How to use the obspy.core.read function in obspy

def test_positive_gradient(self):
        from OP_waveforms import stream_positive_derivative
        from obspy.core import read

        base_path = self.wo.opdict['base_path']
        test_datadir = self.wo.opdict['test_datadir']

        st = read(os.path.join(base_path, test_datadir, 'raw_data',
                               'YA.UV15.00.HHZ.MSEED'))
        tr = st[0]
        npts = len(tr.data)
        dt = tr.stats.delta
        x = np.arange(npts)*dt

        # set up a polynomial function
        y = (3+2*x+4*x*x+5*x*x*x)
        dy_exp = (2+8*x+15*x*x)

        tr.data = y
        st = stream_positive_derivative(st)
        np.testing.assert_almost_equal(tr.data[20:100], dy_exp[20:100], 2)

if file.comp[-1] not in comps:
                    continue
                fullpath = os.path.join(file.path, file.file)
                datafiles[station][file.comp[-1]].append(fullpath)
            else:
                MULTIPLEX = True
                print("Mutliplex mode, reading the files")
                fullpath = os.path.join(file.path, file.file)
                multiplexed = sorted(glob.glob(fullpath))
                for comp in comps:
                    for fn in multiplexed:
                        if fn in MULTIPLEX_files:
                            _ = MULTIPLEX_files[fn]
                        else:
                            # print("Reading %s" % fn)
                            _ = read(fn, format=params.archive_format or None)
                            traces = []
                            for tr in _:
                                if "%s.%s" % (tr.stats.network, tr.stats.station) in stations and tr.stats.channel[-1] in comps:
                                    traces.append(tr)
                            del _
                            _ = Stream(traces=traces)
                            MULTIPLEX_files[fn] = _
                        datafiles[station][comp].append(_)

    for istation, station in enumerate(stations):
        net, sta = station.split(".")
        for comp in comps:
            files = eval("datafiles['%s']['%s']" % (station, comp))
            if len(files) != 0:
                logger.debug("%s.%s Reading %i Files" %
                              (station, comp, len(files)))

def read(pathname_or_url, *args, ** kwargs):  # format=None, headonly=False,
    """
    Read waveform files into an Stream object.

    Doc of obspy.core.read:
    """
    pathname_or_url, ext = os.path.splitext(pathname_or_url)
    ms = obspy.core.read(pathname_or_url + ext, *args, ** kwargs)
    ignore_starttime = kwargs.get('ignore_starttime', False)
    content = []
    hatfiles = glob.glob(pathname_or_url + '.HAT')
    hatfiles.sort()
    for hatfile in hatfiles:
        with open(hatfile, 'r') as file_:
            file_content = file_.read().strip('\n')
            file_content = file_content.replace('nan', 'np.nan')
            if file_content != '':
                content.extend(file_content.split('\n'))
    if len(content) > 0 and len(content) == len(ms):
        for i in range(len(ms)):
            try:
                st = eval(content[i])  # quiet slow and of course very bad
            except NameError as ex:
                if 'masked' in content[i]:

ofid.write('\nHi I am rank number %d and I am processing the following files for you: \n' %rank)
        for fname in mycontent:
            ofid.write(fname+'\n')
        
    for filepath in mycontent:
        
        filename=filepath.split('/')[-1]
  
        if verbose==True:
            ofid.write('\n========================================================================================\n')
            ofid.write('opening file: '+filepath+'\n')
            t=time.time()-t0
            ofid.write('Time elapsed since start: '+str(t)+'\n')
        #- read data
        try:
            data=read(filepath)
        except TypeError:
            if verbose==True: 
                ofid.write('file could not be opened, skip.')
            continue
        except IOError:
            if verbose: 
                ofid.write('file could not be opened, skip.')
            continue
        
        #- initialize a stream that is plotted in case check option is set
        if check==True:
            cstr=Stream()
        #- initialize the stream that recollects the trace segments
        colloc_data=Stream()
        
