def load_surface(input_fn,
freesurfer_dir,
which='pial',
fsaverage='fsaverage6'):
"""Automatically load pial surface given infile"""
hemi = re.findall('hemi-([LR])', input_fn)[0]
surf_fn = '{0}h.{1}.gii'.format(hemi.lower(), which)
surf_fn = os.path.join(freesurfer_dir, fsaverage, 'SUMA', surf_fn)
print("Loading {}".format(surf_fn))
return surf.read(surf_fn)
def test_surf_voxel_selection(self):
vol_shape = (10, 10, 10)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
vg = volgeom.VolGeom(vol_shape, vol_affine)
density = 10
outer = surf.generate_sphere(density) * 25. + 15
inner = surf.generate_sphere(density) * 20. + 15
vs = volsurf.VolSurfMaximalMapping(vg, outer, inner)
nv = outer.nvertices
# select under variety of parameters
# parameters are distance metric (dijkstra or euclidean),
# radius, and number of searchlight centers
params = [('d', 1., 10), ('d', 1., 50), ('d', 1., 100), ('d', 2., 100),
('e', 2., 100), ('d', 2., 100), ('d', 20, 100),
('euclidean', 5, None), ('dijkstra', 10, None)]
# function that indicates for which parameters the full test is run
test_full = lambda x: len(x[0]) > 1 or x[2] == 100
expected_labs = ['grey_matter_position', 'center_distances']
voxcount = []
tested_double_features = False
for param in params:
distance_metric, radius, ncenters = param
srcs = range(0, nv, nv // (ncenters or nv))
sel = surf_voxel_selection.voxel_selection(
vs,
radius,
source_surf_nodes=srcs,
distance_metric=distance_metric)
# see how many voxels were selected
vg = sel.volgeom
datalin = np.zeros((vg.nvoxels, 1))
mp = sel
for k, idxs in mp.iteritems():
if idxs is not None:
datalin[idxs] = 1
voxcount.append(np.sum(datalin))
if test_full(param):
assert_equal(np.sum(datalin), np.sum(sel.get_mask()))
assert_true(len('%s%r' % (sel, sel)) > 0)
# see if voxels containing inner and outer
# nodes were selected
for sf in [inner, outer]:
for k, idxs in mp.iteritems():
xyz = np.reshape(sf.vertices[k, :], (1, 3))
linidx = vg.xyz2lin(xyz)
# only required if xyz is actually within the volume
assert_equal(linidx in idxs, vg.contains_lin(linidx))
# check that it has all the attributes
labs = sel.aux_keys()
assert_true(all([lab in labs for lab in expected_labs]))
if externals.exists('h5py'):
# some I/O testing
fd, fn = tempfile.mkstemp('.h5py', 'test')
os.close(fd)
h5save(fn, sel)
sel2 = h5load(fn)
os.remove(fn)
assert_equal(sel, sel2)
else:
sel2 = sel
# check that mask is OK even after I/O
assert_array_equal(sel.get_mask(), sel2.get_mask())
# test I/O with surfaces
# XXX the @tempfile decorator only supports a single filename
# hence this method does not use it
fd, outerfn = tempfile.mkstemp('outer.asc', 'test')
os.close(fd)
fd, innerfn = tempfile.mkstemp('inner.asc', 'test')
os.close(fd)
fd, volfn = tempfile.mkstemp('vol.nii', 'test')
os.close(fd)
surf.write(outerfn, outer, overwrite=True)
surf.write(innerfn, inner, overwrite=True)
img = sel.volgeom.get_empty_nifti_image()
img.to_filename(volfn)
sel3 = surf_voxel_selection.run_voxel_selection(
radius,
volfn,
innerfn,
outerfn,
source_surf_nodes=srcs,
distance_metric=distance_metric)
outer4 = surf.read(outerfn)
inner4 = surf.read(innerfn)
vsm4 = vs = volsurf.VolSurfMaximalMapping(vg, inner4, outer4)
# check that two ways of voxel selection match
sel4 = surf_voxel_selection.voxel_selection(
vsm4,
radius,
source_surf_nodes=srcs,
distance_metric=distance_metric)
assert_equal(sel3, sel4)
os.remove(outerfn)
os.remove(innerfn)
os.remove(volfn)
# compare sel3 with other selection results
# NOTE: which voxels are precisely selected by sel can be quite
# off from those in sel3, as writing the surfaces imposes
# rounding errors and the sphere is very symmetric, which
# means that different neighboring nodes are selected
# to select a certain number of voxels.
sel3cmp_difference_ratio = [(sel, .2), (sel4, 0.)]
for selcmp, ratio in sel3cmp_difference_ratio:
nunion = ndiff = 0
for k in selcmp.keys():
p = set(sel3.get(k))
q = set(selcmp.get(k))
nunion += len(p.union(q))
ndiff += len(p.symmetric_difference(q))
assert_true(float(ndiff) / float(nunion) <= ratio)
# check searchlight call
# as of late Aug 2012, this is with the fancy query engine
# as implemented by Yarik
mask = sel.get_mask()
keys = None if ncenters is None else sel.keys()
dset_data = np.reshape(np.arange(vg.nvoxels), vg.shape)
dset_img = nb.Nifti1Image(dset_data, vg.affine)
dset = fmri_dataset(samples=dset_img, mask=mask)
qe = queryengine.SurfaceVerticesQueryEngine(
sel,
# you can optionally add additional
# information about each near-disk-voxels
add_fa=['center_distances', 'grey_matter_position'])
# test i/o ensuring that when loading it is still trained
if externals.exists('h5py'):
fd, qefn = tempfile.mkstemp('qe.hdf5', 'test')
os.close(fd)
h5save(qefn, qe)
qe = h5load(qefn)
os.remove(qefn)
assert_false('ERROR' in repr(qe)) # to check if repr works
voxelcounter = _Voxel_Count_Measure()
searchlight = Searchlight(
