def dataTest3():
DATA_PATH1 = pyCGM2.TEST_DATA_PATH + "GaitData\\Patient\\session 1 - CGM1\\"
modelledFilenames1 = ["20180706_CS_PONC_S_NNNN dyn 02.c3d",
"20180706_CS_PONC_S_NNNN dyn 03.c3d",
"20180706_CS_PONC_S_NNNN dyn 05.c3d"]
analysisInstance1 = analysis.makeAnalysis(DATA_PATH1,
modelledFilenames1,
type="Gait",
emgChannels = emgChannels,
pointLabelSuffix=None,
subjectInfo=None, experimentalInfo=None,modelInfo=None,
)
DATA_PATH2 = pyCGM2.TEST_DATA_PATH + "GaitData\\Patient\\session 2 - CGM23\\"
modelledFilenames2 = ["20200729-SC-PONC-S-NNNN dyn 04.c3d",
"20200729-SC-PONC-S-NNNN dyn 06.c3d"]
analysisInstance2 = analysis.makeAnalysis(DATA_PATH2,
modelledFilenames2,
type="Gait",
emgChannels = emgChannels,
pointLabelSuffix=None,
subjectInfo=None, experimentalInfo=None,modelInfo=None,
)
return DATA_PATH1,modelledFilenames1,analysisInstance1,DATA_PATH2,modelledFilenames2,analysisInstance2
def test_gaitMeanOnlyKineticPlotPanel(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
analysis1 = analysis.makeAnalysis(DATA_PATH,modelledFilenames)
analysis2 = analysis.makeAnalysis(DATA_PATH,modelledFilenames)
kv = ComparisonPlotViewers.KineticsPlotComparisonViewer([analysis1,analysis2],"Right",
["ana1","ana2"])
kv.setConcretePlotFunction(plot.gaitMeanPlot)
kv.setNormativeDataset(normativeDatasets.Schwartz2008("Free"))
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
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 = analysis.makeAnalysis("Gait", "CGM1.0", DATA_PATH,
modelledFilenames, None, None, None)
analysis2 = analysis.makeAnalysis("Gait", "CGM1.0", DATA_PATH,
modelledFilenames, None, None, None)
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 test_consistencyPlot_OneModelOutputPlot(self):
"""
Plot only one Model output
"""
# ----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)
fig = plt.figure()
ax = plt.gca()
plot.gaitConsistencyPlot(ax,
analysisInstance.kinematicStats,
"LPelvisAngles",
"Left",
0,
color="blue",
title="",
xlabel="",
ylabel="",
ylim=None,
customLimits=None)
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(DATA_PATH, modelledFilenames,
None, None, None)
# viewer
kv = plotViewers.SpatioTemporalPlotViewer(analysisInstance)
kv.setNormativeDataset(normativeDatasets.NormalSTP())
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setExport(DATA_PATH, "stp", "pdf")
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
analysisInstance = analysis.makeAnalysis("Gait", "CGM1.0", DATA_PATH,modelledFilenames,None, None, None)
# viewer
kv = plotViewers.LowerLimbKinematicsPlotViewer(analysisInstance)
kv.setConcretePlotFunction(plot.gaitDescriptivePlot)
kv.setNormativeDataset(normativeDatasets.Schwartz2008("Free"))
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
plt.show()
def test_gaitConsistencyKinematicPlotPanel(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)
# viewer
kv = plotViewers.NormalizedKinematicsPlotViewer(analysisInstance)
kv.setConcretePlotFunction(plot.gaitConsistencyPlot)
kv.setNormativeDataset(normativeDatasets.Schwartz2008("Free"))
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
def test_descriptiveKinematicPlotPanel_savePngAndPdf(self):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"GaitData\CGM1-NormalGaitData-Events\Hånnibøl Lecter\\"
modelledFilenames = ["gait Trial 01.c3d","gait Trial 02.c3d"]
DATA_PATH_OUT = pyCGM2.TEST_DATA_PATH_OUT+"GaitData\CGM1-NormalGaitData-Events\Hånnibøl Lecter\\"
files.createDir(DATA_PATH_OUT)
modelInfo=None
subjectInfo=None
experimentalInfo=None
analysisInstance = analysis.makeAnalysis(DATA_PATH,modelledFilenames)
# viewer
kv = plotViewers.NormalizedKinematicsPlotViewer(analysisInstance)
kv.setConcretePlotFunction(plot.descriptivePlot)
kv.setNormativeDataset(normativeDatasets.Schwartz2008("Free"))
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setExport(DATA_PATH_OUT,"test_descriptiveKinematicPlotPanel","png")
pf.plot()
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setExport(DATA_PATH_OUT,"test_descriptiveKinematicPlotPanel","pdf")
pf.plot()
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 dataTest1():
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitData//CGM1-NormalGaitData-Events//Hannibal Lecter\\"
modelledFilenames = ["gait Trial 01.c3d", "gait Trial 02.c3d"]
analysisInstance = analysis.makeAnalysis(DATA_PATH,
modelledFilenames,
type="Gait")
return DATA_PATH,analysisInstance
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.perFilePyCGM2tspStats = {path.basename(name).replace(".c3d", ""): analysis.makeAnalysis(
workingDirectory + "\\", [path.basename(name)]).stpStats for name in self.fileNames}
def test_meanPlot_OneModelOutputPlot(self):
"""
Plot only one Model output
"""
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitData\CGM1-NormalGaitData-Events\Hånnibøl Lecter\\"
modelledFilenames1 = ["gait Trial 01.c3d"]
modelledFilenames2 = ["gait Trial 02.c3d"]
#---- Analysis
#--------------------------------------------------------------------------
modelInfo = None
subjectInfo = None
experimentalInfo = None
analysis1 = analysis.makeAnalysis(DATA_PATH, modelledFilenames1)
analysis2 = analysis.makeAnalysis(DATA_PATH, modelledFilenames2)
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()
def main():
plt.close("all")
parser = argparse.ArgumentParser(description='CGM plot stp')
parser.add_argument('-ps',
'--pointSuffix',
type=str,
help='suffix added to pyCGM2 outputs')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED:
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)
# ----- 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
plot.plot_spatioTemporal(DATA_PATH,
analysisInstance,
exportPdf=True,
outputName=modelledFilename)
else:
raise Exception("NO Nexus connection. Turn on Nexus")
def main(args):
DATA_PATH = os.getcwd()+"\\"
userSettings = files.openFile(DATA_PATH,args.userFile)
manager = ProcessingManager.GaitProcessingConfigManager(userSettings,modelVersion=None)
modelledTrials = [str(trialFilename[:-4]+"-pyCGM2modelled.c3d") for trialFilename in manager.modelledTrials]
analysisInstance = analysis.makeAnalysis(
DATA_PATH,modelledTrials,
subjectInfo=manager.subjectInfo,
experimentalInfo=manager.experimentalInfo,
modelInfo=None,
pointLabelSuffix=manager.pointSuffix)
plot.plot_spatioTemporal(DATA_PATH,analysisInstance,
exportPdf=True,
outputName=manager.title)
for body in manager.bodyPart:
if not manager.consistencyFlag:
plot.plot_DescriptiveKinematic(DATA_PATH,analysisInstance,body,
manager.normativeData,
exportPdf=True,
outputName=manager.title,
pointLabelSuffix=manager.pointSuffix)
try:
plot.plot_DescriptiveKinetic(DATA_PATH,analysisInstance,body,
manager.normativeData,
exportPdf=True,outputName=manager.title,
pointLabelSuffix=manager.pointSuffix)
except:
pass
else:
plot.plot_ConsistencyKinematic(DATA_PATH,analysisInstance,body,
manager.normativeData,
exportPdf=True,
outputName=manager.title,
pointLabelSuffix=manager.pointSuffix)
try:
plot.plot_ConsistencyKinetic(DATA_PATH,analysisInstance,body,
manager.normativeData,
exportPdf=True,outputName=manager.title,
pointLabelSuffix=manager.pointSuffix)
except:
pass
plot.plot_MAP(DATA_PATH,analysisInstance,manager.normativeData,exportPdf=True,outputName=manager.title,pointLabelSuffix=manager.pointSuffix)
def dataTest2():
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitData\\Patient\\session 1 - CGM1\\"
modelledFilenames = ["20180706_CS_PONC_S_NNNN dyn 02.c3d",
"20180706_CS_PONC_S_NNNN dyn 03.c3d",
"20180706_CS_PONC_S_NNNN dyn 05.c3d"]
analysisInstance = analysis.makeAnalysis(DATA_PATH,
modelledFilenames,
type="Gait",
emgChannels = emgChannels,
pointLabelSuffix=None,
subjectInfo=None, experimentalInfo=None,modelInfo=None,
)
return DATA_PATH,modelledFilenames,analysisInstance
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
analysisInstance = analysis.makeAnalysis("Gait", "CGM1.0", DATA_PATH,
modelledFilenames, None, None,
None)
fig = plt.figure()
ax = plt.gca()
plot.gaitConsistencyPlot(ax,
analysisInstance.kinematicStats,
"LPelvisAngles",
"Left",
0,
color="blue",
title="",
xlabel="",
ylabel="",
ylim=None,
customLimits=None)
plt.show()
