MIL Component - MILModel

[myron]

Fix #3163

A wrapper around backbone CNN classification model suitable for MIL

[bhashemian]

Hi @myron, all your git commits need to be signed for MONAI. You should use -s in ALL your commits:

git commit -sm "Add commit message"

https://github.com/Project-MONAI/MONAI/pull/3236/checks?check_run_id=4074346048

[myron]

Hi @myron, all your git commits need to be signed for MONAI. You should use -s in ALL your commits:

git commit -sm "Add commit message"

https://github.com/Project-MONAI/MONAI/pull/3236/checks?check_run_id=4074346048

even for draft PRs ? I thought this is just to have an initial discussion

[myron]

Ok, signed and pushed

[bhashemian]

Thank you @myron. The draft PR is the work in progress to let the repo maintainer know what is being developed. So you can continue to improve it until it is ready to review (and passing all the tests)

I will try to give my comments earlier but please work on addressing the tests that are not passing. You can start from the easy one like code formatting. Please let me know if you have any question.

[Nic-Ma]

Hi @myron ,

Please add guys in reviewers instead of assignees.

Thanks.

[myron]

I've updated this model, added enum and moved some options into arguments
@drbeh does it look better?

[myron]

I ran into another JIT issue, it fails the test on the older Pytorch version (1.7, over a year old), it looks like at that time Enum wasn't supported in JIT.

@wyli @Nic-Ma any suggestions?
we can remove Enum, and use strings for MilMode, or we can skip this test ?

thanks

RuntimeError:
Module 'MILModel' has no attribute 'mil_mode' (This attribute exists on the Python module, but we failed to convert Python type: 'monai.networks.nets.milmodel.MilMode' to a TorchScript type.):
  File "/mnt/amproj/Code/MONAI/monai/networks/nets/milmodel.py", line 161
        sh = x.shape

        if self.mil_mode == MilMode.MEAN:

[bhashemian]

I ran into another JIT issue, it fails the test on the older Pytorch version (1.7, over a year old), it looks like at that time Enum wasn't supported in JIT.

@wyli @Nic-Ma any suggestions? we can remove Enum, and use strings for MilMode, or we can skip this test ?

thanks

RuntimeError:
Module 'MILModel' has no attribute 'mil_mode' (This attribute exists on the Python module, but we failed to convert Python type: 'monai.networks.nets.milmodel.MilMode' to a TorchScript type.):
  File "/mnt/amproj/Code/MONAI/monai/networks/nets/milmodel.py", line 161
        sh = x.shape

        if self.mil_mode == MilMode.MEAN:

@myron considering the tight deadline for the next release, let's use string instead of enum if it can fix the issue and move on.

[bhashemian]

@myron it looks good to me. Could you please take a look at the checks that are failing?

[bhashemian]

@Nic-Ma @wyli do you have any other commnet?

[myron]

@myron it looks good to me. Could you please take a look at the checks that are failing?

I don't know why it's failing. There is only 1 failed check, that seems to be unrelated to my PR

2021-11-14 16:01:06,684 - ERROR - check_hash failed 938869fb71b05f5ba345ab36dfbbc4388f53a550.
clang-format: 1.86MB [00:00, 2.41MB/s]                           
Download /__w/MONAI/MONAI/.clang-format-bin/clang-format failed: sha1 check of downloaded file failed: URL=https://oss-clang-format.s3.us-east-2.amazonaws.com/linux64/clang-format-linux64, filepath=/__w/MONAI/MONAI/.clang-format-bin/clang-format, expected sha1=9073602de1c4e1748f2feea5a0782417b20e3043.
Please remove /__w/MONAI/MONAI/.clang-format-bin/clang-format and retry.

[Nic-Ma]

@myron it looks good to me. Could you please take a look at the checks that are failing?

I don't know why it's failing. There is only 1 failed check, that seems to be unrelated to my PR

2021-11-14 16:01:06,684 - ERROR - check_hash failed 938869fb71b05f5ba345ab36dfbbc4388f53a550.
clang-format: 1.86MB [00:00, 2.41MB/s]                           
Download /__w/MONAI/MONAI/.clang-format-bin/clang-format failed: sha1 check of downloaded file failed: URL=https://oss-clang-format.s3.us-east-2.amazonaws.com/linux64/clang-format-linux64, filepath=/__w/MONAI/MONAI/.clang-format-bin/clang-format, expected sha1=9073602de1c4e1748f2feea5a0782417b20e3043.
Please remove /__w/MONAI/MONAI/.clang-format-bin/clang-format and retry.

Hi @myron ,

I already submitted PR to fix it.

Thanks.

[yiheng-wang-nv]

Looks good on me.

[bhashemian]

@Nic-Ma @wyli could you please run Blossom CI here?

[Nic-Ma]

/build

[Nic-Ma]

Thanks for the great feature.
Looks good to me, I will slightly adjust the doc related things later.

Thanks.