/**
* The results of the {@link SR_EELS_CharacterisationPlugin} plugin are parsed.
*
* <p>This function extracts the values that describe the width of a spectrum depending on its
* position on the camera.
*
* @return a polynomial that fits the given data points
*/
private SR_EELS_Polynomial_2D getFunctionWidth() {
final double[][] vals = new double[importer.size()][3];
int i = 0;
for (final float[] point : importer) {
// The width of the spectrum -> z value
vals[i][0] = point[8];
// Coordinate on the energy dispersive axis -> x value
// The same value for top, centre and bottom.
vals[i][1] = point[0] - CameraSetup.getFullWidth() / 2;
// coordinate on the lateral axis -> y value
// The indices for centre, top and bottom are 2, 4 and 6.
vals[i][2] = point[2] - CameraSetup.getFullHeight() / 2;
i++;
}
/*
* Define the orders of the 2D polynomial.
*/
final int m = 2;
final int n = 2;
final SR_EELS_Polynomial_2D func = new SR_EELS_Polynomial_2D(m, n);
final double[] b_fit = new double[(m + 1) * (n + 1)];
Arrays.fill(b_fit, 1.);
final LMA lma = new LMA(func, b_fit, vals);
lma.fit();
/*
* TODO: Output information about the fit using IJ.log
*/
return new SR_EELS_Polynomial_2D(m, n, b_fit);
}
/**
* The results of the {@link SR_EELS_CharacterisationPlugin} plugin are parsed.
*
* <p>This function extracts the values that describe the pathway of the borders of a spectrum.
*
* @return a polynomial that fits the given data points
*/
private SR_EELS_Polynomial_2D getFunctionBorders() {
final double[][] vals = new double[3 * importer.size()][3];
int i = 0;
for (final float[] point : importer) {
for (int j = 0; j < 3; j++) {
// y coordinate of the fit function at the centre of the
// image/camera ->
// z value
vals[i + j][0] = point[2 + 2 * j] - CameraSetup.getFullWidth() / 2;
// Coordinate on the energy dispersive axis -> x value
// The same value for top, centre and bottom.
vals[i + j][1] = point[0] - CameraSetup.getFullHeight() / 2;
// coordinate on the lateral axis -> y value
// The indices for centre, top and bottom are 2, 4 and 6.
vals[i + j][2] =
importer.getYInterceptPoint(i / 3)[11 + j] - CameraSetup.getFullHeight() / 2;
}
i += 3;
}
/*
* Define the orders of the 2D polynomial.
*/
final int m = 3;
final int n = 2;
final SR_EELS_Polynomial_2D func = new SR_EELS_Polynomial_2D(m, n);
final double[] a_fit = new double[(m + 1) * (n + 1)];
Arrays.fill(a_fit, 1.);
final LMA lma = new LMA(func, a_fit, vals);
lma.fit();
/*
* TODO: Output information about the fit using IJ.log
*/
return new SR_EELS_Polynomial_2D(m, n, a_fit);
}