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view m-toolbox/classes/@ao/fromDatafile.m @ 35:4be5f7a5316f database-connection-manager
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author | Daniele Nicolodi <nicolodi@science.unitn.it> |
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date | Mon, 05 Dec 2011 16:20:06 +0100 |
parents | f0afece42f48 |
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% FROMDATAFILE Construct an ao from filename AND parameter list %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % FUNCTION: fromDatafile % % DESCRIPTION: Construct an ao from filename AND parameter list % % CALL: a = fromFilenameAndPlist(a, pli) % % PARAMETER: a: empty ao-object % pli: plist-object (must contain the filename) % % VERSION: $Id: fromDatafile.m,v 1.51 2011/10/12 20:30:51 mauro Exp $ % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function a = fromDatafile(ain, pli) utils.helper.msg(utils.const.msg.PROC1, 'constructing from filename and/or plist'); VERSION = '$Id: fromDatafile.m,v 1.51 2011/10/12 20:30:51 mauro Exp $'; % get AO info mi = ao.getInfo('ao', 'From ASCII File'); % Set the method version string in the minfo object mi.setMversion([VERSION '-->' mi.mversion]); % Get filename file_name = find(pli, 'filename'); file_path = find(pli, 'filepath'); [filePath, fileName, ext] = fileparts(file_name); % Add the file extenstion to the fileName fileName = strcat(fileName, ext); % Define the path of the if ~isempty(file_path) && ~isempty(filePath) % Do nothing because we will use filePath elseif ~isempty(file_path) filePath = file_path; elseif ~isempty(filePath) % Do nothing because we will use filePath else filePath = pwd(); end absolutePathname = fullfile(filePath, fileName); % Check if the abolute Pathname exist if ~exist(absolutePathname, 'file') absolutePathname = fileName; end %%%%%%%%%% Get default parameter list %%%%%%%%%% dpl = ao.getDefaultPlist('From ASCII File'); pl = applyDefaults(dpl, pli); pl = pset(pl, 'filename', fileName); pl = pset(pl, 'filepath', filePath); data_type = find(pl, 'type'); columns = find(pl, 'columns'); maxLines = find(pl, 'maxlines'); comment_char = find(pl, 'comment_char'); delimiter = find(pl, 'delimiter'); use_fs = find(pl, 'fs'); a = []; orig_col = columns; % necessary for the history t0 = find(pl, 't0'); %%%% if strcmpi(data_type, 'cdata') use_fs = 1; end %%%%%%%%%% read file %%%%%%%%%% [fid,msg] = fopen (absolutePathname, 'r'); if (fid < 0) error ('### can not open file: %s \n### error msg: %s', absolutePathname, msg); end try %%%%%%%%%% create scan format: '%f %f %f %f %f %*[^\n]' %%%%%%%%%% scan_format = ''; read_col = 0; %%%%%%%%%% Read first comment and empty lines %%%%%%%%%% while ~feof(fid) fidPos = ftell(fid); fline = fgetl(fid); % check if there was an error reading the file [errmsg, errnum] = ferror(fid); if errnum ~= 0 error('### an error happened reading the first part of the file: %s', errmsg) end if fline == -1 % we hit the end of file error('### the file is empty!') end fline = strtrim(fline); if ~isempty(fline) && ~(~isempty(comment_char) && strncmp(fline, comment_char, numel(comment_char))) fseek(fid, fidPos, 'bof'); break; end end %%%%%%%%%% Get/Count max number of lines %%%%%%%%%% if isempty(maxLines) maxLines = numLines(fid); utils.helper.msg(utils.const.msg.PROC2, 'Counting lines: %d', maxLines); end %%%%%%%%%% Check max number of columns %%%%%%%%%% maxColumns = numCols(fid, delimiter); if isempty(columns) && strcmpi(data_type, 'cdata') columns = 1:maxColumns; orig_col = columns; end if maxColumns < max(columns) error('### The file doesn''t have more than [%d] columns. But you want to read the column [%d].', maxColumns, max(columns)); end %%%%%%%%%% Check number of columns %%%%%%%%%% if isempty(columns) && ~strcmpi(data_type, 'cdata') error('### Please specify at least one column number to read the data file.'); end %%% preallocate data array f_data = zeros(maxLines, numel(unique(columns))); %%% check if using robust read: 'yes'/'no' or true/false or 'true'/'false' robust = utils.prog.yes2true(find(pl, 'Robust')); if robust f_data = robustRead(fid, f_data, columns, orig_col); else %%% Based on skipping the not used columns we have to transform the columns. %%% We must transform the columns [ 2 5 2 6 5 7] to [ 1 2 1 3 2 4] %%% In each loop we have to replace the corresponding value. In the first loop %%% the first minimum, in the second loop the second minimum, ... with the %%% current loop number. sort_col = sort(columns); for jj = 1:max(columns) if ismember(jj, columns) scan_format = [scan_format '%n']; read_col = read_col + 1; replace = min(sort_col); columns (columns == replace) = read_col; sort_col(sort_col == replace) = []; else scan_format = [scan_format '%*n']; end end scan_format = [deblank(scan_format) '%*[^\n]']; %%%%%%%%%% Read data %%%%%%%%%% readlines = min(50000, maxLines); nlines = 0; %%% read file to end while ~feof(fid) && nlines < maxLines if isempty(comment_char) && isempty(delimiter) C = textscan(fid, scan_format, readlines); elseif isempty(comment_char) && ~isempty(delimiter) C = textscan(fid, scan_format, readlines, 'Delimiter', delimiter); elseif ~isempty(comment_char) && isempty(delimiter) C = textscan(fid, scan_format, readlines, 'CommentStyle', comment_char); else C = textscan(fid, scan_format, readlines, 'CommentStyle', comment_char, 'Delimiter', delimiter); end if isempty(C{1}) && nlines == 0 error('\n### There are no data.\n### Did you use the right comment character?\n### The current comment character is: [%s]\n### Use a parameter list with the parameter:\n### plist(''comment_char'', ''%%'')', comment_char); end f_data(nlines+1:nlines+size(C{1},1),:) = cell2mat(C); nlines = nlines + length(C{1}); utils.helper.msg(utils.const.msg.PROC2, 'read %09d lines of %09d', nlines, maxLines); end %%% get only the data we want if size(f_data,1) > nlines f_data = f_data(1:nlines, :); end end catch ME % An error occurred during the scan fclose(fid); rethrow(ME); end % The scan was successful fclose(fid); %%%%%%%%%% Create for each column pair the data object %%%%%%%%%% % This is a list of keys which support multiple values. We need to % process the history plist to account for this so that the hisotry of a % single object only contains the value that the user intended that % object to get. % TODO: find a nicer way to specify this? keys = {'name', 'description', 'xunits', 'yunits', 't0'}; if isempty(use_fs) %%%%%%%%%% The numbers in columns must be even %%%%%%%%%% if length(columns) == 1 if ~strcmp(data_type, 'cdata') error('A single column file with no sample rate set can only be used to build a cdata AO'); end else if mod(length(columns),2) ~= 0 error('### The numbers in columns must be even or you forgot to specify the ''fs'' parameter'); end end N = length(columns)/2; for lauf = 1:N data_x_axes = f_data(:, columns(lauf*2-1)); data_y_axes = f_data(:, columns(lauf*2)); % create data object corresponding to the parameter list ao_data = []; switch lower(data_type) case 'tsdata' ao_data = tsdata(data_x_axes, data_y_axes); case 'fsdata' ao_data = fsdata(data_x_axes, data_y_axes); case 'cdata' error('### This should not happen!'); case 'xydata' ao_data = xydata(data_x_axes, data_y_axes); otherwise error('### unknown data type ''%s''', data_type); end aa = ao(ao_data); % set up the history plist for this object plhist = pl.processForHistory(N, lauf, keys); plhist.pset('columns', [orig_col(lauf*2-1) orig_col(lauf*2)]); % Add history aa.addHistory(mi, plhist, [], []); a = [a aa]; end %%%%%%%%%% Create for each column AND fs a data object %%%%%%%%%% else % isempty(use_fs) N = length(columns); for lauf = 1:N data_y_axes = f_data(:, columns(lauf)); % create data object corresponding to the parameter list ao_data = []; switch lower(data_type) case 'tsdata' ao_data = tsdata(data_y_axes, use_fs); case 'fsdata' ao_data = fsdata(data_y_axes, use_fs); case 'cdata' % Special case for cdata-objects. % Is the user specify some columns then he will get for each % column an AO. If don't specify a columns then he will all data % in a single AO. if isempty(pl.find('columns')) % Create only one AO with all data a = ao(f_data); a.name = fileName; a.addHistory(mi, pl, [], []); break else % Create for each column a single AO ao_data = cdata(data_y_axes); end case 'xydata' ao_data = xydata(data_y_axes); otherwise error('### unknown data type ''%s''', data_type); end aa = ao(ao_data); % set up the history plist for this object plhist = pl.processForHistory(N, lauf, keys); plhist.pset('columns', orig_col(lauf)); % Add history aa.addHistory(mi, plhist, [], []); a = [a aa]; end end % for tsdata and fsdata we support setting the t0 if any(strcmpi(data_type, {'tsdata', 'fsdata'})) a.setT0(t0); end % set xunits if we don't have a cdata if ~strcmpi(data_type, 'cdata') xunits = pl.find('xunits'); if isempty(xunits) if strcmpi(data_type, 'tsdata') xunits = 's'; elseif strcmpi(data_type, 'fsdata') xunits = 'Hz'; else % do nothing end end a.setXunits(xunits); end % set yunits a.setYunits(pl.find('yunits')); % Set object properties a.setObjectProperties(pl); end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Local Functions % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % FUNCTION: numLines % % SYNTAX: count = numLines(fid); % % DESCRIPTION: Returns the number of lines in an ASCII file. This method % doesn't change the position of the file identifier (fid) % % HISTORY: 02-08-2002 Peter Acklam, CSSM post % Creation. % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function lines = numLines(fid) fidPos = ftell(fid); block = []; lines = 0; % number of lines in file nlchr = uint8(sprintf('\n')); % newline chr as uint8 bsize = 4 * 256 * 8192; % block size to read while ~feof(fid) block = fread(fid, bsize, '*uint8'); lines = lines + sum(block == nlchr); end if ~isempty(block) % in case file is empty lines = lines + double(block(end) ~= nlchr); end fseek(fid, fidPos, 'bof'); end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % FUNCTION: numCols % % SYNTAX: count = numCols(fid); % % DESCRIPTION: Returns the number of columns in an ASCII file. This method % doesn't change the position of the file identifier (fid) % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function ncols = numCols(fid, delimiter) fidPos = ftell(fid); line = fgetl(fid); if ischar(line) if nargin == 1 || isempty(delimiter) C = textscan(line, '%s'); else C = textscan(line, '%s', 'Delimiter', delimiter); end C = C{1}; ncols = numel(C); else ncols = 0; end fseek(fid, fidPos, 'bof'); end % A robust and slow data reader function f_data = robustRead(fid, f_data, columns, orig_cols) cols = unique(columns); ocols = unique(orig_cols); Nline = 1; while ~feof(fid) % read and parse line tokens = sscanf(fgets(fid), '%f'); % parse tokens if ~isempty(tokens) f_data(Nline, cols) = tokens(ocols); if mod(Nline, 1000) == 0 utils.helper.msg(utils.const.msg.PROC2, 'lines read: %d', Nline); end Nline = Nline + 1; end end % drop empty lines f_data = f_data(1:Nline-1, :); end