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; }
angles.add( new Angle( a, angleNameList.get( a ) ) );
for ( int a = 0; a < rotations.length; ++a ) final Angle angle = new Angle( a, String.valueOf( rotations[ a ] ) );
angleList.add( new Angle( a, angleNameList.get( a ) ) );
e = new Angle( 0 ); viewSetup.setAttribute( e );
for ( int a = 0; a < meta.numAngles(); ++a ) final Angle angle = new Angle( a, meta.rotationAngle( a ) );
if ( angle == null ) angle = new Angle( angleId ); angles.put( angleId, angle );
for ( int a = 0; a < meta.numAngles(); ++a ) final Angle angle = new Angle( a, meta.angles()[ a ] );
Angle aI = new Angle( angleId, angleId.toString() );
for ( int a = 0; a < meta.numAngles(); ++a ) final Angle angle = new Angle( a, meta.rotationAngle( a ) );
for ( int a = 0; a < meta.numAngles(); ++a ) final Angle angle = new Angle( a, meta.angles()[ a ] );
final Angle angle = new Angle( conf.angles[ angleIndex ] ); final Illumination illumination = new Illumination( conf.illuminations[ illuminationIndex ] );