c3d-parser 0.3.4__tar.gz → 0.4.0__tar.gz

{c3d_parser-0.3.4/src/c3d_parser.egg-info → c3d_parser-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 0.3.4
+Version: 0.4.0
 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
@@ -12,10 +12,12 @@ 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>=0.1.19
+Requires-Dist: opensim-model-creator>=0.2.0
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors
+Requires-Dist: pyvistaqt
+Requires-Dist: ll-visualiser
 Dynamic: license-file
 
 # C3D-parser

{c3d_parser-0.3.4 → c3d_parser-0.4.0}/requirements.txt

@@ -3,7 +3,9 @@ numpy==1.26.4
 pandas
 c3d==0.5.2
 trc-data-reader
-opensim-model-creator>=0.1.19
+opensim-model-creator>=0.2.0
 PySide6
 matplotlib
 mplcursors
+pyvistaqt
+ll-visualiser

c3d_parser-0.4.0/src/c3d_parser/__init__.py

@@ -0,0 +1,2 @@
+
+__version__ = "0.4.0"

{c3d_parser-0.3.4 → c3d_parser-0.4.0}/src/c3d_parser/core/c3d_parser.py

@@ -329,6 +329,8 @@ def harmonise_markers(frame_data, lab, required_markers):
     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:
@@ -382,8 +384,10 @@ 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
@@ -597,6 +601,14 @@ def extract_data(file_path, start_frame, end_frame):
     return analog_data, reader.analog_rate, trimmed_events, plate_count, corners
 
 
+# TODO: Georgio asked if we could maybe provide a way to approximate some of these values (from markers),
+#   if they haven't measured them.
+#   ...
+#   Thor suggests taking this value from the model.
+#   ...
+#   Discuss this with Elyse to see if she's Ok with this/
+#   If she can get the other labs to agree/
+#   See how each lab measures this.
 def extract_static_data(file_path):
     with open(file_path, 'rb') as handle:
         reader = c3d.Reader(handle)
@@ -1410,6 +1422,11 @@ def add_medial_knee_markers(frame_data, left_knee_width, right_knee_width, marke
 def create_osim_model(static_trc, dynamic_trc, static_marker_data, marker_diameter, static_data,
                       output_directory, optimise_knee_axis, progress_tracker):
 
+    # TODO: Lazy import this here.
+    #   Reduce startup time.
+    #   We might be able to "warm up" this import in the background before we get here as well.
+    # from opensim_model_creator.Create_Model import create_model
+
     static_marker_data = static_marker_data.drop("Time").to_dict()
     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()}

{c3d_parser-0.3.4 → c3d_parser-0.4.0}/src/c3d_parser/core/osim.py

@@ -18,6 +18,11 @@ def perform_ik(osim_file, trc_file, output_file):
     ik_tool.setModel(model)
     ik_tool.setMarkerDataFileName(trc_file)
     ik_tool.set_IKTaskSet(osim.IKTaskSet(IK_TASK_SET))
+
+    # TODO: Fix Teresa's OpenSim issue.
+    # ik_tool.setResultsDir(r"C:\Users\MyUser\AppData\Local\MyApp\results")
+    # ik_tool.setResultsDir(output_directory)
+
     ik_tool.setOutputMotionFileName(output_file)
     ik_tool.set_report_errors(False)
     ik_tool.run()
@@ -34,9 +39,13 @@ def perform_id(osim_file, ik_file, grf_file, output_file):
     id_tool = osim.InverseDynamicsTool()
     id_tool.setModel(model)
     id_tool.setCoordinatesFileName(ik_file)
+
+    # TODO: Temporarily disable.
     id_tool.setExternalLoadsFileName(external_loads_file)
+    
     id_tool.setResultsDir(output_directory)
     id_tool.setOutputGenForceFileName(output_file_name)
+    # TODO: We shouldn't need this since the data (IK results) are already filtered.
     id_tool.setLowpassCutoffFrequency(6)
     id_tool.setStartTime(time_values[0])
     id_tool.setEndTime(time_values[-1])

{c3d_parser-0.3.4 → c3d_parser-0.4.0}/src/c3d_parser/view/main_window.py

@@ -12,6 +12,8 @@ from PySide6.QtWidgets import (QApplication, QMainWindow, QMenu, QFileDialog, QL
                                QWidget, QVBoxLayout, QHBoxLayout)
 from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg
 from matplotlib.figure import Figure
+from pyvistaqt import QtInteractor
+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_kinematics, write_normalised_kinetics, write_spatiotemporal_data)
@@ -53,6 +55,13 @@ 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):
@@ -86,6 +95,7 @@ class MainWindow(QMainWindow):
         self._load_settings()
         self._setup_progress_bar()
         self._validate_directory()
+        self._setup_visualiser()
 
         self._grf_curves = GaitCurves(self._grf_canvas)
         self._kinematic_curves = GaitCurves(self._kinematic_canvas)
@@ -96,6 +106,14 @@ class MainWindow(QMainWindow):
         self._progress_value = 0
         self._ui.progressBar.setVisible(False)
 
