Add NrrdWriter for multi-channel arrays #779

markus-hinsche · 2022-05-12T11:35:13Z

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:

After the NRRD reader, writer also makes sense, see issues:
- see issue Implement NrrdReader for nrrd and seg.nrrd files MONAI#4238 with PR Implement NrrdReader MONAI#4259
seg.nrrd tooling with 3D Slicer
- Add support for .seg.nrrd in UpdateSegmentationMask() of the Slicer extension #768

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

Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

* 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>

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>

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

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>

Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

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>

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>

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

SachidanandAlle · 2022-05-13T12:34:02Z

Thanks for raising the PR.. will be look into this asap..

SachidanandAlle · 2022-05-13T12:35:24Z

monailabel/transform/writer.py

+def write_seg_nrrd(
+    image_np: np.ndarray,
+    output_file: str,
+    dtype: type,


may be u can have default value for dtype

We tried to make this function's signature similar to the write_itk(). It is probably best to also have a default there as well then, would you agree?

SachidanandAlle · 2022-05-13T12:36:46Z

monailabel/transform/writer.py


+            if self.is_multichannel_image(image_np):
+                if ext != ".seg.nrrd":
+                    logger.debug(


this can be logger info or warning

SachidanandAlle · 2022-05-13T12:41:18Z

monailabel/transform/writer.py

        return output_file, output_json

+    def is_multichannel_image(self, image_np):
+        return len(image_np.shape) == 4 and image_np.shape[-1] > 1


channel last? normally all images/labels/predictions are processed as channel first in post transform... we better cross check by running some examples e2e..

@diazandr3s can u help to verify this feature...

Happy to help :)
Should we wait until this PR (Project-MONAI/MONAI#4259) is merged?

you can checkout the remote branch and verify..

Project-MONAI/MONAI#4259 is merged now. I merged upstream/main into this branch

Indeed this seemed wrong, I updated the code to check the first dimension instead.

FYI:

pynrrd choses the following convention

default index_order='F' nrrd.writer.write(data) index_order : {'C', 'F'}, optional Specifies the index order used for writing. Either 'C' (C-order) where the dimensions are ordered from slowest-varying to fastest-varying (e.g. (z, y, x)), 'F' (Fortran-order) where the dimensions are ordered from fastest-varying to slowest-varying (e.g. (x, y, z)).

We chose 'C' as a default here

torch has the following convention: NxCxHxW

At the moment, in our monailabel-app, we use (5, 4280, 3520, 1) = (channels, width, height, batch)

diazandr3s · 2022-05-13T13:39:58Z

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:

* After the NRRD reader, writer also makes sense, see issues:
  
  * see issues: [Implement `NrrdReader` for `nrrd` and `seg.nrrd` files  MONAI#4238](https://github.com/Project-MONAI/MONAI/issues/4238) and [Implement NrrdReader MONAI#4259](https://github.com/Project-MONAI/MONAI/pull/4259)

* `seg.nrrd` tooling with 3D Slicer
  
  * [Add support for .seg.nrrd in UpdateSegmentationMask() of the Slicer extension #768](https://github.com/Project-MONAI/MONAILabel/pull/768)

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

Thanks, @markus-hinsche
This may also help to solve this issue #22

CC @lassoan

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

* 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>

…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>

Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

* 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>

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

SachidanandAlle · 2022-05-17T12:24:16Z

can you please fix the base branch.. it complains out-of-date and can't be done through UI

markus-hinsche · 2022-05-17T12:53:52Z

can you please fix the base branch.. it complains out-of-date and can't be done through UI

I am not sure what the problem is. Feel free to elaborate

diazandr3s

Thanks for the PR. Looks good to me.

markus-hinsche · 2022-05-19T12:19:12Z

Great! Thanks for the feedback

SachidanandAlle · 2022-05-19T12:23:08Z

Can't merge as it says out of date

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

SachidanandAlle · 2022-05-19T19:34:14Z

I see the problem.. u have forked the forked repo..
https://github.com/jlvahldiek/MONAILabel => yours..
this is bit confusing for github itself..

can you please fix the fork and resolve the conflicts correct.. if possible i suggest please fork from the original repo..

markus-hinsche · 2022-05-19T19:44:29Z

Closing in favor of #793

SachidanandAlle and others added 15 commits May 12, 2022 14:10

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>

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>

Add unit test for NRRD writer

b8a5f81

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Polish

02359fe

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

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>

update docstrings

3355bde

Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

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>

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>

Fix typo

03b8744

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Add pynrrd==0.4.2 to setup.cfg

31b8852

Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

fix check for multi-channel label

f323fe3

Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

fix unit test

9c2d055

Signed-off-by: Janis Vahldiek <janis@vahldiek.info> Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Fix multichannel problem

5364d17

Signed-off-by: Markus Hinsche Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Reformat code

4cf50dd

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

markus-hinsche force-pushed the nrrd-writer branch from dfc2011 to 4cf50dd Compare May 12, 2022 12:11

markus-hinsche added 3 commits May 12, 2022 14:14

Make mypy happy

8985562

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Merge remote-tracking branch 'upstream/main' into nrrd-writer

4b32b01

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Fix merge conflict

38b2dea

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

SachidanandAlle reviewed May 13, 2022

View reviewed changes

kbressem mentioned this pull request May 13, 2022

Implement NrrdReader Project-MONAI/MONAI#4259

Merged

6 tasks

markus-hinsche and others added 5 commits May 17, 2022 13:30

Use logger.warning instead logger.debug

5a5f80f

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

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>

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 added 2 commits May 17, 2022 13:30

Fix: Check first dimension for multichannel

71f5aa4

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

Polish unit test to be more specific about dimensions

2606586

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

markus-hinsche force-pushed the nrrd-writer branch from 26d96f9 to 2606586 Compare May 17, 2022 11:31

markus-hinsche requested review from SachidanandAlle and diazandr3s May 17, 2022 11:57

diazandr3s approved these changes May 17, 2022

View reviewed changes

SachidanandAlle approved these changes May 19, 2022

View reviewed changes

Merge remote-tracking branch 'upstream/main' into nrrd-writer

0479aa5

Signed-off-by: Markus Hinsche <m.hinsche@gmail.com>

markus-hinsche mentioned this pull request May 19, 2022

Add NrrdWriter for multi-channel arrays #793

Merged

markus-hinsche closed this May 19, 2022

jlvahldiek mentioned this pull request Nov 4, 2022

ITKWriter can write nrrd files #1115

Closed

Add NrrdWriter for multi-channel arrays #779

Add NrrdWriter for multi-channel arrays #779

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