def concat(input, axis, fname_output, pixdim):
"""Concatenate NIfTIs along the specified dimension.
input: Input paths of the files to concatenate. Separate the files by a space.
"""
# Create nii list
list_nii = []
for fname_file in input:
nii_input = nib.load(fname_file)
list_nii.append(nii_input)
# Call concat API
dim_list = AXES
index = dim_list.index(axis)
nii_out = concat_data(list_nii, index, pixdim)
# Save image
nib.save(nii_out, fname_output)
def test_concat_100(self):
"""Use a list of more than 100 files"""
out = concat_data(self.list_nii * 34, 4)
assert out.shape == self.list_nii[0].shape + (1, len(self.list_nii) * 34) # (128, 68, 20, 1, 3)
def test_concat_pixdim(self):
pixdim = 0.2
out = concat_data(self.list_nii, 2, pixdim=pixdim)
assert np.all(np.isclose(out.header['pixdim'], [-1, 2.1875, 2.1875, 0.2, 1, 0, 0, 0]))
def test_concat_dim_1(self):
out = concat_data(self.list_nii, 1)
assert out.shape == (128, 204, 20)
def test_concat_dim_4(self):
out = concat_data(self.list_nii, 4)
assert out.shape == self.list_nii[0].shape + (1, len(self.list_nii)) # (128, 68, 20, 1, 3)
def test_concat_dim_def(self):
out = concat_data(self.list_nii)
assert out.shape == self.list_nii[0].shape + (len(self.list_nii),) # (128, 68, 20, 3)