Sn lab ephys JL

.gitignore

@@ -1,4 +1,6 @@
 # Byte-compiled / optimized / DLL files
+.DS_Store
+
 __pycache__/
 *.py[cod]
 *$py.class

behavior/metagen_tools/meta.csv

@@ -0,0 +1,49 @@
+subid,basepath3,genotype,age,session_date,dob,vidname,basename,exposure,maze_width_cm,maze_length_cm,maze_type,maze_color,cue_position,task_name,condition,treatment,objects,paradigm,moved_object,trial_start_1,trial_stop_1,trial_start_2,trial_stop_2,trial_start_3,trial_stop_3,trial_start_4,trial_stop_4
+3764,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3764/3764_pairing_day02,,,07/19/23,,3764B_pairing2_A-07192023091159.avi,3764_pairing_day02,3,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3764,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3764/3764_pairing_day02,,,07/19/23,,3764B_pairing2_B-07192023093033.avi,3764_pairing_day02,3,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3764,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3764/3764_pairing_posttest_day03,,,07/20/23,,3764B_pairing3_A-07202023085140.avi,3764_pairing_posttest_day03,4,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3764,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3764/3764_pairing_posttest_day03,,,07/20/23,,3764B_pairing3_B-07202023091025.avi,3764_pairing_posttest_day03,4,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3764,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3764/3764_pairing_posttest_day03,,,07/20/23,,3764B_posttest-07202023112613.avi,3764_pairing_posttest_day03,5,70.5,39,dual_open_field,multi,none,cpp,posttest,none,none,none,none,,,,,,,,
+3764,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3764/3764_pretest_pairing_day01,,,07/18/23,,3764B_pretest-07182023081455.avi,3764_pretest_pairing_day01,1,70.5,39,dual_open_field,multi,none,cpp,pretest,none,none,none,none,,,,,,,,
+3764,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3764/3764_pretest_pairing_day01,,,07/18/23,,3764B_pairing1_A-07182023111801.avi,3764_pretest_pairing_day01,2,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3764,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3764/3764_pretest_pairing_day01,,,07/18/23,,3764B_pairing1_B-07182023113748.avi,3764_pretest_pairing_day01,2,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3771,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3771/3771_pairing_day02,,,07/19/23,,3771B_pairing2_B-07192023083410.avi,3771_pairing_day02,3,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3771,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3771/3771_pairing_day02,,,07/19/23,,3771B_pairing2_A-07192023085211.avi,3771_pairing_day02,3,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3771,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3771/3771_pairing_posttest_day03,,,07/20/23,,3771B_pairing3_B-07202023081500.avi,3771_pairing_posttest_day03,4,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3771,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3771/3771_pairing_posttest_day03,,,07/20/23,,3771B_pairing3_A-07202023083358.avi,3771_pairing_posttest_day03,4,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3771,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3771/3771_pairing_posttest_day03,,,07/20/23,,3771B_posttest-07202023105132.avi,3771_pairing_posttest_day03,5,70.5,39,dual_open_field,multi,none,cpp,posttest,none,none,none,none,,,,,,,,
+3771,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3771/3771_pretest_pairing_day01,,,07/18/23,,3771B_pretest-07182023075122.avi,3771_pretest_pairing_day01,1,70.5,39,dual_open_field,multi,none,cpp,pretest,none,none,none,none,,,,,,,,
+3771,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3771/3771_pretest_pairing_day01,,,07/18/23,,3771B_pairing1_B-07182023104044.avi,3771_pretest_pairing_day01,2,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3771,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3771/3771_pretest_pairing_day01,,,07/18/23,,3771B_pairing1_A-07182023105905.avi,3771_pretest_pairing_day01,2,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3772,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3772/3772_pairing_day02,,,07/19/23,,3772_2L_pairing2_A-07192023094939.avi,3772_pairing_day02,3,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3772,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3772/3772_pairing_day02,,,07/19/23,,3772_2L_pairing2_B-07192023100822.avi,3772_pairing_day02,3,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3772,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3772/3772_pairing_posttest_day03,,,07/20/23,,37722L_pairing3_A-07202023122808.avi,3772_pairing_posttest_day03,4,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3772,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3772/3772_pairing_posttest_day03,,,07/20/23,,37722L_pairing3_B-07202023124648.avi,3772_pairing_posttest_day03,4,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3772,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3772/3772_pairing_posttest_day03,,,07/20/23,,3772_2L_posttest-07202023145207.avi,3772_pairing_posttest_day03,5,70.5,39,dual_open_field,multi,none,cpp,posttest,none,none,none,none,,,,,,,,
+3772,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3772/3772_pretest_pairing_day01,,,07/18/23,,3772_2L_pretest-07182023090021.avi,3772_pretest_pairing_day01,1,70.5,39,dual_open_field,multi,none,cpp,pretest,none,none,none,none,,,,,,,,
+3772,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3772/3772_pretest_pairing_day01,,,07/18/23,,3772_2L_pairing1_A-07182023123224.avi,3772_pretest_pairing_day01,2,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3772,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3772/3772_pretest_pairing_day01,,,07/18/23,,3772_2L_pairing1_B-07182023125037.avi,3772_pretest_pairing_day01,2,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3773,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3773/3773_pairing_day02,,,07/19/23,,3773_2R_pairing2_A-07192023102757.avi,3773_pairing_day02,3,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3773,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3773/3773_pairing_day02,,,07/19/23,,3773_2R_pairing2_B-07192023104612.avi,3773_pairing_day02,3,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3773,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3773/3773_pairing_posttest_day03,,,07/20/23,,37732R_pairing3_A-07202023115142.avi,3773_pairing_posttest_day03,4,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3773,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3773/3773_pairing_posttest_day03,,,07/20/23,,37732R_pairing3_B-07202023121018.avi,3773_pairing_posttest_day03,4,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3773,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3773/3773_pairing_posttest_day03,,,07/20/23,,37732R_posttest-07202023143003.avi,3773_pairing_posttest_day03,5,70.5,39,dual_open_field,multi,none,cpp,posttest,none,none,none,none,,,,,,,,
+3773,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3773/3773_pretest_pairing_day01,,,07/18/23,,3773_2R_pretest-07182023083909.avi,3773_pretest_pairing_day01,1,70.5,39,dual_open_field,multi,none,cpp,pretest,none,none,none,none,,,,,,,,
+3773,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3773/3773_pretest_pairing_day01,,,07/18/23,,3773_2R_pairing1_A-07182023115612.avi,3773_pretest_pairing_day01,2,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3773,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3773/3773_pretest_pairing_day01,,,07/18/23,,3773_2R_pairing1_B-07182023121418.avi,3773_pretest_pairing_day01,2,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3774,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3774/3774_pairing_day02,,,07/19/23,,3774_1L2R_pairing2_A-07192023072034.avi,3774_pairing_day02,3,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3774,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3774/3774_pairing_day02,,,07/19/23,,3774_1L2R_pairing2_B-07192023073959.avi,3774_pairing_day02,3,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3774,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3774/3774_pairing_posttest_day03,,,07/20/23,,3774_1L2R_pairing3_A-07202023070217.avi,3774_pairing_posttest_day03,4,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3774,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3774/3774_pairing_posttest_day03,,,07/20/23,,3774_1L2R_pairing3_B-07202023072019.avi,3774_pairing_posttest_day03,4,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3774,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3774/3774_pairing_posttest_day03,,,07/20/23,,3774_1L2R_posttest-07202023093643.avi,3774_pairing_posttest_day03,5,70.5,39,dual_open_field,multi,none,cpp,posttest,none,none,none,none,,,,,,,,
+3774,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3774/3774_pretest_pairing_day01,,,07/18/23,,3774_1L2R_pretest-07182023071222.avi,3774_pretest_pairing_day01,1,70.5,39,dual_open_field,multi,none,cpp,pretest,none,none,none,none,,,,,,,,
+3774,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3774/3774_pretest_pairing_day01,,,07/18/23,,3774_2L1R_pairing1_A-07182023092833.avi,3774_pretest_pairing_day01,2,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
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+3803,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3803/3803_pairing_day02,,,07/19/23,,3803R_pairing2_B-07192023075828.avi,3803_pairing_day02,3,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3803,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3803/3803_pairing_day02,,,07/19/23,,3803R_pairing2_A-07192023081608.avi,3803_pairing_day02,3,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3803,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3803/3803_pairing_posttest_day03,,,07/20/23,,3803R_pairing3_B-07202023073811.avi,3803_pairing_posttest_day03,4,23,39,open_field,blue,none,cpp,pairing,none,none,none,none,,,,,,,,
+3803,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3803/3803_pairing_posttest_day03,,,07/20/23,,3803R_pairing3_A-07202023075635.avi,3803_pairing_posttest_day03,4,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,
+3803,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3803/3803_pairing_posttest_day03,,,07/20/23,,3803R_posttest-07202023101229.avi,3803_pairing_posttest_day03,5,70.5,39,dual_open_field,multi,none,cpp,posttest,none,none,none,none,,,,,,,,
+3803,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3803/3803_pretest_pairing_day01,,,07/18/23,,3803R_pretest-07182023073125.avi,3803_pretest_pairing_day01,1,70.5,39,dual_open_field,multi,none,cpp,pretest,none,none,none,none,,,,,,,,
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+3803,/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3/3803/3803_pretest_pairing_day01,,,07/18/23,,3803R_pairing1_A-07182023102215.avi,3803_pretest_pairing_day01,2,23,39,open_field,yellow,none,cpp,pairing,none,none,none,none,,,,,,,,

behavior/metagen_tools/tablegen.m

@@ -0,0 +1,132 @@
+
+function output = tablegen (basepath)
+    % Get all the videos from the directory
+    file_struct = dir(fullfile(basepath,'*.avi'));
+    %remove hidden files
+    file_struct = file_struct(~startsWith({file_struct.name}, '.'));
+    % Extract base name
+    bstring=char(basepath);
+    File_name=bstring(1+max(strfind(basepath,'/')):end); % ***** edit '\' or '/' depending on mac or windows
+    % Extract the timestamps from the filenames
+    timestamps = regexp({file_struct.name}, '-\d+', 'match');
+    timestamps = cellfun(@(x) extractAfter(x,'-'),timestamps,'UniformOutput',false);
+    timestamps = cellfun(@(x) str2double(x),timestamps,'UniformOutput',false);
+    [~, sortedIndices] = sort( [timestamps{:}]);
+    file_struct=file_struct(sortedIndices);
+    subid=[];
+    basepath3=[];
+    genotype=[];
+    age=[];
+    session_date=[];
+    dob=[];
+    vidname=[];
+    basename=[];
+    exposure=[];
+    maze_width_cm=[];
+    maze_length_cm=[];
+    maze_type=[];
+    maze_color=[];
+    cue_position=[];
+    task_name=[];
+    condition=[];
+    treatment=[];
+    objects=[];
+    paradigm=[];
+    moved_object=[];
+    trial_start_1=[];
+    trial_stop_1=[];
+    trial_start_2=[];
+    trial_stop_2=[];
+    trial_start_3=[];
+    trial_stop_3=[];
+    trial_start_4=[];
+    trial_stop_4=[];
+    % none columns
+    none=[];
+    for i=1:length(sortedIndices)
+        %nones and constant columns
+        maze_length_cm=[maze_length_cm;39];
+        none=[none;"none"];
+        task_name=[task_name;"cpp"];
+        %subid
+        vid=file_struct(i).name;
+        subid=[subid;vid(1:4)];
+        %Basepath
+        pos=find(sortedIndices==i);
+        basepath3=[basepath3;string(basepath)];
+        %Session Date
+        daytemp=extractBefore(file_struct(pos).date," "); 
+        date=datetime(daytemp, 'InputFormat', 'dd-MMM-yyyy');
+        date=datestr(date, 'mm/dd/yy');
+        session_date=[session_date;string(date)];
+        %video name
+        vidname=[vidname;string(vid)];
+        %base name
+        basename=[basename;string(File_name)];
+        %exposure and condition
+
+        if contains(basename,'pretest')
+
+            if contains(vid,'pretest')
+                condition=[condition;"pretest"];
+                exposure=[exposure;1];
+            elseif contains(vid,'pairing')|| contains(vid,'paring')
+                exposure=[exposure;2];
+                condition=[condition;"pairing"];
+            end
+         elseif contains(basename,'posttest')
+            if contains(vid,'posttest')
+                exposure=[exposure;5];
+                condition=[condition;"posttest"];
+
+            elseif contains(vid,'pairing')|| contains(vid,'paring')
+                exposure=[exposure;4];
+                condition=[condition;"pairing"];
+
+            end
+        elseif contains(basename,'day02')
+            condition=[condition;"pairing"];
+            exposure=[exposure;3];
+        else
+            condition=[condition;'pairinadsfafdsfsdg'];
+            exposure=[exposure;9];
+        end
+        %maze width and type and color
+        if contains(vid, 'pairing') || contains(vid, 'paring')
+            maze_width_cm=[maze_width_cm;23];
+            maze_type=[maze_type;"open_field"];
+            if contains(vid, '_A-')
+                maze_color=[maze_color;"yellow"];
+            elseif contains(vid, '_B-')
+                maze_color=[maze_color;"blue"];
+            end
+        else
+            maze_width_cm=[maze_width_cm;70.5];
+            maze_type=[maze_type;"dual_open_field"];
+            maze_color=[maze_color;"multi"];
+        end
+    end
+    %NaN and none columns
+    na=cell(length(none), 1);
+    trial_start_1=na;
+    trial_stop_1=na;
+    trial_start_2=na;
+    trial_stop_2=na;
+    trial_start_3=na;
+    trial_stop_3=na;
+    trial_start_4=na;
+    trial_stop_4=na;
+    genotype=na;
+    age=na;
+    dob=na;
+    objects=none;
+    cue_position=none;
+    paradigm=none;
+    moved_object=none;
+    treatment=none;
+    notes=na;
+    output=table(subid,basepath3,genotype,age,session_date,dob,vidname,basename,exposure,...
+        maze_width_cm,maze_length_cm,maze_type,maze_color,cue_position,task_name,condition,...
+        treatment,objects,paradigm,moved_object,trial_start_1,trial_stop_1,trial_start_2,...
+        trial_stop_2,trial_start_3,trial_stop_3,trial_start_4,trial_stop_4);
+

behavior/metagen_tools/tablegen_script.m

@@ -0,0 +1,59 @@
+% get all the folder paths
+function tablegen_script (cohortpath)
+    basepath=pathGetter(cohortpath);
+    output=table();
+    for i=1:length(basepath)
+        bp=string(basepath(i));
+        output=vertcat(output,tablegen(bp));
+    end
+    csv = 'meta.csv';
+
+    % Write the table to a CSV file
+    writetable(output, csv);
+
+end
+
+
+
+function aviFilePaths = pathGetter (cohortpath)
+%Gets all the filepaths of folders that contain avi files
+%cohortpath: filepath of the main folder
+    tempanimals=dir(fullfile(string(cohortpath),'*'));
+    animals=fullfile(cohortpath,{tempanimals(~startsWith({tempanimals.name}, '.')).name});
+    [~,~,ext]=fileparts(animals);
+    aviFilePaths={};
+    if ismember('.avi',ext)
+        aviFilePaths=[aviFilePaths,cohortpath];
+    elseif isfolder(animals)
+        for x=animals
+            aviFilePaths=[aviFilePaths,pathGetter(x)]; 
+        end
+    end
+end
+% 
+% %List of the animal folder paths ****** edit here
+% cohortpath='/Volumes/sn data server 3/laura_berkowitz/behavior_validation/appps1_cpp/data/cohort3';
+% tempanimals = dir(fullfile(cohortpath,'*'));
+% animals=fullfile(cohortpath,{tempanimals(~startsWith({tempanimals.name}, '.')).name});
+% num=length(animals);
+% basepath={};
+% %Fix order of files   *****change depending on alphabetical ordering
+% order=[3,1,2];
+% for i=1:num
+%     path = string(animals(i));  % Specify the folder path
+%     file_struct = dir(fullfile(path,'*day*'));
+%     paths = fullfile(path, {file_struct.name});
+%     paths = paths(order);
+%     for j=1:length(paths)    
+%         basepath{end+1}=paths(j);
+%     end
+% end
+% output=table();
+% for i=1:length(basepath)
+%     bp=string(basepath(i));
+%     output=vertcat(output,tablegen(bp));
+% end
+% csv = 'meta.csv';
+% 
+% % Write the table to a CSV file
+% writetable(output, csv);