feat: expose min error (#40)

* fix: max simplification error int -> float

* feat: expose min_error to Python

* test: check that setting min_error to 0 gives closer to reduction factor

* fix: use C++ default value

* feat: add id to zmesh.Mesh

ChangeLog

@@ -1,9 +1,13 @@
 CHANGES
 =======
 
+* fix: max simplification error int -> float
+* feat: support more types of obj files
+
 1.7.1
 -----
 
+* fix: some setup issues for py312
 * build: update cibuildwheel
 * fix: re-simplification works
 * fix(simplify): double multiplication by resolution

automated_test.py

@@ -274,3 +274,26 @@ def test_simplified_meshes_remain_the_same(connectomics_labels, order):
     assert np.all(np.isclose(np.sort(old_mesh.vertices[old_mesh.faces], axis=0), np.sort(new_mesh.vertices[new_mesh.faces], axis=0)))
     print(lbl, "ok")
 
+
+@pytest.mark.parametrize("reduction_factor", [2,5,10])
+def test_min_error_skip(reduction_factor):
+  for order in ['C','F']:
+    labels = np.zeros((11, 17, 19), dtype=np.uint8, order=order)
+    labels[1:-1, 1:-1, 1:-1] = 1
+
+    mesher = zmesh.Mesher((4, 4, 40))
+    mesher.mesh(labels)
+
+    original_mesh = mesher.get_mesh(1, normals=False)
+    mesh = mesher.simplify(
+        original_mesh, 
+        reduction_factor=reduction_factor, 
+        max_error=40, 
+        min_error=0,
+        compute_normals=True
+    )
+    factor = len(original_mesh.faces) / len(mesh.faces)
+    assert abs(factor - reduction_factor) < 1
+
+
+

cMesher.hpp

@@ -53,7 +53,8 @@ class CMesher {
     LabelType segid, 
     bool generate_normals,
     int simplification_factor,
-    int max_simplification_error,
+    float max_simplification_error,
+    float min_simplification_error,
     bool transpose = true
   ) {
 
@@ -71,6 +72,7 @@ class CMesher {
       generate_normals,
       simplification_factor,
       max_simplification_error,
+      min_simplification_error,
       transpose
     );
   }
@@ -79,7 +81,8 @@ class CMesher {
       const std::vector< zi::vl::vec< PositionType, 3> >& triangles,
       bool generate_normals,
       int simplification_factor,
-      int max_simplification_error,
+      float max_simplification_error,
+      float min_simplification_error,
 
       // This is to support the old broken version
       // w/ backwards compatibility
@@ -111,7 +114,8 @@ class CMesher {
       // This is the most cpu intensive line
       simplifier_.optimize(
           simplifier_.face_count() / simplification_factor,
-          max_simplification_error
+          max_simplification_error,
+          min_simplification_error
       );
     }
 
@@ -178,7 +182,8 @@ class CMesher {
     const size_t Nv,
     bool generate_normals,
     int simplification_factor,
-    int max_simplification_error
+    float max_simplification_error,
+    float min_simplification_error
   ) {
 
     std::vector< zi::vl::vec< PositionType, 3> > triangles;
@@ -199,6 +204,7 @@ class CMesher {
       generate_normals, 
       simplification_factor, 
       max_simplification_error,
+      min_simplification_error,
       false
     );
   }

templates/mesherclass.j2

@@ -18,8 +18,8 @@ cdef class Mesher{{ position_type }}{{ '%02d' % label_type }}:
   def ids(self):
     return self.ptr.ids()
 
-  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, transpose=True):
-    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, transpose)
+  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, min_simplification_error=(25 * sys.float_info.epsilon), transpose=True):
+    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, min_simplification_error, transpose)
 
   def clear(self):
     self.ptr.clear()

zi_lib/zi/mesh/quadratic_simplifier.hpp

@@ -460,8 +460,11 @@ class simplifier : non_copyable
 
     std::size_t
     optimize(std::size_t target_faces, Float max_error,
-             Float min_error = std::numeric_limits<Float>::epsilon() * 25)
+             Float min_error = -1.0)
     {
+        if (min_error < 0) {
+            min_error = std::numeric_limits<Float>::epsilon() * 25;
+        }
 
         // double no_faces = static_cast< double >( mesh_.face_count() );
 

zmesh/_zmesh.pyx

@@ -8,6 +8,7 @@ from libcpp cimport bool
 
 import operator
 from functools import reduce
+import sys
 
 cimport numpy as cnp
 import numpy as np
@@ -33,7 +34,8 @@ cdef extern from "cMesher.hpp":
       L segid, 
       bool normals,
       int simplification_factor, 
-      int max_simplification_error, 
+      float max_simplification_error, 
+      float min_simplification_error,
       bool transpose
     )
     # NOTE: need to define triangle_t
@@ -42,7 +44,8 @@ cdef extern from "cMesher.hpp":
       size_t Nv, 
       bool normals, 
       int simplification_factor, 
-      int max_simplification_error
+      float max_simplification_error,
+      float min_simplification_error,
     )
     bool erase(L segid)
     void clear()
@@ -180,7 +183,9 @@ class Mesher:
       transpose=False
     )
 
-    return self._normalize_simplified_mesh(mesh, voxel_centered, physical=True)
+    mesh = self._normalize_simplified_mesh(mesh, voxel_centered, physical=True)
+    mesh.id = int(label)
+    return mesh
 
   def _normalize_simplified_mesh(self, mesh, voxel_centered, physical):
     points = np.array(mesh['points'], dtype=np.float32)
@@ -209,16 +214,21 @@ class Mesher:
     """
     return self.simplify(mesh, reduction_factor=0, max_error=0, compute_normals=True)
 
