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S4_inseminations.m
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%% S4_insemination: insemination and fertility data
clear variables
close all
clc
datetime.setDefaultFormats('defaultdate','dd-MM-yyyy HH:mm:ss');
%% STEP D0: detect data files in folder DELAVAL
% directory of txt files with data
cd = 'C:\Users\u0084712\Documents\Box Sync\Documents\MastiMan\Data\Data sets\Backup files\testSQLOUTPUT3txt\'; % all data files in txt format
cd_H = 'C:\Users\u0084712\Documents\Box Sync\Documents\MastiMan\Data\Data sets\Backup files\testSQLOUTPUT3head\'; % all header files
% find all the files in the folder
FNfiles = ls(cd); % this is the list with files in the folder where I saved the MPR results of MCC
ind = []; for i = 1:length(FNfiles); if isempty(find(contains(FNfiles(i,:),'.txt'))) == 1; ind = [ind; i]; end; end % find no filenames
FNfiles(ind,:) = []; clear ind % delete
% find all farmnames = for all files everything before '_'
files = array2table((1:length(FNfiles))','VariableNames',{'No'});
files.Farm(:,:) = repmat({'na'},length(FNfiles),1);
files.Date(:,1) = NaT;
files.Version(:,1) = repmat(0,length(FNfiles),1);
files.Table(:,:) = repmat({'na'},length(FNfiles),1);
files.FN(:,:) = repmat({'na'},length(FNfiles),1);
for i = 1:length(FNfiles(:,1)) % run through all the files in the folder
numLoc = regexp(FNfiles(i,:),'_'); % this functions finds the unique positions of 2 successive numbers in a filename
endLoc = regexp(FNfiles(i,:),'.txt'); % this gives the end of the filename
% Store data in 'files'
files.Farm{i,1} = FNfiles(i,1:numLoc(1)-1); % FarmName:length(FN(i,1:numLoc(1)-1))}
files.Date(i,1) = datetime(FNfiles(i,numLoc(1)+1:numLoc(1)+8),'InputFormat','yyyyMMdd','Format','dd/MM/yyyy'); % Date
files.Version(i,1) = str2double(FNfiles(i,numLoc(3)+1:numLoc(4)-1)); % Version
files.Table{i,1} = FNfiles(i,numLoc(end)+1:endLoc-1); % TableName
files.FN{i,1} = FNfiles(i,1:endLoc-1); % full FileName
end
files = sortrows(files, {'Farm','Date'});
% clear variables
clear i endLoc numLoc
% select tables containing treatment / diagnosis data
selTables = {'EventInsemination','HistoryAnimalReproductionInfo'};
ind = ismember(files.Table, selTables);
selFiles = files(ind,:);
% unique farms in the dataset
Farms = unique(selFiles.Farm); % all unique farms in the dataset
% combine headers with datafiles
for i = 1:height(selFiles)
d = dir([cd selFiles.FN{i} '.txt']);
if d.bytes ~= 0
datapath = [cd selFiles.FN{i} '.txt'];
headerpath = [cd_H selFiles.FN{i} '_headers.txt'];
if month(selFiles.Date(i)) < 10 && day(selFiles.Date(i)) < 10
C = [selFiles.Farm{i} '_' num2str(year(selFiles.Date(i))) '0' num2str(month(selFiles.Date(i))) '0' num2str(day(selFiles.Date(i)))];
savepath = ['C:\Users\u0084712\Documents\Box Sync\Documents\MastiMan\Data\Data sets\Backup files\ALLADD\' selFiles.Farm{i} '_' num2str(year(selFiles.Date(i))) '0' num2str(month(selFiles.Date(i))) '0' num2str(day(selFiles.Date(i))) '_' selFiles.Table{i} '.txt'];
elseif month(selFiles.Date(i)) < 10 && day(selFiles.Date(i)) >= 10
C = [selFiles.Farm{i} '_' num2str(year(selFiles.Date(i))) '0' num2str(month(selFiles.Date(i))) num2str(day(selFiles.Date(i)))];
savepath = ['C:\Users\u0084712\Documents\Box Sync\Documents\MastiMan\Data\Data sets\Backup files\ALLADD\' selFiles.Farm{i} '_' num2str(year(selFiles.Date(i))) '0' num2str(month(selFiles.Date(i))) num2str(day(selFiles.Date(i))) '_' selFiles.Table{i} '.txt'];
