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Pull #199

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weaverba137

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working on PR suggestions

Pull Request Pull Request #199: Add units to a Table

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/py/desiutil/annotate.py

# Licensed under a 3-clause BSD style license - see LICENSE.rst
# -*- coding: utf-8 -*-
"""
=================
desiutil.annotate
=================

Tools for adding units and comments to FITS files.
"""
import csv
import os
import sys
from argparse import ArgumentParser
import yaml
from astropy.io import fits
from astropy.table import Table, QTable
from astropy.units import UnitConversionError
from . import __version__ as desiutilVersion
from .log import get_logger, DEBUG


log = None


def find_column_name(columns, prefix=('unit', )):
    """Find the column that contains unit descriptions, or comments.

    Parameters
    ----------
    columns : iterable
        The column names from a CSV or similar file.
    prefix : :class:`tuple`, optional
        Search for a column matching one or more items in `prefix`.
        The search is case-insensitive.

    Returns
    -------
    :class:`int`
        The index of `columns` that matches.

    Raises
    ------
    IndexError
        If no match was found.
    """
    for i, column in enumerate(columns):
        for s in prefix:
            if s in column.lower():
                return i
    raise IndexError(f"No column matching '{prefix[0]}' found!")


def find_key_name(data, prefix=('unit', )):
    """
    Parameters
    ----------
    data : :class:`dict`
        A dictionary resulting from a parsed YAML file.
    prefix : :class:`tuple`, optional
        Search for a column matching one or more items in `prefix`.
        The search is case-insensitive.

    Returns
    -------
    :class:`str`
        The key of `data` that matches.

    Raises
    ------
    KeyError
        If no match was found.
    """
    for key in data.keys():
        for s in prefix:
            if s in key.lower():
                return key
    raise KeyError(f"No key matching '{prefix[0]}' found!")


def load_csv_units(filename):
    """Parse a CSV file that contains column names and units and optionally comments.

    Table column names are assumed to be in the first column of the CSV file.
    Any column with the name "Unit(s)" (case-insensitive) is assumed to contain FITS-style units.
    Any column with the name "Comment(s)" (case-insensitive) or "Description(s)" is assumed to be the comment.

    Parameters
    ----------
    filename : :class:`str` or :class:`pathlib.Path`
        Read column definitions from `filename`.

    Returns
    -------
    :class:`tuple`
        A tuple containing two :class:`dict` objects for units and comments.
        If no comments are detected, the comments :class:`dict` will be empty.

    Raises
    ------
    ValueError
        If `filename` does not at least contain a "unit" column.
    """
    units = dict()
    comments = dict()
    header = None
    data = list()
    log.debug("filename = '%s'", filename)
    with open(filename, newline='') as f:
        reader = csv.reader(f)
        for row in reader:
            if header is None:
                header = row
            else:
                data.append(row)
    log.debug(header)
    try:
        u = find_column_name(header)
    except IndexError:
        raise ValueError(f"{filename} does not have a unit column!")
    try:
        c = find_column_name(header, prefix=('comment', 'description'))
    except IndexError:
        c = None
    for row in data:
        log.debug("units['%s'] = '%s'", row[0], row[u])
        units[row[0]] = row[u]
        if c:
            log.debug("comments['%s'] = '%s'", row[0], row[c])
            comments[row[0]] = row[c]
    return (units, comments)


def load_yml_units(filename):
    """Parse a YAML file that contains column names and units and optionally comments.

    The YAML file should contain a dictionary with a keyword like 'units' and,
    optionally, a keyword like 'comments' or 'description.

    For backwards-compatibility, the YAML file can be simply a dictionary
    containing column names.

    Parameters
    ----------
    filename : :class:`str` or :class:`pathlib.Path`
        Read column definitions from `filename`.

    Returns
    -------
    :class:`tuple`
        A tuple containing two :class:`dict` objects for units and comments.
        If no comments are detected, the comments :class:`dict` will be empty.
    """
    comments = dict()
    # log.debug("y = yaml.safe_load('%s')", filename)
    with open(filename, newline='') as f:
        y = yaml.safe_load(f)
    try:
        u = find_key_name(y)
    except KeyError:
        log.warning(f"{filename} does not have a unit column, assuming keys are columns!")
        u = None
    try:
        c = find_key_name(y, prefix=('comment', 'description'))
    except KeyError:
        c = None
    if u:
        units = y[u]
    else:
        units = y
    if c:
        comments = y[c]
    return (units, comments)


def annotate_table(table, units, inplace=False):
    """Add annotations to `table`.

    Parameters
    ----------
    table : :class:`astropy.table.Table` or :class:`astropy.table.QTable`
        A data table.
    units : :class:`dict`
        Mapping of table columns to units.
    inplace : :class:`bool`, optional
        If ``True``, modify `table` directly instead of returning a copy.

    Returns
    -------
    :class:`astropy.table.Table`
        An updated version of `table`.

    Notes
    -----
    Currently :class:`~astropy.table.Table` does not support the concept
    of column-specific comments, especially in a way where the comments
    could be written to a file. If this ever changes, this function could
    be extended to add comments.
    """
    if inplace:
        t = table
    else:
        if isinstance(table, QTable):
            t = QTable(table)  # copy=True is the default.
        else:
            t = Table(table)
    for colname in t.colnames:
        if colname not in units:
            log.info("Column '%s' not found in units argument.", colname)
    for column in units:
        if column in t.colnames:
            if len(units[column]) > 0:
                try:
                    log.debug("t['%s'].unit = '%s'", column, units[column])
                    t[column].unit = units[column]
                except AttributeError:
                    #
                    # Can't change .unit if it is already set. Try to convert.
                    #
                    try:
                        log.debug("t.replace_column('%s', t['%s'].to('%s'))", column, column, units[column])
                        t.replace_column(column, t[column].to(units[column]))
                    except UnitConversionError:
                        log.error("Cannot add or replace unit '%s' to column '%s'!", units[column], column)
            else:
                log.debug("Not setting blank unit for column '%s'.", column)
        else:
            log.debug("Column '%s' not present in table.", column)
    return t


def annotate(filename, extension, units=None, comments=None):
    """Add annotations to `filename`.

    If `units` or `comments` is an empty dictionary, it will be ignored.

    Parameters
    ----------
    filename : :class:`str`
        Name of FITS file.
    extension : :class:`str` or :class:`int
        Name or number of extension in `filename`.
    units : :class:`dict`, optional
        Mapping of table columns to units.
    comments : :class:`dict`, optional
        Mapping of table columns to comments.

    Returns
    -------
    :class:`astropy.io.fits.HDUList`
        An updated version of the file.
    """
    new_hdus = list()
    with fits.open(filename, mode='readonly', memmap=False, lazy_load_hdus=False, uint=False, disable_image_compression=True, do_not_scale_image_data=True, character_as_bytes=True, scale_back=True) as hdulist:
        log.debug(hdulist._open_kwargs)
        kwargs = hdulist._open_kwargs.copy()
        for h in hdulist:
            hc = h.copy()
            if hasattr(h, '_do_not_scale_image_data'):
                hc._do_not_scale_image_data = h._do_not_scale_image_data
            if hasattr(h, '_bzero'):
                hc._bzero = h._bzero
            if hasattr(h, '_bscale'):
                hc._bzero = h._bscale
            if hasattr(h, '_scale_back'):
                hc._scale_back = h._scale_back
            if hasattr(h, '_uint'):
                hc._uint = h._uint
            #
            # Work around header comments not copied for BinTableHDU.
            #
            if isinstance(h, fits.BinTableHDU):
                for key in h.header.keys():
                    hc.header.comments[key] = h.header.comments[key]
            #
            # Work around disappearing BZERO and BSCALE keywords.
            #
            if isinstance(h, fits.ImageHDU) and 'BZERO' in h.header and 'BSCALE' in h.header:
                if 'BZERO' not in hc.header or 'BSCALE' not in hc.header:
                    iscale = h.header.index('BSCALE')
                    izero = h.header.index('BZERO')
                    if izero > iscale:
                        hc.header.insert(iscale - 1, ('BSCALE', h.header['BSCALE'], h.header.comments['BSCALE']), after=True)
                        hc.header.insert(iscale, ('BZERO', h.header['BZERO'], h.header.comments['BZERO']), after=True)
                    else:
                        hc.header.insert(izero - 1, ('BZERO', h.header['BZERO'], h.header.comments['BZERO']), after=True)
                        hc.header.insert(izero, ('BSCALE', h.header['BSCALE'], h.header.comments['BSCALE']), after=True)
            new_hdus.append(hc)
    new_hdulist = fits.HDUList(new_hdus)
    new_hdulist._open_kwargs = kwargs
    log.debug(new_hdulist._open_kwargs)
    try:
        ext = int(extension)
    except ValueError:
        ext = extension
    try:
        hdu = new_hdulist[ext]
    except (IndexError, KeyError):
        raise
    return new_hdulist


