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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 # TODO: deprecate in DM-27170, remove in DM-27177
463 def getFilter(datasetType, pythonType, location, dataId):
464 fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
465 return fitsReader.readFilter()
467 setMethods("filter", bypassImpl=getFilter)
469 # TODO: deprecate in DM-27177, remove in DM-27811
470 def getFilterLabel(datasetType, pythonType, location, dataId):
471 fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
472 return fitsReader.readFilterLabel()
474 setMethods("filterLabel", bypassImpl=getFilterLabel)
476 setMethods("detector",
477 mapImpl=lambda dataId, write=False:
478 dafPersist.ButlerLocation(
479 pythonType="lsst.afw.cameraGeom.CameraConfig",
480 cppType="Config",
481 storageName="Internal",
482 locationList="ignored",
483 dataId=dataId,
484 mapper=self,
485 storage=None,
486 ),
487 bypassImpl=lambda datasetType, pythonType, location, dataId:
488 self.camera[self._extractDetectorName(dataId)]
489 )
491 def getBBox(datasetType, pythonType, location, dataId):
492 md = readMetadata(location.getLocationsWithRoot()[0], hdu=1)
493 fix_header(md, translator_class=self.translatorClass)
494 return afwImage.bboxFromMetadata(md)
496 setMethods("bbox", bypassImpl=getBBox)
498 elif name == "images":
499 def getBBox(datasetType, pythonType, location, dataId):
500 md = readMetadata(location.getLocationsWithRoot()[0])
501 fix_header(md, translator_class=self.translatorClass)
502 return afwImage.bboxFromMetadata(md)
503 setMethods("bbox", bypassImpl=getBBox)
505 if subPolicy["storage"] == "FitsCatalogStorage": # a FITS catalog
507 def getMetadata(datasetType, pythonType, location, dataId):
508 md = readMetadata(os.path.join(location.getStorage().root,
509 location.getLocations()[0]), hdu=1)
510 fix_header(md, translator_class=self.translatorClass)
511 return md
513 setMethods("md", bypassImpl=getMetadata)
515 # Sub-images
516 if subPolicy["storage"] == "FitsStorage":
517 def mapSubClosure(dataId, write=False, mapper=weakref.proxy(self), mapping=mapping):
518 subId = dataId.copy()
519 del subId['bbox']
520 loc = mapping.map(mapper, subId, write)
521 bbox = dataId['bbox']
522 llcX = bbox.getMinX()
523 llcY = bbox.getMinY()
524 width = bbox.getWidth()
525 height = bbox.getHeight()
526 loc.additionalData.set('llcX', llcX)
527 loc.additionalData.set('llcY', llcY)
528 loc.additionalData.set('width', width)
529 loc.additionalData.set('height', height)
530 if 'imageOrigin' in dataId:
531 loc.additionalData.set('imageOrigin',
532 dataId['imageOrigin'])
533 return loc
535 def querySubClosure(key, format, dataId, mapping=mapping):
536 subId = dataId.copy()
537 del subId['bbox']
538 return mapping.lookup(format, subId)
539 setMethods("sub", mapImpl=mapSubClosure, queryImpl=querySubClosure)
541 if subPolicy["storage"] == "FitsCatalogStorage":
542 # Length of catalog
544 def getLen(datasetType, pythonType, location, dataId):
545 md = readMetadata(os.path.join(location.getStorage().root,
546 location.getLocations()[0]), hdu=1)
547 fix_header(md, translator_class=self.translatorClass)
548 return md["NAXIS2"]
550 setMethods("len", bypassImpl=getLen)
552 # Schema of catalog
553 if not datasetType.endswith("_schema") and datasetType + "_schema" not in datasets:
554 setMethods("schema", bypassImpl=lambda datasetType, pythonType, location, dataId:
555 afwTable.Schema.readFits(os.path.join(location.getStorage().root,
556 location.getLocations()[0])))
558 def _computeCcdExposureId(self, dataId):
559 """Compute the 64-bit (long) identifier for a CCD exposure.
561 Subclasses must override
563 Parameters
564 ----------
565 dataId : `dict`
566 Data identifier with visit, ccd.
567 """
568 raise NotImplementedError()
570 def _computeCoaddExposureId(self, dataId, singleFilter):
571 """Compute the 64-bit (long) identifier for a coadd.
573 Subclasses must override
575 Parameters
576 ----------
577 dataId : `dict`
578 Data identifier with tract and patch.
579 singleFilter : `bool`
580 True means the desired ID is for a single-filter coadd, in which
581 case dataIdmust contain filter.
582 """
583 raise NotImplementedError()
585 def _search(self, path):
586 """Search for path in the associated repository's storage.
588 Parameters
589 ----------
590 path : string
591 Path that describes an object in the repository associated with
592 this mapper.
593 Path may contain an HDU indicator, e.g. 'foo.fits[1]'. The
594 indicator will be stripped when searching and so will match
595 filenames without the HDU indicator, e.g. 'foo.fits'. The path
596 returned WILL contain the indicator though, e.g. ['foo.fits[1]'].
598 Returns
599 -------
600 string
601 The path for this object in the repository. Will return None if the
602 object can't be found. If the input argument path contained an HDU
603 indicator, the returned path will also contain the HDU indicator.
604 """
605 return self.rootStorage.search(path)
607 def backup(self, datasetType, dataId):
608 """Rename any existing object with the given type and dataId.
610 The CameraMapper implementation saves objects in a sequence of e.g.:
612 - foo.fits
613 - foo.fits~1
614 - foo.fits~2
616 All of the backups will be placed in the output repo, however, and will
617 not be removed if they are found elsewhere in the _parent chain. This
618 means that the same file will be stored twice if the previous version
619 was found in an input repo.
620 """
622 # Calling PosixStorage directly is not the long term solution in this
623 # function, this is work-in-progress on epic DM-6225. The plan is for
624 # parentSearch to be changed to 'search', and search only the storage
625 # associated with this mapper. All searching of parents will be handled
626 # by traversing the container of repositories in Butler.
628 def firstElement(list):
629 """Get the first element in the list, or None if that can't be
630 done.
631 """
632 return list[0] if list is not None and len(list) else None
634 n = 0
635 newLocation = self.map(datasetType, dataId, write=True)
636 newPath = newLocation.getLocations()[0]
637 path = dafPersist.PosixStorage.search(self.root, newPath, searchParents=True)
638 path = firstElement(path)
639 oldPaths = []
640 while path is not None:
641 n += 1
642 oldPaths.append((n, path))
643 path = dafPersist.PosixStorage.search(self.root, "%s~%d" % (newPath, n), searchParents=True)
644 path = firstElement(path)
645 for n, oldPath in reversed(oldPaths):
646 self.rootStorage.copyFile(oldPath, "%s~%d" % (newPath, n))
648 def keys(self):
649 """Return supported keys.
651 Returns
652 -------
653 iterable
654 List of keys usable in a dataset identifier
655 """
656 return iter(self.keyDict.keys())
658 def getKeys(self, datasetType, level):
659 """Return a dict of supported keys and their value types for a given
660 dataset type at a given level of the key hierarchy.
662 Parameters
663 ----------
664 datasetType : `str`
665 Dataset type or None for all dataset types.
666 level : `str` or None
667 Level or None for all levels or '' for the default level for the
668 camera.
670 Returns
671 -------
672 `dict`
673 Keys are strings usable in a dataset identifier, values are their
674 value types.
675 """
677 # not sure if this is how we want to do this. what if None was
678 # intended?
679 if level == '':
680 level = self.getDefaultLevel()
682 if datasetType is None:
683 keyDict = copy.copy(self.keyDict)
684 else:
685 keyDict = self.mappings[datasetType].keys()
686 if level is not None and level in self.levels:
687 keyDict = copy.copy(keyDict)
688 for lev in self.levels[level]:
689 if lev in keyDict:
690 del keyDict[lev]
691 return keyDict
693 def getDefaultLevel(self):
694 return self.defaultLevel
696 def getDefaultSubLevel(self, level):
697 if level in self.defaultSubLevels:
698 return self.defaultSubLevels[level]
699 return None
701 @classmethod
702 def getCameraName(cls):
703 """Return the name of the camera that this CameraMapper is for."""
704 className = str(cls)
705 className = className[className.find('.'):-1]
706 m = re.search(r'(\w+)Mapper', className)
707 if m is None:
708 m = re.search(r"class '[\w.]*?(\w+)'", className)
709 name = m.group(1)
710 return name[:1].lower() + name[1:] if name else ''
712 @classmethod
713 def getPackageName(cls):
714 """Return the name of the package containing this CameraMapper."""
715 if cls.packageName is None:
716 raise ValueError('class variable packageName must not be None')
717 return cls.packageName
719 @classmethod
720 def getGen3Instrument(cls):
721 """Return the gen3 Instrument class equivalent for this gen2 Mapper.
