Reconstruct

class Qiber3D.Reconstruct

Bases: object

classmethod clean(net, sliver_threshold=6)

Clean a Qiber3D.Network from small sliver.

Parameters

  • net (Qiber.Network) – network to smooth

  • sliver_threshold (int) – treat smaller segments

Returns

classmethod create_base_network(image, low_memory=False, distance_voxel_overlap=15)

Create a unoptimized Qiber3D.Network from a binary image.

Parameters

  • image (np.ndarray) – binary image stack

  • low_memory (bool) – split the image for the euclidean distance transformation

  • distance_voxel_overlap (int) – overlap for the low memory euclidean distance transformation in voxel

Returns

Qiber3D.Network

classmethod get_network(image, scale=1.0, input_path=None, sliver_threshold=6, voxel_per_point=10.0, low_memory=False, distance_voxel_overlap=15)

Create a cleaned and smoothed Qiber3D.Network from a binary image.

Parameters

  • image (np.ndarray) – binary image stack

  • scale (float) – ratio between voxel size and length unit

  • input_path (str, Path) – set this path as new imput path of the returning network

  • sliver_threshold (int) – treat smaller segments

  • voxel_per_point (float) – distance between interpolated points

  • low_memory (bool) – low memory mode

  • distance_voxel_overlap (int) – overlap for the low memory euclidean distance transformation in voxel

Returns

Qiber3D.Network

classmethod smooth(net, voxel_per_point=10)

Smooth a Qiber3D.Network in place with a third order spline interpolation.

Parameters

  • net (Qiber.Network) – network to smooth

  • voxel_per_point (float) – distance between interpolated points

Returns

Qiber3D.Network