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

Example 61 with Project

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

the class Project method adjustProperties.

public void adjustProperties() {
    // should be more generic, but for now it'll do
    GenericDialog gd = new GenericDialog("Properties");
    gd.addMessage("Ignore image linking for:");
    boolean link_labels = addBox(gd, DLabel.class);
    boolean nolink_segmentations = "true".equals(ht_props.get("segmentations_nolinks"));
    gd.addCheckbox("Segmentations", nolink_segmentations);
    gd.addMessage("Currently linked objects will remain so\nunless explicitly unlinked.");
    boolean dissector_zoom = "true".equals(ht_props.get("dissector_zoom"));
    gd.addCheckbox("Zoom-invariant markers for Dissector", dissector_zoom);
    gd.addChoice("Image_resizing_mode: ", Loader.MIPMAP_MODES.values().toArray(new String[Loader.MIPMAP_MODES.size()]), Loader.getMipMapModeName(mipmaps_mode));
    gd.addChoice("mipmaps format:", FSLoader.MIPMAP_FORMATS, FSLoader.MIPMAP_FORMATS[loader.getMipMapFormat()]);
    gd.addNumericField("Save mipmap images from level", this.first_mipmap_level_saved, 0);
    boolean layer_mipmaps = "true".equals(ht_props.get("layer_mipmaps"));
    gd.addCheckbox("Layer_mipmaps", layer_mipmaps);
    boolean keep_mipmaps = "true".equals(ht_props.get("keep_mipmaps"));
    // coping with the fact that thee is no Action context ... there should be one in the Worker thread.
    gd.addCheckbox("Keep_mipmaps_when_deleting_images", keep_mipmaps);
    int bucket_side = (int) getProperty("bucket_side", Bucket.MIN_BUCKET_SIZE);
    gd.addNumericField("Bucket side length: ", bucket_side, 0, 6, "pixels");
    boolean no_shutdown_hook = "true".equals(ht_props.get("no_shutdown_hook"));
    gd.addCheckbox("No_shutdown_hook to save the project", no_shutdown_hook);
    int n_undo_steps = getProperty("n_undo_steps", 32);
    gd.addSlider("Undo steps", 32, 200, n_undo_steps);
    boolean flood_fill_to_image_edge = "true".equals(ht_props.get("flood_fill_to_image_edge"));
    gd.addCheckbox("AreaList_flood_fill_to_image_edges", flood_fill_to_image_edge);
    int look_ahead_cache = (int) getProperty("look_ahead_cache", 0);
    gd.addNumericField("Look_ahead_cache:", look_ahead_cache, 0, 6, "layers");
    // default: every 10 minutes
    int autosaving_interval = getProperty("autosaving_interval", 10);
    gd.addNumericField("Autosave every:", autosaving_interval, 0, 6, "minutes");
    int n_mipmap_threads = getProperty("n_mipmap_threads", 1);
    gd.addSlider("Number of threads for mipmaps", 1, n_mipmap_threads, n_mipmap_threads);
    int meshResolution = getProperty("mesh_resolution", 32);
    gd.addSlider("Default mesh resolution for images", 1, 512, meshResolution);
    // 
    gd.showDialog();
    // 
    if (gd.wasCanceled())
        return;
    setLinkProp(link_labels, gd.getNextBoolean(), DLabel.class);
    boolean nolink_segmentations2 = gd.getNextBoolean();
    if (nolink_segmentations) {
        if (!nolink_segmentations2)
            ht_props.remove("segmentations_nolinks");
    } else if (nolink_segmentations2)
        ht_props.put("segmentations_nolinks", "true");
    if (adjustProp("dissector_zoom", dissector_zoom, gd.getNextBoolean())) {
        // TODO: should repaint nested LayerSets as well
        Display.repaint(layer_set);
    }
    this.mipmaps_mode = Loader.getMipMapModeIndex(gd.getNextChoice());
    final int new_mipmap_format = gd.getNextChoiceIndex();
    final int old_mipmap_format = loader.getMipMapFormat();
    if (new_mipmap_format != old_mipmap_format) {
        YesNoDialog yn = new YesNoDialog("MipMaps format", "Changing mipmaps format to '" + FSLoader.MIPMAP_FORMATS[new_mipmap_format] + "'requires regenerating all mipmaps. Proceed?");
        if (yn.yesPressed()) {
            if (loader.setMipMapFormat(new_mipmap_format)) {
                loader.updateMipMapsFormat(old_mipmap_format, new_mipmap_format);
            }
        }
    }
    setFirstMipMapLevelSaved(gd.getNextNumber());
    boolean layer_mipmaps2 = gd.getNextBoolean();
    if (adjustProp("layer_mipmaps", layer_mipmaps, layer_mipmaps2)) {
        if (layer_mipmaps && !layer_mipmaps2) {
        // TODO
        // 1 - ask first
        // 2 - remove all existing images from layer.mipmaps folder
        } else if (!layer_mipmaps && layer_mipmaps2) {
        // TODO
        // 1 - ask first
        // 2 - create de novo all layer mipmaps in a background task
        }
    }
    adjustProp("keep_mipmaps", keep_mipmaps, gd.getNextBoolean());
    Utils.log2("keep_mipmaps: " + getBooleanProperty("keep_mipmaps"));
    // 
    bucket_side = (int) gd.getNextNumber();
    if (bucket_side > Bucket.MIN_BUCKET_SIZE) {
        setProperty("bucket_side", Integer.toString(bucket_side));
        layer_set.recreateBuckets(true);
    }
    adjustProp("no_shutdown_hook", no_shutdown_hook, gd.getNextBoolean());
    n_undo_steps = (int) gd.getNextNumber();
    if (n_undo_steps < 0)
        n_undo_steps = 0;
    setProperty("n_undo_steps", Integer.toString(n_undo_steps));
    adjustProp("flood_fill_to_image_edge", flood_fill_to_image_edge, gd.getNextBoolean());
    double d_look_ahead_cache = gd.getNextNumber();
    if (!Double.isNaN(d_look_ahead_cache) && d_look_ahead_cache >= 0) {
        setProperty("look_ahead_cache", Integer.toString((int) d_look_ahead_cache));
        if (0 == d_look_ahead_cache) {
            Display.clearColumnScreenshots(this.layer_set);
        } else {
            Utils.logAll("WARNING: look-ahead cache is incomplete.\n  Expect issues when editing objects, adding new ones, and the like.\n  Use \"Project - Flush image cache\" to fix any lack of refreshing issues you encounter.");
        }
    } else {
        Utils.log2("Ignoring invalid 'look ahead cache' value " + d_look_ahead_cache);
    }
    double autosaving_interval2 = gd.getNextNumber();
    if (((int) (autosaving_interval2)) == autosaving_interval) {
    // do nothing
    } else if (autosaving_interval2 < 0 || Double.isNaN(autosaving_interval)) {
        Utils.log("IGNORING invalid autosaving interval: " + autosaving_interval2);
    } else {
        setProperty("autosaving_interval", Integer.toString((int) autosaving_interval2));
        restartAutosaving();
    }
    int n_mipmap_threads2 = (int) Math.max(1, gd.getNextNumber());
    if (n_mipmap_threads != n_mipmap_threads2) {
        setProperty("n_mipmap_threads", Integer.toString(n_mipmap_threads2));
        // WARNING: this does it for a static service, affecting all projects!
        FSLoader.restartMipMapThreads(n_mipmap_threads2);
    }
    int meshResolution2 = (int) gd.getNextNumber();
    if (meshResolution != meshResolution2) {
        if (meshResolution2 > 0) {
            setProperty("mesh_resolution", Integer.toString(meshResolution2));
        } else {
            Utils.log("WARNING: ignoring invalid mesh resolution value " + meshResolution2);
        }
    }
}

