allensdk.brain_observatory.r_neuropil module¶
- class allensdk.brain_observatory.r_neuropil.NeuropilSubtract(lam=0.05, dt=1.0, folds=4)[source]¶
Bases:
object
TODO: docs
- allensdk.brain_observatory.r_neuropil.ab_from_diagonals(mat_dict)[source]¶
Constructs value for scipy.linalg.solve_banded
- Parameters:
- mat_dict: dictionary of diagonals keyed by offsets
- Returns:
- ab: value for scipy.linalg.solve_banded
- allensdk.brain_observatory.r_neuropil.estimate_contamination_ratios(F_M, F_N, lam=0.05, folds=4, iterations=3, r_range=[0.0, 2.0], dr=0.1, dr_factor=0.1)[source]¶
Calculates neuropil contamination of ROI
- Parameters:
- F_M: ROI trace
- F_N: Neuropil trace
- Returns:
- dictionary: key-value pairs
‘r’: the contamination ratio – corrected trace = M - r*N
‘err’: RMS error
‘min_error’: minimum error
‘bounds_error’: boolean. True if error or R are outside tolerance
- allensdk.brain_observatory.r_neuropil.get_diagonals_from_sparse(mat)[source]¶
Returns a dictionary of diagonals keyed by offsets
- Parameters:
- mat: scipy.sparse matrix
- Returns:
- dictionary: diagonals keyed by offsets