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 run_makespec(config, env):
'''Generates the SUMA specifcation files for all hemispheres and ld values'''
refdir = config['refdir']
icolds, hemis = _get_hemis_icolds(config)
for icold in icolds:
for hemi in hemis:
# make spec file
surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
if config['overwrite'] or not os.path.exists(specpathfn):
suma_makespec(refdir,
surfprefix,
config['surfformat'],
specpathfn,
removepostfix=config['alsuffix'])
else:
print "Skipping spec for %s" % specpathfn
# make simple script to run afni and suma
runsumafn = '%s/%sh_ico%d_runsuma.sh' % (refdir, hemi, icold)
surfvol = '%(sid)s_SurfVol%(al2expsuffix)s+orig' % config
if config['overwrite'] or not os.path.exists(runsumafn):
suma_makerunsuma(runsumafn, specfn, surfvol)
def run_makespec(config, env):
"""Generates the SUMA specifcation files for all hemispheres and ld values"""
refdir = config["refdir"]
icolds, hemis = _get_hemis_icolds(config)
for icold in icolds:
for hemi in hemis:
# make spec file
surfprefix = "%s%sh" % (config["mi_icopat"] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi, config["alsuffix"])
specpathfn = pathjoin(refdir, specfn)
if config["overwrite"] or not os.path.exists(specpathfn):
suma_makespec(refdir, surfprefix, config["surfformat"], specpathfn, removepostfix=config["alsuffix"])
else:
print "Skipping spec for %s" % specpathfn
# make simple script to run afni and suma
runsumafn = "%s/%sh_ico%d_runsuma.sh" % (refdir, hemi, icold)
surfvol = "%(sid)s_SurfVol%(al2expsuffix)s+orig" % config
if config["overwrite"] or not os.path.exists(runsumafn):
suma_makerunsuma(runsumafn, specfn, surfvol)
def run_makespec(config, env):
'''Generates the SUMA specifcation files for all hemispheres and ld values'''
refdir = config['refdir']
icolds, hemis = _get_hemis_icolds(config)
for icold in icolds:
for hemi in hemis:
# make spec file
surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
if config['overwrite'] or not os.path.exists(specpathfn):
suma_makespec(refdir, surfprefix, specpathfn, removepostfix=config['alsuffix'])
else:
print "Skipping spec for %s" % specpathfn
# make simple script to run afni and suma
runsumafn = '%s/%sh_ico%d_runsuma.sh' % (refdir, hemi, icold)
surfvol = '%(sid)s_SurfVol%(al2expsuffix)s+orig' % config
if config['overwrite'] or not os.path.exists(runsumafn):
suma_makerunsuma(runsumafn, specfn, surfvol)
def run_makesurfmasks(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
if config['sid'] is None:
raise ValueError('Need sid')
sumfn = '%s_qa_surf_mask' % config['sid'] # output file
fullext = config['outvol_fullext']
volor = config['outvol_ext']
sumfn_path = '%s/%s%s' % (refdir, sumfn, fullext)
qafn_path = '%s/%s.png' % (refdir, sumfn)
checkfn_paths = (sumfn_path, qafn_path)
if all(map(os.path.exists, checkfn_paths)) and not overwrite:
print "Already exist: %s" % (", ".join(checkfn_paths))
return
icolds, hemis = _get_hemis_icolds(config)
volexts = ['%s%s' % (volor, e) for e in '.HEAD', '.BRIK*']
sssuffix = config['sssuffix'] if config['expvol_ss'] else ''
expvol_fn = '%s%s%s' % (utils.afni_fileparts(
config['expvol'])[1], sssuffix, volor)
#if overwrite or not os.path.exists('%s/%s' % (refdir, sv_al_nii_fn)):
