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'''
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Created on Set 9, 2015
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@author: roj-idl71 Karim Kuyeng
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'''
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import os
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import sys
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import glob
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import fnmatch
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import datetime
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import time
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import re
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import h5py
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import numpy
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try:
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from gevent import sleep
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except:
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from time import sleep
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from schainpy.model.data.jroheaderIO import RadarControllerHeader, SystemHeader
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from schainpy.model.data.jrodata import Voltage
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from schainpy.model.proc.jroproc_base import ProcessingUnit, Operation, MPDecorator
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from numpy import imag
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class AMISRReader(ProcessingUnit):
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'''
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classdocs
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'''
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def __init__(self):
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'''
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Constructor
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'''
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ProcessingUnit.__init__(self)
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self.set = None
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self.subset = None
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self.extension_file = '.h5'
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self.dtc_str = 'dtc'
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self.dtc_id = 0
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self.status = True
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self.isConfig = False
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self.dirnameList = []
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self.filenameList = []
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self.fileIndex = None
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self.flagNoMoreFiles = False
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self.flagIsNewFile = 0
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self.filename = ''
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self.amisrFilePointer = None
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self.realBeamCode = []
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self.dataShape = None
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self.profileIndex = 0
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self.beamCodeByFrame = None
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self.radacTimeByFrame = None
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self.dataset = None
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self.__firstFile = True
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self.buffer = None
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self.timezone = 'ut'
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self.__waitForNewFile = 20
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self.__filename_online = None
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#Is really necessary create the output object in the initializer
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self.dataOut = Voltage()
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self.dataOut.error=False
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def setup(self,path=None,
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startDate=None,
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endDate=None,
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startTime=None,
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endTime=None,
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walk=True,
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timezone='ut',
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all=0,
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code = None,
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nCode = 0,
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nBaud = 0,
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online=False):
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self.timezone = timezone
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self.all = all
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self.online = online
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self.code = code
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self.nCode = int(nCode)
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self.nBaud = int(nBaud)
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#self.findFiles()
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if not(online):
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#Busqueda de archivos offline
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self.searchFilesOffLine(path, startDate, endDate, startTime, endTime, walk)
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else:
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self.searchFilesOnLine(path, startDate, endDate, startTime,endTime,walk)
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if not(self.filenameList):
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print("There is no files into the folder: %s"%(path))
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sys.exit(-1)
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self.fileIndex = 0
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self.readNextFile(online)
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'''
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Add code
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'''
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self.isConfig = True
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# print("Setup Done")
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pass
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def readAMISRHeader(self,fp):
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if self.isConfig :
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newShape = fp.get('Raw11/Data/Samples/Data').shape
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if self.dataShape != newShape:
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print("\nERROR, NEW FILE IS A DIFFERENT EXPERIMENT \n")
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return 0
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else:
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self.dataShape = fp.get('Raw11/Data/Samples/Data').shape
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header = 'Raw11/Data/RadacHeader'
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self.beamCodeByPulse = fp.get(header+'/BeamCode') # LIST OF BEAMS PER PROFILE, TO BE USED ON REARRANGE
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if (self.startDate> datetime.date(2021, 7, 15)): #Se cambió la forma de extracción de Apuntes el 17
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self.beamcodeFile = fp['Setup/Beamcodefile'][()].decode()
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self.trueBeams = self.beamcodeFile.split("\n")
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self.trueBeams.pop()#remove last
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[self.realBeamCode.append(x) for x in self.trueBeams if x not in self.realBeamCode]
