredentials;
+import software.amazon.awssdk.auth.credentials.StaticCredentialsProvider;
+import software.amazon.awssdk.regions.Region;
+import software.amazon.awssdk.services.s3.S3Client;
+import software.amazon.awssdk.services.s3.S3ClientBuilder;
+import software.amazon.awssdk.services.s3.S3Configuration;
+
+/**
+ *
+ * This class provides a unified interface for accessing Zarr stores from different
+ * storage backends including local filesystem, HTTP/HTTPS endpoints, and S3-compatible
+ * object storage. It offers convenience methods for accessing arrays and groups,
+ * as well as their metadata.
+ *
+ *
+ * Supported URI schemes:
+ *
+ * - file:// or no scheme - Local filesystem storage
+ * - http:// or https:// - HTTP-based storage
+ * - s3:// - S3-compatible object storage (with authentication via URL parameters)
+ *
+ *
+ */
+public class ZarrLocation {
+
+ /** The underlying store handle for accessing Zarr data */
+ StoreHandle store;
+
+ /** The full path to the Zarr store including the .zarr extension */
+ String path;
+
+ /** The name of the Zarr (typically the .zarr directory name) */
+ String name;
+
+ /**
+ * Constructs a ZarrLocation from the given path.
+ *
+ * The path must contain a .zarr extension. The constructor automatically detects
+ * the storage backend based on the URI scheme and initializes the appropriate store.
+ *
+ *
+ * For S3 URIs, authentication parameters can be provided as query parameters:
+ *
+ * - anonymous - Use anonymous access
+ * - accessKeyId and secretAccessKey - Use basic credentials
+ * - region - Specify AWS region (defaults to US_EAST_1)
+ *
+ * Example: s3://host/bucket/path/data.zarr?anonymous=true
+ *
+ *
+ * @param orgPath the path to the Zarr store, must contain .zarr extension
+ * @throws URISyntaxException if the path is not a valid URI
+ * @throws IllegalArgumentException if the path does not contain .zarr or uses an unsupported URI scheme
+ */
+ public ZarrLocation(final String orgPath) throws URISyntaxException, IllegalArgumentException {
+ int i = orgPath.lastIndexOf(".zarr");
+ if (i > 0) {
+ this.path = orgPath.substring(0, i+5);
+ } else {
+ throw new IllegalArgumentException("Path is not a .zarr");
+ }
+
+ URI uri = new URI(path);
+ if (uri.getScheme() == null || uri.getScheme().equals("file")) {
+ int sep = path.lastIndexOf(File.separator);
+ name = path.substring(sep + 1);
+ String storePath = path.substring(0, sep);
+ store = new FilesystemStore(storePath).resolve(name);
+ } else if (uri.getScheme().startsWith("http")) {
+ int sep = path.lastIndexOf("/");
+ name = path.substring(sep + 1);
+ String storePath = path.substring(0, sep);
+ store = new HttpStore(storePath).resolve(name);
+ } else if (uri.getScheme().startsWith("s3")) {
+ String[] tmp = path.replaceFirst("s3://", "").split("/");
+ String host = tmp[0];
+ String bucket = tmp[1];
+ name = tmp[tmp.length - 1];
+ String[] rest = Arrays.copyOfRange(tmp, 2, tmp.length);
+
+ // Extract URL parameters for authentication
+ Map params = new HashMap<>();
+ String query = (new URI(orgPath)).getQuery();
+ if (query != null) {
+ String[] pairs = query.split("&");
+ for (String pair : pairs) {
+ int idx = pair.indexOf("=");
+ if (idx > 0) {
+ params.put(pair.substring(0, idx), pair.substring(idx + 1));
+ }
+ }
+ }
+
+ URI endpoint = new URI("https://" + host);
+ S3ClientBuilder clientBuilder = S3Client.builder()
+ .endpointOverride(endpoint)
+ .region(Region.US_EAST_1); // Default region required even for non-AWS
+
+ S3Configuration s3Config = S3Configuration.builder()
+ .pathStyleAccessEnabled(true)
+ .build();
+ clientBuilder.serviceConfiguration(s3Config);
+
+ if (params.containsKey("anonymous")) {
+ clientBuilder.credentialsProvider(AnonymousCredentialsProvider.create());
+ } else if (params.containsKey("accessKeyId") && params.containsKey("secretAccessKey")) {
+ AwsBasicCredentials credentials = AwsBasicCredentials.create(
+ params.get("accessKeyId"),
+ params.get("secretAccessKey"));
+ clientBuilder.credentialsProvider(StaticCredentialsProvider.create(credentials));
+ }
+ if (params.containsKey("region")) {
+ clientBuilder.region(Region.of(params.get("region")));
+ }
+
+ S3Client client = clientBuilder.build();
+ store = new S3Store(client, bucket, null).resolve(rest);
+ } else {
+ throw new IllegalArgumentException("Unsupported URI scheme: " + uri.getScheme());
+ }
+ }
+
+ /**
+ * Opens and returns a Zarr group at the specified path.
+ *
+ * @param path the relative path to the group within the store (empty string for root group)
+ * @return the opened Group object
+ * @throws IOException if the group cannot be opened or does not exist
+ */
+ public Group getGroup(String path) throws IOException {
+ try {
+ if (path.isEmpty()) {
+ return (Group) Node.open(store);
+ } else {
+ return (Group) Node.open(store.resolve(path.split("/")));
+ }
+ } catch (Exception e) {
+ throw new IOException("Failed to open group at path: "+store+" / " + path, e);
+ }
+ }
+
+ /**
+ * Opens and returns a Zarr array at the specified path.
+ *
+ * @param path the relative path to the array within the store (empty string for root array)
+ * @return the opened Array object
+ * @throws IOException if the array cannot be opened or does not exist
+ */
+ public Array getArray(String path) throws IOException {
+ try {
+ if (path.isEmpty()) {
+ return (Array) Node.open(store);
+ } else {
+ return (Array) Node.open(store.resolve(path.split("/")));
+ }
+ } catch (Exception e) {
+ throw new IOException("Failed to open array at path: "+store+" / " + path, e);
+ }
+ }
+
+ /**
+ * Retrieves metadata from a Zarr array at the specified path.
+ *
+ * @param path the relative path to the array within the store
+ * @return a map containing metadata including shape, chunkShape, dataType, and littleEndian
+ * @throws RuntimeException if the array cannot be accessed or metadata cannot be retrieved
+ */
+ public Map metadataFromArray(String path) {
+ try {
+ Array array = getArray(path);
+ return metadataFromArray(array);
+ } catch (IOException e) {
+ throw new RuntimeException("Failed to get array metadata from path: "+store+" / " + path, e);
+ }
+ }
+
+ /**
+ * Extracts metadata from a Zarr array object.
+ *
+ * The returned map contains:
+ *
+ * - shape - The dimensions of the array
+ * - chunkShape - The chunk dimensions
+ * - dataType - The data type of array elements
+ * - littleEndian - Byte order (Todo: currently always true for v3 arrays)
+ *
+ *
+ *
+ * @param array the Array object to extract metadata from
+ * @return a map containing the array metadata
+ */
+ public Map metadataFromArray(Array array) {
+ Map res = new HashMap<>();
+ ArrayMetadata m = array.metadata();
+ if (array instanceof dev.zarr.zarrjava.v3.Array) {
+ // TODO: Implement!!
+ res.put("littleEndian", true);
+ } else {
+ dev.zarr.zarrjava.v2.ArrayMetadata m2 = (dev.zarr.zarrjava.v2.ArrayMetadata) m;
+ res.put("littleEndian", m2.endianness.equals(Endianness.LITTLE));
+ }
+ res.put("shape", m.shape);
+ res.put("chunkShape", m.chunkShape());
+ res.put("dataType", m.dataType());
+ return res;
+ }
+
+ /**
+ * Retrieves metadata from a Zarr group at the specified path.
