% Laboratory in Oceanography - Data and Methods
% SMAST, UMass Dartmouth
%
% Examples of assigning different data types in Matlab, and of reading
% and writing to and from various formatted data files.
%
% Written by Miles A. Sundermeyer, 2/9/09

% set a breakpoint - use F10 to step line by line in debug mode
keyboard

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% DATA TYPES
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Create arrays of different data types - see what happens when combined
%% double and single
A = [sin(0:2*pi/9:2*pi)]			% double by default

A_single = single(A)		% create a single

AA = [A; A_single]		% combines to one data type 
				% reverts to the simpler data type
whos

%% int8
A_int8 = int8(A)		% create a signed integer(8) array

AA = [A; A_single; A_int8]	% combines to one data type
				% reverts to the simpler data type
whos

%% logical
A_logical = logical(A)		% all non-zero real elements become 1, 
				% zeros become 0, nans not allowed

A_logical = A>0			% using logical operators

disp(A)				% alternate way of displaying to workspace
disp(A_logical)

AA = [A A_logical]		% show the two different logical arrays
				% default here is to convert logical to double
whos

%% char	
A_char = 'drifter.dat'		% array of characters to create a string

whos

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Now store all these different data types in a single cell array
Acell{1} = A
Acell{2} = A_single
Acell{3} = A_int8
Acell{4} = A_logical
Acell{5} = A_char

whos

% show indexing of cell array - note curly brackets, {}'s, as well as ()'s
Acell{1}(1:5)
A(1:5)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Now store these in a structure
Astruct.double = A
Astruct.single = A_single
Astruct.int8 = A_int8
Astruct.logical = A_logical
Astruct.char = A_char

whos

% show indexing of structure 
Astruct.int8(1:5)
A_int8

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Complex Numbers
A_cmplx = 2+A*i			% complex double
whos

A_cmplx = 2+A_single*i		% complex single 
whos

A_cmplx = 2+A_logical*i		% other allowed types convert to double complex
whos

%A_cmplx = 2*A_int8*i		% int not allowed with complex operations

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% More on characters and strings
str = 'Hello';
whos 

% Arrays of chars to create strings
% Examples
msg = 'You''re right!'
name = ['Thomas' ' R. ' 'Lee']
S = {'Hello' 'Yes' 'No' 'Goodbye'}
C = ['Hello  '; 'Yes    '; 'No     '; 'Goodbye']

name = strcat('Thomas',' R.',' Lee')
C = strvcat('Hello','Yes','No','Goodbye')

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Show how Matlab uses numbers for characters
% can use uint8 or double function to convert characters to their numeric values:
str_numeric = uint8(str)

% The char function converts the integer vector back to characters:
str_alpha = char([72 101 108 108 111])

% Show a bunch of characters as an array based on numeric values
char(32:126)				% basic ascii characters
char(170:255)				% various special characters

% Reveal what this array looks like as numbers
C = strvcat('Hello','Yes','No','Goodbye')
uint8(C)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Constructing String Arguments in Code 
% Strings can be combined as arrays in same way as numbers e.g., 
for d=1:3
  fnm = ['drifter' int2str(d) '.dat']
  %load(fnm)
end

% The ‘eval’ Function
% Works with string variables to evaluate strings as Matlab commands, e.g., 
for d=1:3
  s = ['load drifter' int2str(d) '.dat']
  %eval(s)
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% LOADING AND SAVING DATA
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
help fileformats
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Matlab formatted binary data
whos

save test_data A A_char		% save the data A A_char in file test_data.mat
what				% look to see if it's there

% clear all			% clear the Matlab workspace
who 
load test_data A A_char		% reload the data
load('test_data','A','A_char')	% accomplishes same as previous line
fnm = 'test_data'; load(fnm)	% same again

whos				% check for the reloaded data

% Note: 'save' without any arguments saves all variables in file 'matlab.mat'
% 	'load' without any arguments loads entire contents of .mat file
% Note: Can also use '*' wildcard commands with 'load' and 'save'

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% ascii
save test_data.dat -ascii A 
load test_data.dat		% puts data in variable <fnm root>
A = load('test_data.dat')	% puts data in variable A

% Note: The following is problematic since the arrays are different sizes 
% and types - better to use Matlab format in this case
save test_data.dat -ascii A A_char
%load test_data.dat		% gives error

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Structures
% save a structure as it's component variables in a .mat file
save test_data -struct Astruct 
whos -file test_data		% list contents of file 'test_data.mat'
% ASIDE: what 'best practices' rule have I broken in the above example?

% load above data as a structure
S = load('test_data')
whos S				% look at properties of variable S
S				% look at structure elements

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

clear

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% CSV (Comma Separated Values)
% load ONichols_2008_V1.csv		% gives error due to header
S = csvread('ONichols_2008_V1.csv',1,0)	% indices for read are zero based

% alternative using importdata
S = importdata('ONichols_2008_V1.csv')	% more general wrapper for various
					% file type reads
S
fieldnames(S)
S.data
S.textdata
S.colheaders

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% More CSV (Comma Separated Values), but with characters mixed in
% load ONichols_2008.csv		% gives error due to header
load ONichols_2008_noheader.csv % still has trouble with character '/'
				% although no error is encountered
ONichols_2008_noheader(1,:)	% note 1st column is wrong

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Import the file
S = importdata('ONichols_2008.csv',',',1);

header = S.textdata(1,:)
[year month day] = datevec(S.textdata(2:end,1))

% see also datenum and datestr
SS = datenum(S.textdata(2:end,1))
datestr(SS)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Write to a csv file
dlmwrite('ONichols_2008_out.csv',S.data,'delimiter',',')

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

clear

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% XLS files
fnm = 'SHabtes_ABT_2003_data.xls' 

[A, DESCR, FORMAT] = xlsfinfo(fnm)
[NUMERIC,TXT,RAW]=xlsread(fnm,DESCR{1}) 

whos

% Note: NUMERIC contains all cell values that Matlab could interpret as numeric
%	TXT contains all cell values that Matlab interpreted as text, in this
%		case just the header line, so TXT is a 1x8 cell array
% 	RAW contains everything Matlab interpreted as non-empty cell data

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% XLS files again
fnm = 'CPeptitas_Silicate_diatom.xlsx' 

[A, DESCR, FORMAT] = xlsfinfo(fnm)	% gives read error for xlsx files
[NUMERIC,TXT,RAW]=xlsread(fnm,DESCR{1}) 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fnm = 'CPeptitas_Silicate_diatom.xls' 

[A, DESCR, FORMAT] = xlsfinfo(fnm)
[NUMERIC,TXT,RAW]=xlsread(fnm,DESCR{1}) 

whos