ngl_layers extract the neuroglancer layers with
convenience options for selecting layers by characteristics such as
visibility, type etc.
ngl_layers<- sets the layers element of a
ngscene object, taking care of name/class details.
+.ngscene adds segments or layers to a neuroglancer scene
-.ngscene removes segments or whole layers from a
neuroglancer scene. It does not complain if the segment is not present.
Usage
ngl_layers(x, subset = NULL)
ngl_layers(x) <- value
# S3 method for ngscene
+(x, y)
# S3 method for ngscene
-(x, y)Arguments
- x
a neuroglancer scene object (see
ngscene) or an existingnglayersobject (which you probably want to subset).- subset
an expression (evaluated in the style of subset.dataframe) which defined
- value
a list specifying one or more neuroglancer layers. This will usually come from a json fragment or another parsed neuroglancer scene. See examples.
- y
Segments or layers to add or remove from a neuroglancer scene. Segments are provided as character vectors or by applying
ngl_segmentsto a more complex object. Layers to remove should be the layer name. Layers to add should be in the form of an R list returned by ng_layers or a JSON fragment copied from neuroglancer.
Using + and -
There are shortcut methods that allow you to add or subtract segments or layers from neuroglancer scenes. These are designed for convenience in interactive use, but may be a bit fragile for unusual inputs.
See also
ngl_decode_scene, ngl_layers,
ngl_segments, ngl_encode_url
Examples
# \donttest{
u="https://ngl.flywire.ai/?json_url=https://globalv1.flywire-daf.com/nglstate/5409525645443072"
sc=ngl_decode_scene(u)
sc
#> neuroglancer scene with 2 layers and 2 segments (of which 2 shown)
#> name type visible nsegs
#> 1 Production-image image TRUE 0
#> 2 Production-segmentation_with_graph segmentation_with_graph TRUE 2
#> nhidden
#> 1 0
#> 2 0
#> source
#> 1 precomputed://gs://microns-seunglab/drosophila_v0/alignment/image_rechunked
#> 2 graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v31
names(ngl_layers(sc))
#> [1] "Production-image" "Production-segmentation_with_graph"
str(ngl_layers(sc))
#> List of 2
#> $ Production-image :List of 5
#> ..$ source : chr "precomputed://gs://microns-seunglab/drosophila_v0/alignment/image_rechunked"
#> ..$ type : chr "image"
#> ..$ blend : chr "default"
#> ..$ shaderControls: Named list()
#> ..$ name : chr "Production-image"
#> $ Production-segmentation_with_graph:List of 7
#> ..$ source : chr "graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v31"
#> ..$ type : chr "segmentation_with_graph"
#> ..$ segments : chr [1:2] "720575940621039145" "720575940626877799"
#> ..$ skeletonRendering :List of 2
#> .. ..$ mode2d: chr "lines_and_points"
#> .. ..$ mode3d: chr "lines"
#> ..$ graphOperationMarker:List of 2
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> ..$ pathFinder :List of 2
#> .. ..$ color : chr "#ffff00"
#> .. ..$ pathObject:List of 2
#> .. .. ..$ annotationPath:List of 2
#> .. .. .. ..$ annotations: list()
#> .. .. .. ..$ tags : list()
#> .. .. ..$ hasPath : logi FALSE
#> ..$ name : chr "Production-segmentation_with_graph"
#> - attr(*, "class")= chr [1:2] "nglayers" "list"
str(ngl_layers(sc, nsegs>0))
#> List of 1
#> $ Production-segmentation_with_graph:List of 7
#> ..$ source : chr "graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v31"
#> ..$ type : chr "segmentation_with_graph"
#> ..$ segments : chr [1:2] "720575940621039145" "720575940626877799"
#> ..$ skeletonRendering :List of 2
#> .. ..$ mode2d: chr "lines_and_points"
#> .. ..$ mode3d: chr "lines"
#> ..$ graphOperationMarker:List of 2
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> ..$ pathFinder :List of 2
#> .. ..$ color : chr "#ffff00"
#> .. ..$ pathObject:List of 2
#> .. .. ..$ annotationPath:List of 2
#> .. .. .. ..$ annotations: list()
#> .. .. .. ..$ tags : list()
#> .. .. ..$ hasPath : logi FALSE
#> ..$ name : chr "Production-segmentation_with_graph"
#> - attr(*, "class")= chr [1:2] "nglayers" "list"
str(ngl_layers(sc, visible==TRUE))
#> List of 2
#> $ Production-image :List of 5
#> ..$ source : chr "precomputed://gs://microns-seunglab/drosophila_v0/alignment/image_rechunked"
#> ..$ type : chr "image"
#> ..$ blend : chr "default"
#> ..$ shaderControls: Named list()
#> ..$ name : chr "Production-image"
#> $ Production-segmentation_with_graph:List of 7
#> ..$ source : chr "graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v31"
#> ..$ type : chr "segmentation_with_graph"
#> ..$ segments : chr [1:2] "720575940621039145" "720575940626877799"
#> ..$ skeletonRendering :List of 2
#> .. ..$ mode2d: chr "lines_and_points"
#> .. ..$ mode3d: chr "lines"
#> ..$ graphOperationMarker:List of 2
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> ..$ pathFinder :List of 2
#> .. ..$ color : chr "#ffff00"
