def parseInfHeader(filename):
"""Parse the metadata from a presto ``.inf`` file.
:param filename: file containing the header
:type filename: :func:`str`
:return: observational metadata
:rtype: :class:`~sigpyproc.Header.Header`
"""
f = open(filename, "r")
header = {}
lines = f.readlines()
f.close()
for line in lines:
key = line.split("=")[0].strip()
val = line.split("=")[-1].strip()
if not key in conf.inf_to_header.keys():
continue
else:
key, keytype = conf.inf_to_header[key]
header[key] = keytype(val)
header["src_raj"] = float("".join(header["src_raj"].split(":")))
header["src_dej"] = float("".join(header["src_dej"].split(":")))
header["telescope_id"] = conf.telescope_ids.get(header["telescope_id"], 10)
header["machine_id"] = conf.machine_ids.get(header["machine_id"], 9)
header["data_type"] = 2
header["nchans"] = 1
header["nbits"] = 32
header["hdrlen"] = 0
header["nsamples"] = 0
return Header(header)
def readSpec(cls, filename):
"""Read a sigpyproc format ``.spec`` file.
Parameters
----------
filename : str
the name of the ``.spec`` file to read
Returns
-------
:class:`~sigpyproc.FourierSeries.FourierSeries`
an array containing the whole file contents
Notes
-----
This is not setup to handle ``.spec`` files such as are
created by Sigprocs seek module. To do this would require
a new header parser for that file format.
"""
header = Header.parseSigprocHeader(filename)
hdrlen = header["hdrlen"]
f = File(filename, "r", nbits=32)
f.seek(hdrlen)
data = np.fromfile(f, dtype="complex32")
return cls(data, header)
def test_toFFTFile(self, fourier_data, tim_header):
myFS = FourierSeries(fourier_data, Header(tim_header))
fftfile, inffile = myFS.toFFTFile(basename="temp_test")
assert os.path.isfile(fftfile)
assert os.path.isfile(inffile)
os.remove(fftfile)
os.remove(inffile)
def test_toDat(self, tim_data, tim_header):
myTim = TimeSeries(tim_data, Header(tim_header))
datfile, inffile = myTim.toDat(basename="temp_test")
assert os.path.isfile(datfile)
assert os.path.isfile(inffile)
os.remove(datfile)
os.remove(inffile)
def parseSigprocHeader(filename):
"""Parse the metadata from a Sigproc-style file header.
:param filename: file containing the header
:type filename: :func:`str`
:return: observational metadata
:rtype: :class:`~sigpyproc.Header.Header`
"""
f = open(filename, "rb")
header = {}
try:
keylen = unpack("I", f.read(4))[0]
except struct.error:
raise IOError("File Header is not in sigproc format... Is file empty?")
key = f.read(keylen)
if key != b"HEADER_START":
raise IOError("File Header is not in sigproc format")
while True:
keylen = unpack("I", f.read(4))[0]
key = f.read(keylen)
# convert bytestring to unicode
try:
key = key.decode("UTF-8")
except UnicodeDecodeError as e:
print("Could not convert to unicode: {0}".format(str(e)))
# this is basically a sanity check that we haven't passed header_end
if not key in conf.header_keys:
print("'%s' not recognised header key" % (key))
return None
if conf.header_keys[key] == "str":
header[key] = _read_string(f)
elif conf.header_keys[key] == "I":
header[key] = _read_int(f)
elif conf.header_keys[key] == "b":
header[key] = _read_char(f)
elif conf.header_keys[key] == "d":
header[key] = _read_double(f)
if key == "HEADER_END":
break
header["hdrlen"] = f.tell()
f.seek(0, 2)
header["filelen"] = f.tell()
header["nbytes"] = header["filelen"] - header["hdrlen"]
header[
"nsamples"] = 8 * header["nbytes"] / header["nbits"] / header["nchans"]
f.seek(0)
header["filename"] = filename
header["basename"] = os.path.splitext(filename)[0]
f.close()
return Header(header)
def test_readTim(self, tim_data, tim_header):
myTim = TimeSeries(tim_data, Header(tim_header))
outfile = myTim.toFile()
mynewTim = TimeSeries.readTim(filename=outfile)
assert mynewTim.header.nbits == 32
assert mynewTim.header.source_name == "test"
np.testing.assert_allclose(np.mean(mynewTim), 128, atol=0.1)
os.remove(outfile)
def test_makeInf(self, inffile, tmpfile):
myheader = Header.parseInfHeader(filename=inffile)
myheader.makeInf(outfile=tmpfile)
with open(inffile, 'r') as file_inf:
infdata = file_inf.read()
with open(tmpfile, 'r') as file_tmp:
tmpdata = file_tmp.read()
np.testing.assert_string_equal(tmpdata, infdata)
def test_readFFT(self, fourier_data, tim_header):
myFS = FourierSeries(fourier_data, Header(tim_header))
fftfile, inffile = myFS.toFFTFile(basename="temp_test")
mynewFS = FourierSeries.readFFT(filename=fftfile)
assert mynewFS.header.nbits == 32
assert mynewFS.header.source_name == "test"
np.testing.assert_allclose(np.mean(mynewFS), 135.61371, atol=0.01)
os.remove(fftfile)
os.remove(inffile)
def test_readDat(self, tim_data, tim_header):
myTim = TimeSeries(tim_data, Header(tim_header))
datfile, inffile = myTim.toDat(basename="temp_test")
mynewTim = TimeSeries.readDat(filename=datfile)
assert mynewTim.header.nbits == 32
assert mynewTim.header.source_name == "test"
np.testing.assert_allclose(np.mean(mynewTim), 128, atol=0.1)
os.remove(datfile)
os.remove(inffile)
def test_parseSigprocHeader(self, timfile):
header = Header.parseSigprocHeader(filename=timfile)
assert header.nbits == 32
assert header.source_name == "Mystery_PSR"
assert header.telescope_id == 6
assert header.machine_id == 4
assert header.ra == "16:43:38.1000"
assert header.dec == "-12:24:58.7000"
assert header.nsamples == 66250
assert header.nchans == 1
def test_parseInfHeader(self, inffile):
header = Header.parseInfHeader(filename=inffile)
assert header.nbits == 32
assert header.source_name == "Mystery_PSR"
assert header.telescope_id == 6
assert header.machine_id == 9
assert header.src_raj == 164338.1
assert header.src_dej == -122458.7
assert header.nsamples == 66250
assert header.nchans == 1
def __init__(self, filename):
self.filename = filename
self.header = Header.parseSigprocHeader(self.filename)
self._file = File(filename, "r", self.header.nbits)
self.itemsize = np.dtype(self.header.dtype).itemsize
if self.header.nbits in {1, 2, 4}:
self.bitfact = 8 // self.header.nbits
else:
self.bitfact = 1
self.sampsize = self.header.nchans * self.itemsize // self.bitfact
super().__init__()
def parseSigprocHeader(filename):
"""Parse the metadata from a Sigproc-style file header.
:param filename: file containing the header
:type filename: :func:`str`
:return: observational metadata
:rtype: :class:`~sigpyproc.Header.Header`
"""
f = open(filename,"r")
header = {}
try:
keylen = unpack("I",f.read(4))[0]
except struct.error:
raise IOError,"File Header is not in sigproc format... Is file empty?"
key = f.read(keylen)
if key != "HEADER_START":
raise IOError,"File Header is not in sigproc format"
while True:
keylen = unpack("I",f.read(4))[0]
key = f.read(keylen)
if not key in conf.header_keys:
print "'%s' not recognised header key"%(key)
return None
if conf.header_keys[key] == "str":
header[key] = _read_string(f)
elif conf.header_keys[key] == "I":
header[key] = _read_int(f)
elif conf.header_keys[key] == "b":
header[key] = _read_char(f)
elif conf.header_keys[key] == "d":
header[key] = _read_double(f)
if key == "HEADER_END":
break
header["hdrlen"] = f.tell()
f.seek(0,2)
header["filelen"] = f.tell()
header["nbytes"] = header["filelen"]-header["hdrlen"]
header["nsamples"] = 8*header["nbytes"]/header["nbits"]/header["nchans"]
f.seek(0)
header["filename"] = filename
header["basename"] = os.path.splitext(filename)[0]
f.close()
return Header(header)
def readTim(cls, filename):
"""Read a sigproc format ``.tim`` file.
Parameters
----------
filename : str
the name of the ``.tim`` file to read
Returns
-------
:class:`~sigpyproc.TimeSeries.TimeSeries`
a new TimeSeries object
"""
header = Header.parseSigprocHeader(filename)
nbits = header["nbits"]
hdrlen = header["hdrlen"]
f = File(filename, "r", nbits=nbits)
f.seek(hdrlen)
data = np.fromfile(f, dtype=header["dtype"]).astype(np.float32, copy=False)
return cls(data, header)
def readDat(cls, filename, inf=None):
"""Read a presto format ``.dat`` file.
