def test_move_update(self):
child = simulated.Stage("stage", "test", axes=["z"])
# Slow speed to give some chance of the move update to work
child.speed.value = {"z": 100e-6}
stage = AntiBacklashActuator("absact", "abs", {"orig": child},
backlash={"z": 100e-6})
self.called = 0
orig_pos = stage.position.value
stage.position.subscribe(self._on_position)
for i in range(10):
if i % 2:
d = 1
else:
d = -1
dist = d * (i + 1) * 10e-6
f = stage.moveRel({"z": dist}, update=True)
time.sleep(0.05) # 50 ms for 'user update'
f = stage.moveAbs(orig_pos, update=True)
f.result()
# If there is an antibacklash for each move against backlash, we should
# see ~ 16 moves. If only an antibacklash at the last move
# (or integrated in last move), we should see 11 or 12 moves.
self.assertLessEqual(self.called, 12)
test.assert_pos_almost_equal(child.position.value, orig_pos)
stage.terminate()
def test_move_rel(self):
# Test relative moves
self.dev.moveAbs({
'x': 0,
'y': 0,
'z': 0,
'rx': 0,
'ry': 0,
'rz': 0
}).result()
old_pos = self.dev.position.value
shift = {'x': 0.01, 'y': -0.001, 'ry': -0.0003, 'rz': 0}
self.dev.moveRel(shift).result()
new_pos = self.dev.position.value
test.assert_pos_almost_equal(smaract.add_coord(old_pos, shift),
new_pos, **COMP_ARGS)
# Test several relative moves and ensure they are queued up.
old_pos = self.dev.position.value
shift = {
'z': -0.000001,
'rx': 0.00001,
'ry': -0.000001,
'rz': -0.00001
}
self.dev.moveRel(shift)
self.dev.moveRel(shift)
self.dev.moveRel(shift).result()
new_pos = smaract.add_coord(
smaract.add_coord(smaract.add_coord(old_pos, shift), shift), shift)
test.assert_pos_almost_equal(self.dev.position.value, new_pos,
**COMP_ARGS)
def test_auto_update_function(self):
self.dev.moveAbs({"x": 0.0, "y": 0.0, "z": 0.0}).result()
pos_before_move = self.dev.position.value
rel_move = {"z": 5e-6}
expected_pos = pos_before_move.copy()
expected_pos["z"] += rel_move["z"]
self.dev.moveRel(rel_move).result()
# the position updater function is called every 1 sec, wait a bit more.
time.sleep(2)
pos_after_move = self.dev.position.value
test.assert_pos_almost_equal(expected_pos, pos_after_move, **COMP_ARGS)
def test_position_abs(self):
"""
Test moving to an absolute position.
"""
exp_pos = self.dev.position.value.copy()
for pos in (0, 0.1, 0.15, -0.1, 0):
new_pos = {'x': pos}
f = self.dev.moveAbs(new_pos)
f.result()
exp_pos["x"] = pos
test.assert_pos_almost_equal(self.dev.position.value, exp_pos, **COMP_ARGS)
def test_reference_and_deactivate_move(self):
# Set a deactive position and check to be sure that the controller moves to this location
# after a reference move
de_pos = {'x': 0, 'y': -1.2e-4, 'z': 0}
self.dev.updateMetadata({model.MD_FAV_POS_DEACTIVE: de_pos})
f = self.dev.reference(set(self.dev.axes.keys()))
f.result()
test.assert_pos_almost_equal(self.dev.position.value, de_pos,
**COMP_ARGS)
def test_pivot_set(self):
# Test setting the pivot to some value through metadata
old_pos = self.dev.position.value
new_pivot = {'x': 0.05, 'y': 0.05, 'z': 0.01}
self.dev.updateMetadata({model.MD_PIVOT_POS: new_pivot})
test.assert_pos_almost_equal(old_pos, self.dev.position.value, **COMP_ARGS)
old_pos = self.dev.position.value
new_pivot = {'x': 0.01, 'y':-0.05, 'z': 0.01}
self.dev.updateMetadata({model.MD_PIVOT_POS: new_pivot})
test.assert_pos_almost_equal(old_pos, self.dev.position.value, **COMP_ARGS)
def test_moveAbs(self):
# It's optional
if not hasattr(self.dev, "moveAbs"):
self.skipTest("Actuator doesn't support absolute move")
move = {}
# move to the centre
for axis in self.dev.axes:
rng = self.dev.axes[axis].range
move[axis] = (rng[0] + rng[1]) / 2
f = self.dev.moveAbs(move)
f.result() # wait
test.assert_pos_almost_equal(move, self.dev.position.value, atol=1e-7)
def test_offset(self):
# Start near the origin
self.dev.moveAbs({'x': 0.01}).result()
logging.info("POSITION = %s", self.dev.position.value)
# Bad offset
with self.assertRaises(ValueError):
self.dev.updateMetadata({model.MD_POS_COR: 5})
# Test offset #1
old_pos = self.dev.position.value
offset_1 = {'x': 0.05}
self.dev.updateMetadata({model.MD_POS_COR: offset_1})
test.assert_pos_almost_equal(subtract_coord(old_pos, offset_1), self.dev.position.value, **COMP_ARGS)
# Test offset #2
old_pos = self._getRealPosition()
offset_2 = {'x':-0.05}
self.dev.updateMetadata({model.MD_POS_COR: offset_2})
exp_pos = subtract_coord(old_pos, offset_2)
test.assert_pos_almost_equal(exp_pos, self.dev.position.value, **COMP_ARGS)
# now move to the origin
new_pos = {'x': 0}
f = self.dev.moveAbs(new_pos)
f.result()
exp_pos = self.dev.position.value.copy()
exp_pos["x"] = 0
test.assert_pos_almost_equal(exp_pos, self.dev.position.value, **COMP_ARGS)
exp_real = self.dev.position.value.copy()
exp_real.update(offset_2)
test.assert_pos_almost_equal(exp_real, self._getRealPosition(), **COMP_ARGS)
# Remove the offset
self.dev.updateMetadata({model.MD_POS_COR: {'x': 0}})
def test_smaract_stage_fallback_movement(self):
"""
Test behaviour of smaract 5dof stage when the linear axes are near the maximum range
"""
# 1. Move to imaging position
cryoSwitchSamplePosition(IMAGING).result()
# 2. Move the stage linear axes to their max range + move rx from 0
cryoSwitchAlignPosition(LOADING).result()
self.stage.moveAbs({'x': self.stage.axes['x'].range[1], 'y': self.stage.axes['y'].range[1], 'z': self.stage.axes['z'].range[1], 'rx': 0.15}).result()
# 3. Move to loading where the ordered submoves would start from rx/rx, resulting in an invalid move
# exception if it's not handled
cryoSwitchSamplePosition(LOADING).result()
test.assert_pos_almost_equal(self.stage.position.value, self.stage_deactive,
atol=ATOL_LINEAR_POS)
def test_position_rel(self):
"""
Test moving to a relative position.
"""
# Start at the origin to prevent hitting the ends
self.dev.moveAbs({'x': 0.3}).result()
# Test another relative move
for shift in (0, 0.12, -0.12):
new_shift = {'x': shift}
old_pos = self.dev.position.value
f = self.dev.moveRel(new_shift)
f.result()
test.assert_pos_almost_equal(add_coord(old_pos, new_shift), self.dev.position.value, **COMP_ARGS)
def test_moveRel(self):
prev_pos = self.dev.position.value
move = {}
# move by 1%
for axis in self.dev.axes:
move[axis] = self.dev.axes[axis].range[1] * 0.01
expected_pos = {}
for axis in self.dev.axes:
expected_pos[axis] = prev_pos[axis] + move[axis]
f = self.dev.moveRel(move)
f.result() # wait
test.assert_pos_almost_equal(expected_pos, self.dev.position.value, atol=1e-7)
def test_reference_and_deactivate_move(self):
# Set a deactive position and check to be sure that the controller moves to this location
# after a reference move
de_pos = {'x': 3.5801e-4, 'y': 0, 'z': 1e-3, 'rx': -1.2e-6, 'rz': 0.0}
self.dev.updateMetadata({model.MD_FAV_POS_DEACTIVE: de_pos})
f = self.dev.reference()
f.result()
for a, i in self.dev.referenced.value.items():
self.assertTrue(i)
test.assert_pos_almost_equal(self.dev.position.value, de_pos,
**COMP_ARGS)
def test_pivot_set(self):
# Check that the pivot position is available from the beginning
old_pivot = self.dev.getMetadata()[model.MD_PIVOT_POS]
try:
# Test setting the pivot to some value through metadata
old_pos = self.dev.position.value
new_pivot = {'x': 0.05, 'y': 0.05, 'z': 0.01}
self.dev.updateMetadata({model.MD_PIVOT_POS: new_pivot})
test.assert_pos_almost_equal(old_pos, self.dev.position.value,
**COMP_ARGS)
self.dev.moveRelSync({"x": 0}) # WARNING: this can cause a move!
test.assert_pos_almost_equal(old_pos, self.dev.position.value,
**COMP_ARGS)
old_pos = self.dev.position.value
new_pivot = {'x': 0.01, 'y': -0.05, 'z': 0.01}
self.dev.updateMetadata({model.MD_PIVOT_POS: new_pivot})
test.assert_pos_almost_equal(old_pos, self.dev.position.value,
**COMP_ARGS)
self.dev.moveRelSync({"x": 0}) # WARNING: this can cause a move!
