Trying to fix dir problems again

NiChart_DLMUSE/__main__.py

@@ -124,26 +124,20 @@ def main() -> None:
     no_threads = args.cores  # for now
     subfolders = split_data(in_data, no_threads)
 
-    threads = []
-    for i in range(len(subfolders)):
+    ##threads = []
+    ##for i in range(len(subfolders)):
+    ##    curr_out_dir = out_dir + f"split_{i}"
+    ##    curr_thread = threading.Thread(
+    ##        target=run_pipeline, args=(subfolders[i], curr_out_dir, device)
+    ##    )
+    ##    curr_thread.start()
+    ##    threads.append(curr_thread)
+
+    ##for t in threads:
+    ##    t.join()
 
-        if out_dir[len(out_dir) - 1] != '/':
-            # This is because sometimes users don't enter the dir
-            # like this: "output/" but like this "output"
-            out_dir += '/'
-
-        curr_out_dir = out_dir + f"split_{i}"
-        curr_thread = threading.Thread(
-            target=run_pipeline, args=(subfolders[i], curr_out_dir, device)
-        )
-        curr_thread.start()
-        threads.append(curr_thread)
-
-    for t in threads:
-        t.join()
-
-    remove_subfolders(in_data)
     merge_output_data(out_dir)
+    remove_subfolders(in_data)
 
 if __name__ == "__main__":
     main()

NiChart_DLMUSE/utils.py

@@ -169,7 +169,7 @@ def split_data(in_dir: str, N: int) -> list:
 
 
 def remove_subfolders(in_dir: str) -> None:
-    os.system(f"rm -r {in_dir}/split_*")
+    os.system(f"rm -r {in_dir}split_*")
 
 def merge_output_data(in_dir: str) -> None:
     os.system(f"mkdir {in_dir}results")
@@ -181,14 +181,13 @@ def merge_output_data(in_dir: str) -> None:
     os.system(f"mkdir {in_dir}results/s6_combined")
 
     for dir in os.listdir(in_dir):
-        os.system(f"mv {in_dir}{dir}/s1_reorient_lps/* {in_dir}results/s1_reorient_lps/")
-        os.system(f"mv {in_dir}{dir}/s2_dlicv/* {in_dir}results/s2_dlicv/")
-        os.system(f"mv {in_dir}{dir}/s3_masked/* {in_dir}results/s3_masked/")
-        os.system(f"mv {in_dir}{dir}/s4_dlmuse/* {in_dir}results/s4_dlmuse/")
-        os.system(f"mv {in_dir}{dir}/s5_relabeled/* {in_dir}results/s5_relabeled/")
-        os.system(f"mv {in_dir}{dir}/s6_combined/* {in_dir}results/s6_combined/")
-
-    os.system(f"mv {in_dir}*.nii.gz {in_dir}results/")
+        os.system(f"mv {in_dir}{dir}/temp_working_dir/s1_reorient_lps/* {in_dir}results/s1_reorient_lps/")
+        os.system(f"mv {in_dir}{dir}/temp_working_dir/s2_dlicv/* {in_dir}results/s2_dlicv/")
+        os.system(f"mv {in_dir}{dir}/temp_working_dir/s3_masked/* {in_dir}results/s3_masked/")
+        os.system(f"mv {in_dir}{dir}/temp_working_dir/s4_dlmuse/* {in_dir}results/s4_dlmuse/")
+        os.system(f"mv {in_dir}{dir}/temp_working_dir/s5_relabeled/* {in_dir}results/s5_relabeled/")
+        os.system(f"mv {in_dir}{dir}/temp_working_dir/s6_combined/* {in_dir}results/s6_combined/")
+        os.system(f"mv {in_dir}*.nii.gz {in_dir}results/")
 
     for dir in os.listdir(in_dir):
         os.system(f"rm -r {dir}")