FTrack

 FTRACK 
 For all your fly-tracking needs! . See documentation for usage details.

0001 function varargout = FTrack(varargin)
0002 % FTRACK
0003 % For all your fly-tracking needs! . See documentation for usage details.
0004 
0005 % Last Modified by GUIDE v2.5 26-Nov-2007 18:07:29
0006 
0007 % Begin initialization code - DO NOT EDIT
0008 gui_Singleton = 1;
0009 gui_State = struct('gui_Name',       mfilename, ...
0010                    'gui_Singleton',  gui_Singleton, ...
0011                    'gui_OpeningFcn', @FTrack_OpeningFcn, ...
0012                    'gui_OutputFcn',  @FTrack_OutputFcn, ...
0013                    'gui_LayoutFcn',  [] , ...
0014                    'gui_Callback',   []);
0015 if nargin && ischar(varargin{1})
0016     gui_State.gui_Callback = str2func(varargin{1});
0017 end
0018 
0019 if nargout
0020     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
0021 else
0022     gui_mainfcn(gui_State, varargin{:});
0023 end
0024 % End initialization code - DO NOT EDIT
0025 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0026 
0027 % --- Executes just before FTrack is made visible.
0028 function FTrack_OpeningFcn(hObject, eventdata, handles, varargin)
0029 % This function has no output args, see OutputFcn.
0030 % hObject    handle to figure
0031 % eventdata  reserved - to be defined in a future version of MATLAB
0032 % handles    structure with handles and user data (see GUIDATA)
0033 % varargin   command line arguments to FTrack (see VARARGIN)
0034 
0035 % Choose default command line output for FTrack
0036 handles.output = hObject;
0037 
0038 % Update handles structure
0039 guidata(hObject, handles);
0040 disp('Welcome to FTrack!')
0041 warning off all
0042 
0043 % UIWAIT makes FTrack wait for user response (see UIRESUME)
0044 % uiwait(handles.figure1);
0045 
0046 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0047 
0048 % --- Outputs from this function are returned to the command line.
0049 function varargout = FTrack_OutputFcn(hObject, eventdata, handles) 
0050 % varargout  cell array for returning output args (see VARARGOUT);
0051 % hObject    handle to figure
0052 % eventdata  reserved - to be defined in a future version of MATLAB
0053 % handles    structure with handles and user data (see GUIDATA)
0054 
0055 % Get default command line output from handles structure
0056 varargout{1} = handles.output;
0057 
0058 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0059 % --- Executes on button press in load_video.
0060 function load_video_Callback(hObject, eventdata, handles)
0061 % hObject    handle to load_video (see GCBO)
0062 % eventdata  reserved - to be defined in a future version of MATLAB
0063 % handles    structure with handles and user data (see GUIDATA
0064 
0065 
0066 %The following allows the user to select multiple videos to be tracked.
0067 %The videos will be tracked sequentially, not in parallel. The filenames
0068 %will be displayed in the message center.
0069 
0070 [filename, pathname] = uigetfile({'*.avi;*.mpg;*.mp2','Video Files (*.avi,*.mpg,*.mp2)'}, 'Pick a video', 'MultiSelect','on');
0071 if iscell(filename)
0072     NFiles = length(filename);
0073 else
0074     NFiles = 1;
0075     filename = {filename};
0076 end
0077 
0078 if isequal(filename,0) || isequal(pathname,0)
0079     disp('File select canceled')
0080 else
0081     for i = 1:NFiles
0082         disp(['Video selected: ', fullfile(pathname, filename{i})])
0083         handles.filename{i} = fullfile(pathname, filename{i}); 
0084     end
0085 end
0086 
0087 guidata(gcbo,handles);
0088 
0089 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0090 
0091 % --- Executes on button press in viewframe.
0092 function viewframe_Callback(hObject, eventdata, handles)
0093 % hObject    handle to viewframe (see GCBO)
0094 % eventdata  reserved - to be defined in a future version of MATLAB
0095 % handles    structure with handles and user data (see GUIDATA)
0096 
0097 %This is the single frame viewer.  It simply gives the user some info about
0098 %the video (displayed in the message center), and also shows the user a
0099 %single frame of the movie so that they can make sure it looks correct and
0100 %they can get some parameters off of the frame if need be (such as fly size
0101 %or a pixel/cm calilbration).
0102 
0103 filename = handles.filename;
0104 if iscell(filename)
0105     NFiles = length(filename);
0106 else
0107     NFiles = 1;
0108     filename = {filename};
0109 end
0110 
0111 for i = 1:NFiles
0112     video = videoReader(filename{i});
0113     seek(video,1);
0114     info = getinfo(video);
0115     img = getframe(video);
0116     figure
0117     imagesc(img)
0118     title(filename{i})
0119     disp(['Video name:',filename{i}])
0120     disp(['Video dimensions [Width, Height]:  [', num2str(info.width),' , ' num2str(info.height),']'])
0121     disp(['Number of frames:  ',num2str(info.numFrames)])
0122     disp(['Frame rate:  ',num2str(info.fps),' frames/s'])
0123     
0124     handles.VideoInfo(i) = info;
0125 end
0126 
0127 disp('Frame Viewer Finished')
0128 guidata(gcbo, handles);
0129 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0130 
0131 % --- Executes on button press in arena_dims.
0132 function arena_dims_Callback(hObject, eventdata, handles)
0133 % hObject    handle to arena_dims (see GCBO)
0134 % eventdata  reserved - to be defined in a future version of MATLAB
0135 % handles    structure with handles and user data (see GUIDATA)
0136 
0137 filename = handles.filename;
0138 if iscell(filename)
0139     NFiles = length(filename);
0140 else
0141     NFiles = 1;
0142     filename = {filename};
0143 end
0144 
0145 p = [];
0146 q = [];
0147 for i = 1:NFiles
0148     video = videoReader(filename{i});
0149     info = getinfo(video);
0150     seek(video,1);
0151     img = getframe(video);
0152     sz = size(img);
0153     figure
0154     colormap gray
0155     imagesc(img)
0156     axis image
0157     title({filename{i}; 'Left click to select points on boundary of arena. Press return when done.'})
0158  
0159     % Choose points on arena boundary
0160     [p q] = ginput;
0161 
0162     %Find center and radius of arena
0163 
0164     ellipse = fit_ellipse(p',q','y');
0165     semiminor = min(ellipse.a,ellipse.b);
0166     semimajor = max(ellipse.a,ellipse.b);
0167     ellipse.epsilon = sqrt(1-semiminor^2/semimajor^2);
0168     ellipse.psi = asin(ellipse.epsilon);
0169     ellipse.semiminor = semiminor;
0170     ellipse.semimajor = semimajor;
0171 
0172     rotated_ellipse = ellipse.rotated_ellipse;
0173     ellipse.points_selected = [p q];
0174     title('Arena w/ Boundary')
0175     ellipse.boundaries = [ rotated_ellipse(1,:)', info.height-rotated_ellipse(2,:)'];
0176        
0177     info = handles.VideoInfo(i);
0178     figure
0179     title('Masking arena.  Please wait...')
0180     drawnow
0181     disp('Masking arena...')
0182     mask = zeros(info.height, info.width);
0183     for k=1:info.height
0184         for j=1:info.width
0185             rot = inv(ellipse.R)*[j;k];
0186             testpoint = (rot(1)-ellipse.X0).^2/(ellipse.a).^2+(rot(2)-ellipse.Y0).^2/(ellipse.b).^2;
0187             if (testpoint <= 1.01) %giving a little lee-way near boundary
0188                 mask(k,j) = 1;
0189             end
0190         end
0191     end
0192     ellipse.mask =  double(mask);
0193     handles.arena{i} = ellipse;
0194     
0195     imagesc(double(img(:,:,1)).*double(mask))
0196     axis image
0197     colormap gray
0198     title('Portion to be tracked')
0199     
0200 end
0201 
0202 %setting things up to only consider pixels within selected arena...
0203 
0204 disp('Arena Dimensions Calculated')
0205 disp(ellipse)
0206 guidata(gcbo, handles);
0207 
0208 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0209 % --- Executes on button press in input_params.
0210 function input_params_Callback(hObject, eventdata, handles)
0211 % hObject    handle to input_params (see GCBO)
0212 % eventdata  reserved - to be defined in a future version of MATLAB
0213 % handles    structure with handles and user data (see GUIDATA)
0214 
0215 
0216 %Opens up a dialog box so that the user can input relevant parameters for
0217 %each video that is being tracked.  A separate box will open for each
0218 %video.
0219 
0220 filename = handles.filename;
0221 if iscell(filename)
0222     NFiles = length(filename);
0223 else
0224     Nfiles = 1;
0225     filename = {filename};
0226 end
0227 UserIn = [];
0228 
0229 for i = 1:NFiles
0230     first = strvcat(filename{i}, '          ','Output directory');
0231     prompt = {first,'Start Frame (Remember that first frame is indexed 0)','End Frame:', 'Initial background size:', 'Arena radius (cm)', 'Bounding box half-size (in pixels)','Background weight (0.9 < a < 1)'};
0232     dlg_title = ['Input Paramters'];
0233     num_lines = 1;
0234     defaults = {'C:\Documents and Settings\liam\My Documents\LabVIEW Data\FTrack output','0','999', '100','7.5','10','0.9'};
0235     options.Resize='on';
0236     options.WindowStyle='normal';
0237     answer = inputdlg(prompt,dlg_title,num_lines,defaults, options);
0238     UserIn = [UserIn answer];
0239     disp(['Input parameters have been entered for ', filename{i}])
0240     
0241     InputData(i).OutputPath = UserIn{1,i};
0242     InputData(i).StartFrame = str2double(UserIn(2,i));
0243     InputData(i).EndFrame = str2double(UserIn(3,i));
0244     InputData(i).NBackFrames = str2double(UserIn(4,i));
0245     InputData(i).ArenaRadius = str2double(UserIn(5,i));
0246     InputData(i).sqrsize = str2double(UserIn(6,i));
0247     InputData(i).alpha = str2double(UserIn(7,i));
0248 
0249 end
0250 
0251 handles.InputData = InputData;
0252  
0253 guidata(gcbo, handles);
0254 
0255 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0256 % Radio Buttons to select fly finding option
0257 
0258 % --- Executes during object creation, after setting all properties.
0259 function find_opt_CreateFcn(hObject, eventdata, handles)
0260 % hObject    handle to find_opt (see GCBO)
0261 % eventdata  reserved - to be defined in a future version of MATLAB
0262 % handles    empty - handles not created until after all CreateFcns called
0263 
0264 
0265 % --------------------------------------------------------------------
0266 function find_opt_SelectionChangeFcn(hObject, eventdata, handles)
0267 % hObject    handle to find_opt (see GCBO)
0268 % eventdata  reserved - to be defined in a future version of MATLAB
0269 % handles    structure with handles and user data (see GUIDATA)
0270 
0271 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0272 %  Radio buttons to select whether fly is white on black or black on white
0273 
0274 % --- Executes during object creation, after setting all properties.
0275 function neg_opt_CreateFcn(hObject, eventdata, handles)
0276 % hObject    handle to neg_opt (see GCBO)
0277 % eventdata  reserved - to be defined in a future version of MATLAB
0278 % handles    empty - handles not created until after all CreateFcns called
0279 
0280 % --------------------------------------------------------------------
0281 function neg_opt_SelectionChangeFcn(hObject, eventdata, handles)
0282 % hObject    handle to neg_opt (see GCBO)
0283 % eventdata  reserved - to be defined in a future version of MATLAB
0284 % handles    structure with handles and user data (see GUIDATA)
0285 
0286 
0287 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0288 % --- Executes on button press in TrackStart.
0289 function TrackStart_Callback(hObject, eventdata, handles)
0290 % hObject    handle to TrackStart (see GCBO)
0291 % eventdata  reserved - to be defined in a future version of MATLAB
0292 % handles    structure with handles and user data (see GUIDATA)
0293 
0294 %This part of the calls FlyTracker to do the actual tracking.
0295 
0296 %grab the filename and user input parameters
0297 filename = handles.filename;
0298 InputData = handles.InputData;
0299 
0300 if iscell(filename)
0301     NVideos = length(filename);
0302 else
0303     NVideos = 1;
0304     filename = {filename};
0305 end
0306 
0307 neg_opt = get(get(handles.neg_opt,'SelectedObject'), 'Tag');
0308 
0309 % Call FlyTracker
0310 for i=1:NVideos
0311      
0312     %video parameters, just because...
0313     info = handles.VideoInfo(i);
0314     FrameRate = info.fps;
0315     FrameRange = [InputData(i).StartFrame:InputData(i).EndFrame];
0316     
0317     %Track the fly!
0318     [x, y, orientation] = FlyTracker(filename{i}, FrameRange,...
0319                        InputData(i).NBackFrames, neg_opt, InputData(i).sqrsize,...
0320                         InputData(i).alpha, handles.arena{i});
0321                     
0322     %Time vector
0323     if (info.numFrames == InputData(i).EndFrame)
0324         InputData(i).EndFrame = InputData(i).EndFrame-1;
0325     elseif (info.numFrames < InputData(i).EndFrame)
0326         InputData(i).EndFrame = info.numFrames-1;
0327     end
0328     
0329     t = [InputData(i).StartFrame:InputData.EndFrame(i)]/FrameRate;
0330         
0331     %Save data to handles so the rest of the GUI can access it.
0332     handles.x = x;
0333     handles.y = y;
0334     handles.orientation = orientation;
0335     handles.t = t;
0336 
0337     guidata(gcbo, handles);  
0338     %Also, save variables as a .mat file so that the user will be able to
0339     %load in the tracked data later on.
0340     
0341     out = SaveFiles(i,handles);
0342     
0343 end
0344 disp('Tracking Complete.')
0345 
0346 
0347 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0348 
0349 % --- Executes on button press in view_traj.
0350 function view_traj_Callback(hObject, eventdata, handles)
0351 % hObject    handle to view_traj (see GCBO)
0352 % eventdata  reserved - to be defined in a future version of MATLAB
0353 % handles    structure with handles and user data (see GUIDATA)
0354 
0355 [filename, pathname] = ...
0356      uigetfile({'*.mat'},'Select Raw Trajectory Data');
0357 
0358 if isequal(filename,0) || isequal(pathname,0)
0359     disp('File select canceled')
0360     return;
0361 else
0362     fullname = fullfile(pathname, filename);
0363 end
0364 
0365 
0366 load(fullname)
0367 figure
0368 set(gcf,'Name',fullname)
0369 subplot(2,2,1)
0370 plot(t,x)
0371 xlim([0 t(end)])
0372 xlabel('Time (s)')
0373 ylabel('cm')
0374 title('Raw x data')
0375 subplot(2,2,3)
0376 plot(t,y)
0377 xlim([0 t(end)])
0378 xlabel('Time (s)')
0379 ylabel('cm')
0380 title('Raw y data')
0381 subplot(2,2,[2 4])
0382 plot(x,y)
0383 xlabel('x position (cm)')
0384 ylabel('y position (cm)')
0385 title('Raw Trajectory')
0386 axis equal
0387 
0388 handles.filename = filename;
0389 handles.x = x;
0390 handles.y = y;
0391 handles.orientation = orientation;
0392 handles.t = t;
0393 handles.VideoInfo = VideoInfo;
0394 handles.InputData = InputData;
0395 handles.arena{1} = arena;
0396 
0397 guidata(gcbo, handles);  
0398      
0399 
0400 
0401 
0402 % --- Executes on button press in clean_x.
0403 function clean_x_Callback(hObject, eventdata, handles)
0404 % hObject    handle to clean_x (see GCBO)
0405 % eventdata  reserved - to be defined in a future version of MATLAB
0406 % handles    structure with handles and user data (see GUIDATA)
0407 
0408 x = handles.x;
0409 filename = handles.filename;
0410 
0411 %open up plot to examine data
0412 figure
0413 plot(x)
0414 title('Zoom in if necessary.  Press any key to continue.')
0415 xlabel('Frame')
0416 ylabel('cm')
0417 pause
0418 
0419 % This loop runs until the user hits return to exit. We wait for the user
0420 % to click four points on the graph, and then run the CleanData function on
0421 % the region defined by those four points.
0422 
0423 while(1)
0424 title('Define region of data to clean: left, right, baseline, threshold. Hit Return to exit.')
0425 [p q] = ginput(4);
0426 if isempty(p)
0427     close;
0428     disp('X data has been cleaned.')
0429     out = SaveFiles(1,handles);
0430     return;
0431 else
0432     rnge = floor(p(1)):floor(p(2));
0433 end
0434 
0435 if (q(3) > q(4))
0436     choice = 'below';
0437 elseif (q(3) < q(4));
0438     choice = 'above';
0439 end
0440 epsilon = q(4);
0441 
0442 x = CleanData(x, rnge, choice, epsilon);
0443 handles.x = x;
0444 guidata(gcbo, handles)
0445 ax = gca;
0446 xlim_temp = get(ax, 'XLim');
0447 ylim_temp = get(ax, 'YLim');
0448 
0449 %Show plot of clean data
0450 figure
0451 plot(x)
0452 xlim(xlim_temp);
0453 ylim(ylim_temp);
0454 xlabel('Frame')
0455 ylabel('cm')
0456 title('Zoom in if necessary.  Press any key to continue.')
0457 pause
0458 end
0459 
0460 
0461 
0462 % --- Executes on button press in clean_y.
0463 function clean_y_Callback(hObject, eventdata, handles)
0464 % hObject    handle to clean_y (see GCBO)
0465 % eventdata  reserved - to be defined in a future version of MATLAB
0466 % handles    structure with handles and user data (see GUIDATA)
0467 
0468 y = handles.y;
0469 filename = handles.filename;
0470 %open up plot to examine data
0471 figure(2)
0472 plot(y)
0473 xlabel('Frame')
0474 ylabel('cm')
0475 title('Zoom in if necessary.  Press any key to continue.')
0476 pause
0477 
0478 % This loop runs until the user hits return to exit. We wait for the user
0479 % to click four points on the graph, and then run the CleanData function on
0480 % the region defined by those four points.
0481 
0482 while(1)
0483 title('Define region of data to clean: left, right, baseline, threshold. Hit Return to exit.')
0484 [p q] = ginput(4);
0485 if isempty(p)
0486     close;
0487     disp('Y data has been cleaned.')
0488     out = SaveFiles(1,handles);
0489     return;
0490 else
0491     rnge = floor(p(1)):floor(p(2));
0492 end
0493 
0494 if (q(3) > q(4))
0495     choice = 'below';
0496 elseif (q(3) < q(4));
0497     choice = 'above';
0498 end
0499 epsilon = q(4);
0500 
0501 y = CleanData(y, rnge, choice, epsilon);
0502 handles.y = y;
0503 guidata(gcbo, handles)
0504 ax = gca;
0505 xlim_temp = get(ax, 'XLim');
0506 ylim_temp = get(ax, 'YLim');
0507 
0508 %Show plot of clean data
0509 figure(2)
0510 plot(y)
0511 xlim(xlim_temp);
0512 ylim(ylim_temp);
0513 xlabel('Frame')
0514 ylabel('cm')
0515 title('Zoom in if necessary.  Press any key to continue.')
0516 pause
0517 end
0518 
0519 return;
0520 
0521 function out = SaveFiles(i,handles)
0522     
0523     if iscell(handles.filename)
0524         filename = handles.filename{i};
0525     else
0526         filename = handles.filename;
0527     end
0528     
0529     OutputPath = handles.InputData(i).OutputPath; 
0530     x = handles.x;
0531     y = handles.y;
0532     t = handles.t;
0533     orientation = handles.orientation;
0534     InputData = handles.InputData(i);
0535     VideoInfo = handles.VideoInfo(i);
0536     arena =  handles.arena{i};
0537     
0538     [temp, name, ext, versn] = fileparts(filename);
0539     
0540     name_mat = strcat(name,'.mat');
0541     name_xy=strcat(name,'.xy');
0542     name_ori=strcat(name,'.ori');
0543     save_filename = fullfile(OutputPath,name);
0544     save_filename_xy = fullfile(OutputPath,name_xy);
0545     save_filename_ori = fullfile(OutputPath,name_ori);
0546     ori=handles.orientation(1,:)';
0547     xy=[handles.x' handles.y'];
0548     save(save_filename,'x','y','t','orientation','InputData', 'VideoInfo','arena')
0549     disp(['Saved ',save_filename])
0550     save(save_filename_xy,'xy','-ascii','-tabs');
0551     disp(['Saved ',save_filename_xy])
0552     save(save_filename_ori,'ori','-ascii','-tabs');   
0553     disp(['Saved ',save_filename_ori])
0554     out = 1;
0555     
0556 return;
0557 
0558 
0559 % --- Executes on button press in tilt_correct.
0560 function tilt_correct_Callback(hObject, eventdata, handles)
0561 % hObject    handle to tilt_correct (see GCBO)
0562 % eventdata  reserved - to be defined in a future version of MATLAB
0563 % handles    structure with handles and user data (see GUIDATA)
0564 
0565 
0566 %Note.  This is a slightly different version of tilt correction than
0567 %described in the PLoS paper.  I think this is more robust and general.
0568 
0569 x = handles.x;
0570 y = handles.y;
0571 t = handles.t;
0572 ellipse = handles.arena{1};
0573 radius_in_cm = handles.InputData.ArenaRadius;
0574 video = videoReader(handles.VideoInfo.url);
0575 info = getinfo(video);
0576 height = info.height;
0577 
0578 psi = ellipse.psi;
0579 phi = ellipse.phi;
0580 
0581 %redefining coordinate system so center of arena is at (0,0)
0582 rotated_ellipse(:,1) = ellipse.boundaries(:,1)-ellipse.X0_in;
0583 rotated_ellipse(:,2) = ellipse.boundaries(:,2)-(height-ellipse.Y0_in);
0584 
0585 M = [cos(phi) sin(phi);-sin(phi) cos(phi)];  %rotation matrix.
0586 
0587 %stretch ellipse only in shortest dimension to length of longest.
0588 if (ellipse.a > ellipse.b)
0589     L = [1 0; 0 ellipse.a/ellipse.b]; 
0590 else
0591     L = [ellipse.b/ellipse.a 0; 0 1];
0592 end
0593 
0594 T = L*M;  %transformation matrix.  A rotation and a stretch to turn an ellipse into a circle.
0595 
0596 disp('Correcting for camera tilt.  This may take a few minutes, so be patient!')
0597 
0598 z = zeros(1,length(rotated_ellipse(:,1)));
0599 
0600 %Transform boundary line
0601 for j = 1:length(rotated_ellipse(:,1))
0602     temp = T*[rotated_ellipse(j,1); rotated_ellipse(j,2)];
0603     xe(j) = temp(1);
0604     ye(j) = temp(2);      
0605 end
0606 
0607 %fit new ellipse
0608 z = zeros(1,length(x));
0609 new_ellipse = fit_ellipse(xe',ye','n');
0610 
0611 semiminor = min(new_ellipse.a,new_ellipse.b);
0612 semimajor = max(new_ellipse.a,new_ellipse.b);
0613 new_ellipse.epsilon = sqrt(1-semiminor^2/semimajor^2);
0614 new_ellipse.psi = asin(new_ellipse.epsilon);
0615 new_ellipse.semiminor = semiminor;
0616 new_ellipse.semimajor = semimajor;
0617 new_ellipse.boundaries = [xe' ye'];
0618 
0619 %Now transform trajectory
0620 for j = 1:length(x)   
0621         temp = T*[x(j)-ellipse.X0_in; y(j)-(height-ellipse.Y0_in)];
0622         xp(j) = temp(1);
0623         yp(j) = temp(2);              
0624 end
0625 
0626 
0627 if (abs(new_ellipse.b-new_ellipse.a) <= 2) %2 pixel accuracy seems adequate
0628     disp('Tilt corrected')
0629     pixels_in_cm = semimajor/radius_in_cm;
0630 
0631     x = (xp)/pixels_in_cm;
0632     y = (yp)/pixels_in_cm;
0633     
0634     figure
0635     plot(x,y,new_ellipse.boundaries(:,1)/pixels_in_cm,new_ellipse.boundaries(:,2)/pixels_in_cm,'r')
0636     title('Transformed trajectory with boundary')
0637 
0638     handles.arena{1}=new_ellipse;
0639     handles.x = x;
0640     handles.y = y;
0641     handles.InputData.pixels_in_cm =  pixels_in_cm;
0642     out = SaveFiles(1,handles);
0643 else
0644     disp('Something went wrong. Arena is still an ellipse. ')
0645 end
0646 
0647 
0648 guidata(gcbo, handles)
0649 
0650 
0651  
0652  
0653  
0654  
0655