Examples with FitResult uk.ac.sussex.gdsc.smlm.fitting.FitResult used on opensource projects

Example 6 with FitResult

use of uk.ac.sussex.gdsc.smlm.fitting.FitResult in project GDSC-SMLM by aherbert.

the class GaussianFit method fit.

/**
 * Fits a single 2D Gaussian to the data. The fit is initialised at the highest value and then
 * optimised.
 *
 * <p>Data must be arranged in yx block order, i.e. height rows of width.
 *
 * <p>The angle parameter is only set if using elliptical Gaussian fitting.
 *
 * <p>Note: The returned fit coordinates should be offset by 0.5 if the input data represents
 * pixels
 *
 * @param data the data
 * @param width the width
 * @param height the height
 * @return Array containing the fitted curve data: Background, Amplitude, PosX, PosY, StdDevX,
 *         StdDevY, Angle. Null if no fit is possible.
 */
@Nullable
public double[] fit(float[] data, int width, int height) {
    if (data == null || data.length != width * height) {
        return null;
    }
    // Get the limits
    float max = Float.MIN_VALUE;
    int maxIndex = -1;
    for (int i = data.length; i-- > 0; ) {
        final float f = data[i];
        if (max < f) {
            max = f;
            maxIndex = i;
        }
    }
    if (maxIndex < 0) {
        return null;
    }
    final Gaussian2DFitter gf = createGaussianFitter(false);
    final FitResult fitResult = gf.fit(SimpleArrayUtils.toDouble(data), width, height, new int[] { maxIndex });
    if (fitResult.getStatus() == FitStatus.OK) {
        chiSquared = fitResult.getError();
        final double[] params = fitResult.getParameters();
        // Check bounds
        final double x = params[Gaussian2DFunction.X_POSITION];
        final double y = params[Gaussian2DFunction.Y_POSITION];
        if (x < 0 || x >= width || y < 0 || y >= height) {
            return null;
        }
        // Re-arrange order for backwards compatibility with old code.
        final double background = params[Gaussian2DFunction.BACKGROUND];
        final double intensity = params[Gaussian2DFunction.SIGNAL];
        final double sx = params[Gaussian2DFunction.X_SD];
        final double sy = params[Gaussian2DFunction.Y_SD];
        final double angle = params[Gaussian2DFunction.ANGLE];
        final double amplitude = Gaussian2DPeakResultHelper.getAmplitude(intensity, sx, sy);
        return new double[] { background, amplitude, x, y, sx, sy, angle };
    }
    return null;
}