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stn_script.py
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stn_script.py
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'''
Created on Jul 17, 2017
@author: gpetrochenkov
'''
#!/usr/bin/env python3
import sys
import csv
current_path = sys.path[0]
sys.path.append(''.join([current_path,'\\..']))
sys.path.append(''.join([current_path,'\\..\\netCDF_Utils']))
import numpy as np
import netCDF_Utils.nc as nc
from pytz import timezone
from csv_readers import Leveltroll, MeasureSysLogger, House, Hobo, RBRSolo, Waveguage
import unit_conversion as uc
import argparse
from tools.storm_options import StormOptions
from tools.storm_netCDF import Storm_netCDF
from tools.storm_graph import StormGraph, Bool
from tools.storm_statistics import StormStatistics
INSTRUMENTS = {
'LevelTroll': Leveltroll,
'RBRSolo': RBRSolo,
'Wave Guage': Waveguage,
'USGS Homebrew': House,
'MS TruBlue 255': MeasureSysLogger,
'Onset Hobo U20': Hobo }
def convert_to_netcdf(inputs):
translated = translate_inputs(inputs)
instrument = INSTRUMENTS[translated['instrument_name']]()
instrument.user_data_start_flag = 0
for key in translated:
setattr(instrument, key, translated[key])
instrument.read()
instrument.write(pressure_type=translated['pressure_type'])
return instrument.bad_data
DATATYPES = {
'latitude': np.float32,
'longitude': np.float32,
'initial_water_depth': np.float32,
'final_water_depth': np.float32,
'device_depth': np.float32,
'tzinfo': timezone,
'sea_pressure' : bool }
def translate(inputs):
translated = translate_inputs(inputs)
instrument = INSTRUMENTS[translated['instrument_name']]()
instrument.user_data_start_flag = 0
for key in translated:
setattr(instrument, key, translated[key])
def translate_inputs(inputs):
translated = dict()
for key in inputs: # cast everything to the right type
if key in DATATYPES:
translated[key] = DATATYPES[key](inputs[key])
else:
translated[key] = inputs[key]
return translated
def find_index(array, value):
array = np.array(array)
idx = (np.abs(array-value)).argmin()
return idx
def check_file_type(file_name):
index = file_name.rfind('.')
if index == -1:
csv_file = open(file_name)
try:
dialect = csv.Sniffer().sniff(csv_file.read(1024))
return True
except:
return False
else:
if file_name[index:] == '.csv':
return True
else:
return False
def process_file(args):
daylight_savings = False
if args['daylight_savings'].lower() == 'true':
daylight_savings = True
inputs = {
'in_filename' : args['in_fname'],
'out_filename' : args['out_fname'],
'creator_name' : args['creator_name'],
'creator_email' : args['creator_email'],
'creator_url' : args['creator_url'],
'instrument_name' : args['instrument_name'],
'stn_station_number': args['stn_station_number'],
'stn_instrument_id': args['stn_instrument_id'],
'latitude' : args['latitude'],
'longitude' : args['longitude'],
'tz_info' : args['tz_info'],
'daylight_savings': daylight_savings,
'datum': args['datum'],
'initial_sensor_orifice_elevation': args['initial_sensor_orifice_elevation'],
'final_sensor_orifice_elevation': args['final_sensor_orifice_elevation'],
'salinity' : args['salinity'],
'initial_land_surface_elevation': args['initial_land_surface_elevation'],
'final_land_surface_elevation': args['final_land_surface_elevation'],
'deployment_time' : args['deployment_time'],
'retrieval_time' : args['retrieval_time'],
'sea_name' : args['sea_name'],
'pressure_type' : args['pressure_type'],
'good_start_date': args['good_start_date'],
'good_end_date': args['good_end_date'],
}
#checks for the correct file type
if check_file_type(inputs['in_filename']) == False:
return (2, None)
#check for dates in chronological order if sea pressure file
if inputs['pressure_type'] == 'Sea Pressure':
inputs['deployment_time'] = uc.datestring_to_ms(inputs['deployment_time'], '%Y%m%d %H%M', \
inputs['tz_info'],
inputs['daylight_savings'])
inputs['retrieval_time'] = uc.datestring_to_ms(inputs['retrieval_time'], '%Y%m%d %H%M', \
inputs['tz_info'],
inputs['daylight_savings'])
if inputs['retrieval_time'] <= inputs['deployment_time']:
return (3, None)
try:
data_issues = convert_to_netcdf(inputs)
except:
return (5, None)
time = nc.get_time(inputs['out_filename'])
start_index = find_index(time,uc.datestring_to_ms(inputs['good_start_date'], '%Y%m%d %H%M', \
inputs['tz_info'],