+  # adding this causes a cython compilation error as of 3.0.10
+  # @cython.binding(True)
   def simplify(
-    self, mesh, int reduction_factor=0, 
-    int max_error=40, compute_normals=False,
-    voxel_centered=False
+    self, mesh, 
+    int reduction_factor = 0, 
+    float max_error = 40, 
+    compute_normals = False,
+    voxel_centered = False, 
+    float min_error = -1,
   ):
     """
     Mesh simplify(
       mesh, reduction_factor=0, 
       max_error=40, compute_normals=False, 
-      voxel_centered=False
+      voxel_centered=False, min_error = -1
     )
 
     Given a mesh object (either zmesh.Mesh or another object that has
@@ -234,6 +244,13 @@ class Mesher:
         stop short of this target.
       max_error: The maximum allowed displacement of a vertex in physical
         distance.
+      min_error: Continue simplifying until this error target is met OR secondarily 
+        the target number of triangles is met. Set this to 0 to force the 
+        reduction_factor to take precedence. -1 indicates that the c++ default
+        value should be used.
+
+        The c++ default value is std::numeric_limits<Float>::epsilon() * 25
+
       compute_normals: whether or not to also compute the vertex normals
       voxel_centered: By default, the meshes produced will be centered at 
         0,0,0. If enabled, the meshes will be centered in the voxel at 
@@ -278,7 +295,8 @@ class Mesher:
 
     cdef MeshObject result = mesher.simplify_points(
       <uint64_t*>&packed_triangles[0,0], Nv, 
-      <bool>compute_normals, reduction_factor, max_error
+      <bool>compute_normals, reduction_factor, 
+      max_error, min_error
     )
     del mesher
 
@@ -357,8 +375,8 @@ cdef class Mesher3208:
   def ids(self):
     return self.ptr.ids()
 
-  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, transpose=True):
-    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, transpose)
+  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, min_simplification_error=(25 * sys.float_info.epsilon), transpose=True):
+    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, min_simplification_error, transpose)
 
   def clear(self):
     self.ptr.clear()
@@ -386,8 +404,8 @@ cdef class Mesher3216:
   def ids(self):
     return self.ptr.ids()
 
-  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, transpose=True):
-    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, transpose)
+  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, min_simplification_error=(25 * sys.float_info.epsilon), transpose=True):
+    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, min_simplification_error, transpose)
 
   def clear(self):
     self.ptr.clear()
@@ -415,8 +433,8 @@ cdef class Mesher3232:
   def ids(self):
     return self.ptr.ids()
 
-  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, transpose=True):
-    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, transpose)
+  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, min_simplification_error=(25 * sys.float_info.epsilon), transpose=True):
+    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, min_simplification_error, transpose)
 
   def clear(self):
     self.ptr.clear()
@@ -444,8 +462,8 @@ cdef class Mesher3264:
   def ids(self):
     return self.ptr.ids()
 
-  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, transpose=True):
-    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, transpose)
+  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, min_simplification_error=(25 * sys.float_info.epsilon), transpose=True):
+    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, min_simplification_error, transpose)
 
   def clear(self):
     self.ptr.clear()
@@ -473,8 +491,8 @@ cdef class Mesher6408:
   def ids(self):
     return self.ptr.ids()
 
-  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, transpose=True):
-    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, transpose)
+  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, min_simplification_error=(25 * sys.float_info.epsilon), transpose=True):
+    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, min_simplification_error, transpose)
 
   def clear(self):
     self.ptr.clear()
@@ -502,8 +520,8 @@ cdef class Mesher6416:
   def ids(self):
     return self.ptr.ids()
 
-  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, transpose=True):
-    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, transpose)
+  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, min_simplification_error=(25 * sys.float_info.epsilon), transpose=True):
+    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, min_simplification_error, transpose)
 
   def clear(self):
     self.ptr.clear()
@@ -531,8 +549,8 @@ cdef class Mesher6432:
   def ids(self):
     return self.ptr.ids()
 
-  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, transpose=True):
-    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, transpose)
+  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, min_simplification_error=(25 * sys.float_info.epsilon), transpose=True):
+    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, min_simplification_error, transpose)
 
   def clear(self):
     self.ptr.clear()
@@ -560,8 +578,8 @@ cdef class Mesher6464:
   def ids(self):
     return self.ptr.ids()
 
-  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, transpose=True):
-    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, transpose)
+  def get_mesh(self, mesh_id, normals=False, simplification_factor=0, max_simplification_error=40, min_simplification_error=(25 * sys.float_info.epsilon), transpose=True):
+    return self.ptr.get_mesh(mesh_id, normals, simplification_factor, max_simplification_error, min_simplification_error, transpose)
 
   def clear(self):
     self.ptr.clear()

zmesh/mesh.py

@@ -13,10 +13,11 @@ class Mesh:
     ndarray[float32, ndim=2] self.normals:  [ [nx,ny,nz], ... ]
 
   """
-  def __init__(self, vertices, faces, normals):
+  def __init__(self, vertices, faces, normals, id=None):
     self.vertices = vertices
     self.faces = faces
     self.normals = normals
+    self.id = id
 
   def __len__(self):
     return self.vertices.shape[0]