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def dummy_data():
frag0 = np.arange(1, 17, dtype=int).reshape((4, 4))
gt0 = np.array([[1, 1, 2, 2], [1, 1, 2, 2], [3] * 4, [3] * 4], dtype=int)
frag, gt = (ndi.zoom(image, 4, order=0, mode='reflect')
for image in [frag0, gt0])
fman = features.base.Mock(frag, gt)
return frag, gt, fman
import numpy as np
from scipy.misc import comb as nchoosek
from . import base
class Manager(base.Null):
def __init__(self, nmoments=4, use_diff_features=True, oriented=False,
normalize=False, *args, **kwargs):
super(Manager, self).__init__()
self.nmoments = nmoments
self.use_diff_features = use_diff_features
self.oriented = oriented
self.normalize = normalize
@classmethod
def load_dict(cls, fm_info):
obj = cls(fm_info['nmoments'], fm_info['use_diff'],
fm_info['oriented'], fm_info['normalize'])
return obj
def write_fm(self, json_fm={}):
if 'feature_list' not in json_fm:
import numpy as np
from numpy.linalg import eig, norm
from . import base
class Manager(base.Null):
def __init__(self, *args, **kwargs):
super(Manager, self).__init__()
def write_fm(self, json_fm={}):
if 'feature_list' not in json_fm:
json_fm['feature_list'] = []
json_fm['feature_list'].append('orientation')
json_fm['orientation'] = {}
return json_fm
def create_node_cache(self, g, n):
# Get subscripts of extent (morpho.unravel_index was slow)
M = np.zeros_like(g.watershed);
M.ravel()[list(g.extent(n))] = 1
ind = np.array(np.nonzero(M)).T
# Get second moment matrix
from __future__ import absolute_import
# external libraries
import numpy as np
import networkx as nx
# local imports
from . import base
class Manager(base.Null):
def __init__(self, *args, **kwargs):
super(Manager, self).__init__()
def write_fm(self, json_fm={}):
if 'feature_list' not in json_fm:
json_fm['feature_list'] = []
json_fm['feature_list'].append('graph')
json_fm['graph'] = {}
return json_fm
def compute_node_features(self, g, n, cache=None):
deg = g.degree(n)
ndeg = nx.algorithms.average_neighbor_degree(g, nodes=[n])[n]
return np.array([deg, ndeg])
def compute_edge_features(self, g, n1, n2, cache=None):
import numpy as np
from . import base
class Manager(base.Null):
def __init__(self, *args, **kwargs):
super(Manager, self).__init__()
@classmethod
def load_dict(cls, fm_info):
obj = cls()
return obj
def write_fm(self, json_fm={}):
if 'feature_list' not in json_fm:
json_fm['feature_list'] = []
json_fm['feature_list'].append('inclusiveness')
json_fm['inclusiveness'] = {}
return json_fm
def compute_node_features(self, g, n, cache=None):
import numpy as np
from . import base
class Manager(base.Null):
def __init__(self, nbins=4, minval=0.0, maxval=1.0,
compute_percentiles=[], oriented=False,
compute_histogram=True, use_neuroproof=False, *args, **kwargs):
super(Manager, self).__init__()
self.minval = minval
self.maxval = maxval
self.nbins = nbins
self.oriented = oriented
self.compute_histogram = compute_histogram
self.use_neuroproof = use_neuroproof
try:
_ = len(compute_percentiles)
except TypeError: # single percentile value given
compute_percentiles = [compute_percentiles]
self.compute_percentiles = compute_percentiles
# external libraries
import numpy as np
import networkx as nx
# local imports
from . import base
class Manager(base.Null):
def __init__(self, *args, **kwargs):
super(Manager, self).__init__()
def write_fm(self, json_fm={}):
if 'feature_list' not in json_fm:
json_fm['feature_list'] = []
json_fm['feature_list'].append('graph')
json_fm['graph'] = {}
return json_fm
def compute_node_features(self, g, n, cache=None):
deg = g.degree(n)
ndeg = nx.algorithms.average_neighbor_degree(g, nodes=[n])[n]
return np.array([deg, ndeg])
def compute_edge_features(self, g, n1, n2, cache=None):