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myh/dataProcessing/bci/bci_adrian/import_BCIsummary_venice.m
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import_BCIsummary_venice.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_venice.xlsx
% Worksheet: bci_venice
%
% 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 2020/06/16 13:09:30
%% Import the data, extracting spreadsheet dates in Excel serial date format
[~, ~, raw, dates] = xlsread('data\bci_summary_venice.xlsx','bci_venice','','',@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
bcisummaryvenice = table;
%% Allocate imported array to column variable names
bcisummaryvenice.patient_id_ven = data(:,1);
bcisummaryvenice.patient_id_all_sites = data(:,2);
bcisummaryvenice.subject_id = data(:,3);
bcisummaryvenice.sex = categorical(stringVectors(:,1));
bcisummaryvenice.date_of_birth = datetime([dates{:,1}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.lesion_side = categorical(stringVectors(:,2));
bcisummaryvenice.affected_upperlimbside = categorical(stringVectors(:,3));
bcisummaryvenice.lateralisation = categorical(stringVectors(:,4));
bcisummaryvenice.stroke_date = datetime([dates{:,2}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.stroke_location = categorical(stringVectors(:,5));
bcisummaryvenice.treatment = data(:,4);
bcisummaryvenice.questionnaire_motivaton_pre_date = datetime([dates{:,3}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.questionnaire_motivaton_pre = data(:,5);
bcisummaryvenice.fma_pre_date = datetime([dates{:,4}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.fma_prescore = data(:,6);
bcisummaryvenice.arat_pre_date = datetime([dates{:,5}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.arat_prescore = data(:,7);
bcisummaryvenice.jamar_pre_date = datetime([dates{:,6}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.jamar_comment = stringVectors(:,6);
bcisummaryvenice.jamar_ASprescoreKgF = data(:,8);
bcisummaryvenice.jamar_USprescoreKgF = data(:,9);
bcisummaryvenice.ashworth_pre_date = datetime([dates{:,7}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.ashworth_prescore = stringVectors(:,7);
bcisummaryvenice.monofilament_pre_date = datetime([dates{:,8}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.monofilament_comment = stringVectors(:,8);
bcisummaryvenice.monofilament_ASprescore = stringVectors(:,9);
bcisummaryvenice.monofilament_USprescore = categorical(stringVectors(:,10));
bcisummaryvenice.mif_pre_date = datetime([dates{:,9}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.mif_prescore = data(:,10);
bcisummaryvenice.questionnaire_motivaton_post_date = datetime([dates{:,10}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.questionnaire_motivaton_post = stringVectors(:,11);
bcisummaryvenice.tms_pre_date = datetime([dates{:,11}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.tms_preASMT = data(:,11);
bcisummaryvenice.tms_preUSMT = data(:,12);
bcisummaryvenice.tms_post_date = datetime([dates{:,12}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.tms_postASMT = data(:,13);
bcisummaryvenice.tms_postUSMT = data(:,14);
bcisummaryvenice.fma_post_date = datetime([dates{:,13}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.fma_postscore = data(:,15);
bcisummaryvenice.arat_post_date = datetime([dates{:,14}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.arat_postscore = data(:,16);
bcisummaryvenice.jamar_post_date = datetime([dates{:,15}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.jamar_post_comment = stringVectors(:,12);
bcisummaryvenice.jamar_ASpostscoreKgF = data(:,17);
bcisummaryvenice.jamar_USpostscoreKgF = data(:,18);
bcisummaryvenice.ashworth_post_date = datetime([dates{:,16}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.ashworth_postscore = stringVectors(:,13);
bcisummaryvenice.monofilament_post_date = datetime([dates{:,17}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.monofilament_ASpostscore = stringVectors(:,14);
bcisummaryvenice.monofilament_USpostscore = stringVectors(:,15);
bcisummaryvenice.mif_post_date = datetime([dates{:,18}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.mif_postscore = data(:,19);
bcisummaryvenice.fma_3monthpoststroke_date = datetime([dates{:,19}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.fma_3monthpoststrokescore = data(:,20);
bcisummaryvenice.arat_3monthpoststroke_date = datetime([dates{:,20}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.arat_3monthpoststrokescore = data(:,21);
bcisummaryvenice.jamar_3monthpoststroke_date = datetime([dates{:,21}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.jamar_comment1 = stringVectors(:,16);
bcisummaryvenice.jamar_AS3monthpoststrokescoreKgF = data(:,22);
bcisummaryvenice.jamar_US3monthpoststrokescoreKgF = data(:,23);
bcisummaryvenice.ashworth_3monthpoststroke_date = datetime([dates{:,22}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.ashworth_3monthpoststrokescore = stringVectors(:,17);
bcisummaryvenice.monofilament_3monthpoststroke_date = datetime([dates{:,23}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.monofilament_comment1 = stringVectors(:,18);
bcisummaryvenice.monofilament_AS3monthpoststrokescore = stringVectors(:,19);
bcisummaryvenice.monofilament_US3monthpoststrokescore = categorical(stringVectors(:,20));
bcisummaryvenice.mif_3monthpoststroke_date = datetime([dates{:,24}].', 'ConvertFrom', 'Excel');
bcisummaryvenice.mif_3monthpoststrokescore = data(:,24);
bcisummaryvenice.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).
