Add inflate_to_sphere_implicit

civet/extraction/surfaces.py

@@ -48,15 +48,28 @@ class IrregularSurface(GenericSurface[_IS], Generic[_IS]):
     """
     Represents a mesh (`.obj`) with irregular connectivity.
     """
-    def interpolate_with_sphere(self, side: Optional[Side] = None) -> RegularSurface:
+    def interpolate_with_sphere(
+            self,
+            side: Optional[Side] = None,
+            n_inflate: Optional[int] = None,
+            n_smooth: Optional[int] = None
+    ) -> RegularSurface:
         """
         Resample this surface to have a standard number of 81,920 triangles.
+
+        If `n_inflate` and `n_smooth` are given, use `inflate_to_sphere_implicit` instead
+        of `inflate_to_sphere`.
         """
+        options = []
+        if side is not None:
+            options += ['-' + side.value]
+        if (n_inflate is None) ^ (n_smooth is None):
+            raise ValueError('both n_inflate and n_smooth must be specified')
+        if n_inflate is not None and n_smooth is not None:
+            options += ['-inflate', str(n_inflate), str(n_smooth)]
+
         class InterpolatedFromSphere(RegularSurface):
             def command(self, output: str | PathLike
                         ) -> Sequence[str | PathLike | AbstractDataCommand]:
-                side_option = []
-                if side is not None:
-                    side_option = ['-' + side.value]
-                return 'interpolate_surface_with_sphere.pl', *side_option, self.input, output
+                return 'interpolate_surface_with_sphere.pl', *options, self.input, output
         return InterpolatedFromSphere(self)

scripts/interpolate_surface_with_sphere.pl

@@ -1,6 +1,11 @@
 #!/usr/bin/env perl
-# copied from
-# https://github.com/aces/surface-extraction/blob/master/scripts/marching_cubes.pl.in
+
+# For the most part, this was adapted from
+# https://github.com/aces/surface-extraction/blob/7c9c5987a2f8f5fdeb8d3fd15f2f9b636401d9a1/scripts/marching_cubes.pl.in
+#
+# o 2022-05-06
+#   Replaced `inflate_to_sphere` with `inflate_to_sphere_implicit`
+
 
 use strict;
 use warnings "all";
@@ -17,16 +22,18 @@
 LICENSE
 
 my $usage = <<USAGE;
-Usage: $ProgramName [-left|-right] surface_unknown.obj surface_81920.obj
+Usage: $ProgramName [-left|-right] [-inflate 2000 2000] surface_unknown.obj surface_81920.obj
 
 $license
 USAGE
 
 
 my $side = undef;
+my @inflate_args = undef;
 my @options = (
   ['-left', 'const', "Left", \$side, "Surface is a left surface"],
   ['-right', 'const', "Right", \$side, "Surface is a right surface (sphere should be flipped)"],
+  ['-inflate', 'integer', 2, \@inflate_args, "Use inflate_to_sphere_implicit instead of inflate_to_sphere, and pass the given arguments to it."]
 );
 
 GetOptions( \@options, \@ARGV ) or exit 1;
@@ -49,7 +56,13 @@
 # Inflate the white surface onto a unit sphere.
 
 my $white_sphere_sm = "${tmpdir}/white_sphere_sm.obj";
-&run( 'inflate_to_sphere', $white_surface_sm, $white_sphere_sm );
+
+if ( @inflate_args ) {
+  &run( 'inflate_to_sphere_implicit', $white_surface_sm, $white_sphere_sm, $inflate_args[0], $inflate_args[1] );
+}
+else {
+  &run( 'inflate_to_sphere', $white_surface_sm, $white_sphere_sm );
+}
 
 # Interpolate from sphere-to-sphere to resample the white surface
 # using the 40962 vertices on the standard ICBM surface average

setup.py

@@ -15,7 +15,7 @@
 
 setup(
     name='pycivet',
-    version='0.0.8.post1',
+    version='0.0.9',
     description='Object-oriented CIVET bindings for Python',
     long_description=readme,
     long_description_content_type='text/markdown',