Examples with UnicodeReader gdsc.core.utils.UnicodeReader used on opensource projects

Example 1 with UnicodeReader

use of gdsc.core.utils.UnicodeReader in project GDSC-SMLM by aherbert.

the class SMLMTools method createFrame.

private boolean createFrame() {
    // Locate all the GDSC SMLM plugins using the plugins.config:
    InputStream readmeStream = getToolsPluginsConfig();
    ij.Menus.installPlugin("", ij.Menus.PLUGINS_MENU, "-", "", IJ.getInstance());
    // Read into memory
    ArrayList<String[]> plugins = new ArrayList<String[]>();
    int gaps = 0;
    BufferedReader input = null;
    try {
        input = new BufferedReader(new UnicodeReader(readmeStream, null));
        String line;
        while ((line = input.readLine()) != null) {
            if (line.startsWith("#"))
                continue;
            String[] tokens = line.split(",");
            if (tokens.length == 3) {
                // Only copy the entries from the Plugins menu
                if (!ignore(tokens)) {
                    if (!plugins.isEmpty()) {
                        // Multiple gaps indicates a new column
                        if (gaps > 1) {
                            plugins.add(new String[] { "next", "" });
                        }
                    }
                    gaps = 0;
                    plugins.add(new String[] { tokens[1].trim(), tokens[2].trim() });
                }
            } else
                gaps++;
            // Put a spacer between plugins if specified
            if ((tokens.length == 2 && tokens[0].startsWith("Plugins") && tokens[1].trim().equals("\"-\"")) || line.length() == 0) {
                plugins.add(new String[] { "spacer", "" });
            }
        }
    } catch (IOException e) {
    // Ignore 
    } finally {
        if (input != null) {
            try {
                input.close();
            } catch (IOException e) {
            // Ignore
            }
        }
    }
    if (plugins.isEmpty())
        return false;
    // Arrange on a grid
    Panel mainPanel = new Panel();
    GridBagLayout grid = new GridBagLayout();
    mainPanel.setLayout(grid);
    add(mainPanel);
    addSpacer = false;
    int col = 0, row = 0;
    for (String[] plugin : plugins) {
        if (plugin[0].equals("next")) {
            col++;
            row = 0;
        } else if (plugin[0].equals("spacer"))
            addSpacer = true;
        else
            row = addPlugin(mainPanel, grid, plugin[0], plugin[1], col, row);
    }
    return true;
}

Example 2 with UnicodeReader

use of gdsc.core.utils.UnicodeReader in project GDSC-SMLM by aherbert.

the class CreateData method createPhotonDistribution.

/**
	 * @return A photon distribution loaded from a file of floating-point values with the specified population mean.
	 */
private RealDistribution createPhotonDistribution() {
    if (PHOTON_DISTRIBUTION[PHOTON_CUSTOM].equals(settings.photonDistribution)) {
        // Get the distribution file
        String filename = Utils.getFilename("Photon_distribution", settings.photonDistributionFile);
        if (filename != null) {
            settings.photonDistributionFile = filename;
            try {
                InputStream is = new FileInputStream(new File(settings.photonDistributionFile));
                BufferedReader in = new BufferedReader(new UnicodeReader(is, null));
                StoredDataStatistics stats = new StoredDataStatistics();
                try {
                    String str = null;
                    double val = 0.0d;
                    while ((str = in.readLine()) != null) {
                        val = Double.parseDouble(str);
                        stats.add(val);
                    }
                } finally {
                    in.close();
                }
                if (stats.getSum() > 0) {
                    // Update the statistics to the desired mean.
                    double scale = (double) settings.photonsPerSecond / stats.getMean();
                    double[] values = stats.getValues();
                    for (int i = 0; i < values.length; i++) values[i] *= scale;
                    // TODO - Investigate the limits of this distribution. 
                    // How far above and below the input data will values be generated.
                    // Create the distribution using the recommended number of bins
                    final int binCount = stats.getN() / 10;
                    EmpiricalDistribution dist = new EmpiricalDistribution(binCount, createRandomGenerator());
                    dist.load(values);
                    return dist;
                }
            } catch (IOException e) {
            // Ignore
            } catch (NullArgumentException e) {
            // Ignore 
            } catch (NumberFormatException e) {
            // Ignore
            }
        }
        Utils.log("Failed to load custom photon distribution from file: %s. Default to fixed.", settings.photonDistributionFile);
    } else if (PHOTON_DISTRIBUTION[PHOTON_UNIFORM].equals(settings.photonDistribution)) {
        if (settings.photonsPerSecond < settings.photonsPerSecondMaximum) {
            UniformRealDistribution dist = new UniformRealDistribution(createRandomGenerator(), settings.photonsPerSecond, settings.photonsPerSecondMaximum);
            return dist;
        }
    } else if (PHOTON_DISTRIBUTION[PHOTON_GAMMA].equals(settings.photonDistribution)) {
        final double scaleParameter = settings.photonsPerSecond / settings.photonShape;
        GammaDistribution dist = new GammaDistribution(createRandomGenerator(), settings.photonShape, scaleParameter, ExponentialDistribution.DEFAULT_INVERSE_ABSOLUTE_ACCURACY);
        return dist;
    } else if (PHOTON_DISTRIBUTION[PHOTON_CORRELATED].equals(settings.photonDistribution)) {
        // No distribution required
        return null;
    }
    settings.photonDistribution = PHOTON_DISTRIBUTION[PHOTON_FIXED];
    return null;
}

Example 3 with UnicodeReader

use of gdsc.core.utils.UnicodeReader in project GDSC-SMLM by aherbert.

the class BenchmarkFilterAnalysis method readFilterSets.

@SuppressWarnings("unchecked")
private List<FilterSet> readFilterSets() {
    if (extraOptions && BenchmarkSpotFit.multiFilter != null) {
        IDirectFilter f = BenchmarkSpotFit.multiFilter.getFilter();
        if (f instanceof DirectFilter) {
            GenericDialog gd = new GenericDialog(TITLE);
            gd.addMessage("Use an identical filter to " + BenchmarkSpotFit.TITLE);
            gd.enableYesNoCancel();
            gd.hideCancelButton();
            gd.showDialog();
            if (gd.wasOKed()) {
                setLastFile(null);
                List<FilterSet> filterSets = new ArrayList<FilterSet>(1);
                List<Filter> filters = new ArrayList<Filter>(1);
                filters.add((DirectFilter) f);
                FilterSet filterSet = new FilterSet(filters);
                filterSets.add(filterSet);
                resetParametersFromFitting();
                createResultsPrefix2();
                return filterSets;
            }
        }
    }
    GlobalSettings gs = SettingsManager.loadSettings();
    FilterSettings filterSettings = gs.getFilterSettings();
    String filename = Utils.getFilename("Filter_File", filterSettings.filterSetFilename);
    if (filename != null) {
        IJ.showStatus("Reading filters ...");
        filterSettings.filterSetFilename = filename;
        // Allow the filters to be cached
        if (isSameFile(filename)) {
            GenericDialog gd = new GenericDialog(TITLE);
            gd.hideCancelButton();
            gd.addMessage("The same filter file was selected.");
            gd.addCheckbox("Re-use_filters", reUseFilters);
            gd.showDialog();
            if (!gd.wasCanceled()) {
                if ((reUseFilters = gd.getNextBoolean())) {
                    SettingsManager.saveSettings(gs);
                    return filterList;
                }
            }
        }
        BufferedReader input = null;
        setLastFile(null);
        try {
            FileInputStream fis = new FileInputStream(filename);
            input = new BufferedReader(new UnicodeReader(fis, null));
            Object o = XStreamWrapper.getInstance().fromXML(input);
            if (o != null && o instanceof List<?>) {
                SettingsManager.saveSettings(gs);
                List<FilterSet> filterSets = (List<FilterSet>) o;
                if (containsStandardFilters(filterSets)) {
                    IJ.log("Filter sets must contain 'Direct' filters");
                    return null;
                }
                // Check they are not empty lists
                List<FilterSet> filterSets2 = new LinkedList<FilterSet>();
                for (FilterSet filterSet : filterSets) {
                    if (filterSet.size() != 0) {
                        filterSets2.add(filterSet);
                    } else {
                        IJ.log("Filter set empty: " + filterSet.getName());
                    }
                }
                if (filterSets2.isEmpty()) {
                    IJ.log("All Filter sets are empty");
                    return null;
                }
                // Maintain the same list type
                filterSets.clear();
                filterSets.addAll(filterSets2);
                filterList = filterSets;
                // Option to enumerate filters
                expandFilters();
                setLastFile(filename);
                return filterList;
            }
            IJ.log("No filter sets defined in the specified file: " + filename);
        } catch (Exception e) {
            IJ.log("Unable to load the filter sets from file: " + e.getMessage());
        } finally {
            if (input != null) {
                try {
                    input.close();
                } catch (IOException e) {
                // Ignore
                }
            }
            IJ.showStatus("");
        }
    }
    return null;
}

