def dummy_test(infile, expfile):
# load input test data
ifile = open(infile, "br")
idic = pickle.load(ifile)
ifile.close()
surf = {}
if "tri" in idic.keys():
surf["tri"] = idic["tri"]
if "lat" in idic.keys():
surf["lat"] = idic["lat"]
# run mesh_edges
out_edge = mesh_edges(surf)
# load expected outout data
efile = open(expfile, "br")
expdic = pickle.load(efile)
efile.close()
exp_edge = expdic["edg"]
testout = []
comp = np.allclose(out_edge, exp_edge, rtol=1e-05, equal_nan=True)
testout.append(comp)
assert all(flag == True for (flag) in testout)
def test_nifti_input():
nifti = nib.load(
tflow.get("MNI152Lin", resolution="02", desc="brain", suffix="mask"))
edg = mesh_edges(nifti)
assert edg.shape[1] == 2
assert np.amax(edg) <= nifti.get_data().sum() - 1
def get_meshedge_output(surf, foutname):
"""Runs mesh_edges and returns all relevant output."""
# run mesh_edges
surf_out = {}
surf_out["edg"] = mesh_edges(surf)
with open(foutname, "wb") as handle:
pickle.dump(surf_out, handle, protocol=4) #
return
def _unmask(self) -> None:
"""Changes all masked parameters to their input dimensions."""
simple_unmask_parameters = ["t", "coef", "SSE", "r", "ef", "sd", "dfs"]
for key in simple_unmask_parameters:
attr = getattr(self, key)
if attr is not None:
setattr(self, key, undo_mask(attr, self.mask, axis=1))
# slm.resl unmask
if self.resl is not None:
edges = mesh_edges(self.surf)
_, idx = _mask_edges(edges, self.mask)
self.resl = undo_mask(self.resl, idx, axis=0)
def generate_test_data():
np.random.seed(0)
# generate the parameters
tri = np.random.randint(1, int(50), size=(100, 3))
coord = np.random.rand(3, 50)
edg = mesh_edges({"tri": tri})
n_edges = edg.shape[0]
n_vertices = int(tri.shape[0])
cluster_threshold = np.random.rand()
mygrid = [
{
"num_t": [1, 2, 3],
"k": [1, 2, 3],
"df": [1, [1, 1]],
"mask": [False, True],
"reselspvert": [None, True],
},
]
myparamgrid = ParameterGrid(mygrid)
# Generate data.
test_num = 0
for params in myparamgrid:
I = {
"tri": tri,
"edg": edg,
"thresh": cluster_threshold,
"t": np.random.random_sample((params["num_t"], n_vertices)),
"resl": np.random.random_sample((n_edges, 1)),
"k": params["k"],
"df": params["df"],
"coord": coord,
}
if params["mask"] is True:
I["mask"] = np.random.choice(a=[False, True], size=(n_vertices))
else:
I["mask"] = np.ones((n_vertices), dtype=bool)
if params["reselspvert"] is True:
I["reselspvert"] = np.random.rand(n_vertices)
else:
I["reselspvert"] = None
# Here we go: generate slm & run peak_clus & save in-out
slm = generate_random_slm(I)
D = generate_peak_clus_out(slm, I)
test_num += 1
params2files(I, D, test_num)
def _compute_resls(self, Y):
"""Computes the sum over observations of squares of differences of
normalized residuals along each edge.
Parameters
----------
Y : numpy.array
Response variable residual matrix.
Returns
-------
numpy.array
Sum over observations of squares of differences of normalized residuals
along each edge.
dict
Dictionary containing the mesh connections in either triangle or lattice
format. The dictionary's sole key is 'tri' for triangle connections or
'lat' for lattice connections.
"""
if isinstance(self.surf, BSPolyData):
mesh_connections = {"tri": np.array(get_cells(self.surf)) + 1}
else:
key = "tri" if "tri" in self.surf else "lat"
mesh_connections = {key: self.surf[key]}
edges = mesh_edges(self.surf, self.mask)
n_edges = edges.shape[0]
Y = np.atleast_3d(Y)
resl = np.zeros((n_edges, Y.shape[2]))
for j in range(Y.shape[2]):
normr = np.sqrt(self.SSE[((j + 1) * (j + 2) // 2) - 1])
for i in range(Y.shape[0]):
u = Y[i, :, j] / normr
resl[:, j] += np.diff(u[edges], axis=1).ravel()**2
return resl, mesh_connections
