c3d-parser 1.5.2__tar.gz → 1.5.3__tar.gz

{c3d_parser-1.5.2/src/c3d_parser.egg-info → c3d_parser-1.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.5.2
+Version: 1.5.3
 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
@@ -12,7 +12,7 @@ Requires-Dist: numpy==1.26.4
 Requires-Dist: pandas
 Requires-Dist: c3d==0.5.2
 Requires-Dist: trc-data-reader>=0.4.1
-Requires-Dist: opensim-model-creator==0.8.1
+Requires-Dist: opensim-model-creator==0.8.2
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.5.2 → c3d_parser-1.5.3}/requirements.txt

@@ -3,7 +3,7 @@ numpy==1.26.4
 pandas
 c3d==0.5.2
 trc-data-reader>=0.4.1
-opensim-model-creator==0.8.1
+opensim-model-creator==0.8.2
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.5.3/src/c3d_parser/__init__.py

@@ -0,0 +1,2 @@
+
+__version__ = "1.5.3"

{c3d_parser-1.5.2 → c3d_parser-1.5.3}/src/c3d_parser/core/c3d_parser.py

@@ -525,8 +525,10 @@ 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
@@ -1090,6 +1092,8 @@ 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` instead?
 def is_dynamic(file_path):
     with open(file_path, 'rb') as handle:
         try:
@@ -1265,6 +1269,11 @@ 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"]
@@ -1357,6 +1366,9 @@ def write_normalised_data(data, column_names, selected_trials, excluded_cycles,
                     file.write('\n')
 
 
+# TODO: Rework this function to be less sequential.
+#   It should be able to calculate metrics for walking and running gait.
+#   Put this at the start of the sequential bit.
 def calculate_spatiotemporal_data(frame_data, events, static_data):
     stride_lengths = {"Left": {}, "Right": {}}
     step_lengths = {"Left": {}, "Right": {}}
@@ -1379,6 +1391,8 @@ def calculate_spatiotemporal_data(frame_data, events, static_data):
             for event_time, (event_type, event_plate) in stride_events.items():
                 time_ordered_events[event_time][foot] = [event_type, stride_number]
 
+    # TODO: We should be able to use this to calculate ALL measurements non-sequentially.
+    # TODO: Double check that we don't have situations where the events are not ordered in increasing stride number.
     # Add terminal foot-strike to events for each cycle.
     full_cycle_events = copy.deepcopy(events)
     for foot, foot_events in full_cycle_events.items():
@@ -1617,13 +1631,13 @@ def add_medial_knee_markers(frame_data, left_knee_width, right_knee_width, marke
     This function takes a pandas.DataFrame of TRC data, extracts a single frame from the data
     and adds the medial knee markers if they are missing. It returns the frame as a pandas.Series.
 
-    The ``padding`` argument should include skin-padding as well as the thickness of the
-    baseplate used to attach the markers.
+    The ``padding`` values are the thickness of the baseplate used to attach the markers. Knee
+    widths are measured over the skin.
     """
     frame = frame_data.iloc[len(frame_data) // 2].copy()
 
-    medial_padding = 6
-    lateral_padding = 4
+    medial_padding = 2
+    lateral_padding = 2
 
     for side in ['L', 'R']:
         medial_label = f'{side}KNEM'
@@ -1637,7 +1651,7 @@ def add_medial_knee_markers(frame_data, left_knee_width, right_knee_width, marke
             magnitude = np.sqrt((np.array(axix_vector) ** 2.0).sum(-1))
             knee_axis = np.divide(axix_vector, magnitude)
 
-            # Adjust knee width to account for marker-radius, skin-padding.
+            # Adjust knee width to account for marker-radius, baseplate.
             knee_width = left_knee_width if side == 'L' else right_knee_width
             knee_width = knee_width + marker_diameter + medial_padding + lateral_padding
             medial_marker = lateral_marker + knee_width * knee_axis
@@ -1654,7 +1668,7 @@ def create_osim_model(static_trc, dynamic_trc, static_marker_data, marker_diamet
     rotation_matrix = np.array([[1, 0, 0], [0, 0, 1], [0, -1, 0]])
     static_marker_data = {k: np.dot(rotation_matrix, v) for k, v in static_marker_data.items()}
     subject_info = get_subject_info(static_data)
-    marker_radius = marker_diameter / 2
+    marker_radius = marker_diameter / 2 + 2  # Include the 2mm marker baseplate.
 
     model_path = create_model(static_trc, dynamic_trc, output_directory, static_marker_data, subject_info,
                               marker_radius, left_foot_flat, right_foot_flat,

{c3d_parser-1.5.2 → c3d_parser-1.5.3}/src/c3d_parser/core/osim_resources/ik_task_set.xml

@@ -74,6 +74,12 @@
 				<!--Weight given to the task when solving inverse kinematics problems, default is 0.-->
 				<weight>1</weight>
 			</IKMarkerTask>
+			<IKMarkerTask name="SACR">
+				<!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
+				<apply>true</apply>
+				<!--Weight given to the task when solving inverse kinematics problems, default is 0.-->
+				<weight>2</weight>
+			</IKMarkerTask>
 			<IKMarkerTask name="RHEE">
 				<!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
 				<apply>true</apply>

{c3d_parser-1.5.2 → c3d_parser-1.5.3}/src/c3d_parser/view/main_window.py

@@ -57,6 +57,7 @@ class ProgressTracker(QObject):
     progress = Signal(str, str)
 
 
+# TODO: CGM2 event detector on GitHub...?
 class MainWindow(QMainWindow):
 
     def __init__(self):
@@ -258,6 +259,12 @@ 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):
 
         # Temporarily disable spatio-temporal visualisation for running gait.
@@ -903,6 +910,8 @@ class MainWindow(QMainWindow):
                         if (file_name, f"{foot}_{cycle_number}") not in excluded_cycles:
                             counts[foot] += 1
 
+            # TODO: This is being displayed before processing has finished.
+            #   Which should not be happening.
             self._ui.labelCount.setText(f"Cycles: L {counts['Left']} / R {counts['Right']}")
 
         tab = self._ui.tabWidget.currentWidget()
@@ -930,6 +939,7 @@ 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():
@@ -1021,6 +1031,8 @@ 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())
@@ -1225,6 +1237,9 @@ 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-1.5.2 → c3d_parser-1.5.3/src/c3d_parser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.5.2
+Version: 1.5.3
 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
@@ -12,7 +12,7 @@ Requires-Dist: numpy==1.26.4
 Requires-Dist: pandas
 Requires-Dist: c3d==0.5.2
 Requires-Dist: trc-data-reader>=0.4.1
-Requires-Dist: opensim-model-creator==0.8.1
+Requires-Dist: opensim-model-creator==0.8.2
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.5.2 → c3d_parser-1.5.3}/src/c3d_parser.egg-info/requires.txt

@@ -3,7 +3,7 @@ numpy==1.26.4
 pandas
 c3d==0.5.2
 trc-data-reader>=0.4.1
-opensim-model-creator==0.8.1
+opensim-model-creator==0.8.2
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.5.2/src/c3d_parser/__init__.py

@@ -1,2 +0,0 @@
-
-__version__ = "1.5.2"