Coverage for python/lsst/obs/lsst/rawFormatter.py: 97%
101 statements
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« prev ^ index » next coverage.py v6.4.1, created at 2022-06-28 03:03 -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 def readMetadata(self):
59 """Read all header metadata directly into a PropertyList.
61 Specialist version since some of our data does not
62 set INHERIT=T so we have to merge the headers manually.
64 Returns
65 -------
66 metadata : `~lsst.daf.base.PropertyList`
67 Header metadata.
68 """
69 file = self.fileDescriptor.location.path
70 phdu = lsst.afw.fits.readMetadata(file, 0)
71 if "INHERIT" in phdu: 71 ↛ 73line 71 didn't jump to line 73, because the condition on line 71 was never true
72 # Trust the inheritance flag
73 return super().readMetadata()
75 # Merge ourselves
76 md = merge_headers([phdu, lsst.afw.fits.readMetadata(file)],
77 mode="overwrite")
78 fix_header(md)
79 return md
81 def getDetector(self, id):
82 in_detector = self._instrument.getCamera()[id]
83 # The detectors attached to the Camera object represent the on-disk
84 # amplifier geometry, not the assembled raw. But Butler users
85 # shouldn't know or care about what's on disk; they want the Detector
86 # that's equivalent to `butler.get("raw", ...).getDetector()`, so we
87 # adjust it accordingly. This parallels the logic in
88 # fixAmpsAndAssemble, but that function and the ISR AssembleCcdTask it
89 # calls aren't set up to handle bare bounding boxes with no pixels. We
90 # also can't remove those without API breakage. So this is fairly
91 # duplicative, and hence fragile.
92 # We start by fixing amp bounding boxes based on the size of the amp
93 # images themselves, because the camera doesn't have the right overscan
94 # regions for all images.
95 filename = self.fileDescriptor.location.path
96 temp_detector = in_detector.rebuild()
97 temp_detector.clear()
98 with warn_once(filename) as logCmd:
99 for n, in_amp in enumerate(in_detector):
100 reader = lsst.afw.image.ImageFitsReader(filename, hdu=(n + 1))
101 out_amp, _ = fixAmpGeometry(in_amp,
102 bbox=reader.readBBox(),
103 metadata=reader.readMetadata(),
104 logCmd=logCmd)
105 temp_detector.append(out_amp)
106 adjusted_detector = temp_detector.finish()
107 # Now we need to apply flips and offsets to reflect assembly. The
108 # function call that does this in fixAmpsAndAssemble is down inside
109 # ip.isr.AssembleCcdTask.
110 return makeUpdatedDetector(adjusted_detector)
112 def readImage(self):
113 # Docstring inherited.
114 return self.readFull().getImage()
116 def readFull(self):
117 # Docstring inherited.
118 rawFile = self.fileDescriptor.location.path
119 amplifier, detector, _ = standardizeAmplifierParameters(
120 self.checked_parameters,
121 self._instrument.getCamera()[self.observationInfo.detector_num],
122 )
123 if amplifier is not None:
124 # LSST raws are already per-amplifier on disk, and in a different
125 # assembly state than all of the other images we see in
126 # DM-maintained formatters. And we also need to deal with the
127 # on-disk image having different overscans from our nominal
128 # detector. So we can't use afw.cameraGeom.AmplifierIsolator for
129 # most of the implementation (as other formatters do), but we can
130 # call most of the same underlying code to do the work.
132 def findAmpHdu(name):
133 """Find the HDU for the amplifier with the given name,
134 according to cameraGeom.
135 """
136 for hdu, amp in enumerate(detector): 136 ↛ 139line 136 didn't jump to line 139, because the loop on line 136 didn't complete
137 if amp.getName() == name:
138 return hdu + 1
139 raise LookupError(f"Could not find HDU for amp with name {name}.")
141 reader = lsst.afw.image.ImageFitsReader(rawFile, hdu=findAmpHdu(amplifier.getName()))
142 image = reader.read(dtype=np.dtype(np.int32), allowUnsafe=True)
143 with warn_once(rawFile) as logCmd:
144 # Extract an amplifier from the on-disk detector and fix its
145 # overscan bboxes as necessary to match the on-disk bbox.
146 adjusted_amplifier_builder, _ = fixAmpGeometry(
147 detector[amplifier.getName()],
148 bbox=image.getBBox(),
149 metadata=reader.readMetadata(),
150 logCmd=logCmd,
151 )
152 on_disk_amplifier = adjusted_amplifier_builder.finish()
153 # We've now got two Amplifier objects in play:
154 # A) 'amplifier' is what the user wants
155 # B) 'on_disk_amplifier' represents the subimage we have.
156 # The one we want has the orientation/shift state of (A) with
157 # the overscan regions of (B).
158 comparison = amplifier.compareGeometry(on_disk_amplifier)
159 # If the flips or origins differ, we need to modify the image
160 # itself.
161 if comparison & comparison.FLIPPED:
162 from lsst.afw.math import flipImage
163 image = flipImage(
164 image,
165 comparison & comparison.FLIPPED_X,
166 comparison & comparison.FLIPPED_Y,
167 )
168 if comparison & comparison.SHIFTED:
169 image.setXY0(amplifier.getRawBBox().getMin())
170 # Make a single-amplifier detector that reflects the image we're
171 # returning.
172 detector_builder = detector.rebuild()
173 detector_builder.clear()
174 detector_builder.unsetCrosstalk()
175 if comparison & comparison.REGIONS_DIFFER:
176 # We can't just install the amplifier the user gave us, because
177 # that has the wrong overscan regions; instead we transform the
178 # on-disk amplifier to have the same orientation and offsets as
179 # the given one.
180 adjusted_amplifier_builder.transform(
181 outOffset=on_disk_amplifier.getRawXYOffset(),
182 outFlipX=amplifier.getRawFlipX(),
183 outFlipY=amplifier.getRawFlipY(),
184 )
185 detector_builder.append(adjusted_amplifier_builder)
186 detector_builder.setBBox(adjusted_amplifier_builder.getBBox())
187 else:
188 detector_builder.append(amplifier.rebuild())
189 detector_builder.setBBox(amplifier.getBBox())
190 exposure = lsst.afw.image.makeExposure(lsst.afw.image.makeMaskedImage(image))
191 exposure.setDetector(detector_builder.finish())
192 else:
193 ampExps = readRawAmps(rawFile, detector)
194 exposure = fixAmpsAndAssemble(ampExps, rawFile)
195 self.attachComponentsFromMetadata(exposure)
196 return exposure
199class LatissRawFormatter(LsstCamRawFormatter):
200 translatorClass = LatissTranslator
201 _instrument = Latiss
202 filterDefinitions = Latiss.filterDefinitions
203 wcsFlipX = True
206class LsstCamImSimRawFormatter(LsstCamRawFormatter):
207 translatorClass = LsstCamImSimTranslator
208 _instrument = LsstCamImSim
209 filterDefinitions = LsstCamImSim.filterDefinitions
212class LsstCamPhoSimRawFormatter(LsstCamRawFormatter):
213 translatorClass = LsstCamPhoSimTranslator
214 _instrument = LsstCamPhoSim
215 filterDefinitions = LsstCamPhoSim.filterDefinitions
218class LsstTS8RawFormatter(LsstCamRawFormatter):
219 translatorClass = LsstTS8Translator
220 _instrument = LsstTS8
221 filterDefinitions = LsstTS8.filterDefinitions
224class LsstTS3RawFormatter(LsstCamRawFormatter):
225 translatorClass = LsstTS3Translator
226 _instrument = LsstTS3
227 filterDefinitions = LsstTS3.filterDefinitions
230class LsstComCamRawFormatter(LsstCamRawFormatter):
231 translatorClass = LsstComCamTranslator
232 _instrument = LsstComCam
233 filterDefinitions = LsstComCam.filterDefinitions
236class LsstUCDCamRawFormatter(LsstCamRawFormatter):
237 translatorClass = LsstUCDCamTranslator
238 _instrument = LsstUCDCam
239 filterDefinitions = LsstUCDCam.filterDefinitions