solved delimiter issue in data cleaning

valeriocaporioniunipi · May 26, 2024 · 110b0b2 · 110b0b2
1 parent 4c56944
commit 110b0b2
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 10 deletions.
diff --git a/brainage/__pycache__/utils.cpython-311.pyc b/brainage/__pycache__/utils.cpython-311.pyc
diff --git a/brainage/neural_net.py b/brainage/neural_net.py
@@ -357,6 +357,7 @@ def neural_net_parsing():
         p_value_emp(pad_control, pad_asd)
         sites_asd = get_sites(args.filename, site_col = args.site_col, group_col = args.group,
                           group_value = 1) # 1 is for ASD group
+        print(np.mean(pad_control), np.mean(pad_asd))
         sites_barplot(pad_asd, sites_asd)
         if args.plot:
             plt.show()

diff --git a/brainage/utils.py b/brainage/utils.py
@@ -102,7 +102,7 @@ def handle_spurious(df: pd.DataFrame, *args: str) -> pd.DataFrame:
         if isinstance(arg, str):
             df.drop(arg, axis="columns", inplace=True)
         else:
-            print("Invalid argument!")
+            logger.error('Invalid argument')
 
     # Replace -9999 with NaN
     df.replace(-9999, np.nan, inplace=True)
@@ -370,19 +370,15 @@ def sites_barplot(numbers, sites):
     plt.savefig("../plots/bar_plot.png", transparent = True)
 
 if __name__ == "__main__":
-
-    # Uncomment for a rapid test
-
+    df = pd.read_csv('../data/abide.csv', delimiter = ';')
+    ## First step
     # check_for_spurious(df, show = True)
-    # check_site_correlation(df).to_csv("../data/site_correlation.csv")
+    ## Second step
     # df = handle_spurious(df, "FIQ",
     #                      "Left-vessel_Volume_mm3",
     #                      "Right-vessel_Volume_mm3",
     #                      "5th-Ventricle_Volume_mm3")
-    # df.to_csv('../data/abide_clean.csv')
-    # check_site_correlation(df).to_csv("site_correlation_no_spurious.csv")
-    df = pd.read_csv("../data/abide.csv", delimiter = ';')
-    # # handle_spurious(df)
-    get_correlation(df)
+    # df.to_csv('../data/abide_clean.csv', sep=';')
+    # logger.info('Done')