Merge branch 'master' into 'main'

init

See merge request !1

Definition.py

+# -*- coding: utf-8 -*-
+"""
+Created on Mon Sep 23 15:09:43 2019
+
+@author: Mariette Bergere
+"""
+
+#See exemple of command_file. 
+#Respect yaml indentation.
+
+#   method: str. command_file or command_file_Della_Croce
+#   a, E: int. angle and error magnitude
+#   Error_dir: str. AP_ML, AP_DP or ML_DP
+
+
+import numpy as np
+import yaml
+import glob
+import itertools
+
+
+def definition_method(data_path):
+    '''see 2 existing command files'''
+    File=glob.glob(data_path+"\\command_file"+"*.txt")
+    if File==[]: 
+        raise Exception ("command_file not found")
+    else:
+        method=File[0].replace(data_path+"\\",'')
+        method=method.replace(".txt",'')
+    return method
+
+  
+def definition_marker(data_path,method): 
+    '''Takes info of the 1st part of command_file (Markers)'''
+    Ori=[]
+    Dir=[]
+    Seg_name=[]
+    Mark=[]
+    file_path=data_path + '\\' + method+'.txt'
+    
+    if not glob.glob(file_path): 
+        raise Exception ("command_file not found")
+    else:
+        with open(file_path, 'r') as file:      
+            command_file = yaml.load_all(file)
+            for command in command_file:
+                for k,v in command.items():
+                    if k=='Markers':
+                        for m in range(len(v)):
+                            M=v.items()[m][1].items()
+                            for i in M:
+                                if i[0]=='name':
+                                    Mark.append(i[1])
+                                elif i[0]=='dir':
+                                    Dir.append(i[1])
+                                elif i[0]=='segment_name':
+                                    Seg_name.append(i[1])
+                                elif i[0]=='ori':
+                                    Ori.append(i[1])
+    return (Ori, Dir, Seg_name, Mark)
+
+
+
+def definition_combi(data_path):
+    '''Takes info of the 2nd part of command_file (Error) and creates all the 
+    combinaisons of error possible '''
+    MARK=definition_marker(data_path, 'command_file' )[3]
+    Er=[]
+    Angles=[]
+    file_path=data_path + '\\' + 'command_file.txt'
+    
+    if not glob.glob(file_path): 
+        raise Exception ("command_file not found")
+        
+    else:
+        with open(file_path, 'r') as file:      
+            command_file = yaml.load_all(file)
+            for command in command_file:
+                for k,v in command.items():
+                    if k=='Error':
+                        A=v.items()[0][1].items()
+                        E=v.items()[1][1].items()
+                        for ang in A:
+                            Angles.append(ang[1])
+                        for er in E:
+                            Er.append(er[1])
+    Error_Succession=[]
+    Combi=[]
+    Er_poss=[]
+    Combi_er=[]
+    for e in Er:
+        if e==0: 
+            Er_poss.append([0,e])
+        else:
+            for a in Angles:
+                Er_poss.append([a,e])
+    for c in itertools.product(Er_poss,repeat=len(MARK)):
+        Combi_er.append(c)
+        Error_Succession.append(c)
+    for c in Combi_er:
+        Mark_mis=[]
+        for m in range(len(MARK)):
+            Mark_mis.append([MARK[m], c[m]])
+        Combi.append(Mark_mis)
+        
+    return (Combi, Er_poss, Error_Succession)
+
+    
+
+def definition_error(a, E, Error_dir):
+    '''Creates the error vector in the LCS to add to the marker's original values at each frames.'''
+    # a_cos=abs(np.cos(np.deg2rad(a)))
+    # a_sin=abs(np.sin(np.deg2rad(a)))
+    a_cos = np.cos(np.deg2rad(a))
+    a_sin = np.sin(np.deg2rad(a))
+    if Error_dir == 'AP_DP':
+        Error = np.array([[E*a_cos, 0, E*a_sin]])
+    elif Error_dir == 'AP_ML':
+        # Error = np.array([[E*a_cos, E*a_sin, 0]])
+        Error = np.array([[E*a_sin, E*a_cos, 0]])
+    elif Error_dir == 'ML_DP':
+        Error = np.array([[0, E*a_cos, E*a_sin]])
+    return(Error[0])
+    
+def definition_combi_Della_Croce(data_path):
+    '''Takes info of the 2nd part of command_file (Error) and creates all the 
+    combinaisons of error possible '''
+    MARK=definition_marker(data_path, 'command_file_Della_Croce')[3]
+    Magn=[]
+    file_path=data_path + '\\' + 'command_file_Della_Croce.txt'
+    
+    if not glob.glob(file_path): 
+        raise Exception ("command_file not found")
+        
+    else:
+        with open(file_path, 'r') as file:      
+            command_file = yaml.load_all(file)
+            for command in command_file:
+                for k,v in command.items():
+                    if k=='Markers':
+                        for m in range(len(v)):
+                            M=v.items()[m][1].items()
+                            for i,j in M:
+                                if i=='misplacement_magnitude':
+                                    magn_mark=[]
+                                    for magn in range(len(j)):
+                                        m=j.items()[magn][1]
+                                        if m!='None':
+                                            magn_mark.append(j.items()[magn][1])
+                                    Magn.append(magn_mark)
+        file.close()
+    Er_poss=[]
+    
+    for er in Magn:
+        Er_Mark=[[0,0],[0,er[0]],[180,-er[0]],[90,er[1]],[270,-er[1]]]
+        Er_poss.append(Er_Mark)
+    Combi=[]
+    Combi_er=[]
+    for c in itertools.product(Er_poss[0],Er_poss[1],Er_poss[2],Er_poss[3],Er_poss[4],Er_poss[5],Er_poss[6],Er_poss[7]):#[Er_poss[i] for i in range(len(Er_poss))]):#,Er_poss[1],Er_poss[2],Er_poss[3],Er_poss[4],Er_poss[5],Er_poss[6],Er_poss[7]):#len(MARK)
+        Combi_er.append(c)
+    for c in Combi_er:
+        Mark_mis=[]
+        for m in range(len(MARK)):
+            Mark_mis.append([MARK[m], c[m]])
+        Combi.append(Mark_mis)
+    return (Combi,Er_poss)
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
\ No newline at end of file

