Coverage for python/astro_metadata_translator/translator.py: 41%
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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"""Classes and support code for metadata translation"""
14from __future__ import annotations
16__all__ = ("MetadataTranslator", "StubTranslator", "cache_translation")
18import importlib
19import inspect
20import logging
21import math
22import warnings
23from abc import abstractmethod
24from typing import (
25 TYPE_CHECKING,
26 Any,
27 Callable,
28 Dict,
29 FrozenSet,
30 Iterable,
31 Iterator,
32 List,
33 Mapping,
34 MutableMapping,
35 Optional,
36 Sequence,
37 Set,
38 Tuple,
39 Type,
40 Union,
41)
43import astropy.io.fits.card
44import astropy.units as u
45from astropy.coordinates import Angle
47from .properties import PROPERTIES, PropertyDefinition
49if TYPE_CHECKING: 49 ↛ 50line 49 didn't jump to line 50, because the condition on line 49 was never true
50 import astropy.coordinates
51 import astropy.time
53log = logging.getLogger(__name__)
55# Location of the root of the corrections resource files
56CORRECTIONS_RESOURCE_ROOT = "corrections"
58"""Cache of version strings indexed by class."""
59_VERSION_CACHE: Dict[Type, str] = dict()
62def cache_translation(func: Callable, method: Optional[str] = None) -> Callable:
63 """Decorator to cache the result of a translation method.
65 Especially useful when a translation uses many other translation
66 methods. Should be used only on ``to_x()`` methods.
68 Parameters
69 ----------
70 func : `function`
71 Translation method to cache.
72 method : `str`, optional
73 Name of the translation method to cache. Not needed if the decorator
74 is used around a normal method, but necessary when the decorator is
75 being used in a metaclass.
77 Returns
78 -------
79 wrapped : `function`
80 Method wrapped by the caching function.
81 """
82 name = func.__name__ if method is None else method
84 def func_wrapper(self: MetadataTranslator) -> Any:
85 if name not in self._translation_cache:
86 self._translation_cache[name] = func(self)
87 return self._translation_cache[name]
89 func_wrapper.__doc__ = func.__doc__
90 func_wrapper.__name__ = f"{name}_cached"
91 return func_wrapper
94class MetadataTranslator:
95 """Per-instrument metadata translation support
97 Parameters
98 ----------
99 header : `dict`-like
100 Representation of an instrument header that can be manipulated
101 as if it was a `dict`.
102 filename : `str`, optional
103 Name of the file whose header is being translated. For some
104 datasets with missing header information this can sometimes
105 allow for some fixups in translations.
106 """
108 # These are all deliberately empty in the base class.
109 name: Optional[str] = None
110 """The declared name of the translator."""
112 default_search_path: Optional[Sequence[str]] = None
113 """Default search path to use to locate header correction files."""
115 default_resource_package = __name__.split(".")[0]
116 """Module name to use to locate the correction resources."""
118 default_resource_root: Optional[str] = None
119 """Default package resource path root to use to locate header correction
120 files within the ``default_resource_package`` package."""
122 _trivial_map: Dict[str, Union[str, List[str], Tuple[Any, ...]]] = {}
123 """Dict of one-to-one mappings for header translation from standard
124 property to corresponding keyword."""
126 _const_map: Dict[str, Any] = {}
127 """Dict defining a constant for specified standard properties."""
129 translators: Dict[str, Type] = dict()
130 """All registered metadata translation classes."""
132 supported_instrument: Optional[str] = None
133 """Name of instrument understood by this translation class."""
135 all_properties: Dict[str, PropertyDefinition] = {}
136 """All the valid properties for this translator including extensions."""
138 extensions: Dict[str, PropertyDefinition] = {}
139 """Extension properties (`str`: `PropertyDefinition`)
141 Some instruments have important properties beyond the standard set; this is
142 the place to declare that they exist, and they will be treated in the same
143 way as the standard set, except that their names will everywhere be
144 prefixed with ``ext_``.
146 Each property is indexed by name (`str`), with a corresponding
147 `PropertyDefinition`.
148 """
150 # Static typing requires that we define the standard dynamic properties
151 # statically.
