ShapeWorks 6.0 testing

[akenmorris]

Please edit and add a ✅ indicating success and ❌ indicating failure or 🕒 for a test in progress with your username when you complete a task for a given platform. When a test fails, please add a github issue and link it (* the issue when it's fixed and ready to test again). Also, go ahead and add new tasks that might not already be on here.

Please use the most recent release candidate for all testing (be careful which shapeworks is in your $PATH). The most recent is found here:

https://github.com/SCIInstitute/ShapeWorks/releases/tag/v6.0.0-rc10

Example:

	Windows	Mac	Linux
Notebooks		🕒 (@archanasri)
Usecase: Ellipsoid	✅ (@akenmorris )
Usecase: All tiny-test	❌ (#1073)	✅ (@cchriste)

Ok, now the real thing!

	Windows	Mac	Linux
Clean installation	✅ (@cchriste) (#1097, #1098)	✅ (@akenmorris RC10)
Notebooks: getting-started-with-jupyter-notebooks	✅ (@cchriste)	✅ (@akenmorris RC10)	✅ (@jadie1, @riddhishb)
Notebooks: setting-up-shapeworks-environment	✅ (@cchriste)	✅ (@akenmorris RC10)	✅ (@jadie1, @riddhishb)
Notebooks: getting-started-with-segmentations	✅ (@cchriste) (#1113)	✅ (@akenmorris RC10)	✅ (@jadie1 RC10)
Notebooks: getting-started-with-exploring-segmentations	✅ (@cchriste) (#1113)	✅ (@akenmorris RC10)	✅ (@jadie1 RC10)
Notebooks: getting-started-with-meshes	✅ (@cchriste) (#1142)	✅(@akenmorris RC10)	✅ (@jadie1 RC10)
Notebooks: getting-started-with-data-augmentation	✅ (@cchriste)	✅(@akenmorris)	✅ (@jadie1)
Notebooks: getting-started-with-shape-cohort-generation	✅ (@cchriste) (#1113)	✅ (@akenmorris)	✅ (@jadie1 RC10)
Usecase: ellipsoid	✅ (@akenmorris RC10)	✅ (@akenmorris)	✅ (@jadie1 RC10)
Usecase: ellipsoid --tiny_test	✅ (@akenmorris)	✅ (@archanasri)	✅ (@jadie1, @riddhishb)
Usecase: ellipsoid_cut	✅ (@akenmorris RC10)	✅ (@akenmorris)	(✅ @jadie1 RC10)
Usecase: ellipsoid_cut --tiny_test	✅ (@akenmorris)	✅ (@archanasri)	✅ (@jadie1)
Usecase: ellipsoid_evaluate	✅ (@akenmorris) (RC6)	✅ (@akenmorris) (RC6)	✅ (@iyerkrithika21)
Usecase: ellipsoid_fd	✅ (@cchriste)	✅ (@akenmorris)	✅ (@jadie1 RC10, @riddhishb)
Usecase: ellipsoid_mesh	✅ (@iyerkrithika21, @cchriste)	✅ (@archanasri)	✅ (@medakk) (@jadie1 RC10)
Usecase: ellipsoid_mesh --tiny-test	✅ (@iyerkrithika21)	✅ (@archanasri)	✅ (@medakk)
Usecase: femur	✅ (@cchriste)	✅ (@akenmorris RC10)	✅ (@jadie1)
Usecase: femur --tiny-test	✅ (@iyerkrithika21)	✅ (@archanasri)	✅ (@jadie1)
Usecase: femur --groom_images	✅ (@cchriste)	✅ (@akenmorris)	✅ (@jadie1)
Usecase: femur --groom_images --tiny-test	✅ (@iyerkrithika21)	✅ (@archanasri)	✅ (@jadie1)
Usecase: femur_mesh	✅ (@cchriste)	✅ (@archanasri)	✅ (@jadie1)
Usecase: femur_mesh --tiny-test	✅ (@iyerkrithika21)	✅ (@archanasri)	✅ (@jadie1)
Usecase: femur_cut	✅ (@cchriste)	✅ (akenmorris)	✅ (@jadie1)
Usecase: femur_cut --tiny-test	✅ (@iyerkrithika21)	✅ (@archanasri)	✅ (@jadie1)
Usecase: femur_cut --tiny-test (anisotropic)	✅ (@akenmorris)	✅ (@akenmorris)	✅ (@jadie1)
Usecase: left_atrium	✅ (@akenmorris, @cchriste)	✅ (@akenmorris)	✅ (@jadie1)
Usecase: left_atrium --tiny-test	✅ (@akenmorris)	✅ (@archanasri)	✅ (@jadie1)
Usecase: lumps	✅ (@iyerkrithika21, @cchriste)	✅ (@akenmorris)	✅ (@jadie1)
Usecase: lumps --tiny-test	✅ (@iyerkrithika21)	✅ (@archanasri)	✅ (@jadie1)
Usecase: deep_ssm --tiny-test	✅ (@cchriste)	✅ (@akenmorris RC10)	✅ (@jadie1)
Usecase: deep_ssm	✅ (@cchriste)	✅ (@akenmorris RC10)	✅ (@jadie1)
Studio: Ellipsoid Example	✅ (@akenmorris)	✅ (@akenmorris)	✅ (@medakk)
Studio: Feature Map Example	✅ (@akenmorris)	✅ (@akenmorris)	✅ (@medakk)
...

