def meanPlot_OneModelOutputPlot(cls):
"""
Plot only one Model output
"""
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\plot\\gaitPlot\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
modelInfo = None
subjectInfo = None
experimentalInfo = None
analysis1 = gaitSmartFunctions.make_analysis(
trialManager, cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT, modelInfo,
subjectInfo, experimentalInfo)
analysis2 = gaitSmartFunctions.make_analysis(
trialManager, cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT, modelInfo,
subjectInfo, experimentalInfo)
analyses = [analysis1, analysis2]
fig = plt.figure()
ax = plt.gca()
colormap = plt.cm.Reds
colormap_i = [colormap(i) for i in np.linspace(0.2, 1, len(analyses))]
plot.gaitMeanPlot(ax,
analysis1.kinematicStats,
"LPelvisAngles",
"Left",
0,
color=colormap_i[0],
legendLabel="analysis1",
customLimits=None)
plot.gaitMeanPlot(ax,
analysis2.kinematicStats,
"LKneeAngles",
"Left",
0,
color=colormap_i[1],
legendLabel="analysis2",
customLimits=None)
ax.legend()
plt.show()
def Save_and_openAnalysis(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\analysis\\gait\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
# ----INFOS-----
modelInfo = {"Type": "cgm2", "hjc": "hara"}
subjectInfo = {"Id": "1", "Name": "Lecter"}
experimentalInfo = {"Condition": "Barefoot", "context": "block"}
analysis = gaitSmartFunctions.make_analysis(
trialManager, cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT, modelInfo,
subjectInfo, experimentalInfo)
files.saveAnalysis(analysis, DATA_PATH, "Save_and_openAnalysis")
analysis2 = files.loadAnalysis(DATA_PATH, "Save_and_openAnalysis")
def makeAnalysis_oneFile_noInfo(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\analysis\\gait\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
modelInfo = None
subjectInfo = None
experimentalInfo = None
analysis = gaitSmartFunctions.make_analysis(
trialManager, cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT, modelInfo,
subjectInfo, experimentalInfo)
def analysisBasic(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\analysis\\gait\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
# ----INFOS-----
modelInfo = {"Type": "cgm2", "hjc": "hara"}
subjectInfo = {"Id": "1", "Name": "Lecter"}
experimentalInfo = {"Condition": "Barefoot", "context": "block"}
analysis = gaitSmartFunctions.make_analysis(
trialManager, cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT, modelInfo,
subjectInfo, experimentalInfo)
exportFilter = exporter.XlsAnalysisExportFilter()
exportFilter.setAnalysisInstance(analysis)
exportFilter.export("test",
path=DATA_PATH,
excelFormat="xls",
mode="Basic")
def gaitMeanOnlyKineticPlotPanel(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"operations\\plot\\gaitPlot\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
modelInfo=None
subjectInfo=None
experimentalInfo=None
analysis1 = gaitSmartFunctions.make_analysis(trialManager,
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT,
modelInfo,subjectInfo,experimentalInfo)
analysis2 = gaitSmartFunctions.make_analysis(trialManager,
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT,
modelInfo,subjectInfo,experimentalInfo)
kv = plotViewers.multipleAnalyses_LowerLimbKineticsPlotViewer([analysis1,analysis2],"Right",
["ana1","ana2"])
kv.setConcretePlotFunction(plot.gaitMeanPlot)
kv.setNormativeDataset(normativeDatasets.Schwartz2008("Free"))
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
plt.show()
def singleAnalysis(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"operations\\plot\\gaitPlot\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
modelInfo=None
subjectInfo=None
experimentalInfo=None
analysis = gaitSmartFunctions.make_analysis(trialManager,
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT,
modelInfo,subjectInfo,experimentalInfo)
ndp = normativeDatasets.Schwartz2008("Free")
gps =scores.CGM1_GPS()
scf = scores.ScoreFilter(gps,analysis, ndp)
scf.compute()
# viewer
kv = plotViewers.GpsMapPlotViewer(analysis)
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setPath(DATA_PATH)
pf.setPdfName(str("map"))
pf.plot()
plt.show()
def gaitDescriptiveKinematicPlotPanel(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"operations\\plot\\gaitPlot\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
modelInfo=None
subjectInfo=None
experimentalInfo=None
analysis = gaitSmartFunctions.make_analysis(trialManager,
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT,
modelInfo,subjectInfo,experimentalInfo)
# viewer
kv = plotViewers.LowerLimbKinematicsPlotViewer(analysis)
kv.setConcretePlotFunction(plot.gaitDescriptivePlot)
kv.setNormativeDataset(normativeDatasets.Schwartz2008("Free"))
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
ka = annotator.Annotator(pf.fig)
ka.IncreasedRange(0,40,10,40, "Context", timing="Throughout Cycle")
print(ka.getAnnotations())
plt.show()
def consistencyPlot_OneModelOutputPlot(cls):
