Improve MSD calculation #248
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Use MSD method in plots Add MSD test
stefsmeets
approved these changes
Jan 25, 2024
MSD into a function Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>
Simplify traj filtering Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>
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This branch improves the statistics of the MSD calculation, expanding on the idea of the multiple starting points, discussed in #237.
In the limit of infinitely many starting-points, the MSD algorithm can consider all the non-overlapping continuous subtrajectories of length$t_i$ in order to compute all the corresponding $MSD(t_i)$ .
Numerically this can be efficiently implemented following the algorithm introduced in this paper, which is well explained in this stackoverflow thread.
This new MDS-algorithm uses Fast Fourier Transform, and produces estimation which are significantly less sensitive to noise.
These are some plot to showcase the improved performance:
It can also be used for multiple species at the same time:
And also using plotly:
