miblab-ssa 0.0.0__tar.gz

miblab_ssa-0.0.0/LICENSE

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miblab_ssa-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: miblab-ssa
+Version: 0.0.0
+Summary: Statistical shape analysis for medical imaging
+Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://miblab.org/
+Project-URL: Source Code, https://github.com/openmiblab/pckg-miblab-ssa
+Keywords: python,medical imaging,MRI
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: tqdm
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: scikit-image
+Requires-Dist: trimesh
+Requires-Dist: dask
+Requires-Dist: dask-ml
+Requires-Dist: zarr
+Requires-Dist: pyshtools
+Requires-Dist: psutil
+Requires-Dist: vreg
+Dynamic: license-file
+
+# miblab-ssa
+Statistical shape analysis for medical imaging data

miblab_ssa-0.0.0/README.md

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+# miblab-ssa
+Statistical shape analysis for medical imaging data

miblab_ssa-0.0.0/pyproject.toml

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+# https://packaging.python.org/en/latest/specifications/pyproject-toml/#pyproject-toml-spec
+
+[build-system]
+build-backend = 'setuptools.build_meta'
+requires = ['setuptools>=61.2']
+
+[project]
+name = "miblab-ssa"
+version = "0.0.0"
+dependencies = [
+  'tqdm',
+  'numpy',
+  'scipy',
+  'scikit-learn',
+  'scikit-image',
+  'trimesh',
+  'dask',
+  'dask-ml',
+  'zarr',
+  'pyshtools',
+  'psutil',
+  'vreg',
+]
+# optional information
+description = "Statistical shape analysis for medical imaging"
+readme = "README.md"
+authors = [
+  { name = "Steven Sourbron", email = "s.sourbron@sheffield.ac.uk" },
+]
+license = "Apache-2.0"
+classifiers = [
+  # How mature is this project? Common values are
+  #   3 - Alpha
+  #   4 - Beta
+  #   5 - Production/Stable
+  'Development Status :: 3 - Alpha',
+
+  # Indicate who your project is intended for
+  'Intended Audience :: Developers',
+  'Intended Audience :: Science/Research',
+  'Topic :: Scientific/Engineering',
+  'Operating System :: OS Independent',
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3"
+]
+keywords = [
+  'python', 
+  "medical imaging",  
+  "MRI",
+]
+
+
+[project.urls]
+"Homepage" = "https://miblab.org/"
+"Source Code" = "https://github.com/openmiblab/pckg-miblab-ssa"
+
+
+[tool.setuptools.packages.find]
+where = ["src"]

miblab_ssa-0.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

miblab_ssa-0.0.0/src/miblab_ssa/__init__.py

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+from .normalize import (
+    normalize_kidney_mask
+)
+from .ssa import (
+    features_from_dataset_zarr, 
+    pca_from_features_zarr, 
+    coefficients_from_features_zarr,
+    modes_from_pca_zarr,
+)
+from .metrics import (
+    hausdorff_matrix_zarr,
+    dice_matrix_zarr
+)
+from . import sdf_ft, sdf_cheby, lb, zernike

miblab_ssa-0.0.0/src/miblab_ssa/lb.py

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+import numpy as np
+from skimage import measure
+import trimesh
+from scipy.sparse import coo_matrix, diags
+from scipy.sparse.linalg import eigsh
+
+# -------------------------------
+# Helper: convert trimesh to mask
+# -------------------------------
+def mesh_to_mask(mesh, shape):
+    """
+    Rasterize mesh into 3D binary mask
+    """
+    mask = np.zeros(shape, dtype=bool)
+    # Use trimesh voxelization
+    vox = mesh.voxelized(pitch=1.0)
+    indices = vox.sparse_indices
+    mask[indices[:,0], indices[:,1], indices[:,2]] = True
+    return mask
+
+# -------------------------------
+# 1️⃣ Mask → Mesh
+# -------------------------------
+def mask_to_mesh(mask, spacing=(1.0,1.0,1.0)):
+    """
+    Convert 3D binary mask to triangular mesh.
+    """
+    verts, faces, normals, values = measure.marching_cubes(mask.astype(float), level=0.5, spacing=spacing)
+    mesh = trimesh.Trimesh(vertices=verts, faces=faces, process=False)
+    return mesh
+
+
+def mask_to_mesh_fixed_vertices(mask: np.ndarray, spacing: np.ndarray, target_vertices: int = 5000) -> trimesh.Trimesh:
+    """
+    Convert a 3D binary mask to a mesh with a fixed number of vertices.
+
+    Parameters
+    ----------
+    center : bool
+        If True, center the mesh at the origin.
+    spacing : np.ndarray
+        Voxel size
+
+    Returns
+    -------
+    mesh_simplified : trimesh.Trimesh
+        Mesh object with approximately target_vertices vertices.
+    """
+    # Step 1: extract surface using marching cubes
+    verts, faces, normals, _ = measure.marching_cubes(mask.astype(float), level=0.5, spacing=spacing)
+
+    mesh = trimesh.Trimesh(vertices=verts, faces=faces, vertex_normals=normals, process=True)
+
+    # Step 2: simplify / resample to target number of vertices
+    # Needs testing
+    mesh_simplified = mesh.simplify_quadratic_decimation(target_vertices)
+
+    return mesh_simplified
+
+
+# -------------------------------
+# 2️⃣ Preprocessing for invariance (FIXED)
+# -------------------------------
+def preprocess_mesh(mesh):
+    """
+    Apply translation, scaling, and PCA alignment.
+    Returns processed mesh and preprocessing parameters for inverse mapping.
+    """
+    # Center
+    centroid = mesh.vertices.mean(axis=0)
+    mesh_c = mesh.copy()
+    mesh_c.vertices = mesh.vertices - centroid
+
+    # Scale
+    scale = np.sqrt((mesh_c.vertices**2).sum(axis=1).mean())
+    mesh_s = mesh_c.copy()
+    mesh_s.vertices = mesh_c.vertices / scale
+
+    # PCA alignment
+    cov = np.cov(mesh_s.vertices.T)
+    eigvals, eigvecs = np.linalg.eigh(cov)
+    idx = np.argsort(eigvals)[::-1]
+    eigvecs = eigvecs[:, idx]
+    mesh_aligned = mesh_s.copy()
+    mesh_aligned.vertices = mesh_s.vertices @ eigvecs
+
+    # Save parameters for inverse transformation
+    params = {"centroid": centroid, "scale": scale, "pca_eigvecs": eigvecs}
+    return mesh_aligned, params
+
+def inverse_preprocess_mesh(vertices, params):
+    """
+    Map reconstructed vertices back to original coordinates.
+    """
+    v = vertices @ params["pca_eigvecs"].T  # undo PCA
+    v = v * params["scale"]                # undo scaling
+    v = v + params["centroid"]             # undo translation
+    return v
+
+# -------------------------------
+# 3️⃣ Laplace-Beltrami Eigenfunctions
+# -------------------------------
+def cotangent_laplacian(mesh):
+    vertices = mesh.vertices
+    faces = mesh.faces
+
+    def cotangent(a, b, c):
+        ba = b - a
+        ca = c - a
+        cos_angle = np.dot(ba, ca)
+        sin_angle = np.linalg.norm(np.cross(ba, ca))
+        return cos_angle / (sin_angle + 1e-10)
+
+    I, J, V = [], [], []
+    n = len(vertices)
+    for face in faces:
+        i, j, k = face
+        vi, vj, vk = vertices[i], vertices[j], vertices[k]
+        cot_alpha = cotangent(vj, vi, vk)
+        cot_beta  = cotangent(vk, vj, vi)
+        cot_gamma = cotangent(vi, vk, vj)
+        for (p, q, w) in [(i,j,cot_gamma),(j,i,cot_gamma),
+                          (j,k,cot_alpha),(k,j,cot_alpha),
+                          (k,i,cot_beta),(i,k,cot_beta)]:
+            I.append(p)
+            J.append(q)
+            V.append(w/2)
+
+    L = coo_matrix((V, (I, J)), shape=(n, n))
+    L = diags(L.sum(axis=1).A1) - L
+    return L
+        
+def lb_eigen_decomposition(mesh, k=50):
+    L = cotangent_laplacian(mesh)
