From 5ded8517cb230712c8ecd70c9f0c510d2533874a Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 19 Sep 2023 14:33:27 -0400 Subject: [PATCH] RF: Drop triangular meshes for now --- nibabel/pointset.py | 58 ------------- nibabel/tests/test_pointset.py | 152 --------------------------------- 2 files changed, 210 deletions(-) diff --git a/nibabel/pointset.py b/nibabel/pointset.py index 324b76d36..b40449801 100644 --- a/nibabel/pointset.py +++ b/nibabel/pointset.py @@ -144,64 +144,6 @@ def get_coords(self, *, as_homogeneous: bool = False): return coords -class TriangularMesh(Pointset): - def __init__(self, mesh): - if isinstance(mesh, tuple) and len(mesh) == 2: - coords, self._triangles = mesh - elif hasattr(mesh, 'coords') and hasattr(mesh, 'triangles'): - coords = mesh.coords - self._triangles = mesh.triangles - elif hasattr(mesh, 'get_mesh'): - coords, self._triangles = mesh.get_mesh() - else: - raise ValueError('Cannot interpret input as triangular mesh') - super().__init__(coords) - - @property - def n_triangles(self): - """Number of faces - - Subclasses should override with more efficient implementations. - """ - return self._triangles.shape[0] - - def get_triangles(self): - """Mx3 array of indices into coordinate table""" - return self._triangles - - def get_mesh(self, name=None): - return self.get_coords(name=name), self.get_triangles() - - def get_names(self): - """List of surface names that can be passed to - ``get_{coords,triangles,mesh}`` - """ - raise NotImplementedError - - -class TriMeshFamily(TriangularMesh): - def __init__(self, mapping, default=None): - self._triangles = None - self._coords = {} - for name, mesh in dict(mapping).items(): - coords, triangles = TriangularMesh(mesh).get_mesh() - if self._triangles is None: - self._triangles = triangles - self._coords[name] = coords - - if default is None: - default = next(iter(self._coords)) - self._default = default - - def get_names(self): - return list(self._coords) - - def get_coords(self, name=None): - if name is None: - name = self._default - return self._coords[name] - - class Grid(Pointset): r"""A regularly-spaced collection of coordinates diff --git a/nibabel/tests/test_pointset.py b/nibabel/tests/test_pointset.py index 49c51251c..fb9a7c5c8 100644 --- a/nibabel/tests/test_pointset.py +++ b/nibabel/tests/test_pointset.py @@ -182,155 +182,3 @@ def test_to_mask(self): ], ) assert np.array_equal(mask_img.affine, np.eye(4)) - - -class H5ArrayProxy: - def __init__(self, file_like, dataset_name): - self.file_like = file_like - self.dataset_name = dataset_name - with h5.File(file_like, 'r') as h5f: - arr = h5f[dataset_name] - self._shape = arr.shape - self._dtype = arr.dtype - - @property - def is_proxy(self): - return True - - @property - def shape(self): - return self._shape - - @property - def ndim(self): - return len(self.shape) - - @property - def dtype(self): - return self._dtype - - def __array__(self, dtype=None): - with h5.File(self.file_like, 'r') as h5f: - return np.asanyarray(h5f[self.dataset_name], dtype) - - def __getitem__(self, slicer): - with h5.File(self.file_like, 'r') as h5f: - return h5f[self.dataset_name][slicer] - - -class H5Geometry(ps.TriMeshFamily): - """Simple Geometry file structure that combines a single topology - with one or more coordinate sets - """ - - @classmethod - def from_filename(klass, pathlike): - meshes = {} - with h5.File(pathlike, 'r') as h5f: - triangles = H5ArrayProxy(pathlike, '/topology') - for name in h5f['coordinates']: - meshes[name] = (H5ArrayProxy(pathlike, f'/coordinates/{name}'), triangles) - return klass(meshes) - - def to_filename(self, pathlike): - with h5.File(pathlike, 'w') as h5f: - h5f.create_dataset('/topology', data=self.get_triangles()) - for name, coord in self._coords.items(): - h5f.create_dataset(f'/coordinates/{name}', data=coord) - - -class FSGeometryProxy: - def __init__(self, pathlike): - self._file_like = str(Path(pathlike)) - self._offset = None - self._vnum = None - self._fnum = None - - def _peek(self): - from nibabel.freesurfer.io import _fread3 - - with open(self._file_like, 'rb') as fobj: - magic = _fread3(fobj) - if magic != 16777214: - raise NotImplementedError('Triangle files only!') - fobj.readline() - fobj.readline() - self._vnum = np.fromfile(fobj, '>i4', 1)[0] - self._fnum = np.fromfile(fobj, '>i4', 1)[0] - self._offset = fobj.tell() - - @property - def vnum(self): - if self._vnum is None: - self._peek() - return self._vnum - - @property - def fnum(self): - if self._fnum is None: - self._peek() - return self._fnum - - @property - def offset(self): - if self._offset is None: - self._peek() - return self._offset - - @auto_attr - def coords(self): - ap = ArrayProxy(self._file_like, ((self.vnum, 3), '>f4', self.offset)) - ap.order = 'C' - return ap - - @auto_attr - def triangles(self): - offset = self.offset + 12 * self.vnum - ap = ArrayProxy(self._file_like, ((self.fnum, 3), '>i4', offset)) - ap.order = 'C' - return ap - - -class FreeSurferHemisphere(ps.TriMeshFamily): - @classmethod - def from_filename(klass, pathlike): - path = Path(pathlike) - hemi, default = path.name.split('.') - mesh_names = ( - 'orig', - 'white', - 'smoothwm', - 'pial', - 'inflated', - 'sphere', - 'midthickness', - 'graymid', - ) # Often created - if default not in mesh_names: - mesh_names.append(default) - meshes = {} - for mesh in mesh_names: - fpath = path.parent / f'{hemi}.{mesh}' - if fpath.exists(): - meshes[mesh] = FSGeometryProxy(fpath) - hemi = klass(meshes) - hemi._default = default - return hemi - - -def test_FreeSurferHemisphere(): - lh = FreeSurferHemisphere.from_filename(FS_DATA / 'fsaverage/surf/lh.white') - assert lh.n_coords == 163842 - assert lh.n_triangles == 327680 - - -@skipUnless(has_h5py, reason='Test requires h5py') -def test_make_H5Geometry(tmp_path): - lh = FreeSurferHemisphere.from_filename(FS_DATA / 'fsaverage/surf/lh.white') - h5geo = H5Geometry({name: lh.get_mesh(name) for name in ('white', 'pial')}) - h5geo.to_filename(tmp_path / 'geometry.h5') - - rt_h5geo = H5Geometry.from_filename(tmp_path / 'geometry.h5') - assert set(h5geo._coords) == set(rt_h5geo._coords) - assert np.array_equal(lh.get_coords('white'), rt_h5geo.get_coords('white')) - assert np.array_equal(lh.get_triangles(), rt_h5geo.get_triangles())