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Removed deprecated torch.lstsq, replaced by torch.linalg.lstsq #33

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Merged
carloalbertobarbano merged 5 commits into from
Jan 18, 2023
Merged

Removed deprecated torch.lstsq, replaced by torch.linalg.lstsq #33

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f14df82
Removed deprecated torch.lstsq, replaced by torch.linalg.lstsq
raphaelattias Jan 11, 2023
6883215
removed .vscode, revert change to example.py and updated min version …
raphaelattias Jan 11, 2023
26091e4
fix example
raphaelattias Jan 11, 2023
c5b715c
add torch version checking for backward compatibility
raphaelattias Jan 11, 2023
2b4dd90
Added torch version check in the __init__
raphaelattias Jan 17, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/tests_full.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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: [1.8.0, 1.9.0, 1.10.0, 1.11.0, 1.12.0, 1.13.0]
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@andreped andreped Jan 11, 2023

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Great! Just handling new/older torch version in the repo that remains :]

exclude:
- python-version: 3.6
pytorch-version: 1.11.0
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1 change: 0 additions & 1 deletion example.py
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Expand Up @@ -83,7 +83,6 @@
t_ = time.time()
norm, H, E = tf_normalizer.normalize(I=t_to_transform, stains=True)
print("tf runtime:", time.time() - t_)

plt.figure()
plt.suptitle('tensorflow normalizer')
plt.subplot(2, 2, 1)
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10 changes: 7 additions & 3 deletions torchstain/torch/normalizers/macenko.py
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Expand Up @@ -14,7 +14,8 @@ def __init__(self):
[0.7201, 0.8012],
[0.4062, 0.5581]])
self.maxCRef = torch.tensor([1.9705, 1.0308])

self.deprecated_torch = torch.__version__ < (1,9,0)

def __convert_rgb2od(self, I, Io, beta):
I = I.permute(1, 2, 0)

Expand Down Expand Up @@ -49,13 +50,16 @@ def __find_concentration(self, OD, HE):
Y = OD.T

# determine concentrations of the individual stains
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@andreped andreped Jan 11, 2023

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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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@raphaelattias raphaelattias Jan 11, 2023

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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:

https://github.com/pytorch/pytorch/blob/b0c86caa1d46a16195682e2afe5456f97265aa53/torch/_linalg_utils.py#L111

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@andreped andreped Jan 11, 2023

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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__)

return torch.lstsq(Y, HE)[0][:2]
if self.deprecated_torch:
return torch.lstsq(Y, HE)[0][:2]

return torch.linalg.lstsq(HE, Y)[0]

def __compute_matrices(self, I, Io, alpha, beta):
OD, ODhat = self.__convert_rgb2od(I, Io=Io, beta=beta)

# compute eigenvectors
_, eigvecs = torch.symeig(cov(ODhat.T), eigenvectors=True)
_, eigvecs = torch.linalg.eigh(cov(ODhat.T))
eigvecs = eigvecs[:, [1, 2]]

HE = self.__find_HE(ODhat, eigvecs, alpha)
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