+    M = diags(np.ones(mesh.vertices.shape[0]))
+    eigvals, eigvecs = eigsh(L, k=k, M=M, sigma=1e-8, which='LM')
+    return eigvals, eigvecs
+
+def surface_to_coefficients(mesh, k=50):
+    eigvals, eigvecs = lb_eigen_decomposition(mesh, k=k)
+    coords = mesh.vertices
+    coeffs = eigvecs.T @ coords  # shape (k,3)
+    return coeffs, eigvecs, eigvals
+
+
+def rotationally_invariant_lb_coeffs(coeffs, eigvals, k=100):
+    """
+    Compute rotationally invariant Laplace–Beltrami spectral coefficients.
+
+    Parameters
+    ----------
+    mesh : trimesh.Trimesh or similar
+        Input surface mesh with vertices (N, 3)
+    k : int
+        Number of eigenmodes to use
+
+    Returns
+    -------
+    eigvals : (k,) array
+        Laplace–Beltrami eigenvalues
+    invariants : (k,) array
+        Rotationally invariant spectral coefficients
+    """
+    invariants = np.linalg.norm(coeffs, axis=1)  # sqrt(sum over x,y,z)
+    invariants /= np.linalg.norm(invariants)
+
+    # Optional: normalize eigenvalues by first non-zero eigenvalue
+    eigvals = eigvals / eigvals[1] if eigvals[1] != 0 else eigvals
+
+    # Optionally drop the first eigenvalue (zero mode) from descriptor since it's trivial
+    eigvals = eigvals[1:]  # length k-1
+    invariants = invariants[1:]  # skip first mode as it may be trivial
+
+    descriptor = np.concatenate([eigvals[:k], invariants[:k]])
+    descriptor /= np.linalg.norm(descriptor)  # normalize final vector
+
+    return invariants, eigvals
+
+
+# def coefficients_to_surface(coeffs, eigvecs):
+#     reconstructed = eigvecs @ coeffs
+#     return reconstructed
+
+def coefficients_to_surface(coeffs, eigvecs, threshold=None):
+    """
+    Reconstruct surface vertices from coefficients and eigenvectors.
+    
+    Args:
+        coeffs (np.ndarray): shape (k, 3), coefficients from surface_to_coefficients
+        eigvecs (np.ndarray): shape (n, k), eigenvectors of Laplace-Beltrami
+        threshold (float, optional): percentage (0-100).
+            If given, only the top threshold% dominant modes (by coefficient norm)
+            are kept in the reconstruction.
+    
+    Returns:
+        np.ndarray: reconstructed vertices, shape (n, 3)
+    """
+    if threshold is not None:
+        # Compute importance of each eigenfunction
+        norms = np.linalg.norm(coeffs, axis=1)
+        k = len(norms)
+
+        # How many to keep
+        keep = max(1, int(np.ceil(k * threshold / 100.0)))
+
+        # Select indices of the most important modes
+        idx_sorted = np.argsort(norms)[::-1]
+        idx_keep = idx_sorted[:keep]
+
+        # Zero out the others
+        coeffs_filtered = np.zeros_like(coeffs)
+        coeffs_filtered[idx_keep] = coeffs[idx_keep]
+
+        reconstructed = eigvecs @ coeffs_filtered
+    else:
+        reconstructed = eigvecs @ coeffs
+
+    return reconstructed
+
+
+def pipeline(mask, k=50):
+    # mesh = mask_to_mesh(mask)
+    # Fixed number of vertices is necessary to achieve comparable coefficients
+    mesh = mask_to_mesh_fixed_vertices(mask)
+    mesh_proc, params = preprocess_mesh(mesh)
+    coeffs, eigvecs, eigvals = surface_to_coefficients(mesh_proc, k=k)
+    return coeffs, eigvecs, mesh_proc, params
+
+def eigvals(mask, k=100, normalize=False):
+    mesh = mask_to_mesh(mask)
+    coeffs, eigvecs, eigvals = surface_to_coefficients(mesh, k=k)
+    if normalize:
+        # Normalize eigenvalues by first non-zero eigenvalue
+        # eigvals = eigvals / eigvals[1] if eigvals[1] != 0 else eigvals
+        eigvals = eigvals / np.max(eigvals)
+        # Drop the first eigenvalue (zero mode) from descriptor since it's trivial
+        eigvals = eigvals[1:]  # length k-1
+    return eigvals
+
+
+def process(mesh, k=10, threshold=None):
+    mesh_proc, params = preprocess_mesh(mesh)
+
+    # Compute LB coefficients (invariant)
+    coeffs, eigvecs, eigvals = surface_to_coefficients(mesh_proc, k=k)
+
+    # Reconstruct in normalized/aligned space
+    reconstructed_vertices_proc = coefficients_to_surface(coeffs, eigvecs, threshold=threshold)
+
+    # Map reconstruction back to original coordinates
+    reconstructed_vertices_orig = inverse_preprocess_mesh(reconstructed_vertices_proc, params)
+
+    # Build reconstructed mesh
+    reconstructed_mesh = mesh.copy()
+    reconstructed_mesh.vertices = reconstructed_vertices_orig  
+
+    return coeffs, eigvals, reconstructed_mesh  
+
+
+