def test_sanity():
from nipy.modalities.fmri import design, hrf
import nipy.modalities.fmri.fmristat.hrf as fshrf
from nipy.modalities.fmri.fmristat.tests import FIACdesigns
from nipy.modalities.fmri.fmristat.tests.test_FIAC import matchcol
from nipy.algorithms.statistics import formula
from nose.tools import assert_true
"""
Single subject fitting of FIAC model
"""
# Based on file
# subj3_evt_fonc1.txt
# subj3_bloc_fonc3.txt
for subj, run, design_type in [(3, 1, 'event'), (3, 3, 'block')]:
nvol = 191
TR = 2.5
Tstart = 1.25
volume_times = np.arange(nvol) * TR + Tstart
volume_times_rec = formula.make_recarray(volume_times, 't')
path_dict = {'subj': subj, 'run': run}
if exists(
pjoin(DATADIR, "fiac_%(subj)02d", "block",
"initial_%(run)02d.csv") % path_dict):
path_dict['design'] = 'block'
else:
path_dict['design'] = 'event'
experiment = csv2rec(
pjoin(DATADIR, "fiac_%(subj)02d", "%(design)s",
"experiment_%(run)02d.csv") % path_dict)
initial = csv2rec(
pjoin(DATADIR, "fiac_%(subj)02d", "%(design)s",
"initial_%(run)02d.csv") % path_dict)
X_exper, cons_exper = design.event_design(experiment,
volume_times_rec,
hrfs=fshrf.spectral)
X_initial, _ = design.event_design(initial,
volume_times_rec,
hrfs=[hrf.glover])
X, cons = design.stack_designs((X_exper, cons_exper), (X_initial, {}))
# Get original fmristat design
Xf = FIACdesigns.fmristat[design_type]
# Check our new design can be closely matched to the original
for i in range(X.shape[1]):
# Columns can be very well correlated negatively or positively
assert_true(abs(matchcol(X[:, i], Xf)[1]) > 0.999)
def test_block_amplitudes():
# Test event design helper function
# An event design with one event type
onsets = np.array([0, 20, 40, 60])
durations = np.array([2, 3, 4, 5])
offsets = onsets + durations
amplitudes = [3, 2, 1, 4]
t = np.arange(0, 100, 2.5)
def mk_blk_tc(amplitudes=None, hrf=glover):
func_amp = blocks(zip(onsets, offsets), amplitudes)
# Make real time course for block onset / offsets / amplitudes
term = convolve_functions(func_amp, hrf(T),
(-5, 70), # step func support
(0, 30.), # conv kernel support
0.02) # dt
return lambdify_t(term)(t)
no_amps = make_recarray(zip(onsets, offsets), ('start', 'end'))
amps = make_recarray(zip(onsets, offsets, amplitudes),
('start', 'end', 'amplitude'))
X, contrasts = block_amplitudes('ev0', no_amps, t)
assert_almost_equal(X, mk_blk_tc())
assert_dict_almost_equal(contrasts, {'ev0_0': 1})
# Same thing as 2D array
X, contrasts = block_amplitudes('ev0', np.c_[onsets, offsets], t)
assert_almost_equal(X, mk_blk_tc())
assert_dict_almost_equal(contrasts, {'ev0_0': 1})
# Now as list
X, contrasts = block_amplitudes('ev0', list(zip(onsets, offsets)), t)
assert_almost_equal(X, mk_blk_tc())
assert_dict_almost_equal(contrasts, {'ev0_0': 1})
# Add amplitudes
X_a, contrasts_a = block_amplitudes('ev1', amps, t)
assert_almost_equal(X_a, mk_blk_tc(amplitudes=amplitudes))
assert_dict_almost_equal(contrasts_a, {'ev1_0': 1})
# Same thing as 2D array
X_a, contrasts_a = block_amplitudes('ev1',
np.c_[onsets, offsets, amplitudes],
t)
assert_almost_equal(X_a, mk_blk_tc(amplitudes=amplitudes))
assert_dict_almost_equal(contrasts_a, {'ev1_0': 1})
# Add another HRF
X_2, contrasts_2 = block_amplitudes('ev0', no_amps, t, (glover, dglover))
