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Update main from fork #136

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ba44c15
Update nnls.py
Beatricecrudele Apr 14, 2025
9a6e123
Merge pull request #1 from pone-software/Beatricecrudele-dev
Beatricecrudele Apr 28, 2025
ed1374e
Update nnls.py
Beatricecrudele May 22, 2025
c7481bc
Merge branch 'legend-exp:main' into main
Beatricecrudele May 22, 2025
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15 changes: 10 additions & 5 deletions src/dspeed/processors/nnls.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@

@guvectorize(
[
"void(float32[:,::1], float32[::1], float32, float32, boolean, float32, float32[::1])",
"void(float64[:,::1], float64[::1], float64, float32, boolean, float32, float64[::1])",
"void(float32[:,::1], float32[::1], float32, float32, boolean, float32, float32, float32[::1])",
"void(float64[:,::1], float64[::1], float64, float32, boolean, float32, float32, float64[::1])",
],
"(m,n),(m),(),(),(),(),(n)",
"(m,n),(m),(),(),(),(),(),(n)",
nopython=True,
**nb_kwargs,
)
Expand All @@ -23,6 +23,7 @@ def optimize_nnls(
tol: float,
allow_singularity: bool,
min_value: float,
lmb: float,
x: np.ndarray,
) -> None:
"""Solve ``argmin_x || ax - b ||_2`` for ``x>=0``.
Expand All @@ -45,6 +46,10 @@ def optimize_nnls(
If matrix is not solvable (e.g. because of non full rank caused by
float precision), no error is raised but all elements of the
solution vector are set NaN
min_value: float
Threshold for noise reduction
lmb : float
L1 penalty to enforce sparsity in the solution.
x : ndarray
Solution vector.

Expand All @@ -58,7 +63,7 @@ def optimize_nnls(
"module": "dspeed.processors",
"args": ["db.coefficient_matrix",
"wf_blsub",
"1000", "1e-6", "True"
"1000", "1e-6", "True", 0.3, 3e4,
"nnls_solution"],
}
"""
Expand Down Expand Up @@ -100,7 +105,7 @@ def is_singular(matrix):
)

ata = np.transpose(a) @ a
atb = b @ a # Result is 1D - let NumPy figure it out
atb = b @ a - lmb # Result is 1D - let NumPy figure it out

# Initialize vars
x[:] = np.zeros(n, dtype=np.float64)
Expand Down