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Bug 1299 - gtec_mat support disappeared from ft_read_header in svn merged branch
| Status | CLOSED FIXED |
| Reported | 2012-01-31 22:02:00 +0100 |
| Modified | 2012-04-02 16:27:04 +0200 |
| Product: | FieldTrip |
| Component: | fileio |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P3 normal |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Robert Oostenveld - 2012-01-31 22:02:23 +0100
On 31 Jan 2012, at 15:57, Hogervorst, M.A. (Maarten) wrote: Robert, Ik krijg sinds kort fouten bij het inlezen van de matfiles met EEGdata met fieldtrip. Fieldtrip lijkt het format niet te kunnen interpreteren. Als ik jouw import-functies gebruik krijg ik onderstaande error-melding: --------------------------------- ??? Error using ==> ft_read_header at 1531 unsupported header format (gtec_mat) Error in ==> ft_preprocessing at 338 hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat); -------------------------------- Ik gebruik de download fieldtrip-20120106
Robert Oostenveld - 2012-01-31 22:05:14 +0100
I zoomed in on the problem. Revision 4286 has the gtec_mat support, revision 4287 lost it. See http://code.google.com/p/fieldtrip/source/browse/trunk/fileio/ft_read_header.m?spec=svn4286&r=4286 http://code.google.com/p/fieldtrip/source/browse/trunk/fileio/ft_read_header.m?spec=svn4287&r=4287 That is a commit from Jan-Mathijs: r4287 by jansch on Sep 23, 2011 enhancement - #879 redefine the description of the sensor-array, merged the branch that was created for this back into the trunk This suggests that something went wrong with the svn merge. Other files with may also have been affected (i.e. other improvements to code may have been undone) and therefore should also be checked.
Robert Oostenveld - 2012-01-31 22:08:18 +0100
To fix the immediate problem for Maarten, I have copied the relevant parts out of the last working revision into the latest/current revision. The diff is mbp> svn diff ft_read_header.m Index: ft_read_header.m =================================================================== --- ft_read_header.m (revision 5188) +++ ft_read_header.m (working copy) @@ -48,6 +48,7 @@ % NeuroScan (*.eeg, *.cnt, *.avg) % Nexstim (*.nxe) % BrainVision (*.eeg, *.seg, *.dat, *.vhdr, *.vmrk) +% GTec (*.mat) % % The following spike and LFP dataformats are supported (with some limitations) % Plextor (*.nex, *.plx, *.ddt) @@ -120,7 +121,7 @@ fallback = ft_getopt(varargin, 'fallback'); if isempty(cache), - if strcmp(headerformat, 'bci2000_dat') || strcmp(headerformat, 'eyelink_asc') || strcmp(headerformat, 'biosig') + if strcmp(headerformat, 'bci2000_dat') || strcmp(headerformat, 'eyelink_asc') || || strcmp(headerformat, 'gtec_mat') || strcmp(headerformat, 'biosig') cache = true; else cache = false; @@ -950,7 +951,31 @@ hdr = db_select('fieldtrip.header', {'nChans', 'nSamples', 'nSamplesPre', 'Fs', 'label'}, 1); hdr.label = mxDeserialize(hdr.label); end + + case 'gtec_mat' + % this is a simple MATLAB format, it contains a log and a names variable + tmp = load(headerfile); + log = tmp.log; + names = tmp.names; + hdr.label = cellstr(names); + hdr.nChans = size(log,1); + hdr.nSamples = size(log,2); + hdr.nSamplesPre = 0; + hdr.nTrials = 1; % assume continuous data, not epoched + + % compute the sampling frequency from the time channel + sel = strcmp(hdr.label, 'Time'); + time = log(sel,:); + + hdr.Fs = 1./(time(2)-time(1)); + + % also remember the complete data upon request + if cache + hdr.orig.log = log; + hdr.orig.names = names; + end + case {'itab_raw' 'itab_mhd'} % read the full header information frtom the binary header structure header_info = read_itab_mhd(headerfile);
Robert Oostenveld - 2012-01-31 22:12:14 +0100
(In reply to comment #2) mbp> svn commit ft_read_header.m Sending ft_read_header.m Transmitting file data . Committed revision 5189. @Maarten, the updated file will be in the ftp release tomorrow evening (it is too late for it to end up in the 20120131 release). You can also pick up this individual file itself at http://code.google.com/p/fieldtrip/source/browse/trunk/fileio/ft_read_header.m?r=5189
Robert Oostenveld - 2012-01-31 22:14:22 +0100
(In reply to comment #1) Oh my ..., the merging of the branch affected a lot of files. See http://code.google.com/p/fieldtrip/source/detail?spec=svn4287&r=4287
Jan-Mathijs Schoffelen - 2012-02-01 15:35:51 +0100
These are those files: I'll check them to see whether there have been changes that were lost due to the branching Modify /trunk/fileio/ft_chantype.m diff Modify /trunk/fileio/ft_read_header.m diff Modify /trunk/fileio/ft_read_headshape.m diff Modify /trunk/fileio/ft_read_sens.m diff Modify /trunk/forward/ft_apply_montage.m diff Modify /trunk/forward/ft_average_sens.m diff Modify /trunk/forward/ft_compute_leadfield.m diff Modify /trunk/forward/ft_convert_units.m diff Modify /trunk/forward/ft_headmodel_localspheres.m diff Modify /trunk/forward/ft_prepare_vol_sens.m diff Modify /trunk/forward/ft_senstype.m diff Add /trunk/forward/private/channelposition.m diff Add /trunk/forward/private/fixsens.m diff Modify /trunk/forward/private/meg_forward.m diff Modify /trunk/forward/private/meg_ini.m diff Add /trunk/forward/private/undobalancing.m diff Modify /trunk/ft_channelrepair.m diff Modify /trunk/ft_electroderealign.m diff Modify /trunk/ft_headmodelplot.m diff Modify /trunk/ft_headmovement.m diff Modify /trunk/ft_interactiverealign.m diff Modify /trunk/ft_megplanar.m diff Modify /trunk/ft_megrealign.m diff Modify /trunk/ft_neighbourplot.m diff Modify /trunk/ft_prepare_layout.m diff Modify /trunk/ft_prepare_localspheres.m diff Modify /trunk/ft_prepare_neighbours.m diff Modify /trunk/ft_prepare_sourcemodel.m diff Modify /trunk/ft_scalpcurrentdensity.m diff Modify /trunk/ft_sensorrealign.m diff Modify /trunk/plotting/ft_plot_sens.m diff Add /trunk/plotting/private/fixsens.m diff Modify /trunk/plotting/private/ft_apply_montage.m diff Modify /trunk/plotting/private/ft_senstype.m diff Modify /trunk/private/constructplanargrad.m diff Modify /trunk/private/fixsens.m diff Modify /trunk/private/head_surf.m diff Modify /trunk/private/headsurface.m diff Modify /trunk/private/megplanar_fitplane.m diff Modify /trunk/private/megplanar_orig.m diff Modify /trunk/private/megplanar_sincos.m diff Modify /trunk/private/sel50p.m diff Modify /trunk/test/test_ft_megplanar.m diff Modify /trunk/utilities/ft_checkdata.m diff Modify /trunk/utilities/ft_datatype_comp.m diff Modify /trunk/utilities/ft_datatype_freq.m diff Modify /trunk/utilities/ft_datatype_mvar.m diff Modify /trunk/utilities/ft_datatype_raw.m diff Modify /trunk/utilities/ft_datatype_timelock.m diff Modify /trunk/utilities/ft_transform_geometry.m diff
Jan-Mathijs Schoffelen - 2012-02-01 15:50:09 +0100
Created attachment 223 difference between revision 4286 and 4287 svn diff -r 4286:4287 > svndiff4286to4287.txt
Jan-Mathijs Schoffelen - 2012-02-01 15:51:27 +0100
Created attachment 224 summary of modified files
Jan-Mathijs Schoffelen - 2012-02-01 16:22:58 +0100
Created attachment 225 differences between 4286 and 4287 which were present in 4286, and not anymore in 4287