diff --git a/src/main/java/azgracompress/ViewerCompressionOptions.java b/src/main/java/azgracompress/ViewerCompressionOptions.java
deleted file mode 100644
index c74cd3c181a707bb92f4ae775a54c1a846495163..0000000000000000000000000000000000000000
--- a/src/main/java/azgracompress/ViewerCompressionOptions.java
+++ /dev/null
@@ -1,22 +0,0 @@
-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 2756ebff4497eb0a76a7500a94c50651bc83e13d..df3644ad2d832778de00296be7ff84795f47f53f 100644
--- a/src/main/java/bdv/BigDataViewer.java
+++ b/src/main/java/bdv/BigDataViewer.java
@@ -28,7 +28,6 @@
*/
package bdv;
-import azgracompress.ViewerCompressionOptions;
import azgracompress.utilities.ColorConsole;
import bdv.cache.CacheControl;
import bdv.export.ProgressWriter;
@@ -93,619 +92,576 @@ public class BigDataViewer {
protected final RecordMovieDialog movieDialog;
- protected final BrightnessDialog brightnessDialog;
-
- 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 );
-
- viewerFrame = new ViewerFrame( sources, numTimepoints, cache, options.inputTriggerConfig( inputTriggerConfig ) );
- if ( windowTitle != null )
- viewerFrame.setTitle( windowTitle );
- viewer = viewerFrame.getViewerPanel();
-
-// final ConverterSetup.SetupChangeListener requestRepaint = s -> viewer.requestRepaint();
-// for ( final ConverterSetup cs : converterSetups )
-// cs.setupChangeListeners().add( requestRepaint );
-
- manualTransformation = new ManualTransformation( viewer );
- manualTransformationEditor = new ManualTransformationEditor( viewer, viewerFrame.getKeybindings() );
-
- bookmarks = new Bookmarks();
- bookmarkEditor = new BookmarksEditor( viewer, viewerFrame.getKeybindings(), bookmarks );
-
- final ConverterSetups setups = viewerFrame.getConverterSetups();
- if ( converterSetups.size() != sources.size() )
- System.err.println( "WARNING! Constructing BigDataViewer, with converterSetups.size() that is not the same as sources.size()." );
- final int numSetups = Math.min( converterSetups.size(), sources.size() );
- for ( int i = 0; i < numSetups; ++i )
- {
- final SourceAndConverter< ? > source = sources.get( i );
- final ConverterSetup setup = converterSetups.get( i );
- if ( setup != null )
- setups.put( source, setup );
- }
-
- 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().overlays().add( movieDialog );
-
- movieMaxProjectDialog = new RecordMaxProjectionDialog( viewerFrame, viewer, progressWriter );
- // this is just to get updates of window size:
- viewer.getDisplay().overlays().add( movieMaxProjectDialog );
-
- activeSourcesDialog = new VisibilityAndGroupingDialog( viewerFrame, viewer.state() );
-
- 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;
- }
+ protected final BrightnessDialog brightnessDialog;
- public static BigDataViewer open(final String xmlFilename,
+ 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;
+
+ private boolean enableCompression;
+
+ 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);
+
+ viewerFrame = new ViewerFrame(sources, numTimepoints, cache, options.inputTriggerConfig(inputTriggerConfig));
+ if (windowTitle != null)
+ viewerFrame.setTitle(windowTitle);
+ viewer = viewerFrame.getViewerPanel();
+
+ // final ConverterSetup.SetupChangeListener requestRepaint = s -> viewer.requestRepaint();
+ // for ( final ConverterSetup cs : converterSetups )
+ // cs.setupChangeListeners().add( requestRepaint );
+
+ manualTransformation = new ManualTransformation(viewer);
+ manualTransformationEditor = new ManualTransformationEditor(viewer, viewerFrame.getKeybindings());
+
+ bookmarks = new Bookmarks();
+ bookmarkEditor = new BookmarksEditor(viewer, viewerFrame.getKeybindings(), bookmarks);
+
+ final ConverterSetups setups = viewerFrame.getConverterSetups();
+ if (converterSetups.size() != sources.size())
+ System.err.println("WARNING! Constructing BigDataViewer, with converterSetups.size() that is not the same as sources.size().");
+ final int numSetups = Math.min(converterSetups.size(), sources.size());
+ for (int i = 0; i < numSetups; ++i) {
+ final SourceAndConverter<?> source = sources.get(i);
+ final ConverterSetup setup = converterSetups.get(i);
+ if (setup != null)
+ setups.put(source, setup);
+ }
+
+ 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().overlays().add(movieDialog);
+
+ movieMaxProjectDialog = new RecordMaxProjectionDialog(viewerFrame, viewer, progressWriter);
+ // this is just to get updates of window size:
+ viewer.getDisplay().overlays().add(movieMaxProjectDialog);
+
+ activeSourcesDialog = new VisibilityAndGroupingDialog(viewerFrame, viewer.state());
+
+ 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);
+
+ enableCompression = options.values.getCompressionOptions().isEnabled();
+ if (options.values.getCompressionOptions().isEnabled()) {
+ menu = new JMenu("QCMP Compression");
+ menubar.add(menu);
+
+ final JCheckBoxMenuItem enableCompressionCheckBox = new JCheckBoxMenuItem("Enable compression", true);
+ enableCompressionCheckBox.addActionListener(e -> {
+ enableDisableCompression(enableCompressionCheckBox.isSelected());
+ });
+
+ menu.add(enableCompressionCheckBox);
+ }
+
+
+ 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,
- final ViewerCompressionOptions ops) throws SpimDataException {
+ 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;
+ }
+
+ private synchronized void enableDisableCompression(final boolean enabled) {
+ if (this.enableCompression == enabled)
+ return;
+ this.enableCompression = enabled;
+
+
+ }
+ public static BigDataViewer open(final String xmlFilename,
+ final String windowTitle,
+ final ProgressWriter progressWriter,
+ final ViewerOptions options) throws SpimDataException {
final XmlIoSpimDataMinimal xmlIoSpimDataMinimal = new XmlIoSpimDataMinimal();
- xmlIoSpimDataMinimal.setViewerCompressionOptions(ops);
+ xmlIoSpimDataMinimal.setViewerCompressionOptions(options.values.getCompressionOptions());
+
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.viewerFrame );
+ InitializeViewerState.initBrightness(0.001, 0.999, bdv.viewerFrame);
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.viewerFrame );
- 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 ConverterSetups getConverterSetups()
- {
- return viewerFrame.getConverterSetups();
- }
-
- /**
- * @deprecated Instead {@code getViewer().state()} returns the {@link ViewerState} that can be modified directly.
- */
- @Deprecated
- 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 void expandAndFocusCardPanel()
- {
- viewerFrame.getSplitPanel().setCollapsed( false );
- viewerFrame.getSplitPanel().getRightComponent().requestFocusInWindow();
- }
-
- public void collapseCardPanel()
- {
- viewerFrame.getSplitPanel().setCollapsed( true );
- viewer.requestFocusInWindow();
- }
+ 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 ConverterSetups getConverterSetups() {
+ return viewerFrame.getConverterSetups();
+ }
+
+ /**
+ * @deprecated Instead {@code getViewer().state()} returns the {@link ViewerState} that can be modified directly.