152 if TYPE_CHECKING: 152 ↛ 153line 152 didn't jump to line 153, because the condition on line 152 was never true
153 to_telescope: Callable[[MetadataTranslator], str]
154 to_instrument: Callable[[MetadataTranslator], str]
155 to_location: Callable[[MetadataTranslator], astropy.coordinates.EarthLocation]
156 to_exposure_id: Callable[[MetadataTranslator], int]
157 to_visit_id: Callable[[MetadataTranslator], int]
158 to_physical_filter: Callable[[MetadataTranslator], str]
159 to_datetime_begin: Callable[[MetadataTranslator], astropy.time.Time]
160 to_datetime_end: Callable[[MetadataTranslator], astropy.time.Time]
161 to_exposure_time: Callable[[MetadataTranslator], u.Quantity]
162 to_dark_time: Callable[[MetadataTranslator], u.Quantity]
163 to_boresight_airmass: Callable[[MetadataTranslator], float]
164 to_boresight_rotation_angle: Callable[[MetadataTranslator], u.Quantity]
165 to_boresight_rotation_coord: Callable[[MetadataTranslator], str]
166 to_detector_num: Callable[[MetadataTranslator], int]
167 to_detector_name: Callable[[MetadataTranslator], str]
168 to_detector_serial: Callable[[MetadataTranslator], str]
169 to_detector_group: Callable[[MetadataTranslator], Optional[str]]
170 to_detector_exposure_id: Callable[[MetadataTranslator], int]
171 to_object: Callable[[MetadataTranslator], str]
172 to_temperature: Callable[[MetadataTranslator], u.Quantity]
173 to_pressure: Callable[[MetadataTranslator], u.Quantity]
174 to_relative_humidity: Callable[[MetadataTranslator], float]
175 to_tracking_radec: Callable[[MetadataTranslator], astropy.coordinates.SkyCoord]
176 to_altaz_begin: Callable[[MetadataTranslator], astropy.coordinates.AltAz]
177 to_science_program: Callable[[MetadataTranslator], str]
178 to_observation_type: Callable[[MetadataTranslator], str]
179 to_observation_id: Callable[[MetadataTranslator], str]
181 @classmethod
182 def defined_in_this_class(cls, name: str) -> Optional[bool]:
183 """Report if the specified class attribute is defined specifically in
184 this class.
186 Parameters
187 ----------
188 name : `str`
189 Name of the attribute to test.
191 Returns
192 -------
193 in_class : `bool`
194 `True` if there is a attribute of that name defined in this
195 specific subclass.
196 `False` if the method is not defined in this specific subclass
197 but is defined in a parent class.
198 Returns `None` if the attribute is not defined anywhere
199 in the class hierarchy (which can happen if translators have
200 typos in their mapping tables).
202 Notes
203 -----
204 Retrieves the attribute associated with the given name.
205 Then looks in all the parent classes to determine whether that
206 attribute comes from a parent class or from the current class.
207 Attributes are compared using `id()`.
208 """
209 # The attribute to compare.
210 if not hasattr(cls, name):
211 return None
212 attr_id = id(getattr(cls, name))
214 # Get all the classes in the hierarchy
215 mro = list(inspect.getmro(cls))
217 # Remove the first entry from the list since that will be the
218 # current class
219 mro.pop(0)
221 for parent in mro:
222 # Some attributes may only exist in subclasses. Skip base classes
223 # that are missing the attribute (such as object).
224 if hasattr(parent, name):
225 if id(getattr(parent, name)) == attr_id:
226 return False
227 return True
229 @classmethod
230 def _make_const_mapping(cls, property_key: str, constant: Any) -> Callable:
231 """Make a translator method that returns a constant value.
233 Parameters
234 ----------
235 property_key : `str`
236 Name of the property to be calculated (for the docstring).
237 constant : `str` or `numbers.Number`
238 Value to return for this translator.
240 Returns
241 -------
242 f : `function`
243 Function returning the constant.
244 """
246 def constant_translator(self: MetadataTranslator) -> Any:
247 return constant
249 if property_key in cls.all_properties:
250 property_doc = cls.all_properties[property_key].doc
251 return_type = cls.all_properties[property_key].py_type
252 else:
253 return_type = type(constant)
254 property_doc = f"Returns constant value for '{property_key}' property"
256 constant_translator.__doc__ = f"""{property_doc}
258 Returns
259 -------
260 translation : `{return_type}`
261 Translated property.
262 """
263 return constant_translator
265 @classmethod
266 def _make_trivial_mapping(
267 cls,
268 property_key: str,
269 header_key: Union[str, Sequence[str]],
270 default: Optional[Any] = None,
271 minimum: Optional[Any] = None,
272 maximum: Optional[Any] = None,
273 unit: Optional[astropy.unit.Unit] = None,
274 checker: Optional[Callable] = None,
275 ) -> Callable:
276 """Make a translator method returning a header value.
278 The header value can be converted to a `~astropy.units.Quantity`
279 if desired, and can also have its value validated.
281 See `MetadataTranslator.validate_value()` for details on the use
282 of default parameters.
284 Parameters
285 ----------
286 property_key : `str`
287 Name of the translator to be constructed (for the docstring).
288 header_key : `str` or `list` of `str`
289 Name of the key to look up in the header. If a `list` each
290 key will be tested in turn until one matches. This can deal with
291 header styles that evolve over time.
292 default : `numbers.Number` or `astropy.units.Quantity`, `str`, optional
293 If not `None`, default value to be used if the parameter read from
294 the header is not defined or if the header is missing.
295 minimum : `numbers.Number` or `astropy.units.Quantity`, optional
296 If not `None`, and if ``default`` is not `None`, minimum value
297 acceptable for this parameter.
298 maximum : `numbers.Number` or `astropy.units.Quantity`, optional
299 If not `None`, and if ``default`` is not `None`, maximum value
300 acceptable for this parameter.
301 unit : `astropy.units.Unit`, optional
302 If not `None`, the value read from the header will be converted
303 to a `~astropy.units.Quantity`. Only supported for numeric values.
304 checker : `function`, optional
305 Callback function to be used by the translator method in case the
306 keyword is not present. Function will be executed as if it is
307 a method of the translator class. Running without raising an
308 exception will allow the default to be used. Should usually raise
309 `KeyError`.
311 Returns
312 -------
313 t : `function`
314 Function implementing a translator with the specified
315 parameters.
