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pyhrf.parcellation module

class pyhrf.parcellation.Ant(a_id, greed, graph, labels, path_marks, site_marks, pressures, world, verbosity=0)

Bases: pyhrf.parcellation.Talker

action(time)
fix_explosion()
to_conquer()
to_patrol()
class pyhrf.parcellation.Talker(talker_string_id, verbosity=0)
verbose(level, msg)
verbose_array(level, array)
pyhrf.parcellation.Visit_graph_noeud(noeud, graphe, Visited=None)
class pyhrf.parcellation.World(graph, nb_ants, greed=0.05, time_min=100, time_max=None, tolerance=1, verbosity=0, stop_when_all_controlled=False)

Bases: pyhrf.parcellation.Talker

balanced()
force_end()
get_final_labels()
resolve()
site_taken(site)
pyhrf.parcellation.init_edge_data(g, init_value=0)
pyhrf.parcellation.make_parcellation_cubed_blobs_from_file(parcellation_file, output_path, roi_ids=None, bg_parcel=0, skip_existing=False)
pyhrf.parcellation.make_parcellation_from_files(betaFiles, maskFile, outFile, nparcels, method, dry=False, spatial_weight=10.0)
pyhrf.parcellation.make_parcellation_surf_from_files(beta_files, mesh_file, parcellation_file, nbparcel, method, mu=10.0, verbose=0)
pyhrf.parcellation.parcellate_balanced_vol(mask, nb_parcels)
Performs a balanced partitioning on the input mask using a balloon patroling
algorithm [Eurol 2009]. Values with 0 are discarded position in the mask.
Parameters:
  • mask (-) – binary 3D array of valid position to parcellate
  • nb_parcels (-) – the required number of parcels
Returns:

a 3D array of integers
Return type:

  • the parcellation (numpy.ndarray)
pyhrf.parcellation.parcellate_voronoi_vol(mask, nb_parcels, seeds=None)

Produce a parcellation from a Voronoi diagram built on random seeds. The number of seeds is equal to the nb of parcels. Seed are randomly placed within the mask, expect on edge positions

Parameters:
  • mask (-) – binary 3D array of valid position to parcellate
  • nb_parcels (-) – the required number of parcels
  • seeds (-) – TODO
Returns:

a 3D array of integers -
Return type:

  • the parcellation (numpy.ndarray)
pyhrf.parcellation.parcellation_dist(p1, p2, mask=None)

Compute the distance between the two parcellation p1 and p2 as the minimum number of positions to remove in order to obtain equal partitions. “mask” may be a binary mask to limit the distance computation to some specific positions. Important convention: parcel label 0 is treated as background and corresponding positions are discarded if no mask is provided.

Returns:(distance value, parcellation overlap)
pyhrf.parcellation.parcellation_for_jde(fmri_data, avg_parcel_size=250, output_dir=None, method='gkm', glm_drift='Cosine', glm_hfcut=128)

method: gkm, ward, ward_and_gkm

pyhrf.parcellation.parcellation_report(d)
pyhrf.parcellation.parcellation_ward_spatial(func_data, n_clusters, graph=None)

Make parcellation based upon ward hierarchical clustering from scikit-learn

Parameters:
  • func_data (array of shape (nb_positions, dim_feature_1, [dim_feature2, ..])) – functional data:
  • n_clusters – chosen number of clusters to create
  • graph – adjacency list defining neighbours. if None, no connectivity defined: clustering is spatially independent
Returns:
Return type:

parcellation labels
pyhrf.parcellation.permutation(x)

Randomly permute a sequence, or return a permuted range.

If x is a multi-dimensional array, it is only shuffled along its first index.

Parameters:x (int or array_like) – If x is an integer, randomly permute np.arange(x). If x is an array, make a copy and shuffle the elements randomly.
Returns:out – Permuted sequence or array range.
Return type:ndarray

Examples

>>> np.random.permutation(10)
array([1, 7, 4, 3, 0, 9, 2, 5, 8, 6])

>>> np.random.permutation([1, 4, 9, 12, 15])
array([15,  1,  9,  4, 12])

>>> arr = np.arange(9).reshape((3, 3))
>>> np.random.permutation(arr)
array([[6, 7, 8],
       [0, 1, 2],
       [3, 4, 5]])
pyhrf.parcellation.rand(d0, d1, ..., dn)

Random values in a given shape.

Create an array of the given shape and populate it with random samples from a uniform distribution over [0, 1).

Parameters:d1, .., dn (d0,) – The dimensions of the returned array, should all be positive. If no argument is given a single Python float is returned.
Returns:out – Random values.
Return type:ndarray, shape (d0, d1, ..., dn)

See also

random()

Notes

This is a convenience function. If you want an interface that takes a shape-tuple as the first argument, refer to np.random.random_sample .

Examples

>>> np.random.rand(3,2)
array([[ 0.14022471,  0.96360618],  #random
       [ 0.37601032,  0.25528411],  #random
       [ 0.49313049,  0.94909878]]) #random
pyhrf.parcellation.randint(low, high=None, size=None, dtype='l')

Return random integers from low (inclusive) to high (exclusive).

Return random integers from the “discrete uniform” distribution of the specified dtype in the “half-open” interval [low, high). If high is None (the default), then results are from [0, low).

Parameters:
  • low (int) – Lowest (signed) integer to be drawn from the distribution (unless high=None, in which case this parameter is the highest such integer).
  • high (int, optional) – If provided, one above the largest (signed) integer to be drawn from the distribution (see above for behavior if high=None).
  • size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., (m, n, k), then m * n * k samples are drawn. Default is None, in which case a single value is returned.
  • dtype (dtype, optional) –

    Desired dtype of the result. All dtypes are determined by their name, i.e., ‘int64’, ‘int’, etc, so byteorder is not available and a specific precision may have different C types depending on the platform. The default value is ‘np.int’.

    New in version 1.11.0.
Returns:

out – size-shaped array of random integers from the appropriate distribution, or a single such random int if size not provided.
Return type:

int or ndarray of ints

See also

random.random_integers()
similar to randint, only for the closed interval [low, high], and 1 is the lowest value if high is omitted. In particular, this other one is the one to use to generate uniformly distributed discrete non-integers.

Examples

>>> np.random.randint(2, size=10)
array([1, 0, 0, 0, 1, 1, 0, 0, 1, 0])
>>> np.random.randint(1, size=10)
array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0])

Generate a 2 x 4 array of ints between 0 and 4, inclusive:

>>> np.random.randint(5, size=(2, 4))
array([[4, 0, 2, 1],
       [3, 2, 2, 0]])
pyhrf.parcellation.random_pick(a)
pyhrf.parcellation.round_nb_parcels(n)
pyhrf.parcellation.split_big_parcels(parcel_file, output_file, max_size=400)
pyhrf.parcellation.split_parcel(labels, graphs, id_parcel, n_parcels, inplace=False, verbosity=0, balance_tolerance='exact')

balance_tolerance : exact or draft