def test_sdf(self):
"""Test building a SDF from a tarball."""
sdf = metabundle.get_sdf(mdbFile)
def main(args):
# Set the site
site = None
if args.lwa1:
site = 'lwa1'
elif args.lwasv:
site = 'lwasv'
# Open the file and file good data (not raw DRX data)
fh = open(args.filename, 'rb')
try:
for i in xrange(5):
junkFrame = drx.read_frame(fh)
raise RuntimeError("ERROR: '%s' appears to be a raw DRX file, not a DR spectrometer file" % args.filename)
except errors.SyncError:
fh.seek(0)
# Interrogate the file to figure out what frames sizes to expect, now many
# frames there are, and what the transform length is
FRAME_SIZE = drspec.get_frame_size(fh)
nFrames = os.path.getsize(args.filename) // FRAME_SIZE
nChunks = nFrames
LFFT = drspec.get_transform_size(fh)
# Read in the first frame to figure out the DP information
junkFrame = drspec.read_frame(fh)
fh.seek(-FRAME_SIZE, 1)
srate = junkFrame.sample_rate
t0 = junkFrame.time
tInt = junkFrame.header.nints*LFFT/srate
# Offset in frames for beampols beam/tuning/pol. sets
offset = int(round(args.skip / tInt))
fh.seek(offset*FRAME_SIZE, 1)
# Iterate on the offsets until we reach the right point in the file. This
# is needed to deal with files that start with only one tuning and/or a
# different sample rate.
while True:
## Figure out where in the file we are and what the current tuning/sample
## rate is
junkFrame = drspec.read_frame(fh)
srate = junkFrame.sample_rate
t1 = junkFrame.time
tInt = junkFrame.header.nints*LFFT/srate
fh.seek(-FRAME_SIZE, 1)
## See how far off the current frame is from the target
tDiff = t1 - (t0 + args.skip)
## Half that to come up with a new seek parameter
tCorr = -tDiff / 2.0
cOffset = int(round(tCorr / tInt))
offset += cOffset
## If the offset is zero, we are done. Otherwise, apply the offset
## and check the location in the file again/
if cOffset is 0:
break
fh.seek(cOffset*FRAME_SIZE, 1)
# Update the offset actually used
args.skip = t1 - t0
nChunks = (os.path.getsize(args.filename) - fh.tell()) // FRAME_SIZE
# Update the file contents
beam = junkFrame.id
central_freq1, central_freq2 = junkFrame.central_freq
srate = junkFrame.sample_rate
data_products = junkFrame.data_products
t0 = junkFrame.time
tInt = junkFrame.header.nints*LFFT/srate
beginDate = junkFrame.time.datetime
# Report
print("Filename: %s" % args.filename)
if args.metadata is not None:
print("Metadata: %s" % args.metadata)
elif args.sdf is not None:
print("SDF: %s" % args.sdf)
print("Date of First Frame: %s" % beginDate)
print("Beam: %i" % beam)
print("Sample Rate: %i Hz" % srate)
print("Tuning Frequency: %.3f Hz (1); %.3f Hz (2)" % (central_freq1, central_freq2))
print("Data Products: %s" % ','.join(data_products))
print("Frames: %i (%.3f s)" % (nFrames, nFrames*tInt))
print("---")
print("Offset: %.3f s (%i frames)" % (args.skip, offset))
print("Transform Length: %i" % LFFT)
print("Integration: %.3f s" % tInt)
# Setup the output file
outname = os.path.split(args.filename)[1]
outname = os.path.splitext(outname)[0]
outname = '%s-waterfall.hdf5' % outname
if os.path.exists(outname):
if not args.force:
yn = raw_input("WARNING: '%s' exists, overwrite? [Y/n] " % outname)
else:
yn = 'y'
if yn not in ('n', 'N'):
os.unlink(outname)
else:
raise RuntimeError("Output file '%s' already exists" % outname)
f = hdfData.create_new_file(outname)
obsList = {}
if args.metadata is not None:
try:
project = metabundle.get_sdf(args.metadata)
except Exception as e:
if adpReady:
project = metabundleADP.get_sdf(args.metadata)
else:
raise e
sdfBeam = project.sessions[0].drx_beam
spcSetup = project.sessions[0].spcSetup
if sdfBeam != beam:
raise RuntimeError("Metadata is for beam #%i, but data is from beam #%i" % (sdfBeam, beam))
for i,obs in enumerate(project.sessions[0].observations):
sdfStart = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm)
sdfStop = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm + obs.dur)
obsChunks = int(numpy.ceil(obs.dur/1000.0 * drx.FILTER_CODES[obs.filter] / (spcSetup[0]*spcSetup[1])))
obsList[i+1] = (sdfStart, sdfStop, obsChunks)
hdfData.fill_from_metabundle(f, args.metadata)
elif args.sdf is not None:
try:
project = sdf.parse_sdf(args.sdf)
except Exception as e:
if adpReady:
project = sdfADP.parse_sdf(args.sdf)
else:
raise e
sdfBeam = project.sessions[0].drx_beam
spcSetup = project.sessions[0].spcSetup
if sdfBeam != beam:
raise RuntimeError("Metadata is for beam #%i, but data is from beam #%i" % (sdfBeam, beam))
for i,obs in enumerate(project.sessions[0].observations):
sdfStart = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm)
sdfStop = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm + obs.dur)
obsChunks = int(numpy.ceil(obs.dur/1000.0 * drx.FILTER_CODES[obs.filter] / (spcSetup[0]*spcSetup[1])))
obsList[i+1] = (sdfStart, sdfStop, obsChunks)
hdfData.fill_from_sdf(f, args.sdf, station=site)
else:
obsList[1] = (beginDate, datetime(2222,12,31,23,59,59), nChunks)
hdfData.fill_minimum(f, 1, beam, srate, station=site)
data_products = junkFrame.data_products
for o in sorted(obsList.keys()):
for t in (1,2):
hdfData.create_observation_set(f, o, t, numpy.arange(LFFT, dtype=numpy.float64), obsList[o][2], data_products)
f.attrs['FileGenerator'] = 'drspec2hdf.py'
f.attrs['InputData'] = os.path.basename(args.filename)
# Create the various HDF group holders
ds = {}
for o in sorted(obsList.keys()):
obs = hdfData.get_observation_set(f, o)
ds['obs%i' % o] = obs
ds['obs%i-time' % o] = hdfData.get_time(f, o)
for t in (1,2):
ds['obs%i-freq%i' % (o, t)] = hdfData.get_data_set(f, o, t, 'freq')
for p in data_products:
ds["obs%i-%s%i" % (o, p, t)] = hdfData.get_data_set(f, o, t, p)
ds['obs%i-Saturation%i' % (o, t)] = hdfData.get_data_set(f, o, t, 'Saturation')
# Loop over DR spectrometer frames to fill in the HDF5 file
pbar = progress.ProgressBar(max=nChunks)
o = 1
j = 0
firstPass = True
for i in xrange(nChunks):
frame = drspec.read_frame(fh)
cTime = frame.time.datetime
if cTime > obsList[o][1]:
# Increment to the next observation
o += 1
# If we have reached the end, exit...
try:
obsList[o]
firstPass = True
except KeyError:
sys.stdout.write('%s\r' % (' '*pbar.span))
sys.stdout.flush()
print("End of observing block according to SDF, exiting")
break
if cTime < obsList[o][0]:
# Skip over data that occurs before the start of the observation
continue
try:
if frame.time > oTime + 1.001*tInt:
print('Warning: Time tag error at frame %i; %.3f > %.3f + %.3f' % (i, frame.time, oTime, tInt))
except NameError:
pass
oTime = frame.time
if firstPass:
# Otherwise, continue on...
central_freq1, central_freq2 = frame.central_freq
srate = frame.sample_rate
tInt = frame.header.nints*LFFT/srate
freq = numpy.fft.fftshift( numpy.fft.fftfreq(LFFT, d=1.0/srate) )
freq = freq.astype(numpy.float64)
sys.stdout.write('%s\r' % (' '*pbar.span))
sys.stdout.flush()
print("Switching to Obs. #%i" % o)
print("-> Tunings: %.1f Hz, %.1f Hz" % (central_freq1, central_freq2))
print("-> Sample Rate: %.1f Hz" % srate)
print("-> Integration Time: %.3f s" % tInt)
sys.stdout.write(pbar.show()+'\r')
sys.stdout.flush()
j = 0
ds['obs%i-freq1' % o][:] = freq + central_freq1
ds['obs%i-freq2' % o][:] = freq + central_freq2
obs = ds['obs%i' % o]
obs.attrs['tInt'] = tInt
obs.attrs['tInt_Units'] = 's'
obs.attrs['LFFT'] = LFFT
obs.attrs['nChan'] = LFFT
obs.attrs['RBW'] = freq[1]-freq[0]
obs.attrs['RBW_Units'] = 'Hz'
firstPass = False
# Load the data from the spectrometer frame into the HDF5 group
ds['obs%i-time' % o][j] = (frame.time[0], frame.time[1])
ds['obs%i-Saturation1' % o][j,:] = frame.payload.saturations[0:2]
ds['obs%i-Saturation2' % o][j,:] = frame.payload.saturations[2:4]
for t in (1,2):
for p in data_products:
ds['obs%i-%s%i' % (o, p, t)][j,:] = getattr(frame.payload, "%s%i" % (p, t-1), None)
j += 1
# Update the progress bar
pbar.inc()
if i % 10 == 0:
sys.stdout.write(pbar.show()+'\r')
sys.stdout.flush()
sys.stdout.write(pbar.show()+'\n')
sys.stdout.flush()
# Done
fh.close()
# Save the output to a HDF5 file
f.close()
def main(args):
# Get the site and observer
site = stations.lwa1
observer = site.get_observer()
# Filenames in an easier format
inputTGZ = args.filename
# Parse the input file and get the dates of the observations. Be default
# this is for LWA1 but we switch over to LWA-SV if an error occurs.
try:
# LWA1
project = metabundle.get_sdf(inputTGZ)
obsImpl = metabundle.get_observation_spec(inputTGZ)
fileInfo = metabundle.get_session_metadata(inputTGZ)
aspConfigB = metabundle.get_asp_configuration_summary(
inputTGZ, which='Beginning')
aspConfigE = metabundle.get_asp_configuration_summary(inputTGZ,
which='End')
except:
# LWA-SV
## Site changes
site = stations.lwasv
observer = site.get_observer()
## Try again
project = metabundleADP.get_sdf(inputTGZ)
obsImpl = metabundleADP.get_observation_spec(inputTGZ)
fileInfo = metabundleADP.get_session_metadata(inputTGZ)
aspConfigB = metabundleADP.get_asp_configuration_summary(
inputTGZ, which='Beginning')
aspConfigE = metabundleADP.get_asp_configuration_summary(inputTGZ,
which='End')
nObs = len(project.sessions[0].observations)
tStart = [
None,
] * nObs
for i in range(nObs):
tStart[i] = utcjd_to_unix(project.sessions[0].observations[i].mjd +
MJD_OFFSET)
tStart[i] += project.sessions[0].observations[i].mpm / 1000.0
tStart[i] = datetime.utcfromtimestamp(tStart[i])
tStart[i] = _UTC.localize(tStart[i])
# Get the LST at the start
observer.date = (min(tStart)).strftime('%Y/%m/%d %H:%M:%S')
lst = observer.sidereal_time()
# Report on the file
print("Filename: %s" % inputTGZ)
print(" Project ID: %s" % project.id)
print(" Session ID: %i" % project.sessions[0].id)
print(" Observations appear to start at %s" %
(min(tStart)).strftime(_FORMAT_STRING))
print(" -> LST at %s for this date/time is %s" % (site.name, lst))
lastDur = project.sessions[0].observations[nObs - 1].dur
lastDur = timedelta(seconds=int(lastDur / 1000),
microseconds=(lastDur * 1000) % 1000000)
sessionDur = max(tStart) - min(tStart) + lastDur
print(" ")
print(" Total Session Duration: %s" % sessionDur)
print(" -> First observation starts at %s" %
min(tStart).strftime(_FORMAT_STRING))
print(" -> Last observation ends at %s" %
(max(tStart) + lastDur).strftime(_FORMAT_STRING))
if project.sessions[0].observations[0].mode not in ('TBW', 'TBN'):
drspec = 'No'
if project.sessions[0].spcSetup[0] != 0 and project.sessions[
0].spcSetup[1] != 0:
drspec = 'Yes'
drxBeam = project.sessions[0].drx_beam
if drxBeam < 1:
drxBeam = "MCS decides"
else:
drxBeam = "%i" % drxBeam
print(" DRX Beam: %s" % drxBeam)
print(" DR Spectrometer used? %s" % drspec)
if drspec == 'Yes':
print(" -> %i channels, %i windows/integration" %
tuple(project.sessions[0].spcSetup))
else:
tbnCount = 0
tbwCount = 0
for obs in project.sessions[0].observations:
if obs.mode == 'TBW':
tbwCount += 1
else:
tbnCount += 1
if tbwCount > 0 and tbnCount == 0:
print(" Transient Buffer Mode: TBW")
elif tbwCount == 0 and tbnCount > 0:
print(" Transient Buffer Mode: TBN")
else:
print(" Transient Buffer Mode: both TBW and TBN")
print(" ")
print("File Information:")
for obsID in fileInfo.keys():
print(" Obs. #%i: %s" % (obsID, fileInfo[obsID]['tag']))
print(" ")
print("ASP Configuration:")
print(' Beginning')
for k, v in aspConfigB.items():
print(' %s: %i' % (k, v))
print(' End')
for k, v in aspConfigE.items():
print(' %s: %i' % (k, v))
print(" ")
print(" Number of observations: %i" % nObs)
print(" Observation Detail:")
for i in range(nObs):
currDur = project.sessions[0].observations[i].dur
currDur = timedelta(seconds=int(currDur / 1000),
microseconds=(currDur * 1000) % 1000000)
print(" Observation #%i" % (i + 1, ))
currObs = None
for j in range(len(obsImpl)):
if obsImpl[j]['obsID'] == i + 1:
currObs = obsImpl[j]
break
## Basic setup
print(" Target: %s" % project.sessions[0].observations[i].target)
print(" Mode: %s" % project.sessions[0].observations[i].mode)
print(" Start:")
print(" MJD: %i" % project.sessions[0].observations[i].mjd)
print(" MPM: %i" % project.sessions[0].observations[i].mpm)
print(" -> %s" % get_observation_start_stop(
project.sessions[0].observations[i])[0].strftime(_FORMAT_STRING))
print(" Duration: %s" % currDur)
## DP setup
if project.sessions[0].observations[i].mode not in ('TBW', ):
print(" Tuning 1: %.3f MHz" %
(project.sessions[0].observations[i].frequency1 / 1e6, ))
if project.sessions[0].observations[i].mode not in ('TBW', 'TBN'):
print(" Tuning 2: %.3f MHz" %
(project.sessions[0].observations[i].frequency2 / 1e6, ))
if project.sessions[0].observations[i].mode not in ('TBW', ):
print(" Filter code: %i" %
project.sessions[0].observations[i].filter)
if currObs is not None:
if project.sessions[0].observations[i].mode not in ('TBW', ):
if project.sessions[0].observations[i].mode == 'TBN':
print(" Gain setting: %i" % currObs['tbnGain'])
else:
print(" Gain setting: %i" % currObs['drxGain'])
else:
print(
" WARNING: observation specification not found for this observation"
)
## Comments/notes
print(" Observer Comments: %s" %
project.sessions[0].observations[i].comments)
def main(args):
# Parse the command line
filenames = args.filename
# Check if the first argument on the command line is a directory. If so,
# use what is in that directory
if os.path.isdir(filenames[0]):
filenames = [
os.path.join(filenames[0], filename)
for filename in os.listdir(filenames[0])
]
filenames.sort()
# Convert the filenames to absolute paths
filenames = [os.path.abspath(filename) for filename in filenames]
# Open the database connection to NRAO to find the antenna locations
try:
db = database('params')
except Exception as e:
sys.stderr.write("WARNING: %s" % str(e))
sys.stderr.flush()
db = None
# Pass 1 - Get the LWA metadata so we know where we are pointed
context = {
'observer': 'Unknown',
'project': 'Unknown',
'session': None,
'vlaref': None
}
setup = None
sources = []
metadata = {}
lwasite = {}
for filename in filenames:
# Figure out what to do with the file
ext = os.path.splitext(filename)[1]
if ext == '.tgz':
## LWA Metadata
try:
## Extract the SDF
if len(sources) == 0:
try:
sdf = metabundle.get_sdf(filename)
except Exception as e:
sdf = metabundleADP.get_sdf(filename)
context['observer'] = sdf.observer.name
context['project'] = sdf.id
context['session'] = sdf.sessions[0].id
comments = sdf.project_office.sessions[0]
mtch = CORR_CHANNELS.search(comments)
if mtch is not None:
corr_channels = int(mtch.group('channels'), 10)
else:
corr_channels = None
mtch = CORR_INTTIME.search(comments)
if mtch is not None:
corr_inttime = float(mtch.group('inttime'))
else:
corr_inttime = None
mtch = CORR_BASIS.search(comments)
if mtch is not None:
corr_basis = mtch.group('basis')
else:
sys.stderr.write(
"WARNING: No output correlation polarization basis defined, assuming 'linear'.\n"
)
corr_basis = 'linear'
if corr_channels is not None and corr_inttime is not None:
setup = {
'channels': corr_channels,
'inttime': corr_inttime,
'basis': corr_basis
}
else:
sys.stderr.write(
"WARNING: No or incomplete correlation configuration defined, setting to be defined at correlation time.\n"
)
for o, obs in enumerate(sdf.sessions[0].observations):
if type(obs).__name__ == 'Solar':
name = 'Sun'
intent = 'target'
ra = None
dec = None
elif type(obs).__name__ == 'Jovian':
name = 'Jupiter'
intent = 'target'
ra = None
dec = None
else:
name = obs.target
intent = obs.name
ra = ephem.hours(str(obs.ra))
dec = ephem.degrees(str(obs.dec))
tStart = mjdmpm_to_datetime(obs.mjd, obs.mpm)
tStop = mjdmpm_to_datetime(obs.mjd, obs.mpm + obs.dur)
sources.append({
'name': name,
'intent': intent,
'ra2000': ra,
'dec2000': dec,
'start': tStart,
'stop': tStop
})
### Alternate phase centers
comments = sdf.project_office.observations[0][o]
alts = {}
for mtch in ALT_TARGET.finditer(comments):
alt_id = int(mtch.group('id'), 10)
alt_name = mtch.group('target')
try:
alts[alt_id]['name'] = alt_name
except KeyError:
alts[alt_id] = {
'name': alt_name,
'intent': 'dummy',
'ra': None,
'dec': None
}
for mtch in ALT_INTENT.finditer(comments):
alt_id = int(mtch.group('id'), 10)
alt_intent = mtch.group('intent')
try:
alts[alt_id]['intent'] = alt_intent
except KeyError:
alts[alt_id] = {
'name': None,
'intent': alt_intent,
'ra': None,
'dec': None
}
for mtch in ALT_RA.finditer(comments):
alt_id = int(mtch.group('id'), 10)
alt_ra = ephem.hours(mtch.group('ra'))
try:
alts[alt_id]['ra'] = alt_ra
except KeyError:
alts[alt_id] = {
'name': None,
'intent': 'dummy',
'ra': alt_ra,
'dec': None
}
for mtch in ALT_DEC.finditer(comments):
alt_id = int(mtch.group('id'), 10)
alt_dec = ephem.degrees(mtch.group('dec'))
try:
alts[alt_id]['dec'] = alt_dec
except KeyError:
alts[alt_id] = {
'name': None,
'intent': 'dummy',
'ra': None,
'dec': alt_dec
}
for alt_id in sorted(alts.keys()):
alt_name, alt_ra, alt_dec = alts[alt_id]
if alt_name is None or alt_ra is None or alt_dec is None:
sys.stderr.write(
"WARNING: Incomplete alternate phase center %i, skipping.\n"
% alt_id)
else:
sources.append({
'name': alt_name,
'ra2000': alt_ra,
'dec2000': alt_dec,
'start': tStart,
'stop': tStop
})
## Extract the file information so that we can pair things together
fileInfo = metabundle.get_session_metadata(filename)
for obsID in fileInfo.keys():
metadata[fileInfo[obsID]['tag']] = filename
## Figure out LWA1 vs LWA-SV
try:
cs = metabundle.get_command_script(filename)
for c in cs:
if c['subsystem_id'] == 'DP':
site = 'LWA1'
break
elif c['subsystem_id'] == 'ADP':
site = 'LWA-SV'
break
except (RuntimeError, ValueError):
site = 'LWA-SV'
for obsID in fileInfo.keys():
lwasite[fileInfo[obsID]['tag']] = site
except Exception as e:
sys.stderr.write("ERROR reading metadata file: %s\n" % str(e))
sys.stderr.flush()
# Setup what we need to write out a configuration file
corrConfig = {
'context': context,
'setup': setup,
'source': {
'name': '',
'ra2000': '',
'dec2000': ''
},
'inputs': []
}
metadata = {}
for filename in filenames:
#print("%s:" % os.path.basename(filename))
# Skip over empty files
if os.path.getsize(filename) == 0:
continue
# Open the file
fh = open(filename, 'rb')
# Figure out what to do with the file
ext = os.path.splitext(filename)[1]
if ext == '':
## DRX
try:
## Get the site
try:
sitename = lwasite[os.path.basename(filename)]
except KeyError:
sitename = 'LWA1'
## Get the location so that we can set site-specific parameters
if sitename == 'LWA1':
xyz = LWA1_ECEF
off = args.lwa1_offset
elif sitename == 'LWA-SV':
xyz = LWASV_ECEF
off = args.lwasv_offset
else:
raise RuntimeError("Unknown LWA site '%s'" % site)
## Move into the LWA1 coordinate system
### ECEF to LWA1
rho = xyz - LWA1_ECEF
sez = numpy.dot(LWA1_ROT, rho)
enz = sez[[1, 0, 2]] # pylint: disable=invalid-sequence-index
enz[1] *= -1
## Read in the first few frames to get the start time
frames = [drx.read_frame(fh) for i in xrange(1024)]
streams = []
freq1, freq2 = 0.0, 0.0
for frame in frames:
beam, tune, pol = frame.id
if tune == 1:
freq1 = frame.central_freq
else:
freq2 = frame.central_freq
if (beam, tune, pol) not in streams:
streams.append((beam, tune, pol))
tStart = frames[0].time.datetime
tStartAlt = (frames[-1].time - 1023 // len(streams) * 4096 /
frames[-1].sample_rate).datetime
tStartDiff = tStart - tStartAlt
if abs(tStartDiff) > timedelta(microseconds=10000):
sys.stderr.write(
"WARNING: Stale data found at the start of '%s', ignoring\n"
% os.path.basename(filename))
sys.stderr.flush()
tStart = tStartAlt
### ^ Adjustment to the start time to deal with occasional problems
### with stale data in the DR buffers at LWA-SV
## Read in the last few frames to find the end time
fh.seek(os.path.getsize(filename) - 1024 * drx.FRAME_SIZE)
backed = 0
while backed < 2 * drx.FRAME_SIZE:
try:
drx.read_frame(fh)
fh.seek(-drx.FRAME_SIZE, 1)
break
except errors.SyncError:
backed += 1
fh.seek(-drx.FRAME_SIZE - 1, 1)
for i in xrange(32):
try:
frame = drx.read_frame(fh)
beam, tune, _ = frame.id
if tune == 1:
freq1 = frame.central_freq
else:
freq2 = frame.central_freq
except errors.SyncError:
continue
tStop = frame.time.datetime
## Save
corrConfig['inputs'].append({
'file':
filename,
'type':
'DRX',
'antenna':
sitename,
'pols':
'X, Y',
'location': (enz[0], enz[1], enz[2]),
'clockoffset': (off, off),
'fileoffset':
0,
'beam':
beam,
'tstart':
tStart,
'tstop':
tStop,
'freq': (freq1, freq2)
})
except Exception as e:
sys.stderr.write("ERROR reading DRX file: %s\n" % str(e))
sys.stderr.flush()
elif ext == '.vdif':
## VDIF
try:
## Read in the GUPPI header
header = vdif.read_guppi_header(fh)
## Read in the first frame
vdif.FRAME_SIZE = vdif.get_frame_size(fh)
frame = vdif.read_frame(fh)
antID = frame.id[0] - 12300
tStart = frame.time.datetime
nThread = vdif.get_thread_count(fh)
## Read in the last frame
nJump = int(os.path.getsize(filename) / vdif.FRAME_SIZE)
nJump -= 30
fh.seek(nJump * vdif.FRAME_SIZE, 1)
mark = fh.tell()
while True:
try:
frame = vdif.read_frame(fh)
tStop = frame.time.datetime
except Exception as e:
break
## Find the antenna location
pad, edate = db.get_pad('EA%02i' % antID, tStart)
x, y, z = db.get_xyz(pad, tStart)
#print(" Pad: %s" % pad)
#print(" VLA relative XYZ: %.3f, %.3f, %.3f" % (x,y,z))
## Move into the LWA1 coordinate system
### relative to ECEF
xyz = numpy.array([x, y, z])
xyz += VLA_ECEF
### ECEF to LWA1
rho = xyz - LWA1_ECEF
sez = numpy.dot(LWA1_ROT, rho)
enz = sez[[1, 0, 2]] # pylint: disable=invalid-sequence-index
enz[1] *= -1
## Set an apparent position if WiDAR is already applying a delay model
apparent_enz = (None, None, None)
if args.no_vla_delay_model:
apparent_xyz = VLA_ECEF
apparent_rho = apparent_xyz - LWA1_ECEF
apparent_sez = numpy.dot(LWA1_ROT, apparent_rho)
apparent_enz = apparent_sez[[1, 0, 2]] # pylint: disable=invalid-sequence-index
apparent_enz[1] *= -1
## VLA time offset
off = args.vla_offset
## Save
corrConfig['context']['observer'] = header['OBSERVER']
try:
corrConfig['context']['project'] = header[
'BASENAME'].split('_')[0]
corrConfig['context']['session'] = header[
'BASENAME'].split('_')[1].replace('sb', '')
except IndexError:
corrConfig['context']['project'] = header[
'BASENAME'].split('.')[0]
corrConfig['context']['session'] = header[
'BASENAME'].split('.')[1].replace('sb', '')
corrConfig['context']['vlaref'] = re.sub(
'\.[0-9]+\.[0-9]+\.[AB][CD]-.*', '', header['BASENAME'])
corrConfig['source']['name'] = header['SRC_NAME']
corrConfig['source']['intent'] = 'target'
corrConfig['source']['ra2000'] = header['RA_STR']
corrConfig['source']['dec2000'] = header['DEC_STR']
corrConfig['inputs'].append({
'file':
filename,
'type':
'VDIF',
'antenna':
'EA%02i' % antID,
'pols':
'Y, X',
'location': (enz[0], enz[1], enz[2]),
'apparent_location':
(apparent_enz[0], apparent_enz[1], apparent_enz[2]),
'clockoffset': (off, off),
'fileoffset':
0,
'pad':
pad,
'tstart':
tStart,
'tstop':
tStop,
'freq':
header['OBSFREQ']
})
except Exception as e:
sys.stderr.write("ERROR reading VDIF file: %s\n" % str(e))
sys.stderr.flush()
elif ext == '.tgz':
## LWA Metadata
try:
## Extract the file information so that we can pair things together
fileInfo = metabundle.get_session_metadata(filename)
for obsID in fileInfo.keys():
metadata[fileInfo[obsID]['tag']] = filename
except Exception as e:
sys.stderr.write("ERROR reading metadata file: %s\n" % str(e))
sys.stderr.flush()
# Done
fh.close()
# Close out the connection to NRAO
try:
db.close()
except AttributeError:
pass
# Choose a VDIF reference file, if there is one, and mark whether or
# not DRX files were found
vdifRefFile = None
isDRX = False
for cinp in corrConfig['inputs']:
if cinp['type'] == 'VDIF':
if vdifRefFile is None:
vdifRefFile = cinp
elif cinp['type'] == 'DRX':
isDRX = True
# Set a state variable so that we can generate a warning about missing
# DRX files
drxFound = False
# Purge DRX files that don't make sense
toPurge = []
drxFound = False
lwasvFound = False
for cinp in corrConfig['inputs']:
### Sort out multiple DRX files - this only works if we have only one LWA station
if cinp['type'] == 'DRX':
if vdifRefFile is not None:
l0, l1 = cinp['tstart'], cinp['tstop']
v0, v1 = vdifRefFile['tstart'], vdifRefFile['tstop']
ve = (v1 - v0).total_seconds()
overlapWithVDIF = (v0 >= l0 and v0 < l1) or (l0 >= v0
and l0 < v1)
lvo = (min([v1, l1]) - max([v0, l0])).total_seconds()
if not overlapWithVDIF or lvo < 0.25 * ve:
toPurge.append(cinp)
drxFound = True
if cinp['antenna'] == 'LWA-SV':
lwasvFound = True
for cinp in toPurge:
del corrConfig['inputs'][corrConfig['inputs'].index(cinp)]
