Matlab Training Session 5: Importing Data

1. Matlab Training Session 5:Importing Data

2. Course Outline Weeks: • Introduction to Matlab and its Interface (Jan 13 2009) • Fundamentals (Operators) • Fundamentals (Flow) • Importing Data • Functions and M-Files • Plotting (2D and 3D) • Statistical Tools in Matlab • Analysis and Data Structures Course Website: http://www.queensu.ca/neurosci/matlab.php

3. Week 5 Lecture Outline Importing Data A. Week 4 Review B. Simple Import C. Handling Files D. Mini-Project

4. Functions in Matlab • In Matlab, each function is a .m file • It is good protocol to name your .m file the same as your function name, i.e. funcname.m • function outargs=funcname(inargs); Function input output

5. Mini-Project • Raising any number of numbers to the nth power • Inputs: • A vector of numbers to be raised (N1…Nm) • A vector of powers (P1…Pm) • Outputs: • A vector of raised values (N1P1 … NmPm) • An error flag: 1 if error in calculation, 0 if successful • Caveats: • If only one input is provided, the function should square each entry, so output = (N12…Nm2) and error flag is 0 • If the length of N and P are not the same,this is an error, return anything in the output vector and a 1 in the error flag • Make sure to comment and document the function

6. Solution Complex function [y, e] = raise(x,n) y = ones(1,length(x)); if nargin == 1 [y e] = raise(x,2*ones(1,length(x))); return elseif nargin == 2 if(length(x)~=length(n)) y = NaN; e = 1; return end for(i=1:length(x)) for(j=1:n(i)) y(i) = y(i)*x(i); end end e = 0; return end Simple function [y, e] = raise(x,n) if nargin == 1 [y e] = x.^2; return elseif nargin == 2 if(length(x)~=length(n)) y = NaN; e = 1; return end y = x.^n e = 0; end

7. Importing Data • Basic issue: • How do we get data from other sources into Matlab so that we can play with it? • Other Issues: • Where do we get the data? • What types of data can we import • Easily or Not

8. load • Command opens and imports data from a standard ASCII file into a matlab variable • Restrictions • Data must be constantly sized • Data must be ASCII • No other characters

9. load • Consider the simple file below • Create in notepad and save as test1.txt and text2.txt • In matlab, set the path to the correct place (ie. where the file is) and type load(‘test1.txt’) • Now, type x = load(‘test1.txt’) 1 2 3 4 5 2 4 8 16 32 test1

10. load • Now the file is no longer simple because not every row has the same amount of characters • Create in notepad and save as test2.txt and text2.txt • type y = load(‘test2.txt’) • Error! 1 2 3 4 5 4 8 16 32 test2

11. load • Now type in the same thing from test1.txt into Excel and save the workbook as test1.xls • type y = load(‘test1.xls’) • What happens? • Forcing the issue with Excel data test1 1 2 3 4 5 2 4 8 16 32

12. load • Works for simple and unstructured code • Powerful and easy to use but limited • Will likely force you to manually handle simplifying data which is prone to error • More complex functions are more flexible

13. File Handling • f* functions are associated with file opening, reading, manipulating, writing, … • Basic Functions of Interest for opening and reading generic files in matlab • fopen • fclose • fseek/ftell/frewind • fscanf • fgetl

14. fopen • Opens a file object in matlab that points to the file of interest • fid = fopen(‘filepath’) • absolute directory + filename • If file of interest is C:\Andrew\Project_1\file.dat • fid = fopen(‘C:\Andrew\Project_1\file.dat’) • relative path + filename • If your matlab path is set to c:\Andrew\Project_1 • fid = fopen(‘file.dat’) • fid is an integer that represents the file • Can open multiple files and matlab will assign unique fids

15. fclose • When you are done with a file, it is a good idea to close it especially if you are opening many files • fclose(fid)

16. What is a File? • A specific organization of data • In matlab it is identified with a fid • Location is specified with a pointer that can be moved around fid file_name Pointer

17. Moving the Pointer • We already know how to assign a fid (fopen) • To find where the file is pointing: • x = ftell(fid) • To point somewhere else • fseek(fid,offset,origin) • Move pointer in file fid by offset relative to origin • Move pointer by a fixed number of bytes • Origin can be beginning, current, end of file • To point to the beginning • frewind(fid)

18. Getting Data • Why move the pointer around? • Get somewhere in the file from where you want data • [data] = fscanf(fid,format,size) • Format • You have to tell matlab the type of data it should be expecting in the text file so that it can convert it • ‘%d’, ‘%f’, ‘%c’, ‘%s’ • Size • You can specify how to organize the imported data • [m,n] – import the data as m by n, n can be infinite • Be careful because matlab will mangle your data and not tell you

19. Lets Try It • Open text1.txt using the fopen command • Remember to save the fid, we will need it • Create a variable with the data of text1.txt • Now create another variable y with the data of text1.txt in it by using fscanf (do not simply copy x) • What happens here? • Need to set file pointer to beginning using rewind(fid) • Now use the size option to import the data with 5 rows and 2 columns • Try the same thing with test2.txt • It works and fills in the blanks. This is powerful but dangerous

20. Lets Try It • Open text1.txt using the fopen command • Remember to save the fid, we will need it fid = fopen('test1.txt) • Create a variable with the data of text1.txt [x] = fscanf(fid,'%f%f') • Now create another variable y with the data of text1.txt in it by using fscanf (do not simply copy x) [y] = fscanf(fid,'%f%f') • What happens here? • Need to set file pointer to beginning using frewind(fid)

21. Lets Try It • Now use the size option to import the data with 5 rows and 2 columns [data2] = fscanf(fid,'%f%f',[5,2]) - Careful this is the same format as the original data but not the same organization!! frewind(fid) [data3] = fscanf(fid,'%f%f',[2,5]) data3’ - now the data is formatted correctly • Try the same thing with test2.txt • It works and fills in the blanks. This is powerful but dangerous

22. Getting Data • fgetl returns the next line of the file as a character array • You may need to convert these to numbers >> fid1 = fopen(‘test1.txt’); >> a_str = fgetl(fid1) a_str = 1 2 >> a_num = str2num(a_str) a_num = [1 2]

23. Realistic File • A realistic file of data will have header information, labeled columns and other information embedded within it. • See PDXtemp.dat • Option 1: Manually go through deleting this information and import using load of fopen commands. • Option 2: Have matlab delete and format available data on the fly

24. Realistic File • Powerful function textread can be used to input almost any text file • Handles (input variables): • Opening the file • Ignoring Header Information • Accepting Column Labels • Will work for most applications

25. Realistic File • Powerful function textread can be used to input almost any text file Usage: [var1 varN] = textread(‘filename’,’format’,args)

26. Summary • Lots of options to load files • load for basics • fscanf for complex • textread for most things • xlsread for Excel worksheets • Also saving Excel sheets as tab delimitted

27. Mini-Project • Using the textread function, import the full data located in PDXtemp.dat with the stated names and correct data types • Take the resulting temperatures in Fahrenheit and convert to Celsius • Make use of Matlab help to learn about and implement the textread function • Deg_F = 9/5*Deg_C + 32

28. Mini-ProjectSolution % Assume that the textfile is saved in the matlab work directory % which is automatically in the path % read data from PDXtemp.txt into 4 variables (assume PDXtemp.txt is in path) [month, high_F, low_F, avg_F] = … textread('PDXtemp.txt','%4c%f%f%f','headerlines', 6); % convert each temperature variable to celcius high_C = (5/9).*(high_F - 32); Low_C = (5/9).*(low_F - 32); avg_C = (5/9).*(avg_F - 32);

29. Getting Help • Help and Documentation • Digital • Accessible Help from the Matlab Start Menu • Updated online help from the Matlab Mathworks website: • http://www.mathworks.com/access/helpdesk/help/techdoc/matlab.html • Matlab command prompt function lookup • Built in Demo’s • Websites • Hard Copy • Books, Guides, Reference • The Student Edition of Matlab pub. Mathworks Inc.