diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
new file mode 100644
index 00000000..2579abb7
--- /dev/null
+++ b/.git-blame-ignore-revs
@@ -0,0 +1,2 @@
+# Format source code according to checkstyle configuration
+a5da2cad2e1f73c18df90bbfbe5d06f2bbd3357e
diff --git a/build.gradle b/build.gradle
index 9bbbaee6..78270ef6 100644
--- a/build.gradle
+++ b/build.gradle
@@ -2,6 +2,7 @@ plugins {
id 'java-library'
id 'eclipse'
id 'maven-publish'
+ id 'checkstyle'
}
group = 'com.glencoesoftware.omero'
@@ -87,3 +88,7 @@ jar {
)
}
}
+
+checkstyle {
+ toolVersion = "10.26.1"
+}
diff --git a/config/checkstyle/checkstyle.xml b/config/checkstyle/checkstyle.xml
new file mode 100644
index 00000000..b10ab4ca
--- /dev/null
+++ b/config/checkstyle/checkstyle.xml
@@ -0,0 +1,470 @@
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diff --git a/src/main/java/com/glencoesoftware/omero/zarr/OmeroAmazonS3ClientFactory.java b/src/main/java/com/glencoesoftware/omero/zarr/OmeroAmazonS3ClientFactory.java
index 9a85a081..f078056b 100644
--- a/src/main/java/com/glencoesoftware/omero/zarr/OmeroAmazonS3ClientFactory.java
+++ b/src/main/java/com/glencoesoftware/omero/zarr/OmeroAmazonS3ClientFactory.java
@@ -15,14 +15,8 @@
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
-package com.glencoesoftware.omero.zarr;
-import java.net.URI;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Properties;
-
-import org.slf4j.LoggerFactory;
+package com.glencoesoftware.omero.zarr;
import com.amazonaws.auth.AWSCredentialsProvider;
import com.amazonaws.auth.AWSCredentialsProviderChain;
@@ -36,7 +30,15 @@
import com.amazonaws.services.s3.AmazonS3ClientBuilder;
import com.amazonaws.util.AwsHostNameUtils;
import com.upplication.s3fs.AmazonS3ClientFactory;
+import java.net.URI;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+import org.slf4j.LoggerFactory;
+/**
+ * Subclass which maps an URI into a set of credentials to use for the client.
+ */
public class OmeroAmazonS3ClientFactory extends AmazonS3ClientFactory {
private static final org.slf4j.Logger log =
@@ -48,11 +50,11 @@ public class OmeroAmazonS3ClientFactory extends AmazonS3ClientFactory {
protected AWSCredentialsProvider getCredentialsProvider(Properties props) {
// If AWS Environment or System Properties are set, throw an exception
// so users will know they are not supported
- if (System.getenv("AWS_ACCESS_KEY_ID") != null ||
- System.getenv("AWS_SECRET_ACCESS_KEY") != null ||
- System.getenv("AWS_SESSION_TOKEN") != null ||
- System.getProperty("aws.accessKeyId") != null ||
- System.getProperty("aws.secretAccessKey") != null) {
+ if (System.getenv("AWS_ACCESS_KEY_ID") != null
+ || System.getenv("AWS_SECRET_ACCESS_KEY") != null
+ || System.getenv("AWS_SESSION_TOKEN") != null
+ || System.getProperty("aws.accessKeyId") != null
+ || System.getProperty("aws.secretAccessKey") != null) {
throw new RuntimeException("AWS credentials supplied by environment variables"
+ " or Java system properties are not supported."
+ " Please use either named profiles or instance"
@@ -77,6 +79,7 @@ protected AWSCredentialsProvider getCredentialsProvider(Properties props) {
/**
* Retrieves the bucket name from a given URI.
+ *
* @param uri The URI to handle
* @return The bucket name
*/
@@ -90,6 +93,7 @@ private String getBucketFromUri(URI uri) {
/**
* Retrieves the region from a given URI.
+ *
* @param uri The URI to handle
* @return The region
*/
@@ -103,6 +107,7 @@ private String getRegionFromUri(URI uri) {
/**
* Retrieves the endpoint from a given URI.
