def test_vdif_read(self):
"""Test reading in a frame from a VDIF file."""
fh = open(vdifFile, 'rb')
# First frame
frame1 = vdif.read_frame(fh)
# Validate header
station, thread = frame1.id
self.assertEqual(station, 19284)
self.assertEqual(thread, 0)
self.assertEqual(frame1.header.is_legacy, 0)
self.assertEqual(frame1.header.is_invalid, 0)
self.assertEqual(frame1.header.ref_epoch, 30)
self.assertEqual(frame1.header.seconds_from_epoch, 9106862)
self.assertEqual(frame1.header.frame_in_second, 59866)
self.assertEqual(frame1.header.frame_length, 8224 // 8)
self.assertEqual(frame1.header.nchan, 4)
self.assertEqual(frame1.header.bits_per_sample, 2)
self.assertEqual(frame1.header.is_complex, 0)
# Validate (some) data
for k, d in enumerate(
(1.0, -1.0, -1.0, -1.0, 1.0, 1.0, 1.0, 1.0, 1.0, -1.0)):
i = k % frame1.header.nchan
j = k // frame1.header.nchan
self.assertAlmostEqual(frame1.payload.data[i, j], d, 5)
# Second frame
frame2 = vdif.read_frame(fh)
# Validate header
station, thread = frame2.id
self.assertEqual(station, 19284)
self.assertEqual(thread, 0)
self.assertEqual(frame2.header.is_legacy, 0)
self.assertEqual(frame2.header.is_invalid, 0)
self.assertEqual(frame2.header.ref_epoch, 30)
self.assertEqual(frame2.header.seconds_from_epoch, 9106862)
self.assertEqual(frame2.header.frame_in_second, 59867)
self.assertEqual(frame2.header.frame_length, 8224 // 8)
self.assertEqual(frame2.header.nchan, 4)
self.assertEqual(frame2.header.bits_per_sample, 2)
self.assertEqual(frame2.header.is_complex, 0)
# Validate (some) data
for k, d in enumerate(
(-1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0)):
i = k % frame2.header.nchan
j = k // frame2.header.nchan
self.assertAlmostEqual(frame2.payload.data[i, j], d, 5)
fh.close()
def test_vdif_real(self):
"""Test writing real data to VDIF format."""
# Setup the file names
testFile = os.path.join(self.testPath, 'tbw-test-W.fits')
# Get some data
frames = self._get_tbw()
# Write the data
with open(testFile, 'wb') as fh:
for frame in frames:
vFrame = vdif.Frame(frame.id,
frame.time,
bits=8,
data=frame.payload.data[0, :].astype(
numpy.int8),
sample_rate=196e6)
vFrame.write_raw_frame(fh)
# Read it back in
with open(testFile, 'rb') as fh:
for tFrame in frames:
vFrame = vrdr.read_frame(fh, sample_rate=196e6)
self.assertAlmostEqual(vFrame.time, tFrame.time, 6)
numpy.testing.assert_allclose(
(vFrame.payload.data * 256 - 1) / 2,
tFrame.payload.data[0, :].astype(numpy.int8),
atol=1e-6)
def test_vdif_frames_per_second(self):
"""Test reading a VDIF file with a GUPPI header."""
filename = glob.glob('*.vdif')[0]
# Open the file
fh = open(filename, 'rb')
# Read the GUPPI header and a frame
header = vdif.read_guppi_header(fh)
frame0 = vdif.read_frame(fh)
# Find the number of frames per second
fps = vdif.get_frames_per_second(fh)
# Does it make sense?
bw = header['OBSBW']
bw *= 1 if frame0.header.is_complex else 2
calculated_fps = int(bw / frame0.payload.data.size)
self.assertEqual(fps, calculated_fps)
# Find the sample rate
sample_rate = vdif.get_sample_rate(fh)
self.assertAlmostEqual(sample_rate, bw, 6)
fh.close()
def test_vdif_complex(self):
"""Test writing complex data to VIDF format."""
# Setup the file names
testFile = os.path.join(self.testPath, 'tbn-test-W.fits')
# Get some data
frames = self.__getTBN()
# Write the data
fh = open(testFile, 'wb')
for frame in frames:
stand, pol = frame.id
if pol == 1:
continue
vFrame = vdif.Frame(stand,
frame.time,
bits=8,
data=frame.payload.data,
sample_rate=100e3)
vFrame.write_raw_frame(fh)
fh.close()
# Read it back in
fh = open(testFile, 'rb')
for tFrame in frames[::2]:
vFrame = vrdr.read_frame(fh)
for v, t in zip((vFrame.payload.data * 256 - 1 - 1j) / 2,
tFrame.payload.data):
self.assertAlmostEqual(v, t, 6)
fh.close()
def test_vdif_real(self):
"""Test writing real data to VDIF format."""
