Jen practice

Analysis/script_loop_through_data_folders.m

@@ -0,0 +1,67 @@
+% script to calculate scalograms for all of Jen's rats; store in files in
+% the processed data folders
+
+parent_directory = 'X:\Neuro-Leventhal\data\ChoiceTask';
+summary_xls = 'ProbeSite_Mapping_MATLAB.xlsx';
+summary_xls_dir = 'X:\Neuro-Leventhal\data\ChoiceTask\Probe Histology Summary';
+summary_xls = fullfile(summary_xls_dir, summary_xls);
+
+% change the line below to allow looping through multiple trial types,
+% extract left vs right, etc.
+trials_to_analyze = 'correct';
+lfp_types = {'monopolar', 'bipolar'};
+lfp_type = 'monopolar';
+% trials_to_analyze = 'all';
+
+t_window = [-2.5, 2.5];
+event_list = {'cueOn', 'centerIn', 'tone', 'centerOut' 'sideIn', 'sideOut', 'foodClick', 'foodRetrieval'};
+
+probe_type_sheet = 'probe_type';
+probe_types = read_Jen_xls_summary(summary_xls, probe_type_sheet);
+% NOTE - UPDATE FUNCTION read_Jen_xls_summary WHEN WE NEED OTHER
+% INFORMATION OUT OF THAT SPREADSHEET
+
+[rat_nums, ratIDs, ratIDs_goodhisto] = get_rat_list();
+
+num_rats = length(ratIDs);
+
+for i_rat = 1 : num_rats
+    ratID = ratIDs{i_rat};
+    rat_folder = fullfile(parent_directory, ratID);
+
+    if ~isfolder(rat_folder)
+        continue;
+    end
+
+    probe_type = probe_types{probe_types.RatID == ratID, 2};
+    processed_folder = find_data_folder(ratID, 'processed', parent_directory);
+    session_dirs = dir(fullfile(processed_folder, strcat(ratID, '*')));
+    num_sessions = length(session_dirs);
+
+    probe_lfp_type = sprintf('%s_%s', probe_type, lfp_type);
+
+    for i_session = 1 : num_sessions
+
+        session_name = session_dirs(i_session).name;
+        cur_dir = fullfile(session_dirs(i_session).folder, session_name);
+        cd(cur_dir)
+
+        for i_lfptype = 1 : length(lfp_types)
+
+            lfp_type = lfp_types{i_lfptype};
+
+            for i_event = 1 : length(event_list)
+                event_name = event_list{i_event};
+                sprintf('working on session %s, event %s', session_name, event_name)
+
+                scalo_folder = create_scalo_folder(session_name, event_name, parent_directory);
+
+                for i_channel = 1 : num_channels
+
+
+                end
+            end
+        end
+    end
+
+end

Analysis/script_rename_scalos_to_monopolar.m

@@ -0,0 +1,80 @@
+% script to calculate scalograms for all of Jen's rats; store in files in
+% the processed data folders
+
+parent_directory = 'X:\Neuro-Leventhal\data\ChoiceTask';
+summary_xls = 'ProbeSite_Mapping_MATLAB.xlsx';
+summary_xls_dir = 'X:\Neuro-Leventhal\data\ChoiceTask\Probe Histology Summary';
+summary_xls = fullfile(summary_xls_dir, summary_xls);
+
+% change the line below to allow looping through multiple trial types,
+% extract left vs right, etc.
+trials_to_analyze = 'correct';
+lfp_types = {'monopolar', 'bipolar'};
+lfp_type = 'monopolar';
+% trials_to_analyze = 'all';
+
+t_window = [-2.5, 2.5];
+event_list = {'cueOn', 'centerIn', 'tone', 'centerOut' 'sideIn', 'sideOut', 'foodClick', 'foodRetrieval'};
+
+probe_type_sheet = 'probe_type';
+probe_types = read_Jen_xls_summary(summary_xls, probe_type_sheet);
+% NOTE - UPDATE FUNCTION read_Jen_xls_summary WHEN WE NEED OTHER
+% INFORMATION OUT OF THAT SPREADSHEET
+
+[rat_nums, ratIDs, ratIDs_goodhisto] = get_rat_list();
+
+num_rats = length(ratIDs);
+
+for i_rat = 1 : num_rats
+    ratID = ratIDs{i_rat};
+    rat_folder = fullfile(parent_directory, ratID);
+
+    if ~isfolder(rat_folder)
+        continue;
+    end
+
+    probe_type = probe_types{probe_types.ratID == ratID, 2};
+    processed_folder = find_data_folder(ratID, 'processed', parent_directory);
+    session_dirs = dir(fullfile(processed_folder, strcat(ratID, '*')));
+    num_sessions = length(session_dirs);
+
+    probe_lfp_type = sprintf('%s_%s', probe_type, lfp_type);
+
+    for i_session = 1 : num_sessions
+
+        session_name = session_dirs(i_session).name;
+        cur_dir = fullfile(session_dirs(i_session).folder, session_name);
+        cd(cur_dir)
+
+        for i_lfptype = 1 : length(lfp_types)
+
+            lfp_type = lfp_types{i_lfptype};
+
+            for i_event = 1 : length(event_list)
+                event_name = event_list{i_event};
+                sprintf('working on session %s, event %s', session_name, event_name)
+
+                scalo_folder = create_scalo_folder(session_name, event_name, parent_directory);
+                if ~exist(scalo_folder, 'dir')
+                    continue
+                end
+
+                for i_channel = 1 : num_channels
+                    [shank_num, site_num] = get_shank_and_site_num(probe_lfp_type, i_channel);
+
+                    old_scalo_name = sprintf('%s_scalos_%s_shank%02d_site%02d.mat',session_name, event_name, shank_num, site_num);
+                    old_scalo_name = fullfile(scalo_folder, old_scalo_name);
+
+                    if exist(old_scalo_name, 'file')
+                        new_scalo_name = sprintf('%s_scalos_%s_%s_shank%02d_site%02d.mat',session_name, lfp_type, event_name, shank_num, site_num);
+                        new_scalo_name = fullfile(scalo_folder, new_scalo_name);
+
+                        movefile(old_scalo_name, new_scalo_name)
+                    end
+
+                end
+            end
+        end
+    end
+
+end

Analysis/sum_session_correct_trials.m

@@ -0,0 +1,7 @@
+AllTrials = vertcat(trials.correct);
+tone = vertcat(trials.tone);
+C = [AllTrials tone];
+indices = find(C(:,1)==0);
+C(indices,:) = [];
+tone2 = sum( C(:,2)==2 );
+tone1 = sum( C(:,2)==1 );

Analysis/trial_scalograms.m

@@ -0,0 +1,20 @@
+function [event_related_scalos, f, coi] = trial_scalograms(event_triggered_lfps, fb)
+%UNTITLED2 Summary of this function goes here
+% INPUTS
+%   event_triggered_lfps - num_trials x samples_per_event array
+%   Detailed explanation goes here
+
+num_trials = size(event_triggered_lfps, 1);
+samples_per_event = size(event_triggered_lfps, 2);
+
+f = centerFrequencies(fb);
+num_freqs = length(f);
+
+real_event_related_scalos = zeros(num_trials, num_freqs, samples_per_event);
+event_related_scalos = complex(real_event_related_scalos, 0);
+
+for i_trial = 1 : num_trials
+    [event_related_scalos(i_trial, :, :), ~, coi] = wt(fb, squeeze(event_triggered_lfps(i_trial, :)));
+end
+
+end

ChoiceTask_Intan_behavior_analysis/create_and_save_trials_struct_Intan.asv

@@ -0,0 +1,61 @@
+% script create_and_save_trials_struct_Intan
+
+% loop through all rats with valid choice task data, create trials
+% structure for each session, save in the processed data folder to save
+% time
+
+parent_directory = 'Z:\data\ChoiceTask\';
+
+[rat_nums, ratIDs, ratIDs_goodhisto] = get_rat_list();
+
+num_rats = length(ratIDs);
+
+for i_rat = 1 : num_rats
+    ratID = ratIDs{i_rat};
+    rat_folder = fullfile(parent_directory, ratID);
+
+    if ~isfolder(rat_folder)
+        continue;
+    end
+
+    processed_folder = find_data_folder(ratID, 'processed', parent_directory);
+    session_dirs = dir(fullfile(processed_folder, strcat(ratID, '*')));
+    num_sessions = length(session_dirs);
+
+    rawdata_folder = find_data_folder(ratID, 'rawdata', parent_directory);
+
+    for i_session = 1 : num_sessions
+
+        session_name = session_dirs(i_session).name;
+        cur_processed_dir = fullfile(session_dirs(i_session).folder, session_name);
+        cur_rawdata_dir = fullfile(rawdata_folder, session_name);
+        cd(cur_processed_dir)
+
+        lfp_fname = strcat(session_name, '_lfp.mat');
+        if ~isfile(lfp_fname)
+            sprintf('%s not found, skipping', lfp_file)
+            continue
+        end
+
+        trials_name = sprintf('%s_trials.mat', session_name);
+        trials_name = fullfile(cur_processed_dir, trials_name);
+        if exist(trial_name, 'file')
+
+            continue
+        end
+
+        rawdata_ephys_folder = get_rawdata_ephys_folder(rawdata_folder,session_name);
+        nexData = extractEventsFromIntanSystem(rawdata_ephys_folder);
+
+        log_file = find_log_file(session_name, parent_directory);
+        logData = readLogData(log_file);
+
+        sprintf('loaded logData and nexData for %s', session_name)
+
+        trials = createTrialsStruct_simpleChoice_Intan( logData, nexData );
+
+
+
+    end
+
+end

ChoiceTask_Intan_behavior_analysis/create_and_save_trials_struct_Intan.m

@@ -0,0 +1,83 @@
+% script create_and_save_trials_struct_Intan
+
+% loop through all rats with valid choice task data, create trials
+% structure for each session, save in the processed data folder to save
+% time
+
+parent_directory = 'Z:\data\ChoiceTask\';
+
+[rat_nums, ratIDs, ratIDs_goodhisto] = get_rat_list();
+
+num_rats = length(ratIDs);
+
+for i_rat = 1 : num_rats
+    ratID = ratIDs{i_rat};
+    rat_folder = fullfile(parent_directory, ratID);
+
+    if ~isfolder(rat_folder)
+        continue;
+    end
+
+    processed_folder = find_data_folder(ratID, 'processed', parent_directory);
+    session_dirs = dir(fullfile(processed_folder, strcat(ratID, '*')));
+    num_sessions = length(session_dirs);
+
+    rawdata_folder = find_data_folder(ratID, 'rawdata', parent_directory);
+
+    for i_session = 1 : num_sessions
+
+        session_name = session_dirs(i_session).name;
+        cur_processed_dir = fullfile(session_dirs(i_session).folder, session_name);
+        cur_rawdata_dir = fullfile(rawdata_folder, session_name);
+        cd(cur_processed_dir)
+
+        lfp_fname = strcat(session_name, '_lfp.mat');
+        if ~isfile(lfp_fname)
+            sprintf('%s not found, skipping', lfp_file)
+            continue
+        end
+
+        trials_name = sprintf('%s_trials.mat', session_name);
+        trials_name = fullfile(cur_processed_dir, trials_name);
+        if exist(trials_name, 'file')
+            % skip if already calculated
+            sprintf('trials structure already calculated for %s', session_name)
+            continue
+        end
+
+        rawdata_ephys_folder = get_rawdata_ephys_folder(rawdata_folder,session_name);
+        % check that the digitalIn file exists - was missing from some
+        % early sessions
+        digitalin_fname = fullfile(rawdata_ephys_folder, 'digitalin.dat');
+        if ~exist(digitalin_fname, 'file')
+            sprintf('no digital input file found for %s', session_name)
+            continue
+        end
+
+        nexData = extractEventsFromIntanSystem(rawdata_ephys_folder);
+        if isempty(nexData)
+            % something was wrong with the analog/digital input files from
+            % the intan system
+            sprintf('nexData could not be generated for %s', session_name)
+            continue
+        end
+
+        log_file = find_log_file(session_name, parent_directory);
+        logData = readLogData(log_file);
+
+        sprintf('loaded logData and nexData for %s', session_name)
+
+        try
+            trials = createTrialsStruct_simpleChoice_Intan( logData, nexData );
+        catch ME
+            if strcmp(ME.identifier, 'lognexmerge:lognexmismatch')
+                sprintf('mismatch between log and nex files for %s', session_name)
+                continue
+            end
+        end
+
+        save(trials_name, 'trials');
+
+    end
+
+end

ChoiceTask_Intan_behavior_analysis/extractEventsFromIntanSystem.m

@@ -28,6 +28,10 @@
 digital_word = readIntanDigitalFile(dig_in_file);
 toc
 tic
+if ~isfield(intan_info, 'board_adc_channels')
+    nexData = [];
+    return
+end
 ADC_signals = readIntanAnalogFile(analog_in_file,intan_info.board_adc_channels);
 toc