add mesh.non_manifold_faces()

docs/changes.md

@@ -11,14 +11,14 @@
 - add `utils.is_ragged()` to check if an array is homogeneuos (not ragged)
 - fix `shapes.Lines()` class 
 - add `shapes.ThickTube()` as per #800
-- add `settings.backend_autoclose` (default is True) to automatically close `Plotter` after show 
-in jupyter notebooks, #802
+- add `settings.backend_autoclose` (default is True) to automatically close `Plotter` after show() in jupyter notebooks, #802
 - fix k3d backend - remove pinning to 2.7.4 #808
 - in `Text2D` and `Text3D` shortcut to symbols are now formatted as `:gamma` and no more as `\gamma`
 - fix `mesh.stretch()` thanks to @mikaeltulldahl in #807
 - fixes to `cmap()`
 - added `mesh.is_manifold()` method #813
 - added `utils.open3d2vedo()` and `utils.vedo2open3d` converters as per #663
+- added `mesh.non_manifold_faces()` to detect and (try to) remove non-manifold faces of a triangular mesh #813 #663 and https://github.com/SlicerIGT/SlicerBoneReconstructionPlanner/issues/35
 
 
 -------------------------

vedo/mesh.py

@@ -13,8 +13,7 @@
 from vedo.colors import color_map
 from vedo.colors import get_color
 from vedo.pointcloud import Points
-from vedo.utils import buildPolyData
-from vedo.utils import is_sequence, mag, mag2
+from vedo.utils import buildPolyData, is_sequence, mag, mag2
 from vedo.utils import numpy2vtk, vtk2numpy
 
 __docformat__ = "google"
@@ -743,6 +742,66 @@ def is_manifold(self):
         ne = fe.GetOutput().GetNumberOfCells()
         return not bool(ne)
 
+    def non_manifold_faces(self, remove_all=False, remove_boundary=False, collapse_edges=False):
+        """
+        Detect and (try to) remove non-manifold faces of a triangular mesh.
+
+        Leaving all to `False` will add a new cell array with name "NonManifoldCell".
+        Note that "faces" and "cells" are synomyms.
+        """
+        if int(remove_all)+int(remove_boundary)+int(collapse_edges) > 1:
+            raise ValueError("Select only one option")
+        # mark original point and cell ids
+        self.add_ids()
+        nme = self.boundaries(
+            boundary_edges=False,
+            non_manifold_edges=True,
+        )
+        nme_pids = nme.pointdata["PointID"]
+
+        bnd_cids = []
+        if remove_boundary:
+            # find cells sitting on boundaries
+            bnd_cids = self.boundaries(return_cell_ids=True)
+
+        all_nf = []
+        toremove = []
+        faces = self.faces()
+        points = self.points()
+        new_points = np.array(points)
+        for e in vedo.utils.progressbar(nme.lines(), delay=5, title="parsing faces"):
+            ie0, ie1 = e
+            ip0, ip1 = nme_pids[ie0], nme_pids[ie1]
+            for i, f in enumerate(faces):
+                if ip0 in f and ip1 in f:
+                    all_nf.append(i)
+                    if remove_all:
+                        toremove.append(i)
+                    elif remove_boundary:
+                        if i in bnd_cids:
+                            toremove.append(i)
+                    elif collapse_edges:
+                        pass
+                        m = (points[ip0] + points[ip1])/2
+                        new_points[ip0] = m
+                        new_points[ip1] = m
+
+        # print("NF points", nme_pids)
+        # print("NF cells ", nfcells)
+        # print("NF toremove ", toremove)
+
+        if collapse_edges:
+            self.points(new_points)
+            self.clean()
+        elif toremove:
+            self.delete_cells(toremove)
+        else:
+            mark = np.zeros(self.ncells, dtype=np.uint8)
+            mark[all_nf] = 1
+            self.celldata["NonManifoldCell"] = mark
+
+        return self
+
     def shrink(self, fraction=0.85):
         """Shrink the triangle polydata in the representation of the input mesh.
 

vedo/utils.py

@@ -80,6 +80,7 @@ def __init__(
         italic=False,
         title="",
         eta=True,
+        delay=0,
         width=25,
         char="\U00002501",
         char_back="\U00002500",
@@ -120,23 +121,28 @@ def __init__(
         self.percent = 0.0
         self.percent_int = 0
         self.eta = eta
+        self.delay = delay
         self.clock0 = time.time()
         self._remt = 1e10
         self._update(0)
+
         self._counts = 0
         self._oldbar = ""
         self._lentxt = 0
         self._range = np.arange(start, stop, step)
         self._len = len(self._range)
 
-    def print(self, txt="", counts=None, c=None):
+    def print(self, txt="", c=None):
         """Print the progress bar and optional message."""
         if not c:
             c = self.color
-        if counts:
-            self._update(counts)
-        else:
-            self._update(self._counts + self.step)
+
+        self._update(self._counts + self.step)
+
+        if self.delay:
+            if time.time() - self.clock0 < self.delay:
+                return
+
         if self.pbar != self._oldbar:
             self._oldbar = self.pbar
             eraser = [" "] * self._lentxt + ["\b"] * self._lentxt
@@ -223,6 +229,7 @@ def progressbar(
         title="",
         eta=True,
         width=25,
+        delay=0,
     ):
     """
     Function to print a progress bar with optional text message.
@@ -248,7 +255,7 @@ def progressbar(
     pb = ProgressBar(
         0, total, 
         c=c, bold=bold, italic=italic, 
-        title=title, eta=eta, width=width,
+        title=title, eta=eta, delay=delay, width=width,
     )
     for item in iterable:
         pb.print()

vedo/version.py

@@ -1 +1 @@
-_version = '2023.4.3.dev15'
+_version = '2023.4.3.dev16'