Matlab course at. P. Ciuciu 1,2. 1: CEA/NeuroSpin/LNAO 2: IFR49

Transcription

1 Matlab course at NeuroSpin P. Ciuciu 1,2 1: CEA/NeuroSpin/LNAO 2: IFR49 Mar 5, 2009

2 Outline 2/9 Lesson0: Getting started: environment,.m and.mat files Lesson I: Scalar, vectors, matrices and related operations Lesson II: String manipulations, cell array, files, structures Lesson III: Basic coding: instructions, tests (if), loops (for, while, switch) Lesson IV: Visualization tools + Exercises (fft, conv,...) Lesson V: Scripts, functions, API management (varargin, varargout), debugging Lesson VI: Coding sprint and interaction with SPM5

3 Lesson Two II: main String issues manipulation 3/9 Cell Arrays cell(n) is an N-by-N cell array of empty matrices cell(m,n) or cell([m,n]) is an M-by-N cell array A= {[1] [2 3 4]; [5; 9] [6 7 8; ]} ; size(a) B=cell2mat(A) ; Ab=mat2cell(B) C= {[1] [2 3 4]; 'Philippe', B} num2cell(a) : converts the array A into a cell array by placing each element of A into a separate cell.

4 Lesson Two II: main String issues manipulation String types s='this is my first string' creates a character array and assigns the given text string to the variable s name = ['Philippe' 'Ciuciu'] or strcat('philippe','ciuciu') C =char('hello','yes','no','goodbye') or strvcat('hello','yes','no','goodbye') cellstr : cell array of strings : {'Hello', 'Yes', 'No'} Check string definition : ischar, iscellstr Display strings s = 'toto' ; disp(s) displays the content of s Error messages are best displayed with the function error: error('sorry, the matrix must be symmetric') when placed in an M-File, it causes execution to exit the M-file. 4/9

5 Lesson Two II: main String issues manipulation Interactive prompt: iter = input('enter the number of iterations:'); when this prompt message is displayed execution pauses while the user keys in the input data. Upon pressing the return key, the data is assigned to the variable iter and execution resumes. Output formats format short: fixed point with 4 decimal places (the default) format long: fixed point with 14 decimal place format short e: scientific notation with 4 decimal places format long e:scientific notation with 15 decimal places Once invoked, the chosen format remains in effect until changed. format compact will suppress most blank lines 5/9

6 Lesson Two II: main String issues manipulation Write formatted data to string sprintf :[s,errmsg] = sprintf(format,a,...) formats the data in the real part of array A, under control of the specified format string, and returns it in S. errmsg is an optional output argument that returns an error message string if an error occurred. sprintf is the same as fprintf except that it returns the data in a string variable rather than writing it to a file. Examples s=sprintf('%0.5g', (1+sqrt(5))/2) s= s=sprintf('%0.5g',1/eps) s=4.5036e+15 s=sprintf('%15.5f',1/eps) s= s=sprintf('%d',round(pi)) s=3 s= sprintf('%s','hello') s=hello s=sprintf('the array is %dx%d.',2,3) s=the array is 2x3. sprintf('\n') is the line termination character 6/9

7 Write formatted data to screen fprintf :fprintf(fid,format,a,...) write formatted data to file The special formats \n,\r,\t,\b,\f can be used to produce linefeed,carriage return, tab, backspace, and formfeed characters respectively. Use \\ to produce a backslash character and %% to produce the percent character Lesson Two II: main String issues manipulation Tools for string manipulations findstr : find one string within another strmatch: find possible matches for string strcmp/strcmpi/strncmp: compare strings/ ignoring case lower, upper: convert string to lower/upper case deblank: remove trailing blanks regexp, regexpi: match regular expressions 7/9

8 Lesson Two main II: Strings issues in & fmri files 8/9 File string manipulation Platform dependent implementation build filename: fullfile, fileparts build pathname: pathsep, filesep

9 Lesson Two main II: I/O issues management 9/9 File management open file: fid=fopen(filename, permission) close file: fclose(fid) read binary data file: fread(fid, size, precision) read formatted data from bin file: fscanf(fid,format, size) read formatted data from text file: textscan(fid,format) read tex files: fgetl(fid), fgets(fid) (with line terminator) reread from the beginning: frewind(fid) set file position indicator: fseek(fid,offset,origin) write binary data to file: fwrite(fid,a, precision) write formatted data to file:fprintf(fid,format, a, precision) write text file: save toto.dat A ascii

10 Two Lesson main II: issues Structures 10/9 Structure definition Contain pairs of (fields,values) like a dictionary A=struct([]); creates an empty structure A=struct('field1',VALUES1,'field2',VALUES2,...) creates a structure array with the specified fields and values. The value arrays VALUES1, VALUES2, etc. must be cell arrays of the same size, scalar cells or single values. The size of the resulting structure is the same size as the value cell arrays or 1-by-1 if none of the values is a cell. Structure manipulation A = struct('type',{'big','little'},'color','red','x',{3 4}) Get access to struct array elements: A(1), A(2).type A=struct('strings',{{'hello','yes'}},'lengths',[5 3]) checking structure: isstruct fields: getfield, setfield, fieldnames, rmfield, isfield

11 Lesson Two main II: String issues & Structures Structure for path manipulation List directory: dir s=dir('/data/home/i2bm/work/matlabcourse') s(1).name, s(1).date, s(1).bytes, s(1).isdir List MATLAB-specific files in directory: what what('.').path, what('.').m, what('.').mat,... Example with SPM load SPM SPM.xY, SPM.xY.RT, SPM.xY.VY SPM.xX, SPM.xX.X SPM.nscan SPM.Sess SPM.swd SPM.xCon... 11/9