def test_k_and_radius_neighbors_duplicates():
# Test behavior of kneighbors when duplicates are present in query
for algorithm in ALGORITHMS:
nn = neighbors.NearestNeighbors(n_neighbors=1, algorithm=algorithm)
nn.fit([[0], [1]])
# Do not do anything special to duplicates.
kng = nn.kneighbors_graph([[0], [1]], mode='distance')
assert_array_equal(kng.A, np.array([[0., 0.], [0., 0.]]))
assert_array_equal(kng.data, [0., 0.])
assert_array_equal(kng.indices, [0, 1])
dist, ind = nn.radius_neighbors([[0], [1]], radius=1.5)
check_object_arrays(dist, [[0, 1], [1, 0]])
check_object_arrays(ind, [[0, 1], [0, 1]])
rng = nn.radius_neighbors_graph([[0], [1]], radius=1.5)
assert_array_equal(rng.A, np.ones((2, 2)))
rng = nn.radius_neighbors_graph([[0], [1]],
radius=1.5,
mode='distance')
assert_array_equal(rng.A, [[0, 1], [1, 0]])
assert_array_equal(rng.indices, [0, 1, 0, 1])
assert_array_equal(rng.data, [0, 1, 1, 0])
# Mask the first duplicates when n_duplicates > n_neighbors.
X = np.ones((3, 1))
nn = neighbors.NearestNeighbors(n_neighbors=1)
nn.fit(X)
dist, ind = nn.kneighbors()
assert_array_equal(dist, np.zeros((3, 1)))
assert_array_equal(ind, [[1], [0], [1]])
# Test that zeros are explicitly marked in kneighbors_graph.
kng = nn.kneighbors_graph(mode='distance')
assert_array_equal(kng.A, np.zeros((3, 3)))
assert_array_equal(kng.data, np.zeros(3))
assert_array_equal(kng.indices, [1., 0., 1.])
assert_array_equal(
nn.kneighbors_graph().A,
np.array([[0., 1., 0.], [1., 0., 0.], [0., 1., 0.]]))
def test_callable_metric():
def custom_metric(x1, x2):
return np.sqrt(np.sum(x1**2 + x2**2))
X = np.random.RandomState(42).rand(20, 2)
nbrs1 = neighbors.NearestNeighbors(3,
algorithm='auto',
metric=custom_metric)
nbrs2 = neighbors.NearestNeighbors(3,
algorithm='brute',
metric=custom_metric)
nbrs1.fit(X)
nbrs2.fit(X)
dist1, ind1 = nbrs1.kneighbors(X)
dist2, ind2 = nbrs2.kneighbors(X)
assert_array_almost_equal(dist1, dist2)
def __init__(self, dataset, soft_encoding=True):
self.dataset = dataset
self.kernels = bins_centers
self.L_normalize = 100
self.kernel_normalize = np.max(np.abs(self.kernels))
self.num_bins = len(self.kernels)
self.neighborhood = knn.NearestNeighbors(n_neighbors=5).fit(
self.kernels / self.kernel_normalize)
self.soft_encoding = soft_encoding
self.device = torch.device('cuda:0')
def nearest_neighbors(src, dst):
model = neighbors.NearestNeighbors(n_neighbors=1)
# feed dst points to kd-tree
model.fit(dst)
# search nearest points of src in dst
distances, indices = model.kneighbors(src)
return distances, indices
def apply_mask_and_get_affinity(seeds,
niimg,
radius,
allow_overlap,
n_jobs=1,
mask_img=None):
import time
start = time.time()
seeds = list(seeds)
affine = niimg.affine
# Compute world coordinates of all in-mask voxels.
mask_img = check_niimg_3d(mask_img)
mask_img = image.resample_img(mask_img,
target_affine=affine,
target_shape=niimg.shape[:3],
interpolation='nearest')
mask, _ = masking._load_mask_img(mask_img)
mask_coords = list(zip(*np.where(mask != 0)))
X = masking._apply_mask_fmri(niimg, mask_img)
# For each seed, get coordinates of nearest voxel
nearests = joblib.Parallel(n_jobs=n_jobs)(
joblib.delayed(seed_nearest)(seed_chunk, affine, mask_coords)
for thread_id, seed_chunk in enumerate(np.array_split(seeds, n_jobs)))
nearests = [i for j in nearests for i in j]
mask_coords = np.asarray(list(zip(*mask_coords)))
mask_coords = coord_transform(mask_coords[0], mask_coords[1],
mask_coords[2], affine)
mask_coords = np.asarray(mask_coords).T
clf = neighbors.NearestNeighbors(radius=radius)
A = clf.fit(mask_coords).radius_neighbors_graph(seeds)
A = A.tolil()
for i, nearest in enumerate(nearests):
if nearest is None:
continue
A[i, nearest] = True
# Include the voxel containing the seed itself if not masked
mask_coords = mask_coords.astype(int).tolist()
for i, seed in enumerate(seeds):
try:
A[i, mask_coords.index(seed)] = True
except ValueError:
# seed is not in the mask
pass
if not allow_overlap:
if np.any(A.sum(axis=0) >= 2):
raise ValueError('Overlap detected between spheres')
return X, A
def get_transition_matrix(self, k=10, ann=False):
"""
implementation of transition matrix.
:param k: number of each node's neighbors.
"""
# kNN
if ann == False:
nbrs = neighbors.NearestNeighbors(n_neighbors=k,
metric='euclidean',
n_jobs=-1).fit(self.data)
distances, indices = nbrs.kneighbors(self.data)
else: # need to imporve
lshf = neighbors.LSHForest(n_neighbors=3 * k).fit(self.data)
distances, indices = lshf.kneighbors(self.data, n_neighbors=k)
N = self.shape[0]
sqdistances = np.square(distances)
sigmas = distances[:, -1]
self.sigmas = sigmas
# kernel matrix
sigs_mul = np.multiply.outer(sigmas, sigmas)
kernel_matrix = np.zeros((N, k))
for i in range(N):
kernel_matrix[i, :] = np.exp(
-np.divide(sqdistances[i, :], 2 *
(sigs_mul[i, indices[i, :]])))
weights = kernel_matrix
indptr = range(0, (N + 1) * k, k)
weight_matrix = sparse.csr_matrix(
(weights.flatten(), indices.flatten(), indptr),
shape=(N, N)).toarray()
# symmetric
for i, col in enumerate(indices):
for j in col:
if i not in set(indices[j]):
weight_matrix[j, i] = weight_matrix[i, j]
weight_sum = np.power(weight_matrix.sum(axis=0)[:, None],
-1 / 2).flatten()
weight_sum = np.diag(weight_sum)
weight_matrix = weight_sum @ weight_matrix @ weight_sum
M = np.divide(weight_matrix, weight_matrix.sum(axis=1)[:, None])
mevals, mevecs = sp.linalg.eigh(M)
self.M = M
self.mevals = mevals
self.mevecs = mevecs
self.indices = indices
return M
def test_valid_brute_metric_for_auto_algorithm():
X = rng.rand(12, 12)
Xcsr = csr_matrix(X)
# check that there is a metric that is valid for brute
# but not ball_tree (so we actually test something)
assert_in("cosine", VALID_METRICS['brute'])
assert_false("cosine" in VALID_METRICS['ball_tree'])
# Metric which don't required any additional parameter
require_params = ['mahalanobis', 'wminkowski', 'seuclidean']
for metric in VALID_METRICS['brute']:
if metric != 'precomputed' and metric not in require_params:
nn = neighbors.NearestNeighbors(n_neighbors=3, algorithm='auto',
metric=metric).fit(X)
nn.kneighbors(X)
elif metric == 'precomputed':
X_precomputed = rng.random_sample((10, 4))
Y_precomputed = rng.random_sample((3, 4))
DXX = metrics.pairwise_distances(X_precomputed, metric='euclidean')
DYX = metrics.pairwise_distances(Y_precomputed, X_precomputed,
metric='euclidean')
nb_p = neighbors.NearestNeighbors(n_neighbors=3)
nb_p.fit(DXX)
nb_p.kneighbors(DYX)
for metric in VALID_METRICS_SPARSE['brute']:
if metric != 'precomputed' and metric not in require_params:
nn = neighbors.NearestNeighbors(n_neighbors=3, algorithm='auto',
metric=metric).fit(Xcsr)
nn.kneighbors(Xcsr)
# Metric with parameter
VI = np.dot(X, X.T)
list_metrics = [('seuclidean', dict(V=rng.rand(12))),
('wminkowski', dict(w=rng.rand(12))),
('mahalanobis', dict(VI=VI))]
for metric, params in list_metrics:
nn = neighbors.NearestNeighbors(n_neighbors=3, algorithm='auto',
metric=metric,
metric_params=params).fit(X)
nn.kneighbors(X)
def test_non_euclidean_kneighbors():
rng = np.random.RandomState(0)
X = rng.rand(5, 5)
