Merge pull request #371 from jo-mueller/added-binary-fill-to-surface-labelled-droplet-reconstruction

Added binary fill to surface labelled droplet reconstruction

Author: jo-mueller

docs/04_FAQ/bulk_vs_surface.ipynb

@@ -0,0 +1,3 @@
+gamma: 6.0
+max_degree: 20
+n_quadrature_points: 590

docs/04_FAQ/imgs/example_droplet_bulk.png

@@ -0,0 +1,18 @@
+edge_type: interior
+fit_type: fancy
+interpolation_method: linear
+n_points: 256
+n_smoothing_iterations: 15
+n_tracing_iterations: 1
+outlier_tolerance: 1.5
+remove_outliers: true
+resampling_length: 5.0
+sampling_distance: 1.0
+smoothing_sigma: 1.0
+target_voxelsize: 0.2868
+trace_length: 30.0
+return_intermediate_results: true
+voxelsize: !!ndarray
+- 0.47
+- 0.1036
+- 0.1036

docs/04_FAQ/imgs/example_droplet_merge.png

@@ -0,0 +1,18 @@
+edge_type: surface
+fit_type: fancy
+interpolation_method: linear
+n_points: 256
+n_smoothing_iterations: 15
+n_tracing_iterations: 1
+outlier_tolerance: 1.5
+remove_outliers: true
+resampling_length: 5.0
+sampling_distance: 1.0
+smoothing_sigma: 1.0
+target_voxelsize: 0.2868
+trace_length: 30.0
+return_intermediate_results: true
+voxelsize: !!ndarray
+- 0.47
+- 0.1036
+- 0.1036

docs/04_FAQ/imgs/example_droplet_surface.png

@@ -57,6 +57,7 @@ parts:
     chapters:
     - file: 04_FAQ/Installation
     - file: 04_FAQ/Acknowledgement_and_citation
+    - file: 04_FAQ/bulk_vs_surface
     - file: 04_FAQ/Validation
       sections:
       - file: 04_FAQ/validation/validation_stress_paper

docs/04_FAQ/settings_measurement.yaml

@@ -274,6 +274,7 @@ def reconstruct_droplet(
     from skimage import filters, transform
     from .refine_surfaces import resample_pointcloud
     from .patches import iterative_curvature_adaptive_patch_fitting
+    from scipy.ndimage import binary_fill_holes
 
     scaling_factors = voxelsize / target_voxelsize
     rescaled_image = transform.rescale(
@@ -283,6 +284,9 @@ def reconstruct_droplet(
     threshold = filters.threshold_otsu(rescaled_image)
     binarized_image = rescaled_image > threshold
 
+    if edge_type == "surface":
+        binarized_image = binary_fill_holes(binarized_image)
+
     # convert to surface
     label_image = nsbatwm.connected_component_labeling(binarized_image)
     surface = nppas.largest_label_to_surface(label_image)