def fit(self, X, y=None):
"""Fit a dataset, for a transformer.
Parameters
----------
X : iterable
Each element must be an iterable with at most three features and at
least one. The first that is obligatory is a valid graph structure
(adjacency matrix or edge_dictionary) while the second is
node_labels and the third edge_labels (that fitting the given graph
format). The train samples.
y : None
There is no need of a target in a transformer, yet the pipeline API
requires this parameter.
Returns
-------
self : object
Returns self.
"""
self._method_calling = 1
self._is_transformed = False
# Input validation and parsing
self.initialize()
if X is None:
raise ValueError('`fit` input cannot be None')
else:
if not isinstance(X, collections.Iterable):
raise TypeError('input must be an iterable\n')
i = 0
out = list()
gs = list()
self._labels_hash_dict, labels_hash_set = dict(), set()
for (idx, x) in enumerate(iter(X)):
is_iter = isinstance(x, collections.Iterable)
if is_iter:
x = list(x)
if is_iter and len(x) in [0, 1, 2, 3]:
if len(x) == 0:
warnings.warn('Ignoring empty element on index: '
+ str(idx))
continue
elif len(x) == 1:
warnings.warn(
'Ignoring empty element on index: '
+ str(i) + '\nLabels must be provided.')
else:
x = Graph(x[0], x[1], {}, self._graph_format)
vertices = list(x.get_vertices(purpose="any"))
Labels = x.get_labels(purpose="any")
elif type(x) is Graph:
vertices = list(x.get_vertices(purpose="any"))
Labels = x.get_labels(purpose="any")
else:
raise TypeError('each element of X must be either '
'a graph object or a list with at '
'least a graph like object and '
'node labels dict \n')
g = (vertices, Labels,
{n: x.neighbors(n, purpose="any") for n in vertices})
# collect all the labels
labels_hash_set |= set(itervalues(Labels))
gs.append(g)
i += 1
if i == 0:
raise ValueError('parsed input is empty')
# Hash labels
if len(labels_hash_set) > self._max_number:
warnings.warn('Number of labels is smaller than'
'the biggest possible.. '
'Collisions will appear on the '
'new labels.')
# If labels exceed the biggest possible size
nl, nrl = list(), len(labels_hash_set)
while nrl > self._max_number:
nl += self.random_state_.choice(self._max_number,
self._max_number,
replace=False).tolist()
nrl -= self._max_number
if nrl > 0:
nl += self.random_state_.choice(self._max_number,
nrl,
replace=False).tolist()
# unify the collisions per element.
else:
# else draw n random numbers.
nl = self.random_state_.choice(self._max_number, len(labels_hash_set),
replace=False).tolist()
self._labels_hash_dict = dict(zip(labels_hash_set, nl))
# for all graphs
for vertices, labels, neighbors in gs:
new_labels = {v: self._labels_hash_dict[l]
for v, l in iteritems(labels)}
g = (vertices, new_labels, neighbors,)
gr = {0: self.NH_(g)}
for r in range(1, self.R):
gr[r] = self.NH_(gr[r-1])
# save the output for all levels
out.append(gr)
self.X = out
# Return the transformer
return self
def transform(self, X):
"""Calculate the kernel matrix, between given and fitted dataset.
Parameters
----------
X : iterable
Each element must be an iterable with at most three features and at
least one. The first that is obligatory is a valid graph structure
(adjacency matrix or edge_dictionary) while the second is
node_labels and the third edge_labels (that fitting the given graph
format). If None the kernel matrix is calculated upon fit data.
The test samples.
Returns
-------
K : numpy array, shape = [n_targets, n_input_graphs]
corresponding to the kernel matrix, a calculation between
all pairs of graphs between target an features
"""
self._method_calling = 3
# Check is fit had been called
check_is_fitted(self, ['X'])
# Input validation and parsing
if X is None:
raise ValueError('`transform` input cannot be None')
else:
if not isinstance(X, collections.Iterable):
raise TypeError('input must be an iterable\n')
i = 0
out = list()
for (idx, x) in enumerate(iter(X)):
is_iter = isinstance(x, collections.Iterable)
if is_iter:
x = list(x)
if is_iter and len(x) in [0, 1, 2, 3]:
if len(x) == 0:
warnings.warn('Ignoring empty element on index: '
+ str(idx))
continue
elif len(x) == 1:
warnings.warn(
'Ignoring empty element on index: '
+ str(i) + '\nLabels must be provided.')
else:
x = Graph(x[0], x[1], {}, self._graph_format)
vertices = list(x.get_vertices(purpose="any"))
Labels = x.get_labels(purpose="any")
elif type(x) is Graph:
vertices = list(x.get_vertices(purpose="any"))
Labels = x.get_labels(purpose="any")
else:
raise TypeError('each element of X must be either '
'a graph object or a list with at '
'least a graph like object and '
'node labels dict \n')
# Hash based on the labels of fit
new_labels = {v: self._labels_hash_dict.get(l, None)
for v, l in iteritems(Labels)}
# Radix sort the other
g = ((vertices, new_labels) +
({n: x.neighbors(n, purpose="any")
for n in vertices},))
gr = {0: self.NH_(g)}
for r in range(1, self.R):
gr[r] = self.NH_(gr[r-1])
# save the output for all levels
out.append(gr)
i += 1
if i == 0:
raise ValueError('parsed input is empty')
# Transform - calculate kernel matrix
# Output is always normalized
km = self._calculate_kernel_matrix(out)
self._is_transformed = True
return km