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# DynTrack
Python package for the study of particle dynamics from 2D tracks
Installation
------------
```bash
pip install -U dyntrack
```
Usage
-----
```python
import dyntrack as dt
DT = dt.ut.load_data("tracks.csv","Position X","Position Y","Parent","Time","background.tiff")
dt.tl.vector_field(DT)
dt.pl.vector_field(DT)
dt.tl.FTLE(DT, 20000,5)
dt.pl.FTLE(DT)
dt.tl.fit_ppt(DT,seed=1)
dt.pl.fit_ppt(DT)
```
Workflow
--------
Source build and run issues with windows
----------------------------------------
If missing DLL errors occurs while running, or gcc is not available while building from source please install MinGW-w64:
```powershell
choco install mingw
```
Citations and used works
------------------------
### Vector field building
The function `dyntrack.tl.vector_field` uses
[vfkm](https://github.com/nivan/vfkm/) to generate vector fields (see
[license](https://github.com/LouisFaure/dyntrack/blob/main/vfkm/LICENSE)),
please cite the related study if you use it:
Ferreira, N., Klosowski, J. T., Scheidegger, C. & Silva, C.
Vector Field k-Means: Clustering Trajectories by Fitting Multiple Vector Fields.
Comput. Graph. Forum 32, 201–210 (2012).
### FTLE scalar field generation
Code from `dyntrack.tl.FTLE` have been adapted and optimized from [Richard
Galvez's
notebook](https://github.com/richardagalvez/Vortices-Python/blob/master/Vortex-FTLE.ipynb).
### Principal tree fitting with SimplePPT
Code from `dyntrack.tl.fit_ppt` uses SimplePPT algorithm to fit principal trees on each frames.
SimplePPT has been described in the following paper:
Mao et al. (2015), SimplePPT: A simple principal tree algorithm
SIAM International Conference on Data Mining.
