c3d-parser 1.5.4__tar.gz → 1.6.0__tar.gz

{c3d_parser-1.5.4/src/c3d_parser.egg-info → c3d_parser-1.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.5.4
+Version: 1.6.0
 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
@@ -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==0.8.3
+Requires-Dist: opensim-model-creator==0.10.0
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.5.4 → c3d_parser-1.6.0}/requirements.txt

@@ -3,7 +3,7 @@ numpy==1.26.4
 pandas
 c3d==0.5.2
 trc-data-reader>=0.4.1
-opensim-model-creator==0.8.3
+opensim-model-creator==0.10.0
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.6.0/src/c3d_parser/__init__.py

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

{c3d_parser-1.5.4 → c3d_parser-1.6.0}/src/c3d_parser/core/c3d_parser.py

@@ -16,7 +16,6 @@ from decimal import Decimal, ROUND_CEILING, ROUND_FLOOR
 
 from trc import TRCData
 from opensim_model_creator.Create_Model import create_model
-from ll_visualiser.utils import get_fit_metrics, load_landmarks, define_measurements
 
 from c3d_parser.core.c3d_patch import c3d
 from c3d_parser.core.utils import clear_directory
@@ -38,11 +37,15 @@ torso_markers = ["C7", "T2", "T10", "MAN"]
 required_markers = [{"LASI", "RASI"}, {"LKNE", "RKNE"}, {"LANK", "RANK"}, {"LMED", "RMED"}, {"LHEE", "RHEE"},
                     {"LTOE", "RTOE"}, ({"LPSI", "RPSI"}, {"SACR"}), ({"LKNEM", "RKNEM"}, {"LKAX", "RKAX"})]
 
+required_measurements = ['Sex', 'Age', 'Height', 'Weight', 'ASIS Width', 'Left Knee Width', 'Right Knee Width',
+                         'Left Ankle Width', 'Right Ankle Width']
+
 
 def parse_session(static_trial, dynamic_trials, input_directory, output_directory, lab, marker_diameter, static_data,
                   left_foot_flat, right_foot_flat, toe_marker_proximal, optimise_knee_axis, filter_trc, filter_grf,
                   ik_task_set, running_gait, progress_tracker):
 
+    validate_static_data(static_data)
     clear_directory(output_directory)
 
     logger.info(f"Processing session {os.path.normpath(input_directory)}.")
@@ -127,16 +130,26 @@ def approximate_anthropometrics(c3d_file, lab, marker_diameter):
 
 def calculate_anthropometrics(frame_data, marker_diameter):
 
-    def distance(frame, landmark_1, landmark_2):
-        return round(np.linalg.norm(np.array(frame[landmark_1]) - np.array(frame[landmark_2])), 1)
+    def distance(frame, landmark_1, landmark_2, marker_diameter=0):
+        missing = [landmark for landmark in (landmark_1, landmark_2) if landmark not in frame]
+        if missing:
+            logger.warn(f"Unable to approximate distance between {landmark_1} and {landmark_2}. "
+                        f"Missing marker(s): {', '.join(missing)}.")
+            return 0
+
+        point_1 = np.array(frame[landmark_1])
+        point_2 = np.array(frame[landmark_2])
+        length = round(np.linalg.norm(point_1 - point_2), 1)
+
+        return length - marker_diameter
 
     mid_frame = frame_data.iloc[len(frame_data) // 2].copy()
 
     anthropometrics = {
-        'left_knee_width': distance(mid_frame, 'LKNE', 'LKNEM') - marker_diameter,
-        'right_knee_width': distance(mid_frame, 'RKNE', 'RKNEM') - marker_diameter,
-        'left_ankle_width': distance(mid_frame, 'LANK', 'LMED')  - marker_diameter,
-        'right_ankle_width': distance(mid_frame, 'RANK', 'RMED')  - marker_diameter,
+        'left_knee_width': distance(mid_frame, 'LKNE', 'LKNEM', marker_diameter),
+        'right_knee_width': distance(mid_frame, 'RKNE', 'RKNEM', marker_diameter),
+        'left_ankle_width': distance(mid_frame, 'LANK', 'LMED', marker_diameter),
+        'right_ankle_width': distance(mid_frame, 'RANK', 'RMED', marker_diameter),
         'left_leg_length': distance(mid_frame, 'LASI', 'LMED'),
         'right_leg_length': distance(mid_frame, 'RASI', 'RMED'),
         'inter_asis_distance': distance(mid_frame, 'LASI', 'RASI'),
@@ -290,6 +303,8 @@ def write_c3d_parser_history(input_directory, output_directory, static_trial, de
 