def _options():
    """Parse command-line options.
    """
    parser = ArgumentParser(description="Add units or comments to a FITS file.",
                            prog=os.path.basename(sys.argv[0]))
    parser.add_argument('-c', '--comments', action='store', dest='comments', metavar='COMMENTS',
                        help="COMMENTS should have the form COLUMN='comment':COLUMN='comment'.")
    parser.add_argument('-C', '--csv', action='store', dest='csv', metavar='CSV',
                        help="Read annotations from CSV file.")
    parser.add_argument('-e', '--extension', dest='extension', action='store', metavar='EXT', default='1',
                        help="Update FITS extension EXT, which can be a number or an EXTNAME. If not specified, HDU 1 will be updated, which is standard for simple binary tables.")
    parser.add_argument('-o', '--overwrite', dest='overwrite', action='store_true',
                        help='Overwrite the input FITS file.')
    parser.add_argument('-t', '--test', dest='test', action='store_true',
                        help='Test mode; show what would be done but do not change any files.')
    parser.add_argument('-u', '--units', action='store', dest='units', metavar='UNITS',
                        help="UNITS should have the form COLUMN='unit':COLUMN='unit'.")
    parser.add_argument('-v', '--verbose', dest='verbose', action='store_true',
                        help='Print extra debugging information.')
    parser.add_argument('-V', '--version', action='version', version='%(prog)s ' + desiutilVersion)
    parser.add_argument('-Y', '--yaml', action='store', dest='yaml', metavar='YAML',
                        help="Read annotations from YAML file.")
    parser.add_argument('fits', metavar='INPUT_FITS', help='FITS file to modify.')
    parser.add_argument('output', metavar='OUTPUT_FITS', nargs='?',
                        help='Write to new FITS file. If --overwrite is specified, this value is ignored.')
    options = parser.parse_args()
    return options


def main():
    """Entry-point for command-line scripts.

    Returns
    -------
    :class:`int`
        An integer suitable for passing to :func:`sys.exit`.
    """
    global log
    options = _options()
    if options.test or options.verbose:
        log = get_logger(DEBUG)
    else:
        log = get_logger()
    if options.csv:
        units, comments = load_csv_units(options.csv)
    elif options.yaml:
        units, comments = load_yml_units(options.yaml)
    else:
        if options.units:
            units = dict(tuple(c.split('=')) for c in options.units.split(':'))
        else:
            log.warning("No units have been specified!")
            units = dict()
        if options.comments:
            comments = dict(tuple(c.split('=')) for c in options.comments.split(':'))
        else:
            log.debug("No comments have been specified.")
            comments = dict()
    log.debug("units = %s", units)
    log.debug("comments = %s", comments)
    hdulist = annotate(options.fits, options.extension, units, comments)
    if options.overwrite and options.output:
        output = options.output
    elif options.overwrite:
        output = options.fits
    elif options.output:
        output = options.output
    else:
        log.error("--overwrite not specified and no output file specified!")
        return 1
    try:
        hdulist.writeto(output, output_verify='warn', overwrite=options.overwrite, checksum=False)
    except OSError as e:
        if 'overwrite' in e.args[0]:
            log.error("Output file exists and --overwrite was not specified!")
        else:
            log.error(e.args[0])
        return 1
    return 0

1	# Licensed under a 3-clause BSD style license - see LICENSE.rst
2	# -- coding: utf-8 --
3	"""	1✔
4	=================
5	desiutil.annotate
6	=================
7
8	Tools for adding units and comments to FITS files.
9	"""
10	import csv	1✔
11	import os	1✔
12	import sys	1✔
13	from argparse import ArgumentParser	1✔
14	import yaml	1✔
15	from astropy.io import fits	1✔
16	from astropy.table import Table, QTable	1✔
17	from astropy.units import UnitConversionError	1✔
18	from . import __version__ as desiutilVersion	1✔
19	from .log import get_logger, DEBUG	1✔
20
21
22	log = None	1✔
23
24
25	def find_column_name(columns, prefix=('unit', )):	1✔
26	"""Find the column that contains unit descriptions, or comments.
27
28	Parameters
29	----------
30	columns : iterable
31	The column names from a CSV or similar file.
32	prefix : :class:`tuple`, optional
33	Search for a column matching one or more items in `prefix`.
34	The search is case-insensitive.
35
36	Returns
37	-------
38	:class:`int`
39	The index of `columns` that matches.
40
41	Raises
42	------
43	IndexError
44	If no match was found.
45	"""
46	for i, column in enumerate(columns):	1✔
47	for s in prefix:	1✔
48	if s in column.lower():	1✔
49	return i	1✔
50	raise IndexError(f"No column matching '{prefix[0]}' found!")	1✔
51
52
53	def find_key_name(data, prefix=('unit', )):	1✔
54	"""
55	Parameters
56	----------
57	data : :class:`dict`
58	A dictionary resulting from a parsed YAML file.
59	prefix : :class:`tuple`, optional
60	Search for a column matching one or more items in `prefix`.
61	The search is case-insensitive.
62
63	Returns
64	-------
65	:class:`str`
66	The key of `data` that matches.
67
68	Raises
69	------
70	KeyError
71	If no match was found.
72	"""
73	for key in data.keys():	1✔
74	for s in prefix:	1✔
75	if s in key.lower():	1✔
76	return key	1✔
77	raise KeyError(f"No key matching '{prefix[0]}' found!")	1✔
78
79
80	def load_csv_units(filename):	1✔
81	"""Parse a CSV file that contains column names and units and optionally comments.
82
83	Table column names are assumed to be in the first column of the CSV file.
84	Any column with the name "Unit(s)" (case-insensitive) is assumed to contain FITS-style units.
85	Any column with the name "Comment(s)" (case-insensitive) or "Description(s)" is assumed to be the comment.
86
87	Parameters
88	----------
89	filename : :class:`str` or :class:`pathlib.Path`
90	Read column definitions from `filename`.
91
92	Returns
93	-------
94	:class:`tuple`
95	A tuple containing two :class:`dict` objects for units and comments.
96	If no comments are detected, the comments :class:`dict` will be empty.
97
98	Raises
99	------
100	ValueError
101	If `filename` does not at least contain a "unit" column.
102	"""
103	units = dict()	1✔
104	comments = dict()	1✔
105	header = None	1✔
106	data = list()	1✔
107	log.debug("filename = '%s'", filename)	1✔
108	with open(filename, newline='') as f:	1✔
109	reader = csv.reader(f)	1✔
110	for row in reader:	1✔
111	if header is None:	1✔
112	header = row	1✔
113	else:
114	data.append(row)	1✔
115	log.debug(header)	1✔
116	try:	1✔
117	u = find_column_name(header)	1✔
118	except IndexError:	1✔
119	raise ValueError(f"{filename} does not have a unit column!")	1✔
120	try:	1✔
121	c = find_column_name(header, prefix=('comment', 'description'))	1✔
122	except IndexError:	1✔
123	c = None	1✔
124	for row in data:	1✔
125	log.debug("units['%s'] = '%s'", row[0], row[u])	1✔
126	units[row[0]] = row[u]	1✔
127	if c:	1✔
128	log.debug("comments['%s'] = '%s'", row[0], row[c])	1✔
129	comments[row[0]] = row[c]	1✔
130	return (units, comments)	1✔
131
132
133	def load_yml_units(filename):	1✔
134	"""Parse a YAML file that contains column names and units and optionally comments.
135
136	The YAML file should contain a dictionary with a keyword like 'units' and,
137	optionally, a keyword like 'comments' or 'description.
138
139	For backwards-compatibility, the YAML file can be simply a dictionary
140	containing column names.
141
142	Parameters
143	----------
144	filename : :class:`str` or :class:`pathlib.Path`
145	Read column definitions from `filename`.
146
147	Returns
148	-------
149	:class:`tuple`
150	A tuple containing two :class:`dict` objects for units and comments.
151	If no comments are detected, the comments :class:`dict` will be empty.
152	"""