voxelcounter,
queryengine=qe,
roi_ids=keys,
nproc=1,
enable_ca=['roi_feature_ids', 'roi_center_ids'])
sl_dset = searchlight(dset)
selected_count = sl_dset.samples[0, :]
mp = sel
for i, k in enumerate(sel.keys()):
# check that number of selected voxels matches
assert_equal(selected_count[i], len(mp[k]))
assert_equal(searchlight.ca.roi_center_ids, sel.keys())
assert_array_equal(sl_dset.fa['center_ids'], qe.ids)
# check nearest node is *really* the nearest node
allvx = sel.get_targets()
intermediate = outer * .5 + inner * .5
for vx in allvx:
nearest = sel.target2nearest_source(vx)
xyz = intermediate.vertices[nearest, :]
sqsum = np.sum((xyz - intermediate.vertices)**2, 1)
idx = np.argmin(sqsum)
assert_equal(idx, nearest)
if not tested_double_features: # test only once
# see if we have multiple features for the same voxel, we would get them all
dset1 = dset.copy()
dset1.fa['dset'] = [1]
dset2 = dset.copy()
dset2.fa['dset'] = [2]
dset_ = hstack((dset1, dset2), 'drop_nonunique')
dset_.sa = dset1.sa
# dset_.a.imghdr = dset1.a.imghdr
assert_true('imghdr' in dset_.a.keys())
assert_equal(dset_.a['imghdr'].value,
dset1.a['imghdr'].value)
roi_feature_ids = searchlight.ca.roi_feature_ids
sl_dset_ = searchlight(dset_)
# and we should get twice the counts
assert_array_equal(sl_dset_.samples, sl_dset.samples * 2)
# compare old and new roi_feature_ids
assert (len(roi_feature_ids) == len(
searchlight.ca.roi_feature_ids))
nfeatures = dset.nfeatures
for old, new in zip(roi_feature_ids,
searchlight.ca.roi_feature_ids):
# each new ids should comprise of old ones + (old + nfeatures)
# since we hstack'ed two datasets
assert_array_equal(
np.hstack([(x, x + nfeatures) for x in old]), new)
tested_double_features = True
# check whether number of voxels were selected is as expected
expected_voxcount = [22, 93, 183, 183, 183, 183, 183, 183, 183]
assert_equal(voxcount, expected_voxcount)
def test_surf(self, temp_fn):
"""Some simple testing with surfaces
"""
s = surf.generate_sphere(10)
assert_true(s.nvertices == 102)
assert_true(s.nfaces == 200)
v = s.vertices
f = s.faces
assert_true(v.shape == (102, 3))
assert_true(f.shape == (200, 3))
# another surface
t = s * 10 + 2
assert_true(t.same_topology(s))
assert_array_equal(f, t.faces)
assert_array_equal(v * 10 + 2, t.vertices)
# allow updating, but should not affect original array
# CHECKME: maybe we want to throw an exception instead
assert_true((v * 10 + 2 == t.vertices).all().all())
assert_true((s.vertices * 10 + 2 == t.vertices).all().all())
# a few checks on vertices and nodes
v_check = {
40: (0.86511144, -0.28109175, -0.41541501),
10: (0.08706015, -0.26794358, -0.95949297)
}
f_check = {10: (7, 8, 1), 40: (30, 31, 21)}
vf_checks = [(v_check, lambda x: x.vertices),
(f_check, lambda x: x.faces)]
eps = .0001
for cmap, f in vf_checks:
for k, v in cmap.iteritems():
surfval = f(s)[k, :]
assert_true((abs(surfval - v) < eps).all())
# make sure same topology fails with different topology
u = surf.generate_cube()
assert_false(u.same_topology(s))
# check that neighbours are computed correctly
# even if we nuke the topology afterwards
for _ in [0, 1]:
nbrs = s.neighbors
n_check = [(0, 96, 0.284629), (40, 39, 0.56218349),
(100, 99, 0.1741202)]
for i, j, k in n_check:
assert_true(abs(nbrs[i][j] - k) < eps)
def assign_zero(x):
x.faces[:, :] = 0
return None
assert_raises((ValueError, RuntimeError), assign_zero, s)
# see if mapping to high res works
h = surf.generate_sphere(40)
low2high = s.map_to_high_resolution_surf(h, .1)
partmap = {7: 141, 8: 144, 9: 148, 10: 153, 11: 157, 12: 281}
for k, v in partmap.iteritems():
assert_true(low2high[k] == v)
# ensure that slow implementation gives same results as fast one
low2high_slow = s.map_to_high_resolution_surf(h, .1)
for k, v in low2high.iteritems():
assert_true(low2high_slow[k] == v)
# should fail if epsilon is too small
assert_raises(ValueError,
lambda x: x.map_to_high_resolution_surf(h, .01), s)
n2f = s.node2faces
for i in xrange(s.nvertices):
nf = [10] if i < 2 else [5, 6] # number of faces expected
assert_true(len(n2f[i]) in nf)
# test dijkstra distances
ds2 = s.dijkstra_distance(2)
some_ds = {
0: 3.613173280799,
1: 0.2846296765,
2: 0.,
52: 1.87458018,
53: 2.0487004817,
54: 2.222820777,
99: 3.32854360,
100: 3.328543604,
101: 3.3285436042
}
eps = np.finfo('f').eps
for k, v in some_ds.iteritems():
assert_true(abs(v - ds2[k]) < eps)
# test I/O (through ascii files)
surf.write(temp_fn, s, overwrite=True)
s2 = surf.read(temp_fn)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
h5save(temp_fn, s2)
s2 = h5load(temp_fn)
assert_array_almost_equal(s.vertices, s2.vertices, 4)
assert_array_almost_equal(s.faces, s2.faces, 4)
# test plane (new feature end of August 2012)
s3 = surf.generate_plane((0, 0, 0), (2, 0, 0), (0, 1, 0), 10, 20)
assert_equal(s3.nvertices, 200)
assert_equal(s3.nfaces, 342)
assert_array_almost_equal(s3.vertices[-1, :], np.array([18., 19, 0.]))
assert_array_almost_equal(s3.faces[-1, :], np.array([199, 198, 179]))
# test bar
p, q = (0, 0, 0), (100, 0, 0)
s4 = surf.generate_bar(p, q, 10, 12)
assert_equal(s4.nvertices, 26)
assert_equal(s4.nfaces, 48)
def test_surf_gifti(self, fn):
# From section 14.4 in GIFTI Surface Data Format Version 1.0
# (with some adoptions)
test_data = '''<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/1594/gifti.dtd">
<GIFTI
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="http://www.nitrc.org/frs/download.php/1303/GIFTI_Caret.xsd"
Version="1.0"
NumberOfDataArrays="2">
<MetaData>
<MD>
<Name><![CDATA[date]]></Name>
<Value><![CDATA[Thu Nov 15 09:05:22 2007]]></Value>
</MD>
</MetaData>
<LabelTable/>
<DataArray Intent="NIFTI_INTENT_POINTSET"
DataType="NIFTI_TYPE_FLOAT32"
ArrayIndexingOrder="RowMajorOrder"
Dimensionality="2"
Dim0="4"
Dim1="3"
Encoding="ASCII"
Endian="LittleEndian"
ExternalFileName=""
ExternalFileOffset="">
<CoordinateSystemTransformMatrix>
<DataSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></DataSpace>
<TransformedSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></TransformedSpace>
<MatrixData>
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
</MatrixData>
</CoordinateSystemTransformMatrix>
<Data>
10.5 0 0
0 20.5 0
0 0 30.5
0 0 0
</Data>
</DataArray>
<DataArray Intent="NIFTI_INTENT_TRIANGLE"
DataType="NIFTI_TYPE_INT32"
ArrayIndexingOrder="RowMajorOrder"
Dimensionality="2"
Dim0="4"
Dim1="3"
Encoding="ASCII"
Endian="LittleEndian"
ExternalFileName="" ExternalFileOffset="">
<Data>
0 1 2
1 2 3
0 1 3
0 2 3
</Data>
</DataArray>
</GIFTI>'''
with open(fn, 'w') as f:
f.write(test_data)
# test I/O
s = surf.read(fn)
surf.write(fn, s)
s = surf.read(fn)
v = np.zeros((4, 3))
v[0, 0] = 10.5
v[1, 1] = 20.5
v[2, 2] = 30.5
f = np.asarray([[0, 1, 2], [1, 2, 3], [0, 1, 3], [0, 2, 3]],
dtype=np.int32)
assert_array_equal(s.vertices, v)
assert_array_equal(s.faces, f)
print 'Loading and zscore %s hemisphere template took %s seconds' % (hemi, tttt)
# Run Hyperalignment per hemisphere:
hypsource = {}
finalproj = {}
for hemi in ['L','R']:
# Load connectvity profile:
t1 = time.time()
ds = corr[:,ind[hemi]]
source = Dataset(ds)
zscore(source,chunks_attr=None)
# Set 'node_indices' for hyperalignment function:
source.fa['node_indices'] = range(len(ind[hemi]))
source = source[:,maskimg[hemi]]
# Read surface for searchlight vertices:
s = surf.read('%s/resources/10k/S1200.%s.midthickness.10k_fs_LR.surf.gii' % (tempdir,hemi))
surfsel = SurfaceQueryEngine(surface=s,radius=12,distance_metric='dijkstra',fa_node_key='node_indices')
surfsel.train(source)
nfeatures = source.shape[1]
# Searchlight hyperalignment on connectomes:
projmat = np.zeros([nfeatures,nfeatures])
[hypalign(source,target[hemi],node,surfsel,projmat,maskimg[hemi]) for node in maskimg[hemi]]
normproj = projmat.copy()
# Normalise projection matrices to keep scale of values:
for ii in range(len(projmat)):
nnz = np.count_nonzero(normproj[:, ii])
nnz = np.float(nnz)
normproj[:, ii] = normproj[:, ii]/nnz
normproj = np.nan_to_num(normproj)
dd = np.asmatrix(source.samples)
dd = dd - np.mean(dd,axis=0)
def test_surf_voxel_selection(self):
vol_shape = (10, 10, 10)
vol_affine = np.identity(4)
vol_affine[0, 0] = vol_affine[1, 1] = vol_affine[2, 2] = 5
vg = volgeom.VolGeom(vol_shape, vol_affine)
density = 10
outer = surf.generate_sphere(density) * 25. + 15
inner = surf.generate_sphere(density) * 20. + 15
vs = volsurf.VolSurfMaximalMapping(vg, outer, inner)
nv = outer.nvertices
# select under variety of parameters
# parameters are distance metric (dijkstra or euclidean),
# radius, and number of searchlight centers
params = [('d', 1., 10), ('d', 1., 50), ('d', 1., 100), ('d', 2., 100),
('e', 2., 100), ('d', 2., 100), ('d', 20, 100),
('euclidean', 5, None), ('dijkstra', 10, None)]
# function that indicates for which parameters the full test is run
test_full = lambda x:len(x[0]) > 1 or x[2] == 100
expected_labs = ['grey_matter_position',
'center_distances']
voxcount = []
tested_double_features = False
for param in params:
distance_metric, radius, ncenters = param
srcs = range(0, nv, nv // (ncenters or nv))
sel = surf_voxel_selection.voxel_selection(vs, radius,
source_surf_nodes=srcs,
distance_metric=distance_metric)
# see how many voxels were selected
vg = sel.volgeom
datalin = np.zeros((vg.nvoxels, 1))
mp = sel
for k, idxs in mp.iteritems():
if idxs is not None:
datalin[idxs] = 1
voxcount.append(np.sum(datalin))
if test_full(param):
assert_equal(np.sum(datalin), np.sum(sel.get_mask()))
assert_true(len('%s%r' % (sel, sel)) > 0)
# see if voxels containing inner and outer
# nodes were selected
for sf in [inner, outer]:
for k, idxs in mp.iteritems():
xyz = np.reshape(sf.vertices[k, :], (1, 3))
linidx = vg.xyz2lin(xyz)
# only required if xyz is actually within the volume
assert_equal(linidx in idxs, vg.contains_lin(linidx))
# check that it has all the attributes
labs = sel.aux_keys()
assert_true(all([lab in labs for lab in expected_labs]))
if externals.exists('h5py'):
# some I/O testing
fd, fn = tempfile.mkstemp('.h5py', 'test'); os.close(fd)
h5save(fn, sel)
sel2 = h5load(fn)
os.remove(fn)
assert_equal(sel, sel2)
else:
sel2 = sel
# check that mask is OK even after I/O
assert_array_equal(sel.get_mask(), sel2.get_mask())
# test I/O with surfaces
# XXX the @tempfile decorator only supports a single filename
# hence this method does not use it
fd, outerfn = tempfile.mkstemp('outer.asc', 'test'); os.close(fd)
fd, innerfn = tempfile.mkstemp('inner.asc', 'test'); os.close(fd)
fd, volfn = tempfile.mkstemp('vol.nii', 'test'); os.close(fd)
surf.write(outerfn, outer, overwrite=True)
surf.write(innerfn, inner, overwrite=True)
img = sel.volgeom.get_empty_nifti_image()
img.to_filename(volfn)
sel3 = surf_voxel_selection.run_voxel_selection(radius, volfn, innerfn,
outerfn, source_surf_nodes=srcs,
distance_metric=distance_metric)
outer4 = surf.read(outerfn)
inner4 = surf.read(innerfn)
vsm4 = vs = volsurf.VolSurfMaximalMapping(vg, inner4, outer4)
# check that two ways of voxel selection match
sel4 = surf_voxel_selection.voxel_selection(vsm4, radius,
source_surf_nodes=srcs,
distance_metric=distance_metric)
assert_equal(sel3, sel4)
os.remove(outerfn)
os.remove(innerfn)
os.remove(volfn)
# compare sel3 with other selection results
# NOTE: which voxels are precisely selected by sel can be quite
# off from those in sel3, as writing the surfaces imposes
# rounding errors and the sphere is very symmetric, which
# means that different neighboring nodes are selected
# to select a certain number of voxels.
sel3cmp_difference_ratio = [(sel, .2), (sel4, 0.)]
for selcmp, ratio in sel3cmp_difference_ratio:
nunion = ndiff = 0
for k in selcmp.keys():
p = set(sel3.get(k))
q = set(selcmp.get(k))
nunion += len(p.union(q))
ndiff += len(p.symmetric_difference(q))
assert_true(float(ndiff) / float(nunion) <= ratio)
# check searchlight call
# as of late Aug 2012, this is with the fancy query engine
# as implemented by Yarik
mask = sel.get_mask()
keys = None if ncenters is None else sel.keys()
dset_data = np.reshape(np.arange(vg.nvoxels), vg.shape)
dset_img = nb.Nifti1Image(dset_data, vg.affine)
dset = fmri_dataset(samples=dset_img, mask=mask)
qe = queryengine.SurfaceVerticesQueryEngine(sel,
# you can optionally add additional
# information about each near-disk-voxels
add_fa=['center_distances',
'grey_matter_position'])
# test i/o ensuring that when loading it is still trained
if externals.exists('h5py'):
fd, qefn = tempfile.mkstemp('qe.hdf5', 'test'); os.close(fd)
h5save(qefn, qe)
qe = h5load(qefn)
os.remove(qefn)
assert_false('ERROR' in repr(qe)) # to check if repr works
voxelcounter = _Voxel_Count_Measure()
searchlight = Searchlight(voxelcounter, queryengine=qe, roi_ids=keys, nproc=1,
enable_ca=['roi_feature_ids', 'roi_center_ids'])
sl_dset = searchlight(dset)
selected_count = sl_dset.samples[0, :]
mp = sel
for i, k in enumerate(sel.keys()):
# check that number of selected voxels matches
assert_equal(selected_count[i], len(mp[k]))
assert_equal(searchlight.ca.roi_center_ids, sel.keys())
assert_array_equal(sl_dset.fa['center_ids'], qe.ids)
# check nearest node is *really* the nearest node
allvx = sel.get_targets()
intermediate = outer * .5 + inner * .5
for vx in allvx:
nearest = sel.target2nearest_source(vx)
xyz = intermediate.vertices[nearest, :]
sqsum = np.sum((xyz - intermediate.vertices) ** 2, 1)
idx = np.argmin(sqsum)
assert_equal(idx, nearest)
if not tested_double_features: # test only once
# see if we have multiple features for the same voxel, we would get them all
dset1 = dset.copy()
dset1.fa['dset'] = [1]
dset2 = dset.copy()
dset2.fa['dset'] = [2]
dset_ = hstack((dset1, dset2), 'drop_nonunique')
dset_.sa = dset1.sa
#dset_.a.imghdr = dset1.a.imghdr
assert_true('imghdr' in dset_.a.keys())
assert_equal(dset_.a['imghdr'].value, dset1.a['imghdr'].value)
roi_feature_ids = searchlight.ca.roi_feature_ids
sl_dset_ = searchlight(dset_)
# and we should get twice the counts
assert_array_equal(sl_dset_.samples, sl_dset.samples * 2)
# compare old and new roi_feature_ids
assert(len(roi_feature_ids) == len(searchlight.ca.roi_feature_ids))
nfeatures = dset.nfeatures
for old, new in zip(roi_feature_ids,
searchlight.ca.roi_feature_ids):
# each new ids should comprise of old ones + (old + nfeatures)
# since we hstack'ed two datasets
assert_array_equal(np.hstack([(x, x + nfeatures) for x in old]),
new)
tested_double_features = True
# check whether number of voxels were selected is as expected
expected_voxcount = [22, 93, 183, 183, 183, 183, 183, 183, 183]
assert_equal(voxcount, expected_voxcount)
def test_surf(self, temp_fn):
"""Some simple testing with surfaces
"""
s = surf.generate_sphere(10)
assert_true(s.nvertices == 102)
assert_true(s.nfaces == 200)
v = s.vertices
f = s.faces
assert_true(v.shape == (102, 3))
assert_true(f.shape == (200, 3))
# another surface
t = s * 10 + 2
assert_true(t.same_topology(s))
assert_array_equal(f, t.faces)
assert_array_equal(v * 10 + 2, t.vertices)
# allow updating, but should not affect original array
# CHECKME: maybe we want to throw an exception instead
assert_true((v * 10 + 2 == t.vertices).all().all())
assert_true((s.vertices * 10 + 2 == t.vertices).all().all())
# a few checks on vertices and nodes
v_check = {40:(0.86511144 , -0.28109175, -0.41541501),
10:(0.08706015, -0.26794358, -0.95949297)}
f_check = {10:(7, 8, 1), 40:(30, 31, 21)}
vf_checks = [(v_check, lambda x:x.vertices),
(f_check, lambda x:x.faces)]
eps = .0001
for cmap, f in vf_checks:
for k, v in cmap.iteritems():
surfval = f(s)[k, :]
assert_true((abs(surfval - v) < eps).all())
# make sure same topology fails with different topology
u = surf.generate_cube()
assert_false(u.same_topology(s))
# check that neighbours are computed correctly
# even if we nuke the topology afterwards
for _ in [0, 1]:
nbrs = s.neighbors
n_check = [(0, 96, 0.284629),
(40, 39, 0.56218349),
(100, 99, 0.1741202)]
for i, j, k in n_check:
assert_true(abs(nbrs[i][j] - k) < eps)
def assign_zero(x):
x.faces[:, :] = 0
return None
assert_raises((ValueError, RuntimeError), assign_zero, s)
# see if mapping to high res works
h = surf.generate_sphere(40)
low2high = s.map_to_high_resolution_surf(h, .1)
partmap = {7: 141, 8: 144, 9: 148, 10: 153, 11: 157, 12: 281}
for k, v in partmap.iteritems():
assert_true(low2high[k] == v)
# ensure that slow implementation gives same results as fast one
low2high_slow = s.map_to_high_resolution_surf(h, .1)
for k, v in low2high.iteritems():
assert_true(low2high_slow[k] == v)
# should fail if epsilon is too small
assert_raises(ValueError,
lambda x:x.map_to_high_resolution_surf(h, .01), s)
n2f = s.node2faces
for i in xrange(s.nvertices):
nf = [10] if i < 2 else [5, 6] # number of faces expected
assert_true(len(n2f[i]) in nf)
# test dijkstra distances
ds2 = s.dijkstra_distance(2)
some_ds = {0: 3.613173280799, 1: 0.2846296765, 2: 0.,
52: 1.87458018, 53: 2.0487004817, 54: 2.222820777,
99: 3.32854360, 100: 3.328543604, 101: 3.3285436042}
eps = np.finfo('f').eps
for k, v in some_ds.iteritems():
assert_true(abs(v - ds2[k]) < eps)
# test I/O (through ascii files)
surf.write(temp_fn, s, overwrite=True)
s2 = surf.read(temp_fn)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
h5save(temp_fn, s2)
s2 = h5load(temp_fn)
assert_array_almost_equal(s.vertices, s2.vertices, 4)
assert_array_almost_equal(s.faces, s2.faces, 4)
# test plane (new feature end of August 2012)
s3 = surf.generate_plane((0, 0, 0), (2, 0, 0), (0, 1, 0), 10, 20)
assert_equal(s3.nvertices, 200)
assert_equal(s3.nfaces, 342)
assert_array_almost_equal(s3.vertices[-1, :], np.array([18., 19, 0.]))
assert_array_almost_equal(s3.faces[-1, :], np.array([199, 198, 179]))
# test bar
p, q = (0, 0, 0), (100, 0, 0)
s4 = surf.generate_bar(p, q, 10, 12)
assert_equal(s4.nvertices, 26)
assert_equal(s4.nfaces, 48)
def test_surf_gifti(self, fn):
# From section 14.4 in GIFTI Surface Data Format Version 1.0
# (with some adoptions)
test_data = '''<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/1594/gifti.dtd">
<GIFTI
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="http://www.nitrc.org/frs/download.php/1303/GIFTI_Caret.xsd"
Version="1.0"
NumberOfDataArrays="2">
<MetaData>
<MD>
<Name><![CDATA[date]]></Name>
<Value><![CDATA[Thu Nov 15 09:05:22 2007]]></Value>
</MD>
</MetaData>
<LabelTable/>
<DataArray Intent="NIFTI_INTENT_POINTSET"
DataType="NIFTI_TYPE_FLOAT32"
ArrayIndexingOrder="RowMajorOrder"
Dimensionality="2"
Dim0="4"
Dim1="3"
Encoding="ASCII"
Endian="LittleEndian"
ExternalFileName=""
ExternalFileOffset="">
<CoordinateSystemTransformMatrix>
<DataSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></DataSpace>
<TransformedSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></TransformedSpace>
<MatrixData>
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
</MatrixData>
</CoordinateSystemTransformMatrix>
<Data>
10.5 0 0
0 20.5 0
0 0 30.5
0 0 0
</Data>
</DataArray>
<DataArray Intent="NIFTI_INTENT_TRIANGLE"
DataType="NIFTI_TYPE_INT32"
ArrayIndexingOrder="RowMajorOrder"
Dimensionality="2"
Dim0="4"
Dim1="3"
Encoding="ASCII"
Endian="LittleEndian"
ExternalFileName="" ExternalFileOffset="">
<Data>
0 1 2
1 2 3
0 1 3
0 2 3
</Data>
</DataArray>
</GIFTI>'''
with open(fn, 'w') as f:
f.write(test_data)
# test I/O
s = surf.read(fn)
surf.write(fn, s)
s = surf.read(fn)
v = np.zeros((4, 3))
v[0, 0] = 10.5
v[1, 1] = 20.5
v[2, 2] = 30.5
f = np.asarray([[0, 1, 2], [1, 2, 3], [0, 1, 3], [0, 2, 3]],
dtype=np.int32)
assert_array_equal(s.vertices, v)
assert_array_equal(s.faces, f)
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_alignment(config, env):
'''Aligns anat (which is assumed to be aligned with EPI data) to FreeSurfer SurfVol
This function strips the anatomicals (by default), then uses align_epi_anat.py
to estimate the alignment, then applies this transformation to the non-skull-stripped
SurfVol and also to the surfaces. Some alignment headers will be nuked'''
overwrite = config['overwrite']
alignsuffix = config['al2expsuffix']
refdir = config['refdir']
fullext = config['outvol_fullext']
ext = config['outvol_ext']
if config['sid'] is None:
raise ValueError('Need sid')
cmds = []
if not os.path.exists(config['refdir']):
cmds.append('mkdir %(refdir)s' % config)
# two volumes may have to be stripped: the inpput anatomical, and the surfvol.
# put them in a list here and process them similarly
surfvol = '%(refdir)s/%(sid)s_SurfVol%(outvol_fullext)s' % config
surfvol_ss = '%(refdir)s/%(sid)s_SurfVol%(sssuffix)s%(outvol_fullext)s' % config
e_p, e_n, _, _ = utils.afni_fileparts(config['expvol'])
if config['expvol_ss']:
e_n = '%s%s' % (e_n, config['sssuffix'])
expvol = '%s/%s%s' % (refdir, e_n, fullext)
volsin = [surfvol_ss, expvol]
for volin in volsin:
if not os.path.exists(volin):
raise ValueError('File %s does not exist' % volin)
a_n = utils.afni_fileparts(volsin[0])[1] # surfvol input root name
ssalprefix = '%s%s' % (a_n, alignsuffix)
unity = "1 0 0 0 0 1 0 0 0 0 1 0" # we all like unity, don't we?
fullmatrixfn = '%s_mat.aff12.1D' % ssalprefix
aloutfns = ['%s%s' % (ssalprefix, fullext),
fullmatrixfn] # expected output files if alignment worked
if config['overwrite'] or not all(
[os.path.exists('%s/%s' % (refdir, f)) for f in aloutfns]):
alignedfn = '%s/%s%s' % (refdir, ssalprefix, fullext)
if config['identity']:
fullmatrix_content = '"MATRIX(%s)"' % unity.replace(" ", ",")
cmd = 'cd "%s"; cat_matvec %s > %s; 3dcopy -overwrite %s%s %s%s%s' % (
refdir, fullmatrix_content, fullmatrixfn, a_n, ext, a_n,
alignsuffix, ext)
else:
# use different inputs depending on whether expvol is EPI or ANAT
twovolpat = (
'-anat %s -epi %s -anat2epi -epi_base 0 -anat_has_skull no -epi_strip None'
if config['isepi'] else
'-dset1 %s -dset2 %s -dset1to2 -dset1_strip None -dset2_strip None'
)
# use this pattern to generate a suffix
twovolsuffix = twovolpat % (volsin[0], volsin[1])
aea_opts = config['aea_opts']
if config['template']:
aea_opts += " -Allineate_opts '-maxrot 10 -maxshf 10 -maxscl 1.5'"
# align_epi_anat.py
cmd = 'cd "%s"; align_epi_anat.py -overwrite -suffix %s %s %s' % (
refdir, alignsuffix, twovolsuffix, aea_opts)
cmds.append(cmd)
cmds.append(_set_vol_space_cmd(alignedfn, config))
utils.run_cmds(cmds, env)
else:
print "Alignment already done - skipping"
# run these commands first, then check if everything worked properly
cmds = []
# see if the expected transformation file was found
if not config['identity'] and not os.path.exists('%s/%s' %
(refdir, fullmatrixfn)):
raise Exception("Could not find %s in %s" % (fullmatrixfn, refdir))
# now make a 3x4 matrix
matrixfn = '%s%s.A2E.1D' % (a_n, alignsuffix)
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn)):
cmds.append('cd "%s"; cat_matvec %s > %s || exit 1' %
(refdir, fullmatrixfn, matrixfn))
# make an aligned, non-skullstripped version of SurfVol in refdir
alprefix = '%s_SurfVol%s' % (config['sid'], alignsuffix)
svalignedfn = '%s/%s%s' % (refdir, alprefix, fullext)
newgrid = 1 # size of anatomical grid in mm. We'll have to resample, otherwise 3dWarp does
# not respect the corners of the volume (as of April 2012)
if overwrite or not os.path.exists(svalignedfn):
#if not config['fs_sid']:
# raise ValueError("Don't have a freesurfer subject id - cannot continue")
#surfvolfn = '%s/%s_SurfVol+orig' % (config['sumadir'], config['fs_sid'])
surfvolfn = '%s/T1.nii' % config['sumadir']
cmds.append(
'cd "%s";3dWarp -overwrite -newgrid %f -matvec_out2in `cat_matvec -MATRIX %s` -prefix ./%s %s'
% (refdir, newgrid, matrixfn, alprefix, surfvolfn))
cmds.append(
_set_vol_space_cmd('%s/%s+orig' % (refdir, alprefix), config))
else:
print '%s already exists - skipping Warp' % svalignedfn
utils.run_cmds(cmds, env)
cmds = []
# nuke afni headers
headernukefns = ['%s%s' % (f, fullext) for f in [ssalprefix, alprefix]]
headernukefields = [
'ALLINEATE_MATVEC_B2S_000000', 'ALLINEATE_MATVEC_S2B_000000',
'WARPDRIVE_MATVEC_FOR_000000', 'WARPDRIVE_MATVEC_INV_000000'
]
for fn in headernukefns:
for field in headernukefields:
# nuke transformation - otherwise AFNI does this unwanted transformation for us
fullfn = '%s/%s' % (refdir, fn)
if not (os.path.exists(fullfn) or config['identity']):
raise ValueError("File %r does not exist" % fullfn)
refitcmd = "3drefit -atrfloat %s '%s' %s" % (field, unity, fn)
# only refit if not already in AFNI history (which is stored in HEADfile)
cmd = 'cd "%s"; m=`grep "%s" %s | wc -w`; if [ $m -eq 0 ]; then %s; else echo "File %s seems already 3drefitted"; fi' % (
refdir, refitcmd, fn, refitcmd, fn)
cmds.append(cmd)
utils.run_cmds('; '.join(cmds), env)
cmds = []
# run AddEdge so that volumes can be inspected visually for alignment
if config['AddEdge']:
use_ss = config['expvol_ss']
# ae_{e,s}_n are AddEdge names for expvol and surfvol
ae_e_n = utils.afni_fileparts(config['expvol'])[1]
if use_ss:
ae_e_n += config['sssuffix']
ae_s_n = ssalprefix #if use_ss else alprefix
# *_ne have the output extension as well
ae_e_ne = ae_e_n + ext
ae_s_ne = ae_s_n + ext
addedge_fns = ['%s/_ae.ExamineList.log' % refdir]
exts = ['HEAD', 'BRIK']
orig_ext = '+orig'
addedge_rootfns = [
'%s_%s%%s' % (ae_e_n, postfix)
for postfix in ['e3', 'ec', ae_s_n + '_ec']
]
addedge_rootfns.extend(
['%s_%s%%s' % (ae_s_n, postfix) for postfix in ['e3', 'ec']])
addedge_fns_pat = [
'%s.%s' % (fn, e) for fn in addedge_rootfns for e in exts
]
addegde_pathfns_orig = map(lambda x: os.path.join(refdir, x % '+orig'),
addedge_fns_pat) + addedge_fns
addegde_pathfns_ext = map(lambda x: os.path.join(refdir, x % ext),
addedge_fns_pat)
addegde_exists = map(os.path.exists, addegde_pathfns_ext)
if overwrite or not all(addegde_exists):
ae_ns = (ae_e_n, ae_s_n)
cmds.extend(
map(lambda fn: 'if [ -e "%s" ]; then rm "%s"; fi' % (fn, fn),
addegde_pathfns_orig + addegde_pathfns_ext))
cmds.append(';'.join(['cd %s' % refdir] + [
_convert_vol_space_to_orig_cmd('%s/%s%s' % (refdir, n, ext))
for n in ae_ns
] + ['\@AddEdge %s+orig %s+orig' % ae_ns]))
set_space_fns = addegde_pathfns_orig + [
'%s/%s%s.%s' % (refdir, fn, orig_ext, exts[0]) for fn in ae_ns
]
for fn in set_space_fns: #['%s/%s' % (refdir, fn % orig_ext) for fn in addedge_fns_pat]:
if fn.endswith('.log'):
continue
cmds.append('if [ -e %s ]; then %s; fi' %
(fn, _set_vol_space_cmd(fn, config)))
utils.run_cmds(cmds, env)
cmds = []
else:
print "AddEdge seems to have been run already"
sid = config['sid']
plot_slice_fns = [
(ae_e_n + '_e3', ae_s_n + '_e3', '%s_qa_e3.png' % sid),
(None, ae_e_n + '_' + ae_s_n + '_ec', '%s_qa_ec.png' % sid)
]
plot_slice_imgfns = ['%s/%s' % (refdir, fn) for fn in plot_slice_fns]
if overwrite or not all(map(os.path.exists, plot_slice_imgfns)):
slice_dims = [0, 1, 2]
slice_pos = [.35, .45, .55, .65]
for fns in plot_slice_fns:
input_fns = []
for i, fn in enumerate(fns):
if fn is not None:
fn = '%s/%s' % (refdir, fn)
if i <= 1:
fn += ext
input_fns.append(fn)
fn1, fn2, fnout = input_fns
if not os.path.exists(fnout):
_make_slice_plot(fn1, fn2, fnout)
print "QA Image saved to %s" % fnout
else:
print "Already exists: %s" % fnout
else:
print "QA images already exist"
# because AFNI uses RAI orientation but FreeSurfer LPI, make a new
# affine transformation matrix in which the signs of
# x and y coordinates are negated before and after the transformation
matrixfn_LPI2RAI = '%s.A2E_LPI.1D' % ssalprefix
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn_LPI2RAI)):
lpirai = '"MATRIX(-1,0,0,0,0,-1,0,0,0,0,1,0)"'
cmd = (
'cd %s; cat_matvec -ONELINE %s `cat_matvec -MATRIX %s` %s > %s' %
(refdir, lpirai, matrixfn, lpirai, matrixfn_LPI2RAI))
cmds.append(cmd)
# apply transformation to surfaces
[icolds, hemis] = _get_hemis_icolds(config)
sumadir = config['sumadir']
sumafiles = os.listdir(sumadir)
origext = '.asc'
ext = format2extension(config)
tp = format2type(config)
# process all hemispheres and ld values
for icold in icolds:
for hemi in hemis:
pat = '%s%sh.?*%s' % (config['mi_icopat'] % icold, hemi, origext)
for sumafile in sumafiles:
if fnmatch.fnmatch(sumafile, pat):
if not sumafile.endswith(origext):
raise ValueError("%s does not end with %s" %
(sumafile, origext))
#s = sumafile.split(".")
