public static ArrayList< Tile > getAllTilesSorted( final SpimData data, final Collection< ? extends ViewId > viewIds ) { final HashSet< Tile > tileSet = new HashSet<>(); for ( final ViewId v : viewIds ) { final ViewDescription vd = data.getSequenceDescription().getViewDescription( v ); if ( vd.isPresent() ) tileSet.add( vd.getViewSetup().getTile() ); } final ArrayList< Tile > tiles = new ArrayList<>(); tiles.addAll( tileSet ); Collections.sort( tiles ); return tiles; }
protected String nameForGroup( final Group< ViewDescription > group ) { final ViewDescription vd1 = group.iterator().next(); String name = "TP=" + vd1.getTimePointId() + " Angle=" + vd1.getViewSetup().getAngle().getName() + " Channel=" + vd1.getViewSetup().getChannel().getName(); if ( !groupIllums ) name += " Illum=" + vd1.getViewSetup().getChannel().getName(); if ( !groupTiles ) name += " Tile=" + vd1.getViewSetup().getTile().getName(); return name; }
filename += "_Tile" + viewDescription.getViewSetup().getTile().getName();
tiles.add( data.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getTile().getId() );
public static void updateMissingViews( final SpimData2 spimData, final List< ViewId > viewIds ) { for ( final ViewId viewId : viewIds ) { final ViewDescription vd = spimData.getSequenceDescription().getViewDescription( viewId ); if ( !vd.isPresent() ) { for ( final ViewDescription vdc : spimData.getSequenceDescription().getViewDescriptions().values() ) { if ( vd.getViewSetup().getAngle() == vdc.getViewSetup().getAngle() && vd.getViewSetup().getChannel() == vdc.getViewSetup().getChannel() && vd.getViewSetup().getTile() == vdc.getViewSetup().getTile() && vdc.getViewSetupId() != vd.getViewSetupId() ) { System.out.println( "Missing view " + Group.pvid( vd ) + " compensated from " + Group.pvid( vdc ) ); final ViewRegistration vrc = spimData.getViewRegistrations().getViewRegistration( vdc ); vrc.updateModel(); final ViewRegistration vr = spimData.getViewRegistrations().getViewRegistration( vd ); vr.getTransformList().clear(); vr.getTransformList().addAll( vrc.getTransformList() ); vr.updateModel(); } } } } }
tiles.add( data.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getTile().getId() );
public static ViewSetup getViewSetup( final List< ? extends ViewSetup > list, final Channel c, final Angle a, final Illumination i, final Tile x ) { for ( final ViewSetup viewSetup : list ) { if ( viewSetup.getAngle().getId() == a.getId() && viewSetup.getChannel().getId() == c.getId() && viewSetup.getIllumination().getId() == i.getId() && viewSetup.getTile().getId() == x.getId() ) { return viewSetup; } } return null; }
fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ), vs.getTile(), vs.getChannel(), vs.getAngle(),
newTileId = Math.max( vs.getTile().getId(), newTileId ); newChannelId = Math.max( vs.getChannel().getId(), newChannelId ); newAngleId = Math.max( vs.getAngle().getId(), newAngleId ); fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", Util.getArrayFromValue( downsampling, 3 ) ), vs.getTile(), vs.getChannel(), vs.getAngle(),