LSSTApplications  18.1.0
LSSTDataManagementBasePackage
interpImage.py
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22 from contextlib import contextmanager
23 import lsst.pex.config as pexConfig
24 import lsst.geom
25 import lsst.afw.image as afwImage
26 import lsst.afw.math as afwMath
27 import lsst.meas.algorithms as measAlg
28 import lsst.pipe.base as pipeBase
29 
30 __all__ = ["InterpImageConfig", "InterpImageTask"]
31 
32 
33 class InterpImageConfig(pexConfig.Config):
34  """Config for InterpImageTask
35  """
36  modelPsf = measAlg.GaussianPsfFactory.makeField(doc="Model Psf factory")
37 
38  useFallbackValueAtEdge = pexConfig.Field(
39  dtype=bool,
40  doc="Smoothly taper to the fallback value at the edge of the image?",
41  default=True,
42  )
43  fallbackValueType = pexConfig.ChoiceField(
44  dtype=str,
45  doc="Type of statistic to calculate edge fallbackValue for interpolation",
46  allowed={
47  "MEAN": "mean",
48  "MEDIAN": "median",
49  "MEANCLIP": "clipped mean",
50  "USER": "user value set in fallbackUserValue config",
51  },
52  default="MEDIAN",
53  )
54  fallbackUserValue = pexConfig.Field(
55  dtype=float,
56  doc="If fallbackValueType is 'USER' then use this as the fallbackValue; ignored otherwise",
57  default=0.0,
58  )
59  negativeFallbackAllowed = pexConfig.Field(
60  dtype=bool,
61  doc=("Allow negative values for egde interpolation fallbackValue? If False, set "
62  "fallbackValue to max(fallbackValue, 0.0)"),
63  default=False,
64  )
65  transpose = pexConfig.Field(dtype=int, default=False,
66  doc="Transpose image before interpolating? "
67  "This allows the interpolation to act over columns instead of rows.")
68 
69  def validate(self):
70  pexConfig.Config.validate(self)
71  if self.useFallbackValueAtEdge:
72  if (not self.negativeFallbackAllowed and self.fallbackValueType == "USER" and
73  self.fallbackUserValue < 0.0):
74  raise ValueError("User supplied fallbackValue is negative (%.2f) but "
75  "negativeFallbackAllowed is False" % self.fallbackUserValue)
76 
77 
78 class InterpImageTask(pipeBase.Task):
79  """Interpolate over bad image pixels
80  """
81  ConfigClass = InterpImageConfig
82  _DefaultName = "interpImage"
83 
84  def _setFallbackValue(self, mi=None):
85  """Set the edge fallbackValue for interpolation
86 
87  @param[in] mi input maksedImage on which to calculate the statistics
88  Must be provided if fallbackValueType != "USER".
89 
90  @return fallbackValue The value set/computed based on the fallbackValueType
91  and negativeFallbackAllowed config parameters
92  """
93  if self.config.fallbackValueType != 'USER':
94  assert mi, "No maskedImage provided"
95  if self.config.fallbackValueType == 'MEAN':
96  fallbackValue = afwMath.makeStatistics(mi, afwMath.MEAN).getValue()
97  elif self.config.fallbackValueType == 'MEDIAN':
98  fallbackValue = afwMath.makeStatistics(mi, afwMath.MEDIAN).getValue()
99  elif self.config.fallbackValueType == 'MEANCLIP':
100  fallbackValue = afwMath.makeStatistics(mi, afwMath.MEANCLIP).getValue()
101  elif self.config.fallbackValueType == 'USER':
102  fallbackValue = self.config.fallbackUserValue
103  else:
104  raise NotImplementedError("%s : %s not implemented" %
105  ("fallbackValueType", self.config.fallbackValueType))
106 
107  if not self.config.negativeFallbackAllowed and fallbackValue < 0.0:
108  self.log.warn("Negative interpolation edge fallback value computed but "
109  "negativeFallbackAllowed is False: setting fallbackValue to 0.0")
110  fallbackValue = max(fallbackValue, 0.0)
111 
112  self.log.info("fallbackValueType %s has been set to %.4f" %
113  (self.config.fallbackValueType, fallbackValue))
114 
115  return fallbackValue
116 
117  @pipeBase.timeMethod
118  def run(self, image, planeName=None, fwhmPixels=None, defects=None):
119  """!Interpolate in place over pixels in a maskedImage marked as bad
120 
121  Pixels to be interpolated are set by either a mask planeName provided
122  by the caller OR a defects list of type `~lsst.meas.algorithms.Defects`
123  If both are provided an exception is raised.
124 
125  Note that the interpolation code in meas_algorithms currently doesn't
126  use the input PSF (though it's a required argument), so it's not
127  important to set the input PSF parameters exactly. This PSF is set
128  here as the psf attached to the "image" (i.e if the image passed in
129  is an Exposure). Otherwise, a psf model is created using
130  measAlg.GaussianPsfFactory with the value of fwhmPixels (the value
131  passed in by the caller, or the default defaultFwhm set in
132  measAlg.GaussianPsfFactory if None).
133 
134  @param[in,out] image MaskedImage OR Exposure to be interpolated
135  @param[in] planeName name of mask plane over which to interpolate
136  If None, must provide a defects list.
137  @param[in] fwhmPixels FWHM of core star (pixels)
138  If None the default is used, where the default
139  is set to the exposure psf if available
140  @param[in] defects List of defects of type measAlg.Defects
141  over which to interpolate.
142  """
143  try:
144  maskedImage = image.getMaskedImage()
145  except AttributeError:
146  maskedImage = image
147 
148  # set defectList from defects OR mask planeName provided
149  if planeName is None:
150  if defects is None:
151  raise ValueError("No defects or plane name provided")
152  else:
153  if not isinstance(defects, measAlg.Defects):
154  defectList = measAlg.Defects(defects)
155  else:
156  defectList = defects
157  planeName = "defects"
158  else:
159  if defects is not None:
160  raise ValueError("Provide EITHER a planeName OR a list of defects, not both")
161  if planeName not in maskedImage.getMask().getMaskPlaneDict():
162  raise ValueError("maskedImage does not contain mask plane %s" % planeName)
163  defectList = measAlg.Defects.fromMask(maskedImage, planeName)
164 
165  # set psf from exposure if provided OR using modelPsf with fwhmPixels provided
166  try:
167  psf = image.getPsf()
168  self.log.info("Setting psf for interpolation from image")
169  except AttributeError:
170  self.log.info("Creating psf model for interpolation from fwhm(pixels) = %s" %
171  (str(fwhmPixels) if fwhmPixels is not None else
172  (str(self.config.modelPsf.defaultFwhm)) + " [default]"))
173  psf = self.config.modelPsf.apply(fwhm=fwhmPixels)
174 
175  fallbackValue = 0.0 # interpolateOverDefects needs this to be a float, regardless if it is used
176  if self.config.useFallbackValueAtEdge:
177  fallbackValue = self._setFallbackValue(maskedImage)
178 
179  self.interpolateImage(maskedImage, psf, defectList, fallbackValue)
180 
181  self.log.info("Interpolated over %d %s pixels." % (len(defectList), planeName))
182 
183  @contextmanager
184  def transposeContext(self, maskedImage, defects):
185  """Context manager to potentially transpose an image
186 
187  This applies the ``transpose`` configuration setting.
188 
189  Transposing the image allows us to interpolate along columns instead
190  of rows, which is useful when the saturation trails are typically
191  oriented along rows on the warped/coadded images, instead of along
192  columns as they typically are in raw CCD images.
193 
194  Parameters
195  ----------
196  maskedImage : `lsst.afw.image.MaskedImage`
197  Image on which to perform interpolation.
198  defects : `lsst.meas.algorithms.Defects`
199  List of defects to interpolate over.
200 
201  Yields
202  ------
203  useImage : `lsst.afw.image.MaskedImage`
204  Image to use for interpolation; it may have been transposed.
205  useDefects : `lsst.meas.algorithms.Defects`
206  List of defects to use for interpolation; they may have been
207  transposed.
208  """
209  def transposeImage(image):
210  """Transpose an image"""
211  transposed = image.array.T.copy() # Copy to force row-major; required for ndarray+pybind
212  return image.Factory(transposed, False, lsst.geom.Point2I(*reversed(image.getXY0())))
213 
214  useImage = maskedImage
215  useDefects = defects
216  if self.config.transpose:
217  useImage = afwImage.makeMaskedImage(transposeImage(maskedImage.image),
218  transposeImage(maskedImage.mask),
219  transposeImage(maskedImage.variance))
220  useDefects = defects.transpose()
221  yield useImage, useDefects
222  if self.config.transpose:
223  maskedImage.image.array = useImage.image.array.T
224  maskedImage.mask.array = useImage.mask.array.T
225  maskedImage.variance.array = useImage.variance.array.T
226 
227  def interpolateImage(self, maskedImage, psf, defectList, fallbackValue):
228  """Interpolate over defects in an image
229 
230  Parameters
231  ----------
232  maskedImage : `lsst.afw.image.MaskedImage`
233  Image on which to perform interpolation.
234  psf : `lsst.afw.detection.Psf`
235  Point-spread function; currently unused.
236  defectList : `lsst.meas.algorithms.Defects`
237  List of defects to interpolate over.
238  fallbackValue : `float`
239  Value to set when interpolation fails.
240  """
241  if not defectList:
242  return
243  with self.transposeContext(maskedImage, defectList) as (image, defects):
244  measAlg.interpolateOverDefects(image, psf, defects, fallbackValue,
245  self.config.useFallbackValueAtEdge)
Fit spatial kernel using approximate fluxes for candidates, and solving a linear system of equations...
MaskedImage< ImagePixelT, MaskPixelT, VariancePixelT > * makeMaskedImage(typename std::shared_ptr< Image< ImagePixelT >> image, typename std::shared_ptr< Mask< MaskPixelT >> mask=Mask< MaskPixelT >(), typename std::shared_ptr< Image< VariancePixelT >> variance=Image< VariancePixelT >())
A function to return a MaskedImage of the correct type (cf.
Definition: MaskedImage.h:1280
Statistics makeStatistics(lsst::afw::math::MaskedVector< EntryT > const &mv, std::vector< WeightPixel > const &vweights, int const flags, StatisticsControl const &sctrl=StatisticsControl())
The makeStatistics() overload to handle lsst::afw::math::MaskedVector<>
Definition: Statistics.h:520
def transposeContext(self, maskedImage, defects)
Definition: interpImage.py:184
int max
def run(self, image, planeName=None, fwhmPixels=None, defects=None)
Interpolate in place over pixels in a maskedImage marked as bad.
Definition: interpImage.py:118
def interpolateImage(self, maskedImage, psf, defectList, fallbackValue)
Definition: interpImage.py:227
Backwards-compatibility support for depersisting the old Calib (FluxMag0/FluxMag0Err) objects...