Back to the main page.

Bug 1837 - clean up the external/simbio directory

Reported 2012-11-16 10:17:00 +0100
Modified 2012-12-18 10:50:25 +0100
Product: FieldTrip
Component: external
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P3 minor
Assigned to: Johannes Vorwerk
Depends on:
See also:

Robert Oostenveld - 2012-11-16 10:17:19 +0100

there are many files that seem not to be needed any more. I suggest to move everything to a temp directory, run the test scripts, see which files are missing and move them from the temp back to external/simbio, and repeat until everything works again. Or use depfun (see attached).

Johannes Vorwerk - 2012-11-16 10:52:38 +0100

Except for bounding_mesh.m and solid_angle.m (where I have no idea why they are in this folder) I know quite well what could be removed, should I just delete that? If a test fails then, I still have a local copy so that I could add it again. Since we do not want to provide source-codes all *.cpp files could also be removed, right? test/ and vista/ are deprecated,too, and for vgrid it should be sufficient to provide a binary. Some things like write_vista_mesh and read_vista_vol are not needed right now, but still useful for example for Bug 1836, those should probably stay?

Robert Oostenveld - 2012-11-16 11:02:05 +0100

I suggest that in principle anything that is not called from fieldtrip (directly or indirectly) should be removed, except for the README and COPYING. potentially useful things (as write_vista_mesh and read_vista_vol) should stay, but it should be clear what their use is. The bounding_mesh.m and solid_angle.m are FT functions and probably added by Cristiano for testing. They can also go. I am not sure whether vgrid shoud be included here. Where in the pipeline is it currently used? I guess nowhere (yet), but thaht it should become part of ft_prepare_mesh as listed in bug 1833. Perhaps leave vgrid for the moment, but later consider to move it to fieldtrip/external/vgrid.

Johannes Vorwerk - 2012-11-16 11:46:23 +0100

(In reply to comment #2) svn commit . Lösche simbio/bounding_mesh.m Lösche simbio/calc_stiff_matrix_val.F Lösche simbio/read_vista_mesh.cpp Lösche simbio/sb_compile_simbio.m Lösche simbio/sb_compile_vista.m Lösche simbio/sb_read_dip.m Lösche simbio/sb_read_msr.m Lösche simbio/sb_read_transfer.m Lösche simbio/sb_write_dip.m Lösche simbio/sb_write_elc.m Lösche simbio/sb_write_par.m Lösche simbio/sb_write_transfer.m Lösche simbio/solid_angle.m Lösche simbio/solid_angle.mexa64 Lösche simbio/test Lösche simbio/vista Lösche simbio/doc Lösche simbio/vistaprimitive.cpp Lösche simbio/vistaprimitive.h Lösche simbio/write_vista_mesh.cpp Lösche simbio/write_vista_vol.cpp

Johannes Vorwerk - 2012-11-27 11:36:02 +0100

(In reply to comment #3) I think this bug is resolved?

Robert Oostenveld - 2012-11-27 17:13:04 +0100

(In reply to comment #4) how about vgrid? Should we not move that to fieldtrip/external/vgrid?

Robert Oostenveld - 2012-12-13 12:21:30 +0100

*** Bug 959 has been marked as a duplicate of this bug. ***

Robert Oostenveld - 2012-12-13 12:37:32 +0100

(In reply to comment #5) ------------------------------------------------------------------------ r7166 | roboos | 2012-12-13 12:27:09 +0100 (Thu, 13 Dec 2012) | 2 lines restructuring - moved vgrid from simbio to external ------------------------------------------------------------------------ r7165 | roboos | 2012-12-13 12:25:24 +0100 (Thu, 13 Dec 2012) | 2 lines restructuring - moved vgrid from the external/simbio directory to external/vgrid and removed the version number from the directory name ------------------------------------------------------------------------ r7164 | roboos | 2012-12-13 12:23:08 +0100 (Thu, 13 Dec 2012) | 2 lines enhanement - added VERSION file with precise number in it ------------------------------------------------------------------------ r7163 | roboos | 2012-12-13 12:20:09 +0100 (Thu, 13 Dec 2012) | 2 lines restructured - compiled vgrid for 64 bit OS X, moved the binaries to platform specific locations to accomodate linux and osx next to each other

Robert Oostenveld - 2012-12-13 12:49:06 +0100

(In reply to comment #7) moved the linux binary to the right location, it is a 64 bit version. We should also compile a 32 bit version. mac001> svn update A bin/glnxa64 A bin/glnxa64/vgrid D bin/glnx86/vgrid Updated to revision 7170.