Coverage for python/lsst/pipe/tasks/cosmicRayPostDiff.py: 68%

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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/>. 

21 

22import lsst.pex.config as pexConfig 

23import lsst.pipe.base as pipeBase 

24import lsst.pipe.base.connectionTypes as cT 

25from lsst.utils.timer import timeMethod 

26from .repair import RepairTask 

27 

28 

29__all__ = ["CosmicRayPostDiffConfig", "CosmicRayPostDiffTask"] 

30 

31 

32class CosmicRayPostDiffConnections(pipeBase.PipelineTaskConnections, 

33 dimensions=("instrument", "visit", "detector"), 

34 defaultTemplates={"coaddName": "deep", 

35 "fakesType": ""}): 

36 exposure = cT.Input( 

37 doc="Input difference image", 

38 name="{fakesType}{coaddName}Diff_differenceExp", 

39 storageClass="ExposureF", 

40 dimensions=("instrument", "visit", "detector"), 

41 ) 

42 repaired = cT.Output( 

43 doc="Output subtracted image after CR run.", 

44 name="{fakesType}{coaddName}Diff_repairedExp", 

45 storageClass="ExposureF", 

46 dimensions=("instrument", "visit", "detector"), 

47 ) 

48 

49 def adjustQuantum(self, inputs, outputs, label, dataId): 

50 # Docstring inherited from PipelineTaskConnections 

51 try: 

52 return super().adjustQuantum(inputs, outputs, label, dataId) 

53 except pipeBase.ScalarError as err: 

54 raise pipeBase.ScalarError( 

55 "CosmicRayPostDiffTask can at present only be run on visits that are associated with " 

56 "exactly one exposure. Either this is not a valid exposure for this pipeline, or the " 

57 "snap-combination step you probably want hasn't been configured to run between ISR and " 

58 "this task (as of this writing, that would be because it hasn't been implemented yet)." 

59 ) from err 

60 

61 

62class CosmicRayPostDiffConfig(pipeBase.PipelineTaskConfig, 

63 pipelineConnections=CosmicRayPostDiffConnections): 

64 

65 """Config for CosmicRayPostDiffTask""" 

66 repair = pexConfig.ConfigurableField( 

67 target=RepairTask, 

68 doc="Remove cosmic rays", 

69 ) 

70 

71 def setDefaults(self): 

72 super().setDefaults() 

73 

74 

75class CosmicRayPostDiffTask(pipeBase.PipelineTask): 

76 """ Detect and repair cosmic rays on an image difference. 

77 Given an output image from image differencing: 

78 - detect and repair cosmic rays 

79 - At the moment this task does NOT recompute the PSF or re-do source detection. 

80 To invoke the task, Call the `run` method. 

81 """ 

82 

83 ConfigClass = CosmicRayPostDiffConfig 

84 _DefaultName = "cosmicRayPostDiff" 

85 

86 def runQuantum(self, butlerQC, inputRefs, outputRefs): 

87 inputs = butlerQC.get(inputRefs) 

88 outputs = self.run(**inputs) 

89 butlerQC.put(outputs, outputRefs) 

90 

91 def __init__(self, **kwargs): 

92 """Construct a CosmicRayPostDiffTask""" 

93 super().__init__(**kwargs) 

94 self.makeSubtask("repair") 

95 

96 @timeMethod 

97 def run(self, exposure): 

98 """Run cosmic ray detection and repair on imageDifference outputs 

99 

100 Parameters 

101 ---------- 

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

103 The following changes are made to the exposure, 

104 - Blank cosmic ray mask planes, run CR detection and repair, update CR mask plane 

105 

106 Returns 

107 ------- 

108 `lsst.pipe.base.Struct`: 

109 Struct containing the input image with the CR mask plane first blanked, 

110 and then cosmic rays detected, and the mask is updated accordingly. 

111 The PSF model is NOT changed. 

112 """ 

113 

114 self.repair.run(exposure=exposure) 

115 

116 return pipeBase.Struct( 

117 repaired=exposure 

118 )