#s[len(s) - 2] += config['alsuffix'] # insert '_al' just before last dot
#alsumafile = ".".join(s)
extsumafile = sumafile[:-len(origext)]
alsumafile = extsumafile + config['alsuffix'] + ext
if config['overwrite'] or not os.path.exists(
'%s/%s' % (refdir, alsumafile)):
# now apply transformation
cmd = 'cd "%s";ConvertSurface -overwrite -i_fs %s/%s -o_%s ./%s -ixmat_1D %s' % \
(refdir, sumadir, sumafile, tp, alsumafile, matrixfn_LPI2RAI)
cmds.append(cmd)
# as of June 2012 copy the original sphere.reg (not aligned) as well
if sumafile == ('%s.sphere.reg%s' % (pat, ext)):
sumaout = '%s/%s' % (refdir, extsumafile + ext)
if config['overwrite'] or not os.path.exists(sumaout):
s = surf.read('%s/%s' % (sumadir, sumafile))
surf.write(s, sumaout)
#cmds.append('cp %s/%s %s/%s' % (sumadir, sumafile, refdir, sumafile))
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
srcpathfn = os.path.join(sumadir, mapfn)
if os.path.exists(srcpathfn):
trgpathfn = os.path.join(refdir, mapfn)
if not os.path.exists(trgpathfn) or config['overwrite']:
cmds.append('cp %s %s' % (srcpathfn, trgpathfn))
utils.run_cmds(cmds, env)
def average_fs_asc_surfs(fn1, fn2, fnout):
'''averages two surfaces'''
surf1 = surf.read(fn1)
surf2 = surf.read(fn2)
surfavg = surf1 * .5 + surf2 * .5
surf.write(fnout, surfavg)
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
def run_alignment(config, env):
'''Aligns anat (which is assumed to be aligned with EPI data) to FreeSurfer SurfVol
This function strips the anatomicals (by default), then uses align_epi_anat.py
to estimate the alignment, then applies this transformation to the non-skull-stripped
SurfVol and also to the surfaces. Some alignment headers will be nuked'''
overwrite = config['overwrite']
alignsuffix = config['al2expsuffix']
refdir = config['refdir']
fullext = config['outvol_fullext']
ext = config['outvol_ext']
if config['sid'] is None:
raise ValueError('Need sid')
cmds = []
if not os.path.exists(config['refdir']):
cmds.append('mkdir %(refdir)s' % config)
# two volumes may have to be stripped: the inpput anatomical, and the surfvol.
# put them in a list here and process them similarly
surfvol = '%(refdir)s/%(sid)s_SurfVol%(outvol_fullext)s' % config
surfvol_ss = '%(refdir)s/%(sid)s_SurfVol%(sssuffix)s%(outvol_fullext)s' % config
e_p, e_n, _, _ = utils.afni_fileparts(config['expvol'])
if config['expvol_ss']:
e_n = '%s%s' % (e_n, config['sssuffix'])
expvol = '%s/%s%s' % (refdir, e_n, fullext)
volsin = [surfvol_ss, expvol]
for volin in volsin:
if not os.path.exists(volin):
raise ValueError('File %s does not exist' % volin)
a_n = utils.afni_fileparts(volsin[0])[1] # surfvol input root name
ssalprefix = '%s%s' % (a_n, alignsuffix)
unity = "1 0 0 0 0 1 0 0 0 0 1 0" # we all like unity, don't we?
fullmatrixfn = '%s_mat.aff12.1D' % ssalprefix
aloutfns = ['%s%s' % (ssalprefix, fullext), fullmatrixfn] # expected output files if alignment worked
if config['overwrite'] or not all([os.path.exists('%s/%s' % (refdir, f)) for f in aloutfns]):
alignedfn = '%s/%s%s' % (refdir, ssalprefix, fullext)
if config['identity']:
fullmatrix_content = '"MATRIX(%s)"' % unity.replace(" ", ",")
cmd = 'cd "%s"; cat_matvec %s > %s; 3dcopy -overwrite %s%s %s%s%s' % (refdir, fullmatrix_content, fullmatrixfn, a_n, ext, a_n, alignsuffix, ext)
else:
# use different inputs depending on whether expvol is EPI or ANAT
twovolpat = ('-anat %s -epi %s -anat2epi -epi_base 0 -anat_has_skull no -epi_strip None' if config['isepi']
else '-dset1 %s -dset2 %s -dset1to2 -dset1_strip None -dset2_strip None')
# use this pattern to generate a suffix
twovolsuffix = twovolpat % (volsin[0], volsin[1])
aea_opts = config['aea_opts']
if config['template']:
aea_opts += " -Allineate_opts '-maxrot 10 -maxshf 10 -maxscl 1.5'"
# align_epi_anat.py
cmd = 'cd "%s"; align_epi_anat.py -overwrite -suffix %s %s %s' % (refdir, alignsuffix, twovolsuffix, aea_opts)
cmds.append(cmd)
cmds.append(_set_vol_space_cmd(alignedfn, config))
utils.run_cmds(cmds, env)
else:
print "Alignment already done - skipping"
# run these commands first, then check if everything worked properly
cmds = []
# see if the expected transformation file was found
if not config['identity'] and not os.path.exists('%s/%s' % (refdir, fullmatrixfn)):
raise Exception("Could not find %s in %s" % (fullmatrixfn, refdir))
# now make a 3x4 matrix
matrixfn = '%s%s.A2E.1D' % (a_n, alignsuffix)
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn)):
cmds.append('cd "%s"; cat_matvec %s > %s || exit 1' % (refdir, fullmatrixfn, matrixfn))
# make an aligned, non-skullstripped version of SurfVol in refdir
alprefix = '%s_SurfVol%s' % (config['sid'], alignsuffix)
svalignedfn = '%s/%s%s' % (refdir, alprefix, fullext)
newgrid = 1 # size of anatomical grid in mm. We'll have to resample, otherwise 3dWarp does
# not respect the corners of the volume (as of April 2012)
if overwrite or not os.path.exists(svalignedfn):
#if not config['fs_sid']:
# raise ValueError("Don't have a freesurfer subject id - cannot continue")
#surfvolfn = '%s/%s_SurfVol+orig' % (config['sumadir'], config['fs_sid'])
surfvolfn = '%s/T1.nii' % config['sumadir']
cmds.append('cd "%s";3dWarp -overwrite -newgrid %f -matvec_out2in `cat_matvec -MATRIX %s` -prefix ./%s %s' %
(refdir, newgrid, matrixfn, alprefix, surfvolfn))
cmds.append(_set_vol_space_cmd('%s/%s+orig' % (refdir, alprefix), config))
else:
print '%s already exists - skipping Warp' % svalignedfn
utils.run_cmds(cmds, env)
cmds = []
# nuke afni headers
headernukefns = ['%s%s' % (f, fullext) for f in [ssalprefix, alprefix]]
headernukefields = ['ALLINEATE_MATVEC_B2S_000000',
'ALLINEATE_MATVEC_S2B_000000',
