pyrot.eye_modelling.match_sclera_to_markers#

Fit the sclera ellipsoid to a set of markers.

Functions#

`match_sclera_to_markers`(→ None)	Fit an ellipsoid to the markers, without using biometry data.
`calc_sclera_center_to_match_white_to_white`(→ float)	Calculate the ellipsoid center location so it matches the WTW-width at vitreous depth.
`calc_sclera_ellipse_for_center`(…)	Calculate the best-fitting sclera ellipse radii given a marker locations and one or more center translations.
`calc_limbusrad`(→ float \| list)	Calculate limbus half-axes for one or an array of sclera ellipses so they match the vitreous depth.
`rotate_eye_model`(structure_set, eye_model_generators, ...)	Rotates the eye model automatically, based on user input.
`project_point_to_ellipse`(center, axes, point)	Projects a point onto the boundary of an ellipse.
`calc_angle_between_points`(center, from_point, to_point)	Calculate the angle (in degrees) needed to rotate from one point to another, relative to the same center.
`calc_rotation_to_align_points`(→ float)	Calculate the optimal rotation angle (in degrees) to align an ellipse point with a manual input.

Module Contents#

pyrot.eye_modelling.match_sclera_to_markers.match_sclera_to_markers(structure_set: object, eye_model_generators: object, eye_model_parameters: object, eye_shape: str, marker_location: str, center_translation: list | None = None) → None#

Fit an ellipsoid to the markers, without using biometry data.

Parameters#

structure_setobject: The structure set containing the POI geometries.
eye_model_generatorsobject: The eye model containing eye parameters.
eye_model_parametersobject: An object containing only specific eye model parameters.
eye_shapestr: The shape of the eye model. Options are “sphere”, “EYEPLAN”, “ellipsoid”, “ellipsoid_fixedCenter”. “sphere” returns a sphere “EYEPLAN” returns an ellipsoid with the same radii in IS and LR directions “ellipsoid” returns an ellipsoid “ellipsoid_fixedCenter” returns an ellipsoid but uses a predefined shift in ellipsoid center location
marker_locationstr: The location of the markers. Options are ‘clips’, ‘choroid’, ‘nocorrection’. “clips” means the location of the clips, which are sutured on the sclera “choroid” means the markers are localized on the choroid For both “clips” and “choroid”, the relevant correction is performed to obtain the sclera radii
center_translationlist, optional: The translation of the center, by default [0, 0, 0] (but this is defined in the function as to not use mutable data structures for argument defaults).

Raises#

NotImplementedError: If an unsupported eye shape or marker location is provided.

pyrot.eye_modelling.match_sclera_to_markers.calc_sclera_center_to_match_white_to_white(structure_set: object, eye_model_parameters: object, marker_location: str, biometry_data: dict, evaluations_start: float = -0.1, evaluations_stop: float = 0.2, n_evaluations: int = 31) → float#

Calculate the ellipsoid center location so it matches the WTW-width at vitreous depth.

This is to ensure the model’s limbus diameter matches the measured limbus diameter / white-to-white, without compromising the correctness of anterior chamber biometry.

Uses linear interpolation to find this center translation. By default, it calculates one sample per 0.1 mm to account for the nonlinearity of the limbus diameter and center translation relation. Using fewer samples with quadratic interpolation (for example with scipy) would be more efficient and more elegant, but this is not possible in some clinical RayOcular scripting environments.

Parameters#

structure_setobject: The structure set containing the POI geometries.
eye_model_parametersobject: An object containing only specific eye model parameters.
marker_locationstr: The location of the markers. Options are ‘clips’, ‘choroid’, ‘nocorrection’.
biometry_datadict: The biometry data containing measurements like ‘AL’, ‘AD’, ‘AD_offset’, and ‘WTW’.
evaluations_startfloat: The minimal center translation to be evaluated in cm, by default -.1
evaluations_stopfloat: The maximal center translation to be evaluated in cm, by default .2
n_evaluationsint, optional: The number of evaluations for center translations, by default 31.

Returns#

float: The center translation based on the WTW radius.

pyrot.eye_modelling.match_sclera_to_markers.calc_sclera_ellipse_for_center(structure_set: object, eye_model_parameters: object, marker_location: str, center_translations: numpy.ndarray) → numpy.ndarray#

Calculate the best-fitting sclera ellipse radii given a marker locations and one or more center translations.

For each center translation, the sclera ellipse radii are calculated based on fitting an ellipse to the marker locations. If a single center translation is given, a single set of sclera ellipse radii is returned. If multiple center translations are given, a list of the corresponding sclera ellipse radii is returned.

Parameters#

structure_setobject: The structure set containing the POI geometries.
eye_model_parametersobject: The eye model object containing only specific eye parameters.
marker_locationstr: The location of the markers. Options are ‘clips’, ‘choroid’, ‘nocorrection’.
center_translationsnp.ndarray | list[np.ndarray]: The center translations to evaluate.

Returns#

np.ndarray | list[np.ndarray]: A single set of sclera ellipse radii if a single center translation is given, or a list of the corresponding sclera ellipse radii for each center translation if multiple center translations are given.

Raises#

NotImplementedError: If an unsupported marker location is provided.

pyrot.eye_modelling.match_sclera_to_markers.calc_limbusrad(eye_model_parameters: object, biometry_data: dict, radii_list: list) → float | list#

Calculate limbus half-axes for one or an array of sclera ellipses so they match the vitreous depth.

Parameters#

eye_model_parametersobject: An object containing only specific eye parameters.
biometry_datadict: The biometry data containing measurements like ‘AL’, ‘AD’, and ‘AD_offset’.
radii_listlist: List of radii for each center translation.

Returns#

float | list: The limbus half-axes for the given sclera ellipses.

pyrot.eye_modelling.match_sclera_to_markers.rotate_eye_model(structure_set: object, eye_model_generators: object, eye_model_parameters: object, poi_type_on: str, roi_name_od: str, roi_name_vitreous: str, based_on: str = 'optic_disk')#

Rotates the eye model automatically, based on user input.

Parameters#

structure_setobject: The structure set containing the POI geometries.
eye_model_generatorsobject: The eye model containing eye parameters.
eye_model_parametersobject: An object containing specific eye parameters
poi_type_onstr: The poi type the poi that defines the optic nerve/disk location is designated by It is necessary that there is only one poi of this type
based_onstr: What the rotation will be based on. Currently, only ‘optic_disk’ is supported
roi_name_odstr: The name of the ROI of the optic disk in the eye model

Raises#

ValueError: If there are multiple POIs with the specified POI type for the optic nerve/disk location.
NotImplementedError: If the method designated in the ‘based_on’ variable is not supported

pyrot.eye_modelling.match_sclera_to_markers.project_point_to_ellipse(center, axes, point)#

Projects a point onto the boundary of an ellipse.

Does this by first calculating the equation of the line between the point and the center of the sclera. Subsequently, the intersection between this line and the sclera ellipse is calculated.

Parameters#

center (tuple): (x_c, y_c) center of the ellipse.
axes (tuple): (a, b) ellipse semi-axes.
point (tuple): (x, y) coordinates of the point to project.

Returns#

tuple: (x_proj, y_proj) coordinates of the projected point on the ellipse.

Raises#

ValueError: If the point is at the center of the ellipse, as the projection is undefined in this case.

pyrot.eye_modelling.match_sclera_to_markers.calc_angle_between_points(center, from_point, to_point)#

Calculate the angle (in degrees) needed to rotate from one point to another, relative to the same center.

Parameters#

center (tuple): (x_c, y_c) center of rotation.
from_point (tuple): (x1, y1) starting point.
to_point (tuple): (x2, y2) target point.

Returns#

float : Rotation angle in degrees (positive = counter-clockwise).

pyrot.eye_modelling.match_sclera_to_markers.calc_rotation_to_align_points(retina_center: tuple, retina_axes: tuple, optic_disc_eyemodel: tuple, optic_disc_poi: tuple) → float#

Calculate the optimal rotation angle (in degrees) to align an ellipse point with a manual input.

Main wrapper function to compute the optimal rotation angle (in degrees) to align an ellipse_point with the projection of a manual_input.

Parameters#

retina_center (tuple): (x_c, y_c) center of the ellipse.
retina_axes (tuple): (a, b) retina ellipse axes.
optic_disc_eyemodel (tuple): the location of the optic disk of the current eye model
optic_disc_poi (tuple): the clicked POI of the actual location of the optic disk

Returns#

float : Rotation angle in degrees.