/**
* 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);
}
/**
* 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);
}
/**
* Use this method for batch processing. Values that are set up by the GUI have to be passed as
* parameters.
*
* @param input_image is the image to correct.
* @param path2REsults is the text file that contains the characterisation results for the width.
* @return the corrected image.
*/
public ImagePlus correctImage(final ImagePlus input_image, final String path2REsults) {
this.inputProcessor =
new SR_EELS_FloatProcessor(
(FloatProcessor) input_image.getProcessor(),
CameraSetup.getFullWidth() / input_image.getWidth(),
CameraSetup.getFullHeight() / input_image.getHeight(),
input_image.getWidth() / 2,
input_image.getHeight() / 2);
title = StringManipulator.removeExtensionFromTitle(input_image.getTitle());
this.pathResults = path2REsults;
run(null);
return outputImage;
}
/*
* (non-Javadoc)
*
* @see ij.plugin.filter.ExtendedPlugInFilter#showDialog(ij.ImagePlus,
* java.lang.String, ij.plugin.filter.PlugInFilterRunner)
*/
@Override
public int showDialog(final ImagePlus imp, final String command, final PlugInFilterRunner pfr) {
final String searchPath = IJ.getDirectory("image");
final LinkedList<String> foundCharacterisationResults = new LinkedList<>();
findDatasets(searchPath, foundCharacterisationResults, imp.getShortTitle());
final String otherResult = "other...";
foundCharacterisationResults.add(otherResult);
if (foundCharacterisationResults.size() > 1) {
/*
* A dialog is presented to select one of the found files.
*/
final GenericDialog gd =
new GenericDialog(
(command != "") ? command : "Debugging" + " - Select data set", IJ.getInstance());
String[] arrayOfFoundResults = new String[foundCharacterisationResults.size()];
arrayOfFoundResults = foundCharacterisationResults.toArray(arrayOfFoundResults);
gd.addRadioButtonGroup(
SR_EELS.FILENAME_RESULTS,
arrayOfFoundResults,
foundCharacterisationResults.size(),
1,
foundCharacterisationResults.get(0));
gd.setResizable(false);
gd.showDialog();
if (gd.wasCanceled()) {
canceled();
return NO_CHANGES | DONE;
}
if (foundCharacterisationResults.size() > 1) {
pathResults = gd.getNextRadioButton();
}
}
/*
* If only no file has been found, the parameters dialog is shown.
*/
if (foundCharacterisationResults.size() == 0 | pathResults.equals(otherResult)) {
do {
if (showParameterDialog(command) == CANCEL) {
canceled();
return NO_CHANGES | DONE;
}
} while (!pathResults.contains(SR_EELS.FILENAME_RESULTS));
} else {
if (foundCharacterisationResults.size() == 1) {
pathResults = foundCharacterisationResults.getFirst();
} else {
canceled();
return NO_CHANGES | DONE;
}
}
inputProcessor =
new SR_EELS_FloatProcessor(
(FloatProcessor) imp.getProcessor(),
CameraSetup.getFullWidth() / imp.getWidth(),
CameraSetup.getFullHeight() / imp.getHeight(),
imp.getWidth() / 2,
imp.getHeight() / 2);
title = StringManipulator.removeExtensionFromTitle(imp.getTitle());
return FLAGS;
}
