CGM inputs arguments
Calibration
Add the -h to the command (e.g. pycgm2.exe NEXUS CGM1.0 Calibration -h) to know the input arguments of the CGM1.0 calibration process
( replace CGM1.0 for other CGM )
example 1
pycgm2.exe NEXUS CGM1.0 Calibration -l 0 -r 1 -md 16 --check
or
pycgm2.exe NEXUS CGM1.0 Calibration --leftFlatFoot 0 --rightFlatFoot 1 --markerDiameter 16 --check
=> disable the left flat foot option, keep enable the right flat foot option, use 16mm marker diameter and add the suffix _cgm1 to model ouputs
example 2
pycgm2.exe NEXUS CGM2.1 Calibration -forceLHJC 30 50 60
=> position the left hip joint centre relative to the pelvic coordinate system with the coodinates 30 50 and 60
This table resumes all available arguments across CGM
| CGM | long options | short options | Type | Description |
|---|---|---|---|---|
| CGM1.0+ | --leftFlatFoot | -l | int | Left flat foot option |
| CGM1.0+ | --rightFlatFoot | -r | int | Right flat foot option |
| CGM1.0+ | --headFlat | -hf | int | Head flat option |
| CGM1.0+ | --markerDiameter | -md | float | Marker diameter |
| CGM1.0+ | --pointSuffix | -ps | str | Suffix of the model outputs |
| CGM1.0+ | --check | Force cgm version as model output suffix | ||
| CGM1.0+ | --resetMP | Reset the optional anthropometric parameters | ||
| CGM1.0+ | --forceMP | Force the use of the MP offsets to compute knee and ankle joint centres | ||
| CGM1.0+ | --anomalyException | -ae | Raise an exception if an anomaly is detected | |
| CGM1.0+ | --offline | nargs=2 | offline mode, need the subject name and the static c3d filename | |
| CGM2.1+ | --forceLHJC | nargs=3 | Force the position of the left hip joint centre to respect local position into the pelvic coordinate system | |
| CGM2.1+ | --forceRHJC | nargs=3 | Force the position of the right hip joint centre to respect local position into the pelvic coordinate system | |
| CGM2.2 and 2.3 | --musculoSkeletalModel | -msm | enable Musculoskeletal computation | |
| CGM2.3+ | --noIk | disbale kinematic fitting ( aka inverse kinematics) |
Fitting
Add the -h to the command (e.g. pycgm2.exe NEXUS CGM1.0 Fitting -h) to know the input arguments of the CGM1.0 calibration process
( replace CGM1.0 for other CGM )
example 1
pycgm2.exe NEXUS CGM1.0 Fitting -md 16 --proj Proximal --pointSuffix test
=> use 16mm marker diameter, project moment into the proximal coordinate system and add the suffix _test to model ouputs
This table resumes all available arguments across CGM
| CGM | long options | short options | Type | Description |
|---|---|---|---|---|
| CGM1.0+ | --markerDiameter | -md | float | Marker diameter |
| CGM1.0+ | --pointSuffix | -ps | str | Suffix of the model outputs |
| CGM1.0+ | --check | Force cgm version as model output suffix | ||
| CGM1.0+ | --anomalyException | -ae | Raise an exception if an anomaly is detected | |
| CGM1.0+ | --offline | nargs=3 | offline mode, need the subject name and the gait c3d filename and the foot force plate assignment | |
| CGM1.0+ | --frameInit | -fi | int | initial frame to process |
| CGM1.0+ | --frameEnd | -fe | int | last frame to process |
| CGM1.0+ | --proj | str | Referential to project joint moment (choice : Distal,Proximal,Global (and JCS for CGM1.1+)) | |
| CGM2.2 and 2.3 | --musculoSkeletalModel | -msm | enable Musculoskeletal computation | |
| CGM2.3+ | --accuracy | -a | float | inverse kinematic solver accuracy () |
| CGM2.3+ | --noIk | store_true | disbale kinematic fitting ( aka inverse kinematics) |
CGM2.6
Depending your functional knee calibration method, type pycgm2.exe NEXUS CGM2.6 2DOF -h) or pycgm2.exe NEXUS CGM2.6 SARA -h to know the input arguments
pycgm2.exe NEXUS CGM2.6 SARA -fi 300 -fe 600 --side Right
