add fill holes parameter in segmentation surface mesh

src/gnomon_package_tissueimagemesh/algorithm/meshFromImage/segmentationSurfaceMesh.py

@@ -2,7 +2,7 @@ import numpy as np
 
 from skimage.filters.thresholding import threshold_otsu
 
-from dtkcore import d_int, d_inliststring, d_real
+from dtkcore import d_bool, d_int, d_inliststring, d_real
 
 import gnomon.core
 from gnomon.core import gnomonAbstractMeshFromImage
@@ -32,6 +32,8 @@ class segmentationSurfaceMesh(gnomonAbstractMeshFromImage):
         self._parameters = {}
         self._parameters['resampling_voxelsize'] = d_real("Resampling voxelsize", 0, 0, 1, 2, "Cubic voxelsize in which to resample the image before mesh extraction")
         self._parameters['orientation'] = d_inliststring('Orientation', "up", ["up", "down"], "Whether to keep upper or lower part")
+        self._parameters['down_facing_threshold'] = d_real("Normal z threshold", 0, -1, 1, 2, "The z coordinate below which a normal vector is considered to face downwards")
+        self._parameters['fill_holes'] = d_bool("Fill holes", False, "Whether to fill holes in the segmented image to generate the surface mesh")
 
         self._parameter_groups = {}
 
@@ -56,6 +58,8 @@ class segmentationSurfaceMesh(gnomonAbstractMeshFromImage):
                 orientation=(1 if self['orientation']=="up" else -1),
                 surface_matching='cell',
                 padding=False,
+                down_facing_threshold=self['down_facing_threshold'],
+                fill_holes=self['fill_holes']
             )
 
             for degree in [1, 2, 3]: