Added Morpho tps registration for BANC->JRC2018F and BANC-mirror

R/data.R

@@ -36,4 +36,108 @@
 # banc.mesh <- malevnc:::decode_neuroglancer_mesh(bytes)
 # banc.surf <- as.hxsurf(banc.mesh)
 # banc.surf$Vertices[,"Z"] <- banc.surf$Vertices[,"Z"]*0.9462 # scaling Jasper worked out
-# save(banc.surf, file="data/BANC.surf.rda")
+# usethis::use_data(banc.surf, overwrite = TRUE)
+
+#' Thin-Plate Spline Registration from BANC to JRC2018F templatebrain
+#'
+#' @description
+#' A thin-plate spline (TPS) registration object that transforms 3D points
+#' from the BANC nanometer coordinate system
+#' to the D. melanogaster template brain JRC2018F coordinate system.
+#'
+#' @format An object of class \code{tpsCoeff} created using \code{Morpho::computeTransform}.
+#'   It contains the following components:
+#'   \describe{
+#'     \item{Lw}{Matrix of TPS coefficients}
+#'     \item{refmat}{Reference matrix (source landmarks)}
+#'     \item{tarmat}{Target matrix (target landmarks)}
+#'     \item{lattice}{3D array representing the deformation grid}
+#'     \item{lambda}{Smoothing parameter used in the TPS computation}
+#'     \item{scale}{Logical indicating whether scaling was used}
+#'     \item{reflection}{Logical indicating whether reflection was allowed}
+#'   }
+#'
+#' @details
+#' This TPS registration was computed based on landmark correspondences
+#' derived from an Elastix registration between the BANC and JRC2018F spaces.
+#' It provides a smooth, interpolated transformation for any point in the BANC space
+#' to its corresponding location in the JRC2018F space.
+#'
+#' @usage data(banc_to_jrc2018f_tpsreg)
+#'
+#' @source
+#' Derived from Elastix registration results using the \code{banc_to_JRC2018F}
+#' function and landmark correspondences extracted from that registration.
+#'
+#' @examples
+#' \dontrun{
+#' data(banc_to_jrc2018f_tpsreg)
+#'
+#' # Transform BANC points to JRC2018F using the TPS registration
+#' banc_points <- matrix(rnorm(300), ncol=3)  # Example BANC points
+#' jrc2018f_points <- Morpho::tps3d(banc_points, banc_to_jrc2018f_tpsreg)
+#' }
+#'
+#' @seealso
+#' \code{\link{banc_to_JRC2018F}} for the function that performs transformations
+#' between BANC and JRC2018F spaces.
+#' \code{\link[Morpho]{computeTransform}} for details on creating tpsCoeff objects.
+#'
+#' @name banc_to_jrc2018f_tpsreg
+#' @docType data
+"banc_to_jrc2018f_tpsreg"
+
+#' Thin-Plate Spline Registration for Mirroring in BANC Space
+#'
+#' @description
+#' A thin-plate spline (TPS) registration object that mirrors 3D points
+#' within the BANC (Buhmann et al. Adult Neural Connectome) coordinate system.
+#'
+#' @format An object of class \code{tpsCoeff} created using \code{Morpho::computeTransform}.
+#'   It contains the following components:
+#'   \describe{
+#'     \item{Lw}{Matrix of TPS coefficients}
+#'     \item{refmat}{Reference matrix (source landmarks)}
+#'     \item{tarmat}{Target matrix (mirrored landmarks)}
+#'     \item{lattice}{3D array representing the deformation grid}
+#'     \item{lambda}{Smoothing parameter used in the TPS computation}
+#'     \item{scale}{Logical indicating whether scaling was used}
+#'     \item{reflection}{Logical indicating whether reflection was allowed}
+#'   }
+#'
+#' @details
+#' This TPS registration was computed to allow mirroring of points directly within
+#' the BANC coordinate system. It provides a smooth, interpolated transformation
+#' for any point in the BANC space to its mirrored counterpart, accounting for
+#' any asymmetries in the BANC reference brain.
+#'
+#' @usage data(banc_mirror_tpsreg)
+#'
+#' @source
+#' Derived from landmark correspondences between original and mirrored points
+#' in the BANC space, possibly utilizing transformations to and from the
+#' JRC2018F space for accurate mirroring.
+#'
+#' @examples
+#' \dontrun{
+#' data(banc_mirror_tpsreg)
+#'
+#' # Mirror BANC points using the TPS registration
+#' banc_points <- matrix(rnorm(300), ncol=3)  # Example BANC points
+#' mirrored_points <- Morpho::tps3d(banc_points, banc_mirror_tpsreg)
+#' }
+#'
+#' @seealso
+#' \code{\link{banc_mirror}} for the function that performs mirroring
+#' of points in BANC space.
+#' \code{\link{banc_to_jrc2018f_tpsreg}} for the TPS registration between
+#' BANC and JRC2018F spaces.
+#' \code{\link[Morpho]{computeTransform}} for details on creating tpsCoeff objects.
+#'
+#' @name banc_mirror_tpsreg
+#' @docType data
+"banc_mirror_tpsreg"
+
+
+
+

R/xform.R

@@ -451,15 +451,15 @@ banc_mirror <- function(x,
     x.jrc2018f <- banc_to_JRC2018F(x=x, units="um", subset=NULL, inverse=FALSE, transform_file = transform_files[1], method = method)
 
     # Mirror
-    x.jrc2018f.m <- nat.templatebrains::mirror_brain(x.jrc2018f, brain = "JRC2018F", ... )
+    x.jrc2018f.m <-  nat.templatebrains::mirror_brain(x.jrc2018f, brain = nat.flybrains::JRC2018F, transform = "flip")
 
     # Back to BANC
     x.banc.m <- banc_to_JRC2018F(x=x, units="um", subset=NULL, inverse=TRUE , transform_file = transform_files[2], method = method)
 
   }else{
 
     # Use pre-calculated tps reg
-    x.banc.m <- nat::xform(xyzf, reg = banc_miror_tpsreg)
+    x.banc.m <- nat::xform(xyzf, reg = banc_mirror_tpsreg)
 
   }