Coverage for tests / nopytest_convertReferenceCatalog.py: 0%
127 statements
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1# This file is part of meas_algorithms.
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/>.
22# This file is excluded from running through pytest due to concerns about the
23# interaction between multiprocessing as invoked by this code, and the process
24# pool used by pytest.
25#
26# Note that it is invoked independently by SCons, so the tests are still run
27# as part of the build.
29import logging
30import os.path
31import tempfile
32import unittest
33import unittest.mock
35import numpy as np
37import lsst.daf.butler
38from lsst.daf.butler import DatasetType, DeferredDatasetHandle
39from lsst.daf.butler.script import ingest_files
40from lsst.meas.algorithms import (ConvertReferenceCatalogTask, ReferenceObjectLoader)
41from lsst.meas.algorithms.htmIndexer import HtmIndexer
42from lsst.meas.algorithms.convertRefcatManager import ConvertRefcatManager
43from lsst.meas.algorithms.readTextCatalogTask import ReadTextCatalogTask
44from lsst.meas.algorithms.convertReferenceCatalog import addRefCatMetadata
45import lsst.utils
47import convertReferenceCatalogTestBase
50class TestConvertReferenceCatalogParallel(convertReferenceCatalogTestBase.ConvertReferenceCatalogTestBase,
51 lsst.utils.tests.TestCase):
52 """Test converting a refcat with multiprocessing turned on.
54 This significantly overlaps in coverage with
55 ``ReferenceObjectLoaderTestCase`` in ``test_referenceObjectLoader.py``, but
56 focuses on checking the conversion, using the loader to perform that check.
57 """
58 def testIngestTwoFilesTwoCores(self):
59 with (tempfile.TemporaryDirectory() as inPath1, tempfile.TemporaryDirectory() as inPath2,
60 tempfile.TemporaryDirectory() as dataPath):
61 # Generate a second catalog, with different ids
62 skyCatalogFile1, _, skyCatalog1 = self.makeSkyCatalog(inPath1, idStart=25, seed=123)
63 skyCatalogFile2, _, skyCatalog2 = self.makeSkyCatalog(inPath2, idStart=5432, seed=11)
64 # override some field names, and use multiple cores
65 config = convertReferenceCatalogTestBase.makeConvertConfig(withRaDecErr=True,
66 withMagErr=True,
67 withPm=True,
68 withParallax=True,
69 withFullPositionInformation=True)
70 # use a very small HTM pixelization depth to ensure there will be collisions when
71 # ingesting the files in parallel
72 depth = 2
73 config.dataset_config.indexer.active.depth = depth
74 # np.savetxt prepends '# ' to the header lines, so use a reader that understands that
75 config.file_reader.format = 'ascii.commented_header'
76 config.n_processes = 2 # use multiple cores for this test only
77 config.id_name = 'id' # Use the ids from the generated catalogs
78 repoPath = os.path.join(self.outPath, "output_multifile_parallel")
80 # Convert the input data files to our HTM indexed format.
81 converter = ConvertReferenceCatalogTask(output_dir=dataPath, config=config)
82 converter.run([skyCatalogFile1, skyCatalogFile2])
84 # Make a temporary butler to ingest them into.
85 butler = self.makeTemporaryRepo(repoPath, config.dataset_config.indexer.active.depth)
86 dimensions = [f"htm{depth}"]
87 datasetType = DatasetType(config.dataset_config.ref_dataset_name,
88 dimensions,
89 "SimpleCatalog",
90 universe=butler.dimensions,
91 isCalibration=False)
92 butler.registry.registerDatasetType(datasetType)
94 # Ingest the files into the new butler.
95 run = "testingRun"
96 htmTableFile = os.path.join(dataPath, "filename_to_htm.ecsv")
97 ingest_files(repoPath,
98 config.dataset_config.ref_dataset_name,
99 run,
100 htmTableFile,
101 transfer="auto")
103 # Test if we can get back the catalogs, with a new butler.
104 with lsst.daf.butler.Butler.from_config(repoPath) as butler:
105 datasetRefs = list(butler.registry.queryDatasets(config.dataset_config.ref_dataset_name,
106 collections=[run]).expanded())
107 handlers = []
108 for dataRef in datasetRefs:
109 handlers.append(DeferredDatasetHandle(butler=butler, ref=dataRef, parameters=None))
110 loaderConfig = ReferenceObjectLoader.ConfigClass()
111 loader = ReferenceObjectLoader([dataRef.dataId for dataRef in datasetRefs],
112 handlers,
113 name="testRefCat",
114 config=loaderConfig,
115 log=self.logger)
116 self.checkAllRowsInRefcat(loader, skyCatalog1, config)
117 self.checkAllRowsInRefcat(loader, skyCatalog2, config)
120class TestConvertRefcatManager(convertReferenceCatalogTestBase.ConvertReferenceCatalogTestBase,
121 lsst.utils.tests.TestCase):
122 """Unittests of various methods of ConvertRefcatManager.
124 Uses mocks to force particular behavior regarding e.g. catalogs.
125 """
126 def setUp(self):
127 self.rng = np.random.Generator(np.random.MT19937(5))
129 self.tempDir = tempfile.TemporaryDirectory()
130 tempPath = self.tempDir.name
131 self.log = logging.getLogger("lsst.TestConvertRefcatManager")
132 self.config = convertReferenceCatalogTestBase.makeConvertConfig(withRaDecErr=True)
133 self.config.id_name = 'id'
134 self.depth = 2 # very small depth, for as few pixels as possible.
135 self.indexer = HtmIndexer(self.depth)
136 self.htm = lsst.sphgeom.HtmPixelization(self.depth)
137 converter = ConvertReferenceCatalogTask(output_dir=tempPath, config=self.config)
138 dtype = [('id', '<f8'), ('ra', '<f8'), ('dec', '<f8'), ('ra_err', '<f8'), ('dec_err', '<f8'),
139 ('a', '<f8'), ('a_err', '<f8')]
140 self.schema, self.key_map = converter.makeSchema(dtype)
141 self.fileReader = ReadTextCatalogTask()
143 self.fakeInput = self.makeSkyCatalog(outPath=None, size=5, idStart=6543)
144 self.matchedPixels = np.array([1, 1, 2, 2, 3])
145 self.tempDir2 = tempfile.TemporaryDirectory()
146 tempPath = self.tempDir2.name
147 self.filenames = {x: os.path.join(tempPath, "%d.fits" % x) for x in set(self.matchedPixels)}
149 self.worker = ConvertRefcatManager(self.filenames,
150 self.config,
151 self.fileReader,
152 self.indexer,
153 self.schema,
154 self.key_map,
155 self.htm.universe()[0],
156 addRefCatMetadata,
157 self.log)
159 def _createFakeCatalog(self, nOld=5, nNew=0, idStart=42):
160 """Create a fake output SimpleCatalog, populated with nOld+nNew elements.
162 Parameters
163 ----------
164 nOld : `int`, optional
165 The number of filled in sources to put in the catalog.
166 nNew : `int`, optional
167 The number of empty sources to put in the catalog.
168 idStart : `int`, optional
169 The start id of the ``nOld`` sources.
171 Returns
172 -------
173 catalog : `lsst.afw.table.SimpleCatalog`
174 A catalog populated with random data and contiguous ids.
175 """
176 catalog = lsst.afw.table.SimpleCatalog(self.schema)
177 catalog.resize(nOld)
178 for x in self.schema:
179 catalog[x.key] = self.rng.random(nOld)
180 # do the ids separately, so there are no duplicates
181 catalog['id'] = np.arange(idStart, idStart + nOld)
182 catalog.resize(nOld + nNew) # make space for the elements we will add
183 return catalog.copy(deep=True)
185 def test_doOnePixelNewData(self):
186 """Test that we can add new data to an existing catalog."""