316 """
317 if property_key in cls.all_properties: 317 ↛ 321line 317 didn't jump to line 321, because the condition on line 317 was never false
318 property_doc = cls.all_properties[property_key].doc
319 return_type = cls.all_properties[property_key].str_type
320 else:
321 return_type = "str` or `numbers.Number"
322 property_doc = f"Map '{header_key}' header keyword to '{property_key}' property"
324 def trivial_translator(self: MetadataTranslator) -> Any:
325 if unit is not None:
326 q = self.quantity_from_card(
327 header_key, unit, default=default, minimum=minimum, maximum=maximum, checker=checker
328 )
329 # Convert to Angle if this quantity is an angle
330 if return_type == "astropy.coordinates.Angle":
331 q = Angle(q)
332 return q
334 keywords = header_key if isinstance(header_key, list) else [header_key]
335 for key in keywords:
336 if self.is_key_ok(key):
337 value = self._header[key]
338 if default is not None and not isinstance(value, str):
339 value = self.validate_value(value, default, minimum=minimum, maximum=maximum)
340 self._used_these_cards(key)
341 break
342 else:
343 # No keywords found, use default, checking first, or raise
344 # A None default is only allowed if a checker is provided.
345 if checker is not None:
346 try:
347 checker(self)
348 except Exception:
349 raise KeyError(f"Could not find {keywords} in header")
350 return default
351 elif default is not None:
352 value = default
353 else:
354 raise KeyError(f"Could not find {keywords} in header")
356 # If we know this is meant to be a string, force to a string.
357 # Sometimes headers represent items as integers which generically
358 # we want as strings (eg OBSID). Sometimes also floats are
359 # written as "NaN" strings.
360 casts = {"str": str, "float": float, "int": int}
361 if return_type in casts and not isinstance(value, casts[return_type]) and value is not None:
362 value = casts[return_type](value)
364 return value
366 # Docstring inheritance means it is confusing to specify here
367 # exactly which header value is being used.
368 trivial_translator.__doc__ = f"""{property_doc}
370 Returns
371 -------
372 translation : `{return_type}`
373 Translated value derived from the header.
374 """
375 return trivial_translator
377 @classmethod
378 def __init_subclass__(cls, **kwargs: Any) -> None:
379 """Register all subclasses with the base class and create dynamic
380 translator methods.
382 The method provides two facilities. Firstly, every subclass
383 of `MetadataTranslator` that includes a ``name`` class property is
384 registered as a translator class that could be selected when automatic
385 header translation is attempted. Only name translator subclasses that
386 correspond to a complete instrument. Translation classes providing
387 generic translation support for multiple instrument translators should
388 not be named.
390 The second feature of this method is to convert simple translations
391 to full translator methods. Sometimes a translation is fixed (for
392 example a specific instrument name should be used) and rather than
393 provide a full ``to_property()`` translation method the mapping can be
394 defined in a class variable named ``_constMap``. Similarly, for
395 one-to-one trivial mappings from a header to a property,
396 ``_trivialMap`` can be defined. Trivial mappings are a dict mapping a
397 generic property to either a header keyword, or a tuple consisting of
398 the header keyword and a dict containing key value pairs suitable for
399 the `MetadataTranslator.quantity_from_card()` method.
400 """
401 super().__init_subclass__(**kwargs)
403 # Only register classes with declared names
404 if hasattr(cls, "name") and cls.name is not None:
405 if cls.name in MetadataTranslator.translators: 405 ↛ 406line 405 didn't jump to line 406, because the condition on line 405 was never true
406 log.warning(
407 "%s: Replacing %s translator with %s",
408 cls.name,
409 MetadataTranslator.translators[cls.name],
410 cls,
411 )
412 MetadataTranslator.translators[cls.name] = cls
414 # Check that we have not inherited constant/trivial mappings from
415 # parent class that we have already applied. Empty maps are always
416 # assumed okay
417 const_map = cls._const_map if cls._const_map and cls.defined_in_this_class("_const_map") else {}
418 trivial_map = (
419 cls._trivial_map if cls._trivial_map and cls.defined_in_this_class("_trivial_map") else {}
420 )
422 # Check for shadowing
423 trivials = set(trivial_map.keys())
424 constants = set(const_map.keys())
425 both = trivials & constants
426 if both: 426 ↛ 427line 426 didn't jump to line 427, because the condition on line 426 was never true
427 log.warning("%s: defined in both const_map and trivial_map: %s", cls.__name__, ", ".join(both))
429 all = trivials | constants
430 for name in all:
431 if cls.defined_in_this_class(f"to_{name}"): 431 ↛ 434line 431 didn't jump to line 434, because the condition on line 431 was never true
432 # Must be one of trivial or constant. If in both then constant
433 # overrides trivial.
