<div dir="ltr">Thank you, Karthik, Stanislaw,<div><br></div><div>I believe Scott and Hamid are aware of limitations with recent matlab versions.</div><div><br></div><div>Would you be able to add the encountered issue in the project issue tracker? This will allow us to plan the needed work for the next release: <a href="https://github.com/nirfast-admin/NIRFAST/issues">https://github.com/nirfast-admin/NIRFAST/issues</a></div><div><br></div><div>Best,</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><span style="color:rgb(136,136,136);font-size:12.8px">Alexis Girault</span><br style="color:rgb(136,136,136);font-size:12.8px"><span style="color:rgb(136,136,136);font-size:12.8px">R&D Engineer in Medical Computing</span><br style="color:rgb(136,136,136);font-size:12.8px"><span style="color:rgb(136,136,136);font-size:12.8px">Kitware, Inc.</span><br style="color:rgb(136,136,136);font-size:12.8px"><br style="color:rgb(136,136,136);font-size:12.8px"><a href="http://www.kitware.com/" rel="noreferrer" style="color:rgb(17,85,204);font-size:12.8px" target="_blank">http://www.kitware.com</a><br style="color:rgb(136,136,136);font-size:12.8px"><font color="#999999"><a target="_blank"><span style="font-size:12.8px">(919) 969-6990 x3</span>25</a></font><br></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, May 9, 2018 at 6:10 PM Stanislaw Wojtkiewicz <<a href="mailto:s.wojtkiewicz@cs.bham.ac.uk">s.wojtkiewicz@cs.bham.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-GB" link="blue" vlink="purple"><div class="m_-7383975974148153812WordSection1"><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi Karthik<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">I can confirm, the newest Matlab does not like some functions used in NIRFAST.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">The very last issue:<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">“</span><span style="color:red">Error using matlab.graphics.axis.Axes/get</span><br><span style="color:red">There is no x_RenderTransform property on the Axes class.</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">”<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">MathWorks removed the ‘</span><span style="color:red">x_RenderTransform</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">’ axes property starting with Matlab R2014a. More community comments about that here: <a href="https://undocumentedmatlab.com/blog/undocumented-view-transformation-matrix" target="_blank">https://undocumentedmatlab.com/blog/undocumented-view-transformation-matrix</a><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">No easy fix of that (the GUI of source/detector placing might require some refurbishment).<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">However, I might have a solution for you.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Here is how to add source/detector manually (using Matlab commands). Step by step:<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">#0<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Do not place points using a mouse.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">#1<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">@ the left side of the GUI where you have empty lists of sources and detectors: put some values in both. E.g. <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">1 2 3<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">2 4 5<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">For (x y z) coordinates of e.g. 2 sources. Do similar with detectors.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">The 'points placing' with a mouse just reads the (x y z) coordinates from the figure axes and puts them into the lists. You might try to put the exact coordinates if you know them.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">#2<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Save the mesh from the GUI. Step #1 is not necessary. You should be able to save mesh without fiducial points. However, you will have more work later :)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">#3<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Load the mesh in Matlab command window, script, etc.. using the ‘load_mesh’ function (mesh = load_mesh(‘path_to_mesh/mesh_name’);)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">#4<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Adjust your sources and detector.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">The mesh structure should have following fields:<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> source: [1×1 struct]<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> meas: [1×1 struct]<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">e.g.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">>> mesh.source<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">ans = <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> struct with fields:<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> distributed: 0<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> fixed: 0<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> num: 1<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> coord: [47.0244 59.5354 48.0170]<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> fwhm: 0<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">and <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">>> mesh.meas<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">ans = <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> struct with fields:<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> fixed: 0<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> num: [2×1 double]<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> coord: [2×3 double]<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> int_func: [2×5 double]<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Look for the fields meaning on the online documentation. Focus on: coordinates (coord) and numbering (num).<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">#5<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Change the mesh.link field accordingly (using your sources and detectors numbering). The ‘link’ field is explained somewhere online. It is basically a list of source and detector numbers and logical indicator (0, 1) if this pair is considered as active (if the boundary fluence rate should be calculated for that pair).<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">#6<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Save the mesh using the command ‘save_mesh(mesh, ‘path_2_mesh/mesh_name’)’<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">#7<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Enjoy the mesh.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">The source/detector coordinates do not have to be exactly on the mesh surface. Try to put them close to the surface. The load_mesh function will take care of proper positioning if you leave the ‘fixed’ field set to ‘0’.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">I hope I helped.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Consolas;color:#1f497d">Regards<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Consolas;color:#1f497d">Stanislaw Wojtkiewicz, PhD<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Consolas;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Consolas;color:#1f497d">---<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Consolas;color:#1f497d">School of Computer Science<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:Consolas;color:#1f497d">University of Birmingham<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:Consolas;color:#1f497d">B15 2TT<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Vishwanath, Karthik <<a href="mailto:vishwak@miamioh.edu" target="_blank">vishwak@miamioh.edu</a>> <br><b>Sent:</b> 09 May 2018 19:15<br><b>To:</b> <a href="mailto:nirfast@public.kitware.com" target="_blank">nirfast@public.kitware.com</a><br><b>Subject:</b> [Nirfast] Failing while trying to graphically place sources/detectors<u></u><u></u></span></p><p class="MsoNormal"><u></u> <u></u></p><div><div><div><p class="MsoNormal" style="margin-bottom:12.0pt">Hi All,<u></u><u></u></p></div><p class="MsoNormal" style="margin-bottom:12.0pt">Was having trouble creating and placing sources/detectors in a standard slab mesh using NIRFAST-9.0 on a linux system (Ubuntu 16.04.4 LTS; 4.4.0-122-generic x86_64 kernel). My MATLAB version is R2017a. <br><br>I've listed sequence of steps with the messages in the workspace window shown and the fixes I attempted (in blue text) <br><br>==================================================<u></u><u></u></p></div><div><p class="MsoNormal">>> nirfast<u></u><u></u></p></div><div><p class="MsoNormal">Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard<u></u><u></u></p></div><div><p class="MsoNormal" style="margin-bottom:12.0pt">Selected slab and set L/W/H to 20mm and click Done<u></u><u></u></p><div style="margin-left:30.0pt"><p class="MsoNormal"><span style="color:red">Error using textscan<br>Unknown parameter 'bufsize'.<br><br>Error in read_nod_elm (line 45)<br> data = textscan(fid,'%u32 %f %f %f%*[^\n]','bufsize',409500);<br><br>Error in checkerboard3d_mm (line 109)<br> [telem tnode] = read_nod_elm(fnprefix,1);<br><br>Error in make_slab (line 89)<br> mesh = checkerboard3d_mm(fullfile(outputdir,'test_node_ele.ele'),...<br><br><br>Error in create_mesh (line 25)<br> eval(['mesh = make_' lower(shape) '(sizevar);']);<br><br>Error in gui_create_mesh>done_Callback (line 532)<br> mesh = evalin('base',content{end});<br><br>Error in gui_mainfcn (line 95)<br> feval(varargin{:});<br><br>Error in gui_create_mesh (line 42)<br> gui_mainfcn(gui_State, varargin{:});<br><br>Error in<br>matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject))<br>Error while evaluating UIControl Callback.