|
new_dir = np.take(x, indices) |
Current code:
dirs = []
for x in bvec:
new_dir = np.take(x, indices)
dirs.append(new_dir)
new_bvec = np.stack(dirs, axis=0)
Suggested replacement:
new_bvec = bvec[:, indices]
The current implementation loops over all rows in bvec, calling np.take on each one, and appends results to a list before stacking. This introduces significant overhead from:
Python-level iteration;
Repeated function calls;
Intermediate list and array construction.
The optimized version uses NumPy’s advanced indexing to extract the desired columns from all rows at once:
It is fully vectorized, much faster, and more memory efficient;
The result is exactly the same.
AtlasToDiffusionReg/src/CODE/extract_single_shell.py
Line 101 in cfb76fb
Current code:
Suggested replacement:
new_bvec = bvec[:, indices]The current implementation loops over all rows in bvec, calling np.take on each one, and appends results to a list before stacking. This introduces significant overhead from:
Python-level iteration;
Repeated function calls;
Intermediate list and array construction.
The optimized version uses NumPy’s advanced indexing to extract the desired columns from all rows at once:
It is fully vectorized, much faster, and more memory efficient;
The result is exactly the same.