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1# 

2# LSST Data Management System 

3# 

4# Copyright 2008-2017 AURA/LSST. 

5# 

6# This product includes software developed by the 

7# LSST Project (http://www.lsst.org/). 

8# 

9# This program is free software: you can redistribute it and/or modify 

10# it under the terms of the GNU General Public License as published by 

11# the Free Software Foundation, either version 3 of the License, or 

12# (at your option) any later version. 

13# 

14# This program is distributed in the hope that it will be useful, 

15# but WITHOUT ANY WARRANTY; without even the implied warranty of 

16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

17# GNU General Public License for more details. 

18# 

19# You should have received a copy of the LSST License Statement and 

20# the GNU General Public License along with this program. If not, 

21# see <https://www.lsstcorp.org/LegalNotices/>. 

22# 

23 

24__all__ = ["getRefFluxField", "getRefFluxKeys", "LoadReferenceObjectsTask", "LoadReferenceObjectsConfig", 

25 "ReferenceObjectLoader"] 

26 

27import abc 

28import itertools 

29 

30import astropy.time 

31import astropy.units 

32import numpy 

33 

34import lsst.geom 

35import lsst.afw.table as afwTable 

36import lsst.pex.config as pexConfig 

37import lsst.pex.exceptions as pexExceptions 

38import lsst.pipe.base as pipeBase 

39import lsst.pex.exceptions as pexExcept 

40import lsst.log 

41from lsst import geom 

42from lsst import sphgeom 

43from lsst.daf.base import PropertyList 

44 

45 

46def isOldFluxField(name, units): 

47 """Return True if this name/units combination corresponds to an 

48 "old-style" reference catalog flux field. 

49 """ 

50 unitsCheck = units != 'nJy' # (units == 'Jy' or units == '' or units == '?') 

51 isFlux = name.endswith('_flux') 

52 isFluxSigma = name.endswith('_fluxSigma') 

53 isFluxErr = name.endswith('_fluxErr') 

54 return (isFlux or isFluxSigma or isFluxErr) and unitsCheck 

55 

56 

57def hasNanojanskyFluxUnits(schema): 

58 """Return True if the units of all flux and fluxErr are correct (nJy). 

59 """ 

60 for field in schema: 

61 if isOldFluxField(field.field.getName(), field.field.getUnits()): 61 ↛ 62line 61 didn't jump to line 62, because the condition on line 61 was never true

62 return False 

63 return True 

64 

65 

66def getFormatVersionFromRefCat(refCat): 

67 """"Return the format version stored in a reference catalog header. 

68 

69 Parameters 

70 ---------- 

71 refCat : `lsst.afw.table.SimpleCatalog` 

72 Reference catalog to inspect. 

73 

74 Returns 

75 ------- 

76 version : `int` or `None` 

77 Format version integer, or `None` if the catalog has no metadata 

78 or the metadata does not include a "REFCAT_FORMAT_VERSION" key. 

79 """ 

80 md = refCat.getMetadata() 

81 if md is None: 81 ↛ 82line 81 didn't jump to line 82, because the condition on line 81 was never true

82 return None 

83 try: 

84 return md.getScalar("REFCAT_FORMAT_VERSION") 

85 except KeyError: 

86 return None 

87 

88 

89def convertToNanojansky(catalog, log, doConvert=True): 

90 """Convert fluxes in a catalog from jansky to nanojansky. 

91 

92 Parameters 

93 ---------- 

94 catalog : `lsst.afw.table.SimpleCatalog` 

95 The catalog to convert. 

96 log : `lsst.log.Log` 

97 Log to send messages to. 

98 doConvert : `bool`, optional 

99 Return a converted catalog, or just identify the fields that need to be converted? 

100 This supports the "write=False" mode of `bin/convert_to_nJy.py`. 

101 

102 Returns 

103 ------- 

104 catalog : `lsst.afw.table.SimpleCatalog` or None 

105 The converted catalog, or None if ``doConvert`` is False. 

106 

107 Notes 

108 ----- 

109 Support for old units in reference catalogs will be removed after the 

110 release of late calendar year 2019. 

111 Use `meas_algorithms/bin/convert_to_nJy.py` to update your reference catalog. 

112 """ 

113 # Do not share the AliasMap: for refcats, that gets created when the 

114 # catalog is read from disk and should not be propagated. 

115 mapper = lsst.afw.table.SchemaMapper(catalog.schema, shareAliasMap=False) 

116 mapper.addMinimalSchema(lsst.afw.table.SimpleTable.makeMinimalSchema()) 

117 input_fields = [] 

118 output_fields = [] 

119 for field in catalog.schema: 

120 oldName = field.field.getName() 

121 oldUnits = field.field.getUnits() 

122 if isOldFluxField(oldName, oldUnits): 

123 units = 'nJy' 

124 # remap Sigma flux fields to Err, so we can drop the alias 

125 if oldName.endswith('_fluxSigma'): 

126 name = oldName.replace('_fluxSigma', '_fluxErr') 

127 else: 

128 name = oldName 

129 newField = lsst.afw.table.Field[field.dtype](name, field.field.getDoc(), units) 

130 mapper.addMapping(field.getKey(), newField) 

131 input_fields.append(field.field) 

132 output_fields.append(newField) 

133 else: 

134 mapper.addMapping(field.getKey()) 

135 

136 fluxFieldsStr = '; '.join("(%s, '%s')" % (field.getName(), field.getUnits()) for field in input_fields) 

137 

138 if doConvert: 

139 newSchema = mapper.getOutputSchema() 

140 output = lsst.afw.table.SimpleCatalog(newSchema) 

141 output.extend(catalog, mapper=mapper) 

142 for field in output_fields: 

143 output[field.getName()] *= 1e9 

144 log.info(f"Converted refcat flux fields to nJy (name, units): {fluxFieldsStr}") 

145 return output 

146 else: 

147 log.info(f"Found old-style refcat flux fields (name, units): {fluxFieldsStr}") 

148 return None 

149 

150 

151class _FilterCatalog: 

152 """This is a private helper class which filters catalogs by 

153 row based on the row being inside the region used to initialize 

154 the class. 

155 

156 Parameters 

157 ---------- 

158 region : `lsst.sphgeom.Region` 

159 The spatial region which all objects should lie within 

160 """ 

161 def __init__(self, region): 

162 self.region = region 

163 

164 def __call__(self, refCat, catRegion): 

165 """This call method on an instance of this class takes in a reference 

166 catalog, and the region from which the catalog was generated. 

167 

168 If the catalog region is entirely contained within the region used to 

169 initialize this class, then all the entries in the catalog must be 

170 within the region and so the whole catalog is returned. 

171 

172 If the catalog region is not entirely contained, then the location for 

173 each record is tested against the region used to initialize the class. 

174 Records which fall inside this region are added to a new catalog, and 

175 this catalog is then returned. 

176 

177 Parameters 

178 --------- 

179 refCat : `lsst.afw.table.SourceCatalog` 

180 SourceCatalog to be filtered. 

181 catRegion : `lsst.sphgeom.Region` 

182 Region in which the catalog was created 

183 """ 

184 if catRegion.isWithin(self.region): 

185 # no filtering needed, region completely contains refcat 

186 return refCat 

187 

188 filteredRefCat = type(refCat)(refCat.table) 

189 for record in refCat: 

190 if self.region.contains(record.getCoord().getVector()): 

191 filteredRefCat.append(record) 

192 return filteredRefCat 

193 

194 

195class ReferenceObjectLoader: 

196 """ This class facilitates loading reference catalogs with gen 3 middleware 

197 

198 The middleware preflight solver will create a list of datarefs that may 

199 possibly overlap a given region. These datarefs are then used to construct 

200 and instance of this class. The class instance should then be passed into 

201 a task which needs reference catalogs. These tasks should then determine 

202 the exact region of the sky reference catalogs will be loaded for, and 

203 call a corresponding method to load the reference objects. 

