def get_FS_from_paths(path_list, masker): print "Loading first-level images from subjects data..." l = [] niis = check_niimgs(path_list) data4d = niis.get_data() for iimg in range(data4d.shape[3]): masked = masker.transform( nib.Nifti1Image(data4d[..., iimg], niis.get_affine()))[0] l.append(masked) FS_org = np.asarray(l) return FS_org
def test_check_niimgs(): assert_raises(TypeError, _utils.check_niimgs, 0) affine = np.eye(4) niimg = Nifti1Image(np.ones((10, 10, 10)), affine) _utils.check_niimgs([niimg, niimg]) # This should raise an error: a 3D niimg is given and we want a 4D assert_raises(TypeError, _utils.check_niimgs, niimg) # This shouldn't raise an error _utils.check_niimgs(niimg, accept_3d=True) # Test a Niimage that does not hold a shape attribute phony_niimg = PhonyNiimage() _utils.check_niimgs(phony_niimg)
def test_check_niimgs(): assert_raises(TypeError, _utils.check_niimgs, 0) assert_raises(TypeError, _utils.check_niimgs, []) affine = np.eye(4) niimg = Nifti1Image(np.ones((10, 10, 10)), affine) _utils.check_niimgs([niimg, niimg]) # This should raise an error: a 3D niimg is given and we want a 4D assert_raises(TypeError, _utils.check_niimgs, niimg) # This shouldn't raise an error _utils.check_niimgs(niimg, accept_3d=True) # Test a Niimage that does not hold a shape attribute phony_niimg = PhonyNiimage() _utils.check_niimgs(phony_niimg)
def test_check_niimgs(): assert_raises_regexp(TypeError, 'image', _utils.check_niimgs, 0) assert_raises_regexp(TypeError, 'image', _utils.check_niimgs, []) affine = np.eye(4) img_3d = Nifti1Image(np.ones((10, 10, 10)), affine) # Tests with return_iterator=False img_4d_1 = _utils.check_niimgs([img_3d, img_3d]) assert_true(img_4d_1.get_data().shape == (10, 10, 10, 2)) assert_array_equal(img_4d_1.get_affine(), affine) img_4d_2 = _utils.check_niimgs(img_4d_1) assert_array_equal(img_4d_2.get_data(), img_4d_2.get_data()) assert_array_equal(img_4d_2.get_affine(), img_4d_2.get_affine()) # Tests with return_iterator=True img_3d_iterator = _utils.check_niimgs([img_3d, img_3d], return_iterator=True) img_3d_iterator_length = sum(1 for _ in img_3d_iterator) assert_true(img_3d_iterator_length == 2) img_3d_iterator_1 = _utils.check_niimgs([img_3d, img_3d], return_iterator=True) img_3d_iterator_2 = _utils.check_niimgs(img_3d_iterator_1, return_iterator=True) for img_1, img_2 in itertools.izip(img_3d_iterator_1, img_3d_iterator_2): assert_true(img_1.get_data().shape == (10, 10, 10)) assert_array_equal(img_1.get_data(), img_2.get_data()) assert_array_equal(img_1.get_affine(), img_2.get_affine()) img_3d_iterator_1 = _utils.check_niimgs([img_3d, img_3d], return_iterator=True) img_3d_iterator_2 = _utils.check_niimgs(img_4d_1, return_iterator=True) for img_1, img_2 in itertools.izip(img_3d_iterator_1, img_3d_iterator_2): assert_true(img_1.get_data().shape == (10, 10, 10)) assert_array_equal(img_1.get_data(), img_2.get_data()) assert_array_equal(img_1.get_affine(), img_2.get_affine()) # This should raise an error: a 3D img is given and we want a 4D assert_raises_regexp(TypeError, 'image', _utils.check_niimgs, img_3d) # This shouldn't raise an error _utils.check_niimgs(img_3d, accept_3d=True) # Test a Niimage that does not hold a shape attribute phony_img = PhonyNiimage() _utils.check_niimgs(phony_img)
def test_check_niimgs(): with assert_raises(TypeError) as cm: _utils.check_niimgs(0) assert_true('image' in cm.exception.message or 'affine' in cm.exception.message) with assert_raises(TypeError) as cm: _utils.check_niimgs([]) assert_true('image' in cm.exception.message or 'affine' in cm.exception.message) affine = np.eye(4) niimg = Nifti1Image(np.ones((10, 10, 10)), affine) _utils.check_niimgs([niimg, niimg]) with assert_raises(TypeError) as cm: # This should raise an error: a 3D niimg is given and we want a 4D _utils.check_niimgs(niimg) assert_true('image' in cm.exception.message) # This shouldn't raise an error _utils.check_niimgs(niimg, accept_3d=True) # Test a Niimage that does not hold a shape attribute phony_niimg = PhonyNiimage() _utils.check_niimgs(phony_niimg)