21 from __future__
import annotations
23 __all__ = [
"ConvertRepoConfig",
"ConvertRepoTask",
"ConvertRepoSkyMapConfig",
"Rerun"]
27 from dataclasses
import dataclass
28 from typing
import Iterable, Optional, List, Dict
31 from lsst.daf.butler
import (
36 from lsst.pex.config
import Config, ConfigurableField, ConfigDictField, DictField, ListField, Field
37 from lsst.pipe.base
import Task
38 from lsst.skymap
import skyMapRegistry, BaseSkyMap
40 from ..ingest
import RawIngestTask
41 from ..defineVisits
import DefineVisitsTask
42 from .repoConverter
import ConversionSubset
43 from .rootRepoConverter
import RootRepoConverter
44 from .calibRepoConverter
import CalibRepoConverter
45 from .standardRepoConverter
import StandardRepoConverter
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",
266 doc=(
"Fully-qualified Python name of the `Instrument` subclass for "
267 "all converted datasets."),
275 return self.
raws.transfer
279 self.
raws.transfer = value
289 """A task that converts one or more related Gen2 data repositories to a
290 single Gen3 data repository (with multiple collections).
294 config: `ConvertRepoConfig`
295 Configuration for this task.
296 butler3: `lsst.daf.butler.Butler`
297 A writeable Gen3 Butler instance that represents the data repository
298 that datasets will be ingested into. If the 'raw' dataset is
299 configured to be included in the conversion, ``butler3.run`` should be
300 set to the name of the collection raws should be ingested into, and
301 ``butler3.collections`` should include a calibration collection from
302 which the ``camera`` dataset can be loaded, unless a calibration repo
303 is converted and ``doWriteCuratedCalibrations`` is `True`.
305 Other keyword arguments are forwarded to the `Task` constructor.
309 Most of the work of converting repositories is delegated to instances of
310 the `RepoConverter` hierarchy. The `ConvertRepoTask` instance itself holds
311 only state that is relevant for all Gen2 repositories being ingested, while
312 each `RepoConverter` instance holds only state relevant for the conversion
313 of a single Gen2 repository. Both the task and the `RepoConverter`
314 instances are single use; `ConvertRepoTask.run` and most `RepoConverter`
315 methods may only be called once on a particular instance.
318 ConfigClass = ConvertRepoConfig
320 _DefaultName =
"convertRepo"
322 def __init__(self, config=None, *, butler3: Butler3, **kwargs):
329 self.makeSubtask(
"raws", butler=butler3)
330 self.makeSubtask(
"defineVisits", butler=butler3)
337 for name, config
in self.config.skyMaps.items():
338 instance = config.skyMap.apply()
344 def _populateSkyMapDicts(self, name, instance):
345 struct =
ConfiguredSkyMap(name=name, sha1=instance.getSha1(), instance=instance)
350 """Return `True` if configuration indicates that the given dataset type
353 This method is intended to be called primarily by the
354 `RepoConverter` instances used interally by the task.
359 Name of the dataset type.
364 Whether the dataset should be included in the conversion.
367 any(fnmatch.fnmatchcase(datasetTypeName, pattern)
368 for pattern
in self.config.datasetIncludePatterns)
369 and not any(fnmatch.fnmatchcase(datasetTypeName, pattern)
370 for pattern
in self.config.datasetIgnorePatterns)
373 def useSkyMap(self, skyMap: BaseSkyMap, skyMapName: str) -> str:
374 """Indicate that a repository uses the given SkyMap.
376 This method is intended to be called primarily by the
377 `RepoConverter` instances used interally by the task.
381 skyMap : `lsst.skymap.BaseSkyMap`
382 SkyMap instance being used, typically retrieved from a Gen2
385 The name of the gen2 skymap, for error reporting.
390 The name of the skymap in Gen3 data IDs.
395 Raised if the specified skymap cannot be found.
397 sha1 = skyMap.getSha1()
402 except KeyError
as err:
403 msg = f
"SkyMap '{skyMapName}' with sha1={sha1} not included in configuration."
404 raise LookupError(msg)
from err
409 """Register all skymaps that have been marked as used.
411 This method is intended to be called primarily by the
412 `RepoConverter` instances used interally by the task.
416 subset : `ConversionSubset`, optional
417 Object that will be used to filter converted datasets by data ID.
418 If given, it will be updated with the tracts of this skymap that
419 overlap the visits in the subset.
423 struct.instance.register(struct.name, self.
registry)
424 if subset
is not None and self.config.relatedOnly:
425 subset.addSkyMap(self.
registry, struct.name)
428 """Indicate that a repository uses the given SkyPix dimension.
430 This method is intended to be called primarily by the
431 `RepoConverter` instances used interally by the task.
435 dimension : `lsst.daf.butler.SkyPixDimension`
436 Dimension represening a pixelization of the sky.
441 """Register all skymaps that have been marked as used.
443 This method is intended to be called primarily by the
444 `RepoConverter` instances used interally by the task.
448 subset : `ConversionSubset`, optional
449 Object that will be used to filter converted datasets by data ID.
450 If given, it will be updated with the pixelization IDs that
451 overlap the visits in the subset.
453 if subset
is not None and self.config.relatedOnly:
455 subset.addSkyPix(self.
registry, dimension)
457 def run(self, root: str, *,
458 calibs: Dict[str, str] =
None,
460 visits: Optional[Iterable[int]] =
None):
461 """Convert a group of related data repositories.
466 Complete path to the root Gen2 data repository. This should be
467 a data repository that includes a Gen2 registry and any raw files
468 and/or reference catalogs.
470 Dictionary mapping calibration repository path to the
471 `~lsst.daf.butler.CollectionType.RUN` collection that converted
472 datasets within it should be inserted into.
473 reruns : `list` of `Rerun`
474 Specifications for rerun (processing output) collections to
476 visits : iterable of `int`, optional
477 The integer IDs of visits to convert. If not provided, all visits
478 in the Gen2 root repository will be converted.
482 if visits
is not None:
485 if self.config.relatedOnly:
486 self.log.warn(
"config.relatedOnly is True but all visits are being ingested; "
487 "no filtering will be done.")
493 converters.append(rootConverter)
494 for calibRoot, run
in calibs.items():
495 if not os.path.isabs(calibRoot):
496 calibRoot = os.path.join(rootConverter.root, calibRoot)
498 mapper=rootConverter.mapper,
499 subset=rootConverter.subset)
500 converters.append(converter)
503 if not os.path.isabs(runRoot):
504 runRoot = os.path.join(rootConverter.root, runRoot)
506 subset=rootConverter.subset)
507 converters.append(converter)
510 if self.config.doRegisterInstrument:
520 rootConverter.runRawIngest()
527 if self.config.doWriteCuratedCalibrations:
528 for run
in calibs.values():
529 butler3 = Butler3(butler=self.
butler3, run=run)
534 rootConverter.runDefineVisits()
537 for converter
in converters:
550 for converter
in converters:
551 converter.insertDimensionData()
564 for converter
in converters:
565 converter.findDatasets()
568 for converter
in converters:
569 converter.expandDataIds()
572 for converter
in converters:
577 if spec.chainName
is not None:
578 self.
butler3.registry.registerCollection(spec.chainName, type=CollectionType.CHAINED)
579 chain = [spec.runName]
580 chain.extend(spec.parents)
581 chain.extend(rootConverter.getCollectionChain())
582 self.log.info(
"Defining %s from chain %s.", spec.chainName, chain)
583 self.
butler3.registry.setCollectionChain(spec.chainName, chain)