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Feature: Bit behaviour for process_evt_read.m #544

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merged 9 commits into from May 25, 2022
Merged

Feature: Bit behaviour for process_evt_read.m #544

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df9add6
Keep all changes in tracks, not only from 0 to value
rcassani May 11, 2022
dc6ef8f
Remove timeshift for CFT triggers (that code came from FieldTrip's re…
rcassani May 11, 2022
a54ac2a
Bugfix: CMC tutorial: Reject events with less than 2 samples
rcassani May 13, 2022
59cf04f
Process entire event channel instead of blocks
rcassani May 20, 2022
4a79366
Update: Coherence tutorial: Reject events shorter than 10 ms (duratio…
rcassani May 23, 2022
3e94320
Add "set" and "reset" to label in when Bit, zero accepted and min dur…
rcassani May 23, 2022
b39ac31
Updated authors
ftadel May 25, 2022
2da1ba0
Removed date tag
ftadel May 25, 2022
708aeda
Fix progress bar management
ftadel May 25, 2022
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247 changes: 133 additions & 114 deletions toolbox/process/functions/process_evt_read.m
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Expand Up @@ -20,6 +20,8 @@
% =============================================================================@
%
% Authors: Francois Tadel, 2012-2021
% Raymundo Cassani, 2022
% Marc Lalancette, 2022

eval(macro_method);
end
Expand Down Expand Up @@ -222,7 +224,6 @@
StimChan = StimChan(1:end-3);
end
end
trigshift = fix(sFile.prop.sfreq * 9/1200);

% ===== ASK READ MODE =====
if strcmpi(EventsTrackMode, 'ask')
Expand Down Expand Up @@ -263,150 +264,172 @@
% Process by blocks (if not: out of memory)
totalLength = (samplesBounds(2) - samplesBounds(1) + 1);
nbBlocks = ceil(totalLength / blockLength);
% Progress bar
% Progress bar, channels
isProgressBar = bst_progress('isVisible');
bst_progress('start', 'Import events', 'Reading events channels...', 0, nbBlocks);
bst_progress('start', 'Import events', 'Reading events channels...', 0, length(iChannels) * nbBlocks);

trackPrev = [];
nTooShort = 0;
% For each block
for iBlock = 1:nbBlocks
tracks_name = {};
tracks_vals = {};
tracks_smps = {};
% Process each channel
for iChannel = 1 : length(iChannels)
% Increment progress bar
bst_progress('inc', 1);
track_prev = [];
track_vals = [];
track_smps = [];
% Progress bar, blocks
bst_progress('text', ['Reading events in channel ' StimChan{iChannel} ' ...']);
for iBlock = 1:nbBlocks
% Increment progress bar
bst_progress('inc', 1);
% === READ BLOCK ===
% Get samples indices for this block
samplesBlock = samplesBounds(1) + [(iBlock - 1) * blockLength, iBlock * blockLength - 1];
samplesBlock(2) = min(samplesBlock(2), samplesBounds(2));
% Read block of data
[track, ~] = in_fread(sFile, ChannelMat, 1, samplesBlock, iChannels(iChannel));
% Round values
track = fix(track);
% Keep only track changes
if iBlock == 1
track_smps(1) = 1;
track_vals(1) = track(1);
track_prev = track(1);
end
% === KEEP ALL CHANGES ===
ixDiffTrack = find(diff([track_prev, track]));
track_vals = [track_vals, track(ixDiffTrack)];
track_smps = [track_smps, samplesBlock(1) + ixDiffTrack];
% Saving ending state for next block
track_prev = track(end);
end

% === READ BLOCK ===
% Get samples indices for this block
samplesBlock = samplesBounds(1) + [(iBlock - 1) * blockLength, iBlock * blockLength - 1];
samplesBlock(2) = min(samplesBlock(2), samplesBounds(2));
% Read block of data
[tracks, times] = in_fread(sFile, ChannelMat, 1, samplesBlock, iChannels);

% === BLOCK EDITED 16-JUN-2021 ===
% Round values
tracks = fix(tracks);
% CTF: Read separately Upper and Lower bytes
if ismember(sFile.format, {'CTF', 'CTF-CONTINUOUS'})
% Events are read as int32, while they are actually uint32: fix negative values
tracks(tracks<0) = tracks(tracks<0) + 2^32;
track_vals(track_vals<0) = track_vals(track_vals<0) + 2^32;
% Keep only upper or lower bytes
if isCtfUp
tracks = fix(tracks / 2^16);
track_vals = fix(track_vals / 2^16);
elseif isCtfLow
tracks = double(bitand(uint32(tracks), 2^16-1));
track_vals = double(bitand(uint32(track_vals), 2^16-1));
end
% Determine the precise timing of the triggers (from FieldTrip's read_ctf_trigger)
upflank = [0 (diff(tracks)>0 & tracks(1:(end-1))==0)];
tracks = upflank(1:(end-trigshift)).*tracks((1+trigshift):end);
% Other formats
else
% Old code: Might be useless and/or detrimental to the reading of the events
% tracks = reshape(double(typecast(int16(tracks(:)), 'uint16')), size(tracks));
% Use the same fix as for CTF files
tracks(tracks<0) = tracks(tracks<0) + 2^32;
track_vals(track_vals<0) = track_vals(track_vals<0) + 2^32;
end
% =================================

% === ADD INITIAL STATE ===
% Add the initial status of the tracks
if isempty(trackPrev)
tracks = [tracks(:,1), tracks];
else
tracks = [trackPrev, tracks];
end
% Saving ending state for next block
trackPrev = tracks(:,end);

% === SEPARATE TRACKS ===
% Each bit of each channel is interpreted as a track
switch lower(EventsTrackMode)
case 'bit'
tracks_tmp = [];
tracks_name = {};
for iTrack = 1:size(tracks, 1)
% Convert track in binary values
track_bin = double(fliplr(dec2bin(tracks(iTrack, :)))');
track_bin(track_bin == '0') = 0;
track_bin(track_bin == '1') = 1;
% Add those binary tracks to the list
tracks_tmp = [tracks_tmp; track_bin];
% Save name of the tracks
for iBit = 1:size(track_bin, 1)
if (length(StimChan) > 1)
tracks_name{end+1} = sprintf('%s_%d', StimChan{iTrack}, iBit);
else
tracks_name{end+1} = sprintf('%d', iBit);
end
% Convert track in binary values
track_bin = double(fliplr(dec2bin(track_vals))');
track_bin(track_bin == '0') = 0;
track_bin(track_bin == '1') = 1;
nBit = size(track_bin, 1);
tracks_bit_name = cell(1, nBit);
tracks_bit_vals = cell(1, nBit);
tracks_bit_smps = cell(1, nBit);
% Data for each binary track
for iBit = 1 : nBit
if (length(StimChan) > 1)
tracks_bit_name{iBit} = sprintf('%s_%d', StimChan{iChannel}, iBit);
else
tracks_bit_name{iBit} = sprintf('%d', iBit);
end
% Keep changes in each binary tracks
ixDiffTrackBit = find(diff([track_prev, track_bin(iBit, :)]));
tracks_bit_vals{iBit} = track_bin(iBit, ixDiffTrackBit);
tracks_bit_smps{iBit} = track_smps(ixDiffTrackBit);
end
tracks = tracks_tmp;
% Append to other tracks
tracks_name = [tracks_name, tracks_bit_name];
tracks_vals = [tracks_vals, tracks_bit_vals];
tracks_smps = [tracks_smps, tracks_bit_smps];
case 'value'
tracks_name = StimChan;
tracks_name{end+1} = StimChan{iChannel};
tracks_vals{end+1} = track_vals;
tracks_smps{end+1} = track_smps;
case {'ttl', 'rttl'}
tracks_name = StimChan;
tracks = abs(round(tracks));
tracks(tracks ~= 0) = 1;
tracks_name{end+1} = StimChan{iChannel};
track_vals = abs(round(track_vals));
track_vals(track_vals ~= 0) = 1;
tracks_vals{end+1} = track_vals;
tracks_smps{end+1} = track_smps;
end
end

% === GET EVENTS ===
% Get the changes on each track
diffTrack = diff(tracks, [], 2);
% Remove intial state from tracks
tracks(:,1) = [];
% Process each track separately
for iTrack = 1:size(tracks, 1)
% Get the samples where something happens
if strcmpi(EventsTrackMode, 'rttl')
iSmp = find((diffTrack(iTrack,:) ~= 0) & ((tracks(iTrack,:) == 0)));
elseif isAcceptZero
iSmp = find((diffTrack(iTrack,:) ~= 0));
else
iSmp = find((diffTrack(iTrack,:) ~= 0) & ((tracks(iTrack,:) ~= 0)));
end
% Process each change individually
for i = 1:length(iSmp)
% === PROCESS EACH TRACK SEPARATELY ===
nTooShort = 0;
for iTrack = 1:length(tracks_name)
% Get the indices where something happens
if strcmpi(EventsTrackMode, 'rttl')
ixs = find(tracks_vals{iTrack} == 0);
elseif isAcceptZero
ixs = 1 : length(tracks_vals{iTrack});
else
ixs = find(tracks_vals{iTrack} ~= 0);
end
% Process each change individually
for i = 1:length(ixs)
if i < length(ixs)
% Skip if shorter than MinDuration
if (MinDuration > 0) && ((length(tracks) - iSmp(i) < MinDuration) || ~all(tracks(iSmp(i):iSmp(i)+MinDuration) == tracks(iSmp(i))))
duration_i = tracks_smps{iTrack}(ixs(i)+1) - tracks_smps{iTrack}(ixs(i));
if (MinDuration > 0) && (duration_i < MinDuration)
nTooShort = nTooShort + 1;
% Pass start sample to next event longer than MinDuration
tracks_smps{iTrack}(ixs(i)+1) = tracks_smps{iTrack}(ixs(i));
continue;
end
% Build event name
switch lower(EventsTrackMode)
case 'bit'
label = tracks_name{iTrack};
case 'value'
value = tracks(iTrack, iSmp(i));
if (length(StimChan) > 1)
label = sprintf('%s_%d', StimChan{iTrack}, value);
end
% Build event name
switch lower(EventsTrackMode)
case 'bit'
label = tracks_name{iTrack};
if (MinDuration == 0) && isAcceptZero
if tracks_vals{iTrack}(ixs(i)) == 1
label = [label '-set'];
else
label = sprintf('%d', value);
label = [label '-reset'];
end
case {'ttl', 'rttl'}
label = StimChan{iTrack};
end
% Find this event in list of events
if ~isempty(events)
iEvent = find(strcmpi({events.label}, label));
else
iEvent = [];
end
% If event does not exist yet: add it
if isempty(iEvent)
iEvent = length(events) + 1;
events(iEvent).label = label;
events(iEvent).epochs = [];
events(iEvent).times = [];
events(iEvent).reactTimes = [];
events(iEvent).select = 1;
events(iEvent).channels = {};
events(iEvent).notes = {};
end
% Add occurrence of this event
iOcc = length(events(iEvent).times) + 1;
events(iEvent).epochs(iOcc) = 1;
events(iEvent).times(iOcc) = (iSmp(i) + samplesBlock(1) - 1) ./ sFile.prop.sfreq;
events(iEvent).channels{iOcc} = {};
events(iEvent).notes{iOcc} = [];
end
case 'value'
value = tracks_vals{iTrack}(ixs(i));
if (length(StimChan) > 1)
label = sprintf('%s_%d', tracks_name{iTrack}, value);
else
label = sprintf('%d', value);
end
case {'ttl', 'rttl'}
label = tracks_name{iTrack};
end
% Find this event in list of events
if ~isempty(events)
iEvent = find(strcmpi({events.label}, label));
else
iEvent = [];
end
% If event does not exist yet: add it
if isempty(iEvent)
iEvent = length(events) + 1;
events(iEvent).label = label;
events(iEvent).epochs = [];
events(iEvent).times = [];
events(iEvent).reactTimes = [];
events(iEvent).select = 1;
events(iEvent).channels = {};
events(iEvent).notes = {};
end
% Add occurrence of this event
iOcc = length(events(iEvent).times) + 1;
events(iEvent).epochs(iOcc) = 1;
events(iEvent).times(iOcc) = (tracks_smps{iTrack}(ixs(i))-1) ./ sFile.prop.sfreq;
events(iEvent).channels{iOcc} = {};
events(iEvent).notes{iOcc} = [];
end
end
% Display warning with removed events
Expand All @@ -418,7 +441,3 @@
bst_progress('stop');
end
end




2 changes: 1 addition & 1 deletion toolbox/script/tutorial_coherence.m
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Expand Up @@ -116,7 +116,7 @@ function tutorial_coherence(tutorial_dir, reports_dir)
'stimchan', 'Stim', ...
'trackmode', 1, ... % Value: detect the changes of channel value
'zero', 0, ...
'min_duration', 0);
'min_duration', 12);
% Load all Event group labels
DataMat = in_bst_data(sFileRaw.FileName, 'F');
eventList = {DataMat.F.events.label};
Expand Down