Add example CLI

[sarthakpati]

Following conversation with Pallavi, I have added a basic command line interface to get collage features. Items that need to be populated are commented with todo.

[nathanhillyer]

Looks good so far!

[nathanhillyer]

One suggestion– could you put all the files into a cli subfolder, please?

[sarthakpati]

One suggestion– could you put all the files into a cli subfolder, please?

Done. Looking forward to when this is fully functional and ready. 😄

[sarthakpati]

BTW, I was not sure what other input parameters are required for collage (for example, the radius and binning), so those could also part of the CLI.

[nathanhillyer]

@sarthakpati What are you expecting in the output CSV file, and what format would be best for CaPTk to process the features? Would you like our CLI tool to write out image files?

[sarthakpati]

Hi @nathanhillyer,

1. Output CSV can be in the following format (no need to write the parameters used, I will do that when I parser the output from CaPTk):

FeatureName,Value

2. From CaPTk's layer, there is no need to write images. However, if you want to write images, put it up as a parameter that can be controlled (and is preferably disabled by default).

[nathanhillyer]

@sarthakpati Thanks for the feedback, and starter project. We're going to use #87 as the final pull request. Feel free to try it out via pip install collageradiomicscli.

[sarthakpati]

Hi @nathanhillyer, would it be possible for you to merge my commites into your PR? I want my contribution to be recognized in this effort.

[nathanhillyer]

Yes, sure!

[sarthakpati]

Hi @nathanhillyer, I have merged your cli branch with mine and this is now up-to-date: https://github.com/sarthakpati/collageradiomics/tree/add_cli

If you don't mind merging this, it would be great, thanks.