lsst.obs.base  17.0.1-5-gb7d1e01+6
cameraMapper.py
Go to the documentation of this file.
1 #
2 # LSST Data Management System
3 # Copyright 2008, 2009, 2010 LSST Corporation.
4 #
5 # This product includes software developed by the
6 # LSST Project (http://www.lsst.org/).
7 #
8 # This program is free software: you can redistribute it and/or modify
9 # it under the terms of the GNU General Public License as published by
10 # the Free Software Foundation, either version 3 of the License, or
11 # (at your option) any later version.
12 #
13 # This program is distributed in the hope that it will be useful,
14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 # GNU General Public License for more details.
17 #
18 # You should have received a copy of the LSST License Statement and
19 # the GNU General Public License along with this program. If not,
20 # see <http://www.lsstcorp.org/LegalNotices/>.
21 #
22 
23 import copy
24 import os
25 from astropy.io import fits # required by _makeDefectsDict until defects are written as AFW tables
26 import re
27 import weakref
28 import lsst.daf.persistence as dafPersist
29 from . import ImageMapping, ExposureMapping, CalibrationMapping, DatasetMapping
30 import lsst.daf.base as dafBase
31 import lsst.afw.geom as afwGeom
32 import lsst.afw.image as afwImage
33 import lsst.afw.table as afwTable
34 from lsst.afw.fits import readMetadata
35 import lsst.afw.cameraGeom as afwCameraGeom
36 import lsst.log as lsstLog
37 import lsst.pex.exceptions as pexExcept
38 from .exposureIdInfo import ExposureIdInfo
39 from .makeRawVisitInfo import MakeRawVisitInfo
40 from lsst.utils import getPackageDir
41 
42 __all__ = ["CameraMapper", "exposureFromImage"]
43 
44 
45 class CameraMapper(dafPersist.Mapper):
46 
47  """CameraMapper is a base class for mappers that handle images from a
48  camera and products derived from them. This provides an abstraction layer
49  between the data on disk and the code.
50 
51  Public methods: keys, queryMetadata, getDatasetTypes, map,
52  canStandardize, standardize
53 
54  Mappers for specific data sources (e.g., CFHT Megacam, LSST
55  simulations, etc.) should inherit this class.
56 
57  The CameraMapper manages datasets within a "root" directory. Note that
58  writing to a dataset present in the input root will hide the existing
59  dataset but not overwrite it. See #2160 for design discussion.
60 
61  A camera is assumed to consist of one or more rafts, each composed of
62  multiple CCDs. Each CCD is in turn composed of one or more amplifiers
63  (amps). A camera is also assumed to have a camera geometry description
64  (CameraGeom object) as a policy file, a filter description (Filter class
65  static configuration) as another policy file, and an optional defects
66  description directory.
67 
68  Information from the camera geometry and defects are inserted into all
69  Exposure objects returned.
70 
71  The mapper uses one or two registries to retrieve metadata about the
72  images. The first is a registry of all raw exposures. This must contain
73  the time of the observation. One or more tables (or the equivalent)
74  within the registry are used to look up data identifier components that
75  are not specified by the user (e.g. filter) and to return results for
76  metadata queries. The second is an optional registry of all calibration
77  data. This should contain validity start and end entries for each
78  calibration dataset in the same timescale as the observation time.
79 
80  Subclasses will typically set MakeRawVisitInfoClass:
81 
82  MakeRawVisitInfoClass: a class variable that points to a subclass of
83  MakeRawVisitInfo, a functor that creates an
84  lsst.afw.image.VisitInfo from the FITS metadata of a raw image.
85 
86  Subclasses must provide the following methods:
87 
88  _extractDetectorName(self, dataId): returns the detector name for a CCD
89  (e.g., "CFHT 21", "R:1,2 S:3,4") as used in the AFW CameraGeom class given
90  a dataset identifier referring to that CCD or a subcomponent of it.
91 
92  _computeCcdExposureId(self, dataId): see below
93 
94  _computeCoaddExposureId(self, dataId, singleFilter): see below
95 
96  Subclasses may also need to override the following methods:
97 
98  _transformId(self, dataId): transformation of a data identifier
99  from colloquial usage (e.g., "ccdname") to proper/actual usage
100  (e.g., "ccd"), including making suitable for path expansion (e.g. removing
101  commas). The default implementation does nothing. Note that this
102  method should not modify its input parameter.
103 
104  getShortCcdName(self, ccdName): a static method that returns a shortened
105  name suitable for use as a filename. The default version converts spaces
106  to underscores.
107 
108  _getCcdKeyVal(self, dataId): return a CCD key and value
109  by which to look up defects in the defects registry.
110  The default value returns ("ccd", detector name)
111 
112  _mapActualToPath(self, template, actualId): convert a template path to an
113  actual path, using the actual dataset identifier.
114 
115  The mapper's behaviors are largely specified by the policy file.
116  See the MapperDictionary.paf for descriptions of the available items.
117 
118  The 'exposures', 'calibrations', and 'datasets' subpolicies configure
119  mappings (see Mappings class).
120 
121  Common default mappings for all subclasses can be specified in the
122  "policy/{images,exposures,calibrations,datasets}.yaml" files. This
123  provides a simple way to add a product to all camera mappers.
124 
125  Functions to map (provide a path to the data given a dataset
126  identifier dictionary) and standardize (convert data into some standard
127  format or type) may be provided in the subclass as "map_{dataset type}"
128  and "std_{dataset type}", respectively.
129 
130  If non-Exposure datasets cannot be retrieved using standard
131  daf_persistence methods alone, a "bypass_{dataset type}" function may be
132  provided in the subclass to return the dataset instead of using the
133  "datasets" subpolicy.
134 
135  Implementations of map_camera and bypass_camera that should typically be
136  sufficient are provided in this base class.
137 
138  Notes
139  -----
140  TODO:
141 
142  - Handle defects the same was as all other calibration products, using the
143  calibration registry
144  - Instead of auto-loading the camera at construction time, load it from
145  the calibration registry
146  - Rewrite defects as AFW tables so we don't need astropy.io.fits to
147  unpersist them; then remove all mention of astropy.io.fits from this
148  package.
149  """
150  packageName = None
151 
152  # a class or subclass of MakeRawVisitInfo, a functor that makes an
153  # lsst.afw.image.VisitInfo from the FITS metadata of a raw image
154  MakeRawVisitInfoClass = MakeRawVisitInfo
155 
156  # a class or subclass of PupilFactory
157  PupilFactoryClass = afwCameraGeom.PupilFactory
158 
159  def __init__(self, policy, repositoryDir,
160  root=None, registry=None, calibRoot=None, calibRegistry=None,
161  provided=None, parentRegistry=None, repositoryCfg=None):
162  """Initialize the CameraMapper.
163 
164  Parameters
165  ----------
166  policy : daf_persistence.Policy,
167  Policy with per-camera defaults already merged.
168  repositoryDir : string
169  Policy repository for the subclassing module (obtained with
170  getRepositoryPath() on the per-camera default dictionary).