434 location = "by _trivial_map"
435 if name in constants:
436 location = "by _const_map"
437 log.warning(
438 "%s: %s is defined explicitly but will be replaced %s", cls.__name__, name, location
439 )
441 properties = set(PROPERTIES) | set(("ext_" + pp for pp in cls.extensions))
442 cls.all_properties = dict(PROPERTIES)
443 cls.all_properties.update(cls.extensions)
445 # Go through the trival mappings for this class and create
446 # corresponding translator methods
447 for property_key, header_key in trivial_map.items():
448 kwargs = {}
449 if type(header_key) == tuple:
450 kwargs = header_key[1]
451 header_key = header_key[0]
452 translator = cls._make_trivial_mapping(property_key, header_key, **kwargs)
453 method = f"to_{property_key}"
454 translator.__name__ = f"{method}_trivial_in_{cls.__name__}"
455 setattr(cls, method, cache_translation(translator, method=method))
456 if property_key not in properties: 456 ↛ 457line 456 didn't jump to line 457, because the condition on line 456 was never true
457 log.warning(f"Unexpected trivial translator for '{property_key}' defined in {cls}")
459 # Go through the constant mappings for this class and create
460 # corresponding translator methods
461 for property_key, constant in const_map.items():
462 translator = cls._make_const_mapping(property_key, constant)
463 method = f"to_{property_key}"
464 translator.__name__ = f"{method}_constant_in_{cls.__name__}"
465 setattr(cls, method, translator)
466 if property_key not in properties: 466 ↛ 467line 466 didn't jump to line 467, because the condition on line 466 was never true
467 log.warning(f"Unexpected constant translator for '{property_key}' defined in {cls}")
469 def __init__(self, header: Mapping[str, Any], filename: Optional[str] = None) -> None:
470 self._header = header
471 self.filename = filename
472 self._used_cards: Set[str] = set()
474 # Prefix to use for warnings about failed translations
475 self._log_prefix_cache: Optional[str] = None
477 # Cache assumes header is read-only once stored in object
478 self._translation_cache: Dict[str, Any] = {}
480 @classmethod
481 @abstractmethod
482 def can_translate(cls, header: MutableMapping[str, Any], filename: Optional[str] = None) -> bool:
483 """Indicate whether this translation class can translate the
484 supplied header.
486 Parameters
487 ----------
488 header : `dict`-like
489 Header to convert to standardized form.
490 filename : `str`, optional
491 Name of file being translated.
493 Returns
494 -------
495 can : `bool`
496 `True` if the header is recognized by this class. `False`
497 otherwise.
498 """
499 raise NotImplementedError()
501 @classmethod
502 def can_translate_with_options(
503 cls, header: Mapping[str, Any], options: Dict[str, Any], filename: Optional[str] = None
504 ) -> bool:
505 """Helper method for `can_translate` allowing options.
507 Parameters
508 ----------
509 header : `dict`-like
510 Header to convert to standardized form.
511 options : `dict`
512 Headers to try to determine whether this header can
513 be translated by this class. If a card is found it will
514 be compared with the expected value and will return that
515 comparison. Each card will be tried in turn until one is
516 found.
517 filename : `str`, optional
518 Name of file being translated.
520 Returns
521 -------
522 can : `bool`
523 `True` if the header is recognized by this class. `False`
524 otherwise.
526 Notes
527 -----
528 Intended to be used from within `can_translate` implementations
529 for specific translators. Is not intended to be called directly
530 from `determine_translator`.
531 """
532 for card, value in options.items():
533 if card in header:
534 return header[card] == value
535 return False
537 @classmethod
538 def determine_translator(
539 cls, header: Mapping[str, Any], filename: Optional[str] = None
540 ) -> Type[MetadataTranslator]:
541 """Determine a translation class by examining the header
543 Parameters
544 ----------
545 header : `dict`-like
546 Representation of a header.
547 filename : `str`, optional
548 Name of file being translated.
550 Returns
551 -------
552 translator : `MetadataTranslator`
553 Translation class that knows how to extract metadata from
554 the supplied header.
556 Raises
557 ------
558 ValueError
559 None of the registered translation classes understood the supplied
560 header.
561 """
562 file_msg = ""
563 if filename is not None:
564 file_msg = f" from {filename}"
565 for name, trans in cls.translators.items():
566 if trans.can_translate(header, filename=filename):
567 log.debug("Using translation class %s%s", name, file_msg)
568 return trans
569 else:
570 raise ValueError(
571 f"None of the registered translation classes {list(cls.translators.keys())}"
572 f" understood this header{file_msg}"
573 )
575 @classmethod
576 def translator_version(cls) -> str:
577 """Return the version string for this translator class.
579 Returns
580 -------
581 version : `str`
582 String identifying the version of this translator.
584 Notes
585 -----
586 Assumes that the version is available from the ``__version__``
587 variable in the parent module. If this is not the case a translator
588 should subclass this method.
589 """
590 if cls in _VERSION_CACHE:
591 return _VERSION_CACHE[cls]
593 version = "unknown"
594 module_name = cls.__module__
595 components = module_name.split(".")
596 while components:
597 # This class has already been imported so importing it
598 # should work.
599 module = importlib.import_module(".".join(components))
600 if hasattr(module, v := "__version__"):
601 version = getattr(module, v)
602 if version == "unknown":
603 # LSST software will have a fingerprint
604 if hasattr(module, v := "__fingerprint__"):
605 version = getattr(module, v)
606 break
607 else:
608 # Remove last component from module name and try again
609 components.pop()
611 _VERSION_CACHE[cls] = version
612 return version
614 @classmethod
615 def fix_header(
616 cls, header: MutableMapping[str, Any], instrument: str, obsid: str, filename: Optional[str] = None
617 ) -> bool:
618 """Apply global fixes to a supplied header.
