fix bug

DendrouLab · Feb 10, 2025 · 39d3c57 · 39d3c57
1 parent 4d873f2
commit 39d3c57
Showing 1 changed file with 8 additions and 15 deletions.
diff --git a/panpipes/funcs/io.py b/panpipes/funcs/io.py
@@ -171,22 +171,23 @@ def gen_load_spatial_jobs(caf, mode_dictionary = {}, load_raw=True):
                 visium_tissue_positions_file = None
                 visium_scalefactors_file = None
                 spatial_filetype = caf['spatial_filetype'][nn]
+                vpt_cell_by_gene = None
+                vpt_cell_metadata = None
+                vpt_cell_boundaries = None
                 if "vpt_cell_by_gene" in caf.columns:
                     if pd.notna(caf['vpt_cell_by_gene'][nn]):
                         vpt_cell_by_gene = caf['vpt_cell_by_gene'][nn]
-                else:
-                    vpt_cell_by_gene = None
                 if "vpt_cell_metadata" in caf.columns:
                     if pd.notna(caf['vpt_cell_metadata'][nn]):
                         vpt_cell_metadata = caf['vpt_cell_metadata'][nn]
-                else:
-                    vpt_cell_metadata = None
                 if "vpt_cell_boundaries" in caf.columns:
                     if pd.notna(caf['vpt_cell_boundaries'][nn]):
                         vpt_cell_boundaries = caf['vpt_cell_boundaries'][nn]
-                else:
-                    vpt_cell_boundaries = None
             elif caf['spatial_filetype'][nn]=="visium":
+                visium_feature_bc_matrix = None 
+                visium_fullres_image_file = None
+                visium_tissue_positions_file = None
+                visium_scalefactors_file = None
                 vpt_cell_by_gene = None
                 vpt_cell_metadata = None
                 vpt_cell_boundaries = None
@@ -195,26 +196,18 @@ def gen_load_spatial_jobs(caf, mode_dictionary = {}, load_raw=True):
                 if "visium_feature_bc_matrix" in caf.columns:
                     if pd.notna(caf["visium_feature_bc_matrix"][nn]):
                         visium_feature_bc_matrix= caf["visium_feature_bc_matrix"][nn]
-                else:
-                    visium_feature_bc_matrix = None  
                 # fullres image
                 if "visium_fullres_image_file" in caf.columns:
                     if pd.notna(caf["visium_fullres_image_file"][nn]):
                         visium_fullres_image_file= caf["visium_fullres_image_file"][nn]
-                else:
-                    visium_fullres_image_file = None 
                 # tissue position 
                 if "visium_tissue_positions_file" in caf.columns:
                     if pd.notna(caf["visium_tissue_positions_file"][nn]):
                         visium_tissue_positions_file= caf["visium_tissue_positions_file"][nn]
-                else:
-                    visium_tissue_positions_file = None  
                 # scalefactor
                 if "visium_scalefactors_file" in caf.columns:
                     if pd.notna(caf["visium_scalefactors_file"][nn]):
-                        visium_scalefactors_file= caf["visium_scalefactors_file"][nn]
-                else:
-                    visium_scalefactors_file = None  
+                        visium_scalefactors_file= caf["visium_scalefactors_file"][nn] 
         else:
             spatial_path= None
             spatial_filetype = None