assert_almost_equal(X_2, np.c_[mk_blk_tc(), mk_blk_tc(hrf=dglover)])
assert_dict_almost_equal(contrasts_2,
{'ev0_0': [1, 0], 'ev0_1': [0, 1]})
# Errors on bad input
no_start = make_recarray(zip(onsets, offsets), ('begin', 'end'))
assert_raises(ValueError, block_amplitudes, 'ev0', no_start, t)
no_end = make_recarray(zip(onsets, offsets), ('start', 'finish'))
assert_raises(ValueError, block_amplitudes, 'ev0', no_end, t)
funny_amp = make_recarray(zip(onsets, offsets, amplitudes),
('start', 'end', 'intensity'))
assert_raises(ValueError, block_amplitudes, 'ev0', funny_amp, t)
funny_extra = make_recarray(zip(onsets, offsets, amplitudes, onsets),
('start', 'end', 'amplitude', 'extra_field'))
assert_raises(ValueError, block_amplitudes, 'ev0', funny_extra, t)
def test_sanity():
from nipy.modalities.fmri import design, hrf
import nipy.modalities.fmri.fmristat.hrf as fshrf
from nipy.modalities.fmri.fmristat.tests import FIACdesigns
from nipy.modalities.fmri.fmristat.tests.test_FIAC import matchcol
from nipy.algorithms.statistics import formula
from nose.tools import assert_true
"""
Single subject fitting of FIAC model
"""
# Based on file
# subj3_evt_fonc1.txt
# subj3_bloc_fonc3.txt
for subj, run, design_type in [(3, 1, 'event'), (3, 3, 'block')]:
nvol = 191
TR = 2.5
Tstart = 1.25
volume_times = np.arange(nvol)*TR + Tstart
volume_times_rec = formula.make_recarray(volume_times, 't')
path_dict = {'subj':subj, 'run':run}
if exists(pjoin(DATADIR, "fiac_%(subj)02d",
"block", "initial_%(run)02d.csv") % path_dict):
path_dict['design'] = 'block'
else:
path_dict['design'] = 'event'
experiment = csv2rec(pjoin(DATADIR, "fiac_%(subj)02d", "%(design)s", "experiment_%(run)02d.csv")
% path_dict)
initial = csv2rec(pjoin(DATADIR, "fiac_%(subj)02d", "%(design)s", "initial_%(run)02d.csv")
% path_dict)
X_exper, cons_exper = design.event_design(experiment,
volume_times_rec,
hrfs=fshrf.spectral)
X_initial, _ = design.event_design(initial,
volume_times_rec,
hrfs=[hrf.glover])
X, cons = design.stack_designs((X_exper, cons_exper), (X_initial, {}))
# Get original fmristat design
Xf = FIACdesigns.fmristat[design_type]
# Check our new design can be closely matched to the original
for i in range(X.shape[1]):
# Columns can be very well correlated negatively or positively
assert_true(abs(matchcol(X[:,i], Xf)[1]) > 0.999)
def model_generator(formula, data, volume_start_times, iterable=None,
slicetimes=None, model_type=OLSModel,
model_params = lambda x: ()):
"""
Generator for the models for a pass of fmristat analysis.
"""
volume_start_times = make_recarray(volume_start_times.astype(float), 't')
# Generator for slices of the data with time as first axis
axis0_gen = fmri_generator(data, iterable=iterable)
# Iterate over 2D slices of the data
for indexer, indexed_data in matrix_generator(axis0_gen):
model_args = model_params(indexer) # model may depend on i
# Get the design for these volume start times
design = formula.design(volume_start_times, return_float=True)
# Make the model from the design
rmodel = model_type(design, *model_args)
yield indexer, indexed_data, rmodel
def model_generator(formula, data, volume_start_times, iterable=None,
slicetimes=None, model_type=OLSModel,
model_params = lambda x: ()):
"""
Generator for the models for a pass of fmristat analysis.
"""
volume_start_times = make_recarray(volume_start_times.astype(float), 't')
# Generator for slices of the data with time as first axis
axis0_gen = axis0_generator(data, slicers=iterable)
# Iterate over 2D slices of the data
for indexer, indexed_data in matrix_generator(axis0_gen):
model_args = model_params(indexer) # model may depend on i
# Get the design for these volume start times
design = formula.design(volume_start_times, return_float=True)
# Make the model from the design
rmodel = model_type(design, *model_args)
yield indexer, indexed_data, rmodel
def mk_blk_spec(factors, names):
names = ('start', 'end') + tuple(names)
return make_recarray(zip(onsets, offsets, *factors), names)
def mk_ev_spec(factors, names):
names = ('time',) + tuple(names)
if len(factors) == 0:
return make_recarray(onsets, names)
return make_recarray(zip(onsets, *factors), names)
def test_event_design():
# Test event design helper function
# An event design with one event type
onsets = np.array([0, 20, 40, 60])
durations = np.array([2, 3, 4, 5])
offsets = onsets + durations
c_fac = np.array([1, 1, 1, 1]) # constant factor (one level)
fac_1 = np.array([0, 1, 0, 1]) # factor 1, two levels
fac_2 = np.array([0, 0, 1, 1]) # factor 2, two levels
t = np.arange(0, 100, 2)
def mk_ev_spec(factors, names):
names = ('time',) + tuple(names)
if len(factors) == 0:
return make_recarray(onsets, names)
return make_recarray(zip(onsets, *factors), names)
def mk_blk_spec(factors, names):
names = ('start', 'end') + tuple(names)
return make_recarray(zip(onsets, offsets, *factors), names)
def mk_ev_tc(ev_inds):
# Make real time course for given event onsets
return lambdify_t(events(onsets[ev_inds], f=glover))(t)
def mk_blk_tc(ev_inds):
# Make real time course for block onset / offsets
B = blocks(zip(onsets[ev_inds], offsets[ev_inds]))
term = convolve_functions(B, glover(T),
(-5, 70), # step func support
(0, 30.), # conv kernel support
0.02) # dt
return lambdify_t(term)(t)
for d_maker, spec_maker, tc_maker, null_name in (
(event_design, mk_ev_spec, mk_ev_tc, '_event_'),
(block_design, mk_blk_spec, mk_blk_tc, '_block_')):
# Event spec with no event factor -> single column design, no contrasts
spec_0 = spec_maker((), ())
X_0, contrasts_0 = d_maker(spec_0, t)
exp_x_0 = tc_maker(onsets==onsets)
assert_almost_equal(X_0, exp_x_0)
assert_dict_almost_equal(contrasts_0, dict(constant_0=1))
X_0, contrasts_0 = d_maker(spec_0, t, level_contrasts=True)
assert_almost_equal(X_0, exp_x_0)
assert_dict_almost_equal(contrasts_0,
{'constant_0': 1,
null_name + '_1_0': 1})
# Event spec with single factor, but only one level
spec_1c = spec_maker((c_fac,), ('smt',))
X_1c, contrasts_1c = d_maker(spec_1c, t)
assert_almost_equal(X_1c, exp_x_0)
assert_dict_almost_equal(contrasts_1c, dict(constant_0=1))
X_1c, contrasts_1c = d_maker(spec_1c, t, level_contrasts=True)
assert_dict_almost_equal(contrasts_1c, dict(constant_0=1, smt_1_0=1))
# Event spec with single factor, two levels
spec_1d = spec_maker((fac_1,), ('smt',))
exp_x_0 = tc_maker(fac_1 == 0)
exp_x_1 = tc_maker(fac_1 == 1)
X_1d, contrasts_1d = d_maker(spec_1d, t)
assert_almost_equal(X_1d, np.c_[exp_x_0, exp_x_1])
assert_dict_almost_equal(contrasts_1d,
dict(constant_0=[1, 1], smt_0=[1, -1]))
X_1d, contrasts_1d = d_maker(spec_1d, t, level_contrasts=True)
assert_dict_almost_equal(contrasts_1d,
dict(constant_0=1,
smt_0=[1, -1], # main effect
smt_0_0=[1, 0], # level 0, hrf 0
smt_1_0=[0, 1])) # level 1, hrf 0
# Event spec with two factors, one with two levels, another with one
spec_2dc = spec_maker((fac_1, c_fac), ('smt', 'smte'))
X_2dc, contrasts_2dc = d_maker(spec_2dc, t)
assert_almost_equal(X_2dc, np.c_[exp_x_0, exp_x_1])
assert_dict_almost_equal(contrasts_2dc,
{'constant_0': [1, 1],
'smt_0': [1, -1], # main effect
'smt:smte_0': [1, -1], # interaction
})
X_2dc, contrasts_2dc = d_maker(spec_2dc, t, level_contrasts=True)
assert_dict_almost_equal(contrasts_2dc,
{'constant_0': [1, 1],
'smt_0': [1, -1], # main effect
'smt:smte_0': [1, -1], # interaction
'smt_0*smte_1_0': [1, 0], # smt 0, smte 0, hrf 0
'smt_1*smte_1_0': [0, 1], # smt 1, smte 0, hrf 0
})
# Event spec with two factors, both with two levels
spec_2dd = spec_maker((fac_1, fac_2), ('smt', 'smte'))
exp_x_0 = tc_maker((fac_1 == 0) & (fac_2 == 0))
exp_x_1 = tc_maker((fac_1 == 0) & (fac_2 == 1))
exp_x_2 = tc_maker((fac_1 == 1) & (fac_2 == 0))
exp_x_3 = tc_maker((fac_1 == 1) & (fac_2 == 1))
X_2dd, contrasts_2dd = d_maker(spec_2dd, t)
assert_almost_equal(X_2dd, np.c_[exp_x_0, exp_x_1, exp_x_2, exp_x_3])
exp_cons = {'constant_0': [1, 1, 1, 1],
'smt_0': [1, 1, -1, -1], # main effect fac_1
'smte_0': [1, -1, 1, -1], # main effect fac_2
'smt:smte_0': [1, -1, -1, 1], # interaction
}
assert_dict_almost_equal(contrasts_2dd, exp_cons)
X_2dd, contrasts_2dd = d_maker(spec_2dd, t, level_contrasts=True)
level_cons = exp_cons.copy()
level_cons.update({
'smt_0*smte_0_0': [1, 0, 0, 0], # smt 0, smte 0, hrf 0
'smt_0*smte_1_0': [0, 1, 0, 0], # smt 0, smte 1, hrf 0
'smt_1*smte_0_0': [0, 0, 1, 0], # smt 1, smte 0, hrf 0
'smt_1*smte_1_0': [0, 0, 0, 1], # smt 1, smte 1, hrf 0
})
assert_dict_almost_equal(contrasts_2dd, level_cons)
# Test max order >> 2, no error
X_2dd, contrasts_2dd = d_maker(spec_2dd, t, order=100)
assert_almost_equal(X_2dd, np.c_[exp_x_0, exp_x_1, exp_x_2, exp_x_3])
assert_dict_almost_equal(contrasts_2dd, exp_cons)
# Test max order = 1
X_2dd, contrasts_2dd = d_maker(spec_2dd, t, order=1)
assert_almost_equal(X_2dd, np.c_[exp_x_0, exp_x_1, exp_x_2, exp_x_3])
# No interaction
assert_dict_almost_equal(contrasts_2dd,
{'constant_0': [1, 1, 1, 1],
'smt_0': [1, 1, -1, -1], # main effect fac_1
'smte_0': [1, -1, 1, -1], # main effect fac_2
})
# events : test field called "time" is necessary
spec_1d = make_recarray(zip(onsets, fac_1), ('brighteyes', 'smt'))
assert_raises(ValueError, event_design, spec_1d, t)
# blocks : test fields called "start" and "end" are necessary
spec_1d = make_recarray(zip(onsets, offsets, fac_1),
('mister', 'brighteyes', 'smt'))
assert_raises(ValueError, block_design, spec_1d, t)
