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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# (https://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 <https://www.gnu.org/licenses/>.
22import copy
23import os
24import re
25import traceback
26import weakref
28from astro_metadata_translator import fix_header
29from lsst.utils import doImport
30import lsst.daf.persistence as dafPersist
31from . import ImageMapping, ExposureMapping, CalibrationMapping, DatasetMapping
32import lsst.daf.base as dafBase
33import lsst.afw.geom as afwGeom
34import lsst.afw.image as afwImage
35import lsst.afw.table as afwTable
36from lsst.afw.fits import readMetadata
37import lsst.afw.cameraGeom as afwCameraGeom
38import lsst.log as lsstLog
39import lsst.pex.exceptions as pexExcept
40from .exposureIdInfo import ExposureIdInfo
41from .makeRawVisitInfo import MakeRawVisitInfo
42from .utils import createInitialSkyWcs, InitialSkyWcsError
43from lsst.utils import getPackageDir
44from ._instrument import Instrument
46__all__ = ["CameraMapper", "exposureFromImage"]
49class CameraMapper(dafPersist.Mapper):
51 """CameraMapper is a base class for mappers that handle images from a
52 camera and products derived from them. This provides an abstraction layer
53 between the data on disk and the code.
55 Public methods: keys, queryMetadata, getDatasetTypes, map,
56 canStandardize, standardize
58 Mappers for specific data sources (e.g., CFHT Megacam, LSST
59 simulations, etc.) should inherit this class.
61 The CameraMapper manages datasets within a "root" directory. Note that
62 writing to a dataset present in the input root will hide the existing
63 dataset but not overwrite it. See #2160 for design discussion.
65 A camera is assumed to consist of one or more rafts, each composed of
66 multiple CCDs. Each CCD is in turn composed of one or more amplifiers
67 (amps). A camera is also assumed to have a camera geometry description
68 (CameraGeom object) as a policy file, a filter description (Filter class
69 static configuration) as another policy file.
71 Information from the camera geometry and defects are inserted into all
72 Exposure objects returned.
74 The mapper uses one or two registries to retrieve metadata about the
75 images. The first is a registry of all raw exposures. This must contain
76 the time of the observation. One or more tables (or the equivalent)
77 within the registry are used to look up data identifier components that
78 are not specified by the user (e.g. filter) and to return results for
79 metadata queries. The second is an optional registry of all calibration
80 data. This should contain validity start and end entries for each
81 calibration dataset in the same timescale as the observation time.
83 Subclasses will typically set MakeRawVisitInfoClass and optionally the
84 metadata translator class:
86 MakeRawVisitInfoClass: a class variable that points to a subclass of
87 MakeRawVisitInfo, a functor that creates an
88 lsst.afw.image.VisitInfo from the FITS metadata of a raw image.
90 translatorClass: The `~astro_metadata_translator.MetadataTranslator`
91 class to use for fixing metadata values. If it is not set an attempt
92 will be made to infer the class from ``MakeRawVisitInfoClass``, failing
93 that the metadata fixup will try to infer the translator class from the
94 header itself.
96 Subclasses must provide the following methods:
98 _extractDetectorName(self, dataId): returns the detector name for a CCD
99 (e.g., "CFHT 21", "R:1,2 S:3,4") as used in the AFW CameraGeom class given
100 a dataset identifier referring to that CCD or a subcomponent of it.
102 _computeCcdExposureId(self, dataId): see below
104 _computeCoaddExposureId(self, dataId, singleFilter): see below
106 Subclasses may also need to override the following methods:
108 _transformId(self, dataId): transformation of a data identifier
109 from colloquial usage (e.g., "ccdname") to proper/actual usage
110 (e.g., "ccd"), including making suitable for path expansion (e.g. removing
111 commas). The default implementation does nothing. Note that this
112 method should not modify its input parameter.
114 getShortCcdName(self, ccdName): a static method that returns a shortened
115 name suitable for use as a filename. The default version converts spaces
116 to underscores.
118 _mapActualToPath(self, template, actualId): convert a template path to an
119 actual path, using the actual dataset identifier.
121 The mapper's behaviors are largely specified by the policy file.
122 See the MapperDictionary.paf for descriptions of the available items.
124 The 'exposures', 'calibrations', and 'datasets' subpolicies configure
125 mappings (see Mappings class).
127 Common default mappings for all subclasses can be specified in the
128 "policy/{images,exposures,calibrations,datasets}.yaml" files. This
129 provides a simple way to add a product to all camera mappers.
131 Functions to map (provide a path to the data given a dataset
132 identifier dictionary) and standardize (convert data into some standard
133 format or type) may be provided in the subclass as "map_{dataset type}"
134 and "std_{dataset type}", respectively.
136 If non-Exposure datasets cannot be retrieved using standard
137 daf_persistence methods alone, a "bypass_{dataset type}" function may be
138 provided in the subclass to return the dataset instead of using the
139 "datasets" subpolicy.
141 Implementations of map_camera and bypass_camera that should typically be
142 sufficient are provided in this base class.
144 Notes
145 -----
146 .. todo::
148 Instead of auto-loading the camera at construction time, load it from
149 the calibration registry
151 Parameters
152 ----------
153 policy : daf_persistence.Policy,
154 Policy with per-camera defaults already merged.
155 repositoryDir : string
156 Policy repository for the subclassing module (obtained with
157 getRepositoryPath() on the per-camera default dictionary).
158 root : string, optional
159 Path to the root directory for data.
160 registry : string, optional
161 Path to registry with data's metadata.
162 calibRoot : string, optional
163 Root directory for calibrations.
164 calibRegistry : string, optional
165 Path to registry with calibrations' metadata.
166 provided : list of string, optional
167 Keys provided by the mapper.
168 parentRegistry : Registry subclass, optional
169 Registry from a parent repository that may be used to look up
170 data's metadata.
171 repositoryCfg : daf_persistence.RepositoryCfg or None, optional
172 The configuration information for the repository this mapper is
173 being used with.
