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New module to do neuropixel recordings with ArpitSoundCatContinuous
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14 files changed

+422
-4506
lines changed

14 files changed

+422
-4506
lines changed

‎ExperPort/Modules/@NeuropixelNeuroblueprint/NeuropixelNeuroblueprint.asv‎

Lines changed: 0 additions & 1256 deletions
This file was deleted.

‎ExperPort/Modules/@NeuropixelNeuroblueprint/NeuropixelNeuroblueprint.m‎

Lines changed: 57 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -109,17 +109,23 @@
109109
uicontrol(handles.software_group, 'Style', 'radiobutton', 'String', 'SpikeGLX', 'Units', 'normalized', 'Position', [0.5, 0.3, 0.4, 0.4], 'Tag', 'SpikeGLX', 'FontSize', 10);
110110

111111
% Panel 1: Behavior
112-
p1 = uipanel('Title', '1. Behavior', 'FontSize', 12, 'FontWeight', 'bold', 'BorderType', 'etchedin', 'BorderWidth', 1, 'Units', 'normalized', 'Position', [0.02, 0.74, 0.6, 0.13]);
112+
p1 = uipanel('Title', '1. Behavior', 'FontSize', 12, 'FontWeight', 'bold', 'BorderType', 'etchedin', 'BorderWidth', 1, 'Units', 'normalized', 'Position', [0.02, 0.74, 0.6, 0.13]);
113113
uicontrol(p1, 'Style', 'text', 'String', 'Protocol Name:', 'Units', 'normalized', 'Position', [0.05, 0.7, 0.22, 0.25], 'HorizontalAlignment', 'right');
114114
handles.protocol_edit = uicontrol(p1, 'Style', 'edit', 'String', 'ArpitSoundCatContinuous', 'Units', 'normalized', 'Position', [0.3, 0.7, 0.45, 0.25]);
115115
handles.manual_test = uicontrol(p1, 'Style', 'checkbox', 'String', 'Manual Test', 'Value', 1, 'Units', 'normalized', 'Position', [0.78, 0.7, 0.2, 0.25]);
116-
uicontrol(p1, 'Style', 'text', 'String', 'Experimenter:', 'Units', 'normalized', 'Position', [0.05, 0.4, 0.22, 0.25], 'HorizontalAlignment', 'right');
117-
handles.exp_edit = uicontrol(p1, 'Style', 'edit', 'String', 'lida', 'Units', 'normalized', 'Position', [0.3, 0.4, 0.65, 0.25], 'Callback', {@(h,e) feval(mfilename, obj, 'update_subject_id')});
118-
uicontrol(p1, 'Style', 'text', 'String', 'Rat Name:', 'Units', 'normalized', 'Position', [0.05, 0.1, 0.22, 0.25], 'HorizontalAlignment', 'right');
119-
handles.rat_name_edit = uicontrol(p1, 'Style', 'edit', 'String', 'LP12', 'Units', 'normalized', 'Position', [0.3, 0.1, 0.4, 0.25], 'Callback', {@(h,e) feval(mfilename, obj, 'update_subject_id')});
120-
uicontrol(p1, 'Style', 'text', 'String', 'Path:', 'Units', 'normalized', 'Position', [0.72, 0.1, 0.08, 0.25], 'HorizontalAlignment', 'right');
121-
handles.behav_edit = uicontrol(p1, 'Style', 'edit', 'String', 'C:\ratter', 'Units', 'normalized', 'Position', [0.81, 0.1, 0.18, 0.25]);
122-
116+
uicontrol(p1, 'Style', 'text', 'String', 'Experimenter:', 'Units', 'normalized', 'Position', [0.02, 0.4, 0.2, 0.25], 'HorizontalAlignment', 'right');
117+
handles.exp_edit = uicontrol(p1, 'Style', 'edit', 'String', 'lida', 'Units', 'normalized', 'Position', [0.23, 0.4, 0.25, 0.25], 'Callback', {@(h,e) feval(mfilename, obj, 'update_subject_id')});
118+
uicontrol(p1, 'Style', 'text', 'String', 'Rat Name:', 'Units', 'normalized', 'Position', [0.50, 0.4, 0.18, 0.25], 'HorizontalAlignment', 'right');
119+
handles.rat_name_edit = uicontrol(p1, 'Style', 'edit', 'String', 'LP12', 'Units', 'normalized', 'Position', [0.69, 0.4, 0.30, 0.25], 'Callback', {@(h,e) feval(mfilename, obj, 'update_subject_id')});
120+
uicontrol(p1, 'Style', 'text', 'String', 'Distribution:', 'Units', 'normalized', 'Position', [0.02, 0.1, 0.18, 0.25], 'HorizontalAlignment', 'right');
121+
handles.distribution_popup = uicontrol(p1, 'Style', 'popupmenu', ...
122+
'String', {'random', 'Uniform', 'Hard A', 'Hard B'}, ...
123+
'Units', 'normalized', ...
124+
'Position', [0.21, 0.1, 0.35, 0.25]);
125+
uicontrol(p1, 'Style', 'text', 'String', 'Path:', 'Units', 'normalized', 'Position', [0.58, 0.1, 0.1, 0.25], 'HorizontalAlignment', 'right');
126+
handles.behav_edit = uicontrol(p1, 'Style', 'edit', 'String', 'C:\ratter', 'Units', 'normalized', 'Position', [0.69, 0.1, 0.30, 0.25]);%
127+
128+
123129
% Panel 2: NeuroBlueprint Format
124130
p2 = uipanel('Title', '2. NeuroBlueprint Format', 'FontSize', 12, 'FontWeight', 'bold', 'BorderType', 'etchedin', 'BorderWidth', 1, 'Units', 'normalized', 'Position', [0.02, 0.42, 0.6, 0.31]);
125131
uicontrol(p2, 'Style', 'text', 'String', 'Project Name:', 'Units', 'normalized', 'Position', [0.01, 0.85, 0.28, 0.1], 'HorizontalAlignment', 'right');
@@ -317,7 +323,7 @@
317323
else % SpikeGLX
318324
log_message(handles, 'Initializing SpikeGLX controller...');
319325
controller = SpikeGL(params.sglx_host_ip, params.sglx_port);
320-
if ~controller.IsConnected(), error('Failed to connect to SpikeGLX'); end
326+
% if ~controller.IsConnected(), error('Failed to connect to SpikeGLX'); end
321327
end
322328
recording_controller.value = controller;
323329
log_message(handles, sprintf('%s controller initialized successfully.', software));
@@ -344,7 +350,8 @@
344350
if strcmp(software, 'OpenEphys')
345351
controller.setRecordPath(params.oe_rec_node_id, save_path);
346352
else % SpikeGLX
347-
controller.SetDataDir(save_path);
353+
controller = SetDataDir( controller, 0, save_path);
354+
recording_controller.value = controller;
348355
end
349356
log_message(handles, sprintf('Recording path set to: %s', save_path));
350357
catch ME
@@ -374,8 +381,22 @@
374381
else % SpikeGLX
375382
log_message(handles, 'Starting SpikeGLX recording...');
376383
run_name = sprintf('experiment_%s', datestr(now, 'yyyymmdd_HHMMSS'));
377-
controller.SetRunName(run_name);
378-
controller.StartRun();
384+
boolval = IsInitialized( controller);
385+
if boolval
386+
spikeglx_params = GetParams( controller );
387+
controller = SetRunName(controller,run_name); % setting run name
388+
controller = StartRun(controller); % starting acquisition
389+
pause(2);
390+
391+
runningval = false;
392+
while ~runningval % waiting for acquisition to start
393+
runningval = IsRunning( controller );
394+
if runningval
395+
controller = SetRecordingEnable( controller, 1 ); % Start Recording
396+
end
397+
end
398+
recording_controller.value = controller;
399+
end
379400
end
380401

381402
log_message(handles, 'Electrophysiology recording is LIVE.');
@@ -399,7 +420,15 @@
399420
controller.idle();
400421
else % SpikeGLX
401422
log_message(handles, 'Stopping SpikeGLX recording...');
402-
controller.StopRun();
423+
boolval = IsSaving( controller );
424+
if boolval
425+
controller = SetRecordingEnable( controller, 0 );
426+
pause(1); % Brief pause to ensure recording stops
427+
controller = StopRun(controller);
428+
else
429+
controller = StopRun(controller);
430+
end
431+
recording_controller.value = controller;
403432
end
404433

405434
log_message(handles, 'Electrophysiology recording stopped.');
@@ -482,7 +511,7 @@
482511
video_save_dir = fullfile(params.local_path, value(session_base_path), 'behav');
483512
try
484513
log_message(handles, 'Loading main behavioral protocol...');
485-
feval(mfilename, obj, 'behav_control', 'load_main_protocol', params.experimenter, params.rat_name, params.protocol_name, video_save_dir, params.behav_path);
514+
feval(mfilename, obj, 'behav_control', 'load_main_protocol', params.experimenter, params.rat_name, params.protocol_name, video_save_dir, params.behav_path,params.stim_distribution);
486515
log_message(handles, 'Behavior system loaded and ready.');
487516
log_message(handles, '--- LOAD sequence complete. Ready to run. ---');
488517
currentState.value = 'Run';
@@ -546,7 +575,7 @@
546575
switch sub_action
547576
case 'load_main_protocol'
548577
experimenter = args{1}; ratname = args{2}; protocol_name = args{3};
549-
video_save_dir = args{4}; behav_path = args{5};
578+
video_save_dir = args{4}; behav_path = args{5}; stim_distribution = args{6};
550579
log_message(handles, ['Loading protocol: ' protocol_name]);
551580
dispatcher('set_protocol', protocol_name);
552581
rath = get_sphandle('name', 'ratname', 'owner', protocol_name);
@@ -556,6 +585,7 @@
556585
log_message(handles, ['Loading settings for ' ratname]);
557586
[~, sfile] = load_solouiparamvalues(ratname, 'experimenter', experimenter, 'owner', class(protobj), 'interactive', 0);
558587
feval(protocol_name, protobj, 'set_setting_params', ratname, experimenter, sfile, char(datetime('now')), video_save_dir);
588+
feval(protocol_name, protobj, 'set_stim_distribution',stim_distribution);
559589
if ~dispatcher('is_running'), pop_history(class(protobj), 'include_non_gui', 1); feval(protocol_name, protobj, 'prepare_next_trial'); end
560590

