def create_parameter_grid(samples, predictors):
"""Creates a parameter grid for the test function.
Returns
-------
ParameterGrid
All pairings of parameters to be run through the SLM class.
"""
model = [
FixedEffect(1) + FixedEffect(np.random.rand(samples, predictors),
names=["y1", "y2", "y3"])
]
Y_idx = [1, 2, 3]
contrast = [np.random.rand(samples), FixedEffect(np.random.rand(samples))]
surf = [None, read_surface_gz(fetch_surf_fsaverage()["pial_left"])]
mask = [None, np.random.rand(10242) > 0.1]
correction = [None, ["rft", "fdr"]]
two_tailed = [False, True]
param_grid = ParameterGrid({
"Y_idx": Y_idx,
"model": model,
"contrast": contrast,
"surf": surf,
"mask": mask,
"correction": correction,
"two_tailed": two_tailed,
})
return param_grid
def generate_tests():
pial_fs5 = datasets.fetch_surf_fsaverage()["pial_left"]
pial_surf = read_surface_gz(pial_fs5)
tri = np.array(get_cells(pial_surf)) + 1
np.random.seed(0)
data = {"tri": tri, "Y": np.random.uniform(-1, 1, (1, 10242)), "FWHM": 3}
O = generate_smooth_out(data)
params2files(data, O, 1)
def load_training_data(n):
brainstat_dir = os.path.dirname(brainstat.__file__)
data_dir = os.path.join(brainstat_dir, "tutorial")
tutorial_data = fetch_tutorial_data(n_subjects=n, data_dir=data_dir)
age = tutorial_data["demographics"]["AGE"].to_numpy()
iq = tutorial_data["demographics"]["IQ"].to_numpy()
# Reshape the thickness files such that left and right hemispheres are in the same row.
files = np.reshape(np.array(tutorial_data["image_files"]), (-1, 2))
thickness = np.zeros((n, 10242))
for i in range(n):
thickness[i, :] = np.squeeze(nib.load(files[i, 0]).get_fdata())
mask = np.all(thickness != 0, axis=0)
pial = read_surface_gz(fetch_surf_fsaverage()["pial_left"])
return (pial, mask, age, iq, thickness)
def generate_test_data():
pial_fs5 = datasets.fetch_surf_fsaverage()["pial_left"]
pial_surf = read_surface_gz(pial_fs5)
real_tri = np.array(get_cells(pial_surf))
np.random.seed(0)
mygrid = [
{
"Y": [
np.random.randint(1, 10, size=(1, 20)),
np.random.randint(1, 10, size=(2, 20)),
np.random.randint(2, 10, size=(3, 20, 4)),
],
"mask": [None,
np.random.choice(a=[False, True], size=(20, ))],
},
{
"Y": [real_tri],
"mask": [
None,
np.random.choice(a=[False, True], size=(real_tri.shape[1]))
],
},
]
myparamgrid = ParameterGrid(mygrid)
# Here wo go!
# Tests 1-4 : Y is 2D or 3D arrays type int, mask is None or random bool
# Tests 6-8 : Y is pial_fs5 trinagles, mask is None or random bool
test_num = 0
for params in myparamgrid:
test_num += 1
I = {}
for key in params.keys():
I[key] = params[key]
D = generate_mesh_normalize_out(I)
params2files(I, D, test_num)
n = 20
tutorial_data = fetch_tutorial_data(n_subjects=n, data_dir=data_dir)
age = tutorial_data["demographics"]["AGE"].to_numpy()
iq = tutorial_data["demographics"]["IQ"].to_numpy()
# Reshape the thickness files such that left and right hemispheres are in the same row.
files = np.reshape(np.array(tutorial_data["image_files"]), (-1, 2))
# We'll use only the left hemisphere in this tutorial.
thickness = np.zeros((n, 10242))
for i in range(n):
thickness[i, :] = np.squeeze(nib.load(files[i, 0]).get_fdata())
mask = np.all(thickness != 0, axis=0)
pial_left = read_surface_gz(fetch_surf_fsaverage()["pial_left"])
