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""" |
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how to parse data, and assert what data and info goes into |
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creating and updating monthly netcdf files |
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parse data water quality data from ysi 6600 V2 |
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collected on Campbell Scientific DataLogger (loggernet) (csi) |
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parser : sample date and time, |
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water temperature, conductivity, pH, dissolved oxygen, turbidity, and system battery |
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creator : lat, lon, z, time, wtemp, cond, ph, turb, do_sat, do_mg, battvolts |
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updator : time, wtemp, cond, ph, turb, do_sat, do_mg, battvolts |
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Examples |
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-------- |
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>> (parse, create, update) = load_processors('proc_csi_wq_v2') |
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or |
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>> si = get_config(cn+'.sensor_info') |
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>> (parse, create, update) = load_processors(si['adcp']['proc_module']) |
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>> lines = load_data(filename) |
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>> data = parse(platform_info, sensor_info, lines) |
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>> create(platform_info, sensor_info, data) or |
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>> update(platform_info, sensor_info, data) |
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""" |
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from raw2proc import * |
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from procutil import * |
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from ncutil import * |
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now_dt = datetime.utcnow() |
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now_dt.replace(microsecond=0) |
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def parser(platform_info, sensor_info, lines): |
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""" |
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From FSL (CSI datalogger program files): |
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15 Output_Table 15.00 Min |
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1 15 L |
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2 Year_RTM L |
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3 Day_RTM L |
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4 Hour_Minute_RTM L |
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5 Rain15sec_TOT L |
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6 SonLevlft L |
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7 SonFlow L |
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8 PrDepthft L |
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9 PrFlowcfs L |
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1 Output_Table 60.00 Min |
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1 1 L |
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2 Year_RTM L |
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3 Day_RTM L |
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4 Hour_Minute_RTM L |
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5 H2OTempC L |
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6 SpCond L |
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7 DOSat L |
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8 DOmg L |
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9 PH L |
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10 Turb L |
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11 BattVolts L |
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Example data: |
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1,2005,83,1600,16.47,0,.4,.04,8.14,115.5,14.25 |
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15,2005,83,1615,0,4.551,-.547,.897,.885 |
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15,2005,83,1630,0,4.541,.727,.908,1.005 |
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15,2005,83,1645,0,4.537,6.731,.878,.676 |
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15,2005,83,1700,0,4.537,6.731,.83,.167 |
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1,2005,83,1700,16.57,0,.4,.03,8.03,145.7,13.08 |
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15,2005,83,1715,0,4.547,5.29,.847,.347 |
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15,2005,83,1730,0,4.541,.908,.842,.287 |
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15,2005,83,1745,0,4.547,7.3,.853,.407 |
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15,2005,83,1800,0,4.551,6.939,.855,.437 |
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1,2005,83,1800,15.65,0,.2,.02,7.91,111.3,12.98 |
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""" |
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import numpy |
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from datetime import datetime |
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from time import strptime |
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import math |
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fn = sensor_info['fn'] |
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sample_dt_start = filt_datetime(fn) |
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nsamp = 0 |
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for line in lines: |
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m=re.search("^1,", line) |
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if m: |
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nsamp=nsamp+1 |
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N = nsamp |
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data = { |
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'dt' : numpy.array(numpy.ones((N,), dtype=object)*numpy.nan), |
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'time' : numpy.array(numpy.ones((N,), dtype=long)*numpy.nan), |
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'wtemp' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan), |
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'cond' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan), |
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'do_sat' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan), |
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'do_mg' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan), |
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'ph' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan), |
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'turb' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan), |
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'battvolts' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan), |
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} |
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i = 0 |
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for line in lines: |
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csi = [] |
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m=re.search("^1,", line) |
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if m: |
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sw = re.split(',', line) |
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else: |
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continue |
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for s in sw: |
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m = re.search(REAL_RE_STR, s) |
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if m: |
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csi.append(float(m.groups()[0])) |
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if len(csi)==11: |
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yyyy = csi[1] |
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yday = csi[2] |
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(MM, HH) = math.modf(csi[3]/100.) |
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MM = math.ceil(MM*100.) |
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if (HH == 24): |
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yday=yday+1 |
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HH = 0. |
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sample_str = '%04d-%03d %02d:%02d' % (yyyy, yday, HH, MM) |
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sample_dt = scanf_datetime(sample_str, fmt='%Y-%j %H:%M') |
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data['dt'][i] = sample_dt |
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data['time'][i] = dt2es(sample_dt) |
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data['wtemp'][i] = csi[4] |
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data['cond'][i] = csi[5] |
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data['do_sat'][i] = csi[6] |
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data['do_mg'][i] = csi[7] |
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data['ph'][i] = csi[8] |
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data['turb'][i] = csi[9] |
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data['battvolts'][i] = csi[10] |
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i=i+1 |
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keep = numpy.array([type(datetime(1970,1,1)) == type(dt) for dt in data['dt'][:]]) |
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if keep.any(): |
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for param in data.keys(): |
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data[param] = data[param][keep] |
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return data |
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def creator(platform_info, sensor_info, data): |
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title_str = sensor_info['description']+' at '+ platform_info['location'] |
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global_atts = { |
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'title' : title_str, |
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'institution' : 'Unversity of North Carolina at Chapel Hill (UNC-CH)', |
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'institution_url' : 'http://nccoos.unc.edu', |
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'institution_dods_url' : 'http://nccoos.unc.edu', |
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'metadata_url' : 'http://nccoos.unc.edu', |
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'references' : 'http://ehs.unc.edu', |
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'contact' : 'Sara Haines (haines@email.unc.edu)', |
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'station_owner' : 'Environment, Health, and Safety Office', |
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'station_contact' : 'Sharon Myers (samyers@ehs.unc.edu)', |
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'source' : 'fixed-point observation', |
