From 84cc71a55563a279471806f29e282f6546acc7c2 Mon Sep 17 00:00:00 2001
From: Tobias Pietzsch <tobias.pietzsch@gmail.com>
Date: Tue, 24 Jun 2014 16:28:44 +0200
Subject: [PATCH] Dialog to select a bounding box
---
.../bdv/viewer/box/BdvBoundingBoxExample.java | 136 +++++++++++++++++
.../bdv/viewer/box/BoundingBoxDialog.java | 143 ++++++++++++++++++
.../viewer/box/BoxRealRandomAccessible.java | 84 ++++++++++
.../bdv/viewer/box/BoxSelectionPanel.java | 108 +++++++++++++
.../box/RealRandomAccessibleSource.java | 78 ++++++++++
5 files changed, 549 insertions(+)
create mode 100644 core/src/main/java/bdv/viewer/box/BdvBoundingBoxExample.java
create mode 100644 core/src/main/java/bdv/viewer/box/BoundingBoxDialog.java
create mode 100644 core/src/main/java/bdv/viewer/box/BoxRealRandomAccessible.java
create mode 100644 core/src/main/java/bdv/viewer/box/BoxSelectionPanel.java
create mode 100644 core/src/main/java/bdv/viewer/box/RealRandomAccessibleSource.java
diff --git a/core/src/main/java/bdv/viewer/box/BdvBoundingBoxExample.java b/core/src/main/java/bdv/viewer/box/BdvBoundingBoxExample.java
new file mode 100644
index 00000000..e2e11268
--- /dev/null
+++ b/core/src/main/java/bdv/viewer/box/BdvBoundingBoxExample.java
@@ -0,0 +1,136 @@
+package bdv.viewer.box;
+
+import java.util.ArrayList;
+
+import javax.swing.ActionMap;
+import javax.swing.InputMap;
+
+import mpicbg.spim.data.SpimDataException;
+import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
+import net.imglib2.Interval;
+import net.imglib2.util.Intervals;
+import bdv.BigDataViewer;
+import bdv.ViewerImgLoader;
+import bdv.spimdata.SpimDataMinimal;
+import bdv.spimdata.WrapBasicImgLoader;
+import bdv.spimdata.XmlIoSpimDataMinimal;
+import bdv.tools.InitializeViewerState;
+import bdv.tools.ToggleDialogAction;
+import bdv.tools.VisibilityAndGroupingDialog;
+import bdv.tools.brightness.BrightnessDialog;
+import bdv.tools.brightness.ConverterSetup;
+import bdv.tools.brightness.MinMaxGroup;
+import bdv.tools.brightness.RealARGBColorConverterSetup;
+import bdv.tools.brightness.SetupAssignments;
+import bdv.util.AbstractNamedAction.NamedActionAdder;
+import bdv.util.KeyProperties;
+import bdv.util.KeyProperties.KeyStrokeAdder;
+import bdv.viewer.DisplayMode;
+import bdv.viewer.NavigationActions;
+import bdv.viewer.SourceAndConverter;
+import bdv.viewer.ViewerFrame;
+import bdv.viewer.ViewerPanel;
+
+
+public class BdvBoundingBoxExample
+{
+ protected BdvBoundingBoxExample( final String xmlFilename ) throws SpimDataException
+ {
+ // =============== Load spimdata and create sources for display ==================
+
+ final SpimDataMinimal spimData = new XmlIoSpimDataMinimal().load( xmlFilename );
+ if ( WrapBasicImgLoader.wrapImgLoaderIfNecessary( spimData ) )
+ {
+ System.err.println( "WARNING:\nOpening <SpimData> dataset that is not suited for suited for interactive browsing.\nConsider resaving as HDF5 for better performance." );
+ }
+ final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription();
+
+ final ArrayList< ConverterSetup > converterSetups = new ArrayList< ConverterSetup >();
+ final ArrayList< SourceAndConverter< ? > > sources = new ArrayList< SourceAndConverter< ? > >();
+ BigDataViewer.initSetups( spimData, converterSetups, sources );
+
+ final int width = 800;
+ final int height = 600;
