Automatically find Polynomial2D.txt:

The plugin searches the folder (and subfolders) of the current image.
If more than one file has been found, the user can choose one.
1st part of replacing Gnuplot:

The 2D polynominal (width vs position) is fitted automatically
and the parameters are converted for use in the correction.

The next step is to fit the borders automatically.
extended SR-EELS_characterisation.ijm:

I need another data set file to perform the correction.
This file contains the position of the borders.
2st part of replacing Gnuplot:

The Java implementation seems to work.
But there is a problem with the coordinates for the borders.
I have to adjust the macro to use coordinates that fit to the Java
implementation.
Implemented miscellaneous test for fitting functions:

I was not able to fit the 2D polynominal.
Whe Gnuplot is able to fit, my code fails.
Created SR_EELS_CalibrationDataSet.java:

The Class loads all txt files from an folder that begin with 'values_'.
These files contain the data gathered by the characterisation macro.
The fit of the 2D polynomial already works well.

I removed 2 unnecessary files.
Changed parent in pom.xml:

I switched from pom-scijava to pom-fiji.
Now all dependency versions are managed by the parent pom.

https://github.com/fiji/pom-fiji
Added SR-EELS_characterisation.ijm from master:

I updated the characterisation.
Extended SR_EELS_CalibrationDataSet.java:

Additionally to the 2D polynomial it can fit a function series to the
borders.
Merge remote-tracking branch 'origin/master' into additions_to_sreels

Conflicts:
	EFTEMj/src/main/resources/macros/SR-EELS_characterisation.ijm
Tested LMA 2D polynomial fitting:

In SR_EELS_CalibrationDataSet.java I extended the tests:
1. Using the calibration data set from
	https://github.com/EFTEMj/EFTEMj/tree/master/Scripts%2BMacros/examples/SR-EELS_characterisation
2. Generate Gnuplot code to compare Java LAM with Gnuplot LMA.

Polynomial_2D.java contains the methods to create Gnuplot code.
Updated SR-EELS_characterisation.ijm:

I changed a file name from 'Polynomial2D.txt' to 'width.txt'.
The new name describes better what is stored at this file.
Extended SR-EELS_characterisation.ijm:

Settings are saved at the beginning and restored on end of macro.
The jpeg compression is increased.
Jpeg images get binned. User can select a desired image height in px.
Added files for testing SR-EELS LMA:

The files have been created using the current characterisation macro.
The SR-EEL example image have been used.
Load test data set from JAR:

I changed the constructor to be able to load the data set from the JAR.
EFTEMj.java gets a new constant that contains the testing folder (path).

Removed an unnecessary comment from JARTool.java.
Added 2 abstract classes for SR-EELs correction:

I will implement different methods to perform the correction.
All methods will extend these abstract classes.
A combination of 2 classes will result in a complete correction.
One class extends CoordinateCorrector and one IntensityCorrector.
Split Polynomial_2D.java:

There is a new class (SR_EELS_Polynomial_2D.java) that contains the
SR-EELS specific part of the 2D polynomial.

Additionally I reimplemented LMAPolyTest.java.
It uses data from the SR-EELS characterisation that is part of this
repository.
New .gitignore for a subfolder.
Started to implement different correction methods:

NoIntensityCorrection.java and SimpleCoordinateCorrection.java are the
first correction methods to be implemented.

This correction passes, but the result is not satisfying.
Finished first correction method:

The simplest method is running fine.
Some optimisations are still necessary.

I enhanced the Gnuplot code output for polynomial fitting.