+ *
+ * @param path the relative path to the group within the store
+ * @return a map containing the group's attributes
+ * @throws RuntimeException if the group cannot be accessed or metadata cannot be retrieved
+ */
+ public Map metadataFromGroup(String path) {
+ try {
+ Group group = getGroup(path);
+ return metadataFromGroup(group);
+ } catch (IOException e) {
+ throw new RuntimeException("Failed to get group metadata from path: "+store+" / " + path, e);
+ }
+ }
+
+ /**
+ * Extracts metadata attributes from a Zarr group object.
+ *
+ * This method handles both Zarr v2 and v3 group formats.
+ *
+ *
+ * @param group the Group object to extract metadata from
+ * @return a map containing the group's attributes
+ */
+ public Map metadataFromGroup(Group group) {
+ if (group instanceof dev.zarr.zarrjava.v2.Group) {
+ dev.zarr.zarrjava.v2.GroupMetadata m = ((dev.zarr.zarrjava.v2.Group) group).metadata;
+ return m.attributes;
+ } else {
+ dev.zarr.zarrjava.v3.GroupMetadata m = ((dev.zarr.zarrjava.v3.Group) group).metadata;
+ return m.attributes;
+ }
+ }
+
+ /**
+ * Returns the underlying store handle.
+ *
+ * @return the StoreHandle for this Zarr location
+ */
+ public StoreHandle getStoreHandle() {
+ return store;
+ }
+
+ /**
+ * Returns the name of the Zarr.
+ *
+ * @return the name (typically the .zarr directory name)
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Returns the full path to the Zarr.
+ *
+ * @return the complete path including the .zarr extension
+ */
+ public String getPath() {
+ return path;
+ }
+}
diff --git a/src/loci/formats/services/ZarrService.java b/src/loci/formats/services/ZarrService.java
index 13b6c3a..a29a511 100644
--- a/src/loci/formats/services/ZarrService.java
+++ b/src/loci/formats/services/ZarrService.java
@@ -30,21 +30,10 @@
*/
import java.io.IOException;
-import java.util.Map;
-import java.util.Set;
-
import loci.common.services.Service;
import loci.formats.FormatException;
-import loci.formats.meta.MetadataRetrieve;
-import loci.formats.services.ZarrService.Compression;
public interface ZarrService extends Service {
-
- enum Compression {
- NONE,
- ZLIB
- }
-
/**
* Gets the text string for when Zarr implementation has not been found.
@@ -82,31 +71,9 @@ enum Compression {
*/
public Object readBytes(int [] shape, int [] offset) throws FormatException, IOException;
- /**
- * Writes values to the Zarr Array
- * @param buf values to be written in a one dimensional array
- * @param shape int array representing the shape of each dimension
- * @param x the offset for each dimension
- */
- void saveBytes(Object data, int[] shape, int[] offset) throws FormatException, IOException;
-
- public void open(String file) throws IOException, FormatException;
+ public void open(String path) throws IOException, FormatException;
boolean isLittleEndian();
boolean isOpen() throws IOException;
-
- String getID() throws IOException;
-
- public void create(String id, MetadataRetrieve meta, int[] chunks) throws IOException;
-
- void create(String id, MetadataRetrieve meta, int[] chunks, Compression compression) throws IOException;
-
- public Map getGroupAttr(String path) throws IOException, FormatException;
-
- public Map getArrayAttr(String path) throws IOException, FormatException;
-
- public Set getGroupKeys(String path) throws IOException, FormatException;
-
- public Set getArrayKeys(String path) throws IOException, FormatException;
}
diff --git a/test/loci/formats/utests/JZarrServiceImplTest.java b/test/loci/formats/utests/JZarrServiceImplTest.java
