diff --git a/.gitignore b/.gitignore index f042d9ad..86b264e2 100644 --- a/.gitignore +++ b/.gitignore @@ -30,3 +30,6 @@ script/matlab/demos/*.mat # Python build outputs *.egg-info *.whl + +# Mac stuff +.DS_Store diff --git a/CMakeLists.txt b/CMakeLists.txt index 38b7df8a..8389b4bf 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,5 +1,5 @@ -cmake_minimum_required(VERSION 3.0.0) -project(toastmm VERSION 0.9.1) +cmake_minimum_required(VERSION 3.10.0) +project(toastmm VERSION 0.9.2) include(CTest) enable_testing() diff --git a/HISTORY.md b/HISTORY.md index d9894547..7f2df98b 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,5 +1,8 @@ # Toast-- Development History +## v0.9.2 + + - Cleanup (mainline) warning on MacOS ## v0.9.1 diff --git a/script/matlab/demos/toast_demo7.asv b/script/matlab/demos/toast_demo7.asv deleted file mode 100755 index 5c49863b..00000000 --- a/script/matlab/demos/toast_demo7.asv +++ /dev/null @@ -1,427 +0,0 @@ -function varargout = toast_demo7(varargin) -% TOAST_demo7 M-file for toast_demo7.fig -% TOAST_demo7, by itself, creates a new TOAST_demo7 or raises the existing -% singleton*. -% -% H = TOAST_demo7 returns the handle to a new TOAST_demo7 or the handle to -% the existing singleton*. -% -% TOAST_demo7('CALLBACK',hObject,eventData,handles,...) calls the local -% function named CALLBACK in TOAST_demo7.M with the given input arguments. -% -% TOAST_demo7('Property','Value',...) creates a new TOAST_demo7 or raises the -% existing singleton*. Starting from the left, property value pairs are -% applied to the GUI before toast_demo7_OpeningFunction gets called. An -% unrecognized property name or invalid value makes property application -% stop. All inputs are passed to toast_demo7_OpeningFcn via varargin. -% -% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one -% instance to run (singleton)". -% -% See also: GUIDE, GUIDATA, GUIHANDLES - -% Edit the above text to modify the response to help toast_demo7 - -% Last Modified by GUIDE v2.5 08-Apr-2008 12:49:40 - -% Begin initialization code - DO NOT EDIT -gui_Singleton = 1; -gui_State = struct('gui_Name', mfilename, ... - 'gui_Singleton', gui_Singleton, ... - 'gui_OpeningFcn', @toast_demo7_OpeningFcn, ... - 'gui_OutputFcn', @toast_demo7_OutputFcn, ... - 'gui_LayoutFcn', [] , ... - 'gui_Callback', []); -if nargin && ischar(varargin{1}) - gui_State.gui_Callback = str2func(varargin{1}); -end - -if nargout - [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); -else - gui_mainfcn(gui_State, varargin{:}); -end -% End initialization code - DO NOT EDIT - - -% --- Executes just before toast_demo7 is made visible. -function toast_demo7_OpeningFcn(hObject, eventdata, handles, varargin) -% This function has no output args, see OutputFcn. -% hObject handle to figure -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) -% varargin command line arguments to toast_demo7 (see VARARGIN) - -% Choose default command line output for toast_demo7 -handles.output = hObject; - -% Update handles structure -guidata(hObject, handles); - -init(handles); - -% UIWAIT makes toast_demo7 wait for user response (see UIRESUME) -%uiwait(handles.figure1); - - -% --- Outputs from this function are returned to the command line. -function varargout = toast_demo7_OutputFcn(hObject, eventdata, handles) -% varargout cell array for returning output args (see VARARGOUT); -% hObject handle to figure -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% Get default command line output from handles structure -varargout{1} = handles.output; - - -% =========================================================== -function init(handles) - -rand('state',0); -clear prm; -prm.maxch = 4; -prm.maxlambda = 4; -prm.nch = 2; -prm.nlambda = 2; -prm.extinct = [[0.01 0.02 0.03 0.035]; [0.035 0.015 0.01 0.02]; [0.03 0.02 0.02 0.03]; [0.015 0.03 0.035 0.025]]; % extinction coefficient for both chromophores at both wavelengths -prm.bdim = [64 64]; -prm.meshfile = 'circle25_32.msh'; -prm.qmfile = 'circle25_16x16.qm'; -prm.lnampfile = 'fmod_ellips_16x16_100MHz.fem'; -prm.phasefile = 'farg_ellips_16x16_100MHz.fem'; -prm.meas.src = struct('freq',100,'type','Neumann','prof','Gaussian','width',2); -prm.meas.det = struct('prof','Gaussian','width',2); -prm.linsolver.method = 'Direct'; -prm.linsolver.tol = 1e-10; -prm.solver.method = 'LM'; -prm.solver.tol = 1e-8; -prm.solver.step0 = 100; -prm.regul.method = 'None'; -prm.initprm.mua = struct('reset','HOMOG','val',0.025); -prm.initprm.mus = struct('reset','HOMOG','val',2); -prm.initprm.ref = struct('reset','HOMOG','val',1.4); - -prm.edit_extinct.ch = 1; -prm.edit_extinct.lambda = 1; - -prm.callback.context = handles; -prm.callback.iter = @callback_vis; % iteration callback from recon - -prm.hMesh = toastReadMesh(prm.meshfile); -toastReadQM (prm.hMesh,prm.qmfile); - -prm.hBasis = toastSetBasis(prm.hMesh,prm.bdim); -prm.smask = toastSolutionMask(prm.hBasis); -n = toastMeshNodeCount(prm.hMesh); -load toast_demo1.mat -load toast_demo2.mat -prm.bmua = bmua; clear bmua; -prm.bmus = bmus; clear bmus; -prm.mua = toastMapBasisToMesh(prm.hBasis,prm.bmua); -prm.mus = toastMapBasisToMesh(prm.hBasis,prm.bmus); -prm.ref = ones(n,1)*1.4; - -prm.hTgt = zeros(prm.maxch,1); -prm.hMuaTgt = zeros(prm.maxlambda,1); -setappdata(handles.figure1,'prm',prm); -rolltgt (handles); -updategui (handles); - -set(handles.pushbutton1,'String','Run'); -setappdata(handles.figure1,'isBusy',false); - - -% =========================================================== -function show_C_images (handles) -prm = getappdata(handles.figure1,'prm'); -for i=1:4 - if i <= prm.nch - vis = 'on'; - else - vis = 'off'; - end - eval (['set(handles.text' num2str(i) ',''Visible'',''' vis ''')']); - eval (['set(handles.text' num2str(i+4) ',''Visible'',''' vis ''')']); - eval (['set(handles.text' num2str(i+12) ',''Visible'',''' vis ''')']); - - if i <= prm.nch - eval(['axes(handles.axes' num2str(i) ')']); - h = imagesc(reshape(prm.bC_tgt(i,:), prm.bdim(1), prm.bdim(2)),[0,prm.bCmax]); - prm.hTgt(i) = h; - elseif prm.hTgt(i) ~= 0 - delete(prm.hTgt(i)); - prm.hTgt(i) = 0; - end - eval (['set(handles.axes' num2str(i) ',''Visible'',''off'')']); - eval (['set(handles.axes' num2str(i+4) ',''Visible'',''off'')']); - setappdata(handles.figure1,'prm',prm); -end - - -% =========================================================== -function show_mua_images (handles) -prm = getappdata(handles.figure1,'prm'); -for i=1:prm.nlambda - img(i,:) = zeros(1,prod(prm.bdim)); - for j=1:prm.nch - img(i,:) = img(i,:) + prm.bC_tgt(j,:) * prm.extinct(j,i); - end -end -muamax = max(max(img)); -for i=1:4 - if i <= prm.nlambda - vis = 'on'; - else - vis = 'off'; - end - eval (['set(handles.text' num2str(i+8) ',''Visible'',''' vis ''')']); - if i <= prm.nlambda - eval(['axes(handles.axes' num2str(i+8) ')']); - h = imagesc(reshape(img(i,:), prm.bdim(1), prm.bdim(2)),[0,muamax]); - prm.hMuaTgt(i) = h; - elseif prm.hMuaTgt(i) ~= 0 - delete(prm.hMuaTgt(i)); - prm.hMuaTgt(i) = 0; - end - eval (['set(handles.axes' num2str(i+8) ',''Visible'',''off'')']); - setappdata(handles.figure1,'prm',prm); -end -clear img; - - -% =========================================================== -function showExtinct (handles) -prm = getappdata(handles.figure1,'prm'); -col = ['b' 'r' 'g' 'k']; -axes(handles.axes13); -h = plot(prm.extinct(1,1:prm.nlambda),['-o' col(1)]); -set(h,'ButtonDownFcn','toast_demo7(''axes13_ButtonDownFcn'',gcbo,1,guidata(gcbo))'); -hold on -for i=2:prm.nch - h = plot(prm.extinct(i,1:prm.nlambda),['-o' col(i)]); - set(h,'ButtonDownFcn',['toast_demo7(''axes13_ButtonDownFcn'',gcbo,' num2str(i) ',guidata(gcbo))']); -end -hold off - - -% =========================================================== -function updategui (handles) -prm = getappdata(handles.figure1,'prm'); -set(handles.popupmenu1,'Value',prm.nch); -set(handles.popupmenu2,'Value',prm.nlambda); -set(handles.edit1,'String',num2str(prm.extinct(prm.edit_extinct.ch,prm.edit_extinct.lambda))); -show_C_images(handles); -show_mua_images(handles); -showExtinct(handles); - - -% =========================================================== -function rolltgt (handles) -prm = getappdata(handles.figure1,'prm'); -grid = prm.bdim; -solmask = prm.smask; -nch = 4; % generate targets for max. number of chromophores -blstr2num(get(handles.edit2,'String')) -blobtgt = 5; -for c=1:nch - img = ones(grid); - nblob = 3+round(rand()*(blobtgt-3)); - for b=1:nblob - rad(b) = (0.05+rand()*0.15)*grid(1); - cont = true; - while cont - cont = false; - cnt(b,:) = rand(1,2).*grid; - r = norm(cnt(b,:)-grid/2); - if r+rad(b) >= grid(1)/2, cont=true; end - for bb=1:b-1 - if norm(cnt(b,:)-cnt(bb,:)) < rad(b)+rad(bb), cont=true; end - end - end - mag(b) = rand()*2+1; - end - for j=1:grid(2) - for i=1:grid(1) - p = [i j]; - for b=1:nblob - if norm(p-cnt(b,:)) <= rad(b) - img(i,j) = img(i,j) + mag(b); - end - end - end - end - img = reshape(img,[],1); - bC_tgt(c,:) = zeros(prod(grid),1); - bC_tgt(c,solmask) = img(solmask) * 0.3; -end -prm.bC_tgt = bC_tgt; -prm.bCmin = min(min(bC_tgt(:,solmask))); -prm.bCmax = max(max(bC_tgt(:,solmask))); -setappdata(handles.figure1,'prm',prm); - - -% =========================================================== -% --- Executes on button press in pushbutton1. -function pushbutton1_Callback(hObject, eventdata, handles) -% hObject handle to pushbutton1 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -if getappdata(handles.figure1,'isBusy') == false - prm = getappdata(handles.figure1,'prm'); - setappdata(handles.figure1,'isBusy',true); - set(handles.pushbutton1,'String','Stop (may be delayed)'); - toast_demo7_drv(prm); - setappdata(handles.figure1,'isBusy',false); - set(handles.pushbutton1,'String','Run'); -else - global ITR_TERM - ITR_TERM = true; -end - - -% Display reconstruction results for current iteration -function callback_vis(handles,res) -prm = getappdata(handles.figure1,'prm'); -for i=1:prm.nch - eval(['axes(handles.axes' num2str(i+4) ')']); - h = imagesc(reshape(res.bC(i,:), prm.bdim(1), prm.bdim(2)),[0,prm.bCmax]); - eval (['set(handles.axes' num2str(i+4) ',''Visible'',''off'')']); -end -axes(handles.axes14); -semilogy([0:max(1,length(res.of)-1)],res.of); axis tight -set(handles.axes14,'FontSize',7); -drawnow - - -% --- Executes on selection change in popupmenu1. -function popupmenu1_Callback(hObject, eventdata, handles) -% hObject handle to popupmenu1 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% Hints: contents = get(hObject,'String') returns popupmenu1 contents as cell array -% contents{get(hObject,'Value')} returns selected item from popupmenu1 -prm = getappdata(handles.figure1,'prm'); -prm.nch = get(hObject,'Value'); -setappdata(handles.figure1,'prm',prm); -updategui(handles); - - -% --- Executes during object creation, after setting all properties. -function popupmenu1_CreateFcn(hObject, eventdata, handles) -% hObject handle to popupmenu1 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles empty - handles not created until after all CreateFcns called - -% Hint: popupmenu controls usually have a white background on Windows. -% See ISPC and COMPUTER. -if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) - set(hObject,'BackgroundColor','white'); -end - - - - -% --- Executes on selection change in popupmenu2. -function popupmenu2_Callback(hObject, eventdata, handles) -% hObject handle to popupmenu2 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% Hints: contents = get(hObject,'String') returns popupmenu2 contents as cell array -% contents{get(hObject,'Value')} returns selected item from popupmenu2 -prm = getappdata(handles.figure1,'prm'); -prm.nlambda = get(hObject,'Value'); -setappdata(handles.figure1,'prm',prm); -updategui(handles); - - -% --- Executes during object creation, after setting all properties. -function popupmenu2_CreateFcn(hObject, eventdata, handles) -% hObject handle to popupmenu2 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles empty - handles not created until after all CreateFcns called - -% Hint: popupmenu controls usually have a white background on Windows. -% See ISPC and COMPUTER. -if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) - set(hObject,'BackgroundColor','white'); -end - - - - -% --- Executes on button press in pushbutton2. -function pushbutton2_Callback(hObject, eventdata, handles) -% hObject handle to pushbutton2 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) -rolltgt (handles); -updategui(handles); - - -function edit1_Callback(hObject, eventdata, handles) -% hObject handle to edit1 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% Hints: get(hObject,'String') returns contents of edit1 as text -% str2double(get(hObject,'String')) returns contents of edit1 as a double -prm = getappdata(handles.figure1,'prm'); -e = str2num(get(hObject,'String')); -prm.extinct(prm.edit_extinct.ch,prm.edit_extinct.lambda) = e; -setappdata(handles.figure1,'prm',prm); -updategui(handles); - - -% --- Executes during object creation, after setting all properties. -function edit1_CreateFcn(hObject, eventdata, handles) -% hObject handle to edit1 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles empty - handles not created until after all CreateFcns called - -% Hint: edit controls usually have a white background on Windows. -% See ISPC and COMPUTER. -if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) - set(hObject,'BackgroundColor','white'); -end - - -function axes13_ButtonDownFcn(hObject, eventdata, handles) -prm = getappdata(handles.figure1,'prm'); -mouse = get(gca,'currentpoint'); -x = mouse(1,1); -ch = eventdata; -lambda = round(x); -prm.edit_extinct.ch = ch; -prm.edit_extinct.lambda = lambda; -set(handles.text34,'String',sprintf('Chromophore %d, wavelength %0.0f',ch,lambda)); -set(handles.edit1,'String',num2str(prm.extinct(ch,lambda))); -setappdata(handles.figure1,'prm',prm); - - - -function edit2_Callback(hObject, eventdata, handles) -% hObject handle to edit2 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% Hints: get(hObject,'String') returns contents of edit2 as text -% str2double(get(hObject,'String')) returns contents of edit2 as a double - - -% --- Executes during object creation, after setting all properties. -function edit2_CreateFcn(hObject, eventdata, handles) -% hObject handle to edit2 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles empty - handles not created until after all CreateFcns called - -% Hint: edit controls usually have a white background on Windows. -% See ISPC and COMPUTER. -if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) - set(hObject,'BackgroundColor','white'); -end - - diff --git a/script/matlab/demos.xml b/script/matlab/docs/demos.xml similarity index 100% rename from script/matlab/demos.xml rename to script/matlab/docs/demos.xml diff --git a/script/matlab/html/about.html b/script/matlab/docs/html/about.html similarity index 100% rename from script/matlab/html/about.html rename to script/matlab/docs/html/about.html diff --git a/script/matlab/html/background/about_toast.html b/script/matlab/docs/html/background/about_toast.html similarity index 100% rename from script/matlab/html/background/about_toast.html rename to script/matlab/docs/html/background/about_toast.html diff --git a/script/matlab/html/background/about_toolbox.html b/script/matlab/docs/html/background/about_toolbox.html similarity index 100% rename from script/matlab/html/background/about_toolbox.html rename to script/matlab/docs/html/background/about_toolbox.html diff --git a/script/matlab/html/background/background.html b/script/matlab/docs/html/background/background.html similarity index 100% rename from script/matlab/html/background/background.html rename to script/matlab/docs/html/background/background.html diff --git a/script/matlab/html/background/ctproj.gif b/script/matlab/docs/html/background/ctproj.gif similarity index 100% rename from script/matlab/html/background/ctproj.gif rename to script/matlab/docs/html/background/ctproj.gif diff --git a/script/matlab/html/background/dot.html b/script/matlab/docs/html/background/dot.html similarity index 100% rename from script/matlab/html/background/dot.html rename to script/matlab/docs/html/background/dot.html diff --git a/script/matlab/html/background/efield.gif b/script/matlab/docs/html/background/efield.gif similarity index 100% rename from script/matlab/html/background/efield.gif rename to script/matlab/docs/html/background/efield.gif diff --git a/script/matlab/html/background/pmdf_blob.gif b/script/matlab/docs/html/background/pmdf_blob.gif similarity index 100% rename from script/matlab/html/background/pmdf_blob.gif rename to script/matlab/docs/html/background/pmdf_blob.gif diff --git a/script/matlab/html/background/pmdf_homog.gif b/script/matlab/docs/html/background/pmdf_homog.gif similarity index 100% rename from script/matlab/html/background/pmdf_homog.gif rename to script/matlab/docs/html/background/pmdf_homog.gif diff --git a/script/matlab/html/banner.gif b/script/matlab/docs/html/banner.gif similarity index 100% rename from script/matlab/html/banner.gif rename to script/matlab/docs/html/banner.gif diff --git a/script/matlab/html/basis.html b/script/matlab/docs/html/basis.html similarity index 100% rename from script/matlab/html/basis.html rename to script/matlab/docs/html/basis.html diff --git a/script/matlab/html/basis_b.gif b/script/matlab/docs/html/basis_b.gif similarity index 100% rename from script/matlab/html/basis_b.gif rename to script/matlab/docs/html/basis_b.gif diff --git a/script/matlab/html/basis_g.gif b/script/matlab/docs/html/basis_g.gif similarity index 100% rename from script/matlab/html/basis_g.gif rename to script/matlab/docs/html/basis_g.gif diff --git a/script/matlab/html/basis_h.gif b/script/matlab/docs/html/basis_h.gif similarity index 100% rename from script/matlab/html/basis_h.gif rename to script/matlab/docs/html/basis_h.gif diff --git a/script/matlab/html/basis_s.gif b/script/matlab/docs/html/basis_s.gif similarity index 100% rename from script/matlab/html/basis_s.gif rename to script/matlab/docs/html/basis_s.gif diff --git a/script/matlab/html/definitions.html b/script/matlab/docs/html/definitions.html similarity index 100% rename from script/matlab/html/definitions.html rename to script/matlab/docs/html/definitions.html diff --git a/script/matlab/html/demo.css b/script/matlab/docs/html/demo.css similarity index 100% rename from script/matlab/html/demo.css rename to script/matlab/docs/html/demo.css diff --git a/script/matlab/html/helptoc.xml b/script/matlab/docs/html/helptoc.xml similarity index 100% rename from script/matlab/html/helptoc.xml rename to script/matlab/docs/html/helptoc.xml diff --git a/script/matlab/html/images/bkg_text.jpg b/script/matlab/docs/html/images/bkg_text.jpg similarity index 100% rename from script/matlab/html/images/bkg_text.jpg rename to script/matlab/docs/html/images/bkg_text.jpg diff --git a/script/matlab/html/images/menu.png b/script/matlab/docs/html/images/menu.png similarity index 100% rename from script/matlab/html/images/menu.png rename to script/matlab/docs/html/images/menu.png diff --git a/script/matlab/html/images/toast_logo_small.jpg b/script/matlab/docs/html/images/toast_logo_small.jpg similarity index 100% rename from script/matlab/html/images/toast_logo_small.jpg rename to script/matlab/docs/html/images/toast_logo_small.jpg diff --git a/script/matlab/html/images/toastpp_label.png b/script/matlab/docs/html/images/toastpp_label.png similarity index 100% rename from script/matlab/html/images/toastpp_label.png rename to script/matlab/docs/html/images/toastpp_label.png diff --git a/script/matlab/html/prm.html b/script/matlab/docs/html/prm.html similarity index 100% rename from script/matlab/html/prm.html rename to script/matlab/docs/html/prm.html diff --git a/script/matlab/html/toast.css b/script/matlab/docs/html/toast.css similarity index 100% rename from script/matlab/html/toast.css rename to script/matlab/docs/html/toast.css diff --git a/script/matlab/html/toast.html b/script/matlab/docs/html/toast.html similarity index 100% rename from script/matlab/html/toast.html rename to script/matlab/docs/html/toast.html diff --git a/script/matlab/html/toastDataLinkList.html b/script/matlab/docs/html/toastDataLinkList.html similarity index 100% rename from script/matlab/html/toastDataLinkList.html rename to script/matlab/docs/html/toastDataLinkList.html diff --git a/script/matlab/html/toastElmat.html b/script/matlab/docs/html/toastElmat.html similarity index 100% rename from script/matlab/html/toastElmat.html rename to script/matlab/docs/html/toastElmat.html diff --git a/script/matlab/html/toastFields.html b/script/matlab/docs/html/toastFields.html similarity index 100% rename from script/matlab/html/toastFields.html rename to script/matlab/docs/html/toastFields.html diff --git a/script/matlab/html/toastFwd.html b/script/matlab/docs/html/toastFwd.html similarity index 100% rename from script/matlab/html/toastFwd.html rename to script/matlab/docs/html/toastFwd.html diff --git a/script/matlab/html/toastFwdCW.html b/script/matlab/docs/html/toastFwdCW.html similarity index 100% rename from script/matlab/html/toastFwdCW.html rename to script/matlab/docs/html/toastFwdCW.html diff --git a/script/matlab/html/toastGradient.html b/script/matlab/docs/html/toastGradient.html similarity index 100% rename from script/matlab/html/toastGradient.html rename to script/matlab/docs/html/toastGradient.html diff --git a/script/matlab/html/toastImageGradient.html b/script/matlab/docs/html/toastImageGradient.html similarity index 100% rename from script/matlab/html/toastImageGradient.html rename to script/matlab/docs/html/toastImageGradient.html diff --git a/script/matlab/html/toastJacobian.html b/script/matlab/docs/html/toastJacobian.html similarity index 100% rename from script/matlab/html/toastJacobian.html rename to script/matlab/docs/html/toastJacobian.html diff --git a/script/matlab/html/toastKrylov.html b/script/matlab/docs/html/toastKrylov.html similarity index 100% rename from script/matlab/html/toastKrylov.html rename to script/matlab/docs/html/toastKrylov.html diff --git a/script/matlab/html/toastLabelRegion.html b/script/matlab/docs/html/toastLabelRegion.html similarity index 100% rename from script/matlab/html/toastLabelRegion.html rename to script/matlab/docs/html/toastLabelRegion.html diff --git a/script/matlab/html/toastLineSearch.html b/script/matlab/docs/html/toastLineSearch.html similarity index 100% rename from script/matlab/html/toastLineSearch.html rename to script/matlab/docs/html/toastLineSearch.html diff --git a/script/matlab/html/toastMakeMesh.html b/script/matlab/docs/html/toastMakeMesh.html similarity index 100% rename from script/matlab/html/toastMakeMesh.html rename to script/matlab/docs/html/toastMakeMesh.html diff --git a/script/matlab/html/toastMarkMeshBoundary.html b/script/matlab/docs/html/toastMarkMeshBoundary.html similarity index 100% rename from script/matlab/html/toastMarkMeshBoundary.html rename to script/matlab/docs/html/toastMarkMeshBoundary.html diff --git a/script/matlab/html/toastMassmat.html b/script/matlab/docs/html/toastMassmat.html similarity index 100% rename from script/matlab/html/toastMassmat.html rename to script/matlab/docs/html/toastMassmat.html diff --git a/script/matlab/html/toastMeshToBasisMatrix.html b/script/matlab/docs/html/toastMeshToBasisMatrix.html similarity index 100% rename from script/matlab/html/toastMeshToBasisMatrix.html rename to script/matlab/docs/html/toastMeshToBasisMatrix.html diff --git a/script/matlab/html/toastReadParam.html b/script/matlab/docs/html/toastReadParam.html similarity index 100% rename from script/matlab/html/toastReadParam.html rename to script/matlab/docs/html/toastReadParam.html diff --git a/script/matlab/html/toastRecon.html b/script/matlab/docs/html/toastRecon.html similarity index 100% rename from script/matlab/html/toastRecon.html rename to script/matlab/docs/html/toastRecon.html diff --git a/script/matlab/html/toastSysmat.html b/script/matlab/docs/html/toastSysmat.html similarity index 100% rename from script/matlab/html/toastSysmat.html rename to script/matlab/docs/html/toastSysmat.html diff --git a/script/matlab/html/toastSysmatComponent.html b/script/matlab/docs/html/toastSysmatComponent.html similarity index 100% rename from script/matlab/html/toastSysmatComponent.html rename to script/matlab/docs/html/toastSysmatComponent.html diff --git a/script/matlab/html/toast_demo1.html b/script/matlab/docs/html/toast_demo1.html similarity index 100% rename from script/matlab/html/toast_demo1.html rename to script/matlab/docs/html/toast_demo1.html diff --git a/script/matlab/html/toast_demo1.png b/script/matlab/docs/html/toast_demo1.png similarity index 100% rename from script/matlab/html/toast_demo1.png rename to script/matlab/docs/html/toast_demo1.png diff --git a/script/matlab/html/toast_demo1a.html b/script/matlab/docs/html/toast_demo1a.html similarity index 100% rename from script/matlab/html/toast_demo1a.html rename to script/matlab/docs/html/toast_demo1a.html diff --git a/script/matlab/html/toast_demo1a.png b/script/matlab/docs/html/toast_demo1a.png similarity index 100% rename from script/matlab/html/toast_demo1a.png rename to script/matlab/docs/html/toast_demo1a.png diff --git a/script/matlab/html/toast_demo2.html b/script/matlab/docs/html/toast_demo2.html similarity index 100% rename from script/matlab/html/toast_demo2.html rename to script/matlab/docs/html/toast_demo2.html diff --git a/script/matlab/html/toast_demo2.png b/script/matlab/docs/html/toast_demo2.png similarity index 100% rename from script/matlab/html/toast_demo2.png rename to script/matlab/docs/html/toast_demo2.png diff --git a/script/matlab/html/toast_demo3.html b/script/matlab/docs/html/toast_demo3.html similarity index 100% rename from script/matlab/html/toast_demo3.html rename to script/matlab/docs/html/toast_demo3.html diff --git a/script/matlab/html/toast_demo3.png b/script/matlab/docs/html/toast_demo3.png similarity index 100% rename from script/matlab/html/toast_demo3.png rename to script/matlab/docs/html/toast_demo3.png diff --git a/script/matlab/html/toast_demo4.html b/script/matlab/docs/html/toast_demo4.html similarity index 100% rename from script/matlab/html/toast_demo4.html rename to script/matlab/docs/html/toast_demo4.html diff --git a/script/matlab/html/toast_demo4.png b/script/matlab/docs/html/toast_demo4.png similarity index 100% rename from script/matlab/html/toast_demo4.png rename to script/matlab/docs/html/toast_demo4.png diff --git a/script/matlab/html/toast_demo5.html b/script/matlab/docs/html/toast_demo5.html similarity index 100% rename from script/matlab/html/toast_demo5.html rename to script/matlab/docs/html/toast_demo5.html diff --git a/script/matlab/html/toast_demo5.png b/script/matlab/docs/html/toast_demo5.png similarity index 100% rename from script/matlab/html/toast_demo5.png rename to script/matlab/docs/html/toast_demo5.png diff --git a/script/matlab/html/toast_demo6.html b/script/matlab/docs/html/toast_demo6.html similarity index 100% rename from script/matlab/html/toast_demo6.html rename to script/matlab/docs/html/toast_demo6.html diff --git a/script/matlab/html/toast_demo6.png b/script/matlab/docs/html/toast_demo6.png similarity index 100% rename from script/matlab/html/toast_demo6.png rename to script/matlab/docs/html/toast_demo6.png diff --git a/script/matlab/html/toast_demo7.html b/script/matlab/docs/html/toast_demo7.html similarity index 100% rename from script/matlab/html/toast_demo7.html rename to script/matlab/docs/html/toast_demo7.html diff --git a/script/matlab/html/toast_demo7.png b/script/matlab/docs/html/toast_demo7.png similarity index 100% rename from script/matlab/html/toast_demo7.png rename to script/matlab/docs/html/toast_demo7.png diff --git a/script/matlab/html/toast_gui.html b/script/matlab/docs/html/toast_gui.html similarity index 100% rename from script/matlab/html/toast_gui.html rename to script/matlab/docs/html/toast_gui.html diff --git a/script/matlab/html/toast_logo_100.jpg b/script/matlab/docs/html/toast_logo_100.jpg similarity index 100% rename from script/matlab/html/toast_logo_100.jpg rename to script/matlab/docs/html/toast_logo_100.jpg diff --git a/script/matlab/html/toast_logo_150.jpg b/script/matlab/docs/html/toast_logo_150.jpg similarity index 100% rename from script/matlab/html/toast_logo_150.jpg rename to script/matlab/docs/html/toast_logo_150.jpg diff --git a/script/matlab/html/tutorials/back.gif b/script/matlab/docs/html/tutorials/back.gif similarity index 100% rename from script/matlab/html/tutorials/back.gif rename to script/matlab/docs/html/tutorials/back.gif diff --git a/script/matlab/html/tutorials/circle25_32.msh b/script/matlab/docs/html/tutorials/circle25_32.msh similarity index 100% rename from script/matlab/html/tutorials/circle25_32.msh rename to script/matlab/docs/html/tutorials/circle25_32.msh diff --git a/script/matlab/html/tutorials/circle25_32x32.qm b/script/matlab/docs/html/tutorials/circle25_32x32.qm similarity index 100% rename from script/matlab/html/tutorials/circle25_32x32.qm rename to script/matlab/docs/html/tutorials/circle25_32x32.qm diff --git a/script/matlab/html/tutorials/circle25_64.msh b/script/matlab/docs/html/tutorials/circle25_64.msh similarity index 100% rename from script/matlab/html/tutorials/circle25_64.msh rename to script/matlab/docs/html/tutorials/circle25_64.msh diff --git a/script/matlab/html/tutorials/demo1.gif b/script/matlab/docs/html/tutorials/demo1.gif similarity index 100% rename from script/matlab/html/tutorials/demo1.gif rename to script/matlab/docs/html/tutorials/demo1.gif diff --git a/script/matlab/html/tutorials/demo1.png b/script/matlab/docs/html/tutorials/demo1.png similarity index 100% rename from script/matlab/html/tutorials/demo1.png rename to script/matlab/docs/html/tutorials/demo1.png diff --git a/script/matlab/html/tutorials/demo10.gif b/script/matlab/docs/html/tutorials/demo10.gif similarity index 100% rename from script/matlab/html/tutorials/demo10.gif rename to script/matlab/docs/html/tutorials/demo10.gif diff --git a/script/matlab/html/tutorials/demo2.gif b/script/matlab/docs/html/tutorials/demo2.gif similarity index 100% rename from script/matlab/html/tutorials/demo2.gif rename to script/matlab/docs/html/tutorials/demo2.gif diff --git a/script/matlab/html/tutorials/demo3.gif b/script/matlab/docs/html/tutorials/demo3.gif similarity index 100% rename from script/matlab/html/tutorials/demo3.gif rename to script/matlab/docs/html/tutorials/demo3.gif diff --git a/script/matlab/html/tutorials/demo4.gif b/script/matlab/docs/html/tutorials/demo4.gif similarity index 100% rename from script/matlab/html/tutorials/demo4.gif rename to script/matlab/docs/html/tutorials/demo4.gif diff --git a/script/matlab/html/tutorials/demo5.gif b/script/matlab/docs/html/tutorials/demo5.gif similarity index 100% rename from script/matlab/html/tutorials/demo5.gif rename to script/matlab/docs/html/tutorials/demo5.gif diff --git a/script/matlab/html/tutorials/demo6.gif b/script/matlab/docs/html/tutorials/demo6.gif similarity index 100% rename from script/matlab/html/tutorials/demo6.gif rename to script/matlab/docs/html/tutorials/demo6.gif diff --git a/script/matlab/html/tutorials/demo7.gif b/script/matlab/docs/html/tutorials/demo7.gif similarity index 100% rename from script/matlab/html/tutorials/demo7.gif rename to script/matlab/docs/html/tutorials/demo7.gif diff --git a/script/matlab/html/tutorials/demo8.gif b/script/matlab/docs/html/tutorials/demo8.gif similarity index 100% rename from script/matlab/html/tutorials/demo8.gif rename to script/matlab/docs/html/tutorials/demo8.gif diff --git a/script/matlab/html/tutorials/demo9.gif b/script/matlab/docs/html/tutorials/demo9.gif similarity index 100% rename from script/matlab/html/tutorials/demo9.gif rename to script/matlab/docs/html/tutorials/demo9.gif diff --git a/script/matlab/html/tutorials/demo_fluorescence/demo_matlab_fluo1.html b/script/matlab/docs/html/tutorials/demo_fluorescence/demo_matlab_fluo1.html similarity index 100% rename from script/matlab/html/tutorials/demo_fluorescence/demo_matlab_fluo1.html rename to script/matlab/docs/html/tutorials/demo_fluorescence/demo_matlab_fluo1.html diff --git a/script/matlab/html/tutorials/demo_fluorescence/demo_matlab_fluo1.m b/script/matlab/docs/html/tutorials/demo_fluorescence/demo_matlab_fluo1.m similarity index 100% rename from script/matlab/html/tutorials/demo_fluorescence/demo_matlab_fluo1.m rename to script/matlab/docs/html/tutorials/demo_fluorescence/demo_matlab_fluo1.m diff --git a/script/matlab/html/tutorials/demo_fluorescence/img1.png b/script/matlab/docs/html/tutorials/demo_fluorescence/img1.png similarity index 100% rename from script/matlab/html/tutorials/demo_fluorescence/img1.png rename to script/matlab/docs/html/tutorials/demo_fluorescence/img1.png diff --git a/script/matlab/html/tutorials/demo_fluorescence/img2.png b/script/matlab/docs/html/tutorials/demo_fluorescence/img2.png similarity index 100% rename from script/matlab/html/tutorials/demo_fluorescence/img2.png rename to script/matlab/docs/html/tutorials/demo_fluorescence/img2.png diff --git a/script/matlab/html/tutorials/demo_fluorescence/img3.png b/script/matlab/docs/html/tutorials/demo_fluorescence/img3.png similarity index 100% rename from script/matlab/html/tutorials/demo_fluorescence/img3.png rename to script/matlab/docs/html/tutorials/demo_fluorescence/img3.png diff --git a/script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1.html b/script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1.html similarity index 100% rename from script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1.html rename to script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1.html diff --git a/script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1.m b/script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1.m similarity index 100% rename from script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1.m rename to script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1.m diff --git a/script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_1.png b/script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_1.