elseif month(selFiles.Date(i)) >= 10 && day(selFiles.Date(i)) < 10
C = [selFiles.Farm{i} '_' num2str(year(selFiles.Date(i))) num2str(month(selFiles.Date(i))) '0' num2str(day(selFiles.Date(i)))];
savepath = ['C:\Users\u0084712\Documents\Box Sync\Documents\MastiMan\Data\Data sets\Backup files\ALLADD\' selFiles.Farm{i} '_' num2str(year(selFiles.Date(i))) num2str(month(selFiles.Date(i))) '0' num2str(day(selFiles.Date(i))) '_' selFiles.Table{i} '.txt'];
else
C = [selFiles.Farm{i} '_' num2str(year(selFiles.Date(i))) num2str(month(selFiles.Date(i))) num2str(day(selFiles.Date(i)))];
savepath = ['C:\Users\u0084712\Documents\Box Sync\Documents\MastiMan\Data\Data sets\Backup files\ALLADD\' selFiles.Farm{i} '_' num2str(year(selFiles.Date(i))) num2str(month(selFiles.Date(i))) num2str(day(selFiles.Date(i))) '_' selFiles.Table{i} '.txt'];
end
% combine and save
if contains(selFiles.Table{i},'EventInsemination')
EI.(C) = F1_CombineDataHeaders(datapath,headerpath,savepath);
elseif contains(selFiles.Table{i},'HistoryAnimalReproductionInfo')
HARI.(C) = F1_CombineDataHeaders(datapath,headerpath,savepath);
end
end
end
clear ind d C i savepath datapath headerpath
% BA & HA
for i = 1:height(files)
if contains(files.Table{i},'HistoryAnimal') && ~contains(files.Table{i},'HistoryAnimalD') && ~contains(files.Table{i},'HistoryAnimalL') ...
&& ~contains(files.Table{i},'HistoryAnimalR') && ~contains(files.Table{i},'HistoryAnimalT') %&& sum(contains(fieldnames(EI),files.Farm{i}))>=1
datapath = [cd files.FN{i} '.txt'];
headerpath = [cd_H files.FN{i} '_headers.txt'];
if month(files.Date(i)) < 10 && day(files.Date(i)) < 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) '0' num2str(month(files.Date(i))) '0' num2str(day(files.Date(i)))];
elseif month(files.Date(i)) < 10 && day(files.Date(i)) >= 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) '0' num2str(month(files.Date(i))) num2str(day(files.Date(i)))];
elseif month(files.Date(i)) >= 10 && day(files.Date(i)) < 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) num2str(month(files.Date(i))) '0' num2str(day(files.Date(i)))];
else
C = [files.Farm{i} '_' num2str(year(files.Date(i))) num2str(month(files.Date(i))) num2str(day(files.Date(i)))];
end
HA.(C) = F1_CombineDataHeaders(datapath,headerpath);
else
if contains(files.Table{i},'BasicAnimal') && sum(contains(fieldnames(EI),files.Farm{i}))>=1
datapath = [cd files.FN{i} '.txt'];
headerpath = [cd_H files.FN{i} '_headers.txt'];
if month(files.Date(i)) < 10 && day(files.Date(i)) < 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) '0' num2str(month(files.Date(i))) '0' num2str(day(files.Date(i)))];
elseif month(files.Date(i)) < 10 && day(files.Date(i)) >= 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) '0' num2str(month(files.Date(i))) num2str(day(files.Date(i)))];
elseif month(files.Date(i)) >= 10 && day(files.Date(i)) < 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) num2str(month(files.Date(i))) '0' num2str(day(files.Date(i)))];
else
C = [files.Farm{i} '_' num2str(year(files.Date(i))) num2str(month(files.Date(i))) num2str(day(files.Date(i)))];
end
BA.(C) = F1_CombineDataHeaders(datapath,headerpath);
end
end
end
% Load HADD and AHD
for i = 1:height(files)
if contains(files.Table{i},'HistoryAnimalDailyData') %&& sum(contains(fieldnames(EI),files.Farm{i}))>=1
datapath = [cd files.FN{i} '.txt'];
headerpath = [cd_H files.FN{i} '_headers.txt'];
if month(files.Date(i)) < 10 && day(files.Date(i)) < 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) '0' num2str(month(files.Date(i))) '0' num2str(day(files.Date(i)))];
elseif month(files.Date(i)) < 10 && day(files.Date(i)) >= 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) '0' num2str(month(files.Date(i))) num2str(day(files.Date(i)))];
elseif month(files.Date(i)) >= 10 && day(files.Date(i)) < 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) num2str(month(files.Date(i))) '0' num2str(day(files.Date(i)))];
else
C = [files.Farm{i} '_' num2str(year(files.Date(i))) num2str(month(files.Date(i))) num2str(day(files.Date(i)))];
end
HADD.(C) = F1_CombineDataHeaders(datapath,headerpath);
else
if contains(files.Table{i},'AnimalHistoricalData') % && sum(contains(fieldnames(EI),files.Farm{i}))>=1
datapath = [cd files.FN{i} '.txt'];
headerpath = [cd_H files.FN{i} '_headers.txt'];
if month(files.Date(i)) < 10 && day(files.Date(i)) < 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) '0' num2str(month(files.Date(i))) '0' num2str(day(files.Date(i)))];
elseif month(files.Date(i)) < 10 && day(files.Date(i)) >= 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) '0' num2str(month(files.Date(i))) num2str(day(files.Date(i)))];
elseif month(files.Date(i)) >= 10 && day(files.Date(i)) < 10
C = [files.Farm{i} '_' num2str(year(files.Date(i))) num2str(month(files.Date(i))) '0' num2str(day(files.Date(i)))];
else
C = [files.Farm{i} '_' num2str(year(files.Date(i))) num2str(month(files.Date(i))) num2str(day(files.Date(i)))];
end
AHD.(C) = F1_CombineDataHeaders(datapath,headerpath);
end
end
end
clear i C selFiles selTables
%%
% combine information in the different tables
fieldNamesHARI = fieldnames(HARI);
fieldNamesEI = fieldnames(EI);
varsBA = {'OID','Number','Name','BirthDate','ExitDate'};
varsHA = {'OID','Number','Name','BirthDate','ExitDate'};
varsHARI = {'OID','ActualInseminationNumber','Sire','PregCheckDay','CalvingDay','HeatSignDay','InsemDay'};
varsEI = {'OID','MotherID','InseminationNo'};
varsAHD = {'OID','BasicAnimal','DateAndTime'};
varsHADD = {'OID','BasicAnimal','DayDate','Animal','LactationNumber'};
for i = 1:length(fieldNamesEI)
try
% find indices
varindxEI = find(contains(EI.(fieldNamesEI{i}).Properties.VariableNames,varsEI));
varindxAHD = find(contains(AHD.(fieldNamesEI{i}).Properties.VariableNames,varsAHD));
EI2.(fieldNamesEI{i}) = innerjoin(EI.(fieldNamesEI{i})(:,varindxEI),AHD.(fieldNamesEI{i})(:,varindxAHD),'LeftKeys',{'OID'},'RightKeys',{'OID'});
if sum(contains(fieldnames(BA),fieldNamesEI{i}))>0
varindxBA = find(contains(BA.(fieldNamesEI{i}).Properties.VariableNames,varsBA));
% combine tables
EI3.(fieldNamesEI{i}) = innerjoin(EI2.(fieldNamesEI{i}),BA.(fieldNamesEI{i})(:,varindxBA),'LeftKeys',{'BasicAnimal'},'RightKeys',{'OID'});
EI3.(fieldNamesEI{i}) = removevars(EI3.(fieldNamesEI{i}),'OID');
EI3.(fieldNamesEI{i}) = sortrows(EI3.(fieldNamesEI{i}),5);
EI3.(fieldNamesEI{i}) = movevars(EI3.(fieldNamesEI{i}),[4 5 6 7 8 ],'before','MotherID');
else
varindxHA = find(contains(HA.(fieldNamesEI{i}).Properties.VariableNames,varsBA));
lacindx = find(contains(HA.(fieldNamesEI{i}).Properties.VariableNames,'LactationNumber'));
if sum(ismember(varindxHA,lacindx)) > 0
varindxHA(varindxHA == lacindx) = [];
end
% combine tables
EI3.(fieldNamesEI{i}) = innerjoin(EI2.(fieldNamesEI{i}),HA.(fieldNamesEI{i})(:,varindxHA),'LeftKeys',{'BasicAnimal'},'RightKeys',{'OID'});