171  root : string, optional
172  Path to the root directory for data.
173  registry : string, optional
174  Path to registry with data's metadata.
175  calibRoot : string, optional
176  Root directory for calibrations.
177  calibRegistry : string, optional
178  Path to registry with calibrations' metadata.
179  provided : list of string, optional
180  Keys provided by the mapper.
181  parentRegistry : Registry subclass, optional
182  Registry from a parent repository that may be used to look up
183  data's metadata.
184  repositoryCfg : daf_persistence.RepositoryCfg or None, optional
185  The configuration information for the repository this mapper is
186  being used with.
187  """
188 
189  dafPersist.Mapper.__init__(self)
190 
191  self.log = lsstLog.Log.getLogger("CameraMapper")
192 
193  if root:
194  self.root = root
195  elif repositoryCfg:
196  self.root = repositoryCfg.root
197  else:
198  self.root = None
199 
200  repoPolicy = repositoryCfg.policy if repositoryCfg else None
201  if repoPolicy is not None:
202  policy.update(repoPolicy)
203 
204  # Levels
205  self.levels = dict()
206  if 'levels' in policy:
207  levelsPolicy = policy['levels']
208  for key in levelsPolicy.names(True):
209  self.levels[key] = set(levelsPolicy.asArray(key))
210  self.defaultLevel = policy['defaultLevel']
211  self.defaultSubLevels = dict()
212  if 'defaultSubLevels' in policy:
213  self.defaultSubLevels = policy['defaultSubLevels']
214 
215  # Root directories
216  if root is None:
217  root = "."
218  root = dafPersist.LogicalLocation(root).locString()
219 
220  self.rootStorage = dafPersist.Storage.makeFromURI(uri=root)
221 
222  # If the calibRoot is passed in, use that. If not and it's indicated in
223  # the policy, use that. And otherwise, the calibs are in the regular
224  # root.
225  # If the location indicated by the calib root does not exist, do not
226  # create it.
227  calibStorage = None
228  if calibRoot is not None:
229  calibRoot = dafPersist.Storage.absolutePath(root, calibRoot)
230  calibStorage = dafPersist.Storage.makeFromURI(uri=calibRoot,
231  create=False)
232  else:
233  calibRoot = policy.get('calibRoot', None)
234  if calibRoot:
235  calibStorage = dafPersist.Storage.makeFromURI(uri=calibRoot,
236  create=False)
237  if calibStorage is None:
238  calibStorage = self.rootStorage
239 
240  self.root = root
241 
242  # Registries
243  self.registry = self._setupRegistry("registry", "exposure", registry, policy, "registryPath",
244  self.rootStorage, searchParents=False,
245  posixIfNoSql=(not parentRegistry))
246  if not self.registry:
247  self.registry = parentRegistry
248  needCalibRegistry = policy.get('needCalibRegistry', None)
249  if needCalibRegistry:
250  if calibStorage:
251  self.calibRegistry = self._setupRegistry("calibRegistry", "calib", calibRegistry, policy,
252  "calibRegistryPath", calibStorage,
253  posixIfNoSql=False) # NB never use posix for calibs
254  else:
255  raise RuntimeError(
256  "'needCalibRegistry' is true in Policy, but was unable to locate a repo at " +
257  "calibRoot ivar:%s or policy['calibRoot']:%s" %
258  (calibRoot, policy.get('calibRoot', None)))
259  else:
260  self.calibRegistry = None
261 
262  # Dict of valid keys and their value types
263  self.keyDict = dict()
264 
265  self._initMappings(policy, self.rootStorage, calibStorage, provided=None)
266  self._initWriteRecipes()
267 
268  # Camera geometry
269  self.cameraDataLocation = None # path to camera geometry config file
270  self.camera = self._makeCamera(policy=policy, repositoryDir=repositoryDir)
271 
272  # Defect registry and root. Defects are stored with the camera and the registry is loaded from the
273  # camera package, which is on the local filesystem.
274  self.defectRegistry = None
275  if 'defects' in policy:
276  self.defectPath = os.path.join(repositoryDir, policy['defects'])
277  defectRegistryLocation = os.path.join(self.defectPath, "defectRegistry.sqlite3")
278  self.defectRegistry = dafPersist.Registry.create(defectRegistryLocation)
279 
280  # Filter translation table
281  self.filters = None
282 
283  # verify that the class variable packageName is set before attempting
284  # to instantiate an instance
285  if self.packageName is None:
286  raise ValueError('class variable packageName must not be None')
287 
289 
290  def _initMappings(self, policy, rootStorage=None, calibStorage=None, provided=None):
291  """Initialize mappings
292 
293  For each of the dataset types that we want to be able to read, there
294  are methods that can be created to support them:
295  * map_<dataset> : determine the path for dataset
296  * std_<dataset> : standardize the retrieved dataset
297  * bypass_<dataset> : retrieve the dataset (bypassing the usual
298  retrieval machinery)
299  * query_<dataset> : query the registry
300 
301  Besides the dataset types explicitly listed in the policy, we create
302  additional, derived datasets for additional conveniences,
303  e.g., reading the header of an image, retrieving only the size of a
304  catalog.
305 
306  Parameters
307  ----------
308  policy : `lsst.daf.persistence.Policy`
309  Policy with per-camera defaults already merged
310  rootStorage : `Storage subclass instance`
311  Interface to persisted repository data.
312  calibRoot : `Storage subclass instance`
313  Interface to persisted calib repository data
314  provided : `list` of `str`
315  Keys provided by the mapper
316  """
317  # Sub-dictionaries (for exposure/calibration/dataset types)
318  imgMappingPolicy = dafPersist.Policy(dafPersist.Policy.defaultPolicyFile(
319  "obs_base", "ImageMappingDefaults.yaml", "policy"))
320  expMappingPolicy = dafPersist.Policy(dafPersist.Policy.defaultPolicyFile(
321  "obs_base", "ExposureMappingDefaults.yaml", "policy"))
322  calMappingPolicy = dafPersist.Policy(dafPersist.Policy.defaultPolicyFile(
323  "obs_base", "CalibrationMappingDefaults.yaml", "policy"))
324  dsMappingPolicy = dafPersist.Policy()
325 
326  # Mappings
327  mappingList = (
328  ("images", imgMappingPolicy, ImageMapping),
329  ("exposures", expMappingPolicy, ExposureMapping),
330  ("calibrations", calMappingPolicy, CalibrationMapping),
331  ("datasets", dsMappingPolicy, DatasetMapping)
332  )
333  self.mappings = dict()
334  for name, defPolicy, cls in mappingList:
335  if name in policy:
336  datasets = policy[name]
337 
338  # Centrally-defined datasets
339  defaultsPath = os.path.join(getPackageDir("obs_base"), "policy", name + ".yaml")
340  if os.path.exists(defaultsPath):
341  datasets.merge(dafPersist.Policy(defaultsPath))
342 
343  mappings = dict()
344  setattr(self, name, mappings)
345  for datasetType in datasets.names(True):
346  subPolicy = datasets[datasetType]
347  subPolicy.merge(defPolicy)
348 
349  if not hasattr(self, "map_" + datasetType) and 'composite' in subPolicy:
350  def compositeClosure(dataId, write=False, mapper=None, mapping=None,
351  subPolicy=subPolicy):
352  components = subPolicy.get('composite')
353  assembler = subPolicy['assembler'] if 'assembler' in subPolicy else None
354  disassembler = subPolicy['disassembler'] if 'disassembler' in subPolicy else None
355  python = subPolicy['python']
356  butlerComposite = dafPersist.ButlerComposite(assembler=assembler,
357  disassembler=disassembler,
358  python=python,
359  dataId=dataId,
360  mapper=self)
361  for name, component in components.items():
362  butlerComposite.add(id=name,
363  datasetType=component.get('datasetType'),
364  setter=component.get('setter', None),
365  getter=component.get('getter', None),
366  subset=component.get('subset', False),
367  inputOnly=component.get('inputOnly', False))
368  return butlerComposite
369  setattr(self, "map_" + datasetType, compositeClosure)
370  # for now at least, don't set up any other handling for this dataset type.
371  continue
372 
373  if name == "calibrations":
374  mapping = cls(datasetType, subPolicy, self.registry, self.calibRegistry, calibStorage,
375  provided=provided, dataRoot=rootStorage)
376  else:
377  mapping = cls(datasetType, subPolicy, self.registry, rootStorage, provided=provided)
378  self.keyDict.update(mapping.keys())
379  mappings[datasetType] = mapping
380  self.mappings[datasetType] = mapping
381  if not hasattr(self, "map_" + datasetType):
382  def mapClosure(dataId, write=False, mapper=weakref.proxy(self), mapping=mapping):
383  return mapping.map(mapper, dataId, write)
384  setattr(self, "map_" + datasetType, mapClosure)
385  if not hasattr(self, "query_" + datasetType):
386  def queryClosure(format, dataId, mapping=mapping):
387  return mapping.lookup(format, dataId)
388  setattr(self, "query_" + datasetType, queryClosure)
389  if hasattr(mapping, "standardize") and not hasattr(self, "std_" + datasetType):
390  def stdClosure(item, dataId, mapper=weakref.proxy(self), mapping=mapping):
391  return mapping.standardize(mapper, item, dataId)
392  setattr(self, "std_" + datasetType, stdClosure)
393 
394  def setMethods(suffix, mapImpl=None, bypassImpl=None, queryImpl=None):
395  """Set convenience methods on CameraMapper"""
396  mapName = "map_" + datasetType + "_" + suffix
397  bypassName = "bypass_" + datasetType + "_" + suffix
398  queryName = "query_" + datasetType + "_" + suffix
399  if not hasattr(self, mapName):
400  setattr(self, mapName, mapImpl or getattr(self, "map_" + datasetType))
401  if not hasattr(self, bypassName):
402  if bypassImpl is None and hasattr(self, "bypass_" + datasetType):
403  bypassImpl = getattr(self, "bypass_" + datasetType)
404  if bypassImpl is not None:
405  setattr(self, bypassName, bypassImpl)
406  if not hasattr(self, queryName):
407  setattr(self, queryName, queryImpl or getattr(self, "query_" + datasetType))
408 
409  # Filename of dataset
410  setMethods("filename", bypassImpl=lambda datasetType, pythonType, location, dataId:
411  [os.path.join(location.getStorage().root, p) for p in location.getLocations()])
412  # Metadata from FITS file
413  if subPolicy["storage"] == "FitsStorage": # a FITS image
414  setMethods("md", bypassImpl=lambda datasetType, pythonType, location, dataId:
415  readMetadata(location.getLocationsWithRoot()[0]))
416 
417  # Add support for configuring FITS compression
418  addName = "add_" + datasetType
419  if not hasattr(self, addName):
420  setattr(self, addName, self.getImageCompressionSettings)
421 
422  if name == "exposures":
423  def getSkyWcs(datasetType, pythonType, location, dataId):
424  fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
425  return fitsReader.readWcs()
426 
427  setMethods("wcs", bypassImpl=getSkyWcs)
428 
429  setMethods("calib", bypassImpl=lambda datasetType, pythonType, location, dataId:
430  afwImage.Calib(readMetadata(location.getLocationsWithRoot()[0])))
431 
432  def getVisitInfo(datasetType, pythonType, location, dataId):
433  fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
434  return fitsReader.readVisitInfo()
435 
436  setMethods("visitInfo", bypassImpl=getVisitInfo)
437 
438  def getFilter(datasetType, pythonType, location, dataId):
439  fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
440  return fitsReader.readFilter()
441 
442  setMethods("filter", bypassImpl=getFilter)
443 
444  setMethods("detector",
445  mapImpl=lambda dataId, write=False:
446  dafPersist.ButlerLocation(
447  pythonType="lsst.afw.cameraGeom.CameraConfig",
448  cppType="Config",
449  storageName="Internal",
450  locationList="ignored",
451  dataId=dataId,
452  mapper=self,
453  storage=None,
454  ),
455  bypassImpl=lambda datasetType, pythonType, location, dataId:
456  self.camera[self._extractDetectorName(dataId)]
457  )
458  setMethods("bbox", bypassImpl=lambda dsType, pyType, location, dataId:
459  afwImage.bboxFromMetadata(
460  readMetadata(location.getLocationsWithRoot()[0], hdu=1)))
461 
462  elif name == "images":
463  setMethods("bbox", bypassImpl=lambda dsType, pyType, location, dataId:
464  afwImage.bboxFromMetadata(
465  readMetadata(location.getLocationsWithRoot()[0])))
466 
467  if subPolicy["storage"] == "FitsCatalogStorage": # a FITS catalog
468  setMethods("md", bypassImpl=lambda datasetType, pythonType, location, dataId:
469  readMetadata(os.path.join(location.getStorage().root,
470  location.getLocations()[0]), hdu=1))
471 
472  # Sub-images
473  if subPolicy["storage"] == "FitsStorage":
474  def mapSubClosure(dataId, write=False, mapper=weakref.proxy(self), mapping=mapping):
475  subId = dataId.copy()
476  del subId['bbox']
477  loc = mapping.map(mapper, subId, write)
478  bbox = dataId['bbox']
479  llcX = bbox.getMinX()
480  llcY = bbox.getMinY()
481  width = bbox.getWidth()
482  height = bbox.getHeight()
483  loc.additionalData.set('llcX', llcX)
484  loc.additionalData.set('llcY', llcY)
485  loc.additionalData.set('width', width)
486  loc.additionalData.set('height', height)
487  if 'imageOrigin' in dataId:
488  loc.additionalData.set('imageOrigin',
489  dataId['imageOrigin'])
490  return loc
491 
492  def querySubClosure(key, format, dataId, mapping=mapping):
493  subId = dataId.copy()
494  del subId['bbox']
495  return mapping.lookup(format, subId)
496  setMethods("sub", mapImpl=mapSubClosure, queryImpl=querySubClosure)
497 
498  if subPolicy["storage"] == "FitsCatalogStorage":
499  # Length of catalog
500  setMethods("len", bypassImpl=lambda datasetType, pythonType, location, dataId:
501  readMetadata(os.path.join(location.getStorage().root,
502  location.getLocations()[0]),
503  hdu=1).getScalar("NAXIS2"))
504 
505  # Schema of catalog
506  if not datasetType.endswith("_schema") and datasetType + "_schema" not in datasets:
507  setMethods("schema", bypassImpl=lambda datasetType, pythonType, location, dataId:
508  afwTable.Schema.readFits(os.path.join(location.getStorage().root,
509  location.getLocations()[0])))
510 
511  def _computeCcdExposureId(self, dataId):
512  """Compute the 64-bit (long) identifier for a CCD exposure.
513 
514  Subclasses must override
515 
516  Parameters
517  ----------
518  dataId : `dict`
519  Data identifier with visit, ccd.
520  """
521  raise NotImplementedError()
522 
523  def _computeCoaddExposureId(self, dataId, singleFilter):
524  """Compute the 64-bit (long) identifier for a coadd.
525 
526  Subclasses must override
527 
528  Parameters
529  ----------
530  dataId : `dict`
531  Data identifier with tract and patch.
532  singleFilter : `bool`
533  True means the desired ID is for a single-filter coadd, in which
534  case dataIdmust contain filter.
535  """
536  raise NotImplementedError()
537 
538  def _search(self, path):
539  """Search for path in the associated repository's storage.
540 
541  Parameters
542  ----------
543  path : string
544  Path that describes an object in the repository associated with
545  this mapper.
546  Path may contain an HDU indicator, e.g. 'foo.fits[1]'. The
547  indicator will be stripped when searching and so will match
548  filenames without the HDU indicator, e.g. 'foo.fits'. The path
549  returned WILL contain the indicator though, e.g. ['foo.fits[1]'].
550 
551  Returns
552  -------
553  string
554  The path for this object in the repository. Will return None if the
555  object can't be found. If the input argument path contained an HDU
556  indicator, the returned path will also contain the HDU indicator.
557  """
558  return self.rootStorage.search(path)
559 
560  def backup(self, datasetType, dataId):
561  """Rename any existing object with the given type and dataId.
562 
563  The CameraMapper implementation saves objects in a sequence of e.g.:
564 
565  - foo.fits
566  - foo.fits~1
567  - foo.fits~2
568 
569  All of the backups will be placed in the output repo, however, and will
570  not be removed if they are found elsewhere in the _parent chain. This
571  means that the same file will be stored twice if the previous version
572  was found in an input repo.
573  """
574 
575  # Calling PosixStorage directly is not the long term solution in this
576  # function, this is work-in-progress on epic DM-6225. The plan is for
577  # parentSearch to be changed to 'search', and search only the storage
578  # associated with this mapper. All searching of parents will be handled
579  # by traversing the container of repositories in Butler.
580 
581  def firstElement(list):
582  """Get the first element in the list, or None if that can't be
583  done.
584  """
585  return list[0] if list is not None and len(list) else None
586 
587  n = 0
588  newLocation = self.map(datasetType, dataId, write=True)
589  newPath = newLocation.getLocations()[0]
590  path = dafPersist.PosixStorage.search(self.root, newPath, searchParents=True)
591  path = firstElement(path)
592  oldPaths = []
593  while path is not None:
594  n += 1
595  oldPaths.append((n, path))
596  path = dafPersist.PosixStorage.search(self.root, "%s~%d" % (newPath, n), searchParents=True)
597  path = firstElement(path)
598  for n, oldPath in reversed(oldPaths):
599  self.rootStorage.copyFile(oldPath, "%s~%d" % (newPath, n))
600 
601  def keys(self):
602  """Return supported keys.
603 
604  Returns
605  -------
606  iterable
607  List of keys usable in a dataset identifier
608  """
609  return iter(self.keyDict.keys())
610 
611  def getKeys(self, datasetType, level):
612  """Return a dict of supported keys and their value types for a given
613  dataset type at a given level of the key hierarchy.
614 
615  Parameters
616  ----------
617  datasetType : `str`
618  Dataset type or None for all dataset types.
619  level : `str` or None
620  Level or None for all levels or '' for the default level for the
621  camera.
622 
623  Returns
624  -------
625  `dict`
626  Keys are strings usable in a dataset identifier, values are their
627  value types.
628  """
629 
630  # not sure if this is how we want to do this. what if None was intended?
631  if level == '':
632  level = self.getDefaultLevel()
633 
634  if datasetType is None:
635  keyDict = copy.copy(self.keyDict)
636  else:
637  keyDict = self.mappings[datasetType].keys()
638  if level is not None and level in self.levels:
639  keyDict = copy.copy(keyDict)
640  for l in self.levels[level]:
641  if l in keyDict:
642  del keyDict[l]
643  return keyDict
644 
645  def getDefaultLevel(self):
646  return self.defaultLevel
647 
648  def getDefaultSubLevel(self, level):
649  if level in self.defaultSubLevels:
650  return self.defaultSubLevels[level]
651  return None
652 
653  @classmethod
654  def getCameraName(cls):
655  """Return the name of the camera that this CameraMapper is for."""
656  className = str(cls)
657  className = className[className.find('.'):-1]
658  m = re.search(r'(\w+)Mapper', className)
659  if m is None:
660  m = re.search(r"class '[\w.]*?(\w+)'", className)
661  name = m.group(1)
662  return name[:1].lower() + name[1:] if name else ''
663 
664  @classmethod
665  def getPackageName(cls):
666  """Return the name of the package containing this CameraMapper."""
667  if cls.packageName is None:
668  raise ValueError('class variable packageName must not be None')
669  return cls.packageName
670 
671  @classmethod
672  def getPackageDir(cls):
673  """Return the base directory of this package"""
674  return getPackageDir(cls.getPackageName())
675 
676  def map_camera(self, dataId, write=False):
677  """Map a camera dataset."""
678  if self.camera is None:
679  raise RuntimeError("No camera dataset available.")
680  actualId = self._transformId(dataId)
681  return dafPersist.ButlerLocation(
682  pythonType="lsst.afw.cameraGeom.CameraConfig",
683  cppType="Config",
684  storageName="ConfigStorage",
685  locationList=self.cameraDataLocation or "ignored",
686  dataId=actualId,
687  mapper=self,
688  storage=self.rootStorage
689  )
690 
691  def bypass_camera(self, datasetType, pythonType, butlerLocation, dataId):
692  """Return the (preloaded) camera object.
693  """
694  if self.camera is None:
695  raise RuntimeError("No camera dataset available.")
696  return self.camera
697 
698  def map_defects(self, dataId, write=False):
699  """Map defects dataset.
700 
701  Returns
702  -------
703  `lsst.daf.butler.ButlerLocation`
704  Minimal ButlerLocation containing just the locationList field
705  (just enough information that bypass_defects can use it).
706  """
707  defectFitsPath = self._defectLookup(dataId=dataId)
708  if defectFitsPath is None:
709  raise RuntimeError("No defects available for dataId=%s" % (dataId,))
710 
711  return dafPersist.ButlerLocation(None, None, None, defectFitsPath,
712  dataId, self,
713  storage=self.rootStorage)
714 
715  def bypass_defects(self, datasetType, pythonType, butlerLocation, dataId):
716  """Return a defect based on the butler location returned by map_defects
717 
718  Parameters
719  ----------
720  butlerLocation : `lsst.daf.persistence.ButlerLocation`
721  locationList = path to defects FITS file
722  dataId : `dict`
723  Butler data ID; "ccd" must be set.
724 
725  Note: the name "bypass_XXX" means the butler makes no attempt to
726  convert the ButlerLocation into an object, which is what we want for
727  now, since that conversion is a bit tricky.
