Merge pull request #139 from TimMonko/plate-map-leading0s

add leading zeroes to measure_props

src/napari_ndev/_tests/test_measure.py

@@ -187,7 +187,7 @@ def test_map_tx_dict_to_df_id_col():
         }
     )
     id_column = 'well'
-    result = _map_tx_dict_to_df_id_col(tx, tx_n_well, target_df, id_column)
+    result = _map_tx_dict_to_df_id_col(tx, tx_n_well, False, target_df, id_column)
     assert isinstance(result, pd.DataFrame)
     assert 'Treatment1' in result.columns
     assert 'Treatment2' in result.columns

src/napari_ndev/measure.py

@@ -22,7 +22,7 @@
 
 from napari_ndev._plate_mapper import PlateMapper
 
-__all__ = ['measure_regionprops', 'group_and_agg_measurements']
+__all__ = ['group_and_agg_measurements', 'measure_regionprops']
 
 def measure_regionprops(
     label_images: list[ArrayLike] | ArrayLike,
@@ -36,6 +36,7 @@ def measure_regionprops(
     tx_id: str | None = None,
     tx_dict: dict | None = None,
     tx_n_well: int | None = None,
+    tx_leading_zeroes: bool = False,
     save_data_path: PathLike = None,
 ) -> pd.DataFrame:
     """
@@ -88,6 +89,8 @@ def measure_regionprops(
         The treatment dictionary.
     tx_n_well : int or None, optional
         The number of wells in the plate.
+    tx_leading_zeroes : bool, optional
+        Whether to use leading zeroes in the plate map.
     save_data_path : PathLike or None, optional
         The path to save the data.
 
@@ -145,7 +148,7 @@ def measure_regionprops(
             measure_df.insert(2, key, value)
 
     if tx_id is not None and tx_dict is not None:
-        _map_tx_dict_to_df_id_col(tx_dict, tx_n_well, measure_df, tx_id)
+        _map_tx_dict_to_df_id_col(tx_dict, tx_n_well, tx_leading_zeroes, measure_df, tx_id)
 
     if save_data_path is not None:
         measure_df.to_csv(save_data_path, index=False)
@@ -354,6 +357,7 @@ def _rename_intensity_columns(df: pd.DataFrame, intensity_names: list[str]):
 def _map_tx_dict_to_df_id_col(
     tx: dict | None = None,
     tx_n_well: int | None = None,
+    tx_leading_zeroes: bool = False,
     df: pd.DataFrame = None,
     id_column: str | None = None,
 ):
@@ -368,6 +372,8 @@ def _map_tx_dict_to_df_id_col(
         The dictionary of treatments.
     tx_n_well : int or None, optional
         The number of wells in the plate.
+    tx_leading_zeroes : bool, optional
+        Whether to use leading zeroes in the plate map. Default is False.
     df : pd.DataFrame
         The DataFrame to map treatments to.
     id_column : str or None, optional
@@ -380,7 +386,7 @@ def _map_tx_dict_to_df_id_col(
 
     """
     if isinstance(tx_n_well, int):
-        plate = PlateMapper(tx_n_well)
+        plate = PlateMapper(tx_n_well, leading_zeroes=tx_leading_zeroes)
         plate.assign_treatments(tx)
         tx_map = plate.plate_map.set_index('well_id').to_dict(orient='index')
     else: