diff --git a/.gitignore b/.gitignore
index e6ed443baa23e5fd37e6963a07d0840211c3c62a..fa22ae82739dff0ec1ab1de56f62a43ff0fe01cb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,7 +9,8 @@
# Maven #
/target/
+# IntelliJ
.idea/
classes/
-bigdataviewer-server.iml
src/main/resources/META-INF/MANIFEST.MF
+*.iml
diff --git a/pom.xml b/pom.xml
index 7cadc59703f4e2632faef37b6b323bb68f305935..b12c0abeb9461460a554caaf14725a0434e18d29 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,13 +5,13 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
- <version>26.0.0</version>
+ <version>28.0.0</version>
<relativePath />
</parent>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-server</artifactId>
- <version>2.1.1-SNAPSHOT</version>
+ <version>3.0.1-SNAPSHOT</version>
<name>BigDataServer</name>
<description>A web server for BigDataViewer datasets.</description>
@@ -77,6 +77,7 @@
<properties>
<package-name>bdv.server</package-name>
+ <main-class>bdv.server.BigDataServer</main-class>
<license.licenseName>gpl_v3</license.licenseName>
<license.copyrightOwners>BigDataViewer developers.</license.copyrightOwners>
@@ -87,8 +88,10 @@
<stringtemplate.version>3.2.1</stringtemplate.version>
<!-- TODO: Remove these version pins and update the code. -->
- <bigdataviewer-core.version>3.0.3</bigdataviewer-core.version>
- <imglib2.version>3.3.0</imglib2.version>
+ <bigdataviewer-core.version>9.0.3</bigdataviewer-core.version>
+ <imglib2.version>5.9.0</imglib2.version>
+ <imglib2-cache.version>1.0.0-beta-13</imglib2-cache.version>
+ <spim_data.version>2.2.4</spim_data.version>
</properties>
<repositories>
@@ -122,5 +125,67 @@
<artifactId>DataCompressor</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
- </dependencies>
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-simple</artifactId>
+ <version>1.7.28</version>
+ </dependency>
+ </dependencies>
+
+ <profiles>
+ <profile>
+ <id>fatjar</id>
+ <build>
+ <plugins>
+ <!-- Maven shade for Uber Jar -->
+ <!-- https://maven.apache.org/plugins/maven-shade-plugin/shade-mojo.html -->
+ <!-- https://databricks.gitbooks.io/databricks-spark-knowledge-base/content/troubleshooting/missing_dependencies_in_jar_files.html -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <configuration>
+ <!-- Do not minimize for now to speed up packaging. -->
+ <transformers combine.children="append">
+ <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+ <resource>META-INF/json/org.scijava.plugin.Plugin</resource>
+ </transformer>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+ <resource>META-INF/json/mpicbg.spim.data.generic.sequence.ImgLoaderIo</resource>
+ </transformer>
+ </transformers>
+ <!--<minimizeJar>true</minimizeJar> -->
+ <filters>
+ <filter>
+ <artifact>*:*</artifact>
+ <excludes>
+ <exclude>META-INF/*.SF</exclude>
+ <exclude>META-INF/*.DSA</exclude>
+ <exclude>META-INF/*.RSA</exclude>
+ </excludes>
+ </filter>
+ </filters>
+ <!-- Additional configuration. -->
+ <relocations>
+ <relocation>
+ <pattern>org.apache.commons.compress</pattern>
+ <shadedPattern>org.janelia.saalfeldlab.org.apache.commons.compress</shadedPattern>
+ </relocation>
+ </relocations>
+ </configuration>
+ <!-- binds by default to package phase -->
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <!-- Maven shade end -->
+ </plugins>
+ </build>
+ </profile>
+ </profiles>
+
</project>
diff --git a/src/main/java/bdv/server/BigDataServer.java b/src/main/java/bdv/server/BigDataServer.java
index 12e3e875b0967d60fe43c8757f9dca3a8a1b8e04..f5cd0074dc0cc3278d149fa7bf4387a893eec72c 100644
--- a/src/main/java/bdv/server/BigDataServer.java
+++ b/src/main/java/bdv/server/BigDataServer.java
@@ -58,9 +58,20 @@ import java.util.Optional;
public class BigDataServer {
private static final org.eclipse.jetty.util.log.Logger LOG = Log.getLogger(BigDataServer.class);
- // private static ScalarQuantizer quantizer;
+ public static class ExtendedCompressionOptions extends CompressionOptions {
+ private int compressFromMipmapLevel;
+
+ public int getCompressFromMipmapLevel() {
+ return compressFromMipmapLevel;
+ }
+
+ public void setCompressFromMipmapLevel(final int compressFromMipmapLevel) {
+ this.compressFromMipmapLevel = compressFromMipmapLevel;
+ }
+ }
static Parameters getDefaultParameters() {
+
final int port = 8080;
String hostname;
try {
@@ -69,25 +80,68 @@ public class BigDataServer {
hostname = "localhost";
}
final String thumbnailDirectory = null;
+ final String baseUrl = null;
final boolean enableManagerContext = false;
return new Parameters(port,
hostname,
new HashMap<String, String>(),
thumbnailDirectory,
+ baseUrl,
enableManagerContext,
new ExtendedCompressionOptions());
}
- public static class ExtendedCompressionOptions extends CompressionOptions {
- private int compressFromMipmapLevel;
+ public static void main(final String[] args) throws Exception {
+ System.setProperty("org.eclipse.jetty.util.log.class", "org.eclipse.jetty.util.log.StdErrLog");
- public int getCompressFromMipmapLevel() {
- return compressFromMipmapLevel;
- }
+ final Parameters params = processOptions(args, getDefaultParameters());
+ if (params == null)
+ return;
- public void setCompressFromMipmapLevel(final int compressFromMipmapLevel) {
- this.compressFromMipmapLevel = compressFromMipmapLevel;
+ final String thumbnailsDirectoryName = getThumbnailDirectoryPath(params);
+
+ // Threadpool for multiple connections
+ final Server server = new Server(new QueuedThreadPool(200, 8));
+
+ // ServerConnector configuration
+ final ServerConnector connector = new ServerConnector(server);
+ connector.setHost(params.getHostname());
+ connector.setPort(params.getPort());
+ LOG.info("Set connectors: " + connector);
+ server.setConnectors(new Connector[]{connector});
+ final String baseURL = params.getBaseUrl() != null ? params.getBaseUrl() :
+ "http://" + server.getURI().getHost() + ":" + params.getPort();
+ System.out.println("baseURL = " + baseURL);
+
+ // Handler initialization
+ final HandlerCollection handlers = new HandlerCollection();
+
+ final ContextHandlerCollection datasetHandlers = createHandlers(baseURL,
+ params.getDatasets(),
+ thumbnailsDirectoryName,
+ params.getCompressionParams());
+ handlers.addHandler(datasetHandlers);
+ handlers.addHandler(new JsonDatasetListHandler(server, datasetHandlers));
+
+ Handler handler = handlers;
+ if (params.enableManagerContext()) {
+ // Add Statistics bean to the connector
+ final ConnectorStatistics connectorStats = new ConnectorStatistics();
+ connector.addBean(connectorStats);
+
+ // create StatisticsHandler wrapper and ManagerHandler
+ final StatisticsHandler statHandler = new StatisticsHandler();
+ handlers.addHandler(new ManagerHandler(baseURL, server, connectorStats, statHandler, datasetHandlers, thumbnailsDirectoryName));
+ statHandler.setHandler(handlers);
+ handler = statHandler;
}
+
+ LOG.info("Set handler: " + handler);
+ server.setHandler(handler);
+ LOG.info("Server Base URL: " + baseURL);
+ LOG.info("BigDataServer starting");
+ server.start();
+ server.join();
}
/**
@@ -105,19 +159,26 @@ public class BigDataServer {
private final String thumbnailDirectory;
- private final ExtendedCompressionOptions compressionParam;
+ private final String baseUrl;
private final boolean enableManagerContext;
- Parameters(final int port, final String hostname, final Map<String, String> datasetNameToXml,
- final String thumbnailDirectory, final boolean enableManagerContext,
- final ExtendedCompressionOptions customCompressionParameters) {
+ private final ExtendedCompressionOptions compressionParam;
+
+ Parameters(final int port,
+ final String hostname,
+ final Map<String, String> datasetNameToXml,
+ final String thumbnailDirectory,
+ final String baseUrl,
+ final boolean enableManagerContext,
+ final ExtendedCompressionOptions extendedCompressionOptions) {
this.port = port;
this.hostname = hostname;
this.datasetNameToXml = datasetNameToXml;
this.thumbnailDirectory = thumbnailDirectory;
+ this.baseUrl = baseUrl;
this.enableManagerContext = enableManagerContext;
- this.compressionParam = customCompressionParameters;
+ this.compressionParam = extendedCompressionOptions;
}
public int getPort() {
@@ -128,6 +189,10 @@ public class BigDataServer {
return hostname;
}
+ public String getBaseUrl() {
+ return baseUrl;
+ }
+
public String getThumbnailDirectory() {
return thumbnailDirectory;
}
@@ -150,14 +215,15 @@ public class BigDataServer {
}
}
-
@SuppressWarnings("static-access")
static private Parameters processOptions(final String[] args, final Parameters defaultParameters) throws IOException {
+ final String ENABLE_COMPRESSION = "qcmp";
+ final String CompressFromKey = "compressFrom";
+
// create Options object
final Options options = new Options();
final String cmdLineSyntax = "BigDataServer [OPTIONS] [NAME XML] ...\n";
- final String CompressFromKey = "compressFrom";
final String description =
"Serves one or more XML/HDF5 datasets for remote access over HTTP.\n" +
@@ -165,7 +231,6 @@ public class BigDataServer {
"dataset should be made accessible and XML is the path to the XML file of the dataset.\n" +
"If -qcmp option is specified, these options are enabled:\u001b[35m-sq,-vq,-b,-cbc\u001b[0m\n";
-
options.addOption(OptionBuilder
.withDescription("Hostname of the server.\n(default: " + defaultParameters.getHostname() + ")")
.hasArg()
@@ -193,16 +258,14 @@ public class BigDataServer {
.withArgName("DIRECTORY")
.create("t"));
- final String ENABLE_COMPRESSION = "qcmp";
-
- final Option test = OptionBuilder
- .withDescription("Enable QCMP compression")
- .create(ENABLE_COMPRESSION);
-
+ options.addOption(OptionBuilder
+ .withDescription("Base URL under which the server will be made visible (e.g., if behind a proxy)")
+ .hasArg()
+ .withArgName("BASEURL")
+ .create("b"));
int optionOrder = 0;
- options.addOption(new OptionWithOrder(OptionBuilder
- .withDescription("Enable QCMP compression")
+ options.addOption(new OptionWithOrder(OptionBuilder.withDescription("Enable QCMP compression")
.create(ENABLE_COMPRESSION), ++optionOrder));
@@ -228,15 +291,16 @@ public class BigDataServer {
final String portString = cmd.getOptionValue("p", Integer.toString(defaultParameters.getPort()));
final int port = Integer.parseInt(portString);
-
// Getting server name option
final String serverName = cmd.getOptionValue("s", defaultParameters.getHostname());
// Getting thumbnail directory option
final String thumbnailDirectory = cmd.getOptionValue("t", defaultParameters.getThumbnailDirectory());
- final HashMap<String, String> datasets = new HashMap<String, String>(defaultParameters.getDatasets());
+ // Getting base url option
+ final String baseUrl = cmd.getOptionValue("b", defaultParameters.getBaseUrl());
+ final HashMap<String, String> datasets = new HashMap<String, String>(defaultParameters.getDatasets());
final boolean enableQcmpCompression = cmd.hasOption(ENABLE_COMPRESSION);
final ExtendedCompressionOptions compressionOptions = new ExtendedCompressionOptions();
@@ -306,7 +370,6 @@ public class BigDataServer {
enableManagerContext = true;
}
-
if (cmd.hasOption("d")) {
// process the file given with "-d"
final String datasetFile = cmd.getOptionValue("d");
@@ -351,6 +414,7 @@ public class BigDataServer {
serverName,
datasets,
thumbnailDirectory,
+ baseUrl,
enableManagerContext,
enableQcmpCompression ? compressionOptions : null);
} catch (final ParseException | IllegalArgumentException e) {
@@ -416,73 +480,23 @@ public class BigDataServer {
}
private static ContextHandlerCollection createHandlers(final String baseURL,
- final Parameters params,
- final String thumbnailsDirectoryName) throws SpimDataException, IOException {
-
+ final Map<String, String> dataSet,
+ final String thumbnailsDirectoryName,
+ final ExtendedCompressionOptions compressionOps) throws SpimDataException,
+ IOException {
final ContextHandlerCollection handlers = new ContextHandlerCollection();
- final Map<String, String> dataSet = params.getDatasets();
for (final Entry<String, String> entry : dataSet.entrySet()) {
final String name = entry.getKey();
final String xmlpath = entry.getValue();
final String context = "/" + name;
- final CellHandler ctx = new CellHandler(baseURL + context + "/", xmlpath, name,
- thumbnailsDirectoryName,
- params.getCompressionParams());
-
+ final CellHandler ctx = new CellHandler(baseURL + context + "/", xmlpath,
+ name, thumbnailsDirectoryName,
+ compressionOps);
ctx.setContextPath(context);
handlers.addHandler(ctx);
}
return handlers;
}
-
- public static void main(final String[] args) throws Exception {
- System.setProperty("org.eclipse.jetty.util.log.class", "org.eclipse.jetty.util.log.StdErrLog");
-
- final Parameters params = processOptions(args, getDefaultParameters());
- if (params == null)
- return;
-
- final String thumbnailsDirectoryName = getThumbnailDirectoryPath(params);
-
- // Threadpool for multiple connections
- final Server server = new Server(new QueuedThreadPool(200, 8));
-
- // ServerConnector configuration
- final ServerConnector connector = new ServerConnector(server);
- connector.setHost(params.getHostname());
- connector.setPort(params.getPort());
- LOG.info("Set connectors: " + connector);
- server.setConnectors(new Connector[]{connector});
- final String baseURL = "http://" + server.getURI().getHost() + ":" + params.getPort();
-
- // Handler initialization
- final HandlerCollection handlers = new HandlerCollection();
-
- final ContextHandlerCollection datasetHandlers = createHandlers(baseURL, params, thumbnailsDirectoryName);
- handlers.addHandler(datasetHandlers);
- handlers.addHandler(new JsonDatasetListHandler(server, datasetHandlers));
-
- Handler handler = handlers;
- if (params.enableManagerContext()) {
- // Add Statistics bean to the connector
- final ConnectorStatistics connectorStats = new ConnectorStatistics();
- connector.addBean(connectorStats);
-
- // create StatisticsHandler wrapper and ManagerHandler
- final StatisticsHandler statHandler = new StatisticsHandler();
- handlers.addHandler(new ManagerHandler(baseURL, server, connectorStats, statHandler, datasetHandlers, thumbnailsDirectoryName));
- statHandler.setHandler(handlers);
- handler = statHandler;
- }
-
-
- LOG.info("Set handler: " + handler);
- server.setHandler(handler);
- LOG.info("Server Base URL: " + baseURL);
- LOG.info("BigDataServer starting");
- server.start();
- server.join();
- }
}
diff --git a/src/main/java/bdv/server/CellHandler.java b/src/main/java/bdv/server/CellHandler.java
index b96500544a6de1399dcde2f396b9c3be8b03d203..927abd9f7ad034a58f5afc2b581bc558dd87ab3e 100644
--- a/src/main/java/bdv/server/CellHandler.java
+++ b/src/main/java/bdv/server/CellHandler.java
@@ -11,12 +11,7 @@ import azgracompress.io.InputData;
import azgracompress.io.MemoryOutputStream;
import azgracompress.utilities.Stopwatch;
import bdv.BigDataViewer;
-import bdv.cache.CacheHints;
-import bdv.cache.LoadingStrategy;
-import bdv.img.cache.VolatileCell;
import bdv.img.cache.VolatileGlobalCellCache;
-import bdv.img.cache.VolatileGlobalCellCache.Key;
-import bdv.img.cache.VolatileGlobalCellCache.VolatileCellLoader;
import bdv.img.hdf5.Hdf5ImageLoader;
import bdv.img.hdf5.Hdf5VolatileShortArrayLoader;
import bdv.img.remote.AffineTransform3DJsonSerializer;
@@ -28,7 +23,11 @@ import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.util.ThumbnailGenerator;
import com.google.gson.GsonBuilder;
import mpicbg.spim.data.SpimDataException;
+import net.imglib2.cache.CacheLoader;
+import net.imglib2.cache.LoaderCache;
+import net.imglib2.cache.ref.SoftRefLoaderCache;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
+import net.imglib2.img.cell.Cell;
import net.imglib2.realtransform.AffineTransform3D;
import org.eclipse.jetty.server.Request;
import org.eclipse.jetty.server.handler.ContextHandler;
@@ -51,18 +50,71 @@ import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Stack;
+import java.util.concurrent.ExecutionException;
public class CellHandler extends ContextHandler {
- private final long transferedDataSize = 0;
-
private static final org.eclipse.jetty.util.log.Logger LOG = Log.getLogger(CellHandler.class);
- private final int counter = 0;
- private final VolatileGlobalCellCache cache;
+ /**
+ * Key for a cell identified by timepoint, setup, level, and index
+ * (flattened spatial coordinate).
+ */
+ public static class Key {
+ private final int timepoint;
+
+ private final int setup;
+
+ private final int level;
+
+ private final long index;
+
+ private final String[] parts;
+
+ /**
+ * Create a Key for the specified cell. Note that {@code cellDims} and
+ * {@code cellMin} are not used for {@code hashcode()/equals()}.
+ *
+ * @param timepoint timepoint coordinate of the cell
+ * @param setup setup coordinate of the cell
+ * @param level level coordinate of the cell
+ * @param index index of the cell (flattened spatial coordinate of the
+ * cell)
+ */
+ public Key(final int timepoint, final int setup, final int level, final long index, final String[] parts) {
+ this.timepoint = timepoint;
+ this.setup = setup;
+ this.level = level;
+ this.index = index;
+ this.parts = parts;
+
+ int value = Long.hashCode(index);
+ value = 31 * value + level;
+ value = 31 * value + setup;
+ value = 31 * value + timepoint;
+ hashcode = value;
+ }
+
+ @Override
+ public boolean equals(final Object other) {
+ if (this == other)
+ return true;
+ if (!(other instanceof VolatileGlobalCellCache.Key))
+ return false;
+ final Key that = (Key) other;
+ return (this.index == that.index) && (this.timepoint == that.timepoint) && (this.setup == that.setup) && (this.level == that.level);
+ }
+
+ final int hashcode;
+
+ @Override
+ public int hashCode() {
+ return hashcode;
+ }
+ }
- private final Hdf5VolatileShortArrayLoader loader;
+ private final CacheLoader<Key, Cell<?>> loader;
- private final CacheHints cacheHints;
+ private final LoaderCache<Key, Cell<?>> cache;
/**
* Full path of the dataset xml file this {@link CellHandler} is serving.
