Merge pull request #8 from adriensizaret/main-new-metrics-dev

MoS Adjustements

gaitalytics/features.py

@@ -256,7 +256,7 @@ def _get_progression_vector(self, trial: model.Trial) -> xr.DataArray:
     def _get_sagittal_vector(self, trial: model.Trial) -> xr.DataArray:
         """Calculate the sagittal vector for a trial.
 
-        The sagittal vector is the vector normal to the sagittal plane.
+        The sagittal vector is the vector normal to the sagittal plane. Note that this vector will always be pointing towards the right side of the body.
 
         Args:
             trial: The trial for which to calculate the sagittal vector.
@@ -507,19 +507,23 @@ class SpatialFeatures(_PointDependentFeature):
     - step_width
     - minimal_toe_clearance
     - AP_margin_of_stability
+    - AP_base_of_support
+    - AP_xcom
     - ML_margin_of_stability
+    - ML_base_of_support
+    - ML_xcom
     """
 
     def _calculate(self, trial: model.Trial) -> xr.DataArray:
         """Calculate the spatial features for a trial.
 
         Definitions of the spatial features:
         Step length & Step width: Hollmann et al. 2011 (doi: 10.1016/j.gaitpost.2011.03.024)
-        Margin of stability: Jinfeng et al. 2021 (doi: 10.1152/jn.00091.2021)
+        Margin of stability: Jinfeng et al. 2021 (doi: 10.1152/jn.00091.2021), Curtze et al. 2024 (doi: 10.1016/j.jbiomech.2024.112045)
         Minimal toe clearance: Schulz 2017 (doi: 10.1016/j.jbiomech.2017.02.024)
 
         Args:
-            trial: The trial for which to calculate the features.
+            trial: The trial for which to calculate the features. 
 
         Returns:
             An xarray DataArray containing the calculated features.
@@ -567,9 +571,9 @@ def _calculate(self, trial: model.Trial) -> xr.DataArray:
             results_dict.update(
                 self._calculate_ap_margin_of_stability(
                     trial,
-                    marker_dict["ipsi_toe_2"],  # type: ignore
+                    marker_dict["ipsi_heel"],  # type: ignore
                     marker_dict["contra_toe_2"],  # type: ignore
-                    marker_dict["xcom"],
+                    marker_dict["xcom"]
                 )
             )
 
@@ -578,7 +582,7 @@ def _calculate(self, trial: model.Trial) -> xr.DataArray:
                     trial,
                     marker_dict["ipsi_ankle"],
                     marker_dict["contra_ankle"],
-                    marker_dict["xcom"],
+                    marker_dict["xcom"]
                 )
             )
         except KeyError:
@@ -704,7 +708,7 @@ def _calculate_stride_length(
         ipsi_marker: mapping.MappedMarkers,
         contra_marker: mapping.MappedMarkers,
     ) -> dict[str, np.ndarray]:
-        """Calculate the stride length for a trial.
+        """Calculate the stride length for a trial. It is computed as the two consecutive step lengths constituting the gait cycle.
 
         Args:
             trial: The trial for which to calculate the stride length.
@@ -838,26 +842,28 @@ def _find_mtc_index(
 
         return None if not mtc_i else min(mtc_i, key=lambda i: toe_z[i])  # type: ignore
 
-    def _calculate_ap_margin_of_stability(
-        self,
-        trial: model.Trial,
-        ipsi_toe_marker: mapping.MappedMarkers,
-        contra_toe_marker: mapping.MappedMarkers,
-        xcom_marker: mapping.MappedMarkers,
-    ) -> dict[str, np.ndarray]:
-        """Calculate the anterior-posterior margin of stability at heel strike
+    def _calculate_ap_margin_of_stability(self,
+                            trial: model.Trial,
+                            ipsi_heel_marker: mapping.MappedMarkers,
+                            contra_toe_marker: mapping.MappedMarkers,
+                            xcom_marker: mapping.MappedMarkers,
+                        ) -> dict[str, np.ndarray]:
+        """Calculate the anterio-posterior margin of stability at heel strike. Result should be interpreted according to Curtze et al. (2024)
         Args:
             trial: The trial for which to calculate the AP margin of stability
-            ipsi_toe_marker: The ipsi-lateral toe marker
-            contra_toe_marker: The contra-lateral toe marker
+            ipsi_heel_marker: The ipsi-lateral heel marker
+            contra_marker: The contra-lateral toe marker
             xcom_marker: The extrapolated center of mass marker
 
         Returns:
-            The calculated anterior-posterior margin of stability in a dict
+            dict: A dictionary containing:
+                - "AP_margin_of_stability": The calculated anterio-posterior margin of stability.
+                - "AP_base_of_support": The calculated anterio-posterior base of support.
+                - "AP_XCOM": The calculated anterio-posterior position of the extrapolated center of mass relative to the back foot.
         """
         event_times = self.get_event_times(trial.events)
 
-        ipsi_toe = self._get_marker_data(trial, ipsi_toe_marker).sel(
+        ipsi_heel = self._get_marker_data(trial, ipsi_heel_marker).sel(
             time=event_times[0], method="nearest"
         )
         contra_toe = self._get_marker_data(trial, contra_toe_marker).sel(
@@ -866,37 +872,42 @@ def _calculate_ap_margin_of_stability(
         xcom = self._get_marker_data(trial, xcom_marker).sel(
             time=event_times[0], method="nearest"
         )
-
+        
         progress_axis = self._get_progression_vector(trial)
         progress_axis = linalg.normalize_vector(progress_axis)
-
-        projected_ipsi = linalg.project_point_on_vector(ipsi_toe, progress_axis)
-        projected_contra = linalg.project_point_on_vector(contra_toe, progress_axis)
-        projected_xcom = linalg.project_point_on_vector(xcom, progress_axis)
-
-        bos_len = linalg.calculate_distance(projected_ipsi, projected_contra).values
-        xcom_len = linalg.calculate_distance(projected_contra, projected_xcom).values
-
-        mos = bos_len - xcom_len
-
-        return {"AP_margin_of_stability": mos}
-
-    def _calculate_ml_margin_of_stability(
-        self,
-        trial: model.Trial,
-        ipsi_ankle_marker: mapping.MappedMarkers,
-        contra_ankle_marker: mapping.MappedMarkers,
-        xcom_marker: mapping.MappedMarkers,
-    ) -> dict[str, np.ndarray]:
-        """Calculate the medio-lateral margin of stability at heel strike
+
+        front_marker = linalg.get_point_in_front(ipsi_heel, contra_toe, progress_axis)
+        back_marker = linalg.get_point_behind(ipsi_heel, contra_toe, progress_axis)
+
+        bos_vect = front_marker - back_marker
+        xcom_vect = xcom - back_marker
+
+        bos_proj = abs(linalg.signed_projection_norm(bos_vect, progress_axis))
+        xcom_proj = linalg.signed_projection_norm(xcom_vect, progress_axis)
+        mos = bos_proj - xcom_proj
+
+        return {"AP_margin_of_stability": mos, 
+                "AP_base_of_support": bos_proj,
+                "AP_xcom": xcom_proj}
+
+    def _calculate_ml_margin_of_stability(self,
+                            trial: model.Trial,
+                            ipsi_ankle_marker: mapping.MappedMarkers,
+                            contra_ankle_marker: mapping.MappedMarkers,
+                            xcom_marker: mapping.MappedMarkers
+                            ) -> dict[str, np.ndarray]:
+        """Calculate the medio-lateral margin of stability at heel strike. Result should be interpreted according to Curtze et al. (2024)
         Args:
-            trial: The trial for which to calculate the AP margin of stability
-            ipsi_ankle_marker: The ipsi-lateral lateral ankle marker
-            contra_ankle_marker: The contra-lateral lateral ankle marker
+            trial: The trial for which to calculate the ml margin of stability
+            ipsi_toe_marker: The ipsi-lateral lateral ankle marker
+            contra_marker: The contra-lateral lateral ankle marker
             xcom_marker: The extrapolated center of mass marker
 
         Returns:
-            The calculated anterio-posterior margin of stability in a dict
+            dict: A dictionary containing:
+                - "ML_margin_of_stability": The calculated medio-lateral margin of stability.
+                - "ML_base_of_support": The calculated medio-lateral base of support.
+                - "ML_xcom": The calculated medio-lateral position of the extrapolated center of mass relative to the back foot.
         """
         event_times = self.get_event_times(trial.events)
 
