def test_surf_fs_asc(self, temp_fn):
s = surf.generate_sphere(5) * 100
surf_fs_asc.write(temp_fn, s, overwrite=True)
t = surf_fs_asc.read(temp_fn)
assert_array_almost_equal(s.vertices, t.vertices)
assert_array_almost_equal(s.vertices, t.vertices)
theta = np.asarray([0, 0., 180.])
r = s.rotate(theta, unit='deg')
l2r = surf.get_sphere_left_right_mapping(s, r)
l2r_expected = [
0, 1, 2, 6, 5, 4, 3, 11, 10, 9, 8, 7, 15, 14, 13, 12, 16, 19, 18,
17, 21, 20, 23, 22, 26, 25, 24
]
assert_array_equal(l2r, np.asarray(l2r_expected))
sides_facing = 'apism'
for side_facing in sides_facing:
l, r = surf.reposition_hemisphere_pairs(s + 10., t + (-10.),
side_facing)
m = surf.merge(l, r)
# not sure at the moment why medial rotation
# messes up - but leave for now
eps = 666 if side_facing == 'm' else .001
assert_true((abs(m.center_of_mass) < eps).all())
def test_surf_fs_asc(self, temp_fn):
s = surf.generate_sphere(5) * 100
surf_fs_asc.write(temp_fn, s, overwrite=True)
t = surf_fs_asc.read(temp_fn)
assert_array_almost_equal(s.vertices, t.vertices)
assert_array_almost_equal(s.vertices, t.vertices)
theta = np.asarray([0, 0., 180.])
r = s.rotate(theta, unit='deg')
l2r = surf.get_sphere_left_right_mapping(s, r)
l2r_expected = [0, 1, 2, 6, 5, 4, 3, 11, 10, 9, 8, 7, 15, 14, 13, 12,
16, 19, 18, 17, 21, 20, 23, 22, 26, 25, 24]
assert_array_equal(l2r, np.asarray(l2r_expected))
sides_facing = 'apism'
for side_facing in sides_facing:
l, r = surf.reposition_hemisphere_pairs(s + 10., t + (-10.),
side_facing)
m = surf.merge(l, r)
# not sure at the moment why medial rotation
# messes up - but leave for now
eps = 666 if side_facing == 'm' else .001
assert_true((abs(m.center_of_mass) < eps).all())
def test_surf_ring_queryengine(self):
s = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1), 4, 5)
# add second layer
s2 = surf.merge(s, (s + (.01, 0, 0)))
ds = Dataset(samples=np.arange(20)[np.newaxis],
fa=dict(node_indices=np.arange(39, 0, -2)))
# add more features (with shared node indices)
ds3 = hstack((ds, ds, ds))
radius = 2.5
inner_radius = 1.0
# Makes sure it raises error if inner_radius is >= radius
assert_raises(ValueError,
lambda: queryengine.SurfaceRingQueryEngine(surface=s2,
inner_radius=2.5,
radius=radius))
distance_metrics = ('euclidean', 'dijkstra', 'euclidean', 'dijkstra')
for distance_metric, include_center in zip(distance_metrics, [True, False]*2):
qe = queryengine.SurfaceRingQueryEngine(surface=s2, radius=radius,
inner_radius=inner_radius, distance_metric=distance_metric,
include_center=include_center)
# untrained qe should give errors
assert_raises(ValueError, lambda: qe.ids)
assert_raises(ValueError, lambda: qe.query_byid(0))
# node index out of bounds should give error
ds_ = ds.copy()
ds_.fa.node_indices[0] = 100
assert_raises(ValueError, lambda: qe.train(ds_))
# lack of node indices should give error
ds_.fa.pop('node_indices')
assert_raises(ValueError, lambda: qe.train(ds_))
# train the qe
qe.train(ds3)
for node in np.arange(-1, s2.nvertices + 1):