# Find a reasonable radius.
dist_array = pairwise_distances(X).flatten()
np.sort(dist_array)
radius = dist_array[15]
# Test kneighbors_graph
for metric in ['manhattan', 'chebyshev']:
nbrs_graph = neighbors.kneighbors_graph(X,
3,
metric=metric,
mode='connectivity',
include_self=True).toarray()
nbrs1 = neighbors.NearestNeighbors(3, metric=metric).fit(X)
assert_array_equal(nbrs_graph, nbrs1.kneighbors_graph(X).toarray())
# Test radiusneighbors_graph
for metric in ['manhattan', 'chebyshev']:
nbrs_graph = neighbors.radius_neighbors_graph(
X, radius, metric=metric, mode='connectivity',
include_self=True).toarray()
nbrs1 = neighbors.NearestNeighbors(metric=metric, radius=radius).fit(X)
assert_array_equal(nbrs_graph, nbrs1.radius_neighbors_graph(X).A)
# Raise error when wrong parameters are supplied,
X_nbrs = neighbors.NearestNeighbors(3, metric='manhattan')
X_nbrs.fit(X)
assert_raises(ValueError,
neighbors.kneighbors_graph,
X_nbrs,
3,
metric='euclidean')
X_nbrs = neighbors.NearestNeighbors(radius=radius, metric='manhattan')
X_nbrs.fit(X)
assert_raises(ValueError,
neighbors.radius_neighbors_graph,
X_nbrs,
radius,
metric='euclidean')
def median_kneighbour_distance(X, k=5):
"""Calculate the median distance between a set of random datapoints and
their kth nearest neighbours. This is a heuristic for setting the
kernel length scale."""
N_all = X.shape[0]
N_subset = min(N_all, 2000)
sample_idx_train = np.random.permutation(N_all)[:N_subset]
nn = neighbors.NearestNeighbors(k)
nn.fit(X[sample_idx_train, :])
d, idx = nn.kneighbors(X[sample_idx_train, :])
return np.median(d[:, -1])
def __init__(self,NN,sigma,km_filepath='',cc=-1):
if(check_value(cc,-1)):
self.cc = np.load(km_filepath)
else:
self.cc = cc
self.K = self.cc.shape[0]
self.NN = int(NN)
self.sigma = sigma
self.nbrs = nn.NearestNeighbors(n_neighbors=NN, algorithm='ball_tree').fit(self.cc)
self.alreadyUsed = False
def finalize(self):
if self.nn is None:
if not self.observations:
raise Exception('no observations')
if not self.observations[0][0]:
# 0-length vectors are not allowed
xs = [[0] for _ in self.observations]
else:
xs = [x for (x, _) in self.observations]
self.nn = neighbors.NearestNeighbors()
self.nn.fit(xs)
def __init__(self, split):
self.split = split
self.folder = 'data/{}'.format(split)
self.files = [f for f in os.listdir(self.folder) if f.lower().endswith('.jpeg')]
# Load the array of quantized ab value
q_ab = np.load("data/pts_in_hull.npy")
self.nb_q = q_ab.shape[0]
# Fit a NN to q_ab
self.nn_finder = nn.NearestNeighbors(n_neighbors=nb_neighbors, algorithm='ball_tree').fit(q_ab)
def buildTree(self):
arr = np.array(self.values)
if self.se2:
arr = np.reshape(arr, [-1, 6])
else:
arr = np.reshape(arr, [-1, 7])
self.nn = sk.NearestNeighbors(n_jobs=-1,
algorithm='brute',
leaf_size=100,
metric=self.metric)
self.nn.fit(arr)
def knn_diversity_stats(training_set, generated_imgs, k=3):
"""
Find the k=3 nearest neighnors of an image in the training set and
returns the average distance
:param array training_set: the training set of images according to which we will find the nearest neighbours
:param array generated_imgs: the images whose nearest neighbours we wish to find
"""
knn = neighbors.NearestNeighbors(n_neighbors=k)
knn.fit(training_set, y=np.zeros(shape=(len(training_set), )))
dists, idxs = knn.kneighbors(generated_imgs)
return np.average(dists)
def __k_neighbor(k_n, algm, feature):
