def participation_coef(cmatrix, Ci):
""" Computes nodal participation coefficient for a binary graph and its
corresponding community structure. For a directed graph, computes "out-
neighbor" participation coefficient.
Only for binary networks.
Parameters
----------
cmatrix : adjacency matrix
Ci : community structure vector Ci
Returns
-------
P : Participation coefficient
Output for directed graphs: "out-neighbor" participation coef
Reference: Guimera R, Amaral L. Nature (2005) 433:895-900.
Mika Rubinov, UNSW, 2008
"""
m = bct.to_gslm(cmatrix.tolist())
cil = bct.to_gslv(Ci.tolist())
str = bct.participation_coef(m, cil)
strnp = bct.from_gsl(str)
bct.gsl_free(m)
bct.gsl_free(str)
return np.asarray(strnp)
def participation_coef(cmatrix, Ci):
""" Computes nodal participation coefficient for a binary graph and its
corresponding community structure. For a directed graph, computes "out-
neighbor" participation coefficient.
Only for binary networks.
Parameters
----------
cmatrix : adjacency matrix
Ci : community structure vector Ci
Returns
-------
P : Participation coefficient
Output for directed graphs: "out-neighbor" participation coef
Reference: Guimera R, Amaral L. Nature (2005) 433:895-900.
Mika Rubinov, UNSW, 2008
"""
m = bct.to_gslm(cmatrix.tolist())
cil = bct.to_gslv(Ci.tolist())
str = bct.participation_coef(m, cil)
strnp = bct.from_gsl(str)
bct.gsl_free(m)
bct.gsl_free(str)
return np.asarray(strnp)
def module_degree_zscore(cmatrix, Ci):
""" Computes 'within module degree z-score'
Computes z-score for a binary graph and its corresponding community
structure. For a directed graph, computes out-neighbor z-score.
Degree based measures for classifying nodes in the context of community
structure. The z-score describes how well the nodes are connected to other
nodes within their modules.
Note that, for directed networks, these functions compute the measures
based on the out-degree.
function Z=module_degree_zscore(A,Ci)
Parameters
---------
cmatrix : binary adjacency matrix
Ci : community structure vector
Returns
-------
Z : z-score
Output for directed graphs: "out-neighbor" z-score.
Reference: Guimera R, Amaral L. Nature (2005) 433:895-900.
Mika Rubinov, UNSW, 2008
"""
m = bct.to_gslm(cmatrix.tolist())
cil = bct.to_gslv(Ci.tolist())
str = bct.module_degree_zscore(m, cil)
strnp = bct.from_gsl(str)
bct.gsl_free(m)
bct.gsl_free(str)
return np.asarray(strnp)
def module_degree_zscore(cmatrix, Ci):
""" Computes 'within module degree z-score'
Computes z-score for a binary graph and its corresponding community
structure. For a directed graph, computes out-neighbor z-score.
Degree based measures for classifying nodes in the context of community
structure. The z-score describes how well the nodes are connected to other
nodes within their modules.
Note that, for directed networks, these functions compute the measures
based on the out-degree.
function Z=module_degree_zscore(A,Ci)
Parameters
---------
cmatrix : binary adjacency matrix
Ci : community structure vector
Returns
-------
Z : z-score
Output for directed graphs: "out-neighbor" z-score.
Reference: Guimera R, Amaral L. Nature (2005) 433:895-900.
Mika Rubinov, UNSW, 2008
"""
m = bct.to_gslm(cmatrix.tolist())
cil = bct.to_gslv(Ci.tolist())
str = bct.module_degree_zscore(m, cil)
strnp = bct.from_gsl(str)
bct.gsl_free(m)
bct.gsl_free(str)
return np.asarray(strnp)
def to_gslv(*args): return _bct.to_gslv(*args)
def to_gslv(*args):
return _bct.to_gslv(*args)
def to_gslv(*args):
"""
to_gslv(double array, int size) -> gsl_vector
to_gslv(PyObject list) -> gsl_vector
"""
return _bct.to_gslv(*args)
def findpaths(cmatrix, sources, qmax):
""" Paths are sequences of linked nodes, that never visit a single
node more than once. This function finds all paths that start at a
set of source vertices, up to a specified length. Warning: very
memory-intensive.
C++ Comment
Finds paths from a set of source nodes up to a given length. Note that
there is no savepths argument; if all paths are desired, pass a valid
pointer as he allpths argument. There is also no tpath argument as its
value may overflow a C++ long. Since 0 is a valid node index in C++, -1
is used as the "filler" value in allpths rather than 0 as in MATLAB.
Pq (the main return), plq, and util are indexed by path length.
They therefore have (qmax + 1) elements and contain no valid data
at index 0.
function [Pq,tpath,plq,qstop,allpths,util] =
findpaths(CIJ,sources,qmax,savepths)
Parameters
----------
cmatrix : connection/adjacency matrix
qmax : maximal path length
sources : source units from which paths are grown
savepths : set to 1 if all paths are to be collected in
'allpths'
Returns
-------
Pq : 3D matrix, with P(i,j,q) = number of paths from
'i' to 'j' of length 'q'.
Not returned by the C++ function:
tpath total number of paths found (lengths 1 to 'qmax')
plq path length distribution as a function of 'q'
qstop path length at which 'findpaths' is stopped
allpths a matrix containing all paths up to 'qmax'
util node use index
Note that Pq[:,:,N] can only carry entries on the diagonal, as all "legal"
paths of length N-1 must terminate. Cycles of length N are possible, with
all vertices visited exactly once (except for source and target).
'qmax = N' can wreak havoc (due to memory problems).
Note: Weights are discarded.
Note: I am fairly certain that this algorithm is rather inefficient -
suggestions for improvements are welcome.
Olaf Sporns, Indiana University, 2002/2007/2008
"""
# XXX: work on docstring
m = bct.to_gslm(cmatrix.tolist())
cil = bct.to_gslv(sources.tolist())
pq, plq, qstop, allpths, util = bct.findpaths(m, cil, qmax)
pqret = bct.from_gsl(pq)
print pqret[0]
print np.asarray(pqret[1])
print plq
print qstop
print allpths
print util
bct.gsl_free(m)
bct.gsl_free(pq)
bct.gsl_free(plq)
bct.gsl_free(allpths)
bct.gsl_free(util)
#logging.error("What to do with std::vector<gsl_matrix*> ??")
return
def to_gslv(*args):
"""
to_gslv(double array, int size) -> gsl_vector
to_gslv(PyObject list) -> gsl_vector
"""
return _bct.to_gslv(*args)
def findpaths(cmatrix, sources, qmax):
""" Paths are sequences of linked nodes, that never visit a single
node more than once. This function finds all paths that start at a
set of source vertices, up to a specified length. Warning: very
memory-intensive.
C++ Comment
Finds paths from a set of source nodes up to a given length. Note that
there is no savepths argument; if all paths are desired, pass a valid
pointer as he allpths argument. There is also no tpath argument as its
value may overflow a C++ long. Since 0 is a valid node index in C++, -1
is used as the "filler" value in allpths rather than 0 as in MATLAB.
Pq (the main return), plq, and util are indexed by path length.
They therefore have (qmax + 1) elements and contain no valid data
at index 0.
function [Pq,tpath,plq,qstop,allpths,util] =
findpaths(CIJ,sources,qmax,savepths)
Parameters
----------
cmatrix : connection/adjacency matrix
qmax : maximal path length
sources : source units from which paths are grown
savepths : set to 1 if all paths are to be collected in
'allpths'
Returns
-------
Pq : 3D matrix, with P(i,j,q) = number of paths from
'i' to 'j' of length 'q'.
Not returned by the C++ function:
tpath total number of paths found (lengths 1 to 'qmax')
plq path length distribution as a function of 'q'
qstop path length at which 'findpaths' is stopped
allpths a matrix containing all paths up to 'qmax'
util node use index
Note that Pq[:,:,N] can only carry entries on the diagonal, as all "legal"
paths of length N-1 must terminate. Cycles of length N are possible, with
all vertices visited exactly once (except for source and target).
'qmax = N' can wreak havoc (due to memory problems).
Note: Weights are discarded.
Note: I am fairly certain that this algorithm is rather inefficient -
suggestions for improvements are welcome.
Olaf Sporns, Indiana University, 2002/2007/2008
"""
# XXX: work on docstring
m = bct.to_gslm(cmatrix.tolist())
cil = bct.to_gslv(sources.tolist())
pq, plq, qstop, allpths, util = bct.findpaths(m, cil, qmax)
pqret = bct.from_gsl(pq)
print pqret[0]
print np.asarray(pqret[1])
print plq
print qstop
print allpths
print util
bct.gsl_free(m)
bct.gsl_free(pq)
bct.gsl_free(plq)
bct.gsl_free(allpths)
bct.gsl_free(util)
#logging.error("What to do with std::vector<gsl_matrix*> ??")
return
