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'''
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Created on Dec 27, 2017
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@author: Juan C. Espinoza
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'''
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import os
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import sys
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import time
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import json
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import glob
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import datetime
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import tarfile
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import numpy
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from netCDF4 import Dataset
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from schainpy.model.io.jroIO_base import JRODataReader
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from schainpy.model.proc.jroproc_base import ProcessingUnit, Operation
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from schainpy.model.data.jrodata import Parameters
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from schainpy.utils import log
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UT1970 = datetime.datetime(1970, 1, 1) - datetime.timedelta(seconds=time.timezone)
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def load_json(obj):
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'''
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Parse json as string instead of unicode
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'''
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if isinstance(obj, str):
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iterable = json.loads(obj)
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else:
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iterable = obj
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if isinstance(iterable, dict):
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return {str(k): load_json(v) if isinstance(v, dict) else str(v) if isinstance(v, unicode) else v
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for k, v in iterable.items()}
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elif isinstance(iterable, (list, tuple)):
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return [str(v) if isinstance(v, unicode) else v for v in iterable]
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return iterable
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class NCDFReader(JRODataReader, ProcessingUnit):
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def __init__(self, **kwargs):
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ProcessingUnit.__init__(self, **kwargs)
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self.dataOut = Parameters()
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self.counter_records = 0
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self.nrecords = None
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self.flagNoMoreFiles = 0
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self.isConfig = False
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self.filename = None
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self.intervals = set()
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self.ext = ('.nc', '.tgz')
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self.online_mode = False
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def setup(self,
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path=None,
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startDate=None,
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endDate=None,
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format=None,
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startTime=datetime.time(0, 0, 0),
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endTime=datetime.time(23, 59, 59),
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walk=False,
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**kwargs):
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self.path = path
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self.startDate = startDate
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self.endDate = endDate
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self.startTime = startTime
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self.endTime = endTime
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self.datatime = datetime.datetime(1900,1,1)
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self.walk = walk
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self.nTries = kwargs.get('nTries', 3)
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self.online = kwargs.get('online', False)
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self.delay = kwargs.get('delay', 30)
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self.ele = kwargs.get('ext', '')
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if self.path is None:
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raise ValueError, 'The path is not valid'
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self.search_files(path, startDate, endDate, startTime, endTime, walk)
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self.cursor = 0
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self.counter_records = 0
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if not self.files:
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raise Warning, 'There is no files matching these date in the folder: {}. \n Check startDate and endDate'.format(path)
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def search_files(self, path, startDate, endDate, startTime, endTime, walk):
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'''
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Searching for NCDF files in path
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Creating a list of files to procces included in [startDate,endDate]
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Input:
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path - Path to find files
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'''
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log.log('Searching files {} in {} '.format(self.ext, path), 'NCDFReader')
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if walk:
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paths = [os.path.join(path, p) for p in os.listdir(path) if os.path.isdir(os.path.join(path, p))]
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paths.sort()
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else:
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paths = [path]
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fileList0 = []
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for subpath in paths:
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fileList0 += [os.path.join(subpath, s) for s in glob.glob1(subpath, '*') if os.path.splitext(s)[-1] in self.ext and 'E{}'.format(self.ele) in s]
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fileList0.sort()
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if self.online:
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fileList0 = fileList0[-1:]
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self.files = {}
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startDate = startDate - datetime.timedelta(1)
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endDate = endDate + datetime.timedelta(1)
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for fullname in fileList0:
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thisFile = fullname.split('/')[-1]
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year = thisFile[3:7]
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if not year.isdigit():
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continue
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month = thisFile[7:9]
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if not month.isdigit():
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continue
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day = thisFile[9:11]
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if not day.isdigit():
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continue
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year, month, day = int(year), int(month), int(day)
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dateFile = datetime.date(year, month, day)
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timeFile = datetime.time(int(thisFile[12:14]), int(thisFile[14:16]), int(thisFile[16:18]))
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if (startDate > dateFile) or (endDate < dateFile):
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continue
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dt = datetime.datetime.combine(dateFile, timeFile)
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if dt not in self.files:
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self.files[dt] = []
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self.files[dt].append(fullname)
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self.dates = self.files.keys()
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self.dates.sort()
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return
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def search_files_online(self):
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'''
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Searching for NCDF files in online mode path
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Creating a list of files to procces included in [startDate,endDate]
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Input:
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path - Path to find files
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'''
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self.files = {}
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for n in range(self.nTries):
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if self.walk:
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paths = [os.path.join(self.path, p) for p in os.listdir(self.path) if os.path.isdir(os.path.join(self.path, p))]
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path = paths[-1]
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else:
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paths = self.path
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new_files = [os.path.join(path, s) for s in glob.glob1(path, '*') if os.path.splitext(s)[-1] in self.ext and 'E{}'.format(self.ele) in s]
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new_files.sort()
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for fullname in new_files:
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thisFile = fullname.split('/')[-1]
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year = thisFile[3:7]
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if not year.isdigit():
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continue
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month = thisFile[7:9]
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if not month.isdigit():
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continue
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day = thisFile[9:11]
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if not day.isdigit():
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continue
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year, month, day = int(year), int(month), int(day)
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dateFile = datetime.date(year, month, day)
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timeFile = datetime.time(int(thisFile[12:14]), int(thisFile[14:16]), int(thisFile[16:18]))
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dt = datetime.datetime.combine(dateFile, timeFile)
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if self.dt >= dt:
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continue
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if dt not in self.files:
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self.dt = dt
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self.files[dt] = []
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self.files[dt].append(fullname)
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break
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if self.files:
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break
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else:
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log.warning('Waiting {} seconds for the next file, try {} ...'.format(self.delay, n + 1), 'NCDFReader')
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time.sleep(self.delay)
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if not self.files:
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return 0
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self.dates = self.files.keys()
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self.dates.sort()
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self.cursor = 0
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return 1
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def parseFile(self):
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'''
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'''
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self.header = {}
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for attr in self.fp.ncattrs():
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self.header[str(attr)] = getattr(self.fp, attr)
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self.data[self.header['TypeName']] = numpy.array(self.fp.variables[self.header['TypeName']])
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if 'Azimuth' not in self.data:
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self.data['Azimuth'] = numpy.array(self.fp.variables['Azimuth'])
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def setNextFile(self):
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'''
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Open next files for the current datetime
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'''
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cursor = self.cursor
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if not self.online_mode:
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if cursor == len(self.dates):
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if self.online:
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cursor = 0
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self.dt = self.dates[cursor]
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self.online_mode = True
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if not self.search_files_online():
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log.success('No more files', 'NCDFReader')
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return 0
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else:
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log.success('No more files', 'NCDFReader')
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self.flagNoMoreFiles = 1
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return 0
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else:
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if not self.search_files_online():
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return 0
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cursor = self.cursor
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log.log(
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'Opening: {}\'s files'.format(self.dates[cursor]),
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'NCDFReader'
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)
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self.data = {}
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for fullname in self.files[self.dates[cursor]]:
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if os.path.splitext(fullname)[-1] == '.tgz':
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tar = tarfile.open(fullname, 'r:gz')
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tar.extractall('/tmp')
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files = [os.path.join('/tmp', member.name) for member in tar.getmembers()]
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else:
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files = [fullname]
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for filename in files:
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if self.filename is not None:
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self.fp.close()
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self.filename = filename
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self.filedate = self.dates[cursor]
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self.fp = Dataset(self.filename, 'r')
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self.parseFile()
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self.counter_records += 1
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self.cursor += 1
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return 1
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def readNextFile(self):
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while True:
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self.flagDiscontinuousBlock = 0
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if not self.setNextFile():
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return 0
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self.datatime = datetime.datetime.utcfromtimestamp(self.header['Time'])
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if (self.datatime < datetime.datetime.combine(self.startDate, self.startTime)) or \
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(self.datatime > datetime.datetime.combine(self.endDate, self.endTime)):
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log.warning(
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'Reading Record No. {}/{} -> {} [Skipping]'.format(
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self.counter_records,
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self.nrecords,
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self.datatime.ctime()),
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'NCDFReader')
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continue
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break
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log.log(
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'Reading Record No. {}/{} -> {}'.format(
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self.counter_records,
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self.nrecords,
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self.datatime.ctime()),
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'NCDFReader')
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return 1
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def set_output(self):
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'''
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Storing data from buffer to dataOut object
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'''
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self.dataOut.heightList = self.data.pop('Azimuth')
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log.log('Parameters found: {}'.format(','.join(self.data.keys())),
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'PXReader')
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self.dataOut.data_param = numpy.array(self.data.values())
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self.dataOut.data_param[self.dataOut.data_param == -99900.] = numpy.nan
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self.dataOut.parameters = self.data.keys()
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self.dataOut.utctime = self.header['Time']
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self.dataOut.utctimeInit = self.dataOut.utctime
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self.dataOut.useLocalTime = False
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self.dataOut.flagNoData = False
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self.dataOut.flagDiscontinuousBlock = self.flagDiscontinuousBlock
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def getData(self):
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'''
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Storing data from databuffer to dataOut object
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'''
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if self.flagNoMoreFiles:
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self.dataOut.flagNoData = True
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log.error('No file left to process', 'NCDFReader')
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return 0
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if not self.readNextFile():
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self.dataOut.flagNoData = True
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return 0
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self.set_output()
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return 1
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