### Setup Vicon Nexus Packages

Source: https://pycgm2.netlify.app/installation/pycgm2_installation

Executes setup scripts for Vicon Nexus integration. The first command installs Python packages into Nexus, and the second generates a ready-to-use pipeline.

```bash
pyCGM2-setup_NexusPackages.exe
```

```bash
pyCGM2-generate_pyCGM2_Nexus.exe
```

--------------------------------

### Example CGM Settings Configuration

Source: https://pycgm2.netlify.app/faq/4.cgmdefaultsettings

This is an example of how to configure settings within the CGM settings file, such as disabling flat foot options.

```ini
Calibration:
    HJC:
        Left: Hara #[string](choice: Hara only)
        Right: Hara
    Left flat foot: 0 #[integer](choice: 0 or 1)
    Right flat foot: 0
    Head flat : 0
```

--------------------------------

### Install Vicon Nexus API and Utils

Source: https://pycgm2.netlify.app/installation/known-issues

Run these batch commands in the Miniconda prompt (as administrator) after activating your environment and navigating to the SDK folder to fix 'viconnexusapi' installation failures.

```batch
install_vicon_nexus_api.bat
```

```batch
install_vicon_nexus_utils.bat
```

--------------------------------

### Example EMG Configuration Snippet

Source: https://pycgm2.netlify.app/faq/5.emgsettings

This is an example of how to modify the emg.settings file to change muscle assignments for EMG channels. Adjust the 'Muscle' and 'Context' fields as needed.

```ini
CHANNELS:
    Voltage.EMG1 :
        Muscle : GLUMED 
        Context : Left 
        NormalActivity : GLUMED 

    Voltage.EMG2 :
        Muscle : GLUMED
        Context : Right
        NormalActivity : GLUMED
```

--------------------------------

### CGM2 Modelling via Start Processing Menu

Source: https://pycgm2.netlify.app/nexusqualisys/qtm-apps

Applies a specific CGM#i model to trials by selecting the 'CGM2 modelling' command from the QTM Start processing menu and choosing the desired CGM model.

```bash
CGM2 modelling
```

--------------------------------

### Install Package with Pip Trusted Hosts

Source: https://pycgm2.netlify.app/installation/known-issues

When installing a package with pip under a secure proxy, add these arguments to bypass SSL warnings.

```bash
pip install . --trusted-host pypi.org --trusted-host files.pythonhosted.org
```

--------------------------------

### Get Conda Installation Path

Source: https://pycgm2.netlify.app/faq/2.condapath

Open a Conda console and execute 'conda info' to display details about your Conda installation, including its path.

```bash
conda info
copy
```

--------------------------------

### CGM2 Processing via Start Processing Menu

Source: https://pycgm2.netlify.app/nexusqualisys/qtm-apps

Finalizes the analysis by running 'CGM2 processing' from the QTM Start processing menu. This processes model outputs, generates a PDF report, and exports time-normalized data.

```bash
CGM2 processing
```

--------------------------------

### Install pyCGM2 from Conda Channel

Source: https://pycgm2.netlify.app/installation/pycgm2_installation

Installs pyCGM2 and its dependencies from the official pyCGM2 conda channel. This is the standard installation method for users.

```bash
conda install -c pycgm2 pycgm2
```

--------------------------------

### Processing Specific Model Outputs

Source: https://pycgm2.netlify.app/api/gait-applications/gaitprocessing

This example demonstrates how to process only specific kinematic or kinetic parameters by providing dictionaries that map labels to desired outputs. This allows for time-normalization of selected CGM outputs based on gait events.

```python
analysisInstance = analysis.makeAnalysis(DATA_PATH,
                    modelledFilenames,
                    kinematicLabelsDict = {"Left":["LHipAngles","LKneeAngles"],"Right":["RHipAngles","RKneeAngles"]},
                    kineticLabelsDict   = {"Left":["LHipMoment","LKneePower"],"Right":["RHipMoment","RKneePower"]},
                    emgChannels = None,
                    subjectInfo={"Name":"Hannibal"},
                    experimentalInfo={"Context":"Post-Toxin"},
                    modelInfo={"model":"CGM"},
                    )

```

--------------------------------

### Create Conda Environment from YAML

Source: https://pycgm2.netlify.app/installation/pycgm2_installation

Creates a conda environment based on the 'environment.yml' file, typically used for developer installations. An optional name can be specified.

```bash
conda env create -f environment.yml
```

```bash
conda env create -f environment.yml -n newName
```

--------------------------------

### Navigate to pyCGM2 Folder

Source: https://pycgm2.netlify.app/installation/pycgm2_installation

Changes the current directory to the pyCGM2 source code folder. This is required for developer mode installation.

```bash
cd path/to/my/pycgm2/folder
```

