863 lines
38 KiB
Matlab
863 lines
38 KiB
Matlab
% readlocs() - read electrode location coordinates and other information from a file.
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% Several standard file formats are supported. Users may also specify
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% a custom column format. Defined format examples are given below
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% (see File Formats).
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% Usage:
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% >> eloc = readlocs( filename );
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% >> EEG.chanlocs = readlocs( filename, 'key', 'val', ... );
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% >> [eloc, labels, theta, radius, indices] = ...
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% readlocs( filename, 'key', 'val', ... );
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% Inputs:
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% filename - Name of the file containing the electrode locations
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% {default: 2-D polar coordinates} (see >> help topoplot )
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%
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% Optional inputs:
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% 'filetype' - ['loc'|'sph'|'sfp'|'xyz'|'asc'|'polhemus'|'besa'|'chanedit'|'custom']
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% Type of the file to read. By default the file type is determined
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% using the file extension (see below under File Formats),
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% 'loc' an EEGLAB 2-D polar coordinates channel locations file
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% Coordinates are theta and radius (see definitions below).
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% 'sph' Matlab spherical coordinates (Note: spherical
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% coordinates used by Matlab functions are different
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% from spherical coordinates used by BESA - see below).
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% 'sfp' EGI Cartesian coordinates (NOT Matlab Cartesian - see below).
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% 'xyz' Matlab/EEGLAB Cartesian coordinates (NOT EGI Cartesian).
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% z is toward nose; y is toward left ear; z is toward vertex
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% 'asc' Neuroscan polar coordinates.
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% 'polhemus' or 'polhemusx' - Polhemus electrode location file recorded
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% with 'X' on sensor pointing to subject (see below and readelp()).
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% 'polhemusy' - Polhemus electrode location file recorded with
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% 'Y' on sensor pointing to subject (see below and readelp()).
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% 'besa' BESA-'.elp' spherical coordinates. (Not MATLAB spherical -
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% see below).
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% 'chanedit' - EEGLAB channel location file created by pop_chanedit().
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% 'custom' - Ascii file with columns in user-defined 'format' (see below).
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% 'importmode' - ['eeglab'|'native'] for location files containing 3-D cartesian electrode
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% coordinates, import either in EEGLAB format (nose pointing toward +X).
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% This may not always be possible since EEGLAB might not be able to
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% determine the nose direction for scanned electrode files. 'native' import
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% original carthesian coordinates (user can then specify the position of
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% the nose when calling the topoplot() function; in EEGLAB the position
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% of the nose is stored in the EEG.chaninfo structure). {default 'eeglab'}
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% 'format' - [cell array] Format of a 'custom' channel location file (see above).
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% {default: if no file type is defined. The cell array contains
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% labels defining the meaning of each column of the input file.
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% 'channum' [positive integer] channel number.
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% 'labels' [string] channel name (no spaces).
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% 'theta' [real degrees] 2-D angle in polar coordinates.
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% positive => rotating from nose (0) toward left ear
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% 'radius' [real] radius for 2-D polar coords; 0.5 is the head
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% disk radius and limit for topoplot() plotting).
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% 'X' [real] Matlab-Cartesian X coordinate (to nose).
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% 'Y' [real] Matlab-Cartesian Y coordinate (to left ear).
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% 'Z' [real] Matlab-Cartesian Z coordinate (to vertex).
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% '-X','-Y','-Z' Matlab-Cartesian coordinates pointing opposite
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% to the above.
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% 'sph_theta' [real degrees] Matlab spherical horizontal angle.
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% positive => rotating from nose (0) toward left ear.
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% 'sph_phi' [real degrees] Matlab spherical elevation angle.
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% positive => rotating from horizontal (0) upwards.
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% 'sph_radius' [real] distance from head center (unused).
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% 'sph_phi_besa' [real degrees] BESA phi angle from vertical.
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% positive => rotating from vertex (0) towards right ear.
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% 'sph_theta_besa' [real degrees] BESA theta horiz/azimuthal angle.
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% positive => rotating from right ear (0) toward nose.
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% 'ignore' ignore column}.
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% The input file may also contain other channel information fields.
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% 'type' channel type: 'EEG', 'MEG', 'EMG', 'ECG', others ...
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% 'calib' [real near 1.0] channel calibration value.
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% 'gain' [real > 1] channel gain.
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% 'custom1' custom field #1.