153	comments = dict()	1✔
154	# log.debug("y = yaml.safe_load('%s')", filename)
155	with open(filename, newline='') as f:	1✔
156	y = yaml.safe_load(f)	1✔
157	try:	1✔
158	u = find_key_name(y)	1✔
159	except KeyError:	1✔
160	log.warning(f"{filename} does not have a unit column, assuming keys are columns!")	1✔
161	u = None	1✔
162	try:	1✔
163	c = find_key_name(y, prefix=('comment', 'description'))	1✔
164	except KeyError:	1✔
165	c = None	1✔
166	if u:	1✔
167	units = y[u]	1✔
168	else:
169	units = y	1✔
170	if c:	1✔
171	comments = y[c]	1✔
172	return (units, comments)	1✔
173
174
175	def annotate_table(table, units, inplace=False):	1✔
176	"""Add annotations to `table`.
177
178	Parameters
179	----------
180	table : :class:`astropy.table.Table` or :class:`astropy.table.QTable`
181	A data table.
182	units : :class:`dict`
183	Mapping of table columns to units.
184	inplace : :class:`bool`, optional
185	If ``True``, modify `table` directly instead of returning a copy.
186
187	Returns
188	-------
189	:class:`astropy.table.Table`
190	An updated version of `table`.
191
192	Notes
193	-----
194	Currently :class:`~astropy.table.Table` does not support the concept
195	of column-specific comments, especially in a way where the comments
196	could be written to a file. If this ever changes, this function could
197	be extended to add comments.
198	"""
199	if inplace:	1✔
200	t = table	1✔
201	else:
202	if isinstance(table, QTable):	1✔
203	t = QTable(table) # copy=True is the default.	1✔
204	else:
205	t = Table(table)	1✔
206	for colname in t.colnames:	1✔
207	if colname not in units:	1✔
208	log.info("Column '%s' not found in units argument.", colname)	1✔
209	for column in units:	1✔
210	if column in t.colnames:	1✔
211	if len(units[column]) > 0:	1✔
212	try:	1✔
213	log.debug("t['%s'].unit = '%s'", column, units[column])	1✔
214	t[column].unit = units[column]	1✔
215	except AttributeError:	1✔
216	#
217	# Can't change .unit if it is already set. Try to convert.
218	#
219	try:	1✔
220	log.debug("t.replace_column('%s', t['%s'].to('%s'))", column, column, units[column])	1✔
221	t.replace_column(column, t[column].to(units[column]))	1✔
222	except UnitConversionError:	1✔
223	log.error("Cannot add or replace unit '%s' to column '%s'!", units[column], column)	1✔
224	else:
225	log.debug("Not setting blank unit for column '%s'.", column)	1✔
226	else:
227	log.debug("Column '%s' not present in table.", column)	1✔
228	return t	1✔
229
230
231	def annotate(filename, extension, units=None, comments=None):	1✔
232	"""Add annotations to `filename`.
233
234	If `units` or `comments` is an empty dictionary, it will be ignored.
235
236	Parameters
237	----------
238	filename : :class:`str`
239	Name of FITS file.
240	extension : :class:`str` or :class:`int
241	Name or number of extension in `filename`.
242	units : :class:`dict`, optional
243	Mapping of table columns to units.
244	comments : :class:`dict`, optional
245	Mapping of table columns to comments.
246
247	Returns
248	-------
249	:class:`astropy.io.fits.HDUList`
250	An updated version of the file.
251	"""
252	new_hdus = list()	×
253	with fits.open(filename, mode='readonly', memmap=False, lazy_load_hdus=False, uint=False, disable_image_compression=True, do_not_scale_image_data=True, character_as_bytes=True, scale_back=True) as hdulist:	×
254	log.debug(hdulist._open_kwargs)	×
255	kwargs = hdulist._open_kwargs.copy()	×
256	for h in hdulist:	×
257	hc = h.copy()	×
258	if hasattr(h, '_do_not_scale_image_data'):	×
259	hc._do_not_scale_image_data = h._do_not_scale_image_data	×
260	if hasattr(h, '_bzero'):	×
261	hc._bzero = h._bzero	×
262	if hasattr(h, '_bscale'):	×
263	hc._bzero = h._bscale	×
264	if hasattr(h, '_scale_back'):	×
265	hc._scale_back = h._scale_back	×
266	if hasattr(h, '_uint'):	×
267	hc._uint = h._uint	×
268	#
269	# Work around header comments not copied for BinTableHDU.
270	#
271	if isinstance(h, fits.BinTableHDU):	×
272	for key in h.header.keys():	×
273	hc.header.comments[key] = h.header.comments[key]	×
274	#
275	# Work around disappearing BZERO and BSCALE keywords.
276	#
277	if isinstance(h, fits.ImageHDU) and 'BZERO' in h.header and 'BSCALE' in h.header:	×
278	if 'BZERO' not in hc.header or 'BSCALE' not in hc.header:	×
279	iscale = h.header.index('BSCALE')	×
280	izero = h.header.index('BZERO')	×
281	if izero > iscale:	×