# cmd = 'cd %s; 3dcopy -overwrite %s %s' % (refdir, sv_al_orig_fn, sv_al_nii_fn)
# utils.run_cmds(cmd, env)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
icold = max(icolds)
oneDfn = '__t.1D'
oneDtfn = '__tt.1D' # transposed
cmds = [
'cd %s' % refdir,
'1deval -1D: -num %d -expr 1 > %s' % (icold**2 * 10 + 1, oneDfn),
'1dtranspose %s > %s' % (oneDfn, oneDtfn)
]
utils.run_cmds(';'.join(cmds), env)
tmpfns = [oneDfn, oneDtfn]
s2v_cmd = ('3dSurf2Vol -map_func mask2 -data_expr "a*%%d" -spec %%s %%s -sv %s'
' -grid_parent %s. -prefix %%s -sdata %s -overwrite') % \
(expvol_fn, expvol_fn, oneDtfn)
infix2val = {
'-surf_A pial': 1,
'-surf_A smoothwm': 2,
'-surf_A smoothwm -surf_B pial -f_steps 20': 4
}
volfns = []
for hemi in hemis:
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
for infix, val in infix2val.iteritems():
fnprefix = '__m%d_%sh' % (val, hemi)
cmd = s2v_cmd % (val, specfn, infix, fnprefix)
utils.run_cmds('cd %s;%s' % (refdir, cmd))
tmpfns.extend(['%s%s' % (fnprefix, e) for e in volexts])
volfns.append(fnprefix + volor)
cmds = ['cd %s' % refdir]
catfn = '__cat'
cmds.extend([
'3dTcat -overwrite -prefix %s %s' % (catfn, ' '.join(volfns)),
'3dTstat -overwrite -sum -prefix %s %s%s' % (sumfn, catfn, volor)
])
tmpfns.extend(['%s%s' % (catfn, e) for e in volexts])
cmds.extend('rm %s' % fn for fn in tmpfns)
cmds.append('echo "Surface mask in %s"' % sumfn)
utils.run_cmds(';'.join(cmds), env)
# make plot
if overwrite or not os.path.exists(qafn_path):
expvol_path = '%s/%s' % (refdir, expvol_fn)
_make_slice_plot(expvol_path, sumfn_path, qafn_path)
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_makesurfmasks(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
if config['sid'] is None:
raise ValueError('Need sid')
sumfn = '%s_qa_surf_mask' % config['sid'] # output file
fullext = config['outvol_fullext']
volor = config['outvol_ext']
sumfn_path = '%s/%s%s' % (refdir, sumfn, fullext)
qafn_path = '%s/%s.png' % (refdir, sumfn)
checkfn_paths = (sumfn_path, qafn_path)
if all(map(os.path.exists, checkfn_paths)) and not overwrite:
print "Already exist: %s" % (", ".join(checkfn_paths))
return
icolds, hemis = _get_hemis_icolds(config)
volexts = ['%s%s' % (volor, e) for e in '.HEAD', '.BRIK*']
sssuffix = config['sssuffix'] if config['expvol_ss'] else ''
expvol_fn = '%s%s%s' % (utils.afni_fileparts(config['expvol'])[1],
sssuffix,
volor)
#if overwrite or not os.path.exists('%s/%s' % (refdir, sv_al_nii_fn)):
# cmd = 'cd %s; 3dcopy -overwrite %s %s' % (refdir, sv_al_orig_fn, sv_al_nii_fn)
# utils.run_cmds(cmd, env)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
icold = max(icolds)
oneDfn = '__t.1D'
oneDtfn = '__tt.1D' # transposed
cmds = ['cd %s' % refdir,
'1deval -1D: -num %d -expr 1 > %s' % (icold ** 2 * 10 + 1, oneDfn),
'1dtranspose %s > %s' % (oneDfn, oneDtfn)]
utils.run_cmds(';'.join(cmds), env)
tmpfns = [oneDfn, oneDtfn]
s2v_cmd = ('3dSurf2Vol -map_func mask2 -data_expr "a*%%d" -spec %%s %%s -sv %s'
' -grid_parent %s. -prefix %%s -sdata %s -overwrite') % \
(expvol_fn, expvol_fn, oneDtfn)
infix2val = {'-surf_A pial':1,
'-surf_A smoothwm':2,
'-surf_A smoothwm -surf_B pial -f_steps 20': 4}
volfns = []
for hemi in hemis:
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
for infix, val in infix2val.iteritems():