# Sort the inputs based on the antenna name - this puts LWA1 first,
# LWA-SV second, and the VLA at the end in 'EA' antenna order, i.e.,
# EA01, EA02, etc.
corrConfig['inputs'].sort(key=lambda x: 0 if x['antenna'] == 'LWA1' else (
1 if x['antenna'] == 'LWA-SV' else int(x['antenna'][2:], 10)))
# VDIF/DRX warning check/report
if vdifRefFile is not None and isDRX and not drxFound:
sys.stderr.write(
"WARNING: DRX files provided but none overlapped with VDIF data")
# Duplicate antenna check
antCounts = {}
for cinp in corrConfig['inputs']:
try:
antCounts[cinp['antenna']] += 1
except KeyError:
antCounts[cinp['antenna']] = 1
for ant in antCounts.keys():
if antCounts[ant] != 1:
sys.stderr.write("WARNING: Antenna '%s' is defined %i times" %
(ant, antCounts[ant]))
# Update the file offsets to get things lined up better
tMax = max([cinp['tstart'] for cinp in corrConfig['inputs']])
for cinp in corrConfig['inputs']:
diff = tMax - cinp['tstart']
offset = diff.days * 86400 + diff.seconds + diff.microseconds / 1e6
cinp['fileoffset'] = max([0, offset])
# Reconcile the source lists for when we have eLWA data. This is needed so
# that we use the source information contained in the VDIF files rather than
# the stub information contained in the SDFs
if len(sources) <= 1:
if corrConfig['source']['name'] != '':
## Update the source information with what comes from the VLA
try:
sources[0] = corrConfig['source']
except IndexError:
sources.append(corrConfig['source'])
# Update the dwell time using the minimum on-source time for all inputs if
# there is only one source, i.e., for full eLWA runs
if len(sources) == 1:
sources[0]['start'] = max(
[cinp['tstart'] for cinp in corrConfig['inputs']])
sources[0]['stop'] = min(
[cinp['tstop'] for cinp in corrConfig['inputs']])
# Render the configuration
startRef = sources[0]['start']
s = 0
for source in sources:
startOffset = source['start'] - startRef
startOffset = startOffset.total_seconds()
dur = source['stop'] - source['start']
dur = dur.total_seconds()
## Skip over dummy scans and scans that start after the files end
if source['intent'] in (None, 'dummy'):
continue
if source['start'] > max(
[cinp['tstop'] for cinp in corrConfig['inputs']]):
print(
"Skipping scan of %s which starts at %s, %.3f s after the data end"
% (source['name'], source['start'],
(source['start'] -
max([cinp['tstop']
for cinp in corrConfig['inputs']])).total_seconds()))
continue
## Small correction for the first scan to compensate for stale data at LWA-SV
if lwasvFound and s == 0:
startOffset += 10.0
dur -= 10.0
## Skip over scans that are too short
if dur < args.minimum_scan_length:
continue
## Setup
if args.output is None:
fh = sys.stdout
else:
outname = args.output
if len(sources) > 1:
outname += str(s + 1)
fh = open(outname, 'w')
try:
repo = git.Repo(os.path.dirname(os.path.abspath(__file__)))
try:
branch = repo.active_branch.name
hexsha = repo.active_branch.commit.hexsha
except TypeError:
branch = '<detached>'
hexsha = repo.head.commit.hexsha
shortsha = hexsha[-7:]
dirty = ' (dirty)' if repo.is_dirty() else ''
except git.exc.GitError:
branch = 'unknown'
hexsha = 'unknown'
shortsha = 'unknown'
dirty = ''
## Preamble
fh.write("# Created\n")
fh.write("# on %s\n" % datetime.now())
fh.write("# using %s, revision %s.%s%s\n" %
(os.path.basename(__file__), branch, shortsha, dirty))
fh.write("\n")
## Observation context
fh.write("Context\n")
fh.write(" Observer %s\n" % corrConfig['context']['observer'])
fh.write(" Project %s\n" % corrConfig['context']['project'])
if corrConfig['context']['session'] is not None:
fh.write(" Session %s\n" % corrConfig['context']['session'])
if corrConfig['context']['vlaref'] is not None:
fh.write(" VLARef %s\n" % corrConfig['context']['vlaref'])
fh.write("EndContext\n")
fh.write("\n")
## Configuration, if present
if corrConfig['setup'] is not None:
fh.write("Configuration\n")
fh.write(" Channels %i\n" % corrConfig['setup']['channels'])
fh.write(" IntTime %.3f\n" % corrConfig['setup']['inttime'])
fh.write(" PolBasis %s\n" % corrConfig['setup']['basis'])
fh.write("EndConfiguration\n")
fh.write("\n")
## Source
fh.write("Source\n")
fh.write("# Observation start is %s\n" % source['start'])
fh.write("# Duration is %s\n" % (source['stop'] - source['start'], ))
fh.write(" Name %s\n" % source['name'])
fh.write(" Intent %s\n" % source['intent'].lower())
if source['name'] not in ('Sun', 'Jupiter'):
fh.write(" RA2000 %s\n" % source['ra2000'])
fh.write(" Dec2000 %s\n" % source['dec2000'])
fh.write(" Duration %.3f\n" % dur)
fh.write("SourceDone\n")
fh.write("\n")
## Input files
for cinp in corrConfig['inputs']:
fh.write("Input\n")
fh.write("# Start time is %s\n" % cinp['tstart'])
fh.write("# Stop time is %s\n" % cinp['tstop'])
try:
fh.write("# Beam is %i\n" % cinp['beam'])
except KeyError:
pass
try:
fh.write("# VLA pad is %s\n" % cinp['pad'])
except KeyError:
pass
try:
fh.write("# Frequency tuning 1 is %.3f Hz\n" % cinp['freq'][0])
fh.write("# Frequency tuning 2 is %.3f Hz\n" % cinp['freq'][1])
except TypeError:
fh.write("# Frequency tuning is %.3f Hz\n" % cinp['freq'])
fh.write(" File %s\n" % cinp['file'])
try:
metaname = metadata[os.path.basename(cinp['file'])]
fh.write(" MetaData %s\n" % metaname)
except KeyError:
if cinp['type'] == 'DRX':
sys.stderr.write(
"WARNING: No metadata found for '%s', source %i\n" %
(os.path.basename(cinp['file']), s + 1))
sys.stderr.flush()
pass
fh.write(" Type %s\n" % cinp['type'])
fh.write(" Antenna %s\n" % cinp['antenna'])
fh.write(" Pols %s\n" % cinp['pols'])
fh.write(" Location %.6f, %.6f, %.6f\n" %
cinp['location'])
try:
if cinp['apparent_location'][0] is not None:
fh.write(" ApparentLocation %.6f, %.6f, %.6f\n" %
cinp['apparent_location'])
except KeyError:
pass
fh.write(" ClockOffset %s, %s\n" % cinp['clockoffset'])
fh.write(" FileOffset %.3f\n" %
(startOffset + cinp['fileoffset'], ))
fh.write("InputDone\n")
fh.write("\n")
if fh != sys.stdout:
fh.close()
# Increment the source/file counter
s += 1
def main(args):
# Length of the FFT and the window to use
LFFT = args.fft_length
if args.bartlett:
window = numpy.bartlett
elif args.blackman:
window = numpy.blackman
elif args.hanning:
window = numpy.hanning
else:
window = fxc.null_window
args.window = window
# Open the file and find good data
idf = LWA1DataFile(args.filename,
ignore_timetag_errors=args.ignore_time_errors)
# Metadata
nFramesFile = idf.get_info('nframe')
srate = idf.get_info('sample_rate')
antpols = idf.get_info('nantenna')
# Number of frames to integrate over
nFramesAvg = int(args.average * srate / 512) * antpols
nFramesAvg = int(1.0 * (nFramesAvg // antpols) * 512 /
float(LFFT)) * LFFT / 512 * antpols
args.average = 1.0 * (nFramesAvg // antpols) * 512 / srate
maxFrames = nFramesAvg
# Offset into the file, if needed
offset = idf.offset(args.skip)
# Number of remaining chunks (and the correction to the number of
# frames to read in).
if args.metadata is not None:
args.duration = 0
if args.duration == 0:
args.duration = 1.0 * nFramesFile / antpols * 512 / srate
args.duration -= args.skip
else:
args.duration = int(
round(args.duration * srate * antpols / 512) // antpols * 512 //
srate)
nChunks = int(round(args.duration / args.average))
if nChunks == 0:
nChunks = 1
nFrames = nFramesAvg * nChunks
# Date & Central Frequency
t1 = idf.get_info('start_time')
beginDate = t1.datetime
central_freq1 = idf.get_info('freq1')
# File summary
print("Filename: %s" % args.filename)
print("Date of First Frame: %s" % str(beginDate))
print("Antenna/Pols: %i" % antpols)
print("Sample Rate: %i Hz" % srate)
print("Tuning Frequency: %.3f Hz" % (central_freq1, ))
print("Frames: %i (%.3f s)" %
(nFramesFile, 1.0 * nFramesFile / antpols * 512 / srate))
print("---")
print("Offset: %.3f s (%i frames)" % (args.skip, offset))
print("Integration: %.3f s (%i frames; %i frames per antenna/pol)" %
(args.average, nFramesAvg, nFramesAvg // antpols))
print("Duration: %.3f s (%i frames; %i frames per antenna/pol)" %
(args.average * nChunks, nFrames, nFrames // antpols))
print("Chunks: %i" % nChunks)
print(" ")
# Estimate clip level (if needed)
if args.estimate_clip_level:
estimate = idf.estimate_levels(sigma=5.0)
clip1 = 1.0 * sum(estimate) / len(estimate)
else:
clip1 = args.clip_level
# Get the antennas for Stokes calculation
if args.metadata is not None:
try:
project = metabundle.get_sdf(args.metadata)
station = stations.lwa1
except Exception as e:
project = metabundleADP.get_sdf(args.metadata)
station = stations.lwasv
elif args.lwasv:
station = stations.lwasv
else:
station = stations.lwa1
antennas = station.antennas
# Setup the output file
outname = os.path.split(args.filename)[1]
outname = os.path.splitext(outname)[0]
outname = '%s-tbn-waterfall.hdf5' % outname
if os.path.exists(outname):
if not args.force:
yn = raw_input("WARNING: '%s' exists, overwrite? [Y/n] " % outname)
else:
yn = 'y'
if yn not in ('n', 'N'):
os.unlink(outname)
else:
raise RuntimeError("Output file '%s' already exists" % outname)
f = hdfData.create_new_file(outname)
# Look at the metadata and come up with a list of observations. If
# there are no metadata, create a single "observation" that covers the
# whole file.
obsList = {}
if args.metadata is not None:
try:
project = metabundle.get_sdf(args.metadata)
except Exception as e:
project = metabundleADP.get_sdf(args.metadata)
sdfBeam = project.sessions[0].drx_beam
if sdfBeam != 5:
raise RuntimeError(
"Metadata is for beam #%i, but data is from beam #%i" %
(sdfBeam, 5))
for i, obs in enumerate(project.sessions[0].observations):
sdfStart = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm)
sdfStop = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm + obs.dur)
obsDur = obs.dur / 1000.0
obsSR = tbn.FILTER_CODES[obs.filter]
obsList[i + 1] = (sdfStart, sdfStop, obsDur, obsSR)
print("Observations:")
for i in sorted(obsList.keys()):
obs = obsList[i]
print(" #%i: %s to %s (%.3f s) at %.3f MHz" %
(i, obs[0], obs[1], obs[2], obs[3] / 1e6))
print(" ")
hdfData.fill_from_metabundle(f, args.metadata)
elif args.sdf is not None:
try:
project = sdf.parse_sdf(args.sdf)
except Exception as e:
project = sdfADP.parse_sdf(args.sdf)
sdfBeam = project.sessions[0].drx_beam
if sdfBeam != 5:
raise RuntimeError(
"Metadata is for beam #%i, but data is from beam #%i" %
(sdfBeam, 5))
for i, obs in enumerate(project.sessions[0].observations):
sdfStart = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm)
sdfStop = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm + obs.dur)
obsDur = obs.dur / 1000.0
obsSR = tbn.FILTER_CODES[obs.filter]
obsList[i + 1] = (sdfStart, sdfStop, obsDur, obsSR)
site = 'lwa1'
if args.lwasv:
site = 'lwasv'
hdfData.fill_from_sdf(f, args.sdf, station=site)
else:
obsList[1] = (datetime.utcfromtimestamp(t1),
datetime(2222, 12, 31, 23, 59, 59), args.duration, srate)
site = 'lwa1'
if args.lwasv:
site = 'lwasv'
hdfData.fill_minimum(f, 1, 5, srate, station=site)
if (not args.stokes):
data_products = ['XX', 'YY']
else:
data_products = ['I', 'Q', 'U', 'V']
for o in sorted(obsList.keys()):
for t in range(len(antennas) // 2):
hdfData.create_observation_set(
f, o, t + 1, numpy.arange(LFFT, dtype=numpy.float64),
int(round(obsList[o][2] / args.average)), data_products)
f.attrs['FileGenerator'] = 'tbnWaterfall.py'
f.attrs['InputData'] = os.path.basename(args.filename)
# Create the various HDF group holders
ds = {}
for o in sorted(obsList.keys()):
obs = hdfData.get_observation_set(f, o)
ds['obs%i' % o] = obs
ds['obs%i-time' % o] = hdfData.get_time(f, o)
for t in range(len(antennas) // 2):
ds['obs%i-freq%i' % (o, t + 1)] = hdfData.get_data_set(
f, o, t + 1, 'freq')
for p in data_products:
ds["obs%i-%s%i" % (o, p, t + 1)] = hdfData.get_data_set(
f, o, t + 1, p)
ds['obs%i-Saturation%i' % (o, t + 1)] = hdfData.get_data_set(
f, o, t + 1, 'Saturation')
# Load in the correct analysis function
if (not args.stokes):
process_data = process_data_to_linear
else:
process_data = process_data_to_stokes
# Go!
for o in sorted(obsList.keys()):
try:
process_data(idf,
antennas,
obsList[o][0],
obsList[o][2],
obsList[o][3],
args,
ds,
obsID=o,
clip1=clip1)
except RuntimeError as e:
print("Observation #%i: %s, abandoning this observation" %
(o, str(e)))
# Save the output to a HDF5 file
f.close()
# Close out the data file
idf.close()
def main(args):
# Get the file names
meta = args.metadata
data = args.filename
# Get all observations and their start times
try:
## LWA-1
sdf = metabundle.get_sdf(meta)
ses = metabundle.get_session_spec(meta)
obs = metabundle.get_observation_spec(meta)
except:
## LWA-SV
### Try again
sdf = metabundleADP.get_sdf(meta)
ses = metabundleADP.get_session_spec(meta)
obs = metabundleADP.get_observation_spec(meta)
obs.sort(_obs_comp)
tStart = []
oDetails = []
for i,o in enumerate(obs):
tStart.append( mjdmpm_to_datetime(o['mjd'], o['mpm']) )
oDetails.append( {'m': o['mode'], 'd': o['dur'] / 1000.0, 'f': o['bw'],
'p': o['project_id'], 's': o['session_id'], 'o': o['obs_id'],
't': sdf.sessions[0].observations[o['obs_id']-1].target} )
print("Observation #%i" % (o['obs_id']))
print(" Start: %i, %i -> %s" % (o['mjd'], o['mpm'], tStart[-1]))
print(" Mode: %s" % mode_to_string(o['mode']))
print(" BW: %i" % o['bw'])
print(" Target: %s" % sdf.sessions[0].observations[o['obs_id']-1].target)
print(" ")
# Figure out where in the file the various bits are.
fh = open(data, 'rb')
lf = drx.read_frame(fh)
beam, j, k = lf.id
if beam != obs[0]['drx_beam']:
print('ERROR: Beam mis-match, metadata is for #%i, file is for #%i' % (obs[0]['drx_beam'], beam))
sys.exit()
firstFrame = lf.time.datetime
if abs(firstFrame - min(tStart)) > timedelta(seconds=30):
print('ERROR: Time mis-match, metadata is for %s, file is for %s' % (min(tStart), firstFrame))
sys.exit()
fh.seek(0)
for i in range(len(tStart)):
eof = False
## Get observation properties
oStart = tStart[i]
oMode = mode_to_string(oDetails[i]['m'])
oDur = oDetails[i]['d']
oBW = oDetails[i]['f']
print("Seeking %s observation of %.3f seconds at %s" % (oMode, oDur, oStart))
## Get the correct reader to use
if oMode == 'TBW':
reader = tbw
bwKey = None
bwMult = 520.0 / 400
fCount = 400
elif oMode == 'TBN':
reader = tbn
bwKey = tbn.FILTER_CODES
bwMult = 520.0 / 512
fCount = 512
else:
reader = drx
bwKey = drx.FILTER_CODES
bwMult = 4.0 / 4096
fCount = 4096
## Jump ahead to where the next frame should be, if needed
if i != 0:
pDur = oDetails[i-1]['d']
pBW = oDetails[i-1]['f']
nFramesSkip = int(pDur*bwKey[pBW]*bwMult)
fh.seek(nFramesSkip*reader.FRAME_SIZE, 1)
if fh.tell() >= os.path.getsize(data):
fh.seek(-10*reader.FRAME_SIZE, 2)
## Figure out where we are and make sure we line up on a frame
## NOTE: This should never be needed
fail = True
while fail:
try:
frame = reader.read_frame(fh)
fail = False
except errors.SyncError:
fh.seek(1, 1)
except errors.EOFError:
break
fh.seek(-reader.FRAME_SIZE, 1)
## Go in search of the start of the observation
if frame.time.datetime < oStart:
### We aren't at the beginning yet, seek fowards
print("-> At byte %i, time is %s < %s" % (fh.tell(), frame.time.datetime, oStart))
while frame.time.datetime < oStart:
try:
frame = reader.read_frame(fh)
except errors.SyncError:
fh.seek(1, 1)
except errors.EOFError:
break
#print(frame.time.datetime, oStart)
elif frame.time.datetime > oStart:
### We've gone too far, seek backwards
print("-> At byte %i, time is %s > %s" % (fh.tell(), frame.time.datetime, oStart))
while frame.time.datetime > oStart:
if fh.tell() == 0:
break
fh.seek(-2*reader.FRAME_SIZE, 1)
try:
frame = reader.read_frame(fh)
except errors.SyncError:
fh.seek(-1, 1)
except errors.EOFError:
break
#print(frame.time.datetime, oStart)
else:
### We're there already
print("-> At byte %i, time is %s = %s" % (fh.tell(), frame.time.datetime, oStart))
## Jump back exactly one frame so that the filehandle is in a position
## to read the first frame that is part of the observation
try:
frame = reader.read_frame(fh)
print("-> At byte %i, time is %s = %s" % (fh.tell(), frame.time.datetime, oStart))
fh.seek(-reader.FRAME_SIZE, 1)
except errors.EOFError:
pass
## Update the bytes ranges
if fh.tell() < os.path.getsize(data):
oDetails[i]['b'] = fh.tell()
oDetails[i]['e'] = -1
else:
oDetails[i]['b'] = -1
oDetails[i]['e'] = -1
if i != 0:
oDetails[i-1]['e'] = fh.tell()
## Progress report
if oDetails[i]['b'] >= 0:
print('-> Obs.', oDetails[i]['o'], 'starts at byte', oDetails[i]['b'])
else:
print('-> Obs.', oDetails[i]['o'], 'starts after the end of the file')
print(" ")
# Report
for i in range(len(tStart)):
if oDetails[i]['b'] < 0:
print("%s, Session %i, Observation %i: not found" % (oDetails[i]['p'], oDetails[i]['s'], oDetails[i]['o']))
else:
print("%s, Session %i, Observation %i: %i to %i (%i bytes)" % (oDetails[i]['p'], oDetails[i]['s'], oDetails[i]['o'], oDetails[i]['b'], oDetails[i]['e'], (oDetails[i]['e'] - oDetails[i]['b'])))
print(" ")
# Split
if not args.list:
for i in range(len(tStart)):
if oDetails[i]['b'] < 0:
continue
## Report
print("Working on Observation %i" % (i+1,))
## Create the output name
if args.source:
outname = '%s_%i_%s.dat' % (oDetails[i]['p'], oDetails[i]['s'], oDetails[i]['t'].replace(' ', '').replace('/','').replace('&','and'))
else:
outname = '%s_%i_%i.dat' % (oDetails[i]['p'], oDetails[i]['s'], oDetails[i]['o'])
oMode = mode_to_string(oDetails[i]['m'])
## Get the correct reader to use
if oMode == 'TBW':
reader = tbw
elif oMode == 'TBN':
reader = tbn
else:
reader = drx
## Get the number of frames
if oDetails[i]['e'] > 0:
nFramesRead = (oDetails[i]['e'] - oDetails[i]['b']) // reader.FRAME_SIZE
else:
nFramesRead = (os.path.getsize(data) - oDetails[i]['b']) // reader.FRAME_SIZE
## Split
if os.path.exists(outname):
if not args.force:
yn = input("WARNING: '%s' exists, overwrite? [Y/n] " % outname)
else:
yn = 'y'
if yn not in ('n', 'N'):
os.unlink(outname)
else:
print("WARNING: output file '%s' already exists, skipping" % outname)
continue
fh.seek(oDetails[i]['b'])
t0 = time.time()
oh = open(outname, 'wb')
for sl in [2**i for i in range(17)[::-1]]:
while nFramesRead >= sl:
temp = fh.read(sl*reader.FRAME_SIZE)
oh.write(temp)
nFramesRead -= sl
oh.close()
t1 = time.time()
print(" Copied %i bytes in %.3f s (%.3f MB/s)" % (os.path.getsize(outname), t1-t0, os.path.getsize(outname)/1024.0**2/(t1-t0)))
print(" ")
def main(args):
# Length of the FFT and the window to use
LFFT = args.fft_length
if args.bartlett:
window = numpy.bartlett
elif args.blackman:
window = numpy.blackman
elif args.hanning:
window = numpy.hanning
else:
window = fxc.null_window
args.window = window
# Open the file and find good data (not spectrometer data)
fh = open(args.filename, "rb")
try:
for i in xrange(5):
junkFrame = drspec.read_frame(fh)
raise RuntimeError(
"ERROR: '%s' appears to be a DR spectrometer file, not a raw DRX file"
% args.filename)
except errors.SyncError:
fh.seek(0)
# Good, we seem to have a real DRX file, switch over to the LDP interface
fh.close()
idf = LWA1DataFile(args.filename,
ignore_timetag_errors=args.ignore_time_errors)
# Metadata
nFramesFile = idf.get_info('nframe')
beam = idf.get_info('beam')
srate = idf.get_info('sample_rate')
beampols = idf.get_info('nbeampol')
beams = max([1, beampols // 4])
# Number of frames to integrate over
nFramesAvg = int(args.average * srate / 4096) * beampols
nFramesAvg = int(1.0 * (nFramesAvg // beampols) * 4096 /
float(LFFT)) * LFFT / 4096 * beampols
args.average = 1.0 * (nFramesAvg // beampols) * 4096 / srate
maxFrames = nFramesAvg
# Offset into the file, if needed
offset = idf.offset(args.skip)
