[ci] test v2m_cgalmesh, v2m_simplify and v2s in labeled volumn

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: 0.2.3
+* Version: 0.2.4
 * URL: [https://pypi.org/project/iso2mesh/](https://pypi.org/project/iso2mesh/)
 * Github: [https://github.com/NeuroJSON/pyiso2mesh](https://github.com/NeuroJSON/pyiso2mesh)
 
@@ -85,7 +85,7 @@ the built-in unit-test script inside the downloaded git repository by using this
 inside the `pyiso2mesh` root folder
 
 ```
-python -m unittest test.run_test
+python3 -m unittest test.run_test
 ```
 
 

iso2mesh/__init__.py

@@ -137,7 +137,7 @@
     barycentricgrid,
 )
 
-__version__ = "0.2.3"
+__version__ = "0.2.4"
 __all__ = [
     "advancefront",
     "barycentricgrid",

iso2mesh/core.py

@@ -33,10 +33,17 @@
 import re
 import platform
 import subprocess
-from iso2mesh.trait import surfinterior, surfseeds, surfedge, elemvolume, meshreorient
+from iso2mesh.trait import (
+    surfinterior,
+    surfseeds,
+    surfedge,
+    elemvolume,
+    meshreorient,
+    finddisconnsurf,
+)
 from iso2mesh.utils import *
 from iso2mesh.io import saveoff, readoff, saveinr, readtetgen, savesurfpoly, readmedit
-from iso2mesh.modify import meshcheckrepair, sortmesh
+from iso2mesh.modify import meshcheckrepair, sortmesh, meshresample, removeisolatedsurf
 
 ##====================================================================================
 ## implementations
@@ -732,7 +739,7 @@ def binsurface(img, nface=3):
         )
 
     # Compress the node indices
-    maxid = elem.max() + 1
+    maxid = np.max(elem) + 1
     nodemap = np.zeros(maxid, dtype=int)
     nodemap[elem.ravel(order="F")] = 1
     id = np.where(nodemap)[0]

iso2mesh/io.py

@@ -77,7 +77,7 @@ def saveinr(vol, fname):
 
     # Write the header and the volume data to the file
     fid.write(header.encode("ascii"))
-    fid.write(vol.astype(dtype).tobytes())
+    fid.write(np.transpose(vol, [2, 1, 0]).astype(dtype).tobytes())
 
     # Close the file
     fid.close()

iso2mesh/modify.py

@@ -40,7 +40,7 @@
 import subprocess
 from iso2mesh.utils import *
 from iso2mesh.io import saveoff, readoff
-from iso2mesh.trait import meshconn, mesheuler
+from iso2mesh.trait import meshconn, mesheuler, finddisconnsurf
 
 ##====================================================================================
 ## implementations
@@ -549,17 +549,17 @@ def removeisolatedsurf(v, f, maxdiameter):
     """
     fc = finddisconnsurf(f)
     for i in range(len(fc)):
-        xdia = v[fc[i], 0]
+        xdia = v[fc[i] - 1, 0]
         if np.max(xdia) - np.min(xdia) <= maxdiameter:
             fc[i] = []
             continue
 
-        ydia = v[fc[i], 1]
+        ydia = v[fc[i] - 1, 1]
         if np.max(ydia) - np.min(ydia) <= maxdiameter:
             fc[i] = []
             continue
 
-        zdia = v[fc[i], 2]
+        zdia = v[fc[i] - 1, 2]
         if np.max(zdia) - np.min(zdia) <= maxdiameter:
             fc[i] = []
             continue

setup.py

@@ -6,7 +6,7 @@
 setup(
     name="iso2mesh",
     packages=["iso2mesh"],
-    version="0.2.3",
+    version="0.2.4",
     license='GPLv3+',
     description="Image-based 3D Surface and Volumetric Mesh Generator",
     long_description=readme,

test/run_test.py

@@ -933,6 +933,14 @@ def __init__(self, *args, **kwargs):
         self.im = np.zeros((3, 3, 3))
         self.im[1, 1, 1:3] = 1
 
+        xi, yi, zi = np.meshgrid(
+            np.arange(0, 61), np.arange(0, 58), np.arange(0, 55), indexing="ij"
+        )
+        dist = (xi - 30) ** 2 + (yi - 30) ** 2 + (zi - 30) ** 2
+        self.mask = dist < 400
+        self.mask = self.mask.astype(float)
+        self.mask[25:35, 25:35, :] = 2
+
     def test_binsurface(self):
         no, fc = binsurface(self.im)
         expected_fc = [
@@ -1005,6 +1013,32 @@ def test_cgalv2m(self):
         self.assertEqual(removedupelem(fc[:, :3]).shape[0], 0)
         self.assertAlmostEqual(sum(elemvolume(no[:, :3], el[:, :4])), 0.7455, 3)
 
+    def test_v2s_label(self):
+        no, fc, _, _ = v2s(self.mask, 0.04, 1)
+        self.assertAlmostEqual(
+            sum(elemvolume(no[:, :3], fc[:, :3])) * 0.001, 6.356848339883229, 3
+        )
+
+    def test_v2m_cgalmesh(self):
+        no, el, _ = v2m(
+            self.mask.astype(np.uint8),
+            [],
+            {"radbound": 1, "distbound": 0.5},
+            5,
+            "cgalmesh",
+        )
+        self.assertAlmostEqual(
+            sum(elemvolume(no[:, :3], el[:, :4])) * 0.0001, 3.4780013268627226, 2
+        )
+
+    def test_v2m_simplify(self):
+        no, el, _ = v2m(
+            self.mask.astype(np.uint8), 1.5, {"keepratio": 0.5}, 10, "simplify"
+        )
+        self.assertAlmostEqual(
+            sum(elemvolume(no[:, :3], el[:, :4])), 5456.390624999979, 0
+        )
+
 
 if __name__ == "__main__":
     unittest.main()