Importing XYZ matrix into Matlab

I have a set of 6 XY wavelength/absorption datasets, each with a different concentration. I have formed them into a 312x7 XYZ matrix with the first row holding the Y-variables (concentration), and the first column holding the X-variables (wavelength). I have used this data format quite frequently in other programs, but I cannot figure out how to get Matlab to recognize the data properly. I would like to use Matlab to baseline correct the data and then solve for the molar absorptivity at each wavelength.

Example:

    0    10   25    50    75    100
290 0.0  0.1  0.12  0.15  0.2   0.3
291 0.0  0.11 0.121 0.151 0.21  0.31

Thanks in advance for your help.

Answer 1

[Cedric]

EDIT: see my second solution for a more flexible approach.

=== 1st solution.

 % - Read content.
 fid     = fopen( 'myFile.txt', 'r' ) ;
 content = fscanf( fid, '%f', Inf ) ;
 fclose( fid ) ;

 % - Extact headers and data.
 colHeader = content(1:6).' ;
 content   = reshape( content(7:end), 7, [] ).' ;
 rowHeader = content(:,1) ;
 data      = content(:,2:end) ;

With that, you get..

 >> colHeader
 colHeader =
     0    10    25    50    75   100

 >> rowHeader
 rowHeader =
   290
   291

 >> data
 data =
         0    0.1000    0.1200    0.1500    0.2000    0.3000
         0    0.1100    0.1210    0.1510    0.2100    0.3100

PS: there are other approaches, e.g. based on FGETL for the col. header and then TEXTSCAN, but I personnaly prefer reading the file in one shot and then reshaping/extracting numbers appropriately.

=== 2nd solution.

If the number of columns could vary among files though, I would go for a first step reading the first line of the file and determining dynamically the number of columns, before reading/processing the rest. For example:

 fid = fopen( 'myFile.txt', 'r' ) ;
 colHeader = sscanf( fgetl(fid), '%f' ).' ;     % Read/convert 1st line only.
 nDataCol  = numel( colHeader ) ;               % Determine # of data columns.
 content   = fscanf( fid, '%f', Inf ) ;         % Read rest of the file.
 fclose(fid) ;
 content   = reshape( content, nDataCol+1, [] ).' ;
 rowHeader = content(:,1) ;
 data      = content(:,2:end) ;

[Jan]

@Cedric: "buffer" shadows the built-in function buffer. Although this command can solve some problems in the Matlab forums, I used it only one time for my real-world programs. So perhaps it is recommended to use another name, but I really do not know if the general rule is useful for rarely used functions.

[Cedric]

@Jan: you are right, it's a bad habit of mine actually (that I refuse to loose because the term is so generic that, AFAIK, it was a mistake to name this built-in this way), especially because I know the built-in! However, I shouldn't propagate my bad habits ;-), so I'll update my answer.

I wanted to start a discussion about conflicting function names between toolboxes/libs/etc by the way. I'd love to have something like .. well see Jan's new thread!

[Soren]

Great! The data is in a .csv format. I think this is causing some issues in the parsing scheme.

% - Read content. fid = fopen( 'rawdata_array.csv', 'r' ) ; content = fscanf( fid, '%f', Inf ) ; fclose( fid ) ; % - Extact headers and data. colHeader = content(1:6).' ; buffer = reshape( content(7:end), 7, [] ).' ; rowHeader = buffer(:,1) ; data = buffer(:,2:end) ; Index exceeds matrix dimensions.

Thanks for your help in advance!

[Cedric]

So the separator is the comma and the first line is starting with a comma (empty content for 1st element)? If so, loading the data is much simpler:

 content   = csvread( 'rawdata_array.csv' ) ;
 colHeader = content(1,2:end) ;
 rowHeader = content(2:end,1) ;
 data      = content(2:end,2:end) ;

[Soren]

Thank you very much for your quick and accurate assistance!

Soren

[Cedric]

You're welcome!