Export_Data_csv.py

+#%% 
+import numpy as np
+import pandas as pd
+from pyCGM2 import btk
+import Simplify_acq
+import File_Processing
+
+#%%
+Data_path = 'C:\\Users\\FONSECMI\\OneDrive - unige.ch\\Projects\\MIS\\App\\1_Data\\'
+DataToExport_path = 'C:\\Users\\FONSECMI\\OneDrive - unige.ch\\Projects\\MIS\\App\\2_DataToExport\\'
+ExportCsv_path = 'C:\\Users\\FONSECMI\\OneDrive - unige.ch\\Projects\\MIS\\App\\3_InputData\\'
+
+
+Markers_To_Keep = ['LTOE','LHEE','LMET','LMED','LANK','LTIB',\
+                   'RTOE','RHEE','RMET','RMED','RANK','RTIB','RTTU','RKNE','RTHI',\
+                   'LTTU','LKNE','LTHI','LASI','RASI','LPSI','RPSI']
+Metadata_To_Export = ["Bodymass","Height","LeftLegLength","RightLegLength","LeftKneeWidth","RightKneeWidth","LeftAnkleWidth","RightAnkleWidth","LeftSoleDelta","RightSoleDelta","LeftShoulderOffset","LeftElbowWidth","LeftWristWidth","LeftHandThickness","RightShoulderOffset","RightElbowWidth","RightWristWidth","RightHandThickness"]
+
+#%%
+# static_file = '01_03000_04617_20180423-SBNNN-VDEF-02.C3D'
+# dynamic_file = '01_03000_04617_20180423-GBNNN-VDEF-05.C3D'
+static_file = '03517_05339_20201211-SBNNN-VREF-01.C3D'
+dynamic_file = '03517_05339_20201211-GBNNN-VREF-06.C3D'
+
+#%% Export kinematics
+Angles_to_Export = ['LPelvisAngles_pyCGM2_1', 'RPelvisAngles_pyCGM2_1', 'LHipAngles_pyCGM2_1', 'RHipAngles_pyCGM2_1', 'LKneeAngles_pyCGM2_1', 'RKneeAngles_pyCGM2_1', 'LAnkleAngles_pyCGM2_1', 'RAnkleAngles_pyCGM2_1', 'LFootProgressAngles_pyCGM2_1', 'RFootProgressAngles_pyCGM2_1']
+ptk = np.concatenate((Markers_To_Keep, Angles_to_Export))
+
+#%%
+Simplify_acq.new_dyn(dynamic_file, ptk, Data_path, DataToExport_path)
+acq_dyn = File_Processing.reader(DataToExport_path + dynamic_file)
+acq_sta = File_Processing.reader(Data_path + static_file)
+# %%
+MarkersDyn_df = pd.DataFrame()
+MarkersSta_df = pd.DataFrame()
+
+for marker in Markers_To_Keep:
+    m = acq_dyn.GetPoint(marker).GetValues()
+    MarkersDyn_df[marker+'_X'] = m[:,0]
+    MarkersDyn_df[marker+'_Y'] = m[:,1]
+    MarkersDyn_df[marker+'_Z'] = m[:,2]
+
+    m = acq_sta.GetPoint(marker).GetValues()
+    MarkersSta_df[marker+'_X'] = m[:,0]
+    MarkersSta_df[marker+'_Y'] = m[:,1]
+    MarkersSta_df[marker+'_Z'] = m[:,2]
+
+Angles_df = pd.DataFrame()
+for angles in Angles_to_Export:
+    m = acq_dyn.GetPoint(angles).GetValues()
+    Angles_df[angles+'_X'] = m[:,0]
+    Angles_df[angles+'_Y'] = m[:,1]
+    Angles_df[angles+'_Z'] = m[:,2]
+# %% export markers to csv
+MarkersDyn_df.to_csv(ExportCsv_path+dynamic_file[:-4] + '.csv')
+MarkersSta_df.to_csv(ExportCsv_path+static_file[:-4] + '.csv')
+Angles_df.to_csv(ExportCsv_path+dynamic_file[:-4]+'_kinematics.csv')
+
+# %%
+metadata = acq_sta.GetMetadata()
+Metadata = {}
+Metadata["Bodymass"]=metadata.FindChild("ANALYSIS").value().FindChild("VALUES").value().GetInfo().ToDouble()[0]
+Metadata["Height"]=metadata.FindChild("ANALYSIS").value().FindChild("VALUES").value().GetInfo().ToDouble()[1]
+Metadata["LeftLegLength"]=metadata.FindChild("ANALYSIS").value().FindChild("VALUES").value().GetInfo().ToDouble()[4]
+Metadata["RightLegLength"]=metadata.FindChild("ANALYSIS").value().FindChild("VALUES").value().GetInfo().ToDouble()[7]
+Metadata["LeftKneeWidth"]=metadata.FindChild("ANALYSIS").value().FindChild("VALUES").value().GetInfo().ToDouble()[3]
+Metadata["RightKneeWidth"]=metadata.FindChild("ANALYSIS").value().FindChild("VALUES").value().GetInfo().ToDouble()[6]
+Metadata["LeftAnkleWidth"]=metadata.FindChild("ANALYSIS").value().FindChild("VALUES").value().GetInfo().ToDouble()[2]
+Metadata["RightAnkleWidth"]=metadata.FindChild("ANALYSIS").value().FindChild("VALUES").value().GetInfo().ToDouble()[5]

File_Processing.py

+# -*- coding: utf-8 -*-
+"""
+Created on Fri Oct 25 09:23:14 2019
+
+@author: Mariette Bergere
+MIS2 project
+"""
+
+from pyCGM2 import btk
+
+def reader(file):
+    reader = btk.btkAcquisitionFileReader()
+    reader.SetFilename(file) 
+    reader.Update()
+    acq=reader.GetOutput()
+    return acq
+
+def writer (acq, save_path, new_filename):
+    writer = btk.btkAcquisitionFileWriter()
+    writer.SetInput(acq)
+    writer.SetFilename(save_path + new_filename)
+    writer.Update()  
\ No newline at end of file

