Report

normativeDatasets

Module deals with normative datasets.

Normative datasets are embedded in pyCGM2. they are placed in the folder pyCGM2/Data as a json file.

The construction of a NormativeData instance automatically populate its attribute data, an intuitive dictionary with model ouput as key, reporting mean and standard deviation as sub-key.

The NormativeSTP class replicates the process for the spatio-temporal excel file (normal_stp.xlsx) placed in the folder pyCGM2/Data/stp

class pyCGM2.Report.normativeDatasets.NormalSTP

Normative spatio-temporal dataset.

The instance contruction populates the attribute data which reports normative data as a dictionary

class pyCGM2.Report.normativeDatasets.NormativeData(filenameNoExt, modality)

Normative dataset.

The instance contruction populates the attribute data which reports normative data as a dictionary

Parameters

  • filenameNoExt (str) – filename of the targeted json file.

  • modality (str) – modality.

plot

Module contains low-level plot functions

pyCGM2.Report.plot.addNormalActivationLayer(figAxis, normalActivationLabel, fo)

display normal muscle activation in the background of a time-normalized trace

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • normalActivationLabel (str) – muscle label

  • fo (int) – time-normalized foot off frame

pyCGM2.Report.plot.addTemporalNormalActivationLayer(figAxis, acq, normalActivationLabel, context)

display normal muscle activation in the background of a temporal trace

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • acq (btk.Acquisition) – an acquisition

  • normalActivationLabel (str) – muscle label

  • context (str) – event context

pyCGM2.Report.plot.consistencyPlot(figAxis, analysisStructureItem, pointLabel, contextPointLabel, axis, color=None, title=None, xlabel=None, ylabel=None, ylim=None, legendLabel=None, customLimits=None)

Plot all time-normalized traces from an attribute of an analysis instance

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • analysisStructureItem (pyCGM2.Processing.analysis.Analysis.(attribute)) – an attribute of an analysis instance

  • pointLabel (str) – point label

  • contextPointLabel (str) – event context

  • axis (int) – column index of the point values

  • color (type,Optional[None]) – line color

  • title (type,Optional[None]) – plot title

  • xlabel (type,Optional[None]) – x-axis label

  • ylabel (type,Optional[None]) – y-axis label

  • ylim (list,Optional[None]) – y boundaries

  • legendLabel (type,Optional[None]) – legend

  • customLimits (list,Optional[None]) – horizontal lines

pyCGM2.Report.plot.descriptivePlot(figAxis, analysisStructureItem, pointLabel, contextPointLabel, axis, color=None, title=None, xlabel=None, ylabel=None, ylim=None, legendLabel=None, customLimits=None)

Plot descriptive (average and sd corridor) time-normalized traces from an attribute of an analysis instance

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • analysisStructureItem (pyCGM2.Processing.analysis.Analysis.(attribute)) – an attribute of an analysis instance

  • pointLabel (str) – point label

  • contextPointLabel (str) – event context

  • axis (int) – column index of the point values

  • color (type,Optional[None]) – line color

  • title (type,Optional[None]) – plot title

  • xlabel (type,Optional[None]) – x-axis label

  • ylabel (type,Optional[None]) – y-axis label

  • ylim (list,Optional[None]) – y boundaries

  • legendLabel (type,Optional[None]) – legend

  • customLimits (list,Optional[None]) – horizontal lines

pyCGM2.Report.plot.gaitConsistencyPlot(figAxis, analysisStructureItem, pointLabel, contextPointLabel, axis, color=None, title=None, xlabel=None, ylabel=None, ylim=None, legendLabel=None, customLimits=None)

Plot all gait traces from an attribute of an analysis instance

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • analysisStructureItem (pyCGM2.Processing.analysis.Analysis.(attribute)) – an attribute of an analysis instance

  • pointLabel (str) – point label

  • contextPointLabel (str) – event context

  • axis (int) – column index of the point values

  • color (type,Optional[None]) – line color

  • title (type,Optional[None]) – plot title

  • xlabel (type,Optional[None]) – x-axis label

  • ylabel (type,Optional[None]) – y-axis label

  • ylim (list,Optional[None]) – y boundaries

  • legendLabel (type,Optional[None]) – legend

  • customLimits (list,Optional[None]) – horizontal lines

pyCGM2.Report.plot.gaitDescriptivePlot(figAxis, analysisStructureItem, pointLabel, contextPointLabel, axis, color=None, title=None, xlabel=None, ylabel=None, ylim=None, legendLabel=None, customLimits=None)

Plot descriptive (average and sd corridor) gait traces from an attribute of an analysis instance

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • analysisStructureItem (pyCGM2.Processing.analysis.Analysis.(attribute)) – an attribute of an analysis instance

