Updates to clean and detect

[vsoch]

Description

Opening this PR as start of work to refactor the detect and clean flow, changes include:

• removing the ultrasound regions from the default deid.dicom and adding one specifically for ultrasound
• parsing them into one list, in the order provided, so keepcoordinates (value of 1) and coordinates (0) are respected for the order the user wants
• having the default value set to ones (indicating keep)
• adding an ability to say coordinates all or keepcoordinates all in case the user wants to apply a change to the entire mask (e.g., for the ultrasound we would do coordinates all to blank them first before keeping the Ultrasound region.
• parsing the dicom in clean.py to account for these changes, and also adding image dimension of 2.
• adding documentation that explains this!

cc @wetzelj

Related issues: #149

Please include a summary of the change(s) and if relevant, any related issues above.

Checklist

• [ ] I have commented my code, particularly in hard-to-understand areas
• [ ] My changes generate no new warnings
• [ ] My code follows the style guidelines of this project

Open questions

Questions that require more discussion or to be addressed in future development:

[wetzelj]

@vsoch - Are you okay with having mini, unit-test specific recipe files added for testing clean? If so, would a new "resources" folder under tests be okay?

[vsoch]

Definitely!

[wetzelj]

I have some unit tests written as well as some bug fixes. They're currently committed here, but I can port them to where ever you want if you are okay with the changes.

Just to point out a couple things:

• Removed the looping on line 156 in clean.py.
• Switched the creation of the output folders from a mkdir to makedirs so that the entire tree is created.
• Removed the "cleaned-" prefix from the output header files. This simplifies the merging of the pixel output with header output.

[vsoch]

Great! Let's do the PR against the branch here, then we can merge, make sure all the tests still work, and then merge again and release. Everything sounds good except for:

Removed the "cleaned-" prefix from the output header files. This simplifies the merging of the pixel output with header output.

The concern here is that the user would accidentally rewrite files - I think we should keep the cleaned- prefix. It's also a message that the files were absolutely generated - without the prefix it might not be clear. If you feel strongly that this isn't a good feature, then we could have some kind of input argument for an output prefix, with default to be cleaned- and for your use case setting it to an empty string.

[wetzelj]

Got it.

I don't have a strong preference on the "cleaned-" prefix. Let's just leave it as is.

[wetzelj]

Same here. I will be continuing to test. If I see anything else I'll open another issue.

[vsoch]

I'll give you a day or so to test and report any quick issues, otherwise I'll release after that!