c3d-parser 1.6.1__tar.gz → 1.6.2__tar.gz

{c3d_parser-1.6.1/src/c3d_parser.egg-info → c3d_parser-1.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.6.1
+Version: 1.6.2
 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
@@ -81,7 +81,7 @@ these classifications by right-clicking on the item in question. You can exclude
 from the analysis by using the check-boxes provided.
 
 <p align="center">
-  <img src="res/images/Inputs.png" alt="Inputs Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Inputs.png" alt="Inputs Screenshot"/>
 </p>
 
 You can also specify an "Output" directory if you wish. By default, an output structure will be
@@ -94,7 +94,7 @@ filled using the metadata in your static C3D file. Confirm these values are accu
 any gaps.
 
 <p align="center">
-  <img src="res/images/Anthropometrics.png" alt="Anthropometrics Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Anthropometrics.png" alt="Anthropometrics Screenshot"/>
 </p>
 
 
@@ -107,7 +107,7 @@ The visualisation tab displays the generated model and the predicted landmark po
 these against the (skin-padding adjusted) experimental marker positions.
 
 <p align="center">
-  <img src="res/images/Visualiser.png" alt="Visualiser Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Visualiser.png" alt="Visualiser Screenshot"/>
 </p>
 
 
@@ -127,12 +127,12 @@ select "Exclude Selected Cycles". Similarly, it is also possible to exclude/incl
 sections of data for specific trials by right-clicking on the trial name in the list of trials.
 
 <p align="center">
-  <img src="res/images/Exclusion_01.png" alt="Exclusion 01"/>
-  <img src="res/images/Exclusion_02.png" alt="Exclusion 02"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_01.png" alt="Exclusion 01"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_02.png" alt="Exclusion 02"/>
 </p>
 <p align="center">
-  <img src="res/images/Exclusion_03.png" alt="Exclusion 03"/>
-  <img src="res/images/Exclusion_04.png" alt="Exclusion 04"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_03.png" alt="Exclusion 03"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_04.png" alt="Exclusion 04"/>
 </p>
 
 The "Spatio-temporal" tab supports exclusions in the same manner.
@@ -146,7 +146,7 @@ User settings are available under _View_ -> _Options_.
 All settings are retained after you close the application.
 
 <p align="center">
-  <img src="res/images/Options.png" alt="Options Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Options.png" alt="Options Screenshot"/>
 </p>
 
 **File**  
@@ -172,7 +172,7 @@ please deselect these options.
 **Inverse Kinematics**  
 If you wish to define custom marker weights, you may do so by providing your own IK task set file.
 Please follow the format used in the C3D-Parser
-[default IK task set](src/c3d_parser/core/osim_resources/ik_task_set.xml).
+[default IK task set](https://github.com/musculoskeletal/c3d-parser/blob/main/src/c3d_parser/core/osim_resources/ik_task_set.xml).
 
 
 ## Custom Marker Sets
@@ -182,7 +182,7 @@ not fit your needs you can adjust one of the existing marker sets or create a ne
 using the custom marker set dialog under "Marker" -> "Custom Marker Set".
 
 <p align="center">
-  <img src="res/images/Custom_Marker_Set.png" alt="Custom Marker Set Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Custom_Marker_Set.png" alt="Custom Marker Set Screenshot"/>
 </p>
 
 You can import an initial mapping from one of the existing marker sets using the "Import" button.

{c3d_parser-1.6.1 → c3d_parser-1.6.2}/README.md

@@ -59,7 +59,7 @@ these classifications by right-clicking on the item in question. You can exclude
 from the analysis by using the check-boxes provided.
 
 <p align="center">
-  <img src="res/images/Inputs.png" alt="Inputs Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Inputs.png" alt="Inputs Screenshot"/>
 </p>
 
 You can also specify an "Output" directory if you wish. By default, an output structure will be
@@ -72,7 +72,7 @@ filled using the metadata in your static C3D file. Confirm these values are accu
 any gaps.
 
 <p align="center">
-  <img src="res/images/Anthropometrics.png" alt="Anthropometrics Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Anthropometrics.png" alt="Anthropometrics Screenshot"/>
 </p>
 
 
@@ -85,7 +85,7 @@ The visualisation tab displays the generated model and the predicted landmark po
 these against the (skin-padding adjusted) experimental marker positions.
 
 <p align="center">
-  <img src="res/images/Visualiser.png" alt="Visualiser Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Visualiser.png" alt="Visualiser Screenshot"/>
 </p>
 
 
@@ -105,12 +105,12 @@ select "Exclude Selected Cycles". Similarly, it is also possible to exclude/incl
 sections of data for specific trials by right-clicking on the trial name in the list of trials.
 
 <p align="center">
-  <img src="res/images/Exclusion_01.png" alt="Exclusion 01"/>
-  <img src="res/images/Exclusion_02.png" alt="Exclusion 02"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_01.png" alt="Exclusion 01"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_02.png" alt="Exclusion 02"/>
 </p>
 <p align="center">
-  <img src="res/images/Exclusion_03.png" alt="Exclusion 03"/>
-  <img src="res/images/Exclusion_04.png" alt="Exclusion 04"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_03.png" alt="Exclusion 03"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_04.png" alt="Exclusion 04"/>
 </p>
 
 The "Spatio-temporal" tab supports exclusions in the same manner.
@@ -124,7 +124,7 @@ User settings are available under _View_ -> _Options_.
 All settings are retained after you close the application.
 
 <p align="center">
-  <img src="res/images/Options.png" alt="Options Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Options.png" alt="Options Screenshot"/>
 </p>
 
 **File**  
@@ -150,7 +150,7 @@ please deselect these options.
 **Inverse Kinematics**  
 If you wish to define custom marker weights, you may do so by providing your own IK task set file.
 Please follow the format used in the C3D-Parser
-[default IK task set](src/c3d_parser/core/osim_resources/ik_task_set.xml).
+[default IK task set](https://github.com/musculoskeletal/c3d-parser/blob/main/src/c3d_parser/core/osim_resources/ik_task_set.xml).
 
 
 ## Custom Marker Sets
@@ -160,7 +160,7 @@ not fit your needs you can adjust one of the existing marker sets or create a ne
 using the custom marker set dialog under "Marker" -> "Custom Marker Set".
 
 <p align="center">
-  <img src="res/images/Custom_Marker_Set.png" alt="Custom Marker Set Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Custom_Marker_Set.png" alt="Custom Marker Set Screenshot"/>
 </p>
 
 You can import an initial mapping from one of the existing marker sets using the "Import" button.

c3d_parser-1.6.2/src/c3d_parser/__init__.py

@@ -0,0 +1,2 @@
+
+__version__ = "1.6.2"

{c3d_parser-1.6.1 → c3d_parser-1.6.2}/src/c3d_parser/core/c3d_parser.py

@@ -550,10 +550,8 @@ 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
@@ -1117,8 +1115,6 @@ 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:
@@ -1294,11 +1290,6 @@ 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"]
@@ -1391,9 +1382,6 @@ 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": {}}
@@ -1416,8 +1404,6 @@ 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-1.6.1 → c3d_parser-1.6.2}/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):
@@ -257,12 +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.
@@ -898,8 +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()
@@ -927,7 +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():
@@ -1020,8 +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())
@@ -1226,9 +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-1.6.1 → c3d_parser-1.6.2/src/c3d_parser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: c3d-parser
-Version: 1.6.1
+Version: 1.6.2
 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
@@ -81,7 +81,7 @@ these classifications by right-clicking on the item in question. You can exclude
 from the analysis by using the check-boxes provided.
 
 <p align="center">
-  <img src="res/images/Inputs.png" alt="Inputs Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Inputs.png" alt="Inputs Screenshot"/>
 </p>
 
 You can also specify an "Output" directory if you wish. By default, an output structure will be
@@ -94,7 +94,7 @@ filled using the metadata in your static C3D file. Confirm these values are accu
 any gaps.
 
 <p align="center">
-  <img src="res/images/Anthropometrics.png" alt="Anthropometrics Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Anthropometrics.png" alt="Anthropometrics Screenshot"/>
 </p>
 
 
@@ -107,7 +107,7 @@ The visualisation tab displays the generated model and the predicted landmark po
 these against the (skin-padding adjusted) experimental marker positions.
 
 <p align="center">
-  <img src="res/images/Visualiser.png" alt="Visualiser Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Visualiser.png" alt="Visualiser Screenshot"/>
 </p>
 
 
@@ -127,12 +127,12 @@ select "Exclude Selected Cycles". Similarly, it is also possible to exclude/incl
 sections of data for specific trials by right-clicking on the trial name in the list of trials.
 
 <p align="center">
-  <img src="res/images/Exclusion_01.png" alt="Exclusion 01"/>
-  <img src="res/images/Exclusion_02.png" alt="Exclusion 02"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_01.png" alt="Exclusion 01"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_02.png" alt="Exclusion 02"/>
 </p>
 <p align="center">
-  <img src="res/images/Exclusion_03.png" alt="Exclusion 03"/>
-  <img src="res/images/Exclusion_04.png" alt="Exclusion 04"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_03.png" alt="Exclusion 03"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Exclusion_04.png" alt="Exclusion 04"/>
 </p>
 
 The "Spatio-temporal" tab supports exclusions in the same manner.
@@ -146,7 +146,7 @@ User settings are available under _View_ -> _Options_.
 All settings are retained after you close the application.
 
 <p align="center">
-  <img src="res/images/Options.png" alt="Options Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Options.png" alt="Options Screenshot"/>
 </p>
 
 **File**  
@@ -172,7 +172,7 @@ please deselect these options.
 **Inverse Kinematics**  
 If you wish to define custom marker weights, you may do so by providing your own IK task set file.
 Please follow the format used in the C3D-Parser
-[default IK task set](src/c3d_parser/core/osim_resources/ik_task_set.xml).
+[default IK task set](https://github.com/musculoskeletal/c3d-parser/blob/main/src/c3d_parser/core/osim_resources/ik_task_set.xml).
 
 
 ## Custom Marker Sets
@@ -182,7 +182,7 @@ not fit your needs you can adjust one of the existing marker sets or create a ne
 using the custom marker set dialog under "Marker" -> "Custom Marker Set".
 
 <p align="center">
-  <img src="res/images/Custom_Marker_Set.png" alt="Custom Marker Set Screenshot"/>
+  <img src="https://raw.githubusercontent.com/musculoskeletal/c3d-parser/main/res/images/Custom_Marker_Set.png" alt="Custom Marker Set Screenshot"/>
 </p>
 
 You can import an initial mapping from one of the existing marker sets using the "Import" button.

c3d_parser-1.6.1/src/c3d_parser/__init__.py

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