27from lsstDebug
import getDebugFrame
33 doInterpolate = pexConfig.Field(
35 doc=
"Interpolate over defects? (ignored unless you provide a list of defects)",
38 doCosmicRay = pexConfig.Field(
40 doc=
"Find and mask out cosmic rays?",
43 cosmicray = pexConfig.ConfigField(
44 dtype=measAlg.FindCosmicRaysConfig,
45 doc=
"Options for finding and masking cosmic rays",
47 interp = pexConfig.ConfigurableField(
48 target=InterpImageTask,
49 doc=
"Interpolate over bad image pixels",
53 self.
interp.useFallbackValueAtEdge =
True
54 self.
interp.fallbackValueType =
"MEANCLIP"
55 self.
interp.negativeFallbackAllowed =
True
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
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
96 @section pipe_tasks_repair_Config Configuration parameters
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:
110 <DD> A dictionary containing debug point names
as keys
with frame number
as value. Valid keys are:
113 <DD> display image before any repair
is done
115 <DD> display image after cosmic ray
and defect correction
118 <DD> If
True, display the exposure on display
's frame 1 and overlay bounding boxes around detects CRs.
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.
124 examples/runRepair.py
126 @dontinclude runRepair.py
127 Import the task. There are other imports. Read the source file
for more info.
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.
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).
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>
149 Finally, the exposure can be repaired. Create an instance of the task
and run it. The exposure
150 is modified
in place.
155 To investigate the
@ref pipe_tasks_repair_Debug, put something like
160 if name ==
"lsst.pipe.tasks.repair":
161 di.display = {
'repair.before':2,
'repair.after':3}
167 into your debug.py file
and run runRepair.py
with the
@c --debug flag.
171 Display code should be updated once we settle on a standard way of controlling what
is displayed.
173 ConfigClass = RepairConfig
174 _DefaultName = "repair"
177 pipeBase.Task.__init__(self, **kwargs)
178 if self.config.doInterpolate:
179 self.makeSubtask(
"interp")
182 def run(self, exposure, defects=None, keepCRs=None):
183 """!Repair an Exposure's defects and cosmic rays
187 @param[
in] defects an lsst.meas.algorithms.DefectListT object. If
None, do no
189 @param[
in] keepCRs don
't interpolate over the CR pixels (defer to RepairConfig if None)
191 @throws AssertionError
with the following strings:
194 <DT> No exposure provided
195 <DD> The object provided
as exposure evaluates to
False
197 <DD> The Exposure has no associated Psf
200 assert exposure,
"No exposure provided"
201 psf = exposure.getPsf()
202 assert psf,
"No PSF provided"
204 frame = getDebugFrame(self._display,
"repair.before")
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")
216 afwDisplay.Display(frame).mtv(exposure)
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)
228 assert exposure,
"No exposure provided"
229 psf = exposure.getPsf()
230 assert psf,
"No psf provided"
234 mask = exposure.getMaskedImage().getMask()
235 crBit = mask.getMaskPlane(
"CR")
236 mask.clearMaskPlane(crBit)
241 binSize = self.config.cosmicray.background.binSize
242 nx, ny = exposure.getWidth()/binSize, exposure.getHeight()/binSize
246 medianBg = afwMath.makeStatistics(exposure.getMaskedImage(), afwMath.MEDIAN).getValue()
252 exposure = exposure.Factory(exposure,
True)
253 subtractBackgroundTask = measAlg.SubtractBackgroundTask(config=self.config.cosmicray.background)
254 modelBg = subtractBackgroundTask.run(exposure).background
258 keepCRs = self.config.cosmicray.keepCRs
260 crs = measAlg.findCosmicRays(exposure.getMaskedImage(), psf, medianBg,
261 pexConfig.makePropertySet(self.config.cosmicray), keepCRs)
264 img = exposure.getMaskedImage()
265 img += modelBg.getImageF()
268 exposure0.setMaskedImage(exposure.getMaskedImage())
272 afwDisplay.Display().mtv(exposure0, title=
"Failed CR")
277 mask = exposure0.getMaskedImage().getMask()
278 crBit = mask.getPlaneBitMask(
"CR")
279 afwDet.setMaskFromFootprintList(mask, crs, crBit)
282 if display
and displayCR:
283 disp = afwDisplay.Display()
284 disp.incrDefaultFrame()
285 disp.mtv(exposure0, title=
"Post-CR")
287 with disp.Buffering():
289 afwDisplay.utils.drawBBox(cr.getBBox(), borderWidth=0.55)
291 self.log.info(
"Identified %s cosmic rays.", num)
def __init__(self, **kwargs)
def run(self, exposure, defects=None, keepCRs=None)
Repair an Exposure's defects and cosmic rays.
def cosmicRay(self, exposure, keepCRs=None)