Coverage for /pythoncovmergedfiles/medio/medio/usr/local/lib/python3.8/site-packages/imageio-2.35.1-py3.8.egg/imageio/plugins/feisem.py: 17%

1# -*- coding: utf-8 -*- 

2# imageio is distributed under the terms of the (new) BSD License. 

3 

4"""Read TIFF from FEI SEM microscopes. 

5 

6Backend Library: internal 

7 

8This format is based on :mod:`TIFF <imageio.plugins.tifffile>`, and supports the 

9same parameters. FEI microscopes append metadata as ASCII text at the end of the 

10file, which this reader correctly extracts. 

11 

12Parameters 

13---------- 

14discard_watermark : bool 

15 If True (default), discard the bottom rows of the image, which 

16 contain no image data, only a watermark with metadata. 

17watermark_height : int 

18 The height in pixels of the FEI watermark. The default is 70. 

19 

20See Also 

21-------- 

22 :mod:`imageio.plugins.tifffile` 

23 

24""" 

25 

26 

27from .tifffile import TiffFormat 

28 

29 

30class FEISEMFormat(TiffFormat): 

31 """See :mod:`imageio.plugins.feisem`""" 

32 

33 def _can_write(self, request): 

34 return False # FEI-SEM only supports reading 

35 

36 class Reader(TiffFormat.Reader): 

37 def _get_data(self, index=0, discard_watermark=True, watermark_height=70): 

38 """Get image and metadata from given index. 

39 

40 FEI images usually (always?) contain a watermark at the 

41 bottom of the image, 70 pixels high. We discard this by 

42 default as it does not contain any information not present 

43 in the metadata. 

44 """ 

45 im, meta = super(FEISEMFormat.Reader, self)._get_data(index) 

46 if discard_watermark: 

47 im = im[:-watermark_height] 

48 return im, meta 

49 

50 def _get_meta_data(self, index=None): 

51 """Read the metadata from an FEI SEM TIFF. 

52 

53 This metadata is included as ASCII text at the end of the file. 

54 

55 The index, if provided, is ignored. 

56 

57 Returns 

58 ------- 

59 metadata : dict 

60 Dictionary of metadata. 

61 """ 

62 if hasattr(self, "_fei_meta"): 

63 return self._fei_meta 

64 

65 md = {"root": {}} 

66 current_tag = "root" 

67 reading_metadata = False 

68 filename = self.request.get_local_filename() 

69 with open(filename, encoding="utf8", errors="ignore") as fin: 

70 for line in fin: 

71 if not reading_metadata: 

72 if not line.startswith("Date="): 

73 continue 

74 else: 

75 reading_metadata = True 

76 line = line.rstrip() 

77 if line.startswith("["): 

78 current_tag = line.lstrip("[").rstrip("]") 

79 md[current_tag] = {} 

80 else: 

81 if "=" in line: # ignore empty and irrelevant lines 

82 key, val = line.split("=", maxsplit=1) 

83 for tag_type in (int, float): 

84 try: 

85 val = tag_type(val) 

86 except ValueError: 

87 continue 

88 else: 

89 break 

90 md[current_tag][key] = val 

91 if not md["root"] and len(md) == 1: 

92 raise ValueError("Input file %s contains no FEI metadata." % filename) 

93 

94 self._fei_meta = md 

95 return md