Updated mesh tests.

tests/test_gifti.py

@@ -28,7 +28,7 @@ def test_GiftiMesh_create():
     minbounds = np.array([ 59.50759888,  88.43039703,  72.10890198])
     maxbounds = np.array([ 77.72619629, 128.40600586,  94.82050323])
 
-    minb, maxb = surf.getBounds()
+    minb, maxb = surf.bounds
 
     assert surf.name                  == 'example'
     assert surf.dataSource            == testfile
@@ -47,9 +47,9 @@ def test_GiftiMesh_create_loadAll():
 
     with tempdir() as td:
 
-        vertSets = [op.join(td, 'prefix.1.surf.gii'),
-                    op.join(td, 'prefix.2.surf.gii'),
-                    op.join(td, 'prefix.3.surf.gii')]
+        vertSets = [op.join(td, 'prefix.L.1.surf.gii'),
+                    op.join(td, 'prefix.L.2.surf.gii'),
+                    op.join(td, 'prefix.L.3.surf.gii')]
 
         for vs in vertSets:
             shutil.copy(testfile, vs)
@@ -83,6 +83,27 @@ def test_loadGiftiMesh():
             gifti.loadGiftiSurface(bf)
 
 
+def test_loadVertices():
+
+    testdir  = op.join(op.dirname(__file__), 'testdata')
+    testfile = op.join(testdir, 'example.surf.gii')
+
+    with tempdir():
+
+        mesh = gifti.GiftiMesh(testfile)
+
+        shutil.copy(testfile, 'example2.surf.gii')
+
+
+        verts  = mesh.vertices
+        verts2 = verts * 2
+
+        np.savetxt('verts.txt', verts2)
+
+        assert np.all(np.isclose(mesh.loadVertices('example2.surf.gii'), verts))
+        assert np.all(np.isclose(mesh.loadVertices('verts.txt')        , verts2))
+
+
 def test_GiftiMesh_loadVertexData():
 
     testdir   = op.join(op.dirname(__file__), 'testdata')
@@ -100,7 +121,7 @@ def test_GiftiMesh_loadVertexData():
     assert surf.loadVertexData(txtfile).shape == (642, 1)
 
     # add from memory
-    surf.addVertexData('inmemdata', memdata)
+    assert np.all(np.isclose(surf.addVertexData('inmemdata', memdata), memdata.reshape(-1, 1)))
 
     # check cached
     assert surf.getVertexData(shapefile)  .shape == (642, 1)
@@ -197,12 +218,10 @@ def test_relatedFiles():
             with open(op.join(td, l), 'wt') as f:
                 f.write(l)
 
-        with pytest.raises(Exception):
-            gifti.relatedFiles('nonexistent')
-
         badname = op.join(op.join(td, 'badly-formed-filename'))
 
-        assert len(gifti.relatedFiles(badname)) == 0
+        assert len(gifti.relatedFiles(badname))       == 0
+        assert len(gifti.relatedFiles('nonexistent')) == 0
 
         lsurfaces = [op.join(td, f) for f in lsurfaces]
         rsurfaces = [op.join(td, f) for f in rsurfaces]

tests/test_mesh.py

@@ -68,8 +68,11 @@ def test_mesh_create():
 
     mesh = fslmesh.Mesh(tris, vertices=verts)
 
+    print(str(mesh))
+
     assert mesh.name       == 'mesh'
     assert mesh.dataSource is None
+    assert mesh.nvertices  == 8
     assert np.all(np.isclose(mesh.vertices, verts))
     assert np.all(np.isclose(mesh.indices,  tris))
 
@@ -92,13 +95,13 @@ def test_mesh_addVertices():
     assert mesh.vertexSets() == ['default']
     assert np.all(np.isclose(mesh.vertices, verts))
 
-    mesh.addVertices(verts2, 'twotimes')
+    assert np.all(np.isclose(mesh.addVertices(verts2, 'twotimes'), verts2))
 
     assert mesh.selectedVertices() == 'twotimes'
     assert mesh.vertexSets() == ['default', 'twotimes']
     assert np.all(np.isclose(mesh.vertices, verts2))
 
-    mesh.addVertices(verts3, 'threetimes', select=False)
+    assert np.all(np.isclose(mesh.addVertices(verts3, 'threetimes', select=False), verts3))
 
     assert mesh.selectedVertices() == 'twotimes'
     assert mesh.vertexSets() == ['default', 'twotimes', 'threetimes']
@@ -109,6 +112,32 @@ def test_mesh_addVertices():
     assert mesh.selectedVertices() == 'threetimes'
     assert np.all(np.isclose(mesh.vertices, verts3))
 
+    with pytest.raises(ValueError):
+        mesh.addVertices(verts[:-1, :], 'badverts')
+
+
+def test_loadVertices():
+
+    tris  = np.array(CUBE_TRIANGLES_CCW)
+    verts = np.array(CUBE_VERTICES)
+
+    mesh = fslmesh.Mesh(tris, vertices=verts)
+
+    with tempdir():
+
+        verts2 = verts * 2
+
+        np.savetxt('verts2.txt', verts2)
+
+        assert np.all(np.isclose(mesh.loadVertices('verts2.txt'), verts2))
+
+        assert mesh.selectedVertices() == op.abspath('verts2.txt')
+
+        np.savetxt('badverts.txt', verts2[:-1, :])
+
+        with pytest.raises(ValueError):
+            mesh.loadVertices('badverts.txt')
+
 
 def test_mesh_addVertexData():
 
@@ -122,9 +151,14 @@ def test_mesh_addVertexData():
     data4D   = np.random.randint(1, 100, (nverts, 20))
     dataBad  = np.random.randint(1, 100, (nverts - 1, 20))
 
-    mesh.addVertexData('3d',   data3D)
-    mesh.addVertexData('3_1d', data3_1D)
-    mesh.addVertexData('4d',   data4D)
+    assert np.all(np.isclose(mesh.addVertexData('3d',   data3D),   data3D.reshape(-1, 1)))
+    assert list(mesh.vertexDataSets()) == ['3d']
+
+    assert np.all(np.isclose(mesh.addVertexData('3_1d', data3_1D), data3_1D))
+    assert list(mesh.vertexDataSets()) == ['3d', '3_1d']
+
+    assert np.all(np.isclose(mesh.addVertexData('4d',   data4D),   data4D))
+    assert list(mesh.vertexDataSets()) == ['3d', '3_1d', '4d']
 
     assert mesh.getVertexData('3d')  .shape == (nverts, 1)
     assert mesh.getVertexData('3_1d').shape == (nverts, 1)
@@ -150,7 +184,8 @@ def test_loadVertexData():
     mesh  = fslmesh.Mesh(tris, vertices=verts)
 
     with tempdir():
-        np.savetxt('vdata.txt', vdata)
+        np.savetxt('vdata.txt',    vdata)
+        np.savetxt('badvdata.txt', vdata[:-1])
 
         key = op.abspath('vdata.txt')
 
@@ -159,6 +194,9 @@ def test_loadVertexData():
         assert np.all(np.isclose(mesh.loadVertexData(key, 'vdkey'), vdata))
         assert np.all(np.isclose(mesh.getVertexData(      'vdkey'), vdata))
 
+        with pytest.raises(ValueError):
+            mesh.loadVertexData('badvdata.txt')
+
 
 def test_normals():
 
@@ -217,17 +255,16 @@ def test_needsFixing():
 
 def test_trimesh_no_trimesh():
 
-    verts = np.array(CUBE_VERTICES)
-    tris  = np.array(CUBE_TRIANGLES_CCW)
-
     mods = ['trimesh', 'rtree']
 
     for mod in mods:
         with mock.patch.dict('sys.modules', **{mod : None}):
 
-            mesh = fslmesh.Mesh(tris, vertices=verts)
+            verts = np.array(CUBE_VERTICES)
+            tris  = np.array(CUBE_TRIANGLES_CCW)
+            mesh  = fslmesh.Mesh(tris, vertices=verts)
 
-            assert mesh.trimesh() is None
+            assert mesh.trimesh is None
             locs, tris = mesh.rayIntersection([[0, 0, 0]], [[0, 0, 1]])
             assert locs.size == 0
             assert tris.size == 0
@@ -250,7 +287,7 @@ def test_trimesh():
     tris  = np.array(CUBE_TRIANGLES_CCW)
 
     mesh = fslmesh.Mesh(tris, vertices=verts)
-    assert isinstance(mesh.trimesh(), trimesh.Trimesh)
+    assert isinstance(mesh.trimesh, trimesh.Trimesh)
 
 
 def test_rayIntersection():