mosaic.geometry.VolumeGeometry

class VolumeGeometry(volume=None, volume_sampling_rate=array([1., 1., 1.]), target_resolution=10.0, **kwargs)

Bases: Geometry

Geometry class specialized for 3D volume rendering with isosurfaces.

Parameters:

volumenp.ndarray, optional

3D volume data array.

volume_sampling_ratenp.ndarray, optional

Sampling rates for volume data, by default ones(3).

target_resolutionfloat, optional

Target physical resolution for lowpass filtering. Set to 0 to disable filtering. By default 10.0 (Angstroms).

**kwargs

Additional keyword arguments passed to parent Geometry class.

__init__(volume=None, volume_sampling_rate=array([1., 1., 1.]), target_resolution=10.0, **kwargs)

Methods

__init__([volume, volume_sampling_rate, ...])
change_representation([representation])	Change the visual representation mode of the geometry.
color_points(point_ids, color)	Color specific points in the geometry using set_scalars backend.
get_number_of_points()	Get total number of points in the geometry.
get_point_data()
is_mesh_representation([representation])
merge(geometries)	Merge multiple geometry objects into a single geometry.
set_appearance([isovalue_percentile])	Set visual appearance properties of the geometry.
set_color([color])	Set uniform color for all points in the geometry.
set_scalars(scalars, color_lut[, ...])	Set scalar data for coloring points.
set_visibility([visibility])	Set geometry visibility in the scene.
subset(idx[, copy])
swap_data(points[, normals, faces, ...])	Replace geometry data with new point cloud or mesh data.
update_isovalue(upper[, lower])	Update the isovalue for volume surface rendering.
update_isovalue_quantile(upper_quantile[, ...])	Update isovalue using quantile-based thresholds.
update_target_resolution(resolution)	Update the target physical resolution for lowpass filtering.

Attributes

actor	VTK actor object for rendering.
model
normals	Normal vectors at each point.
points	3D point coordinates of the geometry.
quaternions	Orientation quaternions for each point.
sampling_rate
vertex_properties
visible	Visibility state of the geometry.