From 368cc7c0749ac523597d19985598f662d7520d35 Mon Sep 17 00:00:00 2001
From: Vojtech Moravec <vojtech.moravec.st@vsb.cz>
Date: Fri, 25 Sep 2020 13:06:13 +0200
Subject: [PATCH] Enable usage of multiple decompressors.
This contains functionality to map mipmap level to codebook size. Also -compress-from options is added to set the minimal mipmap level to compress.
Eg. -comress-from 1, means that level 0 is not compressed and levels > 1 are.
---
.../ViewerCompressionOptions.java | 22 ++++
src/main/java/bdv/BigDataViewer.java | 118 +++++++++---------
.../bdv/img/remote/RemoteImageLoader.java | 22 ++--
.../RemoteVolatileShortArrayLoader.java | 53 ++++++--
.../bdv/spimdata/XmlIoSpimDataMinimal.java | 85 ++++++-------
5 files changed, 173 insertions(+), 127 deletions(-)
create mode 100644 src/main/java/azgracompress/ViewerCompressionOptions.java
diff --git a/src/main/java/azgracompress/ViewerCompressionOptions.java b/src/main/java/azgracompress/ViewerCompressionOptions.java
new file mode 100644
index 00000000..c74cd3c1
--- /dev/null
+++ b/src/main/java/azgracompress/ViewerCompressionOptions.java
@@ -0,0 +1,22 @@
+package azgracompress;
+
+public class ViewerCompressionOptions {
+ private boolean enabled = false;
+ private int compressFromMipmapLevel = 0;
+
+ public boolean isEnabled() {
+ return enabled;
+ }
+
+ public void setEnabled(final boolean enable) {
+ this.enabled = enable;
+ }
+
+ public int getCompressFromMipmapLevel() {
+ return compressFromMipmapLevel;
+ }
+
+ public void setCompressFromMipmapLevel(final int compressFrom) {
+ this.compressFromMipmapLevel = compressFrom;
+ }
+}
diff --git a/src/main/java/bdv/BigDataViewer.java b/src/main/java/bdv/BigDataViewer.java
index 88583bc6..e1f6a331 100644
--- a/src/main/java/bdv/BigDataViewer.java
+++ b/src/main/java/bdv/BigDataViewer.java
@@ -29,73 +29,55 @@
*/
package bdv;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.ActionMap;
-import javax.swing.JFileChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuBar;
-import javax.swing.JMenuItem;
-import javax.swing.filechooser.FileFilter;
-
-import azgracompress.cache.ICacheFile;
-import net.imglib2.Volatile;
-import net.imglib2.converter.Converter;
-import net.imglib2.display.ColorConverter;
-import net.imglib2.display.RealARGBColorConverter;
-import net.imglib2.display.ScaledARGBConverter;
-import net.imglib2.type.numeric.ARGBType;
-import net.imglib2.type.numeric.NumericType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.volatiles.VolatileARGBType;
-
-import org.jdom2.Document;
-import org.jdom2.Element;
-import org.jdom2.JDOMException;
-import org.jdom2.input.SAXBuilder;
-import org.jdom2.output.Format;
-import org.jdom2.output.XMLOutputter;
-import org.scijava.ui.behaviour.io.InputTriggerConfig;
-import org.scijava.ui.behaviour.io.yaml.YamlConfigIO;
-
+import azgracompress.ViewerCompressionOptions;
+import azgracompress.utilities.ColorConsole;
import bdv.cache.CacheControl;
import bdv.export.ProgressWriter;
import bdv.export.ProgressWriterConsole;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.WrapBasicImgLoader;
import bdv.spimdata.XmlIoSpimDataMinimal;
-import bdv.tools.HelpDialog;
-import bdv.tools.InitializeViewerState;
-import bdv.tools.RecordMaxProjectionDialog;
-import bdv.tools.RecordMovieDialog;
-import bdv.tools.VisibilityAndGroupingDialog;
+import bdv.tools.*;
import bdv.tools.bookmarks.Bookmarks;
import bdv.tools.bookmarks.BookmarksEditor;
-import bdv.tools.brightness.BrightnessDialog;
-import bdv.tools.brightness.ConverterSetup;
-import bdv.tools.brightness.MinMaxGroup;
-import bdv.tools.brightness.RealARGBColorConverterSetup;
-import bdv.tools.brightness.SetupAssignments;
+import bdv.tools.brightness.*;
import bdv.tools.crop.CropDialog;
import bdv.tools.transformation.ManualTransformation;
import bdv.tools.transformation.ManualTransformationEditor;
import bdv.tools.transformation.TransformedSource;
-import bdv.viewer.NavigationActions;
-import bdv.viewer.SourceAndConverter;
-import bdv.viewer.ViewerFrame;
-import bdv.viewer.ViewerOptions;
-import bdv.viewer.ViewerPanel;
+import bdv.viewer.*;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
import mpicbg.spim.data.sequence.Angle;
import mpicbg.spim.data.sequence.Channel;
+import net.imglib2.Volatile;
+import net.imglib2.converter.Converter;
+import net.imglib2.display.ColorConverter;
+import net.imglib2.display.RealARGBColorConverter;
+import net.imglib2.display.ScaledARGBConverter;
+import net.imglib2.type.numeric.ARGBType;
+import net.imglib2.type.numeric.NumericType;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.type.volatiles.VolatileARGBType;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.JDOMException;
+import org.jdom2.input.SAXBuilder;
+import org.jdom2.output.Format;
+import org.jdom2.output.XMLOutputter;
+import org.scijava.ui.behaviour.io.InputTriggerConfig;
+import org.scijava.ui.behaviour.io.yaml.YamlConfigIO;
+
+import javax.swing.*;
+import javax.swing.filechooser.FileFilter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
public class BigDataViewer {
protected final ViewerFrame viewerFrame;
@@ -465,10 +447,10 @@ public class BigDataViewer {
final String windowTitle,
final ProgressWriter progressWriter,
final ViewerOptions options,
- final boolean allowCompression) throws SpimDataException {
+ final ViewerCompressionOptions ops) throws SpimDataException {
final XmlIoSpimDataMinimal xmlIoSpimDataMinimal = new XmlIoSpimDataMinimal();
- xmlIoSpimDataMinimal.setAllowCompression(allowCompression);
+ xmlIoSpimDataMinimal.setViewerCompressionOptions(ops);
final SpimDataMinimal spimData = xmlIoSpimDataMinimal.load(xmlFilename);
final BigDataViewer bdv = open(spimData, windowTitle, progressWriter, options);
if (!bdv.tryLoadSettings(xmlFilename))
@@ -635,19 +617,37 @@ public class BigDataViewer {
viewer.requestRepaint();
}
- public static void main(final String[] args) {
-
- // Default
- String fn = "http://127.0.0.1:8080/drosophila32";
-
+ public static void main(final String[] args) {
if (args.length < 1) {
System.err.println("Provide path.");
return;
}
+ final String fn = args[0];
+
+ final ViewerCompressionOptions ops = new ViewerCompressionOptions();
+ if (args.length > 1) {
+ for (int i = 1; i < args.length; i++) {
+
+ switch (args[i]) {
+ case "-qcmp":
+ ops.setEnabled(true);
+ break;
+ case "-compress-from":
+ if (args.length <= i + 1) {
+ System.err.println("Missing -compress-from integer parameter.");
+ return;
+ }
+ ops.setCompressFromMipmapLevel(Integer.parseInt(args[++i]));
+ break;
+ }
+
+ }
+ }
- fn = args[0];
- final boolean allowCompression = (args.length > 1) && (args[1].equals("-qcmp"));
+ ColorConsole.printf(ColorConsole.Color.Green, "Compression:\t" + (ops.isEnabled() ? "ON" : "OFF"));
+ if (ops.isEnabled())
+ ColorConsole.printf(ColorConsole.Color.Green, "CompressFrom:\t" + ops.getCompressFromMipmapLevel());
try {
System.setProperty("apple.laf.useScreenMenuBar", "true");
@@ -656,7 +656,7 @@ public class BigDataViewer {
"Server test",
new ProgressWriterConsole(),
ViewerOptions.options(),
- allowCompression);
+ ops);
} 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 e2fb6499..949c7cf3 100644
--- a/src/main/java/bdv/img/remote/RemoteImageLoader.java
+++ b/src/main/java/bdv/img/remote/RemoteImageLoader.java
@@ -29,6 +29,7 @@
*/
package bdv.img.remote;
+import azgracompress.ViewerCompressionOptions;
import azgracompress.cache.ICacheFile;
import azgracompress.cache.QuantizationCacheManager;
import azgracompress.compression.ImageDecompressor;
@@ -77,7 +78,7 @@ public class RemoteImageLoader implements ViewerImgLoader {
/**
* Flag whether we allow the server to send us compressed data.
*/
- private boolean allowCompression;
+ private ViewerCompressionOptions viewerCompressionOptions;
/**
@@ -124,19 +125,15 @@ public class RemoteImageLoader implements ViewerImgLoader {
for (final int setupId : metadata.perSetupMipmapInfo.keySet())
setupImgLoaders.put(setupId, new SetupImgLoader(setupId));
- if (allowCompression) {
+ if (viewerCompressionOptions.isEnabled()) {
setupCompression();
}
}
}
}
- public boolean shouldAllowCompression() {
- return allowCompression;
- }
-
- public void setAllowCompression(final boolean compressionEnabled) {
- this.allowCompression = compressionEnabled;
+ public void setViewerCompressionOptions(final ViewerCompressionOptions ops) {
+ this.viewerCompressionOptions = ops;
}
private void setupCompression() throws IOException {
@@ -166,10 +163,11 @@ public class RemoteImageLoader implements ViewerImgLoader {
ColorConsole.fprintf(ColorConsole.Target.stdout, ColorConsole.Color.Yellow, "Received %d cache files.", cacheFiles.size());
- final ICacheFile cachedCodebook = cacheFiles.get(cacheFiles.size() - 1);
- // TODO(Moravec): Provide all decompressors.
- shortLoader.setDataDecompressor(new ImageDecompressor(cachedCodebook));
- System.out.println("\u001b[33mRemoteImageLoader::setupCompression() - instantiated image decompressor in shortLoader.\u001b[0m");
+ final ImageDecompressor[] decompressors = new ImageDecompressor[cacheFiles.size()];
+ for (int i = 0; i < cacheFiles.size(); i++) {
+ decompressors[i] = new ImageDecompressor(cacheFiles.get(i));
+ }
+ shortLoader.setDataDecompressors(decompressors, metadata.maxNumLevels, viewerCompressionOptions.getCompressFromMipmapLevel());
}
diff --git a/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java b/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
index 0e85c9ce..7a85c86b 100644
--- a/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
+++ b/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
@@ -29,7 +29,9 @@
*/
package bdv.img.remote;
+import azgracompress.compression.CompressorDecompressorBase;
import azgracompress.compression.ImageDecompressor;
+import azgracompress.utilities.ColorConsole;
import bdv.img.cache.CacheArrayLoader;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
@@ -38,12 +40,17 @@ import java.io.InputStream;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.HashMap;
public class RemoteVolatileShortArrayLoader implements CacheArrayLoader<VolatileShortArray> {
private final RemoteImageLoader imgLoader;
private boolean requestCompressedData = false;
- private ImageDecompressor decompressor;
+ private HashMap<Integer, ImageDecompressor> decompressors;
+ private ImageDecompressor lowestResDecompressor;
+ private int compressFromMipmapLevel = 0;
public RemoteVolatileShortArrayLoader(final RemoteImageLoader imgLoader) {
@@ -70,10 +77,9 @@ public class RemoteVolatileShortArrayLoader implements CacheArrayLoader<Volatile
final int setup,
final int level,
final int[] dimensions,
- final long[] min) throws InterruptedException {
+ final long[] min) {
-
- if (requestCompressedData) {
+ if (requestCompressedData && level >= compressFromMipmapLevel) {
return loadArrayFromCompressedDataStream(timepoint, setup, level, dimensions, min);
}
@@ -104,13 +110,13 @@ public class RemoteVolatileShortArrayLoader implements CacheArrayLoader<Volatile
public VolatileShortArray loadArrayFromCompressedDataStream(final int timepoint,
final int setup,
- final int level,
