Add the option to have an image path inside index file

[fefossa]

This PR adds the possibility for the user to give a full path to the image file inside the index.csv file. It's just checking if the FileName is a path; if it's a path, it won't add the root to the FileName.

The user may want to give a full path to the image file instead of moving the images to inputs/images. DeepProfiler expects to have the images inside "inputs/images", and it always adds the root path to the filenames.

Mostly for RunDeepProfiler (discussion and PR) to work on CellProfiler we need to have this function so we don't need to move the images to inputs/images and grab it from the user's inputs.

I've tested this also by giving the inputs as DeepProfiler usually expects (index.csv only having "Plate/FileName") and it worked fine.

[bethac07]

@jccaicedo @Arkkienkeli Any objection to merging this? We'd love to get the CellProfiler DeepProfiler plugin merged? Thanks!

[Arkkienkeli]

@fefossa Hi, did you test it for both full paths and inputs/image paths?

[fefossa]

@Arkkienkeli Yes, I've tested this also by giving the inputs as DeepProfiler usually expects (index.csv only having "Plate/FileName", with the images inside inputs/image) and it worked fine.

[Arkkienkeli]

@fefossa
Do you mind to document this change in the handbook? Specifically, here. I guess, we can merge after that.

[fefossa]

It took me some time, sorry - but I've modified the documentation as requested by @Arkkienkeli. Thanks!

[Arkkienkeli]

Thank you, I have merged both documentation and this PRs.