561591
case 'crashed'
@@ -585,6 +615,7 @@
585615
load_soloparamvalues(ratname, 'experimenter', experimenter, 'owner', protocol_name, 'interactive', 0,'data_file',fullfile(temp_data_dir,temp_data_file));
586616
dispatcher('runstart_enable');
587617
end
618+
feval(protocol_name, protobj, 'psychometricUpdate_aftercrash'); % update parameters for psychometric plots which were not saved so cant be loaded
588619
if ~dispatcher('is_running'), pop_history(class(protobj), 'include_non_gui', 1); feval(protocol_name, protobj, 'prepare_next_trial'); end
589620
catch
590621
log_message(handles, ['Loading settings for ' ratname]);
@@ -1029,6 +1060,8 @@
10291060
params.do_manual_test = get(handles.manual_test, 'Value');
10301061
params.experimenter = get(handles.exp_edit, 'String');
10311062
params.rat_name = get(handles.rat_name_edit, 'String');
1063+
popup_string = get(handles.distribution_popup,'String');
1064+
params.stim_distribution = popup_string{get(handles.distribution_popup,'Value')};
10321065
params.behav_path = get(handles.behav_edit, 'String');
10331066
params.project_name = get(handles.proj_edit, 'String');
10341067
params.subject_id = get(handles.sub_edit, 'String');
@@ -1151,13 +1184,13 @@ function log_message(handles,logStr)
11511184
try
11521185
if ~isfield(handles, 'log_box') || ~isvalid(handles.log_box), return; end
11531186
current_text = get(handles.log_box, 'String');
1154-
timestamp = datestr(now, '[HH:MM:SS] ');
1187+
timestamp = char(datetime('now', 'Format', '[HH:mm:ss] '));
11551188
new_line = [timestamp, logStr];
11561189
new_text = [current_text; {new_line}];
11571190
set(handles.log_box, 'String', new_text, 'Value', numel(new_text));
11581191
drawnow;
11591192
catch
1160-
fprintf('%s: %s\n', datestr(now, '[HH:MM:SS]'), logStr);
1193+
fprintf('%s: %s\n', char(datetime('now', 'Format', '[HH:mm:ss] ')), logStr);
11611194
end
11621195

11631196
function toggle_button_color(~, ~, button_handle)
@@ -1180,18 +1213,20 @@ function commit_to_svn(handles, file_path_data,file_path_settings, root_dir)
11801213
return;
11811214
end
11821215
load(configFilePath, 'svn_user', 'svn_password');
1183-
logmsg = char(strcat('automated commit from GUI for data and settings for ', {' '} ,fname_data,{'@'}));
1216+
logmsg_data = char(strcat('automated commit from GUI for data and settings for ', {' '} ,fname_data,{'@'}));
11841217
% current_dir = cd;
11851218
cd(pname_data);
11861219
add_cmd_data = char(strcat('svn add', {' '}, fname_data, '.mat',{'@'}));
1187-
system(add_cmd_data);
1220+
system(add_cmd_data);
1221+
commit_cmd_data = sprintf('svn ci --username="%s" --password="%s" -m "%s"', svn_user, svn_password, logmsg_data);
1222+
[status, ~] = system(commit_cmd_data);
11881223

11891224
cd(pname_settings);
11901225
add_cmd_settings = char(strcat('svn add', {' '}, fname_settings, '.mat',{'@'}));
11911226
system(add_cmd_settings);
1192-
1193-
commit_cmd = sprintf('svn ci --username="%s" --password="%s" -m "%s"', svn_user, svn_password, logmsg);
1194-
[status, ~] = system(commit_cmd);
1227+
logmsg_setting = char(strcat('automated commit from GUI for data and settings for ', {' '} ,fname_settings,{'@'}));
1228+
commit_cmd_setting = sprintf('svn ci --username="%s" --password="%s" -m "%s"', svn_user, svn_password, logmsg_setting);
1229+
[status, ~] = system(commit_cmd_setting);
11951230

11961231
if status == 0
11971232
log_message(handles, ['SVN commit successful for ' fname_data]);

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