# Setup the file names
testFile = os.path.join(self.testPath, 'tbw-test-W.fits')
# Get some data
frames = self.__getTBW()
# Write the data
fh = open(testFile, 'wb')
for frame in frames:
vFrame = vdif.Frame(frame.id,
frame.time,
bits=8,
data=frame.payload.data[0, :].astype(
numpy.int8))
vFrame.write_raw_frame(fh)
fh.close()
# Read it back in
fh = open(testFile, 'rb')
for tFrame in frames:
vFrame = vrdr.read_frame(fh)
self.assertAlmostEqual(vFrame.time, tFrame.time, 6)
for v, t in zip((vFrame.payload.data * 256 - 1) / 2,
tFrame.payload.data[0, :].astype(numpy.int8)):
self.assertAlmostEqual(v, t, 6)
fh.close()
def test_vdif_errors(self):
"""Test reading in all frames from a truncated VDIF file."""
fh = open(vdifFile, 'rb')
# Frames 1 through 10
for i in range(1, 11):
frame = vdif.read_frame(fh)
# Last frame should be an error (errors.EOFError)
self.assertRaises(errors.EOFError, vdif.read_frame, fh)
fh.close()
def test_vdif_guppi_header(self):
"""Test reading a VDIF file with a GUPPI header."""
filename = glob.glob('*.vdif')[0]
# Open the file
fh = open(filename, 'rb')
# Make sure it is there
self.assertTrue(vdif.has_guppi_header(fh))
# Read the GUPPI header
header = vdif.read_guppi_header(fh)
self.assertEqual(header['NBITS'], 4)
self.assertEqual(header['PKTSIZE'], 5000)
self.assertAlmostEqual(header['OBSBW'], 8.0e6, 6)
# And now read some frames to make sure that everything is ok
frame0 = vdif.read_frame(fh)
frame1 = vdif.read_frame(fh)
self.assertEqual(frame0.payload.data.size, header['PKTSIZE']*8//header['NBITS'])
fh.close()
def test_vdif_sort(self):
"""Test sorting VDIF frames by time tags."""
fh = open(vdifFile, 'rb')
# Frames 1 through 10
frames = []
for i in range(1, 11):
frames.append(vdif.read_frame(fh, sample_rate=16e6))
frames.sort()
frames = frames[::-1]
for i in range(1, len(frames)):
self.assertTrue(frames[i - 1] >= frames[i])
fh.close()
def test_vdif_math(self):
"""Test mathematical operations on VDIF frame data via frames."""
fh = open(vdifFile, 'rb')
# Frames 1 through 10
frames = []
for i in range(1, 11):
frames.append(vdif.read_frame(fh))
fh.close()
nchan, nSamples = frames[0].payload.data.shape
# Multiplication
frameT = frames[0] * 2.0
for i in range(nchan):
for j in range(nSamples):
self.assertAlmostEqual(frameT.payload.data[i, j],
2 * frames[0].payload.data[i, j], 2)
frameT *= 2.0
for i in range(nchan):
for j in range(nSamples):
self.assertAlmostEqual(frameT.payload.data[i, j],
4 * frames[0].payload.data[i, j], 2)
frameT = frames[0] * frames[1]
for i in range(nchan):
for j in range(nSamples):
self.assertAlmostEqual(
frameT.payload.data[i, j], frames[0].payload.data[i, j] *
frames[1].payload.data[i, j], 2)
# Addition
frameA = frames[0] + 2.0
for i in range(nchan):
for j in range(nSamples):
self.assertAlmostEqual(frameA.payload.data[i, j],
2 + frames[0].payload.data[i, j], 2)
frameA += 2.0
for i in range(nchan):
for j in range(nSamples):
self.assertAlmostEqual(frameA.payload.data[i, j],
4 + frames[0].payload.data[i, j], 2)
frameA = frames[0] + frames[1]
for i in range(nchan):
for j in range(nSamples):
self.assertAlmostEqual(
frameA.payload.data[i, j], frames[0].payload.data[i, j] +
frames[1].payload.data[i, j], 2)
def test_vdif_comps(self):
"""Test the VDIF frame comparison operators (>, <, etc.) for time tags."""
fh = open(vdifFile, 'rb')
# Frames 1 through 10
frames = []
for i in range(1, 11):
frames.append(vdif.read_frame(fh, sample_rate=16e6))
fh.close()
self.assertTrue(0 < frames[0])
self.assertFalse(0 > frames[0])
self.assertTrue(frames[-1] >= frames[0])
self.assertFalse(frames[-1] <= frames[0])
self.assertTrue(frames[0] == frames[0])
self.assertFalse(frames[0] == frames[-1])
self.assertFalse(frames[0] != frames[0])
def test_vdif_math(self):
"""Test mathematical operations on VDIF frame data via frames."""
fh = open(vdifFile, 'rb')
# Frames 1 through 10
frames = []
for i in range(1, 11):
frames.append(vdif.read_frame(fh))
fh.close()
nchan, nSamples = frames[0].payload.data.shape
# Multiplication
frameT = frames[0] * 2.0
numpy.testing.assert_allclose(frameT.payload.data,
2 * frames[0].payload.data,
atol=1e-6)
frameT *= 2.0
numpy.testing.assert_allclose(frameT.payload.data,
4 * frames[0].payload.data,
atol=1e-6)
frameT = frames[0] * frames[1]
numpy.testing.assert_allclose(frameT.payload.data,
frames[0].payload.data *
frames[1].payload.data,
atol=1e-6)
# Addition
frameA = frames[0] + 2.0
numpy.testing.assert_allclose(frameA.payload.data,
2 + frames[0].payload.data,
atol=1e-6)
frameA += 2.0
numpy.testing.assert_allclose(frameA.payload.data,
4 + frames[0].payload.data,
atol=1e-6)
frameA = frames[0] + frames[1]
numpy.testing.assert_allclose(frameA.payload.data,
frames[0].payload.data +
frames[1].payload.data,
atol=1e-6)
def get_thread_count(filehandle):
"""
Find out how many thrads are present by examining the first 1024
records. Return the number of threads found.
