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Generate fiji url links and process them: in progress #207

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fde8602
POM: Add slf4j dependency
tpietzsch Mar 25, 2025
f9d8712
Add JsonUtils in particular @JsonIo annotation
tpietzsch Mar 25, 2025
ae1c027
ResourceManager will be used to match ResourceSpecs of pasted links
tpietzsch Feb 27, 2025
9745a44
Move StyleElements to package bdv.ui.settings, make public
tpietzsch Mar 25, 2025
533a6b1
Add ResourceManager to BigDataViewer and track added Sources
tpietzsch Mar 25, 2025
1ae9640
Add copy&paste of BDV state as JSON
tpietzsch Mar 25, 2025
6729e65
fix javadoc error
tpietzsch Mar 25, 2025
8a1ee3f
Make JsonAdapters public
tpietzsch Mar 25, 2025
eea6f1f
generate url links and process them
mzouink May 5, 2025
2d8a2fa
remove debug changes
mzouink May 5, 2025
94a7187
remove link handler, will be a separate project
mzouink May 5, 2025
5b72d6a
remove links dep
mzouink May 5, 2025
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8 changes: 8 additions & 0 deletions pom.xml
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Expand Up @@ -235,6 +235,14 @@
<groupId>org.yaml</groupId>
<artifactId>snakeyaml</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
</dependency>

<!-- Test dependencies -->
<dependency>
Expand Down
181 changes: 141 additions & 40 deletions src/main/java/bdv/BigDataViewer.java
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Expand Up @@ -28,16 +28,6 @@
*/
package bdv;

import bdv.tools.PreferencesDialog;
import bdv.ui.UIUtils;
import bdv.ui.keymap.Keymap;
import bdv.ui.keymap.KeymapManager;
import bdv.ui.keymap.KeymapSettingsPage;
import bdv.viewer.ConverterSetups;
import bdv.viewer.ViewerState;
import bdv.ui.appearance.AppearanceManager;
import bdv.ui.appearance.AppearanceSettingsPage;
import dev.dirs.ProjectDirectories;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
Expand All @@ -53,16 +43,6 @@
import javax.swing.SwingUtilities;
import javax.swing.filechooser.FileFilter;

import net.imglib2.Volatile;
import net.imglib2.converter.Converter;
import net.imglib2.display.ColorConverter;
import net.imglib2.display.RealARGBColorConverter;
import net.imglib2.display.ScaledARGBConverter;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.volatiles.VolatileARGBType;

import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
Expand All @@ -71,6 +51,7 @@
import org.jdom2.output.XMLOutputter;
import org.scijava.ui.behaviour.io.InputTriggerConfig;
import org.scijava.ui.behaviour.io.yaml.YamlConfigIO;
import org.scijava.ui.behaviour.util.Actions;

import bdv.cache.CacheControl;
import bdv.export.ProgressWriter;
Expand All @@ -80,6 +61,7 @@
import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.tools.HelpDialog;
import bdv.tools.InitializeViewerState;
import bdv.tools.PreferencesDialog;
import bdv.tools.RecordMaxProjectionDialog;
import bdv.tools.RecordMovieDialog;
import bdv.tools.VisibilityAndGroupingDialog;
Expand All @@ -91,21 +73,47 @@
import bdv.tools.brightness.RealARGBColorConverterSetup;
import bdv.tools.brightness.SetupAssignments;
import bdv.tools.crop.CropDialog;
import bdv.tools.links.LinkActions;
import bdv.tools.links.PasteSettings;
import bdv.tools.links.ResourceManager;
import bdv.tools.links.resource.SpimDataMinimalFileResource;
import bdv.tools.links.resource.SpimDataSetupSourceResource;
import bdv.tools.links.resource.TransformedSourceResource;
import bdv.tools.transformation.ManualTransformation;
import bdv.tools.transformation.ManualTransformationEditor;
import bdv.tools.transformation.TransformedSource;
import bdv.ui.UIUtils;
import bdv.ui.appearance.AppearanceManager;
import bdv.ui.appearance.AppearanceSettingsPage;
import bdv.ui.keymap.Keymap;
import bdv.ui.keymap.KeymapManager;
import bdv.ui.keymap.KeymapSettingsPage;
import bdv.ui.links.LinkCard;
import bdv.ui.links.LinkSettingsManager;
import bdv.ui.links.LinkSettingsPage;
import bdv.viewer.ConverterSetups;
import bdv.viewer.NavigationActions;
import bdv.viewer.SourceAndConverter;
import bdv.viewer.ViewerFrame;
import bdv.viewer.ViewerOptions;
import bdv.viewer.ViewerPanel;
import bdv.viewer.ViewerState;
import dev.dirs.ProjectDirectories;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
import mpicbg.spim.data.sequence.Angle;
import mpicbg.spim.data.sequence.Channel;
import org.scijava.ui.behaviour.util.Actions;
import net.imglib2.Volatile;
import net.imglib2.converter.Converter;
import net.imglib2.display.ColorConverter;
import net.imglib2.display.RealARGBColorConverter;
import net.imglib2.display.ScaledARGBConverter;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.volatiles.VolatileARGBType;

