Examples with CoordinateTransform mpicbg.trakem2.transform.CoordinateTransform used on opensource projects

Example 16 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class Patch method addAlphaMaskLocal.

/**
 * Add the given area, in local coordinates, to the alpha mask, using the given fill value.
 */
public void addAlphaMaskLocal(final Area aLocal, int value) {
    if (value < 0)
        value = 0;
    if (value > 255)
        value = 255;
    // 
    CoordinateTransform ct = null;
    if (hasCoordinateTransform() && null == (ct = getCT())) {
        return;
    }
    // When the area is larger than the image, sometimes the area fails to be set at all
    // Also, intersection accelerates calls to contains(x,y) for complex polygons
    final Area a = new Area(new Rectangle(0, 0, (int) (width + 1), (int) (height + 1)));
    a.intersect(aLocal);
    if (M.isEmpty(a)) {
        Utils.log("ROI does not intersect the active image!");
        return;
    }
    ByteProcessor mask = getAlphaMask();
    // Use imglib to bypass all the problems with ShapeROI
    // Create a Shape image with background and the Area on it with 'value'
    final int background = (null != mask && 255 == value) ? 0 : 255;
    final ShapeList<UnsignedByteType> shapeList = new ShapeList<UnsignedByteType>(new int[] { (int) width, (int) height, 1 }, new UnsignedByteType(background));
    shapeList.addShape(a, new UnsignedByteType(value), new int[] { 0 });
    final mpicbg.imglib.image.Image<UnsignedByteType> shapeListImage = new mpicbg.imglib.image.Image<UnsignedByteType>(shapeList, shapeList.getBackground(), "mask");
    ByteProcessor rmask = (ByteProcessor) ImageJFunctions.copyToImagePlus(shapeListImage, ImagePlus.GRAY8).getProcessor();
    if (hasCoordinateTransform()) {
        // inverse the coordinate transform
        final TransformMesh mesh = new TransformMesh(ct, meshResolution, o_width, o_height);
        final TransformMeshMapping mapping = new TransformMeshMapping(mesh);
        rmask = (ByteProcessor) mapping.createInverseMappedImageInterpolated(rmask);
    }
    if (null == mask) {
        // There wasn't a mask, hence just set it
        mask = rmask;
    } else {
        final byte[] b1 = (byte[]) mask.getPixels();
        final byte[] b2 = (byte[]) rmask.getPixels();
        // Whatever is not background in the new mask gets set on the old mask
        for (int i = 0; i < b1.length; i++) {
            // background pixel in new mask
            if (background == (b2[i] & 0xff))
                continue;
            // replace old pixel with new pixel
            b1[i] = b2[i];
        }
    }
    setAlphaMask(mask);
}

Example 17 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class Patch method getLocalAffine.

/**
 * Return the local affine transformation for a passed location in world
 * coordinates.   This affine transform is either the global affine
 * transform of the patch or the combined affine transform of the local
 * affine transform in the transform mesh and its global affine transform.
 *
 * @param wx
 * @param wy
 * @return
 */
public AffineTransform getLocalAffine(final double wx, final double wy) {
    final AffineTransform affine = new AffineTransform(at);
    if (hasCoordinateTransform()) {
        final CoordinateTransform ct = getCoordinateTransform();
        final double[] w = new double[] { wx, wy };
        try {
            at.inverseTransform(w, 0, w, 0, 1);
        } catch (final NoninvertibleTransformException e) {
        }
        final TransformMesh mesh = new TransformMesh(ct, meshResolution, o_width, o_height);
        final mpicbg.models.AffineModel2D triangle = mesh.closestTargetAffine(new double[] { w[0], w[1] });
        affine.concatenate(triangle.createAffine());
    }
    return affine;
}

Example 18 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class Patch method createCoordinateTransformedImage.