+ final int numTimepoints = seq.getTimePoints().getTimePointsOrdered().size();
+ final ViewerFrame viewerFrame = new ViewerFrame( width, height, sources, numTimepoints,
+ ( ( ViewerImgLoader< ?, ? > ) seq.getImgLoader() ).getCache() );
+ final ViewerPanel viewer = viewerFrame.getViewerPanel();
+
+
+ // =============== Create SetupAssignments, which encapsulate source color and brightness settings ==================
+
+ for ( final ConverterSetup cs : converterSetups )
+ if ( RealARGBColorConverterSetup.class.isInstance( cs ) )
+ ( ( RealARGBColorConverterSetup ) cs ).setViewer( viewer );
+
+ final SetupAssignments 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 );
+ }
+
+
+ // =============== Dialogs for brightness and visibility&grouping ==================
+
+ final BrightnessDialog brightnessDialog = new BrightnessDialog( viewerFrame, setupAssignments );
+ final VisibilityAndGroupingDialog activeSourcesDialog = new VisibilityAndGroupingDialog( viewerFrame, viewer.getVisibilityAndGrouping() );
+
+
+ // =============== the bounding box dialog ==================
+
+ final int boxSetupId = 9999; // some non-existing setup id
+ final Interval initialInterval = Intervals.createMinMax( 500, 100, -100, 1500, 800, 300 ); // the initially selected bounding box
+ final Interval rangeInterval = Intervals.createMinMax( -500, -500, -500, 3000, 3000, 1000 ); // the range (bounding box of possible bounding boxes)
+ final BoundingBoxDialog boundingBoxDialog = new BoundingBoxDialog( viewerFrame, viewer, setupAssignments, boxSetupId, initialInterval, rangeInterval );
+
+
+ // =============== install standard navigation shortcuts and S/F6/B for brightness/visibility&grouping/boundingbox dialogs ==================
+
+ final KeyProperties keyProperties = KeyProperties.readPropertyFile();
+ NavigationActions.installActionBindings( viewerFrame.getKeybindings(), viewer, keyProperties );
+ final String BRIGHTNESS_SETTINGS = "brightness settings";
+ final String VISIBILITY_AND_GROUPING = "visibility and grouping";
+ final String BOUNDING_BOX_DIALOG = "bounding box";
+ final ActionMap actionMap = new ActionMap();
+ final NamedActionAdder amap = new NamedActionAdder( actionMap );
+ amap.put( new ToggleDialogAction( BRIGHTNESS_SETTINGS, brightnessDialog ) );
+ amap.put( new ToggleDialogAction( VISIBILITY_AND_GROUPING, activeSourcesDialog ) );
+ amap.put( new ToggleDialogAction( BOUNDING_BOX_DIALOG, boundingBoxDialog ) );
+ final InputMap inputMap = new InputMap();
+ final KeyStrokeAdder imap = new KeyProperties( null ).adder( inputMap );
+ imap.put( BRIGHTNESS_SETTINGS, "S" );
+ imap.put( VISIBILITY_AND_GROUPING, "F6" );
+ imap.put( BOUNDING_BOX_DIALOG, "B" );
+ viewerFrame.getKeybindings().addActionMap( "bdvbox", actionMap );
+ viewerFrame.getKeybindings().addInputMap( "bdvbox", inputMap );
+
+ // =============== go to fused mode (overlay all sources) such that bounding box will be visible ==================
+ viewer.setDisplayMode( DisplayMode.FUSED );
+
+ // show viewer window
+ viewerFrame.setVisible( true );
+
+ // initialize transform and brightness
+ InitializeViewerState.initTransform( viewer );
+ InitializeViewerState.initBrightness( 0.001, 0.999, viewer, setupAssignments );
+
+// ( ( Hdf5ImageLoader ) seq.imgLoader ).initCachedDimensionsFromHdf5( false );
+ }
+
+ public static void main( final String[] args )
+ {
+ final String fn = "/Users/Pietzsch/Desktop/bdv example/drosophila 2.xml";
+ try
+ {
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ new BdvBoundingBoxExample( fn );
+ }
+ catch ( final Exception e )
+ {
+ e.printStackTrace();
+ }
+ }
+
+}
diff --git a/core/src/main/java/bdv/viewer/box/BoundingBoxDialog.java b/core/src/main/java/bdv/viewer/box/BoundingBoxDialog.java
new file mode 100644
index 00000000..3ee971db
--- /dev/null
+++ b/core/src/main/java/bdv/viewer/box/BoundingBoxDialog.java
@@ -0,0 +1,143 @@
+package bdv.viewer.box;
+
+import java.awt.BorderLayout;
+import java.awt.Container;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.KeyEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.ActionMap;
+import javax.swing.InputMap;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JDialog;
+import javax.swing.KeyStroke;
+
+import net.imglib2.Interval;
+import net.imglib2.display.RealARGBColorConverter;
+import net.imglib2.type.numeric.ARGBType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+import bdv.tools.brightness.RealARGBColorConverterSetup;
+import bdv.tools.brightness.SetupAssignments;
+import bdv.viewer.SourceAndConverter;
+import bdv.viewer.ViewerPanel;
+
+// dialog to change bounding box
+// while dialog is visible, bounding box is added as a source to the viewer
+public class BoundingBoxDialog extends JDialog
+{
+ private final ViewerPanel viewer;
+
+ private final BoxRealRandomAccessible< UnsignedShortType > boxRealRandomAccessible;
+
+ private final BoxSelectionPanel boxSelectionPanel;
+
+ protected final SourceAndConverter< UnsignedShortType > boxSourceAndConverter;
+
+ protected final RealARGBColorConverterSetup boxConverterSetup;
+
+ public BoundingBoxDialog( final Frame owner, final ViewerPanel viewer, final SetupAssignments setupAssignments, final int boxSetupId, final Interval initialInterval, final Interval rangeInterval )
+ {
+ super( owner, "bounding box", false );
+ this.viewer = viewer;
+
+
+ // create a procedural RealRandomAccessible that will render the bounding box
+ final UnsignedShortType insideValue = new UnsignedShortType( 1000 ); // inside the box pixel value is 1000
+ final UnsignedShortType outsideValue = new UnsignedShortType( 0 ); // outside is 0
+ boxRealRandomAccessible = new BoxRealRandomAccessible< UnsignedShortType >( initialInterval, insideValue, outsideValue );
+
+ // create a bdv.viewer.Source providing data from the bbox RealRandomAccessible
+ final RealRandomAccessibleSource< UnsignedShortType > boxSource = new RealRandomAccessibleSource< UnsignedShortType >( boxRealRandomAccessible, "selection" )
+ {
+ @Override
+ public Interval getInterval( final int t, final int level )
+ {
+ return boxRealRandomAccessible.getInterval();
+ }
+ };
+
+ // set up a converter from the source type (UnsignedShortType in this case) to ARGBType
+ final RealARGBColorConverter< UnsignedShortType > converter = new RealARGBColorConverter.Imp1< UnsignedShortType >( 0, 3000 );
+ converter.setColor( new ARGBType( ARGBType.rgba( 0, 255, 0, 255 ) ) ); // set bounding box color to green
+
+ // create a ConverterSetup (can be used by the brightness dialog to adjust the converter settings)
+ boxConverterSetup = new RealARGBColorConverterSetup( boxSetupId, converter );
+ boxConverterSetup.setViewer( viewer );
+
+ // create a SourceAndConverter (can be added to the viewer for display
+ boxSourceAndConverter = new SourceAndConverter< UnsignedShortType >( boxSource, converter );
+
+
+ // create a JPanel with sliders to modify the bounding box interval (boxRealRandomAccessible.getInterval())
+ boxSelectionPanel = new BoxSelectionPanel( boxRealRandomAccessible.getInterval(), rangeInterval );
+ boxSelectionPanel.addSelectionUpdateListener( new BoxSelectionPanel.SelectionUpdateListener() // listen for updates on the bbox to trigger repainting
+ {
+ @Override
+ public void selectionUpdated()
+ {
+ viewer.requestRepaint();
+ }
+ } );
+
+
+ // button prints the bounding box interval
+ final JButton button = new JButton( "ok" );
+ button.addActionListener( new AbstractAction()
+ {
+ @Override
+ public void actionPerformed( final ActionEvent e )
+ {
+ System.out.println( "bounding box:" + net.imglib2.util.Util.printInterval( boxRealRandomAccessible.getInterval() ) );
+ }
+ } );
+
+
+ // when dialog is made visible, add bbox source
+ // when dialog is hidden, remove bbox source
+ addComponentListener( new ComponentAdapter()
+ {
+ @Override
+ public void componentShown( final ComponentEvent e )
+ {
+ viewer.addSource( boxSourceAndConverter );
+ setupAssignments.addSetup( boxConverterSetup );
+ }
+
+ @Override
+ public void componentHidden( final ComponentEvent e )
+ {
+ viewer.removeSource( boxSourceAndConverter.getSpimSource() );
+ setupAssignments.removeSetup( boxConverterSetup );
+ }
+ } );
+
+
+ // make ESC key hide dialog
+ final ActionMap am = getRootPane().getActionMap();
+ final InputMap im = getRootPane().getInputMap( JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT );
+ final Object hideKey = new Object();
+ final Action hideAction = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed( final ActionEvent e )
+ {
+ setVisible( false );
+ }
+ };
+ im.put( KeyStroke.getKeyStroke( KeyEvent.VK_ESCAPE, 0 ), hideKey );
+ am.put( hideKey, hideAction );
+
+
+ // layout and show dialog
+ final Container content = getContentPane();
+ content.add( boxSelectionPanel, BorderLayout.NORTH );
+ content.add( button, BorderLayout.SOUTH );
+ pack();
+ setDefaultCloseOperation( JDialog.HIDE_ON_CLOSE );
+ }
+}
diff --git a/core/src/main/java/bdv/viewer/box/BoxRealRandomAccessible.java b/core/src/main/java/bdv/viewer/box/BoxRealRandomAccessible.java
new file mode 100644
index 00000000..23de2e29
--- /dev/null
+++ b/core/src/main/java/bdv/viewer/box/BoxRealRandomAccessible.java
@@ -0,0 +1,84 @@
+package bdv.viewer.box;
+
+import net.imglib2.Interval;
+import net.imglib2.RealInterval;
+import net.imglib2.RealPoint;
+import net.imglib2.RealRandomAccess;
+import net.imglib2.RealRandomAccessible;
+import net.imglib2.type.Type;
+import net.imglib2.util.Intervals;
+import bdv.util.ModifiableInterval;
+
+// a simple imglib2 RealRandomAccessible that has one value inside a box and another value outside
+public class BoxRealRandomAccessible< T extends Type< T > > implements RealRandomAccessible< T >
+{
+ private final int n;
+
+ private final ModifiableInterval interval;
+
+ private final T insideValue;
+
+ private final T outsideValue;
+
+ public BoxRealRandomAccessible( final Interval interval, final T insideValue, final T outsideValue )
+ {
+ n = interval.numDimensions();
+ this.interval = new ModifiableInterval( interval );
+ this.insideValue = insideValue.copy();
+ this.outsideValue = outsideValue.copy();
+ }
+
+ @Override
+ public int numDimensions()
+ {
+ return n;
+ }
+
+ public class Access extends RealPoint implements RealRandomAccess< T >
+ {
+ public Access()
+ {
+ super( BoxRealRandomAccessible.this.n );
+ }
+
+ protected Access( final Access a )
+ {
+ super( a );
+ }
+
+ @Override
+ public T get()
+ {
+ return Intervals.contains( interval, this ) ? insideValue : outsideValue;
+ }
+
+ @Override
+ public Access copy()
+ {
+ return new Access( this );
+ }
+
+ @Override
+ public Access copyRealRandomAccess()
+ {
+ return copy();
+ }
+ }
+
+ @Override
+ public RealRandomAccess< T > realRandomAccess()
+ {
+ return new Access();
+ }
+
+ @Override
+ public RealRandomAccess< T > realRandomAccess( final RealInterval interval )
+ {
+ return new Access();
+ }
+
+ public ModifiableInterval getInterval()
+ {
+ return interval;
+ }
+}
diff --git a/core/src/main/java/bdv/viewer/box/BoxSelectionPanel.java b/core/src/main/java/bdv/viewer/box/BoxSelectionPanel.java
new file mode 100644
index 00000000..f88c8c8e
--- /dev/null
+++ b/core/src/main/java/bdv/viewer/box/BoxSelectionPanel.java
@@ -0,0 +1,108 @@
+package bdv.viewer.box;
+
+import java.util.ArrayList;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JPanel;
+
+import net.imglib2.FinalInterval;
+import net.imglib2.Interval;
+import bdv.tools.brightness.SliderPanel;
+import bdv.util.BoundedInterval;
+import bdv.util.ModifiableInterval;
+
+// a JPanel containing X,Y,Z min/max sliders for adjusting an interval
+public class BoxSelectionPanel extends JPanel
+{
+ public static interface SelectionUpdateListener
+ {
+ public void selectionUpdated();
+ }
+
+ private static final long serialVersionUID = 1L;
+
+ private final BoundedInterval[] ranges;
+
+ private final ModifiableInterval selection;
+
+ private final ArrayList< SelectionUpdateListener > listeners;
+
+ public BoxSelectionPanel( final ModifiableInterval selection, final Interval rangeInterval )
+ {
+ final int n = selection.numDimensions();
+ this.selection = selection;
+ ranges = new BoundedInterval[ n ];
+ listeners = new ArrayList< SelectionUpdateListener >();
+
+ setLayout( new BoxLayout( this, BoxLayout.PAGE_AXIS ) );
+ for ( int d = 0; d < n; ++d )
+ {
+ final int rangeMin = ( int ) rangeInterval.min( d );
+ final int rangeMax = ( int ) rangeInterval.max( d );
+ final int initialMin = Math.max( ( int ) selection.min( d ), rangeMin );
+ final int initialMax = Math.min( ( int ) selection.max( d ), rangeMax );
+ final BoundedInterval range = new BoundedInterval( rangeMin, rangeMax, initialMin, initialMax, 1 )
+ {
+ @Override
+ protected void updateInterval( final int min, final int max )
+ {
+ updateSelection();
+ }
+ };
+ final JPanel sliders = new JPanel();
+ sliders.setLayout( new BoxLayout( sliders, BoxLayout.PAGE_AXIS ) );
+ final SliderPanel minPanel = new SliderPanel( "min", range.getMinBoundedValue(), 1 );
+ minPanel.setBorder( BorderFactory.createEmptyBorder( 0, 10, 10, 10 ) );
+ sliders.add( minPanel );
+ final SliderPanel maxPanel = new SliderPanel( "max", range.getMaxBoundedValue(), 1 );
+ maxPanel.setBorder( BorderFactory.createEmptyBorder( 0, 10, 10, 10 ) );
+ sliders.add( maxPanel );
+ add( sliders );
+ ranges[ d ] = range;
+ }
+ }
