Notebook

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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]:

In [6]:

from IPython.display import display, HTML

display(HTML('<link href="//fonts.googleapis.com/css?family=Open+Sans:600,400,300,200|Inconsolata|Ubuntu+Mono:400,700" rel="stylesheet" type="text/css" />'))
display(HTML('<link rel="stylesheet" type="text/css" href="http://help.plot.ly/documentation/all_static/css/ipython-notebook-custom.css">'))

! pip install git+https://github.com/plotly/publisher.git --upgrade
import publisher
publisher.publish(
    'python-Baseline-Subtraction.ipynb', 'python/baseline-subtraction/', 'Baseline Subtraction | plotly',
    'Learn how to subtract baseline estimates from data in Python.',
    title='Baseline Subtraction in Python | plotly',
    name='Baseline Subtraction',
    language='python',
    page_type='example_index', has_thumbnail='false', display_as='peak-analysis', order=2,
    ipynb= '~notebook_demo/118')

Collecting git+https://github.com/plotly/publisher.git
  Cloning https://github.com/plotly/publisher.git to /private/var/folders/tc/bs9g6vrd36q74m5t8h9cgphh0000gn/T/pip-req-build-GOxp_4
Building wheels for collected packages: publisher
  Running setup.py bdist_wheel for publisher ... done
  Stored in directory: /private/var/folders/tc/bs9g6vrd36q74m5t8h9cgphh0000gn/T/pip-ephem-wheel-cache-FJUFJi/wheels/99/3e/a0/fbd22ba24cca72bdbaba53dbc23c1768755fb17b3af0f33966
Successfully built publisher
Installing collected packages: publisher
  Found existing installation: publisher 0.11
    Uninstalling publisher-0.11:
      Successfully uninstalled publisher-0.11
Successfully installed publisher-0.11

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/nbconvert.py:13: ShimWarning:

The `IPython.nbconvert` package has been deprecated since IPython 4.0. You should import from nbconvert instead.

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/publisher/publisher.py:53: UserWarning:

Did you "Save" this notebook before running this command? Remember to save, always save.

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