def test_parcel_write(self):
parcelmap = np.zeros(self.img3.shape)
parcelmap[0,0,0] = 1
parcelmap[1,1,1] = 1
parcelmap[2,2,2] = 1
parcelmap[1,2,1] = 2
parcelmap[2,3,2] = 2
parcelmap[0,1,0] = 2
parcelseq = (0, 1, 2, 3)
expected = [np.product(self.img3.shape) - 6, 3, 3, 0]
iterator = gen.parcels(parcelmap, labels=parcelseq)
for i, s in enumerate(iterator):
value = np.arange(expected[i])
self.img3[s] = value
iterator = gen.parcels(parcelmap, labels=parcelseq)
for i, pair in enumerate(gen.data_generator(self.img3, iterator)):
s, d = pair
self.assertEqual((expected[i],), d.shape)
assert_equal(d, np.arange(expected[i]))
iterator = gen.parcels(parcelmap)
for i, s in enumerate(iterator):
value = np.arange(expected[i])
self.img3[s] = value
iterator = gen.parcels(parcelmap)
for i, pair in enumerate(gen.data_generator(self.img3, iterator)):
s, d = pair
self.assertEqual((expected[i],), d.shape)
assert_equal(d, np.arange(expected[i]))
def test_iterate_over_image(self):
# Fit a model, iterating over the slices of an array
# associated to an FmriImage.
c = np.zeros(self.fd.shape[1:]) + 0.5
fd = self.fd
res_gen = result_generator(flatten_generator(fmri_generator(fd)))
write_data(c, unflatten_generator(contrast_generator(res_gen)))
# Fit a model, iterating over the array associated to an
# FmriImage, iterating over a list of ROIs defined by binary
# regions of the same shape as a frame of FmriImage
# this might really be an anatomical image or AR(1) coefficients
a = np.asarray(fd[0])
p = np.greater(a, a.mean())
d = np.ones(fd.shape[1:]) * 2.0
flat_gen = flatten_generator(fmri_generator(fd, parcels(p)))
write_data(d, contrast_generator(result_generator(flat_gen)))
yield assert_array_almost_equal, d, c
e = np.zeros(fd.shape[1:]) + 3.0
flat_gen2 = flatten_generator(fmri_generator(fd, parcels(p)))
write_data(e, f_generator(contrast, result_generator(flat_gen2)))
yield assert_array_almost_equal, d, e
def test_parcel_copy(self):
parcelmap = np.zeros(self.img3.shape)
parcelmap[0,0,0] = 1
parcelmap[1,1,1] = 1
parcelmap[2,2,2] = 1
parcelmap[1,2,1] = 2
parcelmap[2,3,2] = 2
parcelmap[0,1,0] = 2
parcelseq = (0, 1, 2, 3)
expected = [np.product(self.img3.shape) - 6, 3, 3, 0]
iterator = gen.parcels(parcelmap, labels=parcelseq)
tmp = Image(np.asarray(self.img3), self.img3.coordmap)
gen_parcels = gen.parcels(parcelmap, labels=parcelseq)
new_iterator = gen.data_generator(tmp, gen_parcels)
for i, slice_ in enumerate(new_iterator):
self.assertEqual((expected[i],), slice_[1].shape)
def test_parcel(self):
parcelmap = np.zeros(self.img3.shape)
parcelmap[0,0,0] = 1
parcelmap[1,1,1] = 1
parcelmap[2,2,2] = 1
parcelmap[1,2,1] = 2
parcelmap[2,3,2] = 2
parcelmap[0,1,0] = 2
parcelseq = (0, 1, 2, 3)
expected = [np.product(self.img3.shape) - 6, 3, 3, 0]
iterator = gen.data_generator(self.img3,
gen.parcels(parcelmap, labels=parcelseq))
for i, pair in enumerate(iterator):
s, d = pair
self.assertEqual((expected[i],), d.shape)
iterator = gen.data_generator(self.img3, gen.parcels(parcelmap))
for i, pair in enumerate(iterator):
s, d = pair
self.assertEqual((expected[i],), d.shape)
