- Author:
- JuliaMusgrave <jmus753@aucklanduni.ac.nz>
- Date:
- 2025-07-28 16:16:19+12:00
- Desc:
- Jupyter Notebook and alternate modes of the model to implement work-loop simulations
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d52/rawfile/7a0de368661d5f1fe8812a21e2ba6984aca7e3c3/CellML/piecewise_Ca.py
'''
Short script to help prepare CellML code with piecewise Calcium as an input.
Reads the csv files containing Ca data and outputs a text file suitable for copying into CellML text editor
Useful if data can not be easily captured with a fitted function.
'''
import csv
import numpy as np
ca_time = []
nd_ca = []
d_ca = []
with open('nd_ca.csv', 'r') as file:
csv_reader = csv.reader(file)
next(csv_reader)
for row in csv_reader:
ca_time.append(float(row[0]))
nd_ca.append(float(row[1]))
with open('d_ca.csv', 'r') as file:
csv_reader = csv.reader(file)
next(csv_reader)
for row in csv_reader:
d_ca.append(float(row[1]))
dt = 0.001 # sampling frequency
T = 1 # period
with open('nd_step.txt', 'w') as fp:
fp.write("Ca = sel\n")
for t in np.linspace(0, T, int(T/dt)+1):
ca_i = np.interp(t, ca_time, nd_ca)
fp.write(f"case t_twitch < {t+dt/2:.4f}{{second}}:\n"
f" {ca_i:.4f}{{micromolar}};\n")
fp.write("endsel;\n")
with open('d_step.txt', 'w') as fp:
fp.write("Ca = sel\n")
for t in np.linspace(0, T, int(T/dt)+1):
ca_i = np.interp(t, ca_time, d_ca)
fp.write(f"case t_twitch < {t+dt/2:.4f}{{second}}:\n"
f" {ca_i:.4f}{{micromolar}};\n")
fp.write("endsel;\n")
