small corrections

features_analysis.py

@@ -841,9 +841,12 @@ if __name__ == "__main__":
     # selected_features = []
     # selected_df = df[selected_features]
     ## TODO Or use the csv with dropped features
-    selected_df = pd_.read_csv(f"{save_in}\\df_drop_highly_corr_feat.csv")
-    # selected_df = pd_.read_csv(f"{save_in}\\df_drop_highly_corr_feat_6H.csv")
-    ## If an error raises, only run the part until FeaturesStatistics included, and then run the last part.
+    try:
+        selected_df = pd_.read_csv(f"{save_in}\\df_drop_highly_corr_feat.csv")
+        # selected_df = pd_.read_csv(f"{save_in}\\df_drop_highly_corr_feat_6H.csv")
+    except:
+        raise("Only run the part until FeaturesStatistics included to generate df_drop_highly_corr_feat.csv, and then run the last part.")
+        ## If an error raises, only run the part until FeaturesStatistics included, and then run the last part.
 
     # if other columns need to be dropped:
     try:

nutrimorph.py

@@ -229,8 +229,8 @@ def NutriMorph(data_path: str,
     print("\n--- Soma Detection")
 
     # Change the soma parameters from micron to pixel dimensions, using the previously determined voxel size
-    soma_min_area_c = in_.ToPixel(soma_min_area_c, size_voxel_in_micron, dimension=(0, 1))
-    soma_max_area_c = in_.ToPixel(soma_max_area_c, size_voxel_in_micron, dimension=(0, 1))
+    soma_min_area_c = in_.ToPixel(soma_min_area_c, size_voxel_in_micron, dimension=(0, 1, 2))
+    soma_max_area_c = in_.ToPixel(soma_max_area_c, size_voxel_in_micron, dimension=(0, 1, 2))
     soma_selem_c = mp_.disk(in_.ToPixel(soma_selem_micron_c, size_voxel_in_micron))
 
     # - Create the maps for enhancing and detecting the soma
@@ -283,7 +283,7 @@ def NutriMorph(data_path: str,
     image_for_ext[del_soma] = 0
 
     # Change the extensions parameters from micron to pixel dimensions
-    ext_min_area_c = in_.ToPixel(ext_min_area_c, size_voxel_in_micron, dimension=(0, 1))
+    ext_min_area_c = in_.ToPixel(ext_min_area_c, size_voxel_in_micron, dimension=(0, 1, 2))
 
     if ext_selem_micron_c == 0:
         ext_selem_pixel_c = None

parameters.ini

@@ -74,8 +74,11 @@ soma_low_c                 :    0.15
 soma_high_c                :    0.7126
 ; this is a coefficient => not in micron
 soma_selem_micron_c        :    0.481
-soma_min_area_c            :    58
-soma_max_area_c            :    580
+; below, area correspond to a volume
+soma_min_area_c            :    116
+# 58 if ToPixel (0,1)
+soma_max_area_c            :    1160
+# 580 if ToPixel (0,1)
 
 [Extensions]
 adapt_hist_equalization    :    False
@@ -84,7 +87,9 @@ ext_low_c                  :    10
 ext_high_c                 :    0.6
 ; for morphological cleaning
 ext_selem_micron_c         :    0.2405
-ext_min_area_c             :    5.7840
+;below, area correspond to a volume
+ext_min_area_c             :    11.568
+# 5.7840 if ToPixel (0,1)
 
 [Connexions]
 max_straight_sq_dist_c     :    217