def test_singleAnalysis(self):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitData\CGM1-NormalGaitData-Events\Hånnibøl Lecter\\"
modelledFilenames = ["gait Trial 01.c3d", "gait Trial 02.c3d"]
#---- Analysis
#--------------------------------------------------------------------------
modelInfo = None
subjectInfo = None
experimentalInfo = None
analysisInstance = analysis.makeAnalysis(DATA_PATH, modelledFilenames)
ndp = normativeDatasets.Schwartz2008("Free")
gps = scores.CGM1_GPS()
scf = scores.ScoreFilter(gps, analysisInstance, ndp)
scf.compute()
# viewer
kv = plotViewers.GpsMapPlotViewer(analysisInstance)
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
def test_CGM1(self):
# results = {'Overall': {'std': array([0.2023908]), 'values': array([5.84457972, 5.35628479, 5.98072926, 5.92348919, 5.73983361,
# 5.75431847]), 'median': array([5.79944909]), 'mean': array([5.76653917])}, 'Context': {'Right': {'std': array([0.24414746]), 'values': array([5.84457972, 5.35628479]), 'median': array([5.60043226]), 'mean': array([5.60043226])}, 'Left': {'std': array([0.10462042]), 'values': array([5.98072926, 5.92348919, 5.73983361, 5.75431847]), 'median': array([5.83890383]), 'mean': array([5.84959263])}}}
DATA_PATH,analysisInstance = dataTest1()
gps =scores.CGM1_GPS()
scf = scores.ScoreFilter(gps,analysisInstance, newNormativeDataset)
scf.compute()
def plot_MAP(DATA_PATH,
analysis,
normativeDataset,
exportPdf=False,
outputName=None,
pointLabelSuffix=None,
show=True,
title=None,
exportPng=False):
"""
plot_MAP : display the Movement Analysis Profile
:param DATA_PATH [str]: path to your data
:param analysis [pyCGM2.Processing.analysis.Analysis]: pyCGM2 analysis instance
:param normativeDataset [pyCGM2.Report.normativeDatasets]: pyCGM2 normative dataset instance
**optional**
:param pointLabelSuffix [string]: (None) suffix added to outputs
:param exportPdf [bool]: save as pdf (False[default])
:param outputName [string]: name of your pdf file (None[default] export your pdf with name : Global Analysis)
:param show [bool]: enable matplotlib show function
:param title [string]: change default title of the plot panel
"""
if outputName is None:
outputName = "PyCGM2-Analysis"
if exportPdf or exportPng:
filenameOut = outputName + "-Map"
#compute
gps = scores.CGM1_GPS(pointSuffix=pointLabelSuffix)
scf = scores.ScoreFilter(gps, analysis, normativeDataset)
scf.compute()
#plot
kv = plotViewers.GpsMapPlotViewer(analysis,
pointLabelSuffix=pointLabelSuffix)
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
if exportPdf: pf.setExport(DATA_PATH, filenameOut, "pdf")
if title is not None: pf.setTitle(title + "-Map")
fig = pf.plot()
if show: plt.show()
if exportPng:
fig.savefig(DATA_PATH + filenameOut + ".png")
return fig, filenameOut + ".png"
else:
return fig
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 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
analysisInstance = analysis.makeAnalysis("Gait", "CGM1.0", DATA_PATH,
modelledFilenames, None, None,
None)
ndp = normativeDatasets.Schwartz2008("Free")
gps = scores.CGM1_GPS()
scf = scores.ScoreFilter(gps, analysisInstance, ndp)
scf.compute()
# viewer
kv = plotViewers.GpsMapPlotViewer(analysisInstance)
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setPath(DATA_PATH)
pf.setPdfName(str("map"))
pf.plot()
plt.show()
def __init__(self, workingDirectory):
self.workingDirectory = workingDirectory
self.null = None
c3dValObj = c3dValidation.c3dValidation(workingDirectory)
