openflexure_microscope_server.scan

class documentation

class ScanPlanner: (source)

Known subclasses: openflexure_microscope_server.scan_planners.SmartSpiral

Constructor: ScanPlanner(initial_position, planner_settings)

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A base class for a scan planner.

This should never be used directly for a scan, it should be subclassed.

Each subclass should implement at least the methods with NotImplementedError set:

_parse() - to parse the planner_settings dictionary, saving values to class

variables
_initial_location_list() - Sets the list of locations for the scan to follow

For a simple scan pattern this should be sufficient. For more complex ones that dynamically adjust the path it is suggested to override mark_location_visited() calling super().mark_location_visited() at the start of the method so that all locations are adjusted.

When subclassing be sure to use enforce_xy_tuple and enforce_xyz_tuple on any user data before running.

Method	`__init__`	Set up lists for the path planning, and scan history.
Method	`closest_focus_site`	Return the xyz position of the closest site where focus was achieved.
Method	`get_next_location_and_z_estimate`	Return the next location to scan and its estimated z-position.
Method	`get_visited_location`	Return the scan location from the history that matches the input position.
Method	`mark_location_visited`	Mark the location as visited.
Method	`position_planned`	Return True if input scan position position is planned.
Method	`position_visited`	Return True if input scan position has been visited before.
Property	`focused_locations`	Property to access a copy of the focused_locations.
Property	`imaged_locations`	Property to access a copy of the imaged_locations.
Property	`path_history`	Property to access a copy of the path_history.
Property	`remaining_locations`	Property to access a copy of the remaining_locations.
Property	`scan_complete`	Return True if there are no locations left to scan.
Method	`_initial_location_list`	Set the initial list of locations for this scan planner.
Method	`_parse`	Parse any settings sent to this planner and store them if needed.
Instance Variable	`_initial_position`	Undocumented
Instance Variable	`_path_history`	Undocumented
Instance Variable	`_remaining_locations`	Undocumented

def __init__(self, initial_position: XYPos, planner_settings: dict | None = None): (source) ¶

overridden in openflexure_microscope_server.scan_planners.SmartSpiral

Set up lists for the path planning, and scan history.

def closest_focus_site(self, xy_pos: XYPos) -> XYZPos | None: (source) ¶

Return the xyz position of the closest site where focus was achieved.

The most recently taken image is returned in the case of a tie.

Returns None if there if no focussed locations are present

Parameters
xy_pos:`XYPos`	The xy_position which the returned position should be closest to.

Returns
`XYZPos \| None`	Undocumented

def get_next_location_and_z_estimate(self) -> tuple[XYPos, int | None]: (source) ¶

overridden in openflexure_microscope_server.scan_planners.SmartSpiral

Return the next location to scan and its estimated z-position.

Note z-position may be None! This indicates that the current z, position should be used.

def get_visited_location(self, position: XYPos | XYZPos | FutureScanLocation) -> VisitedScanLocation: (source) ¶

Return the scan location from the history that matches the input position.

def mark_location_visited(self, xyz_pos: XYZPos, imaged: bool, focused: bool): (source) ¶

overridden in openflexure_microscope_server.scan_planners.SmartSpiral

Mark the location as visited.

Parameters
xyz_pos:`XYZPos`	the x_y_z position
imaged:`bool`	true if an image was taken, false if not (due to background detect)
focused:`bool`	true if autofocus completed successfully