Coverage for python/lsst/faro/base/BaseSubTasks.py: 44%

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1# This file is part of faro. 

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 

22from lsst.afw.table import SourceCatalog 

23from lsst.pipe.base import Struct, Task 

24from lsst.pex.config import Field, DictField 

25from lsst.verify import Measurement 

26 

27from lsst.faro.utils.matcher import mergeCatalogs 

28from lsst.faro.utils.calibrated_catalog import CalibratedCatalog 

29from lsst.faro.base.ConfigBase import MeasurementTaskConfig 

30import astropy.units as u 

31import numpy as np 

32from typing import Dict, List 

33 

34__all__ = ( 

35 "NumSourcesTask", 

36 "NumSourcesConfig", 

37 "NumSourcesMatchedTask", 

38 "NumSourcesMergeTask", 

39 "NumpySummaryConfig", 

40 "NumpySummaryTask", 

41) 

42 

43 

44class NumSourcesConfig(MeasurementTaskConfig): 

45 doPrimary = Field( 

46 doc="Only count sources where detect_isPrimary is True.", 

47 dtype=bool, 

48 default=False, 

49 ) 

50 columns = DictField( 

51 doc="""Columns required for metric calculation. Should be all columns in SourceTable contexts, 

52 and columns that do not change name with band in ObjectTable contexts""", 

53 keytype=str, 

54 itemtype=str, 

55 default={"detect_isPrimary": "detect_isPrimary"} 

56 ) 

57 columnsBand = DictField( 

58 doc="""Columns required for metric calculation that change with band in ObjectTable contexts""", 

59 keytype=str, 

60 itemtype=str, 

61 default={} 

62 ) 

63 

64 

65class NumSourcesTask(Task): 

66 r"""Simple default task to count the number of sources/objects in catalog.""" 

67 

68 ConfigClass = NumSourcesConfig 

69 _DefaultName = "numSourcesTask" 

70 

71 def run(self, metricName, catalog, **kwargs): 

72 """Run NumSourcesTask 

73 Parameters 

74 ---------- 

75 metricName : `str` 

76 The name of the metric to measure. 

77 catalog : `dict` 

78 `lsst.afw.table` Catalog type 

79 kwargs 

80 Extra keyword arguments used to construct the task. 

81 Returns 

82 ------- 

83 measurement : `Struct` 

84 The measured value of the metric. 

85 """ 

86 self.log.info("Measuring %s", metricName) 

87 if self.config.doPrimary: 

88 nSources = np.sum(catalog[self.config._getColumnName("detect_isPrimary")] is True) 

89 else: 

90 nSources = len(catalog) 

91 self.log.info("Number of sources (nSources) = %i" % nSources) 

92 meas = Measurement("nsrcMeas", nSources * u.count) 

93 return Struct(measurement=meas) 

94 

95 

96class NumSourcesMatchedTask(NumSourcesTask): 

97 r"""Extension of NumSourcesTask to count sources in a matched catalog""" 

98 

99 # The only purpose of this task is to call NumSourcesTask's run method 

100 # TODO: Review the necessity of this in DM-31061 

101 def run(self, metricName: str, matchedCatalog: SourceCatalog, **kwargs): 

102 return super().run(metricName, matchedCatalog, **kwargs) 

103 

104 

105class NumSourcesMergeTask(Task): 

106 

107 ConfigClass = MeasurementTaskConfig 

108 _DefaultName = "numSourcesMergeTask" 

109 

110 def run(self, metricName: str, data: Dict[str, List[CalibratedCatalog]]): 

111 bands = list(data.keys()) 

112 if len(bands) != 1: 

113 raise RuntimeError(f'NumSourcesMergeTask task got bands: {bands} but expecting exactly one') 

114 else: 

115 data = data[list(bands)[0]] 

116 self.log.info("Measuring %s", metricName) 

117 catalog = mergeCatalogs( 

118 [x.catalog for x in data], 

119 [x.photoCalib for x in data], 

120 [x.astromCalib for x in data], 

121 ) 

122 nSources = len(catalog) 

123 meas = Measurement("nsrcMeas", nSources * u.count) 

124 return Struct(measurement=meas) 

125 

126 

127class NumpySummaryConfig(MeasurementTaskConfig): 

128 summary = Field( 

129 dtype=str, default="median", doc="Aggregation to use for summary metrics" 

130 ) 

131 

132 

133class NumpySummaryTask(Task): 

134 

135 ConfigClass = NumpySummaryConfig 

136 _DefaultName = "numpySummaryTask" 

137 

138 def run(self, measurements, agg_name, package, metric): 

139 agg = agg_name.lower() 

140 if agg == "summary": 

141 agg = self.config.summary 

142 self.log.info("Computing the %s of %s_%s values", agg, package, metric) 

143 

144 if len(measurements) == 0: 

145 self.log.info("Received zero length measurements list. Returning NaN.") 

146 # In the case of an empty list, there is nothing we can do other than 

147 # to return a NaN 

148 value = u.Quantity(np.nan) 

149 else: 

150 unit = measurements[0].quantity.unit 

151 value = getattr(np, agg)( 

152 u.Quantity( 

153 [x.quantity for x in measurements if np.isfinite(x.quantity)] 

154 ) 

155 ) 

156 # Make sure return has same unit as inputs 

157 # In some cases numpy can return a NaN and the unit gets dropped 

158 value = value.value * unit 

159 return Struct( 

160 measurement=Measurement( 

161 f"metricvalue_{agg_name.lower()}_{package}_{metric}", value 

162 ) 

163 )