Add QuickModelAlign extension

[seanchoi0519]

New extension

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[jamesobutler]

Does it make sense to include this Slicer module as part of SlicerMorph since it is based on the ALPACA module in SlicerMorph and therefore could benefit from the same maintenance activities? I worry about future maintenance of the code. For example there was some discussion about open3d usage being problematic at times and Murat indicating a switch to an ITK based ALPACA instead (see https://discourse.slicer.org/t/alpaca-open3d-error/29483/2). Additionally could this QuickAlign module directly use the ALPACA module in the SlicerMorph extension and apply customizations as needed? cc: @muratmaga, @smrolfe

[seanchoi0519]

Does it make sense to include this Slicer module as part of SlicerMorph since it is based on the ALPACA module in SlicerMorph and therefore could benefit from the same maintenance activities? I worry about future maintenance of the code. For example there was some discussion about open3d usage being problematic at times and Murat indicating a switch to an ITK based ALPACA instead (see https://discourse.slicer.org/t/alpaca-open3d-error/29483/2). Additionally could this QuickAlign module directly use the ALPACA module in the SlicerMorph extension and apply customizations as needed? cc: @muratmaga, @smrolfe

Thanks for your reply. I am curious as to what you guys think.
That being said a lot of modifications have been made to make QuickAlign, I am not sure if we'll be able to achieve compatibility. For example, it does not use the '.ui' widget rather the UI is cutomized via code. The UI is also very simplistic and specific (does not allow for much customization) compared to ALPACA.
I did consider switching to ITK based ALPACA however considering the time I spent on modifying the code (many months) I decided that it may not be worth it at this time.

[smrolfe]

I would recommend at least calling the logic functions directly from ALPACA so that they don't need to be maintained separately. We are only supporting the open3D version temporarily due to the issues mentioned by @jamesobutler.

cc: @agporto

[agporto]

I think there are two ways to go about it.

• Option 1- If there is enough interest from SlicerMorph folks @smrolfe @muratmaga, it wouldn't be a bad idea to incorporate it into SlicerMorph. Sean's extension does something SlicerMorph users frequently ask for (the ability to register two 3D models and compare them using different types of visualization). However, some work would have to be done to integrate the tools to minimize redundancy. I am happy to help, but I would need helps from others as well. The main downside is that Sean might not want that integration, since his focus is on dentistry applications and he might want the UI to be specific to the task.
• Option 2 - The other way to look at it is that it is a completely independent module that will grow into its own ecosystem. As I understand, Sean is regularly using the module in teaching activities and will need to maintain the code to be compatible at least with Slicer stables.

[muratmaga]

I did consider switching to ITK based ALPACA however considering the time I spent on modifying the code (many months) I decided that it may not be worth it at this time.

In that case you will have to revise your code, particularly this section where you are using the wheels from our box server to install the open3d. https://github.com/seanchoi0519/SlicerQuickAlign/blob/main/QuickAlign.py#L76

I will remove these once the current ALPACA is deprecated and ITK-ALPACA becomes the default module in the next stable release. This will break your extension.

I highly encourage you to work with @agporto and @smrolfe to develop this into a full-fledged 3D model registration module. This can be a nice project week activity and I believe there is still time to list new ones.

[seanchoi0519]

Thanks all for your responses.
I'm very happy with the idea of developing an independent full-fledged 3D model registration module. I think this could have potential for applications in many fields & opportunities for publications. This has been my goal for quite a while but I would require help.

@agporto @smrolfe would you guys be on board for this project? I can take charge of the UI and the visual display modes, however I would need help with the ITK backend integration. Let me know!

[seanchoi0519]

I think there are two ways to go about it.
Option 1- If there is enough interest from SlicerMorph folks @smrolfe @muratmaga, it wouldn't be a bad idea to incorporate it into SlicerMorph. Sean's extension does something SlicerMorph users frequently ask for (the ability to register two 3D models and compare them using different types of visualization). However, some work would have to be done to integrate the tools to minimize redundancy. I am happy to help, but I would need helps from others as well. The main downside is that Sean might not want that integration, since his focus is on dentistry applications and he might want the UI to be specific to the task.
Option 2 - The other way to look at it is that it is a completely independent module that will grow into its own ecosystem. As I understand, Sean is regularly using the module in teaching activities and will need to maintain the code to be compatible at least with Slicer stables.

