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New main #53

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merged 366 commits into from
Jan 10, 2024
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e208ed9
changed that ctf is randomly selected at each image
Dingel321 Mar 14, 2023
3698158
changed that ctf is randomly selected at each image
Dingel321 Mar 14, 2023
e348b86
chnaged calculation of ctf (less copying of tensors), add log prior f…
Dingel321 Mar 14, 2023
f4a5e38
chnaged calculation of ctf (less copying of tensors), add log prior f…
Dingel321 Mar 14, 2023
329c538
minor changes to external files
Dingel321 Mar 14, 2023
3b51d1a
minor changes to external files
Dingel321 Mar 14, 2023
377b739
updated readme with training
Dingel321 Mar 14, 2023
2abfbf2
updated readme with training
Dingel321 Mar 14, 2023
9713be0
fix memory error in simulator
Mar 15, 2023
5273692
fix memory error in simulator
Mar 15, 2023
97f3c5e
removed unwanted dir
Mar 15, 2023
3eb19c6
removed unwanted dir
Mar 15, 2023
7430bd4
Merge branch 'iss7' of github.com:DSilva27/cryo_em_SBI into iss7
Mar 15, 2023
03d48d7
Merge branch 'iss7' of github.com:DSilva27/cryo_em_SBI into iss7
Mar 15, 2023
e520b39
fix return error in simulator
Mar 15, 2023
4269889
fix return error in simulator
Mar 15, 2023
4fda03b
update tutorial
Mar 15, 2023
b025278
update tutorial
Mar 15, 2023
1501de7
Merge branch 'develop' into iss6
Mar 15, 2023
8d46d7a
Merge branch 'develop' into iss6
Mar 15, 2023
242fc0f
fixes some default variables in inference methods
Mar 15, 2023
a00524d
fixes some default variables in inference methods
Mar 15, 2023
f31e472
implement unit tests for the simulator
Mar 16, 2023
245766a
implement unit tests for the simulator
Mar 16, 2023
60630b0
Create python-package.yml
DSilva27 Mar 16, 2023
9aa29f8
Create python-package.yml
DSilva27 Mar 16, 2023
d34f9d3
Merge pull request #10 from DSilva27/iss8
DSilva27 Mar 16, 2023
7d27ed9
Merge pull request #10 from DSilva27/iss8
DSilva27 Mar 16, 2023
a67db6a
Revert "Create python-package.yml"
DSilva27 Mar 16, 2023
532e853
Revert "Create python-package.yml"
DSilva27 Mar 16, 2023
e2427f4
Merge pull request #11 from DSilva27/revert-10-iss8
DSilva27 Mar 16, 2023
1b65b6e
Merge pull request #11 from DSilva27/revert-10-iss8
DSilva27 Mar 16, 2023
820a013
add GitHub actions closes #9
Mar 16, 2023
92cd5b4
add GitHub actions closes #9
Mar 16, 2023
787360f
Merge branch 'iss6' of github.com:DSilva27/cryo_em_SBI into iss6
Mar 16, 2023
a83dec6
Merge branch 'iss6' of github.com:DSilva27/cryo_em_SBI into iss6
Mar 16, 2023
ee2384e
fix GitHub actions
Mar 16, 2023
ab16543
fix GitHub actions
Mar 16, 2023
f1ea33c
update Actions
Mar 16, 2023
cd6501f
update Actions
Mar 16, 2023
0975aab
update Actions
Mar 16, 2023
08bf664
update Actions
Mar 16, 2023
30cdae3
update Actions
Mar 16, 2023
6b58d9e
update Actions
Mar 16, 2023
9f4fab4
fix pyporject.toml
Mar 16, 2023
77a4dca
fix pyporject.toml
Mar 16, 2023
5731b8d
fix pyporject.toml
Mar 16, 2023
f2ffedd
fix pyporject.toml
Mar 16, 2023
44a17be
update README
Mar 16, 2023
d868e56
update README
Mar 16, 2023
ac7218a
tidy up repo
Mar 16, 2023
aba5513
tidy up repo
Mar 16, 2023
3c3def1
small chnages and added config_files
Dingel321 Mar 17, 2023
0aa2e74
small chnages and added config_files
Dingel321 Mar 17, 2023
b3fdd30
this commit should resolve merge
Dingel321 Mar 17, 2023
b63eb47
this commit should resolve merge
Dingel321 Mar 17, 2023
11cfaf7
Merge pull request #12 from DSilva27/iss9
Dingel321 Mar 17, 2023
293b47a
Merge pull request #12 from DSilva27/iss9
Dingel321 Mar 17, 2023
6dd5036
deleted dead code from simulator parts
Dingel321 Mar 20, 2023
66ca458
deleted dead code from simulator parts
Dingel321 Mar 20, 2023
8679cfb
simplified simulator and fixed test failure
Dingel321 Mar 20, 2023
2d133a7
simplified simulator and fixed test failure
Dingel321 Mar 20, 2023
94cd6f3
changed hsp90 experiment setup
Dingel321 Mar 20, 2023
756e068
changed hsp90 experiment setup
Dingel321 Mar 20, 2023
64fe1e3
added indexing=ij to ctf calculation in order to remove warning
Dingel321 Mar 20, 2023
b282d48
added indexing=ij to ctf calculation in order to remove warning
Dingel321 Mar 20, 2023
b06d74e
added tests for estimator utils
Dingel321 Mar 20, 2023
d0af69f
added tests for estimator utils
Dingel321 Mar 20, 2023
17ab0ae
small changes to notebooks and config files
Dingel321 Mar 21, 2023
e539a14
small changes to notebooks and config files
Dingel321 Mar 21, 2023
1a6b082
removed output from notebooks
Dingel321 Mar 21, 2023
a750143
removed output from notebooks
Dingel321 Mar 21, 2023
2c9c746
added first prototype to simulate crowded enviroments
Dingel321 Mar 21, 2023
483aa9c
added first prototype to simulate crowded enviroments
Dingel321 Mar 21, 2023
465fab3
file formattings
Dingel321 Mar 21, 2023
028fc95
file formattings
Dingel321 Mar 21, 2023
e7d9aea
Update noise.py
DSilva27 Mar 24, 2023
db1db3c
Update noise.py
DSilva27 Mar 24, 2023
bb6e94e
small changes
Dingel321 Mar 24, 2023
3631ace
small changes
Dingel321 Mar 24, 2023
79216f6
Merge branch 'develop' of https://github.com/DSilva27/cryo_em_SBI int…
Dingel321 Mar 24, 2023
99e6124
Merge branch 'develop' of https://github.com/DSilva27/cryo_em_SBI int…
Dingel321 Mar 24, 2023
67f9136
added noise different types of noise to noise.py
Dingel321 Mar 24, 2023
4f2d384
added noise different types of noise to noise.py
Dingel321 Mar 24, 2023
e85ae9c
chnaged noise back ' just for a couple of days (since test failed)
Dingel321 Mar 24, 2023
8fbfa21
chnaged noise back ' just for a couple of days (since test failed)
Dingel321 Mar 24, 2023
1ec2da3
added way to modify noise in simulator
Dingel321 Mar 27, 2023
35b744c
added way to modify noise in simulator
Dingel321 Mar 27, 2023
34719d9
changed shape inference in noise.py
Dingel321 Mar 27, 2023
4a96a4a
changed shape inference in noise.py
Dingel321 Mar 27, 2023
b1ec79a
added utils for image modifications and added lowpassfilter embedding
Dingel321 Mar 28, 2023
a945d7c
added utils for image modifications and added lowpassfilter embedding
Dingel321 Mar 28, 2023
eb59a27
formatted code
Dingel321 Mar 28, 2023
a648f58
formatted code
Dingel321 Mar 28, 2023
283aa9f
added images utils with function for torch transforms
Dingel321 Mar 31, 2023
1b49e40
added images utils with function for torch transforms
Dingel321 Mar 31, 2023
d559e34
added a range for sigma
Dingel321 Apr 1, 2023
fc10aa8
added a range for sigma
Dingel321 Apr 1, 2023
654ff33
new embedding with image masking
Dingel321 Apr 3, 2023
9167281
new embedding with image masking
Dingel321 Apr 3, 2023
ae7d654
Update pyproject.toml
DSilva27 Apr 3, 2023
e86e07a
Update pyproject.toml
DSilva27 Apr 3, 2023
a5b519d
added embedding and config files for posteriors
Dingel321 Apr 3, 2023
1626c98
added embedding and config files for posteriors
Dingel321 Apr 3, 2023
89592f6
added new embedding and some utils functions
Dingel321 Apr 6, 2023
0ae8e12
added new embedding and some utils functions
Dingel321 Apr 6, 2023
3e54ba3
organized and deleted some unused files
Dingel321 Apr 14, 2023
a6646d4
organized and deleted some unused files
Dingel321 Apr 14, 2023
de4906f
added current notebooks
Dingel321 Apr 14, 2023
529bfc0
added current notebooks
Dingel321 Apr 14, 2023
2d2f838
added documentation in image utils
Dingel321 Apr 17, 2023
994ec58
added documentation in image utils
Dingel321 Apr 17, 2023
21412dd
added some docstrings
Dingel321 Apr 17, 2023
ac20143
added some docstrings
Dingel321 Apr 17, 2023
4930647
Assed some docstrings.
Dingel321 Apr 17, 2023
45889cd
Assed some docstrings.
Dingel321 Apr 17, 2023
5438474
fixed wrong name in test_utils.py
Dingel321 Apr 17, 2023
232a7a8
fixed wrong name in test_utils.py
Dingel321 Apr 17, 2023
e3c58b9
added doc strings for almost all functions
Dingel321 Apr 17, 2023
e4f9529
added doc strings for almost all functions
Dingel321 Apr 17, 2023
730d7b3
added function for implicit water
Dingel321 Apr 24, 2023
e415e6b
added function for implicit water
Dingel321 Apr 24, 2023
4ea335e
updated image utils documentation
Dingel321 May 11, 2023
2262b5f
updated image utils documentation
Dingel321 May 11, 2023
6ca42e5
reformatted code
Dingel321 May 11, 2023
f2cb7e2
reformatted code
Dingel321 May 11, 2023
190d2f5
cleaned up code
Dingel321 May 11, 2023
cea2265
cleaned up code
Dingel321 May 11, 2023
9ca2577
removed unused imports and a bug
Dingel321 May 15, 2023
cd57001
removed unused imports and a bug
Dingel321 May 15, 2023
e05b11a
changed workflow back
Dingel321 May 15, 2023
c7229cb
changed workflow back
Dingel321 May 15, 2023
747973b
cleaned simulator code
Dingel321 May 15, 2023
1413aa4
cleaned simulator code
Dingel321 May 15, 2023
dc3707d
add documentation for inference functions
Dingel321 May 15, 2023
4c75625
add documentation for inference functions
Dingel321 May 15, 2023
9f674bf
formatted code for inference functions
Dingel321 May 15, 2023
4e49820
formatted code for inference functions
Dingel321 May 15, 2023
ba9ffd5
updated image utils
Dingel321 May 16, 2023
4dce962
updated image utils
Dingel321 May 16, 2023
03d49db
updated image param files in 6wxb experiment
Dingel321 May 16, 2023
0697ca9
updated image param files in 6wxb experiment
Dingel321 May 16, 2023
477fb48
formatted code and added micrograph utils
Dingel321 May 16, 2023
e4e5abf
formatted code and added micrograph utils
Dingel321 May 16, 2023
10ad26a
Merge pull request #15 from DSilva27/whitend_images
Dingel321 May 16, 2023
3d494b5
Merge pull request #15 from DSilva27/whitend_images
Dingel321 May 16, 2023
5625aa7
cleaned impoerts up
Dingel321 May 16, 2023
44b6833
cleaned impoerts up
Dingel321 May 16, 2023
a98da10
Merge branch 'develop' into clean_up
Dingel321 May 16, 2023
0d223ac
Merge branch 'develop' into clean_up
Dingel321 May 16, 2023
51049df
Merge pull request #16 from DSilva27/clean_up
Dingel321 May 16, 2023
fdefea1
Merge pull request #16 from DSilva27/clean_up
Dingel321 May 16, 2023
facb127
cleaned inference code
Dingel321 May 16, 2023
071d021
cleaned inference code
Dingel321 May 16, 2023
a1018ac
cleaned generate training set code
Dingel321 May 16, 2023
a9cdf66
cleaned generate training set code
Dingel321 May 16, 2023
b4dc604
added command line options fromtraining and new models
Dingel321 May 16, 2023
92ba23d
added command line options fromtraining and new models
Dingel321 May 16, 2023
84ef25d
added specific gitignore to notebook folder
Dingel321 May 16, 2023
9687897
added specific gitignore to notebook folder
Dingel321 May 16, 2023
38f53c6
contains updated type hints and all updated notebooks
