def __init__(self, filename=None):
if filename is None:
filename = self.builtin_mat
if _is_url(filename):
self.filename = download_file(filename, cache=True)
else:
self.filename = filename
mat = spio.loadmat(self.filename, matlab_compatible=True)
# Pull out the information we need.
# FIXME: No mapInfoDV nor commented stuff below in SourceForge version
key = 'mapInfoDV'
# key = 'map'
self.n_dim = mat[key]['nDim'][0][0][0][0]
self.Ymap = mat[key]['Ymap'][0][0][0][0]
self.YmapMapping = self.Ymap['mapping']
self.YmapMean = self.YmapMapping['mean'][0][0][0]
self.YmapM = self.YmapMapping['M'][0][0]
self.YmapMapped = self.Ymap['mapped']
self.knn = mat[key]['knn'][0][0][0][0]
self.knnGood = mat[key]['knnGood'][0][0][:, 0]
self.mappedPeriods = mat[key]['periods'][0][0][0]
self.mappedMes = mat[key]['mes'][0][0][0]
self.nPsample = mat[key]['nPsample'][0][0][0][
0] # number to sample # noqa: E501
self.nPercentil = mat[key]['npercentilTM'][0][0][0][0]
self.dymeans = mat[key]['dymean'][0][0][0]
self.ntrfr = 2.0
self.npts = 80.0
def from_builtin(cls, name):
"""Vega spectrum from a built-in `sbpy` source.
Parameters
----------
name : string
The name of a Vega spectrum parameter set in
`sbpy.spectroscopy.vega.sources`.
"""
from astropy.utils.data import _is_url
try:
parameters = getattr(sources, name).copy()
if not _is_url(parameters['filename']):
# find in the module's location
parameters['filename'] = get_pkg_data_filename(
os.path.join('data', parameters['filename']))
vega = Vega.from_file(**parameters)
except AttributeError:
msg = 'Unknown Vega spectrum "{}". Valid spectra:\n{}'.format(
name, sources.available)
raise ValueError(msg)
return vega
def from_builtin(cls, name):
"""Spectrum from a built-in `sbpy` source.
Parameters
----------
name : string
The name of the spectrum. See `show_builtin()` for
available sources.
"""
from astropy.utils.data import _is_url
try:
parameters = getattr(cls._sources, name).copy()
except AttributeError:
msg = 'Unknown spectrum "{}". Valid spectra:\n'.format(
name) + cls.show_builtin(print=False)
raise UndefinedSourceError(msg)
if not _is_url(parameters['filename']):
# find in the module's location
parameters['filename'] = get_pkg_data_filename(
os.path.join('data', parameters['filename']))
return cls.from_file(**parameters)
def from_builtin(cls, name):
"""Solar spectrum from a built-in `sbpy` source.
Parameters
----------
name : string
The name of a solar spectrum parameter set in
`sbpy.spectroscopy.sun.sources`.
"""
from astropy.utils.data import _is_url
try:
parameters = getattr(sources, name).copy()
if not _is_url(parameters['filename']):
# find in the module's location
path = os.path.dirname(__file__)
parameters['filename'] = os.sep.join(
(path, 'data', parameters['filename']))
return Sun.from_file(**parameters)
except AttributeError:
msg = 'Unknown solar spectrum "{}". Valid spectra:\n{}'.format(
name, sources.available)
raise ValueError(msg)
def from_file(cls,
filename,
wave_unit=None,
flux_unit=None,
cache=True,
**kwargs):
"""Load the source spectrum from a file.
NaNs are dropped.
Parameters
----------
filename : string
The name of the file. See
`~synphot.SourceSpectrum.from_file` for details.
wave_unit, flux_unit : str or `~astropy.units.Unit`, optional
Wavelength and flux units in the file.
cache : bool, optional
If ``True``, cache the contents of URLs.
**kwargs
Passed to object initialization.
"""
try:
import synphot
except ImportError:
raise ImportError('synphot required for {}.'.format(cls.__name__))
from astropy.utils.data import download_file, _is_url
if filename.lower().endswith(('.fits', '.fit', '.fz')):
read_spec = synphot.specio.read_fits_spec
else:
read_spec = synphot.specio.read_ascii_spec
# URL cache because synphot.SourceSpectrum.from_file does not
if _is_url(filename):
fn = download_file(filename, cache=True)
else:
fn = filename
spec = read_spec(fn, wave_unit=wave_unit, flux_unit=flux_unit)
i = np.isfinite(spec[1] * spec[2])
source = synphot.SourceSpectrum(synphot.Empirical1D,
points=spec[1][i],
lookup_table=spec[2][i],
meta={'header': spec[0]})
return cls(source, **kwargs)
def from_file(cls, filename, wave_unit=None, flux_unit=None,
cache=True, **kwargs):
"""Load the source spectrum from a file.
Parameters
----------
filename : string
The name of the file. See
`~synphot.SourceSpectrum.from_file` for details.
wave_unit, flux_unit : str or `~astropy.units.core.Unit`, optional
Wavelength and flux units.
cache : bool, optional
If `True`, cache the contents of URLs.
**kwargs
Passed to `Sun` initialization.
"""
from astropy.utils.data import download_file
from astropy.utils.data import _is_url
import synphot
from synphot.specio import read_fits_spec, read_ascii_spec
# URL cache because synphot.SourceSpectrum.from_file does not
if _is_url(filename):
if filename.lower().endswith(('.fits', '.fit')):
read_spec = read_fits_spec
else:
read_spec = read_ascii_spec
fn = download_file(filename, cache=True)
spec = read_spec(fn, wave_unit=wave_unit, flux_unit=flux_unit)
source = synphot.SourceSpectrum(
synphot.Empirical1D, points=spec[1], lookup_table=spec[2],
meta={'header': spec[0]})
else:
source = synphot.SourceSpectrum.from_file(
filename, wave_unit=wave_unit, flux_unit=flux_unit)
return cls(source, **kwargs)
def __init__(self,
fileobj=None,
mode=None,
memmap=None,
overwrite=False,
cache=True):
self.strict_memmap = bool(memmap)
memmap = True if memmap is None else memmap
self._file = None
self.closed = False
self.binary = True
self.mode = mode
self.memmap = memmap
self.compression = None
self.readonly = False
self.writeonly = False
# Should the object be closed on error: see
# https://github.com/astropy/astropy/issues/6168
self.close_on_error = False
# Holds mmap instance for files that use mmap
self._mmap = None
if fileobj is None:
self.simulateonly = True
return
else:
self.simulateonly = False
# If fileobj is of type pathlib.Path
if isinstance(fileobj, pathlib.Path):
fileobj = str(fileobj)
if mode is not None and mode not in IO_FITS_MODES:
raise ValueError(f"Mode '{mode}' not recognized")
if isfile(fileobj):
objmode = _normalize_fits_mode(fileobj_mode(fileobj))
if mode is not None and mode != objmode:
raise ValueError(
"Requested FITS mode '{}' not compatible with open file "
"handle mode '{}'".format(mode, objmode))
mode = objmode
if mode is None:
mode = 'readonly'
# Handle raw URLs
if (isinstance(fileobj, (str, bytes))
and mode not in ('ostream', 'append', 'update')
and _is_url(fileobj)):
self.name = download_file(fileobj, cache=cache)
# Handle responses from URL requests that have already been opened
elif isinstance(fileobj, http.client.HTTPResponse):
if mode in ('ostream', 'append', 'update'):
raise ValueError(f"Mode {mode} not supported for HTTPResponse")
fileobj = io.BytesIO(fileobj.read())
else:
self.name = fileobj_name(fileobj)
self.mode = mode
# Underlying fileobj is a file-like object, but an actual file object
self.file_like = False
# Initialize the internal self._file object
if isfile(fileobj):
self._open_fileobj(fileobj, mode, overwrite)
elif isinstance(fileobj, (str, bytes)):
self._open_filename(fileobj, mode, overwrite)
else:
self._open_filelike(fileobj, mode, overwrite)
self.fileobj_mode = fileobj_mode(self._file)
if isinstance(fileobj, gzip.GzipFile):
self.compression = 'gzip'
elif isinstance(fileobj, zipfile.ZipFile):
# Reading from zip files is supported but not writing (yet)
self.compression = 'zip'
elif _is_bz2file(fileobj):
self.compression = 'bzip2'
if (mode in ('readonly', 'copyonwrite', 'denywrite')
or (self.compression and mode == 'update')):
self.readonly = True
elif (mode == 'ostream' or (self.compression and mode == 'append')):
self.writeonly = True
# For 'ab+' mode, the pointer is at the end after the open in
# Linux, but is at the beginning in Solaris.
if (mode == 'ostream' or self.compression
or not hasattr(self._file, 'seek')):
# For output stream start with a truncated file.
# For compressed files we can't really guess at the size
self.size = 0
else:
pos = self._file.tell()
self._file.seek(0, 2)
self.size = self._file.tell()
self._file.seek(pos)
if self.memmap:
if not isfile(self._file):
self.memmap = False
elif not self.readonly and not self._mmap_available:
# Test mmap.flush--see
# https://github.com/astropy/astropy/issues/968
self.memmap = False
def __init__(self,
fileobj=None,
mode=None,
memmap=None,
overwrite=False,
cache=True):
self.strict_memmap = bool(memmap)
memmap = True if memmap is None else memmap
if fileobj is None:
self._file = None
self.closed = False
self.binary = True
self.mode = mode
self.memmap = memmap
self.compression = None
self.readonly = False
self.writeonly = False
self.simulateonly = True
self.close_on_error = False
return
else:
self.simulateonly = False
# If fileobj is of type pathlib.Path
if isinstance(fileobj, pathlib.Path):
fileobj = str(fileobj)
elif isinstance(fileobj, bytes):
# Using bytes as filename is tricky, it's deprecated for Windows
# in Python 3.5 (because it could lead to false-positives) but
# was fixed and un-deprecated in Python 3.6.
# However it requires that the bytes object is encoded with the
# file system encoding.
# Probably better to error out and ask for a str object instead.
# TODO: This could be revised when Python 3.5 support is dropped
# See also: https://github.com/astropy/astropy/issues/6789
raise TypeError("names should be `str` not `bytes`.")
# Holds mmap instance for files that use mmap
self._mmap = None
if mode is not None and mode not in IO_FITS_MODES:
raise ValueError(f"Mode '{mode}' not recognized")
if isfile(fileobj):
objmode = _normalize_fits_mode(fileobj_mode(fileobj))
if mode is not None and mode != objmode:
raise ValueError(
"Requested FITS mode '{}' not compatible with open file "
"handle mode '{}'".format(mode, objmode))
mode = objmode
if mode is None:
mode = 'readonly'
# Handle raw URLs
if (isinstance(fileobj, str)
and mode not in ('ostream', 'append', 'update')
and _is_url(fileobj)):
self.name = download_file(fileobj, cache=cache)
# Handle responses from URL requests that have already been opened
elif isinstance(fileobj, http.client.HTTPResponse):
if mode in ('ostream', 'append', 'update'):
raise ValueError(f"Mode {mode} not supported for HTTPResponse")
fileobj = io.BytesIO(fileobj.read())
else:
self.name = fileobj_name(fileobj)
self.closed = False
self.binary = True
self.mode = mode
self.memmap = memmap
# Underlying fileobj is a file-like object, but an actual file object
self.file_like = False
# Should the object be closed on error: see
# https://github.com/astropy/astropy/issues/6168
self.close_on_error = False
# More defaults to be adjusted below as necessary
self.compression = None
self.readonly = False
self.writeonly = False
# Initialize the internal self._file object
if isfile(fileobj):
self._open_fileobj(fileobj, mode, overwrite)
elif isinstance(fileobj, str):
self._open_filename(fileobj, mode, overwrite)
else:
self._open_filelike(fileobj, mode, overwrite)
self.fileobj_mode = fileobj_mode(self._file)
if isinstance(fileobj, gzip.GzipFile):
self.compression = 'gzip'
elif isinstance(fileobj, zipfile.ZipFile):
# Reading from zip files is supported but not writing (yet)
self.compression = 'zip'
elif isinstance(fileobj, bz2.BZ2File):
self.compression = 'bzip2'
if (mode in ('readonly', 'copyonwrite', 'denywrite')
or (self.compression and mode == 'update')):
self.readonly = True
elif (mode == 'ostream' or (self.compression and mode == 'append')):
self.writeonly = True
# For 'ab+' mode, the pointer is at the end after the open in
# Linux, but is at the beginning in Solaris.
if (mode == 'ostream' or self.compression
or not hasattr(self._file, 'seek')):
# For output stream start with a truncated file.
# For compressed files we can't really guess at the size
self.size = 0
else:
pos = self._file.tell()
self._file.seek(0, 2)
self.size = self._file.tell()
self._file.seek(pos)
if self.memmap:
if not isfile(self._file):
self.memmap = False
elif not self.readonly and not self._mmap_available:
# Test mmap.flush--see
# https://github.com/astropy/astropy/issues/968
self.memmap = False