204 """ 

205 def __init__(self, dataIds, refCats, config, log=None): 

206 """ Constructs an instance of ReferenceObjectLoader 

207 

208 Parameters 

209 ---------- 

210 dataIds : iterable of `lsst.daf.butler.DataIds` 

211 An iterable object of DataSetRefs which point to reference catalogs 

212 in a gen 3 repository 

213 refCats : Iterable of `lsst.daf.butler.DeferedDatasetHandle` 

214 Handles to load refCats on demand 

215 log : `lsst.log.Log` 

216 Logger object used to write out messages. If `None` (default) the default 

217 lsst logger will be used 

218 

219 """ 

220 self.dataIds = dataIds 

221 self.refCats = refCats 

222 self.log = log or lsst.log.Log.getDefaultLogger() 

223 self.config = config 

224 

225 @staticmethod 

226 def _makeBoxRegion(BBox, wcs, BBoxPadding): 

227 outerLocalBBox = geom.Box2D(BBox) 

228 innerLocalBBox = geom.Box2D(BBox) 

229 

230 # Grow the bounding box to make sure the spherical geometry bbox will contain 

231 # the same region, as non-padded boxes may contain different regions because of optical distortion. 

232 # Also create an inner region that is sure to be inside the bbox 

233 outerLocalBBox.grow(BBoxPadding) 

234 innerLocalBBox.grow(-1*BBoxPadding) 

235 

236 # Handle the fact that the inner bounding box shrunk to a zero sized region in at least one 

237 # dimension, in which case all reference catalogs must be checked fully against the input 

238 # bounding box 

239 if innerLocalBBox.getDimensions() == geom.Extent2D(0, 0): 

240 innerSkyRegion = sphgeom.Box() 

241 else: 

242 innerBoxCorners = innerLocalBBox.getCorners() 

243 innerSphCorners = [wcs.pixelToSky(corner).getVector() for corner in innerBoxCorners] 

244 

245 innerSkyRegion = sphgeom.ConvexPolygon(innerSphCorners) 

246 

247 # Convert the corners of the box to sky coordinates 

248 outerBoxCorners = outerLocalBBox.getCorners() 

249 outerSphCorners = [wcs.pixelToSky(corner).getVector() for corner in outerBoxCorners] 

250 

251 outerSkyRegion = sphgeom.ConvexPolygon(outerSphCorners) 

252 

253 return innerSkyRegion, outerSkyRegion, innerSphCorners, outerSphCorners 

254 

255 def loadPixelBox(self, bbox, wcs, filterName=None, epoch=None, photoCalib=None, bboxPadding=100): 

256 """Load reference objects that are within a pixel-based rectangular region 

257 

258 This algorithm works by creating a spherical box whose corners correspond 

259 to the WCS converted corners of the input bounding box (possibly padded). 

260 It then defines a filtering function which will look at a reference 

261 objects pixel position and accept objects that lie within the specified 

262 bounding box. 

263 

264 The spherical box region and filtering function are passed to the generic 

265 loadRegion method which will load and filter the reference objects from 

266 the datastore and return a single catalog containing all reference objects 

267 

268 Parameters 

269 ---------- 

270 bbox : `lsst.geom.box2I` 

271 Box which bounds a region in pixel space 

272 wcs : `lsst.afw.geom.SkyWcs` 

273 Wcs object defining the pixel to sky (and inverse) transform for the space 

274 of pixels of the supplied bbox 

275 filterName : `str` 

276 Name of camera filter, or None or blank for the default filter 

277 epoch : `astropy.time.Time` (optional) 

278 Epoch to which to correct proper motion and parallax, 

279 or None to not apply such corrections. 

280 photoCalib : None 

281 Deprecated and ignored, only included for api compatibility 

282 bboxPadding : `int` 

283 Number describing how much to pad the input bbox by (in pixels), defaults 

284 to 100. This parameter is necessary because optical distortions in telescopes 

285 can cause a rectangular pixel grid to map into a non "rectangular" spherical 

286 region in sky coordinates. This padding is used to create a spherical 

287 "rectangle", which will for sure enclose the input box. This padding is only 

288 used to determine if the reference catalog for a sky patch will be loaded from 

289 the data store, this function will filter out objects which lie within the 

290 padded region but fall outside the input bounding box region. 

291 

292 Returns 

293 ------- 

294 referenceCatalog : `lsst.afw.table.SimpleCatalog` 

295 Catalog containing reference objects inside the specified bounding box 

296 

297 Raises 

298 ------ 

299 `lsst.pex.exception.RuntimeError` 

300 Raised if no reference catalogs could be found for the specified region 

301 

302 `lsst.pex.exception.TypeError` 

303 Raised if the loaded reference catalogs do not have matching schemas 

304 """ 

305 innerSkyRegion, outerSkyRegion, _, _ = self._makeBoxRegion(bbox, wcs, bboxPadding) 

306 

307 def _filterFunction(refCat, region): 

308 # Add columns to the reference catalog relating to center positions and use afwTable 

309 # to populate those columns 

310 refCat = self.remapReferenceCatalogSchema(refCat, position=True) 

311 afwTable.updateRefCentroids(wcs, refCat) 

312 # no need to filter the catalog if it is sure that it is entirely contained in the region 

313 # defined by given bbox 

314 if innerSkyRegion.contains(region): 

315 return refCat 

316 # Create a new reference catalog, and populate it with records which fall inside the bbox 

317 filteredRefCat = type(refCat)(refCat.table) 

318 centroidKey = afwTable.Point2DKey(refCat.schema['centroid']) 

319 for record in refCat: 

320 pixCoords = record[centroidKey] 

321 if bbox.contains(geom.Point2I(pixCoords)): 

322 filteredRefCat.append(record) 

323 return filteredRefCat 

324 return self.loadRegion(outerSkyRegion, filtFunc=_filterFunction, epoch=epoch, filterName=filterName) 

325 

326 def loadRegion(self, region, filtFunc=None, filterName=None, epoch=None): 

327 """ Load reference objects within a specified region 

328 

329 This function loads the DataIds used to construct an instance of this class 

330 which intersect or are contained within the specified region. The reference 

331 catalogs which intersect but are not fully contained within the input region are 

332 further filtered by the specified filter function. This function will return a 

333 single source catalog containing all reference objects inside the specified region. 

334 

335 Parameters 

336 ---------- 

337 region : `lsst.sphgeom.Region` 

338 This can be any type that is derived from `lsst.sphgeom.region` and should 

339 define the spatial region for which reference objects are to be loaded. 

340 filtFunc : callable 

341 This optional parameter should be a callable object that takes a reference 

342 catalog and its corresponding region as parameters, filters the catalog by 

343 some criteria and returns the filtered reference catalog. If the value is 

344 left as the default (None) than an internal filter function is used which 

345 filters according to if a reference object falls within the input region. 

346 filterName : `str` 

347 Name of camera filter, or None or blank for the default filter 

348 epoch : `astropy.time.Time` (optional) 

349 Epoch to which to correct proper motion and parallax, 

350 or None to not apply such corrections. 

