A R-package for 3D Gait data Processing

Code/CodeIndex.md

@@ -1,8 +1,9 @@
 # Code Index
-A list of the code contributed by our community members. This is either hosted here on the CMAS open-code repository, or externally. 
+A list of the code contributed by our community members. This is either hosted here on the CMAS open-code repository, or externally.
 When you add a new entry, make sure you include a link to the code, the required software, and your name, so we know who to thank! :heart::clap:
 
-- [Gait Profile Score & Movement Analysis Profile](https://github.com/cmasuki/open-code/tree/master/Code/Gait_profile_score) by [Neil Postans](https://github.com/npostans). 
+- [Gait Profile Score & Movement Analysis Profile](https://github.com/cmasuki/open-code/tree/master/Code/Gait_profile_score) by [Neil Postans](https://github.com/npostans).
 Needs Python 2.7 (32 bit version) & Vicon Nexus 2.x
 - [Local Dynamic Stability code (Rosensteins Algorithm)](https://github.com/SjoerdBruijn/LocalDynamicStability) by [Sjoerd Bruijn](https://github.com/SjoerdBruijn) Needs Matlab (any version)
 - [Code to read accelerometry data from a mobile phone via Matlab in realtime](https://github.com/SjoerdBruijn/StreamPhoneData) by [Sjoerd Bruijn](https://github.com/SjoerdBruijn) Needs Matlab (any version)
+- [visualisation and statistical processing of 3D gait data with R](https://github.com/pyCGM2/rCGM2) bu [Fabien Leboeuf](https://github.com/pyCGM2/rCGM2) Needs Rstudio

Code/anonymising c3d/matlab/ChangeSubjectName-btk.m

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+function ChangeSubjectName
+% change the name of subject in C3D files associated with models, markers,
+% events
+% vsk file should have the same name of the new name of the subject.
+DefaultName = '\\DEFAULT PATH'; % TO EDIT
+[C3D_filename,C3D_path]=uigetfile({'*.C3D'},'Select C3D file',DefaultName,'MultiSelect','on');
+nbre_fichier = size(C3D_filename,2);
+
+f=findstr(C3D_path,'\');
+def=C3D_path(f(end-2)+1:f(end-1)-1);
+subject = inputdlg('Name of the new subject','Name of the new subject',1,{def});
+subject=char(subject);
+
+for t=1:nbre_fichier
+    C3D_file=char(C3D_filename(t));
+
+    if nbre_fichier ==1
+        C3D_file = C3D_filename;
+    end
+    acq= btkReadAcquisition(char([C3D_path C3D_file]));
+    METADATA = btkGetMetaData(acq);
+    I1=struct();
+    I3=struct();
+    info1=struct();
+    info3=struct();
+    B={};
+    % change subject name in the metadata
+    if isfield(METADATA.children,'SUBJECTS')==1
+        info1=METADATA.children.SUBJECTS.children.NAMES.info;
+        I1 = btkMetaDataInfo('Char', {subject});
+        btkAppendMetaData(acq,'SUBJECTS','NAMES',I1);
+        info2=METADATA.children.POINT.children.ANGLES.info;
+        I2 = btkMetaDataInfo('Char', {subject});
+        btkAppendMetaData(acq,'POINT','ANGLES',I2);
+    end
+
+    % change subject name in the events
+    n_event=btkGetEventNumber(acq);
+    if isempty(n_event)==0
+        if n_event>0
+            for i=1:n_event
+                btkSetEventSubject(acq, i, subject);
+            end
+        end
+    end
+
+    % change subject name in analysis
+    if isfield(METADATA.children,'ANALYSIS')==1
+        info3=METADATA.children.ANALYSIS.children.SUBJECTS.info;
+        if info3.dims(2)>0
+            for i=1:info3.dims(2)
+                B{i}=subject;
+            end
+            I3 = btkMetaDataInfo('Char', B');
+            btkAppendMetaData(acq,'ANALYSIS','SUBJECTS',I3);
+        end
+    end
+
+    btkWriteAcquisition(acq,(char([C3D_path C3D_file])));
+    disp(['Write - ' char([C3D_path C3D_file])]);
+end
+disp('Change Name finished')

Code/anonymising c3d/matlab/changeSubjectName-btk.readme

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+**DESCRIPTION**
+change subject name of a several c3d files
+
+**SYNOPSIS**
+
+
+
+**AUTHOR**
+
+Stephane Armand : HUG - Geneva (SW)
+
+
+
+**REQUIREMENT**
+
+  * BTK ( matlab) 0
+
+
+
+**CHANGELOG**
+
+  * *[2018-05-07]* proposal to CMASUKI
+
+
+**TODO**
+
+
+
+**HOW TO**
+
+  1. Run the m file
+  2. Select your c3d set i the dialog box

Code/anonymising c3d/python/anonymising-pyCGM2.py

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+# -*- coding: utf-8 -*-
+
+import os
+from pyCGM2.Tools import btkTools
+
+
+if __name__ == "__main__":
+
+    c3dFilename = "TO EDIT"
+    DATA_PATH = os.getcwd() + "//"
+
+    btkAcq = btkTools.smartReader(DATA_PATH+c3dFilename)
+    btkAcqUn = btkTools.changeSubjectName(btkAcq,subjectName)
+    btkTools.smartWriter(btkAcqUn, DATA_PATH+c3dFilename[:-4]+"-Anonymised.c3d")

Code/anonymising c3d/python/anonymising-pyCGM2.readme

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+**DESCRIPTION**
+change name of the subject into the c3d
+
+(@CarolineORLAUKeele : ready to sell your scripted USB stick on ebay :-) )
+
+**SYNOPSIS**
+
+When you export a c3d, from Vicon Nexus for instance, the name of the subject is defined in different sections of the c3d.
+This function allows to change the subject name everywhere and export a new c3d with *-anonymised" as suffix
+
+
+
+**AUTHOR**
+
+Fabien Leboeuf : University Salford (UK)
+
+
+
+**REQUIREMENT**
+
+  * this function need installation of [pyCGM2](https://pycgm2.github.io)
+  * compatible python2.7 only
+
+
+**CHANGELOG**
+
+  * *[2018-05-07]* proposal to CMASUKI
+
+
+**TODO**
+
+
+
+**HOW TO**
+
+  1. place the script "anonymising-pyCGM2.py" into your data folder
+  2. open it with either your python editor pycharmm, spyder or  a text editor like notepad
+  3. edit you c3d filename (replace TOEDIT)
+  4 run the python script ( double click on "anonymising-pyCGM2.py") if *python.exe* is associated with *.py file or use the run command of your python IDE)