class Superell(Primitive):
def __init__(self,name, center=(0, 0, 0), a=(1, 0, 0), b=(0, 1, 0), c=(0, 0, 1), n=0, e=0, copy=False):
Primitive.__init__(self, name=name)
self.center = Vector(center, copy)
self.a = Vector(a, copy)
self.b = Vector(b, copy)
self.c = Vector(c, copy)
self.n = n
self.e = e
def __repr__(self):
result = "{}({}, v={}, a={}, b={}, c={}, n={}, e={} )"
return result.format(
self.__class__.__name__, self.name, repr(self.center), repr(self.a),
repr(self.b), repr(self.c), self.n, self.e
)
def update_params(self, params):
params.update({
"center": self.center,
"a": self.a,
"b": self.b,
"c": self.c,
"n": self.n,
"e": self.e
})
def copy(self):
return Superell(self.name, self.center, self.a, self.b, self.c, self.n, self.e, copy=True)
def has_same_data(self, other):
return self.e == other.e and \
self.n == other.n and \
self.center.is_same(other.center) and \
self.a.is_same(other.a) and \
self.b.is_same(other.b) and \
self.c.is_same(other.c)
@staticmethod
def from_wdb(name, data):
return Superell(
name=name,
center=data.v,
a=data.a,
b=data.b,
c=data.c,
n=data.n,
e=data.e,
)
def check_tgc(self, name, expected_points):
shape = self.lookup_shape(name)
expected = Vector(expected_points)
actual = cta.flatten_numbers(
[shape.base, shape.height, shape.a, shape.b, shape.c, shape.d])
if not expected.is_same(actual):
self.fail("{0} != {1}".format(expected, actual))
class Grip(Primitive):
def __init__(self,
name,
center=(0, 0, 0),
normal=(1, 0, 0),
magnitude=1,
copy=False):
Primitive.__init__(self, name=name)
self.center = Vector(center, copy=copy)
self.normal = Vector(normal, copy=copy)
self.magnitude = magnitude
def __repr__(self):
result = "{}({}, center={}, normal={}, magnitude={})"
return result.format(self.__class__.__name__, self.name, self.center,
self.normal, self.magnitude)
def update_params(self, params):
params.update({
"center": self.center,
"normal": self.normal,
"magnitude": self.magnitude
})
def copy(self):
return Grip(self.name,
self.center,
self.normal,
self.magnitude,
copy=True)
def has_same_data(self, other):
return self.center.is_same(other.center) and \
self.normal.is_same(other.normal) and \
self.magnitude == other.magnitude
@staticmethod
def from_wdb(name, data):
return Grip(name=name,
center=data.center,
normal=data.normal,
magnitude=data.mag)
class Grip(Primitive):
def __init__(self, name, center=(0, 0, 0), normal=(1, 0, 0), magnitude=1, copy=False):
Primitive.__init__(self, name=name)
self.center = Vector(center, copy=copy)
self.normal = Vector(normal, copy=copy)
self.magnitude = magnitude
def __repr__(self):
result = "{}({}, center={}, normal={}, magnitude={})"
return result.format(
self.__class__.__name__, self.name, self.center, self.normal, self.magnitude
)
def update_params(self, params):
params.update({
"center": self.center,
"normal": self.normal,
"magnitude": self.magnitude
})
def copy(self):
return Grip(self.name, self.center, self.normal, self.magnitude, copy=True)
def has_same_data(self, other):
return self.center.is_same(other.center) and \
self.normal.is_same(other.normal) and \
self.magnitude == other.magnitude
@staticmethod
def from_wdb(name, data):
return Grip(
name=name,
center=data.center,
normal=data.normal,
magnitude=data.mag
)
class VOL(Primitive):
def __init__(
self,
name,
file_name,
x_dim=1,
y_dim=1,
z_dim=1,
low_thresh=0,
high_thresh=128,
cell_size=(1, 1, 1),
mat=Transform.unit(),
copy=False,
):
Primitive.__init__(self, name=name)
if not os.path.isfile(file_name):
raise ValueError("File {} does not exist !".format(file_name))
self.file_name = file_name
self.x_dim = x_dim
self.y_dim = y_dim
self.z_dim = z_dim
self.low_thresh = low_thresh
self.high_thresh = high_thresh
self.cell_size = Vector(cell_size, copy=copy)
self.mat = Transform(mat, copy=copy, force=True)
def __repr__(self):
result = (
"{}({}, file_name={}, x_dim={}, y_dim={}, z_dim={}, " "low_thresh={}, high_thresh={} cell_size={}, mat={})"
)
return result.format(
self.__class__.__name__,
self.file_name,
self.name,
self.x_dim,
self.y_dim,
self.z_dim,
self.low_thresh,
self.high_thresh,
repr(self.cell_size),
repr(self.mat),
)
def update_params(self, params):
params.update(
{
"file_name": self.file_name,
"x_dim": self.x_dim,
"y_dim": self.y_dim,
"z_dim": self.z_dim,
"low_thresh": self.low_thresh,
"high_thresh": self.high_thresh,
"cell_size": self.cell_size,
"mat": self.mat,
}
)
def copy(self):
return VOL(
self.name,
file_name=self.file_name,
x_dim=self.x_dim,
y_dim=self.y_dim,
z_dim=self.z_dim,
low_thresh=self.low_thresh,
high_thresh=self.high_thresh,
cell_size=self.cell_size,
mat=self.mat,
copy=True,
)
def has_same_data(self, other):
if not (
self.file_name == other.file_name,
self.x_dim == other.x_dim
and self.y_dim == other.y_dim
and self.z_dim == other.z_dim
and self.low_thresh == other.low_thresh
and self.high_thresh == other.high_thresh,
):
return False
return self.cell_size.is_same(other.cell_size) and np.allclose(self.mat, other.mat)
@staticmethod
def from_wdb(name, data):
return VOL(
name=name,
file_name=data.file,
x_dim=data.xdim,
y_dim=data.ydim,
z_dim=data.zdim,
low_thresh=data.lo,
high_thresh=data.hi,
cell_size=data.cellsize,
mat=cta.transform_from_pointer(data.mat),
)
class VOL(Primitive):
def __init__(self,
name,
file_name,
x_dim=1,
y_dim=1,
z_dim=1,
low_thresh=0,
high_thresh=128,
cell_size=(1, 1, 1),
mat=Transform.unit(),
copy=False):
Primitive.__init__(self, name=name)
if not os.path.isfile(file_name):
raise ValueError("File {} does not exist !".format(file_name))
self.file_name = file_name
self.x_dim = x_dim
self.y_dim = y_dim
self.z_dim = z_dim
self.low_thresh = low_thresh
self.high_thresh = high_thresh
self.cell_size = Vector(cell_size, copy=copy)
self.mat = Transform(mat, copy=copy, force=True)
def __repr__(self):
result = "{}({}, file_name={}, x_dim={}, y_dim={}, z_dim={}, " \
"low_thresh={}, high_thresh={} cell_size={}, mat={})"
return result.format(self.__class__.__name__, self.file_name,
self.name, self.x_dim, self.y_dim, self.z_dim,
self.low_thresh, self.high_thresh,
repr(self.cell_size), repr(self.mat))
def update_params(self, params):
params.update({
"file_name": self.file_name,
"x_dim": self.x_dim,
"y_dim": self.y_dim,
"z_dim": self.z_dim,
"low_thresh": self.low_thresh,
"high_thresh": self.high_thresh,
"cell_size": self.cell_size,
"mat": self.mat
})
def copy(self):
return VOL(self.name,
file_name=self.file_name,
x_dim=self.x_dim,
y_dim=self.y_dim,
z_dim=self.z_dim,
low_thresh=self.low_thresh,
high_thresh=self.high_thresh,
cell_size=self.cell_size,
mat=self.mat,
copy=True)
def has_same_data(self, other):
if not (self.file_name == other.file_name, self.x_dim == other.x_dim
and self.y_dim == other.y_dim and self.z_dim == other.z_dim
and self.low_thresh == other.low_thresh
and self.high_thresh == other.high_thresh):
return False
return self.cell_size.is_same(other.cell_size) and np.allclose(
self.mat, other.mat)
@staticmethod
def from_wdb(name, data):
return VOL(name=name,
file_name=data.file,
x_dim=data.xdim,
y_dim=data.ydim,
z_dim=data.zdim,
low_thresh=data.lo,
high_thresh=data.hi,
cell_size=data.cellsize,
mat=cta.transform_from_pointer(data.mat))
def check_tgc(self, name, expected_points):
shape = self.lookup_shape(name)
expected = Vector(expected_points)
actual = cta.flatten_numbers([shape.base, shape.height, shape.a, shape.b, shape.c, shape.d])
if not expected.is_same(actual):
self.fail("{0} != {1}".format(expected, actual))
def check_arb(self, name, expected_points):
shape = self.lookup_shape(name)
expected = Vector(expected_points)
if not expected.is_same(shape.points):
self.fail("{0} != {1}".format(expected, shape.points))
def test_arbn_defaults(self):
shape = self.lookup_shape("arbn.s")
expected = Vector((1, 0, 0, 1, -1, 0, 0, 1, 0, 1, 0, 1, 0, -1, 0, 1, 0, 0, 1, 1, 0, 0, -1, 1))
self.assertTrue(expected.is_same(cta.flatten_numbers(shape.planes)))
def check_arb(self, name, expected_points):
shape = self.lookup_shape(name)
expected = Vector(expected_points)
if not expected.is_same(shape.points):
self.fail("{0} != {1}".format(expected, shape.points))
def test_arbn_defaults(self):
shape = self.lookup_shape("arbn.s")
expected = Vector((1, 0, 0, 1, -1, 0, 0, 1, 0, 1, 0, 1, 0, -1, 0, 1, 0,
0, 1, 1, 0, 0, -1, 1))
self.assertTrue(expected.is_same(cta.flatten_numbers(shape.planes)))
