diff --git a/Distributed_Source_Localization.fig b/Distributed_Source_Localization.fig index 0f8bf2d..559aab4 100644 Binary files a/Distributed_Source_Localization.fig and b/Distributed_Source_Localization.fig differ diff --git a/FP_FEM.fig b/FP_FEM.fig index 92e333f..de3bbe5 100644 Binary files a/FP_FEM.fig and b/FP_FEM.fig differ diff --git a/FP_FEM.m b/FP_FEM.m index 8047f47..d9a5afe 100644 --- a/FP_FEM.m +++ b/FP_FEM.m @@ -162,11 +162,32 @@ function editMeshName_CreateFcn(hObject, eventdata, handles) function set_session_changed(handles) % call when any change is made to the session edit boxes -if (handles.session_changed ~= 1) - set(handles.sessionProgressText,'String','Value Changed!'); +% if (handles.session_changed ~= 1) +% set(handles.sessionProgressText,'String','Value Changed!'); +% set(handles.pushbuttonCreateModel,'Enable','on'); +% end +% handles.session_changed = 1; + +set(handles.pushbuttonCreateModel,'Enable','off'); +name = get(handles.editModelName,'String'); +cond1 = str2num(get(handles.editScalpCond, 'String')); +cond2 = str2num(get(handles.editSkullCond, 'String')); +cond3 = str2num(get(handles.editCSFCond, 'String')); +cond4 = str2num(get(handles.editBrainCond, 'String')); + +if isempty(get(handles.editMeshName,'String')) + set(handles.sessionProgressText,'String', 'Please load a mesh.'); +elseif isempty(name) + set(handles.sessionProgressText,'String', 'Please enter session name.'); +elseif ~isfield(handles, 'sensors') + set(handles.sessionProgressText,'String', 'Please load sensors.'); +elseif (isempty(cond1) || isempty(cond2) || isempty(cond4)) + set(handles.sessionProgressText,'String', 'Please Enter Conductivities'); +else + set(handles.sessionProgressText,'String', 'Ready to create Model'); set(handles.pushbuttonCreateModel,'Enable','on'); end -handles.session_changed = 1; + guidata(handles.figure1, handles); @@ -298,7 +319,7 @@ function pushbuttonCreateModel_Callback(hObject, eventdata, handles) errordlg('Mesh must have at least 3 layers'); return end -name = get(handles.editModelName(),'String'); +name = get(handles.editModelName,'String'); if (isempty(name)) errordlg('Please Enter Session Name'); return @@ -593,8 +614,8 @@ function pushbuttonLoadSensors_Callback(hObject, eventdata, handles) end end %set_session_changed(handles); -update_display(handles); -%set_session_changed(handles); +%update_display(handles); +set_session_changed(handles); % @@ -689,12 +710,7 @@ function update_display(handles) %set(handles.editScalpCond,'String',[]); %set(handles.editSkullCond,'String',[]); %set(handles.editCSFCond,'String',[]); - %set(handles.editBrainCond,'String',[]); - - set(handles.sessionProgressText,'String','No Session'); - set(handles.pushbuttonCreateModel,'Enable','off'); - handles.session_changed = 0; - guidata(handles.figure1, handles); + %set(handles.editBrainCond,'String',[]); else set(handles.editModelName,'String',handles.session.name); set(handles.editScalpCond,'String',handles.session.cond(1)); @@ -708,6 +724,7 @@ function update_display(handles) end set(handles.sessionProgressText,'String','FEM Session Loaded'); end +set_session_changed(handles); if isfield(handles,'sensors') set(handles.editNumberofSensors,'String',length(handles.sensors)); @@ -720,7 +737,7 @@ function update_display(handles) set(handles.uipanelCSF, 'visible', 'off') end end - + % -------------------------------------------------------------------- function Load_Mesh_Menu_Callback(hObject, eventdata, handles) % hObject handle to Load_Mesh_Menu (see GCBO) diff --git a/Forward_Problem_Solution.fig b/Forward_Problem_Solution.fig index 512f833..cffd2a5 100644 Binary files a/Forward_Problem_Solution.fig and b/Forward_Problem_Solution.fig differ diff --git a/Forward_Problem_Solution.m b/Forward_Problem_Solution.m index adcc5a0..b9d3fa4 100644 --- a/Forward_Problem_Solution.m +++ b/Forward_Problem_Solution.m @@ -418,7 +418,7 @@ function pushbuttonCreateModel_Callback(hObject, eventdata, handles) errordlg('Mesh must have at least 3 layers'); return end -name = get(handles.editModelName(),'String'); +name = get(handles.editModelName,'String'); if (isempty(name)) errordlg('Please Enter Model Name'); return diff --git a/Forward_Problem_Solution.m~ b/Forward_Problem_Solution.m~ deleted file mode 100644 index 04e4565..0000000 --- a/Forward_Problem_Solution.m~ +++ /dev/null @@ -1,1151 +0,0 @@ -function varargout = Forward_Problem_Solution(varargin) -% FORWARD_PROBLEM_SOLUTION M-file for Forward_Problem_Solution.fig -% FORWARD_PROBLEM_SOLUTION, by itself, creates a new FORWARD_PROBLEM_SOLUTION or raises the existing -% singleton*. -% -% H = FORWARD_PROBLEM_SOLUTION returns the handle to a new FORWARD_PROBLEM_SOLUTION or the handle to -% the existing singleton*. -% -% FORWARD_PROBLEM_SOLUTION('CALLBACK',hObject,eventData,handles,...) calls the local -% function named CALLBACK in FORWARD_PROBLEM_SOLUTION.M with the given input arguments. -% -% FORWARD_PROBLEM_SOLUTION('Property','Value',...) creates a new FORWARD_PROBLEM_SOLUTION or raises the -% existing singleton*. Starting from the left, property value pairs are -% applied to the GUI before Forward_Problem_Solution_OpeningFunction gets called. An -% unrecognized property name or invalid value makes property application -% stop. All inputs are passed to Forward_Problem_Solution_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 -% -% Author: Zeynep Akalin Acar, SCCN, 2008 - -% Copyright (C) 2007 Zeynep Akalin Acar, SCCN, zeynep@sccn.ucsd.edu -% -% This program is free software; you can redistribute it and/or modify -% it under the terms of the GNU General Public License as published by -% the Free Software Foundation; either version 2 of the License, or -% (at your option) any later version. -% -% This program is distributed in the hope that it will be useful, -% but WITHOUT ANY WARRANTY; without even the implied warranty of -% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -% GNU General Public License for more details. -% -% You should have received a copy of the GNU General Public License -% along with this program; if not, write to the Free Software -% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - - -% Edit the above text to modify the response to help Forward_Problem_Solution - -% Last Modified by GUIDE v2.5 20-Mar-2008 12:14:54 - -% Begin initialization code - DO NOT EDIT -gui_Singleton = 1; -gui_State = struct('gui_Name', mfilename, ... - 'gui_Singleton', gui_Singleton, ... - 'gui_OpeningFcn', @Forward_Problem_Solution_OpeningFcn, ... - 'gui_OutputFcn', @Forward_Problem_Solution_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 Forward_Problem_Solution is made visible. -function Forward_Problem_Solution_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 Forward_Problem_Solution (see VARARGIN) - - -% Parse arguments and set handles as necessary -for i = 1:length(varargin) - if strcmp(varargin{i}, 'subjectdir') - i = i + 1; - handles.OutputFolder = varargin{i}; - elseif strcmp(varargin{i}, 'subject') - i = i + 1; - handles.arg_subject = varargin{i}; - elseif strcmp(varargin{i}, 'session') - i = i + 1; - handles.arg_session = varargin{i}; - end -end - - -handles.session_changed = 0; -handles.model_changed = 0; - - -if isfield(handles,'OutputFolder') - - % change dir - path = handles.OutputFolder; - lof = length(path); - if path(lof) ~= '/'; path(lof+1) = '/'; end; - cd(path) % change directory - % try to load mesh, model or session - if ~isempty(handles.arg_subject) && ~isempty(handles.arg_session) - % try to load session - file = [handles.arg_session '.session']; - try - ssave = load(file, '-MAT'); - handles = load_model(hObject,handles, [path ssave.model_name, '.model']); - handles.session = bem_create_session(ssave.name, handles.model, ssave.Smatrix); - handles.session = bem_load_transfer_matrix(handles.session, 'tmte'); - handles.sensors = sensMatToCoord(handles.session.Smatrix, handles.mesh.coord); - catch - try - % try to load model - file = [handles.arg_subject '.model']; - handles = load_model(hObject,handles, file); - handles.session = []; - catch - try - % try to load mesh - file = handles.arg_subject; - handles.mesh = bem_load_mesh(file); - handles.model = []; - handles.session = []; - catch - handles.mesh = []; - handles.model = []; - handles.model_changed = 0; - handles.session = []; - handles.session_changed = 0; - rethrow(lasterror); - end - end - end - elseif ~isempty(handles.arg_subject) - try - % try to load model - file = [handles.arg_subject '.model']; - handles = load_model(hObject,handles, file); - handles.session = []; - catch - try - % try to load mesh - file = handles.arg_subject; - handles.mesh = bem_load_mesh(file); - handles.model = []; - handles.session = []; - catch - handles.mesh = []; - handles.model = []; - handles.model_changed = 0; - handles.session = []; - handles.session_changed = 0; - end - end - else % ~isfield(handles,'arg_subject') & ~isfield(handles,'arg_session') - handles.mesh = []; - handles.model = []; - handles.model_changed = 0; - handles.session = []; - handles.session_changed = 0; - end %if isfield(handles, 'arg_subject') & isfield(handles,'arg_session') - - % try loading source space - try - file = 'sourcespace.dip'; -% handles.dipoles_name = file(1:length(file)-4); - handles.dipoles.pos = load([file], '-ascii'); - handles.dipoles.sym = 0; - set(handles.editNumberofdipoles,'String',size(handles.dipoles.pos,1)); - end -else % if no output folder is specified - % XXX check! - - % Choose default command line output for Forward_Problem_Solution - handles.mesh = []; - handles.model = []; - handles.model_changed = 0; - handles.session = []; - handles.session_changed = 0; -end - -handles.output = hObject; - -update_display(handles); - -if isfield(handles, 'arg_subject') && ~isempty(handles.arg_subject) - set(handles.editModelName,'String',handles.arg_subject); - set_model_changed(handles); -end -if isfield(handles,'arg_session') && ~isempty(handles.arg_session) - set(handles.editSessionName,'String',handles.arg_session); - set_session_changed(handles); -end - -% Update handles structure -guidata(hObject, handles); - - - -% UIWAIT makes Forward_Problem_Solution wait for user response (see UIRESUME) -% uiwait(handles.figure1); - - -% --- Outputs from this function are returned to the command line. -function varargout = Forward_Problem_Solution_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 editMeshName_Callback(hObject, eventdata, handles) -% hObject handle to editMeshName (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 editMeshName as text -% str2double(get(hObject,'String')) returns contents of editMeshName as a double - - -% --- Executes during object creation, after setting all properties. -function editMeshName_CreateFcn(hObject, eventdata, handles) -% hObject handle to editMeshName (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 set_model_changed(handles) -% call when any change is made to the model edit boxes -if (handles.model_changed ~= 1) - set(handles.modelProgressText,'String','Value Changed!'); - set(handles.pushbuttonCreateModel,'Enable','on'); -end -handles.model_changed = 1; -guidata(handles.figure1, handles); - - -function editModelName_Callback(hObject, eventdata, handles) -% hObject handle to editModelName (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 editModelName as text -% str2double(get(hObject,'String')) returns contents of editModelName as a double -set_model_changed(handles); - -% --- Executes during object creation, after setting all properties. -function editModelName_CreateFcn(hObject, eventdata, handles) -% hObject handle to editModelName (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 set_session_changed(handles) -% call when any change is made to the model edit boxes -if (handles.session_changed ~= 1) - set(handles.sessionProgressText, 'String', 'Value Changed!'); -end -if (isempty(handles.session) && ~isempty(get(handles.editSessionName,'String'))... - && isfield(handles,'sensors') && ~isempty(handles.model)) - set(handles.pushbuttonGenerateTM, 'Enable', 'on'); -else - set(handles.pushbuttonGenerateTM, 'Enable', 'off'); -end - -handles.session_changed = 1; -guidata(handles.figure1, handles); - - -function editSessionName_Callback(hObject, eventdata, handles) -% hObject handle to editSessionName (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 editSessionName as text -% str2double(get(hObject,'String')) returns contents of editSessionName as a double -set_session_changed(handles); - -% --- Executes during object creation, after setting all properties. -function editSessionName_CreateFcn(hObject, eventdata, handles) -% hObject handle to editSessionName (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 editScalpCond_Callback(hObject, eventdata, handles) -% hObject handle to editScalpCond (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 editScalpCond as text -% str2double(get(hObject,'String')) returns contents of editScalpCond as a double -set_model_changed(handles); - -% --- Executes during object creation, after setting all properties. -function editScalpCond_CreateFcn(hObject, eventdata, handles) -% hObject handle to editScalpCond (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 editCSFCond_Callback(hObject, eventdata, handles) -% hObject handle to editCSFCond (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 editCSFCond as text -% str2double(get(hObject,'String')) returns contents of editCSFCond as a double -set_model_changed(handles); - -% --- Executes during object creation, after setting all properties. -function editCSFCond_CreateFcn(hObject, eventdata, handles) -% hObject handle to editCSFCond (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 editBrainCond_Callback(hObject, eventdata, handles) -% hObject handle to editBrainCond (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 editBrainCond as text -% str2double(get(hObject,'String')) returns contents of editBrainCond as a double -set_model_changed(handles); - -% --- Executes during object creation, after setting all properties. -function editBrainCond_CreateFcn(hObject, eventdata, handles) -% hObject handle to editBrainCond (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 editSkullCond_Callback(hObject, eventdata, handles) -% hObject handle to editSkullCond (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 editSkullCond as text -% str2double(get(hObject,'String')) returns contents of editSkullCond as a double -set_model_changed(handles); - -% --- Executes during object creation, after setting all properties. -function editSkullCond_CreateFcn(hObject, eventdata, handles) -% hObject handle to editSkullCond (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 - - -% --- Executes on button press in checkbox1. -function checkbox1_Callback(hObject, eventdata, handles) -% hObject handle to checkbox1 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% Hint: get(hObject,'Value') returns toggle state of checkbox1 -set_model_changed(handles); - -% --- Executes on button press in pushbuttonCreateModel. -function pushbuttonCreateModel_Callback(hObject, eventdata, handles) -% hObject handle to pushbuttonCreateModel (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) -if (isempty(handles.mesh)) - errordlg('Please Load a Mesh first'); - return -end -if (handles.mesh.num_boundaries < 3) - errordlg('Mesh must have at least 3 layers'); - return -end -name = get(handles.editModelName(),'String'); -if (isempty(name)) - errordlg('Please Enter Model Name'); - return -end -if (handles.mesh.num_boundaries < 3) - errordlg('Mesh must have at least 3 layers'); - return -end - -if handles.mesh.num_boundaries == 3 - set(handles.editCSFCond, 'String' ,''); -end - -cond1 = str2num(get(handles.editScalpCond, 'String')); -cond2 = str2num(get(handles.editSkullCond, 'String')); -cond3 = str2num(get(handles.editCSFCond, 'String')); -cond4 = str2num(get(handles.editBrainCond, 'String')); - -if (handles.mesh.num_boundaries == 3 && ~isempty(cond3)) - errordlg('Mesh has no CSF layer'); - return -end -cond = [cond1 cond2 cond3 cond4]; - -if (isempty(cond1) || isempty(cond2) || isempty(cond4)) - errordlg('Please Enter Scalp, Skull and Brain Conductivities'); - return -end - -if (handles.mesh.num_boundaries == 4 && isempty(cond3)) - errordlg('Please Enter CSF Conductivity'); - return -end - -if (get(handles.checkbox1, 'Value') == 1) - mod = 3; -else - mod = -1; -end -handles.model = bem_create_model(name, handles.mesh, cond, mod); -set(handles.modelProgressText,'String','Generating matrices...'); -pause(0.5); -bem_generate_eeg_matrices(handles.model); -set(handles.modelProgressText,'String','BEM Model Created'); - -% save model -msave.name = handles.model.name; -msave.mesh_name = handles.model.mesh.name; -msave.cond = handles.model.cond; -msave.mod = handles.model.mod; -save([handles.model.name '.model'], '-STRUCT', 'msave') - -vol = mesh2volstr(handles.model.name); -vol.cond = handles.model.cond; -vol.type = 'metubem'; -save([handles.arg_subject '_vol.mat'], 'vol'); - - -set(handles.pushbuttonCreateModel,'Enable','off'); -handles.model_changed = 0; -guidata(handles.figure1, handles); - -function edit9_Callback(hObject, eventdata, handles) -% hObject handle to edit9 (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 edit9 as text -% str2double(get(hObject,'String')) returns contents of edit9 as a double - - -% --- Executes during object creation, after setting all properties. -function edit9_CreateFcn(hObject, eventdata, handles) -% hObject handle to edit9 (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 - - -% --- Executes on button press in pushbuttonGenerateTM. -function pushbuttonGenerateTM_Callback(hObject, eventdata, handles) -% hObject handle to pushbuttonGenerateTM (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -if (isempty(handles.mesh)) - errordlg('Please load a mesh first'); - return -end -if (isempty(handles.model)) - errordlg('Please load or generate a model first'); - return -end -name = get(handles.editSessionName,'String'); -if (isempty(name)) - errordlg('Please Enter Session Name'); - return -end - -if (isempty(handles.sensors)) - errordlg('Please Load a Sensor file'); - return -end - -a = dir(['ori_sen_loc.mat']); -if size(a,1) > 0 - load ori_sen_loc - handles.elocfn = sens_fn; - eloc = readlocs(sens_fn); -end - -sens.pnt = handles.sensors; -nsens = size(handles.sensors,1); -ind = handles.sensorindex; -% -if isfield(handles, 'sensorindex') & isfield(handles,'elocfn') - for ii=1:nsens - sens.label{ii} = eloc(ind(ii)).labels; - end -end - - -if isvector(handles.sensors) - Smatrix = bem_smatrix_from_nodes(handles.mesh, handles.sensors); -elseif size(handles.sensors,2) == 3 - Smatrix = bem_smatrix_from_coordinates(handles.mesh, handles.sensors); -end - -handles.session = bem_create_session(name, handles.model, Smatrix); -set(handles.sessionProgressText,'String','Generating matrices...'); - -handles.session = bem_generate_eeg_transfer_matrix(handles.session); -set(handles.sessionProgressText,'String','Session Created'); - -% save session -ssave.name = handles.session.name; -ssave.model_name = handles.session.model.name; -ssave.Smatrix = Smatrix; -ssave.sens = sens; -%ssave.tmte = handles.session.tmte; -save([handles.session.name '.session'], '-STRUCT', 'ssave'); - -set(handles.pushbuttonGenerateTM,'Enable','off'); -handles.session_changed = 0; -guidata(handles.figure1, handles); - -update_display(handles); - -function edit10_Callback(hObject, eventdata, handles) -% hObject handle to edit10 (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 edit10 as text -% str2double(get(hObject,'String')) returns contents of edit10 as a double - - -% --- Executes during object creation, after setting all properties. -function edit10_CreateFcn(hObject, eventdata, handles) -% hObject handle to edit10 (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 - - -% --- Executes on button press in pushbutton4. -function pushbutton4_Callback(hObject, eventdata, handles) -% hObject handle to pushbutton4 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - - -% --- Executes on button press in pushbutton5. -function pushbutton5_Callback(hObject, eventdata, handles) -% hObject handle to pushbutton5 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) -set(handles.textComputeLFM,'String','Computing...'); -pause(0.5); -[handles.potentials, handles.session] = bem_solve_lfm_eeg(handles.session, handles.dipoles.pos); -set(handles.textComputeLFM,'String','LFM Computed'); -guidata(hObject, handles); -update_display(handles); - -f = handles.session.name; -if handles.dipoles.sym == 0 - LFM = handles.potentials; - save([f '_LFM.mat'],'LFM'); - clear LFM; -else % symmetric dipoles - Np = size(handles.dipoles.pos,1); - LFM1 = handles.potentials(:,1:Np/2); - LFM2 = handles.potentials(:,Np/2+1:Np); - LFM = LFM1+ LFM2; - save([f '_sLFM.mat'],'LFM'); - clear LFM*; -end - - -% --- Executes on button press in pushbuttonShowMesh. -function pushbuttonShowMesh_Callback(hObject, eventdata, handles) -% hObject handle to pushbuttonShowMesh (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) -coordt = handles.mesh.coord; -ma = mean(coordt); -coordt = coordt - ones(length(coordt),1) * ma; -h = eeglab_plotmesh(handles.mesh.elem, coordt); -set(gcf, 'Name', 'Figure: Mesh', 'NumberTitle', 'off', 'Color', [0.925 0.957 1]); - - -function editNumberofLayers_Callback(hObject, eventdata, handles) -% hObject handle to editNumberofLayers (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 editNumberofLayers as text -% str2double(get(hObject,'String')) returns contents of editNumberofLayers as a double - - -% --- Executes during object creation, after setting all properties. -function editNumberofLayers_CreateFcn(hObject, eventdata, handles) -% hObject handle to editNumberofLayers (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 editNumberofNodes_Callback(hObject, eventdata, handles) -% hObject handle to editNumberofNodes (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 editNumberofNodes as text -% str2double(get(hObject,'String')) returns contents of editNumberofNodes as a double - - -% --- Executes during object creation, after setting all properties. -function editNumberofNodes_CreateFcn(hObject, eventdata, handles) -% hObject handle to editNumberofNodes (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 editNumberofElements_Callback(hObject, eventdata, handles) -% hObject handle to editNumberofElements (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 editNumberofElements as text -% str2double(get(hObject,'String')) returns contents of editNumberofElements as a double - - -% --- Executes during object creation, after setting all properties. -function editNumberofElements_CreateFcn(hObject, eventdata, handles) -% hObject handle to editNumberofElements (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 editNumberofNE_Callback(hObject, eventdata, handles) -% hObject handle to editNumberofNE (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 editNumberofNE as text -% str2double(get(hObject,'String')) returns contents of editNumberofNE as a double - - -% --- Executes during object creation, after setting all properties. -function editNumberofNE_CreateFcn(hObject, eventdata, handles) -% hObject handle to editNumberofNE (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 - - -% --- Executes on button press in pushbuttonLoadSensors. -function pushbuttonLoadSensors_Callback(hObject, eventdata, handles) -% hObject handle to pushbuttonLoadSensors (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% XXX control node list -if get(handles.radiobuttonNodeList, 'Value') == 1 - [file, path] = uigetfile('*.dat'); - if ~isequal(file, 0) && length(file) > 5 - % remove .dat extension - file = [path file(1:length(file)-4)]; - handles.sensors = load([file '.dat'], '-ascii'); - % Update handles structure - guidata(hObject, handles); - set(handles.editNumberofSensors,'String',length(handles.sensors)); - end -% XXX control coordinate list 1. size =(Nx3) 2. on the mesh? -else % load from coordinates - [file, path] = uigetfile('*.sens; *.sensors'); - if ~isequal(file, 0) && length(file) > 6 - if file(length(file)-3:length(file)) == 'sens' - % remove .sens extension - filen = [path file(1:length(file)-5)]; - handles.sensors = load([filen '.sens'], '-ascii'); - fileind = [path file(1:length(file)-16)]; % clear headsensors.sens - handles.sensorindex = load([fileind 'sensorindex'], '-ascii'); - % Update handles structure - guidata(hObject, handles); - set(handles.editNumberofSensors,'String',length(handles.sensors)); - else - sens = load([path file],'-mat'); - handles.sensors = sens.pnt; - handles.sensorindex = sens.ind; - % Update handles structure - guidata(hObject, handles); - set(handles.editNumberofSensors,'String',length(handles.sensors)); - end - end -end -set_session_changed(handles); -%update_display(handles); -%set_model_changed(handles); -set(handles.uipanelSensLoad,'visible','on') -% - -function editNumberofSensors_Callback(hObject, eventdata, handles) -% hObject handle to editNumberofSensors (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 editNumberofSensors as text -% str2double(get(hObject,'String')) returns contents of editNumberofSensors as a double - - -% --- Executes during object creation, after setting all properties. -function editNumberofSensors_CreateFcn(hObject, eventdata, handles) -% hObject handle to editNumberofSensors (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 - -% --- Convert sensMat to Electrode coordinates. -function C = sensMatToCoord(S, Coord) -% S Sens Mat -% Coord Mesh Coordinates -idx = unique(S(:, 1)); -C = zeros(length(idx), 3); - -for i = 1:length(idx) - si = find(S(:,1) == idx(i)); - C(i,:) = S(si, 3)' * Coord(S(si,2),:); -end - -% --- Executes on button press in pushbutton8. -function pushbutton8_Callback(hObject, eventdata, handles) -% hObject handle to pushbutton8 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) -if ~isfield(handles,'sensors') - handles.sensors = sensMatToCoord(handles.session.Smatrix, handles.mesh.coord); -end - -if size(handles.sensors, 2) == 3 - eloc = handles.sensors; -else - eloc = handles.mesh.coord(handles.sensors,:); -end - -dipnum = str2num(get(handles.editDipoleNumber, 'String')); -szdip = size(handles.potentials,2); -if dipnum < 1 - dipnum == 1 -elseif dipnum > szdip - dipnum == szdip; -end -dipnum = round(dipnum); -set(handles.editDipoleNumber, 'String', dipnum); - -figure; -utilbem_headplot(handles.potentials(:,dipnum), handles.mesh, eloc); -set(gcf, 'Name', 'Figure: Potential distribution', 'NumberTitle', 'off', 'Color', [0.925 0.957 1]); - -% --- Executes on button press in pushbuttonLoadDipoles. -function pushbuttonLoadDipoles_Callback(hObject, eventdata, handles) -% hObject handle to pushbuttonLoadDipoles (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - - -[file, path] = uigetfile('*.dip;*.sdip'); -if ~isequal(file, 0) && length(file) > 5 - if file(length(file)-3)=='s' %sdip - handles.dipoles_name = file(1:length(file)-5); - file = [path file(1:length(file)-5)]; - handles.dipoles.pos = load([file '.sdip'], '-ascii'); - handles.dipoles.sym = 1; - - else % dip - handles.dipoles_name = file(1:length(file)-4); - file = [path file(1:length(file)-4)]; - handles.dipoles.pos = load([file '.dip'], '-ascii'); - handles.dipoles.sym = 0; - end - % Update handles structure - guidata(hObject, handles); - set(handles.editNumberofdipoles,'String',size(handles.dipoles.pos,1)); -end -%update_display(handles); -%set_model_changed(handles); -set(handles.uipanelDipLoad,'visible','on') -set(handles.textComputeLFM,'String',' '); - -% -------------------------------------------------------------------- -function File_Menu_Callback(hObject, eventdata, handles) -% hObject handle to File_Menu (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - - -% -------------------------------------------------------------------- -function Untitled_2_Callback(hObject, eventdata, handles) -% hObject handle to Untitled_2 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% -------------------------------------------------------------------- -function update_display(handles) -if (isempty(handles.mesh)) - set(handles.editMeshName,'String',[]); - set(handles.editNumberofLayers,'String',[]); - set(handles.editNumberofNodes,'String',[]); - set(handles.editNumberofElements,'String',[]); - set(handles.editNumberofNE,'String',[]); - set(handles.pushbuttonShowMesh,'Enable','off'); -else - set(handles.editMeshName,'String',handles.mesh.name); - set(handles.editNumberofLayers,'String',handles.mesh.num_boundaries); - set(handles.editNumberofNodes,'String',handles.mesh.num_nodes); - set(handles.editNumberofElements,'String',handles.mesh.num_elements); - set(handles.editNumberofNE,'String',handles.mesh.num_node_elem); - set(handles.pushbuttonShowMesh,'Enable','on'); -end - -if (isempty(handles.model)) - set(handles.editModelName,'String',[]); - %set(handles.editScalpCond,'String',[]); - %set(handles.editSkullCond,'String',[]); - %set(handles.editCSFCond,'String',[]); - %set(handles.editBrainCond,'String',[]); - set(handles.checkbox1,'Value',1); - set(handles.modelProgressText,'String','No Model'); - set(handles.pushbuttonCreateModel,'Enable','off'); - handles.model_changed = 0; - guidata(handles.figure1, handles); -else - set(handles.editModelName,'String',handles.model.name); - set(handles.editScalpCond,'String',handles.model.cond(1)); - set(handles.editSkullCond,'String',handles.model.cond(2)); - if length(handles.model.cond) == 3 - set(handles.editCSFCond,'String',[]); - set(handles.editBrainCond,'String',handles.model.cond(3)); - elseif length(handles.model.cond) == 4 - set(handles.editCSFCond,'String',handles.model.cond(3)); - set(handles.editBrainCond,'String',handles.model.cond(4)); - end - set(handles.modelProgressText,'String','BEM Model Loaded'); -end - -if (isempty(handles.session)) - set(handles.editSessionName,'String',[]); - set(handles.pushbuttonGenerateTM,'Enable','off'); - set(handles.sessionProgressText,'String','No Session'); - set(handles.pushbutton5, 'Enable', 'off'); -else - set(handles.editSessionName,'String',handles.session.name); - set(handles.editNumberofSensors,'String',length(unique(handles.session.Smatrix(:,1)))); - set(handles.sessionProgressText,'String','Session Loaded'); - if ~isfield(handles.session,'tmte') - set(handles.pushbuttonGenerateTM,'Enable','on'); - end - set(handles.pushbutton5, 'Enable', 'on'); -end -if ~isfield(handles,'potentials') - set(handles.editDipoleNumber,'Enable','off'); - set(handles.pushbutton8,'Enable','off') -else - set(handles.editDipoleNumber,'Enable','on'); - set(handles.pushbutton8,'Enable','on') -end -if (isfield(handles,'sensors')) - set(handles.uipanelSensLoad, 'visible', 'on') -else - set(handles.uipanelSensLoad, 'visible', 'off') -end -if isfield(handles.mesh,'num_boundaries') - if handles.mesh.num_boundaries == 4 - set(handles.uipanelCSF, 'visible', 'on') - elseif handles.mesh.num_boundaries == 3 - set(handles.uipanelCSF, 'visible', 'off') - end -end - -% -------------------------------------------------------------------- -function Load_Mesh_Menu_Callback(hObject, eventdata, handles) -% hObject handle to Load_Mesh_Menu (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - - -[file, path] = uigetfile('*.bei'); -if ~isequal(file, 0) && length(file) > 5 - % remove .bei extension - file = [path file(1:length(file)-4)]; - handles.mesh = bem_load_mesh(file); - handles.model = []; - handles.session = []; - % Update handles structure - guidata(hObject, handles); -end -update_display(handles); - - -function handles = load_model(hObject,handles, file) - msave = load(file, '-MAT'); - handles.mesh = bem_load_mesh(msave.mesh_name); - handles.model = bem_create_model(msave.name, handles.mesh, msave.cond, msave.mod); - handles.session = []; - % Update handles structure - guidata(hObject, handles); % comment out - - -% -------------------------------------------------------------------- -function Load_Model_Menu_Callback(hObject, eventdata, handles) -% hObject handle to Load_Model_Menu (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -[file, path] = uigetfile('*.model'); -if ~isequal(file, 0) && length(file) > 7 - file = [path file]; - handles = load_model(hObject,handles, file); -end -update_display(handles); - - -% -------------------------------------------------------------------- -function Load_Session_Menu_Callback(hObject, eventdata, handles) -% hObject handle to Load_Session_Menu (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -[file, path] = uigetfile('*.session'); -if ~isequal(file, 0) && length(file) > 9 - file = [path file];l - ssave = load(file, '-MAT'); - handles = load_model(hObject,handles, [path ssave.mode_name, '.model']); - handles.session = bem_create_session(ssave.name, handles.model, ssave.Smatrix); - handles.session = bem_load_transfer_matrix(handles.session, 'tmte'); - handles.sensors = sensMatToCoord(handles.session.Smatrix, handles.mesh.coord); - % Update handles structure - guidata(hObject, handles); -end -update_display(handles); - - -function editNumberofdipoles_Callback(hObject, eventdata, handles) -% hObject handle to editNumberofdipoles (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 editNumberofdipoles as text -% str2double(get(hObject,'String')) returns contents of editNumberofdipoles as a double - - -% --- Executes during object creation, after setting all properties. -function editNumberofdipoles_CreateFcn(hObject, eventdata, handles) -% hObject handle to editNumberofdipoles (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 uipanel5_SelectionChangeFcn(hObject, eventdata, handles) -% hObject handle to uipanel5 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) -%get(handles.uipanel5); -%if get(handles.radiobuttonNodeList, 'Value') == 1 -% handles.LoadfromNodeList = 1; -%elseif get(handles.radiobuttonCoordinates, 'Value') == 1 -% handles.LoadfromNodeList = 0; -%end -%update_display(handles); - - - - - -% -------------------------------------------------------------------- -function uipanel6_ButtonDownFcn(hObject, eventdata, handles) -% hObject handle to uipanel6 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - - -% -------------------------------------------------------------------- -function uipanel6_SelectionChangeFcn(hObject, eventdata, handles) -% hObject handle to uipanel6 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - - - - -% --- Executes on button press in radiobuttonNodeList. -function radiobuttonNodeList_Callback(hObject, eventdata, handles) -% hObject handle to radiobuttonNodeList (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% Hint: get(hObject,'Value') returns toggle state of radiobuttonNodeList - - -% -------------------------------------------------------------------- -function uipanel5_SelectionChangeFcn(hObject, eventdata, handles) -% hObject handle to uipanel5 (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - - - - - -function editDipoleNumber_Callback(hObject, eventdata, handles) -% hObject handle to editDipoleNumber (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 editDipoleNumber as text -% str2double(get(hObject,'String')) returns contents of editDipoleNumber as a double - - -% --- Executes during object creation, after setting all properties. -function editDipoleNumber_CreateFcn(hObject, eventdata, handles) -% hObject handle to editDipoleNumber (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 - - - - -% --- Executes on button press in pushbuttonShowSensors. -function pushbuttonShowSensors_Callback(hObject, eventdata, handles) -% hObject handle to pushbuttonShowSensors (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -if ~isfield(handles,'sensors') - handles.sensors = sensMatToCoord(handles.session.Smatrix, handles.mesh.coord); -end - -coordt = handles.mesh.coord; -ma = mean(coordt); -coordt = coordt - ones(length(coordt),1)*ma; -%figure; -h = eeglab_plotmesh(handles.mesh.elem, coordt); -set(gcf, 'Name', 'Figure: Sensors', 'NumberTitle', 'off', 'Color', [0.925 0.957 1]); -hold - -if size(handles.sensors, 2) == 3 - eloc = handles.sensors; -else - eloc = handles.mesh.coord(handles.sensors,:); -end -eloc = eloc - ones(length(eloc),1)*ma; -plot3(eloc(:,1),eloc(:,2),eloc(:,3),'ko','LineWidth',2,'MarkerEdgeColor',... - 'k','MarkerFaceColor','r','MarkerSize',6); - diff --git a/Mesh_generation.fig b/Mesh_generation.fig index 16a8d6c..c51348e 100644 Binary files a/Mesh_generation.fig and b/Mesh_generation.fig differ diff --git a/Neuroelectromagnetic_Forward_Modeling_Toolbox.fig b/Neuroelectromagnetic_Forward_Modeling_Toolbox.fig index d90150f..5f73754 100644 Binary files a/Neuroelectromagnetic_Forward_Modeling_Toolbox.fig and b/Neuroelectromagnetic_Forward_Modeling_Toolbox.fig differ diff --git a/ReadSMF.m b/ReadSMF.m new file mode 100644 index 0000000..1fc1555 --- /dev/null +++ b/ReadSMF.m @@ -0,0 +1,25 @@ +function [Coord, Elem]=ReadSMF(name,x,y,z,sc); +fid=fopen(name, 'r'); +nnp=0; nel=0; +line=1; +while line~=-1 + line=fgets(fid); + if line(1)=='v'; + nnp=nnp+1; + [A,count,ERRMSG,NEXTINDEX] = sscanf(line,'%c %f %f %f',4); + Coord(nnp,1)=nnp; + Coord(nnp,2:4)=A(2:4)'; + elseif (line(1)=='t')|(line(1)=='f'); + nel=nel+1; + [A,count,ERRMSG,NEXTINDEX] = sscanf(line,'%c %d %d %d',4); + Elem(nel,1)=nel; + Elem(nel,2:4)=A(2:4)'; + end +end +fclose(fid); + +Coord(:,4)=Coord(:,4)/sc+z; +Coord(:,2)=Coord(:,2)+x; +Coord(:,3)=Coord(:,3)+y; + + \ No newline at end of file diff --git a/Segmentation.fig b/Segmentation.fig index f428fe7..ed0485c 100644 Binary files a/Segmentation.fig and b/Segmentation.fig differ diff --git a/Segmentation.m b/Segmentation.m index 3edb88e..fd01ed7 100644 --- a/Segmentation.m +++ b/Segmentation.m @@ -297,6 +297,13 @@ function OpenMenuItem_Callback(hObject, eventdata, handles) % remove .hdr extension file = [path file(1:length(file)-4)]; [x,y,z] = segm_readanalyze(file); + [K,L,M]=size(x); + if K==L && L==M && M==K && y(1)==1 && y(2)==1 && y(3)==1 + else + error_msg = ['Please run Freesurfer pre-processing on the MR image: \n',... + 'https://sccn.ucsd.edu/wiki/Chapter_02:_Head_Modeling_from_MR_Images']; + error( 'u:stuffed:it' , error_msg) + end set(handles.pbinhomog,'Enable','on'); if get(handles.checkboxLRflip, 'Value') == 1 % flip image left-right (image is flipped during MR acquisition) @@ -554,7 +561,7 @@ function Runbutton_Callback(hObject, eventdata, handles) if handles.CurrentOperation == 1 iter = str2num(get(handles.editNumberofIter, 'String')); % ts = str2num(get(handles.editTimeStep, 'String')); - ts = 0.0625; + ts = 0.0625; cond = str2num(get(handles.editConductance, 'String')); handles.parameters.filter.iter = iter; handles.parameters.filter.cond = cond; diff --git a/Source_space_generation.fig b/Source_space_generation.fig index dac9488..85ca409 100644 Binary files a/Source_space_generation.fig and b/Source_space_generation.fig differ diff --git a/bem_solve_lfm_eeg.m b/bem_solve_lfm_eeg.m index 5a784e4..4dbaf61 100644 --- a/bem_solve_lfm_eeg.m +++ b/bem_solve_lfm_eeg.m @@ -57,7 +57,7 @@ rhs = zeros(mesh.num_nodes, size(dipoles,1)); if model.mod < 1 - for k = 1:size(dipoles,1) % parfor + parfor k = 1:size(dipoles,1) rhs(:,k) = utilbem_pot_unbound(mesh.coord, model.node_cond, dipoles(k,:)); end else @@ -74,7 +74,7 @@ model = session.model; s2 = model.cond(mesh.bnd(model.mod,3)); % outer s3 = model.cond(mesh.bnd(model.mod,2)); % inner - for k = 1:size(dipoles,1) % parfor + parfor k = 1:size(dipoles,1) rhs(:,k) = utilbem_multilayer_rhs(mesh.coord, model.node_cond, model.ind_mod, ... model.ind_imesh, model.ind_imesh_mod, model.iinv, model.dmt, s2, s3, dipoles(k,:)); end diff --git a/eeglab_dipplot.m b/eeglab_dipplot.m index cfa9a3c..bd76808 100644 --- a/eeglab_dipplot.m +++ b/eeglab_dipplot.m @@ -624,12 +624,12 @@ %adding log message % -function [outsources, XX, YY, ZZ, XO, YO, ZO] = dipplot( sourcesori, varargin ) +function [outsources, XX, YY, ZZ, XO, YO, ZO] = eeglab_dipplot( sourcesori, varargin ) DEFAULTVIEW = [0 0 1]; if nargin < 1 - help dipplot; + help eeglab_dipplot; return; end; @@ -757,13 +757,13 @@ end; end; -% if strcmpi(g.coordformat, 'spherical') -% dat.sph2spm = sph2spm; -% elseif strcmpi(g.coordformat, 'CTF') -% dat.sph2spm = traditionaldipfit([0 0 0 0 0 0 10 -10 10]); -% else -% dat.sph2spm = []; %traditional([0 0 0 0 0 pi 1 1 1]); -% end; + if strcmpi(g.coordformat, 'spherical') + dat.sph2spm = sph2spm; + elseif strcmpi(g.coordformat, 'CTF') + dat.sph2spm = traditionaldipfit([0 0 0 0 0 0 10 -10 10]); + else + dat.sph2spm = []; %traditional([0 0 0 0 0 pi 1 1 1]); + end; dat.sph2spm=eye(4); % zeynep @@ -888,9 +888,9 @@ pos1 = [0 0 0.5 0.5]; pos2 = [0 0.5 0.5 .5]; pos3 = [.5 .5 0.5 .5]; if strcmp(g.summary, 'on2'), tmp = pos1; pos1 =pos3; pos3 = tmp; end; - axes('position', pos1); newsources = dipplot(sourcesori, 'view', [1 0 0] , options{:}); axis off; - axes('position', pos2); newsources = dipplot(sourcesori, 'view', [0 0 1] , options{:}); axis off; - axes('position', pos3); newsources = dipplot(sourcesori, 'view', [0 -1 0], options{:}); axis off; + axes('position', pos1); newsources = eeglab_dipplot(sourcesori, 'view', [1 0 0] , options{:}); axis off; + axes('position', pos2); newsources = eeglab_dipplot(sourcesori, 'view', [0 0 1] , options{:}); axis off; + axes('position', pos3); newsources = eeglab_dipplot(sourcesori, 'view', [0 -1 0], options{:}); axis off; axes('position', [0.5 0 0.5 0.5]); colorcount = 1; if isfield(newsources, 'component') @@ -928,9 +928,9 @@ 'coordformat' g.coordformat 'mri' g.mri 'meshdata' g.meshdata 'axistight' g.axistight }; figure('position', [ 100 600 600 200 ]); axes('position', [-0.1 -0.1 1.2 1.2], 'color', 'k'); axis off; blackimg = zeros(10,10,3); image(blackimg); - axes('position', [0 0 1/3 1], 'tag', 'rear'); dipplot(sourcesori, options{:}, 'holdon', 'on'); view([0 -1 0]); - axes('position', [1/3 0 1/3 1], 'tag', 'top' ); dipplot(sourcesori, options{:}, 'holdon', 'on'); view([0 0 1]); - axes('position', [2/3 0 1/3 1], 'tag', 'side'); dipplot(sourcesori, options{:}, 'holdon', 'on'); view([1 -0.01 0]); + axes('position', [0 0 1/3 1], 'tag', 'rear'); eeglab_dipplot(sourcesori, options{:}, 'holdon', 'on'); view([0 -1 0]); + axes('position', [1/3 0 1/3 1], 'tag', 'top' ); eeglab_dipplot(sourcesori, options{:}, 'holdon', 'on'); view([0 0 1]); + axes('position', [2/3 0 1/3 1], 'tag', 'side'); eeglab_dipplot(sourcesori, options{:}, 'holdon', 'on'); view([1 -0.01 0]); set(gcf, 'paperpositionmode', 'auto'); return; end; @@ -1307,7 +1307,7 @@ ' for tmpi = 1:' nbsrc ',' ... ' set(findobj(''parent'', gca, ''tag'', [ ''dipole'' int2str(tmpi) ]), ''visible'', ''off'');' ... ' end; clear tmpi;' ... - ' dipplot(gcbf);' ... + ' eeglab_dipplot(gcbf);' ... ' set(gcbo, ''string'', ''Plot all'');' ... 'else,' ... ' for tmpi = 1:' nbsrc ',' ... @@ -1324,7 +1324,7 @@ 'tmpuserdat.axistight = ~tmpuserdat.axistight;' ... 'set(gca, ''userdata'', tmpuserdat);' ... 'clear tmpuserdat;' ... - 'dipplot(gcbf);' ]; + 'eeglab_dipplot(gcbf);' ]; viewstring = fastif(dat.axistight, 'Loose view', 'Tight view'); enmesh = fastif(isempty(g.meshdata) & strcmpi(g.coordformat, 'MNI'), 'off', 'on'); if strcmpi(g.coordformat, 'CTF'), viewcor = 'view([0 1 0]);'; viewtop = 'view([0 0 -1]);'; vis = 'off'; @@ -1363,7 +1363,7 @@ 'style', 'text', 'string', ''); h = uicontrol( 'unit', 'normalized', 'position', [0 0.62 .15 .05], 'tag', 'tmp', 'userdata', 'editor', ... 'style', 'edit', 'string', '1', 'callback', ... - [ 'dipplot(gcbf);' ] ); + [ 'eeglab_dipplot(gcbf);' ] ); h = uicontrol( 'unit', 'normalized', 'position', [0 0.67 .15 .05], 'tag', 'tmp', ... 'style', 'pushbutton', 'string', 'Keep|Prev', 'callback', ... [ 'editobj = findobj(''parent'', gcf, ''userdata'', ''editor'');' ... @@ -1382,14 +1382,14 @@ 'style', 'pushbutton', 'string', 'Next', 'callback', ... [ 'editobj = findobj(''parent'', gcf, ''userdata'', ''editor'');' ... 'set(editobj, ''string'', num2str(str2num(get(editobj, ''string''))+1));' ... - 'dipplot(gcbf);' ... + 'eeglab_dipplot(gcbf);' ... 'clear editobj;' ]); h = uicontrol( 'unit', 'normalized', 'position', [0 0.82 .15 .05], 'tag', 'tmp', ... 'style', 'pushbutton', 'string', 'Keep|Next', 'callback', ... [ 'editobj = findobj(''parent'', gcf, ''userdata'', ''editor'');' ... 'set(editobj, ''string'', num2str(str2num(get(editobj, ''string''))+1));' ... 'tmpobj = get(gcf, ''userdata'');' ... - 'dipplot(gcbf);' ... + 'eeglab_dipplot(gcbf);' ... 'set(tmpobj, ''visible'', ''on'');' ... 'clear editobj tmpobj;' ]); h = uicontrol( 'unit', 'normalized', 'position', [0 0.87 .15 .05], 'tag', 'tmp', ... diff --git a/eegplugin_nft.m b/eegplugin_nft.m index c21aead..4e90188 100644 --- a/eegplugin_nft.m +++ b/eegplugin_nft.m @@ -29,12 +29,9 @@ % $Log: eegplugin_nft.m,v $ function vers = eegplugin_nft(fig, trystrs, catchstrs) - -%path = '/data/projects/zeynep/NFT/NFT-2.1'; -% addpath(path) - vers = 'nft2.2'; + vers = 'nft2.3'; if nargin < 3 error('eegplugin_nft requires 3 arguments'); end; diff --git a/forward.orig b/forward.orig deleted file mode 100755 index f2f0019..0000000 Binary files a/forward.orig and /dev/null differ diff --git a/freesurfer_read_surf.m b/freesurfer_read_surf.m new file mode 100644 index 0000000..5501259 --- /dev/null +++ b/freesurfer_read_surf.m @@ -0,0 +1,156 @@ +function [vertices, faces] = freesurfer_read_surf(fname) + +% freesurfer_read_surf - FreeSurfer I/O function to read a surface file +% +% [vertices, faces] = freesurfer_read_surf(fname) +% +% Reads the vertex coordinates (mm) and face lists from a surface file. +% +% Surface files are stored as either triangulations or quadrangulations. +% That is, for a triangulation, each face is defined by 3 vertices. For a +% quadrangulation, each face is defined by 4 vertices. The rows of 'faces' +% contain indices into the rows of 'vertices', the latter holds the XYZ +% coordinates of each vertex. +% +% The freesurfer faces index the vertices in counter-clockwise order (when +% viewed from the outside of the surface). This is consistent with a +% right-hand rule. If we have vertices +% +% C B +% +% +% A +% +% Then we can calculate an edge vector from A to B (ie, AB = B - A) and +% another edge vector from A to C (ie, AC = C - A). If you form a "gun" +% with your thumb and forefinger of the right hand, then align your thumb +% with the AB vector and your forefinger with the AC vector, your palm is +% facing out of the screen and extending your middle finger in the +% orthogonal direction to the plane of the screen will give the outward +% surface normal of the triangle ABC. (If you lookup "triangle" on +% Wolfram's mathworld, you can see that AB is referred to as c and AC is +% referred to as b.) +% +% However, if this surface is read into matlab, it will give INWARD surface +% normals in the matlab patch command. For some reason, matlab is not +% following the right hand rule. To get OUTWARD normals with the matlab +% patch command, use faces(:,[1 3 2]) (see below). +% +% The vertex coordinates are in mm. The FreeSurfer coordinate +% system for surfaces is quite simple, but relating to their MRI +% cor-??? files is too confusing to explain here; see the FreeSurfer +% homepage or google the documentation by Graham Wideman. For the +% surfaces, at least, the origin is somewhere in the center of the +% head, and the vertex XYZ coordinates are oriented such that +X is +% right, +Y is anterior and +Z is superior (this is the +% FreeSurfer RAS coordinate system). +% +% Note that reading the faces of a quad file can take a long +% time due to their compact storage format. In this case, the return of +% vertices can be faster if the face output variable is not specified; in +% this case, the faces are not read. +% +% Try this to visualize the surface: +% Hp = patch('vertices',vertices,'faces',faces(:,[1 3 2]),... +% 'facecolor',[.5 .5 .5],'edgecolor','none') +% camlight('headlight','infinite') +% vertnormals = get(Hp,'vertexnormals'); +% +% See also freesurfer_write_surf, freesurfer_read_curv, +% freesurfer_read_wfile +% + +% $Revision: 1.1.2.1 $ $Date: 2007/12/09 22:50:25 $ + +% Copyright (C) 2000 Darren L. Weber +% +% This program is free software; you can redistribute it and/or +% modify it under the terms of the GNU General Public License +% as published by the Free Software Foundation; either version 2 +% of the License, or (at your option) any later version. +% +% This program is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License for more details. +% +% You should have received a copy of the GNU General Public License +% along with this program; if not, write to the Free Software +% Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, +% USA. + +% History: 08/2000, Darren.Weber_at_radiology.ucsf.edu +% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +ver = '$Revision: 1.1.2.1 $ $Date: 2007/12/09 22:50:25 $'; +fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15)); + +if(nargin < 1) + help freesurfer_read_surf; + return; +end + +%QUAD_FILE_MAGIC_NUMBER = (-1 & 0x00ffffff) ; +%NEW_QUAD_FILE_MAGIC_NUMBER = (-3 & 0x00ffffff) ; + +TRIANGLE_FILE_MAGIC_NUMBER = 16777214; +QUAD_FILE_MAGIC_NUMBER = 16777215; + + +% open it as a big-endian file +fid = fopen(fname, 'rb', 'b'); +if (fid < 0), + str = sprintf('could not open surface file %s.', fname); + error(str); +end + +fprintf('...reading surface file: %s\n', fname); +tic; + +magic = freesurfer_fread3(fid); + +if (magic == QUAD_FILE_MAGIC_NUMBER), + Nvertices = freesurfer_fread3(fid); + Nfaces = freesurfer_fread3(fid); + fprintf('...reading %d quad file vertices\n',Nvertices); + vertices = fread(fid, Nvertices*3, 'int16') ./ 100 ; + if (nargout > 1), + fprintf('...reading %d quad file faces (please wait)\n',Nfaces); + faces = zeros(Nfaces,4); + for iface = 1:Nfaces, + for n=1:4, + faces(iface,n) = freesurfer_fread3(fid) ; + end + if(~rem(iface, 10000)), fprintf(' %7.0f',iface); end + if(~rem(iface,100000)), fprintf('\n'); end + end + end +elseif (magic == TRIANGLE_FILE_MAGIC_NUMBER), + fprintf('...reading triangle file\n'); + tline = fgets(fid); % read creation date text line + tline = fgets(fid); % read info text line + + Nvertices = fread(fid, 1, 'int32'); % number of vertices + Nfaces = fread(fid, 1, 'int32'); % number of faces + + % vertices are read in column format and reshaped below + vertices = fread(fid, Nvertices*3, 'float32'); + + % faces are read in column format and reshaped + faces = fread(fid, Nfaces*3, 'int32'); + faces = reshape(faces, 3, Nfaces)'; +else + str = sprintf('unknown magic number in surface file %s.', fname); + error(str); +end + +vertices = reshape(vertices, 3, Nvertices)'; +fclose(fid); + +fprintf('...adding 1 to face indices for matlab compatibility.\n'); +faces = faces + 1; + +t=toc; fprintf('...done (%6.2f sec)\n\n',t); + +return \ No newline at end of file diff --git a/geodesic/create_flat_triangular_mesh.m b/geodesic/create_flat_triangular_mesh.m new file mode 100644 index 0000000..82162b0 --- /dev/null +++ b/geodesic/create_flat_triangular_mesh.m @@ -0,0 +1,33 @@ +%good mesh to catch possible bugs in geodesic algorithms +%Copyright (c) 2007 Danil Kirsanov +function [p,tri] = create_flat_triangular_mesh(step, smoothness) + +x = -1:step:1; +y = x; + +N_p = length(x)*length(y); %regular grid +p = zeros(N_p,3); +N_t = (length(x)-1)*(length(y)-1)*2; %two triangles per square +tri = zeros(N_t,3); + +n_p = 1; +n_t = 1; +for i=1:length(x); + for j=1:length(y); + p(n_p,:) = [x(i) y(j) 0]; + + if i 1 + p(i,:) = p(i,:)/max(abs(p(i,:))); + end + + scale = abs(p(i,1))*waist + (1 - waist); + p(i,2:3) = p(i,2:3)*scale; % add "waist" on x-axis +end; diff --git a/geodesic/create_subdivision_pattern.m b/geodesic/create_subdivision_pattern.m new file mode 100644 index 0000000..6b26e70 --- /dev/null +++ b/geodesic/create_subdivision_pattern.m @@ -0,0 +1,33 @@ +%regular subdivision pattern of a triangle +%used in drawing approximate equidistant lines in example5.m +%Copyright (c) 2007 Danil Kirsanov +function [weights,tri] = create_subdivision_pattern(level) %"level" is the number of additional vertices per edge + +step = 1/(level + 1); +N = level + 2; %total number of points per edge + +N_p = (N^2 + N)/2; %number of vertices in the regular grid +N_t = (N-1)^2; %two triangles per square +weights = zeros(N_p,3); +tri = zeros(N_t,3); + +n_p = 1; +n_t = 1; +for i=1:N; + K = N-i+1; + for j=1:K + c = step*[j-1, i-1]; + weights(n_p,:) = [c, 1-sum(c)]; + + if i 1e10); %find vertices for which the distances are undefined +defined = find(distances < 1e10); +distances(undefined) = max(distances(defined))*1.1; %plot undefined distances with white +colormap('winter'); +c_map = colormap; +c_map(end,:) = 1; +colormap(c_map); + +hold off; +trisurf(faces,vertices(:,1),vertices(:,2),vertices(:,3),distances, 'FaceColor', 'interp', 'EdgeColor', 'k'); %plot the mesh +hold on; +daspect([1 1 1]); + +for i=1:length(path) %plot paths to all vertices with finite distances + [x,y,z] = extract_coordinates_from_path(path{i}); + plot3(x,y,z,'r'); +end; + +for i=1:length(stop_points); %show stop vertices + h = plot3(stop_points{i}.x,stop_points{i}.y,stop_points{i}.z,'ro','MarkerSize',5, 'MarkerFaceColor', 'r'); +end; +legend(h, 'stop vertices'); + +geodesic_delete; diff --git a/geodesic/example5.m b/geodesic/example5.m new file mode 100644 index 0000000..f88d7be --- /dev/null +++ b/geodesic/example5.m @@ -0,0 +1,94 @@ +% Simple application: drawing approximate piece-wise linear isodistance curves (isolines). +% In theory, isolines on a triangular mesh are piecewise second-order curves. +% Here, we draw piecewise linear approximation of these curves. The distance function +% of the mesh is sampled at the subdivision vertices within each triangle and +% represented as a linear function within each subdivision triangle. +% This particular method works well only for 'exact' geodesic method, +% because for the approximate methods the distance field is discontinuous +% on the edges of the mesh. +% Danil Kirsanov, 09/2007 + +subdivision_level = 5; %number of additional vertices per edge; each mesh triangle will have roughly speaking subdivision_level^2 number of subdivision triangles +number_of_isolines = 10; + +rand('state', 0); %comment this statement if you want to produce random mesh every time + +[vertices,faces] = create_flat_triangular_mesh(0.2, 0); +N = length(vertices); +% N = 300; %number of points in a mesh +% [vertices,faces] = create_hedgehog_mesh(N, 0.1); %create "noisy sphere" mesh; "vertices" contains 3D vertex coordinates; "faces" contains vertex id's for every triangle + +hold off; +trisurf(faces,vertices(:,1),vertices(:,2),vertices(:,3), 'FaceColor', 'w', 'EdgeColor', 'k', 'FaceAlpha', 0.99); %plot the mesh +hold on; + +mesh = geodesic_new_mesh(vertices,faces); %initilize new mesh +algorithm = geodesic_new_algorithm(mesh, 'exact'); %initialize new geodesic algorithm + +source_points = {}; +for vertex_id = [26,N-5, floor(N/2)-3, floor(N/2)+3]; %create source points + source_points{end+1} = geodesic_create_surface_point('vertex',vertex_id, vertices(vertex_id,:)); +end; + +geodesic_propagate(algorithm, source_points); + +[sub_weights,sub_tri] = create_subdivision_pattern(subdivision_level); %coordinates of the subdivision triangles + +[source_id, distances] = geodesic_distance_and_source(algorithm); %find distances for all vertices of the mesh +max_distance = max(distances); + +isolines_step = max_distance/number_of_isolines; +isolines_distances = isolines_step/2 : isolines_step : max_distance; + +[known_distances, tmp] = find(sub_weights > 0.999); %we already know the distances to the actual vertices of the mesh +unknown_distances = setdiff([1:size(sub_weights,1)], known_distances); +for face_id = 1:size(faces,1) + vertex_ids = faces(face_id,:); + sub_vertices = sub_weights*vertices(vertex_ids,:); %find coordinates of subdivision vertices + sub_distances = zeros(size(sub_vertices,1),1); + + sub_distances(known_distances) = distances(vertex_ids); %no need to reevaluate distance finction for the vertices of the face + %for sub_index = 1:size(sub_vertices,1) %find distances at all subdivision vertices + for sub_index = unknown_distances %find distances at all internal subdivision vertices + q = geodesic_create_surface_point('face',face_id,sub_vertices(sub_index,:)); + [source_id, d] = geodesic_distance_and_source(algorithm, q); + sub_distances(sub_index) = d; + end; + + selected_distances = find(isolines_distances >= min(sub_distances) & ... + isolines_distances <= max(sub_distances)); + selected_distances = isolines_distances(selected_distances); + + for tri_index = 1:size(sub_tri,1) %intersection of the equidistance curve with every subdivision triangle is approximated as a straight line + for isodistance = selected_distances + p = []; + for i = 1:3 + index1 = sub_tri(tri_index, i); + index2 = sub_tri(tri_index, mod(i,3) + 1); + d1 = sub_distances(index1); + d2 = sub_distances(index2); + + if d1 == isodistance %special case when isodistance paths exactly through the vertex + p(end+1,:) = sub_vertices(index1,:); + end + + if isodistance > min(d1,d2) & isodistance < max(d1,d2) %draw equidistant curve + a = (isodistance - d2)/(d1 - d2); % I believe that division by zero will never happen here + p(end+1,:) = a*sub_vertices(index1,:) + (1-a)*sub_vertices(index2,:); + end; + end + if size(p,1) == 2 + plot3(p(:,1), p(:,2),p(:,3),'b', 'LineWidth', 2); + end + end + end; +end; + +for i=1:length(source_points); + h = plot3(source_points{i}.x,source_points{i}.y,source_points{i}.z,'ro','MarkerSize',5, 'MarkerFaceColor', 'r'); +end; + +campos([0, 0, 5]) +legend(h, 'sources'); + +geodesic_delete; \ No newline at end of file diff --git a/geodesic/extract_coordinates_from_path.m b/geodesic/extract_coordinates_from_path.m new file mode 100644 index 0000000..9ad0e4a --- /dev/null +++ b/geodesic/extract_coordinates_from_path.m @@ -0,0 +1,17 @@ +function [x,y,z] = extract_coordinates_from_path(path) + +%this elegant way is incompatible with the older versions of matlab +% x = cellfun(@(p) p.x, path); %the simplest way to extract coordinates from the path +% y = cellfun(@(p) p.y, path); %if it looks complicated, you can use "for" similar to example1.m +% z = cellfun(@(p) p.z, path); + +x = zeros(length(path),1); +y = x; +z = y; + +for i=1:length(path) + x(i) = path{i}.x; + y(i) = path{i}.y; + z(i) = path{i}.z; +end; + diff --git a/geodesic/geodesic.mexa64 b/geodesic/geodesic.mexa64 new file mode 100644 index 0000000..9170bb2 Binary files /dev/null and b/geodesic/geodesic.mexa64 differ diff --git a/geodesic/geodesic.mexmaci64 b/geodesic/geodesic.mexmaci64 new file mode 100644 index 0000000..41b61c7 Binary files /dev/null and b/geodesic/geodesic.mexmaci64 differ diff --git a/geodesic/geodesic.mexw64 b/geodesic/geodesic.mexw64 new file mode 100644 index 0000000..975e745 Binary files /dev/null and b/geodesic/geodesic.mexw64 differ diff --git a/geodesic/geodesic_convert_surface_points.m b/geodesic/geodesic_convert_surface_points.m new file mode 100644 index 0000000..f24fdfd --- /dev/null +++ b/geodesic/geodesic_convert_surface_points.m @@ -0,0 +1,46 @@ +%internal geodesic function +%conversion between C++ and matlab surface point representation +% Danil Kirsanov, 09/2007 + +function q = geodesic_convert_surface_points(p) + +if isempty(p) + q = []; + return; +end; + +point_types = {'vertex', 'edge', 'face'}; + +if ~isa(p,'numeric') %convert from matlab to C++ + num_points = length(p); + q = zeros(num_points*5, 1); + for i = 1:num_points + shift = (i-1)*5; + q(shift + 1) = p{i}.x; + q(shift + 2) = p{i}.y; + q(shift + 3) = p{i}.z; + q(shift + 5) = p{i}.id - 1; + + type = find(strcmp(point_types, p{i}.type)); + if isempty(type) + disp('error: point type is incorrect'); + q = []; + return; + else + q(shift + 4) = type - 1; + end + end +else %convert from C++ to matlab + num_points = length(p)/5; + q = cell(num_points, 1); + for i = 1:num_points + shift = (i-1)*5; + point.x = p(shift + 1); + point.y = p(shift + 2); + point.z = p(shift + 3); + point.type = point_types(p(shift + 4) + 1); + point.id = p(shift + 5) + 1; + + q{i} = point; + end; +end; diff --git a/geodesic/geodesic_create_surface_point.m b/geodesic/geodesic_create_surface_point.m new file mode 100644 index 0000000..5bb1927 --- /dev/null +++ b/geodesic/geodesic_create_surface_point.m @@ -0,0 +1,14 @@ +function p = geodesic_create_surface_point(type,id,x,y,z) + +p.type = type; +p.id = id; + +if nargin == 3 + p.x = x(1); + p.y = x(2); + p.z = x(3); +else + p.x = x; + p.y = y; + p.z = z; +end diff --git a/geodesic/geodesic_delete.m b/geodesic/geodesic_delete.m new file mode 100644 index 0000000..e05bbc8 --- /dev/null +++ b/geodesic/geodesic_delete.m @@ -0,0 +1,14 @@ +% delete mesh, algorithm, or everything at once +% Danil Kirsanov, 09/2007 + +function object = geodesic_delete(object) + +if nargin == 0 % the simplest way to delete everything is + clear geodesic; % to unload the library +elseif strcmp(object.object_type, 'mesh') + geodesic('delete_mesh', object.id); % delete mesh and corresponding algorithms +else + geodesic('delete_algorithm', object.id); % delete a single algorithm +end + +object = []; diff --git a/geodesic/geodesic_distance_and_source.m b/geodesic/geodesic_distance_and_source.m new file mode 100644 index 0000000..f5f7779 --- /dev/null +++ b/geodesic/geodesic_distance_and_source.m @@ -0,0 +1,14 @@ +%finds best source and distance to the best source +% if distance is negative, the best source cannot be found (for example, because the propagation was stopped before it reached this point) +% Danil Kirsanov, 09/2007 + +function [source_id, distance] = geodesic_distance_and_source(algorithm, destination) + +if nargin == 2 + d = geodesic_convert_surface_points({destination}); + [source_id, distance] = geodesic('distance_and_source', algorithm.id, d); +else %return distances and sources for all vertices + [source_id, distance] = geodesic('distance_and_source', algorithm.id); +end + +source_id = source_id + 1; diff --git a/geodesic/geodesic_new_algorithm.m b/geodesic/geodesic_new_algorithm.m new file mode 100644 index 0000000..a0485ae --- /dev/null +++ b/geodesic/geodesic_new_algorithm.m @@ -0,0 +1,21 @@ +function algorithm = geodesic_new_algorithm(mesh, type, subdivision) + +if nargin == 2 + subdivision = 0; +end + +if strcmp(type, 'subdivision') & subdivision == 0 + type = 'dijkstra'; +end; + +algorithm_types = {'exact', 'subdivision', 'dijkstra'}; +type_id = find(strcmp(type, algorithm_types)); +if isempty(type_id) + disp('error: algorithm type is incorrect'); + return; +end +type_id = type_id - 1; + +algorithm.id = geodesic('new_algorithm', mesh.id, type_id, subdivision); +algorithm.type = type; +algorithm.object_type = 'algorithm'; diff --git a/geodesic/geodesic_new_mesh.m b/geodesic/geodesic_new_mesh.m new file mode 100644 index 0000000..01993f3 --- /dev/null +++ b/geodesic/geodesic_new_mesh.m @@ -0,0 +1,18 @@ +function [mesh, edge_to_vertex, edge_to_face] = geodesic_new_mesh(points, tri) + +dim = find(size(points) == 3); +if dim == 2 + points = points'; +end; + +dim = find(size(tri) == 3); +if dim == 2 + tri = tri'; +end; + +[mesh_id, edges] = geodesic('new_mesh', points, tri - 1); + +mesh.id = mesh_id; +mesh.object_type = 'mesh'; +edge_to_vertex = (edges(1:2,:) + 1)'; +edge_to_face = (edges(3:4,:) + 1)'; diff --git a/geodesic/geodesic_propagate.m b/geodesic/geodesic_propagate.m new file mode 100644 index 0000000..05fd5c0 --- /dev/null +++ b/geodesic/geodesic_propagate.m @@ -0,0 +1,16 @@ +function geodesic_propagate(algorithm, source_points, stop_points, max_distance) + +global geodesic_library; + +if nargin < 4 + max_distance = 1e100; +end + +if nargin < 3 + stop_points = []; +end + +sources = geodesic_convert_surface_points(source_points); +stops = geodesic_convert_surface_points(stop_points); + +geodesic('propagate', algorithm.id, sources, stops, max_distance); diff --git a/geodesic/geodesic_trace_back.m b/geodesic/geodesic_trace_back.m new file mode 100644 index 0000000..0a1fe40 --- /dev/null +++ b/geodesic/geodesic_trace_back.m @@ -0,0 +1,8 @@ +function path = geodesic_trace_back(algorithm, destination) + +global geodesic_library; + +tmp{1} = destination; +d = geodesic_convert_surface_points(tmp); + +path = geodesic_convert_surface_points(geodesic('trace_back', algorithm.id, d)); \ No newline at end of file diff --git a/geodesic/mesh_geodesic_distance.m b/geodesic/mesh_geodesic_distance.m new file mode 100644 index 0000000..ddff21f --- /dev/null +++ b/geodesic/mesh_geodesic_distance.m @@ -0,0 +1,22 @@ +function geo_distance = mesh_geodesic_distance(mesh, algorithm, vertices, faces); + +Nn = size(vertices,1); +geo_distance = zeros(Nn,Nn); +hh = waitbar(0, 'computing geodesic distance ...'); +for i = 1:Nn + waitbar(i/Nn) + vertex_from = i; + source_points = {geodesic_create_surface_point('vertex',vertex_from,vertices(vertex_from,:))}; + %stop_points = {geodesic_create_surface_point('vertex',vertex_to,vertices(vertex_id,:))}; + + stop_points = []; + stop_distance = 10000000; + geodesic_propagate(algorithm, source_points, stop_points, stop_distance); + + %find distances to all vertices of the mesh; in this example we have a single source, so source_id is always equal to 1... + [source_id, distances] = geodesic_distance_and_source(algorithm); + geo_distance(:,i) = distances; +end +close(hh) + + diff --git a/geodesic/mesh_geodesic_distancep.m b/geodesic/mesh_geodesic_distancep.m new file mode 100644 index 0000000..b34b6fa --- /dev/null +++ b/geodesic/mesh_geodesic_distancep.m @@ -0,0 +1,22 @@ +function geo_distance = mesh_geodesic_distancep(mesh, algorithm, vertices, faces); + +Nn = size(vertices,1); +geo_distance = zeros(Nn,Nn); +hh = waitbar(0, 'computing geodesic distance ...'); +parfor i = 1:Nn + waitbar(i/Nn) + vertex_from = i; + source_points = {geodesic_create_surface_point('vertex',vertex_from,vertices(vertex_from,:))}; + %stop_points = {geodesic_create_surface_point('vertex',vertex_to,vertices(vertex_id,:))}; + + stop_points = []; + stop_distance = 10000000; + geodesic_propagate(algorithm, source_points, stop_points, stop_distance); + + %find distances to all vertices of the mesh; in this example we have a single source, so source_id is always equal to 1... + [source_id, distances] = geodesic_distance_and_source(algorithm); + geo_distance(:,i) = distances; +end +close(hh) + + diff --git a/geodesic/readme_sccn.txt b/geodesic/readme_sccn.txt new file mode 100644 index 0000000..3e08088 --- /dev/null +++ b/geodesic/readme_sccn.txt @@ -0,0 +1,15 @@ +This is a modification of geodesic implementation by Danil Kirsanov to +make it compile as a MATLAB MEX file rather than a shared object. The +toolbox .m files are modified to call the mex file. + +The original C++ source code is available at +https://code.google.com/archive/p/geodesic/ and the Matlab toolbox can +be downloaded from MathWorks File Exchange. + +Compilation Instructions: + + $ mex geodesic.cpp strlcpy.c + +requires MATLAB and the boost library to be installed. + +Zeynep Akalin Acar, April 2021 diff --git a/geodesic/src/example0.cpp b/geodesic/src/example0.cpp new file mode 100644 index 0000000..e2d770c --- /dev/null +++ b/geodesic/src/example0.cpp @@ -0,0 +1,86 @@ +/* read mesh from file and + - if one vertex is specified, for all vertices of the mesh print their distances to this vertex + - if two vertices are specified, print the shortest path between these vertices + + Danil Kirsanov, 01/2008 +*/ +#include +#include + +#include "geodesic_algorithm_exact.h" + + +int main(int argc, char **argv) +{ + if(argc < 2) + { + std::cout << "usage: mesh_file_name [first_vertex] [second_vertex]" << std::endl; //try: "hedgehog_mesh.txt 3 14" or "flat_triangular_mesh.txt 1" + return 0; + } + + std::vector points; + std::vector faces; + + bool success = geodesic::read_mesh_from_file(argv[1],points,faces); + if(!success) + { + std::cout << "something is wrong with the input file" << std::endl; + return 0; + } + + geodesic::Mesh mesh; + mesh.initialize_mesh_data(points, faces); //create internal mesh data structure including edges + + geodesic::GeodesicAlgorithmExact algorithm(&mesh); //create exact algorithm for the mesh + + unsigned source_vertex_index = (argc == 2) ? 0 : atol(argv[2]); + + geodesic::SurfacePoint source(&mesh.vertices()[source_vertex_index]); //create source + std::vector all_sources(1,source); //in general, there could be multiple sources, but now we have only one + + if(argc > 3) //target vertex specified, compute single path + { + unsigned target_vertex_index = atol(argv[3]); + geodesic::SurfacePoint target(&mesh.vertices()[target_vertex_index]); //create source + + std::vector path; //geodesic path is a sequence of SurfacePoints + + bool const lazy_people_flag = false; //there are two ways to do exactly the same + if(lazy_people_flag) + { + algorithm.geodesic(source, target, path); //find a single source-target path + } + else //doing the same thing explicitly for educational reasons + { + double const distance_limit = geodesic::GEODESIC_INF; // no limit for propagation + std::vector stop_points(1, target); //stop propagation when the target is covered + algorithm.propagate(all_sources, distance_limit, &stop_points); //"propagate(all_sources)" is also fine, but take more time because covers the whole mesh + + algorithm.trace_back(target, path); //trace back a single path + } + + print_info_about_path(path); + for(unsigned i = 0; i +#include +#include + +#include "geodesic_algorithm_dijkstra.h" +#include "geodesic_algorithm_subdivision.h" +#include "geodesic_algorithm_exact.h" + +int main(int argc, char **argv) +{ + std::vector points; + std::vector faces; + geodesic::read_mesh_from_file("hedgehog_mesh.txt",points,faces); + + geodesic::Mesh mesh; + mesh.initialize_mesh_data(points, faces); //create internal mesh data structure including edges + + geodesic::GeodesicAlgorithmExact exact_algorithm(&mesh); //exact algorithm + geodesic::GeodesicAlgorithmDijkstra dijkstra_algorithm(&mesh); //simplest approximate algorithm: path only allowed on the edges of the mesh + unsigned const subdivision_level = 3; //three additional vertices per every edge in subdivision algorithm + geodesic::GeodesicAlgorithmSubdivision subdivision_algorithm(&mesh,2); //with subdivision_level=0 this algorithm becomes Dijkstra, with subdivision_level->infinity it becomes exact + + std::vector all_algorithms; //for simplicity, store all possible geodesic algorithms here + all_algorithms.push_back(&dijkstra_algorithm); + all_algorithms.push_back(&subdivision_algorithm); + all_algorithms.push_back(&exact_algorithm); + + std::vector sources; + sources.push_back(geodesic::SurfacePoint(&mesh.vertices()[0])); //one source is located at vertex zero + sources.push_back(geodesic::SurfacePoint(&mesh.edges()[12])); //second source is located in the middle of edge 12 + sources.push_back(geodesic::SurfacePoint(&mesh.faces()[20])); //third source is located in the middle of face 20 + + std::vector targets; //same thing with targets + targets.push_back(geodesic::SurfacePoint(&mesh.vertices().back())); + targets.push_back(geodesic::SurfacePoint(&mesh.edges()[10])); + targets.push_back(geodesic::SurfacePoint(&mesh.faces()[3])); + + for(unsigned index=0; indexname() << std::endl; + + algorithm->propagate(sources); //cover the whole mesh + algorithm->print_statistics(); + + //------------------first task: compute the pathes to the targets---- + std::vector path; + for(int i=0; itrace_back(targets[i], path); + print_info_about_path(path); + } + + //------------------second task: for each source, find the furthest vertex that it covers ---- + std::vector max_distance(sources.size(), 0.0); //distance to the furthest vertex that is covered by the given source + for(int i=0; ibest_source(p,distance); + + max_distance[best_source] = std::max(max_distance[best_source], distance); + } + + std::cout << std::endl; + for(int i=0; i +#include +#include +#include + +#include "mex.h" + +#define Xassert(expr) ((expr) ? (void) (0) : Xassert_fail(#expr, __FILE__, __LINE__)) + +void Xassert_fail(const char *, const char *, unsigned int); + +#include "geodesic_mesh.h" +#include "geodesic_algorithm_dijkstra_alternative.h" +#include "geodesic_algorithm_dijkstra.h" +#include "geodesic_algorithm_subdivision.h" +#include "geodesic_algorithm_exact.h" + +#ifdef _MSC_VER +#define strcasecmp _stricmp +#endif + +extern "C" { +size_t strlcpy(char *dst, const char *src, size_t siz); +} + +typedef std::shared_ptr mesh_shared_pointer; +std::vector meshes; + +typedef std::shared_ptr algorithm_shared_pointer; +std::vector algorithms; + +void gd_help( int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[]); + +void +Xassert_fail(const char *expr, const char *file, unsigned int line) +{ + char buf[256]; + snprintf(buf, sizeof(buf), "%s:%u assert(%s) failed!", file, line, expr); + mexErrMsgTxt(buf); +} + +static +std::size_t find_mesh_id(geodesic::Mesh* mesh) +{ + for(std::size_t i=0; i 2) + mexErrMsgTxt("expecting at most two output arguments"); + + if ( ! mxIsDouble(prhs[0]) || mxGetNumberOfDimensions(prhs[0]) != 2 ) + mexErrMsgTxt("expecting points (arg 1) to be a matrix"); + + if ( ! mxIsDouble(prhs[1]) || mxGetNumberOfDimensions(prhs[1]) != 2 ) + mexErrMsgTxt("expecting tri (arg 1) to be a matrix"); + + size = mxGetDimensions(prhs[0]); + if (size[0] != 3) + mexErrMsgTxt("points: invalid size (expected 3 columns)"); + + num_points = size[1]; + points = mxGetPr(prhs[0]); + + size = mxGetDimensions(prhs[1]); + if (size[0] != 3) + mexErrMsgTxt("tri: invalid size (expected 3 columns)"); + num_triangles = size[1]; + triangles = mxGetPr(prhs[1]); + + mesh_shared_pointer new_mesh = mesh_shared_pointer(new geodesic::Mesh); + meshes.push_back(new_mesh); + + new_mesh->initialize_mesh_data(num_points, + points, + num_triangles, + triangles); + + // mesh_id + plhs[0] = mxCreateDoubleScalar(meshes.size() - 1); + + if (nlhs < 2 ) + return; + + num_edges = new_mesh->edges().size(); + + plhs[1] = mxCreateDoubleMatrix(4, num_edges, mxREAL); + + edges = mxGetPr(plhs[1]); + + if (edges == NULL) + mexErrMsgTxt("Failed to allocate edges!"); + + for(std::size_t i=0; iedges()[i]; + double* buffer = edges + 4*i; + + buffer[0] = edge.adjacent_vertices()[0]->id(); + buffer[1] = edge.adjacent_vertices()[1]->id(); + buffer[2] = edge.adjacent_faces()[0]->id(); + buffer[3] = edge.adjacent_faces().size() == 2 ? + edge.adjacent_faces()[1]->id() : -1; + } +} + +// algorithm_id = geodesic('new_algorithm', mesh_id, type_id, subdivision); +void +gd_new_algorithm(int nlhs, mxArray *plhs[], + int nrhs, const mxArray*prhs[]) +{ + long mesh_id, type_id, subdivision; + + if (nrhs != 3) + mexErrMsgTxt("expecting three input arguments"); + + if (nlhs != 1) + mexErrMsgTxt("expecting one output argument"); + + if (! (mxIsNumeric(prhs[0]) && mxIsScalar(prhs[0]))) + mexErrMsgTxt("expecting mesh_id (arg 1) to be a scalar"); + + if (! (mxIsNumeric(prhs[1]) && mxIsScalar(prhs[1]))) + mexErrMsgTxt("expecting type_id (arg 2) to be a scalar"); + + if (! (mxIsNumeric(prhs[2]) && mxIsScalar(prhs[2]))) + mexErrMsgTxt("expecting subdividion (arg 3) to be a scalar"); + + mesh_id = mxGetScalar(prhs[0]); + type_id = mxGetScalar(prhs[1]); + subdivision = mxGetScalar(prhs[2]); + + if (mesh_id < 0 || mesh_id >= meshes.size()) + mexErrMsgTxt("invalid mesh_id"); + + if (subdivision == 0 && type_id == 1) + type_id = 2; + + geodesic::Mesh* mesh = meshes[mesh_id].get(); + geodesic::GeodesicAlgorithmBase* algorithm; + + switch(type_id) { + case 2: //DIJKSTRA + { + algorithm = new geodesic::GeodesicAlgorithmDijkstra(mesh); + break; + } + case 1: //SUBDIVISION: + { + algorithm = new geodesic::GeodesicAlgorithmSubdivision(mesh, subdivision); + break; + } + default: // EXACT + { + algorithm = new geodesic::GeodesicAlgorithmExact(mesh); + break; + } + } + + algorithms.push_back(algorithm_shared_pointer(algorithm)); + + // mesh_id + plhs[0] = mxCreateDoubleScalar(algorithms.size() - 1); +} + +// geodesic('delete_mesh', mesh_id); +void +gd_delete_mesh(int nlhs, mxArray *plhs[], + int nrhs, const mxArray*prhs[]) +{ + long mesh_id; + + if (nrhs != 1) + mexErrMsgTxt("expecting one input argument"); + + if (! (mxIsNumeric(prhs[0]) && mxIsScalar(prhs[0]))) + mexErrMsgTxt("expecting mesh_id (arg 1) to be a scalar"); + + mesh_id = mxGetScalar(prhs[0]); + + if (mesh_id < 0 || mesh_id >= meshes.size()) + mexErrMsgTxt("invalid mesh_id"); + + geodesic::Mesh* mesh = meshes[mesh_id].get(); + for(std::size_t i=0; imesh() == mesh) + { + algorithms[i] = algorithm_shared_pointer(); + } + } + + meshes[mesh_id] = mesh_shared_pointer(); +} + +// geodesic('delete_algorithm', algorithm_id); +void +gd_delete_algorithm(int nlhs, mxArray *plhs[], + int nrhs, const mxArray*prhs[]) +{ + long id; + + if (nrhs != 1) + mexErrMsgTxt("expecting one input argument"); + + if (! (mxIsNumeric(prhs[0]) && mxIsScalar(prhs[0]))) + mexErrMsgTxt("expecting algorithm_id (arg 1) to be a scalar"); + + id = mxGetScalar(prhs[0]); + + if (id < 0 || id >= algorithms.size()) + mexErrMsgTxt("invalid algorithm_id"); + + algorithms[id] = algorithm_shared_pointer(); +} + +// geodesic('propagate', algorithm, source_points, stop_points, max_distance); +void +gd_propagate(int nlhs, mxArray *plhs[], + int nrhs, const mxArray*prhs[]) +{ + const mwSize *size; + mwSize num_sources, num_stop_points; + double *source_points, *stop_points = NULL, max_distance; + long id; + + if (nrhs != 4) + mexErrMsgTxt("expecting four input arguments"); + + if (! (mxIsNumeric(prhs[0]) && mxIsScalar(prhs[0]))) + mexErrMsgTxt("expecting algorithm_id (arg 1) to be a scalar"); + + if (! mxIsDouble(prhs[1]) || mxGetNumberOfDimensions(prhs[1]) != 2 ) + mexErrMsgTxt("expecting source_points (arg 2) to be a matrix/vector"); + else { + size = mxGetDimensions(prhs[1]); + num_sources = size[0] * size[1]; + if ((num_sources % 5) != 0) + mexErrMsgTxt("source_points: invalid size (expected multiple of 5 )"); + num_sources = num_sources / 5; + } + + if (mxIsEmpty(prhs[2])) + num_stop_points = 0; + else if (! mxIsDouble(prhs[2]) || mxGetNumberOfDimensions(prhs[2]) != 2 ) + mexErrMsgTxt("expecting stop_points (arg 3) to be a matrix/vector"); + else { + size = mxGetDimensions(prhs[2]); + num_stop_points = size[0] * size[1]; + if ((num_stop_points % 5) != 0) + mexErrMsgTxt("stop_points: invalid size (expected multiple of 5 )"); + num_stop_points = num_stop_points / 5; + } + + if (! (mxIsNumeric(prhs[3]) && mxIsScalar(prhs[3]))) + mexErrMsgTxt("expecting max_distance (arg 4) to be a scalar"); + + id = mxGetScalar(prhs[0]); + source_points = mxGetPr(prhs[1]); + if (num_stop_points > 0) + stop_points = mxGetPr(prhs[2]); + + max_distance = mxGetScalar(prhs[3]); + + if (id < 0 || id >= algorithms.size()) + mexErrMsgTxt("invalid algorithm_id"); + + std::vector sources(num_sources); + + geodesic::Mesh* mesh = algorithms[id]->mesh(); + for(std::size_t i=0; i stop(num_stop_points); + for(std::size_t i=0; ipropagate(sources, + max_distance, + &stop); +} + +// path = geodesic('trace_back', algorithm_id, destination); +void +gd_trace_back(int nlhs, mxArray *plhs[], + int nrhs, const mxArray*prhs[]) +{ + const mwSize *size; + double *destination, *path; + long id; + + if (nrhs != 2) + mexErrMsgTxt("expecting two input arguments"); + + if (nlhs != 1) + mexErrMsgTxt("expecting one output argument"); + + if (!(mxIsNumeric(prhs[0]) && mxIsScalar(prhs[0]))) + mexErrMsgTxt("expecting algorithm_id (arg 1) to be a scalar"); + + id = mxGetScalar(prhs[0]); + if (id < 0 || id >= algorithms.size()) + mexErrMsgTxt("invalid algorithm_id"); + + if (! mxIsDouble(prhs[1]) || mxGetNumberOfDimensions(prhs[1]) != 2 ) + mexErrMsgTxt("expecting destination (arg 2) to be a matrix/vector"); + + size = mxGetDimensions(prhs[1]); + long num_dest = size[0] * size[1]; + if (num_dest != 5) + mexErrMsgTxt("destination: must be a single point"); + destination = mxGetPr(prhs[1]); + + geodesic::SurfacePoint point; + geodesic::GeodesicAlgorithmBase* algorithm = algorithms[id].get(); + std::vector output_path; + + geodesic::fill_surface_point_structure(&point, + destination, + algorithm->mesh()); + + algorithm->trace_back(point, output_path); + + std::size_t mesh_id = find_mesh_id(algorithm->mesh()); + + plhs[0] = mxCreateDoubleMatrix(1, output_path.size()*5, mxREAL); + + path = mxGetPr(plhs[0]); + + for(std::size_t i=0; i 2) + mexErrMsgTxt("expecting at most two input arguments"); + + if (nlhs > 2) + mexErrMsgTxt("expecting at most two output arguments"); + + if (!(mxIsNumeric(prhs[0]) && mxIsScalar(prhs[0]))) + mexErrMsgTxt("expecting algorithm_id (arg 1) to be a scalar"); + + id = mxGetScalar(prhs[0]); + if (id < 0 || id >= algorithms.size()) + mexErrMsgTxt("invalid algorithm_id"); + + geodesic::GeodesicAlgorithmBase* algorithm = algorithms[id].get(); + geodesic::Mesh* mesh = algorithm->mesh(); + + if (nrhs < 2) { // for all vertices + plhs[0] = mxCreateDoubleMatrix(1, mesh->vertices().size(), mxREAL); + plhs[1] = mxCreateDoubleMatrix(1, mesh->vertices().size(), mxREAL); + double *sources = mxGetPr(plhs[0]); + double *distances = mxGetPr(plhs[1]); + + for(std::size_t i = 0; i < mesh->vertices().size(); ++i) { + geodesic::SurfacePoint point(&mesh->vertices()[i]); + sources[i] = algorithm->best_source(point, distances[i]); + } + } else { + // for destination vertex + if (! mxIsDouble(prhs[1]) || mxGetNumberOfDimensions(prhs[1]) != 2 ) + mexErrMsgTxt("expecting destination (arg 2) to be a matrix/vector"); + + size = mxGetDimensions(prhs[1]); + long num_dest = size[0] * size[1]; + if (num_dest != 5) + mexErrMsgTxt("destination: must be a single point"); + destination = mxGetPr(prhs[1]); + + geodesic::SurfacePoint point; + geodesic::fill_surface_point_structure(&point, destination, mesh); + double best_source_distance; + std::size_t best_source = algorithm->best_source(point, best_source_distance); + + plhs[0] = mxCreateDoubleScalar(best_source); + plhs[1] = mxCreateDoubleScalar(best_source_distance); + } +} + +struct command { + const char *cm_name; + const char *cm_proto; + const char *cm_desc; + void (*cm_func)(int, mxArray *[], int, const mxArray*[]); +}; + + +struct command gd_commands[] = { + {"new_mesh", "[mesh_id, edges] = geodesic('new_mesh', points, triangles)", + "creates new mesh", gd_new_mesh}, + {"new_algorithm", "algorithm_id = geodesic('new_algorithm', mesh_id, type_id, subdivision)", + "creates a geodesic algorithm for a given mesh", gd_new_algorithm}, + {"delete_mesh", "geodesic('delete_mesh', mesh_id)", + "delete mesh and all associated algorithms", gd_delete_mesh}, + {"delete_algorithm","geodesic('delete_algorithm', algorithm_id)", + "deletes a given algorithm", gd_delete_algorithm}, + {"propagate", "geodesic('propagate', algorithm, source_points, stop_points, max_distance)", + "compute distance field for given source points", gd_propagate}, + {"trace_back", "path = geodesic('trace_back', algorithm_id, destination)", + "using procomputed distance field, compute a shortest path from destination to the closest source", + gd_trace_back}, + {"distance_and_source", + "[source_id, distances] = geodesic('distance_and_source', algorithm_id, destination)", + "quickly find what source this point beints to and what is the distance to this source", + gd_distance_and_source}, + {"help", "geodesic('help')", "show help text", gd_help}, + {"", "", "", NULL}}; + +void +gd_help( int nlhs, mxArray *plhs[], + int nrhs, const mxArray*prhs[]) +{ + mexPrintf("usage: geodesic('command', ...);\n\n"); + mexPrintf("where 'command' is:\n"); + + for (struct command *c = gd_commands; c->cm_func; c++) { + mexPrintf(" '%s': %s\n", c->cm_name, c->cm_desc); + mexPrintf(" %s\n", c->cm_proto); + } +} + + +void +mexFunction( int nlhs, mxArray *plhs[], + int nrhs, const mxArray*prhs[] ) +{ + static int need_setup = 1; + const char *errmsg = NULL; + struct command *c; + char cmd[32], *cp; + + cp = NULL; + + if (nrhs < 1) + mexErrMsgTxt("Usage: geodesic('command', ...)"); + + cp = mxArrayToString(prhs[0]); + + if (cp == NULL) { + errmsg = "expecting command (arg 1) to be a string"; + goto exit; + } + if (strlcpy(cmd, cp, sizeof(cmd)) >= sizeof(cmd)) { + errmsg = "invalid command, use 'help' for a list."; + mxFree(cp); + goto exit; + } + + mxFree(cp); + + prhs++; + nrhs--; + + for (c = gd_commands; c->cm_func; c++) { + if (strcasecmp(cmd, c->cm_name) == 0) { + c->cm_func(nlhs, plhs, nrhs, prhs); + goto exit; + } + } + + errmsg = "unknown command, use 'help' for a list."; + +exit: + if (errmsg) + mexErrMsgTxt(errmsg); +} diff --git a/geodesic/src/geodesic_algorithm_base.h b/geodesic/src/geodesic_algorithm_base.h new file mode 100644 index 0000000..b7c7b89 --- /dev/null +++ b/geodesic/src/geodesic_algorithm_base.h @@ -0,0 +1,191 @@ +//Copyright (C) 2008 Danil Kirsanov, MIT License + +#ifndef GEODESIC_ALGORITHM_BASE_122806 +#define GEODESIC_ALGORITHM_BASE_122806 + +#include "geodesic_mesh.h" +#include "geodesic_constants_and_simple_functions.h" +#include +#include + +namespace geodesic{ + +class GeodesicAlgorithmBase +{ +public: + enum AlgorithmType + { + EXACT, + DIJKSTRA, + SUBDIVISION, + UNDEFINED_ALGORITHM + }; + + GeodesicAlgorithmBase(geodesic::Mesh* mesh): + m_type(UNDEFINED_ALGORITHM), + m_max_propagation_distance(1e100), + m_mesh(mesh) + {}; + + virtual ~GeodesicAlgorithmBase(){}; + + virtual void propagate(std::vector& sources, + double max_propagation_distance = GEODESIC_INF, //propagation algorithm stops after reaching the certain distance from the source + std::vector* stop_points = NULL) = 0; //or after ensuring that all the stop_points are covered + + virtual void trace_back(SurfacePoint& destination, //trace back piecewise-linear path + std::vector& path) = 0; + + void geodesic(SurfacePoint& source, + SurfacePoint& destination, + std::vector& path); //lazy people can find geodesic path with one function call + + void geodesic(std::vector& sources, + std::vector& destinations, + std::vector >& paths); //lazy people can find geodesic paths with one function call + + virtual unsigned best_source(SurfacePoint& point, //after propagation step is done, quickly find what source this point belongs to and what is the distance to this source + double& best_source_distance) = 0; + + virtual void print_statistics() //print info about timing and memory usage in the propagation step of the algorithm + { + std::cout << "propagation step took " << m_time_consumed << " seconds " << std::endl; + }; + + AlgorithmType type(){return m_type;}; + + virtual std::string name(); + + geodesic::Mesh* mesh(){return m_mesh;}; +protected: + + void set_stop_conditions(std::vector* stop_points, + double stop_distance); + double stop_distance() + { + return m_max_propagation_distance; + } + + AlgorithmType m_type; // type of the algorithm + + typedef std::pair stop_vertex_with_distace_type; + std::vector m_stop_vertices; // algorithm stops propagation after covering certain vertices + double m_max_propagation_distance; // or reaching the certain distance + + geodesic::Mesh* m_mesh; + + double m_time_consumed; //how much time does the propagation step takes + double m_propagation_distance_stopped; //at what distance (if any) the propagation algorithm stopped +}; + +inline double length(std::vector& path) +{ + double length = 0; + if(!path.empty()) + { + for(unsigned i=0; i& path) +{ + std::cout << "number of the points in the path = " << path.size() + << ", length of the path = " << length(path) + << std::endl; +} + +inline std::string GeodesicAlgorithmBase::name() +{ + switch(m_type) + { + case EXACT: + return "exact"; + case DIJKSTRA: + return "dijkstra"; + case SUBDIVISION: + return "subdivision"; + default: + case UNDEFINED_ALGORITHM: + return "undefined"; + } +} + +inline void GeodesicAlgorithmBase::geodesic(SurfacePoint& source, + SurfacePoint& destination, + std::vector& path) //lazy people can find geodesic path with one function call +{ + std::vector sources(1, source); + std::vector stop_points(1, destination); + double const max_propagation_distance = GEODESIC_INF; + + propagate(sources, + max_propagation_distance, + &stop_points); + + trace_back(destination, path); +} + +inline void GeodesicAlgorithmBase::geodesic(std::vector& sources, + std::vector& destinations, + std::vector >& paths) //lazy people can find geodesic paths with one function call +{ + double const max_propagation_distance = GEODESIC_INF; + + propagate(sources, + max_propagation_distance, + &destinations); //we use desinations as stop points + + paths.resize(destinations.size()); + + for(unsigned i=0; i* stop_points, + double stop_distance) +{ + m_max_propagation_distance = stop_distance; + + if(!stop_points) + { + m_stop_vertices.clear(); + return; + } + + m_stop_vertices.resize(stop_points->size()); + + std::vector possible_vertices; + for(unsigned i = 0; i < stop_points->size(); ++i) + { + SurfacePoint* point = &(*stop_points)[i]; + + possible_vertices.clear(); + m_mesh->closest_vertices(point, &possible_vertices); + + vertex_pointer closest_vertex = NULL; + double min_distance = 1e100; + for(unsigned j = 0; j < possible_vertices.size(); ++j) + { + double distance = point->distance(possible_vertices[j]); + if(distance < min_distance) + { + min_distance = distance; + closest_vertex = possible_vertices[j]; + } + } + Xassert(closest_vertex); + + m_stop_vertices[i].first = closest_vertex; + m_stop_vertices[i].second = min_distance; + } +} + +}//geodesic + +#endif //GEODESIC_ALGORITHM_BASE_122806 diff --git a/geodesic/src/geodesic_algorithm_dijkstra.h b/geodesic/src/geodesic_algorithm_dijkstra.h new file mode 100644 index 0000000..e37c21e --- /dev/null +++ b/geodesic/src/geodesic_algorithm_dijkstra.h @@ -0,0 +1,139 @@ +//Copyright (C) 2008 Danil Kirsanov, MIT License +#ifndef GEODESIC_ALGORITHM_DIJKSTRA_010506 +#define GEODESIC_ALGORITHM_DIJKSTRA_010506 + +#include "geodesic_algorithm_graph_base.h" +#include "geodesic_mesh_elements.h" +#include +#include + +namespace geodesic{ + +class DijkstraNode +{ + typedef DijkstraNode* node_pointer; +public: + DijkstraNode(){}; + ~DijkstraNode(){}; + + double& distance_from_source(){return m_distance;}; + node_pointer& previous(){return m_previous;}; + unsigned& source_index(){return m_source_index;}; + vertex_pointer& vertex(){return m_vertex;}; + + void clear() + { + m_distance = GEODESIC_INF; + m_previous = NULL; + } + + bool operator()(node_pointer const s1, node_pointer const s2) const + { + return s1->distance_from_source() != s2->distance_from_source() ? + s1->distance_from_source() < s2->distance_from_source() : + s1->vertex()->id() < s2->vertex()->id(); + }; + + double distance(SurfacePoint* p) + { + return m_vertex->distance(p); + } + + SurfacePoint surface_point() + { + return SurfacePoint(m_vertex); + } + +private: + double m_distance; //distance to the closest source + unsigned m_source_index; //closest source index + node_pointer m_previous; //previous node in the geodesic path + vertex_pointer m_vertex; //correspoding vertex +}; + +class GeodesicAlgorithmDijkstra: public GeodesicAlgorithmGraphBase +{ +public: + typedef DijkstraNode Node; + typedef Node* node_pointer; + + GeodesicAlgorithmDijkstra(geodesic::Mesh* mesh): + GeodesicAlgorithmGraphBase(mesh) + { + m_type = DIJKSTRA; + + m_nodes.resize(mesh->vertices().size()); + for(unsigned i=0; ivertices()[i]; + } + }; + + ~GeodesicAlgorithmDijkstra(){}; + +protected: + + void list_nodes_visible_from_source(MeshElementBase* p, + std::vector& storage); //list all nodes that belong to this mesh element + + void list_nodes_visible_from_node(node_pointer node, //list all nodes that belong to this mesh element + std::vector& storage, + std::vector& distances, + double threshold_distance); //list only the nodes whose current distance is larger than the threshold +}; + +void GeodesicAlgorithmDijkstra::list_nodes_visible_from_source(MeshElementBase* p, + std::vector& storage) +{ + Xassert(p->type() != UNDEFINED_POINT); + + if(p->type() == FACE) + { + face_pointer f = static_cast(p); + for(unsigned i=0; i<3; ++i) + { + vertex_pointer v = f->adjacent_vertices()[i]; + storage.push_back(&m_nodes[node_index(v)]); + } + } + else if(p->type() == EDGE) + { + edge_pointer e = static_cast(p); + for(unsigned i=0; i<2; ++i) + { + vertex_pointer v = e->adjacent_vertices()[i]; + storage.push_back(&m_nodes[node_index(v)]); + } + } + else //VERTEX + { + vertex_pointer v = static_cast(p); + storage.push_back(&m_nodes[node_index(v)]); + } +} + +inline void GeodesicAlgorithmDijkstra::list_nodes_visible_from_node(node_pointer node, //list all nodes that belong to this mesh element + std::vector& storage, + std::vector& distances, + double threshold_distance) +{ + vertex_pointer v = node->vertex(); + Xassert(storage.size() == distances.size()); + + for(unsigned i=0; iadjacent_edges().size(); ++i) + { + edge_pointer e = v->adjacent_edges()[i]; + vertex_pointer new_v = e->opposite_vertex(v); + node_pointer new_node = &m_nodes[node_index(new_v)]; + + if(new_node->distance_from_source() > threshold_distance + e->length()) + { + storage.push_back(new_node); + distances.push_back(e->length()); + } + } +} + +} //geodesic + +#endif //GEODESIC_ALGORITHM_DIJKSTRA_010506 diff --git a/geodesic/src/geodesic_algorithm_dijkstra_alternative.h b/geodesic/src/geodesic_algorithm_dijkstra_alternative.h new file mode 100644 index 0000000..137a618 --- /dev/null +++ b/geodesic/src/geodesic_algorithm_dijkstra_alternative.h @@ -0,0 +1,282 @@ +//Copyright (C) 2008 Danil Kirsanov, MIT License +#ifndef GEODESIC_ALGORITHM_DIJKSTRA_ALTERNATIVE_010506 +#define GEODESIC_ALGORITHM_DIJKSTRA_ALTERNATIVE_010506 + +#include "geodesic_algorithm_base.h" +#include "geodesic_mesh_elements.h" +#include +#include + +namespace geodesic{ + +class DijkstraNode1 +{ + typedef DijkstraNode1* node_pointer; +public: + DijkstraNode1(){}; + ~DijkstraNode1(){}; + + double& distance_from_source(){return m_distance;}; + node_pointer& previous(){return m_previous;}; + unsigned& source_index(){return m_source_index;}; + vertex_pointer& vertex(){return m_vertex;}; + + void clear() + { + m_distance = GEODESIC_INF; + m_previous = NULL; + } + + bool operator()(node_pointer const s1, node_pointer const s2) const + { + return s1->distance_from_source() != s2->distance_from_source() ? + s1->distance_from_source() < s2->distance_from_source() : + s1->vertex()->id() < s2->vertex()->id(); + }; + +private: + double m_distance; //distance to the closest source + unsigned m_source_index; //closest source index + node_pointer m_previous; //previous node in the geodesic path + vertex_pointer m_vertex; //correspoding vertex +}; + +class GeodesicAlgorithmDijkstraAlternative: public GeodesicAlgorithmBase +{ +public: + typedef DijkstraNode1 Node; + typedef Node* node_pointer; + + GeodesicAlgorithmDijkstraAlternative(geodesic::Mesh* mesh = NULL): + GeodesicAlgorithmBase(mesh), + m_nodes(mesh->vertices().size()) + { + m_type = DIJKSTRA; + for(unsigned i=0; ivertices()[i]; + } + }; + + ~GeodesicAlgorithmDijkstraAlternative(){}; + + virtual void propagate(std::vector& sources, + double max_propagation_distance = GEODESIC_INF, //propagation algorithm stops after reaching the certain distance from the source + std::vector* stop_points = NULL); //or after ensuring that all the stop_points are covered + + virtual void trace_back(SurfacePoint& destination, //trace back piecewise-linear path + std::vector& path); + + virtual unsigned best_source(SurfacePoint& point, //quickly find what source this point belongs to and what is the distance to this source + double& best_source_distance); +private: + + void set_sources(std::vector& sources) + { + m_sources = sources; + } + + bool check_stop_conditions(unsigned& index); + + std::vector m_nodes; //nodes of the subdivision graph located on the vertices + + std::vector m_sources; //for simplicity, we keep sources as they are + + typedef std::set queue_type; + queue_type m_queue; +}; + +inline unsigned GeodesicAlgorithmDijkstraAlternative::best_source(SurfacePoint& point, //quickly find what source this point belongs to and what is the distance to this source + double& best_source_distance) +{ + if(point.type() == VERTEX) + { + vertex_pointer v = (vertex_pointer)point.base_element(); + node_pointer node = &m_nodes[v->id()]; + best_source_distance = node->distance_from_source(); + return node->source_index(); + } + else + { + std::vector possible_vertices; //initialize vertices directly visible from sources + m_mesh->closest_vertices(&point, &possible_vertices); + + best_source_distance = GEODESIC_INF; + vertex_pointer min_vertex = NULL; + for(unsigned i=0; iid()].distance_from_source(); + double distance_from_dest = v->distance(&point); + if(distance_from_source + distance_from_dest < best_source_distance) + { + best_source_distance = distance_from_source + distance_from_dest; + min_vertex = v; + } + } + Xassert(min_vertex); + node_pointer node = &m_nodes[min_vertex->id()]; + return node->source_index(); + } +} + +inline void GeodesicAlgorithmDijkstraAlternative::trace_back(SurfacePoint& destination, //trace back piecewise-linear path + std::vector& path) +{ + path.clear(); + path.push_back(destination); + + if(destination.type() != VERTEX) //snap to the closest vertex + { + std::vector possible_vertices; //initialize vertices directly visible from sources + m_mesh->closest_vertices(&destination, &possible_vertices); + + double min_distance = GEODESIC_INF; + vertex_pointer min_vertex = NULL; + for(unsigned i=0; iid()].distance_from_source(); + double distance_from_dest = v->distance(&destination); + if(distance_from_source + distance_from_dest < min_distance) + { + min_distance = distance_from_source + distance_from_dest; + min_vertex = v; + } + } + Xassert(min_vertex); + path.push_back(SurfacePoint(min_vertex)); + } + + node_pointer node = &m_nodes[path.back().base_element()->id()]; + while(node->previous()) //follow the path + { + node = node->previous(); + path.push_back(SurfacePoint(node->vertex())); + } + + SurfacePoint& source = m_sources[node->source_index()]; //add source to the path if it is not already there + if(source.type() != VERTEX || + source.base_element()->id() != node->vertex()->id()) + { + path.push_back(source); + } +} + +inline void GeodesicAlgorithmDijkstraAlternative::propagate(std::vector& sources, + double max_propagation_distance, //propagation algorithm stops after reaching the certain distance from the source + std::vector* stop_points) //or after ensuring that all the stop_points are covered +{ + set_stop_conditions(stop_points, max_propagation_distance); + set_sources(sources); + + m_queue.clear(); //clear everything + for(unsigned i=0; i visible_vertices; //initialize vertices directly visible from sources + for(unsigned i=0; iclosest_vertices(s, &visible_vertices); + for(unsigned j=0; jdistance(v); + + node_pointer node = &m_nodes[v->id()]; + if(distance < node->distance_from_source()) + { + node->distance_from_source() = distance; + node->source_index() = i; + node->previous() = NULL; + } + } + visible_vertices.clear(); + } + + for(unsigned i=0; idistance_from_source()<< std::endl; + } + + node_pointer min_node = *m_queue.begin(); + m_queue.erase(m_queue.begin()); + + vertex_pointer v = min_node->vertex(); + + for(unsigned i=0; iadjacent_edges().size(); ++i) //update all the adgecent vertices + { + edge_pointer e = v->adjacent_edges()[i]; + vertex_pointer next_v = e->opposite_vertex(v); + node_pointer next_node = &m_nodes[next_v->id()]; + //double current_distance = + if(next_node->distance_from_source() > min_node->distance_from_source() + e->length()) + { + if(next_node->distance_from_source() < GEODESIC_INF) //remove it from the queue + { + queue_type::iterator iter = m_queue.find(next_node); + Xassert(iter != m_queue.end()); + m_queue.erase(iter); + } + next_node->distance_from_source() = min_node->distance_from_source() + e->length(); + next_node->source_index() = min_node->source_index(); + next_node->previous() = min_node; + m_queue.insert(next_node); + } + } + } + //std::cout << std::endl; + + clock_t finish = clock(); + m_time_consumed = (static_cast(finish)-static_cast(start))/CLOCKS_PER_SEC; +} + +inline bool GeodesicAlgorithmDijkstraAlternative::check_stop_conditions(unsigned& index) +{ + double queue_min_distance = (*m_queue.begin())->distance_from_source(); + + if(queue_min_distance < m_max_propagation_distance) + { + return false; + } + + while(index < m_stop_vertices.size()) + { + vertex_pointer v = m_stop_vertices[index].first; + Node& node = m_nodes[v->id()]; + if(queue_min_distance < node.distance_from_source() + m_stop_vertices[index].second) + { + return false; + } + ++index; + } + return true; +} + +} //geodesic + +#endif //GEODESIC_ALGORITHM_DIJKSTRA_ALTERNATIVE_010506 diff --git a/geodesic/src/geodesic_algorithm_exact.h b/geodesic/src/geodesic_algorithm_exact.h new file mode 100644 index 0000000..de05e85 --- /dev/null +++ b/geodesic/src/geodesic_algorithm_exact.h @@ -0,0 +1,1381 @@ +//Copyright (C) 2008 Danil Kirsanov, MIT License +#ifndef GEODESIC_ALGORITHM_EXACT_20071231 +#define GEODESIC_ALGORITHM_EXACT_20071231 + +#include "geodesic_memory.h" +#include "geodesic_algorithm_base.h" +#include "geodesic_algorithm_exact_elements.h" +#include +#include +#include + +#include + +namespace geodesic{ + +class GeodesicAlgorithmExact : public GeodesicAlgorithmBase +{ +public: + GeodesicAlgorithmExact(geodesic::Mesh* mesh): + GeodesicAlgorithmBase(mesh), + m_memory_allocator(mesh->edges().size(), mesh->edges().size()), + m_edge_interval_lists(mesh->edges().size()) + { + m_type = EXACT; + + for(unsigned i=0; iedges()[i]); + } + }; + + ~GeodesicAlgorithmExact(){}; + + void propagate(std::vector& sources, + double max_propagation_distance = GEODESIC_INF, //propagation algorithm stops after reaching the certain distance from the source + std::vector* stop_points = NULL); //or after ensuring that all the stop_points are covered + + void trace_back(SurfacePoint& destination, //trace back piecewise-linear path + std::vector& path); + + unsigned best_source(SurfacePoint& point, //quickly find what source this point belongs to and what is the distance to this source + double& best_source_distance); + + void print_statistics(); + +private: + typedef std::set IntervalQueue; + + void update_list_and_queue(list_pointer list, + IntervalWithStop* candidates, //up to two candidates + unsigned num_candidates); + + unsigned compute_propagated_parameters(double pseudo_x, + double pseudo_y, + double d, //parameters of the interval + double start, + double end, //start/end of the interval + double alpha, //corner angle + double L, //length of the new edge + bool first_interval, //if it is the first interval on the edge + bool last_interval, + bool turn_left, + bool turn_right, + IntervalWithStop* candidates); //if it is the last interval on the edge + + void construct_propagated_intervals(bool invert, + edge_pointer edge, + face_pointer face, //constructs iNew from the rest of the data + IntervalWithStop* candidates, + unsigned& num_candidates, + interval_pointer source_interval); + + double compute_positive_intersection(double start, + double pseudo_x, + double pseudo_y, + double sin_alpha, + double cos_alpha); //used in construct_propagated_intervals + + unsigned intersect_intervals(interval_pointer zero, + IntervalWithStop* one); //intersecting two intervals with up to three intervals in the end + + interval_pointer best_first_interval(SurfacePoint& point, + double& best_total_distance, + double& best_interval_position, + unsigned& best_source_index); + + bool check_stop_conditions(unsigned& index); + + void clear() + { + m_memory_allocator.clear(); + m_queue.clear(); + for(unsigned i=0; iid()]; + }; + + void set_sources(std::vector& sources) + { + m_sources.initialize(sources); + } + + void initialize_propagation_data(); + + void list_edges_visible_from_source(MeshElementBase* p, + std::vector& storage); //used in initialization + + long visible_from_source(SurfacePoint& point); //used in backtracing + + void best_point_on_the_edge_set(SurfacePoint& point, + std::vector const& storage, + interval_pointer& best_interval, + double& best_total_distance, + double& best_interval_position); + + void possible_traceback_edges(SurfacePoint& point, + std::vector& storage); + + bool erase_from_queue(interval_pointer p); + + IntervalQueue m_queue; //interval queue + + MemoryAllocator m_memory_allocator; //quickly allocate and deallocate intervals + std::vector m_edge_interval_lists; //every edge has its interval data + + enum MapType {OLD, NEW}; //used for interval intersection + MapType map[5]; + double start[6]; + interval_pointer i_new[5]; + + unsigned m_queue_max_size; //used for statistics + unsigned m_iterations; //used for statistics + + SortedSources m_sources; +}; + +inline void GeodesicAlgorithmExact::best_point_on_the_edge_set(SurfacePoint& point, + std::vector const& storage, + interval_pointer& best_interval, + double& best_total_distance, + double& best_interval_position) +{ + best_total_distance = 1e100; + for(unsigned i=0; ifind_closest_point(&point, + offset, + distance, + interval); + + if(distance < best_total_distance) + { + best_interval = interval; + best_total_distance = distance; + best_interval_position = offset; + } + } +} + +inline void GeodesicAlgorithmExact::possible_traceback_edges(SurfacePoint& point, + std::vector& storage) +{ + storage.clear(); + + if(point.type() == VERTEX) + { + vertex_pointer v = static_cast(point.base_element()); + for(unsigned i=0; iadjacent_faces().size(); ++i) + { + face_pointer f = v->adjacent_faces()[i]; + storage.push_back(f->opposite_edge(v)); + } + } + else if(point.type() == EDGE) + { + edge_pointer e = static_cast(point.base_element()); + for(unsigned i=0; iadjacent_faces().size(); ++i) + { + face_pointer f = e->adjacent_faces()[i]; + + storage.push_back(f->next_edge(e,e->v0())); + storage.push_back(f->next_edge(e,e->v1())); + } + } + else + { + face_pointer f = static_cast(point.base_element()); + storage.push_back(f->adjacent_edges()[0]); + storage.push_back(f->adjacent_edges()[1]); + storage.push_back(f->adjacent_edges()[2]); + } +} + + +inline long GeodesicAlgorithmExact::visible_from_source(SurfacePoint& point) //negative if not visible +{ + Xassert(point.type() != UNDEFINED_POINT); + + if(point.type() == EDGE) + { + edge_pointer e = static_cast(point.base_element()); + list_pointer list = interval_list(e); + double position = std::min(point.distance(e->v0()), e->length()); + interval_pointer interval = list->covering_interval(position); + //Xassert(interval); + if(interval && interval->visible_from_source()) + { + return (long)interval->source_index(); + } + else + { + return -1; + } + } + else if(point.type() == FACE) + { + return -1; + } + else if(point.type() == VERTEX) + { + vertex_pointer v = static_cast(point.base_element()); + for(unsigned i=0; iadjacent_edges().size(); ++i) + { + edge_pointer e = v->adjacent_edges()[i]; + list_pointer list = interval_list(e); + + double position = e->v0()->id() == v->id() ? 0.0 : e->length(); + interval_pointer interval = list->covering_interval(position); + if(interval && interval->visible_from_source()) + { + return (long)interval->source_index(); + } + } + + return -1; + } + + Xassert(0); + return 0; +} + +inline double GeodesicAlgorithmExact::compute_positive_intersection(double start, + double pseudo_x, + double pseudo_y, + double sin_alpha, + double cos_alpha) +{ + Xassert(pseudo_y < 0); + + double denominator = sin_alpha*(pseudo_x - start) - cos_alpha*pseudo_y; + if(denominator<0.0) + { + return -1.0; + } + + double numerator = -pseudo_y*start; + + if(numerator < 1e-30) + { + return 0.0; + } + + if(denominator < 1e-30) + { + return -1.0; + } + + return numerator/denominator; +} + +inline void GeodesicAlgorithmExact::list_edges_visible_from_source(MeshElementBase* p, + std::vector& storage) +{ + Xassert(p->type() != UNDEFINED_POINT); + + if(p->type() == FACE) + { + face_pointer f = static_cast(p); + for(unsigned i=0; i<3; ++i) + { + storage.push_back(f->adjacent_edges()[i]); + } + } + else if(p->type() == EDGE) + { + edge_pointer e = static_cast(p); + storage.push_back(e); + } + else //VERTEX + { + vertex_pointer v = static_cast(p); + for(unsigned i=0; iadjacent_edges().size(); ++i) + { + storage.push_back(v->adjacent_edges()[i]); + } + + } +} + +inline bool GeodesicAlgorithmExact::erase_from_queue(interval_pointer p) +{ + if(p->min() < GEODESIC_INF/10.0)// && p->min >= queue->begin()->first) + { + Xassert(m_queue.count(p)<=1); //the set is unique + + IntervalQueue::iterator it = m_queue.find(p); + + if(it != m_queue.end()) + { + m_queue.erase(it); + return true; + } + } + + return false; +} + +inline unsigned GeodesicAlgorithmExact::intersect_intervals(interval_pointer zero, + IntervalWithStop* one) //intersecting two intervals with up to three intervals in the end +{ + Xassert(zero->edge()->id() == one->edge()->id()); + Xassert(zero->stop() > one->start() && zero->start() < one->stop()); + Xassert(one->min() < GEODESIC_INF/10.0); + + double const local_epsilon = SMALLEST_INTERVAL_RATIO*one->edge()->length(); + + unsigned N=0; + if(zero->min() > GEODESIC_INF/10.0) + { + start[0] = zero->start(); + if(zero->start() < one->start() - local_epsilon) + { + map[0] = OLD; + start[1] = one->start(); + map[1] = NEW; + N = 2; + } + else + { + map[0] = NEW; + N = 1; + } + + if(zero->stop() > one->stop() + local_epsilon) + { + map[N] = OLD; //"zero" interval + start[N++] = one->stop(); + } + + start[N+1] = zero->stop(); + return N; + } + + double const local_small_epsilon = 1e-8*one->edge()->length(); + + double D = zero->d() - one->d(); + double x0 = zero->pseudo_x(); + double x1 = one->pseudo_x(); + double R0 = x0*x0 + zero->pseudo_y()*zero->pseudo_y(); + double R1 = x1*x1 + one->pseudo_y()*one->pseudo_y(); + + double inter[2]; //points of intersection + char Ninter=0; //number of the points of the intersection + + if(std::abs(D)local_small_epsilon) + { + inter[0] = (R1 - R0)/(2.*denom); //one solution + Ninter = 1; + } + } + else + { + double D2 = D*D; + double Q = 0.5*(R1-R0-D2); + double X = x0 - x1; + + double A = X*X - D2; + double B = Q*X + D2*x0; + double C = Q*Q - D2*R0; + + if (std::abs(A)local_small_epsilon) + { + inter[0] = -C/B; //one solution + Ninter = 1; + } + } + else + { + double det = B*B-A*C; + if(det>local_small_epsilon*local_small_epsilon) //two roots + { + det = sqrt(det); + if(A>0.0) //make sure that the roots are ordered + { + inter[0] = (-B - det)/A; + inter[1] = (-B + det)/A; + } + else + { + inter[0] = (-B + det)/A; + inter[1] = (-B - det)/A; + } + + if(inter[1] - inter[0] > local_small_epsilon) + { + Ninter = 2; + } + else + { + Ninter = 1; + } + } + else if(det>=0.0) //single root + { + inter[0] = -B/A; + Ninter = 1; + } + } + } + //---------------------------find possible intervals--------------------------------------- + double left = std::max(zero->start(), one->start()); //define left and right boundaries of the intersection of the intervals + double right = std::min(zero->stop(), one->stop()); + + double good_start[4]; //points of intersection within the (left, right) limits +"left" + "right" + good_start[0] = left; + char Ngood_start=1; //number of the points of the intersection + + for(char i=0; i left + local_epsilon && x < right - local_epsilon) + { + good_start[Ngood_start++] = x; + } + } + good_start[Ngood_start++] = right; + + MapType mid_map[3]; + for(char i=0; isignal(mid) <= one->signal(mid) ? OLD : NEW; + } + + //-----------------------------------output---------------------------------- + N = 0; + if(zero->start() < left - local_epsilon) //additional "zero" interval + { + if(mid_map[0] == OLD) //first interval in the map is already the old one + { + good_start[0] = zero->start(); + } + else + { + map[N] = OLD; //"zero" interval + start[N++] = zero->start(); + } + } + + for(long i=0;istop() > one->stop() + local_epsilon) + { + if(N==0 || map[N-1] == NEW) + { + map[N] = OLD; //"zero" interval + start[N++] = one->stop(); + } + } + + start[0] = zero->start(); // just to make sure that epsilons do not damage anything + //start[N] = zero->stop(); + + return N; +} + +inline void GeodesicAlgorithmExact::initialize_propagation_data() +{ + clear(); + + IntervalWithStop candidate; + std::vector edges_visible_from_source; + for(unsigned i=0; ibase_element(), + edges_visible_from_source); + + for(unsigned j=0; jlength(); + candidate.compute_min_distance(candidate.stop()); + candidate.direction() = Interval::FROM_SOURCE; + + update_list_and_queue(interval_list(e), &candidate, 1); + } + } +} + +inline void GeodesicAlgorithmExact::propagate(std::vector& sources, + double max_propagation_distance, //propagation algorithm stops after reaching the certain distance from the source + std::vector* stop_points) +{ + set_stop_conditions(stop_points, max_propagation_distance); + set_sources(sources); + initialize_propagation_data(); + + clock_t start = clock(); + + unsigned satisfied_index = 0; + + m_iterations = 0; //for statistics + m_queue_max_size = 0; + + IntervalWithStop candidates[2]; + + while(!m_queue.empty()) + { + m_queue_max_size = std::max((unsigned int)m_queue.size(), m_queue_max_size); + + unsigned const check_period = 10; + if(++m_iterations % check_period == 0) //check if we covered all required vertices + { + if (check_stop_conditions(satisfied_index)) + { + break; + } + } + + interval_pointer min_interval = *m_queue.begin(); + m_queue.erase(m_queue.begin()); + edge_pointer edge = min_interval->edge(); + list_pointer list = interval_list(edge); + + Xassert(min_interval->d() < GEODESIC_INF); + + bool const first_interval = min_interval->start() == 0.0; + //bool const last_interval = min_interval->stop() == edge->length(); + bool const last_interval = min_interval->next() == NULL; + + bool const turn_left = edge->v0()->saddle_or_boundary(); + bool const turn_right = edge->v1()->saddle_or_boundary(); + + for(unsigned i=0; iadjacent_faces().size(); ++i) //two possible faces to propagate + { + if(!edge->is_boundary()) //just in case, always propagate boundary edges + { + if((i == 0 && min_interval->direction() == Interval::FROM_FACE_0) || + (i == 1 && min_interval->direction() == Interval::FROM_FACE_1)) + { + continue; + } + } + + face_pointer face = edge->adjacent_faces()[i]; //if we come from 1, go to 2 + edge_pointer next_edge = face->next_edge(edge,edge->v0()); + + unsigned num_propagated = compute_propagated_parameters(min_interval->pseudo_x(), + min_interval->pseudo_y(), + min_interval->d(), //parameters of the interval + min_interval->start(), + min_interval->stop(), //start/end of the interval + face->vertex_angle(edge->v0()), //corner angle + next_edge->length(), //length of the new edge + first_interval, //if it is the first interval on the edge + last_interval, + turn_left, + turn_right, + candidates); //if it is the last interval on the edge + bool propagate_to_right = true; + + if(num_propagated) + { + if(candidates[num_propagated-1].stop() != next_edge->length()) + { + propagate_to_right = false; + } + + bool const invert = next_edge->v0()->id() != edge->v0()->id(); //if the origins coinside, do not invert intervals + + construct_propagated_intervals(invert, //do not inverse + next_edge, + face, + candidates, + num_propagated, + min_interval); + + update_list_and_queue(interval_list(next_edge), + candidates, + num_propagated); + } + + if(propagate_to_right) + { + //propogation to the right edge + double length = edge->length(); + next_edge = face->next_edge(edge,edge->v1()); + + num_propagated = compute_propagated_parameters(length - min_interval->pseudo_x(), + min_interval->pseudo_y(), + min_interval->d(), //parameters of the interval + length - min_interval->stop(), + length - min_interval->start(), //start/end of the interval + face->vertex_angle(edge->v1()), //corner angle + next_edge->length(), //length of the new edge + last_interval, //if it is the first interval on the edge + first_interval, + turn_right, + turn_left, + candidates); //if it is the last interval on the edge + + if(num_propagated) + { + bool const invert = next_edge->v0()->id() != edge->v1()->id(); //if the origins coinside, do not invert intervals + + construct_propagated_intervals(invert, //do not inverse + next_edge, + face, + candidates, + num_propagated, + min_interval); + + update_list_and_queue(interval_list(next_edge), + candidates, + num_propagated); + } + } + } + } + + m_propagation_distance_stopped = m_queue.empty() ? GEODESIC_INF : (*m_queue.begin())->min(); + clock_t stop = clock(); + m_time_consumed = (static_cast(stop)-static_cast(start))/CLOCKS_PER_SEC; + +/* for(unsigned i=0; ifirst(); + Xassert(p->start() == 0.0); + while(p->next()) + { + Xassert(p->stop() == p->next()->start()); + Xassert(p->d() < GEODESIC_INF); + p = p->next(); + } + }*/ +} + + +inline bool GeodesicAlgorithmExact::check_stop_conditions(unsigned& index) +{ + double queue_distance = (*m_queue.begin())->min(); + if(queue_distance < stop_distance()) + { + return false; + } + + while(index < m_stop_vertices.size()) + { + vertex_pointer v = m_stop_vertices[index].first; + edge_pointer edge = v->adjacent_edges()[0]; //take any edge + + double distance = edge->v0()->id() == v->id() ? + interval_list(edge)->signal(0.0) : + interval_list(edge)->signal(edge->length()); + + if(queue_distance < distance + m_stop_vertices[index].second) + { + return false; + } + + ++index; + } + return true; +} + + +inline void GeodesicAlgorithmExact::update_list_and_queue(list_pointer list, + IntervalWithStop* candidates, //up to two candidates + unsigned num_candidates) +{ + Xassert(num_candidates <= 2); + //Xassert(list->first() != NULL); + edge_pointer edge = list->edge(); + double const local_epsilon = SMALLEST_INTERVAL_RATIO * edge->length(); + + if(list->first() == NULL) + { + interval_pointer* p = &list->first(); + IntervalWithStop* first; + IntervalWithStop* second; + + if(num_candidates == 1) + { + first = candidates; + second = candidates; + first->compute_min_distance(first->stop()); + } + else + { + if(candidates->start() <= (candidates+1)->start()) + { + first = candidates; + second = candidates+1; + } + else + { + first = candidates+1; + second = candidates; + } + Xassert(first->stop() == second->start()); + + first->compute_min_distance(first->stop()); + second->compute_min_distance(second->stop()); + } + + if(first->start() > 0.0) + { + *p = m_memory_allocator.allocate(); + (*p)->initialize(edge); + p = &(*p)->next(); + } + + *p = m_memory_allocator.allocate(); + memcpy(*p,first,sizeof(Interval)); + m_queue.insert(*p); + + if(num_candidates == 2) + { + p = &(*p)->next(); + *p = m_memory_allocator.allocate(); + memcpy(*p,second,sizeof(Interval)); + m_queue.insert(*p); + } + + if(second->stop() < edge->length()) + { + p = &(*p)->next(); + *p = m_memory_allocator.allocate(); + (*p)->initialize(edge); + (*p)->start() = second->stop(); + } + else + { + (*p)->next() = NULL; + } + return; + } + + bool propagate_flag; + + for(unsigned i=0; ifirst(); + Xassert(p->start() == 0.0); + + while(p != NULL && p->stop() - local_epsilon < q->start()) + { + p = p->next(); + } + + while(p != NULL && p->start() < q->stop() - local_epsilon) //go through all old intervals + { + unsigned const N = intersect_intervals(p, q); //interset two intervals + + if(N == 1) + { + if(map[0]==OLD) //if "p" is always better, we do not need to update anything) + { + if(previous) //close previous interval and put in into the queue + { + previous->next() = p; + previous->compute_min_distance(p->start()); + m_queue.insert(previous); + previous = NULL; + } + + p = p->next(); + + } + else if(previous) //extend previous interval to cover everything; remove p + { + previous->next() = p->next(); + erase_from_queue(p); + m_memory_allocator.deallocate(p); + + p = previous->next(); + } + else //p becomes "previous" + { + previous = p; + interval_pointer next = p->next(); + erase_from_queue(p); + + memcpy(previous,q,sizeof(Interval)); + + previous->start() = start[0]; + previous->next() = next; + + p = next; + } + continue; + } + + //update_flag = true; + + Interval swap(*p); //used for swapping information + propagate_flag = erase_from_queue(p); + + for(unsigned j=1; jnext() = p; + previous->compute_min_distance(previous->stop()); + m_queue.insert(previous); + previous = NULL; + } + i_new[0] = p; + p->next() = i_new[1]; + p->start() = start[0]; + } + else if(previous) //extend previous interval to cover everything; remove p + { + i_new[0] = previous; + previous->next() = i_new[1]; + m_memory_allocator.deallocate(p); + previous = NULL; + } + else //p becomes "previous" + { + i_new[0] = p; + memcpy(p,q,sizeof(Interval)); + + p->next() = i_new[1]; + p->start() = start[0]; + } + + Xassert(!previous); + + for(unsigned j=1; jnext() = swap.next(); + } + else + { + current_interval->next() = i_new[j+1]; + } + + current_interval->start() = start[j]; + } + + for(unsigned j=0; jcompute_min_distance(current_interval->stop()); //compute minimal distance + + if(map[j]==NEW || (map[j]==OLD && propagate_flag)) + { + m_queue.insert(current_interval); + } + } + } + + p = swap.next(); + } + + if(previous) //close previous interval and put in into the queue + { + previous->compute_min_distance(previous->stop()); + m_queue.insert(previous); + previous = NULL; + } + } +} + +inline unsigned GeodesicAlgorithmExact::compute_propagated_parameters(double pseudo_x, + double pseudo_y, + double d, //parameters of the interval + double begin, + double end, //start/end of the interval + double alpha, //corner angle + double L, //length of the new edge + bool first_interval, //if it is the first interval on the edge + bool last_interval, + bool turn_left, + bool turn_right, + IntervalWithStop* candidates) //if it is the last interval on the edge +{ + Xassert(pseudo_y<=0.0); + Xassert(dstart() = 0.0; + p->stop() = L; + p->d() = d - pseudo_x; + p->pseudo_x() = 0.0; + p->pseudo_y() = 0.0; + return 1; + } + else if(last_interval && pseudo_x >= end) + { + p->start() = 0.0; + p->stop() = L; + p->d() = d + pseudo_x-end; + p->pseudo_x() = end*cos(alpha); + p->pseudo_y() = -end*sin(alpha); + return 1; + } + else if(pseudo_x >= begin && pseudo_x <= end) + { + p->start() = 0.0; + p->stop() = L; + p->d() = d; + p->pseudo_x() = pseudo_x*cos(alpha); + p->pseudo_y() = -pseudo_x*sin(alpha); + return 1; + } + else + { + return 0; + } + } + + double sin_alpha = sin(alpha); + double cos_alpha = cos(alpha); + + //important: for the first_interval, this function returns zero only if the new edge is "visible" from the source + //if the new edge can be covered only after turn_over, the value is negative (-1.0) + double L1 = compute_positive_intersection(begin, + pseudo_x, + pseudo_y, + sin_alpha, + cos_alpha); + + if(L1 < 0 || L1 >= L) + { + if(first_interval && turn_left) + { + p->start() = 0.0; + p->stop() = L; + p->d() = d + sqrt(pseudo_x*pseudo_x + pseudo_y*pseudo_y); + p->pseudo_y() = 0.0; + p->pseudo_x() = 0.0; + return 1; + } + else + { + return 0; + } + } + + double L2 = compute_positive_intersection(end, + pseudo_x, + pseudo_y, + sin_alpha, + cos_alpha); + + if(L2 < 0 || L2 >= L) + { + p->start() = L1; + p->stop() = L; + p->d() = d; + p->pseudo_x() = cos_alpha*pseudo_x + sin_alpha*pseudo_y; + p->pseudo_y() = -sin_alpha*pseudo_x + cos_alpha*pseudo_y; + + return 1; + } + + p->start() = L1; + p->stop() = L2; + p->d() = d; + p->pseudo_x() = cos_alpha*pseudo_x + sin_alpha*pseudo_y; + p->pseudo_y() = -sin_alpha*pseudo_x + cos_alpha*pseudo_y; + Xassert(p->pseudo_y() <= 0.0); + + if(!(last_interval && turn_right)) + { + return 1; + } + else + { + p = candidates + 1; + + p->start() = L2; + p->stop() = L; + double dx = pseudo_x - end; + p->d() = d + sqrt(dx*dx + pseudo_y*pseudo_y); + p->pseudo_x() = end*cos_alpha; + p->pseudo_y() = -end*sin_alpha; + + return 2; + } +} + +inline void GeodesicAlgorithmExact::construct_propagated_intervals(bool invert, + edge_pointer edge, + face_pointer face, //constructs iNew from the rest of the data + IntervalWithStop* candidates, + unsigned& num_candidates, + interval_pointer source_interval) //up to two candidates +{ + double edge_length = edge->length(); + double local_epsilon = SMALLEST_INTERVAL_RATIO * edge_length; + + //kill very small intervals in order to avoid precision problems + if(num_candidates == 2) + { + double start = std::min(candidates->start(), (candidates+1)->start()); + double stop = std::max(candidates->stop(), (candidates+1)->stop()); + if(candidates->stop()-candidates->start() < local_epsilon) // kill interval 0 + { + *candidates = *(candidates+1); + num_candidates = 1; + candidates->start() = start; + candidates->stop() = stop; + } + else if ((candidates+1)->stop() - (candidates+1)->start() < local_epsilon) + { + num_candidates = 1; + candidates->start() = start; + candidates->stop() = stop; + } + } + + IntervalWithStop* first; + IntervalWithStop* second; + if(num_candidates == 1) + { + first = candidates; + second = candidates; + } + else + { + if(candidates->start() <= (candidates+1)->start()) + { + first = candidates; + second = candidates+1; + } + else + { + first = candidates+1; + second = candidates; + } + Xassert(first->stop() == second->start()); + } + + if(first->start() < local_epsilon) + { + first->start() = 0.0; + } + if(edge_length - second->stop() < local_epsilon) + { + second->stop() = edge_length; + } + + //invert intervals if necessary; fill missing data and set pointers correctly + Interval::DirectionType direction = edge->adjacent_faces()[0]->id() == face->id() ? + Interval::FROM_FACE_0 : + Interval::FROM_FACE_1; + + if(!invert) //in this case everything is straighforward, we do not have to invert the intervals + { + for(unsigned i=0; inext() = (i == num_candidates - 1) ? NULL : candidates + i + 1; + p->edge() = edge; + p->direction() = direction; + p->source_index() = source_interval->source_index(); + + p->min() = 0.0; //it will be changed later on + + Xassert(p->start() < p->stop()); + } + } + else //now we have to invert the intervals + { + for(unsigned i=0; inext() = (i == 0) ? NULL : candidates + i - 1; + p->edge() = edge; + p->direction() = direction; + p->source_index() = source_interval->source_index(); + + double length = edge_length; + p->pseudo_x() = length - p->pseudo_x(); + + double start = length - p->stop(); + p->stop() = length - p->start(); + p->start() = start; + + p->min() = 0; + + Xassert(p->start() < p->stop()); + Xassert(p->start() >= 0.0); + Xassert(p->stop() <= edge->length()); + } + } +} + + +inline unsigned GeodesicAlgorithmExact::best_source(SurfacePoint& point, //quickly find what source this point belongs to and what is the distance to this source + double& best_source_distance) +{ + double best_interval_position; + unsigned best_source_index; + + best_first_interval(point, + best_source_distance, + best_interval_position, + best_source_index); + + return best_source_index; +} + +inline interval_pointer GeodesicAlgorithmExact::best_first_interval(SurfacePoint& point, + double& best_total_distance, + double& best_interval_position, + unsigned& best_source_index) +{ + Xassert(point.type() != UNDEFINED_POINT); + + interval_pointer best_interval = NULL; + best_total_distance = GEODESIC_INF; + + if(point.type() == EDGE) + { + edge_pointer e = static_cast(point.base_element()); + list_pointer list = interval_list(e); + + best_interval_position = point.distance(e->v0()); + best_interval = list->covering_interval(best_interval_position); + if(best_interval) + { + //Xassert(best_interval && best_interval->d() < GEODESIC_INF); + best_total_distance = best_interval->signal(best_interval_position); + best_source_index = best_interval->source_index(); + } + } + else if(point.type() == FACE) + { + face_pointer f = static_cast(point.base_element()); + for(unsigned i=0; i<3; ++i) + { + edge_pointer e = f->adjacent_edges()[i]; + list_pointer list = interval_list(e); + + double offset; + double distance; + interval_pointer interval; + + list->find_closest_point(&point, + offset, + distance, + interval); + + if(interval && distance < best_total_distance) + { + best_interval = interval; + best_total_distance = distance; + best_interval_position = offset; + best_source_index = interval->source_index(); + } + } + + //check for all sources that might be located inside this face + SortedSources::sorted_iterator_pair local_sources = m_sources.sources(f); + for(SortedSources::sorted_iterator it=local_sources.first; it != local_sources.second; ++it) + { + SurfacePointWithIndex* source = *it; + double distance = point.distance(source); + if(distance < best_total_distance) + { + best_interval = NULL; + best_total_distance = distance; + best_interval_position = 0.0; + best_source_index = source->index(); + } + } + } + else if(point.type() == VERTEX) + { + vertex_pointer v = static_cast(point.base_element()); + for(unsigned i=0; iadjacent_edges().size(); ++i) + { + edge_pointer e = v->adjacent_edges()[i]; + list_pointer list = interval_list(e); + + double position = e->v0()->id() == v->id() ? 