723 Returns
724 -------
725 instr : `type`
726 A `~lsst.obs.base.Instrument` class.
727 """
728 if cls._gen3instrument is None:
729 raise NotImplementedError("Please provide a specific implementation for your instrument"
730 " to enable conversion of this gen2 repository to gen3")
731 if isinstance(cls._gen3instrument, str):
732 # Given a string to convert to an instrument class
733 cls._gen3instrument = doImport(cls._gen3instrument)
734 if not issubclass(cls._gen3instrument, Instrument):
735 raise ValueError(f"Mapper {cls} has declared a gen3 instrument class of {cls._gen3instrument}"
736 " but that is not an lsst.obs.base.Instrument")
737 return cls._gen3instrument
739 @classmethod
740 def getPackageDir(cls):
741 """Return the base directory of this package"""
742 return getPackageDir(cls.getPackageName())
744 def map_camera(self, dataId, write=False):
745 """Map a camera dataset."""
746 if self.camera is None:
747 raise RuntimeError("No camera dataset available.")
748 actualId = self._transformId(dataId)
749 return dafPersist.ButlerLocation(
750 pythonType="lsst.afw.cameraGeom.CameraConfig",
751 cppType="Config",
752 storageName="ConfigStorage",
753 locationList=self.cameraDataLocation or "ignored",
754 dataId=actualId,
755 mapper=self,
756 storage=self.rootStorage
757 )
759 def bypass_camera(self, datasetType, pythonType, butlerLocation, dataId):
760 """Return the (preloaded) camera object.
761 """
762 if self.camera is None:
763 raise RuntimeError("No camera dataset available.")
764 return self.camera
766 def map_expIdInfo(self, dataId, write=False):
767 return dafPersist.ButlerLocation(
768 pythonType="lsst.obs.base.ExposureIdInfo",
769 cppType=None,
770 storageName="Internal",
771 locationList="ignored",
772 dataId=dataId,
773 mapper=self,
774 storage=self.rootStorage
775 )
777 def bypass_expIdInfo(self, datasetType, pythonType, location, dataId):
778 """Hook to retrieve an lsst.obs.base.ExposureIdInfo for an exposure"""
779 expId = self.bypass_ccdExposureId(datasetType, pythonType, location, dataId)
780 expBits = self.bypass_ccdExposureId_bits(datasetType, pythonType, location, dataId)
781 return ExposureIdInfo(expId=expId, expBits=expBits)
783 def std_bfKernel(self, item, dataId):
784 """Disable standardization for bfKernel
786 bfKernel is a calibration product that is numpy array,
787 unlike other calibration products that are all images;
788 all calibration images are sent through _standardizeExposure
789 due to CalibrationMapping, but we don't want that to happen to bfKernel
790 """
791 return item
793 def std_raw(self, item, dataId):
794 """Standardize a raw dataset by converting it to an Exposure instead
795 of an Image"""
796 return self._standardizeExposure(self.exposures['raw'], item, dataId,
797 trimmed=False, setVisitInfo=True)
799 def map_skypolicy(self, dataId):
800 """Map a sky policy."""
801 return dafPersist.ButlerLocation("lsst.pex.policy.Policy", "Policy",
802 "Internal", None, None, self,
803 storage=self.rootStorage)
805 def std_skypolicy(self, item, dataId):
806 """Standardize a sky policy by returning the one we use."""
807 return self.skypolicy
809###############################################################################
810#
811# Utility functions
812#
813###############################################################################
815 def _setupRegistry(self, name, description, path, policy, policyKey, storage, searchParents=True,
816 posixIfNoSql=True):
817 """Set up a registry (usually SQLite3), trying a number of possible
818 paths.
820 Parameters
821 ----------
822 name : string
823 Name of registry.
824 description: `str`
825 Description of registry (for log messages)
826 path : string
827 Path for registry.
828 policy : string
829 Policy that contains the registry name, used if path is None.
830 policyKey : string
831 Key in policy for registry path.
832 storage : Storage subclass
833 Repository Storage to look in.
834 searchParents : bool, optional
835 True if the search for a registry should follow any Butler v1
836 _parent symlinks.
837 posixIfNoSql : bool, optional
838 If an sqlite registry is not found, will create a posix registry if
839 this is True.
841 Returns
842 -------
843 lsst.daf.persistence.Registry
844 Registry object
845 """
846 if path is None and policyKey in policy:
847 path = dafPersist.LogicalLocation(policy[policyKey]).locString()
848 if os.path.isabs(path):
849 raise RuntimeError("Policy should not indicate an absolute path for registry.")
