files not visible in mac docker

[kateharline]

Hi, I'm using the mac docker image on Monterey 12.0.1, I'm able to get the PlantSeg GUI to load with % docker run -it --rm -v PATH_TO_DATASET:/Users/kateharline/workspace/20210627 -e DISPLAY=10.48.88.110:0 wolny/plantseg

However, when I try to navigate to the directory with my image files or load an individual file, none are visible. The log reads 2021-11-30 18:17:02,546 - Executing pipeline step: 'preprocessing'. Parameters: '{'state': True, 'save_directory': 'PreProcessing', 'factor': [1.0, 1.0, 1.0], 'order': 2, 'crop_volume': '[:, :, :]', 'filter': {'state': False, 'type': 'gaussian', 'filter_param': 1.0}}'. Files [].

and it throws AssertionError: Input file paths cannot be empty

(Fair enough)

I have tried this with my image files as .tif and .h5

[bipashadey]

I have the same error! any leads?

[wolny]

Hi @kateharline, thanks for raising the issue. I see the error in your docker command: you've incorrectly mounted your files inside the docker container. As explained in the documentation (https://github.com/hci-unihd/plant-seg#mac-os) the PATH_TO_DATASET is the directory from host which you want to mount. So it should be /Users/kateharline/workspace/20210627. The second argument (after the colon) is the directory inside the container, e.g. /root/datasets. This is where you should navigate the PlantSeg GUI to load the files.

So basically your command should be:

docker run -it --rm -v /Users/kateharline/workspace/20210627:/root/datasets -e DISPLAY=10.48.88.110:0 wolny/plantseg

and then you should navigate to the /root/datasets to find your files.