Merge pull request #34 from EveCharbie/env

Fixed the environment issues (some dependency updates changed the test values, so I made the scaling test less sensitive and changed the joint center tool tests values).

Author: EveCharbie

.github/workflows/copilot-setup-steps.yml

@@ -20,6 +20,9 @@ jobs:
   # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
   copilot-setup-steps:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: Checkout code with submodule
         uses: actions/checkout@v4
@@ -31,19 +34,29 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
-
-      - name: Set up Python
-        run: |
-          conda install -cconda-forge python=3.11.11 pip 
+          activate-environment: biobuddy
+          python-version: 3.11.11
 
       - name: Install dependencies
         run: | 
           pip install . && pip uninstall -y biobuddy
-          pip install scipy==1.15.1 numpy lxml ezc3d
+          pip install scipy==1.15.2 numpy==1.25.2 lxml ezc3d
 
       - name: Install test dependencies
         run: |
-          pip install pytest pytest-cov codecov pyomeca black
+          pip install pytest pytest-cov codecov black
           conda install -c opensim-org opensim=4.5.1
           conda install -c conda-forge biorbd=1.11.2 deepdiff
-  
+
+      - name: Set environment variables for Copilot
+        run: |
+          echo "CONDA_PREFIX=$CONDA_PREFIX" >> $GITHUB_ENV
+          echo "PYTHONPATH=$CONDA_PREFIX/lib/python3.11/site-packages:$PYTHONPATH" >> $GITHUB_ENV
+          echo "PATH=$CONDA_PREFIX/bin:$PATH" >> $GITHUB_ENV
+
+      - name: Verify environment setup
+        run: |
+          echo "Python location: $(which python)"
+          echo "Conda prefix: $CONDA_PREFIX"
+          echo "Python path: $PYTHONPATH"
+          python -c "import sys; print('Python sys.path:'); [print(f'  {p}') for p in sys.path]"

.github/workflows/run_tests.yml

@@ -62,11 +62,11 @@ jobs:
       - name: Install dependencies
         run: | 
           pip install . && pip uninstall -y biobuddy
-          pip install scipy==1.15.1 numpy==1.25.2 lxml ezc3d
+          pip install scipy==1.15.1 numpy==1.25.2 lxml ezc3d matplotlib
 
       - name: Install test dependencies
         run: |
-          pip install pytest pytest-cov codecov pyomeca
+          pip install pytest pytest-cov codecov
           conda install -c opensim-org opensim=4.5.1
           conda install -c conda-forge biorbd=1.11.2 deepdiff
 

README.md

@@ -19,11 +19,12 @@ If you are a user, you can set up your environment with minimal dependencies.
 conda install -c conda-forge python=3.11.11 pip
 pip install scipy==1.15.1 numpy==1.25.2 lxml ezc3d
 ```
+Note: On mac, you might need to add `conda install conda-forge::libcxx`
 
 However, if you are a developer and want to contribute, you will need to set up your environment using the following command:
 Due to the OpenSim dependency used only in BioBuddy's tests, we recommend using python=3.11.
 ```bash
-pip install pytest pytest-cov codecov pyomeca
+pip install pytest pytest-cov codecov
 conda install -c opensim-org opensim=4.5.1
 conda install -c conda-forge biorbd=1.11.2 deepdiff
 ```
@@ -60,7 +61,7 @@ from biobuddy import ScaleTool
 scale_tool = ScaleTool(original_model=original_model).from_xml(filepath=xml_filepath)
 
 # Performing the scaling based on a static trial
-scaled_model_CAC = scale_tool.scale(filepath=static_c3d_filepath, first_frame=100, last_frame=200, mass=mass)
+scaled_model = scale_tool.scale(static_c3d=C3dData(filepath), mass=mass)
 ```
 
 **Joint center identification:**
@@ -75,25 +76,21 @@ joint_center_tool = JointCenterTool(scaled_model)
 # Example for the right hip
 joint_center_tool.add(
     Score(
-        filepath=hip_movement_c3d_filepath,
+        functional_c3d=C3dData(c3d_filepath, first_frame=100, last_frame=900),
         parent_name="pelvis",
         child_name="femur_r",
         parent_marker_names=["RASIS", "LASIS", "LPSIS", "RPSIS"],
         child_marker_names=["RGT", "RUB_Leg", "RUF_Leg", "FBF_Leg", "RMFE", "RLFE"],
-        first_frame=100,
-        last_frame=900,
     )
 )
 # Example for the right knee
 joint_center_tool.add(
     Sara(
-        filepath=knee_movement_c3d_filepath,
+        functional_c3d=C3dData(c3d_filepath),
         parent_name="femur_r",
         child_name="tibia_r",
         parent_marker_names=["RGT", "RUB_Leg", "RUF_Leg", "FBF_Leg"],
         child_marker_names=["RATT", "RUB_Tib", "RDF_Tib", "RDB_Tib", "RSPH", "RLM"],
-        first_frame=100,
-        last_frame=900,
     )
 )
 

biobuddy/model_modifiers/joint_center_tool.py

@@ -12,7 +12,6 @@
 from ..utils.c3d_data import C3dData
 from ..utils.linear_algebra import (
     RotoTransMatrix,
-    get_closest_rt_matrix,
     mean_unit_vector,
     RotoTransMatrixTimeSeries,
     point_from_local_to_global,
@@ -27,21 +26,19 @@
 class RigidSegmentIdentification:
     def __init__(
         self,
-        filepath: str,
+        functional_c3d: C3dData,
         parent_name: str,
         child_name: str,
         parent_marker_names: list[str],
         child_marker_names: list[str],
-        first_frame: int = None,
-        last_frame: int = None,
         initialize_whole_trial_reconstruction: bool = False,
         animate_rt: bool = False,
     ):
         """
         Parameters
         ----------
-        filepath
-            The path to the .c3d file containing the functional trial.
+        functional_c3d
+            The .c3d file containing the functional trial.
         parent_name
             The name of the joint's parent segment.
         child_name
@@ -50,24 +47,18 @@ def __init__(
             The name of the markers in the parent segment to consider during the SCoRE algorithm.
         child_marker_names
             The name of the markers in the child segment to consider during the SCoRE algorithm.
-        first_frame
-            The first frame to consider in the functional trial.
-        last_frame
-            The last frame to consider in the functional trial.
         initialize_whole_trial_reconstruction
             If True, the whole trial is reconstructed using whole body inverse kinematics to initialize the segments' rt in the global reference frame.
         animate_rt
             If True, it animates the segment rt reconstruction using pyomeca and pyorerun.
         """
 
         # Original attributes
-        self.filepath = filepath
+        self.c3d_data = functional_c3d
         self.parent_name = parent_name
         self.child_name = child_name
         self.parent_marker_names = parent_marker_names
         self.child_marker_names = child_marker_names
-        self.first_frame = first_frame
-        self.last_frame = last_frame
         self.initialize_whole_trial_reconstruction = initialize_whole_trial_reconstruction
         self.animate_rt = animate_rt
 
@@ -78,7 +69,6 @@ def __init__(
         self.child_static_markers_in_local: np.ndarray = None
         self.parent_markers_global: np.ndarray = None
         self.child_markers_global: np.ndarray = None
-        self.c3d_data: C3dData = None
         self.marker_name: list[str] = None
         self.marker_positions: np.ndarray = None
 
@@ -101,22 +91,15 @@ def _check_c3d_functional_trial_file(self):
         """
         Check that the file format is appropriate and that there is a functional movement in the trial (aka the markers really move).
         """
-        # Check file format
-        if self.filepath.endswith(".c3d"):
-            # Load the c3d file
-            self.c3d_data = C3dData(self.filepath, self.first_frame, self.last_frame)
-            self.marker_names = self.c3d_data.marker_names
-            self.marker_positions = self.c3d_data.all_marker_positions[:3, :, :]
-        else:
-            if self.filepath.endswith(".trc"):
-                raise NotImplementedError(".trc files cannot be read yet.")
-            else:
-                raise RuntimeError("The filepath (static trial) must be a .c3d file in a static posture.")
+        self.marker_names = self.c3d_data.marker_names
+        self.marker_positions = self.c3d_data.all_marker_positions[:3, :, :]
 
         # Check that the markers move
         std = []
         for marker_name in self.parent_marker_names + self.child_marker_names:
             std += self.c3d_data.std_marker_position(marker_name)
+        if len(std) == 0:
+            raise RuntimeError("There are no markers in the functional trial. Please check the trial again.")
         if all(np.array(std) < 0.01):
             raise RuntimeError(
                 f"The markers {self.parent_marker_names + self.child_marker_names} are not moving in the functional trial (markers std = {std}). "
@@ -676,28 +659,24 @@ def perform_task(
 class Sara(RigidSegmentIdentification):
     def __init__(
         self,
-        filepath: str,
+        functional_c3d: C3dData,
         parent_name: str,
         child_name: str,
         parent_marker_names: list[str],
         child_marker_names: list[str],
         joint_center_markers: list[str],
         distal_markers: list[str],
         is_longitudinal_axis_from_jcs_to_distal_markers: bool,
-        first_frame: int = None,
-        last_frame: int = None,
         initialize_whole_trial_reconstruction: bool = False,
         animate_rt: bool = False,
     ):
 
         super(Sara, self).__init__(
-            filepath=filepath,
+            functional_c3d=functional_c3d,
             parent_name=parent_name,
             child_name=child_name,
             parent_marker_names=parent_marker_names,
             child_marker_names=child_marker_names,
-            first_frame=first_frame,
-            last_frame=last_frame,
             animate_rt=animate_rt,
             initialize_whole_trial_reconstruction=initialize_whole_trial_reconstruction,
         )

biobuddy/model_modifiers/scale_tool.py

@@ -70,9 +70,7 @@ def add_marker_weight(self, marker_weight: MarkerWeight):
 
     def scale(
         self,
-        filepath: str,
-        first_frame: int,
-        last_frame: int,
+        static_c3d: C3dData,
         mass: float,
         q_regularization_weight: float = None,
         initial_static_pose: np.ndarray = None,
@@ -85,12 +83,8 @@ def scale(
 
