Examples with Montage ini.trakem2.utils.Montage used on opensource projects

Example 11 with Montage

use of ini.trakem2.utils.Montage in project TrakEM2 by trakem2.

the class Loader method importGrid.

/**
 * Import a grid of images and put them in the layer. If the directory (@param dir) is null, it'll be asked for.
 */
public Bureaucrat importGrid(final Layer layer, String dir) {
    try {
        String file = null;
        if (null == dir) {
            final String[] dn = Utils.selectFile("Select first image");
            if (null == dn)
                return null;
            dir = dn[0];
            file = dn[1];
        }
        // char digit digit
        String convention = "cdd";
        boolean chars_are_columns = true;
        // examine file name
        /*
		if (file.matches("\\A[a-zA-Z]\\d\\d.*")) { // one letter, 2 numbers
			//means:
			//	\A		- beggining of input
			//	[a-zA-Z]	- any letter upper or lower case
			//	\d\d		- two consecutive digits
			//	.*		- any row of chars
			ini_grid_convention = true;
		}
		*/
        // ask for chars->rows, numbers->columns or viceversa
        final GenericDialog gd = new GenericDialog("Conventions");
        gd.addStringField("file_name_contains:", "");
        gd.addNumericField("base_x: ", 0, 3);
        gd.addNumericField("base_y: ", 0, 3);
        gd.addMessage("Use: x(any), c(haracter), d(igit)");
        gd.addStringField("convention: ", convention);
        final String[] cr = new String[] { "columns", "rows" };
        gd.addChoice("characters are: ", cr, cr[0]);
        gd.addMessage("[File extension ignored]");
        // as asked by Joachim Walter
        gd.addNumericField("bottom-top overlap: ", 0, 3);
        gd.addNumericField("left-right overlap: ", 0, 3);
        gd.addCheckbox("link_images", false);
        gd.addCheckbox("montage with phase correlation", false);
        gd.addCheckbox("homogenize_contrast", true);
        final Component[] c = { (Component) gd.getSliders().get(gd.getSliders().size() - 2), (Component) gd.getNumericFields().get(gd.getNumericFields().size() - 2), (Component) gd.getSliders().get(gd.getSliders().size() - 1), (Component) gd.getNumericFields().get(gd.getNumericFields().size() - 1), (Component) gd.getChoices().get(gd.getChoices().size() - 1) };
        // enable the checkbox to control the slider and its associated numeric field:
        Utils.addEnablerListener((Checkbox) gd.getCheckboxes().get(gd.getCheckboxes().size() - 1), c, null);
        // gd.addCheckbox("Apply non-linear deformation", false);
        gd.showDialog();
        if (gd.wasCanceled()) {
            return null;
        }
        // collect data
        // filter away files not containing this tag
        final String regex = gd.getNextString();
        // the base x,y of the whole grid
        final double bx = gd.getNextNumber();
        final double by = gd.getNextNumber();
        // if (!ini_grid_convention) {
        convention = gd.getNextString().toLowerCase();
        // }
        if (/*!ini_grid_convention && */
        (null == convention || convention.equals("") || -1 == convention.indexOf('c') || -1 == convention.indexOf('d'))) {
            // TODO check that the convention has only 'cdx' chars and also that there is an island of 'c's and of 'd's only.
            Utils.showMessage("Convention '" + convention + "' needs both c(haracters) and d(igits), optionally 'x', and nothing else!");
            return null;
        }
        chars_are_columns = (0 == gd.getNextChoiceIndex());
        final double bt_overlap = gd.getNextNumber();
        final double lr_overlap = gd.getNextNumber();
        final boolean link_images = gd.getNextBoolean();
        final boolean stitch_tiles = gd.getNextBoolean();
        final boolean homogenize_contrast = gd.getNextBoolean();
        // start magic
        // get ImageJ-openable files that comply with the convention
        final File images_dir = new File(dir);
        if (!(images_dir.exists() && images_dir.isDirectory())) {
            Utils.showMessage("Something went wrong:\n\tCan't find directory " + dir);
            return null;
        }
        final String[] file_names = images_dir.list(new ImageFileFilter(regex, convention));
        if (null == file && file_names.length > 0) {
            // the 'selected' file
            file = file_names[0];
        }
        Utils.showStatus("Adding " + file_names.length + " patches.", false);
        if (0 == file_names.length) {
            Utils.log("Zero files match the convention '" + convention + "'");
            return null;
        }
        // How to: select all files, and order their names in a double array as they should be placed in the Display. Then place them, displacing by offset, and resizing if necessary.
        // gather image files:
        final Montage montage = new Montage(convention, chars_are_columns);
        montage.addAll(file_names);
        // an array of Object[] arrays, of unequal length maybe, each containing a column of image file names
        final ArrayList<String[]> cols = montage.getCols();
        // !@#$%^&*
        final String dir_ = dir;
        final double bt_overlap_ = bt_overlap;
        final double lr_overlap_ = lr_overlap;
        final String file_ = file;
        return Bureaucrat.createAndStart(new Worker.Task("Insert grid", true) {

            @Override
            public void exec() {
                StitchingTEM.PhaseCorrelationParam pc_param = null;
                if (stitch_tiles) {
                    pc_param = new StitchingTEM.PhaseCorrelationParam();
                    pc_param.setup(layer);
                }
                insertGrid(layer, dir_, file_, file_names.length, cols, bx, by, bt_overlap_, lr_overlap_, link_images, stitch_tiles, homogenize_contrast, pc_param, this);
            }
        }, layer.getProject());
    } catch (final Exception e) {
        IJError.print(e);
    }
    return null;
}

Example 12 with Montage

use of ini.trakem2.utils.Montage in project TrakEM2 by trakem2.

the class StitchingTEM method montageWithPhaseCorrelation.

/**
 * Perform montage based on phase correlation
 * @param col collection of patches
 * @param param phase correlation parameters
 */
public static void montageWithPhaseCorrelation(final Collection<Patch> col, final PhaseCorrelationParam param) {
    if (null == col || col.size() < 1)
        return;
    final ArrayList<Patch> al = new ArrayList<Patch>(col);
    final ArrayList<AbstractAffineTile2D<?>> tiles = new ArrayList<AbstractAffineTile2D<?>>();
    final ArrayList<AbstractAffineTile2D<?>> fixed_tiles = new ArrayList<AbstractAffineTile2D<?>>();
    for (final Patch p : al) {
        // Pre-check: just a warning
        final int aff_type = p.getAffineTransform().getType();
        switch(p.getAffineTransform().getType()) {
            case AffineTransform.TYPE_IDENTITY:
            case AffineTransform.TYPE_TRANSLATION:
                // ok
                break;
            default:
                Utils.log2("WARNING: patch with a non-translation transform: " + p);
                break;
        }
        // create tiles
        final TranslationTile2D tile = new TranslationTile2D(new TranslationModel2D(), p);
        tiles.add(tile);
        if (p.isLocked2()) {
            Utils.log("Added fixed (locked) tile " + p);
            fixed_tiles.add(tile);
        }
    }
    // Get acceptable values
    double cc_scale = param.cc_scale;
    if (cc_scale < 0 || cc_scale > 1) {
        Utils.log("Unacceptable cc_scale of " + param.cc_scale + ". Using 1 instead.");
        cc_scale = 1;
    }
    float overlap = param.overlap;
    if (overlap < 0 || overlap > 1) {
        Utils.log("Unacceptable overlap of " + param.overlap + ". Using 1 instead.");
        overlap = 1;
    }
    for (int i = 0; i < al.size(); i++) {
        final Patch p1 = al.get(i);
        final Rectangle r1 = p1.getBoundingBox();
        // find overlapping, add as connections
        for (int j = i + 1; j < al.size(); j++) {
            if (Thread.currentThread().isInterrupted())
                return;
            final Patch p2 = al.get(j);
            final Rectangle r2 = p2.getBoundingBox();
            if (r1.intersects(r2)) {
                // Skip if it's a diagonal overlap
                final int dx = Math.abs(r1.x - r2.x);
                final int dy = Math.abs(r1.y - r2.y);
                if (dx > r1.width / 2 && dy > r1.height / 2) {
                    // skip diagonal match
                    Utils.log2("Skipping diagonal overlap between " + p1 + " and " + p2);
                    continue;
                }
                p1.getProject().getLoader().releaseToFit((long) (p1.getWidth() * p1.getHeight() * 25));
                final double[] R;
                if (1 == overlap) {
                    R = correlate(p1, p2, overlap, cc_scale, TOP_BOTTOM, 0, 0, param.min_R);
                    if (SUCCESS == R[2]) {
                        addMatches(tiles.get(i), tiles.get(j), R[0], R[1]);
                    }
                } else {
                    switch(getClosestOverlapLocation(p1, p2)) {
                        case // p1 overlaps p2 from the left
                        0:
                            R = correlate(p1, p2, overlap, cc_scale, LEFT_RIGHT, 0, 0, param.min_R);
                            if (SUCCESS == R[2]) {
                                addMatches(tiles.get(i), tiles.get(j), R[0], R[1]);
                            }
                            break;
                        case // p1 overlaps p2 from the top
                        1:
                            R = correlate(p1, p2, overlap, cc_scale, TOP_BOTTOM, 0, 0, param.min_R);
                            if (SUCCESS == R[2]) {
                                addMatches(tiles.get(i), tiles.get(j), R[0], R[1]);
                            }
                            break;
                        case // p1 overlaps p2 from the right
                        2:
                            R = correlate(p2, p1, overlap, cc_scale, LEFT_RIGHT, 0, 0, param.min_R);
                            if (SUCCESS == R[2]) {
                                addMatches(tiles.get(j), tiles.get(i), R[0], R[1]);
                            }
                            break;
                        case // p1 overlaps p2 from the bottom
                        3:
                            R = correlate(p2, p1, overlap, cc_scale, TOP_BOTTOM, 0, 0, param.min_R);
                            if (SUCCESS == R[2]) {
                                addMatches(tiles.get(j), tiles.get(i), R[0], R[1]);
                            }
                            break;
                        default:
                            Utils.log("Unknown overlap direction!");
                            continue;
                    }
                }
            }
        }
    }
    if (param.remove_disconnected || param.hide_disconnected) {
        for (final Iterator<AbstractAffineTile2D<?>> it = tiles.iterator(); it.hasNext(); ) {
            final AbstractAffineTile2D<?> t = it.next();
            if (null != t.getMatches() && t.getMatches().isEmpty()) {
                if (param.hide_disconnected)
                    t.getPatch().setVisible(false);
                else if (param.remove_disconnected)
                    t.getPatch().remove(false);
                it.remove();
            }
        }
    }
    // Optimize tile configuration by removing bad matches
    optimizeTileConfiguration(tiles, fixed_tiles, param);
    for (final AbstractAffineTile2D<?> t : tiles) t.getPatch().setAffineTransform(t.getModel().createAffine());
    try {
        Display.repaint(al.get(0).getLayer());
    } catch (final Exception e) {
    }
}

