# -*- coding: utf-8 -*-
"""
Copyright (c) 2010-2018 CNRS / Centre de Recherche Astrophysique de Lyon
Copyright (c) 2015-2016 Laure Piqueras <laure.piqueras@univ-lyon1.fr>
Copyright (c) 2015-2018 Simon Conseil <simon.conseil@univ-lyon1.fr>
Copyright (c) 2016 Martin Shepherd <martin.shepherd@univ-lyon1.fr>
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors
may be used to endorse or promote products derived from this software
without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""
import astropy.units as u
import fnmatch
import logging
import numpy as np
import os
from astropy.io import fits
from ..version import __version__
__all__ = ('add_mpdaf_method_keywords', 'add_mpdaf_keywords_to_file',
'fix_unit_read', 'fix_unit_write', 'copy_header', 'copy_keywords',
'is_valid_fits_file', 'read_slice_from_fits')
FITS_EXTENSIONS = ("fits", "fits.gz", "fits.fz")
[docs]def add_mpdaf_method_keywords(header, method, params, values, comments):
"""Add keywords in a FITS header to describe the method and the
corresponding parameters.
Parameters
----------
header : pyfits.Header
FITS header.
method : string
MPDAF method identifier
params : list of strings
Names of parameters
values : list
Values of parameters
comments : list of strings
parameters description
"""
i = 1
while 'MPDAF METH%d ID' % i in header:
i += 1
header['HIERARCH MPDAF METH%d VERSION' % i] = (__version__,
'MPDAF version')
header['HIERARCH MPDAF METH%d ID' % i] = (method,
'MPDAF method identifier')
n = len(params)
for p in range(n):
header['HIERARCH MPDAF METH%d PARAM%d NAME' % (i, p + 1)] = (
params[p], comments[p])
keyword = 'HIERARCH MPDAF METH%d PARAM%d VALUE' % (i, p + 1)
if isinstance(values[p], str):
n = 80 - len(keyword) - 14
s = values[p][0:n]
header[keyword] = s
else:
header[keyword] = values[p]
[docs]def add_mpdaf_keywords_to_file(path, method, params, values, comments, ext=0):
"""Add keywords in a FITS file header to describe the method and the
corresponding parameters.
Parameters
----------
path : str
File path.
method : string
MPDAF method identifier
params : list of strings
Names of parameters
values : list
Values of parameters
comments : list of strings
parameters description
"""
with fits.open(path, mode='update') as hdul:
add_mpdaf_method_keywords(hdul[ext].header, method,
params, values, comments)
hdul.flush()
[docs]def fix_unit_read(x):
x = x.replace('10**(-20)', '1e-20')
x = x.replace('*', ' ')
x = x.replace('mum', 'micron')
return x
[docs]def fix_unit_write(x):
x = x.replace('1e-20', '10**(-20)')
return x
[docs]def copy_keywords(srchdr, dsthdr, keys):
"""Copy a list of FITS keywords from one header to another.
Parameters
----------
srchdr : `astropy.io.fits.Header`
Source header
dsthdr : `astropy.io.fits.Header`
Destination header
keys : list
List of keys
"""
for key in keys:
if key in srchdr:
dsthdr[key] = (srchdr[key], srchdr.comments[key])
[docs]def is_valid_fits_file(filename):
"""Return True is a file exist and is a valid FITS file (based on its
extension)."""
return os.path.isfile(filename) and filename.endswith(FITS_EXTENSIONS)
[docs]def read_slice_from_fits(filename_or_hdu, item=None, ext='DATA', mask_ext=None,
dtype=None, convert_float64=True):
"""Read data from a FITS file."""
try:
if isinstance(filename_or_hdu, fits.HDUList):
close_hdu = False
hdulist = filename_or_hdu
else:
hdulist = fits.open(filename_or_hdu)
close_hdu = True
data = hdulist[ext].data
if item is not None:
data = data[item]
data = np.asarray(data, dtype=dtype)
# Force data to be in double instead of float
if convert_float64 and data.dtype.type == np.float32:
data = data.astype(np.float64)
# mask extension
if mask_ext is not None and mask_ext in hdulist:
mask = hdulist[mask_ext].data
if item is not None:
mask = mask[item]
mask = np.asarray(mask, dtype=bool)
else:
mask = None
finally:
if close_hdu:
hdulist.close()
return data, mask