public class BigDataViewer
{
Expand Down Expand Up @@ -137,6 +145,10 @@ public class BigDataViewer

private final AppearanceManager appearanceManager;

private final LinkSettingsManager linkSettingsManager;

private final ResourceManager resourceManager;

protected final PreferencesDialog preferencesDialog;

protected final ManualTransformationEditor manualTransformationEditor;
Expand Down Expand Up @@ -257,49 +269,103 @@ public static ConverterSetup createConverterSetup( final SourceAndConverter< ? >
*/
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() );
return wrapWithTransformedSource( soc, null );
}

@SuppressWarnings( "unchecked" )
final SourceAndConverter< V > vsoc = ( SourceAndConverter< V > ) soc.asVolatile();
/**
* 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.
*
* @param soc
* source to decorate
* @param resources
* if non-null, a {@code ResourceSpec} for the created {@code TransformedSource} wrapper.
*
* @return {@code TransformedSource} wrapper around {@code soc}
*/
public static < T, V extends Volatile< T > > SourceAndConverter< T > wrapWithTransformedSource( final SourceAndConverter< T > soc, final ResourceManager resources )
{
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() ) );

final SourceAndConverter< V > vtsoc;
if ( soc.asVolatile() == null )
{
vtsoc = null;
}
else
{
@SuppressWarnings( "unchecked" )
final SourceAndConverter< V > vsoc = ( SourceAndConverter< V > ) soc.asVolatile();
final TransformedSource< V > vts = new TransformedSource<>( vsoc.getSpimSource(), ts );
vtsoc = new SourceAndConverter<>( vts, vsoc.getConverter() );
}

final SourceAndConverter< T > tsoc = new SourceAndConverter<>( ts, soc.getConverter(), vtsoc );
if (resources != null)
{
final TransformedSourceResource.Spec spec = new TransformedSourceResource.Spec(
resources.getResourceSpec( soc ) );
resources.put( tsoc, spec );
resources.keepAlive( tsoc, soc );
}
return tsoc;
}

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 List< SourceAndConverter< ? > > sources,
final ResourceManager resources )
{
final int setupId = setup.getId();
final String setupName = createSetupName( setup );
final SourceAndConverter< T > soc = createSetupSourceNumericType( spimData, setupId, setupName, resources );
final SourceAndConverter< T > tsoc = wrapWithTransformedSource( soc, resources );
sources.add( tsoc );

final ConverterSetup converterSetup = createConverterSetup( tsoc, setupId );
if ( converterSetup != null )
converterSetups.add( converterSetup );
}

public static < T extends NumericType< T >, V extends Volatile< T > & NumericType< V > > SourceAndConverter< T > createSetupSourceNumericType(
final AbstractSpimData< ? > spimData,
final int setupId,
final String name,
final ResourceManager resources )
{
final ViewerImgLoader imgLoader = ( ViewerImgLoader ) spimData.getSequenceDescription().getImgLoader();
@SuppressWarnings( "unchecked" )
final ViewerSetupImgLoader< T, V > setupImgLoader = ( ViewerSetupImgLoader< T, V > ) imgLoader.getSetupImgLoader( setupId );
if ( setupImgLoader == null )
throw new IllegalArgumentException( "No SetupImgLoader for setup ID " + setupId + " found." );

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 );
final VolatileSpimSource< V > vs = new VolatileSpimSource<>( spimData, setupId, name );
vsoc = new SourceAndConverter<>( vs, createConverterToARGB( volatileType ) );
}

final SpimSource< T > s = new SpimSource<>( spimData, setupId, setupName );
final SpimSource< T > s = new SpimSource<>( spimData, setupId, name );
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 );
if (resources != null)
{
final SpimDataSetupSourceResource.Spec spec = new SpimDataSetupSourceResource.Spec(
resources.getResourceSpec( spimData ),
setupId, name );
resources.put( soc, spec );
resources.keepAlive( soc, spimData );
}
return soc;
}

public static void initSetups(
Expand All @@ -308,7 +374,17 @@ public static void initSetups(
final List< SourceAndConverter< ? > > sources )
{
for ( final BasicViewSetup setup : spimData.getSequenceDescription().getViewSetupsOrdered() )
initSetupNumericType( spimData, setup, converterSetups, sources );
initSetupNumericType( spimData, setup, converterSetups, sources, null );
}

public static void initSetups(
final AbstractSpimData< ? > spimData,
final List< ConverterSetup > converterSetups,
final List< SourceAndConverter< ? > > sources,
final ResourceManager resources )
{
for ( final BasicViewSetup setup : spimData.getSequenceDescription().getViewSetupsOrdered() )
initSetupNumericType( spimData, setup, converterSetups, sources, resources );
}