public final Patch.PatchImage createCoordinateTransformedImage() {
    if (!hasCoordinateTransform())
        return null;
    final CoordinateTransform ct = getCoordinateTransform();
    final ImageProcessor source = getImageProcessor();
    // some error occurred
    if (null == source)
        return null;
    // Utils.log2("source image dimensions: " + source.getWidth() + ", " + source.getHeight());
    final TransformMesh mesh = new TransformMesh(ct, meshResolution, o_width, o_height);
    final Rectangle box = mesh.getBoundingBox();
    /* We can calculate the exact size of the image to be rendered, so let's do it */
    // project.getLoader().releaseToFit(o_width, o_height, type, 5);
    final long b = // outside and mask source
    2 * o_width * o_height + // outside and mask target
    2 * box.width * box.height + // image source
    5 * o_width * o_height + // image target
    5 * box.width * box.height;
    project.getLoader().releaseToFit(b);
    final TransformMeshMapping mapping = new TransformMeshMapping(mesh);
    final ImageProcessorWithMasks target = mapping.createMappedMaskedImageInterpolated(source, getAlphaMask());
    // Set the LUT
    target.ip.setColorModel(source.getColorModel());
    return new PatchImage(target.ip, (ByteProcessor) target.mask, target.outside, box, true);
}

Example 19 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class AlignTask method alignMultiLayerMosaicTask.

@SuppressWarnings({ "unchecked", "rawtypes" })
public static final void alignMultiLayerMosaicTask(final List<Layer> layerRange, final Patch nail, final Align.Param cp, final Align.ParamOptimize p, final Align.ParamOptimize pcp, final boolean tilesAreInPlaceIn, final boolean largestGraphOnlyIn, final boolean hideDisconnectedTilesIn, final boolean deleteDisconnectedTilesIn, final boolean deformIn) {
    /* register */
    final List<AbstractAffineTile2D<?>> allTiles = new ArrayList<AbstractAffineTile2D<?>>();
    final List<AbstractAffineTile2D<?>> allFixedTiles = new ArrayList<AbstractAffineTile2D<?>>();
    final List<AbstractAffineTile2D<?>> previousLayerTiles = new ArrayList<AbstractAffineTile2D<?>>();
    final HashMap<Patch, PointMatch> tileCenterPoints = new HashMap<Patch, PointMatch>();
    final Collection<Patch> fixedPatches = new HashSet<Patch>();
    if (null != nail)
        fixedPatches.add(nail);
    Layer previousLayer = null;
    for (final Layer layer : layerRange) {
        /* align all tiles in the layer */
        final List<Patch> patches = new ArrayList<Patch>();
        for (// ignore hidden tiles
        final Displayable a : // ignore hidden tiles
        layer.getDisplayables(Patch.class, true)) if (a instanceof Patch)
            patches.add((Patch) a);
        final List<AbstractAffineTile2D<?>> currentLayerTiles = new ArrayList<AbstractAffineTile2D<?>>();
        final List<AbstractAffineTile2D<?>> fixedTiles = new ArrayList<AbstractAffineTile2D<?>>();
        Align.tilesFromPatches(p, patches, fixedPatches, currentLayerTiles, fixedTiles);
        // Will consider graphs and hide/delete tiles when all cross-layer graphs are found.
        alignTiles(p, currentLayerTiles, fixedTiles, tilesAreInPlaceIn, false, false, false);
        if (Thread.currentThread().isInterrupted())
            return;
        /* connect to the previous layer */
        /* generate tiles with the cross-section model from the current layer tiles */
        /* ------------------------------------------------------------------------ */
        /* TODO step back and make tiles bare containers for a patch and a model such that by changing the model the tile can be reused */
        final HashMap<Patch, AbstractAffineTile2D<?>> currentLayerPatchTiles = new HashMap<Patch, AbstractAffineTile2D<?>>();
        for (final AbstractAffineTile2D<?> t : currentLayerTiles) currentLayerPatchTiles.put(t.getPatch(), t);
        final List<AbstractAffineTile2D<?>> csCurrentLayerTiles = new ArrayList<AbstractAffineTile2D<?>>();
        final Set<AbstractAffineTile2D<?>> csFixedTiles = new HashSet<AbstractAffineTile2D<?>>();
        Align.tilesFromPatches(cp, patches, fixedPatches, csCurrentLayerTiles, csFixedTiles);
        final HashMap<Tile<?>, AbstractAffineTile2D<?>> tileTiles = new HashMap<Tile<?>, AbstractAffineTile2D<?>>();
        for (final AbstractAffineTile2D<?> t : csCurrentLayerTiles) tileTiles.put(currentLayerPatchTiles.get(t.getPatch()), t);
        for (final AbstractAffineTile2D<?> t : currentLayerTiles) {
            final AbstractAffineTile2D<?> csLayerTile = tileTiles.get(t);
            csLayerTile.addMatches(t.getMatches());
            for (final Tile<?> ct : t.getConnectedTiles()) csLayerTile.addConnectedTile(tileTiles.get(ct));
        }
        /* add a fixed tile only if there was a Patch selected */
        allFixedTiles.addAll(csFixedTiles);
        /* first, align connected graphs to each other */
        /* graphs in the current layer */
        final List<Set<Tile<?>>> currentLayerGraphs = AbstractAffineTile2D.identifyConnectedGraphs(csCurrentLayerTiles);
        if (Thread.currentThread().isInterrupted())
            return;
        // /* TODO just for visualization */
        // for ( final Set< Tile< ? > > graph : currentLayerGraphs )
        // {
        // Display.getFront().getSelection().clear();
        // Display.getFront().setLayer( ( ( AbstractAffineTile2D< ? > )graph.iterator().next() ).getPatch().getLayer() );
        // 
        // for ( final Tile< ? > tile : graph )
        // {
        // Display.getFront().getSelection().add( ( ( AbstractAffineTile2D< ? > )tile ).getPatch() );
        // Display.repaint();
        // }
        // Utils.showMessage( "OK" );
        // }
        /* graphs from the whole system that are present in the previous layer */
        final List<Set<Tile<?>>> graphs = AbstractAffineTile2D.identifyConnectedGraphs(allTiles);
        final HashMap<Set<Tile<?>>, Set<Tile<?>>> graphGraphs = new HashMap<Set<Tile<?>>, Set<Tile<?>>>();
        for (final Set<Tile<?>> graph : graphs) {
            if (Thread.currentThread().isInterrupted())
                return;
            final Set<Tile<?>> previousLayerGraph = new HashSet<Tile<?>>();
