[FIX] fix parameter estimation for edge cases

make sure that the parameter estimation array goes beyond the value 1.0 and
catch cases where no optimal solution can be found
[NOP] rename files in test folder
[FEATURE] add linear and interpolation transformation

- add a linear transformation
- add an interpolation transformation
[FEATURE] add the transformed data to output on disk

- also write the transformed data on disk, e.g. the timepoints in the
  transformed space
[FEATURE] add option to only consider a single run
cleanup spline aligner
small refactor