test: add get to some tests

seung-lab · william-silversmith · Jun 23, 2023 · Jun 20, 2023 · Jun 20, 2023 · Jun 21, 2023
commit 8535be1a3434592e52b6e1cf0d6252fca512c6d0
diff --git a/README.md b/README.md
@@ -15,16 +15,19 @@ mesher.mesh(labels, close=False)
 meshes = []
 for obj_id in mesher.ids():
   meshes.append(
-    mesher.get_mesh(
+    mesher.get(
       obj_id, 
       normals=False, # whether to calculate normals or not
 
       # tries to reduce triangles by this factor
       # 0 disables simplification
-      simplification_factor=100, 
+      reduction_factor=100, 
 
       # Max tolerable error in physical distance
-      max_simplification_error=8,
+      # note: if max_error is not set, the max error
+      # will be set equivalent to one voxel along the 
+      # smallest dimension.
+      max_error=8,
       # whether meshes should be centered in the voxel
       # on (0,0,0) [False] or (0.5,0.5,0.5) [True]
       voxel_centered=False, 
@@ -39,7 +42,7 @@ mesh = mesher.simplify(
   mesh, 
   # same as simplification_factor in get_mesh
   reduction_factor=100, 
-  # same as max_simplification_error in get_mesh
+  # same as max_error in get
   max_error=40, 
   compute_normals=False, # whether to also compute face normals
 ) # apply simplifier to a pre-existing mesh
@@ -65,6 +68,8 @@ with open('10001001:0', 'wb') as f:
   f.write(mesh.to_precomputed())
 ```
 
+Note: As of the latest version, `mesher.get_mesh` has been deprecated in favor of `mesher.get` which fixes a long standing bug where you needed to transpose your data in order to get a mesh in the correct orientation.
+
 ## Installation 
 
 If binaries are not available for your system, ensure you have a C++ compiler installed.

diff --git a/automated_test.py b/automated_test.py
@@ -20,7 +20,7 @@ def fanc_label():
 @pytest.mark.parametrize("dtype", DTYPE)
 @pytest.mark.parametrize("close", [ False, True ])
 @pytest.mark.parametrize("order", [ 'C', 'F' ])
-def test_executes(dtype, close, order):
+def test_executes_legacy(dtype, close, order):
   labels = np.zeros( (11,17,19), dtype=dtype, order=order)
   labels[1:-1, 1:-1, 1:-1] = 1
 
@@ -37,6 +37,27 @@ def test_executes(dtype, close, order):
   assert len(mesh.faces) > 0
   assert len(mesh.normals) > 0
 
+
+@pytest.mark.parametrize("dtype", DTYPE)
+@pytest.mark.parametrize("close", [ False, True ])
+@pytest.mark.parametrize("order", [ 'C', 'F' ])
+def test_executes(dtype, close, order):
+  labels = np.zeros( (11,17,19), dtype=dtype, order=order)
+  labels[1:-1, 1:-1, 1:-1] = 1
+
+  mesher = zmesh.Mesher( (4,4,40) )
+  mesher.mesh(labels, close=close)
+
+  mesh = mesher.get(1, normals=False)
+  assert len(mesh.vertices) > 0
+  assert len(mesh.faces) > 0
+  assert mesh.normals is None
+
+  mesh = mesher.get(1, normals=True)
+  assert len(mesh.vertices) > 0
+  assert len(mesh.faces) > 0
+  assert len(mesh.normals) > 0
+
 @pytest.mark.parametrize("dtype", DTYPE)
 @pytest.mark.parametrize("order", [ 'C', 'F' ])
 def test_simplify(dtype, order):
@@ -83,7 +104,7 @@ def test_simplify(dtype, order):
     pass
 
 @pytest.mark.parametrize("dtype", DTYPE)
-def test_precomputed(dtype):
+def test_precomputed_legacy(dtype):
   labels = np.zeros( (11,17,19), dtype=dtype)
   labels[1:-1, 1:-1, 1:-1] = 1
 
@@ -101,13 +122,32 @@ def test_precomputed(dtype):
   reconstituted = zmesh.Mesh.from_precomputed(precomputed_mesh)
   assert reconstituted != mesh # Precomputed doesn't preserve normals
 
+@pytest.mark.parametrize("dtype", DTYPE)
+def test_precomputed(dtype):
+  labels = np.zeros( (11,17,19), dtype=dtype)
+  labels[1:-1, 1:-1, 1:-1] = 1
+
+  mesher = zmesh.Mesher( (4,4,40) )
+  mesher.mesh(labels)
+  mesh = mesher.get(1, normals=False)
+
+  precomputed_mesh = mesh.to_precomputed()
+  reconstituted = zmesh.Mesh.from_precomputed(precomputed_mesh)
+  assert reconstituted == mesh
+
+  mesh = mesher.get(1, normals=True)
+
+  precomputed_mesh = mesh.to_precomputed()
+  reconstituted = zmesh.Mesh.from_precomputed(precomputed_mesh)
+  assert reconstituted != mesh # Precomputed doesn't preserve normals
+
 def test_obj_import():
   labels = np.zeros( (11,17,19), dtype=np.uint32)
   labels[1:-1, 1:-1, 1:-1] = 1
 
   mesher = zmesh.Mesher( (4,4,40) )
   mesher.mesh(labels)
-  mesh = mesher.get_mesh(1, normals=False)
+  mesh = mesher.get(1, normals=False)
 
   obj_str = mesh.to_obj()
   mesh2 = zmesh.Mesh.from_obj(obj_str)
@@ -120,14 +160,14 @@ def test_ply_import():
 
   mesher = zmesh.Mesher( (4,4,40) )
   mesher.mesh(labels)
-  mesh = mesher.get_mesh(1, normals=False)
+  mesh = mesher.get(1, normals=False)
 
   plydata = mesh.to_ply()
   mesh2 = zmesh.Mesh.from_ply(plydata)
 
   assert mesh == mesh2
 
-def test_C_F_meshes_same(connectomics_labels):
+def test_C_F_meshes_same_legacy(connectomics_labels):
   connectomics_labels = connectomics_labels[102:,31:,17:]
 
   fdata = np.asfortranarray(connectomics_labels)
@@ -166,8 +206,8 @@ def test_fanc_bug(fanc_label, transpose):
   assert c_mesher.ids() == f_mesher.ids()
 
   for label in c_mesher.ids():
-    c_mesh = c_mesher.get_mesh(label, normals=False, simplification_factor=0)
-    f_mesh = f_mesher.get_mesh(label, normals=False, simplification_factor=0)
+    c_mesh = c_mesher.get(label, normals=False, reduction_factor=0)
+    f_mesh = f_mesher.get(label, normals=False, reduction_factor=0)
     assert np.isclose(c_mesh.vertices.mean(), f_mesh.vertices.mean())
 
 @pytest.mark.parametrize("order", [ 'C', 'F' ])