Example 4 with UnicodeReader

use of gdsc.core.utils.UnicodeReader in project GDSC-SMLM by aherbert.

the class PeakResultsReader method readRapidSTORM.

private MemoryPeakResults readRapidSTORM() {
    MemoryPeakResults results = createResults();
    results.setName(new File(filename).getName());
    BufferedReader input = null;
    try {
        FileInputStream fis = new FileInputStream(filename);
        FileChannel channel = fis.getChannel();
        input = new BufferedReader(new UnicodeReader(fis, null));
        String line;
        int errors = 0;
        // Skip the header
        while ((line = input.readLine()) != null) {
            if (line.length() == 0)
                continue;
            if (line.charAt(0) != '#') {
                // This is the first record
                if (!addRapidSTORMResult(results, line))
                    errors = 1;
                break;
            }
        }
        int c = 0;
        while ((line = input.readLine()) != null) {
            if (line.length() == 0)
                continue;
            if (line.charAt(0) == '#')
                continue;
            if (!addRapidSTORMResult(results, line)) {
                if (++errors >= 10) {
                    break;
                }
            }
            if (++c % 512 == 0)
                showProgress(channel);
        }
    } catch (IOException e) {
    // ignore
    } finally {
        try {
            if (input != null)
                input.close();
        } catch (IOException e) {
        // Ignore
        }
    }
    return results;
}

Example 5 with UnicodeReader

use of gdsc.core.utils.UnicodeReader in project GDSC-SMLM by aherbert.

the class PeakResultsReader method readText.

private MemoryPeakResults readText() {
    MemoryPeakResults results = createResults();
    BufferedReader input = null;
    try {
        FileInputStream fis = new FileInputStream(filename);
        FileChannel channel = fis.getChannel();
        input = new BufferedReader(new UnicodeReader(fis, null));
        String line;
        int errors = 0;
        // Read different versions
        int version = (readAmplitude) ? 1 : 2;
        // Skip the header
        while ((line = input.readLine()) != null) {
            if (line.length() == 0)
                continue;
            if (line.charAt(0) != '#') {
                // This is the first record
                if (!addPeakResult(results, line, version))
                    errors = 1;
                break;
            }
        }
        int c = 0;
        while ((line = input.readLine()) != null) {
            if (line.length() == 0)
                continue;
            if (line.charAt(0) == '#')
                continue;
            if (!addPeakResult(results, line, version)) {
                if (++errors >= 10) {
                    break;
                }
            }
            if (++c % 512 == 0)
                showProgress(channel);
        }
    } catch (IOException e) {
    // ignore
    } finally {
        try {
            if (input != null)
                input.close();
        } catch (IOException e) {
        // Ignore
        }
    }
    return results;
}