Add mirror_banc

DESCRIPTION

@@ -26,7 +26,8 @@ Imports:
     jsonlite,
     pbapply,
     dplyr,
-    checkmate
+    checkmate,
+    utils
 Suggests: 
     testthat (>= 3.0.0),
     reticulate,

NAMESPACE

@@ -29,6 +29,7 @@ export(fanc_segid_from_cellid)
 export(fanc_set_token)
 export(fanc_voxdims)
 export(fanc_xyz2id)
+export(mirror_banc)
 export(read_fanc_meshes)
 export(transform_fanc2manc)
 export(with_banc)

R/data.R

@@ -45,3 +45,15 @@
 #' boundingbox(BANC)
 "BANC"
 
+#' Provisional mirroring registration for BANC (lanmarks+thin plate splines)
+#'
+#' @name mirror_banc_lm
+#' @docType data
+#' @description This is calibrated in nm. See \code{data-raw/mirror_banc.R} for
+#'   details of how it was generated. It is still provisional pending synpase
+#'   cloud-based registrations.
+#'
+#' @examples
+#' utils::str(mirror_banc_lm)
+"mirror_banc_lm"
+

R/xform.R

@@ -82,3 +82,53 @@ transform_fanc2manc <- function(x, inverse = F, ...) {
   reg = fanc_to_manc_reg()
   xform(x, reg=reg, swap=inverse,... )
 }
+
+
+#' Mirror points, neurons in BANC space
+#'
+#' @param x Points, neurons or other objects compatible with \code{xyzmatrix}
+#' @param units Units for both input \emph{and} output data.
+#' @param subset Optional argument to transform only a subset of a neuron list.
+#'
+#' @return Trge transformed object (calibrated according to the units argument)
+#' @export
+#'
+#' @examples
+#' BANC.surf.m <- mirror_banc(BANC.surf)
+#' \dontrun{
+#' library(nat)
+#' wire3d(BANC.surf)
+#' # clearly not great in some places, especially optic lobe, but still useful
+#' wire3d(BANC.surf.m, col='red')
+#' }
+mirror_banc <- function(x, units=c("nm", "microns", "raw"), subset=NULL) {
+  units=match.arg(units)
+
+  if(!is.null(subset)) {
+    xs=x[subset]
+    xst=mirror_banc(xs, units = units, mirror_reg = fancr::mirror_banc_lm)
+    x[subset]=xst
+    return(x)
+  }
+  BANCmesh=templatebrain("BANC",
+                     BoundingBox = structure(c(79392.9, 966179.9, 35524.5, 1131169.6, -62.8, 315466.7
+                     ), dim = 2:3, class = "boundingbox"))
+  # convert to nm if necessary
+  xyz=xyzmatrix(x)
+  if(units=='microns')
+    xyz=xyz*1e3
+  else if(units=='raw')
+    xyz=banc_raw2nm(xyz)
+
+  xyzf=mirror_brain(x, brain = BANCmesh, mirrorAxis = 'X', transform = 'flip')
+  xyzf2=xform(xyzf, reg = fancr::mirror_banc_lm)
+
+  # convert from nm to original units if necessary
+  if(units=='microns')
+    xyzf2=xyzf2/1e3
+  else if(units=='raw')
+    xyzf2=banc_nm2raw(xyzf2)
+
+  xyzmatrix(x)=xyzf2
+  x
+}

data-raw/mirror-banc.R

@@ -0,0 +1,17 @@
+# construct a mirroring registration from landmarks
+mirror_banc_tps <- function(anns) {
+  if(is.character(anns)) {
+    anns=ngl_annotations(anns)
+  }
+  AB=rbind(banc_raw2nm(anns$pointA), banc_raw2nm(anns$pointB))
+  BA=rbind(banc_raw2nm(anns$pointB), banc_raw2nm(anns$pointA))
+  # have decided to use this rather than "official" space
+  BANCmesh=nat.templatebrains::templatebrain("BANC",
+    BoundingBox = structure(c(79392.9, 966179.9, 35524.5, 1131169.6, -62.8, 315466.7), dim = 2:3, class = "boundingbox"))
+  ABf=nat.templatebrains::mirror_brain(AB, brain = BANCmesh, mirrorAxis = 'X', transform = 'flip')
+  delta=BA-ABf
+  tpsreg(sample = ABf, reference = BA)
+}
+mirror_banc_lm=mirror_banc_tps('https://spelunker.cave-explorer.org/#!middleauth+https://global.daf-apis.com/nglstate/api/v1/5486159028289536')
+
+usethis::use_data(mirror_banc_lm, overwrite = TRUE)