174 """
175 packageName = None
177 # a class or subclass of MakeRawVisitInfo, a functor that makes an
178 # lsst.afw.image.VisitInfo from the FITS metadata of a raw image
179 MakeRawVisitInfoClass = MakeRawVisitInfo
181 # a class or subclass of PupilFactory
182 PupilFactoryClass = afwCameraGeom.PupilFactory
184 # Class to use for metadata translations
185 translatorClass = None
187 # Gen3 instrument corresponding to this mapper
188 # Can be a class or a string with the full name of the class
189 _gen3instrument = None
191 def __init__(self, policy, repositoryDir,
192 root=None, registry=None, calibRoot=None, calibRegistry=None,
193 provided=None, parentRegistry=None, repositoryCfg=None):
195 dafPersist.Mapper.__init__(self)
197 self.log = lsstLog.Log.getLogger("CameraMapper")
199 if root:
200 self.root = root
201 elif repositoryCfg:
202 self.root = repositoryCfg.root
203 else:
204 self.root = None
206 repoPolicy = repositoryCfg.policy if repositoryCfg else None
207 if repoPolicy is not None:
208 policy.update(repoPolicy)
210 # Levels
211 self.levels = dict()
212 if 'levels' in policy:
213 levelsPolicy = policy['levels']
214 for key in levelsPolicy.names(True):
215 self.levels[key] = set(levelsPolicy.asArray(key))
216 self.defaultLevel = policy['defaultLevel']
217 self.defaultSubLevels = dict()
218 if 'defaultSubLevels' in policy:
219 self.defaultSubLevels = policy['defaultSubLevels']
221 # Root directories
222 if root is None:
223 root = "."
224 root = dafPersist.LogicalLocation(root).locString()
226 self.rootStorage = dafPersist.Storage.makeFromURI(uri=root)
228 # If the calibRoot is passed in, use that. If not and it's indicated in
229 # the policy, use that. And otherwise, the calibs are in the regular
230 # root.
231 # If the location indicated by the calib root does not exist, do not
232 # create it.
233 calibStorage = None
234 if calibRoot is not None:
235 calibRoot = dafPersist.Storage.absolutePath(root, calibRoot)
236 calibStorage = dafPersist.Storage.makeFromURI(uri=calibRoot,
237 create=False)
238 else:
239 calibRoot = policy.get('calibRoot', None)
240 if calibRoot:
241 calibStorage = dafPersist.Storage.makeFromURI(uri=calibRoot,
242 create=False)
243 if calibStorage is None:
244 calibStorage = self.rootStorage
246 self.root = root
248 # Registries
249 self.registry = self._setupRegistry("registry", "exposure", registry, policy, "registryPath",
250 self.rootStorage, searchParents=False,
251 posixIfNoSql=(not parentRegistry))
252 if not self.registry:
253 self.registry = parentRegistry
254 needCalibRegistry = policy.get('needCalibRegistry', None)
255 if needCalibRegistry:
256 if calibStorage:
257 self.calibRegistry = self._setupRegistry("calibRegistry", "calib", calibRegistry, policy,
258 "calibRegistryPath", calibStorage,
259 posixIfNoSql=False) # NB never use posix for calibs
260 else:
261 raise RuntimeError(
262 "'needCalibRegistry' is true in Policy, but was unable to locate a repo at "
263 f"calibRoot ivar:{calibRoot} or policy['calibRoot']:{policy.get('calibRoot', None)}")
264 else:
265 self.calibRegistry = None
267 # Dict of valid keys and their value types
268 self.keyDict = dict()
270 self._initMappings(policy, self.rootStorage, calibStorage, provided=None)
271 self._initWriteRecipes()
273 # Camera geometry
274 self.cameraDataLocation = None # path to camera geometry config file
275 self.camera = self._makeCamera(policy=policy, repositoryDir=repositoryDir)
277 # Filter translation table
278 self.filters = None
280 # verify that the class variable packageName is set before attempting
281 # to instantiate an instance
282 if self.packageName is None:
283 raise ValueError('class variable packageName must not be None')
285 self.makeRawVisitInfo = self.MakeRawVisitInfoClass(log=self.log)
287 # Assign a metadata translator if one has not been defined by
288 # subclass. We can sometimes infer one from the RawVisitInfo
289 # class.
290 if self.translatorClass is None and hasattr(self.makeRawVisitInfo, "metadataTranslator"):
291 self.translatorClass = self.makeRawVisitInfo.metadataTranslator
293 def _initMappings(self, policy, rootStorage=None, calibStorage=None, provided=None):
294 """Initialize mappings
296 For each of the dataset types that we want to be able to read, there
297 are methods that can be created to support them:
298 * map_<dataset> : determine the path for dataset
299 * std_<dataset> : standardize the retrieved dataset
300 * bypass_<dataset> : retrieve the dataset (bypassing the usual
301 retrieval machinery)
302 * query_<dataset> : query the registry
304 Besides the dataset types explicitly listed in the policy, we create
305 additional, derived datasets for additional conveniences,
306 e.g., reading the header of an image, retrieving only the size of a
307 catalog.
309 Parameters
310 ----------
311 policy : `lsst.daf.persistence.Policy`
312 Policy with per-camera defaults already merged
313 rootStorage : `Storage subclass instance`
314 Interface to persisted repository data.
315 calibRoot : `Storage subclass instance`
316 Interface to persisted calib repository data
317 provided : `list` of `str`
318 Keys provided by the mapper
319 """
320 # Sub-dictionaries (for exposure/calibration/dataset types)
321 imgMappingPolicy = dafPersist.Policy(dafPersist.Policy.defaultPolicyFile(
322 "obs_base", "ImageMappingDefaults.yaml", "policy"))
323 expMappingPolicy = dafPersist.Policy(dafPersist.Policy.defaultPolicyFile(
324 "obs_base", "ExposureMappingDefaults.yaml", "policy"))
325 calMappingPolicy = dafPersist.Policy(dafPersist.Policy.defaultPolicyFile(
326 "obs_base", "CalibrationMappingDefaults.yaml", "policy"))
327 dsMappingPolicy = dafPersist.Policy()
329 # Mappings
330 mappingList = (
331 ("images", imgMappingPolicy, ImageMapping),
332 ("exposures", expMappingPolicy, ExposureMapping),
333 ("calibrations", calMappingPolicy, CalibrationMapping),
334 ("datasets", dsMappingPolicy, DatasetMapping)
335 )
336 self.mappings = dict()
337 for name, defPolicy, cls in mappingList:
338 if name in policy:
339 datasets = policy[name]
341 # Centrally-defined datasets
342 defaultsPath = os.path.join(getPackageDir("obs_base"), "policy", name + ".yaml")
343 if os.path.exists(defaultsPath):
344 datasets.merge(dafPersist.Policy(defaultsPath))
346 mappings = dict()
347 setattr(self, name, mappings)
348 for datasetType in datasets.names(True):
349 subPolicy = datasets[datasetType]
350 subPolicy.merge(defPolicy)
352 if not hasattr(self, "map_" + datasetType) and 'composite' in subPolicy:
353 def compositeClosure(dataId, write=False, mapper=None, mapping=None,
354 subPolicy=subPolicy):
355 components = subPolicy.get('composite')
356 assembler = subPolicy['assembler'] if 'assembler' in subPolicy else None
357 disassembler = subPolicy['disassembler'] if 'disassembler' in subPolicy else None
358 python = subPolicy['python']
359 butlerComposite = dafPersist.ButlerComposite(assembler=assembler,
360 disassembler=disassembler,
361 python=python,
362 dataId=dataId,
363 mapper=self)
364 for name, component in components.items():
365 butlerComposite.add(id=name,
366 datasetType=component.get('datasetType'),
367 setter=component.get('setter', None),
368 getter=component.get('getter', None),
369 subset=component.get('subset', False),
370 inputOnly=component.get('inputOnly', False))
371 return butlerComposite
372 setattr(self, "map_" + datasetType, compositeClosure)
373 # for now at least, don't set up any other handling for
374 # this dataset type.
375 continue
377 if name == "calibrations":
378 mapping = cls(datasetType, subPolicy, self.registry, self.calibRegistry, calibStorage,
379 provided=provided, dataRoot=rootStorage)
380 else:
381 mapping = cls(datasetType, subPolicy, self.registry, rootStorage, provided=provided)
383 if datasetType in self.mappings:
384 raise ValueError(f"Duplicate mapping policy for dataset type {datasetType}")
385 self.keyDict.update(mapping.keys())
386 mappings[datasetType] = mapping
387 self.mappings[datasetType] = mapping
388 if not hasattr(self, "map_" + datasetType):
389 def mapClosure(dataId, write=False, mapper=weakref.proxy(self), mapping=mapping):
390 return mapping.map(mapper, dataId, write)
391 setattr(self, "map_" + datasetType, mapClosure)
392 if not hasattr(self, "query_" + datasetType):
393 def queryClosure(format, dataId, mapping=mapping):
394 return mapping.lookup(format, dataId)
395 setattr(self, "query_" + datasetType, queryClosure)
396 if hasattr(mapping, "standardize") and not hasattr(self, "std_" + datasetType):
397 def stdClosure(item, dataId, mapper=weakref.proxy(self), mapping=mapping):
398 return mapping.standardize(mapper, item, dataId)
399 setattr(self, "std_" + datasetType, stdClosure)
401 def setMethods(suffix, mapImpl=None, bypassImpl=None, queryImpl=None):
402 """Set convenience methods on CameraMapper"""
403 mapName = "map_" + datasetType + "_" + suffix
404 bypassName = "bypass_" + datasetType + "_" + suffix
405 queryName = "query_" + datasetType + "_" + suffix
406 if not hasattr(self, mapName):
407 setattr(self, mapName, mapImpl or getattr(self, "map_" + datasetType))
408 if not hasattr(self, bypassName):
409 if bypassImpl is None and hasattr(self, "bypass_" + datasetType):
410 bypassImpl = getattr(self, "bypass_" + datasetType)
411 if bypassImpl is not None:
412 setattr(self, bypassName, bypassImpl)
413 if not hasattr(self, queryName):
414 setattr(self, queryName, queryImpl or getattr(self, "query_" + datasetType))
416 # Filename of dataset
417 setMethods("filename", bypassImpl=lambda datasetType, pythonType, location, dataId:
418 [os.path.join(location.getStorage().root, p) for p in location.getLocations()])
419 # Metadata from FITS file
420 if subPolicy["storage"] == "FitsStorage": # a FITS image
421 def getMetadata(datasetType, pythonType, location, dataId):
422 md = readMetadata(location.getLocationsWithRoot()[0])
423 fix_header(md, translator_class=self.translatorClass)
424 return md
426 setMethods("md", bypassImpl=getMetadata)
428 # Add support for configuring FITS compression
429 addName = "add_" + datasetType
430 if not hasattr(self, addName):
431 setattr(self, addName, self.getImageCompressionSettings)
433 if name == "exposures":
434 def getSkyWcs(datasetType, pythonType, location, dataId):
435 fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
436 return fitsReader.readWcs()
438 setMethods("wcs", bypassImpl=getSkyWcs)
440 def getRawHeaderWcs(datasetType, pythonType, location, dataId):
441 """Create a SkyWcs from the un-modified raw
442 FITS WCS header keys."""
443 if datasetType[:3] != "raw":
444 raise dafPersist.NoResults("Can only get header WCS for raw exposures.",
445 datasetType, dataId)
446 return afwGeom.makeSkyWcs(readMetadata(location.getLocationsWithRoot()[0]))
448 setMethods("header_wcs", bypassImpl=getRawHeaderWcs)
450 def getPhotoCalib(datasetType, pythonType, location, dataId):
451 fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
452 return fitsReader.readPhotoCalib()
454 setMethods("photoCalib", bypassImpl=getPhotoCalib)
456 def getVisitInfo(datasetType, pythonType, location, dataId):
457 fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
458 return fitsReader.readVisitInfo()
460 setMethods("visitInfo", bypassImpl=getVisitInfo)
462 def getFilter(datasetType, pythonType, location, dataId):
463 fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
464 return fitsReader.readFilter()
466 setMethods("filter", bypassImpl=getFilter)
468 setMethods("detector",
469 mapImpl=lambda dataId, write=False:
470 dafPersist.ButlerLocation(
471 pythonType="lsst.afw.cameraGeom.CameraConfig",
472 cppType="Config",
473 storageName="Internal",
474 locationList="ignored",
475 dataId=dataId,
476 mapper=self,
477 storage=None,
478 ),
479 bypassImpl=lambda datasetType, pythonType, location, dataId:
480 self.camera[self._extractDetectorName(dataId)]
481 )
483 def getBBox(datasetType, pythonType, location, dataId):
484 md = readMetadata(location.getLocationsWithRoot()[0], hdu=1)
485 fix_header(md, translator_class=self.translatorClass)
486 return afwImage.bboxFromMetadata(md)
488 setMethods("bbox", bypassImpl=getBBox)
490 elif name == "images":
491 def getBBox(datasetType, pythonType, location, dataId):
492 md = readMetadata(location.getLocationsWithRoot()[0])
493 fix_header(md, translator_class=self.translatorClass)
494 return afwImage.bboxFromMetadata(md)
495 setMethods("bbox", bypassImpl=getBBox)
497 if subPolicy["storage"] == "FitsCatalogStorage": # a FITS catalog
499 def getMetadata(datasetType, pythonType, location, dataId):
500 md = readMetadata(os.path.join(location.getStorage().root,
501 location.getLocations()[0]), hdu=1)
502 fix_header(md, translator_class=self.translatorClass)
503 return md
505 setMethods("md", bypassImpl=getMetadata)
507 # Sub-images
508 if subPolicy["storage"] == "FitsStorage":
509 def mapSubClosure(dataId, write=False, mapper=weakref.proxy(self), mapping=mapping):
510 subId = dataId.copy()
511 del subId['bbox']
512 loc = mapping.map(mapper, subId, write)
513 bbox = dataId['bbox']
514 llcX = bbox.getMinX()
515 llcY = bbox.getMinY()
516 width = bbox.getWidth()
517 height = bbox.getHeight()
518 loc.additionalData.set('llcX', llcX)
519 loc.additionalData.set('llcY', llcY)
520 loc.additionalData.set('width', width)
521 loc.additionalData.set('height', height)
522 if 'imageOrigin' in dataId:
523 loc.additionalData.set('imageOrigin',
524 dataId['imageOrigin'])
525 return loc
527 def querySubClosure(key, format, dataId, mapping=mapping):
528 subId = dataId.copy()
529 del subId['bbox']
530 return mapping.lookup(format, subId)
531 setMethods("sub", mapImpl=mapSubClosure, queryImpl=querySubClosure)
533 if subPolicy["storage"] == "FitsCatalogStorage":
534 # Length of catalog
536 def getLen(datasetType, pythonType, location, dataId):
537 md = readMetadata(os.path.join(location.getStorage().root,
538 location.getLocations()[0]), hdu=1)
539 fix_header(md, translator_class=self.translatorClass)
540 return md["NAXIS2"]
542 setMethods("len", bypassImpl=getLen)
544 # Schema of catalog
545 if not datasetType.endswith("_schema") and datasetType + "_schema" not in datasets:
546 setMethods("schema", bypassImpl=lambda datasetType, pythonType, location, dataId:
547 afwTable.Schema.readFits(os.path.join(location.getStorage().root,
548 location.getLocations()[0])))
550 def _computeCcdExposureId(self, dataId):
551 """Compute the 64-bit (long) identifier for a CCD exposure.
553 Subclasses must override
555 Parameters
556 ----------
557 dataId : `dict`
558 Data identifier with visit, ccd.
559 """
560 raise NotImplementedError()
562 def _computeCoaddExposureId(self, dataId, singleFilter):
563 """Compute the 64-bit (long) identifier for a coadd.
565 Subclasses must override
567 Parameters
568 ----------
569 dataId : `dict`
570 Data identifier with tract and patch.
571 singleFilter : `bool`
572 True means the desired ID is for a single-filter coadd, in which
573 case dataIdmust contain filter.
574 """
575 raise NotImplementedError()
577 def _search(self, path):
578 """Search for path in the associated repository's storage.
580 Parameters
581 ----------
582 path : string
583 Path that describes an object in the repository associated with
584 this mapper.
585 Path may contain an HDU indicator, e.g. 'foo.fits[1]'. The
586 indicator will be stripped when searching and so will match
587 filenames without the HDU indicator, e.g. 'foo.fits'. The path
588 returned WILL contain the indicator though, e.g. ['foo.fits[1]'].
590 Returns
591 -------
592 string
593 The path for this object in the repository. Will return None if the
594 object can't be found. If the input argument path contained an HDU
595 indicator, the returned path will also contain the HDU indicator.
596 """
597 return self.rootStorage.search(path)
599 def backup(self, datasetType, dataId):
600 """Rename any existing object with the given type and dataId.
602 The CameraMapper implementation saves objects in a sequence of e.g.:
604 - foo.fits
605 - foo.fits~1
606 - foo.fits~2
608 All of the backups will be placed in the output repo, however, and will
609 not be removed if they are found elsewhere in the _parent chain. This
610 means that the same file will be stored twice if the previous version
611 was found in an input repo.
612 """
614 # Calling PosixStorage directly is not the long term solution in this
615 # function, this is work-in-progress on epic DM-6225. The plan is for
616 # parentSearch to be changed to 'search', and search only the storage
617 # associated with this mapper. All searching of parents will be handled
618 # by traversing the container of repositories in Butler.
620 def firstElement(list):
621 """Get the first element in the list, or None if that can't be
622 done.
623 """
624 return list[0] if list is not None and len(list) else None
626 n = 0
627 newLocation = self.map(datasetType, dataId, write=True)
628 newPath = newLocation.getLocations()[0]
629 path = dafPersist.PosixStorage.search(self.root, newPath, searchParents=True)
630 path = firstElement(path)
631 oldPaths = []
632 while path is not None:
633 n += 1
634 oldPaths.append((n, path))
635 path = dafPersist.PosixStorage.search(self.root, "%s~%d" % (newPath, n), searchParents=True)
636 path = firstElement(path)
637 for n, oldPath in reversed(oldPaths):
638 self.rootStorage.copyFile(oldPath, "%s~%d" % (newPath, n))
640 def keys(self):
641 """Return supported keys.
643 Returns
644 -------
645 iterable
646 List of keys usable in a dataset identifier
647 """
648 return iter(self.keyDict.keys())
650 def getKeys(self, datasetType, level):
651 """Return a dict of supported keys and their value types for a given
652 dataset type at a given level of the key hierarchy.
654 Parameters
655 ----------
656 datasetType : `str`
657 Dataset type or None for all dataset types.
658 level : `str` or None
659 Level or None for all levels or '' for the default level for the
660 camera.
662 Returns
663 -------
664 `dict`
665 Keys are strings usable in a dataset identifier, values are their
666 value types.
667 """
669 # not sure if this is how we want to do this. what if None was
670 # intended?
671 if level == '':
672 level = self.getDefaultLevel()
674 if datasetType is None:
675 keyDict = copy.copy(self.keyDict)
676 else:
677 keyDict = self.mappings[datasetType].keys()
678 if level is not None and level in self.levels:
679 keyDict = copy.copy(keyDict)
680 for lev in self.levels[level]:
681 if lev in keyDict:
682 del keyDict[lev]
683 return keyDict
685 def getDefaultLevel(self):
686 return self.defaultLevel
688 def getDefaultSubLevel(self, level):
689 if level in self.defaultSubLevels:
690 return self.defaultSubLevels[level]
691 return None
693 @classmethod
694 def getCameraName(cls):
695 """Return the name of the camera that this CameraMapper is for."""
696 className = str(cls)
697 className = className[className.find('.'):-1]
698 m = re.search(r'(\w+)Mapper', className)
699 if m is None:
700 m = re.search(r"class '[\w.]*?(\w+)'", className)
701 name = m.group(1)
702 return name[:1].lower() + name[1:] if name else ''
704 @classmethod
705 def getPackageName(cls):
706 """Return the name of the package containing this CameraMapper."""
707 if cls.packageName is None:
708 raise ValueError('class variable packageName must not be None')
709 return cls.packageName
711 @classmethod
712 def getGen3Instrument(cls):
713 """Return the gen3 Instrument class equivalent for this gen2 Mapper.
