Coverage for tests/test_readers.py : 13%

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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
27import lsst.utils.tests
28from lsst.daf.base import PropertyList
29from lsst.geom import Box2I, Point2I, Extent2I, Point2D, Box2D, SpherePoint, degrees
30from lsst.afw.geom import makeSkyWcs, Polygon
31from lsst.afw.table import ExposureTable
32from lsst.afw.image import (Image, Mask, Exposure, LOCAL, PARENT, MaskPixel, VariancePixel,
33 ImageFitsReader, MaskFitsReader, MaskedImageFitsReader, ExposureFitsReader,
34 Filter, FilterLabel, PhotoCalib, ApCorrMap, VisitInfo, TransmissionCurve,
35 CoaddInputs, ExposureInfo)
36from lsst.afw.image.utils import defineFilter
37from lsst.afw.detection import GaussianPsf
38from lsst.afw.cameraGeom.testUtils import DetectorWrapper
40TESTDIR = os.path.abspath(os.path.dirname(__file__))
43class FitsReaderTestCase(lsst.utils.tests.TestCase):
45 def setUp(self):
46 self.dtypes = [np.dtype(t) for t in (np.uint16, np.int32, np.float32, np.float64)]
47 self.bbox = Box2I(Point2I(2, 1), Extent2I(5, 7))
48 self.args = [
49 (),
50 (Box2I(Point2I(3, 4), Extent2I(2, 1)),),
51 (Box2I(Point2I(3, 4), Extent2I(2, 1)), PARENT),
52 (Box2I(Point2I(1, 0), Extent2I(3, 2)), LOCAL),
53 ]
55 def testImageFitsReader(self):
56 for n, dtypeIn in enumerate(self.dtypes):
57 with self.subTest(dtypeIn=dtypeIn):
58 imageIn = Image(self.bbox, dtype=dtypeIn)
59 imageIn.array[:, :] = np.random.randint(low=1, high=5, size=imageIn.array.shape)
60 with lsst.utils.tests.getTempFilePath(".fits") as fileName:
61 imageIn.writeFits(fileName)
62 reader = ImageFitsReader(fileName)
63 self.assertEqual(reader.readBBox(), self.bbox)
64 self.assertEqual(reader.readDType(), dtypeIn)
65 self.assertEqual(reader.fileName, fileName)
66 for args in self.args:
67 with self.subTest(args=args):
68 array1 = reader.readArray(*args)
69 image1 = reader.read(*args)
70 subIn = imageIn.subset(*args) if args else imageIn
71 self.assertEqual(dtypeIn, array1.dtype)
72 self.assertTrue(np.all(subIn.array == array1))
73 self.assertEqual(subIn.getXY0(), reader.readXY0(*args))
74 self.assertImagesEqual(subIn, image1)
75 for dtype2 in self.dtypes[n:]:
76 for args in self.args:
77 with self.subTest(dtype2=dtype2, args=args):
78 subIn = imageIn.subset(*args) if args else imageIn
79 array2 = reader.readArray(*args, dtype=dtype2)
80 image2 = reader.read(*args, dtype=dtype2)
81 self.assertEqual(dtype2, array2.dtype)
82 self.assertTrue(np.all(subIn.array == array2))
83 self.assertEqual(subIn.getXY0(), reader.readXY0(*args))
84 self.assertEqual(subIn.getBBox(), image2.getBBox())
85 self.assertTrue(np.all(image2.array == array2))
87 def testMaskFitsReader(self):
88 maskIn = Mask(self.bbox, dtype=MaskPixel)
89 maskIn.array[:, :] = np.random.randint(low=1, high=5, size=maskIn.array.shape)
90 with lsst.utils.tests.getTempFilePath(".fits") as fileName:
91 maskIn.writeFits(fileName)
92 reader = MaskFitsReader(fileName)
93 self.assertEqual(reader.readBBox(), self.bbox)
94 self.assertEqual(reader.readDType(), MaskPixel)
95 self.assertEqual(reader.fileName, fileName)
96 for args in self.args:
97 with self.subTest(args=args):
98 array = reader.readArray(*args)
99 mask = reader.read(*args)
100 subIn = maskIn.subset(*args) if args else maskIn
101 self.assertEqual(MaskPixel, array.dtype)
102 self.assertTrue(np.all(subIn.array == array))
103 self.assertEqual(subIn.getXY0(), reader.readXY0(*args))
104 self.assertImagesEqual(subIn, mask)
106 def checkMultiPlaneReader(self, reader, objectIn, fileName, dtypesOut, compare):
107 """Test operations common to MaskedImageFitsReader and ExposureFitsReader.
109 Parameters
110 ----------
111 reader : `MaskedImageFitsReader` or `ExposureFitsReader` instance
112 Reader object to test.
113 objectIn : `MaskedImage` or `Exposure`
114 Object originally saved, to compare against.
115 fileName : `str`
116 Name of the file the reader is reading.
117 dtypesOut : sequence of `numpy.dype`
118 Compatible image pixel types to try to read in.
119 compare : callable
120 Callable that compares objects of the same type as objectIn and
121 asserts if they are not equal.
122 """
123 dtypeIn = objectIn.image.dtype
124 self.assertEqual(reader.readBBox(), self.bbox)
125 self.assertEqual(reader.readImageDType(), dtypeIn)
126 self.assertEqual(reader.readMaskDType(), MaskPixel)
127 self.assertEqual(reader.readVarianceDType(), VariancePixel)
128 self.assertEqual(reader.fileName, fileName)
129 for args in self.args:
130 with self.subTest(args=args):
131 object1 = reader.read(*args)
132 subIn = objectIn.subset(*args) if args else objectIn
133 self.assertEqual(object1.image.array.dtype, dtypeIn)
134 self.assertEqual(object1.mask.array.dtype, MaskPixel)
135 self.assertEqual(object1.variance.array.dtype, VariancePixel)
136 self.assertImagesEqual(subIn.image, reader.readImage(*args))
137 self.assertImagesEqual(subIn.mask, reader.readMask(*args))
138 self.assertImagesEqual(subIn.variance, reader.readVariance(*args))
139 compare(subIn, object1)
140 for dtype2 in dtypesOut:
141 with self.subTest(dtype2=dtype2, args=args):
142 object2 = reader.read(*args, dtype=dtype2)
143 image2 = reader.readImage(*args, dtype=dtype2)
144 self.assertEqual(object2.image.array.dtype, dtype2)
145 self.assertEqual(object2.mask.array.dtype, MaskPixel)
146 self.assertEqual(object2.variance.array.dtype, VariancePixel)
147 self.assertImagesEqual(subIn.image, Image(image2, deep=True, dtype=dtypeIn))
148 self.assertImagesEqual(image2, object2.image)
149 compare(subIn, object2)
151 def checkMaskedImageFitsReader(self, exposureIn, fileName, dtypesOut):
152 """Test MaskedImageFitsReader.
154 Parameters
155 ----------
156 exposureIn : `Exposure`
157 Object originally saved, to compare against.
158 fileName : `str`
159 Name of the file the reader is reading.
160 dtypesOut : sequence of `numpy.dype`
161 Compatible image pixel types to try to read in.
162 """
163 reader = MaskedImageFitsReader(fileName)
164 self.checkMultiPlaneReader(reader, exposureIn.maskedImage, fileName, dtypesOut,
165 compare=self.assertMaskedImagesEqual)
167 def checkExposureFitsReader(self, exposureIn, fileName, dtypesOut):
168 """Test ExposureFitsReader.