# Number of remaining chunks (and the correction to the number of
# frames to read in).
if args.metadata is not None:
args.duration = 0
if args.duration == 0:
args.duration = 1.0 * nFramesFile / beampols * 4096 / srate
args.duration -= args.skip
else:
args.duration = int(
round(args.duration * srate * beampols / 4096) / beampols * 4096 /
srate)
nChunks = int(round(args.duration / args.average))
if nChunks == 0:
nChunks = 1
nFrames = nFramesAvg * nChunks
# Date & Central Frequency
t1 = idf.get_info('start_time')
beginDate = t1.datetime
central_freq1 = idf.get_info('freq1')
central_freq2 = idf.get_info('freq2')
# File summary
print("Filename: %s" % args.filename)
print("Date of First Frame: %s" % str(beginDate))
print("Beams: %i" % beams)
print("Tune/Pols: %i" % beampols)
print("Sample Rate: %i Hz" % srate)
print("Tuning Frequency: %.3f Hz (1); %.3f Hz (2)" %
(central_freq1, central_freq2))
print("Frames: %i (%.3f s)" %
(nFramesFile, 1.0 * nFramesFile / beampols * 4096 / srate))
print("---")
print("Offset: %.3f s (%i frames)" % (args.skip, offset))
print("Integration: %.3f s (%i frames; %i frames per beam/tune/pol)" %
(args.average, nFramesAvg, nFramesAvg / beampols))
print("Duration: %.3f s (%i frames; %i frames per beam/tune/pol)" %
(args.average * nChunks, nFrames, nFrames / beampols))
print("Chunks: %i" % nChunks)
print(" ")
# Estimate clip level (if needed)
if args.estimate_clip_level:
estimate = idf.estimate_levels(fh, sigma=5.0)
clip1 = (estimate[0] + estimate[1]) / 2.0
clip2 = (estimate[2] + estimate[3]) / 2.0
else:
clip1 = args.clip_level
clip2 = args.clip_level
# Make the pseudo-antennas for Stokes calculation
antennas = []
for i in xrange(4):
if i // 2 == 0:
newAnt = stations.Antenna(1)
else:
newAnt = stations.Antenna(2)
if i % 2 == 0:
newAnt.pol = 0
else:
newAnt.pol = 1
antennas.append(newAnt)
# Setup the output file
outname = os.path.split(args.filename)[1]
outname = os.path.splitext(outname)[0]
outname = '%s-waterfall.hdf5' % outname
if os.path.exists(outname):
if not args.force:
yn = raw_input("WARNING: '%s' exists, overwrite? [Y/n] " % outname)
else:
yn = 'y'
if yn not in ('n', 'N'):
os.unlink(outname)
else:
raise RuntimeError("Output file '%s' already exists" % outname)
f = hdfData.create_new_file(outname)
# Look at the metadata and come up with a list of observations. If
# there are no metadata, create a single "observation" that covers the
# whole file.
obsList = {}
if args.metadata is not None:
try:
project = metabundle.get_sdf(args.metadata)
except Exception as e:
project = metabundleADP.get_sdf(args.metadata)
sdfBeam = project.sessions[0].drx_beam
spcSetup = project.sessions[0].spcSetup
if sdfBeam != beam:
raise RuntimeError(
"Metadata is for beam #%i, but data is from beam #%i" %
(sdfBeam, beam))
for i, obs in enumerate(project.sessions[0].observations):
sdfStart = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm)
sdfStop = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm + obs.dur)
obsDur = obs.dur / 1000.0
obsSR = drx.FILTER_CODES[obs.filter]
obsList[i + 1] = (sdfStart, sdfStop, obsDur, obsSR)
print("Observations:")
for i in sorted(obsList.keys()):
obs = obsList[i]
print(" #%i: %s to %s (%.3f s) at %.3f MHz" %
(i, obs[0], obs[1], obs[2], obs[3] / 1e6))
print(" ")
hdfData.fill_from_metabundle(f, args.metadata)
elif args.sdf is not None:
try:
project = sdf.parse_sdf(args.sdf)
except Exception as e:
project = sdfADP.parse_sdf(args.sdf)
sdfBeam = project.sessions[0].drx_beam
spcSetup = project.sessions[0].spcSetup
if sdfBeam != beam:
raise RuntimeError(
"Metadata is for beam #%i, but data is from beam #%i" %
(sdfBeam, beam))
for i, obs in enumerate(project.sessions[0].observations):
sdfStart = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm)
sdfStop = mcs.mjdmpm_to_datetime(obs.mjd, obs.mpm + obs.dur)
obsDur = obs.dur / 1000.0
obsSR = drx.FILTER_CODES[obs.filter]
obsList[i + 1] = (sdfStart, sdfStop, obsDur, obsSR)
site = 'lwa1'
if args.lwasv:
site = 'lwasv'
hdfData.fill_from_sdf(f, args.sdf, station=site)
else:
obsList[1] = (datetime.utcfromtimestamp(t1),
datetime(2222, 12, 31, 23, 59, 59), args.duration, srate)
site = 'lwa1'
if args.lwasv:
site = 'lwasv'
hdfData.fill_minimum(f, 1, beam, srate, station=site)
if (not args.stokes):
data_products = ['XX', 'YY']
else:
data_products = ['I', 'Q', 'U', 'V']
for o in sorted(obsList.keys()):
for t in (1, 2):
hdfData.create_observation_set(
f, o, t, numpy.arange(LFFT, dtype=numpy.float64),
int(round(obsList[o][2] / args.average)), data_products)
f.attrs['FileGenerator'] = 'hdfWaterfall.py'
f.attrs['InputData'] = os.path.basename(args.filename)
# Create the various HDF group holders
ds = {}
for o in sorted(obsList.keys()):
obs = hdfData.get_observation_set(f, o)
ds['obs%i' % o] = obs
ds['obs%i-time' % o] = hdfData.get_time(f, o)
for t in (1, 2):
ds['obs%i-freq%i' % (o, t)] = hdfData.get_data_set(f, o, t, 'freq')
for p in data_products:
ds["obs%i-%s%i" % (o, p, t)] = hdfData.get_data_set(f, o, t, p)
ds['obs%i-Saturation%i' % (o, t)] = hdfData.get_data_set(
f, o, t, 'Saturation')
# Load in the correct analysis function
if (not args.stokes):
processDataBatch = processDataBatchLinear
else:
processDataBatch = processDataBatchStokes
# Go!
for o in sorted(obsList.keys()):
try:
processDataBatch(idf,
antennas,
obsList[o][0],
obsList[o][2],
obsList[o][3],
args,
ds,
obsID=o,
clip1=clip1,
clip2=clip2)
except RuntimeError as e:
print("Observation #%i: %s, abandoning this observation" %
(o, str(e)))
# Save the output to a HDF5 file
f.close()
# Close out the data file
idf.close()