+ */
+ @Deprecated
+ 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 void expandAndFocusCardPanel() {
+ viewerFrame.getSplitPanel().setCollapsed(false);
+ viewerFrame.getSplitPanel().getRightComponent().requestFocusInWindow();
+ }
+
+ public void collapseCardPanel() {
+ viewerFrame.getSplitPanel().setCollapsed(true);
+ viewer.requestFocusInWindow();
+ }
public static void main(final String[] args) {
if (args.length < 1) {
@@ -714,29 +670,22 @@ public class BigDataViewer {
}
final String fn = args[0];
- final ViewerCompressionOptions ops = new ViewerCompressionOptions();
+ final ViewerOptions viewerOptions = ViewerOptions.options();
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]));
+ viewerOptions.values.getCompressionOptions().setEnabled(true);
break;
}
}
}
- ColorConsole.printf(ColorConsole.Color.Green, "Compression:\t" + (ops.isEnabled() ? "ON" : "OFF"));
- if (ops.isEnabled())
- ColorConsole.printf(ColorConsole.Color.Green, "CompressFrom:\t" + ops.getCompressFromMipmapLevel());
+ ColorConsole.printf(ColorConsole.Color.Green, "Compression:\t" +
+ (viewerOptions.values.getCompressionOptions().isEnabled() ? "ON" : "OFF"));
+
try {
System.setProperty("apple.laf.useScreenMenuBar", "true");
@@ -744,8 +693,7 @@ public class BigDataViewer {
final BigDataViewer bdv = open(fn,
"Server test",
new ProgressWriterConsole(),
- ViewerOptions.options(),
- ops);
+ viewerOptions);
} 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 01835d7790c86af1b55466e22a035fd41c4964cc..74178125e057eb7c88ec721b2cb5209057873afc 100644
--- a/src/main/java/bdv/img/remote/RemoteImageLoader.java
+++ b/src/main/java/bdv/img/remote/RemoteImageLoader.java
@@ -28,7 +28,6 @@
*/
package bdv.img.remote;
-import azgracompress.ViewerCompressionOptions;
import azgracompress.cache.ICacheFile;
import azgracompress.cache.QuantizationCacheManager;
import azgracompress.compression.ImageDecompressor;
@@ -41,6 +40,7 @@ import bdv.img.hdf5.DimsAndExistence;
import bdv.img.hdf5.MipmapInfo;
import bdv.img.hdf5.ViewLevelId;
import bdv.util.ConstantRandomAccessible;
+import bdv.viewer.ViewerOptions;
import com.google.gson.GsonBuilder;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
import net.imglib2.FinalInterval;
@@ -77,7 +77,7 @@ public class RemoteImageLoader implements ViewerImgLoader {
/**
* Flag whether we allow the server to send us compressed data.
*/
- private ViewerCompressionOptions viewerCompressionOptions;
+ private ViewerOptions.CompressionOptions viewerCompressionOptions;
/**
@@ -131,7 +131,7 @@ public class RemoteImageLoader implements ViewerImgLoader {
}
}
- public void setViewerCompressionOptions(final ViewerCompressionOptions ops) {
+ public void setViewerCompressionOptions(final ViewerOptions.CompressionOptions ops) {
this.viewerCompressionOptions = ops;
}
@@ -146,7 +146,9 @@ public class RemoteImageLoader implements ViewerImgLoader {
return;
}
final ArrayList<ICacheFile> cacheFiles = new ArrayList<>();
+ int compressFromMipmapLevel = 0;
try (final DataInputStream dis = new DataInputStream(connection.getInputStream())) {
+ compressFromMipmapLevel = dis.readByte();
final int codebookCount = dis.readByte();
for (int cbIndex = 0; cbIndex < codebookCount; cbIndex++) {
final ICacheFile readCacheFile = QuantizationCacheManager.readCacheFile(dis);
@@ -160,13 +162,15 @@ public class RemoteImageLoader implements ViewerImgLoader {
}
}
ColorConsole.fprintf(ColorConsole.Target.stdout, ColorConsole.Color.Yellow, "Received %d cache files.", cacheFiles.size());
+ ColorConsole.fprintf(ColorConsole.Target.stdout, ColorConsole.Color.Yellow,
+ "Decompressing from mipmap level %d.", compressFromMipmapLevel);
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());
+ shortLoader.setDataDecompressors(decompressors, metadata.maxNumLevels, compressFromMipmapLevel);
}
diff --git a/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java b/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java
index 2d5daf3cb1bde2824b930c8d4f23f52438f5b5d9..a2baab0cac95f8e82215d1e8b322790cf7e4c9e1 100644
--- a/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java
+++ b/src/main/java/bdv/spimdata/XmlIoSpimDataMinimal.java