% bcisummaryveniceS1.date_of_birth=datenum(bcisummaryveniceS1.date_of_birth);bcisummaryveniceS1.stroke_date=datenum(bcisummaryveniceS1.stroke_date);
% bcisummaryveniceS1.questionnaire_motivaton_pre_date=datenum(bcisummaryveniceS1.questionnaire_motivaton_pre_date);bcisummaryveniceS1.fma_pre_date=datenum(bcisummaryveniceS1.fma_pre_date);
% bcisummaryveniceS1.arat_pre_date=datenum(bcisummaryveniceS1.arat_pre_date);bcisummaryveniceS1.jamar_pre_date=datenum(bcisummaryveniceS1.jamar_pre_date);bcisummaryveniceS1.ashworth_pre_date=datenum(bcisummaryveniceS1.ashworth_pre_date);bcisummaryveniceS1.monofilament_pre_date=datenum(bcisummaryveniceS1.monofilament_pre_date);bcisummaryveniceS1.mif_pre_date=datenum(bcisummaryveniceS1.mif_pre_date);
% bcisummaryveniceS1.questionnaire_motivaton_post_date=datenum(bcisummaryveniceS1.questionnaire_motivaton_post_date);bcisummaryveniceS1.tms_pre_date=datenum(bcisummaryveniceS1.tms_pre_date);
% bcisummaryveniceS1.tms_post_date=datenum(bcisummaryveniceS1.tms_post_date);bcisummaryveniceS1.fma_post_date=datenum(bcisummaryveniceS1.fma_post_date);bcisummaryveniceS1.arat_post_date=datenum(bcisummaryveniceS1.arat_post_date);bcisummaryveniceS1.jamar_post_date=datenum(bcisummaryveniceS1.jamar_post_date);bcisummaryveniceS1.ashworth_post_date=datenum(bcisummaryveniceS1.ashworth_post_date);bcisummaryveniceS1.monofilament_post_date=datenum(bcisummaryveniceS1.monofilament_post_date);bcisummaryveniceS1.mif_post_date=datenum(bcisummaryveniceS1.mif_post_date);bcisummaryveniceS1.fma_3monthpoststroke_date=datenum(bcisummaryveniceS1.fma_3monthpoststroke_date);bcisummaryveniceS1.arat_3monthpoststroke_date=datenum(bcisummaryveniceS1.arat_3monthpoststroke_date);bcisummaryveniceS1.jamar_3monthpoststroke_date=datenum(bcisummaryveniceS1.jamar_3monthpoststroke_date);bcisummaryveniceS1.ashworth_3monthpoststroke_date=datenum(bcisummaryveniceS1.ashworth_3monthpoststroke_date);bcisummaryveniceS1.monofilament_3monthpoststroke_date=datenum(bcisummaryveniceS1.monofilament_3monthpoststroke_date);bcisummaryveniceS1.mif_3monthpoststroke_date=datenum(bcisummaryveniceS1.mif_3monthpoststroke_date);
%% Clear temporary variables
clearvars data raw dates stringVectors R;
% Change the treatment naming
treatmentinstring = categorical(bcisummaryvenice.treatment);
treatmentinstring(treatmentinstring == '0') = 'sham';
treatmentinstring(treatmentinstring == '1') = 'bci';
bcisummaryvenice.treatment = treatmentinstring;
% Add sites label
experiment_site = categorical(cellstr(repmat('VEN', size(bcisummaryvenice, 1), 1)));
bcisummaryvenice.experiment_site = categorical(experiment_site);
bcisummaryvenice = movevars(bcisummaryvenice, 'experiment_site', 'After', 'subject_id');
% Change first variable name
bcisummaryvenice.Properties.VariableNames{'patient_id_ven'} = 'patient_id';
save data\raw_bcisummary_venice bcisummaryvenice
% save 'D:/Sinergia/Data collection (BCI and tDCS)/bci/dataProcessing/data/raw_bcisummary' bcisummary;
clearvars treatmentinstring experiment_site
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