Code

Static dev#3

Code

Open

mat10d wants to merge 138 commits intomainCryaaa/embed_time:mainfrom static_devCryaaa/embed_time:static_devCopy head branch name to clipboard

+15,798-3

Commits

Commits on Aug 30, 2024

• first commit of dataset for non-time

  mat10d

  committed
  bbd10c1

  Copy full SHA for bbd10c1

• moved dataset static to src

  mat10d

  committed
  01cc47b

  Copy full SHA for 01cc47b

• added dataloader

  mat10d

  committed
  3d22b75

  Copy full SHA for 3d22b75

• tested static dataset

  mat10d

  committed
  3edf003

  Copy full SHA for 3edf003

• add pyproject commit

  mat10d

  committed
  6a5fca1

  Copy full SHA for 6a5fca1

• added data split code

  mat10d

  committed
  cb99bc1

  Copy full SHA for cb99bc1

• example vae mnist

  

  akila-14

  committed
  76349cd

  Copy full SHA for 76349cd

• finalized dataloader/splitter for static data

  mat10d

  committed
  f3418d5

  Copy full SHA for f3418d5

Commits on Aug 31, 2024

• added dataloader for static

  mat10d

  committed
  3b893dd

  Copy full SHA for 3b893dd

• Update README.md

  Show description for 70c076a
  

  ijan780

  authored and

  akila-14

  committed
  70c076a

  Copy full SHA for 70c076a

• Add black linter

  

  adjavon

  authored and

  akila-14

  committed
  fb57eca

  Copy full SHA for fb57eca

• Add dev setup

  

  adjavon

  authored and

  akila-14

  committed
  2b30da6

  Copy full SHA for 2b30da6

• Add dummy model

  

  adjavon

  authored and

  akila-14

  committed
  e518d29

  Copy full SHA for e518d29

• Add VAE tests

  

  adjavon

  authored and

  akila-14

  committed
  5583578

  Copy full SHA for 5583578

• Add test CI

  

  adjavon

  authored and

  akila-14

  committed
  cc62e47

  Copy full SHA for cc62e47

• Add black linter

  

  adjavon

  authored and

  mat10d

  committed
  e6c0f49

  Copy full SHA for e6c0f49

• fix pyproject

  mat10d

  committed
  71007aa

  Copy full SHA for 71007aa

• Add dummy model

  

  adjavon

  authored and

  mat10d

  committed
  0dabae3

  Copy full SHA for 0dabae3

• Add VAE tests

  

  adjavon

  authored and

  mat10d

  committed
  1f5d0cc

  Copy full SHA for 1f5d0cc

• Add test CI

  

  adjavon

  authored and

  mat10d

  committed
  9865435

  Copy full SHA for 9865435

• new training test notebook

  mat10d

  committed
  70659a4

  Copy full SHA for 70659a4

• notebooks with code to read neuromast dataset

  akila-14

  committed
  d9ea4b1

  Copy full SHA for d9ea4b1

• Merge branch 'static_dev' into Akila

  akila-14

  committed
  aeb9a6c

  Copy full SHA for aeb9a6c

• first training loop!

  mat10d

  committed
  5553fbd

  Copy full SHA for 5553fbd

• Merge branch 'static_dev' into Akila

  akila-14

  committed
  b6dbe4a

  Copy full SHA for b6dbe4a

• overnight changes (minimal)

  mat10d

  committed
  7cabe65

  Copy full SHA for 7cabe65

• cleaned datasets (temp)

  mat10d

  committed
  dac03c5

  Copy full SHA for dac03c5

• preliminary normalization

  mat10d

  committed
  9330d2a

  Copy full SHA for 9330d2a

• commit to save files

  akila-14

  committed
  4a48864

  Copy full SHA for 4a48864

• commit to save

  akila-14

  committed
  d7c59d0

  Copy full SHA for d7c59d0

• pre training

  

  Alecampoy

  authored and

  akila-14

  committed
  a70c677

  Copy full SHA for a70c677

• overnight changes (minimal)

  

  mat10d

  authored and

  akila-14

  committed
  97b5327

  Copy full SHA for 97b5327

• training loop.py

  

  Alecampoy

  authored and

  akila-14

  committed
  0ab9aa8

  Copy full SHA for 0ab9aa8

• test

  

  Alecampoy

  authored and

  akila-14

  committed
  16bfd53

  Copy full SHA for 16bfd53

• Add dev setup

  

  adjavon

  authored and

  akila-14

  committed
  6ab7cb1

  Copy full SHA for 6ab7cb1

• Added dataloader for live-TLS dataset and Notebook to check functionality

  

  Cryaaa

  authored and

  akila-14

  committed
  124c5e3

  Copy full SHA for 124c5e3

• Added notebook entries to test normalization, added those functions to a transforms file

  

  Cryaaa

  authored and

  akila-14

  committed
  405a7d6

  Copy full SHA for 405a7d6

• Fixed dependencies.

  

  ijan780

  authored and

  akila-14

  committed
  3f6c7e0

  Copy full SHA for 3f6c7e0

• Added dependencies.

  

  ijan780

  authored and

  akila-14

  committed
  d827e85

  Copy full SHA for d827e85

• added custom transform for selecting timepoint and added notebook for dataset normalisation

  

  Cryaaa

  authored and

  akila-14

  committed
  05d648a

  Copy full SHA for 05d648a

• Confirmed SelectRandomTimepoint Transform in notebook

  

  Cryaaa

  authored and

  akila-14

  committed
  2e755d4

  Copy full SHA for 2e755d4

• Added UNet based Autoencoder

  

  Cryaaa

  authored and

  akila-14

  committed
  58d4d54

  Copy full SHA for 58d4d54

• adding notebook changes and small space diffs

  

  Cryaaa

  authored and

  akila-14

  committed
  346c27d

  Copy full SHA for 346c27d

• WPI: decoder.

  

  ijan780

  authored and

  akila-14

  committed
  156ddfa

  Copy full SHA for 156ddfa

• Add dev setup

  

  adjavon

  authored and

  akila-14

  committed
  3dc0e60

  Copy full SHA for 3dc0e60

• Added dataloader for live-TLS dataset and Notebook to check functionality

  

  Cryaaa

  authored and

  akila-14

  committed
  c7de5a9

  Copy full SHA for c7de5a9

• Fixed dependencies.

  

  ijan780

  authored and

  akila-14

  committed
  e6bdf3a

  Copy full SHA for e6bdf3a

• added notebook for splitting into train test set

  

  Cryaaa

  authored and

  akila-14

  committed
  a084af0

  Copy full SHA for a084af0

• Remove annoying file (finally)

  

  ijan780

  authored and

  akila-14

  committed
  11740fc

  Copy full SHA for 11740fc

• Added train & Ian's data loader (WPI)

  

  ijan780

  authored and

  akila-14

  committed
  7c69c61

  Copy full SHA for 7c69c61

• added unet based decoder code still unfinished, implemented first training loop with vanilla model

  

  Cryaaa

  authored and

  akila-14

  committed
  f443fe0

  Copy full SHA for f443fe0

• add final convolution to decoder

  

  Cryaaa

  authored and

  akila-14

  committed
  a018a65

  Copy full SHA for a018a65

• Renamed encoder decoder code to something more useful

  

  Cryaaa

  authored and

  akila-14

  committed
  b47dde1

  Copy full SHA for b47dde1

• renaming dataloader

  

  Cryaaa

  authored and

  akila-14

  committed
  5a693f8

  Copy full SHA for 5a693f8

• added folder to scripts to discriminate our work on main

  

  Cryaaa

  authored and

  akila-14

  committed
  81bdfd6

  Copy full SHA for 81bdfd6

• added unsaved changes in train loop

  

  Cryaaa

  authored and

  akila-14

  committed
  8fcf005

  Copy full SHA for 8fcf005

• notebooks with code to read neuromast dataset

  akila-14

  committed
  4058b4e

  Copy full SHA for 4058b4e

• add pyproject commit

  

  mat10d

  authored and

  akila-14

  committed
  508f875

  Copy full SHA for 508f875

• fix pyproject

  

  mat10d

  authored and

  akila-14

  committed
  e18e79e

  Copy full SHA for e18e79e

• fix pyproject.toml

  

  mat10d

  authored and

  akila-14

  committed
  7059180

  Copy full SHA for 7059180

• commit to save files

  akila-14

  committed
  df8a5f2

  Copy full SHA for df8a5f2

• fixing some rebase errors

  akila-14

  committed
  ab50c99

  Copy full SHA for ab50c99

• fixed bug in static

  mat10d

  committed
  09be91a

  Copy full SHA for 09be91a

Commits on Sep 1, 2024

• final normalization push

  mat10d

  committed
  3f93956

  Copy full SHA for 3f93956

• pre training

  

  Alecampoy

  authored and

  mat10d

  committed
  c0ff440

  Copy full SHA for c0ff440

• training loop.py

  

  Alecampoy

  authored and

  mat10d

  committed
  17ada70

  Copy full SHA for 17ada70

• test

  

  Alecampoy

  authored and

  mat10d

  committed
  c19faaf

  Copy full SHA for c19faaf

• cleaned datasets (temp)

  mat10d

  committed
  e097e93

  Copy full SHA for e097e93

• final normalization push

  mat10d

  committed
  3ec5bc7

  Copy full SHA for 3ec5bc7

• version to keep

  mat10d

  committed
  94cabea

  Copy full SHA for 94cabea

• Revert "final normalization push"

  Show description for 385b70f
  mat10d

  committed
  385b70f

  Copy full SHA for 385b70f

• add the script dataset_static

  mat10d

  committed
  9ffe213

  Copy full SHA for 9ffe213

• remove notebooks

  mat10d

  committed
  501b114

  Copy full SHA for 501b114

• training loop with embeddings in tensor board

  akila-14

  committed
  655b109

  Copy full SHA for 655b109

• updated training loop with checkpoints

  akila-14

  committed
  5062ccc

  Copy full SHA for 5062ccc

• added cropping for images

  

  Cryaaa

  authored and

  akila-14

  committed
  1b5fb70

  Copy full SHA for 1b5fb70

• rename first training script

  

  Cryaaa

  authored and

  akila-14

  committed
  992162a

  Copy full SHA for 992162a

• make second train loop and rename UNet encoder name

  

  Cryaaa

  authored and

  akila-14

  committed
  2c19d86

  Copy full SHA for 2c19d86

• removed print statements and fixed bug in decoder training loop of first unet test finished

  

  Cryaaa

  authored and

  akila-14

  committed
  1adff03

  Copy full SHA for 1adff03

• Created model dictionary

  

  ijan780

  authored and

  akila-14

  committed
  6f1ae03

  Copy full SHA for 6f1ae03

• added notebook to check model outs

  

  Cryaaa

  authored and

  akila-14

  committed
  1c5987c

  Copy full SHA for 1c5987c

• added notebook to explore resnet encoder

  

  Cryaaa

  authored and

  akila-14

  committed
  eeae1d7

  Copy full SHA for eeae1d7

• first test with simclr

  

  afoix

  authored and

  akila-14

  committed
  fd1611f

  Copy full SHA for fd1611f

• first serve of the dataloader

  

  afoix

  authored and

  akila-14

  committed
  9bbca88

  Copy full SHA for 9bbca88

• working state dataloader

  

  afoix

  authored and

  akila-14

  committed
  64c2047

  Copy full SHA for 64c2047

• VAE_resnet18 model to test

  

  afoix

  authored and

  akila-14

  committed
  d7511df

  Copy full SHA for d7511df

• fix VAEResnet

  

  afoix

  authored and

  akila-14

  committed
  81274bc

  Copy full SHA for 81274bc

• no bugs, yet to train

  

  Ben-Salmon

  authored and

  akila-14

  committed
  7f78430

  Copy full SHA for 7f78430

• remove in place operations

  

  Ben-Salmon

  authored and

  akila-14

  committed
  f2896bd

  Copy full SHA for f2896bd

• new training on resnet

  Alecampoy

  committed
  4cadf68

  Copy full SHA for 4cadf68

• added resnet taining loop and resnet test notebook

  akila-14

  committed
  27cab32

  Copy full SHA for 27cab32

• cleanup of dataset, sunday

  mat10d

  committed
  7524ad7

  Copy full SHA for 7524ad7

• new trainintg loop

  Alecampoy

  committed
  d598a87

  Copy full SHA for d598a87

• new training on resnet

  

  Alecampoy

  authored and

  adjavon

  committed
  9bae23a

  Copy full SHA for 9bae23a

• new trainintg loop

  