620 Parameters
621 ----------
622 header : `dict`
623 The header to correct. Correction is in place.
624 instrument : `str`
625 The name of the instrument.
626 obsid : `str`
627 Unique observation identifier associated with this header.
628 Will always be provided.
629 filename : `str`, optional
630 Filename associated with this header. May not be set since headers
631 can be fixed independently of any filename being known.
633 Returns
634 -------
635 modified : `bool`
636 `True` if a correction was applied.
638 Notes
639 -----
640 This method is intended to support major discrepancies in headers
641 such as:
643 * Periods of time where headers are known to be incorrect in some
644 way that can be fixed either by deriving the correct value from
645 the existing value or understanding the that correction is static
646 for the given time. This requires that the date header is
647 known.
648 * The presence of a certain value is always wrong and should be
649 corrected with a new static value regardless of date.
651 It is assumed that one off problems with headers have been applied
652 before this method is called using the per-obsid correction system.
654 Usually called from `astro_metadata_translator.fix_header`.
656 For log messages, do not assume that the filename will be present.
657 Always write log messages to fall back on using the ``obsid`` if
658 ``filename`` is `None`.
659 """
660 return False
662 @staticmethod
663 def _construct_log_prefix(obsid: str, filename: Optional[str] = None) -> str:
664 """Construct a log prefix string from the obsid and filename.
666 Parameters
667 ----------
668 obsid : `str`
669 The observation identifier.
670 filename : `str`, optional
671 The filename associated with the header being translated.
672 Can be `None`.
673 """
674 if filename:
675 return f"{filename}({obsid})"
676 return obsid
678 @property
679 def _log_prefix(self) -> str:
680 """Standard prefix that can be used for log messages to report
681 useful context.
683 Will be either the filename and obsid, or just the obsid depending
684 on whether a filename is known.
686 Returns
687 -------
688 prefix : `str`
689 The prefix to use.
690 """
691 if self._log_prefix_cache is None:
692 # Protect against the unfortunate event of the obsid failing to
693 # be calculated. This should be rare but should not prevent a log
694 # message from appearing.
695 try:
696 obsid = self.to_observation_id()
697 except Exception:
698 obsid = "unknown_obsid"
699 self._log_prefix_cache = self._construct_log_prefix(obsid, self.filename)
700 return self._log_prefix_cache
702 def _used_these_cards(self, *args: str) -> None:
703 """Indicate that the supplied cards have been used for translation.
705 Parameters
706 ----------
707 args : sequence of `str`
708 Keywords used to process a translation.
709 """
710 self._used_cards.update(set(args))
712 def cards_used(self) -> FrozenSet[str]:
713 """Cards used during metadata extraction.
715 Returns
716 -------
717 used : `frozenset` of `str`
718 Cards used when extracting metadata.
719 """
720 return frozenset(self._used_cards)
722 @staticmethod
723 def validate_value(
724 value: float, default: float, minimum: Optional[float] = None, maximum: Optional[float] = None
725 ) -> float:
726 """Validate the supplied value, returning a new value if out of range
728 Parameters
729 ----------
730 value : `float`
731 Value to be validated.
732 default : `float`
733 Default value to use if supplied value is invalid or out of range.
734 Assumed to be in the same units as the value expected in the
735 header.
736 minimum : `float`
737 Minimum possible valid value, optional. If the calculated value
738 is below this value, the default value will be used.
739 maximum : `float`
740 Maximum possible valid value, optional. If the calculated value
741 is above this value, the default value will be used.
743 Returns
744 -------
745 value : `float`
746 Either the supplied value, or a default value.
747 """
748 if value is None or math.isnan(value):
749 value = default
750 else:
751 if minimum is not None and value < minimum:
752 value = default
753 elif maximum is not None and value > maximum:
754 value = default
755 return value
757 @staticmethod
758 def is_keyword_defined(header: Mapping[str, Any], keyword: Optional[str]) -> bool:
759 """Return `True` if the value associated with the named keyword is
760 present in the supplied header and defined.
762 Parameters
763 ----------
764 header : `dict`-lik
765 Header to use as reference.
766 keyword : `str`
767 Keyword to check against header.
769 Returns
770 -------
771 is_defined : `bool`
772 `True` if the header is present and not-`None`. `False` otherwise.
773 """
774 if keyword is None or keyword not in header:
775 return False
777 if header[keyword] is None:
778 return False
780 # Special case Astropy undefined value
781 if isinstance(header[keyword], astropy.io.fits.card.Undefined):
782 return False
784 return True
786 def resource_root(self) -> Tuple[Optional[str], Optional[str]]:
787 """Package resource to use to locate correction resources within an
788 installed package.
790 Returns
791 -------
792 resource_package : `str`
793 Package resource name. `None` if no package resource are to be
794 used.
795 resource_root : `str`
796 The name of the resource root. `None` if no package resources
797 are to be used.
798 """
799 return (self.default_resource_package, self.default_resource_root)
801 def search_paths(self) -> List[str]:
802 """Search paths to use when searching for header fix up correction
803 files.
805 Returns
806 -------
807 paths : `list`
808 Directory paths to search. Can be an empty list if no special
809 directories are defined.
