c3d-parser 1.5.0__tar.gz → 1.5.2__tar.gz

{c3d_parser-1.5.0/src/c3d_parser.egg-info → c3d_parser-1.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.5.0
+Version: 1.5.2
 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==0.8.0
+Requires-Dist: opensim-model-creator==0.8.1
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.5.0 → c3d_parser-1.5.2}/requirements.txt

@@ -3,7 +3,7 @@ numpy==1.26.4
 pandas
 c3d==0.5.2
 trc-data-reader>=0.4.1
-opensim-model-creator==0.8.0
+opensim-model-creator==0.8.1
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.5.2/src/c3d_parser/__init__.py

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

{c3d_parser-1.5.0 → c3d_parser-1.5.2}/src/c3d_parser/core/c3d_parser.py

@@ -525,10 +525,8 @@ 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 +1090,6 @@ 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 +1265,6 @@ 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 +1357,6 @@ 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 +1379,6 @@ 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():

{c3d_parser-1.5.0 → c3d_parser-1.5.2}/src/c3d_parser/view/main_window.py

@@ -57,7 +57,6 @@ class ProgressTracker(QObject):
     progress = Signal(str, str)
 
 
-# TODO: CGM2 event detector on GitHub...?
 class MainWindow(QMainWindow):
 
     def __init__(self):
@@ -118,6 +117,10 @@ class MainWindow(QMainWindow):
         self._kinematic_curves.signals.cycles_included.connect(self._grf_curves.include_cycles)
         self._kinetic_curves.signals.cycles_excluded.connect(self._grf_curves.exclude_cycles)
         self._kinetic_curves.signals.cycles_included.connect(self._grf_curves.include_cycles)
+        self._kinematic_curves.signals.cycles_excluded.connect(self._update_cycle_count)
+        self._kinematic_curves.signals.cycles_included.connect(self._update_cycle_count)
+        self._kinetic_curves.signals.cycles_excluded.connect(self._update_cycle_count)
+        self._kinetic_curves.signals.cycles_included.connect(self._update_cycle_count)
 
     def _setup_progress_bar(self):
         self._progress_text = ""
@@ -255,12 +258,6 @@ 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.
@@ -351,6 +348,8 @@ class MainWindow(QMainWindow):
         self._ui.lineEditInputDirectory.textChanged.connect(self._validate_input_directory)
         self._ui.lineEditOutputDirectory.textChanged.connect(self._validate_directory)
         self._ui.listWidgetFiles.itemChanged.connect(self._update_plot_visibility)
+        self._ui.tabWidget.currentChanged.connect(self._update_cycle_count)
+        self._ui.listWidgetFiles.itemChanged.connect(self._update_cycle_count)
         self._ui.pushButtonInputDirectoryChooser.clicked.connect(self._open_input_directory_chooser)
         self._ui.pushButtonOutputDirectoryChooser.clicked.connect(self._open_output_directory_chooser)
         self._ui.pushButtonParseData.clicked.connect(self._parse_c3d_data)
@@ -380,6 +379,7 @@ class MainWindow(QMainWindow):
         if directory_valid:
             self._scan_directory()
 
+            self._clear_curves()
             self._reset_grf_plots()
             self._reset_kinematic_plots()
             self._reset_kinetic_plots()
@@ -398,6 +398,8 @@ class MainWindow(QMainWindow):
         self._ui.pushButtonParseData.setEnabled(input_directory_valid and output_directory_valid)
         self._ui.pushButtonFinalise.setEnabled(False)
 
+        self._ui.labelCount.setVisible(not (input_directory_valid and output_directory_valid))
+
         return input_directory_valid
 
     def _open_input_directory_chooser(self):
@@ -633,6 +635,7 @@ class MainWindow(QMainWindow):
     def _parse_finished(self, result):
         self._grf_data, self._kinematic_data, self._kinetic_data, self._s_t_data, self._deidentified_file_names = result
 
+        self._clear_curves()
         self._visualise_grf_data(self._grf_data)
         self._visualise_kinematic_data(self._kinematic_data)
         self._visualise_kinetic_data(self._kinetic_data)
@@ -640,9 +643,12 @@ class MainWindow(QMainWindow):
         self._visualise_model()
 
         self._show_selected_trials()
+        self._update_cycle_count()
         logger.info("Process completed successfully.")
         self._progress_tracker.progress.emit("Process completed successfully", "green")
 
+        self._ui.labelCount.setVisible(True)
+
         self._ui.pushButtonParseData.setEnabled(True)
         self._ui.pushButtonFinalise.setEnabled(True)
         self._ui.progressBar.setVisible(False)
@@ -703,6 +709,11 @@ class MainWindow(QMainWindow):
         logger.info(f"Final outputs written to {self._output_directory}.")
         self._progress_tracker.progress.emit(f"Final outputs written to {self._output_directory}", "green")
 
+    def _clear_curves(self):
+        self._grf_curves.clear()
+        self._kinematic_curves.clear()
+        self._kinetic_curves.clear()
+
     def _reset_grf_plots(self):
         self._plot_x.clear()
         self._plot_y.clear()
@@ -795,10 +806,8 @@ class MainWindow(QMainWindow):
                 plot.set_ylim(-30, 70)
             elif i == 6:
                 plot.set_ylim(-15, 75)
-            elif i in [7, 8]:
+            elif i == 7:
                 plot.set_ylim(-50, 30)
-            elif i == 9:
-                plot.set_ylim(-60, 30)
             else:
                 plot.set_ylim(-30, 30)
             plot.axhline(y=0, color='gray', linewidth=1.0, zorder=1)
@@ -880,6 +889,30 @@ class MainWindow(QMainWindow):
             item = self._ui.listWidgetFiles.item(i)
             self._update_plot_visibility(item)
 
