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Fixes #1174
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@tischi
tischi committed Jul 10, 2024
1 parent 6ab81ca commit 1b653d2
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Showing 16 changed files with 86 additions and 95 deletions.
34 changes: 1 addition & 33 deletions src/main/java/org/embl/mobie/command/context/ConfigureImageRenderingCommand.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,11 +31,9 @@
import bdv.util.BdvHandle;
import bdv.viewer.SourceAndConverter;
import org.embl.mobie.command.CommandConstants;
import org.embl.mobie.lib.bdv.blend.BlendingMode;
import org.embl.mobie.lib.volume.ImageVolumeViewer;
import org.scijava.Initializable;
import org.scijava.command.DynamicCommand;
import org.scijava.module.MutableModuleItem;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand;
Expand All @@ -50,20 +48,15 @@ public class ConfigureImageRenderingCommand extends DynamicCommand implements Bd
{
static { net.imagej.patcher.LegacyInjector.preinit(); }

protected static ISourceAndConverterService sourceAndConverterService = SourceAndConverterServices.getSourceAndConverterService();

@Parameter
protected BdvHandle bdvh;
protected BdvHandle bdvHandle;

@Parameter
protected SourceAndConverter< ? >[] sourceAndConverters;

@Parameter
protected ImageVolumeViewer volumeViewer;

@Parameter( label = "Blending mode", choices = { BlendingMode.SUM, BlendingMode.ALPHA }, persist = false )
String blendingMode = BlendingMode.SUM;

@Parameter ( label = "Volume rendering", choices = { AUTO, USE_BELOW_RESOLUTION } )
public String volumeRenderingMode = AUTO;

Expand All @@ -73,40 +66,15 @@ public class ConfigureImageRenderingCommand extends DynamicCommand implements Bd
@Override
public void initialize()
{
initBlendingModeItem();
}

private void initBlendingModeItem()
{
final MutableModuleItem< String > blendingModeItem = getInfo().getMutableInput("blendingMode", String.class );

for ( SourceAndConverter sourceAndConverter : sourceAndConverters )
{
final BlendingMode blendingMode = ( BlendingMode ) sourceAndConverterService.getMetadata( sourceAndConverter, BlendingMode.class.getName() );
final String toString = blendingMode.toString();
blendingModeItem.setValue( this, toString );
return;
}
}

@Override
public void run()
{
updateBlendingMode();

updateVolumeRendering();
}

private void updateBlendingMode()
{
for ( SourceAndConverter< ? > sourceAndConverter : sourceAndConverters )
{
final BlendingMode blendingMode = BlendingMode.valueOf( this.blendingMode );
SourceAndConverterServices.getSourceAndConverterService().setMetadata( sourceAndConverter, BlendingMode.class.getName(), blendingMode );
}
bdvh.getViewerPanel().requestRepaint();
}

private void updateVolumeRendering()
{
if ( volumeViewer == null ) return;
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/embl/mobie/lib/bdv/ScreenShotMaker.java
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Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@ public void run( List< SourceAndConverter< ? > > sacs, double targetVoxelSpacing
screenshotDimensions,
blockSize );

IJ.log( ThreadHelper.getNumIoThreads() + " threads working on blocks of " + Arrays.toString( blockSize ) );
// IJ.log( ThreadHelper.getNumIoThreads() + " threads working on blocks of " + Arrays.toString( blockSize ) );
final long currentTimeMillis = System.currentTimeMillis();
for ( SourceAndConverter< ? > sac : sacs )
{
Expand Down
145 changes: 84 additions & 61 deletions src/main/java/org/embl/mobie/ui/UserInterfaceHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@
import org.embl.mobie.io.util.IOHelper;
import org.embl.mobie.MoBIE;
import org.embl.mobie.lib.bdv.AutoContrastAdjuster;
import org.embl.mobie.lib.bdv.blend.BlendingMode;
import org.embl.mobie.lib.io.FileLocation;
import org.embl.mobie.lib.MoBIEInfo;
import org.embl.mobie.lib.Services;
Expand All @@ -71,6 +72,8 @@
import org.embl.mobie.lib.transform.viewer.ViewerTransform;
import org.embl.mobie.lib.volume.ImageVolumeViewer;
import org.embl.mobie.lib.volume.SegmentVolumeViewer;
import org.jetbrains.annotations.NotNull;
import org.scijava.plugin.Parameter;
import sc.fiji.bdvpg.services.ISourceAndConverterService;
import sc.fiji.bdvpg.services.SourceAndConverterServices;
import sc.fiji.bdvpg.sourceandconverter.display.ColorChanger;
Expand Down Expand Up @@ -458,37 +461,13 @@ public static JFrame showOpacityAndContrastLimitsDialog(
BdvHandle bdvHandle,
boolean addContrastLimitUI )
{
ISourceAndConverterService service = SourceAndConverterServices.getSourceAndConverterService();

