class JLineGenerator2D(JavaIteratorWrapper):
"""
Create a 2D LineGenerator and wrap the points into java Point objects
"""
def __init__(self, names, units, start, stop, num_points, alternate_direction=False):
super(JLineGenerator2D, self).__init__()
start = start.tolist() # Convert from array to list
stop = stop.tolist()
self.names = names
self.generator = LineGenerator(names, units, start, stop, num_points, alternate_direction)
logging.debug(self.generator.to_dict())
def _iterator(self):
for point in self.generator.iterator():
index = point.indexes[0]
x_name = self.names[0]
y_name = self.names[1]
x_position = point.positions[x_name]
y_position = point.positions[y_name]
java_point = Point(x_name, index, x_position,
y_name, index, y_position, False)
# Set is2D=False
yield java_point
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_configure(self):
xs = LineGenerator("x", "mm", 0.0, 0.5, 3000, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2000)
generator = CompoundGenerator([ys, xs], [], [], 0.1)
generator.prepare()
completed_steps = 0
steps_to_do = 2000 * 3000
# We wait to be armed, so set this here
self.set_attributes(self.child, acquiring=True)
# This is what the detector does when exposure and acquirePeriod are
# both set to 0.1
self.set_attributes(self.child, exposure=0.1, acquirePeriod=0.105)
self.o.configure(self.context,
completed_steps,
steps_to_do, {},
generator=generator)
assert self.child.handled_requests.mock_calls == [
call.put('exposure', 0.1),
call.put('acquirePeriod', 0.1),
call.put('arrayCallbacks', True),
call.put('arrayCounter', 0),
# duration - readout - fudge_factor - crystal offset
call.put('exposure', pytest.approx(0.1 - 0.005 - 0.0014 - 5e-6)),
call.put('imageMode', 'Multiple'),
call.put('numImages', 6000000),
call.put('acquirePeriod', 0.1 - 5e-6),
call.post('start')
]
def test_load_more_positions(self):
task = MagicMock()
current_index = 1
# Haven't done point 4 or 5 yet
self.o.end_index = 4
self.o.steps_up_to = 6
xs = LineGenerator("x", "mm", 0.0, 0.5, 3, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2)
self.o.generator = CompoundGenerator([ys, xs], [], [])
self.o.generator.prepare()
self.o.load_more_positions(current_index, task)
expected_xml = """<?xml version="1.0" ?>
<pos_layout>
<dimensions>
<dimension name="d0" />
<dimension name="d1" />
<dimension name="FilePluginClose" />
</dimensions>
<positions>
<position FilePluginClose="0" d0="1" d1="1" />
<position FilePluginClose="1" d0="1" d1="0" />
</positions>
</pos_layout>""".replace("\n", "")
task.put.assert_called_once_with(self.child["xml"], expected_xml)
self.assertEqual(self.o.end_index, 6)
def test_validate(self):
line1 = LineGenerator('y', 'mm', 0, 2, 3)
line2 = LineGenerator('x', 'mm', 0, 2, 2)
compound = CompoundGenerator([line1, line2], [], [])
actual = self.b.validate(generator=compound, axesToMove=['x'])
self.assertEqual(actual["generator"], compound)
self.assertEqual(actual["axesToMove"], ('x', ))
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_array_positions_from_line_non_matching_bounds(self):
genone = LineGenerator("x", "mm", 1.0, 9.0, 5)
gentwo = LineGenerator("x", "mm", 20, 24, 5)
g = ConcatGenerator([genone, gentwo])
g.prepare_positions()
with self.assertRaises(AssertionError):
g.prepare_bounds()
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 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_configure_with_breakpoints(self):
xs = LineGenerator("x", "mm", 0.0, 0.5, 3, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2)
