jroIO_HDF5.py
1005 lines
| 30.0 KiB
| text/x-python
|
PythonLexer
Julio Valdez
|
r514 | import numpy | ||
| import time | ||||
| import os | ||||
| import h5py | ||||
| import re | ||||
|
Julio Valdez
|
r608 | import tables | ||
|
Julio Valdez
|
r514 | |||
Miguel Valdez
|
r568 | from schainpy.model.data.jrodata import * | ||
| from schainpy.model.proc.jroproc_base import ProcessingUnit, Operation | ||||
| from schainpy.model.io.jroIO_base import * | ||||
|
Julio Valdez
|
r514 | |||
| class HDF5Reader(ProcessingUnit): | ||||
| ext = ".hdf5" | ||||
| optchar = "D" | ||||
| timezone = None | ||||
|
Julio Valdez
|
r543 | secStart = None | ||
| secEnd = None | ||||
|
Julio Valdez
|
r514 | fileIndex = None | ||
| blockIndex = None | ||||
|
Julio Valdez
|
r543 | blocksPerFile = None | ||
|
Julio Valdez
|
r514 | path = None | ||
|
Julio Valdez
|
r543 | #List of Files | ||
| filenameList = None | ||||
| datetimeList = None | ||||
|
Julio Valdez
|
r514 | #Hdf5 File | ||
| fpMetadata = None | ||||
|
Julio Valdez
|
r543 | pathMeta = None | ||
|
Julio Valdez
|
r514 | listMetaname = None | ||
|
Julio Valdez
|
r543 | listMeta = None | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | listDataname = None | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | listData = None | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | listShapes = None | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | fp = None | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | #dataOut reconstruction | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | dataOut = None | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | nRecords = None | ||
|
Julio Valdez
|
r514 | |||
| def __init__(self): | ||||
|
Julio Valdez
|
r543 | self.dataOut = self.__createObjByDefault() | ||
|
Julio Valdez
|
r514 | return | ||
|
Julio Valdez
|
r543 | |||
| def __createObjByDefault(self): | ||||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | dataObj = Parameters() | ||
| return dataObj | ||||
|
Julio Valdez
|
r514 | 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, | ||||
| ext=None): | ||||
| if ext==None: | ||||
| ext = self.ext | ||||
| self.timezone = timezone | ||||
| # self.all = all | ||||
| # self.online = online | ||||
| self.path = path | ||||
|
Julio Valdez
|
r543 | |||
| startDateTime = datetime.datetime.combine(startDate,startTime) | ||||
| endDateTime = datetime.datetime.combine(endDate,endTime) | ||||
| secStart = (startDateTime-datetime.datetime(1970,1,1)).total_seconds() | ||||
| secEnd = (endDateTime-datetime.datetime(1970,1,1)).total_seconds() | ||||
| self.secStart = secStart | ||||
| self.secEnd = secEnd | ||||
|
Julio Valdez
|
r514 | |||
| if not(online): | ||||
| #Busqueda de archivos offline | ||||
|
Julio Valdez
|
r543 | self.__searchFilesOffline(path, startDate, endDate, ext, startTime, endTime, secStart, secEnd, walk) | ||
|
Julio Valdez
|
r514 | 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.__setNextFileOffline() | ||||
| self.__readMetadata() | ||||
| self.blockIndex = 0 | ||||
| return | ||||
| def __searchFilesOffline(self, | ||||
| path, | ||||
| startDate, | ||||
| endDate, | ||||
| ext, | ||||
| startTime=datetime.time(0,0,0), | ||||
| endTime=datetime.time(23,59,59), | ||||
|
Julio Valdez
|
r543 | secStart = 0, | ||
| secEnd = numpy.inf, | ||||
|
Julio Valdez
|
r514 | 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]) | ||||
| pathList = [] | ||||
| if not walk: | ||||
| #pathList.append(path) | ||||
| multi_path = path.split(',') | ||||
| for single_path in multi_path: | ||||
| pathList.append(single_path) | ||||
| else: | ||||
| #dirList = [] | ||||
| multi_path = path.split(',') | ||||
| for single_path in multi_path: | ||||
| dirList = [] | ||||
| for thisPath in os.listdir(single_path): | ||||
