Coverage for tests/test_calibrateImage.py: 19%
183 statements
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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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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
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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 self.truth_exposure, self.truth_cat = dataset.realize(noise=noise, schema=schema)
79 # To make it look like a version=1 (nJy fluxes) refcat
80 self.truth_cat = self.truth_exposure.photoCalib.calibrateCatalog(self.truth_cat)
81 self.ref_loader = testUtils.MockReferenceObjectLoaderFromMemory([self.truth_cat])
82 metadata = lsst.daf.base.PropertyList()
83 metadata.set("REFCAT_FORMAT_VERSION", 1)
84 self.truth_cat.setMetadata(metadata)
86 # TODO: a cosmic ray (need to figure out how to insert a fake-CR)
87 # self.truth_exposure.image.array[10, 10] = 100000
88 # self.truth_exposure.variance.array[10, 10] = 100000/noise
90 # Copy the truth exposure, because CalibrateImage modifies the input.
91 # Post-ISR ccds only contain: initial WCS, VisitInfo, filter
92 self.exposure = afwImage.ExposureF(self.truth_exposure.maskedImage)
93 self.exposure.setWcs(self.truth_exposure.wcs)
94 self.exposure.info.setVisitInfo(self.truth_exposure.visitInfo)
95 # "truth" filter, to match the "truth" refcat.
96 self.exposure.setFilter(lsst.afw.image.FilterLabel(physical='truth', band="truth"))
98 # Test-specific configuration:
99 self.config = CalibrateImageTask.ConfigClass()
100 # We don't have many sources, so have to fit simpler models.
101 self.config.psf_detection.background.approxOrderX = 1
102 self.config.star_detection.background.approxOrderX = 1
103 # Use PCA psf fitter, as psfex fails if there are only 4 stars.
104 self.config.psf_measure_psf.psfDeterminer = 'pca'
105 # We don't have many test points, so can't match on complicated shapes.
106 self.config.astrometry.matcher.numPointsForShape = 3
107 # ApFlux has more noise than PsfFlux (the latter unrealistically small
108 # in this test data), so we need to do magnitude rejection at higher
109 # sigma, otherwise we can lose otherwise good sources.
110 # TODO DM-39203: Once we are using Compensated Gaussian Fluxes, we
111 # will use those fluxes here, and hopefully can remove this.
112 self.config.astrometry.magnitudeOutlierRejectionNSigma = 9.0
114 # Something about this test dataset prefers the older fluxRatio here.
115 self.config.star_catalog_calculation.plugins['base_ClassificationExtendedness'].fluxRatio = 0.925
117 def test_run(self):
118 """Test that run() returns reasonable values to be butler put.
119 """
120 calibrate = CalibrateImageTask(config=self.config)
121 calibrate.astrometry.setRefObjLoader(self.ref_loader)
122 calibrate.photometry.match.setRefObjLoader(self.ref_loader)
123 result = calibrate.run(exposure=self.exposure)
125 # Background should have 4 elements: 3 from compute_psf and one from
126 # re-estimation during source detection.
127 self.assertEqual(len(result.background), 4)
129 # Check that the summary statistics are reasonable.
130 summary = self.exposure.info.getSummaryStats()
131 self.assertFloatsAlmostEqual(self.exposure.info.getSummaryStats().psfSigma, 2.0, rtol=1e-2)
132 self.assertFloatsAlmostEqual(summary.ra, self.sky_center.getRa().asDegrees(), rtol=1e-7)
133 self.assertFloatsAlmostEqual(summary.dec, self.sky_center.getDec().asDegrees(), rtol=1e-7)
135 # Returned photoCalib should be the applied value, not the ==1 one on the exposure.
136 self.assertFloatsAlmostEqual(result.applied_photo_calib.getCalibrationMean(),
137 self.photo_calib, rtol=2e-3)
138 # Should have flux/magnitudes in the catalog.
139 self.assertIn("slot_PsfFlux_flux", result.stars.schema)
140 self.assertIn("slot_PsfFlux_mag", result.stars.schema)
142 # Check that all necessary fields are in the output.
143 lsst.pipe.base.testUtils.assertValidOutput(calibrate, result)
145 def test_compute_psf(self):
146 """Test that our brightest sources are found by _compute_psf(),
147 that a PSF is assigned to the expopsure.
148 """
149 calibrate = CalibrateImageTask(config=self.config)
150 sources, background, candidates = calibrate._compute_psf(self.exposure)
152 # Background should have 3 elements: initial subtraction, and two from
153 # re-estimation during the two detection passes.
154 self.assertEqual(len(background), 3)
156 # Only the point-sources with S/N > 50 should be in this output.
157 self.assertEqual(sources["calib_psf_used"].sum(), 3)
158 # Sort in order of brightness, to easily compare with expected positions.
159 sources.sort(sources.getPsfFluxSlot().getMeasKey())
160 for record, flux, center in zip(sources[::-1], self.fluxes, self.centroids[self.fluxes > 50]):
161 self.assertFloatsAlmostEqual(record.getX(), center[0], rtol=0.01)
162 self.assertFloatsAlmostEqual(record.getY(), center[1], rtol=0.01)
163 # PsfFlux should match the values inserted.
164 self.assertFloatsAlmostEqual(record["slot_PsfFlux_instFlux"], flux, rtol=0.01)
166 # TODO: While debugging DM-32701, we're using PCA instead of psfex.
167 # Check that we got a useable PSF.
168 # self.assertIsInstance(self.exposure.psf, lsst.meas.extensions.psfex.PsfexPsf)
169 self.assertIsInstance(self.exposure.psf, lsst.meas.algorithms.PcaPsf)
170 # TestDataset sources have PSF radius=2 pixels.
171 radius = self.exposure.psf.computeShape(self.exposure.psf.getAveragePosition()).getDeterminantRadius()
172 self.assertFloatsAlmostEqual(radius, 2.0, rtol=1e-2)
174 # To look at images for debugging (`setup display_ds9` and run ds9):
175 # import lsst.afw.display
176 # display = lsst.afw.display.getDisplay()
177 # display.mtv(self.exposure)
179 def test_measure_aperture_correction(self):
180 """Test that _measure_aperture_correction() assigns an ApCorrMap to the
181 exposure.
182 """
183 calibrate = CalibrateImageTask(config=self.config)
184 sources, background, candidates = calibrate._compute_psf(self.exposure)
186 # First check that the exposure doesn't have an ApCorrMap.
187 self.assertIsNone(self.exposure.apCorrMap)
188 calibrate._measure_aperture_correction(self.exposure, sources)
189 self.assertIsInstance(self.exposure.apCorrMap, afwImage.ApCorrMap)
191 def test_find_stars(self):
192 """Test that _find_stars() correctly identifies the S/N>10 stars
193 in the image and returns them in the output catalog.
194 """
195 calibrate = CalibrateImageTask(config=self.config)
196 sources, background, candidates = calibrate._compute_psf(self.exposure)
197 calibrate._measure_aperture_correction(self.exposure, sources)
199 stars = calibrate._find_stars(self.exposure, background)
201 # Background should have 4 elements: 3 from compute_psf and one from
202 # re-estimation during source detection.
203 self.assertEqual(len(background), 4)
205 # Only psf-like sources with S/N>10 should be in the output catalog.
206 self.assertEqual(len(stars), 4)
207 self.assertTrue(sources.isContiguous())
208 # Sort in order of brightness, to easily compare with expected positions.
209 sources.sort(sources.getPsfFluxSlot().getMeasKey())
210 for record, flux, center in zip(sources[::-1], self.fluxes, self.centroids[self.fluxes > 50]):
211 self.assertFloatsAlmostEqual(record.getX(), center[0], rtol=0.01)
212 self.assertFloatsAlmostEqual(record.getY(), center[1], rtol=0.01)
213 self.assertFloatsAlmostEqual(record["slot_PsfFlux_instFlux"], flux, rtol=0.01)
215 def test_astrometry(self):
216 """Test that the fitted WCS gives good catalog coordinates.
217 """
218 calibrate = CalibrateImageTask(config=self.config)
219 calibrate.astrometry.setRefObjLoader(self.ref_loader)
220 sources, background, candidates = calibrate._compute_psf(self.exposure)
221 calibrate._measure_aperture_correction(self.exposure, sources)
222 stars = calibrate._find_stars(self.exposure, background)
224 calibrate._fit_astrometry(self.exposure, stars)
226 # Check that we got reliable matches with the truth coordinates.