 
 def define_metrics_and_measurements(output_directory):
+    from ll_visualiser.utils import get_fit_metrics, load_landmarks, define_measurements
+
     model_directory = os.path.join(output_directory, "Models", "Meshes")
     left_predicted_landmark_file = os.path.join(model_directory, 'predicted_lms_left.txt')
     right_predicted_landmark_file = os.path.join(model_directory, 'predicted_lms_right.txt')
@@ -525,10 +540,8 @@ 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
@@ -1092,8 +1105,6 @@ 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` instead?
 def is_dynamic(file_path):
     with open(file_path, 'rb') as handle:
         try:
@@ -1269,11 +1280,6 @@ 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"]
@@ -1366,9 +1372,6 @@ 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": {}}
@@ -1391,8 +1394,6 @@ 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():
@@ -1700,3 +1701,23 @@ def get_subject_info(static_data):
         'right_malleolar_width'
     ])
     return info
+
+
+def height_to_mm(height):
+    if 0 < height < 300:
+        logger.info(f"Subject height ({height}) assumed to be in cm. Converting to mm.")
+        return height * 10
+
+    return height
+
+
+def validate_static_data(static_data):
+    missing = [key for key in required_measurements if not static_data.get(key)]
+    if missing:
+        raise ParserError("Subject measurements missing:\n- " + "\n- ".join(missing))
+
+    static_data['Height'] = height_to_mm(static_data['Height'])
+
+    # Cap age at 18.
+    # Current shape model is paediatric only, ages over 18 can give strange results.
+    static_data['Age'] = min(static_data['Age'], 18)

{c3d_parser-1.5.4 → c3d_parser-1.6.0}/src/c3d_parser/view/main_window.py

@@ -17,7 +17,7 @@ from ll_visualiser.visualiser import visualise_model
 
 from c3d_parser.core.c3d_parser import (parse_session, extract_static_data, extract_marker_names, is_dynamic,
     CancelException, write_normalised_grfs, write_normalised_kinematics, write_normalised_kinetics,
-    write_spatiotemporal_data, approximate_anthropometrics)
+    write_spatiotemporal_data, approximate_anthropometrics, height_to_mm)
 from c3d_parser.settings.general import (APPLICATION_NAME, VERSION, DEFAULT_STYLE_SHEET, INVALID_STYLE_SHEET,
                                          get_marker_maps_dir)
 from c3d_parser.view.ui.ui_main_window import Ui_MainWindow
@@ -57,7 +57,6 @@ class ProgressTracker(QObject):
     progress = Signal(str, str)
 
 
-# TODO: CGM2 event detector on GitHub...?
 class MainWindow(QMainWindow):
 
     def __init__(self):
@@ -124,7 +123,6 @@ class MainWindow(QMainWindow):
         self._kinetic_curves.signals.cycles_included.connect(self._update_cycle_count)
 
     def _setup_progress_bar(self):
-        self._progress_text = ""
         self._progress_value = 0
         self._ui.progressBar.setVisible(False)
 
@@ -160,7 +158,6 @@ class MainWindow(QMainWindow):
         self._plotter.clear_actors()
 
     def _clear_progress_bar(self):
-        self._progress_text = ""
         self._ui.labelProgress.setText("")
         self._progress_value = 0
         self._ui.progressBar.setValue(0)
@@ -259,12 +256,6 @@ 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):
 
         # Temporarily disable spatio-temporal visualisation for running gait.
@@ -460,33 +451,32 @@ class MainWindow(QMainWindow):
                 self._set_subject_info(static_trial)
                 self._static_trial = static_trial
 
