Coverage for python / lsst / obs / base / formatters / fitsExposure.py: 17%
338 statements
« prev ^ index » next coverage.py v7.13.2, created at 2026-02-19 01:06 -0800
1# This file is part of obs_base.
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 COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <http://www.gnu.org/licenses/>.
22__all__ = (
23 "FitsExposureFormatter",
24 "FitsImageFormatter",
25 "FitsImageFormatterBase",
26 "FitsMaskFormatter",
27 "FitsMaskedImageFormatter",
28 "StandardFitsImageFormatterBase",
29 "standardizeAmplifierParameters",
30)
32import hashlib
33import json
34import logging
35import threading
36import uuid
37import warnings
38from abc import abstractmethod
39from collections.abc import Mapping, Set
40from io import BytesIO
41from typing import TYPE_CHECKING, Any, ClassVar, NamedTuple, Protocol
43import astropy.io.fits
44import numpy as np
46import lsst.geom
47from lsst.afw.cameraGeom import AmplifierGeometryComparison, AmplifierIsolator
48from lsst.afw.fits import CompressionOptions, MemFileManager
49from lsst.afw.geom.wcsUtils import getImageXY0FromMetadata
50from lsst.afw.image import (
51 ExposureFitsReader,
52 ExposureInfo,
53 FilterLabel,
54 ImageFitsReader,
55 MaskedImageFitsReader,
56 MaskFitsReader,
57)
59# Needed for ApCorrMap to resolve properly
60from lsst.afw.math import BoundedField # noqa: F401
61from lsst.daf.base import PropertyList
62from lsst.daf.butler import DatasetProvenance, FormatterV2
63from lsst.resources import ResourcePath
64from lsst.utils.classes import cached_getter
65from lsst.utils.introspection import find_outside_stacklevel
67from ..utils import add_provenance_to_fits_header
69if TYPE_CHECKING:
70 import lsst.afw.cameraGeom
73_LOG = logging.getLogger(__name__)
75_ALWAYS_USE_ASTROPY_FOR_COMPONENT_READ = False
76"""If True, the astropy code will always be used to read component and cutouts
77even if the file is local, the cutout is too large, or the dataset type is
78wrong. This should mostly be used for testing.
79"""
82class _ReaderClassLike(Protocol):
83 def __init__(self, path: str) -> None: ...
84 def readBBox(self) -> lsst.geom.Box2I: ...
85 def read(self, bbox: lsst.geom.Box2I = lsst.geom.Box2I(), dtype: Any = None) -> Any: ...
86 def readImage(self, bbox: lsst.geom.Box2I = lsst.geom.Box2I(), dtype: Any = None) -> Any: ...
87 def readMask(self, bbox: lsst.geom.Box2I = lsst.geom.Box2I(), dtype: Any = None) -> Any: ...
88 def readVariance(self, bbox: lsst.geom.Box2I = lsst.geom.Box2I(), dtype: Any = None) -> Any: ...
89 def readDetector(self) -> lsst.afw.cameraGeom.Detector: ...
90 def readComponent(self, component: str) -> Any: ...
91 def readMetadata(self) -> PropertyList: ...
92 def readSerializationVersion(self) -> int: ...
95class FitsImageFormatterBase(FormatterV2):
96 """Base class formatter for image-like storage classes stored via FITS.
98 Notes
99 -----
100 This class makes no assumptions about how many HDUs are used to represent
101 the image on disk, and includes no support for writing. It's really just a
102 collection of miscellaneous boilerplate common to all FITS image
103 formatters.
105 Concrete subclasses must implement `readComponent`, `readFull`, and
106 `write_local_file` (even if just to disable them by raising an exception).
107 """
109 can_read_from_local_file = True
110 default_extension = ".fits"
111 supported_extensions: ClassVar[Set[str]] = frozenset({".fits", ".fits.gz", ".fits.fz", ".fz", ".fit"})
113 unsupported_parameters: ClassVar[Set[str]] = frozenset()
114 """Support all parameters."""
116 _reader = None
117 _reader_path: str | None = None
119 ReaderClass: type[_ReaderClassLike] # must be set by concrete subclasses
120 """Class to use for reading FITS files in the expected way.
121 (e.g., `type` [`lsst.afw.image.ImageFitsReader])
122 """
124 @property
125 def reader(self) -> _ReaderClassLike:
126 """The reader object that backs this formatter's read operations.
128 This is computed on first use and then cached. It should never be
129 accessed when writing. Currently assumes a local file.
130 """
131 if self._reader is None:
132 if self._reader_path is None:
133 raise RuntimeError("Internal error in formatter; failing to set path.")
134 self._reader = self.ReaderClass(self._reader_path)
135 return self._reader
137 @property
138 @cached_getter
139 def checked_parameters(self) -> dict[str, Any]:
140 """The parameters passed by the butler user, after checking them
141 against the storage class and transforming `None` into an empty `dict`
142 (`dict`).
144 This is computed on first use and then cached. It should never be
145 accessed when writing. Subclasses that need additional checking should
146 delegate to `super` and then check the result before returning it.
147 """
148 parameters = self.file_descriptor.parameters
149 if parameters is None:
150 parameters = {}
151 self.file_descriptor.storageClass.validateParameters(parameters)
152 return parameters
154 @property
155 def storageClass_dtype(self) -> np.dtype | None:
156 """The numpy data type associated with the storage class."""
157 dtype: np.dtype | None = None
158 try:
159 # lsst.afw.image.Exposure is generic base class and does not have
160 # the dtype attribute.
161 dtype = np.dtype(self.file_descriptor.storageClass.pytype.dtype) # type: ignore[attr-defined]
162 except AttributeError:
163 pass
164 return dtype
166 def read_from_local_file(self, path: str, component: str | None = None, expected_size: int = -1) -> Any:
167 # Docstring inherited.
168 # The methods doing the reading all currently assume local file
169 # and assume that the file descriptor refers to a local file.
170 # With FormatterV2 that file descriptor does not refer to a local
171 # file.
172 self._reader_path = path
173 self._reader = None # Ensure the reader class is reset.
174 try:
175 if component is not None:
176 in_memory_dataset = self.readComponent(component)
177 else:
178 in_memory_dataset = self.readFull()
179 finally:
180 self._reader = None # Release the file handle.
181 return in_memory_dataset
183 @abstractmethod
184 def readComponent(self, component: str) -> Any:
185 """Read a component dataset.
187 Parameters
188 ----------
189 component : `str`, optional
190 Component to read from the file.
192 Returns
193 -------
194 obj : `typing.Any`
195 In-memory component object.
197 Raises
198 ------
199 KeyError
200 Raised if the requested component cannot be handled.
201 """
202 raise NotImplementedError()
204 @abstractmethod
205 def readFull(self) -> Any:
206 """Read the full dataset (while still accounting for parameters).
208 Returns
209 -------
210 obj : `typing.Any`
211 In-memory component object.
213 """
214 raise NotImplementedError()
217class StandardFitsImageFormatterBase(FitsImageFormatterBase):
218 """Base class interface for image-like storage stored via FITS,
219 written using LSST code.
221 Notes
222 -----
223 Concrete subclasses must provide at least the ``ReaderClass`` attribute.
225 The provided implementation of `readComponent` handles only the 'bbox',
226 'dimensions', and 'xy0' components common to all image-like storage
227 classes. Subclasses with additional components should handle them first,
228 then delegate to ``super()`` for these (or, if necessary, delegate first
229 and catch `KeyError`).
231 The provided implementation of `readFull` handles only parameters that
232 can be forwarded directly to the reader class (usually ``bbox`` and
233 ``origin``). Concrete subclasses that need to handle additional parameters
234 should generally reimplement without delegating (the implementation is
235 trivial).
237 This Formatter supports write recipes, and assumes its in-memory type has
238 ``writeFits`` and (for write recipes) ``writeFitsWithOptions`` methods.
240 Each ``StandardFitsImageFormatterBase`` recipe for FITS compression should
241 define ``image``, ``mask`` and ``variance`` entries, each of which may
242 contain entries supported by
243 `lsst.afw.fits.CompressionOptions.from_mapping` (``null`` disables
244 compression).
246 A very simple example YAML recipe (for the `lsst.afw.image.Exposure`
247 specialization):
249 .. code-block:: yaml
251 lsst.obs.base.fitsExposureFormatter.FitsExposureFormatter:
252 default:
253 image: &default
254 algorithm: GZIP_2
255 mask: *default
256 variance: *default
258 """
260 supported_write_parameters = frozenset({"recipe"})
262 def readComponent(self, component: str) -> Any:
263 # Docstring inherited.
264 if component in ("bbox", "dimensions", "xy0"):
265 bbox = self.reader.readBBox()
266 if component == "dimensions":
267 return bbox.getDimensions()
268 elif component == "xy0":
269 return bbox.getMin()
270 else:
271 return bbox
272 else:
273 raise KeyError(f"Unknown component requested: {component}")
275 def readFull(self) -> Any:
276 # Docstring inherited.
277 return self.reader.read(**self.checked_parameters, dtype=self.storageClass_dtype)
279 def write_local_file(self, in_memory_dataset: Any, uri: ResourcePath) -> None:
280 """Serialize the image to FITS.
282 Parameters
283 ----------
284 in_memory_dataset : `object`
285 Image to write. Must support a ``writeFits`` or
286 ``writeFitsWithOptions`` interface.
287 uri : `lsst.resources.ResourcePath`
288 Location to write the local file.
289 """
290 # check to see if we have a recipe requested
291 recipeName = self.write_parameters.get("recipe")
292 recipe = self.get_image_compression_settings(recipeName)
293 if recipe:
294 in_memory_dataset.writeFitsWithOptions(uri.ospath, options=recipe)
295 else:
296 in_memory_dataset.writeFits(uri.ospath)
298 def get_image_compression_settings(self, recipeName: str | None) -> dict:
299 """Retrieve the relevant compression settings for this recipe.
301 Parameters
302 ----------
303 recipeName : `str` or `None`
304 Label associated with the collection of compression parameters
305 to select.
307 Returns
308 -------
309 settings : `dict`
310 The selected settings.
311 """
312 # if no recipe has been provided and there is no default
313 # return immediately
314 if not recipeName:
315 if "default" not in self.write_recipes:
316 return {}
317 recipeName = "default"
319 if recipeName not in self.write_recipes:
320 raise RuntimeError(f"Unrecognized recipe option given for compression: {recipeName}")
322 recipe = self.write_recipes[recipeName]
323 if recipe is None:
324 return {}
325 seed: int | None = None
326 for plane in ("image", "mask", "variance"):
327 if plane in recipe and (quantization := recipe[plane].get("quantization")) is not None:
328 if quantization.get("seed", 0) == 0:
329 if seed is None:
330 # Set the seed based on data ID. We can't just use
331 # 'hash', since like 'set' that's not deterministic.
332 # And we can't rely on a DimensionPacker because those
333 # are only defined for certain combinations of
334 # dimensions. Doing an MD5 of the JSON feels like
335 # overkill but I don't really see anything much
336 # simpler.
337 hash_bytes = hashlib.md5(
338 json.dumps(list(self.data_id.required_values)).encode(),
339 usedforsecurity=False,
340 ).digest()
341 # And it *really* feels like overkill when we squash
342 # that into the [1, 10000] range allowed by FITS.
343 seed = 1 + int.from_bytes(hash_bytes) % 9999
344 _LOG.debug(
345 "Setting compression quantization seed for %s %s %s to %s.",
346 self.data_id,
347 self.dataset_ref.datasetType.name,
348 plane,
349 seed,
350 )
351 quantization["seed"] = seed
352 else:
353 _LOG.warning(
354 "Compression quantization seed for %s %s %s was set explicitly to %s.",
355 self.dataset_ref.datasetType.name,
356 self.data_id,
357 plane,
358 quantization["seed"],
359 )
360 else:
361 _LOG.debug(
362 "No quantization found for %s %s %s.",
363 self.dataset_ref.datasetType.name,
364 self.data_id,
365 plane,
366 )
367 return recipe
369 @classmethod
370 def validate_write_recipes(cls, recipes: Mapping[str, Any] | None) -> Mapping[str, Any] | None:
371 """Validate supplied recipes for this formatter.
373 The recipes are supplemented with default values where appropriate.
375 Parameters
376 ----------
377 recipes : `dict` or `None`
378 Recipes to validate. Can be empty dict or `None`.
380 Returns
381 -------
382 validated : `dict`
383 Validated recipes. Returns what was given if there are no
384 recipes listed.
386 Raises
387 ------
388 RuntimeError
389 Raised if validation fails.
390 """
391 if not recipes:
392 # We can not insist on recipes being specified.
393 return recipes
395 validated: dict[str, Any] = {}
396 for name, recipe in recipes.items():
397 if recipe is not None:
398 validated[name] = {}
399 for plane in ["image", "mask", "variance"]:
400 try:
401 options = CompressionOptions.from_mapping(recipe[plane])
402 except Exception as err:
403 err.add_note(f"Validating write recipe {name!r} ({plane!r} section).")
404 raise
405 validated[name][plane] = options.to_dict()
406 else:
407 validated[name] = None
408 return validated
411class FitsImageFormatter(StandardFitsImageFormatterBase):
412 """Concrete formatter for reading/writing `~lsst.afw.image.Image`
413 from/to FITS.
414 """
416 ReaderClass = ImageFitsReader
419class FitsMaskFormatter(StandardFitsImageFormatterBase):
420 """Concrete formatter for reading/writing `~lsst.afw.image.Mask`
421 from/to FITS.
422 """
424 ReaderClass = MaskFitsReader
427class FitsMaskedImageFormatter(StandardFitsImageFormatterBase):
428 """Concrete formatter for reading/writing `~lsst.afw.image.MaskedImage`
429 from/to FITS.
430 """
432 ReaderClass = MaskedImageFitsReader
434 def readComponent(self, component: str) -> Any:
435 # Docstring inherited.
436 if component == "image":
437 return self.reader.readImage(**self.checked_parameters, dtype=self.storageClass_dtype)
438 elif component == "mask":
439 return self.reader.readMask(**self.checked_parameters)
440 elif component == "variance":
441 return self.reader.readVariance(**self.checked_parameters, dtype=self.storageClass_dtype)
442 else:
443 # Delegate to base for bbox, dimensions, xy0.
444 return super().readComponent(component)
447def standardizeAmplifierParameters(
448 parameters: dict[str, Any], on_disk_detector: lsst.afw.cameraGeom.Detector | None
449) -> tuple[lsst.afw.cameraGeom.Amplifier, lsst.afw.cameraGeom.Detector, bool]:
450 """Preprocess the Exposure storage class's "amp" and "detector" parameters.
452 This checks the given objects for consistency with the on-disk geometry and
453 converts amplifier IDs/names to Amplifier instances.
455 Parameters
456 ----------
457 parameters : `dict`
458 Dictionary of parameters passed to formatter. See the Exposure storage
459 class definition in daf_butler for allowed keys and values.
460 on_disk_detector : `lsst.afw.cameraGeom.Detector` or `None`
461 Detector that represents the on-disk image being loaded, or `None` if
462 this is unknown (and hence the user must provide one in
463 ``parameters`` if "amp" is in ``parameters``).
465 Returns
466 -------
467 amplifier : `lsst.afw.cameraGeom.Amplifier` or `None`
468 An amplifier object that defines a subimage to load, or `None` if there
469 was no "amp" parameter.
470 detector : `lsst.afw.cameraGeom.Detector` or `None`
471 A detector object whose amplifiers are in the same s/orientation
472 state as the on-disk image. If there is no "amp" parameter,
473 ``on_disk_detector`` is simply passed through.
474 regions_differ : `bool`
475 `True` if the on-disk detector and the detector given in the parameters
476 had different bounding boxes for one or more regions. This can happen
477 if the true overscan region sizes can only be determined when the image
478 is actually read, but otherwise it should be considered user error.
479 """
480 if (amplifier := parameters.get("amp")) is None:
481 return None, on_disk_detector, False
482 if "bbox" in parameters or "origin" in parameters:
483 raise ValueError("Cannot pass 'amp' with 'bbox' or 'origin'.")
484 if isinstance(amplifier, int | str):
485 amp_key = amplifier
486 target_amplifier = None
487 else:
488 amp_key = amplifier.getName()
489 target_amplifier = amplifier
490 if (detector := parameters.get("detector")) is not None:
491 if on_disk_detector is not None:
492 # User passed a detector and we also found one on disk. Check them
493 # for consistency. Note that we are checking the amps we'd get
494 # from the two detectors against each other, not the amplifier we
495 # got directly from the user, as the latter is allowed to differ in
496 # assembly/orientation state.
497 comparison = on_disk_detector[amp_key].compareGeometry(detector[amp_key])
498 if comparison & comparison.ASSEMBLY_DIFFERS:
499 raise ValueError(
500 "The given 'detector' has a different assembly state and/or orientation from "
501 f"the on-disk one for amp {amp_key}."
502 )
503 else:
504 if on_disk_detector is None:
505 raise ValueError(
506 f"No on-disk detector and no detector given; cannot load amplifier from key {amp_key}. "
507 "Please provide either a 'detector' parameter or an Amplifier instance in the "
508 "'amp' parameter."
509 )
510 comparison = AmplifierGeometryComparison.EQUAL
511 detector = on_disk_detector
512 if target_amplifier is None:
513 target_amplifier = detector[amp_key]
514 return target_amplifier, detector, comparison & comparison.REGIONS_DIFFER
517class _ComponentCache(NamedTuple):
518 id_: uuid.UUID | None = None
519 reader: ExposureFitsReader | None = None
520 bbox: lsst.geom.Box2I | None = None
521 mem: MemFileManager | None = None
524class FitsExposureFormatter(FitsMaskedImageFormatter):
525 """Concrete formatter for reading/writing `~lsst.afw.image.Exposure`
526 from/to FITS.
528 Notes
529 -----
530 This class inherits from `FitsMaskedImageFormatter` even though
531 `lsst.afw.image.Exposure` doesn't inherit from
532 `lsst.afw.image.MaskedImage`; this is just an easy way to be able to
533 delegate to `FitsMaskedImageFormatter` for component-handling, and
534 should be replaced with e.g. both calling a free function if that slight
535 type covariance violation ever becomes a practical problem.
536 """
538 can_read_from_uri = True
539 ReaderClass = ExposureFitsReader
540 # TODO: Remove MemFileManager from cache when DM-49640 is fixed.
541 _lock = threading.Lock()
542 _cached_fits: _ComponentCache = _ComponentCache()
544 def read_from_uri(self, uri: ResourcePath, component: str | None = None, expected_size: int = -1) -> Any:
545 # For now only support small non-pixel components. In future
546 # could work with cutouts.
547 self._reader = None # Guarantee things are reset.
549 # Full read, always use local file read.
550 if not component and not self.checked_parameters:
551 return NotImplemented
553 if not _ALWAYS_USE_ASTROPY_FOR_COMPONENT_READ and uri.isLocal:
554 # For a local URI allow afw to read it directly.
555 return NotImplemented
556 pixel_components = ("mask", "image", "variance")
558 if component in pixel_components:
559 # For pixel access currently this can not be cached in memory
560 # and the performance gains are unclear. Assume local file
561 # read with file caching for now.
562 return NotImplemented
564 # With current file layouts the non-pixel extensions account for 1/3
565 # of the file size and it is more efficient to download the entire
566 # file.
567 if not (
568 _ALWAYS_USE_ASTROPY_FOR_COMPONENT_READ
569 or self._dataset_ref.dataId.mapping.keys().isdisjoint({"tract", "patch"})
570 ):
571 return NotImplemented
573 # Cutouts can be optimized. For now only use this optimization
574 # if bbox is the only parameter and the number of pixels in the
575 # bounding box is reasonable.
576 bbox = None
577 origin = lsst.afw.image.PARENT
578 if not component:
579 # Try to support PARENT and LOCAL origin but if there are any
580 # other parameters do not attempt a cutout.
