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comparison m-toolbox/classes/@ao/fromDatafile.m @ 0:f0afece42f48

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author Daniele Nicolodi <nicolodi@science.unitn.it>
date Wed, 23 Nov 2011 19:22:13 +0100
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1 % FROMDATAFILE Construct an ao from filename AND parameter list
2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3 %
4 % FUNCTION: fromDatafile
5 %
6 % DESCRIPTION: Construct an ao from filename AND parameter list
7 %
8 % CALL: a = fromFilenameAndPlist(a, pli)
9 %
10 % PARAMETER: a: empty ao-object
11 % pli: plist-object (must contain the filename)
12 %
13 % VERSION: $Id: fromDatafile.m,v 1.51 2011/10/12 20:30:51 mauro Exp $
14 %
15 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
16
17 function a = fromDatafile(ain, pli)
18
19 utils.helper.msg(utils.const.msg.PROC1, 'constructing from filename and/or plist');
20
21 VERSION = '$Id: fromDatafile.m,v 1.51 2011/10/12 20:30:51 mauro Exp $';
22
23 % get AO info
24 mi = ao.getInfo('ao', 'From ASCII File');
25
26 % Set the method version string in the minfo object
27 mi.setMversion([VERSION '-->' mi.mversion]);
28
29 % Get filename
30 file_name = find(pli, 'filename');
31 file_path = find(pli, 'filepath');
32
33 [filePath, fileName, ext] = fileparts(file_name);
34
35 % Add the file extenstion to the fileName
36 fileName = strcat(fileName, ext);
37
38 % Define the path of the
39 if ~isempty(file_path) && ~isempty(filePath)
40 % Do nothing because we will use filePath
41 elseif ~isempty(file_path)
42 filePath = file_path;
43 elseif ~isempty(filePath)
44 % Do nothing because we will use filePath
45 else
46 filePath = pwd();
47 end
48
49 absolutePathname = fullfile(filePath, fileName);
50
51 % Check if the abolute Pathname exist
52 if ~exist(absolutePathname, 'file')
53 absolutePathname = fileName;
54 end
55
56 %%%%%%%%%% Get default parameter list %%%%%%%%%%
57 dpl = ao.getDefaultPlist('From ASCII File');
58 pl = applyDefaults(dpl, pli);
59
60 pl = pset(pl, 'filename', fileName);
61 pl = pset(pl, 'filepath', filePath);
62
63 data_type = find(pl, 'type');
64 columns = find(pl, 'columns');
65 maxLines = find(pl, 'maxlines');
66 comment_char = find(pl, 'comment_char');
67 delimiter = find(pl, 'delimiter');
68 use_fs = find(pl, 'fs');
69 a = [];
70 orig_col = columns; % necessary for the history
71 t0 = find(pl, 't0');
72
73 %%%%
74 if strcmpi(data_type, 'cdata')
75 use_fs = 1;
76 end
77
78 %%%%%%%%%% read file %%%%%%%%%%
79 [fid,msg] = fopen (absolutePathname, 'r');
80 if (fid < 0)
81 error ('### can not open file: %s \n### error msg: %s', absolutePathname, msg);
82 end
83
84
85 try
86
87 %%%%%%%%%% create scan format: '%f %f %f %f %f %*[^\n]' %%%%%%%%%%
88 scan_format = '';
89 read_col = 0;
90
91 %%%%%%%%%% Read first comment and empty lines %%%%%%%%%%
92 while ~feof(fid)
93 fidPos = ftell(fid);
94 fline = fgetl(fid);
95 % check if there was an error reading the file
96 [errmsg, errnum] = ferror(fid);
97 if errnum ~= 0
98 error('### an error happened reading the first part of the file: %s', errmsg)
99 end
100 if fline == -1
101 % we hit the end of file
102 error('### the file is empty!')
103 end
104 fline = strtrim(fline);
105 if ~isempty(fline) && ~(~isempty(comment_char) && strncmp(fline, comment_char, numel(comment_char)))
106 fseek(fid, fidPos, 'bof');
107 break;
108 end
109 end
110
111 %%%%%%%%%% Get/Count max number of lines %%%%%%%%%%
112 if isempty(maxLines)
113 maxLines = numLines(fid);
114 utils.helper.msg(utils.const.msg.PROC2, 'Counting lines: %d', maxLines);
115 end
116
117 %%%%%%%%%% Check max number of columns %%%%%%%%%%
118 maxColumns = numCols(fid, delimiter);
119 if isempty(columns) && strcmpi(data_type, 'cdata')
120 columns = 1:maxColumns;
121 orig_col = columns;
122 end
123 if maxColumns < max(columns)
124 error('### The file doesn''t have more than [%d] columns. But you want to read the column [%d].', maxColumns, max(columns));
125 end
126
127 %%%%%%%%%% Check number of columns %%%%%%%%%%
128 if isempty(columns) && ~strcmpi(data_type, 'cdata')
129 error('### Please specify at least one column number to read the data file.');
130 end
131
132 %%% preallocate data array
133 f_data = zeros(maxLines, numel(unique(columns)));
134
135 %%% check if using robust read: 'yes'/'no' or true/false or 'true'/'false'
136 robust = utils.prog.yes2true(find(pl, 'Robust'));
137
138 if robust
139 f_data = robustRead(fid, f_data, columns, orig_col);
140 else
141
142 %%% Based on skipping the not used columns we have to transform the columns.
143 %%% We must transform the columns [ 2 5 2 6 5 7] to [ 1 2 1 3 2 4]
144 %%% In each loop we have to replace the corresponding value. In the first loop
145 %%% the first minimum, in the second loop the second minimum, ... with the
146 %%% current loop number.
147 sort_col = sort(columns);
148 for jj = 1:max(columns)
149 if ismember(jj, columns)
150 scan_format = [scan_format '%n'];
151 read_col = read_col + 1;
152 replace = min(sort_col);
153
154 columns (columns == replace) = read_col;
155 sort_col(sort_col == replace) = [];
156 else
157 scan_format = [scan_format '%*n'];
158 end
159 end
160 scan_format = [deblank(scan_format) '%*[^\n]'];
161
162 %%%%%%%%%% Read data %%%%%%%%%%
163 readlines = min(50000, maxLines);
164 nlines = 0;
165
166 %%% read file to end
167 while ~feof(fid) && nlines < maxLines
168
169 if isempty(comment_char) && isempty(delimiter)
170 C = textscan(fid, scan_format, readlines);
171 elseif isempty(comment_char) && ~isempty(delimiter)
172 C = textscan(fid, scan_format, readlines, 'Delimiter', delimiter);
173 elseif ~isempty(comment_char) && isempty(delimiter)
174 C = textscan(fid, scan_format, readlines, 'CommentStyle', comment_char);
175 else
176 C = textscan(fid, scan_format, readlines, 'CommentStyle', comment_char, 'Delimiter', delimiter);
177 end
178
179 if isempty(C{1}) && nlines == 0
180 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);
181 end
182
183 f_data(nlines+1:nlines+size(C{1},1),:) = cell2mat(C);
184 nlines = nlines + length(C{1});
185
186 utils.helper.msg(utils.const.msg.PROC2, 'read %09d lines of %09d', nlines, maxLines);
187 end
188
189 %%% get only the data we want
190 if size(f_data,1) > nlines
191 f_data = f_data(1:nlines, :);
192 end
193 end
194
195 catch ME
196 % An error occurred during the scan
197 fclose(fid);
198 rethrow(ME);
199 end
200
201 % The scan was successful
202 fclose(fid);
203
204
205 %%%%%%%%%% Create for each column pair the data object %%%%%%%%%%
206
207 % This is a list of keys which support multiple values. We need to
208 % process the history plist to account for this so that the hisotry of a
209 % single object only contains the value that the user intended that
210 % object to get.
211 % TODO: find a nicer way to specify this?
212 keys = {'name', 'description', 'xunits', 'yunits', 't0'};
213
214 if isempty(use_fs)
215
216 %%%%%%%%%% The numbers in columns must be even %%%%%%%%%%
217 if length(columns) == 1
218 if ~strcmp(data_type, 'cdata')
219 error('A single column file with no sample rate set can only be used to build a cdata AO');
220 end
221 else
222 if mod(length(columns),2) ~= 0
223 error('### The numbers in columns must be even or you forgot to specify the ''fs'' parameter');
224 end
225 end
226
227 N = length(columns)/2;
228 for lauf = 1:N
229
230 data_x_axes = f_data(:, columns(lauf*2-1));
231 data_y_axes = f_data(:, columns(lauf*2));
232
233 % create data object corresponding to the parameter list
234 ao_data = [];
235 switch lower(data_type)
236 case 'tsdata'
237 ao_data = tsdata(data_x_axes, data_y_axes);
238 case 'fsdata'
239 ao_data = fsdata(data_x_axes, data_y_axes);
240 case 'cdata'
241 error('### This should not happen!');
242 case 'xydata'
243 ao_data = xydata(data_x_axes, data_y_axes);
244 otherwise
245 error('### unknown data type ''%s''', data_type);
246 end
247 aa = ao(ao_data);
248
249 % set up the history plist for this object
250 plhist = pl.processForHistory(N, lauf, keys);
251 plhist.pset('columns', [orig_col(lauf*2-1) orig_col(lauf*2)]);
252
253
254 % Add history
255 aa.addHistory(mi, plhist, [], []);
256
257 a = [a aa];
258
259 end
260
261 %%%%%%%%%% Create for each column AND fs a data object %%%%%%%%%%
262 else % isempty(use_fs)
263
264 N = length(columns);
265 for lauf = 1:N
266
267 data_y_axes = f_data(:, columns(lauf));
268
269 % create data object corresponding to the parameter list
270 ao_data = [];
271 switch lower(data_type)
272 case 'tsdata'
273 ao_data = tsdata(data_y_axes, use_fs);
274 case 'fsdata'
275 ao_data = fsdata(data_y_axes, use_fs);
276 case 'cdata'
277 % Special case for cdata-objects.
278 % Is the user specify some columns then he will get for each
279 % column an AO. If don't specify a columns then he will all data
280 % in a single AO.
281 if isempty(pl.find('columns'))
282 % Create only one AO with all data
283 a = ao(f_data);
284 a.name = fileName;
285 a.addHistory(mi, pl, [], []);
286 break
287 else
288 % Create for each column a single AO
289 ao_data = cdata(data_y_axes);
290 end
291 case 'xydata'
292 ao_data = xydata(data_y_axes);
293 otherwise
294 error('### unknown data type ''%s''', data_type);
295 end
296 aa = ao(ao_data);
297
298 % set up the history plist for this object
299 plhist = pl.processForHistory(N, lauf, keys);
300 plhist.pset('columns', orig_col(lauf));
301
302
303 % Add history
304 aa.addHistory(mi, plhist, [], []);
305
306 a = [a aa];
307
308 end
309
310 end
311
312 % for tsdata and fsdata we support setting the t0
313 if any(strcmpi(data_type, {'tsdata', 'fsdata'}))
314 a.setT0(t0);
315 end
316
317 % set xunits if we don't have a cdata
318 if ~strcmpi(data_type, 'cdata')
319 xunits = pl.find('xunits');
320 if isempty(xunits)
321 if strcmpi(data_type, 'tsdata')
322 xunits = 's';
323 elseif strcmpi(data_type, 'fsdata')
324 xunits = 'Hz';
325 else
326 % do nothing
327 end
328 end
329 a.setXunits(xunits);
330 end
331
332 % set yunits
333 a.setYunits(pl.find('yunits'));
334
335 % Set object properties
336 a.setObjectProperties(pl);
337
338 end
339
340 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
341 % Local Functions %
342 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
343
344 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
345 %
346 % FUNCTION: numLines
347 %
348 % SYNTAX: count = numLines(fid);
349 %
350 % DESCRIPTION: Returns the number of lines in an ASCII file. This method
351 % doesn't change the position of the file identifier (fid)
352 %
353 % HISTORY: 02-08-2002 Peter Acklam, CSSM post
354 % Creation.
355 %
356 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
357
358 function lines = numLines(fid)
359
360 fidPos = ftell(fid);
361 block = [];
362 lines = 0; % number of lines in file
363 nlchr = uint8(sprintf('\n')); % newline chr as uint8
364 bsize = 4 * 256 * 8192; % block size to read
365
366 while ~feof(fid)
367 block = fread(fid, bsize, '*uint8');
368 lines = lines + sum(block == nlchr);
369 end
370 if ~isempty(block) % in case file is empty
371 lines = lines + double(block(end) ~= nlchr);
372 end
373 fseek(fid, fidPos, 'bof');
374 end
375
376 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
377 %
378 % FUNCTION: numCols
379 %
380 % SYNTAX: count = numCols(fid);
381 %
382 % DESCRIPTION: Returns the number of columns in an ASCII file. This method
383 % doesn't change the position of the file identifier (fid)
384 %
385 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
386
387 function ncols = numCols(fid, delimiter)
388
389 fidPos = ftell(fid);
390 line = fgetl(fid);
391 if ischar(line)
392 if nargin == 1 || isempty(delimiter)
393 C = textscan(line, '%s');
394 else
395 C = textscan(line, '%s', 'Delimiter', delimiter);
396 end
397 C = C{1};
398 ncols = numel(C);
399 else
400 ncols = 0;
401 end
402 fseek(fid, fidPos, 'bof');
403 end
404
405
406 % A robust and slow data reader
407 function f_data = robustRead(fid, f_data, columns, orig_cols)
408
409 cols = unique(columns);
410 ocols = unique(orig_cols);
411 Nline = 1;
412 while ~feof(fid)
413 % read and parse line
414 tokens = sscanf(fgets(fid), '%f');
415 % parse tokens
416 if ~isempty(tokens)
417 f_data(Nline, cols) = tokens(ocols);
418 if mod(Nline, 1000) == 0
419 utils.helper.msg(utils.const.msg.PROC2, 'lines read: %d', Nline);
420 end
421 Nline = Nline + 1;
422 end
423 end
424
425 % drop empty lines
426 f_data = f_data(1:Nline-1, :);
427
428 end