0.0 : e->length(); + interval_pointer interval = list->covering_interval(position); + if(interval) + { + double distance = interval->signal(position); + + if(distance < best_total_distance) + { + best_interval = interval; + best_total_distance = distance; + best_interval_position = position; + best_source_index = interval->source_index(); + } + } + } + } + + if(best_total_distance > m_propagation_distance_stopped) //result is unreliable + { + best_total_distance = GEODESIC_INF; + return NULL; + } + else + { + return best_interval; + } +} + +inline void GeodesicAlgorithmExact::trace_back(SurfacePoint& destination, //trace back piecewise-linear path + std::vector& path) +{ + path.clear(); + double best_total_distance; + double best_interval_position; + unsigned source_index = std::numeric_limits::max(); + interval_pointer best_interval = best_first_interval(destination, + best_total_distance, + best_interval_position, + source_index); + + if(best_total_distance >= GEODESIC_INF/2.0) //unable to find the right path + { + return; + } + + path.push_back(destination); + + if(best_interval) //if we did not hit the face source immediately + { + std::vector possible_edges; + possible_edges.reserve(10); + + while(visible_from_source(path.back()) < 0) //while this point is not in the direct visibility of some source (if we are inside the FACE, we obviously hit the source) + { + SurfacePoint& q = path.back(); + + possible_traceback_edges(q, possible_edges); + + interval_pointer interval; + double total_distance; + double position; + + best_point_on_the_edge_set(q, + possible_edges, + interval, + total_distance, + position); + + //std::cout << total_distance + length(path) << std::endl; + Xassert(total_distancesource_index(); + + edge_pointer e = interval->edge(); + double local_epsilon = SMALLEST_INTERVAL_RATIO*e->length(); + if(position < local_epsilon) + { + path.push_back(SurfacePoint(e->v0())); + } + else if(position > e->length()-local_epsilon) + { + path.push_back(SurfacePoint(e->v1())); + } + else + { + double normalized_position = position/e->length(); + path.push_back(SurfacePoint(e, normalized_position)); + } + } + } + + SurfacePoint& source = static_cast(m_sources[source_index]); + if(path.back().distance(&source) > 0) + { + path.push_back(source); + } +} + +inline void GeodesicAlgorithmExact::print_statistics() +{ + GeodesicAlgorithmBase::print_statistics(); + + unsigned interval_counter = 0; + for(unsigned i=0; i +#include +#include + +namespace geodesic{ + +class Interval; +class IntervalList; +typedef Interval* interval_pointer; +typedef IntervalList* list_pointer; + +class Interval //interval of the edge +{ +public: + + Interval(){}; + ~Interval(){}; + + enum DirectionType + { + FROM_FACE_0, + FROM_FACE_1, + FROM_SOURCE, + UNDEFINED_DIRECTION + }; + + double signal(double x) //geodesic distance function at point x + { + Xassert(x>=0.0 && x <= m_edge->length()); + + if(m_d == GEODESIC_INF) + { + return GEODESIC_INF; + } + else + { + double dx = x - m_pseudo_x; + if(m_pseudo_y == 0.0) + { + return m_d + std::abs(dx); + } + else + { + return m_d + sqrt(dx*dx + m_pseudo_y*m_pseudo_y); + } + } + } + + double max_distance(double end) + { + if(m_d == GEODESIC_INF) + { + return GEODESIC_INF; + } + else + { + double a = std::abs(m_start - m_pseudo_x); + double b = std::abs(end - m_pseudo_x); + + return a > b ? m_d + sqrt(a*a + m_pseudo_y*m_pseudo_y): + m_d + sqrt(b*b + m_pseudo_y*m_pseudo_y); + } + } + + void compute_min_distance(double stop) //compute min, given c,d theta, start, end. + { + Xassert(stop > m_start); + + if(m_d == GEODESIC_INF) + { + m_min = GEODESIC_INF; + } + else if(m_start > m_pseudo_x) + { + m_min = signal(m_start); + } + else if(stop < m_pseudo_x) + { + m_min = signal(stop); + } + else + { + Xassert(m_pseudo_y<=0); + m_min = m_d - m_pseudo_y; + } + } + //compare two intervals in the queue + bool operator()(interval_pointer const x, interval_pointer const y) const + { + if(x->min() != y->min()) + { + return x->min() < y->min(); + } + else if(x->start() != y->start()) + { + return x->start() < y->start(); + } + else + { + return x->edge()->id() < y->edge()->id(); + } + } + + double stop() //return the endpoint of the interval + { + return m_next ? m_next->start() : m_edge->length(); + } + + double hypotenuse(double a, double b) + { + return sqrt(a*a + b*b); + } + + void find_closest_point(double const x, + double const y, + double& offset, + double& distance); //find the point on the interval that is closest to the point (alpha, s) + + double& start(){return m_start;}; + double& d(){return m_d;}; + double& pseudo_x(){return m_pseudo_x;}; + double& pseudo_y(){return m_pseudo_y;}; + double& min(){return m_min;}; + interval_pointer& next(){return m_next;}; + edge_pointer& edge(){return m_edge;}; + DirectionType& direction(){return m_direction;}; + bool visible_from_source(){return m_direction == FROM_SOURCE;}; + unsigned& source_index(){return m_source_index;}; + + void initialize(edge_pointer edge, + SurfacePoint* point = NULL, + unsigned source_index = 0); + +protected: + double m_start; //initial point of the interval on the edge + double m_d; //distance from the source to the pseudo-source + double m_pseudo_x; //coordinates of the pseudo-source in the local coordinate system + double m_pseudo_y; //y-coordinate should be always negative + double m_min; //minimum distance on the interval + + interval_pointer m_next; //pointer to the next interval in the list + edge_pointer m_edge; //edge that the interval belongs to + unsigned m_source_index; //the source it belongs to + DirectionType m_direction; //where the interval is coming from +}; + +struct IntervalWithStop : public Interval +{ +public: + double& stop(){return m_stop;}; +protected: + double m_stop; +}; + +class IntervalList //list of the of intervals of the given edge +{ +public: + IntervalList(){m_first = NULL;}; + ~IntervalList(){}; + + void clear() + { + m_first = NULL; + }; + + void initialize(edge_pointer e) + { + m_edge = e; + m_first = NULL; + }; + + interval_pointer covering_interval(double offset) //returns the interval that covers the offset + { + Xassert(offset >= 0.0 && offset <= m_edge->length()); + + interval_pointer p = m_first; + while(p && p->stop() < offset) + { + p = p->next(); + } + + return p;// && p->start() <= offset ? p : NULL; + }; + + void find_closest_point(SurfacePoint* point, + double& offset, + double& distance, + interval_pointer& interval) + { + interval_pointer p = m_first; + distance = GEODESIC_INF; + interval = NULL; + + double x,y; + m_edge->local_coordinates(point, x, y); + + while(p) + { + if(p->min()find_closest_point(x, y, o, d); + if(d < distance) + { + distance = d; + offset = o; + interval = p; + } + } + p = p->next(); + } + }; + + unsigned number_of_intervals() + { + interval_pointer p = m_first; + unsigned count = 0; + while(p) + { + ++count; + p = p->next(); + } + return count; + } + + interval_pointer last() + { + interval_pointer p = m_first; + if(p) + { + while(p->next()) + { + p = p->next(); + } + } + return p; + } + + double signal(double x) + { + interval_pointer interval = covering_interval(x); + + return interval ? interval->signal(x) : GEODESIC_INF; + } + + interval_pointer& first(){return m_first;}; + edge_pointer& edge(){return m_edge;}; +private: + interval_pointer m_first; //pointer to the first member of the list + edge_pointer m_edge; //edge that owns this list +}; + +class SurfacePointWithIndex : public SurfacePoint +{ +public: + unsigned index(){return m_index;}; + + void initialize(SurfacePoint& p, unsigned index) + { + SurfacePoint::initialize(p); + m_index = index; + } + + bool operator()(SurfacePointWithIndex* x, SurfacePointWithIndex* y) const //used for sorting + { + Xassert(x->type() != UNDEFINED_POINT && y->type() !=UNDEFINED_POINT); + + if(x->type() != y->type()) + { + return x->type() < y->type(); + } + else + { + return x->base_element()->id() < y->base_element()->id(); + } + } + +private: + unsigned m_index; +}; + +class SortedSources : public std::vector +{ +private: + typedef std::vector sorted_vector_type; +public: + typedef sorted_vector_type::iterator sorted_iterator; + typedef std::pair sorted_iterator_pair; + + sorted_iterator_pair sources(base_pointer mesh_element) + { + m_search_dummy.base_element() = mesh_element; + + return equal_range(m_sorted.begin(), + m_sorted.end(), + &m_search_dummy, + m_compare_less); + } + + void initialize(std::vector& sources) //we initialize the sources by copie + { + resize(sources.size()); + m_sorted.resize(sources.size()); + for(unsigned i=0; ilength(); + if(std::abs(hs+hc) < local_epsilon) + { + if(rs<=m_start) + { + r = m_start; + d_out = signal(m_start) + std::abs(rs - m_start); + } + else if(rs>=end) + { + r = end; + d_out = signal(end) + fabs(end - rs); + } + else + { + r = rs; + d_out = signal(rs); + } + } + else + { + double ri = (rs*hc + hs*rc)/(hs+hc); + + if(riend) + { + r = end; + d_out = signal(end) + hypotenuse(end - rs, hs); + } + else + { + r = ri; + d_out = m_d + hypotenuse(rc - rs, hc + hs); + } + } + } + + +inline void Interval::initialize(edge_pointer edge, + SurfacePoint* source, + unsigned source_index) +{ + m_next = NULL; + //m_geodesic_previous = NULL; + m_direction = UNDEFINED_DIRECTION; + m_edge = edge; + m_source_index = source_index; + + m_start = 0.0; + //m_stop = edge->length(); + if(!source) + { + m_d = GEODESIC_INF; + m_min = GEODESIC_INF; + return; + } + m_d = 0; + + if(source->base_element()->type() == VERTEX) + { + if(source->base_element()->id() == edge->v0()->id()) + { + m_pseudo_x = 0.0; + m_pseudo_y = 0.0; + m_min = 0.0; + return; + } + else if(source->base_element()->id() == edge->v1()->id()) + { + m_pseudo_x = stop(); + m_pseudo_y = 0.0; + m_min = 0.0; + return; + } + } + + edge->local_coordinates(source, m_pseudo_x, m_pseudo_y); + m_pseudo_y = -m_pseudo_y; + + compute_min_distance(stop()); +} + +} //geodesic + +#endif //GEODESIC_ALGORITHM_EXACT_ELEMENTS_20071231 diff --git a/geodesic/src/geodesic_algorithm_graph_base.h b/geodesic/src/geodesic_algorithm_graph_base.h new file mode 100644 index 0000000..460895a --- /dev/null +++ b/geodesic/src/geodesic_algorithm_graph_base.h @@ -0,0 +1,278 @@ +#ifndef GEODESIC_ALGORITHM_GRAPH_BASE_010907 +#define GEODESIC_ALGORITHM_GRAPH_BASE_010907 + +#include "geodesic_algorithm_base.h" +#include "geodesic_mesh_elements.h" +#include +#include + +namespace geodesic{ + +template +class GeodesicAlgorithmGraphBase: public GeodesicAlgorithmBase +{ +public: + typedef Node* node_pointer; + + GeodesicAlgorithmGraphBase(geodesic::Mesh* mesh): + GeodesicAlgorithmBase(mesh) + {}; + + ~GeodesicAlgorithmGraphBase(){}; + + void propagate(std::vector& sources, + double max_propagation_distance = GEODESIC_INF, //propagation algorithm stops after reaching the certain distance from the source + std::vector* stop_points = NULL); //or after ensuring that all the stop_points are covered + + void trace_back(SurfacePoint& destination, //trace back piecewise-linear path + std::vector& path); + + unsigned best_source(SurfacePoint& point, //quickly find what source this point belongs to and what is the distance to this source + double& best_source_distance); + + void print_statistics() + { + GeodesicAlgorithmBase::print_statistics(); + + double memory = m_nodes.size()*sizeof(Node); + std::cout << "uses about " << memory/1e6 << "Mb of memory" <id(); + }; + + void set_sources(std::vector& sources) + { + m_sources = sources; + } + + node_pointer best_first_node(SurfacePoint& point, double& best_total_distance) + { + node_pointer best_node = NULL; + if(point.type() == VERTEX) + { + vertex_pointer v = (vertex_pointer)point.base_element(); + best_node = &m_nodes[node_index(v)]; + best_total_distance = best_node->distance_from_source(); + } + else + { + std::vector possible_nodes; + list_nodes_visible_from_source(point.base_element(), possible_nodes); + + best_total_distance = GEODESIC_INF; + for(unsigned i=0; idistance(&point); + if(node->distance_from_source() + distance_from_dest < best_total_distance) + { + best_total_distance = node->distance_from_source() + distance_from_dest; + best_node = node; + } + } + } + + //Xassert(best_node); + //Xassert(best_total_distance m_propagation_distance_stopped) //result is unreliable + { + best_total_distance = GEODESIC_INF; + return NULL; + } + else + { + return best_node; + } + }; //quickly find what node will be the next one in geodesic path + + bool check_stop_conditions(unsigned& index); //check when propagation should stop + + virtual void list_nodes_visible_from_source(MeshElementBase* p, + std::vector& storage) = 0; //list all nodes that belong to this mesh element + + virtual void list_nodes_visible_from_node(node_pointer node, //list all nodes that belong to this mesh element + std::vector& storage, + std::vector& distances, + double threshold_distance) = 0; //list only the nodes whose current distance is larger than the threshold + + std::vector m_nodes; //nodes of the graph + + typedef std::set queue_type; + queue_type m_queue; + + std::vector m_sources; //for simplicity, we keep sources as they are +}; + +template +void GeodesicAlgorithmGraphBase::propagate(std::vector& sources, + double max_propagation_distance, //propagation algorithm stops after reaching the certain distance from the source + std::vector* stop_points) //or after ensuring that all the stop_points are covered +{ + set_stop_conditions(stop_points, max_propagation_distance); + set_sources(sources); + + m_queue.clear(); + m_propagation_distance_stopped = GEODESIC_INF; + for(unsigned i=0; i visible_nodes; //initialize vertices directly visible from sources + for(unsigned i=0; ibase_element(), + visible_nodes); + + for(unsigned j=0; jdistance(source); + if(distance < node->distance_from_source()) + { + node->distance_from_source() = distance; + node->source_index() = i; + node->previous() = NULL; + } + } + visible_nodes.clear(); + } + + for(unsigned i=0; i distances_between_nodes; + while(!m_queue.empty()) //main cycle + { + if(counter++ % 10 == 0) //check if we covered all required vertices + { + if (check_stop_conditions(satisfied_index)) + { + break; + } + } + + node_pointer min_node = *m_queue.begin(); + m_queue.erase(m_queue.begin()); + Xassert(min_node->distance_from_source() < GEODESIC_INF); + + visible_nodes.clear(); + distances_between_nodes.clear(); + list_nodes_visible_from_node(min_node, + visible_nodes, + distances_between_nodes, + min_node->distance_from_source()); + + for(unsigned i=0; idistance_from_source() > min_node->distance_from_source() + + distances_between_nodes[i]) + { + if(next_node->distance_from_source() < GEODESIC_INF) //remove it from the queue + { + typename queue_type::iterator iter = m_queue.find(next_node); + Xassert(iter != m_queue.end()); + m_queue.erase(iter); + } + next_node->distance_from_source() = min_node->distance_from_source() + + distances_between_nodes[i]; + next_node->source_index() = min_node->source_index(); + next_node->previous() = min_node; + m_queue.insert(next_node); + } + } + } + + m_propagation_distance_stopped = m_queue.empty() ? GEODESIC_INF : (*m_queue.begin())->distance_from_source(); + clock_t finish = clock(); + m_time_consumed = (static_cast(finish)-static_cast(start))/CLOCKS_PER_SEC; + //std::cout << std::endl; +} + +template +inline bool GeodesicAlgorithmGraphBase::check_stop_conditions(unsigned& index) +{ + double queue_min_distance = (*m_queue.begin())->distance_from_source(); + + if(queue_min_distance < m_max_propagation_distance) + { + return false; + } + + while(index < m_stop_vertices.size()) + { + vertex_pointer v = m_stop_vertices[index].first; + Node& node = m_nodes[node_index(v)]; + if(queue_min_distance < node.distance_from_source() + m_stop_vertices[index].second) + { + return false; + } + ++index; + } + return true; +} + +template +inline void GeodesicAlgorithmGraphBase::trace_back(SurfacePoint& destination, //trace back piecewise-linear path + std::vector& path) +{ + path.clear(); + + double total_path_length; + node_pointer node = best_first_node(destination, total_path_length); + + if(total_path_length>GEODESIC_INF/2.0) //unable to find the path + { + return; + } + + path.push_back(destination); + + if(node->distance(&destination) > 1e-50) + { + path.push_back(node->surface_point()); + } + + while(node->previous()) //follow the path + { + node = node->previous(); + path.push_back(node->surface_point()); + } + + SurfacePoint& source = m_sources[node->source_index()]; //add source to the path if it is not already there + if(node->distance(&source) > 1e-50) + { + path.push_back(source); + } +} + + +template +inline unsigned GeodesicAlgorithmGraphBase::best_source(SurfacePoint& point, //quickly find what source this point belongs to and what is the distance to this source + double& best_source_distance) +{ + node_pointer node = best_first_node(point, best_source_distance); + return node ? node->source_index() : 0; +}; + +} //geodesic + +#endif //GEODESIC_ALGORITHM_GRAPH_BASE_010907 diff --git a/geodesic/src/geodesic_algorithm_subdivision.h b/geodesic/src/geodesic_algorithm_subdivision.h new file mode 100644 index 0000000..e4abb4f --- /dev/null +++ b/geodesic/src/geodesic_algorithm_subdivision.h @@ -0,0 +1,269 @@ +//Copyright (C) 2008 Danil Kirsanov, MIT License +#ifndef GEODESIC_ALGORITHM_SUBDIVISION_122806 +#define GEODESIC_ALGORITHM_SUBDIVISION_122806 + +#include "geodesic_algorithm_graph_base.h" +#include "geodesic_mesh_elements.h" +#include +#include + +namespace geodesic{ + +class SubdivisionNode: public SurfacePoint +{ + typedef SubdivisionNode* node_pointer; +public: + SubdivisionNode(){}; + + template + SubdivisionNode(Pointer p): + SurfacePoint(p), + m_previous(NULL), + m_distance(0.0) + {}; + + template + SubdivisionNode(Pointer p, Parameter param): + SurfacePoint(p, param), + m_previous(NULL), + m_distance(0.0) + {}; + + ~SubdivisionNode(){}; + + double& distance_from_source(){return m_distance;}; + node_pointer& previous(){return m_previous;}; + unsigned& source_index(){return m_source_index;}; + + void clear() + { + m_distance = GEODESIC_INF; + m_previous = NULL; + } + + bool operator()(node_pointer const s1, node_pointer const s2) const + { + if(s1 == s2) + { + return false; + } + if(s1->distance_from_source() != s2->distance_from_source()) + { + return s1->distance_from_source() < s2->distance_from_source(); + } +/* if(s1->type() != s2->type()) + { + return s1->type() < s2->type(); + } + if(s1->base_element()->id() != s2->base_element()->id()) + { + return s1->base_element()->id() < s2->base_element()->id(); + } */ + if(s1->x() != s2->x()) //two nodes cannot be located in the same space + { + return s1->x() < s2->x(); + } + if(s1->y() != s2->y()) + { + return s1->y() < s2->y(); + } + if(s1->z() != s2->z()) + { + return s1->z() < s2->z(); + } + + Xassert(0); + return true; + }; + + SurfacePoint& surface_point(){return static_cast(*this);}; + +private: + double m_distance; //distance to the closest source + unsigned m_source_index; //closest source index + node_pointer m_previous; //previous node in the geodesic path +}; + +class GeodesicAlgorithmSubdivision: public GeodesicAlgorithmGraphBase +{ + typedef SubdivisionNode Node; +public: + GeodesicAlgorithmSubdivision(geodesic::Mesh* mesh = NULL, + unsigned subdivision_level = 0): + GeodesicAlgorithmGraphBase(mesh) + { + m_type = SUBDIVISION; + + m_nodes.reserve(mesh->vertices().size()); + for(unsigned i=0; ivertices().size(); ++i) + { + vertex_pointer v = &mesh->vertices()[i]; + m_nodes.push_back(Node(v)); //!! + } + + set_subdivision_level(subdivision_level); + }; + + ~GeodesicAlgorithmSubdivision(){}; + + unsigned subdivision_level(){return m_subdivision_level;}; + + void set_subdivision_level(unsigned subdivision_level) + { + m_subdivision_level = subdivision_level; + + m_nodes.resize(m_mesh->vertices().size()); + m_nodes.reserve(m_mesh->vertices().size() + + m_mesh->edges().size()*subdivision_level); + + for(unsigned i=0; iedges().size(); ++i) + { + edge_pointer e = &m_mesh->edges()[i]; + for(unsigned i=0; i& storage); //list all nodes that belong to this mesh element + + void list_nodes_visible_from_node(node_pointer node, //list all nodes that belong to this mesh element + std::vector& storage, + std::vector& distances, + double threshold_distance); //list only the nodes whose current distance is larger than the threshold + + unsigned node_indexx(edge_pointer e) + { + return e->id()*m_subdivision_level + m_mesh->vertices().size(); + }; + +private: + void list_nodes(MeshElementBase* p, //list nodes that belong to this mesh element + std::vector& storage, + double threshold_distance = -1.0); //list only the nodes whose current distance is larger than the threshold + + unsigned m_subdivision_level; //when level is equal to 1, this algorithm corresponds to the Dijkstra algorithm +}; + +inline void GeodesicAlgorithmSubdivision::list_nodes(MeshElementBase* p, + std::vector& storage, + double threshold_distance) +{ + Xassert(p->type() != UNDEFINED_POINT); + + if(p->type() == VERTEX) + { + vertex_pointer v = static_cast(p); + node_pointer node = &m_nodes[node_index(v)]; + if(node->distance_from_source() > threshold_distance) + { + storage.push_back(node); + } + } + else if(p->type() == EDGE) + { + edge_pointer e = static_cast(p); + unsigned node_index = node_indexx(e); + for(unsigned i=0; idistance_from_source() > threshold_distance) + { + storage.push_back(node); + } + } + } + //FACE has no nodes +} + +void GeodesicAlgorithmSubdivision::list_nodes_visible_from_source(MeshElementBase* p, + std::vector& storage) +{ + Xassert(p->type() != UNDEFINED_POINT); + + if(p->type() == FACE) + { + face_pointer f = static_cast(p); + for(unsigned i=0; i<3; ++i) + { + list_nodes(f->adjacent_vertices()[i],storage); + list_nodes(f->adjacent_edges()[i],storage); + } + } + else if(p->type() == EDGE) + { + list_nodes(p,storage); + list_nodes(p->adjacent_vertices()[0],storage); + list_nodes(p->adjacent_vertices()[1],storage); + } + else //VERTEX + { + list_nodes(p,storage); + } +} + +void GeodesicAlgorithmSubdivision::list_nodes_visible_from_node(node_pointer node, //list all nodes that belong to this mesh element + std::vector& storage, + std::vector& distances, + double threshold_distance) +{ + MeshElementBase* p = node->base_element(); + Xassert(p->type() != UNDEFINED_POINT); + Xassert(storage.size() == distances.size()); + + if(p->type() == VERTEX) + { + vertex_pointer v = static_cast(p); + + for(unsigned i=0; iadjacent_edges().size(); ++i) + { + edge_pointer e = v->adjacent_edges()[i]; + vertex_pointer v_opposite = e->opposite_vertex(v); + list_nodes(e, storage, threshold_distance); + list_nodes(v_opposite, storage, threshold_distance); + } + for(unsigned i=0; iadjacent_faces().size(); ++i) + { + face_pointer f = v->adjacent_faces()[i]; + edge_pointer e = f->opposite_edge(v); + list_nodes(e, storage, threshold_distance); + } + } + else if(p->type() == EDGE) + { + edge_pointer e = static_cast(p); + + vertex_pointer v0 = e->adjacent_vertices()[0]; + vertex_pointer v1 = e->adjacent_vertices()[1]; + list_nodes(v0, storage, threshold_distance); + list_nodes(v1, storage, threshold_distance); + + for(unsigned i=0; iadjacent_faces().size(); ++i) + { + face_pointer f = e->adjacent_faces()[i]; + + list_nodes(f->next_edge(e,v0), storage, threshold_distance); + list_nodes(f->next_edge(e,v1), storage, threshold_distance); + list_nodes(f->opposite_vertex(e), storage, threshold_distance); + } + } + else + { + Xassert(0); + } + + unsigned index = distances.size(); + distances.resize(storage.size()); + for(; indexdistance(&storage[index]->surface_point()); + } +} + +} //geodesic + +#endif //GEODESIC_ALGORITHM_SUBDIVISION_122806 diff --git a/geodesic/src/geodesic_constants_and_simple_functions.h b/geodesic/src/geodesic_constants_and_simple_functions.h new file mode 100644 index 0000000..1db17eb --- /dev/null +++ b/geodesic/src/geodesic_constants_and_simple_functions.h @@ -0,0 +1,80 @@ +//Copyright (C) 2008 Danil Kirsanov, MIT License +#ifndef GEODESIC_CONSTANTS_20071231 +#define GEODESIC_CONSTANTS_20071231 + +// some constants and simple math functions + +#include +#include +#include + +namespace geodesic{ + +#ifndef M_PI +#define M_PI 3.14159265358979323846 +#endif + +//double const GEODESIC_INF = std::numeric_limits::max(); +double const GEODESIC_INF = 1e100; + +//in order to avoid numerical problems with "infinitely small" intervals, +//we drop all the intervals smaller than SMALLEST_INTERVAL_RATIO*edge_length +double const SMALLEST_INTERVAL_RATIO = 1e-6; +//double const SMALL_EPSILON = 1e-10; + + +inline double cos_from_edges(double const a, //compute the cosine of the angle given the lengths of the edges + double const b, + double const c) +{ + Xassert(a>1e-50); + Xassert(b>1e-50); + Xassert(c>1e-50); + + double result = (b*b + c*c - a*a)/(2.0*b*c); + result = std::max(result, -1.0); + return std::min(result, 1.0); +} + +inline double angle_from_edges(double const a, //compute the cosine of the angle given the lengths of the edges + double const b, + double const c) +{ + return acos(cos_from_edges(a,b,c)); +} + +template +inline bool read_mesh_from_file(char* filename, + Points& points, + Faces& faces) +{ + std::ifstream file(filename); + Xassert(file.is_open()); + if(!file.is_open()) return false; + + unsigned num_points; + file >> num_points; + Xassert(num_points>=3); + + unsigned num_faces; + file >> num_faces; + + points.resize(num_points*3); + for(typename Points::iterator i=points.begin(); i!=points.end(); ++i) + { + file >> *i; + } + + faces.resize(num_faces*3); + for(typename Faces::iterator i=faces.begin(); i!=faces.end(); ++i) + { + file >> *i; + } + file.close(); + + return true; +} + +} //geodesic + +#endif //GEODESIC_CONSTANTS_20071231 diff --git a/geodesic/src/geodesic_matlab_api.cpp b/geodesic/src/geodesic_matlab_api.cpp new file mode 100644 index 0000000..285148d --- /dev/null +++ b/geodesic/src/geodesic_matlab_api.cpp @@ -0,0 +1,234 @@ +#ifdef _WIN32_ +#define GEODESIC_DLL_IMPORT __declspec(dllexport) +#endif + +#include + +#include +#include +#include + +#include "geodesic_mesh.h" +#include "geodesic_algorithm_dijkstra_alternative.h" +#include "geodesic_algorithm_dijkstra.h" +#include "geodesic_algorithm_subdivision.h" +#include "geodesic_algorithm_exact.h" +#include "geodesic_matlab_api.h" + +typedef boost::shared_ptr mesh_shared_pointer; +std::vector meshes; + +typedef boost::shared_ptr algorithm_shared_pointer; +std::vector algorithms; + +std::vector output_path; +geodesic::OutputBuffer output_buffer, output_buffer1; + + +std::size_t find_mesh_id(geodesic::Mesh* mesh) +{ + for(std::size_t i=0; imesh()); + geodesic::fill_surface_point_structure(&point, + destination, + algorithm->mesh()); + + std::size_t best_source = algorithm->best_source(point, + *best_source_distance); + return best_source; +} + +GEODESIC_DLL_IMPORT int distance_and_source_for_all_vertices(int algorithm_id, //same idea as in the previous function + double** distances, //list distance/source info for all vertices of the mesh + int** sources) +{ + + geodesic::GeodesicAlgorithmBase* algorithm = algorithms[algorithm_id].get(); + geodesic::Mesh* mesh = algorithm->mesh(); + + output_buffer.allocate(mesh->vertices().size()); //allocate space for distances + *distances = output_buffer.get(); + + output_buffer1.allocate(mesh->vertices().size()); //allocate space for sources + *sources = output_buffer1.get(); + + + for(std::size_t i = 0; i < mesh->vertices().size(); ++i) + { + geodesic::SurfacePoint point(&mesh->vertices()[i]); + double* distace_location = *distances + i; + (*sources)[i] = algorithm->best_source(point, *distace_location); + } + + return mesh->vertices().size(); +} + + +GEODESIC_DLL_IMPORT int trace_back(int algorithm_id, + double* destination, + double** path) +{ + geodesic::SurfacePoint point; + geodesic::GeodesicAlgorithmBase* algorithm = algorithms[algorithm_id].get(); + geodesic::fill_surface_point_structure(&point, + destination, + algorithm->mesh()); + + algorithm->trace_back(point, + output_path); + + std::size_t mesh_id = find_mesh_id(algorithm->mesh()); + output_buffer.allocate(output_path.size()*5); + for(std::size_t i=0; i() + 5*i, + mesh_id); + } + + *path = output_buffer.get(); + + return output_path.size(); +} + +GEODESIC_DLL_IMPORT void propagate(int algorithm_id, + double* source_points, + int num_sources, + double* stop_points, + int num_stop_points, + double max_propagation_distance) +{ + std::vector sources(num_sources); + + geodesic::Mesh* mesh = algorithms[algorithm_id]->mesh(); + for(std::size_t i=0; i stop(num_stop_points); + for(std::size_t i=0; ipropagate(sources, + max_propagation_distance, + &stop); +} + + +GEODESIC_DLL_IMPORT int new_mesh(int num_points, + double* points, + int num_triangles, + int* triangles, + int* num_edges, + double** edges) +{ + mesh_shared_pointer new_mesh = mesh_shared_pointer(new geodesic::Mesh); + meshes.push_back(new_mesh); + + new_mesh->initialize_mesh_data(num_points, + points, + num_triangles, + triangles); + + *num_edges = new_mesh->edges().size(); + + output_buffer.allocate(*num_edges * 4); + *edges = output_buffer.get(); + + for(std::size_t i=0; i<*num_edges; ++i) + { + geodesic::Edge& edge = new_mesh->edges()[i]; + double* buffer = *edges + 4*i; + + buffer[0] = edge.adjacent_vertices()[0]->id(); + buffer[1] = edge.adjacent_vertices()[1]->id(); + buffer[2] = edge.adjacent_faces()[0]->id(); + buffer[3] = edge.adjacent_faces().size() == 2 ? + edge.adjacent_faces()[1]->id() : + -1.0; + } + + return meshes.size() - 1; +} + +GEODESIC_DLL_IMPORT int new_algorithm(int mesh_id, + int type, + int subdivision) +{ + if(subdivision == 0 && type == 1)//SUBDIVISION) + { + type = 2; //DIJKSTRA; + } + + geodesic::Mesh* mesh = meshes[mesh_id].get(); + geodesic::GeodesicAlgorithmBase* algorithm; + switch(type) + { + case 2: //DIJKSTRA + { + algorithm = new geodesic::GeodesicAlgorithmDijkstra(mesh); + break; + } + case 1: //SUBDIVISION: + { + algorithm = new geodesic::GeodesicAlgorithmSubdivision(mesh, subdivision); + break; + } + case 0://EXACT: + default: + { + algorithm = new geodesic::GeodesicAlgorithmExact(mesh); + break; + } + } + + algorithms.push_back(algorithm_shared_pointer(algorithm)); + + return algorithms.size() - 1; +} + +GEODESIC_DLL_IMPORT void delete_mesh(int id) //delete mesh and all related algorithms +{ + assert(id < meshes.size()); + + geodesic::Mesh* mesh = meshes[id].get(); + for(std::size_t i=0; imesh() == mesh) + { + algorithms[i] = algorithm_shared_pointer(); + } + } + + meshes[id] = mesh_shared_pointer(); +} + +GEODESIC_DLL_IMPORT void delete_algorithm(int id) +{ + if(id < algorithms.size()) + { + algorithms[id] = algorithm_shared_pointer(); + } +} diff --git a/geodesic/src/geodesic_matlab_api.h b/geodesic/src/geodesic_matlab_api.h new file mode 100644 index 0000000..95ceace --- /dev/null +++ b/geodesic/src/geodesic_matlab_api.h @@ -0,0 +1,50 @@ +#ifndef GEODESIC_DLL_HEADER_HPP_234232 +#define GEODESIC_DLL_HEADER_HPP_234232 + +#ifndef GEODESIC_DLL_IMPORT +#define GEODESIC_DLL_IMPORT +#endif + +#ifdef __cplusplus +extern "C" { +#endif + +GEODESIC_DLL_IMPORT int new_mesh(int num_points, //creates new mesh + double* points, + int num_triangles, + int* triangles, + int* num_edges, + double** edges); + +GEODESIC_DLL_IMPORT int new_algorithm(int mesh_id, //creates a geodesic algorithm for a given mesh + int type, + int subdivision); + +GEODESIC_DLL_IMPORT void delete_algorithm(int id); + +GEODESIC_DLL_IMPORT void delete_mesh(int id); //delete mesh and all associated algorithms + +GEODESIC_DLL_IMPORT void propagate(int algorithm_id, //compute distance field for given source points + double* source_points, + int num_sources, + double* stop_points, //limitations on distance field propagation + int num_stop_points, + double max_propagation_distance); + +GEODESIC_DLL_IMPORT int trace_back(int algorithm_id, //using procomputed distance field, compute a shortest path from destination to the closest source + double* destination, + double** path); + +GEODESIC_DLL_IMPORT int distance_and_source(int algorithm_id, //quickly find what source this point beints to and what is the distance to this source + double* destination, + double* best_source_distance); + +GEODESIC_DLL_IMPORT int distance_and_source_for_all_vertices(int algorithm_id, //same idea as in the previous function + double** distances, //list distance/source info for all vertices of the mesh + int** sources); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/geodesic/src/geodesic_memory.h b/geodesic/src/geodesic_memory.h new file mode 100644 index 0000000..9ba6683 --- /dev/null +++ b/geodesic/src/geodesic_memory.h @@ -0,0 +1,193 @@ +//Copyright (C) 2008 Danil Kirsanov, MIT License +#ifndef _GEODESIC_MEMORY_20071231 +#define _GEODESIC_MEMORY_20071231 + +//two fast and simple memory allocators + +#include +#include + +namespace geodesic{ + +template //quickly allocates multiple elements of a given type; no deallocation +class SimlpeMemoryAllocator +{ +public: + typedef T* pointer; + + SimlpeMemoryAllocator(unsigned block_size = 0, + unsigned max_number_of_blocks = 0) + { + reset(block_size, + max_number_of_blocks); + }; + + ~SimlpeMemoryAllocator(){}; + + void reset(unsigned block_size, + unsigned max_number_of_blocks) + { + m_block_size = block_size; + m_max_number_of_blocks = max_number_of_blocks; + + + m_current_position = 0; + + m_storage.reserve(max_number_of_blocks); + m_storage.resize(1); + m_storage[0].resize(block_size); + }; + + pointer allocate(unsigned const n) //allocate n units + { + Xassert(n < m_block_size); + + if(m_current_position + n >= m_block_size) + { + m_storage.push_back( std::vector() ); + m_storage.back().resize(m_block_size); + m_current_position = 0; + } + pointer result = & m_storage.back()[m_current_position]; + m_current_position += n; + + return result; + }; +private: + std::vector > m_storage; + unsigned m_block_size; //size of a single block + unsigned m_max_number_of_blocks; //maximum allowed number of blocks + unsigned m_current_position; //first unused element inside the current block +}; + + +template //quickly allocates and deallocates single elements of a given type +class MemoryAllocator +{ +public: + typedef T* pointer; + + MemoryAllocator(unsigned block_size = 1024, + unsigned max_number_of_blocks = 1024) + { + reset(block_size, + max_number_of_blocks); + }; + + ~MemoryAllocator(){}; + + void clear() + { + reset(m_block_size, + m_max_number_of_blocks); + } + + void reset(unsigned block_size, + unsigned max_number_of_blocks) + { + m_block_size = block_size; + m_max_number_of_blocks = max_number_of_blocks; + + Xassert(m_block_size > 0); + Xassert(m_max_number_of_blocks > 0); + + m_current_position = 0; + + m_storage.reserve(max_number_of_blocks); + m_storage.resize(1); + m_storage[0].resize(block_size); + + m_deleted.clear(); + m_deleted.reserve(2*block_size); + }; + + pointer allocate() //allocates single unit of memory + { + pointer result; + if(m_deleted.empty()) + { + if(m_current_position + 1 >= m_block_size) + { + m_storage.push_back( std::vector() ); + m_storage.back().resize(m_block_size); + m_current_position = 0; + } + result = & m_storage.back()[m_current_position]; + ++m_current_position; + } + else + { + result = m_deleted.back(); + m_deleted.pop_back(); + } + + return result; + }; + + void deallocate(pointer p) //allocate n units + { + if(m_deleted.size() < m_deleted.capacity()) + { + m_deleted.push_back(p); + } + }; + +private: + std::vector > m_storage; + unsigned m_block_size; //size of a single block + unsigned m_max_number_of_blocks; //maximum allowed number of blocks + unsigned m_current_position; //first unused element inside the current block + + std::vector m_deleted; //pointers to deleted elemets +}; + + +class OutputBuffer +{ +public: + OutputBuffer(): + m_num_bytes(0) + {} + + void clear() + { + m_num_bytes = 0; + m_buffer = std::unique_ptr(); + } + + template + T* allocate(unsigned n) + { + double wanted = n*sizeof(T); + if(wanted > m_num_bytes) + { + unsigned new_size = (unsigned) ceil(wanted / (double)sizeof(double)); + m_buffer = std::unique_ptr(new double[new_size]); + m_num_bytes = new_size*sizeof(double); + } + + return (T*)m_buffer.get(); + } + + template + T* get() + { + return (T*)m_buffer.get(); + } + + template + unsigned capacity() + { + return (unsigned)floor((double)m_num_bytes/(double)sizeof(T)); + }; + +private: + + std::unique_ptr m_buffer; + unsigned m_num_bytes; +}; + + +} //geodesic + +#endif //_GEODESIC_MEMORY_20071231 diff --git a/geodesic/src/geodesic_mesh.h b/geodesic/src/geodesic_mesh.h new file mode 100644 index 0000000..fcac8bf --- /dev/null +++ b/geodesic/src/geodesic_mesh.h @@ -0,0 +1,528 @@ +//Copyright (C) 2008 Danil Kirsanov, MIT License +#ifndef GEODESIC_MESH_20071231 +#define GEODESIC_MESH_20071231 + +#include +#include +#include +#include +#include +#include + +#include "geodesic_mesh_elements.h" +#include "geodesic_memory.h" +#include "geodesic_constants_and_simple_functions.h" + +namespace geodesic{ + +struct edge_visible_from_source +{ + unsigned source; + edge_pointer edge; +}; + +class Mesh +{ +public: + Mesh() + {}; + + ~Mesh(){}; + + template + void initialize_mesh_data(unsigned num_vertices, + Points& p, + unsigned num_faces, + Faces& tri); //build mesh from regular point-triangle representation + + template + void initialize_mesh_data(Points& p, Faces& tri); //build mesh from regular point-triangle representation + + std::vector& vertices(){return m_vertices;}; + std::vector& edges(){return m_edges;}; + std::vector& faces(){return m_faces;}; + + unsigned closest_vertices(SurfacePoint* p, + std::vector* storage = NULL); //list vertices closest to the point + +private: + + void build_adjacencies(); //build internal structure of the mesh + bool verify(); //verifies connectivity of the mesh and prints some debug info + + typedef void* void_pointer; + void_pointer allocate_pointers(unsigned n) + { + return m_pointer_allocator.allocate(n); + } + + std::vector m_vertices; + std::vector m_edges; + std::vector m_faces; + + SimlpeMemoryAllocator m_pointer_allocator; //fast memory allocating for Face/Vertex/Edge cross-references +}; + +inline unsigned Mesh::closest_vertices(SurfacePoint* p, + std::vector* storage) +{ + Xassert(p->type() != UNDEFINED_POINT); + + if(p->type() == VERTEX) + { + if(storage) + { + storage->push_back(static_cast(p->base_element())); + } + return 1; + } + else if(p->type() == FACE) + { + if(storage) + { + vertex_pointer* vp= p->base_element()->adjacent_vertices().begin(); + storage->push_back(*vp); + storage->push_back(*(vp+1)); + storage->push_back(*(vp+2)); + } + return 2; + } + else if(p->type() == EDGE) //for edge include all 4 adjacent vertices + { + edge_pointer edge = static_cast(p->base_element()); + + if(storage) + { + storage->push_back(edge->adjacent_vertices()[0]); + storage->push_back(edge->adjacent_vertices()[1]); + + for(unsigned i = 0; i < edge->adjacent_faces().size(); ++i) + { + face_pointer face = edge->adjacent_faces()[i]; + storage->push_back(face->opposite_vertex(edge)); + } + } + return 2 + edge->adjacent_faces().size(); + } + + Xassert(0); + return 0; +} + +template +void Mesh::initialize_mesh_data(Points& p, Faces& tri) //build mesh from regular point-triangle representation +{ + Xassert(p.size() % 3 == 0); + unsigned const num_vertices = p.size() / 3; + Xassert(tri.size() % 3 == 0); + unsigned const num_faces = tri.size() / 3; + + initialize_mesh_data(num_vertices, p, num_faces, tri); +} + +template +void Mesh::initialize_mesh_data(unsigned num_vertices, + Points& p, + unsigned num_faces, + Faces& tri) +{ + unsigned const approximate_number_of_internal_pointers = (num_vertices + num_faces)*4; + unsigned const max_number_of_pointer_blocks = 100; + m_pointer_allocator.reset(approximate_number_of_internal_pointers, + max_number_of_pointer_blocks); + + m_vertices.resize(num_vertices); + for(unsigned i=0; iadjacent Faces + std::vector count(m_vertices.size()); //count adjacent vertices + for(unsigned i=0; iid(); + Xassert(vertex_id < m_vertices.size()); + count[vertex_id]++; + } + } + + for(unsigned i=0; iadjacent_faces()[count[v->id()]++] = &f; + } + } + + //find all edges + //i.e. find all half-edges, sort and combine them into edges + std::vector half_edges(m_faces.size()*3); + unsigned k = 0; + for(unsigned i=0; iid(); + unsigned vertex_id_2 = f.adjacent_vertices()[(j+1) % 3]->id(); + half_edges[k].vertex_0 = std::min(vertex_id_1, vertex_id_2); + half_edges[k].vertex_1 = std::max(vertex_id_1, vertex_id_2); + + k++; + } + } + std::sort(half_edges.begin(), half_edges.end()); + + unsigned number_of_edges = 1; + for(unsigned i=1; iadjacent Vertices and Faces + m_edges.resize(number_of_edges); + unsigned edge_id = 0; + for(unsigned i=0; idistance(e.adjacent_vertices()[1]); + Xassert(e.length() > 1e-100); //algorithm works well with non-degenerate meshes only + + if(i != half_edges.size()-1 && half_edges[i] == half_edges[i+1]) //double edge + { + e.adjacent_faces().set_allocation(allocate_pointers(2),2); + e.adjacent_faces()[0] = &m_faces[half_edges[i].face_id]; + e.adjacent_faces()[1] = &m_faces[half_edges[i+1].face_id]; + i += 2; + } + else //single edge + { + e.adjacent_faces().set_allocation(allocate_pointers(1),1); //one adjucent faces + e.adjacent_faces()[0] = &m_faces[half_edges[i].face_id]; + i += 1; + } + } + + // Vertices->adjacent Edges + std::fill(count.begin(), count.end(), 0); + for(unsigned i=0; iid()]++; + count[e.adjacent_vertices()[1]->id()]++; + } + for(unsigned i=0; iadjacent_edges()[count[v->id()]++] = &e; + } + } + + // Faces->adjacent Edges + for(unsigned i=0; iid()]<3); + f->adjacent_edges()[count[f->id()]++] = &e; + } + } + + //compute angles for the faces + for(unsigned i=0; ilength(); + } + + double angle = angle_from_edges(abc[0], abc[1], abc[2]); + Xassert(angle>1e-5); //algorithm works well with non-degenerate meshes only + + f.corner_angles()[j] = angle; + sum += angle; + } + Xassert(std::abs(sum - M_PI) < 1e-5); //algorithm works well with non-degenerate meshes only + } + + //define m_turn_around_flag for vertices + std::vector total_vertex_angle(m_vertices.size()); + for(unsigned i=0; iid()] += f.corner_angles()[j]; + } + } + + for(unsigned i=0; i 2.0*M_PI - 1e-5); + } + + for(unsigned i=0; isaddle_or_boundary() = true; + e.adjacent_vertices()[1]->saddle_or_boundary() = true; + } + } + + Xassert(verify()); +} + +inline bool Mesh::verify() //verifies connectivity of the mesh and prints some debug info +{ + std::cout << std::endl; + // make sure that all vertices are mentioned at least once. + // though the loose vertex is not a bug, it most likely indicates that something is wrong with the mesh + std::vector map(m_vertices.size(), false); + for(unsigned i=0; iadjacent_vertices()[0]->id()] = true; + map[e->adjacent_vertices()[1]->id()] = true; + } + Xassert(std::find(map.begin(), map.end(), false) == map.end()); + + //make sure that the mesh is connected trough its edges + //if mesh has more than one connected component, it is most likely a bug + std::vector stack(1,&m_faces[0]); + stack.reserve(m_faces.size()); + + map.resize(m_faces.size()); + std::fill(map.begin(), map.end(), false); + map[0] = true; + + while(!stack.empty()) + { + face_pointer f = stack.back(); + stack.pop_back(); + + for(unsigned i=0; i<3; ++i) + { + edge_pointer e = f->adjacent_edges()[i]; + face_pointer f_adjacent = e->opposite_face(f); + if(f_adjacent && !map[f_adjacent->id()]) + { + map[f_adjacent->id()] = true; + stack.push_back(f_adjacent); + } + } + } + if (std::find(map.begin(), map.end(), false) != map.end()) + std::cout << "Warning: mesh has multiple components!\n"; + + //print some mesh statistics that can be useful in debugging + std::cout << "mesh has " << m_vertices.size() + << " vertices, " << m_faces.size() + << " faces, " << m_edges.size() + << " edges\n"; + + unsigned total_boundary_edges = 0; + double longest_edge = 0; + double shortest_edge = 1e100; + for(unsigned i=0; iset(data); + unsigned type = (unsigned) data[3]; + unsigned id = (unsigned) data[4]; + + + if(type == 0) //vertex + { + point->base_element() = &mesh->vertices()[id]; + } + else if(type == 1) //edge + { + point->base_element() = &mesh->edges()[id]; + } + else //face + { + point->base_element() = &mesh->faces()[id]; + } +} + +inline void fill_surface_point_double(geodesic::SurfacePoint* point, + double* data, + long mesh_id) +{ + data[0] = point->x(); + data[1] = point->y(); + data[2] = point->z(); + data[4] = point->base_element()->id(); + + if(point->type() == VERTEX) //vertex + { + data[3] = 0; + } + else if(point->type() == EDGE) //edge + { + data[3] = 1; + } + else //face + { + data[3] = 2; + } +} + +} //geodesic + +#endif diff --git a/geodesic/src/geodesic_mesh_elements.h b/geodesic/src/geodesic_mesh_elements.h new file mode 100644 index 0000000..3df9577 --- /dev/null +++ b/geodesic/src/geodesic_mesh_elements.h @@ -0,0 +1,421 @@ +//Copyright (C) 2008 Danil Kirsanov, MIT License +#ifndef GEODESIC_MESH_ELEMENTS_20071231 +#define GEODESIC_MESH_ELEMENTS_20071231 + +// here we define the building elements of the mesh: +// 3D-points, vertices, edges, faces, and surface points + +#include + +namespace geodesic{ + +class Vertex; +class Edge; +class Face; +class Mesh; +class MeshElementBase; + +typedef Vertex* vertex_pointer; +typedef Edge* edge_pointer; +typedef Face* face_pointer; +typedef Mesh* mesh_pointer; +typedef MeshElementBase* base_pointer; + +template //simple vector that stores info about mesh references +class SimpleVector //for efficiency, it uses an outside memory allocator +{ +public: + SimpleVector(): + m_size(0), + m_begin(NULL) + {}; + + typedef Data* iterator; + + unsigned size(){return m_size;}; + iterator begin(){return m_begin;}; + iterator end(){return m_begin + m_size;}; + + template + void set_allocation(DataPointer begin, unsigned size) + { + Xassert(begin != NULL || size == 0); + m_size = size; + m_begin = (iterator)begin; + } + + Data& operator[](unsigned i) + { + Xassert(i < m_size); + return *(m_begin + i); + } + + void clear() + { + m_size = 0; + m_begin = NULL; + } + +private: + unsigned m_size; + Data* m_begin; +}; + +enum PointType +{ + VERTEX, + EDGE, + FACE, + UNDEFINED_POINT +}; + +class MeshElementBase //prototype of vertices, edges and faces +{ +public: + typedef SimpleVector vertex_pointer_vector; + typedef SimpleVector edge_pointer_vector; + typedef SimpleVector face_pointer_vector; + + MeshElementBase(): + m_id(0), + m_type(UNDEFINED_POINT) + {}; + + vertex_pointer_vector& adjacent_vertices(){return m_adjacent_vertices;}; + edge_pointer_vector& adjacent_edges(){return m_adjacent_edges;}; + face_pointer_vector& adjacent_faces(){return m_adjacent_faces;}; + + unsigned& id(){return m_id;}; + PointType type(){return m_type;}; + +protected: + vertex_pointer_vector m_adjacent_vertices; //list of the adjacent vertices + edge_pointer_vector m_adjacent_edges; //list of the adjacent edges + face_pointer_vector m_adjacent_faces; //list of the adjacent faces + + unsigned m_id; //unique id + PointType m_type; //vertex, edge or face +}; + +class Point3D //point in 3D and corresponding operations +{ +public: + Point3D(){}; + Point3D(Point3D* p) + { + x() = p->x(); + y() = p->y(); + z() = p->z(); + }; + + double* xyz(){return m_coordinates;}; + double& x(){return *m_coordinates;}; + double& y(){return *(m_coordinates+1);}; + double& z(){return *(m_coordinates+2);}; + + void set(double new_x, double new_y, double new_z) + { + x() = new_x; + y() = new_y; + z() = new_z; + } + + void set(double* data) + { + x() = *data; + y() = *(data+1); + z() = *(data+2); + } + + double distance(double* v) + { + double dx = m_coordinates[0] - v[0]; + double dy = m_coordinates[1] - v[1]; + double dz = m_coordinates[2] - v[2]; + + return sqrt(dx*dx + dy*dy + dz*dz); + }; + + double distance(Point3D* v) + { + return distance(v->xyz()); + }; + + void add(Point3D* v) + { + x() += v->x(); + y() += v->y(); + z() += v->z(); + }; + + void multiply(double v) + { + x() *= v; + y() *= v; + z() *= v; + }; + +private: + double m_coordinates[3]; //xyz +}; + +class Vertex: public MeshElementBase, public Point3D +{ +public: + Vertex() + { + m_type = VERTEX; + }; + + ~Vertex(){}; + + bool& saddle_or_boundary(){return m_saddle_or_boundary;}; +private: + //this flag speeds up exact geodesic algorithm + bool m_saddle_or_boundary; //it is true if total adjacent angle is larger than 2*PI or this vertex belongs to the mesh boundary +}; + + +class Face: public MeshElementBase +{ +public: + Face() + { + m_type = FACE; + }; + + ~Face(){}; + + edge_pointer opposite_edge(vertex_pointer v); + vertex_pointer opposite_vertex(edge_pointer e); + edge_pointer next_edge(edge_pointer e, vertex_pointer v); + + double vertex_angle(vertex_pointer v) + { + for(unsigned i=0; i<3; ++i) + { + if(adjacent_vertices()[i]->id() == v->id()) + { + return m_corner_angles[i]; + } + } + Xassert(0); + return 0; + } + + double* corner_angles(){return m_corner_angles;}; + +private: + double m_corner_angles[3]; //triangle angles in radians; angles correspond to vertices in m_adjacent_vertices +}; + +class Edge: public MeshElementBase +{ +public: + Edge() + { + m_type = EDGE; + }; + + ~Edge(){}; + + double& length(){return m_length;}; + + face_pointer opposite_face(face_pointer f) + { + if(adjacent_faces().size() == 1) + { + Xassert(adjacent_faces()[0]->id() == f->id()); + return NULL; + } + + Xassert(adjacent_faces()[0]->id() == f->id() || + adjacent_faces()[1]->id() == f->id()); + + return adjacent_faces()[0]->id() == f->id() ? + adjacent_faces()[1] : adjacent_faces()[0]; + }; + + vertex_pointer opposite_vertex(vertex_pointer v) + { + Xassert(belongs(v)); + + return adjacent_vertices()[0]->id() == v->id() ? + adjacent_vertices()[1] : adjacent_vertices()[0]; + }; + + bool belongs(vertex_pointer v) + { + return adjacent_vertices()[0]->id() == v->id() || + adjacent_vertices()[1]->id() == v->id(); + } + + bool is_boundary(){return adjacent_faces().size() == 1;}; + + vertex_pointer v0(){return adjacent_vertices()[0];}; + vertex_pointer v1(){return adjacent_vertices()[1];}; + + void local_coordinates(Point3D* point, + double& x, + double& y) + { + double d0 = point->distance(v0()); + if(d0 < 1e-50) + { + x = 0.0; + y = 0.0; + return; + } + + double d1 = point->distance(v1()); + if(d1 < 1e-50) + { + x = m_length; + y = 0.0; + return; + } + + x = m_length/2.0 + (d0*d0 - d1*d1)/(2.0*m_length); + y = sqrt(std::max(0.0, d0*d0 - x*x)); + return; + } + +private: + double m_length; //length of the edge +}; + +class SurfacePoint:public Point3D //point on the surface of the mesh +{ +public: + SurfacePoint(): + m_p(NULL) + {}; + + SurfacePoint(vertex_pointer v): //set the surface point in the vertex + SurfacePoint::Point3D(v), + m_p(v) + {}; + + SurfacePoint(face_pointer f): //set the surface point in the center of the face + m_p(f) + { + set(0,0,0); + add(f->adjacent_vertices()[0]); + add(f->adjacent_vertices()[1]); + add(f->adjacent_vertices()[2]); + multiply(1./3.); + }; + + SurfacePoint(edge_pointer e, //set the surface point in the middle of the edge + double a = 0.5): + m_p(e) + { + double b = 1 - a; + + vertex_pointer v0 = e->adjacent_vertices()[0]; + vertex_pointer v1 = e->adjacent_vertices()[1]; + + x() = b*v0->x() + a*v1->x(); + y() = b*v0->y() + a*v1->y(); + z() = b*v0->z() + a*v1->z(); + }; + + SurfacePoint(base_pointer g, + double x, + double y, + double z, + PointType t = UNDEFINED_POINT): + m_p(g) + { + set(x,y,z); + }; + + void initialize(SurfacePoint const& p) + { + *this = p; + } + + ~SurfacePoint(){}; + + PointType type(){return m_p ? m_p->type() : UNDEFINED_POINT;}; + base_pointer& base_element(){return m_p;}; +protected: + base_pointer m_p; //could be face, vertex or edge pointer +}; + +inline edge_pointer Face::opposite_edge(vertex_pointer v) +{ + for(unsigned i=0; i<3; ++i) + { + edge_pointer e = adjacent_edges()[i]; + if(!e->belongs(v)) + { + return e; + } + } + Xassert(0); + return NULL; +} + +inline vertex_pointer Face::opposite_vertex(edge_pointer e) +{ + for(unsigned i=0; i<3; ++i) + { + vertex_pointer v = adjacent_vertices()[i]; + if(!e->belongs(v)) + { + return v; + } + } + Xassert(0); + return NULL; +} + +inline edge_pointer Face::next_edge(edge_pointer e, vertex_pointer v) +{ + Xassert(e->belongs(v)); + + for(unsigned i=0; i<3; ++i) + { + edge_pointer next = adjacent_edges()[i]; + if(e->id() != next->id() && next->belongs(v)) + { + return next; + } + } + Xassert(0); + return NULL; +} + +struct HalfEdge //prototype of the edge; used for mesh construction +{ + unsigned face_id; + unsigned vertex_0; //adjacent vertices sorted by id value + unsigned vertex_1; //they are sorted, vertex_0 < vertex_1 +}; + +inline bool operator < (const HalfEdge &x, const HalfEdge &y) +{ + if(x.vertex_0 == y.vertex_0) + { + return x.vertex_1 < y.vertex_1; + } + else + { + return x.vertex_0 < y.vertex_0; + } +} + +inline bool operator != (const HalfEdge &x, const HalfEdge &y) +{ + return x.vertex_0 != y.vertex_0 || x.vertex_1 != y.vertex_1; +} + +inline bool operator == (const HalfEdge &x, const HalfEdge &y) +{ + return x.vertex_0 == y.vertex_0 && x.vertex_1 == y.vertex_1; +} + +} //geodesic + +#endif diff --git a/geodesic/src/strlcpy.c b/geodesic/src/strlcpy.c new file mode 100644 index 0000000..2d52390 --- /dev/null +++ b/geodesic/src/strlcpy.c @@ -0,0 +1,51 @@ +/* $OpenBSD: strlcpy.c,v 1.11 2006-05-05 15:27:38 millert Exp $ */ + +/* + * Copyright (c) 1998 Todd C. Miller + * + * Permission to use, copy, modify, and distribute this software for any + * purpose with or without fee is hereby granted, provided that the above + * copyright notice and this permission notice appear in all copies. + * + * THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES + * WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF + * MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR + * ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES + * WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN + * ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF + * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + */ + +#include +#include + +/* + * Copy src to string dst of size siz. At most siz-1 characters + * will be copied. Always NUL terminates (unless siz == 0). + * Returns strlen(src); if retval >= siz, truncation occurred. + */ +size_t +strlcpy(char *dst, const char *src, size_t siz) +{ + char *d = dst; + const char *s = src; + size_t n = siz; + + /* Copy as many bytes as will fit */ + if (n != 0) { + while (--n != 0) { + if ((*d++ = *s++) == '\0') + break; + } + } + + /* Not enough room in dst, add NUL and traverse rest of src */ + if (n == 0) { + if (siz != 0) + *d = '\0'; /* NUL-terminate dst */ + while (*s++) + ; + } + + return(s - src - 1); /* count does not include NUL */ +} diff --git a/matitk.mexmaci64 b/matitk.mexmaci64 new file mode 100644 index 0000000..4bea158 Binary files /dev/null and b/matitk.mexmaci64 differ diff --git a/metufem.mexa64 b/metufem.mexa64 index 1771927..e7ebf5e 100755 Binary files a/metufem.mexa64 and b/metufem.mexa64 differ diff --git a/metufem.mexa64.orig b/metufem.mexa64.orig deleted file mode 100755 index e7ebf5e..0000000 Binary files a/metufem.mexa64.orig and /dev/null differ diff --git a/metufem.mexw64 b/metufem.mexw64 new file mode 100644 index 0000000..305459f Binary files /dev/null and b/metufem.mexw64 differ diff --git a/nft_dipfit/ft_datatype.m b/nft_dipfit/ft_datatype.m new file mode 100644 index 0000000..24041ea --- /dev/null +++ b/nft_dipfit/ft_datatype.m @@ -0,0 +1,232 @@ +function [type, dimord] = ft_datatype(data, desired) + +% FT_DATATYPE determines the type of data represented in a FieldTrip data +% structure and returns a string with raw, freq, timelock source, comp, +% spike, source, volume, dip. +% +% Use as +% [type, dimord] = ft_datatype(data) +% [status] = ft_datatype(data, desired) +% +% See also FT_DATATYPE_COMP FT_DATATYPE_FREQ FT_DATATYPE_MVAR +% FT_DATATYPE_SEGMENTATION FT_DATATYPE_PARCELLATION FT_DATATYPE_SOURCE +% FT_DATATYPE_TIMELOCK FT_DATATYPE_DIP FT_DATATYPE_HEADMODEL +% FT_DATATYPE_RAW FT_DATATYPE_SENS FT_DATATYPE_SPIKE FT_DATATYPE_VOLUME + +% Copyright (C) 2008-2012, Robert Oostenveld +% +% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip +% for the documentation and details. +% +% FieldTrip is free software: you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation, either version 3 of the License, or +% (at your option) any later version. +% +% FieldTrip is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License for more details. +% +% You should have received a copy of the GNU General Public License +% along with FieldTrip. If not, see . +% +% $Id: ft_datatype.m 7599 2013-03-06 15:50:17Z jansch $ + +% determine the type of input data, this can be raw, freq, timelock, comp, spike, source, volume, dip, segmentation, parcellation +israw = isfield(data, 'label') && isfield(data, 'time') && isa(data.time, 'cell') && isfield(data, 'trial') && isa(data.trial, 'cell') && ~isfield(data,'trialtime'); +isfreq = (isfield(data, 'label') || isfield(data, 'labelcmb')) && isfield(data, 'freq') && ~isfield(data,'trialtime') && ~isfield(data,'origtrial'); %&& (isfield(data, 'powspctrm') || isfield(data, 'crsspctrm') || isfield(data, 'cohspctrm') || isfield(data, 'fourierspctrm') || isfield(data, 'powcovspctrm')); +istimelock = isfield(data, 'label') && isfield(data, 'time') && ~isfield(data, 'freq') && ~isfield(data,'trialtime'); %&& ((isfield(data, 'avg') && isnumeric(data.avg)) || (isfield(data, 'trial') && isnumeric(data.trial) || (isfield(data, 'cov') && isnumeric(data.cov)))); +iscomp = isfield(data, 'label') && isfield(data, 'topo') || isfield(data, 'topolabel'); +isvolume = isfield(data, 'transform') && isfield(data, 'dim'); +issource = isfield(data, 'pos'); +isdip = isfield(data, 'dip'); +ismvar = isfield(data, 'dimord') && ~isempty(strfind(data.dimord, 'lag')); +isfreqmvar = isfield(data, 'freq') && isfield(data, 'transfer'); +ischan = isfield(data, 'dimord') && strcmp(data.dimord, 'chan') && ~isfield(data, 'time') && ~isfield(data, 'freq'); +issegmentation = check_segmentation(data); +isparcellation = check_parcellation(data); + +if ~isfreq + % this applies to a ferq structure from 2003 up to early 2006 + isfreq = all(isfield(data, {'foi', 'label', 'dimord'})) && ~isempty(strfind(data.dimord, 'frq')); +end + +% check if it is a spike structure +spk_hastimestamp = isfield(data,'label') && isfield(data, 'timestamp') && isa(data.timestamp, 'cell'); +spk_hastrials = isfield(data,'label') && isfield(data, 'time') && isa(data.time, 'cell') && isfield(data, 'trial') && isa(data.trial, 'cell') && isfield(data, 'trialtime') && isa(data.trialtime, 'numeric'); +spk_hasorig = isfield(data,'origtrial') && isfield(data,'origtime'); % for compatibility +isspike = isfield(data, 'label') && (spk_hastimestamp || spk_hastrials || spk_hasorig); + +% check if it is a sensor array +isgrad = isfield(data, 'label') && isfield(data, 'coilpos') && isfield(data, 'chanpos') && isfield(data, 'coilori'); +iselec = isfield(data, 'label') && isfield(data, 'elecpos') && isfield(data, 'chanpos'); + +if iscomp + % comp should conditionally go before raw, otherwise the returned ft_datatype will be raw + type = 'comp'; +elseif israw + type = 'raw'; +elseif isfreqmvar + % freqmvar should conditionally go before freq, otherwise the returned ft_datatype will be freq in the case of frequency mvar data + type = 'freqmvar'; +elseif isfreq + type = 'freq'; +elseif ismvar + type = 'mvar'; +elseif isdip + % dip should conditionally go before timelock, otherwise the ft_datatype will be timelock + type = 'dip'; +elseif istimelock + type = 'timelock'; +elseif isspike + type = 'spike'; +elseif issegmentation + % a segmentation data structure is a volume data structure, but in general not vice versa + % segmentation should conditionally go before volume, otherwise the returned ft_datatype will be volume + type = 'segmentation'; +elseif isvolume + type = 'volume'; +elseif isparcellation + % a parcellation data structure is a source data structure, but in general not vice versa + % parcellation should conditionally go before source, otherwise the returned ft_datatype will be source + type = 'parcellation'; +elseif issource + type = 'source'; +elseif ischan + % this results from avgovertime/avgoverfreq after timelockstatistics or freqstatistics + type = 'chan'; +elseif iselec + type = 'elec'; +elseif isgrad + type = 'grad'; +else + type = 'unknown'; +end + +if nargin>1 + % return a boolean value + switch desired + case 'raw' + type = any(strcmp(type, {'raw', 'comp'})); + case 'volume' + type = any(strcmp(type, {'volume', 'segmentation'})); + case 'source' + type = any(strcmp(type, {'source', 'parcellation'})); + case 'sens' + type = any(strcmp(type, {'elec', 'grad'})); + otherwise + type = strcmp(type, desired); + end % switch +end + +if nargout>1 + % also return the dimord of the input data + if isfield(data, 'dimord') + dimord = data.dimord; + else + dimord = 'unknown'; + end +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% SUBFUNCTION +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function [res] = check_segmentation(volume) +res = false; + +if ~isfield(volume, 'dim') + return +end + +if isfield(volume, 'pos') + return +end + +if any(isfield(volume, {'seg', 'csf', 'white', 'gray', 'skull', 'scalp', 'brain'})) + res = true; + return +end + +fn = fieldnames(volume); +isboolean = []; +cnt = 0; +for i=1:length(fn) + if isfield(volume, [fn{i} 'label']) + res = true; + return + else + if (islogical(volume.(fn{i})) || isnumeric(volume.(fn{i}))) && isequal(size(volume.(fn{i})),volume.dim) + cnt = cnt+1; + if islogical(volume.(fn{i})) + isboolean(cnt) = true; + else + isboolean(cnt) = false; + end + end + end +end +if ~isempty(isboolean) + res = all(isboolean); +end + + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% SUBFUNCTION +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function [res] = check_parcellation(source) +res = false; + +if ~isfield(source, 'pos') + return +end + +fn = fieldnames(source); +fb = false(size(fn)); +npos = size(source.pos,1); +for i=1:numel(fn) + % for each of the fields check whether it might be a logical array with the size of the number of sources + tmp = source.(fn{i}); + fb(i) = numel(tmp)==npos && islogical(tmp); +end +if sum(fb)>1 + % the presence of multiple logical arrays suggests it is a parcellation + res = true; +end + +if res == false % check if source has more D elements + check = 0; + for i = 1: length(fn) + fname = fn{i}; + switch fname + case 'tri' + npos = size(source.tri,1); + check = 1; + case 'hex' + npos = size(source.hex,1); + check = 1; + case 'tet' + npos = size(source.tet,1); + check = 1; + end + end + if check == 1 % check if elements are labelled + for i=1:numel(fn) + tmp = source.(fn{i}); + fb(i) = numel(tmp)==npos && islogical(tmp); + end + if sum(fb)>1 + res = true; + end + end +end + +fn = fieldnames(source); +for i=1:length(fn) + if isfield(source, [fn{i} 'label']) + res = true; + return + end +end diff --git a/nft_dipfit/ft_senstype.m b/nft_dipfit/ft_senstype.m new file mode 100644 index 0000000..85ec10e --- /dev/null +++ b/nft_dipfit/ft_senstype.m @@ -0,0 +1,417 @@ +function [type] = ft_senstype(input, desired) + +% FT_SENSTYPE determines the type of acquisition device by looking at the +% channel names and comparing them with predefined lists. +% +% Use as +% [type] = ft_senstype(sens) +% [flag] = ft_senstype(sens, desired) +% +% The output type can be any of the following +% 'ctf64' +% 'ctf151' +% 'ctf151_planar' +% 'ctf275' +% 'ctf275_planar' +% 'bti148' +% 'bti148_planar' +% 'bti248' +% 'bti248_planar' +% 'bti248grad' +% 'bti248grad_planar' +% 'itab28' +% 'itab153' +% 'itab153_planar' +% 'yokogawa9' +% 'yokogawa64' +% 'yokogawa64_planar' +% 'yokogawa160' +% 'yokogawa160_planar' +% 'yokogawa440' +% 'yokogawa440'_planar +% 'neuromag122' +% 'neuromag306' +% 'egi32' +% 'egi64' +% 'egi128' +% 'egi256' +% 'biosemi64' +% 'biosemi128' +% 'biosemi256' +% 'ext1020' +% 'plexon' +% 'electrode' +% 'magnetometer' +% +% The optional input argument for the desired type can be any of the above, +% or any of the following +% 'eeg' +% 'meg' +% 'meg_planar' +% 'meg_axial' +% 'ctf' +% 'bti' +% 'neuromag' +% 'yokogawa' +% If you specify the desired type, this function will return a boolean +% true/false depending on the input data. +% +% Besides specifiying a sensor definition (i.e. a grad or elec structure, +% see FT_DATATYPE_SENS), it is also possible to give a data structure +% containing a grad or elec field, or giving a list of channel names (as +% cell-arrray). So assuming that you have a FieldTrip data structure, any +% of the following calls would also be fine. +% ft_senstype(hdr) +% ft_senstype(data) +% ft_senstype(data.label) +% ft_senstype(data.grad) +% ft_senstype(data.grad.label) +% +% See also FT_SENSLABEL, FT_CHANTYPE, FT_READ_SENS, FT_COMPUTE_LEADFIELD, FT_DATATYPE_SENS + +% Copyright (C) 2007-2011, Robert Oostenveld +% +% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip +% for the documentation and details. +% +% FieldTrip is free software: you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation, either version 3 of the License, or +% (at your option) any later version. +% +% FieldTrip is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License for more details. +% +% You should have received a copy of the GNU General Public License +% along with FieldTrip. If not, see . +% +% $Id: ft_senstype.m 7496 2013-02-19 09:25:34Z roboos $ + +% these are for remembering the type on subsequent calls with the same input arguments +persistent previous_argin previous_argout + +% this is to avoid a recursion loop +persistent recursion +if isempty(recursion) + recursion = false; +end + +if iscell(input) && numel(input)<4 && ~all(cellfun(@ischar, input)) + % this might represent combined EEG, ECoG and/or MEG + type = cell(size(input)); + if nargin<2 + desired = cell(size(input)); % empty elements + end + for i=1:numel(input) + type{i} = ft_senstype(input{i}, desired{i}); + end + return +end + +if nargin<2 + % ensure that all input arguments are defined + desired = []; +end + +current_argin = {input, desired}; +if isequal(current_argin, previous_argin) + % don't do the type detection again, but return the previous output from cache + type = previous_argout{1}; + return +end + +% FIXME the detection of the type of input structure should perhaps be done using the datatype function +isdata = isa(input, 'struct') && isfield(input, 'hdr'); +isheader = isa(input, 'struct') && isfield(input, 'label') && isfield(input, 'Fs'); +isgrad = isa(input, 'struct') && isfield(input, 'label') && isfield(input, 'pnt') && isfield(input, 'ori'); % old style +isgrad = (isa(input, 'struct') && isfield(input, 'label') && isfield(input, 'coilpos')) || isgrad; % new style +iselec = isa(input, 'struct') && isfield(input, 'label') && isfield(input, 'pnt') && ~isfield(input, 'ori'); % old style +iselec = (isa(input, 'struct') && isfield(input, 'label') && isfield(input, 'elecpos')) || iselec; % new style +islabel = isa(input, 'cell') && ~isempty(input) && isa(input{1}, 'char'); +isfreq = isa(input, 'struct') && (isfield(input, 'fourierspctrm') || isfield(input, 'powspctrm')); +haslabel = isa(input, 'struct') && isfield(input, 'label'); + +if ~isdata && ~isheader + % timelock or freq structures don't have the header structure + % the header is also removed from raw data after megrealign + % the gradiometer definition is lost after megplanar+combineplanar + isdata = isa(input, 'struct') && (isfield(input, 'grad') || isfield(input, 'elec')); +end + +if ~(isdata || isheader || isgrad || iselec || islabel || haslabel) && isfield(input, 'hdr') + input = input.hdr; + isheader = true; +end + +% the input may be a data structure which then contains a grad/elec structure, a header or only the labels +if isdata + % preferably look at the data and not the header for the grad, because it might be re-balanced and/or planar + if isfield(input, 'grad') + sens = input.grad; + isgrad = true; + elseif isfield(input, 'elec') + sens = input.elec; + iselec = true; + elseif issubfield(input, 'hdr.grad') + sens = input.hdr.grad; + isgrad = true; + elseif issubfield(input, 'hdr.elec') + sens = input.hdr.elec; + iselec = true; + elseif issubfield(input, 'hdr.label') + sens.label = input.hdr.label; + islabel = true; + elseif isfield(input, 'label') + sens.label = input.label; + islabel = true; + end +elseif isfreq + type = 'unknown'; +elseif isheader + if isfield(input, 'grad') + sens = input.grad; + isgrad = true; + elseif isfield(input, 'elec') + sens = input.elec; + iselec = true; + elseif isfield(input, 'label') + sens.label = input.label; + islabel = true; + end +elseif isgrad + sens = input; +elseif iselec + sens = input; +elseif islabel + sens.label = input; +elseif haslabel + % it does not resemble anything that we had expected at this location, but it does have channel labels + % the channel labels can be used to determine the type of sensor array + sens.label = input.label; + islabel = true; +else + sens = []; +end + +if exist('sens') + if isfield(sens,'type') + istypefield = 1; + else + istypefield = 0; + end +else + istypefield = 0; +end + +if istypefield + % preferably the structure specifies its own type + type = sens.type; +elseif isfield(input, 'nChans') && input.nChans==1 && isfield(input, 'label') && ~isempty(regexp(input.label{1}, '^csc', 'once')) + % this is a single channel header that was read from a Neuralynx file, might be fcdc_matbin or neuralynx_nsc + type = 'neuralynx'; + +elseif issubfield(input, 'orig.FileHeader') && issubfield(input, 'orig.VarHeader') + % this is a complete header that was read from a Plexon *.nex file using read_plexon_nex + type = 'plexon'; + +elseif issubfield(input, 'orig.stname') + % this is a complete header that was read from an ITAB dataset + type = 'itab'; + +elseif issubfield(input, 'orig.sys_name') + % this is a complete header that was read from a Yokogawa dataset + if strcmp(input.orig.sys_name, '9ch Biomagnetometer System') || input.orig.channel_count<20 + % this is the small animal system that is installed at the UCL Ear Institute + % see http://www.ucl.ac.uk/news/news-articles/0907/09070101 + type = 'yokogawa9'; + elseif input.orig.channel_count<160 + type = 'yokogawa64'; + elseif input.orig.channel_count<300 + type = 'yokogawa160'; + else + % FIXME this might fail if there are many bad channels + type = 'yokogawa440'; + end + +elseif issubfield(input, 'orig.FILE.Ext') && strcmp(input.orig.FILE.Ext, 'edf') + % this is a complete header that was read from an EDF or EDF+ dataset + type = 'electrode'; + +else + % start with unknown, then try to determine the proper type by looking at the labels + type = 'unknown'; + + if isgrad && isfield(sens, 'type') + type = sens.type; + + elseif isgrad + % this looks like MEG + % revert the component balancing that was previously applied + if isfield(sens, 'balance') && strcmp(sens.balance.current, 'comp') + sens = undobalancing(sens); + end + + % determine the type of magnetometer/gradiometer system based on the channel names alone + % this uses a recursive call to the "islabel" section further down + type = ft_senstype(sens.label); + if strcmp(type, 'unknown') + % although we don't know the type, we do know that it is MEG + type = 'meg'; + end + + elseif iselec + % this looks like EEG + + % determine the type of electrode/acquisition system based on the channel names alone + % this uses a recursive call to the "islabel" section further down + type = ft_senstype(sens.label); + if strcmp(type, 'unknown') + % although we don't know the type, we do know that it is EEG + type = 'eeg'; + end + + elseif islabel + % look only at the channel labels + if (mean(ismember(ft_senslabel('ctf275'), sens.label)) > 0.8) + type = 'ctf275'; + elseif (mean(ismember(ft_senslabel('ctfheadloc'), sens.label)) > 0.8) % look at the head localization channels + type = 'ctf275'; + elseif (mean(ismember(ft_senslabel('ctf151'), sens.label)) > 0.8) + type = 'ctf151'; + elseif (mean(ismember(ft_senslabel('ctf64'), sens.label)) > 0.8) + type = 'ctf64'; + elseif (mean(ismember(ft_senslabel('ctf275_planar'), sens.label)) > 0.8) + type = 'ctf275_planar'; + elseif (mean(ismember(ft_senslabel('ctf151_planar'), sens.label)) > 0.8) + type = 'ctf151_planar'; + elseif (mean(ismember(ft_senslabel('bti248'), sens.label)) > 0.8) % note that it might also be a bti248grad system + type = 'bti248'; + elseif (mean(ismember(ft_senslabel('bti148'), sens.label)) > 0.8) + type = 'bti148'; + elseif (mean(ismember(ft_senslabel('bti248_planar'), sens.label)) > 0.8) % note that it might also be a bti248grad_planar system + type = 'bti248_planar'; + elseif (mean(ismember(ft_senslabel('bti148_planar'), sens.label)) > 0.8) + type = 'bti148_planar'; + elseif (mean(ismember(ft_senslabel('itab28'), sens.label)) > 0.8) + type = 'itab28'; + elseif (mean(ismember(ft_senslabel('itab153'), sens.label)) > 0.8) + type = 'itab153'; + elseif (mean(ismember(ft_senslabel('itab153_planar'), sens.label)) > 0.8) + type = 'itab153_planar'; + + % the order is important for the different yokogawa systems, because they all share the same channel names + elseif (mean(ismember(ft_senslabel('yokogawa440'), sens.label)) > 0.7) + type = 'yokogawa440'; + elseif (mean(ismember(ft_senslabel('yokogawa440_planar'), sens.label)) > 0.7) + type = 'yokogawa440_planar'; + elseif (mean(ismember(ft_senslabel('yokogawa160'), sens.label)) > 0.4) + type = 'yokogawa160'; + elseif (mean(ismember(ft_senslabel('yokogawa160_planar'), sens.label)) > 0.4) + type = 'yokogawa160_planar'; + elseif (mean(ismember(ft_senslabel('yokogawa64'), sens.label)) > 0.4) + type = 'yokogawa64'; + elseif (mean(ismember(ft_senslabel('yokogawa64_planar'), sens.label)) > 0.4) + type = 'yokogawa64_planar'; + + elseif any(mean(ismember(ft_senslabel('neuromag306'), sens.label)) > 0.8) + type = 'neuromag306'; + elseif any(mean(ismember(ft_senslabel('neuromag306alt'),sens.label)) > 0.8) % an alternative set without spaces in the name + type = 'neuromag306'; + elseif any(mean(ismember(ft_senslabel('neuromag122'), sens.label)) > 0.8) + type = 'neuromag122'; + elseif any(mean(ismember(ft_senslabel('neuromag122alt'),sens.label)) > 0.8) % an alternative set without spaces in the name + type = 'neuromag122'; + elseif (mean(ismember(ft_senslabel('biosemi256'), sens.label)) > 0.8) + type = 'biosemi256'; + elseif (mean(ismember(ft_senslabel('biosemi128'), sens.label)) > 0.8) + type = 'biosemi128'; + elseif (mean(ismember(ft_senslabel('biosemi64'), sens.label)) > 0.8) + type = 'biosemi64'; + elseif (mean(ismember(ft_senslabel('egi256'), sens.label)) > 0.8) + type = 'egi256'; + elseif (mean(ismember(ft_senslabel('egi128'), sens.label)) > 0.8) + type = 'egi128'; + elseif (mean(ismember(ft_senslabel('egi64'), sens.label)) > 0.8) + type = 'egi64'; + elseif (mean(ismember(ft_senslabel('egi32'), sens.label)) > 0.8) + type = 'egi32'; + elseif (sum(ismember(sens.label, ft_senslabel('eeg1005'))) > 10) % Otherwise it's not even worth recognizing + type = 'ext1020'; + elseif any(ismember(ft_senslabel('btiref'), sens.label)) + type = 'bti'; % it might be 148 or 248 channels + elseif any(ismember(ft_senslabel('ctfref'), sens.label)) + type = 'ctf'; % it might be 151 or 275 channels + end + + end % look at label, ori and/or pnt +end % if isfield(sens, 'type') + +if strcmp(type, 'unknown') && ~recursion + % try whether only lowercase channel labels makes a difference + if islabel + recursion = true; + type = ft_senstype(lower(input)); + recursion = false; + elseif isfield(input, 'label') + input.label = lower(input.label); + recursion = true; + type = ft_senstype(input); + recursion = false; + end +end + +if strcmp(type, 'unknown') && ~recursion + % try whether only uppercase channel labels makes a difference + if islabel + recursion = true; + type = ft_senstype(upper(input)); + recursion = false; + elseif isfield(input, 'label') + input.label = upper(input.label); + recursion = true; + type = ft_senstype(input); + recursion = false; + end +end + +if ~isempty(desired) + % return a boolean flag + switch desired + case 'eeg' + type = any(strcmp(type, {'eeg' 'electrode' 'biosemi64' 'biosemi128' 'biosemi256' 'egi32' 'egi64' 'egi128' 'egi256' 'ext1020'})); + case 'biosemi' + type = any(strcmp(type, {'biosemi64' 'biosemi128' 'biosemi256'})); + case 'egi' + type = any(strcmp(type, {'egi64' 'egi128' 'egi256'})); + case 'meg' + type = any(strcmp(type, {'meg' 'magnetometer' 'ctf' 'bti' 'ctf64' 'ctf151' 'ctf275' 'ctf151_planar' 'ctf275_planar' 'neuromag122' 'neuromag306' 'bti148' 'bti148_planar' 'bti248' 'bti248_planar' 'bti248grad' 'bti248grad_planar' 'yokogawa160' 'yokogawa160_planar' 'yokogawa64' 'yokogawa64_planar' 'yokogawa440' 'yokogawa440_planar' 'itab' 'itab28' 'itab153' 'itab153_planar'})); + case 'ctf' + type = any(strcmp(type, {'ctf' 'ctf64' 'ctf151' 'ctf275' 'ctf151_planar' 'ctf275_planar'})); + case 'bti' + type = any(strcmp(type, {'bti' 'bti148' 'bti148_planar' 'bti248' 'bti248_planar' 'bti248grad' 'bti248grad_planar'})); + case 'neuromag' + type = any(strcmp(type, {'neuromag122' 'neuromag306'})); + case 'yokogawa' + type = any(strcmp(type, {'yokogawa160' 'yokogawa160_planar' 'yokogawa64' 'yokogawa64_planar' 'yokogawa440' 'yokogawa440_planar'})); + case 'itab' + type = any(strcmp(type, {'itab' 'itab28' 'itab153' 'itab153_planar'})); + case 'meg_axial' + % note that neuromag306 is mixed planar and axial + type = any(strcmp(type, {'magnetometer' 'neuromag306' 'ctf64' 'ctf151' 'ctf275' 'bti148' 'bti248' 'bti248grad' 'yokogawa160' 'yokogawa64' 'yokogawa440'})); + case 'meg_planar' + % note that neuromag306 is mixed planar and axial + type = any(strcmp(type, {'neuromag122' 'neuromag306' 'ctf151_planar' 'ctf275_planar' 'bti148_planar' 'bti248_planar' 'bti248grad_planar' 'yokogawa160_planar' 'yokogawa64_planar' 'yokogawa440_planar'})); + otherwise + type = any(strcmp(type, desired)); + end % switch desired +end % detemine the correspondence to the desired type + +% remember the current input and output arguments, so that they can be +% reused on a subsequent call in case the same input argument is given +current_argout = {type}; +previous_argin = current_argin; +previous_argout = current_argout; + +return % ft_senstype main() diff --git a/nft_dipfit/ft_voltype.m b/nft_dipfit/ft_voltype.m new file mode 100644 index 0000000..d04efb8 --- /dev/null +++ b/nft_dipfit/ft_voltype.m @@ -0,0 +1,143 @@ +function [type] = ft_voltype(vol, desired) + +% FT_VOLTYPE determines the type of volume conduction model of the head +% +% Use as +% [type] = ft_voltype(vol) +% to get a string describing the type, or +% [flag] = ft_voltype(vol, desired) +% to get a boolean value. +% +% For EEG the following volume conduction models are recognized +% singlesphere analytical single sphere model +% concentricspheres analytical concentric sphere model with up to 4 spheres +% halfspace infinite homogenous medium on one side, vacuum on the other +% openmeeg boundary element method, based on the OpenMEEG software +% bemcp boundary element method, based on the implementation from Christophe Phillips +% dipoli boundary element method, based on the implementation from Thom Oostendorp +% asa boundary element method, based on the (commercial) ASA software +% simbio finite element method, based on the SimBio software +% fns finite difference method, based on the FNS software +% interpolate interpolate the potential based on pre-computed leadfields +% +% and for MEG the following volume conduction models are recognized +% singlesphere analytical single sphere model +% localspheres local spheres model for MEG, one sphere per channel +% singleshell realisically shaped single shell approximation, based on the implementation from Guido Nolte +% infinite magnetic dipole in an infinite vacuum +% interpolate interpolate the potential based on pre-computed leadfields +% +% See also FT_COMPUTE_LEADFIELD, FT_READ_VOL, FT_HEADMODEL_BEMCP, +% FT_HEADMODEL_ASA, FT_HEADMODEL_DIPOLI, FT_HEADMODEL_SIMBIO, +% FT_HEADMODEL_FNS, FT_HEADMODEL_HALFSPACE, FT_HEADMODEL_INFINITE, +% FT_HEADMODEL_OPENMEEG, FT_HEADMODEL_SINGLESPHERE, +% FT_HEADMODEL_CONCENTRICSPHERES, FT_HEADMODEL_LOCALSPHERES, +% FT_HEADMODEL_SINGLESHELL, FT_HEADMODEL_INTERPOLATE + +% Copyright (C) 2007-2012, Robert Oostenveld +% +% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip +% for the documentation and details. +% +% FieldTrip is free software: you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation, either version 3 of the License, or +% (at your option) any later version. +% +% FieldTrip is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License for more details. +% +% You should have received a copy of the GNU General Public License +% along with FieldTrip. If not, see . +% +% $Id: ft_voltype.m 7402 2013-01-23 16:23:43Z roevdmei $ + +% these are for remembering the type on subsequent calls with the same input arguments +persistent previous_argin previous_argout + +if iscell(vol) && numel(vol)<4 + % this might represent combined EEG, ECoG and/or MEG + type = cell(size(vol)); + if nargin<2 + desired = cell(size(vol)); % empty elements + end + for i=1:numel(vol) + type{i} = ft_voltype(vol{i}, desired{i}); + end + return +end + +if nargin<2 + % ensure that all input arguments are defined + desired = []; +end + +current_argin = {vol, desired}; +if isequal(current_argin, previous_argin) + % don't do the type detection again, but return the previous values from cache + type = previous_argout{1}; + return +end + +% check whether input is a grad or elec array, also containing types +% Note: currently, ft_datatype cannot detect several volumes, and cannot be used here for checking volumness +issens = ft_datatype(vol,'grad') || ft_datatype(vol,'sens'); + + +if isfield(vol, 'type') && ~issens + % preferably the structure specifies its own type + type = vol.type; + +elseif isfield(vol, 'r') && numel(vol.r)==1 && ~isfield(vol, 'label') + type = 'singlesphere'; + +elseif isfield(vol, 'r') && isfield(vol, 'o') && isfield(vol, 'label') + % this is before the spheres have been assigned to the coils + % and every sphere is still associated with a channel + type = 'localspheres'; + +elseif isfield(vol, 'r') && isfield(vol, 'o') && size(vol.r,1)==size(vol.o,1) && size(vol.r,1)>4 + % this is after the spheres have been assigned to the coils + % note that this one is easy to confuse with the concentric one + type = 'localspheres'; + +elseif isfield(vol, 'r') && numel(vol.r)>=2 && ~isfield(vol, 'label') + type = 'concentricspheres'; + +elseif isfield(vol, 'bnd') && isfield(vol, 'mat') + type = 'bem'; % it could be dipoli, asa, bemcp or openmeeg + +elseif isfield(vol, 'bnd') && isfield(vol, 'forwpar') + type = 'singleshell'; + +elseif isfield(vol, 'bnd') && numel(vol.bnd)==1 + type = 'singleshell'; + +elseif isempty(vol) || (isstruct(vol) && isequal(fieldnames(vol), {'unit'})) + % it is empty, or only contains a specification of geometrical units + type = 'infinite'; + +else + type = 'unknown'; + +end % if isfield(vol, 'type') + +if ~isempty(desired) + % return a boolean flag + switch desired + case 'bem' + type = any(strcmp(type, {'bem', 'dipoli', 'asa', 'bemcp', 'openmeeg'})); + otherwise + type = any(strcmp(type, desired)); + end % switch desired +end % determine the correspondence to the desired type + +% remember the current input and output arguments, so that they can be +% reused on a subsequent call in case the same input argument is given +current_argout = {type}; +previous_argin = current_argin; +previous_argout = current_argout; + +return % voltype main() diff --git a/nft_dipfit/issubfield.m b/nft_dipfit/issubfield.m new file mode 100644 index 0000000..bfb0ea1 --- /dev/null +++ b/nft_dipfit/issubfield.m @@ -0,0 +1,42 @@ +function [r] = issubfield(s, f) + +% ISSUBFIELD tests for the presence of a field in a structure just like the standard +% Matlab ISFIELD function, except that you can also specify nested fields +% using a '.' in the fieldname. The nesting can be arbitrary deep. +% +% Use as +% f = issubfield(s, 'fieldname') +% or as +% f = issubfield(s, 'fieldname.subfieldname') +% +% This function returns true if the field is present and false if the field +% is not present. +% +% See also ISFIELD, GETSUBFIELD, SETSUBFIELD + +% Copyright (C) 2005, Robert Oostenveld +% +% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip +% for the documentation and details. +% +% FieldTrip is free software: you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation, either version 3 of the License, or +% (at your option) any later version. +% +% FieldTrip is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License for more details. +% +% You should have received a copy of the GNU General Public License +% along with FieldTrip. If not, see . +% +% $Id: issubfield.m 7123 2012-12-06 21:21:38Z roboos $ + +try + getsubfield(s, f); % if this works, then the subfield must be present + r = true; +catch + r = false; % apparently the subfield is not present +end diff --git a/nft_inverse_problem_solution.m b/nft_inverse_problem_solution.m index 4b8e4d6..7777ec0 100644 --- a/nft_inverse_problem_solution.m +++ b/nft_inverse_problem_solution.m @@ -18,7 +18,7 @@ % ss_name : sourcespace name (default: [subject_name '_sourcespace.dip']) % % Outputs: -% dip1 - dipole structure with fields posxyzsymm, momxyz, rv +% dip1 - dipole structure with fields posxyz, momxyz, rv % % % Author: Zeynep Akalin Acar, SCCN, 2012 diff --git a/readme.txt b/readme.txt new file mode 100644 index 0000000..46e1a63 --- /dev/null +++ b/readme.txt @@ -0,0 +1,53 @@ +This is an implementation of geodesic (shortest path) algorithm for triangular mesh (triangulated surface) first described by Mitchell, Mount and Papadimitriou in 1987[1] with some minor improvements, extensions and simplifications. The algorithm has O(n^2 log n) worst-case time complexity, but in practice can work with million-node meshes in reasonable time. For the quick overview, see [2]. + +The basic idea of the algorithm is very similar to Dijkstra's algorithm for finding shortest path on a weighted graph. It has two steps: +- propagation of the distance field from sources over the surface of the mesh (slow) +- tracing back the shortest path from target point to the closest source (fast) + +For debugging and comparison purposes I also implemented two approximate algorithms +- Dijkstra shortest path on the graph created by the vertices and edges of the mesh +- Subdivision (put N additional vertices on every edge of the mesh, directly connect all vertices belonging to the same face, run Dijkstra on the resulting graph) +The nice property of the subdivision algorithm is that it becomes Dijkstra when N=0 and computes exact distances when N->infinity. + +The input mesh is represented as two arrays: vertices (each vertex has tree coordinates) and faces (each face is represented as indices of its vertices). Most of the communication with the algorithms is done through SurfacePoints (points on the surface of the mesh; they have three coordinates and a pointer to a mesh element they belong). + +The algorithms are available as C++ code (downloadable at http://code.google.com/p/geodesic/) and Matlab toolbox (downloadable at MathWorks File Exchange). + +C++ NOTES +The base class of for all algorithms is GeodesicAlgorithmBase (defined in geodesic_algorithm_base.h). The most important functions defined in this class are +- propagate(...). It is possible to stop propagation after it reaches certain distance or covers certain points on the surface of the mesh; O(n^2 log n). +- trace_back(…). It traces the shortest path from target to the nearest source; O(n) . +- best_source(…). For a given point on the surface of the mesh, this function reports the closest source and the distance to this source; O(1). +Read example0.cpp and example1.cpp – they are self-explanatory. + +MATLAB NOTES +- you do not have to compile anything; the algorithm is already available as C library (it has _debug and _release versions) +- just in case, the header of the library is geodesic_matlab_api.h; all the functions are instantiated in geodesic_matlab_api.c (this is the only file you have to compile for the library). +- only Windows version of the library is provided. If you need them on other operating systems, you are on your own – download C++ code and compile geodesic_matlab_api.c into a library +Play with example1.m – example5.m; they are self-explanatory. + +Limitations and known issues. + +The mesh should be edge-connected. I.e. for every two faces of the mesh there should exist a connecting path on the surface of the mesh that does not go through any vertex. This property implies the simple connectivity of the mesh. In particular, there should be no vertices that are not used by any of the triangles. + +There is a list of possible features and improvements that could be done to the algorithm. +- Memory is currently a bottleneck for large meshes. In theory, it is possible to overcome it if all destinations are known BEFORE the propagation step. +- For large flat parts of the mesh (vertices whose total adjacent angles sum up to exactly 2*pi) the current version of the algorithm uses more time and memory than necessary. + +ACKNOWLEDGEMENTS +I am very grateful to Steven Gortler without whom this project would never exist. Hugues Hoppe helped to develop the early version of the algorithm by providing his mesh processing code as well as many helpful advices. Tatiana and Vitaly Surazhsky did a great job analyzing the complexity of the algorithm for the “regular” meshes. + +REPORTING BUGS AND SENDING LOVE/HATE MAIL +If you have a bug, first check your mesh and run the algorithm in debug mode. Most likely, the mesh is numbered incorrectly or disconnected or of somehow degenerate. +Usually, I am not very good communicating with people, but you can try reaching me at exact.geodesic@gmail.com + +Best, +Danil Kirsanov, 01/2008 + +[1] J.S.B. Mitchell, D.~M. Mount, and C.~H. Papadimitriou. SIAM J. Comput., 16:647--668, 1987. +[2] J. O'Rourke, Computational Geometry Column 35, SIGACT News, 30(2) Issue #111 (1999) 31-32, 1993 (could be found at citeseer.ist.psu.edu) + + +CHANGES ON 03/03/08 +- fixed libpointer conflict with matlab 2007b +- fixed cellfun error with earlier versions of matlab \ No newline at end of file diff --git a/replay_pid18352.log b/replay_pid18352.log deleted file mode 100644 index 1edf356..0000000 --- a/replay_pid18352.log +++ /dev/null @@ -1,10213 +0,0 @@ -JvmtiExport can_access_local_variables 0 -JvmtiExport can_hotswap_or_post_breakpoint 0 -JvmtiExport can_post_on_exceptions 0 -# 597 ciObject found -instanceKlass java/util/concurrent/locks/ReentrantReadWriteLock$Sync$HoldCounter -instanceKlass com/mathworks/cmlink/management/cache/transaction/FolderCacheTransaction -instanceKlass com/mathworks/cmlink/management/cache/transaction/FileUpdateTransaction -instanceKlass com/mathworks/mwswing/datatransfer/MJTransferable$CompoundTransferable -instanceKlass 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12 12 12 1 1 1 1 12 12 12 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield java/lang/invoke/DirectMethodHandle IMPL_NAMES Ljava/lang/invoke/MemberName$Factory; java/lang/invoke/MemberName$Factory -staticfield java/lang/invoke/DirectMethodHandle ACCESSOR_FORMS [Ljava/lang/invoke/LambdaForm; 132 [Ljava/lang/invoke/LambdaForm; -staticfield java/lang/invoke/DirectMethodHandle $assertionsDisabled Z 1 -ciInstanceKlass java/lang/invoke/MemberName 1 1 654 7 7 100 10 10 10 9 9 10 9 10 10 10 10 10 10 10 9 10 100 7 10 8 10 10 10 10 9 8 10 7 7 10 10 7 7 7 10 9 100 8 10 10 10 10 10 10 10 10 10 8 8 8 10 10 9 3 10 10 10 10 10 10 10 10 10 7 8 10 10 8 9 8 9 10 8 10 10 10 10 10 100 10 10 8 10 10 8 10 10 100 10 10 8 8 10 10 10 10 10 10 10 10 10 3 10 3 10 3 3 3 3 3 3 10 100 10 3 10 3 10 10 10 10 10 10 10 10 10 10 10 10 100 10 10 10 100 10 10 10 10 100 10 10 8 10 10 10 10 10 10 10 10 10 10 10 100 10 100 8 10 10 10 10 10 10 10 8 8 8 8 10 10 10 8 8 10 8 10 10 10 8 8 10 10 8 8 100 10 8 8 8 8 10 7 7 7 10 100 10 7 10 9 10 100 100 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 3 1 3 1 3 1 3 1 3 1 1 1 1 1 1 1 1 3 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 100 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 100 1 1 1 1 1 100 1 1 1 100 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 7 1 1 12 12 12 12 12 12 12 12 12 12 12 12 12 12 100 12 12 1 1 12 1 12 12 12 12 12 1 100 12 1 1 12 1 1 1 12 12 1 1 12 12 12 12 12 12 12 12 12 1 1 1 100 12 12 12 12 12 12 12 12 12 12 12 1 12 12 100 100 12 1 12 12 12 12 12 1 12 12 1 12 12 1 12 12 1 12 12 1 1 12 12 12 12 12 12 12 12 12 12 12 100 1 1 7 12 12 12 12 12 7 12 12 12 12 12 12 1 12 1 12 12 1 12 100 12 100 12 12 12 12 12 12 12 1 12 1 1 7 12 12 7 12 12 12 1 1 1 1 12 12 12 1 1 12 1 12 12 1 1 12 1 1 1 1 1 1 1 12 1 1 1 1 1 7 12 12 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield java/lang/invoke/MemberName $assertionsDisabled Z 1 -ciInstanceKlass java/lang/invoke/MethodHandleNatives 1 1 442 100 10 9 10 100 10 10 10 10 8 8 8 8 8 8 8 8 8 8 7 10 7 10 10 100 10 10 8 10 8 10 8 10 9 8 10 100 10 100 100 8 7 7 10 10 7 9 10 10 10 7 10 10 10 10 100 10 9 8 10 8 10 8 8 8 100 8 10 10 10 10 10 100 10 10 8 8 10 10 10 8 10 8 8 9 10 10 10 100 100 10 10 10 100 100 10 10 100 10 10 100 100 10 10 10 10 100 10 10 10 10 10 10 10 8 8 100 10 100 10 10 10 10 7 10 10 10 9 10 10 10 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 100 100 1 1 100 100 100 100 1 1 100 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 100 100 100 100 1 1 1 100 100 1 1 1 1 1 1 1 1 1 12 12 12 1 12 12 12 1 1 1 1 1 1 1 1 1 1 1 12 1 12 100 12 1 12 1 12 1 12 1 12 100 12 1 100 12 1 12 1 1 1 1 1 12 1 7 12 12 12 7 12 1 12 7 12 12 12 1 100 12 12 1 12 1 12 1 1 1 1 1 12 12 12 12 12 1 12 12 1 1 12 12 1 100 12 1 1 7 12 12 12 12 1 1 12 1 1 1 1 1 100 12 12 1 12 7 12 12 12 12 12 1 1 1 12 1 12 12 12 12 1 12 12 12 12 7 12 12 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield java/lang/invoke/MethodHandleNatives COUNT_GWT Z 1 -staticfield java/lang/invoke/MethodHandleNatives $assertionsDisabled Z 1 -ciInstanceKlass java/lang/invoke/LambdaForm 1 1 986 7 100 9 10 10 9 9 10 100 10 9 10 9 10 7 9 10 9 9 9 10 7 10 10 10 10 10 10 10 9 10 8 10 10 10 10 7 10 10 8 10 10 10 100 8 10 10 10 10 10 7 10 7 10 10 9 9 10 10 100 10 10 10 10 10 10 10 10 10 10 8 10 10 8 8 9 9 9 10 10 10 9 10 10 10 10 10 10 10 10 8 8 8 8 8 8 8 8 10 9 10 10 10 10 10 10 10 7 10 10 9 10 10 10 10 10 10 8 10 100 100 10 10 10 10 11 11 11 7 10 10 10 10 7 10 8 10 10 8 10 10 10 7 10 8 10 9 10 10 8 8 10 10 8 8 8 10 10 9 10 8 8 9 10 10 8 8 8 100 8 100 8 100 8 10 8 10 9 10 10 9 10 10 10 10 10 10 10 10 10 10 8 100 10 10 9 10 8 8 100 8 8 9 8 8 8 10 8 8 8 10 10 8 8 8 10 8 10 8 8 8 8 8 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 9 8 10 11 11 9 9 9 9 9 10 10 8 10 8 9 7 10 100 10 7 10 9 10 10 10 10 9 10 10 9 10 9 10 9 7 9 9 10 100 10 10 10 10 9 100 1 100 1 100 1 1 1 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 3 1 3 1 1 1 3 1 1 1 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 100 100 1 1 1 1 1 1 100 1 1 1 1 1 1 1 100 100 100 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 100 1 100 100 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 100 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 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1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield java/lang/invoke/LambdaForm COMPILE_THRESHOLD I 0 -staticfield java/lang/invoke/LambdaForm INTERNED_ARGUMENTS [[Ljava/lang/invoke/LambdaForm$Name; 5 [[Ljava/lang/invoke/LambdaForm$Name; -staticfield java/lang/invoke/LambdaForm IMPL_NAMES Ljava/lang/invoke/MemberName$Factory; java/lang/invoke/MemberName$Factory -staticfield java/lang/invoke/LambdaForm LF_identityForm [Ljava/lang/invoke/LambdaForm; 6 [Ljava/lang/invoke/LambdaForm; -staticfield java/lang/invoke/LambdaForm LF_zeroForm [Ljava/lang/invoke/LambdaForm; 6 [Ljava/lang/invoke/LambdaForm; -staticfield java/lang/invoke/LambdaForm NF_identity [Ljava/lang/invoke/LambdaForm$NamedFunction; 6 [Ljava/lang/invoke/LambdaForm$NamedFunction; -staticfield java/lang/invoke/LambdaForm NF_zero [Ljava/lang/invoke/LambdaForm$NamedFunction; 6 [Ljava/lang/invoke/LambdaForm$NamedFunction; -staticfield java/lang/invoke/LambdaForm DEBUG_NAME_COUNTERS Ljava/util/HashMap; null -staticfield java/lang/invoke/LambdaForm TRACE_INTERPRETER Z 0 -staticfield java/lang/invoke/LambdaForm $assertionsDisabled Z 1 -ciInstanceKlass java/lang/invoke/MethodType 1 1 608 7 10 10 10 9 10 7 9 9 10 9 8 10 10 9 9 10 7 10 8 10 10 10 100 8 10 100 10 10 10 10 11 9 11 7 10 9 10 10 10 10 10 9 7 10 7 10 10 10 10 10 10 10 10 10 10 8 8 10 9 100 10 10 10 10 10 10 10 10 10 8 10 10 10 10 10 11 10 10 10 10 10 7 10 10 10 10 9 7 10 10 10 10 10 10 10 10 8 8 10 8 10 10 9 10 10 10 10 10 10 10 10 10 10 10 10 9 7 10 10 10 10 10 8 10 11 9 10 10 10 10 10 10 10 10 10 9 9 10 9 10 7 10 7 9 8 10 10 8 100 100 10 100 1 1 1 1 1 5 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 3 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 100 1 1 1 1 1 1 1 100 1 1 100 1 1 1 1 1 1 100 100 1 100 1 1 1 1 1 100 1 1 100 1 1 1 1 1 1 1 100 1 1 1 12 12 12 12 7 12 12 12 7 12 7 12 1 7 12 12 7 7 12 1 1 12 12 12 1 1 12 1 12 12 12 7 12 12 12 1 7 12 12 12 12 12 12 12 12 1 12 1 12 12 100 12 12 12 12 12 12 12 12 1 1 12 12 1 12 12 12 12 100 12 12 12 1 12 12 7 12 12 12 12 12 12 12 12 12 1 12 12 12 12 1 12 7 12 12 7 12 12 12 1 1 12 1 100 12 12 12 12 12 12 12 12 12 100 12 12 12 12 12 12 1 12 12 12 7 12 12 1 7 12 12 12 12 12 100 12 12 12 100 12 12 100 12 12 12 7 12 12 12 1 1 12 12 12 1 1 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield java/lang/invoke/MethodType internTable Ljava/lang/invoke/MethodType$ConcurrentWeakInternSet; java/lang/invoke/MethodType$ConcurrentWeakInternSet -staticfield java/lang/invoke/MethodType NO_PTYPES [Ljava/lang/Class; 0 [Ljava/lang/Class; -staticfield java/lang/invoke/MethodType objectOnlyTypes [Ljava/lang/invoke/MethodType; 20 [Ljava/lang/invoke/MethodType; -staticfield java/lang/invoke/MethodType serialPersistentFields [Ljava/io/ObjectStreamField; 0 [Ljava/io/ObjectStreamField; -staticfield java/lang/invoke/MethodType rtypeOffset J 12 -staticfield java/lang/invoke/MethodType ptypesOffset J 16 -staticfield java/lang/invoke/MethodType $assertionsDisabled Z 1 -ciInstanceKlass java/lang/BootstrapMethodError 0 0 39 10 10 10 10 10 100 100 1 1 1 5 0 1 1 1 1 1 1 1 1 100 100 1 1 12 12 12 100 12 12 1 1 1 1 1 1 1 1 -instanceKlass java/lang/invoke/VolatileCallSite -instanceKlass java/lang/invoke/MutableCallSite -instanceKlass java/lang/invoke/ConstantCallSite -ciInstanceKlass java/lang/invoke/CallSite 1 1 322 10 10 9 10 10 100 7 10 7 10 10 10 100 100 10 10 10 8 10 10 10 9 10 10 10 10 100 8 10 10 10 100 10 9 10 10 10 10 9 9 10 10 9 10 10 10 10 10 10 7 10 10 10 10 10 10 7 100 8 10 10 10 10 10 7 100 8 10 10 100 8 10 7 10 10 10 8 10 10 8 10 10 100 10 8 10 10 100 100 10 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 100 1 1 1 1 1 100 100 100 100 100 100 100 1 1 1 1 1 1 1 1 100 100 1 1 12 12 12 12 12 1 1 12 1 12 12 12 1 1 100 12 12 1 12 12 12 12 12 100 12 12 1 1 12 12 1 12 12 12 12 12 100 12 7 12 12 7 12 12 7 12 12 12 12 12 7 12 12 1 12 12 12 12 12 12 1 1 1 12 12 100 12 12 1 1 1 12 1 1 12 1 12 12 7 12 12 12 12 12 1 12 12 12 1 1 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield java/lang/invoke/CallSite GET_TARGET Ljava/lang/invoke/MethodHandle; java/lang/invoke/DirectMethodHandle -staticfield java/lang/invoke/CallSite THROW_UCS Ljava/lang/invoke/MethodHandle; java/lang/invoke/MethodHandleImpl$AsVarargsCollector -staticfield java/lang/invoke/CallSite TARGET_OFFSET J 12 -ciInstanceKlass java/lang/invoke/ConstantCallSite 1 1 42 10 9 10 100 10 9 100 10 10 7 7 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 12 12 12 1 12 12 1 12 1 1 1 1 1 1 -ciInstanceKlass java/lang/invoke/MutableCallSite 0 0 57 10 10 9 10 10 10 9 10 10 100 10 100 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 12 12 12 12 12 12 12 12 100 12 1 12 1 1 1 1 1 1 1 1 1 1 1 1 1 -ciInstanceKlass java/lang/invoke/VolatileCallSite 0 0 33 10 10 10 10 10 10 100 100 1 1 1 1 1 1 1 1 1 1 1 12 12 12 12 12 12 1 1 1 1 1 1 1 -instanceKlass java/lang/StringBuilder -instanceKlass java/lang/StringBuffer -ciInstanceKlass java/lang/AbstractStringBuilder 1 1 318 7 10 9 9 10 10 10 7 3 10 3 100 10 100 10 10 10 10 100 10 10 10 8 10 10 10 10 10 10 10 10 10 10 10 7 10 11 10 8 100 10 8 10 10 8 8 10 10 11 3 8 10 10 7 5 0 8 10 10 10 10 10 10 10 10 100 10 8 8 10 10 10 8 8 8 10 10 8 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 7 100 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 12 12 12 12 12 7 12 1 12 1 1 12 12 7 12 12 1 12 12 1 12 7 12 12 12 12 12 12 100 1 12 12 1 1 1 12 12 1 1 12 12 1 12 12 1 1 12 12 7 12 12 12 12 12 1 1 1 12 12 12 1 1 1 12 12 1 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -ciInstanceKlass java/lang/StringBuffer 1 1 371 10 10 10 11 10 10 9 9 10 10 9 10 100 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 7 10 10 8 10 8 10 8 10 10 10 10 7 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 7 10 9 9 9 7 7 100 100 1 1 1 1 1 5 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 12 12 12 12 12 12 12 12 12 12 1 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 7 12 1 12 100 12 1 100 12 1 12 1 12 12 100 12 100 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 1 12 7 12 7 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield java/lang/StringBuffer serialPersistentFields [Ljava/io/ObjectStreamField; 3 [Ljava/io/ObjectStreamField; -ciInstanceKlass java/lang/StringBuilder 1 1 326 10 10 10 11 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 7 9 9 10 10 10 10 10 10 10 100 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 7 7 100 100 1 1 1 5 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 1 12 12 12 100 12 12 12 100 12 12 12 1 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -ciInstanceKlass sun/misc/Unsafe 1 1 390 10 10 10 10 100 8 10 9 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 100 10 10 7 7 8 10 10 7 10 9 7 9 7 9 7 9 7 9 7 9 7 9 7 9 7 9 10 9 9 9 9 9 9 9 9 9 10 9 7 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 12 7 12 7 12 7 12 1 1 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 100 12 100 12 12 12 12 12 12 12 12 12 12 12 1 12 1 1 12 1 12 12 1 12 1 12 1 12 1 12 1 12 1 12 1 12 1 12 12 12 12 12 12 12 12 12 12 12 12 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield sun/misc/Unsafe theUnsafe Lsun/misc/Unsafe; sun/misc/Unsafe -staticfield sun/misc/Unsafe ARRAY_BOOLEAN_BASE_OFFSET I 16 -staticfield sun/misc/Unsafe ARRAY_BYTE_BASE_OFFSET I 16 -staticfield sun/misc/Unsafe ARRAY_SHORT_BASE_OFFSET I 16 -staticfield sun/misc/Unsafe ARRAY_CHAR_BASE_OFFSET I 16 -staticfield sun/misc/Unsafe ARRAY_INT_BASE_OFFSET I 16 -staticfield sun/misc/Unsafe ARRAY_LONG_BASE_OFFSET I 16 -staticfield sun/misc/Unsafe ARRAY_FLOAT_BASE_OFFSET I 16 -staticfield sun/misc/Unsafe ARRAY_DOUBLE_BASE_OFFSET I 16 -staticfield sun/misc/Unsafe ARRAY_OBJECT_BASE_OFFSET I 16 -staticfield sun/misc/Unsafe ARRAY_BOOLEAN_INDEX_SCALE I 1 -staticfield sun/misc/Unsafe ARRAY_BYTE_INDEX_SCALE I 1 -staticfield sun/misc/Unsafe ARRAY_SHORT_INDEX_SCALE I 2 -staticfield sun/misc/Unsafe ARRAY_CHAR_INDEX_SCALE I 2 -staticfield sun/misc/Unsafe ARRAY_INT_INDEX_SCALE I 4 -staticfield sun/misc/Unsafe ARRAY_LONG_INDEX_SCALE I 8 -staticfield sun/misc/Unsafe ARRAY_FLOAT_INDEX_SCALE I 4 -staticfield sun/misc/Unsafe ARRAY_DOUBLE_INDEX_SCALE I 8 -staticfield sun/misc/Unsafe ARRAY_OBJECT_INDEX_SCALE I 4 -staticfield sun/misc/Unsafe ADDRESS_SIZE I 8 -instanceKlass org/eclipse/jgit/util/io/AutoCRLFInputStream -instanceKlass org/eclipse/jgit/util/io/AutoLFInputStream -instanceKlass org/eclipse/jgit/lib/ObjectStream -instanceKlass sun/net/www/http/ChunkedInputStream -instanceKlass com/sun/imageio/plugins/common/InputStreamAdapter -instanceKlass sun/security/ssl/HandshakeInStream -instanceKlass sun/security/ssl/AppInputStream -instanceKlass java/io/ObjectInputStream$PeekInputStream -instanceKlass java/io/ObjectInputStream$BlockDataInputStream -instanceKlass 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java/util/Locale -staticfield java/util/Locale SIMPLIFIED_CHINESE Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale TRADITIONAL_CHINESE Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale FRANCE Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale GERMANY Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale ITALY Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale JAPAN Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale KOREA Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale CHINA Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale PRC Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale TAIWAN Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale UK Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale US Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale CANADA Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale CANADA_FRENCH Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale ROOT Ljava/util/Locale; java/util/Locale -staticfield java/util/Locale serialPersistentFields [Ljava/io/ObjectStreamField; 6 [Ljava/io/ObjectStreamField; -staticfield java/util/Locale $assertionsDisabled Z 1 -ciInstanceKlass java/util/concurrent/ConcurrentHashMap 1 1 1036 7 7 3 3 100 10 100 10 100 11 11 11 9 9 9 10 7 10 10 10 100 10 3 10 9 10 10 5 0 10 5 0 10 10 9 10 9 9 10 9 10 9 10 100 10 100 10 10 10 10 10 10 10 100 10 10 10 11 10 11 11 11 11 100 11 11 10 10 9 10 9 10 9 10 5 0 9 7 10 9 7 10 9 100 10 100 10 10 8 10 10 100 11 100 7 4 10 10 8 10 8 10 8 10 10 10 10 5 0 7 100 10 9 9 10 9 11 11 7 10 11 10 100 10 100 10 10 9 10 10 9 10 9 10 9 9 10 10 9 9 10 10 9 9 9 9 10 7 9 9 100 10 9 10 9 7 10 9 10 100 5 0 10 100 10 10 10 100 10 10 100 100 10 10 10 100 10 10 100 10 10 100 10 100 10 10 10 100 10 10 10 100 10 10 100 10 10 100 10 10 100 10 10 100 10 10 100 10 10 100 10 10 100 10 10 100 10 10 100 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java/util/concurrent/ConcurrentHashMap MAX_RESIZERS I 65535 -staticfield java/util/concurrent/ConcurrentHashMap RESIZE_STAMP_SHIFT I 16 -staticfield java/util/concurrent/ConcurrentHashMap NCPU I 32 -staticfield java/util/concurrent/ConcurrentHashMap serialPersistentFields [Ljava/io/ObjectStreamField; 3 [Ljava/io/ObjectStreamField; -staticfield java/util/concurrent/ConcurrentHashMap U Lsun/misc/Unsafe; sun/misc/Unsafe -staticfield java/util/concurrent/ConcurrentHashMap SIZECTL J 20 -staticfield java/util/concurrent/ConcurrentHashMap TRANSFERINDEX J 32 -staticfield java/util/concurrent/ConcurrentHashMap BASECOUNT J 24 -staticfield java/util/concurrent/ConcurrentHashMap CELLSBUSY J 36 -staticfield java/util/concurrent/ConcurrentHashMap CELLVALUE J 144 -staticfield java/util/concurrent/ConcurrentHashMap ABASE J 16 -staticfield java/util/concurrent/ConcurrentHashMap ASHIFT I 2 -instanceKlass sun/net/www/protocol/http/Handler -instanceKlass sun/net/www/protocol/jar/Handler -instanceKlass 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sun/misc/URLClassPath$JarLoader zipAccess Lsun/misc/JavaUtilZipFileAccess; java/util/zip/ZipFile$1 -instanceKlass java/util/jar/JarFile -ciInstanceKlass java/util/zip/ZipFile 1 1 527 7 100 10 10 10 10 10 10 10 9 10 9 10 9 9 10 10 9 7 10 7 10 9 10 10 7 10 7 10 9 100 100 10 8 10 10 10 10 10 10 10 10 100 8 10 10 9 10 10 9 10 10 10 10 10 10 10 9 10 10 8 10 10 9 8 10 9 9 10 7 10 10 11 5 0 5 0 5 0 5 0 10 7 10 100 8 10 11 7 10 10 10 11 7 10 10 100 10 10 10 10 10 8 10 10 9 10 9 9 9 9 10 9 11 100 10 11 11 11 11 11 100 11 100 10 11 10 10 10 100 8 10 8 8 10 8 10 10 8 10 8 8 7 10 10 7 100 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 3 1 3 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 100 1 1 1 1 100 100 100 100 100 1 1 1 1 100 100 100 1 1 100 1 1 1 1 1 100 100 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 1 12 1 12 7 12 12 12 1 1 12 1 1 1 12 100 12 12 12 7 12 100 12 12 1 1 7 12 12 12 12 12 12 7 12 12 12 12 12 12 12 12 12 12 12 12 1 12 12 12 1 12 12 7 12 12 1 12 1 1 7 12 1 12 12 12 12 1 12 12 1 100 12 100 12 12 12 1 12 12 12 12 12 12 12 12 12 12 12 1 12 12 12 100 12 100 12 12 1 1 12 1 12 12 12 12 1 1 1 1 12 1 7 12 100 12 1 12 1 1 1 7 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield java/util/zip/ZipFile usemmap Z 1 -staticfield java/util/zip/ZipFile ensuretrailingslash Z 1 -instanceKlass org/eclipse/jgit/errors/UnmergedPathException -instanceKlass org/eclipse/jgit/errors/IndexReadException -instanceKlass java/util/zip/ZipException -instanceKlass org/eclipse/jgit/errors/UnsupportedPackVersionException -instanceKlass org/eclipse/jgit/errors/UnsupportedPackIndexVersionException -instanceKlass org/eclipse/jgit/errors/UnpackException -instanceKlass org/eclipse/jgit/errors/NoPackSignatureException -instanceKlass org/eclipse/jgit/errors/PackInvalidException -instanceKlass org/eclipse/jgit/util/io/AutoLFInputStream$IsBinaryException -instanceKlass org/eclipse/jgit/errors/MissingObjectException -instanceKlass org/eclipse/jgit/errors/PackMismatchException -instanceKlass org/eclipse/jgit/errors/LockFailedException -instanceKlass org/eclipse/jgit/errors/AmbiguousObjectException -instanceKlass org/eclipse/jgit/errors/IncorrectObjectTypeException -instanceKlass org/eclipse/jgit/errors/TransportException -instanceKlass java/nio/charset/CharacterCodingException -instanceKlass org/eclipse/jgit/errors/CorruptObjectException -instanceKlass java/net/UnknownHostException -instanceKlass java/net/ProtocolException -instanceKlass java/rmi/RemoteException -instanceKlass java/io/InterruptedIOException -instanceKlass javax/net/ssl/SSLException -instanceKlass org/apache/commons/httpclient/HttpException -instanceKlass java/net/SocketException 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10 7 10 10 9 10 9 10 9 10 9 9 9 10 9 7 8 10 10 7 9 9 7 10 10 8 10 8 8 8 8 8 8 8 8 8 8 10 10 100 10 10 10 10 10 100 10 10 100 10 10 11 100 10 10 100 10 9 10 10 10 10 100 10 7 10 10 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 100 1 1 1 1 1 1 100 1 1 1 1 1 1 1 1 100 100 1 100 100 1 1 100 100 100 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 100 1 1 1 1 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 12 12 12 1 12 1 12 12 12 12 12 12 1 12 12 1 12 12 12 1 12 1 12 12 1 1 12 1 12 12 1 100 12 100 12 12 7 12 12 1 12 1 1 1 12 1 1 12 7 12 12 1 1 1 12 12 12 1 12 1 100 12 12 12 1 12 1 7 12 7 12 7 12 1 12 12 1 1 12 12 12 12 12 7 12 12 12 12 12 12 12 12 1 1 7 12 1 12 12 1 12 12 1 12 1 1 1 1 1 1 1 1 1 1 12 1 12 12 12 12 12 1 12 12 1 12 12 100 12 1 12 1 12 12 12 12 12 1 1 7 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield java/util/jar/JarFile CLASSPATH_CHARS [C 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1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -staticfield sun/misc/PerfCounter perf Lsun/misc/Perf; sun/misc/Perf -ciInstanceKlass sun/misc/PerfCounter$CoreCounters 1 1 53 10 8 10 9 8 9 8 9 8 9 8 9 8 9 7 100 1 1 1 1 1 1 1 1 1 1 1 1 1 1 12 1 7 12 12 1 12 1 12 1 12 1 12 1 12 1 1 1 1 1 1 1 -staticfield sun/misc/PerfCounter$CoreCounters pdt Lsun/misc/PerfCounter; sun/misc/PerfCounter -staticfield sun/misc/PerfCounter$CoreCounters lc Lsun/misc/PerfCounter; sun/misc/PerfCounter -staticfield sun/misc/PerfCounter$CoreCounters lct Lsun/misc/PerfCounter; sun/misc/PerfCounter -staticfield sun/misc/PerfCounter$CoreCounters rcbt Lsun/misc/PerfCounter; sun/misc/PerfCounter -staticfield sun/misc/PerfCounter$CoreCounters zfc Lsun/misc/PerfCounter; sun/misc/PerfCounter -staticfield sun/misc/PerfCounter$CoreCounters zfot Lsun/misc/PerfCounter; sun/misc/PerfCounter -instanceKlass java/nio/DirectLongBufferU -ciInstanceKlass java/nio/LongBuffer 1 1 179 10 9 9 10 100 10 100 10 10 100 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(Ljava/net/URLClassLoader;Ljava/lang/String;Lsun/misc/Resource;)Ljava/lang/Class; 2 7814 orig 264 80 90 188 138 53 43 0 0 24 140 161 189 53 43 0 0 64 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 124 0 0 0 81 240 0 0 1 0 0 0 173 18 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0 255 255 255 255 2 0 3 0 0 0 0 0 data 2 0x30002 0x1e0a oops 0 -ciMethodData java/net/URLClassLoader defineClass (Ljava/lang/String;Lsun/misc/Resource;)Ljava/lang/Class; 2 7814 orig 264 80 90 188 138 53 43 0 0 192 131 161 189 53 43 0 0 56 4 0 0 192 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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[Ljava/security/cert/Certificate; 73 [Ljava/security/cert/Certificate; -ciMethodData java/util/ArrayList toArray ([Ljava/lang/Object;)[Ljava/lang/Object; 2 5139 orig 264 80 90 188 138 53 43 0 0 152 241 165 189 53 43 0 0 64 2 0 0 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 16 0 0 0 25 160 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 8 0 2 0 0 0 240 0 0 0 255 255 255 255 7 0 6 0 0 0 0 0 data 30 0x60007 0xb24 0x90 0x8df 0x120005 0x5f 0x2b3624671d30 0x87f 0x2b3624671e40 0x1 0x150002 0x8df 0x180004 0x0 0x2b3624671f50 0x26 0x2b3624671f90 0x1 0x270002 0xb24 0x300007 0xb23 0x50 0x1 0x390104 0x0 0x0 0x0 0x0 0x0 oops 4 6 [Ljava/awt/Component; 8 [Lsun/security/jca/ProviderConfig; 14 [Ljava/lang/Class; 16 [Ljava/lang/invoke/MethodHandle; -ciMethodData java/net/URLStreamHandler getHostAddress (Ljava/net/URL;)Ljava/net/InetAddress; 2 5392 orig 264 80 90 188 138 53 43 0 0 136 72 181 189 53 43 0 0 56 2 0 0 160 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 113 160 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 14 0 2 0 0 0 232 0 0 0 255 255 255 255 7 0 4 0 0 0 0 0 data 29 0x40007 0x140e 0x20 0x0 0xd0005 0x0 0x2b358eeb9530 0x140e 0x0 0x0 0x120007 0x0 0x70 0x140e 0x180005 0x0 0x2b358d8a8930 0x140e 0x0 0x0 0x1b0007 0x0 0x20 0x140e 0x220002 0x0 0x280003 0x0 0x18 oops 2 6 java/net/URL 16 java/lang/String -ciMethodData java/util/jar/Manifest (Ljava/io/InputStream;)V 1 411 orig 264 80 90 188 138 53 43 0 0 8 212 161 189 53 43 0 0 176 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 0 0 0 145 11 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 3 0 2 0 0 0 96 0 0 0 255 255 255 255 2 0 1 0 0 0 0 0 data 12 0x10002 0x172 0x90002 0x172 0x140002 0x172 0x1c0005 0x0 0x2b358eeb95c0 0x172 0x0 0x0 oops 1 8 java/util/jar/Manifest -ciMethodData java/lang/ClassLoader getPackage (Ljava/lang/String;)Ljava/lang/Package; 2 5412 orig 264 80 90 188 138 53 43 0 0 96 93 154 189 53 43 0 0 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java/util/HashMap 8 java/lang/Package 25 sun/misc/Launcher$ExtClassLoader 27 sun/misc/Launcher$AppClassLoader 40 java/util/HashMap 56 java/util/HashMap -ciMethodData java/security/CodeSource hashCode ()I 2 5427 orig 264 80 90 188 138 53 43 0 0 200 29 162 189 53 43 0 0 152 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 153 161 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 9 0 2 0 0 0 80 0 0 0 255 255 255 255 7 0 4 0 0 0 0 0 data 10 0x40007 0x2 0x50 0x1431 0xb0005 0x0 0x2b358eeb9530 0x1431 0x0 0x0 oops 1 6 java/net/URL -ciMethodData java/net/URL hashCode ()I 2 5425 orig 264 80 90 188 138 53 43 0 0 16 183 161 189 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(Ljava/security/CodeSource;)Ljava/security/ProtectionDomain; 2 7976 orig 264 80 90 188 138 53 43 0 0 0 77 155 189 53 43 0 0 152 3 0 0 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 128 1 0 0 65 237 0 0 1 0 0 0 19 20 0 0 0 0 0 0 2 0 0 0 0 0 21 0 2 0 0 0 72 2 0 0 255 255 255 255 7 0 1 0 0 0 0 0 data 73 0x10007 0x1da8 0x20 0x0 0x140005 0x0 0x2b3604b21070 0x1da8 0x0 0x0 0x170104 0x0 0x2b358d8a8ff0 0x1d28 0x0 0x0 0x1c0007 0x1d28 0x1b0 0x81 0x210005 0x3 0x2b358eeb96e0 0x73 0x2b358eeb94a0 0xb 0x2f0002 0x81 0x390005 0x0 0x2b3604b21070 0x81 0x0 0x0 0x400007 0x81 0x120 0x0 0x4a0002 0x0 0x4f0005 0x0 0x0 0x0 0x0 0x0 0x530005 0x0 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data 8 0x90002 0x22ca 0xc0005 0x29 0x2b358eeb96e0 0x2255 0x2b358eeb94a0 0x4c oops 2 4 sun/misc/Launcher$AppClassLoader 6 java/net/URLClassLoader -ciMethodData java/lang/ClassLoader defineClass (Ljava/lang/String;[BIILjava/security/ProtectionDomain;)Ljava/lang/Class; 2 7826 orig 264 80 90 188 138 53 43 0 0 16 66 154 189 53 43 0 0 136 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 129 1 0 0 137 232 0 0 1 0 0 0 84 25 0 0 0 0 0 0 2 0 0 0 0 0 15 0 2 0 0 0 64 0 0 0 255 255 255 255 2 0 4 0 0 0 0 0 data 8 0x40002 0x1d11 0xc0002 0x1d12 0x1b0002 0x1d12 0x250002 0x1d13 oops 0 -ciMethodData java/security/ProtectionDomain (Ljava/security/CodeSource;Ljava/security/PermissionCollection;Ljava/lang/ClassLoader;[Ljava/security/Principal;)V 1 605 orig 264 80 90 188 138 53 43 0 0 216 16 155 189 53 43 0 0 16 3 0 0 240 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 0 0 0 249 17 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 13 0 2 0 0 0 168 1 0 0 255 255 255 255 2 0 1 0 0 0 0 0 data 53 0x10002 0x23f 0xe0002 0x23f 0x1a0007 0x1be 0xf0 0x81 0x260005 0x0 0x2b36081f8df0 0x81 0x0 0x0 0x2a0004 0x0 0x2b36081f8df0 0x81 0x0 0x0 0x2d0007 0x0 0x70 0x81 0x310004 0x0 0x2b36081f8df0 0x81 0x0 0x0 0x370007 0x80 0x20 0x1 0x470007 0x23f 0x98 0x0 0x4c0005 0x0 0x0 0x0 0x0 0x0 0x4f0004 0x0 0x0 0x0 0x0 0x0 0x520003 0x0 0x18 oops 3 10 java/security/Permissions 16 java/security/Permissions 26 java/security/Permissions -ciMethodData java/lang/ClassLoader preDefineClass (Ljava/lang/String;Ljava/security/ProtectionDomain;)Ljava/security/ProtectionDomain; 2 8125 orig 264 80 90 188 138 53 43 0 0 232 63 154 189 53 43 0 0 56 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 129 1 0 0 225 241 0 0 1 0 0 0 32 25 0 0 0 0 0 0 2 0 0 0 0 0 16 0 2 0 0 0 224 2 0 0 255 255 255 255 2 0 2 0 0 0 0 0 data 92 0x20002 0x1e3c 0x50007 0x1e3d 0xd0 0x0 0x100002 0x0 0x150005 0x0 0x0 0x0 0x0 0x0 0x190005 0x0 0x0 0x0 0x0 0x0 0x1c0005 0x0 0x0 0x0 0x0 0x0 0x1f0002 0x0 0x240007 0x11 0x180 0x1e2c 0x2a0005 0x130 0x2b358d8a8930 0x1cfc 0x0 0x0 0x2d0007 0x1e2c 0x130 0x0 0x380002 0x0 0x3d0005 0x0 0x0 0x0 0x0 0x0 0x450005 0x0 0x0 0x0 0x0 0x0 0x480005 0x0 0x0 0x0 0x0 0x0 0x4b0005 0x0 0x0 0x0 0x0 0x0 0x4e0005 0x0 0x0 0x0 0x0 0x0 0x510002 0x0 0x56e007 0x1e02 0x20 0x3c 0x5f0007 0x11 0x60 0x1e2d 0x650005 0x131 0x2b358d8a8ff0 0x1cfc 0x0 0x0 0x680002 0x1e2d oops 2 34 java/lang/String 86 java/security/ProtectionDomain -ciMethodData java/lang/ClassLoader checkCerts (Ljava/lang/String;Ljava/security/CodeSource;)V 2 6805 orig 264 80 90 188 138 53 43 0 0 56 71 154 189 53 43 0 0 112 5 0 0 136 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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0x0 0x0 0x0 0xbe0002 0x0 oops 8 2 java/lang/String 15 java/lang/String 25 java/security/CodeSource 35 java/util/Hashtable 58 java/util/Hashtable 70 java/util/concurrent/ConcurrentHashMap 83 java/util/concurrent/ConcurrentHashMap 89 [Ljava/security/cert/Certificate; -ciMethodData java/lang/ClassLoader defineClassSourceLocation (Ljava/security/ProtectionDomain;)Ljava/lang/String; 2 7827 orig 264 80 90 188 138 53 43 0 0 152 64 154 189 53 43 0 0 80 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 129 1 0 0 145 232 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 8 0 2 0 0 0 0 1 0 0 255 255 255 255 5 0 1 0 0 0 0 0 data 32 0x10005 0x2 0x2b358d8a8ff0 0x1d10 0x0 0x0 0x80007 0x0 0xd0 0x1d12 0xc0005 0x2 0x2b358eeb9800 0x1d10 0x0 0x0 0xf0007 0x41 0x80 0x1cd1 0x130005 0x2 0x2b358eeb9800 0x1ccf 0x0 0x0 0x160005 0x2 0x2b358eeb9530 0x1ccf 0x0 0x0 oops 4 2 java/security/ProtectionDomain 12 java/security/CodeSource 22 java/security/CodeSource 28 java/net/URL -ciMethod java/net/InetAddress hashCode ()I 0 0 1 0 -1 -ciMethodData java/security/PermissionCollection setReadOnly ()V 1 156 orig 264 80 90 188 138 53 43 0 0 232 181 192 189 53 43 0 0 32 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 255 255 255 255 0 0 0 0 0 0 0 0 data 0 oops 0 -ciMethodData java/security/ProtectionDomain$Key ()V 1 607 orig 264 80 90 188 138 53 43 0 0 96 119 181 189 53 43 0 0 48 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 68 79 32 101 120 116 114 97 32 100 97 116 97 32 108 111 99 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 249 10 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 3 0 2 0 0 0 16 0 0 0 255 255 255 255 2 0 1 0 0 0 0 0 data 2 0x10002 0x15f oops 0 -compile java/net/URLClassLoader$1 run ()Ljava/lang/Class; -1 4 inline 254 0 -1 java/net/URLClassLoader$1 run ()Ljava/lang/Class; 1 8 java/lang/String replace (CC)Ljava/lang/String; 2 121 java/lang/String ([CZ)V 3 1 java/lang/Object ()V 1 13 java/lang/String concat (Ljava/lang/String;)Ljava/lang/String; 2 1 java/lang/String length ()I 2 24 java/util/Arrays copyOf ([CI)[C 2 33 java/lang/String getChars ([CI)V 2 43 java/lang/String ([CZ)V 3 1 java/lang/Object ()V 1 21 java/net/URLClassLoader access$000 (Ljava/net/URLClassLoader;)Lsun/misc/URLClassPath; 1 43 java/net/URLClassLoader access$100 (Ljava/net/URLClassLoader;Ljava/lang/String;Lsun/misc/Resource;)Ljava/lang/Class; 2 3 java/net/URLClassLoader defineClass (Ljava/lang/String;Lsun/misc/Resource;)Ljava/lang/Class; 3 7 java/lang/String lastIndexOf (I)I 4 9 java/lang/String lastIndexOf (II)I 3 13 sun/misc/URLClassPath$JarLoader$2 getCodeSourceURL ()Ljava/net/URL; 4 4 sun/misc/URLClassPath$JarLoader access$600 (Lsun/misc/URLClassPath$JarLoader;)Ljava/net/URL; 3 28 java/lang/String substring (II)Ljava/lang/String; 4 75 java/lang/String ([CII)V 5 1 java/lang/Object ()V 5 75 java/util/Arrays copyOfRange ([CII)[C 3 34 sun/misc/URLClassPath$JarLoader$2 getManifest ()Ljava/util/jar/Manifest; 4 4 sun/misc/URLClassPath$JarLoader access$700 (Lsun/misc/URLClassPath$JarLoader;)Ljava/util/jar/JarFile; 4 7 java/util/jar/JarFile getManifest ()Ljava/util/jar/Manifest; 5 1 java/util/jar/JarFile getManifestFromReference ()Ljava/util/jar/Manifest; 6 11 java/lang/ref/SoftReference get ()Ljava/lang/Object; 6 27 java/util/jar/JarFile getManEntry ()Ljava/util/jar/JarEntry; 7 11 java/util/jar/JarFile getJarEntry (Ljava/lang/String;)Ljava/util/jar/JarEntry; 8 2 java/util/jar/JarFile getEntry (Ljava/lang/String;)Ljava/util/zip/ZipEntry; 9 16 java/util/jar/JarFile$JarFileEntry (Ljava/util/jar/JarFile;Ljava/util/zip/ZipEntry;)V 10 7 java/util/jar/JarEntry (Ljava/util/zip/ZipEntry;)V 7 63 java/util/jar/JarFile getJarEntry (Ljava/lang/String;)Ljava/util/jar/JarEntry; 8 2 java/util/jar/JarFile getEntry (Ljava/lang/String;)Ljava/util/zip/ZipEntry; 9 16 java/util/jar/JarFile$JarFileEntry (Ljava/util/jar/JarFile;Ljava/util/zip/ZipEntry;)V 10 7 java/util/jar/JarEntry (Ljava/util/zip/ZipEntry;)V 6 44 java/util/jar/JarFile getBytes (Ljava/util/zip/ZipEntry;)[B 7 10 java/util/zip/ZipEntry getSize ()J 6 57 java/io/ByteArrayInputStream ([B)V 7 1 java/io/InputStream ()V 8 1 java/lang/Object ()V 6 60 java/util/jar/Manifest (Ljava/io/InputStream;)V 7 1 java/lang/Object ()V 7 9 java/util/jar/Attributes ()V 8 3 java/util/jar/Attributes (I)V 9 1 java/lang/Object ()V 9 10 java/util/HashMap (I)V 10 4 java/util/HashMap (IF)V 7 20 java/util/HashMap ()V 8 1 java/util/AbstractMap ()V 9 1 java/lang/Object ()V 6 77 java/util/jar/JarVerifier ([B)V 7 1 java/lang/Object ()V 7 29 java/lang/Object ()V 7 40 java/util/HashMap ()V 8 1 java/util/AbstractMap ()V 9 1 java/lang/Object ()V 7 51 java/util/HashMap ()V 8 1 java/util/AbstractMap ()V 9 1 java/lang/Object ()V 7 71 java/util/jar/JarVerifier$3 (Ljava/util/jar/JarVerifier;)V 8 6 java/lang/Object ()V 7 87 java/util/Hashtable ()V 8 5 java/util/Hashtable (IF)V 9 1 java/util/Dictionary ()V 10 1 java/lang/Object ()V 9 47 java/lang/Float isNaN (F)Z 9 106 java/lang/Math min (FF)F 7 98 java/util/Hashtable ()V 8 5 java/util/Hashtable (IF)V 9 1 java/util/Dictionary ()V 10 1 java/lang/Object ()V 9 47 java/lang/Float isNaN (F)Z 9 106 java/lang/Math min (FF)F 7 111 java/util/Hashtable (I)V 8 4 java/util/Hashtable (IF)V 9 1 java/util/Dictionary ()V 10 1 java/lang/Object ()V 9 47 java/lang/Float isNaN (F)Z 9 106 java/lang/Math min (FF)F 7 122 java/util/ArrayList ()V 8 1 java/util/AbstractList ()V 9 1 java/util/AbstractCollection ()V 10 1 java/lang/Object ()V 7 133 java/io/ByteArrayOutputStream ()V 8 3 java/io/ByteArrayOutputStream (I)V 9 1 java/io/OutputStream ()V 10 1 java/lang/Object ()V 7 144 java/util/ArrayList ()V 8 1 java/util/AbstractList ()V 9 1 java/util/AbstractCollection ()V 10 1 java/lang/Object ()V 6 95 java/util/jar/Manifest (Ljava/io/InputStream;)V 7 1 java/lang/Object ()V 7 9 java/util/jar/Attributes ()V 8 3 java/util/jar/Attributes (I)V 9 1 java/lang/Object ()V 9 10 java/util/HashMap (I)V 10 4 java/util/HashMap (IF)V 7 20 java/util/HashMap ()V 8 1 java/util/AbstractMap ()V 9 1 java/lang/Object ()V 6 105 java/lang/ref/SoftReference (Ljava/lang/Object;)V 7 2 java/lang/ref/Reference (Ljava/lang/Object;)V 8 3 java/lang/ref/Reference (Ljava/lang/Object;Ljava/lang/ref/ReferenceQueue;)V 9 1 java/lang/Object ()V 3 50 sun/misc/Resource getByteBuffer ()Ljava/nio/ByteBuffer; 3 103 sun/misc/URLClassPath$JarLoader$2 getCodeSigners ()[Ljava/security/CodeSigner; 4 4 java/util/jar/JarFile$JarFileEntry getCodeSigners ()[Ljava/security/CodeSigner; 5 4 java/util/jar/JarFile access$200 (Ljava/util/jar/JarFile;)V 6 1 java/util/jar/JarFile maybeInstantiateVerifier ()V 7 45 java/lang/String endsWith (Ljava/lang/String;)Z 8 13 java/lang/String startsWith (Ljava/lang/String;I)Z 7 54 java/lang/String endsWith (Ljava/lang/String;)Z 8 13 java/lang/String startsWith (Ljava/lang/String;I)Z 7 63 java/lang/String endsWith (Ljava/lang/String;)Z 8 13 java/lang/String startsWith (Ljava/lang/String;I)Z 7 72 java/lang/String endsWith (Ljava/lang/String;)Z 8 13 java/lang/String startsWith (Ljava/lang/String;I)Z 7 79 java/util/jar/JarFile getManifest ()Ljava/util/jar/Manifest; 8 1 java/util/jar/JarFile getManifestFromReference ()Ljava/util/jar/Manifest; 9 11 java/lang/ref/SoftReference get ()Ljava/lang/Object; 9 27 java/util/jar/JarFile getManEntry ()Ljava/util/jar/JarEntry; 10 11 java/util/jar/JarFile getJarEntry (Ljava/lang/String;)Ljava/util/jar/JarEntry; 10 63 java/util/jar/JarFile getJarEntry (Ljava/lang/String;)Ljava/util/jar/JarEntry; 9 44 java/util/jar/JarFile getBytes (Ljava/util/zip/ZipEntry;)[B 10 10 java/util/zip/ZipEntry getSize ()J 9 57 java/io/ByteArrayInputStream ([B)V 10 1 java/io/InputStream ()V 9 60 java/util/jar/Manifest (Ljava/io/InputStream;)V 10 1 java/lang/Object ()V 10 9 java/util/jar/Attributes ()V 10 20 java/util/HashMap ()V 9 77 java/util/jar/JarVerifier ([B)V 10 1 java/lang/Object ()V 10 29 java/lang/Object ()V 10 40 java/util/HashMap ()V 10 51 java/util/HashMap ()V 10 71 java/util/jar/JarVerifier$3 (Ljava/util/jar/JarVerifier;)V 10 87 java/util/Hashtable ()V 10 98 java/util/Hashtable ()V 10 111 java/util/Hashtable (I)V 10 122 java/util/ArrayList ()V 10 133 java/io/ByteArrayOutputStream ()V 10 144 java/util/ArrayList ()V 9 95 java/util/jar/Manifest (Ljava/io/InputStream;)V 10 1 java/lang/Object ()V 10 9 java/util/jar/Attributes ()V 10 20 java/util/HashMap ()V 9 105 java/lang/ref/SoftReference (Ljava/lang/Object;)V 10 2 java/lang/ref/Reference (Ljava/lang/Object;)V 5 31 java/util/jar/JarFile access$300 (Ljava/util/jar/JarFile;)Ljava/util/jar/JarVerifier; 3 116 java/security/CodeSource (Ljava/net/URL;[Ljava/security/CodeSigner;)V 4 1 java/lang/Object ()V 3 121 sun/misc/PerfCounter getReadClassBytesTime ()Lsun/misc/PerfCounter; 3 125 sun/misc/PerfCounter addElapsedTimeFrom (J)V 4 6 sun/misc/PerfCounter add (J)V 5 1 sun/misc/PerfCounter get ()J 6 5 java/nio/DirectLongBufferU get (I)J 7 6 java/nio/Buffer checkIndex (I)I 7 9 java/nio/DirectLongBufferU ix (I)J 5 13 java/nio/DirectLongBufferU put (IJ)Ljava/nio/LongBuffer; 6 6 java/nio/Buffer checkIndex (I)I 6 9 java/nio/DirectLongBufferU ix (I)J 3 138 java/security/SecureClassLoader defineClass (Ljava/lang/String;[BIILjava/security/CodeSource;)Ljava/lang/Class; 4 9 java/security/SecureClassLoader getProtectionDomain (Ljava/security/CodeSource;)Ljava/security/ProtectionDomain; 5 20 java/util/HashMap get (Ljava/lang/Object;)Ljava/lang/Object; 6 2 java/util/HashMap hash (Ljava/lang/Object;)I 7 9 java/security/CodeSource hashCode ()I 8 11 java/net/URL hashCode ()I 6 6 java/util/HashMap getNode (ILjava/lang/Object;)Ljava/util/HashMap$Node; 7 59 java/security/CodeSource equals (Ljava/lang/Object;)Z 8 45 java/net/URL equals (Ljava/lang/Object;)Z 8 56 java/security/CodeSource matchCerts (Ljava/security/CodeSource;Z)Z 7 126 java/security/CodeSource equals (Ljava/lang/Object;)Z 8 45 java/net/URL equals (Ljava/lang/Object;)Z 8 56 java/security/CodeSource matchCerts (Ljava/security/CodeSource;Z)Z 5 47 java/security/ProtectionDomain (Ljava/security/CodeSource;Ljava/security/PermissionCollection;Ljava/lang/ClassLoader;[Ljava/security/Principal;)V 6 1 java/lang/Object ()V 6 14 java/security/ProtectionDomain$Key ()V 7 1 java/lang/Object ()V 6 38 java/security/PermissionCollection setReadOnly ()V 5 57 java/util/HashMap put (Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object; 6 2 java/util/HashMap hash (Ljava/lang/Object;)I 7 9 java/security/CodeSource hashCode ()I 8 11 java/net/URL hashCode ()I 4 12 java/lang/ClassLoader defineClass (Ljava/lang/String;[BIILjava/security/ProtectionDomain;)Ljava/lang/Class; 5 4 java/lang/ClassLoader preDefineClass (Ljava/lang/String;Ljava/security/ProtectionDomain;)Ljava/security/ProtectionDomain; 6 2 java/lang/ClassLoader checkName (Ljava/lang/String;)Z 7 5 java/lang/String length ()I 7 16 java/lang/String indexOf (I)I 8 3 java/lang/String indexOf (II)I 7 23 sun/misc/VM allowArraySyntax ()Z 7 31 java/lang/String charAt (I)C 6 42 java/lang/String startsWith (Ljava/lang/String;)Z 7 3 java/lang/String startsWith (Ljava/lang/String;I)Z 6 101 java/security/ProtectionDomain getCodeSource ()Ljava/security/CodeSource; 5 12 java/lang/ClassLoader defineClassSourceLocation (Ljava/security/ProtectionDomain;)Ljava/lang/String; 6 1 java/security/ProtectionDomain getCodeSource ()Ljava/security/CodeSource; 6 12 java/security/CodeSource getLocation ()Ljava/net/URL; 6 19 java/security/CodeSource getLocation ()Ljava/net/URL; 6 22 java/net/URL toString ()Ljava/lang/String; 7 1 java/net/URL toExternalForm ()Ljava/lang/String; 8 5 java/net/URLStreamHandler toExternalForm (Ljava/net/URL;)Ljava/lang/String; 9 1 java/net/URL getProtocol ()Ljava/lang/String; 9 4 java/lang/String length ()I 9 11 java/net/URL getAuthority ()Ljava/lang/String; 9 18 java/net/URL getAuthority ()Ljava/lang/String; 9 21 java/lang/String length ()I 9 30 java/net/URL getAuthority ()Ljava/lang/String; 9 33 java/lang/String length ()I 9 40 java/net/URL getPath ()Ljava/lang/String; 9 48 java/net/URL getPath ()Ljava/lang/String; 9 51 java/lang/String length ()I 9 57 java/net/URL getQuery ()Ljava/lang/String; 9 66 java/net/URL getQuery ()Ljava/lang/String; 9 69 java/lang/String length ()I 9 76 java/net/URL getRef ()Ljava/lang/String; 9 99 java/lang/StringBuffer (I)V 10 2 java/lang/AbstractStringBuilder (I)V 9 105 java/net/URL getProtocol ()Ljava/lang/String; 9 108 java/lang/StringBuffer append (Ljava/lang/String;)Ljava/lang/StringBuffer; 10 7 java/lang/AbstractStringBuilder append (Ljava/lang/String;)Ljava/lang/AbstractStringBuilder; 9 115 java/lang/StringBuffer append (Ljava/lang/String;)Ljava/lang/StringBuffer; 10 7 java/lang/AbstractStringBuilder append (Ljava/lang/String;)Ljava/lang/AbstractStringBuilder; 9 120 java/net/URL getAuthority ()Ljava/lang/String; 9 127 java/net/URL getAuthority ()Ljava/lang/String; 9 130 java/lang/String length ()I 9 139 java/lang/StringBuffer append (Ljava/lang/String;)Ljava/lang/StringBuffer; 10 7 java/lang/AbstractStringBuilder append (Ljava/lang/String;)Ljava/lang/AbstractStringBuilder; 9 145 java/net/URL getAuthority ()Ljava/lang/String; 9 148 java/lang/StringBuffer append (Ljava/lang/String;)Ljava/lang/StringBuffer; 10 7 java/lang/AbstractStringBuilder append (Ljava/lang/String;)Ljava/lang/AbstractStringBuilder; 9 153 java/net/URL getPath ()Ljava/lang/String; 9 161 java/net/URL getPath ()Ljava/lang/String; 9 164 java/lang/StringBuffer append (Ljava/lang/String;)Ljava/lang/StringBuffer; 10 7 java/lang/AbstractStringBuilder append (Ljava/lang/String;)Ljava/lang/AbstractStringBuilder; 9 169 java/net/URL getQuery ()Ljava/lang/String; 9 184 java/net/URL getQuery ()Ljava/lang/String; 9 192 java/net/URL getRef ()Ljava/lang/String; 9 215 java/lang/StringBuffer toString ()Ljava/lang/String; 10 17 java/util/Arrays copyOfRange ([CII)[C 10 32 java/lang/String ([CZ)V 5 37 java/lang/ClassLoader postDefineClass (Ljava/lang/Class;Ljava/security/ProtectionDomain;)V 6 1 java/security/ProtectionDomain getCodeSource ()Ljava/security/CodeSource; 6 8 java/security/ProtectionDomain getCodeSource ()Ljava/security/CodeSource; 6 11 java/security/CodeSource getCertificates ()[Ljava/security/cert/Certificate; 7 29 java/util/ArrayList ()V 8 1 java/util/AbstractList ()V 9 1 java/util/AbstractCollection ()V 10 1 java/lang/Object ()V 7 51 java/security/CodeSigner getSignerCertPath ()Ljava/security/cert/CertPath; 7 54 sun/security/provider/certpath/X509CertPath getCertificates ()Ljava/util/List; 7 70 java/util/ArrayList size ()I 6 22 java/lang/ClassLoader setSigners (Ljava/lang/Class;[Ljava/lang/Object;)V diff --git a/segm_brain.m b/segm_brain.m index 391c3b6..e2f5224 100644 --- a/segm_brain.m +++ b/segm_brain.m @@ -10,6 +10,18 @@ % sl,st - fill level and threshold for watershed segmentation % % Outputs: +% Bra - brain mask% Segm_brain() - Performs brain segmentation +% +% Usage: +% >> [Bra] = Segm_brain(b,Sca, sli, WMp,sl, st); +% +% Inputs: +% b - input image (filtered MR image) +% sli - lowest point for crebellum +% WMp - White matter point +% sl,st - fill level and threshold for watershed segmentation +% +% Outputs: % Bra - brain mask % % Author: Zeynep Akalin Acar, SCCN, 2008 diff --git a/ss_cortex_gaus.m b/ss_cortex_gaus.m new file mode 100644 index 0000000..232bc61 --- /dev/null +++ b/ss_cortex_gaus.m @@ -0,0 +1,32 @@ +function ss_sparse = ss_cortex_gaus(mesh,algorithm, vertices, faces, stop_distance); +Nn = size(vertices,1); +%ss_sparse = sparse(Nn,Nn); +ss_sparse = sparse([],[],[],Nn,Nn,Nn*1000); % allocate 1000 nonzero spaces + +sigma = stop_distance/3; % standard deviation + +hh = waitbar(0,'computing patches ...'); +for vertex_id = 1:Nn + waitbar(vertex_id/Nn) + + source_points = {geodesic_create_surface_point('vertex',vertex_id,vertices(vertex_id,:))}; + + stop_points = []; + + geodesic_propagate(algorithm, source_points, stop_points, stop_distance); + + [source_id, distances] = geodesic_distance_and_source(algorithm); %find distances to all vertices of the mesh; in this example we have a single source, so source_id is always equal to 1 + k1 = find(distances < 1.0000e+100); + k2 = find(distances == 1.0000e+100); + + max_d = max(distances(k1)); + deg = distances; + deg(k2) = 0; + deg(k1) = 1/sigma/sqrt(2*pi) * exp(-0.5/sigma^2*(max_d - distances(k1)).^2); + deg(k1) = max(deg(k1)) - deg(k1); + ss_sparse(vertex_id,:) = sparse(deg); + +end +close(hh) + +