def validate_gantry_calibration(gantry_cal: List[List[float]]):
"""
This function determines whether the gantry calibration is valid
or not based on the following use-cases:
"""
curr_cal = np.array(gantry_cal)
row, _ = curr_cal.shape
rank = np.linalg.matrix_rank(curr_cal)
id_matrix = linal.identity_deck_transform()
z = abs(curr_cal[2][-1])
outofrange = z < 16 or z > 34
if row != rank:
# Check that the matrix is non-singular
return DeckTransformState.SINGULARITY
elif np.array_equal(curr_cal, id_matrix):
# Check that the matrix is not an identity
return DeckTransformState.IDENTITY
elif outofrange:
# Check that the matrix is not out of range.
return DeckTransformState.BAD_CALIBRATION
else:
# Transform as it stands is sufficient.
return DeckTransformState.OK
def _determine_calibration_to_use(deck_cal_to_check, api_v1):
"""
The default calibration loaded in simulation is not
a valid way to check whether labware exceeds a given
height. As a workaround, we should load the identity
matrix with a Z offset if we are not running on a
robot.
"""
id_matrix = linal.identity_deck_transform()
deck_cal_to_use = deck_cal_to_check
if not config.IS_ROBOT and not api_v1:
if not deck_cal_to_check:
deck_cal_to_use = DEFAULT_SIMULATION_CALIBRATION
elif deck_cal_to_check and\
array_equal(array(deck_cal_to_check), id_matrix):
deck_cal_to_use = deck_cal_to_check
return deck_cal_to_use
def __init__(self, hardware):
self.id = _get_uuid()
self.pipettes = {}
self.current_mount = None
self.current_model = None
self.tip_length = None
self.points = {k: None for k in expected_points().keys()}
self.z_value = None
self.cp = None
self.pipette_id = None
self.adapter = hardware.sync
self.current_transform = identity_deck_transform()
robot_configs.backup_configuration(self.adapter.config)
# Start from fresh identity matrix every calibration session
self.adapter.update_config(gantry_calibration=list(
map(lambda i: list(i), self.current_transform)))
def __init__(self, hardware):
self.id = _get_uuid()
self.pipettes = {}
self.current_mount = None
self.current_model = None
self.tip_length = None
self.points = {k: None for k in expected_points().keys()}
self.z_value = None
self.cp = None
self.pipette_id = None
self.adapter = hardware
self.current_transform = identity_deck_transform()
if feature_flags.use_protocol_api_v2():
self.adapter = hardware_control.adapters.SynchronousAdapter(
hardware)
# Start from fresh identity matrix every calibration session
self.adapter.update_config(gantry_calibration=self.current_transform)
def __init__(self,
point_set,
hardware,
pickup_tip=None,
loop=None,
log_level=None):
# URWID user interface objects
if not loop:
loop = asyncio.get_event_loop()
loop = urwid.main_loop.AsyncioEventLoop(loop=loop)
controls = '\n'.join([
'arrow keys: move the gantry',
'q/a: move the pipette up/down',
'=/-: increase/decrease the distance moved on each step',
'1/2/3: go to calibration point 1/2/3',
'enter: confirm current calibration point position',
'space: save data (after confirming all 3 points)',
'p: perform tip probe (after saving calibration data)',
'esc: exit calibration tool',
'?: Full Instructions'
])
self._tip_text_box = urwid.Text(controls)
self._status_text_box = urwid.Text('')
self._pile = urwid.Pile([self._tip_text_box, self._status_text_box])
self._filler = urwid.Filler(self._pile, 'top')
self.hardware = hardware
self._pipettes = {}
if not feature_flags.use_protocol_api_v2():
self._current_mount = right
else:
self._current_mount = types.Mount.RIGHT
self.update_pipette_models()
self.current_transform = identity_deck_transform()
self._tip_length = DEFAULT_TIP_LENGTH
# Other state
if not pickup_tip:
self._tip_length =\
self._pipettes[self._current_mount]._fallback_tip_length
if feature_flags.use_protocol_api_v2():
self.hardware.add_tip(types.Mount.RIGHT, self._tip_length)
if self._pipettes[types.Mount.LEFT]:
self.hardware.add_tip(
types.Mount.LEFT,
self._pipettes[types.Mount.LEFT]._fallback_tip_length)
else:
for pip in self._pipettes.values():
if pip:
pip._add_tip(pip._tip_length)
self.current_position = (0, 0, 0)
self._steps = [0.1, 0.25, 0.5, 1, 5, 10, 20, 40, 80]
self._steps_index = 2
self._current_point = 1
self.model_offset = self._pipettes[self._current_mount].model_offset
deck_height = 0
if not feature_flags.use_protocol_api_v2():
deck_height = self._tip_length
self.actual_points = {1: (0, 0), 2: (0, 0), 3: (0, 0)}
self._expected_points = self.set_deck_height_expected_points(
deck_height, point_set)
self._test_points = self.set_deck_height_test_points(deck_height)
slot5 = self._test_points['slot5']
log_val = self.hardware.config.log_level
if log_level:
log_val = log_level.upper()
logging_config.log_init(log_val)
self.key_map = {
'-':
lambda: self.decrease_step(),
'=':
lambda: self.increase_step(),
'z':
lambda: self.save_z_value(),
'p':
lambda: self.probe(slot5),
'enter':
lambda: self.save_point(),
'\\':
lambda: self.home(),
' ':
lambda: self.save_transform(),
'esc':
lambda: self.exit(),
'q':
lambda: self._jog(self._current_mount, +1, self.current_step()),
'a':
lambda: self._jog(self._current_mount, -1, self.current_step()),
'n':
lambda: self.update_pipette_models(),
'up':
lambda: self._jog('Y', +1, self.current_step()),
'down':
lambda: self._jog('Y', -1, self.current_step()),
'left':
lambda: self._jog('X', -1, self.current_step()),
'right':
lambda: self._jog('X', +1, self.current_step()),
'm':
lambda: self.validate_mount_offset(),
's':
lambda: self.switch_mounts(),
't':
lambda: self.try_pickup_tip(),
'1':
lambda: self.validate(self._expected_points[1], 1, self.
_current_mount),
'2':
lambda: self.validate(self._expected_points[2], 2, self.
_current_mount),
'3':
lambda: self.validate(self._expected_points[3], 3, self.
_current_mount),
'4':
lambda: self.validate(self._test_points['slot5'], 4, self.
_current_mount),
'5':
lambda: self.validate(self._test_points['corner3'], 5, self.
_current_mount),
'6':
lambda: self.validate(self._test_points['corner8'], 6, self.
_current_mount),
'7':
lambda: self.validate(self._test_points['corner9'], 7, self.
_current_mount),
'?':
lambda: self.print_instructions(),
}
self.ui_loop = urwid.MainLoop(self._filler,
handle_mouse=False,
unhandled_input=self._on_key_press,
event_loop=loop)
log.debug("Starting gantry calibration command line interface (CLI)")