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Feature/write mesh fixes #514

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merged 3 commits into from
Oct 9, 2023
Merged

Feature/write mesh fixes #514

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5c3b51f
handle ply format when name does not end in ply
jefferis Oct 6, 2023
5d1bd0f
examples writing meshes
jefferis Oct 6, 2023
0660ee9
error if using write.neurons for single object
jefferis Oct 6, 2023
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17 changes: 16 additions & 1 deletion R/neuron-io.R
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Original file line number Diff line number Diff line change
Expand Up @@ -672,6 +672,14 @@ is.swc<-function(f, TrustSuffix=TRUE) {
#'
#' # write out "myneuron.am" in Amira hxlineset format
#' write.neuron(Cell07PNs[[1]], format = 'hxlineset', file='myneuron')
#'
#' # write a mesh in Stanford ply
#' write.neuron(MBL.surf, file = 'MBL.surf.ply')
#' # ... or Wavefront obj format
#' write.neuron(MBL.surf, file = 'MBL.surf.obj')
#' # specify the format directly if not evident from file suffix
#' # not recommended though as will probably just cause trouble when reading
#' write.neuron(MBL.surf, file = 'MBL.surf', format='obj')
#' }
write.neuron<-function(n, file=NULL, dir=NULL, format=NULL, ext=NULL,
Force=FALSE, MakeDir=TRUE, metadata=NULL, ...){
Expand Down Expand Up @@ -891,7 +899,14 @@ write.neurons<-function(nl, dir, format=NULL, subdir=NULL,
INDICES=names(nl), files=NULL,
include.data.frame=FALSE,
metadata=FALSE,
Force=FALSE, cl=NULL, ...){
Force=FALSE, cl=NULL, ...) {
if(!inherits(nl, 'neuronlist')) {
# check if this looks like some of the other kinds of object we might
# write by accident
single_object_classes <- c("mesh3d", "neuron", "dotprops", "hxsurf")
if(any(single_object_classes %in% class(nl)))
stop("Please use `write.neuron` to write a single neuron/mesh object!")
}
if(grepl("\\.zip", dir)) {
zip_file=dir
# check if file exists (and we want to overwrite)
Expand Down
10 changes: 9 additions & 1 deletion R/neuron-mesh.R
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Expand Up @@ -43,8 +43,16 @@ write.neuron.mesh <- function(x, file, format=c("ply", "obj"), ...) {
if(!inherits(x, 'mesh3d')) {
x=tryCatch(as.mesh3d(x), error=function(e) stop("Unable to convert x to mesh3d object! Only neuron meshes can be written in ",format," format!"))
}
if(format=="ply")
if(format=="ply") {
if(!isTRUE(tools::file_ext(file)=="ply")) {
# ply format must end in .ply
origfile=file
file=tempfile(fileext = '.ply')
on.exit(file.copy(file, origfile, overwrite = T), add = T)
on.exit(unlink(file), add = T)
}
Rvcg::vcgPlyWrite(x, filename=file, writeCol = F, writeNormals = F, ...)
}
else if(format=="obj")
Rvcg::vcgObjWrite(x, filename=file, writeNormals=F, ...)
else stop("Unknown format")
Expand Down
8 changes: 8 additions & 0 deletions man/write.neuron.Rd
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6 changes: 6 additions & 0 deletions tests/testthat/test-neuron-mesh.R
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Expand Up @@ -13,13 +13,19 @@ test_that("read/write works", {
md5.2=tools::md5sum(ff2)
expect_equal(md5.1, md5.2)

# error if we try to write one object with write.neurons
expect_error(write.neurons(bl[[1]], dir=td, format='ply'))

expect_is(bl2 <- read.neurons(td, format='ply'), 'neuronlist')
expect_equal(sbl <- summary(bl), summary(bl2))

expect_is(sbl, 'data.frame')
expect_known_value(sbl, file = 'testdata/summary_bl.rds')

expect_error(write.neurons(Cell07PNs[1:3], format = 'ply'))

write.neuron(MBL.surf, file=file.path(td, "MBL.surf.ply"), format = 'ply')
expect_equal(read.neuron(file.path(td, "MBL.surf.ply")), as.mesh3d(MBL.surf), tolerance = 1e-6)
})

skip_if_not_installed('readobj')
Expand Down
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