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Merges main into pytorch_dlc #2828

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Merged
n-poulsen merged 3 commits into from
Jan 8, 2025
Merged

Merges main into pytorch_dlc #2828

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d4da23a
Pins `numpy<2`, fix svd for `scipy>=1.11.0` (#2827)
n-poulsen Jan 7, 2025
5473c6f
Merge branch 'main' into niels/merge_main_20250107
n-poulsen Jan 7, 2025
6ca069f
unpin scipy
n-poulsen Jan 7, 2025
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12 changes: 8 additions & 4 deletions deeplabcut/refine_training_dataset/stitch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -412,10 +412,14 @@ def estimate_rank(self, tol):
The optimal hard threshold for singular values is 4/sqrt(3)
"""
mat = self.to_hankelet()
# nrows, ncols = mat.shape
# beta = nrows / ncols
# omega = 0.56 * beta ** 3 - 0.95 * beta ** 2 + 1.82 * beta + 1.43
_, s, _ = sli.svd(mat, min(10, min(mat.shape)))
if np.any(mat): # check that the matrix contains non-zero entries
# nrows, ncols = mat.shape
# beta = nrows / ncols
# omega = 0.56 * beta ** 3 - 0.95 * beta ** 2 + 1.82 * beta + 1.43
_, s, _ = sli.svd(mat, min(10, min(mat.shape)))
else:
s = np.zeros(min(10, min(mat.shape)))

# return np.argmin(s > omega * np.median(s))
eigen = s**2
diff = np.abs(np.diff(eigen / eigen[0]))
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4 changes: 2 additions & 2 deletions requirements.txt
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Expand Up @@ -16,13 +16,13 @@ imgaug>=0.4.0
numba>=0.54.0
matplotlib>=3.3, <3.8.4
networkx>=2.6
numpy>=1.18.5
numpy>=1.18.5,<2.0.0
pandas>=1.0.1,!=1.5.0
Pillow>=7.1
pyyaml
scikit-image>=0.17
scikit-learn>=1.0
scipy>=1.4,<1.11.0
scipy>=1.9
statsmodels>=0.11
tensorflow>=2.0,<2.13.0
tables==3.8.0
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4 changes: 2 additions & 2 deletions setup.py
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Expand Up @@ -66,11 +66,11 @@ def pytorch_config_paths() -> list[str]:
"numba>=0.54",
"matplotlib>=3.3,<3.9,!=3.7.0,!=3.7.1",
"networkx>=2.6",
"numpy>=1.18.5",
"numpy>=1.18.5,<2.0.0",
"pandas>=1.0.1,!=1.5.0",
"scikit-image>=0.17",
"scikit-learn>=1.0",
"scipy>=1.4,<1.11.0",
"scipy>=1.9",
"statsmodels>=0.11",
"tables==3.8.0",
"timm",
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