#!/usr/bin/env python
# coding: utf-8

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# #### Imports
# The tutorial below imports [NumPy](http://www.numpy.org/), [Pandas](https://plotly.com/pandas/intro-to-pandas-tutorial/), [SciPy](https://www.scipy.org/) and [PeakUtils](http://pythonhosted.org/PeakUtils/).

# In[1]:


import plotly.plotly as py
import plotly.graph_objs as go
import plotly.figure_factory as ff

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


# #### Import Data
# For 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')


# #### Plot with Baseline

# In[3]:


# calculate baseline y values
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='#B292EA',
    ),
    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')


# In[4]:


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">'))

get_ipython().system(' pip install git+https://github.com/plotly/publisher.git --upgrade')
import publisher
publisher.publish(
    'python-Baseline-Detection.ipynb', 'python/baseline-detection/', 'Baseline Detection | plotly',
    'Learn how to detect baselines on data in Python.',
    title='Baseline Detection in Python | plotly',
    name='Baseline Detection',
    language='python',
    page_type='example_index', has_thumbnail='false', display_as='peak-analysis', order=1,
    ipynb= '~notebook_demo/117')


# In[ ]: