92 """Set the edge fallbackValue for interpolation
96 mi : `lsst.afw.image.MaskedImage`, optional
97 Input maskedImage on which to calculate the statistics
98 Must be provided if fallbackValueType != "USER".
102 fallbackValue : `float`
103 The value set/computed based on the fallbackValueType
104 and negativeFallbackAllowed config parameters.
106 if self.config.fallbackValueType !=
'USER':
107 assert mi,
"No maskedImage provided"
108 if self.config.fallbackValueType ==
'MEAN':
109 fallbackValue = afwMath.makeStatistics(mi, afwMath.MEAN).getValue()
110 elif self.config.fallbackValueType ==
'MEDIAN':
111 fallbackValue = afwMath.makeStatistics(mi, afwMath.MEDIAN).getValue()
112 elif self.config.fallbackValueType ==
'MEANCLIP':
113 fallbackValue = afwMath.makeStatistics(mi, afwMath.MEANCLIP).getValue()
114 elif self.config.fallbackValueType ==
'USER':
115 fallbackValue = self.config.fallbackUserValue
117 raise NotImplementedError(
"%s : %s not implemented" %
118 (
"fallbackValueType", self.config.fallbackValueType))
120 if not self.config.negativeFallbackAllowed
and fallbackValue < 0.0:
121 self.log.warning(
"Negative interpolation edge fallback value computed but "
122 "negativeFallbackAllowed is False: setting fallbackValue to 0.0")
123 fallbackValue = max(fallbackValue, 0.0)
125 self.log.info(
"fallbackValueType %s has been set to %.4f",
126 self.config.fallbackValueType, fallbackValue)
131 def run(self, image, planeName=None, fwhmPixels=None, defects=None):
132 """Interpolate in place over pixels in a maskedImage marked as bad
134 Pixels to be interpolated are set by either a mask planeName provided
135 by the caller OR a defects list of type `~lsst.meas.algorithms.Defects`
136 If both are provided an exception is raised.
138 Note that the interpolation code in meas_algorithms currently doesn't
139 use the input PSF (though it's a required argument), so it's not
140 important to set the input PSF parameters exactly. This PSF is set
141 here as the psf attached to the "image" (i.e if the image passed in
142 is an Exposure). Otherwise, a psf model is created using
143 measAlg.GaussianPsfFactory with the value of fwhmPixels (the value
144 passed in by the caller, or the default defaultFwhm set in
145 measAlg.GaussianPsfFactory if None).
149 image : `lsst.afw.image.MaskedImage` or `lsst.afw.image.exposure.Exposure`
150 MaskedImage OR Exposure to be interpolated.
151 planeName : `str`, optional
152 Name of mask plane over which to interpolate.
153 If None, must provide a defects list.
154 fwhmPixels : `int`, optional
155 FWHM of core star (pixels).
156 If None the default is used, where the default
157 is set to the exposure psf if available.
158 defects : `lsst.meas.algorithms.Defects`, optional
159 List of defects of type ipIsr.Defects
160 over which to interpolate.
163 maskedImage = image.getMaskedImage()
164 except AttributeError:
168 if planeName
is None:
170 raise ValueError(
"No defects or plane name provided")
172 if not isinstance(defects, ipIsr.Defects):
173 defectList = ipIsr.Defects(defects)
176 planeName =
"defects"
178 if defects
is not None:
179 raise ValueError(
"Provide EITHER a planeName OR a list of defects, not both")
180 if planeName
not in maskedImage.getMask().getMaskPlaneDict():
181 raise ValueError(
"maskedImage does not contain mask plane %s" % planeName)
182 defectList = ipIsr.Defects.fromMask(maskedImage, planeName)
187 self.log.info(
"Setting psf for interpolation from image")
188 except AttributeError:
189 self.log.info(
"Creating psf model for interpolation from fwhm(pixels) = %s",
190 str(fwhmPixels)
if fwhmPixels
is not None else
191 (str(self.config.modelPsf.defaultFwhm)) +
" [default]")
192 psf = self.config.modelPsf.apply(fwhm=fwhmPixels)
195 if self.config.useFallbackValueAtEdge:
200 self.log.info(
"Interpolated over %d %s pixels.", len(defectList), planeName)
204 """Context manager to potentially transpose an image
206 This applies the ``transpose`` configuration setting.
208 Transposing the image allows us to interpolate along columns instead
209 of rows, which is useful when the saturation trails are typically
210 oriented along rows on the warped/coadded images, instead of along
211 columns as they typically are in raw CCD images.
215 maskedImage : `lsst.afw.image.MaskedImage`
216 Image on which to perform interpolation.
217 defects : `lsst.meas.algorithms.Defects`
218 List of defects to interpolate over.
222 useImage : `lsst.afw.image.MaskedImage`
223 Image to use for interpolation; it may have been transposed.
224 useDefects : `lsst.meas.algorithms.Defects`
225 List of defects to use for interpolation; they may have been
228 def transposeImage(image):
229 """Transpose an image
235 transposed = image.array.T.copy()
236 return image.Factory(transposed,
False,
lsst.geom.Point2I(*reversed(image.getXY0())))
238 useImage = maskedImage
240 if self.config.transpose:
241 useImage = afwImage.makeMaskedImage(transposeImage(maskedImage.image),
242 transposeImage(maskedImage.mask),
243 transposeImage(maskedImage.variance))
244 useDefects = defects.transpose()
245 yield useImage, useDefects
246 if self.config.transpose:
247 maskedImage.image.array = useImage.image.array.T
248 maskedImage.mask.array = useImage.mask.array.T
249 maskedImage.variance.array = useImage.variance.array.T
252 """Interpolate over defects in an image
256 maskedImage : `lsst.afw.image.MaskedImage`
257 Image on which to perform interpolation.
258 psf : `lsst.afw.detection.Psf`
259 Point-spread function; currently unused.
260 defectList : `lsst.meas.algorithms.Defects`
261 List of defects to interpolate over.
262 fallbackValue : `float`
263 Value to set when interpolation fails.
268 measAlg.interpolateOverDefects(image, psf, defects, fallbackValue,
269 self.config.useFallbackValueAtEdge)