diff --git a/.gitignore b/.gitignore
index 14803ad980956b04712d46c855bc6e3c3454ee29..8098709b36f8f384501bb23e156756dfaf4d9eab 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,7 +8,7 @@
.project
.settings
/target
-
+classes/
# IntelliJ
.idea/
*.iml
diff --git a/pom.xml b/pom.xml
index ce3fdd41dccd46e2b398c2e0220c433fe7883eac..3bcf22161bb8852cd056600496f0306a6ebff91e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -201,5 +201,11 @@
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
- </dependencies>
+ <dependency>
+ <groupId>org.azgra</groupId>
+ <artifactId>DataCompressor</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ <scope>compile</scope>
+ </dependency>
+ </dependencies>
</project>
diff --git a/src/main/java/bdv/BigDataViewer.java b/src/main/java/bdv/BigDataViewer.java
index 266aa8d8d2ec0f26c04c913fa7daba7e3f9a61c7..9f2390ba1f9e6d395970af9e094bbf07c15180f2 100644
--- a/src/main/java/bdv/BigDataViewer.java
+++ b/src/main/java/bdv/BigDataViewer.java
@@ -43,6 +43,7 @@ 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;
@@ -96,628 +97,589 @@ import mpicbg.spim.data.generic.sequence.BasicViewSetup;
import mpicbg.spim.data.sequence.Angle;
import mpicbg.spim.data.sequence.Channel;
-public class BigDataViewer
-{
- protected final ViewerFrame viewerFrame;
+public class BigDataViewer {
+ protected final ViewerFrame viewerFrame;
- protected final ViewerPanel viewer;
+ protected final ViewerPanel viewer;
- protected final SetupAssignments setupAssignments;
-
- protected final ManualTransformation manualTransformation;
-
- protected final Bookmarks bookmarks;
-
- protected final BrightnessDialog brightnessDialog;
-
- protected final CropDialog cropDialog;
-
- protected final RecordMovieDialog movieDialog;
-
- protected final RecordMaxProjectionDialog movieMaxProjectDialog;
-
- protected final VisibilityAndGroupingDialog activeSourcesDialog;
-
- protected final HelpDialog helpDialog;
-
- protected final ManualTransformationEditor manualTransformationEditor;
-
- protected final BookmarksEditor bookmarkEditor;
-
- protected final JFileChooser fileChooser;
-
- protected File proposedSettingsFile;
-
- public void toggleManualTransformation()
- {
- manualTransformationEditor.toggle();
- }
-
- public void initSetBookmark()
- {
- bookmarkEditor.initSetBookmark();
- }
-
- public void initGoToBookmark()
- {
- bookmarkEditor.initGoToBookmark();
- }
-
- public void initGoToBookmarkRotation()
- {
- bookmarkEditor.initGoToBookmarkRotation();
- }
-
- private static String createSetupName( final BasicViewSetup setup )
- {
- if ( setup.hasName() )
- return setup.getName();
-
- String name = "";
-
- final Angle angle = setup.getAttribute( Angle.class );
- if ( angle != null )
- name += ( name.isEmpty() ? "" : " " ) + "a " + angle.getName();
-
- final Channel channel = setup.getAttribute( Channel.class );
- if ( channel != null )
- name += ( name.isEmpty() ? "" : " " ) + "c " + channel.getName();
-
- return name;
- }
-
- /**
- * Create standard converter from the given {@code type} to ARGB:
- * <ul>
- * <li>For {@code RealType}s a {@link RealARGBColorConverter} is
- * returned.</li>
- * <li>For {@code ARGBType}s a {@link ScaledARGBConverter.ARGB} is
- * returned.</li>
- * <li>For {@code VolatileARGBType}s a
- * {@link ScaledARGBConverter.VolatileARGB} is returned.</li>
- * </ul>
- */
- @SuppressWarnings( "unchecked" )
- public static < T extends NumericType< T > > Converter< T, ARGBType > createConverterToARGB( final T type )
- {
- if ( type instanceof RealType )
- {
- final RealType< ? > t = ( RealType< ? > ) type;
- final double typeMin = Math.max( 0, Math.min( t.getMinValue(), 65535 ) );
- final double typeMax = Math.max( 0, Math.min( t.getMaxValue(), 65535 ) );
- return ( Converter< T, ARGBType > ) RealARGBColorConverter.create( t, typeMin, typeMax );
- }
- else if ( type instanceof ARGBType )
- return ( Converter< T, ARGBType > ) new ScaledARGBConverter.ARGB( 0, 255 );
- else if ( type instanceof VolatileARGBType )
- return ( Converter< T, ARGBType > ) new ScaledARGBConverter.VolatileARGB( 0, 255 );
- else
- throw new IllegalArgumentException( "ImgLoader of type " + type.getClass() + " not supported." );
- }
-
- /**
- * Create a {@code ConverterSetup} for the given {@code SourceAndConverter}.
- * {@link SourceAndConverter#asVolatile() Nested volatile}
- * {@code SourceAndConverter} are added to the {@code ConverterSetup} if
- * present. If {@code SourceAndConverter} does not comprise a
- * {@code ColorConverter}, returns {@code null}.
- *
- * @param soc
- * {@code SourceAndConverter} for which to create a
- * {@code ConverterSetup}
- * @param setupId
- * setupId of the created {@code ConverterSetup}
- * @return a new {@code ConverterSetup} or {@code null}
- */
- public static ConverterSetup createConverterSetup( final SourceAndConverter< ? > soc, final int setupId )
- {
- final List< ColorConverter > converters = new ArrayList<>();
-
- final Converter< ?, ARGBType > c = soc.getConverter();
- if ( c instanceof ColorConverter )
- converters.add( ( ColorConverter ) c );
-
- final SourceAndConverter< ? extends Volatile< ? > > vsoc = soc.asVolatile();
- if ( vsoc != null )
- {
- final Converter< ?, ARGBType > vc = vsoc.getConverter();
- if ( vc instanceof ColorConverter )
- converters.add( ( ColorConverter ) vc );
- }
-
- if ( converters.isEmpty() )
- return null;
- else
- return new RealARGBColorConverterSetup( setupId, converters );
- }
-
- /**
- * Decorate source with an extra transformation, that can be edited manually
- * in this viewer. {@link SourceAndConverter#asVolatile() Nested volatile}
- * {@code SourceAndConverter} are wrapped as well, if present.
- */
- public static < T, V extends Volatile< T > > SourceAndConverter< T > wrapWithTransformedSource( final SourceAndConverter< T > soc )
- {
- if ( soc.asVolatile() == null )
- return new SourceAndConverter<>( new TransformedSource<>( soc.getSpimSource() ), soc.getConverter() );
-
- @SuppressWarnings( "unchecked" )
- final SourceAndConverter< V > vsoc = ( SourceAndConverter< V > ) soc.asVolatile();
- final TransformedSource< T > ts = new TransformedSource<>( soc.getSpimSource() );
- final TransformedSource< V > vts = new TransformedSource<>( vsoc.getSpimSource(), ts );
- return new SourceAndConverter<>( ts, soc.getConverter(), new SourceAndConverter<>( vts, vsoc.getConverter() ) );
- }
-
- private static < T extends NumericType< T >, V extends Volatile< T > & NumericType< V > > void initSetupNumericType(
- final AbstractSpimData< ? > spimData,
- final BasicViewSetup setup,
- final List< ConverterSetup > converterSetups,
- final List< SourceAndConverter< ? > > sources )
- {
- final int setupId = setup.getId();
- final ViewerImgLoader imgLoader = ( ViewerImgLoader ) spimData.getSequenceDescription().getImgLoader();
- @SuppressWarnings( "unchecked" )
- final ViewerSetupImgLoader< T, V > setupImgLoader = ( ViewerSetupImgLoader< T, V > ) imgLoader.getSetupImgLoader( setupId );
- final T type = setupImgLoader.getImageType();
- final V volatileType = setupImgLoader.getVolatileImageType();
-
- if ( ! ( type instanceof NumericType ) )
- throw new IllegalArgumentException( "ImgLoader of type " + type.getClass() + " not supported." );
-
- final String setupName = createSetupName( setup );
-
- SourceAndConverter< V > vsoc = null;
- if ( volatileType != null )
- {
- final VolatileSpimSource< V > vs = new VolatileSpimSource<>( spimData, setupId, setupName );
- vsoc = new SourceAndConverter<>( vs, createConverterToARGB( volatileType ) );
- }
-
- final SpimSource< T > s = new SpimSource<>( spimData, setupId, setupName );
- final SourceAndConverter< T > soc = new SourceAndConverter<>( s, createConverterToARGB( type ), vsoc );
- final SourceAndConverter< T > tsoc = wrapWithTransformedSource( soc );
- sources.add( tsoc );
-
- final ConverterSetup converterSetup = createConverterSetup( tsoc, setupId );
- if ( converterSetup != null )
- converterSetups.add( converterSetup );
- }
-
- public static void initSetups(
- final AbstractSpimData< ? > spimData,
- final List< ConverterSetup > converterSetups,
- final List< SourceAndConverter< ? > > sources )
- {
- for ( final BasicViewSetup setup : spimData.getSequenceDescription().getViewSetupsOrdered() )
- initSetupNumericType( spimData, setup, converterSetups, sources );
- }
-
- /**
- *
- * @param converterSetups
- * list of {@link ConverterSetup} that control min/max and color
- * of sources.
- * @param sources
- * list of pairs of source of some type and converter from that
- * type to ARGB.
- * @param spimData
- * may be null. The {@link AbstractSpimData} of the dataset (if
- * there is one). If it exists, it is used to set up a "Crop"
- * dialog.
- * @param numTimepoints
- * the number of timepoints in the dataset.
- * @param cache
- * handle to cache. This is used to control io timing.
- * @param windowTitle
- * title of the viewer window.
- * @param progressWriter
- * a {@link ProgressWriter} to which BDV may report progress
- * (currently only used in the "Record Movie" dialog).
- * @param options
- * optional parameters.
- */
- public BigDataViewer(
- final ArrayList< ConverterSetup > converterSetups,
- final ArrayList< SourceAndConverter< ? > > sources,
- final AbstractSpimData< ? > spimData,
- final int numTimepoints,
- final CacheControl cache,
- final String windowTitle,
- final ProgressWriter progressWriter,
- final ViewerOptions options )
- {
- final InputTriggerConfig inputTriggerConfig = getInputTriggerConfig( options );
- if ( options.values.getTransformEventHandlerFactory() instanceof BehaviourTransformEventHandlerFactory )
- ( ( BehaviourTransformEventHandlerFactory< ? > ) options.values.getTransformEventHandlerFactory() ).setConfig( inputTriggerConfig );
-
- viewerFrame = new ViewerFrame( sources, numTimepoints, cache, options );
- if ( windowTitle != null )
- viewerFrame.setTitle( windowTitle );
- viewer = viewerFrame.getViewerPanel();
-
- for ( final ConverterSetup cs : converterSetups )
- cs.setViewer( viewer );
-
- manualTransformation = new ManualTransformation( viewer );
- manualTransformationEditor = new ManualTransformationEditor( viewer, viewerFrame.getKeybindings() );
-
- bookmarks = new Bookmarks();
- bookmarkEditor = new BookmarksEditor( viewer, viewerFrame.getKeybindings(), bookmarks );
-
- setupAssignments = new SetupAssignments( converterSetups, 0, 65535 );
- if ( setupAssignments.getMinMaxGroups().size() > 0 )
- {
- final MinMaxGroup group = setupAssignments.getMinMaxGroups().get( 0 );
- for ( final ConverterSetup setup : setupAssignments.getConverterSetups() )
- setupAssignments.moveSetupToGroup( setup, group );
- }
-
- brightnessDialog = new BrightnessDialog( viewerFrame, setupAssignments );
-
- if (spimData != null )
- viewer.getSourceInfoOverlayRenderer().setTimePointsOrdered( spimData.getSequenceDescription().getTimePoints().getTimePointsOrdered() );
-
- cropDialog = ( spimData == null ) ? null : new CropDialog( viewerFrame, viewer, spimData.getSequenceDescription() );
-
- movieDialog = new RecordMovieDialog( viewerFrame, viewer, progressWriter );
- // this is just to get updates of window size:
- viewer.getDisplay().addOverlayRenderer( movieDialog );
-
- movieMaxProjectDialog = new RecordMaxProjectionDialog( viewerFrame, viewer, progressWriter );
- // this is just to get updates of window size:
- viewer.getDisplay().addOverlayRenderer( movieMaxProjectDialog );
-
- activeSourcesDialog = new VisibilityAndGroupingDialog( viewerFrame, viewer.getVisibilityAndGrouping() );
-
- helpDialog = new HelpDialog( viewerFrame );
-
- fileChooser = new JFileChooser();
- fileChooser.setFileFilter( new FileFilter()
- {
- @Override
- public String getDescription()
- {
- return "xml files";
- }
-
- @Override
- public boolean accept( final File f )
- {
- if ( f.isDirectory() )
- return true;
- if ( f.isFile() )
- {
- final String s = f.getName();
- final int i = s.lastIndexOf( '.' );
- if ( i > 0 && i < s.length() - 1 )
- {
- final String ext = s.substring( i + 1 ).toLowerCase();
- return ext.equals( "xml" );
- }
- }
- return false;
- }
- } );
-
- NavigationActions.installActionBindings( viewerFrame.getKeybindings(), viewer, inputTriggerConfig );
- BigDataViewerActions.installActionBindings( viewerFrame.getKeybindings(), this, inputTriggerConfig );
-
- final JMenuBar menubar = new JMenuBar();
- JMenu menu = new JMenu( "File" );
- menubar.add( menu );
-
- final ActionMap actionMap = viewerFrame.getKeybindings().getConcatenatedActionMap();
- final JMenuItem miLoadSettings = new JMenuItem( actionMap.get( BigDataViewerActions.LOAD_SETTINGS ) );
- miLoadSettings.setText( "Load settings" );
- menu.add( miLoadSettings );
-
- final JMenuItem miSaveSettings = new JMenuItem( actionMap.get( BigDataViewerActions.SAVE_SETTINGS ) );
- miSaveSettings.setText( "Save settings" );
- menu.add( miSaveSettings );
-
- menu = new JMenu( "Settings" );
- menubar.add( menu );
-
- final JMenuItem miBrightness = new JMenuItem( actionMap.get( BigDataViewerActions.BRIGHTNESS_SETTINGS ) );
- miBrightness.setText( "Brightness & Color" );
- menu.add( miBrightness );
-
- final JMenuItem miVisibility = new JMenuItem( actionMap.get( BigDataViewerActions.VISIBILITY_AND_GROUPING ) );
- miVisibility.setText( "Visibility & Grouping" );
- menu.add( miVisibility );
-
- menu = new JMenu( "Tools" );
- menubar.add( menu );
-
- if ( cropDialog != null )
- {
- final JMenuItem miCrop = new JMenuItem( actionMap.get( BigDataViewerActions.CROP ) );
- miCrop.setText( "Crop" );
- menu.add( miCrop );
- }
-
- final JMenuItem miMovie = new JMenuItem( actionMap.get( BigDataViewerActions.RECORD_MOVIE ) );
- miMovie.setText( "Record Movie" );
- menu.add( miMovie );
-
- final JMenuItem miMaxProjectMovie = new JMenuItem( actionMap.get( BigDataViewerActions.RECORD_MAX_PROJECTION_MOVIE ) );
- miMaxProjectMovie.setText( "Record Max-Projection Movie" );
- menu.add( miMaxProjectMovie );
-
- final JMenuItem miManualTransform = new JMenuItem( actionMap.get( BigDataViewerActions.MANUAL_TRANSFORM ) );
- miManualTransform.setText( "Manual Transform" );
- menu.add( miManualTransform );
-
- menu = new JMenu( "Help" );
- menubar.add( menu );
-
- final JMenuItem miHelp = new JMenuItem( actionMap.get( BigDataViewerActions.SHOW_HELP ) );
- miHelp.setText( "Show Help" );
- menu.add( miHelp );
-
- viewerFrame.setJMenuBar( menubar );
- }
-
- public static BigDataViewer open( final AbstractSpimData< ? > spimData, final String windowTitle, final ProgressWriter progressWriter, final ViewerOptions options )
- {
- if ( WrapBasicImgLoader.wrapImgLoaderIfNecessary( spimData ) )
- {
- System.err.println( "WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider resaving as HDF5 for better performance." );
- }
-
- final ArrayList< ConverterSetup > converterSetups = new ArrayList<>();
- final ArrayList< SourceAndConverter< ? > > sources = new ArrayList<>();
- initSetups( spimData, converterSetups, sources );
-
- final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription();
- final int numTimepoints = seq.getTimePoints().size();
- final CacheControl cache = ( ( ViewerImgLoader ) seq.getImgLoader() ).getCacheControl();
-
- final BigDataViewer bdv = new BigDataViewer( converterSetups, sources, spimData, numTimepoints, cache, windowTitle, progressWriter, options );
-
- WrapBasicImgLoader.removeWrapperIfPresent( spimData );
-
- bdv.viewerFrame.setVisible( true );
- InitializeViewerState.initTransform( bdv.viewer );
- return bdv;
- }
-
- public static BigDataViewer open( final String xmlFilename, final String windowTitle, final ProgressWriter progressWriter, final ViewerOptions options ) throws SpimDataException
- {
- final SpimDataMinimal spimData = new XmlIoSpimDataMinimal().load( xmlFilename );
- final BigDataViewer bdv = open( spimData, windowTitle, progressWriter, options );
- if ( !bdv.tryLoadSettings( xmlFilename ) )
- InitializeViewerState.initBrightness( 0.001, 0.999, bdv.viewer, bdv.setupAssignments );
- return bdv;
- }
-
- public static BigDataViewer open(
- final ArrayList< ConverterSetup > converterSetups,
- final ArrayList< SourceAndConverter< ? > > sources,
- final int numTimepoints,
- final CacheControl cache,
- final String windowTitle,
- final ProgressWriter progressWriter,
- final ViewerOptions options )
- {
- final BigDataViewer bdv = new BigDataViewer( converterSetups, sources, null, numTimepoints, cache, windowTitle, progressWriter, options );
- bdv.viewerFrame.setVisible( true );
- InitializeViewerState.initTransform( bdv.viewer );
- return bdv;
- }
-
- public ViewerPanel getViewer()
- {
- return viewer;
- }
-
- public ViewerFrame getViewerFrame()
- {
- return viewerFrame;
- }
-
- public SetupAssignments getSetupAssignments()
- {
- return setupAssignments;
- }
-
- public ManualTransformationEditor getManualTransformEditor()
- {
- return manualTransformationEditor;
- }
-
- public boolean tryLoadSettings( final String xmlFilename )
- {
- proposedSettingsFile = null;
- if( xmlFilename.startsWith( "http://" ) )
- {
- // load settings.xml from the BigDataServer
- final String settings = xmlFilename + "settings";
- {
- try
- {
- loadSettings( settings );
- return true;
- }
- catch ( final FileNotFoundException e )
- {}
- catch ( final Exception e )
- {
- e.printStackTrace();
- }
- }
- }
- else if ( xmlFilename.endsWith( ".xml" ) )
- {
- final String settings = xmlFilename.substring( 0, xmlFilename.length() - ".xml".length() ) + ".settings" + ".xml";
- proposedSettingsFile = new File( settings );
- if ( proposedSettingsFile.isFile() )
- {
- try
- {
- loadSettings( settings );
- return true;
- }
- catch ( final Exception e )
- {
- e.printStackTrace();
- }
- }
- }
- return false;
- }
-
- public void saveSettings()
- {
- fileChooser.setSelectedFile( proposedSettingsFile );
- final int returnVal = fileChooser.showSaveDialog( null );
- if ( returnVal == JFileChooser.APPROVE_OPTION )
- {
- proposedSettingsFile = fileChooser.getSelectedFile();
- try
- {
- saveSettings( proposedSettingsFile.getCanonicalPath() );
- }
- catch ( final IOException e )
- {
- e.printStackTrace();
- }
- }
- }
-
- public void saveSettings( final String xmlFilename ) throws IOException
- {
- final Element root = new Element( "Settings" );
- root.addContent( viewer.stateToXml() );
- root.addContent( setupAssignments.toXml() );
- root.addContent( manualTransformation.toXml() );
- root.addContent( bookmarks.toXml() );
- final Document doc = new Document( root );
- final XMLOutputter xout = new XMLOutputter( Format.getPrettyFormat() );
- xout.output( doc, new FileWriter( xmlFilename ) );
- }
-
- /**
- * If {@code options} doesn't define a {@link InputTriggerConfig}, try to
- * load it from files in this order:
- * <ol>
- * <li>"bdvkeyconfig.yaml" in the current directory.
- * <li>".bdv/bdvkeyconfig.yaml" in the user's home directory.
- * <li>legacy "bigdataviewer.keys.properties" in current directory (will be
- * also written to "bdvkeyconfig.yaml").
- * </ol>
- *
- * @param options
- * @return
- */
- public static InputTriggerConfig getInputTriggerConfig( final ViewerOptions options )
- {
- InputTriggerConfig conf = options.values.getInputTriggerConfig();
-
- // try "bdvkeyconfig.yaml" in current directory
- if ( conf == null && new File( "bdvkeyconfig.yaml" ).isFile() )
- {
- try
- {
- conf = new InputTriggerConfig( YamlConfigIO.read( "bdvkeyconfig.yaml" ) );
- }
- catch ( final IOException e )
- {}
- }
-
- // try "~/.bdv/bdvkeyconfig.yaml"
- if ( conf == null )
- {
- final String fn = System.getProperty( "user.home" ) + "/.bdv/bdvkeyconfig.yaml";
- if ( new File( fn ).isFile() )
- {
- try
- {
- conf = new InputTriggerConfig( YamlConfigIO.read( fn ) );
- }
- catch ( final IOException e )
- {}
- }
- }
-
- if ( conf == null )
- {
- conf = new InputTriggerConfig();
- }
-
- return conf;
- }
-
- public void loadSettings()
- {
- fileChooser.setSelectedFile( proposedSettingsFile );
- final int returnVal = fileChooser.showOpenDialog( null );
- if ( returnVal == JFileChooser.APPROVE_OPTION )
- {
- proposedSettingsFile = fileChooser.getSelectedFile();
- try
- {
- loadSettings( proposedSettingsFile.getCanonicalPath() );
- }
- catch ( final Exception e )
- {
- e.printStackTrace();
- }
- }
- }
-
- public void loadSettings( final String xmlFilename ) throws IOException, JDOMException
- {
- final SAXBuilder sax = new SAXBuilder();
- final Document doc = sax.build( xmlFilename );
- final Element root = doc.getRootElement();
- viewer.stateFromXml( root );
- setupAssignments.restoreFromXml( root );
- manualTransformation.restoreFromXml( root );
- bookmarks.restoreFromXml( root );
- activeSourcesDialog.update();
- viewer.requestRepaint();
- }
-
- 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";
- try
- {
- System.setProperty( "apple.laf.useScreenMenuBar", "true" );
-
- final BigDataViewer bdv = open( fn, new File( fn ).getName(), new ProgressWriterConsole(), ViewerOptions.options() );
-
-// DumpInputConfig.writeToYaml( System.getProperty( "user.home" ) + "/.bdv/bdvkeyconfig.yaml", bdv.getViewerFrame() );
- }
- catch ( final Exception e )
- {
- e.printStackTrace();
- }
- }
+ protected final SetupAssignments setupAssignments;
+
+ protected final ManualTransformation manualTransformation;
+
+ protected final Bookmarks bookmarks;
+
+ protected final BrightnessDialog brightnessDialog;
+
+ protected final CropDialog cropDialog;
+
+ protected final RecordMovieDialog movieDialog;
+
+ protected final RecordMaxProjectionDialog movieMaxProjectDialog;
+
+ protected final VisibilityAndGroupingDialog activeSourcesDialog;
+
+ protected final HelpDialog helpDialog;
+
+ protected final ManualTransformationEditor manualTransformationEditor;
+
+ protected final BookmarksEditor bookmarkEditor;
+
+ protected final JFileChooser fileChooser;
+
+ protected File proposedSettingsFile;
+
+ public void toggleManualTransformation() {
+ manualTransformationEditor.toggle();
+ }
+
+ public void initSetBookmark() {
+ bookmarkEditor.initSetBookmark();
+ }
+
+ public void initGoToBookmark() {
+ bookmarkEditor.initGoToBookmark();
+ }
+
+ public void initGoToBookmarkRotation() {
+ bookmarkEditor.initGoToBookmarkRotation();
+ }
+
+ private static String createSetupName(final BasicViewSetup setup) {
+ if (setup.hasName())
+ return setup.getName();
+
+ String name = "";
+
+ final Angle angle = setup.getAttribute(Angle.class);
+ if (angle != null)
+ name += (name.isEmpty() ? "" : " ") + "a " + angle.getName();
+
+ final Channel channel = setup.getAttribute(Channel.class);
+ if (channel != null)
+ name += (name.isEmpty() ? "" : " ") + "c " + channel.getName();
+
+ return name;
+ }
+
+ /**
+ * Create standard converter from the given {@code type} to ARGB:
+ * <ul>
+ * <li>For {@code RealType}s a {@link RealARGBColorConverter} is
+ * returned.</li>
+ * <li>For {@code ARGBType}s a {@link ScaledARGBConverter.ARGB} is
+ * returned.</li>
+ * <li>For {@code VolatileARGBType}s a
+ * {@link ScaledARGBConverter.VolatileARGB} is returned.</li>
+ * </ul>
+ */
+ @SuppressWarnings("unchecked")
+ public static <T extends NumericType<T>> Converter<T, ARGBType> createConverterToARGB(final T type) {
+ if (type instanceof RealType) {
+ final RealType<?> t = (RealType<?>) type;
+ final double typeMin = Math.max(0, Math.min(t.getMinValue(), 65535));
+ final double typeMax = Math.max(0, Math.min(t.getMaxValue(), 65535));
+ return (Converter<T, ARGBType>) RealARGBColorConverter.create(t, typeMin, typeMax);
+ } else if (type instanceof ARGBType)
+ return (Converter<T, ARGBType>) new ScaledARGBConverter.ARGB(0, 255);
+ else if (type instanceof VolatileARGBType)
+ return (Converter<T, ARGBType>) new ScaledARGBConverter.VolatileARGB(0, 255);
+ else
+ throw new IllegalArgumentException("ImgLoader of type " + type.getClass() + " not supported.");
+ }
+
+ /**
+ * Create a {@code ConverterSetup} for the given {@code SourceAndConverter}.