JFrame frame = new JFrame( name );
frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE );
JPanel panel = new JPanel();
panel.setLayout( new BoxLayout( panel, BoxLayout.PAGE_AXIS ) );

ISourceAndConverterService service = SourceAndConverterServices.getSourceAndConverterService();

// Opacity Slider
//
// TODO: This cast requires that the sourceAndConverter implements
// an OpacityAdjuster; how to do this more cleanly?
// Maybe we should rather operate on the coloring model that is
// wrapped in the converter?
final double current = ( ( OpacityAdjuster ) sacs.get( 0 ).getConverter()).getOpacity();

final BoundedValueDouble selection =
new BoundedValueDouble(
0.0,
1.0,
current );

final SliderPanelDouble opacitySlider = new SliderPanelDouble( "Opacity", selection, 0.05 );
opacitySlider.setNumColummns( 3 );
opacitySlider.setDecimalFormat( "#.##" );

final OpacityUpdateListener opacityUpdateListener =
new OpacityUpdateListener( selection, opacitySlider, sacs, bdvHandle );

selection.setUpdateListener( opacityUpdateListener );
panel.add( opacitySlider );

if ( addContrastLimitUI )
{
// Contrast Limits
Expand Down Expand Up @@ -547,6 +526,7 @@ public static JFrame showOpacityAndContrastLimitsDialog(
panel.add( minSlider );
panel.add( maxSlider );


JButton autoButton = new JButton("Auto Contrast");
autoButton.addActionListener( e ->
{
Expand All @@ -555,7 +535,9 @@ public static JFrame showOpacityAndContrastLimitsDialog(
min.setCurrentValue( minMax[ 0 ] );
max.setCurrentValue( minMax[ 1 ] );
});
panel.add( autoButton );
JPanel autoPanel = SwingHelper.horizontalLayoutPanel();
autoPanel.add( autoButton );
panel.add( autoPanel );

boolean isInvert = false;
for ( Converter< ?, ARGBType > converter : converters )
Expand All @@ -580,9 +562,56 @@ public static JFrame showOpacityAndContrastLimitsDialog(
}
bdvHandle.getViewerPanel().requestRepaint();
} );
panel.add( invertCheckBox );
JPanel invertPanel = SwingHelper.horizontalLayoutPanel();
invertPanel.add( invertCheckBox );
panel.add( invertPanel );
panel.add( new JLabel("") ); // create some Luft
}

// Blending mode
JPanel blendingPanel = SwingHelper.horizontalLayoutPanel();
blendingPanel.add( new JLabel("Blending ") );
JComboBox< BlendingMode > blendingModeComboBox = new JComboBox<>(
new BlendingMode[]{ BlendingMode.Sum, BlendingMode.Alpha } );
BlendingMode currentBlendingMode = ( BlendingMode ) service.getMetadata( sacs.get( 0 ), BlendingMode.class.getName() );
blendingModeComboBox.setSelectedItem( currentBlendingMode );
blendingModeComboBox.addActionListener( e ->
{
for ( SourceAndConverter< ? > sourceAndConverter : sacs )
{
service.setMetadata( sourceAndConverter,
BlendingMode.class.getName(),
blendingModeComboBox.getSelectedItem() );
}
bdvHandle.getViewerPanel().requestRepaint();
} );
blendingPanel.add( blendingModeComboBox );
panel.add( blendingPanel );

// Opacity Slider
//
// TODO: This cast requires that the sourceAndConverter implements
// an OpacityAdjuster; how to do this more cleanly?
// Maybe we should rather operate on the coloring model that is
// wrapped in the converter?
final double current = ( ( OpacityAdjuster ) sacs.get( 0 ).getConverter()).getOpacity();

final BoundedValueDouble selection =
new BoundedValueDouble(
0.0,
1.0,
current );

final SliderPanelDouble opacitySlider = new SliderPanelDouble( "Opacity", selection, 0.05 );
opacitySlider.setNumColummns( 3 );
opacitySlider.setDecimalFormat( "#.##" );

final OpacityUpdateListener opacityUpdateListener =
new OpacityUpdateListener( selection, opacitySlider, sacs, bdvHandle );

selection.setUpdateListener( opacityUpdateListener );
panel.add( opacitySlider );

