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Dp kidney #549

Merged
merged 21 commits into from
Jan 12, 2024
Merged

Dp kidney #549

merged 21 commits into from
Jan 12, 2024

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daniellepace
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Adding:

  1. tensorization and tensormap options for pancreas image segmentation
  2. additional options for machine learning setup and median T1 time inference, created to emulate Marcus's setup (although in the end these were not used, they might be useful for other projects?)
  3. various bug fixes

lucidtronix and others added 19 commits December 5, 2023 16:27
@lucidtronix
add pancreas
57e43c4
@lucidtronix
add pancreas
943909c
@daniellepace
use pancreas for pngs
804015b
@daniellepace
WIP
9181099
@daniellepace
New manifest file
8753ece
@daniellepace
Fix view creation
b9321cb
@daniellepace
Prevent tensorize from overwriting
afaab76
@daniellepace
Add tensormaps for pancreas mris
87258a3
@daniellepace
Add elements of Marcus's setup - L2 weight_decay and cosine decay lea…
e7cd9f0 
…rning rate schedule
@daniellepace
FIX: Fix bug when a generator has 0 ids
3050729
@daniellepace
FIX: Fix bug when key_prefix is not given
4a951e9
@daniellepace
ENH: Allow for no testing during model training
e6684e4
@daniellepace
FIX: Fix typo
78839dd
@daniellepace
FIX: Fix parser for boolean arguments
6e70e83
@daniellepace
STYLE: Remove unneeded comment
4b86543
@daniellepace
WIP
05c4f77
@daniellepace
FIX error (which kills a thread and prevents subsequent pngs from bei…
ca2e89b 
…ng written) if the image size is wrong
@daniellepace
Tensorize can create empty tensors if there are no good series, makin…
05c5975 
…g you think it's working when it isn't. At least give a warning
@daniellepace
Don't commit code to interpet this specific manifest_tsv file
8eaa344
lucidtronix
lucidtronix approved these changes Jan 12, 2024
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lgtm!

ml4h/arguments.py Outdated Show resolved Hide resolved
ml4h/models/layer_wrappers.py Show resolved Hide resolved
@daniellepace daniellepace merged commit 0064b83 into master Jan 12, 2024
3 checks passed
@daniellepace daniellepace deleted the dp_kidney branch January 12, 2024 16:53
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@lucidtronix lucidtronix lucidtronix approved these changes

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@daniellepace @lucidtronix