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O2vae integration #1

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O2vae integration #1

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@ctr26 ctr26 commented Oct 1, 2024

test

ctr26 and others added 30 commits January 15, 2024 15:07
@ctr26
Removing umap feature compression
7b43109
@ctr26
Merge pull request uhlmanngroup#19 from ctr26/decoder_fix
e58fbac 
Decoder fix
@ctr26
Merge pull request uhlmanngroup#21 from ctr26/no_umap
38cf94d 
Removing umap feature compression
@ctr26
Indexation augmentation (forgot this wasnt in here)
b17827a
@ctr26
Fixed the import issue
5cf77fc
@ctr26
missing import
9273f8c
@ctr26
Merge pull request uhlmanngroup#17 from ctr26/indexation_aug
1abc9d6 
Indexation augmentation (forgot this wasnt in here)
@ctr26
Fixing tests
5f46b74
@ctr26
First attempt at setting up the testing cicd
0fc9066
@ctr26
adding windows back in?
8a2d14d
@ctr26
commented instead I think this makes more sense
74f2d13
@ctr26
removing snakemake from env
c190e04
@ctr26
Forgot to remove sourceing
1e657fd
@ctr26
Merge pull request uhlmanngroup#22 from ctr26/cicd
9a61af2 
First attempt at setting up the testing cicd
@ctr26
Generalised the logging a bit
510aa04
@ctr26
First attempt as arg hashing for checkpoints
3b37ca9
@ctr26
Early stopping on val loss to stop overfitting
8e18943
@ctr26
Attempt at cli
397abe8
@afoix
Merge remote-tracking branch 'origin/hashing_model_args' into all_tog…
8534143 
…ether
@ctr26
Merge pull request uhlmanngroup#34 from ctr26/logger_improve
e4e26a9 
Generalised the logging a bit
@ctr26
Merge pull request uhlmanngroup#35 from ctr26/hashing_model_args
820b816 
First attempt as arg hashing for checkpoints
@ctr26
Early stopping on val loss to stop overfitting
4bf27f9
@ctr26
adding branch prose back
4ca9dd0
@afoix
Merge branch 'master' into all_together
0068fa0
@afoix
Merge remote-tracking branch 'origin/early_stopping' into all_together
26bf58c
@afoix
Merge remote-tracking branch 'origin/readme_edits' into all_together
1d5c49c
@afoix
local changes to run
a34ee72
@afoix
command line arguments
9135043
@afoix
enable testing + uncomment dataset
43c6ed0
@afoix
added a slurm python script
e4e0aae
afoix added 28 commits July 21, 2024 23:36
@afoix
Split model name in two columns if there are model args
d802f9a
@afoix
remove stale import
663cc52
@afoix
experiment with plots
7d328d9
@afoix
keep exploring potential plots
e3796ba
@afoix
more graphs
cecde4e
@afoix
fix model name in shapeembed output csv
344cff1
@afoix
Added loss / mse to shapeembed's generated csv
6846ce1
@afoix
updated slurm script with regex filtering of squeue output
7a8972f
@afoix
added a simple latex table to the gather_run_results script
d9c87a3
@afoix
minor refactor in efd
cced4e9
@afoix
minor refactor in regionprops
3e6e4c9
@afoix
generated plots and more tables in gather_run_results
2908c15
@afoix
added regionprops and efd to gather results script
41d4603
@afoix
Updated graphs titles
251d85f
@afoix
fake beta column if necessary and filter out regionprops and efd for …
932b13a 
…f1 Vs Mse comparison
@afoix
updated datasets + only find jobs and scores if corresponding filter …
61f8e17 
…active
@afoix
bugfix overwriting loop dataframe
583e835
@afoix
dded a clarg to control region prop properties
07bb89c
@afoix
Added random order to efd and regionprops
a35490c
@afoix
force different markers for scatter plot F1vMSE
83a7679
@afoix
updated scatterplot
b9c64d5
@afoix
add standard deviation to the report for regions props and efd
d51a120
@afoix
modification slurm script
c0232c7
@afoix
changes to test o2vae integration XXX relies on an adapted o2vae repo…
870aa42 
… present in bioimage_embed/modles/o2vae
@afoix
off-by-one in square recrop
6fa5cc9
@afoix
added drop_last for uneven dataset sizes
85ce853
@afoix
specialized slurm script
db3a4fb
@afoix
added o2vae repo patch
c45b884
@ctr26 ctr26 changed the base branch from main to dev October 1, 2024 15:24
@ctr26 ctr26 changed the base branch from dev to main October 1, 2024 15:26
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2 participants
@ctr26 @afoix