nc.py

import os
import sys
import logging
import pandas as pd
from datetime import datetime as dt
from aosstower.l00 import parser
from netCDF4 import Dataset
import numpy as np 
import platform
from aosstower import station

LOG = logging.getLogger(__name__)

# The purpose of this function is to write the dimensions
# for the nc file
# no parameters
# no returns

def writeDimensions(ncFile):
    ncFile.createDimension('time', None)
    ncFile.createDimension('max_len_station_name', 32)

    return ncFile

def createVariables(ncFile, firstStamp, chunksizes, zlib):
    #base_time long name
    btln = 'base time as unix timestamp'

    #base time units
    btu = 'seconds since 1970-01-01 00:00:00'

    #base time string
    bts = firstStamp.strftime('%Y-%m-%d 00:00:00Z')

    #time long name
    tln = 'time offset from base_time'

    #time units
    tu = 'seconds since ' + firstStamp.strftime('%Y-%m-%d 00:00:00Z')

    

    coordinates = {
                      #fields: type, dimension, fill, valid_min, std_name, longname, units, valid_max, cf_role, axis
                      'lon': [np.float32, None, float(-999), '-180L', 'longitude', None, 'degrees_east', '180L', None],
                      'lat': [np.float32, None, float(-999), '-90L', 'latitude', None, 'degrees_north', '90L', None],
                      'alt': [np.float32, None, float(-999), None, 'height', 'vertical distance', 'm', None, None],
                      'base_time': [np.float32, None, float(-999), None, 'time', btln, btu, None, None],
                      'time_offset': [np.float32, 'time', float(-999), None, 'time', tln, tu, None, None],
                      'station_name': ['c', 'max_len_station_name', '-', None, None, 'station name', None, None, 'timeseries_id'],   
                      'time': [np.float32, 'time', float(-999), None, None, "Time offset from epoch", "seconds since 1970-01-01 00:00:00Z", None, None, None]
                  }

    for key in coordinates:
        attr = coordinates[key]

        if(attr[1]):
            if attr[1] == 'max_len_station_name':
                if (chunksizes) and chunksizes[0] > 32:
                    variable = ncFile.createVariable(key, attr[0], dimensions=(attr[1]), fill_value=attr[2], zlib=zlib, chunksizes=[32])

                else:
                    variable = ncFile.createVariable(key, attr[0], dimensions=(attr[1]), fill_value=attr[2], zlib=zlib, chunksizes=chunksizes)

            else:
                variable = ncFile.createVariable(key, attr[0], dimensions=(attr[1]), fill_value=attr[2], zlib=zlib, chunksizes=chunksizes)
        else:
            variable = ncFile.createVariable(key, attr[0], fill_value=attr[1], zlib=zlib, chunksizes=chunksizes)

        #create var attributes
        if key == 'alt':
            variable.positive = 'up'
            variable.axis = 'Z'

        if(attr[3]):
            variable.valid_min = attr[3]
            variable.valid_max = attr[7]

        if(attr[4]):
            variable.standard_name = attr[4]

        if(attr[5]):
            variable.long_name = attr[5]

        if(attr[6]):
            variable.units = attr[6]

        if(attr[8]):
             variable.cf_role = attr[8]

        if key == 'base_time':
            variable.string = bts

    for entry in parser.database:
        if(entry == 'stamp'):
            continue

        varTup = parser.database[entry]
        
        variable = ncFile.createVariable(entry, np.float32,
        dimensions=('time'), fill_value=float(-999), zlib=zlib, chunksizes=chunksizes)
        variable.standard_name = varTup[1]
        variable.description = varTup[3]
        variable.units = varTup[4]

    #create global attributes
    ncFile.source = 'surface observation'
    ncFile.conventions = 'ARM-1.2 CF-1.6'
    ncFile.institution = 'UW SSEC'
    ncFile.featureType = 'timeSeries'
    ncFile.data_level = 'a0'
    ncFile.datastream = 'aoss.tower.nc.la0.v00'
    ncFile.software_version = '00'

    #generate history
    ncFile.history = ' '.join(platform.uname()) + " " + os.path.basename(__file__)
    
    return ncFile

def minuteAverages(frame):
    frame['minute'] = [ts.replace(second=0) for ts in frame.index]
    newFrame = frame.groupby('minute').mean()
    newFrame.index.names = ['']
    
    columns = list(newFrame.columns.values)
    if 'wind_speed' in columns:
        del newFrame['wind_speed']

    if 'wind_direction' in columns:
        del newFrame['wind_direction']

    del frame['minute']

    return newFrame.fillna(-99999)

def getData(inputFiles):
    dictData = {}

    for filename in inputFiles:
        getFrames = list(parser.read_frames(filename))

        for frame in getFrames:
            if 'stamp' not in frame:
                continue

            stamp = frame['stamp']
            del frame['stamp']

            dictData[stamp] = frame

    return pd.DataFrame(dictData).transpose().replace(-99999, np.nan)

def writeVars(ncFile, frame):
    stamps = list(frame.index)

    baseDTObj = dt.strptime(str(stamps[0]).split(' ')[0], '%Y-%m-%d')

    #find out how much time elapsed
    #since the origin to the start of the day
    #in seconds
    baseTimeValue = baseDTObj - dt(1970,1,1)
    baseTimeValue = baseTimeValue.total_seconds()

    #create time numpy
    timeNumpy = np.empty(len(stamps), dtype='float32')

    counter = 0

    #write stamps in, yo

    for stamp in stamps:
        stampObj = dt.strptime(str(stamp), '%Y-%m-%d %H:%M:%S')
        timeValue = (stampObj - baseDTObj).total_seconds()

        timeNumpy[counter] = timeValue
        counter += 1

    fileVar = ncFile.variables

    fileVar['base_time'].assignValue(baseTimeValue)
    fileVar['time_offset'][:] = timeNumpy
    fileVar['time'][:] = timeNumpy + baseTimeValue

