Create movie file. The view point is top side of cortex.
F
L R : Front, Back, Left, Right
B
[Input]
fiber_tracking_file : [input file] fiber tracking result file.
current_file : [input file] MAR dynamics file.
movie_file : [output file] output movie file.(empty : no output)
Timefrom : [optional] Time starts from (ms).
Tfreq : [optional] time frequency(Hz) : default:1000
[History]
2014-11-10 Masa-aki Sato Created as a test_ar_cylinder.m
2015-12-07 rhayashi Rename, fine-tuning and added all arguments.
2017-12-12 Yusuke Takeda Modified details
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function movie_top_view_create(fiber_tracking_file, ... 0002 current_file, movie_file, Timefrom, Tfreq) 0003 % Create movie file. The view point is top side of cortex. 0004 % F 0005 % L R : Front, Back, Left, Right 0006 % B 0007 % 0008 % [Input] 0009 % fiber_tracking_file : [input file] fiber tracking result file. 0010 % current_file : [input file] MAR dynamics file. 0011 % movie_file : [output file] output movie file.(empty : no output) 0012 % Timefrom : [optional] Time starts from (ms). 0013 % Tfreq : [optional] time frequency(Hz) : default:1000 0014 % 0015 % 0016 % [History] 0017 % 2014-11-10 Masa-aki Sato Created as a test_ar_cylinder.m 0018 % 2015-12-07 rhayashi Rename, fine-tuning and added all arguments. 0019 % 2017-12-12 Yusuke Takeda Modified details 0020 % 0021 % Copyright (C) 2011, ATR All Rights Reserved. 0022 % License : New BSD License(see VBMEG_LICENSE.txt) 0023 0024 % 0025 % --- Previous check 0026 % 0027 if exist(fiber_tracking_file, 'file') ~= 2 0028 error('fiber_tracking_file not found.'); 0029 end 0030 if exist(current_file, 'file') ~= 2 0031 error('current_file not found.'); 0032 end 0033 if ~exist('movie_file', 'var') 0034 movie_file = []; 0035 elseif ~isempty(movie_file) 0036 [p_, f_, e_] = fileparts(movie_file); 0037 if exist(p_, 'dir') ~= 7 0038 mkdir(p_); 0039 end 0040 end 0041 0042 if ~exist('Timefrom', 'var') 0043 Timefrom = 0; % [ms] 0044 end 0045 if ~exist('Tfreq', 'var') 0046 Tfreq = 1000; % [Hz] 0047 end 0048 0049 % 0050 % --- Main Procedure 0051 % 0052 0053 %------- Plot parameter 0054 plot_para.conn_file = fiber_tracking_file; 0055 plot_para.curr_file = current_file; 0056 0057 %--- figure parameter 0058 plot_para.fig_unit = 'pixels'; 0059 plot_para.fig_pos = [200, 200, 768, 720]; 0060 0061 %--- brain surface 0062 plot_para.faceclr = [0.8 0.7 0.6]; 0063 plot_para.faceclr0 = [1 1 1];% face color of brain 0064 plot_para.alpha = [0.1 0.1 0.01];% alpha value of brain 0065 0066 %--- face surface 0067 plot_para.face_on = 1; % =1:plot face 0068 plot_para.alpha_face = 0.5; % Initial alpha value of face 0069 plot_para.face_file = which('Subject.face.mat'); 0070 plot_para.zoom_factor= 1.3; % zoom factor when a face disappears 0071 0072 %--- area surface 0073 plot_para.alpha_area = [0.8 0.08 0.01]; % alpha value of area 0074 plot_para.cbox = 0; % show area color update dialog 0075 0076 %--- view angle 0077 plot_para.angle = [0 90];% initial view angle 0078 plot_para.dang = [0 0];% increment of view angle in one step 0079 plot_para.Ntime = 0;% number of times for rotation 0080 0081 %--- ROI area surface 0082 plot_para.roi = 0; %=1: show ROI surface 0083 0084 % Time length & speed 0085 plot_para.Tfreq = Tfreq; 0086 plot_para.Timefrom= Timefrom; % time (ms) starts from (for display) 0087 plot_para.Tstay = 100; % time length (sample) for first non-rotate state 0088 plot_para.Tstop = 600; % time point (sample) of stop rotation. 0089 0090 %--- connection line 0091 plot_para.Nskip = 1;% skip number for connections selection 0092 plot_para.Nstep = 1;% skip number along path (neighbor distance= Nstep*0.2mm) 0093 %plot_para.Ndivide = 50;% number of division of connection line 0094 %plot_para.Nperiod = 100;% time window length 0095 0096 %--- activity transition movie 0097 plot_para.pmove = 1;%=1: show activity transition movie 0098 plot_para.pause1 = 0.01;% pause time(sec) 0099 plot_para.pause2 = 0.05;% (sec) 0100 0101 plot_para.dN = 10;% number of cylinder points 0102 plot_para.dr = 0.3;% radius of cylinder [mm] 0103 %plot_para.sigma = 0.1;% input noise sd 0104 plot_para.omega = 0.5;% oscillation speed of dynamics [no dynamics file case] 0105 0106 plot_para.show_max = 1; % max value for caxis 0107 plot_para.abs_mode = 1;%=1: show absolute value of activity 0108 plot_para.max_norm = 1;%=1: normalize activity by max value for each vertex 0109 plot_para.wmulti = 0; %=1: multiply MAR weight 0110 plot_para.vertex_show = 2;% =1: show vertex activity 0111 plot_para.Msize = 10; % marker size 0112 plot_para.th_show = 0.8; % threshold to show vertex activity 0113 0114 %--- message box for stop rotation 0115 plot_para.mbox = 0; 0116 plot_para.video = 0; 0117 if ~isempty(movie_file) 0118 plot_para.video = 1; 0119 plot_para.video_dir = p_; 0120 end 0121 0122 % color map for connection line 0123 color_parm.Nlevel = 64; % gradation color level 0124 color_parm.Nwidth = 13; % active color region length 0125 color_parm.Ncycle = 20; % cycle length 0126 color_parm.Nrepeat = 5; % repeat number of active cycle 0127 color_parm.Nback = 21; % repeat number of background cycle 0128 color_parm.mode = 'gradation'; % color map mode ('gradation','jet','hot') 0129 0130 %----- colormap for connection 0131 color_parm.active_color = 'white'; % color name for active state 0132 color_parm.rest_color = 'navyblue'; % color name for rest state 0133 color_parm.back_color = 'blue'; % color name for background 0134 0135 %---> Set colormap 0136 %C1 = cmap_move(color_parm); 0137 C1 = cmap_move2(color_parm); 0138 %colorbar; colormap(C1); 0139 0140 %----- colormap for vertex 0141 color_parm.active_color = 'yellow'; % color name for active state 0142 color_parm.rest_color = 'orange'; % color name for rest state 0143 color_parm.back_color = 'bottlegreen'; % color name for background 0144 %---> Set colormap 0145 C2 = cmap_move2(color_parm); 0146 0147 %----- set colormap 0148 plot_para.cmap = C1; 0149 plot_para.cmap2 = C2; 0150 0151 %----- Load Connection data 0152 connection = load_connection_from_vmni_connect_file(plot_para.conn_file); 0153 0154 %----- Create movie 0155 close all; 0156 [hfig, Q, id] = plot_cylinder_prepare(connection, plot_para); 0157 set(gca, 'Position', [0.1300 0.2300 0.7750 0.8150]); 0158 % colorbar; 0159 plot_cylinder_anime(plot_para, hfig, Q, id); 0160 0161 if plot_para.video 0162 [success, message] = movefile(fullfile(p_, 'cylinder.avi'), movie_file); 0163 if success 0164 disp(['top view: ' movie_file ' was created.']); 0165 else 0166 error(message); 0167 end 0168 end