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1# This file is part of astro_metadata_translator.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (http://www.lsst.org).
6# See the LICENSE file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# Use of this source code is governed by a 3-clause BSD-style
10# license that can be found in the LICENSE file.
12"""Code to support header manipulation operations."""
14__all__ = ("merge_headers", "fix_header")
16import pkg_resources
17import posixpath
18import logging
19import itertools
20import copy
21import os
22import yaml
23from collections.abc import Mapping
24from collections import Counter
26from .translator import MetadataTranslator
27from .translators import FitsTranslator
29log = logging.getLogger(__name__)
31ENV_VAR_NAME = "METADATA_CORRECTIONS_PATH"
32"""Name of environment variable containing search path for header fix up."""
35def merge_headers(headers, mode="overwrite", sort=False, first=None, last=None):
36 """Merge multiple headers into a single dict.
38 Given a list of dict-like data headers, combine them following the
39 specified mode.
41 Parameters
42 ----------
43 headers : `list` of `dict` (or `dict`-like)
44 Collection of headers to combine. `~lsst.daf.base.PropertyList`
45 is supported.
46 mode : `str`
47 Scheme to use when a header has the same key as another header
48 but different value. Options are:
50 - ``'overwrite'`` : Value in later header overwrites earlier value.
51 - ``'drop'`` : Entire key is dropped. If a key only appears in a
52 subset of the headers, and is identical in those, it will be
53 retained.
54 - ``'diff'`` : As for ``drop`` but the dropped values are stored in a
55 `list` of `dict` in the returned merged header in key
56 ``__DIFF__``. The order used matches the supplied order or
57 the sorted order if specified. This allows a simple header diff
58 to be performed and associated with the original headers. Only
59 keys that appear in all headers will be retained in the merged one.
60 Unlike for ``'drop'`` headers that are identical and only present in
61 a subset will always be included in the diff.
62 - ``'first'`` : Retain first value encountered.
63 - ``'append'`` : Convert value to list with a value for each header
64 (`None` if the key was not present). If the value is
65 identical in multiple headers but key is missing in
66 some, then the single identical header is stored.
67 sort : `bool`, optional
68 If `True`, sort the supplied headers into date order if possible.
69 This affects the resulting merged output depending on the requested
70 merge mode. An attempt will be made to extract a date from the
71 headers.
72 first : `list` or `tuple`, optional
73 Keys to retain even if they differ. For all modes excepting ``append``
74 (where it is ignored) the value in the merged header will always be
75 the value first encountered. This is usually to allow time-dependent
76 headers such as ``DATE-OBS`` and ``AZSTART`` to be retained to allow
77 the header to indicate the range of values. No exception is raised if
78 a key can not be found in a header since this allows a range of
79 expected headers to be listed covering multiple instruments.
80 last : `list` or `tuple`, optional
81 Keys to retain even if they differ. For all modes excepting ``append``
82 (where it is ignored) the value in the merged header will always be
83 the final value encountered. This is usually to allow time-dependent
84 headers such as ``DATE-END`` and ``AZEND`` to be retained to allow
85 the header to indicate the range of values. No exception is raised if
86 a key can not be found in a header since this allows a range of
87 expected headers to be listed covering multiple instruments.
89 Returns
90 -------
91 merged : `dict`
92 Single `dict` combining all the headers using the specified
93 combination mode.
95 Notes
96 -----
97 If ``first`` and ``last`` are supplied, the keys from ``first`` are
98 handled first, followed by the keys from ``last``. No check is made to
99 ensure that the keys do not overlap.
100 """
101 if not headers:
102 raise ValueError("No headers supplied.")
104 # Copy the input list because we will be reorganizing it
105 headers = list(headers)
107 # With a single header provided return a copy immediately
108 if len(headers) == 1:
109 return copy.deepcopy(headers[0])
111 if sort:
112 def key_func(hdr):
113 translator_class = None
114 try:
115 translator_class = MetadataTranslator.determine_translator(hdr)
116 except ValueError:
117 # Try the FITS translator
118 translator_class = FitsTranslator
119 translator = translator_class(hdr)
120 return translator.to_datetime_begin()
122 headers = sorted(headers, key=key_func)
124 log.debug("Received %d headers for merging", len(headers))
126 # Pull out first header
127 first_hdr = headers.pop(0)
129 # Seed the merged header with a copy
130 merged = copy.deepcopy(first_hdr)
132 if mode == "overwrite":
133 for h in headers:
134 merged.update(h)
136 elif mode == "first":
137 # Reversing the headers and using overwrite mode would result in the
138 # header order being inconsistent dependent on mode.
