package cmd;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashMap;

import java.util.List;

import java.util.concurrent.Callable;

import java.util.concurrent.ExecutorService;

import java.util.concurrent.Executors;

import javax.swing.SwingUtilities;

import align.Pairwise;

import analyze.Entropy;

import analyze.ExtractGeneLists;

import bdv.ui.splitpanel.SplitPanel;

import bdv.util.BdvStackSource;

import bdv.viewer.DisplayMode;

import bdv.viewer.SourceGroup;

import bdv.viewer.SynchronizedViewerState;

import gui.DisplayScaleOverlay;

import gui.STDataAssembly;

import gui.bdv.AddedGene;

import gui.bdv.AddedGene.Rendering;

import gui.bdv.STIMCard;

import gui.bdv.STIMCardAlignICP;

import gui.bdv.STIMCardAlignSIFT;

import gui.bdv.STIMCardFilter;

import gui.bdv.STIMCardManualAlign;

import io.SpatialDataContainer;

import io.SpatialDataIO;

import net.imglib2.RandomAccessibleInterval;

import net.imglib2.type.numeric.ARGBType;

import net.imglib2.type.numeric.real.DoubleType;

import net.imglib2.util.Pair;

import picocli.CommandLine;

import picocli.CommandLine.Option;

import util.Threads;

import org.apache.logging.log4j.Logger;

import util.LoggerUtil;

// -c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180531_22.n5 -d2 Puck_180531_23.n5 -n 4 -sk 2

// -c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180602_15.n5 -d2 Puck_180602_16.n5 -n 4 -sk 2

// -c visium.n5 -d1 slice1.h5ad -d2 slice2.n5 -n 9 -sk 14

// align all

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180528_22.n5 -d2 Puck_180528_20.n5 -n 4 -sk 2 // huge shift

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180531_13.n5 -d2 Puck_180528_22.n5 -n 4 -sk 2

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180531_17.n5 -d2 Puck_180531_13.n5 -n 4 -sk 2

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180531_18.n5 -d2 Puck_180531_17.n5 -n 4 -sk 2

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180531_19.n5 -d2 Puck_180531_18.n5 -n 4 -sk 2 --ffSingleSpot 1.5

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180531_22.n5 -d2 Puck_180531_19.n5 -n 8 -sk 2 --ffSingleSpot 1.5

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180531_23.n5 -d2 Puck_180531_22.n5 -n 8 -sk 2 --ffSingleSpot 1.5

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180602_15.n5 -d2 Puck_180531_23.n5 -n 8 -sk 2 --ffSingleSpot 1.5

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180602_16.n5 -d2 Puck_180602_15.n5 -n 8 -sk 2 --ffSingleSpot 1.5

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180602_17.n5 -d2 Puck_180602_16.n5 -n 8 -sk 2 --ffSingleSpot 1.5

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180602_18.n5 -d2 Puck_180602_17.n5 -n 8 -sk 2 --ffSingleSpot 1.5

//-c /Users/preibischs/Documents/BIMSB/Publications/imglib2-st/slide-seq/raw/slide-seq.n5 -d1 Puck_180602_20.n5 -d2 Puck_180602_18.n5 -n 8 -sk 2 --ffSingleSpot 1.5

public class InteractiveAlignment implements Callable<Void> {

private static final Logger logger = LoggerUtil.getLogger();

@Option(names = {"-c", "--container"}, required = true, description = "input N5 container path, e.g. -c /home/ssq.n5.")

private String inputPath = null;

@Option(names = {"-f", "--fixed"}, required = false, description = "the fixed dataset (slice), e.g. -f 'Puck_180528_20'")

private String fixedDataset = null;

@Option(names = {"-m", "--moving"}, required = false, description = "the moving dataset (slice), e.g. -m 'Puck_180528_22'")

private String movingDataset = null;

@Option(names = {"-s", "--scale"}, required = false, description = "initial scaling factor for rendering the coordinates into images, can be changed interactively (default: 0.05 for slideseq data)")

private double scale = 0.05;

