[port] test surf2vol, surf2volz, s2v, bump version to 0.3.8

fangq · fangq · commit cf2f35920a72 · 2025-07-09T17:48:54.000-04:00
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 
 * **Copyright**: (C) Qianqian Fang (2024-2025) <q.fang at neu.edu>
 * **License**: GNU Public License V3 or later
-* **Version**: 0.3.7
+* **Version**: 0.3.8
 * **URL**: [https://pypi.org/project/iso2mesh/](https://pypi.org/project/iso2mesh/)
 * **Homepage**: [https://iso2mesh.sf.net](https://iso2mesh.sf.net)
 * **Github**: [https://github.com/NeuroJSON/pyiso2mesh](https://github.com/NeuroJSON/pyiso2mesh)
@@ -187,21 +187,21 @@ tracked in https://github.com/NeuroJSON/pyiso2mesh/issues/1
 | ✅ `v2m.m` | ✅ tested |                    | ✅ `saveasc.m` | ⭕️ tested |
 | ✅ `v2s.m` | ✅ tested |                    | ✅ `savedxf.m` | ⭕️ tested |
 | ✅ `s2m.m` | ✅ tested |                    | ✅ `savestl.m` | ⭕️ tested |
-| ✅ `s2v.m` | ⭕️ tested |                    | ✅ `savebinstl.m` | ⭕️ tested |
+| ✅ `s2v.m` | ✅ tested |                    | ✅ `savebinstl.m` | ⭕️ tested |
 | ✅ `m2v.m` | ⭕️ tested |                    | ✅ `saveinr.m` | ⭕️ tested |
 | ✅ `sms.m` | ✅ tested |                    | ✅ `saveoff.m` | ✅ tested |
 | > Streamlined mesh generation| |            | ⭕️ `savesmf.m` | ⭕️ tested |
 | ✅ `vol2mesh.m` | ✅ tested |               | ✅ `savesurfpoly.m` | ✅ tested |
 | ✅ `vol2surf.m` | ✅ tested |               | ⭕️ `savegts.m` | ⭕️ tested |
 | ✅ `surf2mesh.m` | ✅ tested |              | ⭕️ `readgts.m` | ⭕️ tested |
-| ✅ `surf2vol.m` | ⭕️ tested |               | ⭕️ `savemsh.m` | ⭕️ tested |
+| ✅ `surf2vol.m` | ✅ tested |               | ⭕️ `savemsh.m` | ⭕️ tested |
 | ✅ `mesh2vol.m` | ⭕️ tested |               | ⭕️ `savevrml.m` | ⭕️ tested |
 | > Iso2mesh main function backend| |         | ✅ `readasc.m` | ⭕️ tested |
 | ✅ `binsurface.m` | ✅ tested |             | ⭕️ `readinr.m` | ⭕️ tested |
 | ✅ `cgalv2m.m` | ✅ tested |                | ✅ `readmedit.m` | ⭕️ tested |
 | ✅ `cgals2m.m` | ⭕️ tested |                | ✅ `readoff.m` | ✅ tested |
 | ✅ `vol2restrictedtri.m` | ✅ tested |      | ⭕️ `readsmf.m` | ⭕️ tested |
-| ✅ `surf2volz.m` | ⭕️ tested |              | ✅ `readtetgen.m` | ✅ tested |
+| ✅ `surf2volz.m` | ✅ tested |              | ✅ `readtetgen.m` | ✅ tested |
 | ✅ `mesh2mask.m` | ⭕️ tested |              | ✅ `deletemeshfile.m` | ✅ tested |
 | > Iso2mesh primitive meshing|           |   | ✅ `mcpath.m` | ✅ tested |
 | ✅ `meshabox.m` | ✅ tested |               | ✅ `mwpath.m` | ✅ tested |
@@ -273,7 +273,7 @@ tracked in https://github.com/NeuroJSON/pyiso2mesh/issues/1
 | ⭕️ `closestnode.m` | ⭕️ tested |            | ⭕️ `soa2aos.m` | ⭕️ tested |
 | > Mesh resampling and optimization| |
 | ✅ `meshresample.m` | ✅ tested |
-| ✅ `remeshsurf.m` | ⭕️ tested |
+| ✅ `remeshsurf.m` | ✅ tested |
 | ✅ `smoothsurf.m` | ✅ tested |
 | ✅ `sortmesh.m` | ⭕️ tested |
 | ✅ `mergemesh.m` | ⭕️ tested |
diff --git a/iso2mesh/__init__.py b/iso2mesh/__init__.py
@@ -157,7 +157,7 @@
     regpt2surf,
 )
 
-__version__ = "0.3.7"
+__version__ = "0.3.8"
 __all__ = [
     "advancefront",
     "barycentricgrid",
diff --git a/iso2mesh/core.py b/iso2mesh/core.py
@@ -200,15 +200,15 @@ def s2m(
     return node, elem, face
 
 
-def s2v(node, face, div=50, *args):
+def s2v(node, face, div=50, **kwargs):
     """
     Convert a surface mesh to a volumetric binary image.
 
     Parameters:
     node   : array-like, the vertices of the triangular surface (Nx3 for x, y, z)
     face   : array-like, the triangle node indices (Mx3, each row is a triangle)
     div    : int, division number along the shortest edge of the mesh (resolution)
-    *args  : additional arguments for the surf2vol function
+    kwargs  : additional arguments for the surf2vol function
 
     Returns:
     img    : volumetric binary image
@@ -232,9 +232,9 @@ def s2v(node, face, div=50, *args):
     yi = np.arange(p0[1] - dx, p1[1] + dx, dx)
     zi = np.arange(p0[2] - dx, p1[2] + dx, dx)
 
-    img, v2smap = surf2vol(node, face, xi, yi, zi, *args)
+    img = surf2vol(node, face, xi, yi, zi, **kwargs)
 
-    return img, v2smap
+    return img
 
 
 def vol2mesh(img, ix, iy, iz, opt, maxvol, dofix, method="cgalsurf", isovalues=None):
@@ -586,7 +586,10 @@ def surf2volz(node, face, xi, yi, zi):
     maxz = np.max(node[:, 2])
 
     # Determine the z index range
-    iz = np.histogram([minz, maxz], bins=zi)[0]
+    iz, _ = np.histogram(
+        [minz, maxz],
+        bins=np.append(zi - np.diff(zi)[0] / 2, zi[-1] + np.diff(zi)[-1] / 2),
+    )
     hz = np.nonzero(iz)[0]
     iz = np.arange(hz[0], min(len(zi), hz[-1] + 1))
 
diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 setup(
     name="iso2mesh",
     packages=["iso2mesh"],
-    version="0.3.7",
+    version="0.3.8",
     license="GPLv3+",
     description="One-liner 3D Surface and Tetrahedral Mesh Generation Toolbox",
     long_description=readme,
diff --git a/test/run_test.py b/test/run_test.py
@@ -1070,6 +1070,7 @@ def __init__(self, *args, **kwargs):
         self.mask = self.dist < 400
         self.mask = self.mask.astype(float)
         self.mask[25:35, 25:35, :] = 2
+        self.no, self.fc, _, _ = v2s(self.dist < 100, 0.5, 2)
 
         self.plcno = (
             np.array(
@@ -1221,15 +1222,43 @@ def test_remeshsurf(self):
         no, fc, _, _ = v2s(self.dist, 100, 2)
         no1, fc1 = remeshsurf(no, fc, 1)
         self.assertAlmostEqual(
-            sum(elemvolume(no[:, :3], fc[:, :3])) * 0.0001, 2.034550093898604, 4
+            sum(elemvolume(no[:, :3], fc[:, :3])) * 0.0001, 2.034550093898604, 3
         )
 
-    # def test_surf2vol(self):
-    #     no, fc, _, _ = v2s(self.dist < 100, 0.5, 2)
-    #     vol = surf2vol(
-    #         no, fc, np.arange(19, 42, 1), np.arange(19, 42, 1), np.arange(19, 42, 1)
-    #     )
-    #     self.assertAlmostEqual(np.sum(vol.astype(np.float32)), 2.034550093898604, 4)
+    def test_surf2volz(self):
+        vol = surf2volz(
+            self.no,
+            self.fc,
+            np.arange(19, 42, 1),
+            np.arange(19, 42, 1),
+            np.arange(19, 42, 1),
+        )
+        self.assertAlmostEqual(np.sum(vol.astype(np.float32)) * 0.001, 1.099, 2)
+
+    def test_surf2vol(self):
+        vol = surf2vol(
+            self.no,
+            self.fc,
+            np.arange(19, 42, 1),
+            np.arange(19, 42, 1),
+            np.arange(19, 42, 1),
+        )
+        self.assertAlmostEqual(np.sum(vol.astype(np.float32)) * 0.001, 1.704, 2)
+
+    def test_surf2vol_fill(self):
+        vol = surf2vol(
+            self.no,
+            self.fc,
+            np.arange(19, 42, 1),
+            np.arange(19, 42, 1),
+            np.arange(19, 42, 1),
+            fill=1,
+        )
+        self.assertAlmostEqual(np.sum(vol.astype(np.float32)) * 0.001, 4.903, 2)
+
+    def test_s2v(self):
+        vol = s2v(self.no, self.fc, fill=1)
+        self.assertAlmostEqual(np.sum(vol.astype(np.float32)) * 0.0001, 7.8651, 2)
 
 
 @unittest.skipIf(

Original file line number	Diff line number	Diff line change
`@@ -157,7 +157,7 @@`
`157`	`157`	`regpt2surf,`
`158`	`158`	`)`
`159`	`159`
`160`		`-__version__ = "0.3.7"`
	`160`	`+__version__ = "0.3.8"`
`161`	`161`	`__all__ = [`
`162`	`162`	`"advancefront",`
`163`	`163`	`"barycentricgrid",`