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1# This file is part of obs_base. 

2# 

3# Developed for the LSST Data Management System. 

4# This product includes software developed by the LSST Project 

5# (http://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 <http://www.gnu.org/licenses/>. 

21 

22__all__ = ("FitsExposureFormatter", "FitsImageFormatter", "FitsMaskFormatter", 

23 "FitsMaskedImageFormatter") 

24 

25from astro_metadata_translator import fix_header 

26from lsst.daf.base import PropertySet 

27from lsst.daf.butler import Formatter 

28# Do not use ExposureFitsReader.readMetadata because that strips 

29# out lots of headers and there is no way to recover them 

30from lsst.afw.fits import readMetadata 

31from lsst.afw.image import ExposureFitsReader, ImageFitsReader, MaskFitsReader, MaskedImageFitsReader 

32# Needed for ApCorrMap to resolve properly 

33from lsst.afw.math import BoundedField # noqa: F401 

34 

35 

36class FitsExposureFormatter(Formatter): 

37 """Interface for reading and writing Exposures to and from FITS files. 

38 

39 This Formatter supports write recipes. 

40 

41 Each ``FitsExposureFormatter`` recipe for FITS compression should 

42 define ``image``, ``mask`` and ``variance`` entries, each of which may 

43 contain ``compression`` and ``scaling`` entries. Defaults will be 

44 provided for any missing elements under ``compression`` and 

45 ``scaling``. 

46 

47 The allowed entries under ``compression`` are: 

48 

49 * ``algorithm`` (`str`): compression algorithm to use 

50 * ``rows`` (`int`): number of rows per tile (0 = entire dimension) 

51 * ``columns`` (`int`): number of columns per tile (0 = entire dimension) 

52 * ``quantizeLevel`` (`float`): cfitsio quantization level 

53 

54 The allowed entries under ``scaling`` are: 

55 

56 * ``algorithm`` (`str`): scaling algorithm to use 

57 * ``bitpix`` (`int`): bits per pixel (0,8,16,32,64,-32,-64) 

58 * ``fuzz`` (`bool`): fuzz the values when quantising floating-point values? 

59 * ``seed`` (`int`): seed for random number generator when fuzzing 

60 * ``maskPlanes`` (`list` of `str`): mask planes to ignore when doing 

61 statistics 

62 * ``quantizeLevel`` (`float`): divisor of the standard deviation for 

63 ``STDEV_*`` scaling 

64 * ``quantizePad`` (`float`): number of stdev to allow on the low side (for 

65 ``STDEV_POSITIVE``/``NEGATIVE``) 

66 * ``bscale`` (`float`): manually specified ``BSCALE`` 

67 (for ``MANUAL`` scaling) 

68 * ``bzero`` (`float`): manually specified ``BSCALE`` 

69 (for ``MANUAL`` scaling) 

70 

71 A very simple example YAML recipe: 

72 

73 .. code-block:: yaml 

74 

75 lsst.obs.base.fitsExposureFormatter.FitsExposureFormatter: 

76 default: 

77 image: &default 

78 compression: 

79 algorithm: GZIP_SHUFFLE 

80 mask: *default 

81 variance: *default 

82 

83 """ 

84 supportedExtensions = frozenset({".fits", ".fits.gz", ".fits.fz", ".fz", ".fit"}) 

85 extension = ".fits" 

86 _metadata = None 

87 supportedWriteParameters = frozenset({"recipe"}) 

88 _readerClass = ExposureFitsReader 

89 

90 unsupportedParameters = {} 

91 """Support all parameters.""" 

92 

93 @property 

94 def metadata(self): 

95 """The metadata read from this file. It will be stripped as 

96 components are extracted from it 

97 (`lsst.daf.base.PropertyList`). 

98 """ 

99 if self._metadata is None: 

100 self._metadata = self.readMetadata() 

101 return self._metadata 

102 

103 def readMetadata(self): 

104 """Read all header metadata directly into a PropertyList. 

105 

106 Returns 

107 ------- 

108 metadata : `~lsst.daf.base.PropertyList` 

109 Header metadata. 

110 """ 

111 md = readMetadata(self.fileDescriptor.location.path) 

112 fix_header(md) 

113 return md 

114 

115 def stripMetadata(self): 

116 """Remove metadata entries that are parsed into components. 

117 

118 This is only called when just the metadata is requested; stripping 

119 entries there forces code that wants other components to ask for those 

120 components directly rather than trying to extract them from the 

121 metadata manually, which is fragile. This behavior is an intentional 

122 change from Gen2. 

123 

124 Parameters 

125 ---------- 

126 metadata : `~lsst.daf.base.PropertyList` 

127 Header metadata, to be modified in-place. 

128 """ 

129 # TODO: make sure this covers everything, by delegating to something 

130 # that doesn't yet exist in afw.image.ExposureInfo. 