@@ -125,19 +177,32 @@ public class CellHandler extends ContextHandler {
return uncompressedAccumulation;
}
- public CellHandler(final String baseUrl, final String xmlFilename, final String datasetName, final String thumbnailsDirectory,
- final BigDataServer.ExtendedCompressionOptions compressionParams) throws SpimDataException, IOException {
+ public CellHandler(final String baseUrl,
+ final String xmlFilename,
+ final String datasetName,
+ final String thumbnailsDirectory,
+ final BigDataServer.ExtendedCompressionOptions compressionOps) throws SpimDataException, IOException {
final XmlIoSpimDataMinimal io = new XmlIoSpimDataMinimal();
final SpimDataMinimal spimData = io.load(xmlFilename);
final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
-
final Hdf5ImageLoader imgLoader = (Hdf5ImageLoader) seq.getImgLoader();
- this.compressionParams = compressionParams;
+ this.compressionParams = compressionOps;
- cache = imgLoader.getCacheControl();
- loader = imgLoader.getShortArrayLoader();
- cacheHints = new CacheHints(LoadingStrategy.BLOCKING, 0, false);
+ final Hdf5VolatileShortArrayLoader cacheArrayLoader = imgLoader.getShortArrayLoader();
+ loader = key -> {
+ final int[] cellDims = new int[]{
+ Integer.parseInt(key.parts[5]),
+ Integer.parseInt(key.parts[6]),
+ Integer.parseInt(key.parts[7])};
+ final long[] cellMin = new long[]{
+ Long.parseLong(key.parts[8]),
+ Long.parseLong(key.parts[9]),
+ Long.parseLong(key.parts[10])};
+ return new Cell<>(cellDims, cellMin, cacheArrayLoader.loadArray(key.timepoint, key.setup, key.level, cellDims, cellMin));
+ };
+
+ cache = new SoftRefLoaderCache<>();
// dataSetURL property is used for providing the XML file by replace
// SequenceDescription>ImageLoader>baseUrl
@@ -145,14 +210,12 @@ public class CellHandler extends ContextHandler {
baseFilename = xmlFilename.endsWith(".xml") ? xmlFilename.substring(0, xmlFilename.length() - ".xml".length()) : xmlFilename;
dataSetURL = baseUrl;
- final int numberOfMipmapLevels = imgLoader.getSetupImgLoader(0).numMipmapLevels();
-
datasetXmlString = buildRemoteDatasetXML(io, spimData, baseUrl);
metadataJson = buildMetadataJsonString(imgLoader, seq);
settingsXmlString = buildSettingsXML(baseFilename);
thumbnailFilename = createThumbnail(spimData, baseFilename, datasetName, thumbnailsDirectory);
-
+ final int numberOfMipmapLevels = imgLoader.getSetupImgLoader(0).numMipmapLevels();
initializeCompression(numberOfMipmapLevels);
}
@@ -221,31 +284,11 @@ public class CellHandler extends ContextHandler {
cachedBuffers.push(buffer);
}
- private short[] getCachedVolatileCellData(final String[] parts, final int[] cellDims, final int level) {
- final int index = Integer.parseInt(parts[1]);
- final int timepoint = Integer.parseInt(parts[2]);
- final int setup = Integer.parseInt(parts[3]);
- final Key key = new VolatileGlobalCellCache.Key(timepoint, setup, level, index);
- VolatileCell<?> cell = cache.getLoadingVolatileCache().getIfPresent(key, cacheHints);
-
- final long[] cellMin = new long[]{
- Long.parseLong(parts[8]),
- Long.parseLong(parts[9]),
- Long.parseLong(parts[10])};
- if (cell == null) {
- cell = cache.getLoadingVolatileCache().get(key,
- cacheHints,
- new VolatileCellLoader<>(loader, timepoint, setup, level, cellDims, cellMin));
- }
- //noinspection unchecked
- return ((VolatileCell<VolatileShortArray>) cell).getData().getCurrentStorageArray();
- }
-
private FlatBufferInputData createInputDataObject(final short[] data, final int[] cellDims) {
return new FlatBufferInputData(data, new V3i(cellDims[0], cellDims[1], cellDims[2]), InputData.PixelType.Gray16, this.baseFilename);
}
- private void responseWithShortArray(final HttpServletResponse response, final short[] data) throws IOException {
+ private void respondWithShortArray(final HttpServletResponse response, final short[] data) throws IOException {
final OutputStream responseStream = response.getOutputStream();
final byte[] buf = new byte[2 * data.length];
@@ -259,6 +302,22 @@ public class CellHandler extends ContextHandler {
responseStream.close();
}
+ private short[] getCachedVolatileCellData(final String[] parts, final int level) {
+ final int index = Integer.parseInt(parts[1]);
+ final int timepoint = Integer.parseInt(parts[2]);
+ final int setup = Integer.parseInt(parts[3]);
+
+ final Key key = new Key(timepoint, setup, level, index, parts);
+ short[] data;
+ try {
+ final Cell<?> cell = cache.get(key, loader);
+ data = ((VolatileShortArray) cell.getData()).getCurrentStorageArray();
+ } catch (final ExecutionException e) {
+ data = new short[0];
+ }
+ return data;
+ }
+
@Override
public void doHandle(final String target,
final Request baseRequest,
@@ -281,28 +340,23 @@ public class CellHandler extends ContextHandler {
respondWithString(baseRequest, response, "application/xml", datasetXmlString);
return;
}
+
final String[] parts = cellString.split("/");
if (parts[0].equals("cell")) {
- final int level = Integer.parseInt(parts[4]);
- final int[] cellDims = new int[]{
- Integer.parseInt(parts[5]),
- Integer.parseInt(parts[6]),
- Integer.parseInt(parts[7])};
-
- final short[] data = getCachedVolatileCellData(parts, cellDims, level);
- responseWithShortArray(response, data);
+ final int level = Integer.parseInt(parts[4]);
+ final short[] data = getCachedVolatileCellData(parts, level);
+ respondWithShortArray(response, data);
response.setContentType("application/octet-stream");
response.setStatus(HttpServletResponse.SC_OK);
baseRequest.setHandled(true);
-
} else if (parts[0].equals("cell_qcmp")) {
final Stopwatch stopwatch = Stopwatch.startNew();
final int mipmapLevel = Integer.parseInt(parts[4]);
final int[] cellDims = new int[]{Integer.parseInt(parts[5]), Integer.parseInt(parts[6]), Integer.parseInt(parts[7])};
- final short[] data = getCachedVolatileCellData(parts, cellDims, mipmapLevel);
+ final short[] data = getCachedVolatileCellData(parts, mipmapLevel);
assert (compressors != null && !compressors.isEmpty());
final FlatBufferInputData inputData = createInputDataObject(data, cellDims);
@@ -349,6 +403,23 @@ public class CellHandler extends ContextHandler {
}
}
+ private void provideThumbnail(final Request baseRequest, final HttpServletResponse response) throws IOException {
+ final Path path = Paths.get(thumbnailFilename);
+ if (Files.exists(path)) {
+ final byte[] imageData = Files.readAllBytes(path);
+ if (imageData != null) {
+ response.setContentType("image/png");
+ response.setContentLength(imageData.length);
+ response.setStatus(HttpServletResponse.SC_OK);
+ baseRequest.setHandled(true);
+
+ final OutputStream os = response.getOutputStream();
+ os.write(imageData);
+ os.close();
+ }
+ }
+ }
+
private void respondWithCompressionInfo(final Request baseRequest, final HttpServletResponse response) throws IOException {
if (cachedCodebooks == null || cachedCodebooks.isEmpty()) {
LOG.info("QCMP initialization request was refused, QCMP compression is not enabled.");
@@ -369,23 +440,6 @@ public class CellHandler extends ContextHandler {
baseRequest.setHandled(true);
}
- private void provideThumbnail(final Request baseRequest, final HttpServletResponse response) throws IOException {
- final Path path = Paths.get(thumbnailFilename);
- if (Files.exists(path)) {
- final byte[] imageData = Files.readAllBytes(path);
- if (imageData != null) {
- response.setContentType("image/png");
- response.setContentLength(imageData.length);
- response.setStatus(HttpServletResponse.SC_OK);
- baseRequest.setHandled(true);
-
- final OutputStream os = response.getOutputStream();
- os.write(imageData);
- os.close();
- }
- }
- }
-
public String getXmlFile() {
return xmlFilename;
}
@@ -506,4 +560,4 @@ public class CellHandler extends ContextHandler {
ow.write(string);
ow.close();
}
-}
+}
\ No newline at end of file
diff --git a/src/main/java/bdv/util/ThumbnailGenerator.java b/src/main/java/bdv/util/ThumbnailGenerator.java
index 92c0f322bce7e29f9406fd1d063dba49b65e25f5..f8d64a61efc32e9f4be13b7bee888a998077ea9a 100644
--- a/src/main/java/bdv/util/ThumbnailGenerator.java
+++ b/src/main/java/bdv/util/ThumbnailGenerator.java
@@ -114,7 +114,7 @@ public class ThumbnailGenerator
final int numGroups = 10;
final ArrayList< SourceGroup > groups = new ArrayList< SourceGroup >( numGroups );
for ( int i = 0; i < numGroups; ++i )
- groups.add( new SourceGroup( "", null ) );
+ groups.add( new SourceGroup( "" ) );
state = new ViewerState( sources, groups, numTimePoints );
if ( !sources.isEmpty() )