@Override public VoxelDimensions getVoxelSize(ViewId view) { return new FinalVoxelDimensions( "pixel", 1, 1, 1 ); }
@Override public VoxelDimensions getVoxelSize( final ViewId view ) { return new FinalVoxelDimensions( "pixel", 1, 1, 1 ); }
protected void updateMetaDataCache( final ViewId viewId, final int w, final int h, final int d, final double calX, final double calY, final double calZ ) { imageMetaDataCache.put( viewId, new ValuePair< Dimensions, VoxelDimensions >( new FinalDimensions( new long[] { w, h, d } ), new FinalVoxelDimensions( "", calX, calY, calZ ) ) ); // links the viewSetupId to the last added viewId, overwrites earlier entries viewIdLookUp.put( viewId.getViewSetupId(), viewId ); }
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; }
protected ArrayList< ViewSetup > createViewSetups( final DHMMetaData meta ) { final ArrayList< Channel > channels = new ArrayList< Channel >(); channels.add( new Channel( meta.getAmpChannelId(), meta.getAmplitudeDir() ) ); channels.add( new Channel( meta.getPhaseChannelId(), meta.getPhaseDir() ) ); final ArrayList< Illumination > illuminations = new ArrayList< Illumination >(); illuminations.add( new Illumination( 0, String.valueOf( 0 ) ) ); final ArrayList< Angle > angles = new ArrayList< Angle >(); angles.add( new Angle( 0, String.valueOf( 0 ) ) ); final ArrayList< ViewSetup > viewSetups = new ArrayList< ViewSetup >(); for ( final Channel c : channels ) for ( final Illumination i : illuminations ) for ( final Angle a : angles ) { final VoxelDimensions voxelSize = new FinalVoxelDimensions( meta.calUnit, meta.calX, meta.calY, meta.calZ ); final Dimensions dim = new FinalDimensions( new long[]{ meta.getWidth(), meta.getHeight(), meta.getDepth() } ); viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) ); } return viewSetups; }
final VoxelDimensions voxelSize = new FinalVoxelDimensions( cal.calUnit, cal.calX, cal.calY, cal.calZ );
for ( final Angle a : angles ) final VoxelDimensions voxelSize = new FinalVoxelDimensions( "pixels", 1, 1, 1 ); final Dimensions dim = new FinalDimensions( new long[]{ range.max( 0 ) - range.min( 0 ), range.max( 1 ) - range.min( 1 ), range.max( 2 ) - range.min( 2 ) } ); viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) );
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 ) );
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 );
for ( final Angle a : angles ) final VoxelDimensions voxelSize = new FinalVoxelDimensions( meta.calUnit(), meta.calX(), meta.calY(), meta.calZ() ); final Dimensions dim = new FinalDimensions( new long[]{ meta.width(), meta.height(), meta.depth() } ); viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) );
final double ph = XmlHelpers.getDouble( elem, "pixelHeight" ); final double pd = XmlHelpers.getDouble( elem, "pixelDepth" ); final VoxelDimensions voxelSize = new FinalVoxelDimensions( "px", pw, ph, pd );
final Angle theAngle = angles.get( meta.getAngleMap().get( at ) ); final VoxelDimensions voxelSize = new FinalVoxelDimensions( meta.calUnit(), meta.calX(), meta.calY(), meta.calZ() ); final Dimensions dim = new FinalDimensions( meta.imageSizes().get( t.getId() ) ); viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, t, c, theAngle, i ) );
for ( final Angle a : angles ) final VoxelDimensions voxelSize = new FinalVoxelDimensions( meta.calUnit(), meta.calX(), meta.calY(), meta.calZ() ); final Dimensions dim = new FinalDimensions( new long[]{ meta.width(), meta.height(), meta.depth() } ); viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) );
public static void applyCal( final Cal maxCal, final SpimData spimData, final List< ViewId > viewIds ) { // this is the same for all timepoints, we are just interested in the ViewSetup final TimePoint t = spimData.getSequenceDescription().getTimePoints().getTimePointsOrdered().get( 0 ); for ( final ViewId viewId : viewIds ) { if ( viewId.getTimePointId() != t.getId() ) continue; final ViewDescription desc = spimData.getSequenceDescription().getViewDescriptions().get( viewId ); final ViewSetup viewSetup = desc.getViewSetup(); viewSetup.setVoxelSize( new FinalVoxelDimensions( maxCal.unit(), maxCal.getCal()[ 0 ], maxCal.getCal()[ 1 ], maxCal.getCal()[ 2 ] ) ); } }
}; final String unit = access.readImarisAttributeString( path, "Unit" ); final VoxelDimensions voxelSize = new FinalVoxelDimensions( unit, new double[] { ( extMax[ 0 ] - extMin[ 0 ] ) / imageSize[ 0 ], ( extMax[ 1 ] - extMin[ 1 ] ) / imageSize[ 1 ],
c.getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ), new Tile( 0 ), c, channels.get( c ).getName() + "_" + illums.get( i ).getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ), new Tile( 0 ), channels.get( c ), "Fused", fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ), new Tile( 0 ), new Channel( 0 ), vs.getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ), vs.getTile(), vs.getChannel(),
for ( final Angle a : angles ) final VoxelDimensions voxelSize = new FinalVoxelDimensions( meta.calUnit(), meta.calX(), meta.calY(), meta.calZ() ); final Dimensions dim = new FinalDimensions( meta.imageSizes().get( a.getId() ) ); viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) );
final Pair< Dimensions, VoxelDimensions > pairNew = new ValuePair< Dimensions, VoxelDimensions >( pairOld.getA(), new FinalVoxelDimensions( calUnit, calX, calY, calZ ) ); state.getDimensionMap().put( key, pairNew );
c.getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", Util.getArrayFromValue( downsampling, 3 ) ), new Tile( newTileId ), c, channels.get( c ).getName() + "_" + illums.get( i ).getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", Util.getArrayFromValue( downsampling, 3 ) ), new Tile( newTileId ), channels.get( newChannelId ), "Fused", fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", Util.getArrayFromValue( downsampling, 3 ) ), new Tile( newTileId ), new Channel( newChannelId ), vs.getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", Util.getArrayFromValue( downsampling, 3 ) ), vs.getTile(), vs.getChannel(),
protected boolean updateProposedMipmaps( final String fusionDirectory, final SPIMConfiguration conf ) { final Pair< String, Integer > pair = detectPatternAndNumSlices( new File ( fusionDirectory ), conf.timepoints[0] ); if ( pair != null ) { final String filenamePattern = pair.getA(); final int numSlices = pair.getB(); final String fn = fusionDirectory + "/" + String.format( filenamePattern, conf.timepoints[0], conf.channels[0], 0 ); final ImagePlus imp = new ImagePlus( fn ); final int width = imp.getWidth(); final int height = imp.getHeight(); imp.close(); final Dimensions size = new FinalDimensions( new int[] { width, height, numSlices } ); final VoxelDimensions voxelSize = new FinalVoxelDimensions( "px", 1, 1, 1 ); final ExportMipmapInfo info = ProposeMipmaps.proposeMipmaps( new BasicViewSetup( 0, "", size, voxelSize ) ); autoSubsampling = ProposeMipmaps.getArrayString( info.getExportResolutions() ); autoChunkSizes = ProposeMipmaps.getArrayString( info.getSubdivisions() ); return true; } else return false; }