715 Returns
716 -------
717 instr : `type`
718 A `~lsst.obs.base.Instrument` class.
719 """
720 if cls._gen3instrument is None:
721 raise NotImplementedError("Please provide a specific implementation for your instrument"
722 " to enable conversion of this gen2 repository to gen3")
723 if isinstance(cls._gen3instrument, str):
724 # Given a string to convert to an instrument class
725 cls._gen3instrument = doImport(cls._gen3instrument)
726 if not issubclass(cls._gen3instrument, Instrument):
727 raise ValueError(f"Mapper {cls} has declared a gen3 instrument class of {cls._gen3instrument}"
728 " but that is not an lsst.obs.base.Instrument")
729 return cls._gen3instrument
731 @classmethod
732 def getPackageDir(cls):
733 """Return the base directory of this package"""
734 return getPackageDir(cls.getPackageName())
736 def map_camera(self, dataId, write=False):
737 """Map a camera dataset."""
738 if self.camera is None:
739 raise RuntimeError("No camera dataset available.")
740 actualId = self._transformId(dataId)
741 return dafPersist.ButlerLocation(
742 pythonType="lsst.afw.cameraGeom.CameraConfig",
743 cppType="Config",
744 storageName="ConfigStorage",
745 locationList=self.cameraDataLocation or "ignored",
746 dataId=actualId,
747 mapper=self,
748 storage=self.rootStorage
749 )
751 def bypass_camera(self, datasetType, pythonType, butlerLocation, dataId):
752 """Return the (preloaded) camera object.
753 """
754 if self.camera is None:
755 raise RuntimeError("No camera dataset available.")
756 return self.camera
758 def map_expIdInfo(self, dataId, write=False):
759 return dafPersist.ButlerLocation(
760 pythonType="lsst.obs.base.ExposureIdInfo",
761 cppType=None,
762 storageName="Internal",
763 locationList="ignored",
764 dataId=dataId,
765 mapper=self,
766 storage=self.rootStorage
767 )
769 def bypass_expIdInfo(self, datasetType, pythonType, location, dataId):
770 """Hook to retrieve an lsst.obs.base.ExposureIdInfo for an exposure"""
771 expId = self.bypass_ccdExposureId(datasetType, pythonType, location, dataId)
772 expBits = self.bypass_ccdExposureId_bits(datasetType, pythonType, location, dataId)
773 return ExposureIdInfo(expId=expId, expBits=expBits)
775 def std_bfKernel(self, item, dataId):
776 """Disable standardization for bfKernel
778 bfKernel is a calibration product that is numpy array,
779 unlike other calibration products that are all images;
780 all calibration images are sent through _standardizeExposure
781 due to CalibrationMapping, but we don't want that to happen to bfKernel
782 """
783 return item
785 def std_raw(self, item, dataId):
786 """Standardize a raw dataset by converting it to an Exposure instead
787 of an Image"""
788 return self._standardizeExposure(self.exposures['raw'], item, dataId,
789 trimmed=False, setVisitInfo=True)
791 def map_skypolicy(self, dataId):
792 """Map a sky policy."""
793 return dafPersist.ButlerLocation("lsst.pex.policy.Policy", "Policy",
794 "Internal", None, None, self,
795 storage=self.rootStorage)
797 def std_skypolicy(self, item, dataId):
798 """Standardize a sky policy by returning the one we use."""
799 return self.skypolicy
801###############################################################################
802#
803# Utility functions
804#
805###############################################################################
807 def _setupRegistry(self, name, description, path, policy, policyKey, storage, searchParents=True,
808 posixIfNoSql=True):
809 """Set up a registry (usually SQLite3), trying a number of possible
810 paths.
812 Parameters
813 ----------
814 name : string
815 Name of registry.
816 description: `str`
817 Description of registry (for log messages)
818 path : string
819 Path for registry.
820 policy : string
821 Policy that contains the registry name, used if path is None.
822 policyKey : string
823 Key in policy for registry path.
824 storage : Storage subclass
825 Repository Storage to look in.
826 searchParents : bool, optional
827 True if the search for a registry should follow any Butler v1
828 _parent symlinks.
829 posixIfNoSql : bool, optional
830 If an sqlite registry is not found, will create a posix registry if
831 this is True.
833 Returns
834 -------
835 lsst.daf.persistence.Registry
836 Registry object
837 """
838 if path is None and policyKey in policy:
839 path = dafPersist.LogicalLocation(policy[policyKey]).locString()
840 if os.path.isabs(path):
841 raise RuntimeError("Policy should not indicate an absolute path for registry.")
842 if not storage.exists(path):
843 newPath = storage.instanceSearch(path)
845 newPath = newPath[0] if newPath is not None and len(newPath) else None
846 if newPath is None:
847 self.log.warn("Unable to locate registry at policy path (also looked in root): %s",
848 path)
849 path = newPath
850 else:
851 self.log.warn("Unable to locate registry at policy path: %s", path)
852 path = None
854 # Old Butler API was to indicate the registry WITH the repo folder,
855 # New Butler expects the registry to be in the repo folder. To support
856 # Old API, check to see if path starts with root, and if so, strip
857 # root from path. Currently only works with PosixStorage
858 try:
859 root = storage.root
860 if path and (path.startswith(root)):
861 path = path[len(root + '/'):]
862 except AttributeError:
863 pass
865 # determine if there is an sqlite registry and if not, try the posix
866 # registry.
867 registry = None
869 def search(filename, description):
870 """Search for file in storage
872 Parameters
873 ----------
874 filename : `str`
875 Filename to search for
876 description : `str`
877 Description of file, for error message.
879 Returns
880 -------
881 path : `str` or `None`
882 Path to file, or None
883 """
884 result = storage.instanceSearch(filename)
885 if result:
886 return result[0]
887 self.log.debug("Unable to locate %s: %s", description, filename)
888 return None
890 # Search for a suitable registry database
891 if path is None:
892 path = search("%s.pgsql" % name, "%s in root" % description)
893 if path is None:
894 path = search("%s.sqlite3" % name, "%s in root" % description)
895 if path is None:
896 path = search(os.path.join(".", "%s.sqlite3" % name), "%s in current dir" % description)
898 if path is not None:
899 if not storage.exists(path):
900 newPath = storage.instanceSearch(path)
901 newPath = newPath[0] if newPath is not None and len(newPath) else None
902 if newPath is not None:
903 path = newPath
904 localFileObj = storage.getLocalFile(path)
905 self.log.info("Loading %s registry from %s", description, localFileObj.name)
906 registry = dafPersist.Registry.create(localFileObj.name)
907 localFileObj.close()
908 elif not registry and posixIfNoSql:
909 try:
910 self.log.info("Loading Posix %s registry from %s", description, storage.root)
911 registry = dafPersist.PosixRegistry(storage.root)
912 except Exception:
913 registry = None
915 return registry
917 def _transformId(self, dataId):
918 """Generate a standard ID dict from a camera-specific ID dict.
920 Canonical keys include:
921 - amp: amplifier name
922 - ccd: CCD name (in LSST this is a combination of raft and sensor)
923 The default implementation returns a copy of its input.
925 Parameters
926 ----------
927 dataId : `dict`
928 Dataset identifier; this must not be modified
930 Returns
931 -------
932 `dict`
933 Transformed dataset identifier.
934 """
936 return dataId.copy()
938 def _mapActualToPath(self, template, actualId):
939 """Convert a template path to an actual path, using the actual data
940 identifier. This implementation is usually sufficient but can be
941 overridden by the subclass.
943 Parameters
944 ----------
945 template : `str`
946 Template path
947 actualId : `dict`
948 Dataset identifier
950 Returns
951 -------
952 `str`
953 Pathname
954 """
956 try:
957 transformedId = self._transformId(actualId)
958 return template % transformedId
959 except Exception as e:
960 raise RuntimeError("Failed to format %r with data %r: %s" % (template, transformedId, e))
962 @staticmethod
963 def getShortCcdName(ccdName):
964 """Convert a CCD name to a form useful as a filename
966 The default implementation converts spaces to underscores.
967 """
968 return ccdName.replace(" ", "_")
970 def _extractDetectorName(self, dataId):
971 """Extract the detector (CCD) name from the dataset identifier.
973 The name in question is the detector name used by lsst.afw.cameraGeom.
975 Parameters
976 ----------
977 dataId : `dict`
978 Dataset identifier.
980 Returns
981 -------
982 `str`
983 Detector name
984 """
985 raise NotImplementedError("No _extractDetectorName() function specified")
987 def _setAmpDetector(self, item, dataId, trimmed=True):
988 """Set the detector object in an Exposure for an amplifier.
990 Defects are also added to the Exposure based on the detector object.
992 Parameters
993 ----------
994 item : `lsst.afw.image.Exposure`
995 Exposure to set the detector in.
996 dataId : `dict`
997 Dataset identifier
998 trimmed : `bool`
999 Should detector be marked as trimmed? (ignored)
1000 """
1002 return self._setCcdDetector(item=item, dataId=dataId, trimmed=trimmed)
1004 def _setCcdDetector(self, item, dataId, trimmed=True):
1005 """Set the detector object in an Exposure for a CCD.
1007 Parameters
1008 ----------
1009 item : `lsst.afw.image.Exposure`
1010 Exposure to set the detector in.
1011 dataId : `dict`
1012 Dataset identifier
1013 trimmed : `bool`
1014 Should detector be marked as trimmed? (ignored)
1015 """
1016 if item.getDetector() is not None:
1017 return
1019 detectorName = self._extractDetectorName(dataId)
1020 detector = self.camera[detectorName]
1021 item.setDetector(detector)
1023 def _setFilter(self, mapping, item, dataId):
1024 """Set the filter object in an Exposure. If the Exposure had a FILTER
1025 keyword, this was already processed during load. But if it didn't,
1026 use the filter from the registry.
1028 Parameters
1029 ----------
1030 mapping : `lsst.obs.base.Mapping`
1031 Where to get the filter from.
1032 item : `lsst.afw.image.Exposure`
1033 Exposure to set the filter in.
1034 dataId : `dict`
1035 Dataset identifier.
1036 """
1038 if not (isinstance(item, afwImage.ExposureU) or isinstance(item, afwImage.ExposureI)
1039 or isinstance(item, afwImage.ExposureF) or isinstance(item, afwImage.ExposureD)):
1040 return
1042 if item.getFilter().getId() != afwImage.Filter.UNKNOWN:
1043 return
1045 actualId = mapping.need(['filter'], dataId)
1046 filterName = actualId['filter']
1047 if self.filters is not None and filterName in self.filters:
1048 filterName = self.filters[filterName]
1049 try:
1050 item.setFilter(afwImage.Filter(filterName))
1051 except pexExcept.NotFoundError:
1052 self.log.warn("Filter %s not defined. Set to UNKNOWN." % (filterName))
1054 def _standardizeExposure(self, mapping, item, dataId, filter=True,
1055 trimmed=True, setVisitInfo=True):
1056 """Default standardization function for images.
1058 This sets the Detector from the camera geometry
1059 and optionally set the Filter. In both cases this saves
1060 having to persist some data in each exposure (or image).
1062 Parameters
1063 ----------
1064 mapping : `lsst.obs.base.Mapping`
1065 Where to get the values from.
1066 item : image-like object
1067 Can be any of lsst.afw.image.Exposure,
1068 lsst.afw.image.DecoratedImage, lsst.afw.image.Image
1069 or lsst.afw.image.MaskedImage
1071 dataId : `dict`
1072 Dataset identifier
1073 filter : `bool`
1074 Set filter? Ignored if item is already an exposure
1075 trimmed : `bool`
1076 Should detector be marked as trimmed?
1077 setVisitInfo : `bool`
1078 Should Exposure have its VisitInfo filled out from the metadata?
1080 Returns
1081 -------
1082 `lsst.afw.image.Exposure`
1083 The standardized Exposure.
1084 """
1085 try:
1086 exposure = exposureFromImage(item, dataId, mapper=self, logger=self.log,
1087 setVisitInfo=setVisitInfo)
1088 except Exception as e:
1089 self.log.error("Could not turn item=%r into an exposure: %s" % (repr(item), e))
1090 raise
1092 if mapping.level.lower() == "amp":
1093 self._setAmpDetector(exposure, dataId, trimmed)
1094 elif mapping.level.lower() == "ccd":
1095 self._setCcdDetector(exposure, dataId, trimmed)
1097 # We can only create a WCS if it doesn't already have one and
1098 # we have either a VisitInfo or exposure metadata.
1099 # Do not calculate a WCS if this is an amplifier exposure
1100 if mapping.level.lower() != "amp" and exposure.getWcs() is None and \
1101 (exposure.getInfo().getVisitInfo() is not None or exposure.getMetadata().toDict()):
1102 self._createInitialSkyWcs(exposure)
1104 if filter:
1105 self._setFilter(mapping, exposure, dataId)
1107 return exposure
1109 def _createSkyWcsFromMetadata(self, exposure):
1110 """Create a SkyWcs from the FITS header metadata in an Exposure.
1112 Parameters
1113 ----------
1114 exposure : `lsst.afw.image.Exposure`
1115 The exposure to get metadata from, and attach the SkyWcs to.
1116 """
1117 metadata = exposure.getMetadata()
1118 fix_header(metadata, translator_class=self.translatorClass)
1119 try:
1120 wcs = afwGeom.makeSkyWcs(metadata, strip=True)
1121 exposure.setWcs(wcs)
1122 except pexExcept.TypeError as e:
1123 # See DM-14372 for why this is debug and not warn (e.g. calib
1124 # files without wcs metadata).
