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

Example 21 with Worker

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

the class Display method importNextImage.

protected Bureaucrat importNextImage() {
    final Worker worker = new // / all this verbosity is what happens when functions are not first class citizens. I could abstract it away by passing a string name "importImage" and invoking it with reflection, but that is an even bigger PAIN
    Worker(// / all this verbosity is what happens when functions are not first class citizens. I could abstract it away by passing a string name "importImage" and invoking it with reflection, but that is an even bigger PAIN
    "Import image") {

        @Override
        public void run() {
            startedWorking();
            try {
                final Rectangle srcRect = canvas.getSrcRect();
                // - imp.getWidth() / 2;
                final int x = srcRect.x + srcRect.width / 2;
                // - imp.getHeight()/ 2;
                final int y = srcRect.y + srcRect.height / 2;
                final Patch p = project.getLoader().importNextImage(project, x, y);
                if (null == p) {
                    Utils.showMessage("Could not open next image.");
                    finishedWorking();
                    return;
                }
                Display.this.getLayerSet().addLayerContentStep(layer);
                // will add it to the proper Displays
                layer.add(p);
                Display.this.getLayerSet().addLayerContentStep(layer);
            } catch (final Exception e) {
                IJError.print(e);
            }
            finishedWorking();
        }
    };
    return Bureaucrat.createAndStart(worker, getProject());
}

Example 22 with Worker

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

the class ProjectTree method actionPerformed.

public void actionPerformed(final ActionEvent ae) {
    if (!project.isInputEnabled())
        return;
    super.dispatcher.exec(new Runnable() {

        public void run() {
            try {
                if (null == selected_node)
                    return;
                final Object ob = selected_node.getUserObject();
                if (!(ob instanceof ProjectThing))
                    return;
                final ProjectThing thing = (ProjectThing) ob;
                int i_position = 0;
                String command = ae.getActionCommand();
                final Object obd = thing.getObject();
                if (command.startsWith("new ") || command.equals("Duplicate")) {
                    ProjectThing new_thing = null;
                    if (command.startsWith("new ")) {
                        // if it's a Displayable, it will be added to whatever layer is in the front Display
                        new_thing = thing.createChild(command.substring(4));
                    } else if (command.equals("Duplicate")) {
                        // just to keep myself from screwing in the future
                        if (Project.isBasicType(thing.getType()) && null != thing.getParent()) {
                            new_thing = ((ProjectThing) thing.getParent()).createClonedChild(thing);
                        }
                        // adjust parent
                        selected_node = (DefaultMutableTreeNode) selected_node.getParent();
                    }
                    // add it to the tree
                    if (null != new_thing) {
                        DefaultMutableTreeNode new_node = new DefaultMutableTreeNode(new_thing);
                        ((DefaultTreeModel) ProjectTree.this.getModel()).insertNodeInto(new_node, selected_node, i_position);
                        TreePath treePath = new TreePath(new_node.getPath());
                        ProjectTree.this.scrollPathToVisible(treePath);
                        ProjectTree.this.setSelectionPath(treePath);
                    }
                    // bring the display to front
                    if (new_thing.getObject() instanceof Displayable) {
                        Display.getFront().getFrame().toFront();
                    }
                } else if (command.equals("many...")) {
                    ArrayList<TemplateThing> children = thing.getTemplate().getChildren();
                    if (null == children || 0 == children.size())
                        return;
                    String[] cn = new String[children.size()];
                    int i = 0;
                    for (final TemplateThing child : children) {
                        cn[i] = child.getType();
                        i++;
                    }
                    GenericDialog gd = new GenericDialog("Add many children");
                    gd.addNumericField("Amount: ", 1, 0);
                    gd.addChoice("New child: ", cn, cn[0]);
                    gd.addCheckbox("Recursive", true);
                    gd.showDialog();
                    if (gd.wasCanceled())
                        return;
                    int amount = (int) gd.getNextNumber();
                    if (amount < 1) {
                        Utils.showMessage("Makes no sense to create less than 1 child!");
                        return;
                    }
                    project.getRootLayerSet().addChangeTreesStep();
                    final ArrayList<ProjectThing> nc = thing.createChildren(cn[gd.getNextChoiceIndex()], amount, gd.getNextBoolean());
                    addLeafs(nc, new Runnable() {

                        public void run() {
                            project.getRootLayerSet().addChangeTreesStep();
                        }
                    });
                } else if (command.equals("Unhide")) {
                    thing.setVisible(true);
                } else if (command.equals("Select in display")) {
                    boolean shift_down = 0 != (ae.getModifiers() & ActionEvent.SHIFT_MASK);
                    selectInDisplay(thing, shift_down);
                } else if (command.equals("Show centered in Display")) {
                    if (obd instanceof Displayable) {
                        Displayable displ = (Displayable) obd;
                        Display.showCentered(displ.getLayer(), displ, true, 0 != (ae.getModifiers() & ActionEvent.SHIFT_MASK));
                    }
                } else if (command.equals("Show tabular view")) {
                    ((Tree<?>) obd).createMultiTableView();
                } else if (command.equals("Show in 3D")) {
                    Display3D.showAndResetView(thing);
                } else if (command.equals("Remove from 3D view")) {
                    Display3D.removeFrom3D(thing);
                } else if (command.equals("Hide")) {
                    // find all Thing objects in this subtree starting at Thing and hide their Displayable objects.
                    thing.setVisible(false);
                } else if (command.equals("Delete...")) {
                    // store old state
                    project.getRootLayerSet().addChangeTreesStep();
                    remove(true, thing, selected_node);
                    // store new state
                    project.getRootLayerSet().addChangeTreesStep();
                    return;
                } else if (command.equals("Rename...")) {
                    // if (!Project.isBasicType(thing.getType())) {
                    rename(thing);
                // }
                } else if (command.equals("Measure")) {
                    // block displays while measuring
                    Bureaucrat.createAndStart(new Worker("Measuring") {

                        public void run() {
                            startedWorking();
                            try {
                                thing.measure();
                            } catch (Throwable e) {
                                IJError.print(e);
                            } finally {
                                finishedWorking();
                            }
                        }
                    }, thing.getProject());
                } else /* else if (command.equals("Export 3D...")) {
				GenericDialog gd = ControlWindow.makeGenericDialog("Export 3D");
				String[] choice = new String[]{".svg [preserves links and hierarchical grouping]", ".shapes [limited to one profile per layer per profile_list]"};
				gd.addChoice("Export to: ", choice, choice[0]);
				gd.addNumericField("Z scaling: ", 1, 2);
				gd.showDialog();
				if (gd.wasCanceled()) return;
				double z_scale = gd.getNextNumber();
				switch (gd.getNextChoiceIndex()) {
					case 0:
						Render.exportSVG(thing, z_scale);
						break;
					case 1:
						new Render(thing).save(z_scale);
						break;
				}
			}*/
                if (command.equals("Export project...") || command.equals("Save as...")) {
                    // "Save as..." is for a FS project
                    Utils.log2("Calling export project at " + System.currentTimeMillis());
                    thing.getProject().getLoader().saveTask(thing.getProject(), "Save as...");
                } else if (command.equals("Save")) {
                    // overwrite the xml file of a FSProject
                    // Just do the same as in "Save as..." but without saving the images and overwritting the XML file without asking.
                    thing.getProject().getLoader().saveTask(thing.getProject(), "Save");
                } else if (command.equals("Info")) {
                    showInfo(thing);
                    return;
                } else if (command.equals("Move up")) {
                    move(selected_node, -1);
                } else if (command.equals("Move down")) {
                    move(selected_node, 1);
                } else if (command.equals("Collapse nodes of children nodes")) {
                    if (null == selected_node)
                        return;
                    Enumeration<?> c = selected_node.children();
                    while (c.hasMoreElements()) {
                        DefaultMutableTreeNode child = (DefaultMutableTreeNode) c.nextElement();
                        if (child.isLeaf())
                            continue;
                        collapsePath(new TreePath(child.getPath()));
                    }
                } else if (command.equals("Sibling project")) {
                    sendToSiblingProjectTask(selected_node);
                } else {
                    Utils.log("ProjectTree.actionPerformed: don't know what to do with the command: " + command);
                    return;
                }
            } catch (Exception e) {
                IJError.print(e);
            }
        }
    });
}

Example 23 with Worker

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

the class Polyline method mousePressed.

