def __init__(self, resource, db="pickle"):
if isinstance(resource, six.string_types):
# Resource is a filename
if not os.path.isfile(resource):
raise (PE.PyAFileError(resource, "ne"))
self.file = resource
if not (re.match(".*\.hdf5", resource) is None):
db = "hdf5"
if not (re.match(".*\.zlib", resource) is None):
db = "hdf5"
if not (re.match(".*\.emcee", resource) is None):
db = "emcee"
if db == "pickle":
self.dbtype = "pymc"
self._checkPackage("pymc")
self.db = pymc.database.pickle.load(resource)
self.stateDic = self.db.getstate()
self.tracesDic = self.db._traces
elif db == "hdf5":
self.dbtype = "pymc"
self._checkPackage("pymc")
self.db = pymc.database.hdf5.load(resource)
self.stateDic = self.db.getstate()
self.tracesDic = self.db._traces
elif db == "emcee":
self.dbtype = "emcee"
self._loadEMCEEChain(resource)
else:
raise (PE.PyAValError("Database type '" + db +
"' is currently not supported."))
elif isinstance(resource, pymc.database.base.Database):
self.db = resource
else:
raise (PE.PyAValError(
"'resource' must be a filename or a pymc database object.",
where="TraceAnalysis::__init__"))
# Set default burn-in and thinning
self.burn = 0
self.thin = 1
def write1dFitsSpec(fn,
flux,
wvl=None,
waveParams=None,
fluxErr=None,
header=None,
clobber=False,
refFileName=None,
refFileExt=0):
"""
Write a 1d spectrum with equidistant binning to a fits file.
Write a 1d-spectrum to a file. Wavelength axis and header keywords
are related through the following expression:
wvl = ((np.arange(N) + 1.0) - CRPIX1) * CDELT1 + CRVAL1,
where CRPIX1, CDELT1, and CRVAL1 are the
relevant header keywords.
The function allows to specify an existing fits extension, from
which the header will be cloned. Alternatively, an arbitrary,
user-defined header may be given.
Parameters
----------
fn : string
Filename
flux : array
Flux array
wvl : array, optional
Wavelength array. Either the wavelength array or the header
keywords have to be provided (see `waveParams`).
waveParams : dict, optional
Wavelength information required in the fits-header.
Required keys are CDELT, CRVAL, CRPIX or (CDELT1, CRVAL1, CRPIX1).
fluxErr : array, optional
Flux errors. If given, the error will be stored in an additional extension.
header : dict, optional
Dictionary with header information to be transfered to the new file.
Note that the wavelength information will be overwritten
by the information given to this routine.
If both, a reference file to clone the header from and the header parameters
are given, the cloned header from the reference file will be overwritten and
extended by the keywords specified here.
refFileName : string, optional
Clone header keywords from a reference file.
Note that the wavelength information will be overwritten by the information
by the information given to this routine.
refFileExt : int, optional
Reference-file extension to be used for cloning the header keywords.
The default is 0.
"""
reservedKeyWords = [
"BITPIX", "SIMPLE", "NAXIS", "NAXIS1", "CDELT1", "CRPIX1", "CRVAL1",
"EXTEND"
]
if (not _ic.check["pyfits"]) and (not _ic.check["astropy.io.fits"]):
raise (PE.PyARequiredImport(
"Could neither import module 'pyfits' and 'astropy.io.fits'.",
where="write1dFitsSpec",
solution=
"Install pyfits: http://www.stsci.edu/institute/software_hardware/pyfits"
))
if wvl is None and waveParams is None:
raise (PE.PyAValError(
"The wavelength axis is not defined, i.e., neither \'wvl\' nor \'waveParams\' is specified.",
where="write1dFitsSpec",
solution=
"Provide wavelength array as \'wvl\' or wavelength information as \'waveParams\'."
))
if wvl is not None and waveParams is not None:
raise (PE.PyAValError(
"You provided the wavelength axis as \'wvl\' AND wavelength information as \'waveParams\'. Don't know which to use.",
where="write1dFitsSpec",
solution=
"Provide only wavelength array via \'wvl\' or wavelength information via \'waveParams\'."
))
if wvl is not None:
# Check whether the wavelength axis is equidistant
dwl = wvl[1:] - wvl[0:-1]
if (np.max(dwl) - np.min(dwl)) / np.max(dwl) > 1e-6:
raise (PE.PyAValError(
"Wavelength axis seems not to be equidistant.",
where="write1dFitsSpec",
solution=[
"Check wavelength array.",
"Consider passing wavelength information via `waveParams`."
]))
if os.path.isfile(fn) and not clobber:
raise (PE.PyAFileError(
fn,
"ae",
where="write1dFitsSpec",
solution="File exists; set clobber=True to overwrite."))
if _ic.check["pyfits"]:
import pyfits
else:
import astropy.io.fits as pyfits
# Put the flux into the output file.
# Generate primary HDU
hdu = pyfits.PrimaryHDU(flux)
if refFileName:
# If the is a reference file, its header will be used to populate
# the header of the file to be written.
if not os.path.isfile(refFileName):
raise (PE.PyAFileError(str(refFileName),
"ne",
where="write1dFitsSpec",
solution="Check file name."))
ff = pyfits.open(refFileName)[refFileExt]
for k in ff.header.keys():
if k not in reservedKeyWords and k != "COMMENT":
try:
if len(k) > 8:
hdu.header["HIERARCH " + k] = ff.header[k]
else:
hdu.header[k] = ff.header[k]
except:
PE.warn(
PE.PyAValError("Cannot write keyword <" + str(k) +
"> with content " + str(ff.header[k])))
if header is not None:
# A use-defined header was specified
for k in header.keys():
hdu.header[k] = header[k]
# Header keywords relevant for wavelength axis
hk = {}
# The only allowed type here
hk["CTYPE1"] = "Linear"
# If wavelength array is provided, create header keywords:
if wvl is not None:
hk["CRPIX1"] = 1
hk["CRVAL1"] = wvl[0]
hk["CDELT1"] = float(wvl[-1] - wvl[0]) / (len(wvl) - 1)
elif waveParams is not None:
requiredKeys = ["CRPIX", "CRVAL", "CDELT"]
# Counts whether all required keywords are provided
count = 0
for k in requiredKeys:
subCount = 0
for p in six.iterkeys(waveParams):
if p.upper() == k or p.upper() == k + "1":
hk[k + "1"] = waveParams[p]
subCount += 1
if subCount == 1:
count += 1
else:
# This occurs if, e.g., both "CRVAL" and "CRVAL1" are present
raise (PE.PyAValError(
"The wavelength parameters provided via \'waveParams\' contain ambiguous parameters. "
+ "You provided multiple values for " + k + ".",
where="write1dFitsSpec",
solution=
"Check content of \'waveParams\' so that only one value for "
+ k +
" is provided (including lower/upper case and presence of a trailing \'1\'."
))
if count < 3:
raise (PE.PyAValError(
"You provided an incomplete set of waveParams.",
where="write1dFitsSpec",
solution="Required keywords are CRPIX, CRVAL, and CDELT."))
# (Over-)Write wavelength-related header information
for k in hk.keys():
hdu.header[k] = hk[k]
if not fluxErr is None:
# An error on the flux was given
hdue = pyfits.ImageHDU(fluxErr)
for k in hk.keys():
# Add wavelength information to error header
hdue.header[k] = hk[k]
hdulist = pyfits.HDUList([hdu, hdue])
else:
hdulist = pyfits.HDUList([hdu])
hdulist.writeto(fn, overwrite=clobber)
def read1dFitsSpec(fn, hdu=0, fullout=False, CRPIX1=None, keymap={}):
"""
Read a simple 1d spectrum from fits file.
Reads a 1d-spectrum from a file and constructs the
associated wavelength axis. To this end, the expression:
wvl = ((np.arange(N) + 1.0) - CRPIX1) * CDELT1 + CRVAL1
will be evaluated, where N is the number of bins and
CRPIX1, CDELT1, and CRVAL1 are header keywords.
Parameters
----------
fn : string
Filename
hdu : int, optional
The number of the HDU to be used. The default
is 0, i.e., the primary HDU.
fullout : boolean, optional
If True, the header keywords used to construct
the wavelength axis will be returned. The default
is False.
CRPIX1 : int, optional
Can be used to circumvent missing CRPIX1 entry.
keymap : dict, optional
Can be used to map header keywords
Returns
-------
wvl : array
The wavelength array.
flx : array
The flux array.
Examples
--------
::
from PyAstronomy import pyasl
wvl, flx = pyasl.read1dFitsSpec("mySpectrum.fits")
"""
if (not _ic.check["pyfits"]) and (not _ic.check["astropy.io.fits"]):
raise(PE.PyARequiredImport("Could neither import module 'pyfits' and 'astropy.io.fits'.",
where="read1dFitsSpec",
solution="Install pyfits: http://www.stsci.edu/institute/software_hardware/pyfits"))
if not os.path.isfile(fn):
raise(PE.PyAFileError(fn, "ne",
where="read1dFitsSpec",
solution="Check file name."))
if _ic.check["pyfits"]:
import pyfits
else:
import astropy.io.fits as pyfits
hl = pyfits.open(fn)
naxis = hl[hdu].header["NAXIS"]
if hl[hdu].header["NAXIS"] != 1:
if hl[hdu].header["NAXIS"] == 2 and hl[hdu].header["NAXIS2"] == 1:
pass
else:
raise(PE.PyAValError("There is more than one axis (NAXIS = " + str(naxis) + ", actual value is " + str(hl[hdu].header["NAXIS"]) + ").",
where="read1dFitsSpec",
solution="Check file and HDU."))
hkeys = {"CRVAL1": None, "CRPIX1": CRPIX1, "CDELT1": None}
for k in hkeys.keys():
if k not in keymap:
keymap[k] = k
for k in hkeys.keys():
if hkeys[k] is not None:
continue
if not keymap[k] in hl[hdu].header:
raise(PE.PyAValError("Header does not contain required keyword '" + str(keymap[k]) + "'",
where="read1dFitsSpec",
solution="Check file and HDU."))
hkeys[k] = hl[hdu].header[keymap[k]]
N = int(hl[hdu].header["NAXIS1"])
# Construct wvl axis
wvl = ((np.arange(N) + 1.0) - hkeys["CRPIX1"]
) * hkeys["CDELT1"] + hkeys["CRVAL1"]
# Get flux
if naxis == 1:
flx = np.array(hl[hdu].data)
elif naxis == 2:
flx = np.array(hl[hdu].data[0])
if fullout:
# Full output
return wvl, flx, hkeys
return wvl, flx