Examples with Project ini.trakem2.Project used on opensource projects

Example 11 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class DBLoader method getProjects.

/**
 * Fetch all existing projects from the database.
 */
public Project[] getProjects() {
    synchronized (db_lock) {
        // connect if disconnected
        if (!connectToDatabase()) {
            return null;
        }
        Project[] projects = null;
        try {
            ResultSet r = connection.prepareStatement("SELECT title, id FROM ab_projects ORDER BY id").executeQuery();
            ArrayList<Project> al_projects = new ArrayList<Project>();
            while (r.next()) {
                al_projects.add(new Project(r.getLong("id"), r.getString("title")));
            }
            r.close();
            projects = new Project[al_projects.size()];
            al_projects.toArray(projects);
        } catch (Exception e) {
            IJError.print(e);
            return null;
        }
        return projects;
    }
}

Example 12 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class DBLoader method upgradeProjectsTable.

/**
 * Used to upgrade old databases.
 */
private boolean upgradeProjectsTable() throws Exception {
    // Upgrade database if necessary: set a version field, create the TemplateThing entries in the database for each project from its XML template file, and delete the xml_template column
    // Check columns: see if trakem2_version is there
    ResultSet r = connection.prepareStatement("SELECT column_name FROM information_schema.columns WHERE table_name='ab_projects' AND column_name='xml_template'").executeQuery();
    if (r.next()) {
        YesNoCancelDialog yn = new YesNoCancelDialog(IJ.getInstance(), "Upgrade", "Need to upgrade table projects.\nNo data will be lost, but reorganized.\nProceed?");
        if (!yn.yesPressed()) {
            return false;
        }
        // retrieve and parse XML template from each project
        ResultSet r1 = connection.prepareStatement("SELECT * FROM ab_projects").executeQuery();
        while (r1.next()) {
            long project_id = r1.getLong("id");
            // parse the XML file stored in the db and save the TemplateThing into the ab_things table
            InputStream xml_stream = null;
            try {
                String query = "SELECT xml_template FROM ab_projects WHERE id=" + project_id;
                ResultSet result = connection.prepareStatement(query).executeQuery();
                if (result.next()) {
                    xml_stream = result.getBinaryStream("xml_template");
                }
                result.close();
            } catch (Exception e) {
                IJError.print(e);
                return false;
            }
            if (null == xml_stream) {
                Utils.showMessage("Failed to upgrade the database schema: XML template stream is null.");
                return false;
            }
            TemplateThing template_root = new TrakEM2MLParser(xml_stream).getTemplateRoot();
            if (null == template_root) {
                Utils.showMessage("Failed to upgrade the database schema: root TemplateThing is null.");
                return false;
            }
            Project project = new Project(project_id, r1.getString("title"));
            project.setTempLoader(this);
            template_root.addToDatabase(project);
        }
        r1.close();
        // remove the XML column
        connection.prepareStatement("ALTER TABLE ab_projects DROP xml_template").execute();
        // org.postgresql.util.PSQLException: ERROR: adding columns with defaults is not implemented in 7.4.* (only in 8.1.4+)
        // connection.prepareStatement("ALTER TABLE ab_projects ADD version text default '" + Utils.version + "'").execute();
        // so: workaround
        connection.prepareStatement("ALTER TABLE ab_projects ADD version TEXT").execute();
        connection.prepareStatement("ALTER TABLE ab_projects ALTER COLUMN version SET DEFAULT '" + Utils.version + "'").execute();
    }
    r.close();
    // success!
    return true;
}

Example 13 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class DBLoader method getRootLayerThing.

/**
 * Fetches the root LayerSet, fills it with children (recursively) and uses the profiles, pipes, etc., from the project_thing. Will reconnect the links and open Displays for the layers that have one.
 */
public LayerThing getRootLayerThing(Project project, ProjectThing project_thing, TemplateThing layer_set_tt, TemplateThing layer_tt) {
    synchronized (db_lock) {
        // connect if disconnected
        if (!connectToDatabase()) {
            return null;
        }
        HashMap hs_pt = new HashMap();
        unpack(project_thing, hs_pt);
        LayerThing root = null;
        try {
            // -1 signals root
            ResultSet r = connection.prepareStatement("SELECT * FROM ab_things WHERE project_id=" + project.getId() + " AND type='layer_set' AND parent_id=-1").executeQuery();
            if (r.next()) {
                root = getLayerThing(r, project, hs_pt, layer_set_tt, layer_tt);
            }
            r.close();
            if (null == root) {
                Utils.log("Loader.getRootLayerThing: can't find it for project id=" + project.getId());
                return null;
            }
            // Redo the links! hs_pt contains now all Displayable objects.
            ResultSet rl = connection.prepareStatement("SELECT * FROM ab_links WHERE project_id=" + project.getId()).executeQuery();
            while (rl.next()) {
                Long id1 = new Long(rl.getLong("id1"));
                Long id2 = new Long(rl.getLong("id2"));
                Object ob1 = hs_pt.get(id1);
                Object ob2 = hs_pt.get(id2);
                if (null != ob1 && null != ob2) {
                    Displayable d = (Displayable) ob1;
                    d.link((Displayable) ob2, false);
                } else {
                    Utils.log("Loader: broken link between " + id1 + " and " + id2);
                }
            }
            rl.close();
        } catch (Exception e) {
            IJError.print(e);
            return null;
        }
        return root;
    }
}

Example 14 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class NeuroML method exportNeuroML.

/**
 * Export to NeuroML 1.8.3, with synapses.
 * Every {@link Tree} is represented by a <cell>, and an instance of that <cell>
 * is represented by a <population> of one single cell.
 */
public static final void exportNeuroML(final Set<Tree<?>> trees, final Writer w) throws Exception {
    if (trees.isEmpty())
        return;
    // Header
    w.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<!-- Exported from TrakEM2 '" + Utils.version + "' at " + new Date() + "\nTrakEM2 software by Albert Cardona, Institute of Neuroinformatics of the University of Zurich and ETH Zurich -->\n" + "<neuroml xmlns=\"http://morphml.org/neuroml/schema\"\n" + " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n" + " xmlns:net=\"http://morphml.org/networkml/schema\"\n" + " xmlns:mml=\"http://morphml.org/morphml/schema\"\n" + " xmlns:meta=\"http://morphml.org/metadata/schema\"\n" + " xmlns:bio=\"http://morphml.org/biophysics/schema\"\n" + " xmlns:cml=\"http://morphml.org/channelml/schema\"\n" + " xsi:schemaLocation=\"http://morphml.org/neuroml/schema http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd\"\n" + " length_units=\"micrometer\">\n");
    final List<HalfSynapse> presynaptic = new ArrayList<HalfSynapse>();
    final List<HalfSynapse> postsynaptic = new ArrayList<HalfSynapse>();
    // Scale units to micrometers
    final Calibration cal = trees.iterator().next().getLayerSet().getCalibration();
    final double scale = scaleToMicrometers(cal);
    final AffineTransform scale2d = new AffineTransform(cal.pixelWidth * scale, 0, 0, cal.pixelHeight * scale, 0, 0);
    // not pixelDepth
    final double zScale = cal.pixelWidth * scale;
    w.write("<cells>\n");
    // Each Tree is a cell
    for (final Tree<?> t : trees) {
        if (null == t.getRoot())
            continue;
        exportMorphMLCell(w, t, trees, presynaptic, postsynaptic, scale2d, zScale);
    }
    w.write("</cells>\n");
    // Write a a population of cell for every Tree, where each population has only one cell at 0,0,0.
    // If the id=10, then the name is p10 and the type is t10.
    w.write("<populations xmlns=\"http://morphml.org/networkml/schema\">\n");
    for (final Tree<?> t : trees) {
        w.write(" <population name=\"p");
        final String sid = Long.toString(t.getId());
        w.write(sid);
        w.write("\" cell_type=\"t");
        w.write(sid);
        w.write("\">\n  <instances size=\"1\">\n   <instance id=\"0\"><location x=\"0\" y=\"0\" z=\"0\"/></instance>\n  </instances>\n </population>\n");
    }
    w.write("</populations>\n");
    // Write a project group with all the synapses among the members of the set of trees.
    w.write("<projections units=\"Physiological Units\" xmlns=\"http://morphml.org/networkml/schema\">\n");
    // Figure out which pre connect to which post: the Connector instance is shared, so use it as key
    final Map<Connector, HalfSynapse> cpre = new HashMap<Connector, HalfSynapse>();
    for (final HalfSynapse syn : presynaptic) {
        cpre.put(syn.c, syn);
    }
    final Map<TreePair, List<Synapse>> pairs = new HashMap<TreePair, List<Synapse>>();
    for (final HalfSynapse post : postsynaptic) {
        final HalfSynapse pre = cpre.get(post.c);
        // Does not originate within the set of trees
        if (null == pre)
            continue;
        // pre and post share the same Connector
        final TreePair pair = new TreePair(pre.t, post.t);
        List<Synapse> ls = pairs.get(pair);
        if (null == ls) {
            ls = new ArrayList<Synapse>();
            pairs.put(pair, ls);
        }
        ls.add(new Synapse(pre, post));
    }
    for (final Map.Entry<TreePair, List<Synapse>> e : pairs.entrySet()) {
        // Write synapse between pre and post
        final TreePair pair = e.getKey();
        w.write("  <projection name=\"NetworkConnection\" source=\"p");
        w.write(Long.toString(pair.source.getId()));
        w.write("\" target=\"p");
        w.write(Long.toString(pair.target.getId()));
        w.write("\">\n");
        w.write("   <synapse_props synapse_type=\"DoubExpSynA\" internal_delay=\"5\" weight=\"1\" threshold=\"-20\"/>\n");
        w.write("   <connections size=\"");
        final List<Synapse> ls = e.getValue();
        w.write(Integer.toString(ls.size()));
        w.write("\">\n");
        int cid = 0;
        for (final Synapse syn : ls) {
            w.write("    <connection id=\"");
            w.write(Integer.toString(cid));
            w.write("\" pre_cell_id=\"0\" pre_segment_id=\"");
            w.write(Long.toString(syn.pre.segmentId));
            w.write("\" pre_fraction_along=\"0.5\" post_cell_id=\"0\" post_segment_id=\"");
            w.write(Long.toString(syn.post.segmentId));
            w.write("\"/>\n");
            cid += 1;
        }
        w.write("   </connections>\n");
        w.write("  </projection>\n");
    }
    w.write(" </projections>\n");
    w.write("</neuroml>\n");
}

Example 15 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class AlignTask method createTransformPropertiesTable.

/**
 * Creates a map only for visible patches that intersect vdata.
 *  @param src_vdata represents the VectorData instances in original form, of the original project and layer set.
 *  @param tgt_vdata if not null, it must have the same size as src_data and their elements correspond one-to-one (as in, tgt element a clone of src element at the same index).
 *  @param lids_to_operate The id of the layers on which any operation will be done
 *  tgt_data enables transformVectorData to apply the transforms to copies of the src_vdata in another project.
 */
public static final ReferenceData createTransformPropertiesTable(final List<Displayable> src_vdata, final List<Displayable> tgt_vdata, final Set<Long> lids_to_operate) {
    if (src_vdata.isEmpty())
        return null;
    final Map<Long, Patch.TransformProperties> tp = new HashMap<Long, Patch.TransformProperties>();
    // A map of Displayable vs a map of Layer id vs list of Patch ids in that Layer that lay under the Patch, sorted by stack index
    final Map<Displayable, Map<Long, TreeMap<Integer, Long>>> underlying = new HashMap<Displayable, Map<Long, TreeMap<Integer, Long>>>();
    // The set of layers used
    final Set<Long> src_layer_lids_used = new HashSet<Long>();
    // Parallelize! This operation can be insanely expensive
    final int nproc = Runtime.getRuntime().availableProcessors();
    final ExecutorService exec = Utils.newFixedThreadPool(nproc, "AlignTask-createTransformPropertiesTable");
    final List<Future<?>> dtasks = new ArrayList<Future<?>>();
    final List<Future<?>> ltasks = new ArrayList<Future<?>>();
    final Thread current = Thread.currentThread();
    try {
        for (int i = src_vdata.size() - 1; i > -1; i--) {
            final Displayable src_d = src_vdata.get(i);
            // filter out
            if (!(src_d instanceof VectorData))
                continue;
            // use src_d if tgt_vdata is null
            final Displayable tgt_d = null == tgt_vdata ? src_d : tgt_vdata.get(i);
            // Some checking
            if (!(tgt_d instanceof VectorData)) {
                Utils.log("WARNING ignoring provided tgt_vdata " + tgt_d + " which is NOT a VectorData instance!");
                continue;
            }
            if (src_d.getClass() != tgt_d.getClass()) {
                Utils.log("WARNING src_d and tgt_d are instances of different classes:\n  src_d :: " + src_d + "\n  tgt_d :: " + tgt_d);
            }
            dtasks.add(exec.submit(new Runnable() {

