c3d-parser 1.1.2__tar.gz → 1.2.0__tar.gz

{c3d_parser-1.1.2/src/c3d_parser.egg-info → c3d_parser-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.1.2
+Version: 1.2.0
 Summary: C3D parser for gait data harmonisation.
 Author-email: Timothy Salemink <tim.nicolas@outlook.com>, Sally Jack <sallyjaack@gmail.com>
 License-Expression: Apache-2.0
@@ -11,8 +11,8 @@ Requires-Dist: scipy
 Requires-Dist: numpy==1.26.4
 Requires-Dist: pandas
 Requires-Dist: c3d==0.5.2
-Requires-Dist: trc-data-reader
-Requires-Dist: opensim-model-creator==0.6.0
+Requires-Dist: trc-data-reader>=0.4.1
+Requires-Dist: opensim-model-creator==0.7.0
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.1.2 → c3d_parser-1.2.0}/requirements.txt

@@ -2,8 +2,8 @@ scipy
 numpy==1.26.4
 pandas
 c3d==0.5.2
-trc-data-reader
-opensim-model-creator==0.6.0
+trc-data-reader>=0.4.1
+opensim-model-creator==0.7.0
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.2.0/src/c3d_parser/__init__.py

@@ -0,0 +1,2 @@
+
+__version__ = "1.2.0"

{c3d_parser-1.1.2 → c3d_parser-1.2.0}/src/c3d_parser/core/c3d_parser.py

@@ -18,7 +18,7 @@ from opensim_model_creator.Create_Model import create_model
 
 from c3d_parser.core.c3d_patch import c3d
 from c3d_parser.core.utils import clear_directory
-from c3d_parser.core.osim import perform_ik, perform_id
+from c3d_parser.core.osim import perform_ik, perform_id, calculate_foot_progression_angles
 from c3d_parser.settings.general import get_marker_maps_dir
 from c3d_parser.settings.logging import logger
 from c3d_parser.settings.general import VERSION
@@ -53,7 +53,6 @@ def parse_session(static_trial, dynamic_trials, input_directory, output_director
     grf_data = {}
     event_data = {}
     spatiotemporal_data = {}
-    foot_progression_data = {}
     kinematic_data = {}
     kinetic_data = {}
 
@@ -66,7 +65,7 @@ def parse_session(static_trial, dynamic_trials, input_directory, output_director
     for trial_index, trial in enumerate(dynamic_trials, start=1):
         file_path = os.path.normpath(os.path.join(input_directory, trial))
         try:
-            analog_data, events, foot_progression, s_t_data, trc_file_path, grf_file_path = \
+            analog_data, events, s_t_data, trc_file_path, grf_file_path = \
                 parse_dynamic_trial(file_path, lab, output_directory, trial_index, marker_data_rate, static_data,
                                     filter_trc, filter_grf)
         except ParserError as e:
@@ -76,7 +75,6 @@ def parse_session(static_trial, dynamic_trials, input_directory, output_director
         grf_data[trial] = analog_data
         event_data[trial] = events
         spatiotemporal_data[trial] = s_t_data
-        foot_progression_data[trial] = foot_progression
 
         trc_file_paths[trial] = trc_file_path
         grf_file_paths[trial] = grf_file_path
@@ -96,9 +94,12 @@ def parse_session(static_trial, dynamic_trials, input_directory, output_director
 
     for trial in trc_file_paths.keys():
         logger.info(f"Running IK and ID for {trial}.")
-        ik_data, ik_output = run_ik(osim_model, trc_file_paths[trial], output_directory, marker_data_rate, ik_task_set)
-        ik_data = pd.concat([ik_data, foot_progression_data[trial]], axis=1)
-        id_data = run_id(osim_model, ik_data, ik_output, grf_file_paths[trial], output_directory, marker_data_rate, event_data[trial], weight)
+        ik_data, ik_output = run_ik(osim_model, trc_file_paths[trial], output_directory, ik_task_set)
+        foot_progression = calculate_foot_progression_angles(osim_model, ik_output)
+        ik_data = pd.concat([ik_data, foot_progression], axis=1)
+        filter_data(ik_data, marker_data_rate)
+
+        id_data = run_id(osim_model, ik_data, ik_output, grf_file_paths[trial], output_directory, event_data[trial], weight)
 
         kinematic_data[trial] = ik_data
         kinetic_data[trial] = id_data
@@ -220,12 +221,9 @@ def parse_dynamic_trial(c3d_file, lab, output_directory, trial_index, marker_dat
     set_marker_data(trc_data, frame_data, rate=marker_data_rate)
     trc_file_path = write_trc_data(trc_data, output_file_name, output_directory)
 
