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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 from YSI 6600 V2-2 on an automated veritical profiler (avp) |
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parser : date and time, water_depth for each profile |
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sample time, sample depth, as cast measures water |
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temperature, conductivity, salinity, pH, dissolved oxygen, |
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turbidity, and chlorophyll |
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creator : lat, lon, z, stime, (time, water_depth), water_temp, cond, |
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salin, ph, turb, chl, do |
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updator : z, stime, (time, water_depth), water_temp, cond, salin, ph, |
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turb, chl, do |
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using fixed profiler CDL but modified to have raw data for each cast |
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along each column |
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Examples |
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-------- |
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>> (parse, create, update) = load_processors('proc_avp_ysi_6600_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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parse Automated Vertical Profile Station (AVP) Water Quality Data |
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month, day, year, hour, min, sec, temp (deg. C), conductivity |
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(mS/cm), salinity (ppt or PSU), depth (meters), pH, turbidity (NTU), |
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chlorophyll (micrograms per liter), DO (micrograms per liter) |
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Notes |
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----- |
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1. Column Format |
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temp, cond, salin, depth, pH, turb, chl, DO |
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(C), (mS/cm), (ppt), (m), pH, (NTU), (ug/l), (ug/l) |
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Profile Time: 00:30:00 |
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Profile Date: 08/18/2008 |
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Profile Depth: 255.0 cm |
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Profile Location: Stones Bay Serial No: 00016B79, ID: AVP1_SERDP |
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08/18/08 00:30:06 26.94 41.87 26.81 0.134 8.00 3.4 4.5 6.60 |
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08/18/08 00:30:07 26.94 41.87 26.81 0.143 8.00 3.4 4.8 6.59 |
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08/18/08 00:30:08 26.94 41.87 26.81 0.160 8.00 3.4 4.8 6.62 |
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08/18/08 00:30:09 26.94 41.87 26.81 0.183 8.00 3.4 4.8 6.66 |
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2. Use a ragged array to store each uniquely measured param at each |
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time and depth but not gridded, so this uses fixed profiler CDL |
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but modified to have raw data for each cast along each column. |
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For plotting, the data will need to be grid at specified depth bins. |
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|
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Tony Whipple at IMS says 'The AVPs sample at one second intervals. |
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Between the waves and the instrument descending from a spool of |
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line with variable radius it works out to about 3-5 cm between |
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observations on average. When I process the data to make the |
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images, I bin the data every 10 cm and take the average of however |
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many observations fell within that bin.' |
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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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fn = sensor_info['fn'] |
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sample_dt_start = filt_datetime(fn) |
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nprof = 0 |
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for line in lines: |
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m=re.search("Profile Time:", line) |
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if m: |
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nprof=nprof+1 |
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for i in range(len(lines[0:40])): |
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if re.search("^ \r\n", lines[i]): |
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blank_line = lines.pop(i) |
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lines.append(' \r\n') |
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for i, line in enumerate(lines): |
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if re.search(r"Profile Time", line, re.IGNORECASE): |
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if not re.search("^ \r\n", lines[i-1]): |
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lines.insert(i, " \r\n") |
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N = nprof |
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nbins = sensor_info['nbins'] |
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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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'z' : numpy.array(numpy.ones((N,nbins), dtype=float)*numpy.nan), |
