def test_superpose(self):
# create a few test sets with random data points, including degenerate
# situations. (e.g. one point, two points, linear points)
references = [ # a list of 2-tuples: (points, degenerate)
(numpy.random.normal(0, 5, (n, 3)), False) for n in xrange(4, 40)
] + [
#(numpy.array([[0,0,1]], float), True),
#(numpy.array([[0,0,0],[0,0,1]], float), True),
#(numpy.array([[0,0,0],[0,0,1],[0,0,2]], float), True),
#(numpy.array([[0,0,0],[0,0,1],[0,0,2],[0,0,4]], float), True),
#(numpy.random.normal(0, 5, (3, 3)), True)
]
# Do a random transformation on the points
randomized = []
for points, degenerate in references:
#points[:] -= points.mean(axis=0)
axis = random_unit(3)
angle = numpy.random.uniform(0, numpy.pi * 2)
transformation = Complete()
transformation.set_rotation_properties(angle, axis, False)
transformation.t[:] = numpy.random.normal(0, 5, 3)
randomized.append(
(numpy.array([transformation.vector_apply(p)
for p in points]), transformation))
for (ref_points, degenerate), (tr_points,
transf) in zip(references, randomized):
check_transf = superpose(ref_points, tr_points)
# check whether the rotation matrix is orthogonal
self.assertArraysAlmostEqual(
numpy.dot(check_transf.r, check_transf.r.transpose()),
numpy.identity(3, float), 1e-5)
# first check whether check_transf brings the tr_points back to the ref_points
check_points = numpy.dot(
tr_points, check_transf.r.transpose()) + check_transf.t
self.assertArraysAlmostEqual(ref_points,
check_points,
1e-5,
doabs=True)
if not degenerate:
# if the set of points is not degenerate, check whether transf and check_transf
# are each other inverses
tmp = Complete()
tmp.apply_before(transf)
tmp.apply_before(check_transf)
self.assertArraysAlmostEqual(
numpy.dot(transf.r, check_transf.r),
numpy.identity(3, float), 1e-5)
self.assertArrayAlmostZero(tmp.t, 1e-5)
# Add some distortion to the transformed points
randomized = []
for tr_points, transf in randomized:
tr_points[:] += numpy.random.normal(0, 1.0, len(tr_points))
# Do a blind test
for (ref_points, degenerate), (tr_points,
transf) in zip(references, randomized):
superpose(ref_points, tr_points)
def setUp(self):
self.test_transformations = []
for i in xrange(20):
test_transformation = Complete()
test_transformation.set_rotation_properties(random.random()*math.pi*2, numpy.random.uniform(-3, 3, 3), random.sample([True, False], 1)[0])
test_transformation.t = numpy.random.uniform(-3, 3, 3)
self.test_transformations.append(test_transformation)
def setUp(self):
self.test_transformations = []
for i in xrange(20):
test_transformation = Complete()
test_transformation.set_rotation_properties(
random.random() * math.pi * 2, numpy.random.uniform(-3, 3, 3),
random.sample([True, False], 1)[0])
test_transformation.t = numpy.random.uniform(-3, 3, 3)
self.test_transformations.append(test_transformation)
def test_superpose(self):
# create a few test sets with random data points, including degenerate
# situations. (e.g. one point, two points, linear points)
references = [ # a list of 2-tuples: (points, degenerate)
(numpy.random.normal(0, 5, (n, 3)), False) for n in xrange(4, 40)
] + [
#(numpy.array([[0,0,1]], float), True),
#(numpy.array([[0,0,0],[0,0,1]], float), True),
#(numpy.array([[0,0,0],[0,0,1],[0,0,2]], float), True),
#(numpy.array([[0,0,0],[0,0,1],[0,0,2],[0,0,4]], float), True),
#(numpy.random.normal(0, 5, (3, 3)), True)
]
# Do a random transformation on the points
randomized = []
for points, degenerate in references:
#points[:] -= points.mean(axis=0)
axis = random_unit(3)
angle = numpy.random.uniform(0, numpy.pi*2)
transformation = Complete()
transformation.set_rotation_properties(angle, axis, False)
transformation.t[:] = numpy.random.normal(0, 5, 3)
randomized.append((
numpy.array([transformation.vector_apply(p) for p in points]),
transformation
))
for (ref_points, degenerate), (tr_points, transf) in zip(references, randomized):
check_transf = superpose(ref_points, tr_points)
# check whether the rotation matrix is orthogonal
self.assertArraysAlmostEqual(numpy.dot(check_transf.r, check_transf.r.transpose()), numpy.identity(3, float), 1e-5)
# first check whether check_transf brings the tr_points back to the ref_points
check_points = numpy.dot(tr_points, check_transf.r.transpose()) + check_transf.t
self.assertArraysAlmostEqual(ref_points, check_points, 1e-5, doabs=True)
if not degenerate:
# if the set of points is not degenerate, check whether transf and check_transf
# are each other inverses
tmp = Complete()
tmp.apply_before(transf)
tmp.apply_before(check_transf)
self.assertArraysAlmostEqual(numpy.dot(transf.r, check_transf.r), numpy.identity(3, float), 1e-5)
self.assertArrayAlmostZero(tmp.t, 1e-5)
# Add some distortion to the transformed points
randomized = []
for tr_points, transf in randomized:
tr_points[:] += numpy.random.normal(0, 1.0, len(tr_points))
# Do a blind test
for (ref_points, degenerate), (tr_points, transf) in zip(references, randomized):
superpose(ref_points, tr_points)
def do_test(self, coordinates, masses, expected_is):
reference = MolecularDescriptorTV1(coordinates, masses)
self.assert_(reference.inversion_symmetric == expected_is)
for counter in xrange(3):
transformation = Complete()
transformation.set_rotation_properties(
random.uniform(0, 2 * math.pi),
numpy.random.uniform(-1, 1, (3, )),
False,
)
transformation.t = numpy.random.uniform(-5, 5, (3, ))
new_coordinates = numpy.array([
transformation.vector_apply(coordinate)
for coordinate in coordinates
], float)
new_descriptor = MolecularDescriptorTV1(new_coordinates, masses)
self.assert_(reference.compare_structure(new_descriptor))
self.assert_(not reference.compare_global_rotation(new_descriptor))
self.assert_(
not reference.compare_global_translation(new_descriptor))
def do_test(self, coordinates, masses, expected_is):
reference = MolecularDescriptorTV1(coordinates, masses)
self.assert_(reference.inversion_symmetric == expected_is)
for counter in xrange(3):
transformation = Complete()
transformation.set_rotation_properties(
random.uniform(0, 2*math.pi),
numpy.random.uniform(-1, 1, (3,)),
False,
)
transformation.t = numpy.random.uniform(-5, 5, (3,))
new_coordinates = numpy.array([
transformation.vector_apply(coordinate)
for coordinate
in coordinates
], float)
new_descriptor = MolecularDescriptorTV1(new_coordinates, masses)
self.assert_(reference.compare_structure(new_descriptor))
self.assert_(not reference.compare_global_rotation(new_descriptor))
self.assert_(not reference.compare_global_translation(new_descriptor))
class Vector(GLReferentBase):
#
# State
#
def initnonstate(self):
GLReferentBase.initnonstate(self)
self.orientation = Complete()
self.set_children([
SpatialReference(prefix="Begin"),
SpatialReference(prefix="End")
])
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo("Basic", (0, 2), fields.read.VectorLength(
label_text="Vector length"
)),
])
#
# Draw
#
def draw(self):
self.calc_vector_dimensions()
context.application.vis_backend.transform(self.orientation)
#
# Revalidation
#
def revalidate_total_list(self):
if self.gl_active:
vb = context.application.vis_backend
vb.begin_list(self.total_list)
if self.visible:
vb.push_name(self.draw_list)
vb.push_matrix()
self.draw_selection()
vb.call_list(self.draw_list)
vb.pop_matrix()
vb.pop_name()
vb.end_list()
self.total_list_valid = True
def revalidate_draw_list(self):
if self.gl_active:
GLReferentBase.revalidate_draw_list(self)
def revalidate_boundingbox_list(self):
if self.gl_active:
vb = context.application.vis_backend
#print "Compiling selection list (" + str(self.boundingbox_list) + "): " + str(self.name)
vb.begin_list(self.boundingbox_list)
vb.push_matrix()
vb.transform(self.orientation)
self.revalidate_bounding_box()
self.bounding_box.draw()
vb.pop_matrix()
vb.end_list()
self.boundingbox_list_valid = True
#
# Frame
#
def get_bounding_box_in_parent_frame(self):
return self.bounding_box.transformed(self.orientation)
#
# Vector
#
def shortest_vector_relative_to(self, other):
b = self.children[0].translation_relative_to(other)
e = self.children[1].translation_relative_to(other)
if (b is None) or (e is None):
return None
else:
return self.parent.shortest_vector(e - b)
def calc_vector_dimensions(self):
relative_translation = self.shortest_vector_relative_to(self.parent)
if relative_translation is None:
self.length = 0
else:
self.length = math.sqrt(numpy.dot(relative_translation, relative_translation))
if self.length > 0:
self.orientation.t = self.children[0].translation_relative_to(self.parent)
#axis = numpy.cross(relative_translation, numpy.array([1.0, 0.0, 0.0]))
c = relative_translation[2] / self.length
if c >= 1.0:
self.orientation.set_rotation_properties(0, numpy.array([1.0, 0.0, 0.0]), False)
elif c <= -1.0:
self.orientation.set_rotation_properties(math.pi, numpy.array([1.0, 0.0, 0.0]), False)
else:
x, y = relative_translation[0], relative_translation[1]
if abs(x) < abs(y):
signy = {True: 1, False: -1}[y >= 0]
a = -signy
b = signy * x / y
else:
signx = {True: 1, False: -1}[x >= 0]
a = -signx * y / x
b = signx
self.orientation.set_rotation_properties(math.acos(c), numpy.array([a, b, 0.0]), False)
def define_target(self, reference, new_target):
GLReferentBase.define_target(self, reference, new_target)
self.invalidate_boundingbox_list()
self.invalidate_draw_list()
def target_moved(self, reference, target):
GLReferentBase.target_moved(self, reference, target)
self.invalidate_boundingbox_list()
self.invalidate_draw_list()
