feat: add adaptive sampling, motion registration, MEDL, and e2e ADS configs - #316

Open

georgeyiasemis wants to merge 105 commits into

mainfrom

feature/adaptive-registration

Commits on Jul 22, 2024

Add reg module
georgeyiasemis
committed
4d27859

Commits on Jul 25, 2024

Update reg and add integration
georgeyiasemis
committed
4700070
Add smooth loss
georgeyiasemis
committed
0643b1e
Update transforms
georgeyiasemis
committed
dc1655e
Minor fix
georgeyiasemis
committed
89d3e62
Minor fix
georgeyiasemis
committed
952b710

Commits on Aug 1, 2024

Add option to save mask
georgeyiasemis
committed
f555921
Minor fix
georgeyiasemis
committed
e0a1eef
Add recon and eval
georgeyiasemis
committed
a4be1d9
Add adpt
georgeyiasemis
committed
741e700

Commits on Aug 5, 2024

Option to use acs as mask
georgeyiasemis
committed
8020099
Forgotten return
georgeyiasemis
committed
e319efc
Recover if error
georgeyiasemis
committed
f468869

Commits on Aug 12, 2024

Visualize registration items
georgeyiasemis
committed
8742423

Commits on Aug 13, 2024

Return registered image if registration
georgeyiasemis
committed
cbf5a56

Commits on Aug 21, 2024

Add traditional recon as models
georgeyiasemis
committed
2eaed0b
Choose if calculate displacement
georgeyiasemis
committed
6392c3c
Minor fix
georgeyiasemis
committed
e840963
Minor fix
georgeyiasemis
committed
f75f8e8
Minor fix
georgeyiasemis
committed
d912b9e

Commits on Sep 21, 2024

Add 3d models

George Yiasemis
authored and
George Yiasemis
committed
d7a2975
Add 3d varnet and 3d kspace varnet

George Yiasemis
authored and
George Yiasemis
committed
64e0345
Minor fixes
georgeyiasemis
committed
8a7d731
Update for registration
georgeyiasemis
committed
6f52a4b

Commits on Oct 20, 2024

Add vit transformers module
georgeyiasemis
committed
10124c5
Rename
georgeyiasemis
committed
842dd87
Minor fix
georgeyiasemis
committed
8d7cd07
Minor fix
georgeyiasemis
committed
d7ca4a5
Isort
georgeyiasemis
committed
d14e00f
Minor fix
georgeyiasemis
committed
930e2e5
Minor fix
georgeyiasemis
committed
a96907a
Rename
georgeyiasemis
committed
9a45371

Commits on Oct 24, 2024

No torchvision version
georgeyiasemis
committed
5c2fea3
Allow for non end to end training
georgeyiasemis
committed
adb18fd

Commits on Nov 4, 2024

Add voxelmorph model
georgeyiasemis
committed
b16eff6
isort, add vit reg
georgeyiasemis
committed
5ca113b
Minor fix
georgeyiasemis
committed
f0a2b4f

Commits on Nov 21, 2024

Changes for saving registered images, minor fixes
georgeyiasemis
committed
86fd9f4

Commits on Jan 28, 2025

Allow decoupled training if registration
georgeyiasemis
committed
0a8af40
Minor fix
georgeyiasemis
committed
d49a24b

Commits on Feb 7, 2025

Add MEDL model
georgeyiasemis
committed
29d216a
Minor fic
georgeyiasemis
committed
b96b184
Minor fix
georgeyiasemis
committed
b1d3fba

Commits on Aug 5, 2026

feat: integrate adaptive sampling and end-to-end registration from main

georgeyiasemis
and
cursoragent
committed
9773d44
fix: normalize paper experiment configs for main schema

georgeyiasemis
and
cursoragent
committed
8d729f2
fix: drop obsolete keys from adpt experiment dumps

georgeyiasemis
and
cursoragent
committed
e2742aa
fix: restore optimizer eps and finish adpt config cleanup

georgeyiasemis
and
cursoragent
committed
9fd2e3d
fix: sanitize remaining adpt masking keys for MaskFuncMode API

georgeyiasemis
and
cursoragent
committed
217468c
fix: rebuild broken inference transforms in adpt config dumps

georgeyiasemis
and
cursoragent
committed
6ac9c3a
fix: rewrite inference blocks in remaining adpt config dumps

georgeyiasemis
and
cursoragent
committed
3fda588
fix: drop VarNet k-space and harden adaptive MPS/smoke paths

georgeyiasemis
and
cursoragent
committed
27be1b2
chore: remove mini experiment configs from the branch

georgeyiasemis
and
cursoragent
committed
3643c38

Commits on Aug 6, 2026

chore: flatten paper experiment configs to named yaml files

georgeyiasemis
and
cursoragent
committed
10581c8
chore: remove mini configs reintroduced by flatten commit

georgeyiasemis
and
cursoragent
committed
226ac4c
chore: drop no_df_loss from e2e_ads_reg experiment config names

georgeyiasemis
and
cursoragent
committed
fb97825
chore: remove mini configs accidentally re-added

georgeyiasemis
and
cursoragent
committed
f0a179c
chore: gitignore local e2e_ads mini configs

georgeyiasemis
and
cursoragent
committed
a7c0572
chore: remove and gitignore local e2e_ads smoke configs

georgeyiasemis
and
cursoragent
committed
8e824b9
chore: remove local mini/smoke paths from .gitignore

georgeyiasemis
and
cursoragent
committed
f4a9cd7
fix: drop training.eps from config and experiment dumps

georgeyiasemis
and
cursoragent
committed
94643d3
chore: require Python 3.12 and build elasticdeform from source

