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Update external/fieldtrip to FieldTrip cfdad9b80 #156

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2 changes: 1 addition & 1 deletion external/fieldtrip/.fieldtrip-version
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@@ -1 +1 @@
adf8a8b58f88ae194ecab4e18e2615f332694dbd
cfdad9b80757f9394404680d54ecb6e452fcc43b
5 changes: 0 additions & 5 deletions external/fieldtrip/connectivity/private/ft_platform_supports.m
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Expand Up @@ -134,11 +134,6 @@
root_dir = fileparts(which('ft_defaults'));
if ~isempty(root_dir)
external_stats_dir = fullfile(root_dir, 'external', 'stats');
% these files are only used by the other functions in the external/stats directory
exclude_mfiles = {
'common_size.m'
'iscomplex.m'
};
tf = has_all_functions_in_dir(external_stats_dir, exclude_mfiles);
else
% this probably only works for MATLAB, not for Octave
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16 changes: 8 additions & 8 deletions external/fieldtrip/data2bids.m
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Expand Up @@ -1583,7 +1583,7 @@
end
end % if emptyroom

elseif isfield(hdr, 'grad') && ft_senstype(hdr.grad, 'neuromag')
elseif isfield(hdr, 'grad') && (ft_senstype(hdr.grad, 'neuromag') || ft_senstype(hdr.grad, 'fieldline_v3'))

if ~issubfield(hdr, 'orig.dig')
% the data was not read using the default Neuromag import function
Expand All @@ -1594,17 +1594,17 @@
ft_notice('this seems to be an empty room recording')
coordsystem_json.MEGCoordinateSystem = 'Other';
coordsystem_json.MEGCoordinateUnits = 'm';
coordsystem_json.MEGCoordinateSystemDescription = 'ElektaNeuromag dewar coordinates, orientation RAS';
coordsystem_json.MEGCoordinateSystemDescription = 'NeuromagElekta dewar coordinates, orientation RAS';
else
% coordinate system for MEG sensors
coordsystem_json.MEGCoordinateSystem = 'ElektaNeuromagMEGIN';
coordsystem_json.MEGCoordinateSystem = 'NeuromagElektaMEGIN';
coordsystem_json.MEGCoordinateUnits = 'm';
coordsystem_json.MEGCoordinateSystemDescription = 'ElektaNeuromag head coordinates, orientation RAS, origin between the ears';
coordsystem_json.MEGCoordinateSystemDescription = 'NeuromagElekta head coordinates, orientation RAS, origin between the ears';
% coordinate system for head localization coils
coordsystem_json.HeadCoilCoordinates = []; % see below
coordsystem_json.HeadCoilCoordinateSystem = 'ElektaNeuromagMEGIN';
coordsystem_json.HeadCoilCoordinateSystem = 'NeuromagElektaMEGIN';
coordsystem_json.HeadCoilCoordinateUnits = 'm';
coordsystem_json.HeadCoilCoordinateSystemDescription = 'ElektaNeuromag head coordinates, orientation RAS, origin between the ears';
coordsystem_json.HeadCoilCoordinateSystemDescription = 'NeuromagElekta head coordinates, orientation RAS, origin between the ears';
if isempty(coordsystem_json.HeadCoilCoordinates)
idxHPI = find([hdr.orig.dig.kind] == 2); % count the kind==2 (HLU in the Elekta/Megin system), usually 4 or 5
for i=1:length(idxHPI)
Expand All @@ -1614,9 +1614,9 @@
end
% coordinates of the anatomical landmarks (LPA/RPA/NAS)
coordsystem_json.AnatomicalLandmarkCoordinates = []; % see below
coordsystem_json.AnatomicalLandmarkCoordinateSystem = 'ElektaNeuromagMEGIN';
coordsystem_json.AnatomicalLandmarkCoordinateSystem = 'NeuromagElektaMEGIN';
coordsystem_json.AnatomicalLandmarkCoordinateUnits = 'm';
coordsystem_json.AnatomicalLandmarkCoordinateSystemDescription = 'ElektaNeuromag head coordinates, orientation RAS, origin between the ears';
coordsystem_json.AnatomicalLandmarkCoordinateSystemDescription = 'NeuromagElekta head coordinates, orientation RAS, origin between the ears';
if isempty(coordsystem_json.AnatomicalLandmarkCoordinates)
coordsystem_json = rmfield(coordsystem_json, 'AnatomicalLandmarkCoordinates'); % needed to set the names afterwards
coordsystem_json.AnatomicalLandmarkCoordinates.lpa = hdr.orig.dig(1).r';
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15 changes: 9 additions & 6 deletions external/fieldtrip/fileio/ft_read_data.m
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Expand Up @@ -766,15 +766,18 @@
dat = dat.data(chanindx,:); % select the desired channels

case 'eyelink_asc'
if isfield(hdr.orig, 'dat')
% this is inefficient, since it keeps the complete data in memory
% but it does speed up subsequent read operations without the user
% having to care about it
if isfield(hdr, 'orig')
asc = hdr.orig;
else
asc = read_eyelink_asc(filename);
% for some reason the orig is not present, but needed
hdr = read_eyelink_asc(filename);
asc = hdr.orig;
end
if checkboundary && (asc.trialidx(begsample)~=asc.trialidx(endsample))
ft_error('requested data segment extends over a discontinuous trial boundary');
end
dat = asc.dat(chanindx,begsample:endsample);
asc = read_eyelink_asc(filename, asc, begsample, endsample, chanindx);
dat = asc.dat;

case 'fcdc_buffer'
% read from a networked buffer for realtime analysis
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65 changes: 1 addition & 64 deletions external/fieldtrip/fileio/ft_read_event.m
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Expand Up @@ -1183,71 +1183,8 @@
end

case 'eyelink_asc'
if isempty(hdr)
hdr = ft_read_header(filename, 'headerformat', headerformat);
end
if isfield(hdr.orig, 'input')
% this is inefficient, since it keeps the complete data in memory
% but it does speed up subsequent read operations without the user
% having to care about it
asc = hdr.orig;
else
asc = read_eyelink_asc(filename);
end

% the input events are handled differently (because they already
% contain a timestamp and value, as per read_eyelink_asc
if ~isempty(asc.input)
timestamp = asc.input.timestamp;
value = asc.input.value;
sample = (timestamp-hdr.FirstTimeStamp)/hdr.TimeStampPerSample + 1;

% note that in this dataformat the first input trigger can be before
% the start of the data acquisition
for i=1:length(timestamp)
event(end+1).type = 'INPUT';
event(end ).sample = sample(i);
event(end ).timestamp = timestamp(i);
event(end ).value = value(i);
event(end ).duration = 1;
event(end ).offset = 0;
end
end

% these fields are dealt with a bit differently, the 'e' -events
% contain more information than the 's' -events
fnames = {'eblink', 'efix', 'esacc'};
tnames = {'BLINK', 'FIX', 'SACC'};
if isfield(asc, 'msg') && istable(asc.msg) && size(asc.msg,2)==2
fnames(end+1) = {'msg'};
tnames(end+1) = {'MSG'};
end
for k=1:length(fnames)
if isfield(asc, fnames{k}) && ~isempty(asc.(fnames{k}))
bfs = asc.(fnames{k});

timestamp = bfs.stime;
sample = (timestamp-hdr.FirstTimeStamp)/hdr.TimeStampPerSample + 1;
if ~strcmp(fnames{k}, 'msg')
value = bfs.eye;
duration = bfs.dur;
else
value = bfs.message;
duration = nan(size(bfs,1),1);
end
[hdr, event] = read_eyelink_asc(filename); % hdr and event are both returned in FT-style

% note that in this dataformat the first input trigger can be before
% the start of the data acquisition
for i=1:length(timestamp)
event(end+1).type = tnames{k};
event(end ).sample = sample(i);
event(end ).timestamp = timestamp(i);
event(end ).value = value(i);
event(end ).duration = duration(i);
event(end ).offset = 0;
end
end
end
case 'fcdc_global'
event = event_queue;

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24 changes: 2 additions & 22 deletions external/fieldtrip/fileio/ft_read_header.m
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Expand Up @@ -970,28 +970,8 @@
hdr.orig = orig;

case 'eyelink_asc'
asc = read_eyelink_asc(filename);
hdr.nChans = size(asc.dat,1);
hdr.nSamples = size(asc.dat,2);
hdr.nSamplesPre = 0;
hdr.nTrials = 1;
hdr.FirstTimeStamp = asc.dat(1,1);
hdr.TimeStampPerSample = median(diff(asc.dat(1,:)));
hdr.Fs = 1000/hdr.TimeStampPerSample; % these timestamps are in miliseconds
% give this warning only once
ft_warning('creating fake channel names');
for i=1:hdr.nChans
hdr.label{i} = sprintf('%d', i);
end

% remember all header and data details upon request
if cache
hdr.orig = asc;
else
% remember the original header details
hdr.orig = removefields(asc, 'dat');
end

hdr = read_eyelink_asc(filename);

case 'spmeeg_mat'
hdr = read_spmeeg_header(filename);

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17 changes: 12 additions & 5 deletions external/fieldtrip/fileio/private/bids_sidecar.m
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Expand Up @@ -137,14 +137,21 @@
% sort them to get the tsv files first in the list, followed by the json files
filelist = [filelist(endsWith(filelist', 'tsv')) filelist(endsWith(filelist', 'json'))];

% we are searching for a file with the datatype as suffix and that ends with json
% we are searching for a file with the same suffix and the extension tsv or json
evidence = zeros(size(filelist));
for i=1:numel(filelist)
[p, f, x] = fileparts(filelist{i});
tmp = split(f, '_');
% check the file extension, the suffix and the entities of each candidate file
if ismember(x, {'.tsv', '.json'}) && strcmp(tmp{end}, suffix) && all(ismember(tmp(1:end-1), entities))
ft_info('found matching BIDS sidecar ''%s''', filelist{i})
sidecar = filelist{i};
break % do not consider any of the other potential matches
if ismember(x, {'.tsv', '.json'}) && strcmp(tmp{end}, suffix) && sum(ismember(entities, tmp(1:end-1)))>0
% count how many entities of the sidecar match with the data file
evidence(i) = sum(ismember(entities, tmp(1:end-1)));
end
end

if any(evidence)
% take the first sidecar file that has most matching entities
[dum, sel] = max(evidence);
ft_info('found matching BIDS sidecar ''%s''', filelist{sel});
sidecar = filelist{sel};
end
2 changes: 1 addition & 1 deletion external/fieldtrip/fileio/private/ft_hastoolbox.m
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Expand Up @@ -304,7 +304,7 @@
case 'COMM'
dependency = {has_license('communication_toolbox'), 'de2bi', 'fskmod', 'pskmod'}; % also check the availability of a toolbox license
case 'SIGNAL'
dependency = {has_license('signal_toolbox'), 'window', 'hanning'}; % also check the availability of a toolbox license
dependency = {has_license('signal_toolbox'), 'medfilt1', 'freqz'}; % these must not be functions that external/signal provides
case 'IMAGES'
dependency = {has_license('image_toolbox'), 'imerode', 'imdilate'}; % also check the availability of a toolbox license
case 'VISION'
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5 changes: 0 additions & 5 deletions external/fieldtrip/fileio/private/ft_platform_supports.m
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Expand Up @@ -134,11 +134,6 @@
root_dir = fileparts(which('ft_defaults'));
if ~isempty(root_dir)
external_stats_dir = fullfile(root_dir, 'external', 'stats');
% these files are only used by the other functions in the external/stats directory
exclude_mfiles = {
'common_size.m'
'iscomplex.m'
};
tf = has_all_functions_in_dir(external_stats_dir, exclude_mfiles);
else
% this probably only works for MATLAB, not for Octave
Expand Down
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