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data_import.py
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data_import.py
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import csv
import sys
import dateutil.parser
from os import listdir
from os.path import isfile, join
import argparse
import datetime
class ImportData:
'''
Class for importing and parsing data for time series
'''
def __init__(self, data_csv):
'''
Class constructor, read value and time from input file
'''
self._time = []
self._value = []
# Use a handle to determine how to summarize duplicated values
# Default set to 0 meaning sum the duplicated
self._dedup = 0
if 'hr' in data_csv or 'smbg' in data_csv or 'cgm' in data_csv or \
'basal' in data_csv:
self._dedup = 1
# open file, create a reader from csv.DictReader,
# and read input times and values
with open(data_csv, 'r') as fhandle:
reader = csv.DictReader(fhandle)
for row in reader:
if 'time' not in row.keys() or 'value' not in row.keys():
raise ValueError('Input data needs contain time, values')
if (row['time'] == ''):
continue
try:
if row['value'] == 'low':
row['value'] = 40.0
elif row['value'] == 'high':
row['value'] = 300.0
val = float(row['value'])
if val is not None:
self._time.append(dateutil.parser.parse(row['time']))
self._value.append(val)
except ValueError:
print('Skipping value' + row['value'])
fhandle.close()
def linear_search_value(self, key_time):
'''
Linear search to find key in the self._time vector
'''
# return list of value(s) associated with key_time
# if none, return -1 and error message
out_list = []
for i in range(len(self._time)):
if self._time[i] == key_time:
out_list.append(self._value[i])
if len(out_list) == 0:
print('The specified time key is not found.')
return(-1)
else:
return(out_list)
def binary_search_value(self, key_time):
pass
# optional extra credit
# return list of value(s) associated with key_time
# if none, return -1 and error message
def roundTimeArray(obj, res):
'''
Inputs: obj (ImportData Object) and res (rounding resoultion)
objective:
create a list of datetime entries and associated values
with the times rounded to the nearest rounding resolution (res)
ensure no duplicated times
handle duplicated values for a single timestamp based on instructions in
the assignment
return: iterable zip object of the two lists
note: you can create additional variables to help with this task
which are not returned
'''
times = []
values = []
# Rounding time
for i in range(len(obj._time)):
time = obj._time[i]
bad_entry = datetime.timedelta(minutes=time.minute % res,
seconds=time.second)
time -= bad_entry
if (bad_entry >= datetime.timedelta(minutes=res/2)):
time += datetime.timedelta(minutes=res)
obj._time[i] = time
if len(obj._time) > 0:
times.append(obj._time[0])
search = obj.linear_search_value(obj._time[0])
if obj._dedup == 0:
values.append(sum(search))
elif obj._dedup == 1:
values.append(sum(search)/len(search))
# Check for duplciates
for i in range(1, len(obj._time)):
if obj._time[i] == obj._time[i - 1]:
continue
else:
times.append(obj._time[i])
search = obj.linear_search_value(obj._time[i])
if obj._dedup == 0:
values.append(sum(search))
elif obj._dedup == 1:
values.append(sum(search)/len(search))
return zip(times, values)
def printArray(data_list, annotation_list, base_name, key_file):
# combine and print on the key_file
key_list = []
out = []
annotation = []
if key_file not in annotation_list:
raise ValueError("Key_file not found!")
else:
for i in range(len(annotation_list)):
if (annotation_list[i] == key_file):
key_list.append(data_list[i])
else:
annotation.append(annotation_list[i])
out.append(data_list[i])
with open(base_name+'.csv', mode='w') as output:
writer = csv.writer(output, delimiter=',')
writer.writerow(['time', key_file] + annotation)
for (time, val) in key_list[0]:
old = []
for data in out:
start_length = len(old)
for (timex, valsx) in data:
if time == timex:
old.append(valsx)
if len(old) == start_length:
old.append(0)
writer.writerow([time, val] + old)
return(0)
if __name__ == '__main__':
# adding arguments
parser = argparse.ArgumentParser(description='import time stuff',
prog='dataImport')
parser.add_argument('folder_name', type=str, help='Name of the folder')
parser.add_argument('output_file', type=str, help='Name of Output file')
parser.add_argument('sort_key', type=str, help='File to sort on')
parser.add_argument('--number_of_files', type=int,
help="Number of Files", required=False)
args = parser.parse_args()
# pull all the folders in the file
folder_path = args.folder_name
try:
# append file list while checking to see if file exists
files_lst = [f for f in listdir(folder_path)
if isfile(join(folder_path, f))]
except FileNotFoundError:
print('Specified input folder not found.')
sys.exit(1)
# import all the files into a list of ImportData objects (in a loop!)
data_lst = []
for files in files_lst:
data_lst.append(ImportData(folder_path + '/' + files))
# create two new lists of zip objects
# do this in a loop, where you loop through the data_lst
data_5 = [] # a list with time rounded to 5min
data_15 = [] # a list with time rounded to 15min
for i in data_lst:
data_5.append(roundTimeArray(i, 5))
data_15.append(roundTimeArray(i, 15))
# print to a csv file
printArray(data_5, files_lst, args.output_file+'_5', args.sort_key)
printArray(data_15, files_lst, args.output_file+'_15', args.sort_key)