+    def _setup_visualiser(self):
+        self._plotter = QtInteractor(self._ui.tabVisualiser)
+        self._plotter.set_background('#2b2b2b')
+        self._ui.tabVisualiser.layout().addWidget(self._plotter.interactor)
+
+    def _clear_visualiser(self):
+        self._plotter.clear_actors()
+
     def _clear_progress_bar(self):
         self._progress_text = ""
         self._ui.labelProgress.setText("")
@@ -303,6 +321,7 @@ class MainWindow(QMainWindow):
             self._reset_kinematic_plots()
             self._reset_kinetic_plots()
             self._clear_spatiotemporal_data()
+            self._clear_visualiser()
 
     def _validate_directory(self):
         input_directory = self._ui.lineEditInputDirectory.text()
@@ -514,6 +533,7 @@ class MainWindow(QMainWindow):
         self._visualise_kinematic_data(self._kinematic_data)
         self._visualise_kinetic_data(self._kinetic_data)
         self._visualise_spatiotemporal_data()
+        self._visualise_model()
 
         self._show_selected_trials()
         self._progress_tracker.progress.emit("Process completed successfully", "green")
@@ -543,6 +563,15 @@ class MainWindow(QMainWindow):
         self._progress_value = min(self._progress_value + 20, 100)
         self._ui.progressBar.setValue(self._progress_value)
 
+    def _visualise_model(self):
+        model_directory = os.path.join(self._output_directory, "Models", "Meshes")
+        left_original_landmark_file = os.path.join(model_directory, 'original_lms_left.txt')
+        right_original_landmark_file = os.path.join(model_directory, 'original_lms_right.txt')
+        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')
+        visualise_model(self._plotter, model_directory, left_original_landmark_file, right_original_landmark_file,
+                        left_predicted_landmark_file, right_predicted_landmark_file)
+
     @handle_runtime_error
     def _harmonise_data(self):
         selected = self._get_selected_trials()

{c3d_parser-0.3.4 → c3d_parser-0.4.0}/src/c3d_parser/view/ui/ui_main_window.py

@@ -522,6 +522,11 @@ class Ui_MainWindow(object):
         self.verticalLayout_8.addWidget(self.scrollArea)
 
         self.tabWidget.addTab(self.tabSpatiotemporal, "")
+        self.tabVisualiser = QWidget()
+        self.tabVisualiser.setObjectName(u"tabVisualiser")
+        self.verticalLayout_13 = QVBoxLayout(self.tabVisualiser)
+        self.verticalLayout_13.setObjectName(u"verticalLayout_13")
+        self.tabWidget.addTab(self.tabVisualiser, "")
 
         self.verticalLayout_3.addWidget(self.tabWidget)
 
@@ -638,6 +643,7 @@ class Ui_MainWindow(object):
         self.tabWidget.setTabText(self.tabWidget.indexOf(self.tabKinetic), QCoreApplication.translate("MainWindow", u"Kinetic", None))
         self.tabWidget.setTabText(self.tabWidget.indexOf(self.tabGRF), QCoreApplication.translate("MainWindow", u"GRF", None))
         self.tabWidget.setTabText(self.tabWidget.indexOf(self.tabSpatiotemporal), QCoreApplication.translate("MainWindow", u"Spatio-temporal", None))
+        self.tabWidget.setTabText(self.tabWidget.indexOf(self.tabVisualiser), QCoreApplication.translate("MainWindow", u"Visualiser", None))
         self.labelProgress.setText("")
         self.menuFile.setTitle(QCoreApplication.translate("MainWindow", u"File", None))
         self.menuView.setTitle(QCoreApplication.translate("MainWindow", u"View", None))

{c3d_parser-0.3.4 → c3d_parser-0.4.0/src/c3d_parser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 0.3.4
+Version: 0.4.0
 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
@@ -12,10 +12,12 @@ 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>=0.1.19
+Requires-Dist: opensim-model-creator>=0.2.0
 Requires-Dist: PySide6
 Requires-Dist: matplotlib
 Requires-Dist: mplcursors
+Requires-Dist: pyvistaqt
+Requires-Dist: ll-visualiser
 Dynamic: license-file
 
 # C3D-parser

{c3d_parser-0.3.4 → c3d_parser-0.4.0}/src/c3d_parser.egg-info/requires.txt

@@ -3,7 +3,9 @@ numpy==1.26.4
 pandas
 c3d==0.5.2
 trc-data-reader
-opensim-model-creator>=0.1.19
+opensim-model-creator>=0.2.0
 PySide6
 matplotlib
 mplcursors
+pyvistaqt
+ll-visualiser

c3d_parser-0.3.4/src/c3d_parser/__init__.py

@@ -1,2 +0,0 @@
-
-__version__ = "0.3.4"