Coverage for tests/test_isPrimaryFlag.py: 26%

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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 os 

23import unittest 

24import numpy as np 

25import logging 

26 

27from lsst.geom import Point2I, Box2I, Extent2I 

28from lsst.skymap import TractInfo 

29from lsst.skymap.patchInfo import PatchInfo 

30import lsst.afw.image as afwImage 

31import lsst.utils.tests 

32from lsst.utils import getPackageDir 

33from lsst.pipe.tasks.characterizeImage import CharacterizeImageTask, CharacterizeImageConfig 

34from lsst.pipe.tasks.calibrate import CalibrateTask, CalibrateConfig 

35from lsst.meas.algorithms import SourceDetectionTask, SkyObjectsTask 

36from lsst.meas.extensions.scarlet.scarletDeblendTask import ScarletDeblendTask 

37from lsst.meas.base import SingleFrameMeasurementTask 

38from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask, getPseudoSources 

39from lsst.afw.table import SourceCatalog 

40 

41 

42class NullTract(TractInfo): 

43 """A Tract not contained in the MockSkyMap. 

44 

45 BaseSkyMap.findTract(coord) will always return a Tract, 

46 even if the coord isn't located in the Tract. 

47 In order to mimick this functionality we create a 

48 NullTract for regions of the MockSkyMap that 

49 aren't contained in any of the tracts. 

50 """ 

51 def __init__(self): 

52 pass 

53 

54 def getId(self): 

55 return None 

56 

57 

58class MockTractInfo: 

59 """A Tract based on a bounding box and WCS. 

60 

61 Testing is made easier when we can specifically define 

62 a Tract in terms of its bounding box in pixel coordinates 

63 along with a WCS for the exposure. 

64 

65 Only the relevant methods from `TractInfo` needed to make 

66 test pass are implemented here. Since this is just for 

67 testing, it isn't sophisticated and requires developers to 

68 ensure that the size of the bounding box is evenly divisible 

69 by the number of patches in the Tract. 

70 """ 

71 def __init__(self, name, bbox, wcs, numPatches): 

72 self.name = name 

73 self.bbox = bbox 

74 self.wcs = wcs 

75 self._numPatches = numPatches 

76 assert bbox.getWidth()%numPatches[0] == 0 

77 assert bbox.getHeight()%numPatches[1] == 0 

78 self.patchWidth = bbox.getWidth()//numPatches[0] 

79 self.patchHeight = bbox.getHeight()//numPatches[1] 

80 

81 def contains(self, coord): 

82 pixel = self.wcs.skyToPixel(coord) 

83 return self.bbox.contains(Point2I(pixel)) 

84 

85 def getId(self): 

86 return self.name 

87 

88 def getNumPatches(self): 

89 return self._numPatches 

90 

91 def getPatchInfo(self, index): 

92 x, y = index 

93 width = self.patchWidth 

94 height = self.patchHeight 

95 

96 x = x*self.patchWidth 

97 y = y*self.patchHeight 

98 

99 bbox = Box2I(Point2I(x, y), Extent2I(width, height)) 

100 

101 nx, ny = self._numPatches 

102 sequentialIndex = nx*y + x 

103 

104 patchInfo = PatchInfo( 

105 index=index, 

106 innerBBox=bbox, 

107 outerBBox=bbox, 

108 sequentialIndex=sequentialIndex, 

109 tractWcs=self.wcs 

110 ) 

111 return patchInfo 

112 

113 def __getitem__(self, index): 

114 return self.getPatchInfo(index) 

115 

116 def __iter__(self): 

117 xNum, yNum = self.getNumPatches() 

118 for y in range(yNum): 

119 for x in range(xNum): 

120 yield self.getPatchInfo((x, y)) 

121 

122 

123class MockSkyMap: 

124 """A SkyMap based on a list of bounding boxes. 

125 

126 Testing is made easier when we can specifically define 

127 a Tract in terms of its bounding box in pixel coordinates 

128 along with a WCS for the exposure. This class allows us 

129 to define the tract(s) in the SkyMap and create 

130 them. 

131 """ 

132 def __init__(self, bboxes, wcs, numPatches): 

133 self.bboxes = bboxes 

134 self.wcs = wcs 

135 self.numPatches = numPatches 

136 

137 def __iter__(self): 

138 for b, bbox in enumerate(self.bboxes): 

139 yield self.generateTract(b) 

140 

141 def __getitem__(self, index): 

142 return self.generateTract(index) 

143 

144 def generateTract(self, index): 

145 return MockTractInfo(index, self.bboxes[index], self.wcs, self.numPatches) 

146 

147 def findTract(self, coord): 

148 for tractInfo in self: 

149 if tractInfo.contains(coord): 

150 return tractInfo 

151 

152 return NullTract() 

153 

154 

155class IsPrimaryTestCase(lsst.utils.tests.TestCase): 

156 

157 def setUp(self): 

158 # Load sample input from disk 

159 expPath = os.path.join(getPackageDir("pipe_tasks"), "tests", "data", "v695833-e0-c000-a00.sci.fits") 

160 self.exposure = afwImage.ExposureF(expPath) 

161 

162 # Characterize the image (create PSF, etc.) 

163 charImConfig = CharacterizeImageConfig() 

164 charImTask = CharacterizeImageTask(config=charImConfig) 

165 self.charImResults = charImTask.run(self.exposure) 

166 

167 # set log level so that warnings do not display 

168 logging.getLogger("lsst.calibrate").setLevel(logging.ERROR) 

169 

170 def tearDown(self): 

171 del self.exposure 

172 self.charImResults 

173 

174 def testIsSinglePrimaryFlag(self): 

175 """Tests detect_isPrimary column gets added when run, and that sources 

176 labelled as detect_isPrimary are not sky sources and have no children. 

177 """ 

178 calibConfig = CalibrateConfig() 

179 calibConfig.doAstrometry = False 

180 calibConfig.doPhotoCal = False 

181 calibConfig.doComputeSummaryStats = False 

182 calibTask = CalibrateTask(config=calibConfig) 

183 calibResults = calibTask.run(self.charImResults.exposure) 

184 outputCat = calibResults.outputCat 

185 self.assertTrue("detect_isPrimary" in outputCat.schema.getNames()) 

186 # make sure all sky sources are flagged as not primary 

187 self.assertEqual(sum((outputCat["detect_isPrimary"]) & (outputCat["sky_source"])), 0) 

188 # make sure all parent sources are flagged as not primary 

189 self.assertEqual(sum((outputCat["detect_isPrimary"]) & (outputCat["deblend_nChild"] > 0)), 0) 

190 

191 with self.assertRaises(KeyError): 

192 outputCat.getSchema().find("detect_isDelendedModelPrimary") 

193 

194 def testIsScarletPrimaryFlag(self): 

195 """Test detect_isPrimary column when scarlet is used as the deblender 

196 """ 

197 # We need a multiband coadd for scarlet, 

198 # even though there is only one band 

199 coadds = afwImage.MultibandExposure.fromExposures(["test"], [self.exposure]) 

200 

201 # Create a SkyMap with a tract that contains a portion of the image, 

202 # subdivided into 3x3 patches 

203 wcs = self.exposure.getWcs() 

204 tractBBox = Box2I(Point2I(100, 100), Extent2I(900, 900)) 

205 skyMap = MockSkyMap([tractBBox], wcs, (3, 3)) 

206 tractInfo = skyMap[0] 

207 patchInfo = tractInfo[0, 0] 

208 patchBBox = patchInfo.getInnerBBox() 

209 

210 schema = SourceCatalog.Table.makeMinimalSchema() 

211 # Initialize the detection task 

212 detectionTask = SourceDetectionTask(schema=schema) 

213 

214 # Initialize the fake source injection task 

215 skyConfig = SkyObjectsTask.ConfigClass() 

216 skySourcesTask = SkyObjectsTask(name="skySources", config=skyConfig) 

217 schema.addField("merge_peak_sky", type="Flag") 

218 

219 # Initialize the deblender task 

220 scarletConfig = ScarletDeblendTask.ConfigClass() 

221 scarletConfig.maxIter = 20 

222 scarletConfig.columnInheritance["merge_peak_sky"] = "merge_peak_sky" 

223 deblendTask = ScarletDeblendTask(schema=schema, config=scarletConfig) 

224 

225 # We'll customize the configuration of measurement to just run the 

226 # minimal number of plugins to make setPrimaryFlags work. 

