From 33a89608d452c1aa1ab130c453d57a1f07999706 Mon Sep 17 00:00:00 2001
From: cakester <hanna.ma@motioncorrect.com>
Date: Sat, 19 Nov 2022 21:33:25 -0500
Subject: [PATCH] Add TypeHint for loader/film.py (#1151)

---
 ivadomed/loader/film.py | 39 +++++++++++++++++++++++++++------------
 1 file changed, 27 insertions(+), 12 deletions(-)

diff --git a/ivadomed/loader/film.py b/ivadomed/loader/film.py
index 3d5403db5..13f04039b 100644
--- a/ivadomed/loader/film.py
+++ b/ivadomed/loader/film.py
@@ -1,6 +1,8 @@
+from __future__ import annotations
 import json
 from pathlib import Path
 from copy import deepcopy
+from typing import List, Union
 
 import numpy as np
 from loguru import logger
@@ -9,6 +11,14 @@
 from sklearn.neighbors import KernelDensity
 from sklearn.preprocessing import OneHotEncoder
 from ivadomed.keywords import MetadataKW
+import typing
+
+if typing.TYPE_CHECKING:
+    from ivadomed.loader.bids_dataset import BidsDataset
+    from ivadomed.loader.bids3d_dataset import Bids3DDataset
+    from ivadomed.loader.mri2d_segmentation_dataset import MRI2DSegmentationDataset
+
+    import torch.nn as nn
 
 from ivadomed import __path__
 
@@ -19,12 +29,16 @@
                      "acq-MToff_MTS": 3, "acq-MTon_MTS": 4, "acq-T1w_MTS": 5}
 
 
-def normalize_metadata(ds_in, clustering_models, debugging, metadata_type, train_set=False):
+def normalize_metadata(ds_in: Union[BidsDataset, Bids3DDataset, MRI2DSegmentationDataset],
+                       clustering_models: dict,
+                       debugging: bool,
+                       metadata_type: str,
+                       train_set: bool = False) -> (list, OneHotEncoder) | list:
     """Categorize each metadata value using a KDE clustering method, then apply a one-hot-encoding.
 
     Args:
-         ds_in (BidsDataset): Dataset with metadata.
-         clustering_models: Pre-trained clustering model that has been trained on metadata of the training set.
+         ds_in (BidsDataset): Dataset BidsDataset, Bids3D, MRI2D with metadata.
+         clustering_models (dict): Pre-trained clustering model that has been trained on metadata of the training set.
          debugging (bool): If True, extended verbosity and intermediate outputs.
          metadata_type (str): Choice between 'mri_params', 'constrasts' or the name of a column from the
             participants.tsv file.
@@ -105,11 +119,11 @@ class Kde_model():
         kde (sklearn.neighbors.KernelDensity):
         minima (float): Local minima.
     """
-    def __init__(self):
+    def __init__(self) -> None:
         self.kde = KernelDensity()
         self.minima = None
 
-    def train(self, data, value_range, gridsearch_bandwidth_range):
+    def train(self, data: list, value_range: np.ndarray, gridsearch_bandwidth_range: np.ndarray) -> None:
         # reshape data to fit sklearn
         data = np.array(data).reshape(-1, 1)
 
@@ -130,18 +144,18 @@ def train(self, data, value_range, gridsearch_bandwidth_range):
         # find local minima
         self.minima = s[argrelextrema(e, np.less)[0]]
 
-    def predict(self, data):
+    def predict(self, data: float) -> int:
         x = [i for i, m in enumerate(self.minima) if data < m]
         pred = min(x) if len(x) else len(self.minima)
         return pred
 
 
-def clustering_fit(dataset, key_lst):
+def clustering_fit(dataset: list, key_lst: List[str]) -> dict:
     """This function creates clustering models for each metadata type,
     using Kernel Density Estimation algorithm.
 
     Args:
-        datasets (list): data
+        dataset (list): data
         key_lst (list of str): names of metadata to cluster
 
     Returns:
@@ -192,7 +206,7 @@ def check_isMRIparam(mri_param_type: str, mri_param: dict, subject: str, metadat
         return True
 
 
-def get_film_metadata_models(ds_train, metadata_type, debugging=False):
+def get_film_metadata_models(ds_train: MRI2DSegmentationDataset, metadata_type: str, debugging: bool = False):
     """Get FiLM models.
 
     This function pulls the clustering and one-hot encoder models that are used by FiLMedUnet.
@@ -221,7 +235,8 @@ def get_film_metadata_models(ds_train, metadata_type, debugging=False):
     return ds_train, train_onehotencoder, metadata_clustering_models
 
 
-def store_film_params(gammas, betas, metadata_values, metadata, model, film_layers, depth, film_metadata):
+def store_film_params(gammas: dict, betas: dict, metadata_values: list, metadata: list, model: nn.Module,
+                      film_layers: list, depth: int, film_metadata: str) -> (dict, dict, list):
     """Store FiLM params.
 
     Args:
@@ -235,7 +250,7 @@ def store_film_params(gammas, betas, metadata_values, metadata, model, film_laye
         film_metadata (str): Metadata of interest used to modulate the network (e.g., contrast, tumor_type).
 
     Returns:
-        dict, dict: gammas, betas
+        dict, dict, list: gammas, betas, metadata_values
     """
     new_input = [metadata[k][0][film_metadata] for k in range(len(metadata))]
     metadata_values.append(new_input)
@@ -255,7 +270,7 @@ def store_film_params(gammas, betas, metadata_values, metadata, model, film_laye
     return gammas, betas, metadata_values
 
 
-def save_film_params(gammas, betas, metadata_values, depth, ofolder):
+def save_film_params(gammas: dict, betas: dict, metadata_values: list, depth: int, ofolder: str) -> None:
     """Save FiLM params as npy files.
 
     These parameters can be further used for visualisation purposes. They are saved in the `ofolder` with `.npy` format.