//Display the window.
frame.setContentPane( panel );
frame.setBounds( MouseInfo.getPointerInfo().getLocation().x,
Expand All @@ -604,7 +633,7 @@ public JPanel createRegionDisplaySettingsPanel( RegionDisplay display )
// Buttons
panel.add( space() );
panel.add( createFocusButton( display, display.sliceViewer.getBdvHandle(), sourceAndConverters.stream().map( sac -> sac.getSpimSource() ).collect( Collectors.toList() ) ) );
panel.add( createOpacityAndContrastLimitsButton( sourceAndConverters, display.getName(), display.sliceViewer.getBdvHandle(), false ) );
panel.add( createContrastButton( sourceAndConverters, display.getName(), display.sliceViewer.getBdvHandle(), false ) );
panel.add( createButtonPlaceholder() ); // color
panel.add( createLabelRenderingSettingsButton( sourceAndConverters ) ); // special settings
panel.add( createRemoveButton( display ) );
Expand All @@ -625,7 +654,7 @@ public JPanel createSpotDisplaySettingsPanel( SpotDisplay display )
// Buttons
panel.add( space() );
panel.add( createFocusButton( display, display.sliceViewer.getBdvHandle(), sourceAndConverters.stream().map( sac -> sac.getSpimSource() ).collect( Collectors.toList() ) ) );
panel.add( createOpacityAndContrastLimitsButton( sourceAndConverters, display.getName(), display.sliceViewer.getBdvHandle(), false ) );
panel.add( createContrastButton( sourceAndConverters, display.getName(), display.sliceViewer.getBdvHandle(), false ) );
panel.add( createButtonPlaceholder() ); // color
panel.add( createSpotSettingsButton( sourceAndConverters ) ); // special settings
panel.add( createRemoveButton( display ) );
Expand Down Expand Up @@ -712,7 +741,7 @@ public JPanel createImageDisplaySettingsPanel( ImageDisplay< ? > display )
// Buttons
panel.add( space() );
panel.add( createFocusButton( display, display.sliceViewer.getBdvHandle(), sourceAndConverters.stream().map( sac -> sac.getSpimSource() ).collect( Collectors.toList() ) ) );
panel.add( createOpacityAndContrastLimitsButton( sourceAndConverters, display.getName(), display.sliceViewer.getBdvHandle(), true ) );
panel.add( createContrastButton( sourceAndConverters, display.getName(), display.sliceViewer.getBdvHandle(), true ) );
panel.add( createColorButton( panel, sourceAndConverters, display.sliceViewer.getBdvHandle() ) );
//panel.add( createImageDisplayBrightnessButton( display ) );
panel.add( createImageRenderingSettingsButton( sourceAndConverters, display.imageVolumeViewer ) );
Expand Down Expand Up @@ -758,7 +787,7 @@ public JPanel createSegmentationDisplaySettingsPanel( SegmentationDisplay displa

panel.add( space() );
panel.add( createFocusButton( display, display.sliceViewer.getBdvHandle(), sourceAndConverters.stream().map( sac -> sac.getSpimSource() ).collect( Collectors.toList() ) ) );
panel.add( createOpacityAndContrastLimitsButton( sourceAndConverters, display.getName(), display.sliceViewer.getBdvHandle(), false ) );
panel.add( createContrastButton( sourceAndConverters, display.getName(), display.sliceViewer.getBdvHandle(), false ) );
panel.add( createButtonPlaceholder() );
panel.add( createSegmentRenderingSettingsButton( sourceAndConverters, display.segmentVolumeViewer ) );
panel.add( createRemoveButton( display ) );
Expand Down Expand Up @@ -787,10 +816,7 @@ public JPanel createSegmentationDisplaySettingsPanel( SegmentationDisplay displa

private JButton createImageRenderingSettingsButton( List< ? extends SourceAndConverter< ? > > sourceAndConverters, ImageVolumeViewer imageVolumeViewer )
{
final URL resource = UserInterfaceHelper.class.getResource( "/settings_19.png" );
final ImageIcon imageIcon = new ImageIcon( resource );
JButton button = new JButton( imageIcon );
button.setPreferredSize( PREFERRED_BUTTON_SIZE );
JButton button = getIconButton( "settings.png" );
button.addActionListener( e ->
{
SwingUtilities.invokeLater( () ->
Expand All @@ -807,15 +833,15 @@ private JButton createImageRenderingSettingsButton( List< ? extends SourceAndCon

private JButton createLabelRenderingSettingsButton( List< SourceAndConverter< ? > > sourceAndConverters )
{
JButton button = new JButton( "S" );
JButton button = getIconButton( "settings.png" );
button.setPreferredSize( PREFERRED_BUTTON_SIZE );
button.addActionListener( e -> Services.commandService.run( ConfigureLabelRenderingCommand.class, true, "sourceAndConverters", sourceAndConverters.toArray( new SourceAndConverter[ 0 ] ) ) );
return button;
}

private JButton createSegmentRenderingSettingsButton( List< SourceAndConverter< ? > > sourceAndConverters, SegmentVolumeViewer< ? > segmentVolumeViewer )
{
JButton button = new JButton( "S" );
JButton button = getIconButton( "settings.png" );
button.setPreferredSize( PREFERRED_BUTTON_SIZE );
button.addActionListener( e -> Services.commandService.run( ConfigureSegmentRenderingCommand.class, true, "sourceAndConverters", sourceAndConverters.toArray( new SourceAndConverter[ 0 ] ), "volumeViewer", segmentVolumeViewer ) );
return button;
Expand Down Expand Up @@ -1225,11 +1251,8 @@ public static JButton createFocusButton( AbstractDisplay< ? > sourceDisplay,
BdvHandle bdvHandle,
List< Source< ? > > sources )
{
final URL resource = UserInterfaceHelper.class.getResource( "/focus_19.png" );
final ImageIcon imageIcon = new ImageIcon( resource );
JButton button = new JButton( imageIcon );
JButton button = getIconButton( "focus.png" );
button.setToolTipText( "Show whole dataset" );
button.setPreferredSize( PREFERRED_BUTTON_SIZE );

button.addActionListener( e ->
{
Expand All @@ -1254,9 +1277,8 @@ public static JButton createFocusButton( AbstractDisplay< ? > sourceDisplay,

public static JButton createImageDisplayBrightnessButton( ImageDisplay< ? > imageDisplay )
{
JButton button = new JButton( "B" );
JButton button = getIconButton( "contrast.png" );
button.setToolTipText( "Change brightness/contrast" );
button.setPreferredSize( PREFERRED_BUTTON_SIZE );

button.addActionListener( e ->
{
Expand All @@ -1270,17 +1292,14 @@ public static JButton createImageDisplayBrightnessButton( ImageDisplay< ? > imag
return button;
}

public static JButton createOpacityAndContrastLimitsButton(
public static JButton createContrastButton(
List< ? extends SourceAndConverter< ? > > sourceAndConverters,
String name,
BdvHandle bdvHandle,
boolean addContrastLimitUI )
{
final URL resource = UserInterfaceHelper.class.getResource( "/contrast_19.png" );
final ImageIcon imageIcon = new ImageIcon( resource );
JButton button = new JButton( imageIcon );
JButton button = getIconButton( "contrast.png" );
button.setToolTipText( "Change opacity and contrast limits" );
button.setPreferredSize( PREFERRED_BUTTON_SIZE );

button.addActionListener( e ->
{
Expand All @@ -1296,16 +1315,23 @@ public static JButton createOpacityAndContrastLimitsButton(
return button;
}

private static JButton createColorButton( JPanel parentPanel, List< ? extends SourceAndConverter< ? > > sourceAndConverters, BdvHandle bdvHandle )
@NotNull
private static JButton getIconButton( final String iconResource )
{
final URL resource = UserInterfaceHelper.class.getResource( "/color_19.png" );
final ImageIcon imageIcon = new ImageIcon( resource );
JButton colorButton = new JButton( imageIcon );
colorButton.setToolTipText( "Change color" );
final URL resource = UserInterfaceHelper.class.getResource( "/" + iconResource );
Image scaledInstance = new ImageIcon( resource ).getImage().getScaledInstance( 19, 19, Image.SCALE_SMOOTH );
ImageIcon imageIcon = new ImageIcon( scaledInstance );
JButton button = new JButton( imageIcon );
button.setPreferredSize( PREFERRED_BUTTON_SIZE);
return button;
}

colorButton.setPreferredSize( PREFERRED_BUTTON_SIZE);
private static JButton createColorButton( JPanel parentPanel, List< ? extends SourceAndConverter< ? > > sourceAndConverters, BdvHandle bdvHandle )
{
JButton button = getIconButton( "color.png" );
button.setToolTipText( "Change color" );

colorButton.addActionListener( e ->
button.addActionListener( e ->
{
Color color = JColorChooser.showDialog( null, "", null );
if ( color == null ) return;
Expand All @@ -1320,7 +1346,7 @@ private static JButton createColorButton( JPanel parentPanel, List< ? extends So
bdvHandle.getViewerPanel().requestRepaint();
} );

return colorButton;
return button;
}

private void setPanelColor( JPanel panel, ARGBType argbType )
Expand All @@ -1345,11 +1371,8 @@ private void setPanelColor( JPanel panel, String colorString )

private JButton createRemoveButton( Display display )
{
final URL resource = UserInterfaceHelper.class.getResource( "/delete_19.png" );
final ImageIcon imageIcon = new ImageIcon( resource );
JButton button = new JButton( imageIcon );
JButton button = getIconButton( "delete.png" );
button.setToolTipText( "Remove dataset" );
button.setPreferredSize( PREFERRED_BUTTON_SIZE );

button.addActionListener( e ->
{
Expand Down
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