Model

anthropometricMeasurement

bodySegmentParameters

class pyCGM2.Model.bodySegmentParameters.Bsp(iModel)

Body Segment Parameter of the lower limb according Dempster 1995

Reference

Dempster. (1955). Body Segment Parameter Data for 2-D Studies

compute(): Compute body segment parameters of a Model

classmethod setParameters(bspSegmentLabel, segmentLength, bodymass)

Compute body parameter of a selected lower limb segment

Parameters

bspSegmentLabel (str) – segment label defined in the class object TABLE
segmentLength (double) – length of the segment
bodymass (double) – mass of the subject

pyCGM2.Model.bodySegmentParameters.updateFromcustomMp(model, custom_mp)

update the anthropometric parameters fo your model

Parameters

model (pyCGM2.Model) – a model instance.
custom_mp (dict) – mp from the file mp.settings

frame

this module gathers two classes (Node and Frame), important for the construction of a model

A Frame is a representation of a coordinate system at a specific time. Its main attributes are the rotation matrix and the translation vectors.

A Frame can collect Node instances. A Node represents a 3d point expressed in a local coordinate system

class pyCGM2.Model.frame.Frame

A Frame represents a coordinate system

addNode(nodeLabel, position, positionType='Global', desc='')

Append a Node to a Frame

Parameters

nodeLabel (str) – node label
position (array(3,)) – a translation vector
positionType (str,Optional) – two choice Global or Local
desc (str,Optional) – description

copyNode(nodeLabel, nodeToCopy)

Copy a node and add it or update a existant node

Parameters

nodeLabel (str) – the node label
nodeToCopy (str) – the label of the node to copy

eraseNodes(): Erase all nodes

getAngleAxis(): Get the angle axis

getGlobalPosition(nodeLabel)

Return the global position

Parameters: nodeLabel (str) – the node label

getNodeIndex(nodeLabel)

Get the node index

Parameters: nodeLabel (str) – the node label

getNodeLabels(display=True): Display all node labels

getNode_byIndex(index)

Get a node from its index

Parameters: index (int) – index of the node within the list

getNode_byLabel(label)

Get a node from its label

Args:
label(str): the node label

getNodes(): Return all node instances

getRotation()

Get rotation matrix

Returns: array ((3,3) – a rotation matrix

getTranslation(): Get translation vector

isNodeExist(nodeLabel)

Check if a node exists from its label

Parameters: nodeLabel (str) – the node label

setRotation(R)

Set the rotation matrix

Parameters: R (array(3,3) – a rotation matrix

setTranslation(t)

Set the translation vector

Parameters: t (array(3,)) – a translation vector

update(R, t)

Update both the rotation matrix and the translation vector

Parameters

R (array(3,3) – a rotation matrix
t (array(3,)) – a translation vector

updateAxisFromRotation(R)

Update the rotation matrix

Parameters: R (array(3,3) – a rotation matrix

updateNode(nodeLabel, localArray, globalArray, desc='')

Update a node

Parameters

nodeLabel (str) – the node label
localArray (array(3)) – local position
globalArray (array(3)) – global position
desc (str,Optional) – description

class pyCGM2.Model.frame.Node(label, desc='')

A node is a local position of a 3D point in a coordinate system

Note

Automatically, the suffix “_node” ends the node label

Parameters

label (str) – desired label of the node
desc (str,Optional) – description

computeGlobal(rot, t)

Compute global position from local

Parameters

rot (array((3,3)) – a rotation matrix
t (array((1,3)) – a translation vector

computeLocal(rot, t)

Compute local position from global position

Parameters

rot (array(3,3)) – a rotation matrix
t (array((1,3))) – a translation vector

getDescription(): Get the node description

getGlobal(): Get the global coordinates of the node

getLabel(): Get the node label

getLocal(): Get the local coordinates of the node

setDescription(description)

Set description of the node

Parameters: description (str) – description

pyCGM2.Model.frame.angleAxisFromQuaternion(Quaternion)

Calculates the AngleAxis representation from a quaternion

Parameters: Quaternion (array(4)) – a quaternion

pyCGM2.Model.frame.getQuaternionFromMatrix(RotMat)

Calculates the quaternion representation from a rotation matrix.

Algorithm in Ken Shoemake’s article in 1987 SIGGRAPH course notes article “Quaternion Calculus and Fast Animation”.

Parameters: RotMat (array(3,3)) – Rotation matrix

pyCGM2.Model.frame.setFrameData(a1, a2, sequence)

Set axes and rotation matrix of a coordinate system from 2 vectors and a sequence

The sequence can be all combinaison of XYZ. If the second letter is prefixed by i, the opposite vector to the cross product a1, a2 is considered

Parameters

a1 (array(1,3)) – first vector
a2 (array(1,3)) – second vector
sequence (str) – construction sequence (XYZ, XYiZ,…)

model

modelDecorator

modelFilters

modelQualityFilter

motion

This module contains pose algorithms

pyCGM2.Model.motion.segmentalLeastSquare(A, B)

Compute the transformation between two coordinate systems using SVD.

Parameters

A (numpy.array(n,3)) –
B (numpy.array(n,3)) –

CGM2

cgm

cgm2

decorators

Opensim

opensimFilters

osimProcessing

This module contains convenient functions and classes for working with opensim.

pyCGM2.Model.Opensim.osimProcessing.globalTransformationLabToOsim(acq, R_LAB_OSIM)

transform all markers into the the opensim global coordinate system

Parameters

acq (Btk.Acquisition) – an acquisition
R_LAB_OSIM (array(3,3)) – rotation matrix for passing from the lab to opensim coordinate sytem

pyCGM2.Model.Opensim.osimProcessing.mot2pointValues(motFilename, labels, orientation=[1, 1, 1])

convert an element of an opensim mot file into a btk-point values (ie array(n,3) with n: the number of frames)

Parameters

motFilename (str) – full filename of the mot file
label (str) – label to convert
orientation (list) – scales to apply before returning final values. Default is [1,1,1]

pyCGM2.Model.Opensim.osimProcessing.setGlobalTransormation_lab_osim(axis, forwardProgression)

return the rotation matrix expressing the opensim global coordinate system to the laboratory coordinate system

Parameters

axis (str) – defined progression axis (ie X or Y ).
forwardProgression (bool) – forward progression flag.
True ((if) –
of (the movement progression is along the positive value) –
) (your progression axis) –

pyCGM2.Model.Opensim.osimProcessing.smartTrcExport(acq, filenameNoExt)

save as a trc file

Parameters

acq (Btk.Acquisition) – an acquisition
filenameNoExt (str) – filename without extension

pyCGM2.Model.Opensim.osimProcessing.sto2pointValues(storageObject, label, R_LAB_OSIM)

transform an element of a storage instance into the Laboratory coordinate system.

Parameters

storageObject (opensim.Storage) – an opensim storage instance.
label (str) – label to extract from the storage instance
R_LAB_OSIM (array(3,3)) – rotation matrix for passing from the lab to opensim coordinate sytem