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Countoscope in python

Codes to count particles in boxes and calculate statistics of these the fluctuating counts

Use and citation

If you use this code please cite our paper available on ArXiv (https://arxiv.org/abs/2311.00647), and soon on Phys. Rev. X.

[1] Mackay, E. K., Marbach, S., Sprinkle, B., & Thorneywork, A. L. (2023). The Countoscope: Measuring Self and Collective Dynamics without Trajectories. arXiv preprint arXiv:2311.00647.

and we will come up shortly with a Zenodo release for the code which you can cite as well

Installation

To install, clone this directory into your site-packages directory (eg cd ~/.local/lib/python3.10/site-packages && git clone https://github.com/Countoscope/countoscope_PRX/ countoscope) or simply download the codes

Content

  • example_runcounting.py * example code to run the counting algorithm and plot relevant curves
  • test_data/example_dataset.txt * example data set simulated from Brownian motion of non-interacting particles
  • Box_Count_Stats.py * source codes to count particles in boxes and calculate statistics
  • Numba_Box_Count_stats.py * same as above but with just-in-time-compilation. Sometimes numba is not compatible with some machines.
  • LICENSE * licence agreement
  • Old_Codes/ * old codes directory

Use

To use

import countoscope as countoscope

results = countoscope.calculate_nmsd(data=f"data.dat", window_size_x=217.6, window_size_y=174, box_sizes=Box_Ls, sep_sizes=sep)

See the full example in example_runcounting.py (which also includes plotting)

The parameters to calculate_nmsd are:

  • data. Either:
    • data should be a string, the address of a text file containing rows of x, y, t values, whitespace separated.
    • or data should be provided as a 2D array where data[i, 0:2] is [x, y, t]
    • the t values should be the index of the frame. They can be 0-based or 1-based (or any other), and can be supplied as floats or integers.
  • window_size_x and window_size_y optional, the dimensions of the viewing window. If not supplied, the maximum x and y coordinate over all frames and particles will be used instead.
    • it is assumed that the particles lie in 0 <= x <= window_size_x and 0 <= y <= window_size_y. Viewing windows not cornered at the origin are not currently supported.
  • The box sizes are specified as:
    • if only box_sizes is provided, the boxes will be square, width and height of box i equal to box_sizes[i].
    • if box_sizes_x and box_sizes_y are provided, box i will be of shape box_sizes_x[i] * box_sizes_y[i].
    • however, if you want one of the width or height to be constant, you can just pass a single value to one of box_sizes_x or box_sizes_y and then all boxes will have the same width or height.
  • sep_sizes should be an array of the same size as box_sizes/box_sizes_x/box_sizes_y
    • if any elements of sep_sizes are negative, the boxes will overlap. This causes the library to use a different algorithm to count the particles which is substantially slower. You should be careful when choosing the overlaps; if the overlap is a rational fraction of the box size then some boxes' edges will touch, leaving the counts correlated.

The return object:

Property Shape Description
results.N2_mean len(box_sizes) * Nframes number displacement fluctuations (N(t) - N(0))^2 mean value
results.N2_std len(box_sizes) * Nframes number displacement fluctuations (N(t) - N(0))^2 mean value
results.N_mean len(box_sizes) mean particles per box, averaged over all boxes
results.N_mean_std len(box_sizes) standard deviation of (mean particles per box in time) over all boxes
results.N_var len(box_sizes) variance of all counts
results.N_var_sem_ub len(box_sizes)
results.N_var_sem_lb len(box_sizes)
results.N_var_mod len(box_sizes) variance of number of particles in box over time, averaged over all boxes
results.N_var_mod_std len(box_sizes) standard deviation of (variance of number of particles in box over time) over all boxes
results.num_boxes len(box_sizes) number of boxes used for each box size
results.counts len(box_sizes) * max_boxes_y * max_boxes_x * num_timesteps the raw counts in each box
results.box_coords len(box_sizes) * max_boxes_y * max_boxes_x * 2 the (x, y) positions of the lower-left corner of each box

Dependencies

numpy, scipy, and numba. By default, numba will run using as many threads as you have cores on your machine. Use NUMBA_NUM_THREADS=16 python .... to limit numba to a certain number of threads if you don't want it to use all your cores. If tqdm is installed, we will use it for nice progress bars.

Debugging

If you get an annoying C error like Segmentation fault, try running with NUMBA_DISABLE_JIT=1 python myscript.py to disable numba compilation (it will take much longer), and see if you get any pure Python errors