Add remove small parts filter

README.md

@@ -67,6 +67,7 @@ After all the image processing is finished, the volume is converted to a VTK ima
 Then the following VTK pipeline is executed:
 * [Extract a surface mesh](https://vtk.org/doc/nightly/html/classvtkContourFilter.html) from the VTK image
 * Apply the [clean mesh filter](https://vtk.org/doc/nightly/html/classvtkCleanPolyData.html)
+* [Remove small parts](https://vtk.org/doc/nightly/html/classvtkPolyDataConnectivityFilter.html) which connect to little other parts
 * Apply the [smooth mesh filter](https://vtk.org/doc/nightly/html/classvtkSmoothPolyDataFilter.html)
 * Apply the [reduce mesh filter](https://vtk.org/doc/nightly/html/classvtkQuadricDecimation.html)
 * [Write out an STL file](https://vtk.org/doc/nightly/html/classvtkSTLWriter.html)

dicom2stl.py

@@ -326,16 +326,25 @@ def elapsedTime(start_time):
 mesh = vtkutils.extractSurface(vtkimg, isovalue)
 vtkimg = None
 gc.collect()
+
 if args.debug:
     print("Cleaning mesh")
 mesh2 = vtkutils.cleanMesh(mesh, connectivityFilter)
 mesh = None
 gc.collect()
+
 if args.debug:
-    print("Smoothing mesh", args.smooth, "iterations")
-mesh3 = vtkutils.smoothMesh(mesh2, args.smooth)
+    print(f"Cleaning small parts ratio{args.small}")
+mesh_cleaned_parts =  vtkutils.removeSmallObjects(mesh2, args.small)
 mesh2 = None
 gc.collect()
+
+if args.debug:
+    print("Smoothing mesh", args.smooth, "iterations")
+mesh3 = vtkutils.smoothMesh(mesh_cleaned_parts, args.smooth)
+mesh_cleaned_parts = None
+gc.collect()
+
 if args.debug:
     print("Simplifying mesh")
 mesh4 = vtkutils.reduceMesh(mesh3, args.reduce)

parseargs.py

@@ -105,6 +105,10 @@ def parseargs():
                             type=float, default=.9,
                             help='Mesh reduction factor (default=.9)')
 
+    mesh_group.add_argument('--clean-small', '-x', action='store', dest='small',
+                            type=float, default=.05,
+                            help='Clean small parts factor (default=.05)')
+
     # Filtering options
     filter_group = parser.add_argument_group('Filtering options')
     filter_group.add_argument('--enable', action='append', dest='filters',

utils/vtkutils.py

@@ -186,6 +186,54 @@ def reduceMesh(mymesh, reductionFactor):
         traceback.print_exception(
             exc_type, exc_value, exc_traceback, limit=2, file=sys.stdout)
     return None
+
+
+# from https://github.com/AOT-AG/DicomToMesh/blob/master/lib/src/meshRoutines.cpp#L109
+# MIT License
+def removeSmallObjects(mesh, ratio):
+    """
+    Remove small parts which are not of interest
+    @param ratio A floating-point value between 0.0 and 1.0, the higher the stronger effect
+    """
+
+    # do nothing if ratio is 0
+    if ratio == 0:
+        return mesh
+
+    try:
+        t = time.perf_counter()
+        conn_filter = vtk.vtkPolyDataConnectivityFilter()
+        conn_filter.SetInputData(mesh)
+        conn_filter.SetExtractionModeToAllRegions()
+        conn_filter.Update()
+
+        # remove objects consisting of less than ratio vertexes of the biggest object
+        region_sizes = conn_filter.GetRegionSizes()
+
+        # find object with most vertices
+        max_size = 0
+        for i in range(conn_filter.GetNumberOfExtractedRegions()):
+            if region_sizes.GetValue(i) > max_size:
+                max_size = region_sizes.GetValue(i)
+
+        # append regions of sizes over the threshold
+        conn_filter.SetExtractionModeToSpecifiedRegions()
+        for i in range(conn_filter.GetNumberOfExtractedRegions()):
+            if region_sizes.GetValue(i) > max_size * ratio:
+                conn_filter.AddSpecifiedRegion(i)
+
+        conn_filter.Update()
+        processed_mesh = conn_filter.GetOutput()
+        print("Small parts cleaned")
+        print("    ", processed_mesh.GetNumberOfPolys(), "polygons")
+        elapsedTime(t)
+        return processed_mesh
+
+    except BaseException:
+        print("Remove small objects failed")
+        exc_type, exc_value, exc_traceback = sys.exc_info()
+        traceback.print_exception(
+            exc_type, exc_value, exc_traceback, limit=2, file=sys.stdout)
 
 
 #