georgeyiasemis
and
cursoragent
committed
f7e3923
docs: modernize adaptive sampling package docs and typing

georgeyiasemis
and
cursoragent
committed
d05fb2e
docs: modernize registration packages and lazy-load elasticdeform

georgeyiasemis
and
cursoragent
committed
7471105
docs: modernize MEDL docs and switch to torch.amp autocast

georgeyiasemis
and
cursoragent
committed
0f7e3bd
feat: add key-based losses and displacement-field TensorBoard viz

georgeyiasemis
and
cursoragent
committed
37fb806
fix: catch adaptive rejection sampling via typed exception

georgeyiasemis
and
cursoragent
committed
4cd87cc
chore: drop empty inference.metrics dump noise from experiment configs

georgeyiasemis
and
cursoragent
committed
2a7b6b1
style: reformat e2e_ads experiment YAMLs with 4-space indent

georgeyiasemis
and
cursoragent
committed
7f67336
chore: remove df_0_01 displacement-loss ablation configs

georgeyiasemis
and
cursoragent
committed
4d02d24
chore: remove df_loss displacement-loss ablation configs

georgeyiasemis
and
cursoragent
committed
219f31b
chore: rename e2e_ads experiment configs to a concise scheme

georgeyiasemis
and
cursoragent
committed
643975d
chore: drop accidentally committed e2e_ads mini/smoke configs

georgeyiasemis
and
cursoragent
committed
b98e50a

Commits on Aug 8, 2026

fix: handle float adaptive masks in DC fill and masking

georgeyiasemis
and
cursoragent
committed
5e722c6
fix: dynamic init masks and normalize reference_kspace

georgeyiasemis
and
cursoragent
committed
b02c892
fix: adaptive policy budgeting for static ACS with dynamic k-space

georgeyiasemis
and
cursoragent
committed
ed394cc
fix: load paper checkpoints after ModConv bias defaults

georgeyiasemis
and
cursoragent
committed
c24e69e
test: unpack extra evaluate visualization return from MRI engine

georgeyiasemis
and
cursoragent
committed
61d96ab
chore: keep validated paper YAMLs; rename e2e_ads_recon_reg

georgeyiasemis
and
cursoragent
committed
316dda5
docs: expand e2e_ads_recon(_reg) READMEs with paper method figures

georgeyiasemis
and
cursoragent
committed
834a92c
docs: retitle e2e_ads READMEs to paper names and clean usage notes

georgeyiasemis
and
cursoragent
committed
46ea2e6
docs: fix broken RST titles and tables in e2e_ads READMEs

georgeyiasemis
and
cursoragent
committed
340d602
chore: rename dyn configs to frame-/phase-specific per papers

georgeyiasemis
and
cursoragent
committed
22c0a50
chore: drop accidental kosmos_ref_predict artifacts from rename

georgeyiasemis
and
cursoragent
committed
a7c16ac
chore: stop tracking e2e_ads project .gitignore files

georgeyiasemis
and
cursoragent
committed
f50f9aa
revert: restore torch.where in apply_mask

georgeyiasemis
and
cursoragent
committed
8795af4
refactor: remove unused centered weight norm convolutions

georgeyiasemis
and
cursoragent
committed
aac5c74
fix: pass time dim to DYNAMIC CreateSamplingMask

georgeyiasemis
and
cursoragent
committed
58fafc9
feat: make training log flush interval configurable

georgeyiasemis
and
cursoragent
committed
c545506
Merge branch 'main' into feature/adaptive-registration

georgeyiasemis
and
cursoragent
committed
799391e

Commits on Aug 9, 2026

Add sibling inference YAMLs for e2e ADS projects with commented rates.

georgeyiasemis
and
cursoragent
committed
f17cb2f
Support inference-only configs and harden model/config wiring.

georgeyiasemis
and
cursoragent
committed
25a71c1
Remove .hf_staging from shared .gitignore; keep it local only.

georgeyiasemis
and
cursoragent
committed
c163b7f
Drop local scratch path ignores from shared .gitignore.

georgeyiasemis
and
cursoragent
committed
e918866
Merge branch main into feature/adaptive-registration.

georgeyiasemis
and
cursoragent
committed
5d633c8
fix: silence ty errors and add tests for adaptive/registration modules.

georgeyiasemis
and
cursoragent
committed
0e63f63
test: expand coverage for adaptive, MEDL, and registration modules.

georgeyiasemis
and
cursoragent
committed
d9f3896
fix: address Codacy and ruff findings in adaptive/registration paths.

georgeyiasemis
and
cursoragent
committed
93f826a

Commits on Aug 10, 2026

test: raise coverage on writers, engines, VarNet3D, and adaptive utils.

georgeyiasemis
and
cursoragent
committed
551185d
chore: keep minimize_inference_yaml.py local-only.

georgeyiasemis
and
cursoragent
committed
dec79dc
chore: drop minimize_inference_yaml.py from .gitignore.

georgeyiasemis
and
cursoragent
committed
2a7389f
chore: drop redundant engine_name: null from project YAMLs.

georgeyiasemis
and
cursoragent
committed
5efb96a
feat: visualize and save ADS initial vs predicted masks.

georgeyiasemis
and
cursoragent
committed
eadb1fb
feat: print ASCII DIRECT logo when logging starts.

georgeyiasemis
and
cursoragent
committed
f6c0e3e
fix: print ASCII logo after the clinical-use warning.

georgeyiasemis
and
cursoragent
committed
5f9b593
chore: update ASCII DIRECT logo art.

georgeyiasemis
and
cursoragent
committed
7d25ab2