Add Active Learning strategies to DeepEdit#782
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SachidanandAlle merged 2 commits intomainfrom May 15, 2022
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Signed-off-by: Andres Diaz-Pinto <[email protected]>
Signed-off-by: Andres Diaz-Pinto <[email protected]>
SachidanandAlle
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May 15, 2022
markus-hinsche
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May 17, 2022
* 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]>
SachidanandAlle
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May 19, 2022
* 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]>
DaoMaoDuc
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Jun 1, 2022
* 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: Duc <[email protected]>
DaoMaoDuc
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Jun 1, 2022
* 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]>
Douwe-Spaanderman
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Dec 9, 2022
* 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]>
Douwe-Spaanderman
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Dec 9, 2022
* 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]>
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Signed-off-by: Andres Diaz-Pinto [email protected]
Still not clear how to use these configuration flags:
Edit:
This flag (MONAI_LABEL_AUTO_UPDATE_SCORING) disables the use of active learning strategies:
https://github.com/Project-MONAI/MONAILabel/blob/main/monailabel/config.py#L52