Merge branch 'master' of https://github.com/spatialtopology/spacetop-…

…prep

spacetop_prep/datalad/rename_sub-0075_ses-01_task-social.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+set -eu
+
+# Define the rename function (assuming it's located at ../../../code/rename_file)
+RENAME_FUNC="/Users/h/Documents/projects_local/1076_spacetop/code/rename_file"
+
+# Define the base file name pattern
+SUBPATH="/Users/h/Documents/projects_local/1076_spacetop/sub-0075/ses-01/func"
+PATTERN="sub-0075_ses-01_task-social_acq-mb8_run"
+
+# Rename files
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-04_bold.json" "${SUBPATH}/${PATTERN}-06_bold.json"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-04_bold.nii.gz" "${SUBPATH}/${PATTERN}-06_bold.nii.gz"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-04_sbref.json" "${SUBPATH}/${PATTERN}-06_sbref.json"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-04_sbref.nii.gz" "${SUBPATH}/${PATTERN}-06_sbref.nii.gz"
+
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-03_bold.json" "${SUBPATH}/${PATTERN}-04_bold.json"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-03_bold.nii.gz" "${SUBPATH}/${PATTERN}-04_bold.nii.gz"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-03_sbref.json" "${SUBPATH}/${PATTERN}-04_sbref.json"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-03_sbref.nii.gz" "${SUBPATH}/${PATTERN}-04_sbref.nii.gz"
+
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-02_bold.json" "${SUBPATH}/${PATTERN}-03_bold.json"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-02_bold.nii.gz" "${SUBPATH}/${PATTERN}-03_bold.nii.gz"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-02_sbref.json" "${SUBPATH}/${PATTERN}-03_sbref.json"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-02_sbref.nii.gz" "${SUBPATH}/${PATTERN}-03_sbref.nii.gz"
+
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-01_bold.json" "${SUBPATH}/${PATTERN}-02_bold.json"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-01_bold.nii.gz" "${SUBPATH}/${PATTERN}-02_bold.nii.gz"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-01_sbref.json" "${SUBPATH}/${PATTERN}-02_sbref.json"
+$RENAME_FUNC "${SUBPATH}/${PATTERN}-01_sbref.nii.gz" "${SUBPATH}/${PATTERN}-02_sbref.nii.gz"

spacetop_prep/datalad/resolve_missingevents/s03_sub_0001_task_alignvideo.m

@@ -0,0 +1,111 @@
+function s03_sub_0001_task_alignvideo()
+% Define the run ranges and maximum rows per run
+run_ranges = {1:4, 5:8, 9:12, 13:14};
+max_rows_per_run = [4, 4, 4, 2];  % Specify the number of rows for each run
+
+% Define the list of video filenames corresponding to the runs
+param_video_filename_list = {
+    'ses-01_run-01_order-01_content-idiots.mp4',
+    'ses-01_run-01_order-02_content-wanderers.mp4',
+    'ses-01_run-01_order-03_content-lioncubs.mp4',
+    'ses-01_run-01_order-04_content-parkour.mp4',
+    'ses-01_run-02_order-01_content-harrymetsally.mp4',
+    'ses-01_run-02_order-02_content-HB.mp4',
+    'ses-01_run-02_order-03_content-islamophobia.mp4',
+    'ses-01_run-02_order-04_content-beachsunset.mp4',
+    'ses-01_run-03_order-01_content-huggingpets.mp4',
+    'ses-01_run-03_order-02_content-bestfriendsweating.mp4',
+    'ses-01_run-03_order-03_content-cupstacking.mp4',
+    'ses-01_run-03_order-04_content-dancewithdeath.mp4',
+    'ses-01_run-04_order-01_content-beatbox.mp4',
+    'ses-01_run-04_order-02_content-angrygrandpa.mp4'
+    };
+
+% Loop over each run number
+for run_num = 1:4
+    % Select the relevant filenames for this run
+    filename_range = run_ranges{run_num};
+    selected_filenames = param_video_filename_list(filename_range)';
+
+    % Load the corresponding data file
+    file_path = sprintf('/Users/h/Documents/projects_local/1076_spacetop/sourcedata/d_beh/sub-0001/task-alignvideos/ses-01/sub-0001_ses-01_task-alignvideos_run-%02d_beh.mat', run_num);
+    load(file_path)
+
+    % initialize values by getting correct dataframe size
+    selected_range = run_ranges{run_num};
+    num_items = numel(explog.rating.times{selected_range(1)});
+    rating_onset = zeros(numel(selected_range), num_items);
+    rating_value = zeros(numel(selected_range), num_items);
+    rating_RT = zeros(numel(selected_range), num_items);
+    biopac_displayonset = NaN(numel(selected_range), num_items);
+    biopac_response = NaN(numel(selected_range), num_items);
+
+    for i = 1:num_items
+        for j = 1:numel(selected_range)
+            rating_onset(j, i) = explog.rating.times{selected_range(j)}(i);
+            rating_value(j, i) = explog.rating.ratings{selected_range(j)}(i);
+            rating_RT(j, i) = explog.rating.RT{selected_range(j)}(i);
+        end
+    end
+
+    % Number of rows for this run
+    num_rows = max_rows_per_run(run_num);
+
+    % Create the table dynamically without padding
+    T = table();
+    % Assuming rating_onset, rating_value, and rating_RT are already defined as 4x7 matrices
+    num_items = size(rating_onset, 2); % Number of items (7 in your case)
+    num_rows = size(rating_onset, 1); % Number of rows (4 in your case)
+
+    % Initialize the cell array for column names
+    col_names = cell(1, num_items * 5);
+
+    % Populate the column names
+    for i = 1:num_items
+        col_names{i} = sprintf('event02_rating0%d_displayonset', i);
+        col_names{num_items + i} = sprintf('event02_rating0%d_rating', i);
+        col_names{2*num_items + i} = sprintf('event02_rating0%d_RT', i);
+        col_names{3*num_items + i} = sprintf('event02_rating0%d_biopac_displayonset', i);
+        col_names{4*num_items + i} = sprintf('event02_rating0%d_biopac_response', i);
+    end
+    % Concatenate the data into one matrix in the correct order
+    data_matrix = [rating_onset, rating_value, rating_RT, biopac_displayonset, biopac_response];
+
+    % Convert the matrix to a table
+    T = array2table(data_matrix, 'VariableNames', col_names);
+
+    %% combine the rating dataframe with another dataframe with parameter and video onset data
+    src_subject_id = repmat(1, num_rows, 1);
+    session_id = repmat(1, num_rows, 1);
+    param_run_num = repmat(run_num, num_rows, 1);
+    param_trigger_onset = repmat(explog.param_trigger_onset(run_num), num_rows, 1);
+    param_start_biopac = NaN(num_rows, 1);
+    param_video_filename = selected_filenames';
+
+    % Derive event01_video_onset and event01_video_end
+    event01_video_onset = NaN(num_rows, 1);
+    event01_video_end = NaN(num_rows, 1);
+    range_idx = run_ranges{run_num};
+    event01_video_onset(1:numel(range_idx)) = explog.movie_start(range_idx);
+    event01_video_end(1:numel(range_idx)) = explog.movie_end(range_idx);
+    event01_video_biopac = NaN(num_rows, 1);
+
+    % Create the new columns table
+    new_columns = table(src_subject_id, session_id, param_run_num, param_trigger_onset, ...
+        param_start_biopac, param_video_filename, event01_video_onset, event01_video_biopac, event01_video_end);
+
+    % Ensure that the new_columns and T have the same number of rows before concatenating
+    if size(new_columns, 1) == size(T, 1)
+        combinedT = [new_columns T];
+    else
+        error('Row mismatch between new_columns and T for run %d', run_num);
+    end
+
+    new_order = {'src_subject_id','session_id','param_run_num','param_trigger_onset','param_start_biopac','param_video_filename','event01_video_onset','event01_video_biopac','event01_video_end','event02_rating01_displayonset','event02_rating02_displayonset','event02_rating03_displayonset'	'event02_rating04_displayonset','event02_rating05_displayonset','event02_rating06_displayonset','event02_rating07_displayonset','event02_rating01_rating','event02_rating02_rating','event02_rating03_rating','event02_rating04_rating','event02_rating05_rating','event02_rating06_rating','event02_rating07_rating','event02_rating01_RT','event02_rating02_RT','event02_rating03_RT','event02_rating04_RT','event02_rating05_RT','event02_rating06_RT','event02_rating07_RT','event02_rating01_biopac_displayonset','event02_rating02_biopac_displayonset','event02_rating03_biopac_displayonset','event02_rating04_biopac_displayonset',	'event02_rating05_biopac_displayonset','event02_rating06_biopac_displayonset',	'event02_rating07_biopac_displayonset','event02_rating01_biopac_response','event02_rating02_biopac_response','event02_rating03_biopac_response','event02_rating04_biopac_response','event02_rating05_biopac_response','event02_rating06_biopac_response',	'event02_rating07_biopac_response'};
+    T_reordered = combinedT(:, new_order);
+    % Save the table to a file
+    filename = sprintf('/Users/h/Documents/projects_local/1076_spacetop/sourcedata/d_beh/sub-0001/task-alignvideos/ses-01/sub-0001_ses-01_task-alignvideos_run-%02d_beh.csv', run_num);
+    writetable(T_reordered, filename);
+end
+end
+%%%%%%%

spacetop_prep/events/bidsify_social_factorize_ENH.py

@@ -257,12 +257,12 @@ def process_task(task_name, filtered_file_list, logger, metadata_df):
             except Exception as e:
                 logger.error(f"An error occurred while processing the trajectory file: {e}")
         else:
-            if args.bids_string:
-                beh_df['event02_expect_fillna'] = 'n/a'
-                beh_df['event04_outcome_fillna'] = 'n/a'
-                logger.info(f"Skipping trajectory processing for {args.bids_string} as no trajectory file exists.")
-            else:
-                logger.warning(f"No trajectory data found for {sub_bids}, {ses_bids}, {run_bids}. No BIDS string provided.")
+            # if args.bids_string:
+            beh_df['event02_expect_fillna'] = 'n/a'
+            beh_df['event04_outcome_fillna'] = 'n/a'
+            # logger.info(f"Skipping trajectory processing for {args.bids_string} as no trajectory file exists.")
+            # else:
+            logger.warning(f"No trajectory data found for {sub_bids}, {ses_bids}, {run_bids}. No BIDS string provided.")
 
         # Process cue, expect, stim, outcome, and save to CSV
         process_behavioral_data(cue, expect, stim, outcome, beh_df, traj_df, trigger, task_name, beh_savedir, sub_bids, ses_bids, run_bids, logger)
@@ -455,7 +455,7 @@ def main():
             run = extract_bids(fname, 'run')
 
             filtered_file_list = glob.glob(
-                str(Path(beh_inputdir) / sub / '**' / 'task-social' / '**' / f'*{args.bids_string}*.csv'),
+                str(Path(beh_inputdir) / sub / '**' / 'task-social' / '**' / f'*{sub}*{ses}*task-social*{run}*.csv'),
                 recursive=True)
 
             if not filtered_file_list: