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Commit 0b59586b authored by Vojtech Moravec's avatar Vojtech Moravec
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Prepare Viewer to handle QCMP compressed data.

parent 9236e585
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src/main/java/bdv/BigDataViewer.java
+ 9
− 29
View file @ 0b59586b
......@@ -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();
}
......
src/main/java/bdv/img/remote/RemoteImageLoader.java
+ 24
− 7
View file @ 0b59586b
......@@ -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");
}
......
src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
+ 102
− 52
View file @ 0b59586b
......@@ -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;
}
}
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