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Baseline Subtraction in Python

Learn how to subtract baseline estimates from data in Python.

New to Plotly?¶

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Imports¶

The tutorial below imports NumPy, Pandas, SciPy and PeakUtils.

In [1]:
import plotly.plotly as py
import plotly.graph_objs as go
import plotly.tools as tools
import plotly.figure_factory as ff

import numpy as np
import pandas as pd
import scipy
import peakutils

Import Data¶

As with our baseline detection example, we will import some data on milk production by month:

In [2]:
milk_data = pd.read_csv('https://raw.githubusercontent.com/plotly/datasets/master/monthly-milk-production-pounds.csv')
time_series = milk_data['Monthly milk production (pounds per cow)']
time_series = np.asarray(time_series)

df = milk_data[0:15]

table = ff.create_table(df)
py.iplot(table, filename='milk-production-dataframe')
Out[2]:

Plot with Baseline¶

To subtact a baseline estimate from our data, it is a good idea to first we must first calculate the baseline values then plot the data with the baseline drawn in.

In [4]:
baseline_values = peakutils.baseline(time_series)

trace = go.Scatter(
    x=[j for j in range(len(time_series))],
    y=time_series,
    mode='lines',
    marker=dict(
        color='#547C66',
    ),
    name='Original Plot'
)

trace2 = go.Scatter(
    x=[j for j in range(len(time_series))],
    y=baseline_values,
    mode='markers',
    marker=dict(
        size=3,
        color='#EB55BF',
        symbol='circle-open'
    ),
    name='Baseline'
)

data = [trace, trace2]
py.iplot(data, filename='milk-production-plot-with-baseline')
Out[4]:

Baseline Subtraction¶

In [5]:
baseline_values = peakutils.baseline(time_series)

trace = go.Scatter(
    x=[j for j in range(len(time_series))],
    y=time_series,
    mode='lines',
    marker=dict(
        color='#547C66',
    ),
    name='Original Plot'
)

trace2 = go.Scatter(
    x=[j for j in range(len(time_series))],
    y=baseline_values,
    mode='markers',
    marker=dict(
        size=3,
        color='#EB55BF',
        symbol='circle-open'
    ),
    name='Baseline'
)

data = [trace, trace2]
py.iplot(data, filename='milk-production-plot-with-baseline')
Out[5]:
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