850 if not storage.exists(path):
851 newPath = storage.instanceSearch(path)
853 newPath = newPath[0] if newPath is not None and len(newPath) else None
854 if newPath is None:
855 self.log.warn("Unable to locate registry at policy path (also looked in root): %s",
856 path)
857 path = newPath
858 else:
859 self.log.warn("Unable to locate registry at policy path: %s", path)
860 path = None
862 # Old Butler API was to indicate the registry WITH the repo folder,
863 # New Butler expects the registry to be in the repo folder. To support
864 # Old API, check to see if path starts with root, and if so, strip
865 # root from path. Currently only works with PosixStorage
866 try:
867 root = storage.root
868 if path and (path.startswith(root)):
869 path = path[len(root + '/'):]
870 except AttributeError:
871 pass
873 # determine if there is an sqlite registry and if not, try the posix
874 # registry.
875 registry = None
877 def search(filename, description):
878 """Search for file in storage
880 Parameters
881 ----------
882 filename : `str`
883 Filename to search for
884 description : `str`
885 Description of file, for error message.
887 Returns
888 -------
889 path : `str` or `None`
890 Path to file, or None
891 """
892 result = storage.instanceSearch(filename)
893 if result:
894 return result[0]
895 self.log.debug("Unable to locate %s: %s", description, filename)
896 return None
898 # Search for a suitable registry database
899 if path is None:
900 path = search("%s.pgsql" % name, "%s in root" % description)
901 if path is None:
902 path = search("%s.sqlite3" % name, "%s in root" % description)
903 if path is None:
904 path = search(os.path.join(".", "%s.sqlite3" % name), "%s in current dir" % description)
906 if path is not None:
907 if not storage.exists(path):
908 newPath = storage.instanceSearch(path)
909 newPath = newPath[0] if newPath is not None and len(newPath) else None
910 if newPath is not None:
911 path = newPath
912 localFileObj = storage.getLocalFile(path)
913 self.log.info("Loading %s registry from %s", description, localFileObj.name)
914 registry = dafPersist.Registry.create(localFileObj.name)
915 localFileObj.close()
916 elif not registry and posixIfNoSql:
917 try:
918 self.log.info("Loading Posix %s registry from %s", description, storage.root)
919 registry = dafPersist.PosixRegistry(storage.root)
920 except Exception:
921 registry = None
923 return registry
925 def _transformId(self, dataId):
926 """Generate a standard ID dict from a camera-specific ID dict.
928 Canonical keys include:
929 - amp: amplifier name
930 - ccd: CCD name (in LSST this is a combination of raft and sensor)
931 The default implementation returns a copy of its input.
933 Parameters
934 ----------
935 dataId : `dict`
936 Dataset identifier; this must not be modified
938 Returns
939 -------
940 `dict`
941 Transformed dataset identifier.
942 """
944 return dataId.copy()
946 def _mapActualToPath(self, template, actualId):
947 """Convert a template path to an actual path, using the actual data
948 identifier. This implementation is usually sufficient but can be
949 overridden by the subclass.
951 Parameters
952 ----------
953 template : `str`
954 Template path
955 actualId : `dict`
956 Dataset identifier
958 Returns
959 -------
960 `str`
961 Pathname
962 """
964 try:
965 transformedId = self._transformId(actualId)
966 return template % transformedId
967 except Exception as e:
968 raise RuntimeError("Failed to format %r with data %r: %s" % (template, transformedId, e))
970 @staticmethod
971 def getShortCcdName(ccdName):
972 """Convert a CCD name to a form useful as a filename
974 The default implementation converts spaces to underscores.
975 """
976 return ccdName.replace(" ", "_")
978 def _extractDetectorName(self, dataId):
979 """Extract the detector (CCD) name from the dataset identifier.
981 The name in question is the detector name used by lsst.afw.cameraGeom.
983 Parameters
984 ----------
985 dataId : `dict`
986 Dataset identifier.
988 Returns
989 -------
990 `str`
991 Detector name
992 """
993 raise NotImplementedError("No _extractDetectorName() function specified")
995 def _setAmpDetector(self, item, dataId, trimmed=True):
996 """Set the detector object in an Exposure for an amplifier.
998 Defects are also added to the Exposure based on the detector object.
1000 Parameters
1001 ----------
1002 item : `lsst.afw.image.Exposure`
1003 Exposure to set the detector in.
1004 dataId : `dict`
1005 Dataset identifier
1006 trimmed : `bool`
1007 Should detector be marked as trimmed? (ignored)
1008 """
1010 return self._setCcdDetector(item=item, dataId=dataId, trimmed=trimmed)
1012 def _setCcdDetector(self, item, dataId, trimmed=True):
1013 """Set the detector object in an Exposure for a CCD.
