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Scale resampling length #351

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Scale resampling length #351

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f753a8a
scaled resampling length by voxelsize for robustness in case of highe…
jo-mueller Dec 21, 2023
483091b
used pure vedo instead of nppas
jo-mueller Dec 21, 2023
4be69b5
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 21, 2023
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18 changes: 8 additions & 10 deletions src/napari_stress/_reconstruction/toolbox.py
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Original file line number Diff line number Diff line change
Expand Up @@ -261,7 +261,7 @@ def reconstruct_droplet(
- droplet center: center of droplet

"""
import copy
import vedo
import napari_process_points_and_surfaces as nppas
import napari_segment_blobs_and_things_with_membranes as nsbatwm
from napari_stress import reconstruction
Expand All @@ -280,20 +280,18 @@ def reconstruct_droplet(
# convert to surface
label_image = nsbatwm.connected_component_labeling(binarized_image)
surface = nppas.largest_label_to_surface(label_image)
surface = nppas.remove_duplicate_vertices(surface)

# Smooth and decimate
surface = nppas.smooth_surface(
surface, n_smoothing_iterations, feature_angle=120, edge_angle=90
vedo_mesh = (
vedo.Mesh(surface)
.clean()
.smooth(niter=n_smoothing_iterations, feature_angle=120, edge_angle=90)
)
surface = nppas.decimate_quadric(surface, number_of_vertices=n_points)
points_first_guess = surface[0]
points = copy.deepcopy(points_first_guess)
vedo_mesh.decimate(method="quadric", n=n_points)
points = vedo_mesh.vertices

# repeat tracing `n_tracing_iterations` times
for i in range(n_tracing_iterations):
resampled_points = resample_pointcloud(
points, sampling_length=resampling_length
points, sampling_length=resampling_length / (target_voxelsize**2)
)

traced_points, trace_vectors = reconstruction.trace_refinement_of_surface(
Expand Down