From 91148e641f2224eb2b004001755987d2f2433261 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 21 Jan 2018 12:35:39 +0000
Subject: [PATCH] Mesh unit tests updated
---
tests/test_mesh.py | 251 ++++++++++++++++++++++-----------------------
1 file changed, 121 insertions(+), 130 deletions(-)
diff --git a/tests/test_mesh.py b/tests/test_mesh.py
index ce47c09fe..bfbffafaf 100644
--- a/tests/test_mesh.py
+++ b/tests/test_mesh.py
@@ -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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