'WARPDRIVE_MATVEC_FOR_000000',
'WARPDRIVE_MATVEC_INV_000000']
for fn in headernukefns:
for field in headernukefields:
# nuke transformation - otherwise AFNI does this unwanted transformation for us
fullfn = '%s/%s' % (refdir, fn)
if not (os.path.exists(fullfn) or config['identity']):
raise ValueError("File %r does not exist" % fullfn)
refitcmd = "3drefit -atrfloat %s '%s' %s" % (field, unity, fn)
# only refit if not already in AFNI history (which is stored in HEADfile)
cmd = 'cd "%s"; m=`grep "%s" %s | wc -w`; if [ $m -eq 0 ]; then %s; else echo "File %s seems already 3drefitted"; fi' % (refdir, refitcmd, fn, refitcmd, fn)
cmds.append(cmd)
utils.run_cmds('; '.join(cmds), env)
cmds = []
# run AddEdge so that volumes can be inspected visually for alignment
if config['AddEdge']:
use_ss = config['expvol_ss']
# ae_{e,s}_n are AddEdge names for expvol and surfvol
ae_e_n = utils.afni_fileparts(config['expvol'])[1]
if use_ss:
ae_e_n += config['sssuffix']
ae_s_n = ssalprefix #if use_ss else alprefix
# *_ne have the output extension as well
ae_e_ne = ae_e_n + ext
ae_s_ne = ae_s_n + ext
addedge_fns = ['%s/_ae.ExamineList.log' % refdir]
exts = ['HEAD', 'BRIK']
orig_ext = '+orig'
addedge_rootfns = ['%s_%s%%s' % (ae_e_n, postfix)
for postfix in ['e3', 'ec', ae_s_n + '_ec']]
addedge_rootfns.extend(['%s_%s%%s' % (ae_s_n, postfix)
for postfix in ['e3', 'ec']])
addedge_fns_pat = ['%s.%s' % (fn, e) for fn in addedge_rootfns for e in exts]
addegde_pathfns_orig = map(lambda x:pathjoin(refdir, x % '+orig'), addedge_fns_pat) + addedge_fns
addegde_pathfns_ext = map(lambda x:pathjoin(refdir, x % ext), addedge_fns_pat)
addegde_exists = map(os.path.exists, addegde_pathfns_ext)
if overwrite or not all(addegde_exists):
ae_ns = (ae_e_n, ae_s_n)
cmds.extend(map(lambda fn : 'if [ -e "%s" ]; then rm "%s"; fi' % (fn, fn), addegde_pathfns_orig + addegde_pathfns_ext))
cmds.append(';'.join(['cd %s' % refdir] +
[_convert_vol_space_to_orig_cmd('%s/%s%s' % (refdir, n, ext))
for n in ae_ns] +
['\@AddEdge %s+orig %s+orig' % ae_ns]))
set_space_fns = addegde_pathfns_orig + ['%s/%s%s.%s' % (refdir, fn, orig_ext, exts[0]) for fn in ae_ns]
for fn in set_space_fns: #['%s/%s' % (refdir, fn % orig_ext) for fn in addedge_fns_pat]:
if fn.endswith('.log'):
continue
cmds.append('if [ -e %s ]; then %s; fi' % (fn, _set_vol_space_cmd(fn, config)))
utils.run_cmds(cmds, env)
cmds = []
else:
print "AddEdge seems to have been run already"
sid = config['sid']
plot_slice_fns = [(ae_e_n + '_e3', ae_s_n + '_e3', '%s_qa_e3.png' % sid),
(None, ae_e_n + '_' + ae_s_n + '_ec', '%s_qa_ec.png' % sid)]
plot_slice_imgfns = ['%s/%s' % (refdir, fn) for fn in plot_slice_fns]
if overwrite or not all(map(os.path.exists, plot_slice_imgfns)):
slice_dims = [0, 1, 2]
slice_pos = [.35, .45, .55, .65]
for fns in plot_slice_fns:
input_fns = []
for i, fn in enumerate(fns):
if fn is not None:
fn = '%s/%s' % (refdir, fn)
if i <= 1:
fn += ext
input_fns.append(fn)
fn1, fn2, fnout = input_fns
if not os.path.exists(fnout):
_make_slice_plot(fn1, fn2, fnout)
print "QA Image saved to %s" % fnout
else:
print "Already exists: %s" % fnout
else:
print "QA images already exist"
# because AFNI uses RAI orientation but FreeSurfer LPI, make a new
# affine transformation matrix in which the signs of
# x and y coordinates are negated before and after the transformation
matrixfn_LPI2RAI = '%s.A2E_LPI.1D' % ssalprefix
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn_LPI2RAI)):
lpirai = '"MATRIX(-1,0,0,0,0,-1,0,0,0,0,1,0)"'
cmd = ('cd %s; cat_matvec -ONELINE %s `cat_matvec -MATRIX %s` %s > %s' %
(refdir, lpirai, matrixfn, lpirai, matrixfn_LPI2RAI))
cmds.append(cmd)
# apply transformation to surfaces
[icolds, hemis] = _get_hemis_icolds(config)
sumadir = config['sumadir']
sumafiles = os.listdir(sumadir)
origext = '.asc'
ext = format2extension(config)
tp = format2type(config)
# process all hemispheres and ld values
for icold in icolds:
for hemi in hemis:
pat = '%s%sh.?*%s' % (config['mi_icopat'] % icold, hemi, origext)
for sumafile in sumafiles:
if fnmatch.fnmatch(sumafile, pat):
if not sumafile.endswith(origext):
raise ValueError("%s does not end with %s" % (sumafile, origext))
#s = sumafile.split(".")
#s[len(s) - 2] += config['alsuffix'] # insert '_al' just before last dot
#alsumafile = ".".join(s)
extsumafile = sumafile[:-len(origext)]
alsumafile = extsumafile + config['alsuffix'] + ext
if config['overwrite'] or not os.path.exists('%s/%s' % (refdir, alsumafile)):
# now apply transformation
cmd = 'cd "%s";ConvertSurface -overwrite -i_fs %s/%s -o_%s ./%s -ixmat_1D %s' % \
(refdir, sumadir, sumafile, tp, alsumafile, matrixfn_LPI2RAI)
cmds.append(cmd)
# as of June 2012 copy the original sphere.reg (not aligned) as well
if sumafile == ('%s.sphere.reg%s' % (pat, ext)):
sumaout = '%s/%s' % (refdir, extsumafile + ext)
if config['overwrite'] or not os.path.exists(sumaout):
s = surf.read('%s/%s' % (sumadir, sumafile))
surf.write(s, sumaout)
#cmds.append('cp %s/%s %s/%s' % (sumadir, sumafile, refdir, sumafile))
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
srcpathfn = pathjoin(sumadir, mapfn)
if os.path.exists(srcpathfn):
trgpathfn = pathjoin(refdir, mapfn)
if not os.path.exists(trgpathfn) or config['overwrite']:
cmds.append('cp %s %s' % (srcpathfn, trgpathfn))
utils.run_cmds(cmds, env)
def average_fs_asc_surfs(fn1, fn2, fnout):
'''averages two surfaces'''
surf1 = surf.read(fn1)
surf2 = surf.read(fn2)
surfavg = surf1 * .5 + surf2 * .5
surf.write(fnout, surfavg)
def average_fs_asc_surfs(fn1, fn2, fnout):
"""averages two surfaces"""
surf1 = surf.read(fn1)
surf2 = surf.read(fn2)
surfavg = surf1 * 0.5 + surf2 * 0.5
surf.write(fnout, surfavg)