test.assert_pos_almost_equal(old_pos, self.dev.position.value,
**COMP_ARGS)
finally:
self.dev.updateMetadata({model.MD_PIVOT_POS: old_pivot})
self.dev.moveRelSync({"x": 0})
def test_move_abs(self):
pos1 = {'x': 0, 'y': 0, 'z': 0, 'rx': 0.001, 'rz': 0.001}
pos2 = {'x': 0, 'y': 0, 'z': 0, 'rx': 0, 'rz': 0}
pos3 = {
'x': 3.5218e-4,
'y': 1.785e-5,
'z': 1e-3,
'rx': -1e-6,
'rz': -1.253e-6
}
# test where not all axes are defined
pos4 = {'x': 1e-3, 'rx': 1e-5, 'rz': 0}
self.dev.moveAbs(pos1).result()
test.assert_pos_almost_equal(self.dev.position.value, pos1,
**COMP_ARGS)
self.dev.moveAbs(pos2).result()
test.assert_pos_almost_equal(self.dev.position.value, pos2,
**COMP_ARGS)
self.dev.moveAbs(pos3).result()
test.assert_pos_almost_equal(self.dev.position.value, pos3,
**COMP_ARGS)
self.dev.moveAbs(pos4).result()
# add missing axes to do the comparison
pos4['y'] = pos3['y']
pos4['z'] = pos3['z']
test.assert_pos_almost_equal(self.dev.position.value, pos4,
**COMP_ARGS)
def test_move_abs(self):
pos1 = {'x': 0, 'y': 0, 'z': 0, 'rx': 0, 'ry': 0, 'rz': 0.0005}
pos2 = {
'x': -0.0102,
'y': 0,
'z': 0.0,
'rx': 0.0001,
'ry': 0.0001,
'rz': 0
}
pos3 = {'x': 0.0102, 'y': -0.00002, 'z': 0, 'rx': 0, 'ry': 0, 'rz': 0}
# test where not all axes are defined
pos4 = {'x': 1e-3, 'rx': 1e-5, 'ry': 0, 'rz': 0}
self.dev.moveAbs(pos1).result()
test.assert_pos_almost_equal(self.dev.position.value, pos1,
**COMP_ARGS)
self.dev.moveAbs(pos2).result()
test.assert_pos_almost_equal(self.dev.position.value, pos2,
**COMP_ARGS)
self.dev.moveAbs(pos3).result()
test.assert_pos_almost_equal(self.dev.position.value, pos3,
**COMP_ARGS)
self.dev.moveAbs(pos4).result()
# add missing axes to do the comparison
pos4['y'] = pos3['y']
pos4['z'] = pos3['z']
test.assert_pos_almost_equal(self.dev.position.value, pos4,
**COMP_ARGS)
logging.debug(self.dev.position.value)
def test_move(self):
"""
Check it's possible to move the stage
"""
pos = self.stage.position.value
f = self.stage.moveRel({"x":-100e-6, "y":-100e-6}) # 1 mm
f.result()
# FIXME: this should fail
self.assertNotEqual(self.stage.position.value, pos)
time.sleep(1)
f = self.stage.moveRel({"x":100e-6, "y":100e-6}) # 1 mm
f.result()
test.assert_pos_almost_equal(self.stage.position.value, pos)
def test_navcam_focus(self):
"""
Check it's possible to change the overview focus
"""
pos = self.navcam_focus.position.value
f = self.navcam_focus.moveRel({"z": 0.1e-3}) # 1 mm
f.result()
self.assertNotEqual(self.navcam_focus.position.value, pos)
time.sleep(1)
# restore original position
f = self.navcam_focus.moveAbs(pos)
f.result()
test.assert_pos_almost_equal(self.navcam_focus.position.value, pos)
def test_position_rel(self):
"""
Test moving to a relative position.
"""
# Start at the origin to prevent hitting the ends
self.dev.moveAbs({'x': 0}).result()
# Test another relative move
for shift in (0, 0.12, -0.12):
new_shift = {'x': shift}
old_pos = self.dev.position.value
f = self.dev.moveRel(new_shift)
f.result()
test.assert_pos_almost_equal(add_coord(old_pos, new_shift), self.dev.position.value, **COMP_ARGS)
def test_move(self):
"""
Check it's possible to move the stage
"""
pos = self.stage.position.value
f = self.stage.moveRel({"x": -100e-6, "y": -100e-6}) # 1 mm
f.result()
# FIXME: this should fail
self.assertNotEqual(self.stage.position.value, pos)
time.sleep(1)
f = self.stage.moveRel({"x": 100e-6, "y": 100e-6}) # 1 mm
f.result()
test.assert_pos_almost_equal(self.stage.position.value, pos)
def test_multimove(self):
"""
Test running multimoves
"""
# start at origin
self.dev.moveAbs({'x': 0}).result()
orig_pos = self.dev.position.value
f1 = self.dev.moveRel({'x': 0.15})
time.sleep(0.02)
f2 = self.dev.moveRel({'x':-0.15})
f2.result()
test.assert_pos_almost_equal(orig_pos, self.dev.position.value, **COMP_ARGS)
def test_navcam_focus(self):
"""
Check it's possible to change the overview focus
"""
f = self.pressure.moveAbs({"pressure":1e04}) # move to NavCam
f.result()
pos = self.navcam_focus.position.value
f = self.navcam_focus.moveRel({"z":0.1e-3}) # 1 mm
f.result()
self.assertNotEqual(self.navcam_focus.position.value, pos)
time.sleep(1)
# restore original position
f = self.navcam_focus.moveAbs(pos)
f.result()
test.assert_pos_almost_equal(self.navcam_focus.position.value, pos)
def test_stop(self):
"""
Check it's possible to move the stage
"""
pos = self.stage.position.value.copy()
logging.info("Initial pos = %s", pos)
f = self.stage.moveRel({"y": 50e-3})
exppos = pos.copy()
exppos["y"] += 50e-3
time.sleep(0.5) # abort after 0.5 s
f.cancel()
time.sleep(6) # wait for position to update
self.assertNotEqual(self.stage.position.value, pos)
self.assertNotEqual(self.stage.position.value, exppos)
f = self.stage.moveAbs(pos) # Back to orig pos
f.result()
time.sleep(6) # wait for position to update
test.assert_pos_almost_equal(self.stage.position.value,
pos,
atol=0.1e-6)
# Same thing, but using stop() method
pos = self.stage.position.value.copy()
f = self.stage.moveRel({"y": 10e-3})
time.sleep(0.5)
self.stage.stop()
with self.assertRaises(CancelledError):
f.result()
exppos = pos.copy()
exppos["y"] += 10e-3
self.assertNotEqual(self.stage.position.value, pos)
self.assertNotEqual(self.stage.position.value, exppos)
f = self.stage.moveAbs(pos) # Back to orig pos
f.result()
time.sleep(6)
test.assert_pos_almost_equal(self.stage.position.value,
pos,
atol=0.1e-6)
def test_move_rel(self):
# Test relative moves
self.dev.moveAbs({'x': 0, 'y': 0, 'z': 0, 'rx': 0, 'ry': 0, 'rz': 0}).result()
old_pos = self.dev.position.value
shift = {'x': 0.01, 'y':-0.001, 'ry':-0.0003, 'rz': 0}
self.dev.moveRel(shift).result()
new_pos = self.dev.position.value
test.assert_pos_almost_equal(smarpod.add_coord(old_pos, shift), new_pos, **COMP_ARGS)
# Test several relative moves and ensure they are queued up.
old_pos = self.dev.position.value
shift = {'z':-0.000001, 'rx': 0.00001, 'ry':-0.000001, 'rz':-0.00001}
self.dev.moveRel(shift)
self.dev.moveRel(shift)
self.dev.moveRel(shift).result()
new_pos = smarpod.add_coord(smarpod.add_coord(smarpod.add_coord(old_pos, shift), shift), shift)
test.assert_pos_almost_equal(self.dev.position.value, new_pos, **COMP_ARGS)
def test_move_to_tiles(self):
"""
Test moving the stage to a tile based on its index
"""
area = (-0.001, -0.001, 0.001, 0.001)
overlap = 0.2
tiled_acq_task = TiledAcquisitionTask(
self.fm_streams,
self.stage,
area=area,
overlap=overlap,
future=model.InstantaneousFuture())
fov = compute_camera_fov(self.ccd)
exp_shift = fov[0] * (1 - overlap), fov[1] * (1 - overlap)
# move to starting position (left, top)
starting_pos = tiled_acq_task._starting_pos
self.stage.moveAbs(starting_pos).result()
logging.debug("Starting position: %s", starting_pos)
# no change in movement
tiled_acq_task._moveToTile((0, 0), (0, 0), fov)
assert_pos_almost_equal(self.stage.position.value,
starting_pos,
atol=100e-9,
match_all=False)
# Note that we cannot predict precisely, as the algorithm may choose to spread
# more or less the tiles to fit within the area.
tiled_acq_task._moveToTile((1, 0), (0, 0), fov) # move right on x
exp_pos = {'x': starting_pos["x"] + exp_shift[0] / 2}
assert_pos_almost_equal(self.stage.position.value,
exp_pos,
atol=10e-6,
match_all=False)
tiled_acq_task._moveToTile((1, 1), (1, 0), fov) # move down on y
exp_pos = {
'x': starting_pos["x"] + exp_shift[0] / 2,
'y': starting_pos["y"] - exp_shift[1] / 2
}
assert_pos_almost_equal(self.stage.position.value,
exp_pos,
atol=10e-6,
match_all=False)
tiled_acq_task._moveToTile((0, 1), (1, 1), fov) # move back on x
exp_pos = {
'x': starting_pos["x"],
'y': starting_pos["y"] - exp_shift[1] / 2
}
assert_pos_almost_equal(self.stage.position.value,
exp_pos,
atol=10e-6,
match_all=False)
def test_tilting_procedures(self):
"""
Test moving the sample stage from imaging position to tilting position and back to imaging
"""
stage = self.stage
align = self.aligner
# Test tilting from imaging
# Get the stage to imaging position
cryoSwitchSamplePosition(LOADING).result()
cryoSwitchSamplePosition(IMAGING).result()
# Tilt the stage on rx only
f = cryoTiltSample(rx=self.rx_angle)
f.result()
test.assert_pos_almost_equal(stage.position.value,
{'rx': self.rx_angle},
match_all=False,
atol=ATOL_ROTATION_POS)
# Tilt the stage on rx and rz
f = cryoTiltSample(rx=self.rx_angle, rz=self.rz_angle)
f.result()
test.assert_pos_almost_equal(stage.position.value, {
'rx': self.rx_angle,
'rz': self.rz_angle
},
match_all=False,
atol=ATOL_ROTATION_POS)
