% READLOCS - read electrode location coordinates and other information from a file.
% Several standard file formats are supported. Users may also specify
% a custom column format. Defined format examples are given below
% (see File Formats).
% Usage:
% >> eloc = readlocs( filename );
% >> EEG.chanlocs = readlocs( filename, 'key', 'val', ... );
% >> [eloc, labels, theta, radius, indices] = ...
% readlocs( filename, 'key', 'val', ... );
% Inputs:
% filename - Name of the file containing the electrode locations
% {default: 2-D polar coordinates} (see >> help topoplot )
%
% Optional inputs:
% 'filetype' - ['loc'|'sph'|'sfp'|'xyz'|'asc'|'polhemus'|'besa'|'chanedit'|'custom']
% Type of the file to read. By default the file type is determined
% using the file extension (see below under File Formats),
% 'loc' an EEGLAB 2-D polar coordinates channel locations file
% Coordinates are theta and radius (see definitions below).
% 'sph' Matlab spherical coordinates (Note: spherical
% coordinates used by Matlab functions are different
% from spherical coordinates used by BESA - see below).
% 'sfp' EGI Cartesian coordinates (NOT Matlab Cartesian - see below).
% 'xyz' Matlab/EEGLAB Cartesian coordinates (NOT EGI Cartesian).
% z is toward nose; y is toward left ear; z is toward vertex
% 'asc' Neuroscan polar coordinates.
% 'polhemus' or 'polhemusx' - Polhemus electrode location file recorded
% with 'X' on sensor pointing to subject (see below and READELP).
% 'polhemusy' - Polhemus electrode location file recorded with
% 'Y' on sensor pointing to subject (see below and READELP).
% 'besa' BESA-'.elp' spherical coordinates. (Not MATLAB spherical -
% see below).
% 'chanedit' - EEGLAB channel location file created by POP_CHANEDIT.
% 'custom' - Ascii file with columns in user-defined 'format' (see below).
% 'importmode' - ['eeglab'|'native'] for location files containing 3-D cartesian electrode
% coordinates, import either in EEGLAB format (nose pointing toward +X).
% This may not always be possible since EEGLAB might not be able to
% determine the nose direction for scanned electrode files. 'native' import
% original cartesian coordinates (user can then specify the position of
% the nose when calling the TOPOPLOT function; in EEGLAB the position
% of the nose is stored in the EEG.chaninfo structure). {default 'eeglab'}
% 'format' - [cell array] Format of a 'custom' channel location file (see above).
% {default: if no file type is defined. The cell array contains
% labels defining the meaning of each column of the input file.
% 'channum' [positive integer] channel number.
% 'labels' [string] channel name (no spaces).
% 'theta' [real degrees] 2-D angle in polar coordinates.
% positive => rotating from nose (0) toward left ear
% 'radius' [real] radius for 2-D polar coords; 0.5 is the head
% disk radius and limit for TOPOPLOT plotting).
% 'X' [real] Matlab-Cartesian X coordinate (to nose).
% 'Y' [real] Matlab-Cartesian Y coordinate (to left ear).
% 'Z' [real] Matlab-Cartesian Z coordinate (to vertex).
% '-X','-Y','-Z' Matlab-Cartesian coordinates pointing opposite
% to the above.
% 'sph_theta' [real degrees] Matlab spherical horizontal angle.
% positive => rotating from nose (0) toward left ear.
% 'sph_phi' [real degrees] Matlab spherical elevation angle.
% positive => rotating from horizontal (0) upwards.
% 'sph_radius' [real] distance from head center (unused).
% 'sph_phi_besa' [real degrees] BESA phi angle from vertical.
% positive => rotating from vertex (0) towards right ear.
% 'sph_theta_besa' [real degrees] BESA theta horiz/azimuthal angle.
% positive => rotating from right ear (0) toward nose.
% 'ignore' ignore column}.
% The input file may also contain other channel information fields.
% 'type' channel type: 'EEG', 'MEG', 'EMG', 'ECG', others ...
% 'calib' [real near 1.0] channel calibration value.
% 'gain' [real > 1] channel gain.
% 'custom1' custom field #1.
% 'custom2', 'custom3', 'custom4', etc. more custom fields
% 'skiplines' - [integer] Number of header lines to skip (in 'custom' file types only).
% Note: Characters on a line following '%' will be treated as comments.
% 'readchans' - [integer array] indices of electrodes to read. {default: all}
% 'center' - [(1,3) real array or 'auto'] center of xyz coordinates for conversion
% to spherical or polar, Specify the center of the sphere here, or 'auto'.
% This uses the center of the sphere that best fits all the electrode
% locations read. {default: [0 0 0]}. [Deprecated]
% Outputs:
% eloc - structure containing the channel names and locations (if present).
% It has three fields: 'eloc.labels', 'eloc.theta' and 'eloc.radius'
% identical in meaning to the EEGLAB struct 'EEG.chanlocs'.
% labels - cell array of strings giving the names of the electrodes. NOTE: Unlike the
% three outputs below, includes labels of channels *without* location info.
% theta - vector (in degrees) of polar angles of the electrode locations.
% radius - vector of polar-coordinate radii (arc_lengths) of the electrode locations
% indices - indices, k, of channels with non-empty 'locs(k).theta' coordinate
%
% File formats:
% If 'filetype' is unspecified, the file extension determines its type.
%
% '.loc' or '.locs' or '.eloc':
% polar coordinates. Notes: angles in degrees:
% right ear is 90; left ear -90; head disk radius is 0.5.
% Fields: N angle radius label
% Sample: 1 -18 .511 Fp1
% 2 18 .511 Fp2
% 3 -90 .256 C3
% 4 90 .256 C4
% ...
% Note: In previous releases, channel labels had to contain exactly
% four characters (spaces replaced by '.'). This format still works,
% though dots are no longer required.
% '.sph':
% Matlab spherical coordinates. Notes: theta is the azimuthal/horizontal angle
% in deg.: 0 is toward nose, 90 rotated to left ear. Following this, performs
% the elevation (phi). Angles in degrees.
% Fields: N theta phi label
% Sample: 1 18 -2 Fp1
% 2 -18 -2 Fp2
% 3 90 44 C3
% 4 -90 44 C4
% ...
% '.elc':
% Cartesian 3-D electrode coordinates scanned using the EETrak software.
% See READEETRAKLOCS.
% '.elp':
% Polhemus-.'elp' Cartesian coordinates. By default, an .elp extension is read
% as PolhemusX-elp in which 'X' on the Polhemus sensor is pointed toward the
% subject. Polhemus files are not in columnar format (see READELP).
% '.elp':
% BESA-'.elp' spherical coordinates: Need to specify 'filetype','besa'.
% The elevation angle (phi) is measured from the vertical axis. Positive
% rotation is toward right ear. Next, perform azimuthal/horizontal rotation
% (theta): 0 is toward right ear; 90 is toward nose, -90 toward occiput.
% Angles are in degrees. If labels are absent or weights are given in
% a last column, READLOCS adjusts for this. Default labels are E1, E2, ...
% Fields: Type label phi theta
% Sample: EEG Fp1 -92 -72
% EEG Fp2 92 72
% EEG C3 -46 0
% EEG C4 46 0
% ...
% '.xyz':
% Matlab/EEGLAB Cartesian coordinates. Here. x is towards the nose,
% y is towards the left ear, and z towards the vertex. Note that the first
% column (x) is -Y in a Matlab 3-D plot, the second column (y) is X in a
% matlab 3-D plot, and the third column (z) is Z.
% Fields: channum x y z label
% Sample: 1 .950 .308 -.035 Fp1
% 2 .950 -.308 -.035 Fp2
% 3 0 .719 .695 C3
% 4 0 -.719 .695 C4
% ...
% '.asc', '.dat':
% Neuroscan-.'asc' or '.dat' Cartesian polar coordinates text file.
% '.mat':
% Brainstrom or fieldtrip channel location/layout file.
% '.lay':
% Fieldtrip layout file.
% '.txt':
% Fieldtrip electore file.
% Fields: label phi theta
% Sample: Fp1 -92 -72
% Fp2 92 72
% C3 -46 0
% C4 46 0
% '.sfp':
% BESA/EGI-xyz Cartesian coordinates. Notes: For EGI, x is toward right ear,
% y is toward the nose, z is toward the vertex. EEGLAB converts EGI
% Cartesian coordinates to Matlab/EEGLAB xyz coordinates.
% Fields: label x y z
% Sample: Fp1 -.308 .950 -.035
% Fp2 .308 .950 -.035
% C3 -.719 0 .695
% C4 .719 0 .695
% ...
% '.ced':
% ASCII file saved by POP_CHANEDIT. Contains multiple MATLAB/EEGLAB formats.
% Cartesian coordinates are as in the 'xyz' format (above).
% Fields: channum label theta radius x y z sph_theta sph_phi ...
% Sample: 1 Fp1 -18 .511 .950 .308 -.035 18 -2 ...
% 2 Fp2 18 .511 .950 -.308 -.035 -18 -2 ...
% 3 C3 -90 .256 0 .719 .695 90 44 ...
% 4 C4 90 .256 0 -.719 .695 -90 44 ...
% ...
% The last columns of the file may contain any other defined fields (gain,
% calib, type, custom).
%
% Fieldtrip structure:
% If a Fieltrip structure is given as input, an EEGLAB
% chanlocs structure is returned
% Brainstrom Matlab file:
% If a Brainstrom Matlab file is given as input, an EEGLAB
% chanlocs structure is returned
%
% Author: Arnaud Delorme, Salk Institute, 8 Dec 2002
%
% See also: READELP, WRITELOCS, TOPO2SPH, SPH2TOPO, SPH2CART
% Copyright (C) Arnaud Delorme, CNL / Salk Institute, 28 Feb 2002
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
%
% 1. Redistributions of source code must retain the above copyright notice,
% this list of conditions and the following disclaimer.
%
% 2. Redistributions in binary form must reproduce the above copyright notice,
% this list of conditions and the following disclaimer in the documentation
% and/or other materials provided with the distribution.
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
% THE POSSIBILITY OF SUCH DAMAGE.
function [eloc, labels, theta, radius, indices] = readlocs( filename, varargin );
if nargin < 1
help readlocs;
return;
end
% NOTE: To add a new channel format:
% ----------------------------------
% 1) Add a new element to the structure 'chanformat' (see 'ADD NEW FORMATS HERE' below):
% 2) Enter a format 'type' for the new file format,
% 3) Enter a (short) 'typestring' description of the format
% 4) Enter a longer format 'description' (possibly multiline, see ex. (1) below)
% 5) Enter format file column labels in the 'importformat' field (see ex. (2) below)
% 6) Enter the number of header lines to skip (if any) in the 'skipline' field
% 7) Document the new channel format in the help message above.
% 8) After testing, please send the new version of readloca.m to us
% at eeglab@sccn.ucsd.edu with a sample locs file.
% The 'chanformat' structure is also used (automatically) by the WRITELOCS
% and POP_READLOCS functions. You do not need to edit these functions.
chanformat(1).type = 'polhemus';
chanformat(1).typestring = 'Polhemus native .elp file';
chanformat(1).description = [ 'Polhemus native coordinate file containing scanned electrode positions. ' ...
'User must select the direction ' ...
'for the nose after importing the data file.' ];
chanformat(1).importformat = 'readelp() function';
% ---------------------------------------------------------------------------------------------------
chanformat(2).type = 'besa';
chanformat(2).typestring = 'BESA spherical .elp file';
chanformat(2).description = [ 'BESA spherical coordinate file. Note that BESA spherical coordinates ' ...
'are different from Matlab spherical coordinates' ];
chanformat(2).skipline = 0; % some BESA files do not have headers
chanformat(2).importformat = { 'type' 'labels' 'sph_theta_besa' 'sph_phi_besa' 'sph_radius' };
% ---------------------------------------------------------------------------------------------------
chanformat(3).type = 'xyz';
chanformat(3).typestring = 'Matlab .xyz file';
chanformat(3).description = [ 'Standard 3-D cartesian coordinate files with electrode numbers in ' ...
'the first column and X, Y, and Z coordinates in columns 2, 3, and 4' ...
' and channel labels in column 5' ];
chanformat(3).importformat = { 'channum' '-Y' 'X' 'Z' 'labels'};
% ---------------------------------------------------------------------------------------------------
chanformat(4).type = 'sfp';
chanformat(4).typestring = 'BESA or EGI 3-D cartesian .sfp file';
chanformat(4).description = [ 'Standard BESA 3-D cartesian coordinate files with electrode labels in ' ...
'the first column and X, Y, and Z coordinates in columns 2, 3, and 4.' ...
'Coordinates are re-oriented to fit the EEGLAB standard of having the ' ...
'nose along the +X axis.' ];
chanformat(4).importformat = { 'labels' '-Y' 'X' 'Z' };
chanformat(4).skipline = 0;
% ---------------------------------------------------------------------------------------------------
chanformat(5).type = 'loc';
chanformat(5).typestring = 'EEGLAB polar .loc file';
chanformat(5).description = [ 'EEGLAB polar .loc file' ];
chanformat(5).importformat = { 'channum' 'theta' 'radius' 'labels' };
% ---------------------------------------------------------------------------------------------------
chanformat(6).type = 'sph';
chanformat(6).typestring = 'Matlab .sph spherical file';
chanformat(6).description = [ 'Standard 3-D spherical coordinate files in Matlab format' ];
chanformat(6).importformat = { 'channum' 'sph_theta' 'sph_phi' 'labels' };
% ---------------------------------------------------------------------------------------------------
chanformat(7).type = 'asc';
chanformat(7).typestring = 'Neuroscan polar .asc file';
chanformat(7).description = [ 'Neuroscan polar .asc file, automatically recentered to fit EEGLAB standard' ...
'of having ''Cz'' at (0,0).' ];
chanformat(7).importformat = 'readneurolocs';
% ---------------------------------------------------------------------------------------------------
chanformat(8).type = 'dat';
chanformat(8).typestring = 'Neuroscan 3-D .dat file';
chanformat(8).description = [ 'Neuroscan 3-D cartesian .dat file. Coordinates are re-oriented to fit ' ...
'the EEGLAB standard of having the nose along the +X axis.' ];
chanformat(8).importformat = 'readneurodat';
% ---------------------------------------------------------------------------------------------------
chanformat(9).type = 'elc';
chanformat(9).typestring = 'ASA .elc 3-D file';
chanformat(9).description = [ 'ASA .elc 3-D coordinate file containing scanned electrode positions. ' ...
'User must select the direction ' ...
'for the nose after importing the data file.' ];
chanformat(9).importformat = 'readeetraklocs';
% ---------------------------------------------------------------------------------------------------
chanformat(10).type = 'chanedit';
chanformat(10).typestring = 'EEGLAB complete 3-D file';
chanformat(10).description = [ 'EEGLAB file containing polar, cartesian 3-D, and spherical 3-D ' ...
'electrode locations.' ];
chanformat(10).importformat = { 'channum' 'labels' 'theta' 'radius' 'X' 'Y' 'Z' 'sph_theta' 'sph_phi' ...
'sph_radius' 'type' };
chanformat(10).skipline = 1;
% ---------------------------------------------------------------------------------------------------
chanformat(11).type = 'tsv';
chanformat(11).typestring = 'BIDS .tsv file';
chanformat(11).description = [ 'Standard 3-D cartesian coordinate files with electrode labels in ' ...
'the first column and X, Y, and Z coordinates in columns 2, 3, and 4' ];
chanformat(11).importformat = { 'labels' 'X' 'Y' 'Z' };
chanformat(11).skipline = 1;
% ---------------------------------------------------------------------------------------------------
chanformat(12).type = 'mat';
chanformat(12).typestring = 'Brainstorm Matlab file format';
chanformat(12).description = 'Custom Matlab file.';
chanformat(12).importformat = '';
% ---------------------------------------------------------------------------------------------------
chanformat(13).type = 'lay';
chanformat(13).typestring = 'Fieldtrip layout file';
chanformat(13).description = 'Fieldtrip layout file';
chanformat(13).importformat = '';
% ---------------------------------------------------------------------------------------------------
chanformat(14).type = 'txt';
chanformat(14).typestring = 'Fieldtrip .txt spherical file';
chanformat(14).description = [ 'Standard 3-D spherical coordinate files in text format' ];
chanformat(14).importformat = { 'labels' 'sph_theta_besa' 'sph_phi_besa' };
% ---------------------------------------------------------------------------------------------------
chanformat(15).type = 'custom';
chanformat(15).typestring = 'Custom file format';
chanformat(15).description = 'Custom ASCII file format where user can define content for each file columns.';
chanformat(15).importformat = '';
% ---------------------------------------------------------------------------------------------------
% ----- ADD MORE FORMATS HERE -----------------------------------------------------------------------
% ---------------------------------------------------------------------------------------------------
listcolformat = { 'labels' 'channum' 'theta' 'radius' 'sph_theta' 'sph_phi' ...
'sph_radius' 'sph_theta_besa' 'sph_phi_besa' 'gain' 'calib' 'type' ...
'X' 'Y' 'Z' '-X' '-Y' '-Z' 'custom1' 'custom2' 'custom3' 'custom4' 'ignore' 'not def' };
% ----------------------------------
% special mode for getting the info
% ----------------------------------
if ischar(filename) && strcmp(filename, 'getinfos')
eloc = chanformat;
labels = listcolformat;
return;
end
g = finputcheck( varargin, ...
