[Update] Updated docstrings for DLMUSE and DLICV

NiChart_DLMUSE/CalcROIVol.py

@@ -109,6 +109,17 @@ def create_roi_csv(
 ) -> None:
     """
     Creates a csv file with the results of the roi calculations
+
+    :param mrid: the input mrid
+    :type mrid: Any
+    :param in_roi: the input ROI
+    :type in_roi: Any
+    :param map_derived_roi: derived roi map file
+    :type map_derived_roi: Any
+    :param out_csv: output csv filename
+    :type out_csv: str
+
+    :rtype: None
     """
 
     # Calculate MUSE ROIs
@@ -140,6 +151,19 @@ def apply_create_roi_csv(
 ) -> None:
     """
     Apply roi volume calc to all images
+
+    :param df_img: the passed dataframe
+    :type df_img: pd.DataFrame
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :type in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suff: the output suffix
+    :type out_suff: str
+
+    :rtype: None
     """
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
@@ -158,6 +182,19 @@ def combine_roi_csv(
 ) -> None:
     """
     Combine csv files
+
+    :param df_img: passed dataframe
+    :type df_img: pd.DataFrame
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :type in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_name: the desired output filename
+    :type out_name: str
+
+    :rtype: None
     """
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)

NiChart_DLMUSE/SegmentImage.py

@@ -6,12 +6,30 @@
 
 def run_dlicv(
     in_dir: str,
-    in_suff: Any,
+    in_suff: str,
     out_dir: str,
-    out_suff: Any,
+    out_suff: str,
     device: str,
     extra_args: str = "",
 ) -> None:
+    """
+    Run dlicv with the passed images
+
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :type in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suff: the output suffix
+    :type out_suff: str
+    :param device: cuda/mps for GPU acceleration otherwise cpu
+    :type device: str
+    :param extra_args: extra arguments for DLICV package
+    :type extra_args: str
+
+    :rtype: None
+    """
     # Call DLICV
     os.system(f"DLICV -i {in_dir} -o {out_dir} -device {device} " + extra_args)
 
@@ -28,6 +46,24 @@ def run_dlmuse(
     device: str,
     extra_args: str = "",
 ) -> None:
+    """
+    Run dlmuse with the passed images
+
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :type in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suff: the output suffix
+    :type out_suff: str
+    :param device: cuda/mps for GPU acceleration otherwise cpu
+    :type device: str
+    :param extra_args: extra arguments for DLMUSE package
+    :type extra_args: str
+
+    :rtype: None
+    """
     # Call DLMUSE
     os.system(f"DLMUSE -i {in_dir} -o {out_dir} -device {device} " + extra_args)
 

NiChart_DLMUSE/dlmuse_pipeline.py

@@ -45,6 +45,21 @@ def run_pipeline(
 ) -> None:
     """
     NiChart pipeline
+
+    :param in_data: the input directory
+    :type in_data: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param device: conda/mps for GPU acceleration otherwise cpu
+    :type device: str
+    :param dlmuse_extra_args: extra arguments for DLMUSE package
+    :type dlmuse_extra_args: str
+    :param dlicv_extra_args: extra arguments for DLICV package
+    :type dlicv_extra_args: str
+    :param sub_fldr: the number of subfolders(default = 1)
+    :type sub_fldr: int
+
+    :rtype: None
     """
     logging.info(f"Starting the pipeline on folder {sub_fldr}")
     logging.info(f"Detecting input images for batch [{sub_fldr}]...")