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% 'custom2', 'custom3', 'custom4', etc. more custom fields
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% 'skiplines' - [integer] Number of header lines to skip (in 'custom' file types only).
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% Note: Characters on a line following '%' will be treated as comments.
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% 'readchans' - [integer array] indices of electrodes to read. {default: all}
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% 'center' - [(1,3) real array or 'auto'] center of xyz coordinates for conversion
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% to spherical or polar, Specify the center of the sphere here, or 'auto'.
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% This uses the center of the sphere that best fits all the electrode
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% locations read. {default: [0 0 0]}
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% Outputs:
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% eloc - structure containing the channel names and locations (if present).
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% It has three fields: 'eloc.labels', 'eloc.theta' and 'eloc.radius'
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% identical in meaning to the EEGLAB struct 'EEG.chanlocs'.
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% labels - cell array of strings giving the names of the electrodes. NOTE: Unlike the
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% three outputs below, includes labels of channels *without* location info.
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% theta - vector (in degrees) of polar angles of the electrode locations.
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% radius - vector of polar-coordinate radii (arc_lengths) of the electrode locations
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% indices - indices, k, of channels with non-empty 'locs(k).theta' coordinate
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%
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% File formats:
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% If 'filetype' is unspecified, the file extension determines its type.
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%
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% '.loc' or '.locs' or '.eloc':
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% polar coordinates. Notes: angles in degrees:
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% right ear is 90; left ear -90; head disk radius is 0.5.
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% Fields: N angle radius label
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% Sample: 1 -18 .511 Fp1
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% 2 18 .511 Fp2
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% 3 -90 .256 C3
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% 4 90 .256 C4
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% ...
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% Note: In previous releases, channel labels had to contain exactly
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% four characters (spaces replaced by '.'). This format still works,
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% though dots are no longer required.
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% '.sph':
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% Matlab spherical coordinates. Notes: theta is the azimuthal/horizontal angle
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% in deg.: 0 is toward nose, 90 rotated to left ear. Following this, performs
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% the elevation (phi). Angles in degrees.
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% Fields: N theta phi label
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% Sample: 1 18 -2 Fp1
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% 2 -18 -2 Fp2
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% 3 90 44 C3
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% 4 -90 44 C4
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% ...
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% '.elc':
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% Cartesian 3-D electrode coordinates scanned using the EETrak software.
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% See readeetraklocs().
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% '.elp':
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% Polhemus-.'elp' Cartesian coordinates. By default, an .elp extension is read
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% as PolhemusX-elp in which 'X' on the Polhemus sensor is pointed toward the
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% subject. Polhemus files are not in columnar format (see readelp()).
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% '.elp':
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% BESA-'.elp' spherical coordinates: Need to specify 'filetype','besa'.
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% The elevation angle (phi) is measured from the vertical axis. Positive
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% rotation is toward right ear. Next, perform azimuthal/horizontal rotation
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% (theta): 0 is toward right ear; 90 is toward nose, -90 toward occiput.
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% Angles are in degrees. If labels are absent or weights are given in
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% a last column, readlocs() adjusts for this. Default labels are E1, E2, ...
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% Fields: label phi theta
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% Sample: Fp1 -92 -72
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% Fp2 92 72
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% C3 -46 0
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% C4 46 0
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% ...
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% '.xyz':
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% Matlab/EEGLAB Cartesian coordinates. Here. x is towards the nose,
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% y is towards the left ear, and z towards the vertex. Note that the first
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% column (x) is -Y in a Matlab 3-D plot, the second column (y) is X in a
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% matlab 3-D plot, and the third column (z) is Z.
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% Fields: channum x y z label
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% Sample: 1 .950 .308 -.035 Fp1
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% 2 .950 -.308 -.035 Fp2
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% 3 0 .719 .695 C3
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% 4 0 -.719 .695 C4
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% ...
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% '.asc', '.dat':
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% Neuroscan-.'asc' or '.dat' Cartesian polar coordinates text file.
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% '.sfp':
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% BESA/EGI-xyz Cartesian coordinates. Notes: For EGI, x is toward right ear,
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% y is toward the nose, z is toward the vertex. EEGLAB converts EGI
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% Cartesian coordinates to Matlab/EEGLAB xyz coordinates.
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% Fields: label x y z
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% Sample: Fp1 -.308 .950 -.035
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% Fp2 .308 .950 -.035
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% C3 -.719 0 .695
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% C4 .719 0 .695
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% ...
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% '.ced':
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% ASCII file saved by pop_chanedit(). Contains multiple MATLAB/EEGLAB formats.
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% Cartesian coordinates are as in the 'xyz' format (above).
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% Fields: channum label theta radius x y z sph_theta sph_phi ...
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% Sample: 1 Fp1 -18 .511 .950 .308 -.035 18 -2 ...
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% 2 Fp2 18 .511 .950 -.308 -.035 -18 -2 ...
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% 3 C3 -90 .256 0 .719 .695 90 44 ...
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% 4 C4 90 .256 0 -.719 .695 -90 44 ...
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% ...
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% The last columns of the file may contain any other defined fields (gain,
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% calib, type, custom).
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%
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% Author: Arnaud Delorme, Salk Institute, 8 Dec 2002 (expanded from the previous EEG/ICA
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% toolbox function)
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%
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% See also: readelp(), writelocs(), topo2sph(), sph2topo(), sph2cart()
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%123456789012345678901234567890123456789012345678901234567890123456789012
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% Copyright (C) Arnaud Delorme, CNL / Salk Institute, 28 Feb 2002
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%
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% This program is free software; you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as published by
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% the Free Software Foundation; either version 2 of the License, or
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% (at your option) any later version.
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%
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% This program is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License
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% along with this program; if not, write to the Free Software
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% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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% $Log: readlocs.m,v $
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% Revision 1.102 2009/09/27 05:14:55 arno
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% Fix rereading CED file
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%
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% Revision 1.101 2009/05/12 18:15:40 arno
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% nasion list
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%
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% Revision 1.100 2007/08/23 23:25:38 arno
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% encode type for neuroscan channel electrode files
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%
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% Revision 1.99 2007/08/15 22:28:10 arno
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% changing SFP not to skip any lines
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%
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% Revision 1.98 2007/05/22 13:56:50 arno
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% type for custom sphbesa
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%
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% Revision 1.97 2007/05/01 21:35:58 arno
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% fix typo
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%
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% Revision 1.96 2007/03/22 23:22:07 toby
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% help2html
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%
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% Revision 1.95 2007/03/22 23:17:28 toby
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% for help2html
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%
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% Revision 1.94 2007/03/22 23:09:45 toby
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% edit to accomodate help2html
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%
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% Revision 1.93 2007/03/22 21:22:34 arno
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% same
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%
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% Revision 1.92 2007/03/22 21:18:47 arno
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% indices of non empty channels
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%
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% Revision 1.91 2007/02/05 16:18:43 arno
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% reading channel types for .ced format
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%
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% Revision 1.90 2006/11/09 20:46:51 arno
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% fixing readling .elp files
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%
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% Revision 1.89 2006/11/07 02:31:21 arno
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% better documentation for .xyz
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%
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% Revision 1.88 2006/11/06 22:15:46 arno
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% loading besa format
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%
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% Revision 1.87 2006/06/01 17:40:50 arno
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% updating header
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%
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% Revision 1.86 2006/05/26 15:59:35 scott
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% worked on text of instructions for adding a channel type -- NOTE: chaninfo is
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% discussed in help message, but NOT implemented!?
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%
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% Revision 1.85 2006/04/14 21:19:08 arno
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% fixing skipping lines
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%
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% Revision 1.84 2006/03/31 03:11:13 toby
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% made '.eloc' equivalent to '.loc' as a filetype
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%
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% Revision 1.83 2006/02/14 00:01:18 arno
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% change xyz format
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%
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% Revision 1.82 2006/01/20 22:37:08 arno
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% default for BESA and polhemus
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%
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% Revision 1.81 2006/01/12 23:22:39 arno
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% fixing indices
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%
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% Revision 1.80 2006/01/12 22:03:51 arno
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% fiducial type
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%
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% Revision 1.79 2006/01/10 22:56:17 arno
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% adding defaultelp option
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%
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% Revision 1.78 2006/01/10 22:53:49 arno
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% [6~[6~changing default besa format
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%
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% Revision 1.77 2005/11/30 18:31:40 arno
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% same
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%
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% Revision 1.76 2005/11/30 18:29:48 arno
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% same
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%
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% Revision 1.75 2005/11/30 18:28:37 arno
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% reformat outputs
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%
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% Revision 1.74 2005/10/29 03:49:50 scott
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% NOTE: there is no mention of 'chantype' - should at least add a help mention after line 69 -sm
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%
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% Revision 1.73 2005/09/27 22:08:41 arno
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% fixing reading .ced files
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%
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% Revision 1.72 2005/05/24 17:07:05 arno
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% cell2mat - celltomat
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%
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% Revision 1.71 2005/03/10 17:42:11 arno
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% new format for channel location info
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%
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% Revision 1.70 2005/03/08 23:19:24 arno
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% using old function to read asa format
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%
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% Revision 1.69 2005/03/04 23:17:22 arno
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% use fieldtrip readeetrack
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%
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% Revision 1.65 2004/10/27 01:01:05 arno
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% msg format
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%
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% Revision 1.64 2004/03/23 00:37:56 scott
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% clarifying help msg re meaning of 'indices' output
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%
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% Revision 1.63 2004/03/23 00:22:51 scott
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% clarified meaning of output 'indices'
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%
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% Revision 1.62 2004/02/24 17:17:32 arno
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% dbug message
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%
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% Revision 1.61 2004/01/01 19:12:08 scott
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% help message edits
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%
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% Revision 1.60 2004/01/01 18:57:26 scott
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% edit text outputs
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%
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% Revision 1.59 2004/01/01 01:47:34 scott
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% franglais -> anglais
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%
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% Revision 1.58 2003/12/17 00:55:07 arno
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% debug last
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%
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% Revision 1.57 2003/12/17 00:50:10 arno
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% adding index for non-empty electrodes
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%
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% Revision 1.56 2003/12/05 18:37:56 arno
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% debug polhemus x and y fixed
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%
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% Revision 1.55 2003/12/02 03:21:39 arno
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% neuroscan format
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%
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% Revision 1.54 2003/11/27 00:38:13 arno
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% conversion elc
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%
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% Revision 1.53 2003/11/27 00:31:30 arno
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% debuging elc format
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%
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% Revision 1.52 2003/11/27 00:25:51 arno
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% automatically detecting elc files
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%
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% Revision 1.51 2003/11/05 17:20:23 arno
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% first convert spherical instead of carthesian
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%
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% Revision 1.50 2003/09/18 00:07:05 arno
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% further checks for neuroscan
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%
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% Revision 1.49 2003/07/16 18:52:21 arno
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% allowing file type locs
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%
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% Revision 1.48 2003/06/30 15:00:43 arno
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% fixing inputcheck problem
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%
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% Revision 1.47 2003/05/13 23:31:25 arno
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% number of lines to skip in chanedit format
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%
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% Revision 1.46 2003/05/13 22:09:01 arno
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% updating sph format
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%
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% Revision 1.45 2003/05/13 22:07:07 arno
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% removing labels in sfp format
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%
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% Revision 1.44 2003/05/13 21:14:11 arno
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% only write a subset of file format
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%
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% Revision 1.43 2003/03/10 16:28:12 arno
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% removing help for elc
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%
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% Revision 1.42 2003/03/10 16:26:59 arno
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% adding then removing .elc format
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%
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% Revision 1.41 2003/03/08 17:36:13 arno
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% import spherical EGI files correctly
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%
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% Revision 1.40 2003/03/05 15:38:15 arno
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% fixing '.' bug
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%
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% Revision 1.39 2003/03/04 20:04:44 arno
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% adding neuroscan .asc format
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%
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% Revision 1.38 2003/01/30 16:45:12 arno
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% debugging ced format
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%
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% Revision 1.37 2003/01/10 17:40:11 arno
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% removing trailing dots
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%
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% Revision 1.36 2003/01/03 22:47:00 arno
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% typo in warning messages
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%
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% Revision 1.35 2003/01/03 22:45:48 arno
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% adding another warning message
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%
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% Revision 1.34 2003/01/03 22:41:38 arno
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% autodetect format .sfp
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%
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% Revision 1.33 2003/01/03 22:38:39 arno
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% adding warning message
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%
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% Revision 1.32 2002/12/29 23:04:00 scott
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% header
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%
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% Revision 1.31 2002/12/29 22:37:15 arno
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% txt -> ced
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%
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% Revision 1.30 2002/12/29 22:35:35 arno
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% adding coords. info for file format in header, programming .sph, ...
