diff --git a/src/main/java/bdv/BigDataViewer.java b/src/main/java/bdv/BigDataViewer.java
index 9f2390ba1f9e6d395970af9e094bbf07c15180f2..88583bc6fb0e130ccce577f2521562b4a9bceeac 100644
--- a/src/main/java/bdv/BigDataViewer.java
+++ b/src/main/java/bdv/BigDataViewer.java
@@ -243,7 +243,7 @@ public class BigDataViewer {
final ViewerImgLoader imgLoader = (ViewerImgLoader) spimData.getSequenceDescription().getImgLoader();
@SuppressWarnings("unchecked") final ViewerSetupImgLoader<T, V> setupImgLoader =
(ViewerSetupImgLoader<T, V>) imgLoader.getSetupImgLoader(
- setupId);
+ setupId);
final T type = setupImgLoader.getImageType();
final V volatileType = setupImgLoader.getVolatileImageType();
@@ -636,38 +636,19 @@ public class BigDataViewer {
}
public static void main(final String[] args) {
- // final String fn = "http://tomancak-mac-17.mpi-cbg.de:8080/openspim/";
- // final String fn = "/Users/Pietzsch/Desktop/openspim/datasetHDF.xml";
- // final String fn = "/Users/pietzsch/workspace/data/111010_weber_full.xml";
- // final String fn = "/Users/Pietzsch/Desktop/spimrec2/dataset.xml";
- // final String fn = "/Users/pietzsch/Desktop/HisYFP-SPIM/dataset.xml";
- // final String fn = "/Users/Pietzsch/Desktop/bdv example/drosophila 2.xml";
- // final String fn = "/Users/pietzsch/Desktop/data/clusterValia/140219-1/valia-140219-1.xml";
- // final String fn = "/Users/Pietzsch/Desktop/data/catmaid.xml";
- // final String fn = "src/main/resources/openconnectome-bock11-neariso.xml";
- // final String fn = "/home/saalfeld/catmaid.xml";
- // final String fn = "/home/saalfeld/catmaid-fafb00-v9.xml";
- // final String fn = "/home/saalfeld/catmaid-fafb00-sample_A_cutout_3k.xml";
- // final String fn = "/home/saalfeld/catmaid-thorsten.xml";
- // final String fn = "/home/saalfeld/knossos-example.xml";
- // final String fn = "/Users/Pietzsch/Desktop/data/catmaid-confocal.xml";
- // final String fn = "/Users/pietzsch/desktop/data/BDV130418A325/BDV130418A325_NoTempReg.xml";
- // final String fn = "/Users/pietzsch/Desktop/data/valia2/valia.xml";
- // final String fn = "/Users/pietzsch/workspace/data/fast fly/111010_weber/combined.xml";
- // final String fn = "/Users/pietzsch/workspace/data/mette/mette.xml";
- // final String fn = "/Users/tobias/Desktop/openspim.xml";
- // final String fn = "/Users/pietzsch/Desktop/data/fibsem.xml";
- // final String fn = "/Users/pietzsch/Desktop/data/fibsem-remote.xml";
- // final String fn = "/Users/pietzsch/Desktop/url-valia.xml";
- // final String fn = "/Users/pietzsch/Desktop/data/clusterValia/140219-1/valia-140219-1.xml";
- // final String fn = "/Users/pietzsch/workspace/data/111010_weber_full.xml";
- // final String fn = "/Volumes/projects/tomancak_lightsheet/Mette/ZeissZ1SPIM/Maritigrella/021013_McH2BsGFP_CAAX-mCherry/11-use/hdf5/021013_McH2BsGFP_CAAX-mCherry-11-use.xml";
+
+ // Default
+ String fn = "http://127.0.0.1:8080/drosophila32";
+
+
if (args.length < 1) {
System.err.println("Provide path.");
return;
}
- final String fn = args[0];
+
+ fn = args[0];
final boolean allowCompression = (args.length > 1) && (args[1].equals("-qcmp"));
+
try {
System.setProperty("apple.laf.useScreenMenuBar", "true");
@@ -677,7 +658,6 @@ public class BigDataViewer {
ViewerOptions.options(),
allowCompression);
- // DumpInputConfig.writeToYaml( System.getProperty( "user.home" ) + "/.bdv/bdvkeyconfig.yaml", bdv.getViewerFrame() );
} catch (final Exception e) {
e.printStackTrace();
}
diff --git a/src/main/java/bdv/img/remote/RemoteImageLoader.java b/src/main/java/bdv/img/remote/RemoteImageLoader.java
index 2d5247a2995966d20952922aeada3d75252c9188..839771a63baba5790423be74050370c78a5e0c5d 100644
--- a/src/main/java/bdv/img/remote/RemoteImageLoader.java
+++ b/src/main/java/bdv/img/remote/RemoteImageLoader.java
@@ -31,6 +31,7 @@ package bdv.img.remote;
import azgracompress.cache.ICacheFile;
import azgracompress.cache.QuantizationCacheManager;
+import azgracompress.compression.ImageDecompressor;
import bdv.AbstractViewerSetupImgLoader;
import bdv.ViewerImgLoader;
import bdv.img.cache.VolatileCachedCellImg;
@@ -55,6 +56,7 @@ import net.imglib2.view.Views;
import java.io.IOException;
import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
import java.net.URL;
import java.util.HashMap;
@@ -69,7 +71,12 @@ public class RemoteImageLoader implements ViewerImgLoader {
protected RemoteVolatileShortArrayLoader shortLoader;
+ /**
+ * Flag whether we allow the server to send us compressed data.
+ */
private boolean allowCompression;
+
+
/**
* TODO
*/
@@ -102,10 +109,6 @@ public class RemoteImageLoader implements ViewerImgLoader {
return;
isOpen = true;
- if (allowCompression) {
- receiveCompressionInfo();
- }
-
final URL url = new URL(baseUrl + "?p=init");
final GsonBuilder gsonBuilder = new GsonBuilder();
gsonBuilder.registerTypeAdapter(AffineTransform3D.class, new AffineTransform3DJsonSerializer());
@@ -117,6 +120,10 @@ public class RemoteImageLoader implements ViewerImgLoader {
cellsDimensions = metadata.createCellsDimensions();
for (final int setupId : metadata.perSetupMipmapInfo.keySet())
setupImgLoaders.put(setupId, new SetupImgLoader(setupId));
+
+ if (allowCompression) {
+ setupCompression();
+ }
}
}
}
@@ -129,10 +136,20 @@ public class RemoteImageLoader implements ViewerImgLoader {
this.allowCompression = compressionEnabled;
}
- private void receiveCompressionInfo() throws IOException {
+ private void setupCompression() throws IOException {
final URL url = new URL(baseUrl + "?p=init_qcmp");
- final ICacheFile cachedCodebook = QuantizationCacheManager.readCacheFile(url.openStream());
- System.out.println("\u001b[33mRemoteImageLoader::receiveCompressionInfo() - received cache file. '" + cachedCodebook.toString() + "'\u001b[0m");
+ final HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+ connection.setRequestMethod("GET");
+ connection.connect();
+
+ if (connection.getResponseCode() != HttpURLConnection.HTTP_OK) {
+ System.out.println("\u001b[33mRemoteImageLoader::setupCompression() - Server doesn't provide compressed data.\u001b[0m");
+ return;
+ }
+ final ICacheFile cachedCodebook = QuantizationCacheManager.readCacheFile(connection.getInputStream());
+ System.out.println("\u001b[33mRemoteImageLoader::setupCompression() - received cache file. '" + cachedCodebook + "'\u001b[0m");
+ shortLoader.setDataDecompressor(new ImageDecompressor(cachedCodebook));
+ System.out.println("\u001b[33mRemoteImageLoader::setupCompression() - instantiated image decompressor in shortLoader.\u001b[0m");
}
diff --git a/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java b/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
index ea2582129362c2f21434d88805fc8e97b6539167..600780828a5b4d6ae6d1696ed370f0ffb0bde510 100644
--- a/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
+++ b/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
@@ -31,67 +31,117 @@ package bdv.img.remote;
import java.io.IOException;
import java.io.InputStream;
+import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
+import azgracompress.compression.ImageDecompressor;
import bdv.img.cache.CacheArrayLoader;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
-public class RemoteVolatileShortArrayLoader implements CacheArrayLoader< VolatileShortArray >
-{
- private final RemoteImageLoader imgLoader;
-
- public RemoteVolatileShortArrayLoader( final RemoteImageLoader imgLoader )
- {
- this.imgLoader = imgLoader;
- }
-
- @Override
- public VolatileShortArray loadArray( final int timepoint, final int setup, final int level, final int[] dimensions, final long[] min ) throws InterruptedException
- {
- final int index = imgLoader.getCellIndex( timepoint, setup, level, min );
- final short[] data = new short[ dimensions[ 0 ] * dimensions[ 1 ] * dimensions[ 2 ] ];
- try
- {
- final URL url = new URL(String.format("%s?p=cell/%d/%d/%d/%d/%d/%d/%d/%d/%d/%d",
- imgLoader.baseUrl,
- index,
- timepoint,
- setup,
- level,
- dimensions[0],
- dimensions[1],
- dimensions[2],
- min[0],
- min[1],
- min[2]));
- final InputStream s = url.openStream();
-// System.out.println("Request URL=" + url);
+public class RemoteVolatileShortArrayLoader implements CacheArrayLoader<VolatileShortArray> {
+ private final RemoteImageLoader imgLoader;
+
+ private ImageDecompressor decompressor;
+ private boolean requestCompressedData = false;
+
+ public RemoteVolatileShortArrayLoader(final RemoteImageLoader imgLoader) {
+ this.imgLoader = imgLoader;
+ }
+
+ private String constructRequestUrl(final String baseParam,
+ final int timepoint,
+ final int setup,
+ final int level,
+ final int[] dimensions,
+ final long[] min) {
+ final int index = imgLoader.getCellIndex(timepoint, setup, level, min);
+ return String.format("%s?p=%s/%d/%d/%d/%d/%d/%d/%d/%d/%d/%d",
+ imgLoader.baseUrl, baseParam,
+ index, timepoint, setup, level,
+ dimensions[0], dimensions[1], dimensions[2],
+ min[0], min[1], min[2]);
+ }
+
+
+ @Override
+ public VolatileShortArray loadArray(final int timepoint,
+ final int setup,
+ final int level,
+ final int[] dimensions,
+ final long[] min) throws InterruptedException {
+
+
+ if (requestCompressedData) {
+ return loadArrayFromCompressedDataStream(timepoint, setup, level, dimensions, min);
+ }
+
+ short[] data = new short[dimensions[0] * dimensions[1] * dimensions[2]];
+ try {
+ final URL url = new URL(constructRequestUrl("cell", timepoint, setup, level, dimensions, min));
+
final byte[] buf = new byte[data.length * 2];
+ final InputStream urlStream = url.openStream();
- // NOTE(Moravec): Decompression place!
- for (int i = 0, l = s.read(buf, 0, buf.length);
- l > 0;
- i += l, l = s.read(buf, i, buf.length - i))
- ;
+ //noinspection StatementWithEmptyBody
+ for (int i = 0, l = urlStream.read(buf, 0, buf.length);
+ l > 0;
+ i += l, l = urlStream.read(buf, i, buf.length - i))
+ ;
for (int i = 0, j = 0; i < data.length; ++i, j += 2)
data[i] = (short) (((buf[j] & 0xff) << 8) | (buf[j + 1] & 0xff));
- s.close();
- }
- catch ( final MalformedURLException e )
- {
- e.printStackTrace();
- }
- catch ( final IOException e )
- {
- e.printStackTrace();
- }
- return new VolatileShortArray( data, true );
- }
-
- @Override
- public int getBytesPerElement() {
- return 2;
- }
+
+ urlStream.close();
+ } catch (final MalformedURLException e) {
+ e.printStackTrace();
+ } catch (final IOException e) {
+ e.printStackTrace();
+ }
+ return new VolatileShortArray(data, true);
+ }
+
+ public VolatileShortArray loadArrayFromCompressedDataStream(final int timepoint,
+ final int setup,
+ final int level,
+ final int[] dimensions,
+ final long[] min) {
+
+ short[] data = null;
+ try {
+ final URL url = new URL(constructRequestUrl("cell_qcmp", timepoint, setup, level, dimensions, min));
+
+ final HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+ connection.setRequestMethod("GET");
+ connection.connect();
+
+ final byte[] buf = new byte[connection.getContentLength()];
+ final InputStream urlStream = connection.getInputStream();
+
+ //noinspection StatementWithEmptyBody
+ for (int i = 0, l = urlStream.read(buf, 0, buf.length);
+ l > 0;
+ i += l, l = urlStream.read(buf, i, buf.length - i))
+ ;
+
+
+ data = decompressor.decompressStream(urlStream);
+
+ urlStream.close();
+ } catch (final Exception e) {
+ e.printStackTrace();
+ }
+
+ return new VolatileShortArray(data, true);
+ }
+
+ @Override
+ public int getBytesPerElement() {
+ return 2;
+ }
+
+ public void setDataDecompressor(final ImageDecompressor imageDecompressor) {
+ this.decompressor = imageDecompressor;
+ requestCompressedData = true;
+ }
}