-    foot_progression = calculate_foot_progression_angles(frame_data)
-    resample_data(foot_progression, trc_data['DataRate'], marker_data_rate)
-
     s_t_data = calculate_spatiotemporal_data(frame_data, events, static_data)
 
-    return analog_data, events, foot_progression, s_t_data, trc_file_path, grf_file_path
+    return analog_data, events, s_t_data, trc_file_path, grf_file_path
 
 
 def write_c3d_parser_history(input_directory, static_trial, deidentified_file_names):
@@ -248,7 +246,7 @@ def write_c3d_parser_history(input_directory, static_trial, deidentified_file_na
         raise ParserError("Could not write c3d_parser_history.log")
 
 
-def run_ik(osim_model, trc_file_path, output_directory, marker_data_rate, ik_task_set):
+def run_ik(osim_model, trc_file_path, output_directory, ik_task_set):
     # Perform inverse kinematics.
     file_name = os.path.splitext(os.path.basename(trc_file_path))[0]
     ik_directory = os.path.join(output_directory, 'ik')
@@ -257,12 +255,11 @@ def run_ik(osim_model, trc_file_path, output_directory, marker_data_rate, ik_tas
     ik_output = os.path.join(ik_directory, f"{file_name}_IK.mot")
     perform_ik(osim_model, trc_file_path, ik_output, ik_task_set)
     ik_data = read_data(ik_output)
-    filter_data(ik_data, marker_data_rate)
 
     return ik_data, ik_output
 
 
-def run_id(osim_model, ik_data, ik_output, grf_file_path, output_directory, marker_data_rate, events, subject_mass):
+def run_id(osim_model, ik_data, ik_output, grf_file_path, output_directory, events, subject_mass):
     # Perform inverse dynamics.
     file_name = os.path.basename(grf_file_path).replace("_grf.mot", "")
     id_directory = os.path.join(output_directory, 'id')
@@ -384,21 +381,18 @@ def convert_old_marker_map(map_file, marker_mapping):
     return marker_set
 
 
-# TODO: The marker set should not be so sensitive to case...!
 def harmonise_markers(frame_data, lab, required_markers):
     marker_set = get_marker_map(lab)
 
     # Harmonise marker labels.
-    reversed_mapping = {value: key for key, value in marker_set.items() if value is not None}
-    header_mapping = {header: reversed_mapping.get(header, None) for header in frame_data.columns[1:]}
+    reversed_mapping = {value.upper(): key for key, value in marker_set.items() if value is not None}
+    header_mapping = {header: reversed_mapping.get(header.upper(), None) for header in frame_data.columns[1:]}
     frame_data.rename(columns=header_mapping, inplace=True)
 
     # Filter out non-harmonised data points.
     if None in frame_data.columns:
         frame_data.drop(columns=frame_data.columns[frame_data.columns.isna()], inplace=True)
 
-    # TODO: This error window does not indicate which trial has the issue.
-    #   Update this.
     # Ensure required markers are present.
     available = set(frame_data.columns)
     for item in required_markers:
@@ -454,10 +448,8 @@ def trim_frames(frame_data):
     if not drop_frames.empty:
         frame_data.drop(drop_frames, inplace=True)
 
-    # TODO: If we convert this to a dictionary we can keep the markers that are missing and check if they are required.
     remaining_frames = [frame for frame in incomplete_frames.keys() if trim_start <= frame <= trim_end]
     if remaining_frames:
-        # TODO: We should raise a ParserError (skip this trial) if the missing markers are required...?
         logger.warn(f"Frames {remaining_frames} are incomplete.")
 
     return trim_start, trim_end
@@ -633,11 +625,6 @@ def extract_data(file_path, start_frame, end_frame):
                 analog_data[label].extend(analog[j - 1])
         analog_data = pd.DataFrame(analog_data)
 
-        # TODO: ACTUALLY, this would also be a good place to just apply the channel order to the analog columns...
-        #   ???
-        #   We will need this if we want to support the files with the deleted plates...!
-        #   And their new force plate setup...!
-
         # Extract event information.
         event_group = get_metadata(reader, 'EVENT')
         event_count = get_metadata(event_group, 'USED').int8_value
@@ -664,6 +651,7 @@ def extract_data(file_path, start_frame, end_frame):
         stride_numbers = {"Left": 0, "Right": 0}
         for foot, event in events.items():
             for event_time, event_type in event.items():
+                event_type = event_type.title()
                 if event_type == "Foot Strike":
                     stride_numbers[foot] += 1
                 stride_number = stride_numbers[foot]
@@ -1019,8 +1007,6 @@ def scale_grf_data(analog_data):
     analog_data[columns] = analog_data[columns] / 1000
 
 
-# TODO: This incorrectly classifies Adelaide's static trials as dynamic.
-#   Use `calculate_distance_covered`...?
 def is_dynamic(file_path):
     with open(file_path, 'rb') as handle:
         try:
@@ -1187,11 +1173,6 @@ def normalise_kinetics(kinetic_data, events):
                         normalised_data[foot][file_name] = {}
                     data_segment = data.iloc[start:frame, 1:]
 
-                    # TODO: If the model +tve and -tve are wrong, then we can't just flip these.
-                    #   Because the non-GRF parts of the moments would also be flipped.
-                    #   Just visually check the results against some clinical kinetics.
-                    #   ...
-                    #   Looks pretty good so far.
                     # Perform sign transformations.
                     data_segment[f"hip_flexion_{side}_moment"] = -data_segment[f"hip_flexion_{side}_moment"]
                     data_segment[f"hip_adduction_{side}_moment"] = -data_segment[f"hip_adduction_{side}_moment"]
@@ -1425,33 +1406,6 @@ def calculate_walking_direction(frame_data):
     return walking_direction
 
 
-# TODO: First, we need to calculate the static flexion angle between the foot vector (heel to toe) and the floor.
-#   (before this function)
-#   Then, when we do this, we should adjust the heel position using a rotation matrix defined by that flexion angle.
-#   (before projecting on to the floor)
-def calculate_foot_progression_angles(frame_data):
-    walking_direction = calculate_walking_direction(frame_data)
-    walking_angle = np.arctan2(walking_direction[1], walking_direction[0])
-
-    foot_progression = pd.DataFrame()
-    for foot in ['Left', 'Right']:
-        side = foot[0]
-        heel_xz = np.stack(frame_data[f"{side}HEE"].values)[:, [0, 2]]
-        toe_xz = np.stack(frame_data[f"{side}TOE"].values)[:, [0, 2]]
-
-        foot_vectors = toe_xz - heel_xz
-        foot_unit_vectors = foot_vectors / np.linalg.norm(foot_vectors, axis=1, keepdims=True)
-        foot_angles = np.arctan2(foot_unit_vectors[:, 1], foot_unit_vectors[:, 0])
-        angles = np.degrees(foot_angles - walking_angle)
-
-        if foot == 'Right':
-            angles = -angles
-
-        foot_progression[f'foot_progression_{side.lower()}'] = angles
-
-    return foot_progression
-
-
 def normalise_angle(angle):
     if angle < -180:
         angle += 360

{c3d_parser-1.1.2 → c3d_parser-1.2.0}/src/c3d_parser/core/osim.py

@@ -1,9 +1,13 @@
 
 import os
 import copy
+import numpy as np
+import pandas as pd
 import opensim as osim
 import xml.etree.ElementTree as ET
 
+from scipy.spatial.transform import Rotation
+
 from c3d_parser.settings.logging import logger
 
 
@@ -95,3 +99,59 @@ def setup_external_loads(output_directory, grf_file):
     tree.write(external_loads_file)
 
     return external_loads_file
+
+
+def calculate_foot_progression_angles(model_file, ik_file):
+
+    # Load model information.
+    model = osim.Model(model_file)
+    model.initSystem()
+    coordinate_set = model.getCoordinateSet()
+    n_coordinates = coordinate_set.getSize()
+
+    # Load IK solution.
+    storage = osim.Storage(ik_file)
+    labels = storage.getColumnLabels()
+    n_frames = storage.getSize()
+
+    foot_progression = {"l": [], "r": []}
+    for i in range(n_frames):
+
+        # Build a state vector from the IK solution at this frame.
+        time_stamp = storage.getStateVector(i).getTime()
+        state = model.initSystem()
+        state.setTime(time_stamp)
+        ik_row = storage.getStateVector(i).getData()
+
+        # Set body coordinates from the IK solution.
+        for j in range(n_coordinates):
+            coordinate = coordinate_set.get(j)
+            coordinate_name = coordinate.getName()
+            column_index = labels.findIndex(coordinate_name)
+            if column_index >= 0:
+                value = ik_row.get(column_index - 1)
+
+                if coordinate.getMotionType() == osim.Coordinate.Rotational:
+                    value = np.deg2rad(value)
+                coordinate.setValue(state, value)
+        model.realizePosition(state)
+
+        # Extract foot segment rotation.
+        for side in foot_progression.keys():
+            foot_body = model.getBodySet().get(f"calcn_{side}")
+            transform = foot_body.getTransformInGround(state)
+
+            # Decompose rotation matrix into ZXY Euler angles.
+            rotation_matrix = np.array([[transform.R().get(row, col) for col in range(3)] for row in range(3)])
+            angles = Rotation.from_matrix(rotation_matrix).as_euler('ZXY')
+            foot_progression_angle = np.rad2deg(angles[2])
+
+            if side == "l":
+                foot_progression_angle = -foot_progression_angle
+            foot_progression[side].append(foot_progression_angle)
+
+    data_frame = pd.DataFrame({
+        "foot_progression_l": foot_progression["l"],
+        "foot_progression_r": foot_progression["r"],
+    })
+    return data_frame

