Merge pull request #47 from CBICA/spiros-dev

Fixing issues with parallelization

NiChart_DLMUSE/__main__.py

@@ -133,12 +133,16 @@ def main() -> None:
     print(args)
     print()
 
+    if len(os.listdir(out_dir)) != 0:
+        print(f"Emptying output folder: {out_dir}...")
+        os.system(f"rm -r {out_dir}/*")
+
     if args.clear_cache:
         os.system("DLICV -i ./dummy -o ./dummy --clear_cache")
         os.system("DLMUSE -i ./dummy -o ./dummy --clear_cache")
 
     # Run pipeline
-    no_threads = args.cores  # for now
+    no_threads = int(args.cores)  # for now
     subfolders = split_data(in_data, no_threads)
 
     threads = []
@@ -163,6 +167,7 @@ def main() -> None:
 
     merge_output_data(out_dir)
     remove_subfolders(in_data)
+    remove_subfolders(out_dir)
 
 
 if __name__ == "__main__":

NiChart_DLMUSE/utils.py

@@ -150,11 +150,14 @@ def dir_size(in_dir: str) -> int:
 
 def split_data(in_dir: str, N: int) -> list:
     """
-    Splits the input data directory into subfolders of size N
+    Splits the input data directory into subfolders of size.
+    N should be > 0 and the number of files in each subfolder should be > 0 as well.
     """
     assert N > 0
     data_size = dir_size(in_dir)
-    no_files_in_folders = data_size / N if (data_size % N == 0) else (data_size / N) + 1
+    no_files_in_folders = (
+        data_size // N if (data_size % N == 0) else (data_size // N) + 1
+    )
     assert no_files_in_folders > 0
     subfolders = []
 
@@ -177,10 +180,18 @@ def split_data(in_dir: str, N: int) -> list:
 
 
 def remove_subfolders(in_dir: str) -> None:
+    """
+    Removes all the split_* subolders from the input folder
+    """
     os.system(f"rm -r {in_dir}/split_*")
 
 
 def merge_output_data(in_dir: str) -> None:
+    """
+    Takes all the results from the temp_working_fir and moves them into
+    the results/ subfolder in the output folder
+    """
+
     os.system(f"mkdir {in_dir}/results")
     os.system(f"mkdir {in_dir}/results/s1_reorient_lps")
     os.system(f"mkdir {in_dir}/results/s2_dlicv")
@@ -212,5 +223,3 @@ def merge_output_data(in_dir: str) -> None:
             f"mv {in_dir}/{dir}/temp_working_dir/s6_combined/* {in_dir}/results/s6_combined/"
         )
         os.system(f"mv {in_dir}/{dir}/*.nii.gz {in_dir}/results/")
-
-    os.system(f"rm -r {in_dir}/split_*")

requirements.txt

@@ -1,8 +1,8 @@
 torch>=2.2.1
-DLICV>=1.0.1
-DLMUSE>=1.0.1
+DLICV
+DLMUSE
 nibabel>=5.2
 huggingface_hub
 argparse
 scipy
-pathlib
+pathlib

setup.py

@@ -1,12 +1,11 @@
 from pathlib import Path
 
-import setuptools
 from setuptools import find_packages, setup
 
 this_directory = Path(__file__).parent
 long_description = (this_directory / "README.md").read_text()
 
-with open('requirements.txt') as f:
+with open("requirements.txt") as f:
     required = f.read().splitlines()
 
 
@@ -42,6 +41,6 @@
         "nnunet",
     ],
     package_data={
-        'NiChart_DLMUSE': ['**/*.csv', '**/*.json'],
+        "NiChart_DLMUSE": ["**/*.csv", "**/*.json"],
     },
 )