self.measurementNames = c3dValObj.getValidC3dList(True)
self.fileNames = c3dValObj.getValidC3dList(False)
self.normative_dataset = normativeDatasets.NormativeData(
"Schwartz2008", "Free")
analysis_per_file = {
path.basename(name).replace(".c3d", ""):
analysis.makeAnalysis(workingDirectory + "\\",
[path.basename(name)])
for name in self.fileNames
}
self.scores = {}
for filename, analysis_obj in analysis_per_file.items():
gps = scores.CGM1_GPS(pointSuffix=None)
scf = scores.ScoreFilter(gps, analysis_obj, self.normative_dataset)
scf.compute()
self.scores[filename] = analysis_obj
def GpsCGM1Test(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\analysis\\gps\\"
reconstructedFilenameLabelledNoExt = "gait Trial 03 - viconName"
reconstructedFilenameLabelled = reconstructedFilenameLabelledNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("reconstructed file: " + reconstructedFilenameLabelled)
modelledFilenames = [reconstructedFilenameLabelled]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- GAIT CYCLES FILTER
#--------------------------------------------------------------------------
cycleBuilder = cycle.GaitCyclesBuilder(
spatioTemporalTrials=trialManager.spatioTemporal["Trials"],
kinematicTrials=trialManager.kinematic["Trials"],
kineticTrials=trialManager.kinetic["Trials"],
emgTrials=trialManager.emg["Trials"])
cyclefilter = cycle.CyclesFilter()
cyclefilter.setBuilder(cycleBuilder)
cycles = cyclefilter.build()
#---- GAIT ANALYSIS FILTER
#--------------------------------------------------------------------------
# ----INFOS-----
modelInfo = {"type": "S01"}
subjectInfo = None
experimentalInfo = None
pointLabelSuffix = ""
pointLabelSuffixPlus = pointLabelSuffix if pointLabelSuffix == "" else "_" + pointLabelSuffix
kinematicLabelsDict = {
'Left': [
"LHipAngles" + pointLabelSuffixPlus,
"LKneeAngles" + pointLabelSuffixPlus,
"LAnkleAngles" + pointLabelSuffixPlus,
"LFootProgressAngles" + pointLabelSuffixPlus,
"LPelvisAngles" + pointLabelSuffixPlus
],
'Right': [
"RHipAngles" + pointLabelSuffixPlus,
"RKneeAngles" + pointLabelSuffixPlus,
"RAnkleAngles" + pointLabelSuffixPlus,
"RFootProgressAngles" + pointLabelSuffixPlus,
"RPelvisAngles" + pointLabelSuffixPlus
]
}
kineticLabelsDict = {
'Left': [
"LHipMoment" + pointLabelSuffixPlus,
"LKneeMoment" + pointLabelSuffixPlus,
"LAnkleMoment" + pointLabelSuffixPlus,
"LHipPower" + pointLabelSuffixPlus,
"LKneePower" + pointLabelSuffixPlus,
"LAnklePower" + pointLabelSuffixPlus
],
'Right': [
"RHipMoment" + pointLabelSuffixPlus,
"RKneeMoment" + pointLabelSuffixPlus,
"RAnkleMoment" + pointLabelSuffixPlus,
"RHipPower" + pointLabelSuffixPlus,
"RKneePower" + pointLabelSuffixPlus,
"RAnklePower" + pointLabelSuffixPlus
]
}
analysisBuilder = analysis.GaitAnalysisBuilder(
cycles,
kinematicLabelsDict=kinematicLabelsDict,
kineticLabelsDict=kineticLabelsDict,
subjectInfos=subjectInfo,
modelInfos=modelInfo,
experimentalInfos=experimentalInfo)
analysisFilter = analysis.AnalysisFilter()
analysisFilter.setBuilder(analysisBuilder)
analysisFilter.setInfo(model=modelInfo)
analysisFilter.build()
analysisInstance = analysisFilter.analysis
## --- GPS ----
ndp = normativeDatasets.Schwartz2008("Free")
gps = scores.CGM1_GPS()
scf = scores.ScoreFilter(gps, analysisInstance, ndp)
scf.compute()
xlsExport = exporter.XlsAnalysisExportFilter()
xlsExport.setAnalysisInstance(analysisInstance)
xlsExport.export("gpsTest2", path=DATA_PATH, mode="Advanced")
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
