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Add grapher branch view #323

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merged 6 commits into from
Sep 23, 2024
Merged

Add grapher branch view #323

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b45f26e
Add a new class GrapherInitializer
stefanhahmann Sep 5, 2024
b661805
Initialize UI of MamutViewGrapher using GrapherInitiliazer
stefanhahmann Sep 5, 2024
a641600
Add a new Window that can show a plot of features on the branch graph
stefanhahmann Sep 5, 2024
4b4c92a
Rename variables in grapher screen transform handler
stefanhahmann Sep 19, 2024
5d1afe8
Introduce parameter minScaleX and minScaleY to InertialScreenTransfor…
stefanhahmann Sep 19, 2024
75be135
Set smaller min scale values for in MamutBranchViewGrapher so that fu…
stefanhahmann Sep 19, 2024
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288 changes: 288 additions & 0 deletions src/main/java/org/mastodon/mamut/views/grapher/GrapherInitializer.java
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package org.mastodon.mamut.views.grapher;

import net.imglib2.loops.LoopBuilder;
import org.apache.commons.lang3.function.TriFunction;
import org.mastodon.Ref;
import org.mastodon.app.ui.MastodonFrameViewActions;
import org.mastodon.app.ui.SearchVertexLabel;
import org.mastodon.app.ui.ViewMenu;
import org.mastodon.app.ui.ViewMenuBuilder;
import org.mastodon.graph.Edge;
import org.mastodon.graph.Vertex;
import org.mastodon.grouping.GroupHandle;
import org.mastodon.mamut.MainWindow;
import org.mastodon.mamut.MamutMenuBuilder;
import org.mastodon.mamut.ProjectModel;
import org.mastodon.mamut.UndoActions;
import org.mastodon.mamut.model.Model;
import org.mastodon.mamut.views.MamutViewI;
import org.mastodon.model.AutoNavigateFocusModel;
import org.mastodon.model.FocusModel;
import org.mastodon.model.HasLabel;
import org.mastodon.model.HighlightModel;
import org.mastodon.model.NavigationHandler;
import org.mastodon.model.SelectionModel;
import org.mastodon.spatial.HasTimepoint;
import org.mastodon.ui.EditTagActions;
import org.mastodon.ui.ExportViewActions;
import org.mastodon.ui.FocusActions;
import org.mastodon.ui.SelectionActions;
import org.mastodon.ui.coloring.ColorBarOverlay;
import org.mastodon.ui.coloring.ColoringModel;
import org.mastodon.ui.coloring.GraphColorGeneratorAdapter;
import org.mastodon.views.context.ContextChooser;
import org.mastodon.views.grapher.datagraph.DataContextListener;
import org.mastodon.views.grapher.datagraph.DataEdge;
import org.mastodon.views.grapher.datagraph.DataGraph;
import org.mastodon.views.grapher.datagraph.DataGraphLayout;
import org.mastodon.views.grapher.datagraph.DataVertex;
import org.mastodon.views.grapher.display.DataDisplayFrame;
import org.mastodon.views.grapher.display.DataDisplayOptions;
import org.mastodon.views.grapher.display.DataDisplayPanel;
import org.mastodon.views.grapher.display.DataDisplayZoom;
import org.mastodon.views.grapher.display.FeatureGraphConfig;
import org.mastodon.views.grapher.display.OffsetAxes;
import org.mastodon.views.grapher.display.style.DataDisplayStyle;
import org.mastodon.views.grapher.display.style.DataDisplayStyleManager;
import org.mastodon.views.trackscheme.display.TrackSchemeNavigationActions;
import org.scijava.ui.behaviour.util.Actions;
import org.scijava.ui.behaviour.util.Behaviours;

import javax.swing.ActionMap;
import javax.swing.JPanel;
import java.util.function.BiConsumer;

import static org.mastodon.app.ui.ViewMenuBuilder.item;
import static org.mastodon.app.ui.ViewMenuBuilder.separator;
import static org.mastodon.mamut.MamutMenuBuilder.colorMenu;
import static org.mastodon.mamut.MamutMenuBuilder.colorbarMenu;
import static org.mastodon.mamut.MamutMenuBuilder.editMenu;
import static org.mastodon.mamut.MamutMenuBuilder.fileMenu;
import static org.mastodon.mamut.MamutMenuBuilder.tagSetMenu;
import static org.mastodon.mamut.MamutMenuBuilder.viewMenu;

public class GrapherInitializer< V extends Vertex< E > & HasTimepoint & HasLabel & Ref< V >, E extends Edge< V > & Ref< E > >
{
private final DataGraph< V, E > viewGraph;

