Coverage for python/lsst/summit/utils/utils.py: 18%

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1# This file is part of summit_utils. 

2# 

3# Developed for the LSST Data Management System. 

4# This product includes software developed by the LSST Project 

5# (https://www.lsst.org). 

6# See the COPYRIGHT file at the top-level directory of this distribution 

7# for details of code ownership. 

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 GNU General Public License 

20# along with this program. If not, see <https://www.gnu.org/licenses/>. 

21 

22import os 

23from typing import Iterable 

24import numpy as np 

25import logging 

26from scipy.ndimage import gaussian_filter 

27import lsst.afw.image as afwImage 

28import lsst.afw.detection as afwDetect 

29from lsst.afw.detection import Footprint, FootprintSet 

30import lsst.afw.math as afwMath 

31import lsst.daf.base as dafBase 

32import lsst.geom as geom 

33import lsst.pipe.base as pipeBase 

34import lsst.utils.packages as packageUtils 

35from lsst.daf.butler.cli.cliLog import CliLog 

36import datetime 

37from dateutil.tz import gettz 

38 

39from lsst.obs.lsst.translators.lsst import FILTER_DELIMITER 

40from lsst.obs.lsst.translators.latiss import AUXTEL_LOCATION 

41 

42from astro_metadata_translator import ObservationInfo 

43from astropy.coordinates import SkyCoord, AltAz 

44from astropy.coordinates.earth import EarthLocation 

45import astropy.units as u 

46from astropy.time import Time 

47 

48from .astrometry.utils import genericCameraHeaderToWcs 

49 

50__all__ = ["SIGMATOFWHM", 

51 "FWHMTOSIGMA", 

52 "EFD_CLIENT_MISSING_MSG", 

53 "GOOGLE_CLOUD_MISSING_MSG", 

54 "AUXTEL_LOCATION", 

55 "countPixels", 

56 "quickSmooth", 

57 "argMax2d", 

58 "getImageStats", 

59 "detectObjectsInExp", 

60 "humanNameForCelestialObject", 

61 "getFocusFromHeader", 

62 "dayObsIntToString", 

63 "dayObsSeqNumToVisitId", 

64 "setupLogging", 

65 "getCurrentDayObs_datetime", 

66 "getCurrentDayObs_int", 

67 "getCurrentDayObs_humanStr", 

68 "getSite", 

69 "getExpPositionOffset", 

70 "starTrackerFileToExposure", 

71 "getAirmassSeeingCorrection", 

72 "getFilterSeeingCorrection", 

73 "getCdf", 

74 "getQuantiles", 

75 "digitizeData", 

76 ] 

77 

78 

79SIGMATOFWHM = 2.0*np.sqrt(2.0*np.log(2.0)) 

80FWHMTOSIGMA = 1/SIGMATOFWHM 

81 

82EFD_CLIENT_MISSING_MSG = ('ImportError: lsst_efd_client not found. Please install with:\n' 

83 ' pip install lsst-efd-client') 

84 

85GOOGLE_CLOUD_MISSING_MSG = ('ImportError: Google cloud storage not found. Please install with:\n' 

86 ' pip install google-cloud-storage') 

87 

88 

89def countPixels(maskedImage, maskPlane): 

90 """Count the number of pixels in an image with a given mask bit set. 

91 

92 Parameters 

93 ---------- 

94 maskedImage : `lsst.afw.image.MaskedImage` 

95 The masked image, 

96 maskPlane : `str` 

97 The name of the bitmask. 

98 

99 Returns 

100 ------- 

101 count : `int`` 

102 The number of pixels in with the selected mask bit 

103 """ 

104 bit = maskedImage.mask.getPlaneBitMask(maskPlane) 

105 return len(np.where(np.bitwise_and(maskedImage.mask.array, bit))[0]) 

106 

107 

108def quickSmooth(data, sigma=2): 

109 """Perform a quick smoothing of the image. 

110 

111 Not to be used for scientific purposes, but improves the stretch and 

112 visual rendering of low SNR against the sky background in cutouts. 

113 

114 Parameters 

115 ---------- 

116 data : `np.array` 

117 The image data to smooth 

118 sigma : `float`, optional 

119 The size of the smoothing kernel. 

120 

121 Returns 

122 ------- 

123 smoothData : `np.array` 

124 The smoothed data 

125 """ 

126 kernel = [sigma, sigma] 

127 smoothData = gaussian_filter(data, kernel, mode='constant') 

128 return smoothData 

129 

130 

131def argMax2d(array): 

132 """Get the index of the max value of an array and whether it's unique. 