Parameters
----------
filename : str
the name of the ``.dat`` file to read
inf : str, optional
the name of the corresponding ``.inf`` file, by default None
Returns
-------
:class:`~sigpyproc.TimeSeries.TimeSeries`
a new TimeSeries object
Raises
------
IOError
If no ``.inf`` file found in the same directory of ``.dat`` file.
Notes
-----
If inf=None, then the associated .inf file must be in the same directory.
"""
datfile = os.path.realpath(filename)
basename, ext = os.path.splitext(datfile)
if inf is None:
inf = f"{basename}.inf"
if not os.path.isfile(inf):
raise IOError("No corresponding .inf file found")
header = Header.parseInfHeader(inf)
f = File(filename, "r", nbits=32)
data = np.fromfile(f, dtype=np.float32)
header["basename"] = basename
header["inf"] = inf
header["filename"] = filename
header["nsamples"] = data.size
return cls(data, header)
def readFFT(cls, filename, inf=None):
"""Read a presto format ``.fft`` file.
Parameters
----------
filename : str
the name of the ``.fft`` file to read
inf : str, optional
the name of the corresponding ``.inf`` file, by default None
Returns
-------
:class:`~sigpyproc.FourierSeries.FourierSeries`
an array containing the whole file contents
Raises
------
IOError
If no ``.inf`` file found in the same directory of ``.fft`` file.
Notes
-----
If inf=None, then the associated .inf file must be in the same directory.
"""
fftfile = os.path.realpath(filename)
basename, ext = os.path.splitext(fftfile)
if inf is None:
inf = f"{basename}.inf"
if not os.path.isfile(inf):
raise IOError("No corresponding inf file found")
header = Header.parseInfHeader(inf)
f = File(filename, "r", nbits=32)
data = np.fromfile(f, dtype="float32")
header["basename"] = basename
header["inf"] = inf
header["filename"] = filename
return cls(data, header)
def test_prepOutfile(self, filfile, tmpfile):
myheader = Header.parseSigprocHeader(filename=filfile)
outfile = myheader.prepOutfile(tmpfile)
out_header = Header.parseSigprocHeader(filename=outfile.name)
np.testing.assert_equal(out_header.SPPHeader(), myheader.SPPHeader())
def test_fourierSeries(self, fourier_data, tim_header):
myFS = FourierSeries(fourier_data, Header(tim_header))
assert myFS.header.nbits == 32
assert myFS.header.source_name == "test"
assert myFS.shape == (10002, )
np.testing.assert_allclose(np.mean(myFS), 135.61371, atol=0.01)
def test_getDMdelays(self, filfile):
header = Header.parseSigprocHeader(filename=filfile)
delays_time = header.getDMdelays(dm=100, in_samples=False)
delays_samp = header.getDMdelays(dm=100, in_samples=True)
np.testing.assert_equal(delays_samp.mean(), 193.3125)
np.testing.assert_allclose(delays_time.mean(), 0.013913)
def test_toFile(self, fourier_data, tim_header):
myFS = FourierSeries(fourier_data, Header(tim_header))
outfile = myFS.toFile()
assert os.path.isfile(outfile)
os.remove(outfile)
def test_iFFT(self, fourier_data, tim_header, tim_data):
myFS = FourierSeries(fourier_data, Header(tim_header))
myTim = myFS.iFFT()
np.testing.assert_allclose(myTim, tim_data, atol=0.01)
def test_runningMedian(self, tim_data, tim_header):
myTim = TimeSeries(tim_data, Header(tim_header))
median_filter = myTim.runningMedian(window=101)
np.testing.assert_allclose(np.mean(median_filter), 128, atol=0.1)
def test_downsample(self, tim_data, tim_header):
myTim = TimeSeries(tim_data, Header(tim_header))
downsampled = myTim.downsample(factor=16)
np.testing.assert_allclose(np.mean(downsampled), 128, atol=0.1)
def test_toFile(self, tim_data, tim_header):
myTim = TimeSeries(tim_data, Header(tim_header))
outfile = myTim.toFile()
assert os.path.isfile(outfile)
os.remove(outfile)
def test_timeseries(self, tim_data, tim_header):
myTim = TimeSeries(tim_data, Header(tim_header))
assert myTim.header.nbits == 32
assert myTim.header.source_name == "test"
np.testing.assert_allclose(np.mean(myTim), 128, atol=0.1)