jroIO_madrigal.py
580 lines
| 19.2 KiB
| text/x-python
|
PythonLexer
Juan C. Espinoza
|
r1010 | ''' | ||
| Created on Aug 1, 2017 | ||||
| @author: Juan C. Espinoza | ||||
| ''' | ||||
| import os | ||||
| import sys | ||||
| import time | ||||
|
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|
r1021 | import json | ||
| r1065 | import glob | |||
|
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|
r1010 | import datetime | ||
| import numpy | ||||
| r1065 | import h5py | |||
|
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|
r1010 | |||
| try: | ||||
| import madrigal | ||||
| import madrigal.cedar | ||||
| except: | ||||
| print 'You should install "madrigal library" module if you want to read/write Madrigal data' | ||||
| r1065 | from schainpy.model.io.jroIO_base import JRODataReader | |||
| from schainpy.model.proc.jroproc_base import ProcessingUnit, Operation | ||||
|
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|
r1021 | from schainpy.model.data.jrodata import Parameters | ||
| r1065 | from schainpy.utils import log | |||
|
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|
r1021 | |||
| DEF_CATALOG = { | ||||
| 'principleInvestigator': 'Marco Milla', | ||||
| 'expPurpose': None, | ||||
| 'expMode': None, | ||||
| 'cycleTime': None, | ||||
| 'correlativeExp': None, | ||||
| 'sciRemarks': None, | ||||
| 'instRemarks': None | ||||
| } | ||||
| DEF_HEADER = { | ||||
| 'kindatDesc': None, | ||||
| 'analyst': 'Jicamarca User', | ||||
| 'comments': None, | ||||
| 'history': None | ||||
| } | ||||
| MNEMONICS = { | ||||
| 10: 'jro', | ||||
| 11: 'jbr', | ||||
| 840: 'jul', | ||||
| 13: 'jas', | ||||
| 1000: 'pbr', | ||||
| 1001: 'hbr', | ||||
| 1002: 'obr', | ||||
| } | ||||
| r1065 | UT1970 = datetime.datetime(1970, 1, 1) - datetime.timedelta(seconds=time.timezone) | |||
|
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|
r1021 | def load_json(obj): | ||
| ''' | ||||
| Parse json as string instead of unicode | ||||
| ''' | ||||
| if isinstance(obj, str): | ||||
| r1065 | iterable = json.loads(obj) | |||
| if isinstance(iterable, dict): | ||||
| return {str(k): load_json(v) if isinstance(v, dict) else str(v) if isinstance(v, unicode) else v | ||||
| for k, v in iterable.items()} | ||||
| elif isinstance(iterable, (list, tuple)): | ||||
| return [str(v) if isinstance(v, unicode) else v for v in iterable] | ||||
| return iterable | ||||
| class MADReader(JRODataReader, ProcessingUnit): | ||||
| def __init__(self, **kwargs): | ||||
| ProcessingUnit.__init__(self, **kwargs) | ||||
| self.dataOut = Parameters() | ||||
| self.counter_records = 0 | ||||
| self.nrecords = None | ||||
| self.flagNoMoreFiles = 0 | ||||
| self.isConfig = False | ||||
| self.filename = None | ||||
| self.intervals = set() | ||||
| def setup(self, | ||||
| path=None, | ||||
| startDate=None, | ||||
| endDate=None, | ||||
| format=None, | ||||
| startTime=datetime.time(0, 0, 0), | ||||
| endTime=datetime.time(23, 59, 59), | ||||
| **kwargs): | ||||
| self.started = True | ||||
| self.path = path | ||||
| self.startDate = startDate | ||||
| self.endDate = endDate | ||||
| self.startTime = startTime | ||||
| self.endTime = endTime | ||||
| self.datatime = datetime.datetime(1900,1,1) | ||||
| self.oneDDict = load_json(kwargs.get('oneDDict', | ||||
| "{\"GDLATR\":\"lat\", \"GDLONR\":\"lon\"}")) | ||||
| self.twoDDict = load_json(kwargs.get('twoDDict', | ||||
| "{\"GDALT\": \"heightList\"}")) | ||||
| self.ind2DList = load_json(kwargs.get('ind2DList', | ||||
| "[\"GDALT\"]")) | ||||
| if self.path is None: | ||||
| raise ValueError, 'The path is not valid' | ||||
| if format is None: | ||||
| raise ValueError, 'The format is not valid choose simple or hdf5' | ||||
| elif format.lower() in ('simple', 'txt'): | ||||
| self.ext = '.txt' | ||||
| elif format.lower() in ('cedar',): | ||||
| self.ext = '.001' | ||||
| else: | ||||
| self.ext = '.hdf5' | ||||
| self.search_files(self.path) | ||||
| self.fileId = 0 | ||||
| if not self.fileList: | ||||
| raise Warning, 'There is no files matching these date in the folder: {}. \n Check startDate and endDate'.format(path) | ||||
| self.setNextFile() | ||||
| def search_files(self, path): | ||||
| ''' | ||||
| Searching for madrigal files in path | ||||
| Creating a list of files to procces included in [startDate,endDate] | ||||
| Input: | ||||
| path - Path to find files | ||||
| ''' | ||||
| print 'Searching files {} in {} '.format(self.ext, path) | ||||
| foldercounter = 0 | ||||
| fileList0 = glob.glob1(path, '*{}'.format(self.ext)) | ||||
| fileList0.sort() | ||||
| self.fileList = [] | ||||
| self.dateFileList = [] | ||||
| startDate = self.startDate - datetime.timedelta(1) | ||||
| endDate = self.endDate + datetime.timedelta(1) | ||||
| for thisFile in fileList0: | ||||
| year = thisFile[3:7] | ||||
| if not year.isdigit(): | ||||
| continue | ||||
| month = thisFile[7:9] | ||||
| if not month.isdigit(): | ||||
| continue | ||||
| day = thisFile[9:11] | ||||
| if not day.isdigit(): | ||||
| continue | ||||
| year, month, day = int(year), int(month), int(day) | ||||
| dateFile = datetime.date(year, month, day) | ||||
| if (startDate > dateFile) or (endDate < dateFile): | ||||
| continue | ||||
| self.fileList.append(thisFile) | ||||
| self.dateFileList.append(dateFile) | ||||
| return | ||||
| def parseHeader(self): | ||||
| ''' | ||||
| ''' | ||||
| self.output = {} | ||||
| self.version = '2' | ||||
| s_parameters = None | ||||
| if self.ext == '.txt': | ||||
| self.parameters = [s.strip().lower() for s in self.fp.readline().strip().split(' ') if s] | ||||
| elif self.ext == '.hdf5': | ||||
| metadata = self.fp['Metadata'] | ||||
| data = self.fp['Data']['Array Layout'] | ||||
| if 'Independent Spatial Parameters' in metadata: | ||||
| s_parameters = [s[0].lower() for s in metadata['Independent Spatial Parameters']] | ||||
| self.version = '3' | ||||
| one = [s[0].lower() for s in data['1D Parameters']['Data Parameters']] | ||||
| one_d = [1 for s in one] | ||||
| two = [s[0].lower() for s in data['2D Parameters']['Data Parameters']] | ||||
| two_d = [2 for s in two] | ||||
| self.parameters = one + two | ||||
| self.parameters_d = one_d + two_d | ||||
| log.success('Parameters found: {}'.format(','.join(self.parameters)), | ||||
| 'MADReader') | ||||
| if s_parameters: | ||||
| log.success('Spatial parameters: {}'.format(','.join(s_parameters)), | ||||
| 'MADReader') | ||||
| for param in self.oneDDict.keys(): | ||||
| if param.lower() not in self.parameters: | ||||
| print('\x1b[33m[Warning]\x1b[0m Parameter \x1b[1;32m{}\x1b[0m not found will be ignored'.format( | ||||
| param | ||||
| )) | ||||
| self.oneDDict.pop(param, None) | ||||
| for param, value in self.twoDDict.items(): | ||||
| if param.lower() not in self.parameters: | ||||
| print('\x1b[33m[Warning]\x1b[0m Parameter \x1b[1;32m{}\x1b[0m not found will be ignored'.format( | ||||
| param | ||||
| )) | ||||
| self.twoDDict.pop(param, None) | ||||
| continue | ||||
| if isinstance(value, list): | ||||
| if value[0] not in self.output: | ||||
| self.output[value[0]] = [] | ||||
| self.output[value[0]].append(None) | ||||
| def parseData(self): | ||||
| ''' | ||||
| ''' | ||||
|
Juan C. Espinoza
|
r1021 | |||
| r1065 | if self.ext == '.txt': | |||
| self.data = numpy.genfromtxt(self.fp, missing_values=('missing')) | ||||
| self.nrecords = self.data.shape[0] | ||||
| self.ranges = numpy.unique(self.data[:,self.parameters.index(self.ind2DList[0].lower())]) | ||||
| elif self.ext == '.hdf5': | ||||
| self.data = self.fp['Data']['Array Layout'] | ||||
| self.nrecords = len(self.data['timestamps'].value) | ||||
| self.ranges = self.data['range'].value | ||||
| def setNextFile(self): | ||||
| ''' | ||||
| ''' | ||||
| file_id = self.fileId | ||||
| if file_id == len(self.fileList): | ||||
| print '\nNo more files in the folder' | ||||
| print 'Total number of file(s) read : {}'.format(self.fileId) | ||||
| self.flagNoMoreFiles = 1 | ||||
| return 0 | ||||
| print('\x1b[32m[Info]\x1b[0m Opening: {}'.format( | ||||
| self.fileList[file_id] | ||||
| )) | ||||
| filename = os.path.join(self.path, self.fileList[file_id]) | ||||
| if self.filename is not None: | ||||
| self.fp.close() | ||||
| self.filename = filename | ||||
| self.filedate = self.dateFileList[file_id] | ||||
| if self.ext=='.hdf5': | ||||
| self.fp = h5py.File(self.filename, 'r') | ||||
| else: | ||||
| self.fp = open(self.filename, 'rb') | ||||
| self.parseHeader() | ||||
| self.parseData() | ||||
| self.sizeOfFile = os.path.getsize(self.filename) | ||||
| self.counter_records = 0 | ||||
| self.flagIsNewFile = 0 | ||||
| self.fileId += 1 | ||||
| return 1 | ||||
| def readNextBlock(self): | ||||
| while True: | ||||
| if self.flagIsNewFile: | ||||
| if not self.setNextFile(): | ||||
| return 0 | ||||
| self.readBlock() | ||||
| if (self.datatime < datetime.datetime.combine(self.startDate, self.startTime)) or \ | ||||
| (self.datatime > datetime.datetime.combine(self.endDate, self.endTime)): | ||||
| print "\x1b[32m[Reading]\x1b[0m Record No. %d/%d -> %s \x1b[33m[Skipping]\x1b[0m" %( | ||||
| self.counter_records, | ||||
| self.nrecords, | ||||
| self.datatime.ctime()) | ||||
| continue | ||||
| break | ||||
| print "\x1b[32m[Reading]\x1b[0m Record No. %d/%d -> %s" %( | ||||
| self.counter_records, | ||||
| self.nrecords, | ||||
| self.datatime.ctime()) | ||||
| return 1 | ||||
| def readBlock(self): | ||||
| ''' | ||||
| ''' | ||||
| dum = [] | ||||
| if self.ext == '.txt': | ||||
| dt = self.data[self.counter_records][:6].astype(int) | ||||
| self.datatime = datetime.datetime(dt[0], dt[1], dt[2], dt[3], dt[4], dt[5]) | ||||
| while True: | ||||
| dt = self.data[self.counter_records][:6].astype(int) | ||||
| datatime = datetime.datetime(dt[0], dt[1], dt[2], dt[3], dt[4], dt[5]) | ||||
| if datatime == self.datatime: | ||||
| dum.append(self.data[self.counter_records]) | ||||
| self.counter_records += 1 | ||||
| if self.counter_records == self.nrecords: | ||||
| self.flagIsNewFile = True | ||||
| break | ||||
| continue | ||||
| self.intervals.add((datatime-self.datatime).seconds) | ||||
| break | ||||
| elif self.ext == '.hdf5': | ||||
| datatime = datetime.datetime.utcfromtimestamp( | ||||
| self.data['timestamps'][self.counter_records]) | ||||
| nHeights = len(self.ranges) | ||||
| for n, param in enumerate(self.parameters): | ||||
| if self.parameters_d[n] == 1: | ||||
| dum.append(numpy.ones(nHeights)*self.data['1D Parameters'][param][self.counter_records]) | ||||
| else: | ||||
| if self.version == '2': | ||||
| dum.append(self.data['2D Parameters'][param][self.counter_records]) | ||||
| else: | ||||
| tmp = self.data['2D Parameters'][param].value.T | ||||
| dum.append(tmp[self.counter_records]) | ||||
| self.intervals.add((datatime-self.datatime).seconds) | ||||
| self.datatime = datatime | ||||
| self.counter_records += 1 | ||||
| if self.counter_records == self.nrecords: | ||||
| self.flagIsNewFile = True | ||||
| self.buffer = numpy.array(dum) | ||||
| return | ||||
| def set_output(self): | ||||
| ''' | ||||
| Storing data from buffer to dataOut object | ||||
| ''' | ||||
| parameters = [None for __ in self.parameters] | ||||
| for param, attr in self.oneDDict.items(): | ||||
| x = self.parameters.index(param.lower()) | ||||
| setattr(self.dataOut, attr, self.buffer[0][x]) | ||||
| for param, value in self.twoDDict.items(): | ||||
| x = self.parameters.index(param.lower()) | ||||
| if self.ext == '.txt': | ||||
| y = self.parameters.index(self.ind2DList[0].lower()) | ||||
| ranges = self.buffer[:,y] | ||||
| if self.ranges.size == ranges.size: | ||||
| continue | ||||
| index = numpy.where(numpy.in1d(self.ranges, ranges))[0] | ||||
| dummy = numpy.zeros(self.ranges.shape) + numpy.nan | ||||
| dummy[index] = self.buffer[:,x] | ||||
| else: | ||||
| dummy = self.buffer[x] | ||||
| if isinstance(value, str): | ||||
| if value not in self.ind2DList: | ||||
| setattr(self.dataOut, value, dummy.reshape(1,-1)) | ||||
| elif isinstance(value, list): | ||||
| self.output[value[0]][value[1]] = dummy | ||||
| parameters[value[1]] = param | ||||
| for key, value in self.output.items(): | ||||
| setattr(self.dataOut, key, numpy.array(value)) | ||||
| self.dataOut.parameters = [s for s in parameters if s] | ||||
| self.dataOut.heightList = self.ranges | ||||
| self.dataOut.utctime = (self.datatime - UT1970).total_seconds() | ||||
| self.dataOut.utctimeInit = self.dataOut.utctime | ||||
| self.dataOut.paramInterval = min(self.intervals) | ||||
| self.dataOut.useLocalTime = False | ||||
| self.dataOut.flagNoData = False | ||||
| self.dataOut.started = self.started | ||||
| def getData(self): | ||||
| ''' | ||||
| Storing data from databuffer to dataOut object | ||||
| ''' | ||||
| if self.flagNoMoreFiles: | ||||
| self.dataOut.flagNoData = True | ||||
| print 'No file left to process' | ||||
| return 0 | ||||
| if not self.readNextBlock(): | ||||
| self.dataOut.flagNoData = True | ||||
| return 0 | ||||
| self.set_output() | ||||
| return 1 | ||||
|
Juan C. Espinoza
|
r1021 | |||
|
Juan C. Espinoza
|
r1010 | |||
|
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|
r1021 | class MAD2Writer(Operation): | ||
| r1065 | ||||
| missing = -32767 | ||||
| ext = '.dat' | ||||
|
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r1010 | |||
|
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|
r1021 | def __init__(self, **kwargs): | ||
|
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|
r1010 | |||
|
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r1021 | Operation.__init__(self, **kwargs) | ||
|
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|
r1010 | self.dataOut = Parameters() | ||
| self.path = None | ||||
| self.dataOut = None | ||||
| r1065 | def run(self, dataOut, path, oneDDict, ind2DList='[]', twoDDict='{}', metadata='{}', **kwargs): | |||
|
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|
r1021 | ''' | ||
| Inputs: | ||||
| path - path where files will be created | ||||
