public static ArrayList< ViewSetup > createViewSetupsFromImgLoader(SimulatedBeadsImgLoader2 imgLoader) { final ArrayList< ViewSetup > viewSetups = new ArrayList< ViewSetup >(); SimulateBeads2 sb = imgLoader.getSimulateBeads(); int vid = 0; for (int a : new ArrayList<>(sb.angleTransforms.keySet()).stream().sorted().collect( Collectors.toList() )) for (int channel : new ArrayList<>(sb.channelTransforms.keySet()).stream().sorted().collect( Collectors.toList() )) for (int illum : new ArrayList<>(sb.illumTransforms.keySet()).stream().sorted().collect( Collectors.toList() )) for (int tile : new ArrayList<>(sb.tileTransforms.keySet()).stream().sorted().collect( Collectors.toList() )) { final VoxelDimensions voxelSize = new FinalVoxelDimensions( "pixels", 1, 1, 1 ); final Dimensions dim = imgLoader.getSimulateBeads().getImg( 0, a, channel, tile, illum ); viewSetups.add( new ViewSetup( vid++, Integer.toString( vid ), dim, voxelSize, new Tile(tile), new Channel(channel), new Angle(a), new Illumination(illum) ) ); } return viewSetups; }
protected ArrayList< ViewSetup > createViewSetups( final DHMMetaData meta ) { final ArrayList< Channel > channels = new ArrayList< Channel >(); channels.add( new Channel( meta.getAmpChannelId(), meta.getAmplitudeDir() ) ); channels.add( new Channel( meta.getPhaseChannelId(), meta.getPhaseDir() ) ); final ArrayList< Illumination > illuminations = new ArrayList< Illumination >(); illuminations.add( new Illumination( 0, String.valueOf( 0 ) ) ); final ArrayList< Angle > angles = new ArrayList< Angle >(); angles.add( new Angle( 0, String.valueOf( 0 ) ) ); final ArrayList< ViewSetup > viewSetups = new ArrayList< ViewSetup >(); for ( final Channel c : channels ) for ( final Illumination i : illuminations ) for ( final Angle a : angles ) { final VoxelDimensions voxelSize = new FinalVoxelDimensions( meta.calUnit, meta.calX, meta.calY, meta.calZ ); final Dimensions dim = new FinalDimensions( new long[]{ meta.getWidth(), meta.getHeight(), meta.getDepth() } ); viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) ); } return viewSetups; }
final VoxelDimensions voxelSize = new FinalVoxelDimensions( cal.calUnit, cal.calX, cal.calY, cal.calZ ); viewSetups.add( new ViewSetup( viewSetups.size(), Integer.toString( viewSetups.size() ), null, voxelSize, t, c, a, i ) );
viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) );
viewSetups.add( new ViewSetup( viewSetups.size(), null, null, voxelSize, x, c, a, i ) );
viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) );
final VoxelDimensions voxelSize = new FinalVoxelDimensions( "px", pw, ph, pd ); final ViewSetup setup = new ViewSetup( id, null, size, voxelSize, channel, angle, illumination ); setups.put( id, setup );
viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, t, c, theAngle, i ) );
ViewSetup vs = new ViewSetup( viewSetupId, viewSetupId.toString(), state.getDimensionMap().get( (viewList.get( 0 ))).getA(),
viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) );
viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) );
setups.add( new ViewSetup( setup_id++, name, size, voxelSize, channel, angle, illumination ) );