1015 Parameters
1016 ----------
1017 item : `lsst.afw.image.Exposure`
1018 Exposure to set the detector in.
1019 dataId : `dict`
1020 Dataset identifier
1021 trimmed : `bool`
1022 Should detector be marked as trimmed? (ignored)
1023 """
1024 if item.getDetector() is not None:
1025 return
1027 detectorName = self._extractDetectorName(dataId)
1028 detector = self.camera[detectorName]
1029 item.setDetector(detector)
1031 def _setFilter(self, mapping, item, dataId):
1032 """Set the filter object in an Exposure. If the Exposure had a FILTER
1033 keyword, this was already processed during load. But if it didn't,
1034 use the filter from the registry.
1036 Parameters
1037 ----------
1038 mapping : `lsst.obs.base.Mapping`
1039 Where to get the filter from.
1040 item : `lsst.afw.image.Exposure`
1041 Exposure to set the filter in.
1042 dataId : `dict`
1043 Dataset identifier.
1044 """
1046 if not (isinstance(item, afwImage.ExposureU) or isinstance(item, afwImage.ExposureI)
1047 or isinstance(item, afwImage.ExposureF) or isinstance(item, afwImage.ExposureD)):
1048 return
1050 if item.getFilter().getId() != afwImage.Filter.UNKNOWN:
1051 return
1053 actualId = mapping.need(['filter'], dataId)
1054 filterName = actualId['filter']
1055 if self.filters is not None and filterName in self.filters:
1056 filterName = self.filters[filterName]
1057 try:
1058 item.setFilter(afwImage.Filter(filterName))
1059 except pexExcept.NotFoundError:
1060 self.log.warn("Filter %s not defined. Set to UNKNOWN." % (filterName))
1062 def _standardizeExposure(self, mapping, item, dataId, filter=True,
1063 trimmed=True, setVisitInfo=True):
1064 """Default standardization function for images.
1066 This sets the Detector from the camera geometry
1067 and optionally set the Filter. In both cases this saves
1068 having to persist some data in each exposure (or image).
1070 Parameters
1071 ----------
1072 mapping : `lsst.obs.base.Mapping`
1073 Where to get the values from.
1074 item : image-like object
1075 Can be any of lsst.afw.image.Exposure,
1076 lsst.afw.image.DecoratedImage, lsst.afw.image.Image
1077 or lsst.afw.image.MaskedImage
1079 dataId : `dict`
1080 Dataset identifier
1081 filter : `bool`
1082 Set filter? Ignored if item is already an exposure
1083 trimmed : `bool`
1084 Should detector be marked as trimmed?
1085 setVisitInfo : `bool`
1086 Should Exposure have its VisitInfo filled out from the metadata?
1088 Returns
1089 -------
1090 `lsst.afw.image.Exposure`
1091 The standardized Exposure.
1092 """
1093 try:
1094 exposure = exposureFromImage(item, dataId, mapper=self, logger=self.log,
1095 setVisitInfo=setVisitInfo)
1096 except Exception as e:
1097 self.log.error("Could not turn item=%r into an exposure: %s" % (repr(item), e))
1098 raise
1100 if mapping.level.lower() == "amp":
1101 self._setAmpDetector(exposure, dataId, trimmed)
1102 elif mapping.level.lower() == "ccd":
1103 self._setCcdDetector(exposure, dataId, trimmed)
1105 # We can only create a WCS if it doesn't already have one and
1106 # we have either a VisitInfo or exposure metadata.
1107 # Do not calculate a WCS if this is an amplifier exposure
1108 if mapping.level.lower() != "amp" and exposure.getWcs() is None and \
1109 (exposure.getInfo().getVisitInfo() is not None or exposure.getMetadata().toDict()):
1110 self._createInitialSkyWcs(exposure)
1112 if filter:
1113 self._setFilter(mapping, exposure, dataId)
1115 return exposure
1117 def _createSkyWcsFromMetadata(self, exposure):
1118 """Create a SkyWcs from the FITS header metadata in an Exposure.
1120 Parameters
1121 ----------
1122 exposure : `lsst.afw.image.Exposure`
1123 The exposure to get metadata from, and attach the SkyWcs to.
1124 """
1125 metadata = exposure.getMetadata()
1126 fix_header(metadata, translator_class=self.translatorClass)
1127 try:
1128 wcs = afwGeom.makeSkyWcs(metadata, strip=True)
1129 exposure.setWcs(wcs)
1130 except pexExcept.TypeError as e:
1131 # See DM-14372 for why this is debug and not warn (e.g. calib
1132 # files without wcs metadata).