deleted file mode 100644
index 220b223..0000000
--- a/test/loci/formats/utests/JZarrServiceImplTest.java
+++ /dev/null
@@ -1,281 +0,0 @@
-package test.loci.formats.utests;
-
-/*-
- * #%L
- * Implementation of Bio-Formats readers for the next-generation file formats
- * %%
- * Copyright (C) 2020 - 2022 Open Microscopy Environment
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.nio.ByteOrder;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import org.mockito.Mock;
-import org.mockito.MockedStatic;
-import org.mockito.Mockito;
-import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.when;
-
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.DataProvider;
-import org.testng.annotations.Test;
-
-import com.bc.zarr.DataType;
-import com.bc.zarr.ZarrArray;
-import com.bc.zarr.ZarrGroup;
-
-import loci.formats.FormatException;
-import loci.formats.FormatTools;
-import loci.formats.services.JZarrServiceImpl;
-import ucar.ma2.InvalidRangeException;
-
-public class JZarrServiceImplTest {
-
- JZarrServiceImpl jzarrService;
- String testID = "testID";
- private static MockedStatic zarrGroupStatic;
- private static MockedStatic zarrArrayStatic;
-
- @Mock
- ZarrArray zarrArray;
-
- @Mock
- ZarrGroup zarrGroup;
-
- @BeforeMethod
- public void setup() {
- jzarrService = new JZarrServiceImpl(null);
- zarrArray = Mockito.mock(ZarrArray.class);
- zarrGroup = Mockito.mock(ZarrGroup.class);
- jzarrService.open(testID, zarrArray);
-
- zarrGroupStatic = Mockito.mockStatic(ZarrGroup.class);
- zarrGroupStatic.when(() -> ZarrGroup.open("path")).thenReturn(zarrGroup);
-
- zarrArrayStatic = Mockito.mockStatic(ZarrArray.class);
- zarrArrayStatic.when(() -> ZarrArray.open("path")).thenReturn(zarrArray);
- }
-
- @AfterMethod
- public void teardown() {
- try {
- jzarrService.close();
- zarrGroupStatic.close();
- zarrArrayStatic.close();
- } catch (IOException e) {
- fail("IOException thrown while closing JZarrServiceImpl");
- }
- }
-
- @DataProvider(name = "pixelTypes")
- public Object[][] createPixelTypes() {
- return new Object[][] {
- {FormatTools.INT8, DataType.i1},
- {FormatTools.INT16, DataType.i2},
- {FormatTools.INT32, DataType.i4},
- {FormatTools.UINT8, DataType.u1},
- {FormatTools.UINT16, DataType.u2},
- {FormatTools.UINT32, DataType.u4},
- {FormatTools.FLOAT, DataType.f4},
- {FormatTools.DOUBLE, DataType.f8},
- };
- }
-
- @Test(dataProvider = "pixelTypes")
- public void testZarrPixelType(int omePixelType, DataType jzarrPixelType) {
- assertEquals(jzarrPixelType, jzarrService.getZarrPixelType(omePixelType));
- }
-
- @Test(dataProvider = "pixelTypes")
- public void testOMEPixelType(int omePixelType, DataType jzarrPixelType) {
- assertEquals(omePixelType, jzarrService.getOMEPixelType(jzarrPixelType));
- }
-
- @Test(dataProvider = "pixelTypes")
- public void testPixelType(int omePixelType, DataType jzarrPixelType) {
- when(zarrArray.getDataType()).thenReturn(jzarrPixelType);
- assertEquals(omePixelType, jzarrService.getPixelType());
- }
-
- @Test
- public void testIsLittleEndian() {
- when(zarrArray.getByteOrder()).thenReturn(ByteOrder.BIG_ENDIAN);
- assertEquals(false, jzarrService.isLittleEndian());
- when(zarrArray.getByteOrder()).thenReturn(ByteOrder.LITTLE_ENDIAN);
- assertEquals(true, jzarrService.isLittleEndian());
- }
-
- @Test
- public void testGetNoZarrMessage() {
- assertEquals(JZarrServiceImpl.NO_ZARR_MSG, jzarrService.getNoZarrMsg());
- }
-
- @Test
- public void testGetShape() {