GDI.py

+# -*- coding: utf-8 -*-
+"""
+Created on Mon Feb 10 15:52:29 2020
+
+@author: MCDF
+"""
+
+import scipy.io
+import numpy as np
+
+def calculate_GDI(g):
+    ''' calculate Gait deviation index (Schwartz) 
+        g - kinemtatics of the patient (vector 459*9)
+    '''
+    
+    G = scipy.io.loadmat('G.mat')
+    GG = np.transpose(G['G'])
+    features = scipy.io.loadmat('features.mat') #matrix of clean values
+    ff = features['features']
+    
+    C = GG.dot(ff)
+    
+    for i in range(len(C)):
+        if np.all(C[i,:] == np.zeros(len(C[2]))):
+            CC = C[:i, :]
+            break
+        
+    meanC = CC.mean(0)   
+    
+    deltaC = CC
+    for i in range(len(CC)):
+        deltaC[i,:] = CC[i,:]-meanC
+    
+    d = np.sqrt(np.sum(deltaC*deltaC,1))
+    lnd = np.log(d)
+    m_lnd = np.mean(lnd)
+    sd_lnd = np.std(lnd)    
+    Csubject = g.dot(ff)
+    Cdiff = Csubject - meanC
+    lnd = np.log(np.sqrt(np.sum(np.sum(Cdiff*Cdiff))))
+    zlnd = (lnd-m_lnd)/(sd_lnd)    
+    GDI = 100-(10*zlnd)
+    
+    return GDI
+