"""
# Save the current position in the file so we can return to that point
fhStart = filehandle.tell()
# Make sure we have a frame size to work with
try:
vdif.FRAME_SIZE
except AttributeError:
vdif.FRAME_SIZE = vdif.get_frame_size(filehandle)
# Build up the list-of-lists that store ID codes and loop through 1024
# frames. In each case, parse pull the thread ID and append the thread
# ID to the relevant thread array if it is not already there.
threads = []
i = 0
while i < 1024:
try:
cFrame = vdif.read_frame(filehandle)
except errors.SyncError:
filehandle.seek(vdif.FRAME_SIZE, 1)
continue
except errors.EOFError:
continue
cID = cFrame.header.thread_id
if cID not in threads:
threads.append(cID)
i += 1
# Return to the place in the file where we started
filehandle.seek(fhStart)
# Return the number of threads found
return len(threads)
def test_vdif_complex(self):
"""Test writing complex data to VIDF format."""
# Setup the file names
testFile = os.path.join(self.testPath, 'tbn-test-W.fits')
# Get some data
frames = self._get_tbn()
# Write the data
with open(testFile, 'wb') as fh:
for frame in frames:
stand, pol = frame.id
if pol == 1:
continue
## We need an integer number of frame per second so adjust the sample rate
vFrame = vdif.Frame(stand,
frame.time,
bits=8,
data=frame.payload.data,
sample_rate=102.4e3)
vFrame.write_raw_frame(fh)
# Read it back in
with open(testFile, 'rb') as fh:
for tFrame in frames:
stand, pol = tFrame.id
if pol == 1:
continue
vFrame = vrdr.read_frame(fh, sample_rate=102.4e3)
self.assertAlmostEqual(vFrame.time, tFrame.time, 6)
vData = vFrame.payload.data
vData.real = (vData.real * 256 - 1).astype(numpy.int8) // 2
vData.imag = (vData.imag * 256 - 1).astype(numpy.int8) // 2
numpy.testing.assert_allclose(vData,
tFrame.payload.data,
atol=1e-6)
def main(args):
if args[0] == '-s':
skip = float(args[1])
filename = args[2]
else:
skip = 0
filename = args[0]
fh = open(filename, 'rb')
header = vdif.read_guppi_header(fh)
vdif.FRAME_SIZE = vdif.get_frame_size(fh)
nThreads = get_thread_count(fh)
nFramesFile = os.path.getsize(filename) // vdif.FRAME_SIZE
nFramesSecond = get_frames_per_second(fh)
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
sample_rate = junkFrame.sample_rate
vdif.DATA_LENGTH = junkFrame.payload.data.size
nSampsFrame = vdif.DATA_LENGTH
station, thread = junkFrame.id
tunepols = nThreads
beampols = tunepols
fh.seek(-vdif.FRAME_SIZE, 1)
# Store the information about the first frame
prevDate = junkFrame.time.datetime
prevTime = junkFrame.header.seconds_from_epoch
prevFrame = junkFrame.header.frame_in_second
# Skip ahead
fh.seek(int(skip * sample_rate / vdif.DATA_LENGTH) * vdif.FRAME_SIZE, 1)
# Report on the file
print("Filename: %s" % os.path.basename(args[0]))
print(" Station: %i" % station)
print(" Thread count: %i" % nThreads)
print(" Date of first frame: %i -> %s" % (prevTime, str(prevDate)))
print(" Samples per frame: %i" % vdif.DATA_LENGTH)
print(" Frames per second: %i" % nFramesSecond)
print(" Sample rate: %i Hz" % sample_rate)
print(" Bit Depth: %i" % junkFrame.header.bits_per_sample)
print(" ")
if skip != 0:
print("Skipping ahead %i frames (%.6f seconds)" %
(int(skip * sample_rate / vdif.DATA_LENGTH) * 4,
int(skip * sample_rate / vdif.DATA_LENGTH) * vdif.DATA_LENGTH /
sample_rate))
print(" ")
prevDate = ['' for i in xrange(nThreads)]
prevTime = [0 for i in xrange(nThreads)]
prevFrame = [0 for i in xrange(nThreads)]
for i in xrange(nThreads):
currFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
station, thread = currFrame.id
prevDate[thread] = currFrame.time.datetime
prevTime[thread] = currFrame.header.seconds_from_epoch
prevFrame[thread] = currFrame.header.frame_in_second
inError = False
while True:
try:
currFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
if inError:
print("ERROR: sync. error cleared @ byte %i" %
(fh.tell() - vdif.FRAME_SIZE, ))
inError = False
except errors.SyncError:
if not inError:
print("ERROR: invalid frame (sync. word error) @ byte %i" %
fh.tell())
inError = True
fh.seek(vdif.FRAME_SIZE, 1)
continue
except errors.EOFError:
break
station, thread = currFrame.id
currDate = currFrame.time.datetime
currTime = currFrame.header.seconds_from_epoch
currFrame = currFrame.header.frame_in_second
if thread == 0 and currTime % 10 == 0 and currFrame == 0:
print("station %i, thread %i: t.t. %i @ frame %i -> %s" %
(station, thread, currTime, currFrame, currDate))
deltaT = (currTime - prevTime[thread]) * nFramesSecond + (
currFrame - prevFrame[thread])
#print(station, thread, deltaT, fh.tell())
if deltaT < 1:
print("ERROR: t.t. %i @ frame %i < t.t. %i @ frame %i + 1" %
(currTime, currFrame, prevTime[thread], prevFrame[thread]))
print(" -> difference: %i (%.5f seconds); %s" %
(deltaT, deltaT * nSampsFrame / sample_rate, str(currDate)))
print(" -> station %i, thread %i" % (station, thread))
elif deltaT > 1:
print("ERROR: t.t. %i @ frame %i > t.t. %i @ frame %i + 1" %
(currTime, currFrame, prevTime[thread], prevFrame[thread]))