if node < 0 or node >= s2.nvertices:
assert_raises(KeyError, lambda: qe.query_byid(node))
continue
feature_ids = np.asarray(qe.query_byid(node))
# node indices relative to ds
base_ids = feature_ids[feature_ids < 20]
# should have multiples of 20
assert_equal(set(feature_ids),
set((base_ids[np.newaxis].T + \
[0, 20, 40]).ravel()))
node_indices = s2.circlearound_n2d(node,
radius, distance_metric or 'dijkstra')
fa_indices = [fa_index for fa_index, inode in
enumerate(ds3.fa.node_indices)
if inode in node_indices and node_indices[inode] > inner_radius]
if include_center and node in ds3.fa.node_indices:
fa_indices += np.where(ds3.fa.node_indices == node)[0].tolist()
assert_equal(set(feature_ids), set(fa_indices))
def run_makespec_bothhemis(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
icolds, hemis = _get_hemis_icolds(config)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
for icold in icolds:
specs = []
for hemi in hemis:
#surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
specs.append(afni_suma_spec.read(specpathfn))
specs = afni_suma_spec.hemi_pairs_add_views(specs,
'inflated',
refdir,
overwrite=overwrite)
specs = afni_suma_spec.hemi_pairs_add_views(specs,
'sphere.reg',
refdir,
overwrite=overwrite)
spec_both = afni_suma_spec.combine_left_right(specs)
# generate spec files for both hemispheres
hemiboth = 'b'
specfn = afni_suma_spec.canonical_filename(icold, hemiboth,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
spec_both.write(specpathfn, overwrite=overwrite)
# merge left and right into one surface
# and generate the spec files as well
hemimerged = 'm'
specfn = afni_suma_spec.canonical_filename(icold, hemimerged,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
if config['overwrite'] or not os.path.exists(specpathfn):
spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(
spec_both)
spec_merged.write(specpathfn, overwrite=overwrite)
full_path = lambda x: os.path.join(refdir, x)
for fn_out, fns_in in surfs_to_join.iteritems():
surfs_in = [surf_fs_asc.read(full_path(fn)) for fn in fns_in]
surf_merged = surf.merge(*surfs_in)
if config['overwrite'] or not os.path.exists(
full_path(fn_out)):
surf_fs_asc.write(surf_merged,
full_path(fn_out),
overwrite=overwrite)
print "Merged surfaces written to %s" % fn_out
def run_makespec_bothhemis(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
icolds, hemis = _get_hemis_icolds(config)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
for icold in icolds:
specs = []
for hemi in hemis:
#surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
specs.append(afni_suma_spec.read(specpathfn))
specs = afni_suma_spec.hemi_pairs_add_views(specs,
'inflated', refdir, overwrite=overwrite)
specs = afni_suma_spec.hemi_pairs_add_views(specs,
'sphere.reg', refdir, overwrite=overwrite)
spec_both = afni_suma_spec.combine_left_right(specs)
# generate spec files for both hemispheres
hemiboth = 'b'
specfn = afni_suma_spec.canonical_filename(icold, hemiboth, config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
spec_both.write(specpathfn, overwrite=overwrite)
# merge left and right into one surface
# and generate the spec files as well
hemimerged = 'm'
specfn = afni_suma_spec.canonical_filename(icold, hemimerged, config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
if config['overwrite'] or not os.path.exists(specpathfn):
spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(spec_both)
spec_merged.write(specpathfn, overwrite=overwrite)
full_path = lambda x:os.path.join(refdir, x)
for fn_out, fns_in in surfs_to_join.iteritems():
surfs_in = [surf_fs_asc.read(full_path(fn)) for fn in fns_in]
surf_merged = surf.merge(*surfs_in)
if config['overwrite'] or not os.path.exists(full_path(fn_out)):
surf_fs_asc.write(surf_merged, full_path(fn_out),
overwrite=overwrite)
print "Merged surfaces written to %s" % fn_out
def test_surf_pairs(self):
o, x, y = map(np.asarray, [(0, 0, 0), (0, 1, 0), (1, 0, 0)])
d = np.asarray((0, 0, .1))
n = 10
s1 = surf.generate_plane(o, x, y, n, n)
s2 = surf.generate_plane(o + d, x, y, n, n)
s = surf.merge(s1, s2)
# try for small surface
eps = .0000001
pw = s.pairwise_near_nodes(.5)
for i in xrange(n ** 2):
d = pw.pop((i, i + 100))
assert_array_almost_equal(d, .1)
assert_true(len(pw) == 0)
pw = s.pairwise_near_nodes(.5)
for i in xrange(n ** 2):
d = pw.pop((i, i + 100))
assert_array_almost_equal(d, .1)
assert_true(len(pw) == 0)
# bigger one
pw = s.pairwise_near_nodes(1.4)
for i in xrange(n ** 2):
p, q = i // n, i % n
offsets = sum(([] if q == 0 else [-1],
[] if q == n - 1 else [+1],
[] if p == 0 else [-n],
[] if p == n - 1 else [n],
[0]), [])
for offset in offsets:
ii = i + offset + n ** 2
d = pw.pop((i, ii))
assert_true((d < .5) ^ (offset > 0))
assert_true(len(pw) == 0)
def test_surf_pairs(self):
o, x, y = map(np.asarray, [(0, 0, 0), (0, 1, 0), (1, 0, 0)])
d = np.asarray((0, 0, .1))
n = 10
s1 = surf.generate_plane(o, x, y, n, n)
s2 = surf.generate_plane(o + d, x, y, n, n)
s = surf.merge(s1, s2)
# try for small surface
eps = .0000001
pw = s.pairwise_near_nodes(.5)
for i in xrange(n ** 2):
d = pw.pop((i, i + 100))
assert_array_almost_equal(d, .1)
assert_true(len(pw) == 0)
pw = s.pairwise_near_nodes(.5)
for i in xrange(n ** 2):
d = pw.pop((i, i + 100))
assert_array_almost_equal(d, .1)
assert_true(len(pw) == 0)
# bigger one
pw = s.pairwise_near_nodes(1.4)
for i in xrange(n ** 2):
p, q = i // n, i % n
offsets = sum(([] if q == 0 else [-1],
[] if q == n - 1 else [+1],
[] if p == 0 else [-n],
[] if p == n - 1 else [n],
[0]), [])
for offset in offsets:
ii = i + offset + n ** 2
d = pw.pop((i, ii))
assert_true((d < .5) ^ (offset > 0))
assert_true(len(pw) == 0)
def test_surf_queryengine(self, qefn):
s = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1), 4, 5)
# add second layer
s2 = surf.merge(s, (s + (.01, 0, 0)))
ds = Dataset(samples=np.arange(20)[np.newaxis],
fa=dict(node_indices=np.arange(39, 0, -2)))
# add more features (with shared node indices)
ds3 = hstack((ds, ds, ds))
radius = 2.5
# Note: sweepargs it not used to avoid re-generating the same
# surface and dataset multiple times.
for distance_metric in ('euclidean', 'dijkstra', '<illegal>', None):
builder = lambda: queryengine.SurfaceQueryEngine(
s2, radius, distance_metric)
if distance_metric in ('<illegal>', None):
assert_raises(ValueError, builder)
continue
qe = builder()
# test i/o and ensure that the untrained instance is not trained
if externals.exists('h5py'):
h5save(qefn, qe)
qe = h5load(qefn)
# untrained qe should give errors
assert_raises(ValueError, lambda: qe.ids)
assert_raises(ValueError, lambda: qe.query_byid(0))
# node index out of bounds should give error
ds_ = ds.copy()
ds_.fa.node_indices[0] = 100
assert_raises(ValueError, lambda: qe.train(ds_))
# lack of node indices should give error
ds_.fa.pop('node_indices')
assert_raises(ValueError, lambda: qe.train(ds_))
# train the qe
qe.train(ds3)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
h5save(qefn, qe)
qe = h5load(qefn)
for node in np.arange(-1, s2.nvertices + 1):
if node < 0 or node >= s2.nvertices:
assert_raises(KeyError, lambda: qe.query_byid(node))
continue
feature_ids = np.asarray(qe.query_byid(node))
# node indices relative to ds
base_ids = feature_ids[feature_ids < 20]
# should have multiples of 20
assert_equal(set(feature_ids),
set((base_ids[np.newaxis].T + \
[0, 20, 40]).ravel()))
node_indices = list(
s2.circlearound_n2d(node, radius, distance_metric
or 'dijkstra'))
fa_indices = [
fa_index
for fa_index, node in enumerate(ds3.fa.node_indices)
if node in node_indices
]
assert_equal(set(feature_ids), set(fa_indices))
# smoke tests
assert_true('SurfaceQueryEngine' in '%s' % qe)
assert_true('SurfaceQueryEngine' in '%r' % qe)
def test_surf_queryengine(self, qefn):
s = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1), 4, 5)
# add scond layer
s2 = surf.merge(s, (s + (.01, 0, 0)))
ds = Dataset(samples=np.arange(20)[np.newaxis],
fa=dict(node_indices=np.arange(39, 0, -2)))
# add more features (with shared node indices)
ds3 = hstack((ds, ds, ds))
radius = 2.5
# Note: sweepargs it not used to avoid re-generating the same
# surface and dataset multiple times.
for distance_metric in ('euclidean', 'dijkstra', '<illegal>', None):
builder = lambda: queryengine.SurfaceQueryEngine(s2, radius,
distance_metric)
if distance_metric in ('<illegal>', None):
assert_raises(ValueError, builder)
continue
qe = builder()
# test i/o and ensure that the untrained instance is not trained
if externals.exists('h5py'):
fd, qefn = tempfile.mkstemp('qe.hdf5', 'test'); os.close(fd)
h5save(qefn, qe)
qe = h5load(qefn)
os.remove(qefn)
# untrained qe should give errors
assert_raises(ValueError, lambda:qe.ids)
assert_raises(ValueError, lambda:qe.query_byid(0))
# node index out of bounds should give error
ds_ = ds.copy()
ds_.fa.node_indices[0] = 100
assert_raises(ValueError, lambda: qe.train(ds_))
# lack of node indices should give error
ds_.fa.pop('node_indices')
assert_raises(ValueError, lambda: qe.train(ds_))
# train the qe
qe.train(ds3)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
h5save(qefn, qe)
qe = h5load(qefn)
for node in np.arange(-1, s2.nvertices + 1):
if node < 0 or node >= s2.nvertices:
assert_raises(KeyError, lambda: qe.query_byid(node))
continue
feature_ids = np.asarray(qe.query_byid(node))
# node indices relative to ds
base_ids = feature_ids[feature_ids < 20]
# should have multiples of 20
assert_equal(set(feature_ids),
set((base_ids[np.newaxis].T + \
[0, 20, 40]).ravel()))
node_indices = list(s2.circlearound_n2d(node,
radius, distance_metric or 'dijkstra'))
fa_indices = [fa_index for fa_index, node in
enumerate(ds3.fa.node_indices)
if node in node_indices]
assert_equal(set(feature_ids), set(fa_indices))
# smoke tests
assert_true('SurfaceQueryEngine' in '%s' % qe)
assert_true('SurfaceQueryEngine' in '%r' % qe)
def run_makespec_bothhemis(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
icolds, hemis = _get_hemis_icolds(config)
ext = format2extension(config)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
for icold in icolds:
specs = []
for hemi in hemis:
#surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
s = afni_suma_spec.read(specpathfn)
specs.append(afni_suma_spec.read(specpathfn))
add_states = ['inflated', 'full.patch.flat', 'sphere.reg']
add_states_required = [True, False, True] # flat surface is optional
for add_state, is_req in zip(add_states, add_states_required):
has_state = all([
len(spec.find_surface_from_state(add_state)) == 1
for spec in specs
])
if not has_state:
if is_req:
error('cannot find state %s' % add_state)
else:
# skip this state
print "Optional state %s not found - skipping" % add_state
continue
specs = afni_suma_spec.hemi_pairs_add_views(specs,
add_state,
ext,
refdir,
overwrite=overwrite)
spec_both = afni_suma_spec.combine_left_right(specs)
# generate spec files for both hemispheres
hemiboth = 'b'
specfn = afni_suma_spec.canonical_filename(icold, hemiboth,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
spec_both.write(specpathfn, overwrite=overwrite)
# merge left and right into one surface
# and generate the spec files as well
hemimerged = 'm'
specfn = afni_suma_spec.canonical_filename(icold, hemimerged,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
if config['overwrite'] or not os.path.exists(specpathfn):
spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(
spec_both)
spec_merged.write(specpathfn, overwrite=overwrite)
full_path = lambda x: os.path.join(refdir, x)
for fn_out, fns_in in surfs_to_join.iteritems():
surfs_in = [surf.read(full_path(fn)) for fn in fns_in]
if all(['full.patch.flat' in fn for fn in fns_in]):
# left hemi of flat; rotate 180 degrees, reposition again
surfs_in[0] = surfs_in[0] * [-1, -1, 1]
surfs_in = surf.reposition_hemisphere_pairs(
surfs_in[0], surfs_in[1], 'm')
surf_merged = surf.merge(*surfs_in)
if config['overwrite'] or not os.path.exists(
full_path(fn_out)):
surf.write(full_path(fn_out), surf_merged)
print "Merged surfaces written to %s" % fn_out
def run_makespec_bothhemis(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
icolds, hemis = _get_hemis_icolds(config)
ext = format2extension(config)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
for icold in icolds:
specs = []
for hemi in hemis:
#surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
specpathfn = pathjoin(refdir, specfn)
s = afni_suma_spec.read(specpathfn)
specs.append(afni_suma_spec.read(specpathfn))
add_states = ['inflated', 'full.patch.flat', 'sphere.reg']
add_states_required = [True, False, True] # flat surface is optional
for add_state, is_req in zip(add_states, add_states_required):
has_state = all([len(spec.find_surface_from_state(add_state)) == 1
for spec in specs])
if not has_state:
if is_req:
error('cannot find state %s' % add_state)
else:
# skip this state
print "Optional state %s not found - skipping" % add_state
continue
specs = afni_suma_spec.hemi_pairs_add_views(specs,
add_state, ext, refdir, overwrite=overwrite)
spec_both = afni_suma_spec.combine_left_right(specs)
# generate spec files for both hemispheres
hemiboth = 'b'
specfn = afni_suma_spec.canonical_filename(icold, hemiboth, config['alsuffix'])
specpathfn = pathjoin(refdir, specfn)
spec_both.write(specpathfn, overwrite=overwrite)
# merge left and right into one surface
# and generate the spec files as well
hemimerged = 'm'
specfn = afni_suma_spec.canonical_filename(icold, hemimerged, config['alsuffix'])
specpathfn = pathjoin(refdir, specfn)
if config['overwrite'] or not os.path.exists(specpathfn):
spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(spec_both)
spec_merged.write(specpathfn, overwrite=overwrite)
full_path = lambda x:pathjoin(refdir, x)
for fn_out, fns_in in surfs_to_join.iteritems():
surfs_in = [surf.read(full_path(fn)) for fn in fns_in]
if all(['full.patch.flat' in fn for fn in fns_in]):
# left hemi of flat; rotate 180 degrees, reposition again
surfs_in[0] = surfs_in[0] * [-1, -1, 1]
surfs_in = surf.reposition_hemisphere_pairs(surfs_in[0], surfs_in[1], 'm')
surf_merged = surf.merge(*surfs_in)
if config['overwrite'] or not os.path.exists(full_path(fn_out)):
surf.write(full_path(fn_out), surf_merged)
print "Merged surfaces written to %s" % fn_out
