Coverage for src/deepdraw/data/montgomery/__init__.py: 94%

1# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch> 

2# 

3# SPDX-License-Identifier: GPL-3.0-or-later 

4 

5"""Montgomery County dataset for Lung Segmentation. 

6 

7The database includes 58 cases with manifestation of tuberculosis, and 80 

8normal cases. It contains a total of 138 resolution of 4020 x 4892, or 

94892 x 4020. One set of ground-truth lung annotations is available. 

10 

11* Reference: [MC-2014]_ 

12* Original resolution (height x width): 4020 x 4892, or 4892 x 4020 

13* Configuration resolution: 512 x 512 (after rescaling) 

14* Split reference: [GAAL-2020]_ 

15* Protocol ``default``: 

16 

17 * Training samples: 96 (including labels) 

18 * Validation samples: 14 (including labels) 

19 * Test samples: 28 (including labels) 

20""" 

21 

22import os 

23 

24import numpy as np 

25import pkg_resources 

26 

27from PIL import Image 

28 

29from ...data.dataset import JSONDataset 

30from ...utils.rc import load_rc 

31from ..loader import load_pil_1, load_pil_rgb, make_delayed 

32 

33_protocols = [ 

34 pkg_resources.resource_filename(__name__, "default.json"), 

35] 

36 

37_root_path = load_rc().get("datadir.montgomery", os.path.realpath(os.curdir)) 

38 

39 

40def _raw_data_loader(sample): 

41 return dict( 

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

43 label=Image.fromarray( 

44 np.ma.mask_or( 

45 np.asarray( 

46 load_pil_1(os.path.join(_root_path, sample["label_l"])) 

47 ), 

48 np.asarray( 

49 load_pil_1(os.path.join(_root_path, sample["label_r"])) 

50 ), 

51 ) 

52 ), 

53 ) 

54 

55 

56def _loader(context, sample): 

57 # "context" is ignored in this case - database is homogeneous 

58 # we returned delayed samples to avoid loading all images at once 

59 return make_delayed(sample, _raw_data_loader) 

60 

61 

62dataset = JSONDataset( 

63 protocols=_protocols, 

64 fieldnames=("data", "label_l", "label_r"), 

65 loader=_loader, 

66) 

67 

68"""Montgomery County dataset object"""