[test] add cgalmesh v2m test, accept radbound/distbound via opt

Author: fangq

README.md

@@ -4,7 +4,7 @@
 
 * Copyright: (C) Qianqian Fang (2024-2025) <q.fang at neu.edu>, Edward Xu (2024) <xu.ed at northeastern.edu>
 * License: GNU Public License V3 or later
-* Version: 0.2.1
+* Version: 0.2.2
 * URL: [https://pypi.org/project/iso2mesh/](https://pypi.org/project/iso2mesh/)
 * Github: [https://github.com/NeuroJSON/pyiso2mesh](https://github.com/NeuroJSON/pyiso2mesh)
 
@@ -130,6 +130,10 @@ i2m.plotmesh(no, el, 'x < 0', shade=False, edgecolor='r')
 # creating and plotting polyhedral solids (PLCs)
 mesh = i2m.latticegrid([0,1],[0,1,2], [0,2])
 i2m.plotmesh(mesh[0], mesh[1], alpha=0.5, linestyle='--')
+
+# mesh and label PLC based domains using tetgen1.5
+mesh2 = i2m.s2m(mesh[0], mesh[1], 1, 0.03, method='tetgen1.5')
+i2m.plotmesh(mesh2[0], mesh2[1], alpha=0.5)
 ```
 
 `pyiso2mesh` subdivides all functions into sub-modules (**core, geometry, plot,

iso2mesh/__init__.py

@@ -137,7 +137,7 @@
     barycentricgrid,
 )
 
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 __all__ = [
     "advancefront",
     "barycentricgrid",

iso2mesh/core.py

@@ -793,7 +793,7 @@ def cgalv2m(vol, opt, maxvol):
     if not isinstance(opt, dict):
         ssize = opt
 
-    if isinstance(opt, dict) and len(opt) == 1:
+    if isinstance(opt, dict):
         ssize = opt.get("radbound", ssize)
         ang = opt.get("angbound", ang)
         approx = opt.get("distbound", approx)
@@ -806,7 +806,7 @@ def cgalv2m(vol, opt, maxvol):
 
     cmd = f'"{mcpath("cgalmesh", exesuff)}" "{mwpath("pre_cgalmesh.inr")}" "{mwpath("post_cgalmesh.mesh")}" {ang} {ssize} {approx} {reratio} {maxvol} {randseed}'
 
-    os.system(cmd)
+    status, str_output = subprocess.getstatusoutput(cmd)
 
     if not os.path.exists(mwpath("post_cgalmesh.mesh")):
         raise RuntimeError(f"Output file was not found. Command failed: {cmd}")

iso2mesh/trait.py

@@ -373,21 +373,21 @@ def elemvolume(node, elem, option=None):
     """
 
     # Convert 1-based indices to 0-based for Python indexing
-    v1 = node[elem[:, 0] - 1, :]
-    v2 = node[elem[:, 1] - 1, :]
-    v3 = node[elem[:, 2] - 1, :]
+    v1 = node[elem[:, 0] - 1, :3]
+    v2 = node[elem[:, 1] - 1, :3]
+    v3 = node[elem[:, 2] - 1, :3]
 
     edge1 = v2 - v1
     edge2 = v3 - v1
 
-    if elem.shape[1] == node.shape[1]:
+    if elem.shape[1] == 3:
         # Triangle area in 2D or area in 3D projected onto a plane
         det12 = np.cross(edge1, edge2)
         det12 = np.sum(det12 * det12, axis=1)
         vol = 0.5 * np.sqrt(det12)
         return vol
 
-    v4 = node[elem[:, 3] - 1, :]
+    v4 = node[elem[:, 3] - 1, :3]
     edge3 = v4 - v1
 
     # Compute signed volume of tetrahedron

setup.py

@@ -6,7 +6,7 @@
 setup(
     name="iso2mesh",
     packages=["iso2mesh"],
-    version="0.2.1",
+    version="0.2.2",
     license='GPLv3+',
     description="Image-based 3D Surface and Volumetric Mesh Generator",
     long_description=readme,
@@ -16,16 +16,14 @@
     maintainer="Qianqian Fang",
     url="https://github.com/NeuroJSON/pyiso2mesh",
     keywords=[
-        "JSON",
-        "iso2mesh",
-        "UBJSON",
-        "Biso2mesh",
-        "Openiso2mesh",
-        "NeuroJSON",
-        "JNIfTI",
-        "JMesh",
-        "Encoder",
-        "Decoder",
+        "Iso2Mesh",
+        "Mesh generation",
+        "FEM",
+        "MATLAB",
+        "Mesh-based Monte Carlo",
+        "CGAL",
+        "Tetgen",
+        "CSG",
     ],
     platforms="any",
     install_requires=["numpy>=1.8.0", "matplotlib"],

test/run_test.py

@@ -596,11 +596,11 @@ def test_surfboolean_second(self):
         no3, el3 = surfboolean(self.no1, self.el1, "second", self.no2, self.el2)
         no3, el3 = meshcheckrepair(no3, el3, "dup", tolerance=1e-4)
         node, elem, _ = s2m(no3, el3, 1, 100, "tetgen", np.array([2.6, 2.6, 2.6]))
-        self.assertEqual(
-            round(sum(elemvolume(node, elem[elem[:, 4] == 1, :4])), 5), 7.973
+        self.assertAlmostEqual(
+            sum(elemvolume(node, elem[elem[:, 4] == 1, :4])), 7.973, 5
         )
-        self.assertEqual(
-            round(sum(elemvolume(node, elem[elem[:, 4] == 0, :4])), 5), 0.027
+        self.assertAlmostEqual(
+            sum(elemvolume(node, elem[elem[:, 4] == 0, :4])), 0.027, 5
         )
 
     def test_surfboolean_resolve(self):
@@ -609,14 +609,14 @@ def test_surfboolean_resolve(self):
         node, elem, _ = s2m(
             no3, el3, 1, 100, "tetgen", np.array([[1.5, 1.5, 1.5], [2.6, 2.6, 2.6]])
         )
-        self.assertEqual(
-            round(sum(elemvolume(node, elem[elem[:, 4] == 0, :4])), 5), 0.027
+        self.assertAlmostEqual(
+            sum(elemvolume(node, elem[elem[:, 4] == 0, :4])), 0.027, 5
         )
-        self.assertEqual(
-            round(sum(elemvolume(node, elem[elem[:, 4] == 1, :4])), 5), 0.973
+        self.assertAlmostEqual(
+            sum(elemvolume(node, elem[elem[:, 4] == 1, :4])), 0.973, 5
         )
-        self.assertEqual(
-            round(sum(elemvolume(node, elem[elem[:, 4] == 2, :4])), 5), 7.973
+        self.assertAlmostEqual(
+            sum(elemvolume(node, elem[elem[:, 4] == 2, :4])), 7.973, 5
         )
 
     def test_surfboolean_self(self):
@@ -683,13 +683,24 @@ def test_binsurface0(self):
 
     def test_v2s(self):
         no, fc, _, _ = v2s(self.im, 0.5, 0.03)
-        self.assertAlmostEqual(round(sum(elemvolume(no, fc[:, :3])), 2), 5.01)
+        self.assertAlmostEqual(sum(elemvolume(no, fc[:, :3])), 5.01, 2)
 
     def test_v2m(self):
         no, el, fc = v2m(self.im, 0.5, 0.03, 10)
         self.assertAlmostEqual(round(sum(elemvolume(no, fc[:, :3])), 2), 5.01)
         self.assertAlmostEqual(round(sum(elemvolume(no, el[:, :4])), 4), 0.8786)
 
+    def test_cgalv2m(self):
+        no, el, fc = v2m(
+            self.im.astype(np.uint8),
+            [],
+            {"radbound": 0.03, "distbound": 0.2},
+            10,
+            "cgalmesh",
+        )
+        self.assertEqual(removedupelem(fc[:, :3]).shape[0], 0)
+        self.assertAlmostEqual(sum(elemvolume(no[:, :3], el[:, :4])), 0.7455, 4)
+
 
 if __name__ == "__main__":
     unittest.main()