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Add highest dct order #449

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08e74ea
Add cosine drifts with period up to equal to the requested cut period
takhs91 Dec 20, 2018
c043a46
Add docstring changes
takhs91 Dec 20, 2018
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8 changes: 4 additions & 4 deletions nipy/modalities/fmri/design_matrix.py
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Expand Up @@ -75,7 +75,7 @@ def _cosine_drift(period_cut, frametimes):
Returns
-------
cdrift: array of shape(n_scans, n_drifts)
cosin drifts plus a constant regressor at cdrift[:,0]
cosine drifts plus a constant regressor at cdrift[:,-1]

Ref: http://en.wikipedia.org/wiki/Discrete_cosine_transform DCT-II
"""
Expand All @@ -85,13 +85,13 @@ def _cosine_drift(period_cut, frametimes):

dt = frametimes[1] - frametimes[0] # frametimes.max() should be (len_tim-1)*dt
order = int(np.floor(2*len_tim*hfcut*dt)) # s.t. hfcut = 1/(2*dt) yields len_tim
cdrift = np.zeros((len_tim, order))
cdrift = np.zeros((len_tim, order + 1))
nfct = np.sqrt(2.0/len_tim)

for k in range(1, order):
for k in range(1, order + 1):
cdrift[:,k-1] = nfct * np.cos((np.pi/len_tim)*(n_times + .5)*k)

cdrift[:,order-1] = 1. # or 1./sqrt(len_tim) to normalize
cdrift[:, -1] = 1. # or 1./sqrt(len_tim) to normalize
return cdrift


Expand Down
10 changes: 5 additions & 5 deletions nipy/modalities/fmri/realfuncs.py
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Expand Up @@ -27,7 +27,7 @@ def dct_ii_basis(volume_times, order=None, normcols=False):
Returns
-------
dct_basis : array
Shape ``(len(volume_times), order)`` array with DCT-II basis up to
Shape ``(len(volume_times), order + 1)`` array with DCT-II basis up to
order `order`.

Raises
Expand All @@ -43,11 +43,11 @@ def dct_ii_basis(volume_times, order=None, normcols=False):
raise ValueError("DCT basis assumes continuous regular sampling")
n = np.arange(N)
cycle = np.pi * (n + 0.5) / N
dct_basis = np.zeros((N, order))
for k in range(0, order):
dct_basis = np.zeros((N, order + 1))
for k in range(0, order + 1):
dct_basis[:, k] = np.cos(cycle * k)
if normcols: # Set column lengths to 1
lengths = np.ones(order) * np.sqrt(N / 2.)
lengths = np.ones(order + 1) * np.sqrt(N / 2.)
lengths[0:1] = np.sqrt(N) # Allow order=0
dct_basis /= lengths
return dct_basis
Expand Down Expand Up @@ -80,6 +80,6 @@ def dct_ii_cut_basis(volume_times, cut_period):
# Always return constant column
if order == 0:
return np.ones((N, 1))
basis = np.ones((N, order))
basis = np.ones((N, order + 1))
basis[:, :-1] = dct_ii_basis(volume_times, order, normcols=True)[:, 1:]
return basis
6 changes: 3 additions & 3 deletions nipy/modalities/fmri/tests/test_dmtx.py
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Expand Up @@ -85,7 +85,7 @@ def test_cosine_drift():
tim = np.arange(20)
P = 10 # period is half the time, gives us an order 4
nipy_drifts = _cosine_drift(P, tim) #
assert_almost_equal(spm_drifts[:,1:], nipy_drifts[:,:-1])
assert_almost_equal(spm_drifts[:,1:], nipy_drifts[:, :-2])
# nipy_drifts is placing the constant at the end [:,:-1]


Expand Down Expand Up @@ -205,7 +205,7 @@ def test_dmtx2():
hrf_model = 'Canonical'
X, names= dmtx_light(frametimes, paradigm, hrf_model=hrf_model,
drift_model='cosine', hfcut=63)
assert_equal(len(names), 7) # was 8 with old cosine
assert_equal(len(names), 8)

def test_dmtx3():
# idem test_dmtx1 with a different drift term
Expand Down Expand Up @@ -416,7 +416,7 @@ def test_dmtx20():
drift_model='cosine')

# check that the drifts are not constant
assert_true(np.all(np.diff(X[:, -2]) != 0))
assert_true(np.any(np.diff(X[:, -2]) != 0))


def test_fir_block():
Expand Down
11 changes: 6 additions & 5 deletions nipy/modalities/fmri/tests/test_realfuncs.py
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Expand Up @@ -23,7 +23,8 @@ def test_dct_ii_basis():
spm_fname = pjoin(HERE, 'dct_{0}.txt'.format(N))
spm_mtx = np.loadtxt(spm_fname)
vol_times = np.arange(N) * 15. + 3.2
our_dct = dct_ii_basis(vol_times)
# :-1 is needed because one extra drift was added
our_dct = dct_ii_basis(vol_times)[:, :-1]
# Check dot products of columns
sq_col_lengths = np.ones(N) * N / 2.
sq_col_lengths[0] = N
Expand All @@ -32,13 +33,13 @@ def test_dct_ii_basis():
col_lengths = np.sqrt(sq_col_lengths)
assert_almost_equal(our_dct / col_lengths, spm_mtx)
# Normalize length
our_normed_dct = dct_ii_basis(vol_times, normcols=True)
our_normed_dct = dct_ii_basis(vol_times, normcols=True)[:, :-1]
assert_almost_equal(our_normed_dct, spm_mtx)
assert_almost_equal(our_normed_dct.T.dot(our_normed_dct), np.eye(N))
for i in range(N):
assert_almost_equal(dct_ii_basis(vol_times, i) / col_lengths[:i],
assert_almost_equal(dct_ii_basis(vol_times, i)[:, :-1] / col_lengths[:i],
spm_mtx[:, :i])
assert_almost_equal(dct_ii_basis(vol_times, i, True),
assert_almost_equal(dct_ii_basis(vol_times, i, True)[:, :-1],
spm_mtx[:, :i])
vol_times[0] += 0.1
assert_raises(ValueError, dct_ii_basis, vol_times)
Expand All @@ -55,6 +56,6 @@ def test_dct_ii_cut_basis():
if order == 0:
assert_array_equal(dct_vals, np.ones((N, 1)))
continue
dct_expected = np.ones((N, order))
dct_expected = np.ones((N, order + 1))
dct_expected[:, :-1] = dct_ii_basis(times, order, normcols=True)[:, 1:]
assert_array_equal(dct_vals, dct_expected)