# align should be in deactive position
test.assert_pos_almost_equal(align.position.value,
self.align_deactive,
atol=ATOL_LINEAR_POS)
def test_tilting_procedures(self):
"""
Test moving the sample stage from imaging position to tilting position and back to imaging
"""
stage = self.stage
# Test tilting from imaging
# Get the stage to imaging position
f = cryoLoadSample(LOADING)
f.result()
f = cryoLoadSample(IMAGING)
f.result()
# Tilt the stage on rx only
f = cryoTiltSample(rx=self.rx_angle)
f.result()
test.assert_pos_almost_equal(stage.position.value, {'rx': self.rx_angle, 'rz': 0},
match_all=False,
atol=ATOL_ROTATION_POS)
# Tilt the stage on rx and rz
f = cryoTiltSample(rx=self.rx_angle, rz=self.rz_angle)
f.result()
test.assert_pos_almost_equal(stage.position.value, {'rx': self.rx_angle, 'rz': self.rz_angle},
match_all=False,
atol=ATOL_ROTATION_POS)
# Test imaging from tilting
f = cryoTiltSample(rx=0, rz=0)
f.result()
test.assert_pos_almost_equal(stage.position.value, self.stage_active, atol=ATOL_LINEAR_POS)
def test_stop(self):
"""
Check it's possible to move the stage
"""
pos = self.stage.position.value.copy()
logging.info("Initial pos = %s", pos)
f = self.stage.moveRel({"y": 50e-3})
exppos = pos.copy()
exppos["y"] += 50e-3
time.sleep(0.5) # abort after 0.5 s
f.cancel()
time.sleep(6) # wait for position to update
self.assertNotEqual(self.stage.position.value, pos)
self.assertNotEqual(self.stage.position.value, exppos)
f = self.stage.moveAbs(pos) # Back to orig pos
f.result()
time.sleep(6) # wait for position to update
test.assert_pos_almost_equal(self.stage.position.value, pos, atol=0.1e-6)
# Same thing, but using stop() method
pos = self.stage.position.value.copy()
f = self.stage.moveRel({"y": 10e-3})
time.sleep(0.5)
self.stage.stop()
with self.assertRaises(CancelledError):
f.result()
exppos = pos.copy()
exppos["y"] += 10e-3
self.assertNotEqual(self.stage.position.value, pos)
self.assertNotEqual(self.stage.position.value, exppos)
f = self.stage.moveAbs(pos) # Back to orig pos
f.result()
time.sleep(6)
test.assert_pos_almost_equal(self.stage.position.value, pos, atol=0.1e-6)
def test_align_switch_procedures(self):
"""
Test moving the sample stage from loading position to both imaging, alignment and coating, then back to loading
"""
align = self.aligner
# Get the stage to loading position
f = cryoSwitchAlignPosition(LOADING)
f.result()
test.assert_pos_almost_equal(align.position.value,
self.align_deactive,
atol=ATOL_LINEAR_POS)
# Get the stage to imaging position
f = cryoSwitchAlignPosition(IMAGING)
f.result()
test.assert_pos_almost_equal(align.position.value,
self.align_active,
atol=ATOL_LINEAR_POS)
# Get the stage to imaging position
f = cryoSwitchAlignPosition(ALIGNMENT)
f.result()
test.assert_pos_almost_equal(align.position.value,
self.align_alignment,
atol=ATOL_LINEAR_POS)
def test_ab_rotation(self):
"""
Test typical rotation stage for the SECOM v1 A/B alignment
"""
child = simulated.Stage("stage", "test", axes=["a", "b"])
stage = ConvertStage("inclined", "align", {"orig": child},
axes=["b", "a"], rotation=math.radians(-135))
f = stage.moveRel({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 1e-06, "y": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"a":-2.1213203435596424e-06,
"b": 7.071067811865477e-07})
f = stage.moveRel({"x": -1e-06, "y": -2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
test.assert_pos_almost_equal(child.position.value, {"a": 0, "b": 0})
def test_move_abs(self):
pos1 = {'x': 0, 'y': 0, 'z': 0, 'rx': 0, 'ry': 0, 'rz': 0.0005}
pos2 = {'x':-0.0102, 'y': 0, 'z': 0.0, 'rx': 0.0001, 'ry': 0.0001, 'rz': 0}
pos3 = {'x': 0.0102, 'y':-0.00002, 'z': 0, 'rx': 0, 'ry': 0, 'rz': 0}
self.dev.moveAbs(pos1).result()
test.assert_pos_almost_equal(self.dev.position.value, pos1, **COMP_ARGS)
self.dev.moveAbs(pos2).result()
test.assert_pos_almost_equal(self.dev.position.value, pos2, **COMP_ARGS)
self.dev.moveAbs(pos3).result()
test.assert_pos_almost_equal(self.dev.position.value, pos3, **COMP_ARGS)
logging.debug(self.dev.position.value)
def test_move_to_tiles(self):
"""
Test moving the stage to a tile based on its index
"""
area = (-0.001, -0.001, 0.001, 0.001)
overlap = 0.2
tiled_acq_task = TiledAcquisitionTask(
self.fm_streams,
self.stage,
area=area,
overlap=overlap,
future=model.InstantaneousFuture())
fov = (10**-5, 10**-5)
self.stage.moveAbs({'x': -0.001, 'y': -0.001}).result()
tiled_acq_task._moveToTile((0, 0), (0, 0), fov)
exp_pos = {'x': -0.001, 'y': -0.001}
assert_pos_almost_equal(self.stage.position.value,
exp_pos,
atol=100e-9,
match_all=False)
tiled_acq_task._moveToTile((1, 0), (0, 0), fov) # move right on x
exp_pos = {'x': -0.000992}
assert_pos_almost_equal(self.stage.position.value,
exp_pos,
atol=100e-9,
match_all=False)
tiled_acq_task._moveToTile((1, 1), (1, 0), fov) # move down on y
exp_pos = {'x': -0.000992, 'y': -0.001008}
assert_pos_almost_equal(self.stage.position.value,
exp_pos,
atol=100e-9,
match_all=False)
tiled_acq_task._moveToTile((0, 1), (1, 1), fov) # move back on x
exp_pos = {'x': -0.001, 'y': -0.001008}
assert_pos_almost_equal(self.stage.position.value,
exp_pos,
atol=100e-9,
match_all=False)
def test_move_abs(self):
pos1 = {'x': 0, 'y': 0, 'z': 0}
pos2 = {'x': 0, 'y': -1.2e-4, 'z': 0}
pos3 = {'x': 0.643e-3, 'y': 0, 'z': 1e-3}
self.dev.moveAbs(pos1).result()
test.assert_pos_almost_equal(self.dev.position.value, pos1,
**COMP_ARGS)
self.dev.moveAbs(pos2).result()
test.assert_pos_almost_equal(self.dev.position.value, pos2,
**COMP_ARGS)
self.dev.moveAbs(pos3).result()
test.assert_pos_almost_equal(self.dev.position.value, pos3,
**COMP_ARGS)
logging.debug(self.dev.position.value)
def test_unreachable_position_error(self):
edge_move = {'x': 1.6e-2, 'y': 1.5e-2, 'z': -0.002, 'rx': 0, 'rz': 0}
rot_move = {'rx': 0.001, 'rz': 0.001}
zero_move = {'x': 0, 'y': 0, 'z': 0}
# move the stage to the maximum range
self.dev.moveAbs(edge_move).result()
test.assert_pos_almost_equal(self.dev.position.value,
edge_move,
match_all=False)
# moving rx/rz would throw unreachable move exception
with self.assertRaises(IndexError):
self.dev.moveAbs(rot_move).result()
# moving all linear axes from range then moving rx/rz would be fine
self.dev.moveAbs(zero_move).result()
test.assert_pos_almost_equal(self.dev.position.value,
zero_move,
match_all=False)
self.dev.moveAbs(rot_move).result()
test.assert_pos_almost_equal(self.dev.position.value,
rot_move,
match_all=False)
def test_simple(self):
child = simulated.Stage("stage", "test", axes=["x", "y"])
stage = AntiBacklashActuator("absact", "align", {"orig": child},
backlash={"x": 100e-6, "y": -80e-6})
# moves should just go the same positions
# abs
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
f = stage.moveAbs({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 1e-06, "y": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"x": 1e-06, "y": 2e-06})
f = stage.moveAbs({"x": 0, "y": 0})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
test.assert_pos_almost_equal(child.position.value, {"x": 0, "y": 0})
f = stage.moveAbs({"x": -23e-06, "y": -15e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x":-23e-06, "y":-15e-06})
test.assert_pos_almost_equal(child.position.value, {"x":-23e-06, "y":-15e-06})
# rel
f = stage.moveAbs({"x": 0, "y": 0})
f = stage.moveRel({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 1e-06, "y": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"x": 1e-06, "y": 2e-06})
f = stage.moveRel({"x": 0, "y": 0})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 1e-06, "y": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"x": 1e-06, "y": 2e-06})
f = stage.moveRel({"x": -1e-06, "y": -2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
test.assert_pos_almost_equal(child.position.value, {"x": 0, "y": 0})
def test_move(self):
"""
Check it's possible to move the stage
"""
pos = self.stage.position.value.copy()
f = self.stage.moveRel({"x":2e-6, "y":3e-6})
f.result()
self.assertNotEqual(self.stage.position.value, pos)
time.sleep(6) # wait until .position is updated
self.assertNotEqual(self.stage.position.value, pos)
f = self.stage.moveRel({"x":-2e-6, "y":-3e-6})
f.result()
test.assert_pos_almost_equal(self.stage.position.value, pos, atol=0.1e-6)
time.sleep(6)
test.assert_pos_almost_equal(self.stage.position.value, pos, atol=0.1e-6)
# Try a relative move outside of the range (less than min)
axes = self.stage.axes
toofar = {"x": axes["x"].range[0] - pos["x"] - 10e-6}
f = self.stage.moveRel(toofar)
with self.assertRaises(ValueError):
f.result()
test.assert_pos_almost_equal(self.stage.position.value, pos, atol=0.1e-6)
time.sleep(6)
test.assert_pos_almost_equal(self.stage.position.value, pos, atol=0.1e-6)
# Try a relative move outside of the range (more than max)
toofar = {"y": axes["y"].range[1] - pos["y"] + 10e-6}
f = self.stage.moveRel(toofar)
with self.assertRaises(ValueError):
f.result()
test.assert_pos_almost_equal(self.stage.position.value, pos, atol=0.1e-6)
time.sleep(6)
test.assert_pos_almost_equal(self.stage.position.value, pos, atol=0.1e-6)
# f = self.stage.moveRel({"z": 4e-3}) # 100 µm
# time.sleep(15) # wait for stage move
# f.result()
# self.assertNotEqual(self.stage.position.value, pos)
#
# f = self.stage.moveRel({"z":-4e-3}) # 100 µm
# time.sleep(15) # wait for stage move
# f.result()
# test.assert_pos_almost_equal(self.stage.position.value, pos, atol=10e-6)
with self.assertRaises(ValueError):
f = self.stage.moveRel({"x":-200e-3})
p = self.stage.position.value.copy()
subpos = self.stage.position.value.copy()
subpos["x"] += 50e-6
f = self.stage.moveAbs(subpos)
f.result()
test.assert_pos_almost_equal(self.stage.position.value, subpos)
time.sleep(6)
test.assert_pos_almost_equal(self.stage.position.value, subpos)
subpos = self.stage.position.value.copy()
subpos.pop("y")
subpos["x"] -= 50e-6
self.stage.moveAbsSync(subpos)
test.assert_pos_almost_equal(self.stage.position.value, p)
time.sleep(6)
test.assert_pos_almost_equal(self.stage.position.value, p)
def assertXYAlmostEqual(self, actual, expected, *args, **kwargs):
pos = {"x": actual["x"], "y": actual["y"]}
test.assert_pos_almost_equal(pos, expected, *args, **kwargs)
def test_move_abs(self):
child = simulated.Stage("stage", "test", axes=["x", "y"])
# no transformation
stage = ConvertStage("conv", "align", {"orig": child}, axes=["x", "y"])
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
f = stage.moveAbs({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 1e-06, "y": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"x": 1e-06, "y": 2e-06})
f = stage.moveAbs({"x": 0, "y": 0})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
test.assert_pos_almost_equal(child.position.value, {"x": 0, "y": 0})
# scaling
stage = ConvertStage("conv", "align", {"orig": child}, axes=["x", "y"],
scale=(10, 10))
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
f = stage.moveAbs({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 1e-06, "y": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"x": 1e-05, "y": 2e-05})
f = stage.moveAbs({"x": 0, "y": 0})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
test.assert_pos_almost_equal(child.position.value, {"x": 0, "y": 0})
# rotation
stage = ConvertStage("conv", "align", {"orig": child}, axes=["x", "y"],
rotation=math.pi / 2)
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
f = stage.moveAbs({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 1e-06, "y": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"x":-2e-06, "y": 1e-06})
f = stage.moveAbs({"x": 0, "y": 0})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
test.assert_pos_almost_equal(child.position.value, {"x": 0, "y": 0})
# offset
stage = ConvertStage("conv", "align", {"orig": child}, axes=["x", "y"],
translation=(1e-06, 2e-06))
test.assert_pos_almost_equal(stage.position.value, {"x":-1e-06, "y":-2e-06})
f = stage.moveAbs({"x": 0, "y": 0})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
test.assert_pos_almost_equal(child.position.value, {"x": 1e-06, "y": 2e-06})
f = stage.moveAbs({"x": -1e-06, "y": -2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x":-1e-06, "y":-2e-06})
test.assert_pos_almost_equal(child.position.value, {"x": 0, "y": 0})
# offset + scaling
stage = ConvertStage("conv", "align", {"orig": child}, axes=["x", "y"],
translation=(1e-06, 2e-06),
scale=(10, 10))
test.assert_pos_almost_equal(stage.position.value, {"x":-1e-06, "y":-2e-06})
f = stage.moveAbs({"x": 0, "y": 0})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"x": 0, "y": 0})
test.assert_pos_almost_equal(child.position.value, {"x": 1e-05, "y": 2e-05})
def test_move_abs(self):
stage = self.stage
sem_stage = self.sem_stage
align = self.align
tmcm = self.tmcm
# axes = set(["x", "y"])
# f = stage.reference(axes)
# f.result()
# no transformation
stage.updateMetadata({model.MD_ROTATION_COR: 0,
model.MD_POS_COR: (0, 0),
model.MD_PIXEL_SIZE_COR: (1, 1)})
f = stage.moveAbs({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(align.position.value, {"x": 1e-06, "y": 2e-06}, atol=1e-7)
test.assert_pos_almost_equal(sem_stage.position.value, {"x": 1e-06, "y": 2e-06}, atol=1e-7)
self.assertXYAlmostEqual(tmcm.position.value, {"x":-1e-06, "y":-2e-06}, atol=1e-7)
# scaling
stage.updateMetadata({model.MD_ROTATION_COR: 0})
stage.updateMetadata({model.MD_POS_COR: (0, 0)})
stage.updateMetadata({model.MD_PIXEL_SIZE_COR: (10, 10)})
f = stage.moveAbs({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(align.position.value, {"x": 1e-06, "y": 2e-06}, atol=1e-7)
test.assert_pos_almost_equal(sem_stage.position.value, {"x": 1e-05, "y": 2e-05}, atol=1e-7)
self.assertXYAlmostEqual(tmcm.position.value, {"x":-1e-06, "y":-2e-06}, atol=1e-7)
# rotation
stage.updateMetadata({model.MD_ROTATION_COR: math.pi / 2})
stage.updateMetadata({model.MD_POS_COR: (0, 0)})
stage.updateMetadata({model.MD_PIXEL_SIZE_COR: (1, 1)})
f = stage.moveAbs({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(align.position.value, {"x": 1e-06, "y": 2e-06}, atol=1e-7)
test.assert_pos_almost_equal(sem_stage.position.value, {"x":-2e-06, "y": 1e-06}, atol=1e-7)
self.assertXYAlmostEqual(tmcm.position.value, {"x":-1e-06, "y":-2e-06}, atol=1e-7)
# offset
stage.updateMetadata({model.MD_ROTATION_COR: 0})
stage.updateMetadata({model.MD_POS_COR: (-1e-06, -2e-06)})
stage.updateMetadata({model.MD_PIXEL_SIZE_COR: (1, 1)})
f = stage.moveAbs({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(align.position.value, {"x": 1e-06, "y": 2e-06}, atol=1e-7)
test.assert_pos_almost_equal(sem_stage.position.value, {"x": 0, "y": 0}, atol=1e-7)
self.assertXYAlmostEqual(tmcm.position.value, {"x":-1e-06, "y":-2e-06}, atol=1e-7)
# offset + scaling
stage.updateMetadata({model.MD_ROTATION_COR: 0})
stage.updateMetadata({model.MD_POS_COR: (-1e-06, -2e-06)})
stage.updateMetadata({model.MD_PIXEL_SIZE_COR: (10, 10)})
f = stage.moveAbs({"x": 1e-06, "y": 2e-06})
f.result()
test.assert_pos_almost_equal(align.position.value, {"x": 1e-06, "y": 2e-06}, atol=1e-7)
test.assert_pos_almost_equal(sem_stage.position.value, {"x": 0, "y": 0}, atol=1e-7)
self.assertXYAlmostEqual(tmcm.position.value, {"x":-1e-06, "y":-2e-06}, atol=1e-7)
f = stage.moveAbs({"x": 0, "y": 0})
f.result()
def test_limited_backlash(self):
"""
Test when backlash doesn't involve all axes
"""
child = simulated.Stage("stage", "test", axes=["a", "b"])
stage = AntiBacklashActuator("absact", "align", {"orig": child},
backlash={"a": 100e-6})
# moves should just go the same positions
# abs
test.assert_pos_almost_equal(stage.position.value, {"a": 0, "b": 0})
f = stage.moveAbs({"a": 1e-06, "b": 2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"a": 1e-06, "b": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"a": 1e-06, "b": 2e-06})
f = stage.moveAbs({"b": 0})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"a": 1e-06, "b": 0})
test.assert_pos_almost_equal(child.position.value, {"a": 1e-06, "b": 0})
f = stage.moveAbs({"a": -23e-06, "b": -15e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"a":-23e-06, "b":-15e-06})
test.assert_pos_almost_equal(child.position.value, {"a":-23e-06, "b":-15e-06})
f = stage.moveAbs({"a": -20e-06}) # negative position but positive move
f.result()
test.assert_pos_almost_equal(stage.position.value, {"a":-20e-06, "b":-15e-06})
test.assert_pos_almost_equal(child.position.value, {"a":-20e-06, "b":-15e-06})
# rel
f = stage.moveAbs({"a": 0})
f = stage.moveAbs({"b": 0})
f = stage.moveRel({"a": 1e-06, "b": 2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"a": 1e-06, "b": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"a": 1e-06, "b": 2e-06})
f = stage.moveRel({"a": 0, "b": 0})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"a": 1e-06, "b": 2e-06})
test.assert_pos_almost_equal(child.position.value, {"a": 1e-06, "b": 2e-06})
f = stage.moveRel({"a": -1e-06, "b": -2e-06})
f.result()
test.assert_pos_almost_equal(stage.position.value, {"a": 0, "b": 0})
test.assert_pos_almost_equal(child.position.value, {"a": 0, "b": 0})