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myh/dataProcessing/bci/import_BCIsummary.m
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import_BCIsummary.m
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%% Import data from spreadsheet
% Script for importing data from the following spreadsheet:
%
% Workbook: D:\Sinergia\Data collection (BCI and tDCS)\bci\clinical_analyses\data\bci_summary.xlsx
% Worksheet: bci
%
% To extend the code for use with different selected data or a different
% spreadsheet, generate a function instead of a script.
% Auto-generated by MATLAB on 2020/06/15 15:43:04
%% Import the data, extracting spreadsheet dates ins Excel serial date format
% in xlsread function, the range has to be change according to the number
% of line of the .xlsx file
% [~, ~, raw, dates] = xlsread('data/bci_summary.xlsx','bci','A2:BQ28','',@convertSpreadsheetExcelDates);
[~, ~, raw, dates] = xlsread('data/bci_summary.xlsx','bci','','',@convertSpreadsheetExcelDates);
raw(cellfun(@(x) ~isempty(x) && isnumeric(x) && isnan(x),raw)) = {''};
stringVectors = string(raw(:,[4,6,7,8,10,19,23,25,26,27,31,43,47,49,50,58,62,64,65,66,69]));
stringVectors(ismissing(stringVectors)) = '';
raw = raw(:,[1,2,3,11,13,15,17,20,21,29,33,34,36,37,39,41,44,45,52,54,56,59,60,68]);
dates = dates(:,[5,9,12,14,16,18,22,24,28,30,32,35,38,40,42,46,48,51,53,55,57,61,63,67]);
%% Replace non-numeric cells with NaN
R = cellfun(@(x) ~isnumeric(x) && ~islogical(x),raw); % Find non-numeric cells
raw(R) = {NaN}; % Replace non-numeric cells
R = cellfun(@(x) ~isnumeric(x) && ~islogical(x),dates); % Find non-numeric cells
dates(R) = {NaN}; % Replace non-numeric Excel dates with NaN
%% Create output variable
data = reshape([raw{:}],size(raw));
%% Create table
bcisummary = table;
%% Allocate imported array to column variable names
bcisummary.patient_id_hug = data(:,1);
bcisummary.patient_id_all_sites = data(:,2);
bcisummary.subject_id = data(:,3);
bcisummary.sex = categorical(stringVectors(:,1));
bcisummary.date_of_birth = datetime([dates{:,1}].', 'ConvertFrom', 'Excel');
bcisummary.lesion_side = categorical(stringVectors(:,2));
bcisummary.affected_upperlimbside = categorical(stringVectors(:,3));
bcisummary.lateralisation = categorical(stringVectors(:,4));
bcisummary.stroke_date = datetime([dates{:,2}].', 'ConvertFrom', 'Excel');
bcisummary.stroke_location = categorical(stringVectors(:,5));
bcisummary.treatment = data(:,4);
bcisummary.questionnaire_motivaton_pre_date = datetime([dates{:,3}].', 'ConvertFrom', 'Excel');
bcisummary.questionnaire_motivaton_pre = data(:,5);
bcisummary.fma_pre_date = datetime([dates{:,4}].', 'ConvertFrom', 'Excel');
bcisummary.fma_prescore = data(:,6);
bcisummary.arat_pre_date = datetime([dates{:,5}].', 'ConvertFrom', 'Excel');
bcisummary.arat_prescore = data(:,7);
bcisummary.jamar_pre_date = datetime([dates{:,6}].', 'ConvertFrom', 'Excel');
bcisummary.jamar_comment = stringVectors(:,6);
bcisummary.jamar_ASprescoreKgF = data(:,8);
bcisummary.jamar_USprescoreKgF = data(:,9);
bcisummary.ashworth_pre_date = datetime([dates{:,7}].', 'ConvertFrom', 'Excel');
bcisummary.ashworth_prescore = stringVectors(:,7);
bcisummary.monofilament_pre_date = datetime([dates{:,8}].', 'ConvertFrom', 'Excel');
bcisummary.monofilament_comment = stringVectors(:,8);
bcisummary.monofilament_ASprescore = stringVectors(:,9);
bcisummary.monofilament_USprescore = categorical(stringVectors(:,10));
bcisummary.mif_pre_date = datetime([dates{:,9}].', 'ConvertFrom', 'Excel');
bcisummary.mif_prescore = data(:,10);
bcisummary.questionnaire_motivaton_post_date = datetime([dates{:,10}].', 'ConvertFrom', 'Excel');
bcisummary.questionnaire_motivaton_post = stringVectors(:,11);
bcisummary.tms_pre_date = datetime([dates{:,11}].', 'ConvertFrom', 'Excel');
bcisummary.tms_preASMT = data(:,11);
bcisummary.tms_preUSMT = data(:,12);
bcisummary.tms_post_date = datetime([dates{:,12}].', 'ConvertFrom', 'Excel');
bcisummary.tms_postASMT = data(:,13);
bcisummary.tms_postUSMT = data(:,14);
bcisummary.fma_post_date = datetime([dates{:,13}].', 'ConvertFrom', 'Excel');
bcisummary.fma_postscore = data(:,15);
bcisummary.arat_post_date = datetime([dates{:,14}].', 'ConvertFrom', 'Excel');
bcisummary.arat_postscore = data(:,16);
bcisummary.jamar_post_date = datetime([dates{:,15}].', 'ConvertFrom', 'Excel');
bcisummary.jamar_post_comment = stringVectors(:,12);
bcisummary.jamar_ASpostscoreKgF = data(:,17);
bcisummary.jamar_USpostscoreKgF = data(:,18);
bcisummary.ashworth_post_date = datetime([dates{:,16}].', 'ConvertFrom', 'Excel');