170 Parameters
171 ----------
172 exposureIn : `Exposure`
173 Object originally saved, to compare against.
174 fileName : `str`
175 Name of the file the reader is reading.
176 dtypesOut : sequence of `numpy.dype`
177 Compatible image pixel types to try to read in.
178 """
179 reader = ExposureFitsReader(fileName)
180 self.assertIn('EXPINFO_V', reader.readMetadata().toDict(), "metadata is automatically versioned")
181 reader.readMetadata().remove('EXPINFO_V')
182 self.assertGreaterEqual(reader.readSerializationVersion(), 0)
183 self.assertEqual(exposureIn.getMetadata().toDict(), reader.readMetadata().toDict())
184 self.assertWcsAlmostEqualOverBBox(exposureIn.getWcs(), reader.readWcs(), self.bbox,
185 maxDiffPix=0, maxDiffSky=0*degrees)
186 self.assertWcsAlmostEqualOverBBox(exposureIn.getWcs(),
187 reader.readComponent(ExposureInfo.KEY_WCS),
188 self.bbox,
189 maxDiffPix=0, maxDiffSky=0*degrees)
190 self.assertEqual(exposureIn.getFilter(), reader.readFilter())
191 self.assertEqual(exposureIn.getFilterLabel(), reader.readFilterLabel())
192 self.assertEqual(exposureIn.getFilterLabel(),
193 reader.readComponent(ExposureInfo.KEY_FILTER))
194 self.assertEqual(exposureIn.getPhotoCalib(), reader.readPhotoCalib())
195 self.assertEqual(exposureIn.getPhotoCalib(),
196 reader.readComponent(ExposureInfo.KEY_PHOTO_CALIB))
197 self.assertImagesEqual(exposureIn.getPsf().computeImage(), reader.readPsf().computeImage())
198 self.assertImagesEqual(exposureIn.getPsf().computeImage(),
199 reader.readComponent('PSF').computeImage())
200 self.assertEqual(exposureIn.getInfo().getValidPolygon(), reader.readValidPolygon())
201 self.assertEqual(exposureIn.getInfo().getValidPolygon(),
202 reader.readComponent(ExposureInfo.KEY_VALID_POLYGON))
203 self.assertCountEqual(exposureIn.getInfo().getApCorrMap(), reader.readApCorrMap())
204 self.assertCountEqual(exposureIn.getInfo().getApCorrMap(),
205 reader.readComponent(ExposureInfo.KEY_AP_CORR_MAP))
206 self.assertEqual(exposureIn.getInfo().getVisitInfo().getExposureTime(),
207 reader.readVisitInfo().getExposureTime())
208 point = Point2D(2.3, 3.1)
209 wavelengths = np.linspace(4000, 5000, 5)
210 self.assertFloatsEqual(exposureIn.getInfo().getTransmissionCurve().sampleAt(point, wavelengths),
211 reader.readTransmissionCurve().sampleAt(point, wavelengths))
212 # Note: readComponent(ExposureInfo.KEY_TRANSMISSION_CURVE) returns a generic Storable
213 # rather than a TransmissionCurve object.
215 # Because we persisted the same instances, we should get back the same
216 # instances for *archive* components, and hence equality comparisons
217 # should work even if it just amounts to C++ pointer equality.
218 record = reader.readCoaddInputs().ccds[0]
219 self.assertEqual(record.getWcs(), reader.readWcs())
220 self.assertEqual(record.getPsf(), reader.readPsf())
221 self.assertEqual(record.getValidPolygon(), reader.readValidPolygon())
222 self.assertEqual(record.getApCorrMap(), reader.readApCorrMap())
223 self.assertEqual(record.getPhotoCalib(), reader.readPhotoCalib())
224 self.assertEqual(record.getDetector(), reader.readDetector())
225 self.checkMultiPlaneReader(
226 reader, exposureIn, fileName, dtypesOut,
227 compare=lambda a, b: self.assertMaskedImagesEqual(a.maskedImage, b.maskedImage)
228 )
230 def testCompressedSinglePlaneExposureFitsReader(self):
231 """Test that a compressed single plane image can be read as exposure.
