Not able to define output folder

[GabeK-L]

Perhaps I am missing something but it would be great if there was a way to define an output folder for the processed images because I like to keep my raw data in read only folders. I want to be able to read that data with dw and save the output in a new folder. Is that possible? Thanks!

[elgw]

Hello,

You are on top of everything. Currently it is not possible to specify an output folder.

However, the whole name of the output file can be specified with the --out command line argument, for example --out /some/where/file.tif, in that case the log file will be called /some/where/file.tif.log.txt.

Beware of a bug (just stumbled upon it): The program crashes a folder name is given to --out. I think that it would make sense that --out accepted a folder names as well. Or possibly to make a distinction between --outfile and --outfolder. Let me know if you need this and if you have any suggestions for how it should work.

Cheers,
Erik

[GabeK-L]

Thanks for the info! I can make that work for now. Having --out accept a folder name would be great, I don't see myself at least needing to have the --outfile and --outfolder distinction.

Thanks!
Gabe

[elgw]

Great, thanks for the feedback! Will fix that.

Erik

[WisdomUfondu27]

I personally am able to get around this through the use of a Python-encoded GUI that allows me to process input images in batches and save each output in a desired folder. If you would like me to share the script (for windows 11), I can do that as well!

Cheers,
Wisdom

[elgw]

Nice!

Most of the times I use the scripts generated by nd2tool but that is linux (and possibly) mac only at the moment and, of course, tailored to my needs. Everyone will have their own workflow :)

If you put it in a public repo I'd be happy to link to it.

Cheers,
Erik

[elgw]

This is fixed in the 0.4.4_rc3

Since we don't use separate arguments for outfolder and outfile, please make sure that the folder exists, otherwise what is passed to --out will be interpreted as a file name.

If no prefix is wanted, simply pass an empty string to --prefix. How that is done depends on the shell, for example on windows powershell

--prefix `"`"`

can be used.

I will put the installer under the Releases page.

Cheers,
Erik

dw0.4.4_rc3_win11.zip

[GabeK-L]

@elgw Awesome! Thanks for the update!

@WisdomUfondu27. I would love to check that script out. I did something similar in ImageJ to fit into one of my workflows but having it in python would be better.

Gabe