spec_1d = make_recarray(zip(onsets, offsets, fac_1),
('start', 'brighteyes', 'smt'))
assert_raises(ValueError, block_design, spec_1d, t)
spec_1d = make_recarray(zip(onsets, offsets, fac_1),
('mister', 'end', 'smt'))
assert_raises(ValueError, block_design, spec_1d, t)
def mk_blk_spec(factors, names):
names = ('start', 'end') + tuple(names)
return make_recarray(zip(onsets, offsets, *factors), names)
def mk_ev_spec(factors, names):
names = ('time',) + tuple(names)
if len(factors) == 0:
return make_recarray(onsets, names)
return make_recarray(zip(onsets, *factors), names)
def test_event_design():
# Test event design helper function
# An event design with one event type
onsets = np.array([0, 20, 40, 60])
durations = np.array([2, 3, 4, 5])
offsets = onsets + durations
c_fac = np.array([1, 1, 1, 1]) # constant factor (one level)
fac_1 = np.array([0, 1, 0, 1]) # factor 1, two levels
fac_2 = np.array([0, 0, 1, 1]) # factor 2, two levels
t = np.arange(0, 100, 2)
def mk_ev_spec(factors, names):
names = ('time',) + tuple(names)
if len(factors) == 0:
return make_recarray(onsets, names)
return make_recarray(zip(onsets, *factors), names)
def mk_blk_spec(factors, names):
names = ('start', 'end') + tuple(names)
return make_recarray(zip(onsets, offsets, *factors), names)
def mk_ev_tc(ev_inds):
# Make real time course for given event onsets
return lambdify_t(events(onsets[ev_inds], f=glover))(t)
def mk_blk_tc(ev_inds):
# Make real time course for block onset / offsets
B = blocks(zip(onsets[ev_inds], offsets[ev_inds]))
term = convolve_functions(B, glover(T),
(-5, 70), # step func support
(0, 30.), # conv kernel support
0.02) # dt
return lambdify_t(term)(t)
for d_maker, spec_maker, tc_maker, null_name in (
(event_design, mk_ev_spec, mk_ev_tc, '_event_'),
(block_design, mk_blk_spec, mk_blk_tc, '_block_')):
# Event spec with no event factor -> single column design, no contrasts
spec_0 = spec_maker((), ())
X_0, contrasts_0 = d_maker(spec_0, t)
exp_x_0 = tc_maker(onsets==onsets)
assert_almost_equal(X_0, exp_x_0)
assert_dict_almost_equal(contrasts_0, dict(constant_0=1))
X_0, contrasts_0 = d_maker(spec_0, t, level_contrasts=True)
assert_almost_equal(X_0, exp_x_0)
assert_dict_almost_equal(contrasts_0,
{'constant_0': 1,
null_name + '_1_0': 1})
# Event spec with single factor, but only one level
spec_1c = spec_maker((c_fac,), ('smt',))
X_1c, contrasts_1c = d_maker(spec_1c, t)
assert_almost_equal(X_1c, exp_x_0)
assert_dict_almost_equal(contrasts_1c, dict(constant_0=1))
X_1c, contrasts_1c = d_maker(spec_1c, t, level_contrasts=True)
assert_dict_almost_equal(contrasts_1c, dict(constant_0=1, smt_1_0=1))
# Event spec with single factor, two levels
spec_1d = spec_maker((fac_1,), ('smt',))
exp_x_0 = tc_maker(fac_1 == 0)
exp_x_1 = tc_maker(fac_1 == 1)
X_1d, contrasts_1d = d_maker(spec_1d, t)
assert_almost_equal(X_1d, np.c_[exp_x_0, exp_x_1])
assert_dict_almost_equal(contrasts_1d,
dict(constant_0=[1, 1], smt_0=[1, -1]))
X_1d, contrasts_1d = d_maker(spec_1d, t, level_contrasts=True)