+ *
* @param uri The URI to handle
* @return The endpoint
*/
@@ -112,7 +117,7 @@ public String getEndPointFromUri(URI uri) {
@Override
public synchronized AmazonS3 getAmazonS3(URI uri, Properties props) {
- //Check if we have a S3 client for this bucket
+ // Check if we have a S3 client for this bucket
String bucket = getBucketFromUri(uri);
if (bucketClientMap.containsKey(bucket)) {
log.info("Found bucket " + bucket);
@@ -120,11 +125,12 @@ public synchronized AmazonS3 getAmazonS3(URI uri, Properties props) {
}
log.info("Creating client for bucket " + bucket);
AmazonS3 client = AmazonS3ClientBuilder.standard()
- .withCredentials(getCredentialsProvider(props))
- .withClientConfiguration(getClientConfiguration(props))
- .withMetricsCollector(getRequestMetricsCollector(props))
- .withEndpointConfiguration(new EndpointConfiguration(getEndPointFromUri(uri), getRegionFromUri(uri)))
- .build();
+ .withCredentials(getCredentialsProvider(props))
+ .withClientConfiguration(getClientConfiguration(props))
+ .withMetricsCollector(getRequestMetricsCollector(props))
+ .withEndpointConfiguration(
+ new EndpointConfiguration(getEndPointFromUri(uri), getRegionFromUri(uri)))
+ .build();
bucketClientMap.put(bucket, client);
return client;
}
diff --git a/src/main/java/com/glencoesoftware/omero/zarr/OmeroS3FileSystem.java b/src/main/java/com/glencoesoftware/omero/zarr/OmeroS3FileSystem.java
index c4f02d1a..2af84c49 100644
--- a/src/main/java/com/glencoesoftware/omero/zarr/OmeroS3FileSystem.java
+++ b/src/main/java/com/glencoesoftware/omero/zarr/OmeroS3FileSystem.java
@@ -15,16 +15,18 @@
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
-package com.glencoesoftware.omero.zarr;
-import java.io.IOException;
+package com.glencoesoftware.omero.zarr;
import com.amazonaws.services.s3.AmazonS3;
import com.upplication.s3fs.S3FileSystem;
import com.upplication.s3fs.S3FileSystemProvider;
+import java.io.IOException;
+/** Subclass of S3FileSystem with performance optimizations. */
public class OmeroS3FileSystem extends S3FileSystem {
+ /** Default constructor. */
public OmeroS3FileSystem(S3FileSystemProvider provider, String key,
AmazonS3 client, String endpoint) {
super(provider, key, client, endpoint);
@@ -32,11 +34,11 @@ public OmeroS3FileSystem(S3FileSystemProvider provider, String key,
@Override
public void close() throws IOException {
- //No-op
+ // No-op
}
@Override
public boolean isOpen() {
- return true; //Not possible to be closed
+ return true; // Not possible to be closed
}
}
diff --git a/src/main/java/com/glencoesoftware/omero/zarr/OmeroS3ReadOnlySeekableByteChannel.java b/src/main/java/com/glencoesoftware/omero/zarr/OmeroS3ReadOnlySeekableByteChannel.java
index 8dbc1671..8fd8e1c3 100644
--- a/src/main/java/com/glencoesoftware/omero/zarr/OmeroS3ReadOnlySeekableByteChannel.java
+++ b/src/main/java/com/glencoesoftware/omero/zarr/OmeroS3ReadOnlySeekableByteChannel.java
@@ -15,9 +15,14 @@
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
-package com.glencoesoftware.omero.zarr;
+package com.glencoesoftware.omero.zarr;
+import com.amazonaws.services.s3.model.GetObjectRequest;
+import com.amazonaws.services.s3.model.S3Object;
+import com.amazonaws.services.s3.model.S3ObjectInputStream;
+import com.upplication.s3fs.S3Path;
+import com.upplication.s3fs.S3ReadOnlySeekableByteChannel;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
@@ -32,14 +37,8 @@
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
-
import org.perf4j.slf4j.Slf4JStopWatch;
-import com.amazonaws.services.s3.model.GetObjectRequest;
-import com.amazonaws.services.s3.model.S3Object;
-import com.amazonaws.services.s3.model.S3ObjectInputStream;
-import com.upplication.s3fs.S3Path;
-import com.upplication.s3fs.S3ReadOnlySeekableByteChannel;
/**
* Overridden, hybrid version of the implementation from
@@ -61,15 +60,15 @@ public class OmeroS3ReadOnlySeekableByteChannel implements SeekableByteChannel {
* entire object in full from S3 without checks for length during
* object construction.
*/
- public OmeroS3ReadOnlySeekableByteChannel(S3Path path, Set options) throws IOException {
+ public OmeroS3ReadOnlySeekableByteChannel(S3Path path, Set options)
+ throws IOException {
this.options = Collections.unmodifiableSet(new HashSet<>(options));
- if (
- this.options.contains(StandardOpenOption.WRITE) ||
- this.options.contains(StandardOpenOption.CREATE) ||
- this.options.contains(StandardOpenOption.CREATE_NEW) ||
- this.options.contains(StandardOpenOption.APPEND)
- ) {
+ if (this.options.contains(StandardOpenOption.WRITE)
+ || this.options.contains(StandardOpenOption.CREATE)
+ || this.options.contains(StandardOpenOption.CREATE_NEW)
+ || this.options.contains(StandardOpenOption.APPEND)
+ ) {
throw new ReadOnlyFileSystemException();
}
@@ -92,10 +91,10 @@ public OmeroS3ReadOnlySeekableByteChannel(S3Path path, Set
// the stream closed as quickly as possible. See
// https://docs.aws.amazon.com/AWSJavaSDK/latest/javadoc/com/amazonaws/services/s3/model/S3Object.html#getObjectContent--
try (S3ObjectInputStream s3Stream = s3Object.getObjectContent()) {
- byte[] read_buf = new byte[1024*1024];
- int read_len = 0;
- while ((read_len = s3Stream.read(read_buf)) > 0) {
- outputStream.write(read_buf, 0, read_len);
+ byte[] readBuf = new byte[1024 * 1024];
+ int readLen = 0;
+ while ((readLen = s3Stream.read(readBuf)) > 0) {
+ outputStream.write(readBuf, 0, readLen);
}
}
this.data = outputStream.toByteArray();
@@ -124,7 +123,9 @@ public boolean isOpen() {
* private visibility.
*/
@Override
- public long position() { return position; }
+ public long position() {
+ return position;
+ }
/**
* Overridden, hybrid version of the implementation from
@@ -133,8 +134,7 @@ public boolean isOpen() {
*/
@Override
public SeekableByteChannel position(long targetPosition)
- throws IOException
- {
+ throws IOException {
throw new UnsupportedOperationException();
}
diff --git a/src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java b/src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java
index 4ff6b989..4cd2bee7 100644
--- a/src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java
+++ b/src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java
@@ -18,6 +18,10 @@
package com.glencoesoftware.omero.zarr;
+import com.bc.zarr.DataType;
+import com.bc.zarr.ZarrArray;
+import com.github.benmanes.caffeine.cache.AsyncLoadingCache;
+import com.github.benmanes.caffeine.cache.Caffeine;
import java.awt.Dimension;
import java.io.IOException;
import java.nio.BufferOverflowException;
@@ -31,22 +35,18 @@
import java.util.Map;
import java.util.concurrent.ExecutionException;
import java.util.stream.IntStream;
-
-import org.slf4j.LoggerFactory;
-
-import com.bc.zarr.DataType;
-import com.bc.zarr.ZarrArray;
-import com.github.benmanes.caffeine.cache.AsyncLoadingCache;
-import com.github.benmanes.caffeine.cache.Caffeine;
-
import loci.formats.FormatTools;
import ome.io.nio.DimensionsOutOfBoundsException;
import ome.io.nio.PixelBuffer;
import ome.io.nio.RomioPixelBuffer;
import ome.model.core.Pixels;
import ome.util.PixelData;
+import org.slf4j.LoggerFactory;
import ucar.ma2.InvalidRangeException;
+/**
+ * Subclass of ome.io.nio.PixelBuffer handling OME-Zarr data.
+ **/
public class ZarrPixelBuffer implements PixelBuffer {
private static final org.slf4j.Logger log =
@@ -55,25 +55,25 @@ public class ZarrPixelBuffer implements PixelBuffer {
/** Reference to the pixels. */
private final Pixels pixels;
- /** Root of the OME-NGFF multiscale we are operating on */
+ /** Root of the OME-NGFF multiscale we are operating on. */
private final Path root;
- /** Requested resolution level */
+ /** Requested resolution level. */
private int resolutionLevel;
- /** Total number of resolution levels */
+ /** Total number of resolution levels. */
private final int resolutionLevels;
- /** Max Plane Width */
+ /** Max Plane Width. */
private final Integer maxPlaneWidth;
- /** Max Plane Height */
+ /** Max Plane Height. */
private final Integer maxPlaneHeight;
- /** Zarr attributes present on the root group */
+ /** Zarr attributes present on the root group. */
private final Map rootGroupAttributes;
- /** Zarr array corresponding to the current resolution level */
+ /** Zarr array corresponding to the current resolution level. */
private ZarrArray array;
/**
@@ -82,34 +82,32 @@ public class ZarrPixelBuffer implements PixelBuffer {
*/
private Map zIndexMap;
- /** { resolutionLevel, z, c, t, x, y, w, h } vs. tile byte array cache */
+ /** { resolutionLevel, z, c, t, x, y, w, h } vs. tile byte array cache. */
private final AsyncLoadingCache, byte[]> tileCache;
- /** Whether or not the Zarr is on S3 or similar */
+ /** Whether or not the Zarr is on S3 or similar. */
private final boolean isRemote;
- /** Root path vs. metadata cache */
+ /** Root path vs. metadata cache. */
private final
AsyncLoadingCache> zarrMetadataCache;
- /** Array path vs. ZarrArray cache */
+ /** Array path vs. ZarrArray cache. */
private final AsyncLoadingCache zarrArrayCache;
- /** Supported axes, X and Y are essential */
+ /** Supported axes, X and Y are essential. */
public enum Axis {
X, Y, Z, C, T;
}
- /** Maps axes to their corresponding indexes */
+ /** Maps axes to their corresponding indexes. */
private Map axesOrder;
/**
- * Default constructor
+ * Default constructor.
+ *
* @param pixels Pixels metadata for the pixel buffer
* @param root The root of this buffer
- * @param maxTileLength Maximum tile length that can be used during
- * read operations
- * @throws IOException
*/
public ZarrPixelBuffer(Pixels pixels, Path root, Integer maxPlaneWidth,
Integer maxPlaneHeight,
@@ -121,10 +119,10 @@ public ZarrPixelBuffer(Pixels pixels, Path root, Integer maxPlaneWidth,
this.root = root;
this.zarrMetadataCache = zarrMetadataCache;
this.zarrArrayCache = zarrArrayCache;
- this.isRemote = root.toString().startsWith("s3://")? true : false;
+ this.isRemote = root.toString().startsWith("s3://") ? true : false;
try {
rootGroupAttributes = this.zarrMetadataCache.get(this.root).get();
- } catch (ExecutionException|InterruptedException e) {
+ } catch (ExecutionException | InterruptedException e) {
throw new IOException(e);
}
if (!rootGroupAttributes.containsKey("multiscales")) {
@@ -162,6 +160,7 @@ public ZarrPixelBuffer(Pixels pixels, Path root, Integer maxPlaneWidth,
/**
* Get Bio-Formats/OMERO pixels type for buffer.
+ *
* @return See above.
*/
public int getPixelsType() {
@@ -191,11 +190,11 @@ public int getPixelsType() {
/**
* Calculates the pixel length of a given NumPy like "shape".
+ *
* @param shape the NumPy like "shape" to calculate the length of
* @return See above
- * @see
- * numpy.shape documentation
+ * @see numpy.shape
+ * documentation
*/
private long length(int[] shape) {
return IntStream.of(shape)
@@ -269,7 +268,7 @@ private void read(byte[] buffer, int[] shape, int[] offset)
default:
throw new IllegalArgumentException(
"Data type " + dataType + " not supported");
- }
+ }
}
} catch (InvalidRangeException e) {
log.error("Error reading Zarr data", e);
@@ -294,8 +293,8 @@ private PixelData toPixelData(byte[] buffer) {
/**
* Retrieves the array chunk sizes of all subresolutions of this multiscale
* buffer.
+ *
* @return See above.
- * @throws IOException
*/
public int[][] getChunks() throws IOException {
List> datasets = getDatasets();
@@ -312,6 +311,7 @@ public int[][] getChunks() throws IOException {
/**
* Retrieves the datasets metadata of the first multiscale from the root
* group attributes.
+ *
* @return See above.
* @see #getRootGroupAttributes()
* @see #getMultiscalesMetadata()
@@ -322,7 +322,8 @@ public List> getDatasets() {
}
/**
- * Retrieves the axes order of the first multiscale
+ * Retrieves the axes order of the first multiscale.
+ *
* @return See above.
*/
public Map getAxesOrder() {
@@ -330,7 +331,8 @@ public Map getAxesOrder() {
return axesOrder;
}
axesOrder = new HashMap();
- List> axesData = (List>) getMultiscalesMetadata().get(0).get("axes");
+ List> axesData =
+ (List>) getMultiscalesMetadata().get(0).get("axes");
if (axesData == null) {
log.warn("No axes metadata found, defaulting to standard axes TCZYX");
axesOrder.put(Axis.T, 0);
@@ -345,7 +347,8 @@ public Map getAxesOrder() {
try {
axesOrder.put(Axis.valueOf(name), i);
} catch (IllegalArgumentException e) {
- throw new IllegalArgumentException("Invalid axis name (only T,C,Z,Y,X are supported): " + name);
+ throw new IllegalArgumentException(
+ "Invalid axis name (only T,C,Z,Y,X are supported): " + name);
}
}
}
@@ -357,6 +360,7 @@ public Map getAxesOrder() {
/**
* Retrieves the multiscales metadata from the root group attributes.
+ *
* @return See above.
* @see #getRootGroupAttributes()
* @see #getDatasets()
@@ -368,6 +372,7 @@ public List> getMultiscalesMetadata() {
/**
* Returns the current Zarr root group attributes for this buffer.
+ *
* @return See above.
* @see #getMultiscalesMetadata()
* @see #getDatasets()
@@ -385,6 +390,7 @@ public void close() throws IOException {
/**
* Implemented as specified by {@link PixelBuffer} I/F.
+ *
* @see PixelBuffer#checkBounds(Integer, Integer, Integer, Integer, Integer)
*/
@Override
@@ -416,6 +422,9 @@ public void checkBounds(Integer x, Integer y, Integer z, Integer c,
}
}
+ /**
+ * Checks the shape to read does not exceed the maximum plane size.
+ **/
public void checkReadSize(int[] shape) {
long length = length(shape);
long maxLength = maxPlaneWidth * maxPlaneHeight;
@@ -522,14 +531,14 @@ public PixelData getTile(
Integer z, Integer c, Integer t, Integer x, Integer y,
Integer w, Integer h)
throws IOException {
- //Check origin indices > 0
+ // Check origin indices > 0
checkBounds(x, y, z, c, t);
- //Check check bottom-right of tile in bounds
+ // Check check bottom-right of tile in bounds
checkBounds(x + w - 1, y + h - 1, z, c, t);
- //Check planar read size (sizeX and sizeY only), essential that this
- //happens before the similar check in read(). Otherwise we will
- //potentially allocate massive inner buffers in the tile cache
- //asynchronous entry builder that will never be used.
+ // Check planar read size (sizeX and sizeY only), essential that this
+ // happens before the similar check in read(). Otherwise we will
+ // potentially allocate massive inner buffers in the tile cache
+ // asynchronous entry builder that will never be used.
checkReadSize(new int[] { w, h });
List> keys = new ArrayList>();
@@ -537,7 +546,7 @@ public PixelData getTile(
List channels = Arrays.asList(new Integer[] { c });
if (getSizeC() == 3 && isRemote) {
// Guessing that we are in RGB mode
- channels = Arrays.asList(new Integer[] { 0, 1 ,2 });
+ channels = Arrays.asList(new Integer[] { 0, 1, 2 });
}
for (Integer channel : channels) {
List v = Arrays.asList(
@@ -561,9 +570,9 @@ public byte[] getTileDirect(
Integer z, Integer c, Integer t, Integer x, Integer y,
Integer w, Integer h, byte[] buffer) throws IOException {
try {
- //Check origin indices > 0
+ // Check origin indices > 0
checkBounds(x, y, z, c, t);
- //Check check bottom-right of tile in bounds
+ // Check check bottom-right of tile in bounds
checkBounds(x + w - 1, y + h - 1, z, c, t);
int[] shape = new int[axesOrder.size()];
@@ -680,9 +689,9 @@ public byte[] getStackDirect(Integer c, Integer t, byte[] buffer)
int w = getSizeX();
int h = getSizeY();
- //Check origin indices > 0
+ // Check origin indices > 0
checkBounds(x, y, z, c, t);
- //Check check bottom-right of tile in bounds
+ // Check check bottom-right of tile in bounds
checkBounds(x + w - 1, y + h - 1, z, c, t);
int[] shape = new int[axesOrder.size()];
@@ -727,9 +736,9 @@ public byte[] getTimepointDirect(Integer t, byte[] buffer)
int w = getSizeX();
int h = getSizeY();
- //Check origin indices > 0
+ // Check origin indices > 0
checkBounds(x, y, z, c, t);
- //Check check bottom-right of tile in bounds
+ // Check check bottom-right of tile in bounds
checkBounds(x + w - 1, y + h - 1, z, c, t);
int[] shape = new int[axesOrder.size()];
@@ -828,8 +837,8 @@ public void setTimepoint(byte[] buffer, Integer t)
@Override
public byte[] calculateMessageDigest() throws IOException {
throw new UnsupportedOperationException(
- "Zarr pixel buffer does not support message digest " +
- "calculation");
+ "Zarr pixel buffer does not support message digest "
+ + "calculation");
}
@Override
@@ -877,6 +886,8 @@ public int getSizeZ() {
}
/**
+ * Returns the real Z size for the current resolution level.