@@ -908,18 +919,27 @@ def _calculate_ml_margin_of_stability(
         )
         xcom = self._get_marker_data(trial, xcom_marker).sel(
             time=event_times[0], method="nearest"
-        )
+        )            
 
         sagittal_axis = self._get_sagittal_vector(trial)
         sagittal_axis = linalg.normalize_vector(sagittal_axis)
-
-        projected_ipsi = linalg.project_point_on_vector(ipsi_ankle, sagittal_axis)
-        projected_contra = linalg.project_point_on_vector(contra_ankle, sagittal_axis)
-        projected_xcom = linalg.project_point_on_vector(xcom, sagittal_axis)
-
-        bos_len = linalg.calculate_distance(projected_contra, projected_ipsi).values
-        xcom_len = linalg.calculate_distance(projected_contra, projected_xcom).values
-
-        mos = bos_len - xcom_len
-
-        return {"ML_margin_of_stability": mos}
+
+        if trial.events.attrs["context"] == "Left":
+            #Rotate sagittal axis so it points towards the left side of the body
+            sagittal_axis = -sagittal_axis
+
+        # Lateral is the furthest point in the direction of the sagittal axis
+        lateral_point = linalg.get_point_in_front(ipsi_ankle, contra_ankle, sagittal_axis)
+        # Medial is the closest point in the direction of the sagittal axis
+        medial_point = linalg.get_point_behind(ipsi_ankle, contra_ankle, sagittal_axis)
+
+        bos_vect = lateral_point - medial_point
+        xcom_vect = xcom - medial_point
+
+        bos_proj = abs(linalg.signed_projection_norm(bos_vect, sagittal_axis))
+        xcom_proj = linalg.signed_projection_norm(xcom_vect, sagittal_axis)
+        mos = bos_proj - xcom_proj
+
+        return {"ML_margin_of_stability": mos,
+                "ML_base_of_support": bos_proj,
+                "ML_xcom": xcom_proj}

gaitalytics/io.py

@@ -1,5 +1,4 @@
 """This module provides classes for reading biomechanical file-types."""
-
 import math
 from abc import abstractmethod, ABC
 from pathlib import Path

gaitalytics/utils/linalg.py

@@ -30,8 +30,26 @@ def project_point_on_vector(point: xr.DataArray, vector: xr.DataArray) -> xr.Dat
     """
     return vector * point.dot(vector, dim="axis")
 
+def signed_projection_norm(vector: xr.DataArray, onto: xr.DataArray) -> xr.DataArray:
+    """Compute the signed norm of the projection of a vector onto another vector. <br>
+    If the projection is in the same direction as the onto vector, the norm is positive. <br>
+    If the projection is in the opposite direction, the norm is negative. <br>
 
-def get_normal_vector(vector1: xr.DataArray, vector2: xr.DataArray):
+    Args:
+        vector: The vector to be projected.
+        onto: The vector to project onto.
+
+    Returns:
+        An xarray DataArray containing the signed norm of the projected vector.
+    """
+    projection = onto * vector.dot(onto, dim="axis") / onto.dot(onto, dim="axis")
+    projection_norm = projection.meca.norm(dim="axis")
+    sign = xr.where(vector.dot(onto, dim="axis") > 0, 1, -1)
+    sign = xr.where(vector.dot(onto, dim="axis") == 0, 0, sign)
+    return projection_norm * sign
+
+
+def get_normal_vector(vector1: xr.DataArray, vector2: xr.DataArray) -> xr.DataArray:
     """Create a vector with norm = 1 normal to two other vectors.
 
     Args:
@@ -80,4 +98,38 @@ def calculate_speed_norm(position: xr.DataArray, dt: float = 0.01) -> np.ndarray
     speed_values = np.sqrt(velocity_squared_sum)
     speed_values = np.append(speed_values, speed_values[-1])
 
-    return speed_values
+    return xr.DataArray(speed_values, dims=["time"], coords={"time": position.coords["time"]})
+
+def get_point_in_front(point_a: xr.DataArray, point_b: xr.DataArray, direction_vector: xr.DataArray) -> xr.DataArray:
+    """Determine which point is in front of the other according to the direction vector.
+
+    Args:
+        point_a: The first point.
+        point_b: The second point.
+        direction_vector: The direction vector.
+
+    Returns:
+        The point that is in front according to the direction vector.
+    """
+    direction_vector = direction_vector / direction_vector.meca.norm(dim="axis")
+    vector_b_to_a = point_a - point_b
+    signed_distance = vector_b_to_a.dot(direction_vector, dim="axis")
+
+    return point_a if signed_distance > 0 else point_b
+
+def get_point_behind(point_a: xr.DataArray, point_b: xr.DataArray, direction_vector: xr.DataArray) -> xr.DataArray:
+    """Determine which point is behind the other according to the direction vector.
+
+    Args:
+        point_a: The first point.
+        point_b: The second point.
+        direction_vector: The direction vector.
+
+    Returns:
+        The point that is behind according to the direction vector.
+    """
+    direction_vector = direction_vector / direction_vector.meca.norm(dim="axis")
+    vector_b_to_a = point_a - point_b
+    signed_distance = vector_b_to_a.dot(direction_vector, dim="axis")
+
+    return point_b if signed_distance > 0 else point_a

tests/full/test_linalg.py

@@ -0,0 +1,74 @@
+import pytest
+import xarray as xr
+import numpy as np
+
+from gaitalytics.utils.linalg import (
+    calculate_distance,
+    project_point_on_vector,
+    signed_projection_norm,
+    get_normal_vector,
+    normalize_vector,
+    calculate_speed_norm, 
+    get_point_in_front, 
+    get_point_behind
+)
+
+@pytest.fixture
+def sample_data():
+    point_a = xr.DataArray([1, 2, 3], dims=["axis"], coords={"axis": ["x", "y", "z"]})
+    point_b = xr.DataArray([4, 5, 6], dims=["axis"], coords={"axis": ["x", "y", "z"]})
+    vector_a = xr.DataArray([1, 0, 0], dims=["axis"], coords={"axis": ["x", "y", "z"]})
+    vector_b = xr.DataArray([0, 1, 0], dims=["axis"], coords={"axis": ["x", "y", "z"]})
+    return point_a, point_b, vector_a, vector_b
+
+def test_calculate_distance(sample_data):
+    point_a, point_b, _, _ = sample_data
+    distance = calculate_distance(point_a, point_b)
+    expected_distance = np.sqrt(27)
+    assert distance == pytest.approx(expected_distance)
+
+def test_project_point_on_vector(sample_data):
+    point_a, _, vector_a, _ = sample_data
+    projected_point = project_point_on_vector(point_a, vector_a)
+    expected_projection = xr.DataArray([1, 0, 0], dims=["axis"], coords={"axis": ["x", "y", "z"]})
+    xr.testing.assert_allclose(projected_point, expected_projection)
+
+def test_signed_projection_norm(sample_data):
+    _, _, vector_a, vector_b = sample_data
+    signed_norm = signed_projection_norm(vector_a, vector_b)
+    expected_signed_norm = 0.0
+    assert signed_norm == pytest.approx(expected_signed_norm)
+
+def test_get_normal_vector(sample_data):
+    _, _, vector_a, vector_b = sample_data
+    normal_vector = get_normal_vector(vector_a, vector_b)
+    expected_normal_vector = xr.DataArray([0, 0, 1], dims=["axis"], coords={"axis": ["x", "y", "z"]})
+    xr.testing.assert_allclose(normal_vector, expected_normal_vector)
+
+def test_normalize_vector(sample_data):
+    _, _, vector_a, _ = sample_data
+    normalized_vector = normalize_vector(vector_a)
+    expected_normalized_vector = xr.DataArray([1, 0, 0], dims=["axis"], coords={"axis": ["x", "y", "z"]})
+    xr.testing.assert_allclose(normalized_vector, expected_normalized_vector)
+
+def test_calculate_speed_norm():
+    position = xr.DataArray(
+        np.array([[0, 1, 2], [0, 1, 2], [0, 1, 2]]),
+        dims=["axis", "time"],
+        coords={"axis": ["x", "y", "z"], "time": [0, 1, 2]}
+    )
+    speed = calculate_speed_norm(position, dt=1.0)
+    expected_speed = xr.DataArray([np.sqrt(3), np.sqrt(3), np.sqrt(3)], dims=["time"], coords={"time": [0, 1, 2]})
+    xr.testing.assert_allclose(speed, expected_speed)
+
+def test_get_point_in_front(sample_data):
+    point_a, point_b, vector_a, _ = sample_data
+    point_in_front = get_point_in_front(point_a, point_b, vector_a)
+    expected_point_in_front = point_b
+    xr.testing.assert_allclose(point_in_front, expected_point_in_front)
+
+def test_get_point_behind(sample_data):
+    point_a, point_b, vector_a, _ = sample_data
+    point_behind = get_point_behind(point_a, point_b, vector_a)
+    expected_point_behind = point_a
+    xr.testing.assert_allclose(point_behind, expected_point_behind)