Please keep comments on this issue to a minimum. Let's try to keep the status in the table and not in the comments.

[akenmorris]

Do we have instructions anywhere for how to test (say) notebooks? Just open and run them?

I think so. There are instructions in them for the most part. They typically require that you go download data and put it in the right place. You can't just blindly open and run everything.

[jadie1]

Regarding #1102, should the answer be yes or no?
The currently running test was answered yes (use isotropic spacing for mesh rasterization).

For testing? It should work either way, testing with both yes and no on the tiny test only should be sufficient though. No need to test the entire use case with both.

[akenmorris]

I've disabled that now, but is there some way we can tell Windows to stay awake when shapeworks is running?

I would recommend disabling sleep in power options until you're finished testing shapeworks.

Are you asking if there is a windows API for disabling sleep, that a user program can alter? Even if there is, I would recommend against pursuing that.

[sheryjoe]

@jadie1 didn't we add the violin plots for data augmentation viz?

[jadie1]

@jadie1 didn't we add the violin plots for data augmentation viz?

Yes and it is used in the data augmentation notebook. I didn't change the DeepSSM use case to use it, I can if you'd like.

[akenmorris]

@jadie1 , should this be considered success? Can we close the issue and mark it as successful above?

[jadie1]

@jadie1 , should this be considered success? Can we close the issue and mark it as successful above?

Yes, if on windows or no GPU that is the expected output.

[sheryjoe]

@jadie1 didn't we add the violin plots for data augmentation viz?

Yes and it is used in the data augmentation notebook. I didn't change the DeepSSM use case to use it, I can if you'd like.

@jadie1 for consistency, let's add the violin plots to the deep ssm use case. it is also a better viz to convey the augmentation results.

[akenmorris]

@cchriste , looks good to me.

[cchriste]

@jadie1 , should this be considered success? Can we close the issue and mark it as successful above?

Yes, if on windows or no GPU that is the expected output.

Is there a github issue to enable utilization of the GPU(s) on Windows? This box has two of them and they're really bored.

It will work on windows if the user installs the correct version of Pytorch themselves to the ShapeWorks environment following this doc: PyTorch GPU Support for ShapeWorks. It seems there is no reliable way to automatically detect CUDA version on Windows which is why we don't have conda_installs.bat install it with GPU support. We can make an issue but I am not sure if there is currently a solution.

Unfortunately those instructions don't provide any method for determining the CUDA version available on Windows (something will need to be installed, so it's a process likely starting here. I will look into it more when I have a chance.

[cchriste]

I think we're down to just the two ellipsoid use cases for this release. Might anyone have ideas for things we just haven't thought to test yet? Anything in particular we should be sure to run again on any particular platform?

[jadie1]

The ellipsoid use case and notebook are working on the one_mode_ellipsoid branch (issue #1133). The only thing we are waiting on is the parameters need to be tuned for the ellipsoid_cut use case because the correspondence is still not great (issue #1104). @HeavenlyBerserker an @akenmorris Should I make a PR now for the one_mode_ellipsoid branch? Or wait in case the ellipsoid_cut params get updated?

[jadie1]

I did not find any issues with RC10 on Linux!

[akenmorris]

Done!