Skip to content
Open

Dev #658

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
187 commits
Select commit Hold shift + click to select a range
8886a13
Merge release 2.0.2 #573
ashleve May 2, 2023
467a974
Lightning + Aim dependency fix in conda environment.yaml and setup.py…
tesfaldet May 11, 2023
ca07865
Change "pytorch_lightning" to "lightning" in instantiators.py (#577)
tesfaldet May 12, 2023
9355a5d
Fix WandB config improper hierarchical display of keys (#583)
dreaquil Jun 21, 2023
b987605
Remove yaml extension from hydra defaults lists (#584)
tesfaldet Jul 29, 2023
e70291d
Docstrings revamp (#589)
tesfaldet Jul 29, 2023
21313a9
Rename `pyrootutils` to `rootutils` (#592)
ashleve Jul 29, 2023
8055898
Fix `.log` being saved in project root dir instead of log dir (#588)
tesfaldet Jul 29, 2023
271972c
Fix accelerator in `tests/test_train.py` (#595)
caplett Aug 24, 2023
429947f
Update Lightning DDP documentation links in `README.md` (#601)
amorehead Sep 1, 2023
2654bad
Fix `torch.compile` on `nn.module` instead of on `LightningModule` (#…
tesfaldet Sep 1, 2023
07ce4b7
Update function arguments typing (#603)
amorehead Sep 9, 2023
1fb5405
DDP-related improvements to datamodule and logging (#594)
tesfaldet Sep 18, 2023
bddbc24
Add FSDP support to `MNISTLitModule` (#604)
amorehead Sep 25, 2023
7347707
++ first try to implement Natalia's code for reconstruction was succe…
amirshamaei Oct 5, 2023
0ce5f16
++ readme.md was updated
amirshamaei Oct 5, 2023
b374175
++ direct toolkit was added
amirshamaei Oct 5, 2023
4106af9
++ change requirements
amirshamaei Oct 5, 2023
58a91d0
++ change requirements
amirshamaei Oct 5, 2023
cd16e0a
++ add experiment_linux.yaml
amirshamaei Oct 6, 2023
46cb1c8
++ experiment_linux.yaml changed to cpu
amirshamaei Oct 6, 2023
c6360ea
++ add masks to git
amirshamaei Oct 6, 2023
058f6d9
++ experiment_linux.yaml got changed
amirshamaei Oct 6, 2023
3329ce4
++ experiment_linux.yaml got changed
amirshamaei Oct 6, 2023
38c21bd
++ .to('cuda') is removed from natalia's code, so runs on cpu
amirshamaei Oct 6, 2023
6577dfa
++ nothing important
amirshamaei Oct 6, 2023
06b8837
++ nothing important
amirshamaei Oct 6, 2023
83e7e69
++ nothing important
amirshamaei Oct 6, 2023
7068faa
++ nothing important
amirshamaei Oct 6, 2023
5602fe2
++ testing ddp
amirshamaei Oct 6, 2023
6c56f55
++ direct tk has been added and tested on C2 dataset
amirshamaei Oct 9, 2023
a5dd9f8
++ RecVarNet from direct has been added.
amirshamaei Oct 10, 2023
5024f54
++ changes in yaml experiment_recvarnet.yaml
amirshamaei Oct 10, 2023
cbf3734
++ changes in yaml experiment_recvarnet.yaml + support of matmul prec…
amirshamaei Oct 10, 2023
6f5f30f
++ epoch sized got changed
amirshamaei Oct 10, 2023
78bce71
++ testing check point
amirshamaei Oct 10, 2023
eb11021
++ small changes from previous commit
amirshamaei Oct 10, 2023
51ccaac
++ recurrentvarnet_adaptor.py has been updated to estimate the sensit…
amirshamaei Oct 11, 2023
af8a8ce
++ slurm file updated
amirshamaei Oct 11, 2023
b54ea45
++ slurm file updated
amirshamaei Oct 11, 2023
72b4598
++ slurm file updated
amirshamaei Oct 11, 2023
0a7c86b
++ slurm file updated
amirshamaei Oct 11, 2023
24c53b8
++ direct and fastMRI are relocated
amirshamaei Oct 11, 2023
2ac1d37
++ recvarnet mri_direct.yaml has been updated by parameters in the pr…
amirshamaei Oct 12, 2023
ef03e48
++ add calgary campinas datamodule without testing
amirshamaei Oct 16, 2023
3cce2eb
from ai2lab1
amirshamaei Oct 17, 2023
4b3fcce
+ calgary_campinas_dataset.py class now is working. I created a tempr…
amirshamaei Oct 18, 2023
e6fdd38
+ dataloader works. tested with target with rss
amirshamaei Nov 1, 2023
7b42d65
+ some changes to paths
amirshamaei Nov 1, 2023
50dc577
+ some changes to paths
amirshamaei Nov 1, 2023
41cdd8f
+ some changes to paths
amirshamaei Nov 1, 2023
3015702
+ to run as a job
amirshamaei Nov 2, 2023
3cfbd94
+ to run as a job
amirshamaei Nov 2, 2023
fe87c93
+ to run as a job
amirshamaei Nov 2, 2023
b24fb9a
+ to run as a job
amirshamaei Nov 2, 2023
d726af5
+ to run as a job
amirshamaei Nov 2, 2023
67382de
+ to run as a job
amirshamaei Nov 2, 2023
83d6cd8
+ to run as a job
amirshamaei Nov 2, 2023
4dd9c74
+ to run as a job
amirshamaei Nov 2, 2023
832081f
+ to run as a job
amirshamaei Nov 2, 2023
91be900
+ to run as a job
amirshamaei Nov 2, 2023
6cd7905
+ to run as a job
amirshamaei Nov 2, 2023
7786882
+ to run as a job
amirshamaei Nov 2, 2023
97bb600
+ to run as a job
amirshamaei Nov 2, 2023
993895c
+ to run as a job
amirshamaei Nov 3, 2023
b330a51
+ to run as a job
amirshamaei Nov 3, 2023
7202a21
+ to run as a job
amirshamaei Nov 3, 2023
819608e
+ to run as a job
amirshamaei Nov 3, 2023
1792754
+ to run as a job
amirshamaei Nov 3, 2023
b3f499f
+ add r2 loss
amirshamaei Nov 3, 2023
e128eb6
+ add r2 loss
amirshamaei Nov 3, 2023
24ae268
+ add r2 loss
amirshamaei Nov 5, 2023
583cd92
+ refine exp
amirshamaei Nov 5, 2023
05b84ac
+ refine exp
amirshamaei Nov 5, 2023
476c92c
+ refine exp
amirshamaei Nov 5, 2023
1525d85
+ refine exp
amirshamaei Nov 5, 2023
a3eae2b
+ refine exp
amirshamaei Nov 5, 2023
6beff36
+ 3d ecperiment has been added
amirshamaei Nov 6, 2023
b4ebe4c
+ 3d ecperiment has been added
amirshamaei Nov 7, 2023
de152d8
+ make eval testing
amirshamaei Nov 7, 2023
575846c
+ testing in case of ckpt is provided is fixed
amirshamaei Nov 7, 2023
fb1dc41
+ testing in case of ckpt is provided is fixed
amirshamaei Nov 7, 2023
c64e971
+ testing in case of ckpt is provided is fixed
amirshamaei Nov 7, 2023
8136ea2
+ testing in case of ckpt is provided is fixed
amirshamaei Nov 7, 2023
b21cfe6
+ 3d training with new arch
amirshamaei Nov 7, 2023
c482679
+ 3d training with new arch
amirshamaei Nov 7, 2023
545ea3f
+ longitudinal experiment has been added
amirshamaei Nov 10, 2023
16c21b4
+ 3d model compared with normal
amirshamaei Nov 10, 2023
7a86108
+ add check point
amirshamaei Nov 11, 2023
af6270f
+ add check point
amirshamaei Nov 11, 2023
dc4fddf
+ trying to test one subj as one batch
amirshamaei Nov 11, 2023
0481df4
+ trying to test one subj as one batch
amirshamaei Nov 11, 2023
216e2b2
+ trying to test one subj as one batch
amirshamaei Nov 11, 2023
600d720
+ trying to test one subj as one batch
amirshamaei Nov 12, 2023
2f19ba2
+ trying to test one subj as one batch
amirshamaei Nov 12, 2023
2cd1493
+ multivisit tested but result is not good
amirshamaei Nov 14, 2023
33916b1
+ start of fine tuning
amirshamaei Nov 17, 2023
011a376
+ start of fine tuning
amirshamaei Nov 17, 2023
04ddcc5
+ test without r2
amirshamaei Nov 17, 2023
78aa97d
+ transformers has been added
amirshamaei Nov 17, 2023
4296176
+ transformers has been added
amirshamaei Nov 19, 2023
d5ca9bf
+ matplotlib outofmemeory got fixed
amirshamaei Nov 22, 2023
fe9db21
+ R15 sampling has been added
amirshamaei Nov 22, 2023
4edae47
+ R15 sampling has been fixed
amirshamaei Nov 23, 2023
c39fe7b
+ R15 sampling has been added
amirshamaei Nov 30, 2023
193f8e6
+ testing mutivisit.py on cluster
amirshamaei Dec 1, 2023
5c918e1
fromarc
amirshamaei Dec 3, 2023
4902bff
from_arc
amirshamaei Dec 4, 2023
5a946d9
+ stable diffusion cross attention
amirshamaei Dec 5, 2023
8b227a5
+ stable diffusion cross attention
amirshamaei Dec 5, 2023
eccad6d
+ stable diffusion cross attention
amirshamaei Dec 5, 2023
4b60361
+ yousef's work has been added mv_reg
amirshamaei Dec 7, 2023
f5f9435
from_arc
amirshamaei Dec 7, 2023
d0fdaf7
+ new idea of cross attention
amirshamaei Dec 8, 2023
50ba16c
+ new idea of cross attention
amirshamaei Dec 8, 2023
55e05f0
+ new idea of cross attention
amirshamaei Dec 8, 2023
b932918
+rich prog bar removed
amirshamaei Dec 8, 2023
b313e9f
+ new idea of cross attention
amirshamaei Dec 8, 2023
5164b2f
+ meta file got corrected
amirshamaei Dec 8, 2023
689113d
+ new idea of cross attention
amirshamaei Dec 8, 2023
4691915
+ new idea of cross attention
amirshamaei Dec 8, 2023
c3139b1
+ new idea of cross attention
amirshamaei Dec 8, 2023
7bf7c32
+ new idea of cross attention
amirshamaei Dec 11, 2023
9f0ac30
+ new idea of cross attention
amirshamaei Dec 11, 2023
ad7ef1e
from_arc
amirshamaei Dec 21, 2023
f533ed8
++ baysian modeling is added
amirshamaei Dec 21, 2023
188ca5d
++ baysian modeling is added
amirshamaei Dec 21, 2023
96f15fc
++ self supervised added + new self supervised idea
amirshamaei Dec 22, 2023
2bfd738
++ self supervised with ratio masking
amirshamaei Dec 22, 2023
8ed42cd
from_arc
amirshamaei Jan 4, 2024
f85691b
++ self supervised with ratio masking
amirshamaei Jan 5, 2024
8968f67
from_arc
amirshamaei Jan 9, 2024
293a3aa
++ bayes
amirshamaei Jan 9, 2024
6aac9ae
merge branch 'main' of https://github.com/amirshamaei/MRI_REC_template
amirshamaei Jan 9, 2024
66912bd
from_arc
amirshamaei Jan 9, 2024
60af913
++ bayes
amirshamaei Jan 9, 2024
aec5e48
from_arc
amirshamaei Jan 11, 2024
90701de
++ csvs updated
amirshamaei Jan 11, 2024
742246e
from_arc
amirshamaei Jan 12, 2024
09183cf
some_change_from_Arc
amirshamaei Jan 15, 2024
a617cc2
++ csvs updated
amirshamaei Jan 15, 2024
7f26464
++ csvs updated
amirshamaei Jan 17, 2024
ec8b022
from arc
amirshamaei Jan 18, 2024
db5bc51
++ csvs updated
amirshamaei Jan 18, 2024
1739166
stash
amirshamaei Jan 18, 2024
b0b96e2
Merge branch 'main' of https://github.com/amirshamaei/MRI_REC_template
amirshamaei Jan 18, 2024
2f2336f
++ csvs updated
amirshamaei Jan 18, 2024
eaa52cf
Merge branch 'main' of https://github.com/amirshamaei/MRI_REC_template
amirshamaei Jan 18, 2024
84e0bed
++ csvs updated
amirshamaei Jan 22, 2024
3bd1730
Merge branch 'main' of https://github.com/amirshamaei/MRI_REC_template
amirshamaei Jan 22, 2024
7fdfe01
+ new idea of cross attention
amirshamaei Feb 8, 2024
7251f96
+ with new data from roberto
amirshamaei Feb 15, 2024
ab1a682
from_arc
amirshamaei Feb 15, 2024
d3a3816
from_arc
amirshamaei Feb 15, 2024
80e755b
+ with unetr
amirshamaei Feb 17, 2024
c8c7e91
Merge branch 'main' of https://github.com/amirshamaei/MRI_REC_template
amirshamaei Feb 17, 2024
85e2c7f
+ with tryon unet
amirshamaei Feb 18, 2024
5772d17
Merge branch 'main' of https://github.com/amirshamaei/MRI_REC_template
amirshamaei Feb 18, 2024
4422ef1
+ with stable diffusion
amirshamaei Feb 20, 2024
846917a
Merge branch 'main' of https://github.com/amirshamaei/MRI_REC_template
amirshamaei Feb 20, 2024
b0df756
+ 2d vs 3d roberto
amirshamaei Feb 22, 2024
3a4730d
Merge branch 'main' of https://github.com/amirshamaei/MRI_REC_template
amirshamaei Feb 22, 2024
12bc0c7
with_DiT
amirshamaei Mar 8, 2024
50c24c7
with_DiT
amirshamaei Mar 11, 2024
757f9a3
+ with DiT 3d
amirshamaei Mar 11, 2024
afa25e4
+ with DiT 3d
amirshamaei Mar 11, 2024
439cf8e
dit_outperformed
amirshamaei Apr 28, 2024
1e9a516
large update with baysian
amirshamaei Sep 15, 2024
cccf71f
update_on_Arc
amirshamaei Sep 22, 2024
f9b01af
++ add experiment for windows
amirshamaei Sep 22, 2024
d5c4f9a
from narval
Sep 24, 2024
e2db6fa
++ add experiment for windows
amirshamaei Sep 24, 2024
fc7e1c2
++ add noise transform
amirshamaei Sep 25, 2024
7a1776e
++ add affine transform
amirshamaei Sep 25, 2024
4ed202a
++ add elastic deformation
amirshamaei Sep 25, 2024
dd0e702
from narval after getting results
Oct 14, 2024
94efdba
++ add mcdo for narval
amirshamaei Oct 14, 2024
5cf6d54
some small changes in mcdo
Oct 15, 2024
0c9fe25
MCDO_RESULTS
amirshamaei Oct 19, 2024
8993eec
update gitignore from arc
amirshamaei Oct 19, 2024
506c309
++ first try of synthRec
amirshamaei Oct 28, 2024
104a269
Update mri_calgary_campinas_module_mv.py
amirshamaei Jan 19, 2025
e438fac
Update mri_calgary_campinas_module.py
amirshamaei Jan 19, 2025
b980d0f
Update mri_calgary_campinas_module.py
amirshamaei Jan 19, 2025
d880fa6
Update calgary_campinas_datamodule.py
amirshamaei Jan 19, 2025
03790d6
Update calgary_campinas_datamodule.py
amirshamaei Jan 19, 2025
a90091f
Update calgary_campinas_datamodule.py
amirshamaei Jan 19, 2025
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
10 changes: 9 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -146,9 +146,17 @@ dmypy.json

# Lightning-Hydra-Template
configs/local/default.yaml
/data/

/logs/
.env

# Aim logging
.aim

/data/MNIST/


/bayesian-torch/
projects/uncertainty/2024-07-16_18-49-40/
projects/uncertainty/2024-07-16_19-18-17/
projects/uncertainty/R20/
30 changes: 27 additions & 3 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -40,10 +40,33 @@ repos:

# python docstring formatting
- repo: https://github.com/myint/docformatter
rev: v1.5.1
rev: v1.7.4
hooks:
- id: docformatter
args: [--in-place, --wrap-summaries=99, --wrap-descriptions=99]
args:
[
--in-place,
--wrap-summaries=99,
--wrap-descriptions=99,
--style=sphinx,
--black,
]

# python docstring coverage checking
- repo: https://github.com/econchick/interrogate
rev: 1.5.0 # or master if you're bold
hooks:
- id: interrogate
args:
[
--verbose,
--fail-under=80,
--ignore-init-module,
--ignore-init-method,
--ignore-module,
--ignore-nested-functions,
-vv,
]

# python check (PEP8), programming errors and code complexity
- repo: https://github.com/PyCQA/flake8
Expand All @@ -53,10 +76,11 @@ repos:
args:
[
"--extend-ignore",
"E203,E402,E501,F401,F841",
"E203,E402,E501,F401,F841,RST2,RST301",
"--exclude",
"logs/*,data/*",
]
additional_dependencies: [flake8-rst-docstrings==0.3.0]

# python security linter
- repo: https://github.com/PyCQA/bandit
Expand Down
Loading
Loading