From dd1d1af47ce26dc91c9a6cd3de5d1ed212cf59e0 Mon Sep 17 00:00:00 2001
From: shanemckeon <sdm63@pitt.edu>
Date: Fri, 22 Nov 2024 16:27:13 -0500
Subject: [PATCH] updating gitignore and preproc function

---
 .gitignore                                    |  2 ++
 Preprocessing_Functions/all_remarked_set.m    |  2 +-
 .../preprocessing_pipeline.m                  |  6 ++--
 .../run_preprocessing_pipeline.m              | 29 +++++++------------
 4 files changed, 17 insertions(+), 22 deletions(-)

diff --git a/.gitignore b/.gitignore
index 91af1de..d50bb39 100755
--- a/.gitignore
+++ b/.gitignore
@@ -52,3 +52,5 @@ choice-landscape/
 0c43526d20387f01a0f149d0888f1f5d27d85850
 preprocessed_data/
 Signal_Complexity/
+EEGcoordinates/
+attic/
diff --git a/Preprocessing_Functions/all_remarked_set.m b/Preprocessing_Functions/all_remarked_set.m
index 9fbd30c..45bd666 100755
--- a/Preprocessing_Functions/all_remarked_set.m
+++ b/Preprocessing_Functions/all_remarked_set.m
@@ -1,4 +1,4 @@
-function [setfiles] = all_remarked_set(setfilesDir, varargin)
+function [setfiles] = all_remarked_set(setfilesDir,varargin)
 % ALL_REMARKED_SET - return cell array of paths to initial set files
  % handle options
     p = inputParser;
diff --git a/Preprocessing_Functions/preprocessing_pipeline.m b/Preprocessing_Functions/preprocessing_pipeline.m
index 0f46090..1d01937 100755
--- a/Preprocessing_Functions/preprocessing_pipeline.m
+++ b/Preprocessing_Functions/preprocessing_pipeline.m
@@ -15,8 +15,8 @@
 subj_files = file_locs(inputfile, outpath, task);
 
 % to know how far your script is with running
-fprintf('==========\n%s:\n\t Initial Preprocessing(%s,%f,%f,%s)\n',...
-    currentName, inputfile, lowBP, topBP, outpath)
+fprintf('==========\n%s:\n\t Initial Preprocessing(%s,%f,%f,%s,%s)\n',...
+    currentName, inputfile, lowBP, topBP, outpath,task)
 
 
 % where to save things
@@ -61,7 +61,7 @@
     return
 end
 
-if condition == 1
+if condition == 1 
     xEEG = load_if_exists(subj_files.filter);
 end
 
diff --git a/Preprocessing_Functions/run_preprocessing_pipeline.m b/Preprocessing_Functions/run_preprocessing_pipeline.m
index 1358118..07c76f5 100755
--- a/Preprocessing_Functions/run_preprocessing_pipeline.m
+++ b/Preprocessing_Functions/run_preprocessing_pipeline.m
@@ -33,32 +33,24 @@
 % gather all file paths for all subjects remarked data 
 setfilesDir = [taskdirectory, '/remarked/1*_20*.set'];    
 setfiles = all_remarked_set(setfilesDir);
-
 n = size(setfiles,1); %number of EEG sets to preprocess
 
-% first steps of preprocessing then epoch anti data first so we do not lose events 
-if task == "anti"
-    path_data = [taskdirectory '/remarked/'];
-    epoch_folder = [taskdirectory '/epoched/'];
-    EEGfileNames = dir([path_data, '/*_Rem.set']);
-
-    revisar = {};
-    for currentEEG = 1:size(EEGfileNames,1)
-        % skipping weird participants for now (38 = 11632_201901001, 87 = 11681_2018011, 100 = 11688-20190614, 291 = 11821_320210630)
-        if currentEEG == 38 || currentEEG == 87 || currentEEG == 100 || currentEEG == 291
-            continue
-        end
-        filename = [EEGfileNames(currentEEG).name];
-        inputfile = [path_data,filename];
-        revisar{currentEEG} = epochAS(inputfile,epoch_folder,task,taskdirectory,condition,lowBP,topBP);
-    end
+% some participants are left out from lines 33 and 34 for AS
+if task=="anti"
+    setfilesDir = [taskdirectory, '/remarked/*.set'];
+    setfiles = all_remarked_setAS(setfilesDir);
+    n = length(setfiles);
 end
 
 % loop through every subject to preprocess
 for i = 1:n
     inputfile = setfiles{i};
     try
-      preprocessing_pipeline(inputfile, taskdirectory, lowBP, topBP, FLAG, condition, task)
+        if task ~= "anti"
+            preprocessing_pipeline(inputfile, taskdirectory, lowBP, topBP, FLAG, condition, task)
+        elseif task == "anti"
+            preprocessing_pipelineAS(inputfile,taskdirectory,lowBP,topBP,FLAG,condition,task)
+        end
    catch e
       fprintf('Error processing "%s": %s\n',inputfile, e.message)
       for s=e.stack
@@ -67,6 +59,7 @@
    end
 end
 
+
 %% select ICA values to reject
 
 ICA_Path = [taskdirectory '/ICAwhole'];