Nothing
update_igraph <- FALSE
.onLoad <- function(libname, pkgname) {
try(cmtk.bindir(set=TRUE,check=TRUE),silent=TRUE)
# Register file formats: neuron tracings
registerformat('swc', read=read.neuron.swc, write=write.neuron.swc,
class='neuron')
# nb we cannot (yet) register formats with the same name but different classes
registerformat('swcng', ext='.swc', read=read.ngraph.swc, class='ngraph')
registerformat('neuroml', ext=c('.xml','.nml'), read=read.neuron.neuroml,
class='neuron', magic=is.neuroml, magiclen=8L)
registerformat('fijitraces', ext=c('.traces','.xml'), read=read.neuron.fiji,
class='neuron', magic=is.fijitraces, magiclen=5L)
registerformat('rds', read=readRDS, write=saveRDS, class='neuron')
registerformat('hxskel', ext='.am', read=read.neuron.hxskel,
write=write.neuron.hxskel, magic=is.hxskel,
class='neuron', magiclen=14L)
registerformat('hxlineset', ext='.am', read=read.neuron.hxlineset,
write=write.neuron.hxlineset, magic=is.hxlineset,
class='neuron', magiclen=14L)
registerformat('vtk', ext='.vtk', write=write.vtk.neuron, class='neuron')
# image formats
registerformat('nrrd', ext=c('.nrrd','.nhdr'), read=read.im3d.nrrd,
write=write.nrrd, magic=is.nrrd,
class='im3d', magiclen=8L)
registerformat('amiramesh', ext=c('.am','.amiramesh'), read=read.im3d.amiramesh,
write=write.amiramesh, magic=is.amiramesh.im3d,
class='im3d', magiclen=14L)
registerformat('vaa3draw', ext=c('.v3d','.v3draw'), read=read.im3d.vaa3draw,
magic=is.vaa3draw, class='im3d', magiclen=24L)
# landmarks
registerformat('amiralandmarks', ext=c('.landmarkAscii','.landmarkBin','.am','.amiramesh'),
read=read.landmarks.amira, write=write.landmarks.amira,
magic=is.amiratype("LandmarkSet"),
class='landmarks', magiclen=14L)
registerformat('fijilandmarks', ext=c('.points'), read=read.landmarks.fiji,
write=write.landmarks.fiji,
magic=is.fijilandmarks, class='landmarks', magiclen=5L)
registerformat('cmtklandmarks', ext=c('.landmarks'), read=read.landmarks.cmtk,
write=write.landmarks.cmtk, magic=is.cmtklandmarks,
class='landmarks', magiclen=13L)
# surfaces
registerformat('hxsurf', ext=c('.surf', '.am','.amiramesh'), read=read.hxsurf,
write=write.hxsurf, magic=is.amiratype("HxSurface"),
class='hxsurf', magiclen=14L)
# deal with slow vertex sequences in igraph
pvi <- packageVersion('igraph')
if (pvi < "1.0.0") {
# this is fast by default
} else if (pvi > "1.0.1") {
# we can turn off expensive vs.es return sequences
igraph::igraph_options(return.vs.es = FALSE)
} else {
update_igraph <- TRUE
}
invisible()
}
.onAttach <- function(libname, pkgname) {
if(is.null(cmtk.bindir()))
{
packageStartupMessage("Some nat functions depend on a CMTK installation. ",
"See ?cmtk and README.md for details.")
}
# igraph_options fails for v 1.0.0/1.0.1 so need to hack the function
if(update_igraph)
packageStartupMessage("nat: upgrading to igraph >1.0.1 is recommended to ",
"increase the speed of graph operations on neurons.")
invisible()
}
# will store information about formats that we can read
.fileformats <- new.env()
# Will store stack of plotted rgl objects, ready for popping
.plotted3d <- new.env()
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