I was able to fix the problem by replacing the xlsread/xlswrite functions with equivalent ActiveX functions. I didn't want to use ActivX at first because it seemed more complicated, but once you know which commands to use, it's relatively easy. I haven't seen any of those java errors since I've been using ActiveX, and my code is running faster since Excel doesn't need to close between subsequent read/write operations to the same file.
The ActiveX commands I used to replace xlsread/xlswrite can be found below. The basic replacement version is given first. If you need to create sheets and files or open multiple files at once, some advanced examples are in my 'testing function' at the end.
So here's the basic version:
%define file path
filepath = [pwd '\testExcel_TE.xlsx'];
%open Excel
Excelhandle = actxserver('excel.application');
Excelhandle.Visible = 1; %0 if you want to run Excel in the background
set(Excelhandle, 'DisplayAlerts', 0); % Stop dialog (do you wish to overwrite...)
%open your file
TE_filehandle = Excelhandle.Workbooks.Open(filepath);
%create a handle to the sheets in your file
Sheets = TE_filehandle.Sheets;
%your data should have the format of a cell array
dataToWrite = num2cell([10,5,3,6,7,9]);
%basic XLSWRITE
%write cell array 'dataToWrite' to Excel file in sheet 'Sheet1', range B3:G3
ActivesheetRange = get(Sheets.Item('Sheet1'), 'Range', 'B3:G3');
set(ActivesheetRange, 'Value', dataToWrite);
%Notes:
% - make sure the dimensions of your variable and the Excel range match;
% - if the Sheet doesn't exist yet, you'll need to create it first (see testing function)
%basic XLSREAD
%read cell array from Excel file and store it in 'readDataCell'
ActivesheetRange = get(Sheets.Item('Sheet1'), 'Range', 'B3:G3');
readDataCell = ActivesheetRange.value;
%save workbook, close workbook, close Excel
TE_filehandle.Save();
Excelhandle.Workbooks.Close;
Excelhandle.Quit;
To use the testing function below, manually create two Excel files in your MATLAB working directory, one named testExcel.xlsx, the other secondtestExcel.xlsx and place some strings, numbers, formulas... in the cells you're going to read.
Example:
testExcel.xlsx
Sheet2, row1A-G: this; is; a; test; 1; 2; 3
Sheet2, row3A-G: 1; 2; 3; 4; 5; 6; 7
Sheet3, C2: =A2+B2
secondtestExcel.xlsx
(empty)
function testingExcel
%store Excel file location in filepath variable
filepath = [pwd '\testExcel.xlsx']; %pwd returns the current Matlab folder
filepath2 = [pwd '\secondtestExcel.xlsx'];
%open Excel
Excelhandle = actxserver('excel.application');
%you can make it visible (then you can actually see Excel changing the values in the cells, which is useful for debugging). Set this to 0 to hide Excel and run it in the background.
Excelhandle.Visible = 1;
%The following line is very important when you want to have your code run without interruptions: it stops Excel from asking confirmation when saving or overwriting files. If you don't include this line, every time you want to save a file you'll have to confirm it manually by clicking 'Yes' in the Excel dialog.
set(Excelhandle, 'DisplayAlerts', 0);
%Open your file in Excel and create a handle to your file
exlFile = Excelhandle.Workbooks.Open(filepath);
%Alternatively, you can create a new blank file
% Workbooks = Excelhandle.Workbooks;
% exlFile = invoke(Workbooks, 'Add');
% Get the list of sheets in the workbook
Sheets = exlFile.Sheets;
%Put a cell array into Excel (specify sheet + position)
A = {'apple', 'pear' ; 6, 4};
ActivesheetRange = get(Sheets.Item('Sheet3'), 'Range', 'A1:B2');
set(ActivesheetRange, 'Value', A);
%Get a range from the Excel file as a cell array.
ActivesheetRange = get(Sheets.Item('Sheet3'), 'Range', 'C2');
sixplusfour = ActivesheetRange.value; %if you inserted the formula =A2+B2 manually in C2 when you created testExcel.xlsx, this should return the sum of the values you wrote in A2 and B2
display(sixplusfour);
%Add a sheet
% Newsheet = invoke(Sheets, 'Add');
% Newsheet.Name = 'New sheet X';
%Rename the first sheet
Sheets.Item(1).Name = 'This is sheet 1';
%Create a handle to the sheet called 'Sheet2'
exlSheet2 = exlFile.Sheets.Item('Sheet2');
%Read data in A1:G3 in Sheet2, it's returned as a cell array
dat_range = ['A1:G3'];
rngObj = exlSheet2.Range(dat_range);
exlData = rngObj.Value; %this returns a cell array
display(exlData);
%Save the file
% Excel.ActiveWorkbook.Save();
%Save as
invoke(Excelhandle.ActiveWorkbook, 'SaveAs', [pwd '\mynewfile.xlsx']);
%You can create a new handle (start another instance of Excel) to work on another file at the same time
Excelhandle2 = actxserver('excel.application');
Excelhandle2.Visible = 1;
set(Excelhandle2, 'DisplayAlerts', 0);
%Open the second file
Excelhandle2.Workbooks.Open(filepath2);
%Close all workbooks opened by the first Excel handle (in this case, this will close testExcel.xlsx)
Excelhandle.Workbooks.Close;
%Close all workbooks opened by the second Excel handle (in this case, this will close secondtestExcel.xlsx)
Excelhandle2.Workbooks.Close;
%Quit Excel, delete the related objects if needed
Excelhandle.Quit;
Excelhandle2.Quit;
clear Excel;
clear Sheets;
%...
