Add hemibrain_neuron_meshes

DESCRIPTION

@@ -23,7 +23,8 @@ Suggests:
     elmr,
     dbscan,
     RColorBrewer,
-    nat.hdf5
+    nat.hdf5,
+    Rvcg
 VignetteBuilder: knitr
 Depends:
     R (>= 3.1),

NAMESPACE

@@ -148,6 +148,7 @@ export(hemibrain_meta)
 export(hemibrain_multi3d)
 export(hemibrain_nblast)
 export(hemibrain_neuron_bodyids)
+export(hemibrain_neuron_meshes)
 export(hemibrain_neurons)
 export(hemibrain_overlap_locality)
 export(hemibrain_prune_online)
@@ -207,6 +208,7 @@ importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
 importFrom(dplyr,select)
+importFrom(fafbseg,flywire_cloudvolume)
 importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")
 importFrom(googledrive,as_id)

R/hemibrain_neuron_meshes.R

@@ -0,0 +1,99 @@
+# convert cloudvolume python mesh to an R mesh3d object
+# method vf just uses the vertex and face arrays
+# ply writes out to Stanford ply format and reads back in again
+#' @importFrom
+cvmesh2mesh <- function(x, method=c('vf', 'ply'), ...) {
+  method=match.arg(method)
+  if(method=='vf') {
+    verts=t(x$vertices)
+    stopifnot(nrow(verts)==3)
+    faces=t(x$faces+1)
+    stopifnot(max(faces)<=ncol(verts))
+    stopifnot(min(faces)>0)
+    stopifnot(nrow(faces)==3)
+    m=rgl::tmesh3d(vertices = verts, indices = faces, homogeneous = F)
+  } else {
+    bytes=x$to_ply()
+    tf=tempfile(fileext = paste0('.', method))
+    on.exit(unlink(tf))
+    writeBin(bytes, con = tf)
+    m=Rvcg::vcgPlyRead(tf, ...)
+  }
+  m
+}
+
+#' Read hemibrain neurite or mitochondrial meshes into an R neuronlist object
+#'
+#' @description \code{hemibrain_neuron_meshes} reads standard neuron meshes
+#'
+#' @param bodyids One more hemibrain body ids (including as expressions passed
+#'   to \code{\link{neuprint_ids}})
+#' @param lod the level of detail (highest resolution is 0, default of 2 gives a
+#'   good overall morphology while 3 is also useful and smaller still)
+#' @param cloudvolume.url Optional a specific URL from which to download mesh
+#'   data.
+#' @param conn A neuprint connection to the hemibrain dataset
+#' @param dataset Optionally specify which version of the hemibrain dataset to
+#'   use (when \code{NULL} uses the most recent)
+#' @param ... Additional arguments passed to \code{\link{nlapply}}
+#'
+#' @return A \code{\link{neuronlist}} object
+#' @export
+#'
+#' @examples
+#' \donttest{
+#' da2.lod3=hemibrain_neuron_meshes("DA2_lPN", lod=3)
+#' da2.lod3
+#' }
+#' \dontrun{
+#' da2=hemibrain_neuron_meshes("DA2_lPN")
+#' # lod 2 ~ 5x bigger than lod 3 but does look nicer
+#' da2
+#' plot3d(da2)
+#'
+#' da2mito=hemibrain_mito_meshes("DA2_lPN")
+#'
+#' # if you just wanted one neuron (as a mesh3d object) rather than neuronlist
+#' dl4=hemibrain_neuron_meshes("name:DL4_adPN_R")[[1]]
+#' }
+#' @importFrom fafbseg flywire_cloudvolume
+hemibrain_neuron_meshes <- function(bodyids, lod=2L, cloudvolume.url=NULL, conn=NULL, dataset=NULL, ...) {
+  dataset = neuprintr:::check_dataset(dataset, conn = conn)
+  bodyids = neuprintr::neuprint_ids(bodyids, conn = conn, dataset = dataset)
+  if(is.null(cloudvolume.url)) {
+    cloudvolume.url = sprintf(
+      "precomputed://gs://neuroglancer-janelia-flyem-%s/segmentation",
+      sub(":", "/", dataset, fixed = T)
+    )
+  }
+  # in case they are integer64
+  bodyids=as.character(bodyids)
+  nn=bodyids;names(nn) <- bodyids
+  res=nlapply(nn, hemibrain_neuron_mesh, lod=lod, cloudvolume.url=cloudvolume.url, ...)
+  res[,] <- neuprint_get_meta(names(res), conn=conn, dataset = dataset)
+  return(res)
+}
+
+hemibrain_neuron_mesh <- function(bodyids, lod, cloudvolume.url, method='vf') {
+  cv=fafbseg::flywire_cloudvolume(cloudvolume.url = cloudvolume.url)
+  # convert to python longint if necessary
+  li=reticulate::py_eval(bodyids, convert = F)
+  lod=as.integer(lod)
+  cm=cv$mesh$get(li, lod = lod)
+  if(!any(bodyids %in% names(cm))) {
+    stop("Failed to read segid: ", bodyids)
+  }
+  # we get back a dict where the key is a python 64 bit int
+  cmesh=reticulate::py_get_item(cm, li)
+  m=cvmesh2mesh(cmesh, method=method)
+  m
+}
+
+
+#' @rdname hemibrain_neuron_meshes
+#' @description \code{hemibrain_mito_meshes} reads mitochondrial meshes
+hemibrain_mito_meshes <- function(bodyids, lod=2L, ...) {
+  cvu="precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.2/mito-objects-grouped"
+  hemibrain_neuron_meshes(bodyids, lod=lod, cloudvolume.url = cvu, ...)
+}
+

_pkgdown.yml

@@ -33,11 +33,12 @@ reference:
     - 'hemibrain_somas'
     - '`hemibrain_reroot`'
     - 'hemilineages'
-  - title: Synapses and meshes
+  - title: Synapses and neuron and ROI meshes
     desc: ~
     contents:
     - '`hemibrain_extract_synapses`'
     - '`hemibrain_remove_bad_synapses`'
+    - '`hemibrain_neuron_meshes`'
     - '`hemibrain_roi_meshes`'
     - 'hemibrain.surf'
     - 'hemibrain_al.surf'