def circlearound_n2d(self, src, radius, metric="euclidean"):
shortmetric = metric[0].lower()
if shortmetric == "e":
v = self.vertices
# make sure src is a 1x3 array
if type(src) is tuple and len(src) == 3:
src = np.asarray(src)
if isinstance(src, np.ndarray):
if src.shape not in ((1, 3), (3,), (3, 1)):
raise ValueError("Illegal shape: should have 3 elements")
src_coord = src if src.shape == (1, 3) else np.reshape(src, (1, 3))
else:
src_coord = np.reshape(v[src, :], (1, 3))
# ensure it is a float
src_coord = np.asanyarray(src_coord, dtype=np.float)
# make a mask around center
voxel2world = self._vg.affine
world2voxel = np.linalg.inv(voxel2world)
nrm = np.linalg.norm(voxel2world, 2)
max_extent = np.ceil(radius / nrm + 1)
src_ijk = self._vg.xyz2ijk(src_coord)
# min and max ijk coordinates
mn = (src_ijk.ravel() - max_extent).astype(np.int_)
mx = (src_ijk.ravel() + max_extent).astype(np.int_)
# set boundaries properly
mn[mn < 0] = 0
sh = np.asarray(self._vg.shape[:3])
mx[mx > sh] = sh[mx > sh]
msk_ijk = np.zeros(self._vg.shape[:3], np.int)
msk_ijk[mn[0] : mx[0], mn[1] : mx[1], mn[2] : mx[2]] = 1
msk_lin = msk_ijk.ravel()
# indices of voxels around the mask
idxs = np.nonzero(msk_lin)[0]
d = volgeom.distance(src_coord, v[idxs])[0, :]
n = d.size
node2dist = dict((idxs[i], d[i]) for i in np.arange(n) if d[i] <= radius)
return node2dist
elif shortmetric == "d":
return {src: 0.0}
else:
raise ValueError("Illegal metric: %s" % metric)
def target2nearest_source(self, target, fallback_euclidean_distance=False):
"""Find the voxel nearest to a mask center
Parameters
==========
target: int
linear index of a voxel
fallback_euclidean_distance: bool (default: False)
Whether to use a euclidean distance metric if target is not in
any of the masks in this instance
Returns
=======
src: int
key index for the mask that contains target and is nearest to
target. If target is not contained in any mask, then None is
returned if fallback_euclidean_distance is False, and the
index of the source nearest to target using a Euclidean distance
metric is returned if fallback_euclidean_distance is True
"""
targets = []
if type(target) in (list, tuple):
for t in target:
targets.append(t)
else:
targets = [target]
xyz_trg = self.xyz_target(np.asarray(targets))
src = self.target2sources(targets)
flat_srcs = []
for s in src:
if s:
for j in s:
flat_srcs.append(j)
if not flat_srcs:
if fallback_euclidean_distance:
flat_srcs = self.keys()
else:
return None
xyz_srcs = self.xyz_source(flat_srcs)
d = volgeom.distance(xyz_srcs, xyz_trg)
i = np.argmin(d)
# d is a 2D array, get the row number with the lowest d
source = flat_srcs[i // xyz_trg.shape[0]]
return source
def target2nearest_source(self, target, fallback_euclidean_distance=False):
"""Find the voxel nearest to a mask center
Parameters
==========
target: int
linear index of a voxel
fallback_euclidean_distance: bool (default: False)
Whether to use a euclidean distance metric if target is not in
any of the masks in this instance
Returns
=======
src: int
key index for the mask that contains target and is nearest to
target. If target is not contained in any mask, then None is
returned if fallback_euclidean_distance is False, and the
index of the source nearest to target using a Euclidean distance
metric is returned if fallback_euclidean_distance is True
"""
targets = []
if type(target) in (list, tuple):
for t in target:
targets.append(t)
else:
targets = [target]
xyz_trg = self.xyz_target(np.asarray(targets))
src = self.target2sources(targets)
flat_srcs = []
for s in src:
if s:
for j in s:
flat_srcs.append(j)
if not flat_srcs:
if fallback_euclidean_distance:
flat_srcs = self.keys()
else:
return None
xyz_srcs = self.xyz_source(flat_srcs)
d = volgeom.distance(xyz_srcs, xyz_trg)
i = np.argmin(d)
# d is a 2D array, get the row number with the lowest d
source = flat_srcs[i // xyz_trg.shape[0]]
return source
def source2nearest_target(self, source):
"""Find the voxel nearest to a mask center
Parameters
==========
src: int
mask index
Returns
=======
target: int
linear index of the voxel that is contained in the mask associated
with src and nearest (Euclidean distance) to src.
"""
trgs = self.__getitem__(source)
trg_xyz = self.xyz_target(trgs)
src_xyz = self.xyz_source(source)
d = volgeom.distance(trg_xyz, src_xyz)
i = np.argmin(d)
return trgs[i / src_xyz.shape[0]]
def source2nearest_target(self, source):
"""Finds the voxel nearest to a mask center
Parameters
==========
src: int
mask index
Returns
=======
target: int
linear index of the voxel that is contained in the mask associated
with src and nearest (Euclidian distance) to src.
"""
trgs = self.__getitem__(source)
trg_xyz = self.xyz_target(trgs)
src_xyz = self.xyz_source(source)
d = volgeom.distance(trg_xyz, src_xyz)
i = np.argmin(d)
return trgs[i / src_xyz.shape[0]]
def test_volume_mask_dict(self):
# also tests the outside_node_margin feature
sh = (10, 10, 10)
msk = np.zeros(sh)
for i in xrange(0, sh[0], 2):
msk[i, :, :] = 1
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 2
vg = volgeom.VolGeom(sh, vol_affine, mask=msk)
density = 10
outer = surf.generate_sphere(density) * 10. + 5
inner = surf.generate_sphere(density) * 5. + 5
intermediate = outer * .5 + inner * .5
xyz = intermediate.vertices
radius = 50
outside_node_margins = [None, 0, 100., np.inf, True]
expected_center_count = [87] * 2 + [intermediate.nvertices] * 3
for k, outside_node_margin in enumerate(outside_node_margins):
sel = surf_voxel_selection.run_voxel_selection(
radius,
vg,
inner,
outer,
outside_node_margin=outside_node_margin)
assert_equal(intermediate, sel.source)
assert_equal(len(sel.keys()), expected_center_count[k])
assert_true(
set(sel.aux_keys()).issubset(
set(['center_distances', 'grey_matter_position'])))
msk_lin = msk.ravel()
sel_msk_lin = sel.get_mask().ravel()
for i in xrange(vg.nvoxels):
if msk_lin[i]:
src = sel.target2nearest_source(i)
assert_false((src is None) ^ (sel_msk_lin[i] == 0))
if src is None:
continue
# index of node nearest to voxel i
src_anywhere = sel.target2nearest_source(
i, fallback_euclidean_distance=True)
# coordinates of node nearest to voxel i
xyz_src = xyz[src_anywhere]
# coordinates of voxel i
xyz_trg = vg.lin2xyz(np.asarray([i]))
# distance between node nearest to voxel i, and voxel i
# this should be the smallest distancer
d = volgeom.distance(np.reshape(xyz_src, (1, 3)), xyz_trg)
# distances between all nodes and voxel i
ds = volgeom.distance(xyz, xyz_trg)
# order of the distances
is_ds = np.argsort(ds.ravel())
# go over all the nodes
# require that the node is in the volume
# mask
# index of node nearest to voxel i
ii = np.argmin(ds)
xyz_min = xyz[ii]
lin_min = vg.xyz2lin([xyz_min])
# linear index of voxel that contains xyz_src
lin_src = vg.xyz2lin(np.reshape(xyz_src, (1, 3)))
# when using multi-core support,
# pickling and unpickling can reduce the precision
# a little bit, causing rounding errors
eps = 1e-14
delta = np.abs(ds[ii] - d)
assert_false(delta > eps and ii in sel and i in sel[ii]
and vg.contains_lin(lin_min))
def test_volume_mask_dict(self):
# also tests the outside_node_margin feature
sh = (10, 10, 10)
msk = np.zeros(sh)
for i in xrange(0, sh[0], 2):
msk[i, :, :] = 1
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 2
vg = volgeom.VolGeom(sh, vol_affine, mask=msk)
density = 10
outer = surf.generate_sphere(density) * 10. + 5
inner = surf.generate_sphere(density) * 5. + 5