private final ProjectModel appModel;

private final Model model;

private final DataDisplayFrame< V, E > frame;

private final DataDisplayPanel< V, E > panel;

private final DataGraphLayout< V, E > layout;

private final DataDisplayStyle forwardDefaultStyle;

private final DataDisplayStyle.UpdateListener styleUpdateListener;

private final ContextChooser< V > contextChooser;

private ColoringModel coloringModel;

private ColorBarOverlay colorBarOverlay;

private final GraphColorGeneratorAdapter< V, E, DataVertex, DataEdge > coloringAdapter;

private final AutoNavigateFocusModel< DataVertex, DataEdge > navigateFocusModel;

private final SelectionModel< DataVertex, DataEdge > selectionModel;

private final NavigationHandler< DataVertex, DataEdge > navigationHandler;

private final FocusModel< DataVertex > focusModel;

GrapherInitializer( final DataGraph< V, E > graph, final ProjectModel appModel,
final SelectionModel< DataVertex, DataEdge > selectionModel, final NavigationHandler< DataVertex, DataEdge > navigationHandler,
final FocusModel< DataVertex > focusModel, final HighlightModel< DataVertex, DataEdge > highlightModel,
final GroupHandle groupHandle
)
{
this.viewGraph = graph;
this.appModel = appModel;
this.model = appModel.getModel();
this.selectionModel = selectionModel;
this.navigationHandler = navigationHandler;
this.focusModel = focusModel;

// The layout.
layout = new DataGraphLayout<>( viewGraph, selectionModel );

// ContextChooser
final DataContextListener< V > contextListener = new DataContextListener<>( viewGraph );
contextChooser = new ContextChooser<>( contextListener );

// Style
final DataDisplayStyleManager dataDisplayStyleManager = appModel.getWindowManager().getManager( DataDisplayStyleManager.class );
forwardDefaultStyle = dataDisplayStyleManager.getForwardDefaultStyle();

// A reference on the {@code GraphColorGeneratorAdapter} created and registered with this instance/window
coloringAdapter = new GraphColorGeneratorAdapter<>( viewGraph.getVertexMap(), viewGraph.getEdgeMap() );

// Options
final DataDisplayOptions options = DataDisplayOptions.options()
.shareKeyPressedEvents( appModel.getKeyPressedManager() )
.style( forwardDefaultStyle )
.graphColorGenerator( coloringAdapter );

// Navigation
navigateFocusModel = new AutoNavigateFocusModel<>( focusModel, navigationHandler );

// Frame
this.frame = new DataDisplayFrame<>(
viewGraph,
appModel.getModel().getFeatureModel(),
appModel.getSharedBdvData().getSources().size(),
layout,
highlightModel,
navigateFocusModel,
selectionModel,
navigationHandler,
model,
groupHandle,
contextChooser,
options );

// Panel
this.panel = frame.getDataDisplayPanel();
contextListener.setContextListener( panel );

// Style listener
styleUpdateListener = panel::repaint;
forwardDefaultStyle.updateListeners().add( styleUpdateListener );

// Label listener
appModel.getModel().getGraph().addVertexLabelListener( vertex -> panel.entitiesAttributesChanged() );
}

void setOnClose( final MamutViewI view )
{
view.onClose( () -> forwardDefaultStyle.updateListeners().remove( styleUpdateListener ) );
}

void initFeatureConfig( final FeatureGraphConfig featureGraphConfig )
{
frame.getVertexSidePanel().setGraphConfig( featureGraphConfig );
panel.graphChanged();
}

void addMenusAndRegisterColors(
final TriFunction< ViewMenuBuilder.JMenuHandle, GraphColorGeneratorAdapter< V, E, DataVertex, DataEdge >,
DataDisplayPanel< V, E >, ColoringModel > colorModelRegistration,
final LoopBuilder.TriConsumer< ColorBarOverlay, ViewMenuBuilder.JMenuHandle,
DataDisplayPanel< V, E > > colorBarRegistration,
final BiConsumer< ViewMenuBuilder.JMenuHandle, DataDisplayPanel< V, E > > tagSetMenuRegistration,
final String[] keyConfigContexts )
{
final ViewMenu viewMenu = new ViewMenu( frame.getJMenuBar(), appModel.getKeymap(), keyConfigContexts );
final ActionMap actionMap = frame.getKeybindings().getConcatenatedActionMap();

final ViewMenuBuilder.JMenuHandle coloringMenuHandle = new ViewMenuBuilder.JMenuHandle();
final ViewMenuBuilder.JMenuHandle colorbarMenuHandle = new ViewMenuBuilder.JMenuHandle();
final ViewMenuBuilder.JMenuHandle tagSetMenuHandle = new ViewMenuBuilder.JMenuHandle();

