FILE I/O: Low-level

1. FILE I/O: Low-level General Ideas. High vs. low-level Opening a file Closing a file Writing data to the file Reading data from the file(numerical, strings..Etc)

2. 1. High vs low level High level Low level Requires at least 3 lines! clc clear %open the file __ = fopen(_________); %grab the data ‘properly’ ______(a lot of options)_____ %close the file fclose(_____); %ready to analyze the data… • “1 line of code opens the file, reads/write the data, closes the file” clc clear %upload data from file data = dlmread(‘myfile.dat’); %ready to analyze the data..

3. 1. Low-Level, cont. • Some files are mixed format that are not readable by high-level functions such as xlsread() and dlmread()! • Since the data is not easily recognized by any high-level function, every step to read the file requires a separate MATLAB command: • Open a file, either to read-from or to write-to • Read or writedata from/to the file with the specific delimiters • Close the file

4. The order of today.. • first, learn the fopen() command • then, learn the fclose() command • dump data to a file - fprintf() • read string data - fgets() and fgetl() • read numerical data -fscanf() • read combination of numerical and string - textscan()

5. 2. Opening / Closing Files • "Open a file" • Program requests access to a file (from the OS) for reading and/or writing data to/from the file. • "Close a file" • Inform the OS that the program is finished working with the file.

6. 2. Opening a file • There are many syntaxes possible (from the doc file): • The most commonly used ones (in EGR115): Description fileID= fopen(filename); %opens the file filename for read access, and returns an integer file identifier. fileID= fopen(filename, permission); %opens the file with the specified permission.

7. 2. Opening a file • Syntax to open a file fileID = fopen( filename , permission ); • fileID is known as a file identifier. It is like a "nickname" and is used instead of the filename when actually working with the file. • filename represents a string that is the name of the file with its extension (the letters after the dot). It can either be hardcoded, or within a variable • permission is a string that describes the type of access for the file >> why is this needed?

8. 2. Opening Files:permission • The “permission” indicates how MATLAB will use the file after being opened. • Since the operating system has permissions (read-only, write-only) assigned to files, when you request access to a file you must tell the system in what mode you will be using the file. • The strings used for this tell the OS what it needs to know, and has an impact on how MATLAB will use the file.

9. 2. Opening Files: permission • The most commonly used stringsare ‘r’ Open file for reading (default). ‘w’ Open or create new file for writing. Discard existing contents, if any. ‘a’ Open or create new file for writing. Append data to the end of the file. • There are MANY more >> doc fopen<enter>

10. 2. Opening Files: File Position Pointer • What happens when MATLAB opens a file to read or write? • When a file is opened, a “file position pointer” is created. The system keeps track of the point in the file to which your program has read or written. • Think of it like a cursor that moves as you read or write the file. • The file position pointer is set initially to different locations depending on the permission granted.

11. 2. Opening Files: File Position Pointer • Depending on the access-mode, does a file get “wiped” or not, “created” or not? • You should be able to reason this out – memorization is not the key here! Access Mode Delete Content? Create File? r w a This is the only ‘tricky’ one. Think: ‘w’=write=wipe.

12. 2. Opening Files: Choosing a permission • Trivia A “log file” is a file that keeps a history of events. Many programs keep log files. They help programmers see what occurred in the past so that a problem can be fixed. For example, swiping for attendance creates a log-file. If your program is going to keep a log file, what is the best mode to use when opening this file? Why?

13. 2. Closing Files • Syntax: fclose(fid); %usually ignore the return value • After working with a file, it is important to close the file. Other than being good form, it is critical when writing to the file. • Remember this? "Safe remove" warning on USB drives. • When the OS is supposed to put information on disk it frequently waits until it determines the best time. This is known as "write caching". • Windows may wait to write data. If your program finishes and Windows hasn't written this data, it will not be written at all! >> Closing the file forces Windows to write the data to the disk.

14. 2. Examples of opening and closing % Example 1) open a file from which to read fileGrades = fopen('grades.txt', 'r'); %hardcode the filename <code block to be inserted here> %close file fclose(fileGrades); % Example 2) ask user for a filename, then open it to read nameFile = uigetfile(‘*.txt’); fileGrades = fopen(nameFile, 'r'); <code block to be inserted here> %close file fclose(fileGrades); Use the file handle – not the file name! no quotes: a variable Notice that the file handle variable can be any acceptable variable name

15. 3. Writing to Text Files fprintf(<file handle>, … The rest is as usual...); Don’t forget the semi-colon! Otherwise, MATLAB displays in the command window a number! fprintf() default output is how many characters were printed. Example: fh = fopen('log_file.txt', 'a'); for k = 1:nbEvents fprintf(fh,'Event #%d: %15s %s\n',k,events{k,1},events{k,2}); end fclose(fh); File handle – not the file name!

