def interactiveCropping_fromCropped(cls):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
DATA_PATH = "C:\\Users\\HLS501\\Documents\\VICON DATA\\pyCGM2-Data\\NexusAPI\\BtkAcquisitionCreator\\sample_NOx2d\\"
filenameNoExt = "gait_cropped"
NEXUS.OpenTrial(str(DATA_PATH + filenameNoExt), 30)
NEXUS.SetTrialRegionOfInterest(300, 400)
subject = NEXUS.GetSubjectNames()[0]
trialConstructorFilter = nexusFilters.NexusConstructTrialFilter(
DATA_PATH, filenameNoExt, subject)
trial = trialConstructorFilter.build()
ma.io.write(trialConstructorFilter.m_root,
"TestsNOX2d_interactiveCropping_fromCropped_openMA.c3d")
trial0 = trialTools.smartTrialReader(
DATA_PATH,
"forCheckingInteractiveCropped\\gait_Cropped - 300-400.c3d")
np.testing.assert_array_almost_equal(
trial0.findChild(ma.T_TimeSequence, "LTHI").data(),
trial.findChild(ma.T_TimeSequence, "LTHI").data(),
decimal=2)
np.testing.assert_array_almost_equal(
trial0.findChild(ma.T_TimeSequence, "Voltage.EMG1").data(),
trial.findChild(ma.T_TimeSequence, "Voltage.EMG1").data(),
decimal=2)
def noCroppedC3d(cls):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
DATA_PATH = "C:\\Users\\HLS501\\Documents\\VICON DATA\\pyCGM2-Data\\NexusAPI\\BtkAcquisitionCreator\\sample0\\"
filenameNoExt = "gait_noCropped"
NEXUS.OpenTrial(str(DATA_PATH + filenameNoExt), 30)
subject = NEXUS.GetSubjectNames()[0]
trialConstructorFilter = nexusFilters.NexusConstructTrialFilter(
filenameNoExt, subject)
root = trialConstructorFilter.build()
trial0 = trialTools.smartTrialReader(DATA_PATH,
str(filenameNoExt + ".c3d"))
# firstFrame = (root.findChild(ma.T_TimeSequence,"LTHI").startTime()+0.01)*100.0
# firstFrame0 = (trial0.findChild(ma.T_TimeSequence,"LTHI").startTime()+0.01)*100.0
#
# lastFrame = root.findChild(ma.T_TimeSequence,"LTHI").duration()*100.0
# lastFrame0 = trial0.findChild(ma.T_TimeSequence,"LTHI").duration()*100.0
#
# np.testing.assert_equal(firstFrame,firstFrame0)
# np.testing.assert_equal(lastFrame,lastFrame0)
np.testing.assert_array_almost_equal(
trial0.findChild(ma.T_TimeSequence, "LTHI").data(),
root.findChild(ma.T_TimeSequence, "LTHI").data(),
decimal=2)
np.testing.assert_array_almost_equal(
trial0.findChild(ma.T_TimeSequence, "Voltage.EMG1").data(),
root.findChild(ma.T_TimeSequence, "Voltage.EMG1").data(),
decimal=2)
ma.io.write(root, "gait_noCropped_checked.c3d")
def croppedC3d(cls):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
DATA_PATH = "C:\\Users\\HLS501\\Documents\\VICON DATA\\pyCGM2-Data\\NexusAPI\\BtkAcquisitionCreator\\sample_withx2d\\"
filenameNoExt = "gait_cropped"
NEXUS.OpenTrial(str(DATA_PATH + filenameNoExt), 30)
subject = NEXUS.GetSubjectNames()[0]
trialConstructorFilter = nexusFilters.NexusConstructTrialFilter(
DATA_PATH, filenameNoExt, subject)
trial = trialConstructorFilter.build()
ma.io.write(trialConstructorFilter.m_root,
"TestsX2d_croppedC3d_openma.c3d")
trial0 = trialTools.smartTrialReader(DATA_PATH,
str(filenameNoExt + ".c3d"))
np.testing.assert_array_almost_equal(
trial0.findChild(ma.T_TimeSequence, "LTHI").data(),
trial.findChild(ma.T_TimeSequence, "LTHI").data(),
decimal=2)
np.testing.assert_array_almost_equal(
trial0.findChild(ma.T_TimeSequence, "Voltage.EMG1").data(),
trial.findChild(ma.T_TimeSequence, "Voltage.EMG1").data(),
decimal=2)
def main():
plt.close("all")
parser = argparse.ArgumentParser(description='CGM plot temporal Kinetics')
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:
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()
# --------------------pyCGM2 MODEL ------------------------------
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plotTemporalKinetic(DATA_PATH,
modelledFilename,
"LowerLimb",
pointLabelSuffix=pointSuffix,
exportPdf=True,
openmaTrial=openmaTrial)
# if model.m_bodypart in [enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody]:
# plot.plotTemporalKinetic(DATA_PATH, modelledFilename,"Trunk", pointLabelSuffix=pointSuffix,exportPdf=True)
# 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 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 modelOutputs(cls):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
DATA_PATH = "C:\\Users\\HLS501\\Documents\\VICON DATA\\pyCGM2-Data\\NexusAPI\\BtkAcquisitionCreator\\sample0\\"
filenameNoExt = "gait_cropped_ModelOutputDynamic"
NEXUS.OpenTrial(str(DATA_PATH + filenameNoExt), 30)
subject = NEXUS.GetSubjectNames()[0]
trialConstructorFilter = nexusFilters.NexusConstructTrialFilter(
filenameNoExt, subject)
root = trialConstructorFilter.build()
trial0 = trialTools.smartTrialReader(DATA_PATH,
str(filenameNoExt + ".c3d"))
np.testing.assert_array_almost_equal(
trial0.findChild(ma.T_TimeSequence, "LTHI").data(),
root.findChild(ma.T_TimeSequence, "LTHI").data(),
decimal=2)
ma.io.write(root, str("modelOutputsOpenMA_checked.c3d"))
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")
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")