Thank you Arthur, that's correct. The end users in my mind are regular students & professors who may not have technical expertise. Hence I'd be looking to keep the user interface quite specific and simple. Yes, I do plan on regularly maintaining the code.

[muratmaga]

Hence I'd be looking to keep the user interface quite specific and simple

I think the goal would be to develeop a general purpose point cloud based registration tool, on which you can simply do a lightweight UI specific to your use case(s).

[seanchoi0519]

Hi Murat
That's correct, and there are UI pictures I've uploaded on README file available to see what I meant by the UI.

[seanchoi0519]

Hello @jamesobutler ,
A suggestion - I am happy to update the module with the SlicerMorph rigid registration pipeline (once it is done), however for now is it possible to have the extension available on the Slicer extension repository - compared to waiting for possibly many weeks for the update (which I'm very excited for) as I do have a network of dental institutions that could benefit from using this extension immediately. Let me know!

[muratmaga]

now is it possible to have the extension available on the Slicer extension repository

Are you aware of the Extension Wizard install method? That's you can provide a zip file of the repo to your users, which they can unzip and user the built in extension wizard to add to their slicer. It is essentially one more action (unzipping) compared to the extension catalog install. It might be good interim solution.

[seanchoi0519]

now is it possible to have the extension available on the Slicer extension repository

Are you aware of the Extension Wizard install method? That's you can provide a zip file of the repo to your users, which they can unzip and user the built in extension wizard to add to their slicer. It is essentially one more action (unzipping) compared to the extension catalog install. It might be good interim solution.

Thanks Murat, I guess I can do that, but again I keep in mind my target users may lack technical expertise and my goal would be to keep the installation process as simple as possible.

Would it be a hassle to make it available on extension repository for now? Meanwhile I could work to update the code, perhaps something like quickalign_preview, similar to the ALPACA. Let me know your thoughts,

Sean

[muratmaga]

Would it be a hassle to make it available on extension

That's really not for me to say as i dont review these or make the decisions. All i can say @agporto and @chz31 are looking into building the general purpose mesh registration tool and probably join this PW (remotely)

[lassoan]

Adding/renaming/removing extensions have significant long-term impact. If an extension appears in the extension catalog for a few months and it shows up in some youtube videos or forum posts then and then the extension is renamed or removed then for years we need to keep explaining users where that extension went, why, what to use instead.

Therefore, I would avoid adding a separate extension for mesh registration if it later will be folded into SlicerMorph. However, if the plan is to keep it as a separate extension then it is OK to create a separate extension for it now (and dependency with SlicerMorph can be sorted out later - extension dependencies are mostly internal implementation details).

One important change is needed in the extension name. In Slicer you can align many kind of data sets in many parameter spaces, so if the scope of the extension is spatial alignment of models then that must be included in the name. Something like QuickModelAlign, QuickAlignSurface, ModelQuickAlign, etc. would be sufficient.

[seanchoi0519]

Thank you @lassoan
I will implement the extension name change, this is not a problem.
Whether this module will be integrated to 3DSlicer as a seperate module or folded into Slicermorph, I'm happy for @agporto to decide!

[agporto]

Hi @seanchoi0519, you should do what you think is best. Given the focus of your module, my suggestion would be to keep it as a separate extension that will eventually use SlicerMorph's model registration module (for ease of maintenance).

[seanchoi0519]

Thank you @agporto, I'm happy to move forward with that
What would be the next steps? Is everyone OK with this module being added as a seperate extension in the preview release? Then it will be eventually merged with SlicerMorph's model registration module?

[seanchoi0519]

Hello everyone,

Following Arthur's advice, I do feel happy to publish the module as is. I will update the module once the rigid registration approach from SlicerMorph is published.

I've also amended the name to "QuickModelAlign." @lassoan
Please let me know if there's anything further to do on my end.

Many thanks to everyone!
@jamesobutler

[muratmaga]

Hello everyone,

Following Arthur's advice, I do feel happy to publish the module as is. I will update the module once the rigid registration approach from SlicerMorph is published.

I've also amended the name to "QuickModelAlign." @lassoan Please let me know if there's anything further to do on my end.

Many thanks to everyone! @jamesobutler

Sean, @chz31 is going to a demo of the separate registration module tomorrow to our monthly SlicerMorph user group. Feel free to join. It is on 11 (PT), here is the webex link. I think the module will be pushed to SlicerMorph by the end of the week.

https://seattlechildrens.webex.com/seattlechildrens/j.php?MTID=me662604e1ffd9c40f25888d048fcc0de

[seanchoi0519]

Hello everyone,
Following Arthur's advice, I do feel happy to publish the module as is. I will update the module once the rigid registration approach from SlicerMorph is published.
I've also amended the name to "QuickModelAlign." @lassoan Please let me know if there's anything further to do on my end.
Many thanks to everyone! @jamesobutler

Sean, @chz31 is going to a demo of the separate registration module tomorrow to our monthly SlicerMorph user group. Feel free to join. It is on 11 (PT), here is the webex link. I think the module will be pushed to SlicerMorph by the end of the week.

https://seattlechildrens.webex.com/seattlechildrens/j.php?MTID=me662604e1ffd9c40f25888d048fcc0de

Sounds good, will be there!

[seanchoi0519]

Hi @muratmaga @jamesobutler

Got to check out the "FastModelAlign" today (lol nice name), code looks great
I think it'd be great if we add the display & animation capabilities that my "QuickModelAlign" offers.
Imo it is one capability to register 2 models, but another to actually allow visual comparison of the output

I would either be looking to:

1. collaborate with @chz31 to add this capability
2. As mentioned before, I think the visualization aspect has big use cases in education field (I am partnering up with multiple universities at the moment in dental education), which is why I want to publish it as a seperate module.

Please advise

[muratmaga]

Imo it is one capability to register 2 models, but another to actually allow visual comparison of the output

I think we will keep the module strictly for registration. I agree visualizations are important but it will be different for everyone. So my suggestion, continue maintaining your extension in the way that will help you customize the visualizations whichever way you want, simply add SlicerMorph as a dependency for it.

This way you don't have to worry about maintaining the registration code, libraries, etc. The only requirement for you would be making sure that user did in fact run ITK-ALPACA (which brings the automatically necessary ITK python module). There is an example doing that programmatically that we can provide you.

[seanchoi0519]

Imo it is one capability to register 2 models, but another to actually allow visual comparison of the output

I think we will keep the module strictly for registration. I agree visualizations are important but it will be different for everyone. So my suggestion, continue maintaining your extension in the way that will help you customize the visualizations whichever way you want, simply add SlicerMorph as a dependency for it.

This way you don't have to worry about maintaining the registration code, libraries, etc. The only requirement for you would be making sure that user did in fact run ITK-ALPACA (which brings the automatically necessary ITK python module). There is an example doing that programmatically that we can provide you.

Hello murat, thanks and I'd be happy to check out the example code.

[smrolfe]

You can use

slicer.util.selectModule(slicer.modules.alpaca)

to switch to the ALPACA module, which will initiate install of the dependencies. Then switch back to your module on completion.

[muratmaga]

@seanchoi0519 FastModelAlign module is now incorporated to SlicerMorph (as a testing module) and if all goes well, will be available with tomorrow's build.

[jcfr]

FastModelAlign module is now available in SlicerMorph ✔️

@seanchoi0519 Did you have a chance to work on the QuickModelAlign extension ?

[lassoan]

We are cleaning out our backlog of open pull requests. We have introduced tiers for extensions, making it easier to add experimental extensions to the index. @seanchoi0519 if you want your extension to be added to the index then let us know and we can add it as a tier 1. If we don't hear from you then we will close the pull request (but you can reopen it anytime).