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