1125 self.log.debug("wcs set to None; missing information found in metadata to create a valid wcs:"
1126 " %s", e.args[0])
1127 # ensure any WCS values stripped from the metadata are removed in the
1128 # exposure
1129 exposure.setMetadata(metadata)
1131 def _createInitialSkyWcs(self, exposure):
1132 """Create a SkyWcs from the boresight and camera geometry.
1134 If the boresight or camera geometry do not support this method of
1135 WCS creation, this falls back on the header metadata-based version
1136 (typically a purely linear FITS crval/crpix/cdmatrix WCS).
1138 Parameters
1139 ----------
1140 exposure : `lsst.afw.image.Exposure`
1141 The exposure to get data from, and attach the SkyWcs to.
1142 """
1143 # Always use try to use metadata first, to strip WCS keys from it.
1144 self._createSkyWcsFromMetadata(exposure)
1146 if exposure.getInfo().getVisitInfo() is None:
1147 msg = "No VisitInfo; cannot access boresight information. Defaulting to metadata-based SkyWcs."
1148 self.log.warn(msg)
1149 return
1150 try:
1151 newSkyWcs = createInitialSkyWcs(exposure.getInfo().getVisitInfo(), exposure.getDetector())
1152 exposure.setWcs(newSkyWcs)
1153 except InitialSkyWcsError as e:
1154 msg = "Cannot create SkyWcs using VisitInfo and Detector, using metadata-based SkyWcs: %s"
1155 self.log.warn(msg, e)
1156 self.log.debug("Exception was: %s", traceback.TracebackException.from_exception(e))
1157 if e.__context__ is not None:
1158 self.log.debug("Root-cause Exception was: %s",
1159 traceback.TracebackException.from_exception(e.__context__))
1161 def _makeCamera(self, policy, repositoryDir):
1162 """Make a camera (instance of lsst.afw.cameraGeom.Camera) describing
1163 the camera geometry
1165 Also set self.cameraDataLocation, if relevant (else it can be left
1166 None).
1168 This implementation assumes that policy contains an entry "camera"
1169 that points to the subdirectory in this package of camera data;
1170 specifically, that subdirectory must contain:
1171 - a file named `camera.py` that contains persisted camera config
1172 - ampInfo table FITS files, as required by
1173 lsst.afw.cameraGeom.makeCameraFromPath
1175 Parameters
1176 ----------
1177 policy : `lsst.daf.persistence.Policy`
1178 Policy with per-camera defaults already merged
1179 (PexPolicy only for backward compatibility).
1180 repositoryDir : `str`
1181 Policy repository for the subclassing module (obtained with
1182 getRepositoryPath() on the per-camera default dictionary).
1183 """
1184 if 'camera' not in policy:
1185 raise RuntimeError("Cannot find 'camera' in policy; cannot construct a camera")
1186 cameraDataSubdir = policy['camera']
1187 self.cameraDataLocation = os.path.normpath(
1188 os.path.join(repositoryDir, cameraDataSubdir, "camera.py"))
1189 cameraConfig = afwCameraGeom.CameraConfig()
1190 cameraConfig.load(self.cameraDataLocation)
1191 ampInfoPath = os.path.dirname(self.cameraDataLocation)
1192 return afwCameraGeom.makeCameraFromPath(
1193 cameraConfig=cameraConfig,
1194 ampInfoPath=ampInfoPath,
1195 shortNameFunc=self.getShortCcdName,
1196 pupilFactoryClass=self.PupilFactoryClass
1197 )
1199 def getRegistry(self):
1200 """Get the registry used by this mapper.
1202 Returns
1203 -------
1204 Registry or None
1205 The registry used by this mapper for this mapper's repository.
1206 """
1207 return self.registry
1209 def getImageCompressionSettings(self, datasetType, dataId):
1210 """Stuff image compression settings into a daf.base.PropertySet
1212 This goes into the ButlerLocation's "additionalData", which gets
1213 passed into the boost::persistence framework.
1215 Parameters
1216 ----------
1217 datasetType : `str`
1218 Type of dataset for which to get the image compression settings.
1219 dataId : `dict`
1220 Dataset identifier.
1222 Returns
1223 -------
1224 additionalData : `lsst.daf.base.PropertySet`
1225 Image compression settings.
1226 """
1227 mapping = self.mappings[datasetType]
1228 recipeName = mapping.recipe
1229 storageType = mapping.storage
1230 if storageType not in self._writeRecipes:
1231 return dafBase.PropertySet()
1232 if recipeName not in self._writeRecipes[storageType]:
1233 raise RuntimeError("Unrecognized write recipe for datasetType %s (storage type %s): %s" %
1234 (datasetType, storageType, recipeName))
1235 recipe = self._writeRecipes[storageType][recipeName].deepCopy()
1236 seed = hash(tuple(dataId.items())) % 2**31
1237 for plane in ("image", "mask", "variance"):
1238 if recipe.exists(plane + ".scaling.seed") and recipe.getScalar(plane + ".scaling.seed") == 0:
1239 recipe.set(plane + ".scaling.seed", seed)
1240 return recipe
1242 def _initWriteRecipes(self):
1243 """Read the recipes for writing files
1245 These recipes are currently used for configuring FITS compression,
1246 but they could have wider uses for configuring different flavors
1247 of the storage types. A recipe is referred to by a symbolic name,
1248 which has associated settings. These settings are stored as a
1249 `PropertySet` so they can easily be passed down to the
1250 boost::persistence framework as the "additionalData" parameter.
1252 The list of recipes is written in YAML. A default recipe and
1253 some other convenient recipes are in obs_base/policy/writeRecipes.yaml
1254 and these may be overridden or supplemented by the individual obs_*
1255 packages' own policy/writeRecipes.yaml files.
1257 Recipes are grouped by the storage type. Currently, only the
1258 ``FitsStorage`` storage type uses recipes, which uses it to
1259 configure FITS image compression.
1261 Each ``FitsStorage`` recipe for FITS compression should define
1262 "image", "mask" and "variance" entries, each of which may contain
1263 "compression" and "scaling" entries. Defaults will be provided for
1264 any missing elements under "compression" and "scaling".
1266 The allowed entries under "compression" are:
1268 * algorithm (string): compression algorithm to use
1269 * rows (int): number of rows per tile (0 = entire dimension)
1270 * columns (int): number of columns per tile (0 = entire dimension)
1271 * quantizeLevel (float): cfitsio quantization level
1273 The allowed entries under "scaling" are:
1275 * algorithm (string): scaling algorithm to use
1276 * bitpix (int): bits per pixel (0,8,16,32,64,-32,-64)
1277 * fuzz (bool): fuzz the values when quantising floating-point values?
