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