Example 62 with Project

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

the class Project method saveTask.

public Bureaucrat saveTask(final String command) {
    return Bureaucrat.createAndStart(new Worker.Task("Saving") {

        public void exec() {
            if (command.equals("Save")) {
                save();
            } else if (command.equals("Save as...")) {
                XMLOptions options = new XMLOptions();
                options.overwriteXMLFile = false;
                options.export_images = false;
                options.include_coordinate_transform = true;
                options.patches_dir = null;
                // Will open a file dialog
                loader.saveAs(project, options);
                restartAutosaving();
            // 
            } else if (command.equals("Save as... without coordinate transforms")) {
                YesNoDialog yn = new YesNoDialog("WARNING", "You are about to save an XML file that lacks the information for the coordinate transforms of each image.\n" + "These transforms are referred to with the attribute 'ct_id' of each 't2_patch' entry in the XML document,\n" + "and the data for the transform is stored in an individual file under the folder 'trakem2.cts/'.\n" + " \n" + "It is advised to keep a complete XML file with all coordinate transforms included along with this new copy.\n" + "Please check NOW that you have such a complete XML copy.\n" + " \n" + "Proceed?");
                if (!yn.yesPressed())
                    return;
                saveWithoutCoordinateTransforms();
            // 
            } else if (command.equals("Delete stale files...")) {
                setTaskName("Deleting stale files");
                GenericDialog gd = new GenericDialog("Delete stale files");
                gd.addMessage("You are about to remove all files under the folder 'trakem2.cts/' which are not referred to from the\n" + "currently loaded project. If you have sibling XML files whose 't2_patch' entries (the images) refer,\n" + "via 'ct_id' attributes, to coordinate transforms in 'trakem2.cts/' that this current XML doesn't,\n" + "they may be LOST FOREVER. Unless you have a version of the XML file with the coordinate transforms\n" + "written in it, as can be obtained by using the 'Project - Save' command.\n" + " \n" + "The same is true for the .zip files that store alpha masks, under folder 'trakem2.masks/'\n" + "and which are referred to from the 'alpha_mask_id' attribute of 't2_patch' entries.\n" + " \n" + "Do you have such complete XML file? Check *NOW*.\n" + " \n" + "Proceed with deleting:");
                gd.addCheckbox("Delete stale coordinate transform files", true);
                gd.addCheckbox("Delete stale alpha mask files", true);
                gd.showDialog();
                if (gd.wasCanceled())
                    return;
                project.getLoader().deleteStaleFiles(gd.getNextBoolean(), gd.getNextBoolean());
            }
        }
    }, project);
}

Example 63 with Project

use of ini.trakem2.Project in project openstack4j by ContainX.

the class KeystoneProjectServiceTests method projects_getByName_not_exist_test.

public void projects_getByName_not_exist_test() throws Exception {
    respondWith(JSON_PROJECTS_GET_BY_NAME_EMPTY);
    Project project = osv3().identity().projects().getByName(PROJECT_NAME, PROJECT_DOMAIN_ID);
    assertNull(project);
}

Example 64 with Project

use of ini.trakem2.Project in project openstack4j by ContainX.

the class KeystoneProjectServiceTests method projects_crud_test.

public void projects_crud_test() throws Exception {
    Project project = Builders.project().name(PROJECT_NAME).description(PROJECT_DESCRIPTION).domainId(PROJECT_DOMAIN_ID).setExtra(PROJECT_EXTRA_KEY_1, PROJECT_EXTRA_VALUE_1).enabled(true).build();
    respondWith(JSON_PROJECTS_CREATE);
    Project newProject = osv3().identity().projects().create(project);
    assertEquals(newProject.getName(), PROJECT_NAME);
    assertEquals(newProject.getDomainId(), PROJECT_DOMAIN_ID);
    assertEquals(newProject.getDescription(), PROJECT_DESCRIPTION);
    assertEquals(newProject.getExtra(PROJECT_EXTRA_KEY_1), PROJECT_EXTRA_VALUE_1);
    PROJECT_ID = newProject.getId();
    respondWith(JSON_PROJECTS_GET_BYID);
    Project project_setToUpdate = osv3().identity().projects().get(PROJECT_ID);
    respondWith(JSON_PROJECTS_UPDATE);
    Project updatedProject = osv3().identity().projects().update(project_setToUpdate.toBuilder().description(PROJECT_DESCRIPTION_UPDATE).setExtra(PROJECT_EXTRA_KEY_2, PROJECT_EXTRA_VALUE_2).build());
    assertEquals(updatedProject.getId(), PROJECT_ID);
    assertEquals(updatedProject.getName(), PROJECT_NAME);
    assertEquals(updatedProject.getDomainId(), PROJECT_DOMAIN_ID);
    assertEquals(updatedProject.getDescription(), PROJECT_DESCRIPTION_UPDATE);
    assertEquals(updatedProject.getExtra(PROJECT_EXTRA_KEY_1), PROJECT_EXTRA_VALUE_1);
    assertEquals(updatedProject.getExtra(PROJECT_EXTRA_KEY_2), PROJECT_EXTRA_VALUE_2);
}

Example 65 with Project

use of ini.trakem2.Project in project camel by apache.

the class ProjectProducer method doCreate.

private void doCreate(Exchange exchange) {
    final Project in = messageToProject(exchange.getIn());
    final Project out = osV3Client.identity().projects().create(in);
    exchange.getIn().setBody(out);
}