c3d-parser 1.6.0__tar.gz → 1.6.1__tar.gz

{c3d_parser-1.6.0/src/c3d_parser.egg-info → c3d_parser-1.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.6.0
+Version: 1.6.1
 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==0.10.0
+Requires-Dist: opensim-model-creator==0.10.1
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.6.0 → c3d_parser-1.6.1}/requirements.txt

@@ -3,7 +3,7 @@ numpy==1.26.4
 pandas
 c3d==0.5.2
 trc-data-reader>=0.4.1
-opensim-model-creator==0.10.0
+opensim-model-creator==0.10.1
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.6.1/src/c3d_parser/__init__.py

@@ -0,0 +1,2 @@
+
+__version__ = "1.6.1"

{c3d_parser-1.6.0 → c3d_parser-1.6.1}/src/c3d_parser/core/c3d_parser.py

@@ -92,7 +92,8 @@ def parse_session(static_trial, dynamic_trials, input_directory, output_director
                                    output_directory, left_foot_flat, right_foot_flat, toe_marker_proximal,
                                    optimise_knee_axis, progress_tracker)
 
-    write_c3d_parser_history(input_directory, output_directory, static_trial, deidentified_file_names, static_data)
+    write_c3d_parser_history(input_directory, output_directory, lab, static_trial, deidentified_file_names, static_data,
+                             left_foot_flat, right_foot_flat, toe_marker_proximal)
 
     if not trc_file_paths:
         raise CancelException("No dynamic trials found.")
@@ -251,15 +252,18 @@ def parse_dynamic_trial(c3d_file, lab, output_directory, trial_index, marker_dat
     return analog_data, events, s_t_data, trc_file_path, grf_file_path
 
 
-def write_c3d_parser_history(input_directory, output_directory, static_trial, deidentified_file_names, static_data):
+def write_c3d_parser_history(input_directory, output_directory, lab, static_trial, deidentified_file_names, static_data,
+                             left_foot_flat, right_foot_flat, toe_marker_proximal):
     log_path = os.path.join(input_directory, "c3d_parser_history.log")
     timestamp = datetime.now().strftime("%Y-%m-%d %H:%M")
 
     try:
         with open(log_path, "w", encoding="utf-8") as f:
             f.write("C3D-Parser History\n")
-            f.write(f"Last Run: {timestamp}\n\n")
+            f.write(f"Last Run: {timestamp}\n")
+            f.write(f"C3D-Parser Version: {VERSION}\n\n")
 
+            f.write(f"Lab: {lab}\n")
             f.write(f"Static trial: {static_trial}\n\n")
 
             if deidentified_file_names:
@@ -286,6 +290,12 @@ def write_c3d_parser_history(input_directory, output_directory, static_trial, de
                     unit = f" {units[key]}" if key in units else ""
                     f.write(f"{label}: {value}{unit}\n")
 
+            f.write("\n")
+            f.write("Foot Settings:\n")
+            f.write(f"Toe Marker: {'Proximal' if toe_marker_proximal else '2nd/3rd Met'}\n")
+            f.write(f"Left Foot Flat: {left_foot_flat}\n")
+            f.write(f"Right Foot Flat: {right_foot_flat}\n")
+
             metrics, measurements = define_metrics_and_measurements(output_directory)
             if metrics:
                 f.write("\n")
@@ -540,8 +550,10 @@ 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
@@ -1105,6 +1117,8 @@ 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:
@@ -1280,6 +1294,11 @@ 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"]
@@ -1372,6 +1391,9 @@ 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": {}}
@@ -1394,6 +1416,8 @@ 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():

{c3d_parser-1.6.0 → c3d_parser-1.6.1}/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):
@@ -256,6 +257,12 @@ 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.
@@ -891,6 +898,8 @@ 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()
@@ -918,6 +927,7 @@ 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():
@@ -1010,6 +1020,8 @@ 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())
@@ -1214,6 +1226,9 @@ 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-1.6.0 → c3d_parser-1.6.1/src/c3d_parser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.6.0
+Version: 1.6.1
 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==0.10.0
+Requires-Dist: opensim-model-creator==0.10.1
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.6.0 → c3d_parser-1.6.1}/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==0.10.0
+opensim-model-creator==0.10.1
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.6.0/src/c3d_parser/__init__.py

@@ -1,2 +0,0 @@
-
-__version__ = "1.6.0"