Coverage for tests/test_readTextCatalog.py: 25%

1# 

2# LSST Data Management System 

3# 

4# Copyright 2008-2016 AURA/LSST. 

5# 

6# This product includes software developed by the 

7# LSST Project (http://www.lsst.org/). 

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 LSST License Statement and 

20# the GNU General Public License along with this program. If not, 

21# see <https://www.lsstcorp.org/LegalNotices/>. 

22# 

23 

24import os 

25import unittest 

26 

27import numpy as np 

28 

29from lsst.meas.algorithms.readTextCatalogTask import ReadTextCatalogTask 

30import lsst.utils.tests 

31 

32# If you want to update the FITS table used for this test: 

33# - modify makeFitsTable to create the table as you want it 

34# - set SaveTextCatalog = True 

35# - sun the test once to create the new file 

36# - set SaveTextCatalog = False again 

37SaveTextCatalog = False # construct and save a new text table file? 

38TestDir = os.path.dirname(__file__) 

39TextPath = os.path.join(TestDir, "data", "testReadTextCatalog.csv") 

40 

41 

42def makeCatalog(): 

43 """Create an object catalog as a numpy structured array 

44 

45 dtypes are chosen to match how the data is read back in, for ease in testing 

46 Including a '£' in demonstates that we can round-trip UTF-8 rather than 

47 being limited to ASCII. 

48 """ 

49 dtype = [("name", "U8"), ("ra", "float64"), ("dec", "float64"), 

50 ("counts", "int64"), ("flux", "float64"), ("resolved", "int64")] 

51 data = [ 

52 ("£object1", -5, 10, 1000, 1.1, True), 

53 ("£object2", 45, 5, 2000, 1.2, False), 

54 ] 

55 return np.array(data, dtype=dtype) 

56 

57 

58if SaveTextCatalog: 58 ↛ 59line 58 didn't jump to line 59, because the condition on line 58 was never true

59 print("Warning: writing a new text catalog file; to stop this set SaveTextCatalog = False") 

60 arr = makeCatalog() 

61 with open(TextPath, "w") as f: 

62 f.write(", ".join(arr.dtype.names)) 

63 f.write("\n") 

64 for row in arr: 

65 f.write(", ".join(str(val) for val in row)) 

66 f.write("\n") 

67 

68 

69class ReadTextCatalogTaskTestCase(lsst.utils.tests.TestCase): 

70 """Test ReadTextCatalogTask""" 

71 

72 def setUp(self): 

73 self.arr = makeCatalog() 

74 

75 def testDefaultNames(self): 

76 """Test reading without renaming 

77 """ 

78 task = ReadTextCatalogTask() 

79 arr = task.run(TextPath) 

80 self.assertTrue(np.array_equal(arr, self.arr)) 

81 self.assertEqual(len(arr), 2) 

82 

83 def testGivenNames(self): 

84 """Test reading with column names in the config 

85 """ 

86 colnames = ("id", "ra_deg", "dec_deg", "total_counts", "total_flux", "is_resolved") 

87 config = ReadTextCatalogTask.ConfigClass() 

88 config.colnames = colnames 

89 config.header_lines = 1 

90 task = ReadTextCatalogTask(config=config) 

91 arr = task.run(TextPath) 

92 self.assertEqual(arr.dtype.names, colnames) 

93 self.assertEqual(len(arr), 2) 

94 for inname, outname in zip(self.arr.dtype.names, colnames): 

95 self.assertTrue(np.array_equal(self.arr[inname], arr[outname])) 

96 

97 def testBadPath(self): 

98 """Test that an invalid path causes an error""" 

99 task = ReadTextCatalogTask() 

100 badPath = "does/not/exists.garbage" 

101 with self.assertRaises(IOError): 

102 task.run(badPath) 

103 

104 def testTooFewColumnNames(self): 

105 """Test that too few names in config.colnames causes an error""" 

106 config = ReadTextCatalogTask.ConfigClass() 

107 for badColNames in ( 

108 ["name", "ra", "dec", "counts", "flux"], 

109 ["name"], 

110 ): 

111 config.colnames = badColNames 

112 config.header_lines = 1 

113 task = ReadTextCatalogTask(config=config) 

114 with self.assertRaises(ValueError): 

115 task.run(TextPath) 

116 

117 def testNullValues(self): 

118 """Test that missing values designated by a string are converted to 

119 zeros and that their column has the appropriate data type.""" 

120 config = ReadTextCatalogTask.ConfigClass() 

121 config.fill_values = ['null', '0'] 

122 config.replace_missing_floats_with_nan = True 

123 task = ReadTextCatalogTask(config=config) 

124 nullValuesFile = os.path.join(TestDir, "data", "testReadTextCatalog_nullValues.csv") 

125 arr = task.run(nullValuesFile) 

126 dtype = [("name", "U7"), ("ra", "float64"), ("dec", "float64"), 

127 ("counts", "int64"), ("flux", "float64"), ("resolved", "int64")] 

128 

129 for (name, dt) in dtype: 

130 self.assertEqual(dt, arr.dtype[name]) 

131 

132 self.assertTrue(np.isnan(arr['flux'][1])) 

133 self.assertEqual(arr['resolved'][1], 0) 

134 

135 

136class TestMemory(lsst.utils.tests.MemoryTestCase): 

137 pass 

138 

139 

140def setup_module(module): 

141 lsst.utils.tests.init() 

142 

143 

144if __name__ == "__main__": 144 ↛ 145line 144 didn't jump to line 145, because the condition on line 144 was never true

145 lsst.utils.tests.init() 

146 unittest.main()