c3d-parser 0.3.0__tar.gz → 0.4.0__tar.gz

{c3d_parser-0.3.0/src/c3d_parser.egg-info → c3d_parser-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 0.3.0
+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>=0.1.18
+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-0.3.0 → 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>=0.1.18
+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-0.3.0 → c3d_parser-0.4.0}/src/c3d_parser/application.py

@@ -2,9 +2,6 @@
 import sys
 import ctypes
 
-from PySide6.QtWidgets import QApplication
-
-from c3d_parser.view.main_window import MainWindow
 from c3d_parser.settings.general import (set_applications_settings, application_instance_exists,
     start_application_server, setup_marker_maps_dir)
 from c3d_parser.settings.logging import initialise_logger, filter_c3d_warnings
@@ -15,7 +12,14 @@ def main():
         my_app_id = 'Motion_Connect.C3D_Parser'
         ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(my_app_id)
 
+    from PySide6.QtWidgets import QApplication
     app = QApplication(sys.argv)
+
+    from c3d_parser.splashscreen import SplashScreen
+    splash = SplashScreen()
+    splash.show()
+
+    splash.showMessage("Loading settings ...", 5)
     set_applications_settings(app)
     setup_marker_maps_dir()
 
@@ -25,12 +29,20 @@ def main():
         sys.exit(1)
     app_server = start_application_server()
 
+    splash.showMessage('Initialising logger ...', 20)
     initialise_logger()
     filter_c3d_warnings()
 
+    splash.showMessage('Importing dependencies ...', 40)
+    from c3d_parser.view.main_window import MainWindow
+    splash.showMessage('Creating main window ...', 80)
     window = MainWindow()
+    splash.showMessage('Showing main window ...', 90)
     window.show()
 
+    splash.showMessage('Load complete ...', 100)
+    splash.finish(window)
+
     sys.exit(app.exec())
 
 

{c3d_parser-0.3.0 → c3d_parser-0.4.0}/src/c3d_parser/core/c3d_parser.py

@@ -76,11 +76,11 @@ def parse_session(static_trial, dynamic_trials, input_directory, output_director
         grf_file_paths[trial] = grf_file_path
         deidentified_file_names[trial] = os.path.basename(trc_file_path).rsplit(".", 1)[0]
 
-    dynamic_trc_path = list(trc_file_paths.values())[0] if dynamic_trials else ""
+    dynamic_trc_path = list(trc_file_paths.values())[0] if trc_file_paths else ""
     osim_model = create_osim_model(static_trc_path, dynamic_trc_path, frame, marker_diameter, static_data,
                                    output_directory, optimise_knee_axis, progress_tracker)
 
-    if not dynamic_trials:
+    if not trc_file_paths:
         raise CancelException("No dynamic trials found.")
 
     progress_tracker.progress.emit("Running IK and ID", "black")
@@ -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
@@ -408,7 +412,7 @@ def resample_data(frame_data, data_rate, frequency=100):
 
     start_time = frame_data.iloc[:, 0].iat[0]
     end_time = frame_data.iloc[:, 0].iat[-1]
-    number_of_frames = int((end_time - start_time) * frequency)
+    number_of_frames = round((end_time - start_time) * frequency) + 1
     time_array = np.linspace(start_time, end_time, number_of_frames)
 
     resampled_frame_data = pd.DataFrame(columns=frame_data.columns)
@@ -435,7 +439,7 @@ def resample_data(frame_data, data_rate, frequency=100):
         for i in range(resampled_trajectory.shape[0]):
             flattened_array[i] = resampled_trajectory[i]
         resampled_frame_data.loc[:, column] = flattened_array
-        resampled_frame_data.index = pd.RangeIndex(start=1, stop=len(resampled_frame_data) + 1, step=1)
+        resampled_frame_data.index = pd.RangeIndex(start=0, stop=len(resampled_frame_data), step=1)
 
     return resampled_frame_data
 
@@ -552,9 +556,12 @@ def extract_data(file_path, start_frame, end_frame):
 
         for i in range(event_count):
             foot = contexts[i].strip()
-            label = labels[i].strip()
-            event_time = times[i][1]
-            events[foot][event_time] = label
+            if foot:
+                label = labels[i].strip()
+                event_time = times[i][1]
+                events[foot][event_time] = label
+        if not any(events.values()):
+            raise ParserError("Event context (side) missing.")
 
         for foot in events.keys():
             events[foot] = dict(sorted(events[foot].items()))
@@ -594,6 +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)
@@ -1407,6 +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-0.3.0 → 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])