def sens_xyz_ori(v: numpy.ndarray, f: numpy.ndarray,
l: numpy.ndarray) -> numpy.ndarray:
surface = Surface(v, f, [], None)
vn = surface.vertex_normals()
pos = numpy.zeros((n_sens, 6))
numpy.add.at(pos, l, numpy.c_[v, vn])
return pos / numpy.bincount(l)[:, numpy.newaxis]
def merge_surfaces(self, surfaces):
"""
Merge several surfaces, and their region mappings.
:return: the merge result surface and region mapping.
"""
n_surfaces = len(surfaces)
out_surface = Surface([], [])
# TODO: how to deal with the metadata of merged surfaces, so that freesurfer.io can handle them, e.g., write them
# i.e., we need to have a final unique version of the metadata, not a list of them, as I am doing here in the
# commented code
# out_surface_attributes=dict()
# for attribute in ["vertices_coord_system", "generic_metadata", "vertices_metadata", "triangles_metadata"]:
# out_surface_attributes[attribute]=[]
for i_srf in range(n_surfaces):
out_surface.add_vertices_and_triangles(surfaces[i_srf].vertices,
surfaces[i_srf].triangles,
surfaces[i_srf].area_mask)
if len(surfaces[i_srf].center_ras) == 0:
pass
elif len(out_surface.center_ras) == 0:
out_surface.center_ras = surfaces[i_srf].center_ras
elif numpy.any(
out_surface.center_ras != surfaces[i_srf].center_ras):
raise ValueError(
"At least two surfaces have different -non empty- centers in RAS coordinates!"
)
# #TODO: think about how to better merge these fields
# for attribute in ["vertices_coord_system", "generic_metadata", "vertices_metadata", "triangles_metadata"]:
# out_surface_attributes[attribute].append(getattr(surfaces[i_srf],attribute))
# setattr(out_surface,attribute,out_surface_attributes[attribute])
return out_surface
def gen_dipoles(self, pos, ori_or_face=None, out_fname=None):
"Generate dipoles (or equiv. file) for OpenMEEG."
if ori_or_face is None:
pos, ori = self.gen_dipole_triplets(pos)
else:
if ori_or_face.dtype in numpy.floattypes:
ori = ori_or_face
else:
surface = Surface(pos, ori_or_face, [], None)
ori = surface.vertex_normals()
numpy.savetxt(out_fname, numpy.c_[pos, ori], fmt='%f')
def gen_dipoles(self, pos: Union[numpy.ndarray, list], ori_or_face: Optional[numpy.float]=None,
out_fname: Optional[os.PathLike]=None) -> numpy.ndarray:
"Generate dipoles (or equiv. file) for OpenMEEG."
if ori_or_face is None:
pos, ori = self.gen_dipole_triplets(pos)
else:
if ori_or_face.dtype is not None:
ori = ori_or_face
else:
surface = Surface(pos, ori_or_face, [], None)
ori = surface.vertex_normals()
dipoles = numpy.c_[pos, ori]
numpy.savetxt(out_fname, dipoles, fmt='%f')
return dipoles
def read(self, surface_path, use_center_surface):
vertices, triangles, metadata = read_geometry(surface_path,
read_metadata=True)
self.logger.info("From the file %s the extracted metadata is %s",
surface_path, metadata)
if use_center_surface:
cras = [0, 0, 0]
self.logger.info(
"The --center_ras flag was specified, so the ras centering point is %s",
cras)
else:
if CENTER_RAS_FS_SURF in metadata:
cras = metadata[CENTER_RAS_FS_SURF]
self.logger.info(
"The ras centering point for surface %s is %s",
surface_path, cras)
else:
cras = [0, 0, 0]
self.logger.warning(
"Could not read the ras centering point from surface %s header. "
"The cras will be %s", surface_path, cras)
return Surface(vertices,
triangles,
area_mask=None,
center_ras=cras,
generic_metadata=metadata)
def extract_subsurf(self, surface, verts_mask, output='surface'):
"""
Extracts a sub-surface that contains only the masked vertices and the corresponding faces.
An important step is to replace old vertices indexes of faces to the new ones.
:param: surface: input surface object
:param: verts_mask: mask of the sub-surface to be extracted
:return: output surface object
"""
verts_out = surface.vertices[verts_mask]
triangles_mask = numpy.c_[verts_mask[surface.triangles[:, 0]],
verts_mask[surface.triangles[:, 1]],
verts_mask[surface.triangles[:,
2]]].all(axis=1)
triangles_out = numpy.array(surface.triangles[triangles_mask, :])
verts_out_inds, = numpy.where(verts_mask)
for triang_idx in range(triangles_out.shape[0]):
for vertex_idx in range(3):
triangles_out[triang_idx, vertex_idx], = \
numpy.where(
triangles_out[triang_idx, vertex_idx] == verts_out_inds)
if output == 'surface':
out_surface = Surface(
verts_out,
triangles_out,
area_mask=surface.area_mask[verts_out_inds],
center_ras=surface.center_ras,
vertices_coord_system=surface.vertices_coord_system,
generic_metadata=surface.generic_metadata,
vertices_metadata=surface.vertices_metadata,
triangles_metadata=surface.triangles_metadata)
return out_surface
else:
return (verts_out, triangles_out,
surface.area_mask[verts_out_inds])
def compute_areas_for_regions(self, regions: list, surface: Surface, region_mapping: list) -> numpy.array:
"""Compute the areas of given regions"""
region_surface_area = numpy.zeros(len(regions))
avt = numpy.array(surface.get_vertex_triangles())
# NOTE: Slightly overestimates as it counts overlapping border triangles,
# but, not really a problem provided triangle-size << region-size.
for i, k in enumerate(regions):
regs = list(map(set, avt[numpy.array(region_mapping) == k]))
if len(regs) == 0:
continue
region_triangles = set.union(*regs)
if region_triangles:
region_surface_area[i] = surface.get_triangle_areas()[list(region_triangles)].sum()
return region_surface_area
def read(self, data_file, use_center_surface):
gifti_image = giftiio.read(data_file)
image_metadata = gifti_image.meta.metadata
self.logger.info(
"From the file %s the extracted metadata is %s", data_file, image_metadata)
data_arrays = gifti_image.darrays
vertices = data_arrays[0].data
triangles = data_arrays[1].data
vol_geom_center_ras = [0, 0, 0]
vertices_metadata = data_arrays[0].metadata
self.logger.info(
"The metadata from vertices data array is %s", vertices_metadata)
vertices_coord_system = data_arrays[0].coordsys
self.logger.info(
"The coordinate system transform matrix from vertices data array is %s", vertices_coord_system)
triangles_metadata = data_arrays[1].metadata
self.logger.info(
"The metadata from triangles data array is %s", triangles_metadata)
if use_center_surface:
vol_geom_center_ras = [0, 0, 0]
else:
vol_geom_center_ras[0] = float(
vertices_metadata[CENTER_RAS_GIFTI_SURF[0]])
vol_geom_center_ras[1] = float(
vertices_metadata[CENTER_RAS_GIFTI_SURF[1]])
vol_geom_center_ras[2] = float(
vertices_metadata[CENTER_RAS_GIFTI_SURF[2]])
return Surface(vertices, triangles, area_mask=None,
center_ras=vol_geom_center_ras, vertices_coord_system=vertices_coord_system,
generic_metadata=image_metadata, vertices_metadata=vertices_metadata,
triangles_metadata=triangles_metadata)
def merge_surfaces(self, surfaces: Surface) -> Surface:
"""
Merge several surfaces, and their region mappings.
:return: the merge result surface and region mapping.
"""
n_surfaces = len(surfaces)
out_surface = Surface([], [])
# TODO: how to deal with the metadata of merged surfaces, so that freesurfer.io can handle them, e.g., write them
# i.e., we need to have a final unique version of the metadata, not a list of them, as I am doing here in the
# commented code
# out_surface_attributes=dict()
# for attribute in ["vertices_coord_system", "generic_metadata", "vertices_metadata", "triangles_metadata"]:
# out_surface_attributes[attribute]=[]
for i_srf in range(n_surfaces):
out_surface.add_vertices_and_triangles(surfaces[i_srf].vertices,
surfaces[i_srf].triangles,
surfaces[i_srf].area_mask)
if out_surface.get_main_metadata() is None:
out_surface.set_main_metadata(surfaces[i_srf].get_main_metadata())
if len(surfaces[i_srf].center_ras) == 0:
pass
elif len(out_surface.center_ras) == 0:
out_surface.center_ras = surfaces[i_srf].center_ras
elif numpy.any(out_surface.center_ras != surfaces[i_srf].center_ras):
self.logger.warn("At least two surfaces have different -non empty- centers in RAS coordinates!")
# #TODO: think about how to better merge these fields
# for attribute in ["vertices_coord_system", "generic_metadata", "vertices_metadata", "triangles_metadata"]:
# out_surface_attributes[attribute].append(getattr(surfaces[i_srf],attribute))
# setattr(out_surface,attribute,out_surface_attributes[attribute])
return out_surface
def write_surface_with_annotation(self,
surface: Surface,
annot: Annotation,
result_name: str,
positions: list = [(0, 0), (0, 90),
(0, 180), (0, 270),
(90, 0), (270, 0)]):
x = surface.vertices[:, 0]
y = surface.vertices[:, 1]
z = surface.vertices[:, 2]
fig = pyplot.figure()
ax = Axes3D(fig)
min = numpy.min([numpy.min(x), numpy.min(y), numpy.min(z)])
max = numpy.max([numpy.max(x), numpy.max(y), numpy.max(z)])
ax.set_xlim3d(min, max)
ax.set_ylim3d(min, max)
ax.set_zlim3d(min, max)
if annot is not None:
face_colors = annot.compute_face_colors(surface.triangles)
normals = surface.compute_normals()
face_colors = ax._shade_colors(face_colors, normals)
poly_line = ax.plot_trisurf(x, y, z, triangles=surface.triangles)
if annot is not None:
poly_line.set_edgecolor(face_colors)
poly_line.set_facecolor(face_colors)
pyplot.axis('off')
snapshot_index = 0
for e, a in positions:
ax.view_init(elev=e, azim=a)
ax.dist = 6
pyplot.savefig(self.get_path(result_name + str(snapshot_index)),
dpi=fig.dpi)
snapshot_index += 1
self.logger.info("The 6 snapshots were generated")
def write_surface_with_annotation(self, surface: Surface, annot: Annotation, result_name:str,
positions: list=[(0, 0), (0, 90), (0, 180), (0, 270), (90, 0), (270, 0)]):
x = surface.vertices[:, 0]
y = surface.vertices[:, 1]
z = surface.vertices[:, 2]
fig = pyplot.figure()
ax = Axes3D(fig, aspect='equal')
min = numpy.min([numpy.min(x), numpy.min(y), numpy.min(z)])
max = numpy.max([numpy.max(x), numpy.max(y), numpy.max(z)])
ax.set_xlim3d(min, max)
ax.set_ylim3d(min, max)
ax.set_zlim3d(min, max)
if annot is not None:
face_colors = annot.compute_face_colors(surface.triangles)
normals = surface.compute_normals()
face_colors = ax._shade_colors(face_colors, normals)
poly_line = ax.plot_trisurf(x, y, z, triangles=surface.triangles)
if annot is not None:
poly_line.set_edgecolor(face_colors)
poly_line.set_facecolor(face_colors)
pyplot.axis('off')
snapshot_index = 0
for e, a in positions:
ax.view_init(elev=e, azim=a)
ax.dist = 6
pyplot.savefig(self.get_path(
result_name + str(snapshot_index)), dpi=fig.dpi)
snapshot_index += 1
self.logger.info("The 6 snapshots were generated")
def compute_seeg_gain_matrix(self, seeg_xyz: os.PathLike, cort_file: os.PathLike, subcort_file: os.PathLike,
cort_rm: os.PathLike, subcort_rm: os.PathLike,
out_gain_mat: os.PathLike) -> numpy.ndarray:
genericIO = GenericIO()
sensors = numpy.genfromtxt(seeg_xyz, usecols=[1, 2, 3])
cort_vertices = genericIO.read_field_from_zip("vertices.txt", cort_file)
cort_triangles = genericIO.read_field_from_zip("triangles.txt", cort_file, dtype="i")
cort_surf = Surface(cort_vertices, cort_triangles)
cort_normals = cort_surf.vertex_normals()
cort_areas = cort_surf.get_vertex_areas()
subcort_vertices = genericIO.read_field_from_zip("vertices.txt", subcort_file)
subcort_triangles = genericIO.read_field_from_zip("triangles.txt", subcort_file, dtype="i")
subcort_surf = Surface(subcort_vertices, subcort_triangles)
subcort_areas = subcort_surf.get_vertex_areas()
cort_rm = list(numpy.genfromtxt(cort_rm, usecols=[0], dtype='i'))
subcort_rm = list(numpy.genfromtxt(subcort_rm, usecols=[0], dtype='i'))
region_list = numpy.unique(cort_rm + subcort_rm)
nr_regions = len(region_list)
nr_vertices = cort_surf.vertices.shape[0] + subcort_surf.vertices.shape[0]
verts_regions_mat = self._get_verts_regions_matrix(nr_vertices, nr_regions, cort_rm + subcort_rm)
gain_matrix = self._gain_matrix_dipole(cort_surf.vertices, cort_normals, cort_areas, sensors)
gain_matrix_subcort = self._gain_matrix_inv_square(subcort_surf.vertices, subcort_areas, sensors)
gain_total = numpy.concatenate((gain_matrix, gain_matrix_subcort), axis=1)
gain_out = gain_total @ verts_regions_mat
numpy.savetxt(out_gain_mat, gain_out)
return gain_out
def read(self, h5_path, use_center_surface=False):
h5_file = h5py.File(h5_path, 'r', libver='latest')
vertices = h5_file['/vertices'][()]
triangles = h5_file['/triangles'][()]
h5_file.close()
return Surface(vertices, triangles)