vkhodygo / am_tools

Python scripts for active matter analysis

Active matter tools

version number: 0.0.1 author: Vladimir Khodygo

Overview

A collection of Python scripts for active matter statistical analysis.

Installation / Usage

To install use pip:

$ pip install am_tools

Or clone the repo:

$ git clone https://github.com/vkhodygo/am_tools.git
$ python setup.py install

Contributing

TBD

Example

TBD

am_tools's Issues

UPD: pwlf routine for piecewise linear fit

Here, I need to finish two functions, the first one uses pwlf to approximate a set of points w/ lines, the other one cleans data.
I also need to compare the results of approximation before and after cleaning.

[FIXME]: correct evaluation of GDF

General commentaries on the theory
There is no consistent way to measure GDF as far as I'm aware, at least I couldn't find enough respectable references.
The way I saw and understood that initially was to get mean system density first (that is the number of particles per box).
Next step was to find deviations per cell, average over cells and time.

Apparently, this is not the case. The way it works in unbounded square domains is the following (see, for instance, this): we pick a square sub-volume of increasing linear size measure the time average of the number of particles inside and calculate its rms.

After some talks I was convinced that was the right choice, at least for non-equilibrium systems such as mine.
Different parts of confined domains have different (time) average values of density.
We can use the same approach that is square sub-domains, but for strongly anisotropic domain shapes that leaves us with a very limited number of points. In the case of narrow channels it is up to half-width (or width if we really need those points at the end of the scale).

My idea is to use regular cells of some suitable shape (squares and rectangles at the moment) to tile the whole domain.
That provides a lot of data points but - again - leaves us with a limited number of cell sizes and shapes.
The question is what to do next. The data itself looks correlated since particles leaving one cell immediately move into one of the adjacent.
Regardless of that, first step is to calculate time average for each cells, average over cells next?

• check the code used in thesis to make sure what method I used.
• what numerical approach should be used here: measure variance or std? averaging all variances and getting a square root of the result is not the same as getting square roots of all variances and averaging over them.
• what about system average, is it a good idea to get a single value per cell? what about different systems with the same parameters, do we (weight) average at all (on a cell basis or on a system basis)?

Methods
This method is based on 2d- (3d-) histograms, but numpy and fast-histogram methods both have the same peculiar implementation: due to round-off errors some points in the rightmost column (and/or topmost row) can be marked as out-of-domain thus decreasing the overall number of particles within the system. That and a particular implementation (that should be the fastest one) leads to square roots of negative numbers.

Useful links
Check this, there is a chance I mix standard deviation and standard error.
https://stats.stackexchange.com/questions/222655/average-of-average-quantities-and-their-associated-error
https://stackoverflow.com/questions/19391149/numpy-mean-and-variance-from-single-function
https://ned.ipac.caltech.edu/level5/Leo/Stats4_5.html

[ENH]: add method for unbounded domains

There should be another method of the class for domains w/o boundaries,
where we can pick a zone and gradually scale the only bin.

UPD: parallel processing of gdf

Two versions are required, one for parallel processing of a single file, the other one is for parallel processing of multiple files.

[FIXME]: remove concatenation out of loop

Reading file involves concatenation at

am_tools/am_tools/modules/giant_density_fluctuations.py

Line 70 in 643953a

df_ = concat([df_, x], ignore_index=True)

That behaviour is undesired as discussed here: 1 and 2 (see also this discussion).

FIX: add other geometries

gdf works only for rectangular domains at the moment, this requires further investigation and code update

[ENH]: GDF parameter validation

Add parameter validation, unified approach is preferred.

FIX: replace the license

The default one from the template is not the one I need