+ *
* @return Z size of the current underlying Zarr array
*/
private int getTrueSizeZ() {
@@ -930,8 +941,7 @@ public void setResolutionLevel(int resolutionLevel) {
if (zIndexMap == null) {
zIndexMap = new HashMap();
- }
- else {
+ } else {
zIndexMap.clear();
}
try {
diff --git a/src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java b/src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java
index 4a3ef1a8..d34e0c16 100644
--- a/src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java
+++ b/src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java
@@ -18,6 +18,12 @@
package com.glencoesoftware.omero.zarr;
+import com.bc.zarr.ZarrArray;
+import com.bc.zarr.ZarrGroup;
+import com.github.benmanes.caffeine.cache.AsyncLoadingCache;
+import com.github.benmanes.caffeine.cache.Caffeine;
+import com.google.common.base.Splitter;
+import com.upplication.s3fs.OmeroS3FilesystemProvider;
import java.io.File;
import java.io.IOException;
import java.net.URI;
@@ -28,18 +34,6 @@
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
-
-import org.perf4j.StopWatch;
-import org.perf4j.slf4j.Slf4JStopWatch;
-import org.slf4j.LoggerFactory;
-
-import com.google.common.base.Splitter;
-import com.upplication.s3fs.OmeroS3FilesystemProvider;
-import com.bc.zarr.ZarrArray;
-import com.bc.zarr.ZarrGroup;
-import com.github.benmanes.caffeine.cache.AsyncLoadingCache;
-import com.github.benmanes.caffeine.cache.Caffeine;
-
import ome.api.IQuery;
import ome.conditions.LockTimeout;
import ome.io.nio.BackOff;
@@ -51,11 +45,15 @@
import ome.model.core.Pixels;
import ome.model.meta.ExternalInfo;
import ome.model.roi.Mask;
+import org.perf4j.StopWatch;
+import org.perf4j.slf4j.Slf4JStopWatch;
+import org.slf4j.LoggerFactory;
/**
* Subclass which overrides series retrieval to avoid the need for
* an injected {@link IQuery}.
- * @author Chris Allan
+ *
+ * @author Chris Allan
*
*/
public class ZarrPixelsService extends ome.io.nio.PixelsService {
@@ -66,25 +64,26 @@ public class ZarrPixelsService extends ome.io.nio.PixelsService {
public static final String NGFF_ENTITY_TYPE = "com.glencoesoftware.ngff:multiscales";
public static final long NGFF_ENTITY_ID = 3;
- /** Max Plane Width */
+ /** Max Plane Width. */
protected final Integer maxPlaneWidth;
- /** Max Plane Height */
+ /** Max Plane Height. */
protected final Integer maxPlaneHeight;
- /** Zarr metadata and array cache size */
+ /** Zarr metadata and array cache size. */
private final long zarrCacheSize;
- /** Copy of private IQuery also provided to ome.io.nio.PixelsService */
+ /** Copy of private IQuery also provided to ome.io.nio.PixelsService. */
private final IQuery iQuery;
- /** Root path vs. metadata cache */
+ /** Root path vs. metadata cache. */
private final
AsyncLoadingCache> zarrMetadataCache;
/** Array path vs. ZarrArray cache */
private final AsyncLoadingCache zarrArrayCache;
+ /** Default constructor. */
public ZarrPixelsService(
String path, boolean isReadOnlyRepo, File memoizerDirectory,
long memoizerWait, FilePathResolver resolver, BackOff backOff,
@@ -110,9 +109,9 @@ public ZarrPixelsService(
/**
* Retrieves Zarr metadata from a given path.
- * @param root path to get Zarr metadata from
+ *
+ * @param path path to get Zarr metadata from
* @return See above.
- * @throws IOException
*/
public static Map getZarrMetadata(Path path)
throws IOException {
@@ -124,9 +123,9 @@ public static Map getZarrMetadata(Path path)
/**
* Opens a Zarr array at a given path.
- * @param root path to open a Zarr array from
+ *
+ * @param path path to open a Zarr array from
* @return See above.
- * @throws IOException
*/
public static ZarrArray getZarrArray(Path path) throws IOException {
return ZarrArray.open(path);
@@ -134,11 +133,11 @@ public static ZarrArray getZarrArray(Path path) throws IOException {
/**
* Converts an NGFF root string to a path, initializing a {@link FileSystem}
- * if required
+ * if required.
+ *
* @param ngffDir NGFF directory root
* @return Fully initialized path or null if the NGFF root
- * directory has not been specified in configuration.
- * @throws IOException
+ * directory has not been specified in configuration.
*/
public static Path asPath(String ngffDir) throws IOException {
if (ngffDir.isEmpty()) {
@@ -189,25 +188,27 @@ public static Path asPath(String ngffDir) throws IOException {
/**
* Retrieve {@link Mask} or {@link Image} URI stored under {@link ExternalInfo}.
+ *
* @param object loaded {@link Mask} or {@link Image} to check for a URI
* @return the value of {@link ExternalInfo.lsid}, null if the object
- * does not have an {@link ExternalInfo} with a valid {@link ExternalInfo.lsid} atttribute
- * or if {@link ExternalInfo.entityType} is not equal to {@link NGFF_ENTITY_TYPE} or if
- * {@link ExternalInfo.entityId} is not equal to {@link NGFF_ENTITY_ID}.