+
+ public void setBoundsInterval( final Interval interval )
+ {
+ final int n = selection.numDimensions();
+ for ( int d = 0; d < n; ++d )
+ ranges[ d ].setRange( ( int ) interval.min( d ), ( int ) interval.max( d ) );
+ }
+
+ public void addSelectionUpdateListener( final SelectionUpdateListener l )
+ {
+ listeners.add( l );
+ }
+
+ public void updateSelection()
+ {
+ final int n = selection.numDimensions();
+ final long[] min = new long[ n ];
+ final long[] max = new long[ n ];
+ for ( int d = 0; d < n; ++d )
+ {
+ min[ d ] = ranges[ d ].getMinBoundedValue().getCurrentValue();
+ max[ d ] = ranges[ d ].getMaxBoundedValue().getCurrentValue();
+ }
+ selection.set( new FinalInterval( min, max ) );
+ for ( final SelectionUpdateListener l : listeners )
+ l.selectionUpdated();
+ }
+
+ public void updateSliders( final Interval interval )
+ {
+ final int n = selection.numDimensions();
+ if ( interval.numDimensions() != n )
+ throw new IllegalArgumentException();
+ final long[] min = new long[ n ];
+ final long[] max = new long[ n ];
+ interval.min( min );
+ interval.max( max );
+ for ( int d = 0; d < n; ++d )
+ {
+ ranges[ d ].getMinBoundedValue().setCurrentValue( ( int ) min[ d ] );
+ ranges[ d ].getMaxBoundedValue().setCurrentValue( ( int ) max[ d ] );
+ }
+ }
+}
diff --git a/core/src/main/java/bdv/viewer/box/RealRandomAccessibleSource.java b/core/src/main/java/bdv/viewer/box/RealRandomAccessibleSource.java
new file mode 100644
index 00000000..2f06af37
--- /dev/null
+++ b/core/src/main/java/bdv/viewer/box/RealRandomAccessibleSource.java
@@ -0,0 +1,78 @@
+package bdv.viewer.box;
+
+import net.imglib2.Interval;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.RealRandomAccessible;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.Type;
+import net.imglib2.util.Util;
+import net.imglib2.view.Views;
+import bdv.viewer.Interpolation;
+import bdv.viewer.Source;
+
+/**
+ * A {@link Source} wrapping some {@link RealRandomAccessible}.
+ *
+ * @param <T>
+ *
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ */
+public abstract class RealRandomAccessibleSource< T extends Type< T > > implements Source< T >
+{
+ protected RealRandomAccessible< T > accessible;
+
+ protected final T type;
+
+ protected final String name;
+
+ public RealRandomAccessibleSource( final RealRandomAccessible< T > accessible, final String name )
+ {
+ this.accessible = accessible;
+ this.type = Util.getTypeFromRealRandomAccess( accessible ).createVariable();
+ this.name = name;
+ }
+
+ @Override
+ public boolean isPresent( final int t )
+ {
+ return true;
+ }
+
+ public abstract Interval getInterval( final int t, final int level );
+
+ @Override
+ public RandomAccessibleInterval< T > getSource( final int t, final int level )
+ {
+ return Views.interval( Views.raster( accessible ), getInterval( t, level ) );
+ }
+
+ @Override
+ public RealRandomAccessible< T > getInterpolatedSource( final int t, final int level, final Interpolation method )
+ {
+ return accessible;
+ }
+
+ @Override
+ public AffineTransform3D getSourceTransform( final int t, final int level )
+ {
+ return new AffineTransform3D();
+ }
+
+ @Override
+ public T getType()
+ {
+ return type;
+ }
+
+ @Override
+ public String getName()
+ {
+ return name;
+ }
+
+ @Override
+ public int getNumMipmapLevels()
+ {
+ return 1;
+ }
+}
--
GitLab