"""
General input/output methods.
.. include:: ../include/links.rst
"""
from pathlib import Path
import warnings
from IPython import embed
import numpy
from skimage import io
from astropy.io import fits
[docs]def bench_image(ifile, ext=0):
"""
Read an image from a bench imaging camera.
Args:
ifile (:obj:`str`, `Path`_):
File name
ext (:obj:`int`, optional):
If the file is a multi-extension fits file, this selects the
extension with the relevant data.
Returns:
`numpy.ndarray`_: Array with the (floating-point) image data.
"""
if ifile is None:
return None
_ifile = Path(ifile).resolve()
if not _ifile.exists():
raise FileNotFoundError(f'{_ifile} does not exist!')
if any([s in ['.fit', '.fits'] for s in _ifile.suffixes]):
return fits.open(_ifile)[ext].data.astype(float)
return io.imread(_ifile).astype(float)
[docs]def gather_collimated_file_list(root, par=None, threshold=None):
"""
Gather the list of collimated farfield output files to analyze.
Args:
root (:obj:`str`, `Path`_):
Root directory with files.
par (:obj:`str`, `Path`_, optional):
Name of a file that provides 2 or 3 columns: (1) the files to
analyze, (2) the background image to use for each file, and (3) the
threshold to use for each file. If this file is provided, any
threshold is ignored and the root directory is not trolled for all
bg*, z*, and a* files. The last column with the thresholds can be
omitted, which means the code will use the value provided on the
command line (or its default).
threshold (:obj:`float`, optional):
If ``par`` is not provided or it has no 3nd column, this is the
threshold to use for all files.
Returns:
:obj:`tuple`: Provides (1) the z0 file, (2) its background file, (3) its
threshold, (4) the z1 file, (5) its background file, (6) its threshold,
(7) the list of a* files, (8) their background files, and (9) their
thresholds.
"""
if par is None:
z0, z1, bg, afiles = find_collimated_farfield_files(root)
na = len(afiles)
return z0, bg, threshold, z1, bg, threshold, afiles, [bg]*na, [threshold]*na
return parse_file_list(root, par, threshold)
[docs]def gather_fullcone_file_list(root, par=None, threshold=None):
"""
Gather the list of full-cone farfield output files to analyze.
Args:
root (:obj:`str`, `Path`_):
Root directory with files.
par (:obj:`str`, `Path`_, optional):
Name of a file that provides 2 or 3 columns: (1) the files to
analyze, (2) the background image to use for each file, and (3) the
threshold to use for each file. If this file is provided, any
threshold is ignored and the root directory is not trolled for all
bg*, z*, and a* files. The last column with the thresholds can be
omitted, which means the code will use the value provided on the
command line (or its default).
threshold (:obj:`float`, optional):
If ``par`` is not provided or it has no 3nd column, this is the
threshold to use for all files.
Returns:
:obj:`tuple`: Provides (1) the z0 file, (2) its background file, (3) its
threshold, (4) the z1 file, (5) its background file, (6) its threshold,
(7) the list of a* files, (8) their background files, and (9) their
thresholds.
"""
if par is None:
z0, z1, bg = find_fullcone_farfield_files(root)
return z0, bg, threshold, z1, bg, threshold
return parse_file_list(root, par, threshold)[:6]
[docs]def find_collimated_farfield_files(root):
"""
Find the set of collimated far-field output files according to the expected
nomenclature.
Args:
root (:obj:`str`, `Path`_):
Root directory with files.
Returns:
:obj:`tuple`: Full paths to (1) the z0 image, (2) the z1 image, (3) the
background image, and (4) the list of a* files.
"""
# Set the root directory
_root = Path(root).resolve()
if not _root.exists():
raise FileNotFoundError(f'{_root} is not a valid directory.')
# Find the z0 and z1 images
z0 = sorted(list(_root.glob('z0*')))
if len(z0) > 1:
raise ValueError('More than one z0 image found. Directory should only have one of '
f'the following: {[f.name for f in z0]}')
if len(z0) == 0:
raise ValueError('Could not find z0 image.')
z0 = z0[0]
z1 = sorted(list(_root.glob('z1*')))
if len(z1) > 1:
raise ValueError('More than one z1 image found. Directory should only have one of '
f'the following: {[f.name for f in z1]}')
if len(z1) == 0:
raise ValueError('Could not find z1 image.')
z1 = z1[0]
# Attempt to find a background image
bg = sorted(list(_root.glob('bg*')))
if len(bg) >= 1:
if len(bg) > 1:
warnings.warn(f'Found more than one background image: {[f.name for f in bg]}. '
'Using the first one.')
bg = bg[0]
else:
warnings.warn('No background images found. Will attempt to use main image to set '
'background level.')
bg = None
afiles = sorted(list(_root.glob('a*')))
return z0, z1, bg, afiles
[docs]def find_fullcone_farfield_files(root):
"""
Find a set of fullcone far-field output files according to the expected
nomenclature.
Args:
root (:obj:`str`, `Path`_):
Root directory with files.
Returns:
:obj:`tuple`: Full paths to (1) the z0 image, (2) the z1 image, and (3)
the background image.
"""
# Set the root directory
_root = Path(root).resolve()
if not _root.exists():
raise FileNotFoundError(f'{_root} is not a valid directory.')
# Find the z0 and z1 images
z0 = sorted(list(_root.glob('z0*')))
if len(z0) > 1:
raise ValueError('More than one z0 image found. Directory should only have one of '
f'the following: {[f.name for f in z0]}')
if len(z0) == 0:
raise ValueError('Could not find z0 image.')
z0 = z0[0]
z1 = sorted(list(_root.glob('z1*')))
if len(z1) > 1:
raise ValueError('More than one z1 image found. Directory should only have one of '
f'the following: {[f.name for f in z1]}')
if len(z1) == 0:
raise ValueError('Could not find z1 image.')
z1 = z1[0]
# Attempt to find a background image
bg = sorted(list(_root.glob('bg*')))
for i in range(len(bg)):
if bg[i].is_dir():
bg[i] = sorted(list(bg[i].glob('bg*')))
bg = numpy.concatenate(bg).tolist()
if len(bg) >= 1:
if len(bg) > 1:
warnings.warn(f'Found more than one background image: {[f.name for f in bg]}. '
'Using the first one.')
bg = bg[0]
else:
warnings.warn('No background images found. Will attempt to use main image to set '
'background level.')
bg = None
return z0, z1, bg
[docs]def parse_file_list(root, par, threshold):
"""
Parse a file with the set of data files to analyze.
Args:
root (:obj:`str`, `Path`_):
Root directory with files.
par (:obj:`str`, `Path`_):
Name of a file that provides 2 or 3 columns: (1) the files to
analyze, (2) the background image to use for each file, and (3) the
threshold to use for each file. The last column with the thresholds
can be omitted, which means the code will use the value provided on
the command line (or its default).
threshold (:obj:`float`, optional):
If ``par`` has no 3nd column, this is the threshold to use for all
files.
Returns:
:obj:`tuple`: Provides (1) the z0 file, (2) its background file, (3) its
threshold, (4) the z1 file, (5) its background file, (6) its threshold,
(7) the list of a* files, (8) their background files, and (9) their
thresholds.
"""
# Set the root directory
_root = Path(root).resolve()
if not _root.exists():
raise FileNotFoundError(f'{_root} is not a valid directory.')
_par = Path(par).resolve()
if not _par.exists():
raise FileNotFoundError(f'{_par} does not exist!')
# Use numpy to read the file
db = numpy.genfromtxt(str(_par), dtype=str)
if db.shape[1] not in [2, 3]:
raise ValueError(f'{_par} must only contain 2 or 3 columns!')
nfiles = db.shape[0]
if db.shape[1] == 2:
imgs, bkgs = db.T
thresh = [threshold]*nfiles
else:
imgs, bkgs, thresh = db.T
thresh = thresh.astype(float)
# Check the files exist in the root directory
for i in range(nfiles):
if not (_root / imgs[i]).exists():
raise FileNotFoundError(f'{imgs[i]} is not a file in {_root}.')
if not (_root / bkgs[i]).exists():
raise FileNotFoundError(f'{bkgs[i]} is not a file in {_root}.')
# Find the z0 file
indx = numpy.where([i[:2] == 'z0' for i in imgs])[0]
if len(indx) != 1:
raise ValueError('There should one and only one file that starts with "z0".')
z0 = _root / imgs[indx[0]]
z0_bg = _root / bkgs[indx[0]]
z0_thresh = thresh[indx[0]]
# Find the z1 file
indx = numpy.where([i[:2] == 'z1' for i in imgs])[0]
if len(indx) != 1:
raise ValueError('There should one and only one file that starts with "z1".')
z1 = _root / imgs[indx[0]]
z1_bg = _root / bkgs[indx[0]]
z1_thresh = thresh[indx[0]]
# Find the angle-sweep files
indx = numpy.where([i[0] == 'a' for i in imgs])[0]
if nfiles != indx.size + 2:
warnings.warn(f'Could not parse {nfiles - 2 - indx.size} files in {_par}.')
if indx.size == 0:
warnings.warn(f'Could not find any angle-sweep files.')
return z0, z0_bg, z0_thresh, z1, z1_bg, z1_thresh, \
_root / imgs[indx], _root / bkgs[indx], thresh[indx]