21 from __future__
import annotations
23 __all__ = [
"ConvertRepoConfig",
"ConvertRepoTask",
"ConvertRepoSkyMapConfig"]
27 from dataclasses
import dataclass
28 from typing
import Iterable, Optional, List, Dict
31 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 .repoConverter
import ConversionSubset
41 from .rootRepoConverter
import RootRepoConverter
42 from .calibRepoConverter
import CalibRepoConverter
43 from .standardRepoConverter
import StandardRepoConverter
48 """Struct containing information about a skymap that may appear in a Gen2 53 """Name of the skymap used in Gen3 data IDs. 57 """Hash computed by `BaseSkyMap.getSha1`. 61 """Name of the skymap used in Gen3 data IDs. 65 """Whether this skymap has been found in at least one repository being 71 """Sub-config used to hold the parameters of a SkyMap. 75 This config only needs to exist because we can't put a 76 `~lsst.pex.config.RegistryField` directly inside a 77 `~lsst.pex.config.ConfigDictField`. 79 It needs to have its only field named "skyMap" for compatibility with the 80 configuration of `lsst.pipe.tasks.MakeSkyMapTask`, which we want so we can 81 use one config file in an obs package to configure both. 83 This name leads to unfortunate repetition with the field named 84 "skymap" that holds it - "skyMap[name].skyMap" - but that seems 87 skyMap = skyMapRegistry.makeField(
88 doc=
"Type and parameters for the SkyMap itself.",
94 raws = ConfigurableField(
95 "Configuration for subtask responsible for ingesting raws and adding " 96 "visit and exposure dimension entries.",
99 skyMaps = ConfigDictField(
100 "Mapping from Gen3 skymap name to the parameters used to construct a " 101 "BaseSkyMap instance. This will be used to associate names with " 102 "existing skymaps found in the Gen2 repo.",
104 itemtype=ConvertRepoSkyMapConfig,
107 rootSkyMapName = Field(
108 "Name of a Gen3 skymap (an entry in ``self.skyMaps``) to assume for " 109 "datasets in the root repository when no SkyMap is found there. ",
114 collections = DictField(
115 "Special collections (values) for certain dataset types (keys). " 116 "These are used in addition to rerun collections for datasets in " 117 "reruns. The 'raw' dataset must have an entry here if it is to be " 122 "deepCoadd_skyMap":
"skymaps",
123 "brightObjectMask":
"masks",
126 storageClasses = DictField(
127 "Mapping from dataset type name or Gen2 policy entry (e.g. 'python' " 128 "or 'persistable') to the Gen3 StorageClass name.",
135 "defects":
"Defects",
136 "BaseSkyMap":
"SkyMap",
137 "BaseCatalog":
"Catalog",
138 "BackgroundList":
"Background",
140 "MultilevelParquetTable":
"DataFrame",
141 "ParquetTable":
"DataFrame",
145 doRegisterInstrument = Field(
146 "If True (default), add dimension records for the Instrument and its " 147 "filters and detectors to the registry instead of assuming they are " 152 doWriteCuratedCalibrations = Field(
153 "If True (default), ingest human-curated calibrations directly via " 154 "the Instrument interface. Note that these calibrations are never " 155 "converted from Gen2 repositories.",
160 "The names of reference catalogs (subdirectories under ref_cats) to " 165 fileIgnorePatterns = ListField(
166 "Filename globs that should be ignored instead of being treated as " 169 default=[
"README.txt",
"*~?",
"butler.yaml",
"gen3.sqlite3",
170 "registry.sqlite3",
"calibRegistry.sqlite3",
"_mapper",
171 "_parent",
"repositoryCfg.yaml"]
173 datasetIncludePatterns = ListField(
174 "Glob-style patterns for dataset type names that should be converted.",
178 datasetIgnorePatterns = ListField(
179 "Glob-style patterns for dataset type names that should not be " 180 "converted despite matching a pattern in datasetIncludePatterns.",
185 "Key used for the Gen2 equivalent of 'detector' in data IDs.",
190 "If True (default), only convert datasets that are related to the " 191 "ingested visits. Ignored unless a list of visits is passed to " 196 curatedCalibrations = ListField(
197 "Dataset types that are handled by `Instrument.writeCuratedCalibrations()` " 198 "and thus should not be converted using the standard calibration " 199 "conversion system.",
202 "transmission_sensor",
203 "transmission_filter",
204 "transmission_optics",
205 "transmission_atmosphere",
211 return self.
raws.transfer
215 self.
raws.transfer = value
219 return self.
raws.instrument
223 self.
raws.instrument = value
233 """A task that converts one or more related Gen2 data repositories to a 234 single Gen3 data repository (with multiple collections). 238 config: `ConvertRepoConfig` 239 Configuration for this task. 240 butler3: `lsst.daf.butler.Butler` 241 Gen3 Butler instance that represents the data repository datasets will 242 be ingested into. The collection and/or run associated with this 243 Butler will be ignored in favor of collections/runs passed via config 246 Other keyword arguments are forwarded to the `Task` constructor. 250 Most of the work of converting repositories is delegated to instances of 251 the `RepoConverter` hierarchy. The `ConvertRepoTask` instance itself holds 252 only state that is relevant for all Gen2 repositories being ingested, while 253 each `RepoConverter` instance holds only state relevant for the conversion 254 of a single Gen2 repository. Both the task and the `RepoConverter` 255 instances are single use; `ConvertRepoTask.run` and most `RepoConverter` 256 methods may only be called once on a particular instance. 259 ConfigClass = ConvertRepoConfig
261 _DefaultName =
"convertRepo" 263 def __init__(self, config=None, *, butler3: Butler3, **kwds):
270 self.makeSubtask(
"raws", butler=butler3)
274 self.
instrument = doImport(self.config.instrument)()
277 for name, config
in self.config.skyMaps.items():
278 instance = config.skyMap.apply()
282 def _populateSkyMapDicts(self, name, instance):
283 struct =
ConfiguredSkyMap(name=name, sha1=instance.getSha1(), instance=instance)
288 """Return `True` if configuration indicates that the given dataset type 291 This method is intended to be called primarily by the 292 `RepoConverter` instances used interally by the task. 297 Name of the dataset type. 302 Whether the dataset should be included in the conversion. 305 any(fnmatch.fnmatchcase(datasetTypeName, pattern)
306 for pattern
in self.config.datasetIncludePatterns)
307 and not any(fnmatch.fnmatchcase(datasetTypeName, pattern)
308 for pattern
in self.config.datasetIgnorePatterns)
311 def useSkyMap(self, skyMap: BaseSkyMap, skyMapName: str) -> str:
312 """Indicate that a repository uses the given SkyMap. 314 This method is intended to be called primarily by the 315 `RepoConverter` instances used interally by the task. 319 skyMap : `lsst.skymap.BaseSkyMap` 320 SkyMap instance being used, typically retrieved from a Gen2 323 The name of the gen2 skymap, for error reporting. 328 The name of the skymap in Gen3 data IDs. 333 Raised if the specified skymap cannot be found. 335 sha1 = skyMap.getSha1()
340 except KeyError
as err:
341 msg = f
"SkyMap '{skyMapName}' with sha1={sha1} not included in configuration." 342 raise LookupError(msg)
from err
347 """Register all skymaps that have been marked as used. 349 This method is intended to be called primarily by the 350 `RepoConverter` instances used interally by the task. 354 subset : `ConversionSubset`, optional 355 Object that will be used to filter converted datasets by data ID. 356 If given, it will be updated with the tracts of this skymap that 357 overlap the visits in the subset. 361 struct.instance.register(struct.name, self.
registry)
362 if subset
is not None and self.config.relatedOnly:
363 subset.addSkyMap(self.
registry, struct.name)
366 """Indicate that a repository uses the given SkyPix dimension. 368 This method is intended to be called primarily by the 369 `RepoConverter` instances used interally by the task. 373 dimension : `lsst.daf.butler.SkyPixDimension` 374 Dimension represening a pixelization of the sky. 379 """Register all skymaps that have been marked as used. 381 This method is intended to be called primarily by the 382 `RepoConverter` instances used interally by the task. 386 subset : `ConversionSubset`, optional 387 Object that will be used to filter converted datasets by data ID. 388 If given, it will be updated with the pixelization IDs that 389 overlap the visits in the subset. 391 if subset
is not None and self.config.relatedOnly:
393 subset.addSkyPix(self.
registry, dimension)
395 def run(self, root: str, collections: List[str], *,
396 calibs: Dict[str, List[str]] =
None,
397 reruns: Dict[str, List[str]] =
None,
398 visits: Optional[Iterable[int]] =
None):
399 """Convert a group of related data repositories. 404 Complete path to the root Gen2 data repository. This should be 405 a data repository that includes a Gen2 registry and any raw files 406 and/or reference catalogs. 407 collections : `list` of `str` 408 Gen3 collections that datasets from the root repository should be 409 associated with. This should include any rerun collection that 410 these datasets should also be considered to be part of; because of 411 structural difference between Gen2 parent/child relationships and 412 Gen3 collections, these cannot be reliably inferred. 414 Dictionary mapping calibration repository path to the collections 415 that the repository's datasets should be associated with. The path 416 may be relative to ``root`` or absolute. Collections should 417 include child repository collections as appropriate (see 418 documentation for ``collections``). 420 Dictionary mapping rerun repository path to the collections that 421 the repository's datasets should be associated with. The path may 422 be relative to ``root`` or absolute. Collections should include 423 child repository collections as appropriate (see documentation for 425 visits : iterable of `int`, optional 426 The integer IDs of visits to convert. If not provided, all visits 427 in the Gen2 root repository will be converted. 434 if visits
is not None:
437 if self.config.relatedOnly:
438 self.log.warn(
"config.relatedOnly is True but all visits are being ingested; " 439 "no filtering will be done.")
447 if self.config.doRegisterInstrument:
455 rootConverter =
RootRepoConverter(task=self, root=root, collections=collections, subset=subset)
457 converters.append(rootConverter)
459 for root, collections
in calibs.items():
460 if not os.path.isabs(root):
461 root = os.path.join(rootConverter.root, root)
463 mapper=rootConverter.mapper,
464 subset=rootConverter.subset)
466 converters.append(converter)
468 for root, collections
in reruns.items():
469 if not os.path.isabs(root):
470 root = os.path.join(rootConverter.root, root)
472 subset=rootConverter.subset)
474 converters.append(converter)
491 for converter
in converters:
492 converter.insertDimensionData()
505 for converter
in converters:
506 converter.findDatasets()
509 for converter
in converters:
510 converter.expandDataIds()
513 for converter
in converters:
def isDatasetTypeIncluded
def _populateSkyMapDicts(self, name, instance)