+ final int mipmapLevel,
final int[] dimensions,
final long[] min) {
short[] data = null;
try {
- final URL url = new URL(constructRequestUrl("cell_qcmp", timepoint, setup, level, dimensions, min));
+ final URL url = new URL(constructRequestUrl("cell_qcmp", timepoint, setup, mipmapLevel, dimensions, min));
final HttpURLConnection connection = (HttpURLConnection) url.openConnection();
connection.setRequestMethod("GET");
@@ -119,7 +125,7 @@ public class RemoteVolatileShortArrayLoader implements CacheArrayLoader<Volatile
final int contentLength = connection.getContentLength();
final InputStream urlStream = connection.getInputStream();
- data = decompressor.decompressStream(urlStream, contentLength);
+ data = getDecompressorForMipmapLevel(mipmapLevel).decompressStream(urlStream, contentLength);
urlStream.close();
} catch (final Exception e) {
@@ -134,8 +140,35 @@ public class RemoteVolatileShortArrayLoader implements CacheArrayLoader<Volatile
return 2;
}
- public void setDataDecompressor(final ImageDecompressor imageDecompressor) {
- this.decompressor = imageDecompressor;
- requestCompressedData = true;
+ private ImageDecompressor getDecompressorForMipmapLevel(final int mipmapLevel) {
+ assert (decompressors != null && !decompressors.isEmpty());
+ if (decompressors.containsKey(mipmapLevel)) {
+ return decompressors.get(mipmapLevel);
+ }
+ return lowestResDecompressor;
+ }
+
+ public void setDataDecompressors(final ImageDecompressor[] imageDecompressors,
+ final int levelCount,
+ final int compressFromMipmapLevel) {
+ Arrays.sort(imageDecompressors, Comparator.comparingInt(CompressorDecompressorBase::getBitsPerCodebookIndex));
+
+
+ final int numberOfDecompressionLevels = Math.min((levelCount - compressFromMipmapLevel), imageDecompressors.length);
+ decompressors = new HashMap<>(numberOfDecompressionLevels);
+
+ for (int mipmapLevel = 0; mipmapLevel < numberOfDecompressionLevels; mipmapLevel++) {
+ final ImageDecompressor decompressor = imageDecompressors[(imageDecompressors.length - 1) - mipmapLevel];
+ final int cbSize = (int) Math.pow(2, decompressor.getBitsPerCodebookIndex());
+ final int actualKey = mipmapLevel + compressFromMipmapLevel;
+ decompressors.put(actualKey, decompressor);
+
+ ColorConsole.fprintf(ColorConsole.Target.stdout, ColorConsole.Color.Yellow,
+ "Created decompressor for mipmap level %d with codebook of size %d.",
+ actualKey, cbSize);
+ lowestResDecompressor = decompressor;
+ }
+ this.compressFromMipmapLevel = compressFromMipmapLevel;
+ requestCompressedData = !decompressors.isEmpty();
}
}
diff --git a/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java b/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java
index 8737c521..2988d6d2 100644
--- a/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java
+++ b/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java
@@ -29,11 +29,9 @@
*/
package bdv.spimdata;
-import static mpicbg.spim.data.XmlKeys.SPIMDATA_TAG;
-
-import java.io.File;
-
+import azgracompress.ViewerCompressionOptions;
import bdv.img.remote.RemoteImageLoader;
+import bdv.spimdata.legacy.XmlIoSpimDataMinimalLegacy;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.SpimDataIOException;
import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
@@ -43,58 +41,53 @@ import mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetups;
import mpicbg.spim.data.registration.XmlIoViewRegistrations;
import mpicbg.spim.data.sequence.XmlIoMissingViews;
