Improvements to SR-EELS_Correction:

I removed ghost images that occured because of negative areas during
integration. 'SR-EELS_Exception.java' is part of this fix.
The correction can be performed on images with different binning values.
Yet only binning 4 was possible.
When reading the parameters file, lines with commends (char #) are
ignored.
The plugin estimates the remaining time.
The calculation of the bounding rectangle is more save now.
Improvements to SR-EELS_Correction:

I removed the oversampling and implemented a morphological filter. By
using dilate and erode holes in the binary image are closed. This is
much faster than oversampling and removes an intensity problem I was not
able to comprehend.
The display of the remaining time has a 5 seconds delay to avoid wrong
values at the start.
Improved compatibility with Java 1.6:

I removed a method that is only available for never versions of Java.
Fixed the intensity correction:

I implemented my own closing operation that uses a 1x3 kernel instead of
the default 3x3 kernel.
I had to add a border to my BinaryProcessor to not generate artefacts
when running the closing.
The debug mode has been optimized.
'binning' is passed to 'SR_EELS_CorrectionFunction':

I removed all calculations from 'SR_EELS_Correction' that in included
the binning.
When I only pass the binning to 'SR_EELS_CorrectionFunction', the code
is easier to understand.
Small error fixes:

- DEBUG was still set to 'true'.
- The time-out of the ExecutorService was to low (60min -> 24h).
- Added '1.0*' to an integer division.
Optimized debug options.
Extended the correction function to use the full polynomial to calculate
yn.
Added comments (not yet finished).
Added Optimization_Example.java:

This plugin is an example from Fiji.
I had to correct it, to make it work.
I will try to use the curve fitting for my SR-EELS characterisation.
Optimized the ParametricUnivariateFunction.
Using FastMath for 'asinh':

FastMath is part of commons-math:
https://commons.apache.org/proper/commons-math/userguide/utilities.html
Optimize_Example: new commit with GitHub for Win

GitHub for Windows want's to commit the file again.
Added levenberg-marquardt algorithm:

http://scribblethink.org/Computer/Javanumeric/index.html
I added a 3D-polynomial and tested it with my SR-EELS values.
The Java implementation of LM gives the same results as Gnuplot.
I updated the LM classes:

There is a new class (Polynomial_2D) that I will use for fitting the
distortion in SR-EELS.
LMfunc is now devided into LM_Function and LM_TestFunction.
Fix line endings:

Eclipse does not use the correct line endings when reating new files. I
have to fix this soon.
Run the SR-EELS characterisation macro as a plugin:

1. I created a new PlugIn to run the macro.
2. JARTool is used to load the contend of a text file that is included
in the jar.
3. Moved code from Tutorial_Drift to JARTool
Mergeconflict free files.
Merge files with conflicts:

I selected the code from additions_to_sreels, as this is the most recent
code for the SR-EELs correction.