def cgm24(cls): """ """ MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\markerDecomposition\\CGM24decomposeTracking\\" # staticFilename = "PN01OP01S01STAT.c3d" acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model=cgm2.CGM2_4LowerLimbs() model.setVersion("CGM2.4e") model.configure() markerDiameter=14 mp={ 'Bodymass' : 83.0, 'LeftLegLength' : 874.0, 'RightLegLength' : 876.0 , 'LeftKneeWidth' : 106.0, 'RightKneeWidth' : 103.0, 'LeftAnkleWidth' : 74.0, 'RightAnkleWidth' : 72.0, 'LeftSoleDelta' : 0, 'RightSoleDelta' : 0, } model.addAnthropoInputParameters(mp) # CALIBRATION scp=modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp,acqStatic,model, leftFlatFoot = 1, rightFlatFoot = 1, markerDiameter=markerDiameter, ).compute() modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="left") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left") modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="right") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right") modelDecorator.HipJointCenterDecorator(model).hara(side = "Both") scp=modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp,acqStatic,model, leftFlatFoot = 1, rightFlatFoot = 1, markerDiameter=markerDiameter, ).compute() # --- Test 1 Motion Axe X ------- gaitFilename="PN01OP01S01SS01.c3d" acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename)) modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,pyCGM2Enums.motionMethod.Sodervisk ) modMotion.compute() mtf = modelFilters.TrackingMarkerDecompositionFilter(model,acqGait) mtf.decompose() btkTools.smartWriter(acqGait, "cgm24-decompose.c3d")
def noIK_6dof(cls): MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\fullBody\\" staticFilename = "PN01OP01S01STAT.c3d" gaitFilename = "PN01OP01S01STAT.c3d" markerDiameter = 14 mp = { 'Bodymass': 83.0, 'LeftLegLength': 874.0, 'RightLegLength': 876.0, 'LeftKneeWidth': 106.0, 'RightKneeWidth': 103.0, 'LeftAnkleWidth': 74.0, 'RightAnkleWidth': 72.0, 'LeftSoleDelta': 0, 'RightSoleDelta': 0, } # --- Calibration --- acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) translators = files.getTranslators(MAIN_PATH, "CGM2_4.translators") acqStatic = btkTools.applyTranslators(acqStatic, translators) model = cgm2.CGM2_4() model.configure() model.addAnthropoInputParameters(mp) # ---- Calibration ---- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() print "----" print model.getSegment("Left Shank").getReferential( "TF").relativeMatrixAnatomic print "----" # # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # # # final modelFilters.ModelCalibrationFilter( scp, acqStatic, model, markerDiameter=markerDiameter).compute() # ------ Fitting ------- acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename)) acqGait = btkTools.applyTranslators(acqGait, translators) # Motion FILTER modMotion = modelFilters.ModelMotionFilter( scp, acqGait, model, enums.motionMethod.Sodervisk) modMotion.compute() btkTools.smartWriter(acqGait, "cgm24_noIK6dof_staticMotion.c3d")
def applyHJCDecorators(model,method): if method["Left"] == "Hara": logging.info("[pyCGM2] Left HJC : Hara") modelDecorator.HipJointCenterDecorator(model).hara(side = "left") elif len(method["Left"]) == 3: logging.info("[pyCGM2] Left HJC : Custom") logging.warning(method["Left"]) modelDecorator.HipJointCenterDecorator(model).custom(position_Left = np.array(method["Left"]), methodDesc = "custom",side="left") if method["Right"] == "Hara": logging.info("[pyCGM2] Right HJC : Hara") modelDecorator.HipJointCenterDecorator(model).hara(side = "right") elif len(method["Right"]) == 3: logging.info("[pyCGM2] Right HJC : Custom") logging.warning(method["Right"]) modelDecorator.HipJointCenterDecorator(model).custom(position_Right = np.array(method["Right"]), methodDesc = "custom",side="right")