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_1.png rename to script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_1.png diff --git a/script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_2.png b/script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_2.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_2.png rename to script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_2.png diff --git a/script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_3.png b/script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_3.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_3.png rename to script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_3.png diff --git a/script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_4.png b/script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_4.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_4.png rename to script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_4.png diff --git a/script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_5.png b/script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_5.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_5.png rename to script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_5.png diff --git a/script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_eq1.png b/script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_eq1.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_eq1.png rename to script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_eq1.png diff --git a/script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_eq2.png b/script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_eq2.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd1/demo_matlab_fwd1_eq2.png rename to script/matlab/docs/html/tutorials/demo_fwd1/demo_matlab_fwd1_eq2.png diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2.html b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2.html similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2.html rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2.html diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2.m b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2.m similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2.m rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2.m diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_3.png b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_3.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_3.png rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_3.png diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_4.png b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_4.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_4.png rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_4.png diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_5.png b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_5.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_5.png rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_5.png diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_6.png b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_6.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_6.png rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_6.png diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_7.png b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_7.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_7.png rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_7.png diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_8.png b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_8.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_8.png rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_8.png diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_9.png b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_9.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_9.png rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_9.png diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_mua.png b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_mua.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_mua.png rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_mua.png diff --git a/script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_mus.png b/script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_mus.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd2/demo_matlab_fwd2_mus.png rename to script/matlab/docs/html/tutorials/demo_fwd2/demo_matlab_fwd2_mus.png diff --git a/script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3.html b/script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3.html similarity index 100% rename from script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3.html rename to script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3.html diff --git a/script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3.m b/script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3.m similarity index 100% rename from script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3.m rename to script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3.m diff --git a/script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3_1.png b/script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3_1.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3_1.png rename to script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3_1.png diff --git a/script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3_2.png b/script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3_2.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3_2.png rename to script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3_2.png diff --git a/script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3_eq1.png b/script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3_eq1.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3_eq1.png rename to script/matlab/docs/html/tutorials/demo_fwd3/demo_matlab_fwd3_eq1.png diff --git a/script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4.html b/script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4.html similarity index 100% rename from script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4.html rename to script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4.html diff --git a/script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4.m b/script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4.m similarity index 100% rename from script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4.m rename to script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4.m diff --git a/script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4_1.png b/script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4_1.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4_1.png rename to script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4_1.png diff --git a/script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq1.png b/script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq1.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq1.png rename to script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq1.png diff --git a/script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq2.png b/script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq2.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq2.png rename to script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq2.png diff --git a/script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq3.png b/script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq3.png similarity index 100% rename from script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq3.png rename to script/matlab/docs/html/tutorials/demo_fwd4/demo_matlab_fwd4_eq3.png diff --git a/script/matlab/html/tutorials/demo_matlab_fwd5.m b/script/matlab/docs/html/tutorials/demo_matlab_fwd5.m similarity index 100% rename from script/matlab/html/tutorials/demo_matlab_fwd5.m rename to script/matlab/docs/html/tutorials/demo_matlab_fwd5.m diff --git a/script/matlab/html/tutorials/demo_matlab_rec2.m b/script/matlab/docs/html/tutorials/demo_matlab_rec2.m similarity index 99% rename from script/matlab/html/tutorials/demo_matlab_rec2.m rename to script/matlab/docs/html/tutorials/demo_matlab_rec2.m index 24efbb48..8f969698 100755 --- a/script/matlab/html/tutorials/demo_matlab_rec2.m +++ b/script/matlab/docs/html/tutorials/demo_matlab_rec2.m @@ -189,8 +189,8 @@ x = exp(logx); % Map parameters back to mesh - scmua = x(1:size(x)/2); - sckap = x(size(x)/2+1:size(x)); + scmua = x(1:size(x,1)/2); + sckap = x(size(x,1)/2+1:size(x,1)); smua = scmua/cm; skap = sckap/cm; smus = 1./(3*skap) - smua; diff --git a/script/matlab/html/tutorials/demo_meshgen1/demo_meshgen1.html b/script/matlab/docs/html/tutorials/demo_meshgen1/demo_meshgen1.html similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/demo_meshgen1.html rename to script/matlab/docs/html/tutorials/demo_meshgen1/demo_meshgen1.html diff --git a/script/matlab/html/tutorials/demo_meshgen1/gmsh1.png b/script/matlab/docs/html/tutorials/demo_meshgen1/gmsh1.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/gmsh1.png rename to script/matlab/docs/html/tutorials/demo_meshgen1/gmsh1.png diff --git a/script/matlab/html/tutorials/demo_meshgen1/gmsh2.png b/script/matlab/docs/html/tutorials/demo_meshgen1/gmsh2.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/gmsh2.png rename to script/matlab/docs/html/tutorials/demo_meshgen1/gmsh2.png diff --git a/script/matlab/html/tutorials/demo_meshgen1/gmsh3.png b/script/matlab/docs/html/tutorials/demo_meshgen1/gmsh3.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/gmsh3.png rename to script/matlab/docs/html/tutorials/demo_meshgen1/gmsh3.png diff --git a/script/matlab/html/tutorials/demo_meshgen1/gmsh4.png b/script/matlab/docs/html/tutorials/demo_meshgen1/gmsh4.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/gmsh4.png rename to script/matlab/docs/html/tutorials/demo_meshgen1/gmsh4.png diff --git a/script/matlab/html/tutorials/demo_meshgen1/gmsh5.png b/script/matlab/docs/html/tutorials/demo_meshgen1/gmsh5.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/gmsh5.png rename to script/matlab/docs/html/tutorials/demo_meshgen1/gmsh5.png diff --git a/script/matlab/html/tutorials/demo_meshgen1/gmsh6.png b/script/matlab/docs/html/tutorials/demo_meshgen1/gmsh6.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/gmsh6.png rename to script/matlab/docs/html/tutorials/demo_meshgen1/gmsh6.png diff --git a/script/matlab/html/tutorials/demo_meshgen1/gmsh7.png b/script/matlab/docs/html/tutorials/demo_meshgen1/gmsh7.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/gmsh7.png rename to script/matlab/docs/html/tutorials/demo_meshgen1/gmsh7.png diff --git a/script/matlab/html/tutorials/demo_meshgen1/gmsh8.png b/script/matlab/docs/html/tutorials/demo_meshgen1/gmsh8.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/gmsh8.png rename to script/matlab/docs/html/tutorials/demo_meshgen1/gmsh8.png diff --git a/script/matlab/html/tutorials/demo_meshgen1/toast_mesh.png b/script/matlab/docs/html/tutorials/demo_meshgen1/toast_mesh.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen1/toast_mesh.png rename to script/matlab/docs/html/tutorials/demo_meshgen1/toast_mesh.png diff --git a/script/matlab/html/tutorials/demo_meshgen2/demo_meshgen2.html b/script/matlab/docs/html/tutorials/demo_meshgen2/demo_meshgen2.html similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen2/demo_meshgen2.html rename to script/matlab/docs/html/tutorials/demo_meshgen2/demo_meshgen2.html diff --git a/script/matlab/html/tutorials/demo_meshgen2/gmsh1.png b/script/matlab/docs/html/tutorials/demo_meshgen2/gmsh1.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen2/gmsh1.png rename to script/matlab/docs/html/tutorials/demo_meshgen2/gmsh1.png diff --git a/script/matlab/html/tutorials/demo_meshgen2/gmsh2.png b/script/matlab/docs/html/tutorials/demo_meshgen2/gmsh2.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen2/gmsh2.png rename to script/matlab/docs/html/tutorials/demo_meshgen2/gmsh2.png diff --git a/script/matlab/html/tutorials/demo_meshgen2/gmsh3.png b/script/matlab/docs/html/tutorials/demo_meshgen2/gmsh3.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen2/gmsh3.png rename to script/matlab/docs/html/tutorials/demo_meshgen2/gmsh3.png diff --git a/script/matlab/html/tutorials/demo_meshgen2/toast_region.png b/script/matlab/docs/html/tutorials/demo_meshgen2/toast_region.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen2/toast_region.png rename to script/matlab/docs/html/tutorials/demo_meshgen2/toast_region.png diff --git a/script/matlab/html/tutorials/demo_meshgen3/demo_meshgen3.html b/script/matlab/docs/html/tutorials/demo_meshgen3/demo_meshgen3.html similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen3/demo_meshgen3.html rename to script/matlab/docs/html/tutorials/demo_meshgen3/demo_meshgen3.html diff --git a/script/matlab/html/tutorials/demo_meshgen3/mesh1.png b/script/matlab/docs/html/tutorials/demo_meshgen3/mesh1.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen3/mesh1.png rename to script/matlab/docs/html/tutorials/demo_meshgen3/mesh1.png diff --git a/script/matlab/html/tutorials/demo_meshgen3/mesh2.png b/script/matlab/docs/html/tutorials/demo_meshgen3/mesh2.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen3/mesh2.png rename to script/matlab/docs/html/tutorials/demo_meshgen3/mesh2.png diff --git a/script/matlab/html/tutorials/demo_meshgen3/mesh3.png b/script/matlab/docs/html/tutorials/demo_meshgen3/mesh3.png similarity index 100% rename from script/matlab/html/tutorials/demo_meshgen3/mesh3.png rename to script/matlab/docs/html/tutorials/demo_meshgen3/mesh3.png diff --git a/script/matlab/html/tutorials/demo_nonunique/circle_blob.msh b/script/matlab/docs/html/tutorials/demo_nonunique/circle_blob.msh similarity index 100% rename from script/matlab/html/tutorials/demo_nonunique/circle_blob.msh rename to script/matlab/docs/html/tutorials/demo_nonunique/circle_blob.msh diff --git a/script/matlab/html/tutorials/demo_nonunique/demo_nonunique.html b/script/matlab/docs/html/tutorials/demo_nonunique/demo_nonunique.html similarity index 100% rename from script/matlab/html/tutorials/demo_nonunique/demo_nonunique.html rename to script/matlab/docs/html/tutorials/demo_nonunique/demo_nonunique.html diff --git a/script/matlab/html/tutorials/demo_nonunique/fig1a.jpg b/script/matlab/docs/html/tutorials/demo_nonunique/fig1a.jpg similarity index 100% rename from script/matlab/html/tutorials/demo_nonunique/fig1a.jpg rename to script/matlab/docs/html/tutorials/demo_nonunique/fig1a.jpg diff --git a/script/matlab/html/tutorials/demo_nonunique/fig1b.jpg b/script/matlab/docs/html/tutorials/demo_nonunique/fig1b.jpg similarity index 100% rename from script/matlab/html/tutorials/demo_nonunique/fig1b.jpg rename to script/matlab/docs/html/tutorials/demo_nonunique/fig1b.jpg diff --git a/script/matlab/html/tutorials/demo_nonunique/fig2.jpg b/script/matlab/docs/html/tutorials/demo_nonunique/fig2.jpg similarity index 100% rename from script/matlab/html/tutorials/demo_nonunique/fig2.jpg rename to script/matlab/docs/html/tutorials/demo_nonunique/fig2.jpg diff --git a/script/matlab/html/tutorials/demo_nonunique/fig3.jpg b/script/matlab/docs/html/tutorials/demo_nonunique/fig3.jpg similarity index 100% rename from script/matlab/html/tutorials/demo_nonunique/fig3.jpg rename to script/matlab/docs/html/tutorials/demo_nonunique/fig3.jpg diff --git a/script/matlab/html/tutorials/demo_nonunique/nonuniqueness.m b/script/matlab/docs/html/tutorials/demo_nonunique/nonuniqueness.m similarity index 100% rename from script/matlab/html/tutorials/demo_nonunique/nonuniqueness.m rename to script/matlab/docs/html/tutorials/demo_nonunique/nonuniqueness.m diff --git a/script/matlab/html/tutorials/demo_pmdf1/demo_matlab_pmdf1.html b/script/matlab/docs/html/tutorials/demo_pmdf1/demo_matlab_pmdf1.html similarity index 100% rename from script/matlab/html/tutorials/demo_pmdf1/demo_matlab_pmdf1.html rename to script/matlab/docs/html/tutorials/demo_pmdf1/demo_matlab_pmdf1.html diff --git a/script/matlab/html/tutorials/demo_rec1/demo_matlab_rec1.html b/script/matlab/docs/html/tutorials/demo_rec1/demo_matlab_rec1.html similarity index 100% rename from script/matlab/html/tutorials/demo_rec1/demo_matlab_rec1.html rename to script/matlab/docs/html/tutorials/demo_rec1/demo_matlab_rec1.html diff --git a/script/matlab/html/tutorials/demo_rec1/demo_matlab_rec1.m b/script/matlab/docs/html/tutorials/demo_rec1/demo_matlab_rec1.m similarity index 100% rename from script/matlab/html/tutorials/demo_rec1/demo_matlab_rec1.m rename to script/matlab/docs/html/tutorials/demo_rec1/demo_matlab_rec1.m diff --git a/script/matlab/html/tutorials/demo_rec1/demo_matlab_rec1_1.png b/script/matlab/docs/html/tutorials/demo_rec1/demo_matlab_rec1_1.png similarity index 100% rename from script/matlab/html/tutorials/demo_rec1/demo_matlab_rec1_1.png rename to script/matlab/docs/html/tutorials/demo_rec1/demo_matlab_rec1_1.png diff --git a/script/matlab/html/tutorials/demos_matlab.html b/script/matlab/docs/html/tutorials/demos_matlab.html similarity index 100% rename from script/matlab/html/tutorials/demos_matlab.html rename to script/matlab/docs/html/tutorials/demos_matlab.html diff --git a/script/matlab/html/tutorials/images/bluearrow.gif b/script/matlab/docs/html/tutorials/images/bluearrow.gif similarity index 100% rename from script/matlab/html/tutorials/images/bluearrow.gif rename to script/matlab/docs/html/tutorials/images/bluearrow.gif diff --git a/script/matlab/html/tutorials/images/toast_label.jpg b/script/matlab/docs/html/tutorials/images/toast_label.jpg similarity index 100% rename from script/matlab/html/tutorials/images/toast_label.jpg rename to script/matlab/docs/html/tutorials/images/toast_label.jpg diff --git a/script/matlab/html/tutorials/images/ucl.gif b/script/matlab/docs/html/tutorials/images/ucl.gif similarity index 100% rename from script/matlab/html/tutorials/images/ucl.gif rename to script/matlab/docs/html/tutorials/images/ucl.gif diff --git a/script/matlab/html/tutorials/quickstart/quickstart.html b/script/matlab/docs/html/tutorials/quickstart/quickstart.html similarity index 100% rename from script/matlab/html/tutorials/quickstart/quickstart.html rename to script/matlab/docs/html/tutorials/quickstart/quickstart.html diff --git a/script/matlab/html/tutorials/quickstart/quickstart1.jpg b/script/matlab/docs/html/tutorials/quickstart/quickstart1.jpg similarity index 100% rename from script/matlab/html/tutorials/quickstart/quickstart1.jpg rename to script/matlab/docs/html/tutorials/quickstart/quickstart1.jpg diff --git a/script/matlab/info.xml b/script/matlab/docs/info.xml similarity index 95% rename from script/matlab/info.xml rename to script/matlab/docs/info.xml index d6909517..159e02d4 100755 --- a/script/matlab/info.xml +++ b/script/matlab/docs/info.xml @@ -9,7 +9,7 @@ html -