21 from __future__
import annotations
23 __all__ = [
"ConvertRepoConfig",
"ConvertRepoTask",
"ConvertRepoSkyMapConfig",
"Rerun"]
27 from dataclasses
import dataclass
28 from typing
import Iterable, Optional, List, Dict
30 from lsst.daf.butler
import (
35 from lsst.pex.config
import Config, ConfigurableField, ConfigDictField, DictField, ListField, Field
36 from lsst.pipe.base
import Task
37 from lsst.skymap
import skyMapRegistry, BaseSkyMap
39 from ..ingest
import RawIngestTask
40 from ..defineVisits
import DefineVisitsTask
41 from .repoConverter
import ConversionSubset
42 from .rootRepoConverter
import RootRepoConverter
43 from .calibRepoConverter
import CalibRepoConverter
44 from .standardRepoConverter
import StandardRepoConverter
45 from .._instrument
import Instrument
50 """Struct containing information about a skymap that may appear in a Gen2
55 """Name of the skymap used in Gen3 data IDs.
59 """Hash computed by `BaseSkyMap.getSha1`.
63 """Name of the skymap used in Gen3 data IDs.
67 """Whether this skymap has been found in at least one repository being
74 """Specification for a Gen2 processing-output repository to convert.
78 """Absolute or relative (to the root repository) path to the Gen2
83 """Name of the `~lsst.daf.butler.CollectionType.RUN` collection datasets
84 will be inserted into (`str`).
87 chainName: Optional[str]
88 """Name of a `~lsst.daf.butler.CollectionType.CHAINED` collection that will
89 combine this repository's datasets with those of its parent repositories
94 """Collection names associated with parent repositories, used to define the
95 chained collection (`list` [ `str` ]).
97 Ignored if `chainName` is `None`. Runs used in the root repo are
98 automatically included.
103 """Sub-config used to hold the parameters of a SkyMap.
107 This config only needs to exist because we can't put a
108 `~lsst.pex.config.RegistryField` directly inside a
109 `~lsst.pex.config.ConfigDictField`.
111 It needs to have its only field named "skyMap" for compatibility with the
112 configuration of `lsst.pipe.tasks.MakeSkyMapTask`, which we want so we can
113 use one config file in an obs package to configure both.
115 This name leads to unfortunate repetition with the field named
116 "skymap" that holds it - "skyMap[name].skyMap" - but that seems
119 skyMap = skyMapRegistry.makeField(
120 doc=
"Type and parameters for the SkyMap itself.",
126 raws = ConfigurableField(
127 "Configuration for subtask responsible for ingesting raws and adding "
128 "exposure dimension entries.",
129 target=RawIngestTask,
131 defineVisits = ConfigurableField(
132 "Configuration for the subtask responsible for defining visits from "
134 target=DefineVisitsTask,
136 skyMaps = ConfigDictField(
137 "Mapping from Gen3 skymap name to the parameters used to construct a "
138 "BaseSkyMap instance. This will be used to associate names with "
139 "existing skymaps found in the Gen2 repo.",
141 itemtype=ConvertRepoSkyMapConfig,
144 rootSkyMapName = Field(
145 "Name of a Gen3 skymap (an entry in ``self.skyMaps``) to assume for "
146 "datasets in the root repository when no SkyMap is found there. ",
152 "A mapping from dataset type name to the RUN collection they should "
153 "be inserted into. This must include all datasets that can be found "
154 "in the root repository; other repositories will use per-repository "
159 "deepCoadd_skyMap":
"skymaps",
160 "brightObjectMask":
"masks",
163 storageClasses = DictField(
164 "Mapping from dataset type name or Gen2 policy entry (e.g. 'python' "
165 "or 'persistable') to the Gen3 StorageClass name.",
172 "defects":
"Defects",
173 "crosstalk":
"CrosstalkCalib",
174 "BaseSkyMap":
"SkyMap",
175 "BaseCatalog":
"Catalog",
176 "BackgroundList":
"Background",
178 "MultilevelParquetTable":
"DataFrame",
179 "ParquetTable":
"DataFrame",
183 formatterClasses = DictField(
184 "Mapping from dataset type name to formatter class. "
185 "By default these are derived from the formatters listed in the"
186 " Gen3 datastore configuration.",
191 targetHandlerClasses = DictField(
192 "Mapping from dataset type name to target handler class.",
197 doRegisterInstrument = Field(
