Uploaded code content and initial documentation

data/BodyParts3D/LICENSE_content

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+Summary: Creative Commons License Creative Commons Attribution-Inheritance 2.1 Japan (CC BY-SA)
+
+Original: http://lifesciencedb.jp/bp3d/info_en/license/index.html
+
+Translation: https://creativecommons.org/licenses/by-sa/2.1/jp/deed.en
+
+About terms of use and credit description:
+The standard licenses for the contents (including images created by Anatomography) published on this site (http://lifesciencedb.jp/bp3d, http://lifesciencedb.jp/ag) are as follows.
+
+Creative Commons License Creative Commons Attribution-Inheritance 2.1 Japan
+
+Please be sure to display the following credits before using.
+
+BodyParts3D, Copyrightc 2008 Life Science Integrated Database Center licensed by CC Display-Inheritance 2.1 Japan

mcode/A_BodyParts3D_convert_STL_to_MAT.m

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+clear; close all; clc;
+
+%% Description
+% This code parses all STL files in the /stl folder and exports them as MAT
+% files to the /mat folder.
+%
+% This code requires the GIBBON MATLAB toolbox
+% <www.gibboncode.org>
+
+%% Control parameters
+
+% Path names
+projectFolder = fileparts(fileparts(mfilename('fullpath'))); %Main code path
+loadFolder=fullfile(projectFolder,'data','BodyParts3D','stl'); %The STL loading folder
+saveFolder=fullfile(projectFolder,'data','BodyParts3D','mat'); %The MAT saving folder
+
+%%
+
+%Get list of all STL files
+fileList = dir(fullfile(loadFolder,['*','stl']));
+fileList={fileList(1:end).name};
+
+Dc=readtable(fullfile(projectFolder,'data','BodyParts3D','FMA_ID_label_obj.csv'));
+P=lower(Dc.FMAID);
+
+%Convert all STL files to MAT
+numFiles=numel(fileList); %Number of files to parse
+for q=1:1:numFiles %Loop over all files
+    %Get file name
+    [~,fileNameClean,~]=fileparts(fileList{q}); %File name without path or extension
+
+    %Prepare STL file name
+    fileNameLoad=fullfile(loadFolder,fileList{q}); %STL file name
+
+    %Prepare save file name
+    fileNameSave=fullfile(saveFolder,[fileNameClean,'.mat']); %MAT file name
+
+    %Get FMAID code
+    FMAID=sscanf(fileNameClean,'FMA%d');
+
+    %Get preferred name
+    logicFMAID=P==FMAID;
+    preferredName=Dc.preferredName{logicFMAID};
+
+    %Parse STL import
+    disp(['Parsing file ', num2str(q),' of ',num2str(numFiles),', ',sprintf('%3.0f',round(100*q/numFiles)),'% done, ',fileNameClean,', ',preferredName])    
+    try %MATLAB's stlread
+        TR = stlread(fileNameLoad);
+        v=TR.Points;
+        f=TR.ConnectivityList;
+    catch %GIBBON's importer
+        [stlStruct] = import_STL_bin(fileNameLoad);
+        v=stlStruct.solidVertices{1};
+        f=stlStruct.solidFaces{1};
+    end
+
+    %Merge vertices
+    [f,v]=mergeVertices(f,v);
+
+    %Build model structure
+    model.sourceName=fileList{q};
+    model.preferredName=preferredName;
+    model.faces=f;
+    model.vertices=v;
+
+    %Export MAT file
+    save(fileNameSave,'-struct','model');    
+end
+