assert_dict_almost_equal(contrasts_1d,
dict(constant_0=1,
smt_0=[1, -1], # main effect
smt_0_0=[1, 0], # level 0, hrf 0
smt_1_0=[0, 1])) # level 1, hrf 0
# Event spec with two factors, one with two levels, another with one
spec_2dc = spec_maker((fac_1, c_fac), ('smt', 'smte'))
X_2dc, contrasts_2dc = d_maker(spec_2dc, t)
assert_almost_equal(X_2dc, np.c_[exp_x_0, exp_x_1])
assert_dict_almost_equal(contrasts_2dc,
{'constant_0': [1, 1],
'smt_0': [1, -1], # main effect
'smt:smte_0': [1, -1], # interaction
})
X_2dc, contrasts_2dc = d_maker(spec_2dc, t, level_contrasts=True)
assert_dict_almost_equal(contrasts_2dc,
{'constant_0': [1, 1],
'smt_0': [1, -1], # main effect
'smt:smte_0': [1, -1], # interaction
'smt_0*smte_1_0': [1, 0], # smt 0, smte 0, hrf 0
'smt_1*smte_1_0': [0, 1], # smt 1, smte 0, hrf 0
})
# Event spec with two factors, both with two levels
spec_2dd = spec_maker((fac_1, fac_2), ('smt', 'smte'))
exp_x_0 = tc_maker((fac_1 == 0) & (fac_2 == 0))
exp_x_1 = tc_maker((fac_1 == 0) & (fac_2 == 1))
exp_x_2 = tc_maker((fac_1 == 1) & (fac_2 == 0))
exp_x_3 = tc_maker((fac_1 == 1) & (fac_2 == 1))
X_2dd, contrasts_2dd = d_maker(spec_2dd, t)
assert_almost_equal(X_2dd, np.c_[exp_x_0, exp_x_1, exp_x_2, exp_x_3])
exp_cons = {'constant_0': [1, 1, 1, 1],
'smt_0': [1, 1, -1, -1], # main effect fac_1
'smte_0': [1, -1, 1, -1], # main effect fac_2
'smt:smte_0': [1, -1, -1, 1], # interaction
}
assert_dict_almost_equal(contrasts_2dd, exp_cons)
X_2dd, contrasts_2dd = d_maker(spec_2dd, t, level_contrasts=True)
level_cons = exp_cons.copy()
level_cons.update({
'smt_0*smte_0_0': [1, 0, 0, 0], # smt 0, smte 0, hrf 0
'smt_0*smte_1_0': [0, 1, 0, 0], # smt 0, smte 1, hrf 0
'smt_1*smte_0_0': [0, 0, 1, 0], # smt 1, smte 0, hrf 0
'smt_1*smte_1_0': [0, 0, 0, 1], # smt 1, smte 1, hrf 0
})
assert_dict_almost_equal(contrasts_2dd, level_cons)
# Test max order >> 2, no error
X_2dd, contrasts_2dd = d_maker(spec_2dd, t, order=100)
assert_almost_equal(X_2dd, np.c_[exp_x_0, exp_x_1, exp_x_2, exp_x_3])
assert_dict_almost_equal(contrasts_2dd, exp_cons)
# Test max order = 1
X_2dd, contrasts_2dd = d_maker(spec_2dd, t, order=1)
assert_almost_equal(X_2dd, np.c_[exp_x_0, exp_x_1, exp_x_2, exp_x_3])
# No interaction
assert_dict_almost_equal(contrasts_2dd,
{'constant_0': [1, 1, 1, 1],
'smt_0': [1, 1, -1, -1], # main effect fac_1
'smte_0': [1, -1, 1, -1], # main effect fac_2
})
# events : test field called "time" is necessary
spec_1d = make_recarray(zip(onsets, fac_1), ('brighteyes', 'smt'))
assert_raises(ValueError, event_design, spec_1d, t)
# blocks : test fields called "start" and "end" are necessary
spec_1d = make_recarray(zip(onsets, offsets, fac_1),
('mister', 'brighteyes', 'smt'))
assert_raises(ValueError, block_design, spec_1d, t)
spec_1d = make_recarray(zip(onsets, offsets, fac_1),
('start', 'brighteyes', 'smt'))
assert_raises(ValueError, block_design, spec_1d, t)
spec_1d = make_recarray(zip(onsets, offsets, fac_1),
('mister', 'end', 'smt'))
assert_raises(ValueError, block_design, spec_1d, t)