inputs['daylight_savings']))
end_index = find_index(time,uc.datestring_to_ms(inputs['good_end_date'], '%Y%m%d %H%M', \
inputs['tz_info'],
inputs['daylight_savings']))
#checks for chronological order of dates
if end_index <= start_index:
return (3, None)
air_pressure = False
if args['pressure_type'] == 'Air Pressure':
air_pressure = True
try:
nc.chop_netcdf(inputs['out_filename'], ''.join([inputs['out_filename'],'chop.nc']),
start_index, end_index, air_pressure)
except:
return (5, None)
if data_issues:
return (1, ''.join([inputs['out_filename'],'chop.nc']))
else:
return (0, ''.join([inputs['out_filename'],'chop.nc']))
#will be either 0 for perfect overlap or 1 for slicing some data
def process_storm_files(args):
so = StormOptions()
so.air_fname = args['air_fname']
so.sea_fname = args['sea_fname']
#check to see if the correct type of files were uploaded
if so.check_file_types() == False:
return 2
so.wind_fname = None
so.format_output_fname(args['out_fname'])
so.timezone = args['tz_info']
so.daylight_savings = args['daylight_savings']
if 'baro_y_min' in args and args['baro_y_min'] is not None:
so.baroYLims = []
so.baroYLims.append(args['baro_y_min'])
so.baroYLims.append(args['baro_y_max'])
if 'wl_y_min' in args and args['wl_y_min'] is not None:
so.wlYLims = []
so.wlYLims.append(args['wl_y_min'])
so.wlYLims.append(args['wl_y_max'])
#check to see if the time series of the water and air file overlap
overlap = so.time_comparison()
#if there is no overlap
if overlap == 2:
return 4
try:
snc = Storm_netCDF()
so.netCDF['Storm Tide with Unfiltered Water Level'] = Bool(True)
so.netCDF['Storm Tide Water Level'] = Bool(True)
snc.process_netCDFs(so)
sg = StormGraph()
so.graph['Storm Tide with Wind Data'] = Bool(False)
so.graph['Storm Tide with Unfiltered Water Level'] = Bool(True)
so.graph['Storm Tide Water Level'] = Bool(True)
so.graph['Atmospheric Pressure'] = Bool(True)
sg.process_graphs(so)
if args['sea_4hz'].lower() == 'true':
so.int_units = False
so.high_cut = 1.0
so.low_cut = 0.045
so.from_water_level_file = False
ss = StormStatistics()
for y in so.statistics:
so.statistics[y] = Bool(False)
so.statistics['H1/3'] = Bool(True)
so.statistics['Average Z Cross'] = Bool(True)
so.statistics['PSD Contour'] = Bool(True)
ss.process_graphs(so)
return 0
except:
return 5
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('sea_fname',
help='directory location of raw sea pressure csv file')
parser.add_argument('air_fname',
help='directory location of raw air pressure csv file')
parser.add_argument('out_fname',
help='directory location to output netCDF file')
parser.add_argument('creator_name',
help='name of user running the script')
parser.add_argument('creator_email',
help='email of user running the script')
parser.add_argument('creator_url',
help='url of organization the user running the script belongs to')
parser.add_argument('sea_instrument_name',
help='name of the instrument used to measure pressure')
parser.add_argument('air_instrument_name',
help='name of the instrument used to measure pressure')
parser.add_argument('sea_stn_station_number',
help='STN Site ID')
parser.add_argument('air_stn_station_number',
help='STN Site ID')
parser.add_argument('sea_stn_instrument_id',
help='STN Instrument ID')
parser.add_argument('air_stn_instrument_id',
help='STN Instrument ID')
parser.add_argument('sea_latitude', type=float,
help='latitude of instrument')
parser.add_argument('air_latitude', type=float,
help='latitude of instrument')
parser.add_argument('sea_longitude', type=float,
help='longitude of instrument')
parser.add_argument('air_longitude', type=float,
help='longitude of instrument')
parser.add_argument('tz_info',
help='time zone of instrument output dates')
parser.add_argument('daylight_savings',
help='if time zone is in daylight savings')
parser.add_argument('datum',
help='geospatial vertical reference point')
parser.add_argument('sea_initial_sensor_orifice_elevation', type=float,
help='tape down to sensor at deployment time')
parser.add_argument('air_initial_sensor_orifice_elevation', type=float,
help='tape down to sensor at deployment time')
parser.add_argument('sea_final_sensor_orifice_elevation', type=float,
help='tape down to sensor at retrieval time')
parser.add_argument('air_final_sensor_orifice_elevation', type=float,
help='tape down to sensor at retrieval time')
