def test_components_img():
shape = (6, 8, 10, 5)
affine = np.eye(4)
rng = np.random.RandomState(0)
# Create a "multi-subject" dataset
data = []
for i in range(8):
this_data = rng.normal(size=shape)
# Create fake activation to get non empty mask
this_data[2:4, 2:4, 2:4, :] += 10
data.append(nibabel.Nifti1Image(this_data, affine))
mask_img = nibabel.Nifti1Image(np.ones(shape[:3], dtype=np.int8), affine)
n_components = 3
multi_pca = MultiPCA(mask=mask_img,
n_components=n_components,
random_state=0)
# fit to the data and test for components images
multi_pca.fit(data)
components_img = multi_pca.components_img_
assert_true(isinstance(components_img, nibabel.Nifti1Image))
check_shape = data[0].shape[:3] + (n_components, )
assert_equal(components_img.shape, check_shape)
assert_equal(len(components_img.shape), 4)
def subject_pca(subject_dir, n_components=512, smoothing_fwhm=6,
mask_img='gm_mask.nii'):
files = sorted(glob.glob(os.path.join(
subject_dir, 'rfMRI_REST?_??/rfMRI_REST?_??.nii.gz')))
confounds = get_confounds(subject_dir, files, mask_img=mask_img)
multi_pca = MultiPCA(mask=mask_img, smoothing_fwhm=smoothing_fwhm,
t_r=.7, low_pass=.1,
n_components=n_components, do_cca=False,
n_jobs=N_JOBS, verbose=12)
multi_pca.fit(files, confounds=confounds)
return multi_pca.components_ * multi_pca.variance_[:, np.newaxis]
def test_with_globbing_patterns_with_single_image():
# With single image
data_4d = np.zeros((40, 40, 40, 3))
data_4d[20, 20, 20] = 1
img_4d = nibabel.Nifti1Image(data_4d, affine=np.eye(4))
multi_pca = MultiPCA(n_components=3)
with write_tmp_imgs(img_4d, create_files=True, use_wildcards=True) as img:
input_image = _tmp_dir() + img
multi_pca.fit(input_image)
components_img = multi_pca.components_img_
assert_true(isinstance(components_img, nibabel.Nifti1Image))
# n_components = 3
check_shape = img_4d.shape[:3] + (3, )
assert_equal(components_img.shape, check_shape)
assert_equal(len(components_img.shape), 4)
def test_with_globbing_patterns_with_single_image():
# With single image
data_4d = np.zeros((40, 40, 40, 3))
data_4d[20, 20, 20] = 1
img_4d = nibabel.Nifti1Image(data_4d, affine=np.eye(4))
multi_pca = MultiPCA(n_components=3)
with write_tmp_imgs(img_4d, create_files=True, use_wildcards=True) as img:
input_image = _tmp_dir() + img
multi_pca.fit(input_image)
components_img = multi_pca.components_img_
assert_true(isinstance(components_img, nibabel.Nifti1Image))
# n_components = 3
check_shape = img_4d.shape[:3] + (3,)
assert_equal(components_img.shape, check_shape)
assert_equal(len(components_img.shape), 4)
def __init__(self,
method,
n_parcels=50,
random_state=0,
mask=None,
smoothing_fwhm=4.,
standardize=False,
detrend=False,
low_pass=None,
high_pass=None,
t_r=None,
target_affine=None,
target_shape=None,
mask_strategy='epi',
mask_args=None,
memory=Memory(cachedir=None),
memory_level=0,
n_jobs=1,
verbose=1):
self.method = method
self.n_parcels = n_parcels
MultiPCA.__init__(self,
n_components=200,
random_state=random_state,
mask=mask,
memory=memory,
smoothing_fwhm=smoothing_fwhm,
standardize=standardize,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
target_affine=target_affine,
target_shape=target_shape,
mask_strategy=mask_strategy,
mask_args=mask_args,
memory_level=memory_level,
n_jobs=n_jobs,
verbose=verbose)
def __init__(self, algorithm, n_parcels=50, n_components=100,
linkage='ward', init='k-means++', connectivity=None,
random_state=0, mask=None, target_affine=None,
target_shape=None,
low_pass=None, high_pass=None, t_r=None,
smoothing_fwhm=None, standardize=False,
detrend=False, memory=Memory(cachedir=None),
memory_level=0, n_jobs=1, verbose=1,
shelve=False):
self.algorithm = algorithm
self.n_parcels = n_parcels
self.linkage = linkage
self.init = init
self.connectivity = connectivity
self.shelve = shelve
MultiPCA.__init__(self, n_components=n_components,
random_state=random_state,
mask=mask, memory=memory,
memory_level=memory_level,
n_jobs=n_jobs,
verbose=verbose)
def fit(self, imgs, y=None, confounds=None):
""" Fit the clustering technique to fmri images
Parameters
----------
X : List of Niimg-like objects
Data from which parcellations will be returned.
"""
if self.algorithm is None:
raise ValueError("Parcellation algorithm must be specified in "
"['minibatchkmeans', 'featureagglomeration'].")
valid_algorithms = self.VALID_ALGORITHMS
if self.algorithm not in valid_algorithms:
raise ValueError("Invalid algorithm={0} is provided. Please one "
"among them {1}".format(self.algorithm,
valid_algorithms))
if not hasattr(imgs, '__iter__'):
imgs = [imgs]
if isinstance(self.mask, (NiftiMasker, MultiNiftiMasker)):
if self.memory is None and self.mask.memory is not None:
self.memory = self.mask.memory
if self.memory_level is None and \
self.mask.memory_level is not None:
self.memory_level = self.mask.memory_level
if self.n_jobs is None and self.mask.n_jobs is not None:
self.n_jobs = self.mask.n_jobs
MultiPCA.fit(self, imgs)
if self.verbose:
print("[Parcellations] Learning the data")
self._fit_method(self.components_)
return self
def test_components_img():
shape = (6, 8, 10, 5)
affine = np.eye(4)
rng = np.random.RandomState(0)
# Create a "multi-subject" dataset
data = []
for i in range(8):
this_data = rng.normal(size=shape)
# Create fake activation to get non empty mask
this_data[2:4, 2:4, 2:4, :] += 10
data.append(nibabel.Nifti1Image(this_data, affine))
mask_img = nibabel.Nifti1Image(np.ones(shape[:3], dtype=np.int8), affine)
n_components = 3
multi_pca = MultiPCA(mask=mask_img, n_components=n_components,
random_state=0)
# fit to the data and test for components images
multi_pca.fit(data)
components_img = multi_pca.components_img_
assert_true(isinstance(components_img, nibabel.Nifti1Image))
check_shape = data[0].shape[:3] + (n_components,)
assert_equal(components_img.shape, check_shape)
assert_equal(len(components_img.shape), 4)
def _raw_fit(self, data):
group = self.group
sub_num = self.sub_num
if group:
data = MultiPCA._raw_fit(self, data).T
else:
data = data.reshape((3, self.n_components, -1))
data = data[sub_num - 1]
# plt.plot(data[:, :3])
# plt.tight_layout()
# plt.show()
self.hvmf_fit(data.T)
return self
def test_multi_pca():
# Smoke test the MultiPCA
# XXX: this is mostly a smoke test
shape = (6, 8, 10, 5)
affine = np.eye(4)
rng = np.random.RandomState(0)
# Create a "multi-subject" dataset
data = []
for i in range(8):
this_data = rng.normal(size=shape)
# Create fake activation to get non empty mask
this_data[2:4, 2:4, 2:4, :] += 10
data.append(nibabel.Nifti1Image(this_data, affine))
mask_img = nibabel.Nifti1Image(np.ones(shape[:3], dtype=np.int8), affine)
multi_pca = MultiPCA(mask=mask_img, n_components=3)
# Test that the components are the same if we put twice the same data
components1 = multi_pca.fit(data).components_
components2 = multi_pca.fit(2 * data).components_
np.testing.assert_array_almost_equal(components1, components2)
# Smoke test fit with 'confounds' argument
confounds = [np.arange(10).reshape(5, 2)] * 8
multi_pca.fit(data, confounds=confounds)
# Smoke test that multi_pca also works with single subject data
multi_pca.fit(data[0])
# Check that asking for too little components raises a ValueError
multi_pca = MultiPCA()
nose.tools.assert_raises(ValueError, multi_pca.fit, data[:2])
# Smoke test the use of a masker and without CCA
multi_pca = MultiPCA(mask=MultiNiftiMasker(mask_args=dict(opening=0)),
do_cca=False, n_components=3)
multi_pca.fit(data[:2])
# Smoke test the transform and inverse_transform
multi_pca.inverse_transform(multi_pca.transform(data[-2:]))
def test_multi_pca_score():
shape = (6, 8, 10, 5)
affine = np.eye(4)
rng = np.random.RandomState(0)
