Coverage for tests/test_readers.py: 14%
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1# This file is part of afw.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (http://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 <http://www.gnu.org/licenses/>.
22import unittest
24import os
25import numpy as np
26import astropy.io.fits
28import lsst.utils.tests
29from lsst.daf.base import PropertyList
30from lsst.geom import Box2I, Point2I, Extent2I, Point2D, Box2D, SpherePoint, degrees
31from lsst.afw.geom import makeSkyWcs, Polygon
32from lsst.afw.table import ExposureTable
33from lsst.afw.image import (Image, Mask, Exposure, LOCAL, PARENT, MaskPixel, VariancePixel,
34 ImageFitsReader, MaskFitsReader, MaskedImageFitsReader, ExposureFitsReader,
35 Filter, FilterLabel, PhotoCalib, ApCorrMap, VisitInfo, TransmissionCurve,
36 CoaddInputs, ExposureInfo)
37from lsst.afw.image.utils import defineFilter
38from lsst.afw.detection import GaussianPsf
39from lsst.afw.cameraGeom.testUtils import DetectorWrapper
41TESTDIR = os.path.abspath(os.path.dirname(__file__))
44class FitsReaderTestCase(lsst.utils.tests.TestCase):
46 def setUp(self):
47 self.dtypes = [np.dtype(t) for t in (np.uint16, np.int32, np.float32, np.float64)]
48 self.bbox = Box2I(Point2I(2, 1), Extent2I(5, 7))
49 self.args = [
50 (),
51 (Box2I(Point2I(3, 4), Extent2I(2, 1)),),
52 (Box2I(Point2I(3, 4), Extent2I(2, 1)), PARENT),
53 (Box2I(Point2I(1, 0), Extent2I(3, 2)), LOCAL),
54 ]
56 def testImageFitsReader(self):
57 for n, dtypeIn in enumerate(self.dtypes):
58 with self.subTest(dtypeIn=dtypeIn):
59 imageIn = Image(self.bbox, dtype=dtypeIn)
60 imageIn.array[:, :] = np.random.randint(low=1, high=5, size=imageIn.array.shape)
61 with lsst.utils.tests.getTempFilePath(".fits") as fileName:
62 imageIn.writeFits(fileName)
63 reader = ImageFitsReader(fileName)
64 self.assertEqual(reader.readBBox(), self.bbox)
65 self.assertEqual(reader.readDType(), dtypeIn)
66 self.assertEqual(reader.fileName, fileName)
67 for args in self.args:
68 with self.subTest(args=args):
69 array1 = reader.readArray(*args)
70 image1 = reader.read(*args)
71 subIn = imageIn.subset(*args) if args else imageIn
72 self.assertEqual(dtypeIn, array1.dtype)
73 self.assertTrue(np.all(subIn.array == array1))
74 self.assertEqual(subIn.getXY0(), reader.readXY0(*args))
75 self.assertImagesEqual(subIn, image1)
76 for dtype2 in self.dtypes[n:]:
77 for args in self.args:
78 with self.subTest(dtype2=dtype2, args=args):
79 subIn = imageIn.subset(*args) if args else imageIn
80 array2 = reader.readArray(*args, dtype=dtype2)
81 image2 = reader.read(*args, dtype=dtype2)
82 self.assertEqual(dtype2, array2.dtype)
83 self.assertTrue(np.all(subIn.array == array2))
84 self.assertEqual(subIn.getXY0(), reader.readXY0(*args))
85 self.assertEqual(subIn.getBBox(), image2.getBBox())
86 self.assertTrue(np.all(image2.array == array2))
88 def testMaskFitsReader(self):
89 maskIn = Mask(self.bbox, dtype=MaskPixel)
90 maskIn.array[:, :] = np.random.randint(low=1, high=5, size=maskIn.array.shape)
91 with lsst.utils.tests.getTempFilePath(".fits") as fileName:
92 maskIn.writeFits(fileName)
93 reader = MaskFitsReader(fileName)
94 self.assertEqual(reader.readBBox(), self.bbox)
95 self.assertEqual(reader.readDType(), MaskPixel)
96 self.assertEqual(reader.fileName, fileName)
97 for args in self.args:
98 with self.subTest(args=args):
99 array = reader.readArray(*args)
100 mask = reader.read(*args)
101 subIn = maskIn.subset(*args) if args else maskIn
102 self.assertEqual(MaskPixel, array.dtype)
103 self.assertTrue(np.all(subIn.array == array))
104 self.assertEqual(subIn.getXY0(), reader.readXY0(*args))
105 self.assertImagesEqual(subIn, mask)
107 def checkMultiPlaneReader(self, reader, objectIn, fileName, dtypesOut, compare):
108 """Test operations common to MaskedImageFitsReader and ExposureFitsReader.
