### About

Model of Ictal and Interictal discharges during epilepsy. Please see [this article](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006186) for details.

### Dictionary
**Epileptiform** - The term is used to connote EEG patterns believed to be associated with a relatively high risk for having seizures.
**Ictal** event - Event during seizure.
**Interictal** event - Event between seizures.
Focal event -
Tonic seizure -
Clonic seizure -

### Run

#### Install
You need [Python](https://www.python.org/downloads/) of version 3.6 or higher. Also I highly recommend to use environments for work. [Anaconda](https://www.anaconda.com/distribution/) is a good choice. The required dependencies are:
    - matplotlib, scipy, numpy, numba, pyyaml

#### 2D case
- Adjust params as you need in `params_0d.py` and `params_2d.py`. 
- Execute `python epileptor/model_2d_full.py`. It gives 3 files as the result in `results` dir. These files have names: `<YYYY-mm-dd_HH.MM>_plain.npz`, `<YYYY-mm-dd_HH.MM>_points.npz`, `<YYYY-mm-dd_HH.MM>_params.yml` correspondingly, where `<YYYY-mm-dd_HH.MM>` is the date/time when your execution ended.
- To display results execute `python -d results/<YYYY-mm-dd_HH.MM> epileptor/display_2D.py`.
- Look up the display results in `media` directory. They all have `<YYYY-mm-dd_HH.MM>` part in common.

**Example**
Your execution successfully ended. You have 3 results: `2019-01-27_17.14_plain.npz`, `2019-01-27_17.14_points.npz`, `2019-01-27_17.14_params.yml`. `<YYYY-mm-dd_HH.MM>` is represented as `2019-01-27_17.14`.

### Velocity

Default params: `gKleak=1, gE=5, gE_normal=1, dK_reset=0.04, roK_roNa=20, lamb=0.1, tau_K=100, gL=1, ro_pump=0.0002, Gain=20, tau_Na=20000, NoiseAmpl=25`

| Var name | diffusion, uninoise | diffusion, rndnoise | synaptic, uninoise | synaptic, rndnoise |
| -------- |:-------------------:| -------------------:| ------------------:| ------------------:|
| base velocity| Mean: 0.029387, STD: 0.000997 | Mean: 0.027642, STD: 0.002180 | Mean: 0.049463, STD: 0.001814 | |
| `gKleak=0.5`| No wave | | | |
| `gKleak=2`| Up, Mean: 0.105585, STD: 0.033166 | | Up, 0.464241, STD: 0.104938, wave length > `yh` | |
| `gE=10`| No UP. Wave more often | | | |
| `gE_normal=2`| No UP. Baseline gets up the same as the peak | | | |
| `dK_reset=0.08`| Invalid results, NaN | | | |
| `roK_roNa=10`| Up, Mean: 0.043350, STD: 0.008512 | | | |
| `lamb=0.2`|  | | Up significantly, wave length > `yh` | |
| `tau_K=150`|  | Down |  | |
| `gKLeak=2, roK_roNa=5` || Wave is minor. Everything goes up pretty fast. | | |
| `gL=0.5;0.8` || No wave. Many noise mini waves going up everywhere. | | |
| `gL=2` || No wave |  | |
| `ro_pump=0.0001` || UP. Mean: 0.030930, STD: 0.001174. Increases wave amplitude.| | |
| `ro_pump=0.0004` || Down. Decreases wave amplitude.| | |
| `Gain=10` || Up. Noisy wave ends. Decreases wave amplitude. Mean: 0.042021, STD: 0.000897.| | |
| `tau_Na=10000` || No UP. Amplitude is higher. MEAN: 0.025406, STD: 0.000305| | |
| `tau_Na=40000` || No UP. Amplitude is lower. MEAN: 0.024776, STD: 0.000714| | |
| `NoiseAmpl=40` || UP. Noisy wave ends. Mean: 0.048747, STD: 0.001611| | |

- assuming gKLeak = 2 increase of tau_Na with any of params that increase velocity (like NoiseAmpl to 40, Gain to 10)
- `gE` or `gE_normal` do not affect velocity. They rather affect amplitude only.
- Increase of roK_roNa leads to a smaller wave peak and narrow wave length. Example: roK_roNa = 40 => peak about 13.
- Velocity is about 0.5 with NoiseAmpl = 40, Gain = 10, gKleak = 2, roK_roNa = 40. But the wave is noisy