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Python 2to3, Spectra (all operations) working
Python 2to3, Spectra (all operations) working

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jroIO_amisr.py
691 lines | 24.1 KiB | text/x-python | PythonLexer
'''
@author: Daniel Suarez
'''
import os
import sys
import glob
import fnmatch
import datetime
import time
import re
import h5py
import numpy
from schainpy.model.proc.jroproc_base import ProcessingUnit, Operation
from schainpy.model.data.jroamisr import AMISR
try:
from gevent import sleep
except:
from time import sleep
class RadacHeader():
def __init__(self, fp):
header = 'Raw11/Data/RadacHeader'
self.beamCodeByPulse = fp.get(header+'/BeamCode')
self.beamCode = fp.get('Raw11/Data/Beamcodes')
self.code = fp.get(header+'/Code')
self.frameCount = fp.get(header+'/FrameCount')
self.modeGroup = fp.get(header+'/ModeGroup')
self.nsamplesPulse = fp.get(header+'/NSamplesPulse')
self.pulseCount = fp.get(header+'/PulseCount')
self.radacTime = fp.get(header+'/RadacTime')
self.timeCount = fp.get(header+'/TimeCount')
self.timeStatus = fp.get(header+'/TimeStatus')
self.nrecords = self.pulseCount.shape[0] #nblocks
self.npulses = self.pulseCount.shape[1] #nprofile
self.nsamples = self.nsamplesPulse[0,0] #ngates
self.nbeams = self.beamCode.shape[1]
def getIndexRangeToPulse(self, idrecord=0):
#indexToZero = numpy.where(self.pulseCount.value[idrecord,:]==0)
#startPulseCountId = indexToZero[0][0]
#endPulseCountId = startPulseCountId - 1
#range1 = numpy.arange(startPulseCountId,self.npulses,1)
#range2 = numpy.arange(0,startPulseCountId,1)
#return range1, range2
zero = 0
npulse = max(self.pulseCount[0,:]+1)-1
looking_index = numpy.where(self.pulseCount.value[idrecord,:]==npulse)[0]
getLastIndex = looking_index[-1]
index_data = numpy.arange(0,getLastIndex+1,1)
index_buffer = numpy.arange(getLastIndex+1,self.npulses,1)
return index_data, index_buffer
class AMISRReader(ProcessingUnit):
path = None
startDate = None
endDate = None
startTime = None
endTime = None
walk = None
isConfig = False
def __init__(self):
self.set = None
self.subset = None
self.extension_file = '.h5'
self.dtc_str = 'dtc'
self.dtc_id = 0
self.status = True
self.isConfig = False
self.dirnameList = []
self.filenameList = []
self.fileIndex = None
self.flagNoMoreFiles = False
self.flagIsNewFile = 0
self.filename = ''
self.amisrFilePointer = None
self.radacHeaderObj = None
self.dataOut = self.__createObjByDefault()
self.datablock = None
self.rest_datablock = None
self.range = None
self.idrecord_count = 0
self.profileIndex = 0
self.index_amisr_sample = None
self.index_amisr_buffer = None
self.beamCodeByFrame = None
self.radacTimeByFrame = None
#atributos originales tal y como esta en el archivo de datos
self.beamCodesFromFile = None
self.radacTimeFromFile = None
self.rangeFromFile = None
self.dataByFrame = None
self.dataset = None
self.beamCodeDict = {}
self.beamRangeDict = {}
#experiment cgf file
self.npulsesint_fromfile = None
self.recordsperfile_fromfile = None
self.nbeamcodes_fromfile = None
self.ngates_fromfile = None
self.ippSeconds_fromfile = None
self.frequency_h5file = None
self.__firstFile = True
self.buffer_radactime = None
self.index4_schain_datablock = None
self.index4_buffer = None
self.schain_datablock = None
self.buffer = None
self.linear_pulseCount = None
self.npulseByFrame = None
self.profileIndex_offset = None
self.timezone = 'ut'
self.__waitForNewFile = 20
self.__filename_online = None
def __createObjByDefault(self):
dataObj = AMISR()
return dataObj
def __setParameters(self,path='', startDate='',endDate='',startTime='', endTime='', walk=''):
self.path = path
self.startDate = startDate
self.endDate = endDate
self.startTime = startTime
self.endTime = endTime
self.walk = walk
def __checkPath(self):
if os.path.exists(self.path):
self.status = 1
else:
self.status = 0
print('Path:%s does not exists'%self.path)
return
def __selDates(self, amisr_dirname_format):
try:
year = int(amisr_dirname_format[0:4])
month = int(amisr_dirname_format[4:6])
dom = int(amisr_dirname_format[6:8])
thisDate = datetime.date(year,month,dom)
if (thisDate>=self.startDate and thisDate <= self.endDate):
return amisr_dirname_format
except:
return None
def __findDataForDates(self,online=False):
if not(self.status):
return None
pat = '\d+.\d+'
dirnameList = [re.search(pat,x) for x in os.listdir(self.path)]
dirnameList = [x for x in dirnameList if x!=None]
dirnameList = [x.string for x in dirnameList]
if not(online):
dirnameList = [self.__selDates(x) for x in dirnameList]
dirnameList = [x for x in dirnameList if x!=None]
if len(dirnameList)>0:
self.status = 1
self.dirnameList = dirnameList
self.dirnameList.sort()
else:
self.status = 0
return None
def __getTimeFromData(self):
startDateTime_Reader = datetime.datetime.combine(self.startDate,self.startTime)
endDateTime_Reader = datetime.datetime.combine(self.endDate,self.endTime)
print('Filtering Files from %s to %s'%(startDateTime_Reader, endDateTime_Reader))
print('........................................')
