def test_fixed_effect_contrast_nonzero_effect():
X, y = make_regression(n_features=5, n_samples=20, random_state=0)
y = y[:, None]
labels, results = run_glm(y, X, 'ols')
coef = LinearRegression(fit_intercept=False).fit(X, y).coef_
for i in range(X.shape[1]):
contrast = np.zeros(X.shape[1])
contrast[i] = 1.
fixed_effect = _compute_fixed_effect_contrast(
[labels],
[results],
[contrast],
)
assert_almost_equal(fixed_effect.effect_size(), coef.ravel()[i])
fixed_effect = _compute_fixed_effect_contrast([labels] * 3,
[results] * 3,
[contrast] * 3)
assert_almost_equal(fixed_effect.effect_size(), coef.ravel()[i])
def test_fixed_effect_contrast():
n, p, q = 100, 80, 10
X, Y = np.random.randn(p, q), np.random.randn(p, n)
lab, res = run_glm(Y, X, 'ols')
c1, c2 = np.eye(q)[0], np.eye(q)[1]
con = _compute_fixed_effect_contrast([lab, lab], [res, res], [c1, c2])
z_vals = con.z_score()
assert_almost_equal(z_vals.mean(), 0, 0)
assert_almost_equal(z_vals.std(), 1, 0)
def test_fixed_effect_contrast():
rng = np.random.RandomState(42)
n, p, q = 100, 80, 10
X, Y = rng.standard_normal(size=(p, q)), rng.standard_normal(size=(p, n))
lab, res = run_glm(Y, X, 'ols')
c1, c2 = np.eye(q)[0], np.eye(q)[1]
con = _compute_fixed_effect_contrast([lab, lab], [res, res], [c1, c2])
z_vals = con.z_score()
assert_almost_equal(z_vals.mean(), 0, 0)
assert_almost_equal(z_vals.std(), 1, 0)
def compute_contrast(self, contrast_def, stat_type=None,
output_type='z_score'):
"""Generate different outputs corresponding to
the contrasts provided e.g. z_map, t_map, effects and variance.
In multi-session case, outputs the fixed effects map.
Parameters
----------
contrast_def : str or array of shape (n_col) or list of (string or
array of shape (n_col))
where ``n_col`` is the number of columns of the design matrix,
(one array per run). If only one array is provided when there
are several runs, it will be assumed that the same contrast is
desired for all runs. The string can be a formula compatible with
`pandas.DataFrame.eval`. Basically one can use the name of the
conditions as they appear in the design matrix of the fitted model
combined with operators +- and combined with numbers
with operators +-`*`/.
stat_type : {'t', 'F'}, optional
type of the contrast
output_type : str, optional
Type of the output map. Can be 'z_score', 'stat', 'p_value',
'effect_size', 'effect_variance' or 'all'
Returns
-------
output : Nifti1Image or dict
The desired output image(s). If ``output_type == 'all'``, then
the output is a dictionary of images, keyed by the type of image.
"""
if self.labels_ is None or self.results_ is None:
raise ValueError('The model has not been fit yet')
if isinstance(contrast_def, (np.ndarray, str)):
con_vals = [contrast_def]
elif isinstance(contrast_def, (list, tuple)):
con_vals = contrast_def
else:
raise ValueError('contrast_def must be an array or str or list of'
' (array or str)')
# Translate formulas to vectors
for cidx, (con, design_mat) in enumerate(zip(con_vals,
self.design_matrices_)
):
design_columns = design_mat.columns.tolist()
if isinstance(con, str):
con_vals[cidx] = expression_to_contrast_vector(
con, design_columns)
n_runs = len(self.labels_)
if len(con_vals) != n_runs:
warn('One contrast given, assuming it for all %d runs' % n_runs)
con_vals = con_vals * n_runs
valid_types = ['z_score', 'stat', 'p_value', 'effect_size',
'effect_variance']
valid_types.append('all') # ensuring 'all' is the final entry.
if output_type not in valid_types:
raise ValueError(
'output_type must be one of {}'.format(valid_types))
contrast = _compute_fixed_effect_contrast(self.labels_, self.results_,
con_vals, stat_type)
output_types = (valid_types[:-1]
if output_type == 'all' else [output_type])
outputs = {}
for output_type_ in output_types:
estimate_ = getattr(contrast, output_type_)()
# Prepare the returned images
output = self.masker_.inverse_transform(estimate_)
contrast_name = str(con_vals)
output.header['descrip'] = (
'%s of contrast %s' % (output_type_, contrast_name))
outputs[output_type_] = output
return outputs if output_type == 'all' else output