Examples with FSLoader ini.trakem2.persistence.FSLoader used on opensource projects

Example 1 with FSLoader

use of ini.trakem2.persistence.FSLoader in project TrakEM2 by trakem2.

the class MatchIntensities method run.

/**
 * @param layers
 * @param radius
 * @param scale
 * @param numCoefficients
 * @param lambda1
 * @param lambda2
 * @param neighborWeight
 * @param roi
 */
public <M extends Model<M> & Affine1D<M>> void run(final List<Layer> layers, final int radius, final double scale, final int numCoefficients, final double lambda1, final double lambda2, final double neighborWeight, final Rectangle roi) throws InterruptedException, ExecutionException {
    final int firstLayerIndex = layerset.getLayerIndex(layers.get(0).getId());
    final int lastLayerIndex = layerset.getLayerIndex(layers.get(layers.size() - 1).getId());
    // final PointMatchFilter filter = new RansacRegressionFilter();
    final PointMatchFilter filter = new RansacRegressionReduceFilter();
    /* collect patches */
    Utils.log("Collecting patches ... ");
    final ArrayList<Patch> patches = new ArrayList<Patch>();
    for (final Layer layer : layers) patches.addAll((Collection) layer.getDisplayables(Patch.class, roi));
    /* delete existing intensity coefficients */
    Utils.log("Clearing existing intensity maps ... ");
    for (final Patch p : patches) p.clearIntensityMap();
    /* generate coefficient tiles for all patches
		 * TODO consider offering alternative models */
    final HashMap<Patch, ArrayList<Tile<? extends M>>> coefficientsTiles = (HashMap) generateCoefficientsTiles(patches, new InterpolatedAffineModel1D<InterpolatedAffineModel1D<AffineModel1D, TranslationModel1D>, IdentityModel>(new InterpolatedAffineModel1D<AffineModel1D, TranslationModel1D>(new AffineModel1D(), new TranslationModel1D(), lambda1), new IdentityModel(), lambda2), numCoefficients * numCoefficients);
    /* completed patches */
    final HashSet<Patch> completedPatches = new HashSet<Patch>();
    /* collect patch pairs */
    Utils.log("Collecting patch pairs ... ");
    final ArrayList<ValuePair<Patch, Patch>> patchPairs = new ArrayList<ValuePair<Patch, Patch>>();
    for (final Patch p1 : patches) {
        completedPatches.add(p1);
        final Rectangle box1 = p1.getBoundingBox().intersection(roi);
        final ArrayList<Patch> p2s = new ArrayList<Patch>();
        /* across adjacent layers */
        final int layerIndex = layerset.getLayerIndex(p1.getLayer().getId());
        for (int i = Math.max(firstLayerIndex, layerIndex - radius); i <= Math.min(lastLayerIndex, layerIndex + radius); ++i) {
            final Layer layer = layerset.getLayer(i);
            if (layer != null)
                p2s.addAll((Collection) layer.getDisplayables(Patch.class, box1));
        }
        for (final Patch p2 : p2s) {
            /*
				 * if this patch had been processed earlier, all matches are
				 * already in
				 */
            if (completedPatches.contains(p2))
                continue;
            patchPairs.add(new ValuePair<Patch, Patch>(p1, p2));
        }
    }
    final int numThreads = Integer.parseInt(layerset.getProperty("n_mipmap_threads", Integer.toString(Runtime.getRuntime().availableProcessors())));
    Utils.log("Matching intensities using " + numThreads + " threads ... ");
    final ExecutorService exec = Executors.newFixedThreadPool(numThreads);
    final ArrayList<Future<?>> futures = new ArrayList<Future<?>>();
    for (final ValuePair<Patch, Patch> patchPair : patchPairs) {
