Extracting information from file

I am trying to extract information from the attached file and write them into a matrix with one column each from sample name, number of cells and porosity. I have been trying textscan and sscanf, but am not sure how to search the structure of the text.

[per isakson]

• Is &nbsp cutTDM400_111_111_000_000_000 &nbsp a sample name?
• Does &nbsp [1;33m--- Initializing LBM Domain &nbsp indicate the beginning of a "cell" ?
• I would use fileread and regexp

[Julia]

• yes, cutTDM400_111_111_000_000_000 is a sample name (and I want to extract the Num of cells and Porosity).
• The beginning of a cell is indicated by e.g. Running sample cutTDM400_111_111_000_000_000, after that it is solved three times, but the Num of cells and porosity value are the same.
• So the next row would be the values for cutTDM200_111_111_111_000_000.

[per isakson]

Now, I think I understand. The word "cells" in "Num of cells" has nothing to do with the word "cell" in "beginning of a cell is indicated".

First, I thought you wanted to count some kind of "sections" of the file. I missed "Num of cells = 32000000" when I first browsed the file.

Answer 1

[per isakson]

This is one way to read the your file

>> tic, sas = nohup, toc
sas = 
1x1173 struct array with fields:
    SampleName
    NumOfCells
    Porosity
Elapsed time is 27.000338 seconds.
>> ix = find( strcmp( {sas.SampleName}, 'cutTDM050_111_121_221_222_122' ) )
ix =
   583
>> sas(ix).Porosity
ans =
    0.0828    0.0828    0.0828
>> sas(ix).NumOfCells
ans =
      125000      125000      125000

where (in one m-file)

function    sas = nohup
%%    
    str = fileread( 'nohup.txt' ); 
%%
    heading_string  = 'Running Sample';
    trailing_string = '=============================================='; 
    %
    xpr = sprintf( '(?<=%s).+?(?=%s)', heading_string, trailing_string );
    cac = regexp( str, xpr, 'match' );
%% 
    sas = struct( 'SampleName',repmat({''},[1,length(cac)]) ...
                , 'NumOfCells',{[]}, 'Porosity', {[]}       );
    for jj = 1 : length( cac )
        sas(jj) = nohup_( cac{jj} ); 
    end
end
function    sas = nohup_( str )
    %
    sas.SampleName ... 
    =   regexp( str, 'cutTDM\d{3}_\d{3}_\d{3}_\d{3}_\d{3}_\d{3}', 'match', 'once' );
    %
    cac = regexp( str, '(?<=Num of cells +\= *)\d+', 'match' ); 
    sas.NumOfCells = str2double( cac );
    %
    cac = regexp( str, '(?<=Porosity +\= *)[\d+\.]+', 'match' ); 
    sas.Porosity = str2double( cac );
end

&nbsp

Comments:

The function is slow. Nearly all the time is spend with regexp searching for "Num of cells" and "Porosity". "the Num of cells and porosity value are the same." may be used improve speed. Adding 'once' to these two calls of regexp increases the speed forty times. That's much more than I anticipated; I don't understand; I cannot see what's taking all the extra time.

>> tic, sas = nohup, toc
sas = 
1x1173 struct array with fields:
    SampleName
    NumOfCells
    Porosity
Elapsed time is 0.645206 seconds.
>> ix = find( strcmp( {sas.SampleName}, 'cutTDM050_111_121_221_222_122' ) )
ix =
   583
>> sas(ix).Porosity
ans =
    0.0828
>> sas(ix).NumOfCells
ans =
      125000
>>

[Julia]

Great, thank you very much.