view rDiff/src/octave/importdata.m @ 1:08d3a6143873

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## Copyright (C) 2012 Erik Kjellson
##
## This file is part of Octave.
##
## Octave is free software; you can redistribute it and/or modify it
## under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or (at
## your option) any later version.
##
## Octave is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
## General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with Octave; see the file COPYING.  If not, see
## <http://www.gnu.org/licenses/>.

## -*- texinfo -*-
## @deftypefn  {Function File} {@var{A} =} importdata (@var{fname})
## @deftypefnx {Function File} {@var{A} =} importdata (@var{fname}, @var{delimiter})
## @deftypefnx {Function File} {@var{A} =} importdata (@var{fname}, @var{delimiter},  @var{header_rows})
## @deftypefnx {Function File} {[@var{A}, @var{delimiter}] =} importdata (...)
## @deftypefnx {Function File} {[@var{A}, @var{delimiter}, @var{header_rows}] =} importdata (...)
## Importing data from file.
##
## Importing the contents of file @var{fname} into workspace.
##
## Input parameters:
## @itemize
## @item @var{fname}
## The file name for the file to import.
## 
## @item @var{delimiter}
## The character separating columns of data. Use @code{\t} for tab.
## (Only valid for ascii files)
##
## @item @var{header_rows}
## Number of header rows before the data begins. (Only valid for ascii files)
## @end itemize
##
## Different file types are supported:
## @itemize
## @item Ascii table
##
## Importing ascii table using the specified number of header rows and
## the specified delimiter.
##
## @item Image file
##
## @item @sc{Matlab} file
##
## @item Spreadsheet files (depending on external software)
##
## @item Wav file
##
## @end itemize
##
## @seealso{textscan, dlmread, csvread, load}
## @end deftypefn

## Author: Erik Kjellson <[e-mail]>

function [output, delimiter, header_rows] = importdata (varargin)

    
  ## Default values
  fname   = "";
  delimiter  = "";
  header_rows = -1;

  ##########

  ## Check input arguments

  if (nargin < 1)
    print_usage ();
  endif

  fname = varargin{1};
  ## Check that the file name really is a string
  if (! ischar (fname))
    error ("importdata: file name needs to be a string");
  endif
  if ( strcmpi (fname, "-pastespecial"))
    error ("importdata: option -pastespecial not implemented");
  endif

  if (nargin > 1)
    delimiter = varargin{2};
    ## Check that the delimiter really is a string
    if (!ischar (delimiter))
      error("importdata: delimiter needs to be a character");
    endif
    if (length (delimiter) > 1 && !strcmpi (delimiter, "\\t"))
      error("importdata: delimiter cannot be longer than 1 character");
    endif
    if (strcmpi (delimiter, "\\"))
      delimiter = "\\\\";
    endif
  endif

  if (nargin > 2)
    header_rows = varargin{3};
    if (!isnumeric (header_rows) || header_rows < 0)
      error ("importdata: number of header rows needs to be an integer number >= 0");
    endif
  endif

  if (nargin > 3)
    error ("importdata: too many input arguments");
  endif

  ##########

  ## Check file format
  ## Get the extension from the file name.
  [d n fileExt v] = fileparts (fname);
  ## Make sure file extension is in lower case.
  fileExt = lower (fileExt);

  switch fileExt
    case {".au", ".snd"}
      error (sprintf ("importdata: not implemented for file format %s", 
                      fileExt));
    case ".avi"
      error (sprintf ("importdata: not implemented for file format %s", 
                      fileExt));
    case {".bmp", ".cur", ".gif", ".hdf", ".ico", ".jpe", ".jpeg", ".jpg", \
          ".pbm", ".pcx", ".pgm", ".png", ".pnm", ".ppm", ".ras", \
          ".tif", ".tiff", ".xwd"}
      delimiter  = NaN;
      header_rows = 0;
      [output.cdata, output.colormap, output.alpha] = imread (fname);
    case ".mat"
      delimiter  = NaN;
      header_rows = 0;
      output = load (fname);
    case {".wk1", ".xls", ".xlsx", ".dbf", ".pxl"}
      ## If there's no Excel file support simply fall back to unimplemented.m
      output = xlsread (fname);
    case {".ods", ".sxc", ".fods", ".uos", ".xml"}
      ## unimplemented.m only knows ML functions; odsread isn't one but is in OF
      try
        output = odsread (fname);
      catch
        ## Fall back to unimplemented.m.
        output = xlsread (fname);
      end_try_catch
    case {".wav", ".wave"}
      delimiter  = NaN;
      header_rows = 0;
      [output.data, output.fs] = wavread (fname);
    otherwise
      ## Assume the file is in ascii format.
      [output, delimiter, header_rows]  = \
          importdata_ascii (fname, delimiter, header_rows);
  endswitch

  ## If there are any empty fields in the output structure, then remove them
  if (isstruct (output) && length (output) == 1)
    fields = fieldnames (output);
    for i=1:length (fields)
      if (isempty (getfield (output, fields{i})))
        output = rmfield (output, fields{i});
      endif
    endfor

    ## If only one field is left, replace the structure with the field,
    ## i.e. output = output.onlyFieldLeft

    ## Update the list of fields
    fields = fieldnames (output);
    if (length (fields) == 1)
      output = getfield (output, fields{1});
    endif
  endif
endfunction


########################################

function [output, delimiter, header_rows] = \
      importdata_ascii (fname, delimiter, header_rows)

  ## Define the fields in the output structure so that the order will be
  ## correct.

  output.data       = [];
  output.textdata   = [];
  output.rowheaders = [];
  output.colheaders = [];

  ## Read file into string and count the number of header rows
  #file_content = fileread (fname);
  file_content_rows={};
  fid=fopen(fname);
  currline=0;
  firstline=1;
  while 1==1
      if not(isempty(currline))
          if currline==-1
              break
          end
      end     
      currline=fgetl(fid);
      file_content_rows{end+1}=currline;
  end
  fclose(fid);
  file_content_rows={file_content_rows{1:(end-1)}};
  
  ## Split the file into rows (using \r\n or \n as delimiters between rows).
  #file_content_rows = regexp (file_content, "\r?\n", "split");

  ## FIXME: guess delimiter, if it isn't defined
  if (isempty (delimiter))
    error ("importdata: Guessing delimiter is not implemented yet, you have to specify it.");
  endif

  ## FIXME: A more intelligent way to count number of header rows. This
  ## is needed e.g. when delimiter=' ' and the header contains spaces...

  ## If number of header rows is undefined, then count the number of
  ## header rows by step through row by row and look for the delimiter.
  ## Assume that the header can't contain any delimiter.
  if (header_rows < 0)
    header_rows = 0;
    for i=1:length (file_content_rows)
      if (isempty (regexp(file_content_rows{i}, delimiter, "once")))
        header_rows++;
      else
        ## Data part has begun and therefore no more header rows can be
        ## found
        break;
      endif
    endfor
  endif

  ## Put the header rows in output.textdata.
  if (header_rows > 0)
    output.textdata   = file_content_rows (1:header_rows)';
  endif

  ## If space is the delimiter, then remove spaces in the beginning of
  ## each data row.
  if (strcmpi (delimiter, " "))
    for i=(header_rows+1):length (file_content_rows)
      ## strtrim does not only remove the leading spaces but also the
      ## tailing spaces, but that doesn't really matter.
      file_content_rows{i} = strtrim (file_content_rows{i});
    endfor
  endif

  ## Remove empty data rows. Go through them backwards so that you wont
  ## get out of bounds.
  for i=length (file_content_rows):-1:(header_rows + 1)
    if (length (file_content_rows{i}) < 1)
      file_content_rows = [file_content_rows(1:i-1), \
                           file_content_rows(i+1:length(file_content_rows))];
    endif
  endfor

  ## Count the number of data columns. If there are different number of
  ## columns, use the greatest value.
  data_columns = 0;
  delimiter_pattern = delimiter;
  ## If space is the delimiter, then multiple spaces should count as ONE
  ## delimiter. Also ignore leading spaces.
  if (strcmpi (delimiter, " "))
    delimiter_pattern = ' +';
  endif
  for i=(header_rows+1):length(file_content_rows)
    data_columns = max (data_columns,
                        length (regexp (file_content_rows{i},
                                        delimiter_pattern, "split")));
  endfor

  ## Go through the data and put it in either output.data or
  ## output.textdata depending on if it is numeric or not.
  output.data = NaN (length (file_content_rows) - header_rows, data_columns);

  cut_rows=zeros(1,data_columns);
  for i=(header_rows+1):length(file_content_rows)
    ## Only use the row if it contains anything other than white-space
    ## characters.
    if (any (file_content_rows{i} != " "))
      row_data = regexp (file_content_rows{i}, delimiter_pattern, "split");

      for j=1:length(row_data)
        ## Try to convert the column to a number, if it works put it in
        ## output.data, otherwise in output.textdata
        if (!isempty (row_data{j}))
          data_numeric = str2double (row_data{j});
          if and(!isempty (data_numeric),not(isnan(data_numeric)))
            output.data(i-header_rows, j) = data_numeric;
            if not(isnan(data_numeric))
                cut_rows(j)=1;
            end
          else
            output.textdata{i,j} = row_data{j};
          endif
        endif
      endfor

    endif
  endfor
  output.data=output.data(:,cut_rows>0);
  
  ## Check wether rowheaders or colheaders should be used
  if ((header_rows == data_columns) && (size (output.textdata, 2) == 1))
    output.rowheaders = output.textdata;
  elseif (size (output.textdata, 2) == data_columns)
    output.colheaders = output.textdata(end,:);
  endif

  ## When delimiter = "\\t" convert it to a tab, done for Matlab compatibility.
  if (strcmp (delimiter, '\t'))
    delimiter = "\t";
  endif

endfunction


function [RET]=regexp(ARG1,ARG2,ARG3)
%ARG3 is always 'split' in this context
  if (strcmp (ARG2, '\t'))
    ARG2 = "\t";
  endif
  RET = strsplit(ARG1,"\t",fixed=true);
endfunction

########################################

%!test
%! # Comma separated values
%! A = [3.1 -7.2 0; 0.012 6.5 128];
%! fn  = tmpnam ();
%! fid = fopen (fn, "w");
%! fputs (fid, "3.1,-7.2,0\n0.012,6.5,128");
%! fclose (fid);
%! [a,d,h] = importdata (fn, ",");
%! unlink (fn);
%! assert (a, A);
%! assert (d, ",");
%! assert (h, 0);

%!test
%! # Tab separated values
%! A = [3.1 -7.2 0; 0.012 6.5 128];
%! fn  = tmpnam ();
%! fid = fopen (fn, "w");
%! fputs (fid, "3.1\t-7.2\t0\n0.012\t6.5\t128");
%! fclose (fid);
%! [a,d,h] = importdata (fn, "\\t");
%! unlink (fn);
%! assert (a, A);
%! assert (d, "\t");
%! assert (h, 0);

%!test
%! # Space separated values, using multiple spaces to align in columns.
%! A = [3.1 -7.2 0; 0.012 6.5 128];
%! fn  = tmpnam ();
%! fid = fopen (fn, "w");
%! fprintf (fid, "%10.3f %10.3f %10.3f\n", A(1,:));
%! fprintf (fid, "%10.3f %10.3f %10.3f\n", A(2,:));
%! fclose (fid);
%! [a,d,h] = importdata (fn, " ");
%! unlink (fn);
%! assert (a, A);
%! assert (d, " ");
%! assert (h, 0);

%!test
%! # Header
%! A.data = [3.1 -7.2 0; 0.012 6.5 128];
%! A.textdata = {"This is a header row."; \
%!               "this row does not contain any data, but the next one does."};
%! fn  = tmpnam ();
%! fid = fopen (fn, "w");
%! fputs (fid, [A.textdata{1} "\n"]);
%! fputs (fid, [A.textdata{2} "\n"]);
%! fputs (fid, "3.1\t-7.2\t0\n0.012\t6.5\t128");
%! fclose (fid);
%! [a,d,h] = importdata (fn, "\\t");
%! unlink (fn);
%! assert (a, A);
%! assert (d, "\t");
%! assert (h, 2);

%!test
%! # Ignore empty rows containing only spaces
%! A = [3.1 -7.2 0; 0.012 6.5 128];
%! fn  = tmpnam ();
%! fid = fopen (fn, "w");
%! fprintf (fid, "%10.3f %10.3f %10.3f\n", A(1,:));
%! fputs (fid, "      ");
%! fprintf (fid, "%10.3f %10.3f %10.3f\n", A(2,:));
%! fclose (fid);
%! [a,d,h] = importdata (fn, " ");
%! unlink (fn);
%! assert (a, A);
%! assert (d, " ");
%! assert (h, 0);

%!test
%! # Exponentials
%! A = [3.1 -7.2 0; 0.012 6.5 128];
%! fn  = tmpnam ();
%! fid = fopen (fn, "w");
%! fputs (fid, "+3.1e0\t-72E-1\t0\n12e-3\t6.5\t128");
%! fclose (fid);
%! [a,d,h] = importdata (fn, "\\t");
%! unlink (fn);
%! assert (a, A);
%! assert (d, "\t");
%! assert (h, 0);

%!test
%! # Missing values
%! A = [3.1 NaN 0; 0.012 6.5 128];
%! fn  = tmpnam ();
%! fid = fopen (fn, "w");
%! fputs (fid, "3.1\t\t0\n0.012\t6.5\t128");
%! fclose (fid);
%! [a,d,h] = importdata (fn, "\\t");
%! unlink (fn);
%! assert (a, A);
%! assert (d, "\t");
%! assert (h, 0);

%!test
%! # CRLF for line breaks
%! A = [3.1 -7.2 0; 0.012 6.5 128];
%! fn  = tmpnam ();
%! fid = fopen (fn, "w");
%! fputs (fid, "3.1\t-7.2\t0\r\n0.012\t6.5\t128");
%! fclose (fid);
%! [a,d,h] = importdata (fn, "\\t");
%! unlink (fn);
%! assert (a, A);
%! assert (d, "\t");
%! assert (h, 0);