refactor signs into weights

sed/calibrator/delay.py

@@ -271,7 +271,7 @@ def add_offsets(
                 df=df,
                 target_column=delay_column,
                 offset_columns=columns,
-                signs=weights,
+                weights=weights,
                 preserve_mean=preserve_mean,
                 reductions=reductions,
             )

sed/calibrator/energy.py

@@ -1474,7 +1474,7 @@ def add_offsets(
         df: Union[pd.DataFrame, dask.dataframe.DataFrame] = None,
         constant: float = None,
         columns: Union[str, Sequence[str]] = None,
-        signs: Union[int, Sequence[int]] = None,
+        weights: Union[int, Sequence[int]] = None,
         preserve_mean: Union[bool, Sequence[bool]] = False,
         reductions: Union[str, Sequence[str]] = None,
         energy_column: str = None,
@@ -1491,8 +1491,8 @@ def add_offsets(
             df (Union[pd.DataFrame, dask.dataframe.DataFrame]): Dataframe to use.
             constant (float, optional): The constant to shift the energy axis by.
             columns (Union[str, Sequence[str]]): Name of the column(s) to apply the shift from.
-            signs (Union[int, Sequence[int]]): Sign of the shift to apply. (+1 or -1) A positive
-                sign shifts the energy axis to higher kinetic energies. Defaults to +1.
+            weights (Union[int, Sequence[int]]): weight of the shift to apply. (+1 or -1) A positive
+                weight shifts the energy axis to higher kinetic energies. Defaults to +1.
             preserve_mean (bool): Whether to subtract the mean of the column before applying the
                 shift. Defaults to False.
             reductions (str): The reduction to apply to the column. Should be an available method
@@ -1512,7 +1512,7 @@ def add_offsets(
         if columns is None and constant is None:
             # load from config
             columns = []
-            signs = []
+            weights = []
             preserve_mean = []
             reductions = []
             for k, v in self.offsets.items():
@@ -1521,9 +1521,9 @@ def add_offsets(
                 else:
                     columns.append(k)
                     try:
-                        signs.append(v["sign"])
+                        weights.append(v["weight"])
                     except KeyError as exc:
-                        raise KeyError(f"Missing sign for offset column {k} in config.") from exc
+                        raise KeyError(f"Missing weight for offset column {k} in config.") from exc
                     pm = v.get("preserve_mean", False)
                     if str(pm).lower() in ["false", "0", "no"]:
                         pm = False
@@ -1549,45 +1549,45 @@ def add_offsets(
         # apply offset
         if columns is not None:
             # use passed parameters
-            if isinstance(signs, int):
-                signs = [signs]
-            elif not isinstance(signs, Sequence):
-                raise TypeError(f"Invalid type for signs: {type(signs)}")
-            if not all(isinstance(s, int) for s in signs):
-                raise TypeError(f"Invalid type for signs: {type(signs)}")
-            # flip signs if binding energy scale
-            signs = [s * scale_sign for s in signs]
+            if isinstance(weights, int):
+                weights = [weights]
+            elif not isinstance(weights, Sequence):
+                raise TypeError(f"Invalid type for weights: {type(weights)}")
+            if not all(isinstance(s, int) for s in weights):
+                raise TypeError(f"Invalid type for weights: {type(weights)}")
+            # flip weights if binding energy scale
+            weights = [s * scale_sign for s in weights]
 
             df = dfops.offset_by_other_columns(
                 df=df,
                 target_column=energy_column,
                 offset_columns=columns,
-                signs=signs,
+                weights=weights,
                 preserve_mean=preserve_mean,
                 reductions=reductions,
                 inplace=True,
             )
             metadata["energy_column"] = energy_column
             metadata["columns"] = columns
-            metadata["signs"] = signs
+            metadata["weights"] = weights
             metadata["preserve_mean"] = preserve_mean
             metadata["reductions"] = reductions
 
             # overwrite the current offset dictionary with the parameters used
             if not isinstance(columns, Sequence):
                 columns = [columns]
-            if not isinstance(signs, Sequence):
-                signs = [signs]
+            if not isinstance(weights, Sequence):
+                weights = [weights]
             if isinstance(preserve_mean, bool):
                 preserve_mean = [preserve_mean] * len(columns)
             if not isinstance(reductions, Sequence):
                 reductions = [reductions]
             if len(reductions) == 1:
                 reductions = [reductions[0]] * len(columns)
 
-            for col, sign, pmean, red in zip(columns, signs, preserve_mean, reductions):
+            for col, weight, pmean, red in zip(columns, weights, preserve_mean, reductions):
                 self.offsets[col] = {
-                    "sign": sign,
+                    "weight": weight,
                     "preserve_mean": pmean,
                     "reduction": red,
                 }

sed/core/dfops.py

@@ -269,7 +269,7 @@ def offset_by_other_columns(
     df: dask.dataframe.DataFrame,
     target_column: str,
     offset_columns: Union[str, Sequence[str]],
-    signs: Union[int, Sequence[int]],
+    weights: Union[float, Sequence[float]],
     reductions: Union[str, Sequence[str]] = None,
     preserve_mean: Union[bool, Sequence[bool]] = False,
     inplace: bool = True,
@@ -281,7 +281,7 @@ def offset_by_other_columns(
         df (dask.dataframe.DataFrame): Dataframe to use. Currently supports only dask dataframes.
         target_column (str): Name of the column to apply the offset to.
         offset_columns (str): Name of the column(s) to use for the offset.
-        signs (int): Sign of the offset.
+        weights (int): weights to apply on each column before adding. Used also for changing sign.
         reductions (str, optional): Reduction function to use for the offset. Defaults to "mean".
             Currently, only mean is supported.
         preserve_mean (bool, optional): Whether to subtract the mean of the offset column.
@@ -304,13 +304,13 @@ def offset_by_other_columns(
     if any(c not in df.columns for c in offset_columns):
         raise KeyError(f"{offset_columns} not in dataframe!")
 
-    if isinstance(signs, int):
-        signs = [signs]
-    elif not isinstance(signs, Sequence):
-        raise TypeError(f"Invalid type for signs: {type(signs)}")
-    if len(signs) != len(offset_columns):
+    if isinstance(weights, int):
+        weights = [weights]
+    elif not isinstance(weights, Sequence):
+        raise TypeError(f"Invalid type for signs: {type(weights)}")
+    if len(weights) != len(offset_columns):
         raise ValueError("signs and offset_columns must have the same length!")
-    signs_dict = dict(zip(offset_columns, signs))
+    signs_dict = dict(zip(offset_columns, weights))
 
     if isinstance(reductions, str) or reductions is None:
         reductions = [reductions] * len(offset_columns)

sed/core/processor.py

@@ -1270,7 +1270,7 @@ def add_energy_offset(
         self,
         constant: float = None,
         columns: Union[str, Sequence[str]] = None,
-        signs: Union[int, Sequence[int]] = None,
+        weights: Union[float, Sequence[float]] = None,
         reductions: Union[str, Sequence[str]] = None,
         preserve_mean: Union[bool, Sequence[bool]] = None,
     ) -> None:
@@ -1279,7 +1279,7 @@ def add_energy_offset(
         Args:
             constant (float, optional): The constant to shift the energy axis by.
             columns (Union[str, Sequence[str]]): Name of the column(s) to apply the shift from.
-            signs (Union[int, Sequence[int]]): Sign of the shift to apply. (+1 or -1) A positive
+            weights (Union[int, Sequence[int]]): Sign of the shift to apply. (+1 or -1) A positive
                 sign shifts the energy axis to higher kinetic energies. Defaults to +1.
             preserve_mean (bool): Whether to subtract the mean of the column before applying the
                 shift. Defaults to False.
@@ -1304,7 +1304,7 @@ def add_energy_offset(
                 constant=constant,
                 columns=columns,
                 energy_column=energy_column,
-                signs=signs,
+                weights=weights,
                 reductions=reductions,
                 preserve_mean=preserve_mean,
             )
@@ -1315,7 +1315,7 @@ def add_energy_offset(
                         constant=constant,
                         columns=columns,
                         energy_column=energy_column,
-                        signs=signs,
+                        weights=weights,
                         reductions=reductions,
                         preserve_mean=preserve_mean,
                     )
@@ -1517,7 +1517,7 @@ def add_delay_offset(
         constant: float = None,
         flip_delay_axis: bool = None,
         columns: Union[str, Sequence[str]] = None,
-        signs: Union[int, Sequence[int]] = None,
+        weights: Union[float, Sequence[float]] = None,
         reductions: Union[str, Sequence[str]] = None,
         preserve_mean: Union[bool, Sequence[bool]] = None,
         inplace: bool = False,
@@ -1528,7 +1528,7 @@ def add_delay_offset(
         Args:
             constant (float, optional): The constant to shift the delay axis by.
             columns (Union[str, Sequence[str]]): Name of the column(s) to apply the shift from.
-            signs (Union[int, Sequence[int]]): Sign of the shift to apply. (+1 or -1) A positive
+            weights (Union[float, Sequence[float]]): Weight of the shift to apply. A positive
                 sign shifts the delay axis to higher values. Defaults to +1.
             preserve_mean (bool): Whether to subtract the mean of the column before applying the
                 shift. Defaults to False.
@@ -1557,7 +1557,7 @@ def add_delay_offset(
                 flip_delay_axis=flip_delay_axis,
                 columns=columns,
                 delay_column=delay_column,
-                weights=signs,
+                weights=weights,
                 reductions=reductions,
                 preserve_mean=preserve_mean,
                 inplace=inplace,
@@ -1571,7 +1571,7 @@ def add_delay_offset(
                     flip_delay_axis=flip_delay_axis,
                     columns=columns,
                     delay_column=delay_column,
-                    weights=signs,
+                    weights=weights,
                     reductions=reductions,
                     preserve_mean=preserve_mean,
                     inplace=inplace,

tests/calibrator/test_energy.py

@@ -583,11 +583,11 @@ def test_add_offsets_functionality():
                 "offset": {
                     "constant": 1,
                     "off1": {
-                        "sign": 1,
+                        "weight": 1,
                         "preserve_mean": True,
                     },
-                    "off2": {"sign": -1, "preserve_mean": False},
-                    "off3": {"sign": 1, "preserve_mean": False, "reduction": "mean"},
+                    "off2": {"weight": -1, "preserve_mean": False},
+                    "off3": {"weight": 1, "preserve_mean": False, "reduction": "mean"},
                 },
             },
         },
@@ -599,7 +599,7 @@ def test_add_offsets_functionality():
         "constant": 1,
         "energy_column": "energy",
         "columns": ["off1", "off2", "off3"],
-        "signs": [1, -1, 1],
+        "weights": [1, -1, 1],
         "preserve_mean": [True, False, False],
         "reductions": [None, None, "mean"],
     }
@@ -648,9 +648,9 @@ def test_add_offset_raises():
             },
             "offset": {
                 "constant": 1,
-                "off1": {"sign": -1, "preserve_mean": True},
-                "off2": {"sign": -1, "preserve_mean": False},
-                "off3": {"sign": 1, "preserve_mean": False, "reduction": "mean"},
+                "off1": {"weight": -1, "preserve_mean": True},
+                "off2": {"weight": -1, "preserve_mean": False},
+                "off3": {"weight": 1, "preserve_mean": False, "reduction": "mean"},
             },
         },
     }
@@ -667,7 +667,7 @@ def test_add_offset_raises():
     # no sign in config
     with pytest.raises(KeyError):
         cfg = deepcopy(cfg_dict)
-        cfg["energy"]["offset"]["off1"].pop("sign")
+        cfg["energy"]["offset"]["off1"].pop("weight")
         config = parse_config(config=cfg, folder_config={}, user_config={}, system_config={})
         ec = EnergyCalibrator(config=cfg, loader=get_loader("flash", config=config))
         _ = ec.add_offsets(t_df)
@@ -691,7 +691,7 @@ def test_add_offset_raises():
     # invalid sign
     with pytest.raises(TypeError):
         cfg = deepcopy(cfg_dict)
-        cfg["energy"]["offset"]["off1"]["sign"] = "wrong_type"
+        cfg["energy"]["offset"]["off1"]["weight"] = "wrong_type"
         config = parse_config(config=cfg, folder_config={}, user_config={}, system_config={})
         ec = EnergyCalibrator(config=cfg, loader=get_loader("flash", config=config))
         _ = ec.add_offsets(t_df)

tests/test_dfops.py

@@ -263,7 +263,7 @@ def test_offset_by_other_columns_functionality():
         df=t_df.copy(),
         target_column="target",
         offset_columns=["off1"],
-        signs=[1],
+        weights=[1],
     )
     expected = [11, 22, 33, 44, 55, 66]
     np.testing.assert_allclose(res["target"].values, expected)
@@ -272,7 +272,7 @@ def test_offset_by_other_columns_functionality():
         df=t_df.copy(),
         target_column="target",
         offset_columns=["off1", "off2"],
-        signs=[1, -1],
+        weights=[1, -1],
     )
     expected = [10.9, 21.8, 32.7, 43.6, 54.5, 65.4]
     np.testing.assert_allclose(res["target"].values, expected)
@@ -281,7 +281,7 @@ def test_offset_by_other_columns_functionality():
         df=t_df.copy(),
         target_column="target",
         offset_columns=["off3"],
-        signs=[1],
+        weights=[1],
         preserve_mean=True,
     )
     expected = [9.75, 19.85, 29.95, 40.05, 50.15, 60.25]
@@ -291,7 +291,7 @@ def test_offset_by_other_columns_functionality():
         df=t_df.copy(),
         target_column="target",
         offset_columns=["off3"],  # off3 has mean of 10
-        signs=[1],
+        weights=[1],
         reductions="mean",
     )
     expected = [20, 30, 40, 50, 60, 70]
@@ -315,7 +315,7 @@ def test_offset_by_other_columns_pandas_not_working():
             df=pd_df,
             target_column="target",
             offset_columns=["off1"],
-            signs=[1],
+            weights=[1],
         )