root/raw2proc/trunk/raw2proc/proc_cr1000_wq.py

#!/usr/bin/env python
# Last modified:  Time-stamp: <2009-12-15 08:31:52 haines>
"""
how to parse data, and assert what data and info goes into
creating and updating monthly netcdf files

parse data water level and flow data (sontek argonaut and pressure
sensor) collected on Campbell Scientific DataLogger (loggernet) (csi)

parser : sample date and time, water_depth and flow from sontek and pressure

creator : lat, lon, z, time, sontek_wl, sontek_flow, press_wl, press_flow
updator : time, sontek_wl, sontek_flow, press_wl, press_flow


Examples
--------

>> (parse, create, update) = load_processors('proc_csi_adcp_v2')
or
>> si = get_config(cn+'.sensor_info')
>> (parse, create, update) = load_processors(si['adcp']['proc_module'])

>> lines = load_data(filename)
>> data = parse(platform_info, sensor_info, lines)
>> create(platform_info, sensor_info, data) or
>> update(platform_info, sensor_info, data)

"""


from raw2proc import *
from procutil import *
from ncutil import *

now_dt = datetime.utcnow()
now_dt.replace(microsecond=0)

def parser(platform_info, sensor_info, lines):
    """
    "TOA5","CR1000_CBC","CR1000","5498","CR1000.Std.11","CPU:UNC_CrowBranch.CR1","1554","DataHourly"
    "TIMESTAMP","RECORD","SondeTempC","SpCond","DOSat","DOmg","pH","Turb","BattVolt_Min"
    "TS","RN","","","","","","",""
    "","","Smp","Smp","Smp","Smp","Smp","Smp","Min"
    "2009-06-01 00:00:00",3066,20.54,0.551,7.17,-10.3,30.5,0,12.88
    "2009-06-01 01:00:00",3067,20.38,0.551,7.16,-9.7,29.7,0,12.86
    "2009-06-01 02:00:00",3068,20.18,0.55,7.15,-9.2,30.1,0,12.84
    "2009-06-01 03:00:00",3069,19.99,0.549,7.16,-9.5,27.6,0,12.83
    "2009-06-01 04:00:00",3070,"NaN",0.549,7.16,-9.5,27.6,0,12.83
    """

    import numpy
    from datetime import datetime
    from time import strptime

    # get sample datetime from filename
    fn = sensor_info['fn']
    sample_dt_start = filt_datetime(fn)[0]

    # how many samples (don't count header 4 lines)
    nsamp = len(lines[4:])

    N = nsamp
    data = {
        'dt' : numpy.array(numpy.ones((N,), dtype=object)*numpy.nan),
        'time' : numpy.array(numpy.ones((N,), dtype=long)*numpy.nan),
        'wtemp' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
        'cond' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
        'do_sat' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
        'do_mg' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
        'ph' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
        'turb' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
        'battvolts' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),

        }

    # sample count
    i = 0

    for line in lines[4:]:
        csi = []
        # split line
        sw = re.split(',', line)
        if len(sw)<=0:
            print ' ... skipping line %d ' % (i,)
            continue

        # replace "NAN"
        for index, s in enumerate(sw):
            m = re.search(NAN_RE_STR, s)
            if m:
                sw[index] = '-99999'

        # parse date-time, and all other float and integers
        for s in sw[1:]:
            m = re.search(REAL_RE_STR, s)
            if m:
                csi.append(float(m.groups()[0]))

        if  sensor_info['utc_offset']:
            sample_dt = scanf_datetime(sw[0], fmt='"%Y-%m-%d %H:%M:%S"') + \
                        timedelta(hours=sensor_info['utc_offset'])
        else:
            sample_dt = scanf_datetime(sw[0], fmt='"%Y-%m-%d %H:%M:%S"')

        data['dt'][i] = sample_dt # sample datetime
        data['time'][i] = dt2es(sample_dt) # sample time in epoch seconds

        if len(csi)==8:
            # 
            data['wtemp'][i] =  csi[1] # water temperature (C)
            data['cond'][i] = csi[2] # specific conductivity (mS/cm)
            data['ph'][i] = csi[3]   # ph
            data['turb'][i] = csi[5] # turbidity (NTU)
            data['do_sat'][i] = csi[6]   # saturated dissolved oxygen (% air sat)
            data['do_mg'][i] = csi[4]   # dissolved oxygen (mg/l)
            data['battvolts'][i] = csi[7]   # battery (volts)
            i=i+1
        else:
            print ' ... skipping line %d -- %s ' % (i,line)
            continue            
            

        # if re.search
    # for line

    # check that no data[dt] is set to Nan or anything but datetime
    # keep only data that has a resolved datetime
    keep = numpy.array([type(datetime(1970,1,1)) == type(dt) for dt in data['dt'][:]])
    if keep.any():
        for param in data.keys():
            data[param] = data[param][keep]

    return data

def creator(platform_info, sensor_info, data):
    #
    # 
    title_str = sensor_info['description']+' at '+ platform_info['location']
    global_atts = { 
        'title' : title_str,
        'institution' : 'Unversity of North Carolina at Chapel Hill (UNC-CH)',
        'institution_url' : 'http://nccoos.unc.edu',
        'institution_dods_url' : 'http://nccoos.unc.edu',
        'metadata_url' : 'http://nccoos.unc.edu',
        'references' : 'http://ehs.unc.edu',
        'contact' : 'Sara Haines (haines@email.unc.edu)',
        'station_owner' : 'Environment, Health, and Safety Office',
        'station_contact' : 'Sharon Myers (samyers@ehs.unc.edu)',
        # 
        'source' : 'fixed-point observation',
        'history' : 'raw2proc using ' + sensor_info['process_module'],
        'comment' : 'File created using pycdf'+pycdfVersion()+' and numpy '+pycdfArrayPkg(),
        # conventions
        'Conventions' : 'CF-1.0; SEACOOS-CDL-v2.0',
        # SEACOOS CDL codes
        'format_category_code' : 'fixed-point',
        'institution_code' : platform_info['institution'],
        'platform_code' : platform_info['id'],
        'package_code' : sensor_info['id'],
        # institution specific
        'project' : 'Environment, Health, and Safety (EHS)',
        'project_url' : 'http://ehs.unc.edu/environment/water_quality',
        # timeframe of data contained in file yyyy-mm-dd HH:MM:SS
        # first date in monthly file
        'start_date' : data['dt'][0].strftime("%Y-%m-%d %H:%M:%S"),
        # last date in monthly file
        'end_date' : data['dt'][-1].strftime("%Y-%m-%d %H:%M:%S"), 
        'release_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
        #
        'creation_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
        'modification_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
        'process_level' : 'level1',
        #
        # must type match to data (e.g. fillvalue is real if data is real)
        '_FillValue' : -99999.,
        }

    var_atts = {
        # coordinate variables
        'time' : {'short_name': 'time',
                  'long_name': 'Time',
                  'standard_name': 'time',
                  'units': 'seconds since 1970-1-1 00:00:00 -0', # UTC
                  'axis': 'T',
                  },
        'lat' : {'short_name': 'lat',
             'long_name': 'Latitude',
             'standard_name': 'latitude',
             'reference':'geographic coordinates',
             'units': 'degrees_north',
             'valid_range':(-90.,90.),
             'axis': 'Y',
             },
        'lon' : {'short_name': 'lon',
                 'long_name': 'Longitude',
                 'standard_name': 'longitude',
                 'reference':'geographic coordinates',
                 'units': 'degrees_east',
                 'valid_range':(-180.,180.),
                 'axis': 'Y',
                 },
        'z' : {'short_name': 'z',
               'long_name': 'Height',
               'standard_name': 'height',
               'reference':'zero at sea-surface',
               'positive' : 'up',
               'units': 'm',
               'axis': 'Z',
               },
        # data variables
        'wtemp': {'short_name': 'wtemp',
                  'long_name': 'Water Temperature',
                  'standard_name': 'water_temperature',                          
                  'units': 'degrees_Celsius',
                  },
        'cond': {'short_name': 'cond',
                 'long_name': 'Conductivity',
                 'standard_name': 'conductivity',                          
                 'units': 'mS cm-1',
                 },
        'turb': {'short_name': 'turb',
                 'long_name': 'Turbidity',
                 'standard_name': 'turbidity',                          
                 'units': 'NTU',
                 },
        'ph': {'short_name': 'ph',
               'long_name': 'pH',
               'standard_name': 'ph',                          
               'units': '',
               },
        'do_mg': {'short_name': 'do_mg',
               'long_name': 'ROX Optical Dissolved Oxygen, Derived Concentration',
               'standard_name': 'dissolved_oxygen_concentration',                          
               'units': 'mg l-1',
               },
        'do_sat': {'short_name': 'do_sat',
               'long_name': 'ROX Optical Dissolved Oxygen, Percent of Air Saturation',
               'standard_name': 'dissolved_oxygen_relative_to_air_saturation',                          
               'units': '%',
               },
        'battvolts': {'short_name': 'battery',
               'long_name': 'Battery Voltage of the Station',
               'standard_name': 'battery_voltage',                          
               'units': 'volts',
               },
        }

    # dimension names use tuple so order of initialization is maintained
    dim_inits = (
        ('ntime', NC.UNLIMITED),
        ('nlat', 1),
        ('nlon', 1),
        ('nz', 1),
        )
    
    # using tuple of tuples so order of initialization is maintained
    # using dict for attributes order of init not important
    # use dimension names not values
    # (varName, varType, (dimName1, [dimName2], ...))
    var_inits = (
        # coordinate variables
        ('time', NC.INT, ('ntime',)),
        ('lat', NC.FLOAT, ('nlat',)),
        ('lon', NC.FLOAT, ('nlon',)),
        ('z',  NC.FLOAT, ('nz',)),
        # data variables
        ('wtemp', NC.FLOAT, ('ntime',)),
        ('cond', NC.FLOAT, ('ntime',)),
        ('turb', NC.FLOAT, ('ntime',)),
        ('ph', NC.FLOAT, ('ntime',)),
        ('do_mg', NC.FLOAT, ('ntime',)),
        ('do_sat', NC.FLOAT, ('ntime',)),
        ('battvolts', NC.FLOAT, ('ntime',)),
        )

    # subset data only to month being processed (see raw2proc.process())
    i = data['in']
    
    # var data 
    var_data = (
        ('lat',  platform_info['lat']),
        ('lon', platform_info['lon']),
        ('z', platform_info['altitude']),
        #
        ('time', data['time'][i]),
        #
        ('wtemp', data['wtemp'][i]),
        ('cond', data['cond'][i]),
        ('turb', data['turb'][i]),
        ('ph', data['ph'][i]),
        ('do_mg', data['do_mg'][i]),
        ('do_sat', data['do_sat'][i]),
        ('battvolts', data['battvolts'][i]),
        )

    return (global_atts, var_atts, dim_inits, var_inits, var_data)

def updater(platform_info, sensor_info, data):
    #
    global_atts = { 
        # update times of data contained in file (yyyy-mm-dd HH:MM:SS)
        # last date in monthly file
        'end_date' : data['dt'][-1].strftime("%Y-%m-%d %H:%M:%S"), 
        'release_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
        #
        'modification_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
        }

    # data variables
    # update any variable attributes like range, min, max
    var_atts = {}
    # var_atts = {
    #    'wtemp': {'max': max(data.u),
    #          'min': min(data.v),
    #          },
    #    'cond': {'max': max(data.u),
    #          'min': min(data.v),
    #          },
    #    }
    
    # subset data only to month being processed (see raw2proc.process())
    i = data['in']

    # data 
    var_data = (
        ('time', data['time'][i]),
        ('wtemp', data['wtemp'][i]),
        ('cond', data['cond'][i]),
        ('turb', data['turb'][i]),
        ('ph', data['ph'][i]),
        ('do_mg', data['do_mg'][i]),
        ('do_sat', data['do_sat'][i]),
        ('battvolts', data['battvolts'][i]),
        )

    return (global_atts, var_atts, var_data)
#