{ 'filetype' 'string' {} '';
'importmode' 'string' { 'eeglab','native' } 'eeglab';
'defaultelp' 'string' { 'besa','polhemus' } 'polhemus';
'skiplines' 'integer' [0 Inf] [];
'elecind' 'integer' [1 Inf] [];
'format' 'cell' [] {} }, 'readlocs');
if ischar(g), error(g); end
if ~isempty(g.format), g.filetype = 'custom'; end
if ischar(filename)
% format auto detection
% --------------------
if strcmpi(g.filetype, 'autodetect'), g.filetype = ''; end
g.filetype = strtok(g.filetype);
[~,~,fileextension] = fileparts(filename);
fileextension = fileextension(2:end);
g.filetype = lower(g.filetype);
if isempty(g.filetype)
switch lower(fileextension)
case {'loc' 'locs' 'eloc'}, g.filetype = 'loc'; % 5/27/2014 Ramon: 'eloc' option introduced.
case 'xyz', g.filetype = 'xyz';
fprintf( [ 'WARNING: Matlab Cartesian coord. file extension (".xyz") detected.\n' ...
'If importing EGI Cartesian coords, force type "sfp" instead.\n'] );
case 'sph', g.filetype = 'sph';
case 'ced', g.filetype = 'chanedit';
case 'elp', g.filetype = g.defaultelp;
case 'asc', g.filetype = 'asc';
case 'dat', g.filetype = 'dat';
case 'elc', g.filetype = 'elc';
case 'eps', g.filetype = 'besa';
case 'txt', g.filetype = 'txt';
case 'sfp', g.filetype = 'sfp';
case 'tsv', g.filetype = 'tsv';
case 'mat', g.filetype = 'mat';
case 'lay', g.filetype = 'lay';
otherwise, g.filetype = '';
end
fprintf('readlocs(): ''%s'' format assumed from file extension\n', g.filetype);
else
if strcmpi(g.filetype, 'locs'), g.filetype = 'loc'; end
if strcmpi(g.filetype, 'eloc'), g.filetype = 'loc'; end
end
% assign format from filetype
% ---------------------------
if ~isempty(g.filetype) && ~strcmpi(g.filetype, 'custom') ...
& ~strcmpi(g.filetype, 'asc') & ~strcmpi(g.filetype, 'elc') & ~strcmpi(g.filetype, 'dat')
indexformat = strmatch(lower(g.filetype), { chanformat.type }, 'exact');
g.format = chanformat(indexformat).importformat;
if isempty(g.skiplines)
g.skiplines = chanformat(indexformat).skipline;
end
if isempty(g.filetype)
error( ['readlocs() error: The filetype cannot be detected from the \n' ...
' file extension, and custom format not specified']);
end
end
% import file
% -----------
if strcmp(g.filetype, 'mat')
elocIn = load('-mat', filename );
if isfield(elocIn, 'Channel')
% brainstorm file
for iChan = 1:length(elocIn.Channel)
eloc(iChan).labels = elocIn.Channel(iChan).Name;
eloc(iChan).X = elocIn.Channel(iChan).Loc(1);
eloc(iChan).Y = elocIn.Channel(iChan).Loc(2);
eloc(iChan).Z = elocIn.Channel(iChan).Loc(3);
eloc(iChan).type = elocIn.Channel(iChan).Type;
end
if isfield(elocIn, 'SCS')
chans = { 'NAS' 'LPA' 'RPA' };
for iChan = 1:length(chans)
if isfield(elocIn.SCS, chans{iChan}) && ~isempty(elocIn.SCS.(chans{iChan}))
eloc(end+1).labels = chans{iChan};
eloc(end).X = elocIn.SCS.(chans{iChan})(1);
eloc(end).Y = elocIn.SCS.(chans{iChan})(2);
eloc(end).Z = elocIn.SCS.(chans{iChan})(3);
eloc(end).type = elocIn.Channel(iChan).Type;
end
end
end
else
% fieldtrip layout file
fprintf(2, 'Warning: You are a 2-D Layout file, do not use channel coordinates for source localization\n');
if isfield(elocIn, 'layout') && ~isfield(elocIn, 'lay')
elocIn.lay = elocIn.layout;
end
if any(elocIn.lay.pos(:,1) > 700)
elocIn.lay.pos = (elocIn.lay.pos - 400)/800;
elseif any(elocIn.lay.pos(:,1) > 400)
elocIn.lay.pos = (elocIn.lay.pos - 250)/500;
