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Mesoscope ibl #319

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Mesoscope ibl #319

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68e97e7
Prepare IBL experiment on Timeline PC
k1o0 Dec 1, 2023
78e9a92
Minor fixes
Dec 1, 2023
60c5687
Fix Timeline y axis label formatting
k1o0 Dec 19, 2023
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13 changes: 10 additions & 3 deletions +hw/Timeline.m
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Original file line number Diff line number Diff line change
Expand Up @@ -494,12 +494,17 @@ function stop(obj)
% timebase for Alyx and optionally into universal timebase if
% conversion is provided. TODO: Make timelineToALF a class method
if exist('+alf/timelineToALF','file') && exist('writeNPY','file')
alf.timelineToALF(obj.Data, [],...
fileparts(dat.expFilePath(obj.Data.expRef, 'timeline', 'master')))
% save only to master repo as data are redundent
masterSavePath = fileparts(dat.expFilePath(obj.Data.expRef, 'timeline', 'master'));
ALFpath = fullfile(masterSavePath, 'raw_sync_data');
if ~exist(ALFpath, 'dir')
mkdir(ALFpath)
end
alf.timelineToALF(obj.Data, [], fullfile(masterSavePath, 'raw_sync_data'))
else
warning('did not write files into alf format. Check that alyx-matlab and npy-matlab repositories are in path');
end

%Register ALF components and hardware structures to Alyx
%database. TODO: Make this process more robust.
subject = dat.parseExpRef(obj.Data.expRef);
Expand Down Expand Up @@ -643,6 +648,8 @@ function livePlot(obj, data)
if isempty(obj.Axes)
f = figure('Units', 'Normalized');
obj.Axes = gca; % store a handle to the axes
% ensure underscores in channel names not interpreted as underscores
obj.Axes.TickLabelInterpreter = 'none';
if isprop(obj, 'FigurePosition') && ~isempty(obj.FigurePosition)
set(f, 'Position', obj.FigurePosition); % set the figure position
end
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13 changes: 13 additions & 0 deletions cortexlab/+tl/bindMpepServer.m
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Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,11 @@ function processMpep(listener, msg)
tls.AlyxInstance = ai;
case 'expstart'
% create a file path & experiment ref based on experiment info
stubsPaths = prepareExperiment(info.expRef, 'timeline', ...
'fullPathInSettings', true, 'computerID', 'timeline');
tlSavePath = fileparts(dat.expFilePath(info.expRef, 'timeline', 'master'));
assert(tlSavePath == fileparts(stubsPaths{1}), ...
'iblrig local data path does not match dat.paths master repo location')
try % start Timeline
assert(~tlObj.IsRunning, ...
'Rigbox:tl:bindMpepServer:timelineAlreadyRunning', ...
Expand All @@ -101,6 +106,14 @@ function processMpep(listener, msg)
end
case 'expend'
tlObj.stop(); % stop Timeline
% Touch a flag file to disk for the copy script to find
masterSavePath = fileparts(dat.expFilePath(info.expRef, 'timeline', 'master'));
[fID, errmsg] = fopen(fullfile(masterSavePath, 'transfer_me.flag'), 'w');
if isempty(errmsg)
fclose(fID);
else
warning('Failed to create transfer flag: %s', errmsg)
end
case 'expinterrupt'
tlObj.stop(); % stop Timeline
end
Expand Down