- int[] expectedShape = {1024, 1024, 32, 32, 32};
- when(zarrArray.getShape()).thenReturn(expectedShape);
- assertEquals(expectedShape, jzarrService.getShape());
- }
-
- @Test
- public void testGetChunkSize() {
- int[] expectedChunks = {256, 256, 8, 8, 8};
- when(zarrArray.getChunks()).thenReturn(expectedChunks);
- assertEquals(expectedChunks, jzarrService.getChunkSize());
- }
-
- @Test
- public void testGetGroupAttributes() {
- Map emptyAttributes = new HashMap();
- Map attributes = new HashMap();
- attributes.put("AttributeKey1", "AttributeValue1");
- attributes.put("AttributeKey2", "AttributeValue2");
-
- try {
- assertEquals(jzarrService.getGroupAttr("path"), emptyAttributes);
- when(zarrGroup.getAttributes()).thenReturn(attributes);
- assertEquals(jzarrService.getGroupAttr("path"), attributes);
- } catch (IOException | FormatException e) {
- fail("Unexpected exception thrown while retrieving group attributes");
- e.printStackTrace();
- }
- }
-
- @Test
- public void testGetGroupKeys() {
- Set emptyKeys = new HashSet();
- Set keys = new HashSet();
- keys.add("Key1");
- keys.add("Key2");
-
- try {
- assertEquals(jzarrService.getGroupKeys("path"), emptyKeys);
- when(zarrGroup.getGroupKeys()).thenReturn(keys);
- assertEquals(jzarrService.getGroupKeys("path"), keys);
- } catch (IOException | FormatException e) {
- fail("Unexpected exception thrown while retrieving group keys");
- e.printStackTrace();
- }
- }
-
- @Test
- public void testGetArrayAttributes() {
- Map emptyAttributes = new HashMap();
- Map attributes = new HashMap();
- attributes.put("AttributeKey1", "AttributeValue1");
- attributes.put("AttributeKey2", "AttributeValue2");
-
- try {
- assertEquals(jzarrService.getArrayAttr("path"), emptyAttributes);
- when(zarrArray.getAttributes()).thenReturn(attributes);
- assertEquals(jzarrService.getArrayAttr("path"), attributes);
- } catch (IOException | FormatException e) {
- fail("Unexpected exception thrown while retrieving array attributes");
- e.printStackTrace();
- }
- }
-
- @Test
- public void testGetArrayKeys() {
- Set emptyKeys = new HashSet();
- Set keys = new HashSet();
- keys.add("Key1");
- keys.add("Key2");
-
- try {
- assertEquals(jzarrService.getArrayKeys("path"), emptyKeys);
- when(zarrGroup.getArrayKeys()).thenReturn(keys);
- assertEquals(jzarrService.getArrayKeys("path"), keys);
- } catch (IOException | FormatException e) {
- fail("Unexpected exception thrown while retrieving array keys");
- e.printStackTrace();
- }
- }
-
- @Test
- public void testGetID() {
- assertEquals(testID, jzarrService.getID());
- JZarrServiceImpl nullJzarrService = new JZarrServiceImpl(null);
- assertEquals(null, nullJzarrService.getID());
- nullJzarrService.open("TestGetID", zarrArray);
- assertEquals("TestGetID", nullJzarrService.getID());
- }
-
- @Test
- public void testIsOpen() {
- assertEquals(true, jzarrService.isOpen());
- JZarrServiceImpl nullJzarrService = new JZarrServiceImpl(null);
- assertEquals(false, nullJzarrService.isOpen());
- nullJzarrService.open("isOpenTestID", zarrArray);
- assertEquals(true, nullJzarrService.isOpen());
- }
-
- @Test
- public void testReadBytes() {
- int[] expectedBytes = {256, 256, 8, 8, 8};
- int[] shape = {1024, 1024, 32, 32, 32};
- int[] offset = {0, 0, 0, 0, 0};
- try {
- when(zarrArray.read(shape, offset)).thenReturn(expectedBytes);
- assertEquals(expectedBytes, jzarrService.readBytes(shape, offset));
- } catch (IOException e) {
- fail("Unexpected exception on JZarrServiceImpl readBytes");
- e.printStackTrace();
- } catch (InvalidRangeException e) {
- fail("Unexpected InvalidRangeException on ZarrArray read");
- e.printStackTrace();
- } catch (FormatException e) {
- fail("Unexpected FormatException on JZarrServiceImpl readBytes");
- e.printStackTrace();
- }
- }
-
- @Test
- public void testSaveBytes() {
- int[] data = {256, 256, 8, 8, 8};
- int[] shape = {1024, 1024, 32, 32, 32};
- int[] offset = {0, 0, 0, 0, 0};
- try {
- jzarrService.saveBytes(data, shape, offset);
- verify(zarrArray).write(data, shape, offset);
- } catch (IOException e) {
- fail("Unexpected IOException on JZarrServiceImpl saveBytes");
- e.printStackTrace();
- } catch (InvalidRangeException e) {
- fail("Unexpected InvalidRangeException on ZarrArray write");
- e.printStackTrace();
- } catch (FormatException e) {
- fail("Unexpected FormatException on JZarrServiceImpl saveBytes");
- e.printStackTrace();
- }
- }
-}
diff --git a/test/loci/formats/utests/ZarrReaderMock.java b/test/loci/formats/utests/ZarrReaderMock.java
deleted file mode 100644
index bc0cd23..0000000
--- a/test/loci/formats/utests/ZarrReaderMock.java
+++ /dev/null
@@ -1,50 +0,0 @@
-package test.loci.formats.utests;
-
-/*-
- * #%L
- * Implementation of Bio-Formats readers for the next-generation file formats
- * %%
- * Copyright (C) 2020 - 2022 Open Microscopy Environment
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-
-import java.io.IOException;
-
-import loci.formats.FormatException;
-import loci.formats.in.ZarrReader;
-import loci.formats.services.ZarrService;
-
-public class ZarrReaderMock extends ZarrReader {
-
- private ZarrService mockService;
-
- public ZarrReaderMock(ZarrService zarrService) {
- mockService = zarrService;
- }
-
- @Override
- protected void initializeZarrService() throws IOException, FormatException {
- zarrService = mockService;
- }
-}
diff --git a/test/loci/formats/utests/ZarrReaderTest.java b/test/loci/formats/utests/ZarrReaderTest.java
deleted file mode 100644
index 7c45fe1..0000000
--- a/test/loci/formats/utests/ZarrReaderTest.java
+++ /dev/null
@@ -1,289 +0,0 @@
-package test.loci.formats.utests;
-
-/*-
- * #%L
- * Implementation of Bio-Formats readers for the next-generation file formats
- * %%
- * Copyright (C) 2020 - 2022 Open Microscopy Environment
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
-
-import static org.junit.Assert.*;
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.AssertJUnit.assertFalse;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import org.mockito.InjectMocks;
-import org.mockito.Mock;
-import org.mockito.Mockito;
-
-import static org.mockito.Mockito.when;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-import loci.common.DataTools;
-import loci.common.Location;
-import loci.formats.FormatException;
-import loci.formats.FormatTools;
-import loci.formats.in.ZarrReader;
-import loci.formats.services.ZarrService;
-
-
-/**
- * Tests the functionality of ZarrReader
- */
-public class ZarrReaderTest {
-
- @Mock
- private ZarrService zarrService;
-
- @InjectMocks
- private ZarrReaderMock reader;
-
- private File file;
- private int[] shape = {8, 16, 32, 512, 1024};
-
- @BeforeClass
- public void setUp() throws Exception {
- zarrService = Mockito.mock(ZarrService.class);
- reader = new ZarrReaderMock(zarrService);
- file = File.createTempFile("tileTest", ".zarr");
- String rootPath = file.getAbsolutePath();
- String canonicalPath = new Location(rootPath).getCanonicalPath();
-
- Map topLevelAttributes = new HashMap();
- ArrayList