25 from astropy.io
import fits
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
38 from .exposureIdInfo
import ExposureIdInfo
39 from .makeRawVisitInfo
import MakeRawVisitInfo
42 __all__ = [
"CameraMapper",
"exposureFromImage"]
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. 51 Public methods: keys, queryMetadata, getDatasetTypes, map, 52 canStandardize, standardize 54 Mappers for specific data sources (e.g., CFHT Megacam, LSST 55 simulations, etc.) should inherit this class. 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. 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. 68 Information from the camera geometry and defects are inserted into all 69 Exposure objects returned. 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. 80 Subclasses will typically set MakeRawVisitInfoClass: 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. 86 Subclasses must provide the following methods: 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. 92 _computeCcdExposureId(self, dataId): see below 94 _computeCoaddExposureId(self, dataId, singleFilter): see below 96 Subclasses may also need to override the following methods: 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. 104 getShortCcdName(self, ccdName): a static method that returns a shortened 105 name suitable for use as a filename. The default version converts spaces 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) 112 _mapActualToPath(self, template, actualId): convert a template path to an 113 actual path, using the actual dataset identifier. 115 The mapper's behaviors are largely specified by the policy file. 116 See the MapperDictionary.paf for descriptions of the available items. 118 The 'exposures', 'calibrations', and 'datasets' subpolicies configure 119 mappings (see Mappings class). 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. 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. 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. 135 Implementations of map_camera and bypass_camera that should typically be 136 sufficient are provided in this base class. 142 - Handle defects the same was as all other calibration products, using the 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 154 MakeRawVisitInfoClass = MakeRawVisitInfo
157 PupilFactoryClass = afwCameraGeom.PupilFactory
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. 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 184 repositoryCfg : daf_persistence.RepositoryCfg or None, optional 185 The configuration information for the repository this mapper is 189 dafPersist.Mapper.__init__(self)
191 self.
log = lsstLog.Log.getLogger(
"CameraMapper")
196 self.
root = repositoryCfg.root
200 repoPolicy = repositoryCfg.policy
if repositoryCfg
else None 201 if repoPolicy
is not None:
202 policy.update(repoPolicy)
206 if 'levels' in policy:
207 levelsPolicy = policy[
'levels']
208 for key
in levelsPolicy.names(
True):
209 self.
levels[key] = set(levelsPolicy.asArray(key))
212 if 'defaultSubLevels' in policy:
218 root = dafPersist.LogicalLocation(root).locString()
228 if calibRoot
is not None:
229 calibRoot = dafPersist.Storage.absolutePath(root, calibRoot)
230 calibStorage = dafPersist.Storage.makeFromURI(uri=calibRoot,
233 calibRoot = policy.get(
'calibRoot',
None)
235 calibStorage = dafPersist.Storage.makeFromURI(uri=calibRoot,
237 if calibStorage
is None:
245 posixIfNoSql=(
not parentRegistry))
248 needCalibRegistry = policy.get(
'needCalibRegistry',
None)
249 if needCalibRegistry:
252 "calibRegistryPath", calibStorage,
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)))
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)
286 raise ValueError(
'class variable packageName must not be None')
290 def _initMappings(self, policy, rootStorage=None, calibStorage=None, provided=None):
291 """Initialize mappings 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 299 * query_<dataset> : query the registry 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 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 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()
328 (
"images", imgMappingPolicy, ImageMapping),
329 (
"exposures", expMappingPolicy, ExposureMapping),
330 (
"calibrations", calMappingPolicy, CalibrationMapping),
331 (
"datasets", dsMappingPolicy, DatasetMapping)
334 for name, defPolicy, cls
in mappingList:
336 datasets = policy[name]
339 defaultsPath = os.path.join(
getPackageDir(
"obs_base"),
"policy", name +
".yaml")
340 if os.path.exists(defaultsPath):
341 datasets.merge(dafPersist.Policy(defaultsPath))
344 setattr(self, name, mappings)
345 for datasetType
in datasets.names(
True):
346 subPolicy = datasets[datasetType]
347 subPolicy.merge(defPolicy)
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,
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)
373 if name ==
"calibrations":
375 provided=provided, dataRoot=rootStorage)
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)
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))
410 setMethods(
"filename", bypassImpl=
lambda datasetType, pythonType, location, dataId:
411 [os.path.join(location.getStorage().root, p)
for p
in location.getLocations()])
413 if subPolicy[
"storage"] ==
"FitsStorage":
414 setMethods(
"md", bypassImpl=
lambda datasetType, pythonType, location, dataId:
415 readMetadata(location.getLocationsWithRoot()[0]))
418 addName =
"add_" + datasetType
419 if not hasattr(self, addName):
422 if name ==
"exposures":
423 def getSkyWcs(datasetType, pythonType, location, dataId):
424 fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
425 return fitsReader.readWcs()
427 setMethods(
"wcs", bypassImpl=getSkyWcs)
429 setMethods(
"calib", bypassImpl=
lambda datasetType, pythonType, location, dataId:
430 afwImage.Calib(readMetadata(location.getLocationsWithRoot()[0])))
432 def getVisitInfo(datasetType, pythonType, location, dataId):
433 fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
434 return fitsReader.readVisitInfo()
436 setMethods(
"visitInfo", bypassImpl=getVisitInfo)
438 def getFilter(datasetType, pythonType, location, dataId):
439 fitsReader = afwImage.ExposureFitsReader(location.getLocationsWithRoot()[0])
440 return fitsReader.readFilter()
442 setMethods(
"filter", bypassImpl=getFilter)
444 setMethods(
"detector",
445 mapImpl=
lambda dataId, write=
False:
446 dafPersist.ButlerLocation(
447 pythonType=
"lsst.afw.cameraGeom.CameraConfig",
449 storageName=
"Internal",
450 locationList=
"ignored",
455 bypassImpl=
lambda datasetType, pythonType, location, dataId:
458 setMethods(
"bbox", bypassImpl=
lambda dsType, pyType, location, dataId:
459 afwImage.bboxFromMetadata(
460 readMetadata(location.getLocationsWithRoot()[0], hdu=1)))
462 elif name ==
"images":
463 setMethods(
"bbox", bypassImpl=
lambda dsType, pyType, location, dataId:
464 afwImage.bboxFromMetadata(
465 readMetadata(location.getLocationsWithRoot()[0])))
467 if subPolicy[
"storage"] ==
"FitsCatalogStorage":
468 setMethods(
"md", bypassImpl=
lambda datasetType, pythonType, location, dataId:
469 readMetadata(os.path.join(location.getStorage().root,
470 location.getLocations()[0]), hdu=1))
473 if subPolicy[
"storage"] ==
"FitsStorage":
474 def mapSubClosure(dataId, write=False, mapper=weakref.proxy(self), mapping=mapping):
475 subId = dataId.copy()
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'])
492 def querySubClosure(key, format, dataId, mapping=mapping):
493 subId = dataId.copy()
495 return mapping.lookup(format, subId)
496 setMethods(
"sub", mapImpl=mapSubClosure, queryImpl=querySubClosure)
498 if subPolicy[
"storage"] ==
"FitsCatalogStorage":
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"))
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])))
511 def _computeCcdExposureId(self, dataId):
512 """Compute the 64-bit (long) identifier for a CCD exposure. 514 Subclasses must override 519 Data identifier with visit, ccd. 521 raise NotImplementedError()
523 def _computeCoaddExposureId(self, dataId, singleFilter):
524 """Compute the 64-bit (long) identifier for a coadd. 526 Subclasses must override 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. 536 raise NotImplementedError()
538 def _search(self, path):
539 """Search for path in the associated repository's storage. 544 Path that describes an object in the repository associated with 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]']. 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. 561 """Rename any existing object with the given type and dataId. 563 The CameraMapper implementation saves objects in a sequence of e.g.: 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. 581 def firstElement(list):
582 """Get the first element in the list, or None if that can't be 585 return list[0]
if list
is not None and len(list)
else None 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)
593 while path
is not None:
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))
602 """Return supported keys. 607 List of keys usable in a dataset identifier 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. 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 626 Keys are strings usable in a dataset identifier, values are their 634 if datasetType
is None:
635 keyDict = copy.copy(self.
keyDict)
638 if level
is not None and level
in self.
levels:
639 keyDict = copy.copy(keyDict)
640 for l
in self.
levels[level]:
655 """Return the name of the camera that this CameraMapper is for.""" 657 className = className[className.find(
'.'):-1]
658 m = re.search(
r'(\w+)Mapper', className)
660 m = re.search(
r"class '[\w.]*?(\w+)'", className)
662 return name[:1].lower() + name[1:]
if name
else '' 666 """Return the name of the package containing this CameraMapper.""" 668 raise ValueError(
'class variable packageName must not be None')
673 """Return the base directory of this package""" 677 """Map a camera dataset.""" 679 raise RuntimeError(
"No camera dataset available.")
681 return dafPersist.ButlerLocation(
682 pythonType=
"lsst.afw.cameraGeom.CameraConfig",
684 storageName=
"ConfigStorage",
692 """Return the (preloaded) camera object. 695 raise RuntimeError(
"No camera dataset available.")
699 """Map defects dataset. 703 `lsst.daf.butler.ButlerLocation` 704 Minimal ButlerLocation containing just the locationList field 705 (just enough information that bypass_defects can use it). 708 if defectFitsPath
is None:
709 raise RuntimeError(
"No defects available for dataId=%s" % (dataId,))
711 return dafPersist.ButlerLocation(
None,
None,
None, defectFitsPath,
716 """Return a defect based on the butler location returned by map_defects 720 butlerLocation : `lsst.daf.persistence.ButlerLocation` 721 locationList = path to defects FITS file 723 Butler data ID; "ccd" must be set. 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. 730 defectsFitsPath = butlerLocation.locationList[0]
731 with fits.open(defectsFitsPath)
as hduList:
732 for hdu
in hduList[1:]:
733 if hdu.header[
"name"] != detectorName:
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'])),
742 defectList.append(afwImage.DefectBase(bbox))
745 raise RuntimeError(
"No defects for ccd %s in %s" % (detectorName, defectsFitsPath))
748 return dafPersist.ButlerLocation(
749 pythonType=
"lsst.obs.base.ExposureIdInfo",
751 storageName=
"Internal",
752 locationList=
"ignored",
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)
765 """Disable standardization for bfKernel 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 775 """Standardize a raw dataset by converting it to an Exposure instead 778 trimmed=
False, setVisitInfo=
True)
781 """Map a sky policy.""" 782 return dafPersist.ButlerLocation(
"lsst.pex.policy.Policy",
"Policy",
783 "Internal",
None,
None, self,
787 """Standardize a sky policy by returning the one we use.""" 788 return self.skypolicy
796 def _getCcdKeyVal(self, dataId):
797 """Return CCD key and value used to look a defect in the defect 800 The default implementation simply returns ("ccd", full detector name) 804 def _setupRegistry(self, name, description, path, policy, policyKey, storage, searchParents=True,
806 """Set up a registry (usually SQLite3), trying a number of possible 814 Description of registry (for log messages) 818 Policy that contains the registry name, used if path is None. 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 826 posixIfNoSql : bool, optional 827 If an sqlite registry is not found, will create a posix registry if 832 lsst.daf.persistence.Registry 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)
842 newPath = newPath[0]
if newPath
is not None and len(newPath)
else None 844 self.
log.warn(
"Unable to locate registry at policy path (also looked in root): %s",
848 self.
log.warn(
"Unable to locate registry at policy path: %s", path)
856 if path
and (path.startswith(root)):
857 path = path[len(root +
'/'):]
858 except AttributeError:
864 def search(filename, description):
865 """Search for file in storage 870 Filename to search for 872 Description of file, for error message. 876 path : `str` or `None` 877 Path to file, or None 879 result = storage.instanceSearch(filename)
882 self.
log.debug(
"Unable to locate %s: %s", description, filename)
887 path = search(
"%s.pgsql" % name,
"%s in root" % description)
889 path = search(
"%s.sqlite3" % name,
"%s in root" % description)
891 path = search(os.path.join(
".",
"%s.sqlite3" % name),
"%s in current dir" % description)
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:
899 localFileObj = storage.getLocalFile(path)
900 self.
log.info(
"Loading %s registry from %s", description, localFileObj.name)
901 registry = dafPersist.Registry.create(localFileObj.name)
903 elif not registry
and posixIfNoSql:
905 self.