EI3.(fieldNamesEI{i}) = removevars(EI3.(fieldNamesEI{i}),'OID');
EI3.(fieldNamesEI{i}) = sortrows(EI3.(fieldNamesEI{i}),5);
EI3.(fieldNamesEI{i}) = movevars(EI3.(fieldNamesEI{i}),[4 5 6 7 8 ],'before','MotherID');
end
catch
% do nothing
end
end
for i = 1:length(fieldNamesHARI)
try
% find indices
varindxHARI = find(contains(HARI.(fieldNamesHARI{i}).Properties.VariableNames,varsHARI));
varindxHADD = find(contains(HADD.(fieldNamesHARI{i}).Properties.VariableNames,varsHADD));
HARI2.(fieldNamesHARI{i}) = innerjoin(HARI.(fieldNamesHARI{i})(:,varindxHARI),HADD.(fieldNamesHARI{i})(:,varindxHADD),'LeftKeys',{'OID'},'RightKeys',{'OID'});
if sum(contains(fieldnames(HA),fieldNamesHARI{i}))>0
varindxHA = find(contains(HA.(fieldNamesHARI{i}).Properties.VariableNames,varsHA));
lacindx = find(contains(HA.(fieldNamesHARI{i}).Properties.VariableNames,'LactationNumber'));
if sum(ismember(varindxHA,lacindx)) > 0
varindxHA(varindxHA == lacindx) = [];
end
% combine tables
HARI3.(fieldNamesHARI{i}) = innerjoin(HARI2.(fieldNamesHARI{i}),HA.(fieldNamesHARI{i})(:,varindxHA),'LeftKeys',{'Animal'},'RightKeys',{'OID'});
HARI3.(fieldNamesHARI{i}) = removevars(HARI3.(fieldNamesHARI{i}),'OID');
HARI3.(fieldNamesHARI{i}) = sortrows(HARI3.(fieldNamesHARI{i}),8);
HARI3.(fieldNamesHARI{i}) = movevars(HARI3.(fieldNamesHARI{i}),[8 9 10 11 12 13],'before','ActualInseminationNumber');
end
catch
% do nothing
end
end
clear test varindxAHD varindxEI varindxHADD varsAHD varsBA varsHARI varsHA varsEI varsHADD i ind varindxBA varindxHA selTables varindxHARI fieldnamesHAT C datapath headerpath savepath d selFiles EI2 fieldNamesEI fieldNamesHARI ans lacindx
% merge farm files and save per farm
fieldNamesHAT = fieldnames(HAT2);
previousFarm = 'random';
for i = 1:length(fieldNamesHAT)
numLoc = regexp(fieldNamesHAT{i,:},'_'); % this functions finds the unique positions of 2 successive numbers in a filename
currentFarm = fieldNamesHAT(i,:); % farmname
currentFarm = currentFarm{:};
currentFarm = currentFarm(1,1:numLoc-1);
if ~contains(fieldNamesHAT{i},previousFarm) & height(HAT2.(fieldNamesHAT{i})) > 10
HAT3.(currentFarm) = HAT2.(fieldNamesHAT{i});
elseif height(HAT2.(fieldNamesHAT{i})) > 10
try
HAT3.(currentFarm) = unique([HAT3.(currentFarm); HAT2.(fieldNamesHAT{i})],'rows');
catch
HAT3.(currentFarm).Name(:,1) = HAT2.(fieldNamesHAT{i}).Name(1);
HAT3.(currentFarm) = unique([HAT3.(currentFarm); HAT2.(fieldNamesHAT{i})],'rows');
end
end
previousFarm = currentFarm;
end
clear ans I
% save in excel
fieldNamesHAT = fieldnames(HAT3);
for i = 1:length(fieldNamesHAT)
writetable(HAT3.(fieldNamesHAT{i}), 'C:\Users\u0084712\Documents\Box Sync\Documents\MastiMan\Data\Data sets\Backup files\ALLADD\TreatmentRegisters.xlsx','Sheet',fieldNamesHAT{i}); % write table in each sep tablad per MPR period
end
% Delete default sheets
% Open Excel file.
objExcel = actxserver('Excel.Application');
objExcel.Workbooks.Open(fullfile(cd_SV, FN1)); % Full path is necessary! FN 1
% Delete sheets.
try
% Throws an error if the sheets do not exist.
objExcel.ActiveWorkbook.Worksheets.Item('Sheet1').Delete;
objExcel.ActiveWorkbook.Worksheets.Item('Sheet2').Delete;
objExcel.ActiveWorkbook.Worksheets.Item('Sheet3').Delete;
catch
% Do nothing.
end
% Save, close and clean up.
objExcel.ActiveWorkbook.Save;
objExcel.ActiveWorkbook.Close;
objExcel.Quit;
objExcel.delete;
clear cd cd_H