Coverage for /scratch/builds/bob/bob.ip.binseg/miniconda/conda-bld/bob.ip.binseg_1673966692152/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.10/site-packages/bob/ip/common/test/test_refuge.py: 47%

1#!/usr/bin/env python 

2# coding=utf-8 

3 

4 

5"""Tests for REFUGE""" 

6 

7import numpy 

8import pytest 

9 

10from ...binseg.data.refuge import dataset 

11from .utils import count_bw 

12 

13 

14def test_protocol_consistency(): 

15 

16 for protocol in ("optic-disc", "optic-cup"): 

17 

18 subset = dataset.subsets(protocol) 

19 assert len(subset) == 3 

20 

21 assert "train" in subset 

22 assert len(subset["train"]) == 400 

23 for s in subset["train"]: 

24 assert s.key.startswith("Training400") 

25 

26 assert "validation" in subset 

27 assert len(subset["validation"]) == 400 

28 for s in subset["validation"]: 

29 assert s.key.startswith("REFUGE-Validation400") 

30 

31 assert "test" in subset 

32 assert len(subset["test"]) == 400 

33 for s in subset["test"]: 

34 assert s.key.startswith("Test400") 

35 

36 

37@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.refuge.datadir") 

38@pytest.mark.slow 

39def test_loading(): 

40 def _check_sample( 

41 s, image_size, glaucoma_label, entries, bw_threshold_label 

42 ): 

43 

44 data = s.data 

45 assert isinstance(data, dict) 

46 assert len(data) == entries 

47 

48 assert "data" in data 

49 assert data["data"].size == image_size 

50 assert data["data"].mode == "RGB" 

51 

52 assert "label" in data 

53 assert data["label"].size == image_size 

54 assert data["label"].mode == "1" 

55 b, w = count_bw(data["label"]) 

56 assert (b + w) == numpy.prod(image_size), ( 

57 f"Counts of black + white ({b}+{w}) do not add up to total " 

58 f"image size ({numpy.prod(image_size)}) at '{s.key}':label" 

59 ) 

60 assert (w / b) < bw_threshold_label, ( 

61 f"The proportion between black and white pixels " 

62 f"({w}/{b}={w/b:.3f}) is larger than the allowed threshold " 

63 f"of {bw_threshold_label} at '{s.key}':label - this could " 

64 f"indicate a loading problem!" 

65 ) 

66 

67 assert "mask" in data 

68 assert data["mask"].size == image_size 

69 assert data["mask"].mode == "1" 

70 

71 if glaucoma_label: 

72 assert "glaucoma" in data 

73 

74 # to visualize images, uncomment the folowing code 

75 # it should display an image with a faded background representing the 

76 # original data, blended with green labels. 

77 # from ..data.utils import overlayed_image 

78 # display = overlayed_image(data["data"], data["label"]) 

79 # display.show() 

80 # import ipdb; ipdb.set_trace() 

81 

82 return w / b 

83 

84 limit = None # use this to limit testing to first images only 

85 subset = dataset.subsets("optic-disc") 

86 proportions = [ 

87 _check_sample(s, (2124, 2056), True, 4, 0.029) 

88 for s in subset["train"][:limit] 

89 ] 

90 # print(f"max label proportions = {max(proportions)}") 

91 proportions = [ 

92 _check_sample(s, (1634, 1634), False, 3, 0.043) 

93 for s in subset["validation"][:limit] 

94 ] 

95 # print(f"max label proportions = {max(proportions)}") 

96 proportions = [ 

97 _check_sample(s, (1634, 1634), True, 4, 0.026) 

98 for s in subset["test"][:limit] 

99 ] 

100 # print(f"max label proportions = {max(proportions)}") 

101 

102 subset = dataset.subsets("optic-cup") 

103 proportions = [ 

104 _check_sample(s, (2124, 2056), True, 4, 0.018) 

105 for s in subset["train"][:limit] 

106 ] 

107 # print(f"max label proportions = {max(proportions)}") 

108 proportions = [ 

109 _check_sample(s, (1634, 1634), False, 3, 0.030) 

110 for s in subset["validation"][:limit] 

111 ] 

112 # print(f"max label proportions = {max(proportions)}") 

113 proportions = [ 

114 _check_sample(s, (1634, 1634), True, 4, 0.017) 

115 for s in subset["test"][:limit] 

116 ] 

117 # print(f"max label proportions = {max(proportions)}") 

118 del proportions # only to satisfy flake8 

119 

120 

121@pytest.mark.skip_if_rc_var_not_set("bob.ip.binseg.refuge.datadir") 

122@pytest.mark.slow 

123def test_check(): 

124 assert dataset.check() == 0