R/neuron-io.R
If file is not specified the neuron's InputFileName field will be checked
(for a dotprops object it will be the 'file'
attribute). If this is
missing there will be an error. If dir is specified it will be combined with
basename(file). If file is specified but format is not, it will be inferred
from file's extension.
write.neuron(n, file = NULL, dir = NULL, format = NULL, ext = NULL, Force = FALSE, MakeDir = TRUE, ...)
n | A neuron |
---|---|
file | Path to output file |
dir | Path to directory (this will replace dirname(file) if specified) |
format | Unique abbreviation of one of the registered file formats for neurons including 'swc', 'hxlineset', 'hxskel' |
ext | Will replace the default extension for the filetype and should
include the period eg |
Force | Whether to overwrite an existing file |
MakeDir | Whether to create directory implied by |
... | Additional arguments passed to selected writer function |
return value
Note that if file
does not have an extension then the default
extension for the specified format
will be appended. This behaviour
can be suppressed by setting ext=NA
.
If you find that some software rejects your SWC files, try setting
normalise.ids=TRUE
(see examples). This will ensure that the vertex
ids are sequentially ascending integers (1:N). The default value of
normalise.ids=NA
will normalise PointNo
vertex ids only when
a vertex is connected (by the Parent
field) to a vertex that had not
yet been defined. Many readers make the assumption that this is true. When
normalise.ids=F
the vertex ids will not be touched.
write.neuron
, fileformats
,
saveRDS
# show the currently registered file formats that we can write fileformats(class='neuron', write=TRUE)#> [1] "hxlineset" "hxskel" "rds" "swc" "vtk"# NOT RUN { # write out "myneuron.swc" in SWC format write.neuron(Cell07PNs[[1]], file='myneuron.swc') # write out "myneuron.swc" in SWC format, normalising the integer ids that # label every node (this is required by some SWC readers e.g. Fiji) write.neuron(Cell07PNs[[1]], file='myneuron.swc', normalise.ids=TRUE) # write out "myneuron.amiramesh" in Amira hxlineset format write.neuron(Cell07PNs[[1]], format = 'hxlineset', file='myneuron.amiramesh') # write out "myneuron.am" in Amira hxlineset format write.neuron(Cell07PNs[[1]], format = 'hxlineset', file='myneuron') # }