@Deprecated
Expand Down Expand Up @@ -353,8 +429,11 @@ public BigDataViewer(
{
final KeymapManager optionsKeymapManager = options.values.getKeymapManager();
final AppearanceManager optionsAppearanceManager = options.values.getAppearanceManager();
final LinkSettingsManager optionsLinkSettingsManager = options.values.getLinkSettingsManager();
keymapManager = optionsKeymapManager != null ? optionsKeymapManager : new KeymapManager( configDir );
appearanceManager = optionsAppearanceManager != null ? optionsAppearanceManager : new AppearanceManager( configDir );
linkSettingsManager = optionsLinkSettingsManager != null ? optionsLinkSettingsManager : new LinkSettingsManager( configDir );
resourceManager = options.values.getResourceManager();

InputTriggerConfig inputTriggerConfig = options.values.getInputTriggerConfig();
final Keymap keymap = this.keymapManager.getForwardSelectedKeymap();
Expand Down Expand Up @@ -442,6 +521,7 @@ public boolean accept( final File f )
preferencesDialog = new PreferencesDialog( viewerFrame, keymap, new String[] { KeyConfigContexts.BIGDATAVIEWER } );
preferencesDialog.addPage( new AppearanceSettingsPage( "Appearance", appearanceManager ) );
preferencesDialog.addPage( new KeymapSettingsPage( "Keymap", this.keymapManager, this.keymapManager.getCommandDescriptions() ) );
preferencesDialog.addPage( new LinkSettingsPage( "Links", linkSettingsManager ) );
appearanceManager.appearance().updateListeners().add( viewerFrame::repaint );
appearanceManager.addLafComponent( fileChooser );
SwingUtilities.invokeLater(() -> appearanceManager.updateLookAndFeel());
Expand All @@ -454,9 +534,17 @@ public boolean accept( final File f )
bdvActions.install( viewerFrame.getKeybindings(), "bdv" );
BigDataViewerActions.install( bdvActions, this );

final Actions linkActions = new Actions( inputTriggerConfig, "bdv" );
linkActions.install( viewerFrame.getKeybindings(), "links" );
final PasteSettings pasteSettings = linkSettingsManager.linkSettings().pasteSettings();
LinkActions.install( linkActions, viewerFrame.getViewerPanel(), viewerFrame.getConverterSetups(), pasteSettings, resourceManager );

LinkCard.install( linkSettingsManager.linkSettings(), viewerFrame.getCardPanel() );

keymap.updateListeners().add( () -> {
navigationActions.updateKeyConfig( keymap.getConfig() );
bdvActions.updateKeyConfig( keymap.getConfig() );
linkActions.updateKeyConfig( keymap.getConfig() );
viewerFrame.getTransformBehaviours().updateKeyConfig( keymap.getConfig() );
} );

Expand Down Expand Up @@ -531,7 +619,8 @@ public static BigDataViewer open( final AbstractSpimData< ? > spimData, final St

final ArrayList< ConverterSetup > converterSetups = new ArrayList<>();
final ArrayList< SourceAndConverter< ? > > sources = new ArrayList<>();
initSetups( spimData, converterSetups, sources );
final ResourceManager resources = options.values.getResourceManager();
initSetups( spimData, converterSetups, sources, resources );

final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription();
final int numTimepoints = seq.getTimePoints().size();
Expand All @@ -549,6 +638,8 @@ public static BigDataViewer open( final AbstractSpimData< ? > spimData, final St
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 ResourceManager resources = options.values.getResourceManager();
resources.put( spimData, new SpimDataMinimalFileResource.Spec( xmlFilename ) );
final BigDataViewer bdv = open( spimData, windowTitle, progressWriter, options );
if ( !bdv.tryLoadSettings( xmlFilename ) )
InitializeViewerState.initBrightness( 0.001, 0.999, bdv.viewerFrame );
Expand Down Expand Up @@ -609,6 +700,16 @@ public AppearanceManager getAppearanceManager()
return appearanceManager;
}

public LinkSettingsManager getLinkSettingsManager()
{
return linkSettingsManager;
}

public ResourceManager getResourceManager()
{
return resourceManager;
}

public boolean tryLoadSettings( final String xmlFilename )
{
proposedSettingsFile = null;
Expand Down
2 changes: 2 additions & 0 deletions src/main/java/bdv/img/remote/AffineTransform3DJsonSerializer.java
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Expand Up @@ -30,6 +30,7 @@

import java.lang.reflect.Type;

import bdv.tools.JsonUtils;
import net.imglib2.realtransform.AffineTransform3D;

import com.google.gson.JsonDeserializationContext;
Expand All @@ -39,6 +40,7 @@
import com.google.gson.JsonSerializationContext;
import com.google.gson.JsonSerializer;

@JsonUtils.JsonIo( jsonType = "AffineTransform3D.Anchor", type = AffineTransform3D.class )
public class AffineTransform3DJsonSerializer implements JsonDeserializer< AffineTransform3D >, JsonSerializer< AffineTransform3D >
{
@Override
Expand Down
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