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20th August 2020
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
Who? | Discussion Points | Next |
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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 (NiftyReg is no longer maintained, does MONAI do registration?)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 |
Apologies from NB
YH
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Keen to submit 1st Sept or nearest
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Item to discuss next week: dissemination and promotion
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ZB & NB agreed to PYPI implementation - not time-sensitive (post/pre-r1)
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EB demo requirements still unresolved. Provisional measures required
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Demo plot requirements need clearer guidelines that incorporate predictor output: cases for and against including live demo plots
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Live plotting is difficult on remote vs. clarity of highlighting selected output
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People who have never performed demos will be assigned to review demos for ~30 mins. And to comment
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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
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YF will have a serious look at the loaders and can feedback to AG
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Main concern is to ensure all lines of code are parsed and to test both Nifti and h5 loaders
YH
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Quick review remaining issues prior to release, documentation is paramount
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Unet tensorboard - fix post-r1
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Config file (yaml) structure is complicated - fix post-r1
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Testing issues to be discussed offline with NB
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AG to test tf numpy (two instances in codebase)
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#242 assigned to YH
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Readthedocs is high priority YF will review
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AC recommends to include more loss parameters (post-r1)
NB
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Requirements text needs volunteers
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JOSS paper comment: expanded commentary on state of the field required (needs clarification with NB)
YH
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Demo authors restructured, with main authors left as primary contacts
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DeepReg promotion activities raise suggestions
NO OUTSTANDING QUESTIONS
tables: for google docs --> markdown, use tablesgenerator.org
formatting: for google docs --> markdown, use stackedit