end
radius = sqrt(elocIn.lay.pos(:,1).^2 + elocIn.lay.pos(:,2).^2);
theta = atan2d(elocIn.lay.pos(:,1), elocIn.lay.pos(:,2));
for iChan = 1:length(elocIn.lay.label)
eloc(iChan).labels = elocIn.lay.label{iChan};
eloc(iChan).theta = theta(iChan);
eloc(iChan).radius = radius(iChan);
end
end
elseif strcmp(g.filetype, 'lay')
layout = readtable(filename, 'filetype', 'text');
fprintf(2, 'Warning: You are a 2-D Layout file, do not use channel coordinates for source localization\n');
radius = sqrt([layout{:,2}].^2 + [layout{:,3}].^2);
theta = atan2d([layout{:,2}], [layout{:,3}]);
for iChan = 1:length(radius)
eloc(iChan).labels = layout{iChan,1};
if isnumeric(eloc(iChan).labels)
eloc(iChan).labels = num2str(eloc(iChan).labels);
end
eloc(iChan).theta = theta(iChan);
eloc(iChan).radius = radius(iChan);
end
elseif strcmp(g.filetype, 'asc') || strcmp(g.filetype, 'dat')
eloc = readneurolocs( filename );
if isfield(eloc, 'type')
for index = 1:length(eloc)
eloc(index).labels = strtrim(eloc(index).labels);
type = eloc(index).type;
if ~ischar(type) && ~isempty(type)
if type == 69, eloc(index).type = 'EEG';
elseif type == 88, eloc(index).type = 'REF';
elseif type >= 76 && type <= 82, eloc(index).type = 'FID';
else eloc(index).type = num2str(eloc(index).type);
end
end
end
end
elseif strcmp(g.filetype, 'txt')
elocTmp = readtable(filename, 'filetype', 'text');
for iChan = 1:size(elocTmp,1)
eloc(iChan).labels = elocTmp{iChan,1};
if isnumeric(eloc(iChan).labels)
eloc(iChan).labels = num2str(eloc(iChan).labels);
end
if iscell( eloc(iChan).labels)
eloc(iChan).labels = eloc(iChan).labels{1};
end
eloc(iChan).sph_theta_besa = elocTmp{iChan,2};
eloc(iChan).sph_phi_besa = elocTmp{iChan,3};
end
eloc = convertlocs(eloc, 'sphbesa2all');
eloc = rmfield(eloc, 'sph_theta'); % for the conversion below
eloc = rmfield(eloc, 'sph_theta_besa'); % for the conversion below
elseif strcmp(g.filetype, 'elc')
eloc = readeetraklocs( filename );
eloc = convertlocs(eloc, 'cart2all');
eloc = rmfield(eloc, 'sph_theta'); % for the conversion below
eloc = rmfield(eloc, 'sph_theta_besa'); % for the conversion below
eloc = convertlocs(eloc, 'cart2all');
eloc = rmfield(eloc, 'sph_theta'); % for the conversion below
eloc = rmfield(eloc, 'sph_theta_besa'); % for the conversion below
elseif strcmp(lower(g.filetype(1:end-1)), 'polhemus') || ...
strcmp(g.filetype, 'polhemus')
try,
[eloc labels X Y Z]= readelp( filename );
if strcmp(g.filetype, 'polhemusy')
tmp = X; X = Y; Y = tmp;
end
for index = 1:length( eloc )
eloc(index).X = X(index);
eloc(index).Y = Y(index);
eloc(index).Z = Z(index);
end
catch,
disp('readlocs(): Could not read Polhemus coords. Trying to read BESA .elp file.');
[eloc, labels, theta, radius, indices] = readlocs( filename, 'defaultelp', 'besa', varargin{:} );
end
else
% importing file
% --------------
if isempty(g.skiplines), g.skiplines = 0; end
if strcmpi(g.filetype, 'chanedit')
array = loadtxt( filename, 'delim', 9, 'skipline', g.skiplines, 'blankcell', 'off');
else
array = load_file_or_array( filename, g.skiplines);
end
if size(array,2) < length(g.format)
fprintf(['readlocs() warning: Fewer columns in the input than expected.\n' ...
' See >> help readlocs\n']);
elseif size(array,2) > length(g.format)
fprintf(['readlocs() warning: More columns in the input than expected.\n' ...
