organoid_tracker.core.spline module

class organoid_tracker.core.spline.Spline

Bases: object

A curve (curved line) trough the positions. This can be used to measure how far the positions are along this curve.

An offset specifies the zero-point of the axis. A checkpoint (relative to the offset) specifies some point after which a newregion starts. For example, in intestinal organoids this is used to mark the boundary between the crypt and the villus.

add_point(x: float, y: float, z: float): Adds a new point to the path.

copy() → Spline: Returns a copy of this path. Changes to this path will not affect the copy and vice versa.

from_position_on_axis(path_position: float) → Optional[Tuple[float, float, float]]: Given a path position, this returns the corresponding x, y and z coordinates. Returns None for positions outside of the line.

get_direction_marker() → str: Returns a char thar represents the general direction of this path: “>”, “<”, “^” or “v”. The (0,0) coord is assumed to be in the top left.

get_interpolation_2d() → Tuple[List[float], List[float]]: Returns a (cached) list of x and y values that are used for interpolation.

get_interpolation_3d() → Tuple[List[float], List[float], List[float]]: Returns a (cached) list of x, y and z values that are used for interpolation.

get_offset() → float: Gets the offset used in calls to get_path_position_2d and path_position_to_xy. Note that these methods apply the offset automatically, so except for saving/loading purposes there should be no need to call this method.

get_points_2d() → Tuple[List[float], List[float]]: Gets all explicitly added points (no interpolation) without the z coord.

get_points_3d() → Tuple[List[float], List[float], List[float]]: Gets all explicitly added points (no interpolation) including the z coord.

get_z() → int: Gets the average Z coord of this path. Raises ValueError if the path has no points.

length() → float: Gets the length of the spline.

move_points(delta: Position): Translates all points in this path with the specified amount.

remove_point(x: float, y: float): Removes the point that is (within 1 px) at the given coords. Does nothing if there is no such point.

set_offset(offset: float): Manually sets the offset used in calls to get_path_position_2d and path_position_to_xy. See also update_offset_for_positions.

to_position_on_axis(position: Position) → Optional[SplinePosition]: Interprets this spline as an axis. Gets the closest position on this axis and the distance to the axis, both in pixels. Returns None if this spline has fewer than 2 points.

update_offset_for_positions(positions: Iterable[Position]): Updates the offset of this spline such that the lowest path position that is ever returned by get_path_position_2d is exactly 0.

class organoid_tracker.core.spline.SplineCollection

Bases: object

Holds the paths of all time points in an experiment.

add_spline(time_point: TimePoint, path: Spline, spline_id: Optional[int]) → int: Adds a new spline to the given time point. If another spline with that id already exists in the time point, it is overwritten. If spline_id is None, a new id will be assigned. The spline_id is then returned.

all_splines() → Iterable[Tuple[int, TimePoint, Spline]]: Gets all paths. Note that a single time point can have multiple paths.

exists(path: Spline, time_point: TimePoint) → bool: Returns True if the path exists in this path collection at the given time point, False otherwise.

first_time_point() → Optional[TimePoint]: Gets the first time point that contains data axes, or None if there are no axes stored.

first_time_point_number() → Optional[int]: Gets the first time point that contains data axes, or None if there are no axes stored.

get_marker_name(axis_id: int) → Optional[str]: Gets the marker of the data axes with the given id.

get_marker_names() → Iterable[Tuple[int, str]]: Gets all registered axis markers as (id, name).

get_spline(time_point: TimePoint, spline_id: int) → Optional[Spline]: Gets the spline with the given id and time point. Returns None if not found.

has_splines() → bool: Returns True if there are any paths stored in this collection.

is_axis(spline_id: int) → bool: Returns true if the spline with the given id is an axis.

last_time_point() → Optional[TimePoint]: Gets the last time point (inclusive) that contains data axes, or None if there are no axes stored.

last_time_point_number() → Optional[int]: Gets the last time point (inclusive) that contains data axes, or None if there are no axes stored.

move_in_time(time_point_delta: int): Moves all splines the specified amount of time points in time.

of_time_point(time_point: TimePoint) → Iterable[Tuple[int, Spline]]: Gets the data axes of the time point along with their id, or an empty collection if that time point has no paths defined.

reference_time_point(number: Optional[TimePoint] = None) → Optional[TimePoint]: Gets or sets the reference time point number. The reference time point is used to define the “original” axis on which a point resides. Returns None when getting the time point number if there are no data axes provided.

remove_spline(time_point: TimePoint, spline_to_remove: Spline): Removes the given data axis from the given time point. Does nothing if the data axis is not used for the given time point.

set_marker(axis_id: int, axis_marker: Optional[Marker]): Sets the marker of the specified data axes across all time points. High-level version of set_marker_name. If the marker has the extra data “is_axis”: true, then the spline will be used as an axis.

set_marker_name(axis_id: int, axis_marker: Optional[str], is_data_axis: bool): Sets the marker of the specified data axes across all time points

time_points() → Iterable[TimePoint]: Gets all time points with data axes in them, from first to last.

to_position_on_original_axis(links: Links, position: Position) → Optional[SplinePosition]: Gets the position on the axis that was closest in the first time point this position appeared. In this way, every position is assigned to a single axis, and will never switch to another axis during its lifetime.

to_position_on_spline(position: Position, only_axis=False) → Optional[SplinePosition]

update_for_changed_positions(time_point: TimePoint, new_positions: Iterable[Position]): If the positions of a time point have changed, this method must be called to update the zero point of all axes.

class organoid_tracker.core.spline.SplinePosition(axis: Spline, pos: float, distance: float)

Bases: object

Records a position projected on a spline: both the spline, its id, the position on the spline and the distance to the spline are recorded.

calculate_angle(position: Position, resolution: ImageResolution) → float: Calculates the angle from this point on the data axis to the given position.

distance: float

pos: float

spline: Spline

spline_id: int