Rename l1_ratio parameter for clarity

flatironinstitute · Jan 14, 2025 · 52dfd57 · 52dfd57
1 parent 56ffa62
commit 52dfd57
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/caiman/source_extraction/cnmf/initialization.py b/caiman/source_extraction/cnmf/initialization.py
@@ -148,7 +148,7 @@ def initialize_components(Y, K=30, gSig=[5, 5], gSiz=None, ssub=1, tsub=1, nIter
                           min_corr=0.8, min_pnr=10, seed_method='auto', ring_size_factor=1.5,
                           center_psf=False, ssub_B=2, init_iter=2, remove_baseline = True,
                           SC_kernel='heat', SC_sigma=1, SC_thr=0, SC_normalize=True, SC_use_NN=False,
-                          SC_nnn=20, lambda_gnmf=1, l1_ratio:float=0.0):
+                          SC_nnn=20, lambda_gnmf=1, snmf_l1_ratio:float=0.0):
     """
     Initialize components. This function initializes the spatial footprints, temporal components,
     and background which are then further refined by the CNMF iterations. There are four
@@ -256,7 +256,7 @@ def initialize_components(Y, K=30, gSig=[5, 5], gSiz=None, ssub=1, tsub=1, nIter
         init_iter: int, optional
             number of iterations for 1-photon imaging initialization
 
-        l1_ratio: float
+        snmf_l1_ratio: float
             Used only by sparse NMF, passed to NMF call
 
     Returns:
@@ -337,7 +337,7 @@ def initialize_components(Y, K=30, gSig=[5, 5], gSiz=None, ssub=1, tsub=1, nIter
     elif method == 'sparse_nmf':
         Ain, Cin, _, b_in, f_in = sparseNMF(
             Y_ds, nr=K, nb=nb, max_iter_snmf=max_iter_snmf, alpha=alpha_snmf,
-            sigma_smooth=sigma_smooth_snmf, remove_baseline=remove_baseline, perc_baseline=perc_baseline_snmf, l1_ratio=l1_ratio)
+            sigma_smooth=sigma_smooth_snmf, remove_baseline=remove_baseline, perc_baseline=perc_baseline_snmf, l1_ratio=snmf_l1_ratio)
 
     elif method == 'compressed_nmf':
         Ain, Cin, _, b_in, f_in = compressedNMF(

diff --git a/caiman/source_extraction/cnmf/params.py b/caiman/source_extraction/cnmf/params.py
@@ -719,7 +719,7 @@ def __init__(self, fnames=None, dims=None, dxy=(1, 1),
             'init_iter': init_iter,
             'kernel': None,           # user specified template for greedyROI
             'lambda_gnmf': 1,         # regularization weight for graph NMF
-            'l1_ratio': 0.0,
+            'snmf_l1_ratio': 0.0,     # L1 ratio, used by sparse nmf mode only
             'maxIter': 5,             # number of HALS iterations
             'max_iter_snmf': 500,
             'method_init': method_init,    # can be greedy_roi, corr_pnr sparse_nmf, local_NMF