' See >> help readlocs\n']);
end
% removing lines BESA
% -------------------
if isempty(array{1,2})
disp('BESA header detected, skipping three lines...');
array = load_file_or_array( filename, g.skiplines-1);
if isempty(array{1,2})
array = load_file_or_array( filename, g.skiplines-1);
end
end
% xyz format, is the first col absent
% -----------------------------------
if strcmp(g.filetype, 'xyz')
if size(array, 2) == 4
array(:, 2:5) = array(:, 1:4);
end
end
% removing comments and empty lines
% ---------------------------------
indexbeg = 1;
while isempty(array{indexbeg,1}) || ...
(ischar(array{indexbeg,1}) && array{indexbeg,1}(1) == '%' )
indexbeg = indexbeg+1;
end
array = array(indexbeg:end,:);
% converting file
% ---------------
for indexcol = 1:min(size(array,2), length(g.format))
[str, mult] = checkformat(g.format{indexcol});
for indexrow = 1:size( array, 1)
if mult ~= 1
% eval ( [ 'eloc(indexrow).' str '= -array{indexrow, indexcol};' ]);
eloc(indexrow).(str)= -array{indexrow, indexcol};
else
% eval ( [ 'eloc(indexrow).' str '= array{indexrow, indexcol};' ]);
eloc(indexrow).(str)= array{indexrow, indexcol};
end
end
end
end
% handling BESA coordinates
% -------------------------
if isfield(eloc, 'sph_theta_besa')
if isfield(eloc, 'type')
if isnumeric(eloc(1).type)
disp('BESA format detected ( Theta | Phi )');
for index = 1:length(eloc)
eloc(index).sph_phi_besa = eloc(index).labels;
eloc(index).sph_theta_besa = eloc(index).type;
eloc(index).labels = '';
eloc(index).type = '';
end
eloc = rmfield(eloc, 'labels');
end
end
if isfield(eloc, 'labels')
if isnumeric(eloc(1).labels)
disp('BESA format detected ( Elec | Theta | Phi )');
for index = 1:length(eloc)
eloc(index).sph_phi_besa = eloc(index).sph_theta_besa;
eloc(index).sph_theta_besa = eloc(index).labels;
eloc(index).labels = eloc(index).type;
eloc(index).type = '';
eloc(index).radius = 1;
end
end
end
try
eloc = convertlocs(eloc, 'sphbesa2all');
eloc = convertlocs(eloc, 'topo2all'); % problem with some EGI files (not BESA files)
catch, disp('Warning: coordinate conversion failed'); end
fprintf('Readlocs: BESA spherical coords. converted, now deleting BESA fields\n');
fprintf(' to avoid confusion (these fields can be exported, though)\n');
eloc = rmfield(eloc, 'sph_phi_besa');
eloc = rmfield(eloc, 'sph_theta_besa');
% converting XYZ coordinates to polar
% -----------------------------------
elseif isfield(eloc, 'sph_theta') && any(~cellfun(@isempty, { eloc.sph_theta }))
try
eloc = convertlocs(eloc, 'sph2all');
catch, disp('Warning: coordinate conversion failed'); end
elseif isfield(eloc, 'X')
try
eloc = convertlocs(eloc, 'cart2all');
catch, disp('Warning: coordinate conversion failed'); end
else
try
eloc = convertlocs(eloc, 'topo2all');
catch, disp('Warning: coordinate conversion failed'); end
end
% inserting labels if no labels
% -----------------------------
if ~isfield(eloc, 'labels')
fprintf('readlocs(): Inserting electrode labels automatically.\n');
for index = 1:length(eloc)
eloc(index).labels = [ 'E' int2str(index) ];
end
else
% remove trailing '.'
for index = 1:length(eloc)
if ischar(eloc(index).labels)
tmpdots = find( eloc(index).labels == '.' );
eloc(index).labels(tmpdots) = [];
end
end
end
% resorting electrodes if number not-sorted
% -----------------------------------------
if isfield(eloc, 'channum')
if ~isnumeric(eloc(1).channum)
error('Channel numbers must be numeric');
end
allchannum = [ eloc.channum ];
if any( sort(allchannum) ~= allchannum )
fprintf('readlocs(): Re-sorting channel numbers based on ''channum'' column indices\n');
[tmp newindices] = sort(allchannum);
eloc = eloc(newindices);
end
eloc = rmfield(eloc, 'channum');
end
else
if isstruct(filename)
% detect Fieldtrip structure and convert it
% -----------------------------------------
if isfield(filename, 'pnt')
neweloc = [];
for index = 1:length(filename.label)
neweloc(index).labels = filename.label{index};
neweloc(index).X = filename.pnt(index,1);
neweloc(index).Y = filename.pnt(index,2);
neweloc(index).Z = filename.pnt(index,3);
end
eloc = neweloc;
eloc = convertlocs(eloc, 'cart2all');
else
eloc = filename;
end
else
disp('readlocs(): input variable must be a string or a structure');
end;
end
if ~isempty(g.elecind)
eloc = eloc(g.elecind);
end
if nargout > 2
if isfield(eloc, 'theta')
tmptheta = { eloc.theta }; % check which channels have (polar) coordinates set
else tmptheta = cell(1,length(eloc));
end
if isfield(eloc, 'theta')
tmpx = { eloc.X }; % check which channels have (polar) coordinates set
else tmpx = cell(1,length(eloc));
end
indices = find(~cellfun('isempty', tmptheta));
indices = intersect_bc(find(~cellfun('isempty', tmpx)), indices);
indices = sort(indices);
indbad = setdiff_bc(1:length(eloc), indices);
tmptheta(indbad) = { NaN };
theta = [ tmptheta{:} ];
end
if nargout > 3
if isfield(eloc, 'theta')
tmprad = { eloc.radius }; % check which channels have (polar) coordinates set
else tmprad = cell(1,length(eloc));
end
tmprad(indbad) = { NaN };
radius = [ tmprad{:} ];
end
%tmpnum = find(~cellfun('isclass', { eloc.labels }, 'char'));
%disp('Converting channel labels to string');
for index = 1:length(eloc)
if ~ischar(eloc(index).labels)
eloc(index).labels = int2str(eloc(index).labels);
end
end
labels = { eloc.labels };
if isfield(eloc, 'ignore')
eloc = rmfield(eloc, 'ignore');
end
% process fiducials if any
% ------------------------
fidnames = { 'nz' 'lpa' 'rpa' 'nasion' 'left' 'right' 'nazion' 'fidnz' 'fidt9' 'fidt10' 'cms' 'drl' 'nas' 'lht' 'rht' 'lhj' 'rhj' };
for index = 1:length(fidnames)
ind = strmatch(fidnames{index}, lower(labels), 'exact');
if ~isempty(ind), for iInd = 1:length(ind), eloc(ind(iInd)).type = 'FID'; end; end
end
return;
% interpret the variable name
% ---------------------------
function array = load_file_or_array( varname, skiplines )
if isempty(skiplines)
skiplines = 0;
end
if exist( varname ) == 2
array = loadtxt(varname,'verbose','off','skipline',skiplines,'blankcell','off');
else % variable in the global workspace
% --------------------------
try, array = evalin('base', varname);
catch, error('readlocs(): cannot find the named file or variable, check syntax');
end
end
return
% check field format
% ------------------
function [str, mult] = checkformat(str)
mult = 1;
if strcmpi(str, 'labels'), str = lower(str); return; end
if strcmpi(str, 'channum'), str = lower(str); return; end
if strcmpi(str, 'theta'), str = lower(str); return; end
if strcmpi(str, 'radius'), str = lower(str); return; end
if strcmpi(str, 'ignore'), str = lower(str); return; end
if strcmpi(str, 'sph_theta'), str = lower(str); return; end
if strcmpi(str, 'sph_phi'), str = lower(str); return; end
if strcmpi(str, 'sph_radius'), str = lower(str); return; end
if strcmpi(str, 'sph_theta_besa'), str = lower(str); return; end
if strcmpi(str, 'sph_phi_besa'), str = lower(str); return; end
if strcmpi(str, 'gain'), str = lower(str); return; end
if strcmpi(str, 'calib'), str = lower(str); return; end
if strcmpi(str, 'type') , str = lower(str); return; end
if strcmpi(str, 'X'), str = upper(str); return; end
if strcmpi(str, 'Y'), str = upper(str); return; end
if strcmpi(str, 'Z'), str = upper(str); return; end
if strcmpi(str, '-X'), str = upper(str(2:end)); mult = -1; return; end
if strcmpi(str, '-Y'), str = upper(str(2:end)); mult = -1; return; end
if strcmpi(str, '-Z'), str = upper(str(2:end)); mult = -1; return; end
if strcmpi(str, 'custom1'), return; end
if strcmpi(str, 'custom2'), return; end
if strcmpi(str, 'custom3'), return; end
if strcmpi(str, 'custom4'), return; end
error(['readlocs(): undefined field ''' str '''']);
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