-            # Fill in any anthropometric gaps.
-            if self._approximate_anthropometrics:
-                input_directory = self._ui.lineEditInputDirectory.text()
-                lab = self._ui.comboBoxLab.currentText()
-                marker_diameter = self._ui.doubleSpinBoxMarkerDiameter.value()
-                c3d_file = os.path.normpath(os.path.join(input_directory, static_trial))
-                anthropometrics = approximate_anthropometrics(c3d_file, lab, marker_diameter)
-
-                if not self._ui.doubleSpinBoxASISWidth.value():
-                    self._ui.doubleSpinBoxASISWidth.setValue(anthropometrics['inter_asis_distance'])
-                if not self._ui.doubleSpinBoxLeftLegLength.value():
-                    self._ui.doubleSpinBoxLeftLegLength.setValue(anthropometrics['left_leg_length'])
-                if not self._ui.doubleSpinBoxLeftKneeWidth.value():
-                    self._ui.doubleSpinBoxLeftKneeWidth.setValue(anthropometrics['left_knee_width'])
-                if not self._ui.doubleSpinBoxLeftAnkleWidth.value():
-                    self._ui.doubleSpinBoxLeftAnkleWidth.setValue(anthropometrics['left_ankle_width'])
-                if not self._ui.doubleSpinBoxRightLegLength.value():
-                    self._ui.doubleSpinBoxRightLegLength.setValue(anthropometrics['right_leg_length'])
-                if not self._ui.doubleSpinBoxRightKneeWidth.value():
-                    self._ui.doubleSpinBoxRightKneeWidth.setValue(anthropometrics['right_knee_width'])
-                if not self._ui.doubleSpinBoxRightAnkleWidth.value():
-                    self._ui.doubleSpinBoxRightAnkleWidth.setValue(anthropometrics['right_ankle_width'])
+                # Fill in any anthropometric gaps.
+                if self._approximate_anthropometrics:
+                    input_directory = self._ui.lineEditInputDirectory.text()
+                    lab = self._ui.comboBoxLab.currentText()
+                    marker_diameter = self._ui.doubleSpinBoxMarkerDiameter.value()
+                    c3d_file = os.path.normpath(os.path.join(input_directory, static_trial))
+                    anthropometrics = approximate_anthropometrics(c3d_file, lab, marker_diameter)
+
+                    if not self._ui.doubleSpinBoxASISWidth.value():
+                        self._ui.doubleSpinBoxASISWidth.setValue(anthropometrics['inter_asis_distance'])
+                    if not self._ui.doubleSpinBoxLeftLegLength.value():
+                        self._ui.doubleSpinBoxLeftLegLength.setValue(anthropometrics['left_leg_length'])
+                    if not self._ui.doubleSpinBoxLeftKneeWidth.value():
+                        self._ui.doubleSpinBoxLeftKneeWidth.setValue(anthropometrics['left_knee_width'])
+                    if not self._ui.doubleSpinBoxLeftAnkleWidth.value():
+                        self._ui.doubleSpinBoxLeftAnkleWidth.setValue(anthropometrics['left_ankle_width'])
+                    if not self._ui.doubleSpinBoxRightLegLength.value():
+                        self._ui.doubleSpinBoxRightLegLength.setValue(anthropometrics['right_leg_length'])
+                    if not self._ui.doubleSpinBoxRightKneeWidth.value():
+                        self._ui.doubleSpinBoxRightKneeWidth.setValue(anthropometrics['right_knee_width'])
+                    if not self._ui.doubleSpinBoxRightAnkleWidth.value():
+                        self._ui.doubleSpinBoxRightAnkleWidth.setValue(anthropometrics['right_ankle_width'])
 
         # Check height units.
         height = self._ui.doubleSpinBoxHeight.value()
-        if height < 250:
-            self._ui.doubleSpinBoxHeight.setValue(height * 10)
+        self._ui.doubleSpinBoxHeight.setValue(height_to_mm(height))
 
 
     def _clear_subject_info(self):
@@ -586,10 +576,6 @@ class MainWindow(QMainWindow):
             'Right Leg Length': self._ui.doubleSpinBoxRightLegLength.value(),
         }
 
-        # Cap age at 18.
-        # Current shape model is paediatric only, ages over 18 can give strange results.
-        static_data['Age'] = min(static_data['Age'], 18)
-
         missing = [key for key, value in static_data.items() if not value]
         if 'Left Leg Length' in missing or 'Right Leg Length' in missing:
             reply = QMessageBox.warning(self, "Warning", "Leg length measurements missing. You can continue "
@@ -604,10 +590,6 @@ class MainWindow(QMainWindow):
             QMessageBox.warning(self, "Warning", "Subject measurements missing:\n- " + "\n- ".join(missing))
             return
 
-        if static_data['Height'] < 300:
-            QMessageBox.warning(self, "Warning", "Please ensure subject height is in mm.")
-            return
-
         optimise_knee_axis = self._optimise_knee_axis
         if not dynamic_trials:
             reply = QMessageBox.information(self, "No Dynamic Trials",
@@ -685,7 +667,6 @@ class MainWindow(QMainWindow):
 
     def _update_progress(self, message, color):
         self._ui.labelProgress.setText(message)
-        self._progress_text = message
         self._ui.labelProgress.setStyleSheet(f"color: {color};")
 
         self._progress_value = min(self._progress_value + 20, 100)
@@ -910,8 +891,6 @@ 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()
@@ -939,7 +918,6 @@ 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():
@@ -1010,6 +988,7 @@ class MainWindow(QMainWindow):
         dlg.exec()
         self._reset_lab_combo_box()
 
+    @handle_runtime_error
     def _handle_error(self, e):
         raise e
 
@@ -1031,8 +1010,6 @@ 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())
@@ -1237,9 +1214,6 @@ 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-1.5.4 → c3d_parser-1.6.0/src/c3d_parser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.5.4
+Version: 1.6.0
 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
@@ -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==0.8.3
+Requires-Dist: opensim-model-creator==0.10.0
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.5.4 → c3d_parser-1.6.0}/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==0.8.3
+opensim-model-creator==0.10.0
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.5.4/src/c3d_parser/__init__.py

@@ -1,2 +0,0 @@
-
-__version__ = "1.5.4"