        futures.add(exec.submit(new Matcher(roi, patchPair, (HashMap) coefficientsTiles, filter, scale, numCoefficients)));
    }
    for (final Future<?> future : futures) future.get();
    /* connect tiles within patches */
    Utils.log("Connecting coefficient tiles in the same patch  ... ");
    for (final Patch p1 : completedPatches) {
        /* get the coefficient tiles */
        final ArrayList<Tile<? extends M>> p1CoefficientsTiles = coefficientsTiles.get(p1);
        for (int y = 1; y < numCoefficients; ++y) {
            final int yr = numCoefficients * y;
            final int yr1 = yr - numCoefficients;
            for (int x = 0; x < numCoefficients; ++x) {
                identityConnect(p1CoefficientsTiles.get(yr1 + x), p1CoefficientsTiles.get(yr + x), neighborWeight);
            }
        }
        for (int y = 0; y < numCoefficients; ++y) {
            final int yr = numCoefficients * y;
            for (int x = 1; x < numCoefficients; ++x) {
                final int yrx = yr + x;
                identityConnect(p1CoefficientsTiles.get(yrx), p1CoefficientsTiles.get(yrx - 1), neighborWeight);
            }
        }
    }
    /* optimize */
    Utils.log("Optimizing ... ");
    final TileConfiguration tc = new TileConfiguration();
    for (final ArrayList<Tile<? extends M>> coefficients : coefficientsTiles.values()) {
        // for ( final Tile< ? > t : coefficients )
        // if ( t.getMatches().size() == 0 )
        // IJ.log( "bang" );
        tc.addTiles(coefficients);
    }
    try {
        tc.optimize(0.01f, iterations, iterations, 0.75f);
    } catch (final NotEnoughDataPointsException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (final IllDefinedDataPointsException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    /* save coefficients */
    final double[] ab = new double[2];
    final FSLoader loader = (FSLoader) layerset.getProject().getLoader();
    final String itsDir = loader.getUNUIdFolder() + "trakem2.its/";
    for (final Entry<Patch, ArrayList<Tile<? extends M>>> entry : coefficientsTiles.entrySet()) {
        final FloatProcessor as = new FloatProcessor(numCoefficients, numCoefficients);
        final FloatProcessor bs = new FloatProcessor(numCoefficients, numCoefficients);
        final Patch p = entry.getKey();
        final double min = p.getMin();
        final double max = p.getMax();
        final ArrayList<Tile<? extends M>> tiles = entry.getValue();
        for (int i = 0; i < numCoefficients * numCoefficients; ++i) {
            final Tile<? extends M> t = tiles.get(i);
            final Affine1D<?> affine = t.getModel();
            affine.toArray(ab);
            /* coefficients mapping into existing [min, max] */
            as.setf(i, (float) ab[0]);
            bs.setf(i, (float) ((max - min) * ab[1] + min - ab[0] * min));
        }
        final ImageStack coefficientsStack = new ImageStack(numCoefficients, numCoefficients);
        coefficientsStack.addSlice(as);
        coefficientsStack.addSlice(bs);
        final String itsPath = itsDir + FSLoader.createIdPath(Long.toString(p.getId()), "it", ".tif");
        new File(itsPath).getParentFile().mkdirs();
        IJ.saveAs(new ImagePlus("", coefficientsStack), "tif", itsPath);
    }
    /* update mipmaps */
    for (final Patch p : patches) p.getProject().getLoader().decacheImagePlus(p.getId());
    final ArrayList<Future<Boolean>> mipmapFutures = new ArrayList<Future<Boolean>>();
    for (final Patch p : patches) mipmapFutures.add(p.updateMipMaps());
    for (final Future<Boolean> f : mipmapFutures) f.get();
    Utils.log("Matching intensities done.");
}