        #- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

#if options.keybindings:
    #    PickingGUI()
    #    for i in self.dictKeybindings.items():
    #        print i
    #    return

    if options.local:
        streams=[]
        streams.append(read('20091227_105240_Z.RJOB'))
        streams[0].append(read('20091227_105240_N.RJOB')[0])
        streams[0].append(read('20091227_105240_E.RJOB')[0])
        streams.append(read('20091227_105240_Z.RMOA'))
        streams[1].append(read('20091227_105240_N.RMOA')[0])
        streams[1].append(read('20091227_105240_E.RMOA')[0])
        streams.append(read('20091227_105240_Z.RNON'))
        streams[2].append(read('20091227_105240_N.RNON')[0])
        streams[2].append(read('20091227_105240_E.RNON')[0])
        streams.append(read('20091227_105240_Z.RTBE'))
        streams[3].append(read('20091227_105240_N.RTBE')[0])
        streams[3].append(read('20091227_105240_E.RTBE')[0])
        streams.append(read('20091227_105240_Z.RWMO'))
        streams[4].append(read('20091227_105240_N.RWMO')[0])
        streams[4].append(read('20091227_105240_E.RWMO')[0])
        #streams=[]
        #streams.append(read('RJOB_061005_072159.ehz.new'))
        #streams[0].append(read('RJOB_061005_072159.ehn.new')[0])
        #streams[0].append(read('RJOB_061005_072159.ehe.new')[0])
        #streams.append(read('RNON_160505_000059.ehz.new'))
        #streams.append(read('RMOA_160505_014459.ehz.new'))
        #streams[2].append(read('RMOA_160505_014459.ehn.new')[0])
        #streams[2].append(read('RMOA_160505_014459.ehe.new')[0])
    else:

def _getRA(self,ftc,evedf,sta):
        CorDF=pd.DataFrame(index=evedf.Event.values,columns=['Xcor','STALTA','TimeStamp','SampRate','MaxCC','MaxSTALTA','threshold','Nc'])
        #CorDF['FilesToCorr']=FilesToCorr
        
        conStream=self._applyFilter(obspy.core.read(ftc),condat=True)
        if not isinstance(conStream,obspy.core.stream.Stream):
            return None,None
        CorDF['Nc']=len(list(set([x.stats.channel for x in conStream])))
        CorDF['SampRate']=conStream[0].stats.sampling_rate
        MPcon,TR=self.multiplex(conStream,evedf.Nc.median(),retTR=True)
        CorDF['TimeStamp']=min([x.stats.starttime.timestamp for x in TR])
        #get continous data parameters for Xcor
        MPconFD=scipy.fftpack.fft(MPcon,n=2**int(evedf.reqlen.median()).bit_length())
        n = int(np.median([len(x) for x in evedf.MPtem])) ##TODO This assumes all templates are of equal length, if not will break
        a = pd.rolling_mean(MPcon, n)[n-1:]
        b = pd.rolling_std(MPcon, n)[n-1:]
        b *= np.sqrt((n-1.0) / n)

            
        for corevent,corrow in CorDF.iterrows():
            evrow=evedf[evedf.Event==corevent].iloc[0]

#    PickingGUI()
    #    for i in self.dictKeybindings.items():
    #        print i
    #    return

    if options.local:
        streams=[]
        streams.append(read('20091227_105240_Z.RJOB'))
        streams[0].append(read('20091227_105240_N.RJOB')[0])
        streams[0].append(read('20091227_105240_E.RJOB')[0])
        streams.append(read('20091227_105240_Z.RMOA'))
        streams[1].append(read('20091227_105240_N.RMOA')[0])
        streams[1].append(read('20091227_105240_E.RMOA')[0])
        streams.append(read('20091227_105240_Z.RNON'))
        streams[2].append(read('20091227_105240_N.RNON')[0])
        streams[2].append(read('20091227_105240_E.RNON')[0])
        streams.append(read('20091227_105240_Z.RTBE'))
        streams[3].append(read('20091227_105240_N.RTBE')[0])
        streams[3].append(read('20091227_105240_E.RTBE')[0])
        streams.append(read('20091227_105240_Z.RWMO'))
        streams[4].append(read('20091227_105240_N.RWMO')[0])
        streams[4].append(read('20091227_105240_E.RWMO')[0])
        #streams=[]
        #streams.append(read('RJOB_061005_072159.ehz.new'))
        #streams[0].append(read('RJOB_061005_072159.ehn.new')[0])
        #streams[0].append(read('RJOB_061005_072159.ehe.new')[0])
        #streams.append(read('RNON_160505_000059.ehz.new'))
        #streams.append(read('RMOA_160505_014459.ehz.new'))
        #streams[2].append(read('RMOA_160505_014459.ehn.new')[0])
        #streams[2].append(read('RMOA_160505_014459.ehe.new')[0])
    else:
        try:

(options, args) = parser.parse_args()
    for req in ['-d','-t','-i']:
        if not getattr(parser.values,parser.get_option(req).dest):
            parser.print_help()
            return
    
    #if options.keybindings:
    #    PickingGUI()
    #    for i in self.dictKeybindings.items():
    #        print i
    #    return

    if options.local:
        streams=[]
        streams.append(read('20091227_105240_Z.RJOB'))
        streams[0].append(read('20091227_105240_N.RJOB')[0])
        streams[0].append(read('20091227_105240_E.RJOB')[0])
        streams.append(read('20091227_105240_Z.RMOA'))
        streams[1].append(read('20091227_105240_N.RMOA')[0])
        streams[1].append(read('20091227_105240_E.RMOA')[0])
        streams.append(read('20091227_105240_Z.RNON'))
        streams[2].append(read('20091227_105240_N.RNON')[0])
        streams[2].append(read('20091227_105240_E.RNON')[0])
        streams.append(read('20091227_105240_Z.RTBE'))
        streams[3].append(read('20091227_105240_N.RTBE')[0])
        streams[3].append(read('20091227_105240_E.RTBE')[0])
        streams.append(read('20091227_105240_Z.RWMO'))
        streams[4].append(read('20091227_105240_N.RWMO')[0])
        streams[4].append(read('20091227_105240_E.RWMO')[0])
        #streams=[]
        #streams.append(read('RJOB_061005_072159.ehz.new'))
        #streams[0].append(read('RJOB_061005_072159.ehn.new')[0])

:param stream: unfiltered obspy.core.stream.Stream object.
    :param id_: the id of the stream to read.
    :param startdate: the startdate configuration value.
    :param enddate: the enddate configuration value.
    :param goal_sampling_rate: the sampling rate.
    :paran logger: the logger instance to use for logging.
    """
    added = 0
    modified = 0
    unchanged = 0
    for basename in files:
        pathname = os.path.join(folder, basename)
        # logger.debug('reading file %s' % pathname)
        try:
            # Note: if format is None or unknown, obspy will use auto-detection.
            stream = obspy.core.read(pathname, headonly=True,
                                     format=archive_format or None)
            for id in set([t.id for t in stream]):
                update_rv = process_stream(db, folder, basename, stream, id,
                                           startdate, enddate,
                                           goal_sampling_rate)
                if update_rv == 1:
                    added += 1
                elif update_rv == -1:
                    modified += 1
                else:
                    unchanged += 1
        except obspy.io.mseed.ObsPyMSEEDFilesizeTooSmallError as e:
            logger.warning("Ignoring possible empty file '%s'."
                           ' Got error %s: %s' %
                           (pathname, e.__class__.__name__, str(e)))
        except OSError as e:

#- Create a trace object and fill in the basic information
            tr_correlation_stack=Trace()


            tr_correlation_stack.stats.sampling_rate=dat1.stats.sampling_rate
            tr_correlation_stack.data=correlation_stack

            #- open file and write correlation function
            fileid_correlation_stack=outdir+'/stacks/'+fn1+'.'+fn2+'.'+corr_type+'.'+corrname+'.'+tformat
            
            
            #- linear stack
            if os.path.exists(fileid_correlation_stack)==True:
                if verbose: 
                    print "Correlation stack already exists. Add to previous one."
                tr_old=read(fileid_correlation_stack)[0]
                tr_correlation_stack.data=tr_correlation_stack.data+tr_old.data
                
                if tformat=='SAC':
                    tr_correlation_stack.stats=tr_old.stats
                    tr_correlation_stack.stats.sac['user0']+=n
                    tr_correlation_stack.stats.sac['user1']+=tslen
                tr_correlation_stack.write(fileid_correlation_stack, format=tformat)
            else:
                if tformat=='SAC':
                    tr_correlation_stack.stats.sac={}
                    tr_correlation_stack.stats.starttime=UTCDateTime(2000, 01, 01)-maxlag
                    tr_correlation_stack.stats.network=dat1.stats.network
                    tr_correlation_stack.stats.station=dat2.stats.station
                    tr_correlation_stack.stats.channel=dat1.stats.channel
                    
                    tr_correlation_stack.stats.sac['b']=-maxlag