[Nirfast] Failing while trying to graphically place sources/detectors
Alexis Girault
alexis.girault at kitware.com
Fri Jun 22 13:49:46 EDT 2018
Thank you, Karthik, Stanislaw,
I believe Scott and Hamid are aware of limitations with recent
matlab versions.
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:
https://github.com/nirfast-admin/NIRFAST/issues
Best,
Alexis Girault
R&D Engineer in Medical Computing
Kitware, Inc.
http://www.kitware.com
(919) 969-6990 x325
On Wed, May 9, 2018 at 6:10 PM Stanislaw Wojtkiewicz <
s.wojtkiewicz at cs.bham.ac.uk> wrote:
> Hi Karthik
>
>
>
> I can confirm, the newest Matlab does not like some functions used in
> NIRFAST.
>
>
>
> The very last issue:
>
> “Error using matlab.graphics.axis.Axes/get
> There is no x_RenderTransform property on the Axes class.”
>
> MathWorks removed the ‘x_RenderTransform’ axes property starting with
> Matlab R2014a. More community comments about that here:
> https://undocumentedmatlab.com/blog/undocumented-view-transformation-matrix
>
>
>
> No easy fix of that (the GUI of source/detector placing might require some
> refurbishment).
>
>
>
> However, I might have a solution for you.
>
>
>
> Here is how to add source/detector manually (using Matlab commands). Step
> by step:
>
>
>
> #0
>
> Do not place points using a mouse.
>
>
>
> #1
>
> @ the left side of the GUI where you have empty lists of sources and
> detectors: put some values in both. E.g.
>
> 1 2 3
>
> 2 4 5
>
> For (x y z) coordinates of e.g. 2 sources. Do similar with detectors.
>
> 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.
>
> #2
>
> 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 :)
>
> #3
>
> Load the mesh in Matlab command window, script, etc.. using the
> ‘load_mesh’ function (mesh = load_mesh(‘path_to_mesh/mesh_name’);)
>
> #4
>
> Adjust your sources and detector.
>
> The mesh structure should have following fields:
>
> source: [1×1 struct]
>
> meas: [1×1 struct]
>
>
>
> e.g.
>
> >> mesh.source
>
>
>
> ans =
>
>
>
> struct with fields:
>
>
>
> distributed: 0
>
> fixed: 0
>
> num: 1
>
> coord: [47.0244 59.5354 48.0170]
>
> fwhm: 0
>
>
>
> and
>
>
>
> >> mesh.meas
>
>
>
> ans =
>
>
>
> struct with fields:
>
>
>
> fixed: 0
>
> num: [2×1 double]
>
> coord: [2×3 double]
>
> int_func: [2×5 double]
>
>
>
> Look for the fields meaning on the online documentation. Focus on:
> coordinates (coord) and numbering (num).
>
>
>
> #5
>
> 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).
>
>
>
> #6
>
> Save the mesh using the command ‘save_mesh(mesh, ‘path_2_mesh/mesh_name’)’
>
>
>
> #7
>
> Enjoy the mesh.
>
> 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’.
>
>
>
> I hope I helped.
>
>
>
>
>
>
>
> Regards
>
> Stanislaw Wojtkiewicz, PhD
>
>
>
> ---
>
> School of Computer Science
>
> University of Birmingham
>
> B15 2TT
>
>
>
> *From:* Vishwanath, Karthik <vishwak at miamioh.edu>
> *Sent:* 09 May 2018 19:15
> *To:* nirfast at public.kitware.com
> *Subject:* [Nirfast] Failing while trying to graphically place
> sources/detectors
>
>
>
> Hi All,
>
> 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.
>
> I've listed sequence of steps with the messages in the workspace window
> shown and the fixes I attempted (in blue text)
>
> ==================================================
>
> >> nirfast
>
> Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard
>
> Selected slab and set L/W/H to 20mm and click Done
>
> Error using textscan
> Unknown parameter 'bufsize'.
>
> Error in read_nod_elm (line 45)
> data = textscan(fid,'%u32 %f %f %f%*[^\n]','bufsize',409500);
>
> Error in checkerboard3d_mm (line 109)
> [telem tnode] = read_nod_elm(fnprefix,1);
>
> Error in make_slab (line 89)
> mesh = checkerboard3d_mm(fullfile(outputdir,'test_node_ele.ele'),...
>
>
> Error in create_mesh (line 25)
> eval(['mesh = make_' lower(shape) '(sizevar);']);
>
> Error in gui_create_mesh>done_Callback (line 532)
> mesh = evalin('base',content{end});
>
> Error in gui_mainfcn (line 95)
> feval(varargin{:});
>
> Error in gui_create_mesh (line 42)
> gui_mainfcn(gui_State, varargin{:});
>
> Error in
>
> matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject))
> Error while evaluating UIControl Callback.
>
>
>
> ==================================================
>
> Changed line 45 in "toolbox/meshing/tools/read_nod_elm.m" to: data =
> textscan(fid,'%u32 %f %f %f%*[^\n]')
>
>
> Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard
>
> Selected slab and set L/W/H to 20mm and click Done
>
>
>
> Added Shield: 0.0010 s
> Delaunay Triangulation Time: 0.7141 s
> Connectivity Time: 0.0359 s
> Circumcenters Time: 0.0129 s
> 47 th level was reached
> 100.0000 % of Tetraedroms were checked
> Walking Time: 0.0399 s
> Manifold extraction Time: 0.4239 s
> Total Time: 1.2299 s
> Writing data to file...Done writing mesh to:
> Path: /home/karthik/Research/Matlab/lib/nirfast
> Filename: test_node_ele.node/.ele
>
>
> --> Beginning mesh generation process, please wait...
> Done with sub-volume separation.
> ===========================================
> Calculating desired length at boundary nodes.. done.
> Calculating prism normals and bounding boxes.. done.
> Sealing boundary buffer zone.. done.
>
> Tagging interior nodes... done
> -----> Running BSP tree to filter out nodes.
>
> -----> done.
> Writing data to file.Done writing the nodes to:
> Path: /tmp
> Filename: input4delaunay.a.node
>
> Writing data to file... Done writing surface to a poly file:
> Path: /tmp
> Filename: input4delaunay.poly
>
> ---------> Running Delaunay, please wait.../bin/bash:
> /home/karthik/Research/Matlab/lib/nirfast/NIRFAST-9.0/toolbox/meshing/bin/delaunaygen-linux64.exe:
> Permission denied
> Warning: Delaunay Generator failed. Trying again...
> > In checkerboard3d (line 181)
> In checkerboard3d_mm (line 167)
> In make_slab (line 89)
> In create_mesh (line 25)
> In gui_create_mesh>done_Callback (line 532)
> In gui_mainfcn (line 95)
> In gui_create_mesh (line 42)
> In
> matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject))
>
> /bin/bash:
> /home/karthik/Research/Matlab/lib/nirfast/NIRFAST-9.0/toolbox/meshing/bin/delaunaygen-linux64.exe:
> Permission denied
> Error using checkerboard3d (line 186)
> Delaunay Generator failed again. Check your input setting!
>
> Error in checkerboard3d_mm (line 167)
> [mesh.elements, mesh.nodes] = checkerboard3d(telem(:,1:3),tnode,myargs);
>
> Error in make_slab (line 89)
> mesh = checkerboard3d_mm(fullfile(outputdir,'test_node_ele.ele'),...
>
>
> Error in create_mesh (line 25)
> eval(['mesh = make_' lower(shape) '(sizevar);']);
>
> Error in gui_create_mesh>done_Callback (line 532)
> mesh = evalin('base',content{end});
>
> Error in gui_mainfcn (line 95)
> feval(varargin{:});
>
> Error in gui_create_mesh (line 42)
> gui_mainfcn(gui_State, varargin{:});
>
> Error in
> matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject))
>
> Error while evaluating UIControl Callback.
>
> ==================================================
>
> In shell:
>
> $ chmod +x
> /home/karthik/Research/Matlab/lib/nirfast/NIRFAST-9.0/toolbox/meshing/bin/delaunaygen-linux64.exe
>
>
>
> Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard
>
> Selected slab and set L/W/H to 20mm and click Done
>
>
>
> Added Shield: 0.0003 s
> Delaunay Triangulation Time: 0.4179 s
> Connectivity Time: 0.0214 s
> Circumcenters Time: 0.0032 s
> Warning: Brute continuation necessary
> > In MyRobustCrust>Marking (line 408)
> In MyRobustCrust (line 134)
> In make_slab (line 85)
> In create_mesh (line 25)
> In gui_create_mesh>done_Callback (line 532)
> In gui_mainfcn (line 95)
> In gui_create_mesh (line 42)
> In
> matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject))
>
> Warning: 1000 th level was reached\n
> > In MyRobustCrust>Marking (line 440)
> In MyRobustCrust (line 134)
> In make_slab (line 85)
> In create_mesh (line 25)
> In gui_create_mesh>done_Callback (line 532)
> In gui_mainfcn (line 95)
> In gui_create_mesh (line 42)
> In
> matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject))
>
> 99.7824 % of Tetraedroms were checked
> Walking Time: 0.0985 s
> Manifold extraction Time: 0.2470 s
> Total Time: 0.7971 s
> Writing data to file...Done writing mesh to:
> Path: /home/karthik/Research/Matlab/lib/nirfast
> Filename: test_node_ele.node/.ele
>
>
> --> Beginning mesh generation process, please wait...
> Done with sub-volume separation.
> ===========================================
> Calculating desired length at boundary nodes.. done.
> Calculating prism normals and bounding boxes.. done.
> Sealing boundary buffer zone.. done.
>
> Tagging interior nodes... done
> -----> Running BSP tree to filter out nodes.
>
> -----> done.
> Writing data to file.Done writing the nodes to:
> Path: /tmp
> Filename: input4delaunay.a.node
>
> Writing data to file... Done writing surface to a poly file:
> Path: /tmp
> Filename: input4delaunay.poly
>
> ---------> Running Delaunay, please wait... done. <---------
>
>
>
> --> Finished mesh generation.
> Undefined function or variable 'myflag'.
>
> Error in optimize_mesh_gui>optimize_mesh_gui_OpeningFcn (line 78)
> if myflag
>
> Error in gui_mainfcn (line 220)
> feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure),
> varargin{:});
>
> Error in optimize_mesh_gui (line 40)
> [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
>
> Error in gui_create_mesh>done_Callback
>
> Error in gui_mainfcn (line 95)
> feval(varargin{:});
>
> Error in gui_create_mesh (line 42)
> gui_mainfcn(gui_State, varargin{:});
>
> Error in
> matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_create_mesh('done_Callback',hObject,eventdata,guidata(hObject))
>
> Error while evaluating UIControl Callback.
>
>
>
> ==================================================
>
> Added line 64 in toolbox/meshing/tools/optimize_mesh_gui.m:
>
> 64 myflag='';
> 65 if(nargin > 3)
>
> Selected menu in GUI: Mesh->Create Mesh ->Simple Shapes -> Standard
>
> Selected slab and set L/W/H to 20mm and click Done
>
>
>
> The mesh is generated and the figure dialog for "Place sources and
> detectors" comes up.
>
> 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:
>
> Error using matlab.graphics.axis.Axes/get
> There is no x_RenderTransform property on the Axes class.
>
> Error in select3d>local_Data2PixelTransform (line 361)
> xform = get(ax,'x_RenderTransform');
>
>
> Error in select3d (line 208)
> xvert = local_Data2PixelTransform(ax,vert)';
>
>
> Error in gui_place_sources_detectors>figure1_WindowButtonDownFcn (line 386)
> p = select3d;
>
> Error in gui_mainfcn (line 95)
> feval(varargin{:});
>
> Error in gui_place_sources_detectors (line 42)
> gui_mainfcn(gui_State, varargin{:});
>
> Error in
> matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gui_place_sources_detectors('figure1_WindowButtonDownFcn',hObject,eventdata,guidata(hObject))
>
> Error while evaluating Figure WindowButtonDownFcn.
>
>
> ==================================================
>
>
>
> Was not sure how to proceed from there. Let me know if there is any other
> information needed to help track/fix this.
>
> Thanks,
>
> --
> Karthik Vishwanath, PhD
> James C. & Carole E. Garland Professorship
>
> Office: 109 Kreger Hall
>
> Dept. of Physics, Miami University, Oxford OH
>
> Tel: (513) 529-2315
>
> Web: OSIM Lab <http://users.miamioh.edu/vishwak/>
>
>
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