def test_three_dim_middle_alternates(self):
tg = LineGenerator("t", "mm", 1, 5, 5)
zg = LineGenerator("z", "mm", -1, 3, 5, True)
spiral = SpiralGenerator(["s1", "s2"], "mm", [1, 1], 2, 1, True)
yg = LineGenerator("y", "mm", 0, 4, 5)
xg = LineGenerator("x", "mm", 0, 4, 5)
r1 = CircularROI([0, 0], 1)
e1 = ROIExcluder([r1], ["s1", "z"])
e2 = ROIExcluder([r1], ["y", "x"])
g = CompoundGenerator([tg, zg, spiral, yg, xg], [e2, e1], [])
g.prepare()
it = 0
iz = 0
iy = 0
ix = 0
tzs = []
points = []
for t in range_(1, 6):
for z in (range_(-1, 4) if it % 2 == 0 else range_(3, -2, -1)):
s1p = spiral.positions["s1"] if iz % 2 == 0 else spiral.positions["s1"][::-1]
s2p = spiral.positions["s2"] if iz % 2 == 0 else spiral.positions["s2"][::-1]
points += [(x, y, s1, s2, z, t) for (s1, s2) in zip(s1p, s2p)
for y in range(0, 5) for x in range(0, 5)
if s1*s1 + z*z <= 1 and y*y + x*x <= 1]
iz += 1
it += 1
expected = [{"x":float(x), "y":float(y), "s1":s1, "s2":s2, "z":float(z), "t":float(t)}
for (x, y, s1, s2, z, t) in points]
actual = [p.positions for p in list(g.iterator())]
for e, a in zip(expected, actual):
self.assertEqual(e, a)
def test_alternating_three_axis(self):
z = LineGenerator("z", "mm", 1, 2, 2)
y = LineGenerator("y", "mm", 1, 2, 2, True)
x = LineGenerator("x", "mm", 3, 1, 3, True)
g = CompoundGenerator([z, y, x], [], [])
g.prepare()
expected = []
expected_idx = []
expected_lower = []
expected_upper = []
y_f = True
x_f = True
for z in range_(1, 3):
y_r = range_(1, 3) if y_f else range_(2, 0, -1)
y_f = not y_f
for y in y_r:
x_r = range_(3, 0, -1) if x_f else range_(1, 4)
for x in x_r:
expected.append({
"x": float(x),
"y": float(y),
"z": float(z)
})
expected_idx.append([z - 1, y - 1, 3 - x])
expected_lower.append(x + (0.5 if x_f else -0.5))
expected_upper.append(x + (-0.5 if x_f else 0.5))
x_f = not x_f
points = list(g.iterator())
self.assertEqual(expected, [p.positions for p in points])
self.assertEqual(expected_idx, [p.indexes for p in points])
self.assertEqual(expected_lower, [p.lower["x"] for p in points])
self.assertEqual(expected_upper, [p.upper["x"] for p in points])
def test_complex_masks(self):
tg = LineGenerator("t", "mm", 1, 5, 5)
zg = LineGenerator("z", "mm", 0, 4, 5, alternate=True)
yg = LineGenerator("y", "mm", 1, 5, 5, alternate=True)
xg = LineGenerator("x", "mm", 2, 6, 5, alternate=True)
r1 = CircularROI([4., 4.], 1.5)
e1 = ROIExcluder([r1], ["y", "x"])
e2 = ROIExcluder([r1], ["z", "y"])
g = CompoundGenerator([tg, zg, yg, xg], [e1, e2], [])
g.prepare()
t_mask = [True] * 5
iy = 0
ix = 0
xyz_mask = []
xyz = []
for z in range_(0, 5):
for y in (range_(1, 6) if iy % 2 == 0 else range_(5, 0, -1)):
for x in (range_(2, 7) if ix % 2 == 0 else range_(6, 1, -1)):
xyz_mask.append( (x-4)**2 + (y-4)**2 <= 1.5**2 \
and (y-4)**2 + (z-4)**2 <= 1.5**2)
xyz.append((x, y, z))
ix += 1
iy += 1
self.assertEqual(t_mask, g.dimensions[0].mask.tolist())
self.assertEqual(xyz_mask, g.dimensions[1].mask.tolist())
def test_get_point_large_scan(self):
s = SpiralGenerator(["x", "y"], "mm", [0, 0], 6, 1) #114 points
z = LineGenerator("z", "mm", 0, 1, 100)
w = LineGenerator("w", "mm", 0, 1, 5)
t = LineGenerator("t", "mm", 0, 1, 5)
rad1 = 2.8
r1 = CircularROI([1., 1.], rad1)
e1 = ROIExcluder([r1], ["x", "y"])
rad2 = 2
r2 = CircularROI([0.5, 0.5], rad2)
e2 = ROIExcluder([r2], ["y", "z"])
rad3 = 0.5
r3 = CircularROI([0.5, 0.5], rad3)
e3 = ROIExcluder([r3], ["w", "t"])
g = CompoundGenerator([t, w, z, s], [e1, e2, e3], [])
g.prepare()
spiral = [(x, y) for (x, y) in zip(s.positions["x"], s.positions["y"])]
zwt = [(z/99., w/4., t/4.) for t in range_(0, 5)
for w in range_(0, 5)
for z in range_(0, 100)]
expected = [(x, y, z, w, t) for (z, w, t) in zwt for (x, y) in spiral]
expected = [{"x":x, "y":y, "z":z, "w":w, "t":t}
for (x,y,z,w,t) in expected if
(x-1)*(x-1) + (y-1)*(y-1) <= rad1*rad1 and
(y-0.5)*(y-0.5) + (z-0.5)*(z-0.5) <= rad2*rad2 and
(w-0.5)*(w-0.5) + (t-0.5)*(t-0.5) <= rad3*rad3]
points = [g.get_point(n) for n in range_(0, g.size)]
pos = [p.positions for p in points]
# assertEqual on a sequence of dicts is *really* slow
for (e, p) in zip(expected, pos):
self.assertEquals(e.keys(), p.keys())
for k in e.keys():
self.assertAlmostEqual(e[k], p[k])
def test_alternating_regions_2(self):
z = LineGenerator("z", "mm", 1, 5, 5)
y = LineGenerator("y", "mm", 1, 5, 5, True)
x = LineGenerator("x", "mm", 1, 5, 5, True)
r1 = CircularROI([3, 3], 1.5)
e1 = ROIExcluder([r1], ["x", "y"])
e2 = ROIExcluder([r1], ["z", "y"])
g = CompoundGenerator([z, y, x], [e1, e2], []) #20 points
g.prepare()
actual = [p.positions for p in list(g.iterator())]
expected = []
yf = True
xf = True
for z in range_(1, 6):
yr = range_(1, 6) if yf else range_(5, 0, -1)
yf = not yf
for y in yr:
xr = range_(1, 6) if xf else range_(5, 0, -1)
xf = not xf
for x in xr:
expected.append({
"x": float(x),
"y": float(y),
"z": float(z)
})
expected = [
p for p in expected if (p["x"] - 3)**2 +
(p["y"] - 3)**2 <= 1.5**2 and (p["z"] - 3)**2 +
(p["y"] - 3)**2 <= 1.5**2
]
self.assertEqual(expected, actual)
def test_double_spiral_scan(self):
line1 = LineGenerator(["l1"], "mm", -1, 2, 5)
spiral_s = SpiralGenerator(["s1", "s2"], "mm", [1, 2], 5, 2.5, True)
spiral_t = SpiralGenerator(["t1", "t2"], "mm", [0, 0], 5, 2.5, True)
line2 = LineGenerator(["l2"], "mm", -1, 2, 5, True)
r = CircularROI([0, 0], 1)
e1 = ROIExcluder([r], ["s1", "l1"])
e2 = ROIExcluder([r], ["l2", "t1"])
g = CompoundGenerator([line1, spiral_s, spiral_t, line2], [e1, e2], [])
g.prepare()
points = []
l1s = []
tl2 = []
s_f = True
for l1 in line1.positions["l1"]:
sp = zip(spiral_s.positions['s1'], spiral_s.positions['s2'])
sp = sp if s_f else list(sp)[::-1]
s_f = not s_f
l1s += [(s1, s2, l1) for (s1, s2) in sp]
l2_f = True
for (t1, t2) in zip(spiral_t.positions['t1'], spiral_t.positions['t2']):
l2p = line2.positions['l2'] if l2_f else line2.positions['l2'][::-1]
l2pu = line2.bounds['l2'][1:len(line2.positions['l2'])+1]
l2pl = line2.bounds['l2'][0:len(line2.positions['l2'])]
if not l2_f:
l2pu, l2pl = l2pl[::-1], l2pu[::-1]
l2_f = not l2_f
tl2 += [(l2, l2u, l2l, t1, t2) for (l2, l2u, l2l) in
zip(l2p, l2pu, l2pl) if l2*l2 + t1*t1 <= 1]
t_f = True
for (s1, s2, l1) in l1s:
inner = tl2 if t_f else tl2[::-1]
t_f = not t_f
points += [(l2, l2u, l2l, t1, t2, s1, s2, l1)
for (l2, l2u, l2l, t1, t2) in inner if s1*s1 + l1*l1 <= 1]
l1s_original = l1s
l1s = [(s1, s2, l1) for (s1, s2, l1) in l1s if s1*s1 + l1*l1 <= 1]
expected = [{"l2":l2, "t1":t1, "t2":t2, "s1":s1, "s2":s2, "l1":l1}
for (l2, l2u, l2l, t1, t2, s1, s2, l1) in points]
expected_idx = []
t_f = (l1s_original.index(l1s[0])) % 2 == 0 # t_f is False
for d1 in range_(len(l1s)):
expected_idx += [[d1, d2] for d2 in (range_(len(tl2)) if t_f else
range_(len(tl2) - 1, -1, -1))]
t_f = not t_f
expected_l2_lower = [l2l for (l2, l2u, l2l, t1, t2, s1, s2, l1) in points]
expected_l2_upper = [l2u for (l2, l2u, l2l, t1, t2, s1, s2, l1) in points]
gpoints = list(g.iterator())
self.assertEqual(expected, [p.positions for p in gpoints])
self.assertEqual(expected_idx, [p.indexes for p in gpoints])
self.assertEqual(expected_l2_lower, [p.lower["l2"] for p in gpoints])
self.assertEqual(expected_l2_upper, [p.upper["l2"] for p in gpoints])
def test_simple_mask(self):
x = LineGenerator("x", "mm", -1.0, 1.0, 5, False)
y = LineGenerator("y", "mm", -1.0, 1.0, 5, False)
r = CircularROI([0, 0], 1)
e = ROIExcluder([r], ["x", "y"])
g = CompoundGenerator([y, x], [e], [])
g.prepare()
p = [(x / 2., y / 2.) for y in range_(-2, 3) for x in range_(-2, 3)]
expected_mask = [x * x + y * y <= 1 for (x, y) in p]
self.assertEqual(expected_mask, g.dimensions[0].mask.tolist())
def test_iterator(self):
x = LineGenerator("x", "mm", 1.0, 2.0, 5, False)
y = LineGenerator("y", "mm", 1.0, 2.0, 5, False)
g = CompoundGenerator([y, x], [], [])
g.prepare()
points = list(g.iterator())
expected_pos = [{"x":x/4., "y":y/4.}
for y in range_(4, 9) for x in range_(4, 9)]
self.assertEqual(expected_pos, [p.positions for p in points])
expected_indexes = [[y, x] for y in range_(0, 5) for x in range_(0, 5)]
self.assertEqual(expected_indexes, [p.indexes for p in points])
def iterator(self):
for i in range_(self.num):
point = Point()
for axis_index in range_(self.num_axes):
point.positions[self.name[axis_index]] = self._calc(i, axis_index)
point.lower[self.name[axis_index]] = self._calc(i - 0.5, axis_index)
point.upper[self.name[axis_index]] = self._calc(i + 0.5, axis_index)
point.indexes = [i]
yield point
def test_double_mask(self):
x = LineGenerator("x", "mm", -1.0, 1.0, 5, False)
y = LineGenerator("y", "mm", -1.0, 1.0, 5, False)
z = LineGenerator("z", "mm", -1.0, 1.0, 5, False)
r = CircularROI([0.1, 0.2], 1)
e1 = ROIExcluder([r], ["x", "y"])
e2 = ROIExcluder([r], ["y", "z"])
g = CompoundGenerator([z, y, x], [e1, e2], [])
g.prepare()
p = [(x / 2., y / 2., z / 2.) for z in range_(-2, 3)
for y in range_(-2, 3) for x in range_(-2, 3)]
m1 = [(x - 0.1)**2 + (y - 0.2)**2 <= 1 for (x, y, z) in p]
m2 = [(y - 0.1)**2 + (z - 0.2)**2 <= 1 for (x, y, z) in p]
expected_mask = [(b1 and b2) for (b1, b2) in zip(m1, m2)]
self.assertEqual(expected_mask, g.dimensions[0].mask.tolist())
def iterator(self):
for i in range_(self.num):
point = Point()
for axis_index in range_(self.num_axes):
axis_name = self.name[axis_index]
start = self.start[axis_index]
step = self.step[axis_index]
point.positions[axis_name] = start + i * step
point.lower[axis_name] = start + (i - 0.5) * step
point.upper[axis_name] = start + (i + 0.5) * step
point.indexes = [i]
yield point
def test_staticpointgen_in_alternating(self):
x = LineGenerator("x", "mm", 0, 1, 3, True)
y = LineGenerator("y", "cm", 2, 3, 4, False)
m = StaticPointGenerator(5)
r = CircularROI((0.5, 2.5), 0.4)
e = ROIExcluder([r], ["x", "y"])
g = CompoundGenerator([y, m, x], [e], [])
g.prepare()
expected_positions = []
x_positions = [0.0, 0.5, 1.0]
direction = 1
for yp in [2.0, 2 + 1. / 3, 2 + 2. / 3, 3.0]:
for mp in range_(5):
for xp in x_positions[::direction]:
if (xp - 0.5)**2 + (yp - 2.5)**2 <= 0.4**2:
expected_positions.append({"y": yp, "x": xp})
direction *= -1
positions = [point.positions for point in g.iterator()]
self.assertEqual(expected_positions, positions)
self.assertEqual(len(expected_positions), g.size)
self.assertEqual((len(expected_positions), ), g.shape)
self.assertEqual(["y", "x"], g.axes)
self.assertEqual({"y": "cm", "x": "mm"}, g.units)
self.assertEqual(1, len(g.dimensions))
def produce_points(self):
self.points = {}
self.points_lower = {}
self.points_upper = {}
for axis in range_(self.num_axes):
axis_name = self.name[axis]
start = self.start[axis]
stop = self.stop[axis]
d = stop - start
if self.num == 1:
self.points[axis_name] = np.array([start])
self.points_upper[axis_name] = np.array([start + 0.5 * d])
self.points_lower[axis_name] = np.array([start - 0.5 * d])
else:
n = self.num - 1.
s = d / n
upper_start = start + 0.5 * d / n
upper_stop = stop + 0.5 * d / n
lower_start = start - 0.5 * d / n
lower_stop = stop - 0.5 * d / n
self.points[axis_name] = np.linspace(
float(start), float(stop), self.num)
self.points_upper[axis_name] = np.linspace(
float(upper_start), float(upper_stop), self.num)
self.points_lower[axis_name] = np.linspace(
float(lower_start), float(lower_stop), self.num)
def test_simple_mask_alternating(self):
x = LineGenerator("x", "mm", -1.0, 1.0, 5, alternate=True)
y = LineGenerator("y", "mm", -1.0, 1.0, 5, alternate=True)
r = CircularROI([0.5, 0], 1)
e = ROIExcluder([r], ["x", "y"])
g = CompoundGenerator([y, x], [e], [])
g.prepare()
reverse = False
p = []
for y in range_(-2, 3):
if reverse:
p += [(x / 2., y / 2.) for x in range_(2, -3, -1)]
else:
p += [(x / 2., y / 2.) for x in range_(-2, 3)]
reverse = not reverse
expected_mask = [(x - 0.5)**2 + y**2 <= 1**2 for (x, y) in p]
self.assertEqual(expected_mask, g.dimensions[0].mask.tolist())
def point_gen():
for n in range_(10):
p = Point()
p.indexes = [n]
p.positions = {"x": n / 10.}
p.lower = {"x": (n - 0.5) / 10.}
p.upper = {"x": (n + 0.5) / 10.}
yield p
def __init__(self,
name,
units,
start,
stop,
num,
alternate_direction=False):
"""
Args:
name (str/list(str)): The scannable name(s) E.g. "x" or ["x", "y"]
units (str): The scannable units. E.g. "mm"
start (float/list(float)): The first position to be generated.
e.g. 1.0 or [1.0, 2.0]
stop (float or list(float)): The first position to be generated.
e.g. 5.0 or [5.0, 10.0]
num (int): The number of points to generate. E.g. 5
alternate_direction(bool): Specifier to reverse direction if
generator is nested
"""
self.name = to_list(name)
self.start = to_list(start)
self.stop = to_list(stop)
self.alternate_direction = alternate_direction
if len(self.name) != len(set(self.name)):
raise ValueError("Axis names cannot be duplicated; given %s" %
name)
if len(self.name) != len(self.start) or \
len(self.name) != len(self.stop):
raise ValueError("Dimensions of name, start and stop do not match")
self.num = num
self.num_axes = len(self.name)
self.step = []
if self.num < 2:
self.step = [0] * len(self.start)
else:
for axis in range_(len(self.start)):
self.step.append(
(self.stop[axis] - self.start[axis]) / (self.num - 1))
self.position_units = dict()
for dimension in self.name:
self.position_units[dimension] = units
self.index_dims = [self.num]
if len(self.name) > 1:
gen_name = "Line"
for axis_name in self.name[::-1]:
gen_name = axis_name + "_" + gen_name
self.index_names = [gen_name]
else:
self.index_names = self.name
self.axes = self.name # For GDA
def test_separate_indexes(self):
x1 = LineGenerator("x1", "mm", -1.0, 1.0, 5, False)
y1 = LineGenerator("y1", "mm", -1.0, 1.0, 5, False)
z1 = LineGenerator("z1", "mm", -1.0, 1.0, 5, False)
x2 = LineGenerator("x2", "mm", -1.0, 1.0, 5, False)
y2 = LineGenerator("y2", "mm", -1.0, 1.0, 5, False)
x3 = LineGenerator("x3", "mm", 0, 1.0, 5, False)
y3 = LineGenerator("y3", "mm", 0, 1.0, 5, False)
r = CircularROI([0, 0], 1)
e1 = ROIExcluder([r], ["x1", "y1"])
e2 = ROIExcluder([r], ["y1", "z1"])
e3 = ROIExcluder([r], ["x1", "y1"])
e4 = ROIExcluder([r], ["x2", "y2"])
e5 = ROIExcluder([r], ["x3", "y3"])
g = CompoundGenerator([x3, y3, y2, x2, z1, y1, x1],
[e1, e2, e3, e4, e5], [])
g.prepare()
p = [(x / 2., y / 2., z / 2.) for z in range_(-2, 3)
for y in range_(-2, 3) for x in range_(-2, 3)]
m1 = [x * x + y * y <= 1 for (x, y, z) in p]
m2 = [y * y + z * z <= 1 for (x, y, z) in p]
expected_mask = [(b1 and b2) for (b1, b2) in zip(m1, m2)]
self.assertEqual(expected_mask, g.dimensions[2].mask.tolist())
p = [(x / 2., y / 2.) for y in range_(-2, 3) for x in range_(-2, 3)]
expected_mask = [x * x + y * y <= 1 for (x, y) in p]
self.assertEqual(expected_mask, g.dimensions[1].mask.tolist())
p = [(x / 4., y / 4.) for y in range_(0, 5) for x in range_(0, 5)]
expected_mask = [x * x + y * y <= 1 for (x, y) in p]
self.assertEqual(expected_mask, g.dimensions[0].mask.tolist())
def test_triple_alternating_linked_gen(self):
tg = LineGenerator("t", "mm", 1, 5, 5)
zg = LineGenerator("z", "mm", -1, 3, 5, True)
yg = LineGenerator("y", "mm", 0, 4, 5, True)
xg = LineGenerator("x", "mm", 0, 4, 5, True)
r1 = RectangularROI([-1, -1], 5.5, 3.5)
r2 = RectangularROI([1, 0], 2.5, 2.5)
e1 = ROIExcluder([r1], ["z", "y"])
e2 = ROIExcluder([r2], ["x", "y"])
g = CompoundGenerator([tg, zg, yg, xg], [e1, e2], [])
g.prepare()
zf = True
yf = True
xf = True
expected = []
for t in range_(1, 6):
zr = range_(-1, 4) if zf else range_(3, -2, -1)
zf = not zf
for z in zr:
yr = range_(0, 5) if yf else range_(4, -1, -1)
yf = not yf
for y in yr:
xr = range_(0, 5) if xf else range_(4, -1, -1)
xf = not xf
for x in xr:
if z >= -1 and z < 4.5 and y >= 0 and y < 2.5 \
and x >= 1 and x < 3.5:
expected.append({"x":float(x), "y":float(y),
"z":float(z), "t":float(t)})
actual = [p.positions for p in g.iterator()]
self.assertEqual(len(expected), len(actual))
for e, a in zip(expected, actual):
self.assertEqual(e, a)
def test_alternating_complex(self):
tg = LineGenerator("t", "mm", 1, 5, 5)
zg = LineGenerator("z", "mm", 1, 5, 5, True)
yg = LineGenerator("y", "mm", 1, 5, 5, True)
xg = LineGenerator("x", "mm", 1, 5, 5, True)
r1 = RectangularROI([3., 3.], 2., 2.)
e1 = ROIExcluder([r1], ["y", "x"])
e2 = ROIExcluder([r1], ["z", "y"])
g = CompoundGenerator([tg, zg, yg, xg], [e1, e2], [])
g.debug = True
g.prepare()
points = [p.positions for p in list(g.iterator())]
expected = []
zf, yf, xf = True, True, True
for t in range_(1, 6):
r_1 = range_(1,6) if zf else range_(5, 0, -1)
zf = not zf
for z in r_1:
r_2 = range_(1,6) if yf else range_(5, 0, -1)
yf = not yf
for y in r_2:
r_3 = range_(1, 6) if xf else range_(5, 0, -1)
xf = not xf
for x in r_3:
expected.append(
{"t":float(t), "z":float(z),
"y":float(y), "x":float(x)})
expected = [p for p in expected if
(p["y"] >= 3 and p["y"] <= 5 and p["x"] >= 3 and p["x"] <= 5) and
(p["z"] >= 3 and p["z"] <= 5 and p["y"] >= 3 and p["y"] <= 5)]
self.assertEqual(expected, points)
def iterator(self):
for i in range_(self.num):
p = Point()
p.positions[self.names[0]], p.positions[self.names[1]] = self._calc(i)
p.lower[self.names[0]], p.lower[self.names[1]] = self._calc(i - 0.5)
p.upper[self.names[0]], p.upper[self.names[1]] = self._calc(i + 0.5)
p.indexes = [i]
yield p
def __init__(self, name, units, start, stop, num, alternate_direction=False):
"""
Args:
name (str/list(str)): The scannable name(s) E.g. "x" or ["x", "y"]
units (str): The scannable units. E.g. "mm"
start (float/list(float)): The first position to be generated.
e.g. 1.0 or [1.0, 2.0]
stop (float or list(float)): The first position to be generated.
e.g. 5.0 or [5.0, 10.0]
num (int): The number of points to generate. E.g. 5
alternate_direction(bool): Specifier to reverse direction if
generator is nested
"""
self.name = to_list(name)
self.start = to_list(start)
self.stop = to_list(stop)
self.alternate_direction = alternate_direction
self.points = None
self.points_lower = None
self.points_upper = None
self.units = units
if len(self.name) != len(set(self.name)):
raise ValueError("Axis names cannot be duplicated; given %s" %
name)
if len(self.name) != len(self.start) or \
len(self.name) != len(self.stop):
raise ValueError(
"Dimensions of name, start and stop do not match")
self.num = num
self.num_axes = len(self.name)
self.step = []
if self.num < 2:
self.step = [0]*len(self.start)
else:
for axis in range_(len(self.start)):
self.step.append(
(self.stop[axis] - self.start[axis])/(self.num - 1))
self.position_units = dict()
for dimension in self.name:
self.position_units[dimension] = units
self.index_dims = [self.num]
if len(self.name) > 1:
gen_name = "Line"
for axis_name in self.name[::-1]:
gen_name = axis_name + "_" + gen_name
self.index_names = [gen_name]
else:
self.index_names = self.name
self.axes = self.name # For GDA
def iterator(self):
for i in range_(self.num):
p = Point()
p.positions[self.names[0]], p.positions[self.names[1]] = self._calc(i)
p.lower[self.names[0]], p.lower[self.names[1]] = self._calc(i - 0.5)
p.upper[self.names[0]], p.upper[self.names[1]] = self._calc(i + 0.5)
p.indexes = [i]
yield p
def iterator(self):
"""
Iterator yielding generator positions at each scan point
Yields:
Point: The next point
"""
if not self._prepared:
raise ValueError("CompoundGenerator has not been prepared")
it = (self.get_point(n) for n in range_(self.size))
for p in it:
yield p
def test_alternating_with_region(self):
y = LineGenerator("y", "mm", 1, 5, 5, True)
x = LineGenerator("x", "mm", 1, 5, 5, True)
r1 = CircularROI([3, 3], 1.5)
e1 = ROIExcluder([r1], ["y", "x"])
g = CompoundGenerator([y, x], [e1], [])
g.prepare()
expected = []
x_f = True
for y in range_(1, 6):
r = range_(1, 6) if x_f else range(5, 0, -1)
x_f = not x_f
for x in r:
expected.append({"y":float(y), "x":float(x)})
expected = [p for p in expected if
((p["x"]-3)**2 + (p["y"]-3)**2 <= 1.5**2)]
expected_idx = [[xy] for xy in range_(len(expected))]
points = list(g.iterator())
self.assertEqual(expected, [p.positions for p in points])
self.assertEqual(expected_idx, [p.indexes for p in points])
self.assertEqual((len(expected),), g.shape)
def test_get_point(self):
x = LineGenerator("x", "mm", -1., 1, 5, False)
y = LineGenerator("y", "mm", -1., 1, 5, False)
z = LineGenerator("z", "mm", -1., 1, 5, False)
r = CircularROI([0., 0.], 1)
e = ROIExcluder([r], ["x", "y"])
g = CompoundGenerator([z, y, x], [e], [])
g.prepare()
points = [g.get_point(n) for n in range(0, g.size)]
pos = [p.positions for p in points]
idx = [p.indexes for p in points]
xy_expected = [(x/2., y/2.) for y in range_(-2, 3)
for x in range_(-2, 3)]
xy_expected = [(x, y) for (x, y) in xy_expected
if x*x + y*y <= 1]
expected = [{"x":x, "y":y, "z":z/2.} for z in range_(-2, 3)
for (x, y) in xy_expected]
self.assertEqual(expected, pos)
expected_idx = [[z, xy] for z in range_(5)
for xy in range_(len(xy_expected))]
self.assertEqual(expected_idx, idx)
def iterator(self):
for i in range_(0, self._end_point(self.radius) + 1):
p = Point()
p.indexes = [i]
i += 0.5 # Offset so lower bound of first point is not less than 0
p.positions[self.names[0]], p.positions[self.names[1]] = self._calc(i)
p.upper[self.names[0]], p.upper[self.names[1]] = self._calc(i + 0.5)
p.lower[self.names[0]], p.lower[self.names[1]] = self._calc(i - 0.5)
yield p
def iterator(self):
for i in range_(0, self._end_point(self.radius) + 1):
p = Point()
p.indexes = [i]
i += 0.5 # Offset so lower bound of first point is not less than 0
