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refactoring of the laplace beltrami rule (#371)
- splits into different rules for extracting the boundary, and getting distances to src/sink masks - those new rules now produce surface maps (for easier introspection), which are passed along to the laplace beltrami rule - the dentate AP src in bbhist hemi-L was problematic with existing approach, since the PD src/sink were always closer than the AP src, so no vertices were being labelled with AP src. - in this version, we do things a little different: 1. AP and PD are done independently now 2. Instead of nearest neighbor, we use a distance threshold, which is defined based on a signed distance transform of the mask, mapped to the surface. 3. Actually there is a minimum distance, and maximum distance, along with the minimum number of vertices required in the src/sink. The threshold is swept until the desired number is reached, to deal with cases such as the above. - TODO: the get_boundary_vertices script could be further improved to perform connected components and picking the largest one, to avoid being affected by holes or other defects.. - TODO: the laplace beltrami solver doesn't take as long to run now that I am decimating alot, but if we want to further optimize things, I think the step of altering the laplacian based on the boundary conditions, after it has been made a sparse matrix, is where the inefficiency lies (based on profiling). Could try to avoid setting those weights in the first place instead of setting it after the fact.. - NOTE: solve_laplace_beltrami_open_mesh() is kept as is (except for some logging statements)
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| Original file line number | Diff line number | Diff line change |
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| import pyvista as pv | ||
| import numpy as np | ||
| import nibabel as nib | ||
| import nibabel.gifti as gifti | ||
| from collections import defaultdict | ||
| from lib.utils import setup_logger | ||
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| # Setup logger | ||
| log_file = snakemake.log[0] if snakemake.log else None | ||
| logger = setup_logger(log_file) | ||
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| def find_boundary_vertices(mesh): | ||
| """ | ||
| Find boundary vertices of a 3D mesh. | ||
| Args: | ||
| mesh | ||
| Returns: | ||
| list: List of vertex indices that are boundary vertices, sorted in ascending order. | ||
| """ | ||
| vertices = mesh.points | ||
| faces = mesh.faces.reshape((-1, 4))[:, 1:4] # Extract triangle indices | ||
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| edge_count = defaultdict(int) | ||
| # Step 1: Count edge occurrences | ||
| for face in faces: | ||
| # Extract edges from the face, ensure consistent ordering (min, max) | ||
| edges = [ | ||
| tuple(sorted((face[0], face[1]))), | ||
| tuple(sorted((face[1], face[2]))), | ||
| tuple(sorted((face[2], face[0]))), | ||
| ] | ||
| for edge in edges: | ||
| edge_count[edge] += 1 | ||
| # Step 2: Identify boundary edges | ||
| boundary_edges = [edge for edge, count in edge_count.items() if count == 1] | ||
| # Step 3: Collect boundary vertices | ||
| boundary_vertices = set() | ||
| for edge in boundary_edges: | ||
| boundary_vertices.update(edge) | ||
| # Convert the set to a sorted list (array) | ||
| return np.array(sorted(boundary_vertices), dtype=np.int32) | ||
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| def read_surface_from_gifti(surf_gii): | ||
| """Load a surface mesh from a GIFTI file.""" | ||
| surf = nib.load(surf_gii) | ||
| vertices = surf.agg_data("NIFTI_INTENT_POINTSET") | ||
| faces = surf.agg_data("NIFTI_INTENT_TRIANGLE") | ||
| faces_pv = np.hstack([np.full((faces.shape[0], 1), 3), faces]) # PyVista format | ||
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| return pv.PolyData(vertices, faces_pv) | ||
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| logger.info("Loading surface from GIFTI...") | ||
| surface = read_surface_from_gifti(snakemake.input.surf_gii) | ||
| logger.info(f"Surface loaded: {surface.n_points} vertices, {surface.n_faces} faces.") | ||
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| logger.info("Find boundary vertices") | ||
| boundary_indices = find_boundary_vertices(surface) | ||
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| boundary_scalars = np.zeros(surface.n_points, dtype=np.int32) # Default is 0 | ||
| boundary_scalars[boundary_indices] = 1 # Set boundary vertices to 1 | ||
| logger.info( | ||
| f"Boundary scalar array created. {np.sum(boundary_scalars)} boundary vertices marked." | ||
| ) | ||
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| logger.info("Saving GIFTI label file...") | ||
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| # Create a GIFTI label data array | ||
| gii_data = gifti.GiftiDataArray(boundary_scalars, intent="NIFTI_INTENT_LABEL") | ||
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| # Create a Label Table (LUT) | ||
| label_table = gifti.GiftiLabelTable() | ||
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| # Define Background label (key 0) | ||
| background_label = gifti.GiftiLabel( | ||
| key=0, red=1.0, green=1.0, blue=1.0, alpha=0.0 | ||
| ) # Transparent | ||
| background_label.label = "Background" | ||
| label_table.labels.append(background_label) | ||
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| # Define Boundary label (key 1) | ||
| boundary_label = gifti.GiftiLabel( | ||
| key=1, red=1.0, green=0.0, blue=0.0, alpha=1.0 | ||
| ) # Red color | ||
| boundary_label.label = "Boundary" | ||
| label_table.labels.append(boundary_label) | ||
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| # Assign label table to GIFTI image | ||
| gii_img = gifti.GiftiImage(darrays=[gii_data], labeltable=label_table) | ||
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| # Save the label file | ||
| gii_img.to_filename(snakemake.output.label_gii) | ||
| logger.info(f"GIFTI label file saved as '{snakemake.output.label_gii}'.") |
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