--------------------------------

### Get Help for Specific Gait Plot Command

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/gait-plots

Use this command to view detailed input arguments and options for a specific plot command, such as plotting normalized kinematics. Refer to the API documentation for further details.

```bash
pycgm2.exe NEXUS Plots Kinematics Normalized -h
```

--------------------------------

### Run Kalman Gap Filling Method

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/gaps

Load your gait trial data and then execute the pyCGM2 command to perform gap filling using the Kalman method. Use the `-h` flag for input arguments or consult the API documentation.

```bash
pyCGM2.exe NEXUS Gaps Kalman
```

--------------------------------

### Run Gloersen Gap Filling Method

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/gaps

Load your gait trial data and then execute the pyCGM2 command to perform gap filling using the Gloersen method. Use the `-h` flag for input arguments or consult the API documentation.

```bash
pyCGM2.exe NEXUS Gaps Gloersen
```

--------------------------------

### Calibrate Static Trial with CGM1.0

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines

Use this command to perform calibration on a static trial using the CGM1.0 model within Nexus. Ensure Nexus is open and the static file is loaded.

```bash
pyCGM2.exe NEXUS CGM1.0 Calibration
```

--------------------------------

### Install pyCGM2 in Editable Mode

Source: https://pycgm2.netlify.app/installation/pycgm2_installation

Installs pyCGM2 in 'editable' mode using pip. This allows changes in the source code to be immediately reflected without reinstallation, ideal for developers.

```bash
pip install -e .
```

--------------------------------

### Activate Conda Environment

Source: https://pycgm2.netlify.app/installation/pycgm2_installation

Activates the specified conda environment. This command is used in both user and developer installation modes.

```bash
conda activate pycgm310
```

--------------------------------

### Display pyCGM2 Nexus Commands Help

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines

Run this command to view all available pyCGM2 commands for interacting with Nexus, including options for CGM models, event detection, data gap filling, plotting, and system information.

```bash
pycgm2.exe NEXUS -h
```

--------------------------------

### Run Zeni Gait Event Detection

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/events

Use this command to detect gait events using the Zeni et al 2008 algorithm. This method requires pelvic and foot markers.

```bash
pyCGM2.exe NEXUS Events Zeni
```

--------------------------------

### Fit Gait Trial and Plot Kinematics

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines

Execute these commands sequentially to fit a gait trial using CGM1.0 and then generate time-normalized kinematics plots. This is typically done after calibration.

```bash
pyCGM2.exe NEXUS CGM1.0 Fitting
```

```bash
pyCGM2.exe NEXUS Plots Kinematics Normalized
```

--------------------------------

### Getting Help for CGM Commands

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/cgm

To view the input arguments for any CGM command, append the '-h' flag to the command. This is useful for understanding and modifying default settings.

```bash
pycgm2.exe NEXUS CGM1.0 Calibration -h
```

```bash
pycgm2.exe NEXUS CGM1.0 Fitting -h
```

--------------------------------

### Run CGM Commands with Input Arguments

Source: https://pycgm2.netlify.app/faq/4.cgmdefaultsettings

Use these commands to run CGM2.3 calibration or fitting directly by specifying input arguments.

```bash
pycgm2.exe NEXUS CGM2.3 Calibration
```

```bash
pycgm2.exe NEXUS CGM2.3 Fitting
```

--------------------------------

### Create Python 3.10 Conda Environment

Source: https://pycgm2.netlify.app/installation/pycgm2_installation

Creates a new conda environment named 'pycgm310' with Python 3.10. This is a prerequisite for installing pyCGM2 in user mode.

```bash
conda create --name pycgm310 python=3.10
```

--------------------------------

### Create Environment Activation Script

Source: https://pycgm2.netlify.app/faq/3.nexusoperationpipeline

This batch script activates a Conda virtual environment. Ensure 'CONDA_PATH' and 'ENV_NAME' are set to your specific Miniconda installation and environment name.

```batch
@echo off
   
rem Set the path to your Miniconda installation directory
set "CONDA_PATH=C:\Users\fleboeuf\Miniconda3"
   
rem Set the name of your virtual environment
set "ENV_NAME=pycgm39"
   
call "%CONDA_PATH%\Scripts\activate.bat" %ENV_NAME%

```

--------------------------------

### CGM Calibration Commands (1.0-2.5)

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/cgm

Use these commands to calibrate static files for CGM models from version 1.0 to 2.5. Ensure your virtual Python environment is activated before running. Note that the calibration process does not accept gaps; crop or fill gaps in your trial data.

```bash
pycgm2.exe NEXUS CGM1.0 Calibration
```

```bash
pycgm2.exe NEXUS CGM1.1 Calibration
```

```bash
pycgm2.exe NEXUS CGM2.1 Calibration
```

```bash
pycgm2.exe NEXUS CGM2.2 Calibration
```

```bash
pycgm2.exe NEXUS CGM2.3 Calibration
```

```bash
pycgm2.exe NEXUS CGM2.4 Calibration
```

```bash
pycgm2.exe NEXUS CGM2.5 Calibration
```

--------------------------------

### List Available Gait Plot Commands

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/gait-plots

Run this command to see all available plot commands and their options. Ensure your virtual Python environment is activated before execution.

```bash
pycgm2.exe NEXUS Plots -h
```

--------------------------------

### Generate Session in QTM

Source: https://pycgm2.netlify.app/nexusqualisys/qtm-apps

Initiates a new session in QTM, creating the settings.xml file and exporting C3D files for selected trials.

```bash
generate session
```

--------------------------------

### Basic Gait Data Processing and Reporting

Source: https://pycgm2.netlify.app/api/gait-applications/gaitprocessing

This snippet demonstrates the fundamental process of creating an analysis instance from C3D files, generating descriptive kinematic and kinetic plots, spatio-temporal parameter plots, and exporting the results to a spreadsheet. It requires specifying the data path and filenames.

```python
import pyCGM2
from pyCGM2.Report import normativeDatasets
from pyCGM2.Lib import analysis
from pyCGM2.Lib import plot

# data
DATA_PATH = "c:\\pathTomydata\\"
modelledFilenames = ["gait Trial 01.c3d", "gait Trial 02.c3d"] # two gait trials with both gait event and CGMi model ouptuts


analysisInstance = analysis.makeAnalysis(DATA_PATH, modelledFilenames,
                                          emgChannels=None) # construction of the analysis instance.
normativeDataset = normativeDatasets.NormativeData("Schwartz2008","Free") # selected normative dataset

# plots
plot.plot_DescriptiveKinematic(DATA_PATH,analysisInstance,"LowerLimb",normativeDataset)
plot.plot_DescriptiveKinetic(DATA_PATH,analysisInstance,"LowerLimb",normativeDataset)
plot.plot_spatioTemporal(DATA_PATH,analysisInstance)

# export as spreadsheet
analysis.exportAnalysis(analysisInstance,DATA_PATH,"spreadsheet")

```

--------------------------------

### CGM Fitting Commands (1.0-2.5)

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/cgm

Execute these commands to fit CGM models to gait trials for versions 1.0 through 2.5. The projection of joint moments differs between CGM1.0 and later versions (1.1-2.5).

```bash
pycgm2.exe NEXUS CGM1.0 Fitting
```

```bash
pycgm2.exe NEXUS CGM1.1 Fitting
```

```bash
pycgm2.exe NEXUS CGM2.1 Fitting
```

```bash
pycgm2.exe NEXUS CGM2.2 Fitting
```

```bash
pycgm2.exe NEXUS CGM2.3 Fitting
```

```bash
pycgm2.exe NEXUS CGM2.4 Fitting
```

```bash
pycgm2.exe NEXUS CGM2.5 Fitting
```

--------------------------------

### Run Intellevent Gait Event Detection

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/events

Use this command to detect gait events using the Intellevent algorithm (Dumphart et al 2023). This deep learning-based method requires foot markers.

```bash
pyCGM2.exe NEXUS Events Intellevent
```

--------------------------------

### CGM1.0 Fitting with Custom Options

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/3argumentreferences

Configure CGM1.0 fitting with a specific marker diameter, projection method, and output suffix.

```bash
pycgm2.exe NEXUS CGM1.0 Fitting -md 16 --proj Proximal --pointSuffix test
copy
```

--------------------------------

### CGM1.0 Calibration with Short Options

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/3argumentreferences

Use short options for CGM1.0 calibration, specifying left and right flat foot, marker diameter, and enabling a check.

```bash
pycgm2.exe NEXUS CGM1.0 Calibration -l 0 -r 1 -md 16 --check
copy
```

--------------------------------

### Generate Kinematics Time-Normalized Panel

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/3argumentreferences

Creates a time-normalized kinematics panel that displays all cycles rather than the average and standard deviation corridor. It uses model outputs suffixed with '_test_' and incorporates a specific modality from a normative dataset.

```bash
pycgm2.exe NEXUS Plots Kinematics Normalized --consistency -ps test -nd Schwartz2008 -ndm VerySlow
```

--------------------------------

### Apply CGM2.1 to C3D Trials

Source: https://pycgm2.netlify.app/api/gait-applications/gaitmodelling

This code demonstrates how to apply the CGM2.1 model to C3D files for gait analysis. It includes steps for calibration and fitting, using settings from a configuration file. Ensure the necessary C3D files and settings are accessible.

```python
# -*- coding: utf-8 -*-
import os
import pyCGM2
from pyCGM2.Utils import files
from pyCGM2.Tools import btkTools
from pyCGM2.ForcePlates import forceplates
from pyCGM2 import enums
from pyCGM2.Lib.CGM import cgm2_1

LOGGER = pyCGM2.LOGGER


# data
DATA_PATH = "C:\\myPATH\\"
staticFile ="03367_05136_20200604-SBNNN-VDEF-02.c3d" # static trial
trialName = "03367_05136_20200604-GBNNN-VDEF-01.c3d" # gait trial


# setting
settings = files.loadModelSettings(DATA_PATH,"CGM2_1-pyCGM2.settings")

# CGM2.1 CALIBRATION
#-------------------

acqStatic = btkTools.smartReader(DATA_PATH+staticFile) # construct the btk.Acquisition instance

# calibration options from settings
leftFlatFoot = settings["Calibration"]["Left flat foot"]
rightFlatFoot= settings["Calibration"]["Right flat foot"]
headFlat= settings["Calibration"]["Head flat"]
translators = settings["Translators"]
markerDiameter = settings["Global"]["Marker diameter"]
HJC = settings["Calibration"]["HJC"]
pointSuffix = settings["Global"]["Point suffix"]

# anthropometric parameters
required_mp = dict()
required_mp["Bodymass"] = 75.0
required_mp["Height"]= 1750
required_mp["LeftLegLength"] = 800
required_mp["LeftKneeWidth"] = 90
required_mp["RightLegLength"] = 800
required_mp["RightKneeWidth"] = 90
required_mp["LeftAnkleWidth"] = 60
required_mp["RightAnkleWidth"] = 60
required_mp["LeftSoleDelta"] = 0
required_mp["RightSoleDelta"] = 0
required_mp["LeftShoulderOffset"] = 0
required_mp["LeftElbowWidth"] = 0
required_mp["LeftWristWidth"] = 0
required_mp["LeftHandThickness"] = 0
required_mp["RightShoulderOffset"] = 0
required_mp["RightElbowWidth"] = 0
required_mp["RightWristWidth"] = 0
required_mp["RightHandThickness"]= 0

optional_mp = dict()
optional_mp["InterAsisDistance"]= 0
optional_mp["LeftAsisTrocanterDistance"]= 0
optional_mp["LeftTibialTorsion"]= 0
optional_mp["LeftThighRotation"]= 0
optional_mp["LeftShankRotation"]= 0
optional_mp["RightAsisTrocanterDistance"]= 0
optional_mp["RightTibialTorsion"]= 0
optional_mp["RightThighRotation"]= 0
optional_mp["RightShankRotation"]= 0

# calibrate function
model,finalAcqStatic,error = cgm2_1.calibrate(DATA_PATH,
    staticFile,
    translators,
    required_mp,
    optional_mp,
    leftFlatFoot,
    rightFlatFoot,
    headFlat,
    markerDiameter,
    HJC,
    pointSuffix)

# CGM2.1 FITTING
#----------------

# fitting options from settings
momentProjection = enums.enumFromtext(settings["Fitting"]["Moment Projection"],enums.MomentProjection)
pointSuffix = settings["Global"]["Point suffix"]

# force plate assignement
acq = btkTools.smartReader(DATA_PATH+trialName) # btk.Acquisition instance
графии = forceplates.matchingFootSideOnForceplate(acq) #detect correct foot contact with a force plate

# fitting function

acqGait,detectAnomaly = cgm2_1.fitting(model,DATA_PATH, trialName,
    translators,
    markerDiameter,
    pointSuffix,
    mfpa,
    momentProjection,
    frameInit= None, frameEnd= None )# acqGait updated with CGM2.1 ouputs ( kinematics and kinetics)

# EXPORT
# ------- 
btkTools.smartWriter(acqGait, DATA_PATH+trialName[:-4]+"-modelled.c3d") # save the btk.Acquisition instance as a new c3d with the suffix "-modelled"

copy

```

--------------------------------

### View EMG Plot Commands Help

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/emg

To discover available EMG plot commands and their options, execute this command in your activated virtual Python environment.

```bash
pycgm2.exe NEXUS Plots EMG -h
copy
```