@Override
public void mousePressed(final MouseEvent me, final Layer layer, int x_p, int y_p, final double mag) {
    // transform the x_p, y_p to the local coordinates
    final int x_pd = x_p;
    final int y_pd = y_p;
    if (!this.at.isIdentity()) {
        final Point2D.Double po = inverseTransformPoint(x_p, y_p);
        x_p = (int) po.x;
        y_p = (int) po.y;
    }
    final int tool = ProjectToolbar.getToolId();
    final Display display = ((DisplayCanvas) me.getSource()).getDisplay();
    final long layer_id = layer.getId();
    index = findPoint(x_p, y_p, layer_id, mag);
    if (ProjectToolbar.PENCIL == tool && n_points > 0 && -1 == index && !me.isShiftDown() && !Utils.isControlDown(me)) {
        // Check that there are any images -- otherwise may hang. TODO
        if (layer_set.getDisplayables(Patch.class).isEmpty()) {
            Utils.log("No images are present!");
            return;
        }
        final double scale = layer_set.getVirtualizationScale();
        // Ok now with all found images, create a virtual stack that provides access to them all, with caching.
        final Worker[] worker = new Worker[2];
        final TraceParameters tr_ = tr_map.get(layer_set);
        final TraceParameters tr = null == tr_ ? new TraceParameters() : tr_;
        if (null == tr_) {
            synchronized (tr_map) {
                tr_map.put(layer_set, tr);
            }
        }
        if (tr.update) {
            worker[0] = new Worker("Preparing Hessian...") {

                @Override
                public void run() {
                    startedWorking();
                    try {
                        Utils.log("Push ESCAPE key to cancel autotrace anytime.");
                        final ImagePlus virtual = new LayerStack(layer_set, scale, ImagePlus.GRAY8, Patch.class, display.getDisplayChannelAlphas(), Segmentation.fmp.SNT_invert_image).getImagePlus();
                        // virtual.show();
                        final Calibration cal = virtual.getCalibration();
                        double minimumSeparation = 1;
                        if (cal != null)
                            minimumSeparation = Math.min(cal.pixelWidth, Math.min(cal.pixelHeight, cal.pixelDepth));
                        final ComputeCurvatures hessian = new ComputeCurvatures(virtual, minimumSeparation, null, cal != null);
                        hessian.run();
                        tr.virtual = virtual;
                        // tr.scale = scale;
                        tr.hessian = hessian;
                        tr.update = false;
                    } catch (final Exception e) {
                        IJError.print(e);
                    }
                    finishedWorking();
                }
            };
            Bureaucrat.createAndStart(worker[0], project);
        }
        final Point2D.Double po = transformPoint(p[0][n_points - 1], p[1][n_points - 1]);
        final int start_x = (int) po.x;
        final int start_y = (int) po.y;
        // 0-based
        final int start_z = layer_set.indexOf(layer_set.getLayer(p_layer[n_points - 1]));
        // must transform into virtual space
        final int goal_x = (int) (x_pd * scale);
        final int goal_y = (int) (y_pd * scale);
        final int goal_z = layer_set.indexOf(layer);
        /*
			Utils.log2("x_pd, y_pd : " + x_pd + ", " + y_pd);
			Utils.log2("scale: " + scale);
			Utils.log2("start: " + start_x + "," + start_y + ", " + start_z);
			Utils.log2("goal: " + goal_x + "," + goal_y + ", " + goal_z);
			Utils.log2("virtual: " + tr.virtual);
			*/
        final boolean simplify = me.isAltDown();
        worker[1] = new Worker("Tracer - waiting on hessian") {

            @Override
            public void run() {
                startedWorking();
                try {
                    if (null != worker[0]) {
                        // Wait until hessian is ready
                        worker[0].join();
                    }
                    setTaskName("Tracing path");
                    final int reportEveryMilliseconds = 2000;
                    tr.tracer = new TracerThread(tr.virtual, 0, 255, // timeout seconds
                    120, reportEveryMilliseconds, start_x, start_y, start_z, goal_x, goal_y, goal_z, // reciproal pix values at start and goal
                    true, tr.virtual.getStackSize() == 1, tr.hessian, null == tr.hessian ? 1 : 4, null, null != tr.hessian);
                    tr.tracer.addProgressListener(new SearchProgressCallback() {

                        @Override
                        public void pointsInSearch(final SearchInterface source, final int inOpen, final int inClosed) {
                            worker[1].setTaskName("Tracing path: open=" + inOpen + " closed=" + inClosed);
                        }

                        @Override
                        public void finished(final SearchInterface source, final boolean success) {
                            if (!success) {
                                Utils.logAll("Could NOT trace a path");
                            }
                        }

                        @Override
                        public void threadStatus(final SearchInterface source, final int currentStatus) {
                            // This method gets called every reportEveryMilliseconds
                            if (worker[1].hasQuitted()) {
                                source.requestStop();
                            }
                        }
                    });
                    tr.tracer.run();
                    final Path result = tr.tracer.getResult();
                    tr.tracer = null;
                    if (null == result) {
                        // : "+
                        Utils.log("Finding a path failed");
                        // not public //SearchThread.exitReasonStrings[tracer.getExitReason()]);
                        return;
                    }
                    // TODO: precise_x_positions etc are likely to be broken (calibrated or something)
                    // Remove bogus points: those at the end with 0,0 coords
                    int len = result.points;
                    final double[][] pos = result.getXYZUnscaled();
                    for (int i = len - 1; i > -1; i--) {
                        if (0 == pos[0][i] && 0 == pos[1][i]) {
                            len--;
                        } else
                            break;
                    }
                    // Transform points: undo scale, and bring to this Polyline AffineTransform:
                    final AffineTransform aff = new AffineTransform();
                    /* Inverse order: */
                    /* 2 */
                    aff.concatenate(Polyline.this.at.createInverse());
                    /* 1 */
                    aff.scale(1 / scale, 1 / scale);
                    final double[] po = new double[len * 2];
                    for (int i = 0, j = 0; i < len; i++, j += 2) {
                        po[j] = pos[0][i];
                        po[j + 1] = pos[1][i];
                    }
                    final double[] po2 = new double[len * 2];
                    // what a stupid format: consecutive x,y pairs
                    aff.transform(po, 0, po2, 0, len);
                    long[] p_layer_ids = new long[len];
                    double[] pox = new double[len];
                    double[] poy = new double[len];
                    for (int i = 0, j = 0; i < len; i++, j += 2) {
                        // z_positions in 0-(N-1), not in 1-N like slices!
                        p_layer_ids[i] = layer_set.getLayer((int) pos[2][i]).getId();
                        pox[i] = po2[j];
                        poy[i] = po2[j + 1];
                    }
                    // Simplify path: to steps of 5 calibration units, or 5 pixels when not calibrated.
                    if (simplify) {
                        setTaskName("Simplifying path");
                        final Object[] ob = Polyline.simplify(pox, poy, p_layer_ids, 10000, layer_set);
                        pox = (double[]) ob[0];
                        poy = (double[]) ob[1];
                        p_layer_ids = (long[]) ob[2];
                        len = pox.length;
                    }
                    // Record the first newly-added autotraced point index:
                    last_autotrace_start = Polyline.this.n_points;
                    Polyline.this.appendPoints(pox, poy, p_layer_ids, len);
                    Polyline.this.repaint(true, null);
                    Utils.logAll("Added " + len + " new points.");
                } catch (final Exception e) {
                    IJError.print(e);
                }
                finishedWorking();
            }
        };
        Bureaucrat.createAndStart(worker[1], project);
        index = -1;
        return;
    }
    if (ProjectToolbar.PEN == tool || ProjectToolbar.PENCIL == tool) {
        if (Utils.isControlDown(me) && me.isShiftDown()) {
            final long lid = Display.getFrontLayer(this.project).getId();
            if (-1 == index || lid != p_layer[index]) {
                index = findNearestPoint(x_p, y_p, layer_id);
            }
            if (-1 != index) {
                // delete point
                removePoint(index);
                index = -1;
                repaint(false, null);
            }
            // In any case, terminate
            return;
        }
        if (// disable!
        -1 != index && layer_id != p_layer[index])
            // disable!
            index = -1;
        else // if no conditions are met, attempt to add point
        if (-1 == index && !me.isShiftDown() && !me.isAltDown()) {
            // add a new point
            index = addPoint(x_p, y_p, layer_id, mag);
            is_new_point = true;
            repaint(false, null);
            return;
        }
    }
}

Example 24 with Worker

use of ini.trakem2.utils.Worker 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 25 with Worker

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

the class DistortionCorrectionTask method correctDistortionFromSelection.

public static final Bureaucrat correctDistortionFromSelection(final Selection selection) {
    final List<Patch> patches = new ArrayList<Patch>();
    for (final Displayable d : Display.getFront().getSelection().getSelected()) if (d instanceof Patch)
        patches.add((Patch) d);
    if (patches.size() < 2) {
        Utils.log("No images in the selection.");
        return null;
    }
    final Worker worker = new Worker("Lens correction") {

        @Override
        public final void run() {
            try {
                startedWorking();
                if (!correctDistortionFromSelectionParam.setup(selection))
                    return;
                DistortionCorrectionTask.run(correctDistortionFromSelectionParam.clone(), patches, selection.getActive(), selection.getLayer(), null);
                Display.repaint();
            } catch (final Exception e) {
                IJError.print(e);
            } finally {
                finishedWorking();
            }
        }
    };
    return Bureaucrat.createAndStart(worker, selection.getProject());
}