Added missing dependencies

private/addtrirep.m

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+function tNew = addtrirep(varargin)
+%ADDTRIREP creates a new TriRep that contains tA and tB.
+% Usage:
+%   tNew = addtrirep(tA, tB, tC ....)
+%   tNew = addtrirep({tA, tB, tC ...})
+% Where:
+%   tA,tB etc are TriRep
+%
+% ADDTRIREP creates a new TriRep that contains tA and tB.
+%
+% Author: Nick Linton (2011)
+% Modifications - 
+
+    if nargin == 1
+        tCell = varargin{1};
+    else
+        tCell = varargin;
+    end
+
+    nV = 0;
+    nT = 0;
+    for i = 1:length(tCell)
+        if ~isa(tCell{i},'TriRep')
+            error('ADDTRIREP: the input must be TriRep objects or a cell array of TriRep objects.')
+        end
+        nV = nV + size(tCell{i}.X,1);
+        nT = nT + size(tCell{i}.Triangulation,1);
+    end
+
+    newT = zeros(nT,3);
+    newX = zeros(nV,3);
+
+    currentV = 1;
+    currentT = 1;
+    for i = 1:length(tCell)
+        if ~isa(tCell{i},'TriRep')
+            error('ADDTRIREP: the input must be TriRep objects or a cell array of TriRep objects.')
+        end
+        nV = size(tCell{i}.X,1);
+        nT = size(tCell{i}.Triangulation,1);
+        newX(currentV:(currentV+nV-1),:) = tCell{i}.X;
+        newT(currentT:(currentT+nT-1),:) = tCell{i}.Triangulation + currentV-1;
+        currentV = currentV+nV;
+        currentT = currentT+nT;
+    end
+
+    tNew = TriRep(newT, newX);
+
+end
+
+
+

private/colorBrewer.m

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+function rgb = colorBrewer(name)
+% COLORBREWER Returns RGB data for the nice colors
+%
+% Usage:
+%   rgb = colorBrewer(name)
+% Where:
+%   name - is 'r'|'g'|'b'|'p'|'o'|'y'
+%   rgb - is the RGB colorspec
+%
+% COLORBREWER See http://colorbrewer2.org/
+%
+% Author: Steven Williams (2014)
+% Modifications -
+%
+% Info on Code Testing:
+% ---------------------------------------------------------------
+% test code
+% ---------------------------------------------------------------
+%
+% ---------------------------------------------------------------
+% code
+% ---------------------------------------------------------------
+
+if isnumeric(name)
+    if name==1
+        rgb = [228 26 28]/256;
+    elseif name==2
+        rgb = [55 126 184]/256;
+    elseif name==3
+        rgb = [77 175 74]/256;
+    elseif name==4
+        rgb = [152 78 163]/256;
+    elseif name==5
+        rgb = [255 127 0]/256;
+    elseif name==6
+        rgb = [255 255 51]/256;
+    elseif name==7
+        rgb = [166 86 40]/256;
+    elseif name==8
+        rgb = [247 129 191]/256;
+    elseif name==9
+        rgb = [153 153 153]/256;
+    end
+else
+    switch name
+        case 'r'
+            rgb = [228 26 28]/256;
+        case 'g'
+            rgb = [77 175 74]/256;
+        case 'b'
+            rgb = [55 126 184]/256;
+        case 'p'
+            rgb = [152 78 163]/256;
+        case 'o'
+            rgb = [255 127 0]/256;
+        case 'y'
+            rgb = [255 255 51]/256;
+        case 'g1'
+            rgb = [27 158 119]/256;
+        case 'o1'
+            rgb = [217 95 2]/256;
+        case 'p1'
+            rgb = [117 112 179]/256;
+    end
+end

private/deleteFolder.m

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+function deleteFolder( folderPath, varargin )
+% DELETEFOLDER Deletes the folder folderPath
+%
+% Usage:
+%   deleteFolder( folderPath )
+% Where:
+%   folderPath - the full path to the folder
+%
+% DELETEFOLDER Detailed description goes here
+%
+% DELETEFOLDER accepts the following parameter-value pairs
+%   'verbose'     {false}|true
+%
+% Author: Steven Williams (2020)
+% Modifications -
+%
+% Info on Code Testing:
+% ---------------------------------------------------------------
+% test code
+% ---------------------------------------------------------------
+%
+% ---------------------------------------------------------------
+% code
+% ---------------------------------------------------------------
+
+% Parse input
+nStandardArgs = 1; % UPDATE VALUE
+verbose = false;
+if nargin > nStandardArgs
+    for i = nStandardArgs+1:2:nargin
+        switch varargin{i}
+            case 'verbose'
+                verbose = varargin{i+1};
+        end
+    end
+end
+
+% Check to make sure that folder actually exists.  Warn user if it doesn't.
+if ~isdir(folderPath)
+  error('DELETEFOLDER: Specified path does not exist')
+  return;
+end
+
+% Get a list of all files in the folder with the desired file name pattern.
+theFiles = nameFiles(folderPath);
+
+% Delete each file one by one
+for k = 1 : length(theFiles)
+  fullFileName = fullfile(folderPath, theFiles{k});
+  if verbose
+    fprintf(1, 'Now deleting %s\n', fullFileName);
+  end
+  delete(fullFileName);
+end
+
+% Remove the directory
+rmdir(folderPath)
+
+end

private/du.m

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+function cmdout = du( argument )
+% DU is a wrapper function for the Unix file system tool du
+%
+% Usage:
+%   cmdout = du(argument)
+% Where:
+%   argument - is the input provided to do
+%   cmdout - is the information returned by du in a string
+%
+% DU Detailed description goes here
+%
+% Author: Steven Williams (2020)
+% Modifications -
+%
+% Info on Code Testing:
+% ---------------------------------------------------------------
+% test code
+% ---------------------------------------------------------------
+%
+% ---------------------------------------------------------------
+% code
+% ---------------------------------------------------------------
+
+%create the system call
+arg = ['du ' argument];
+
+%system call
+[status, cmdout] = system(arg);
+
+%remove the carriage return from the end of cmdout
+cmdout(end) = [];
+
+end

private/editTriangulation.m

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+function [tr2, isVertUsed] = editTriangulation(tr)
+% EDITTRIANGULATION Graphically remove triangles from a TriRep object
+%
+% Usage:
+%   tr2 = editTriangulation(tr)
+% Where:
+%   tr  - is the original triangulation
+%   tr2 - is the new triangulation with elements removed
+%   isVertUsed - indexes into tr.X for vertices that are used in the new
+%   triangulation, tr2
+%
+% EDITTRIANGULATION uses GET3DFACES to remove triangles from a TriRep
+% object. Controls:
+%   Left click          - select triangles to remove
+%   Shift-Left click    - select triangles to keep
+%   Ctrl-Left click     - select area up to the boundary
+%   d                   - done
+%
+% Author: Steven Williams (2013)
+% Modifications -
+%   2016 - refactored by moving userdata manipulation into a separate fcn
+%
+% Info on Code Testing:
+% ---------------------
+%
+% ---------------------
+%
+% ---------------------------------------------------------------
+% code
+% ---------------------------------------------------------------
+
+% Edit to remove the valve orifice
+disp('E D I T   T R I A N G U L A T I O N');
+disp('-----------------------------------');
+disp('Left click - select triangles to remove (shift to undo)');
+disp('Cltr-left - select area');
+disp('Press d when done');
+disp('');
+
+editFig = figure;
+
+% Construct the trirep
+no = tr.X; %node
+el = tr.Triangulation; %element
+
+hP = trisurf(tr);
+set(hP, 'FaceVertexCData', zeros(length(tr.Triangulation),3)+0.7 ...
+    ,'FaceColor', 'flat' ...
+    );
+axis equal vis3d
+light
+
+get3dfaces(hP,'on');
+
+%Wait until a key is pressed, then only progressif it was 'd'
+key = get(editFig, 'CurrentCharacter');
+while ~strcmpi(key, 'd')
+    pause;
+    key = get(editFig, 'CurrentCharacter');
+end
+
+% Now, continue by creating the new TriRep
+iRemove = get3dfaces(hP);
+close(editFig);
+
+el(iRemove, :) = [];
+tr2 = repack(TriRep(el, no));
+
+[tr2, isVertUsed] = repack(tr2);
+end

private/extract_coordinates_from_path.m

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+function [x,y,z] = extract_coordinates_from_path(path)
+
+%this elegant way is incompatible with the older versions of matlab
+% x = cellfun(@(p) p.x, path);    %the simplest way to extract coordinates from the path
+% y = cellfun(@(p) p.y, path);    %if it looks complicated, you can use "for" similar to example1.m
+% z = cellfun(@(p) p.z, path);
+
+x = zeros(length(path),1);
+y = x; 
+z = y;
+
+for i=1:length(path)
+    x(i) = path{i}.x;
+    y(i) = path{i}.y;
+    z(i) = path{i}.z;
+end;
+