Processing

analysis

analysisHandler

pyCGM2.Processing.analysisHandler.getAnalysisSection(analysisInstance, label, context)

return the section ( ie kinematic, kinetic or emg) of a given label and its context

Parameters

analysisInstance (pyCGM2.Processing.analysis.Analysis) – an analysis instance
label (str) – givel ouput label (eg LKneeAngles)
context (str) – event context

pyCGM2.Processing.analysisHandler.getNumberOfCycle(analysisInstance, label, context)

return the number of cycle from a given ouput and its event context.

Parameters

analysisInstance (pyCGM2.Processing.analysis.Analysis) – an analysis instance
label (str) – givel ouput label (eg LKneeAngles)
context (str) – event context

pyCGM2.Processing.analysisHandler.getPhases(dataStats, context='Both')

get phases

Parameters

dataStats (pyCGM2.Processing.analysis.Analysis.kinematicStats.data) – data level
instance (of the kinematicStats or kineticStats attributes of an Analysis) –
context (str) – event context

pyCGM2.Processing.analysisHandler.getValues(analysisInstance, label, context)

return the values from a given ouput and its event context.

Parameters

analysisInstance (pyCGM2.Processing.analysis.Analysis) – an analysis instance
label (str) – givel ouput label (eg LKneeAngles)
context (str) – event context

pyCGM2.Processing.analysisHandler.isKeyExist(analysisInstance, label, context, exceptionMode=False)

check if the combinaison label/context exist in the analysis instance

Parameters

analysisInstance (pyCGM2.Processing.analysis.Analysis) – an analysis instance
label (str) – givel ouput label (eg LKneeAngles)
context (str) – event context
exceptionMode (bool) – enable exception raising

analysisProcessing

cycle

exporter

This module contains 2 classes (XlsAnalysisExportFilter and AnalysisExportFilter) for exporting an analysis instance in xls fomat and json respectively.

the class XlsExportDataFrameFilter is a generic filter for exporting Pandas.DataFrame in xls.

class pyCGM2.Processing.exporter.AnalysisExportFilter

Filter exporting an analysis instance as json.

export(outputName, path=None)

Export as json

Parameters

outputName (str) – filename without extension
path (str) – Path

setAnalysisInstance(analysisInstance)

set the analysis instance

Parameters: analysisInstance (pyCGM2.analysis.Analysis) – an analysis instance

class pyCGM2.Processing.exporter.XlsAnalysisExportFilter

Filter exporting an analysis instance as spreadheet.

Exported spreadsheet can organize either by row (Advanced mode) or column (basic mode). In Advanced mode, a row is made up of 101 columns representing a time normalized cycle.

export(outputName, path=None, excelFormat='xls', mode='Advanced')

Export spreadsheet

Parameters

outputName (str) – filename without extension
path (str) – Path
excelFormat (str) – format (xls,xlsx)
mode (str) – structure mode of the spreadsheet (Advanced,Basic)

setAnalysisInstance(analysisInstance)

set the analysis instance

Parameters: analysisInstance (pyCGM2.analysis.Analysis) – an analysis instance

class pyCGM2.Processing.exporter.XlsExportDataFrameFilter

Filter exporting a pandas.dataFrame or a list of pandas.dataFrame as xls spreadsheet(s)

export(outputName, path=None, excelFormat='xls')

Export spreadsheet

Parameters

outputName (str) – filename without extension
path (str) – Path
excelFormat (str) – format (xls,xlsx)

setDataFrames(dataframes)

Set the dataFrame

Parameters: dataframes (pandas.dataFrame or list) – dataframe or list of dataframe

c3dManager

c3dManagerFilters

c3dManagerProcedures

Classification

classificationFilters

classificationProcedures

DiscretePoints

discretePointFilters

A discrete point is a value at a specific frame of a cycle.

In this module, through the filter DiscretePointsFilter, the goal is to get series of discrete values extracted according a specific strategy (ie a procedure). For instance, the BenedettiProcedure extracts dicrete points recommanded in Benededdi et al (1998):

References:

Benedetti, M. G.; Catani, F.; Leardini, A.; Pignotti, E.; Giannini, S. (1998) Data management in gait analysis for clinical applications. In : Clinical biomechanics (Bristol, Avon), vol. 13, n° 3, p. 204–215. DOI: 10.1016/s0268-0033(97)00041-7.

class pyCGM2.Processing.DiscretePoints.discretePointFilters.DiscretePointsFilter(discretePointProcedure, analysis, modelInfo=None, subjInfo=None, condExpInfo=None)

Discrete point filter

Parameters

discretePointProcedure (pyCGM2.Processing.DiscrePoints.discretePointProcedures.DiscretePointProcedure) – a procedure
analysis (pyCGM2.Processing.analysis.Analysis) – an analysis instance
modelInfo (dict) – information about the model
subjInfo (dict) – information about the subject
condExpInfo (dict) – information about the experiment

getOutput(): get the output dataframe with all discrete values according to the procedure

setCondExpInf(condExpInfo)

Set experimental information

Parameters: condExpInfo (dict) – experimental information

setModelInfo(modelInfo)

Set model information

Parameters: modelInfo (dict) – model information

setSubjInfo(subjInfo)

Set subject information

Parameters: subjInfo (dict) – subject information

discretePointProcedures

class pyCGM2.Processing.DiscretePoints.discretePointProcedures.BenedettiProcedure(pointSuffix=None)

discrete points recommanded by benededdi et al(1998).

Parameters: pointSuffix (str) – suffix added to model ouputs

References:

Benedetti, M. G.; Catani, F.; Leardini, A.; Pignotti, E.; Giannini, S. (1998) Data management in gait analysis for clinical applications. In : Clinical biomechanics (Bristol, Avon), vol. 13, n° 3, p. 204–215. DOI: 10.1016/s0268-0033(97)00041-7.

detect(analysisInstance)

extract discrete points

Parameters: analysisInstance (pyCGM2.Processing.analysis.Analysis) – an analysis instance

class pyCGM2.Processing.DiscretePoints.discretePointProcedures.GoldbergProcedure(pointSuffix=None)

discrete points recommanded by Goldberg et al(1998).

Parameters: pointSuffix (str) – suffix added to model ouputs

References:

Goldberg, Saryn R.; Ounpuu, Sylvia; Arnold, Allison S.; Gage, James R.; Delp, Scott L. (2006) Kinematic and kinetic factors that correlate with improved knee flexion following treatment for stiff-knee gait. In : Journal of biomechanics, vol. 39, n° 4, p. 689–698. DOI: 10.1016/j.jbiomech.2005.01.015.

detect(analysisInstance)

extract discrete points

Parameters: analysisInstance (pyCGM2.Processing.analysis.Analysis) – an analysis instance

class pyCGM2.Processing.DiscretePoints.discretePointProcedures.MaxMinProcedure(pointSuffix=None)

extract extrema values.

Parameters: pointSuffix (str) – suffix added to model ouputs

detect(analysisInstance)

extract discrete points

Parameters: analysisInstance (pyCGM2.Processing.analysis.Analysis) – an analysis instance

JointPatterns

jointPatternFilters

class pyCGM2.Processing.JointPatterns.jointPatternFilters.JointPatternFilter(jointPatternProcedure, analysis)

jointPatternProcedures

ProgressionFrame

progressionFrameFilters

progressionFrameProcedures

Representative

representativeFilters

representativeProcedures

Scores

scoreFilters

This module is dedicated to the quantification of a Score, i e a Global index caracterizing the movement performed

The filter ScoreFilter calls a specific procedure, and return scores values.

class pyCGM2.Processing.Scores.scoreFilters.ScoreFilter(scoreProcedure, analysis, normativeDataSet)

the score filter

Parameters

scoreProcedure (pyCGM2.processing.Scores.scoreProcedures.ScoreProcedure) – a procedure instance
analysis (pyCGM2.Processing.analysis.Analysis) – and analysis instance
normativeDataSet (pyCGM2.Report.normativeDatasets.NormativeData) – normative data instance

scoreProcedures

class pyCGM2.Processing.Scores.scoreProcedures.CGM1_GPS(pointSuffix=None)

Gait profile score accordin Baker et al. 2009

Parameters: pointSuffix (str,Optional[None]) – suffix added to model ouputs

Reference

Baker, Richard; McGinley, Jennifer L.; Schwartz, Michael H.; Beynon, Sarah; Rozumalski, Adam; Graham, H. Kerr; Tirosh, Oren (2009) The gait profile score and movement analysis profile. In : Gait & posture, vol. 30, n° 3, p. 265–269. DOI: 10.1016/j.gaitpost.2009.05.020.