filter_filenameList = []
self.filenameList.sort()
for i in range(len(self.filenameList)-1):
filename = self.filenameList[i]
fp = h5py.File(filename,'r')
time_str = fp.get('Time/RadacTimeString')
startDateTimeStr_File = time_str[0][0].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)
endDateTimeStr_File = time_str[-1][-1].split('.')[0]
junk = time.strptime(endDateTimeStr_File, '%Y-%m-%d %H:%M:%S')
endDateTime_File = datetime.datetime(junk.tm_year,junk.tm_mon,junk.tm_mday,junk.tm_hour, junk.tm_min, junk.tm_sec)
fp.close()
if self.timezone == 'lt':
startDateTime_File = startDateTime_File - datetime.timedelta(minutes = 300)
endDateTime_File = endDateTime_File - datetime.timedelta(minutes = 300)
if (endDateTime_File>=startDateTime_Reader and endDateTime_File<endDateTime_Reader):
#self.filenameList.remove(filename)
filter_filenameList.append(filename)
filter_filenameList.sort()
self.filenameList = filter_filenameList
return 1
def __filterByGlob1(self, dirName):
filter_files = glob.glob1(dirName, '*.*%s'%self.extension_file)
filterDict = {}
filterDict.setdefault(dirName)
filterDict[dirName] = filter_files
return filterDict
def __getFilenameList(self, fileListInKeys, dirList):
for value in fileListInKeys:
dirName = list(value.keys())[0]
for file in value[dirName]:
filename = os.path.join(dirName, file)
self.filenameList.append(filename)
def __selectDataForTimes(self, online=False):
#aun no esta implementado el filtro for tiempo
if not(self.status):
return None
dirList = [os.path.join(self.path,x) for x in self.dirnameList]
fileListInKeys = [self.__filterByGlob1(x) for x in dirList]
self.__getFilenameList(fileListInKeys, dirList)
if not(online):
#filtro por tiempo
if not(self.all):
self.__getTimeFromData()
if len(self.filenameList)>0:
self.status = 1
self.filenameList.sort()
else:
self.status = 0
return None
else:
#get the last file - 1
self.filenameList = [self.filenameList[-2]]
new_dirnameList = []
for dirname in self.dirnameList:
junk = numpy.array([dirname in x for x in self.filenameList])
junk_sum = junk.sum()
if junk_sum > 0:
new_dirnameList.append(dirname)
self.dirnameList = new_dirnameList
return 1
def searchFilesOnLine(self,
path,
walk=True):
startDate = datetime.datetime.utcnow().date()
endDate = datetime.datetime.utcnow().date()
self.__setParameters(path=path, startDate=startDate, endDate=endDate, walk=walk)
self.__checkPath()
self.__findDataForDates(online=True)
self.dirnameList = [self.dirnameList[-1]]
self.__selectDataForTimes(online=True)
return
def searchFilesOffLine(self,
path,
startDate,
endDate,
startTime=datetime.time(0,0,0),
endTime=datetime.time(23,59,59),
walk=True):
self.__setParameters(path, startDate, endDate, startTime, endTime, walk)
self.__checkPath()
self.__findDataForDates()
self.__selectDataForTimes()
for i in range(len(self.filenameList)):
print("%s" %(self.filenameList[i]))
return
def __setNextFileOffline(self):
idFile = self.fileIndex
while (True):
idFile += 1
if not(idFile < len(self.filenameList)):
self.flagNoMoreFiles = 1
print("No more Files")
return 0
filename = self.filenameList[idFile]
amisrFilePointer = h5py.File(filename,'r')
break
self.flagIsNewFile = 1
self.fileIndex = idFile
self.filename = filename
self.amisrFilePointer = amisrFilePointer
print("Setting the file: %s"%self.filename)
return 1
def __setNextFileOnline(self):
filename = self.filenameList[0]
if self.__filename_online != None:
self.__selectDataForTimes(online=True)
filename = self.filenameList[0]
while self.__filename_online == filename:
print('waiting %d seconds to get a new file...'%(self.__waitForNewFile))
sleep(self.__waitForNewFile)
self.__selectDataForTimes(online=True)
filename = self.filenameList[0]
self.__filename_online = filename
self.amisrFilePointer = h5py.File(filename,'r')
self.flagIsNewFile = 1
self.filename = filename
print("Setting the file: %s"%self.filename)
return 1
def __readHeader(self):
self.radacHeaderObj = RadacHeader(self.amisrFilePointer)
#update values from experiment cfg file
if self.radacHeaderObj.nrecords == self.recordsperfile_fromfile:
self.radacHeaderObj.nrecords = self.recordsperfile_fromfile
self.radacHeaderObj.nbeams = self.nbeamcodes_fromfile
self.radacHeaderObj.npulses = self.npulsesint_fromfile
self.radacHeaderObj.nsamples = self.ngates_fromfile
#looking index list for data
start_index = self.radacHeaderObj.pulseCount[0,:][0]
end_index = self.radacHeaderObj.npulses
range4data = list(range(start_index, end_index))
self.index4_schain_datablock = numpy.array(range4data)
buffer_start_index = 0
buffer_end_index = self.radacHeaderObj.pulseCount[0,:][0]
range4buffer = list(range(buffer_start_index, buffer_end_index))
self.index4_buffer = numpy.array(range4buffer)
self.linear_pulseCount = numpy.array(range4data + range4buffer)
self.npulseByFrame = max(self.radacHeaderObj.pulseCount[0,:]+1)
#get tuning frequency
frequency_h5file_dataset = self.amisrFilePointer.get('Rx'+'/TuningFrequency')
self.frequency_h5file = frequency_h5file_dataset[0,0]
self.flagIsNewFile = 1
def __getBeamCode(self):
self.beamCodeDict = {}
self.beamRangeDict = {}
beamCodeMap = self.amisrFilePointer.get('Setup/BeamcodeMap')
for i in range(len(self.radacHeaderObj.beamCode[0,:])):
self.beamCodeDict.setdefault(i)
self.beamRangeDict.setdefault(i)
beamcodeValue = self.radacHeaderObj.beamCode[0,i]
beamcodeIndex = numpy.where(beamCodeMap[:,0] == beamcodeValue)[0][0]
x = beamCodeMap[beamcodeIndex][1]
y = beamCodeMap[beamcodeIndex][2]
z = beamCodeMap[beamcodeIndex][3]
self.beamCodeDict[i] = [beamcodeValue, x, y, z]
just4record0 = self.radacHeaderObj.beamCodeByPulse[0,:]
for i in range(len(list(self.beamCodeDict.values()))):
xx = numpy.where(just4record0==list(self.beamCodeDict.values())[i][0])
indexPulseByBeam = self.linear_pulseCount[xx[0]]
self.beamRangeDict[i] = indexPulseByBeam
def __getExpParameters(self):
if not(self.status):
return None
experimentCfgPath = os.path.join(self.path, self.dirnameList[0], 'Setup')
expFinder = glob.glob1(experimentCfgPath,'*.exp')
if len(expFinder)== 0:
self.status = 0
return None
experimentFilename = os.path.join(experimentCfgPath,expFinder[0])
f = open(experimentFilename)
lines = f.readlines()
f.close()
parmsList = ['npulsesint*','recordsperfile*','nbeamcodes*','ngates*']
filterList = [fnmatch.filter(lines, x) for x in parmsList]
values = [re.sub(r'\D',"",x[0]) for x in filterList]
self.npulsesint_fromfile = int(values[0])
self.recordsperfile_fromfile = int(values[1])
self.nbeamcodes_fromfile = int(values[2])
self.ngates_fromfile = int(values[3])
tufileFinder = fnmatch.filter(lines, 'tufile=*')
tufile = tufileFinder[0].split('=')[1].split('\n')[0]
tufile = tufile.split('\r')[0]
tufilename = os.path.join(experimentCfgPath,tufile)
f = open(tufilename)
lines = f.readlines()
f.close()
self.ippSeconds_fromfile = float(lines[1].split()[2])/1E6
self.status = 1
