Add NrrdWriter for multi-channel arrays#793
Merged
SachidanandAlle merged 27 commits intoProject-MONAI:mainfrom May 19, 2022
Merged
Add NrrdWriter for multi-channel arrays#793SachidanandAlle merged 27 commits intoProject-MONAI:mainfrom
SachidanandAlle merged 27 commits intoProject-MONAI:mainfrom
Conversation
Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Markus Hinsche <[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: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]> Co-authored-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]>
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]>
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]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Janis Vahldiek <[email protected]> Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
* 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]>
…I#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]>
Signed-off-by: SACHIDANAND ALLE <[email protected]> Signed-off-by: Markus Hinsche <[email protected]>
* 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]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
Signed-off-by: Markus Hinsche <[email protected]>
SachidanandAlle
approved these changes
May 19, 2022
DaoMaoDuc
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to jlvahldiek/MONAILabel
that referenced
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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
pushed a commit
to Douwe-Spaanderman/MONAILabel
that referenced
this pull request
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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Motivation
The
Writerclass (inmonailabel/transform/writer.py) can't handle multi-channel arrays. The ITK reader and writer both can't handle multi-channel arrays, therefore we want to introduce a new writer that can do this.Related PRs
This work is related to other works in this area:
NrrdReaderfornrrdandseg.nrrdfiles MONAI#4238 with PR Implement NrrdReader MONAI#4259seg.nrrdtooling with 3D SlicerChanges
write_seg_nrrd()(similar towrite_itk())pynrrdpip dependency to projectSee PR review comments from predecessor PR #779