GPS.py

+# -*- coding: utf-8 -*-
+"""
+Created on Wed Feb 12 12:59:41 2020
+
+@author: MCDF
+"""
+
+import scipy.io
+import numpy as np
+
+def calculate_GPS(Data_patient):
+    ''' calculate GPS 
+        g - kinemtatics of the patient (vector 459*9)
+        warning: only left leg considered 
+    '''
+   
+#    G = scipy.io.loadmat('G.mat')
+#    GG = np.transpose(G['G'])
+#    features = scipy.io.loadmat('features.mat') #matrix of clean values
+#    ff = features['features']
+    Gmean = scipy.io.loadmat('Gmean')
+    G_m = Gmean['G']
+    G_mean = np.transpose(G_m.reshape(9,51))
+#    # prepare patient data [matrix of 15  columns PT,2HF,2KF,2AF,PO,2HA,PR,2HR,2FP] interp to 51 points
+#    data_f = data[1:,1:13]
+#    data_ff = data_f.astype(np.float)
+#    tn = np.linspace(0,50,51) # interpolate into 51 points
+#    LPelvisAngles_interp = np.zeros((51,3))
+#    LHipAngles_interp = np.zeros((51,3))
+#    LKneeAngles_interp = np.zeros((51,1))
+#    LAnkleAngles_interp = np.zeros((51,1))
+#    LFootProgAngles_interp = np.zeros((51,1))
+#    LGC1t = np.linspace(0, 50, len(data[1:,1:4]))
+#    for i in range(3):
+#        LPelvisAngles_interp[:,i] = np.interp(tn, LGC1t, data_ff[:,i])
+#        LHipAngles_interp[:,i] = np.interp(tn, LGC1t, data_ff[:,i+3])
+#    LKneeAngles_interp[:,0] = np.interp(tn, LGC1t, data_ff[:,6])
+#    LAnkleAngles_interp[:,0] = np.interp(tn, LGC1t, data_ff[:,9])
+#    LFootProgAngles_interp[:,0] = np.interp(tn, LGC1t, data_ff[:,11])
+#    
+#    Data_patient = np.transpose(np.array([LPelvisAngles_interp[:,0], LHipAngles_interp[:,0], LKneeAngles_interp[:,0], \
+#                    LAnkleAngles_interp[:,0], LPelvisAngles_interp[:,1], LHipAngles_interp[:,1],\
+#                    LPelvisAngles_interp[:,2],  LHipAngles_interp[:,2], LFootProgAngles_interp[:,0]]))
+
+    # prepare control data [matrix of 15  columns PT,HF,KF,AF,PO,HA,PR,HR,FP] 
+    Data_control = np.transpose(np.array([G_mean[:,0], G_mean[:,3], G_mean[:,6], G_mean[:,7], G_mean[:,1], \
+                             G_mean[:,4], G_mean[:,2], G_mean[:,5], G_mean[:,8]]))
+    
+#    fig, axs = plt.subplots(3,3)
+#    axs[0,0].plot(LPelvisAngles_interp[:,0], 'r')
+#    axs[0,0].plot(Data_Control[:,0], 'b')
