Coverage for python/lsst/obs/lsst/rawFormatter.py: 97%
110 statements
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« prev ^ index » next coverage.py v6.5.0, created at 2022-10-04 03:29 -0700
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/>.
22"""Gen3 Butler Formatters for LSST raw data.
23"""
25__all__ = (
26 "LsstCamRawFormatter",
27 "LatissRawFormatter",
28 "LsstCamImSimRawFormatter",
29 "LsstCamPhoSimRawFormatter",
30 "LsstTS8RawFormatter",
31 "LsstTS3RawFormatter",
32 "LsstComCamRawFormatter",
33 "LsstUCDCamRawFormatter",
34)
36import numpy as np
37from astro_metadata_translator import fix_header, merge_headers
39import lsst.afw.fits
40from lsst.obs.base import FitsRawFormatterBase
41from lsst.obs.base.formatters.fitsExposure import standardizeAmplifierParameters
42from lsst.afw.cameraGeom import makeUpdatedDetector
44from ._instrument import LsstCam, Latiss, \
45 LsstCamImSim, LsstCamPhoSim, LsstTS8, \
46 LsstTS3, LsstUCDCam, LsstComCam
47from .translators import LatissTranslator, LsstCamTranslator, \
48 LsstUCDCamTranslator, LsstTS3Translator, LsstComCamTranslator, \
49 LsstCamPhoSimTranslator, LsstTS8Translator, LsstCamImSimTranslator
50from .assembly import fixAmpsAndAssemble, fixAmpGeometry, readRawAmps, warn_once
53class LsstCamRawFormatter(FitsRawFormatterBase):
54 translatorClass = LsstCamTranslator
55 filterDefinitions = LsstCam.filterDefinitions
56 _instrument = LsstCam
58 # These named HDUs' headers will be checked for and added to metadata.
59 _extraFitsHeaders = ["REB_COND", "CONFIG_COND"]
61 def readMetadata(self):
62 """Read all header metadata directly into a PropertyList.
64 Specialist version since some of our data does not
65 set INHERIT=T so we have to merge the headers manually.
67 Returns
68 -------
69 metadata : `~lsst.daf.base.PropertyList`
70 Header metadata.
71 """
72 file = self.fileDescriptor.location.path
73 phdu = lsst.afw.fits.readMetadata(file, 0)
75 if "INHERIT" in phdu: 75 ↛ 77line 75 didn't jump to line 77, because the condition on line 75 was never true
76 # Trust the inheritance flag
77 base_md = super().readMetadata()
79 # Merge ourselves
80 else:
81 base_md = merge_headers([phdu, lsst.afw.fits.readMetadata(file)],
82 mode="overwrite")
84 ehdrs = []
85 for hduname in self._extraFitsHeaders:
86 try:
87 ehdr = lsst.afw.fits.readMetadata(file, hduname)
88 except lsst.afw.fits.FitsError:
89 # We can ignore this, the header doesn't exist in this file.
90 continue
91 else:
92 ehdrs.append(ehdr)
94 final_md = merge_headers([base_md] + ehdrs, mode="first")
95 fix_header(final_md)
96 return final_md
98 def getDetector(self, id):
99 in_detector = self._instrument.getCamera()[id]
100 # The detectors attached to the Camera object represent the on-disk
101 # amplifier geometry, not the assembled raw. But Butler users
102 # shouldn't know or care about what's on disk; they want the Detector
103 # that's equivalent to `butler.get("raw", ...).getDetector()`, so we
104 # adjust it accordingly. This parallels the logic in
105 # fixAmpsAndAssemble, but that function and the ISR AssembleCcdTask it
106 # calls aren't set up to handle bare bounding boxes with no pixels. We
107 # also can't remove those without API breakage. So this is fairly
108 # duplicative, and hence fragile.
109 # We start by fixing amp bounding boxes based on the size of the amp
110 # images themselves, because the camera doesn't have the right overscan
111 # regions for all images.
112 filename = self.fileDescriptor.location.path
113 temp_detector = in_detector.rebuild()
114 temp_detector.clear()
115 with warn_once(filename) as logCmd:
116 for n, in_amp in enumerate(in_detector):
117 reader = lsst.afw.image.ImageFitsReader(filename, hdu=(n + 1))
118 out_amp, _ = fixAmpGeometry(in_amp,
119 bbox=reader.readBBox(),
120 metadata=reader.readMetadata(),
121 logCmd=logCmd)
122 temp_detector.append(out_amp)
123 adjusted_detector = temp_detector.finish()
124 # Now we need to apply flips and offsets to reflect assembly. The
125 # function call that does this in fixAmpsAndAssemble is down inside
126 # ip.isr.AssembleCcdTask.
127 return makeUpdatedDetector(adjusted_detector)
129 def readImage(self):
130 # Docstring inherited.
131 return self.readFull().getImage()
133 def readFull(self):
134 # Docstring inherited.
135 rawFile = self.fileDescriptor.location.path
136 amplifier, detector, _ = standardizeAmplifierParameters(
137 self.checked_parameters,
138 self._instrument.getCamera()[self.observationInfo.detector_num],
139 )
140 if amplifier is not None:
141 # LSST raws are already per-amplifier on disk, and in a different
142 # assembly state than all of the other images we see in
143 # DM-maintained formatters. And we also need to deal with the
144 # on-disk image having different overscans from our nominal
145 # detector. So we can't use afw.cameraGeom.AmplifierIsolator for
146 # most of the implementation (as other formatters do), but we can
147 # call most of the same underlying code to do the work.
149 def findAmpHdu(name):
150 """Find the HDU for the amplifier with the given name,
151 according to cameraGeom.
152 """
153 for hdu, amp in enumerate(detector): 153 ↛ 156line 153 didn't jump to line 156, because the loop on line 153 didn't complete
154 if amp.getName() == name:
155 return hdu + 1
156 raise LookupError(f"Could not find HDU for amp with name {name}.")
158 reader = lsst.afw.image.ImageFitsReader(rawFile, hdu=findAmpHdu(amplifier.getName()))
159 image = reader.read(dtype=np.dtype(np.int32), allowUnsafe=True)
160 with warn_once(rawFile) as logCmd:
161 # Extract an amplifier from the on-disk detector and fix its
162 # overscan bboxes as necessary to match the on-disk bbox.
163 adjusted_amplifier_builder, _ = fixAmpGeometry(
164 detector[amplifier.getName()],
165 bbox=image.getBBox(),
166 metadata=reader.readMetadata(),
167 logCmd=logCmd,
168 )
169 on_disk_amplifier = adjusted_amplifier_builder.finish()
170 # We've now got two Amplifier objects in play:
171 # A) 'amplifier' is what the user wants
172 # B) 'on_disk_amplifier' represents the subimage we have.
173 # The one we want has the orientation/shift state of (A) with
174 # the overscan regions of (B).
175 comparison = amplifier.compareGeometry(on_disk_amplifier)
176 # If the flips or origins differ, we need to modify the image
177 # itself.
178 if comparison & comparison.FLIPPED:
179 from lsst.afw.math import flipImage
180 image = flipImage(
181 image,
182 comparison & comparison.FLIPPED_X,
183 comparison & comparison.FLIPPED_Y,
184 )
185 if comparison & comparison.SHIFTED:
186 image.setXY0(amplifier.getRawBBox().getMin())
187 # Make a single-amplifier detector that reflects the image we're
188 # returning.
189 detector_builder = detector.rebuild()
190 detector_builder.clear()
191 detector_builder.unsetCrosstalk()
192 if comparison & comparison.REGIONS_DIFFER:
193 # We can't just install the amplifier the user gave us, because
194 # that has the wrong overscan regions; instead we transform the
195 # on-disk amplifier to have the same orientation and offsets as
196 # the given one.
197 adjusted_amplifier_builder.transform(
198 outOffset=on_disk_amplifier.getRawXYOffset(),
199 outFlipX=amplifier.getRawFlipX(),
200 outFlipY=amplifier.getRawFlipY(),
201 )
202 detector_builder.append(adjusted_amplifier_builder)
203 detector_builder.setBBox(adjusted_amplifier_builder.getBBox())
204 else:
205 detector_builder.append(amplifier.rebuild())
206 detector_builder.setBBox(amplifier.getBBox())
207 exposure = lsst.afw.image.makeExposure(lsst.afw.image.makeMaskedImage(image))
208 exposure.setDetector(detector_builder.finish())
209 else:
210 ampExps = readRawAmps(rawFile, detector)
211 exposure = fixAmpsAndAssemble(ampExps, rawFile)
212 self.attachComponentsFromMetadata(exposure)
213 return exposure
216class LatissRawFormatter(LsstCamRawFormatter):
217 translatorClass = LatissTranslator
218 _instrument = Latiss
219 filterDefinitions = Latiss.filterDefinitions
220 wcsFlipX = True
223class LsstCamImSimRawFormatter(LsstCamRawFormatter):
224 translatorClass = LsstCamImSimTranslator
225 _instrument = LsstCamImSim
226 filterDefinitions = LsstCamImSim.filterDefinitions
229class LsstCamPhoSimRawFormatter(LsstCamRawFormatter):
230 translatorClass = LsstCamPhoSimTranslator
231 _instrument = LsstCamPhoSim
232 filterDefinitions = LsstCamPhoSim.filterDefinitions
235class LsstTS8RawFormatter(LsstCamRawFormatter):
236 translatorClass = LsstTS8Translator
237 _instrument = LsstTS8
238 filterDefinitions = LsstTS8.filterDefinitions
241class LsstTS3RawFormatter(LsstCamRawFormatter):
242 translatorClass = LsstTS3Translator
243 _instrument = LsstTS3
244 filterDefinitions = LsstTS3.filterDefinitions
247class LsstComCamRawFormatter(LsstCamRawFormatter):
248 translatorClass = LsstComCamTranslator
249 _instrument = LsstComCam
250 filterDefinitions = LsstComCam.filterDefinitions
253class LsstUCDCamRawFormatter(LsstCamRawFormatter):
254 translatorClass = LsstUCDCamTranslator
255 _instrument = LsstUCDCam
256 filterDefinitions = LsstUCDCam.filterDefinitions