Add type hint bids_dataframe.py (#1154)

Co-authored-by: Yang Ding <yang.ding@motioncorrect.com>

ivadomed/loader/bids_dataframe.py

@@ -31,7 +31,7 @@ class BidsDataframe:
         df (pd.DataFrame): Dataframe containing dataset information
     """
 
-    def __init__(self, loader_params: dict, path_output: str, derivatives: bool, split_method: str = None):
+    def __init__(self, loader_params: dict, path_output: str, derivatives: bool, split_method: str = None) -> None:
 
         # paths_data from loader parameters
         self.paths_data = loader_params['path_data']
@@ -74,7 +74,7 @@ def __init__(self, loader_params: dict, path_output: str, derivatives: bool, spl
         # Save dataframe as csv file
         self.save(str(Path(path_output, "bids_dataframe.csv")))
 
-    def create_bids_dataframe(self):
+    def create_bids_dataframe(self) -> None:
         """Generate the dataframe."""
 
         for path_data in self.paths_data:
@@ -194,7 +194,7 @@ def create_bids_dataframe(self):
         # Drop columns with all null values
         self.df.dropna(axis=1, inplace=True, how='all')
 
-    def add_tsv_metadata(self, df: pd.DataFrame, path_data: str, layout: pybids.BIDSLayout):
+    def add_tsv_metadata(self, df: pd.DataFrame, path_data: str, layout: pybids.BIDSLayout) -> pd.DataFrame:
         """Add tsv files metadata to dataframe.
 
         Args:
@@ -253,7 +253,7 @@ def add_tsv_metadata(self, df: pd.DataFrame, path_data: str, layout: pybids.BIDS
 
         return df
 
-    def get_subjects_with_derivatives(self):
+    def get_subjects_with_derivatives(self) -> (list, list):
         """Get lists of subject filenames with available derivatives.
 
         Returns:
@@ -284,23 +284,23 @@ def get_subjects_with_derivatives(self):
 
         return has_deriv, deriv
 
-    def get_subject_fnames(self):
+    def get_subject_fnames(self) -> list:
         """Get the list of subject filenames in dataframe.
 
         Returns:
             list: subject filenames.
         """
         return self.df[~self.df['path'].str.contains('derivatives')]['filename'].to_list()
 
-    def get_deriv_fnames(self):
+    def get_deriv_fnames(self) -> list:
         """Get the list of derivative filenames in dataframe.
 
         Returns:
             list: derivative filenames.
         """
         return self.df[self.df['path'].str.contains('derivatives')]['filename'].tolist()
 
-    def get_derivatives(self, subject_fname: str, deriv_fnames: list):
+    def get_derivatives(self, subject_fname: str, deriv_fnames: list) -> list:
         """Return list of available derivative filenames for a subject filename.
 
         Args:
@@ -313,7 +313,7 @@ def get_derivatives(self, subject_fname: str, deriv_fnames: list):
         prefix_fname = subject_fname.split('.')[0]
         return [d for d in deriv_fnames if prefix_fname in d]
 
-    def save(self, path: str):
+    def save(self, path: str) -> None:
         """Save the dataframe into a csv file.
 
         Args:
@@ -325,7 +325,7 @@ def save(self, path: str):
         except FileNotFoundError:
             logger.error(f"Wrong path, bids_dataframe.csv could not be saved in {path}.")
 
-    def write_derivatives_dataset_description(self, path_data: str):
+    def write_derivatives_dataset_description(self, path_data: str) -> None:
         """Writes default dataset_description.json file if not found in path_data/derivatives folder
 
         Args: