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_afni_suma_spec(self, temp_dir):
# XXX this function generates quite a few temporary files,
# which are removed at the end.
# the decorator @with_tempfile seems unsuitable as it only
# supports a single temporary file
# make temporary directory
os.mkdir(temp_dir)
# generate surfaces
inflated_surf = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1),
10, 10)
white_surf = inflated_surf + 1.
# helper function
_tmp = lambda x:pathjoin(temp_dir, x)
# filenames for surfaces and spec file
inflated_fn = _tmp('_lh_inflated.asc')
white_fn = _tmp('_lh_white.asc')
spec_fn = _tmp('lh.spec')
spec_dir = os.path.split(spec_fn)[0]
# generate SUMA-like spec dictionary
white = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=white_fn,
Anatomical='Y',
LocalCurvatureParent='SAME',
LocalDomainParent='SAME',
SurfaceState='smoothwm')
inflated = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=inflated_fn,
Anatomical='N',
LocalCurvatureParent=white_fn,
LocalDomainParent=white_fn,
SurfaceState='inflated')
# make SurfaceSpec object
spec = afni_suma_spec.SurfaceSpec([white], directory=spec_dir)
spec.add_surface(inflated)
# test __str__ and __repr__
assert_true('SurfaceSpec instance with 2 surfaces'
', 2 states ' in '%s' % spec)
assert_true(('%r' % spec).startswith('SurfaceSpec'))
# test finding surfaces
inflated_ = spec.find_surface_from_state('inflated')
assert_equal([(1, inflated)], inflated_)
empty = spec.find_surface_from_state('unknown')
assert_equal(empty, [])
# test .same_states
minimal = afni_suma_spec.SurfaceSpec([dict(SurfaceState=s)
for s in ('smoothwm', 'inflated')])
assert_true(spec.same_states(minimal))
assert_false(spec.same_states(afni_suma_spec.SurfaceSpec(dict())))
# test 'smart' surface file matching
assert_equal(spec.get_surface_file('smo'), white_fn)
assert_equal(spec.get_surface_file('inflated'), inflated_fn)
assert_equal(spec.get_surface_file('this should be None'), None)
# test i/o
spec.write(spec_fn)
spec_ = afni_suma_spec.from_any(spec_fn)
# prepare for another (right-hemisphere) spec file
lh_spec = spec
rh_spec_fn = spec_fn.replace('lh', 'rh')
rh_inflated_fn = _tmp(os.path.split(inflated_fn)[1].replace('_lh',
'_rh'))
rh_white_fn = _tmp(os.path.split(white_fn)[1].replace('_lh',
'_rh'))
rh_spec_fn = _tmp('rh.spec')
rh_white = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=rh_white_fn,
Anatomical='Y',
LocalCurvatureParent='SAME',
LocalDomainParent='SAME',
SurfaceState='smoothwm')
rh_inflated = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=rh_inflated_fn,
Anatomical='N',
LocalCurvatureParent=rh_white_fn,
LocalDomainParent=rh_white_fn,
SurfaceState='inflated')
rh_spec = afni_suma_spec.SurfaceSpec([rh_white], directory=spec_dir)
rh_spec.add_surface(rh_inflated)
# write files
all_temp_fns = [spec_fn, rh_spec_fn]
for fn, s in [(rh_inflated_fn, inflated_surf),
(rh_white_fn, white_surf),
(inflated_fn, inflated_surf),
(white_fn, white_surf)]:
surf.write(fn, s)
all_temp_fns.append(fn)
# test adding views
added_specs = afni_suma_spec.hemi_pairs_add_views((lh_spec, rh_spec),
'inflated', '.asc')
for hemi, added_spec in zip(('l', 'r'), added_specs):
states = ['smoothwm', 'inflated'] + ['CoM%sinflated' % i
for i in 'msiap']
assert_equal(states, [s['SurfaceState']
for s in added_specs[0].surfaces])
all_temp_fns.extend([s['SurfaceName']
for s in added_spec.surfaces])
# test combining specs (bh=both hemispheres)
bh_spec = afni_suma_spec.combine_left_right(added_specs)
# test merging specs (mh=merged hemispheres)
mh_spec, mh_surfs = afni_suma_spec.merge_left_right(bh_spec)
assert_equal([s['SurfaceState'] for s in mh_spec.surfaces],
['smoothwm'] + ['CoM%sinflated' % i for i in 'msiap'])
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
def test_afni_suma_spec(self, temp_dir):
# XXX this function generates quite a few temporary files,
# which are removed at the end.
# the decorator @with_tempfile seems unsuitable as it only
# supports a single temporary file
# make temporary directory
os.mkdir(temp_dir)
# generate surfaces
inflated_surf = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1),
10, 10)
white_surf = inflated_surf + 1.
# helper function
_tmp = lambda x: os.path.join(temp_dir, x)
# filenames for surfaces and spec file
inflated_fn = _tmp('_lh_inflated.asc')
white_fn = _tmp('_lh_white.asc')
spec_fn = _tmp('lh.spec')
spec_dir = os.path.split(spec_fn)[0]
# generate SUMA-like spec dictionary
white = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=white_fn,
Anatomical='Y',
LocalCurvatureParent='SAME',
LocalDomainParent='SAME',
SurfaceState='smoothwm')
inflated = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=inflated_fn,
Anatomical='N',
LocalCurvatureParent=white_fn,
LocalDomainParent=white_fn,
SurfaceState='inflated')
# make SurfaceSpec object
spec = afni_suma_spec.SurfaceSpec([white], directory=spec_dir)
spec.add_surface(inflated)
# test __str__ and __repr__
assert_true('SurfaceSpec instance with 2 surfaces'
', 2 states ' in '%s' % spec)
assert_true(('%r' % spec).startswith('SurfaceSpec'))
# test finding surfaces
inflated_ = spec.find_surface_from_state('inflated')
assert_equal([(1, inflated)], inflated_)
empty = spec.find_surface_from_state('unknown')
assert_equal(empty, [])
# test .same_states
minimal = afni_suma_spec.SurfaceSpec(
[dict(SurfaceState=s) for s in ('smoothwm', 'inflated')])
assert_true(spec.same_states(minimal))
assert_false(spec.same_states(afni_suma_spec.SurfaceSpec(dict())))
# test 'smart' surface file matching
assert_equal(spec.get_surface_file('smo'), white_fn)
assert_equal(spec.get_surface_file('inflated'), inflated_fn)
assert_equal(spec.get_surface_file('this should be None'), None)
# test i/o
spec.write(spec_fn)
spec_ = afni_suma_spec.from_any(spec_fn)
# prepare for another (right-hemisphere) spec file
lh_spec = spec
rh_spec_fn = spec_fn.replace('lh', 'rh')
rh_inflated_fn = _tmp(
os.path.split(inflated_fn)[1].replace('_lh', '_rh'))
rh_white_fn = _tmp(os.path.split(white_fn)[1].replace('_lh', '_rh'))
rh_spec_fn = _tmp('rh.spec')
rh_white = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=rh_white_fn,
Anatomical='Y',
LocalCurvatureParent='SAME',
LocalDomainParent='SAME',
SurfaceState='smoothwm')
rh_inflated = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=rh_inflated_fn,
Anatomical='N',
LocalCurvatureParent=rh_white_fn,
LocalDomainParent=rh_white_fn,
SurfaceState='inflated')
rh_spec = afni_suma_spec.SurfaceSpec([rh_white], directory=spec_dir)
rh_spec.add_surface(rh_inflated)
# write files
all_temp_fns = [spec_fn, rh_spec_fn]
for fn, s in [(rh_inflated_fn, inflated_surf),
(rh_white_fn, white_surf), (inflated_fn, inflated_surf),
(white_fn, white_surf)]:
surf.write(fn, s)
all_temp_fns.append(fn)
# test adding views
added_specs = afni_suma_spec.hemi_pairs_add_views((lh_spec, rh_spec),
'inflated', '.asc')
for hemi, added_spec in zip(('l', 'r'), added_specs):
states = ['smoothwm', 'inflated'
] + ['CoM%sinflated' % i for i in 'msiap']
assert_equal(states,
[s['SurfaceState'] for s in added_specs[0].surfaces])
all_temp_fns.extend(
[s['SurfaceName'] for s in added_spec.surfaces])
# test combining specs (bh=both hemispheres)
bh_spec = afni_suma_spec.combine_left_right(added_specs)
# test merging specs (mh=merged hemispheres)
mh_spec, mh_surfs = afni_suma_spec.merge_left_right(bh_spec)
assert_equal([s['SurfaceState'] for s in mh_spec.surfaces],
['smoothwm'] + ['CoM%sinflated' % i for i in 'msiap'])