Example 2 with FSLoader

use of ini.trakem2.persistence.FSLoader in project TrakEM2 by trakem2.

the class Patch method exportXML.

/**
 * Opens and closes the tag and exports data. The image is saved in the directory provided in @param any as a String.
 */
@Override
public void exportXML(final StringBuilder sb_body, final String indent, final XMLOptions options) {
    // TODO the Loader should handle the saving of images, not this class.
    final String in = indent + "\t";
    String path = null;
    String path2 = null;
    if (options.export_images) {
        path = options.patches_dir + title;
        // save image without overwriting, and add proper extension (.zip)
        path2 = project.getLoader().exportImage(this, path, false);
    // path2 will be null if the file exists already
    }
    sb_body.append(indent).append("<t2_patch\n");
    String rel_path = null;
    if (null != path && path.equals(path2)) {
        // this happens when a DB project is exported. It may be a different path when it's a FS loader
        // Utils.log2("p id=" + id + "  path==path2");
        rel_path = path2;
        // TrakEM2 uses paths that always have '/' and never '\', so using java.io.File.separatorChar would be an error.
        int i_slash = rel_path.lastIndexOf('/');
        if (i_slash > 0) {
            i_slash = rel_path.lastIndexOf('/', i_slash - 1);
            if (-1 != i_slash) {
                rel_path = rel_path.substring(i_slash + 1);
            }
        }
    } else {
        // Utils.log2("Setting rel_path to " + path2);
        rel_path = path2;
    }
    // For FSLoader projects, saving a second time will save images as null unless calling it
    if (null == rel_path) {
        // Utils.log2("path2 was null");
        final Object ob = project.getLoader().getPath(this);
        path2 = null == ob ? null : (String) ob;
        if (null == path2) {
            // Utils.log2("ERROR: No path for Patch id=" + id + " and title: " + title);
            // at least some clue for recovery
            rel_path = title;
        } else {
            rel_path = path2;
        }
    }
    // Utils.log("Patch path is: " + rel_path);
    super.exportXML(sb_body, in, options);
    final String[] RGB = Utils.getHexRGBColor(color);
    int type = this.type;
    if (-1 == this.type) {
        Utils.log2("Retrieving type for p = " + this);
        final ImagePlus imp = project.getLoader().fetchImagePlus(this);
        if (null != imp)
            type = imp.getType();
    }
    sb_body.append(in).append("type=\"").append(type).append("\"\n").append(in).append("file_path=\"").append(rel_path).append("\"\n").append(in).append("style=\"fill-opacity:").append(alpha).append(";stroke:#").append(RGB[0]).append(RGB[1]).append(RGB[2]).append(";\"\n").append(in).append("o_width=\"").append(o_width).append("\"\n").append(in).append("o_height=\"").append(o_height).append("\"\n");
    if (null != original_path) {
        sb_body.append(in).append("original_path=\"").append(original_path).append("\"\n");
    }
    sb_body.append(in).append("min=\"").append(min).append("\"\n");
    sb_body.append(in).append("max=\"").append(max).append("\"\n");
    final String pps = getPreprocessorScriptPath();
    if (null != pps)
        sb_body.append(in).append("pps=\"").append(project.getLoader().makeRelativePath(pps)).append("\"\n");
    sb_body.append(in).append("mres=\"").append(meshResolution).append("\"\n");
    if (hasCoordinateTransform()) {
        sb_body.append(in).append("ct_id=\"").append(ct_id).append("\"\n");
    }
    if (hasAlphaMask()) {
        sb_body.append(in).append("alpha_mask_id=\"").append(alpha_mask_id).append("\"\n");
    }
    sb_body.append(indent).append(">\n");
    if (hasCoordinateTransform()) {
        if (options.include_coordinate_transform) {
            // Write an XML entry for the CoordinateTransform
            char[] ct_chars = null;
            try {
                ct_chars = readCoordinateTransformFile();
            } catch (final Exception e) {
                IJError.print(e);
            }
            if (null != ct_chars) {
                sb_body.append(ct_chars).append('\n');
            } else {
                Utils.log("ERROR: could not write the CoordinateTransform to the XML file!");
            }
        }
    }
    if (null != filters && filters.length > 0) {
        // specify their own line termination
        for (final IFilter f : filters) sb_body.append(f.toXML(in));
    }
    super.restXML(sb_body, in, options);
    sb_body.append(indent).append("</t2_patch>\n");
}

Example 3 with FSLoader

use of ini.trakem2.persistence.FSLoader in project TrakEM2 by trakem2.

the class FSLoader method deleteStaleFiles.

/**
 * Delete stale files under the {@link FSLoader#unuid} folder.
 * These include "*.ct" files (for {@link CoordinateTransform})
 * and "*.zip" files (for alpha mask images) that are not referenced from any {@link Patch}.
 */
@Override
public boolean deleteStaleFiles(boolean coordinate_transforms, boolean alpha_masks) {
    boolean b = true;
    final Project project = Project.findProject(this);
    if (coordinate_transforms)
        b = b && StaleFiles.deleteCoordinateTransforms(project);
    if (alpha_masks)
        b = b && StaleFiles.deleteAlphaMasks(project);
    return b;
}

Example 4 with FSLoader

use of ini.trakem2.persistence.FSLoader in project TrakEM2 by trakem2.

the class Project method newFSProject.

public static Project newFSProject(String arg, TemplateThing template_root, String storage_folder, boolean autocreate_one_layer) {
    if (Utils.wrongImageJVersion())
        return null;
    FSLoader loader = null;
    try {
        String dir_project = storage_folder;
        if (null == dir_project || !new File(dir_project).isDirectory()) {
            DirectoryChooser dc = new DirectoryChooser("Select storage folder");
            dir_project = dc.getDirectory();
            // user cancelled dialog
            if (null == dir_project)
                return null;
            if (!Loader.canReadAndWriteTo(dir_project)) {
                Utils.showMessage("Can't read/write to the selected storage folder.\nPlease check folder permissions.");
                return null;
            }
            if (IJ.isWindows())
                dir_project = dir_project.replace('\\', '/');
        }
        loader = new FSLoader(dir_project);
        Project project = createNewProject(loader, !("blank".equals(arg) || "amira".equals(arg)), template_root);
        // help the helpless users:
        if (autocreate_one_layer && null != project && ControlWindow.isGUIEnabled()) {
            Utils.log2("Creating automatic Display.");
            // add a default layer
            Layer layer = new Layer(project, 0, 1, project.layer_set);
            project.layer_set.add(layer);
            project.layer_tree.addLayer(project.layer_set, layer);
            layer.recreateBuckets();
            Display.createDisplay(project, layer);
        }
        try {
            // waiting cheaply for asynchronous swing calls
            Thread.sleep(200);
        } catch (InterruptedException ie) {
            ie.printStackTrace();
        }
        if ("amira".equals(arg) || "stack".equals(arg)) {
            // forks into a task thread
            loader.importStack(project.layer_set.getLayer(0), null, true);
        }
        project.restartAutosaving();
        return project;
    } catch (Exception e) {
        IJError.print(e);
        if (null != loader)
            loader.destroy();
    }
    return null;
}

Example 5 with FSLoader

use of ini.trakem2.persistence.FSLoader in project TrakEM2 by trakem2.

the class Project method createSubproject.

/**
 * Create a new subproject for the given layer range and ROI.
 *   Create a new Project using the given project as template. This means the DTD of the given project is copied, as well as the storage and mipmaps folders; everything else is empty in the new project.
 */
public Project createSubproject(final Rectangle roi, final Layer first, final Layer last, final boolean ignore_hidden_patches) {
    try {
        // The order matters.
        final Project pr = new Project(new FSLoader(this.getLoader().getStorageFolder()));
        pr.id = this.id;
        // copy properties
        pr.title = this.title;
        pr.ht_props.putAll(this.ht_props);
        // copy template
        pr.root_tt = this.root_tt.clone(pr, true);
        pr.template_tree = new TemplateTree(pr, pr.root_tt);
        synchronized (pr.ht_unique_tt) {
            pr.ht_unique_tt.clear();
            pr.ht_unique_tt.putAll(root_tt.getUniqueTypes(new HashMap<String, TemplateThing>()));
        }
        TemplateThing project_template = new TemplateThing("project");
        project_template.addChild(pr.root_tt);
        pr.ht_unique_tt.put("project", project_template);
        // create the layers templates
        pr.createLayerTemplates();
        // copy LayerSet and all involved Displayable objects
        // (A two-step process to provide the layer_set pointer and all Layer pointers to the ZDisplayable to copy and crop.)
        pr.layer_set = (LayerSet) this.layer_set.clone(pr, first, last, roi, false, true, ignore_hidden_patches);
        LayerSet.cloneInto(this.layer_set, first, last, pr, pr.layer_set, roi, true);
        // create layer tree
        pr.root_lt = new LayerThing(Project.layer_set_template, pr, pr.layer_set);
        pr.layer_tree = new LayerTree(pr, pr.root_lt);
        // add layer nodes to the layer tree (solving chicken-and-egg problem)
        pr.layer_set.updateLayerTree();
        // copy project tree
        pr.root_pt = this.root_pt.subclone(pr);
        pr.project_tree = new ProjectTree(pr, pr.root_pt);
        // not copying node expanded state.
        // register
        al_open_projects.add(pr);
        // add to gui:
        ControlWindow.add(pr, pr.template_tree, pr.project_tree, pr.layer_tree);
        // Above, the id of each object is preserved from this project into the subproject.
        // The abstract structure should be copied in full regardless, without the basic objects
        // included if they intersect the roi.
        // Regenerate mipmaps (blocks GUI from interaction other than navigation)
        pr.loader.regenerateMipMaps(pr.layer_set.getDisplayables(Patch.class));
        pr.restartAutosaving();
        return pr;
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}