1#!/usr/bin/env python 

2# coding=utf-8 

3 

4"""REFUGE for Optic Disc and Cup Segmentation 

5 

6The dataset consists of 1200 color fundus photographs, created for a MICCAI 

7challenge. The goal of the challenge is to evaluate and compare automated 

8algorithms for glaucoma detection and optic disc/cup segmentation on a common 

9dataset of retinal fundus images. 

10 

11* Reference (including train/dev/test split): [REFUGE-2018]_ 

12* Protocols ``optic-disc`` and ``cup``: 

13 

14 * Training samples: 

15 

16 * 400 

17 * includes optic-disc and cup labels 

18 * includes label: glaucomatous and non-glaucomatous 

19 * original resolution: 2056 x 2124 

20 

21 * Validation samples: 

22 

23 * 400 

24 * includes optic-disc and cup labels 

25 * original resolution: 1634 x 1634 

26 

27 * Test samples: 

28 

29 * 400 

30 * includes optic-disc and cup labels 

31 * includes label: glaucomatous and non-glaucomatous 

32 * original resolution: 

33""" 

34 

35import os 

36 

37import pkg_resources 

38 

39import bob.extension 

40 

41from ..dataset import JSONDataset 

42from ..loader import load_pil_1, load_pil_rgb, make_delayed 

43 

44_protocols = { 

45 "optic-disc": pkg_resources.resource_filename(__name__, "default.json"), 

46 "optic-cup": pkg_resources.resource_filename(__name__, "default.json"), 

47} 

48 

49_root_path = bob.extension.rc.get( 

50 "bob.ip.binseg.refuge.datadir", os.path.realpath(os.curdir) 

51) 

52_pkg_path = pkg_resources.resource_filename(__name__, "masks") 

53 

54 

55def _disc_loader(sample): 

56 retval = dict( 

57 data=load_pil_rgb(os.path.join(_root_path, sample["data"])), 

58 label=load_pil_rgb(os.path.join(_root_path, sample["label"])), 

59 mask=load_pil_1(os.path.join(_pkg_path, sample["mask"])), 

60 ) 

61 if "glaucoma" in sample: 

62 retval["glaucoma"] = sample["glaucoma"] 

63 retval["label"] = retval["label"].convert("L") 

64 retval["label"] = retval["label"].point(lambda p: p <= 150, mode="1") 

65 return retval 

66 

67 

68def _cup_loader(sample): 

69 retval = dict( 

70 data=load_pil_rgb(os.path.join(_root_path, sample["data"])), 

71 label=load_pil_rgb(os.path.join(_root_path, sample["label"])), 

72 mask=load_pil_1(os.path.join(_pkg_path, sample["mask"])), 

73 ) 

74 if "glaucoma" in sample: 

75 retval["glaucoma"] = sample["glaucoma"] 

76 retval["label"] = retval["label"].convert("L") 

77 retval["label"] = retval["label"].point(lambda p: p <= 100, mode="1") 

78 return retval 

79 

80 

81def _loader(context, sample): 

82 

83 if context["subset"] == "train": 

84 # adds binary metadata for glaucoma/non-glaucoma patients 

85 sample["glaucoma"] = os.path.basename(sample["label"]).startswith("g") 

86 elif context["subset"] == "test": 

87 sample["glaucoma"] = sample["label"].split(os.sep)[-2] == "G" 

88 elif context["subset"] == "validation": 

89 pass 

90 else: 

91 raise RuntimeError(f"Unknown subset {context['subset']}") 

92 

93 # optic disc is drawn with gray == 128 and includes the cup, drawn with 

94 # black == 0. The rest is white == 255. 

95 if context["protocol"] == "optic-disc": 

96 return make_delayed(sample, _disc_loader) 

97 elif context["protocol"] == "optic-cup": 

98 return make_delayed(sample, _cup_loader) 

99 else: 

100 raise RuntimeError(f"Unknown protocol {context['protocol']}") 

101 

102 

103dataset = JSONDataset( 

104 protocols=_protocols, 

105 fieldnames=("data", "label", "mask"), 

106 loader=_loader, 

107) 

108"""REFUGE dataset object"""