{

/*

public static class STIMStack

{

public RealRandomAccessible< DoubleType > rra;

public Interval interval;

public double minDisplay, maxDisplay;

}

public static BdvStackSource<?> render2d( final STDataAssembly stdata )

{

final List< FilterFactory< DoubleType, DoubleType > > filterFactorys = new ArrayList<>();

//filterFactorys.add( new MedianFilterFactory<>( new DoubleType( 0 ), 50.0 ) );

//filterFactorys.add( new GaussianFilterFactory<>( new DoubleType( 0 ), 50.0, WeightType.BY_SUM_OF_WEIGHTS ) );

//filterFactorys.add( new MeanFilterFactory<>( new DoubleType( 0 ), 50.0 ) );

filterFactorys.add( new SingleSpotRemovingFilterFactory<>( new DoubleType( 0 ), stdata.statistics().getMedianDistance() * 1.5 ) );

final String gene = "Calm2";

final RealRandomAccessible< DoubleType > renderRRA = Render.getRealRandomAccessible( stdata, gene, 1.0, filterFactorys );

final Interval interval =

STDataUtils.getIterableInterval(

new TransformedIterableRealInterval<>(

stdata.data(),

stdata.transform() ) );

final double brightnessMin = 0.0;

final double brightnessMax = 0.5;

final double[] minmax = AddedGene.minmax( stdata.data().getExprData( gene ) );

double minDisplay = AddedGene.getDisplayMin( minmax[ 0 ], minmax[ 1 ], brightnessMin );

double maxDisplay = AddedGene.getDisplayMax( minmax[ 1 ], brightnessMax );

final BdvOptions options = BdvOptions.options().is2D().numRenderingThreads( Runtime.getRuntime().availableProcessors() / 2 );

BdvStackSource<?> bdv = BdvFunctions.show( renderRRA, interval, gene, options );

bdv.setDisplayRangeBounds( minDisplay, minmax[ 1 ] );

bdv.setDisplayRange( minDisplay, maxDisplay );

//bdv.setColor( new ARGBType( ARGBType.rgba( 255, 0, 0, 0 ) ) );

//bdv.getBdvHandle().getViewerPanel().setDisplayMode( DisplayMode.SINGLE );

//bdv.setCurrent();

return bdv;

}

public static RandomAccessibleInterval< DoubleType > render3d_IJ( final List< STDataAssembly > stdata, final String gene, final double scale )

{

final DoubleType outofbounds = new DoubleType( 0 );

final List< FilterFactory< DoubleType, DoubleType > > filterFactorys = new ArrayList<>();

filterFactorys.add( new MedianFilterFactory<>( new DoubleType( 0 ), 20.0 ) );

//filterFactorys.add( new GaussianFilterFactory<>( new DoubleType( 0 ), 50.0, WeightType.BY_SUM_OF_WEIGHTS ) );

//filterFactorys.add( new MeanFilterFactory<>( new DoubleType( 0 ), 50.0 ) );

filterFactorys.add( new SingleSpotRemovingFilterFactory<>( outofbounds, 30 ) );

final STIMStack stack = createStack( stdata, gene, outofbounds, 4.0, 0, 0.5, Rendering.Gauss, 1, filterFactorys );

if ( scale != 1.0 )

{

final AffineGet scaleTransform = new Scale3D( scale, scale, scale );

final RandomAccessible< DoubleType > scaledImg = RealViews.affine( stack.rra, scaleTransform );

return Views.interval( scaledImg, Intervals.smallestContainingInterval( Intervals.scale( Intervals.expand( stack.interval, 200, 2 ), scale ) ) );

}

else

{

return Views.interval( Views.raster( stack.rra ), stack.interval );

}

}

public static BdvStackSource< ? > render3d( final List< STDataAssembly > stdata )

{

final DoubleType outofbounds = new DoubleType( 0 );

final List< FilterFactory< DoubleType, DoubleType > > filterFactorys = new ArrayList<>();

filterFactorys.add( new MedianFilterFactory<>( new DoubleType( 0 ), 20.0 ) );

//filterFactorys.add( new GaussianFilterFactory<>( new DoubleType( 0 ), 50.0, WeightType.BY_SUM_OF_WEIGHTS ) );

//filterFactorys.add( new MeanFilterFactory<>( new DoubleType( 0 ), 50.0 ) );

filterFactorys.add( new SingleSpotRemovingFilterFactory<>( outofbounds, 30 ) );

final STIMStack stack = createStack( stdata, "Calm2", outofbounds, 4.0, 0, 0.5, Rendering.Gauss, 2, filterFactorys );

final Interval interval = stack.interval;

final BdvOptions options = BdvOptions.options().numRenderingThreads( Runtime.getRuntime().availableProcessors() );

BdvStackSource< ? > source = BdvFunctions.show( stack.rra, interval, "Calm2", options );

source.setDisplayRangeBounds( stack.minDisplay, stack.maxDisplay * 2 );

source.setDisplayRange( stack.minDisplay, stack.maxDisplay );

//source.getBdvHandle().getViewerPanel().setDisplayMode( DisplayMode.SINGLE );

//source.setCurrent();

return source;

}

public static void renderMovie3d( final List< STDataAssembly > stdata, final BdvStackSource< ? > source )

{

final List< String > genesToVisualize = new ArrayList<>();

genesToVisualize.add( "Actb" );

genesToVisualize.add( "Ubb" );

genesToVisualize.add( "Hpca" );

genesToVisualize.add( "Calm2" );

genesToVisualize.add( "Mbp" );

genesToVisualize.add( "Fth1" );

genesToVisualize.add( "Pcp4" );

genesToVisualize.add( "Ptgds" );

genesToVisualize.add( "Ttr" );

genesToVisualize.add( "Calm1" );

genesToVisualize.add( "Fkbp1a" );

final DoubleType outofbounds = new DoubleType( 0 );

setupRecordMovie(

source,

(i, oldSource) ->

{

if ( i % 20 == 0 && i <= 220 )

{

final int newGeneIndex = ( i == 220 ) ? 0 : i / 20;

final STIMStack stack =

createStack( stdata, genesToVisualize.get( newGeneIndex ), outofbounds, 4.0, 0, 0.5, Rendering.Gauss, 2.0, null );

BdvStackSource<?> newSource =

BdvFunctions.show(

stack.rra,

stack.interval,

genesToVisualize.get( newGeneIndex ),

BdvOptions.options().numRenderingThreads( Runtime.getRuntime().availableProcessors() ) );

newSource.setDisplayRange( stack.minDisplay, stack.maxDisplay );

newSource.getBdvHandle().getViewerPanel().setDisplayMode( DisplayMode.SINGLE );

if ( oldSource != null )

oldSource.close();

return newSource;

}

else

{

return oldSource;

} } );

}

/*

public static STIMStack createStack(

final List< STDataAssembly > stdata,

final String gene,

final DoubleType outofbounds,

final double spacingFactor,

final double brightnessMin,

final double brightnessMax,

final Rendering renderType,

final double renderingFactor,

final List< FilterFactory< DoubleType, DoubleType > > filterFactorys )

{

final ArrayList< IterableRealInterval< DoubleType > > slices = new ArrayList<>();

double minDisplay = Double.MAX_VALUE;

double maxDisplay = -Double.MAX_VALUE;

for (STDataAssembly stdatum : stdata) {

final IterableRealInterval<DoubleType> data = Render.getRealIterable(stdatum, gene, filterFactorys);

final double[] minmax = AddedGene.minmax(data);

minDisplay = Math.min(minDisplay, AddedGene.getDisplayMin(minmax[0], minmax[1], brightnessMin));

maxDisplay = Math.max(maxDisplay, AddedGene.getDisplayMax(minmax[1], brightnessMax));

slices.add(data);

}

// we need to re-compute the statistics because the transformation might have changed it

final double medianDistance = new STDataStatistics( stdata.get( 0 ).data() ).getMedianDistance();

final double spacing = medianDistance * spacingFactor;

final Interval interval2d = STDataUtils.getCommonIterableInterval( slices );

final long padding = Math.round(Math.ceil(medianDistance * 3));

final long[] minI = new long[] { interval2d.min(0 ), interval2d.min(1 ), -padding};

final long[] maxI = new long[] { interval2d.max( 0 ), interval2d.max( 1 ), Math.round( ( stdata.size() - 1 ) * spacing ) + padding};

final Interval interval = new FinalInterval( minI, maxI );

final StackedIterableRealInterval< DoubleType > stack = new StackedIterableRealInterval<>( slices, spacing );

final STIMStack stimStack = new STIMStack();

stimStack.rra = RenderImage.createRRA( stack, medianDistance, renderType, renderingFactor );

stimStack.interval = interval;

stimStack.minDisplay = minDisplay;

stimStack.maxDisplay = maxDisplay;

return stimStack;

}

public static void setupRecordMovie( final BdvStackSource<?> bdvSource, final CallbackBDV callback )

{

final ActionMap ksActionMap = new ActionMap();

final InputMap ksInputMap = new InputMap();

// default input trigger config, disables "control button1" drag in bdv

// (collides with default of "move annotation")

final InputTriggerConfig config = new InputTriggerConfig(

Collections.singletonList(

new InputTriggerDescription(

new String[]{"not mapped"}, "drag rotate slow", "bdv")));

final KeyStrokeAdder ksKeyStrokeAdder = config.keyStrokeAdder(ksInputMap, "persistence");

new AbstractNamedAction( "Record movie" )

{

private static final long serialVersionUID = 3640052275162419689L;

@Override

public void actionPerformed(ActionEvent e)

{

new Thread( ()-> BDVFlyThrough.record( bdvSource, callback ) ).start();

}

public void register() {

put(ksActionMap);

ksKeyStrokeAdder.put(name(), "ctrl R" );

}

}.register();

new AbstractNamedAction( "Add Current Viewer Transform" )

{

private static final long serialVersionUID = 3620052275162419689L;

@Override

public void actionPerformed(ActionEvent e)

{

BDVFlyThrough.addCurrentViewerTransform( bdvSource.getBdvHandle().getViewerPanel() );

}

public void register() {

put(ksActionMap);

ksKeyStrokeAdder.put(name(), "ctrl A" );

}

}.register();

new AbstractNamedAction( "Clear All Viewer Transforms" )

{

private static final long serialVersionUID = 3620052275162419689L;

@Override

public void actionPerformed(ActionEvent e)

{

BDVFlyThrough.clearAllViewerTransform();

}

public void register() {

put(ksActionMap);

ksKeyStrokeAdder.put(name(), "ctrl X" );

}

}.register();

bdvSource.getBdvHandle().getKeybindings().addActionMap("persistence", ksActionMap);

bdvSource.getBdvHandle().getKeybindings().addInputMap("persistence", ksInputMap);

}

public static ImagePlus visualizeIJ(final List<STDataAssembly> puckData, final boolean useTransform )

{

final List< STData > data = new ArrayList<>();

final List< AffineTransform2D > transforms = new ArrayList<>();

for ( final STDataAssembly stda : puckData )

{

data.add( stda.data() );

transforms.add( useTransform ? stda.transform() : new AffineTransform2D() );

}

return AlignTools.visualizeList( data, transforms, AlignTools.defaultScale, Rendering.Gauss, AlignTools.defaultSmoothnessFactor, AlignTools.defaultGene, true );

}

public static void main( String[] args ) throws IOException

{

final ExecutorService service = Executors.newFixedThreadPool(8);

final List<STDataAssembly> puckData =

SpatialDataContainer.openForReading(Path.getPath() + "slide-seq-test.n5", service).openAllDatasets().stream()

.map(sdio ->

{try {return sdio.readData();} catch (IOException e) {throw new RuntimeException(e);}})

.collect(Collectors.toList());

new ImageJ();

// Display as full 3D ImageJ image

RandomAccessibleInterval<DoubleType> img = render3d_IJ( puckData, "Ptgds", 0.4 );

ImageJFunctions.show( img, Executors.newFixedThreadPool( 8 ) ).setTitle("Ptgds");

// Display as 2D slices (each slice a 2D image)

AlignTools.defaultGene = "Ptgds";//"Calm2";//"Mbp";//;

AlignTools.defaultScale = 0.1;

AlignTools.defaultSmoothnessFactor = 2.0;

ImagePlus imp = visualizeIJ( puckData, true );

imp.show();

// Display interactively with BDV

render2d( puckData.get( 0 ) );

// Display 3D interactively with BDV

BdvStackSource< ? > bdv = render3d( puckData );

service.shutdown();

}