581 if self.checked_parameters.keys() - {"bbox", "origin"}:
582 return NotImplemented
583 bbox = self.checked_parameters["bbox"]
584 origin = self.checked_parameters.get("origin", lsst.afw.image.PARENT)
585 # For larger cutouts use the full file.
586 max_cutout_size = 500 * 500
587 if not _ALWAYS_USE_ASTROPY_FOR_COMPONENT_READ and bbox.width * bbox.height > max_cutout_size:
588 return NotImplemented
590 # We only cache component reads since those are small.
591 if component:
592 with self._lock:
593 cache = type(self)._cached_fits
594 if self.dataset_ref.id == cache.id_:
595 if component in {"xy0", "dimensions", "bbox"} and cache.bbox is not None:
596 match component:
597 case "xy0":
598 return cache.bbox.getMin()
599 case "dimensions":
600 return cache.bbox.getDimensions()
601 case "bbox":
602 return cache.bbox
603 else:
604 self._reader = cache.reader
605 return self.readComponent(component)
607 try:
608 fs, fspath = uri.to_fsspec()
609 except Exception:
610 # fsspec cannot be initialized, fall back to downloading the file.
611 return NotImplemented
613 bbox_component = None
614 try:
615 hdul = []
616 with fs.open(fspath) as f, astropy.io.fits.open(f) as fits_obj:
617 # Read all non-pixel components and cache.
618 for hdu in fits_obj:
619 hdr = hdu.header
620 extname = hdr.get("EXTNAME")
621 # Older files have IMAGE in EXTNAME in PRIMARY so check
622 # for EXTEND=T.
623 extend = hdr.get("EXTEND")
624 if not extend and extname and extname.lower() in pixel_components:
625 # Calculate the dimensional components for later
626 # caching. Do not derive from cached FITS reader
627 # because they depend on the dimensionality of the
628 # pixel data and we do not want to cache the pixel
629 # data.
630 if bbox_component is None:
631 shape = hdu.shape
632 dimensions = lsst.geom.Extent2I(shape[1], shape[0])
634 # XY0 is defined in the A WCS.
635 pl = PropertyList()
636 pl.update(hdr)
637 xy0 = getImageXY0FromMetadata(pl, "A", strip=False)
639 # This is the PARENT bbox.
640 bbox_component = lsst.geom.Box2I(xy0, dimensions)
642 # Handle cutout request.
643 if bbox:
644 if origin == lsst.afw.image.PARENT:
645 full_bbox = bbox_component
646 else:
647 full_bbox = lsst.geom.Box2I(
648 lsst.geom.Point2I(0, 0), bbox_component.getDimensions
649 )
650 minX = bbox.getBeginX() - full_bbox.getBeginX()
651 maxX = bbox.getEndX() - full_bbox.getBeginX()
652 minY = bbox.getBeginY() - full_bbox.getBeginY()
653 maxY = bbox.getEndY() - full_bbox.getBeginY()
654 data = hdu.section[minY:maxY, minX:maxX]
656 # Must correct the header WCS to take into
657 # account the offset.
658 if (k := "CRPIX1") in hdr:
659 hdr[k] -= minX
660 if (k := "CRPIX2") in hdr:
661 hdr[k] -= minY
662 if (k := "LTV1") in hdr:
663 hdr[k] = -bbox.getBeginX()
664 if (k := "LTV2") in hdr:
665 hdr[k] = -bbox.getBeginY()
666 if (k := "CRVAL1A") in hdr:
667 hdr[k] = bbox.getBeginX()
668 if (k := "CRVAL2A") in hdr:
669 hdr[k] = bbox.getBeginY()
670 else:
671 data = np.zeros([1, 1], dtype=np.int32)
673 # Construct a new HDU and copy the header.
674 stripped_hdu = astropy.io.fits.ImageHDU(data=data, header=hdr)
675 hdul.append(stripped_hdu)
676 else:
677 hdul.append(hdu)
678 stripped_fits = astropy.io.fits.HDUList(hdus=hdul)
679 # Write the FITS file to in-memory FITS.
680 buffer = BytesIO()
681 stripped_fits.writeto(buffer)
682 except Exception as e:
683 # For some reason we can't open the remote file so fall back.
684 _LOG.debug(
685 "Attempted remote read of components but encountered an error. "
686 "Falling back to file download. Error: %s",
687 str(e),
688 )
689 return NotImplemented
691 # Pass the new FITS buffer to the reader class without going through
692 # a temporary file. We can assume this is relatively small for
693 # components.
694 fits_data = buffer.getvalue()
695 mem = MemFileManager(len(fits_data))
696 mem.setData(fits_data, len(fits_data))
697 self._reader = self.ReaderClass(mem)
699 if component:
700 with self._lock:
701 type(self)._cached_fits = _ComponentCache(
702 id_=self.dataset_ref.id,
703 reader=self._reader,
704 mem=mem,
705 bbox=bbox_component,
706 )
707 match component:
708 case "xy0":
709 if bbox_component is None: # For mypy.
710 return None
711 return bbox_component.getMin()
712 case "dimensions":
713 if bbox_component is None:
714 return None
715 return bbox_component.getDimensions()
716 case "bbox":
717 return bbox_component
718 case _:
719 return self.readComponent(component)
720 else:
721 # Must be a cutout. We have applied the bbox parameter so no
722 # parameters should be passed here.
723 cutout = self.reader.read(dtype=self.storageClass_dtype)
724 cutout.getInfo().setFilter(self._fixFilterLabels(cutout.getInfo().getFilter()))
725 return cutout
727 def add_provenance(
728 self, in_memory_dataset: Any, /, *, provenance: DatasetProvenance | None = None
729 ) -> Any:
730 # Add provenance via FITS headers.
731 add_provenance_to_fits_header(in_memory_dataset.metadata, self.dataset_ref, provenance)
732 return in_memory_dataset
734 def readComponent(self, component: str) -> Any:
735 # Docstring inherited.
736 # Generic components can be read via a string name; DM-27754 will make
737 # this mapping larger at the expense of the following one.
738 genericComponents = {
739 "summaryStats": ExposureInfo.KEY_SUMMARY_STATS,
740 }
741 if (genericComponentName := genericComponents.get(component)) is not None:
742 return self.reader.readComponent(genericComponentName)
743 # Other components have hard-coded method names, but don't take
744 # parameters.
745 standardComponents = {
746 "id": "readExposureId",
747 "metadata": "readMetadata",
748 "wcs": "readWcs",
749 "coaddInputs": "readCoaddInputs",
750 "psf": "readPsf",
751 "photoCalib": "readPhotoCalib",
752 "filter": "readFilter",
753 "validPolygon": "readValidPolygon",
754 "apCorrMap": "readApCorrMap",
755 "visitInfo": "readVisitInfo",
756 "transmissionCurve": "readTransmissionCurve",
757 "detector": "readDetector",
758 "exposureInfo": "readExposureInfo",
759 }
760 if (methodName := standardComponents.get(component)) is not None:
761 result = getattr(self.reader, methodName)()
762 if component == "filter":
763 return self._fixFilterLabels(result)
764 return result
765 # Delegate to MaskedImage and ImageBase implementations for the rest.
766 return super().readComponent(component)
768 def readFull(self) -> Any:
769 # Docstring inherited.
770 amplifier, detector, _ = standardizeAmplifierParameters(
771 self.checked_parameters,
772 self.reader.readDetector(),
773 )
774 if amplifier is not None:
775 amplifier_isolator = AmplifierIsolator(
776 amplifier,
777 self.reader.readBBox(),
778 detector,
779 )
780 result = amplifier_isolator.transform_subimage(
781 self.reader.read(bbox=amplifier_isolator.subimage_bbox, dtype=self.storageClass_dtype)
782 )
783 result.setDetector(amplifier_isolator.make_detector())
784 else:
785 result = self.reader.read(**self.checked_parameters, dtype=self.storageClass_dtype)
786 result.getInfo().setFilter(self._fixFilterLabels(result.getInfo().getFilter()))
787 return result
789 def _fixFilterLabels(
790 self, file_filter_label: lsst.afw.image.FilterLabel, should_be_standardized: bool | None = None
791 ) -> lsst.afw.image.FilterLabel:
792 """Compare the filter label read from the file with the one in the
793 data ID.
795 Parameters
796 ----------
797 file_filter_label : `lsst.afw.image.FilterLabel` or `None`
798 Filter label read from the file, if there was one.
799 should_be_standardized : `bool`, optional
800 If `True`, expect ``file_filter_label`` to be consistent with the
801 data ID and warn only if it is not. If `False`, expect it to be
802 inconsistent and warn only if the data ID is incomplete and hence
803 the `FilterLabel` cannot be fixed. If `None` (default) guess
804 whether the file should be standardized by looking at the
805 serialization version number in file, which requires this method to
806 have been run after `readFull` or `readComponent`.
808 Returns
809 -------
810 filter_label : `lsst.afw.image.FilterLabel` or `None`
811 The preferred filter label; may be the given one or one built from
812 the data ID. `None` is returned if there should never be any
813 filters associated with this dataset type.
815 Notes
816 -----
817 Most test coverage for this method is in ci_hsc_gen3, where we have
818 much easier access to test data that exhibits the problems it attempts
819 to solve.
820 """
821 # Remember filter data ID keys that weren't in this particular data ID,
822 # so we can warn about them later.
823 missing = []
824 band = None
825 physical_filter = None
826 if "band" in self.data_id.dimensions.names:
827 band = self.data_id.get("band")
828 # band isn't in the data ID; is that just because this data ID
829 # hasn't been filled in with everything the Registry knows, or
830 # because this dataset is never associated with a band?
831 if band is None and not self.data_id.hasFull() and "band" in self.data_id.dimensions.implied:
832 missing.append("band")
833 if "physical_filter" in self.data_id.dimensions.names:
834 physical_filter = self.data_id.get("physical_filter")
835 # Same check as above for band, but for physical_filter.
836 if (
837 physical_filter is None
838 and not self.data_id.hasFull()
839 and "physical_filter" in self.data_id.dimensions.implied
840 ):
841 missing.append("physical_filter")
842 if should_be_standardized is None:
843 version = self.reader.readSerializationVersion()
844 should_be_standardized = version >= 2
845 if missing:
846 # Data ID identifies a filter but the actual filter label values
847 # haven't been fetched from the database; we have no choice but
848 # to use the one in the file.
849 # Warn if that's more likely than not to be bad, because the file
850 # predates filter standardization.
851 if not should_be_standardized:
852 warnings.warn(
853 f"Data ID {self.data_id} is missing (implied) value(s) for {missing}; "
854 "the correctness of this Exposure's FilterLabel cannot be guaranteed. "
855 "Call Registry.expandDataId before Butler.get to avoid this.",
856 # Report the warning from outside of middleware or the
857 # relevant runQuantum method.
858 stacklevel=find_outside_stacklevel(
859 "lsst.obs.base", "lsst.pipe.base", "lsst.daf.butler", allow_methods={"runQuantum"}
860 ),
861 )
862 return file_filter_label
863 if band is None and physical_filter is None:
864 data_id_filter_label = None
865 else:
866 data_id_filter_label = FilterLabel(band=band, physical=physical_filter)
867 if data_id_filter_label != file_filter_label and should_be_standardized:
868 # File was written after FilterLabel and standardization, but its
869 # FilterLabel doesn't agree with the data ID: this indicates a bug
870 # in whatever code produced the Exposure (though it may be one that
871 # has been fixed since the file was written).
872 warnings.warn(
873 f"Reading {self.file_descriptor.location} with data ID {self.data_id}: "
874 f"filter label mismatch (file is {file_filter_label}, data ID is "
875 f"{data_id_filter_label}). This is probably a bug in the code that produced it.",
876 stacklevel=find_outside_stacklevel(
877 "lsst.obs.base", "lsst.pipe.base", "lsst.daf.butler", allow_methods={"runQuantum"}
878 ),
879 )
880 return data_id_filter_label