Example 13 with Montage

use of ini.trakem2.utils.Montage in project TrakEM2 by trakem2.

the class StitchingTEM method montageWithPhaseCorrelation.

/**
 * @param layers
 * @param worker Optional, the {@link Worker} running this task.
 */
public static void montageWithPhaseCorrelation(final List<Layer> layers, final Worker worker) {
    final PhaseCorrelationParam param = new PhaseCorrelationParam();
    final Collection<Displayable> col = layers.get(0).getDisplayables(Patch.class);
    if (!param.setup(col.size() > 0 ? (Patch) col.iterator().next() : null)) {
        return;
    }
    final int i = 1;
    for (final Layer la : layers) {
        if (Thread.currentThread().isInterrupted() || (null != worker && worker.hasQuitted()))
            return;
        if (null != worker)
            worker.setTaskName("Montage layer " + i + "/" + layers.size());
        final Collection<Patch> patches = (Collection<Patch>) (Collection) la.getDisplayables(Patch.class);
        AlignTask.transformPatchesAndVectorData(patches, new Runnable() {

            @Override
            public void run() {
                montageWithPhaseCorrelation(patches, param);
            }
        });
    }
}

Example 14 with Montage

use of ini.trakem2.utils.Montage in project TrakEM2 by trakem2.

the class AlignTask method montageLayers.

@SuppressWarnings({ "rawtypes", "unchecked" })
public static final void montageLayers(final Align.ParamOptimize p, final List<Layer> layers, final boolean tilesAreInPlaceIn, final boolean largestGraphOnlyIn, final boolean hideDisconnectedTilesIn, final boolean deleteDisconnectedTilesIn, final boolean sloppyOverlapTest) {
    int i = 0;
    for (final Layer layer : layers) {
        if (Thread.currentThread().isInterrupted())
            return;
        final Collection<Displayable> patches = layer.getDisplayables(Patch.class, true);
        if (patches.isEmpty())
            continue;
        for (final Displayable patch : patches) {
            if (patch.isLinked() && !patch.isOnlyLinkedTo(Patch.class)) {
                Utils.log("Cannot montage layer " + layer + "\nReason: at least one Patch is linked to non-image data: " + patch);
                continue;
            }
        }
        Utils.log("====\nMontaging layer " + layer);
        Utils.showProgress(((double) i) / layers.size());
        i++;
        alignPatches(p, new ArrayList<Patch>((Collection<Patch>) (Collection) patches), new ArrayList<Patch>(), tilesAreInPlaceIn, largestGraphOnlyIn, hideDisconnectedTilesIn, deleteDisconnectedTilesIn, sloppyOverlapTest);
        Display.repaint(layer);
    }
}