</span><u></u><u></u></p></div><p class="MsoNormal" style="margin-bottom:12.0pt"><br><br>==================================================<u></u><u></u></p></div><div><p class="MsoNormal"><span style="color:blue">Changed line 45 in "toolbox/meshing/tools/read_nod_elm.m" to: data = textscan(fid,'%u32 %f %f %f%*[^\n]')</span><u></u><u></u></p></div><div><p class="MsoNormal"><br>Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard<u></u><u></u></p></div><div><p class="MsoNormal">Selected slab and set L/W/H to 20mm and click Done<u></u><u></u></p></div><div><p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p><div style="margin-left:30.0pt"><p class="MsoNormal" style="margin-bottom:12.0pt">Added Shield: 0.0010 s<br>Delaunay Triangulation Time: 0.7141 s<br>Connectivity Time: 0.0359 s<br>Circumcenters Time: 0.0129 s<br> 47 th level was reached<br>100.0000 % of Tetraedroms were checked<br>Walking Time: 0.0399 s<br>Manifold extraction Time: 0.4239 s<br>Total Time: 1.2299 s<br>Writing data to file...Done writing mesh to:<br> Path: /home/karthik/Research/Matlab/lib/nirfast<br> Filename: test_node_ele.node/.ele<br><br><br>--> Beginning mesh generation process, please wait...<br> Done with sub-volume separation.<br>===========================================<br> Calculating desired length at boundary nodes.. done.<br> Calculating prism normals and bounding boxes.. done.<br> Sealing boundary buffer zone.. done.<br><br> Tagging interior nodes... done<br>-----> Running BSP tree to filter out nodes.<br><br>-----> done.<br>Writing data to file.Done writing the nodes to:<br> Path: /tmp<br> Filename: input4delaunay.a.node<br><br>Writing data to file... Done writing surface to a poly file:<br> Path: /tmp<br> Filename: input4delaunay.poly<br><br>---------> Running Delaunay, please wait.../bin/bash: /home/karthik/Research/Matlab/lib/nirfast/NIRFAST-9.0/toolbox/meshing/bin/delaunaygen-linux64.exe: Permission denied<br>Warning: Delaunay Generator failed. Trying again... <br><span style="color:red">> In checkerboard3d (line 181)<br> In checkerboard3d_mm (line 167)<br> In make_slab (line 89)<br> In create_mesh (line 25)<br> In gui_create_mesh>done_Callback (line 532)<br> In gui_mainfcn (line 95)<br> In gui_create_mesh (line 42)<br> In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject)) <br></span><span style="color:black">/bin/bash: /home/karthik/Research/Matlab/lib/nirfast/NIRFAST-9.0/toolbox/meshing/bin/delaunaygen-linux64.exe: Permission denied</span><span style="color:red"><br>Error using checkerboard3d (line 186)<br> Delaunay Generator failed again. Check your input setting!<br><br>Error in checkerboard3d_mm (line 167)<br>[mesh.elements, mesh.nodes] = checkerboard3d(telem(:,1:3),tnode,myargs);<br><br>Error in make_slab (line 89)<br> mesh = checkerboard3d_mm(fullfile(outputdir,'test_node_ele.ele'),...<br><br><br>Error in create_mesh (line 25)<br> eval(['mesh = make_' lower(shape) '(sizevar);']);<br><br>Error in gui_create_mesh>done_Callback (line 532)<br> mesh = evalin('base',content{end});<br><br>Error in gui_mainfcn (line 95)<br> feval(varargin{:});<br><br>Error in gui_create_mesh (line 42)<br> gui_mainfcn(gui_State, varargin{:});<br><br>Error in<br>matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject)) <br>Error while evaluating UIControl Callback.</span><u></u><u></u></p></div><p class="MsoNormal">==================================================<br><br><span style="color:blue">In shell:</span><u></u><u></u></p></div><div><p class="MsoNormal"><span style="color:blue">$ chmod +x /home/karthik/Research/Matlab/lib/nirfast/NIRFAST-9.0/toolbox/meshing/bin/delaunaygen-linux64.exe</span><u></u><u></u></p></div><div><div><div><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal">Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard<u></u><u></u></p></div><div><p class="MsoNormal">Selected slab and set L/W/H to 20mm and click Done<u></u><u></u></p></div><p class="MsoNormal"><u></u> <u></u></p><div style="margin-left:30.0pt"><p class="MsoNormal">Added Shield: 0.0003 s<br>Delaunay Triangulation Time: 0.4179 s<br>Connectivity Time: 0.0214 s<br>Circumcenters Time: 0.0032 s<br><span style="color:red">Warning: Brute continuation necessary <br>> In MyRobustCrust>Marking (line 408)<br> In MyRobustCrust (line 134)<br> In make_slab (line 85)<br> In create_mesh (line 25)<br> In gui_create_mesh>done_Callback (line 532)<br> In gui_mainfcn (line 95)<br> In gui_create_mesh (line 42)<br> In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject)) <br>Warning: 1000 th level was reached\n <br>> In MyRobustCrust>Marking (line 440)<br> In MyRobustCrust (line 134)<br> In make_slab (line 85)<br> In create_mesh (line 25)<br> In gui_create_mesh>done_Callback (line 532)<br> In gui_mainfcn (line 95)<br> In gui_create_mesh (line 42)<br> In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject)) </span><br>99.7824 % of Tetraedroms were checked<br>Walking Time: 0.0985 s<br>Manifold extraction Time: 0.2470 s<br>Total Time: 0.7971 s<br>Writing data to file...Done writing mesh to:<br> Path: /home/karthik/Research/Matlab/lib/nirfast<br> Filename: test_node_ele.node/.ele<br><br><br>--> Beginning mesh generation process, please wait...<br> Done with sub-volume separation.<br>===========================================<br> Calculating desired length at boundary nodes.. done.<br> Calculating prism normals and bounding boxes.. done.<br> Sealing boundary buffer zone.. done.<br><br> Tagging interior nodes... done<br>-----> Running BSP tree to filter out nodes.<br><br>-----> done.<br>Writing data to file.Done writing the nodes to:<br> Path: /tmp<br> Filename: input4delaunay.a.node<br><br>Writing data to file... Done writing surface to a poly file:<br> Path: /tmp<br> Filename: input4delaunay.poly<br><br>---------> Running Delaunay, please wait... done. <---------<br><br><br><br>--> Finished mesh generation.<br><span style="color:red">Undefined function or variable 'myflag'.<br><br>Error in optimize_mesh_gui>optimize_mesh_gui_OpeningFcn (line 78)<br>if myflag<br><br>Error in gui_mainfcn (line 220)<br> feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});<br><br>Error in optimize_mesh_gui (line 40)<br> [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});<br><br>Error in gui_create_mesh>done_Callback<br><br>Error in gui_mainfcn (line 95)<br> feval(varargin{:});<br><br>Error in gui_create_mesh (line 42)<br> gui_mainfcn(gui_State, varargin{:});<br><br>Error in<br>matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject)) <br>Error while evaluating UIControl Callback.</span><u></u><u></u></p></div><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal">==================================================<br><span style="color:blue"><br>Added line 64 in toolbox/meshing/tools/optimize_mesh_gui.m: <br><br>64 myflag='';<br>65 if(nargin > 3)<br></span><br>Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard<u></u><u></u></p></div><div><p class="MsoNormal">Selected slab and set L/W/H to 20mm and click Done<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal" style="margin-bottom:12.0pt">The mesh is generated and the figure dialog for "Place sources and detectors" comes up. <u></u><u></u></p></div><div><p class="MsoNormal" style="margin-bottom:12.0pt">The mesh is viewable, can be rotated and panned using the tools in the figure window. However, clicking on the mesh generates the following error:<u></u><u></u></p></div><div style="margin-left:30.0pt"><p class="MsoNormal"><span style="color:red">Error using matlab.graphics.axis.Axes/get</span><br><span style="color:red">There is no x_RenderTransform property on the Axes class.</span><br><br><span style="color:red">Error in select3d>local_Data2PixelTransform (line 361)</span><br><span style="color:red">xform = get(ax,'x_RenderTransform');</span><br><br><br><span style="color:red">Error in select3d (line 208)</span><br><span style="color:red">xvert = local_Data2PixelTransform(ax,vert)';</span><br><br><br><span style="color:red">Error in gui_place_sources_detectors>figure1_WindowButtonDownFcn (line 386)</span><br><span style="color:red"> p = select3d;</span><br><br><span style="color:red">Error in gui_mainfcn (line 95)</span><br><span style="color:red"> feval(varargin{:});</span><br><br><span style="color:red">Error in gui_place_sources_detectors (line 42)</span><br><span style="color:red"> gui_mainfcn(gui_State, varargin{:});</span><br><br><span style="color:red">Error in</span><br><span style="color:red">matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_place_sources_detectors('figure1_WindowButtonDownFcn',hObject,eventdata,guidata(hObject)) </span><br><span style="color:red">Error while evaluating Figure WindowButtonDownFcn.</span><u></u><u></u></p></div><p class="MsoNormal"><br>==================================================<u></u><u></u></p></div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal" style="margin-bottom:12.0pt">Was not sure how to proceed from there. Let me know if there is any other information needed to help track/fix this. <br><br><u></u><u></u></p></div><p class="MsoNormal" style="margin-bottom:12.0pt">Thanks,<u></u><u></u></p></div><div><div><p class="MsoNormal">--<br>Karthik Vishwanath, PhD<br>James C. & Carole E. Garland Professorship<u></u><u></u></p><div><p class="MsoNormal">Office: 109 Kreger Hall<u></u><u></u></p></div><p class="MsoNormal">Dept. of Physics, Miami University, Oxford OH<u></u><u></u></p></div><p class="MsoNormal">Tel: (513) 529-2315<u></u><u></u></p><div><p class="MsoNormal">Web: <a href="http://users.miamioh.edu/vishwak/" target="_blank">OSIM Lab</a><u></u><u></u></p></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><div id="m_-7383975974148153812DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2"><br>
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