+#    axs[0,1].plot(LPelvisAngles_interp[:,1], 'r')
+#    axs[0,1].plot(Data_Control[:,1], 'b')
+#    axs[0,2].plot(LPelvisAngles_interp[:,2], 'r')
+#    axs[0,2].plot(Data_Control[:,2], 'b')
+#    axs[1,0].plot( LHipAngles_interp[:,0],'r')
+#    axs[1,0].plot(Data_Control[:,3], 'b')
+#    axs[1,1].plot( LHipAngles_interp[:,1],'r')
+#    axs[1,1].plot(Data_Control[:,4], 'b')
+#    axs[1,2].plot( LHipAngles_interp[:,2],'r')
+#    axs[1,2].plot(Data_Control[:,5], 'b')
+#    axs[2,0].plot( LKneeAngles_interp[:,0],'r')
+#    axs[2,0].plot(Data_Control[:,6], 'b')
+#    axs[2,1].plot( LAnkleAngles_interp[:,0],'r') 
+#    axs[2,1].plot(Data_Control[:,7], 'b')
+#    axs[2,2].plot( LFootProgAngles_interp[:,0],'r')
+#    axs[2,2].plot(Data_Control[:,8], 'b')
+#    
+    
+
+    # Calculation GPS MAP for left leg (consider only left cycle)
+    MAP = np.zeros([1,len(G_mean[1])+2])
+    for n in range(0,len(G_mean[1])):
+        MAP[:,n] = np.sqrt(np.mean( (Data_control[:,n] - Data_patient[:,n])**2) )
+        
+     # MAP 15, 16, 17 are Left, Right & Overall GPS
+    MAP[:,9] = np.sqrt( (MAP[:,0]**2+MAP[:,2]**2+MAP[:,1]**2+MAP[:,3]**2+MAP[:,4]**2+MAP[:,5]**2+MAP[:,6]**2+MAP[:,7]**2+MAP[:,8]**2)/9 ) 
+    MAP[:,10] = np.sqrt(np.mean(MAP[:,0:8]**2))
+
+#    MAP[15,t] = np.sqrt( (MAP[0,t]**2+MAP[1,t]**2+MAP[3,t]**2+MAP[5,t]**2+MAP[7,t]**2+MAP[8,t]**2+MAP[10,t]**2+MAP[11,t]**2+MAP[13,t]**2)/9 ) 
+#    MAP[16,t] = np.sqrt( (MAP[0,t]**2+MAP[2,t]**2+MAP[4,t]**2+MAP[6,t]**2+MAP[7,t]**2+MAP[9,t]**2+MAP[10,t]**2+MAP[12,t]**2+MAP[14,t]**2)/9 ) 
+#    MAP[17,t] = np.sqrt(np.mean(MAP[0:15,t]**2))
+    return MAP
\ No newline at end of file

Manage_acq.py

+import pandas as pd
+from pyCGM2 import btk
+import numpy as np
+
+def acq_to_df(acq, list_angles, ev_fs, ff, xt, tn):
+
+    df = pd.DataFrame()    
+    for ang in list_angles:
+        print(ang)
+        angle = acq.GetPoint(ang+'Angles')
+        angle = angle.GetValues()
+        df[ang + '_x'] = np.interp(tn, xt, angle[ev_fs[0]-ff:ev_fs[1]-ff,0])
+        df[ang + '_y'] = np.interp(tn, xt, angle[ev_fs[0]-ff:ev_fs[1]-ff,1])
+        df[ang + '_z'] = np.interp(tn, xt, angle[ev_fs[0]-ff:ev_fs[1]-ff,2])
+
+
+    return df
\ No newline at end of file

MarkMis.prj

+<deployment-project plugin="plugin.ezdeploy" plugin-version="1.0">
+  <configuration file="C:\Users\FONSECMI\OneDrive - unige.ch\Projects\MIS\App\MarkMis.prj" location="C:\Users\FONSECMI\OneDrive - unige.ch\Projects\MIS\App" name="MarkMis" target="target.ezdeploy.standalone" target-name="Application Compiler">
+    <param.appname>MarkMis</param.appname>
+    <param.icon />
+    <param.icons />
+    <param.version>1.0</param.version>
+    <param.authnamewatermark>Mickael Fonseca</param.authnamewatermark>
+    <param.email>mickael.cardosofonseca@hcuge.ch</param.email>
+    <param.company>Laboratory of Kinesiology</param.company>
+    <param.summary>blabla</param.summary>
+    <param.description>blabla</param.description>
+    <param.screenshot />
+    <param.guid />
+    <param.installpath.string>\Laboratory of Kinesiology\MarkMis\</param.installpath.string>
+    <param.installpath.combo>option.installpath.programfiles</param.installpath.combo>
+    <param.logo />
+    <param.install.notes>blabla</param.install.notes>
+    <param.target.install.notes />
+    <param.intermediate>${PROJECT_ROOT}\MarkMis\for_testing</param.intermediate>
+    <param.files.only>${PROJECT_ROOT}\MarkMis\for_redistribution_files_only</param.files.only>
+    <param.output>${PROJECT_ROOT}\MarkMis\for_redistribution</param.output>
+    <param.logdir>${PROJECT_ROOT}\MarkMis</param.logdir>
+    <param.enable.clean.build>false</param.enable.clean.build>
+    <param.user.defined.mcr.options />
+    <param.target.type>subtarget.standalone</param.target.type>
+    <param.support.packages />
+    <param.web.mcr>true</param.web.mcr>
+    <param.package.mcr>false</param.package.mcr>
+    <param.no.mcr>false</param.no.mcr>
+    <param.web.mcr.name>MyAppInstaller_web</param.web.mcr.name>
+    <param.package.mcr.name>MyAppInstaller_mcr</param.package.mcr.name>
+    <param.no.mcr.name>MyAppInstaller_app</param.no.mcr.name>
+    <param.windows.command.prompt>false</param.windows.command.prompt>
+    <param.create.log>false</param.create.log>
+    <param.log.file />
+    <param.native.matlab>false</param.native.matlab>
+    <param.checkbox>false</param.checkbox>
+    <param.example />
+    <param.help.text>Syntax 
+	 test_Matexe -? 
+	 test_Matexe input 
+ Input Arguments 
+	 -?  print help on how to use the application 
+	 input  input arguments 
+ Description 
+ 	 blabla</param.help.text>
+    <unset>
+      <param.icon />
+      <param.icons />
+      <param.version />
+      <param.screenshot />
+      <param.guid />
+      <param.installpath.string />
+      <param.installpath.combo />
+      <param.logo />
+      <param.target.install.notes />
+      <param.intermediate />
+      <param.files.only />
+      <param.output />
+      <param.logdir />
+      <param.enable.clean.build />
+      <param.user.defined.mcr.options />
+      <param.target.type />
+      <param.support.packages />
+      <param.web.mcr />
+      <param.package.mcr />
+      <param.no.mcr />
+      <param.web.mcr.name />
+      <param.package.mcr.name />
+      <param.no.mcr.name />
+      <param.create.log />
+      <param.log.file />
+      <param.native.matlab />
+      <param.checkbox />
+      <param.example />
+    </unset>
+    <fileset.main>
+      <file>${PROJECT_ROOT}\test_Matexe.m</file>
+    </fileset.main>
+    <fileset.resources>
+      <file>${PROJECT_ROOT}\test_Matexe.m</file>
+    </fileset.resources>
+    <fileset.package />
+    <fileset.depfun />
+    <build-deliverables>
+      <file location="${PROJECT_ROOT}\MarkMis\for_testing" name="MarkMis.exe" optional="false">C:\Users\FONSECMI\OneDrive - unige.ch\Projects\MIS\App\MarkMis\for_testing\MarkMis.exe</file>
+      <file location="${PROJECT_ROOT}\MarkMis\for_testing" name="splash.png" optional="false">C:\Users\FONSECMI\OneDrive - unige.ch\Projects\MIS\App\MarkMis\for_testing\splash.png</file>
+      <file location="${PROJECT_ROOT}\MarkMis\for_testing" name="readme.txt" optional="true">C:\Users\FONSECMI\OneDrive - unige.ch\Projects\MIS\App\MarkMis\for_testing\readme.txt</file>
+    </build-deliverables>
+    <workflow />
+    <matlab>
+      <root>C:\Program Files\MATLAB\R2021a</root>
+      <toolboxes>
+        <toolbox name="neuralnetwork" />
+      </toolboxes>
+      <toolbox>
+        <neuralnetwork>
+          <enabled>true</enabled>
+        </neuralnetwork>
+      </toolbox>
+    </matlab>
+    <platform>
+      <unix>false</unix>
+      <mac>false</mac>
+      <windows>true</windows>
+      <win2k>false</win2k>
+      <winxp>false</winxp>
+      <vista>false</vista>
+      <linux>false</linux>
+      <solaris>false</solaris>
+      <osver>10.0</osver>
+      <os32>false</os32>
+      <os64>true</os64>
+      <arch>win64</arch>
+      <matlab>true</matlab>
+    </platform>
+  </configuration>
+</deployment-project>
\ No newline at end of file

Misplacement.py

+import numpy as np
+import Rotation_Matrix
+import Definition
+import File_Processing
+from pyCGM2 import btk
+
+
+def move(c3d_path, c3d_filename, Marker_list, Mag_list, Angle_list, Segment_list, Origin_list, sagital, coronal, transversal):
+    # seg: segment name (e.g. PELVIS, LFEMUR) - <string>
+    # ori: origin marker (e.g. LHJC, LKJC) - <string>
+    # marker: marker name (e.g. LASI, LANK) - <string>
+    # ang: misplacement angle (from 0 to 360) - <int>
+    # mag: magnitude misplacement - <int>
+    # plane: plane code of misplacement (options: ML_AP for transversal, ML_DP for sagital, AP_DP for coronal) - <string>
+
+    # SEGMENT_origin=Definition.definition_marker(current_path, method)[0][m]
+    # Error_dir=Definition.definition_marker(current_path, method)[1][m]
+    # SEGMENT_name=Definition.definition_marker(current_path, method)[2][m]
+    acq = File_Processing.reader(c3d_path+c3d_filename)
+    for i in range(len(Marker_list)):
+        marker =  Marker_list[i]
+        mag    =  Mag_list[i]
+        angle  =  Angle_list[i]
+        seg    =  Segment_list[i]
+        ori    =  Origin_list[i]
+        
+        # LASI correction
+        if marker == 'LASI' and angle == 'Medial':
+            angle = 'Lateral'
+        elif marker  == 'LASI' and angle == 'Lateral':
+            angle = 'Medial'
+
+        if angle == 'Original':
+            mag = 0
+            ang = 0
+        if marker in sagital:
+            plane = 'AP_DP'
+            if angle == 'Anterior':
+                ang = 0
+            elif angle == 'Proximal':
+                ang = 90
+            elif angle == 'Posterior':
+                ang = 180
+            elif angle == 'Distal':
+                ang = 270
+
+        elif marker in coronal:
+            plane = 'ML_DP'
+            if angle == 'Medial':
+                ang = 0
+            elif angle == 'Proximal':
+                ang = 90
+            elif angle == 'Lateral':
+                ang = 180
+            elif angle == 'Distal':
+                ang = 270
+
+        elif marker in transversal:
+            plane = 'AP_ML'
+            if angle == 'Medial':
+                ang = 0
+            elif angle == 'Anterior':
+                ang = 90
+            elif angle == 'Lateral':
+                ang = 180
+            elif angle == 'Posterior':
+                ang = 270
+        if angle != 'Original':
+            Segment_proximal = seg + '_Z'
+            Segment_lateral  = seg + '_Y'