Ctrl+K

tyssue.particles package

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)[source]#

Bases: object

Container class to ease discretisation along the edges

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

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)[source]#

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)[source]#
update_all()[source]#
update_offset()[source]#
update_offset_lut(offset_lut=None)[source]#

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

  • grid (Default is a shifted regular) –

  • `np.arange(0.5 –

  • num` (num+0.5) /) –

update_particles()[source]#

  • 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()[source]#

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()[source]#
class tyssue.particles.point_cloud.FaceGrid(edges_df, base, **kwargs)[source]#

Bases: object

face_point_cloud(coords=['x', 'y', 'z'], dcoords=['dx', 'dy', 'dz'])[source]#
update_grid()[source]#
tyssue.particles.point_cloud.get_edge_bases(eptm, base=('face', 'srce', 'trgt'))[source]#

Module contents#

Epithelium subsegmentation system

Contents