+ * does not have an {@link ExternalInfo} with a valid {@link ExternalInfo.lsid} atttribute
+ * or if {@link ExternalInfo.entityType} is not equal to {@link NGFF_ENTITY_TYPE} or if
+ * {@link ExternalInfo.entityId} is not equal to {@link NGFF_ENTITY_ID}.
*/
public String getUri(IObject object) {
return getUri(object, NGFF_ENTITY_TYPE, NGFF_ENTITY_ID);
}
/**
- * Retrieve {@link Mask} or {@link Image} URI stored under {@link ExternalInfo}
+ * Retrieve {@link Mask} or {@link Image} URI stored under {@link ExternalInfo}.
+ *
* @param object loaded {@link Mask} or {@link Image} to check for a URI
* @param targetEntityType expected entityType in the object {@link ExternalInfo}
* @param targetEntityId expected entityType in the object {@link ExternalInfo}
* @return the value of {@link ExternalInfo.lsid}, null if the object
- * does not have an {@link ExternalInfo} with a valid {@link ExternalInfo.lsid} atttribute
- * or if {@link ExternalInfo.entityType} is not equal to targetEntityType or if
- * {@link ExternalInfo.entityId} is not equal to targetEntityId .
+ * does not have an {@link ExternalInfo} with a valid {@link ExternalInfo.lsid} atttribute
+ * or if {@link ExternalInfo.entityType} is not equal to targetEntityType or if
+ * {@link ExternalInfo.entityId} is not equal to targetEntityId .
*/
public String getUri(IObject object, String targetEntityType, Long targetEntityId) {
ExternalInfo externalInfo = object.getDetails().getExternalInfo();
@@ -259,6 +260,7 @@ public String getUri(IObject object, String targetEntityType, Long targetEntityI
/**
* Retrieve the {@link Image} for a particular set of pixels. Where
* possible, does not initiate a query.
+ *
* @param pixels Pixels set to retrieve the {@link Image} for.
* @return See above.
*/
@@ -273,9 +275,10 @@ protected Image getImage(Pixels pixels) {
/**
* Retrieves the series for a given set of pixels. Where possible, does not
* initiate a query.
+ *
* @param pixels Set of pixels to return the series for.
* @return The series as specified by the pixels parameters or
- * 0 (the first series).
+ * 0 (the first series).
*/
@Override
protected int getSeries(Pixels pixels) {
@@ -288,9 +291,9 @@ protected int getSeries(Pixels pixels) {
/**
* Returns a label image NGFF pixel buffer if it exists.
+ *
* @param mask Mask to retrieve a pixel buffer for.
* @return A pixel buffer instance.
- * @throws IOException
*/
public ZarrPixelBuffer getLabelImagePixelBuffer(Mask mask)
throws IOException {
@@ -312,11 +315,12 @@ pixels, asPath(root), maxPlaneWidth, maxPlaneHeight,
/**
* Creates an NGFF pixel buffer for a given set of pixels.
+ *
* @param pixels Pixels set to retrieve a pixel buffer for.
- * true opens as read-write, false opens as
- * read-only.
+ * true opens as read-write, false opens as
+ * read-only.
* @return An NGFF pixel buffer instance or null if one cannot
- * be found.
+ * be found.
*/
protected ZarrPixelBuffer createOmeNgffPixelBuffer(Pixels pixels) {
StopWatch t0 = new Slf4JStopWatch("createOmeNgffPixelBuffer()");
@@ -326,7 +330,7 @@ protected ZarrPixelBuffer createOmeNgffPixelBuffer(Pixels pixels) {
if (uri == null) {
// Quick exit if we think we're OME-NGFF but there is no URI
if (image.getFormat() != null && "OMEXML".equals(image.getFormat().getValue())) {
- throw new LockTimeout("Import in progress.", 15*1000, 0);
+ throw new LockTimeout("Import in progress.", 15 * 1000, 0);
}
log.debug("No OME-NGFF root");
return null;
@@ -341,8 +345,8 @@ protected ZarrPixelBuffer createOmeNgffPixelBuffer(Pixels pixels) {
return v;
} catch (Exception e) {
log.warn(
- "Getting OME-NGFF pixel buffer failed - " +
- "attempting to get local data", e);
+ "Getting OME-NGFF pixel buffer failed - "
+ + "attempting to get local data", e);
}
} catch (IOException e1) {
log.debug(
@@ -358,10 +362,11 @@ protected ZarrPixelBuffer createOmeNgffPixelBuffer(Pixels pixels) {
* Returns a pixel buffer for a given set of pixels. Either an NGFF pixel
* buffer, a proprietary ROMIO pixel buffer or a specific pixel buffer
* implementation.
+ *
* @param pixels Pixels set to retrieve a pixel buffer for.
* @param write Whether or not to open the pixel buffer as read-write.
- * true opens as read-write, false opens as
- * read-only.
+ * true opens as read-write, false opens as
+ * read-only.
* @return A pixel buffer instance.