351 

352 Returns 

353 ------- 

354 referenceCatalog : `lsst.afw.table.SourceCatalog` 

355 Catalog containing reference objects which intersect the input region, 

356 filtered by the specified filter function 

357 

358 Raises 

359 ------ 

360 `lsst.pex.exception.RuntimeError` 

361 Raised if no reference catalogs could be found for the specified region 

362 

363 `lsst.pex.exception.TypeError` 

364 Raised if the loaded reference catalogs do not have matching schemas 

365 

366 """ 

367 regionBounding = region.getBoundingBox() 

368 self.log.info("Loading reference objects from region bounded by {}, {} lat lon".format( 

369 regionBounding.getLat(), regionBounding.getLon())) 

370 if filtFunc is None: 

371 filtFunc = _FilterCatalog(region) 

372 # filter out all the regions supplied by the constructor that do not overlap 

373 overlapList = [] 

374 for dataId, refCat in zip(self.dataIds, self.refCats): 

375 # SphGeom supports some objects intersecting others, but is not symmetric, 

376 # try the intersect operation in both directions 

377 try: 

378 intersects = dataId.region.intersects(region) 

379 except TypeError: 

380 intersects = region.intersects(dataId.region) 

381 

382 if intersects: 

383 overlapList.append((dataId, refCat)) 

384 

385 if len(overlapList) == 0: 

386 raise pexExceptions.RuntimeError("No reference tables could be found for input region") 

387 

388 firstCat = overlapList[0][1].get() 

389 refCat = filtFunc(firstCat, overlapList[0][0].region) 

390 trimmedAmount = len(firstCat) - len(refCat) 

391 

392 # Load in the remaining catalogs 

393 for dataId, inputRefCat in overlapList[1:]: 

394 tmpCat = inputRefCat.get() 

395 

396 if tmpCat.schema != firstCat.schema: 

397 raise pexExceptions.TypeError("Reference catalogs have mismatching schemas") 

398 

399 filteredCat = filtFunc(tmpCat, dataId.region) 

400 refCat.extend(filteredCat) 

401 trimmedAmount += len(tmpCat) - len(filteredCat) 

402 

403 self.log.debug(f"Trimmed {trimmedAmount} out of region objects, leaving {len(refCat)}") 

404 self.log.info(f"Loaded {len(refCat)} reference objects") 

405 

406 # Ensure that the loaded reference catalog is continuous in memory 

407 if not refCat.isContiguous(): 

408 refCat = refCat.copy(deep=True) 

409 

410 if epoch is not None and "pm_ra" in refCat.schema: 

411 # check for a catalog in a non-standard format 

412 if isinstance(refCat.schema["pm_ra"].asKey(), lsst.afw.table.KeyAngle): 

413 applyProperMotionsImpl(self.log, refCat, epoch) 

414 else: 

415 self.log.warn("Catalog pm_ra field is not an Angle; not applying proper motion") 

416 

417 # Verify the schema is in the correct units and has the correct version; automatically convert 

418 # it with a warning if this is not the case. 

419 if not hasNanojanskyFluxUnits(refCat.schema) or not getFormatVersionFromRefCat(refCat) >= 1: 

420 self.log.warn("Found version 0 reference catalog with old style units in schema.") 

421 self.log.warn("run `meas_algorithms/bin/convert_refcat_to_nJy.py` to convert fluxes to nJy.") 

422 self.log.warn("See RFC-575 for more details.") 

423 refCat = convertToNanojansky(refCat, self.log) 

424 

425 expandedCat = self.remapReferenceCatalogSchema(refCat, position=True) 

426 

427 # Add flux aliases 

428 expandedCat = self.addFluxAliases(expandedCat, self.config.defaultFilter, self.config.filterMap) 

429 

430 # Ensure that the returned reference catalog is continuous in memory 

431 if not expandedCat.isContiguous(): 

432 expandedCat = expandedCat.copy(deep=True) 

433 

434 fluxField = getRefFluxField(schema=expandedCat.schema, filterName=filterName) 

435 return pipeBase.Struct(refCat=expandedCat, fluxField=fluxField) 

436 

437 def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None): 

438 """Load reference objects that lie within a circular region on the sky 

439 

440 This method constructs a circular region from an input center and angular radius, 

441 loads reference catalogs which are contained in or intersect the circle, and 

442 filters reference catalogs which intersect down to objects which lie within 

443 the defined circle. 

444 

445 Parameters 

446 ---------- 

447 ctrCoord : `lsst.geom.SpherePoint` 

448 Point defining the center of the circular region 

449 radius : `lsst.geom.Angle` 

450 Defines the angular radius of the circular region 

451 filterName : `str` 

452 Name of camera filter, or None or blank for the default filter 

453 epoch : `astropy.time.Time` (optional) 

454 Epoch to which to correct proper motion and parallax, 

455 or None to not apply such corrections. 

456 

457 Returns 

458 ------- 

459 referenceCatalog : `lsst.afw.table.SourceCatalog` 

460 Catalog containing reference objects inside the specified bounding box 

461 

462 Raises 

463 ------ 

464 `lsst.pex.exception.RuntimeError` 

465 Raised if no reference catalogs could be found for the specified region 

466 

467 `lsst.pex.exception.TypeError` 

468 Raised if the loaded reference catalogs do not have matching schemas 

469 

470 """ 

471 centerVector = ctrCoord.getVector() 

472 sphRadius = sphgeom.Angle(radius.asRadians()) 

473 circularRegion = sphgeom.Circle(centerVector, sphRadius) 

474 return self.loadRegion(circularRegion, filterName=filterName, epoch=epoch) 

475 

476 def joinMatchListWithCatalog(self, matchCat, sourceCat): 

477 """Relink an unpersisted match list to sources and reference 

478 objects. 

479 

480 A match list is persisted and unpersisted as a catalog of IDs 

481 produced by afw.table.packMatches(), with match metadata 

482 (as returned by the astrometry tasks) in the catalog's metadata 

483 attribute. This method converts such a match catalog into a match 

484 list, with links to source records and reference object records. 

485 

486 Parameters 

487 ---------- 

488 matchCat : `lsst.afw.table.BaseCatalog` 

489 Unpersisted packed match list. 

490 ``matchCat.table.getMetadata()`` must contain match metadata, 

491 as returned by the astrometry tasks. 

492 sourceCat : `lsst.afw.table.SourceCatalog` 

493 Source catalog. As a side effect, the catalog will be sorted 

494 by ID. 

495 

496 Returns 

497 ------- 

498 matchList : `lsst.afw.table.ReferenceMatchVector` 

499 Match list. 

500 """ 

501 return joinMatchListWithCatalogImpl(self, matchCat, sourceCat) 

502 

503 @classmethod 

504 def getMetadataBox(cls, bbox, wcs, filterName=None, photoCalib=None, epoch=None, bboxPadding=100): 

505 """Return metadata about the load 

506 

507 This metadata is used for reloading the catalog (e.g., for 

508 reconstituting a normalised match list.) 

509 

510 Parameters 

511 ---------- 

512 bbox : `lsst.geom.Box2I` 

513 Bounding bos for the pixels 

514 wcs : `lsst.afw.geom.SkyWcs 

515 WCS object 

516 filterName : `str` or None 

517 filterName of the camera filter, or None or blank for the default filter 

518 photoCalib : None 

519 Deprecated, only included for api compatibility 

520 epoch : `astropy.time.Time` (optional) 

521 Epoch to which to correct proper motion and parallax, 

522 or None to not apply such corrections. 

523 bboxPadding : `int` 

524 Number describing how much to pad the input bbox by (in pixels), defaults 

525 to 100. This parameter is necessary because optical distortions in telescopes 

526 can cause a rectangular pixel grid to map into a non "rectangular" spherical 

527 region in sky coordinates. This padding is used to create a spherical 

528 "rectangle", which will for sure enclose the input box. This padding is only 

529 used to determine if the reference catalog for a sky patch will be loaded from 

530 the data store, this function will filter out objects which lie within the 

531 padded region but fall outside the input bounding box region. 

532 Returns 

533 ------- 

534 md : `lsst.daf.base.PropertyList` 

535 """ 

536 _, _, innerCorners, outerCorners = cls._makeBoxRegion(bbox, wcs, bboxPadding) 

537 md = PropertyList() 

538 for box, corners in zip(("INNER", "OUTER"), (innerCorners, outerCorners)): 

539 for (name, corner) in zip(("UPPER_LEFT", "UPPER_RIGHT", "LOWER_LEFT", "LOWER_RIGHT"), 

540 corners): 

541 md.add(f"{box}_{name}_RA", geom.SpherePoint(corner).getRa().asDegrees(), f"{box}_corner") 

542 md.add(f"{box}_{name}_DEC", geom.SpherePoint(corner).getDec().asDegrees(), f"{box}_corner") 

543 md.add("SMATCHV", 1, 'SourceMatchVector version number') 

544 filterName = "UNKNOWN" if filterName is None else str(filterName) 

545 md.add('FILTER', filterName, 'filter name for photometric data') 

546 md.add('EPOCH', "NONE" if epoch is None else epoch.mjd, 'Epoch (TAI MJD) for catalog') 

547 return md 

548 

549 @staticmethod 

550 def getMetadataCircle(coord, radius, filterName, photoCalib=None, epoch=None): 

551 """Return metadata about the load 

552 

553 This metadata is used for reloading the catalog (e.g. for reconstituting 

554 a normalized match list.) 

