Merge pull request #88 from daisybio/feature_loading

Feature loading from_csv to_csv for FeatureDataset

Author: JudithBernett

drevalpy/datasets/dataset.py

@@ -15,7 +15,6 @@
 
 import copy
 import os
-from abc import ABC, abstractmethod
 from pathlib import Path
 from typing import Any, Callable
 
@@ -31,30 +30,7 @@
 np.set_printoptions(threshold=6)
 
 
-class Dataset(ABC):
-    """Abstract wrapper class for datasets."""
-
-    @classmethod
-    @abstractmethod
-    def from_csv(cls: type["Dataset"], input_file: str | Path, dataset_name: str = "unknown") -> "Dataset":
-        """
-        Loads the dataset from data.
-
-        :param input_file: Path to the csv file containing the data to be loaded
-        :param dataset_name: Optional name to associate the dataset with, default = "unknown"
-        :returns: Dataset object containing data from provided csv file.
-        """
-
-    @abstractmethod
-    def save(self, path: str):
-        """
-        Saves the dataset to data.
-
-        :param path: path to the dataset
-        """
-
-
-class DrugResponseDataset(Dataset):
+class DrugResponseDataset:
     """Drug response dataset."""
 
     _response: np.ndarray
@@ -226,7 +202,7 @@ def to_dataframe(self) -> pd.DataFrame:
             data["predictions"] = self.predictions
         return pd.DataFrame(data)
 
-    def save(self, path: str | Path):
+    def to_csv(self, path: str | Path):
         """
         Stores the drug response dataset on disk.
 
@@ -412,7 +388,7 @@ def save_splits(self, path: str):
             ]:
                 if mode in split:
                     split_path = os.path.join(path, f"cv_split_{i}_{mode}.csv")
-                    split[mode].save(path=split_path)
+                    split[mode].to_csv(path=split_path)
 
     def load_splits(self, path: str) -> None:
         """
@@ -720,25 +696,70 @@ def _leave_group_out_cv(
     return cv_sets
 
 
-class FeatureDataset(Dataset):
+class FeatureDataset:
     """Class for feature datasets."""
 
     _meta_info: dict[str, Any] = {}
     _features: dict[str, dict[str, Any]] = {}
 
     @classmethod
     def from_csv(
-        cls: type["FeatureDataset"], input_file: str | Path, dataset_name: str = "unknown"
-    ) -> "FeatureDataset":
+        cls: type["FeatureDataset"],
+        path_to_csv: str | Path,
+        id_column: str,
+        view_name: str,
+        drop_columns: list[str] | None = None,
+    ):
+        """Load a one-view feature dataset from a csv file.
+
+        Load a feature dataset from a csv file. The rows of the csv file represent the instances (cell lines or drugs),
+        the columns represent the features. A column named id_column contains the identifiers of the instances.
+        All unrelated columns (e.g. other id columns) should be provided as drop_columns,
+        that will be removed from the dataset.
+
+        :param path_to_csv: path to the csv file containing the data to be loaded
+        :param view_name: name of the view (e.g. gene_expression)
+        :param id_column: name of the column containing the identifiers
+        :param drop_columns: list of columns to drop (e.g. other identifier columns)
+        :returns: FeatureDataset object containing data from provided csv file.
+        """
+        data = pd.read_csv(path_to_csv)
+        ids = data[id_column].values
+        data_features = data.drop(columns=(drop_columns or []))
+        data_features = data_features.set_index(id_column)
+        # remove duplicate feature rows (rows with the same index)
+        data_features = data_features[~data_features.index.duplicated(keep="first")]
+        features = {}
+
+        for identifier in ids:
+            features_for_instance = data_features.loc[identifier].values
+            features[identifier] = {view_name: features_for_instance}
+
+        return cls(features=features)
+
+    def to_csv(self, path: str | Path, id_column: str, view_name: str):
         """
-        Load a feature dataset from a csv file.
+        Save the feature dataset to a CSV file.
 
-        This function creates a FeatureDataset from a provided input file in csv format.
-        :param input_file: Path to the csv file containing the data to be loaded
-        :param dataset_name: Optional name to associate the dataset with, default = "unknown"
-        :raises NotImplementedError: This method is currently not implemented.
+        :param path: Path to the CSV file.
+        :param id_column: Name of the column containing the identifiers.
+        :param view_name: Name of the view (e.g., gene_expression).
+
+        :raises ValueError: If the view is not found for an identifier.
         """
-        raise NotImplementedError
+        data = []
+        for identifier, feature_dict in self.features.items():
+            # Get the feature vector for the specified view
+            if view_name in feature_dict:
+                row = {id_column: identifier}
+                row.update({f"feature_{i}": value for i, value in enumerate(feature_dict[view_name])})
+                data.append(row)
+            else:
+                raise ValueError(f"View {view_name!r} not found for identifier {identifier!r}.")
+
+        # Convert to DataFrame and save to CSV
+        df = pd.DataFrame(data)
+        df.to_csv(path, index=False)
 
     @property
     def meta_info(self) -> dict[str, Any]:
@@ -798,15 +819,6 @@ def __init__(
                 raise AssertionError(f"Meta keys {meta_info.keys()} not in view names {self.view_names}")
             self._meta_info = meta_info
 
-    def save(self, path: str):
-        """
-        Saves the feature dataset to data.
-
-        :param path: path to the dataset
-        :raises NotImplementedError: if method is not implemented
-        """
-        raise NotImplementedError("save method not implemented")
-
     def randomize_features(self, views_to_randomize: str | list[str], randomization_type: str) -> None:
         """
         Randomizes the feature vectors.