Coverage for python/lsst/pipe/tasks/repair.py : 19%

Hot-keys on this page
r m x p toggle line displays
j k next/prev highlighted chunk
0 (zero) top of page
1 (one) first highlighted chunk
1# This file is part of pipe_tasks.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://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 <https://www.gnu.org/licenses/>.
22import lsst.pex.config as pexConfig
23import lsst.afw.math as afwMath
24import lsst.afw.detection as afwDet
25import lsst.meas.algorithms as measAlg
26import lsst.pipe.base as pipeBase
27from lsstDebug import getDebugFrame
28import lsst.afw.display as afwDisplay
29from lsst.pipe.tasks.interpImage import InterpImageTask
32class RepairConfig(pexConfig.Config):
33 doInterpolate = pexConfig.Field(
34 dtype=bool,
35 doc="Interpolate over defects? (ignored unless you provide a list of defects)",
36 default=True,
37 )
38 doCosmicRay = pexConfig.Field(
39 dtype=bool,
40 doc="Find and mask out cosmic rays?",
41 default=True,
42 )
43 cosmicray = pexConfig.ConfigField(
44 dtype=measAlg.FindCosmicRaysConfig,
45 doc="Options for finding and masking cosmic rays",
46 )
47 interp = pexConfig.ConfigurableField(
48 target=InterpImageTask,
49 doc="Interpolate over bad image pixels",
50 )
52 def setDefaults(self):
53 self.interp.useFallbackValueAtEdge = True
54 self.interp.fallbackValueType = "MEANCLIP"
55 self.interp.negativeFallbackAllowed = True
57## @addtogroup LSST_task_documentation
58## @{
59## @page RepairTask
60## @ref RepairTask_ "RepairTask"
61## @copybrief RepairTask
62## @}
65class RepairTask(pipeBase.Task):
66 r"""!
67 @anchor RepairTask_
69 @brief Interpolate over defects in an exposure and handle cosmic rays
71 @section pipe_tasks_repair_Contents Contents
73 - @ref pipe_tasks_repair_Purpose
74 - @ref pipe_tasks_repair_Initialize
75 - @ref pipe_tasks_repair_IO
76 - @ref pipe_tasks_repair_Config
77 - @ref pipe_tasks_repair_Debug
78 - @ref pipe_tasks_repair_Example
80 @section pipe_tasks_repair_Purpose Description
82 @copybrief RepairTask
84 This task operates on an lsst.afw.image.Exposure in place to interpolate over a set of
85 lsst.meas.algorithms.Defect objects.
86 It will also, optionally, find and interpolate any cosmic rays in the lsst.afw.image.Exposure.
88 @section pipe_tasks_repair_Initialize Task initialization
90 See: lsst.pipe.base.task.Task.__init__
92 @section pipe_tasks_repair_IO Inputs/Outputs to the run method
94 @copydoc run
96 @section pipe_tasks_repair_Config Configuration parameters
98 See @ref RepairConfig
100 @section pipe_tasks_repair_Debug Debug variables
102 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
103 flag @c -d to import @b debug.py from your @c PYTHONPATH; see <a
104 href="https://developer.lsst.io/stack/debug.html">Debugging Tasks with lsstDebug</a> for more
105 about @b debug.py files.
107 The available variables in RepairTask are:
108 <DL>
109 <DT> @c display
110 <DD> A dictionary containing debug point names as keys with frame number as value. Valid keys are:
111 <DL>
112 <DT> repair.before
113 <DD> display image before any repair is done
114 <DT> repair.after
115 <DD> display image after cosmic ray and defect correction
116 </DL>
117 <DT> @c displayCR
118 <DD> If True, display the exposure on display's frame 1 and overlay bounding boxes around detects CRs.
119 </DL>
120 @section pipe_tasks_repair_Example A complete example of using RepairTask
122 This code is in runRepair.py in the examples directory, and can be run as @em e.g.
123 @code
124 examples/runRepair.py
125 @endcode
126 @dontinclude runRepair.py
127 Import the task. There are other imports. Read the source file for more info.
128 @skipline RepairTask
130 For this example, we manufacture a test image to run on.
132 First, create a pure Poisson noise image and a Psf to go with it. The mask plane
133 and variance can be constructed at the same time.
134 @skip poisson
135 @until mask
137 Inject some cosmic rays and generate the Exposure. Exposures are MaskedImages (image + mask + variance)
138 with other metadata (e.g. Psf and Wcs objects).
139 @skip some CRs
140 @until setPsf
142 Defects are represented as bad columns of random lengths. A defect list must be constructed to pass
143 on to the RepairTask.
144 @bug This is addressed in <a href="https://jira.lsstcorp.org/browse/DM-963"> DM-963</a>
146 @skip addDefects
147 @until push_back
149 Finally, the exposure can be repaired. Create an instance of the task and run it. The exposure
150 is modified in place.
151 @skip RepairTask
152 @until repair.run
154 <HR>
155 To investigate the @ref pipe_tasks_repair_Debug, put something like
156 @code{.py}
157 import lsstDebug
158 def DebugInfo(name):
159 di = lsstDebug.getInfo(name) # N.b. lsstDebug.Info(name) would call us recursively
160 if name == "lsst.pipe.tasks.repair":
161 di.display = {'repair.before':2, 'repair.after':3}
162 di.displayCR = True
163 return di
165 lsstDebug.Info = DebugInfo
166 @endcode
167 into your debug.py file and run runRepair.py with the @c --debug flag.
170 Conversion notes:
171 Display code should be updated once we settle on a standard way of controlling what is displayed.
172 """
173 ConfigClass = RepairConfig
174 _DefaultName = "repair"
176 def __init__(self, **kwargs):
177 pipeBase.Task.__init__(self, **kwargs)
178 if self.config.doInterpolate:
179 self.makeSubtask("interp")
181 @pipeBase.timeMethod
182 def run(self, exposure, defects=None, keepCRs=None):
183 """!Repair an Exposure's defects and cosmic rays
185 @param[in, out] exposure lsst.afw.image.Exposure to process. Exposure must have a valid Psf.
186 Modified in place.
187 @param[in] defects an lsst.meas.algorithms.DefectListT object. If None, do no
188 defect correction.
189 @param[in] keepCRs don't interpolate over the CR pixels (defer to RepairConfig if None)
191 @throws AssertionError with the following strings:
193 <DL>
194 <DT> No exposure provided
195 <DD> The object provided as exposure evaluates to False
196 <DT> No PSF provided
197 <DD> The Exposure has no associated Psf
198 </DL>
199 """
200 assert exposure, "No exposure provided"
201 psf = exposure.getPsf()
202 assert psf, "No PSF provided"
204 frame = getDebugFrame(self._display, "repair.before")
205 if frame:
206 afwDisplay.Display(frame).mtv(exposure)
208 if defects is not None and self.config.doInterpolate:
209 self.interp.run(exposure, defects=defects)
211 if self.config.doCosmicRay:
212 self.cosmicRay(exposure, keepCRs=keepCRs)
214 frame = getDebugFrame(self._display, "repair.after")
215 if frame:
216 afwDisplay.Display(frame).mtv(exposure)
218 def cosmicRay(self, exposure, keepCRs=None):
219 """Mask cosmic rays
221 @param[in,out] exposure Exposure to process
222 @param[in] keepCRs Don't interpolate over the CR pixels (defer to pex_config if None)
223 """
224 import lsstDebug
225 display = lsstDebug.Info(__name__).display
226 displayCR = lsstDebug.Info(__name__).displayCR
228 assert exposure, "No exposure provided"
229 psf = exposure.getPsf()
230 assert psf, "No psf provided"
232 # Blow away old mask
233 try:
234 mask = exposure.getMaskedImage().getMask()
235 crBit = mask.getMaskPlane("CR")
236 mask.clearMaskPlane(crBit)
237 except Exception:
238 pass
240 exposure0 = exposure # initial value of exposure
241 binSize = self.config.cosmicray.background.binSize
242 nx, ny = exposure.getWidth()/binSize, exposure.getHeight()/binSize
243 # Treat constant background as a special case to avoid the extra complexity in calling
244 # measAlg.SubtractBackgroundTask().
245 if nx*ny <= 1:
246 medianBg = afwMath.makeStatistics(exposure.getMaskedImage(), afwMath.MEDIAN).getValue()
247 modelBg = None
248 else:
249 # make a deep copy of the exposure before subtracting its background,
250 # because this routine is only allowed to modify the exposure by setting mask planes
251 # and interpolating over defects, not changing the background level
252 exposure = exposure.Factory(exposure, True)
253 subtractBackgroundTask = measAlg.SubtractBackgroundTask(config=self.config.cosmicray.background)
254 modelBg = subtractBackgroundTask.run(exposure).background
255 medianBg = 0.0
257 if keepCRs is None:
258 keepCRs = self.config.cosmicray.keepCRs
259 try:
260 crs = measAlg.findCosmicRays(exposure.getMaskedImage(), psf, medianBg,
261 pexConfig.makePropertySet(self.config.cosmicray), keepCRs)
262 if modelBg:
263 # Add back background image
264 img = exposure.getMaskedImage()
265 img += modelBg.getImageF()
266 del img
267 # Replace original image with CR subtracted image
268 exposure0.setMaskedImage(exposure.getMaskedImage())
270 except Exception:
271 if display:
272 afwDisplay.Display().mtv(exposure0, title="Failed CR")
273 raise
275 num = 0
276 if crs is not None:
277 mask = exposure0.getMaskedImage().getMask()
278 crBit = mask.getPlaneBitMask("CR")
279 afwDet.setMaskFromFootprintList(mask, crs, crBit)
280 num = len(crs)
282 if display and displayCR:
283 disp = afwDisplay.Display()
284 disp.incrDefaultFrame()
285 disp.mtv(exposure0, title="Post-CR")
287 with disp.Buffering():
288 for cr in crs:
289 afwDisplay.utils.drawBBox(cr.getBBox(), borderWidth=0.55)
291 self.log.info("Identified %s cosmic rays.", num)