#> .. ..$ pathObject:List of 2
#> .. .. ..$ annotationPath:List of 2
#> .. .. .. ..$ annotations: list()
#> .. .. .. ..$ tags : list()
#> .. .. ..$ hasPath : logi FALSE
#> ..$ name : chr "Production-segmentation_with_graph"
#> - attr(*, "class")= chr [1:2] "nglayers" "list"
str(ngl_layers(sc, !visible))
#> Named list()
#> - attr(*, "class")= chr [1:2] "nglayers" "list"
# flywire segmentation
str(ngl_layers(sc, type=="segmentation_with_graph"))
#> List of 1
#> $ Production-segmentation_with_graph:List of 7
#> ..$ source : chr "graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v31"
#> ..$ type : chr "segmentation_with_graph"
#> ..$ segments : chr [1:2] "720575940621039145" "720575940626877799"
#> ..$ skeletonRendering :List of 2
#> .. ..$ mode2d: chr "lines_and_points"
#> .. ..$ mode3d: chr "lines"
#> ..$ graphOperationMarker:List of 2
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> ..$ pathFinder :List of 2
#> .. ..$ color : chr "#ffff00"
#> .. ..$ pathObject:List of 2
#> .. .. ..$ annotationPath:List of 2
#> .. .. .. ..$ annotations: list()
#> .. .. .. ..$ tags : list()
#> .. .. ..$ hasPath : logi FALSE
#> ..$ name : chr "Production-segmentation_with_graph"
#> - attr(*, "class")= chr [1:2] "nglayers" "list"
# image or segmentation
str(ngl_layers(sc, type %in% c("image", "segmentation_with_graph")))
#> List of 2
#> $ Production-image :List of 5
#> ..$ source : chr "precomputed://gs://microns-seunglab/drosophila_v0/alignment/image_rechunked"
#> ..$ type : chr "image"
#> ..$ blend : chr "default"
#> ..$ shaderControls: Named list()
#> ..$ name : chr "Production-image"
#> $ Production-segmentation_with_graph:List of 7
#> ..$ source : chr "graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v31"
#> ..$ type : chr "segmentation_with_graph"
#> ..$ segments : chr [1:2] "720575940621039145" "720575940626877799"
#> ..$ skeletonRendering :List of 2
#> .. ..$ mode2d: chr "lines_and_points"
#> .. ..$ mode3d: chr "lines"
#> ..$ graphOperationMarker:List of 2
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> .. ..$ :List of 2
#> .. .. ..$ annotations: list()
#> .. .. ..$ tags : list()
#> ..$ pathFinder :List of 2
#> .. ..$ color : chr "#ffff00"
#> .. ..$ pathObject:List of 2
#> .. .. ..$ annotationPath:List of 2
#> .. .. .. ..$ annotations: list()
#> .. .. .. ..$ tags : list()
#> .. .. ..$ hasPath : logi FALSE
#> ..$ name : chr "Production-segmentation_with_graph"
#> - attr(*, "class")= chr [1:2] "nglayers" "list"
# }
# get a sample flywire neuroglancer scene
sc=ngl_decode_scene(system.file("flywire-annotations.json" ,
package = 'fafbseg'))
sc
#> neuroglancer scene with 4 layers and 43 segments (of which 1 shown)
#> name type visible nsegs
#> 1 Production-image image TRUE 0
#> 2 Production-segmentation_with_graph segmentation_with_graph TRUE 1
#> 3 annotation annotation TRUE 0
#> 4 jfrc_mesh_test segmentation FALSE 1
#> nhidden
#> 1 0
#> 2 42
#> 3 0
#> 4 1
#> source
#> 1 precomputed://gs://microns-seunglab/drosophila_v0/alignment/image_rechunked
#> 2 graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v31
#> 3 <NA>
#> 4 precomputed://https://spine.itanna.io/files/eric/jfrc_mesh_test
# save a copy
sc.orig <- sc
# remove a layer
ngl_layers(sc)=ngl_layers(sc)[-3]
# or using convenient - notation
sc.noann <- sc.orig - "annotation"
# reverse layer order
ngl_layers(sc)=ngl_layers(sc)[2:1]
# keep visible only
ngl_layers(sc) <- ngl_layers(sc, visible)
# visible + multiple segments
ngl_layers(sc) <- ngl_layers(sc, visible & nsegs>0)
# flywire segmentation
ngl_layers(sc) <- ngl_layers(sc, type=="segmentation_with_graph")
# combine layers using + convenience method
sc.noann + ngl_layers(sc.orig)['annotation']
#> neuroglancer scene with 4 layers and 43 segments (of which 1 shown)
#> name type visible nsegs
#> 1 Production-image image TRUE 0
#> 2 Production-segmentation_with_graph segmentation_with_graph TRUE 1
#> 3 jfrc_mesh_test segmentation FALSE 1
#> 4 annotation annotation TRUE 0
#> nhidden
#> 1 0
#> 2 42
#> 3 1
#> 4 0
#> source
#> 1 precomputed://gs://microns-seunglab/drosophila_v0/alignment/image_rechunked
#> 2 graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v31
#> 3 precomputed://https://spine.itanna.io/files/eric/jfrc_mesh_test
#> 4 <NA>
if (FALSE) {
# combine layers from two scenes
ngl_layers(sc) <- c(ngl_layers(sc), ngl_layers(sc2))
ngl_layers(sc) <- c(ngl_layers(sc)[-(3:4)], ngl_layers(sc2)[3:4])
ngl_layers(sc) <- c(ngl_layers(sc), ngl_layers(sc2)[-1])
ngl_layers(sc) <- c(ngl_layers(sc), ngl_layers(sc2)['annotation'])
sc
# another way to add a single scene
ngl_layers(sc)[[4]] <- ngl_layers(sc2)[[4]]
# add a new layer to a scene by parsing some JSON from the clipboard
# note the double brackets are essential here
ngl_layers(sc)[['jfrc_mesh']] <- jsonlite::fromJSON(clipr::read_clip())
}