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Bug 1056 - move ft_spike* functions to fieldtrip/contrib/spike
| Status | CLOSED FIXED |
| Reported | 2011-10-18 21:19:00 +0200 |
| Modified | 2012-08-23 10:33:54 +0200 |
| Product: | FieldTrip |
| Component: | spike |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P1 normal |
| Assigned to: | Robert Oostenveld |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Robert Oostenveld - 2011-10-18 21:19:32 +0200
and create a README and COPYING file After the move I have to check for the function dependencies. If needed, some fieldtrip/private functions have to be copied to contrib/spike/private.
Robert Oostenveld - 2011-11-11 11:23:20 +0100
convert to using ft_preamble and ft_postamble
Robert Oostenveld - 2011-11-11 11:32:18 +0100
to get consistent behaviour in all ft_spike functions I have removed the cfg.inputfile and cfg.outputfile options. I don't think anyone is using the loadvar/savevar options at the moment. They can be added back at a later stage (using ft_preamble loadvar and ft_postamble savevar), but that should then be done for all functions where it applies. I removed it from the documentation, from the code and added a "checkconfig forbidden" for them.
Robert Oostenveld - 2011-11-11 12:35:53 +0100
I have cleaned up the documentation and copyrights of all ft_spikexxx functions. In the process, I have fixed some function names and where appropriate replaced spikestation with spike. I also added some FT prefixes here and there. Furthermore I have autoindented all of them. Better make sure that you do an svn update before you continue developing these functions!!
Robert Oostenveld - 2011-11-11 12:37:01 +0100
(In reply to comment #3) Committed revision 4724.
Robert Oostenveld - 2011-11-27 15:30:50 +0100
I have changed all ft_spike*.m functions to use ft_preamble and ft_postamble. Furthermore some small cosmetic changes to the layout of the code (e.g. whitespace and documentation) mbp> svn commit ft_spike*.m Sending ft_spike_data2spike.m Sending ft_spike_isihist.m Sending ft_spike_jpsth.m Sending ft_spike_maketrials.m Sending ft_spike_plot_isi.m Sending ft_spike_plot_isireturn.m Sending ft_spike_plot_jpsth.m Sending ft_spike_plot_psth.m Sending ft_spike_plot_raster.m Sending ft_spike_psth.m Sending ft_spike_rate.m Sending ft_spike_rate_condition.m Sending ft_spike_rate_orituning.m Sending ft_spike_spike2data.m Sending ft_spike_sub_defaultcfg.m Sending ft_spike_triggeredspectrum.m Sending ft_spike_xcorr.m Sending ft_spikeanalysis.m Sending ft_spikedensity.m Sending ft_spikedetection.m Sending ft_spikedownsample.m Sending ft_spikefixdmafile.m Sending ft_spikesimulation.m Sending ft_spikesorting.m Sending ft_spikesplitting.m Sending ft_spiketriggeredaverage.m Sending ft_spiketriggeredinterpolation.m Sending ft_spiketriggeredspectrum.m Sending ft_spiketriggeredspectrum_tfr.m Transmitting file data ............................. Committed revision 4816.
Robert Oostenveld - 2011-11-27 15:32:21 +0100
(In reply to comment #1) > convert to using ft_preamble and ft_postamble This has now been done, see previous comment.
Robert Oostenveld - 2012-06-05 12:56:08 +0200
I am in the process of moving the functions. This requires that all fieldtrip/private functions are duplicated in fieldtrip/contrib/spike/private (with autosync). Using mydepfun and a fixme directory, I have found the following private dependencies '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/isrealvec.m' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/nanmean.mexmaci64' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/nanstd.mexmaci64' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/nansum.mexmaci64' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/nanvar.mexmaci64' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/isrealmat.m' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/tinv.m' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/spike_crossx.mexmaci64' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/offset2time.m' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/peakdetect3.m' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/preproc.m' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/smartinput.m' '/Volumes/Data/roboos/matlab/misc/cluster_ward.m' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/read_neuralynx_dma.m' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/sine_taper.m' '/Volumes/Data/roboos/matlab/fieldtrip-clean/contrib/spike/fixme/specest_nanfft.m'
Robert Oostenveld - 2012-06-05 13:02:53 +0200
I have made the move, and dealt with all private functions (except for this unexpected cluster_ward function with is elsewhere on my path). still to do: - update the ft_defaults with the new path manzana> svn commit Adding contrib/spike/ft_spike_isihist.m Adding contrib/spike/ft_spike_jpsth.m Adding contrib/spike/ft_spike_maketrials.m Adding contrib/spike/ft_spike_plot_isi.m Adding contrib/spike/ft_spike_plot_isireturn.m Adding contrib/spike/ft_spike_plot_jpsth.m Adding contrib/spike/ft_spike_plot_psth.m Adding contrib/spike/ft_spike_plot_raster.m Adding contrib/spike/ft_spike_psth.m Adding contrib/spike/ft_spike_rate.m Adding contrib/spike/ft_spike_rate_condition.m Adding contrib/spike/ft_spike_rate_orituning.m Adding contrib/spike/ft_spike_waveform_descriptive.m Adding contrib/spike/ft_spike_xcorr.m Adding contrib/spike/ft_spikedensity.m Adding contrib/spike/ft_spikedetection.m Adding contrib/spike/ft_spikedownsample.m Adding contrib/spike/ft_spikefixdmafile.m Adding contrib/spike/ft_spikesimulation.m Adding contrib/spike/ft_spikesorting.m Adding contrib/spike/ft_spikesplitting.m Adding contrib/spike/ft_spiketriggeredaverage.m Adding contrib/spike/ft_spiketriggeredinterpolation.m Adding contrib/spike/ft_spiketriggeredspectrum.m Adding contrib/spike/ft_spiketriggeredspectrum_convol.m Adding contrib/spike/ft_spiketriggeredspectrum_fft.m Adding contrib/spike/ft_spiketriggeredspectrum_stat.m Adding contrib/spike/private Adding contrib/spike/private/isrealmat.m Adding contrib/spike/private/isrealvec.m Adding (bin) contrib/spike/private/nanmean.mexa64 Adding (bin) contrib/spike/private/nanmean.mexmaci Adding (bin) contrib/spike/private/nanmean.mexmaci64 Adding (bin) contrib/spike/private/nanmean.mexw32 Adding (bin) contrib/spike/private/nanmean.mexw64 Adding (bin) contrib/spike/private/nanstd.mexa64 Adding (bin) contrib/spike/private/nanstd.mexmaci Adding (bin) contrib/spike/private/nanstd.mexmaci64 Adding (bin) contrib/spike/private/nanstd.mexw32 Adding (bin) contrib/spike/private/nanstd.mexw64 Adding (bin) contrib/spike/private/nansum.mexa64 Adding (bin) contrib/spike/private/nansum.mexmaci Adding (bin) contrib/spike/private/nansum.mexmaci64 Adding (bin) contrib/spike/private/nansum.mexw32 Adding (bin) contrib/spike/private/nansum.mexw64 Adding (bin) contrib/spike/private/nanvar.mexa64 Adding (bin) contrib/spike/private/nanvar.mexmaci Adding (bin) contrib/spike/private/nanvar.mexmaci64 Adding (bin) contrib/spike/private/nanvar.mexw32 Adding (bin) contrib/spike/private/nanvar.mexw64 Adding contrib/spike/private/offset2time.m Adding contrib/spike/private/peakdetect3.m Adding contrib/spike/private/preproc.m Adding contrib/spike/private/read_neuralynx_dma.m Adding contrib/spike/private/sine_taper.m Adding contrib/spike/private/smartinput.m Adding contrib/spike/private/specest_nanfft.m Adding (bin) contrib/spike/private/spike_crossx.mexmaci Adding (bin) contrib/spike/private/spike_crossx.mexmaci64 Adding (bin) contrib/spike/private/spike_crossx.mexw32 Adding (bin) contrib/spike/private/spike_crossx.mexw64 Adding contrib/spike/private/tinv.m Deleting ft_spike_isihist.m Deleting ft_spike_jpsth.m Deleting ft_spike_maketrials.m Deleting ft_spike_plot_isi.m Deleting ft_spike_plot_isireturn.m Deleting ft_spike_plot_jpsth.m Deleting ft_spike_plot_psth.m Deleting ft_spike_plot_raster.m Deleting ft_spike_psth.m Deleting ft_spike_rate.m Deleting ft_spike_rate_condition.m Deleting ft_spike_rate_orituning.m Deleting ft_spike_waveform_descriptive.m Deleting ft_spike_xcorr.m Deleting ft_spikedensity.m Deleting ft_spikedetection.m Deleting ft_spikedownsample.m Deleting ft_spikefixdmafile.m Deleting ft_spikesimulation.m Deleting ft_spikesorting.m Deleting ft_spikesplitting.m Deleting ft_spiketriggeredaverage.m Deleting ft_spiketriggeredinterpolation.m Deleting ft_spiketriggeredspectrum.m Deleting ft_spiketriggeredspectrum_convol.m Deleting ft_spiketriggeredspectrum_fft.m Deleting ft_spiketriggeredspectrum_stat.m Sending private/isrealmat.m Sending private/isrealvec.m Sending private/peakdetect3.m Sending private/preproc.m Sending private/sine_taper.m Sending private/specest_nanfft.m Sending private/spike_crossx.mexmaci Sending private/spike_crossx.mexmaci64 Sending private/spike_crossx.mexw32 Sending private/spike_crossx.mexw64 Committed revision 5886.
Robert Oostenveld - 2012-06-05 14:39:55 +0200
I have added a README and a COPYING file. Martin (sitting next to me) has tested the code. All seems fine, so I close the bug.