#! /usr/bin/env python
"""
Module with various fits handling functions (same as in ``VIP``)
"""
__author__ = 'Carlos Alberto Gomez Gonzalez'
__all__ = ['open_fits',
'info_fits',
'write_fits']
import os
import numpy as np
from astropy.io import fits as ap_fits
[docs]def open_fits(fitsfilename, n=0, header=False, ignore_missing_end=False,
precision=np.float32, return_memmap=False, verbose=True,
**kwargs):
"""
Load a fits file into a memory as numpy array.
Parameters
----------
fitsfilename : string or pathlib.Path
Name of the fits file or ``pathlib.Path`` object
n : int, optional
It chooses which HDU to open. Default is the first one.
header : bool, optional
Whether to return the header along with the data or not.
precision : numpy dtype, optional
Float precision, by default np.float32 or single precision float.
ignore_missing_end : bool optional
Allows to open fits files with a header missing END card.
return_memmap : bool, optional
If True, the function returns the handle to the FITS file opened by
mmap. With the hdulist, array data of each HDU to be accessed with mmap,
rather than being read into memory all at once. This is particularly
useful for working with very large arrays that cannot fit entirely into
physical memory.
verbose : bool, optional
If True prints message of completion.
**kwargs: optional
Optional arguments to the astropy.io.fits.open() function. E.g.
"output_verify" can be set to ignore, in case of non-standard header.
Returns
-------
hdulist : hdulist
[memmap=True] FITS file ``n`` hdulist.
data : numpy ndarray
[memmap=False] Array containing the frames of the fits-cube.
header : dict
[memmap=False, header=True] Dictionary containing the fits header.
"""
fitsfilename = str(fitsfilename)
if not os.path.isfile(fitsfilename):
fitsfilename += '.fits'
hdulist = ap_fits.open(fitsfilename, ignore_missing_end=ignore_missing_end,
memmap=True, **kwargs)
if return_memmap:
return hdulist[n]
else:
data = hdulist[n].data
data = np.array(data, dtype=precision)
if header:
header = hdulist[0].header
if verbose:
print("Fits HDU-{} data and header successfully loaded. "
"Data shape: {}".format(n, data.shape))
return data, header
else:
if verbose:
print("Fits HDU-{} data successfully loaded. "
"Data shape: {}".format(n, data.shape))
return data
[docs]def info_fits(fitsfilename, **kwargs):
"""
Print the information about a fits file.
Parameters
----------
fitsfilename : str
Path to the fits file.
**kwargs: optional
Optional arguments to the astropy.io.fits.open() function. E.g.
"output_verify" can be set to ignore, in case of non-standard header.
"""
with ap_fits.open(fitsfilename, memmap=True, **kwargs) as hdulist:
hdulist.info()
[docs]def write_fits(fitsfilename, array, header=None, output_verify='exception',
precision=np.float32, verbose=True):
"""
Write array and header into FITS file.
If there is a previous file with the same filename then it's replaced.
Parameters
----------
fitsfilename : string
Full path of the fits file to be written.
array : numpy ndarray
Array to be written into a fits file.
header : numpy ndarray, optional
Array with header.
output_verify : str, optional
{"fix", "silentfix", "ignore", "warn", "exception"}
Verification options:
https://docs.astropy.org/en/stable/io/fits/api/verification.html
precision : numpy dtype, optional
Float precision, by default np.float32 or single precision float.
verbose : bool, optional
If True prints message.
"""
array = array.astype(precision, copy=False)
if not fitsfilename.endswith('.fits'):
fitsfilename += '.fits'
if os.path.exists(fitsfilename):
os.remove(fitsfilename)
ap_fits.writeto(fitsfilename, array, header, output_verify)
if verbose:
print("Fits file successfully overwritten")
else:
ap_fits.writeto(fitsfilename, array, header, output_verify)
if verbose:
print("Fits file successfully saved")