"""
Plot only one Model output
"""
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\plot\\gaitPlot\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
modelInfo = None
subjectInfo = None
experimentalInfo = None
analysis = gaitSmartFunctions.make_analysis(
trialManager, cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT, modelInfo,
subjectInfo, experimentalInfo)
fig = plt.figure()
ax = plt.gca()
plot.gaitConsistencyPlot(ax,
analysis.kinematicStats,
"LPelvisAngles",
"Left",
0,
color="blue",
title="",
xlabel="",
ylabel="",
ylim=None,
customLimits=None)
plt.show()
def gaitDescriptiveKinematicPlotPanel_recorded(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"operations\\plot\\gaitPlot\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
modelInfo=None
subjectInfo=None
experimentalInfo=None
analysis = gaitSmartFunctions.make_analysis(trialManager,
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT,
modelInfo,subjectInfo,experimentalInfo)
# viewer
kv = plotViewers.LowerLimbKinematicsPlotViewer(analysis)
kv.setConcretePlotFunction(plot.gaitDescriptivePlot)
kv.setNormativeDataset(normativeDatasets.Schwartz2008("Free"))
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setExport("C:\\Users\\HLS501\\Desktop\\","test","png")
pf.plot()
plt.show()
def singleAnalysis(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\plot\\gaitPlot\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
modelInfo = None
subjectInfo = None
experimentalInfo = None
analysis = gaitSmartFunctions.make_analysis(
trialManager, cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT, modelInfo,
subjectInfo, experimentalInfo)
# viewer
kv = plotViewers.SpatioTemporalPlotViewer(analysis)
kv.setNormativeDataset(normativeDatasets.NormalSTP())
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setExport(DATA_PATH, "stp", "pdf")
pf.plot()
plt.show()
def gaitProcessing(DATA_PATH, modelledFilenames, modelVersion,
modelInfo, subjectInfo, experimentalInfo,
normativeData,
pointSuffix,
outputPath=None,
outputFilename="gaitProcessing",
exportXls=False,
plot=True,
plotDisplay=True):
if outputPath is None:
outputPath= DATA_PATH
if isinstance(modelledFilenames,str) or isinstance(modelledFilenames,unicode):
modelledFilenames = [modelledFilenames]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- make analysis
#-----------------------------------------------------------------------
# pycgm2-filter pipeline are gathered in a single function
if modelVersion in["CGM1.0","CGM1.1","CGM2.1","CGM2.2","CGM2.2e","CGM2.3","CGM2.3e","CGM2.4","CGM2.4e"]:
if modelVersion in ["CGM2.4","CGM2.4e"]:
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT["Left"].append("LForeFootAngles")
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT["Right"].append("RForeFootAngles")
analysis = gaitSmartFunctions.make_analysis(trialManager,
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT,
modelInfo, subjectInfo, experimentalInfo,
pointLabelSuffix=pointSuffix)
#---- normative dataset
#-----------------------------------------------------------------------
if normativeData["Author"] == "Schwartz2008":
chosenModality = normativeData["Modality"]
nds = normativeDatasets.Schwartz2008(chosenModality) # modalites : "Very Slow" ,"Slow", "Free", "Fast", "Very Fast"
elif normativeData["Author"] == "Pinzone2014":
chosenModality = normativeData["Modality"]
nds = normativeDatasets.Pinzone2014(chosenModality) # modalites : "Center One" ,"Center Two"
#---- GPS
gps =scores.CGM1_GPS(pointSuffix= pointSuffix)
scf = scores.ScoreFilter(gps,analysis, nds)
scf.compute()
#---- export
#-----------------------------------------------------------------------
files.saveAnalysis(analysis,outputPath,outputFilename)
if exportXls:
exportFilter = exporter.XlsAnalysisExportFilter()
exportFilter.setAnalysisInstance(analysis)
exportFilter.export(outputFilename, path=outputPath,excelFormat = "xls",mode="Advanced")
#---- plot panels
#-----------------------------------------------------------------------
if plot:
gaitSmartFunctions.cgm_gaitPlots(modelVersion,analysis,trialManager.kineticFlag,
outputPath,outputFilename,
pointLabelSuffix=pointSuffix,
normativeDataset=nds )
if plotDisplay:
plt.show()
return analysis
subjectInfo = None
experimentalInfo = None
modelVersion = "CGM2.4"
pointSuffix = ""
# analysis constructor-------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,
modelledFiles)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
analysis = gaitSmartFunctions.make_analysis(trialManager,
None,
None,
modelInfo,
subjectInfo,
experimentalInfo,
modelVersion="CGM2.4",
pointLabelSuffix=pointSuffix)
# end analysis -------
normativeDataset = normativeDatasets.Schwartz2008("Free")
kv = plotViewers.LowerLimbMultiFootKinematicsPlotViewer(
analysis, pointLabelSuffix=pointSuffix)
kv.setConcretePlotFunction(plot.gaitDescriptivePlot)
kv.setNormativeDataset(normativeDataset)
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