mcode/B_BodyParts3D_remesh_surfaces.m

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+clear; close all; clc;
+
+%% Description 
+% This code parses a selection of MAT files in the /mat folder for surface
+% meshes, and remeshes them at a desired point spacing. The remeshed
+% surfaces are exported to the /post folder. 
+%
+% This code requires the GIBBON MATLAB toolbox 
+% <www.gibboncode.org>
+
+%% Plotting settings
+lineWidth=0.5;
+
+%% Control parameters
+
+% Path names
+projectFolder = fileparts(fileparts(mfilename('fullpath'))); %Main code path
+loadFolder=fullfile(projectFolder,'data','BodyParts3D','mat'); %The MAT loading folder
+saveFolder=fullfile(projectFolder,'data','BodyParts3D','post'); %The MAT saving folder for processed data
+
+fileNames_FMA={'FMA16586','FMA24474','FMA24477','FMA24480','FMA24486'};
+
+pointSpacings=[4 4 4 3 3];
+
+optionStructRemesh.disp_on=0; % Turn off command window text display
+
+saveOn=0;
+
+%%
+
+for q=1:1:numel(fileNames_FMA)
+
+    %% Import mesh
+    fileName_FMA=fileNames_FMA{q};    
+    fileName_mat=fullfile(loadFolder,[fileName_FMA,'.mat']);
+
+    model=load(fileName_mat);
+    F=model.faces;
+    V=model.vertices;
+
+    %% Remesh
+    optionStructRemesh.pointSpacing=pointSpacings(q); %Set desired point spacing
+    [Fn,Vn]=ggremesh(F,V,optionStructRemesh);
+
+    %% Visualisation
+
+    cFigure;
+    gtitle([fileName_FMA,' ',model.preferredName])
+    subplot(1,2,1); 
+    title('Raw');
+    gpatch(F,V,'w','r',1,lineWidth);
+    axisGeom;
+    camlight headlight;
+
+    subplot(1,2,2);
+    title('Remeshed');
+    gpatch(Fn,Vn,'w','g',1,lineWidth);
+    axisGeom;
+    camlight headlight;
+    gdrawnow;
+
+    %% Saving
+
+    modelNew.source=model;
+    modelNew.faces=Fn;
+    modelNew.vertices=Vn;
+    modelNew.pointSpacing=pointSpacings(q);
+
+    if saveOn==1
+        %Create save name with lowercase letters and underscores instead of spaces
+        saveNameMesh=regexprep(lower(model.preferredName),' ','_');        
+        saveName_mat=fullfile(saveFolder,[saveNameMesh,'.mat']);
+        save(saveName_mat,'-struct','modelNew')
+    end
+
+end

mcode/C_BodyParts3D_isolateLegOuterSkinSurface.asv

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+clear; close all; clc; 
+
+%% Description 
+% This code processes the MAT file for the skin surface (found in the /mat
+% folder), since it contains both the inner and outer skin surfaces. The
+% inner surface is removed and the outer surface is processed to produce a
+% single "water tight" mesh. The surface is also remeshed using ggremesh.
+% The remeshed surface is exported to the /post folder. 
+%
+% This code requires the GIBBON MATLAB toolbox 
+% <www.gibboncode.org>
+
+%% Plotting settings
+lineWidth=0.5;
+
+%% Control parameters
+
+% Path names
+projectFolder = fileparts(fileparts(mfilename('fullpath'))); %Main code path
+loadFolder=fullfile(projectFolder,'data','BodyParts3D','mat'); %The MAT loading folder
+saveFolder=fullfile(projectFolder,'data','BodyParts3D','post'); %The MAT saving folder for processed data
+
+fileName_FMA='FMA7163';
+saveNameMesh='skin_leg_right';
+
+pointSpacing=4; 
+cutHeight=675;
+saveOn=1;
+
+%%
+
+fileName_mat=fullfile(loadFolder,[fileName_FMA,'.mat']);
+
+model=load(fileName_mat);
+F=model.faces;
+V=model.vertices;
+
+%%
+
+logicVertices=V(:,1)<0 & V(:,3)<=cutHeight+mean(patchEdgeLengths(F,V));
+logicFaces=any(logicVertices(F),2);
+logicFaces=triSurfLogicSharpFix(F,logicFaces); 
+Fs=F(logicFaces,:); 
+[Fs,Vs]=patchCleanUnused(Fs,V);
+
+optionStruct.outputType='label';
+[G,~,groupSize]=tesgroup(Fs,optionStruct);
+[~,indMax]=max(groupSize);
+logicKeep=G==indMax;
+Fs=Fs(logicKeep,:); 
+[Fs,Vs]=patchCleanUnused(Fs,Vs);
+
+snapTolerance=mean(patchEdgeLengths(Fs,Vs))/100; 
+n=vecnormalize([0 0 1]); %Normal direction to plane
+P=[0 0 cutHeight]; %Point on plane
+[Fc,Vc,~,logicSide]=triSurfSlice(Fs,Vs,[],P,n,snapTolerance);
+[Fc,Vc]=patchCleanUnused(Fc(logicSide,:),Vc);
+
+%%
+
+shp = alphaShape(Vc,max(patchEdgeLengths(Fc,Vc)),'HoleThreshold',500,'RegionThreshold',1);
+[Fa,Va] = boundaryFacets(shp);
+[Fa,Va]=patchCleanUnused(Fa,Va);
+
+optionStruct2.pointSpacing=pointSpacing; %Set desired point spacing
+optionStruct2.disp_on=1; % Turn off command window text display
+[Fn,Vn]=ggremesh(Fa,Va,optionStruct2);
+
+%% Visualisation
+
+cFigure; 
+subplot(1,2,1); hold on; 
+gpatch(F,V,'w','none',0.25);
+gpatch(Fn,Vn,'bw','none');
+axisGeom; 
+camlight headlight; 
+
+subplot(1,2,2); hold on; 
+gpatch(Fn,Vn,'bw','k',1,lineWidth);
+axisGeom; 
+camlight headlight; 
+gdrawnow; 
+
+%% Store model in structure
+
+modelNew.source=fileName_FMA;
+modelNew.faces=Fn;
+modelNew.vertices=Vn;
+modelNew.pointSpacing=pointSpacing; 
+modelNew.cutHeight=cutHeight;
+
+%% Save model
+
+if saveOn==1
+    saveName_mat=fullfile(saveFolder,[saveNameMesh,'.mat']);
+    save(saveName_mat,'-struct','modelNew')
+end