187 pixelId = 1 # the pixel we are going to test
189 nOld = 5
190 nNew = sum(self.matchedPixels == pixelId)
191 catalog = self._createFakeCatalog(nOld=nOld, nNew=nNew)
192 self.worker.getCatalog = unittest.mock.Mock(self.worker.getCatalog, return_value=catalog)
194 self.worker._doOnePixel(self.fakeInput, self.matchedPixels, pixelId, {}, {})
195 newcat = lsst.afw.table.SimpleCatalog.readFits(self.filenames[pixelId])
197 # check that the "pre" catalog is unchanged, exactly
198 np.testing.assert_equal(newcat[:nOld]['id'], catalog[:nOld]['id'])
199 self.assertFloatsEqual(newcat[:nOld]['coord_ra'], catalog[:nOld]['coord_ra'])
200 self.assertFloatsEqual(newcat[:nOld]['coord_dec'], catalog[:nOld]['coord_dec'])
202 # check that the new catalog elements are set correctly
203 newElements = self.fakeInput[self.matchedPixels == pixelId]
204 np.testing.assert_equal(newcat[nOld:]['id'], newElements['id'])
205 self.assertFloatsAlmostEqual(newcat[nOld:]['coord_ra'], newElements['ra']*np.pi/180)
206 self.assertFloatsAlmostEqual(newcat[nOld:]['coord_dec'], newElements['dec']*np.pi/180)
208 def test_doOnePixelNoData(self):
209 """Test that we can put new data into an empty catalog."""
210 pixelId = 2
212 nOld = 0
213 nNew = sum(self.matchedPixels == pixelId)
214 catalog = self._createFakeCatalog(nOld=nOld, nNew=nNew)
215 self.worker.getCatalog = unittest.mock.Mock(self.worker.getCatalog, return_value=catalog)
217 self.worker._doOnePixel(self.fakeInput, self.matchedPixels, pixelId, {}, {})
218 newcat = lsst.afw.table.SimpleCatalog.readFits(self.filenames[pixelId])
220 # check that the new catalog elements are set correctly
221 newElements = self.fakeInput[self.matchedPixels == pixelId]
222 np.testing.assert_equal(newcat['id'], newElements['id'])
223 self.assertFloatsAlmostEqual(newcat['coord_ra'], newElements['ra']*np.pi/180)
224 self.assertFloatsAlmostEqual(newcat['coord_dec'], newElements['dec']*np.pi/180)
226 def test_getCatalog(self):
227 """Test that getCatalog returns a properly expanded new catalog."""
228 pixelId = 3
229 nOld = 10
230 nNewElements = 5
231 # save a catalog to disk that we can check against the getCatalog()'s return
232 catalog = self._createFakeCatalog(nOld=nOld, nNew=0)
233 catalog.writeFits(self.filenames[pixelId])
234 newcat = self.worker.getCatalog(pixelId, self.schema, nNewElements)
236 self.assertEqual(len(newcat), nOld + nNewElements)
238 np.testing.assert_equal(newcat[:len(catalog)]['id'], catalog['id'])
239 self.assertFloatsEqual(newcat[:len(catalog)]['coord_ra'], catalog['coord_ra'])
240 self.assertFloatsEqual(newcat[:len(catalog)]['coord_dec'], catalog['coord_dec'])
242 def test_setCoordinateCovariance(self):
243 catalog = self._createFakeCatalog(nOld=10, nNew=0)
245 with self.assertRaises(NotImplementedError):
246 self.worker._setCoordinateCovariance(catalog[0], self.fakeInput[0])
248 def tearDown(self):
249 self.tempDir.cleanup()
250 self.tempDir2.cleanup()
253class TestMemory(lsst.utils.tests.MemoryTestCase):
254 pass
257def setup_module(module):
258 lsst.utils.tests.init()
261if __name__ == "__main__":
262 lsst.utils.tests.init()
263 unittest.main()