555 

556 Parameters 

557 ---------- 

558 coord : `lsst.geom.SpherePoint` 

559 ICRS center of a circle 

560 radius : `lsst.geom.angle` 

561 radius of a circle 

562 filterName : `str` or None 

563 filterName of the camera filter, or None or blank for the default filter 

564 photoCalib : None 

565 Deprecated, only included for api compatibility 

566 epoch : `astropy.time.Time` (optional) 

567 Epoch to which to correct proper motion and parallax, 

568 or None to not apply such corrections. 

569 

570 Returns 

571 ------- 

572 md : `lsst.daf.base.PropertyList` 

573 """ 

574 md = PropertyList() 

575 md.add('RA', coord.getRa().asDegrees(), 'field center in degrees') 

576 md.add('DEC', coord.getDec().asDegrees(), 'field center in degrees') 

577 md.add('RADIUS', radius.asDegrees(), 'field radius in degrees, minimum') 

578 md.add('SMATCHV', 1, 'SourceMatchVector version number') 

579 filterName = "UNKNOWN" if filterName is None else str(filterName) 

580 md.add('FILTER', filterName, 'filter name for photometric data') 

581 md.add('EPOCH', "NONE" if epoch is None else epoch.mjd, 'Epoch (TAI MJD) for catalog') 

582 return md 

583 

584 @staticmethod 

585 def addFluxAliases(refCat, defaultFilter, filterReferenceMap): 

586 """This function creates a new catalog containing the information of the input refCat 

587 as well as added flux columns and aliases between camera and reference flux. 

588 

589 Parameters 

590 ---------- 

591 refCat : `lsst.afw.table.SimpleCatalog` 

592 Catalog of reference objects 

593 defaultFilter : `str` 

594 Name of the default reference filter 

595 filterReferenceMap : `dict` of `str` 

596 Dictionary with keys corresponding to a filter name, and values which 

597 correspond to the name of the reference filter. 

598 

599 Returns 

600 ------- 

601 refCat : `lsst.afw.table.SimpleCatalog` 

602 Reference catalog with columns added to track reference filters 

603 

604 Raises 

605 ------ 

606 `RuntimeError` 

607 If specified reference filter name is not a filter specifed as a key in the 

608 reference filter map. 

609 """ 

610 refCat = ReferenceObjectLoader.remapReferenceCatalogSchema(refCat, 

611 filterNameList=filterReferenceMap.keys()) 

612 aliasMap = refCat.schema.getAliasMap() 

613 if filterReferenceMap is None: 

614 filterReferenceMap = {} 

615 for filterName, refFilterName in itertools.chain([(None, defaultFilter)], 

616 filterReferenceMap.items()): 

617 if refFilterName: 

618 camFluxName = filterName + "_camFlux" if filterName is not None else "camFlux" 

619 refFluxName = refFilterName + "_flux" 

620 if refFluxName not in refCat.schema: 

621 raise RuntimeError("Unknown reference filter %s" % (refFluxName,)) 

622 aliasMap.set(camFluxName, refFluxName) 

623 

624 refFluxErrName = refFluxName + "Err" 

625 camFluxErrName = camFluxName + "Err" 

626 aliasMap.set(camFluxErrName, refFluxErrName) 

627 

628 return refCat 

629 

630 @staticmethod 

631 def remapReferenceCatalogSchema(refCat, *, filterNameList=None, position=False, photometric=False): 

632 """This function takes in a reference catalog and creates a new catalog with additional 

633 columns defined the remaining function arguments. 

634 

635 Parameters 

636 ---------- 

637 refCat : `lsst.afw.table.SimpleCatalog` 

638 Reference catalog to map to new catalog 

639 

640 Returns 

641 ------- 

642 expandedCat : `lsst.afw.table.SimpleCatalog` 

643 Deep copy of input reference catalog with additional columns added 

644 """ 

645 mapper = afwTable.SchemaMapper(refCat.schema, True) 

646 mapper.addMinimalSchema(refCat.schema, True) 

647 mapper.editOutputSchema().disconnectAliases() 

648 if filterNameList: 

649 for filterName in filterNameList: 

650 mapper.editOutputSchema().addField(f"{filterName}_flux", 

651 type=numpy.float64, 

652 doc=f"flux in filter {filterName}", 

653 units="Jy" 

654 ) 

655 mapper.editOutputSchema().addField(f"{filterName}_fluxErr", 

656 type=numpy.float64, 

657 doc=f"flux uncertanty in filter {filterName}", 

658 units="Jy" 

659 ) 

660 

661 if position: 

662 mapper.editOutputSchema().addField("centroid_x", type=float, doReplace=True) 

663 mapper.editOutputSchema().addField("centroid_y", type=float, doReplace=True) 

664 mapper.editOutputSchema().addField("hasCentroid", type="Flag", doReplace=True) 

665 mapper.editOutputSchema().getAliasMap().set("slot_Centroid", "centroid") 

666 

667 if photometric: 

668 mapper.editOutputSchema().addField("photometric", 

669 type="Flag", 

670 doc="set if the object can be used for photometric" 

671 "calibration", 

672 ) 

673 mapper.editOutputSchema().addField("resolved", 

674 type="Flag", 

675 doc="set if the object is spatially resolved" 

676 ) 

677 mapper.editOutputSchema().addField("variable", 

678 type="Flag", 

679 doc="set if the object has variable brightness" 

680 ) 

681 

682 expandedCat = afwTable.SimpleCatalog(mapper.getOutputSchema()) 

683 expandedCat.setMetadata(refCat.getMetadata()) 

684 expandedCat.extend(refCat, mapper=mapper) 

685 

686 return expandedCat 

687 

688 

689def getRefFluxField(schema, filterName=None): 

690 """Get the name of a flux field from a schema. 

691 

692 return the alias of "anyFilterMapsToThis", if present 

693 else if filterName is specified: 

694 return "*filterName*_camFlux" if present 

695 else return "*filterName*_flux" if present (camera filter name 

696 matches reference filter name) 

697 else throw RuntimeError 

698 else: 

699 return "camFlux", if present, 

700 else throw RuntimeError 

701 

702 Parameters 

703 ---------- 

704 schema : `lsst.afw.table.Schema` 

705 Reference catalog schema. 

706 filterName : `str`, optional 

707 Name of camera filter. If not specified, ``defaultFilter`` needs to be 

708 set in the refcat loader config. 

709 

710 Returns 

711 ------- 

712 fluxFieldName : `str` 

713 Name of flux field. 

714 

715 Raises 

716 ------ 

717 RuntimeError 

718 If an appropriate field is not found. 

719 """ 

720 if not isinstance(schema, afwTable.Schema): 720 ↛ 721line 720 didn't jump to line 721, because the condition on line 720 was never true

721 raise RuntimeError("schema=%s is not a schema" % (schema,)) 

722 try: 

723 return schema.getAliasMap().get("anyFilterMapsToThis") 

724 except LookupError: 

725 pass # try the filterMap next 

726 

727 if filterName: 727 ↛ 730line 727 didn't jump to line 730, because the condition on line 727 was never false

728 fluxFieldList = [filterName + "_camFlux", filterName + "_flux"] 

729 else: 

730 fluxFieldList = ["camFlux"] 

731 for fluxField in fluxFieldList: 731 ↛ 735line 731 didn't jump to line 735, because the loop on line 731 didn't complete

732 if fluxField in schema: 

733 return fluxField 

734 

735 raise RuntimeError("Could not find flux field(s) %s" % (", ".join(fluxFieldList))) 

736 

737 

738def getRefFluxKeys(schema, filterName=None): 

739 """Return keys for flux and flux error. 

