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
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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
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rename from script/matlab/html/tutorials/demo_fwd3/demo_matlab_fwd3.html
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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
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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
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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
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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
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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
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rename from script/matlab/html/tutorials/demo_fwd4/demo_matlab_fwd4.m
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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
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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
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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
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rename from script/matlab/html/tutorials/demos_matlab.html
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diff --git a/script/matlab/html/tutorials/images/ucl.gif b/script/matlab/docs/html/tutorials/images/ucl.gif
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rename from script/matlab/html/tutorials/images/ucl.gif
rename to script/matlab/docs/html/tutorials/images/ucl.gif
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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
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rename from script/matlab/html/tutorials/quickstart/quickstart1.jpg
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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
-