###################################################################
# Next, we can create a BrainStat linear model by declaring these variables as
# terms. The term class requires two things: 1) an array or scalar, and 2) a
# variable name for each column. Lastly, we can create the model by simply
# adding the terms together.
from brainstat.stats.terms import Term
term_intercept = Term(1, names="intercept")
term_age = Term(age, "age")
term_iq = Term(iq, "iq")
model = term_intercept + term_age + term_iq
###################################################################
def generate_tests():
# Test 01
# ['tri'] will be a np array, shape (4, 3), int64
np.random.seed(0)
rand_dict = {}
rand_dict["tri"] = np.random.randint(1, int(10), size=(4, 3))
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 1)
# Test 02
# ['tri'] :np array, shape (4, 3), int64
# ['resl'] :np array, shape (8, 6), float64
np.random.seed(0)
rand_dict = {}
n_vertices = 6
rand_dict["tri"] = np.random.randint(1, n_vertices, size=(4, 3))
rand_dict["resl"] = np.random.random_sample((8, n_vertices))
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 2)
# Test 03
# ['tri'] :np array, shape (4, 3), int64
# ['resl'] :np array, shape (8, 6), float64
# ['mask'] :np array, shape (5,), bool
np.random.seed(0)
rand_dict = {}
n_vertices = 6
rand_dict["tri"] = np.random.randint(1, n_vertices, size=(4, 3))
rand_dict["resl"] = np.random.random_sample((8, n_vertices))
rand_dict["mask"] = np.random.choice(
a=[True, False], size=(rand_dict["tri"].max(),)
)
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 3)
# Test 04
# ['lat'] :np array, shape (10, 10, 10), float64
np.random.seed(0)
rand_dict = {}
rand_dict["lat"] = np.ones((10, 10, 10))
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 4)
# Test 05
# ['lat'] :np array, shape (10, 10, 10), bool
np.random.seed(0)
rand_dict = {}
rand_dict["lat"] = np.random.choice(a=[False, True], size=(10, 10, 10))
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 5)
# Test 06
# ['tri] :np array, shape (1000,3)
# ['mask'] :np array, shape (['tri'].max(),), bool
np.random.seed(0)
rand_dict = {}
rand_dict["tri"] = np.random.randint(1, n_vertices, size=(1000, 3))
rand_dict["mask"] = np.random.choice(
a=[True, False], size=(rand_dict["tri"].max(),)
)
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 6)
# Test 07
# ['lat'] :np array, shape (10, 10, 10), bool
# ['resl'] :np array, shape (1359, 1), float64
np.random.seed(0)
rand_dict = {}
rand_dict["lat"] = np.random.choice(a=[False, True], size=(10, 10, 10))
rand_dict["resl"] = np.random.random_sample((1359, 1))
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 7)
# Test 08
# ['tri] :np array, shape (1000,3)
# ['mask'] :np array, shape (499,), bool
np.random.seed(1)
rand_dict = {}
rand_dict["tri"] = np.random.randint(1, 499, size=(1000, 3))
rand_dict["mask"] = np.random.choice(
a=[True, False], size=(rand_dict["tri"].max(),)
)
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 8)
# Test 09
# ['lat'] :np array, shape (10, 10, 10), bool
# ['resl'] :np array, shape (1198, 1), float64
np.random.seed(1)
rand_dict = {}
rand_dict["lat"] = np.random.choice(a=[False, True], size=(10, 10, 10))
rand_dict["resl"] = np.random.random_sample((1198, 1))
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 9)
# Test 10
# ['tri'] is pial_fs5, shape (20480, 3)
pial_fs5 = datasets.fetch_surf_fsaverage()["pial_left"]
pial_surf = read_surface_gz(pial_fs5)
n_vertices = get_points(pial_surf).shape[0]
rand_dict = {}
rand_dict["tri"] = np.array(get_cells(pial_surf)) + 1
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 10)
# Test 11
# ['tri'] :pial_fs5, shape (20480, 3)
# ['mask'] :np array, shape (['tri'].max(),), bool
np.random.seed(0)
rand_dict = {}
rand_dict["tri"] = np.array(get_cells(pial_surf)) + 1
rand_dict["mask"] = np.random.choice(
a=[True, False], size=(rand_dict["tri"].max(),)
)
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 11)
# Test 12
# ['tri'] :pial_fs5, shape (20480, 3) --> shuffle
# ['mask'] :np array, shape (['tri'].max(),), bool
np.random.seed(5)
rand_dict = {}
rand_dict["tri"] = np.array(get_cells(pial_surf)) + 1
np.random.shuffle(rand_dict["tri"])
rand_dict["mask"] = np.random.choice(
a=[True, False], size=(rand_dict["tri"].max(),)
)
In, Out = generate_random_slm(rand_dict)
params2files(In, Out, 12)
def generate_test_data():