    #write coordinate var values to file
    #alt might not be right, need to verify
    fileVar['lon'].assignValue(station.LONGITUDE)
    fileVar['lat'].assignValue(station.LATITUDE)
    fileVar['alt'].assignValue(328)

    #might change
    stationName = ("AOSS Tower")
    
    #transfer station name into array of chars
    statChars = list(stationName)
    statNumpy = np.asarray(statChars)

    #write station name to file
    fileVar['station_name'][0:len(statNumpy)] = statNumpy

    #writes data into file
    for varName in frame:
        dataList = frame[varName].tolist()
        dataArray = np.asarray(dataList)
        fileVar[varName][:] = dataArray
        
    return ncFile

#The purpose of this method is to take a begin date, and end date
# input filenames and output filename and create a netCDF file 
# based upon that
# @param start time - a start datetime object
# @param end time - an end datetime object
# @param input filenames - list of filenames
# @param output filename - filename of the netcdf file

def createGiantNetCDF(start, end, inputFiles, outputName, zlib, chunkSize):
    default = False

    if(chunkSize):
        chunksizes = [chunkSize]

    else:
        default = True

    frame = getData(inputFiles)

    newFrame = minuteAverages(frame)

    print(newFrame)

    if(frame.empty):
        return False
    
    else:
        if(start and end):
            frame = frame[start.strftime('%Y-%m-%d %H:%M:%S'): end.strftime('%Y-%m-%d %H:%M:%S')]

        if(default):
            chunksizes = [len(list(frame.index))]

        firstStamp = dt.strptime(str(list(frame.index)[0]), '%Y-%m-%d %H:%M:%S')

        ncFile = Dataset(outputName, 'w', format='NETCDF4_CLASSIC')

        ncFile = writeDimensions(ncFile)

        ncFile = createVariables(ncFile, firstStamp, chunksizes, zlib)
 
        ncFile.inputFiles = ', '.join(inputFiles)

        ncFile = writeVars(ncFile, frame)

        ncFile.close()
        
        return True

def createMultiple(filenames, outputFilenames, zlib, chunkSize):
    if(outputFilenames and len(filenames) != len(outputFilenames)):
        print('USAGE: number of output filenames must equal number of input filenames when start and end times are not specified')
        exit(0)
    
    results = []

    for idx, filename in enumerate(filenames):
        results.append(createGiantNetCDF(None, None, [filename], outputFilenames[idx], zlib, chunkSize))

    print(results)

    allFalse = True

    for result in results:
        if result == True:
            print('here')
            print(result)
            allFalse = False

    if allFalse == True:
        raise IOError('All ASCII files were empty')

#The purpose of this method is to take a string in the format
# YYYY-mm-ddTHH:MM:SS and convert that to a datetime object
# used in coordination with argparse -s and -e params
# @param datetime string
# @return datetime object

def _dt_convert(datetime_str):
    #parse datetime string, return datetime object
    try: 
        return dt.strptime(datetime_str, '%Y-%m-%dT%H:%M:%S')
    except:
        return dt.strptime(datetime_str, '%Y-%m-%d')
 
def main():
    import argparse

    #argparse description
    parser = argparse.ArgumentParser(description="Convert level_00 aoss tower data to level_a0")

    #argparse verbosity info
    parser.add_argument('-v', '--verbose', action="count", default=int(os.environ.get("VERBOSITY", 2)),
                         dest='verbosity',
                         help='each occurrence increases verbosity 1 level through ERROR-WARNING-INFO-DEBUG (default INFO)')

    #argparse start and end times
    parser.add_argument('-s', '--start-time', type=_dt_convert, 
        help="Start time of massive netcdf file, if only -s is given, a netcdf file for only that day is given" + 
        ". Formats allowed: \'YYYY-MM-DDTHH:MM:SS\', \'YYYY-MM-DD\'")
    parser.add_argument('-e', '--end-time', type=_dt_convert, help='End time of massive netcdf file. Formats allowed:' +
        "\'YYYY-MM-DDTHH:MM:SS\', \'YYYY-MM-DD\'")
    parser.add_argument('-cs', '--chunk-size', type=int, help='chunk Size for the netCDF file')
    parser.add_argument('-z', '--zlib', action='store_true', help='compress netCDF file with zlib')

    parser.add_argument("input_files", nargs="+",
                         help="aoss_tower level_00 paths")

    parser.add_argument('-o', '--output', required=True, nargs="+", help="filename pattern or filename. " +
    "Should be along the lines of <filepath>/aoss_tower.YYYY-MM-DD.nc")
    args = parser.parse_args()

    levels = [logging.ERROR, logging.WARN, logging.INFO, logging.DEBUG]
    level=levels[min(3, args.verbosity)]
    logging.basicConfig(level=level)


    if(args.start_time and args.end_time):
        result = createGiantNetCDF(args.start_time, args.end_time, args.input_files, args.output[0], args.zlib, args.chunk_size)
        if(result == False):
            raise IOError('An empty ASCII file was found')

    elif(args.start_time):
        end_time = args.start_time.replace(hour=23, minute=59, second=59)
        result = createGiantNetCDF(args.start_time, end_time, args.input_files, args.output[0], args.zlib, args.chunk_size)
        if(result == False):
            raise IOError('An empty ASCII file was found')

    elif(args.end_time):
        print('USAGE: start time must be specified when end time is specified')

    else:
        createMultiple(args.input_files, args.output, args.zlib, args.chunk_size)
if __name__ == "__main__":
    main()