def noIK_6dof_Garches(cls): MAIN_PATH = pyCGM2.TEST_DATA_PATH + "Datasets Tests\\didier\\08_02_18_Vincent Pere\\" staticFilename = "08_02_18_Vincent_Pere_Statique_000_MOKKA.c3d" gaitFilename = "08_02_18_Vincent_Pere_Statique_000_MOKKA.c3d" markerDiameter = 14 mp = { 'Bodymass': 70.0, 'LeftLegLength': 890.0, 'RightLegLength': 890.0, 'LeftKneeWidth': 150.0, 'RightKneeWidth': 150.0, 'LeftAnkleWidth': 88.0, 'RightAnkleWidth': 99.0, 'LeftSoleDelta': 0, 'RightSoleDelta': 0, } # --- Calibration --- acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model = cgm2.CGM2_4() model.configure() model.addAnthropoInputParameters(mp) # ---- Calibration ---- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() print "----" print model.getSegment("Left Shank").getReferential( "TF").relativeMatrixAnatomic print "----" # # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # # # final modelFilters.ModelCalibrationFilter( scp, acqStatic, model, markerDiameter=markerDiameter).compute() # ------ Fitting ------- acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename)) # Motion FILTER modMotion = modelFilters.ModelMotionFilter( scp, acqGait, model, enums.motionMethod.Sodervisk) modMotion.compute() btkTools.smartWriter(acqGait, "cgm24_noIK6dof_staticMotion_Garches.c3d")
def calibration_FlatFoot(cls): MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\medial\\" staticFilename = "static.c3d" markerDiameter = 14 mp = { 'Bodymass': 69.0, 'LeftLegLength': 930.0, 'RightLegLength': 930.0, 'LeftKneeWidth': 94.0, 'RightKneeWidth': 64.0, 'LeftAnkleWidth': 67.0, 'RightAnkleWidth': 62.0, 'LeftSoleDelta': 0, 'RightSoleDelta': 0, "LeftToeOffset": 0, "RightToeOffset": 0, } # --- Calibration --- acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model = cgm2.CGM2_4() model.configure() model.addAnthropoInputParameters(mp) # ---- Calibration ---- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # final modelFilters.ModelCalibrationFilter(scp, acqStatic, model, markerDiameter=markerDiameter, leftFlatFoot=True, rightFlatFoot=True).compute() # display CS csp = modelFilters.ModelCoordinateSystemProcedure(model) csf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqStatic) csf.setStatic(True) csf.display() btkTools.smartWriter(acqStatic, "cgm2.4_FlatFoot.c3d")
def calibration_GarchesFlatFoot(cls): MAIN_PATH = pyCGM2.TEST_DATA_PATH + "Datasets Tests\\didier\\08_02_18_Vincent Pere\\" staticFilename = "08_02_18_Vincent_Pere_Statique_000_MOKKA.c3d" markerDiameter = 14 mp = { 'Bodymass': 70.0, 'LeftLegLength': 890.0, 'RightLegLength': 890.0, 'LeftKneeWidth': 150.0, 'RightKneeWidth': 150.0, 'LeftAnkleWidth': 88.0, 'RightAnkleWidth': 99.0, 'LeftSoleDelta': 0, 'RightSoleDelta': 0, "LeftToeOffset": 0, "RightToeOffset": 0, } # --- Calibration --- acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model = cgm2.CGM2_4() model.configure() model.addAnthropoInputParameters(mp) # ---- Calibration ---- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # final modelFilters.ModelCalibrationFilter(scp, acqStatic, model, markerDiameter=markerDiameter, leftFlatFoot=True, rightFlatFoot=True).compute() # display CS csp = modelFilters.ModelCoordinateSystemProcedure(model) csf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqStatic) csf.setStatic(True) csf.display() btkTools.smartWriter(acqStatic, "cgm2.4_GarchesFlatFoot.c3d")
def customLocalPosition(cls): """ GOAL : compare Joint centres and foot Offset """ MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.1\\native\\" staticFilename = "static.c3d" acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model=cgm2.CGM2_1LowerLimbs() model.configure() markerDiameter=14 mp={ 'Bodymass' : 71.0, 'LeftLegLength' : 860.0, 'RightLegLength' : 865.0 , 'LeftKneeWidth' : 102.0, 'RightKneeWidth' : 103.4, 'LeftAnkleWidth' : 75.3, 'RightAnkleWidth' : 72.9, 'LeftSoleDelta' : 0, 'RightSoleDelta' : 0, } model.addAnthropoInputParameters(mp) # -----------CGM STATIC CALIBRATION-------------------- # initial scp=modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute() pos0_L = model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("LHJC").getLocal() pos0_R = model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("RHJC").getLocal() # cgm decorator modelDecorator.HipJointCenterDecorator(model).custom(position_Left = np.array([1,2,3]), position_Right = np.array([1,2,3]), methodDesc = "us") # add node to pelvis # final modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute() pos_L = model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("LHJC").getLocal() pos_R = model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("RHJC").getLocal() # ---- tests ---- np.testing.assert_equal(model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("LHJC").getDescription() ,"us") np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LHJC").getDescription() ,"us") np.testing.assert_equal(model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("RHJC").getDescription() ,"us") np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RHJC").getDescription() ,"us") np.testing.assert_equal(np.all(pos_L == pos0_L) == False, True) np.testing.assert_equal(np.all(pos_R == pos0_R) ==False, True)
def applyHJCDecorators(model, method): if model.getBodyPart() != enums.BodyPart.UpperLimb: if method["Left"] == "Hara": LOGGER.logger.info("[pyCGM2] Left HJC : Hara") modelDecorator.HipJointCenterDecorator(model).hara(side="left") elif len(method["Left"]) == 3: LOGGER.logger.info("[pyCGM2] Left HJC : Custom") LOGGER.logger.debug(method["Left"]) modelDecorator.HipJointCenterDecorator(model).custom( position_Left=np.array(method["Left"]), methodDesc="custom", side="left") if method["Right"] == "Hara": LOGGER.logger.info("[pyCGM2] Right HJC : Hara") modelDecorator.HipJointCenterDecorator(model).hara(side="right") elif len(method["Right"]) == 3: LOGGER.logger.info("[pyCGM2] Right HJC : Custom") LOGGER.logger.debug(method["Right"]) modelDecorator.HipJointCenterDecorator(model).custom( position_Right=np.array(method["Right"]), methodDesc="custom", side="right")
def CGM2_4_SARA_test(cls): MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\Knee Calibration\\" staticFilename = "static.c3d" funcFilename = "functional.c3d" gaitFilename = "gait trial 01.c3d" markerDiameter = 14 mp = { 'Bodymass': 69.0, 'LeftLegLength': 930.0, 'RightLegLength': 930.0, 'LeftKneeWidth': 94.0, 'RightKneeWidth': 64.0, 'LeftAnkleWidth': 67.0, 'RightAnkleWidth': 62.0, 'LeftSoleDelta': 0, 'RightSoleDelta': 0, "LeftToeOffset": 0, "RightToeOffset": 0, } acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model = cgm2.CGM2_4LowerLimbs() model.configure() model.addAnthropoInputParameters(mp) # --- INITIAL CALIBRATION --- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both", cgm1Behaviour=True) modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # final modelFilters.ModelCalibrationFilter( scp, acqStatic, model, seLeftHJCnode="LHJC_Hara", useRightHJCnode="RHJC_Hara", useLeftKJCnode="LKJC_mid", useLeftAJCnode="LAJC_mid", useRightKJCnode="RKJC_mid", useRightAJCnode="RAJC_mid", markerDiameter=markerDiameter).compute() # ------ LEFT KNEE CALIBRATION ------- acqFunc = btkTools.smartReader(str(MAIN_PATH + funcFilename)) # Motion of only left modMotionLeftKnee = modelFilters.ModelMotionFilter( scp, acqFunc, model, pyCGM2Enums.motionMethod.Sodervisk) modMotionLeftKnee.segmentalCompute(["Left Thigh", "Left Shank"]) # decorator modelDecorator.KneeCalibrationDecorator(model).sara( "Left", indexFirstFrame=831, indexLastFrame=1280) # ----add Point into the c3d---- Or_inThigh = model.getSegment("Left Thigh").getReferential( "TF").getNodeTrajectory("KneeFlexionOri") axis_inThigh = model.getSegment("Left Thigh").getReferential( "TF").getNodeTrajectory("KneeFlexionAxis") btkTools.smartAppendPoint(acqFunc, "Left" + "_KneeFlexionOri", Or_inThigh) btkTools.smartAppendPoint(acqFunc, "Left" + "_KneeFlexionAxis", axis_inThigh) # ------ RIGHT KNEE CALIBRATION ------- # Motion of only left modMotionRightKnee = modelFilters.ModelMotionFilter( scp, acqFunc, model, pyCGM2Enums.motionMethod.Sodervisk) modMotionRightKnee.segmentalCompute(["Right Thigh", "Right Shank"]) # decorator modelDecorator.KneeCalibrationDecorator(model).sara("Right", indexFirstFrame=61, indexLastFrame=551) # ----add Point into the c3d---- Or_inThigh = model.getSegment("Right Thigh").getReferential( "TF").getNodeTrajectory("KneeFlexionOri") axis_inThigh = model.getSegment("Right Thigh").getReferential( "TF").getNodeTrajectory("KneeFlexionAxis") btkTools.smartAppendPoint(acqFunc, "Right" + "_KneeFlexionOri", Or_inThigh) btkTools.smartAppendPoint(acqFunc, "Right" + "_KneeFlexionAxis", axis_inThigh) btkTools.smartWriter(acqFunc, "acqFunc-Sara.c3d") #--- FINAL CALIBRATION --- modelFilters.ModelCalibrationFilter( scp, acqStatic, model, useLeftHJCnode="LHJC_Hara", useRightHJCnode="RHJC_Hara", useLeftKJCnode="KJC_Sara", useLeftAJCnode="LAJC_mid", useRightKJCnode="KJC_Sara", useRightAJCnode="RAJC_mid", markerDiameter=markerDiameter, RotateLeftThighFlag=True, RotateRightThighFlag=True).compute() # save static c3d with update KJC btkTools.smartWriter(acqStatic, "Static-SARA.c3d") # ------ Fitting ------- acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename)) # Motion FILTER modMotion = modelFilters.ModelMotionFilter( scp, acqGait, model, pyCGM2Enums.motionMethod.Determinist) modMotion.compute() # relative angles modelFilters.ModelJCSFilter(model, acqGait).compute( description="vectoriel", pointLabelSuffix="cgm1_6dof") # absolute angles longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers( acqGait, ["LASI", "RASI", "RPSI", "LPSI"]) modelFilters.ModelAbsoluteAnglesFilter( model, acqGait, segmentLabels=["Left HindFoot", "Right HindFoot", "Pelvis"], angleLabels=["LFootProgress", "RFootProgress", "Pelvis"], eulerSequences=["TOR", "TOR", "ROT"], globalFrameOrientation=globalFrame, forwardProgression=forwardProgression).compute( pointLabelSuffix="cgm1_6dof") # ------- OPENSIM IK -------------------------------------- # --- osim builder --- cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures( model) markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-markerset.xml" osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim" oscf = opensimFilters.opensimCalibrationFilter( osimfile, model, cgmCalibrationprocedure) oscf.addMarkerSet(markersetFile) scalingOsim = oscf.build(exportOsim=False) # --- fitting --- #procedure cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model) iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-ikSetUp_template.xml" osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim, cgmFittingProcedure, MAIN_PATH) acqIK = osrf.run(acqGait, str(MAIN_PATH + gaitFilename), exportSetUp=False) # -------- NEW MOTION FILTER ON IK MARKERS ------------------ modMotion_ik = modelFilters.ModelMotionFilter( scp, acqIK, model, pyCGM2Enums.motionMethod.Sodervisk, useForMotionTest=True) modMotion_ik.compute() finalJcs = modelFilters.ModelJCSFilter(model, acqIK) finalJcs.setFilterBool(False) finalJcs.compute(description="ik", pointLabelSuffix="2_ik") # btkTools.smartWriter(acqIK, "gait trial 01 - Fitting.c3d")
def calibrate(self, aquiStatic, dictRef, dictAnatomic, options=None): # add markers valSACR = (aquiStatic.GetPoint("LPSI").GetValues() + aquiStatic.GetPoint("RPSI").GetValues()) / 2.0 btkTools.smartAppendPoint(aquiStatic, "SACR", valSACR, desc="") valMidAsis = (aquiStatic.GetPoint("LASI").GetValues() + aquiStatic.GetPoint("RASI").GetValues()) / 2.0 btkTools.smartAppendPoint(aquiStatic, "midASIS", valMidAsis, desc="") valLMET = (aquiStatic.GetPoint("LFMH").GetValues() + aquiStatic.GetPoint("LVMH").GetValues()) / 2.0 btkTools.smartAppendPoint(aquiStatic, "LMET", valLMET, desc="") valRMET = (aquiStatic.GetPoint("RFMH").GetValues() + aquiStatic.GetPoint("RVMH").GetValues()) / 2.0 btkTools.smartAppendPoint(aquiStatic, "RMET", valRMET, desc="") ff = aquiStatic.GetFirstFrame() lf = aquiStatic.GetLastFrame() frameInit = ff - ff frameEnd = lf - ff + 1 # calibrate technical self._calibrateTechnicalSegment(aquiStatic, "Pelvis", dictRef, frameInit, frameEnd, options=options) self._calibrateTechnicalSegment(aquiStatic, "Left Thigh", dictRef, frameInit, frameEnd, options=options) self._calibrateTechnicalSegment(aquiStatic, "Right Thigh", dictRef, frameInit, frameEnd, options=options) self._calibrateTechnicalSegment(aquiStatic, "Left Shank", dictRef, frameInit, frameEnd, options=options) self._calibrateTechnicalSegment(aquiStatic, "Right Shank", dictRef, frameInit, frameEnd, options=options) self._calibrateTechnicalSegment(aquiStatic, "Left Foot", dictRef, frameInit, frameEnd, options=options) self._calibrateTechnicalSegment(aquiStatic, "Right Foot", dictRef, frameInit, frameEnd, options=options) # # ---- decorator ---- modelDecorator.HipJointCenterDecorator(self).greatTrochanterOffset( aquiStatic) modelDecorator.KneeCalibrationDecorator(self).midCondyles(aquiStatic) modelDecorator.AnkleCalibrationDecorator(self).midMaleolus(aquiStatic) # calibrate anatomic self._calibrateAnatomicalSegment(aquiStatic, "Pelvis", dictAnatomic, frameInit, frameEnd, options=options) self._calibrateAnatomicalSegment(aquiStatic, "Left Thigh", dictAnatomic, frameInit, frameEnd, options=options) self._calibrateAnatomicalSegment(aquiStatic, "Right Thigh", dictAnatomic, frameInit, frameEnd, options=options) self._calibrateAnatomicalSegment(aquiStatic, "Left Shank", dictAnatomic, frameInit, frameEnd, options=options) self._calibrateAnatomicalSegment(aquiStatic, "Right Shank", dictAnatomic, frameInit, frameEnd, options=options) self._calibrateAnatomicalSegment(aquiStatic, "Left Foot", dictAnatomic, frameInit, frameEnd, options=options) self._calibrateAnatomicalSegment(aquiStatic, "Right Foot", dictAnatomic, frameInit, frameEnd, options=options)
def full_IK(cls): MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\medial\\" staticFilename = "static.c3d" gaitFilename = "gait Trial 01.c3d" markerDiameter = 14 mp = { 'Bodymass': 69.0, 'LeftLegLength': 930.0, 'RightLegLength': 930.0, 'LeftKneeWidth': 94.0, 'RightKneeWidth': 64.0, 'LeftAnkleWidth': 67.0, 'RightAnkleWidth': 62.0, 'LeftSoleDelta': 0, 'RightSoleDelta': 0, "LeftToeOffset": 0, "RightToeOffset": 0, } # --- Calibration --- acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model = cgm2.CGM2_4LowerLimbs() model.configure() model.addAnthropoInputParameters(mp) # ---- Calibration ---- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # final modelFilters.ModelCalibrationFilter( scp, acqStatic, model, markerDiameter=markerDiameter).compute() # ------ Fitting ------- acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename)) # Motion FILTER modMotion = modelFilters.ModelMotionFilter( scp, acqGait, model, pyCGM2Enums.motionMethod.Sodervisk) modMotion.compute() # relative angles modelFilters.ModelJCSFilter(model, acqGait).compute( description="vectoriel", pointLabelSuffix="cgm1_6dof") # absolute angles longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers( acqGait, ["LASI", "RASI", "RPSI", "LPSI"]) modelFilters.ModelAbsoluteAnglesFilter( model, acqGait, segmentLabels=["Left Foot", "Right Foot", "Pelvis"], angleLabels=["LFootProgress", "RFootProgress", "Pelvis"], eulerSequences=["TOR", "TOR", "ROT"], globalFrameOrientation=globalFrame, forwardProgression=forwardProgression).compute( pointLabelSuffix="cgm1_6dof") # ---Marker decomp filter---- mtf = modelFilters.TrackingMarkerDecompositionFilter(model, acqGait) mtf.decompose() # ------- OPENSIM IK -------------------------------------- # --- osim builder --- cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures( model) markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-markerset - expert.xml" osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim" oscf = opensimFilters.opensimCalibrationFilter( osimfile, model, cgmCalibrationprocedure, MAIN_PATH) oscf.addMarkerSet(markersetFile) scalingOsim = oscf.build(exportOsim=False) # --- fitting --- #procedure cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure( model, expertMode=True) iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-expert-ikSetUp_template.xml" osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim, cgmFittingProcedure, MAIN_PATH) acqIK = osrf.run(acqGait, str(MAIN_PATH + gaitFilename), exportSetUp=False) # -------- NEW MOTION FILTER ON IK MARKERS ------------------ modMotion_ik = modelFilters.ModelMotionFilter( scp, acqIK, model, pyCGM2Enums.motionMethod.Sodervisk, useForMotionTest=True) modMotion_ik.compute() finalJcs = modelFilters.ModelJCSFilter(model, acqIK) finalJcs.setFilterBool(False) finalJcs.compute(description="ik", pointLabelSuffix="2_ik") # btkTools.smartWriter(acqIK, "cgm24e_fullIK.c3d")
pointLabelOrigin="LHEE") gcp.setDefinition("Right Foot", "TF", sequence="ZXY", pointLabel1="RSMH", pointLabel2="RHEE", pointLabel3="RVMH", pointLabelOrigin="RHEE") #---Initial Calibration Filter--- smf0 = modelFilters.ModelCalibrationFilter(gcp, acqStatic, bioMechModel) smf0.setBoolOption("technicalReferentialOnly") smf0.compute() # ---- decorator ---- modelDecorator.HipJointCenterDecorator(bioMechModel).greatTrochanterOffset( acqStatic) modelDecorator.KneeCalibrationDecorator(bioMechModel).midCondyles( acqStatic) modelDecorator.AnkleCalibrationDecorator(bioMechModel).midMaleolus( acqStatic) gcp.setAnatomicalDefinition("Pelvis", sequence="YZX", nodeLabel1="RASI", nodeLabel2="LASI", nodeLabel3="SACR", nodeLabelOrigin="midASIS") gcp.setAnatomicalDefinition("Left Thigh", sequence="ZXiY", nodeLabel1="LKJC_mid", nodeLabel2="LHJC_gt",
} # --- Calibration --- acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model = cgm2.CGM2_2LowerLimbs() model.configure() model.addAnthropoInputParameters(mp) # ------ calibration ------- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # final modelFilters.ModelCalibrationFilter( scp, acqStatic, model, markerDiameter=markerDiameter).compute() # ------ Fitting ------- acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename)) # Motion FILTER modMotion = modelFilters.ModelMotionFilter( scp, acqGait, model, pyCGM2Enums.motionMethod.Determinist)
def test_lowLevel(self): DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM2.3\\Hannibal-medial\\" staticFilename = "static.c3d" gaitFilename= "gait1.c3d" markerDiameter=14 required_mp={ 'Bodymass' : 71.0, 'LeftLegLength' : 860.0, 'RightLegLength' : 865.0 , 'LeftKneeWidth' : 102.0, 'RightKneeWidth' : 103.4, 'LeftAnkleWidth' : 75.3, 'RightAnkleWidth' : 72.9, 'LeftSoleDelta' : 0, 'RightSoleDelta' : 0, 'LeftShoulderOffset' : 0, 'RightShoulderOffset' : 0, 'LeftElbowWidth' : 0, 'LeftWristWidth' : 0, 'LeftHandThickness' : 0, 'RightElbowWidth' : 0, 'RightWristWidth' : 0, 'RightHandThickness' : 0 } optional_mp = { 'LeftTibialTorsion' : 0, 'LeftThighRotation' : 0, 'LeftShankRotation' : 0, 'RightTibialTorsion' : 0, 'RightThighRotation' : 0, 'RightShankRotation' : 0 } # --- Calibration --- # ---check marker set used---- acqStatic = btkTools.smartReader(DATA_PATH + staticFilename) dcm = cgm.CGM.detectCalibrationMethods(acqStatic) model=cgm2.CGM2_3() model.configure(detectedCalibrationMethods=dcm) model.addAnthropoInputParameters(required_mp,optional=optional_mp) # ---- Calibration ---- scp=modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute() # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="both") # final modelFilters.ModelCalibrationFilter(scp,acqStatic,model, markerDiameter=markerDiameter).compute() # ------ Fitting ------- acqGait = btkTools.smartReader(DATA_PATH + gaitFilename) # Motion FILTER modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,enums.motionMethod.Sodervisk) modMotion.compute() # ------- OPENSIM IK -------------------------------------- # --- osim builder --- cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(model) markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-markerset.xml" osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim" oscf = opensimFilters.opensimCalibrationFilter(osimfile, model, cgmCalibrationprocedure, DATA_PATH) oscf.addMarkerSet(markersetFile) scalingOsim = oscf.build(exportOsim=False) # --- fitting --- #procedure cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model) iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-ikSetUp_template.xml" osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim, cgmFittingProcedure, DATA_PATH, acqGait ) acqIK = osrf.run(str(DATA_PATH + gaitFilename ),exportSetUp=False) # -------- NEW MOTION FILTER ON IK MARKERS ------------------ modMotion_ik=modelFilters.ModelMotionFilter(scp,acqIK,model,enums.motionMethod.Sodervisk, useForMotionTest=True) modMotion_ik.compute() finalJcs =modelFilters.ModelJCSFilter(model,acqIK) finalJcs.compute(description="ik", pointLabelSuffix = "2_ik")# btkTools.smartWriter(acqIK,"cgm23_fullIK_Motion.c3d")
