Coverage for src/deepdraw/data/jsrt/__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"""Japanese Society of Radiological Technology dataset for Lung Segmentation. 

6 

7The database includes 154 nodule and 93 non-nodule images. It contains a total 

8of 247 resolution of 2048 x 2048. One set of ground-truth lung annotations is 

9available. 

10 

11* Reference: [JSRT-2000]_ 

12* Original resolution (height x width): 2048 x 2048 

13* Configuration resolution: 1024 x 1024 (after rescaling) 

14* Split reference: [GAAL-2020]_ 

15* Protocol ``default``: 

16 

17 * Training samples: 172 (including labels) 

18 * Validation samples: 25 (including labels) 

19 * Test samples: 50 (including labels) 

20""" 

21 

22import os 

23 

24import numpy 

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_raw_12bit_jsrt, make_delayed 

32 

33_protocols = [ 

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

35] 

36 

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

38 

39 

40def _raw_data_loader(sample): 

41 return dict( 

42 data=load_pil_raw_12bit_jsrt( 

43 os.path.join(_root_path, sample["data"]), 1024 

44 ), 

45 label=Image.fromarray( 

46 numpy.ma.mask_or( 

47 numpy.asarray( 

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

49 ), 

50 numpy.asarray( 

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

52 ), 

53 ) 

54 ), 

55 ) 

56 

57 

58def _loader(context, sample): 

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

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

61 return make_delayed(sample, _raw_data_loader) 

62 

63 

64dataset = JSONDataset( 

65 protocols=_protocols, 

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

67 loader=_loader, 

68) 

69"""Japanese Society of Radiological Technology dataset object."""