Coverage for python/lsst/obs/lsst/rawFormatter.py: 96%

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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"""Gen3 Butler Formatters for LSST raw data. 

23""" 

24 

25__all__ = ( 

26 "LsstCamRawFormatter", 

27 "LatissRawFormatter", 

28 "LsstCamImSimRawFormatter", 

29 "LsstCamPhoSimRawFormatter", 

30 "LsstTS8RawFormatter", 

31 "LsstTS3RawFormatter", 

32 "LsstComCamRawFormatter", 

33 "LsstComCamSimRawFormatter", 

34 "LsstUCDCamRawFormatter", 

35) 

36 

37import numpy as np 

38from astro_metadata_translator import fix_header, merge_headers 

39 

40import lsst.afw.fits 

41from lsst.obs.base import FitsRawFormatterBase 

42from lsst.obs.base.formatters.fitsExposure import standardizeAmplifierParameters 

43from lsst.afw.cameraGeom import makeUpdatedDetector 

44 

45from ._instrument import LsstCam, Latiss, \ 

46 LsstCamImSim, LsstCamPhoSim, LsstTS8, \ 

47 LsstTS3, LsstUCDCam, LsstComCam, LsstComCamSim 

48from .translators import LatissTranslator, LsstCamTranslator, \ 

49 LsstUCDCamTranslator, LsstTS3Translator, LsstComCamTranslator, \ 

50 LsstCamPhoSimTranslator, LsstTS8Translator, LsstCamImSimTranslator, \ 

51 LsstComCamSimTranslator 

52from .assembly import fixAmpsAndAssemble, fixAmpGeometry, readRawAmps, warn_once 

53 

54 

55class LsstCamRawFormatter(FitsRawFormatterBase): 

56 translatorClass = LsstCamTranslator 

57 filterDefinitions = LsstCam.filterDefinitions 

58 _instrument = LsstCam 

59 

60 # These named HDUs' headers will be checked for and added to metadata. 

61 _extraFitsHeaders = ["REB_COND"] 

62 

63 def readMetadata(self): 

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

65 

66 Will merge additional headers if required. 

67 

68 Returns 

69 ------- 

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

71 Header metadata. 

72 """ 

73 file = self.fileDescriptor.location.path 

74 

75 with lsst.afw.fits.Fits(file, "r") as hdu: 

76 hdu.setHdu(0) 

77 base_md = hdu.readMetadata() 

78 

79 # Any extra HDUs we need to read. 

80 ehdrs = [] 

81 for hduname in self._extraFitsHeaders: 

82 try: 

83 hdu.setHdu(hduname) 

84 ehdr = hdu.readMetadata() 

85 except lsst.afw.fits.FitsError: 

86 # The header doesn't exist in this file. Skip. 

87 continue 

88 else: 

89 ehdrs.append(ehdr) 

90 

91 final_md = merge_headers([base_md] + ehdrs, mode="overwrite") 

92 fix_header(final_md, translator_class=self.translatorClass) 

93 return final_md 

94 

95 def stripMetadata(self): 

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

97 if "CRVAL1" not in self.metadata: 

98 # No need to strip WCS since we do not seem to have any WCS. 

99 return 

100 super().stripMetadata() 

101 

102 def getDetector(self, id): 

103 in_detector = self._instrument.getCamera()[id] 

104 # The detectors attached to the Camera object represent the on-disk 

105 # amplifier geometry, not the assembled raw. But Butler users 

106 # shouldn't know or care about what's on disk; they want the Detector 

107 # that's equivalent to `butler.get("raw", ...).getDetector()`, so we 

108 # adjust it accordingly. This parallels the logic in 

109 # fixAmpsAndAssemble, but that function and the ISR AssembleCcdTask it 

110 # calls aren't set up to handle bare bounding boxes with no pixels. We 

111 # also can't remove those without API breakage. So this is fairly 

112 # duplicative, and hence fragile. 

113 # We start by fixing amp bounding boxes based on the size of the amp 

114 # images themselves, because the camera doesn't have the right overscan 

115 # regions for all images. 

116 filename = self.fileDescriptor.location.path 

117 temp_detector = in_detector.rebuild() 

118 temp_detector.clear() 

119 with warn_once(filename) as logCmd: 

120 for n, in_amp in enumerate(in_detector): 

121 reader = lsst.afw.image.ImageFitsReader(filename, hdu=(n + 1)) 

122 out_amp, _ = fixAmpGeometry(in_amp, 

123 bbox=reader.readBBox(), 

124 metadata=reader.readMetadata(), 

125 logCmd=logCmd) 

126 temp_detector.append(out_amp) 

127 adjusted_detector = temp_detector.finish() 

128 # Now we need to apply flips and offsets to reflect assembly. The 

129 # function call that does this in fixAmpsAndAssemble is down inside 

130 # ip.isr.AssembleCcdTask. 

131 return makeUpdatedDetector(adjusted_detector) 

132 

133 def readImage(self): 

134 # Docstring inherited. 

135 return self.readFull().getImage() 

136 

137 def readFull(self): 

138 # Docstring inherited. 

139 rawFile = self.fileDescriptor.location.path 

140 amplifier, detector, _ = standardizeAmplifierParameters( 

141 self.checked_parameters, 

142 self._instrument.getCamera()[self.observationInfo.detector_num], 

143 ) 

144 if amplifier is not None: 

145 # LSST raws are already per-amplifier on disk, and in a different 

146 # assembly state than all of the other images we see in 

147 # DM-maintained formatters. And we also need to deal with the 

148 # on-disk image having different overscans from our nominal 

149 # detector. So we can't use afw.cameraGeom.AmplifierIsolator for 

150 # most of the implementation (as other formatters do), but we can 

151 # call most of the same underlying code to do the work. 

152 

153 def findAmpHdu(name): 

154 """Find the HDU for the amplifier with the given name, 

155 according to cameraGeom. 

156 """ 

157 for hdu, amp in enumerate(detector): 157 ↛ 160line 157 didn't jump to line 160, because the loop on line 157 didn't complete

158 if amp.getName() == name: 

159 return hdu + 1 

160 raise LookupError(f"Could not find HDU for amp with name {name}.") 

161 

162 reader = lsst.afw.image.ImageFitsReader(rawFile, hdu=findAmpHdu(amplifier.getName())) 

163 image = reader.read(dtype=np.dtype(np.int32), allowUnsafe=True) 

164 with warn_once(rawFile) as logCmd: 

165 # Extract an amplifier from the on-disk detector and fix its 

166 # overscan bboxes as necessary to match the on-disk bbox. 

167 adjusted_amplifier_builder, _ = fixAmpGeometry( 

168 detector[amplifier.getName()], 

169 bbox=image.getBBox(), 

170 metadata=reader.readMetadata(), 

171 logCmd=logCmd, 

172 ) 

173 on_disk_amplifier = adjusted_amplifier_builder.finish() 

174 # We've now got two Amplifier objects in play: 

175 # A) 'amplifier' is what the user wants 

176 # B) 'on_disk_amplifier' represents the subimage we have. 

177 # The one we want has the orientation/shift state of (A) with 

178 # the overscan regions of (B). 

179 comparison = amplifier.compareGeometry(on_disk_amplifier) 

180 # If the flips or origins differ, we need to modify the image 

181 # itself. 

182 if comparison & comparison.FLIPPED: 

183 from lsst.afw.math import flipImage 

184 image = flipImage( 

185 image, 

186 comparison & comparison.FLIPPED_X, 

187 comparison & comparison.FLIPPED_Y, 

188 ) 

189 if comparison & comparison.SHIFTED: 

190 image.setXY0(amplifier.getRawBBox().getMin()) 

191 # Make a single-amplifier detector that reflects the image we're 

192 # returning. 

193 detector_builder = detector.rebuild() 

194 detector_builder.clear() 

195 detector_builder.unsetCrosstalk() 

196 if comparison & comparison.REGIONS_DIFFER: 196 ↛ 201line 196 didn't jump to line 201, because the condition on line 196 was never true

197 # We can't just install the amplifier the user gave us, because 

198 # that has the wrong overscan regions; instead we transform the 

199 # on-disk amplifier to have the same orientation and offsets as 

200 # the given one. 

201 adjusted_amplifier_builder.transform( 

202 outOffset=on_disk_amplifier.getRawXYOffset(), 

203 outFlipX=amplifier.getRawFlipX(), 

204 outFlipY=amplifier.getRawFlipY(), 

205 ) 

206 detector_builder.append(adjusted_amplifier_builder) 

207 detector_builder.setBBox(adjusted_amplifier_builder.getBBox()) 

208 else: 

209 detector_builder.append(amplifier.rebuild()) 

210 detector_builder.setBBox(amplifier.getBBox()) 

211 exposure = lsst.afw.image.makeExposure(lsst.afw.image.makeMaskedImage(image)) 

212 exposure.setDetector(detector_builder.finish()) 

213 else: 

214 ampExps = readRawAmps(rawFile, detector) 

215 exposure = fixAmpsAndAssemble(ampExps, rawFile) 

216 self.attachComponentsFromMetadata(exposure) 

217 return exposure 

218 

219 

220class LatissRawFormatter(LsstCamRawFormatter): 

221 translatorClass = LatissTranslator 

222 _instrument = Latiss 

223 filterDefinitions = Latiss.filterDefinitions 

224 wcsFlipX = True 

225 

226 

227class LsstCamImSimRawFormatter(LsstCamRawFormatter): 

228 translatorClass = LsstCamImSimTranslator 

229 _instrument = LsstCamImSim 

230 filterDefinitions = LsstCamImSim.filterDefinitions 

231 

232 

233class LsstCamPhoSimRawFormatter(LsstCamRawFormatter): 

234 translatorClass = LsstCamPhoSimTranslator 

235 _instrument = LsstCamPhoSim 

236 filterDefinitions = LsstCamPhoSim.filterDefinitions 

237 _extraFitsHeaders = [1] 

238 

239 

240class LsstTS8RawFormatter(LsstCamRawFormatter): 

241 translatorClass = LsstTS8Translator 

242 _instrument = LsstTS8 

243 filterDefinitions = LsstTS8.filterDefinitions 

244 

245 

246class LsstTS3RawFormatter(LsstCamRawFormatter): 

247 translatorClass = LsstTS3Translator 

248 _instrument = LsstTS3 

249 filterDefinitions = LsstTS3.filterDefinitions 

250 

251 

252class LsstComCamRawFormatter(LsstCamRawFormatter): 

253 translatorClass = LsstComCamTranslator 

254 _instrument = LsstComCam 

255 filterDefinitions = LsstComCam.filterDefinitions 

256 

257 

258class LsstComCamSimRawFormatter(LsstCamRawFormatter): 

259 translatorClass = LsstComCamSimTranslator 

260 _instrument = LsstComCamSim 

261 filterDefinitions = LsstComCamSim.filterDefinitions 

262 

263 

264class LsstUCDCamRawFormatter(LsstCamRawFormatter): 

265 translatorClass = LsstUCDCamTranslator 

266 _instrument = LsstUCDCam 

267 filterDefinitions = LsstUCDCam.filterDefinitions