            for (final Tile<?> tile : previousLayerTiles) {
                if (graph.contains(tile)) {
                    graphGraphs.put(graph, previousLayerGraph);
                    previousLayerGraph.add(tile);
                }
            }
        }
        final Collection<Set<Tile<?>>> previousLayerGraphs = graphGraphs.values();
        // /* TODO just for visualization */
        // for ( final Set< Tile< ? > > graph : previousLayerGraphs )
        // {
        // Display.getFront().getSelection().clear();
        // Display.getFront().setLayer( ( ( AbstractAffineTile2D< ? > )graph.iterator().next() ).getPatch().getLayer() );
        // 
        // for ( final Tile< ? > tile : graph )
        // {
        // Display.getFront().getSelection().add( ( ( AbstractAffineTile2D< ? > )tile ).getPatch() );
        // Display.repaint();
        // }
        // Utils.showMessage( "OK" );
        // }
        /* generate snapshots of the graphs and preregister them using the parameters defined in cp */
        final List<AbstractAffineTile2D<?>[]> crossLayerTilePairs = new ArrayList<AbstractAffineTile2D<?>[]>();
        for (final Set<Tile<?>> currentLayerGraph : currentLayerGraphs) {
            for (final Set<Tile<?>> previousLayerGraph : previousLayerGraphs) {
                if (Thread.currentThread().isInterrupted())
                    return;
                alignGraphs(cp, layer, previousLayer, currentLayerGraph, previousLayerGraph);
                /* TODO this is pointless data shuffling just for type incompatibility---fix this at the root */
                final ArrayList<AbstractAffineTile2D<?>> previousLayerGraphTiles = new ArrayList<AbstractAffineTile2D<?>>();
                previousLayerGraphTiles.addAll((Set) previousLayerGraph);
                final ArrayList<AbstractAffineTile2D<?>> currentLayerGraphTiles = new ArrayList<AbstractAffineTile2D<?>>();
                currentLayerGraphTiles.addAll((Set) currentLayerGraph);
                AbstractAffineTile2D.pairOverlappingTiles(previousLayerGraphTiles, currentLayerGraphTiles, crossLayerTilePairs);
            }
        }
        /* ------------------------------------------------------------------------ */
        /* this is without the affine/rigid approximation per graph */
        // AbstractAffineTile2D.pairTiles( previousLayerTiles, csCurrentLayerTiles, crossLayerTilePairs );
        Align.connectTilePairs(cp, csCurrentLayerTiles, crossLayerTilePairs, Runtime.getRuntime().availableProcessors());
        if (Thread.currentThread().isInterrupted())
            return;
        // for ( final AbstractAffineTile2D< ? >[] tilePair : crossLayerTilePairs )
        // {
        // Display.getFront().setLayer( tilePair[ 0 ].getPatch().getLayer() );
        // Display.getFront().getSelection().clear();
        // Display.getFront().getSelection().add( tilePair[ 0 ].getPatch() );
        // Display.getFront().getSelection().add( tilePair[ 1 ].getPatch() );
        // 
        // Utils.showMessage( "1: OK?" );
        // 
        // Display.getFront().setLayer( tilePair[ 1 ].getPatch().getLayer() );
        // Display.getFront().getSelection().clear();
        // Display.getFront().getSelection().add( tilePair[ 0 ].getPatch() );
        // Display.getFront().getSelection().add( tilePair[ 1 ].getPatch() );
        // 
        // Utils.showMessage( "2: OK?" );
        // }
        /* prepare the next loop */
        allTiles.addAll(csCurrentLayerTiles);
        previousLayerTiles.clear();
        previousLayerTiles.addAll(csCurrentLayerTiles);
        /* optimize */
        Align.optimizeTileConfiguration(pcp, allTiles, allFixedTiles);
        if (Thread.currentThread().isInterrupted())
            return;
        for (final AbstractAffineTile2D<?> t : allTiles) t.getPatch().setAffineTransform(t.getModel().createAffine());
        previousLayer = layer;
    }
    final List<Set<Tile<?>>> graphs = AbstractAffineTile2D.identifyConnectedGraphs(allTiles);
    final List<AbstractAffineTile2D<?>> interestingTiles = new ArrayList<AbstractAffineTile2D<?>>();
    if (largestGraphOnlyIn && (hideDisconnectedTilesIn || deleteDisconnectedTilesIn)) {
        if (Thread.currentThread().isInterrupted())
            return;
        /* find largest graph. */
        Set<Tile<?>> largestGraph = null;
        for (final Set<Tile<?>> graph : graphs) if (largestGraph == null || largestGraph.size() < graph.size())
            largestGraph = graph;
        final Set<AbstractAffineTile2D<?>> tiles_to_keep = new HashSet<AbstractAffineTile2D<?>>();
        for (final Tile<?> t : largestGraph) tiles_to_keep.add((AbstractAffineTile2D<?>) t);
        if (hideDisconnectedTilesIn)
            for (final AbstractAffineTile2D<?> t : allTiles) if (!tiles_to_keep.contains(t))
                t.getPatch().setVisible(false);
        if (deleteDisconnectedTilesIn)
            for (final AbstractAffineTile2D<?> t : allTiles) if (!tiles_to_keep.contains(t))
                t.getPatch().remove(false);
        interestingTiles.addAll(tiles_to_keep);
    } else
        interestingTiles.addAll(allTiles);
    if (deformIn) {
        /* ############################################ */
        /* experimental: use the center points of all tiles to define a MLS deformation from the pure intra-layer registration to the globally optimal */
        Utils.log("deforming...");
        /* store the center location of each single tile for later deformation */
        for (final AbstractAffineTile2D<?> t : interestingTiles) {
            final double[] c = new double[] { t.getWidth() / 2.0, t.getHeight() / 2.0 };
            t.getModel().applyInPlace(c);
            final Point q = new Point(c);
            tileCenterPoints.put(t.getPatch(), new PointMatch(q.clone(), q));
        }
        for (final Layer layer : layerRange) {
            Utils.log("layer" + layer);
            if (Thread.currentThread().isInterrupted())
                return;
            /* again, align all tiles in the layer */
            final List<Patch> patches = new ArrayList<Patch>();
            for (final Displayable a : layer.getDisplayables(Patch.class)) if (a instanceof Patch)
                patches.add((Patch) a);
            final List<AbstractAffineTile2D<?>> currentLayerTiles = new ArrayList<AbstractAffineTile2D<?>>();
            final List<AbstractAffineTile2D<?>> fixedTiles = new ArrayList<AbstractAffineTile2D<?>>();
            Align.tilesFromPatches(p, patches, fixedPatches, currentLayerTiles, fixedTiles);
            /* add a fixed tile only if there was a Patch selected */
            allFixedTiles.addAll(fixedTiles);
            // will consider graphs and hide/delete tiles when all cross-layer graphs are found
            alignTiles(p, currentLayerTiles, fixedTiles, true, false, false, false);
            /* for each independent graph do an independent transform */
            final List<Set<Tile<?>>> currentLayerGraphs = AbstractAffineTile2D.identifyConnectedGraphs(currentLayerTiles);
            for (final Set<Tile<?>> graph : currentLayerGraphs) {
                /* update the tile-center pointmatches */
                final Collection<PointMatch> matches = new ArrayList<PointMatch>();
                final Collection<AbstractAffineTile2D<?>> toBeDeformedTiles = new ArrayList<AbstractAffineTile2D<?>>();
                for (final AbstractAffineTile2D<?> t : (Collection<AbstractAffineTile2D<?>>) (Collection) graph) {
                    final PointMatch pm = tileCenterPoints.get(t.getPatch());
                    if (pm == null)
                        continue;
                    final double[] pl = pm.getP1().getL();
                    pl[0] = t.getWidth() / 2.0;
                    pl[1] = t.getHeight() / 2.0;
                    t.getModel().applyInPlace(pl);
                    matches.add(pm);
                    toBeDeformedTiles.add(t);
                }
                for (final AbstractAffineTile2D<?> t : toBeDeformedTiles) {
                    if (Thread.currentThread().isInterrupted())
                        return;
                    try {
                        final Patch patch = t.getPatch();
                        final Rectangle pbox = patch.getCoordinateTransformBoundingBox();
                        final AffineTransform pat = new AffineTransform();
                        pat.translate(-pbox.x, -pbox.y);
                        pat.preConcatenate(patch.getAffineTransform());
                        final mpicbg.trakem2.transform.AffineModel2D toWorld = new mpicbg.trakem2.transform.AffineModel2D();
                        toWorld.set(pat);
                        final MovingLeastSquaresTransform2 mlst = Align.createMLST(matches, 1.0f);
                        final CoordinateTransformList<CoordinateTransform> ctl = new CoordinateTransformList<CoordinateTransform>();
                        ctl.add(toWorld);
                        ctl.add(mlst);
                        ctl.add(toWorld.createInverse());
                        patch.appendCoordinateTransform(ctl);
                        patch.getProject().getLoader().regenerateMipMaps(patch);
                    } catch (final Exception e) {
                        e.printStackTrace();
                    }
                }
            }
        }
    }
    layerRange.get(0).getParent().setMinimumDimensions();
    IJ.log("Done: register multi-layer mosaic.");
    return;
}

