Coverage for tests/test_transformDiaSourceCatalog.py: 19%

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1# This file is part of ap_association 

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 os 

23import unittest 

24 

25import numpy as np 

26 

27from lsst.ap.association.transformDiaSourceCatalog import (TransformDiaSourceCatalogConfig, 

28 TransformDiaSourceCatalogTask) 

29from lsst.afw.cameraGeom.testUtils import DetectorWrapper 

30import lsst.daf.base as dafBase 

31import lsst.afw.image as afwImage 

32import lsst.geom as geom 

33import lsst.meas.base.tests as measTests 

34from lsst.pipe.base import Struct 

35from lsst.utils import getPackageDir 

36import lsst.utils.tests 

37 

38from lsst.ap.association.transformDiaSourceCatalog import UnpackApdbFlags 

39 

40 

41class TestTransformDiaSourceCatalogTask(unittest.TestCase): 

42 def setUp(self): 

43 # The first source will be a sky source. 

44 self.nSources = 10 

45 # Default PSF size (psfDim in makeEmptyExposure) in TestDataset results 

46 # in an 18 pixel wide source box. 

47 self.bboxSize = 18 

48 self.yLoc = 100 

49 self.bbox = geom.Box2I(geom.Point2I(0, 0), 

50 geom.Extent2I(1024, 1153)) 

51 dataset = measTests.TestDataset(self.bbox) 

52 for srcIdx in range(self.nSources-1): 

53 # Place sources at (index, yLoc), so we can distinguish them later. 

54 dataset.addSource(100000.0, geom.Point2D(srcIdx, self.yLoc)) 

55 # Ensure the last source has no peak `significance` field. 

56 dataset.addSource(100000.0, geom.Point2D(srcIdx+1, self.yLoc), setPeakSignificance=False) 

57 schema = dataset.makeMinimalSchema() 

58 schema.addField("base_PixelFlags_flag", type="Flag") 

59 schema.addField("base_PixelFlags_flag_offimage", type="Flag") 

60 schema.addField("sky_source", type="Flag", doc="Sky objects.") 

61 self.exposure, self.inputCatalog = dataset.realize(10.0, schema, randomSeed=1234) 

62 self.inputCatalog[0]['sky_source'] = True 

63 # Create schemas for use in initializing the TransformDiaSourceCatalog task. 

64 self.initInputs = {"diaSourceSchema": Struct(schema=schema)} 

65 self.initInputsBadFlags = {"diaSourceSchema": Struct(schema=dataset.makeMinimalSchema())} 

66 

67 self.expId = 4321 

68 self.date = dafBase.DateTime(nsecs=1400000000 * 10**9) 

69 detector = DetectorWrapper(id=23, bbox=self.exposure.getBBox()).detector 

70 visit = afwImage.VisitInfo( 

71 exposureId=self.expId, 

72 exposureTime=200., 

73 date=self.date) 

74 self.exposure.info.id = self.expId 

75 self.exposure.setDetector(detector) 

76 self.exposure.getInfo().setVisitInfo(visit) 

77 self.filterName = 'g' 

78 self.exposure.setFilter(afwImage.FilterLabel(band=self.filterName, physical='g.MP9401')) 

79 scale = 2 

80 scaleErr = 1 

81 self.photoCalib = afwImage.PhotoCalib(scale, scaleErr) 

82 self.exposure.setPhotoCalib(self.photoCalib) 

83 

84 self.config = TransformDiaSourceCatalogConfig() 

85 self.config.flagMap = os.path.join(getPackageDir("ap_association"), 

86 "tests", "data", "test-flag-map.yaml") 

87 self.config.functorFile = os.path.join(getPackageDir("ap_association"), 

88 "tests", 

89 "data", 

90 "testDiaSource.yaml") 

91 

92 def test_run(self): 

93 """Test output dataFrame is created and values are correctly inserted 

94 from the exposure. 

95 """ 

96 transformTask = TransformDiaSourceCatalogTask(initInputs=self.initInputs, 

97 config=self.config) 

98 result = transformTask.run(self.inputCatalog, 

99 self.exposure, 

100 self.filterName, 

101 ccdVisitId=self.expId) 

102 

103 self.assertEqual(len(result.diaSourceTable), len(self.inputCatalog)) 

104 np.testing.assert_array_equal(result.diaSourceTable["bboxSize"], [self.bboxSize]*self.nSources) 

105 np.testing.assert_array_equal(result.diaSourceTable["ccdVisitId"], [self.expId]*self.nSources) 

106 np.testing.assert_array_equal(result.diaSourceTable["filterName"], [self.filterName]*self.nSources) 

107 np.testing.assert_array_equal(result.diaSourceTable["midPointTai"], 

108 [self.date.get(system=dafBase.DateTime.MJD)]*self.nSources) 

109 np.testing.assert_array_equal(result.diaSourceTable["diaObjectId"], [0]*self.nSources) 

110 np.testing.assert_array_equal(result.diaSourceTable["x"], np.arange(self.nSources)) 

111 # The final snr value should be NaN because it doesn't have a peak significance field. 

112 expect_snr = [397.887353515625]*9 

113 expect_snr.append(np.nan) 

114 # Have to use allclose because assert_array_equal doesn't support equal_nan. 

