dalmouiee
commented
2 years ago Hey @pchlap, I've updated the cli to work with configurable PACS, web and test as standalone sub commands which can retrieve the data to the local filesystem using the relevant method, or run the entire pipeline with one of those input methods. I've tested the PACS, web, test and filesystem inputs but the TCIA will be a bit tricky to implement if we have multiples of patient ids, modalities (but is possible), so I left it out of the cli for now.
It is already handy for me, as I need to redownload the test data everytime I chop and change it during dev and the cli subcommand is great for this in my case. Let me know what you think, thanks! :)
Hey @pchlap, made the first version of what a CLI tool for pydicer might be. Currently, it can run 2 commands; the pipeline as a whole, and the input module alone.
We have the potential for input for the user to select which input method they want (for now only the 'testinput' method has been implemented). For the other modules, it could be useful to have them run separately and in the case of debugging, you could run modules singularly and export their output into files when you run the CLI. So potentially, if it is meaningful to get other modules to be run on the CLI, we can build in the other modules easily using this structure.
Open to ideas and other design approaches to this, cheers! :)