[WIP] 2620 Add ITKWriter for other formats

[Nic-Ma]

Fixes #2620 .

Description

This PR added ITKWriter to support more image formats.

Status

Work in progress

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• Breaking change (fix or new feature that would cause existing functionality to change).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
• Quick tests passed locally by running ./runtests.sh --quick --unittests.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[Nic-Ma]

Hi @rijobro @wyli @ericspod ,

I am blocked by an issue that I didn't find the API to set affine matrix in ITK image, already filed a ticket to ITK repo:
InsightSoftwareConsortium/ITK#2663
Do you guys have any experience or ideas?
Actually, if someone can share a detailed python tutorial or example to save numpy array into many different formats(PNG, DICOM, DICOM series, NIfTI, etc.) with ITK, that would be extremely helpful for us. CC @thewtex

Thanks in advance.

[madil90]

/build

[madil90]

/build

[wyli]

I can work on this feature because I revised the reader recently and now familiar with these

[Nic-Ma]

I can work on this feature because I revised the reader recently and now familiar with these

That would be great.
I almost finished this PR for the basic saving with ITK, just blocked by the multi-channels case now, maybe I can complete this PR as initial part of writers? Then you can enhance with more your ideas?

Thanks.

[wyli]

We haven't started the review yet, I think this basic implementation needs some more work. I'll start a new PR on this, using some ideas from this PR, what do you think?

[Nic-Ma]

We haven't started the review yet, I think this basic implementation needs some more work. I'll start a new PR on this, using some ideas from this PR, what do you think?

OK, plan sounds good.

Thanks.

[madil90]

/build

[madil90]

/build

[madil90]

/build

[madil90]

/build

[thewtex]

Hi @rijobro @wyli @ericspod ,

I am blocked by an issue that I didn't find the API to set affine matrix in ITK image, already filed a ticket to ITK repo:
InsightSoftwareConsortium/ITK#2663
Do you guys have any experience or ideas?
Actually, if someone can share a detailed python tutorial or example to save numpy array into many different formats(PNG, DICOM, DICOM series, NIfTI, etc.) with ITK, that would be extremely helpful for us. CC @thewtex

Thanks in advance.

Discussed more in InsightSoftwareConsortium/ITK#2663, but https://gist.github.com/thewtex/9503448d2ad1dfacc2cbd620d95d3dac is hopefully helpful.

[madil90]

/build

[madil90]

/build

[madil90]

/build

[madil90]

/build

[lukasfolle]

Any updates on this? I would really appreciate a Dicom out support for MONAI.

[dyollb]

Any update on this? I was thinking of writing a custom ImageWriter for our in-house file format based on hdf5.

[Nic-Ma]

Hi @dyollb ,

As @wyli said in #2647 (comment), I think we need more discussion about this topic.

Thanks.

[wyli]

thanks, I'm closing this in favour of #3674.