Pydicer tool class

[pchlap]

Hi @dalmouiee, so here is a contribution providing a wrapper class to manage your entire pydicer project. The idea is that a user will create and run the input classes as required. Then once all DICOM is in the PyDicer class will help them orchestrate the rest.

For now, this just provides the basics. But I think we can add a lot more in here. For example functionality to:

• prepare data for nnUNet
• map structures names for consistency
• adding a new data object (such as an auto segmentation). I've got a placeholder for that function in already since I will work on that next.
• loading of images/structures etc...
• and probably lots more....

Curious to hear what you think. PipelineExample.ipynb or the pipeline automated test is probably the best place to see how the pipeline is called using the new PyDicer class :)

[pchlap]

@fahimirfanalam here's the pull request I was just talking about in case you'd like to take a look :)

[pchlap]

This is awesome thanks a lot @pchlap! Makes things much easier to handle for sure. Happy for a merge, I just added some comments regarding style but nothing essential :)

Thanks for the review @dalmouiee, some really useful tips. I've implemented most of them but have left out a few for now to be addressed later. I'll merge this through once everything is passing :)