+ * {@link SourceAndConverter#asVolatile() Nested volatile}
+ * {@code SourceAndConverter} are added to the {@code ConverterSetup} if
+ * present. If {@code SourceAndConverter} does not comprise a
+ * {@code ColorConverter}, returns {@code null}.
+ *
+ * @param soc {@code SourceAndConverter} for which to create a
+ * {@code ConverterSetup}
+ * @param setupId setupId of the created {@code ConverterSetup}
+ * @return a new {@code ConverterSetup} or {@code null}
+ */
+ public static ConverterSetup createConverterSetup(final SourceAndConverter<?> soc, final int setupId) {
+ final List<ColorConverter> converters = new ArrayList<>();
+
+ final Converter<?, ARGBType> c = soc.getConverter();
+ if (c instanceof ColorConverter)
+ converters.add((ColorConverter) c);
+
+ final SourceAndConverter<? extends Volatile<?>> vsoc = soc.asVolatile();
+ if (vsoc != null) {
+ final Converter<?, ARGBType> vc = vsoc.getConverter();
+ if (vc instanceof ColorConverter)
+ converters.add((ColorConverter) vc);
+ }
+
+ if (converters.isEmpty())
+ return null;
+ else
+ return new RealARGBColorConverterSetup(setupId, converters);
+ }
+
+ /**
+ * Decorate source with an extra transformation, that can be edited manually
+ * in this viewer. {@link SourceAndConverter#asVolatile() Nested volatile}
+ * {@code SourceAndConverter} are wrapped as well, if present.
+ */
+ public static <T, V extends Volatile<T>> SourceAndConverter<T> wrapWithTransformedSource(final SourceAndConverter<T> soc) {
+ if (soc.asVolatile() == null)
+ return new SourceAndConverter<>(new TransformedSource<>(soc.getSpimSource()), soc.getConverter());
+
+ @SuppressWarnings("unchecked") final SourceAndConverter<V> vsoc = (SourceAndConverter<V>) soc.asVolatile();
+ final TransformedSource<T> ts = new TransformedSource<>(soc.getSpimSource());
+ final TransformedSource<V> vts = new TransformedSource<>(vsoc.getSpimSource(), ts);
+ return new SourceAndConverter<>(ts, soc.getConverter(), new SourceAndConverter<>(vts, vsoc.getConverter()));
+ }
+
+ private static <T extends NumericType<T>, V extends Volatile<T> & NumericType<V>> void initSetupNumericType(
+ final AbstractSpimData<?> spimData,
+ final BasicViewSetup setup,
+ final List<ConverterSetup> converterSetups,
+ final List<SourceAndConverter<?>> sources) {
+ final int setupId = setup.getId();
+ final ViewerImgLoader imgLoader = (ViewerImgLoader) spimData.getSequenceDescription().getImgLoader();
+ @SuppressWarnings("unchecked") final ViewerSetupImgLoader<T, V> setupImgLoader =
+ (ViewerSetupImgLoader<T, V>) imgLoader.getSetupImgLoader(
+ setupId);
+ final T type = setupImgLoader.getImageType();
+ final V volatileType = setupImgLoader.getVolatileImageType();
+
+ if (!(type instanceof NumericType))
+ throw new IllegalArgumentException("ImgLoader of type " + type.getClass() + " not supported.");
+
+ final String setupName = createSetupName(setup);
+
+ SourceAndConverter<V> vsoc = null;
+ if (volatileType != null) {
+ final VolatileSpimSource<V> vs = new VolatileSpimSource<>(spimData, setupId, setupName);
+ vsoc = new SourceAndConverter<>(vs, createConverterToARGB(volatileType));
+ }
+
+ final SpimSource<T> s = new SpimSource<>(spimData, setupId, setupName);
+ final SourceAndConverter<T> soc = new SourceAndConverter<>(s, createConverterToARGB(type), vsoc);
+ final SourceAndConverter<T> tsoc = wrapWithTransformedSource(soc);
+ sources.add(tsoc);
+
+ final ConverterSetup converterSetup = createConverterSetup(tsoc, setupId);
+ if (converterSetup != null)
+ converterSetups.add(converterSetup);
+ }
+
+ public static void initSetups(
+ final AbstractSpimData<?> spimData,
+ final List<ConverterSetup> converterSetups,
+ final List<SourceAndConverter<?>> sources) {
+ for (final BasicViewSetup setup : spimData.getSequenceDescription().getViewSetupsOrdered())
+ initSetupNumericType(spimData, setup, converterSetups, sources);
+ }
+
+ /**
+ * @param converterSetups list of {@link ConverterSetup} that control min/max and color
+ * of sources.
+ * @param sources list of pairs of source of some type and converter from that
+ * type to ARGB.
+ * @param spimData may be null. The {@link AbstractSpimData} of the dataset (if
+ * there is one). If it exists, it is used to set up a "Crop"
+ * dialog.
+ * @param numTimepoints the number of timepoints in the dataset.
+ * @param cache handle to cache. This is used to control io timing.
+ * @param windowTitle title of the viewer window.
+ * @param progressWriter a {@link ProgressWriter} to which BDV may report progress
+ * (currently only used in the "Record Movie" dialog).
+ * @param options optional parameters.
+ */
+ public BigDataViewer(
+ final ArrayList<ConverterSetup> converterSetups,
+ final ArrayList<SourceAndConverter<?>> sources,
+ final AbstractSpimData<?> spimData,
+ final int numTimepoints,
+ final CacheControl cache,
+ final String windowTitle,
+ final ProgressWriter progressWriter,
+ final ViewerOptions options) {
+ final InputTriggerConfig inputTriggerConfig = getInputTriggerConfig(options);
+ if (options.values.getTransformEventHandlerFactory() instanceof BehaviourTransformEventHandlerFactory)
+ ((BehaviourTransformEventHandlerFactory<?>) options.values.getTransformEventHandlerFactory()).setConfig(
+ inputTriggerConfig);
+
+ viewerFrame = new ViewerFrame(sources, numTimepoints, cache, options);
+ if (windowTitle != null)
+ viewerFrame.setTitle(windowTitle);
+ viewer = viewerFrame.getViewerPanel();
+
+ for (final ConverterSetup cs : converterSetups)
+ cs.setViewer(viewer);
+
+ manualTransformation = new ManualTransformation(viewer);
+ manualTransformationEditor = new ManualTransformationEditor(viewer, viewerFrame.getKeybindings());
+
+ bookmarks = new Bookmarks();
+ bookmarkEditor = new BookmarksEditor(viewer, viewerFrame.getKeybindings(), bookmarks);
+
+ setupAssignments = new SetupAssignments(converterSetups, 0, 65535);
+ if (setupAssignments.getMinMaxGroups().size() > 0) {
+ final MinMaxGroup group = setupAssignments.getMinMaxGroups().get(0);
+ for (final ConverterSetup setup : setupAssignments.getConverterSetups())
+ setupAssignments.moveSetupToGroup(setup, group);
+ }
+
+ brightnessDialog = new BrightnessDialog(viewerFrame, setupAssignments);
+
+ if (spimData != null)
+ viewer.getSourceInfoOverlayRenderer().setTimePointsOrdered(spimData.getSequenceDescription().getTimePoints().getTimePointsOrdered());
+
+ cropDialog = (spimData == null) ? null : new CropDialog(viewerFrame, viewer, spimData.getSequenceDescription());
+
+ movieDialog = new RecordMovieDialog(viewerFrame, viewer, progressWriter);
+ // this is just to get updates of window size:
+ viewer.getDisplay().addOverlayRenderer(movieDialog);
+
+ movieMaxProjectDialog = new RecordMaxProjectionDialog(viewerFrame, viewer, progressWriter);
+ // this is just to get updates of window size:
+ viewer.getDisplay().addOverlayRenderer(movieMaxProjectDialog);
+
+ activeSourcesDialog = new VisibilityAndGroupingDialog(viewerFrame, viewer.getVisibilityAndGrouping());
+
+ helpDialog = new HelpDialog(viewerFrame);
+
+ fileChooser = new JFileChooser();
+ fileChooser.setFileFilter(new FileFilter() {
+ @Override
+ public String getDescription() {
+ return "xml files";
+ }
+
+ @Override
+ public boolean accept(final File f) {
+ if (f.isDirectory())
+ return true;
+ if (f.isFile()) {
+ final String s = f.getName();
+ final int i = s.lastIndexOf('.');
+ if (i > 0 && i < s.length() - 1) {
+ final String ext = s.substring(i + 1).toLowerCase();
+ return ext.equals("xml");
+ }
+ }
+ return false;
+ }
+ });
+
+ NavigationActions.installActionBindings(viewerFrame.getKeybindings(), viewer, inputTriggerConfig);
+ BigDataViewerActions.installActionBindings(viewerFrame.getKeybindings(), this, inputTriggerConfig);
+
+ final JMenuBar menubar = new JMenuBar();
+ JMenu menu = new JMenu("File");
+ menubar.add(menu);
+
+ final ActionMap actionMap = viewerFrame.getKeybindings().getConcatenatedActionMap();
+ final JMenuItem miLoadSettings = new JMenuItem(actionMap.get(BigDataViewerActions.LOAD_SETTINGS));
+ miLoadSettings.setText("Load settings");
+ menu.add(miLoadSettings);
+
+ final JMenuItem miSaveSettings = new JMenuItem(actionMap.get(BigDataViewerActions.SAVE_SETTINGS));
+ miSaveSettings.setText("Save settings");
+ menu.add(miSaveSettings);
+
+ menu = new JMenu("Settings");
+ menubar.add(menu);
+
+ final JMenuItem miBrightness = new JMenuItem(actionMap.get(BigDataViewerActions.BRIGHTNESS_SETTINGS));
+ miBrightness.setText("Brightness & Color");
+ menu.add(miBrightness);
+
+ final JMenuItem miVisibility = new JMenuItem(actionMap.get(BigDataViewerActions.VISIBILITY_AND_GROUPING));
+ miVisibility.setText("Visibility & Grouping");
+ menu.add(miVisibility);
+
+ menu = new JMenu("Tools");
+ menubar.add(menu);
+
+ if (cropDialog != null) {
+ final JMenuItem miCrop = new JMenuItem(actionMap.get(BigDataViewerActions.CROP));
+ miCrop.setText("Crop");
+ menu.add(miCrop);
+ }
+
+ final JMenuItem miMovie = new JMenuItem(actionMap.get(BigDataViewerActions.RECORD_MOVIE));
+ miMovie.setText("Record Movie");
+ menu.add(miMovie);
+
+ final JMenuItem miMaxProjectMovie =
+ new JMenuItem(actionMap.get(BigDataViewerActions.RECORD_MAX_PROJECTION_MOVIE));
+ miMaxProjectMovie.setText("Record Max-Projection Movie");
+ menu.add(miMaxProjectMovie);
+
+ final JMenuItem miManualTransform = new JMenuItem(actionMap.get(BigDataViewerActions.MANUAL_TRANSFORM));
+ miManualTransform.setText("Manual Transform");
+ menu.add(miManualTransform);
+
+ menu = new JMenu("Help");
+ menubar.add(menu);
+
+ final JMenuItem miHelp = new JMenuItem(actionMap.get(BigDataViewerActions.SHOW_HELP));
+ miHelp.setText("Show Help");
+ menu.add(miHelp);
+
+ viewerFrame.setJMenuBar(menubar);
+ }
+
+ public static BigDataViewer open(final AbstractSpimData<?> spimData,
+ final String windowTitle,
+ final ProgressWriter progressWriter,
+ final ViewerOptions options) {
+ if (WrapBasicImgLoader.wrapImgLoaderIfNecessary(spimData)) {
+ System.err.println(
+ "WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider " +
+ "resaving as HDF5 for better performance.");
+ }
+
+ final ArrayList<ConverterSetup> converterSetups = new ArrayList<>();
+ final ArrayList<SourceAndConverter<?>> sources = new ArrayList<>();
+ initSetups(spimData, converterSetups, sources);
+
+ final AbstractSequenceDescription<?, ?, ?> seq = spimData.getSequenceDescription();
+ final int numTimepoints = seq.getTimePoints().size();
+ final CacheControl cache = ((ViewerImgLoader) seq.getImgLoader()).getCacheControl();
+
+ final BigDataViewer bdv = new BigDataViewer(converterSetups,
+ sources,
+ spimData,
+ numTimepoints,
+ cache,
+ windowTitle,
+ progressWriter,
+ options);
+
+ WrapBasicImgLoader.removeWrapperIfPresent(spimData);
+
+ bdv.viewerFrame.setVisible(true);
+ InitializeViewerState.initTransform(bdv.viewer);
+ return bdv;
+ }
+
+ public static BigDataViewer open(final String xmlFilename,
+ final String windowTitle,
+ final ProgressWriter progressWriter,
+ final ViewerOptions options,
+ final boolean allowCompression) throws SpimDataException {
+
+ final XmlIoSpimDataMinimal xmlIoSpimDataMinimal = new XmlIoSpimDataMinimal();
+ xmlIoSpimDataMinimal.setAllowCompression(allowCompression);
+ final SpimDataMinimal spimData = xmlIoSpimDataMinimal.load(xmlFilename);
+ final BigDataViewer bdv = open(spimData, windowTitle, progressWriter, options);
+ if (!bdv.tryLoadSettings(xmlFilename))
+ InitializeViewerState.initBrightness(0.001, 0.999, bdv.viewer, bdv.setupAssignments);
+ return bdv;
+ }
+
+ public static BigDataViewer open(
+ final ArrayList<ConverterSetup> converterSetups,
+ final ArrayList<SourceAndConverter<?>> sources,
+ final int numTimepoints,
+ final CacheControl cache,
+ final String windowTitle,
+ final ProgressWriter progressWriter,
+ final ViewerOptions options) {
+ final BigDataViewer bdv = new BigDataViewer(converterSetups,
+ sources,
+ null,
+ numTimepoints,
+ cache,
+ windowTitle,
+ progressWriter,
+ options);
+ bdv.viewerFrame.setVisible(true);
+ InitializeViewerState.initTransform(bdv.viewer);
+ return bdv;
+ }
+
+ public ViewerPanel getViewer() {
+ return viewer;
+ }
+
+ public ViewerFrame getViewerFrame() {
+ return viewerFrame;
+ }
+
+ public SetupAssignments getSetupAssignments() {
+ return setupAssignments;
+ }
+
+ public ManualTransformationEditor getManualTransformEditor() {
+ return manualTransformationEditor;
+ }
+
+ public boolean tryLoadSettings(final String xmlFilename) {
+ proposedSettingsFile = null;
+ if (xmlFilename.startsWith("http://")) {
+ // load settings.xml from the BigDataServer
+ final String settings = xmlFilename + "settings";
+ {
+ try {
+ loadSettings(settings);
+ return true;
+ } catch (final FileNotFoundException e) {
+ } catch (final Exception e) {
+ e.printStackTrace();
+ }
+ }
+ } else if (xmlFilename.endsWith(".xml")) {
+ final String settings = xmlFilename.substring(0,
+ xmlFilename.length() - ".xml".length()) + ".settings" +
+ ".xml";
+ proposedSettingsFile = new File(settings);
+ if (proposedSettingsFile.isFile()) {
+ try {
+ loadSettings(settings);
+ return true;
+ } catch (final Exception e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ return false;
+ }
+
+ public void saveSettings() {
+ fileChooser.setSelectedFile(proposedSettingsFile);
+ final int returnVal = fileChooser.showSaveDialog(null);
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ proposedSettingsFile = fileChooser.getSelectedFile();
+ try {
+ saveSettings(proposedSettingsFile.getCanonicalPath());
+ } catch (final IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ public void saveSettings(final String xmlFilename) throws IOException {
+ final Element root = new Element("Settings");
+ root.addContent(viewer.stateToXml());
+ root.addContent(setupAssignments.toXml());
+ root.addContent(manualTransformation.toXml());
+ root.addContent(bookmarks.toXml());
+ final Document doc = new Document(root);
+ final XMLOutputter xout = new XMLOutputter(Format.getPrettyFormat());
+ xout.output(doc, new FileWriter(xmlFilename));
+ }
+
+ /**
+ * If {@code options} doesn't define a {@link InputTriggerConfig}, try to
+ * load it from files in this order:
+ * <ol>
+ * <li>"bdvkeyconfig.yaml" in the current directory.
+ * <li>".bdv/bdvkeyconfig.yaml" in the user's home directory.
+ * <li>legacy "bigdataviewer.keys.properties" in current directory (will be
+ * also written to "bdvkeyconfig.yaml").
+ * </ol>
+ *
+ * @param options
+ * @return
+ */
+ public static InputTriggerConfig getInputTriggerConfig(final ViewerOptions options) {
+ InputTriggerConfig conf = options.values.getInputTriggerConfig();
+
+ // try "bdvkeyconfig.yaml" in current directory
+ if (conf == null && new File("bdvkeyconfig.yaml").isFile()) {
+ try {
+ conf = new InputTriggerConfig(YamlConfigIO.read("bdvkeyconfig.yaml"));
+ } catch (final IOException e) {
+ }
+ }
+
+ // try "~/.bdv/bdvkeyconfig.yaml"
+ if (conf == null) {
+ final String fn = System.getProperty("user.home") + "/.bdv/bdvkeyconfig.yaml";
+ if (new File(fn).isFile()) {
+ try {
+ conf = new InputTriggerConfig(YamlConfigIO.read(fn));
+ } catch (final IOException e) {
+ }
+ }
+ }
+
+ if (conf == null) {
+ conf = new InputTriggerConfig();
+ }
+
+ return conf;
+ }
+
+ public void loadSettings() {
+ fileChooser.setSelectedFile(proposedSettingsFile);
+ final int returnVal = fileChooser.showOpenDialog(null);
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ proposedSettingsFile = fileChooser.getSelectedFile();
+ try {
+ loadSettings(proposedSettingsFile.getCanonicalPath());
+ } catch (final Exception e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ public void loadSettings(final String xmlFilename) throws IOException, JDOMException {
+ final SAXBuilder sax = new SAXBuilder();
+ final Document doc = sax.build(xmlFilename);
+ final Element root = doc.getRootElement();
+ viewer.stateFromXml(root);
+ setupAssignments.restoreFromXml(root);
+ manualTransformation.restoreFromXml(root);
+ bookmarks.restoreFromXml(root);
+ activeSourcesDialog.update();
+ viewer.requestRepaint();
+ }
+
+ 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";
+ if (args.length < 1) {
+ System.err.println("Provide path.");
+ return;
+ }
+ final String fn = args[0];
+ final boolean allowCompression = (args.length > 1) && (args[1].equals("-qcmp"));
+ try {
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+
+ final BigDataViewer bdv = open(fn,
+ "Server test",
+ new ProgressWriterConsole(),
+ 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 b485a68a4bed4b180909602d39fa5fe7d82de5db..2d5247a2995966d20952922aeada3d75252c9188 100644
--- a/src/main/java/bdv/img/remote/RemoteImageLoader.java
+++ b/src/main/java/bdv/img/remote/RemoteImageLoader.java
@@ -7,13 +7,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
- *
+ *
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
- *
+ *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -29,13 +29,8 @@
*/
package bdv.img.remote;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.URL;
-import java.util.HashMap;
-
-import com.google.gson.GsonBuilder;
-
+import azgracompress.cache.ICacheFile;
+import azgracompress.cache.QuantizationCacheManager;
import bdv.AbstractViewerSetupImgLoader;
import bdv.ViewerImgLoader;
import bdv.img.cache.VolatileCachedCellImg;
@@ -44,6 +39,7 @@ import bdv.img.hdf5.DimsAndExistence;
import bdv.img.hdf5.MipmapInfo;
import bdv.img.hdf5.ViewLevelId;
import bdv.util.ConstantRandomAccessible;
+import com.google.gson.GsonBuilder;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
import net.imglib2.FinalInterval;
import net.imglib2.RandomAccessibleInterval;
@@ -57,211 +53,213 @@ import net.imglib2.type.volatiles.VolatileUnsignedShortType;
import net.imglib2.util.IntervalIndexer;
import net.imglib2.view.Views;
-public class RemoteImageLoader implements ViewerImgLoader
-{
- protected String baseUrl;
-
- protected RemoteImageLoaderMetaData metadata;
-
- protected HashMap< ViewLevelId, int[] > cellsDimensions;
-
- protected VolatileGlobalCellCache cache;
-
- protected RemoteVolatileShortArrayLoader shortLoader;
-
- /**
- * TODO
- */
- protected final HashMap< Integer, SetupImgLoader > setupImgLoaders;
-
- public RemoteImageLoader( final String baseUrl ) throws IOException
- {
- this( baseUrl, true );
- }
-
- public RemoteImageLoader( final String baseUrl, final boolean doOpen ) throws IOException
- {
- this.baseUrl = baseUrl;
- setupImgLoaders = new HashMap<>();
- if ( doOpen )
- open();
- }
-
- @Override
- public SetupImgLoader getSetupImgLoader( final int setupId )
- {
- tryopen();
- return setupImgLoaders.get( setupId );
- }
-
- private boolean isOpen = false;
-
- private void open() throws IOException
- {
- if ( ! isOpen )
- {
- synchronized ( this )
- {
- if ( isOpen )
- return;
- isOpen = true;
-
- final URL url = new URL( baseUrl + "?p=init" );
- final GsonBuilder gsonBuilder = new GsonBuilder();
- gsonBuilder.registerTypeAdapter( AffineTransform3D.class, new AffineTransform3DJsonSerializer() );
- metadata = gsonBuilder.create().fromJson(
- new InputStreamReader( url.openStream() ),
- RemoteImageLoaderMetaData.class );
- shortLoader = new RemoteVolatileShortArrayLoader( this );
- cache = new VolatileGlobalCellCache( metadata.maxNumLevels, 10 );
- cellsDimensions = metadata.createCellsDimensions();
- for ( final int setupId : metadata.perSetupMipmapInfo.keySet() )
- setupImgLoaders.put( setupId, new SetupImgLoader( setupId ) );
- }
- }
- }
-
- private void tryopen()
- {
- try
- {
- open();
- }
- catch ( final IOException e )
- {
- throw new RuntimeException( e );
- }
- }
-
- @Override
- public VolatileGlobalCellCache getCacheControl()
- {
- tryopen();
- return cache;
- }
-
- public MipmapInfo getMipmapInfo( final int setupId )
- {
- tryopen();
- return metadata.perSetupMipmapInfo.get( setupId );
- }
-
- /**
- * Checks whether the given image data is present on the server.
- *
- * @return true, if the given image data is present.
- */
- public boolean existsImageData( final ViewLevelId id )
- {
- return getDimsAndExistence( id ).exists();
- }
-
- /**
- * For images that are missing in the hdf5, a constant image is created. If
- * the dimension of the missing image is known (see
- * {@link #getDimsAndExistence(ViewLevelId)}) then use that. Otherwise
- * create a 1x1x1 image.
- */
- protected < T > RandomAccessibleInterval< T > getMissingDataImage( final ViewLevelId id, final T constant )
- {
- final long[] d = getDimsAndExistence( id ).getDimensions();
- return Views.interval( new ConstantRandomAccessible<>( constant, 3 ), new FinalInterval( d ) );
- }
-
- public DimsAndExistence getDimsAndExistence( final ViewLevelId id )
- {
- tryopen();
- return metadata.dimsAndExistence.get( id );
- }
-
- int getCellIndex( final int timepoint, final int setup, final int level, final long[] globalPosition )
- {
- final int[] cellDims = cellsDimensions.get( new ViewLevelId( timepoint, setup, level ) );
- final int[] cellSize = getMipmapInfo( setup ).getSubdivisions()[ level ];
- final int[] cellPos = new int[] {
- ( int ) globalPosition[ 0 ] / cellSize[ 0 ],
- ( int ) globalPosition[ 1 ] / cellSize[ 1 ],
- ( int ) globalPosition[ 2 ] / cellSize[ 2 ] };
- return IntervalIndexer.positionToIndex( cellPos, cellDims );
- }
-
- /**
- * Create a {@link VolatileCachedCellImg} backed by the cache. The
- * {@code type} should be either {@link UnsignedShortType} and
- * {@link VolatileUnsignedShortType}.
- */
- protected < T extends NativeType< T > > RandomAccessibleInterval< T > prepareCachedImage(
- final ViewLevelId id,
- final LoadingStrategy loadingStrategy,
- final T type )
- {
- tryopen();
- if ( cache == null )
- throw new RuntimeException( "no connection open" );
-
-// final ViewLevelId id = new ViewLevelId( timepointId, setupId, level );
- if ( ! existsImageData( id ) )
- {
- System.err.println( String.format(
- "image data for timepoint %d setup %d level %d could not be found.",
- id.getTimePointId(), id.getViewSetupId(), id.getLevel() ) );
- return getMissingDataImage( id, type );
- }
-
- final int timepointId = id.getTimePointId();
- final int setupId = id.getViewSetupId();
- final int level = id.getLevel();
- final MipmapInfo mipmapInfo = metadata.perSetupMipmapInfo.get( setupId );
-
- final long[] dimensions = metadata.dimsAndExistence.get( id ).getDimensions();
- final int[] cellDimensions = mipmapInfo.getSubdivisions()[ level ];
- final CellGrid grid = new CellGrid( dimensions, cellDimensions );
-
- final int priority = mipmapInfo.getMaxLevel() - level;
- final CacheHints cacheHints = new CacheHints( loadingStrategy, priority, false );
- return cache.createImg( grid, timepointId, setupId, level, cacheHints, shortLoader, type );
- }
-
- public class SetupImgLoader extends AbstractViewerSetupImgLoader< UnsignedShortType, VolatileUnsignedShortType >
- {
- private final int setupId;
-
- protected SetupImgLoader( final int setupId )
- {
- super( new UnsignedShortType(), new VolatileUnsignedShortType() );
- this.setupId = setupId;
- }
-
- @Override
- public RandomAccessibleInterval< UnsignedShortType > getImage( final int timepointId, final int level, final ImgLoaderHint... hints )
- {
- final ViewLevelId id = new ViewLevelId( timepointId, setupId, level );
- return prepareCachedImage( id, LoadingStrategy.BLOCKING, type );
- }
-
- @Override
- public RandomAccessibleInterval< VolatileUnsignedShortType > getVolatileImage( final int timepointId, final int level, final ImgLoaderHint... hints )
- {
- final ViewLevelId id = new ViewLevelId( timepointId, setupId, level );
- return prepareCachedImage( id, LoadingStrategy.BUDGETED, volatileType );
- }
-
- @Override
- public double[][] getMipmapResolutions()
- {
- return getMipmapInfo( setupId ).getResolutions();
- }
-
- @Override
- public AffineTransform3D[] getMipmapTransforms()
- {
- return getMipmapInfo( setupId ).getTransforms();
- }
-
- @Override
- public int numMipmapLevels()
- {
- return getMipmapInfo( setupId ).getNumLevels();
- }
- }
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.HashMap;
+
+public class RemoteImageLoader implements ViewerImgLoader {
+ protected String baseUrl;
+
+ protected RemoteImageLoaderMetaData metadata;
+
+ protected HashMap<ViewLevelId, int[]> cellsDimensions;
+
+ protected VolatileGlobalCellCache cache;
+
+ protected RemoteVolatileShortArrayLoader shortLoader;
+
+ private boolean allowCompression;
+ /**
+ * TODO
+ */
+ protected final HashMap<Integer, SetupImgLoader> setupImgLoaders;
+
+ public RemoteImageLoader(final String baseUrl) throws IOException {
+ this(baseUrl, true);
+ }
+
+ public RemoteImageLoader(final String baseUrl,
+ final boolean doOpen) throws IOException {
+ this.baseUrl = baseUrl;
+ setupImgLoaders = new HashMap<>();
+ if (doOpen)
+ open();
+ }
+
+ @Override
+ public SetupImgLoader getSetupImgLoader(final int setupId) {
+ tryopen();
+ return setupImgLoaders.get(setupId);
+ }
+
+ private boolean isOpen = false;
+
+ private void open() throws IOException {
+ if (!isOpen) {
+ synchronized (this) {
+ if (isOpen)
+ 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());
+ metadata = gsonBuilder.create().fromJson(
+ new InputStreamReader(url.openStream()),
+ RemoteImageLoaderMetaData.class);
+ shortLoader = new RemoteVolatileShortArrayLoader(this);
+ cache = new VolatileGlobalCellCache(metadata.maxNumLevels, 10);
+ cellsDimensions = metadata.createCellsDimensions();
+ for (final int setupId : metadata.perSetupMipmapInfo.keySet())
+ setupImgLoaders.put(setupId, new SetupImgLoader(setupId));
+ }
+ }
+ }
+
+ public boolean shouldAllowCompression() {
+ return allowCompression;
+ }
+
+ public void setAllowCompression(final boolean compressionEnabled) {
+ this.allowCompression = compressionEnabled;
+ }
+
+ private void receiveCompressionInfo() 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");
+ }
+
+
+ private void tryopen() {
+ try {
+ open();
+ } catch (final IOException e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+ @Override
+ public VolatileGlobalCellCache getCacheControl() {
+ tryopen();
+ return cache;
+ }
+
+ public MipmapInfo getMipmapInfo(final int setupId) {
+ tryopen();
+ return metadata.perSetupMipmapInfo.get(setupId);
+ }
+
+ /**
+ * Checks whether the given image data is present on the server.
+ *
+ * @return true, if the given image data is present.
+ */
+ public boolean existsImageData(final ViewLevelId id) {
+ return getDimsAndExistence(id).exists();
+ }
+
+ /**
+ * For images that are missing in the hdf5, a constant image is created. If
+ * the dimension of the missing image is known (see
+ * {@link #getDimsAndExistence(ViewLevelId)}) then use that. Otherwise
+ * create a 1x1x1 image.
+ */
+ protected <T> RandomAccessibleInterval<T> getMissingDataImage(final ViewLevelId id, final T constant) {
+ final long[] d = getDimsAndExistence(id).getDimensions();
+ return Views.interval(new ConstantRandomAccessible<>(constant, 3), new FinalInterval(d));
+ }
+
+ public DimsAndExistence getDimsAndExistence(final ViewLevelId id) {
+ tryopen();
+ return metadata.dimsAndExistence.get(id);
+ }
+
+ int getCellIndex(final int timepoint, final int setup, final int level, final long[] globalPosition) {
+ final int[] cellDims = cellsDimensions.get(new ViewLevelId(timepoint, setup, level));
+ final int[] cellSize = getMipmapInfo(setup).getSubdivisions()[level];
+ final int[] cellPos = new int[]{
+ (int) globalPosition[0] / cellSize[0],
+ (int) globalPosition[1] / cellSize[1],
+ (int) globalPosition[2] / cellSize[2]};
+ return IntervalIndexer.positionToIndex(cellPos, cellDims);
+ }
+
+ /**
+ * Create a {@link VolatileCachedCellImg} backed by the cache. The
+ * {@code type} should be either {@link UnsignedShortType} and
+ * {@link VolatileUnsignedShortType}.
+ */
+ protected <T extends NativeType<T>> RandomAccessibleInterval<T> prepareCachedImage(
+ final ViewLevelId id,
+ final LoadingStrategy loadingStrategy,
+ final T type) {
+ tryopen();
+ if (cache == null)
+ throw new RuntimeException("no connection open");
+
+ // final ViewLevelId id = new ViewLevelId( timepointId, setupId, level );
+ if (!existsImageData(id)) {
+ System.err.println(String.format(
+ "image data for timepoint %d setup %d level %d could not be found.",
+ id.getTimePointId(), id.getViewSetupId(), id.getLevel()));
+ return getMissingDataImage(id, type);
+ }
+
+ final int timepointId = id.getTimePointId();
+ final int setupId = id.getViewSetupId();
+ final int level = id.getLevel();
+ final MipmapInfo mipmapInfo = metadata.perSetupMipmapInfo.get(setupId);
+
+ final long[] dimensions = metadata.dimsAndExistence.get(id).getDimensions();
+ final int[] cellDimensions = mipmapInfo.getSubdivisions()[level];
+ final CellGrid grid = new CellGrid(dimensions, cellDimensions);
+
+ final int priority = mipmapInfo.getMaxLevel() - level;
+ final CacheHints cacheHints = new CacheHints(loadingStrategy, priority, false);
+ return cache.createImg(grid, timepointId, setupId, level, cacheHints, shortLoader, type);
+ }
+
+ public class SetupImgLoader extends AbstractViewerSetupImgLoader<UnsignedShortType, VolatileUnsignedShortType> {
+ private final int setupId;
+
+ protected SetupImgLoader(final int setupId) {
+ super(new UnsignedShortType(), new VolatileUnsignedShortType());
+ this.setupId = setupId;
+ }
+
+ @Override
+ public RandomAccessibleInterval<UnsignedShortType> getImage(final int timepointId, final int level, final ImgLoaderHint... hints) {
+ final ViewLevelId id = new ViewLevelId(timepointId, setupId, level);
+ return prepareCachedImage(id, LoadingStrategy.BLOCKING, type);
+ }
+
+ @Override
+ public RandomAccessibleInterval<VolatileUnsignedShortType> getVolatileImage(final int timepointId,
+ final int level,
+ final ImgLoaderHint... hints) {
+ final ViewLevelId id = new ViewLevelId(timepointId, setupId, level);
+ return prepareCachedImage(id, LoadingStrategy.BUDGETED, volatileType);
+ }
+
+ @Override
+ public double[][] getMipmapResolutions() {
+ return getMipmapInfo(setupId).getResolutions();
+ }
+
+ @Override
+ public AffineTransform3D[] getMipmapTransforms() {
+ return getMipmapInfo(setupId).getTransforms();
+ }
+
+ @Override
+ public int numMipmapLevels() {
+ return getMipmapInfo(setupId).getNumLevels();
+ }
+ }
}
diff --git a/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java b/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
index e6da148df6fa8b212dbffed20e0edc525fc26a43..ea2582129362c2f21434d88805fc8e97b6539167 100644
--- a/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
+++ b/src/main/java/bdv/img/remote/RemoteVolatileShortArrayLoader.java
@@ -7,13 +7,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
- *
+ *
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
- *
+ *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -53,24 +53,31 @@ public class RemoteVolatileShortArrayLoader implements CacheArrayLoader< Volatil
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 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();
- final byte[] buf = new byte[ data.length * 2 ];
- for ( int i = 0, l = s.read( buf, 0, buf.length ); l > 0; i += l, l = s.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();
+// System.out.println("Request URL=" + url);
+ final byte[] buf = new byte[data.length * 2];
+
+ // 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))
+ ;
+
+ 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 )
{
diff --git a/src/main/java/bdv/img/remote/XmlIoRemoteImageLoader.java b/src/main/java/bdv/img/remote/XmlIoRemoteImageLoader.java
index 3cf39d3afda23219f8d7bd47fbba570d83f3fe63..6b9b8a03b3687b30b4f0345429dfe455298770e0 100644
--- a/src/main/java/bdv/img/remote/XmlIoRemoteImageLoader.java
+++ b/src/main/java/bdv/img/remote/XmlIoRemoteImageLoader.java
@@ -7,13 +7,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
- *
+ *
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
- *
+ *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -41,31 +41,36 @@ import mpicbg.spim.data.generic.sequence.XmlIoBasicImgLoader;
import org.jdom2.Element;
-@ImgLoaderIo( format = "bdv.remote", type = RemoteImageLoader.class )
-public class XmlIoRemoteImageLoader implements XmlIoBasicImgLoader< RemoteImageLoader >
-{
+@ImgLoaderIo(format = "bdv.remote", type = RemoteImageLoader.class)
+public class XmlIoRemoteImageLoader implements XmlIoBasicImgLoader<RemoteImageLoader> {
- @Override
- public Element toXml( final RemoteImageLoader imgLoader, final File basePath )
- {
- final Element elem = new Element( "ImageLoader" );
- elem.setAttribute( IMGLOADER_FORMAT_ATTRIBUTE_NAME, "bdv.remote" );
- elem.addContent( XmlHelpers.textElement( "baseUrl", imgLoader.baseUrl ) );
- return elem;
- }
+ private boolean allowCompression = false;
- @Override
- public RemoteImageLoader fromXml( final Element elem, final File basePath, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
- {
- final String baseUrl = elem.getChildText( "baseUrl" );
- try
- {
- return new RemoteImageLoader( baseUrl );
- }
- catch ( final IOException e )
- {
- throw new RuntimeException( e );
- }
- }
+ @Override
+ public Element toXml(final RemoteImageLoader imgLoader, final File basePath) {
+ final Element elem = new Element("ImageLoader");
+ elem.setAttribute(IMGLOADER_FORMAT_ATTRIBUTE_NAME, "bdv.remote");
+ elem.addContent(XmlHelpers.textElement("baseUrl", imgLoader.baseUrl));
+ return elem;
+ }
+ @Override
+ public RemoteImageLoader fromXml(final Element elem,
+ final File basePath,
+ final AbstractSequenceDescription<?, ?, ?> sequenceDescription) {
+ final String baseUrl = elem.getChildText("baseUrl");
+ try {
+ return new RemoteImageLoader(baseUrl, allowCompression);
+ } catch (final IOException e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+ public boolean shouldAllowCompression() {
+ return allowCompression;
+ }
+
+ public void setAllowCompression(boolean allowCompression) {
+ this.allowCompression = allowCompression;
+ }
}
diff --git a/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java b/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java
index c36211563a3c68d88448d3bf1837fa0f2fb06c30..8737c5210f73452ebbc869418cc3cd878868edb0 100644
--- a/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java
+++ b/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java
@@ -7,13 +7,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
- *
+ *
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
- *
+ *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -33,6 +33,7 @@ import static mpicbg.spim.data.XmlKeys.SPIMDATA_TAG;
import java.io.File;
+import bdv.img.remote.RemoteImageLoader;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.SpimDataIOException;
import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
@@ -51,6 +52,8 @@ import bdv.spimdata.legacy.XmlIoSpimDataMinimalLegacy;
public class XmlIoSpimDataMinimal extends XmlIoAbstractSpimData< SequenceDescriptionMinimal, SpimDataMinimal >
{
+ private boolean allowCompression = false;
+
public XmlIoSpimDataMinimal()
{
super( SpimDataMinimal.class,
@@ -62,6 +65,10 @@ public class XmlIoSpimDataMinimal extends XmlIoAbstractSpimData< SequenceDescrip
new XmlIoViewRegistrations() );
}
+ public void setAllowCompression(final boolean allowCompression) {
+ this.allowCompression = allowCompression;
+ }
+
@Override
public SpimDataMinimal load( final String xmlFilename ) throws SpimDataException
{
@@ -83,6 +90,11 @@ public class XmlIoSpimDataMinimal extends XmlIoAbstractSpimData< SequenceDescrip
if ( root.getName() != SPIMDATA_TAG )
throw new RuntimeException( "expected <" + SPIMDATA_TAG + "> root element. wrong file?" );
- return fromXml( root, new File( xmlFilename ) );
+ 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;
}
}
diff --git a/src/main/java/bdv/spimdata/legacy/XmlIoSpimDataMinimalLegacy.java b/src/main/java/bdv/spimdata/legacy/XmlIoSpimDataMinimalLegacy.java
index 7f0ffefcea08cc066abd4488e48f7cb5a4641c88..a59c57b3d11f2b6225474398994294219a909c36 100644
--- a/src/main/java/bdv/spimdata/legacy/XmlIoSpimDataMinimalLegacy.java
+++ b/src/main/java/bdv/spimdata/legacy/XmlIoSpimDataMinimalLegacy.java
@@ -165,6 +165,7 @@ public class XmlIoSpimDataMinimalLegacy
{
final Element elem = sequenceDescriptionElem.getChild( "ImageLoader" );
final String classn = elem.getAttributeValue( "class" );
+
if ( classn.equals( "viewer.hdf5.Hdf5ImageLoader" ) || classn.equals( "bdv.img.hdf5.Hdf5ImageLoader" ) )
{
final String path = loadPath( elem, "hdf5", basePath ).toString();