110 Parameters
111 ----------
112 reader : `MaskedImageFitsReader` or `ExposureFitsReader` instance
113 Reader object to test.
114 objectIn : `MaskedImage` or `Exposure`
115 Object originally saved, to compare against.
116 fileName : `str`
117 Name of the file the reader is reading.
118 dtypesOut : sequence of `numpy.dype`
119 Compatible image pixel types to try to read in.
120 compare : callable
121 Callable that compares objects of the same type as objectIn and
122 asserts if they are not equal.
123 """
124 dtypeIn = objectIn.image.dtype
125 self.assertEqual(reader.readBBox(), self.bbox)
126 self.assertEqual(reader.readImageDType(), dtypeIn)
127 self.assertEqual(reader.readMaskDType(), MaskPixel)
128 self.assertEqual(reader.readVarianceDType(), VariancePixel)
129 self.assertEqual(reader.fileName, fileName)
130 for args in self.args:
131 with self.subTest(args=args):
132 object1 = reader.read(*args)
133 subIn = objectIn.subset(*args) if args else objectIn
134 self.assertEqual(object1.image.array.dtype, dtypeIn)
135 self.assertEqual(object1.mask.array.dtype, MaskPixel)
136 self.assertEqual(object1.variance.array.dtype, VariancePixel)
137 self.assertImagesEqual(subIn.image, reader.readImage(*args))
138 self.assertImagesEqual(subIn.mask, reader.readMask(*args))
139 self.assertImagesEqual(subIn.variance, reader.readVariance(*args))
140 compare(subIn, object1)
141 for dtype2 in dtypesOut:
142 with self.subTest(dtype2=dtype2, args=args):
143 object2 = reader.read(*args, dtype=dtype2)
144 image2 = reader.readImage(*args, dtype=dtype2)
145 self.assertEqual(object2.image.array.dtype, dtype2)
146 self.assertEqual(object2.mask.array.dtype, MaskPixel)
147 self.assertEqual(object2.variance.array.dtype, VariancePixel)
148 self.assertImagesEqual(subIn.image, Image(image2, deep=True, dtype=dtypeIn))
149 self.assertImagesEqual(image2, object2.image)
150 compare(subIn, object2)
152 def checkMaskedImageFitsReader(self, exposureIn, fileName, dtypesOut):
153 """Test MaskedImageFitsReader.
155 Parameters
156 ----------
157 exposureIn : `Exposure`
158 Object originally saved, to compare against.
159 fileName : `str`
160 Name of the file the reader is reading.
161 dtypesOut : sequence of `numpy.dype`
162 Compatible image pixel types to try to read in.
163 """
164 reader = MaskedImageFitsReader(fileName)
165 self.checkMultiPlaneReader(reader, exposureIn.maskedImage, fileName, dtypesOut,
166 compare=self.assertMaskedImagesEqual)
168 def checkExposureFitsReader(self, exposureIn, fileName, dtypesOut):
169 """Test ExposureFitsReader.
171 Parameters
172 ----------
173 exposureIn : `Exposure`
174 Object originally saved, to compare against.
175 fileName : `str`
176 Name of the file the reader is reading.
177 dtypesOut : sequence of `numpy.dype`
178 Compatible image pixel types to try to read in.
179 """
180 reader = ExposureFitsReader(fileName)
181 self.assertIn('EXPINFO_V', reader.readMetadata().toDict(), "metadata is automatically versioned")
182 reader.readMetadata().remove('EXPINFO_V')
183 # ensure EXTNAMEs can be read and make sense
184 extnames = set(('PRIMARY', 'IMAGE', 'MASK', 'VARIANCE', 'ARCHIVE_INDEX',
185 'Detector', 'TransformMap', 'TransformPoint2ToPoint2',
186 'FilterLabel', 'SkyWcs', 'ApCorrMap', 'PhotoCalib',
187 'ChebyshevBoundedField', 'CoaddInputs', 'GaussianPsf',
188 'Polygon', 'VisitInfo'))
189 with astropy.io.fits.open(fileName) as astropyReadFile:
190 for hdu in astropyReadFile:
191 self.assertIn(hdu.name, extnames)
192 self.assertIn('EXTNAME', reader.readMetadata().toDict(), "EXTNAME is added upon writing")
193 reader.readMetadata().remove('EXTNAME')
194 self.assertGreaterEqual(reader.readSerializationVersion(), 0)
195 self.assertEqual(exposureIn.getMetadata().toDict(), reader.readMetadata().toDict())
196 self.assertWcsAlmostEqualOverBBox(exposureIn.getWcs(), reader.readWcs(), self.bbox,
197 maxDiffPix=0, maxDiffSky=0*degrees)
198 self.assertWcsAlmostEqualOverBBox(exposureIn.getWcs(),
199 reader.readComponent(ExposureInfo.KEY_WCS),
200 self.bbox,
201 maxDiffPix=0, maxDiffSky=0*degrees)
202 self.assertEqual(exposureIn.getFilter(), reader.readFilter())
203 self.assertEqual(exposureIn.getFilterLabel(), reader.readFilterLabel())
204 self.assertEqual(exposureIn.getFilterLabel(),
205 reader.readComponent(ExposureInfo.KEY_FILTER))
206 self.assertEqual(exposureIn.getPhotoCalib(), reader.readPhotoCalib())
207 self.assertEqual(exposureIn.getPhotoCalib(),
208 reader.readComponent(ExposureInfo.KEY_PHOTO_CALIB))
209 self.assertImagesEqual(exposureIn.getPsf().computeImage(), reader.readPsf().computeImage())
210 self.assertImagesEqual(exposureIn.getPsf().computeImage(),
211 reader.readComponent('PSF').computeImage())
212 self.assertEqual(exposureIn.getInfo().getValidPolygon(), reader.readValidPolygon())
213 self.assertEqual(exposureIn.getInfo().getValidPolygon(),
214 reader.readComponent(ExposureInfo.KEY_VALID_POLYGON))
215 self.assertCountEqual(exposureIn.getInfo().getApCorrMap(), reader.readApCorrMap())
216 self.assertCountEqual(exposureIn.getInfo().getApCorrMap(),
217 reader.readComponent(ExposureInfo.KEY_AP_CORR_MAP))
218 self.assertEqual(exposureIn.getInfo().getVisitInfo().getExposureTime(),
219 reader.readVisitInfo().getExposureTime())
220 point = Point2D(2.3, 3.1)
221 wavelengths = np.linspace(4000, 5000, 5)
222 self.assertFloatsEqual(exposureIn.getInfo().getTransmissionCurve().sampleAt(point, wavelengths),
223 reader.readTransmissionCurve().sampleAt(point, wavelengths))
224 # Note: readComponent(ExposureInfo.KEY_TRANSMISSION_CURVE) returns a generic Storable
225 # rather than a TransmissionCurve object.
227 # Because we persisted the same instances, we should get back the same
228 # instances for *archive* components, and hence equality comparisons
229 # should work even if it just amounts to C++ pointer equality.
230 record = reader.readCoaddInputs().ccds[0]
231 self.assertEqual(record.getWcs(), reader.readWcs())
232 self.assertEqual(record.getPsf(), reader.readPsf())
233 self.assertEqual(record.getValidPolygon(), reader.readValidPolygon())
234 self.assertEqual(record.getApCorrMap(), reader.readApCorrMap())
235 self.assertEqual(record.getPhotoCalib(), reader.readPhotoCalib())
236 self.assertEqual(record.getDetector(), reader.readDetector())
237 self.checkMultiPlaneReader(
238 reader, exposureIn, fileName, dtypesOut,
239 compare=lambda a, b: self.assertMaskedImagesEqual(a.maskedImage, b.maskedImage)
240 )
242 def testCompressedSinglePlaneExposureFitsReader(self):
243 """Test that a compressed single plane image can be read as exposure.
244 """
245 uncompressed_file = os.path.join(TESTDIR, "data", "ticketdm26260.fits")
246 compressed_file = os.path.join(TESTDIR, "data", "ticketdm26260.fits.fz")
247 uncompressed = ExposureFitsReader(uncompressed_file).read()
248 compressed = ExposureFitsReader(compressed_file).read()
250 self.assertMaskedImagesEqual(uncompressed.maskedImage, compressed.maskedImage)
252 def testMultiPlaneFitsReaders(self):
253 """Run tests for MaskedImageFitsReader and ExposureFitsReader.
254 """
255 metadata = PropertyList()
256 metadata.add("FIVE", 5)
257 metadata.add("SIX", 6.0)
258 wcs = makeSkyWcs(Point2D(2.5, 3.75), SpherePoint(40.0*degrees, 50.0*degrees),
259 np.array([[1E-5, 0.0], [0.0, -1E-5]]))
260 defineFilter("test_readers_filter", lambdaEff=470.0)
261 calib = PhotoCalib(2.5E4)
262 psf = GaussianPsf(21, 21, 8.0)
263 polygon = Polygon(Box2D(self.bbox))
264 apCorrMap = ApCorrMap()
265 visitInfo = VisitInfo(exposureTime=5.0)
266 transmissionCurve = TransmissionCurve.makeIdentity()
267 coaddInputs = CoaddInputs(ExposureTable.makeMinimalSchema(), ExposureTable.makeMinimalSchema())
268 detector = DetectorWrapper().detector
269 record = coaddInputs.ccds.addNew()
270 record.setWcs(wcs)
271 record.setPhotoCalib(calib)
272 record.setPsf(psf)
273 record.setValidPolygon(polygon)
274 record.setApCorrMap(apCorrMap)
275 record.setVisitInfo(visitInfo)
276 record.setTransmissionCurve(transmissionCurve)
277 record.setDetector(detector)
278 for n, dtypeIn in enumerate(self.dtypes):
279 with self.subTest(dtypeIn=dtypeIn):
280 exposureIn = Exposure(self.bbox, dtype=dtypeIn)
281 shape = exposureIn.image.array.shape
282 exposureIn.image.array[:, :] = np.random.randint(low=1, high=5, size=shape)
283 exposureIn.mask.array[:, :] = np.random.randint(low=1, high=5, size=shape)
284 exposureIn.variance.array[:, :] = np.random.randint(low=1, high=5, size=shape)
285 exposureIn.setMetadata(metadata)
286 exposureIn.setWcs(wcs)
287 exposureIn.setFilter(Filter("test_readers_filter"))
288 exposureIn.setFilterLabel(FilterLabel(physical="test_readers_filter"))
289 exposureIn.setPhotoCalib(calib)
290 exposureIn.setPsf(psf)
291 exposureIn.getInfo().setValidPolygon(polygon)
292 exposureIn.getInfo().setApCorrMap(apCorrMap)
293 exposureIn.getInfo().setVisitInfo(visitInfo)
294 exposureIn.getInfo().setTransmissionCurve(transmissionCurve)
295 exposureIn.getInfo().setCoaddInputs(coaddInputs)
296 exposureIn.setDetector(detector)
297 with lsst.utils.tests.getTempFilePath(".fits") as fileName:
298 exposureIn.writeFits(fileName)
299 self.checkMaskedImageFitsReader(exposureIn, fileName, self.dtypes[n:])
300 self.checkExposureFitsReader(exposureIn, fileName, self.dtypes[n:])
303class TestMemory(lsst.utils.tests.MemoryTestCase):
304 pass
307def setup_module(module):
308 lsst.utils.tests.init()
311if __name__ == "__main__": 311 ↛ 312line 311 didn't jump to line 312, because the condition on line 311 was never true
312 import sys
313 setup_module(sys.modules[__name__])
314 unittest.main()