generator = CompoundGenerator([ys, xs], [], [], 0.1)
generator.prepare()
completed_steps = 0
steps_to_do = 3
info = ExposureDeadtimeInfo(0.01, 1000, 0.0)
part_info = dict(anyname=[info])
self.set_attributes(self.child, triggerMode="Internal")
self.o.on_configure(
self.context,
completed_steps,
steps_to_do,
part_info,
generator,
fileDir="/tmp",
breakpoints=[3, 3],
exposure=info.calculate_exposure(generator.duration),
)
assert self.child.handled_requests.mock_calls == [
call.put("arrayCallbacks", True),
call.put("arrayCounter", 0),
call.put("exposure", 0.1 - 0.01 - 0.0001),
call.put("imageMode", "Multiple"),
call.put("numImages", 3),
call.put("acquirePeriod", 0.1 - 0.0001),
]
assert not self.o.is_hardware_triggered
def test_validate(self):
params = MagicMock()
xs = LineGenerator("x", "mm", 0.0, 0.5, 3, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2)
params.generator = CompoundGenerator([ys, xs], [], [], 0.1)
params.generator.prepare()
self.o.validate(ANY, ANY, params)
def test_minimum_profile(self):
# tests that a turnaround that is >= minturnaround
# is reduced to a start and end point only
# this supports keeping the turnaround really short where
# the motors are fast e.g. j15
axes_to_scan = ["x", "y"]
duration = 0.005
self.set_motor_attributes(
0.0,
0.0,
"mm",
x_acceleration=100.0,
x_velocity=2.0,
y_acceleration=100.0,
y_velocity=2.0,
)
steps_to_do = 1 * len(axes_to_scan)
xs = LineGenerator("x", "mm", 0, 0.0001, 2)
ys = LineGenerator("y", "mm", 0, 0, 2)
generator = CompoundGenerator([ys, xs], [], [],
duration,
continuous=False)
generator.prepare()
m = [MinTurnaroundInfo(0.002, 0.002)]
self.o.on_configure(self.context, 0, steps_to_do, {"part": m},
generator, axes_to_scan)
action, func, args = self.child.handled_requests.mock_calls[-1]
assert args["a"] == pytest.approx(
[0, 0, 0, 0.0001, 0.0001, 0.0001, 0.0001])
assert args["b"] == pytest.approx([0, 0, 0, 0, 0, 0, 0])
assert args["timeArray"] == pytest.approx(
[2000, 2500, 2500, 2000, 2500, 2500, 2000])
# now make the acceleration slower so that the turnaround takes
# longer than the minimum interval
self.set_motor_attributes(
0.0,
0.0,
"mm",
x_acceleration=10.0,
x_velocity=2.0,
y_acceleration=100.0,
y_velocity=2.0,
)
self.o.on_configure(self.context, 0, steps_to_do, {"part": m},
generator, axes_to_scan)
# this generates one mid point between the 1st upper and 2nd lower
# bounds. Note that the point is not exactly central due to time
# quantization
action, func, args = self.child.handled_requests.mock_calls[-1]
assert args["a"] == pytest.approx(
[0, 0, 0, 5.0e-05, 0.0001, 0.0001, 0.0001, 0.0001])
assert args["b"] == pytest.approx([0, 0, 0, 0, 0, 0, 0, 0])
assert args["timeArray"] == pytest.approx(
[2000, 2500, 2500, 6000, 6000, 2500, 2500, 2000])
def test_post_run_armed_with_hardware_trigger_and_breakpoints(self):
xs = LineGenerator("x", "mm", 0.0, 0.5, 100, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 5)
generator = CompoundGenerator([ys, xs], [], [], 0.1)
generator.prepare()
info = ExposureDeadtimeInfo(0.01, 1000, 0.0)
part_info = dict(anyname=[info])
breakpoints = [100, 400]
# This would have been done by initial configure
self.o.is_hardware_triggered = True
self.o.done_when_reaches = 100
self.o.on_post_run_armed(self.context, 100, 400, part_info, generator,
breakpoints)
assert self.child.handled_requests.mock_calls == [
call.put("arrayCallbacks", True),
call.put("arrayCounter", 100),
call.put("imageMode", "Multiple"),
call.put("numImages", 400),
call.put("acquirePeriod", 0.1 - 0.0001),
call.post("start"),
call.when_value_matches("acquiring", True, None),
]
assert self.o.done_when_reaches == 500
def long_configure(self, row_gate=False):
# test 4,000,000 points configure - used to check performance
if row_gate:
infos = [
MotionTriggerInfo(MotionTrigger.ROW_GATE),
]
else:
infos = None
self.set_motor_attributes(
0,
0,
"mm",
x_velocity=300,
y_velocity=300,
x_acceleration=30,
y_acceleration=30,
)
axes_to_scan = ["x", "y"]
x_steps, y_steps = 4000, 1000
steps_to_do = x_steps * y_steps
xs = LineGenerator("x", "mm", 0.0, 10, x_steps, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 8, y_steps)
generator = CompoundGenerator([ys, xs], [], [], 0.0001)
generator.prepare()
start = datetime.now()
self.o.on_configure(self.context, 0, steps_to_do, {"part": infos},
generator, axes_to_scan)
elapsed = datetime.now() - start
# todo goal was sub 1 second but we achieved sub 3 secs
assert elapsed.total_seconds() < 3.5
def test_configure_software_trigger_succeeds(self):
xs = LineGenerator("x", "mm", 0.0, 0.5, 3, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2)
duration = 0.1
generator = CompoundGenerator([ys, xs], [], [], duration)
generator.prepare()
completed_steps = 0
steps_to_do = 6
# We wait to be armed, so set this here
self.set_attributes(self.child,
acquiring=True,
triggerOffCondition="Always On")
self.o.on_configure(self.context,
completed_steps,
steps_to_do, {},
generator,
fileDir="/tmp")
# We expect only these calls (no arming in software trigger mode)
assert self.child.handled_requests.mock_calls == [
call.put("arrayCallbacks", True),
call.put("arrayCounter", 0),
call.put("imageMode", "Multiple"),
call.put("numImages", 6),
call.put("postCount", 1000),
]
def test_configure_with_hardware_start_trigger_succeeds(self):
xs = LineGenerator("x", "mm", 0.0, 0.5, 3, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2)
generator = CompoundGenerator([ys, xs], [], [], 0.1)
generator.prepare()
completed_steps = 0
steps_to_do = 6
# We are not gated
self.o.gated_trigger = False
# We want to be armed and in a hardware trigger mode
self.set_attributes(self.child,
acquiring=True,
triggerMode="Rising Edge")
self.o.on_configure(self.context,
completed_steps,
steps_to_do, {},
generator,
fileDir="/tmp")
assert self.child.handled_requests.mock_calls == [
call.put("arrayCallbacks", True),
call.put("arrayCounter", 0),
call.put("imageMode", "Multiple"),
call.put("numImages", 6),
call.put("postCount", 999),
call.post("start"),
call.when_value_matches("acquiring", True, None),
]
def test_configure_continuous(self):
xs = LineGenerator("x", "mm", 0.0, 0.3, 4, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2)
generator = CompoundGenerator([ys, xs], [], [], 1.0)
self.set_motor_attributes()
axes_to_move = ["x", "y"]
seq_rows = self.get_sequencer_rows(generator, axes_to_move)
# Triggers
GT = Trigger.POSA_GT
IT = Trigger.IMMEDIATE
LT = Trigger.POSA_LT
# Half a frame
hf = 62500000
# Half how long to be blind for
hb = 22500000
expected = SequencerRows()
expected.add_seq_entry(count=1,
trigger=LT,
position=50,
half_duration=hf,
live=1,
dead=0)
expected.add_seq_entry(3, IT, 0, hf, 1, 0)
expected.add_seq_entry(1, IT, 0, hb, 0, 1)
expected.add_seq_entry(1, GT, -350, hf, 1, 0)
expected.add_seq_entry(3, IT, 0, hf, 1, 0)
expected.add_seq_entry(1, IT, 0, MIN_PULSE, 0, 1)
expected.add_seq_entry(0, IT, 0, MIN_PULSE, 0, 0)
assert seq_rows.as_tuples() == expected.as_tuples()
def grid_check():
x = LineGenerator("x", "mm", 0.0, 4.0, 5, alternate=True)
y = LineGenerator("y", "mm", 0.0, 3.0, 4)
gen = CompoundGenerator([y, x], [], [])
plot_generator(gen)
def grid_fly(flyer, y, ystart, ystop, ynum, x, xstart, xstop, xnum):
generator = CompoundGenerator(
generators=[
LineGenerator(y.name, "mm", ystart, ystop, ynum),
LineGenerator(x.name, "mm", xstart, xstop, xnum),
],
duration=0.1,
)
mapping.configure(dict(generator=generator))
md = dict(
hints=dict(
gridding="rectilinear",
dimensions=[([y.name], "primary"), ([x.name], "primary")],
),
shape=(ynum, xnum),
extents=([ystart, ystop], [xstart, xstop]),
)
uid = yield from bps.open_run(md)
yield from bps.kickoff(flyer, wait=True)
yield from bps.collect(flyer, stream=True)
yield from bps.checkpoint()
yield from bps.complete(flyer, group="flyer")
for _ in range(int(ynum * xnum * 0.1)):
yield from bps.sleep(1)
yield from bps.collect(flyer, stream=True)
yield from bps.checkpoint()
yield from bps.wait(group="flyer")
yield from bps.collect(flyer, stream=True)
yield from bps.close_run()
return uid
def test_validate(self):
line1 = LineGenerator('y', 'mm', 0, 2, 3)
line2 = LineGenerator('x', 'mm', 0, 2, 2)
compound = CompoundGenerator([line1, line2], [], [])
actual = self.b.validate(generator=compound, axesToMove=['x'])
assert actual["generator"].to_dict() == compound.to_dict()
assert actual["axesToMove"] == ['x']
def test_configure(self):
xs = LineGenerator("x", "mm", 0.0, 0.5, 3000, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2000)
generator = CompoundGenerator([ys, xs], [], [], 0.1)
generator.prepare()
completed_steps = 0
steps_to_do = 2000 * 3000
# We wait to be armed, so set this here
self.set_attributes(self.child, acquiring=True, fanStateReady=1)
self.o.on_configure(
self.context,
completed_steps,
steps_to_do,
{},
generator=generator,
fileDir="/tmp",
)
assert self.child.handled_requests.mock_calls == [
call.put("arrayCallbacks", True),
call.put("arrayCounter", 0),
call.put("imageMode", "Multiple"),
call.put("numImages", 6000000),
call.put("numImagesPerSeries", 1),
call.post("start"),
]
def prepare_half_run(self, duration=0.01, exception=0):
line1 = LineGenerator('y', 'mm', 0, 2, 3)
line2 = LineGenerator('x', 'mm', 0, 2, 2)
compound = CompoundGenerator([line1, line2], [], [], duration)
self.b.configure(generator=compound,
axesToMove=['x'],
exceptionStep=exception)
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_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 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_init(self):
genone = LineGenerator("x", "mm", 1.0, 9.0, 5)
gentwo = LineGenerator("x", "mm", 13, 20, 5)
g = ConcatGenerator([genone, gentwo])
self.assertEqual(["x"], g.axes)
self.assertEqual(dict(x="mm"), g.axis_units())
self.assertEqual(10, g.size)
def test_configure_and_run_prepare_components(self, buffer_class):
buffer_instance = buffer_class.return_value
buffer_instance.run.return_value = []
xs = LineGenerator("x", "mm", 0.0, 0.3, 4, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2)
generator = CompoundGenerator([ys, xs], [], [], 1.0)
generator.prepare()
completed_steps = 0
steps_to_do = generator.size
self.set_motor_attributes()
axes_to_move = ["x", "y"]
self.o.on_configure(self.context, completed_steps, steps_to_do, {},
generator, axes_to_move)
assert self.o.generator is generator
assert self.o.loaded_up_to == completed_steps
assert self.o.scan_up_to == completed_steps + steps_to_do
# Other unit tests check that the sequencer rows used here are correct
buffer_instance.configure.assert_called_once()
self.gate_part.enable_set.assert_not_called()
buffer_instance.run.assert_not_called()
# The SRGate should only be enabled by on_pre_run() here.
self.o.on_pre_run(self.context)
self.o.on_run(self.context)
self.gate_part.enable_set.assert_called_once()
buffer_instance.run.assert_called_once()
def test_configure(self):
task = MagicMock()
params = MagicMock()
xs = LineGenerator("x", "mm", 0.0, 0.5, 3, alternate=True)
ys = LineGenerator("y", "mm", 0.0, 0.1, 2)
params.generator = CompoundGenerator([ys, xs], [], [])
params.generator.prepare()
completed_steps = 2
steps_to_do = 4
part_info = ANY
self.o.configure(task, completed_steps, steps_to_do, part_info, params)
self.assertEqual(
task.post_async.call_args_list,
[call(self.child["delete"]),
call(self.child["start"])])
task.put_many_async.assert_called_once_with(
self.child, dict(enableCallbacks=True, idStart=3))
expected_xml = """<?xml version="1.0" ?>
<pos_layout>
<dimensions>
<dimension name="d0" />
<dimension name="d1" />
<dimension name="FilePluginClose" />
</dimensions>
<positions>
<position FilePluginClose="0" d0="0" d1="2" />
<position FilePluginClose="0" d0="1" d1="2" />
<position FilePluginClose="0" d0="1" d1="1" />
<position FilePluginClose="1" d0="1" d1="0" />
</positions>
</pos_layout>""".replace("\n", "")
task.put.assert_called_once_with(self.child["xml"], expected_xml)
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 test_excluder_spread_axes(self):
sp = SpiralGenerator(["s1", "s2"], ["mm", "mm"], centre=[0, 0], radius=1, scale=0.5, alternate=True)
y = LineGenerator("y", "mm", 0, 1, 3, True)
z = LineGenerator("z", "mm", -2, 3, 6, True)
e = ROIExcluder([CircularROI([0., 0.], 1.0)], ["s1", "z"])
g = CompoundGenerator([z, y, sp], [e], [])
g.prepare()
s1_pos, s2_pos = sp.positions["s1"], sp.positions["s2"]
s1_pos = np.tile(np.append(s1_pos, s1_pos[::-1]), 9)
s2_pos = np.tile(np.append(s2_pos, s2_pos[::-1]), 9)
y_pos = np.tile(np.repeat(np.array([0, 0.5, 1.0, 1.0, 0.5, 0]), sp.size), 3)
z_pos = np.repeat(np.array([-2, -1, 0, 1, 2, 3]), sp.size * 3)
mask_func = lambda ps1, pz: ps1**2 + pz**2 <= 1
mask = mask_func(s1_pos, z_pos)
expected_s1 = s1_pos[mask]
expected_s2 = s2_pos[mask]
expected_y = y_pos[mask]
expected_z = z_pos[mask]
expected_positions = [{'s1':ps1, 's2':ps2, 'y':py, 'z':pz}
for (ps1, ps2, py, pz) in zip(expected_s1, expected_s2, expected_y, expected_z)]
positions = [point.positions for point in list(g.iterator())]
self.assertEqual(positions, expected_positions)
def __init__(self, names, units, start, stop, num_points, alternate_direction=False):
super(JLineGenerator2D, self).__init__()
start = start.tolist() # Convert from array to list
stop = stop.tolist()
self.names = names
self.generator = LineGenerator(names, units, start, stop, num_points, alternate_direction)
logging.debug(self.generator.to_dict())
class JLineGenerator1D(JavaIteratorWrapper):
"""
Create a 1D LineGenerator and wrap the points into java Scalar objects
"""
def __init__(self, name, units, start, stop, num_points, alternate_direction=False):
super(JLineGenerator1D, self).__init__()
self.name = name
self.generator = LineGenerator(name, units, start, stop, num_points, alternate_direction)
logging.debug(self.generator.to_dict())
def _iterator(self):
for point in self.generator.iterator():
index = point.indexes[0]
position = point.positions[self.name]
java_point = Scalar(self.name, index, position)
yield java_point
class LineGeneratorTest(ScanPointGeneratorTest):
def setUp(self):
self.g = LineGenerator("x", "mm", 1, 0.1, 5)
def test_init(self):
self.assertEqual(self.g.position_units, dict(x="mm"))
self.assertEqual(self.g.index_dims, [5])
self.assertEqual(self.g.index_names, ["x"])
def test_iterator(self):
positions = [1.0, 1.1, 1.2, 1.3, 1.4]
lower = [0.95, 1.05, 1.15, 1.25, 1.35]
upper = [1.05, 1.15, 1.25, 1.35, 1.45]
indexes = [0, 1, 2, 3, 4]
for i, p in enumerate(self.g.iterator()):
self.assertEqual(p.positions, dict(x=positions[i]))
self.assertEqual(p.lower, dict(x=lower[i]))
self.assertEqual(p.upper, dict(x=upper[i]))
self.assertEqual(p.indexes, [indexes[i]])
self.assertEqual(i, 4)
def setUp(self):
self.g = LineGenerator("x", "mm", 1, 0.1, 5)
def __init__(self, name, units, start, stop, num_points, alternate_direction=False):
super(JLineGenerator1D, self).__init__()
self.name = name
self.generator = LineGenerator(name, units, start, stop, num_points, alternate_direction)
logging.debug(self.generator.to_dict())