133 

134 If its not unique, returns a list of the other locations containing the 

135 maximum value, e.g. returns 

136 

137 (12, 34), False, [(56,78), (910, 1112)] 

138 

139 Parameters 

140 ---------- 

141 array : `np.array` 

142 The data 

143 

144 Returns 

145 ------- 

146 maxLocation : `tuple` 

147 The coords of the first instance of the max value 

148 unique : `bool` 

149 Whether it's the only location 

150 otherLocations : `list` of `tuple` 

151 List of the other max values' locations, empty if False 

152 """ 

153 uniqueMaximum = False 

154 maxCoords = np.where(array == np.max(array)) 

155 maxCoords = [coord for coord in zip(*maxCoords)] # list of coords as tuples 

156 if len(maxCoords) == 1: # single unambiguous value 

157 uniqueMaximum = True 

158 

159 return maxCoords[0], uniqueMaximum, maxCoords[1:] 

160 

161 

162def dayObsIntToString(dayObs): 

163 """Convert an integer dayObs to a dash-delimited string. 

164 

165 e.g. convert the hard to read 20210101 to 2021-01-01 

166 

167 Parameters 

168 ---------- 

169 dayObs : `int` 

170 The dayObs. 

171 

172 Returns 

173 ------- 

174 dayObs : `str` 

175 The dayObs as a string. 

176 """ 

177 assert isinstance(dayObs, int) 

178 dStr = str(dayObs) 

179 assert len(dStr) == 8 

180 return '-'.join([dStr[0:4], dStr[4:6], dStr[6:8]]) 

181 

182 

183def dayObsSeqNumToVisitId(dayObs, seqNum): 

184 """Get the visit id for a given dayObs/seqNum. 

185 

186 Parameters 

187 ---------- 

188 dayObs : `int` 

189 The dayObs. 

190 seqNum : `int` 

191 The seqNum. 

192 

193 Returns 

194 ------- 

195 visitId : `int` 

196 The visitId. 

197 

198 Notes 

199 ----- 

200 TODO: Remove this horrible hack once DM-30948 makes this possible 

201 programatically/via the butler. 

202 """ 

203 if dayObs < 19700101 or dayObs > 35000101: 

204 raise ValueError(f'dayObs value {dayObs} outside plausible range') 

205 return int(f"{dayObs}{seqNum:05}") 

206 

207 

208def getImageStats(exp): 

209 """Calculate a grab-bag of stats for an image. Must remain fast. 

210 

211 Parameters 

212 ---------- 

213 exp : `lsst.afw.image.Exposure` 

214 The input exposure. 

215 

216 Returns 

217 ------- 

218 stats : `lsst.pipe.base.Struct` 

219 A container with attributes containing measurements and statistics 

220 for the image. 

221 """ 

222 result = pipeBase.Struct() 

223 

224 vi = exp.visitInfo 

225 expTime = vi.exposureTime 

226 md = exp.getMetadata() 

227 

228 obj = vi.object 

229 mjd = vi.getDate().get() 

230 result.object = obj 

231 result.mjd = mjd 

232 

233 fullFilterString = exp.filter.physicalLabel 

234 filt = fullFilterString.split(FILTER_DELIMITER)[0] 

235 grating = fullFilterString.split(FILTER_DELIMITER)[1] 

236 

237 airmass = vi.getBoresightAirmass() 

238 rotangle = vi.getBoresightRotAngle().asDegrees() 

239 

240 azAlt = vi.getBoresightAzAlt() 

241 az = azAlt[0].asDegrees() 

242 el = azAlt[1].asDegrees() 

243 

244 result.expTime = expTime 

245 result.filter = filt 

246 result.grating = grating 

247 result.airmass = airmass 

248 result.rotangle = rotangle 

249 result.az = az 

250 result.el = el 

251 result.focus = md.get('FOCUSZ') 

252 

253 data = exp.image.array 

254 result.maxValue = np.max(data) 

255 

256 peak, uniquePeak, otherPeaks = argMax2d(data) 

257 result.maxPixelLocation = peak 

258 result.multipleMaxPixels = uniquePeak 

259 

260 result.nBadPixels = countPixels(exp.maskedImage, 'BAD') 

261 result.nSatPixels = countPixels(exp.maskedImage, 'SAT') 

262 result.percentile99 = np.percentile(data, 99) 

263 result.percentile9999 = np.percentile(data, 99.99) 

264 

265 sctrl = afwMath.StatisticsControl() 

266 sctrl.setNumSigmaClip(5) 

267 sctrl.setNumIter(2) 

268 statTypes = afwMath.MEANCLIP | afwMath.STDEVCLIP 

269 stats = afwMath.makeStatistics(exp.maskedImage, statTypes, sctrl) 

270 std, stderr = stats.getResult(afwMath.STDEVCLIP) 

271 mean, meanerr = stats.getResult(afwMath.MEANCLIP) 

272 

273 result.clippedMean = mean 

274 result.clippedStddev = std 

275 

276 return result 

277 

278 

279def detectObjectsInExp(exp, nSigma=10, nPixMin=10, grow=0): 

280 """Quick and dirty object detection for an exposure. 

281 

282 Return the footPrintSet for the objects in a preferably-postISR exposure. 

283 

284 Parameters 

285 ---------- 

286 exp : `lsst.afw.image.Exposure` 

287 The exposure to detect objects in. 

288 nSigma : `float` 

289 The number of sigma for detection. 

290 nPixMin : `int` 

291 The minimum number of pixels in an object for detection. 

292 grow : `int` 

293 The number of pixels to grow the footprint by after detection. 

294 

295 Returns 

296 ------- 

297 footPrintSet : `lsst.afw.detection.FootprintSet` 

298 The set of footprints in the image. 

299 """ 

300 median = np.nanmedian(exp.image.array) 

301 exp.image -= median 

302 

303 threshold = afwDetect.Threshold(nSigma, afwDetect.Threshold.STDEV) 

304 footPrintSet = afwDetect.FootprintSet(exp.getMaskedImage(), threshold, "DETECTED", nPixMin) 

305 if grow > 0: 

306 isotropic = True 

307 footPrintSet = afwDetect.FootprintSet(footPrintSet, grow, isotropic) 

308 

309 exp.image += median # add back in to leave background unchanged 

310 return footPrintSet 

311 

312 

313def fluxesFromFootprints(footprints, parentImage, subtractImageMedian=False): 

314 """Calculate the flux from a set of footprints, given the parent image, 

315 optionally subtracting the whole-image median from each pixel as a very 

316 rough background subtraction. 

317 

318 Parameters 

319 ---------- 

320 footprints : `lsst.afw.detection.FootprintSet` or 

321 `lsst.afw.detection.Footprint` or 

322 `iterable` of `lsst.afw.detection.Footprint` 

323 The footprints to measure. 

324 parentImage : `lsst.afw.image.Image` 

325 The parent image. 

326 subtractImageMedian : `bool`, optional 

327 Subtract a whole-image median from each pixel in the footprint when 

328 summing as a very crude background subtraction. Does not change the 

329 original image. 

330 

331 Returns 

332 ------- 

333 fluxes : `list` of `float` 

334 The fluxes for each footprint. 

335 

336 Raises 

337 ------ 

338 TypeError : raise for unsupported types. 

339 """ 

340 median = 0 

341 if subtractImageMedian: 

342 median = np.nanmedian(parentImage.array) 

343 

344 # poor person's single dispatch 

345 badTypeMsg = ("This function works with FootprintSets, single Footprints, and iterables of Footprints. " 

346 f"Got {type(footprints)}: {footprints}") 

347 if isinstance(footprints, FootprintSet): 

348 footprints = footprints.getFootprints() 

349 elif isinstance(footprints, Iterable): 

350 if not isinstance(footprints[0], Footprint): 

351 raise TypeError(badTypeMsg) 

352 elif isinstance(footprints, Footprint): 

353 footprints = [footprints] 

354 else: 

355 raise TypeError(badTypeMsg) 

356 

357 return np.array([fluxFromFootprint(fp, parentImage, backgroundValue=median) for fp in footprints]) 

358 

359 

360def fluxFromFootprint(footprint, parentImage, backgroundValue=0): 

361 """Calculate the flux from a footprint, given the parent image, optionally 

362 subtracting a single value from each pixel as a very rough background 

363 subtraction, e.g. the image median. 

364 

365 Parameters 

366 ---------- 

367 footprint : `lsst.afw.detection.Footprint` 

368 The footprint to measure. 

369 parentImage : `lsst.afw.image.Image` 

370 Image containing the footprint. 

371 backgroundValue : `bool`, optional 

372 The value to subtract from each pixel in the footprint when summing 

373 as a very crude background subtraction. Does not change the original 

374 image. 

375 

376 Returns 

377 ------- 

378 flux : `float` 

379 The flux in the footprint 

380 """ 

381 if backgroundValue: # only do the subtraction if non-zero for speed 

382 xy0 = parentImage.getBBox().getMin() 

383 return footprint.computeFluxFromArray(parentImage.array - backgroundValue, xy0) 

384 return footprint.computeFluxFromImage(parentImage) 

385 

386 

387def humanNameForCelestialObject(objName): 

388 """Returns a list of all human names for obj, or [] if none are found. 