## Fetch global data and settings.
# Global test settings
basename = "xstatp"
test_num = 1
np.random.seed(0)
# Fetch surface data.
pial_fs5 = datasets.fetch_surf_fsaverage()["pial_left"]
pial_surf = read_surface_gz(pial_fs5)
n_vertices = get_points(pial_surf).shape[0]
## Define the test parameter grids.
# Variable types to test
var_types = {
"t": [np.float64],
"df": [int, np.uint16],
"k": [int, np.uint8],
"resl": [np.float64],
"tri": [np.int64],
}
type_parameter_grid = ParameterGrid(var_types)
# Optional variable test.
var_optional = {
"dfs": [None, np.random.randint(1, 100, (1, n_vertices))],
"cluster_threshold": [0.1, 2],
"mask": [None, np.random.rand(n_vertices) > 0.1],
"k": [1, 3],
}
# Nonsense variables to add.
var_nonsense = ["X", "coef", "SSE", "c", "ef", "sd"]
## Generate test data
# Variable type tests
for params in type_parameter_grid:
slm = generate_random_slm(pial_surf)
for key in list(params.keys()):
attr = getattr(slm, key)
setattr(slm, key, params[key](attr))
slm2files(slm, basename, test_num)
test_num += 1
# Additional variable tests.
additional_parameter_grid = ParameterGrid(var_optional)
for params in additional_parameter_grid:
slm = generate_random_slm(pial_surf)
for key in list(params.keys()):
setattr(slm, key, params[key])
slm2files(slm, basename, test_num)
test_num += 1
# Nonsense variable tests.
slm = generate_random_slm(pial_surf)
slm.dfs = np.random.randint(1, 100, (1, n_vertices))
slm.mask = np.random.rand(n_vertices) > 0.1
for key in var_nonsense:
if getattr(slm, key) is None:
setattr(
slm,
key,
np.random.rand(np.random.randint(1, 10),
np.random.randint(1, 10)),
)
slm2files(slm, basename, test_num)
test_num += 1
def generate_test_data():
np.random.seed(0)
# these are the sizes of array, which will be looped in Parameter Grid
mygrid_xy = [{"x": [3], "y": [1]}, {"x": [6], "y": [6]}, {"x": [5], "y": [2]}]
myparamgrid_xy = ParameterGrid(mygrid_xy)
# Here wo go!
# Tests 1-12: randomly generated arrays for all input params
test_num = 0
for params_xy in list(myparamgrid_xy):
x = params_xy["x"]
y = params_xy["y"]
mygrid = [
{
"X": [np.random.rand(x, y)],
"df": [int(y - 1)],
"coef": [
np.random.rand(y, x),
],
"SSE": [np.random.rand(1, x)],
"contrast": [np.random.rand(1, y), np.random.rand(1, 1)],
"dr": [None, int(y + 1)],
}
]
# here goes the actual Parameter Grid
myparamgrid = ParameterGrid(mygrid)
for params in myparamgrid:
test_num += 1
I = {}
for key in params.keys():
if params[key] is not None:
I[key] = params[key]
D = generate_t_test_out(I)
params2files(I, D, test_num)
# get some real data for the triangle coordinates
pial_fs5 = datasets.fetch_surf_fsaverage()["pial_left"]
surf = read_surface_gz(pial_fs5)
tri = np.array(get_cells(surf))
realgrid = [
{
"X": [np.random.randint(0, 1000, size=(20, 9))],
"df": [np.random.randint(1, 9)],
"coef": [np.random.rand(9, int(tri.shape[0])) - 0.7],
"SSE": [np.random.rand(1, int(tri.shape[0]))],
"tri": [tri],
"resl": [np.random.rand(int(tri.shape[0]), 1)],
"contrast": [np.random.randint(21, 48, size=(20, 1))],
}
]
# Test 13: triangle coordinates are real, from pial_fs5, rest is random
myrealgrid = ParameterGrid(realgrid)
for params in myrealgrid:
test_num += 1
I = {}
for key in params.keys():
if params[key] is not None:
I[key] = params[key]
D = generate_t_test_out(I)
params2files(I, D, test_num)