Examples with Pair mpicbg.trakem2.util.Pair used on opensource projects

Example 46 with Pair

use of mpicbg.trakem2.util.Pair in project LibreraReader by foobnix.

the class MultyDocSearchDialog method getDialogView.

public static View getDialogView(final FragmentActivity c) {
    View inflate = LayoutInflater.from(c).inflate(R.layout.dialog_multy_search, null, false);
    inflate.setKeepScreenOn(true);
    final EditText editPath = (EditText) inflate.findViewById(R.id.editPath);
    final Button buttonPath = (Button) inflate.findViewById(R.id.buttonPath);
    final EditText editSearchText = (EditText) inflate.findViewById(R.id.editSearchText);
    final Button searchStart = (Button) inflate.findViewById(R.id.searchStart);
    final Button searchStop = (Button) inflate.findViewById(R.id.searchStop);
    infoView1 = (TextView) inflate.findViewById(R.id.infoView1);
    final ListView listView = (ListView) inflate.findViewById(R.id.listView);
    final CheckBox searchInTheSubfolders = (CheckBox) inflate.findViewById(R.id.searchInTheSubfolders);
    final BaseItemLayoutAdapter adapter = new BaseItemLayoutAdapter<Pair<String, Integer>>(c, android.R.layout.simple_list_item_1, Model.get().res) {

        @Override
        public void populateView(View layout, int position, final Pair<String, Integer> item) {
            final File file = new File(item.first);
            TextView t = (TextView) layout.findViewById(android.R.id.text1);
            t.setText(file.getName() + " [" + (item.second == -1 ? "not found" : (item.second + 1)) + "]");
            t.setOnClickListener(new OnClickListener() {

                @Override
                public void onClick(View v) {
                    ExtUtils.showDocument(c, file, item.second + 1);
                }
            });
        }
    };
    listView.setAdapter(adapter);
    buttonPath.setOnClickListener(new OnClickListener() {

        @Override
        public void onClick(View v) {
            ChooserDialogFragment.chooseFolder(c, Model.get().path).setOnSelectListener(new ResultResponse2<String, Dialog>() {

                @Override
                public boolean onResultRecive(String nPath, Dialog dialog) {
                    Model.get().path = nPath;
                    AppState.get().dirLastPath = nPath;
                    editPath.setText(Model.get().path);
                    dialog.dismiss();
                    return false;
                }
            });
        }
    });
    editPath.setText(Model.get().path);
    final Handler updater2 = new Handler() {

        @Override
        public void handleMessage(Message msg) {
            adapter.notifyDataSetChanged();
        }
    };
    final Handler updater1 = new Handler() {

        @Override
        public void handleMessage(Message msg) {
            infoView1.setText((Model.get().currentPage + 1) + "/" + Model.get().currentPagesCount + " " + Model.get().currentDoc);
        }
    };
    searchStart.setOnClickListener(new OnClickListener() {

        @Override
        public void onClick(View v) {
            Model.get().text = editSearchText.getText().toString().trim();
            if (TxtUtils.isEmpty(Model.get().text)) {
                Toast.makeText(c, R.string.incorrect_value, Toast.LENGTH_SHORT).show();
                return;
            }
            if (Model.get().text.contains(" ")) {
                Toast.makeText(c, R.string.you_can_search_only_one_word, Toast.LENGTH_SHORT).show();
                return;
            }
            if (Model.get().isSearcingRun) {
                Toast.makeText(c, R.string.searching_please_wait_, Toast.LENGTH_SHORT).show();
                return;
            }
            Model.get().isSearcingRun = true;
            new MyTask(updater1, updater2, c, searchInTheSubfolders.isChecked()).execute();
            infoView1.setText("");
            Model.get().res.clear();
            adapter.notifyDataSetChanged();
            Keyboards.close(editSearchText);
        }
    });
    editSearchText.setOnEditorActionListener(new OnEditorActionListener() {

        @Override
        public boolean onEditorAction(TextView v, int actionId, KeyEvent event) {
            boolean handled = false;
            if (actionId == EditorInfo.IME_ACTION_SEARCH) {
                searchStart.performClick();
                handled = true;
            }
            return handled;
        }
    });
    editSearchText.setOnKeyListener(new OnKeyListener() {

        @Override
        public boolean onKey(View v, int keyCode, KeyEvent event) {
            if (keyCode == KeyEvent.KEYCODE_ENTER) {
                searchStart.performClick();
                return true;
            }
            return false;
        }
    });
    searchStop.setOnClickListener(new OnClickListener() {

        @Override
        public void onClick(View v) {
            Model.get().isSearcingRun = false;
            infoView1.setText("");
        }
    });
    infoView1.setText("");
    Model.get().res.clear();
    adapter.notifyDataSetChanged();
    return inflate;
}

Example 47 with Pair

use of mpicbg.trakem2.util.Pair in project repseqio by repseqio.

the class MarkovInsertModel method create.

@Override
public InsertGenerator create(RandomGenerator random, final boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes) {
    Map<Byte, List<Pair<Byte, Double>>> distParams = new HashMap<>();
    for (Map.Entry<String, Double> s : distribution.entrySet()) {
        String[] split = s.getKey().split(">");
        if (split.length != 2 || split[0].length() != 1 || split[1].length() != 1)
            throw new IllegalArgumentException("Illegal distribution key: " + s.getKey() + ". " + "Expected something like \"A>C\"");
        byte codeFrom = NucleotideSequence.ALPHABET.symbolToCode(split[0].charAt(0));
        byte codeTo = NucleotideSequence.ALPHABET.symbolToCode(split[1].charAt(0));
        if (codeFrom == -1 || codeTo == -1)
            throw new IllegalArgumentException("Illegal nucleotide in: " + s.getKey() + ".");
        List<Pair<Byte, Double>> pairs = distParams.get(codeFrom);
        if (pairs == null)
            distParams.put(codeFrom, pairs = new ArrayList<>());
        pairs.add(new Pair<>(codeTo, s.getValue()));
    }
    final Map<Byte, EnumeratedDistribution<Byte>> dists = new HashMap<>();
    for (byte from = 0; from < NucleotideSequence.ALPHABET.basicSize(); from++) {
        List<Pair<Byte, Double>> d = distParams.get(from);
        if (d == null)
            throw new IllegalArgumentException("No distribution for letter: " + NucleotideSequence.ALPHABET.codeToSymbol(from));
        dists.put(from, new EnumeratedDistribution<>(random, d));
    }
    final IndependentIntGenerator lengthDist = lengthDistribution.create(random);
    return new InsertGenerator() {

        @Override
        public NucleotideSequence generate(GGene gene) {
            ReferencePoint point = beginPoint(fromLeft, v);
            int pointPosition = gene.getPartitioning().getPosition(point);
            if (pointPosition == -1)
                throw new RuntimeException("Point " + point + " is not available for gene " + gene);
            byte letter = gene.getSequence(new Range(pointPosition, pointPosition + 1)).codeAt(0);
            int length = lengthDist.sample();
            byte[] array = new byte[length];
            for (int i = 0; i < length; i++) {
                byte cLetter = dists.get(letter).sample();
                array[i] = cLetter;
                letter = cLetter;
            }
            if (!fromLeft)
                ArraysUtils.reverse(array);
            return NucleotideSequence.ALPHABET.createBuilder().ensureCapacity(length).append(array).createAndDestroy();
        }
    };
}

Example 48 with Pair

use of mpicbg.trakem2.util.Pair in project androidApp by InspectorIncognito.

the class GetBusesRequest method processResult.

@NonNull
@Override
public Pair<ArrayList<MapBus>, ArrayList<Event>> processResult(@NonNull String result) {
    ArrayList<MapBus> busResponse = new ArrayList<>();
    ArrayList<Event> eventResponse = new ArrayList<>();
    try {
        JSONObject response = new JSONObject(result);
        JSONArray buses = response.getJSONArray("servicios");
        JSONArray events = response.getJSONArray("eventos");
        Log.d("Callback events", events.toString());
        for (int i = 0; i < buses.length(); i++) {
            try {
                MapBus bus = new MapBus(buses.getJSONObject(i));
                busResponse.add(bus);
            } catch (JSONException ignored) {
            }
        }
        for (int i = 0; i < events.length(); i++) {
        // Event event = new Event(events.getJSONObject(i));
        // eventResponse.add(event);
        }
        return new Pair<>(busResponse, eventResponse);
    } catch (JSONException e) {
        e.printStackTrace();
        Log.e("GetBusesRequest", result);
    }
    return new Pair<>(busResponse, eventResponse);
}

Example 49 with Pair

use of mpicbg.trakem2.util.Pair in project TrakEM2 by trakem2.

the class ElasticLayerAlignment method exec.

/**
 * @param param
 * @param layerRange
 * @param fixedLayers
 * @param emptyLayers
 * @param box
 * @param filter
 * @param useTps true if using TPS transforms, otherwise MLS
 * @throws Exception
 */
@SuppressWarnings("deprecation")
public final void exec(final Param param, final Project project, final List<Layer> layerRange, final Set<Layer> fixedLayers, final Set<Layer> emptyLayers, final Rectangle box, final boolean propagateTransformBefore, final boolean propagateTransformAfter, final Filter<Patch> filter) throws Exception {
    final ExecutorService service = ExecutorProvider.getExecutorService(1.0f);
    /* create tiles and models for all layers */
    final ArrayList<Tile<?>> tiles = new ArrayList<Tile<?>>();
    for (int i = 0; i < layerRange.size(); ++i) {
        switch(param.desiredModelIndex) {
            case 0:
                tiles.add(new Tile<TranslationModel2D>(new TranslationModel2D()));
                break;
            case 1:
                tiles.add(new Tile<RigidModel2D>(new RigidModel2D()));
                break;
            case 2:
                tiles.add(new Tile<SimilarityModel2D>(new SimilarityModel2D()));
                break;
            case 3:
                tiles.add(new Tile<AffineModel2D>(new AffineModel2D()));
                break;
            case 4:
                tiles.add(new Tile<HomographyModel2D>(new HomographyModel2D()));
                break;
            default:
                return;
        }
    }
    /* collect all pairs of slices for which a model could be found */
    final ArrayList<Triple<Integer, Integer, AbstractModel<?>>> pairs = new ArrayList<Triple<Integer, Integer, AbstractModel<?>>>();
    if (!param.isAligned) {
        preAlignStack(param, project, layerRange, box, filter, pairs);
    } else {
        for (int i = 0; i < layerRange.size(); ++i) {
            final int range = Math.min(layerRange.size(), i + param.maxNumNeighbors + 1);
            for (int j = i + 1; j < range; ++j) {
                pairs.add(new Triple<Integer, Integer, AbstractModel<?>>(i, j, new TranslationModel2D()));
            }
        }
    }
    /* Elastic alignment */
    /* Initialization */
    final TileConfiguration initMeshes = new TileConfiguration();
    final int meshWidth = (int) Math.ceil(box.width * param.layerScale);
    final int meshHeight = (int) Math.ceil(box.height * param.layerScale);
    final ArrayList<SpringMesh> meshes = new ArrayList<SpringMesh>(layerRange.size());
    for (int i = 0; i < layerRange.size(); ++i) {
        meshes.add(new SpringMesh(param.resolutionSpringMesh, meshWidth, meshHeight, param.stiffnessSpringMesh, param.maxStretchSpringMesh * param.layerScale, param.dampSpringMesh));
    }
    // final int blockRadius = Math.max( 32, meshWidth / p.resolutionSpringMesh / 2 );
    final int blockRadius = Math.max(16, mpicbg.util.Util.roundPos(param.layerScale * param.blockRadius));
    Utils.log("effective block radius = " + blockRadius);
    final ArrayList<Future<BlockMatchPairCallable.BlockMatchResults>> futures = new ArrayList<Future<BlockMatchPairCallable.BlockMatchResults>>(pairs.size());
    for (final Triple<Integer, Integer, AbstractModel<?>> pair : pairs) {
        /* free memory */
        project.getLoader().releaseAll();
        final SpringMesh m1 = meshes.get(pair.a);
        final SpringMesh m2 = meshes.get(pair.b);
        final ArrayList<Vertex> v1 = m1.getVertices();
        final ArrayList<Vertex> v2 = m2.getVertices();
        final Layer layer1 = layerRange.get(pair.a);
        final Layer layer2 = layerRange.get(pair.b);
        final boolean layer1Fixed = fixedLayers.contains(layer1);
        final boolean layer2Fixed = fixedLayers.contains(layer2);
        if (!(layer1Fixed && layer2Fixed)) {
            final BlockMatchPairCallable bmpc = new BlockMatchPairCallable(pair, layerRange, layer1Fixed, layer2Fixed, filter, param, v1, v2, box);
            futures.add(service.submit(bmpc));
        }
    }
    for (final Future<BlockMatchPairCallable.BlockMatchResults> future : futures) {
        final BlockMatchPairCallable.BlockMatchResults results = future.get();
        final Collection<PointMatch> pm12 = results.pm12, pm21 = results.pm21;
        final Triple<Integer, Integer, AbstractModel<?>> pair = results.pair;
        final Tile<?> t1 = tiles.get(pair.a);
        final Tile<?> t2 = tiles.get(pair.b);
        final SpringMesh m1 = meshes.get(pair.a);
        final SpringMesh m2 = meshes.get(pair.b);
        final double springConstant = 1.0 / (pair.b - pair.a);
        final boolean layer1Fixed = results.layer1Fixed;
        final boolean layer2Fixed = results.layer2Fixed;
        if (layer1Fixed) {
            initMeshes.fixTile(t1);
        } else {
            if (param.useLocalSmoothnessFilter) {
                Utils.log(pair.a + " > " + pair.b + ": " + pm12.size() + " candidates passed local smoothness filter.");
            } else {
                Utils.log(pair.a + " > " + pair.b + ": found " + pm12.size() + " correspondences.");
            }
            for (final PointMatch pm : pm12) {
                final Vertex p1 = (Vertex) pm.getP1();
                final Vertex p2 = new Vertex(pm.getP2());
                p1.addSpring(p2, new Spring(0, springConstant));
                m2.addPassiveVertex(p2);
            }
            /*
                * adding Tiles to the initialing TileConfiguration, adding a Tile
                * multiple times does not harm because the TileConfiguration is
                * backed by a Set.
                */
            if (pm12.size() > pair.c.getMinNumMatches()) {
                initMeshes.addTile(t1);
                initMeshes.addTile(t2);
                t1.connect(t2, pm12);
            }
        }
        if (layer2Fixed)
            initMeshes.fixTile(t2);
        else {
            if (param.useLocalSmoothnessFilter) {
                Utils.log(pair.a + " < " + pair.b + ": " + pm21.size() + " candidates passed local smoothness filter.");
            } else {
                Utils.log(pair.a + " < " + pair.b + ": found " + pm21.size() + " correspondences.");
            }
            for (final PointMatch pm : pm21) {
                final Vertex p1 = (Vertex) pm.getP1();
                final Vertex p2 = new Vertex(pm.getP2());
                p1.addSpring(p2, new Spring(0, springConstant));
                m1.addPassiveVertex(p2);
            }
            /*
                * adding Tiles to the initialing TileConfiguration, adding a Tile
                * multiple times does not harm because the TileConfiguration is
                * backed by a Set.
                */
            if (pm21.size() > pair.c.getMinNumMatches()) {
                initMeshes.addTile(t1);
                initMeshes.addTile(t2);
                t2.connect(t1, pm21);
            }
        }
        Utils.log(pair.a + " <> " + pair.b + " spring constant = " + springConstant);
    }
    /* pre-align by optimizing a piecewise linear model */
    initMeshes.optimize(param.maxEpsilon * param.layerScale, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh);
    for (int i = 0; i < layerRange.size(); ++i) meshes.get(i).init(tiles.get(i).getModel());
    /* optimize the meshes */
    try {
        final long t0 = System.currentTimeMillis();
        Utils.log("Optimizing spring meshes...");
        if (param.useLegacyOptimizer) {
            Utils.log("  ...using legacy optimizer...");
            SpringMesh.optimizeMeshes2(meshes, param.maxEpsilon * param.layerScale, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
        } else {
            SpringMesh.optimizeMeshes(meshes, param.maxEpsilon * param.layerScale, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
        }
        Utils.log("Done optimizing spring meshes. Took " + (System.currentTimeMillis() - t0) + " ms");
    } catch (final NotEnoughDataPointsException e) {
        Utils.log("There were not enough data points to get the spring mesh optimizing.");
        e.printStackTrace();
        return;
    }
    /* translate relative to bounding box */
    for (final SpringMesh mesh : meshes) {
        for (final PointMatch pm : mesh.getVA().keySet()) {
            final Point p1 = pm.getP1();
            final Point p2 = pm.getP2();
            final double[] l = p1.getL();
            final double[] w = p2.getW();
            l[0] = l[0] / param.layerScale + box.x;
            l[1] = l[1] / param.layerScale + box.y;
            w[0] = w[0] / param.layerScale + box.x;
            w[1] = w[1] / param.layerScale + box.y;
        }
    }
    /* free memory */
    project.getLoader().releaseAll();
    final Layer first = layerRange.get(0);
    final List<Layer> layers = first.getParent().getLayers();
    final LayerSet ls = first.getParent();
    final Area infArea = AreaUtils.infiniteArea();
    final List<VectorData> vectorData = new ArrayList<VectorData>();
    for (final Layer layer : ls.getLayers()) {
        vectorData.addAll(Utils.castCollection(layer.getDisplayables(VectorData.class, false, true), VectorData.class, true));
    }
    vectorData.addAll(Utils.castCollection(ls.getZDisplayables(VectorData.class, true), VectorData.class, true));
    /* transfer layer transform into patch transforms and append to patches */
    if (propagateTransformBefore || propagateTransformAfter) {
        if (propagateTransformBefore) {
            final ThinPlateSplineTransform tps = makeTPS(meshes.get(0).getVA().keySet());
            final int firstLayerIndex = first.getParent().getLayerIndex(first.getId());
            for (int i = 0; i < firstLayerIndex; ++i) {
                applyTransformToLayer(layers.get(i), tps, filter);
                for (final VectorData vd : vectorData) {
                    vd.apply(layers.get(i), infArea, tps);
                }
            }
        }
        if (propagateTransformAfter) {
            final Layer last = layerRange.get(layerRange.size() - 1);
            final CoordinateTransform ct;
            if (param.useTps)
                ct = makeTPS(meshes.get(meshes.size() - 1).getVA().keySet());
            else {
                final MovingLeastSquaresTransform2 mls = new MovingLeastSquaresTransform2();
                mls.setMatches(meshes.get(meshes.size() - 1).getVA().keySet());
                ct = mls;
            }
            final int lastLayerIndex = last.getParent().getLayerIndex(last.getId());
            for (int i = lastLayerIndex + 1; i < layers.size(); ++i) {
                applyTransformToLayer(layers.get(i), ct, filter);
                for (final VectorData vd : vectorData) {
                    vd.apply(layers.get(i), infArea, ct);
                }
            }
        }
    }
    for (int l = 0; l < layerRange.size(); ++l) {
        IJ.showStatus("Applying transformation to patches ...");
        IJ.showProgress(0, layerRange.size());
        final Layer layer = layerRange.get(l);
        final ThinPlateSplineTransform tps = makeTPS(meshes.get(l).getVA().keySet());
        applyTransformToLayer(layer, tps, filter);
        for (final VectorData vd : vectorData) {
            vd.apply(layer, infArea, tps);
        }
        if (Thread.interrupted()) {
            Utils.log("Interrupted during applying transformations to patches.  No all patches have been updated.  Re-generate mipmaps manually.");
        }
        IJ.showProgress(l + 1, layerRange.size());
    }
    /* update patch mipmaps */
    final int firstLayerIndex;
    final int lastLayerIndex;
    if (propagateTransformBefore)
        firstLayerIndex = 0;
    else {
        firstLayerIndex = first.getParent().getLayerIndex(first.getId());
    }
    if (propagateTransformAfter)
        lastLayerIndex = layers.size() - 1;
    else {
        final Layer last = layerRange.get(layerRange.size() - 1);
        lastLayerIndex = last.getParent().getLayerIndex(last.getId());
    }
    for (int i = firstLayerIndex; i <= lastLayerIndex; ++i) {
        final Layer layer = layers.get(i);
        if (!(emptyLayers.contains(layer) || fixedLayers.contains(layer))) {
            for (final Patch patch : AlignmentUtils.filterPatches(layer, filter)) patch.updateMipMaps();
        }
    }
    Utils.log("Done.");
}

Example 50 with Pair

use of mpicbg.trakem2.util.Pair in project TrakEM2 by trakem2.

the class ElasticMontage method exec.

@SuppressWarnings("deprecation")
public final void exec(final Param param, final List<Patch> patches, final Set<Patch> fixedPatches) throws Exception {
    /* free memory */
    patches.get(0).getProject().getLoader().releaseAll();
    /* create tiles and models for all patches */
    final ArrayList<AbstractAffineTile2D<?>> tiles = new ArrayList<AbstractAffineTile2D<?>>();
    final ArrayList<AbstractAffineTile2D<?>> fixedTiles = new ArrayList<AbstractAffineTile2D<?>>();
    Align.tilesFromPatches(param.po, patches, fixedPatches, tiles, fixedTiles);
    if (!param.isAligned) {
        Align.alignTiles(param.po, tiles, fixedTiles, param.tilesAreInPlace, param.maxNumThreads);
        /* Apply the estimated affine transform to patches */
        for (final AbstractAffineTile2D<?> t : tiles) t.getPatch().setAffineTransform(t.createAffine());
        Display.update();
    }
    /* generate tile pairs for all by now overlapping tiles */
    final ArrayList<AbstractAffineTile2D<?>[]> tilePairs = new ArrayList<AbstractAffineTile2D<?>[]>();
    AbstractAffineTile2D.pairOverlappingTiles(tiles, tilePairs);
    /* check if there was any pair */
    if (tilePairs.size() == 0) {
        Utils.log("Elastic montage could not find any overlapping patches after pre-montaging.");
        return;
    }
    Utils.log(tilePairs.size() + " pairs of patches will be block-matched...");
    /* make pairwise global models local */
    final ArrayList<Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform>> pairs = new ArrayList<Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform>>();
    /*
		 * The following casting madness is necessary to get this code compiled
		 * with Sun/Oracle Java 6 which otherwise generates an inconvertible
		 * type exception.
		 *
		 * TODO Remove as soon as this bug is fixed in Sun/Oracle javac.
		 */
    for (final AbstractAffineTile2D<?>[] pair : tilePairs) {
        final AbstractAffineModel2D<?> m;
        switch(param.po.desiredModelIndex) {
            case 0:
                final TranslationModel2D t = (TranslationModel2D) (Object) pair[1].getModel().createInverse();
                t.concatenate((TranslationModel2D) (Object) pair[0].getModel());
                m = t;
                break;
            case 1:
                final RigidModel2D r = (RigidModel2D) (Object) pair[1].getModel().createInverse();
                r.concatenate((RigidModel2D) (Object) pair[0].getModel());
                m = r;
                break;
            case 2:
                final SimilarityModel2D s = (SimilarityModel2D) (Object) pair[1].getModel().createInverse();
                s.concatenate((SimilarityModel2D) (Object) pair[0].getModel());
                m = s;
                break;
            case 3:
                final AffineModel2D a = (AffineModel2D) (Object) pair[1].getModel().createInverse();
                a.concatenate((AffineModel2D) (Object) pair[0].getModel());
                m = a;
                break;
            default:
                m = null;
        }
        pairs.add(new Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform>(pair[0], pair[1], m));
    }
    /* Elastic alignment */
    /* Initialization */
    final double springTriangleHeightTwice = 2 * Math.sqrt(0.75 * param.springLengthSpringMesh * param.springLengthSpringMesh);
    final ArrayList<SpringMesh> meshes = new ArrayList<SpringMesh>(tiles.size());
    final HashMap<AbstractAffineTile2D<?>, SpringMesh> tileMeshMap = new HashMap<AbstractAffineTile2D<?>, SpringMesh>();