def full_IK(cls): MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.3\\fullBody\\" staticFilename = "PN01OP01S01STAT.c3d" gaitFilename = "PN01OP01S01SS01.c3d" markerDiameter = 14 mp = { 'Bodymass': 83.0, 'LeftLegLength': 874.0, 'RightLegLength': 876.0, 'LeftKneeWidth': 106.0, 'RightKneeWidth': 103.0, 'LeftAnkleWidth': 74.0, 'RightAnkleWidth': 72.0, 'LeftSoleDelta': 0, 'RightSoleDelta': 0, } # --- Calibration --- acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) translators = files.getTranslators(MAIN_PATH, "CGM2_3.translators") acqStatic = btkTools.applyTranslators(acqStatic, translators) model = cgm2.CGM2_3LowerLimbs() model.configure() model.addAnthropoInputParameters(mp) # ---- Calibration ---- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # final modelFilters.ModelCalibrationFilter( scp, acqStatic, model, markerDiameter=markerDiameter).compute() # ------ Fitting ------- acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename)) acqGait = btkTools.applyTranslators(acqGait, translators) # Motion FILTER modMotion = modelFilters.ModelMotionFilter( scp, acqGait, model, enums.motionMethod.Sodervisk) modMotion.compute() # ------- OPENSIM IK -------------------------------------- # --- osim builder --- cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures( model) markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-markerset.xml" osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim" oscf = opensimFilters.opensimCalibrationFilter( osimfile, model, cgmCalibrationprocedure, MAIN_PATH) oscf.addMarkerSet(markersetFile) scalingOsim = oscf.build(exportOsim=False) # --- fitting --- #procedure cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model) iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-ikSetUp_template.xml" osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim, cgmFittingProcedure, MAIN_PATH) acqIK = osrf.run(acqGait, str(MAIN_PATH + gaitFilename), exportSetUp=False) # -------- NEW MOTION FILTER ON IK MARKERS ------------------ modMotion_ik = modelFilters.ModelMotionFilter( scp, acqIK, model, enums.motionMethod.Sodervisk, useForMotionTest=True) modMotion_ik.compute() finalJcs = modelFilters.ModelJCSFilter(model, acqIK) finalJcs.setFilterBool(False) finalJcs.compute(description="ik", pointLabelSuffix="2_ik") # btkTools.smartWriter(acqIK, "cgm23_fullIK_Motion.c3d")
def CGM2_4_SARA_test(cls): MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\Knee Calibration\\" staticFilename = "static.c3d" funcFilename = "functional.c3d" gaitFilename = "gait trial 01.c3d" markerDiameter = 14 mp = { 'Bodymass': 69.0, 'LeftLegLength': 930.0, 'RightLegLength': 930.0, 'LeftKneeWidth': 94.0, 'RightKneeWidth': 64.0, 'LeftAnkleWidth': 67.0, 'RightAnkleWidth': 62.0, 'LeftSoleDelta': 0, 'RightSoleDelta': 0, "LeftToeOffset": 0, "RightToeOffset": 0, } acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model = cgm2.CGM2_4() model.configure() model.addAnthropoInputParameters(mp) # --- INITIAL CALIBRATION --- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # final modelFilters.ModelCalibrationFilter( scp, acqStatic, model, seLeftHJCnode="LHJC_Hara", useRightHJCnode="RHJC_Hara", useLeftKJCnode="LKJC_mid", useLeftAJCnode="LAJC_mid", useRightKJCnode="RKJC_mid", useRightAJCnode="RAJC_mid", markerDiameter=markerDiameter).compute() # ------ LEFT KNEE CALIBRATION ------- acqFunc = btkTools.smartReader(str(MAIN_PATH + funcFilename)) # Motion of only left modMotionLeftKnee = modelFilters.ModelMotionFilter( scp, acqFunc, model, enums.motionMethod.Sodervisk) modMotionLeftKnee.segmentalCompute(["Left Thigh", "Left Shank"]) # decorator modelDecorator.KneeCalibrationDecorator(model).sara( "Left", indexFirstFrame=831, indexLastFrame=1280) # ----add Point into the c3d---- Or_inThigh = model.getSegment("Left Thigh").getReferential( "TF").getNodeTrajectory("KneeFlexionOri") axis_inThigh = model.getSegment("Left Thigh").getReferential( "TF").getNodeTrajectory("KneeFlexionAxis") btkTools.smartAppendPoint(acqFunc, "Left" + "_KneeFlexionOri", Or_inThigh) btkTools.smartAppendPoint(acqFunc, "Left" + "_KneeFlexionAxis", axis_inThigh) # ------ RIGHT KNEE CALIBRATION ------- # Motion of only left modMotionRightKnee = modelFilters.ModelMotionFilter( scp, acqFunc, model, enums.motionMethod.Sodervisk) modMotionRightKnee.segmentalCompute(["Right Thigh", "Right Shank"]) # decorator modelDecorator.KneeCalibrationDecorator(model).sara("Right", indexFirstFrame=61, indexLastFrame=551) # ----add Point into the c3d---- Or_inThigh = model.getSegment("Right Thigh").getReferential( "TF").getNodeTrajectory("KneeFlexionOri") axis_inThigh = model.getSegment("Right Thigh").getReferential( "TF").getNodeTrajectory("KneeFlexionAxis") btkTools.smartAppendPoint(acqFunc, "Right" + "_KneeFlexionOri", Or_inThigh) btkTools.smartAppendPoint(acqFunc, "Right" + "_KneeFlexionAxis", axis_inThigh) btkTools.smartWriter(acqFunc, "acqFunc-Sara.c3d") #--- FINAL CALIBRATION --- modelFilters.ModelCalibrationFilter( scp, acqStatic, model, useLeftHJCnode="LHJC_Hara", useRightHJCnode="RHJC_Hara", useLeftKJCnode="KJC_Sara", useLeftAJCnode="LAJC_mid", useRightKJCnode="KJC_Sara", useRightAJCnode="RAJC_mid", markerDiameter=markerDiameter).compute() # save static c3d with update KJC btkTools.smartWriter(acqStatic, "Static-SARA.c3d") # print functional Offsets print model.mp_computed["LeftKneeFuncCalibrationOffset"] print model.mp_computed["RightKneeFuncCalibrationOffset"]
def CGM23_2DOF_test(cls): MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.3\\Knee Calibration\\" staticFilename = "Static.c3d" leftKneeFilename = "Left Knee.c3d" rightKneeFilename = "Right Knee.c3d" gaitFilename = "gait trial 01.c3d" markerDiameter = 14 mp = { 'Bodymass': 71.0, 'LeftLegLength': 860.0, 'RightLegLength': 865.0, 'LeftKneeWidth': 102.0, 'RightKneeWidth': 103.4, 'LeftAnkleWidth': 75.3, 'RightAnkleWidth': 72.9, 'LeftSoleDelta': 0, 'RightSoleDelta': 0, } acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename)) model = cgm2.CGM2_3() model.configure() model.addAnthropoInputParameters(mp) # --- INITIAL CALIBRATION --- scp = modelFilters.StaticCalibrationProcedure(model) modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute() # cgm decorator modelDecorator.HipJointCenterDecorator(model).hara() modelDecorator.KneeCalibrationDecorator(model).midCondyles( acqStatic, markerDiameter=markerDiameter, side="both") modelDecorator.AnkleCalibrationDecorator(model).midMaleolus( acqStatic, markerDiameter=markerDiameter, side="both") # final modelFilters.ModelCalibrationFilter( scp, acqStatic, model, seLeftHJCnode="LHJC_Hara", useRightHJCnode="RHJC_Hara", useLeftKJCnode="LKJC_mid", useLeftAJCnode="LAJC_mid", useRightKJCnode="RKJC_mid", useRightAJCnode="RAJC_mid", markerDiameter=markerDiameter).compute() # ------ LEFT KNEE CALIBRATION ------- acqLeftKnee = btkTools.smartReader(str(MAIN_PATH + leftKneeFilename)) # Motion of only left modMotionLeftKnee = modelFilters.ModelMotionFilter( scp, acqLeftKnee, model, enums.motionMethod.Sodervisk) modMotionLeftKnee.segmentalCompute(["Left Thigh", "Left Shank"]) # decorator modelDecorator.KneeCalibrationDecorator(model).calibrate2dof( "Left", indexFirstFrame=489, indexLastFrame=1451) # ----add Point into the c3d---- btkTools.smartWriter(acqLeftKnee, "Left Knee-2dof.c3d") # ------ RIGHT KNEE CALIBRATION ------- acqRightKnee = btkTools.smartReader(str(MAIN_PATH + rightKneeFilename)) # Motion of only left modMotionRightKnee = modelFilters.ModelMotionFilter( scp, acqRightKnee, model, enums.motionMethod.Sodervisk) modMotionRightKnee.segmentalCompute(["Right Thigh", "Right Shank"]) # decorator modelDecorator.KneeCalibrationDecorator(model).calibrate2dof( "Right", indexFirstFrame=25, indexLastFrame=1060) # ----add Point into the c3d---- btkTools.smartWriter(acqRightKnee, "Right Knee-2dof.c3d") #--- FINAL CALIBRATION --- modelFilters.ModelCalibrationFilter( scp, acqStatic, model, useLeftHJCnode="LHJC_Hara", useRightHJCnode="RHJC_Hara", useLeftKJCnode="KJC_Sara", useLeftAJCnode="LAJC_mid", useRightKJCnode="KJC_Sara", useRightAJCnode="RAJC_mid", markerDiameter=markerDiameter).compute() # save static c3d with update KJC btkTools.smartWriter(acqStatic, "Static-2DOF.c3d")