20th August 2020

Meeting 20/08/2020

Agenda

Chair: YH

Minutes: AG

Attendance:

Yunguan Fu YF

Ester Bonmati EB

Zac Baum ZB

Shaheer Saeed SS

Adria Casamitjana AC

Yipeng Hu YH

Qianye Yang QY

Matt Clarkson MC

Alex Grimwood AG

Zhe Min ZM

Remi Delaunay RD

Apologies:

Nina Montana Brown NMB

Updates and next tasks

Who?	Discussion Points	Next
Zac Baum		Pypi release
Ester Bonmati	Demo: requirements and demo_plot Command line vs python	Review docu
Adria Casamitjana		Demo proofread
Matt Clarkson
Remi Delaunay
Yunguan Fu
Alex Grimwood	@YF & NB: Happy to add suggested improvements to #126 paired loader tomorrow @YF & NB: Are there any outstanding tasks/improvements for #124 grouped loader I can help with?	Move minutes to Wiki (niftinet provides a good example) Test keras numpy functions
Yipeng Hu	Proofreading / demo-testing (human) starts this weekend Review pre-r1 remaining issues From Nina: Add requirements.txt, this is something we are missing and has been flagged during review for several JOSS papers. State of the field: we do not discuss how this package contributes/lives in the OS environment for deep neural nets for registration, we should probably point to NiftyReg and MONAI, and how our package fills a niche. (NiftyReg is no longer maintained, does MONAI do registration?) Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)? (Sort of? read the docs incoming..) PyPi release: ie automated installation vs repo clone. Demo authors	#242 assigned to YH
Nina Montana Brown
Saeed Shaheer
Qianye Yang
Zhe Min

Minutes

Apologies from NB

YH

• Keen to submit 1st Sept or nearest

• Item to discuss next week: dissemination and promotion

• ZB & NB agreed to PYPI implementation - not time-sensitive (post/pre-r1)

• EB demo requirements still unresolved. Provisional measures required

• Demo plot requirements need clearer guidelines that incorporate predictor output: cases for and against including live demo plots

• Live plotting is difficult on remote vs. clarity of highlighting selected output

• People who have never performed demos will be assigned to review demos for ~30 mins. And to comment

• Command line vs python - either acceptable as a matter of preference. Ideally both implemented in each demo, but workload of maintaining both is acknowledged

AG

• YF will have a serious look at the loaders and can feedback to AG

• Main concern is to ensure all lines of code are parsed and to test both Nifti and h5 loaders

YH

• Quick review remaining issues prior to release, documentation is paramount

• Unet tensorboard - fix post-r1

• Config file (yaml) structure is complicated - fix post-r1

• Testing issues to be discussed offline with NB

• AG to test tf numpy (two instances in codebase)

• #242 assigned to YH

• Readthedocs is high priority YF will review

• AC recommends to include more loss parameters (post-r1)

NB

• Requirements text needs volunteers

• JOSS paper comment: expanded commentary on state of the field required (needs clarification with NB)

YH

• Demo authors restructured, with main authors left as primary contacts

• DeepReg promotion activities raise suggestions

NO OUTSTANDING QUESTIONS