728  """
729  detectorName = self._extractDetectorName(dataId)
730  defectsFitsPath = butlerLocation.locationList[0]
731  with fits.open(defectsFitsPath) as hduList:
732  for hdu in hduList[1:]:
733  if hdu.header["name"] != detectorName:
734  continue
735 
736  defectList = []
737  for data in hdu.data:
738  bbox = afwGeom.Box2I(
739  afwGeom.Point2I(int(data['x0']), int(data['y0'])),
740  afwGeom.Extent2I(int(data['width']), int(data['height'])),
741  )
742  defectList.append(afwImage.DefectBase(bbox))
743  return defectList
744 
745  raise RuntimeError("No defects for ccd %s in %s" % (detectorName, defectsFitsPath))
746 
747  def map_expIdInfo(self, dataId, write=False):
748  return dafPersist.ButlerLocation(
749  pythonType="lsst.obs.base.ExposureIdInfo",
750  cppType=None,
751  storageName="Internal",
752  locationList="ignored",
753  dataId=dataId,
754  mapper=self,
755  storage=self.rootStorage
756  )
757 
758  def bypass_expIdInfo(self, datasetType, pythonType, location, dataId):
759  """Hook to retrieve an lsst.obs.base.ExposureIdInfo for an exposure"""
760  expId = self.bypass_ccdExposureId(datasetType, pythonType, location, dataId)
761  expBits = self.bypass_ccdExposureId_bits(datasetType, pythonType, location, dataId)
762  return ExposureIdInfo(expId=expId, expBits=expBits)
763 
764  def std_bfKernel(self, item, dataId):
765  """Disable standardization for bfKernel
766 
767  bfKernel is a calibration product that is numpy array,
768  unlike other calibration products that are all images;
769  all calibration images are sent through _standardizeExposure
770  due to CalibrationMapping, but we don't want that to happen to bfKernel
771  """
772  return item
773 
774  def std_raw(self, item, dataId):
775  """Standardize a raw dataset by converting it to an Exposure instead
776  of an Image"""
777  return self._standardizeExposure(self.exposures['raw'], item, dataId,
778  trimmed=False, setVisitInfo=True)
779 
780  def map_skypolicy(self, dataId):
781  """Map a sky policy."""
782  return dafPersist.ButlerLocation("lsst.pex.policy.Policy", "Policy",
783  "Internal", None, None, self,
784  storage=self.rootStorage)
785 
786  def std_skypolicy(self, item, dataId):
787  """Standardize a sky policy by returning the one we use."""
788  return self.skypolicy
789 
790 
795 
796  def _getCcdKeyVal(self, dataId):
797  """Return CCD key and value used to look a defect in the defect
798  registry
799 
800  The default implementation simply returns ("ccd", full detector name)
801  """
802  return ("ccd", self._extractDetectorName(dataId))
803 
804  def _setupRegistry(self, name, description, path, policy, policyKey, storage, searchParents=True,
805  posixIfNoSql=True):
806  """Set up a registry (usually SQLite3), trying a number of possible
807  paths.
808 
809  Parameters
810  ----------
811  name : string
812  Name of registry.
813  description: `str`
814  Description of registry (for log messages)
815  path : string
816  Path for registry.
817  policy : string
818  Policy that contains the registry name, used if path is None.
819  policyKey : string
820  Key in policy for registry path.
821  storage : Storage subclass
822  Repository Storage to look in.
823  searchParents : bool, optional
824  True if the search for a registry should follow any Butler v1
825  _parent symlinks.
826  posixIfNoSql : bool, optional
827  If an sqlite registry is not found, will create a posix registry if
828  this is True.
829 
830  Returns
831  -------
832  lsst.daf.persistence.Registry
833  Registry object
834  """
835  if path is None and policyKey in policy:
836  path = dafPersist.LogicalLocation(policy[policyKey]).locString()
837  if os.path.isabs(path):
838  raise RuntimeError("Policy should not indicate an absolute path for registry.")
839  if not storage.exists(path):
840  newPath = storage.instanceSearch(path)
841 
842  newPath = newPath[0] if newPath is not None and len(newPath) else None
843  if newPath is None:
844  self.log.warn("Unable to locate registry at policy path (also looked in root): %s",
845  path)
846  path = newPath
847  else:
848  self.log.warn("Unable to locate registry at policy path: %s", path)
849  path = None
850 
851  # Old Butler API was to indicate the registry WITH the repo folder, New Butler expects the registry to
852  # be in the repo folder. To support Old API, check to see if path starts with root, and if so, strip
853  # root from path. Currently only works with PosixStorage
854  try:
855  root = storage.root
856  if path and (path.startswith(root)):
857  path = path[len(root + '/'):]
858  except AttributeError:
859  pass
860 
861  # determine if there is an sqlite registry and if not, try the posix registry.
862  registry = None
863 
864  def search(filename, description):
865  """Search for file in storage
866 
867  Parameters
868  ----------
869  filename : `str`
870  Filename to search for
871  description : `str`
872  Description of file, for error message.
873 
874  Returns
875  -------
876  path : `str` or `None`
877  Path to file, or None
878  """
879  result = storage.instanceSearch(filename)
880  if result:
881  return result[0]
882  self.log.debug("Unable to locate %s: %s", description, filename)
883  return None
884 
885  # Search for a suitable registry database
886  if path is None:
887  path = search("%s.pgsql" % name, "%s in root" % description)
888  if path is None:
889  path = search("%s.sqlite3" % name, "%s in root" % description)
890  if path is None:
891  path = search(os.path.join(".", "%s.sqlite3" % name), "%s in current dir" % description)
892 
893  if path is not None:
894  if not storage.exists(path):
895  newPath = storage.instanceSearch(path)
896  newPath = newPath[0] if newPath is not None and len(newPath) else None
897  if newPath is not None:
898  path = newPath
899  localFileObj = storage.getLocalFile(path)
900  self.log.info("Loading %s registry from %s", description, localFileObj.name)
901  registry = dafPersist.Registry.create(localFileObj.name)
902  localFileObj.close()
903  elif not registry and posixIfNoSql:
904  try:
905  self.log.info("Loading Posix %s registry from %s", description, storage.root)
906  registry = dafPersist.PosixRegistry(storage.root)
907  except Exception:
908  registry = None
909 
910  return registry
911 
912  def _transformId(self, dataId):
913  """Generate a standard ID dict from a camera-specific ID dict.
914 
915  Canonical keys include:
916  - amp: amplifier name
917  - ccd: CCD name (in LSST this is a combination of raft and sensor)
918  The default implementation returns a copy of its input.
919 
920  Parameters
921  ----------
922  dataId : `dict`
923  Dataset identifier; this must not be modified
924 
925  Returns
926  -------
927  `dict`
928  Transformed dataset identifier.
929  """
930 
931  return dataId.copy()
932 
933  def _mapActualToPath(self, template, actualId):
934  """Convert a template path to an actual path, using the actual data
935  identifier. This implementation is usually sufficient but can be
936  overridden by the subclass.
937 
938  Parameters
939  ----------
940  template : `str`
941  Template path
942  actualId : `dict`
943  Dataset identifier
944 
945  Returns
946  -------
947  `str`
948  Pathname
949  """
950 
951  try:
952  transformedId = self._transformId(actualId)
953  return template % transformedId
954  except Exception as e:
955  raise RuntimeError("Failed to format %r with data %r: %s" % (template, transformedId, e))
956 
957  @staticmethod
958  def getShortCcdName(ccdName):
959  """Convert a CCD name to a form useful as a filename
960 
961  The default implementation converts spaces to underscores.
962  """
963  return ccdName.replace(" ", "_")
964 
965  def _extractDetectorName(self, dataId):
966  """Extract the detector (CCD) name from the dataset identifier.
967 
968  The name in question is the detector name used by lsst.afw.cameraGeom.
969 
970  Parameters
971  ----------
972  dataId : `dict`
973  Dataset identifier.
974 
975  Returns
976  -------
977  `str`
978  Detector name
979  """
980  raise NotImplementedError("No _extractDetectorName() function specified")
981 
982  def _extractAmpId(self, dataId):
983  """Extract the amplifier identifer from a dataset identifier.
984 
985  .. note:: Deprecated in 11_0
986 
987  amplifier identifier has two parts: the detector name for the CCD
988  containing the amplifier and index of the amplifier in the detector.
989 
990  Parameters
991  ----------
992  dataId : `dict`
993  Dataset identifer
994 
995  Returns
996  -------
997  `tuple`
998  Amplifier identifier
999  """
1000 
1001  trDataId = self._transformId(dataId)
1002  return (trDataId["ccd"], int(trDataId['amp']))
1003 
1004  def _setAmpDetector(self, item, dataId, trimmed=True):
1005  """Set the detector object in an Exposure for an amplifier.
1006 
1007  Defects are also added to the Exposure based on the detector object.
1008 
1009  Parameters
1010  ----------
1011  item : `lsst.afw.image.Exposure`
1012  Exposure to set the detector in.
1013  dataId : `dict`
1014  Dataset identifier
1015  trimmed : `bool`
1016  Should detector be marked as trimmed? (ignored)
1017  """
1018 
1019  return self._setCcdDetector(item=item, dataId=dataId, trimmed=trimmed)
1020 
1021  def _setCcdDetector(self, item, dataId, trimmed=True):
1022  """Set the detector object in an Exposure for a CCD.
1023 
1024  Parameters
1025  ----------
1026  item : `lsst.afw.image.Exposure`
1027  Exposure to set the detector in.
1028  dataId : `dict`
1029  Dataset identifier
1030  trimmed : `bool`
1031  Should detector be marked as trimmed? (ignored)
1032  """
1033  if item.getDetector() is not None:
1034  return
1035 
1036  detectorName = self._extractDetectorName(dataId)
1037  detector = self.camera[detectorName]
1038  item.setDetector(detector)
1039 
1040  def _setFilter(self, mapping, item, dataId):
1041  """Set the filter object in an Exposure. If the Exposure had a FILTER
1042  keyword, this was already processed during load. But if it didn't,
1043  use the filter from the registry.
1044 
1045  Parameters
1046  ----------
1047  mapping : `lsst.obs.base.Mapping`
1048  Where to get the filter from.
1049  item : `lsst.afw.image.Exposure`
1050  Exposure to set the filter in.
1051  dataId : `dict`
1052  Dataset identifier.
1053  """
1054 
1055  if not (isinstance(item, afwImage.ExposureU) or isinstance(item, afwImage.ExposureI) or
1056  isinstance(item, afwImage.ExposureF) or isinstance(item, afwImage.ExposureD)):
1057  return
1058 
1059  if item.getFilter().getId() != afwImage.Filter.UNKNOWN:
1060  return
1061 
1062  actualId = mapping.need(['filter'], dataId)
1063  filterName = actualId['filter']
1064  if self.filters is not None and filterName in self.filters:
1065  filterName = self.filters[filterName]
1066  item.setFilter(afwImage.Filter(filterName))
1067 
1068  # Default standardization function for exposures
1069  def _standardizeExposure(self, mapping, item, dataId, filter=True,
1070  trimmed=True, setVisitInfo=True):
1071  """Default standardization function for images.
1072 
1073  This sets the Detector from the camera geometry
1074  and optionally set the Fiter. In both cases this saves
1075  having to persist some data in each exposure (or image).
1076 
1077  Parameters
1078  ----------
1079  mapping : `lsst.obs.base.Mapping`
1080  Where to get the values from.
1081  item : image-like object
1082  Can be any of lsst.afw.image.Exposure,
1083  lsst.afw.image.DecoratedImage, lsst.afw.image.Image
1084  or lsst.afw.image.MaskedImage
1085 
1086  dataId : `dict`
1087  Dataset identifier
1088  filter : `bool`
1089  Set filter? Ignored if item is already an exposure
1090  trimmed : `bool`
1091  Should detector be marked as trimmed?
1092  setVisitInfo : `bool`
1093  Should Exposure have its VisitInfo filled out from the metadata?
1094 
1095  Returns
1096  -------
1097  `lsst.afw.image.Exposure`
1098  The standardized Exposure.
1099  """
1100  try:
1101  item = exposureFromImage(item, dataId, mapper=self, logger=self.log, setVisitInfo=setVisitInfo)
1102  except Exception as e:
1103  self.log.error("Could not turn item=%r into an exposure: %s" % (repr(item), e))
1104  raise
1105 
1106  if mapping.level.lower() == "amp":
1107  self._setAmpDetector(item, dataId, trimmed)
1108  elif mapping.level.lower() == "ccd":
1109  self._setCcdDetector(item, dataId, trimmed)
1110 
1111  if filter:
1112  self._setFilter(mapping, item, dataId)
1113 
1114  return item
1115 
1116  def _defectLookup(self, dataId):
1117  """Find the defects for a given CCD.
1118 
1119  Parameters
1120  ----------
1121  dataId : `dict`
1122  Dataset identifier
1123 
1124  Returns
1125  -------
1126  `str`
1127  Path to the defects file or None if not available.
1128  """
1129  if self.defectRegistry is None:
1130  return None
1131  if self.registry is None:
1132  raise RuntimeError("No registry for defect lookup")
1133 
1134  ccdKey, ccdVal = self._getCcdKeyVal(dataId)
1135 
1136  dataIdForLookup = {'visit': dataId['visit']}
1137  # .lookup will fail in a posix registry because there is no template to provide.
1138  rows = self.registry.lookup(('taiObs'), ('raw_visit'), dataIdForLookup)
1139  if len(rows) == 0:
1140  return None
1141  assert len(rows) == 1
1142  taiObs = rows[0][0]
1143 
1144  # Lookup the defects for this CCD serial number that are valid at the exposure midpoint.
1145  rows = self.defectRegistry.executeQuery(("path",), ("defect",),
1146  [(ccdKey, "?")],
1147  ("DATETIME(?)", "DATETIME(validStart)", "DATETIME(validEnd)"),
1148  (ccdVal, taiObs))
1149  if not rows or len(rows) == 0:
1150  return None
1151  if len(rows) == 1:
1152  return os.path.join(self.defectPath, rows[0][0])
1153  else:
1154  raise RuntimeError("Querying for defects (%s, %s) returns %d files: %s" %
1155  (ccdVal, taiObs, len(rows), ", ".join([_[0] for _ in rows])))
1156 
1157  def _makeCamera(self, policy, repositoryDir):
1158  """Make a camera (instance of lsst.afw.cameraGeom.Camera) describing
1159  the camera geometry
1160 
1161  Also set self.cameraDataLocation, if relevant (else it can be left
1162  None).
1163 
1164  This implementation assumes that policy contains an entry "camera"
1165  that points to the subdirectory in this package of camera data;
1166  specifically, that subdirectory must contain:
1167  - a file named `camera.py` that contains persisted camera config
1168  - ampInfo table FITS files, as required by
1169  lsst.afw.cameraGeom.makeCameraFromPath
1170 
1171  Parameters
1172  ----------
1173  policy : `lsst.daf.persistence.Policy`
1174  Policy with per-camera defaults already merged
1175  (PexPolicy only for backward compatibility).
1176  repositoryDir : `str`
1177  Policy repository for the subclassing module (obtained with
1178  getRepositoryPath() on the per-camera default dictionary).
1179  """
1180  if 'camera' not in policy:
1181  raise RuntimeError("Cannot find 'camera' in policy; cannot construct a camera")
1182  cameraDataSubdir = policy['camera']
1183  self.cameraDataLocation = os.path.normpath(
1184  os.path.join(repositoryDir, cameraDataSubdir, "camera.py"))
1185  cameraConfig = afwCameraGeom.CameraConfig()
1186  cameraConfig.load(self.cameraDataLocation)
1187  ampInfoPath = os.path.dirname(self.cameraDataLocation)
1188  return afwCameraGeom.makeCameraFromPath(
1189  cameraConfig=cameraConfig,
1190  ampInfoPath=ampInfoPath,
1191  shortNameFunc=self.getShortCcdName,
1192  pupilFactoryClass=self.PupilFactoryClass
1193  )
1194 
1195  def getRegistry(self):
1196  """Get the registry used by this mapper.
1197 
1198  Returns
1199  -------
1200  Registry or None
1201  The registry used by this mapper for this mapper's repository.
1202  """
1203  return self.registry
1204 
1205  def getImageCompressionSettings(self, datasetType, dataId):
1206  """Stuff image compression settings into a daf.base.PropertySet
1207 
1208  This goes into the ButlerLocation's "additionalData", which gets
1209  passed into the boost::persistence framework.
1210 
1211  Parameters
1212  ----------
1213  datasetType : `str`
1214  Type of dataset for which to get the image compression settings.
1215  dataId : `dict`
1216  Dataset identifier.
1217 
1218  Returns
1219  -------
1220  additionalData : `lsst.daf.base.PropertySet`
1221  Image compression settings.
1222  """
1223  mapping = self.mappings[datasetType]
1224  recipeName = mapping.recipe
1225  storageType = mapping.storage
1226  if storageType not in self._writeRecipes:
1227  return dafBase.PropertySet()
1228  if recipeName not in self._writeRecipes[storageType]:
1229  raise RuntimeError("Unrecognized write recipe for datasetType %s (storage type %s): %s" %
1230  (datasetType, storageType, recipeName))
1231  recipe = self._writeRecipes[storageType][recipeName].deepCopy()
1232  seed = hash(tuple(dataId.items())) % 2**31
1233  for plane in ("image", "mask", "variance"):
1234  if recipe.exists(plane + ".scaling.seed") and recipe.getScalar(plane + ".scaling.seed") == 0:
1235  recipe.set(plane + ".scaling.seed", seed)
1236  return recipe
1237 
1238  def _initWriteRecipes(self):
1239  """Read the recipes for writing files
1240 
1241  These recipes are currently used for configuring FITS compression,
1242  but they could have wider uses for configuring different flavors
1243  of the storage types. A recipe is referred to by a symbolic name,
1244  which has associated settings. These settings are stored as a
1245  `PropertySet` so they can easily be passed down to the
1246  boost::persistence framework as the "additionalData" parameter.
1247 
1248  The list of recipes is written in YAML. A default recipe and
1249  some other convenient recipes are in obs_base/policy/writeRecipes.yaml
1250  and these may be overridden or supplemented by the individual obs_*
1251  packages' own policy/writeRecipes.yaml files.
1252 
1253  Recipes are grouped by the storage type. Currently, only the
1254  ``FitsStorage`` storage type uses recipes, which uses it to
1255  configure FITS image compression.
1256 
1257  Each ``FitsStorage`` recipe for FITS compression should define
1258  "image", "mask" and "variance" entries, each of which may contain
1259  "compression" and "scaling" entries. Defaults will be provided for
1260  any missing elements under "compression" and "scaling".
1261 
1262  The allowed entries under "compression" are:
1263 
1264  * algorithm (string): compression algorithm to use
1265  * rows (int): number of rows per tile (0 = entire dimension)
1266  * columns (int): number of columns per tile (0 = entire dimension)
1267  * quantizeLevel (float): cfitsio quantization level
1268 
1269  The allowed entries under "scaling" are:
1270 
1271  * algorithm (string): scaling algorithm to use
1272  * bitpix (int): bits per pixel (0,8,16,32,64,-32,-64)
1273  * fuzz (bool): fuzz the values when quantising floating-point values?
1274  * seed (long): seed for random number generator when fuzzing
1275  * maskPlanes (list of string): mask planes to ignore when doing
1276  statistics
1277  * quantizeLevel: divisor of the standard deviation for STDEV_* scaling
1278  * quantizePad: number of stdev to allow on the low side (for
1279  STDEV_POSITIVE/NEGATIVE)
1280  * bscale: manually specified BSCALE (for MANUAL scaling)
1281  * bzero: manually specified BSCALE (for MANUAL scaling)
1282 
1283  A very simple example YAML recipe:
1284 
1285  FitsStorage:
1286  default:
1287  image: &default
1288  compression:
1289  algorithm: GZIP_SHUFFLE
1290  mask: *default
1291  variance: *default
1292  """
1293  recipesFile = os.path.join(getPackageDir("obs_base"), "policy", "writeRecipes.yaml")
1294  recipes = dafPersist.Policy(recipesFile)
1295  supplementsFile = os.path.join(self.getPackageDir(), "policy", "writeRecipes.yaml")
1296  validationMenu = {'FitsStorage': validateRecipeFitsStorage, }
1297  if os.path.exists(supplementsFile) and supplementsFile != recipesFile:
1298  supplements = dafPersist.Policy(supplementsFile)
1299  # Don't allow overrides, only supplements
1300  for entry in validationMenu:
1301  intersection = set(recipes[entry].names()).intersection(set(supplements.names()))
1302  if intersection:
1303  raise RuntimeError("Recipes provided in %s section %s may not override those in %s: %s" %
1304  (supplementsFile, entry, recipesFile, intersection))
1305  recipes.update(supplements)
1306 
1307  self._writeRecipes = {}
1308  for storageType in recipes.names(True):
1309  if "default" not in recipes[storageType]:
1310  raise RuntimeError("No 'default' recipe defined for storage type %s in %s" %
1311  (storageType, recipesFile))
1312  self._writeRecipes[storageType] = validationMenu[storageType](recipes[storageType])
1313 
1314 
1315 def exposureFromImage(image, dataId=None, mapper=None, logger=None, setVisitInfo=True):
1316  """Generate an Exposure from an image-like object
1317 
1318  If the image is a DecoratedImage then also set its WCS and metadata
1319  (Image and MaskedImage are missing the necessary metadata
1320  and Exposure already has those set)
1321 
1322  Parameters
1323  ----------
1324  image : Image-like object
1325  Can be one of lsst.afw.image.DecoratedImage, Image, MaskedImage or
1326  Exposure.
1327 
1328  Returns
1329  -------
1330  `lsst.afw.image.Exposure`
1331  Exposure containing input image.
1332  """
1333  metadata = None
1334  if isinstance(image, afwImage.MaskedImage):
1335  exposure = afwImage.makeExposure(image)
1336  elif isinstance(image, afwImage.DecoratedImage):
1337  exposure = afwImage.makeExposure(afwImage.makeMaskedImage(image.getImage()))
1338  metadata = image.getMetadata()
1339  try:
1340  wcs = afwGeom.makeSkyWcs(metadata, strip=True)
1341  exposure.setWcs(wcs)
1342  except pexExcept.TypeError as e:
1343  # raised on failure to create a wcs (and possibly others)
1344  if logger is None:
1345  logger = lsstLog.Log.getLogger("CameraMapper")
1346  logger.debug("wcs set to None; insufficient information found in metadata to create a valid wcs:"
1347  " %s", e.args[0])
1348 
1349  exposure.setMetadata(metadata)
1350  elif isinstance(image, afwImage.Exposure):
1351  # Exposure
1352  exposure = image
1353  metadata = exposure.getMetadata()
1354  else:
1355  # Image
1356  exposure = afwImage.makeExposure(afwImage.makeMaskedImage(image))
1357  #
1358  # set VisitInfo if we can
1359  #
1360  if setVisitInfo and exposure.getInfo().getVisitInfo() is None:
1361  if metadata is not None:
1362  if mapper is None:
1363  if not logger:
1364  logger = lsstLog.Log.getLogger("CameraMapper")
1365  logger.warn("I can only set the VisitInfo if you provide a mapper")
1366  else:
1367  exposureId = mapper._computeCcdExposureId(dataId)
1368  visitInfo = mapper.makeRawVisitInfo(md=metadata, exposureId=exposureId)
1369 
1370  exposure.getInfo().setVisitInfo(visitInfo)
1371 
1372  return exposure
1373 
1374 
1376  """Validate recipes for FitsStorage
1377 
1378  The recipes are supplemented with default values where appropriate.
1379 
1380  TODO: replace this custom validation code with Cerberus (DM-11846)
1381 
1382  Parameters
1383  ----------
1384  recipes : `lsst.daf.persistence.Policy`
1385  FitsStorage recipes to validate.
1386 
1387  Returns
1388  -------
1389  validated : `lsst.daf.base.PropertySet`
1390  Validated FitsStorage recipe.
1391 
1392  Raises
1393  ------
1394  `RuntimeError`
1395  If validation fails.
1396  """
1397  # Schemas define what should be there, and the default values (and by the default
1398  # value, the expected type).
1399  compressionSchema = {
1400  "algorithm": "NONE",
1401  "rows": 1,
1402  "columns": 0,
1403  "quantizeLevel": 0.0,
1404  }
1405  scalingSchema = {
1406  "algorithm": "NONE",
1407  "bitpix": 0,
1408  "maskPlanes": ["NO_DATA"],
1409  "seed": 0,
1410  "quantizeLevel": 4.0,
1411  "quantizePad": 5.0,
1412  "fuzz": True,
1413  "bscale": 1.0,
1414  "bzero": 0.0,
1415  }
1416 
1417  def checkUnrecognized(entry, allowed, description):
1418  """Check to see if the entry contains unrecognised keywords"""
1419  unrecognized = set(entry.keys()) - set(allowed)
1420  if unrecognized:
1421  raise RuntimeError(
1422  "Unrecognized entries when parsing image compression recipe %s: %s" %
1423  (description, unrecognized))
1424 
1425  validated = {}
1426  for name in recipes.names(True):
1427  checkUnrecognized(recipes[name], ["image", "mask", "variance"], name)
1428  rr = dafBase.PropertySet()
1429  validated[name] = rr
1430  for plane in ("image", "mask", "variance"):
1431  checkUnrecognized(recipes[name][plane], ["compression", "scaling"],
1432  name + "->" + plane)
1433 
1434  for settings, schema in (("compression", compressionSchema),
1435  ("scaling", scalingSchema)):
1436  prefix = plane + "." + settings
1437  if settings not in recipes[name][plane]:
1438  for key in schema:
1439  rr.set(prefix + "." + key, schema[key])
1440  continue
1441  entry = recipes[name][plane][settings]
1442  checkUnrecognized(entry, schema.keys(), name + "->" + plane + "->" + settings)
1443  for key in schema:
1444  value = type(schema[key])(entry[key]) if key in entry else schema[key]
1445  rr.set(prefix + "." + key, value)
1446  return validated
def _makeCamera(self, policy, repositoryDir)
def map_expIdInfo(self, dataId, write=False)
def _setAmpDetector(self, item, dataId, trimmed=True)
def validateRecipeFitsStorage(recipes)
def _standardizeExposure(self, mapping, item, dataId, filter=True, trimmed=True, setVisitInfo=True)
def _setFilter(self, mapping, item, dataId)
def _setCcdDetector(self, item, dataId, trimmed=True)
def bypass_defects(self, datasetType, pythonType, butlerLocation, dataId)
def std_bfKernel(self, item, dataId)
def getKeys(self, datasetType, level)
def getImageCompressionSettings(self, datasetType, dataId)
def map_defects(self, dataId, write=False)
def map_camera(self, dataId, write=False)
def backup(self, datasetType, dataId)
def _setupRegistry(self, name, description, path, policy, policyKey, storage, searchParents=True, posixIfNoSql=True)
def std_skypolicy(self, item, dataId)
def bypass_camera(self, datasetType, pythonType, butlerLocation, dataId)
def _initMappings(self, policy, rootStorage=None, calibStorage=None, provided=None)
def __init__(self, policy, repositoryDir, root=None, registry=None, calibRoot=None, calibRegistry=None, provided=None, parentRegistry=None, repositoryCfg=None)
def bypass_expIdInfo(self, datasetType, pythonType, location, dataId)
def exposureFromImage(image, dataId=None, mapper=None, logger=None, setVisitInfo=True)
def _getCcdKeyVal(self, dataId)
Utility functions.