fnprefix = '__m%d_%sh' % (val, hemi)
cmd = s2v_cmd % (val, specfn, infix, fnprefix)
utils.run_cmds('cd %s;%s' % (refdir, cmd))
tmpfns.extend(['%s%s' % (fnprefix, e) for e in volexts])
volfns.append(fnprefix + volor)
cmds = ['cd %s' % refdir]
catfn = '__cat'
cmds.extend(['3dTcat -overwrite -prefix %s %s' % (catfn, ' '.join(volfns)),
'3dTstat -overwrite -sum -prefix %s %s%s' % (sumfn, catfn, volor)])
tmpfns.extend(['%s%s' % (catfn, e) for e in volexts])
cmds.extend('rm %s' % fn for fn in tmpfns)
cmds.append('echo "Surface mask in %s"' % sumfn)
utils.run_cmds(';'.join(cmds), env)
# make plot
if overwrite or not os.path.exists(qafn_path):
expvol_path = '%s/%s' % (refdir, expvol_fn)
_make_slice_plot(expvol_path,
sumfn_path,
qafn_path)
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_makesurfmasks(config, env):
refdir = config["refdir"]
overwrite = config["overwrite"]
if config["sid"] is None:
raise ValueError("Need sid")
sumfn = "%s_qa_surf_mask" % config["sid"] # output file
fullext = config["outvol_fullext"]
volor = config["outvol_ext"]
sumfn_path = "%s/%s%s" % (refdir, sumfn, fullext)
qafn_path = "%s/%s.png" % (refdir, sumfn)
checkfn_paths = (sumfn_path, qafn_path)
if all(map(os.path.exists, checkfn_paths)) and not overwrite:
print "Already exist: %s" % (", ".join(checkfn_paths))
return
icolds, hemis = _get_hemis_icolds(config)
volexts = ["%s%s" % (volor, e) for e in ".HEAD", ".BRIK*"]
sssuffix = config["sssuffix"] if config["expvol_ss"] else ""
expvol_fn = "%s%s%s" % (utils.afni_fileparts(config["expvol"])[1], sssuffix, volor)
# if overwrite or not os.path.exists('%s/%s' % (refdir, sv_al_nii_fn)):
# cmd = 'cd %s; 3dcopy -overwrite %s %s' % (refdir, sv_al_orig_fn, sv_al_nii_fn)
# utils.run_cmds(cmd, env)
if hemis != ["l", "r"]:
raise ValueError("Cannot run without left and right hemisphere")
icold = max(icolds)
oneDfn = "__t.1D"
oneDtfn = "__tt.1D" # transposed
cmds = [
"cd %s" % refdir,
"1deval -1D: -num %d -expr 1 > %s" % (icold ** 2 * 10 + 1, oneDfn),
"1dtranspose %s > %s" % (oneDfn, oneDtfn),
]
utils.run_cmds(";".join(cmds), env)
tmpfns = [oneDfn, oneDtfn]
s2v_cmd = (
'3dSurf2Vol -map_func mask2 -data_expr "a*%%d" -spec %%s %%s -sv %s'
" -grid_parent %s. -prefix %%s -sdata %s -overwrite"
) % (expvol_fn, expvol_fn, oneDtfn)
infix2val = {"-surf_A pial": 1, "-surf_A smoothwm": 2, "-surf_A smoothwm -surf_B pial -f_steps 20": 4}
volfns = []
for hemi in hemis:
specfn = afni_suma_spec.canonical_filename(icold, hemi, config["alsuffix"])
for infix, val in infix2val.iteritems():
fnprefix = "__m%d_%sh" % (val, hemi)
cmd = s2v_cmd % (val, specfn, infix, fnprefix)
utils.run_cmds("cd %s;%s" % (refdir, cmd))
tmpfns.extend(["%s%s" % (fnprefix, e) for e in volexts])
volfns.append(fnprefix + volor)
cmds = ["cd %s" % refdir]
catfn = "__cat"
cmds.extend(
[
"3dTcat -overwrite -prefix %s %s" % (catfn, " ".join(volfns)),
"3dTstat -overwrite -sum -prefix %s %s%s" % (sumfn, catfn, volor),
]
)
tmpfns.extend(["%s%s" % (catfn, e) for e in volexts])
cmds.extend("rm %s" % fn for fn in tmpfns)
cmds.append('echo "Surface mask in %s"' % sumfn)
utils.run_cmds(";".join(cmds), env)
# make plot
if overwrite or not os.path.exists(qafn_path):
expvol_path = "%s/%s" % (refdir, expvol_fn)
_make_slice_plot(expvol_path, sumfn_path, qafn_path)