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Commit 91148e64 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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Mesh unit tests updated

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tests/test_mesh.py
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......@@ -6,10 +6,6 @@
#
import os.path as op
import shutil
import tempfile
import numpy as np
import mock
import pytest
......@@ -18,9 +14,6 @@ import fsl.utils.transform as transform
import fsl.data.mesh as fslmesh
datadir = op.join(op.dirname(__file__), 'testdata')
# vertices of a cube
CUBE_VERTICES = np.array([
[-1, -1, -1],
......@@ -49,119 +42,96 @@ CUBE_TRIANGLES_CW = np.array([
CUBE_TRIANGLES_CCW = np.array(CUBE_TRIANGLES_CW)
CUBE_TRIANGLES_CCW[:, [1, 2]] = CUBE_TRIANGLES_CCW[:, [2, 1]]
CUBE_CCW_FACE_NORMALS = np.array([
[ 0, 0, -1], [ 0, 0, -1],
[ 0, 0, 1], [ 0, 0, 1],
[ 0, -1, 0], [ 0, -1, 0],
[ 0, 1, 0], [ 0, 1, 0],
[-1, 0, 0], [-1, 0, 0],
[ 1, 0, 0], [ 1, 0, 0],
])
def test_create_mesh():
# Test:
# - create from file
# - create from inmem data
testbase = 'test_mesh.vtk'
testfile = op.join(datadir, testbase)
verts, lens, indices = fslmesh.loadVTKPolydataFile(testfile)
mesh1 = fslmesh.TriangleMesh(testfile)
mesh2 = fslmesh.TriangleMesh(verts, indices)
assert mesh1.name == testbase
assert mesh2.name == 'TriangleMesh'
assert mesh1.dataSource == testfile
assert mesh2.dataSource is None
assert mesh1.vertices.shape == (642, 3)
assert mesh2.vertices.shape == (642, 3)
assert mesh1.indices.shape == (1280, 3)
assert mesh2.indices.shape == (1280, 3)
minbounds = np.array([ 59.50759888, 88.43039703, 72.10890198])
maxbounds = np.array([ 77.72619629, 128.40600586, 94.82050323])
mesh1Bounds = mesh1.getBounds()
mesh2Bounds = mesh2.getBounds()
assert np.all(np.isclose(mesh1Bounds[0], minbounds))
assert np.all(np.isclose(mesh1Bounds[1], maxbounds))
assert np.all(np.isclose(mesh2Bounds[0], minbounds))
assert np.all(np.isclose(mesh2Bounds[1], maxbounds))
CUBE_CCW_VERTEX_NORMALS = np.zeros((8, 3))
for i in range(8):
faces = np.where(CUBE_TRIANGLES_CCW == i)[0]
CUBE_CCW_VERTEX_NORMALS[i] = CUBE_CCW_FACE_NORMALS[faces].sum(axis=0)
CUBE_CCW_VERTEX_NORMALS = transform.normalise(CUBE_CCW_VERTEX_NORMALS)
def test_mesh_loadVertexData():
meshfile = op.join(datadir, 'test_mesh.vtk')
datafile = op.join(datadir, 'test_mesh_data.txt')
memdata = np.random.randint(1, 100, 642)
mesh = fslmesh.TriangleMesh(meshfile)
def test_mesh_create():
assert mesh.loadVertexData(datafile).shape == (642,)
assert np.all(mesh.loadVertexData('inmemdata', memdata) == memdata)
verts = np.array(CUBE_VERTICES)
tris = np.array(CUBE_TRIANGLES_CCW)
assert mesh.getVertexData(datafile).shape == (642,)
assert np.all(mesh.getVertexData('inmemdata') == memdata)
mesh = fslmesh.Mesh(tris, vertices=verts)
mesh.clearVertexData()
assert mesh.name == 'mesh'
assert mesh.dataSource is None
assert np.all(np.isclose(mesh.vertices, verts))
assert np.all(np.isclose(mesh.indices, tris))
assert mesh.getVertexData(datafile).shape == (642,)
assert np.all(mesh.loadVertexData('inmemdata', memdata) == memdata)
blo, bhi = mesh.bounds
assert np.all(np.isclose(blo, verts.min(axis=0)))
assert np.all(np.isclose(bhi, verts.max(axis=0)))
def test_loadVTKPolydataFile():
testfile = op.join(datadir, 'test_mesh.vtk')
verts, lens, indices = fslmesh.loadVTKPolydataFile(testfile)
def test_mesh_addVertices():
assert verts.shape == (642, 3)
assert indices.shape == (3840, )
assert lens.shape == (1280, )
assert np.all(lens == 3)
tris = np.array(CUBE_TRIANGLES_CCW)
verts = np.array(CUBE_VERTICES)
verts2 = np.array(CUBE_VERTICES) * 2
verts3 = np.array(CUBE_VERTICES) * 3
mesh = fslmesh.Mesh(tris, vertices=verts)
def test_getFIRSTPrefix():
assert mesh.selectedVertices() == 'default'
assert np.all(np.isclose(mesh.vertices, verts))
failures = [
'blob.txt',
'blob.vtk',
'blob.nii.gz']
mesh.addVertices(verts2, 'twotimes')
passes = [
('blurgh-L_Thal_first.vtk', 'blurgh'),
('blurgh-L_Accu_first.vtk', 'blurgh'),
('blurgh_bufuu-R_Hipp_first.vtk', 'blurgh_bufuu'),
]
assert mesh.selectedVertices() == 'twotimes'
assert np.all(np.isclose(mesh.vertices, verts2))
for f in failures:
with pytest.raises(ValueError):
fslmesh.getFIRSTPrefix(f)
mesh.addVertices(verts3, 'threetimes', select=False)
for fname, expected in passes:
assert fslmesh.getFIRSTPrefix(fname) == expected
assert mesh.selectedVertices() == 'twotimes'
assert np.all(np.isclose(mesh.vertices, verts2))
mesh.vertices = 'threetimes'
assert mesh.selectedVertices() == 'threetimes'
assert np.all(np.isclose(mesh.vertices, verts3))
def test_findReferenceImage():
testdir = tempfile.mkdtemp()
vtkfiles = ['struc-L_Thal_first.vtk',
'struc_first-L_Thal_first.vtk']
def test_mesh_addVertexData():
assert fslmesh.findReferenceImage('nofile') is None
mesh = fslmesh.Mesh(np.array(CUBE_TRIANGLES_CCW),
vertices=np.array(CUBE_VERTICES))
try:
nverts = CUBE_VERTICES.shape[0]
for fname in vtkfiles:
data3D = np.random.randint(1, 100, nverts)
data3_1D = np.random.randint(1, 100, (nverts, 1))
data4D = np.random.randint(1, 100, (nverts, 20))
assert fslmesh.findReferenceImage(fname) is None
mesh.addVertexData('3d', data3D)
mesh.addVertexData('3_1d', data3_1D)
mesh.addVertexData('4d', data4D)
prefix = fslmesh.getFIRSTPrefix(fname)
imgfname = op.join(testdir, '{}.nii.gz'.format(prefix))
fname = op.join(testdir, fname)
assert mesh.getVertexData('3d') .shape == (nverts, 1)
assert mesh.getVertexData('3_1d').shape == (nverts, 1)
assert mesh.getVertexData('4d') .shape == (nverts, 20)
with open(fname, 'wt') as f: f.write(fname)
with open(imgfname, 'wt') as f: f.write(imgfname)
assert np.all(np.isclose(data3D.reshape(-1, 1), mesh.getVertexData('3d')))
assert np.all(np.isclose(data3_1D, mesh.getVertexData('3_1d')))
assert np.all(np.isclose(data4D, mesh.getVertexData('4d')))
assert fslmesh.findReferenceImage(fname) == imgfname
mesh.clearVertexData()
finally:
shutil.rmtree(testdir)
with pytest.raises(KeyError): mesh.getVertexData('3d')
with pytest.raises(KeyError): mesh.getVertexData('3_1d')
with pytest.raises(KeyError): mesh.getVertexData('4d')
def test_normals():
......@@ -170,34 +140,18 @@ def test_normals():
verts = np.array(CUBE_VERTICES)
triangles_cw = np.array(CUBE_TRIANGLES_CW)
triangles_ccw = np.array(CUBE_TRIANGLES_CCW)
fnormals = np.array(CUBE_CCW_FACE_NORMALS)
vnormals = np.array(CUBE_CCW_VERTEX_NORMALS)
cw_nofix = fslmesh.Mesh(np.array(triangles_cw))
cw_fix = fslmesh.Mesh(np.array(triangles_cw))
ccw_nofix = fslmesh.Mesh(np.array(triangles_ccw))
ccw_fix = fslmesh.Mesh(np.array(triangles_ccw))
# face normals
fnormals = np.array([
[ 0, 0, -1], [ 0, 0, -1],
[ 0, 0, 1], [ 0, 0, 1],
[ 0, -1, 0], [ 0, -1, 0],
[ 0, 1, 0], [ 0, 1, 0],
[-1, 0, 0], [-1, 0, 0],
[ 1, 0, 0], [ 1, 0, 0],
])
# vertex normals
vnormals = np.zeros((8, 3))
for i in range(8):
faces = np.where(triangles_cw == i)[0]
vnormals[i] = fnormals[faces].sum(axis=0)
vnormals = transform.normalise(vnormals)
cw_nofix = fslmesh.TriangleMesh(np.array(verts),
np.array(triangles_cw))
cw_fix = fslmesh.TriangleMesh(np.array(verts),
np.array(triangles_cw),
fixWinding=True)
ccw_nofix = fslmesh.TriangleMesh(np.array(verts),
np.array(triangles_ccw))
ccw_fix = fslmesh.TriangleMesh(np.array(verts),
np.array(triangles_ccw),
fixWinding=True)
cw_nofix .addVertices(np.array(verts))
cw_fix .addVertices(np.array(verts), fixWinding=True)
ccw_nofix.addVertices(np.array(verts))
ccw_fix .addVertices(np.array(verts), fixWinding=True)
# ccw triangles should give correct
# normals without unwinding
......@@ -206,29 +160,54 @@ def test_normals():
assert np.all(np.isclose(cw_fix .normals, fnormals))
assert np.all(np.isclose(cw_fix .vnormals, vnormals))
assert np.all(np.isclose(ccw_nofix.normals, fnormals))
assert np.all(np.isclose(ccw_nofix.vnormals, vnormals))
assert np.all(np.isclose(ccw_nofix.vnormals, vnormals))
assert np.all(np.isclose(ccw_fix .normals, fnormals))
assert np.all(np.isclose(ccw_fix .vnormals, vnormals))
# Test standalone calcFaceNormals/
# calcVertexNormals functions
assert np.all(np.isclose(
-fnormals, fslmesh.calcFaceNormals(verts, triangles_cw)))
assert np.all(np.isclose(
fnormals, fslmesh.calcFaceNormals(verts, triangles_ccw)))
assert np.all(np.isclose(
-vnormals, fslmesh.calcVertexNormals(verts, triangles_cw, -fnormals)))
assert np.all(np.isclose(
vnormals, fslmesh.calcVertexNormals(verts, triangles_ccw, fnormals)))
def test_needsFixing():
verts = np.array(CUBE_VERTICES)
tris_cw = np.array(CUBE_TRIANGLES_CW)
tris_ccw = np.array(CUBE_TRIANGLES_CCW)
fnormals = np.array(CUBE_CCW_VERTEX_NORMALS)
blo = verts.min(axis=0)
bhi = verts.max(axis=0)
assert not fslmesh.needsFixing(verts, tris_ccw, fnormals, blo, bhi)
assert fslmesh.needsFixing(verts, tris_cw, -fnormals, blo, bhi)
def test_trimesh_no_trimesh():
testbase = 'test_mesh.vtk'
testfile = op.join(datadir, testbase)
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.TriangleMesh(testfile)
mesh = fslmesh.Mesh(tris, vertices=verts)
assert mesh.trimesh() is None
locs, tris = mesh.rayIntersection([[0, 0, 0]], [[0, 0, 1]])
assert locs.size == 0
assert tris.size == 0
verts, idxs, dists = mesh.nearestVertex([[0, 0, 0]])
assert verts.size == 0
nverts, idxs, dists = mesh.nearestVertex([[0, 0, 0]])
assert nverts.size == 0
assert idxs.size == 0
assert dists.size == 0
......@@ -241,9 +220,10 @@ def test_trimesh():
import trimesh
testbase = 'test_mesh.vtk'
testfile = op.join(datadir, testbase)
mesh = fslmesh.TriangleMesh(testfile)
verts = np.array(CUBE_VERTICES)
tris = np.array(CUBE_TRIANGLES_CCW)
mesh = fslmesh.Mesh(tris, vertices=verts)
assert isinstance(mesh.trimesh(), trimesh.Trimesh)
......@@ -251,7 +231,7 @@ def test_rayIntersection():
verts = np.array(CUBE_VERTICES)
triangles = np.array(CUBE_TRIANGLES_CCW)
mesh = fslmesh.TriangleMesh(verts, triangles)
mesh = fslmesh.Mesh(triangles, vertices=verts)
for axis in range(3):
rayOrigin = [0, 0, 0]
......@@ -279,7 +259,7 @@ def test_nearestVertex():
verts = np.array(CUBE_VERTICES)
triangles = np.array(CUBE_TRIANGLES_CCW)
mesh = fslmesh.TriangleMesh(verts, triangles)
mesh = fslmesh.Mesh(triangles, vertices=verts)
nverts, nidxs, ndists = mesh.nearestVertex(verts * 2)
......@@ -292,7 +272,7 @@ def test_planeIntersection():
verts = np.array(CUBE_VERTICES)
triangles = np.array(CUBE_TRIANGLES_CCW)
mesh = fslmesh.TriangleMesh(verts, triangles)
mesh = fslmesh.Mesh(triangles, vertices=verts)
normal = [0, 0, 1]
origin = [0, 0, 0]
......@@ -357,3 +337,14 @@ def test_planeIntersection():
assert np.all(np.isclose(lines, expLines))
assert np.all(np.isclose(faces, expFaces))
assert np.all(np.isclose(dists, expDists))
normal = [0, 0, 1]
origin = [3, 3, 3]
lines, faces, dists = mesh.planeIntersection(normal,
origin,
distances=True)
assert lines.shape == (0, 2, 3)
assert faces.shape == (0, )
assert dists.shape == (0, 2, 3)
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