this will be useful to bypass tifffile / tiffslide on images that raise an error (traceback below). i am not sure why this error is being raised...
Traceback (most recent call last):
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/wsinfer/patchlib/__init__.py", line 357, in segment_and_patch_directory_of_slides
segment_and_patch_one_slide(
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/wsinfer/patchlib/__init__.py", line 106, in segment_and_patch_one_slide
mpp = get_avg_mpp(slide_path)
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/wsinfer/wsi.py", line 217, in get_avg_mpp
mppx, mppy = _get_mpp_tiffslide(slide_path)
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/wsinfer/wsi.py", line 145, in _get_mpp_tiffslide
tiffslide.PROPERTY_NAME_MPP_X in slide.properties
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/functools.py", line 981, in __get__
val = self.func(instance)
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/tiffslide/tiffslide.py", line 233, in properties
return _PropertyParser(self._tifffile).parse()
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/tiffslide/tiffslide.py", line 750, in parse
return getattr(self, f"parse_{fmt}")() # type: ignore
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/tiffslide/tiffslide.py", line 836, in parse_generic_tiff
series0 = self._tf.series[0]
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/functools.py", line 981, in __get__
val = self.func(instance)
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/tifffile/tifffile.py", line 4444, in series
series = getattr(self, '_series_' + kind)()
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/tifffile/tifffile.py", line 4814, in _series_imagej
page_list = pages[:]
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/tifffile/tifffile.py", line 7613, in __getitem__
return [getitem(i) for i in range(*key.indices(len(pages)))]
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/tifffile/tifffile.py", line 7613, in <listcomp>
return [getitem(i) for i in range(*key.indices(len(pages)))]
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/tifffile/tifffile.py", line 7579, in _getitem
page = tiffpage(self.parent, index=pageindex, keyframe=self._keyframe)
File "/home/jkaczmar/mambaforge/envs/wsinfer/lib/python3.10/site-packages/tifffile/tifffile.py", line 10247, in __init__
raise RuntimeError('incompatible keyframe')
RuntimeError: incompatible keyframe
this will be useful to bypass tifffile / tiffslide on images that raise an error (traceback below). i am not sure why this error is being raised...