pyvivc 1.0

numerical deconvolution and convolution methods working for inequal and incompatible timepoints between impulse and response curves for application in IVIVC level A

Pyvivc

Version 1.0

Stephen Checkley, October 2021.

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Description

A Python 3 port of the Rivivc R package for IVIVC linear level A by Aleksander Mendyk and Sebastian Polak. The package contains a numerical deconvolution method working for inequal and incompatible timepoints between impulse and response curves. A numerical convolution method is also included.

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Installation

Clone the repository and install with pip:

pip install .

or install with pip from the PyPi repository:

pip install pyvivc

Pyvivc example

from pyvivc import *
from scipy.interpolate import pchip_interpolate as pchip
from scipy.optimize import minimize
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
import seaborn as sns
sns.set()
matplotlib.use('TkAgg')


impulse = pd.read_csv('data/impulse.csv')
response = pd.read_csv('data/resp.csv')
inp = pd.read_csv('data/input.csv')

out = pyivivc(inp,impulse,response,explicit_interpolation=10,implicit_interpolation=5)

rsquare_text = str('R squared = ') + str(round(out[0].rvalue,2))

plt.subplot(1, 2, 1)
plt.plot(inp['C'][0:len(inp)-1], out[1]['par'],'o', label='data')
plt.plot(out[1]['par'], out[0].intercept + out[0].slope*out[1]['par'], 'r')
plt.annotate(rsquare_text, (0,0.8), horizontalalignment='left', verticalalignment='top', fontsize=8) # these are the coordinates to position the label
plt.xlabel('input data (#)')
plt.ylabel('deconvolved input (#)')
plt.legend()

plt.subplot(1, 2, 2)
plt.plot(out[1]['time'], out[1]['par'], 'r', label='deconvolution')
plt.plot(inp['time'][0:len(inp)-1], inp['C'][0:len(inp)-1], 'o', label='data')
plt.xlabel('Time')
plt.ylabel('discovered input (%)')
plt.legend()

plt.show()