Unable to detect files and directories

[alasdairball]

Hi, This is probably a basic issue but I am running into an error at the first steps of using steinbock, where it seems to be unable to detect files and directories that definitely exist. I've tried with my own data and the workshop data as below:

Y:\path\to\ImagingWorkshop2023\data\steinbock-new>doskey steinbock=docker run -v 
"Y:\path\to\ImagingWorkshop2023\data\steinbock-new":/data ghcr.io/bodenmillergroup/steinbock:0.15.0 $*

Y:\pah\to\ImagingWorkshop2023\data\steinbock-new>steinbock --version
steinbock, version 0.15.0

Y:\path\to\ImagingWorkshop2023\data\steinbock-new>steinbock preprocess imc panel --unzip
Error: No panel/.mcd/.txt file found

Y:\path\to\ImagingWorkshop2023\data\steinbock-new>steinbock preprocess imc images --unzip --hpf 50
Usage: steinbock preprocess imc images [OPTIONS]
Try 'steinbock preprocess imc images --help' for help.

Error: Invalid value for '--mcd': Directory 'raw' does not exist.

Y:\path\to\ImagingWorkshop2023\data\steinbock-new>dir
Volume in drive Y is rdsprojects
Volume Serial Number is B0BC-99C7

 Directory of Y:\path\to\ImagingWorkshop2023\data\steinbock-new

31/08/2023  15:13    <DIR>          .
31/08/2023  15:12    <DIR>          ..
31/08/2023  15:13    <DIR>          raw
               0 File(s)              0 bytes
               3 Dir(s)  13,784,781,422,592 bytes free

Any help or advice would be much appreciated.

[nilseling]

Hi @alasdairball

could you please send us a screenshot of the contents of Y:\path\to\ImagingWorkshop2023\data\steinbock-new\raw? Ideally, you would place the files somewhere on your system and adjust the \path\to part in the doskey call by the path where the files are located instead of creating a new directory structure called \path\to.

[alasdairball]

Thanks @nilseling

doskey steinbock=docker run -v "Y:\Alasdair\IMC\steinbock\ImagingWorkshop2023\data\steinbock-new":/data 
ghcr.io/bodenmillergroup/steinbock:0.15.0 $*
steinbock --version

Steinbock will print the version correctly but can't find the directory with the below commands

steinbock preprocess imc panel --unzip

steinbock preprocess imc images --unzip --hpf 50

[nilseling]

Thanks. But I was wondering what's inside the raw folder.

[alasdairball]

Currently zipped files from the workshop.

[jwindhager]

Is Y: a network drive?

[alasdairball]

Yes it is.

Is it docker that I would need to give permissions to access the network drive or steinbock, or both?

[jwindhager]

If the network drive is indeed the issue, I'm not sure whether it can be easily resolved by fixing permissions (you would need to assign correct permissions for: the Windows user that mapped the network drive, the Windows user with which you're running Docker, the Docker daemon user, the steinbock user within the Docker container). There may also be some funky WSL2 stuff involved. Before going there, I would try whether the problem disappears when working on a local copy of the data.

[alasdairball]

I don't have permissions to access the local C: drive on my university computer, but testing on my home drive U: gives this result:

Which suggests (given that it reports it can't access U:) it is able to access the Y: network drive. I will have to try from my laptop.

[Milad4849]

Closing due to inactivity