Coverage for python/lsst/obs/lsst/assembly.py: 12%

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1# This file is part of obs_lsst 

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__ = ("attachRawWcsFromBoresight", "fixAmpGeometry", "assembleUntrimmedCcd", 

23 "fixAmpsAndAssemble", "readRawAmps") 

24 

25import logging 

26from contextlib import contextmanager 

27import numpy as np 

28import lsst.afw.image as afwImage 

29from lsst.obs.base import bboxFromIraf, MakeRawVisitInfoViaObsInfo, createInitialSkyWcs 

30from lsst.geom import Box2I, Extent2I 

31from lsst.ip.isr import AssembleCcdTask 

32from astro_metadata_translator import ObservationInfo 

33 

34logger = logging.getLogger(__name__) 

35 

36 

37def attachRawWcsFromBoresight(exposure, dataIdForErrMsg=None): 

38 """Attach a WCS by extracting boresight, rotation, and camera geometry from 

39 an Exposure. 

40 

41 Parameters 

42 ---------- 

43 exposure : `lsst.afw.image.Exposure` 

44 Image object with attached metadata and detector components. 

45 

46 Return 

47 ------ 

48 attached : `bool` 

49 If True, a WCS component was successfully created and attached to 

50 ``exposure``. 

51 """ 

52 md = exposure.getMetadata() 

53 # Use the generic version since we do not have a mapper available to 

54 # tell us a specific translator to use. 

55 obsInfo = ObservationInfo(md) 

56 visitInfo = MakeRawVisitInfoViaObsInfo.observationInfo2visitInfo(obsInfo, log=logger) 

57 exposure.getInfo().setVisitInfo(visitInfo) 

58 exposure.info.id = obsInfo.detector_exposure_id 

59 

60 # LATISS (and likely others) need flipping, DC2 etc do not 

61 flipX = False 

62 if obsInfo.instrument in ("LATISS",): 

63 flipX = True 

64 

65 if visitInfo.getBoresightRaDec().isFinite(): 

66 exposure.setWcs(createInitialSkyWcs(visitInfo, exposure.getDetector(), flipX=flipX)) 

67 return True 

68 

69 if obsInfo.observation_type == "science": 

70 logger.warning("Unable to set WCS from header as RA/Dec/Angle are unavailable%s", 

71 ("" if dataIdForErrMsg is None else " for dataId %s" % dataIdForErrMsg)) 

72 return False 

73 

74 

75def fixAmpGeometry(inAmp, bbox, metadata, logCmd=None): 

76 """Make sure a camera geometry amplifier matches an on-disk bounding box. 

77 

78 Bounding box differences that are consistent with differences in overscan 

79 regions are assumed to be overscan regions, which gives us enough 

80 information to correct the camera geometry. 

81 

82 Parameters 

83 ---------- 

84 inAmp : `lsst.afw.cameraGeom.Amplifier` 

85 Amplifier description from camera geometry. 

86 bbox : `lsst.geom.Box2I` 

87 The on-disk bounding box of the amplifer image. 

88 metadata : `lsst.daf.base.PropertyList` 

89 FITS header metadata from the amplifier HDU. 

90 logCmd : `function`, optional 

91 Call back to use to issue log messages about patching. Arguments to 

92 this function should match arguments to be accepted by normal logging 

93 functions. Warnings about bad EXTNAMES are always sent directly to 

94 the module-level logger. 

95 

96 Return 

97 ------ 

98 outAmp : `~lsst.afw.cameraGeom.Amplifier.Builder` 

99 modified : `bool` 

100 `True` if ``amp`` was modified; `False` otherwise. 

101 

102 Raises 

103 ------ 

104 RuntimeError 

105 Raised if the bounding boxes differ in a way that is not consistent 

106 with just a change in overscan. 

107 """ 

108 if logCmd is None: 

109 # Define a null log command 

110 def logCmd(*args): 

111 return 

112 

113 # check that the book-keeping worked and we got the correct EXTNAME 

114 extname = metadata.get("EXTNAME") 

115 predictedExtname = f"Segment{inAmp.getName()[1:]}" 

116 if extname is not None and predictedExtname != extname: 

117 logger.warning('expected to see EXTNAME == "%s", but saw "%s"', predictedExtname, extname) 

118 

119 modified = False 

120 

121 outAmp = inAmp.rebuild() 

122 if outAmp.getRawBBox() != bbox: # Oh dear. cameraGeom is wrong -- probably overscan 

123 if outAmp.getRawDataBBox().getDimensions() != outAmp.getBBox().getDimensions(): 

124 raise RuntimeError("Active area is the wrong size: %s v. %s" % 

125 (outAmp.getRawDataBBox().getDimensions(), outAmp.getBBox().getDimensions())) 

126 

127 logCmd("outAmp.getRawBBox() != data.getBBox(); patching. (%s v. %s)", outAmp.getRawBBox(), bbox) 

128 

129 w, h = bbox.getDimensions() 

130 ow, oh = outAmp.getRawBBox().getDimensions() # "old" (cameraGeom) dimensions 

131 # 

132 # We could trust the BIASSEC keyword, or we can just assume that 

133 # they've changed the number of overscan pixels (serial and/or 

134 # parallel). As Jim Chiang points out, the latter is safer 

135 # 

136 fromCamGeom = outAmp.getRawHorizontalOverscanBBox() 

137 hOverscanBBox = Box2I(fromCamGeom.getBegin(), 

138 Extent2I(w - fromCamGeom.getBeginX(), fromCamGeom.getHeight())) 

139 fromCamGeom = outAmp.getRawVerticalOverscanBBox() 

140 vOverscanBBox = Box2I(fromCamGeom.getBegin(), 

141 Extent2I(fromCamGeom.getWidth(), h - fromCamGeom.getBeginY())) 

142 outAmp.setRawBBox(bbox) 

143 outAmp.setRawHorizontalOverscanBBox(hOverscanBBox) 

144 outAmp.setRawVerticalOverscanBBox(vOverscanBBox) 

145 # 

146 # This gets all the geometry right for the amplifier, but the size 

147 # of the untrimmed image will be wrong and we'll put the amp sections 

148 # in the wrong places, i.e. 

149 # outAmp.getRawXYOffset() 

150 # will be wrong. So we need to recalculate the offsets. 

151 # 

152 xRawExtent, yRawExtent = outAmp.getRawBBox().getDimensions() 

153 

154 x0, y0 = outAmp.getRawXYOffset() 

155 ix, iy = x0//ow, y0/oh 

156 x0, y0 = ix*xRawExtent, iy*yRawExtent 

157 outAmp.setRawXYOffset(Extent2I(ix*xRawExtent, iy*yRawExtent)) 

158 

159 modified = True 

160 

161 # 

162 # Check the "IRAF" keywords, but don't abort if they're wrong 

163 # 

164 # Only warn about the first amp, use debug for the others 

165 # 

166 d = metadata.toDict() 

167 detsec = bboxFromIraf(d["DETSEC"]) if "DETSEC" in d else None 

168 datasec = bboxFromIraf(d["DATASEC"]) if "DATASEC" in d else None 

169 biassec = bboxFromIraf(d["BIASSEC"]) if "BIASSEC" in d else None 

170 

171 if detsec and outAmp.getBBox() != detsec: 

172 logCmd("DETSEC doesn't match (%s != %s)", outAmp.getBBox(), detsec) 

173 if datasec and outAmp.getRawDataBBox() != datasec: 

174 logCmd("DATASEC doesn't match for (%s != %s)", outAmp.getRawDataBBox(), detsec) 

175 if biassec and outAmp.getRawHorizontalOverscanBBox() != biassec: 

176 logCmd("BIASSEC doesn't match for (%s != %s)", outAmp.getRawHorizontalOverscanBBox(), detsec) 

177 

178 return outAmp, modified 

179 

180 

181def assembleUntrimmedCcd(ccd, exposures): 

182 """Assemble an untrimmmed CCD from per-amp Exposure objects. 

183 

184 Parameters 

185 ---------- 

186 ccd : `~lsst.afw.cameraGeom.Detector` 

187 The detector geometry for this ccd that will be used as the 

188 framework for the assembly of the input amplifier exposures. 

189 exposures : sequence of `lsst.afw.image.Exposure` 

190 Per-amplifier images, in the same order as ``amps``. 

191 

192 Returns 

193 ------- 

194 ccd : `lsst.afw.image.Exposure` 

195 Assembled CCD image. 

196 """ 

197 ampDict = {} 

198 for amp, exposure in zip(ccd, exposures): 

199 ampDict[amp.getName()] = exposure 

200 config = AssembleCcdTask.ConfigClass() 

201 config.doTrim = False 

202 assembleTask = AssembleCcdTask(config=config) 

203 return assembleTask.assembleCcd(ampDict) 

204 

205 

206@contextmanager 

207def warn_once(msg): 

208 """Return a context manager around a log-like object that emits a warning 

209 the first time it is used and a debug message all subsequent times. 

210 

211 Parameters 

212 ---------- 

213 msg : `str` 

214 Message to prefix all log messages with. 

215 

216 Returns 

217 ------- 

218 logger 

219 A log-like object that takes a %-style format string and positional 

220 substition args. 

221 """ 

222 warned = False 

223 

224 def logCmd(s, *args): 

225 nonlocal warned 

226 log_msg = f"{msg}: {s}" 

227 if warned: 

228 logger.debug(log_msg, *args) 

229 else: 

230 logger.warning(log_msg, *args) 

231 warned = True 

232 

233 yield logCmd 

234 

235 

236def fixAmpsAndAssemble(ampExps, msg): 

237 """Fix amp geometry and assemble into exposure. 

238 

239 Parameters 

240 ---------- 

241 ampExps : sequence of `lsst.afw.image.Exposure` 

242 Per-amplifier images. 

243 msg : `str` 

244 Message to add to log and exception output. 

245 

246 Returns 

247 ------- 

248 exposure : `lsst.afw.image.Exposure` 

249 Exposure with the amps combined into a single image. 

250 

251 Notes 

252 ----- 

253 The returned exposure does not have any metadata or WCS attached. 

254 

255 """ 

256 if not len(ampExps): 

257 raise RuntimeError(f"Unable to read raw_amps for {msg}") 

258 

259 ccd = ampExps[0].getDetector() # the same (full, CCD-level) Detector is attached to all ampExps 

260 # 

261 # Check that the geometry in the metadata matches cameraGeom 

262 # 

263 with warn_once(msg) as logCmd: 

264 # Rebuild the detector and the amplifiers to use their corrected 

265 # geometry. 

266 tempCcd = ccd.rebuild() 

267 tempCcd.clear() 

268 for amp, ampExp in zip(ccd, ampExps): 

269 outAmp, _ = fixAmpGeometry(amp, 

270 bbox=ampExp.getBBox(), 

271 metadata=ampExp.getMetadata(), 

272 logCmd=logCmd) 

273 tempCcd.append(outAmp) 

274 ccd = tempCcd.finish() 

275 

276 # Update the data to be combined to point to the newly rebuilt detector. 

277 for ampExp in ampExps: 

278 ampExp.setDetector(ccd) 

279 

280 exposure = assembleUntrimmedCcd(ccd, ampExps) 

281 return exposure 

282 

283 

284def readRawAmps(fileName, detector): 

285 """Given a file name read the amps and attach the detector. 

286 

287 Parameters 

288 ---------- 

289 fileName : `str` 

290 The full path to a file containing data from a single CCD. 

291 detector : `lsst.afw.cameraGeom.Detector` 

292 Detector to associate with the amps. 

293 

294 Returns 

295 ------- 

296 ampExps : `list` of `lsst.afw.image.Exposure` 

297 All the individual amps read from the file. 

298 """ 

299 amps = [] 

300 for hdu in range(1, len(detector)+1): 

301 reader = afwImage.ImageFitsReader(fileName, hdu=hdu) 

302 exp = afwImage.makeExposure(afwImage.makeMaskedImage(reader.read(dtype=np.dtype(np.int32), 

303 allowUnsafe=True))) 

304 exp.setDetector(detector) 

305 exp.setMetadata(reader.readMetadata()) 

306 amps.append(exp) 

307 return amps