96 lines
3.3 KiB
Python
96 lines
3.3 KiB
Python
|
# -*- coding: utf-8 -*-
|
||
|
|
# imageio is distributed under the terms of the (new) BSD License.
|
||
|
|
|
||
|
|
"""Read TIFF from FEI SEM microscopes.
|
||
|
|
|
||
|
|
Backend Library: internal
|
||
|
|
|
||
|
|
This format is based on :mod:`TIFF <imageio.plugins.tifffile>`, and supports the
|
||
|
|
same parameters. FEI microscopes append metadata as ASCII text at the end of the
|
||
|
|
file, which this reader correctly extracts.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
discard_watermark : bool
|
||
|
|
If True (default), discard the bottom rows of the image, which
|
||
|
|
contain no image data, only a watermark with metadata.
|
||
|
|
watermark_height : int
|
||
|
|
The height in pixels of the FEI watermark. The default is 70.
|
||
|
|
|
||
|
|
See Also
|
||
|
|
--------
|
||
|
|
:mod:`imageio.plugins.tifffile`
|
||
|
|
|
||
|
|
"""
|
||
|
|
|
||
|
|
|
||
|
|
from .tifffile import TiffFormat
|
||
|
|
|
||
|
|
|
||
|
|
class FEISEMFormat(TiffFormat):
|
||
|
|
"""See :mod:`imageio.plugins.feisem`"""
|
||
|
|
|
||
|
|
def _can_write(self, request):
|
||
|
|
return False # FEI-SEM only supports reading
|
||
|
|
|
||
|
|
class Reader(TiffFormat.Reader):
|
||
|
|
def _get_data(self, index=0, discard_watermark=True, watermark_height=70):
|
||
|
|
"""Get image and metadata from given index.
|
||
|
|
|
||
|
|
FEI images usually (always?) contain a watermark at the
|
||
|
|
bottom of the image, 70 pixels high. We discard this by
|
||
|
|
default as it does not contain any information not present
|
||
|
|
in the metadata.
|
||
|
|
"""
|
||
|
|
im, meta = super(FEISEMFormat.Reader, self)._get_data(index)
|
||
|
|
if discard_watermark:
|
||
|
|
im = im[:-watermark_height]
|
||
|
|
return im, meta
|
||
|
|
|
||
|
|
def _get_meta_data(self, index=None):
|
||
|
|
"""Read the metadata from an FEI SEM TIFF.
|
||
|
|
|
||
|
|
This metadata is included as ASCII text at the end of the file.
|
||
|
|
|
||
|
|
The index, if provided, is ignored.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
metadata : dict
|
||
|
|
Dictionary of metadata.
|
||
|
|
"""
|
||
|
|
if hasattr(self, "_fei_meta"):
|
||
|
|
return self._fei_meta
|
||
|
|
|
||
|
|
md = {"root": {}}
|
||
|
|
current_tag = "root"
|
||
|
|
reading_metadata = False
|
||
|
|
filename = self.request.get_local_filename()
|
||
|
|
with open(filename, encoding="utf8", errors="ignore") as fin:
|
||
|
|
for line in fin:
|
||
|
|
if not reading_metadata:
|
||
|
|
if not line.startswith("Date="):
|
||
|
|
continue
|
||
|
|
else:
|
||
|
|
reading_metadata = True
|
||
|
|
line = line.rstrip()
|
||
|
|
if line.startswith("["):
|
||
|
|
current_tag = line.lstrip("[").rstrip("]")
|
||
|
|
md[current_tag] = {}
|
||
|
|
else:
|
||
|
|
if "=" in line: # ignore empty and irrelevant lines
|
||
|
|
key, val = line.split("=", maxsplit=1)
|
||
|
|
for tag_type in (int, float):
|
||
|
|
try:
|
||
|
|
val = tag_type(val)
|
||
|
|
except ValueError:
|
||
|
|
continue
|
||
|
|
else:
|
||
|
|
break
|
||
|
|
md[current_tag][key] = val
|
||
|
|
if not md["root"] and len(md) == 1:
|
||
|
|
raise ValueError("Input file %s contains no FEI metadata." % filename)
|
||
|
|
|
||
|
|
self._fei_meta = md
|
||
|
|
return md
|