# Create a "multi-subject" dataset
imgs = []
for i in range(8):
this_img = rng.normal(size=shape)
imgs.append(nibabel.Nifti1Image(this_img, affine))
mask_img = nibabel.Nifti1Image(np.ones(shape[:3], dtype=np.int8), affine)
# Assert that score is between zero and one
multi_pca = MultiPCA(mask=mask_img,
random_state=0,
memory_level=0,
n_components=3)
multi_pca.fit(imgs)
s = multi_pca.score(imgs)
assert_true(np.all(s <= 1))
assert_true(np.all(0 <= s))
# Assert that score does not fail with single subject data
multi_pca = MultiPCA(mask=mask_img,
random_state=0,
memory_level=0,
n_components=3)
multi_pca.fit(imgs[0])
s = multi_pca.score(imgs[0])
assert_true(isinstance(s, float))
assert (0. <= s <= 1.)
# Assert that score is one for n_components == n_sample
# in single subject configuration
multi_pca = MultiPCA(mask=mask_img,
random_state=0,
memory_level=0,
n_components=5)
multi_pca.fit(imgs[0])
s = multi_pca.score(imgs[0])
assert_almost_equal(s, 1., 1)
# Per component score
multi_pca = MultiPCA(mask=mask_img,
random_state=0,
memory_level=0,
n_components=5)
multi_pca.fit(imgs[0])
masker = NiftiMasker(mask_img).fit()
s = multi_pca._raw_score(masker.transform(imgs[0]), per_component=True)
assert_equal(s.shape, (5, ))
assert_true(np.all(s <= 1))
assert_true(np.all(0 <= s))
def test_multi_pca():
# Smoke test the MultiPCA
# XXX: this is mostly a smoke test
shape = (6, 8, 10, 5)
affine = np.eye(4)
rng = np.random.RandomState(0)
# Create a "multi-subject" dataset
data = []
for i in range(8):
this_data = rng.normal(size=shape)
# Create fake activation to get non empty mask
this_data[2:4, 2:4, 2:4, :] += 10
data.append(nibabel.Nifti1Image(this_data, affine))
mask_img = nibabel.Nifti1Image(np.ones(shape[:3], dtype=np.int8), affine)
multi_pca = MultiPCA(mask=mask_img, n_components=3, random_state=0)
# fit to the data and test for masker attributes
multi_pca.fit(data)
assert_true(multi_pca.mask_img_ == mask_img)
assert_true(multi_pca.mask_img_ == multi_pca.masker_.mask_img_)
# Test that the components are the same if we put twice the same data, and
# that fit output is deterministic
components1 = multi_pca.components_
components2 = multi_pca.fit(data).components_
components3 = multi_pca.fit(2 * data).components_
np.testing.assert_array_equal(components1, components2)
np.testing.assert_array_almost_equal(components1, components3)
# Smoke test fit with 'confounds' argument
confounds = [np.arange(10).reshape(5, 2)] * 8
multi_pca.fit(data, confounds=confounds)
# Smoke test that multi_pca also works with single subject data
multi_pca.fit(data[0])
# Check that asking for too little components raises a ValueError
multi_pca = MultiPCA()
assert_raises(ValueError, multi_pca.fit, data[:2])
# Test fit on data with the use of a masker
masker = MultiNiftiMasker()
multi_pca = MultiPCA(mask=masker, n_components=3)
multi_pca.fit(data)
assert_true(multi_pca.mask_img_ == multi_pca.masker_.mask_img_)
# Smoke test the use of a masker and without CCA
multi_pca = MultiPCA(mask=MultiNiftiMasker(mask_args=dict(opening=0)),
do_cca=False,
n_components=3)
multi_pca.fit(data[:2])
# Smoke test the transform and inverse_transform
multi_pca.inverse_transform(multi_pca.transform(data[-2:]))
# Smoke test to fit with no img
assert_raises(TypeError, multi_pca.fit)
multi_pca = MultiPCA(mask=mask_img, n_components=3)
assert_raises_regex(
ValueError, "Object has no components_ attribute. "
"This is probably because fit has not been called",
multi_pca.transform, data)
# Test if raises an error when empty list of provided.
assert_raises_regex(
ValueError, 'Need one or more Niimg-like objects as input, '
'an empty list was given.', multi_pca.fit, [])
# Test passing masker arguments to estimator
multi_pca = MultiPCA(target_affine=affine,
target_shape=shape[:3],
n_components=3,
mask_strategy='background')
multi_pca.fit(data)
def test_multi_pca_score():
shape = (6, 8, 10, 5)
affine = np.eye(4)
rng = np.random.RandomState(0)
# Create a "multi-subject" dataset
imgs = []
for i in range(8):
this_img = rng.normal(size=shape)
imgs.append(nibabel.Nifti1Image(this_img, affine))
mask_img = nibabel.Nifti1Image(np.ones(shape[:3], dtype=np.int8), affine)
# Assert that score is between zero and one
multi_pca = MultiPCA(mask=mask_img, random_state=0, memory_level=0,
n_components=3)
multi_pca.fit(imgs)
s = multi_pca.score(imgs)
assert_true(np.all(s <= 1))
assert_true(np.all(0 <= s))
# Assert that score does not fail with single subject data
multi_pca = MultiPCA(mask=mask_img, random_state=0, memory_level=0,
n_components=3)
multi_pca.fit(imgs[0])
s = multi_pca.score(imgs[0])
assert_true(isinstance(s, float))
assert(0. <= s <= 1.)
# Assert that score is one for n_components == n_sample
# in single subject configuration
multi_pca = MultiPCA(mask=mask_img, random_state=0, memory_level=0,
n_components=5)
multi_pca.fit(imgs[0])
s = multi_pca.score(imgs[0])
assert_almost_equal(s, 1., 1)
# Per component score
multi_pca = MultiPCA(mask=mask_img, random_state=0, memory_level=0,
n_components=5)
multi_pca.fit(imgs[0])
masker = NiftiMasker(mask_img).fit()
s = multi_pca._raw_score(masker.transform(imgs[0]), per_component=True)
assert_equal(s.shape, (5,))
assert_true(np.all(s <= 1))
assert_true(np.all(0 <= s))
def _raw_fit(self, data):
""" Fits the parcellation method on this reduced data.
Data are coming from a base decomposition estimator which computes
the mask and reduces the dimensionality of images using
randomized_svd.
Parameters
----------
data : ndarray
Shape (n_samples, n_features)
Returns
-------
labels_ : numpy.ndarray
Labels to each cluster in the brain.
connectivity_ : numpy.ndarray
voxel-to-voxel connectivity matrix computed from a mask.
Note that, this attribute is returned only for selected methods
such as 'ward', 'complete', 'average'.
"""
valid_methods = self.VALID_METHODS
if self.method is None:
raise ValueError("Parcellation method is specified as None. "
"Please select one of the method in "
"{0}".format(valid_methods))
if self.method is not None and self.method not in valid_methods:
raise ValueError("The method you have selected is not implemented "
"'{0}'. Valid methods are in {1}".format(
self.method, valid_methods))
# we delay importing Ward or AgglomerativeClustering and same
# time import plotting module before that.
# Because sklearn.cluster imports scipy hierarchy and hierarchy imports
# matplotlib. So, we force import matplotlib first using our
# plotting to avoid backend display error with matplotlib
# happening in Travis
try:
from nilearn import plotting
except:
pass
components = MultiPCA._raw_fit(self, data)
mask_img_ = self.masker_.mask_img_
if self.verbose:
print("[{0}] computing {1}".format(self.__class__.__name__,
self.method))
if self.method == 'kmeans':
from sklearn.cluster import MiniBatchKMeans
kmeans = MiniBatchKMeans(n_clusters=self.n_parcels,
init='k-means++',
random_state=self.random_state,
verbose=max(0, self.verbose - 1))
labels = self._cache(_estimator_fit,
func_memory_level=1)(components.T, kmeans)
else:
mask_ = _safe_get_data(mask_img_).astype(np.bool)
shape = mask_.shape
connectivity = image.grid_to_graph(n_x=shape[0],
n_y=shape[1],
n_z=shape[2],
mask=mask_)
# from data.new_agglo import NewAgglomerativeClustering as AgglomerativeClustering
from sklearn.cluster import AgglomerativeClustering
agglomerative = AgglomerativeClustering(n_clusters=self.n_parcels,
connectivity=connectivity,
linkage=self.method,
memory=self.memory,
compute_full_tree=True)
labels = self._cache(_estimator_fit,
func_memory_level=1)(components.T,
agglomerative)
self.agglomerative = agglomerative
self.connectivity_ = connectivity
# Avoid 0 label
labels = labels + 1
self.labels_img_ = self.masker_.inverse_transform(labels)
return self
# Avoid 0 label
labels = labels + 1
self.labels_img_ = self.masker_.inverse_transform(labels)
return self
def test_multi_pca():
# Smoke test the MultiPCA
# XXX: this is mostly a smoke test
shape = (6, 8, 10, 5)
affine = np.eye(4)
rng = np.random.RandomState(0)
# Create a "multi-subject" dataset
data = []
for i in range(8):
this_data = rng.normal(size=shape)
# Create fake activation to get non empty mask
this_data[2:4, 2:4, 2:4, :] += 10
data.append(nibabel.Nifti1Image(this_data, affine))
mask_img = nibabel.Nifti1Image(np.ones(shape[:3], dtype=np.int8), affine)
multi_pca = MultiPCA(mask=mask_img, n_components=3,
random_state=0)
# fit to the data and test for masker attributes
multi_pca.fit(data)
assert_true(multi_pca.mask_img_ == mask_img)
assert_true(multi_pca.mask_img_ == multi_pca.masker_.mask_img_)
# Test that the components are the same if we put twice the same data, and
# that fit output is deterministic
components1 = multi_pca.components_
components2 = multi_pca.fit(data).components_
components3 = multi_pca.fit(2 * data).components_
np.testing.assert_array_equal(components1, components2)
np.testing.assert_array_almost_equal(components1, components3)
# Smoke test fit with 'confounds' argument
confounds = [np.arange(10).reshape(5, 2)] * 8
multi_pca.fit(data, confounds=confounds)
# Smoke test that multi_pca also works with single subject data
multi_pca.fit(data[0])
# Check that asking for too little components raises a ValueError
multi_pca = MultiPCA()
assert_raises(ValueError, multi_pca.fit, data[:2])
# Test fit on data with the use of a masker
masker = MultiNiftiMasker()
multi_pca = MultiPCA(mask=masker, n_components=3)
multi_pca.fit(data)
assert_true(multi_pca.mask_img_ == multi_pca.masker_.mask_img_)
# Smoke test the use of a masker and without CCA
multi_pca = MultiPCA(mask=MultiNiftiMasker(mask_args=dict(opening=0)),
do_cca=False, n_components=3)
multi_pca.fit(data[:2])
# Smoke test the transform and inverse_transform
multi_pca.inverse_transform(multi_pca.transform(data[-2:]))
# Smoke test to fit with no img
assert_raises(TypeError, multi_pca.fit)
multi_pca = MultiPCA(mask=mask_img, n_components=3)
assert_raises_regex(ValueError,
"Object has no components_ attribute. "
"This is probably because fit has not been called",
multi_pca.transform, data)
# Test if raises an error when empty list of provided.
assert_raises_regex(ValueError,
'Need one or more Niimg-like objects as input, '
'an empty list was given.',
multi_pca.fit, [])
# Test passing masker arguments to estimator
multi_pca = MultiPCA(target_affine=affine,
target_shape=shape[:3],
n_components=3,
mask_strategy='background')
multi_pca.fit(data)