def test_fullBody(self):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"GaitData\\CGM1-NormalGaitData-Events\\cgm1-fullbody\\"
modelledFilenames = ["gait1.c3d","gait2.c3d"]
DATA_PATH_OUT = pyCGM2.TEST_DATA_PATH_OUT+"GaitData\\CGM1-NormalGaitData-Events\\cgm1-fullbody\\"
files.createDir(DATA_PATH_OUT)
nds = normativeDatasets.Schwartz2008("Free")
analysisInstance = analysis.makeAnalysis(DATA_PATH,modelledFilenames)
plot.plot_DescriptiveKinematic(DATA_PATH,analysisInstance,"LowerLimb",
nds,
pointLabelSuffix=None,
type="Gait",
exportPdf=False,
outputName=None,
show=True,
title=None)
plot.plot_DescriptiveKinematic(DATA_PATH,analysisInstance,"Trunk",
nds,
pointLabelSuffix=None,
type="Gait",
exportPdf=False,
outputName=None,
show=True,
title=None)
plot.plot_DescriptiveKinematic(DATA_PATH,analysisInstance,"UpperLimb",
nds,
pointLabelSuffix=None,
type="Gait",
exportPdf=False,
outputName=None,
show=True,
title=None)
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 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)
# viewer
kv = plotViewers.SpatioTemporalPlotViewer(analysisInstance)
kv.setNormativeDataset(normativeDatasets.NormalSTP())
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
def main():
logging.info("------------------------------------------------")
logging.info("------------QTM - pyCGM2 Workflow---------------")
logging.info("------------------------------------------------")
file = "session.xml"
sessionXML = files.readXml(os.getcwd() + "\\", file)
sessionDate = files.getFileCreationDate(os.getcwd() + "\\" + file)
#---------------------------------------------------------------------------
#management of the Processed folder
DATA_PATH = os.getcwd() + "\\" + "processed\\"
files.createDir(DATA_PATH)
staticMeasurement = qtmTools.findStatic(sessionXML)
calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement)
if not os.path.isfile(DATA_PATH + calibrateFilenameLabelled):
shutil.copyfile(os.getcwd() + "\\" + calibrateFilenameLabelled,
DATA_PATH + calibrateFilenameLabelled)
logging.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(calibrateFilenameLabelled))
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
for dynamicMeasurement in dynamicMeasurements:
reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement)
if not os.path.isfile(DATA_PATH + reconstructFilenameLabelled):
shutil.copyfile(os.getcwd() + "\\" + reconstructFilenameLabelled,
DATA_PATH + reconstructFilenameLabelled)
logging.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(reconstructFilenameLabelled))
acq = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
if btkTools.checkForcePlateExist(acq):
if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM",
"TYPE"):
forceplates.correctForcePlateType5(acq)
acq, zeniState = eventDetector.zeni(acq)
if zeniState:
btkTools.smartWriter(
acq, str(DATA_PATH + reconstructFilenameLabelled))
cmd = "Mokka.exe \"%s\"" % (str(DATA_PATH +
reconstructFilenameLabelled))
os.system(cmd)
# --------------------------GLOBAL SETTINGS ------------------------------------
# global setting ( in user/AppData)
if os.path.isfile(pyCGM2.PYCGM2_APPDATA_PATH + "CGM2_2-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM2_2-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM2_2-pyCGM2.settings")
# --------------------------MP ------------------------------------
required_mp, optional_mp = qtmTools.SubjectMp(sessionXML)
# --Check MP
inspectprocedure = inspectProcedures.AnthropometricDataQualityProcedure(
required_mp)
inspector = inspectFilters.QualityFilter(inspectprocedure)
inspector.run()
# translators management
translators = files.getTranslators(os.getcwd() + "\\",
"CGM2_2.translators")
if not translators: translators = settings["Translators"]
# ikweight
ikWeight = files.getIKweightSet(DATA_PATH, "CGM2_2.ikw")
if not ikWeight: ikWeight = settings["Fitting"]["Weight"]
# --------------------------MODEL CALIBRATION -----------------------
logging.info(
"--------------------------MODEL CALIBRATION -----------------------")
staticMeasurement = qtmTools.findStatic(sessionXML)
calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement)
logging.info("----- CALIBRATION- static file [%s]--" %
(calibrateFilenameLabelled))
leftFlatFoot = toBool(
staticMeasurement.Left_foot_normalised_to_static_trial.text)
rightFlatFoot = toBool(
staticMeasurement.Right_foot_normalised_to_static_trial.text)
headFlat = toBool(staticMeasurement.Head_normalised_to_static_trial.text)
markerDiameter = float(staticMeasurement.Marker_diameter.text) * 1000.0
hjcMethod = settings["Calibration"]["HJC"]
pointSuffix = None
# Calibration checking
# --------------------
acqStatic = btkTools.smartReader(DATA_PATH + calibrateFilenameLabelled)
for key in MARKERSETS.keys():
logging.info("[pyCGM2] Checking of the %s" % (key))
# presence
ip_presence = inspectProcedures.MarkerPresenceQualityProcedure(
acqStatic, markers=MARKERSETS[key])
inspector = inspectFilters.QualityFilter(ip_presence)
inspector.run()
if ip_presence.markersIn != []:
ip_gap = inspectProcedures.GapQualityProcedure(
acqStatic, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_gap)
inspector.run()
ip_swap = inspectProcedures.SwappingMarkerQualityProcedure(
acqStatic, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_swap)
inspector.run()
ip_pos = inspectProcedures.MarkerPositionQualityProcedure(
acqStatic, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_pos)
# Calibration operation
# --------------------
logging.info("[pyCGM2] --- calibration operation ---")
model, acqStatic = cgm2_2.calibrate(DATA_PATH, calibrateFilenameLabelled,
translators, settings, required_mp,
optional_mp, False, leftFlatFoot,
rightFlatFoot, headFlat,
markerDiameter, hjcMethod, pointSuffix)
logging.info("----- CALIBRATION- static file [%s]-----> DONE" %
(calibrateFilenameLabelled))
# --------------------------MODEL FITTING ----------------------------------
logging.info(
"--------------------------MODEL FITTING ----------------------------------"
)
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
modelledC3ds = list()
eventInspectorStates = list()
for dynamicMeasurement in dynamicMeasurements:
reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement)
logging.info("----Processing of [%s]-----" %
(reconstructFilenameLabelled))
mfpa = qtmTools.getForcePlateAssigment(dynamicMeasurement)
momentProjection_text = dynamicMeasurement.Moment_Projection.text
if momentProjection_text == "Default":
momentProjection_text = settings["Fitting"]["Moment Projection"]
if momentProjection_text == "Distal":
momentProjection = enums.MomentProjection.Distal
elif momentProjection_text == "Proximal":
momentProjection = enums.MomentProjection.Proximal
elif momentProjection_text == "Global":
momentProjection = enums.MomentProjection.Global
elif momentProjection_text == "JCS":
momentProjection = enums.MomentProjection.JCS
acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled)
# Fitting checking
# --------------------
for key in MARKERSETS.keys():
if key != "Calibration markers":
logging.info("[pyCGM2] Checking of the %s" % (key))
# presence
ip_presence = inspectProcedures.MarkerPresenceQualityProcedure(
acq, markers=MARKERSETS[key])
inspector = inspectFilters.QualityFilter(ip_presence)
inspector.run()
if ip_presence.markersIn != []:
ip_gap = inspectProcedures.GapQualityProcedure(
acq, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_gap)
inspector.run()
ip_swap = inspectProcedures.SwappingMarkerQualityProcedure(
acq, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_swap)
inspector.run()
ip_pos = inspectProcedures.MarkerPositionQualityProcedure(
acq, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_pos)
# filtering
# -----------------------
# marker
order = int(float(dynamicMeasurement.Marker_lowpass_filter_order.text))
fc = float(dynamicMeasurement.Marker_lowpass_filter_frequency.text)
signal_processing.markerFiltering(acq, order=order, fc=fc)
# management of force plate type 5 and force plate filtering
order = int(
float(dynamicMeasurement.Forceplate_lowpass_filter_order.text))
fc = float(dynamicMeasurement.Forceplate_lowpass_filter_frequency.text)
if order != 0 and fc != 0:
acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled)
if btkTools.checkForcePlateExist(acq):
if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM",
"TYPE"):
forceplates.correctForcePlateType5(acq)
signal_processing.markerFiltering(acq, order=order, fc=fc)
else:
if btkTools.checkForcePlateExist(acq):
if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM",
"TYPE"):
forceplates.correctForcePlateType5(acq)
btkTools.smartWriter(acq, DATA_PATH + reconstructFilenameLabelled)
# event checking
# -----------------------
inspectprocedureEvents = inspectProcedures.GaitEventQualityProcedure(
acq)
inspector = inspectFilters.QualityFilter(inspectprocedureEvents)
inspector.run()
eventInspectorStates.append(inspectprocedureEvents.state)
# fitting operation
# -----------------------
logging.info("[pyCGM2] --- Fitting operation ---")
acqGait = cgm2_2.fitting(model, DATA_PATH, reconstructFilenameLabelled,
translators, settings, markerDiameter,
pointSuffix, mfpa, momentProjection)
outFilename = reconstructFilenameLabelled #[:-4] + "_CGM1.c3d"
btkTools.smartWriter(acqGait, str(DATA_PATH + outFilename))
modelledC3ds.append(outFilename)
logging.info("----Processing of [%s]-----> DONE" %
(reconstructFilenameLabelled))
# --------------------------GAIT PROCESSING -----------------------
if not all(eventInspectorStates):
raise Exception(
"[pyCGM2] Impossible to run Gait processing. Badly gait event detection. check the log file"
)
logging.info(
"---------------------GAIT PROCESSING -----------------------")
nds = normativeDatasets.Schwartz2008("Free")
types = qtmTools.detectMeasurementType(sessionXML)
for type in types:
modelledTrials = list()
for dynamicMeasurement in dynamicMeasurements:
if qtmTools.isType(dynamicMeasurement, type):
filename = qtmTools.getFilename(dynamicMeasurement)
modelledTrials.append(filename) #.replace(".c3d","_CGM1.c3d"))
subjectMd = {
"patientName":
sessionXML.find("Last_name").text + " " +
sessionXML.find("First_name").text,
"bodyHeight":
sessionXML.find("Height").text,
"bodyWeight":
sessionXML.find("Weight").text,
"diagnosis":
sessionXML.find("Diagnosis").text,
"dob":
sessionXML.find("Date_of_birth").text,
"sex":
sessionXML.find("Sex").text,
"test condition":
type,
"gmfcs":
sessionXML.find("Gross_Motor_Function_Classification").text,
"fms":
sessionXML.find("Functional_Mobility_Scale").text
}
analysisInstance = analysis.makeAnalysis(DATA_PATH,
modelledTrials,
subjectInfo=None,
experimentalInfo=None,
modelInfo=None,
pointLabelSuffix=None)
title = type
# spatiotemporal
plot.plot_spatioTemporal(DATA_PATH,
analysisInstance,
exportPdf=True,
outputName=title,
show=None,
title=title)
#Kinematics
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
if model.m_bodypart in [
enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"Trunk",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"Trunk",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
if model.m_bodypart in [
enums.BodyPart.UpperLimb, enums.BodyPart.FullBody
]:
pass # TODO plot upperlimb panel
#Kinetics
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
plot.plot_ConsistencyKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
#MAP
plot.plot_MAP(DATA_PATH,
analysisInstance,
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
plt.show(False)
logging.info("----- Gait Processing -----> DONE")
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 process_pdf_report(data_path,
modelled_trials,
title,
model,
normative_dataset,
point_suffix=None):
analysisInstance = analysis.makeAnalysis(data_path + "\\",
modelled_trials,
subjectInfo=None,
experimentalInfo=None,
modelInfo=None,
pointLabelSuffix=None)
# spatiotemporal
plot.plot_spatioTemporal(data_path,
analysisInstance,
exportPdf=True,
outputName=title,
show=None,
title=title)
# Kinematics
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(data_path,
analysisInstance,
"LowerLimb",
normative_dataset,
exportPdf=True,
outputName=title,
pointLabelSuffix=point_suffix,
show=False,
title=title)
plot.plot_ConsistencyKinematic(data_path,
analysisInstance,
"LowerLimb",
normative_dataset,
exportPdf=True,
outputName=title,
pointLabelSuffix=point_suffix,
show=False,
title=title)
if model.m_bodypart in [
enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(data_path,
analysisInstance,
"Trunk",
normative_dataset,
exportPdf=True,
outputName=title,
pointLabelSuffix=point_suffix,
show=False,
title=title)
plot.plot_ConsistencyKinematic(data_path,
analysisInstance,
"Trunk",
normative_dataset,
exportPdf=True,
outputName=title,
pointLabelSuffix=point_suffix,
show=False,
title=title)
if model.m_bodypart in [enums.BodyPart.UpperLimb, enums.BodyPart.FullBody]:
pass # TODO plot upperlimb panel
# Kinetics
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinetic(data_path,
analysisInstance,
"LowerLimb",
normative_dataset,
exportPdf=True,
outputName=title,
pointLabelSuffix=point_suffix,
show=False,
title=title)
plot.plot_ConsistencyKinetic(data_path,
analysisInstance,
"LowerLimb",
normative_dataset,
exportPdf=True,
outputName=title,
pointLabelSuffix=point_suffix,
show=False,
title=title)
# MAP
plot.plot_MAP(data_path,
analysisInstance,
normative_dataset,
exportPdf=True,
outputName=title,
pointLabelSuffix=point_suffix,
show=False,
title=title)
plt.show(False)
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 not NEXUS_PYTHON_CONNECTED:
raise Exception("Vicon Nexus is not running")
#-----------------------SETTINGS---------------------------------------
pointSuffix = args.pointSuffix
#-----------------------SETTINGS---------------------------------------
normativeData = {
"Author": args.normativeData,
"Modality": args.normativeDataModality
}
if normativeData["Author"] == "Schwartz2008":
chosenModality = normativeData["Modality"]
elif normativeData["Author"] == "Pinzone2014":
chosenModality = normativeData["Modality"]
nds = normativeDatasets.NormativeData(normativeData["Author"],
chosenModality)
#--------------------------Data Location and subject-------------------------------------
if eclipse.getCurrentMarkedNodes() is not None:
LOGGER.logger.info(
"[pyCGM2] - Script worked with marked node of Vicon Eclipse")
# --- acquisition file and path----
DATA_PATH, modelledFilenames = eclipse.getCurrentMarkedNodes()
ECLIPSE_MODE = True
if not ECLIPSE_MODE:
LOGGER.logger.info(
"[pyCGM2] - Script works with the loaded c3d in vicon Nexus")
# --- acquisition file and path----
DATA_PATH, modelledFilenameNoExt = NEXUS.GetTrialName()
modelledFilename = modelledFilenameNoExt + ".c3d"
LOGGER.logger.info("data Path: " + DATA_PATH)
LOGGER.logger.info("file: " + modelledFilename)
# ----- Subject -----
# need subject to find input files
subject = nexusTools.getActiveSubject(NEXUS)
LOGGER.logger.info("Subject name : " + subject)
if not ECLIPSE_MODE:
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, modelledFilenameNoExt, subject)
acq = nacf.build()
# --------------------------PROCESSING --------------------------------
analysisInstance = analysis.makeAnalysis(DATA_PATH, [modelledFilename],
type="Gait",
kineticLabelsDict=None,
emgChannels=None,
pointLabelSuffix=pointSuffix,
btkAcqs=[acq],
subjectInfo=None,
experimentalInfo=None,
modelInfo=None)
outputName = modelledFilename
else:
analysisInstance = analysis.makeAnalysis(DATA_PATH,
type="Gait",
kineticLabelsDict=None,
emgChannels=None,
pointLabelSuffix=pointSuffix,
subjectInfo=None,
experimentalInfo=None,
modelInfo=None)
outputName = "Eclipse-MAP"
plot.plot_MAP(DATA_PATH,
analysisInstance,
nds,
exportPdf=True,
outputName=outputName,
pointLabelSuffix=pointSuffix)
def pdfGaitReport(DATA_PATH,
model,
modelledTrials,
normativeDataset,
pointSuffix,
title="gait report"):
analysisInstance = analysis.makeAnalysis(DATA_PATH,
modelledTrials,
subjectInfo=None,
experimentalInfo=None,
modelInfo=None,
pointLabelSuffix=None)
with PdfPages(DATA_PATH + title + ".pdf") as pdf:
# spatiotemporal
plot.plot_spatioTemporal(DATA_PATH,
analysisInstance,
exportPdf=False,
outputName=title,
show=None,
title=title)
pdf.savefig()
#Kinematics
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
if model.m_bodypart in [
enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"Trunk",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"Trunk",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