1133 self.log.debug("wcs set to None; missing information found in metadata to create a valid wcs:"
1134 " %s", e.args[0])
1135 # ensure any WCS values stripped from the metadata are removed in the
1136 # exposure
1137 exposure.setMetadata(metadata)
1139 def _createInitialSkyWcs(self, exposure):
1140 """Create a SkyWcs from the boresight and camera geometry.
1142 If the boresight or camera geometry do not support this method of
1143 WCS creation, this falls back on the header metadata-based version
1144 (typically a purely linear FITS crval/crpix/cdmatrix WCS).
1146 Parameters
1147 ----------
1148 exposure : `lsst.afw.image.Exposure`
1149 The exposure to get data from, and attach the SkyWcs to.
1150 """
1151 # Always use try to use metadata first, to strip WCS keys from it.
1152 self._createSkyWcsFromMetadata(exposure)
1154 if exposure.getInfo().getVisitInfo() is None:
1155 msg = "No VisitInfo; cannot access boresight information. Defaulting to metadata-based SkyWcs."
1156 self.log.warn(msg)
1157 return
1158 try:
1159 newSkyWcs = createInitialSkyWcs(exposure.getInfo().getVisitInfo(), exposure.getDetector())
1160 exposure.setWcs(newSkyWcs)
1161 except InitialSkyWcsError as e:
1162 msg = "Cannot create SkyWcs using VisitInfo and Detector, using metadata-based SkyWcs: %s"
1163 self.log.warn(msg, e)
1164 self.log.debug("Exception was: %s", traceback.TracebackException.from_exception(e))
1165 if e.__context__ is not None:
1166 self.log.debug("Root-cause Exception was: %s",
1167 traceback.TracebackException.from_exception(e.__context__))
1169 def _makeCamera(self, policy, repositoryDir):
1170 """Make a camera (instance of lsst.afw.cameraGeom.Camera) describing
1171 the camera geometry
1173 Also set self.cameraDataLocation, if relevant (else it can be left
1174 None).
1176 This implementation assumes that policy contains an entry "camera"
1177 that points to the subdirectory in this package of camera data;
1178 specifically, that subdirectory must contain:
1179 - a file named `camera.py` that contains persisted camera config
1180 - ampInfo table FITS files, as required by
1181 lsst.afw.cameraGeom.makeCameraFromPath
1183 Parameters
1184 ----------
1185 policy : `lsst.daf.persistence.Policy`
1186 Policy with per-camera defaults already merged
1187 (PexPolicy only for backward compatibility).
1188 repositoryDir : `str`
1189 Policy repository for the subclassing module (obtained with
1190 getRepositoryPath() on the per-camera default dictionary).
1191 """
1192 if 'camera' not in policy:
1193 raise RuntimeError("Cannot find 'camera' in policy; cannot construct a camera")
1194 cameraDataSubdir = policy['camera']
1195 self.cameraDataLocation = os.path.normpath(
1196 os.path.join(repositoryDir, cameraDataSubdir, "camera.py"))
1197 cameraConfig = afwCameraGeom.CameraConfig()
1198 cameraConfig.load(self.cameraDataLocation)
1199 ampInfoPath = os.path.dirname(self.cameraDataLocation)
1200 return afwCameraGeom.makeCameraFromPath(
1201 cameraConfig=cameraConfig,
1202 ampInfoPath=ampInfoPath,
1203 shortNameFunc=self.getShortCcdName,
1204 pupilFactoryClass=self.PupilFactoryClass
1205 )
1207 def getRegistry(self):
1208 """Get the registry used by this mapper.
1210 Returns
1211 -------
1212 Registry or None
1213 The registry used by this mapper for this mapper's repository.
1214 """
1215 return self.registry
1217 def getImageCompressionSettings(self, datasetType, dataId):
1218 """Stuff image compression settings into a daf.base.PropertySet
1220 This goes into the ButlerLocation's "additionalData", which gets
1221 passed into the boost::persistence framework.
