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fix SmartSPIM to skip tiles with skip=0 in metadata.json #89

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Merged
StephanPreibisch merged 1 commit into from
Nov 5, 2025
Merged

fix SmartSPIM to skip tiles with skip=0 in metadata.json #89

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104 changes: 61 additions & 43 deletions src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/SmartSPIM.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,12 +27,7 @@
import java.io.IOException;
import java.lang.reflect.Type;
import java.net.URI;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.*;
import java.util.Map.Entry;
import java.util.stream.Collectors;

Expand Down Expand Up @@ -162,11 +157,13 @@ protected ArrayList< ViewSetup > createViewSetups( final SmartSPIMMetaData meta,
for ( int y = 0; y < meta.yTileLocations.size(); ++y )
for ( int x = 0; x < meta.xTileLocations.size(); ++x )
{
final Tile tile = new Tile( i, "x" + x + "_y" + y );
tile.setLocation( new double[] { meta.xTileLocations.get( x ) * scaleFactor, meta.yTileLocations.get( y ) * scaleFactor, 0 } );
if (meta.tileMap.get(meta.xTileLocations.get( x )).contains(meta.yTileLocations.get( y ))) {
final Tile tile = new Tile(i, "x" + x + "_y" + y);
tile.setLocation(new double[]{meta.xTileLocations.get(x) * scaleFactor, meta.yTileLocations.get(y) * scaleFactor, 0});

tiles.add( tile );
++i;
tiles.add(tile);
++i;
}
}

final ArrayList< ViewSetup > viewSetups = new ArrayList< ViewSetup >();
Expand All @@ -190,45 +187,48 @@ public static boolean populateImageSize( final SmartSPIMMetaData metadata, final
for ( int xTile = 0; xTile < metadata.xTileLocations.size(); ++ xTile)
for ( int yTile = 0; yTile < metadata.yTileLocations.size(); ++ yTile)
{
final URI imageDir = metadata.folderFor(
metadata.channels.get( channel ),
metadata.xTileLocations.get( xTile ),
metadata.yTileLocations.get( yTile ) );
if (metadata.tileMap.get(metadata.xTileLocations.get( xTile ))
.contains(metadata.yTileLocations.get( yTile ))) {
final URI imageDir = metadata.folderFor(
metadata.channels.get( channel ),
metadata.xTileLocations.get( xTile ),
metadata.yTileLocations.get( yTile ) );

IOFunctions.println( "Directory: " + imageDir );
IOFunctions.println( "Directory: " + imageDir );

final Pair< long[], List< String > > stackData =
metadata.loadImageSize( channel, xTile, yTile );
final Pair< long[], List< String > > stackData =
metadata.loadImageSize( channel, xTile, yTile );

final long[] dimensions = stackData.getA();
final long[] dimensions = stackData.getA();

IOFunctions.println( "dimensions: " + Util.printCoordinates( dimensions ) );
IOFunctions.println( "dimensions: " + Util.printCoordinates( dimensions ) );

if ( dimensions == null )
return false;
if ( dimensions == null )
return false;

if ( metadata.dimensions == null )
{
metadata.dimensions = dimensions;
metadata.sortedFileNames = stackData.getB();
}
if ( metadata.dimensions == null )
{
metadata.dimensions = dimensions;
metadata.sortedFileNames = stackData.getB();
}

if ( !confirmAllImages )
return true;
if ( !confirmAllImages )
return true;

if ( !Arrays.equals( metadata.dimensions, dimensions ) )
{
IOFunctions.println( "dimensions are not equal. Stopping: " + Util.printCoordinates( dimensions ) + ", " + Util.printCoordinates( metadata.dimensions ) );
return false;
}
if ( !Arrays.equals( metadata.dimensions, dimensions ) )
{
IOFunctions.println( "dimensions are not equal. Stopping: " + Util.printCoordinates( dimensions ) + ", " + Util.printCoordinates( metadata.dimensions ) );
return false;
}

if ( !areListsEqual( metadata.sortedFileNames, stackData.getB() ) )
{
IOFunctions.println( "file names are not equal. Stopping." );
return false;
}

}
if ( !areListsEqual( metadata.sortedFileNames, stackData.getB() ) )
{
IOFunctions.println( "file names are not equal. Stopping." );
return false;
}

}
}

return true;
}
Expand Down Expand Up @@ -293,6 +293,7 @@ public static SmartSPIMMetaData parseMetaDataFile( final URI md )
IOFunctions.println( "number of tiles: " + tiles.size() );

metadata.channels = SmartSPIM_Tile.channels( tiles.values() );
metadata.tileMap = SmartSPIM_Tile.tileMap( tiles.values() );
metadata.xTileLocations = SmartSPIM_Tile.xTileLocations( tiles.values() );
metadata.yTileLocations = SmartSPIM_Tile.yTileLocations( tiles.values() );
metadata.zOffsets = SmartSPIM_Tile.zOffsets( tiles.values() );
Expand Down Expand Up @@ -380,6 +381,7 @@ public static class SmartSPIMMetaData
public List<Long> xTileLocations;
public List<Long> yTileLocations;
public List<Long> zOffsets;
public HashMap<Long, Set<Long>> tileMap;

public SmartSPIMMetaData( final URI metadataFile ) throws SpimDataIOException
{
Expand Down Expand Up @@ -472,11 +474,27 @@ private static class SmartSPIM_Tile
public int Skip;
public int Filter;

public static List< Long > xTileLocations( final Collection< SmartSPIM_Tile > tiles )
public static HashMap<Long, Set<Long>> tileMap( final Collection< SmartSPIM_Tile > tiles )
{
return tiles.stream().map( t -> t.X ).distinct().sorted().collect(Collectors.toList());
HashMap<Long, Set<Long>> getTiles = new HashMap<Long, Set<Long>>(xTileLocations(tiles).size());
for (SmartSPIM_Tile t : tiles) {
if (t.Skip == 1) {
getTiles.computeIfAbsent(t.X, k -> new HashSet<>()).add(t.Y);
}
}

System.out.println("Valid X/Y Combos:");
getTiles.forEach((key, value) -> {
System.out.println("X: " + key + ", Ys: " + value);
});
return getTiles;
}

public static List< Long > xTileLocations( final Collection< SmartSPIM_Tile > tiles )
{
return tiles.stream().map( t -> t.X ).distinct().sorted().collect(Collectors.toList());
}

public static List< Long > yTileLocations( final Collection< SmartSPIM_Tile > tiles )
{
return tiles.stream().map( t -> t.Y ).distinct().sorted().collect(Collectors.toList());
Expand All @@ -502,7 +520,7 @@ public static void main( String[] args )
{
//parseMetaDataFile( URITools.toURI("/Users/preibischs/Documents/Janelia/Projects/BigStitcher/SmartSPIM/metadata.json"));
SmartSPIMMetaData metadata =
parseMetaDataFile( URITools.toURI( "/Volumes/johnsonlab/LM/20241031_11_59_44_RJ_mouse_2_vDisco_hindleg_right_Destripe_DONE/metadata.json") );
parseMetaDataFile( URITools.toURI( "/Volumes/johnsonlab/LM/20240826_15_33_26_RJ_mouse_1_anterior_ventral_Destripe_DONE/metadata.json") );

//populateImageSize( metadata, true );
}
Expand Down