Merge pull request #11 from sredford/master

Tidy and improvements of ComputeAlignment.py
Merge pull request #12 from sredford/master

Added CountPixelMapRepeats function.
Merge pull request #13 from sredford/master

Speed increase in ComputeAlignment.py, without use of scaler.
Fixed histogram name typo
Merge pull request #14 from esicking/master

Fixed histogram name typo
Modified PerformPreAlignement function to allow for inputing an initial rotation and add it to the alignment file
Added the possibility of setting the tolerance for the rotation optimisation, helps with slow convergence or convergence failure to relax this, it is not useful to optimize more than the accuracy of the dataset
Reimplemented find sigma min to do a brute force minimum search for the best sigma to use for eta correction
commented out unused field in tree data, chip number, it is not written anymore in the new version of the tbtrack Eutelescope processor
Added safety check to not fill more than 500 fired pixels, this is a limitation of the array used to fill the tree, maxn can be increased if needed
Merge pull request #15 from mathieubenoit/master

A few improvements and modification for compatibility with Timepix3 data