if model.m_bodypart in [
enums.BodyPart.UpperLimb, enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"UpperLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"UpperLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
#Kinetics
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_ConsistencyKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
#MAP
plot.plot_MAP(DATA_PATH,
analysisInstance,
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plt.show(False)
logging.info("----- Gait Processing -----> DONE")
def main():
plt.close("all")
parser = argparse.ArgumentParser(description='CGM plot stp')
parser.add_argument('-ps',
'--pointSuffix',
type=str,
help='suffix added to pyCGM2 outputs')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
ECLIPSE_MODE = False
if not NEXUS_PYTHON_CONNECTED:
raise Exception("Vicon Nexus is not running")
pointSuffix = args.pointSuffix
#--------------------------Data Location and subject-------------------------------------
if eclipse.getCurrentMarkedNodes() is not None:
LOGGER.logger.info(
"[pyCGM2] - Script worked with marked node of Vicon Eclipse")
# --- acquisition file and path----
DATA_PATH, modelledFilenames = eclipse.getCurrentMarkedNodes()
ECLIPSE_MODE = True
if not ECLIPSE_MODE:
LOGGER.logger.info(
"[pyCGM2] - Script works with the loaded c3d in vicon Nexus")
# --------------------------INPUTS ------------------------------------
DATA_PATH, modelledFilenameNoExt = NEXUS.GetTrialName()
modelledFilename = modelledFilenameNoExt + ".c3d"
LOGGER.logger.info("data Path: " + DATA_PATH)
LOGGER.logger.info("file: " + modelledFilename)
# ----- Subject -----
# need subject to find input files
# subjects = NEXUS.GetSubjectNames()
subject = nexusTools.getActiveSubject(NEXUS)
LOGGER.logger.info("Subject name : " + subject)
if not ECLIPSE_MODE:
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, modelledFilenameNoExt, subject)
acq = nacf.build()
# --------------------------PROCESSING --------------------------------
analysisInstance = analysis.makeAnalysis(DATA_PATH, [modelledFilename],
type="Gait",
kineticLabelsDict=None,
emgChannels=None,
pointLabelSuffix=pointSuffix,
btkAcqs=[acq],
subjectInfo=None,
experimentalInfo=None,
modelInfo=None)
outputName = modelledFilename
else:
# --------------------------PROCESSING --------------------------------
analysisInstance = analysis.makeAnalysis(DATA_PATH,
modelledFilenames,
type="Gait",
kineticLabelsDict=None,
emgChannels=None,
pointLabelSuffix=pointSuffix,
subjectInfo=None,
experimentalInfo=None,
modelInfo=None)
outputName = "Eclipse - SpatioTemporal parameters"
plot.plot_spatioTemporal(DATA_PATH,
analysisInstance,
exportPdf=True,
outputName=outputName)
def pdfGaitReport(DATA_PATH,
model,
modelledTrials,
normativeDataset,
pointSuffix,
title="gait report"):
analysisInstance = analysis.makeAnalysis(
DATA_PATH,
modelledTrials,
type="Gait",
emgChannels=None,
pointLabelSuffix=None,
subjectInfo=None,
experimentalInfo=None,
modelInfo=None,
)
analysis.exportAnalysis(analysisInstance,
DATA_PATH,
title,
mode="Advanced")
with PdfPages(DATA_PATH + title + ".pdf") as pdf:
# spatiotemporal
plot.plot_spatioTemporal(DATA_PATH,
analysisInstance,
exportPdf=False,
outputName=title,
show=None,
title=title)
pdf.savefig()
#Kinematics
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"Trunk",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"Trunk",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"UpperLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"UpperLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
#Kinetics
plot.plot_DescriptiveKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
plot.plot_ConsistencyKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
#MAP
plot.plot_MAP(DATA_PATH,
analysisInstance,
normativeDataset,
exportPdf=False,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
pdf.savefig()
def main():
parser = argparse.ArgumentParser(description='EMG-plot_temporalEMG')
parser.add_argument('-bpf', '--BandpassFrequencies', nargs='+',help='bandpass filter')
parser.add_argument('-elf','--EnvelopLowpassFrequency', type=int, help='cutoff frequency for emg envelops')
parser.add_argument('-c','--consistency', action='store_true', help='consistency plots')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
ECLIPSE_MODE = False
if not NEXUS_PYTHON_CONNECTED:
raise Exception("Vicon Nexus is not running")
#--------------------------Data Location-------------------------------------
if eclipse.getCurrentMarkedNodes() is not None:
LOGGER.logger.info("[pyCGM2] - Script worked with marked node of Vicon Eclipse")
# --- acquisition file and path----
DATA_PATH, inputFiles =eclipse.getCurrentMarkedNodes()
ECLIPSE_MODE = True
if not ECLIPSE_MODE:
LOGGER.logger.info("[pyCGM2] - Script works with the loaded c3d in vicon Nexus")
# --- acquisition file and path----
DATA_PATH, inputFileNoExt = NEXUS.GetTrialName()
inputFile = inputFileNoExt+".c3d"
LOGGER.set_file_handler(DATA_PATH+"pyCGM2.log")
#--------------------------settings-------------------------------------
if os.path.isfile(DATA_PATH + "emg.settings"):
emgSettings = files.openFile(DATA_PATH,"emg.settings")
LOGGER.logger.warning("[pyCGM2]: emg.settings detected in the data folder")
else:
emgSettings = None
manager = EmgManager.EmgConfigManager(None,localInternalSettings=emgSettings)
manager.contruct()
# ----------------------INPUTS-------------------------------------------
bandPassFilterFrequencies = manager.BandpassFrequencies#emgSettings["Processing"]["BandpassFrequencies"]
if args.BandpassFrequencies is not None:
if len(args.BandpassFrequencies) != 2:
raise Exception("[pyCGM2] - bad configuration of the bandpass frequencies ... set 2 frequencies only")
else:
bandPassFilterFrequencies = [float(args.BandpassFrequencies[0]),float(args.BandpassFrequencies[1])]
LOGGER.logger.info("Band pass frequency set to %i - %i instead of 20-200Hz",bandPassFilterFrequencies[0],bandPassFilterFrequencies[1])
envelopCutOffFrequency = manager.EnvelopLowpassFrequency#emgSettings["Processing"]["EnvelopLowpassFrequency"]
if args.EnvelopLowpassFrequency is not None:
envelopCutOffFrequency = args.EnvelopLowpassFrequency
LOGGER.logger.info("Cut-off frequency set to %i instead of 6Hz ",envelopCutOffFrequency)
consistencyFlag = True if args.consistency else False
# --------------emg Processing--------------
EMG_LABELS,EMG_MUSCLES,EMG_CONTEXT,NORMAL_ACTIVITIES = manager.getEmgConfiguration()
if not ECLIPSE_MODE:
# --------------------------SUBJECT ------------------------------------
subject = nexusTools.getActiveSubject(NEXUS)
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(DATA_PATH,inputFileNoExt,subject)
acq = nacf.build()
emg.processEMG_fromBtkAcq(acq, EMG_LABELS,
highPassFrequencies=bandPassFilterFrequencies,
envelopFrequency=envelopCutOffFrequency) # high pass then low pass for all c3ds
# emgAnalysis = analysis.makeEmgAnalysis(DATA_PATH, [inputFile], EMG_LABELS,btkAcqs = [acq])
emgAnalysis = analysis.makeAnalysis(DATA_PATH,
[inputFile],
type="Gait",
kinematicLabelsDict=None,
kineticLabelsDict=None,
emgChannels = EMG_LABELS,
pointLabelSuffix=None,
btkAcqs=[acq],
subjectInfo=None, experimentalInfo=None,modelInfo=None,
)
outputName = inputFile
else:
emg.processEMG(DATA_PATH, inputFiles, EMG_LABELS, highPassFrequencies=bandPassFilterFrequencies,
envelopFrequency=envelopCutOffFrequency)
emgAnalysis = analysis.makeAnalysis(DATA_PATH,
[inputFile],
type="Gait",
kinematicLabelsDict=None,
kineticLabelsDict=None,
emgChannels = EMG_LABELS,
pointLabelSuffix=None,
subjectInfo=None, experimentalInfo=None,modelInfo=None,
)
outputName = "Eclipse - NormalizedEMG"
if not consistencyFlag:
plot.plotDescriptiveEnvelopEMGpanel(DATA_PATH,emgAnalysis, EMG_LABELS,EMG_MUSCLES,EMG_CONTEXT, NORMAL_ACTIVITIES, normalized=False,exportPdf=True,outputName=outputName)
else:
plot.plotConsistencyEnvelopEMGpanel(DATA_PATH,emgAnalysis, EMG_LABELS,EMG_MUSCLES,EMG_CONTEXT, NORMAL_ACTIVITIES, normalized=False,exportPdf=True,outputName=outputName)
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 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")