AlbertDominguez
commented
4 months ago Hi! Hmm... I just tried it in some images of mine and it does work (although the filesystem is not mounted through sftp). The loading is done by another lib (skimage), which in turn resorts to another library (tifffile) to load TIFs, so I don't think it's an issue on our end. How many TIF files do you have in the directory? Could be that one of the files is corrupt and that's why it breaks (and by chance is not the one you are trying). In case you haven't checked all of them, you can try to load them with the following code (in a Python console or as a script, please change the img_dir variable so that it is the directory containing your images!):
from itertools import chain
from pathlib import Path
from skimage.io import imread
ALLOWED_EXTENSIONS = ("tif", "tiff", "png", "jpg", "jpeg")
img_dir = Path("/YOUR/DATA/DIRECTORY/HERE")
image_files = sorted(
tuple(chain(*tuple(img_dir.glob(f"*.{ext}") for ext in ALLOWED_EXTENSIONS)))
)
assert len(image_files) > 0, "No images found in the given folder"
for fname in image_files:
try:
imread(fname)
except Exception as e:
print(f"Could not load image {fname}")
raise e
print("All files read OK!")it should print the filename that's not loading before raising the error, if there is one. If that's the case, then one of the files might be corrupt, or there might be some issue with the SFTP mount. Can you double check that? If all files can be normally loaded, then we can look deeper...
lfra
Dear spotiflow-team, I encounter an error when running spotiflow-predict from the terminal on a folder with TIF files that is located on a remote storage location. The odd thing is when I run spotiflow-predict on a single TIF within that same folder, it works without issues.
Specific example spotiflow-predict /path/to/folder/myfile.tif >> works
spotiflow-predict /path/to/folder >> fails (error message below)
INFO:spotiflow.cli.predict:Spotiflow - version 0.3.2 INFO:spotiflow.model.spotiflow:Loading pretrained model general Traceback (most recent call last): File "/Users/l.m.frank-2/opt/miniconda3/envs/spotiflow/lib/python3.9/site-packages/tifffile/tifffile.py", line 4261, in init byteorder = {b'II': '<', b'MM': '>', b'EP': '<'}[header[:2]] KeyError: b'\x00\x05'
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/Users/l.m.frank-2/opt/miniconda3/envs/spotiflow/bin/spotiflow-predict", line 8, in
sys.exit(main())
File "/Users/l.m.frank-2/opt/miniconda3/envs/spotiflow/lib/python3.9/site-packages/spotiflow/cli/predict.py", line 62, in main
images = [imread(img) for img in image_files]
File "/Users/l.m.frank-2/opt/miniconda3/envs/spotiflow/lib/python3.9/site-packages/spotiflow/cli/predict.py", line 62, in
images = [imread(img) for img in image_files]
File "/Users/l.m.frank-2/opt/miniconda3/envs/spotiflow/lib/python3.9/site-packages/skimage/io/_io.py", line 60, in imread
img = call_plugin('imread', fname, plugin=plugin, *plugin_args)
File "/Users/l.m.frank-2/opt/miniconda3/envs/spotiflow/lib/python3.9/site-packages/skimage/io/manage_plugins.py", line 217, in call_plugin
return func(args, kwargs)
File "/Users/l.m.frank-2/opt/miniconda3/envs/spotiflow/lib/python3.9/site-packages/skimage/io/_plugins/tifffile_plugin.py", line 74, in imread
return tifffile_imread(fname, kwargs)
File "/Users/l.m.frank-2/opt/miniconda3/envs/spotiflow/lib/python3.9/site-packages/tifffile/tifffile.py", line 1239, in imread
with TiffFile(
File "/Users/l.m.frank-2/opt/miniconda3/envs/spotiflow/lib/python3.9/site-packages/tifffile/tifffile.py", line 4263, in init
raise TiffFileError(f'not a TIFF file {header!r}') from exc
tifffile.tifffile.TiffFileError: not a TIFF file b'\x00\x05\x16\x07'
I already tried to see if the TIF files have a strange header/format, but everything seems alright (checked with "file myfile.tif" in terminal and it returns myfile.tif: TIFF image data, little-endian). As mentioned, when running it on a single file, everything works.
When I make a local copy of the folder, it runs normally on all files in the folder upon specifying the folder path - so, could it indeed be a problem on how spotiflow tries to find the TIFs in the folder on the mounted storage?
The storage is mounted via Mountain Duck (sftp). I can access and navigate through the folder without issues both via Finder and the terminal. I do not know if this helps, but this is the path Mountain Duck creates for the folder:
/Users/l.m.frank-2/Library/Group Containers/G69SCX94XU.duck/Library/Application Support/duck/Volumes.noindex/SFTP.xx.xx.localized/storage/myfolder
Thank you very much in advance!
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