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%
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% Revision 1.29 2002/12/29 22:00:10 arno
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% skipline -> skiplines
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%
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% Revision 1.28 2002/12/28 23:46:45 scott
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% header
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%
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% Revision 1.27 2002/12/28 02:02:35 scott
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% header details
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%
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% Revision 1.26 2002/12/28 01:32:41 scott
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% worked on header information - axis details etcetc. -sm & ad
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%
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% Revision 1.25 2002/12/27 23:23:35 scott
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% edit header msg - NEEDS MORE DETAILS -sm
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%
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% Revision 1.24 2002/12/27 22:57:23 arno
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% debugging polhemus
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%
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% Revision 1.23 2002/12/27 17:47:32 arno
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% compatible with more BESA formats
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%
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% Revision 1.22 2002/12/26 16:41:23 arno
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% new release
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%
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% Revision 1.21 2002/12/24 02:51:22 arno
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% new version of readlocs
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%
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function [eloc, labels, theta, radius, indices] = readlocs( filename, varargin );
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if nargin < 1
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help readlocs;
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return;
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end;
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% NOTE: To add a new channel format:
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% ----------------------------------
|
||
% 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 labels in ' ...
|
||
'the first column and X, Y, and Z coordinates in columns 2, 3, and 4' ];
|
||
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 = 'readneurolocs';
|
||
% ---------------------------------------------------------------------------------------------------
|
||
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 = 'custom';
|
||
chanformat(11).typestring = 'Custom file format';
|
||
chanformat(11).description = 'Custom ASCII file format where user can define content for each file columns.';
|
||
chanformat(11).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 isstr(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 isstr(g), error(g); end;
|
||
|
||
if isstr(filename)
|
||
|
||
% format auto detection
|
||
% --------------------
|
||
if strcmpi(g.filetype, 'autodetect'), g.filetype = ''; end;
|
||
g.filetype = strtok(g.filetype);
|
||
periods = find(filename == '.');
|
||
fileextension = filename(periods(end)+1:end);
|
||
g.filetype = lower(g.filetype);
|
||
if isempty(g.filetype)
|
||
switch lower(fileextension),
|
||
case {'loc' 'locs' }, g.filetype = 'loc';
|
||
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 'sfp', g.filetype = 'sfp';
|
||
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, 'asc') | strcmp(g.filetype, 'dat')
|
||
eloc = readneurolocs( filename );
|
||
eloc = rmfield(eloc, 'sph_theta'); % for the conversion below
|
||
eloc = rmfield(eloc, 'sph_theta_besa'); % for the conversion below
|
||
if isfield(eloc, 'type')
|
||
for index = 1:length(eloc)
|
||
type = eloc(index).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;
|
||
elseif strcmp(g.filetype, 'elc')
|
||
eloc = readeetraklocs( filename );
|
||
%eloc = read_asa_elc( filename ); % from fieldtrip
|
||
%eloc = struct('labels', eloc.label, 'X', mattocell(eloc.pnt(:,1)'), 'Y', ...
|
||
% mattocell(eloc.pnt(:,2)'), 'Z', mattocell(eloc.pnt(:,3)'));
|
||
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);
|
||
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;
|
||
|
||
% removing comments and empty lines
|
||
% ---------------------------------
|
||
indexbeg = 1;
|
||
while isempty(array{indexbeg,1}) | ...
|
||
(isstr(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};' ]);
|
||
else
|
||
eval ( [ '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')
|
||
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 isstr(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)
|
||
eloc = filename;
|
||
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
|
||
tmptheta = { eloc.theta }; % check which channels have (polar) coordinates set
|
||
indices = find(~cellfun('isempty', tmptheta));
|
||
tmpx = { eloc.X }; % check which channels have (polar) coordinates set
|
||
indices = intersect(find(~cellfun('isempty', tmpx)), indices);
|
||
indices = sort(indices);
|
||
|
||
indbad = setdiff(1:length(eloc), indices);
|
||
tmptheta(indbad) = { NaN };
|
||
theta = [ tmptheta{:} ];
|
||
end;
|
||
if nargout > 3
|
||
tmprad = { eloc.radius };
|
||
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 ~isstr(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' };
|
||
for index = 1:length(fidnames)
|
||
ind = strmatch(fidnames{index}, lower(labels), 'exact');
|
||
if ~isempty(ind), eloc(ind).type = 'FID'; 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);
|
||
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 '''']);
|
||
|