Removed deprecated torch.lstsq, replaced by torch.linalg.lstsq #33
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| @@ -49,7 +49,7 @@ def __find_concentration(self, OD, HE): | |||
| Y = OD.T | |||
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| # determine concentrations of the individual stains | |||
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Note that I am not sure that doing this is backward compatible, as I believe torch.linalg.lstsq does not exist in older versions of torch. You will need to find a fix that works for all versions.
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By the Torch repo that change was made in Torch 1.9. I suggest bumping the minimum version of Torch required from 1.8 to 1.9 to assure backward compatibility:
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There are surprisingly many people that use older versions of pytorch and tf. Also, 1.9 isn't really that old.
I think a good fix for this is to check which pytorch version that is used and introduce a if statement to handle older versions. You can get the torch version by:
import torch
print(torch.__version__)
.github/workflows/tests_full.yml
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| @@ -73,7 +73,7 @@ jobs: | |||
| matrix: | |||
| os: [ windows-2019, ubuntu-18.04, macos-11 ] | |||
| python-version: [ 3.6, 3.7, 3.8, 3.9 ] | |||
| pytorch-version: [1.8.0, 1.9.0, 1.10.0, 1.11.0, 1.12.0] | |||
| pytorch-version: [1.9.0, 1.10.0, 1.11.0, 1.12.0, 1.13.0] | |||
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Sneaky fix ;) But it would be better if we also supported older versions of pytorch (< 1.9).
| @@ -73,7 +73,7 @@ jobs: | |||
| matrix: | |||
| os: [ windows-2019, ubuntu-18.04, macos-11 ] | |||
| python-version: [ 3.6, 3.7, 3.8, 3.9 ] | |||
| pytorch-version: [1.9.0, 1.10.0, 1.11.0, 1.12.0, 1.13.0] | |||
| pytorch-version: [1.8.0, 1.9.0, 1.10.0, 1.11.0, 1.12.0, 1.13.0] | |||
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Great! Just handling new/older torch version in the repo that remains :]
| @@ -49,7 +49,11 @@ def __find_concentration(self, OD, HE): | |||
| Y = OD.T | |||
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| # determine concentrations of the individual stains | |||
| return torch.linalg.lstsq(HE, Y)[0] | |||
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| if torch.__version__ >= (1,9,0): | |||
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Great! It is a little suboptimal to have this if statement being called every single time this method is called. Might be better to do this only once in the init() or similar. And then, this method knows which lstsq to use, but we can fix that in the near future. LGTM.
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I agree, it should be a rather quick fix to do (in init or in the file header)
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Note that, as I'm not a maintainer of this project, @carloalbertobarbano is needed to:
He will probably return from holiday anytime soon, @raphaelattias :] |
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Hi @raphaelattias, I finally came back from vacation. Thanks for your contribution! I will happily merge it once you refactor the torch version check |
I believe that was already done., I just did not see that in one of my latest comments. See this commit: c5b715c Correct me if I'm wrong. Current version is here, and contains the torch version check: |
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Yes, but I would like the version check to be moved from |
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Oh yeah, sure. I guess you will make that final change yourself in the development branch. Not sure @raphaelattias is available to make that fix right now. |
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Hi @andreped thank you for the feedback, I am working on it :) |
Updated eigen vectors solver
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Thanks for the cooperation @raphaelattias |
As of September 22, torch.lstsq is deprecated (pytorch/pytorch#70980) and has been replaced by torch.linalg.lstsq. This PR solves an issue for Pytorch version 1.13.