mcode/C_BodyParts3D_isolateLegOuterSkinSurface.m

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+clear; close all; clc; 
+
+%% Description 
+% This code processes the MAT file for the skin surface (found in the /mat
+% folder), since it contains both the inner and outer skin surfaces. The
+% inner surface is removed and the outer surface is processed to produce a
+% single "water tight" mesh. The surface is also remeshed using ggremesh.
+% The remeshed surface is exported to the /post folder. 
+%
+% This code requires the GIBBON MATLAB toolbox 
+% <www.gibboncode.org>
+
+%% Plotting settings
+lineWidth=0.5;
+
+%% Control parameters
+
+% Path names
+projectFolder = fileparts(fileparts(mfilename('fullpath'))); %Main code path
+loadFolder=fullfile(projectFolder,'data','BodyParts3D','mat'); %The MAT loading folder
+saveFolder=fullfile(projectFolder,'data','BodyParts3D','post'); %The MAT saving folder for processed data
+
+fileName_FMA='FMA7163';
+saveNameMesh='skin_leg_right';
+
+pointSpacing=4; 
+cutHeight=675;
+saveOn=1;
+
+%%
+
+fileName_mat=fullfile(loadFolder,[fileName_FMA,'.mat']);
+
+model=load(fileName_mat);
+F=model.faces;
+V=model.vertices;
+
+%%
+
+logicVertices=V(:,1)<0 & V(:,3)<=cutHeight+mean(patchEdgeLengths(F,V));
+logicFaces=any(logicVertices(F),2);
+logicFaces=triSurfLogicSharpFix(F,logicFaces); 
+Fs=F(logicFaces,:); 
+[Fs,Vs]=patchCleanUnused(Fs,V);
+
+optionStruct.outputType='label';
+[G,~,groupSize]=tesgroup(Fs,optionStruct);
+[~,indMax]=max(groupSize);
+logicKeep=G==indMax;
+Fs=Fs(logicKeep,:); 
+[Fs,Vs]=patchCleanUnused(Fs,Vs);
+
+snapTolerance=mean(patchEdgeLengths(Fs,Vs))/100; 
+n=vecnormalize([0 0 1]); %Normal direction to plane
+P=[0 0 cutHeight]; %Point on plane
+[Fc,Vc,~,logicSide]=triSurfSlice(Fs,Vs,[],P,n,snapTolerance);
+[Fc,Vc]=patchCleanUnused(Fc(logicSide,:),Vc);
+
+%% Construct alpha shape
+% This deteriorates surface quality (bridges concave regions) but is a
+% termporary "quick-and-dirty" work-around to obtain outer skin surface
+% only. 
+
+shp = alphaShape(Vc,max(patchEdgeLengths(Fc,Vc)),'HoleThreshold',500,'RegionThreshold',1);
+[Fa,Va] = boundaryFacets(shp); %Get boundary faces of alpha shape
+[Fa,Va] = patchCleanUnused(Fa,Va); %Remove unused vertices
+
+%% Remesh alpha shape using |ggremesh|
+optionStructRemesh.pointSpacing=pointSpacing; %Set desired point spacing
+optionStructRemesh.disp_on=1; % Turn off command window text display
+[Fn,Vn]=ggremesh(Fa,Va,optionStructRemesh);
+
+%% Visualisation
+
+cFigure; 
+subplot(1,2,1); hold on; 
+gpatch(F,V,'w','none',0.25);
+gpatch(Fn,Vn,'bw','none');
+axisGeom; 
+camlight headlight; 
+
+subplot(1,2,2); hold on; 
+gpatch(Fn,Vn,'bw','k',1,lineWidth);
+axisGeom; 
+camlight headlight; 
+gdrawnow; 
+
+%% Store model in structure
+
+modelNew.source=fileName_FMA;
+modelNew.faces=Fn;
+modelNew.vertices=Vn;
+modelNew.pointSpacing=pointSpacing; 
+modelNew.cutHeight=cutHeight;
+
+%% Save model
+
+if saveOn==1
+    saveName_mat=fullfile(saveFolder,[saveNameMesh,'.mat']);
+    save(saveName_mat,'-struct','modelNew')
+end