@Option(names = {"-bmin", "--brightnessMin"}, required = false, description = "min initial brightness relative to the maximal value + overall min intensity (default: 0.0)")

private double brightnessMin = 0.0;

@Option(names = {"-bmax", "--brightnessMax"}, required = false, description = "max initial brightness relative to the maximal value (default: 0.5)")

private double brightnessMax = 0.5;

@Option(names = {"-rf", "--renderingFactor"}, required = false, description = "factor for the amount of filtering or radius used for rendering, corresponds to smoothness for Gauss, e.g -rf 2.0 (default: 1.0)")

private double renderingFactor = 1.0;

@Option(names = {"--rendering"}, required = false, description = "inital rendering type (Gauss, Mean, NearestNeighbor, Linear), e.g --rendering Gauss (default: Gauss)")

private Rendering rendering = Rendering.Gauss;

@Option(names = {"-n", "--numGenes"}, required = false, description = "initial number of genes for alignment that have the highest entropy (default: 10)")

private int numGenes = 10;

@Option(names = {"-sk", "--skip"}, required = false, description = "skips the first N genes when selecting by highest entropy, as they can be outliers (default: 10)")

private int skipFirstNGenes = 10;

@Option(names = {"--ffSingleSpot"}, required = false, description = "filter single spots using the median distance between all spots as threshold, e.g. --ffSingleSpot 1.5 (default: no filtering)")

private Double ffSingleSpot = null;

@Option(names = {"--ffMedian"}, required = false, description = "median-filter all spots using a given radius, e.g --ffMedian 5.0 (default: no filtering)")

private Double ffMedian = null;

@Option(names = {"--ffGauss"}, required = false, description = "Gauss-filter all spots using a given radius, e.g --ffGauss 2.0 (default: no filtering)")

private Double ffGauss = null;

@Option(names = {"--ffMean"}, required = false, description = "mean/avg-filter all spots using a given radius, e.g --ffMean 2.5 (default: no filtering)")

private Double ffMean = null;

@Override

public Void call() throws Exception

{

final ExecutorService service = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());

if (!SpatialDataContainer.isCompatibleContainer(inputPath)) {

logger.error("'{}' is not a container. Stopping.", inputPath);

return null;

}

if (numGenes <= 0) {

logger.error("Number of genes must be greater than 0 (is {}). Stopping.", numGenes);

return null;

}

// we might save the transformation, so open for writing

final SpatialDataContainer container = SpatialDataContainer.openExisting(inputPath, service);

logger.info("Opening dataset '{}' in '{}' ...", movingDataset, inputPath);

final SpatialDataIO io1 = container.openDataset(movingDataset);

final STDataAssembly data1 = io1.readData();

//data1.transform().set( new AffineTransform2D() );

logger.debug("Current transform: {}", data1.transform());

logger.info("Opening dataset '{}' in '{}' ...", fixedDataset, inputPath);

final SpatialDataIO io2 = container.openDataset(fixedDataset);

final STDataAssembly data2 = io2.readData();

//data2.transform().set( new AffineTransform2D() );

logger.debug("Current transform: {}", data2.transform());

//

// assemble genes to test

//

logger.info("Assembling initial genes for alignment ({} genes)...", numGenes);

final String stdevLabel = Entropy.STDEV.label();

final List<STDataAssembly> dataToAlign = Arrays.asList(data1, data2);

final List<String> datasetNames = Arrays.asList(movingDataset, fixedDataset);

// ensure that the standard deviation of genes is present for all datasets

logger.info("Retrieving standard deviation of genes for all sections");

for (int i = 0; i < dataToAlign.size(); ++i) {

final STDataAssembly stData = dataToAlign.get(i);

final String datasetName = datasetNames.get(i);

final RandomAccessibleInterval<DoubleType> entropyValues;

if (container.hasEntropyValues(datasetName, Entropy.STDEV)) {

logger.info("Standard deviation of genes for {} already computed. Loading.", datasetName);

entropyValues = container.loadEntropyValues(datasetName, Entropy.STDEV);