p.positions[self.names[0]], p.positions[self.names[1]] = self._calc(i)
p.upper[self.names[0]], p.upper[self.names[1]] = self._calc(i + 0.5)
p.lower[self.names[0]], p.lower[self.names[1]] = self._calc(i - 0.5)
yield p
def test_inner_alternating(self):
z = LineGenerator("z", "mm", 1, 5, 5)
y = LineGenerator("y", "mm", 1, 5, 5, alternate=True)
x = LineGenerator("x", "mm", 1, 5, 5, alternate=True)
r1 = CircularROI([3, 3], 1.5)
e1 = ROIExcluder([r1], ["x", "y"])
g = CompoundGenerator([z, y, x], [e1], [])
g.prepare()
expected = []
xy_expected = []
x_f = True
for y in range_(1, 6):
for x in (range_(1, 6) if x_f else range(5, 0, -1)):
if (x - 3)**2 + (y - 3)**2 <= 1.5**2:
xy_expected.append((x, y))
x_f = not x_f
xy_f = True
for z in range_(1, 6):
for (x, y) in (xy_expected if xy_f else xy_expected[::-1]):
expected.append({"x": float(x), "y": float(y), "z": float(z)})
xy_f = not xy_f
expected_idx = []
xy_f = True
for z in range_(0, 5):
xy_idx = range_(len(xy_expected)) if xy_f \
else range_(len(xy_expected)-1, -1, -1)
expected_idx += [[z, xy] for xy in xy_idx]
xy_f = not xy_f
points = list(g.iterator())
self.assertEqual(expected, [p.positions for p in points])
self.assertEqual(expected_idx, [p.indexes for p in points])
def _base_iterator(self):
"""
Iterator to generate points by nesting each generator in self.generators
Yields:
Point: Base points
"""
for point_num in range_(self.num):
point = Point()
for gen_index, points in enumerate(self.point_sets):
axis_period = self.periods[gen_index]
axis_length = len(points)
# Can't use index_dims in case they have been flattened
# by an excluder
point_index = \
(point_num / (axis_period / axis_length)) % axis_length
loop_number = point_num / axis_period
# Floor floats to ints for indexing
point_index = int(point_index)
loop_number = int(loop_number)
if self.alternate_direction[gen_index] and loop_number % 2:
point_index = (axis_length - 1) - point_index
reverse = True
else:
reverse = False
current_point = points[point_index]
# If innermost generator, use bounds
if gen_index == len(self.point_sets) - 1:
point.positions.update(current_point.positions)
if reverse: # Swap bounds if reversing
point.upper.update(current_point.lower)
point.lower.update(current_point.upper)
else:
point.upper.update(current_point.upper)
point.lower.update(current_point.lower)
else:
point.positions.update(current_point.positions)
point.upper.update(current_point.positions)
point.lower.update(current_point.positions)
point.indexes += current_point.indexes
logging.debug("Current point positions and indexes")
logging.debug([current_point.positions, current_point.indexes])
yield point
def _base_iterator(self):
"""
Iterator to generate points by nesting each generator in self.generators
Yields:
Point: Base points
"""
for point_num in range_(self.num):
point = Point()
for gen_index, points in enumerate(self.point_sets):
axis_period = self.periods[gen_index]
axis_length = len(points)
# Can't use index_dims in case they have been flattened
# by an excluder
point_index = \
(point_num / (axis_period / axis_length)) % axis_length
loop_number = point_num / axis_period
# Floor floats to ints for indexing
point_index = int(point_index)
loop_number = int(loop_number)
if self.alternate_direction[gen_index] and loop_number % 2:
point_index = (axis_length - 1) - point_index
reverse = True
else:
reverse = False
current_point = points[point_index]
# If innermost generator, use bounds
if gen_index == len(self.point_sets) - 1:
point.positions.update(current_point.positions)
if reverse: # Swap bounds if reversing
point.upper.update(current_point.lower)
point.lower.update(current_point.upper)
else:
point.upper.update(current_point.upper)
point.lower.update(current_point.lower)
else:
point.positions.update(current_point.positions)
point.upper.update(current_point.positions)
point.lower.update(current_point.positions)