print(" -> difference: %i (%.5f seconds); %s" %
(deltaT, deltaT * nSampsFrame / sample_rate, str(currDate)))
print(" -> station %i, thread %i" % (station, thread))
else:
pass
prevDate[thread] = currDate
prevTime[thread] = currTime
prevFrame[thread] = currFrame
del currFrame
fh.close()
def main(args):
# Parse the command line
filename = args.filename
# Length of the FFT
LFFT = args.fft_length
fh = open(filename, 'rb')
header = vdif.read_guppi_header(fh)
vdif.FRAME_SIZE = vdif.get_frame_size(fh)
nFramesFile = os.path.getsize(filename) // vdif.FRAME_SIZE
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
srate = junkFrame.sample_rate
vdif.DATA_LENGTH = junkFrame.payload.data.size
beam, pol = junkFrame.id
tunepols = vdif.get_thread_count(fh)
beampols = tunepols
if args.skip != 0:
print("Skipping forward %.3f s" % args.skip)
print("-> %.6f (%s)" % (junkFrame.time, junkFrame.time.datetime))
offset = int(args.skip * srate / vdif.DATA_LENGTH)
fh.seek(beampols * vdif.FRAME_SIZE * offset, 1)
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
fh.seek(-vdif.FRAME_SIZE, 1)
print("-> %.6f (%s)" % (junkFrame.time, junkFrame.time.datetime))
tStart = junkFrame.time
# Get the frequencies
cFreq = 0.0
for j in xrange(4):
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
s, p = junkFrame.id
if p == 0:
cFreq = junkFrame.central_freq
# Set integration time
tInt = args.avg_time
nFrames = int(round(tInt * srate / vdif.DATA_LENGTH))
tInt = nFrames * vdif.DATA_LENGTH / srate
nFrames = int(round(tInt * srate / vdif.DATA_LENGTH))
# Read in some data
tFile = nFramesFile / beampols * vdif.DATA_LENGTH / srate
# Date
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
fh.seek(-vdif.FRAME_SIZE, 1)
beginDate = junkFrame.time.datetime
# Report
print("Filename: %s" % os.path.basename(filename))
print(" Date of First Frame: %s" % beginDate)
print(" Station: %i" % beam)
print(" Sample Rate: %i Hz" % srate)
print(" Tuning 1: %.1f Hz" % cFreq)
print(" Bit Depth: %i" % junkFrame.header.bits_per_sample)
print(" Integration Time: %.3f s" % tInt)
print(" Integrations in File: %i" % int(tFile / tInt))
print(" ")
# Go!
data = numpy.zeros((beampols, vdif.DATA_LENGTH * nFrames),
dtype=numpy.complex64)
count = [0 for i in xrange(data.shape[0])]
for i in xrange(beampols * nFrames):
try:
cFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
except errors.SyncError:
print("Error @ %i" % i)
fh.seek(vdif.FRAME_SIZE, 1)
continue
std, pol = cFrame.id
sid = pol
data[sid, count[sid] * vdif.DATA_LENGTH:(count[sid] + 1) *
vdif.DATA_LENGTH] = cFrame.payload.data
count[sid] += 1
# Transform and trim off the negative frequencies
freq, psd = fxc.SpecMaster(data,
LFFT=2 * LFFT,
sample_rate=srate,
central_freq=header['OBSFREQ'] - srate / 4)
freq, psd = freq[LFFT:], psd[:, LFFT:]
# Plot
fig = plt.figure()
ax = fig.gca()
for i in xrange(psd.shape[0]):
ax.plot(freq / 1e6, numpy.log10(psd[i, :]) * 10, label='%i' % i)
ax.set_title('%i' % beam)
ax.set_xlabel('Frequency [MHz]')
ax.set_ylabel('PSD [arb. dB]')
ax.legend(loc=0)
plt.show()
# Done
fh.close()
def main(args):
# Parse the command line
filename = args.filename
fh = open(filename, 'rb')
header = vdif.read_guppi_header(fh)
vdif.FRAME_SIZE = vdif.get_frame_size(fh)
nFramesFile = os.path.getsize(filename) // vdif.FRAME_SIZE
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
srate = junkFrame.sample_rate
vdif.DATA_LENGTH = junkFrame.payload.data.size
beam, pol = junkFrame.id
tunepols = vdif.get_thread_count(fh)
beampols = tunepols
# Get the frequencies
cFreq = 0.0
for j in xrange(4):
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
s, p = junkFrame.id
if p == 0:
cFreq = junkFrame.central_freq
# Date
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
fh.seek(-vdif.FRAME_SIZE, 1)
beginDate = junkFrame.time.datetime
# Report
print("Filename: %s" % os.path.basename(filename))
print(" Date of First Frame: %s" % beginDate)
print(" Station: %i" % beam)
print(" Sample Rate: %i Hz" % srate)
print(" Bit Depth: %i" % junkFrame.header.bits_per_sample)
print(" Tuning 1: %.1f Hz" % cFreq)
print(" ")
# Determine the clip level
if args.trim_level is None:
if junkFrame.header.bits_per_sample == 1:
args.trim_level = abs(1.0)**2
elif junkFrame.header.bits_per_sample == 2:
args.trim_level = abs(3.3359)**2
elif junkFrame.header.bits_per_sample == 4:
args.trim_level = abs(7 / 2.95)**2
elif junkFrame.header.bits_per_sample == 8:
args.trim_level = abs(255 / 256.)**2
else:
args.trim_level = 1.0
print("Setting clip level to %.3f" % args.trim_level)
print(" ")
# Convert chunk length to total frame count
chunkLength = int(args.length * srate / vdif.DATA_LENGTH * tunepols)
chunkLength = int(1.0 * chunkLength / tunepols) * tunepols
# Convert chunk skip to total frame count
chunkSkip = int(args.skip * srate / vdif.DATA_LENGTH * tunepols)
chunkSkip = int(1.0 * chunkSkip / tunepols) * tunepols
# Output arrays
clipFraction = []
meanPower = []
meanRMS = []
# Go!
i = 1
done = False
print(" | Clipping | Power | RMS |")
print(" | 1X 1Y | 1X 1Y | 1X 1Y |")
print("----+-----------------+---------------+---------------+")
while True:
count = {0: 0, 1: 0}
data = numpy.empty((2, chunkLength * vdif.DATA_LENGTH // tunepols),
dtype=numpy.float32)
for j in xrange(chunkLength):
# Read in the next frame and anticipate any problems that could occur
try:
cFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0,
verbose=False)
except errors.EOFError:
done = True
break
except errors.SyncError:
continue
beam, pol = cFrame.id
aStand = pol
try:
data[aStand,
count[aStand] * vdif.DATA_LENGTH:(count[aStand] + 1) *
vdif.DATA_LENGTH] = cFrame.payload.data
# Update the counters so that we can average properly later on
count[aStand] += 1
except ValueError:
pass
if done:
break
else:
rms = numpy.sqrt((data**2).mean(axis=1))
data = numpy.abs(data)**2
clipFraction.append(numpy.zeros(2))
meanPower.append(data.mean(axis=1))
meanRMS.append(rms)
for j in xrange(2):
bad = numpy.nonzero(data[j, :] > args.trim_level)[0]
clipFraction[-1][j] = 1.0 * len(bad) / data.shape[1]
clip = clipFraction[-1]
power = meanPower[-1]
print("%3i | %6.2f%% %6.2f%% | %6.3f %6.3f | %6.3f %6.3f |" %
(i, clip[0] * 100.0, clip[1] * 100.0, power[0], power[1],
rms[0], rms[1]))
i += 1
fh.seek(vdif.FRAME_SIZE * chunkSkip, 1)
clipFraction = numpy.array(clipFraction)
meanPower = numpy.array(meanPower)
meanRMS = numpy.array(meanRMS)
clip = clipFraction.mean(axis=0)
power = meanPower.mean(axis=0)
rms = meanRMS.mean(axis=0)
print("----+-----------------+---------------+---------------+")
print("%3s | %6.2f%% %6.2f%% | %6.3f %6.3f | %6.3f %6.3f |" %
('M', clip[0] * 100.0, clip[1] * 100.0, power[0], power[1], rms[0],
rms[1]))
def main(args):
# Parse the command line
filename = args.filename
fh = open(filename, 'rb')
header = vdif.read_guppi_header(fh)
vdif.FRAME_SIZE = vdif.get_frame_size(fh)
nFramesFile = os.path.getsize(filename) // vdif.FRAME_SIZE
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
srate = junkFrame.sample_rate
vdif.DATA_LENGTH = junkFrame.payload.data.size
beam, pol = junkFrame.id
tunepols = vdif.get_thread_count(fh)
beampols = tunepols
if args.skip != 0:
print("Skipping forward %.3f s" % args.skip)
print("-> %.6f (%s)" % (junkFrame.time, junkFrame.time.datetime))
offset = int(args.skip * srate / vdif.DATA_LENGTH)
fh.seek(beampols * vdif.FRAME_SIZE * offset, 1)
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
fh.seek(-vdif.FRAME_SIZE, 1)
print("-> %.6f (%s)" % (junkFrame.time, junkFrame.time.datetime))
tStart = junkFrame.time
# Get the frequencies
cFreq = 0.0
for j in xrange(4):
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
s, p = junkFrame.id
if p == 0:
cFreq = junkFrame.central_freq
# Set integration time
tInt = args.avg_time
nFrames = int(round(tInt * srate / vdif.DATA_LENGTH))
tInt = nFrames * vdif.DATA_LENGTH / srate
nFrames = int(round(tInt * srate / vdif.DATA_LENGTH))
# Read in some data
tFile = nFramesFile / beampols * vdif.DATA_LENGTH / srate
# Date
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
fh.seek(-vdif.FRAME_SIZE, 1)
beginDate = junkFrame.time.datetime
# Report
print("Filename: %s" % os.path.basename(filename))
print(" Date of First Frame: %s" % beginDate)
print(" Station: %i" % beam)
print(" Sample Rate: %i Hz" % srate)
print(" Tuning 1: %.1f Hz" % cFreq)
print(" Bit Depth: %i" % junkFrame.header.bits_per_sample)
print(" Integration Time: %.3f s" % tInt)
print(" Integrations in File: %i" % int(tFile / tInt))
print(" ")