--------------------------------

### Detect Gait Events using Zeni Method

Source: https://pycgm2.netlify.app/api/gait-applications/gaitevent

Load a C3D file, detect gait events using the Zeni method, and save the modified file. Ensure the DATA_PATH is correctly set to your trial directory.

```python
import pyCGM2
from pyCGM2.Lib import eventDetector
from pyCGM2.Tools import btkTools

DATA_PATH = "C:\\myPATH\\"

# data
trialName = "03367_05136_20200604-GBNNN-VDEF-01.c3d"
acqGait = btkTools.smartReader(DATA_PATH+trialName)

# function
eventDetector.zeni(acqGait)
btkTools.smartWriter(acqGait, DATA_PATH+trialName[:-4]+"-event.c3d")

copy
```

--------------------------------

### View Normalized EMG Command Arguments

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/emg

To understand the specific input arguments required for normalized EMG commands, use this command. Ensure gait events are identified beforehand for most commands.

```bash
pycgm2.exe NEXUS Plots EMG Normalized -h
copy
```

--------------------------------

### Generate Kinematics Comparison Panel

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/3argumentreferences

Generates a kinematics comparison panel showing all cycles. This command utilizes model outputs suffixed with '_test_' and references a specific modality from a normative dataset.

```bash
pycgm2.exe NEXUS Plots Kinematics Comparison --consistency -ps test -nd Schwartz2008 -ndm VerySlow
```

--------------------------------

### Run Oconnor Gait Event Detection

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/events

Use this command to detect gait events using the Oconnor et al 2007 algorithm. This method requires foot markers.

```bash
pyCGM2.exe NEXUS Events Oconnor
```

--------------------------------

### Zeni et al 2008 Gait Event Detection with Offset

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/3argumentreferences

Apply a systematic offset to all detected foot strikes using the Zeni et al 2008 method for gait event detection.

```bash
pycgm2.exe NEXUS Events Zeni -fso 5
copy
```

--------------------------------

### Adding Metadata to Analysis Instance

Source: https://pycgm2.netlify.app/api/gait-applications/gaitprocessing

This snippet shows how to include subject, experimental, and model metadata when creating the analysis instance. This information will be included as columns in the exported spreadsheet.

```python
analysisInstance = analysis.makeAnalysis(DATA_PATH,
                    modelledFilenames,
                    emgChannels= None,
                    subjectInfo={"Name":"Hannibal"},
                    experimentalInfo={"Context":"Post-Toxin"},
                    modelInfo={"model":"CGM"},
                    )

```

--------------------------------

### Edit EMG Settings via Command Line

Source: https://pycgm2.netlify.app/faq/5.emgsettings

Use this command to edit the emg.settings file from your data folder. Ensure your virtual environment is activated and you are in the correct directory.

```bash
pycgm2.exe SETTINGS Edit -e
```

```bash
pycgm2.exe SETTINGS Edit --emg
```

--------------------------------

### CGM1.0 to CGM2.5 Calibration Commands

Source: https://pycgm2.netlify.app/nexusqualisys/vicon-apps/2commandlines/cgm

These commands are used to calibrate the CGM model. Note that the calibration process does not accept gaps, so trials must be cropped or gaps filled beforehand. Default settings include aligning the longitudinal foot axis with the ground, aligning the head's medio-lateral axis, and considering a 14mm marker diameter. These defaults can be altered using input arguments (type -h for help) or by manipulating setting files.

```APIDOC
## CGM1.0 to CGM2.5 Calibration

### Description
Calibrates the CGM model. Requires trials without gaps.

### Commands
```
pycgm2.exe NEXUS CGM1.0 Calibration
pycgm2.exe NEXUS CGM1.1 Calibration
pycgm2.exe NEXUS CGM2.1 Calibration
pycgm2.exe NEXUS CGM2.2 Calibration
pycgm2.exe NEXUS CGM2.3 Calibration
pycgm2.exe NEXUS CGM2.4 Calibration
pycgm2.exe NEXUS CGM2.5 Calibration
```

### Default Settings
- Align longitudinal foot axis with the ground (flat foot option).
- Align medio-lateral axis of the head (head flat option).
- Consider 14mm marker diameter.

### Customization
- Use input arguments: `pycgm2.exe NEXUS CGM1.0 Calibration -h` (or any CGM version).
- Manipulate setting files (see FAQ).
```

--------------------------------

### Run CGM2 Modelling via Command Line

Source: https://pycgm2.netlify.app/nexusqualisys/qtm-apps

Executes the CGM2 modelling process using the pycgm2.exe command in a conda console. Ensure your virtual environment is activated.

```bash
pycgm2.exe QTM Modelling
```