log.info(
"Loading Posix %s registry from %s", description, storage.root)
906 registry = dafPersist.PosixRegistry(storage.root)
912 def _transformId(self, dataId):
913 """Generate a standard ID dict from a camera-specific ID dict. 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. 923 Dataset identifier; this must not be modified 928 Transformed dataset identifier. 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. 953 return template % transformedId
954 except Exception
as e:
955 raise RuntimeError(
"Failed to format %r with data %r: %s" % (template, transformedId, e))
959 """Convert a CCD name to a form useful as a filename 961 The default implementation converts spaces to underscores. 963 return ccdName.replace(
" ",
"_")
965 def _extractDetectorName(self, dataId):
966 """Extract the detector (CCD) name from the dataset identifier. 968 The name in question is the detector name used by lsst.afw.cameraGeom. 980 raise NotImplementedError(
"No _extractDetectorName() function specified")
982 def _extractAmpId(self, dataId):
983 """Extract the amplifier identifer from a dataset identifier. 985 .. note:: Deprecated in 11_0 987 amplifier identifier has two parts: the detector name for the CCD 988 containing the amplifier and index of the amplifier in the detector. 1002 return (trDataId[
"ccd"], int(trDataId[
'amp']))
1004 def _setAmpDetector(self, item, dataId, trimmed=True):
1005 """Set the detector object in an Exposure for an amplifier. 1007 Defects are also added to the Exposure based on the detector object. 1011 item : `lsst.afw.image.Exposure` 1012 Exposure to set the detector in. 1016 Should detector be marked as trimmed? (ignored) 1019 return self.
_setCcdDetector(item=item, dataId=dataId, trimmed=trimmed)
1021 def _setCcdDetector(self, item, dataId, trimmed=True):
1022 """Set the detector object in an Exposure for a CCD. 1026 item : `lsst.afw.image.Exposure` 1027 Exposure to set the detector in. 1031 Should detector be marked as trimmed? (ignored) 1033 if item.getDetector()
is not None:
1037 detector = self.
camera[detectorName]
1038 item.setDetector(detector)
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. 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. 1055 if not (isinstance(item, afwImage.ExposureU)
or isinstance(item, afwImage.ExposureI)
or 1056 isinstance(item, afwImage.ExposureF)
or isinstance(item, afwImage.ExposureD)):
1059 if item.getFilter().getId() != afwImage.Filter.UNKNOWN:
1062 actualId = mapping.need([
'filter'], dataId)
1063 filterName = actualId[
'filter']
1065 filterName = self.
filters[filterName]
1066 item.setFilter(afwImage.Filter(filterName))
1069 def _standardizeExposure(self, mapping, item, dataId, filter=True,
1070 trimmed=True, setVisitInfo=True):
1071 """Default standardization function for images. 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). 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 1089 Set filter? Ignored if item is already an exposure 1091 Should detector be marked as trimmed? 1092 setVisitInfo : `bool` 1093 Should Exposure have its VisitInfo filled out from the metadata? 1097 `lsst.afw.image.Exposure` 1098 The standardized Exposure. 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))
1106 if mapping.level.lower() ==
"amp":
1108 elif mapping.level.lower() ==
"ccd":
1116 def _defectLookup(self, dataId):
1117 """Find the defects for a given CCD. 1127 Path to the defects file or None if not available. 1132 raise RuntimeError(
"No registry for defect lookup")
1136 dataIdForLookup = {
'visit': dataId[
'visit']}
1138 rows = self.
registry.lookup((
'taiObs'), (
'raw_visit'), dataIdForLookup)
1141 assert len(rows) == 1
1147 (
"DATETIME(?)",
"DATETIME(validStart)",
"DATETIME(validEnd)"),
1149 if not rows
or len(rows) == 0:
1152 return os.path.join(self.
defectPath, rows[0][0])
1154 raise RuntimeError(
"Querying for defects (%s, %s) returns %d files: %s" %
1155 (ccdVal, taiObs, len(rows),
", ".join([_[0]
for _
in rows])))
1157 def _makeCamera(self, policy, repositoryDir):
1158 """Make a camera (instance of lsst.afw.cameraGeom.Camera) describing 1161 Also set self.cameraDataLocation, if relevant (else it can be left 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 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). 1180 if 'camera' not in policy:
1181 raise RuntimeError(
"Cannot find 'camera' in policy; cannot construct a camera")
1182 cameraDataSubdir = policy[
'camera']
1184 os.path.join(repositoryDir, cameraDataSubdir,
"camera.py"))
1185 cameraConfig = afwCameraGeom.CameraConfig()
1188 return afwCameraGeom.makeCameraFromPath(
1189 cameraConfig=cameraConfig,
1190 ampInfoPath=ampInfoPath,
1196 """Get the registry used by this mapper. 1201 The registry used by this mapper for this mapper's repository. 1206 """Stuff image compression settings into a daf.base.PropertySet 1208 This goes into the ButlerLocation's "additionalData", which gets 1209 passed into the boost::persistence framework. 1214 Type of dataset for which to get the image compression settings. 1220 additionalData : `lsst.daf.base.PropertySet` 1221 Image compression settings. 1223 mapping = self.
mappings[datasetType]
1224 recipeName = mapping.recipe
1225 storageType = mapping.storage
1227 return dafBase.PropertySet()
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)
1238 def _initWriteRecipes(self):
1239 """Read the recipes for writing files 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. 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. 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. 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". 1262 The allowed entries under "compression" are: 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 1269 The allowed entries under "scaling" are: 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 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) 1283 A very simple example YAML recipe: 1289 algorithm: GZIP_SHUFFLE 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)
1300 for entry
in validationMenu:
1301 intersection = set(recipes[entry].names()).intersection(set(supplements.names()))
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)
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])
1316 """Generate an Exposure from an image-like object 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) 1324 image : Image-like object 1325 Can be one of lsst.afw.image.DecoratedImage, Image, MaskedImage or 1330 `lsst.afw.image.Exposure` 1331 Exposure containing input image. 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()
1340 wcs = afwGeom.makeSkyWcs(metadata, strip=
True)
1341 exposure.setWcs(wcs)
1342 except pexExcept.TypeError
as e:
1345 logger = lsstLog.Log.getLogger(
"CameraMapper")
1346 logger.debug(
"wcs set to None; insufficient information found in metadata to create a valid wcs:" 1349 exposure.setMetadata(metadata)
1350 elif isinstance(image, afwImage.Exposure):
1353 metadata = exposure.getMetadata()
1356 exposure = afwImage.makeExposure(afwImage.makeMaskedImage(image))
1360 if setVisitInfo
and exposure.getInfo().getVisitInfo()
is None:
1361 if metadata
is not None:
1364 logger = lsstLog.Log.getLogger(
"CameraMapper")
1365 logger.warn(
"I can only set the VisitInfo if you provide a mapper")
1367 exposureId = mapper._computeCcdExposureId(dataId)
1368 visitInfo = mapper.makeRawVisitInfo(md=metadata, exposureId=exposureId)
1370 exposure.getInfo().setVisitInfo(visitInfo)
1376 """Validate recipes for FitsStorage 1378 The recipes are supplemented with default values where appropriate. 1380 TODO: replace this custom validation code with Cerberus (DM-11846) 1384 recipes : `lsst.daf.persistence.Policy` 1385 FitsStorage recipes to validate. 1389 validated : `lsst.daf.base.PropertySet` 1390 Validated FitsStorage recipe. 1395 If validation fails. 1399 compressionSchema = {
1400 "algorithm":
"NONE",
1403 "quantizeLevel": 0.0,
1406 "algorithm":
"NONE",
1408 "maskPlanes": [
"NO_DATA"],
1410 "quantizeLevel": 4.0,
1417 def checkUnrecognized(entry, allowed, description):
1418 """Check to see if the entry contains unrecognised keywords""" 1419 unrecognized = set(entry.keys()) - set(allowed)
1422 "Unrecognized entries when parsing image compression recipe %s: %s" %
1423 (description, unrecognized))
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)
1434 for settings, schema
in ((
"compression", compressionSchema),
1435 (
"scaling", scalingSchema)):
1436 prefix = plane +
"." + settings
1437 if settings
not in recipes[name][plane]:
1439 rr.set(prefix +
"." + key, schema[key])
1441 entry = recipes[name][plane][settings]
1442 checkUnrecognized(entry, schema.keys(), name +
"->" + plane +
"->" + settings)
1444 value = type(schema[key])(entry[key])
if key
in entry
else schema[key]
1445 rr.set(prefix +
"." + key, value)
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 _extractDetectorName(self, dataId)
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 std_raw(self, item, dataId)
def backup(self, datasetType, dataId)
def _setupRegistry(self, name, description, path, policy, policyKey, storage, searchParents=True, posixIfNoSql=True)
def map_skypolicy(self, dataId)
def std_skypolicy(self, item, dataId)
def _defectLookup(self, dataId)
def bypass_camera(self, datasetType, pythonType, butlerLocation, dataId)
def _initMappings(self, policy, rootStorage=None, calibStorage=None, provided=None)
def getDefaultSubLevel(self, level)
def _transformId(self, dataId)
def getDefaultLevel(self)
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 _initWriteRecipes(self)
def getShortCcdName(ccdName)
def _getCcdKeyVal(self, dataId)
Utility functions.