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Avoid 'np.float' Deprecation Error for numpy>=1.20 #21

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Avoid 'np.float' Deprecation Error for numpy>=1.20 #21

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8 changes: 4 additions & 4 deletions spatialdm/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ def pair_selection_matrix(adata, n_perm, sel_ind, method):

# averaged ligand values
L1 = [pd.Series(x[0]).dropna().values for x in ligand.values]
L_mat = [adata[:, L1[l]].X.astype(np.float)[:, 0] for l in range(len(L1))]
L_mat = [adata[:, L1[l]].X.astype(np.float16)[:, 0] for l in range(len(L1))]
for i, k in enumerate(ligand.index):
if len(ligand.loc[k].dropna()) > 1:
if adata.uns['mean'] == 'geometric':
Expand All @@ -185,7 +185,7 @@ def pair_selection_matrix(adata, n_perm, sel_ind, method):

# averaged receptor values
R1 = [pd.Series(x[0]).dropna().values for x in receptor.values]
R_mat = [adata[:, R1[r]].X.astype(np.float)[:, 0] for r in range(len(R1))]
R_mat = [adata[:, R1[r]].X.astype(np.float16)[:, 0] for r in range(len(R1))]
for i, k in enumerate(receptor.index):
if len(receptor.loc[k].dropna()) > 1:
if adata.uns['mean'] == 'geometric':
Expand Down Expand Up @@ -248,7 +248,7 @@ def spot_selection_matrix(adata, ligand, receptor, ind, n_perm, method, scale_X=
if adata.uns['mean'] == 'geometric':
from scipy.stats.mstats import gmean
L1 = [pd.Series(x[0]).dropna().values for x in ligand.values]
L_mat0 = [raw_norm[:, L1[l]].X.A.astype(np.float)[:, 0] for l in range(len(L1))]
L_mat0 = [raw_norm[:, L1[l]].X.A.astype(np.float16)[:, 0] for l in range(len(L1))]
for i, k in enumerate(ligand.index):
if len(ligand.loc[k].dropna()) > 1:
if adata.uns['mean'] == 'geometric':
Expand All @@ -258,7 +258,7 @@ def spot_selection_matrix(adata, ligand, receptor, ind, n_perm, method, scale_X=

# averaged receptor values
R1 = [pd.Series(x[0]).dropna().values for x in receptor.values]
R_mat0 = [raw_norm[:, R1[r]].X.A.astype(np.float)[:, 0] for r in range(len(R1))]
R_mat0 = [raw_norm[:, R1[r]].X.A.astype(np.float16)[:, 0] for r in range(len(R1))]
for i, k in enumerate(receptor.index):
if len(receptor.loc[k].dropna()) > 1:
if adata.uns['mean'] == 'geometric':
Expand Down