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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/>. 

21 

22import math 

23import os 

24import sys 

25import unittest 

26 

27import lsst.geom 

28import lsst.afw.image as afwImage 

29import lsst.afw.math as afwMath 

30import lsst.log.utils as logUtils 

31import lsst.meas.algorithms as algorithms 

32import lsst.pex.config as pexConfig 

33import lsst.utils 

34import lsst.utils.tests 

35 

36# Increase the number for more verbose messages 

37logUtils.traceSetAt("algorithms.CR", 3) 

38 

39try: 

40 display 

41except NameError: 

42 display = False 

43else: 

44 import lsst.afw.display as afwDisplay 

45 afwDisplay.setDefaultMaskTransparency(75) 

46 

47try: 

48 afwdataDir = lsst.utils.getPackageDir('afwdata') 

49 imageFile0 = os.path.join(afwdataDir, "CFHT", "D4", "cal-53535-i-797722_1.fits") 

50except Exception: 

51 imageFile0 = None 

52 

53 

54class CosmicRayTestCase(lsst.utils.tests.TestCase): 

55 """A test case for Cosmic Ray detection.""" 

56 

57 def setUp(self): 

58 self.FWHM = 5 # pixels 

59 self.psf = algorithms.DoubleGaussianPsf(29, 29, self.FWHM/(2*math.sqrt(2*math.log(2)))) 

60 

61 self.mi = afwImage.MaskedImageF(imageFile0) 

62 self.XY0 = lsst.geom.PointI(0, 0) # origin of the subimage we use 

63 

64 if imageFile0: 

65 if True: # use full image, trimmed to data section 

66 self.XY0 = lsst.geom.PointI(32, 2) 

67 self.mi = self.mi.Factory(self.mi, lsst.geom.BoxI(self.XY0, lsst.geom.PointI(2079, 4609)), 

68 afwImage.LOCAL) 

69 self.mi.setXY0(lsst.geom.PointI(0, 0)) 

70 self.nCR = 1076 # number of CRs we should detect 

71 else: # use sub-image 

72 if True: 

73 self.XY0 = lsst.geom.PointI(824, 140) 

74 self.nCR = 10 

75 else: 

76 self.XY0 = lsst.geom.PointI(280, 2750) 

77 self.nCR = 2 

78 self.mi = self.mi.Factory(self.mi, lsst.geom.BoxI(self.XY0, lsst.geom.ExtentI(256, 256), 

79 afwImage.LOCAL)) 

80 self.mi.setXY0(lsst.geom.PointI(0, 0)) 

81 else: 

82 self.nCR = None 

83 

84 self.mi.getMask().addMaskPlane("DETECTED") 

85 

86 def tearDown(self): 

87 del self.mi 

88 del self.psf 

89 

90 @unittest.skipUnless(imageFile0, "afwdata not available") 

91 def testDetection(self): 

92 """Test CR detection.""" 

93 # 

94 # Subtract background 

95 # 

96 bctrl = afwMath.BackgroundControl(afwMath.Interpolate.NATURAL_SPLINE) 

97 bctrl.setNxSample(int(self.mi.getWidth()/256) + 1) 

98 bctrl.setNySample(int(self.mi.getHeight()/256) + 1) 

99 bctrl.getStatisticsControl().setNumSigmaClip(3.0) 

100 bctrl.getStatisticsControl().setNumIter(2) 

101 

102 im = self.mi.getImage() 

103 try: 

104 backobj = afwMath.makeBackground(im, bctrl) 

105 except Exception as e: 

106 print(e, file=sys.stderr) 

107 

108 bctrl.setInterpStyle(afwMath.Interpolate.CONSTANT) 

109 backobj = afwMath.makeBackground(im, bctrl) 

110 

111 im -= backobj.getImageF() 

112 

113 if display: 

114 frame = 0 

115 disp = afwDisplay.Display(frame=frame) 

116 disp.mtv(self.mi, title=self._testMethodName + ": Raw") # raw frame 

117 if self.mi.getWidth() > 256: 

118 disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0()) 

119 # 

120 # Mask known bad pixels 

121 # 

122 measAlgorithmsDir = lsst.utils.getPackageDir('meas_algorithms') 

123 badPixels = algorithms.Defects.readText(os.path.join(measAlgorithmsDir, 

124 "policy", "BadPixels.ecsv")) 

125 # did someone lie about the origin of the maskedImage? If so, adjust bad pixel list 

126 if self.XY0.getX() != self.mi.getX0() or self.XY0.getY() != self.mi.getY0(): 

127 dx = self.XY0.getX() - self.mi.getX0() 

128 dy = self.XY0.getY() - self.mi.getY0() 

129 for bp in badPixels: 

130 bp.shift(-dx, -dy) 

131 

132 algorithms.interpolateOverDefects(self.mi, self.psf, badPixels) 

133 

134 stats = afwMath.makeStatistics(self.mi.getImage(), afwMath.MEANCLIP | afwMath.STDEVCLIP) 

135 background = stats.getValue(afwMath.MEANCLIP) 

136 

137 crConfig = algorithms.FindCosmicRaysConfig() 

138 crs = algorithms.findCosmicRays(self.mi, self.psf, background, pexConfig.makePropertySet(crConfig)) 

139 

140 # Run again using makePolicy and check for warning 

141 with self.assertWarns(FutureWarning): 

142 algorithms.findCosmicRays(self.mi, self.psf, background, pexConfig.makePolicy(crConfig)) 

143 

144 if display: 

145 frame += 1 

146 disp = afwDisplay.Display(frame=frame) 

147 disp.mtv(self.mi, title=self._testMethodName + ": CRs removed") 

148 if self.mi.getWidth() > 256: 

149 disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0()) 

150 

151 print("Detected %d CRs" % len(crs)) 

152 if display and False: 

153 for cr in crs: 

154 bbox = cr.getBBox() 

155 bbox.shift(lsst.geom.ExtentI(-self.mi.getX0(), -self.mi.getY0())) 

156 disp.line([(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5), 

157 (bbox.getMaxX() + 0.5, bbox.getMinY() - 0.5), 

158 (bbox.getMaxX() + 0.5, bbox.getMaxY() + 0.5), 

159 (bbox.getMinX() - 0.5, bbox.getMaxY() + 0.5), 

160 (bbox.getMinX() - 0.5, bbox.getMinY() - 0.5)]) 

161 

162 if self.nCR is not None: 

163 self.assertEqual(len(crs), self.nCR) 

164 

165 

166class CosmicRayNullTestCase(unittest.TestCase): 

167 """A test case for no Cosmic Ray detection.""" 

168 

169 def setUp(self): 

170 self.FWHM = 5 # pixels 

171 self.size = 128 

172 

173 self.psf = algorithms.DoubleGaussianPsf(29, 29, self.FWHM/(2*math.sqrt(2*math.log(2)))) 

174 self.mi = afwImage.MaskedImageF(128, 128) 

175 self.mi.set((0, 0, 1)) 

176 

177 def tearDown(self): 

178 del self.psf 

179 del self.mi 

180 

181 def testDetection(self): 

182 crConfig = algorithms.FindCosmicRaysConfig() 

183 crs = algorithms.findCosmicRays(self.mi, self.psf, 0.0, pexConfig.makePropertySet(crConfig)) 

184 self.assertEqual(len(crs), 0, "Found %d CRs in empty image" % len(crs)) 

185 

186 

187class TestMemory(lsst.utils.tests.MemoryTestCase): 

188 pass 

189 

190 

191def setup_module(module): 

192 lsst.utils.tests.init() 

193 

194 

195if __name__ == "__main__": 195 ↛ 196line 195 didn't jump to line 196, because the condition on line 195 was never true

196 lsst.utils.tests.init() 

197 unittest.main()