MainWindow.addMenus( viewMenu, actionMap );
appModel.getWindowManager().addWindowMenu( viewMenu, actionMap );
MamutMenuBuilder.build( viewMenu, actionMap,
fileMenu(
separator(),
item( ExportViewActions.EXPORT_VIEW_TO_SVG ),
item( ExportViewActions.EXPORT_VIEW_TO_PNG ) ),
viewMenu(
colorMenu( coloringMenuHandle ),
colorbarMenu( colorbarMenuHandle ),
separator(),
item( MastodonFrameViewActions.TOGGLE_SETTINGS_PANEL ) ),
editMenu(
item( UndoActions.UNDO ),
item( UndoActions.REDO ),
separator(),
item( SelectionActions.DELETE_SELECTION ),
item( SelectionActions.SELECT_WHOLE_TRACK ),
item( SelectionActions.SELECT_TRACK_DOWNWARD ),
item( SelectionActions.SELECT_TRACK_UPWARD ),
separator(),
tagSetMenu( tagSetMenuHandle ) ) );
appModel.getPlugins().addMenus( viewMenu );

registerColoring( colorModelRegistration, coloringMenuHandle );
registerColorBar( colorBarRegistration, colorbarMenuHandle );
registerTagSetMenu( tagSetMenuRegistration, tagSetMenuHandle );
}

void layout()
{
layout.layout();
panel.repaint();
panel.getDisplay().requestFocusInWindow();
}

void installActions( final Actions viewActions, final Behaviours viewBehaviours )
{
MastodonFrameViewActions.install( viewActions, () -> frame );
FocusActions.install( viewActions, viewGraph, viewGraph.getLock(), navigateFocusModel, selectionModel );
EditTagActions.install( viewActions, frame.getKeybindings(), frame.getTriggerbindings(), model.getTagSetModel(),
appModel.getSelectionModel(), viewGraph.getLock(), panel, panel.getDisplay(), model );
DataDisplayZoom.install( viewBehaviours, panel );
ExportViewActions.install( viewActions, panel.getDisplay(), frame, frame.getTitle() );

panel.getNavigationActions().install( viewActions, TrackSchemeNavigationActions.NavigatorEtiquette.FINDER_LIKE );
panel.getNavigationBehaviours().install( viewBehaviours );
panel.getTransformEventHandler().install( viewBehaviours );
}

void addSearchPanel( final Actions viewActions )
{
final JPanel searchPanel =
SearchVertexLabel.install( viewActions, viewGraph, navigationHandler, selectionModel, focusModel, panel );
frame.getSettingsPanel().add( searchPanel );
}

private void
registerColoring(
final TriFunction< ViewMenuBuilder.JMenuHandle, GraphColorGeneratorAdapter< V, E, DataVertex, DataEdge >,
DataDisplayPanel< V, E >, ColoringModel > colorModelRegistration,
final ViewMenuBuilder.JMenuHandle coloringMenuHandle )
{
coloringModel = colorModelRegistration.apply( coloringMenuHandle, coloringAdapter, panel );
}

private void registerColorBar( final LoopBuilder.TriConsumer< ColorBarOverlay, ViewMenuBuilder.JMenuHandle,
DataDisplayPanel< V, E > > colorBarRegistration, final ViewMenuBuilder.JMenuHandle colorbarMenuHandle )
{
colorBarOverlay = new ColorBarOverlay( coloringModel, panel::getBackground );
final OffsetAxes offset = panel.getOffsetAxes();
offset.listeners().add( ( w, h ) -> colorBarOverlay.setInsets( 15, w + 15, h + 15, 15 ) );
colorBarRegistration.accept( colorBarOverlay, colorbarMenuHandle, panel );
panel.getDisplay().overlays().add( colorBarOverlay );
}

private void registerTagSetMenu( final BiConsumer< ViewMenuBuilder.JMenuHandle, DataDisplayPanel< V, E > > tagSetMenuRegistration,
final ViewMenuBuilder.JMenuHandle tagSetMenuHandle )
{
tagSetMenuRegistration.accept( tagSetMenuHandle, panel );
}

ContextChooser< V > getContextChooser()
{
return contextChooser;
}

DataDisplayFrame< V, E > getFrame()
{
return frame;
}

ColoringModel getColoringModel()
{
return coloringModel;
}

ColorBarOverlay getColorBarOverlay()
{
return colorBarOverlay;
}
}
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