139 for hdr in headers:
140 for key in hdr:
141 if key not in merged:
142 merged[key] = hdr[key]
144 elif mode == "drop":
145 drop = set()
146 for hdr in headers:
147 for key in hdr:
148 if key not in merged:
149 merged[key] = hdr[key]
150 elif merged[key] != hdr[key]:
151 # Key should be dropped later (not in loop since removing
152 # the key now might add it back for the next header).
153 drop.add(key)
155 for key in drop:
156 del merged[key]
158 elif mode == "diff":
159 dropped_keys = set()
161 # Only want to keep keys in the merged header that are in all the
162 # input headers and identical. Seed with the first header
163 counter = Counter(merged.keys())
165 for hdr in headers:
166 counter.update(hdr.keys())
167 for key in hdr:
168 if key not in merged:
169 merged[key] = hdr[key]
170 elif merged[key] != hdr[key]:
171 # Key should be dropped later (not in loop since removing
172 # the key now might add it back for the next header).
173 dropped_keys.add(key)
175 # Add to the list of dropped keys all the keys that
176 # have a count less than number of input headers (incl first one)
177 n = len(headers) + 1
178 for key in counter:
179 if counter[key] != n:
180 dropped_keys.add(key)
182 # For each dropped key, create a distinct diff header
183 # We must include the first header in this
184 diffs = []
185 for hdr in itertools.chain([first_hdr], headers):
186 # Get a list of all the dropped keys that are in this header
187 # Sometimes a key will only be in some headers. For now
188 # do not include it in the diff at all.
189 diff_keys = dropped_keys & set(hdr)
191 diffs.append({k: hdr[k] for k in diff_keys})
193 # PropertyList does not let us attach a dict to it
194 # so if we encounter this we have to force a type change to dict
195 try:
196 merged["__DIFF__"] = diffs
197 except TypeError:
198 merged = dict(merged)
199 merged["__DIFF__"] = diffs
201 for key in dropped_keys:
202 del merged[key]
204 elif mode == "append":
205 fill = set()
206 for hdr in headers:
207 for key in hdr:
208 if key not in merged:
209 merged[key] = hdr[key]
210 elif not isinstance(merged[key], list) and merged[key] != hdr[key]:
211 # If we detect different values, store an empty list
212 # in the slot and fill it later. Do it at end so
213 # we can pick up earlier values and fill empty with None.
214 merged[key] = []
215 fill.add(key)
217 # Fill the entries that have multiple differing values
218 for key in fill:
219 merged[key] = [h[key] if key in h else None
220 for h in itertools.chain([first_hdr], headers)]
222 else:
223 raise ValueError(f"Unsupported value of '{mode}' for mode parameter.")
225 # Force the first and last values to be inserted
226 #
227 if mode != "append":
228 def retain_value(to_receive, to_retain, sources):
229 if to_retain:
230 for k in to_retain:
231 # Look for values until we find one
232 for h in sources:
233 if k in h:
234 to_receive[k] = h[k]
235 break
237 all_headers = (first_hdr, *headers)
238 retain_value(merged, first, all_headers)
239 retain_value(merged, last, tuple(reversed(all_headers)))
241 return merged
244def _read_yaml(fh, msg):
245 """Read YAML from file descriptor.
247 Parameters
248 ----------
249 fh : `io.IOBase`
250 Open file handle containing the YAML stream
251 msg : `str`
252 Text to include in log file when referring to this stream. Examples
253 could be "file something.yaml" or "resource module:resource".
255 Returns
256 -------
257 parsed : `dict` or `None`
258 The contents of the YAML file if it was a `dict`, else `None` if
259 the contents could not be parsed or the contents were YAML but
260 not a mapping.
261 """
262 try:
263 content = yaml.safe_load(fh)
264 except Exception as e:
265 log.warning("Error parsing YAML header corrections from %s: %s", msg, str(e))
266 return None
268 if not isinstance(content, Mapping):
269 log.warning("YAML Mapping not found in %s. Ignoring contents.", msg)
270 return None
272 return content
275def _find_from_file(header, paths, target_file):
276 """Search file system for matching correction files.
278 Parameters
279 ----------
280 header : `dict`
281 Header to update.
282 paths : `list`
283 Paths to search.
284 target_file : `str`
285 File to locate in the path.
287 Returns
288 -------
289 modified : `bool`
290 `True` if a correction was found. Only the first correction located
291 in a path is used.
292 """
293 for p in paths:
294 correction_file = os.path.join(p, target_file)
295 if os.path.exists(correction_file):
296 with open(correction_file) as fh:
297 log.debug("Applying header corrections from file %s", correction_file)
298 corrections = _read_yaml(fh, f"file {correction_file}")
300 if corrections is None:
301 continue
303 # Apply corrections
304 header.update(corrections)
306 return True
307 return False
310def _find_from_resource(header, package, resource_root, target_file):
311 """Search package resource for correction information.