  Alecampoy

  authored and

  adjavon

  committed
  6a9eb6a

  Copy full SHA for 6a9eb6a

• Merge branch 'Ale_training' into Akila

  adjavon

  committed
  903dd2a

  Copy full SHA for 903dd2a

• Redo Ale's updates

  adjavon

  committed
  69257a0

  Copy full SHA for 69257a0

• Merge branch 'static_dev' into Akila

  adjavon

  committed
  783e37e

  Copy full SHA for 783e37e

• Merge pull request #4 from Cryaaa/Akila

  Show description for 054483f
  adjavon

  authored
  054483f

  Copy full SHA for 054483f

• fixed training loop with new dataset

  mat10d

  committed
  b295299

  Copy full SHA for b295299

• black

  Alecampoy

  committed
  4d2df4e

  Copy full SHA for 4d2df4e

Commits on Sep 2, 2024

• changes in git ignore

  Alecampoy

  committed
  e15bdcd

  Copy full SHA for e15bdcd

• pre training ResVae

  Alecampoy

  committed
  08cf431

  Copy full SHA for 08cf431

• added training loops for md, modified static dataloader

  mat10d

  committed
  92be390

  Copy full SHA for 92be390

• updated training loops to split loss, use small dataset

  mat10d

  committed
  af464cf

  Copy full SHA for af464cf

• updated training loops for logging

  mat10d

  committed
  fefe44b

  Copy full SHA for fefe44b

• speed up data loader in training loops

  mat10d

  committed
  95a90aa

  Copy full SHA for 95a90aa

• add evaluation

  mat10d

  committed
  a75f70d

  Copy full SHA for a75f70d

• linear model AC

  Alecampoy

  committed
  92f36bb

  Copy full SHA for 92f36bb

• Fix errors incurred during rebase

  Alecampoy

  committed
  f5485c5

  Copy full SHA for f5485c5

• Return linear ac model to original state

  Alecampoy

  committed
  360922a

  Copy full SHA for 360922a

• ok linear ac model

  Alecampoy

  committed
  8026281

  Copy full SHA for 8026281

• add sampling for evaluation

  mat10d

  committed
  4098ce9

  Copy full SHA for 4098ce9

Commits on Sep 3, 2024

• adding print model and zarr dataloader

  Alecampoy

  committed
  486a2cd

  Copy full SHA for 486a2cd

• add changes to min normalizing

  mat10d

  committed
  c76be50

  Copy full SHA for c76be50

• Merge branch 'static_dev' of github.com:Cryaaa/embed_time into static_dev

  Alecampoy

  committed
  29a90b0

  Copy full SHA for 29a90b0

• bug fixes for linear model evaluation

  mat10d

  committed
  85430e2

  Copy full SHA for 85430e2

• Add non-targeting experiments

  adjavon

  committed
  6f05288

  Copy full SHA for 6f05288

• zarr dataloader mitocondria

  Alecampoy

  committed
  a24c559

  Copy full SHA for a24c559

• pyproject.toml update

  akila-14

  committed
  0e987ca

  Copy full SHA for 0e987ca

• neuromast dataset notebook with centroids

  akila-14

  committed
  ba3ee67

  Copy full SHA for ba3ee67

• removed a script

  akila-14

  committed
  993bb9a

  Copy full SHA for 993bb9a

• modified training loop and added neuromast metadat scripts

  akila-14

  committed
  43b4058

  Copy full SHA for 43b4058

• training loop for neuromast 2D

  akila-14

  committed
  65be0a1

  Copy full SHA for 65be0a1

• neuromast validation script and dataset class

  akila-14

  committed
  2b7e88f

  Copy full SHA for 2b7e88f

• added test notebook

  akila-14

  committed
  c43fca6

  Copy full SHA for c43fca6

• evaluation neuromast

  akila-14

  committed
  3696e15

  Copy full SHA for 3696e15

Commits on Sep 4, 2024

• evaluation improvements, maybe lost the resnet script

  mat10d

  committed
  79469cb

  Copy full SHA for 79469cb

• updated evaluation

  mat10d

  committed
  285efe3

  Copy full SHA for 285efe3

• Add benchmark dataset creation

  adjavon

  committed
  0daed58

  Copy full SHA for 0daed58

• neuromast class

  akila-14

  committed
  8739de5

  Copy full SHA for 8739de5

• evaluation, classifier

  akila-14

  committed
  3cc0eae

  Copy full SHA for 3cc0eae

• Add visualization

  adjavon

  committed
  28e2634

  Copy full SHA for 28e2634

Commits on Sep 7, 2024

• matteo final commit :/

  mat10d

  committed
  6c03315

  Copy full SHA for 6c03315

Commits on Sep 10, 2024

• fixed error in toml file to hopefully fix tests

  Cryaaa

  committed
  956e338

  Copy full SHA for 956e338

• wasn't quite there yet

  Cryaaa

  committed
  43896f1

  Copy full SHA for 43896f1

• fixed all the duplicate dependancies and misnamed libraries

  Cryaaa

  committed
  bfedf85

  Copy full SHA for bfedf85

• get rid of duplicate dependancies in in dev

  Cryaaa

  committed
  5d55f83

  Copy full SHA for 5d55f83