| r1065 | oneDDict - json of one-dimensional parameters in record where keys | |||
|
Juan C. Espinoza
|
r1021 | are Madrigal codes (integers or mnemonics) and values the corresponding | ||
| dataOut attribute e.g: { | ||||
| 'gdlatr': 'lat', | ||||
| 'gdlonr': 'lon', | ||||
| 'gdlat2':'lat', | ||||
| 'glon2':'lon'} | ||||
| r1065 | ind2DList - list of independent spatial two-dimensional parameters e.g: | |||
| ['heighList'] | ||||
| twoDDict - json of two-dimensional parameters in record where keys | ||||
|
Juan C. Espinoza
|
r1021 | are Madrigal codes (integers or mnemonics) and values the corresponding | ||
| dataOut attribute if multidimensional array specify as tupple | ||||
| ('attr', pos) e.g: { | ||||
| 'gdalt': 'heightList', | ||||
| 'vn1p2': ('data_output', 0), | ||||
| 'vn2p2': ('data_output', 1), | ||||
| 'vn3': ('data_output', 2), | ||||
| 'snl': ('data_SNR', 'db') | ||||
| } | ||||
| metadata - json of madrigal metadata (kinst, kindat, catalog and header) | ||||
| ''' | ||||
| if not self.isConfig: | ||||
| r1065 | self.setup(dataOut, path, oneDDict, ind2DList, twoDDict, metadata, **kwargs) | |||
|
Juan C. Espinoza
|
r1021 | self.isConfig = True | ||
|
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|
r1010 | |||
| self.putData() | ||||
| return | ||||
| r1065 | def setup(self, dataOut, path, oneDDict, ind2DList, twoDDict, metadata, **kwargs): | |||
|
Juan C. Espinoza
|
r1010 | ''' | ||
|
Juan C. Espinoza
|
r1021 | Configure Operation | ||
|
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|
r1010 | ''' | ||
| self.dataOut = dataOut | ||||
|
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|
r1021 | self.nmodes = self.dataOut.nmodes | ||
|
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r1010 | self.path = path | ||
|
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|
r1021 | self.blocks = kwargs.get('blocks', None) | ||
| self.counter = 0 | ||||
| r1065 | self.oneDDict = load_json(oneDDict) | |||
| self.twoDDict = load_json(twoDDict) | ||||
| self.ind2DList = load_json(ind2DList) | ||||
|
Juan C. Espinoza
|
r1021 | meta = load_json(metadata) | ||
| self.kinst = meta.get('kinst') | ||||
| self.kindat = meta.get('kindat') | ||||
| self.catalog = meta.get('catalog', DEF_CATALOG) | ||||
| self.header = meta.get('header', DEF_HEADER) | ||||
| return | ||||
|
Juan C. Espinoza
|
r1010 | def setFile(self): | ||
| ''' | ||||
|
Juan C. Espinoza
|
r1021 | Create new cedar file object | ||
| ''' | ||||
| self.mnemonic = MNEMONICS[self.kinst] #TODO get mnemonic from madrigal | ||||
| date = datetime.datetime.utcfromtimestamp(self.dataOut.utctime) | ||||
| filename = '%s%s_%s%s' % (self.mnemonic, | ||||
| date.strftime('%Y%m%d_%H%M%S'), | ||||
| self.dataOut.mode, | ||||
| self.ext) | ||||
|
Juan C. Espinoza
|
r1010 | |||
|
Juan C. Espinoza
|
r1021 | self.fullname = os.path.join(self.path, filename) | ||
|
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|
r1010 | |||
| if os.path.isfile(self.fullname) : | ||||
| print "Destination path '%s' already exists. Previous file deleted. " %self.fullname | ||||
| os.remove(self.fullname) | ||||
| try: | ||||
|
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|
r1021 | print '[Writing] creating file : %s' % (self.fullname) | ||
|
Juan C. Espinoza
|
r1010 | self.cedarObj = madrigal.cedar.MadrigalCedarFile(self.fullname, True) | ||
|
Juan C. Espinoza
|
r1021 | except ValueError, e: | ||
|
Juan C. Espinoza
|
r1010 | print '[Error]: Impossible to create a cedar object with "madrigal.cedar.MadrigalCedarFile" ' | ||
| return | ||||
| return 1 | ||||
| def writeBlock(self): | ||||
| ''' | ||||
| r1065 | Add data records to cedar file taking data from oneDDict and twoDDict | |||
|
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|
r1021 | attributes. | ||
| Allowed parameters in: parcodes.tab | ||||
|
Juan C. Espinoza
|
r1010 | ''' | ||
|
Juan C. Espinoza
|
r1021 | startTime = datetime.datetime.utcfromtimestamp(self.dataOut.utctime) | ||
| endTime = startTime + datetime.timedelta(seconds=self.dataOut.paramInterval) | ||||
| r1065 | nrows = len(getattr(self.dataOut, self.ind2DList)) | |||
|
Juan C. Espinoza
|
r1021 | |||
| rec = madrigal.cedar.MadrigalDataRecord( | ||||
| self.kinst, | ||||
| self.kindat, | ||||
| startTime.year, | ||||
| startTime.month, | ||||
| startTime.day, | ||||
| startTime.hour, | ||||
| startTime.minute, | ||||
| startTime.second, | ||||
| startTime.microsecond/10000, | ||||
| endTime.year, | ||||
| endTime.month, | ||||
| endTime.day, | ||||
| endTime.hour, | ||||
| endTime.minute, | ||||
| endTime.second, | ||||
| endTime.microsecond/10000, | ||||
| r1065 | self.oneDDict.keys(), | |||
| self.twoDDict.keys(), | ||||
|
Juan C. Espinoza
|
r1021 | nrows | ||
| ) | ||||
|
Juan C. Espinoza
|
r1010 | |||
|
Juan C. Espinoza
|
r1021 | # Setting 1d values | ||
| r1065 | for key in self.oneDDict: | |||
| rec.set1D(key, getattr(self.dataOut, self.oneDDict[key])) | ||||
|
Juan C. Espinoza
|
r1010 | |||
| # Setting 2d values | ||||
|
Juan C. Espinoza
|
r1021 | invalid = numpy.isnan(self.dataOut.data_output) | ||
| r1065 | self.dataOut.data_output[invalid] = self.missing | |||
|
Juan C. Espinoza
|
r1021 | out = {} | ||
| r1065 | for key, value in self.twoDDict.items(): | |||
|
Juan C. Espinoza
|
r1021 | if isinstance(value, str): | ||
| out[key] = getattr(self.dataOut, value) | ||||
| elif isinstance(value, tuple): | ||||
| attr, x = value | ||||
| if isinstance(x, (int, float)): | ||||
| out[key] = getattr(self.dataOut, attr)[int(x)] | ||||
| elif x.lower()=='db': | ||||
| tmp = getattr(self.dataOut, attr) | ||||
| SNRavg = numpy.average(tmp, axis=0) | ||||
| out[key] = 10*numpy.log10(SNRavg) | ||||
| for n in range(nrows): | ||||
| for key in out: | ||||
| rec.set2D(key, n, out[key][n]) | ||||
| self.cedarObj.append(rec) | ||||
|
Juan C. Espinoza
|
r1010 | self.cedarObj.dump() | ||
|
Juan C. Espinoza
|
r1021 | print '[Writing] Record No. {} (mode {}).'.format( | ||
| self.counter, | ||||
| self.dataOut.mode | ||||
| ) | ||||
|
Juan C. Espinoza
|
r1010 | |||
| def setHeader(self): | ||||
| ''' | ||||
|
Juan C. Espinoza
|
r1021 | Create an add catalog and header to cedar file | ||
|
Juan C. Espinoza
|
r1010 | ''' | ||
|
Juan C. Espinoza
|
r1021 | header = madrigal.cedar.CatalogHeaderCreator(self.fullname) | ||
| header.createCatalog(**self.catalog) | ||||
| header.createHeader(**self.header) | ||||
| header.write() | ||||
|
Juan C. Espinoza
|
r1010 | |||
| def putData(self): | ||||
| if self.dataOut.flagNoData: | ||||
| return 0 | ||||
|
Juan C. Espinoza
|
r1021 | if self.counter == 0: | ||
| self.setFile() | ||||
|
Juan C. Espinoza
|
r1010 | |||
|
Juan C. Espinoza
|
r1021 | if self.counter <= self.dataOut.nrecords: | ||
|
Juan C. Espinoza
|
r1010 | self.writeBlock() | ||
|
Juan C. Espinoza
|
r1021 | self.counter += 1 | ||
|
Juan C. Espinoza
|
r1010 | |||
|
Juan C. Espinoza
|
r1021 | if self.counter == self.dataOut.nrecords or self.counter == self.blocks: | ||
|
Juan C. Espinoza
|
r1010 | self.setHeader() | ||
|
Juan C. Espinoza
|
r1021 | self.counter = 0 | ||