"""
k neighbor will compute k-Nearest Neighbors sklearn algorithm
:param k_n: int, integer number for k nearest neighbors groups; '2' set as default
:param algm: str, string name for k-NN's algorithm choice; 'auto' set as default
:param feature: np.array, np.array object with column features
:return: list, python list with numpy array object for each neighbor
"""
n_neighbor = neighbors.NearestNeighbors(n_neighbors=k_n, algorithm=algm)
model_fit = n_neighbor.fit(feature)
return model_fit.kneighbors(feature)
def quantize(inputs, to_points, to_points_one_hot_encoded):
neighbors = nn.NearestNeighbors(n_neighbors=10,
algorithm='auto').fit(to_points)
dists, indices = neighbors.kneighbors(inputs)
end_points = np.zeros((inputs.shape[0], to_points.shape[0]))
sigma = 5.0
wts = np.exp(-dists**2 / (2 * sigma**2))
wts = wts / np.sum(wts, axis=1)[:, np.newaxis]
end_points[np.arange(0, inputs.shape[0], dtype='int')[:, np.newaxis],
indices] = wts
return end_points
def knnThing(matrix, labels):
animals = []
print "\033[1mYou are going to pick 5 animals that are similar to your chosen animal. Pick different animals each time and do not pick your chosen animal itself.\033[0m\n"
inp = -1
while len(animals) < 5:
while inp < 0 or inp >= 50 or inp in animals:
input = raw_input(
"\nGive the index of one of the following animals:\n" +
printAnimalOptions(labels, animals)) + "\n"
try:
inp = int(input)
if inp < 0 or inp >= 50:
print "Please give a value between 0 and 49."
elif inp in animals:
print labels[inp] + " has already been selected!"
except:
print "Please enter only an integer."
print "Ok, " + labels[inp] + " saved."
animals += [inp]
inp = -1
counts = dict()
animals.sort(reverse=True)
animalRows = []
for animal in animals:
animalRows += [[matrix[animal]]]
matrix = np.delete(matrix, animals, axis=0)
labels = np.delete(labels, animals, axis=0)
friendos = neighbors.NearestNeighbors(n_neighbors=5)
friendos.fit(matrix)
for animalRow in animalRows:
fiveClosest = friendos.kneighbors(animalRow, return_distance=False)[0]
for closeAnimal in fiveClosest:
if closeAnimal not in counts:
counts[closeAnimal] = 1
else:
counts[closeAnimal] += 1
maxInd = max(counts, key=counts.get)
print "We predict your animal was " + labels[maxInd] + "."
return
def split_with_wasserstein(texts, test_set_size,
no_of_trials, min_df,
leaf_size):
"""Finds test sets by maximizing Wasserstein distances among the given texts.
This is separating the given texts into training/dev and test sets based on an
approximate Wasserstein method. First all texts are indexed in a nearest
neighbors structure. Then a new test centroid is sampled randomly, from which
the nearest neighbors in Wasserstein space are extracted. Those constitute
the new test set.
Similarity is computed based on document-term counts.
Args:
texts: Texts to split into training/dev and test sets.
test_set_size: Number of elements the new test set should contain.
no_of_trials: Number of test sets requested.
min_df: Mainly for speed-up and memory efficiency. All tokens must occur at
least this many times to be considered in the Wasserstein computation.
leaf_size: Leaf size parameter of the nearest neighbor search. Set high
values for slower, but less memory-heavy computation.
Returns:
Returns a List of test set indices, one for each trial. The indices
correspond to the items in `texts` that should be part of the test set.
"""
vectorizer = feature_extraction.text.CountVectorizer(
dtype=np.int8, min_df=min_df)
logging.info('Creating count vectors.')
text_counts = vectorizer.fit_transform(texts)
text_counts = text_counts.todense()
logging.info('Count vector shape %s.', text_counts.shape)
logging.info('Creating tree structure.')
nn_tree = neighbors.NearestNeighbors(
n_neighbors=test_set_size,
algorithm='ball_tree',
leaf_size=leaf_size,
metric=stats.wasserstein_distance)
nn_tree.fit(text_counts)
logging.info('Sampling test sets.')
test_set_indices = []
for trial in range(no_of_trials):
logging.info('Trial set: %d.', trial)
# Sample random test centroid.
sampled_poind = np.random.randint(
text_counts.max().max() + 1, size=(1, text_counts.shape[1]))
nearest_neighbors = nn_tree.kneighbors(sampled_poind, return_distance=False)
# We queried for only one datapoint.
nearest_neighbors = nearest_neighbors[0]
logging.info(nearest_neighbors[:10])
test_set_indices.append(nearest_neighbors)
return test_set_indices
def dist(self, X, Y=None):
if Y is X or Y is None:
d = neighbors.kneighbors_graph(X,
self.k,
mode='distance',
metric=self.metric)
else:
n = neighbors.NearestNeighbors(metric=self.metric)
n.fit(Y)
d = n.kneighbors_graph(X, self.k, mode='distance')
return d.toarray() # since we cant deal with sparse so far
def fit_history(self, udf_metric, n_cases):
"""
Args:
udf_metric: user-defined metric object
n_cases: int
"""
self.neigh = neighbors.NearestNeighbors(n_neighbors=n_cases,
metric=udf_metric)
self.neigh.fit(self.normalized_history)
self.indices = self.neigh.kneighbors(self.normalized_current,
return_distance=False)[0]
def laplacian_matrix(data, k):
"""
:param data: containing data points,
:param k: the number of neighbors considered (this distance metric is cosine,
and the weights are measured by cosine)
:return:
"""
# import matlab.engine as ME
# import matlab
# engine = ME.start_matlab()
# calling from matllab
# options = dict()
# options.update({'k' : 10})
# options.update({'NeighborMode' : 'KNN'})
#
# options.update({'Metric' : 'Cosine'})
# options.update({'WeightMode' : 'Cosine'})
# options.update({'Metric': 'Euclidean'})
# options.update({'WeightMode': 'HeatKernel'})
# options.update({'t' : 1.0})
# sim = np.array(engine.lapgraph(matlab.double(data.tolist()), options))
# S = [np.sum(row) for row in sim]
#
# for i in range(len(sim)):
# sim[i] = [sim[i][j] / (S[i] * S[j]) ** 0.5 for j in range(len(sim))]
#
# L = np.identity(len(sim)) - sim
# return L
nn = neighbors.NearestNeighbors(n_neighbors=k,
algorithm='brute',
metric='cosine')
nn.fit(data)
dist, nn = nn.kneighbors(return_distance=True)
sim = np.zeros((len(data), len(data)))
for ins_index in range(len(sim)):
dist_row = dist[ins_index]
nn_row = nn[ins_index]
for dist_value, ind_index in zip(dist_row, nn_row):
sim[ins_index][ind_index] = 1.0 - dist_value
sim[ind_index][ins_index] = 1.0 - dist_value
for i in range(len(sim)):
sim[i][i] = 1.0
S = [np.sum(row) for row in sim]
for i in range(len(sim)):
sim[i] = [sim[i][j] / (S[i] * S[j])**0.5 for j in range(len(sim))]
L = np.identity(len(sim)) - sim
return L
def predict_NearestNeighbors(train_data,
train_labels,
test_data,
nb_neighbors=5):
print("Starting to compute Nearest Neighbors")
computeStart = time.time()
convert_to_minutes = False
# Initialization
neighbors_kdtree = neighbors.NearestNeighbors(n_neighbors=nb_neighbors,
algorithm='kd_tree')
# Training
print("Nearest Neighbors : starting training")
neighbors_kdtree.fit(train_data, train_labels)
# Predictions on test_data
print("Nearest Neighbors : starting predictions")
distances, indices = neighbors_kdtree.kneighbors(test_data)
predicted_labels = np.ndarray(shape=(len(test_data)))
for i in range(len(test_data)):
if nb_neighbors == 1:
predicted_labels[i] = indices[i]
else:
mean_distances = {}
for nb in range(nb_neighbors):
actual_label = train_labels[indices[i][nb]]
actual_distance = distances[i][nb]
if actual_label not in mean_distances:
mean_distances[actual_label] = []
mean_distances[actual_label].append(actual_distance)
md_keys = list(mean_distances.keys())
min_label = md_keys[0]
min_distance = np.mean(mean_distances[min_label])
for label in md_keys:
if label != min_label:
actual_distance = np.mean(mean_distances[label])
if actual_distance < min_distance:
min_label = label
min_distance = actual_distance
predicted_labels[i] = min_label
computeDuration = time.time() - computeStart
if computeDuration > 60:
computeDuration = computeDuration / 60
convert_to_minutes = True
unit = " min" if convert_to_minutes else " s"
print("Nearest Neighbors finished, computing duration = " +
str(computeDuration) + unit)
return predicted_labels
def analyze(self, data):
X = data["value"]
Y = data["geofips"].astype(object)
knn = neighbors.KNeighborsClassifier()
neighbor = neighbors.NearestNeighbors(n_neighbors=7, algorithm="brute")
fit = knn.fit(X.to_frame(), Y.to_frame().values.ravel())
p = neighbor.fit(X.to_frame())
pred = p.kneighbors(X.to_frame())
predicted = pred[1]
cols = ["i", "1", "2", "3", "4", "5", "6"]
df = pd.DataFrame(predicted, columns=cols)
df_melt = pd.melt(df, id_vars=["i"])
return df_melt, data
def test_radius_neighbors_boundary_handling():
"""Test whether points lying on boundary are handled consistently"""
X = np.array([[1.5], [3.0], [3.01]])
radius = 3.0
for algorithm in ALGORITHMS:
nbrs = neighbors.NearestNeighbors(radius=radius,
algorithm=algorithm).fit(X)
results = nbrs.radius_neighbors([0.0], return_distance=False)
assert_equal(results.shape, (1, ))
assert_equal(results.dtype, object)
assert_array_equal(results[0], [0, 1])
def build(self, data, k):
self.check_metric(self.metric)
self.index = neighbors.NearestNeighbors(
algorithm="ball_tree",
metric=self.metric,
metric_params=self.metric_params,
n_jobs=self.n_jobs,
)
self.index.fit(data)
# Return the nearest neighbors in the training set
distances, indices = self.index.kneighbors(n_neighbors=k)
return indices, distances
def test_knn_distance(self):
mapper = KeplerMapper()
data = np.random.rand(100, 5)
lens = mapper.project(data, projection="knn_distance_4", scaler=None)
nn = neighbors.NearestNeighbors(n_neighbors=4)
nn.fit(data)
lens_confirm = np.sum(
nn.kneighbors(data, n_neighbors=4, return_distance=True)[0], axis=1
).reshape((-1, 1))
assert lens.shape == (100, 1)
np.testing.assert_array_equal(lens, lens_confirm)
def get_transition_matrix2(self, k=10):
"""
implemantation of transition matrix of DPT.
:param k: number of each node's neighbors.
"""
# kNN
N = self.shape[0]
nbrs = neighbors.NearestNeighbors(n_neighbors=k,
metric='euclidean').fit(self.data)
distances, indices = nbrs.kneighbors(self.data)
sqdistances = np.square(distances)
sigmas = distances[:, -1] / 2
# kernel matrix
sigs_sum = np.add.outer(sigmas**2, sigmas**2)
sig_mul = np.multiply.outer(sigmas, sigmas)
kernel_matrix = np.zeros((N, k))
for i in range(N):
para = np.sqrt(
np.divide(2 * sig_mul[i, indices[i, :]],
sigs_sum[i, indices[i, :]]))
kern = np.exp(-np.divide(sqdistances[i, :],
(sigs_sum[i, indices[i, :]]))) # not *2
kernel_matrix[i, :] = np.multiply(para, kern)
weights = kernel_matrix
indptr = range(0, (N + 1) * k, k)
weight_matrix = sparse.csr_matrix(
(weights.flatten(), indices.flatten(), indptr),
shape=(N, N)).toarray()
# symmetric
for i, row in enumerate(indices):
for j in row:
if i not in set(indices[j]):
weight_matrix[j, i] = weight_matrix[i, j]
# normalization
weight_sum = np.power(weight_matrix.sum(axis=0)[:, None],
-1 / 2).flatten()
weight_sum = np.diag(weight_sum)
M = weight_sum @ weight_matrix @ weight_sum
mevals, mevecs = sp.linalg.eigh(M)
self.M = M
self.mevals = mevals
self.mevecs = mevecs
self.indices = indices
return M
def _apply_mask_and_get_affinity(seeds,
niimg,
radius,
allow_overlap,
mask_img=None):
seeds = list(seeds)
affine = niimg.get_affine()
# Compute world coordinates of all in-mask voxels.
if mask_img is not None:
mask_img = check_niimg_3d(mask_img)
mask_img = image.resample_img(mask_img,
target_affine=affine,
target_shape=niimg.shape[:3],
interpolation='nearest')
mask, _ = masking._load_mask_img(mask_img)
mask_coords = list(np.where(mask != 0))
X = masking._apply_mask_fmri(niimg, mask_img)
else:
mask_coords = list(zip(*np.ndindex(niimg.shape[:3])))
X = niimg.get_data().reshape([-1, niimg.shape[3]]).T
mask_coords = np.asarray(mask_coords)
mask_coords = coord_transform(mask_coords[0], mask_coords[1],
mask_coords[2], affine)
mask_coords = np.asarray(mask_coords).T
if (radius is not None
and LooseVersion(sklearn.__version__) < LooseVersion('0.16')):
# Fix for scikit learn versions below 0.16. See
# https://github.com/scikit-learn/scikit-learn/issues/4072
radius += 1e-6
clf = neighbors.NearestNeighbors(radius=radius)
A = clf.fit(mask_coords).radius_neighbors_graph(seeds)
A = A.tolil()
# Include selfs
mask_coords = mask_coords.astype(int).tolist()
for i, seed in enumerate(seeds):
try:
A[i, mask_coords.index(seed)] = True
except ValueError:
# seed is not in the mask
pass
if not allow_overlap:
if np.any(A.sum(axis=0) >= 2):
raise ValueError('Overlap detected between spheres')
return X, A
def get_positive_neighbors_counts(X, y, k=None, radius=None, positive_label=1):
assert bool(k) ^ bool(radius)
if k:
assert type(k) is int
nn = neighbors.NearestNeighbors(n_neighbors=k + 1, algorithm="auto").fit(X)
else:
assert type(radius) is float
nn = neighbors.NearestNeighbors(radius=radius, algorithm="auto").fit(X)
pos_X_indices = np.where(y == positive_label)[0]
positive_X = X[pos_X_indices]
if k:
neigh = nn.kneighbors(positive_X, return_distance=False)
neigh = neigh[:, 1:] # remove self from neighbors
neigh_targets = np.vectorize(lambda x: y[x])(neigh)
neigh_shape = np.shape(neigh_targets)
neigh_counts = np.full((neigh_shape[0],), np.float(neigh_shape[1]), dtype=np.float)
pos_neigh_counts = np.sum(neigh_targets == positive_label, axis=1)
else:
neigh = nn.radius_neighbors(positive_X, return_distance=False)
neigh = map(lambda tup: np.delete(tup[1], np.where(tup[1] == pos_X_indices[tup[0]])), enumerate(neigh)) # remove self from neighbors
neigh_targets = map(lambda n: np.vectorize(lambda x: y[x])(n) if n.size else np.array([]), neigh)
neigh_counts = np.array(map(lambda n: np.float(np.shape(n)[0]), neigh_targets), dtype=np.float)
pos_neigh_counts = np.array(map(lambda n: np.sum(n == positive_label), neigh_targets))
pos_neigh_proportions = pos_neigh_counts / neigh_counts
pos_neigh_proportions = np.nan_to_num(pos_neigh_proportions) # empty neighborhoods to 0
# # remove empty neighborhoods
# not_nan_indices = ~np.isnan(pos_neigh_proportions)
# avg_pos_neigh_count = np.average(pos_neigh_counts[not_nan_indices])
# avg_pos_neigh_prop = np.average(pos_neigh_proportions[not_nan_indices])
avg_pos_neigh_count = np.average(pos_neigh_counts)
avg_pos_neigh_prop = np.average(pos_neigh_proportions)
return itertools.izip(pos_X_indices, pos_neigh_counts, pos_neigh_proportions), avg_pos_neigh_count, avg_pos_neigh_prop
def simplify_co_occurrence(co, nn=3):
# quintile breaks (crude, still need to account for upper/diagonals)
q = ps.Quantiles(co).yb
q = np.reshape(q, co.shape)
# nearest neighbors graph
knn = neighbors.NearestNeighbors(n_neighbors=nn)
neigh = knn.fit(co)
knn_mat = neigh.kneighbors_graph(co).toarray()
out = np.multiply(q, knn_mat)
return out