#@ String (visibility=MESSAGE, value="Run bigwarp with bigdataviewer n5 images") DOCMSG #@ String(label="Moving n5 base", required=true, style="directory" ) movingN5Base #@ String(label="Moving dataset(s). (Comma separated)", required=true ) movingDatasetsIn #@ String(label="Target n5 base", required=true, style="directory" ) targetN5Base #@ String(label="Target dataset(s). (Comma separated)", required=true ) targetDatasetsIn #@ File(label="Landmark file", required=false, style="extensions:csv") landmarksFile #@ Boolean(label="volatile?", value=true ) useVolatile /** * A script for running bigwarp using image volumes stored with N5 (https://github.com/saalfeldlab/n5). * Requires that the contents N5 fiji update site be installed. * * 2020-Jan-06 : Initial script * 2020-Jan-07 : Add pyramid support * 2021-Jan-19 : Use arbitrary backends, add metadata parsing * * @author John Bogovic */ import java.lang.Exception; import java.util.regex.Pattern; import ij.*; import ij.process.*; import bigwarp.BigWarp; import bigwarp.BigWarpInit; import bigwarp.landmarks.LandmarkTableModel; import bdv.util.*; import bdv.export.*; import bdv.viewer.*; import bdv.util.volatiles.*; import org.janelia.saalfeldlab.n5.*; import org.janelia.saalfeldlab.n5.ij.*; import org.janelia.saalfeldlab.n5.metadata.*; import net.imglib2.*; import net.imglib2.util.*; import net.imglib2.realtransform.*; import mpicbg.spim.data.sequence.*; import org.janelia.saalfeldlab.n5.*; import org.janelia.saalfeldlab.n5.bdv.*; import org.janelia.saalfeldlab.n5.ij.*; import org.janelia.saalfeldlab.n5.imglib2.*; def isPyramid( N5FSReader n5, String group ) { /* * return true if there exists at least one dataset under the group * of the form "s#" where # is a number */ def pattern = Pattern.compile( /s\d/ ); numMatching = 0; subDatasets = n5.list( group ); for( d in subDatasets ) { numMatching += (d =~ pattern).size() } return (numMatching >= 1); } parsers = [ new N5ImagePlusMetadata( "" ), new N5CosemMetadata( "", null, null ), new N5SingleScaleMetadata(), new DefaultMetadata( "", -1 ) ] as N5MetadataParser[]; groupParsers = [ new N5CosemMultiScaleMetadata(), new N5ViewerMultiscaleMetadataParser() ] as N5GroupParser[]; def makeSources( String n5Base, String[] datasets ) { n5 = new N5Importer.N5ViewerReaderFun().apply( n5Base ); num = Runtime.getRuntime().availableProcessors() / 2; if( num < 1 ){ num = 1; } sharedQueue = new SharedQueue( num as int ); sources = []; for( dataset in datasets ) { n5 = new N5Importer.N5ViewerReaderFun().apply( n5Base ); N5MetadataParser[] parsers = new N5MetadataParser[] { new N5ImagePlusMetadata( "" ), new N5CosemMetadata( "", null, null ), new N5SingleScaleMetadata(), new DefaultMetadata( "", -1 ) }; N5GroupParser[] groupParsers = new N5GroupParser[] { new N5CosemMultiScaleMetadata(), new N5ViewerMultiscaleMetadataParser() }; node = new N5TreeNode( dataset, false ); discoverer = new N5DatasetDiscoverer( groupParsers, parsers ); try { discoverer.discoverThreads( n5, node ); Thread.sleep( 1000 ); discoverer.parseGroupsRecursive( node ); } catch ( IOException e ) { e.printStackTrace(); } catch ( InterruptedException e ) { e.printStackTrace(); } String[] datasetsToOpen; AffineTransform3D[] transforms; final N5Metadata metadata = node.getMetadata(); print( metadata ); if (metadata instanceof N5SingleScaleMetadata) { final N5SingleScaleMetadata singleScaleDataset = (N5SingleScaleMetadata) metadata; datasetsToOpen = new String[] {singleScaleDataset.getPath()}; transforms = new AffineTransform3D[] {singleScaleDataset.transform}; } else if (metadata instanceof N5CosemMultiScaleMetadata) { final N5CosemMultiScaleMetadata multiScaleDataset = (N5CosemMultiScaleMetadata) metadata; datasetsToOpen = multiScaleDataset.paths; transforms = multiScaleDataset.transforms; } else if (metadata instanceof ImageplusMetadata ) { ImagePlus iptmp = new ImagePlus( "tmp", new ByteProcessor( 1, 1 )); datasetsToOpen = new String[]{ node.getMetadata().getPath() }; ImageplusMetadata m = ((ImageplusMetadata)node.getMetadata()); m.writeMetadata( ( N5Metadata ) m, iptmp ); AffineTransform3D xfm = new AffineTransform3D(); xfm.set( iptmp.getCalibration().pixelWidth, 0, 0 ); xfm.set( iptmp.getCalibration().pixelHeight, 1, 1 ); xfm.set( iptmp.getCalibration().pixelDepth, 2, 2 ); transforms = new AffineTransform3D[] { xfm }; } else if (metadata == null) { IJ.error("N5 Viewer", "Cannot open dataset where metadata is null"); return; } else { IJ.error("N5 Viewer", "Unknown metadata type: " ); return; } final RandomAccessibleInterval[] images = new RandomAccessibleInterval[datasetsToOpen.length]; double[][] scales = new double[images.length][3]; for ( int s = 0; s < images.length; ++s ) { images[ s ] = N5Utils.openVolatile( n5, datasetsToOpen[s] ); scales[ s ][ 0 ] = transforms[ s ].get( 0, 0 ); scales[ s ][ 1 ] = transforms[ s ].get( 1, 1 ); scales[ s ][ 2 ] = transforms[ s ].get( 2, 2 ); } source = new RandomAccessibleIntervalMipmapSource( images, Util.getTypeFromInterval(images[0]), scales, new mpicbg.spim.data.sequence.FinalVoxelDimensions( "pix", 1, 1, 1), "source"); if( useVolatile ) { sources.add( source.asVolatile(sharedQueue) ); } else { sources.add( source ); } } return sources as Source[]; } // build moving and target sources movingSources = makeSources( movingN5Base, movingDatasetsIn.split(",") as String[] ) targetSources = makeSources( targetN5Base, targetDatasetsIn.split(",") as String[] ) srcNames = [] movingDatasetsIn.split(",").each{ n -> srcNames.add( n )} targetDatasetsIn.split(",").each{ n -> srcNames.add( n )} bwData = BigWarpInit.createBigWarpData( movingSources, targetSources, srcNames as String[] ); try { bw = new BigWarp( bwData, "bigwarp", new ProgressWriterConsole() ); // load the landmark points if they exist if ( landmarksFile != null ) bw.getLandmarkPanel().getTableModel().load( landmarksFile ); } catch(Exception e) { e.printStackTrace(); }