Nuclick train by SachidanandAlle · Pull Request #772 · Project-MONAI/MONAILabel

SachidanandAlle · 2022-05-08T20:36:21Z

Support NuClick training
Use MONAI BUNET

Following is the comparison for BasicUNET (bunet) vs NuClick UNET (nunet) trained over PanNuke dataset (40k+ nuclei for 10 epochs)

This is the log for original training using everything from: https://github.com/mostafajahanifar/nuclick_torch over the same dataset

INFO: Using device cuda
INFO: Network:
	5 input channels
	1 output channels (classes)

INFO: Creating dataset with 44741 examples
INFO: Starting training:
        Network:         UNet
        Epochs:          10
        Batch size:      64
        Learning rate:   0.001
        Training size:   35793
        Validation size: 8948
        Loss function:   Weighted_BCE_Dice
        Checkpoints:     True
        Device:          cuda
        Images scaling:  1
        Mixed Precision: False
    
Epoch 1/10: 100%|################################################################################################| 35793/35793 [02:47<00:00, 213.25img/s, loss (batch)=0.346]
INFO: Validation Dice score: 0.6948385834693909                                                                                                                                                                                                                  
INFO: Checkpoint 1 saved!
Epoch 2/10: 100%|################################################################################################| 35793/35793 [06:08<00:00, 97.15img/s, loss (batch)=0.317]
INFO: Validation Dice score: 0.7801803350448608                                                                                                                                                                                                                  
INFO: Checkpoint 2 saved!
Epoch 3/10: 100%|################################################################################################| 35793/35793 [06:11<00:00, 96.34img/s, loss (batch)=0.284]
INFO: Validation Dice score: 0.813300371170044                                                                                                                                                                                                                   
INFO: Checkpoint 3 saved!
Epoch 4/10: 100%|################################################################################################| 35793/35793 [06:08<00:00, 97.07img/s, loss (batch)=0.262]
INFO: Validation Dice score: 0.8261093497276306                                                                                                                                                                                                                  
INFO: Checkpoint 4 saved!
Epoch 5/10: 100%|################################################################################################| 35793/35793 [06:03<00:00, 98.45img/s, loss (batch)=0.142]
INFO: Validation Dice score: 0.8319364190101624                                                                                                                                                                                                                  
INFO: Checkpoint 5 saved!
Epoch 6/10: 100%|################################################################################################| 35793/35793 [06:00<00:00, 99.33img/s, loss (batch)=0.266]
INFO: Validation Dice score: 0.8355947136878967                                                                                                                                                                                                                  
INFO: Checkpoint 6 saved!
Epoch 7/10: 100%|################################################################################################| 35793/35793 [05:59<00:00, 99.51img/s, loss (batch)=0.175]
INFO: Validation Dice score: 0.8366557955741882                                                                                                                                                                                                                  
INFO: Checkpoint 7 saved!
Epoch 8/10: 100%|################################################################################################| 35793/35793 [05:54<00:00, 101.03img/s, loss (batch)=0.331]
INFO: Validation Dice score: 0.842056930065155                                                                                                                                                                                                                   
INFO: Checkpoint 8 saved!
Epoch 9/10: 100%|################################################################################################| 35793/35793 [05:48<00:00, 102.58img/s, loss (batch)=0.142]
INFO: Validation Dice score: 0.8373238444328308                                                                                                                                                                                                                  
INFO: Checkpoint 9 saved!
Epoch 10/10: 100%|################################################################################################| 35793/35793 [05:55<00:00, 100.70img/s, loss (batch)=0.184]
INFO: Validation Dice score: 0.8469359278678894                                                                                                                                                                                                                  
INFO: Checkpoint 10 saved!

Signed-off-by: Sachidanand Alle <[email protected]>

diazandr3s

This is great

* Draft Training workflow for NuClick Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * Fix nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * rename transform Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * use monai bunet for nuclick Signed-off-by: Sachidanand Alle <[email protected]> * fix log Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Markus Hinsche <[email protected]>

* Only Hide Training area when zero tasks configured (#769) Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Nuclick train (#772) * Draft Training workflow for NuClick Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * Fix nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * rename transform Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * use monai bunet for nuclick Signed-off-by: Sachidanand Alle <[email protected]> * fix log Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Add NRRD writer Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Add unit test for NRRD writer Signed-off-by: Markus Hinsche <[email protected]> * Polish Signed-off-by: Markus Hinsche <[email protected]> * Add labels to data object, Check for label list Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * update docstrings Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * change writer selection write_seg_nrrd() is only needed for 4D multi-channel label arrays. Everything else can be handled by ITK of nifty writer. Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * polish write_seg_nrrd() will only be used for 4D multi-channel label arrays. Thus, removed unnecessary code. Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Fix typo Signed-off-by: Markus Hinsche <[email protected]> * Add pynrrd==0.4.2 to setup.cfg Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <[email protected]> * fix check for multi-channel label Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * fix unit test Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Fix multichannel problem Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <[email protected]> * Reformat code Signed-off-by: Markus Hinsche <[email protected]> * Make mypy happy Signed-off-by: Markus Hinsche <[email protected]> * Fix merge conflict Signed-off-by: Markus Hinsche <[email protected]> * Use logger.warning instead logger.debug Signed-off-by: Markus Hinsche <[email protected]> * Add Active Learning strategies to DeepEdit (#782) * Add Active Learning strategies to DeepEdit Signed-off-by: Andres Diaz-Pinto <[email protected]> * Update readme - commands Active Learning strategies Signed-off-by: Andres Diaz-Pinto <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Prepare MONAI Label for new monai - DeepEdit transforms (#781) * Prepare MONAI Label for new monai - DeepEdit transforms Signed-off-by: Andres Diaz-Pinto <[email protected]> * Add deprecated messages - DeepEdit transforms - interaction Signed-off-by: Andres Diaz-Pinto <[email protected]> Co-authored-by: SACHIDANAND ALLE <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Mention python versions which are supported (#786) Signed-off-by: SACHIDANAND ALLE <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Add original labels option Slicer UI (#785) * Add original labels option Slicer UI Signed-off-by: Andres Diaz-Pinto <[email protected]> * Update Slicer module Signed-off-by: Andres Diaz-Pinto <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Fix: Check first dimension for multichannel Signed-off-by: Markus Hinsche <[email protected]> * Polish unit test to be more specific about dimensions Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: SACHIDANAND ALLE <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Co-authored-by: Andres Diaz-Pinto <[email protected]>

* Draft Training workflow for NuClick Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * Fix nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * rename transform Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * use monai bunet for nuclick Signed-off-by: Sachidanand Alle <[email protected]> * fix log Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Duc <[email protected]>

* Only Hide Training area when zero tasks configured (Project-MONAI#769) Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Nuclick train (Project-MONAI#772) * Draft Training workflow for NuClick Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * Fix nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * rename transform Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * use monai bunet for nuclick Signed-off-by: Sachidanand Alle <[email protected]> * fix log Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Add NRRD writer Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Add unit test for NRRD writer Signed-off-by: Markus Hinsche <[email protected]> * Polish Signed-off-by: Markus Hinsche <[email protected]> * Add labels to data object, Check for label list Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * update docstrings Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * change writer selection write_seg_nrrd() is only needed for 4D multi-channel label arrays. Everything else can be handled by ITK of nifty writer. Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * polish write_seg_nrrd() will only be used for 4D multi-channel label arrays. Thus, removed unnecessary code. Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Fix typo Signed-off-by: Markus Hinsche <[email protected]> * Add pynrrd==0.4.2 to setup.cfg Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <[email protected]> * fix check for multi-channel label Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * fix unit test Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Fix multichannel problem Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <[email protected]> * Reformat code Signed-off-by: Markus Hinsche <[email protected]> * Make mypy happy Signed-off-by: Markus Hinsche <[email protected]> * Fix merge conflict Signed-off-by: Markus Hinsche <[email protected]> * Use logger.warning instead logger.debug Signed-off-by: Markus Hinsche <[email protected]> * Add Active Learning strategies to DeepEdit (Project-MONAI#782) * Add Active Learning strategies to DeepEdit Signed-off-by: Andres Diaz-Pinto <[email protected]> * Update readme - commands Active Learning strategies Signed-off-by: Andres Diaz-Pinto <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Prepare MONAI Label for new monai - DeepEdit transforms (Project-MONAI#781) * Prepare MONAI Label for new monai - DeepEdit transforms Signed-off-by: Andres Diaz-Pinto <[email protected]> * Add deprecated messages - DeepEdit transforms - interaction Signed-off-by: Andres Diaz-Pinto <[email protected]> Co-authored-by: SACHIDANAND ALLE <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Mention python versions which are supported (Project-MONAI#786) Signed-off-by: SACHIDANAND ALLE <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Add original labels option Slicer UI (Project-MONAI#785) * Add original labels option Slicer UI Signed-off-by: Andres Diaz-Pinto <[email protected]> * Update Slicer module Signed-off-by: Andres Diaz-Pinto <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Fix: Check first dimension for multichannel Signed-off-by: Markus Hinsche <[email protected]> * Polish unit test to be more specific about dimensions Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: SACHIDANAND ALLE <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Co-authored-by: Andres Diaz-Pinto <[email protected]> Signed-off-by: Duc <[email protected]>

* Draft Training workflow for NuClick Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * Fix nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * rename transform Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * use monai bunet for nuclick Signed-off-by: Sachidanand Alle <[email protected]> * fix log Signed-off-by: Sachidanand Alle <[email protected]>

* Only Hide Training area when zero tasks configured (Project-MONAI#769) Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Nuclick train (Project-MONAI#772) * Draft Training workflow for NuClick Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * Fix nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * rename transform Signed-off-by: Sachidanand Alle <[email protected]> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <[email protected]> * use monai bunet for nuclick Signed-off-by: Sachidanand Alle <[email protected]> * fix log Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Add NRRD writer Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Add unit test for NRRD writer Signed-off-by: Markus Hinsche <[email protected]> * Polish Signed-off-by: Markus Hinsche <[email protected]> * Add labels to data object, Check for label list Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * update docstrings Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * change writer selection write_seg_nrrd() is only needed for 4D multi-channel label arrays. Everything else can be handled by ITK of nifty writer. Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * polish write_seg_nrrd() will only be used for 4D multi-channel label arrays. Thus, removed unnecessary code. Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Fix typo Signed-off-by: Markus Hinsche <[email protected]> * Add pynrrd==0.4.2 to setup.cfg Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <[email protected]> * fix check for multi-channel label Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * fix unit test Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Fix multichannel problem Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <[email protected]> * Reformat code Signed-off-by: Markus Hinsche <[email protected]> * Make mypy happy Signed-off-by: Markus Hinsche <[email protected]> * Fix merge conflict Signed-off-by: Markus Hinsche <[email protected]> * Use logger.warning instead logger.debug Signed-off-by: Markus Hinsche <[email protected]> * Add Active Learning strategies to DeepEdit (Project-MONAI#782) * Add Active Learning strategies to DeepEdit Signed-off-by: Andres Diaz-Pinto <[email protected]> * Update readme - commands Active Learning strategies Signed-off-by: Andres Diaz-Pinto <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Prepare MONAI Label for new monai - DeepEdit transforms (Project-MONAI#781) * Prepare MONAI Label for new monai - DeepEdit transforms Signed-off-by: Andres Diaz-Pinto <[email protected]> * Add deprecated messages - DeepEdit transforms - interaction Signed-off-by: Andres Diaz-Pinto <[email protected]> Co-authored-by: SACHIDANAND ALLE <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Mention python versions which are supported (Project-MONAI#786) Signed-off-by: SACHIDANAND ALLE <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Add original labels option Slicer UI (Project-MONAI#785) * Add original labels option Slicer UI Signed-off-by: Andres Diaz-Pinto <[email protected]> * Update Slicer module Signed-off-by: Andres Diaz-Pinto <[email protected]> Signed-off-by: Markus Hinsche <[email protected]> * Fix: Check first dimension for multichannel Signed-off-by: Markus Hinsche <[email protected]> * Polish unit test to be more specific about dimensions Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: SACHIDANAND ALLE <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Co-authored-by: Andres Diaz-Pinto <[email protected]>

SachidanandAlle added 7 commits May 5, 2022 05:50

Draft Training workflow for NuClick

a7e02f6

Signed-off-by: Sachidanand Alle <[email protected]>

Sync up changes for nuclick training

692a1ef

Signed-off-by: Sachidanand Alle <[email protected]>

Fix nuclick training

1373b78

Signed-off-by: Sachidanand Alle <[email protected]>

rename transform

7162cbe

Signed-off-by: Sachidanand Alle <[email protected]>

Sync up changes for nuclick training

6b1bf8b

Signed-off-by: Sachidanand Alle <[email protected]>

use monai bunet for nuclick

72cfa15

Signed-off-by: Sachidanand Alle <[email protected]>

fix log

de8b20c

Signed-off-by: Sachidanand Alle <[email protected]>

SachidanandAlle added the 0.4.0 Targeted to Release version 0.4 label May 8, 2022

SachidanandAlle added this to the Pathology annotation function [p0] milestone May 8, 2022

SachidanandAlle requested review from diazandr3s and finalelement May 8, 2022 20:36

Merge branch 'main' into nuclick_train

4751914

diazandr3s approved these changes May 8, 2022

View reviewed changes

SachidanandAlle merged commit a1ca8ff into main May 8, 2022

SachidanandAlle deleted the nuclick_train branch May 8, 2022 21:03

SachidanandAlle mentioned this pull request May 9, 2022

Where to find the dataset used for training pretrained unet model? mostafajahanifar/nuclick_torch#12

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Nuclick train#772

Nuclick train#772
SachidanandAlle merged 8 commits intomainfrom
nuclick_train

SachidanandAlle commented May 8, 2022 •

edited

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SachidanandAlle commented May 8, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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SachidanandAlle commented May 8, 2022 •

edited

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