def prepOutfile(self,filename,headerChanges=None):
outFile = File(filename,"w+")
if headerChanges is not None:
for key,val in headerChanges:
self.modify_header(key,val)
outFile.write(self.write_header())
self.reset_header()
return outFile
def _readTim(self):
"""Read time series from .tim file.
Currently only works with 32-bit time series.
Creates class attribute timBuffer.
"""
f = File(self.file,"r")
f.seek(self.hdrlen)
self.timBuffer = Buffer(self.info["nsamples"],C.c_float)
f.cread(self.timBuffer)
def __init__(self,filename):
"""Create Filterbank instance.
Args:
filename -- string containing name of file to process
"""
Header.__init__(self,filename)
self.f = File(filename,"r",nbits=self.info["nbits"])
infofile = "%s.info"%(self.basename)
if os.path.isfile(infofile):
try:
self.stats = cPickle.load(open(infofile,"r"))
except:
self.stats = None
else:
self.stats = None
if self.ctype == C.c_float:
self.lib = C.CDLL("libSigPyProc32.so")
else:
self.lib = C.CDLL("libSigPyProc8.so")
class Filterbank(Header):
"""Class to handle filterbank files in all their glory.
Parameters
----------
\tfilename -- name of filterbank file
Methods
-------
\tcollapse -- Collapse filterbank in frequency and/or time
\tdedisperse -- Simple dedispersion algorithm (fixed some sigproc bugs)
\tdownsample -- Downsample filterbank in frequency and/or time
"""
def __init__(self,filename):
"""Create Filterbank instance.
Args:
filename -- string containing name of file to process
"""
Header.__init__(self,filename)
self.f = File(filename,"r",nbits=self.info["nbits"])
infofile = "%s.info"%(self.basename)
if os.path.isfile(infofile):
try:
self.stats = cPickle.load(open(infofile,"r"))
except:
self.stats = None
else:
self.stats = None
if self.ctype == C.c_float:
self.lib = C.CDLL("libSigPyProc32.so")
else:
self.lib = C.CDLL("libSigPyProc8.so")
def getDMdelays(self,dm):
"""For a given dispersion measure return delay for each channel
"""
chanFreqs = (numpy.arange(self.info["nchans"])
*self.info['foff'])+self.info['fch1']
chanDelays = (dm * 4.148808e3 *
((chanFreqs**-2)-(self.info['fch1']**-2)
)/self.info["tsamp"]).round().astype("int32")
return chanDelays
def collapse(self,blocksize=512):
"""Collapse a filterbank in frequency.
Args:
blocksize -- number of samples to read in each gulp
Return: TimeSeries instance
"""
readBuffer = Buffer(blocksize*self.info["nchans"],self.ctype)
timBuffer = Buffer(self.info["nsamples"],C.c_float)
passPlan = ReadPlan(self,readBuffer)
passPlan.readOnce(blocksize)
for nsamps,ii in passPlan.makePass():
self.lib.getTim(readBuffer.Cbuffer,timBuffer.Cbuffer,
self.info["nchans"],nsamps,ii*blocksize)
return TimeSeries(self.info.copy(),timBuffer)
def bandpass(self,blocksize=512):
"""Collapse a filterbank in time.
Args:
blocksize -- number of samples to read in each gulp
Return: BandpassFromBuffer instance
"""
readBuffer = Buffer(blocksize*self.info["nchans"],self.ctype)
bpassBuffer = Buffer(self.info["nchans"],C.c_float)
passPlan = ReadPlan(self,readBuffer)
passPlan.readOnce(blocksize)
for nsamps,ii in passPlan.makePass():
self.lib.getBpass(readBuffer.Cbuffer,bpassBuffer.Cbuffer,
self.info["nchans"],blocksize)
return BandpassFromBuffer(self.info.copy(),bpassBuffer)
def dedisperse(self,dm,gulp=10000):
"""Dedisperse filterbank to timeseries.
Args:
dm -- Dispersion measure to dedisperse to
gulp -- size of block to read at a time, if chosen gulp
is less than maximum dispersion delay gulp is taken as 2 * max delay.
Returns: TimeSeries instance
"""
chanDelays = self.getDMdelays(dm)
delayPointer = arrayToPointer(chanDelays)
maxDelay = int(chanDelays.max())
gulp = max(2*maxDelay,gulp)
timLen = self.info["nsamples"]-maxDelay
timBuffer = Buffer(timLen,C.c_float)
readBuffer = Buffer(self.info["nchans"]*gulp,self.ctype)
passPlan = ReadPlan(self,readBuffer)
passPlan.readSkipBack(gulp,maxDelay)
for nsamps,ii in passPlan.makePass():
self.lib.dedisperse(readBuffer.Cbuffer,timBuffer.Cbuffer,delayPointer,
maxDelay, self.info["nchans"], nsamps, ii*(gulp-maxDelay))
timInfo = self.info.copy()
timInfo["nsamples"] = timLen
timInfo["refdm"] = dm
return TimeSeries(timInfo,timBuffer)
def downsample(self,tfactor=1,ffactor=1,filename=None):
"""Downsample filterbank in frequency and/or time.
Args:
tfactor -- Factor to downsample in time
ffactor -- Factor to downsample in frequecy (must be factor of nchans)
filename -- File to write downsampled data to.
Returns: Filterbank instance (from output file)
"""
if filename is None:
filename = "%s_f%d_t%d.fil"%(self.basename,ffactor,tfactor)
self.f.seek(self.hdrlen)
if not self.info["nchans"]%ffactor == 0:
raise ValueError,"Bad frequency factor given"
self.downsample_header(tfactor=tfactor,ffactor=ffactor)
outFile = self.prepOutfile(filename,
(("tsamp",self.info["tsamp"]*tfactor),
("nchans",self.info["nchans"]/ffactor),
("foff",self.info["foff"]*ffactor)))
readBuffer = Buffer(tfactor*self.info["nchans"],self.ctype)
writeBuffer = Buffer(self.info["nchans"]/ffactor,self.ctype)
tempBuffer = Buffer(self.info["nchans"]/ffactor,C.c_int)
self.lib.downsampleFil(self.f.f, outFile.f, readBuffer.Cbuffer,
writeBuffer.Cbuffer,tempBuffer.Cbuffer,
tfactor, ffactor, self.info["nchans"],
self.info["nsamples"])
return Filterbank(filename)
def fold(self,period,dm,nbins=50,nints=32,nbands=32,gulp=10000):
"""Fold filterbank phase bins, subintegrations and subbands.
Args:
period -- period in seconds to fold with
nbins -- number of phase bins in output
nints -- number of subintegrations in output
Returns: FoldedData instance
"""
nbands = min(nbands,self.info["nchans"])
chanDelays = self.getDMdelays(dm)
delayPointer = arrayToPointer(chanDelays)
maxDelay = int(chanDelays.max())
gulp = max(2*maxDelay,gulp)
foldBuffer = Buffer(nbins*nints*nbands,C.c_float)
countBuffer = Buffer(nbins*nints*nbands,C.c_int)
readBuffer = Buffer(self.info["nchans"]*gulp,self.ctype)
passPlan = ReadPlan(self,readBuffer)
passPlan.readSkipBack(gulp,maxDelay)
for nsamps,ii in passPlan.makePass():
self.lib.foldFil(readBuffer.Cbuffer, foldBuffer.Cbuffer, countBuffer.Cbuffer,
delayPointer, maxDelay, C.c_double(self.info["tsamp"]),
C.c_double(period), gulp, self.info["nchans"], nbins,
nints, nbands, ii*(gulp-maxDelay))
parentInfo = self.info.copy()
return FoldedData(parentInfo,foldBuffer,countBuffer,
period,dm,nbins,nints,nbands)
def dropBits32to8(self,gulp=1024,flag=0,clip=0):
if self.stats is None:
raise AttributeError,"First run getStatistics()"
readBuffer = Buffer(self.info["nchans"]*gulp,self.ctype)
writeBuffer = Buffer(self.info["nchans"]*gulp,C.c_ubyte)
passPlan = ReadPlan(self,readBuffer)
passPlan.readOnce(gulp)
if flag is not 0:
flagBuffer = Buffer(self.info["nchans"]*gulp,C.c_ubyte)
flagMax = flag*self.stats["sigma"].astype("float32")
flagMin = -flag*self.stats["sigma"].astype("float32")
if clip is not 0:
chanMax = numpy.array([min(a,b) for a,b in zip(clip*self.stats["sigma"],self.stats["maxima"])])
chanMin = numpy.array([max(a,b) for a,b in zip(-clip*self.stats["sigma"],self.stats["minima"])])
else:
chanMax = self.stats["maxima"]
chanMin = self.stats["minima"]
chanFactor = ((chanMax-chanMin)/255.)
chanPlus = (chanMin/chanFactor)
outFile = self.prepOutfile("%s_8bit.fil"%(self.basename),(("nbits",8)))
if flag is not 0:
changes = (("nbits",8),("source_name","%s_mask"%(self.info["source_name"].split()[0])))
flagFile = self.prepOutfile("%s_8bit_mask.fil"%(self.basename),changes)
for nsamps,ii in passPlan.makePass():
self.lib.to8bit(readBuffer.Cbuffer,writeBuffer.Cbuffer,
arrayToPointer(chanFactor),arrayToPointer(chanPlus),
nsamps,self.info["nchans"])
outFile.cwrite(writeBuffer)
if flag is not 0:
lib.flagBlock(readBuffer.Cbuffer,flagBuffer.Cbuffer,
arrayToPointer(flagMax),arrayToPointer(flagMin),
nsamps,self.info["nchans"])
flagFile.cwrite(flagBuffer)
if flag is not 0:
return(Filterbank(outFile.name),Filterbank(flagFile.name))
else:
return Filterbank(outFile.name)
def getStatistics(self,window=10001,gulp=30003):
if gulp < window: raise ValueError,"gulp must be > window"
readBuffer = Buffer(self.info["nchans"]*gulp,self.ctype)
writeBuffer = Buffer(self.info["nchans"]*gulp,self.ctype)
maximaBuffer = Buffer(self.info["nchans"],C.c_float)
minimaBuffer = Buffer(self.info["nchans"],C.c_float)
meansBuffer = Buffer(self.info["nchans"],C.c_float)
bpassBuffer = Buffer(self.info["nchans"],C.c_float)
stdevBuffer = Buffer(self.info["nchans"],C.c_float)
outFile = self.prepOutfile("%s_RM.fil"%(self.basename))
passPlan = ReadPlan(self,readBuffer)
passPlan.readSkipBack(gulp,window)
for nsamps,ii in passPlan.makePass():
self.lib.getStats(readBuffer.Cbuffer, meansBuffer.Cbuffer,
bpassBuffer.Cbuffer, stdevBuffer.Cbuffer,
writeBuffer.Cbuffer,maximaBuffer.Cbuffer,
minimaBuffer.Cbuffer,self.info["nchans"],nsamps,window,ii)
if ii == 0:
outFile.cwrite(writeBuffer)
elif ii == passPlan.nreads-1:
outFile.cwrite(writeBuffer, nunits=nsamps*self.info["nchans"],
offset=self.info["nchans"]*window)
else:
outFile.cwrite(writeBuffer,
nunits = (gulp-window)*self.info["nchans"],
offset = self.info["nchans"]*window)
stdevBuffer.Ndarray = numpy.sqrt(stdevBuffer.Ndarray/self.info["nsamples"])
infoFile = open("%s_RM.info"%(self.basename),"w+")
info = {"sigma":stdevBuffer.Ndarray,
"bandpass":bpassBuffer.Ndarray,
"maxima":maximaBuffer.Ndarray,
"minima":minimaBuffer.Ndarray}
cPickle.dump(info,infoFile)
infoFile.close()
return Filterbank(outFile.name)
def prepOutfile(self,filename,headerChanges=None):
outFile = File(filename,"w+")
if headerChanges is not None:
for key,val in headerChanges:
self.modify_header(key,val)
outFile.write(self.write_header())
self.reset_header()
return outFile