1223 Parameters
1224 ----------
1225 datasetType : `str`
1226 Type of dataset for which to get the image compression settings.
1227 dataId : `dict`
1228 Dataset identifier.
1230 Returns
1231 -------
1232 additionalData : `lsst.daf.base.PropertySet`
1233 Image compression settings.
1234 """
1235 mapping = self.mappings[datasetType]
1236 recipeName = mapping.recipe
1237 storageType = mapping.storage
1238 if storageType not in self._writeRecipes:
1239 return dafBase.PropertySet()
1240 if recipeName not in self._writeRecipes[storageType]:
1241 raise RuntimeError("Unrecognized write recipe for datasetType %s (storage type %s): %s" %
1242 (datasetType, storageType, recipeName))
1243 recipe = self._writeRecipes[storageType][recipeName].deepCopy()
1244 seed = hash(tuple(dataId.items())) % 2**31
1245 for plane in ("image", "mask", "variance"):
1246 if recipe.exists(plane + ".scaling.seed") and recipe.getScalar(plane + ".scaling.seed") == 0:
1247 recipe.set(plane + ".scaling.seed", seed)
1248 return recipe
1250 def _initWriteRecipes(self):
1251 """Read the recipes for writing files
1253 These recipes are currently used for configuring FITS compression,
1254 but they could have wider uses for configuring different flavors
1255 of the storage types. A recipe is referred to by a symbolic name,
1256 which has associated settings. These settings are stored as a
1257 `PropertySet` so they can easily be passed down to the
1258 boost::persistence framework as the "additionalData" parameter.
1260 The list of recipes is written in YAML. A default recipe and
1261 some other convenient recipes are in obs_base/policy/writeRecipes.yaml
1262 and these may be overridden or supplemented by the individual obs_*
1263 packages' own policy/writeRecipes.yaml files.
1265 Recipes are grouped by the storage type. Currently, only the
1266 ``FitsStorage`` storage type uses recipes, which uses it to
1267 configure FITS image compression.
1269 Each ``FitsStorage`` recipe for FITS compression should define
1270 "image", "mask" and "variance" entries, each of which may contain
1271 "compression" and "scaling" entries. Defaults will be provided for
1272 any missing elements under "compression" and "scaling".
1274 The allowed entries under "compression" are:
1276 * algorithm (string): compression algorithm to use
1277 * rows (int): number of rows per tile (0 = entire dimension)
1278 * columns (int): number of columns per tile (0 = entire dimension)
1279 * quantizeLevel (float): cfitsio quantization level
1281 The allowed entries under "scaling" are:
1283 * algorithm (string): scaling algorithm to use
1284 * bitpix (int): bits per pixel (0,8,16,32,64,-32,-64)
1285 * fuzz (bool): fuzz the values when quantising floating-point values?
1286 * seed (long): seed for random number generator when fuzzing
1287 * maskPlanes (list of string): mask planes to ignore when doing
1288 statistics
1289 * quantizeLevel: divisor of the standard deviation for STDEV_* scaling
1290 * quantizePad: number of stdev to allow on the low side (for
1291 STDEV_POSITIVE/NEGATIVE)
1292 * bscale: manually specified BSCALE (for MANUAL scaling)
1293 * bzero: manually specified BSCALE (for MANUAL scaling)
1295 A very simple example YAML recipe:
1297 FitsStorage:
1298 default:
1299 image: &default
1300 compression:
1301 algorithm: GZIP_SHUFFLE
1302 mask: *default
1303 variance: *default
1304 """
1305 recipesFile = os.path.join(getPackageDir("obs_base"), "policy", "writeRecipes.yaml")
1306 recipes = dafPersist.Policy(recipesFile)
1307 supplementsFile = os.path.join(self.getPackageDir(), "policy", "writeRecipes.yaml")
1308 validationMenu = {'FitsStorage': validateRecipeFitsStorage, }
1309 if os.path.exists(supplementsFile) and supplementsFile != recipesFile:
1310 supplements = dafPersist.Policy(supplementsFile)
1311 # Don't allow overrides, only supplements
1312 for entry in validationMenu:
1313 intersection = set(recipes[entry].names()).intersection(set(supplements.names()))
1314 if intersection:
1315 raise RuntimeError("Recipes provided in %s section %s may not override those in %s: %s" %
1316 (supplementsFile, entry, recipesFile, intersection))
1317 recipes.update(supplements)
1319 self._writeRecipes = {}
1320 for storageType in recipes.names(True):
1321 if "default" not in recipes[storageType]:
1322 raise RuntimeError("No 'default' recipe defined for storage type %s in %s" %
1323 (storageType, recipesFile))
1324 self._writeRecipes[storageType] = validationMenu[storageType](recipes[storageType])
1327def exposureFromImage(image, dataId=None, mapper=None, logger=None, setVisitInfo=True):
1328 """Generate an Exposure from an image-like object
1330 If the image is a DecoratedImage then also set its WCS and metadata
1331 (Image and MaskedImage are missing the necessary metadata
1332 and Exposure already has those set)
