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"""Read TIFF from FEI SEM microscopes. |
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Backend Library: internal |
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This format is based on :mod:`TIFF <imageio.plugins.tifffile>`, and supports the |
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same parameters. FEI microscopes append metadata as ASCII text at the end of the |
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file, which this reader correctly extracts. |
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Parameters |
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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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See Also |
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-------- |
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:mod:`imageio.plugins.tifffile` |
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""" |
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from .tifffile import TiffFormat |
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class FEISEMFormat(TiffFormat): |
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"""See :mod:`imageio.plugins.feisem`""" |
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def _can_write(self, request): |
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return False |
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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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if hasattr(self, "_fei_meta"): |
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return self._fei_meta |
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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: |
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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._fei_meta = md |
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return md |
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