| if not os.path.isdir(os.path.join(single_path,thisPath)): | ||||
| continue | ||||
|
Julio Valdez
|
r608 | if not isDoyFolder(thisPath): | ||
|
Julio Valdez
|
r514 | continue | ||
| dirList.append(thisPath) | ||||
| if not(dirList): | ||||
| return None, None | ||||
| thisDate = startDate | ||||
| while(thisDate <= endDate): | ||||
| year = thisDate.timetuple().tm_year | ||||
| doy = thisDate.timetuple().tm_yday | ||||
| matchlist = fnmatch.filter(dirList, '?' + '%4.4d%3.3d' % (year,doy) + '*') | ||||
| if len(matchlist) == 0: | ||||
| thisDate += datetime.timedelta(1) | ||||
| continue | ||||
| for match in matchlist: | ||||
| pathList.append(os.path.join(single_path,match)) | ||||
| thisDate += datetime.timedelta(1) | ||||
| if pathList == []: | ||||
| print "Any folder was found for the date range: %s-%s" %(startDate, endDate) | ||||
| return None, None | ||||
| print "%d folder(s) was(were) found for the date range: %s - %s" %(len(pathList), startDate, endDate) | ||||
| filenameList = [] | ||||
| datetimeList = [] | ||||
| pathDict = {} | ||||
| filenameList_to_sort = [] | ||||
| for i in range(len(pathList)): | ||||
| thisPath = pathList[i] | ||||
| fileList = glob.glob1(thisPath, "*%s" %ext) | ||||
| fileList.sort() | ||||
| pathDict.setdefault(fileList[0]) | ||||
| pathDict[fileList[0]] = i | ||||
| filenameList_to_sort.append(fileList[0]) | ||||
| filenameList_to_sort.sort() | ||||
| for file in filenameList_to_sort: | ||||
| thisPath = pathList[pathDict[file]] | ||||
| fileList = glob.glob1(thisPath, "*%s" %ext) | ||||
| fileList.sort() | ||||
| for file in fileList: | ||||
| filename = os.path.join(thisPath,file) | ||||
|
Julio Valdez
|
r543 | thisDatetime = self.__isFileinThisTime(filename, secStart, secEnd) | ||
|
Julio Valdez
|
r514 | |||
| if not(thisDatetime): | ||||
| continue | ||||
| filenameList.append(filename) | ||||
| datetimeList.append(thisDatetime) | ||||
| if not(filenameList): | ||||
| print "Any file was found for the time range %s - %s" %(startTime, endTime) | ||||
| return None, None | ||||
| print "%d file(s) was(were) found for the time range: %s - %s" %(len(filenameList), startTime, endTime) | ||||
| for i in range(len(filenameList)): | ||||
| print "%s -> [%s]" %(filenameList[i], datetimeList[i].ctime()) | ||||
| self.filenameList = filenameList | ||||
| self.datetimeList = datetimeList | ||||
| return pathList, filenameList | ||||
|
Julio Valdez
|
r543 | def __isFileinThisTime(self, filename, startSeconds, endSeconds): | ||
|
Julio Valdez
|
r514 | """ | ||
| Retorna 1 si el archivo de datos se encuentra dentro del rango de horas especificado. | ||||
| Inputs: | ||||
| filename : nombre completo del archivo de datos en formato Jicamarca (.r) | ||||
| startTime : tiempo inicial del rango seleccionado en formato datetime.time | ||||
| endTime : tiempo final del rango seleccionado en formato datetime.time | ||||
| Return: | ||||
| Boolean : Retorna True si el archivo de datos contiene datos en el rango de | ||||
| fecha especificado, de lo contrario retorna False. | ||||
| Excepciones: | ||||
| Si el archivo no existe o no puede ser abierto | ||||
| Si la cabecera no puede ser leida. | ||||
| """ | ||||
|
Julio Valdez
|
r543 | |||
|
Julio Valdez
|
r514 | try: | ||
| fp = fp = h5py.File(filename,'r') | ||||
| except IOError: | ||||
| traceback.print_exc() | ||||
| raise IOError, "The file %s can't be opened" %(filename) | ||||
| grp = fp['Data'] | ||||
|
Julio Valdez
|
r543 | timeAux = grp['time'] | ||
| time0 = timeAux[:][0].astype(numpy.float) #Time Vector | ||||
|
Julio Valdez
|
r514 | |||
| fp.close() | ||||
| if self.timezone == 'lt': | ||||
|
Julio Valdez
|
r543 | time0 -= 5*3600 | ||
| boolTimer = numpy.logical_and(time0 >= startSeconds,time0 < endSeconds) | ||||
| if not (numpy.any(boolTimer)): | ||||
|
Julio Valdez
|
r514 | return None | ||
|
Julio Valdez
|
r543 | thisDatetime = datetime.datetime.utcfromtimestamp(time0[0]) | ||
|
Julio Valdez
|
r514 | return thisDatetime | ||
| 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 __setNextFileOffline(self): | ||||
| idFile = self.fileIndex | ||||
| idFile += 1 | ||||
| if not(idFile < len(self.filenameList)): | ||||
| print "No more Files" | ||||
| return 0 | ||||
| filename = self.filenameList[idFile] | ||||
| filePointer = h5py.File(filename,'r') | ||||
| self.flagIsNewFile = 1 | ||||
| self.fileIndex = idFile | ||||
| self.filename = filename | ||||
| self.fp = filePointer | ||||
| print "Setting the file: %s"%self.filename | ||||
| self.__readMetadata() | ||||
|
Julio Valdez
|
r543 | self.__setBlockList() | ||
| # self.nRecords = self.fp['Data'].attrs['blocksPerFile'] | ||||
| self.nRecords = self.fp['Data'].attrs['nRecords'] | ||||
| self.blockIndex = 0 | ||||
|
Julio Valdez
|
r514 | return 1 | ||
|
Julio Valdez
|
r543 | def __setBlockList(self): | ||
| ''' | ||||
| self.fp | ||||
| self.startDateTime | ||||
| self.endDateTime | ||||
| self.blockList | ||||
| self.blocksPerFile | ||||
| ''' | ||||
| filePointer = self.fp | ||||
| secStart = self.secStart | ||||
| secEnd = self.secEnd | ||||
| grp = filePointer['Data'] | ||||
| timeVector = grp['time'].value.astype(numpy.float)[0] | ||||
| if self.timezone == 'lt': | ||||
| timeVector -= 5*3600 | ||||
| ind = numpy.where(numpy.logical_and(timeVector >= secStart , timeVector < secEnd))[0] | ||||
| self.blockList = ind | ||||
| self.blocksPerFile = len(ind) | ||||
| return | ||||
|
Julio Valdez
|
r514 | def __readMetadata(self): | ||
|
Julio Valdez
|
r543 | ''' | ||
| self.pathMeta | ||||
| self.listShapes | ||||
| self.listMetaname | ||||
| self.listMeta | ||||
| ''' | ||||
|
Julio Valdez
|
r514 | grp = self.fp['Data'] | ||
|
Julio Valdez
|
r543 | pathMeta = os.path.join(self.path, grp.attrs['metadata']) | ||
| if pathMeta == self.pathMeta: | ||||
| return | ||||
| else: | ||||
| self.pathMeta = pathMeta | ||||
|
Julio Valdez
|
r514 | filePointer = h5py.File(self.pathMeta,'r') | ||
| groupPointer = filePointer['Metadata'] | ||||
| listMetaname = [] | ||||
| listMetadata = [] | ||||
| for item in groupPointer.items(): | ||||
| name = item[0] | ||||
|
Julio Valdez
|
r543 | if name=='array dimensions': | ||
| table = groupPointer[name][:] | ||||
| listShapes = {} | ||||
| for shapes in table: | ||||
| listShapes[shapes[0]] = numpy.array([shapes[1],shapes[2],shapes[3],shapes[4]]) | ||||
|
Julio Valdez
|
r514 | else: | ||
|
Julio Valdez
|
r543 | data = groupPointer[name].value | ||
|
Julio Valdez
|
r514 | listMetaname.append(name) | ||
| listMetadata.append(data) | ||||
| if name=='type': | ||||
|
Julio Valdez
|
r543 | self.__initDataOut(data) | ||
|
Julio Valdez
|
r514 | |||
| filePointer.close() | ||||
|
Julio Valdez
|
r543 | self.listShapes = listShapes | ||
| self.listMetaname = listMetaname | ||||
| self.listMeta = listMetadata | ||||
|
Julio Valdez
|
r514 | |||
| return | ||||
|
Julio Valdez
|
r543 | def __readData(self): | ||
| grp = self.fp['Data'] | ||||
| listdataname = [] | ||||
| listdata = [] | ||||
| for item in grp.items(): | ||||
| name = item[0] | ||||
| if name == 'time': | ||||
| listdataname.append('utctime') | ||||
| timeAux = grp[name].value.astype(numpy.float)[0] | ||||
| listdata.append(timeAux) | ||||
| continue | ||||
| listdataname.append(name) | ||||
| array = self.__setDataArray(self.nRecords, grp[name],self.listShapes[name]) | ||||
| listdata.append(array) | ||||
| self.listDataname = listdataname | ||||
| self.listData = listdata | ||||
| return | ||||
| def __setDataArray(self, nRecords, dataset, shapes): | ||||
| nChannels = shapes[0] #Dimension 0 | ||||
| nPoints = shapes[1] #Dimension 1, number of Points or Parameters | ||||
| nSamples = shapes[2] #Dimension 2, number of samples or ranges | ||||
| mode = shapes[3] | ||||
| # if nPoints>1: | ||||
| # arrayData = numpy.zeros((nRecords,nChannels,nPoints,nSamples)) | ||||
| # else: | ||||
| # arrayData = numpy.zeros((nRecords,nChannels,nSamples)) | ||||
| # | ||||
| # chn = 'channel' | ||||
| # | ||||
| # for i in range(nChannels): | ||||
| # | ||||
| # data = dataset[chn + str(i)].value | ||||
| # | ||||
| # if nPoints>1: | ||||
| # data = numpy.rollaxis(data,2) | ||||
| # | ||||
| # arrayData[:,i,:] = data | ||||
| arrayData = numpy.zeros((nRecords,nChannels,nPoints,nSamples)) | ||||
| doSqueeze = False | ||||
| if mode == 0: | ||||
| strds = 'channel' | ||||
| nDatas = nChannels | ||||
| newShapes = (nRecords,nPoints,nSamples) | ||||
| if nPoints == 1: | ||||
| doSqueeze = True | ||||
| axisSqueeze = 2 | ||||
| else: | ||||
| strds = 'param' | ||||
| nDatas = nPoints | ||||
| newShapes = (nRecords,nChannels,nSamples) | ||||
| if nChannels == 1: | ||||
| doSqueeze = True | ||||
| axisSqueeze = 1 | ||||
| for i in range(nDatas): | ||||
| data = dataset[strds + str(i)].value | ||||
| data = data.reshape(newShapes) | ||||
| if mode == 0: | ||||
| arrayData[:,i,:,:] = data | ||||
| else: | ||||
| arrayData[:,:,i,:] = data | ||||
| if doSqueeze: | ||||
| arrayData = numpy.squeeze(arrayData, axis=axisSqueeze) | ||||
| return arrayData | ||||
|
Julio Valdez
|
r514 | def __initDataOut(self, type): | ||
|
Julio Valdez
|
r543 | # if type =='Parameters': | ||
| # self.dataOut = Parameters() | ||||
| # elif type =='Spectra': | ||||
| # self.dataOut = Spectra() | ||||
| # elif type =='Voltage': | ||||
| # self.dataOut = Voltage() | ||||
| # elif type =='Correlation': | ||||
| # self.dataOut = Correlation() | ||||
|
Julio Valdez
|
r514 | |||
| return | ||||
| def __setDataOut(self): | ||||
|
Julio Valdez
|
r543 | listMeta = self.listMeta | ||
|
Julio Valdez
|
r514 | listMetaname = self.listMetaname | ||
| listDataname = self.listDataname | ||||
| listData = self.listData | ||||
| blockIndex = self.blockIndex | ||||
|
Julio Valdez
|
r543 | blockList = self.blockList | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | for i in range(len(listMeta)): | ||
| setattr(self.dataOut,listMetaname[i],listMeta[i]) | ||||
|
Julio Valdez
|
r514 | |||
| for j in range(len(listData)): | ||||
|
Julio Valdez
|
r543 | if listDataname[j]=='utctime': | ||
| # setattr(self.dataOut,listDataname[j],listData[j][blockList[blockIndex]]) | ||||
| setattr(self.dataOut,'utctimeInit',listData[j][blockList[blockIndex]]) | ||||
| continue | ||||
| setattr(self.dataOut,listDataname[j],listData[j][blockList[blockIndex],:]) | ||||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | return self.dataOut.data_param | ||
|
Julio Valdez
|
r514 | |||
| def getData(self): | ||||
|
Julio Valdez
|
r543 | # if self.flagNoMoreFiles: | ||
| # self.dataOut.flagNoData = True | ||||
| # print 'Process finished' | ||||
| # return 0 | ||||
| # | ||||
| if self.blockIndex==self.blocksPerFile: | ||||
| if not( self.__setNextFileOffline() ): | ||||
| self.dataOut.flagNoData = True | ||||
| return 0 | ||||
| # | ||||
| # if self.datablock == None: # setear esta condicion cuando no hayan datos por leers | ||||
| # self.dataOut.flagNoData = True | ||||
| # return 0 | ||||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | self.__readData() | ||
|
Julio Valdez
|
r514 | self.__setDataOut() | ||
| self.dataOut.flagNoData = False | ||||
| self.blockIndex += 1 | ||||
|
Julio Valdez
|
r543 | return | ||
|
Julio Valdez
|
r514 | |||
| def run(self, **kwargs): | ||||
| if not(self.isConfig): | ||||
| self.setup(**kwargs) | ||||
|
Julio Valdez
|
r543 | # self.setObjProperties() | ||
|
Julio Valdez
|
r514 | self.isConfig = True | ||
| self.getData() | ||||
| return | ||||
| class HDF5Writer(Operation): | ||||
| ext = ".hdf5" | ||||
| optchar = "D" | ||||
| metaoptchar = "M" | ||||
| metaFile = None | ||||
|
Julio Valdez
|
r608 | filename = None | ||
|
Julio Valdez
|
r514 | path = None | ||
| setFile = None | ||||
| fp = None | ||||
| grp = None | ||||
| ds = None | ||||
| firsttime = True | ||||
| #Configurations | ||||
| blocksPerFile = None | ||||
| blockIndex = None | ||||
| dataOut = None | ||||
| #Data Arrays | ||||
| dataList = None | ||||
| metadataList = None | ||||
|
Julio Valdez
|
r543 | arrayDim = None | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r515 | tableDim = None | ||
|
Julio Valdez
|
r543 | # dtype = [('arrayName', 'S20'),('nChannels', 'i'), ('nPoints', 'i'), ('nSamples', 'i'),('mode', 'b')] | ||
| dtype = [('arrayName', 'S20'),('nDimensions', 'i'), ('dim2', 'i'), ('dim1', 'i'),('dim0', 'i'),('mode', 'b')] | ||||
| mode = None | ||||
| nDatas = None #Number of datasets to be stored per array | ||||
|
Julio Valdez
|
r608 | |||
|
Julio Valdez
|
r543 | nDims = None #Number Dimensions in each dataset | ||
|
Julio Valdez
|
r515 | |||
|
Julio Valdez
|
r608 | nDimsForDs = None | ||
|
Julio Valdez
|
r514 | def __init__(self): | ||
| Operation.__init__(self) | ||||
| self.isConfig = False | ||||
| return | ||||
| def setup(self, dataOut, **kwargs): | ||||
| self.path = kwargs['path'] | ||||
| if kwargs.has_key('ext'): | ||||
| self.ext = kwargs['ext'] | ||||
|
Julio Valdez
|
r543 | |||
|
Julio Valdez
|
r514 | if kwargs.has_key('blocksPerFile'): | ||
| self.blocksPerFile = kwargs['blocksPerFile'] | ||||
| else: | ||||
| self.blocksPerFile = 10 | ||||
|
Julio Valdez
|
r543 | self.metadataList = kwargs['metadataList'] | ||
| self.dataList = kwargs['dataList'] | ||||
|
Julio Valdez
|
r514 | self.dataOut = dataOut | ||
|
Julio Valdez
|
r543 | if kwargs.has_key('mode'): | ||
| mode = kwargs['mode'] | ||||
| if type(mode) == int: | ||||
| mode = numpy.zeros(len(self.dataList)) + mode | ||||
| else: | ||||
| mode = numpy.zeros(len(self.dataList)) | ||||
| self.mode = mode | ||||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | arrayDim = numpy.zeros((len(self.dataList),5)) | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | #Table dimensions | ||
|
Julio Valdez
|
r515 | |||
| dtype0 = self.dtype | ||||
| tableList = [] | ||||
|
Julio Valdez
|
r514 | for i in range(len(self.dataList)): | ||
|
Julio Valdez
|
r543 | dataAux = getattr(self.dataOut, self.dataList[i]) | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | if type(dataAux)==float or type(dataAux)==int: | ||
| arrayDim[i,0] = 1 | ||||
|
Julio Valdez
|
r514 | else: | ||
|
Julio Valdez
|
r543 | arrayDim0 = dataAux.shape | ||
| arrayDim[i,0] = len(arrayDim0) | ||||
| arrayDim[i,4] = mode[i] | ||||
|
Julio Valdez
|
r515 | |||
|
Julio Valdez
|
r543 | if len(arrayDim0) == 3: | ||
| arrayDim[i,1:-1] = numpy.array(arrayDim0) | ||||
| elif len(arrayDim0) == 2: | ||||
| arrayDim[i,2:-1] = numpy.array(arrayDim0) #nHeights | ||||
| elif len(arrayDim0) == 1: | ||||
| arrayDim[i,3] = arrayDim0 | ||||
| elif len(arrayDim0) == 0: | ||||
| arrayDim[i,0] = 1 | ||||
| arrayDim[i,3] = 1 | ||||
| table = numpy.array((self.dataList[i],) + tuple(arrayDim[i,:]),dtype = dtype0) | ||||
|
Julio Valdez
|
r515 | tableList.append(table) | ||
|
Julio Valdez
|
r543 | |||
| self.arrayDim = arrayDim | ||||
|
Julio Valdez
|
r515 | self.tableDim = numpy.array(tableList, dtype = dtype0) | ||
|
Julio Valdez
|
r514 | self.blockIndex = 0 | ||
| return | ||||
| def putMetadata(self): | ||||
| fp = self.createMetadataFile() | ||||
| self.writeMetadata(fp) | ||||
| fp.close() | ||||
| return | ||||
| def createMetadataFile(self): | ||||
| ext = self.ext | ||||
| path = self.path | ||||
| setFile = self.setFile | ||||
| timeTuple = time.localtime(self.dataOut.utctime) | ||||
|
Julio Valdez
|
r608 | |||
| subfolder = '' | ||||
|
Julio Valdez
|
r514 | fullpath = os.path.join( path, subfolder ) | ||
|
Julio Valdez
|
r608 | |||
|
Julio Valdez
|
r514 | if not( os.path.exists(fullpath) ): | ||
| os.mkdir(fullpath) | ||||
| setFile = -1 #inicializo mi contador de seteo | ||||
|
Julio Valdez
|
r608 | |||
| subfolder = 'd%4.4d%3.3d' % (timeTuple.tm_year,timeTuple.tm_yday) | ||||
| fullpath = os.path.join( path, subfolder ) | ||||
| if not( os.path.exists(fullpath) ): | ||||
| os.mkdir(fullpath) | ||||
| setFile = -1 #inicializo mi contador de seteo | ||||
|
Julio Valdez
|
r514 | else: | ||
| filesList = os.listdir( fullpath ) | ||||
|
Julio Valdez
|
r608 | filesList = sorted( filesList, key=str.lower ) | ||
|
Julio Valdez
|
r514 | if len( filesList ) > 0: | ||
|
Julio Valdez
|
r608 | filesList = [k for k in filesList if 'M' in k] | ||
|
Julio Valdez
|
r514 | filen = filesList[-1] | ||
| # el filename debera tener el siguiente formato | ||||
| # 0 1234 567 89A BCDE (hex) | ||||
| # x YYYY DDD SSS .ext | ||||
| if isNumber( filen[8:11] ): | ||||
| setFile = int( filen[8:11] ) #inicializo mi contador de seteo al seteo del ultimo file | ||||
| else: | ||||
| setFile = -1 | ||||
| else: | ||||
| setFile = -1 #inicializo mi contador de seteo | ||||
| setFile += 1 | ||||
|
Julio Valdez
|
r608 | |||
|
Julio Valdez
|
r514 | file = '%s%4.4d%3.3d%3.3d%s' % (self.metaoptchar, | ||
| timeTuple.tm_year, | ||||
| timeTuple.tm_yday, | ||||
| setFile, | ||||
| ext ) | ||||
| filename = os.path.join( path, subfolder, file ) | ||||
| self.metaFile = file | ||||
| #Setting HDF5 File | ||||
| fp = h5py.File(filename,'w') | ||||
| return fp | ||||
| def writeMetadata(self, fp): | ||||
| grp = fp.create_group("Metadata") | ||||
|
Julio Valdez
|
r515 | grp.create_dataset('array dimensions', data = self.tableDim, dtype = self.dtype) | ||
|
Julio Valdez
|
r514 | |||
| for i in range(len(self.metadataList)): | ||||
| grp.create_dataset(self.metadataList[i], data=getattr(self.dataOut, self.metadataList[i])) | ||||
| return | ||||
| def setNextFile(self): | ||||
| ext = self.ext | ||||
| path = self.path | ||||
| setFile = self.setFile | ||||
|
Julio Valdez
|
r543 | mode = self.mode | ||
|
Julio Valdez
|
r608 | |||
|
Julio Valdez
|
r514 | timeTuple = time.localtime(self.dataOut.utctime) | ||
| subfolder = 'd%4.4d%3.3d' % (timeTuple.tm_year,timeTuple.tm_yday) | ||||
| fullpath = os.path.join( path, subfolder ) | ||||
|
Julio Valdez
|
r608 | |||
| if os.path.exists(fullpath): | ||||
|
Julio Valdez
|
r514 | filesList = os.listdir( fullpath ) | ||
|
Julio Valdez
|
r608 | filesList = [k for k in filesList if 'D' in k] | ||
|
Julio Valdez
|
r514 | if len( filesList ) > 0: | ||
| filesList = sorted( filesList, key=str.lower ) | ||||
| filen = filesList[-1] | ||||
| # el filename debera tener el siguiente formato | ||||
| # 0 1234 567 89A BCDE (hex) | ||||
| # x YYYY DDD SSS .ext | ||||
| if isNumber( filen[8:11] ): | ||||
| setFile = int( filen[8:11] ) #inicializo mi contador de seteo al seteo del ultimo file | ||||
| else: | ||||
| setFile = -1 | ||||
| else: | ||||
| setFile = -1 #inicializo mi contador de seteo | ||||
| setFile += 1 | ||||
| file = '%s%4.4d%3.3d%3.3d%s' % (self.optchar, | ||||
| timeTuple.tm_year, | ||||
| timeTuple.tm_yday, | ||||
| setFile, | ||||
| ext ) | ||||
| filename = os.path.join( path, subfolder, file ) | ||||
| #Setting HDF5 File | ||||
| fp = h5py.File(filename,'w') | ||||
| grp = fp.create_group("Data") | ||||
| grp.attrs['metadata'] = self.metaFile | ||||
|
Julio Valdez
|
r543 | # grp.attrs['blocksPerFile'] = 0 | ||
|
Julio Valdez
|
r514 | |||
| ds = [] | ||||
| data = [] | ||||
|
Julio Valdez
|
r608 | nDimsForDs = [] | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | nDatas = numpy.zeros(len(self.dataList)) | ||
| nDims = self.arrayDim[:,0] | ||||
|
Julio Valdez
|
r608 | nDim1 = self.arrayDim[:,2] | ||
| nDim0 = self.arrayDim[:,3] | ||||
|
Julio Valdez
|
r543 | for i in range(len(self.dataList)): | ||
|
Julio Valdez
|
r514 | |||
|
Julio Valdez
|
r543 | if nDims[i]==1: | ||
|
Julio Valdez
|
r608 | # ds0 = grp.create_dataset(self.dataList[i], (1,1), maxshape=(1,self.blocksPerFile) , chunks = True, dtype='S20') | ||
| ds0 = grp.create_dataset(self.dataList[i], (1,1), maxshape=(1,self.blocksPerFile) , chunks = True, dtype=numpy.float64) | ||||
|
Julio Valdez
|
r514 | ds.append(ds0) | ||
| data.append([]) | ||||
|
Julio Valdez
|
r608 | nDimsForDs.append(nDims[i]) | ||
|
Julio Valdez
|
r543 | else: | ||
| if mode[i]==0: | ||||
| strMode = "channel" | ||||
| nDatas[i] = self.arrayDim[i,1] | ||||
| else: | ||||
| strMode = "param" | ||||
| nDatas[i] = self.arrayDim[i,2] | ||||
| if nDims[i]==2: | ||||
| nDatas[i] = self.arrayDim[i,2] | ||||
| grp0 = grp.create_group(self.dataList[i]) | ||||
| for j in range(int(nDatas[i])): | ||||
| tableName = strMode + str(j) | ||||
| if nDims[i] == 3: | ||||
|
Julio Valdez
|
r608 | ds0 = grp0.create_dataset(tableName, (nDim1[i],nDim0[i],1) , data = numpy.zeros((nDim1[i],nDim0[i],1)) ,maxshape=(None,nDim0[i],None), chunks=True) | ||
|
Julio Valdez
|
r543 | else: | ||
|
Julio Valdez
|
r608 | ds0 = grp0.create_dataset(tableName, (1,nDim0[i]), data = numpy.zeros((1,nDim0[i])) , maxshape=(None,nDim0[i]), chunks=True) | ||
|
Julio Valdez
|
r543 | |||
| ds.append(ds0) | ||||
| data.append([]) | ||||
|
Julio Valdez
|
r608 | nDimsForDs.append(nDims[i]) | ||
|
Julio Valdez
|
r543 | self.nDatas = nDatas | ||
| self.nDims = nDims | ||||
|
Julio Valdez
|
r608 | self.nDimsForDs = nDimsForDs | ||
|
Julio Valdez
|
r514 | #Saving variables | ||
| print 'Writing the file: %s'%filename | ||||
|
Julio Valdez
|
r608 | self.filename = filename | ||
|
Julio Valdez
|
r514 | self.fp = fp | ||
| self.grp = grp | ||||
|
Julio Valdez
|
r608 | self.grp.attrs.modify('nRecords', 1) | ||
|
Julio Valdez
|
r514 | self.ds = ds | ||
| self.data = data | ||||
| self.setFile = setFile | ||||
| self.firsttime = True | ||||
| self.blockIndex = 0 | ||||
| return | ||||
| def putData(self): | ||||
|
Julio Valdez
|
r608 | |||
| if not self.firsttime: | ||||
| self.fp.flush() | ||||
| self.fp.close() | ||||
| self.readBlock() | ||||
| if self.blockIndex == self.blocksPerFile: | ||||
| self.setNextFile() | ||||
|
Julio Valdez
|
r514 | self.setBlock() | ||
| self.writeBlock() | ||||
|
Julio Valdez
|
r608 | |||
|
Julio Valdez
|
r514 | return | ||
|
Julio Valdez
|
r608 | def readBlock(self): | ||
| ''' | ||||
| data Array configured | ||||
| self.data | ||||
| ''' | ||||
| ds = self.ds | ||||
| #Setting HDF5 File | ||||
| fp = h5py.File(self.filename,'r+') | ||||
| grp = fp["Data"] | ||||
| ind = 0 | ||||
| # grp.attrs['blocksPerFile'] = 0 | ||||
| for i in range(len(self.dataList)): | ||||
| if self.nDims[i]==1: | ||||
| ds0 = grp[self.dataList[i]] | ||||
| ds[ind] = ds0 | ||||
| ind += 1 | ||||
| else: | ||||
| if self.mode[i]==0: | ||||
| strMode = "channel" | ||||
| else: | ||||
| strMode = "param" | ||||
| grp0 = grp[self.dataList[i]] | ||||
| for j in range(int(self.nDatas[i])): | ||||
| tableName = strMode + str(j) | ||||
| ds0 = grp0[tableName] | ||||
| ds[ind] = ds0 | ||||
| ind += 1 | ||||
| self.fp = fp | ||||
| self.grp = grp | ||||
| self.ds = ds | ||||
| return | ||||
|
Julio Valdez
|
r514 | def setBlock(self): | ||
|
Julio Valdez
|
