Code

ViT UNETR SSL#10

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valosekj wants to merge 100 commits intomainivadomed/model-seg-dcm:mainfrom jv/vit_unetr_sslivadomed/model-seg-dcm:jv/vit_unetr_sslCopy head branch name to clipboard

+3,146

Commits

Commits on Mar 8, 2024

• Add notebook debugging SSL pretraining transformations

  valosekj

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  75a5f85

• Fix typo

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  e37ff59

• Add script for Self-Supervised Pre-training using Vision Transformer (ViT)

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  80fd7db

• Fix typo

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  4dc7e81

• Do sanity dimension check after transformations

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  3a9baef

• Use patch_size=(16, 16, 16) and batch_size = 2

  Show description for 4517f7a
  valosekj

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  4517f7a

Commits on Mar 9, 2024

• rename 'crop_size' to 'spatial_size'

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  a621a9a

• use 'contrast-agnostic' data augmentation for Training of the fine-tuned model

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  516f1ec

• Add script to finetune the 3D Single-Class Spinal Cord Lesion Segmentation Model Using SSL Pre-trained Weights

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  fd8f943

• update description

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  d1b9c3d

• use 'logger.info' instead of 'print'

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  45ef357

• make '--data' arg notrequired

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  0955689

• explicitly specify CUDA GPU number

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  9ea8bca

• change sliding_window_inference roi_size and batch_size

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  3bc999a

• remove 'to_onehot_y=True' and 'softmax=True' because we work with single channel prediction

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Commits on Mar 12, 2024

• add notebook to debug transformations when using SC masks to crop patches

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• rerun the notebook to show different slices

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  622c3f6

• Add 'keys' arg

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  59f4db0

• Add 'keys' arg

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  a3ae050

• Update 'RandCoarseDropoutd' params

  valosekj

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  e1cfad1

• Update comments

  valosekj

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  d4e9995

• Fix imports

  valosekj

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  4c35d42

• Change batch_size and NUM_WORKERS to 4

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  05ab59a

• Make '--data' non required

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  0b12c10

• change 'num_workers' to 0 to prevent 'RuntimeError: received 0 items of ancdata'

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  f5881aa

Commits on Mar 13, 2024

• Update input arg description

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  7aa9858

• Rerun the notebook

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  16691d7

• Print hyper-parameters into the log file

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  56ca187

• Add '--cuda' input arg

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  ce7315a

Commits on Mar 15, 2024

• track and save epoch time

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  1ebf833

• Plot and save input and output validation images to see how the model is learning

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  208b2c1

• Add comment

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  5a9e69a

• Do not plot 'outputs_v2' as it is a hidden representation

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  eca6616

• Include the epoch number as master title

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  8e55985

• Add 'torch.multiprocessing.set_sharing_strategy('file_system')' to solve number of workers issue

  Show description for e7575c5
  valosekj

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  e7575c5

• Create validation_figures directory if it does not exist

  valosekj

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  3b6df14

• Use 3 leading zeros for the epoch number in the figures fname

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  59b061c

• Link issue

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  f2d648b

• Add note for 'RandCropByPosNegLabeld'

  Show description for a6bc6ec
  valosekj

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  a6bc6ec

• Add 'number_of_holes' arg to specify the number of holes to be used for the RandCoarseDropoutd and RandCoarseShuffled transforms

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  c1553d6

Commits on Mar 16, 2024

• typo

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• batch_size = 8

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• NUM_WORKERS = batch_size

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• number_of_holes=5

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  valosekj

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  93c5415

• Update transforms for training of the fine-tuned model

  Show description for a4182b5
  

  valosekj

  and

  naga-karthik

  authored
  a4182b5

• update comment, remove unused imports

  valosekj

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  2573578

• Add notebook with RandCoarseDropoutd transform debug

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  cfb8f12

Commits on Mar 17, 2024

• Fix 'dropout_holes=True' and 'dropout_holes=False' comments

  Show description for 7f27340
  valosekj

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  7f27340

• remove unused 'max_spatial_size' arg

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  74b2f2c

• use 'fill_value=0' for 'RandCoarseDropoutd'

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  bdb2ac1

• Plot also RandCoarseDropoutd dropout_holes=False fill_value=0

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  f7f3689

• Add note that the batch size is actually doubled (8*2=16), because we are using two augmented samples per 3D Volume

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Commits on Mar 18, 2024

• Add '--cuda' input arg

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  b416135

• Remove 'AsDiscrete'

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  0303776

• Remove 'AsDiscrete'

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  4534c57

• Add 'CUDA_NUM=args.cuda'

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  94c8611

• Add TODO to increase batch_size to 16

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  5fb325a

• Use 'roi_size' for 'define_finetune_train_transforms'

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  d1a03c8

• Use 'label_sc' to crop samples around the SC

  Show description for e3d8086
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  e3d8086

• batch_size = 8

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  7e628af

• NUM_WORKERS = batch_size

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  f832c94

• Add 'import torch.multiprocessing'

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  c68d65d

• Fix shape logging

  valosekj

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  a7c7c77

• Change 'img_size' to 'ROI_SIZE'

  valosekj

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  1c6109c

• 'batch["label"]' --> 'batch["label_lesion"]'

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  b92e7d5

• Plot and save input and output validation images to see how the model is learning

  valosekj

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  f174fb9

• Fix ROI_SIZE for sliding_window_inference

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  532e24b

• Crop samples of 64x64x64 also for Validation of the fine-tuned model

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  5c10890

• update docstring

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  d33abfa

• log validation samples shapes

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  efeccf9

• Save validation figure only if it contains a lesion

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  f34ece1

Commits on Mar 19, 2024

• Plot GT together with image

  valosekj

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  e0afafe

• print unique values in the slice to see if it is binary

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  e588a22

• update output fig fname

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  2d0b530

• Add 'AsDiscreted' for Training and Validation of the fine-tuned model

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  988680e

• threshold val_labels_list and val_outputs_list by 0.5 threshold before computing validation dice and plotting

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  f675611

• add normalized relu normalization

  naga-karthik

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  cc78896

• fix binarization bug

  naga-karthik

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  92334ea

• remove 'logger.info(np.unique(output.detach().cpu().numpy()))'

  valosekj

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  2c49ca2

• overlay prediction over input image

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  fbe3dd7

Commits on Mar 20, 2024

• Fix variable when getting probabilities from logits

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  ba39d28

• Add debug lines

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  c8d9a5d

• PEP8

  valosekj

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  ac040a5

• Set validation batch_size to 1

  valosekj

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  1e2b61d

• improve comments

  valosekj

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  8f49545

• fix figure title

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  3a74e28

• comment 'AsDiscreted' transforms

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  dea121c

Commits on Mar 21, 2024

• Make '--pretrained-model' non required to allow training from the scratch

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  013ca65

Commits on Mar 22, 2024

• Add script to create spine-generic MSD dataset

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  f1aae1b

• run notebook again

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  e4c87be

Commits on Mar 23, 2024

• Make 'create_msd_data.py' compatible with other BIDS datasets

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  4448356

• Add note that no testing set is created

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  a354a21

Commits on Mar 24, 2024

• Add README with instructions on how to download T2w images from multiple datasets

  valosekj

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  141c96b

• fix typo

  valosekj

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  7f8e6bb

• remove unused imports

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  46f1bd9

• fix sc suffix for sci-paris

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  afeb7c5

• Use os.path.abspath for 'args.path_data' and 'args.path_out'

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  da1c131

• Update logging message

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  ed42c68

• Fix '.replace' to prevent '//' in the output string

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  7f28fed

• Add 'create_msd_data.py' commands to create MSD-style JSON datalists

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  99a936b