=> calibrate the right knee from frame 300 to 600
for both methods, the input arguments are
| long options | short options | Type | Description | |
|---|---|---|---|---|
--side | -s | str | body side ( Left or Right) | |
--frameInit | -fi | int | initial frame to process | |
--frameEnd | -fe | int | last frame to process |
Events
Zeni et al 2008 - gait event detection
pycgm2.exe NEXUS Events Zeni -fso 5
=> add an offset of 5 to all detected foot strike
| long options | short options | Type | Description | |
|---|---|---|---|---|
--footStrikeOffset | -fso | int | systematic foot strike offset on both side | |
--footOffOffset | -foo | int | systematic foot off offset on both side |
Plots
Spatio temporal plots
pycgm2.exe NEXUS Plots STP -ps test
=> build panel from spatiotemporal variables suffixed test
| long options | short options | Type | Description | |
|---|---|---|---|---|
--pointSuffix | -ps | str | consider model outputs with the given suffix |
Kinematics and kinetics - Temporal plot
pycgm2.exe NEXUS Plots Kinematics Temporal -ps test
pycgm2.exe NEXUS Plots Kinetics Temporal -ps test
=> build panel from model ouputs suffixed test
| long options | short options | Type | Description | |
|---|---|---|---|---|
--pointSuffix | -ps | str | consider model outputs with the given suffix |
Kinematics and kinetics - Time-normalized and Comparison Panels
Time-normalized and Comparison panels share similar arguments
type NEXUS Plots Kinematics Normalized -h or NEXUS Plots Kinematics Comparison -h to know the input arguments ( idem with Kinetics)
pycgm2.exe NEXUS Plots Kinematics Normalized --consistency -ps test -nd Schwartz2008 -ndm VerySlow
pycgm2.exe NEXUS Plots Kinematics Comparison --consistency -ps test -nd Schwartz2008 -ndm VerySlow
=> build kinematic panel from model ouputs suffixed test. the panel render all cycles rather the average and the std corridor. the panel also call the modality Very slow of the open normative dataset from Schwartz2008
| long options | short options | Type | Description | |
|---|---|---|---|---|
--consistency | -c | return consistency trace ( ie all cycles) | ||
--pointSuffix | -ps | str | consider model outputs with the given suffix | |
--normativeData | -nd | str | normative Data set (Schwartz2008 or Pinzone2014) | |
--normativeDataModality | -ndm | str | if Schwartz2008 [VerySlow,Slow,Free,Fast,VeryFast] - if Pinzone2014 [CentreOne,CentreTwo] |
EMG - Temporal plots
type NEXUS Plots EMG Temporal -h to know the input arguments
pycgm2.exe NEXUS Plots EMG Temporal --raw -bpf 200 400
=> render non-rectified emg channels. The process applies a bandpass filter [200-400Hz]
| long options | short options | Type | Description | |
|---|---|---|---|---|
--BandpassFrequencies | -bpf | bandpass frequencies | ||
--EnvelopLowpassFrequency | -elf | envelop lowpass cutoff frequency | ||
--raw | -r | return non-rectified values | ||
--ignoreNormalActivity | -ina | do not display normal activity area in the back ground |
EMG - Time-normalized and Comparison Panels
type NEXUS Plots EMG Normalized -h or NEXUS Plots EMG Comparison -h to know the input arguments
pycgm2.exe NEXUS Plots EMG Normalized --consistency -bpf 200 400 -elp 8.9
=> render all cycles instead of the average and the std corridor. the process applies a bandpass filter [200-400Hz] and construct the emg envelop with a cut-off frequency of 8.9
| long options | short options | Type | Description | |
|---|---|---|---|---|
--BandpassFrequencies | -bpf | bandpass frequencies | ||
--EnvelopLowpassFrequency | -elf | envelop lowpass cutoff frequency | ||
--consistency | -c | return consistency traces ( ie all cycles) |