r515 | ''' | ||
| data Array configured | ||||
|
Julio Valdez
|
r543 | |||
| self.data | ||||
|
Julio Valdez
|
r515 | ''' | ||
|
Julio Valdez
|
r514 | #Creating Arrays | ||
| data = self.data | ||||
|
Julio Valdez
|
r543 | nDatas = self.nDatas | ||
| nDims = self.nDims | ||||
| mode = self.mode | ||||
|
Julio Valdez
|
r514 | ind = 0 | ||
|
Julio Valdez
|
r543 | |||
|
Julio Valdez
|
r514 | for i in range(len(self.dataList)): | ||
| dataAux = getattr(self.dataOut,self.dataList[i]) | ||||
|
Julio Valdez
|
r543 | if nDims[i] == 1: | ||
|
Julio Valdez
|
r608 | # data[ind] = numpy.array([str(dataAux)]).reshape((1,1)) | ||
| data[ind] = dataAux | ||||
| # if not self.firsttime: | ||||
| # data[ind] = numpy.hstack((self.ds[ind][:], self.data[ind])) | ||||
|
Julio Valdez
|
r514 | ind += 1 | ||
|
Julio Valdez
|
r543 | else: | ||
| for j in range(int(nDatas[i])): | ||||
| if (mode[i] == 0) or (nDims[i] == 2): #In case division per channel or Dimensions is only 1 | ||||
| data[ind] = dataAux[j,:] | ||||
| else: | ||||
| data[ind] = dataAux[:,j,:] | ||||
|
Julio Valdez
|
r608 | # if nDims[i] == 3: | ||
| # data[ind] = data[ind].reshape((data[ind].shape[0],data[ind].shape[1],1)) | ||||
|
Julio Valdez
|
r543 | |||
|
Julio Valdez
|
r608 | # if not self.firsttime: | ||
| # data[ind] = numpy.dstack((self.ds[ind][:], data[ind])) | ||||
|
Julio Valdez
|
r543 | |||
|
Julio Valdez
|
r608 | # else: | ||
| # data[ind] = data[ind].reshape((1,data[ind].shape[0])) | ||||
|
Julio Valdez
|
r543 | |||
|
Julio Valdez
|
r608 | # if not self.firsttime: | ||
| # data[ind] = numpy.vstack((self.ds[ind][:], data[ind])) | ||||
|
Julio Valdez
|
r543 | ind += 1 | ||
|
Julio Valdez
|
r608 | |||
|
Julio Valdez
|
r514 | self.data = data | ||
| return | ||||
| def writeBlock(self): | ||||
|
Julio Valdez
|
r515 | ''' | ||
| Saves the block in the HDF5 file | ||||
| ''' | ||||
|
Julio Valdez
|
r514 | for i in range(len(self.ds)): | ||
|
Julio Valdez
|
r608 | if self.firsttime: | ||
| # self.ds[i].resize(self.data[i].shape) | ||||
| # self.ds[i][self.blockIndex,:] = self.data[i] | ||||
| if type(self.data[i]) == numpy.ndarray: | ||||
| nDims1 = len(self.ds[i].shape) | ||||
| if nDims1 == 3: | ||||
| self.data[i] = self.data[i].reshape((self.data[i].shape[0],self.data[i].shape[1],1)) | ||||
| self.ds[i].resize(self.data[i].shape) | ||||
| self.ds[i][:] = self.data[i] | ||||
| else: | ||||
| if self.nDimsForDs[i] == 1: | ||||
| self.ds[i].resize((self.ds[i].shape[0], self.ds[i].shape[1] + 1)) | ||||
| self.ds[i][0,-1] = self.data[i] | ||||
| elif self.nDimsForDs[i] == 2: | ||||
| self.ds[i].resize((self.ds[i].shape[0] + 1,self.ds[i].shape[1])) | ||||
| self.ds[i][self.blockIndex,:] = self.data[i] | ||||
| elif self.nDimsForDs[i] == 3: | ||||
| dataShape = self.data[i].shape | ||||
| dsShape = self.ds[i].shape | ||||
| if dataShape[0]==dsShape[0]: | ||||
| self.ds[i].resize((self.ds[i].shape[0],self.ds[i].shape[1],self.ds[i].shape[2]+1)) | ||||
| self.ds[i][:,:,-1] = self.data[i] | ||||
| else: | ||||
| self.ds[i].resize((self.ds[i].shape[0] + dataShape[0],self.ds[i].shape[1],self.ds[i].shape[2])) | ||||
| self.ds[i][dsShape[0]:,:,0] = self.data[i] | ||||
| # self.ds[i].append(self.data[i]) | ||||
| # self.fp.flush() | ||||
| # if not self.firsttime: | ||||
| # self.fp.root.Data._v_attrs.nRecords = self.blockIndex | ||||
| # if self.firsttime: | ||||
| # self.fp.close() | ||||
| # self.readBlock2() | ||||
|
Julio Valdez
|
r514 | |||
| self.blockIndex += 1 | ||||
| self.firsttime = False | ||||
| return | ||||
| def run(self, dataOut, **kwargs): | ||||
| if not(self.isConfig): | ||||
| self.setup(dataOut, **kwargs) | ||||
| self.isConfig = True | ||||
| self.putMetadata() | ||||
| self.setNextFile() | ||||
| self.putData() | ||||
| return | ||||