load estimated current
USAGE:
[Jinfo,Jact] = ...
vb_load_current(currfile,curr_type,ave_mode,trial,ix_area,verbose)
--- INPUT:
currfile - current file name
--- Optional INPUT:
curr_type - current type
= 0 : J-current : Cortical current excluding zero activity vertex.
= 1 : Z-current : Cortical current on reduced vertex. (bayes_parm_reduce)
= 2 : Current : Cortical current on all vertex. [Default]
= 3 : extra current : Current on extra dipoles (if exist)
ave_mode : trial average mode
= ON : trial average is done [Default]
= OFF : No trial average
trial : trial number to load
if empty, all trials are loaded [Default]
ix_area : (absolute) vertex index to load
if empty, all vertices are loaded [Default]
verbose : verbose mode for trial file loading
0 (No print) , 1 ('.') , 2 ('session , trial')
--- OUTPUT:
Jinfo : structure of current info
.version : Version of current file
.curr_type : current type(0:J-current, 1:Z-current 2:Current)
.tindex : Subsampled indices
.Lact : # of current direction at one vertex in active region
.Wact : Smoothing filter matrix
.ix_act : Vertex index corresponding to Z-current
.ix_act_ex : Vertex index corresponding to J-current
.NJact : # of current vertices
.Tsample : Time sample index for 'Jact'
.Ntrial : # of trials
.Nsession : # of sessions
.jactdir : Current directory
.SampleFreq: Sample Frequency [Hz]
.Pretrigger: Pretrigger period
.Tmsec : Time in msec
.trial : Trial number to load (optional input for this function)
Jact : current timecourse
Jact(Njact,Nsample) for ave_mode = ON
Jact(Njact,Nsample,Ntrials) for ave_mode = OFF
Njact : # of current
- curr_type = 0: Njact = length(Jinfo.ix_act);
- curr_type = 1: Njact = length(Jinfo.ix_act_ex);
- curr_type = 2: Njact = Nvertex(# of all vertex)
Nsample : # of time sample
Ntrials : # of trials in all session
Jact(:, t, :)
Time sample in MEG data : Jinfo.Tsample(t)
Time (ms) in MEG data : Jinfo.Tmsec(t)
Plist : Information of extra dipoles
Jext : estimated current for extra dipoles
2007-3-5 Masa-aki Sato
2008-7-9 Masa-aki Sato
support all file types and old files
2008-09-30 Taku Yoshioka
Minor change for variables in Jinfo
2010-03-01 M. Sato
modified not to use Jinfo.ix_act_ex
2022-05-01 k_suzuki
Merge with vb_load_current_ext
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [Jinfo,Jact,Plist,Jext] = ... 0002 vb_load_current(currfile,curr_type,ave_mode,trial,ix_area,verbose) 0003 % load estimated current 0004 % 0005 % USAGE: 0006 % [Jinfo,Jact] = ... 0007 % vb_load_current(currfile,curr_type,ave_mode,trial,ix_area,verbose) 0008 % 0009 % --- INPUT: 0010 % currfile - current file name 0011 % --- Optional INPUT: 0012 % curr_type - current type 0013 % = 0 : J-current : Cortical current excluding zero activity vertex. 0014 % = 1 : Z-current : Cortical current on reduced vertex. (bayes_parm_reduce) 0015 % = 2 : Current : Cortical current on all vertex. [Default] 0016 % = 3 : extra current : Current on extra dipoles (if exist) 0017 % ave_mode : trial average mode 0018 % = ON : trial average is done [Default] 0019 % = OFF : No trial average 0020 % trial : trial number to load 0021 % if empty, all trials are loaded [Default] 0022 % ix_area : (absolute) vertex index to load 0023 % if empty, all vertices are loaded [Default] 0024 % verbose : verbose mode for trial file loading 0025 % 0 (No print) , 1 ('.') , 2 ('session , trial') 0026 % --- OUTPUT: 0027 % Jinfo : structure of current info 0028 % .version : Version of current file 0029 % .curr_type : current type(0:J-current, 1:Z-current 2:Current) 0030 % .tindex : Subsampled indices 0031 % .Lact : # of current direction at one vertex in active region 0032 % .Wact : Smoothing filter matrix 0033 % .ix_act : Vertex index corresponding to Z-current 0034 % .ix_act_ex : Vertex index corresponding to J-current 0035 % .NJact : # of current vertices 0036 % .Tsample : Time sample index for 'Jact' 0037 % .Ntrial : # of trials 0038 % .Nsession : # of sessions 0039 % .jactdir : Current directory 0040 % .SampleFreq: Sample Frequency [Hz] 0041 % .Pretrigger: Pretrigger period 0042 % .Tmsec : Time in msec 0043 % .trial : Trial number to load (optional input for this function) 0044 % 0045 % Jact : current timecourse 0046 % Jact(Njact,Nsample) for ave_mode = ON 0047 % Jact(Njact,Nsample,Ntrials) for ave_mode = OFF 0048 % Njact : # of current 0049 % - curr_type = 0: Njact = length(Jinfo.ix_act); 0050 % - curr_type = 1: Njact = length(Jinfo.ix_act_ex); 0051 % - curr_type = 2: Njact = Nvertex(# of all vertex) 0052 % Nsample : # of time sample 0053 % Ntrials : # of trials in all session 0054 % 0055 % Jact(:, t, :) 0056 % Time sample in MEG data : Jinfo.Tsample(t) 0057 % Time (ms) in MEG data : Jinfo.Tmsec(t) 0058 % 0059 % Plist : Information of extra dipoles 0060 % Jext : estimated current for extra dipoles 0061 % 0062 % 2007-3-5 Masa-aki Sato 0063 % 2008-7-9 Masa-aki Sato 0064 % support all file types and old files 0065 % 2008-09-30 Taku Yoshioka 0066 % Minor change for variables in Jinfo 0067 % 2010-03-01 M. Sato 0068 % modified not to use Jinfo.ix_act_ex 0069 % 2022-05-01 k_suzuki 0070 % Merge with vb_load_current_ext 0071 % Copyright (C) 2011, ATR All Rights Reserved. 