    for (final AbstractAffineTile2D<?> tile : tiles) {
        final double w = tile.getWidth();
        final double h = tile.getHeight();
        final int numX = Math.max(2, (int) Math.ceil(w / param.springLengthSpringMesh) + 1);
        final int numY = Math.max(2, (int) Math.ceil(h / springTriangleHeightTwice) + 1);
        final double wMesh = (numX - 1) * param.springLengthSpringMesh;
        final double hMesh = (numY - 1) * springTriangleHeightTwice;
        final SpringMesh mesh = new SpringMesh(numX, numY, wMesh, hMesh, param.stiffnessSpringMesh, param.maxStretchSpringMesh * param.bmScale, param.dampSpringMesh);
        meshes.add(mesh);
        tileMeshMap.put(tile, mesh);
    }
    // final int blockRadius = Math.max( 32, Util.roundPos( param.springLengthSpringMesh / 2 ) );
    final int blockRadius = Math.max(Util.roundPos(16 / param.bmScale), param.bmBlockRadius);
    /**
     * TODO set this something more than the largest error by the approximate model
     */
    final int searchRadius = param.bmSearchRadius;
    final AbstractModel<?> localSmoothnessFilterModel = mpicbg.trakem2.align.Util.createModel(param.bmLocalModelIndex);
    for (final Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform> pair : pairs) {
        final AbstractAffineTile2D<?> t1 = pair.a;
        final AbstractAffineTile2D<?> t2 = pair.b;
        final SpringMesh m1 = tileMeshMap.get(t1);
        final SpringMesh m2 = tileMeshMap.get(t2);
        final ArrayList<PointMatch> pm12 = new ArrayList<PointMatch>();
        final ArrayList<PointMatch> pm21 = new ArrayList<PointMatch>();
        final ArrayList<Vertex> v1 = m1.getVertices();
        final ArrayList<Vertex> v2 = m2.getVertices();
        final String patchName1 = patchName(t1.getPatch());
        final String patchName2 = patchName(t2.getPatch());
        final PatchImage pi1 = t1.getPatch().createTransformedImage();
        if (pi1 == null) {
            Utils.log("Patch `" + patchName1 + "' failed generating a transformed image.  Skipping...");
            continue;
        }
        final PatchImage pi2 = t2.getPatch().createTransformedImage();
        if (pi2 == null) {
            Utils.log("Patch `" + patchName2 + "' failed generating a transformed image.  Skipping...");
            continue;
        }
        final FloatProcessor fp1 = (FloatProcessor) pi1.target.convertToFloat();
        final ByteProcessor mask1 = pi1.getMask();
        final FloatProcessor fpMask1 = mask1 == null ? null : scaleByte(mask1);
        final FloatProcessor fp2 = (FloatProcessor) pi2.target.convertToFloat();
        final ByteProcessor mask2 = pi2.getMask();
        final FloatProcessor fpMask2 = mask2 == null ? null : scaleByte(mask2);
        if (!fixedTiles.contains(t1)) {
            BlockMatching.matchByMaximalPMCC(fp1, fp2, fpMask1, fpMask2, param.bmScale, pair.c, blockRadius, blockRadius, searchRadius, searchRadius, param.bmMinR, param.bmRodR, param.bmMaxCurvatureR, v1, pm12, new ErrorStatistic(1));
            if (param.bmUseLocalSmoothnessFilter) {
                Utils.log("`" + patchName1 + "' > `" + patchName2 + "': found " + pm12.size() + " correspondence candidates.");
                localSmoothnessFilterModel.localSmoothnessFilter(pm12, pm12, param.bmLocalRegionSigma, param.bmMaxLocalEpsilon, param.bmMaxLocalTrust);
                Utils.log("`" + patchName1 + "' > `" + patchName2 + "': " + pm12.size() + " candidates passed local smoothness filter.");
            } else {
                Utils.log("`" + patchName1 + "' > `" + patchName2 + "': found " + pm12.size() + " correspondences.");
            }
        } else {
            Utils.log("Skipping fixed patch `" + patchName1 + "'.");
