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

167 datasec = bboxFromIraf(metadata["DATASEC"]) if "DATASEC" in metadata else None 

168 biassec = bboxFromIraf(metadata["BIASSEC"]) if "BIASSEC" in metadata else None 

169 

170 # 2022-11-11: There is a known issue that the header DETSEC have 

171 # the y-axis values flipped between the C0x and C1x entries. This 

172 # is incorrect, and disagrees with the cameraGeom values. 

173 # DM-36115 contains additional details. This test has been 

174 # disabled to remove useless warnings until that is resolved. 

175 # if detsec and outAmp.getBBox() != detsec: 

176 # logCmd("DETSEC doesn't match (%s != %s)", 

177 # outAmp.getBBox(), detsec) 

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

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

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

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

182 

183 return outAmp, modified 

184 

185 

186def assembleUntrimmedCcd(ccd, exposures): 

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

188 

189 Parameters 

190 ---------- 

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

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

193 framework for the assembly of the input amplifier exposures. 

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

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

196 

197 Returns 

198 ------- 

199 ccd : `lsst.afw.image.Exposure` 

200 Assembled CCD image. 

201 """ 

202 ampDict = {} 

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

204 ampDict[amp.getName()] = exposure 

205 config = AssembleCcdTask.ConfigClass() 

206 config.doTrim = False 

207 assembleTask = AssembleCcdTask(config=config) 

208 return assembleTask.assembleCcd(ampDict) 

209 

210 

211@contextmanager 

212def warn_once(msg): 

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

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

215 

216 Parameters 

217 ---------- 

218 msg : `str` 

219 Message to prefix all log messages with. 

220 

221 Returns 

222 ------- 

223 logger 

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

225 substition args. 

226 """ 

227 warned = False 

228 

229 def logCmd(s, *args): 

230 nonlocal warned 

231 log_msg = f"{msg}: {s}" 

232 if warned: 

233 logger.debug(log_msg, *args) 

234 else: 

235 logger.warning(log_msg, *args) 

236 warned = True 

237 

238 yield logCmd 

239 

240 

241def fixAmpsAndAssemble(ampExps, msg): 

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

243 

244 Parameters 

245 ---------- 

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

247 Per-amplifier images. 

248 msg : `str` 

249 Message to add to log and exception output. 

250 

251 Returns 

252 ------- 

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

254 Exposure with the amps combined into a single image. 

255 

256 Notes 

257 ----- 

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

259 

260 """ 

261 if not len(ampExps): 

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

263 

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

265 # 

266 # Check that the geometry in the metadata matches cameraGeom 

267 # 

268 with warn_once(msg) as logCmd: 

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

270 # geometry. 

271 tempCcd = ccd.rebuild() 

272 tempCcd.clear() 

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

274 outAmp, _ = fixAmpGeometry(amp, 

275 bbox=ampExp.getBBox(), 

276 metadata=ampExp.getMetadata(), 

277 logCmd=logCmd) 

278 tempCcd.append(outAmp) 

279 ccd = tempCcd.finish() 

280 

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

282 for ampExp in ampExps: 

283 ampExp.setDetector(ccd) 

284 

285 exposure = assembleUntrimmedCcd(ccd, ampExps) 

286 return exposure 

287 

288 

289def readRawAmps(fileName, detector): 

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

291 

292 Parameters 

293 ---------- 

294 fileName : `str` 

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

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

297 Detector to associate with the amps. 

298 

299 Returns 

300 ------- 

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

302 All the individual amps read from the file. 

303 """ 

304 amps = [] 

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

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

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

308 allowUnsafe=True))) 

309 exp.setDetector(detector) 

310 exp.setMetadata(reader.readMetadata()) 

311 amps.append(exp) 

312 return amps