Examples with AlignTask mpicbg.trakem2.align.AlignTask used on opensource projects

Example 1 with AlignTask

use of mpicbg.trakem2.align.AlignTask 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();
    }
}