Coverage for tests/test_diaPipe.py: 20%

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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 tempfile 

23import unittest 

24from unittest.mock import patch, Mock, MagicMock, DEFAULT 

25import warnings 

26 

27import numpy as np 

28import pandas as pd 

29 

30import lsst.afw.image as afwImage 

31import lsst.afw.table as afwTable 

32import lsst.dax.apdb as daxApdb 

33import lsst.pex.config as pexConfig 

34import lsst.utils.tests 

35from lsst.pipe.base.testUtils import assertValidOutput 

36 

37from lsst.ap.association import DiaPipelineTask 

38from utils_tests import makeExposure, makeDiaObjects 

39 

40 

41def _makeMockDataFrame(): 

42 """Create a new mock of a DataFrame. 

43 

44 Returns 

45 ------- 

46 mock : `unittest.mock.Mock` 

47 A mock guaranteed to accept all operations used by `pandas.DataFrame`. 

48 """ 

49 with warnings.catch_warnings(): 

50 # spec triggers deprecation warnings on DataFrame, but will 

51 # automatically adapt to any removals. 

52 warnings.simplefilter("ignore", category=DeprecationWarning) 

53 return MagicMock(spec=pd.DataFrame()) 

54 

55 

56class TestDiaPipelineTask(unittest.TestCase): 

57 

58 @classmethod 

59 def _makeDefaultConfig(cls, 

60 config_file, 

61 doPackageAlerts=False, 

62 doSolarSystemAssociation=False): 

63 config = DiaPipelineTask.ConfigClass() 

64 config.doConfigureApdb = False 

65 config.apdb_config_url = config_file 

66 config.doPackageAlerts = doPackageAlerts 

67 config.doSolarSystemAssociation = doSolarSystemAssociation 

68 return config 

69 

70 def setUp(self): 

71 # Create an instance of random generator with fixed seed. 

72 rng = np.random.default_rng(1234) 

73 self.rng = rng 

74 

75 # schemas are persisted in both Gen 2 and Gen 3 butler as prototypical catalogs 

76 srcSchema = afwTable.SourceTable.makeMinimalSchema() 

77 srcSchema.addField("base_PixelFlags_flag", type="Flag") 

78 srcSchema.addField("base_PixelFlags_flag_offimage", type="Flag") 

79 self.srcSchema = afwTable.SourceCatalog(srcSchema) 

80 

81 apdb_config = daxApdb.ApdbSql.init_database(db_url="sqlite://") 

82 self.config_file = tempfile.NamedTemporaryFile() 

83 self.addCleanup(self.config_file.close) 

84 apdb_config.save(self.config_file.name) 

85 

86 # TODO: remove on DM-43419 

87 def testConfigApdbNestedOk(self): 

88 config = DiaPipelineTask.ConfigClass() 

89 config.doConfigureApdb = True 

90 with self.assertWarns(FutureWarning): 

91 config.apdb.db_url = "sqlite://" 

92 config.freeze() 

93 config.validate() 

94 

95 # TODO: remove on DM-43419 

96 def testConfigApdbNestedInvalid(self): 

97 config = DiaPipelineTask.ConfigClass() 

98 config.doConfigureApdb = True 

99 # Don't set db_url 

100 config.freeze() 

101 with self.assertRaises(pexConfig.FieldValidationError): 

102 config.validate() 

103 

104 # TODO: remove on DM-43419 

105 def testConfigApdbFileOk(self): 

106 config = DiaPipelineTask.ConfigClass() 

107 config.doConfigureApdb = False 

108 config.apdb_config_url = "some/file/path.yaml" 

109 config.freeze() 

110 config.validate() 

111 

112 # TODO: remove on DM-43419 

113 def testConfigApdbFileInvalid(self): 

114 config = DiaPipelineTask.ConfigClass() 

115 config.doConfigureApdb = False 

116 # Don't set apdb_config_url 

117 config.freeze() 

118 with self.assertRaises(pexConfig.FieldValidationError): 

119 config.validate() 

120 

121 def testRun(self): 

122 """Test running while creating and packaging alerts. 

123 """ 

124 self._testRun(doPackageAlerts=True, doSolarSystemAssociation=True) 

125 

126 def testRunWithSolarSystemAssociation(self): 

127 """Test running while creating and packaging alerts. 

128 """ 

129 self._testRun(doPackageAlerts=False, doSolarSystemAssociation=True) 

130 

131 def testRunWithAlerts(self): 

132 """Test running while creating and packaging alerts. 

133 """ 

134 self._testRun(doPackageAlerts=True, doSolarSystemAssociation=False) 

135 

136 def testRunWithoutAlertsOrSolarSystem(self): 

137 """Test running without creating and packaging alerts. 

138 """ 

139 self._testRun(doPackageAlerts=False, doSolarSystemAssociation=False) 

140 

141 def _testRun(self, doPackageAlerts=False, doSolarSystemAssociation=False): 

142 """Test the normal workflow of each ap_pipe step. 

143 """ 

144 config = self._makeDefaultConfig( 

145 config_file=self.config_file.name, 

146 doPackageAlerts=doPackageAlerts, 

147 doSolarSystemAssociation=doSolarSystemAssociation) 

148 task = DiaPipelineTask(config=config) 

149 # Set DataFrame index testing to always return False. Mocks return 

150 # true for this check otherwise. 

151 task.testDataFrameIndex = lambda x: False 

152 diffIm = Mock(spec=afwImage.ExposureF) 

153 exposure = Mock(spec=afwImage.ExposureF) 

154 template = Mock(spec=afwImage.ExposureF) 

155 diaSrc = _makeMockDataFrame() 

156 ssObjects = _makeMockDataFrame() 

157 ccdExposureIdBits = 32 

158 

159 # Each of these subtasks should be called once during diaPipe 

160 # execution. We use mocks here to check they are being executed 

161 # appropriately. 

162 subtasksToMock = [ 

163 "diaCatalogLoader", 

164 "diaCalculation", 

165 "diaForcedSource", 

166 ] 

167 if doPackageAlerts: 

168 subtasksToMock.append("alertPackager") 

169 else: 

170 self.assertFalse(hasattr(task, "alertPackager")) 

171 

172 if not doSolarSystemAssociation: 

173 self.assertFalse(hasattr(task, "solarSystemAssociator")) 

174 

175 def concatMock(_data, **_kwargs): 

176 return _makeMockDataFrame() 

177 

178 # Mock out the run() methods of these two Tasks to ensure they 

179 # return data in the correct form. 

180 def solarSystemAssociator_run(unAssocDiaSources, solarSystemObjectTable, diffIm): 

181 return lsst.pipe.base.Struct(nTotalSsObjects=42, 

182 nAssociatedSsObjects=30, 

183 ssoAssocDiaSources=_makeMockDataFrame(), 

184 unAssocDiaSources=_makeMockDataFrame()) 

185 

186 def associator_run(table, diaObjects): 

187 return lsst.pipe.base.Struct(nUpdatedDiaObjects=2, nUnassociatedDiaObjects=3, 

188 matchedDiaSources=_makeMockDataFrame(), 

189 unAssocDiaSources=_makeMockDataFrame()) 

190 

191 # apdb isn't a subtask, but still needs to be mocked out for correct 

192 # execution in the test environment. 

193 with patch.multiple(task, **{task: DEFAULT for task in subtasksToMock + ["apdb"]}), \ 

194 patch('lsst.ap.association.diaPipe.pd.concat', side_effect=concatMock), \ 

195 patch('lsst.ap.association.association.AssociationTask.run', 

196 side_effect=associator_run) as mainRun, \ 

197 patch('lsst.ap.association.ssoAssociation.SolarSystemAssociationTask.run', 

198 side_effect=solarSystemAssociator_run) as ssRun: 

199 

200 result = task.run(diaSrc, 

201 ssObjects, 

202 diffIm, 

203 exposure, 

204 template, 

205 ccdExposureIdBits, 

206 "g") 

207 for subtaskName in subtasksToMock: 

208 getattr(task, subtaskName).run.assert_called_once() 

209 assertValidOutput(task, result) 

210 # Exact type and contents of apdbMarker are undefined. 

211 self.assertIsInstance(result.apdbMarker, pexConfig.Config) 

212 meta = task.getFullMetadata() 

213 # Check that the expected metadata has been set. 

214 self.assertEqual(meta["diaPipe.numUpdatedDiaObjects"], 2) 

215 self.assertEqual(meta["diaPipe.numUnassociatedDiaObjects"], 3) 

216 # and that associators ran once or not at all. 

217 mainRun.assert_called_once() 

218 if doSolarSystemAssociation: 

219 ssRun.assert_called_once() 

220 else: 

221 ssRun.assert_not_called() 

222 

223 def test_createDiaObjects(self): 

224 """Test that creating new DiaObjects works as expected. 

225 """ 

226 nSources = 5 

227 diaSources = pd.DataFrame(data=[ 

228 {"ra": 0.04*idx, "dec": 0.04*idx, 

229 "diaSourceId": idx + 1 + nSources, "diaObjectId": 0, 

230 "ssObjectId": 0} 

231 for idx in range(nSources)]) 

232 

233 config = self._makeDefaultConfig(config_file=self.config_file.name, doPackageAlerts=False) 

234 task = DiaPipelineTask(config=config) 

235 result = task.createNewDiaObjects(diaSources) 

236 self.assertEqual(nSources, len(result.newDiaObjects)) 

237 self.assertTrue(np.all(np.equal( 

238 result.diaSources["diaObjectId"].to_numpy(), 

239 result.diaSources["diaSourceId"].to_numpy()))) 

240 self.assertTrue(np.all(np.equal( 

241 result.newDiaObjects["diaObjectId"].to_numpy(), 

242 result.diaSources["diaSourceId"].to_numpy()))) 

243 

244 def test_purgeDiaObjects(self): 

245 """Remove diaOjects that are outside an image's bounding box. 

246 """ 

247 

248 config = self._makeDefaultConfig(config_file=self.config_file.name, doPackageAlerts=False) 

249 task = DiaPipelineTask(config=config) 

250 exposure = makeExposure(False, False) 

251 nObj0 = 20 

252 

253 # Create diaObjects 

254 diaObjects = makeDiaObjects(nObj0, exposure, self.rng) 

255 # Shrink the bounding box so that some of the diaObjects will be outside 

256 bbox = exposure.getBBox() 

257 size = np.minimum(bbox.getHeight(), bbox.getWidth()) 

258 bbox.grow(-size//4) 

259 exposureCut = exposure[bbox] 

260 sizeCut = np.minimum(bbox.getHeight(), bbox.getWidth()) 

261 buffer = 10 

262 bbox.grow(buffer) 

263 

264 def check_diaObjects(bbox, wcs, diaObjects): 

265 raVals = diaObjects.ra.to_numpy() 

266 decVals = diaObjects.dec.to_numpy() 

267 xVals, yVals = wcs.skyToPixelArray(raVals, decVals, degrees=True) 

268 selector = bbox.contains(xVals, yVals) 

269 return selector 

270 

271 selector0 = check_diaObjects(bbox, exposureCut.getWcs(), diaObjects) 

272 nIn0 = np.count_nonzero(selector0) 

273 nOut0 = np.count_nonzero(~selector0) 

274 self.assertEqual(nObj0, nIn0 + nOut0) 

275 

276 diaObjects1 = task.purgeDiaObjects(exposureCut.getBBox(), exposureCut.getWcs(), diaObjects, 

277 buffer=buffer) 

278 # Verify that the bounding box was not changed 

279 sizeCheck = np.minimum(exposureCut.getBBox().getHeight(), exposureCut.getBBox().getWidth()) 

280 self.assertEqual(sizeCut, sizeCheck) 

281 selector1 = check_diaObjects(bbox, exposureCut.getWcs(), diaObjects1) 

282 nIn1 = np.count_nonzero(selector1) 

283 nOut1 = np.count_nonzero(~selector1) 

284 nObj1 = len(diaObjects1) 

285 self.assertEqual(nObj1, nIn0) 

286 # Verify that not all diaObjects were removed 

287 self.assertGreater(nObj1, 0) 

288 # Check that some diaObjects were removed 

289 self.assertLess(nObj1, nObj0) 

290 # Verify that no objects outside the bounding box remain 

291 self.assertEqual(nOut1, 0) 

292 # Verify that no objects inside the bounding box were removed 

293 self.assertEqual(nIn1, nIn0) 

294 

295 

296class MemoryTester(lsst.utils.tests.MemoryTestCase): 

297 pass 

298 

299 

300def setup_module(module): 

301 lsst.utils.tests.init() 

302 

303 

304if __name__ == "__main__": 304 ↛ 305line 304 didn't jump to line 305, because the condition on line 304 was never true

305 lsst.utils.tests.init() 

306 unittest.main()