*/
@Override
diff --git a/src/main/java/com/upplication/s3fs/OmeroS3FilesystemProvider.java b/src/main/java/com/upplication/s3fs/OmeroS3FilesystemProvider.java
index fe85c30a..ce232a34 100644
--- a/src/main/java/com/upplication/s3fs/OmeroS3FilesystemProvider.java
+++ b/src/main/java/com/upplication/s3fs/OmeroS3FilesystemProvider.java
@@ -15,11 +15,17 @@
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
+
package com.upplication.s3fs;
import static com.upplication.s3fs.AmazonS3Factory.ACCESS_KEY;
import static com.upplication.s3fs.AmazonS3Factory.SECRET_KEY;
+import com.glencoesoftware.omero.zarr.OmeroAmazonS3ClientFactory;
+import com.glencoesoftware.omero.zarr.OmeroS3FileSystem;
+import com.glencoesoftware.omero.zarr.OmeroS3ReadOnlySeekableByteChannel;
+import com.google.common.base.Preconditions;
+import com.upplication.s3fs.attribute.S3BasicFileAttributes;
import java.io.IOException;
import java.net.URI;
import java.nio.channels.SeekableByteChannel;
@@ -35,12 +41,8 @@
import java.util.Properties;
import java.util.Set;
-import com.glencoesoftware.omero.zarr.OmeroAmazonS3ClientFactory;
-import com.glencoesoftware.omero.zarr.OmeroS3FileSystem;
-import com.glencoesoftware.omero.zarr.OmeroS3ReadOnlySeekableByteChannel;
-import com.google.common.base.Preconditions;
-import com.upplication.s3fs.attribute.S3BasicFileAttributes;
+/** Subclass of S3FileSystemProvider with performance optimizations. */
public class OmeroS3FilesystemProvider extends S3FileSystemProvider {
/**
@@ -67,7 +69,9 @@ public FileSystem newFileSystem(URI uri, Map env) {
private void validateProperties(Properties props) {
Preconditions.checkArgument(
(props.getProperty(ACCESS_KEY) == null && props.getProperty(SECRET_KEY) == null)
- || (props.getProperty(ACCESS_KEY) != null && props.getProperty(SECRET_KEY) != null), "%s and %s should both be provided or should both be omitted",
+ || (props.getProperty(ACCESS_KEY) != null
+ && props.getProperty(SECRET_KEY) != null),
+ "%s and %s should both be provided or should both be omitted",
ACCESS_KEY, SECRET_KEY);
}
@@ -98,7 +102,8 @@ private Properties getProperties(URI uri, Map env) {
*/
@Override
public S3FileSystem createFileSystem(URI uri, Properties props) {
- return new OmeroS3FileSystem(this, getFileSystemKey(uri, props), getAmazonS3(uri, props), uri.getHost());
+ return new OmeroS3FileSystem(
+ this, getFileSystemKey(uri, props), getAmazonS3(uri, props), uri.getHost());
}
/**
@@ -139,13 +144,16 @@ public boolean exists(S3Path path) {
* {@link OmeroS3ReadOnlySeekableByteChannel}.
*/
@Override
- public SeekableByteChannel newByteChannel(Path path, Set options, FileAttribute... attrs) throws IOException {
+ public SeekableByteChannel newByteChannel(
+ Path path, Set options, FileAttribute... attrs)
+ throws IOException {
S3Path s3Path = toS3Path(path);
if (options.isEmpty() || options.contains(StandardOpenOption.READ)) {
- if (options.contains(StandardOpenOption.WRITE))
+ if (options.contains(StandardOpenOption.WRITE)) {
throw new UnsupportedOperationException(
"Can't read and write one on channel"
);
+ }
return new OmeroS3ReadOnlySeekableByteChannel(s3Path, options);
} else {
return new S3SeekableByteChannel(s3Path, options);
@@ -157,7 +165,8 @@ public SeekableByteChannel newByteChannel(Path path, Set o
* due to its private visibility.
*/
private S3Path toS3Path(Path path) {
- Preconditions.checkArgument(path instanceof S3Path, "path must be an instance of %s", S3Path.class.getName());
+ Preconditions.checkArgument(path instanceof S3Path,
+ "path must be an instance of %s", S3Path.class.getName());
return (S3Path) path;
}
@@ -168,9 +177,11 @@ private S3Path toS3Path(Path path) {
* read-only attributes for every file.
*/
@Override
- public A readAttributes(Path path, Class type, LinkOption... options) throws IOException {
+ public A readAttributes(
+ Path path, Class type, LinkOption... options) throws IOException {
S3Path s3path = (S3Path) path;
- BasicFileAttributes attrs = new S3BasicFileAttributes(s3path.getKey(), null, 0, true, false);
+ BasicFileAttributes attrs = new S3BasicFileAttributes(
+ s3path.getKey(), null, 0, true, false);
return type.cast(attrs);
}
}
diff --git a/src/test/java/com/glencoesoftware/omero/zarr/TestZarr.java b/src/test/java/com/glencoesoftware/omero/zarr/TestZarr.java
index 5b493fad..952ef294 100644
--- a/src/test/java/com/glencoesoftware/omero/zarr/TestZarr.java
+++ b/src/test/java/com/glencoesoftware/omero/zarr/TestZarr.java
@@ -19,6 +19,17 @@
package com.glencoesoftware.omero.zarr;
+import com.bc.zarr.ArrayParams;
+import com.bc.zarr.DataType;
+import com.bc.zarr.DimensionSeparator;
+import com.bc.zarr.ZarrArray;
+import com.bc.zarr.ZarrGroup;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.image.BufferedImage;
+import java.awt.image.DataBufferByte;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
@@ -30,24 +41,11 @@
import java.util.Map;
import java.util.OptionalInt;
import java.util.Random;
-
-import com.bc.zarr.ArrayParams;
-import com.bc.zarr.DataType;
-import com.bc.zarr.DimensionSeparator;
-import com.bc.zarr.ZarrArray;
-import com.bc.zarr.ZarrGroup;
-
import ucar.ma2.InvalidRangeException;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.image.BufferedImage;
-import java.awt.image.DataBufferByte;
-
/**
- * TestZarr is a utility class for creating and populating a Zarr with different number and order of dimensions.
+ * TestZarr is a utility class for creating and populating a Zarr with different number and
+ * order of dimensions.
*/
public class TestZarr {
@@ -71,26 +69,16 @@ public class TestZarr {
/**
* Create a new TestZarr object with default values.
- * @throws IOException
*/
public TestZarr() throws IOException {
}
/**
* Create a new TestZarr object with custom values.
- * @param sizeX
- * @param sizeY
- * @param sizeZ
- * @param sizeT
- * @param sizeC
- * @param order
- * @param path
- * @param dataType
- * @param overwrite
- * @throws IOException
*/
- public TestZarr(int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC,
- String order, String path, DataType dataType, boolean overwrite) throws IOException {
+ public TestZarr(int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC,
+ String order, String path, DataType dataType, boolean overwrite)
+ throws IOException {
this.sizeX = sizeX;
this.sizeY = sizeY;
this.sizeZ = sizeZ;
@@ -104,15 +92,13 @@ public TestZarr(int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC,
/**
* Initialize the Zarr array.
- * @return
- * @throws IOException
*/
public TestZarr init() throws IOException {
if (order == null || order.isEmpty()) {
throw new IllegalArgumentException("Order must specified.");
}
this.order = this.order.toUpperCase();
- if (!order.contains("X") || !order.contains("Y") ) {
+ if (!order.contains("X") || !order.contains("Y")) {
throw new IllegalArgumentException("Order must contain X and Y");
}
if (!order.contains("C")) {
@@ -133,34 +119,37 @@ public TestZarr init() throws IOException {
if (sizeT == 0) {
this.order = order.replace("T", "");
}
- int[] shape = new int[order.length()];
- if (order.contains("C"))
+ int[] shape = new int[order.length()];
+ if (order.contains("C")) {
shape[order.indexOf("C")] = sizeC;
- if (order.contains("T"))
+ }
+ if (order.contains("T")) {
shape[order.indexOf("T")] = sizeT;
- if (order.contains("Z"))
+ }
+ if (order.contains("Z")) {
shape[order.indexOf("Z")] = sizeZ;
+ }
shape[order.indexOf("Y")] = sizeY;
shape[order.indexOf("X")] = sizeX;
if (Files.exists(path)) {
if (overwrite) {
Files.walk(path)
- .sorted(Comparator.reverseOrder())
- .map(Path::toFile)
- .forEach(File::delete);
+ .sorted(Comparator.reverseOrder())
+ .map(Path::toFile)
+ .forEach(File::delete);
} else {
throw new IOException("Path already exists");
}
}
- Path series_path = path.resolve("0"); // image 0 (one image)
- Path img_path = series_path.resolve("0"); // resolution 0 (one resolution)
+ Path seriesPath = path.resolve("0"); // image 0 (one image)
+ Path imgPath = seriesPath.resolve("0"); // resolution 0 (one resolution)
// Create parent directories if they don't exist
- Files.createDirectories(img_path.getParent());
+ Files.createDirectories(imgPath.getParent());
- array = ZarrArray.create(img_path, new ArrayParams()
+ array = ZarrArray.create(imgPath, new ArrayParams()
.shape(shape)
.dataType(dataType)
.dimensionSeparator(DimensionSeparator.SLASH)
@@ -169,34 +158,31 @@ public TestZarr init() throws IOException {
}
/**
- * Fill the Zarr array with pixel data
- * @return
- * @throws IOException
- * @throws InvalidRangeException
+ * Fill the Zarr array with pixel data.
*/
public TestZarr createImage() throws IOException, InvalidRangeException {
for (int c = 0; c < Math.max(1, sizeC); c++) {
for (int t = 0; t < Math.max(1, sizeT); t++) {
for (int z = 0; z < Math.max(1, sizeZ); z++) {
- byte[] plane = generateGreyscaleImageWithText(c, z, t);
int[] sh = new int[order.length()];
int[] off = new int[order.length()];
- if (order.contains("C"))
+ if (order.contains("C")) {
sh[order.indexOf("C")] = 1;
- if (order.contains("T"))
+ off[order.indexOf("C")] = c;
+ }
+ if (order.contains("T")) {
sh[order.indexOf("T")] = 1;
- if (order.contains("Z"))
+ off[order.indexOf("T")] = t;
+ }
+ if (order.contains("Z")) {
sh[order.indexOf("Z")] = 1;
+ off[order.indexOf("Z")] = z;
+ }
sh[order.indexOf("Y")] = sizeY;
sh[order.indexOf("X")] = sizeX;
- if (order.contains("C"))
- off[order.indexOf("C")] = c;
- if (order.contains("T"))
- off[order.indexOf("T")] = t;
- if (order.contains("Z"))
- off[order.indexOf("Z")] = z;
off[order.indexOf("Y")] = 0;
off[order.indexOf("X")] = 0;
+ byte[] plane = generateGreyscaleImageWithText(c, z, t);
array.write(plane, sh, off);
}
}
@@ -206,8 +192,6 @@ public TestZarr createImage() throws IOException, InvalidRangeException {
/**
* Save the image metadata to the Zarr file.
- * @return
- * @throws IOException
*/
public TestZarr createMetadata() throws IOException {
List> axes = new ArrayList<>();
@@ -229,7 +213,6 @@ public TestZarr createMetadata() throws IOException {
axes.add(axisObj);
}
- List> datasets = new ArrayList<>();
Map resObj = new HashMap<>();
resObj.put("path", "0");
List> transforms = new ArrayList<>();
@@ -238,6 +221,7 @@ public TestZarr createMetadata() throws IOException {
trans.put("scale", new int[] {1, 1, 1, 1, 1});
transforms.add(trans);
resObj.put("coordinateTransformations", transforms);
+ List> datasets = new ArrayList<>();
datasets.add(resObj);
List