BRAIN CoGS mini VR rigs

# How to use DB (tips, tricks and more)

# MATLAB

# Prerequesites

  1. U19-pipeline-matlab repo added to MATLAB path
  2. Mounted network cup drives (braininit, u19_dj)
  • Go through U19-pipeline-matlab/tutorials/202103/session01_queries_fetches.mlx to learn basic tips on datajoint.

# Useful scripts and functions for reseacher general use:

# Read behavior file:

  1. Execute: (change key for desired session)
key = struct('subject_fullname', 'testuser_T06', 'session_date', '2022-04-20');
[status,data] = lab.utils.read_behavior_file(key)
  1. If successful status = 1 and data = log behavioral file

# Get behavior file location (local & for spock/scotty)

  1. If you only need to know the path of behavior file use:
key = struct('subject_fullname', 'testuser_T06', 'session_date', '2022-04-20');
baseDir = fetch1(acquisition.SessionStarted & key, 'new_remote_path_behavior_file');
[bucket_path, local_path] =  lab.utils.get_path_from_official_dir(baseDir)

# get_full_trial_data with SpatialTimeBlobs

  • Get trial data (position, velocity, etc) efficiently with DB.
  • New method to retrieve all trial data for multiple sessions faster.
  1. Execute:
key = struct('subject_fullname', 'testuser_T06', 'session_date', '2022-04-20');
get_full_trial_data(key)
  • Get trial data from joined tables as well (e.g. TowersBlock):
key = struct('subject_fullname', 'testuser_T06', 'session_date', '2022-04-20');
get_full_trial_data(key, behavior.TowersBlockTrial * behavior.TowersBlock)
  • Get data from subtasks as well (e.g. Twolickspouts subtask)
key = struct('subject_fullname', 'efonseca_ef114_act114', 'session_date', '2023-01-11');
all_tables = behavior.TowersBlockTrial * behavior.TowersBlock * behavior_subtask.TwolickspoutsBlockTrial * behavior_subtask.TwolickspoutsBlock
get_full_trial_data(key, all_tables)

# get stats from session

  • To get behavior file like stats (on the trial level) for a single or multiple sessions use this function
  • Stats include, but not limited to: (correct_left, correct_right, cum_correct_trials, performance, goodFraction, numPerMin, numRewardsPerMin, bias)
key = struct('subject_fullname', 'testuser_T06', 'session_date', '2022-04-20');
stat_struct = get_stats_from_session(key, "all")

# get behaviorfile as db

  • Function to unnest behavior file structure to get a plain trial table (with block data merged).
key = struct('subject_fullname', 'testuser_T06', 'session_date', '2022-04-20');
data_struct = get_behaviorfile_as_db(key)

# get time from iteration variable

  • Example of how to "translate" a variable from iteration# to trial_time
  • In this case, 1st row of variable licks (iteration#) is translated to lick_times and then added to original trial structure
key = struct('subject_fullname', 'efonseca_ef114_act114', 'session_date', '2023-01-11');
trial_data = get_full_trial_data(key, behavior.TowersBlockTrial * behavior_subtask.TwolickspoutsBlockTrial);
licks_time_struct = struct;
for i=1:length(trial_data)
   licks_time_struct(i,1).lick_times = get_time_from_iter(trial_data(i).trial_time, trial_data(i).licks(1,:));
end
trial_data = cat_struct(trial_data, licks_time_struct);

# plot framerate frequency sessions

  • Plot trial by trial framerate of multiple sessions for comparison
key = 'subject_fullname like "mioffe%" and session_date > "2022-01-01" and session_date < "2022-01-30"';
analyze_iteration_time(key)
Framerate trial by trial sessions

# plot framerate frequency levels and rigs

  • Plot mean framerate by level and rig for multiple sessions
key = 'subject_fullname like "mioffe%" and session_date > "2022-01-01" and session_date < "2022-12-10"';
analyze_iteration_time_level_rig(key)
Mean framerate by level and rig

# plot velocity sessions

  • Plot mean - max range velocity by session for multiple behavior sessions
key = struct('subject_fullname', 'emdiamanti_gps7');
plot_velocity_session(key)
Velocity plot for multiple sessions

# get path table

  1. Get default paths for network cup drives for different OS and spock/scotty (bucket)
key = struct('subject_fullname', 'testuser_T06', 'session_date', '2022-04-20');
baseDir = fetch1(acquisition.SessionStarted & key, 'new_remote_path_behavior_file');
[bucket_path, local_path] =  lab.utils.get_path_from_official_dir(baseDir)
Path table data

# Common errors and troubleshooting

  1. When trying to fetch from a table with external storage and corresponding network cup drive is not mounted:
Error using dj.store_plugins.File (line 89)
Directory `/Volumes/u19_dj/external_dj_blobs` not accessible.

Error in dj.internal.ExternalTable (line 52)
           self.spec = dj.store_plugins.(storePlugin)(config);

Error using fread
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in dj.store_plugins.File.download_buffer (line 63)
           result = fread(fileID);
  • Just mount all cup drives and try agian !!
  1. key reference more than one session when function was supposed to work for single sessions
Error using dj.internal.GeneralRelvar/fetch1 (line 250)
fetch1 can only retrieve a single existing tuple.
  • Just recreate key to reference a single session.

# PYTHON

# Common errors and troubleshooting

← ViRMEn User/Developer Guide →