Feature/bridging graph environment

DESCRIPTION

@@ -19,11 +19,12 @@ Imports:
     igraph,
     digest,
     rappdirs,
-    memoise
+    memoise,
+    purrr
 Suggests:
     testthat (>= 0.10),
     git2r (>= 0.22.1),
     nabor
 URL: https://github.com/jefferislab/nat.templatebrains
-RoxygenNote: 6.1.1
+RoxygenNote: 6.1.1.9000
 Encoding: UTF-8

R/templatebrain.R

@@ -159,9 +159,10 @@ print.templatebrain <- function(x, ...) {
   cat("Sex: ", x$sex, "\n")
   cat(sprintf("Dimensions:%d x %d x %d voxels\n", x$dims[1], x$dims[2], x$dims[3]))
   cat(paste0("Voxel size:\n"))
-  cat("  x =", paste0(x$voxdims[1], " ", x$units[1], "\n"))
-  cat("  y =", paste0(x$voxdims[2], " ", x$units[2], "\n"))
-  cat("  z =", paste0(x$voxdims[3], " ", x$units[3], "\n"))
+  dimension_names = c('x','y','z')
+  for (dimidx in 1:length(x$voxdims)) {
+    cat(" ",dimension_names[dimidx] ,"=", paste0(x$voxdims[dimidx], " ",
+        purrr::pluck(x$units,dimidx,.default = x$units[1]), "\n")) }
   cat(paste0("Bounding box (", x$units[1], "):\n"))
   cat("  x =", paste0(x$BoundingBox[1, 1], ", y = ", x$BoundingBox[1, 2], ", z = ", x$BoundingBox[1, 3], ",\n"))
   cat("  x =", paste0(x$BoundingBox[2, 1], ", y = ", x$BoundingBox[2, 2], ", z = ", x$BoundingBox[2, 3], ".\n"))

R/transformation.R

@@ -185,6 +185,21 @@ allreg_dataframe<-function(regdirs=getOption('nat.templatebrains.regdirs')) {
 #' plot(bridging_graph(), vertex.size=25)
 #' }
 bridging_graph <- function(regdirs=getOption('nat.templatebrains.regdirs'), reciprocal=NA) {
+  sha512=digest(list(regdirs, reciprocal), algo = "sha512")
+  bg=.bridging_graph[[sha512]]
+  if(is.null(bg)){
+    bg=make_bridging_graph(regdirs, reciprocal)
+    .bridging_graph[[sha512]]=bg
+  }
+  bg
+}
+
+set_bridging_graph <- function(bg, regdirs=getOption('nat.templatebrains.regdirs'), reciprocal=NA) {
+  sha512=digest(list(regdirs, reciprocal), algo = "sha512")
+  .bridging_graph[[sha512]]=bg
+}
+
+make_bridging_graph <- function(regdirs, reciprocal) {
   df=allreg_dataframe(regdirs)
   if(nrow(df)==0) return(NULL)
   # just keep the bridging registrations
@@ -205,10 +220,15 @@ bridging_graph <- function(regdirs=getOption('nat.templatebrains.regdirs'), reci
   g
 }
 
+
+
+
+
 #' @importFrom memoise forget memoise
 reset_cache <- function() {
-  memoise::forget(shortest_bridging_seq)
-  memoise::memoise(shortest_bridging_seq)
+  # memoise::forget(shortest_bridging_seq)
+  # memoise::memoise(shortest_bridging_seq)
+  rm(list=ls(.bridging_graph), envir = .bridging_graph)
 }
 
 #' @description \code{shortest_bridging_seq} finds the shortest bridging

R/zzz.R

@@ -7,3 +7,5 @@
 
   invisible()
 }
+
+.bridging_graph <- new.env()

tests/testthat/test-template-brain-data.r

@@ -64,4 +64,9 @@ test_that("as.templatebrain.im3d works", {
 
 test_that("print.templatebrain",{
   expect_output(print(FCWB.demo), "Name: FlyCircuit Whole Brain")
+
+  #Check if it can cycle through units that are not explicity given (for e.g. y and z direction units)
+  dummy_templatebrain <- as.templatebrain(im3d(dims = c(3,4),voxdims = c(2,3,4)), regName="FAFB", name='Full Adult')
+  dummy_templatebrain$units = 'nm'
+  expect_output(print(dummy_templatebrain), "\\nVoxel size:\\n  x = 2 nm\\n  y = 3 nm\\n  z = 4 nm")
 })