intermediate = outer * .5 + inner * .5
xyz = intermediate.vertices
radius = 50
outside_node_margins = [None, 0, 100., np.inf, True]
expected_center_count = [87] * 2 + [intermediate.nvertices] * 3
for k, outside_node_margin in enumerate(outside_node_margins):
sel = surf_voxel_selection.run_voxel_selection(radius, vg, inner,
outer, outside_node_margin=outside_node_margin)
assert_equal(intermediate, sel.source)
assert_equal(len(sel.keys()), expected_center_count[k])
assert_true(set(sel.aux_keys()).issubset(set(['center_distances',
'grey_matter_position'])))
msk_lin = msk.ravel()
sel_msk_lin = sel.get_mask().ravel()
for i in xrange(vg.nvoxels):
if msk_lin[i]:
src = sel.target2nearest_source(i)
assert_false((src is None) ^ (sel_msk_lin[i] == 0))
if src is None:
continue
# index of node nearest to voxel i
src_anywhere = sel.target2nearest_source(i,
fallback_euclidean_distance=True)
# coordinates of node nearest to voxel i
xyz_src = xyz[src_anywhere]
# coordinates of voxel i
xyz_trg = vg.lin2xyz(np.asarray([i]))
# distance between node nearest to voxel i, and voxel i
# this should be the smallest distancer
d = volgeom.distance(np.reshape(xyz_src, (1, 3)), xyz_trg)
# distances between all nodes and voxel i
ds = volgeom.distance(xyz, xyz_trg)
# order of the distances
is_ds = np.argsort(ds.ravel())
# go over all the nodes
# require that the node is in the volume
# mask
# index of node nearest to voxel i
ii = np.argmin(ds)
xyz_min = xyz[ii]
lin_min = vg.xyz2lin([xyz_min])
# linear index of voxel that contains xyz_src
lin_src = vg.xyz2lin(np.reshape(xyz_src, (1, 3)))
# when using multi-core support,
# pickling and unpickling can reduce the precision
# a little bit, causing rounding errors
eps = 1e-14
delta = np.abs(ds[ii] - d)
assert_false(delta > eps and ii in sel and
i in sel[ii] and
vg.contains_lin(lin_min))
def circlearound_n2d(self, src, radius, metric='euclidean'):
shortmetric = metric[0].lower()
if shortmetric == 'e':
v = self.vertices
# make sure src is a 1x3 array
if type(src) is tuple and len(src) == 3:
src = np.asarray(src)
if isinstance(src, np.ndarray):
if src.shape not in ((1, 3), (3, ), (3, 1)):
raise ValueError("Illegal shape: should have 3 elements")
src_coord = src if src.shape == (1, 3) else np.reshape(
src, (1, 3))
else:
src_coord = np.reshape(v[src, :], (1, 3))
# ensure it is a float
src_coord = np.asanyarray(src_coord, dtype=np.float)
# make a mask around center
voxel2world = self._vg.affine
world2voxel = np.linalg.inv(voxel2world)
nrm = np.linalg.norm(voxel2world, 2)
max_extent = np.ceil(radius / nrm + 1)
src_ijk = self._vg.xyz2ijk(src_coord)
# min and max ijk coordinates
mn = (src_ijk.ravel() - max_extent).astype(np.int_)
mx = (src_ijk.ravel() + max_extent).astype(np.int_)
# set boundaries properly
mn[mn < 0] = 0
sh = np.asarray(self._vg.shape[:3])
mx[mx > sh] = sh[mx > sh]
msk_ijk = np.zeros(self._vg.shape[:3], np.int)
msk_ijk[mn[0]:mx[0], mn[1]:mx[1], mn[2]:mx[2]] = 1
msk_lin = msk_ijk.ravel()
# indices of voxels around the mask
idxs = np.nonzero(msk_lin)[0]
d = volgeom.distance(src_coord, v[idxs])[0, :]
n = d.size
node2dist = dict(
(idxs[i], d[i]) for i in np.arange(n) if d[i] <= radius)
return node2dist
elif shortmetric == 'd':
return {src: 0.}
else:
raise ValueError("Illegal metric: %s" % metric)