parser.add_argument('salinity',
help='salinity of the sea surface')
parser.add_argument('initial_land_surface_elevation', type=float,
help='tape down to sea floor at deployment time')
parser.add_argument('final_land_surface_elevation', type=float,
help='tape down to sea floor at retrieval time')
parser.add_argument('deployment_time',
help='time when the instrument was deployed')
parser.add_argument('retrieval_time',
help='time when the instrument was retrieved')
parser.add_argument('sea_name',
help='name of the body of water the instrument was deployed in')
parser.add_argument('sea_good_start_date',
help='first date for chopping the time series')
parser.add_argument('air_good_start_date',
help='first date for chopping the time series')
parser.add_argument('sea_good_end_date',
help='last date for chopping the time series')
parser.add_argument('air_good_end_date',
help='last date for chopping the time series')
parser.add_argument('sea_4hz',
help='True if sea instrument is sampled at 4hz')
parser.add_argument('--baro_y_min',
help='y axis minimum for barometric pressure graph')
parser.add_argument('--bar_y_max',
help='y axis maximum for barometric pressure graph')
parser.add_argument('--wl_y_min',
help='y axis minimum for water level graph')
parser.add_argument('--wl_y_max',
help='y axis maximum for water level graph')
args = vars(parser.parse_args(sys.argv[1:]))
# args = {
# 'sea_fname': 'NCCAR00007_1511451_sea.csv',
# 'air_fname': 'NCCAR12248_9983816_air.csv',
# 'out_fname': 'storm',
# 'creator_name': "greg",
# 'creator_email': '[email protected]',
# 'creator_url': 'g.com',
# 'sea_instrument_name': "MS TruBlue 255",
# 'air_instrument_name': "Onset Hobo U20",
# 'sea_stn_station_number': '1',
# 'air_stn_station_number': '2',
# 'sea_stn_instrument_id': '3',
# 'air_stn_instrument_id': '4',
# 'sea_latitude': 20.0,
# 'air_latitude': 30.0,
# 'sea_longitude': 40.0,
# 'air_longitude': 50.0,
# 'tz_info': 'US/Central',
# 'daylight_savings': 'False',
# 'datum': 'NAVD88',
# 'sea_initial_sensor_orifice_elevation': 1,
# 'air_initial_sensor_orifice_elevation': 1,
# 'sea_final_sensor_orifice_elevation': 1.5,
# 'air_final_sensor_orifice_elevation': 1.5,
# 'salinity': "Salt Water (^> 30 ppt)",
# 'initial_land_surface_elevation': 1,
# 'final_land_surface_elevation': 1.2,
# 'deployment_time': "20151002 0000",
# 'retrieval_time': "20151010 0000",
# 'sea_name': "Chesapeake Bay",
# 'sea_good_start_date': "20161008 0800",
# 'air_good_start_date': "20161008 0800",
# 'sea_good_end_date': "20161010 0800",
# 'air_good_end_date': "20161010 0800",
# 'sea_4hz': 'True'
# }
output = args['out_fname']
args['in_fname'] = args['sea_fname']
args['out_fname'] = ''.join([args['out_fname'], '_sea'])
args['pressure_type'] = 'Sea Pressure'
args['instrument_name'] = args['sea_instrument_name']
args['stn_station_number'] = args['sea_stn_station_number']
args['stn_instrument_id'] = args['sea_stn_instrument_id']
args['latitude'] = args['sea_latitude']
args['longitude'] = args['sea_longitude']
args['initial_sensor_orifice_elevation'] = args['sea_initial_sensor_orifice_elevation']
args['final_sensor_orifice_elevation'] = args['sea_final_sensor_orifice_elevation']
args['good_start_date'] = args['sea_good_start_date']
args['good_end_date'] = args['sea_good_end_date']
sea_code, args['sea_fname'] = process_file(args)
args['out_fname'] = output
args['in_fname'] = args['air_fname']
args['out_fname'] = ''.join([args['out_fname'], '_air'])
args['pressure_type'] = 'Air Pressure'
args['instrument_name'] = args['air_instrument_name']
args['stn_station_number'] = args['air_stn_station_number']
args['stn_instrument_id'] = args['air_stn_instrument_id']
args['latitude'] = args['air_latitude']
args['longitude'] = args['air_longitude']
args['initial_sensor_orifice_elevation'] = args['air_initial_sensor_orifice_elevation']
args['final_sensor_orifice_elevation'] = args['air_final_sensor_orifice_elevation']
args['good_start_date'] = args['air_good_start_date']
args['good_end_date'] = args['air_good_end_date']
air_code, args['air_fname'] = process_file(args)
args['out_fname'] = output
code = process_storm_files(args)
sys.stdout.write(str(sea_code))
sys.stdout.write('\n')
sys.stdout.write(str(air_code))
sys.stdout.write('\n')
sys.stdout.write(str(code))
sys.stdout.write('\n')
sys.stdout.flush()