Prepare MONAI Label for new monai - DeepEdit transforms #781
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Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com>
Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com>
SachidanandAlle
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May 15, 2022
SachidanandAlle
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May 15, 2022
markus-hinsche
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May 17, 2022
…I#781) * Prepare MONAI Label for new monai - DeepEdit transforms Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Add deprecated messages - DeepEdit transforms - interaction Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
SachidanandAlle
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May 19, 2022
* Only Hide Training area when zero tasks configured (#769) Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Nuclick train (#772) * Draft Training workflow for NuClick Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * Fix nuclick training Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * rename transform Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * use monai bunet for nuclick Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * fix log Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add NRRD writer Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> Co-authored-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add unit test for NRRD writer Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Polish Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add labels to data object, Check for label list Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> Co-authored-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * update docstrings Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * 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 <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * polish write_seg_nrrd() will only be used for 4D multi-channel label arrays. Thus, removed unnecessary code. Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix typo Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add pynrrd==0.4.2 to setup.cfg Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * fix check for multi-channel label Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * fix unit test Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix multichannel problem Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Reformat code Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Make mypy happy Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix merge conflict Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Use logger.warning instead logger.debug Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add Active Learning strategies to DeepEdit (#782) * Add Active Learning strategies to DeepEdit Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Update readme - commands Active Learning strategies Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Prepare MONAI Label for new monai - DeepEdit transforms (#781) * Prepare MONAI Label for new monai - DeepEdit transforms Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Add deprecated messages - DeepEdit transforms - interaction Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Mention python versions which are supported (#786) Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add original labels option Slicer UI (#785) * Add original labels option Slicer UI Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Update Slicer module Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix: Check first dimension for multichannel Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Polish unit test to be more specific about dimensions Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Co-authored-by: Janis Vahldiek <janis@vahldiek.info> Co-authored-by: Andres Diaz-Pinto <diazandr3s@gmail.com>
DaoMaoDuc
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Jun 1, 2022
…I#781) * Prepare MONAI Label for new monai - DeepEdit transforms Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Add deprecated messages - DeepEdit transforms - interaction Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: Duc <ducdominhstart@googlemail.com>
DaoMaoDuc
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Jun 1, 2022
* Only Hide Training area when zero tasks configured (Project-MONAI#769) Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Nuclick train (Project-MONAI#772) * Draft Training workflow for NuClick Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * Fix nuclick training Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * rename transform Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * use monai bunet for nuclick Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * fix log Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add NRRD writer Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> Co-authored-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add unit test for NRRD writer Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Polish Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add labels to data object, Check for label list Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> Co-authored-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * update docstrings Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * 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 <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * polish write_seg_nrrd() will only be used for 4D multi-channel label arrays. Thus, removed unnecessary code. Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix typo Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add pynrrd==0.4.2 to setup.cfg Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * fix check for multi-channel label Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * fix unit test Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix multichannel problem Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Reformat code Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Make mypy happy Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix merge conflict Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Use logger.warning instead logger.debug Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add Active Learning strategies to DeepEdit (Project-MONAI#782) * Add Active Learning strategies to DeepEdit Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Update readme - commands Active Learning strategies Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * 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 <diazandr3s@gmail.com> * Add deprecated messages - DeepEdit transforms - interaction Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Mention python versions which are supported (Project-MONAI#786) Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add original labels option Slicer UI (Project-MONAI#785) * Add original labels option Slicer UI Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Update Slicer module Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix: Check first dimension for multichannel Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Polish unit test to be more specific about dimensions Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Co-authored-by: Janis Vahldiek <janis@vahldiek.info> Co-authored-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Signed-off-by: Duc <ducdominhstart@googlemail.com>
Douwe-Spaanderman
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Dec 9, 2022
…I#781) * Prepare MONAI Label for new monai - DeepEdit transforms Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Add deprecated messages - DeepEdit transforms - interaction Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com>
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 <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Nuclick train (Project-MONAI#772) * Draft Training workflow for NuClick Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * Fix nuclick training Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * rename transform Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * Sync up changes for nuclick training Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * use monai bunet for nuclick Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> * fix log Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add NRRD writer Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> Co-authored-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add unit test for NRRD writer Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Polish Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add labels to data object, Check for label list Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> Co-authored-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * update docstrings Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * 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 <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * polish write_seg_nrrd() will only be used for 4D multi-channel label arrays. Thus, removed unnecessary code. Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix typo Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add pynrrd==0.4.2 to setup.cfg Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * fix check for multi-channel label Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * fix unit test Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix multichannel problem Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Reformat code Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Make mypy happy Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix merge conflict Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Use logger.warning instead logger.debug Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add Active Learning strategies to DeepEdit (Project-MONAI#782) * Add Active Learning strategies to DeepEdit Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Update readme - commands Active Learning strategies Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * 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 <diazandr3s@gmail.com> * Add deprecated messages - DeepEdit transforms - interaction Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Mention python versions which are supported (Project-MONAI#786) Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Add original labels option Slicer UI (Project-MONAI#785) * Add original labels option Slicer UI Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> * Update Slicer module Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Fix: Check first dimension for multichannel Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> * Polish unit test to be more specific about dimensions Signed-off-by: Markus Hinsche <m.hinsche@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Co-authored-by: Janis Vahldiek <janis@vahldiek.info> Co-authored-by: Andres Diaz-Pinto <diazandr3s@gmail.com>
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Signed-off-by: Andres Diaz-Pinto diazandr3s@gmail.com