389 

390 Parameters 

391 ---------- 

392 objName : `str` 

393 The/a name of the object. 

394 

395 Returns 

396 ------- 

397 names : `list` of `str` 

398 The names found for the object 

399 """ 

400 from astroquery.simbad import Simbad 

401 results = [] 

402 try: 

403 simbadResult = Simbad.query_objectids(objName) 

404 for row in simbadResult: 

405 if row['ID'].startswith('NAME'): 

406 results.append(row['ID'].replace('NAME ', '')) 

407 return results 

408 except Exception: 

409 return [] # same behavior as for found but un-named objects 

410 

411 

412def _getAltAzZenithsFromSeqNum(butler, dayObs, seqNumList): 

413 """Get the alt, az and zenith angle for the seqNums of a given dayObs. 

414 

415 Parameters 

416 ---------- 

417 butler : `lsst.daf.butler.Butler` 

418 The butler to query. 

419 dayObs : `int` 

420 The dayObs. 

421 seqNumList : `list` of `int` 

422 The seqNums for which to return the alt, az and zenith 

423 

424 Returns 

425 ------- 

426 azimuths : `list` of `float` 

427 List of the azimuths for each seqNum 

428 elevations : `list` of `float` 

429 List of the elevations for each seqNum 

430 zeniths : `list` of `float` 

431 List of the zenith angles for each seqNum 

432 """ 

433 azimuths, elevations, zeniths = [], [], [] 

434 for seqNum in seqNumList: 

435 md = butler.get('raw.metadata', day_obs=dayObs, seq_num=seqNum, detector=0) 

436 obsInfo = ObservationInfo(md) 

437 alt = obsInfo.altaz_begin.alt.value 

438 az = obsInfo.altaz_begin.az.value 

439 elevations.append(alt) 

440 zeniths.append(90-alt) 

441 azimuths.append(az) 

442 return azimuths, elevations, zeniths 

443 

444 

445def getFocusFromHeader(exp): 

446 """Get the raw focus value from the header. 

447 

448 Parameters 

449 ---------- 

450 exp : `lsst.afw.image.exposure` 

451 The exposure. 

452 

453 Returns 

454 ------- 

455 focus : `float` or `None` 

456 The focus value if found, else ``None``. 

457 """ 

458 md = exp.getMetadata() 

459 if 'FOCUSZ' in md: 

460 return md['FOCUSZ'] 

461 return None 

462 

463 

464def checkStackSetup(): 

465 """Check which weekly tag is being used and which local packages are setup. 

466 

467 Designed primarily for use in notbooks/observing, this prints the weekly 

468 tag(s) are setup for lsst_distrib, and lists any locally setup packages and 

469 the path to each. 

470 

471 Notes 

472 ----- 

473 Uses print() instead of logger messages as this should simply print them 

474 without being vulnerable to any log messages potentially being diverted. 

475 """ 

476 packages = packageUtils.getEnvironmentPackages(include_all=True) 

477 

478 lsstDistribHashAndTags = packages['lsst_distrib'] # looks something like 'g4eae7cb9+1418867f (w_2022_13)' 

479 lsstDistribTags = lsstDistribHashAndTags.split()[1] 

480 if len(lsstDistribTags.split()) == 1: 

481 tag = lsstDistribTags.replace('(', '') 

482 tag = tag.replace(')', '') 

483 print(f"You are running {tag} of lsst_distrib") 

484 else: # multiple weekly tags found for lsst_distrib! 

485 print(f'The version of lsst_distrib you have is compatible with: {lsstDistribTags}') 

486 

487 localPackages = [] 

488 localPaths = [] 

489 for package, tags in packages.items(): 

490 if tags.startswith('LOCAL:'): 

491 path = tags.split('LOCAL:')[1] 

492 path = path.split('@')[0] # don't need the git SHA etc 

493 localPaths.append(path) 

494 localPackages.append(package) 

495 

496 if localPackages: 

497 print("\nLocally setup packages:") 

498 print("-----------------------") 

499 maxLen = max(len(package) for package in localPackages) 

500 for package, path in zip(localPackages, localPaths): 

501 print(f"{package:<{maxLen}s} at {path}") 

502 else: 

503 print("\nNo locally setup packages (using a vanilla stack)") 

504 

505 

506def setupLogging(longlog=False): 

507 """Setup logging in the same way as one would get from pipetask run. 

508 

509 Code that isn't run through the butler CLI defaults to WARNING level 

510 messages and no logger names. This sets the behaviour to follow whatever 

511 the pipeline default is, currently 

512 <logger_name> <level>: <message> e.g. 

513 lsst.isr INFO: Masking defects. 

514 """ 

515 CliLog.initLog(longlog=longlog) 

516 

517 

518def getCurrentDayObs_datetime(): 

519 """Get the current day_obs - the observatory rolls the date over at UTC-12 

520 

521 Returned as datetime.date(2022, 4, 28) 

522 """ 

523 utc = gettz("UTC") 

524 nowUtc = datetime.datetime.now().astimezone(utc) 

525 offset = datetime.timedelta(hours=-12) 

526 dayObs = (nowUtc + offset).date() 

527 return dayObs 

528 

529 

530def getCurrentDayObs_int(): 

531 """Return the current dayObs as an int in the form 20220428 

532 """ 

533 return int(getCurrentDayObs_datetime().strftime("%Y%m%d")) 

534 

535 

536def getCurrentDayObs_humanStr(): 

537 """Return the current dayObs as a string in the form '2022-04-28' 

538 """ 

539 return dayObsIntToString(getCurrentDayObs_int()) 

540 

541 

542def getExpRecordAge(expRecord): 

543 """Get the time, in seconds, since the end of exposure. 

544 

545 Parameters 

546 ---------- 

547 expRecord : `lsst.daf.butler.DimensionRecord` 

548 The exposure record. 

549 

550 Returns 

551 ------- 

552 age : `float` 

553 The age of the exposure, in seconds. 

554 """ 

555 return -1 * (expRecord.timespan.end - Time.now()).sec 

556 

557 

558def getSite(): 

559 """Returns where the code is running. 

560 

561 Returns 

562 ------- 

563 location : `str` 

564 One of ['tucson', 'summit', 'base', 'staff-rsp', 'rubin-devl'] 

565 

566 Raises 

567 ------ 

568 ValueError 

569 Raised if location cannot be determined. 

570 """ 

571 # All nublado instances guarantee that EXTERNAL_URL is set and uniquely 

572 # identifies it. 

573 location = os.getenv('EXTERNAL_INSTANCE_URL', "") 

574 if location == "https://tucson-teststand.lsst.codes": 574 ↛ 575line 574 didn't jump to line 575, because the condition on line 574 was never true

575 return 'tucson' 

576 elif location == "https://summit-lsp.lsst.codes": 576 ↛ 577line 576 didn't jump to line 577, because the condition on line 576 was never true

577 return 'summit' 

578 elif location == "https://base-lsp.lsst.codes": 578 ↛ 579line 578 didn't jump to line 579, because the condition on line 578 was never true

579 return 'base' 

580 elif location == "https://usdf-rsp.slac.stanford.edu": 580 ↛ 581line 580 didn't jump to line 581, because the condition on line 580 was never true

581 return 'staff-rsp' 

582 

583 # if no EXTERNAL_URL, try HOSTNAME to see if we're on the dev nodes 

584 # it is expected that this will be extensible to SLAC 

585 hostname = os.getenv('HOSTNAME', "") 

586 if hostname.startswith('sdfrome'): 586 ↛ 587line 586 didn't jump to line 587, because the condition on line 586 was never true

587 return 'rubin-devl' 

588 

589 jenkinsHome = os.getenv('JENKINS_HOME', "") 

590 if jenkinsHome != "": 590 ↛ 591line 590 didn't jump to line 591, because the condition on line 590 was never true

591 return 'jenkins' 

592 

593 # we have failed 

594 raise ValueError('Location could not be determined') 

595 

596 

597def getAltAzFromSkyPosition(skyPos, visitInfo, doCorrectRefraction=False, 

598 wavelength=500.0, 

599 pressureOverride=None, 

600 temperatureOverride=None, 

601 relativeHumidityOverride=None, 

602 ): 

603 """Get the alt/az from the position on the sky and the time and location 

604 of the observation. 

605 

606 The temperature, pressure and relative humidity are taken from the 

607 visitInfo by default, but can be individually overridden as needed. It 

608 should be noted that the visitInfo never contains a nominal wavelength, and 

609 so this takes a default value of 500nm. 

610 

611 Parameters 

612 ---------- 

613 skyPos : `lsst.geom.SpherePoint` 

614 The position on the sky. 

615 visitInfo : `lsst.afw.image.VisitInfo` 

616 The visit info containing the time of the observation. 

617 doCorrectRefraction : `bool`, optional 

618 Correct for the atmospheric refraction? 

619 wavelength : `float`, optional 

620 The nominal wavelength in nanometers (e.g. 500.0), as a float. 

621 pressureOverride : `float`, optional 

622 The pressure, in bars (e.g. 0.770), to override the value supplied in 

623 the visitInfo, as a float. 

624 temperatureOverride : `float`, optional 

625 The temperature, in Celsius (e.g. 10.0), to override the value supplied 

626 in the visitInfo, as a float. 

627 relativeHumidityOverride : `float`, optional 

628 The relativeHumidity in the range 0..1 (i.e. not as a percentage), to 

629 override the value supplied in the visitInfo, as a float. 

630 

631 Returns 

632 ------- 

633 alt : `lsst.geom.Angle` 

634 The altitude. 

635 az : `lsst.geom.Angle` 

636 The azimuth. 

637 """ 

638 skyLocation = SkyCoord(skyPos.getRa().asRadians(), skyPos.getDec().asRadians(), unit=u.rad) 

639 long = visitInfo.observatory.getLongitude() 

640 lat = visitInfo.observatory.getLatitude() 

641 ele = visitInfo.observatory.getElevation() 

642 earthLocation = EarthLocation.from_geodetic(long.asDegrees(), lat.asDegrees(), ele) 

643 

644 refractionKwargs = {} 

645 if doCorrectRefraction: 

646 # wavelength is never supplied in the visitInfo so always take this 

647 wavelength = wavelength * u.nm 

648 

649 if pressureOverride: 

650 pressure = pressureOverride 

651 else: 

652 pressure = visitInfo.weather.getAirPressure() 

653 # ObservationInfos (which are the "source of truth" use pascals) so 

654 # convert from pascals to bars 

655 pressure /= 100000.0 

656 pressure = pressure*u.bar 

657 

658 if temperatureOverride: 

659 temperature = temperatureOverride 

660 else: 

661 temperature = visitInfo.weather.getAirTemperature() 

662 temperature = temperature*u.deg_C 

663 

664 if relativeHumidityOverride: 

665 relativeHumidity = relativeHumidityOverride 

666 else: 

667 relativeHumidity = visitInfo.weather.getHumidity() / 100.0 # this is in percent 

668 relativeHumidity = relativeHumidity*u.deg_C 

669 

670 refractionKwargs = dict(pressure=pressure, 

671 temperature=temperature, 

672 relative_humidity=relativeHumidity, 

673 obswl=wavelength) 

674 

675 # must go via astropy.Time because dafBase.dateTime.DateTime contains 

676 # the timezone, but going straight to visitInfo.date.toPython() loses this. 

677 obsTime = Time(visitInfo.date.toPython(), scale='tai') 

678 altAz = AltAz(obstime=obsTime, 

679 location=earthLocation, 

680 **refractionKwargs) 

681 

682 obsAltAz = skyLocation.transform_to(altAz) 

683 alt = geom.Angle(obsAltAz.alt.degree, geom.degrees) 

684 az = geom.Angle(obsAltAz.az.degree, geom.degrees) 

685 

686 return alt, az 

687 

688 

689def getExpPositionOffset(exp1, exp2, useWcs=True, allowDifferentPlateScales=False): 

690 """Get the change in sky position between two exposures. 

691 

692 Given two exposures, calculate the offset on the sky between the images. 

693 If useWcs then use the (fitted or unfitted) skyOrigin from their WCSs, and 

694 calculate the alt/az from the observation times, otherwise use the nominal 

695 values in the exposures' visitInfos. Note that if using the visitInfo 

696 values that for a given pointing the ra/dec will be ~identical, regardless 

697 of whether astrometric fitting has been performed. 

698 

699 Values are given as exp1-exp2. 

700 

701 Parameters 

702 ---------- 

703 exp1 : `lsst.afw.image.Exposure` 

704 The first exposure. 

705 exp2 : `lsst.afw.image.Exposure` 

706 The second exposure. 

707 useWcs : `bool` 

708 Use the WCS for the ra/dec and alt/az if True, else use the nominal/ 

709 boresight values from the exposures' visitInfos. 

710 allowDifferentPlateScales : `bool`, optional 

711 Use to disable checking that plate scales are the same. Generally, 

712 differing plate scales would indicate an error, but where blind-solving 

713 has been undertaken during commissioning plate scales can be different 

714 enough to warrant setting this to ``True``. 

715 

716 Returns 

717 ------- 

718 offsets : `lsst.pipe.base.Struct` 

719 A struct containing the offsets: 

720 ``deltaRa`` 

721 The diference in ra (`lsst.geom.Angle`) 

722 ``deltaDec`` 

723 The diference in dec (`lsst.geom.Angle`) 

724 ``deltaAlt`` 

725 The diference in alt (`lsst.geom.Angle`) 

726 ``deltaAz`` 

727 The diference in az (`lsst.geom.Angle`) 

728 ``deltaPixels`` 

729 The diference in pixels (`float`) 

730 """ 

731 

732 wcs1 = exp1.getWcs() 

733 wcs2 = exp2.getWcs() 

734 pixScaleArcSec = wcs1.getPixelScale().asArcseconds() 

735 if not allowDifferentPlateScales: 

736 assert np.isclose(pixScaleArcSec, wcs2.getPixelScale().asArcseconds()), \ 

737 "Pixel scales in the exposures differ." 

738 

739 if useWcs: 

740 p1 = wcs1.getSkyOrigin() 

741 p2 = wcs2.getSkyOrigin() 

742 alt1, az1 = getAltAzFromSkyPosition(p1, exp1.getInfo().getVisitInfo()) 

743 alt2, az2 = getAltAzFromSkyPosition(p2, exp2.getInfo().getVisitInfo()) 

744 ra1 = p1[0] 

745 ra2 = p2[0] 

746 dec1 = p1[1] 

747 dec2 = p2[1] 

748 else: 

749 az1 = exp1.visitInfo.boresightAzAlt[0] 

750 az2 = exp2.visitInfo.boresightAzAlt[0] 

751 alt1 = exp1.visitInfo.boresightAzAlt[1] 

752 alt2 = exp2.visitInfo.boresightAzAlt[1] 

753 

754 ra1 = exp1.visitInfo.boresightRaDec[0] 

755 ra2 = exp2.visitInfo.boresightRaDec[0] 

756 dec1 = exp1.visitInfo.boresightRaDec[1] 

757 dec2 = exp2.visitInfo.boresightRaDec[1] 

758 

759 p1 = exp1.visitInfo.boresightRaDec 

760 p2 = exp2.visitInfo.boresightRaDec 

761 

762 angular_offset = p1.separation(p2).asArcseconds() 

763 deltaPixels = angular_offset / pixScaleArcSec 

764 

765 ret = pipeBase.Struct(deltaRa=(ra1-ra2).wrapNear(geom.Angle(0.0)), 

766 deltaDec=dec1-dec2, 

767 deltaAlt=alt1-alt2, 

768 deltaAz=(az1-az2).wrapNear(geom.Angle(0.0)), 

769 deltaPixels=deltaPixels 

770 ) 

771 

772 return ret 

773 

774 

775def starTrackerFileToExposure(filename, logger=None): 

776 """Read the exposure from the file and set the wcs from the header. 

777 

778 Parameters 

779 ---------- 

780 filename : `str` 

781 The full path to the file. 

782 logger : `logging.Logger`, optional 

783 The logger to use for errors, created if not supplied. 

784 

785 Returns 

786 ------- 

787 exp : `lsst.afw.image.Exposure` 

788 The exposure. 

789 """ 

790 if not logger: 

791 logger = logging.getLogger(__name__) 

792 exp = afwImage.ExposureF(filename) 

793 try: 

794 wcs = genericCameraHeaderToWcs(exp) 

795 exp.setWcs(wcs) 

796 except Exception as e: 

797 logger.warning(f"Failed to set wcs from header: {e}") 

798 

799 # for some reason the date isn't being set correctly 

800 # DATE-OBS is present in the original header, but it's being 

801 # stripped out and somehow not set (plus it doesn't give the midpoint 

802 # of the exposure), so set it manually from the midpoint here 

803 try: 

804 md = exp.getMetadata() 

805 begin = datetime.datetime.fromisoformat(md['DATE-BEG']) 

806 end = datetime.datetime.fromisoformat(md['DATE-END']) 

807 duration = end - begin 

808 mid = begin + duration/2 

809 newTime = dafBase.DateTime(mid.isoformat(), dafBase.DateTime.Timescale.TAI) 

810 newVi = exp.visitInfo.copyWith(date=newTime) 

811 exp.info.setVisitInfo(newVi) 

812 except Exception as e: 

813 logger.warning(f"Failed to set date from header: {e}") 

814 

815 return exp 

816 

817 

818def obsInfoToDict(obsInfo): 

819 """Convert an ObservationInfo to a dict. 

820 

821 Parameters 

822 ---------- 

823 obsInfo : `astro_metadata_translator.ObservationInfo` 

824 The ObservationInfo to convert. 

825 

826 Returns 

827 ------- 

828 obsInfoDict : `dict` 

829 The ObservationInfo as a dict. 

830 """ 

831 return {prop: getattr(obsInfo, prop) for prop in obsInfo.all_properties.keys()} 

832 

833 

834def getFieldNameAndTileNumber(field, warn=True, logger=None): 

835 """Get the tile name and number of an observed field. 

836 

837 It is assumed to always be appended, with an underscore, to the rest of the 

838 field name. Returns the name and number as a tuple, or the name unchanged 

839 if no tile number is found. 

840 

841 Parameters 

842 ---------- 

843 field : `str` 

844 The name of the field 

845 

846 Returns 

847 ------- 

848 fieldName : `str` 

849 The name of the field without the trailing tile number, if present. 

850 tileNum : `int` 

851 The number of the tile, as an integer, or ``None`` if not found. 

852 """ 

853 if warn and not logger: 

854 logger = logging.getLogger('lsst.summit.utils.utils.getFieldNameAndTileNumber') 

855 

856 if '_' not in field: 

857 if warn: 

858 logger.warning(f"Field {field} does not contain an underscore," 

859 " so cannot determine the tile number.") 

