def normativeData(self):
normativeData = {
"Author": self._userSettings["NormativeData"]["Author"],
"Modality": self._userSettings["NormativeData"]["Modality"]
}
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)
return nds
def main(args):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED:
#-----------------------SETTINGS---------------------------------------
pointSuffix = args.pointSuffix
normativeData = {
"Author": args.normativeData,
"Modality": args.normativeDataModality
}
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"
consistencyFlag = True if args.consistency else False
# --------------------------INPUTS ------------------------------------
DATA_PATH, modelledFilenameNoExt = NEXUS.GetTrialName()
modelledFilename = modelledFilenameNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("file: " + modelledFilename)
# ----- Subject -----
# need subject to find input files
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.checkActivatedSubject(NEXUS, subjects)
logging.info("Subject name : " + subject)
# ----- construction of the openMA root instance -----
trialConstructorFilter = nexusFilters.NexusConstructTrialFilter(
DATA_PATH, modelledFilenameNoExt, subject)
openmaTrial = trialConstructorFilter.build()
# --------------------pyCGM2 MODEL ------------------------------
model = files.loadModel(DATA_PATH, subject)
modelVersion = model.version
# --------------------------PROCESSING --------------------------------
analysisInstance = analysis.makeAnalysis(
DATA_PATH, [modelledFilename],
pointLabelSuffix=pointSuffix,
openmaTrials=[openmaTrial]
) # analysis structure gathering Time-normalized Kinematic and kinetic CGM outputs
if not consistencyFlag:
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
pointLabelSuffix=pointSuffix,
exportPdf=True,
outputName=modelledFilename)
else:
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_ConsistencyKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
pointLabelSuffix=pointSuffix,
exportPdf=True,
outputName=modelledFilename)
else:
raise Exception("NO Nexus connection. Turn on Nexus")
def main():
plt.close("all")
parser = argparse.ArgumentParser(
description='CGM plot Normalized Kinematics')
parser.add_argument(
'-nd',
'--normativeData',
type=str,
help='normative Data set (Schwartz2008 or Pinzone2014)',
default="Schwartz2008")
parser.add_argument(
'-ndm',
'--normativeDataModality',
type=str,
help=
"if Schwartz2008 [VerySlow,SlowFree,Fast,VeryFast] - if Pinzone2014 [CentreOne,CentreTwo]",
default="Free")
parser.add_argument('-ps',
'--pointSuffix',
type=str,
help='suffix of model outputs')
parser.add_argument('-c',
'--consistency',
action='store_true',
help='consistency plots')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED:
#-----------------------SETTINGS---------------------------------------
normativeData = {
"Author": args.normativeData,
"Modality": args.normativeDataModality
}
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"
consistencyFlag = True if args.consistency else False
pointSuffix = args.pointSuffix
# --------------------------INPUTS ------------------------------------
DATA_PATH, modelledFilenameNoExt = NEXUS.GetTrialName()
modelledFilename = modelledFilenameNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("file: " + modelledFilename)
# ----- Subject -----
# need subject to find input files
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.checkActivatedSubject(NEXUS, subjects)
logging.info("Subject name : " + subject)
# --------------------pyCGM2 MODEL ------------------------------
model = files.loadModel(DATA_PATH, subject)
modelVersion = model.version
# ----- construction of the openMA root instance -----
trialConstructorFilter = nexusFilters.NexusConstructTrialFilter(
DATA_PATH, modelledFilenameNoExt, subject)
openmaTrial = trialConstructorFilter.build()
# --------------------------PROCESSING --------------------------------
analysisInstance = analysis.makeAnalysis(DATA_PATH, [modelledFilename],
pointLabelSuffix=pointSuffix,
openmaTrials=[openmaTrial])
if not consistencyFlag:
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
pointLabelSuffix=pointSuffix,
exportPdf=True,
outputName=modelledFilename)
#plot_DescriptiveKinematic(DATA_PATH,analysis,bodyPart,normativeDataset,pointLabelSuffix=None,type="Gait",exportPdf=False,outputName=None):
if model.m_bodypart in [
enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"Trunk",
nds,
pointLabelSuffix=pointSuffix,
exportPdf=True,
outputName=modelledFilename)
if model.m_bodypart in [
enums.BodyPart.UpperLimb, enums.BodyPart.FullBody
]:
pass # TODO plot upperlimb panel
else:
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
pointLabelSuffix=pointSuffix,
exportPdf=True,
outputName=modelledFilename)
if model.m_bodypart in [
enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody
]:
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"Trunk",
nds,
pointLabelSuffix=pointSuffix,
exportPdf=True,
outputName=modelledFilename)
if model.m_bodypart in [
enums.BodyPart.UpperLimb, enums.BodyPart.FullBody
]:
pass # TODO plot upperlimb panel
else:
raise Exception("NO Nexus connection. Turn on Nexus")
def main():
plt.close("all")
parser = argparse.ArgumentParser(description='CGM plotMAP')
parser.add_argument(
'-nd',
'--normativeData',
type=str,
help='normative Data set (Schwartz2008 or Pinzone2014)',
default="Schwartz2008")
parser.add_argument(
'-ndm',
'--normativeDataModality',
type=str,
help=
"if Schwartz2008 [VerySlow,SlowFree,Fast,VeryFast] - if Pinzone2014 [CentreOne,CentreTwo]",
default="Free")
parser.add_argument('-ps',
'--pointSuffix',
type=str,
help='suffix of model outputs')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED:
#-----------------------SETTINGS---------------------------------------
pointSuffix = args.pointSuffix
normativeData = {
"Author": args.normativeData,
"Modality": args.normativeDataModality
}
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"
# --------------------------INPUTS ------------------------------------
DATA_PATH, modelledFilenameNoExt = NEXUS.GetTrialName()
modelledFilename = modelledFilenameNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("file: " + modelledFilename)
# ----- Subject -----
# need subject to find input files
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.checkActivatedSubject(NEXUS, subjects)
logging.info("Subject name : " + subject)
# ----- construction of the openMA root instance -----
trialConstructorFilter = nexusFilters.NexusConstructTrialFilter(
DATA_PATH, modelledFilenameNoExt, subject)
openmaTrial = trialConstructorFilter.build()
# --------------------pyCGM2 MODEL ------------------------------
model = files.loadModel(DATA_PATH, subject)
modelVersion = model.version
# --------------------------PROCESSING --------------------------------
analysisInstance = analysis.makeAnalysis(
DATA_PATH, [modelledFilename],
None,
None,
None,
pointLabelSuffix=pointSuffix,
openmaTrials=[openmaTrial]
) # analysis structure gathering Time-normalized Kinematic and kinetic CGM outputs
plot.plot_MAP(DATA_PATH,
analysisInstance,
nds,
exportPdf=True,
outputName=modelledFilename,
pointLabelSuffix=pointSuffix)
else:
raise Exception("NO Nexus connection. Turn on Nexus")
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