         Parameters
         ----------
-        filepath
+        static_c3d
             The .c3d or .trc file of the static trial to use for the scaling
-        first_frame
-            The index of the first frame to use in the .c3d file.
-        last_frame
-            The index of the last frame to use in the .c3d file.
         mass
             The mass of the subject
         q_regularization_weight
@@ -105,18 +99,9 @@ def scale(
         method
             The lease square method to use. (default: "lm", other options: "trf" or "dogbox")
         """
+        exp_marker_names = static_c3d.marker_names
+        exp_marker_positions = static_c3d.all_marker_positions[:3, :, :]
 
-        # Check file format
-        if filepath.endswith(".c3d"):
-            # Load the c3d file
-            c3d_data = C3dData(filepath, first_frame, last_frame)
-            exp_marker_names = c3d_data.marker_names
-            exp_marker_positions = c3d_data.all_marker_positions[:3, :, :]
-        else:
-            if filepath.endswith(".trc"):
-                raise NotImplementedError(".trc files cannot be read yet.")
-            else:
-                raise RuntimeError("The filepath (static trial) must be a .c3d file in a static posture.")
         marker_indices = [idx for idx, m in enumerate(exp_marker_names) if m in self.original_model.marker_names]
         marker_names = [exp_marker_names[idx] for idx in marker_indices]
         marker_positions = exp_marker_positions[:, marker_indices, :]

biobuddy/utils/__init__.py

@@ -1,5 +1,5 @@
 from .aliases import Point, Points
-from .c3d_data import C3dData
+from .c3d_data import C3dData, ReferenceFrame
 from .protocols import Data, GenericDynamicModel
 from .rotations import Rotations
 from .translations import Translations
@@ -9,6 +9,7 @@
     "Point",
     "Points",
     C3dData.__name__,
+    ReferenceFrame.__name__,
     Data.__name__,
     GenericDynamicModel.__name__,
     Rotations.__name__,

biobuddy/utils/c3d_data.py

@@ -1,7 +1,17 @@
+from enum import Enum
 import numpy as np
 import ezc3d
 
 
+class ReferenceFrame(Enum):
+    """
+    The reference frame for the C3D data.
+    """
+
+    Z_UP = "z-up"
+    Y_UP = "y-up"
+
+
 class C3dData:
     """
     Implementation of the `Data` protocol from model_creation
@@ -68,3 +78,46 @@ def _to_meter(self, data: np.array) -> np.ndarray:
         data /= factor
         data[3] = 1
         return data
+
+    def change_ref_frame(self, ref_from: ReferenceFrame, ref_to: ReferenceFrame) -> None:
+        """
+        Change the reference frame of the data.
+        """
+        if ref_from == ref_to:
+            return
+
+        if ref_from == ReferenceFrame.Z_UP and ref_to == ReferenceFrame.Y_UP:
+            temporary_data = self.ezc3d_data["data"]["points"].copy()
+            self.ezc3d_data["data"]["points"][0, self.first_frame : self.last_frame, :] = temporary_data[
+                0, self.first_frame : self.last_frame, :
+            ]  # X = X
+            self.ezc3d_data["data"]["points"][1, self.first_frame : self.last_frame, :] = temporary_data[
+                2, self.first_frame : self.last_frame, :
+            ]  # Y = Z
+            self.ezc3d_data["data"]["points"][2, self.first_frame : self.last_frame, :] = -temporary_data[
+                1, self.first_frame : self.last_frame, :
+            ]  # Z = -Y
+
+        elif ref_from == ReferenceFrame.Y_UP and ref_to == ReferenceFrame.Z_UP:
+            temporary_data = self.ezc3d_data["data"]["points"].copy()
+            self.ezc3d_data["data"]["points"][0, self.first_frame : self.last_frame, :] = temporary_data[
+                0, self.first_frame : self.last_frame, :
+            ]  # X = X
+            self.ezc3d_data["data"]["points"][1, self.first_frame : self.last_frame, :] = -temporary_data[
+                2, self.first_frame : self.last_frame, :
+            ]  # Y = -Z
+            self.ezc3d_data["data"]["points"][2, self.first_frame : self.last_frame, :] = temporary_data[
+                1, self.first_frame : self.last_frame, :
+            ]  # Z = Y
+
+        else:
+            raise ValueError(f"Cannot change from {ref_from} to {ref_to}.")
+
+    def save(self, new_path: str):
+        """
+        Save the changes made to the C3D file.
+        """
+        if "meta_points" in self.ezc3d_data["data"]:
+            # Remove meta points if they exist as it might cause issues with some C3D writer
+            del self.ezc3d_data["data"]["meta_points"]
+        self.ezc3d_data.write(new_path)

environment.yml

@@ -80,7 +80,6 @@ dependencies:
       - pillow==11.2.1
       - pluggy==1.6.0
       - pygments==2.19.1
-      - pyomeca==2024.0.2
       - pyparsing==3.2.3
       - pytest==8.4.1
       - pytest-cov==6.2.1