0072 % License : New BSD License(see VBMEG_LICENSE.txt) 0073 0074 0075 if ~exist('curr_type','var'), curr_type = 2; end; 0076 if ~exist('ave_mode','var'), ave_mode = ON; end; 0077 if ~exist('trial','var'), trial = []; end; 0078 if ~exist('ix_area','var'), ix_area = []; end; 0079 if ~exist('verbose','var'), verbose = 0; end; 0080 0081 if curr_type~=3 0082 %----- Load cortical current ----- 0083 whole_vertex = false; 0084 if curr_type == 2 0085 whole_vertex = true; 0086 curr_type = 0; 0087 end 0088 0089 [J_type, file_type] = vb_load_current_type(currfile); 0090 % J_type = 0 : J-current 0091 % J_type = 1 : Z-current 0092 % file_type = 0: single file 0093 % file_type = 1: parent file with trial files 0094 0095 [Jinfo] = vb_load_current_info(currfile); 0096 0097 if ave_mode==OFF && file_type==1 0098 % trial mode & each trial current file 0099 if J_type==1 0100 [Jact,ix_act] = ... 0101 vb_load_current_z_tr(currfile,curr_type,trial,ix_area,verbose); 0102 Jinfo.curr_type = curr_type; 0103 else 0104 if curr_type==1, 0105 fprintf('No Z-current and J-current is returned\n'); 0106 end 0107 [Jact,ix_act] = ... 0108 vb_load_current_j_tr(currfile,trial,ix_area,verbose); 0109 Jinfo.curr_type = 0; 0110 end 0111 else 0112 % single current file 0113 if J_type==1 0114 [Jact,ix_act] = ... 0115 vb_load_current_z(currfile,curr_type,ave_mode,trial,ix_area); 0116 Jinfo.curr_type = curr_type; 0117 else 0118 if curr_type==1, 0119 fprintf('No Z-current and J-current is returned\n'); 0120 end 0121 [Jact,ix_act] = ... 0122 vb_load_current_j(currfile,ave_mode,trial,ix_area); 0123 Jinfo.curr_type = 0; 0124 end 0125 end 0126 0127 Jinfo.trial = trial; 0128 Jinfo.NJact = length(ix_act); 0129 0130 if whole_vertex 0131 % create cortical current on whole vertex. 0132 warning('off', 'MATLAB:load:variableNotFound'); 0133 load(currfile, 'Nvertex'); 0134 warning('on', 'MATLAB:load:variableNotFound'); 0135 if exist('Nvertex', 'var') 0136 [s1, s2, s3] = size(Jact); 0137 Jact_whole = zeros(Nvertex, s2, s3); 0138 Jact_whole(Jinfo.ix_act_ex, :, :) = Jact(:, :, :); 0139 Jact = Jact_whole; 0140 Jinfo.curr_type = 2; 0141 Jinfo.NJact = Nvertex; 0142 else 0143 error('Current file format is old. re-run vb_job_current.'); 0144 end 0145 end 0146 0147 else 0148 %----- Load extra current ----- 0149 load(currfile,'Pointlist'); 0150 if exist('Pointlist', 'var') 0151 Plist = Pointlist; 0152 Jext = inner_load_extra_current(currfile, ave_mode, trial); 0153 Jinfo=[];Jact=[]; 0154 else 0155 warning('Currfile does not contain extra current'); 0156 end 0157 0158 end 0159 0160 end 0161 0162 function Jext = inner_load_extra_current(currfile, ave_mode, ix_trial) 0163 const = vb_define_verbose; 0164 VERBOSE_LEVEL_INFO = const.VERBOSE_LEVEL_INFO; 0165 0166 if ave_mode==OFF 0167 % trial mode 0168 load(currfile,'Jinfo'); 0169 0170 if isfield(Jinfo,'jactdir'), 0171 jactdir = [fileparts(currfile) '/' Jinfo.jactdir]; 0172 if exist(jactdir,'dir')==0, 0173 error('No trial data directory') 0174 end 0175 0176 % Session & Trial number list 0177 session = []; 0178 ntrial = []; 0179 0180 for n=1:Jinfo.Nsession 0181 Ntry = Jinfo.Ntrial(n); 0182 session = [session, repmat(n,1,Ntry)]; 0183 ntrial = [ntrial, 1:Ntry]; 0184 end 0185 0186 % Trial loop 0187 if isempty(ix_trial), ix_trial = 1:length(ntrial); end 0188 Ntrial = length(ix_trial); 0189 0190 for n=1:Ntrial 0191 nt = ix_trial(n); 0192 vb_disp(sprintf('Session: %04d , Trial: %04d', ... 0193 session(nt), ntrial(nt)), VERBOSE_LEVEL_INFO); 0194 %if verbose==1, 0195 % fprintf('.') 0196 %elseif verbose==2, 0197 % fprintf('Session: %04d , Trial: %04d\n',session(nt), ntrial(nt)) 0198 %end 0199 0200 fname = sprintf('data_s%04dt%04d', session(nt), ntrial(nt)); 0201 load([jactdir '/' fname],'Jext'); 0202 Jall(:,:,n) = Jext; 0203 end 0204 0205 Jext = Jall; 0206 else 0207 load(currfile,'Jext'); 0208 if ~isempty(ix_trial), Jext = Jext(:,:,ix_trial); end 0209 end 0210 else 0211 load(currfile,'Jext'); 0212 end 0213 end 0214