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Merged
SachidanandAlle merged 27 commits into from
May 19, 2022
Merged

Add NrrdWriter for multi-channel arrays #793

SachidanandAlle merged 27 commits into from
May 19, 2022

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@markus-hinsche markus-hinsche commented May 19, 2022 •
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Motivation

The Writer class (in monailabel/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:

Changes

  • Add new function write_seg_nrrd() (similar to write_itk())
  • Add condition when to use nrrd writer
  • Add pynrrd pip dependency to project
  • Add unit test for writing multi-channel data

See PR review comments from predecessor PR #779

SachidanandAlle and others added 26 commits May 12, 2022 14:10
@SachidanandAlle @markus-hinsche
Only Hide Training area when zero tasks configured (Project-MONAI#769)
0db62ec 
Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@SachidanandAlle @markus-hinsche
Nuclick train (Project-MONAI#772)
25f95ab 
* 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>
@markus-hinsche @jlvahldiek
Add NRRD writer
83ebf30 
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>
@markus-hinsche
Add unit test for NRRD writer
b8a5f81 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Polish
02359fe 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche @jlvahldiek
Add labels to data object, Check for label list
4f6fee8 
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>
@jlvahldiek @markus-hinsche
update docstrings
3355bde 
Signed-off-by: Janis Vahldiek <janis@vahldiek.info>
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@jlvahldiek @markus-hinsche
change writer selection
f63f3e1 
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>
@jlvahldiek @markus-hinsche
polish
f5ac9c6 
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>
@markus-hinsche
Fix typo
03b8744 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Add pynrrd==0.4.2 to setup.cfg
31b8852 
Signed-off-by: Markus Hinsche
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@jlvahldiek @markus-hinsche
fix check for multi-channel label
f323fe3 
Signed-off-by: Janis Vahldiek <janis@vahldiek.info>
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@jlvahldiek @markus-hinsche
fix unit test
9c2d055 
Signed-off-by: Janis Vahldiek <janis@vahldiek.info>
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Fix multichannel problem
5364d17 
Signed-off-by: Markus Hinsche
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Reformat code
4cf50dd 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Make mypy happy
8985562 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Merge remote-tracking branch 'upstream/main' into nrrd-writer
4b32b01 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Fix merge conflict
38b2dea 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Use logger.warning instead logger.debug
5a5f80f 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@diazandr3s @markus-hinsche
Add Active Learning strategies to DeepEdit (Project-MONAI#782)
b1a0c40 
* 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>
@diazandr3s @SachidanandAlle @markus-hinsche
Prepare MONAI Label for new monai - DeepEdit transforms (Project-MONA…
7c73853 
…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 @markus-hinsche
Mention python versions which are supported (Project-MONAI#786)
acf2f37 
Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com>
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@diazandr3s @markus-hinsche
Add original labels option Slicer UI (Project-MONAI#785)
ec4f069 
* 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>
@markus-hinsche
Fix: Check first dimension for multichannel
71f5aa4 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Polish unit test to be more specific about dimensions
2606586 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche
Merge remote-tracking branch 'upstream/main' into nrrd-writer
0479aa5 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@markus-hinsche markus-hinsche mentioned this pull request May 19, 2022
Closed
@markus-hinsche
Merge remote-tracking branch 'upstream/main' into nrrd-writer
2265678 
Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>
@SachidanandAlle SachidanandAlle merged commit 58dc813 into Project-MONAI:main May 19, 2022
@SachidanandAlle SachidanandAlle added the 0.4.0 Targeted to Release version 0.4 label May 30, 2022
DaoMaoDuc pushed a commit to jlvahldiek/MONAILabel that referenced this pull request Jun 1, 2022
@markus-hinsche @SachidanandAlle
@jlvahldiek @diazandr3s @DaoMaoDuc
Add NrrdWriter for multi-channel arrays (Project-MONAI#793)
7c0d1c1 
* 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 pushed a commit to Douwe-Spaanderman/MONAILabel that referenced this pull request Dec 9, 2022
@markus-hinsche @SachidanandAlle
@jlvahldiek @diazandr3s
Add NrrdWriter for multi-channel arrays (Project-MONAI#793)
b79a276 
* 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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