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

Example 6 with UnicodeReader

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

the class PeakResultsReader method getHeader.

/**
	 * @return The header from the results file
	 */
public String getHeader() {
    if (header == null) {
        BufferedReader input = null;
        try {
            FileInputStream fis = new FileInputStream(filename);
            input = new BufferedReader(new UnicodeReader(fis, null));
            StringBuffer sb = new StringBuffer();
            String line;
            int count = 0;
            while ((line = input.readLine()) != null) {
                count++;
                if (count == 1) {
                    // The NSTORM file format does not have comment characters but does have a single header line
                    if (line.startsWith("Channel Name")) {
                        sb.append(line).append("\n");
                        break;
                    }
                    // User may try and load the text saved directly from the ImageJ Table Results
                    if (line.contains(IMAGEJ_TABLE_RESULTS_HEADER)) {
                        sb.append(line).append("\n");
                        break;
                    }
                }
                if (line.length() == 0)
                    continue;
                if (line.charAt(0) == '#')
                    sb.append(line).append("\n");
                else
                    break;
            }
            header = sb.toString();
            version = getField("FileVersion");
            guessFormat(line);
        } catch (IOException e) {
        // ignore
        } finally {
            try {
                if (input != null)
                    input.close();
            } catch (IOException e) {
            // Ignore
            }
        }
    }
    return header;
}

Example 7 with UnicodeReader

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

the class PeakResultsReader method readMALK.

private MemoryPeakResults readMALK() {
    MemoryPeakResults results = createResults();
    if (Utils.isNullOrEmpty(name))
        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 (!addMALKResult(results, line))
                    errors = 1;
                break;
            }
        }
        int c = 0;
        while ((line = input.readLine()) != null) {
            if (line.length() == 0)
                continue;
            if (line.charAt(0) == '#')
                continue;
            if (!addMALKResult(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
        }
    }
    // The GDSC SMLM code still adds a calibration to the MALK file when saving so we may be able to convert back
    if (getCalibration() != null) {
        if (Maths.isFinite(calibration.getNmPerPixel()) && calibration.getNmPerPixel() > 0) {
            double nmPerPixel = calibration.getNmPerPixel();
            for (PeakResult p : results.getResults()) {
                p.params[Gaussian2DFunction.X_POSITION] /= nmPerPixel;
                p.params[Gaussian2DFunction.Y_POSITION] /= nmPerPixel;
                p.origX = (int) p.params[Gaussian2DFunction.X_POSITION];
                p.origY = (int) p.params[Gaussian2DFunction.Y_POSITION];
            }
        }
    }
    return results;
}

Example 8 with UnicodeReader

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

the class PeakResultsReader method readNSTORM.

private MemoryPeakResults readNSTORM() {
    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 single line header
        input.readLine();
        int c = 0;
        while ((line = input.readLine()) != null) {
            if (line.length() == 0)
                continue;
            if (!addNSTORMResult(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
        }
    }
    // The following relationship holds when length == 1:
    // Area = Height * 2 * pi * (Width / (pixel_pitch*2) )^2
    // => Pixel_pitch = 0.5 * Width / sqrt(Area / (Height * 2 * pi))
    // Try and create a calibration
    Statistics pixelPitch = new Statistics();
    for (PeakResult p : results.getResults()) {
        if (p.getFrame() == p.getEndFrame()) {
            float width = p.params[Gaussian2DFunction.X_SD];
            float height = p.params[Gaussian2DFunction.SIGNAL];
            float area = p.origValue;
            pixelPitch.add(0.5 * width / Math.sqrt(area / (height * 2 * Math.PI)));
            if (pixelPitch.getN() > 100)
                break;
        }
    }
    if (pixelPitch.getN() > 0) {
        final double nmPerPixel = pixelPitch.getMean();
        final double widthConversion = 1.0 / (2 * nmPerPixel);
        // Create a calibration
        calibration = new Calibration();
        calibration.setNmPerPixel(nmPerPixel);
        results.setCalibration(calibration);
        // Convert data
        for (PeakResult p : results.getResults()) {
            p.params[Gaussian2DFunction.X_POSITION] /= nmPerPixel;
            p.params[Gaussian2DFunction.Y_POSITION] /= nmPerPixel;
            // Since the width is 2*pixel pitch
            p.params[Gaussian2DFunction.X_SD] *= widthConversion;
            p.params[Gaussian2DFunction.Y_SD] *= widthConversion;
        }
    }
    // Swap to the intensity stored in the origValue field.
    for (PeakResult p : results.getResults()) {
        final float origValue = p.params[Gaussian2DFunction.SIGNAL];
        p.params[Gaussian2DFunction.SIGNAL] = p.origValue;
        p.origValue = origValue;
    }
    return results;
}

Example 9 with UnicodeReader

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

the class LoadLocalisations method loadLocalisations.

static LocalisationList loadLocalisations(String filename) {
    if (!getFields())
        return null;
    LocalisationList localisations = new LocalisationList(distanceUnit, intensityUnit, gain, pixelPitch, exposureTime);
    final boolean hasComment = !Utils.isNullOrEmpty(comment);
    int errors = 0;
    int count = 0;
    int h = Math.max(0, header);
    BufferedReader input = null;
    try {
        FileInputStream fis = new FileInputStream(filename);
        input = new BufferedReader(new UnicodeReader(fis, null));
        Pattern p = Pattern.compile(delimiter);
        String line;
        while ((line = input.readLine()) != null) {
            // Skip header
            if (h-- > 0)
                continue;
            // Skip empty lines
            if (line.length() == 0)
                continue;
            // Skip comments
            if (hasComment && line.startsWith(comment))
                continue;
            count++;
            final String[] fields = p.split(line);
            Localisation l = new Localisation();
            try {
                if (it >= 0)
                    l.t = Integer.parseInt(fields[it]);
                if (iid >= 0)
                    l.id = Integer.parseInt(fields[iid]);
                l.x = Float.parseFloat(fields[ix]);
                l.y = Float.parseFloat(fields[iy]);
                if (iz >= 0)
                    l.z = Float.parseFloat(fields[iz]);
                if (ii >= 0)
                    l.intensity = Float.parseFloat(fields[ii]);
                if (isx >= 0)
                    l.sy = l.sx = Integer.parseInt(fields[isx]);
                if (isy >= 0)
                    l.sy = Integer.parseInt(fields[isy]);
                if (ip >= 0)
                    l.precision = Float.parseFloat(fields[ip]);
                localisations.add(l);
            } catch (NumberFormatException e) {
                if (errors++ == 0)
                    Utils.log("%s error on record %d: %s", TITLE, count, e.getMessage());
            } catch (IndexOutOfBoundsException e) {
                if (errors++ == 0)
                    Utils.log("%s error on record %d: %s", TITLE, count, e.getMessage());
            }
        }
    } catch (IOException e) {
        Utils.log("%s IO error: %s", TITLE, e.getMessage());
    } finally {
        try {
            if (input != null)
                input.close();
        } catch (IOException e) {
        // Ignore
        }
        if (errors != 0)
            Utils.log("%s has %d / %d error lines", TITLE, errors, count);
    }
    return localisations;
}

Example 10 with UnicodeReader

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

the class FilterAnalysis method readFilterSets.

@SuppressWarnings("unchecked")
private List<FilterSet> readFilterSets() {
    GlobalSettings gs = SettingsManager.loadSettings();
    FilterSettings filterSettings = gs.getFilterSettings();
    String[] path = Utils.decodePath(filterSettings.filterSetFilename);
    OpenDialog chooser = new OpenDialog("Filter_File", path[0], path[1]);
    if (chooser.getFileName() != null) {
        IJ.showStatus("Reading filters ...");
        filterSettings.filterSetFilename = chooser.getDirectory() + chooser.getFileName();
        BufferedReader input = null;
        try {
            FileInputStream fis = new FileInputStream(filterSettings.filterSetFilename);
            input = new BufferedReader(new UnicodeReader(fis, null));
            Object o = XStreamWrapper.getInstance().fromXML(input);
            if (o != null && o instanceof List<?>) {
                SettingsManager.saveSettings(gs);
                return (List<FilterSet>) o;
            }
            IJ.log("No filter sets defined in the specified file: " + filterSettings.filterSetFilename);
        } 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;
}