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'wd' : numpy.array(numpy.ones((N,), dtype=long)*numpy.nan), |
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'wl' : numpy.array(numpy.ones((N,), dtype=long)*numpy.nan), |
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127 |
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128 |
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129 |
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'stime' : numpy.array(numpy.ones((N,nbins), dtype=long)*numpy.nan), |
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'wtemp' : numpy.array(numpy.ones((N,nbins), dtype=float)*numpy.nan), |
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'cond' : numpy.array(numpy.ones((N,nbins), dtype=float)*numpy.nan), |
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'salin' : numpy.array(numpy.ones((N,nbins), dtype=float)*numpy.nan), |
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'turb' : numpy.array(numpy.ones((N,nbins), dtype=float)*numpy.nan), |
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'ph' : numpy.array(numpy.ones((N,nbins), dtype=float)*numpy.nan), |
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'chl' : numpy.array(numpy.ones((N,nbins), dtype=float)*numpy.nan), |
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'do' : numpy.array(numpy.ones((N,nbins), dtype=float)*numpy.nan), |
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} |
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i = 0 |
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have_date = have_time = have_wd = have_location = have_head = False |
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for line in lines: |
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if re.search(r"[\x1a]", line): |
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continue |
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ysi = [] |
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sw = re.split('[\s/\:]*', line) |
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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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ysi.append(float(m.groups()[0])) |
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|
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if re.search("Profile Time:", line): |
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have_time = True |
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HH=ysi[0] |
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MM=ysi[1] |
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SS=ysi[2] |
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elif re.search("Profile Date:", line): |
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have_date = True |
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mm=ysi[0] |
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dd=ysi[1] |
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yyyy=ysi[2] |
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elif re.search("Profile Depth:", line): |
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have_wd = True |
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wd = ysi[0]/100. |
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profile_str = '%02d-%02d-%4d %02d:%02d:%02d' % (mm,dd,yyyy,HH,MM,SS) |
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if sensor_info['utc_offset']: |
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profile_dt = scanf_datetime(profile_str, fmt='%m-%d-%Y %H:%M:%S') + \ |
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timedelta(hours=sensor_info['utc_offset']) |
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else: |
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profile_dt = scanf_datetime(profile_str, fmt='%m-%d-%Y %H:%M:%S') |
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elif re.search("Profile Location:", line): |
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have_location = True |
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179 |
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sw = re.findall(r'\w+:\s(\w+)*', line) |
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181 |
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182 |
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183 |
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wtemp = numpy.array(numpy.ones(nbins,), dtype=float)*numpy.nan |
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depth =numpy.array(numpy.ones(nbins,), dtype=float)*numpy.nan |
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cond = numpy.array(numpy.ones(nbins,), dtype=float)*numpy.nan |
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salin = numpy.array(numpy.ones(nbins,), dtype=float)*numpy.nan |
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turb = numpy.array(numpy.ones(nbins,), dtype=float)*numpy.nan |
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ph = numpy.array(numpy.ones(nbins,), dtype=float)*numpy.nan |
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chl = numpy.array(numpy.ones(nbins,), dtype=float)*numpy.nan |
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do = numpy.array(numpy.ones(nbins,), dtype=float)*numpy.nan |
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stime = numpy.array(numpy.ones(nbins,), dtype=long)*numpy.nan |
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193 |
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j = 0 |
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195 |
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head = numpy.array([have_date, have_time, have_wd, have_location]) |
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have_head = head.all() |
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198 |
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elif (len(ysi)==14 and have_head): |
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if j>=nbins: |
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print 'Sample number (' + str(j) + \ |
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') in profile exceeds maximum value ('+ \ |
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str(nbins) + ') in config' |
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sample_str = '%02d-%02d-%02d %02d:%02d:%02d' % tuple(ysi[0:6]) |
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try: |
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sample_dt = scanf_datetime(sample_str, fmt='%m-%d-%y %H:%M:%S') |
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except ValueError: |
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try: |
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sample_dt = scanf_datetime(sample_str, fmt='%d-%m-%y %H:%M:%S') |
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except: |
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sample_dt = datetime(1970,1,1) |
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216 |
|
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if sample_dt is not None: |
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if sensor_info['utc_offset']: |
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sample_dt = sample_dt + timedelta(hours=sensor_info['utc_offset']) |
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|
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if j<nbins: |
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stime[j] = dt2es(sample_dt) |
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wtemp[j] = ysi[6] |
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cond[j] = ysi[7] |
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salin[j] = ysi[8] |
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depth[j] = ysi[9] |
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228 |
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ph[j] = ysi[10] |
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turb[j] = ysi[11] |
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chl[j] = ysi[12] |
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do[j] = ysi[13] |
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|
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j = j+1 |
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else: |
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print 'skipping line, ill-formed date ... ' + str(line) |
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237 |
|
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238 |
|
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elif (len(ysi)==0 and have_head and i<N): |
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240 |
|
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data['dt'][i] = profile_dt |
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data['time'][i] = dt2es(profile_dt) |
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data['wd'][i] = -1.*wd |
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data['wl'][i] = platform_info['mean_water_depth'] - (-1*wd) |
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245 |
|
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246 |
|
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247 |
|
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data['stime'][i] = stime |
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data['z'][i] = -1.*depth |
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250 |
|
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data['wtemp'][i] = wtemp |
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data['cond'][i] = cond |
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data['salin'][i] = salin |
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data['turb'][i] = turb |
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data['ph'][i] = ph |
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data['chl'][i] = chl |
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data['do'][i] = do |
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258 |
|
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i=i+1 |
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have_date = have_time = have_wd = have_location = False |
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else: |
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print 'skipping bad data line ... ' + str(line) |
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263 |
|
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264 |
|
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265 |
|
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return data |
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267 |
|
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268 |
|
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269 |
def creator(platform_info, sensor_info, data): |
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270 |
|
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271 |
|
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i = data['in'] |
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dt = data['dt'][i] |
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274 |
|
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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://nccoos.unc.edu', |
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'contact' : 'Sara Haines (haines@email.unc.edu)', |
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|
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'source' : 'fixed-automated-profiler 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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288 |
|
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'Conventions' : 'CF-1.0; SEACOOS-CDL-v2.0', |
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290 |
|
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'format_category_code' : 'fixed-profiler-ragged', |
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'institution_code' : platform_info['institution'], |
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293 |
'platform_code' : platform_info['id'], |
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'package_code' : sensor_info['id'], |
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295 |
|
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296 |
'project' : 'North Carolina Coastal Ocean Observing System (NCCOOS)', |
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297 |
'project_url' : 'http://nccoos.unc.edu', |
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298 |
|
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299 |
|
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300 |
'start_date' : dt[0].strftime("%Y-%m-%d %H:%M:%S"), |
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301 |
|
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302 |
'end_date' : dt[-1].strftime("%Y-%m-%d %H:%M:%S"), |
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303 |
'release_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
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304 |
|
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305 |
'creation_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
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306 |
'modification_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
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307 |
'process_level' : 'level1', |
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308 |
|
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309 |
|
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310 |
'_FillValue' : numpy.nan, |
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311 |
} |
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312 |
|
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313 |
var_atts = { |
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314 |
|
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315 |
'time' : {'short_name': 'time', |
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316 |
'long_name': 'Time of Profile', |
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317 |
'standard_name': 'time', |
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318 |
'units': 'seconds since 1970-1-1 00:00:00 -0', |
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319 |
'axis': 'T', |
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320 |
}, |
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321 |
'lat' : {'short_name': 'lat', |
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322 |
'long_name': 'Latitude', |
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323 |
'standard_name': 'latitude', |
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324 |
'reference':'geographic coordinates', |
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325 |
'units': 'degrees_north', |
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326 |
'valid_range':(-90.,90.), |
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327 |
'axis': 'Y', |
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328 |
}, |
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329 |
'lon' : {'short_name': 'lon', |
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330 |
'long_name': 'Longitude', |
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331 |
'standard_name': 'longitude', |
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332 |
'reference':'geographic coordinates', |
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333 |
'units': 'degrees_east', |
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334 |
'valid_range':(-180.,180.), |
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335 |
'axis': 'Y', |
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336 |
}, |
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337 |
'z' : {'short_name': 'z', |
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338 |
'long_name': 'Height', |
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339 |
'standard_name': 'height', |
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340 |
'reference':'zero at sea-surface', |
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341 |
'positive' : 'up', |
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342 |
'units': 'm', |
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343 |
'axis': 'Z', |
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344 |
}, |
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345 |
|
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346 |
'stime' : {'short_name': 'stime', |
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347 |
'long_name': 'Time of Sample ', |
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348 |
'standard_name': 'time', |
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349 |
'units': 'seconds since 1970-1-1 00:00:00 -0', |
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350 |
}, |
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351 |
'wd': {'short_name': 'wd', |
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352 |
'long_name': 'Water Depth', |
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353 |
'standard_name': 'water_depth', |
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354 |
'reference' : 'zero at sea-surface', |
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355 |
'positive' : 'up', |
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356 |
'units': 'm', |
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357 |
}, |
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358 |
'wl': {'short_name': 'wl', |
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359 |
'long_name': 'Water Level', |
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360 |
'standard_name': 'water_level', |
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361 |
'reference':'MSL', |
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362 |
'reference_to_MSL' : 0., |
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363 |
'reference_MSL_datum' : platform_info['mean_water_depth'], |
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364 |
'reference_MSL_datum_time_period' : platform_info['mean_water_depth_time_period'], |
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365 |
'positive' : 'up', |
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366 |
'z' : 0., |
---|
367 |
'units': 'm', |
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368 |
}, |
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369 |
|
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370 |
|
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371 |
|
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372 |
|
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373 |
|
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374 |
|
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375 |
|
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376 |
|
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377 |
'wtemp': {'short_name': 'wtemp', |
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378 |
'long_name': 'Water Temperature', |
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379 |
'standard_name': 'water_temperature', |
---|
380 |
'units': 'degrees_Celsius', |
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381 |
}, |
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382 |
'cond': {'short_name': 'cond', |
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383 |
'long_name': 'Conductivity', |
---|
384 |
'standard_name': 'conductivity', |
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385 |
'units': 'mS cm-1', |
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386 |
}, |
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387 |
'salin': {'short_name': 'salin', |
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388 |
'long_name': 'Salinity', |
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389 |
'standard_name': 'salinity', |
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390 |
'units': 'PSU', |
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391 |
}, |
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392 |
'turb': {'short_name': 'turb', |
---|
393 |
'long_name': 'Turbidity', |
---|
394 |
'standard_name': 'turbidity', |
---|
395 |
'units': 'NTU', |
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396 |
}, |
---|
397 |
'ph': {'short_name': 'ph', |
---|
398 |
'long_name': 'pH', |
---|
399 |
'standard_name': 'ph', |
---|
400 |
'units': '', |
---|
401 |
}, |
---|
402 |
'chl': {'short_name': 'chl', |
---|
403 |
'long_name': 'Chlorophyll', |
---|
404 |
'standard_name': 'chlorophyll', |
---|
405 |
'units': 'ug l-1', |
---|
406 |
}, |
---|
407 |
'do': {'short_name': 'do', |
---|
408 |
'long_name': 'Dissolved Oxygen', |
---|
409 |
'standard_name': 'dissolved_oxygen', |
---|
410 |
'units': 'mg l-1', |
---|
411 |
}, |
---|
412 |
} |
---|
413 |
|
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414 |
|
---|
415 |
dim_inits = ( |
---|
416 |
('time', NC.UNLIMITED), |
---|
417 |
('lat', 1), |
---|
418 |
('lon', 1), |
---|
419 |
('z', sensor_info['nbins']), |
---|
420 |
) |
---|
421 |
|
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422 |
|
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423 |
|
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424 |
|
---|
425 |
|
---|
426 |
var_inits = ( |
---|
427 |
|
---|
428 |
('time', NC.INT, ('time',)), |
---|
429 |
('lat', NC.FLOAT, ('lat',)), |
---|
430 |
('lon', NC.FLOAT, ('lon',)), |
---|
431 |
('z', NC.FLOAT, ('time', 'z',)), |
---|
432 |
|
---|
433 |
('wd', NC.FLOAT, ('time',)), |
---|
434 |
('wl', NC.FLOAT, ('time',)), |
---|
435 |
|
---|
436 |
|
---|
437 |
('stime', NC.FLOAT, ('time', 'z')), |
---|
438 |
('wtemp', NC.FLOAT, ('time', 'z')), |
---|
439 |
('cond', NC.FLOAT, ('time', 'z')), |
---|
440 |
('salin', NC.FLOAT, ('time', 'z')), |
---|
441 |
('turb', NC.FLOAT, ('time', 'z')), |
---|
442 |
('ph', NC.FLOAT, ('time', 'z')), |
---|
443 |
('chl', NC.FLOAT, ('time', 'z')), |
---|
444 |
('do', NC.FLOAT, ('time', 'z')), |
---|
445 |
) |
---|
446 |
|
---|
447 |
|
---|
448 |
var_data = ( |
---|
449 |
('lat', platform_info['lat']), |
---|
450 |
('lon', platform_info['lon']), |
---|
451 |
('time', data['time'][i]), |
---|
452 |
('wd', data['wd'][i]), |
---|
453 |
('wl', data['wl'][i]), |
---|
454 |
|
---|
455 |
|
---|
456 |
('stime', data['stime'][i]), |
---|
457 |
('z', data['z'][i]), |
---|
458 |
|
---|
459 |
('wtemp', data['wtemp'][i]), |
---|
460 |
('cond', data['cond'][i]), |
---|
461 |
('salin', data['salin'][i]), |
---|
462 |
('turb', data['turb'][i]), |
---|
463 |
('ph', data['ph'][i]), |
---|
464 |
('chl', data['chl'][i]), |
---|
465 |
('do', data['do'][i]), |
---|
466 |
) |
---|
467 |
|
---|
468 |
return (global_atts, var_atts, dim_inits, var_inits, var_data) |
---|
469 |
|
---|
470 |
def updater(platform_info, sensor_info, data): |
---|
471 |
|
---|
472 |
|
---|
473 |
i = data['in'] |
---|
474 |
dt = data['dt'][i] |
---|
475 |
|
---|
476 |
global_atts = { |
---|
477 |
|
---|
478 |
|
---|
479 |
'end_date' : dt[-1].strftime("%Y-%m-%d %H:%M:%S"), |
---|
480 |
'release_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
---|
481 |
|
---|
482 |
'modification_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"), |
---|
483 |
} |
---|
484 |
|
---|
485 |
|
---|
486 |
|
---|
487 |
var_atts = {} |
---|
488 |
|
---|
489 |
|
---|
490 |
|
---|
491 |
|
---|
492 |
|
---|
493 |
|
---|
494 |
|
---|
495 |
|
---|
496 |
|
---|
497 |
|
---|
498 |
var_data = ( |
---|
499 |
('time', data['time'][i]), |
---|
500 |
('wd', data['wd'][i]), |
---|
501 |
('wl', data['wl'][i]), |
---|
502 |
|
---|
503 |
|
---|
504 |
('stime', data['stime'][i]), |
---|
505 |
('z', data['z'][i]), |
---|
506 |
|
---|
507 |
('wtemp', data['wtemp'][i]), |
---|
508 |
('cond', data['cond'][i]), |
---|
509 |
('salin', data['salin'][i]), |
---|
510 |
('turb', data['turb'][i]), |
---|
511 |
('ph', data['ph'][i]), |
---|
512 |
('chl', data['chl'][i]), |
---|
513 |
('do', data['do'][i]), |
---|
514 |
) |
---|
515 |
|
---|
516 |
return (global_atts, var_atts, var_data) |
---|
517 |
|
---|
518 |
|
---|