+    def _update_cycle_count(self):
+        def update_count(data, curves):
+            excluded_cycles = curves.get_excluded_cycles()
+            selected_trials = self._get_selected_trials()
+
+            counts = defaultdict(int)
+            for foot, files_dict in data.items():
+                for file_name, cycles in files_dict.items():
+                    if file_name not in selected_trials:
+                        continue
+                    for cycle_number in cycles:
+                        if (file_name, f"{foot}_{cycle_number}") not in excluded_cycles:
+                            counts[foot] += 1
+
+            self._ui.labelCount.setText(f"Cycles: L {counts['Left']} / R {counts['Right']}")
+
+        tab = self._ui.tabWidget.currentWidget()
+        if tab == self._ui.tabKinematic:
+            update_count(self._kinematic_data, self._kinematic_curves)
+        elif tab == self._ui.tabKinetic:
+            update_count(self._kinetic_data, self._kinetic_curves)
+        else:
+            self._ui.labelCount.setText("")
+
     def _get_selected_trials(self):
         selected_trials = []
         for i in range(self._ui.listWidgetFiles.count()):
@@ -897,7 +930,6 @@ 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():
@@ -989,8 +1021,6 @@ 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())
@@ -1195,9 +1225,6 @@ 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):
@@ -1238,10 +1265,14 @@ class GaitCurves(defaultdict):
         self._canvas.draw()
 
     def include_all(self):
+        identifiers = []
         for file_name, cycles in self.items():
+            identifiers.extend((file_name, cycle) for cycle in cycles)
             self.include_trial(file_name)
         self._selected_curves = []
 
+        self.signals.cycles_included.emit(identifiers)
+
     def include_trial(self, file_name):
         for cycle in self[file_name].keys():
             colour = self._colour_left if "Left" in cycle else self._colour_right
@@ -1301,10 +1332,14 @@ class GaitCurves(defaultdict):
         self._canvas.draw()
 
     def exclude_all(self):
+        identifiers = []
         for file_name, cycles in self.items():
+            identifiers.extend((file_name, cycle) for cycle in cycles)
             self.exclude_trial(file_name)
         self._selected_curves = []
 
+        self.signals.cycles_excluded.emit(identifiers)
+
     def exclude_trial(self, file_name):
         for cycle in self[file_name].keys():
             colour = self._colour_left if "Left" in cycle else self._colour_right
@@ -1328,6 +1363,16 @@ class GaitCurves(defaultdict):
     def get_excluded_cycles(self):
         return self._excluded_cycles
 
+    def clear(self):
+        for cursor in self._cursors.values():
+            cursor.remove()
+        self._cursors = {}
+
+        self._selected_curves = []
+        self._excluded_cycles = set()
+
+        super().clear()
+
     def clear_selected(self):
         for (file_name, cycle) in self._selected_curves:
             colour = self._colour_left if "Left" in cycle else self._colour_right

{c3d_parser-1.5.0 → c3d_parser-1.5.2}/src/c3d_parser/view/ui/ui_main_window.py

@@ -637,6 +637,11 @@ class Ui_MainWindow(object):
         self.horizontalLayout_7.setSpacing(8)
         self.horizontalLayout_7.setObjectName(u"horizontalLayout_7")
         self.horizontalLayout_7.setContentsMargins(6, 1, 16, -1)
+        self.labelCount = QLabel(self.frameVisualisation)
+        self.labelCount.setObjectName(u"labelCount")
+
+        self.horizontalLayout_7.addWidget(self.labelCount)
+
         self.horizontalSpacer = QSpacerItem(40, 20, QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Minimum)
 
         self.horizontalLayout_7.addItem(self.horizontalSpacer)
@@ -766,6 +771,7 @@ class Ui_MainWindow(object):
         ___qtablewidgetitem3.setText(QCoreApplication.translate("MainWindow", u"Description", None));
         self.checkBoxSuppressWarnings.setText(QCoreApplication.translate("MainWindow", u"Suppress warnings", None))
         self.tabWidget.setTabText(self.tabWidget.indexOf(self.tabLog), QCoreApplication.translate("MainWindow", u"Log", None))
+        self.labelCount.setText("")
         self.labelProgress.setText("")
         self.menuFile.setTitle(QCoreApplication.translate("MainWindow", u"File", None))
         self.menuView.setTitle(QCoreApplication.translate("MainWindow", u"View", None))

{c3d_parser-1.5.0 → c3d_parser-1.5.2/src/c3d_parser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.5.0
+Version: 1.5.2
 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==0.8.0
+Requires-Dist: opensim-model-creator==0.8.1
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors

{c3d_parser-1.5.0 → c3d_parser-1.5.2}/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==0.8.0
+opensim-model-creator==0.8.1
 PySide6
 matplotlib
 mplcursors

c3d_parser-1.5.0/src/c3d_parser/__init__.py

@@ -1,2 +0,0 @@
-
-__version__ = "1.5.0"