Added and rendered license boiler plate on codes and documentation

.gitignore

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+# Ignore temporary matlab ASV files
+*.asv

docs/docTools/addCodeFooter.m

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+clear; close all; clc;
+
+%%
+
+toolboxPath=fileparts(fileparts(fileparts(mfilename('fullpath'))));
+docPath=fullfile(fileparts(fileparts(fileparts(mfilename('fullpath')))),'docs');
+libPath=fullfile(fileparts(fileparts(fileparts(mfilename('fullpath')))),'mcode');
+docToolsPath=fullfile(fileparts(fileparts(fileparts(mfilename('fullpath')))),'docs','docTools');
+
+pathNames={docToolsPath,libPath,docPath};
+
+%% Prepare boilerplate
+
+licenseBoilerPlate=fullfile(toolboxPath,'licenseBoilerPlate.txt');
+[T]=txtfile2cell(licenseBoilerPlate);
+
+footerTargetText='% _*SimuLimb footer text*_ ';
+
+%%
+
+licenseLink='https://github.com/SimuLimb/simulateAmputation.m/blob/main/LICENSE';
+
+%Add comment symbols
+for q=1:1:numel(T)
+    T{q}=['% ',T{q}];
+end
+
+%Add target header
+T=[{'%% '};{footerTargetText};{'% '};{['% License: <',licenseLink,'>']};T(1:end)];
+
+%%
+
+fileExtension='.m';
+
+%%
+
+numPaths=numel(pathNames); 
+for q_path=1:1:numPaths
+    pathName=pathNames{q_path};     
+    files = dir(fullfile(pathName,'*.m'));
+    files={files(1:end).name};
+    files=sort(files(:));
+    numFiles=numel(files);    
+    for q_file=1:1:numFiles
+        fileName=fullfile(pathName,files{q_file});
+        [T_now]=txtfile2cell(fileName);        
+        T_now(end+1:end+numel(T))=T;
+        cell2txtfile(fileName,T_now,0);        
+    end
+end
+
+%% 
+% _*SimuLimb footer text*_ 
+% 
+% License: <https://github.com/SimuLimb/simulateAmputation.m/blob/main/LICENSE>
+%   
+% Copyright (C) 2006-2021 Kevin Mattheus Moerman and the SimuLimb contributors
+% 
+% Licensed under the Apache License, Version 2.0 (the "License");
+% you may not use this file except in compliance with the License.
+% You may obtain a copy of the License at
+% 
+%     http://www.apache.org/licenses/LICENSE-2.0
+% 
+% Unless required by applicable law or agreed to in writing, software
+% distributed under the License is distributed on an "AS IS" BASIS,
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+% See the License for the specific language governing permissions and
+% limitations under the License.

docs/docTools/removeCodeFooter.m

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+clear; close all; clc;
+
+%% Path names
+
+toolboxPath=fileparts(fileparts(fileparts(mfilename('fullpath'))));
+docPath=fullfile(fileparts(fileparts(fileparts(mfilename('fullpath')))),'docs');
+libPath=fullfile(fileparts(fileparts(fileparts(mfilename('fullpath')))),'mcode');
+docToolsPath=fullfile(fileparts(fileparts(fileparts(mfilename('fullpath')))),'docs','docTools');
+
+pathNames={docToolsPath,libPath,docPath};
+
+%%
+
+fileExtension='.m'; %Extension to remove boilerplate from
+
+footerTargetStart='% _*SimuLimb footer text*_ '; %Target for removal
+
+%N.B. Removal is up to end from the start so make sure the target is
+%appropriately set!!!!!
+
+%% Removing footer text
+
+numPaths=numel(pathNames); 
+for q_path=1:1:numPaths
+    pathName=pathNames{q_path};     
+    files = dir(fullfile(pathName,'*.m'));
+    files={files(1:end).name};
+    files=sort(files(:));
+    numFiles=numel(files);    
+    for q_file=1:1:numFiles
+        fileName=fullfile(pathName,files{q_file});
+        [T_now]=txtfile2cell(fileName);
+        targetStartIndex = find(strcmp(footerTargetStart,T_now));       
+        if ~isempty(targetStartIndex)            
+            targetStartIndex=targetStartIndex(end); %Keep last occurance
+            T_now=T_now(1:targetStartIndex-1-1); %NB -1 is used to remove %% above target 
+            cell2txtfile(fileName,T_now,0,0);
+        end
+    end
+end
+%% 
+% _*SimuLimb footer text*_ 
+% 
+% License: <https://github.com/SimuLimb/simulateAmputation.m/blob/main/LICENSE>
+%   
+% Copyright (C) 2006-2021 Kevin Mattheus Moerman and the SimuLimb contributors
+% 
+% Licensed under the Apache License, Version 2.0 (the "License");
+% you may not use this file except in compliance with the License.
+% You may obtain a copy of the License at
+% 
+%     http://www.apache.org/licenses/LICENSE-2.0
+% 
+% Unless required by applicable law or agreed to in writing, software
+% distributed under the License is distributed on an "AS IS" BASIS,
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+% See the License for the specific language governing permissions and
+% limitations under the License.

licenseBoilerPlate.txt

@@ -0,0 +1,14 @@
+
+Copyright (C) 2006-2021 Kevin Mattheus Moerman and the SimuLimb contributors
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

mcode/A_BodyParts3D_convert_STL_to_MAT.m

@@ -1,69 +1,87 @@
-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
-
+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
+
+%% 
+% _*SimuLimb footer text*_ 
+% 
+% License: <https://github.com/SimuLimb/simulateAmputation.m/blob/main/LICENSE>
+%   
+% Copyright (C) 2006-2021 Kevin Mattheus Moerman and the SimuLimb contributors
+% 
+% Licensed under the Apache License, Version 2.0 (the "License");
+% you may not use this file except in compliance with the License.
+% You may obtain a copy of the License at
+% 
+%     http://www.apache.org/licenses/LICENSE-2.0
+% 
+% Unless required by applicable law or agreed to in writing, software
+% distributed under the License is distributed on an "AS IS" BASIS,
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+% See the License for the specific language governing permissions and
+% limitations under the License.