313 Parameters
314 ----------
315 header : `dict`
316 Header to update.
317 package : `str`
318 Package resource to search.
319 resource_root : `str`
320 Resource root.
321 target_file : `str`
322 Resource to locate.
324 Returns
325 -------
326 modified : `bool`
327 `True` if a correction was found.
328 """
329 if package is not None and resource_root is not None:
330 resource_name = posixpath.join(resource_root, target_file)
331 if pkg_resources.resource_exists(package, resource_name):
332 log.debug("Applying header corrections from package resource %s:%s", package, resource_name)
333 with pkg_resources.resource_stream(package, resource_name) as fh:
334 corrections = _read_yaml(fh, f"package resource {package}:{resource_name}")
336 if corrections is None:
337 return False
339 header.update(corrections)
341 return True
342 return False
345def fix_header(header, search_path=None, translator_class=None, filename=None):
346 """Update, in place, the supplied header with known corrections.
348 Parameters
349 ----------
350 header : `dict`-like
351 Header to correct.
352 search_path : `list` or `str`, optional
353 Explicit directory paths to search for correction files.
354 A single directory path can be given as a string.
355 translator_class : `MetadataTranslator`-class, optional
356 If not `None`, the class to use to translate the supplied headers
357 into standard form. Otherwise each registered translator class will
358 be asked in turn if it knows how to translate the supplied header.
359 filename : `str`, optional
360 Name of the file whose header is being translated. For some
361 datasets with missing header information this can sometimes
362 allow for some fixups in translations.
364 Returns
365 -------
366 fixed : `bool`
367 `True` if the header was updated.
369 Raises
370 ------
371 TypeError
372 Raised if the supplied translation class is not a `MetadataTranslator`.
374 Notes
375 -----
376 In order to determine that a header update is required it is
377 necessary for the header to be handled by the supplied translator
378 class or else support automatic translation class determination.
379 It is also required that the ``observation_id`` and ``instrument``
380 be calculable prior to header fix up. If a translator class can not
381 be found or if there is a problem determining the instrument or
382 observation ID, the function will return without action.
384 Correction files use names of the form ``instrument-obsid.yaml`` (for
385 example ``LATISS-AT_O_20190329_000022.yaml``).
386 The YAML file should have the format of:
388 .. code-block:: yaml
390 EXPTIME: 30.0
391 IMGTYPE: bias
393 where each key/value pair is copied directly into the supplied header,
394 overwriting any previous values.
396 This function searches a number of locations for such a correction file.
397 The search order is:
399 - Any paths explicitly supplied through ``search_path``.
400 - The contents of the PATH-like environment variable
401 ``$METADATA_CORRECTIONS_PATH``.
402 - Any search paths supplied by the matching translator class.
404 The first file located in the search path is used for the correction.
405 """
407 if translator_class is None:
408 try:
409 translator_class = MetadataTranslator.determine_translator(header,
410 filename=filename)
411 except ValueError as e:
412 # if the header is not recognized, we should not complain
413 # and should not proceed further.
414 log.debug("Unable to determine translator class %s -- not fixing header: %e",
415 f"for {filename}" if filename is not None else "", e)
416 return False
417 elif not issubclass(translator_class, MetadataTranslator):
418 raise TypeError(f"Translator class must be a MetadataTranslator, not {translator_class}")
420 # Create an instance for this header
421 translator = translator_class(header, filename=filename)
423 # To determine the file look up we need the observation_id and instrument
424 try:
425 obsid = translator.to_observation_id()
426 instrument = translator.to_instrument()
427 except Exception:
428 # Return without comment if these translations failed
429 return False
431 target_file = f"{instrument}-{obsid}.yaml"
432 log.debug("Checking for header correction file named %s", target_file)
434 # Work out the search path
435 paths = []
436 if search_path is not None:
437 if isinstance(search_path, str):
438 # Allow a single path to be given as a string
439 search_path = [search_path]
440 paths.extend(search_path)
441 if ENV_VAR_NAME in os.environ and os.environ[ENV_VAR_NAME]:
442 paths.extend(os.environ[ENV_VAR_NAME].split(os.path.pathsep))
444 paths.extend(translator.search_paths())
446 # Prioritize file system overrides
447 modified = _find_from_file(header, paths, target_file)
449 # Apply updates from resources only if none found in files
450 if not modified:
451 package, resource_root = translator.resource_root()
452 modified = _find_from_resource(header, package, resource_root, target_file)
454 # Allow a translation class to do local fixups
455 # Allow it to fail but log the failure
456 try:
457 translator_modified = translator_class.fix_header(header, instrument, obsid, filename=filename)
458 except Exception as e:
459 log.fatal("Ignoring translator header fixup of %s %s: %s",
460 instrument, obsid, e)
461 translator_modified = False
463 return modified or translator_modified