282	hc.header.insert(iscale - 1, ('BSCALE', h.header['BSCALE'], h.header.comments['BSCALE']), after=True)	×
283	hc.header.insert(iscale, ('BZERO', h.header['BZERO'], h.header.comments['BZERO']), after=True)	×
284	else:
285	hc.header.insert(izero - 1, ('BZERO', h.header['BZERO'], h.header.comments['BZERO']), after=True)	×
286	hc.header.insert(izero, ('BSCALE', h.header['BSCALE'], h.header.comments['BSCALE']), after=True)	×
287	new_hdus.append(hc)	×
288	new_hdulist = fits.HDUList(new_hdus)	×
289	new_hdulist._open_kwargs = kwargs	×
290	log.debug(new_hdulist._open_kwargs)	×
291	try:	×
292	ext = int(extension)	×
293	except ValueError:	×
294	ext = extension	×
295	try:	×
296	hdu = new_hdulist[ext]	×
297	except (IndexError, KeyError):	×
298	raise	×
299	return new_hdulist	×
300
301
302	def _options():	1✔
303	"""Parse command-line options.
304	"""
305	parser = ArgumentParser(description="Add units or comments to a FITS file.",	1✔
306	prog=os.path.basename(sys.argv[0]))
307	parser.add_argument('-c', '--comments', action='store', dest='comments', metavar='COMMENTS',	1✔
308	help="COMMENTS should have the form COLUMN='comment':COLUMN='comment'.")
309	parser.add_argument('-C', '--csv', action='store', dest='csv', metavar='CSV',	1✔
310	help="Read annotations from CSV file.")
311	parser.add_argument('-e', '--extension', dest='extension', action='store', metavar='EXT', default='1',	1✔
312	help="Update FITS extension EXT, which can be a number or an EXTNAME. If not specified, HDU 1 will be updated, which is standard for simple binary tables.")
313	parser.add_argument('-o', '--overwrite', dest='overwrite', action='store_true',	1✔
314	help='Overwrite the input FITS file.')
315	parser.add_argument('-t', '--test', dest='test', action='store_true',	1✔
316	help='Test mode; show what would be done but do not change any files.')
317	parser.add_argument('-u', '--units', action='store', dest='units', metavar='UNITS',	1✔
318	help="UNITS should have the form COLUMN='unit':COLUMN='unit'.")
319	parser.add_argument('-v', '--verbose', dest='verbose', action='store_true',	1✔
320	help='Print extra debugging information.')
321	parser.add_argument('-V', '--version', action='version', version='%(prog)s ' + desiutilVersion)	1✔
322	parser.add_argument('-Y', '--yaml', action='store', dest='yaml', metavar='YAML',	1✔
323	help="Read annotations from YAML file.")
324	parser.add_argument('fits', metavar='INPUT_FITS', help='FITS file to modify.')	1✔
325	parser.add_argument('output', metavar='OUTPUT_FITS', nargs='?',	1✔
326	help='Write to new FITS file. If --overwrite is specified, this value is ignored.')
327	options = parser.parse_args()	1✔
328	return options	1✔
329
330
331	def main():
332	"""Entry-point for command-line scripts.
333
334	Returns
335	-------
336	:class:`int`
337	An integer suitable for passing to :func:`sys.exit`.
338	"""
339	global log
340	options = _options()
341	if options.test or options.verbose:
342	log = get_logger(DEBUG)
343	else:
344	log = get_logger()
345	if options.csv:
346	units, comments = load_csv_units(options.csv)
347	elif options.yaml:
348	units, comments = load_yml_units(options.yaml)
349	else:
350	if options.units:
351	units = dict(tuple(c.split('=')) for c in options.units.split(':'))
352	else:
353	log.warning("No units have been specified!")
354	units = dict()
355	if options.comments:
356	comments = dict(tuple(c.split('=')) for c in options.comments.split(':'))
357	else:
358	log.debug("No comments have been specified.")
359	comments = dict()
360	log.debug("units = %s", units)
361	log.debug("comments = %s", comments)
362	hdulist = annotate(options.fits, options.extension, units, comments)
363	if options.overwrite and options.output:
364	output = options.output
365	elif options.overwrite:
366	output = options.fits
367	elif options.output:
368	output = options.output
369	else:
370	log.error("--overwrite not specified and no output file specified!")
371	return 1
372	try:
373	hdulist.writeto(output, output_verify='warn', overwrite=options.overwrite, checksum=False)
374	except OSError as e:
375	if 'overwrite' in e.args[0]:
376	log.error("Output file exists and --overwrite was not specified!")
377	else:
378	log.error(e.args[0])
379	return 1
380	return 0

desihub / desiutil / 6041958714

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