860 return field, None 

861 

862 try: 

863 fieldParts = field.split("_") 

864 fieldNum = int(fieldParts[-1]) 

865 except ValueError: 

866 if warn: 

867 logger.warning(f"Field {field} does not contain only an integer after the final underscore" 

868 " so cannot determine the tile number.") 

869 return field, None 

870 

871 return "_".join(fieldParts[:-1]), fieldNum 

872 

873 

874def getAirmassSeeingCorrection(airmass): 

875 """Get the correction factor for seeing due to airmass. 

876 

877 Parameters 

878 ---------- 

879 airmass : `float` 

880 The airmass, greater than or equal to 1. 

881 

882 Returns 

883 ------- 

884 correctionFactor : `float` 

885 The correction factor to apply to the seeing. 

886 

887 Raises 

888 ------ 

889 ValueError raised for unphysical airmasses. 

890 """ 

891 if airmass < 1: 

892 raise ValueError(f"Invalid airmass: {airmass}") 

893 return airmass**(-0.6) 

894 

895 

896def getFilterSeeingCorrection(filterName): 

897 """Get the correction factor for seeing due to a filter. 

898 

899 Parameters 

900 ---------- 

901 filterName : `str` 

902 The name of the filter, e.g. 'SDSSg_65mm'. 

903 

904 Returns 

905 ------- 

906 correctionFactor : `float` 

907 The correction factor to apply to the seeing. 

908 

909 Raises 

910 ------ 

911 ValueError raised for unknown filters. 

912 """ 

913 match filterName: 

914 case 'SDSSg_65mm': 

915 return (477./500.)**0.2 

916 case 'SDSSr_65mm': 

917 return (623./500.)**0.2 

918 case 'SDSSi_65mm': 

919 return (762./500.)**0.2 

920 case _: 

921 raise ValueError(f"Unknown filter name: {filterName}") 

922 

923 

924def getCdf(data, scale): 

925 """Return an approximate cumulative distribution function scaled to 

926 the [0, scale] range. 

927 

928 Parameters 

929 ---------- 

930 data : `np.array` 

931 The input data. 

932 scale : `int` 

933 The scaling range of the output. 

934 

935 Returns 

936 ------- 

937 cdf : `np.array` of `int` 

938 A monotonically increasing sequence that represents a scaled 

939 cumulative distribution function, starting with the value at 

940 minVal, then at (minVal + 1), and so on. 

941 minVal : `float` 

942 An integer smaller than the minimum value in the input data. 

943 maxVal : `float` 

944 An integer larger than the maximum value in the input data. 

945 """ 

946 flatData = data.ravel() 

947 size = flatData.size - np.count_nonzero(np.isnan(flatData)) 

948 

949 minVal = np.floor(np.nanmin(flatData)) 

950 maxVal = np.ceil(np.nanmax(flatData)) + 1.0 

951 

952 hist, binEdges = np.histogram( 

953 flatData, bins=int(maxVal - minVal), range=(minVal, maxVal) 

954 ) 

955 

956 cdf = (scale*np.cumsum(hist)/size).astype(np.int64) 

957 return cdf, minVal, maxVal 

958 

959 

960def getQuantiles(data, nColors): 

961 """Get a set of boundaries that equally distribute data into 

962 nColors intervals. The output can be used to make a colormap 

963 of nColors colors. 

964 

965 This is equivalent to using the numpy function: 

966 np.quantile(data, np.linspace(0, 1, nColors + 1)) 

967 but with a coarser precision, yet sufficient for our use case. 

968 This implementation gives a speed-up. 

969 

970 Parameters 

971 ---------- 

972 data : `np.array` 

973 The input image data. 

974 nColors : `int` 

975 The number of intervals to distribute data into. 

976 

977 Returns 

978 ------- 

979 boundaries: `list` of `float` 

980 A monotonically increasing sequence of size (nColors + 1). 

981 These are the edges of nColors intervals. 

982 """ 

983 cdf, minVal, maxVal = getCdf(data, nColors) 

984 boundaries = np.asarray( 

985 [np.argmax(cdf >= i) + minVal for i in range(nColors)] + [maxVal] 

986 ) 

987 return boundaries 

988 

989 

990def digitizeData(data, nColors=256): 

991 """ 

992 Scale data into nColors using its cumulative distribution function. 

993 

994 Parameters 

995 ---------- 

996 data : `np.array` 

997 The input image data. 

998 nColors : `int` 

999 The number of intervals to distribute data into. 

1000 

1001 Returns 

1002 ------- 

1003 data: `np.array` of `int` 

1004 Scaled data in the [0, nColors - 1] range. 

1005 """ 

1006 cdf, minVal, maxVal = getCdf(data, nColors - 1) 

1007 bins = np.floor((data - minVal)).astype(np.int64) 

1008 return cdf[bins]