Dingel321 May 16, 2023
af7e7ed
contains updated type hints and all updated notebooks
Dingel321 May 16, 2023
fe1957f
Update README.rst
Dingel321 May 16, 2023
036e849
Update README.rst
Dingel321 May 16, 2023
8d4ae7a
removed some final bugs and added minor improvements
Dingel321 May 17, 2023
7d4dd36
removed some final bugs and added minor improvements
Dingel321 May 17, 2023
4c6a7e4
wrong device specified in train.sh
Dingel321 May 17, 2023
9949d31
wrong device specified in train.sh
Dingel321 May 17, 2023
410e74f
some minor reformatting in notebooks
Dingel321 May 17, 2023
572caae
some minor reformatting in notebooks
Dingel321 May 17, 2023
2ab5a7a
add minor optimization with torch.jit.script
Dingel321 May 22, 2023
db199a7
add minor optimization with torch.jit.script
Dingel321 May 22, 2023
9a20480
added optimized torch.jit code
Dingel321 May 23, 2023
be1712c
added optimized torch.jit code
Dingel321 May 23, 2023
5098bb3
optimized image generation
Dingel321 May 23, 2023
9bc020f
optimized image generation
Dingel321 May 23, 2023
5109c2f
formatted image generation
Dingel321 May 23, 2023
cd1f002
formatted image generation
Dingel321 May 23, 2023
b2d91f6
switched to torchs functional nn padding function
Dingel321 May 23, 2023
e415e13
switched to torchs functional nn padding function
Dingel321 May 23, 2023
931d2b0
solved minor bugs
Dingel321 May 23, 2023
93e1055
solved minor bugs
Dingel321 May 23, 2023
9b1d860
final notebooks
Dingel321 May 26, 2023
fbcfd08
final notebooks
Dingel321 May 26, 2023
5e1c2df
cleaned notebook
Dingel321 May 26, 2023
d7315ec
cleaned notebook
Dingel321 May 26, 2023
3aaf742
fromatted notebook
Dingel321 May 26, 2023
69b9359
fromatted notebook
Dingel321 May 26, 2023
04c692c
updated docs in image utils
Dingel321 May 31, 2023
115b1c1
updated docs in image utils
Dingel321 May 31, 2023
2258182
added variable b-factor in the simulator
Dingel321 Jun 1, 2023
e15151f
added variable b-factor in the simulator
Dingel321 Jun 1, 2023
637cc6a
added variable bfactor to ctf adjusted corresponding test
Dingel321 Jun 1, 2023
198b98f
added variable bfactor to ctf adjusted corresponding test
Dingel321 Jun 1, 2023
85fedcc
added image whitening to training
Dingel321 Jun 1, 2023
7f51c1d
added image whitening to training
Dingel321 Jun 1, 2023
573e7f9
updated global .gitignore
Dingel321 Jun 1, 2023
27ce0ca
updated global .gitignore
Dingel321 Jun 1, 2023
03ae15e
formatted code
Dingel321 Jun 1, 2023
89dd364
formatted code
Dingel321 Jun 1, 2023
67021c8
added whitening filter ass command line arg
Dingel321 Jun 2, 2023
6ac69c5
added whitening filter ass command line arg
Dingel321 Jun 2, 2023
171c873
added newest training settings
Jun 2, 2023
ee3c1be
added newest training settings
Jun 2, 2023
edb8e6a
added new pytorch mrc loader and updated training settings
Jun 6, 2023
90c2ace
added new pytorch mrc loader and updated training settings
Jun 6, 2023
706896c
formatted code and added type hints
Jun 6, 2023
706b62e
formatted code and added type hints
Jun 6, 2023
ed56d75
added pztorch dataloader and dataset for mrc files
Dingel321 Jun 8, 2023
7b11aee
added pztorch dataloader and dataset for mrc files
Dingel321 Jun 8, 2023
c2563ca
changed training parameters
Dingel321 Jun 8, 2023
7d2765e
changed training parameters
Dingel321 Jun 8, 2023
52c1e59
fixed problem in model loading
Dingel321 Jun 12, 2023
1586e98
fixed problem in model loading
Dingel321 Jun 12, 2023
1e9c3cd
first gpu implementation
Dingel321 Jun 13, 2023
f9d0971
first gpu implementation
Dingel321 Jun 13, 2023
ed310bc
added newest version of gpu simulator
Dingel321 Jun 15, 2023
4fc4364
deleted all particles npz
Dingel321 Jun 22, 2023
f66ff91
Merge branch 'gpu_simulator' of https://github.com/DSilva27/cryo_em_S…
Dingel321 Jun 22, 2023
65eb909
first prototype
Dingel321 Jul 3, 2023
4ccbe60
corrected noise prior
Dingel321 Jul 3, 2023
095ef93
corrected snr prior
Dingel321 Jul 3, 2023
47c14be
debugging gpu simulator
Dingel321 Jul 3, 2023
7cb0ca0
notebook update
Dingel321 Jul 4, 2023
ca27183
notebook update
Dingel321 Jul 4, 2023
3867c34
added all functions to simulator
Dingel321 Jul 5, 2023
f34e26b
new version gpu simulator
Dingel321 Jul 14, 2023
3debf9a
added backbone of eval_log_prob class
Dingel321 Jul 19, 2023
23e0a65
small bug fixes and changes in the embeddings
Dingel321 Jul 25, 2023
d953d01
include physical information in simulator and implement pdb/traj pars…
DSilva27 Jul 29, 2023
2f03b8c
replace SIGMA for RES in every instance
DSilva27 Jul 29, 2023
2905945
updated all atom branch
Dingel321 Aug 11, 2023
6fc6c22
changed code formatting
Dingel321 Aug 17, 2023
b9f8ddb
fixed bug in traj parser and npewithembedding
Dingel321 Aug 18, 2023
f4e2481
changed definition of atom sigma to bioEM radius
Dingel321 Aug 25, 2023
29353ec
added embedding nets for all expermental setups
Dingel321 Sep 25, 2023
ecf0020
ficed bug in pdb parser
Dingel321 Sep 25, 2023
d8e708e
introduced goarse grained lipid bead
Dingel321 Sep 29, 2023
7a92214
Merge branch 'iss42' of https://github.com/DSilva27/cryo_em_SBI into …
Dingel321 Sep 29, 2023
47631ef
batched simulator in CryoEmSimulator class
Dingel321 Oct 6, 2023
121bb32
all beads are the same in simulator
Dingel321 Oct 20, 2023
1688086
removed old notebooks and experiment files
Dingel321 Oct 20, 2023
c0cffdf
removed deprecated tests and added config files and models for tests
Dingel321 Oct 20, 2023
902805b
updated the readme
Dingel321 Oct 20, 2023
84a5ceb
chnaged title of repo in readme
Dingel321 Oct 20, 2023
4d7002a
titile typo
Dingel321 Oct 20, 2023
9c5b59b
added pdb and traj parser to generate_model.pdb
Dingel321 Oct 20, 2023
6225a18
added eval_log_prob function
Dingel321 Oct 20, 2023
762b900
cleaned train_npe
Dingel321 Dec 6, 2023
a5c9bf9
updated doc strings in generate models
Dingel321 Jan 8, 2024
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notebook update
Dingel321 committed Jul 4, 2023
commit ca2718365c7c883b976437c18e50f3070f3d841b
43 changes: 26 additions & 17 deletions notebooks/Untitled.ipynb

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