Add read/write_catmaid_selection

DESCRIPTION

@@ -20,7 +20,8 @@ Imports:
     rgl,
     dplyr,
     nabor,
-    xml2
+    xml2,
+    grDevices
 Suggests:
     testthat
 Remotes: jefferis/nat

NAMESPACE

@@ -48,11 +48,15 @@ export(connectors)
 export(copy_tags_connectors)
 export(read.neuron.catmaid)
 export(read.neurons.catmaid)
+export(read_catmaid_selection)
+export(write_catmaid_selection)
 import(httr)
 import(nat)
 importFrom(dplyr,as_data_frame)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,right_join)
+importFrom(grDevices,col2rgb)
+importFrom(grDevices,rgb)
 importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,rbind.pages)
 importFrom(nabor,knn)

R/catmaid_selection.R

@@ -0,0 +1,113 @@
+#' Read a CATMAID selection file
+#' 
+#' @param f Path to the \code{.json} file saved by CATMAID
+#' @param readNeurons Whether or not to read the neurons listed in the selection
+#'   file
+#' @param getNames Whether to fetch the names of the neurons (default 
+#'   \code{TRUE}, ignored if neurons are being fetched)
+#' @param ... Connection parameters passed to \code{read.neurons.catmaid}
+#' @return A \code{data.frame} containing the selection information or (if 
+#'   \code{readNeurons=TRUE}) a \code{\link[nat]{neuronlist}} containing this 
+#'   information in the attached metadata. The columns will be \itemize{
+#'   
+#'   \item{skid} The numeric skeleton id
+#'   
+#'   \item{color} The colour of the selected neuron in catmaid
+#'   
+#'   \item{opacity} The opacity (alpha value) of the neuron name
+#'   
+#'   \item{name} Optionally the name of the neuron
+#'   
+#'   }
+#' @export
+#' @examples
+#' f=system.file('catmaid-skeletons.json', package = 'catmaid')
+#' read_catmaid_selection(f, getNames=FALSE)
+#' \dontrun{
+#' # read in the neurons for the selection
+#' x=read_catmaid_selection(f, readNeurons=TRUE)
+#' # plot using the CATMAID colour specifications
+#' plot3d(x, col=color)
+#' }
+#' @seealso \code{\link{write_catmaid_selection}}
+read_catmaid_selection <- function(f, readNeurons=FALSE, getNames=TRUE, ...) {
+  j=jsonlite::read_json(f, simplifyVector = TRUE)
+  colnames(j)[colnames(j)=='skeleton_id']='skid'
+
+  if(readNeurons) {
+    x=read.neurons.catmaid(j$skid, OmitFailures = T, ...)
+    m=merge(x[,], j, by='skid')
+    rownames(m)=names(x)
+    x[,]=m
+    x
+  } else {
+    if(getNames)
+      j$name=catmaid_get_neuronnames(j$skid, ...)
+    class(j)=c(class(j),'catmaid_view')
+    j
+  }
+}
+
+
+#' Make a CATMAID selection file based on neuronlist or skids
+#'
+#' @param x A neuronlist, data.frame or vector of skids
+#' @param f Path to output file (usually ends in .json)
+#' @param color Optional vector of colours in any format understood by col2rgb
+#' @param opacity Optional vector of opacities (alpha values) in range 0-1
+#' @param ... Additional arguments passed to \code{\link[jsonlite]{toJSON}}
+#'
+#' @export
+#' @seealso \code{\link{read_catmaid_selection}}
+#' @examples
+#' \dontrun{
+#' pns=read.neurons.catmaid("annotation:^PN$")
+#' # extract the glomerulus from the name
+#' pns[, 'glomerulus'] = stringr::str_match(pns[, 'name'], 
+#'                                          ".*glomerulus ([A-z0-9]+) .*")[, 2]
+#' pns[, 'glomerulus']=addNA(factor(pns[, 'glomerulus']))
+#' # get the same colours that nat would normally use in a plot
+#' plotres=plot3d(pns, col=glomerulus)
+#' cols=attr(plotres,'df')$col
+#' # write out selection file with those colours
+#' write_catmaid_selection(pns, f='pns-by-glom.json', color=cols)
+#' }
+write_catmaid_selection <- function(x, f, color=NULL, opacity=NULL, ...) {
+  if(is.neuronlist(x))
+    x=as.data.frame(x)
+  if(is.data.frame(x)){
+    df=x
+    x=df$skid
+    # see if the data.frame has colour or opacity information if these are 
+    # missing
+    if(is.null(color)) {
+      colcol=na.omit(match(c("colour", "color", "col"), colnames(df)))
+      if(any(is.finite(colcol)))
+        color=df[[colcol[1]]]
+    }
+    if(is.null(opacity)) {
+      opac_col=na.omit(match(c("opacity","alpha"), colnames(df)))
+      if(any(is.finite(opac_col)))
+        opacity=df[[opac_col[1]]]
+    }
+  }
+  df=data.frame(skeleton_id=x)
+  if(length(color))
+    df$color=normalise_colours(color)
+  if(length(opacity))
+    df$opacity=opacity
+
+  json=jsonlite::toJSON(df, pretty=TRUE, ...)
+  json=gsub("  ", " ", json, fixed = T)
+  writeLines(json, f)
+}
+
+# will take any unitary colour specification ("red", 1, "#FF0000") 
+# and turn into a web style colour specification #FF0000
+#' @importFrom grDevices col2rgb rgb
+normalise_colours <- function(x) {
+  if(is.null(x))
+    return(NULL)
+  cols=apply(col2rgb(x),2, function(x) rgb(x[1], x[2], x[3], maxColorValue = 255))
+  tolower(cols)
+}

inst/catmaid-skeletons.json

@@ -0,0 +1,177 @@
+[
+ {
+  "skeleton_id": 1180353,
+  "color": "#ffff00",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1181286,
+  "color": "#ff00ff",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1182615,
+  "color": "#0000ff",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1313485,
+  "color": "#00ff00",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1334552,
+  "color": "#ffffff",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1334561,
+  "color": "#00ffff",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1371629,
+  "color": "#ff7f00",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 2390270,
+  "color": "#7fff00",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 2390280,
+  "color": "#7f7f7f",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3826596,
+  "color": "#ff0000",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3842618,
+  "color": "#7f7fff",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3853002,
+  "color": "#bfbfbf",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3872709,
+  "color": "#ff7f7f",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4232956,
+  "color": "#7fff7f",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4260599,
+  "color": "#ff007f",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1182625,
+  "color": "#d8a31e",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1273130,
+  "color": "#3fe0d1",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1334538,
+  "color": "#ffbfc9",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 1338786,
+  "color": "#08f62f",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3842350,
+  "color": "#f30b61",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3852709,
+  "color": "#02fc9f",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3908112,
+  "color": "#04fa3f",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3910750,
+  "color": "#ffffff",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3927073,
+  "color": "#57f608",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3930323,
+  "color": "#ff0046",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 3931453,
+  "color": "#98ff00",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4149101,
+  "color": "#89bf3f",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4165941,
+  "color": "#00ff51",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4214127,
+  "color": "#ff9a00",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4233149,
+  "color": "#819cfd",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4260588,
+  "color": "#dfae9f",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4276626,
+  "color": "#fc82f7",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4311394,
+  "color": "#99fa83",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4328317,
+  "color": "#1306f8",
+  "opacity": 1
+ },
+ {
+  "skeleton_id": 4344859,
+  "color": "#790a05",
+  "opacity": 1
+ }
+]