Merge pull request #3 from LiborSoumar/main

Splitting repo into 3 separate examples

Author: LiborSoumar

CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## [1.1.0]
+Split repository into three seperate ones to simplify the code  
+Settings.paf encoding changed to ANSI to better handle special characters  
+Second thorax model file was removed  
+Fix not to include inactive trials in the analysis  
+Fix to missing segment depth for Pelvis Floor segment  
+Update to Readme.md  
+Fix to measurement tagging  
+Option to select Theia c3d file in case the subject is not pose_filt_0.c3d 
+
 ## [1.0.1]
 New Theia settings available in settings.php  
 Analog data are filtered by default (cutoff: 20Hz)

README.md

@@ -1,4 +1,4 @@
-# Qualisys PAF – Theia Markerless example
+# Qualisys PAF – Theia Markerless Basic Example
 
 ## Getting started
 
@@ -10,17 +10,27 @@ To download the latest version (not tested) of the example project to your compu
 
 To download a release version (tested), please [Click here](https://github.com/qualisys/paf-theia-markerless-example/releases)
 
+## Preparing QTM project
+There are two ways how to set up the project for QTM.
+1. Simple method is to unzip the zip file and open the project from QTM (File > Open Project) or by double clicking on Settings.paf in File Explorer.
+2. If you plan to create multiple projects based on this example, unzip the zip file to `C:\Program Files (x86)\Qualisys\Qualisys Track Manager\Packages`, name the folder `Theia Markeless Example` and delete Settings.qtmproj. Then go to QTM > File > New Project and create new project based on Theia Markerless Example.
+
 ## Preparing Qualisys data for Theia3D processing
 
 1. Install [Theia](https://www.theiamarkerless.ca/) and accompanying engine.
 2. In QTM, set Project Options > Miscellaneous > Folder Options for "Theia" to ```C:\Program Files\Theia\Theia3D\Theia3D.exe``` (adapt if Theia is installed at different location).
 3. Install Visual3D.
 4. Set Project Options > Miscellaneous > Folder Options for "Visual 3d" to ```C:\Program Files\Visual3D\Visual3D.exe``` (adapt if Visual3D is installed at different location).
-5. Download data from Qualisys File Library (https://qfl.qualisys.com/#!/project/theiaexample)
-   > Note: Example data include two persons. While **John Doe** can be used with Theia to generate .c3d files (use `Markerless Session`), **Jim Doe** does not include videos and can be used to compare marker-based and markerless data (use `Marker-based vs Markerless Comparison Session`). This sesson type expects data to be captured by combined system of video cameras and marker-based cameras where markers are places on the body for the same trial that is used to capture videos. Script is set to work with sports marker set. If other marker set is required, it is necessary to adapt the script and model files accordingly.
-6. Extract downloaded .zip file into the projects data folder "Theia Markerless Example\Data"
-7. To process the data, you have to first click on **Theia and V3D Processing**
-    > Note: The following Theia specific settings along with their descriptions are available in Templates\settings.php: save_workspace, theia_filter_type, theia_filter_cutoff, enable_knee_rotation, max_people, track_rotated_people and export_type. When saving the workspace, it will create a TheiaFormatData_workspace folder in your session where each subfolder is containing the Theia workspace of a measurement. To open the workspace of a measurement, click on File > Load Workspace and select the subfolder of your choice. If Theia is closed, double-click on the results.p3d included in the subfolder of your choice.
+5. Download data from Qualisys File Library (https://qfl.qualisys.com/#!/project/theiaexample).
+
+   Example data includes three types of data:
+   1. **John Doe** can be used with this example to generate .c3d files,
+   2. **Jim Doe** is intended for markerless vs markerbased comparison example: https://github.com/qualisys/paf-theia-markerless-comparison-example. It does not include videos and can be used to compare marker-based and markerless data and is intended to be used this this repository. This sesson type expects data to be captured by combined system of video cameras and marker-based cameras where markers are places on the body for the same trial that is used to capture videos. Script is set to work with sports marker set. If other marker set is required, it is necessary to adapt the script and model files accordingly. 
+   3. **Joe Doe** is intended for true hybrid example: https://github.com/qualisys/paf-theia-markerless-true-hybrid-example. It does not include videos and can be used as an example for this repository how to add objects to markeless analysis. Objects must have markers on. It is important that both marker cameras and video camera capture at the same rate.
+6. Extract downloaded .zip file into the `Data` folder of the project.
+7. To process the data, you have to click on **Start Processing** button.
+    - The following Theia specific settings along with their descriptions are available in Templates\settings.php: `save_workspace`, `theia_filter_type`, `theia_filter_cutoff`, `enable_knee_rotation`, `max_people`, `track_rotated_people` and `export_type`. When saving the workspace, it will create a TheiaFormatData_workspace folder in your session where each subfolder is containing the Theia workspace of a measurement. To open the workspace of a measurement, click on File > Load Workspace and select the subfolder of your choice. If Theia is closed, double-click on the results.p3d included in the subfolder of your choice.  
+    - Theia can identify and process data for more then one subject if more persons are in the volume. The subject that yields best data is typically selected but sometimes other person is wrongly chosen. If that happens, there is an option to choose which c3d file is actual subject. To select other c3d, activate the measurement, navigate to `Theia c3d file` field and chose number of Theia file. To find out what c3d files Theia has created, go to working directory of active session, open `TheiaFormatData` folder, open folder of active measurement and review `pose_filt_*.c3d` files in Visual3D.
 
 ## Resources for using the Qualisys Project Automation Framework (PAF)
 
@@ -40,6 +50,8 @@ Our official examples for various processing engines:
 - [OpenSim](https://github.com/qualisys/paf-opensim-example)
 - [Python](https://github.com/qualisys/paf-python-example)
 - [Theia Markerless](https://github.com/qualisys/paf-theia-markerless-example)
+- [Theia Markerless Comparison](https://github.com/qualisys/paf-theia-markerless-comparison-example)
+- [Theia Markerless True Hybrid](https://github.com/qualisys/paf-theia-markerless-true-hybrid-example)
 - [Visual3D](https://github.com/qualisys/paf-visual3d-example)
 
 _As of QTM version 2.17, the official Qualisys PAF examples can be used without any additional license. Note that some more advanced analysis types require a license for the "PAF Framework Developer kit" (Article number 150300)._

Settings.paf

@@ -3,7 +3,7 @@ Package Information:
   Name: Theia Markerless Example
   Version: 1.0.1
   Required QTM version: 2020.2.5770
-  Encoding bytes: €€€€€
+  Encoding bytes: �����
 
 Root type: Subject
 Default fields: [Creation date, Creation time]
@@ -26,12 +26,6 @@ Types:
       Analyses: [Theia and V3D Processing]
       Display order: [Session ID, Test condition, Operator, Comments]
       Directory pattern: $Creation date$_Markerless
-    Marker-based vs Markerless Comparison Session:
-      Fields: [Session ID, Test condition, Operator]
-      Measurements: [Static, Dynamic]
-      Analyses: [Theia and V3D Comparison Processing]
-      Display order: [Session ID, Test condition, Operator, Comments]
-      Directory pattern: $Creation date$_Markerless_Comparison
 
 Measurements:
   Fields:
@@ -54,19 +48,6 @@ Analyses:
   Theia and V3D Processing:
     Type: Compound
     Components: [Internal Run Theia, Theia Tools Process, Visual3D Analysis]
-  Theia and V3D Comparison Processing:
-    Type: Compound
-    Components: [Internal Run Theia, Theia Tools Process, Visual3D Comparison]
-  Internal Run Theia:
-    Type: External program
-    Program display name: Theia
-    Do not wait for Application: Yes
-    Arguments: [-path, $TemplateDirectory$Scripts\src\Theia\theia_batch_commands.txt, -force-single-instance]
-  Theia Tools Process:
-    Type: Instantiate template
-    Export session: Yes
-    Template: Templates\Scripts\src\Theia\run_theia_tools.php
-    Export measurements: [c3d,xml settings]
   Visual3D Analysis:
     Type: External program
     Program display name: Visual 3d
@@ -75,14 +56,16 @@ Analyses:
     Arguments: [/s, $WorkingDirectory$create_workspace.v3s]
     Template files: ['*.v3s']
     Do not wait for Application: Yes
-  Visual3D Comparison:
+  Internal Run Theia:
     Type: External program
-    Program display name: Visual 3d
-    Export session: Yes
-    Export measurements: c3d
-    Arguments: [/s, $WorkingDirectory$compare.v3s]
-    Template files: ['*.v3s']
+    Program display name: Theia
     Do not wait for Application: Yes
+    Arguments: [-path, $TemplateDirectory$Scripts\src\Theia\theia_batch_commands.txt, -force-single-instance]
+  Theia Tools Process:
+    Type: Instantiate template
+    Export session: Yes
+    Template: Templates\Scripts\src\Theia\run_theia_tools.php
+    Export measurements: [c3d,xml settings]
 
 Fields:
   ID: