openflexure_microscope_server.things.stage.BaseStage

class documentation

class BaseStage(lt.Thing): (source)

Known subclasses: openflexure_microscope_server.things.stage.dummy.DummyStage, openflexure_microscope_server.things.stage.sangaboard.SangaboardThing

Constructor: BaseStage()

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A base stage class for OpenFlexure translation stages.

This can't be used directly but should reduce boilerplate code when implementing new stages.

Note that the coordinate system used for the microscope may need to have different axis direction as those used by the underlying stage controller.

A minimal working stage must implement _hardware_move_relative and _hardware_move_absolute actions, which update the _hardware_position attribute on completion, and also should implement set_zero_position.

Method	`__init__`	Initialise the stage.
Method	`get_xyz_position`	Return a tuple containing (x, y, z) position.
Method	`invert_axis_direction`	Invert the direction setting of the given axis.
Method	`move_absolute`	Make an absolute move. Keyword arguments should be axis names.
Method	`move_relative`	Make a relative move. Keyword arguments should be axis names.
Method	`move_to_xyz_position`	Move to the location specified by an (x, y, z) tuple.
Method	`set_zero_position`	Make the current position zero in all axes.
Class Variable	`moving`	Whether the stage is in motion.
Instance Variable	`axis_inverted`	Used to convert coordinates between the program frame and the hardware frame.
Property	`axis_names`	The names of the stage's axes, in order.
Property	`position`	Current position of the stage.
Property	`thing_state`	Summary metadata describing the current state of the stage.
Method	`_apply_axis_direction`	Undocumented
Method	`_hardware_move_absolute`	Make a absolute move in the coordinate system used by the physical hardware.
Method	`_hardware_move_relative`	Make a relative move in the coordinate system used by the physical hardware.
Class Variable	`_axis_names`	Undocumented
Instance Variable	`_hardware_position`	Undocumented

def __init__(self): (source) ¶

overridden in openflexure_microscope_server.things.stage.dummy.DummyStage, openflexure_microscope_server.things.stage.sangaboard.SangaboardThing

Initialise the stage.

Raises
`RedefinedBaseMovementError`	if `move_relative` and/or `move_absolute` are overridden. It is recommended to override `_hardware_move_relative` and/or `_hardware_move_absolute` instead so that all code in the child class uses the hardware reference frame.

@lt.thing_action

def get_xyz_position(self) -> tuple[int, int, int]: (source) ¶

Return a tuple containing (x, y, z) position.

This method provides the interface expected by the camera_stage_mapping.

Raises
`KeyError`	if this stage does not have axes named "x", "y", and "z".

@lt.thing_action

def invert_axis_direction(self, axis: Literal['x', 'y', 'z']): (source) ¶

Invert the direction setting of the given axis.

Parameters
axis:`Literal['x', 'y', 'z']`	The axis name (x, y or z) to invert.

@lt.thing_action

def move_absolute(self, cancel: lt.deps.CancelHook, block_cancellation: bool = False, **kwargs: Mapping[str, int]): (source) ¶

Make an absolute move. Keyword arguments should be axis names.

@lt.thing_action

def move_relative(self, cancel: lt.deps.CancelHook, block_cancellation: bool = False, **kwargs: Mapping[str, int]): (source) ¶

Make a relative move. Keyword arguments should be axis names.

@lt.thing_action

def move_to_xyz_position(self, cancel: lt.deps.CancelHook, xyz_pos: tuple[int, int, int]): (source) ¶

Move to the location specified by an (x, y, z) tuple.

This method provides the interface expected by the camera_stage_mapping.

Parameters
cancel:`lt.deps.CancelHook`	A cancel hook for cancelling the move. This dependency should be injected automatically by LabThings-FastAPI
xyz_pos:`tuple[int, int, int]`	The (x, y, z) position to move to.

Raises
`KeyError`	if this stage does not have axes named "x", "y", and "z".

@lt.thing_action

def set_zero_position(self): (source) ¶

overridden in openflexure_microscope_server.things.stage.dummy.DummyStage, openflexure_microscope_server.things.stage.sangaboard.SangaboardThing

Make the current position zero in all axes.

This action does not move the stage, but resets the position to zero. It is intended for use after manually or automatically recentring the stage.

moving = (source) ¶

overridden in openflexure_microscope_server.things.stage.dummy.DummyStage, openflexure_microscope_server.things.stage.sangaboard.SangaboardThing

Whether the stage is in motion.

axis_inverted = (source) ¶

overridden in openflexure_microscope_server.things.stage.dummy.DummyStage, openflexure_microscope_server.things.stage.sangaboard.SangaboardThing

Used to convert coordinates between the program frame and the hardware frame.

@lt.thing_property

axis_names: Sequence[str] = (source) ¶

The names of the stage's axes, in order.

@lt.thing_property

position: Mapping[str, int] = (source) ¶

Current position of the stage.

@property

thing_state = (source) ¶

Summary metadata describing the current state of the stage.

def _apply_axis_direction(self, position: list[int] | tuple[int] | Mapping[str, int]) -> list[int] | Mapping[str, int]: (source) ¶

Undocumented

def _hardware_move_absolute(self, cancel: lt.deps.CancelHook, block_cancellation: bool = False, **kwargs: Mapping[str, int]): (source) ¶

overridden in openflexure_microscope_server.things.stage.dummy.DummyStage, openflexure_microscope_server.things.stage.sangaboard.SangaboardThing

Make a absolute move in the coordinate system used by the physical hardware.

Make sure to use and update self._hardware_position not self.position.

def _hardware_move_relative(self, cancel: lt.deps.CancelHook, block_cancellation: bool = False, **kwargs: Mapping[str, int]): (source) ¶

overridden in openflexure_microscope_server.things.stage.dummy.DummyStage, openflexure_microscope_server.things.stage.sangaboard.SangaboardThing

Make a relative move in the coordinate system used by the physical hardware.

Make sure to use and update self._hardware_position not self.position.

_axis_names: tuple[str, ...] = (source) ¶

Undocumented

_hardware_position = (source) ¶

overridden in openflexure_microscope_server.things.stage.dummy.DummyStage, openflexure_microscope_server.things.stage.sangaboard.SangaboardThing

Undocumented