Case - the fundamental data structure of openep-py

A Case stores all the information obtained during a clinical mapping procedure.

Warning

This class should not be instatiated directly. Instead, a Case can be created using openep.io.readers.load_openep_mat().

Tip

Once you have a Case, you can perform analyses using the functions in openep.case.case_routines. You can also create a 3D mesh using the create_mesh() method.

class openep.data_structures.case.Case

The fundamental OpenEP object.

The class contains all the information on a single case exported from a clinical mapping system.

Parameters

• name (str) – Name to assign to the dataset

• points (ndarray) – 3D coordinates of points on the mesh

• indices (ndarray) – Indices of points that make up each face of the mesh

• fields (Fields) – Numpy arrays of the scalar fields associated with each point on the surface of a mesh

• electtic (Electric) – Electrical data obtained during a clinical mapping procedure.

• ablation (Ablation, optional) – Ablation data obtained during a clinical mapping procedure.

• notes (list, optional) – Notes associated with the dataset.

create_mesh(recenter: bool = True, back_faces: bool = False)

Create a new mesh object from the stored nodes and indices

Parameters

• recenter – if True, recenter the mesh to the origin

• back_faces – if True, calculate back face triangles

Returns

mesh (pyvista.Polydata) – a mesh created from the case’s points and indices

get_surface_data(copy: bool = False) → Tuple[numpy.ndarray, numpy.ndarray]

Extract the surface data for the case.

Parameters

copy (bool, optional) – If True, a copy of the data will be returned. The default is False, in which case a view of the data is returned.

Returns

points (ndarray) – 3D coordinates of points on the mesh indices (ndarray): Indices of points that make up each face of the mesh

get_field(fieldname: str, copy: bool = False) → numpy.ndarray

Extract scalar field data associated with each point on the surface.

Parameters

• fieldname (str) – Must be one of: bipolar_voltage, unipolar_voltage, local_activation_time, impedance, force.

• copy (bool, optional) – If True, a copy of the data will be returned. The default is False, in which case a view of the data is returned.

Returns

field (np.ndarray) – scalar field data

Note

Case contains information on the 3D surface and associated scalar fields, the electrograms, and the ablation sites. These data are, respectively, stored as the following data structures: openep.data_structures.surface.Fields, openep.data_structures.electric.Electric, and openep.data_structures.ablation.Ablation.

Scalar field data

class openep.data_structures.surface.Fields

Class for storing information about the surface of a mesh

Parameters

• bipolar_voltage (np.ndarray) – array of shape N

• unipolar_voltage (np.ndarray) – array of shape N

• local_activation_time (np.ndarray) – array of shape N

• impedance (np.ndarray) – array of shape N

• force (np.ndarray) – array of shape N

Electrical data

class openep.data_structures.electric.Electric

Class for storing electrical data obtained during a clinical mapping procedure.

Parameters

• names (np.ndarray) – The physician-visible names of the points applied during the clinical case.

• internal_names (np.ndarray) – The internal names of the points used by the clinical electroanatomic mapping system.

• bipolar_egm (Electrogram) – The bipolar electrograms, coordinates of mapping points, names of the electrodes, and voltages.

• unipolar_egm (Electrogram) – The unipolar electrograms, coordinates of the two unipole electrodes, names of the two unipole electrodes, and voltages.

• reference_egm (Electrogram) – The reference electrograms for each mapping point.

• ecg (np.ndarray) – The surface electrocardiogram for each mapping point.

• impedance (Impedance) – The time and values of impedance traces for each mapping point

• surface (ElectricSurface) – The position of each mapping point projected to the nearest point on the 3D surface, as well as the normal to the surface at that point.

• annotations (Annotations) – The window of interest, local activation time, and reference activation time for each mapping point.

class openep.data_structures.electric.Electrogram

Class for storing information about electrograms

Parameters

• egm (np.ndarray) – Electrograms

• points (np.ndarray) – 3D coordinates of the associated mapping points.

• voltage (np.ndarray) – The voltage at each mapping point.

• gain (np.ndarray) – gain to apply to each signal

• names (np.ndarray) – Names of the associated electrodes.

class openep.data_structures.electric.Impedance

Class for storing information about impedance traces.

Parameters

• times (np.ndarray) – Times at which the traces were taken.

• values (np.ndarray) – Impedance measurements.

class openep.data_structures.electric.ElectricSurface

Class for storing information about electroanatomic data projected onto the surface mesh.

Parameters

• nearest_point (np.ndarray) – The position of each mapping point projected to the nearest point on the 3D surface constructed by the clinical mapping system.

• normals (np.ndarray) – Normal to the surface at each of the nearest points.

class openep.data_structures.electric.Annotations

Class for storing information about activation times for electrograms.

Parameters

• window_of_interest (np.ndarray) – The window of interest for each mapping point

• local_activation_time (np.ndarray) – The local activation time for each mapping point

• reference_activation_time (np.ndarray) – The reference activation time for each mapping point

Ablation data

class openep.data_structures.ablation.Ablation

Class for storing ablation data.

Parameters

• times (np.ndarray) – array of shape N

• power (np.ndarray) – array of shape N

• impedance (np.ndarray) – array of shape N

• temperature (np.ndarray) – array of shape N

• force (AblationForce) – data on the force at each ablation site. Specifically, the force applied, the time at which it was applied, and axial and lateral angles, and the 3D coordinates of the ablation site.

class openep.data_structures.ablation.AblationForce

Class for storing data on ablation force.

Parameters

• times (np.ndarray) – array of shape N

• force (np.ndarray) – array of shape N

• axial_angle (np.ndarray) – array of shape N

• lateral_angle (np.ndarray) – array of shape N

• points (np.ndarray) – array of shape Nx3