Coverage for python/lsst/meas/algorithms/reinterpolate_pixels.py: 46%

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1# This file is part of meas_algorithms. 

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/>. 

21 

22__all__ = ("ReinterpolatePixelsConfig", "ReinterpolatePixelsTask") 

23 

24import itertools 

25 

26import lsst.afw.detection as afwDetection 

27import lsst.afw.math as afwMath 

28import lsst.pex.config as pexConfig 

29import lsst.pipe.base as pipeBase 

30from lsst.meas.algorithms import Defect, interpolateOverDefects 

31 

32 

33class ReinterpolatePixelsConfig(pexConfig.Config): 

34 """Config for ReinterpolatePixelsTask""" 

35 

36 maskNameList = pexConfig.ListField[str]( 

37 doc="Names of mask planes whose image-plane values should be interpolated.", 

38 default=["SAT"], 

39 ) 

40 

41 fallbackValue = pexConfig.Field[float]( 

42 doc="Value of last resort for interpolation. If not provided (or set to None), it is assigned the " 

43 "clipped mean value of the exposure image.", 

44 default=None, 

45 optional=True, 

46 ) 

47 

48 

49class ReinterpolatePixelsTask(pipeBase.Task): 

50 """Task to reinterpolate pixels""" 

51 

52 ConfigClass = ReinterpolatePixelsConfig 

53 _DefaultName = "reinterpolatePixels" 

54 

55 def run(self, exposure): 

56 """Reinterpolate pixels over ``exposure``. 

57 

58 Parameters 

59 ---------- 

60 exposure : `lsst.afw.image.Exposure` 

61 Exposure to interpolate over. 

62 

63 Notes 

64 ----- 

65 ``exposure`` is modified in place and will become the reinterpolated exposure. 

66 """ 

67 mask = exposure.mask 

68 

69 thresh = afwDetection.Threshold( 

70 mask.getPlaneBitMask(self.config.maskNameList), afwDetection.Threshold.BITMASK 

71 ) 

72 fpSet = afwDetection.FootprintSet(mask, thresh) 

73 defectList = self._fromFootprintList(fpSet.getFootprints()) 

74 self._interpolateDefectList(exposure, defectList) 

75 

76 def _fromFootprintList(self, fpList): 

77 """Compute a defect list from a footprint list. 

78 

79 Parameters 

80 ---------- 

81 fpList : `list` of `lsst.afw.detection.Footprint` 

82 Footprint list to process. 

83 

84 Returns 

85 ------- 

86 defects : `list` of `lsst.meas.algorithms.Defect` 

87 List of defects. 

88 

89 Notes 

90 ----- 

91 By using `itertools.chain.from_iterable()`, the nested iterables are merged into a flat iterable, 

92 allowing convenient iteration over all `lsst.meas.algorithms.Defect` objects. 

93 """ 

94 return list( 

95 itertools.chain.from_iterable(map(Defect, afwDetection.footprintToBBoxList(fp)) for fp in fpList) 

96 ) 

97 

98 def _interpolateDefectList(self, exposure, defectList): 

99 """Interpolate over defects specified in a defect list. 

100 

101 Parameters 

102 ---------- 

103 exposure : `lsst.afw.image.Exposure` 

104 Exposure to process. 

105 defectList : `list` of `lsst.meas.algorithms.Defect` 

106 List of defects to interpolate over. 

107 

108 Notes 

109 ----- 

110 ``exposure`` is modified in place and will become the reinterpolated exposure. 

111 When reinterpolating following the interpolation in ip_isr, be aware that the masks are intentionally 

112 left grown as a side-effect of that interpolation. 

113 """ 

114 

115 # Although `interpolateOverDefects` requires the 

116 # `lsst.afw.detection.Psf` argument to be passed, it does not actually 

117 # utilize it. A dummy `lsst.afw.detection.Psf` object must still be 

118 # provided to prevent a TypeError. 

119 dummyPsf = afwDetection.Psf() 

120 if self.config.fallbackValue is None: 

121 fallbackValue = afwMath.makeStatistics(exposure.image, afwMath.MEANCLIP).getValue() 

122 else: 

123 fallbackValue = self.config.fallbackValue 

124 if "INTRP" not in exposure.mask.getMaskPlaneDict(): 

125 exposure.mask.addMaskPlane("INTRP") 

126 interpolateOverDefects(exposure.maskedImage, dummyPsf, defectList, fallbackValue, True)