131 from lsst.afw.image import bboxFromMetadata 

132 from lsst.afw.geom import makeSkyWcs 

133 

134 # Protect against the metadata being missing 

135 try: 

136 bboxFromMetadata(self.metadata) # always strips 

137 except LookupError: 

138 pass 

139 try: 

140 makeSkyWcs(self.metadata, strip=True) 

141 except Exception: 

142 pass 

143 

144 def readComponent(self, component, parameters=None): 

145 """Read a component held by the Exposure. 

146 

147 Parameters 

148 ---------- 

149 component : `str`, optional 

150 Component to read from the file. 

151 parameters : `dict`, optional 

152 If specified, a dictionary of slicing parameters that 

153 overrides those in ``fileDescriptor``. 

154 

155 Returns 

156 ------- 

157 obj : component-dependent 

158 In-memory component object. 

159 

160 Raises 

161 ------ 

162 KeyError 

163 Raised if the requested component cannot be handled. 

164 """ 

165 

166 # Metadata is handled explicitly elsewhere 

167 componentMap = {'wcs': ('readWcs', False), 

168 'coaddInputs': ('readCoaddInputs', False), 

169 'psf': ('readPsf', False), 

170 'image': ('readImage', True), 

171 'mask': ('readMask', True), 

172 'variance': ('readVariance', True), 

173 'photoCalib': ('readPhotoCalib', False), 

174 'bbox': ('readBBox', True), 

175 'dimensions': ('readBBox', True), 

176 'xy0': ('readXY0', True), 

177 'filter': ('readFilter', False), 

178 'validPolygon': ('readValidPolygon', False), 

179 'apCorrMap': ('readApCorrMap', False), 

180 'visitInfo': ('readVisitInfo', False), 

181 'transmissionCurve': ('readTransmissionCurve', False), 

182 'detector': ('readDetector', False), 

183 'extras': ('readExtraComponents', False), 

184 'exposureInfo': ('readExposureInfo', False), 

185 } 

186 method, hasParams = componentMap.get(component, (None, False)) 

187 

188 if method: 

189 # This reader can read standalone Image/Mask files as well 

190 # when dealing with components. 

191 reader = self._readerClass(self.fileDescriptor.location.path) 

192 caller = getattr(reader, method, None) 

193 

194 if caller: 

195 if parameters is None: 

196 parameters = self.fileDescriptor.parameters 

197 if parameters is None: 

198 parameters = {} 

199 self.fileDescriptor.storageClass.validateParameters(parameters) 

200 

201 if hasParams and parameters: 

202 thisComponent = caller(**parameters) 

203 else: 

204 thisComponent = caller() 

205 if component == "dimensions" and thisComponent is not None: 

206 thisComponent = thisComponent.getDimensions() 

207 return thisComponent 

208 else: 

209 raise KeyError(f"Unknown component requested: {component}") 

210 

211 def readFull(self, parameters=None): 

212 """Read the full Exposure object. 

213 

214 Parameters 

215 ---------- 

216 parameters : `dict`, optional 

217 If specified a dictionary of slicing parameters that overrides 

218 those in ``fileDescriptor``. 

219 

220 Returns 

221 ------- 

222 exposure : `~lsst.afw.image.Exposure` 

223 Complete in-memory exposure. 

224 """ 

225 fileDescriptor = self.fileDescriptor 

226 if parameters is None: 

227 parameters = fileDescriptor.parameters 

228 if parameters is None: 

229 parameters = {} 

230 fileDescriptor.storageClass.validateParameters(parameters) 

231 reader = self._readerClass(fileDescriptor.location.path) 

232 return reader.read(**parameters) 

233 

234 def read(self, component=None): 

235 """Read data from a file. 

236 

237 Parameters 

238 ---------- 

239 component : `str`, optional 

240 Component to read from the file. Only used if the `StorageClass` 

241 for reading differed from the `StorageClass` used to write the 

242 file. 

243 

244 Returns 

245 ------- 

246 inMemoryDataset : `object` 

247 The requested data as a Python object. The type of object 

248 is controlled by the specific formatter. 

249 

250 Raises 

251 ------ 

252 ValueError 

253 Component requested but this file does not seem to be a concrete 

254 composite. 

255 KeyError 

256 Raised when parameters passed with fileDescriptor are not 

257 supported. 

258 """ 

259 fileDescriptor = self.fileDescriptor 

260 if fileDescriptor.readStorageClass != fileDescriptor.storageClass: 

261 if component == "metadata": 

262 self.stripMetadata() 

263 return self.metadata 

264 elif component is not None: 

265 return self.readComponent(component) 

266 else: 

267 raise ValueError("Storage class inconsistency ({} vs {}) but no" 

268 " component requested".format(fileDescriptor.readStorageClass.name, 

269 fileDescriptor.storageClass.name)) 

270 return self.readFull() 

271 

272 def write(self, inMemoryDataset): 

273 """Write a Python object to a file. 

274 

275 Parameters 

276 ---------- 

277 inMemoryDataset : `object` 

278 The Python object to store. 

279 """ 

280 # Update the location with the formatter-preferred file extension 

281 self.fileDescriptor.location.updateExtension(self.extension) 

282 outputPath = self.fileDescriptor.location.path 

283 

284 # check to see if we have a recipe requested 

285 recipeName = self.writeParameters.get("recipe") 

286 recipe = self.getImageCompressionSettings(recipeName) 

287 if recipe: 

288 # Can not construct a PropertySet from a hierarchical 

289 # dict but can update one. 

290 ps = PropertySet() 

291 ps.update(recipe) 

292 inMemoryDataset.writeFitsWithOptions(outputPath, options=ps) 

293 else: 

294 inMemoryDataset.writeFits(outputPath) 

295 

296 def getImageCompressionSettings(self, recipeName): 

297 """Retrieve the relevant compression settings for this recipe. 

298 

299 Parameters 

300 ---------- 

301 recipeName : `str` 

302 Label associated with the collection of compression parameters 

303 to select. 

304 

305 Returns 

306 ------- 

307 settings : `dict` 

308 The selected settings. 

309 """ 

310 # if no recipe has been provided and there is no default 

311 # return immediately 

312 if not recipeName: 

313 if "default" not in self.writeRecipes: 

314 return {} 

315 recipeName = "default" 

316 

317 if recipeName not in self.writeRecipes: 

318 raise RuntimeError(f"Unrecognized recipe option given for compression: {recipeName}") 

319 

320 recipe = self.writeRecipes[recipeName] 

321 

322 # Set the seed based on dataId 

323 seed = hash(tuple(self.dataId.items())) % 2**31 

324 for plane in ("image", "mask", "variance"): 

325 if plane in recipe and "scaling" in recipe[plane]: 

326 scaling = recipe[plane]["scaling"] 

327 if "seed" in scaling and scaling["seed"] == 0: 

328 scaling["seed"] = seed 

329 

330 return recipe 

331 

332 @classmethod 

333 def validateWriteRecipes(cls, recipes): 

334 """Validate supplied recipes for this formatter. 

335 

336 The recipes are supplemented with default values where appropriate. 

337 

338 TODO: replace this custom validation code with Cerberus (DM-11846) 

339 

340 Parameters 

341 ---------- 

342 recipes : `dict` 

343 Recipes to validate. Can be empty dict or `None`. 

344 

345 Returns 

346 ------- 

347 validated : `dict` 

348 Validated recipes. Returns what was given if there are no 

349 recipes listed. 

350 

351 Raises 

352 ------ 

353 RuntimeError 

354 Raised if validation fails. 

355 """ 

356 # Schemas define what should be there, and the default values (and by 

357 # the default value, the expected type). 

358 compressionSchema = { 

359 "algorithm": "NONE", 

360 "rows": 1, 

361 "columns": 0, 

362 "quantizeLevel": 0.0, 

363 } 

364 scalingSchema = { 

365 "algorithm": "NONE", 

366 "bitpix": 0, 

367 "maskPlanes": ["NO_DATA"], 

368 "seed": 0, 

369 "quantizeLevel": 4.0, 

370 "quantizePad": 5.0, 

371 "fuzz": True, 

372 "bscale": 1.0, 

373 "bzero": 0.0, 

374 } 

375 

376 if not recipes: 

377 # We can not insist on recipes being specified 

378 return recipes 

379 

380 def checkUnrecognized(entry, allowed, description): 

381 """Check to see if the entry contains unrecognised keywords""" 

382 unrecognized = set(entry) - set(allowed) 

383 if unrecognized: 

384 raise RuntimeError( 

385 f"Unrecognized entries when parsing image compression recipe {description}: " 

386 f"{unrecognized}") 

387 

388 validated = {} 

389 for name in recipes: 

390 checkUnrecognized(recipes[name], ["image", "mask", "variance"], name) 

391 validated[name] = {} 

392 for plane in ("image", "mask", "variance"): 

393 checkUnrecognized(recipes[name][plane], ["compression", "scaling"], 

394 f"{name}->{plane}") 

395 

396 np = {} 

397 validated[name][plane] = np 

398 for settings, schema in (("compression", compressionSchema), 

399 ("scaling", scalingSchema)): 

400 np[settings] = {} 

401 if settings not in recipes[name][plane]: 

402 for key in schema: 

403 np[settings][key] = schema[key] 

404 continue 

405 entry = recipes[name][plane][settings] 

406 checkUnrecognized(entry, schema.keys(), f"{name}->{plane}->{settings}") 

407 for key in schema: 

408 value = type(schema[key])(entry[key]) if key in entry else schema[key] 

409 np[settings][key] = value 

410 return validated 

411 

412 

413class FitsImageFormatter(FitsExposureFormatter): 

414 """Specialisation for `~lsst.afw.image.Image` reading. 

415 """ 

416 

417 _readerClass = ImageFitsReader 

418 

419 

420class FitsMaskFormatter(FitsExposureFormatter): 

421 """Specialisation for `~lsst.afw.image.Mask` reading. 

422 """ 

423 

424 _readerClass = MaskFitsReader 

425 

426 

427class FitsMaskedImageFormatter(FitsExposureFormatter): 

428 """Specialisation for `~lsst.afw.image.MaskedImage` reading. 

429 """ 

430 

431 _readerClass = MaskedImageFitsReader