import mpicbg.spim.data.sequence.XmlIoTimePoints;
-
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.input.SAXBuilder;
-import bdv.spimdata.legacy.XmlIoSpimDataMinimalLegacy;
+import java.io.File;
+
+import static mpicbg.spim.data.XmlKeys.SPIMDATA_TAG;
-public class XmlIoSpimDataMinimal extends XmlIoAbstractSpimData< SequenceDescriptionMinimal, SpimDataMinimal >
-{
- private boolean allowCompression = false;
+public class XmlIoSpimDataMinimal extends XmlIoAbstractSpimData<SequenceDescriptionMinimal, SpimDataMinimal> {
+ private ViewerCompressionOptions compressionOptions;
- public XmlIoSpimDataMinimal()
- {
- super( SpimDataMinimal.class,
- new XmlIoAbstractSequenceDescription<>(
- SequenceDescriptionMinimal.class,
- new XmlIoTimePoints(),
- new XmlIoBasicViewSetups<>( BasicViewSetup.class ),
- new XmlIoMissingViews() ),
- new XmlIoViewRegistrations() );
- }
+ public XmlIoSpimDataMinimal() {
+ super(SpimDataMinimal.class,
+ new XmlIoAbstractSequenceDescription<>(
+ SequenceDescriptionMinimal.class,
+ new XmlIoTimePoints(),
+ new XmlIoBasicViewSetups<>(BasicViewSetup.class),
+ new XmlIoMissingViews()),
+ new XmlIoViewRegistrations());
+ }
- public void setAllowCompression(final boolean allowCompression) {
- this.allowCompression = allowCompression;
+ public void setViewerCompressionOptions(final ViewerCompressionOptions ops) {
+ this.compressionOptions = ops;
}
- @Override
- public SpimDataMinimal load( final String xmlFilename ) throws SpimDataException
- {
- final SAXBuilder sax = new SAXBuilder();
- Document doc;
- try
- {
- doc = sax.build( xmlFilename );
- }
- catch ( final Exception e )
- {
- throw new SpimDataIOException( e );
- }
- final Element root = doc.getRootElement();
+ @Override
+ public SpimDataMinimal load(final String xmlFilename) throws SpimDataException {
+ final SAXBuilder sax = new SAXBuilder();
+ final Document doc;
+ try {
+ doc = sax.build(xmlFilename);
+ } catch (final Exception e) {
+ throw new SpimDataIOException(e);
+ }
+ final Element root = doc.getRootElement();
- if ( root.getName().equals( "SequenceDescription" ) )
- return XmlIoSpimDataMinimalLegacy.fromXml( root, new File( xmlFilename ) );
+ if (root.getName().equals("SequenceDescription"))
+ return XmlIoSpimDataMinimalLegacy.fromXml(root, new File(xmlFilename));
- if ( root.getName() != SPIMDATA_TAG )
- throw new RuntimeException( "expected <" + SPIMDATA_TAG + "> root element. wrong file?" );
+ if (root.getName() != SPIMDATA_TAG)
+ throw new RuntimeException("expected <" + SPIMDATA_TAG + "> root element. wrong file?");
- SpimDataMinimal spimDataMinimal = fromXml(root, new File(xmlFilename));
- if (spimDataMinimal.getSequenceDescription().getImgLoader() instanceof RemoteImageLoader) {
- final RemoteImageLoader remoteImageLoader = (RemoteImageLoader) spimDataMinimal.getSequenceDescription().getImgLoader();
- remoteImageLoader.setAllowCompression(allowCompression);
- }
- return spimDataMinimal;
- }
+ final SpimDataMinimal spimDataMinimal = fromXml(root, new File(xmlFilename));
+ if (spimDataMinimal.getSequenceDescription().getImgLoader() instanceof RemoteImageLoader) {
+ final RemoteImageLoader remoteImageLoader = (RemoteImageLoader) spimDataMinimal.getSequenceDescription().getImgLoader();
+ remoteImageLoader.setViewerCompressionOptions(compressionOptions);
+ }
+ return spimDataMinimal;
+ }
}
--
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