def test_temporalEmgPlot(self):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"GaitData\\EMG\\Hånnibøl Lecter-nerve block\\"
gaitTrial = "PRE-gait trial 01.c3d"
restTrial = "PRE-repos.c3d"
DATA_PATH_OUT = pyCGM2.TEST_DATA_PATH_OUT+"GaitData\\EMG\\Hånnibøl Lecter-nerve block\\"
files.createDir(DATA_PATH_OUT)
#--------------------------settings-------------------------------------
if os.path.isfile(DATA_PATH + "emg.settings"):
emgSettings = files.openFile(DATA_PATH,"emg.settings")
logging.warning("[pyCGM2]: emg.settings detected in the data folder")
else:
emgSettings = None
manager = EmgManager.EmgConfigManager(None,localInternalSettings=emgSettings)
manager.contruct()
EMG_LABELS,EMG_MUSCLES,EMG_CONTEXT,NORMAL_ACTIVITIES = manager.getEmgConfiguration()
rectifyBool=True
acq = btkTools.smartReader(DATA_PATH+gaitTrial)
analysis.processEMG_fromBtkAcq(acq, EMG_LABELS,
highPassFrequencies=[20,200],
envelopFrequency=6.0)
openmaTrial = trialTools.convertBtkAcquisition(acq)
plot.plotTemporalEMG(DATA_PATH,gaitTrial, EMG_LABELS,EMG_MUSCLES, EMG_CONTEXT, NORMAL_ACTIVITIES,exportPdf=False,rectify=rectifyBool,openmaTrial=openmaTrial)
def test_temporalEmgPlot(self):
DATA_PATH, modelledFilenames,acq = dataTest2()
emg.processEMG(DATA_PATH, modelledFilenames, emgChannels,
highPassFrequencies=[20,200],envelopFrequency=6.0,
fileSuffix=None,outDataPath=None)
figs = plot.plotTemporalEMG(DATA_PATH, modelledFilenames[0],
emgChannels, muscles, contexts, normalActivityEmgs,
rectify = True,
exportPdf=False,outputName=None,show=False,title=None,
btkAcq=None)
if SHOW: plt.show()
return figs[0]
def main():
parser = argparse.ArgumentParser(description='EMG-plot_temporalEMG')
parser.add_argument('-bpf', '--BandpassFrequencies', nargs='+',help='bandpass filter')
parser.add_argument('-ecf','--EnvelopLowpassFrequency', type=int, help='cutoff frequency for emg envelops')
parser.add_argument('-r','--raw', action='store_true', help='rectified data')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
# --- acquisition file and path----
DATA_PATH, inputFileNoExt = NEXUS.GetTrialName()
inputFile = inputFileNoExt+".c3d"
#--------------------------settings-------------------------------------
if os.path.isfile(DATA_PATH + "emg.settings"):
emgSettings = files.openFile(DATA_PATH,"emg.settings")
logging.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])]
logging.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
logging.info("Cut-off frequency set to %i instead of 6Hz ",envelopCutOffFrequency)
rectifyBool = False if args.raw else True
# --------------------------SUBJECT ------------------------------------
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.checkActivatedSubject(NEXUS,subjects)
# btk Acquisition
nacf = nexusFilters.NexusConstructAcquisitionFilter(DATA_PATH,inputFileNoExt,subject)
acq = nacf.build()
# --------------emg Processing--------------
EMG_LABELS,EMG_MUSCLES,EMG_CONTEXT,NORMAL_ACTIVITIES = manager.getEmgConfiguration()
analysis.processEMG_fromBtkAcq(acq, EMG_LABELS,
highPassFrequencies=bandPassFilterFrequencies,
envelopFrequency=envelopCutOffFrequency) # high pass then low pass for all c3ds
openmaTrial = trialTools.convertBtkAcquisition(acq)
plot.plotTemporalEMG(DATA_PATH,inputFile, EMG_LABELS,EMG_MUSCLES, EMG_CONTEXT, NORMAL_ACTIVITIES,exportPdf=True,rectify=rectifyBool,
openmaTrial=openmaTrial)
else:
raise Exception("NO Nexus connection. Turn on Nexus")
def main(args):
DATA_PATH = os.getcwd() + "\\"
# User Settings
if os.path.isfile(DATA_PATH + args.userFile):
userSettings = files.openFile(DATA_PATH, args.userFile)
else:
raise Exception("user setting file not found")
# internal (expert) Settings
if args.expertFile:
if os.path.isfile(DATA_PATH + args.expertFile):
internalSettings = files.openFile(DATA_PATH, args.expertFile)
else:
raise Exception("expert setting file not found")
else:
internalSettings = None
# --- Manager ----
manager = EmgManager.EmgConfigManager(
userSettings, localInternalSettings=internalSettings)
manager.contruct()
finalSettings = manager.getFinalSettings()
files.prettyDictPrint(finalSettings)
# reconfiguration of emg settings as lists
EMG_LABELS, EMG_MUSCLES, EMG_CONTEXT, NORMAL_ACTIVITIES = manager.getEmgConfiguration(
)
#----- rectified view -------
rectTrials = manager.temporal_trials
analysis.processEMG(
DATA_PATH,
rectTrials,
EMG_LABELS,
highPassFrequencies=manager.BandpassFrequencies,
envelopFrequency=manager.EnvelopLowpassFrequency,
fileSuffix=None) # high pass then low pass for all c3ds
for trial in rectTrials:
plot.plotTemporalEMG(DATA_PATH,
trial,
EMG_LABELS,
EMG_MUSCLES,
EMG_CONTEXT,
NORMAL_ACTIVITIES,
exportPdf=True,
rectify=manager.rectifyFlag)
#----- Gait normalized envelop -------
envTrials = manager.gaitNormalized_trials
analysis.processEMG(
DATA_PATH,
envTrials,
EMG_LABELS,
highPassFrequencies=manager.BandpassFrequencies,
envelopFrequency=manager.EnvelopLowpassFrequency,
fileSuffix=None) # high pass then low pass for all c3ds
emgAnalysisInstance = analysis.makeEmgAnalysis(DATA_PATH, envTrials,
EMG_LABELS, None, None)
filename = manager.title
if not manager.consistencyFlag:
plot.plotDescriptiveEnvelopEMGpanel(DATA_PATH,
emgAnalysisInstance,
EMG_LABELS,
EMG_MUSCLES,
EMG_CONTEXT,
NORMAL_ACTIVITIES,
normalized=False,
exportPdf=True,
outputName=filename)
else:
plot.plotConsistencyEnvelopEMGpanel(DATA_PATH,
emgAnalysisInstance,
EMG_LABELS,
EMG_MUSCLES,
EMG_CONTEXT,
NORMAL_ACTIVITIES,
normalized=False,
exportPdf=True,
outputName=filename)
logging.info("=============Writing of final Settings=============")
files.saveJson(DATA_PATH, str(filename + "-EMG.completeSettings"),
finalSettings)
logging.info("---->complete settings (%s) exported" %
(str(filename + "-EMG.completeSettings")))
raw_input("Press return to exit..")