# Go!
data = numpy.zeros((beampols, vdif.DATA_LENGTH * nFrames),
dtype=numpy.complex64)
count = [0 for i in xrange(data.shape[0])]
for i in xrange(beampols * nFrames):
try:
cFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
except errors.SyncError:
print("Error @ %i" % i)
fh.seek(vdif.FRAME_SIZE, 1)
continue
std, pol = cFrame.id
sid = pol
data[sid, count[sid] * vdif.DATA_LENGTH:(count[sid] + 1) *
vdif.DATA_LENGTH] = cFrame.payload.data
count[sid] += 1
# Plot
nBins = 2**junkFrame.header.bits_per_sample
weights = numpy.ones(data.shape[1],
dtype=numpy.float32) * 100.0 / data.shape[1]
fig = plt.figure()
## X
ax = fig.add_subplot(2, 1, 1)
c, b, o = ax.hist(data[0, :].real, bins=nBins, weights=weights)
ax.set_xlim((b[0], b[-1]))
ax.set_xlabel('Value - X')
ax.set_ylabel('Fraction [%]')
## Y
ax = fig.add_subplot(2, 1, 2)
c, b, o = ax.hist(data[1, :].real, bins=nBins, weights=weights)
ax.set_xlim((b[0], b[-1]))
ax.set_xlabel('Value - Y')
ax.set_ylabel('Fraction [%]')
plt.show()
# Done
fh.close()
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 processDataBatchLinear(fh,
header,
antennas,
tStart,
duration,
sample_rate,
args,
dataSets,
obsID=1,
clip1=0,
clip2=0):
"""
Process a chunk of data in a raw vdif file into linear polarization
products and add the contents to an HDF5 file.
"""
# Length of the FFT
LFFT = args.fft_length
# Find the start of the observation
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
srate = junkFrame.sample_rate
t0 = junkFrame.time
fh.seek(-vdif.FRAME_SIZE, 1)
print('Looking for #%i at %s with sample rate %.1f Hz...' %
(obsID, tStart, sample_rate))
while t0.datetime < tStart or srate != sample_rate:
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
srate = junkFrame.sample_rate
t0 = junkFrame.time
print('... Found #%i at %s with sample rate %.1f Hz' %
(obsID, junkFrame.time.datetime, srate))
tDiff = t0.datetime - tStart
try:
duration = duration - tDiff.total_seconds()
except:
duration = duration - (tDiff.seconds + tDiff.microseconds / 1e6)
beam, pol = junkFrame.id
beams = vdif.get_thread_count(fh)
tunepols = vdif.get_thread_count(fh)
tunepol = tunepols
beampols = tunepol
# Make sure that the file chunk size contains is an integer multiple
# of the FFT length so that no data gets dropped. This needs to
# take into account the number of beampols in the data, the FFT length,
# and the number of samples per frame.
maxFrames = int(1.0 * 28000 / beampols * vdif.DATA_LENGTH /
float(2 * LFFT)) * 2 * LFFT // vdif.DATA_LENGTH * beampols
# Number of frames per second
nFramesSecond = int(srate) // vdif.DATA_LENGTH
# Number of frames to integrate over
nFramesAvg = int(round(args.average * srate / vdif.DATA_LENGTH * beampols))
nFramesAvg = int(1.0 * nFramesAvg / beampols * vdif.DATA_LENGTH /
float(2 * LFFT)) * 2 * LFFT // vdif.DATA_LENGTH * beampols
args.average = 1.0 * nFramesAvg / beampols * vdif.DATA_LENGTH / srate
maxFrames = nFramesAvg
# Number of remaining chunks (and the correction to the number of
# frames to read in).
nChunks = int(round(duration / args.average))
if nChunks == 0:
nChunks = 1
nFrames = nFramesAvg * nChunks
# Line up the time tags for the various tunings/polarizations
timetags = []
for i in xrange(16):
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
timetags.append(junkFrame.header.seconds_from_epoch * nFramesSecond +
junkFrame.header.frame_in_second)
fh.seek(-16 * vdif.FRAME_SIZE, 1)
i = 0
if beampols == 4:
while (timetags[i + 0] != timetags[i + 1]) or (
timetags[i + 0] != timetags[i + 2]) or (timetags[i + 0] !=
timetags[i + 3]):
i += 1
fh.seek(vdif.FRAME_SIZE, 1)
elif beampols == 2:
while timetags[i + 0] != timetags[i + 1]:
i += 1
fh.seek(vdif.FRAME_SIZE, 1)
# Date & Central Frequency
beginDate = junkFrame.time.datetime
central_freq1 = 0.0
central_freq2 = 0.0
for i in xrange(4):
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
b, p = junkFrame.id
if p == 0:
central_freq1 = junkFrame.central_freq
elif p == 0:
central_freq2 = junkFrame.central_freq
else:
pass
fh.seek(-4 * vdif.FRAME_SIZE, 1)
freq = numpy.fft.fftshift(numpy.fft.fftfreq(LFFT, d=2 / srate))
if float(fxc.__version__) < 0.8:
freq = freq[1:]
dataSets['obs%i-freq1' % obsID][:] = freq + central_freq1
dataSets['obs%i-freq2' % obsID][:] = freq + central_freq2
obs = dataSets['obs%i' % obsID]
obs.attrs['tInt'] = args.average
obs.attrs['tInt_Unit'] = 's'
obs.attrs['LFFT'] = LFFT
obs.attrs['nchan'] = LFFT - 1 if float(fxc.__version__) < 0.8 else LFFT
obs.attrs['RBW'] = freq[1] - freq[0]
obs.attrs['RBW_Units'] = 'Hz'
# Create the progress bar so that we can keep up with the conversion.
pbar = progress.ProgressBarPlus(max=nChunks)
data_products = ['XX', 'YY']
done = False
for i in xrange(nChunks):
# Find out how many frames remain in the file. If this number is larger
# than the maximum of frames we can work with at a time (maxFrames),
# only deal with that chunk
framesRemaining = nFrames - i * maxFrames
if framesRemaining > maxFrames:
framesWork = maxFrames
else:
framesWork = framesRemaining
count = {0: 0, 1: 0, 2: 0, 3: 0}
data = numpy.zeros((4, framesWork * vdif.DATA_LENGTH // beampols),
dtype=numpy.csingle)
# If there are fewer frames than we need to fill an FFT, skip this chunk
if data.shape[1] < LFFT:
break
# Inner loop that actually reads the frames into the data array
for j in xrange(framesWork):
# Read in the next frame and anticipate any problems that could occur
try:
cFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0,
verbose=False)
except errors.EOFError:
done = True
break
except errors.SyncError:
continue
beam, pol = cFrame.id
aStand = pol
if j is 0:
cTime = cFrame.time
try:
data[aStand,
count[aStand] * vdif.DATA_LENGTH:(count[aStand] + 1) *
vdif.DATA_LENGTH] = cFrame.payload.data
count[aStand] += 1
except ValueError:
raise RuntimeError("Invalid Shape")
# Save out some easy stuff
dataSets['obs%i-time' % obsID][i] = float(cTime)
if not args.without_sats:
sats = ((data.real**2 + data.imag**2) >= 49).sum(axis=1)
dataSets['obs%i-Saturation1' % obsID][i, :] = sats[0:2]
dataSets['obs%i-Saturation2' % obsID][i, :] = sats[2:4]
else:
dataSets['obs%i-Saturation1' % obsID][i, :] = -1
dataSets['obs%i-Saturation2' % obsID][i, :] = -1
# Calculate the spectra for this block of data and then weight the results by
# the total number of frames read. This is needed to keep the averages correct.
if clip1 == clip2:
freq, tempSpec1 = fxc.SpecMaster(data,
LFFT=2 * LFFT,
window=args.window,
verbose=args.verbose,
sample_rate=srate,
clip_level=clip1)
freq, tempSpec1 = freq[LFFT:], tempSpec1[:, LFFT:]
l = 0
for t in (1, 2):
for p in data_products:
dataSets['obs%i-%s%i' %
(obsID, p, t)][i, :] = tempSpec1[l, :]
l += 1
else:
freq, tempSpec1 = fxc.SpecMaster(data[:2, :],
LFFT=2 * LFFT,
window=args.window,
verbose=args.verbose,
sample_rate=srate,
clip_level=clip1)
freq, tempSpec2 = fxc.SpecMaster(data[2:, :],
LFFT=2 * LFFT,
window=args.window,
verbose=args.verbose,
sample_rate=srate,
clip_level=clip2)
freq, tempSpec1, tempSpec2 = freq[
LFFT:], tempSpec1[:, LFFT:], tempSpec2[:, LFFT:]
for l, p in enumerate(data_products):
dataSets['obs%i-%s%i' % (obsID, p, 1)][i, :] = tempSpec1[l, :]
dataSets['obs%i-%s%i' % (obsID, p, 2)][i, :] = tempSpec2[l, :]
# We don't really need the data array anymore, so delete it
del (data)
# Are we done yet?
if done:
break
## Update the progress bar and remaining time estimate
pbar.inc()
sys.stdout.write('%s\r' % pbar.show())
sys.stdout.flush()
pbar.amount = pbar.max
sys.stdout.write('%s\n' % pbar.show())
sys.stdout.flush()
return True
def get_frames_per_second(filehandle):
"""
Find out the number of frames per second in a file by watching how the
headers change. Returns the number of frames in a second.