def __setIdsAndArrays(self):
self.dataByFrame = self.__setDataByFrame()
self.beamCodeByFrame = self.amisrFilePointer.get('Raw11/Data/RadacHeader/BeamCode').value[0, :]
self.readRanges()
self.index_amisr_sample, self.index_amisr_buffer = self.radacHeaderObj.getIndexRangeToPulse(0)
self.radacTimeByFrame = numpy.zeros(self.radacHeaderObj.npulses)
if len(self.index_amisr_buffer) > 0:
self.buffer_radactime = numpy.zeros_like(self.radacTimeByFrame)
def __setNextFile(self,online=False):
if not(online):
newFile = self.__setNextFileOffline()
else:
newFile = self.__setNextFileOnline()
if not(newFile):
return 0
self.__readHeader()
if self.__firstFile:
self.__setIdsAndArrays()
self.__firstFile = False
self.__getBeamCode()
self.readDataBlock()
def setup(self,path=None,
startDate=None,
endDate=None,
startTime=datetime.time(0,0,0),
endTime=datetime.time(23,59,59),
walk=True,
timezone='ut',
all=0,
online=False):
self.timezone = timezone
self.all = all
self.online = online
if not(online):
#Busqueda de archivos offline
self.searchFilesOffLine(path, startDate, endDate, startTime, endTime, walk)
else:
self.searchFilesOnLine(path, walk)
if not(self.filenameList):
print("There is no files into the folder: %s"%(path))
sys.exit(-1)
self.__getExpParameters()
self.fileIndex = -1
self.__setNextFile(online)
# first_beamcode = self.radacHeaderObj.beamCodeByPulse[0,0]
# index = numpy.where(self.radacHeaderObj.beamCodeByPulse[0,:]!=first_beamcode)[0][0]
self.profileIndex_offset = self.radacHeaderObj.pulseCount[0,:][0]
self.profileIndex = self.profileIndex_offset
def readRanges(self):
dataset = self.amisrFilePointer.get('Raw11/Data/Samples/Range')
self.rangeFromFile = numpy.reshape(dataset.value,(-1))
return self.rangeFromFile
def readRadacTime(self,idrecord, range1, range2):
self.radacTimeFromFile = self.radacHeaderObj.radacTime.value
radacTimeByFrame = numpy.zeros((self.radacHeaderObj.npulses))
#radacTimeByFrame = dataset[idrecord - 1,range1]
#radacTimeByFrame = dataset[idrecord,range2]
return radacTimeByFrame
def readBeamCode(self, idrecord, range1, range2):
dataset = self.amisrFilePointer.get('Raw11/Data/RadacHeader/BeamCode')
beamcodeByFrame = numpy.zeros((self.radacHeaderObj.npulses))
self.beamCodesFromFile = dataset.value
#beamcodeByFrame[range1] = dataset[idrecord - 1, range1]
#beamcodeByFrame[range2] = dataset[idrecord, range2]
beamcodeByFrame[range1] = dataset[idrecord, range1]
beamcodeByFrame[range2] = dataset[idrecord, range2]
return beamcodeByFrame
def __setDataByFrame(self):
ndata = 2 # porque es complejo
dataByFrame = numpy.zeros((self.radacHeaderObj.npulses, self.radacHeaderObj.nsamples, ndata))
return dataByFrame
def __readDataSet(self):
dataset = self.amisrFilePointer.get('Raw11/Data/Samples/Data')
return dataset
def __setDataBlock(self,):
real = self.dataByFrame[:,:,0] #asumo que 0 es real
imag = self.dataByFrame[:,:,1] #asumo que 1 es imaginario
datablock = real + imag*1j #armo el complejo
return datablock
def readSamples_version1(self,idrecord):
#estas tres primeras lineas solo se deben ejecutar una vez
if self.flagIsNewFile:
#reading dataset
self.dataset = self.__readDataSet()
self.flagIsNewFile = 0
if idrecord == 0:
self.dataByFrame[self.index4_schain_datablock, : ,:] = self.dataset[0, self.index_amisr_sample,:,:]
self.radacTimeByFrame[self.index4_schain_datablock] = self.radacHeaderObj.radacTime[0, self.index_amisr_sample]
datablock = self.__setDataBlock()
if len(self.index_amisr_buffer) > 0:
self.buffer = self.dataset[0, self.index_amisr_buffer,:,:]
self.buffer_radactime = self.radacHeaderObj.radacTime[0, self.index_amisr_buffer]
return datablock
if len(self.index_amisr_buffer) > 0:
self.dataByFrame[self.index4_buffer,:,:] = self.buffer.copy()
self.radacTimeByFrame[self.index4_buffer] = self.buffer_radactime.copy()
self.dataByFrame[self.index4_schain_datablock,:,:] = self.dataset[idrecord, self.index_amisr_sample,:,:]
self.radacTimeByFrame[self.index4_schain_datablock] = self.radacHeaderObj.radacTime[idrecord, self.index_amisr_sample]
datablock = self.__setDataBlock()
if len(self.index_amisr_buffer) > 0:
self.buffer = self.dataset[idrecord, self.index_amisr_buffer, :, :]
self.buffer_radactime = self.radacHeaderObj.radacTime[idrecord, self.index_amisr_buffer]
return datablock
def readSamples(self,idrecord):
if self.flagIsNewFile:
self.dataByFrame = self.__setDataByFrame()
self.beamCodeByFrame = self.amisrFilePointer.get('Raw11/Data/RadacHeader/BeamCode').value[idrecord, :]
#reading ranges
self.readRanges()
#reading dataset
self.dataset = self.__readDataSet()
self.flagIsNewFile = 0
self.radacTimeByFrame = self.radacHeaderObj.radacTime.value[idrecord, :]
self.dataByFrame = self.dataset[idrecord, :, :, :]
datablock = self.__setDataBlock()
return datablock
def readDataBlock(self):
self.datablock = self.readSamples_version1(self.idrecord_count)
#self.datablock = self.readSamples(self.idrecord_count)
#print 'record:', self.idrecord_count
self.idrecord_count += 1
self.profileIndex = 0
if self.idrecord_count >= self.radacHeaderObj.nrecords:
self.idrecord_count = 0
self.flagIsNewFile = 1
def readNextBlock(self):
self.readDataBlock()
if self.flagIsNewFile:
self.__setNextFile(self.online)
pass
def __hasNotDataInBuffer(self):
#self.radacHeaderObj.npulses debe ser otra variable para considerar el numero de pulsos a tomar en el primer y ultimo record
if self.profileIndex >= self.radacHeaderObj.npulses:
return 1
return 0
def printUTC(self):
print(self.dataOut.utctime)
print('')
def setObjProperties(self):
self.dataOut.heightList = self.rangeFromFile/1000.0 #km
self.dataOut.nProfiles = self.radacHeaderObj.npulses
self.dataOut.nRecords = self.radacHeaderObj.nrecords
self.dataOut.nBeams = self.radacHeaderObj.nbeams
self.dataOut.ippSeconds = self.ippSeconds_fromfile
# self.dataOut.timeInterval = self.dataOut.ippSeconds * self.dataOut.nCohInt
self.dataOut.frequency = self.frequency_h5file
self.dataOut.npulseByFrame = self.npulseByFrame
self.dataOut.nBaud = None
self.dataOut.nCode = None
self.dataOut.code = None
self.dataOut.beamCodeDict = self.beamCodeDict
self.dataOut.beamRangeDict = self.beamRangeDict
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
def getData(self):
if self.flagNoMoreFiles:
self.dataOut.flagNoData = True
print('Process finished')
return 0
if self.__hasNotDataInBuffer():
self.readNextBlock()
if self.datablock is None: # setear esta condicion cuando no hayan datos por leers
self.dataOut.flagNoData = True
return 0
self.dataOut.data = numpy.reshape(self.datablock[self.profileIndex,:],(1,-1))
self.dataOut.utctime = self.radacTimeByFrame[self.profileIndex]
self.dataOut.profileIndex = self.profileIndex
self.dataOut.flagNoData = False
self.profileIndex += 1
return self.dataOut.data
def run(self, **kwargs):
if not(self.isConfig):
self.setup(**kwargs)
self.setObjProperties()
self.isConfig = True
self.getData()