Pipeline: Abdomen resolution fix

nielsboecker / HoloRepository-Core

A system for transforming medical imaging studies into holograms, storing them in the cloud and providing them to other systems.

GNU Affero General Public License v3.0

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Closed ansonwong9695 closed 5 years ago

ansonwong9695 commented 5 years ago

This PR is to address issues from #48

added Y axis flipping function exclusive to abdomen pipeline
added dynamic config update for the resolution of the in dense v net model
updated requirements.txt in dense v net model
updated dockerfile in dense v net model
added comment with explanation and deprecation note to the script that splits apart organs in split_to_seperate_organs.py

nielsboecker commented 5 years ago

Update: #96 implements only one of the two changes proposed here, to reduce the chance of breaking anything.

nielsboecker commented 5 years ago

As discussed, this PR changes too many different things and is too risky to merge at this late stage.

The feature of changing ini config within the NN models can't be sufficiently tested, so we drop it for now.
The Y-axis flip for abdominal_organs_segmentation and the split_organs deprecation node will be integrated with #96