                @SuppressWarnings({ "unchecked", "rawtypes" })
                @Override
                public void run() {
                    final Map<Long, TreeMap<Integer, Long>> under = new HashMap<Long, TreeMap<Integer, Long>>();
                    synchronized (underlying) {
                        underlying.put(tgt_d, under);
                    }
                    if (current.isInterrupted())
                        return;
                    // Iterate the layers in which this VectorData has any data AND which have to be transformed
                    for (final Long olid : src_d.getLayerIds()) {
                        final long lid = olid.longValue();
                        // layer with id 'lid' is not affected
                        if (!lids_to_operate.contains(lid))
                            continue;
                        final Layer la = src_d.getLayerSet().getLayer(lid);
                        final Area a = src_d.getAreaAt(la);
                        if (null == a || a.isEmpty()) {
                            // does not paint in the layer
                            continue;
                        }
                        // The list of patches that lay under VectorData d, sorted by their stack index in the layer
                        final TreeMap<Integer, Long> stacked_patch_ids = new TreeMap<Integer, Long>();
                        synchronized (under) {
                            under.put(lid, stacked_patch_ids);
                        }
                        final boolean[] layer_visited = new boolean[] { false };
                        // Iterate source patches
                        for (final Patch patch : (Collection<Patch>) (Collection) la.getDisplayables(Patch.class, a, true)) {
                            // pick visible patches only
                            if (current.isInterrupted())
                                return;
                            try {
                                ltasks.add(exec.submit(new Runnable() {

                                    @Override
                                    public void run() {
                                        if (current.isInterrupted())
                                            return;
                                        synchronized (patch) {
                                            Patch.TransformProperties props;
                                            synchronized (tp) {
                                                props = tp.get(patch.getId());
                                            }
                                            if (null == props) {
                                                props = patch.getTransformPropertiesCopy();
                                                // Cache the props
                                                synchronized (tp) {
                                                    tp.put(patch.getId(), props);
                                                }
                                            }
                                            // Cache this patch as under the VectorData d
                                            synchronized (stacked_patch_ids) {
                                                // sorted by stack index
                                                stacked_patch_ids.put(la.indexOf(patch), patch.getId());
                                            // Utils.log("Added patch for layer " + la + " with stack index " + la.indexOf(patch) + ", patch " + patch);
                                            }
                                            if (!layer_visited[0]) {
                                                // synch may fail to avoid adding it twice
                                                // but it's ok since it's a Set anyway
                                                layer_visited[0] = true;
                                                synchronized (src_layer_lids_used) {
                                                    src_layer_lids_used.add(la.getId());
                                                }
                                            }
                                        }
                                    }
                                }));
                            } catch (final Throwable t) {
                                IJError.print(t);
                                return;
                            }
                        }
                    }
                }
            }));
        }
        Utils.wait(dtasks);
        Utils.wait(ltasks);
    } catch (final Throwable t) {
        IJError.print(t);
    } finally {
        exec.shutdownNow();
    }
    return new ReferenceData(tp, underlying, src_layer_lids_used);
}