bachelor_thesis/DataAnalysisToolbox/extract_data.m

function dataOut = extract_data(file_nums, filter_choice)
%% Extract and filter data
% The function extracts all data from one or more ".mat" dataset file(s)
% and returns them as one structure per file wrapped in a cell array. If
% requested a filter can be applied to the recording data.
% ------------------------------------------------------------------------
% Input
%   file_num:      number of the required file in the directory
%   filter_choice: selction between two filter options: 
%                       'hn'    applys a hum-noise-remove filter
%                       'hnhfn' additonally applys a low pass filter to
%                               remove high frequency noise
%                       'no'    no filter will be applyed
% ------
% Output
% ------
%   rec_data:   a cell array containing one structure per requested file
%               Each structure contains the following data:
%                 - recordingT  (matrix, containing the recorded membrane
%                                potentials for the T cell for all trials, 
%                                data in mV)
%                 - recordingINT (matrix, containing the recorded membrane
%                                 potentials for the interneuron for all 
%                                 trials, data in mV)
%                 - stimulus (vector, containing the stimulation protocol
%                             of the experiment, data in nA)
%                 - timeVector (vector, suitable vector with time values
%                               for the recorded data, data in s)
%                 - stimulatedT (vector, giving the numbers of the trials
%                                with a stimulated T cell)
% ------------------------------------------------------------------------
% Program by Bjarne Schultze        [last modified 09.12.2021]
% ------------------------------------------------------------------------

%% Directory preparations
% get the current directory
old_cd = cd;

% change into the directory with the datasets and add directory with
% program files
cd ../CleanDatasets
addpath ../'DataAnalysisToolbox'/

%% Preperations for data extraction
% list all '.mat' files in the directory
mat_directory = dir('*.mat');   

% preallocate a cell array for data collection
dataOut = cell(length(file_nums),1);

for fileIndex = 1:length(file_nums)
    % check whether all file indices are in the valid range
    if max(file_nums) > length(mat_directory)
        warning("Index out of range! Check the requested file " + ...
            "index/indices.");
        break
    end

    % load the requested file                 
    load(mat_directory(file_nums(fileIndex)).name, "RecordingData");
    
%% Getting the recorded data and application of filters
    % optional application of a filter
    if isequal(filter_choice, 'hn')
        % filter the hum noise
        [~, RecordingData.recordingT] = ...
            removehumnoise(RecordingData.recordingT, 10000);
        [~, RecordingData.recordingINT] = ...
            removehumnoise(RecordingData.recordingINT, 10000);
    elseif isequal(filter_choice, 'hnhfn')
        % filter the hum noise plus high frequency noise
        [RecordingData.recordingT, ~] = ...
            removehumnoise(RecordingData.recordingT, 10000);
        [RecordingData.recordingINT, ~] = ...
            removehumnoise(RecordingData.recordingINT, 10000);
    end

    % collect the output data in the preallocated cell array
    dataOut{fileIndex, 1} = RecordingData;
end

% reset the current directory to the one from before the function call
cd(old_cd);

% end of function definition
end