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@@ -1,57 +1,25 @@
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### About
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-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.
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-
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-### Dictionary
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-**Epileptiform** - The term is used to connote EEG patterns believed to be associated with a relatively high risk for having seizures.
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-**Ictal** event - Event during seizure.
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-**Interictal** event - Event between seizures.
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-Focal event -
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-Tonic seizure -
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-Clonic seizure -
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-
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-### Run
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+Model of Ictal and Interictal discharges during epilepsy. Please see
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+[this article](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006186)
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+for details.
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#### Install
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-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:
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- - matplotlib, scipy, numpy, numba, pyyaml (`pip install matplotlib scipy numpy numba pyyaml`)
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-
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-#### 2D case
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+You need [Python](https://www.python.org/downloads/) of version 3.6 or
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+higher. Also I highly recommend to use environments for work.
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+[Anaconda](https://www.anaconda.com/distribution/) is a good choice.
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+The required dependencies are: matplotlib, scipy, numpy, numba, pyyaml.
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+```
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+pip install matplotlib scipy numpy numba pyyaml
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+```
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+
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+#### Run
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- Adjust params as you need in `params_0d.py` and `params_2d.py`.
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- 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.
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- To display results execute `python -d results/<YYYY-mm-dd_HH.MM> epileptor/display_2D.py`.
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- Look up the display results in `media` directory. They all have `<YYYY-mm-dd_HH.MM>` part in common.
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**Example**
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-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`.
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-
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-### Velocity
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-
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-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`
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-
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-| Var name | diffusion, uninoise | diffusion, rndnoise | synaptic, uninoise | synaptic, rndnoise |
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-| -------- |:-------------------:| -------------------:| ------------------:| ------------------:|
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-| base velocity| Mean: 0.029387, STD: 0.000997 | Mean: 0.027642, STD: 0.002180 | Mean: 0.049463, STD: 0.001814 | |
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-| `gKleak=0.5`| No wave | | | |
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-| `gKleak=2`| Up, Mean: 0.105585, STD: 0.033166 | | Up, 0.464241, STD: 0.104938, wave length > `yh` | |
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-| `gE=10`| No UP. Wave more often | | | |
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-| `gE_normal=2`| No UP. Baseline gets up the same as the peak | | | |
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-| `dK_reset=0.08`| Invalid results, NaN | | | |
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-| `roK_roNa=10`| Up, Mean: 0.043350, STD: 0.008512 | | | |
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-| `lamb=0.2`| | | Up significantly, wave length > `yh` | |
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-| `tau_K=150`| | Down | | |
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-| `gKLeak=2, roK_roNa=5` || Wave is minor. Everything goes up pretty fast. | | |
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-| `gL=0.5;0.8` || No wave. Many noise mini waves going up everywhere. | | |
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-| `gL=2` || No wave | | |
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-| `ro_pump=0.0001` || UP. Mean: 0.030930, STD: 0.001174. Increases wave amplitude.| | |
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-| `ro_pump=0.0004` || Down. Decreases wave amplitude.| | |
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-| `Gain=10` || Up. Noisy wave ends. Decreases wave amplitude. Mean: 0.042021, STD: 0.000897.| | |
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-| `tau_Na=10000` || No UP. Amplitude is higher. MEAN: 0.025406, STD: 0.000305| | |
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-| `tau_Na=40000` || No UP. Amplitude is lower. MEAN: 0.024776, STD: 0.000714| | |
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-| `NoiseAmpl=40` || UP. Noisy wave ends. Mean: 0.048747, STD: 0.001611| | |
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-
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-- assuming gKLeak = 2 increase of tau_Na with any of params that increase velocity (like NoiseAmpl to 40, Gain to 10)
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-- `gE` or `gE_normal` do not affect velocity. They rather affect amplitude only.
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-- Increase of roK_roNa leads to a smaller wave peak and narrow wave length. Example: roK_roNa = 40 => peak about 13.
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-- Velocity is about 0.5 with NoiseAmpl = 40, Gain = 10, gKleak = 2, roK_roNa = 40. But the wave is noisy
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-
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+Your execution successfully ended. You have 3 results:
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+`2019-01-27_17.14_plain.npz`, `2019-01-27_17.14_points.npz`, `2019-01-27_17.14_params.yml`.
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+`<YYYY-mm-dd_HH.MM>` is represented as `2019-01-27_17.14`.
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