Autoscope2 produces corrupt files

[Charles-Fieseler-Vienna]

@LukasMicroscopy and @Itamar-Lev give a real description

[Charles-Fieseler-Vienna]

Traceback (most recent call last):
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 7807, in init
raise ValueError(f'suspicious number of tags {tagno}')
ValueError: suspicious number of tags 41376

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/charles/.config/JetBrains/PyCharmCE2024.1/scratches/scratch_7.py", line 8, in
print(tif.series, tif.pages)
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/functools.py", line 967, in get
val = self.func(instance)
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 4434, in series
if getattr(self, 'is_' + kind, False):
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/functools.py", line 967, in get
val = self.func(instance)
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 6638, in is_mdgel
or self.pages.get(1, cache=True).is_mdgel
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 7285, in get
return self._getitem(
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 7570, in _getitem
page = tiffpage(self.parent, index=pageindex, keyframe=self._keyframe)
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 7809, in init
raise TiffFileError(
tifffile.tifffile.TiffFileError: corrupted tag list at offset 589824

[Charles-Fieseler-Vienna]

Crashed even on print(tif.series, tif.pages), not even opening the full numpy

[Charles-Fieseler-Vienna]

Also crashes when using the MicroscopeDataReader:

2024-11-21 10:58:02.899 | INFO | imutils.scopereader.microscope_data_reader:_read_raw_tifffile:189 - Reading data from /lisc/scratch/neurobiology/zimmer/brenner/behavior/10052024/data/2024-05-10_10-44_gcy9_gcy31_gcy35_worm1_Ch0 with tifffile
Traceback (most recent call last):
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 7807, in init
raise ValueError(f'suspicious number of tags {tagno}')
ValueError: suspicious number of tags 41893

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/charles/.config/JetBrains/PyCharmCE2024.1/scratches/scratch_7.py", line 8, in
obj = MicroscopeDataReader(fname, as_raw_tiff=True)
File "/home/charles/PycharmProjects/imutils/imutils/scopereader/microscope_data_reader.py", line 54, in init
self._read_raw_tifffile()
File "/home/charles/PycharmProjects/imutils/imutils/scopereader/microscope_data_reader.py", line 193, in _read_raw_tifffile
dask_array = dask.array.from_zarr(self.data_store.aszarr())
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 4380, in aszarr
return self.series[0].aszarr(level=level, **kwargs)
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/functools.py", line 967, in get
val = self.func(instance)
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 4434, in series
if getattr(self, 'is' + kind, False):
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/functools.py", line 967, in get
val = self.func(instance)
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 6638, in is_mdgel
or self.pages.get(1, cache=True).is_mdgel
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 7285, in get
return self._getitem(
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 7570, in _getitem
page = tiffpage(self.parent, index=pageindex, keyframe=self._keyframe)
File "/home/charles/anaconda3/envs/wbfm38/lib/python3.8/site-packages/tifffile/tifffile.py", line 7809, in init
raise TiffFileError(
tifffile.tifffile.TiffFileError: corrupted tag list at offset 589824