1278 * seed (long): seed for random number generator when fuzzing
1279 * maskPlanes (list of string): mask planes to ignore when doing
1280 statistics
1281 * quantizeLevel: divisor of the standard deviation for STDEV_* scaling
1282 * quantizePad: number of stdev to allow on the low side (for
1283 STDEV_POSITIVE/NEGATIVE)
1284 * bscale: manually specified BSCALE (for MANUAL scaling)
1285 * bzero: manually specified BSCALE (for MANUAL scaling)
1287 A very simple example YAML recipe:
1289 FitsStorage:
1290 default:
1291 image: &default
1292 compression:
1293 algorithm: GZIP_SHUFFLE
1294 mask: *default
1295 variance: *default
1296 """
1297 recipesFile = os.path.join(getPackageDir("obs_base"), "policy", "writeRecipes.yaml")
1298 recipes = dafPersist.Policy(recipesFile)
1299 supplementsFile = os.path.join(self.getPackageDir(), "policy", "writeRecipes.yaml")
1300 validationMenu = {'FitsStorage': validateRecipeFitsStorage, }
1301 if os.path.exists(supplementsFile) and supplementsFile != recipesFile:
1302 supplements = dafPersist.Policy(supplementsFile)
1303 # Don't allow overrides, only supplements
1304 for entry in validationMenu:
1305 intersection = set(recipes[entry].names()).intersection(set(supplements.names()))
1306 if intersection:
1307 raise RuntimeError("Recipes provided in %s section %s may not override those in %s: %s" %
1308 (supplementsFile, entry, recipesFile, intersection))
1309 recipes.update(supplements)
1311 self._writeRecipes = {}
1312 for storageType in recipes.names(True):
1313 if "default" not in recipes[storageType]:
1314 raise RuntimeError("No 'default' recipe defined for storage type %s in %s" %
1315 (storageType, recipesFile))
1316 self._writeRecipes[storageType] = validationMenu[storageType](recipes[storageType])
1319def exposureFromImage(image, dataId=None, mapper=None, logger=None, setVisitInfo=True):
1320 """Generate an Exposure from an image-like object
1322 If the image is a DecoratedImage then also set its WCS and metadata
1323 (Image and MaskedImage are missing the necessary metadata
1324 and Exposure already has those set)
1326 Parameters
1327 ----------
1328 image : Image-like object
1329 Can be one of lsst.afw.image.DecoratedImage, Image, MaskedImage or
1330 Exposure.
1332 Returns
1333 -------
1334 `lsst.afw.image.Exposure`
1335 Exposure containing input image.
1336 """
1337 translatorClass = None
1338 if mapper is not None:
1339 translatorClass = mapper.translatorClass
1341 metadata = None
1342 if isinstance(image, afwImage.MaskedImage):
1343 exposure = afwImage.makeExposure(image)
1344 elif isinstance(image, afwImage.DecoratedImage):
1345 exposure = afwImage.makeExposure(afwImage.makeMaskedImage(image.getImage()))
1346 metadata = image.getMetadata()
1347 fix_header(metadata, translator_class=translatorClass)
1348 exposure.setMetadata(metadata)
1349 elif isinstance(image, afwImage.Exposure):
1350 exposure = image
1351 metadata = exposure.getMetadata()
1352 fix_header(metadata, translator_class=translatorClass)
1353 else: # Image
1354 exposure = afwImage.makeExposure(afwImage.makeMaskedImage(image))
1356 # set VisitInfo if we can
1357 if setVisitInfo and exposure.getInfo().getVisitInfo() is None:
1358 if metadata is not None:
1359 if mapper is None:
1360 if not logger:
1361 logger = lsstLog.Log.getLogger("CameraMapper")
1362 logger.warn("I can only set the VisitInfo if you provide a mapper")
1363 else:
1364 exposureId = mapper._computeCcdExposureId(dataId)
1365 visitInfo = mapper.makeRawVisitInfo(md=metadata, exposureId=exposureId)
1367 exposure.getInfo().setVisitInfo(visitInfo)
1369 return exposure
1372def validateRecipeFitsStorage(recipes):
1373 """Validate recipes for FitsStorage
1375 The recipes are supplemented with default values where appropriate.
1377 TODO: replace this custom validation code with Cerberus (DM-11846)
1379 Parameters
1380 ----------
1381 recipes : `lsst.daf.persistence.Policy`
1382 FitsStorage recipes to validate.
1384 Returns
1385 -------
1386 validated : `lsst.daf.base.PropertySet`
1387 Validated FitsStorage recipe.
1389 Raises
1390 ------
1391 `RuntimeError`
1392 If validation fails.
1393 """
1394 # Schemas define what should be there, and the default values (and by the
1395 # default value, the expected type).
1396 compressionSchema = {
1397 "algorithm": "NONE",
1398 "rows": 1,
1399 "columns": 0,
1400 "quantizeLevel": 0.0,
1401 }
1402 scalingSchema = {
1403 "algorithm": "NONE",
1404 "bitpix": 0,
1405 "maskPlanes": ["NO_DATA"],
1406 "seed": 0,
1407 "quantizeLevel": 4.0,
1408 "quantizePad": 5.0,
1409 "fuzz": True,
1410 "bscale": 1.0,
1411 "bzero": 0.0,
1412 }
1414 def checkUnrecognized(entry, allowed, description):
1415 """Check to see if the entry contains unrecognised keywords"""
1416 unrecognized = set(entry.keys()) - set(allowed)
1417 if unrecognized:
1418 raise RuntimeError(
1419 "Unrecognized entries when parsing image compression recipe %s: %s" %
1420 (description, unrecognized))
1422 validated = {}
1423 for name in recipes.names(True):
1424 checkUnrecognized(recipes[name], ["image", "mask", "variance"], name)
1425 rr = dafBase.PropertySet()
1426 validated[name] = rr
1427 for plane in ("image", "mask", "variance"):
1428 checkUnrecognized(recipes[name][plane], ["compression", "scaling"],
1429 name + "->" + plane)
1431 for settings, schema in (("compression", compressionSchema),
1432 ("scaling", scalingSchema)):
1433 prefix = plane + "." + settings
1434 if settings not in recipes[name][plane]:
1435 for key in schema:
1436 rr.set(prefix + "." + key, schema[key])
1437 continue
1438 entry = recipes[name][plane][settings]
1439 checkUnrecognized(entry, schema.keys(), name + "->" + plane + "->" + settings)
1440 for key in schema:
1441 value = type(schema[key])(entry[key]) if key in entry else schema[key]
1442 rr.set(prefix + "." + key, value)
1443 return validated