tiles.add( new Tile( t, tileNameList.get( t ) ) ); t.setLocation( locations.get( new ViewSetupPrecursor( c.getId(), i.getId(), a.getId(), t.getId() ) ) ); final Calibration cal = calibrations.get( new ViewSetupPrecursor( c.getId(), i.getId(), a.getId(), t.getId() ) ); final VoxelDimensions voxelSize = new FinalVoxelDimensions( cal.calUnit, cal.calX, cal.calY, cal.calZ );
protected String[] assembleTiles( final List< Tile > tiles ) { final String[] ts = new String[ tiles.size() ]; for ( int t = 0; t < ts.length; ++t ) ts[ t ] = tiles.get( t ).getName(); return ts; }
tileList.add( new Tile( x, tileNameList.get( x ) ) ); for ( final Tile x : tileList ) final Calibration cal = calibrations.get( new ViewSetupPrecursor( c.getId(), i.getId(), a.getId(), x.getId(), channelNameList, illuminationsNameList, angleNameList, tileNameList ) ); final VoxelDimensions voxelSize = new FinalVoxelDimensions( cal.calUnit, cal.calX, cal.calY, cal.calZ ); viewSetups.add( new ViewSetup( viewSetups.size(), null, null, voxelSize, x, c, a, i ) );
Tile tI = new Tile( tileId, tileId.toString() ); tI.setLocation( new double[] { tInfoI.locationX != null ? tInfoI.locationX : 0, tInfoI.locationY != null ? tInfoI.locationY : 0,
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; }
if (tile.hasLocation()){ final double shiftX = tile.getLocation()[0] / voxelSize.dimension( 0 ) * calX; final double shiftY = tile.getLocation()[1] / voxelSize.dimension( 1 ) * calY; final double shiftZ = tile.getLocation()[2] / voxelSize.dimension( 2 ) * calZ;
for ( int i = 0; i < meta.numTiles(); i++ ) Tile t = new Tile( i, meta.tiles()[ i], meta.tileLocations().get( i ) ); tiles.add( t ); final Dimensions dim = new FinalDimensions( meta.imageSizes().get( t.getId() ) ); viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, t, c, theAngle, i ) );
e = new Tile( 0 ); viewSetup.setAttribute( e );
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; }
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 ) ), new Tile( newTileId ), c, new Angle( newAngleId ), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", Util.getArrayFromValue( downsampling, 3 ) ), new Tile( newTileId ), channels.get( newChannelId ), new Angle( newAngleId ), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", Util.getArrayFromValue( downsampling, 3 ) ), new Tile( newTileId ), new Channel( newChannelId ), new Angle( newAngleId ),
fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ), new Tile( 0 ), c, new Angle( 0 ), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ), new Tile( 0 ), channels.get( c ), new Angle( 0 ), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ), new Tile( 0 ), new Channel( 0 ), new Angle( 0 ),
r.setSeries( t.getId() ); meta.imageSizes().put( t.getId(), new int[]{ width, height, z } ); for ( final ViewSetup vs : sd.getViewSetupsOrdered() ) if ( vs.getTile().getId() == t.getId() ) vs.setSize( new FinalDimensions( meta.imageSizes().get( t.getId() ) ) ); IOFunctions.println( "Resetting image size for viewSetup: " + vs.getId() + ", old: " + width + "x" + height + "x" + depth + ", new: " + width + "x" + height + "x" + z );
protected File getFile( final ViewId view ) { final TimePoint tp = sequenceDescription.getTimePoints().getTimePoints().get( view.getTimePointId() ); final BasicViewSetup vs = sequenceDescription.getViewSetups().get( view.getViewSetupId() ); final String timepoint = tp.getName(); final String angle = vs.getAttribute( Angle.class ).getName(); final String channel = vs.getAttribute( Channel.class ).getName(); final String illum = vs.getAttribute( Illumination.class ).getName(); final String tile = vs.getAttribute( Tile.class ).getName(); final String[] fileName = StackList.getFileNamesFor( fileNamePattern, replaceTimepoints, replaceChannels, replaceIlluminations, replaceAngles, replaceTiles, timepoint, channel, illum, angle, tile, numDigitsTimepoints, numDigitsChannels, numDigitsIlluminations, numDigitsAngles, numDigitsTiles ); // check which of them exists and return it for ( final String fn : fileName ) { final File f = new File( path, fn ); if ( f.exists() ) return f; else IOFunctions.println( "File '" + f.getAbsolutePath() + "' does not exist." ); } IOFunctions.println( "Could not find file for tp=" + timepoint + ", angle=" + angle + ", channel=" + channel + ", ill=" + illum + ", tile=" + tile ); return null; }
tiles.add( data.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getTile().getId() );
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; }
tiles.add( data.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getTile().getId() );
filename += "_Tile" + viewDescription.getViewSetup().getTile().getName();