811 Notes
812 -----
813 Uses the classes ``default_search_path`` property if defined.
814 """
815 if self.default_search_path is not None:
816 return [p for p in self.default_search_path]
817 return []
819 def is_key_ok(self, keyword: Optional[str]) -> bool:
820 """Return `True` if the value associated with the named keyword is
821 present in this header and defined.
823 Parameters
824 ----------
825 keyword : `str`
826 Keyword to check against header.
828 Returns
829 -------
830 is_ok : `bool`
831 `True` if the header is present and not-`None`. `False` otherwise.
832 """
833 return self.is_keyword_defined(self._header, keyword)
835 def are_keys_ok(self, keywords: Iterable[str]) -> bool:
836 """Are the supplied keys all present and defined?
838 Parameters
839 ----------
840 keywords : iterable of `str`
841 Keywords to test.
843 Returns
844 -------
845 all_ok : `bool`
846 `True` if all supplied keys are present and defined.
847 """
848 for k in keywords:
849 if not self.is_key_ok(k):
850 return False
851 return True
853 def quantity_from_card(
854 self,
855 keywords: Union[str, Sequence[str]],
856 unit: u.Unit,
857 default: Optional[float] = None,
858 minimum: Optional[float] = None,
859 maximum: Optional[float] = None,
860 checker: Optional[Callable] = None,
861 ) -> u.Quantity:
862 """Calculate a Astropy Quantity from a header card and a unit.
864 Parameters
865 ----------
866 keywords : `str` or `list` of `str`
867 Keyword to use from header. If a list each keyword will be tried
868 in turn until one matches.
869 unit : `astropy.units.UnitBase`
870 Unit of the item in the header.
871 default : `float`, optional
872 Default value to use if the header value is invalid. Assumed
873 to be in the same units as the value expected in the header. If
874 None, no default value is used.
875 minimum : `float`, optional
876 Minimum possible valid value, optional. If the calculated value
877 is below this value, the default value will be used.
878 maximum : `float`, optional
879 Maximum possible valid value, optional. If the calculated value
880 is above this value, the default value will be used.
881 checker : `function`, optional
882 Callback function to be used by the translator method in case the
883 keyword is not present. Function will be executed as if it is
884 a method of the translator class. Running without raising an
885 exception will allow the default to be used. Should usually raise
886 `KeyError`.
888 Returns
889 -------
890 q : `astropy.units.Quantity`
891 Quantity representing the header value.
893 Raises
894 ------
895 KeyError
896 The supplied header key is not present.
897 """
898 keyword_list = [keywords] if isinstance(keywords, str) else list(keywords)
899 for k in keyword_list:
900 if self.is_key_ok(k):
901 value = self._header[k]
902 keyword = k
903 break
904 else:
905 if checker is not None:
906 try:
907 checker(self)
908 value = default
909 if value is not None:
910 value = u.Quantity(value, unit=unit)
911 return value
912 except Exception:
913 pass
914 raise KeyError(f"Could not find {keywords} in header")
915 if isinstance(value, str):
916 # Sometimes the header has the wrong type in it but this must
917 # be a number if we are creating a quantity.
918 value = float(value)
919 self._used_these_cards(keyword)
920 if default is not None:
921 value = self.validate_value(value, default, maximum=maximum, minimum=minimum)
922 return u.Quantity(value, unit=unit)
924 def _join_keyword_values(self, keywords: Iterable[str], delim: str = "+") -> str:
925 """Join values of all defined keywords with the specified delimiter.
927 Parameters
928 ----------
929 keywords : iterable of `str`
930 Keywords to look for in header.
931 delim : `str`, optional
932 Character to use to join the values together.
934 Returns
935 -------
936 joined : `str`
937 String formed from all the keywords found in the header with
938 defined values joined by the delimiter. Empty string if no
939 defined keywords found.
940 """
941 values = []
942 for k in keywords:
943 if self.is_key_ok(k):
944 values.append(self._header[k])
945 self._used_these_cards(k)
947 if values:
948 joined = delim.join(str(v) for v in values)
949 else:
950 joined = ""
952 return joined
954 @cache_translation
955 def to_detector_unique_name(self) -> str:
956 """Return a unique name for the detector.
958 Base class implementation attempts to combine ``detector_name`` with
959 ``detector_group``. Group is only used if not `None`.
961 Can be over-ridden by specialist translator class.
963 Returns
964 -------
965 name : `str`
966 ``detector_group``_``detector_name`` if ``detector_group`` is
967 defined, else the ``detector_name`` is assumed to be unique.
968 If neither return a valid value an exception is raised.
970 Raises
971 ------
972 NotImplementedError
973 Raised if neither detector_name nor detector_group is defined.
974 """
975 name = self.to_detector_name()
976 group = self.to_detector_group()
978 if group is None and name is None:
979 raise NotImplementedError("Can not determine unique name from detector_group and detector_name")
981 if group is not None:
982 return f"{group}_{name}"
984 return name
986 @cache_translation
987 def to_exposure_group(self) -> Optional[str]:
988 """Return the group label associated with this exposure.
990 Base class implementation returns the ``exposure_id`` in string
991 form. A subclass may do something different.
993 Returns
994 -------
995 name : `str`
996 The ``exposure_id`` converted to a string.
997 """
998 exposure_id = self.to_exposure_id()
999 if exposure_id is None:
1000 # mypy does not think this can ever happen but play it safe
1001 # with subclasses.
1002 return None # type: ignore
1003 else:
1004 return str(exposure_id)
1006 @cache_translation
1007 def to_observation_reason(self) -> str:
1008 """Return the reason this observation was taken.
1010 Base class implementation returns the ``science`` if the
1011 ``observation_type`` is science, else ``unknown``.
1012 A subclass may do something different.
1014 Returns
1015 -------
1016 name : `str`
1017 The reason for this observation.
1018 """
1019 obstype = self.to_observation_type()
1020 if obstype == "science":
1021 return "science"
1022 return "unknown"
1024 @cache_translation
1025 def to_observing_day(self) -> int:
1026 """Return the YYYYMMDD integer corresponding to the observing day.
1028 Base class implementation uses the TAI date of the start of the
1029 observation.
1031 Returns
1032 -------
1033 day : `int`
1034 The observing day as an integer of form YYYYMMDD. If the header
1035 is broken and is unable to obtain a date of observation, ``0``
1036 is returned and the assumption is made that the problem will
1037 be caught elsewhere.
1038 """
1039 datetime_begin = self.to_datetime_begin()
1040 if datetime_begin is None:
1041 return 0
1042 return int(datetime_begin.tai.strftime("%Y%m%d"))
1044 @cache_translation
1045 def to_observation_counter(self) -> int:
1046 """Return an integer corresponding to how this observation relates
1047 to other observations.
1049 Base class implementation returns ``0`` to indicate that it is not
1050 known how an observatory will define a counter. Some observatories
1051 may not use the concept, others may use a counter that increases
1052 for every observation taken for that instrument, and others may
1053 define it to be a counter within an observing day.
1055 Returns
1056 -------
1057 sequence : `int`
1058 The observation counter. Always ``0`` for this implementation.
1059 """
1060 return 0
1062 @cache_translation
1063 def to_group_counter_start(self) -> int:
1064 """Return the observation counter of the observation that began
1065 this group.
1067 The definition of the relevant group is up to the metadata
1068 translator. It can be the first observation in the exposure_group
1069 or the first observation in the visit, but must be derivable
1070 from the metadata of this observation.
1072 Returns
1073 -------
1074 counter : `int`
1075 The observation counter for the start of the relevant group.
1076 Default implementation always returns the observation counter
1077 of this observation.
1078 """
1079 return self.to_observation_counter()
1081 @cache_translation
1082 def to_group_counter_end(self) -> int:
1083 """Return the observation counter of the observation that ends
1084 this group.
1086 The definition of the relevant group is up to the metadata
1087 translator. It can be the last observation in the exposure_group
1088 or the last observation in the visit, but must be derivable
1089 from the metadata of this observation. It is of course possible
1090 that the last observation in the group does not exist if a sequence
1091 of observations was not completed.
1093 Returns
1094 -------
1095 counter : `int`
1096 The observation counter for the end of the relevant group.
1097 Default implementation always returns the observation counter
1098 of this observation.
1099 """
1100 return self.to_observation_counter()
1102 @cache_translation
1103 def to_has_simulated_content(self) -> bool:
1104 """Return a boolean indicating whether any part of the observation
1105 was simulated.
1107 Returns
1108 -------
1109 is_simulated : `bool`
1110 `True` if this exposure has simulated content. This can be
1111 if some parts of the metadata or data were simulated. Default
1112 implementation always returns `False`.
1113 """
1114 return False
1116 @cache_translation
1117 def to_focus_z(self) -> u.Quantity:
1118 """Return a default defocal distance of 0.0 mm if there is no
1119 keyword for defocal distance in the header. The default
1120 keyword for defocal distance is ``FOCUSZ``.
1122 Returns
1123 -------
1124 focus_z: `astropy.units.Quantity`
1125 The defocal distance from header or the 0.0mm default
1126 """
1127 return 0.0 * u.mm
1129 @classmethod
1130 def determine_translatable_headers(
1131 cls, filename: str, primary: Optional[MutableMapping[str, Any]] = None
1132 ) -> Iterator[MutableMapping[str, Any]]:
1133 """Given a file return all the headers usable for metadata translation.
1135 This method can optionally be given a header from the file. This
1136 header will generally be the primary header or a merge of the first
1137 two headers.
1139 In the base class implementation it is assumed that
1140 this supplied header is the only useful header for metadata translation
1141 and it will be returned unchanged if given. This can avoid
1142 unnecesarily re-opening the file and re-reading the header when the
1143 content is already known.
1145 If no header is supplied, a header will be read from the supplied
1146 file using `read_basic_metadata_from_file`, allowing it to merge
1147 the primary and secondary header of a multi-extension FITS file.
1148 Subclasses can read the header from the data file using whatever
1149 technique is best for that instrument.
1151 Subclasses can return multiple headers and ignore the externally
1152 supplied header. They can also merge it with another header and return
1153 a new derived header if that is required by the particular data file.
1154 There is no requirement for the supplied header to be used.
1156 Parameters
1157 ----------
1158 filename : `str`
1159 Path to a file in a format understood by this translator.
1160 primary : `dict`-like, optional
1161 The primary header obtained by the caller. This is sometimes
1162 already known, for example if a system is trying to bootstrap
1163 without already knowing what data is in the file. For many
1164 instruments where the primary header is the only relevant
1165 header, the primary header will be returned with no further
1166 action.
1168 Yields
1169 ------
1170 headers : iterator of `dict`-like
1171 A header usable for metadata translation. For this base
1172 implementation it will be either the supplied primary header
1173 or a header read from the file. This implementation will only
1174 ever yield a single header.
1176 Notes
1177 -----
1178 Each translator class can have code specifically tailored to its
1179 own file format. It is important not to call this method with
1180 an incorrect translator class. The normal paradigm is for the
1181 caller to have read the first header and then called
1182 `determine_translator()` on the result to work out which translator
1183 class to then call to obtain the real headers to be used for
1184 translation.
1185 """
1186 if primary is not None:
1187 yield primary
1188 else:
1189 # Prevent circular import by deferring
1190 from .file_helpers import read_basic_metadata_from_file
1192 # Merge primary and secondary header if they exist.
1193 header = read_basic_metadata_from_file(filename, -1)
1194 assert header is not None # for mypy since can_raise=True
1195 yield header
1198def _make_abstract_translator_method(
1199 property: str, doc: str, return_typedoc: str, return_type: Type
1200) -> Callable:
1201 """Create a an abstract translation method for this property.
1203 Parameters
1204 ----------
1205 property : `str`
1206 Name of the translator for property to be created.
1207 doc : `str`
1208 Description of the property.
1209 return_typedoc : `str`
1210 Type string of this property (used in the doc string).
1211 return_type : `class`
1212 Type of this property.
1214 Returns
1215 -------
1216 m : `function`
1217 Translator method for this property.
1218 """
1220 def to_property(self: MetadataTranslator) -> None:
1221 raise NotImplementedError(f"Translator for '{property}' undefined.")
1223 to_property.__doc__ = f"""Return value of {property} from headers.
1225 {doc}
1227 Returns
1228 -------
1229 {property} : `{return_typedoc}`
1230 The translated property.
1231 """
1232 return to_property
1235# Make abstract methods for all the translators methods.
1236# Unfortunately registering them as abstractmethods does not work
1237# as these assignments come after the class has been created.
1238# Assigning to __abstractmethods__ directly does work but interacts
1239# poorly with the metaclass automatically generating methods from
1240# _trivialMap and _constMap.
1241# Note that subclasses that provide extension properties are assumed to not
1242# need abstract methods created for them.
1244# Allow for concrete translator methods to exist in the base class
1245# These translator methods can be defined in terms of other properties
1246CONCRETE = set()
1248for name, definition in PROPERTIES.items():
1249 method = f"to_{name}"
1250 if not MetadataTranslator.defined_in_this_class(method):
1251 setattr(
1252 MetadataTranslator,
1253 f"to_{name}",
1254 abstractmethod(
1255 _make_abstract_translator_method(
1256 name, definition.doc, definition.str_type, definition.py_type
1257 )
1258 ),
1259 )
1260 else:
1261 CONCRETE.add(method)
1264class StubTranslator(MetadataTranslator):
1265 """Translator where all the translations are stubbed out and issue
1266 warnings.
1268 This translator can be used as a base class whilst developing a new
1269 translator. It allows testing to proceed without being required to fully
1270 define all translation methods. Once complete the class should be
1271 removed from the inheritance tree.
1273 """
1275 pass
1278def _make_forwarded_stub_translator_method(
1279 cls: Type[MetadataTranslator], property: str, doc: str, return_typedoc: str, return_type: Type
1280) -> Callable:
1281 """Create a stub translation method for this property that calls the
1282 base method and catches `NotImplementedError`.
1284 Parameters
1285 ----------
1286 cls : `class`
1287 Class to use when referencing `super()`. This would usually be
1288 `StubTranslator`.
1289 property : `str`
1290 Name of the translator for property to be created.
1291 doc : `str`
1292 Description of the property.
1293 return_typedoc : `str`
1294 Type string of this property (used in the doc string).
1295 return_type : `class`
1296 Type of this property.
1298 Returns
1299 -------
1300 m : `function`
1301 Stub translator method for this property.
1302 """
1303 method = f"to_{property}"
1305 def to_stub(self: MetadataTranslator) -> Any:
1306 parent = getattr(super(cls, self), method, None)
1307 try:
1308 if parent is not None:
1309 return parent()
1310 except NotImplementedError:
1311 pass
1313 warnings.warn(
1314 f"Please implement translator for property '{property}' for translator {self}", stacklevel=3
1315 )
1316 return None
1318 to_stub.__doc__ = f"""Unimplemented forwarding translator for {property}.
1320 {doc}
1322 Calls the base class translation method and if that fails with
1323 `NotImplementedError` issues a warning reminding the implementer to
1324 override this method.
1326 Returns
1327 -------
1328 {property} : `None` or `{return_typedoc}`
1329 Always returns `None`.
1330 """
1331 return to_stub
1334# Create stub translation methods for each property. These stubs warn
1335# rather than fail and should be overridden by translators.
1336for name, description in PROPERTIES.items():
1337 setattr(
1338 StubTranslator,
1339 f"to_{name}",
1340 _make_forwarded_stub_translator_method(
1341 StubTranslator, name, definition.doc, definition.str_type, definition.py_type # type: ignore
1342 ),
1343 )