{c3d_parser-1.1.2 → c3d_parser-1.2.0}/src/c3d_parser/view/main_window.py

@@ -57,13 +57,6 @@ class ProgressTracker(QObject):
     progress = Signal(str, str)
 
 
-# TODO: Add the deidentified name to the column in the file details.
-#   Instead of just "Dynamic", "Dynamic_1" or whatever.
-#   ...
-#   Nah just create local mapping file directly in input directory.
-
-
-# TODO: CGM2 event detector on GitHub...?
 class MainWindow(QMainWindow):
 
     def __init__(self):
@@ -251,12 +244,6 @@ class MainWindow(QMainWindow):
             table.deleteLater()
         self._spatiotemporal_tables = []
 
-    # TODO: The legend is not correctly displayed if the ST tab is open while processing...
-    #   Repositioning and updating the legend do nothing.
-
-    # TODO: The border is still having issues.
-    #   Seems to be related to the area being scrollable.
-    #   Only happens on some PCs/monitors...
     def _visualise_spatiotemporal_data(self):
         layout = self._ui.scrollAreaSpatiotemporal.layout()
         self._clear_spatiotemporal_data()
@@ -882,7 +869,6 @@ class MainWindow(QMainWindow):
             self._update_s_t_colours()
             self._update_legend()
 
-    # TODO: For some reason the legend doesn't get created at all if we are visualising the ST tab while processing...
     def _update_legend(self):
         if self._boxes:
             for side, boxes in self._boxes.items():
@@ -970,8 +956,6 @@ class MainWindow(QMainWindow):
         settings.beginGroup('MainWindow')
         settings.setValue('size', self.size())
         settings.setValue('pos', self.pos())
-        # TODO: The taskbar icon fails if the application opens in full-screen...
-        #   DON'T open in full screen...?
         settings.setValue('is_maximized', self.isMaximized())
         settings.setValue('lab', self._ui.comboBoxLab.currentText())
         settings.setValue('marker_diameter', self._ui.doubleSpinBoxMarkerDiameter.value())
@@ -1158,9 +1142,6 @@ class GaitCurves(defaultdict):
                         line.set_color(colour)
                         line.set_zorder(z_order)
 
-        # TODO: Replace all these with `draw_idle`?
-        #   Just the ones that handle many curves...?
-        #   Probably all...?
         self._canvas.draw()
 
     def show_curve_menu(self, event):

{c3d_parser-1.1.2 → c3d_parser-1.2.0/src/c3d_parser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.1.2
+Version: 1.2.0
 Summary: C3D parser for gait data harmonisation.
 Author-email: Timothy Salemink <tim.nicolas@outlook.com>, Sally Jack <sallyjaack@gmail.com>
 License-Expression: Apache-2.0
@@ -11,8 +11,8 @@ Requires-Dist: scipy
 Requires-Dist: numpy==1.26.4
 Requires-Dist: pandas
 Requires-Dist: c3d==0.5.2
-Requires-Dist: trc-data-reader
-Requires-Dist: opensim-model-creator==0.6.0
+Requires-Dist: trc-data-reader>=0.4.1
+Requires-Dist: opensim-model-creator==0.7.0
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.1.2 → c3d_parser-1.2.0}/src/c3d_parser.egg-info/requires.txt

@@ -2,8 +2,8 @@ scipy
 numpy==1.26.4
 pandas
 c3d==0.5.2
-trc-data-reader
-opensim-model-creator==0.6.0
+trc-data-reader>=0.4.1
+opensim-model-creator==0.7.0
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.1.2/src/c3d_parser/__init__.py

@@ -1,2 +0,0 @@
-
-__version__ = "1.1.2"