16. 3. MS Windows Text files • When writing to a text file, MATLAB will write only a single newline character to the end of a line. • Yet, a Windows software (like Notepad) requires two different characters at the end of a line. • If you choose to open the file in a Windows based software, pad, it will not look like you expect: • But if you open with WordPad…

17. 3. MS Windows Text files • There is nothing wrong with this – unless you intend to work with the file outside of your program (and in Windows). • To make it Windows-ready, write both a carriage return (\r) and a newline (\n):

18. 3. Writing Text Files Inserting data into the middle of a text file Writing to text files is not like working in Word! When you write to a text file, the data added to the file will write over any existing data in the file after the files position pointer – there is no “insert mode”!

19. 3. Writing Text Files What we think should happen…

20. 3. Writing Text Files What REALLY happens…

21. 3. Writing Text Files There is no quick-fix to this problem. You must write code that moves the existing file data so that you can insert the new data. This might mean copying to a new file, or looping and overwriting the old data.

22. 4. Reading text files LAST but not least… • There are many ways to read from a file, due to the infinite possibility of its content. • Numbers? (Remember to use dlmread() if there is ONLY nbs!) • Strings? • Numbers and strings? • Pattern? • No pattern? • Therefore, there are many built-in functions, and ALL can be used in combinations, repeatedly, within a loop… to make it work!

23. 4. Reading files • Examples of files requiring low-level functions • It’s all about moving that cursor from top to bottom, and grabbing the data as you go!

24. Lots of built-in functions • There are many functions out there! Per line in the file: • Some are good with strings fgets() – grabs an entire line including \n fgetl() – grabs entire line, stops cursor before \n • Some are good with numbers fscanf(), textscan() – can return a numerical array • Some are good with strings & numbers textscan() - returns 1 row cell-array EACH OF THESE GRAB DATA AND MOVE THE CURSOR – much like when you read a book!!!!

25. Example1 • Which function to use: • Line 1? _______ • Line 2? _______ • Lines below? _______

26. Move the cursor one line at a time! clc clear %open file fileID = fopen('Electricallab.txt'); %'r' by default %grab data %line1 line1 = fgets(fileID); %line2 line2 = fgets(fileID); %below data = fscanf(fileID,'%f %f',[2,inf])'; %close file fclose(fileID); %now analyze the data! avg_volts = mean(data(:,2)) %somewhere, use line1 and line2… otherwise, ignore the return values above, and don't waste memory. %fgets(fileID); %for line1 %fgets(fileID); %for line2

27. Example2 • We only want columns 1 and 10…

28. Move and Skip*! clc clear %open file fileID = fopen('10Columns.txt'); %'r' by default %grab data %lines1-4 for k = 1:4 fgets(fileID); %notice don't collect. useless. i don't use it later. end %below data = fscanf(fileID,'%f %*d %*f %*f %*d %*d %*d %*f %*f %f',[2,inf])'; %close file fclose(fileID);

29. Example3 line 1? _______ lines 3-end? _____ 

30. textscan() friendly {1} {2} {3} clc clear %open file fileID = fopen('exampleIDName.txt'); %'r' by default %grab data %line1 line1 = fgets(fileID); dataCellArray = textscan(fileID,'%d %s %d'); %CAREFUL. data types of cell1 and 3 are int32!!! use double() to convert. %close file fclose(fileID); %who has highest grade??? %cellplot(dataCellArray) %I PLAY A LOT WITH THIS TO VISUALIZE!! SO COOL! [maxi, rowNb]=max(dataCellArray{3}); nameMax = dataCellArray{2}{rowNb} %{} everywhere, since cell2 contains another cellarray. IdofMax = dataCellArray{1}(rowNb) %regular () since cell1 contains a good old numerical vector columInCell1 = double(dataCellArray{1}); %extract the content of cell1 (which happens to be a vector) (2) (1) (3)

31. EXTREMELY PICKY!!!! • CAUTION: fscanf() and textscan() are EXTREMELY picky when it comes to the format string. Even 1 extra space or missing character could throw MATLAB off. • Consider this file: data=textscan(fid,‘%s %d %d %d AM’); %would not work data=textscan(fid,‘%s %d %d:%d AM’); %would work data=textscan(fid,‘%s %d %d:%d %s’); %would work data=textscan(fid,‘%s %d %d:%d %c%c’); %would work data=textscan(fid,‘%s %d %d:%d %c %c’); %would NOT work

32. More picky examples… File has: Jamie 12:34:44 $45.23 Carol 4:56:54 $23.21 '%s %d:%d:%d $%f' File has: 34-22 - 532.5 *34.53 12-33 - 111.5 *22.34 '%d-%d - %f *%f'

33. If you want… More details about each function

34. 4. Reading text files - Strings • Reading an entire line as a string • including storing the new line character in the variable str = fgets(<file handle>); • without storing the new line character in the variable str = fgetl(<file handle>); >> Both function calls above move the cursor down to the next line (you can use this to “skip” lines by ignoring its return value!)

35. Using fgets() • Includes the new line character in your variable Suppose we had this data file (.txt file) And ran this program: fh = fopen('testdata.txt', 'r'); x = fgets(fh); fprintf(‘->%s<-', x); %old fprintf Notice there are TWO newlines in the variable:

36. Using fgets() • The important idea though is that MATLAB moved the cursor past the first line. Since the file has not been closed, MATLAB is ready to scan the second line! • Use another fgets() to grab the next line.. • Or write a for loop to do repeat the fgets() How can we get rid of the \r\n ?

37. Using fgetl() • Reads past the newline, but DOES NOT include the newline character in your variable And ran this program: fh = fopen('testdata.txt', 'r'); x = fgetl(fh); fprintf('->%s<-', x) %old fprintf

38. 4. Reading text files – Numerical data fscanf() is like the reverse of fprintf(). Specify the format you want to match and fscanf() will read from the file as long as it can match that format. fscanf() is not good for reading strings because it will save the characters as their ASCII equivalents. Returns 1 numerical array (2D if necessary). That’s why it doesn’t like strings, usually of different length!

39. 4. Using fscanf() – part1 of 7 So: After opening the file, and moving the cursor past the first line (using fgets() for example), read the contents using: %open file (read by default) fh = fopen('example.txt'); %move cursor past first line (ignore return value) fgets(fh); %load the numerical data data = fscanf(fh, '%d %d'); fclose(fh); %done with file, close it before continuing…

40. 4. Using fscanf() – part2 However, the result would be: This demonstrates that fscanf() reads the data in line-order, but then stores it as a column. Change this format using one more argument on the function call.

41. 4. Using fscanf() – part3 Change the function call to: data = fscanf(fh, '%d\t%d', [2, 3]) The return-value collected is now: MATLAB is still reading the data in line-order, and still storing the data in column-order, but we've now specified how big the columns will be – two rows each. Add this 3rd argument

42. 4. Using fscanf() – part4 We may want the data to be in the form of the file. Unfortunately, changing the third argument doesn’t help: data = fscanf(fh, '%d\t%d', [3, 2]) • Original file data: • This is because fscanf() is still filling the variable in “column-order” – it fills a column first and then moves onto the next column.

43. 4. Using fscanf() – part5 To fix this, first read it in as a 2x3 matrix: data = fscanf(fh, '%d\t%d', [2, 3]) Then transpose the matrix: data = data'

44. 4. Using fscanf() – part6 Usually, combine all in one line: data = fscanf(fh, '%d\t%d', [2, 3])’

45. 4. Using fscanf() – part7 • Suppose the number of lines in the files is unknown, or more importantly is constantly updated! • Use MATLAB’s inf constant (infinity). It means “as many as needed” data = fscanf(fh, '%d\t%d', [2, inf])’; • Now, if the data file gets larger, the program can still handle it.

46. fscanf() CAUTION • It is impossible to skip to a specific column only. For example: There are 10 columns in the file, and all you need is columns 3 and 7. Too bad.. You must code 10 placeholders no matter what. DO NOT do this: Data = fscanf(fid,’%f %d %f %f %d %d %d’,[7, inf]); That will move the cursor past the 7th column, then start scanning from there again!! Do this: Data = fscanf(fid,’%*f %*d %f %*f %*d %*d %d %*f %*f %*f’,[2, inf]); %the * tells MATLAB to read past this part without storing it within Data. BUT THERE ARE 10 PLACEHOLDERS

47. 5. Reading files – Strings & Numbers • Assume the following file: • Again, move past the first line using fgets() or fgetl(), then how should we grab both integers, and strings? • Remember fscanf() is NOT friendly, it will return ASCII values!

48. 5. Using textscan() • textscan() is similar to fscanf() but is friendly to strings and numbers. There is still 1 return value, but this time it is a cell-array (capable of having strings and numbers of any size!)

49. 5. Using textscan() • Assume this updated data file: • After opening the file, and moving the cursor past the first line (using fgets() for example), read the contents using: data = textscan(fid,'%d %s %d')

50. 5. Using textscan() • The return value is not a 2D cell-array, but rather 1 single row: • To extract the data, simply reference the one cell you’re interested in, using { }. For example: allNames = _________________ allGrades= _________________ allIDs = _________________