Problem running plant-seg on batch mode
Closed this issue · 2 comments
Hello,
When I try to run plant-seg on multiple images in a folder, after completing the predictions for the first image, I get the following message:
[...]
File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py\h5f.pyx", line 106, in h5py.h5f.open
OSError: Unable to open file (file signature not found)
This happens both when I use the GUI and when I try to run plant-seg from the terminal. Do you know what is the problem?
Thanks!
Lucrezia
Hi Lucrezia,
I hope I can help you with your request.
From the error message it seems that the error comes from a wrongly formatted or corrupted h5 file.
Could you try to open the same h5 file using another software like fiji?
When does the error occur? (in the preprocessing, in the cnn predictions or in the segmentation)
Best,
Lorenzo