} else {

logger.info("Computing standard deviation of genes for {} (may take a while)", datasetName);

entropyValues = ExtractGeneLists.computeOrderedEntropy(stData.data(), Entropy.STDEV, Threads.numThreads());

container.saveEntropyValues(entropyValues, datasetName, Entropy.STDEV);

}

stData.data().getGeneAnnotations().put(stdevLabel, entropyValues);

}

final List<Pair<String, Double>> allGenes = Pairwise.allGenes(data1.data(), data2.data(), stdevLabel);

if (allGenes.isEmpty()) {

logger.error("No common genes between both datasets. Stopping.");

return null;

} else {

logger.debug("Automatically identified {} genes that can be used for alignment", allGenes.size());

}

BdvStackSource< ? > lastSource = null;

final HashMap< String, List< AddedGene > > sourceData = new HashMap<>();

logger.info( "Starting BDV ... " );

logger.info("Starting with the top {} genes after skipping the first {} genes (you find them in the 'groups' panel, you can add/remove genes in the GUI.", numGenes, skipFirstNGenes);

for ( int i = skipFirstNGenes; i < numGenes + skipFirstNGenes; ++i )

{

final String gene = allGenes.get( i ).getA(); //"Calm2";

logger.info("Rendering gene (each available as its own source): {}", gene);

final AddedGene addedGene1 = AddedGene.addGene(

inputPath,

movingDataset,

rendering,

lastSource,

data1,

null,

gene,

renderingFactor,

new ARGBType( ARGBType.rgba(0, 255, 0, 0) ),

brightnessMin,

brightnessMax );

final AddedGene addedGene2 = AddedGene.addGene(

inputPath,

fixedDataset,

rendering,

addedGene1.source(),

data2,

null,

gene,

renderingFactor,

new ARGBType( ARGBType.rgba(255, 0, 255, 0) ),

brightnessMin,

brightnessMax );

sourceData.put(gene, new ArrayList<>(Arrays.asList( addedGene1, addedGene2 ) ) );

lastSource = addedGene2.source();

}

final SynchronizedViewerState state = lastSource.getBdvHandle().getViewerPanel().state();

final ArrayList< SourceGroup > oldGroups = new ArrayList<>( state.getGroups() );

final HashMap< String, SourceGroup > geneToBDVSource = new HashMap<>();

for ( int i = 0; i < numGenes; ++i )

{

final String gene = allGenes.get( i + skipFirstNGenes ).getA();

final SourceGroup handle = new SourceGroup();

state.addGroup( handle );

state.setGroupName( handle, gene );

state.setGroupActive( handle, true );

state.addSourceToGroup( state.getSources().get(i*2), handle );

state.addSourceToGroup( state.getSources().get(i*2 + 1), handle );

geneToBDVSource.put( gene, handle );

}

lastSource.getBdvHandle().getViewerPanel().setDisplayMode( DisplayMode.GROUP );

state.removeGroups( oldGroups );

/*

[13:19, 11/21/2023] Tobias Pietzsch: ViewerPanel.state()

[13:20, 11/21/2023] Tobias Pietzsch: und dann in dem ViewerState addSourcesToGroup( Collection< ? extends SourceAndConverter< ? > > collection, SourceGroup group );

[13:20, 11/21/2023] Tobias Pietzsch: und auch im ViewerState setDisplayMode(GROUP)

[13:21, 11/21/2023] Stephan Preibisch: und wie mache ich 10 groups initial?

[13:21, 11/21/2023] Stephan Preibisch: also die SourceGroup objekte

[13:21, 11/21/2023] Tobias Pietzsch: einfach new bdv.viewer.SourceGroup()

[13:22, 11/21/2023] Tobias Pietzsch: das sind quasi nur IDs

[13:22, 11/21/2023] Stephan Preibisch: ok, cool, danke!

[13:22, 11/21/2023] Tobias Pietzsch: dann ViewerState:addGroup(…) ode addGroups(…)

[13:22, 11/21/2023] Stephan Preibisch: ich versuche mein Glück :)

[13:22, 11/21/2023] Tobias Pietzsch: ViewerState.setGroupName(SourceGroup, String)

[13:23, 11/21/2023] Tobias Pietzsch: etc

*/

final double medianDistance = (data1.statistics().getMedianDistance() + data2.statistics().getMedianDistance()) / 2.0;

logger.debug("Median distance of spots: {}", medianDistance);

// the side panel

final SplitPanel splitPanel = lastSource.getBdvHandle().getSplitPanel();

// add scale (so the right size of the images for alignment can be selected)

final DisplayScaleOverlay overlay = new DisplayScaleOverlay();

lastSource.getBdvHandle().getViewerPanel().renderTransformListeners().add(overlay);

lastSource.getBdvHandle().getViewerPanel().getDisplay().overlays().add(overlay);

// show scalebar (so the right error can be selected)

lastSource.getBdvHandle().getAppearanceManager().appearance().setShowScaleBar( true );

// collapse all existing panels (except sources)

lastSource.getBdvHandle().getCardPanel().setCardExpanded(bdv.ui.BdvDefaultCards.DEFAULT_SOURCEGROUPS_CARD, true); // collapse groups panel

lastSource.getBdvHandle().getCardPanel().setCardExpanded(bdv.ui.BdvDefaultCards.DEFAULT_SOURCES_CARD, false); // collapse sources panel

lastSource.getBdvHandle().getCardPanel().setCardExpanded(bdv.ui.BdvDefaultCards.DEFAULT_VIEWERMODES_CARD, false); // collapse display modes panel

// add STIMCard panel

final STIMCard card =

new STIMCard(

new ArrayList<>(Arrays.asList( data1, data2 ) ), allGenes, sourceData, geneToBDVSource, overlay,

medianDistance, rendering, renderingFactor, brightnessMin, brightnessMax, lastSource.getBdvHandle());

lastSource.getBdvHandle().getCardPanel().addCard( "STIM Display Options", "STIM Display Options", card.getPanel(), true );

// add STIMCardFilter panel

final STIMCardFilter cardFilter = new STIMCardFilter( card, ffSingleSpot, ffMedian, ffGauss, ffMean, service );

lastSource.getBdvHandle().getCardPanel().addCard( "STIM Filtering Options", "STIM Filtering Options", cardFilter.getPanel(), false );

// add STIMCardAlignSIFT panel

final STIMCardAlignSIFT cardAlignSIFT =

new STIMCardAlignSIFT(movingDataset, fixedDataset, card, cardFilter, service );

// add STIMCardAlignICP panel

final STIMCardAlignICP cardAlignICP =

new STIMCardAlignICP(movingDataset, fixedDataset, overlay, card, cardFilter, cardAlignSIFT, service );

cardAlignSIFT.setICPCard( cardAlignICP );

final STIMCardManualAlign cardAlignManual = new STIMCardManualAlign(card, cardAlignSIFT, cardAlignICP);

cardAlignSIFT.setManualAlignCard( cardAlignManual );

cardAlignICP.setManualAlignCard( cardAlignManual );

final BdvStackSource<?> source = lastSource;

SwingUtilities.invokeLater( () ->

{

source.getBdvHandle().getCardPanel().addCard( "Manual Alignment", "Manual Alignment", cardAlignManual.getPanel(), false );

source.getBdvHandle().getCardPanel().addCard( "SIFT Alignment", "SIFT Alignment", cardAlignSIFT.getPanel(), true );

source.getBdvHandle().getCardPanel().addCard( "ICP Alignment", "ICP Alignment", cardAlignICP.getPanel(), false );

});

// Expands the split Panel (after waiting 2 secs for the BDV to calm down)

//SimpleMultiThreading.threadWait( 2000 );

SwingUtilities.invokeLater( () -> splitPanel.setCollapsed(false) );

// TODO: BDV should call the transform listener

//SimpleMultiThreading.threadWait( 2000 );

SwingUtilities.invokeLater(cardAlignSIFT::updateMaxOctaveSize);

logger.debug("done");

// service is used in alignment

//service.shutdown();

return null;

}

public static void main(final String... args) {

final CommandLine cmd = new CommandLine(new InteractiveAlignment());

cmd.execute(args);

}

}