@@ -28,9 +28,9 @@
*/
package bdv.spimdata;
-import azgracompress.ViewerCompressionOptions;
import bdv.img.remote.RemoteImageLoader;
import bdv.spimdata.legacy.XmlIoSpimDataMinimalLegacy;
+import bdv.viewer.ViewerOptions;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.SpimDataIOException;
import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
@@ -49,7 +49,7 @@ import java.io.File;
import static mpicbg.spim.data.XmlKeys.SPIMDATA_TAG;
public class XmlIoSpimDataMinimal extends XmlIoAbstractSpimData<SequenceDescriptionMinimal, SpimDataMinimal> {
- private ViewerCompressionOptions compressionOptions;
+ private ViewerOptions.CompressionOptions compressionOptions;
public XmlIoSpimDataMinimal() {
super(SpimDataMinimal.class,
@@ -61,7 +61,7 @@ public class XmlIoSpimDataMinimal extends XmlIoAbstractSpimData<SequenceDescript
new XmlIoViewRegistrations());
}
- public void setViewerCompressionOptions(final ViewerCompressionOptions ops) {
+ public void setViewerCompressionOptions(final ViewerOptions.CompressionOptions ops) {
this.compressionOptions = ops;
}
diff --git a/src/main/java/bdv/viewer/ViewerOptions.java b/src/main/java/bdv/viewer/ViewerOptions.java
index b977c4585e8fdfadafe7b32ffc2efb6bb0a283f4..9561384d069cdcdd6ff0fb5265a08435ba3c6899 100644
--- a/src/main/java/bdv/viewer/ViewerOptions.java
+++ b/src/main/java/bdv/viewer/ViewerOptions.java
@@ -6,13 +6,13 @@
* %%
* 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
@@ -29,285 +29,274 @@
package bdv.viewer;
import bdv.TransformEventHandler3D;
-import java.awt.event.KeyListener;
-
-import org.scijava.ui.behaviour.KeyPressedManager;
-import org.scijava.ui.behaviour.io.InputTriggerConfig;
-
+import bdv.TransformEventHandlerFactory;
import bdv.viewer.animate.MessageOverlayAnimator;
import bdv.viewer.render.AccumulateProjector;
import bdv.viewer.render.AccumulateProjectorARGB;
import bdv.viewer.render.AccumulateProjectorFactory;
import bdv.viewer.render.MultiResolutionRenderer;
-import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.ARGBType;
-import bdv.TransformEventHandlerFactory;
+import org.scijava.ui.behaviour.KeyPressedManager;
+import org.scijava.ui.behaviour.io.InputTriggerConfig;
+
+import java.awt.event.KeyListener;
/**
* Optional parameters for {@link ViewerPanel}.
*
* @author Tobias Pietzsch
*/
-public class ViewerOptions
-{
- public final Values values = new Values();
-
- /**
- * Create default {@link ViewerOptions}.
- * @return default {@link ViewerOptions}.
- */
- public static ViewerOptions options()
- {
- return new ViewerOptions();
- }
-
- /**
- * Set width of {@link ViewerPanel} canvas.
- */
- public ViewerOptions width( final int w )
- {
- values.width = w;
- return this;
- }
-
- /**
- * Set height of {@link ViewerPanel} canvas.
- */
- public ViewerOptions height( final int h )
- {
- values.height = h;
- return this;
- }
-
- /**
- * Set the number and scale factors for scaled screen images.
- *
- * @param s
- * Scale factors from the viewer canvas to screen images of
- * different resolutions. A scale factor of 1 means 1 pixel in
- * the screen image is displayed as 1 pixel on the canvas, a
- * scale factor of 0.5 means 1 pixel in the screen image is
- * displayed as 2 pixel on the canvas, etc.
- * @see MultiResolutionRenderer
- */
- public ViewerOptions screenScales( final double[] s )
- {
- values.screenScales = s;
- return this;
- }
-
- /**
- * Set target rendering time in nanoseconds.
- *
- * @param t
- * Target rendering time in nanoseconds. The rendering time for
- * the coarsest rendered scale should be below this threshold.
- * @see MultiResolutionRenderer
- */
- public ViewerOptions targetRenderNanos( final long t )
- {
- values.targetRenderNanos = t;
- return this;
- }
-
- /**
- * Set how many threads to use for rendering.
- *
- * @param n
- * How many threads to use for rendering.
- * @see MultiResolutionRenderer
- */
- public ViewerOptions numRenderingThreads( final int n )
- {
- values.numRenderingThreads = n;
- return this;
- }
-
- /**
- * Set how many source groups there are initially.
- *
- * @param n
- * How many source groups to create initially.
- */
- public ViewerOptions numSourceGroups( final int n )
- {
- values.numSourceGroups = n;
- return this;
- }
-
- /**
- * Set whether volatile versions of sources should be used if available.
- *
- * @param v
- * whether volatile versions of sources should be used if
- * available.
- * @see MultiResolutionRenderer
- */
- public ViewerOptions useVolatileIfAvailable( final boolean v )
- {
- values.useVolatileIfAvailable = v;
- return this;
- }
-
- public ViewerOptions msgOverlay( final MessageOverlayAnimator o )
- {
- values.msgOverlay = o;
- return this;
- }
-
- public ViewerOptions transformEventHandlerFactory( final TransformEventHandlerFactory f )
- {
- values.transformEventHandlerFactory = f;
- return this;
- }
-
- /**
- * Set the factory for creating {@link AccumulateProjector}. This can be
- * used to customize how sources are combined.
- *
- * @param f
- * factory for creating {@link AccumulateProjector}.
- * @see MultiResolutionRenderer
- */
- public ViewerOptions accumulateProjectorFactory( final AccumulateProjectorFactory< ARGBType > f )
- {
- values.accumulateProjectorFactory = f;
- return this;
- }
-
- /**
- * Set the {@link InputTriggerConfig} from which keyboard and mouse action mapping is loaded.
- *
- * @param c the {@link InputTriggerConfig} from which keyboard and mouse action mapping is loaded
- */
- public ViewerOptions inputTriggerConfig( final InputTriggerConfig c )
- {
- values.inputTriggerConfig = c;
- return this;
- }
-
- /**
- * Set the {@link KeyPressedManager} to share
- * {@link KeyListener#keyPressed(java.awt.event.KeyEvent)} events with other
- * ui-behaviour windows.
- * <p>
- * The goal is to make keyboard click/drag behaviours work like mouse
- * click/drag: When a behaviour is initiated with a key press, the window
- * under the mouse receives focus and the behaviour is handled there.
- * </p>
- *
- * @param manager
- * @return
- */
- public ViewerOptions shareKeyPressedEvents( final KeyPressedManager manager )
- {
- values.keyPressedManager = manager;
- return this;
- }
-
- /**
- * Read-only {@link ViewerOptions} values.
- */
- public static class Values
- {
- private int width = 800;
-
- private int height = 600;
-
- private double[] screenScales = new double[] { 1, 0.75, 0.5, 0.25, 0.125 };
-
- private long targetRenderNanos = 30 * 1000000l;
-
- private int numRenderingThreads = 3;
-
- private int numSourceGroups = 10;
-
- private boolean useVolatileIfAvailable = true;
-
- private MessageOverlayAnimator msgOverlay = new MessageOverlayAnimator( 800 );
-
- private TransformEventHandlerFactory transformEventHandlerFactory = TransformEventHandler3D::new;
-
- private AccumulateProjectorFactory< ARGBType > accumulateProjectorFactory = AccumulateProjectorARGB.factory;
-
- private InputTriggerConfig inputTriggerConfig = null;
-
- private KeyPressedManager keyPressedManager = null;
-
- public ViewerOptions optionsFromValues()
- {
- return new ViewerOptions().
- width( width ).
- height( height ).
- screenScales( screenScales ).
- targetRenderNanos( targetRenderNanos ).
- numRenderingThreads( numRenderingThreads ).
- numSourceGroups( numSourceGroups ).
- useVolatileIfAvailable( useVolatileIfAvailable ).
- msgOverlay( msgOverlay ).
- transformEventHandlerFactory( transformEventHandlerFactory ).
- accumulateProjectorFactory( accumulateProjectorFactory ).
- inputTriggerConfig( inputTriggerConfig );
- }
-
- public int getWidth()
- {
- return width;
- }
-
- public int getHeight()
- {
- return height;
- }
-
- public double[] getScreenScales()
- {
- return screenScales;
- }
-
- public long getTargetRenderNanos()
- {
- return targetRenderNanos;
- }
-
- public int getNumRenderingThreads()
- {
- return numRenderingThreads;
- }
-
- public int getNumSourceGroups()
- {
- return numSourceGroups;
- }
-
- public boolean isUseVolatileIfAvailable()
- {
- return useVolatileIfAvailable;
- }
-
- public MessageOverlayAnimator getMsgOverlay()
- {
- return msgOverlay;
- }
-
- public TransformEventHandlerFactory getTransformEventHandlerFactory()
- {
- return transformEventHandlerFactory;
- }
-
- public AccumulateProjectorFactory< ARGBType > getAccumulateProjectorFactory()
- {
- return accumulateProjectorFactory;
- }
-
- public InputTriggerConfig getInputTriggerConfig()
- {
- return inputTriggerConfig;
- }
-
- public KeyPressedManager getKeyPressedManager()
- {
- return keyPressedManager;
- }
- }
+public class ViewerOptions {
+ public static class CompressionOptions {
+ private boolean enabled = false;
+
+ public boolean isEnabled() {
+ return enabled;
+ }
+
+ public void setEnabled(final boolean enable) {
+ this.enabled = enable;
+ }
+ }
+
+ public final Values values = new Values();
+
+ /**
+ * Create default {@link ViewerOptions}.
+ *
+ * @return default {@link ViewerOptions}.
+ */
+ public static ViewerOptions options() {
+ return new ViewerOptions();
+ }
+
+ /**
+ * Set width of {@link ViewerPanel} canvas.
+ */
+ public ViewerOptions width(final int w) {
+ values.width = w;
+ return this;
+ }
+
+ public ViewerOptions compressionOptions(final CompressionOptions compressionOptions) {
+ values.compressionOptions = compressionOptions;
+ return this;
+ }
+
+ /**
+ * Set height of {@link ViewerPanel} canvas.
+ */
+ public ViewerOptions height(final int h) {
+ values.height = h;
+ return this;
+ }
+
+ /**
+ * Set the number and scale factors for scaled screen images.
+ *
+ * @param s Scale factors from the viewer canvas to screen images of
+ * different resolutions. A scale factor of 1 means 1 pixel in
+ * the screen image is displayed as 1 pixel on the canvas, a
+ * scale factor of 0.5 means 1 pixel in the screen image is
+ * displayed as 2 pixel on the canvas, etc.
+ * @see MultiResolutionRenderer
+ */
+ public ViewerOptions screenScales(final double[] s) {
+ values.screenScales = s;
+ return this;
+ }
+
+ /**
+ * Set target rendering time in nanoseconds.
+ *
+ * @param t Target rendering time in nanoseconds. The rendering time for
+ * the coarsest rendered scale should be below this threshold.
+ * @see MultiResolutionRenderer
+ */
+ public ViewerOptions targetRenderNanos(final long t) {
+ values.targetRenderNanos = t;
+ return this;
+ }
+
+ /**
+ * Set how many threads to use for rendering.
+ *
+ * @param n How many threads to use for rendering.
+ * @see MultiResolutionRenderer
+ */
+ public ViewerOptions numRenderingThreads(final int n) {
+ values.numRenderingThreads = n;
+ return this;
+ }
+
+ /**
+ * Set how many source groups there are initially.
+ *
+ * @param n How many source groups to create initially.
+ */
+ public ViewerOptions numSourceGroups(final int n) {
+ values.numSourceGroups = n;
+ return this;
+ }
+
+ /**
+ * Set whether volatile versions of sources should be used if available.
+ *
+ * @param v whether volatile versions of sources should be used if
+ * available.
+ * @see MultiResolutionRenderer
+ */
+ public ViewerOptions useVolatileIfAvailable(final boolean v) {
+ values.useVolatileIfAvailable = v;
+ return this;
+ }
+
+ public ViewerOptions msgOverlay(final MessageOverlayAnimator o) {
+ values.msgOverlay = o;
+ return this;
+ }
+
+ public ViewerOptions transformEventHandlerFactory(final TransformEventHandlerFactory f) {
+ values.transformEventHandlerFactory = f;
+ return this;
+ }
+
+ /**
+ * Set the factory for creating {@link AccumulateProjector}. This can be
+ * used to customize how sources are combined.
+ *
+ * @param f factory for creating {@link AccumulateProjector}.
+ * @see MultiResolutionRenderer
+ */
+ public ViewerOptions accumulateProjectorFactory(final AccumulateProjectorFactory<ARGBType> f) {
+ values.accumulateProjectorFactory = f;
+ return this;
+ }
+
+ /**
+ * Set the {@link InputTriggerConfig} from which keyboard and mouse action mapping is loaded.
+ *
+ * @param c the {@link InputTriggerConfig} from which keyboard and mouse action mapping is loaded
+ */
+ public ViewerOptions inputTriggerConfig(final InputTriggerConfig c) {
+ values.inputTriggerConfig = c;
+ return this;
+ }
+
+ /**
+ * Set the {@link KeyPressedManager} to share
+ * {@link KeyListener#keyPressed(java.awt.event.KeyEvent)} events with other
+ * ui-behaviour windows.
+ * <p>
+ * The goal is to make keyboard click/drag behaviours work like mouse
+ * click/drag: When a behaviour is initiated with a key press, the window
+ * under the mouse receives focus and the behaviour is handled there.
+ * </p>
+ *
+ * @param manager
+ * @return
+ */
+ public ViewerOptions shareKeyPressedEvents(final KeyPressedManager manager) {
+ values.keyPressedManager = manager;
+ return this;
+ }
+
+ /**
+ * Read-only {@link ViewerOptions} values.
+ */
+ public static class Values {
+ private int width = 800;
+
+ private int height = 600;
+
+ private double[] screenScales = new double[]{1, 0.75, 0.5, 0.25, 0.125};
+
+ private long targetRenderNanos = 30 * 1000000l;
+
+ private int numRenderingThreads = 3;
+
+ private int numSourceGroups = 10;
+
+ private boolean useVolatileIfAvailable = true;
+
+ private MessageOverlayAnimator msgOverlay = new MessageOverlayAnimator(800);
+
+ private TransformEventHandlerFactory transformEventHandlerFactory = TransformEventHandler3D::new;
+
+ private AccumulateProjectorFactory<ARGBType> accumulateProjectorFactory = AccumulateProjectorARGB.factory;
+
+ private InputTriggerConfig inputTriggerConfig = null;
+
+ private KeyPressedManager keyPressedManager = null;
+
+ private CompressionOptions compressionOptions = new CompressionOptions();
+
+ public ViewerOptions optionsFromValues() {
+ return new ViewerOptions().
+ width(width).
+ height(height).
+ screenScales(screenScales).
+ targetRenderNanos(targetRenderNanos).
+ numRenderingThreads(numRenderingThreads).
+ numSourceGroups(numSourceGroups).
+ useVolatileIfAvailable(useVolatileIfAvailable).
+ msgOverlay(msgOverlay).
+ transformEventHandlerFactory(transformEventHandlerFactory).
+ accumulateProjectorFactory(accumulateProjectorFactory).
+ inputTriggerConfig(inputTriggerConfig).
+ compressionOptions(compressionOptions);
+ }
+
+ public int getWidth() {
+ return width;
+ }
+
+ public int getHeight() {
+ return height;
+ }
+
+ public double[] getScreenScales() {
+ return screenScales;
+ }
+
+ public long getTargetRenderNanos() {
+ return targetRenderNanos;
+ }
+
+ public int getNumRenderingThreads() {
+ return numRenderingThreads;
+ }
+
+ public int getNumSourceGroups() {
+ return numSourceGroups;
+ }
+
+ public boolean isUseVolatileIfAvailable() {
+ return useVolatileIfAvailable;
+ }
+
+ public MessageOverlayAnimator getMsgOverlay() {
+ return msgOverlay;
+ }
+
+ public TransformEventHandlerFactory getTransformEventHandlerFactory() {
+ return transformEventHandlerFactory;
+ }
+
+ public AccumulateProjectorFactory<ARGBType> getAccumulateProjectorFactory() {
+ return accumulateProjectorFactory;
+ }
+
+ public InputTriggerConfig getInputTriggerConfig() {
+ return inputTriggerConfig;
+ }
+
+ public KeyPressedManager getKeyPressedManager() {
+ return keyPressedManager;
+ }
+
+ public CompressionOptions getCompressionOptions() {
+ return compressionOptions;
+ }
+ }
}