2_baseline_process.py

# Fetch command line arguments
import sys
my_args = sys.argv
print "Running script:", sys.argv[0]
my_args = sys.argv[1:]
print "Arguments passed to script:", my_args
load_data_fp = my_args[0]
save_data_fp = my_args[1]

import numpy as np
import pandas as pd

#######################################################################
print "Importing data..."
data = pd.read_csv(load_data_fp)
print "Data shape:", data.shape

#######################################################################
print "Dropping all time period 1 because they have no lagged predictors..."
ind = data["timeID"] != 1
data = data[ind]
print "Data shape:", data.shape

print "Setting all the 9999 to NA..."
data[data==9999] = np.nan

print "Dropping rows where the outcome, EVI, is NA..."
data = data[data['EVI'].notnull()]
print "Data shape:", data.shape

data.to_csv(save_data_fp, header=True, index=False)

# Send email
email = False
if(email):
  import smtplib
  GMAIL_USERNAME = None
  GMAIL_PW = None
  RECIP = None
  SMTP_NUM = None
  session = smtplib.SMTP('smtp.gmail.com', SMTP_NUM)
  session.ehlo()
  session.starttls()
  session.login(GMAIL_USERNAME, GMAIL_PW)
  headers = "\r\n".join(["from: " + GMAIL_USERNAME,
                         "subject: " + "Finished running script: " + __file__,
                         "to: " + RECIP,
                         "mime-version: 1.0",
                         "content-type: text/html"])
  content = headers + "\r\n\r\n" + "Done running the script.\n Sent from my Python code."
  session.sendmail(GMAIL_USERNAME, RECIP, content)