  • pointLabel (str) – point label

  • contextPointLabel (str) – event context

  • axis (int) – column index of the point values

  • color (type,Optional[None]) – line color

  • title (type,Optional[None]) – plot title

  • xlabel (type,Optional[None]) – x-axis label

  • ylabel (type,Optional[None]) – y-axis label

  • ylim (list,Optional[None]) – y boundaries

  • legendLabel (type,Optional[None]) – legend

  • customLimits (list,Optional[None]) – horizontal lines

pyCGM2.Report.plot.gaitMeanPlot(figAxis, analysisStructureItem, pointLabel, contextPointLabel, axis, color=None, title=None, xlabel=None, ylabel=None, ylim=None, legendLabel=None, customLimits=None)

Plot average gait traces from an attribute of an analysis instance

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • analysisStructureItem (pyCGM2.Processing.analysis.Analysis.(attribute)) – an attribute of an analysis instance

  • pointLabel (str) – point label

  • contextPointLabel (str) – event context

  • axis (int) – column index of the point values

  • color (type,Optional[None]) – line color

  • title (type,Optional[None]) – plot title

  • xlabel (type,Optional[None]) – x-axis label

  • ylabel (type,Optional[None]) – y-axis label

  • ylim (list,Optional[None]) – y boundaries

  • legendLabel (type,Optional[None]) – legend

  • customLimits (list,Optional[None]) – horizontal lines

pyCGM2.Report.plot.meanPlot(figAxis, analysisStructureItem, pointLabel, contextPointLabel, axis, color=None, title=None, xlabel=None, ylabel=None, ylim=None, legendLabel=None, customLimits=None)

Plot the average time-normalized traces from an attribute of an analysis instance

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • analysisStructureItem (pyCGM2.Processing.analysis.Analysis.(attribute)) – an attribute of an analysis instance

  • pointLabel (str) – point label

  • contextPointLabel (str) – event context

  • axis (int) – column index of the point values

  • color (type,Optional[None]) – line color

  • title (type,Optional[None]) – plot title

  • xlabel (type,Optional[None]) – x-axis label

  • ylabel (type,Optional[None]) – y-axis label

  • ylim (list,Optional[None]) – y boundaries

  • legendLabel (type,Optional[None]) – legend

  • customLimits (list,Optional[None]) – horizontal lines

pyCGM2.Report.plot.stpHorizontalHistogram(figAxis, analysisStructureItem, stpLabel, overall=False, title=None, xlabel=None, xlim=None)

Plot spatio-temporal parameters as histogram from an attribute of an analysis instance

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • analysisStructureItem (pyCGM2.Processing.analysis.Analysis.(attribute)) – an attribute of an analysis instance

  • stpLabel (str) – spatio-temporal label

  • title (type,Optional[None]) – plot title

  • xlabel (type,Optional[None]) – x-axis label

  • xlim (list,Optional[None]) – x boundaries

pyCGM2.Report.plot.temporalPlot(figAxis, acq, pointLabel, axis, pointLabelSuffix=None, color=None, linewidth=None, title=None, xlabel=None, ylabel=None, ylim=None, legendLabel=None, customLimits=None)

Plot temporal traces from an acquisition

Parameters

  • figAxis (matplotlib.pyplot.Axis) – a matplotlib figure axis

  • acq (btk.Acquisition) – an acquisition

  • pointLabel (str) – point label

  • axis (int) – column index of the point values

  • pointLabelSuffix (type,Optional[None]) – suffix added to the point label

  • color (type,Optional[None]) – line color

  • linewidth (type,Optional[None]) – line width

  • title (type,Optional[None]) – plot title

  • xlabel (type,Optional[None]) – x-axis label

  • ylabel (type,Optional[None]) – y-axis label

  • ylim (list,Optional[None]) – y boundaries

  • legendLabel (type,Optional[None]) – legend

  • customLimits (list,Optional[None]) – horizontal lines

plotFilters

This Module contains the pyCGM2 plot filter PlottingFilter.

This PlottingFilter requires a PlotViewer, then displays the plot panel

class pyCGM2.Report.plotFilters.PlottingFilter

The plot filter

plot()

generate plot panel

setAutomaticYlimits()

set Y-axis boundaries to default values

setExport(path, filename, format)

Set filename of the export file

Parameters

  • path (str) – folder path

  • filename (str) – filename

  • format (str) – file format

setHorizontalLine(axisIndex, value, color='black')

set horizontal lines

Parameters

  • axisIndex (int) – index of the matplotlib.figure.axis instance

  • value (double) – y-axis value

  • color (str,Optional[black]) – line color

setTitle(title)

Set the plot panel title

Parameters

title (str) – title

setViewer(concretePlotViewer)

set the plot viewer

Parameters

concretePlotViewer (pyCGM2.report.(Viewers)) – a plot viewer

setYlimits(axisIndex, min, max)

set the y-axis boundaries

Parameters

  • axisIndex (int) – index of the matplotlib.figure.axis instance

  • min (double) – minimum value

  • max (double) – maximum value

plotUtils

Viewers

plotViewers

Module contains plotViewers for displaying convenient gait plot

class pyCGM2.Report.Viewers.plotViewers.GpsMapPlotViewer(iAnalysis, pointLabelSuffix=None)

Plot viewer to display GPS and MAP panel

Parameters

iAnalysis (pyCGM2.Processing.analysis.Analysis) – an analysis instance

plotPanel()

plat the panel

class pyCGM2.Report.Viewers.plotViewers.NormalizedKinematicsPlotViewer(iAnalysis, pointLabelSuffix=None, bodyPart=BodyPartPlot.LowerLimb)

Plot time-Normalized Kinematics

Parameters

  • iAnalysis (pyCGM2.Processing.analysis.Analysis) – an analysis instance

  • pointLabelSuffix (str) – suffix added model outputs

  • bodyPart (enums.BodyPartPlot,Optional[enums.BodyPartPlot.LowerLimb]) – body part

plotPanel()

Plot the panel

setConcretePlotFunction(concreteplotFunction)

set a plot function ( see plot)

Parameters

concreteplotFunction (function) – plot function

setNormativeDataset(iNormativeDataSet)

Set the normative dataset

Parameters

iNormativeDataSet (pyCGM2.Report.normativeDatasets.NormativeData) – a normative dataset instance

class pyCGM2.Report.Viewers.plotViewers.NormalizedKineticsPlotViewer(iAnalysis, pointLabelSuffix=None, bodyPart=BodyPartPlot.LowerLimb)

Plot time-Normalized kinetics

Parameters

  • iAnalysis (pyCGM2.Processing.analysis.Analysis) – an analysis instance

  • pointLabelSuffix (str) – suffix added model outputs

  • bodyPart (enums.BodyPartPlot,Optional[enums.BodyPartPlot.LowerLimb]) – body part

plotPanel()

Plot the panel

setConcretePlotFunction(concreteplotFunction)

set a plot function ( see plot)

Parameters

concreteplotFunction (function) – plot function

setNormativeDataset(iNormativeDataSet)

Set the normative dataset

Parameters

iNormativeDataSet (pyCGM2.Report.normativeDatasets.NormativeData) – a normative dataset instance

class pyCGM2.Report.Viewers.plotViewers.SpatioTemporalPlotViewer(iAnalysis)

Plot viewer to display spatio-temporal parameters as histogram

Parameters

iAnalysis (pyCGM2.Processing.analysis.Analysis) – an analysis instance

plotPanel()

Plot the panel

setNormativeDataset(iNormativeDataSet)

Set the normative dataset

Parameters

iNormativeDataSet (pyCGM2.Report.normativeDatasets.NormalSTP) – a spatio-temporal normative dataset instance

class pyCGM2.Report.Viewers.plotViewers.TemporalKinematicsPlotViewer(iAcq, pointLabelSuffix=None, bodyPart=BodyPartPlot.LowerLimb)

Plot temporal Kinematics

Parameters

  • iAcq (btk.Acquisition) – an acquisition

  • pointLabelSuffix (str) – suffix added model outputs

  • bodyPart (enums.BodyPartPlot,Optional[enums.BodyPartPlot.LowerLimb]) – body part

plotPanel()

Plot the panel

class pyCGM2.Report.Viewers.plotViewers.TemporalKineticsPlotViewer(iAcq, pointLabelSuffix=None, bodyPart=BodyPartPlot.LowerLimb)

Plot temporal Kinetics

Parameters

  • iAcq (btk.Acquisition) – an acquisition

  • pointLabelSuffix (str) – suffix added model outputs

  • bodyPart (enums.BodyPartPlot,Optional[enums.BodyPartPlot.LowerLimb]) – body part

plotPanel()

plot the panel

emgPlotViewers

Module contains plotViewers for displaying emg data

class pyCGM2.Report.Viewers.emgPlotViewers.CoactivationEmgPlotViewer(iAnalysis, pointLabelSuffix=None)

plot coactivation plot

Parameters
plotPanel()

plot the panel

setConcretePlotFunction(concreteplotFunction)

set a concrete plot function

Parameters

concreteplotFunction (pyCGM2.Report.plot) – plot function

setContext(context)

set event context

Parameters

context (str) – event context

setEmgs(label1, label2)

set the 2 emg labels to plot

Parameters

  • label1 (str) – emg channel label

  • label2 (str) – emg channel label

setMuscles(label1, label2)

set the 2 measured muscle names

Parameters

  • label1 (str) – muscle name

  • label2 (str) – muscle name

class pyCGM2.Report.Viewers.emgPlotViewers.EnvEmgGaitPlotPanelViewer(iAnalysis, pointLabelSuffix=None)

plot emg envelops

Parameters
plotPanel()

plot the panel

selectEmgChannels(channelNames)

set the emg channels

Parameters

channelNames (str) – channel labels

setConcretePlotFunction(concreteplotFunction)

set a concrete plot function

Parameters

concreteplotFunction (pyCGM2.Report.plot) – plot function

setEmgManager(emgManager)

set the emgManager instance

Parameters

emgManager (pyCGM2.EMG.EmgManager) – emgManager instance

setNormalizedEmgFlag(flag)

Enable/Disable amplitude-normalized emg

Parameters

flag (bool) – boolean flag

class pyCGM2.Report.Viewers.emgPlotViewers.MultipleAnalysis_EnvEmgPlotPanelViewer(iAnalyses, legends, pointLabelSuffix=None)

plot emg envelops from multiple analysis instances

Parameters

  • iAnalyses (list) – analysis instances

  • legend (str) – label assoaciated to each instance

  • pointLabelSuffix (str,Optional[None]) – suffix added to emg outputs

plotPanel()

plot the panel

selectEmgChannels(channelNames)

set the emg channels

Parameters

channelNames (str) – channel labels

setConcretePlotFunction(concreteplotFunction)

set a concrete plot function

Parameters

concreteplotFunction (pyCGM2.Report.plot) – plot function

setEmgManager(emgManager)

set the emgManager instance

Parameters

emgManager (pyCGM2.EMG.EmgManager) – emgManager instance

setNormalizedEmgFlag(flag)

Enable/Disable amplitude-normalized emg

Parameters

flag (bool) – boolean flag

class pyCGM2.Report.Viewers.emgPlotViewers.TemporalEmgPlotViewer(iAcq, pointLabelSuffix=None)

plot temporal emg plot

Parameters

  • iAcq (btk.Acquisition) – an acquisition

  • pointLabelSuffix (str,Optional[None]) – suffix added to emg outputs

ignoreNormalActivty(bool)

Enable/disable normal actividy display

Parameters

bool (bool) – boolean flag

plotPanel()

plot the panel

selectEmgChannels(channelNames)

set the emg channels

Parameters

channelNames (str) – channel labels

setEmgManager(emgManager)

set the emgManager instance

Parameters

emgManager (pyCGM2.EMG.EmgManager) – emgManager instance

setEmgRectify(flag)

Enable/disable rectify mode

Parameters

flag (bool) – boolean flag

comparisonPlotViewers

Module contains plotViewers for comparing data from different analysis instances

class pyCGM2.Report.Viewers.comparisonPlotViewers.KinematicsPlotComparisonViewer(iAnalyses, context, legends, pointLabelSuffix_lst=None, bodyPart=BodyPartPlot.LowerLimb)

Compare kinematics

Parameters

  • iAnalyses (list) – pyCGM2.Processing.analysis.Analysis instances

  • context (str) – event context

  • pointLabelSuffix (str) –

  • legends (list) – labels caracterizing the analysis instances

  • pointLabelSuffix_lst (list,Optional[None]) – suffix added to model outputs of the analysis instances

  • bodyPart (pyCGM2.enums.BodyPartPlot,Optional[pyCGM2.enums.BodyPartPlot.LowerLimb]) – body part

plotPanel()

plot the panel

setConcretePlotFunction(concreteplotFunction)

set a plot function ( see plot)

Parameters

concreteplotFunction (function) – plot function

setNormativeDataset(iNormativeDataSet)

Set a normative dataset

Parameters

iNormativeDataSet (pyCGM2.Report.normativeDatasets.NormativeData) – normative data instance

class pyCGM2.Report.Viewers.comparisonPlotViewers.KineticsPlotComparisonViewer(iAnalyses, context, legends, pointLabelSuffix_lst=None, bodyPart=BodyPartPlot.LowerLimb)

Compare kinetics

Parameters

  • iAnalyses (list) – pyCGM2.Processing.analysis.Analysis instances

  • context (str) – event context

  • pointLabelSuffix (str) –

  • legends (list) – labels caracterizing the analysis instances

  • pointLabelSuffix_lst (list,Optional[None]) – suffix added to model outputs of the analysis instances

  • bodyPart (pyCGM2.enums.BodyPartPlot,Optional[pyCGM2.enums.BodyPartPlot.LowerLimb]) – body part

plotPanel()

plot the panel

setConcretePlotFunction(concreteplotFunction)

set a plot function ( see plot)

Parameters

concreteplotFunction (function) – plot function

setNormativeDataset(iNormativeDataSet)

Set a normative dataset

Parameters

iNormativeDataSet (pyCGM2.Report.normativeDatasets.NormativeData) – normative data instance