ESS 116 Introduc)on to Data Analysis in Earth Science

Transcription

1 ESS 116 Introduc)on to Data Analysis in Earth Science Instructor: Mike Pritchard (include ESS116 in subject line) Image Credit: NASA Office Hours: 3317 Croul Hall, Tuesdays 1-2pm (exceppon today, 2-3pm)

2 Today s lecture 1. Lecture 2 quick review Matrices/Vectors Plot I/O 2. Lecture 3 MATLAB Programming Program vs script Algorithm example (script) User defined funcpon

3 Lecture 2 - review

4 ClarificaPon from Lab 1 C:\ vs. / for root directories and why it doesn t make sense to use them interchangeably. Make sure you submit test code that runs.

5 Vectors and Matrices Defining matrices in MATLAB: use square brackets mat2x3 = apple >> mat2x3 = [1 3 5; 2 4 6] >> mat2x3 = [1, 3, 5; 2, 4, 6] Matrix Opera/ons: use a dot in front of the operator for element-by-element (or array) operapon: >> A * B %matrix mulpplicapon >> A.* B %array mulpplicapon >> A./ B %array division >> A.^ B %array to a power 2 mat3x2 = >> mat3x2 = [1 4; 2 5; 3 6] >> mat3x2 = [1, 4; 2, 5; 3, 6]

6 Vectors and Matrices Colon operator begin:increment:end >> 0:3:60 %[0, 3, 6, 9,..,60] >> 0:60 %If not specified, the increment is assumed to be 1 Linspace funcpon: linspace(begin,end,n) >> linspace(0,60,21) %Gives 21 evenly spaced values between 0-60 >> linspace(50,-30,17) %Gives 17 evenly spaced values between 50 & -30 zeros, ones and rand >> A = zeros(5,4); %Create a 5x4 matrix of zeros, and assign to variable A >> B = ones(5,6); %Create a 5x6 matrix of zeros, and assign to variable B >> Z = rand(10,1); %Create a 10x1 matrix of random numbers between [0-1] Size : Get matrix >> size(a) >> [m, n] = size(a);

7 Matrix Elements If A is the name of a MATLAB matrix: >> A(3, 1) returns the value of the 3 rd row and 1 st column >> A(2, :) returns the 2 nd row of A >> A(3, 1) = 5; changes the 3 rd row and 1 st column of A to 5 >> A(:, 4) = 2; changes the enpre 4 th column of A to 2 Linear index: 2 (row,col) notapon: 6 4 (1, 1) (1, 2) (1, 3) (2, 1) (2, 2) (2, 3) (3, 1) (3, 2) (3, 3) (4, 1) (4, 2) (4, 3) Linear index: 6 4 (1) (5) (9) (2) (6) (10) (3) (7) (11) (4) (8) (12) >> A(7) will return the same value as A(3,2)

8 Finding Matrix Elements A = B = To find the locapons of 2 in A: >> pos = find(a==2); %linear indices >> [i j] = find(a==2); %rows and columns To find the locapons where B>5 >> pos = find(b>5) ; %linear indices >> [i j] = find(b>5); %rows and columns Combining find and replace: >> PosiPonsWhereALargerThan5 = find(a>5); >> A(PosiPonsWhereALargerThan5) = 5; Combining find and remove: >> PosiPonsWhereBLargerThan5 = find(b>5); >> B(PosiPonsWhereBLargerThan5) = [];

9 i>clicker quespon How would you replace the 5 of A by 42? A = A. A(5) = 42 B. A(3,2) = 42 C. a=find(a==5); A(a)=42; D. All of the above

10 Plot plot(x,y,'-r') Possible colors: 'b' (blue), 'g' (Green), 'k' (black), 'r' (red), Line types: -- (dashed), -. (dash dot), : (doted), - (solid) Markers: o (circle), + (plus), * (asterisk), s (square), ^ (triangle), p (star), plot(x,y,'-.b'); plot(x,y,'g*'); plot(x,y,'*:r');

11 Plot OpPons Line and marker oppons: 'LineWidth' : Changes line width (default is 1) 'MarkerFaceColor': followed by a color (e.g. r ) 'MarkerEdgeColor': followed by a color (e.g. k ) 'MarkerSize': Changes marker size (default is 1) Example: plot(x,y, r+:','markerfacecolor','g','markersize',5, LineWidth,2) axis([xmin xmax ymin ymax]) grid on/grid off Legend('legend line 1','legend line 2');

12 Plot oppons Adding labels and Ptle xlabel( x label (unit)'); ylabel( y label (unit)'); title( This is the plot title'); MulPple lines on the same plot: hold on % After the first plot Plot on mulpple figures call figure(1), figure(2), before plot command MulPple plots on the same figure use subplot(nrows,ncols,number) before plot command example: subplot(2,2,3) is the lower lew subplot of 2x2

13 File I/O Hard Disk Memory (RAM) File output: save command saves a matrix as an ASCII (text) or.mat (binary) file File input: load command loads in an ASCII file or.mat file All data must be numeric, i.e., no text allowed

14 Rocks.dat load cannot open the following file: granite a rhyolite b diorite c andesite d basalt e gabbro f

15 File Input: textscan fopen: opens a file and returns a File IdenPfier used to idenpfy the file later on in your code (-1 signifies an error in opening the file) file = 'rocks.dat'; fid = fopen(file); if fid==-1, error(['error opening ' file]); end cellmat = textscan(fid,'%d %f %s %c'); fclose(fid); textscan: read all the lines of the file and populate variable cellmat (one element per column) %d: integer (e.g., 235) %f: floapng-point number (e.g., ) %s: string (e.g., word) %c: character (e.g., a) fclose: Awer you are finished with a file, you should close it (prevents errors and unwanted behavior).

16 Lecture 3 MATLAB programming

17 Program vs script

18 MATLAB Programming InteracPve MATLAB use only good if problem is simple Owen, many steps are needed We also want to be able to automate repeated tasks Automated data processing is common in Earth science! Automated Earthquake DetecPon and NoPficaPon (USGS) Amazon.com s Automated Kiva Robots Automated Stream Discharge Monitoring (USGS)

19 Program vs. Script Computers only understand low-level language machine code htp://en.wikipedia.org/wiki/machine_code Low-level languages are much faster, but very difficult for humans to write efficiently MATLAB is a high-level language Uses code that is human readable Much easier to write E.g. disp, fprin}, plot, etc Compiler: Translates a high level language into an executable object code program (*.exe in MS Windows) Creates an executable file (binary) from source code (ascii) E.g. Mozilla Firefox and Microsow Office (source code: C++) firefox.exe, winword.exe (machine language executable files) MATLAB does something a litle different

20 Program vs. Script MATLAB is an interpreted language Code is read line by line by an interpreter (not a compiler) Each line of code is translated into machine language and executed on the fly No.exe file is generated (can force MATLAB to make.exe files) Because MATLAB code is not compiled source code is referred to as a script Also called M-files (end in.m) Advantages Don t need to spend Pme compiling the code to use it Don t need to recompile awer you make changes Same script will work on any operapng system with MATLAB Disadvantages Because code is compiled on the fly, some tasks can be slow* Others can change your code*

21 WriPng a script

22 Algorithm Example Before star/ng to write any code, you should break the problem down into a simple algorithm Algorithm: A sequence of steps to solve a problem Example Algorithm: Calculate Volume of a Sphere Get the input: radius of sphere Calculate the result: volume of sphere Display the result Input typically comes from: The user typing in a value when prompted A file on your hard disk Output typically goes to: The screen (i.e. the MATLAB command window) A file on your hard disk

23 Algorithm Example Example Algorithm: Calculate Volume of a Sphere 1. Get the input: radius of sphere Set the radius Store the radius in a variable 2. Calculate the result: volume of sphere Plug radius into volume equapon Store result in variable 3. Display the result We ll do this later

24 To execute a script, enter its name in the command window (don t include the.m ) Simple Script Example The top of all scripts should contain commented documentapon: H1 line: a short comment on what the script does lookfor will read this Subsequent lines Script name Author info Date Details of what the code does Usage (if a funcpon) Leave one blank line before starpng code Read by help

25 DocumenPng Your Code Any line of MATLAB code that begins with % is ignored by the interpreter Referred to as: comments Do not slow down execupon of your code MATLAB doesn t even read comments, but people do Comments allow you to tell yourself and others what you did Typically you can fit most comments into a single line %set the radius value rad = 23; %compute the area Area = pi * (rad ^ 2); %MATLAB ignores commented lines. Use them!!! In this class: uncommented code gets a zero Every line of code must have a brief comment In all scripts, separate into secpons 1) Header/DocumentaPon 2) CalculaPons 3) Plong 4) Output

26 Output statement

27 Output Statements: disp To be a useful, a script must be able to output a result Simplest output: Print to the command window Use either disp or fprin} disp can print strings or numbers disp can only print one thing at a Pme. disp can print variables For this reason, MATLAB also provides fprintf

28 Output Statements: fprin} fprin} has a somewhat confusing syntax Most programming languages have fprin} (or prin}) Syntax was inherited from C / C++ fprin} does not include a new line ( \n ) awer a string, unless you tell it to do so. Use the new line special character, \n You do not need a space before or awer a special character, but adding a space makes code easier to read. fprin} also recognizes these special characters For more info, see doc fprin} and click on the formang strings link near the botom of the page

29 Output Statements: fprin} fprin} can also be used to print variables Can apply special formang to numeric variable (Very Useful!!) When you use fprin} to print a variable, a variable is indicated by a place holder, in this case %d The variable name must be given awer the string. %f indicates that a floapng point number is to be printed. Can print mulpple variables in one line! ( disp can t do this) fprin} recognizes these conversion characters For more info, see doc fprin} and click on the formang strings link near the botom of the page

30 Output Statements: fprin} fprin} and %f can be used to control just about every aspect of the formang of a floapng point number By default, 7 digits are shown, even though MATLAB variables are stored with 17 digits of precision (if needed) MATLAB double variables can hold only 17 digits. Anything beyond the 17 th place gets displayed as a zero and is not stored. Want to print π rounded to two decimal places? Want to print a variable in scienpfic notapon with 5 decimal places? MATLAB uses a compact format by default, so numbers get displayed in scienpfic notapon. fprin} can override this!

31 Output Statements: fprin} fprin} is also great for prinpng out numbers so they are in neat columns. Note the different results. How does this work? %6.2f Leave at least 6 total spaces for each number includes decimals, exponents, and negapve signs Round to 2 decimal places %06.2f Same as above, but show leading zeros Note that fprintf treats matrices/vectors in strange ways!

32 i>clicker quespon I define the following variable in MATLAB: EarthRadius = 6371; I would like MATLAB to print: The radius of the earth is What is the correct command? A. fprintf('the radius of the earth is %d\n',earthradius); B. fprintf('the radius of the earth is %.1f\n',EarthRadius); C. fprintf('the radius of the earth is %7.2f\n',EarthRadius); D. All of the above

33 WriPng a funcpon

34 User-Defined FuncPons You have already used many built in funcpons in MATLAB plot, sin, cos, int8, double, fprin}, linspace, etc For example linspace The Call, or calling the function Arguments Where the returned value is stored

35 User-Defined FuncPons Lets look at the general funcpon setup: Example: ConverPng mph to m/s The func/on header (required for all func/ons) The reserved word, func/on (1 st line must start with this) Name of func/on (iden/cal to name of m-file without.m) Input arguments (must be provided by the user) Value that is returned (not all func/ons need to return something)

36 User-Defined FuncPons FuncPon must be in your pwd or MATLAB path Call by funcpon name no.m at end Same as scripts! Why ans = ? All variables inside a funcpon are local variables Only exist inside the funcpon!! May be confusing at first, but keeps things Pdy User doesn t care about all of the intermediate variables Only wants the returned value Why are v and mph not defined in the command window?

37 User-Defined FuncPons FuncPons can use any number of variables All of these variables are local! The user won t be aware of them unless he/she opens the m-file

38 A Poorly Writen FuncPon Why is this a bad idea? This is NOT how you return a result The result, v, is not accessible to the user

39 Another Poorly Writen FuncPon Why is this even worse?

40 Another Poorly Writen FuncPon Returned value was stored in ans Not illegal, but bad programming Local variables should not be printed to the screen Confusing!! Not accessible to the user PrinPng variables is slow

41 FuncPons That Make Plots FuncPons can Accept more than one argument (separated by commas) Make plots

42 FuncPons That Make Plots FuncPons can Accept more than one argument (separated by commas) Make plots

43 FuncPons That Return MulPple Values FuncPons can return mulpple values Or even matrices!

44 FuncPons That Return MulPple Values FuncPons can return mulpple values Or even matrices! If you only specify one variable, only the first returned value is stored How could we return both x and y as one matrix xy?

45 How could we return both x and y as one matrix xy? Change the the first line from: [x,y]=plotsinwave2(amp,lam,xmin,xmax,numpts) To xy = plotsinwave2(amp,lam,xmin,xmax,numpts) And add one line before end: i>clicker quespon A. xy = x,y; B. xy = [x;y]; C. xy = [x,y]; D. xy = {x,y};

46 A Script That Calls A FuncPon

47 Thoughts on FuncPons Why Make Func/ons? When a task is owen repeated, funcpons save Pme Faster than using prompt When Wri/ng a Func/on Start by sketching out the basic algorithm (pencil & paper) Write algorithm first as a script Difficult to troubleshoot funcpons because variables are local Once the script works, generalize it into a funcpon FuncPons do not need to return a value Some funcpons make plots, print informapon, or write files If a funcpon does not require an input argument It should probably be lew as a script Remember that scripts can call funcpons mulpple Pmes

48 Next Week Lab 3: MATLAB programming DUE: one week awer the lab starts (EEE) Bring a USB drive Lecture 4: SelecPon statements and loops