232 """
233 uncompressed_file = os.path.join(TESTDIR, "data", "ticketdm26260.fits")
234 compressed_file = os.path.join(TESTDIR, "data", "ticketdm26260.fits.fz")
235 uncompressed = ExposureFitsReader(uncompressed_file).read()
236 compressed = ExposureFitsReader(compressed_file).read()
238 self.assertMaskedImagesEqual(uncompressed.maskedImage, compressed.maskedImage)
240 def testMultiPlaneFitsReaders(self):
241 """Run tests for MaskedImageFitsReader and ExposureFitsReader.
242 """
243 metadata = PropertyList()
244 metadata.add("FIVE", 5)
245 metadata.add("SIX", 6.0)
246 wcs = makeSkyWcs(Point2D(2.5, 3.75), SpherePoint(40.0*degrees, 50.0*degrees),
247 np.array([[1E-5, 0.0], [0.0, -1E-5]]))
248 defineFilter("test_readers_filter", lambdaEff=470.0)
249 calib = PhotoCalib(2.5E4)
250 psf = GaussianPsf(21, 21, 8.0)
251 polygon = Polygon(Box2D(self.bbox))
252 apCorrMap = ApCorrMap()
253 visitInfo = VisitInfo(exposureTime=5.0)
254 transmissionCurve = TransmissionCurve.makeIdentity()
255 coaddInputs = CoaddInputs(ExposureTable.makeMinimalSchema(), ExposureTable.makeMinimalSchema())
256 detector = DetectorWrapper().detector
257 record = coaddInputs.ccds.addNew()
258 record.setWcs(wcs)
259 record.setPhotoCalib(calib)
260 record.setPsf(psf)
261 record.setValidPolygon(polygon)
262 record.setApCorrMap(apCorrMap)
263 record.setVisitInfo(visitInfo)
264 record.setTransmissionCurve(transmissionCurve)
265 record.setDetector(detector)
266 for n, dtypeIn in enumerate(self.dtypes):
267 with self.subTest(dtypeIn=dtypeIn):
268 exposureIn = Exposure(self.bbox, dtype=dtypeIn)
269 shape = exposureIn.image.array.shape
270 exposureIn.image.array[:, :] = np.random.randint(low=1, high=5, size=shape)
271 exposureIn.mask.array[:, :] = np.random.randint(low=1, high=5, size=shape)
272 exposureIn.variance.array[:, :] = np.random.randint(low=1, high=5, size=shape)
273 exposureIn.setMetadata(metadata)
274 exposureIn.setWcs(wcs)
275 exposureIn.setFilter(Filter("test_readers_filter"))
276 exposureIn.setFilterLabel(FilterLabel(physical="test_readers_filter"))
277 exposureIn.setPhotoCalib(calib)
278 exposureIn.setPsf(psf)
279 exposureIn.getInfo().setValidPolygon(polygon)
280 exposureIn.getInfo().setApCorrMap(apCorrMap)
281 exposureIn.getInfo().setVisitInfo(visitInfo)
282 exposureIn.getInfo().setTransmissionCurve(transmissionCurve)
283 exposureIn.getInfo().setCoaddInputs(coaddInputs)
284 exposureIn.setDetector(detector)
285 with lsst.utils.tests.getTempFilePath(".fits") as fileName:
286 exposureIn.writeFits(fileName)
287 self.checkMaskedImageFitsReader(exposureIn, fileName, self.dtypes[n:])
288 self.checkExposureFitsReader(exposureIn, fileName, self.dtypes[n:])
291class TestMemory(lsst.utils.tests.MemoryTestCase):
292 pass
295def setup_module(module):
296 lsst.utils.tests.init()
299if __name__ == "__main__": 299 ↛ 300line 299 didn't jump to line 300, because the condition on line 299 was never true
300 import sys
301 setup_module(sys.modules[__name__])
302 unittest.main()