Tutorial/Demo for Modular Patch Inferer

[bhashemian]

Description

This PR adds a notebook to demonstrate how the new modular patch inference can used:

• PatchInferer
• AvgMerger
• SlidingWindowSplitter
• WSISlidingWindowSplitter

Checks

• Avoid including large-size files in the PR.
• Clean up long text outputs from code cells in the notebook.
• For security purposes, please check the contents and remove any sensitive info such as user names and private key.
• Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the ./figure folder
• Notebook runs automatically ./runner.sh -t <path to .ipynb file>

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[Nic-Ma]

Hi @drbeh , do you plan to complete this PR for review?

Thanks.

[bhashemian]

Hi @drbeh , do you plan to complete this PR for review?

Thanks.

Yes, I'll do it shortly.

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KumoLiu commented on 2023-06-01T06:05:48Z
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Duplicated "to" in the first line.

"The core to to a modular patch".

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KumoLiu commented on 2023-06-01T06:05:49Z
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Missing title for this cell and the following cell?

And can we also add a raw image here?

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KumoLiu commented on 2023-06-01T06:05:50Z
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Line #22.    fig.suptitle(f"Patch filtering by a threshold (without padding, {patch_size=})", fontsize=24)

A wrong patch size here for the title.

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Nic-Ma commented on 2023-06-03T09:32:29Z
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I think we usually don't need to put the program code design diagram in tutorial, what do you think?

Thanks.

[Nic-Ma]

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Nic-Ma commented on 2023-06-03T09:32:29Z ----------------------------------------------------------------

I think we usually don't need to put the program code design diagram in tutorial, what do you think?

Thanks.

@wyli @ericspod What do you think?

Thanks.

[ericspod]

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Nic-Ma commented on 2023-06-03T09:32:29Z ----------------------------------------------------------------
I think we usually don't need to put the program code design diagram in tutorial, what do you think?
Thanks.

@wyli @ericspod What do you think?

Thanks.

I'm fine with more information in tutorials especially for a design concept that requires a little explanation. We can do embedded images directly in the notebook rather than linking to a file if you wanted to not have it. Thanks!

[bhashemian]

@KumoLiu @Nic-Ma please let me know if you have any other comments.

[Nic-Ma]

Hi @drbeh ,

I see 1 error in the CI:

    510 elif self.backend == "openslide":
--> 511     self.reader = OpenSlideWSIReader(
    512         level=level,
    513         mpp=mpp,
    514         mpp_rtol=mpp_rtol,
    515         mpp_atol=mpp_atol,
    516         power=power,
    517         power_rtol=power_rtol,
    518         power_atol=power_atol,
    519         channel_dim=channel_dim,
    520         dtype=dtype,
    521         device=device,
    522         mode=mode,
    523         **kwargs,
    524     )
    525 elif self.backend == "tifffile":
    526     self.reader = TiffFileWSIReader(
    527         level=level,
    528         mpp=mpp,
   (...)
    538         **kwargs,
    539     )

File /opt/conda/lib/python3.8/site-packages/monai/utils/module.py:488, in require_pkg.<locals>._decorator.<locals>._wrapper(*args, **kwargs)
    486 err_msg = f"required package `{pkg_name}` is not installed or the version doesn't match requirement."
    487 if raise_error:
--> 488     raise OptionalImportError(err_msg)
    489 else:
    490     warnings.warn(err_msg)

OptionalImportError: required package `openslide` is not installed or the version doesn't match requirement.


Check failed!

If you have any questions about the CI execution env, maybe @mingxin-zheng and @wyli can help.

Thanks in advance.

[bhashemian]

Hi @drbeh ,

I see 1 error in the CI:

    510 elif self.backend == "openslide":
--> 511     self.reader = OpenSlideWSIReader(
    512         level=level,
    513         mpp=mpp,
    514         mpp_rtol=mpp_rtol,
    515         mpp_atol=mpp_atol,
    516         power=power,
    517         power_rtol=power_rtol,
    518         power_atol=power_atol,
    519         channel_dim=channel_dim,
    520         dtype=dtype,
    521         device=device,
    522         mode=mode,
    523         **kwargs,
    524     )
    525 elif self.backend == "tifffile":
    526     self.reader = TiffFileWSIReader(
    527         level=level,
    528         mpp=mpp,
   (...)
    538         **kwargs,
    539     )

File /opt/conda/lib/python3.8/site-packages/monai/utils/module.py:488, in require_pkg.<locals>._decorator.<locals>._wrapper(*args, **kwargs)
    486 err_msg = f"required package `{pkg_name}` is not installed or the version doesn't match requirement."
    487 if raise_error:
--> 488     raise OptionalImportError(err_msg)
    489 else:
    490     warnings.warn(err_msg)

OptionalImportError: required package `openslide` is not installed or the version doesn't match requirement.


Check failed!

If you have any questions about the CI execution env, maybe @mingxin-zheng and @wyli can help.

Thanks in advance.

That's right, @Nic-Ma! I believe openslide library is not being installed in the CI/CD. I can add it but let me see if I can make things work with cucim, so we can avoid additional time that installing the library will take for each test.

[bhashemian]

It passed all tests with cucim. Will merge it.