tyssue.particles package

Submodules

tyssue.particles.point_cloud module

Utilities to generate point clouds

The positions of the points are generated along the architecture of the epithelium.

class tyssue.particles.point_cloud.EdgeSubdiv(edge_df, **kwargs)

Bases: object

Container class to ease discretisation along the edges

Creates an indexer and an offset array to ease discretisation along the edges.

Parameters

• edge_df (pd.DataFrame,) –

• parameters (Keyword) –

• ------------------ –

• density (number of points per edge) –

upcaster

edge indices repeated to match the lookup table

Type

np.ndarray, shape (Np,)

offset

piecewise linear offset along the edges, such that ::math:M_{ij}^n = offset[n]*r_{ij}:

Type

np.ndarray, shape (Np,)

edge_point_cloud(srce_pos, r_ij, offset_modulation=None, modulation_kwargs=None, coords=['x', 'y', 'z'], dcoords=['dx', 'dy', 'dz'])

Generates a point cloud along the edges of the epithelium.

if a offset_modulation function is provided, it is used to transform the offsets

Parameters

• srce_pos (DataFrame of shape (self.Ne, ndim)) – with the origins of the points for each edge (usually the edge upcasted source vertex)

• r_ij (DataFrame of shape (self.Ne, ndim)) – the edge vector coordiantes

• offset_modulation (function of self returning) – an array with shape (self.Np,) containing the modified offsets. self.points[‘offset’] is used by default.

• modulation_kwargs (keyword arguments to the modulation) – function

Returns

points

Return type

(Np, 3) pd.DataFrame with the points positions

static from_eptm_edges(eptm, **kwargs)

Creates an EdgeSubdiv instance and computes the point grid allong the edges from the source vertex to its target. :returns: subdiv :rtype: a EdgeSubdiv instance

upcast(df)

update_all()

update_offset()

update_offset_lut(offset_lut=None)

Updates the density lookup table function.

The offset_lut can be any function with a single num argument

Parameters

• offset_lut (function, default None,) – edge-wise function of the number of points giving the offset positions

• is a shifted regular grid (Default) –

• `np.arange(0.5 –

• / num` (num+0.5)) –

update_particles()

• Updates the number of particles per edge from edges length

and density values: num_particles = length * density * Also updates the self.points df

update_upcaster()

resets the ‘upcaster’ column of self.points,

‘upcaster’ indexes over self.edge_df repeated to upcast data from the edge df to the points df

validate()

class tyssue.particles.point_cloud.FaceGrid(edges_df, base, **kwargs)

Bases: object

face_point_cloud(coords=['x', 'y', 'z'], dcoords=['dx', 'dy', 'dz'])

update_grid()

tyssue.particles.point_cloud.get_edge_bases(eptm, base='face', 'srce', 'trgt')

Module contents

Epithelium subsegmentation system