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

Example 16 with Filter

use of ini.trakem2.utils.Filter in project modules.playframework.org by playframework.

the class Modules method details.

public static Result details(String moduleKey) {
    Result result;
    final Module module = Module.findByModuleKey(moduleKey);
    if (module == null) {
        result = notFound("Module not found: " + moduleKey);
    } else {
        List<ModuleVersion> moduleVersions = ModuleVersion.findByModule(module);
        User user = currentUser();
        Rate rate = null;
        Vote vote = null;
        if (user != null) {
            rate = CollectionUtils.filterFirst(user.rates, new Filter<Rate>() {

                public boolean isAcceptable(Rate rate) {
                    return rate.playModule.id.equals(module.id);
                }
            });
            vote = CollectionUtils.filterFirst(user.votes, new Filter<Vote>() {

                public boolean isAcceptable(Vote vote) {
                    return vote.playModule.id.equals(module.id);
                }
            });
        }
        Set<PlayVersion.MajorVersion> majorVersions = new HashSet<PlayVersion.MajorVersion>();
        for (ModuleVersion moduleVersion : moduleVersions) {
            majorVersions.addAll(moduleVersion.getMajorVersions());
        }
        Ebean.refresh(module.rating);
        result = ok(moduleDetails.render(user, module, moduleVersions, majorVersions, rate, vote));
    }
    return result;
}

Example 17 with Filter

use of ini.trakem2.utils.Filter in project modules.playframework.org by playframework.

the class Modules method rate.

// If a user has already rated, then change the rate, don't add a new one
@RoleHolderPresent
public static Result rate(String moduleKey) {
    Result result;
    Form<RatingForm> form = form(RatingForm.class).bindFromRequest();
    if (form.hasErrors()) {
        result = badRequest(form.errorsAsJson());
    } else {
        RatingForm ratingForm = form.get();
        final Module module = Module.findById(ratingForm.id);
        if (module == null) {
            result = badRequest("Module does not exist");
        } else {
            User user = currentUser();
            Rate rate = null;
            if (user != null) {
                // user shouldn't be null because of @RoleHolderPresent
                rate = CollectionUtils.filterFirst(user.rates, new Filter<Rate>() {

                    @Override
                    public boolean isAcceptable(Rate rate) {
                        return rate.playModule.id.equals(module.id);
                    }
                });
                if (rate != null) {
                    module.rating.subtract(rate);
                } else {
                    rate = new Rate();
                    rate.playModule = module;
                    user.rates.add(rate);
                }
                rate.rating = ratingForm.rating;
                module.rating.add(rate);
                module.rating.calculateAverage();
                module.save();
                user.save();
            }
            RatingResponseForm responseForm = new RatingResponseForm();
            responseForm.totalRatings = module.rating.totalRatings();
            responseForm.averageRating = module.rating.averageRating;
            result = ok(Json.toJson(responseForm));
        }
    }
    return result;
}

Example 18 with Filter

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

the class Loader method preProcess.

protected final void preProcess(final Patch p, ImagePlus imp, final long image_n_bytes) {
    if (null == p)
        return;
    try {
        final String path = preprocessors.get(p);
        boolean update = false;
        if (null != path) {
            final File f = new File(path);
            if (!f.exists()) {
                Utils.log("ERROR: preprocessor script file does NOT exist: " + path);
                return;
            } else if (!f.canRead()) {
                Utils.log("ERROR: can NOT read preprocessor script file at: " + path);
                return;
            }
            if (null == imp) {
                // uninitialized: the script may generate its data
                imp = new ImagePlus();
            } else {
                // Prepare image for pre-processing
                // for 8-bit and RGB images, your problem: setting min and max will expand the range.
                imp.getProcessor().setMinAndMax(p.getMin(), p.getMax());
            }
            // Free 10 times the memory taken by the image, as a gross estimate of memory consumption by the script
            releaseToFit(Math.min(10 * image_n_bytes, MAX_MEMORY / 4));
            // Run the script
            ini.trakem2.scripting.PatchScript.run(p, imp, path);
            // Update Patch image properties:
            if (null != imp.getProcessor() && null != imp.getProcessor().getPixels() && imp.getWidth() > 0 && imp.getHeight() > 0) {
                update = true;
            } else {
                Utils.log("ERROR: preprocessor script failed to create a valid image:" + "\n  ImageProcessor: " + imp.getProcessor() + "\n  pixel array: " + (null == imp.getProcessor() ? null : imp.getProcessor().getPixels()) + "\n  width: " + imp.getWidth() + "\n  height: " + imp.getHeight());
            }
        }
        // Now apply the Patch filters, if any
        final IFilter[] fs = p.getFilters();
        if (null != fs && fs.length > 0) {
            ImageProcessor ip = imp.getProcessor();
            for (final IFilter filter : fs) {
                ip = filter.process(ip);
            }
            if (ip != imp.getProcessor()) {
                imp.setProcessor(ip);
            }
            update = true;
        }
        // Now apply intensity correction if available
        update |= mapIntensities(p, imp);
        if (update) {
            // 1: Tag the ImagePlus as altered (misuses fileFormat field, which is unused in any case)
            final FileInfo fi = imp.getOriginalFileInfo();
            // otherwise, the null original FileInfo is a valid tag by itself in the persistence.Cache
            if (null != fi)
                fi.fileFormat = Loader.PREPROCESSED;
            // 2: cache
            cache(p, imp);
            // 3: update properties of the Patch
            p.updatePixelProperties(imp);
        }
    } catch (final Exception e) {
        IJError.print(e);
    }
}

Example 19 with Filter

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

the class Loader method scaleImage.

public static ImageProcessor scaleImage(final ImagePlus imp, final int level, final boolean quality) {
    if (level <= 0)
        return imp.getProcessor();
    // else, make a properly scaled image:
    // - gaussian blurred for best quality when resizing with nearest neighbor
    // - direct nearest neighbor otherwise
    ImageProcessor ip = imp.getProcessor();
    final int w = ip.getWidth();
    final int h = ip.getHeight();
    final double mag = 1 / Math.pow(2, level);
    // TODO releseToFit !
    if (quality) {
        // apply proper gaussian filter
        // sigma = sqrt(level^2 - 0.5^2)
        final double sigma = Math.sqrt(Math.pow(2, level) - 0.25);
        ip = new FloatProcessorT2(w, h, ImageFilter.computeGaussianFastMirror(new FloatArray2D((float[]) ip.convertToFloat().getPixels(), w, h), (float) sigma).data, ip.getDefaultColorModel(), ip.getMin(), ip.getMax());
        // better while float
        ip = ip.resize((int) (w * mag), (int) (h * mag));
        return Utils.convertTo(ip, imp.getType(), false);
    } else {
        return ip.resize((int) (w * mag), (int) (h * mag));
    }
}

Example 20 with Filter

use of ini.trakem2.utils.Filter 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;
}