198 "If True (default), add dimension records for the Instrument and its "
199 "filters and detectors to the registry instead of assuming they are "
204 doWriteCuratedCalibrations = Field(
205 "If True (default), ingest human-curated calibrations directly via "
206 "the Instrument interface. Note that these calibrations are never "
207 "converted from Gen2 repositories.",
212 "The names of reference catalogs (subdirectories under ref_cats) to "
217 fileIgnorePatterns = ListField(
218 "Filename globs that should be ignored instead of being treated as "
221 default=[
"README.txt",
"*~?",
"butler.yaml",
"gen3.sqlite3",
222 "registry.sqlite3",
"calibRegistry.sqlite3",
"_mapper",
223 "_parent",
"repositoryCfg.yaml"]
225 rawDatasetType = Field(
226 "Gen2 dataset type to use for raw data.",
230 datasetIncludePatterns = ListField(
231 "Glob-style patterns for dataset type names that should be converted.",
235 datasetIgnorePatterns = ListField(
236 "Glob-style patterns for dataset type names that should not be "
237 "converted despite matching a pattern in datasetIncludePatterns.",
242 "Key used for the Gen2 equivalent of 'detector' in data IDs.",
247 "If True (default), only convert datasets that are related to the "
248 "ingested visits. Ignored unless a list of visits is passed to "
253 curatedCalibrations = ListField(
254 "Dataset types that are handled by `Instrument.writeCuratedCalibrations()` "
255 "and thus should not be converted using the standard calibration "
256 "conversion system.",
259 "transmission_sensor",
260 "transmission_filter",
261 "transmission_optics",
262 "transmission_atmosphere",
268 return self.
raws.transfer
272 self.
raws.transfer = value
282 """A task that converts one or more related Gen2 data repositories to a
283 single Gen3 data repository (with multiple collections).
287 config: `ConvertRepoConfig`
288 Configuration for this task.
289 butler3: `lsst.daf.butler.Butler`
290 A writeable Gen3 Butler instance that represents the data repository
291 that datasets will be ingested into. If the 'raw' dataset is
292 configured to be included in the conversion, ``butler3.run`` should be
293 set to the name of the collection raws should be ingested into, and
294 ``butler3.collections`` should include a calibration collection from
295 which the ``camera`` dataset can be loaded, unless a calibration repo
296 is converted and ``doWriteCuratedCalibrations`` is `True`.
298 Other keyword arguments are forwarded to the `Task` constructor.
302 Most of the work of converting repositories is delegated to instances of
303 the `RepoConverter` hierarchy. The `ConvertRepoTask` instance itself holds
304 only state that is relevant for all Gen2 repositories being ingested, while
305 each `RepoConverter` instance holds only state relevant for the conversion
306 of a single Gen2 repository. Both the task and the `RepoConverter`
307 instances are single use; `ConvertRepoTask.run` and most `RepoConverter`
308 methods may only be called once on a particular instance.
311 ConfigClass = ConvertRepoConfig
313 _DefaultName =
"convertRepo"
315 def __init__(self, config=None, *, butler3: Butler3, instrument: Instrument, **kwargs):
322 self.makeSubtask(
"raws", butler=butler3)
323 self.makeSubtask(
"defineVisits", butler=butler3)
330 for name, config
in self.config.skyMaps.items():
331 instance = config.skyMap.apply()
337 def _populateSkyMapDicts(self, name, instance):
338 struct =
ConfiguredSkyMap(name=name, sha1=instance.getSha1(), instance=instance)
343 """Return `True` if configuration indicates that the given dataset type
346 This method is intended to be called primarily by the
347 `RepoConverter` instances used interally by the task.
352 Name of the dataset type.
357 Whether the dataset should be included in the conversion.
360 any(fnmatch.fnmatchcase(datasetTypeName, pattern)
361 for pattern
in self.config.datasetIncludePatterns)
362 and not any(fnmatch.fnmatchcase(datasetTypeName, pattern)
363 for pattern
in self.config.datasetIgnorePatterns)
366 def useSkyMap(self, skyMap: BaseSkyMap, skyMapName: str) -> str:
367 """Indicate that a repository uses the given SkyMap.
369 This method is intended to be called primarily by the
370 `RepoConverter` instances used interally by the task.
374 skyMap : `lsst.skymap.BaseSkyMap`
375 SkyMap instance being used, typically retrieved from a Gen2
378 The name of the gen2 skymap, for error reporting.
383 The name of the skymap in Gen3 data IDs.
388 Raised if the specified skymap cannot be found.
390 sha1 = skyMap.getSha1()
395 except KeyError
as err:
396 msg = f
"SkyMap '{skyMapName}' with sha1={sha1} not included in configuration."
397 raise LookupError(msg)
from err
402 """Register all skymaps that have been marked as used.
404 This method is intended to be called primarily by the
405 `RepoConverter` instances used interally by the task.
409 subset : `ConversionSubset`, optional
410 Object that will be used to filter converted datasets by data ID.
411 If given, it will be updated with the tracts of this skymap that
412 overlap the visits in the subset.
416 struct.instance.register(struct.name, self.
registry)
417 if subset
is not None and self.config.relatedOnly:
418 subset.addSkyMap(self.
registry, struct.name)
421 """Indicate that a repository uses the given SkyPix dimension.
423 This method is intended to be called primarily by the
424 `RepoConverter` instances used interally by the task.
428 dimension : `lsst.daf.butler.SkyPixDimension`
429 Dimension represening a pixelization of the sky.
434 """Register all skymaps that have been marked as used.
436 This method is intended to be called primarily by the
437 `RepoConverter` instances used interally by the task.
441 subset : `ConversionSubset`, optional
442 Object that will be used to filter converted datasets by data ID.
443 If given, it will be updated with the pixelization IDs that
444 overlap the visits in the subset.
446 if subset
is not None and self.config.relatedOnly:
448 subset.addSkyPix(self.
registry, dimension)
450 def run(self, root: str, *,
451 calibs: Dict[str, str] =
None,
453 visits: Optional[Iterable[int]] =
None):
454 """Convert a group of related data repositories.
459 Complete path to the root Gen2 data repository. This should be
460 a data repository that includes a Gen2 registry and any raw files
461 and/or reference catalogs.
463 Dictionary mapping calibration repository path to the
464 `~lsst.daf.butler.CollectionType.RUN` collection that converted
465 datasets within it should be inserted into.
466 reruns : `list` of `Rerun`
467 Specifications for rerun (processing output) collections to
469 visits : iterable of `int`, optional
470 The integer IDs of visits to convert. If not provided, all visits
471 in the Gen2 root repository will be converted.
475 if visits
is not None:
478 if self.config.relatedOnly:
479 self.log.warn(
"config.relatedOnly is True but all visits are being ingested; "
480 "no filtering will be done.")
486 converters.append(rootConverter)
487 for calibRoot, run
in calibs.items():
488 if not os.path.isabs(calibRoot):
489 calibRoot = os.path.join(rootConverter.root, calibRoot)
491 mapper=rootConverter.mapper,
492 subset=rootConverter.subset)
493 converters.append(converter)
496 if not os.path.isabs(runRoot):
497 runRoot = os.path.join(rootConverter.root, runRoot)
499 subset=rootConverter.subset)
500 converters.append(converter)
503 if self.config.doRegisterInstrument:
513 rootConverter.runRawIngest()
520 if self.config.doWriteCuratedCalibrations:
521 for run
in calibs.values():
522 butler3 = Butler3(butler=self.
butler3, run=run)
527 rootConverter.runDefineVisits()
530 for converter
in converters:
543 for converter
in converters:
544 converter.insertDimensionData()
557 for converter
in converters:
558 converter.findDatasets()
561 for converter
in converters:
562 converter.expandDataIds()
565 for converter
in converters:
570 if spec.chainName
is not None:
571 self.
butler3.registry.registerCollection(spec.chainName, type=CollectionType.CHAINED)
572 chain = [spec.runName]
573 chain.extend(spec.parents)
574 chain.extend(rootConverter.getCollectionChain())
575 self.log.info(
"Defining %s from chain %s.", spec.chainName, chain)
576 self.
butler3.registry.setCollectionChain(spec.chainName, chain)