227 fitted = SkyCoord(stars['coord_ra'], stars['coord_dec'], unit="radian")
228 truth = SkyCoord(self.truth_cat['coord_ra'], self.truth_cat['coord_dec'], unit="radian")
229 idx, d2d, _ = fitted.match_to_catalog_sky(truth)
230 np.testing.assert_array_less(d2d.to_value(u.milliarcsecond), 30.0)
232 def test_photometry(self):
233 """Test that the fitted photoCalib matches the one we generated,
234 and that the exposure is calibrated.
235 """
236 calibrate = CalibrateImageTask(config=self.config)
237 calibrate.astrometry.setRefObjLoader(self.ref_loader)
238 calibrate.photometry.match.setRefObjLoader(self.ref_loader)
239 sources, background, candidates = calibrate._compute_psf(self.exposure)
240 calibrate._measure_aperture_correction(self.exposure, sources)
241 stars = calibrate._find_stars(self.exposure, background)
242 calibrate._fit_astrometry(self.exposure, stars)
244 stars, matches, meta, photoCalib = calibrate._fit_photometry(self.exposure, stars)
246 # NOTE: With this test data, PhotoCalTask returns calibrationErr==0,
247 # so we can't check that the photoCal error has been set.
248 self.assertFloatsAlmostEqual(photoCalib.getCalibrationMean(), self.photo_calib, rtol=2e-3)
249 # The exposure should be calibrated by the applied photoCalib.
250 self.assertFloatsAlmostEqual(self.exposure.image.array/self.truth_exposure.image.array,
251 self.photo_calib, rtol=2e-3)
252 # PhotoCalib on the exposure must be identically 1.
253 self.assertEqual(self.exposure.photoCalib.getCalibrationMean(), 1.0)
255 # Check that we got reliable magnitudes and fluxes vs. truth.
256 fitted = SkyCoord(stars['coord_ra'], stars['coord_dec'], unit="radian")
257 truth = SkyCoord(self.truth_cat['coord_ra'], self.truth_cat['coord_dec'], unit="radian")
258 idx, _, _ = fitted.match_to_catalog_sky(truth)
259 # Because the input variance image does not include contributions from
260 # the sources, we can't use fluxErr as a bound on the measurement
261 # quality here.
262 self.assertFloatsAlmostEqual(stars['slot_PsfFlux_flux'], self.truth_cat['truth_flux'][idx], rtol=0.1)
263 self.assertFloatsAlmostEqual(stars['slot_PsfFlux_mag'], self.truth_cat['truth_mag'][idx], rtol=0.01)
266class CalibrateImageTaskRunQuantumTests(lsst.utils.tests.TestCase):
267 """Tests of ``CalibrateImageTask.runQuantum``, which need a test butler,
268 but do not need real images.
269 """
270 def setUp(self):
271 instrument = "testCam"
272 exposure = 101
273 visit = 100101
274 detector = 42
276 # Create a and populate a test butler for runQuantum tests.
277 self.repo_path = tempfile.TemporaryDirectory()
278 self.repo = butlerTests.makeTestRepo(self.repo_path.name)
280 # dataIds for fake data
281 butlerTests.addDataIdValue(self.repo, "instrument", instrument)
282 butlerTests.addDataIdValue(self.repo, "exposure", exposure)
283 butlerTests.addDataIdValue(self.repo, "visit", visit)
284 butlerTests.addDataIdValue(self.repo, "detector", detector)
286 # inputs
287 butlerTests.addDatasetType(self.repo, "postISRCCD", {"instrument", "exposure", "detector"},
288 "ExposureF")
289 butlerTests.addDatasetType(self.repo, "gaia_dr3_20230707", {"htm7"}, "SimpleCatalog")
290 butlerTests.addDatasetType(self.repo, "ps1_pv3_3pi_20170110", {"htm7"}, "SimpleCatalog")
292 # outputs
293 butlerTests.addDatasetType(self.repo, "initial_pvi", {"instrument", "visit", "detector"},
294 "ExposureF")
295 butlerTests.addDatasetType(self.repo, "initial_stars_footprints_detector",
296 {"instrument", "visit", "detector"},
297 "SourceCatalog")
298 butlerTests.addDatasetType(self.repo, "initial_photoCalib_detector",
299 {"instrument", "visit", "detector"},
300 "PhotoCalib")
301 # optional outputs
302 butlerTests.addDatasetType(self.repo, "initial_pvi_background", {"instrument", "visit", "detector"},
303 "Background")
304 butlerTests.addDatasetType(self.repo, "initial_psf_stars_footprints",
305 {"instrument", "visit", "detector"},
306 "SourceCatalog")
307 butlerTests.addDatasetType(self.repo,
308 "initial_astrometry_match_detector",
309 {"instrument", "visit", "detector"},
310 "Catalog")
311 butlerTests.addDatasetType(self.repo,
312 "initial_photometry_match_detector",
313 {"instrument", "visit", "detector"},
314 "Catalog")
316 # dataIds
317 self.exposure_id = self.repo.registry.expandDataId(
318 {"instrument": instrument, "exposure": exposure, "detector": detector})
319 self.visit_id = self.repo.registry.expandDataId(
320 {"instrument": instrument, "visit": visit, "detector": detector})
321 self.htm_id = self.repo.registry.expandDataId({"htm7": 42})
323 # put empty data
324 self.butler = butlerTests.makeTestCollection(self.repo)
325 self.butler.put(afwImage.ExposureF(), "postISRCCD", self.exposure_id)
326 self.butler.put(afwTable.SimpleCatalog(), "gaia_dr3_20230707", self.htm_id)
327 self.butler.put(afwTable.SimpleCatalog(), "ps1_pv3_3pi_20170110", self.htm_id)
329 def tearDown(self):
330 del self.repo_path # this removes the temporary directory
332 def test_runQuantum(self):
333 task = CalibrateImageTask()
334 lsst.pipe.base.testUtils.assertValidInitOutput(task)
336 quantum = lsst.pipe.base.testUtils.makeQuantum(
337 task, self.butler, self.visit_id,
338 {"exposure": self.exposure_id,
339 "astrometry_ref_cat": [self.htm_id],
340 "photometry_ref_cat": [self.htm_id],
341 # outputs
342 "output_exposure": self.visit_id,
343 "stars": self.visit_id,
344 "background": self.visit_id,
345 "psf_stars": self.visit_id,
346 "applied_photo_calib": self.visit_id,
347 "initial_pvi_background": self.visit_id,
348 "astrometry_matches": self.visit_id,
349 "photometry_matches": self.visit_id,
350 })
351 mock_run = lsst.pipe.base.testUtils.runTestQuantum(task, self.butler, quantum)
353 # Ensure the reference loaders have been configured.
354 self.assertEqual(task.astrometry.refObjLoader.name, "gaia_dr3_20230707")
355 self.assertEqual(task.photometry.match.refObjLoader.name, "ps1_pv3_3pi_20170110")
356 # Check that the proper kwargs are passed to run().
357 self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposure"})
359 def test_runQuantum_no_optional_outputs(self):
360 config = CalibrateImageTask.ConfigClass()
361 config.optional_outputs = None
362 task = CalibrateImageTask(config=config)
363 lsst.pipe.base.testUtils.assertValidInitOutput(task)
365 quantum = lsst.pipe.base.testUtils.makeQuantum(
366 task, self.butler, self.visit_id,
367 {"exposure": self.exposure_id,
368 "astrometry_ref_cat": [self.htm_id],
369 "photometry_ref_cat": [self.htm_id],
370 # outputs
371 "output_exposure": self.visit_id,
372 "stars": self.visit_id,
373 "applied_photo_calib": self.visit_id,
374 "background": self.visit_id,
375 })
376 mock_run = lsst.pipe.base.testUtils.runTestQuantum(task, self.butler, quantum)
378 # Ensure the reference loaders have been configured.
379 self.assertEqual(task.astrometry.refObjLoader.name, "gaia_dr3_20230707")
380 self.assertEqual(task.photometry.match.refObjLoader.name, "ps1_pv3_3pi_20170110")
381 # Check that the proper kwargs are passed to run().
382 self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposure"})
384 def test_lintConnections(self):
385 """Check that the connections are self-consistent.
386 """
387 Connections = CalibrateImageTask.ConfigClass.ConnectionsClass
388 lsst.pipe.base.testUtils.lintConnections(Connections)
391def setup_module(module):
392 lsst.utils.tests.init()
395class MemoryTestCase(lsst.utils.tests.MemoryTestCase):
396 pass
399if __name__ == "__main__": 399 ↛ 400line 399 didn't jump to line 400, because the condition on line 399 was never true
400 lsst.utils.tests.init()
401 unittest.main()