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self.beamCode = [int(x, 16) for x in self.realBeamCode]
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else:
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_beamCode= fp.get('Raw11/Data/Beamcodes') #se usa la manera previa al cambio de apuntes
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self.beamCode = _beamCode[0,:]
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#self.code = fp.get(header+'/Code') # NOT USE FOR THIS
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self.frameCount = fp.get(header+'/FrameCount')# NOT USE FOR THIS
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self.modeGroup = fp.get(header+'/ModeGroup')# NOT USE FOR THIS
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self.nsamplesPulse = fp.get(header+'/NSamplesPulse')# TO GET NSA OR USING DATA FOR THAT
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self.pulseCount = fp.get(header+'/PulseCount')# NOT USE FOR THIS
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self.radacTime = fp.get(header+'/RadacTime')# 1st TIME ON FILE ANDE CALCULATE THE REST WITH IPP*nindexprofile
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self.timeCount = fp.get(header+'/TimeCount')# NOT USE FOR THIS
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self.timeStatus = fp.get(header+'/TimeStatus')# NOT USE FOR THIS
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self.rangeFromFile = fp.get('Raw11/Data/Samples/Range')
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self.frequency = fp.get('Rx/Frequency')
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txAus = fp.get('Raw11/Data/Pulsewidth')
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self.nblocks = self.pulseCount.shape[0] #nblocks
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self.nprofiles = self.pulseCount.shape[1] #nprofile
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self.nsa = self.nsamplesPulse[0,0] #ngates
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self.nchannels = len(self.beamCode)
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self.ippSeconds = (self.radacTime[0][1] -self.radacTime[0][0]) #Ipp in seconds
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#self.__waitForNewFile = self.nblocks # wait depending on the number of blocks since each block is 1 sec
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self.__waitForNewFile = self.nblocks * self.nprofiles * self.ippSeconds # wait until new file is created
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#filling radar controller header parameters
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self.__ippKm = self.ippSeconds *.15*1e6 # in km
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self.__txA = (txAus.value)*.15 #(ipp[us]*.15km/1us) in km
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self.__txB = 0
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nWindows=1
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self.__nSamples = self.nsa
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self.__firstHeight = self.rangeFromFile[0][0]/1000 #in km
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self.__deltaHeight = (self.rangeFromFile[0][1] - self.rangeFromFile[0][0])/1000
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#for now until understand why the code saved is different (code included even though code not in tuf file)
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#self.__codeType = 0
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# self.__nCode = None
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# self.__nBaud = None
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self.__code = self.code
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self.__codeType = 0
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if self.code != None:
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self.__codeType = 1
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self.__nCode = self.nCode
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self.__nBaud = self.nBaud
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#self.__code = 0
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#filling system header parameters
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self.__nSamples = self.nsa
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self.newProfiles = self.nprofiles/self.nchannels
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self.__channelList = list(range(self.nchannels))
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self.__frequency = self.frequency[0][0]
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return 1
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def createBuffers(self):
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pass
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def __setParameters(self,path='', startDate='',endDate='',startTime='', endTime='', walk=''):
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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.walk = walk
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def __checkPath(self):
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if os.path.exists(self.path):
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self.status = 1
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else:
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self.status = 0
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print('Path:%s does not exists'%self.path)
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return
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def __selDates(self, amisr_dirname_format):
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try:
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year = int(amisr_dirname_format[0:4])
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month = int(amisr_dirname_format[4:6])
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dom = int(amisr_dirname_format[6:8])
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thisDate = datetime.date(year,month,dom)
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if (thisDate>=self.startDate and thisDate <= self.endDate):
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return amisr_dirname_format
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except:
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return None
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def __findDataForDates(self,online=False):
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if not(self.status):
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return None
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pat = '\d+.\d+'
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dirnameList = [re.search(pat,x) for x in os.listdir(self.path)]
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dirnameList = [x for x in dirnameList if x!=None]
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dirnameList = [x.string for x in dirnameList]
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if not(online):
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dirnameList = [self.__selDates(x) for x in dirnameList]
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dirnameList = [x for x in dirnameList if x!=None]
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if len(dirnameList)>0:
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self.status = 1
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self.dirnameList = dirnameList
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self.dirnameList.sort()
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else:
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self.status = 0
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return None
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def __getTimeFromData(self):
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startDateTime_Reader = datetime.datetime.combine(self.startDate,self.startTime)
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endDateTime_Reader = datetime.datetime.combine(self.endDate,self.endTime)
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print('Filtering Files from %s to %s'%(startDateTime_Reader, endDateTime_Reader))
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print('........................................')
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filter_filenameList = []
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self.filenameList.sort()
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#for i in range(len(self.filenameList)-1):
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for i in range(len(self.filenameList)):
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filename = self.filenameList[i]
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fp = h5py.File(filename,'r')
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time_str = fp.get('Time/RadacTimeString')
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startDateTimeStr_File = time_str[0][0].decode('UTF-8').split('.')[0]
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#startDateTimeStr_File = "2019-12-16 09:21:11"
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junk = time.strptime(startDateTimeStr_File, '%Y-%m-%d %H:%M:%S')
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startDateTime_File = datetime.datetime(junk.tm_year,junk.tm_mon,junk.tm_mday,junk.tm_hour, junk.tm_min, junk.tm_sec)
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#endDateTimeStr_File = "2019-12-16 11:10:11"
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endDateTimeStr_File = time_str[-1][-1].decode('UTF-8').split('.')[0]
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junk = time.strptime(endDateTimeStr_File, '%Y-%m-%d %H:%M:%S')
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endDateTime_File = datetime.datetime(junk.tm_year,junk.tm_mon,junk.tm_mday,junk.tm_hour, junk.tm_min, junk.tm_sec)
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fp.close()
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#print("check time", startDateTime_File)
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if self.timezone == 'lt':
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startDateTime_File = startDateTime_File - datetime.timedelta(minutes = 300)
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endDateTime_File = endDateTime_File - datetime.timedelta(minutes = 300)
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if (endDateTime_File>=startDateTime_Reader and endDateTime_File<endDateTime_Reader):
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#self.filenameList.remove(filename)
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filter_filenameList.append(filename)
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if (endDateTime_File>=endDateTime_Reader):
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break
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filter_filenameList.sort()
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self.filenameList = filter_filenameList
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return 1
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def __filterByGlob1(self, dirName):
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filter_files = glob.glob1(dirName, '*.*%s'%self.extension_file)
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filter_files.sort()
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filterDict = {}
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filterDict.setdefault(dirName)
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filterDict[dirName] = filter_files
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return filterDict
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def __getFilenameList(self, fileListInKeys, dirList):
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for value in fileListInKeys:
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dirName = list(value.keys())[0]
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for file in value[dirName]:
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filename = os.path.join(dirName, file)
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self.filenameList.append(filename)
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def __selectDataForTimes(self, online=False):
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#aun no esta implementado el filtro for tiempo
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if not(self.status):
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return None
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dirList = [os.path.join(self.path,x) for x in self.dirnameList]
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fileListInKeys = [self.__filterByGlob1(x) for x in dirList]
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self.__getFilenameList(fileListInKeys, dirList)
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if not(online):
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#filtro por tiempo
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if not(self.all):
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self.__getTimeFromData()
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if len(self.filenameList)>0:
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self.status = 1
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self.filenameList.sort()
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else:
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self.status = 0
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return None
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else:
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#get the last file - 1
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self.filenameList = [self.filenameList[-2]]
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new_dirnameList = []
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for dirname in self.dirnameList:
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junk = numpy.array([dirname in x for x in self.filenameList])
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junk_sum = junk.sum()
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if junk_sum > 0:
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new_dirnameList.append(dirname)
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self.dirnameList = new_dirnameList
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return 1
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def searchFilesOnLine(self, path, startDate, endDate, startTime=datetime.time(0,0,0),
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endTime=datetime.time(23,59,59),walk=True):
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if endDate ==None:
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startDate = datetime.datetime.utcnow().date()
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endDate = datetime.datetime.utcnow().date()
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self.__setParameters(path=path, startDate=startDate, endDate=endDate,startTime = startTime,endTime=endTime, walk=walk)
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self.__checkPath()
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self.__findDataForDates(online=True)
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self.dirnameList = [self.dirnameList[-1]]
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self.__selectDataForTimes(online=True)
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return
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def searchFilesOffLine(self,
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path,
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startDate,
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endDate,
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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=True):
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self.__setParameters(path, startDate, endDate, startTime, endTime, walk)
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self.__checkPath()
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self.__findDataForDates()
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self.__selectDataForTimes()
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for i in range(len(self.filenameList)):
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print("%s" %(self.filenameList[i]))
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return
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def __setNextFileOffline(self):
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try:
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self.filename = self.filenameList[self.fileIndex]
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self.amisrFilePointer = h5py.File(self.filename,'r')
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self.fileIndex += 1
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except:
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self.flagNoMoreFiles = 1
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print("No more Files")
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return 0
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self.flagIsNewFile = 1
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print("Setting the file: %s"%self.filename)
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return 1
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def __setNextFileOnline(self):
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filename = self.filenameList[0]
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if self.__filename_online != None:
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self.__selectDataForTimes(online=True)
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filename = self.filenameList[0]
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wait = 0
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#self.__waitForNewFile=5 ## DEBUG:
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while self.__filename_online == filename:
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print('waiting %d seconds to get a new file...'%(self.__waitForNewFile))
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if wait == 5:
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self.flagNoMoreFiles = 1
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return 0
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sleep(self.__waitForNewFile)
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self.__selectDataForTimes(online=True)
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filename = self.filenameList[0]
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wait += 1
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self.__filename_online = filename
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self.amisrFilePointer = h5py.File(filename,'r')
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self.flagIsNewFile = 1
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self.filename = filename
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print("Setting the file: %s"%self.filename)
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return 1
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def readData(self):
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buffer = self.amisrFilePointer.get('Raw11/Data/Samples/Data')
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re = buffer[:,:,:,0]
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im = buffer[:,:,:,1]
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dataset = re + im*1j
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self.radacTime = self.amisrFilePointer.get('Raw11/Data/RadacHeader/RadacTime')
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timeset = self.radacTime[:,0]
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return dataset,timeset
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def reshapeData(self):
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#self.beamCodeByPulse, self.beamCode, self.nblocks, self.nprofiles, self.nsa,
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channels = self.beamCodeByPulse[0,:]
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nchan = self.nchannels
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#self.newProfiles = self.nprofiles/nchan #must be defined on filljroheader
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nblocks = self.nblocks
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nsamples = self.nsa
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#Dimensions : nChannels, nProfiles, nSamples
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new_block = numpy.empty((nblocks, nchan, numpy.int_(self.newProfiles), nsamples), dtype="complex64")
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############################################
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for thisChannel in range(nchan):
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new_block[:,thisChannel,:,:] = self.dataset[:,numpy.where(channels==self.beamCode[thisChannel])[0],:]
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new_block = numpy.transpose(new_block, (1,0,2,3))
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new_block = numpy.reshape(new_block, (nchan,-1, nsamples))
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return new_block
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|
def updateIndexes(self):
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|
pass
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def fillJROHeader(self):
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|
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#fill radar controller header
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self.dataOut.radarControllerHeaderObj = RadarControllerHeader(ipp=self.__ippKm,
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txA=self.__txA,
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txB=0,
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nWindows=1,
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|
nHeights=self.__nSamples,
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|
firstHeight=self.__firstHeight,
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|
deltaHeight=self.__deltaHeight,
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|
codeType=self.__codeType,
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|
nCode=self.__nCode, nBaud=self.__nBaud,
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code = self.__code,
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|
|
fClock=1)
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|
|
|
#fill system header
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|
|
self.dataOut.systemHeaderObj = SystemHeader(nSamples=self.__nSamples,
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|
nProfiles=self.newProfiles,
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|
|
nChannels=len(self.__channelList),
|
|
|
adcResolution=14,
|
|
|
pciDioBusWidth=32)
|
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|
|
|
|
self.dataOut.type = "Voltage"
|
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|
|
|
|
self.dataOut.data = None
|
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|
|
|
|
self.dataOut.dtype = numpy.dtype([('real','<i8'),('imag','<i8')])
|
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|
|
|
|
# self.dataOut.nChannels = 0
|
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|
|
|
|
# self.dataOut.nHeights = 0
|
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|
|
|
|
self.dataOut.nProfiles = self.newProfiles*self.nblocks
|
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|
|
|
|
#self.dataOut.heightList = self.__firstHeigth + numpy.arange(self.__nSamples, dtype = numpy.float)*self.__deltaHeigth
|
|
|
ranges = numpy.reshape(self.rangeFromFile.value,(-1))
|
|
|
self.dataOut.heightList = ranges/1000.0 #km
|
|
|
|
|
|
|
|
|
self.dataOut.channelList = self.__channelList
|
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|
|
|
|
self.dataOut.blocksize = self.dataOut.nChannels * self.dataOut.nHeights
|
|
|
|
|
|
# self.dataOut.channelIndexList = None
|
|
|
|
|
|
self.dataOut.flagNoData = True
|
|
|
|
|
|
#Set to TRUE if the data is discontinuous
|
|
|
self.dataOut.flagDiscontinuousBlock = False
|
|
|
|
|
|
self.dataOut.utctime = None
|
|
|
|
|
|
#self.dataOut.timeZone = -5 #self.__timezone/60 #timezone like jroheader, difference in minutes between UTC and localtime
|
|
|
if self.timezone == 'lt':
|
|
|
self.dataOut.timeZone = time.timezone / 60. #get the timezone in minutes
|
|
|
else:
|
|
|
self.dataOut.timeZone = 0 #by default time is UTC
|
|
|
|
|
|
self.dataOut.dstFlag = 0
|
|
|
|
|
|
self.dataOut.errorCount = 0
|
|
|
|
|
|
self.dataOut.nCohInt = 1
|
|
|
|
|
|
self.dataOut.flagDecodeData = False #asumo que la data esta decodificada
|
|
|
|
|
|
self.dataOut.flagDeflipData = False #asumo que la data esta sin flip
|
|
|
|
|
|
self.dataOut.flagShiftFFT = False
|
|
|
|
|
|
self.dataOut.ippSeconds = self.ippSeconds
|
|
|
|
|
|
#Time interval between profiles
|
|
|
#self.dataOut.timeInterval = self.dataOut.ippSeconds * self.dataOut.nCohInt
|
|
|
|
|
|
self.dataOut.frequency = self.__frequency
|
|
|
self.dataOut.realtime = self.online
|
|
|
pass
|
|
|
|
|
|
def readNextFile(self,online=False):
|
|
|
|
|
|
if not(online):
|
|
|
newFile = self.__setNextFileOffline()
|
|
|
else:
|
|
|
newFile = self.__setNextFileOnline()
|
|
|
|
|
|
if not(newFile):
|
|
|
self.dataOut.error = True
|
|
|
return 0
|
|
|
|
|
|
if not self.readAMISRHeader(self.amisrFilePointer):
|
|
|
self.dataOut.error = True
|
|
|
return 0
|
|
|
|
|
|
self.createBuffers()
|
|
|
self.fillJROHeader()
|
|
|
|
|
|
#self.__firstFile = False
|
|
|
|
|
|
|
|
|
|
|
|
self.dataset,self.timeset = self.readData()
|
|
|
|
|
|
if self.endDate!=None:
|
|
|
endDateTime_Reader = datetime.datetime.combine(self.endDate,self.endTime)
|
|
|
time_str = self.amisrFilePointer.get('Time/RadacTimeString')
|
|
|
startDateTimeStr_File = time_str[0][0].decode('UTF-8').split('.')[0]
|
|
|
junk = time.strptime(startDateTimeStr_File, '%Y-%m-%d %H:%M:%S')
|
|
|
startDateTime_File = datetime.datetime(junk.tm_year,junk.tm_mon,junk.tm_mday,junk.tm_hour, junk.tm_min, junk.tm_sec)
|
|
|
if self.timezone == 'lt':
|
|
|
startDateTime_File = startDateTime_File - datetime.timedelta(minutes = 300)
|
|
|
if (startDateTime_File>endDateTime_Reader):
|
|
|
return 0
|
|
|
|
|
|
self.jrodataset = self.reshapeData()
|
|
|
#----self.updateIndexes()
|
|
|
self.profileIndex = 0
|
|
|
|
|
|
return 1
|
|
|
|
|
|
|
|
|
def __hasNotDataInBuffer(self):
|
|
|
if self.profileIndex >= (self.newProfiles*self.nblocks):
|
|
|
return 1
|
|
|
return 0
|
|
|
|
|
|
|
|
|
def getData(self):
|
|
|
|
|
|
if self.flagNoMoreFiles:
|
|
|
self.dataOut.flagNoData = True
|
|
|
return 0
|
|
|
|
|
|
if self.__hasNotDataInBuffer():
|
|
|
if not (self.readNextFile(self.online)):
|
|
|
return 0
|
|
|
|
|
|
|
|
|
if self.dataset is None: # setear esta condicion cuando no hayan datos por leer
|
|
|
self.dataOut.flagNoData = True
|
|
|
return 0
|
|
|
|
|
|
#self.dataOut.data = numpy.reshape(self.jrodataset[self.profileIndex,:],(1,-1))
|
|
|
|
|
|
self.dataOut.data = self.jrodataset[:,self.profileIndex,:]
|
|
|
|
|
|
#print("R_t",self.timeset)
|
|
|
|
|
|
#self.dataOut.utctime = self.jrotimeset[self.profileIndex]
|
|
|
#verificar basic header de jro data y ver si es compatible con este valor
|
|
|
#self.dataOut.utctime = self.timeset + (self.profileIndex * self.ippSeconds * self.nchannels)
|
|
|
indexprof = numpy.mod(self.profileIndex, self.newProfiles)
|
|
|
indexblock = self.profileIndex/self.newProfiles
|
|
|
#print (indexblock, indexprof)
|
|
|
diffUTC = 1.8e4 #UTC diference from peru in seconds --Joab
|
|
|
diffUTC = 0
|
|
|
t_comp = (indexprof * self.ippSeconds * self.nchannels) + diffUTC #
|
|
|
|
|
|
#print("utc :",indexblock," __ ",t_comp)
|
|
|
#print(numpy.shape(self.timeset))
|
|
|
self.dataOut.utctime = self.timeset[numpy.int_(indexblock)] + t_comp
|
|
|
#self.dataOut.utctime = self.timeset[self.profileIndex] + t_comp
|
|
|
#print(self.dataOut.utctime)
|
|
|
self.dataOut.profileIndex = self.profileIndex
|
|
|
self.dataOut.flagNoData = False
|
|
|
# if indexprof == 0:
|
|
|
# print self.dataOut.utctime
|
|
|
|
|
|
self.profileIndex += 1
|
|
|
|
|
|
return self.dataOut.data
|
|
|
|
|
|
|
|
|
def run(self, **kwargs):
|
|
|
'''
|
|
|
This method will be called many times so here you should put all your code
|
|
|
'''
|
|
|
#print("running kamisr")
|
|
|
if not self.isConfig:
|
|
|
self.setup(**kwargs)
|
|
|
self.isConfig = True
|
|
|
|
|
|
self.getData()
|
|
|
|
