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Updated documentation for change in remodeling backup CLI args
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89 changes: 59 additions & 30 deletions
89
hedcode/jupyter_notebooks/remodeling/run_remodel_backup.ipynb
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169 changes: 85 additions & 84 deletions
169
hedcode/matlab_scripts/data_cleaning/runEeglabImportEvents.m
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,88 +1,89 @@ | ||
| %% This imports the _events.tsv into the corresponding EEG.set file | ||
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| %% Set up the specifics for your dataset | ||
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| rootPath = '/XXX/SternbergWorkingPhaseTwo'; | ||
| setname = ''; | ||
| log_name = 'sternberg_12_import_events_log.txt'; | ||
| renameColumns = {'event_type', 'type'; 'onset', 'latency'}; | ||
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| % rootPath = 'G:/AttentionShift/AttentionShiftWorkingPhaseTwo'; | ||
| % setname = 'Auditory Visual Attention Shift'; | ||
| % log_name = 'attention_shift_18_import_events_log.txt'; | ||
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| % rootPath = 's:/bcit/AdvancedGuardDutyWorkingPhaseTwo'; | ||
| % setname = 'BCIT Advanced Guard Duty'; | ||
| % log_name = 'bcit_advanced_guard_duty_10_import_events_log.txt'; | ||
| filename = 'T:SummaryTests/ds004105-download/sub-01/ses-01/eeg/sub-01_ses-01_task-DriveRandomSound_run-1_events.tsv'; | ||
| eventstruct = importevent( filename, [], 1024, 'key1', 'value1', ...); | ||
| % rootPath = '/XXX/SternbergWorkingPhaseTwo'; | ||
| % setname = ''; | ||
| % log_name = 'sternberg_12_import_events_log.txt'; | ||
| % renameColumns = {'event_type', 'type'; 'onset', 'latency'}; | ||
| % | ||
| % rootPath = 's:/bcit/AuditoryCueingWorkingPhaseTwo'; | ||
| % setname = 'BCIT Auditory Cueing'; | ||
| % log_name = 'bcit_auditory_cueing_10_import_events_log.txt'; | ||
|
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| % rootPath = 's:/bcit/BaselineDrivingWorkingPhaseTwo'; | ||
| % setname = 'BCIT Baseline Driving'; | ||
| % log_name = 'bcit_baseline_driving_10_import_events_log.txt'; | ||
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| % rootPath = 's:/bcit/BasicGuardDutyWorkingPhaseTwo'; | ||
| % setname = 'BCIT Basic Guard Duty'; | ||
| % log_name = 'bcit_basic_guard_duty_10_import_events_log.txt'; | ||
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| % rootPath = 's:/bcit/CalibrationDrivingWorkingPhaseTwo'; | ||
| % setname = 'BCIT Calibration Driving'; | ||
| % log_name = 'bcit_calibration_driving_10_import_events_log.txt'; | ||
|
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| % rootPath = 's:/bcit/MindWanderingWorkingPhaseTwo'; | ||
| % setname = 'BCIT Mind Wandering'; | ||
| % log_name = 'bcit_mind_wandering_10_import_events_log.txt'; | ||
|
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| % rootPath = 's:/bcit/SpeedControlWorkingPhaseTwo'; | ||
| % setname = 'BCIT Speed Control'; | ||
| % log_name = 'bcit_speed_control_10_import_events_log.txt'; | ||
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| % rootPath = 's:/bcit/TrafficComplexityWorkingPhaseTwo'; | ||
| % setname = 'BCIT Traffic Complexity'; | ||
| % log_name = 'bcit_traffic_complexity_10_import_events_log.txt'; | ||
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| excludeDirs = {'sourcedata', 'code', 'stimuli'}; | ||
| namePrefix = ''; | ||
| nameSuffix = '_eeg'; | ||
| extensions = {'.set'}; | ||
|
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| % Designate the columns that are numeric (rest are char) | ||
| columnTypes = {'onset', 'double'; 'duration', 'double'; 'sample', 'int32'}; | ||
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| convertLatency = true; | ||
|
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| %% Open the log | ||
| fid = fopen([rootPath filesep 'code/curation_logs', filesep log_name], 'w'); | ||
| fprintf(fid, 'Log of runEeglabEventsImport.m on %s\n', datetime('now')); | ||
|
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||
| %% Generate json file. | ||
| fileList = getFileList(rootPath, namePrefix, nameSuffix, ... | ||
| extensions, excludeDirs); | ||
| for k = 1:length(fileList) | ||
| EEG = pop_loadset(fileList{k}); | ||
| [pathName, basename, ext] = fileparts(fileList{k}); | ||
| fprintf(fid, '%s:\n', basename); | ||
| eventsFile = [pathName filesep basename(1:(end-3)) 'events.tsv']; | ||
| eventTable = getEventTable(eventsFile, columnTypes, renameColumns); | ||
| fprintf(fid, '\tCreate a table from the events file\n'); | ||
| if convertLatency | ||
| eventTable.('latency') = eventTable.('latency')*EEG.srate + 1; | ||
| fprintf(fid, '\tConvert the latency column to samples\n'); | ||
| end | ||
| fprintf('%s: EEG.event has %d events and BIDS event file has %d events\n', ... | ||
| basename, length(EEG.event), size(eventTable,1)); | ||
| EEG.urevent = table2struct(eventTable)'; | ||
| fprintf(fid, '\tSet the EEG.urevent\n'); | ||
| eventTable.('urevent') = transpose(1:size(eventTable)); | ||
| EEG.event = table2struct(eventTable)'; | ||
| fprintf(fid, '\tSet the EEG.event\n'); | ||
| if ~isempty(setname) | ||
| EEG.setname = [setname basename]; | ||
| fprintf(fid, '\tSet the EEG.setname\n'); | ||
| end | ||
| fprintf(fid, '\tResave the EEG.set file\n'); | ||
| EEG = pop_saveset(EEG, 'savemode', 'resave', 'version', '7.3'); | ||
| end | ||
| fclose(fid); | ||
| % % rootPath = 'G:/AttentionShift/AttentionShiftWorkingPhaseTwo'; | ||
| % % setname = 'Auditory Visual Attention Shift'; | ||
| % % log_name = 'attention_shift_18_import_events_log.txt'; | ||
| % | ||
| % % rootPath = 's:/bcit/AdvancedGuardDutyWorkingPhaseTwo'; | ||
| % % setname = 'BCIT Advanced Guard Duty'; | ||
| % % log_name = 'bcit_advanced_guard_duty_10_import_events_log.txt'; | ||
| % % | ||
| % % rootPath = 's:/bcit/AuditoryCueingWorkingPhaseTwo'; | ||
| % % setname = 'BCIT Auditory Cueing'; | ||
| % % log_name = 'bcit_auditory_cueing_10_import_events_log.txt'; | ||
| % | ||
| % % rootPath = 's:/bcit/BaselineDrivingWorkingPhaseTwo'; | ||
| % % setname = 'BCIT Baseline Driving'; | ||
| % % log_name = 'bcit_baseline_driving_10_import_events_log.txt'; | ||
| % | ||
| % % rootPath = 's:/bcit/BasicGuardDutyWorkingPhaseTwo'; | ||
| % % setname = 'BCIT Basic Guard Duty'; | ||
| % % log_name = 'bcit_basic_guard_duty_10_import_events_log.txt'; | ||
| % | ||
| % % rootPath = 's:/bcit/CalibrationDrivingWorkingPhaseTwo'; | ||
| % % setname = 'BCIT Calibration Driving'; | ||
| % % log_name = 'bcit_calibration_driving_10_import_events_log.txt'; | ||
| % | ||
| % % rootPath = 's:/bcit/MindWanderingWorkingPhaseTwo'; | ||
| % % setname = 'BCIT Mind Wandering'; | ||
| % % log_name = 'bcit_mind_wandering_10_import_events_log.txt'; | ||
| % | ||
| % % rootPath = 's:/bcit/SpeedControlWorkingPhaseTwo'; | ||
| % % setname = 'BCIT Speed Control'; | ||
| % % log_name = 'bcit_speed_control_10_import_events_log.txt'; | ||
| % | ||
| % % rootPath = 's:/bcit/TrafficComplexityWorkingPhaseTwo'; | ||
| % % setname = 'BCIT Traffic Complexity'; | ||
| % % log_name = 'bcit_traffic_complexity_10_import_events_log.txt'; | ||
| % | ||
| % excludeDirs = {'sourcedata', 'code', 'stimuli', 'derivatives'}; | ||
| % namePrefix = ''; | ||
| % nameSuffix = '_eeg'; | ||
| % extensions = {'.set'}; | ||
| % | ||
| % % Designate the columns that are numeric (rest are char) | ||
| % columnTypes = {'onset', 'double'; 'duration', 'double'; 'sample', 'int32'}; | ||
| % | ||
| % convertLatency = true; | ||
| % | ||
| % %% Open the log | ||
| % fid = fopen([rootPath filesep 'code/curation_logs', filesep log_name], 'w'); | ||
| % fprintf(fid, 'Log of runEeglabEventsImport.m on %s\n', datetime('now')); | ||
| % | ||
| % %% Generate json file. | ||
| % fileList = getFileList(rootPath, namePrefix, nameSuffix, ... | ||
| % extensions, excludeDirs); | ||
| % for k = 1:length(fileList) | ||
| % EEG = pop_loadset(fileList{k}); | ||
| % [pathName, basename, ext] = fileparts(fileList{k}); | ||
| % fprintf(fid, '%s:\n', basename); | ||
| % eventsFile = [pathName filesep basename(1:(end-3)) 'events.tsv']; | ||
| % eventTable = getEventTable(eventsFile, columnTypes, renameColumns); | ||
| % fprintf(fid, '\tCreate a table from the events file\n'); | ||
| % if convertLatency | ||
| % eventTable.('latency') = eventTable.('latency')*EEG.srate + 1; | ||
| % fprintf(fid, '\tConvert the latency column to samples\n'); | ||
| % end | ||
| % fprintf('%s: EEG.event has %d events and BIDS event file has %d events\n', ... | ||
| % basename, length(EEG.event), size(eventTable,1)); | ||
| % EEG.urevent = table2struct(eventTable)'; | ||
| % fprintf(fid, '\tSet the EEG.urevent\n'); | ||
| % eventTable.('urevent') = transpose(1:size(eventTable)); | ||
| % EEG.event = table2struct(eventTable)'; | ||
| % fprintf(fid, '\tSet the EEG.event\n'); | ||
| % if ~isempty(setname) | ||
| % EEG.setname = [setname basename]; | ||
| % fprintf(fid, '\tSet the EEG.setname\n'); | ||
| % end | ||
| % fprintf(fid, '\tResave the EEG.set file\n'); | ||
| % EEG = pop_saveset(EEG, 'savemode', 'resave', 'version', '7.3'); | ||
| % end | ||
| % fclose(fid); |
88 changes: 88 additions & 0 deletions
88
hedcode/matlab_scripts/data_cleaning/runEeglabImportEventsOld.m
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| %% This imports the _events.tsv into the corresponding EEG.set file | ||
|
|
||
| %% Set up the specifics for your dataset | ||
|
|
||
| rootPath = '/XXX/SternbergWorkingPhaseTwo'; | ||
| setname = ''; | ||
| log_name = 'sternberg_12_import_events_log.txt'; | ||
| renameColumns = {'event_type', 'type'; 'onset', 'latency'}; | ||
|
|
||
| % rootPath = 'G:/AttentionShift/AttentionShiftWorkingPhaseTwo'; | ||
| % setname = 'Auditory Visual Attention Shift'; | ||
| % log_name = 'attention_shift_18_import_events_log.txt'; | ||
|
|
||
| % rootPath = 's:/bcit/AdvancedGuardDutyWorkingPhaseTwo'; | ||
| % setname = 'BCIT Advanced Guard Duty'; | ||
| % log_name = 'bcit_advanced_guard_duty_10_import_events_log.txt'; | ||
| % | ||
| % rootPath = 's:/bcit/AuditoryCueingWorkingPhaseTwo'; | ||
| % setname = 'BCIT Auditory Cueing'; | ||
| % log_name = 'bcit_auditory_cueing_10_import_events_log.txt'; | ||
|
|
||
| % rootPath = 's:/bcit/BaselineDrivingWorkingPhaseTwo'; | ||
| % setname = 'BCIT Baseline Driving'; | ||
| % log_name = 'bcit_baseline_driving_10_import_events_log.txt'; | ||
|
|
||
| % rootPath = 's:/bcit/BasicGuardDutyWorkingPhaseTwo'; | ||
| % setname = 'BCIT Basic Guard Duty'; | ||
| % log_name = 'bcit_basic_guard_duty_10_import_events_log.txt'; | ||
|
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||
| % rootPath = 's:/bcit/CalibrationDrivingWorkingPhaseTwo'; | ||
| % setname = 'BCIT Calibration Driving'; | ||
| % log_name = 'bcit_calibration_driving_10_import_events_log.txt'; | ||
|
|
||
| % rootPath = 's:/bcit/MindWanderingWorkingPhaseTwo'; | ||
| % setname = 'BCIT Mind Wandering'; | ||
| % log_name = 'bcit_mind_wandering_10_import_events_log.txt'; | ||
|
|
||
| % rootPath = 's:/bcit/SpeedControlWorkingPhaseTwo'; | ||
| % setname = 'BCIT Speed Control'; | ||
| % log_name = 'bcit_speed_control_10_import_events_log.txt'; | ||
|
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||
| % rootPath = 's:/bcit/TrafficComplexityWorkingPhaseTwo'; | ||
| % setname = 'BCIT Traffic Complexity'; | ||
| % log_name = 'bcit_traffic_complexity_10_import_events_log.txt'; | ||
|
|
||
| excludeDirs = {'sourcedata', 'code', 'stimuli', 'derivatives'}; | ||
| namePrefix = ''; | ||
| nameSuffix = '_eeg'; | ||
| extensions = {'.set'}; | ||
|
|
||
| % Designate the columns that are numeric (rest are char) | ||
| columnTypes = {'onset', 'double'; 'duration', 'double'; 'sample', 'int32'}; | ||
|
|
||
| convertLatency = true; | ||
|
|
||
| %% Open the log | ||
| fid = fopen([rootPath filesep 'code/curation_logs', filesep log_name], 'w'); | ||
| fprintf(fid, 'Log of runEeglabEventsImport.m on %s\n', datetime('now')); | ||
|
|
||
| %% Generate json file. | ||
| fileList = getFileList(rootPath, namePrefix, nameSuffix, ... | ||
| extensions, excludeDirs); | ||
| for k = 1:length(fileList) | ||
| EEG = pop_loadset(fileList{k}); | ||
| [pathName, basename, ext] = fileparts(fileList{k}); | ||
| fprintf(fid, '%s:\n', basename); | ||
| eventsFile = [pathName filesep basename(1:(end-3)) 'events.tsv']; | ||
| eventTable = getEventTable(eventsFile, columnTypes, renameColumns); | ||
| fprintf(fid, '\tCreate a table from the events file\n'); | ||
| if convertLatency | ||
| eventTable.('latency') = eventTable.('latency')*EEG.srate + 1; | ||
| fprintf(fid, '\tConvert the latency column to samples\n'); | ||
| end | ||
| fprintf('%s: EEG.event has %d events and BIDS event file has %d events\n', ... | ||
| basename, length(EEG.event), size(eventTable,1)); | ||
| EEG.urevent = table2struct(eventTable)'; | ||
| fprintf(fid, '\tSet the EEG.urevent\n'); | ||
| eventTable.('urevent') = transpose(1:size(eventTable)); | ||
| EEG.event = table2struct(eventTable)'; | ||
| fprintf(fid, '\tSet the EEG.event\n'); | ||
| if ~isempty(setname) | ||
| EEG.setname = [setname basename]; | ||
| fprintf(fid, '\tSet the EEG.setname\n'); | ||
| end | ||
| fprintf(fid, '\tResave the EEG.set file\n'); | ||
| EEG = pop_saveset(EEG, 'savemode', 'resave', 'version', '7.3'); | ||
| end | ||
| fclose(fid); |
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