227 measureConfig = SingleFrameMeasurementTask.ConfigClass() 

228 measureConfig.plugins.names = ["base_SdssCentroid", "base_SkyCoord"] 

229 measureConfig.slots.psfFlux = None 

230 measureConfig.slots.apFlux = None 

231 measureConfig.slots.shape = None 

232 measureConfig.slots.modelFlux = None 

233 measureConfig.slots.calibFlux = None 

234 measureConfig.slots.gaussianFlux = None 

235 measureTask = SingleFrameMeasurementTask(config=measureConfig, schema=schema) 

236 primaryConfig = SetPrimaryFlagsTask.ConfigClass() 

237 setPrimaryTask = SetPrimaryFlagsTask(config=primaryConfig, schema=schema, 

238 name="setPrimaryFlags", isSingleFrame=False) 

239 

240 table = SourceCatalog.Table.make(schema) 

241 # detect sources 

242 detectionResult = detectionTask.run(table, coadds["test"]) 

243 catalog = detectionResult.sources 

244 # add fake sources 

245 skySources = skySourcesTask.run(mask=self.exposure.mask, seed=0) 

246 for foot in skySources[:5]: 

247 src = catalog.addNew() 

248 src.setFootprint(foot) 

249 src.set("merge_peak_sky", True) 

250 # deblend 

251 catalog, modelData = deblendTask.run(coadds, catalog) 

252 # Attach footprints to the catalog 

253 modelData.updateCatalogFootprints( 

254 catalog=catalog, 

255 band="test", 

256 psfModel=coadds["test"].getPsf(), 

257 redistributeImage=None, 

258 ) 

259 # measure 

260 measureTask.run(catalog, self.exposure) 

261 outputCat = catalog 

262 # Set the primary flags 

263 setPrimaryTask.run(outputCat, skyMap=skyMap, tractInfo=tractInfo, patchInfo=patchInfo) 

264 

265 # There should be the same number of deblenedPrimary and 

266 # deblendedModelPrimary sources, 

267 # since they both have the same blended sources and only differ 

268 # over which model to use for the isolated sources. 

269 isPseudo = getPseudoSources(outputCat, primaryConfig.pseudoFilterList, schema, setPrimaryTask.log) 

270 self.assertEqual( 

271 np.sum(outputCat["detect_isDeblendedSource"] & ~isPseudo), 

272 np.sum(outputCat["detect_isDeblendedModelSource"])) 

273 

274 # Check that the sources contained in a tract are all marked appropriately 

275 x = outputCat["slot_Centroid_x"] 

276 y = outputCat["slot_Centroid_y"] 

277 tractInner = tractBBox.contains(x, y) 

278 np.testing.assert_array_equal(outputCat["detect_isTractInner"], tractInner) 

279 

280 # Check that the sources contained in a patch are all marked appropriately 

281 patchInner = patchBBox.contains(x, y) 

282 np.testing.assert_array_equal(outputCat["detect_isPatchInner"], patchInner) 

283 

284 # make sure all sky sources are flagged as not primary 

285 self.assertEqual(sum((outputCat["detect_isPrimary"]) & (outputCat["merge_peak_sky"])), 0) 

286 

287 # Check that sky objects have not been deblended 

288 np.testing.assert_array_equal( 

289 isPseudo, 

290 isPseudo & (outputCat["deblend_nChild"] == 0) 

291 ) 

292 

293 

294class MemoryTester(lsst.utils.tests.MemoryTestCase): 

295 pass 

296 

297 

298def setup_module(module): 

299 lsst.utils.tests.init() 

300 

301 

302if __name__ == "__main__": 302 ↛ 303line 302 didn't jump to line 303, because the condition on line 302 was never true

303 lsst.utils.tests.init() 

304 unittest.main()