Examples with InputMismatchException java.util.InputMismatchException used on opensource projects

Example 66 with InputMismatchException

use of java.util.InputMismatchException in project GDSC-SMLM by aherbert.

the class PeakResultsReader method createNSTORMResult.

// So that the fields can be named  
@SuppressWarnings("unused")
private PeakResult createNSTORMResult(String line) {
    //    data then Zc= Z.		
    try {
        Scanner scanner = new Scanner(line);
        scanner.useDelimiter(tabPattern);
        scanner.useLocale(Locale.US);
        String channelName = scanner.next();
        float x = scanner.nextFloat();
        float y = scanner.nextFloat();
        float xc = scanner.nextFloat();
        float yc = scanner.nextFloat();
        float height = scanner.nextFloat();
        float area = scanner.nextFloat();
        float width = scanner.nextFloat();
        float phi = scanner.nextFloat();
        float ax = scanner.nextFloat();
        float bg = scanner.nextFloat();
        float i = scanner.nextFloat();
        int frame = scanner.nextInt();
        int length = scanner.nextInt();
        // These are not needed
        //float link = scanner.nextFloat();
        //float valid = scanner.nextFloat();
        //float z = scanner.nextFloat();
        //float zc = scanner.nextFloat();
        scanner.close();
        // The coordinates are in nm
        // The values are in ADUs. The area value is the signal.
        // 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))
        float[] params = new float[7];
        params[Gaussian2DFunction.BACKGROUND] = bg;
        //params[Gaussian2DFunction.ANGLE] = ax;
        params[Gaussian2DFunction.SIGNAL] = height;
        params[Gaussian2DFunction.X_POSITION] = xc;
        params[Gaussian2DFunction.Y_POSITION] = yc;
        params[Gaussian2DFunction.X_SD] = width;
        params[Gaussian2DFunction.Y_SD] = width;
        // Store the signal as the original value
        return new ExtendedPeakResult(frame, (int) xc, (int) yc, area, 0.0, 0.0f, params, null, frame + length - 1, 0);
    } catch (InputMismatchException e) {
    // Ignore
    } catch (NoSuchElementException e) {
    // Ignore
    }
    return null;
}

Example 67 with InputMismatchException

use of java.util.InputMismatchException in project GDSC-SMLM by aherbert.

the class PeakResultsReader method createRapidSTORMResult.

private PeakResult createRapidSTORMResult(String line) {
    // *Note that the RapidSTORM Amplitude is the signal. To get the Amplitude we must divide by the 2*pi*sx*sy
    try {
        Scanner scanner = new Scanner(line);
        scanner.useDelimiter(spacePattern);
        scanner.useLocale(Locale.US);
        float x = scanner.nextFloat();
        float y = scanner.nextFloat();
        final int peak = scanner.nextInt();
        final float signal = scanner.nextFloat();
        final float sx2 = scanner.nextFloat();
        final float sy2 = scanner.nextFloat();
        @SuppressWarnings("unused") final float kernelImprovement = scanner.nextFloat();
        final double chiSquared = scanner.nextDouble();
        scanner.close();
        // Convert from pm^2 to nm
        float sx = (float) (Math.sqrt(sx2) * 1000);
        float sy = (float) (Math.sqrt(sy2) * 1000);
        // If calibration was found convert to pixels
        if (calibration != null) {
            x /= calibration.getNmPerPixel();
            y /= calibration.getNmPerPixel();
            sx /= calibration.getNmPerPixel();
            sy /= calibration.getNmPerPixel();
        }
        float[] params = new float[7];
        params[Gaussian2DFunction.SIGNAL] = signal;
        params[Gaussian2DFunction.X_POSITION] = x;
        params[Gaussian2DFunction.Y_POSITION] = y;
        params[Gaussian2DFunction.X_SD] = sx;
        params[Gaussian2DFunction.Y_SD] = sy;
        // Store the signal as the original value
        return new PeakResult(peak, (int) x, (int) y, signal, chiSquared, 0.0f, params, null);
    } catch (InputMismatchException e) {
    } catch (NoSuchElementException e) {
    }
    return null;
}

Example 68 with InputMismatchException

use of java.util.InputMismatchException in project GDSC-SMLM by aherbert.

the class DriftCalculator method readDriftFile.

/**
	 * Read the drift file storing the T,X,Y into the class level calculatedTimepoints, lastdx and lastdy
	 * arrays. Ignore any records where T is outside the limits.
	 * 
	 * @param limits
	 * @return The number of records read
	 */
private int readDriftFile(int[] limits) {
    int ok = 0;
    BufferedReader input = null;
    try {
        FileInputStream fis = new FileInputStream(driftFilename);
        input = new BufferedReader(new UnicodeReader(fis, null));
        String line;
        Pattern pattern = Pattern.compile("[\t, ]+");
        while ((line = input.readLine()) != null) {
            if (line.length() == 0)
                continue;
            if (Character.isDigit(line.charAt(0))) {
                try {
                    Scanner scanner = new Scanner(line);
                    scanner.useDelimiter(pattern);
                    scanner.useLocale(Locale.US);
                    final int t = scanner.nextInt();
                    if (t < limits[0] || t > limits[1])
                        continue;
                    final double x = scanner.nextDouble();
                    final double y = scanner.nextDouble();
                    calculatedTimepoints[t] = ++ok;
                    lastdx[t] = x;
                    lastdy[t] = y;
                    scanner.close();
                } catch (InputMismatchException e) {
                } catch (NoSuchElementException e) {
                }
            }
        }
    } catch (IOException e) {
    // ignore
    } finally {
        try {
            if (input != null)
                input.close();
        } catch (IOException e) {
        // Ignore
        }
    }
    return ok;
}

Example 69 with InputMismatchException

use of java.util.InputMismatchException 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;
}

Example 70 with InputMismatchException

use of java.util.InputMismatchException in project Neuronizer by djuelg.

the class EditHeaderInteractorImpl method run.

@Override
public void run() {
    final Optional<TodoListHeader> outDatedItem = repository.todoList().getHeaderById(uuid);
    if (!outDatedItem.isPresent()) {
        throw new InputMismatchException("Item not existing!");
    }
    final TodoListHeader updatedItem = outDatedItem.get().update(title, position, expanded);
    repository.todoList().update(updatedItem);
    final Optional<TodoList> todoList = repository.todoList().getTodoListById(updatedItem.getParentTodoListUuid());
    final TodoListHeader itemFromUI = new TodoListHeader(uuid, title, outDatedItem.get().getCreatedAt(), outDatedItem.get().getChangedAt(), position, expanded, outDatedItem.get().getParentTodoListUuid());
    if (todoList.isPresent() && !outDatedItem.get().equals(itemFromUI))
        repository.todoList().update(todoList.get().updateLastChange());
    mMainThread.post(new Runnable() {

        @Override
        public void run() {
            callback.onHeaderUpdated(updatedItem);
        }
    });
}