1334 Parameters
1335 ----------
1336 image : Image-like object
1337 Can be one of lsst.afw.image.DecoratedImage, Image, MaskedImage or
1338 Exposure.
1340 Returns
1341 -------
1342 `lsst.afw.image.Exposure`
1343 Exposure containing input image.
1344 """
1345 translatorClass = None
1346 if mapper is not None:
1347 translatorClass = mapper.translatorClass
1349 metadata = None
1350 if isinstance(image, afwImage.MaskedImage):
1351 exposure = afwImage.makeExposure(image)
1352 elif isinstance(image, afwImage.DecoratedImage):
1353 exposure = afwImage.makeExposure(afwImage.makeMaskedImage(image.getImage()))
1354 metadata = image.getMetadata()
1355 fix_header(metadata, translator_class=translatorClass)
1356 exposure.setMetadata(metadata)
1357 elif isinstance(image, afwImage.Exposure):
1358 exposure = image
1359 metadata = exposure.getMetadata()
1360 fix_header(metadata, translator_class=translatorClass)
1361 else: # Image
1362 exposure = afwImage.makeExposure(afwImage.makeMaskedImage(image))
1364 # set VisitInfo if we can
1365 if setVisitInfo and exposure.getInfo().getVisitInfo() is None:
1366 if metadata is not None:
1367 if mapper is None:
1368 if not logger:
1369 logger = lsstLog.Log.getLogger("CameraMapper")
1370 logger.warn("I can only set the VisitInfo if you provide a mapper")
1371 else:
1372 exposureId = mapper._computeCcdExposureId(dataId)
1373 visitInfo = mapper.makeRawVisitInfo(md=metadata, exposureId=exposureId)
1375 exposure.getInfo().setVisitInfo(visitInfo)
1377 return exposure
1380def validateRecipeFitsStorage(recipes):
1381 """Validate recipes for FitsStorage
1383 The recipes are supplemented with default values where appropriate.
1385 TODO: replace this custom validation code with Cerberus (DM-11846)
1387 Parameters
1388 ----------
1389 recipes : `lsst.daf.persistence.Policy`
1390 FitsStorage recipes to validate.
1392 Returns
1393 -------
1394 validated : `lsst.daf.base.PropertySet`
1395 Validated FitsStorage recipe.
1397 Raises
1398 ------
1399 `RuntimeError`
1400 If validation fails.
1401 """
1402 # Schemas define what should be there, and the default values (and by the
1403 # default value, the expected type).
1404 compressionSchema = {
1405 "algorithm": "NONE",
1406 "rows": 1,
1407 "columns": 0,
1408 "quantizeLevel": 0.0,
1409 }
1410 scalingSchema = {
1411 "algorithm": "NONE",
1412 "bitpix": 0,
1413 "maskPlanes": ["NO_DATA"],
1414 "seed": 0,
1415 "quantizeLevel": 4.0,
1416 "quantizePad": 5.0,
1417 "fuzz": True,
1418 "bscale": 1.0,
1419 "bzero": 0.0,
1420 }
1422 def checkUnrecognized(entry, allowed, description):
1423 """Check to see if the entry contains unrecognised keywords"""
1424 unrecognized = set(entry.keys()) - set(allowed)
1425 if unrecognized:
1426 raise RuntimeError(
1427 "Unrecognized entries when parsing image compression recipe %s: %s" %
1428 (description, unrecognized))
1430 validated = {}
1431 for name in recipes.names(True):
1432 checkUnrecognized(recipes[name], ["image", "mask", "variance"], name)
1433 rr = dafBase.PropertySet()
1434 validated[name] = rr
1435 for plane in ("image", "mask", "variance"):
1436 checkUnrecognized(recipes[name][plane], ["compression", "scaling"],
1437 name + "->" + plane)
1439 for settings, schema in (("compression", compressionSchema),
1440 ("scaling", scalingSchema)):
1441 prefix = plane + "." + settings
1442 if settings not in recipes[name][plane]:
1443 for key in schema:
1444 rr.set(prefix + "." + key, schema[key])
1445 continue
1446 entry = recipes[name][plane][settings]
1447 checkUnrecognized(entry, schema.keys(), name + "->" + plane + "->" + settings)
1448 for key in schema:
1449 value = type(schema[key])(entry[key]) if key in entry else schema[key]
1450 rr.set(prefix + "." + key, value)
1451 return validated