        }
        if (!fixedTiles.contains(t2)) {
            BlockMatching.matchByMaximalPMCC(fp2, fp1, fpMask2, fpMask1, param.bmScale, pair.c.createInverse(), blockRadius, blockRadius, searchRadius, searchRadius, param.bmMinR, param.bmRodR, param.bmMaxCurvatureR, v2, pm21, new ErrorStatistic(1));
            if (param.bmUseLocalSmoothnessFilter) {
                Utils.log("`" + patchName1 + "' < `" + patchName2 + "': found " + pm21.size() + " correspondence candidates.");
                localSmoothnessFilterModel.localSmoothnessFilter(pm21, pm21, param.bmLocalRegionSigma, param.bmMaxLocalEpsilon, param.bmMaxLocalTrust);
                Utils.log("`" + patchName1 + "' < `" + patchName2 + "': " + pm21.size() + " candidates passed local smoothness filter.");
            } else {
                Utils.log("`" + patchName1 + "' < `" + patchName2 + "': found " + pm21.size() + " correspondences.");
            }
        } else {
            Utils.log("Skipping fixed patch `" + patchName2 + "'.");
        }
        for (final PointMatch pm : pm12) {
            final Vertex p1 = (Vertex) pm.getP1();
            final Vertex p2 = new Vertex(pm.getP2());
            p1.addSpring(p2, new Spring(0, 1.0f));
            m2.addPassiveVertex(p2);
        }
        for (final PointMatch pm : pm21) {
            final Vertex p1 = (Vertex) pm.getP1();
            final Vertex p2 = new Vertex(pm.getP2());
            p1.addSpring(p2, new Spring(0, 1.0f));
            m1.addPassiveVertex(p2);
        }
    }
    /* initialize */
    for (final Map.Entry<AbstractAffineTile2D<?>, SpringMesh> entry : tileMeshMap.entrySet()) entry.getValue().init(entry.getKey().getModel());
    /* optimize the meshes */
    try {
        final long t0 = System.currentTimeMillis();
        IJ.log("Optimizing spring meshes...");
        if (param.useLegacyOptimizer) {
            Utils.log("  ...using legacy optimizer...");
            SpringMesh.optimizeMeshes2(meshes, param.po.maxEpsilon, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
        } else {
            SpringMesh.optimizeMeshes(meshes, param.po.maxEpsilon, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
        }
        IJ.log("Done optimizing spring meshes. Took " + (System.currentTimeMillis() - t0) + " ms");
    } catch (final NotEnoughDataPointsException e) {
        Utils.log("There were not enough data points to get the spring mesh optimizing.");
        e.printStackTrace();
        return;
    }
    /* apply */
    for (final Map.Entry<AbstractAffineTile2D<?>, SpringMesh> entry : tileMeshMap.entrySet()) {
        final AbstractAffineTile2D<?> tile = entry.getKey();
        if (!fixedTiles.contains(tile)) {
            final Patch patch = tile.getPatch();
            final SpringMesh mesh = entry.getValue();
            final Set<PointMatch> matches = mesh.getVA().keySet();
            Rectangle box = patch.getCoordinateTransformBoundingBox();
            /* compensate for existing coordinate transform bounding box */
            for (final PointMatch pm : matches) {
                final Point p1 = pm.getP1();
                final double[] l = p1.getL();
                l[0] += box.x;
                l[1] += box.y;
            }
            final ThinPlateSplineTransform mlt = ElasticLayerAlignment.makeTPS(matches);
            patch.appendCoordinateTransform(mlt);
            box = patch.getCoordinateTransformBoundingBox();
            patch.getAffineTransform().setToTranslation(box.x, box.y);
            patch.updateInDatabase("transform");
            patch.updateBucket();
            patch.updateMipMaps();
        }
    }
    Utils.log("Done.");
}