"""
# Save the current position in the file so we can return to that point
fhStart = filehandle.tell()
# Get the number of threads
nThreads = get_thread_count(filehandle)
# Get the current second counts for all threads
ref = {}
i = 0
while i < nThreads:
try:
cFrame = vdif.read_frame(filehandle)
except errors.SyncError:
filehandle.seek(vdif.FRAME_SIZE, 1)
continue
except errors.EOFError:
continue
cID = cFrame.header.thread_id
cSC = cFrame.header.seconds_from_epoch
ref[cID] = cSC
i += 1
# Read frames until we see a change in the second counter
cur = {}
fnd = []
while True:
## Get a frame
try:
cFrame = vdif.read_frame(filehandle)
except errors.SyncError:
filehandle.seek(vdif.FRAME_SIZE, 1)
continue
except errors.EOFError:
break
## Pull out the relevant metadata
cID = cFrame.header.thread_id
cSC = cFrame.header.seconds_from_epoch
cFC = cFrame.header.frame_in_second
## Figure out what to do with it
if cSC == ref[cID]:
### Same second as the reference, save the frame number
cur[cID] = cFC
else:
### Different second than the reference, we've found something
ref[cID] = cSC
if cID not in fnd:
fnd.append(cID)
if len(fnd) == nThreads:
break
# Return to the place in the file where we started
filehandle.seek(fhStart)
# Pull out the mode
mode = {}
for key in cur.keys():
value = cur[key]
try:
mode[value] += 1
except KeyError:
mode[value] = 1
best, bestValue = 0, 0
for key in mode.keys():
value = mode[key]
if value > bestValue:
best = key
bestValue = value
# Correct for a zero-based counter and return
best += 1
return best
def main(args):
# Length of the FFT
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)
filename = args.filename
fh = open(filename, "rb")
header = vdif.read_guppi_header(fh)
vdif.FRAME_SIZE = vdif.get_frame_size(fh)
nFramesFile = os.path.getsize(filename) // vdif.FRAME_SIZE
while True:
try:
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
try:
srate = junkFrame.sample_rate
t0 = junkFrame.time
vdif.DATA_LENGTH = junkFrame.payload.data.size
break
except ZeroDivisionError:
pass
except errors.SyncError:
fh.seek(-vdif.FRAME_SIZE + 1, 1)
fh.seek(-vdif.FRAME_SIZE, 1)
beam, pol = junkFrame.id
beams = 1
tunepols = vdif.get_thread_count(fh)
tunepol = tunepols
beampols = tunepol
# Offset in frames for beampols beam/tuning/pol. sets
offset = int(args.skip * srate / vdif.DATA_LENGTH * beampols)
offset = int(1.0 * offset / beampols) * beampols
fh.seek(offset * vdif.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 = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
srate = junkFrame.sample_rate
t1 = junkFrame.time
tunepols = (vdif.get_thread_count(fh), )
tunepol = tunepols[0]
beampols = tunepol
fh.seek(-vdif.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(tCorr * srate / vdif.DATA_LENGTH * beampols)
cOffset = int(1.0 * cOffset / beampols) * beampols
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 * vdif.FRAME_SIZE, 1)
# Update the offset actually used
args.skip = t1 - t0
offset = int(round(args.skip * srate / vdif.DATA_LENGTH * beampols))
offset = int(1.0 * offset / beampols) * beampols
# Make sure that the file chunk size contains is an integer multiple
# of the FFT length so that no data gets dropped. This needs to
# take into account the number of beampols in the data, the FFT length,
# and the number of samples per frame.
maxFrames = int(1.0 * 28000 / beampols * vdif.DATA_LENGTH /
float(2 * LFFT)) * 2 * LFFT / vdif.DATA_LENGTH * beampols
# Number of frames to integrate over
nFramesAvg = int(args.average * srate / vdif.DATA_LENGTH * beampols)
nFramesAvg = int(1.0 * nFramesAvg / beampols * vdif.DATA_LENGTH /
float(2 * LFFT)) * 2 * LFFT / vdif.DATA_LENGTH * beampols
args.average = 1.0 * nFramesAvg / beampols * vdif.DATA_LENGTH / srate
maxFrames = nFramesAvg
# Number of remaining chunks (and the correction to the number of
# frames to read in).
if args.duration == 0:
args.duration = 1.0 * nFramesFile / beampols * vdif.DATA_LENGTH / srate
args.duration -= args.skip
else:
args.duration = int(
round(args.duration * srate * beampols / vdif.DATA_LENGTH) /
beampols * vdif.DATA_LENGTH / srate)
nChunks = int(round(args.duration / args.average))
if nChunks == 0:
nChunks = 1
nFrames = nFramesAvg * nChunks
# Date & Central Frequency
t1 = junkFrame.time
beginDate = junkFrame.time.datetime
central_freq1 = 0.0
central_freq2 = 0.0
for i in xrange(4):
junkFrame = vdif.read_frame(fh,
central_freq=header['OBSFREQ'],
sample_rate=header['OBSBW'] * 2.0)
b, p = junkFrame.id
if p == 0:
central_freq1 = junkFrame.central_freq
elif p == 0:
central_freq2 = junkFrame.central_freq
else:
pass
fh.seek(-4 * vdif.FRAME_SIZE, 1)
# File summary
print("Filename: %s" % filename)
print("Date of First Frame: %s" % str(beginDate))
print("Beams: %i" % beams)
print("Tune/Pols: %i" % tunepols)
print("Sample Rate: %i Hz" % srate)
print("Bit Depth: %i" % junkFrame.header.bits_per_sample)
print("Tuning Frequency: %.3f Hz (1); %.3f Hz (2)" %
(central_freq1, central_freq2))
print(
"Frames: %i (%.3f s)" %
(nFramesFile, 1.0 * nFramesFile / beampols * vdif.DATA_LENGTH / 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(" ")
# Get the clip levels
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(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.createNewFile(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 = {}
obsList[1] = (datetime.utcfromtimestamp(t1),
datetime(2222, 12, 31, 23, 59, 59), args.duration, srate)
hdfData.fillMinimum(f, 1, beam, srate)
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.createDataSets(
f, o, t,
numpy.arange(LFFT -
1 if float(fxc.__version__) < 0.8 else LFFT,
dtype=numpy.float32),
int(round(obsList[o][2] / args.average)), data_products)
f.attrs['FileGenerator'] = 'hdfWaterfall.py'
f.attrs['InputData'] = os.path.basename(filename)
# Create the various HDF group holders
ds = {}
for o in sorted(obsList.keys()):
obs = hdfData.getObservationSet(f, o)
ds['obs%i' % o] = obs
ds['obs%i-time' % o] = obs.create_dataset(
'time', (int(round(obsList[o][2] / args.average)), ), 'f8')
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(fh,
header,
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()
