BatchMiniscopeProcessing2.m

% Pipeline for processing the miniscope data
% USAGE: MasterPreProcessing_Intan(folder_name)
% where folder_name is the base name for everything 

function BatchMiniscopeProcessing2(fbasename, varargin)


files = dir();
dirFlags = [files.isdir];
% Extract only those that are directories.
subDirs = files(dirFlags);
subDirsNames = cell(1, numel(subDirs) - 2);
for i=3:numel(subDirs)
    subDirsNames{i-2} = subDirs(i).name;
end

[n_folders,~] = size(subDirsNames');

for ii=1:n_folders
    path = subDirsNames{ii};
    %if strcmp(path(1:4),'2021')
    if isequal(path(1:5), fbasename)
    
        cd(subDirsNames{ii});
        fprintf(path);
        %% Concatenate AVI files
%         spatial_downsampling = 2;

        dirName = pwd;
%         avifolder = [dirName filesep 'Miniscope'];
%         Process_ConcatenateAVI(avifolder, spatial_downsampling);

        %% CLEAN FOLDERS
        % go one folder up and rename
%         idcs = strfind(dirName, filesep);4
%         newDir = dirName(1:idcs(end)-1);
%         cd(newDir);
%         oldfoldername = dirName(idcs(end)+1:end);
%         tmp = erase(oldfoldername, '_');
%         newfoldername = [fbasename '-' tmp(3:end)];
%         mergename = [fbasename '-' tmp(3:end)];

%         movefile([newDir filesep oldfoldername], [newDir filesep newfoldername]);
%         cd([newDir filesep newfoldername]);
% 
%         % rename analogin and tracking
%         files = dir('Take*.csv');
%         if exist(files.name, 'file')
%             fname = files.name;
%             targetFile = fullfile(pwd, [mergename '_0.csv']);
%             movefile(fname, targetFile);
%         end
% 
%         files = dir('Take*.tak');
%         if exist(files.name, 'file')
%             fname = files.name;
%             targetFile = fullfile(pwd, [mergename '_0.tak']);
%             movefile(fname, targetFile);
%         end
% 
% 
%         % Copying analogin file if any exists 
%         intanfolder = dir([fbasename '_*']);
%         analoginfile = [intanfolder.name filesep 'analogin.dat'];
%         targetFile = fullfile(pwd, [mergename '_0_analogin.dat']);
%         movefile(analoginfile, targetFile);
% 
%         % rename raw avi file
%         avifile = dir('*.avi');
%         movefile(avifile.name, fullfile(pwd, [mergename '_raw.avi']));
% 
%         % rename json file
%         jsonfile = dir('*.json');
%         movefile(jsonfile.name, fullfile(pwd, [mergename '.json']));
% 
%         % move miniscope timestamps in case
%         tstamps = dir('Miniscope/*.csv');
% 
%         movefile(fullfile(tstamps.folder, tstamps.name), fullfile(pwd, [mergename '_ms_ts.csv']));
% 
%         %cleaning
%         system(['rm -r ' fullfile(pwd, intanfolder.name)]);
%         system(['rm -r ' fullfile(pwd, 'experiment')]);

        %% Normcorre
        % takes the raw avi file
%         [~,mergename] = fileparts(dirName);
%         avifile = fullfile(pwd, [mergename '_raw.avi']);
%         Process_normcorre(avifile, mergename);
% 
%         % Yf = read_file(fullfile(pwd, [mergename '.h5']));
% 
%         %% CNMF-E
%         neuron = Process_cnmfe(fullfile(pwd, [mergename '.h5']));
% 
% 
%         %% Exporting
%         % save as csv
%         csvwrite(fullfile(pwd, [mergename '_C.csv']), neuron.C);
%         csvwrite(fullfile(pwd, [mergename '_A.csv']), neuron.A);
%         csvwrite(fullfile(pwd, [mergename '_C_raw.csv']), neuron.C_raw);
%         csvwrite(fullfile(pwd, [mergename '_S.csv']), neuron.S);
%         %neuron.save_neurons();
%         neuron.save_results([mergename '_cnmfe.mat']);

        %pwd
        cd('~')
        [basepath, ~] = fileparts(dirName);
        cd(basepath);
    end
end


    

end