def spike_detector(fname, Zalph=5., lZalph=3., histeresis=True, hthres=2., verbose=0):
"""
fname: name of nifti image, time is last dimension
other: see spikes_from_slice_diff function
"""
img = nib.load(fname)
arr = img.get_data()
assert len(arr.shape) == 4 # need a 4d nifti
assert arr.shape[3] > max(arr.shape[:-1]), \
print("time dim should be greater than others and shape is:", arr.shape)
#
qc = time_slice_diffs(arr)
# tsdiffplot.plot_tsdiffs(qc)
smd2 = qc['slice_mean_diff2']
spikes = spikes_from_slice_diff(smd2, Zalph=Zalph, lZalph=lZalph,
histeresis=histeresis, hthres=hthres, verbose=verbose)
final = final_detection(spikes, verbose=verbose)
times_to_correct = np.where(final.sum(axis=1) > 0)[0]
slices_to_correct = {}
for tim in times_to_correct:
slices_to_correct[tim] = np.where(final[tim,:] > 0)[0]
if verbose:
print("total number of outliers found:", spikes.sum())
print("total number of slices to be corrected:", final.sum())
print("number of time to be corrected:", (final.sum(axis=1) > 0).sum())
return qc, spikes, (times_to_correct, slices_to_correct)
def test_against_matlab_results():
fimg = load_image(funcfile)
results = tsd.time_slice_diffs(fimg)
# struct as record only to avoid deprecation warning
tsd_results = sio.loadmat(pjoin(TEST_DATA_PATH, 'tsdiff_results.mat'),
struct_as_record=True, squeeze_me=True)
yield assert_array_almost_equal(
results['volume_means'],
tsd_results['g'])
yield assert_array_almost_equal(
results['volume_mean_diff2'],
tsd_results['imgdiff'])
yield assert_array_almost_equal(
results['slice_mean_diff2'],
tsd_results['slicediff'])
# next tests are from saved, reloaded volumes at 16 bit integer
# precision, so are not exact, but very close, given that the mean
# of this array is around 3200
yield assert_array_almost_equal(
results['diff2_mean_vol'],
tsd_results['diff2_mean_vol'],
decimal=1)
yield assert_array_almost_equal(
results['slice_diff2_max_vol'],
tsd_results['slice_diff2_max_vol'],
decimal=1)
def test_time_slice_diffs():
n_tps = 10
n_slices = 4
slice_shape = (2,3)
slice_size = np.prod(slice_shape)
vol_shape = slice_shape + (n_slices,)
vol_size = np.prod(vol_shape)
ts = np.random.normal(size=vol_shape + (n_tps,)) * 100 + 10
expected = {}
expected['volume_means'] = ts.reshape((vol_size, -1)).mean(0)
# difference over time ^2
diffs2 = np.diff(ts, axis=-1)**2
expected['volume_mean_diff2'] = np.mean(
diffs2.reshape((vol_size, -1)), 0)
expected['slice_mean_diff2'] = np.zeros((n_tps-1, n_slices))
for s in range(n_slices):
v = diffs2[:,:,s,:].reshape((slice_size, -1))
expected['slice_mean_diff2'][:,s] = np.mean(v, 0)
expected['diff2_mean_vol'] = np.mean(diffs2, -1)
max_diff_is = np.argmax(expected['slice_mean_diff2'], 0)
sdmv = np.empty(vol_shape)
for si, dti in enumerate(max_diff_is):
sdmv[:,:,si] = diffs2[:,:,si,dti]
expected['slice_diff2_max_vol'] = sdmv
results = tsd.time_slice_diffs(ts)
for key in expected:
yield assert_array_almost_equal(results[key], expected[key])
# tranposes, reset axes, get the same result
results = tsd.time_slice_diffs(ts.T, 0, 1)
results['diff2_mean_vol'] = results['diff2_mean_vol'].T
results['slice_diff2_max_vol'] = results['slice_diff2_max_vol'].T
for key in expected:
yield assert_array_almost_equal(results[key], expected[key])
ts_t = ts.transpose((1, 3, 0, 2))
results = tsd.time_slice_diffs(ts_t, 1, -1)
results['diff2_mean_vol'] = results['diff2_mean_vol'].transpose(
((1,0,2)))
results['slice_diff2_max_vol'] = results['slice_diff2_max_vol'].transpose(
((1,0,2)))
for key in expected:
yield assert_array_almost_equal(results[key], expected[key])
def one_detection(sh,sli,tim):
arr = make_data(sh)
arr = make_bad_slices(arr, sli, tim)
qc = time_slice_diffs(arr)
smd2 = qc['slice_mean_diff2']
print("\n smd2 ine one detec\n", smd2)
spikes = fqc.spikes_from_slice_diff(smd2, Zalph=5., lZalph=3.,
histeresis=True, hthres=.2, verbose=1)
print("\n spikes ine one detec\n", spikes)
final = fqc.final_detection(spikes, verbose=1)
print("\n final ine one detec\n", final)
times_to_correct = np.where(final.sum(axis=1) > 0)[0]
print("times_to_correct: ",times_to_correct)
slices_to_correct = {}
for ti in times_to_correct:
slices_to_correct[ti] = np.where(final[ti,:] > 0)[0]
return times_to_correct, slices_to_correct
def one_detection(sh, sli, tim):
arr = make_data(sh)
arr = make_bad_slices(arr, sli, tim)
qc = time_slice_diffs(arr)
smd2 = qc['slice_mean_diff2']
print("\n smd2 ine one detec\n", smd2)
spikes = fqc.spikes_from_slice_diff(smd2,
Zalph=5.,
lZalph=3.,
histeresis=True,
hthres=.2,
verbose=1)
print("\n spikes ine one detec\n", spikes)
final = fqc.final_detection(spikes, verbose=1)
print("\n final ine one detec\n", final)
times_to_correct = np.where(final.sum(axis=1) > 0)[0]
print("times_to_correct: ", times_to_correct)
slices_to_correct = {}
for ti in times_to_correct:
slices_to_correct[ti] = np.where(final[ti, :] > 0)[0]
return times_to_correct, slices_to_correct
def spike_detector(fname,
Zalph=5.,
lZalph=3.,
histeresis=True,
hthres=2.,
verbose=0):
"""
fname: name of nifti image, time is last dimension
other: see spikes_from_slice_diff function
"""
img = nib.load(fname)
arr = img.get_data()
assert len(arr.shape) == 4 # need a 4d nifti
assert arr.shape[3] > max(arr.shape[:-1]), \
print("time dim should be greater than others and shape is:", arr.shape)
#
qc = time_slice_diffs(arr)
# tsdiffplot.plot_tsdiffs(qc)
smd2 = qc['slice_mean_diff2']
spikes = spikes_from_slice_diff(smd2,
Zalph=Zalph,
lZalph=lZalph,
histeresis=histeresis,
hthres=hthres,
verbose=verbose)
final = final_detection(spikes, verbose=verbose)
times_to_correct = np.where(final.sum(axis=1) > 0)[0]
slices_to_correct = {}
for tim in times_to_correct:
slices_to_correct[tim] = np.where(final[tim, :] > 0)[0]
if verbose:
print("total number of outliers found:", spikes.sum())
print("total number of slices to be corrected:", final.sum())
print("number of time to be corrected:", (final.sum(axis=1) > 0).sum())
return qc, spikes, (times_to_correct, slices_to_correct)