Introduction to File I/O in Scientific Programming

1. COMP 116: Introduction to Scientific Programming Lecture 29: File I/O

2. Announcements • No class this Friday • Today’s office hours moved to 3pm-4pm

3. Last class • Data types • char, logical, integers, floating point numbers

4. Today • File I/O • Reading, writing MATLAB data files (.mat) • Reading, writing text files

5. Jargon • Input • Loading data from a file into MATLAB • Output • Saving data from MATLAB into a file • Text Mode • Files can be “read” by a human or a computer

6. The fprintf command • Formatted output • Unlike disp, error commands • Usage: fprintf(format, a1, a2 ...) • a1, a2,. … are variables • ‘format’ is a string that specifies how the output has to be formatted

7. Examples • x is an integer with value 5 and y is a floating point real number with value 3.2 >> fprintf(‘Height is %dmeters and %f cms\n', x, y) Height is 5 meters and 3.20000 cms %d says print the corresponding variable as an integer, %f says print the corresponding variable as a floating point number ‘\n’ corresponds to the newline character

8. fprintf format string • %d – print as integer • %f – print as floating point number • %c – print as a character • %s – print as a string • %2.4f would print only upto the 4 digit after decimal • More details doc fprintf

9. Exercise I: What does this code do? % Assume that N is preassigned for i=1:N fprintf('The square root of %d is %f\n', i, sqrt(i)); end

10. File Input Output

11. Variable Storage (.MAT files) • Loading variables • load <filename> • .MAT extensions is assumed • Overwrites any current variables with same name • Writing variable(s) to a file • save <filename> • .MAT extension is automatically added • Saves all current workspace variables • Save only selected variables: • save <filename> var1 var2 var3

12. Variable Storage (.MAT files) • To see what variable(s) are in a .MAT file • who –file <filename> • Appending more variables • save –append <filename>

13. Reading other file formats • You've been given a file with data in it that you need. • …but it's not in the format that MATLAB saves in • You can't get at the data by typing load <filename> • You're going to have to read the file yourself

14. Reading other file formats • Three steps • Open the file, get a file id • Read from (or write to) the file, using the id • Close the file, using the id • That’s not so hard • Just get the syntax right

15. Opening a file fileID = fopen(filename, permission); • filename:the name of the file to open (as a string) • permission:a string saying whether we read or write, and whether the file is text or binary • fileID: a number that we will use later to read from the file • File Permissions • Controls whether reading, writing, or appending is allowed. • How to handle a file that doesn't exist.

16. Opening a file: example fid = fopen(‘somefile.dat’, ‘r’); • Some important (and common) file permissions • ‘r’ – read • ‘w’ – write • ‘a’ – append • ‘r+’ – read and write

17. fopen’s return value • Returns • file “handle” if open was successful • -1, if an error (e.g., trying to read a file that does not exist) • [fid, msg] = fopen('file.dat', 'r'); • if (fid == -1) • % Error opening file • disp(msg); • end

18. Closing a file • Just as important as opening a file • Possibly the thing that’s forgotten the most • Every file that we open needs to be closed when we are done using it fclose( fileId ) • Forgetting to close a file is not an error, but… • If you are writing to a file, the data might not get actually saved until you call fclose. • There is a physical limit to how many files can be open at once.

19. Writing to a file • Easier than reading, so we’ll start with this • Writing in text mode: • The return of the ‘fprintf’ command • fprintf(fid, 'This is the %dth dimension\n', 8); • (i.e., just stick the file-id at the beginning)

20. Writing to a (text) file: example fid = fopen('output.txt', 'wt'); fprintf( fid, 'This is the first line of output\n' ); fprintf( fid, '%d + %d = %d\n', 1, 2, (1 + 2) ); fclose( fid );

21. Exercise 2: What does this code do? % Assume that N is preassigned fid=fopen(‘newfile.txt’, 'w'); for i=1:N fprintf(fid,'The square root of %2d is %2.4f\n', i, sqrt(i)); end fclose(fid);

22. Reading from a file • Text file: • Various options • Read the file line by line, as strings • fgetl() • oneLine = fgetl( fileId ); • Process the line with MATLAB string functions • Returns -1 at end of file

23. Example: Copying a text file % open input and output files fin = fopen( 'my_orig.m', 'rt' ); fout = fopen( 'my_copy.m', 'wt' ); % read and write each line of text textLine = fgetl( fin ); while ischar( textLine ) fprintf( fout, '%s\n', textLine ); textLine = fgetl( fin ); end % close input and output files fclose( fout ); fclose( fin ); This is a very common ‘idiom’ for reading text files

24. Reading from a text file • Read formatted text • [A,count] = fscanf(fid, format, size) • size optional - can specify the size of a matrix, for instance • reads one line at a time • returns data one column at a time dataCol = fscanf( fid, '%f', 2 );

25. Aside: Reading/Writing Excel Files • help xlsread • help xlswrite

26. Common Pitfalls • fopenfails • Is the filename misspelled? • Is the directory misspelled? • Is the file actually in the directory you specified? • Use ‘load’ and ‘save’ when you can, use low level file I/O only when necessary • Use 'a' when trying to append more data to a file • If you just use ‘w’, you’ll overwrite all the data already in the existing file.

27. Programming Guidelines • Always close files that were opened • Always double check that the files were opened successfully before trying to work with them • Make sure all data is read from the file • Implies that you should use a “while” loop, since you typically don’t know how many elements are in the file. • Make sure to use the correct formatting string when using fscanfor textscan • Test on small example string or file first

28. Reminder • Review File I/O • Practice working with text files • Read • From MATLAB Help window, Contents tab, choose MATLAB→ProgrammingFundamentals→Data Import and Export→Using Low-Level File I/O Functions.