bcisummary.ashworth_postscore = stringVectors(:,13);
bcisummary.monofilament_post_date = datetime([dates{:,17}].', 'ConvertFrom', 'Excel');
bcisummary.monofilament_ASpostscore = stringVectors(:,14);
bcisummary.monofilament_USpostscore = stringVectors(:,15);
bcisummary.mif_post_date = datetime([dates{:,18}].', 'ConvertFrom', 'Excel');
bcisummary.mif_postscore = data(:,19);
bcisummary.fma_3monthpoststroke_date = datetime([dates{:,19}].', 'ConvertFrom', 'Excel');
bcisummary.fma_3monthpoststrokescore = data(:,20);
bcisummary.arat_3monthpoststroke_date = datetime([dates{:,20}].', 'ConvertFrom', 'Excel');
bcisummary.arat_3monthpoststrokescore = data(:,21);
bcisummary.jamar_3monthpoststroke_date = datetime([dates{:,21}].', 'ConvertFrom', 'Excel');
bcisummary.jamar_comment1 = stringVectors(:,16);
bcisummary.jamar_AS3monthpoststrokescoreKgF = data(:,22);
bcisummary.jamar_US3monthpoststrokescoreKgF = data(:,23);
bcisummary.ashworth_3monthpoststroke_date = datetime([dates{:,22}].', 'ConvertFrom', 'Excel');
bcisummary.ashworth_3monthpoststrokescore = stringVectors(:,17);
bcisummary.monofilament_3monthpoststroke_date = datetime([dates{:,23}].', 'ConvertFrom', 'Excel');
bcisummary.monofilament_comment1 = stringVectors(:,18);
bcisummary.monofilament_AS3monthpoststrokescore = stringVectors(:,19);
bcisummary.monofilament_US3monthpoststrokescore = categorical(stringVectors(:,20));
bcisummary.mif_3monthpoststroke_date = datetime([dates{:,24}].', 'ConvertFrom', 'Excel');
bcisummary.mif_3monthpoststrokescore = data(:,24);
bcisummary.comments = stringVectors(:,21);
% For code requiring serial dates (datenum) instead of datetime, uncomment
% the following line(s) below to return the imported dates as datenum(s).
% bcisummaryS1.date_of_birth=datenum(bcisummaryS1.date_of_birth);
% bcisummaryS1.stroke_date=datenum(bcisummaryS1.stroke_date);
% bcisummaryS1.questionnaire_motivaton_pre_date=datenum(bcisummaryS1.questionnaire_motivaton_pre_date);bcisummaryS1.fma_pre_date=datenum(bcisummaryS1.fma_pre_date);
% bcisummaryS1.arat_pre_date=datenum(bcisummaryS1.arat_pre_date);
% bcisummaryS1.jamar_pre_date=datenum(bcisummaryS1.jamar_pre_date);
% bcisummaryS1.ashworth_pre_date=datenum(bcisummaryS1.ashworth_pre_date);
% bcisummaryS1.monofilament_pre_date=datenum(bcisummaryS1.monofilament_pre_date);bcisummaryS1.mif_pre_date=datenum(bcisummaryS1.mif_pre_date);
% bcisummaryS1.questionnaire_motivaton_post_date=datenum(bcisummaryS1.questionnaire_motivaton_post_date);bcisummaryS1.tms_pre_date=datenum(bcisummaryS1.tms_pre_date);
% bcisummaryS1.tms_post_date=datenum(bcisummaryS1.tms_post_date);
% bcisummaryS1.fma_post_date=datenum(bcisummaryS1.fma_post_date);
% bcisummaryS1.arat_post_date=datenum(bcisummaryS1.arat_post_date);
% bcisummaryS1.jamar_post_date=datenum(bcisummaryS1.jamar_post_date);
% bcisummaryS1.ashworth_post_date=datenum(bcisummaryS1.ashworth_post_date);
% bcisummaryS1.monofilament_post_date=datenum(bcisummaryS1.monofilament_post_date);bcisummaryS1.mif_post_date=datenum(bcisummaryS1.mif_post_date);
% bcisummaryS1.fma_3monthpoststroke_date=datenum(bcisummaryS1.fma_3monthpoststroke_date);bcisummaryS1.arat_3monthpoststroke_date=datenum(bcisummaryS1.arat_3monthpoststroke_date);bcisummaryS1.jamar_3monthpoststroke_date=datenum(bcisummaryS1.jamar_3monthpoststroke_date);bcisummaryS1.ashworth_3monthpoststroke_date=datenum(bcisummaryS1.ashworth_3monthpoststroke_date);bcisummaryS1.monofilament_3monthpoststroke_date=datenum(bcisummaryS1.monofilament_3monthpoststroke_date);bcisummaryS1.mif_3monthpoststroke_date=datenum(bcisummaryS1.mif_3monthpoststroke_date);
%% Clear temporary variables and NaN rows
clearvars data raw dates stringVectors R;
bcisummary = rmmissing(bcisummary,'DataVariables',{'patient_id_hug'});
%% Modify column
% Change the treatment naming
treatmentinstring = categorical(bcisummary.treatment);
treatmentinstring(treatmentinstring == '0') = 'sham';
treatmentinstring(treatmentinstring == '1') = 'bci';
treatmentinstring(treatmentinstring == '-1') = 'drop-out';
bcisummary.treatment = treatmentinstring;
% Add sites label
experiment_site = categorical(cellstr(repmat('HUG', size(bcisummary, 1), 1)));
bcisummary.experiment_site = categorical(experiment_site);
bcisummary = movevars(bcisummary, 'experiment_site', 'After', 'subject_id');
% Change first variable name
bcisummary.Properties.VariableNames{'patient_id_hug'} = 'patient_id';
save 'data\raw_bcisummary' bcisummary;
clearvars treatmentinstring experiment_site
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