Coverage for tests/test_calibrateImage.py: 19%
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1# This file is part of pipe_tasks.
2#
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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#
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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
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22import unittest
23import tempfile
25import astropy.units as u
26from astropy.coordinates import SkyCoord
27import numpy as np
29import lsst.afw.image as afwImage
30import lsst.afw.table as afwTable
31import lsst.daf.base
32import lsst.daf.butler.tests as butlerTests
33import lsst.geom
34import lsst.meas.algorithms
35from lsst.meas.algorithms import testUtils
36import lsst.meas.extensions.psfex
37import lsst.meas.base.tests
38import lsst.pipe.base.testUtils
39from lsst.pipe.tasks.calibrateImage import CalibrateImageTask
40import lsst.utils.tests
43class CalibrateImageTaskTests(lsst.utils.tests.TestCase):
45 def setUp(self):
46 # Different x/y dimensions so they're easy to distinguish in a plot,
47 # and non-zero minimum, to help catch xy0 errors.
48 bbox = lsst.geom.Box2I(lsst.geom.Point2I(5, 4), lsst.geom.Point2I(205, 184))
49 self.sky_center = lsst.geom.SpherePoint(245.0, -45.0, lsst.geom.degrees)
50 self.photo_calib = 12.3
51 dataset = lsst.meas.base.tests.TestDataset(bbox, crval=self.sky_center, calibration=self.photo_calib)
52 # sqrt of area of a normalized 2d gaussian
53 psf_scale = np.sqrt(4*np.pi*(dataset.psfShape.getDeterminantRadius())**2)
54 noise = 10.0 # stddev of noise per pixel
55 # Sources ordered from faintest to brightest.
56 self.fluxes = np.array((6*noise*psf_scale,
57 12*noise*psf_scale,
58 45*noise*psf_scale,
59 150*noise*psf_scale,
60 400*noise*psf_scale,
61 1000*noise*psf_scale))
62 self.centroids = np.array(((162, 22),
63 (25, 70),
64 (100, 160),
65 (50, 120),
66 (92, 35),
67 (175, 154)), dtype=np.float32)
68 for flux, centroid in zip(self.fluxes, self.centroids):
69 dataset.addSource(instFlux=flux, centroid=lsst.geom.Point2D(centroid[0], centroid[1]))
71 # Bright extended source in the center of the image: should not appear
72 # in any of the output catalogs.
73 center = lsst.geom.Point2D(100, 100)
74 shape = lsst.afw.geom.Quadrupole(8, 9, 3)
75 dataset.addSource(instFlux=500*noise*psf_scale, centroid=center, shape=shape)
77 schema = dataset.makeMinimalSchema()
78 afwTable.CoordKey.addErrorFields(schema)
79 self.truth_exposure, self.truth_cat = dataset.realize(noise=noise, schema=schema)
80 lsst.afw.table.updateSourceCoords(self.truth_exposure.wcs, self.truth_cat)
81 # To make it look like a version=1 (nJy fluxes) refcat
82 self.truth_cat = self.truth_exposure.photoCalib.calibrateCatalog(self.truth_cat)
83 self.ref_loader = testUtils.MockReferenceObjectLoaderFromMemory([self.truth_cat])
84 metadata = lsst.daf.base.PropertyList()
85 metadata.set("REFCAT_FORMAT_VERSION", 1)
86 self.truth_cat.setMetadata(metadata)
88 # TODO: a cosmic ray (need to figure out how to insert a fake-CR)
89 # self.truth_exposure.image.array[10, 10] = 100000
90 # self.truth_exposure.variance.array[10, 10] = 100000/noise
92 # Copy the truth exposure, because CalibrateImage modifies the input.
93 # Post-ISR ccds only contain: initial WCS, VisitInfo, filter
94 self.exposure = afwImage.ExposureF(self.truth_exposure.maskedImage)
95 self.exposure.setWcs(self.truth_exposure.wcs)
96 self.exposure.info.setVisitInfo(self.truth_exposure.visitInfo)
97 # "truth" filter, to match the "truth" refcat.
98 self.exposure.setFilter(lsst.afw.image.FilterLabel(physical='truth', band="truth"))
100 # Test-specific configuration:
101 self.config = CalibrateImageTask.ConfigClass()
102 # We don't have many sources, so have to fit simpler models.
103 self.config.psf_detection.background.approxOrderX = 1
104 self.config.star_detection.background.approxOrderX = 1
105 # Use PCA psf fitter, as psfex fails if there are only 4 stars.
106 self.config.psf_measure_psf.psfDeterminer = 'pca'
107 # We don't have many test points, so can't match on complicated shapes.
108 self.config.astrometry.matcher.numPointsForShape = 3
110 # Something about this test dataset prefers the older fluxRatio here.
111 self.config.star_catalog_calculation.plugins['base_ClassificationExtendedness'].fluxRatio = 0.925
113 def test_run(self):
114 """Test that run() returns reasonable values to be butler put.
115 """
116 calibrate = CalibrateImageTask(config=self.config)
117 calibrate.astrometry.setRefObjLoader(self.ref_loader)
118 calibrate.photometry.match.setRefObjLoader(self.ref_loader)
119 result = calibrate.run(exposure=self.exposure)
121 # Background should have 4 elements: 3 from compute_psf and one from
122 # re-estimation during source detection.
123 self.assertEqual(len(result.background), 4)
125 # Check that the summary statistics are reasonable.
126 summary = self.exposure.info.getSummaryStats()
127 self.assertFloatsAlmostEqual(self.exposure.info.getSummaryStats().psfSigma, 2.0, rtol=1e-2)
128 self.assertFloatsAlmostEqual(summary.ra, self.sky_center.getRa().asDegrees(), rtol=1e-7)
129 self.assertFloatsAlmostEqual(summary.dec, self.sky_center.getDec().asDegrees(), rtol=1e-7)
131 # Returned photoCalib should be the applied value, not the ==1 one on the exposure.
132 self.assertFloatsAlmostEqual(result.applied_photo_calib.getCalibrationMean(),
133 self.photo_calib, rtol=2e-3)
134 # Should have flux/magnitudes in the catalog.
135 self.assertIn("slot_PsfFlux_flux", result.stars.schema)
136 self.assertIn("slot_PsfFlux_mag", result.stars.schema)
138 # Check that all necessary fields are in the output.
139 lsst.pipe.base.testUtils.assertValidOutput(calibrate, result)
141 def test_compute_psf(self):
142 """Test that our brightest sources are found by _compute_psf(),
143 that a PSF is assigned to the expopsure.
144 """
145 calibrate = CalibrateImageTask(config=self.config)
146 sources, background, candidates = calibrate._compute_psf(self.exposure)
148 # Background should have 3 elements: initial subtraction, and two from
149 # re-estimation during the two detection passes.
150 self.assertEqual(len(background), 3)
152 # Only the point-sources with S/N > 50 should be in this output.
153 self.assertEqual(sources["calib_psf_used"].sum(), 3)
154 # Sort in order of brightness, to easily compare with expected positions.
155 sources.sort(sources.getPsfFluxSlot().getMeasKey())
156 for record, flux, center in zip(sources[::-1], self.fluxes, self.centroids[self.fluxes > 50]):
157 self.assertFloatsAlmostEqual(record.getX(), center[0], rtol=0.01)
158 self.assertFloatsAlmostEqual(record.getY(), center[1], rtol=0.01)
159 # PsfFlux should match the values inserted.
160 self.assertFloatsAlmostEqual(record["slot_PsfFlux_instFlux"], flux, rtol=0.01)
162 # TODO: While debugging DM-32701, we're using PCA instead of psfex.
163 # Check that we got a useable PSF.
164 # self.assertIsInstance(self.exposure.psf, lsst.meas.extensions.psfex.PsfexPsf)
165 self.assertIsInstance(self.exposure.psf, lsst.meas.algorithms.PcaPsf)
166 # TestDataset sources have PSF radius=2 pixels.
167 radius = self.exposure.psf.computeShape(self.exposure.psf.getAveragePosition()).getDeterminantRadius()
168 self.assertFloatsAlmostEqual(radius, 2.0, rtol=1e-2)
170 # To look at images for debugging (`setup display_ds9` and run ds9):
171 # import lsst.afw.display
172 # display = lsst.afw.display.getDisplay()
173 # display.mtv(self.exposure)
175 def test_measure_aperture_correction(self):
176 """Test that _measure_aperture_correction() assigns an ApCorrMap to the
177 exposure.
178 """
179 calibrate = CalibrateImageTask(config=self.config)
180 sources, background, candidates = calibrate._compute_psf(self.exposure)
182 # First check that the exposure doesn't have an ApCorrMap.
183 self.assertIsNone(self.exposure.apCorrMap)
184 calibrate._measure_aperture_correction(self.exposure, sources)
185 self.assertIsInstance(self.exposure.apCorrMap, afwImage.ApCorrMap)
187 def test_find_stars(self):
188 """Test that _find_stars() correctly identifies the S/N>10 stars
189 in the image and returns them in the output catalog.
190 """
191 calibrate = CalibrateImageTask(config=self.config)
192 sources, background, candidates = calibrate._compute_psf(self.exposure)
193 calibrate._measure_aperture_correction(self.exposure, sources)
195 stars = calibrate._find_stars(self.exposure, background)
197 # Background should have 4 elements: 3 from compute_psf and one from
198 # re-estimation during source detection.
199 self.assertEqual(len(background), 4)
201 # Only psf-like sources with S/N>10 should be in the output catalog.
202 self.assertEqual(len(stars), 4)
203 self.assertTrue(sources.isContiguous())
204 # Sort in order of brightness, to easily compare with expected positions.
205 sources.sort(sources.getPsfFluxSlot().getMeasKey())
206 for record, flux, center in zip(sources[::-1], self.fluxes, self.centroids[self.fluxes > 50]):
207 self.assertFloatsAlmostEqual(record.getX(), center[0], rtol=0.01)
208 self.assertFloatsAlmostEqual(record.getY(), center[1], rtol=0.01)
209 self.assertFloatsAlmostEqual(record["slot_PsfFlux_instFlux"], flux, rtol=0.01)
211 def test_astrometry(self):
212 """Test that the fitted WCS gives good catalog coordinates.
213 """
214 calibrate = CalibrateImageTask(config=self.config)
215 calibrate.astrometry.setRefObjLoader(self.ref_loader)
216 sources, background, candidates = calibrate._compute_psf(self.exposure)
217 calibrate._measure_aperture_correction(self.exposure, sources)
218 stars = calibrate._find_stars(self.exposure, background)
220 calibrate._fit_astrometry(self.exposure, stars)
222 # Check that we got reliable matches with the truth coordinates.
223 fitted = SkyCoord(stars['coord_ra'], stars['coord_dec'], unit="radian")
224 truth = SkyCoord(self.truth_cat['coord_ra'], self.truth_cat['coord_dec'], unit="radian")
225 idx, d2d, _ = fitted.match_to_catalog_sky(truth)
226 np.testing.assert_array_less(d2d.to_value(u.milliarcsecond), 30.0)
228 def test_photometry(self):
229 """Test that the fitted photoCalib matches the one we generated,
230 and that the exposure is calibrated.
231 """
232 calibrate = CalibrateImageTask(config=self.config)
233 calibrate.astrometry.setRefObjLoader(self.ref_loader)
234 calibrate.photometry.match.setRefObjLoader(self.ref_loader)
235 sources, background, candidates = calibrate._compute_psf(self.exposure)
236 calibrate._measure_aperture_correction(self.exposure, sources)
237 stars = calibrate._find_stars(self.exposure, background)
238 calibrate._fit_astrometry(self.exposure, stars)
240 stars, matches, meta, photoCalib = calibrate._fit_photometry(self.exposure, stars)
242 # NOTE: With this test data, PhotoCalTask returns calibrationErr==0,
243 # so we can't check that the photoCal error has been set.
244 self.assertFloatsAlmostEqual(photoCalib.getCalibrationMean(), self.photo_calib, rtol=2e-3)
245 # The exposure should be calibrated by the applied photoCalib.
246 self.assertFloatsAlmostEqual(self.exposure.image.array/self.truth_exposure.image.array,
247 self.photo_calib, rtol=2e-3)
248 # PhotoCalib on the exposure must be identically 1.
249 self.assertEqual(self.exposure.photoCalib.getCalibrationMean(), 1.0)
251 # Check that we got reliable magnitudes and fluxes vs. truth.
252 fitted = SkyCoord(stars['coord_ra'], stars['coord_dec'], unit="radian")
253 truth = SkyCoord(self.truth_cat['coord_ra'], self.truth_cat['coord_dec'], unit="radian")
254 idx, _, _ = fitted.match_to_catalog_sky(truth)
255 # Because the input variance image does not include contributions from
256 # the sources, we can't use fluxErr as a bound on the measurement
257 # quality here.
258 self.assertFloatsAlmostEqual(stars['slot_PsfFlux_flux'], self.truth_cat['truth_flux'][idx], rtol=0.1)
259 self.assertFloatsAlmostEqual(stars['slot_PsfFlux_mag'], self.truth_cat['truth_mag'][idx], rtol=0.01)
262class CalibrateImageTaskRunQuantumTests(lsst.utils.tests.TestCase):
263 """Tests of ``CalibrateImageTask.runQuantum``, which need a test butler,
264 but do not need real images.
265 """
266 def setUp(self):
267 instrument = "testCam"
268 exposure = 101
269 visit = 100101
270 detector = 42
272 # Create a and populate a test butler for runQuantum tests.
273 self.repo_path = tempfile.TemporaryDirectory()
274 self.repo = butlerTests.makeTestRepo(self.repo_path.name)
276 # dataIds for fake data
277 butlerTests.addDataIdValue(self.repo, "instrument", instrument)
278 butlerTests.addDataIdValue(self.repo, "exposure", exposure)
279 butlerTests.addDataIdValue(self.repo, "visit", visit)
280 butlerTests.addDataIdValue(self.repo, "detector", detector)
282 # inputs
283 butlerTests.addDatasetType(self.repo, "postISRCCD", {"instrument", "exposure", "detector"},
284 "ExposureF")
285 butlerTests.addDatasetType(self.repo, "gaia_dr3_20230707", {"htm7"}, "SimpleCatalog")
286 butlerTests.addDatasetType(self.repo, "ps1_pv3_3pi_20170110", {"htm7"}, "SimpleCatalog")
288 # outputs
289 butlerTests.addDatasetType(self.repo, "initial_pvi", {"instrument", "visit", "detector"},
290 "ExposureF")
291 butlerTests.addDatasetType(self.repo, "initial_stars_footprints_detector",
292 {"instrument", "visit", "detector"},
293 "SourceCatalog")
294 butlerTests.addDatasetType(self.repo, "initial_photoCalib_detector",
295 {"instrument", "visit", "detector"},
296 "PhotoCalib")
297 # optional outputs
298 butlerTests.addDatasetType(self.repo, "initial_pvi_background", {"instrument", "visit", "detector"},
299 "Background")
300 butlerTests.addDatasetType(self.repo, "initial_psf_stars_footprints",
301 {"instrument", "visit", "detector"},
302 "SourceCatalog")
303 butlerTests.addDatasetType(self.repo,
304 "initial_astrometry_match_detector",
305 {"instrument", "visit", "detector"},
306 "Catalog")
307 butlerTests.addDatasetType(self.repo,
308 "initial_photometry_match_detector",
309 {"instrument", "visit", "detector"},
310 "Catalog")
312 # dataIds
313 self.exposure_id = self.repo.registry.expandDataId(
314 {"instrument": instrument, "exposure": exposure, "detector": detector})
315 self.visit_id = self.repo.registry.expandDataId(
316 {"instrument": instrument, "visit": visit, "detector": detector})
317 self.htm_id = self.repo.registry.expandDataId({"htm7": 42})
319 # put empty data
320 self.butler = butlerTests.makeTestCollection(self.repo)
321 self.butler.put(afwImage.ExposureF(), "postISRCCD", self.exposure_id)
322 self.butler.put(afwTable.SimpleCatalog(), "gaia_dr3_20230707", self.htm_id)
323 self.butler.put(afwTable.SimpleCatalog(), "ps1_pv3_3pi_20170110", self.htm_id)
325 def tearDown(self):
326 del self.repo_path # this removes the temporary directory
328 def test_runQuantum(self):
329 task = CalibrateImageTask()
330 lsst.pipe.base.testUtils.assertValidInitOutput(task)
332 quantum = lsst.pipe.base.testUtils.makeQuantum(
333 task, self.butler, self.visit_id,
334 {"exposure": self.exposure_id,
335 "astrometry_ref_cat": [self.htm_id],
336 "photometry_ref_cat": [self.htm_id],
337 # outputs
338 "output_exposure": self.visit_id,
339 "stars": self.visit_id,
340 "background": self.visit_id,
341 "psf_stars": self.visit_id,
342 "applied_photo_calib": self.visit_id,
343 "initial_pvi_background": self.visit_id,
344 "astrometry_matches": self.visit_id,
345 "photometry_matches": self.visit_id,
346 })
347 mock_run = lsst.pipe.base.testUtils.runTestQuantum(task, self.butler, quantum)
349 # Ensure the reference loaders have been configured.
350 self.assertEqual(task.astrometry.refObjLoader.name, "gaia_dr3_20230707")
351 self.assertEqual(task.photometry.match.refObjLoader.name, "ps1_pv3_3pi_20170110")
352 # Check that the proper kwargs are passed to run().
353 self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposure"})
355 def test_runQuantum_no_optional_outputs(self):
356 config = CalibrateImageTask.ConfigClass()
357 config.optional_outputs = None
358 task = CalibrateImageTask(config=config)
359 lsst.pipe.base.testUtils.assertValidInitOutput(task)
361 quantum = lsst.pipe.base.testUtils.makeQuantum(
362 task, self.butler, self.visit_id,
363 {"exposure": self.exposure_id,
364 "astrometry_ref_cat": [self.htm_id],
365 "photometry_ref_cat": [self.htm_id],
366 # outputs
367 "output_exposure": self.visit_id,
368 "stars": self.visit_id,
369 "applied_photo_calib": self.visit_id,
370 "background": self.visit_id,
371 })
372 mock_run = lsst.pipe.base.testUtils.runTestQuantum(task, self.butler, quantum)
374 # Ensure the reference loaders have been configured.
375 self.assertEqual(task.astrometry.refObjLoader.name, "gaia_dr3_20230707")
376 self.assertEqual(task.photometry.match.refObjLoader.name, "ps1_pv3_3pi_20170110")
377 # Check that the proper kwargs are passed to run().
378 self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposure"})
380 def test_lintConnections(self):
381 """Check that the connections are self-consistent.
382 """
383 Connections = CalibrateImageTask.ConfigClass.ConnectionsClass
384 lsst.pipe.base.testUtils.lintConnections(Connections)
387def setup_module(module):
388 lsst.utils.tests.init()
391class MemoryTestCase(lsst.utils.tests.MemoryTestCase):
392 pass
395if __name__ == "__main__": 395 ↛ 396line 395 didn't jump to line 396, because the condition on line 395 was never true
396 lsst.utils.tests.init()
397 unittest.main()