def read(fin: TextIO, alphabet: Alphabet = None) -> SeqList:
"""Read a sequence file and attempt to guess its format.
First the filename extension (if available) is used to infer the format.
If that fails, then we attempt to parse the file using several common
formats.
Note, fin cannot be unseekable stream such as sys.stdin
returns :
SeqList
Raises :
ValueError: If the file cannot be parsed.
ValueError: Sequence do not conform to the alphabet.
"""
alphabet = Alphabet(alphabet)
parsers = _get_parsers(fin)
for p in parsers:
fin.seek(0)
try:
return p.read(fin, alphabet)
except ValueError:
pass
names = ", ".join([p.names[0] for p in parsers])
raise ValueError("Cannot parse sequence file: Tried %s " % names)
def reversed_blocks(f: TextIO, blocksize=4096):
""" Generate blocks of file's contents in reverse order. """
f.seek(0, os.SEEK_END)
here = f.tell()
while 0 < here:
delta = min(blocksize, here)
here -= delta
f.seek(here, os.SEEK_SET)
yield f.read(delta)
def navheader3(f: TextIO) -> Dict[str, Any]:
if isinstance(f, Path):
fn = f
with fn.open('r') as f:
return navheader3(f)
else:
f.seek(0)
hdr = rinexinfo(f)
assert int(hdr['version']) == 3, 'see rinexnav2() for RINEX 2.x files'
assert hdr['filetype'] == 'N', 'Did not detect Nav file'
for ln in f:
if 'END OF HEADER' in ln:
break
kind, content = ln[60:].strip(), ln[:60]
if kind == "IONOSPHERIC CORR":
if kind not in hdr:
hdr[kind] = {}
coefficients_kind = content[:4].strip()
if coefficients_kind == 'GAL':
n_corr = 3
else:
n_corr = 4
coefficients = [
rinex_string_to_float(content[5 + i * 12:5 + (i + 1) * 12])
for i in range(n_corr)
]
hdr[kind][coefficients_kind] = coefficients
elif kind == "LEAP SECONDS":
hdr[kind] = content.split()[0]
else:
hdr[kind] = content
return hdr
def obsheader2(f: TextIO,
useindicators: bool = False,
meas: Sequence[str] = None) -> Dict[str, Any]:
"""
End users should use rinexheader()
"""
if isinstance(f, (str, Path)):
with opener(f, header=True) as h:
return obsheader2(h, useindicators, meas)
f.seek(0)
# %% selection
if isinstance(meas, str):
meas = [meas]
if not meas or not meas[0].strip():
meas = None
hdr = rinexinfo(f)
Nobs = 0 # not None due to type checking
for ln in f:
if "END OF HEADER" in ln:
break
h = ln[60:80].strip()
c = ln[:60]
# %% measurement types
if '# / TYPES OF OBSERV' in h:
if Nobs == 0:
Nobs = int(c[:6])
hdr[h] = c[6:].split()
else:
hdr[h] += c[6:].split()
elif h not in hdr: # Header label
hdr[h] = c # string with info
else: # concatenate
hdr[h] += " " + c
# %% useful values
try:
hdr['systems'] = hdr['RINEX VERSION / TYPE'][40]
except KeyError:
pass
hdr['Nobs'] = Nobs
# 5 observations per line (incorporating LLI, SSI)
hdr['Nl_sv'] = ceil(hdr['Nobs'] / 5)
# %% list with receiver location in x,y,z cartesian ECEF (OPTIONAL)
try:
hdr['position'] = [float(j) for j in hdr['APPROX POSITION XYZ'].split()]
if ecef2geodetic is not None:
hdr['position_geodetic'] = ecef2geodetic(*hdr['position'])
except (KeyError, ValueError):
pass
# %% observation types
try:
hdr['fields'] = hdr['# / TYPES OF OBSERV']
if Nobs != len(hdr['fields']):
raise ValueError(f'{f.name} header read incorrectly')
if isinstance(meas, (tuple, list, np.ndarray)):
ind = np.zeros(len(hdr['fields']), dtype=bool)
for m in meas:
for i, f in enumerate(hdr['fields']):
if f.startswith(m):
ind[i] = True
hdr['fields_ind'] = np.nonzero(ind)[0]
else:
ind = slice(None)
hdr['fields_ind'] = np.arange(Nobs)
hdr['fields'] = np.array(hdr['fields'])[ind].tolist()
except KeyError:
pass
hdr['Nobsused'] = hdr['Nobs']
if useindicators:
hdr['Nobsused'] *= 3
# %%
try:
hdr['# OF SATELLITES'] = int(hdr['# OF SATELLITES'][:6])
except (KeyError, ValueError):
pass
# %% time
try:
hdr['t0'] = _timehdr(hdr['TIME OF FIRST OBS'])
except (KeyError, ValueError):
pass
try:
hdr['t1'] = _timehdr(hdr['TIME OF LAST OBS'])
except (KeyError, ValueError):
pass
try: # This key is OPTIONAL
hdr['interval'] = float(hdr['INTERVAL'][:10])
except (KeyError, ValueError):
pass
return hdr
def obsheader2(f: TextIO,
useindicators: bool = False,
meas: Sequence[str] = None) -> Dict[str, Any]:
"""
End users should use rinexheader()
"""
if isinstance(f, (str, Path)):
with opener(f, header=True) as h:
return obsheader2(h, useindicators, meas)
f.seek(0)
# %% selection
if isinstance(meas, str):
meas = [meas]
if not meas or not meas[0].strip():
meas = None
hdr = rinexinfo(f)