115 np.testing.assert_allclose(result.diaSourceTable["snr"], expect_snr, equal_nan=True, rtol=0) 

116 

117 def test_run_doSkySources(self): 

118 """Test that we get the correct output with doSkySources=True; the one 

119 sky source should be missing, but the other records should be the same. 

120 

121 We only test the fields here that could be different, not the ones that 

122 are the same for all sources. 

123 """ 

124 # Make the sky source have a different significance value, to distinguish it. 

125 self.inputCatalog[0].getFootprint().updatePeakSignificance(5.0) 

126 

127 self.config.doRemoveSkySources = True 

128 task = TransformDiaSourceCatalogTask(initInputs=self.initInputs, config=self.config) 

129 result = task.run(self.inputCatalog, self.exposure, self.filterName, ccdVisitId=self.expId) 

130 

131 self.assertEqual(len(result.diaSourceTable), self.nSources-1) 

132 # 0th source was removed, so x positions of the remaining sources are at x=1,2,3... 

133 np.testing.assert_array_equal(result.diaSourceTable["x"], np.arange(self.nSources-1)+1) 

134 # The final snr value should be NaN because it doesn't have a peak significance field. 

135 expect_snr = [397.887353515625]*8 

136 expect_snr.append(np.nan) 

137 # Have to use allclose because assert_array_equal doesn't support equal_nan. 

138 np.testing.assert_allclose(result.diaSourceTable["snr"], expect_snr, equal_nan=True, rtol=0) 

139 

140 def test_run_dia_source_wrong_flags(self): 

141 """Test that the proper errors are thrown when requesting flag columns 

142 that are not in the input schema. 

143 """ 

144 with self.assertRaises(KeyError): 

145 TransformDiaSourceCatalogTask(initInputs=self.initInputsBadFlags) 

146 

147 def test_computeBBoxSize(self): 

148 transform = TransformDiaSourceCatalogTask(initInputs=self.initInputs, 

149 config=self.config) 

150 boxSizes = transform.computeBBoxSizes(self.inputCatalog) 

151 

152 for size in boxSizes: 

153 self.assertEqual(size, self.bboxSize) 

154 self.assertEqual(len(boxSizes), self.nSources) 

155 

156 def test_bit_unpacker(self): 

157 """Test that the integer bit packer is functioning correctly. 

158 """ 

159 transform = TransformDiaSourceCatalogTask(initInputs=self.initInputs, 

160 config=self.config) 

161 for idx, obj in enumerate(self.inputCatalog): 

162 if idx in [1, 3, 5]: 

163 obj.set("base_PixelFlags_flag", 1) 

164 if idx in [1, 4, 6]: 

165 obj.set("base_PixelFlags_flag_offimage", 1) 

166 outputCatalog = transform.run(self.inputCatalog, 

167 self.exposure, 

168 self.filterName, 

169 ccdVisitId=self.expId).diaSourceTable 

170 

171 unpacker = UnpackApdbFlags(self.config.flagMap, "DiaSource") 

172 flag_values = unpacker.unpack(outputCatalog["flags"], "flags") 

173 

174 for idx, flag in enumerate(flag_values): 

175 if idx in [1, 3, 5]: 

176 self.assertTrue(flag['base_PixelFlags_flag']) 

177 else: 

178 self.assertFalse(flag['base_PixelFlags_flag']) 

179 

180 if idx in [1, 4, 6]: 

181 self.assertTrue(flag['base_PixelFlags_flag_offimage']) 

182 else: 

183 self.assertFalse(flag['base_PixelFlags_flag_offimage']) 

184 

185 def test_flag_existence_check(self): 

186 unpacker = UnpackApdbFlags(self.config.flagMap, "DiaSource") 

187 

188 self.assertTrue(unpacker.flagExists('base_PixelFlags_flag')) 

189 self.assertFalse(unpacker.flagExists('')) 

190 with self.assertRaisesRegex(ValueError, 'column doesNotExist not in flag map'): 

191 unpacker.flagExists('base_PixelFlags_flag', columnName='doesNotExist') 

192 

193 def test_flag_bitmask(self): 

194 """Test that we get the expected bitmask back from supplied flag names. 

195 """ 

196 unpacker = UnpackApdbFlags(self.config.flagMap, "DiaSource") 

197 

198 with self.assertRaisesRegex(ValueError, "flag '' not included"): 

199 unpacker.makeFlagBitMask(['']) 

200 with self.assertRaisesRegex(ValueError, 'column doesNotExist not in flag map'): 

201 unpacker.makeFlagBitMask(['base_PixelFlags_flag'], columnName='doesNotExist') 

202 self.assertEqual(unpacker.makeFlagBitMask(['base_PixelFlags_flag']), np.uint64(1)) 

203 self.assertEqual(unpacker.makeFlagBitMask(['base_PixelFlags_flag_offimage']), np.uint64(2)) 

204 self.assertEqual(unpacker.makeFlagBitMask(['base_PixelFlags_flag', 

205 'base_PixelFlags_flag_offimage']), 

206 np.uint64(3)) 

207 

208 

209class MemoryTester(lsst.utils.tests.MemoryTestCase): 

210 pass 

211 

212 

213def setup_module(module): 

214 lsst.utils.tests.init() 

215 

216 

217if __name__ == "__main__": 217 ↛ 218line 217 didn't jump to line 218, because the condition on line 217 was never true

218 lsst.utils.tests.init() 

219 unittest.main()