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

Example 26 with Bureaucrat

use of ini.trakem2.utils.Bureaucrat 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 27 with Bureaucrat

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

the class Project method openFSProject.

/**
 * Opens a project from an .xml file. If the path is null it'll be asked for.
 *  Only one project may be opened at a time.
 */
@SuppressWarnings("unchecked")
public static synchronized Project openFSProject(final String path, final boolean open_displays) {
    if (Utils.wrongImageJVersion())
        return null;
    final FSLoader loader = new FSLoader();
    final Object[] data = loader.openFSProject(path, open_displays);
    if (null == data) {
        loader.destroy();
        return null;
    }
    final TemplateThing root_tt = (TemplateThing) data[0];
    final ProjectThing root_pt = (ProjectThing) data[1];
    final LayerThing root_lt = (LayerThing) data[2];
    final HashMap<ProjectThing, Boolean> ht_pt_expanded = (HashMap<ProjectThing, Boolean>) data[3];
    final Project project = (Project) root_pt.getObject();
    project.createLayerTemplates();
    project.template_tree = new TemplateTree(project, root_tt);
    project.root_tt = root_tt;
    project.root_pt = root_pt;
    project.project_tree = new ProjectTree(project, project.root_pt);
    project.layer_tree = new LayerTree(project, root_lt);
    project.root_lt = root_lt;
    project.layer_set = (LayerSet) root_lt.getObject();
    // if all when well, register as open:
    al_open_projects.add(project);
    // create the project control window, containing the trees in a double JSplitPane
    ControlWindow.add(project, project.template_tree, project.project_tree, project.layer_tree);
    // set ProjectThing nodes expanded state, now that the trees exist
    try {
        java.lang.reflect.Field f = JTree.class.getDeclaredField("expandedState");
        f.setAccessible(true);
        Hashtable<Object, Object> ht_exp = (Hashtable<Object, Object>) f.get(project.project_tree);
        for (Map.Entry<ProjectThing, Boolean> entry : ht_pt_expanded.entrySet()) {
            ProjectThing pt = entry.getKey();
            Boolean expanded = entry.getValue();
            // project.project_tree.expandPath(new TreePath(project.project_tree.findNode(pt, project.project_tree).getPath()));
            // WARNING the above is wrong in that it will expand the whole thing, not just set the state of the node!!
            // So the ONLY way to do it is to start from the child-most leafs of the tree, and apply the expanding to them upward. This is RIDICULOUS, how can it be so broken
            // so, hackerous:
            DefaultMutableTreeNode nd = DNDTree.findNode(pt, project.project_tree);
            // else Utils.log2("path: " + new TreePath(nd.getPath()));
            if (null == nd) {
                Utils.log2("Can't find node for " + pt);
            } else {
                ht_exp.put(new TreePath(nd.getPath()), expanded);
            }
        }
        // very important!!
        project.project_tree.updateUILater();
    } catch (Exception e) {
        IJError.print(e);
    }
    // open any stored displays
    if (open_displays) {
        final Bureaucrat burro = Display.openLater();
        if (null != burro) {
            final Runnable ru = new Runnable() {

                public void run() {
                    // wait until the Bureaucrat finishes
                    try {
                        burro.join();
                    } catch (InterruptedException ie) {
                    }
                    // restore to non-changes (crude, but works)
                    project.loader.setChanged(false);
                    Utils.log2("C set to false");
                }
            };
            new Thread() {

                public void run() {
                    setPriority(Thread.NORM_PRIORITY);
                    // avoiding "can't call invokeAndWait from the EventDispatch thread" error
                    try {
                        javax.swing.SwingUtilities.invokeAndWait(ru);
                    } catch (Exception e) {
                        Utils.log2("ERROR: " + e);
                    }
                }
            }.start();
            // SO: WAIT TILL THE END OF TIME!
            new Thread() {

                public void run() {
                    try {
                        // ah, the pain in my veins. I can't take this shitty setup anymore.
                        Thread.sleep(4000);
                        javax.swing.SwingUtilities.invokeAndWait(new Runnable() {

                            public void run() {
                                project.getLoader().setChanged(false);
                                Utils.log2("D set to false");
                            }
                        });
                        // repainting to fix gross errors in tree rendering
                        project.getTemplateTree().updateUILater();
                        // idem
                        project.getProjectTree().updateUILater();
                    } catch (Exception ie) {
                    }
                }
            }.start();
        } else {
            // help the helpless users
            Display.createDisplay(project, project.layer_set.getLayer(0));
        }
    }
    project.restartAutosaving();
    return project;
}

Example 28 with Bureaucrat

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

the class Loader method getJobsPopup.

public JPopupMenu getJobsPopup(final Display display) {
    synchronized (jobs) {
        this.popup_jobs = new JPopupMenu("Cancel jobs:");
        int i = 1;
        for (final Bureaucrat burro : jobs) {
            final JMenuItem item = new JMenuItem("Job " + i + ": " + burro.getTaskName());
            item.addActionListener(display);
            popup_jobs.add(item);
            i++;
        }
    }
    return popup_jobs;
}

Example 29 with Bureaucrat

use of ini.trakem2.utils.Bureaucrat 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 30 with Bureaucrat

use of ini.trakem2.utils.Bureaucrat 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());
}