Nobs = 0 # not None due to type checking
for ln in f:
if "END OF HEADER" in ln:
break
h = ln[60:80].strip()
c = ln[:60]
# %% measurement types
if "# / TYPES OF OBSERV" in h:
if Nobs == 0:
Nobs = int(c[:6])
hdr[h] = c[6:].split()
else:
hdr[h] += c[6:].split()
elif h not in hdr: # Header label
hdr[h] = c # string with info
else: # concatenate
hdr[h] += " " + c
# %% useful values
try:
hdr["systems"] = hdr["RINEX VERSION / TYPE"][40]
except KeyError:
pass
hdr["Nobs"] = Nobs
# 5 observations per line (incorporating LLI, SSI)
hdr["Nl_sv"] = ceil(hdr["Nobs"] / 5)
# %% list with receiver location in x,y,z cartesian ECEF (OPTIONAL)
try:
hdr["position"] = [
float(j) for j in hdr["APPROX POSITION XYZ"].split()
]
if ecef2geodetic is not None:
hdr["position_geodetic"] = ecef2geodetic(*hdr["position"])
except (KeyError, ValueError):
pass
# %% observation types
try:
hdr["fields"] = hdr["# / TYPES OF OBSERV"]
if hdr["Nobs"] != len(hdr["fields"]):
logging.error(
f"{f.name} number of observations declared in header does not match fields"
)
hdr["Nobs"] = len(hdr["fields"])
if isinstance(meas, (tuple, list, np.ndarray)):
ind = np.zeros(len(hdr["fields"]), dtype=bool)
for m in meas:
for i, f in enumerate(hdr["fields"]):
if f.startswith(m):
ind[i] = True
hdr["fields_ind"] = np.nonzero(ind)[0]
else:
ind = np.s_[:]
hdr["fields_ind"] = np.arange(hdr["Nobs"])
hdr["fields"] = np.array(hdr["fields"])[ind].tolist()
except KeyError:
pass
hdr["Nobsused"] = hdr["Nobs"]
if useindicators:
hdr["Nobsused"] *= 3
# %%
try:
hdr["# OF SATELLITES"] = int(hdr["# OF SATELLITES"][:6])
except (KeyError, ValueError):
pass
# %% time
try:
hdr["t0"] = _timehdr(hdr["TIME OF FIRST OBS"])
except (KeyError, ValueError):
pass
try:
hdr["t1"] = _timehdr(hdr["TIME OF LAST OBS"])
except (KeyError, ValueError):
pass
try: # This key is OPTIONAL
hdr["interval"] = float(hdr["INTERVAL"][:10])
except (KeyError, ValueError):
pass
try:
s = " "
hdr["rxmodel"] = s.join(hdr["REC # / TYPE / VERS"].split()[1:-1])
except (KeyError, ValueError):
pass
return hdr
def obsheader2(f: TextIO,
useindicators: bool = False,
meas: Sequence[str] = None) -> Dict[str, Any]:
"""
End users should use rinexheader()
"""
if isinstance(f, (str, Path)):
with opener(f, header=True) as h:
return obsheader2(h, useindicators, meas)
f.seek(0)
# %% selection
if isinstance(meas, str):
meas = [meas]
if not meas or not meas[0].strip():
meas = None
hdr = rinexinfo(f)
Nobs = 0 # not None due to type checking
for ln in f:
if "END OF HEADER" in ln:
break
h = ln[60:80].strip()
c = ln[:60]
# %% measurement types
if '# / TYPES OF OBSERV' in h:
if Nobs == 0:
Nobs = int(c[:6])
hdr[h] = c[6:].split()
else:
hdr[h] += c[6:].split()
elif h not in hdr: # Header label
hdr[h] = c # string with info
else: # concatenate
hdr[h] += " " + c
# %% useful values
try:
hdr['systems'] = hdr['RINEX VERSION / TYPE'][40]
except KeyError:
pass
hdr['Nobs'] = Nobs
# 5 observations per line (incorporating LLI, SSI)
hdr['Nl_sv'] = ceil(hdr['Nobs'] / 5)
# %% list with receiver location in x,y,z cartesian ECEF (OPTIONAL)
try:
hdr['position'] = [float(j) for j in hdr['APPROX POSITION XYZ'].split()]
if ecef2geodetic is not None:
hdr['position_geodetic'] = ecef2geodetic(*hdr['position'])
except (KeyError, ValueError):
pass
# %% observation types
try:
hdr['fields'] = hdr['# / TYPES OF OBSERV']
if Nobs != len(hdr['fields']):
raise ValueError(f'{f.name} header read incorrectly')
if isinstance(meas, (tuple, list, np.ndarray)):
ind = np.zeros(len(hdr['fields']), dtype=bool)
for m in meas:
for i, f in enumerate(hdr['fields']):
if f.startswith(m):
ind[i] = True
hdr['fields_ind'] = np.nonzero(ind)[0]
else:
ind = slice(None)
hdr['fields_ind'] = np.arange(Nobs)
hdr['fields'] = np.array(hdr['fields'])[ind].tolist()
except KeyError:
pass
hdr['Nobsused'] = hdr['Nobs']
if useindicators:
hdr['Nobsused'] *= 3
# %%
try:
hdr['# OF SATELLITES'] = int(hdr['# OF SATELLITES'][:6])
except (KeyError, ValueError):
pass
# %% time
try:
hdr['t0'] = _timehdr(hdr['TIME OF FIRST OBS'])
except (KeyError, ValueError):
pass
try:
hdr['t1'] = _timehdr(hdr['TIME OF LAST OBS'])
except (KeyError, ValueError):
pass
try: # This key is OPTIONAL
hdr['interval'] = float(hdr['INTERVAL'][:10])
except (KeyError, ValueError):
pass
return hdr
def set_pos_after_license(file: TextIO) -> None:
for line in file:
if re.search(r"SPDX-License-Identifier", line):
return
file.seek(0, 0)
return