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

Example 16 with UnicodeReader

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

the class PCPALMClusters method loadHistogram.

/**
	 * Load the histogram from the file. Assumes the histogram is [int, float] format and creates a contiguous histogram
	 * from zero
	 * 
	 * @param filename
	 * @return
	 */
private HistogramData loadHistogram(String filename) {
    BufferedReader input = null;
    try {
        int f = 0;
        double a = 0;
        String u = "";
        FileInputStream fis = new FileInputStream(filename);
        input = new BufferedReader(new UnicodeReader(fis, null));
        String line;
        int count = 0;
        ArrayList<float[]> data = new ArrayList<float[]>();
        // Read the header and store the calibration if present
        while ((line = input.readLine()) != null) {
            count++;
            if (line.length() == 0)
                continue;
            if (Character.isDigit(line.charAt(0)))
                // This is the first record
                break;
            String[] fields = line.split("[\t, ]+");
            if (fields[0].equalsIgnoreCase("frames"))
                f = Integer.parseInt(fields[1]);
            if (fields[0].equalsIgnoreCase("area"))
                a = Double.parseDouble(fields[1]);
            if (fields[0].equalsIgnoreCase("units"))
                u = fields[1];
        }
        final Pattern pattern = Pattern.compile("[\t, ]+");
        while (line != null) {
            if (line.length() == 0)
                continue;
            if (!Character.isDigit(line.charAt(0)))
                continue;
            // Extract the first 2 fields
            Scanner scanner = new Scanner(line);
            scanner.useLocale(Locale.US);
            scanner.useDelimiter(pattern);
            try {
                int molecules = scanner.nextInt();
                float frequency = scanner.nextFloat();
                // Check for duplicates
                for (float[] d : data) {
                    if (d[0] == molecules) {
                        error("Duplicate molecules field on line " + count);
                        return null;
                    }
                }
                data.add(new float[] { molecules, frequency });
            } catch (InputMismatchException e) {
                error("Incorrect fields on line " + count);
                return null;
            } catch (NoSuchElementException e) {
                error("Incorrect fields on line " + count);
                return null;
            } finally {
                scanner.close();
            }
            // Get the next line
            line = input.readLine();
            count++;
        }
        if (data.isEmpty()) {
            error("No data in file " + filename);
            return null;
        }
        // Create a contiguous histogram from zero
        int maxN = 0;
        for (float[] d : data) {
            if (maxN < d[0])
                maxN = (int) d[0];
        }
        float[][] hist = new float[2][maxN + 1];
        for (int n = 0; n <= maxN; n++) {
            hist[0][n] = n;
            for (float[] d : data) {
                if (n == d[0])
                    hist[1][n] = d[1];
            }
        }
        HistogramData histogramData = new HistogramData(hist, f, a, u);
        histogramData.filename = filename;
        return histogramData;
    } catch (IOException e) {
        IJ.error(TITLE, "Unable to read from file " + filename);
    } finally {
        try {
            if (input != null)
                input.close();
        } catch (IOException e) {
        // Ignore
        }
    }
    return null;
}