MetaStim DBS in Python

How to use metastim python package

Install Instructions:

1. create python3 virtual environment ( python version required 3.8 or higher)

mkdir  -p  ~/project/metastim  # or any directory  of  your choice
cd project/metastim
python3 -m venv venv

2. Activate the virtual environment

source venv/bin/activate

if above command is scuccess your terminal prompt will change to denote that you are in python virtual environment.

3. Install metastim package

from being in python virtual environment type

pip install metastim

4. start python interactive shell

python3  

5. Test if you can import metastim modules

try to import metastim modules filed_ann and axon_ann as shown below if you do not see any errors , you successfully installed metastim package

>>> from metastim import field_ann, axon_ann

How to Use MetaStim

Sample demo code is provided below, it shows usage of metastim copy this code into let say demo.py in ~/project/metastim folder and run within virtual environment created above

or

alternatively you can download demo.py avialable in this repositoty and run it in the virtual environment created above

python3 demo.py

Here is the complete code.

from metastim import field_ann, axon_ann
from metastim.utils import MetaStimUtil
from metastim import visualization as vis
import os
import numpy as np

if __name__ == "__main__":
    
    lead_id  = '6172'
    electrode_list = [1, 0, 0, 0, -1, 0, 0, 0]
    stimulation_amp = 3 # [V]
    pulse_width = 90 #[us]
    num_axons = 10
    min_distance = 1
    max_distance = 5
    axon_diameter = 6 # [um]

    lead_radius = MetaStimUtil.get_lead_radius(lead_id, electrode_list)

    inl = 100 * axon_diameter / 1e3 # distance between nodes on an axon

    z_base = np.arange(-5, 16, inl)
    num_axon_nodes = z_base.shape[0]

    x_axon = np.repeat(np.linspace(min_distance, max_distance, num=num_axons), num_axon_nodes).reshape(num_axon_nodes, num_axons, order='F') + lead_radius
    y_axon = np.zeros(x_axon.shape)
    z_axon = np.repeat(z_base, num_axons).reshape(num_axon_nodes, num_axons)


    axon_ann_model = axon_ann.AxonANN(electrode_list,  pulse_width, stimulation_amp, num_axons, axon_diameter)
    field_ann_model = field_ann.FieldANN(electrode_list)

    phi_axon = field_ann_model.field_ann(x_axon, y_axon, z_axon)
    axon_act = axon_ann_model.axon_ann(x_axon, y_axon, z_axon, lead_radius)

    visual_demo1 = vis.Visualization(lead_id, stimulation_amp, num_axons, x_axon, z_axon, phi_axon, axon_act)
    visual_demo1.visualize1(electrode_list)

Sample Jupitor Notebook example

A Sample Jupitor note book file is aviable in this repository at demo.ipynb

1. donwload demo.ipynb and copy to ~/projects/metastim folder

2. activate python virtual environment if it is not activated already

cd ~/projects/metastim

source venv/bin/activate

3. Open vscode

code .

4. Run demo.ipynb jupitor notebook file

After vscode opens, open demo.ipynb file and click "Run All" button vscode suggests to install ipython server if ipython is not already installed install ipython by repsonding to vscode prompt.

If ipython server already present in vscode then vscode ask to select environment , select the virtual env