def temporalPlotPanel(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "EMG\\SampleNantes\\"
gaitTrial = "gait.c3d"
restTrial = "repos.c3d"
EMG_LABELS = ['EMG1', 'EMG2', 'EMG3', 'EMG4']
acq = btkTools.smartReader(DATA_PATH + gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq, EMG_LABELS)
bf.setHighPassFrequencies(20.0, 200.0)
bf.run()
btkTools.smartWriter(acq, "testBasicPlot.c3d")
trial = trialTools.smartTrialReader(None, "testBasicPlot.c3d")
# # viewer
kv = emgPlotViewers.TemporalEmgPlotViewer(trial)
kv.setEmgs([["EMG1", "Left"], ["EMG2", "Right"], ["EMG3", "Left"],
["EMG4", "Right"]])
kv.setNormalActivationLabels(["RECFEM", "RECFEM", None, "VASLAT"])
kv.setEmgRectify(True)
# # filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
plt.show()
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 temporalPlotSingleEmg(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "EMG\\SampleNantes\\"
gaitTrial = "gait.c3d"
restTrial = "repos.c3d"
EMG_LABELS = ['EMG1']
acq = btkTools.smartReader(DATA_PATH + gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq, EMG_LABELS)
bf.setHighPassFrequencies(20.0, 200.0)
bf.run()
btkTools.smartWriter(acq, "testBasicPlot.c3d")
trial = trialTools.smartTrialReader(None, "testBasicPlot.c3d")
fig = plt.figure()
ax = plt.gca()
plot.temporalPlot(ax,
trial,
"EMG1_Rectify",
0,
color="blue",
title="test",
xlabel="frame",
ylabel="emg",
ylim=None,
legendLabel=None,
customLimits=None)
plot.addTemporalNormalActivationLayer(ax, trial, "RECFEM", "Left")
plt.show()
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 cgm_staticPlot(modelVersion,
modelledStaticFilename,
DATA_PATH,
outputPath=None,
pdfFilename="staticProcessing",
pointLabelSuffix=""):
# check model is the CGM1
logging.info("loaded model : %s" % (modelVersion))
if outputPath is None:
outputPath = DATA_PATH
trial = trialTools.smartTrialReader(DATA_PATH, modelledStaticFilename)
#viewer
if modelVersion in [
"CGM1.0", "CGM1.1", "CGM2.1", "CGM2.2", "CGM2.2e", "CGM2.3",
"CGM2.3e"
]:
kv = plotViewers.TemporalGaitKinematicsPlotViewer(
trial, pointLabelSuffix=pointLabelSuffix)
else:
raise Exception("[pyCGM2] Model version not known")
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setPath(outputPath)
pf.setPdfName(pdfFilename)
pf.plot()
def test_temporalPlotSingleEmg(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)
EMG_LABELS=['EMG1']
acq = btkTools.smartReader(DATA_PATH +gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq,EMG_LABELS)
bf.setHighPassFrequencies(20.0,200.0)
bf.run()
btkTools.smartWriter(acq,DATA_PATH_OUT+"test_temporalPlotSingleEmg.c3d")
trial =trialTools.smartTrialReader(DATA_PATH_OUT,"test_temporalPlotSingleEmg.c3d")
fig = plt.figure()
ax = plt.gca()
plot.temporalPlot(ax,trial,"EMG1_Rectify",0,
color="blue",
title="test", xlabel="frame", ylabel="emg",ylim=None,legendLabel=None,
customLimits=None)
plot.addTemporalNormalActivationLayer(ax,trial,"RECFEM","Left")
def temporalPlot_OneModelOutputPlot(cls):
"""
Plot only one Model output
"""
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\plot\\gaitPlot\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
trial = trialTools.smartTrialReader(DATA_PATH, modelledFilenames[0])
fig = plt.figure()
ax = plt.gca()
plot.temporalPlot(ax,
trial,
"LPelvisAngles",
0,
color="blue",
title="test",
xlabel="frame",
ylabel="angle",
ylim=None,
legendLabel=None,
customLimits=None)
plt.show()
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 test_temporalPlotPanel(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)
EMG_LABELS=['EMG1','EMG2','EMG3','EMG4']
acq = btkTools.smartReader(DATA_PATH +gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq,EMG_LABELS)
bf.setHighPassFrequencies(20.0,200.0)
bf.run()
btkTools.smartWriter(acq,DATA_PATH_OUT+"test_temporalPlotPanel.c3d")
trial =trialTools.smartTrialReader(DATA_PATH_OUT,"test_temporalPlotPanel.c3d")
# # viewer
kv = emgPlotViewers.TemporalEmgPlotViewer(trial)
kv.setEmgs([["EMG1","Left","RF"],["EMG2","Right","RF"],["EMG3","Left","vaste"],["EMG4","Right","vaste"]])
kv.setNormalActivationLabels(["RECFEM","RECFEM",None,"VASLAT"])
kv. setEmgRectify(True)
# # filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setExport(DATA_PATH_OUT,"hän-test_temporalPlotPanel","png")
pf.plot()
def gaitTrialGarches(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\progression\\"
gaitFilename="gait_garches_issue2.c3d"
trial = trialTools.smartTrialReader(MAIN_PATH,gaitFilename)
longitudinalAxis,forwardProgression,globalFrame = trialTools.findProgression(trial,"RHEE")
np.testing.assert_equal( longitudinalAxis,"Y")
np.testing.assert_equal( forwardProgression,False)
np.testing.assert_equal( globalFrame,"YXZ")
def test_temporalKineticPlotPanel(self):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitData\CGM1-NormalGaitData-Events\Hånnibøl Lecter\\"
modelledFilenames = ["gait Trial 01.c3d", "gait Trial 02.c3d"]
trial = trialTools.smartTrialReader(DATA_PATH, modelledFilenames[0])
# viewer
kv = plotViewers.TemporalKineticsPlotViewer(trial)
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
def temporalKineticPlotPanel(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\plot\\gaitPlot\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
trial = trialTools.smartTrialReader(DATA_PATH, modelledFilenames[0])
# viewer
kv = plotViewers.TemporalGaitKineticsPlotViewer(trial)
# filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
plt.show()
def gaitTrialProgressionY_forward_lateralX(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\progression\\"
gaitFilename = "gait_Y_forward.c3d"
trial = trialTools.smartTrialReader(MAIN_PATH, gaitFilename)
longitudinalAxis, forwardProgression, globalFrame = trialTools.findProgression(
trial, "LPSI")
np.testing.assert_equal(longitudinalAxis, "Y")
np.testing.assert_equal(forwardProgression, True)
np.testing.assert_equal(globalFrame, "YXZ")
longitudinalAxisFoot, forwardProgressionFoot, globalFrameFoot = trialTools.findProgression(
trial, "RHEE")
np.testing.assert_equal(longitudinalAxis, "Y")
np.testing.assert_equal(forwardProgression, True)
np.testing.assert_equal(globalFrame, "YXZ")
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 test_temporalPlot_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"]
trial = trialTools.smartTrialReader(DATA_PATH, modelledFilenames[0])
fig = plt.figure()
ax = plt.gca()
plot.temporalPlot(ax,
trial,
"LPelvisAngles",
0,
color="blue",
title="test",
xlabel="frame",
ylabel="angle",
ylim=None,
legendLabel=None,
customLimits=None)
def plotTemporalKinetic(DATA_PATH,
modelledFilenames,
bodyPart,
pointLabelSuffix=None,
exportPdf=False,
outputName=None,
show=True,
title=None,
openmaTrial=None):
"""
plotTemporalKinetic : display temporal trace of the Kinetics
:param DATA_PATH [str]: path to your data
:param modelledFilenames [string list]: c3d files
:param bodyPart [str]: body part (choice : LowerLimb, Trunk, UpperLimb)
**optional**
:param pointLabelSuffix [string]: suffix previously added to your model outputs
:param exportPdf [bool]: save as pdf (False[default])
:param outputName [string]: name of the output filed
:param show [bool]: enable matplotlib show function
:param title [string]: change default title of the plot panel
:param openmaTrial [openma::Trial]: force use of an openma trial instance
Examples:
"""
if bodyPart == "LowerLimb":
bodyPart = enums.BodyPartPlot.LowerLimb
elif bodyPart == "Trunk":
bodyPart = enums.BodyPartPlot.Trunk
elif bodyPart == "UpperLimb":
bodyPart = enums.BodyPartPlot.UpperLimb
else:
raise Exception(
"[pyCGM2] - bodyPart argument not recognized ( must be LowerLimb, Trunk or UpperLimb) "
)
if exportPdf:
if outputName is None:
filenameOut = str(modelledFilenames + "-Temporal Kinetics[" +
bodyPart.name + "]")
else:
filenameOut = str(outputName + "-Temporal Kinetics [" +
bodyPart.name + "]")
if openmaTrial is not None:
trial = openmaTrial
trialTools.sortedEvents(trial)
else:
trial = trialTools.smartTrialReader(DATA_PATH, modelledFilenames)
kv = plotViewers.TemporalKineticsPlotViewer(
trial, pointLabelSuffix=pointLabelSuffix, bodyPart=bodyPart)
# # filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
if title is not None:
pf.setTitle(str(title + "-Temporal Kinetics [" + bodyPart.name + "]"))
if exportPdf: pf.setExport(DATA_PATH, filenameOut, "pdf")
pf.plot()
if show: plt.show()
def test_reader(self):
trial = trialTools.smartTrialReader(
pyCGM2.TEST_DATA_PATH + "LowLevel\\IO\\Hånnibøl_c3d\\",
"static.c3d")
def plotTemporalEMG(DATA_PATH,
processedEmgfile,
emgChannels,
muscles,
contexts,
normalActivityEmgs,
rectify=True,
exportPdf=False,
outputName=None,
show=True,
title=None,
openmaTrial=None):
"""
plotTemporalEMG : display temporal trace of EMG signals
:param DATA_PATH [str]: path to your data
:param processedEmgfile [string]: c3d file
:param emgChannels [string list]: labels of your emg channels
:param muscles [string list]: muscle labels associated with your emg channels
:param contexts [string list]: contexts associated with your emg channel
:param normalActivityEmgs [string list]: normal activities associated with your emg channels
:param openmaTrial [openma::Trial]: force use of an openma trial instance
**optional**
:param rectify [bool]: plot rectify signals (True[default])
:param exportPdf [bool]: save as pdf (False[default])
:param outputName [string]: name of the output filed
:param show [bool]: enable matplotlib show function
:param title [string]: change default title of the plot panel
"""
if openmaTrial is not None:
trial = openmaTrial
else:
trial = trialTools.smartTrialReader(DATA_PATH, processedEmgfile)
emgChannels_list = [
emgChannels[i:i + 10] for i in range(0, len(emgChannels), 10)
]
contexts_list = [contexts[i:i + 10] for i in range(0, len(contexts), 10)]
muscles_list = [muscles[i:i + 10] for i in range(0, len(muscles), 10)]
normalActivityEmgs_list = [
normalActivityEmgs[i:i + 10]
for i in range(0, len(normalActivityEmgs), 10)
]
pageNumber = len(emgChannels_list)
count = 0
for i in range(0, pageNumber):
if exportPdf and pageNumber > 1:
if outputName is None:
filenameOut = str(
processedEmgfile + "-TemporalEmgPlot" +
"[rectify]-") + str(count) if rectify else str(
processedEmgfile + "-TemporalEmgPlot" +
"[raw]-") + str(count)
else:
filenameOut = str(
outputName + "-TemporalEmgPlot" + "[rectify]-") + str(
count) if rectify else str(title + "-TemporalEmgPlot" +
"[raw]-") + str(count)
else:
if outputName is None:
filenameOut = str(processedEmgfile + "-TemporalEmgPlot" +
"[rectify]") if rectify else str(
processedEmgfile + "-TemporalEmgPlot" +
"[raw]")
else:
filenameOut = str(outputName + "-TemporalEmgPlot" +
"[rectify]") if rectify else str(
title + "-TemporalEmgPlot" + "[raw]")
combinedEMGcontext = []
for j in range(0, len(emgChannels_list[i])):
combinedEMGcontext.append([
emgChannels_list[i][j], contexts_list[i][j], muscles_list[i][j]
])
# # viewer
kv = emgPlotViewers.TemporalEmgPlotViewer(trial)
kv.setEmgs(combinedEMGcontext)
kv.setNormalActivationLabels(normalActivityEmgs_list[i])
kv.setEmgRectify(rectify)
# # filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
if title is not None:
if pageNumber > 1:
pf.setTitle(
str(title + "-TemporalEmgPlot" + "[rectify]-") +
str(count) if rectify else str(title + "-TemporalEmgPlot" +
"[raw]-") + str(count))
else:
pf.setTitle(
str(title + "-TemporalEmgPlot" +
"[rectify]") if rectify else str(title +
"-TemporalEmgPlot" +
"[raw]"))
if exportPdf: pf.setExport(DATA_PATH, filenameOut, "pdf")
pf.plot()
count += 1
if show: plt.show()