Example 20 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class AlignTask method transformVectorData.

public static final void transformVectorData(final ReferenceData rd, /* The transformations of patches before alignment. */
final Collection<Displayable> vdata, /* The VectorData instances to transform along with images. */
final LayerSet target_layerset) /* The LayerSet in which the vdata and the transformed images exist. */
{
    final ExecutorService exec = Utils.newFixedThreadPool("AlignTask-transformVectorData");
    try {
        final Collection<Future<?>> fus = new ArrayList<Future<?>>();
        final HashMap<Long, Layer> lidm = new HashMap<Long, Layer>();
        for (final Long lid : rd.src_layer_lids_used) {
            final Layer la = target_layerset.getLayer(lid.longValue());
            if (null == la) {
                Utils.log("ERROR layer with id " + lid + " NOT FOUND in target layerset!");
                continue;
            }
            lidm.put(lid, la);
        }
        for (final Map.Entry<Displayable, Map<Long, TreeMap<Integer, Long>>> ed : rd.underlying.entrySet()) {
            // The VectorData instance to transform
            final Displayable d = ed.getKey();
            // Process Displayables concurrently:
            fus.add(exec.submit(new Runnable() {

                @SuppressWarnings({ "rawtypes", "unchecked" })
                @Override
                public void run() {
                    for (final Map.Entry<Long, TreeMap<Integer, Long>> el : ed.getValue().entrySet()) {
                        // The entry has the id of the layer and the stack-index-ordered list of Patch that intersect VectorData d in that Layer
                        final Layer layer = lidm.get(el.getKey());
                        if (null == layer) {
                            Utils.log("ERROR layer with id " + el.getKey() + " NOT FOUND in target layerset!");
                            continue;
                        }
                        // Utils.log("Editing Displayable " + d + " at layer " + layer);
                        // list of Patch ids affecting VectorData/Displayable d
                        final ArrayList<Long> pids = new ArrayList<Long>(el.getValue().values());
                        // so now Patch ids are sorted from top to bottom
                        Collections.reverse(pids);
                        // The area already processed in the layer
                        final Area used_area = new Area();
                        // The map of areas vs transforms for each area to apply to the VectorData, to its data within the layer only
                        final VectorDataTransform vdt = new VectorDataTransform(layer);
                        // The list of transforms to apply to each VectorData
                        for (final long pid : pids) {
                            // Find the Patch with id 'pid' in Layer 'la' of the target LayerSet:
                            final DBObject ob = layer.findById(pid);
                            if (null == ob || !(ob instanceof Patch)) {
                                Utils.log("ERROR layer with id " + layer.getId() + " DOES NOT CONTAIN a Patch with id " + pid);
                                continue;
                            }
                            final Patch patch = (Patch) ob;
                            // no need to synch, read only from now on
                            final Patch.TransformProperties props = rd.tp.get(pid);
                            if (null == props) {
                                Utils.log("ERROR: could not find any Patch.TransformProperties for patch " + patch);
                                continue;
                            }
                            final Area a = new Area(props.area);
                            a.subtract(used_area);
                            if (M.isEmpty(a)) {
                                // skipping fully occluded Patch
                                continue;
                            }
                            // Accumulate:
                            used_area.add(props.area);
                            // For the remaining area within this Layer, define a transform
                            // Generate a CoordinateTransformList that includes:
                            // 1 - an inverted transform from Patch coords to world coords
                            // 2 - the CoordinateTransform of the Patch, if any
                            // 3 - the AffineTransform of the Patch
                            // 
                            // The idea is to first send the data from world to pixel space of the Patch, using the old transfroms,
                            // and then from pixel space of the Patch to world, using the new transforms.
                            final CoordinateTransformList tlist = new CoordinateTransformList();
                            // 1. Inverse of the old affine: from world into the old patch mipmap
                            final mpicbg.models.AffineModel2D aff_inv = new mpicbg.models.AffineModel2D();
                            try {
                                aff_inv.set(props.at.createInverse());
                            } catch (final NoninvertibleTransformException nite) {
                                Utils.log("ERROR: could not invert the affine transform for Patch " + patch);
                                IJError.print(nite);
                                continue;
                            }
                            tlist.add(aff_inv);
                            // 2. Inverse of the old coordinate transform of the Patch: from old mipmap to pixels in original image
                            if (null != props.ct) {
                                // The props.ct is a CoordinateTransform, not necessarily an InvertibleCoordinateTransform
                                // So the mesh is necessary to ensure the invertibility
                                final mpicbg.trakem2.transform.TransformMesh mesh = new mpicbg.trakem2.transform.TransformMesh(props.ct, props.meshResolution, props.o_width, props.o_height);
                                /* // Apparently not needed; the inverse affine in step 1 took care of it.
								 * // (the affine of step 1 includes the mesh translation)
							Rectangle box = mesh.getBoundingBox();
							AffineModel2D aff = new AffineModel2D();
							aff.set(new AffineTransform(1, 0, 0, 1, box.x, box.y));
							tlist.add(aff);
								 */
                                tlist.add(new InverseICT(mesh));
                            }
                            // 3. New coordinate transform of the Patch: from original image to new mipmap
                            final mpicbg.trakem2.transform.CoordinateTransform ct = patch.getCoordinateTransform();
                            if (null != ct) {
                                tlist.add(ct);
                                final mpicbg.trakem2.transform.TransformMesh mesh = new mpicbg.trakem2.transform.TransformMesh(ct, patch.getMeshResolution(), patch.getOWidth(), patch.getOHeight());
                                // correct for mesh bounds -- Necessary because it comes from the other side, and the removal of the translation here is re-added by the affine in step 4!
                                final Rectangle box = mesh.getBoundingBox();
                                final AffineModel2D aff = new AffineModel2D();
                                aff.set(new AffineTransform(1, 0, 0, 1, -box.x, -box.y));
                                tlist.add(aff);
                            }
                            // 4. New affine transform of the Patch: from mipmap to world
                            final mpicbg.models.AffineModel2D new_aff = new mpicbg.models.AffineModel2D();
                            new_aff.set(patch.getAffineTransform());
                            tlist.add(new_aff);
                            /*
						// TODO Consider caching the tlist for each Patch, or for a few thousand of them maximum.
						//      But it could blow up memory astronomically.

						// The old part:
						final mpicbg.models.InvertibleCoordinateTransformList old = new mpicbg.models.InvertibleCoordinateTransformList();
						if (null != props.ct) {
							mpicbg.trakem2.transform.TransformMesh mesh = new mpicbg.trakem2.transform.TransformMesh(props.ct, props.meshResolution, props.o_width, props.o_height);
							old.add(mesh);
						}
						final mpicbg.models.AffineModel2D old_aff = new mpicbg.models.AffineModel2D();
						old_aff.set(props.at);
						old.add(old_aff);

						tlist.add(new InverseICT(old));

						// The new part:
						final mpicbg.models.AffineModel2D new_aff = new mpicbg.models.AffineModel2D();
						new_aff.set(patch.getAffineTransform());
						tlist.add(new_aff);
						final mpicbg.trakem2.transform.CoordinateTransform ct = patch.getCoordinateTransform();
						if (null != ct) tlist.add(ct);
							 */
                            vdt.add(a, tlist);
                        }
                        // Apply the map of area vs tlist for the data section of d within the layer:
                        try {
                            ((VectorData) d).apply(vdt);
                        } catch (final Exception t) {
                            Utils.log("ERROR transformation failed for " + d + " at layer " + layer);
                            IJError.print(t);
                        }
                    }
                }
            }));
        }
        Utils.wait(fus);
        Display.repaint();
    } finally {
        exec.shutdown();
    }
}