Input micrographs as file

[rfleiro]

Hi guys, great software :)

It would be great if topaz could take a file with a list of micrographs as input

Is this a possibility at all right now?

[tbepler]

At which stage? Topaz train accepts micrographs listed in an image list file. For downstream steps that expect micrographs to be listed on the command line (i.e. topaz extract), bash can do this for you using $(cat file.txt). For example,

topaz extract $(cat micrograph_list_file.txt)

will pass each line of "micrograph_list_file.txt" to topaz extract as a separate argument.

[rfleiro]

Thanks for the quick reply

I realise now I didn't specify. I was wondering if a list file could be provided for pre-process and denoising

I am indeed passing the input mics using a similar approach, thanks for the suggestion

[tbepler]

I'll add passing micrograph inputs through a file to the list for extra features to add in the future. If this is something you're interested in working on, I'd be happy to accept a pull request with this feature.

In the meantime, the bash approach above seems like the best way to deal with this.

[tbepler]

I added this in commit 752c140