point.indexes += current_point.indexes
logging.debug("Current point positions and indexes")
logging.debug([current_point.positions, current_point.indexes])
yield point
def test_alternating_simple(self):
y = LineGenerator("y", "mm", 1, 5, 5)
x = LineGenerator("x", "mm", 1, 5, 5, alternate=True)
g = CompoundGenerator([y, x], [], [])
g.prepare()
expected = []
expected_idx = []
expected_lower = []
expected_upper = []
for y in range_(1, 6):
x_f = y % 2 == 1
r = range_(1, 6) if x_f else range_(5, 0, -1)
for x in r:
expected.append({"y": float(y), "x": float(x)})
expected_idx.append([y - 1, x - 1])
expected_lower.append(x + (-0.5 if x_f else 0.5))
expected_upper.append(x + (0.5 if x_f else -0.5))
points = list(g.iterator())
self.assertEqual(expected, [p.positions for p in points])
self.assertEqual(expected_idx, [p.indexes for p in points])
self.assertEqual(expected_lower, [p.lower["x"] for p in points])
self.assertEqual(expected_upper, [p.upper["x"] for p in points])
def test_double_mask_spiral(self):
zgen = LineGenerator("z", "mm", 0.0, 4.0, 5)
spiral = SpiralGenerator(['x', 'y'], "mm", [0.0, 0.0], 3) #29 points
r1 = RectangularROI([-2, -2], 4, 3)
r2 = RectangularROI([-2, 0], 4, 3)
e1 = ROIExcluder([r1], ["y", "x"])
e2 = ROIExcluder([r2], ["y", "z"])
g = CompoundGenerator([zgen, spiral], [e1, e2], [])
g.prepare()
p = list(zip(spiral.positions['x'], spiral.positions['y']))
p = [(x, y, z) for z in range_(0, 5) for (x, y) in p]
expected = [x >= -2 and x <= 1 and y >= -2 and y <= 2
and z >= 0 and z <= 3 for (x, y, z) in p]
actual = g.dimensions[0].mask.tolist()
self.assertEqual(expected, actual)
def mask_points(self, points):
x = points[0]
y = points[1]
v1 = self.points[-1]
mask = np.full(len(x), False, dtype=bool)
for i in range_(0, len(self.points)):
v2 = self.points[i]
if (v2[1] == v1[1]):
# skip horizontal edges
v1 = v2
continue
vmask = ((y < v2[1]) & (y >= v1[1])) | ((y < v1[1]) & (y >= v2[1]))
t = (y - v2[1]) / (v2[1] - v1[1])
vmask &= x < v1[0] + t * (v2[0] - v1[0])
mask ^= vmask
v1 = v2
return mask
def test_intermediate_staticpointgen(self):
x = LineGenerator("x", "mm", 0, 1, 3, False)
y = LineGenerator("y", "cm", 2, 3, 4, False)
m = StaticPointGenerator(5)
g = CompoundGenerator([y, m, x], [], [])
g.prepare()
expected_positions = []
for yp in [2.0, 2 + 1. / 3, 2 + 2. / 3, 3.0]:
for mp in range_(5):
for xp in [0.0, 0.5, 1.0]:
expected_positions.append({"y": yp, "x": xp})
positions = [point.positions for point in g.iterator()]
self.assertEqual(expected_positions, positions)
self.assertEqual(60, g.size)
self.assertEqual((4, 5, 3), g.shape)
self.assertEqual(["y", "x"], g.axes)
self.assertEqual({"y": "cm", "x": "mm"}, g.units)
self.assertEqual(3, len(g.dimensions))
def iterator(self):
for i in range_(self.num):
point = Point()
for axis, coordinate in enumerate(self.points[i]):
point.positions[self.name[axis]] = coordinate
if self.upper_bounds is None:
upper = self._calculate_upper_bound(i, axis, coordinate)
else:
upper = self.upper_bounds[i][axis]
point.upper[self.name[axis]] = upper
if self.lower_bounds is None:
lower = self._calculate_lower_bound(i, axis, coordinate)
else:
lower = self.lower_bounds[i][axis]
point.lower[self.name[axis]] = lower
point.indexes = [i]
yield point
def iterator(self):
for i in range_(self.num):
point = Point()
for axis, coordinate in enumerate(self.points[i]):
point.positions[self.name[axis]] = coordinate
if self.upper_bounds is None:
upper = self._calculate_upper_bound(i, axis, coordinate)
else:
upper = self.upper_bounds[i][axis]
point.upper[self.name[axis]] = upper
if self.lower_bounds is None:
lower = self._calculate_lower_bound(i, axis, coordinate)
else:
lower = self.lower_bounds[i][axis]
point.lower[self.name[axis]] = lower
point.indexes = [i]
yield point
def iterator(self):
it = (self.get_point(n) for n in range_(self.num))
for m in self.mutators:
it = m.mutate(it)
for p in it:
yield p