740 

741 Parameters 

742 ---------- 

743 schema : `lsst.afw.table.Schema` 

744 Reference catalog schema. 

745 filterName : `str` 

746 Name of camera filter. 

747 

748 Returns 

749 ------- 

750 keys : `tuple` of (`lsst.afw.table.Key`, `lsst.afw.table.Key`) 

751 Two keys: 

752 

753 - flux key 

754 - flux error key, if present, else None 

755 

756 Raises 

757 ------ 

758 RuntimeError 

759 If flux field not found. 

760 """ 

761 fluxField = getRefFluxField(schema, filterName) 

762 fluxErrField = fluxField + "Err" 

763 fluxKey = schema[fluxField].asKey() 

764 try: 

765 fluxErrKey = schema[fluxErrField].asKey() 

766 except Exception: 

767 fluxErrKey = None 

768 return (fluxKey, fluxErrKey) 

769 

770 

771class LoadReferenceObjectsConfig(pexConfig.Config): 

772 pixelMargin = pexConfig.RangeField( 

773 doc="Padding to add to 4 all edges of the bounding box (pixels)", 

774 dtype=int, 

775 default=300, 

776 min=0, 

777 ) 

778 defaultFilter = pexConfig.Field( 

779 doc=("Default reference catalog filter to use if filter not specified in exposure;" 

780 " if blank then filter must be specified in exposure."), 

781 dtype=str, 

782 default="", 

783 ) 

784 anyFilterMapsToThis = pexConfig.Field( 

785 doc=("Always use this reference catalog filter, no matter whether or what filter name is " 

786 "supplied to the loader. Effectively a trivial filterMap: map all filter names to this filter." 

787 " This can be set for purely-astrometric catalogs (e.g. Gaia DR2) where there is only one " 

788 "reasonable choice for every camera filter->refcat mapping, but not for refcats used for " 

789 "photometry, which need a filterMap and/or colorterms/transmission corrections."), 

790 dtype=str, 

791 default=None, 

792 optional=True 

793 ) 

794 filterMap = pexConfig.DictField( 

795 doc=("Mapping of camera filter name: reference catalog filter name; " 

796 "each reference filter must exist in the refcat." 

797 " Note that this does not perform any bandpass corrections: it is just a lookup."), 

798 keytype=str, 

799 itemtype=str, 

800 default={}, 

801 ) 

802 requireProperMotion = pexConfig.Field( 

803 doc="Require that the fields needed to correct proper motion " 

804 "(epoch, pm_ra and pm_dec) are present?", 

805 dtype=bool, 

806 default=False, 

807 ) 

808 

809 def validate(self): 

810 super().validate() 

811 if self.filterMap != {} and self.anyFilterMapsToThis is not None: 

812 msg = "`filterMap` and `anyFilterMapsToThis` are mutually exclusive" 

813 raise pexConfig.FieldValidationError(LoadReferenceObjectsConfig.anyFilterMapsToThis, 

814 self, msg) 

815 

816 

817class LoadReferenceObjectsTask(pipeBase.Task, metaclass=abc.ABCMeta): 

818 r"""Abstract base class to load objects from reference catalogs 

819 """ 

820 ConfigClass = LoadReferenceObjectsConfig 

821 _DefaultName = "LoadReferenceObjects" 

822 

823 def __init__(self, butler=None, *args, **kwargs): 

824 """Construct a LoadReferenceObjectsTask 

825 

826 Parameters 

827 ---------- 

828 butler : `lsst.daf.persistence.Butler` 

829 Data butler, for access reference catalogs. 

830 """ 

831 pipeBase.Task.__init__(self, *args, **kwargs) 

832 self.butler = butler 

833 

834 @pipeBase.timeMethod 

835 def loadPixelBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None): 

836 """Load reference objects that overlap a rectangular pixel region. 

837 

838 Parameters 

839 ---------- 

840 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D` 

841 Bounding box for pixels. 

842 wcs : `lsst.afw.geom.SkyWcs` 

843 WCS; used to convert pixel positions to sky coordinates 

844 and vice-versa. 

845 filterName : `str` 

846 Name of filter, or `None` or `""` for the default filter. 

847 This is used for flux values in case we have flux limits 

848 (which are not yet implemented). 

849 photoCalib : `lsst.afw.image.PhotoCalib` (optional) 

850 Calibration, or `None` if unknown. 

851 epoch : `astropy.time.Time` (optional) 

852 Epoch to which to correct proper motion and parallax, 

853 or None to not apply such corrections. 

854 

855 Returns 

856 ------- 

857 results : `lsst.pipe.base.Struct` 

858 A Struct containing the following fields: 

859 refCat : `lsst.afw.catalog.SimpleCatalog` 

860 A catalog of reference objects with the standard 

861 schema, as documented in the main doc string for 

862 `LoadReferenceObjects`. 

863 The catalog is guaranteed to be contiguous. 

864 fluxField : `str` 

865 Name of flux field for specified `filterName`. 

866 

867 Notes 

868 ----- 

869 The search algorithm works by searching in a region in sky 

870 coordinates whose center is the center of the bbox and radius 

871 is large enough to just include all 4 corners of the bbox. 

872 Stars that lie outside the bbox are then trimmed from the list. 

873 """ 

874 circle = self._calculateCircle(bbox, wcs) 

875 

876 # find objects in circle 

877 self.log.info("Loading reference objects using center %s and radius %s deg" % 

878 (circle.coord, circle.radius.asDegrees())) 

879 loadRes = self.loadSkyCircle(circle.coord, circle.radius, filterName=filterName, epoch=epoch, 

880 centroids=True) 

881 refCat = loadRes.refCat 

882 numFound = len(refCat) 

883 

884 # trim objects outside bbox 

885 refCat = self._trimToBBox(refCat=refCat, bbox=circle.bbox, wcs=wcs) 

886 numTrimmed = numFound - len(refCat) 

887 self.log.debug("trimmed %d out-of-bbox objects, leaving %d", numTrimmed, len(refCat)) 

888 self.log.info("Loaded %d reference objects", len(refCat)) 

889 

890 # make sure catalog is contiguous 

891 if not refCat.isContiguous(): 

892 loadRes.refCat = refCat.copy(deep=True) 

893 

894 return loadRes 

895 

896 @abc.abstractmethod 

897 def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None, centroids=False): 

898 """Load reference objects that overlap a circular sky region. 

899 

900 Parameters 

901 ---------- 

902 ctrCoord : `lsst.geom.SpherePoint` 

903 ICRS center of search region. 

904 radius : `lsst.geom.Angle` 

905 Radius of search region. 

906 filterName : `str` (optional) 

907 Name of filter, or `None` or `""` for the default filter. 

908 This is used for flux values in case we have flux limits 

909 (which are not yet implemented). 

910 epoch : `astropy.time.Time` (optional) 

911 Epoch to which to correct proper motion and parallax, 

912 or None to not apply such corrections. 

913 centroids : `bool` (optional) 

914 Add centroid fields to the loaded Schema. ``loadPixelBox`` expects 

915 these fields to exist. 

916 

917 Returns 

918 ------- 

919 results : `lsst.pipe.base.Struct` 

920 A Struct containing the following fields: 

921 refCat : `lsst.afw.catalog.SimpleCatalog` 

922 A catalog of reference objects with the standard 

923 schema, as documented in the main doc string for 

924 `LoadReferenceObjects`. 

925 The catalog is guaranteed to be contiguous. 

926 fluxField : `str` 

927 Name of flux field for specified `filterName`. 

928 

929 Notes 

930 ----- 

931 Note that subclasses are responsible for performing the proper motion 

932 correction, since this is the lowest-level interface for retrieving 

933 the catalog. 

934 """ 

935 return 

936 

937 @staticmethod 

938 def _trimToBBox(refCat, bbox, wcs): 

939 """Remove objects outside a given pixel bounding box and set 

940 centroid and hasCentroid fields. 

941 

942 Parameters 

943 ---------- 

944 refCat : `lsst.afw.table.SimpleCatalog` 

945 A catalog of objects. The schema must include fields 

946 "coord", "centroid" and "hasCentroid". 

947 The "coord" field is read. 

948 The "centroid" and "hasCentroid" fields are set. 

949 bbox : `lsst.geom.Box2D` 

950 Pixel region 

951 wcs : `lsst.afw.geom.SkyWcs` 

952 WCS; used to convert sky coordinates to pixel positions. 

953 

954 Returns 

955 ------- 

956 catalog : `lsst.afw.table.SimpleCatalog` 

957 Reference objects in the bbox, with centroid and 

958 hasCentroid fields set. 

959 """ 

960 afwTable.updateRefCentroids(wcs, refCat) 

961 centroidKey = afwTable.Point2DKey(refCat.schema["centroid"]) 

962 retStarCat = type(refCat)(refCat.table) 

963 for star in refCat: 

964 point = star.get(centroidKey) 

965 if bbox.contains(point): 

966 retStarCat.append(star) 

967 return retStarCat 

968 

969 def _addFluxAliases(self, schema): 

970 """Add aliases for camera filter fluxes to the schema. 

971 

972 If self.config.defaultFilter then adds these aliases: 

973 camFlux: <defaultFilter>_flux 

974 camFluxErr: <defaultFilter>_fluxErr, if the latter exists 

975 

976 For each camFilter: refFilter in self.config.filterMap adds these aliases: 

977 <camFilter>_camFlux: <refFilter>_flux 

978 <camFilter>_camFluxErr: <refFilter>_fluxErr, if the latter exists 

979 

980 Parameters 

981 ---------- 

982 schema : `lsst.afw.table.Schema` 

983 Schema for reference catalog. 

984 

985 Raises 

986 ------ 

987 RuntimeError 

988 If any reference flux field is missing from the schema. 

989 """ 

990 aliasMap = schema.getAliasMap() 

991 

992 if self.config.anyFilterMapsToThis is not None: 992 ↛ 993line 992 didn't jump to line 993, because the condition on line 992 was never true

993 refFluxName = self.config.anyFilterMapsToThis + "_flux" 

994 if refFluxName not in schema: 

995 msg = f"Unknown reference filter for anyFilterMapsToThis='{refFluxName}'" 

996 raise RuntimeError(msg) 

997 aliasMap.set("anyFilterMapsToThis", refFluxName) 

998 return # this is mutually exclusive with filterMap 

999 

1000 def addAliasesForOneFilter(filterName, refFilterName): 

1001 """Add aliases for a single filter 

1002 

1003 Parameters 

1004 ---------- 

1005 filterName : `str` (optional) 

1006 Camera filter name. The resulting alias name is 

1007 <filterName>_camFlux, or simply "camFlux" if `filterName` 

1008 is `None` or `""`. 

1009 refFilterName : `str` 

1010 Reference catalog filter name; the field 

1011 <refFilterName>_flux must exist. 

1012 """ 

1013 camFluxName = filterName + "_camFlux" if filterName is not None else "camFlux" 

1014 refFluxName = refFilterName + "_flux" 

1015 if refFluxName not in schema: 

1016 raise RuntimeError("Unknown reference filter %s" % (refFluxName,)) 

1017 aliasMap.set(camFluxName, refFluxName) 

1018 refFluxErrName = refFluxName + "Err" 

1019 if refFluxErrName in schema: 

1020 camFluxErrName = camFluxName + "Err" 

1021 aliasMap.set(camFluxErrName, refFluxErrName) 

1022 

1023 if self.config.defaultFilter: 1023 ↛ 1024line 1023 didn't jump to line 1024, because the condition on line 1023 was never true

1024 addAliasesForOneFilter(None, self.config.defaultFilter) 

1025 

1026 for filterName, refFilterName in self.config.filterMap.items(): 1026 ↛ 1027line 1026 didn't jump to line 1027, because the loop on line 1026 never started

1027 addAliasesForOneFilter(filterName, refFilterName) 

1028 

1029 @staticmethod 

1030 def makeMinimalSchema(filterNameList, *, addCentroid=False, 

1031 addIsPhotometric=False, addIsResolved=False, 

1032 addIsVariable=False, coordErrDim=2, 

1033 addProperMotion=False, properMotionErrDim=2, 

1034 addParallax=False): 

1035 """Make a standard schema for reference object catalogs. 

1036 

1037 Parameters 

1038 ---------- 

1039 filterNameList : `list` of `str` 

1040 List of filter names. Used to create <filterName>_flux fields. 

1041 addIsPhotometric : `bool` 

1042 If True then add field "photometric". 

1043 addIsResolved : `bool` 

1044 If True then add field "resolved". 

1045 addIsVariable : `bool` 

1046 If True then add field "variable". 

1047 coordErrDim : `int` 

1048 Number of coord error fields; must be one of 0, 2, 3: 

1049 

1050 - If 2 or 3: add fields "coord_raErr" and "coord_decErr". 

1051 - If 3: also add field "coord_radecErr". 

1052 addProperMotion : `bool` 

1053 If True add fields "epoch", "pm_ra", "pm_dec" and "pm_flag". 

1054 properMotionErrDim : `int` 

1055 Number of proper motion error fields; must be one of 0, 2, 3; 

1056 ignored if addProperMotion false: 

1057 - If 2 or 3: add fields "pm_raErr" and "pm_decErr". 

1058 - If 3: also add field "pm_radecErr". 

1059 addParallax : `bool` 

1060 If True add fields "epoch", "parallax", "parallaxErr" 

1061 and "parallax_flag". 

1062 

1063 Returns 

1064 ------- 

1065 schema : `lsst.afw.table.Schema` 

1066 Schema for reference catalog, an 

1067 `lsst.afw.table.SimpleCatalog`. 

1068 

1069 Notes 

1070 ----- 

1071 Reference catalogs support additional covariances, such as 

1072 covariance between RA and proper motion in declination, 

1073 that are not supported by this method, but can be added after 

1074 calling this method. 

1075 """ 

1076 schema = afwTable.SimpleTable.makeMinimalSchema() 

1077 if addCentroid: 1077 ↛ 1078line 1077 didn't jump to line 1078, because the condition on line 1077 was never true

1078 afwTable.Point2DKey.addFields( 

1079 schema, 

1080 "centroid", 

1081 "centroid on an exposure, if relevant", 

1082 "pixel", 

1083 ) 

1084 schema.addField( 

1085 field="hasCentroid", 

1086 type="Flag", 

1087 doc="is position known?", 

1088 ) 

1089 for filterName in filterNameList: 

1090 schema.addField( 

1091 field="%s_flux" % (filterName,), 

1092 type=numpy.float64, 

1093 doc="flux in filter %s" % (filterName,), 

1094 units="nJy", 

1095 ) 

1096 for filterName in filterNameList: 

1097 schema.addField( 

1098 field="%s_fluxErr" % (filterName,), 

1099 type=numpy.float64, 

1100 doc="flux uncertainty in filter %s" % (filterName,), 

1101 units="nJy", 

1102 ) 

1103 if addIsPhotometric: 1103 ↛ 1104line 1103 didn't jump to line 1104, because the condition on line 1103 was never true

1104 schema.addField( 

1105 field="photometric", 

1106 type="Flag", 

1107 doc="set if the object can be used for photometric calibration", 

1108 ) 

1109 if addIsResolved: 1109 ↛ 1110line 1109 didn't jump to line 1110, because the condition on line 1109 was never true

1110 schema.addField( 

1111 field="resolved", 

1112 type="Flag", 

1113 doc="set if the object is spatially resolved", 

1114 ) 

1115 if addIsVariable: 1115 ↛ 1116line 1115 didn't jump to line 1116, because the condition on line 1115 was never true

1116 schema.addField( 

1117 field="variable", 

1118 type="Flag", 

1119 doc="set if the object has variable brightness", 

1120 ) 

1121 if coordErrDim not in (0, 2, 3): 1121 ↛ 1122line 1121 didn't jump to line 1122, because the condition on line 1121 was never true

1122 raise ValueError("coordErrDim={}; must be (0, 2, 3)".format(coordErrDim)) 

1123 if coordErrDim > 0: 

1124 afwTable.CovarianceMatrix2fKey.addFields( 

1125 schema=schema, 

1126 prefix="coord", 

1127 names=["ra", "dec"], 

1128 units=["rad", "rad"], 

1129 diagonalOnly=(coordErrDim == 2), 

1130 ) 

1131 

1132 if addProperMotion or addParallax: 

1133 schema.addField( 

1134 field="epoch", 

1135 type=numpy.float64, 

1136 doc="date of observation (TAI, MJD)", 

1137 units="day", 

1138 ) 

1139 

1140 if addProperMotion: 

1141 schema.addField( 

1142 field="pm_ra", 

1143 type="Angle", 

1144 doc="proper motion in the right ascension direction = dra/dt * cos(dec)", 

1145 units="rad/year", 

1146 ) 

1147 schema.addField( 

1148 field="pm_dec", 

1149 type="Angle", 

1150 doc="proper motion in the declination direction", 

1151 units="rad/year", 

1152 ) 

1153 if properMotionErrDim not in (0, 2, 3): 1153 ↛ 1154line 1153 didn't jump to line 1154, because the condition on line 1153 was never true

1154 raise ValueError("properMotionErrDim={}; must be (0, 2, 3)".format(properMotionErrDim)) 

1155 if properMotionErrDim > 0: 1155 ↛ 1163line 1155 didn't jump to line 1163, because the condition on line 1155 was never false

1156 afwTable.CovarianceMatrix2fKey.addFields( 

1157 schema=schema, 

1158 prefix="pm", 

1159 names=["ra", "dec"], 

1160 units=["rad/year", "rad/year"], 

1161 diagonalOnly=(properMotionErrDim == 2), 

1162 ) 

1163 schema.addField( 

1164 field="pm_flag", 

1165 type="Flag", 

1166 doc="Set if proper motion or proper motion error is bad", 

1167 ) 

1168 

1169 if addParallax: 

1170 schema.addField( 

1171 field="parallax", 

1172 type="Angle", 

1173 doc="parallax", 

1174 units="rad", 

1175 ) 

1176 schema.addField( 

1177 field="parallaxErr", 

1178 type="Angle", 

1179 doc="uncertainty in parallax", 

1180 units="rad", 

1181 ) 

1182 schema.addField( 

1183 field="parallax_flag", 

1184 type="Flag", 

1185 doc="Set if parallax or parallax error is bad", 

1186 ) 

1187 return schema 

1188 

1189 def _calculateCircle(self, bbox, wcs): 

1190 """Compute on-sky center and radius of search region. 

1191 

1192 Parameters 

1193 ---------- 

1194 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D` 

1195 Pixel bounding box. 

1196 wcs : `lsst.afw.geom.SkyWcs` 

1197 WCS; used to convert pixel positions to sky coordinates. 

1198 

1199 Returns 

1200 ------- 

1201 results : `lsst.pipe.base.Struct` 

1202 A Struct containing: 

1203 

1204 - coord : `lsst.geom.SpherePoint` 

1205 ICRS center of the search region. 

1206 - radius : `lsst.geom.Angle` 

1207 Radius of the search region. 

1208 - bbox : `lsst.geom.Box2D` 

1209 Bounding box used to compute the circle. 

1210 """ 

1211 bbox = lsst.geom.Box2D(bbox) # make sure bbox is double and that we have a copy 

1212 bbox.grow(self.config.pixelMargin) 

1213 coord = wcs.pixelToSky(bbox.getCenter()) 

1214 radius = max(coord.separation(wcs.pixelToSky(pp)) for pp in bbox.getCorners()) 

1215 return pipeBase.Struct(coord=coord, radius=radius, bbox=bbox) 

1216 

1217 def getMetadataBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None): 

1218 """Return metadata about the load. 

1219 

1220 This metadata is used for reloading the catalog (e.g., for 

1221 reconstituting a normalised match list. 

1222 

1223 Parameters 

1224 ---------- 

1225 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D` 

1226 Pixel bounding box. 

1227 wcs : `lsst.afw.geom.SkyWcs` 

1228 WCS; used to convert pixel positions to sky coordinates. 

1229 filterName : `str` 

1230 Name of camera filter, or `None` or `""` for the default 

1231 filter. 

1232 photoCalib : `lsst.afw.image.PhotoCalib` (optional) 

1233 Calibration, or `None` if unknown. 

1234 epoch : `astropy.time.Time` (optional) 

1235 Epoch to which to correct proper motion and parallax, 

1236 or None to not apply such corrections. 

1237 

1238 Returns 

1239 ------- 

1240 metadata : lsst.daf.base.PropertyList 

1241 Metadata about the load. 

1242 """ 

1243 circle = self._calculateCircle(bbox, wcs) 

1244 return self.getMetadataCircle(circle.coord, circle.radius, filterName, photoCalib=photoCalib, 

1245 epoch=epoch) 

1246 

1247 def getMetadataCircle(self, coord, radius, filterName, photoCalib=None, epoch=None): 

1248 """Return metadata about the load. 

1249 

1250 This metadata is used for reloading the catalog (e.g., for 

1251 reconstituting a normalised match list. 

1252 

1253 Parameters 

1254 ---------- 

1255 coord : `lsst.geom.SpherePoint` 

1256 ICRS center of the search region. 

1257 radius : `lsst.geom.Angle` 

1258 Radius of the search region. 

1259 filterName : `str` 

1260 Name of camera filter, or `None` or `""` for the default 

1261 filter. 

1262 photoCalib : `lsst.afw.image.PhotoCalib` (optional) 

1263 Calibration, or `None` if unknown. 

1264 epoch : `astropy.time.Time` (optional) 

1265 Epoch to which to correct proper motion and parallax, 

1266 or None to not apply such corrections. 

1267 

1268 Returns 

1269 ------- 

1270 metadata : lsst.daf.base.PropertyList 

1271 Metadata about the load 

1272 """ 

1273 md = PropertyList() 

1274 md.add('RA', coord.getRa().asDegrees(), 'field center in degrees') 

1275 md.add('DEC', coord.getDec().asDegrees(), 'field center in degrees') 

1276 md.add('RADIUS', radius.asDegrees(), 'field radius in degrees, minimum') 

1277 md.add('SMATCHV', 1, 'SourceMatchVector version number') 

1278 filterName = "UNKNOWN" if filterName is None else str(filterName) 

1279 md.add('FILTER', filterName, 'filter name for photometric data') 

1280 md.add('EPOCH', "NONE" if epoch is None else epoch.mjd, 'Epoch (TAI MJD) for catalog') 

1281 return md 

1282 

1283 def joinMatchListWithCatalog(self, matchCat, sourceCat): 

1284 """Relink an unpersisted match list to sources and reference 

1285 objects. 

1286 

1287 A match list is persisted and unpersisted as a catalog of IDs 

1288 produced by afw.table.packMatches(), with match metadata 

1289 (as returned by the astrometry tasks) in the catalog's metadata 

1290 attribute. This method converts such a match catalog into a match 

1291 list, with links to source records and reference object records. 

1292 

1293 Parameters 

1294 ---------- 

1295 matchCat : `lsst.afw.table.BaseCatalog` 

1296 Unperisted packed match list. 

1297 ``matchCat.table.getMetadata()`` must contain match metadata, 

1298 as returned by the astrometry tasks. 

1299 sourceCat : `lsst.afw.table.SourceCatalog` 

1300 Source catalog. As a side effect, the catalog will be sorted 

1301 by ID. 

1302 

1303 Returns 

1304 ------- 

1305 matchList : `lsst.afw.table.ReferenceMatchVector` 

1306 Match list. 

1307 """ 

1308 return joinMatchListWithCatalogImpl(self, matchCat, sourceCat) 

1309 

1310 def applyProperMotions(self, catalog, epoch): 

1311 """Apply proper motion correction to a reference catalog. 

1312 

1313 Adjust position and position error in the ``catalog`` 

1314 for proper motion to the specified ``epoch``, 

1315 modifying the catalog in place. 

1316 

1317 Parameters 

1318 ---------- 

1319 catalog : `lsst.afw.table.SimpleCatalog` 

1320 Catalog of positions, containing: 

1321 

1322 - Coordinates, retrieved by the table's coordinate key. 

1323 - ``coord_raErr`` : Error in Right Ascension (rad). 

1324 - ``coord_decErr`` : Error in Declination (rad). 

1325 - ``pm_ra`` : Proper motion in Right Ascension (rad/yr, 

1326 East positive) 

1327 - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional. 

1328 - ``pm_dec`` : Proper motion in Declination (rad/yr, 

1329 North positive) 

1330 - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional. 

1331 - ``epoch`` : Mean epoch of object (an astropy.time.Time) 

1332 epoch : `astropy.time.Time` 

1333 Epoch to which to correct proper motion, 

1334 """ 

1335 if ("epoch" not in catalog.schema or "pm_ra" not in catalog.schema or "pm_dec" not in catalog.schema): 

1336 if self.config.requireProperMotion: 

1337 raise RuntimeError("Proper motion correction required but not available from catalog") 

1338 self.log.warn("Proper motion correction not available from catalog") 

1339 return 

1340 applyProperMotionsImpl(self.log, catalog, epoch) 

1341 

1342 

1343def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat): 

1344 """Relink an unpersisted match list to sources and reference 

1345 objects. 

1346 

1347 A match list is persisted and unpersisted as a catalog of IDs 

1348 produced by afw.table.packMatches(), with match metadata 

1349 (as returned by the astrometry tasks) in the catalog's metadata 

1350 attribute. This method converts such a match catalog into a match 

1351 list, with links to source records and reference object records. 

1352 

1353 Parameters 

1354 ---------- 

1355 refObjLoader 

1356 Reference object loader to use in getting reference objects 

1357 matchCat : `lsst.afw.table.BaseCatalog` 

1358 Unperisted packed match list. 

1359 ``matchCat.table.getMetadata()`` must contain match metadata, 

1360 as returned by the astrometry tasks. 

1361 sourceCat : `lsst.afw.table.SourceCatalog` 

1362 Source catalog. As a side effect, the catalog will be sorted 

1363 by ID. 

1364 

1365 Returns 

1366 ------- 

1367 matchList : `lsst.afw.table.ReferenceMatchVector` 

1368 Match list. 

1369 """ 

1370 matchmeta = matchCat.table.getMetadata() 

1371 version = matchmeta.getInt('SMATCHV') 

1372 if version != 1: 

1373 raise ValueError('SourceMatchVector version number is %i, not 1.' % version) 

1374 filterName = matchmeta.getString('FILTER').strip() 

1375 try: 

1376 epoch = matchmeta.getDouble('EPOCH') 

1377 except (pexExcept.NotFoundError, pexExcept.TypeError): 

1378 epoch = None # Not present, or not correct type means it's not set 

1379 if 'RADIUS' in matchmeta: 

1380 # This is a circle style metadata, call loadSkyCircle 

1381 ctrCoord = lsst.geom.SpherePoint(matchmeta.getDouble('RA'), 

1382 matchmeta.getDouble('DEC'), lsst.geom.degrees) 

1383 rad = matchmeta.getDouble('RADIUS') * lsst.geom.degrees 

1384 refCat = refObjLoader.loadSkyCircle(ctrCoord, rad, filterName, epoch=epoch).refCat 

1385 elif "INNER_UPPER_LEFT_RA" in matchmeta: 

1386 # This is the sky box type (only triggers in the LoadReferenceObject class, not task) 

1387 # Only the outer box is required to be loaded to get the maximum region, all filtering 

1388 # will be done by the unpackMatches function, and no spatial filtering needs to be done 

1389 # by the refObjLoader 

1390 box = [] 

1391 for place in ("UPPER_LEFT", "UPPER_RIGHT", "LOWER_LEFT", "LOWER_RIGHT"): 

1392 coord = lsst.geom.SpherePoint(matchmeta.getDouble(f"OUTER_{place}_RA"), 

1393 matchmeta.getDouble(f"OUTER_{place}_DEC"), 

1394 lsst.geom.degrees).getVector() 

1395 box.append(coord) 

1396 outerBox = sphgeom.ConvexPolygon(box) 

1397 refCat = refObjLoader.loadRegion(outerBox, filterName=filterName, epoch=epoch).refCat 

1398 

1399 refCat.sort() 

1400 sourceCat.sort() 

1401 return afwTable.unpackMatches(matchCat, refCat, sourceCat) 

1402 

1403 

1404def applyProperMotionsImpl(log, catalog, epoch): 

1405 """Apply proper motion correction to a reference catalog. 

1406 

1407 Adjust position and position error in the ``catalog`` 

1408 for proper motion to the specified ``epoch``, 

1409 modifying the catalog in place. 

1410 

1411 Parameters 

1412 ---------- 

1413 log : `lsst.log.Log` 

1414 Log object to write to. 

1415 catalog : `lsst.afw.table.SimpleCatalog` 

1416 Catalog of positions, containing: 

1417 

1418 - Coordinates, retrieved by the table's coordinate key. 

1419 - ``coord_raErr`` : Error in Right Ascension (rad). 

1420 - ``coord_decErr`` : Error in Declination (rad). 

1421 - ``pm_ra`` : Proper motion in Right Ascension (rad/yr, 

1422 East positive) 

1423 - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional. 

1424 - ``pm_dec`` : Proper motion in Declination (rad/yr, 

1425 North positive) 

1426 - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional. 

1427 - ``epoch`` : Mean epoch of object (an astropy.time.Time) 

1428 epoch : `astropy.time.Time` 

1429 Epoch to which to correct proper motion. 

1430 """ 

1431 if "epoch" not in catalog.schema or "pm_ra" not in catalog.schema or "pm_dec" not in catalog.schema: 

1432 log.warn("Proper motion correction not available from catalog") 

1433 return 

1434 if not catalog.isContiguous(): 

1435 raise RuntimeError("Catalog must be contiguous") 

1436 catEpoch = astropy.time.Time(catalog["epoch"], scale="tai", format="mjd") 

1437 log.info("Correcting reference catalog for proper motion to %r", epoch) 

1438 # Use `epoch.tai` to make sure the time difference is in TAI 

1439 timeDiffsYears = (epoch.tai - catEpoch).to(astropy.units.yr).value 

1440 coordKey = catalog.table.getCoordKey() 

1441 # Compute the offset of each object due to proper motion 

1442 # as components of the arc of a great circle along RA and Dec 

1443 pmRaRad = catalog["pm_ra"] 

1444 pmDecRad = catalog["pm_dec"] 

1445 offsetsRaRad = pmRaRad*timeDiffsYears 

1446 offsetsDecRad = pmDecRad*timeDiffsYears 

1447 # Compute the corresponding bearing and arc length of each offset 

1448 # due to proper motion, and apply the offset 

1449 # The factor of 1e6 for computing bearing is intended as 

1450 # a reasonable scale for typical values of proper motion 

1451 # in order to avoid large errors for small values of proper motion; 

1452 # using the offsets is another option, but it can give 

1453 # needlessly large errors for short duration 

1454 offsetBearingsRad = numpy.arctan2(pmDecRad*1e6, pmRaRad*1e6) 

1455 offsetAmountsRad = numpy.hypot(offsetsRaRad, offsetsDecRad) 

1456 for record, bearingRad, amountRad in zip(catalog, offsetBearingsRad, offsetAmountsRad): 

1457 record.set(coordKey, 

1458 record.get(coordKey).offset(bearing=bearingRad*lsst.geom.radians, 

1459 amount=amountRad*lsst.geom.radians)) 

1460 # Increase error in RA and Dec based on error in proper motion 

1461 if "coord_raErr" in catalog.schema: 

1462 catalog["coord_raErr"] = numpy.hypot(catalog["coord_raErr"], 

1463 catalog["pm_raErr"]*timeDiffsYears) 

1464 if "coord_decErr" in catalog.schema: 

1465 catalog["coord_decErr"] = numpy.hypot(catalog["coord_decErr"], 

1466 catalog["pm_decErr"]*timeDiffsYears)