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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Hi Karthik<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>I can confirm, the newest Matlab does not like some functions used in NIRFAST.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>The very last issue:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>“</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;mso-fareast-language:EN-US'>”<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>MathWorks removed the ‘</span><span style='color:red'>x_RenderTransform</span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>’ axes property starting with Matlab R2014a. More community comments about that here: <a href="https://undocumentedmatlab.com/blog/undocumented-view-transformation-matrix">https://undocumentedmatlab.com/blog/undocumented-view-transformation-matrix</a><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>No easy fix of that (the GUI of source/detector placing might require some refurbishment).<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>However, I might have a solution for you.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Here is how to add source/detector manually (using Matlab commands). Step by step:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#0<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Do not place points using a mouse.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#1<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>@ the left side of the GUI where you have empty lists of sources and detectors: put some values in both. E.g. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>1 2 3<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>2 4 5<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>For (x y z) coordinates of e.g. 2 sources. Do similar with detectors.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>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.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#2<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>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 :)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#3<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Load the mesh in Matlab command window, script, etc.. using the ‘load_mesh’ function (mesh = load_mesh(‘path_to_mesh/mesh_name’);)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#4<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Adjust your sources and detector.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>The mesh structure should have following fields:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> source: [1×1 struct]<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> meas: [1×1 struct]<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>e.g.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>>> mesh.source<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>ans = <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> struct with fields:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> distributed: 0<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> fixed: 0<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> num: 1<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> coord: [47.0244 59.5354 48.0170]<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> fwhm: 0<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>and <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>>> mesh.meas<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>ans = <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> struct with fields:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> fixed: 0<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> num: [2×1 double]<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> coord: [2×3 double]<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> int_func: [2×5 double]<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Look for the fields meaning on the online documentation. Focus on: coordinates (coord) and numbering (num).<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#5<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>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).<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#6<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Save the mesh using the command ‘save_mesh(mesh, ‘path_2_mesh/mesh_name’)’<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#7<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Enjoy the mesh.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>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’.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>I hope I helped.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Regards<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Stanislaw Wojtkiewicz, PhD<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>---<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>School of Computer Science<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>University of Birmingham<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>B15 2TT<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></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 <vishwak@miamioh.edu> <br><b>Sent:</b> 09 May 2018 19:15<br><b>To:</b> nirfast@public.kitware.com<br><b>Subject:</b> [Nirfast] Failing while trying to graphically place sources/detectors<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Hi All,<o:p></o:p></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>==================================================<o:p></o:p></p></div><div><p class=MsoNormal>>> nirfast<o:p></o:p></p></div><div><p class=MsoNormal>Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard<o:p></o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Selected slab and set L/W/H to 20mm and click Done<o:p></o:p></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><o:p></o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'><br><br>==================================================<o:p></o:p></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><o:p></o:p></p></div><div><p class=MsoNormal><br>Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard<o:p></o:p></p></div><div><p class=MsoNormal>Selected slab and set L/W/H to 20mm and click Done<o:p></o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></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><o:p></o:p></p></div><p class=MsoNormal>==================================================<br><br><span style='color:blue'>In shell:</span><o:p></o:p></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><o:p></o:p></p></div><div><div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard<o:p></o:p></p></div><div><p class=MsoNormal>Selected slab and set L/W/H to 20mm and click Done<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></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><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></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<o:p></o:p></p></div><div><p class=MsoNormal>Selected slab and set L/W/H to 20mm and click Done<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></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. <o:p></o:p></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:<o:p></o:p></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><o:p></o:p></p></div><p class=MsoNormal><br>==================================================<o:p></o:p></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><o:p> </o:p></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><o:p></o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'>Thanks,<o:p></o:p></p></div><div><div><p class=MsoNormal>--<br>Karthik Vishwanath, PhD<br>James C. & Carole E. Garland Professorship<o:p></o:p></p><div><p class=MsoNormal>Office: 109 Kreger Hall<o:p></o:p></p></div><p class=MsoNormal>Dept. of Physics, Miami University, Oxford OH<o:p></o:p></p></div><p class=MsoNormal>Tel: (513) 529-2315<o:p></o:p></p><div><p class=MsoNormal>Web: <a href="http://users.miamioh.edu/vishwak/" target="_blank">OSIM Lab</a><o:p></o:p></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="DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2"><br />
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