npxpy.nodes.aligners.FiberAligner

Bases: Node

Source code in npxpy/nodes/aligners.py

class FiberAligner(Node):
    def __init__(
        self,
        name: str = "Fiber aligner",
        fiber_radius: Union[float, int] = 63.5,
        center_stage: bool = True,
        action_upon_failure: str = "abort",
        illumination_name: str = "process_led_1",
        core_signal_lower_threshold: Union[float, int] = 0.05,
        core_signal_range: List[Union[float, int]] = [0.1, 0.9],
        detection_margin: Union[float, int] = 6.35,
    ):
        """
        Initialize the fiber aligner with specified parameters.

        Parameters:
            name (str): Name of the fiber aligner.
            fiber_radius (Union[float, int]): Radius of the fiber.
            center_stage (bool): Whether to center the stage.
            action_upon_failure (str): Action upon failure ('abort' or 'ignore').
            illumination_name (str): Name of the illumination source.
            core_signal_lower_threshold (Union[float, int]): Lower threshold for
                the core signal.
            core_signal_range (List[Union[float, int]]): Range for the core
                signal [min, max].
            detection_margin (Union[float, int]): Detection margin.
        """
        super().__init__(
            node_type="fiber_core_alignment",
            name=name,
        )

        # Use setters to handle attributes
        self.fiber_radius = fiber_radius
        self.center_stage = center_stage
        self.action_upon_failure = action_upon_failure
        self.illumination_name = illumination_name
        self.core_signal_lower_threshold = core_signal_lower_threshold
        self.core_signal_range = core_signal_range
        self.detection_margin = detection_margin

        # Default values using setters for consistency
        self.detect_light_direction = False
        self.z_scan_range = [10, 100]
        self.z_scan_range_sample_count = 1
        self.z_scan_range_scan_count = 1

    # Proper setters with validation
    @property
    def fiber_radius(self) -> Union[float, int]:
        return self._fiber_radius

    @fiber_radius.setter
    def fiber_radius(self, value: Union[float, int]):
        if not isinstance(value, (float, int)) or value <= 0:
            raise ValueError("fiber_radius must be a positive number.")
        self._fiber_radius = value

    @property
    def center_stage(self) -> bool:
        return self._center_stage

    @center_stage.setter
    def center_stage(self, value: bool):
        if not isinstance(value, bool):
            raise TypeError("center_stage must be a boolean.")
        self._center_stage = value

    @property
    def action_upon_failure(self) -> str:
        return self._action_upon_failure

    @action_upon_failure.setter
    def action_upon_failure(self, value: str):
        if value not in ["abort", "ignore"]:
            raise ValueError(
                "action_upon_failure must be 'abort' or 'ignore'."
            )
        self._action_upon_failure = value

    @property
    def illumination_name(self) -> str:
        return self._illumination_name

    @illumination_name.setter
    def illumination_name(self, value: str):
        if not isinstance(value, str):
            raise TypeError("illumination_name must be a string.")
        self._illumination_name = value

    @property
    def core_signal_lower_threshold(self) -> Union[float, int]:
        return self._core_signal_lower_threshold

    @core_signal_lower_threshold.setter
    def core_signal_lower_threshold(self, value: Union[float, int]):
        if not isinstance(value, (float, int)):
            raise TypeError(
                "core_signal_lower_threshold must be a float or an int."
            )
        self._core_signal_lower_threshold = value

    @property
    def core_signal_range(self) -> List[Union[float, int]]:
        return self._core_signal_range

    @core_signal_range.setter
    def core_signal_range(self, value: List[Union[float, int]]):
        if not isinstance(value, list) or len(value) != 2:
            raise ValueError(
                "core_signal_range must be a list of two elements."
            )
        if not all(isinstance(val, (float, int)) for val in value):
            raise TypeError(
                "All elements in core_signal_range must be numbers."
            )
        self._core_signal_range = value

    @property
    def detection_margin(self) -> Union[float, int]:
        return self._detection_margin

    @detection_margin.setter
    def detection_margin(self, value: Union[float, int]):
        if not isinstance(value, (float, int)) or value <= 0:
            raise ValueError("detection_margin must be a positive number.")
        self._detection_margin = value

    @property
    def z_scan_range(self) -> List[Union[float, int]]:
        return self._z_scan_range

    @z_scan_range.setter
    def z_scan_range(self, value: List[Union[float, int]]):
        if (
            not isinstance(value, list)
            or len(value) != 2
            or value[1] <= value[0]
        ):
            raise ValueError(
                "z_scan_range must be a list of two elements where the "
                "second element is greater than the first."
            )
        self._z_scan_range = value

    @property
    def z_scan_range_sample_count(self) -> int:
        return self._z_scan_range_sample_count

    @z_scan_range_sample_count.setter
    def z_scan_range_sample_count(self, value: int):
        if not isinstance(value, int) or value <= 0:
            raise ValueError(
                "z_scan_range_sample_count must be a positive integer."
            )
        self._z_scan_range_sample_count = value

    @property
    def z_scan_range_scan_count(self) -> int:
        return self._z_scan_range_scan_count

    @z_scan_range_scan_count.setter
    def z_scan_range_scan_count(self, value: int):
        if not isinstance(value, int) or value <= 0:
            raise ValueError(
                "z_scan_range_scan_count must be a positive integer."
            )
        self._z_scan_range_scan_count = value

    def measure_tilt(
        self,
        z_scan_range: List[Union[float, int]] = [10, 100],
        z_scan_range_sample_count: int = 3,
        z_scan_range_scan_count: int = 1,
    ):
        """
        Measures tilt by setting scan range parameters.

        Parameters:
            z_scan_range (List[Union[float, int]]): Range for the z-scan.
            z_scan_range_sample_count (int): Number of samples in the z-scan.
            z_scan_range_scan_count (int): Number of scans in the z-scan.

        Returns:
            self: The instance of the FiberAligner class.

        """
        self.z_scan_range = z_scan_range
        self.z_scan_range_sample_count = z_scan_range_sample_count
        self.z_scan_range_scan_count = z_scan_range_scan_count
        self.detect_light_direction = True

        return self

    def to_dict(self) -> Dict:
        """
        Converts the current state of the object into a dictionary.

        Returns:
            dict: Dictionary representation of the current state of the object.
        """
        node_dict = super().to_dict()
        # Add custom attributes not covered by super().__init__()
        node_dict.update(
            {
                "fiber_radius": self.fiber_radius,
                "center_stage": self.center_stage,
                "action_upon_failure": self.action_upon_failure,
                "illumination_name": self.illumination_name,
                "core_signal_lower_threshold": self.core_signal_lower_threshold,
                "core_signal_range": self.core_signal_range,
                "core_position_offset_tolerance": self.detection_margin,
                "detect_light_direction": self.detect_light_direction,
                "z_scan_range": self.z_scan_range,
                "z_scan_range_sample_count": self.z_scan_range_sample_count,
                "z_scan_range_scan_count": self.z_scan_range_scan_count,
            }
        )
        return node_dict

__init__(name='Fiber aligner', fiber_radius=63.5, center_stage=True, action_upon_failure='abort', illumination_name='process_led_1', core_signal_lower_threshold=0.05, core_signal_range=[0.1, 0.9], detection_margin=6.35)

Initialize the fiber aligner with specified parameters.

Parameters:

Name	Type	Description	Default
name	str	Name of the fiber aligner.	'Fiber aligner'
fiber_radius	Union[float, int]	Radius of the fiber.	63.5
center_stage	bool	Whether to center the stage.	True
action_upon_failure	str	Action upon failure ('abort' or 'ignore').	'abort'
illumination_name	str	Name of the illumination source.	'process_led_1'
core_signal_lower_threshold	Union[float, int]	Lower threshold for the core signal.	0.05
core_signal_range	List[Union[float, int]]	Range for the core signal [min, max].	[0.1, 0.9]
detection_margin	Union[float, int]	Detection margin.	6.35

Source code in npxpy/nodes/aligners.py

def __init__(
    self,
    name: str = "Fiber aligner",
    fiber_radius: Union[float, int] = 63.5,
    center_stage: bool = True,
    action_upon_failure: str = "abort",
    illumination_name: str = "process_led_1",
    core_signal_lower_threshold: Union[float, int] = 0.05,
    core_signal_range: List[Union[float, int]] = [0.1, 0.9],
    detection_margin: Union[float, int] = 6.35,
):
    """
    Initialize the fiber aligner with specified parameters.

    Parameters:
        name (str): Name of the fiber aligner.
        fiber_radius (Union[float, int]): Radius of the fiber.
        center_stage (bool): Whether to center the stage.
        action_upon_failure (str): Action upon failure ('abort' or 'ignore').
        illumination_name (str): Name of the illumination source.
        core_signal_lower_threshold (Union[float, int]): Lower threshold for
            the core signal.
        core_signal_range (List[Union[float, int]]): Range for the core
            signal [min, max].
        detection_margin (Union[float, int]): Detection margin.
    """
    super().__init__(
        node_type="fiber_core_alignment",
        name=name,
    )

    # Use setters to handle attributes
    self.fiber_radius = fiber_radius
    self.center_stage = center_stage
    self.action_upon_failure = action_upon_failure
    self.illumination_name = illumination_name
    self.core_signal_lower_threshold = core_signal_lower_threshold
    self.core_signal_range = core_signal_range
    self.detection_margin = detection_margin

    # Default values using setters for consistency
    self.detect_light_direction = False
    self.z_scan_range = [10, 100]
    self.z_scan_range_sample_count = 1
    self.z_scan_range_scan_count = 1

measure_tilt(z_scan_range=[10, 100], z_scan_range_sample_count=3, z_scan_range_scan_count=1)

Measures tilt by setting scan range parameters.

Parameters:

Name	Type	Description	Default
z_scan_range	List[Union[float, int]]	Range for the z-scan.	[10, 100]
z_scan_range_sample_count	int	Number of samples in the z-scan.	3
z_scan_range_scan_count	int	Number of scans in the z-scan.	1

Returns:

Name	Type	Description
self		The instance of the FiberAligner class.

Source code in npxpy/nodes/aligners.py

def measure_tilt(
    self,
    z_scan_range: List[Union[float, int]] = [10, 100],
    z_scan_range_sample_count: int = 3,
    z_scan_range_scan_count: int = 1,
):
    """
    Measures tilt by setting scan range parameters.

    Parameters:
        z_scan_range (List[Union[float, int]]): Range for the z-scan.
        z_scan_range_sample_count (int): Number of samples in the z-scan.
        z_scan_range_scan_count (int): Number of scans in the z-scan.

    Returns:
        self: The instance of the FiberAligner class.

    """
    self.z_scan_range = z_scan_range
    self.z_scan_range_sample_count = z_scan_range_sample_count
    self.z_scan_range_scan_count = z_scan_range_scan_count
    self.detect_light_direction = True

    return self

to_dict()

Converts the current state of the object into a dictionary.

Returns:

Name	Type	Description
dict	Dict	Dictionary representation of the current state of the object.

Source code in npxpy/nodes/aligners.py

def to_dict(self) -> Dict:
    """
    Converts the current state of the object into a dictionary.

    Returns:
        dict: Dictionary representation of the current state of the object.
    """
    node_dict = super().to_dict()
    # Add custom attributes not covered by super().__init__()
    node_dict.update(
        {
            "fiber_radius": self.fiber_radius,
            "center_stage": self.center_stage,
            "action_upon_failure": self.action_upon_failure,
            "illumination_name": self.illumination_name,
            "core_signal_lower_threshold": self.core_signal_lower_threshold,
            "core_signal_range": self.core_signal_range,
            "core_position_offset_tolerance": self.detection_margin,
            "detect_light_direction": self.detect_light_direction,
            "z_scan_range": self.z_scan_range,
            "z_scan_range_sample_count": self.z_scan_range_sample_count,
            "z_scan_range_scan_count": self.z_scan_range_scan_count,
        }
    )
    return node_dict