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'history' : 'raw2proc using ' + sensor_info['process_module'], |
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'comment' : 'File created using pycdf'+pycdfVersion()+' and numpy '+pycdfArrayPkg(), |
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'Conventions' : 'CF-1.0; SEACOOS-CDL-v2.0', |
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'format_category_code' : 'fixed-point', |
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'institution_code' : platform_info['institution'], |
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'platform_code' : platform_info['id'], |
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'package_code' : sensor_info['id'], |
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'project' : 'Environment, Health, and Safety (EHS)', |
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'project_url' : 'http://ehs.unc.edu/environment/water_quality', |
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'start_date' : data['dt'][0].strftime("%Y-%m-%d %H:%M:%S"), |
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'end_date' : data['dt'][-1].strftime("%Y-%m-%d %H:%M:%S"), |
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'release_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
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'creation_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
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'modification_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
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'process_level' : 'level1', |
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'_FillValue' : -99999., |
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} |
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var_atts = { |
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'time' : {'short_name': 'time', |
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'long_name': 'Time', |
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'standard_name': 'time', |
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'units': 'seconds since 1970-1-1 00:00:00 -0', |
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'axis': 'T', |
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}, |
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'lat' : {'short_name': 'lat', |
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'long_name': 'Latitude', |
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'standard_name': 'latitude', |
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'reference':'geographic coordinates', |
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'units': 'degrees_north', |
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'valid_range':(-90.,90.), |
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'axis': 'Y', |
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}, |
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'lon' : {'short_name': 'lon', |
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'long_name': 'Longitude', |
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'standard_name': 'longitude', |
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'reference':'geographic coordinates', |
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'units': 'degrees_east', |
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'valid_range':(-180.,180.), |
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'axis': 'Y', |
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}, |
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'z' : {'short_name': 'z', |
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'long_name': 'Height', |
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'standard_name': 'height', |
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'reference':'zero at sea-surface', |
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'positive' : 'up', |
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'units': 'm', |
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'axis': 'Z', |
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}, |
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'wtemp': {'short_name': 'wtemp', |
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'long_name': 'Water Temperature', |
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'standard_name': 'water_temperature', |
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'units': 'degrees_Celsius', |
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}, |
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'cond': {'short_name': 'cond', |
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'long_name': 'Conductivity', |
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'standard_name': 'conductivity', |
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'units': 'mS cm-1', |
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}, |
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'turb': {'short_name': 'turb', |
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'long_name': 'Turbidity', |
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'standard_name': 'turbidity', |
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'units': 'NTU', |
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}, |
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'ph': {'short_name': 'ph', |
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'long_name': 'pH', |
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'standard_name': 'ph', |
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'units': '', |
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}, |
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'do_mg': {'short_name': 'do_mg', |
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'long_name': 'ROX Optical Dissolved Oxygen, Derived Concentration', |
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'standard_name': 'dissolved_oxygen_concentration', |
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'units': 'mg l-1', |
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}, |
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'do_sat': {'short_name': 'do_sat', |
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'long_name': 'ROX Optical Dissolved Oxygen, Percent of Air Saturation', |
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'standard_name': 'dissolved_oxygen_relative_to_air_saturation', |
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'units': '%', |
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}, |
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'battvolts': {'short_name': 'battery', |
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'long_name': 'Battery Voltage of the Station', |
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'standard_name': 'battery_voltage', |
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'units': 'volts', |
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}, |
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} |
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dim_inits = ( |
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('ntime', NC.UNLIMITED), |
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('nlat', 1), |
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('nlon', 1), |
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('nz', 1), |
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) |
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var_inits = ( |
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('time', NC.INT, ('ntime',)), |
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('lat', NC.FLOAT, ('nlat',)), |
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('lon', NC.FLOAT, ('nlon',)), |
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('z', NC.FLOAT, ('nz',)), |
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('wtemp', NC.FLOAT, ('ntime',)), |
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('cond', NC.FLOAT, ('ntime',)), |
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('turb', NC.FLOAT, ('ntime',)), |
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('ph', NC.FLOAT, ('ntime',)), |
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('do_mg', NC.FLOAT, ('ntime',)), |
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('do_sat', NC.FLOAT, ('ntime',)), |
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('battvolts', NC.FLOAT, ('ntime',)), |
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) |
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i = data['in'] |
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var_data = ( |
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('lat', platform_info['lat']), |
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('lon', platform_info['lon']), |
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('z', platform_info['altitude']), |
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('time', data['time'][i]), |
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('wtemp', data['wtemp'][i]), |
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('cond', data['cond'][i]), |
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('turb', data['turb'][i]), |
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('ph', data['ph'][i]), |
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('do_mg', data['do_mg'][i]), |
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('do_sat', data['do_sat'][i]), |
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('battvolts', data['battvolts'][i]), |
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) |
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return (global_atts, var_atts, dim_inits, var_inits, var_data) |
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def updater(platform_info, sensor_info, data): |
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global_atts = { |
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'end_date' : data['dt'][-1].strftime("%Y-%m-%d %H:%M:%S"), |
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'release_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
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'modification_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
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} |
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var_atts = {} |
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358 |
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i = data['in'] |
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var_data = ( |
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('time', data['time'][i]), |
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('wtemp', data['wtemp'][i]), |
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('cond', data['cond'][i]), |
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('turb', data['turb'][i]), |
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('ph', data['ph'][i]), |
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('do_mg', data['do_mg'][i]), |
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('do_sat', data['do_sat'][i]), |
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('battvolts', data['battvolts'][i]), |
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) |
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return (global_atts, var_atts, var_data) |
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