pointsinside() winding-number test via natcpp; macOS CI on CRAN binaries (v1.11.1)

.github/workflows/R-CMD-check.yaml

@@ -40,7 +40,11 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
-          use-public-rspm: true
+          # Public RSPM (Posit Package Manager) binaries only on Linux, where
+          # they are the big win. macOS/Windows fall back to CRAN binaries:
+          # P3M's macOS arm64 Rvcg build currently fails to load with a missing
+          # libomp symbol (___kmpc_dispatch_init_4u), and CRAN's build is clean.
+          use-public-rspm: ${{ startsWith(matrix.config.os, 'ubuntu') }}
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nat
 Type: Package
 Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
-Version: 1.11.0
+Version: 1.11.1
 Authors@R: c(
     person("Gregory","Jefferis", email="jefferis@gmail.com", 
     role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0587-9355")),

NEWS.md

@@ -1,3 +1,13 @@
+# nat 1.11.1
+
+* `pointsinside()` now uses natcpp's (>= 0.3.2) generalised winding-number test
+  for logical results when the natcpp package is installed. This is independent
+  of face normals, so it is robust to inconsistently oriented meshes that could
+  previously give spurious inside/outside classifications with the normal-based
+  `Rvcg` test. The `Rvcg` path remains the fallback and still handles
+  `rval="distance"` and `rval="mesh3d"`; set `options(nat.use_natcpp=FALSE)` to
+  force it.
+
 # nat 1.11.0
 
 This release bundles together a large number of changes and is targeting a CRAN

R/hxsurf.R

@@ -613,9 +613,18 @@ NULL
 #'   testing repeatedly against the same surface, it may make sense to
 #'   pre-convert.
 #'
-#'   \code{pointsinside} depends on the face normals for each face pointing out
-#'   of the object (see example). The face normals are defined by the order of
-#'   the three vertices making up a triangular face. You can flip the face
+#'   When the \href{https://natverse.org/natcpp/}{natcpp} package (>= 0.3.2) is
+#'   installed, logical results (\code{rval="logical"} or
+#'   \code{"consistent_logical"}) use its generalised (solid-angle)
+#'   winding-number test. This does not depend on face normals and is therefore
+#'   robust to inconsistently oriented faces, so the face-normal caveats below
+#'   apply only to the \code{Rvcg} fallback (used when natcpp is unavailable and
+#'   for \code{rval="distance"} or \code{"mesh3d"}). Set
+#'   \code{options(nat.use_natcpp=FALSE)} to force the \code{Rvcg} path.
+#'
+#'   The \code{Rvcg} fallback depends on the face normals for each face pointing
+#'   out of the object (see example). The face normals are defined by the order
+#'   of the three vertices making up a triangular face. You can flip the face
 #'   normal for a face by permuting the vertices (i.e. 1,2,3 -> 1,3,2). If you
 #'   find for a given surface that points are outside when you expect them to be
 #'   inside then the face normals are probably all the wrong way round. You can
@@ -719,14 +728,23 @@ pointsinside.default<-function(x, surf, ..., rval=c('logical','distance',
       stop("Only logical return values are currently possible ",
            "with boundingbox objects!")
   }
-
-  if(!requireNamespace('Rvcg', quietly = TRUE))
-    stop("Please install suggested library Rvcg to use pointsinside")
-
+
   if(!inherits(surf,'mesh3d')) {
     surf=as.mesh3d(surf, ...)
   }
 
+  # Fast, normal-independent path for logical results: natcpp's generalised
+  # winding-number test (>= 0.3.2, method="auto"). Unlike the Rvcg signed
+  # distance it does not depend on face normals, so it avoids spurious results
+  # near thin/sharp features. distance and mesh3d still require Rvcg below.
+  if(rval=='consistent_logical' && !is.null(surf$it) &&
+     use_natcpp(version='0.3.2')) {
+    return(natcpp::c_pointsinside(xyzmatrix(x), xyzmatrix(surf), t(surf$it)))
+  }
+
+  if(!requireNamespace('Rvcg', quietly = TRUE))
+    stop("Please install suggested library Rvcg to use pointsinside")
+
   pts=xyzmatrix(x)
   rmesh=Rvcg::vcgClostKD(pts, surf, sign = TRUE)
   switch(rval,

R/utils.R

@@ -19,7 +19,12 @@ nat_progress <- function (x, max = 100, message = NULL) {
 
 # to check if we should use natcpp
 # always=TRUE => use if installed even if option says otherwise
-use_natcpp <- function(always=FALSE) {
+# version => optional minimum natcpp version required (character or numeric_version)
+use_natcpp <- function(always=FALSE, version=NULL) {
   opcheck <- isTRUE(always) || !isFALSE(getOption('nat.use_natcpp'))
-  opcheck && requireNamespace('natcpp', quietly = TRUE)
+  if(!opcheck || !requireNamespace('natcpp', quietly = TRUE))
+    return(FALSE)
+  if(!is.null(version) && utils::packageVersion('natcpp') < version)
+    return(FALSE)
+  TRUE
 }