def make_graphml_tensor_graph(graphs):
"""
Make a tensor graph from a series (may be just 2) of graphs.
@param graphs: A list of fully qualified file names for graphs.
@param output: The name of the tensor graph output.
"""
base_graph = igraph_io.read_arbitrary(graphs[0], informat="graphml")
for attr in base_graph.attributes(): del attr # get rid of attrs other than weight
ecount = base_graph.ecount() # This is where edge attributes for appended graphs should start
base_graph.es["weight0"] = base_graph.es["weight"]
base_graph["time_idx"] = "0: %s" % os.path.splitext(os.path.basename(graphs[0]))[0]
base_graph["num_edges"] = "0: %d" % base_graph.ecount() # Keep track of all the graphs in a
del base_graph.es["weight"] # get rid of old attr
for time_slot, graph_fn in enumerate(graphs[1:]): # Note start index
g = igraph_io.read_arbitrary(graph_fn, informat="graphml")
base_graph += g.get_edgelist() # Add new edges to current graph at eid old_ecount:new_ecount
new_edges = [None]*ecount # Mask out all old edges
ecount = base_graph.ecount() # Update edge count
new_edges.extend(g.es["weight"]) # Assemble new edge weights for eids base.old_ecount:base.new_ecount
base_graph.es["weight%d" % (time_slot+1)] = new_edges
base_graph["time_idx"] += ", %d: %s" % \
(time_slot+1, os.path.splitext(os.path.basename(graphs[time_slot+1]))[0])
base_graph["num_edges"] += ", %d: %d" % (time_slot+1, g.ecount())
return base_graph
def main():
parser = argparse.ArgumentParser(
description="Verify that given a big graph I can\
obtain the equivalent small graph")
parser.add_argument("biggfn",
action="store",
help="The big graph filename")
parser.add_argument("--b",
"--bigformat",
default="graphml",
help="The format of\
the big graph")
parser.add_argument("smallgfn",
action="store",
help="The small graph filename")
parser.add_argument("--s",
"--smallformat",
default="graphml",
help="The format\
of the small graph")
parser.add_argument("-a",
"--atlasfn",
action="store",
default=os.path.join(os.path.dirname(__file__),
"desikan_atlas.nii"),
help="The desikan atlas filename")
result = parser.parse_args()
gsmall = igraph_io.read_arbitrary(result.smallgfn, result.smallformat)
gbig = igraph_io.read_arbitrary(result.biggfn, result.bigformat)
atlas = Atlas(result.atlasfn)
verify(gsmall, gbig, atlas)
def make_graphml_tensor_graph(graphs):
"""
Make a tensor graph from a series (may be just 2) of graphs.
@param graphs: A list of fully qualified file names for graphs.
@param output: The name of the tensor graph output.
"""
base_graph = igraph_io.read_arbitrary(graphs[0], informat="graphml")
for attr in base_graph.attributes():
del attr # get rid of attrs other than weight
ecount = base_graph.ecount(
) # This is where edge attributes for appended graphs should start
base_graph.es["weight0"] = base_graph.es["weight"]
base_graph["time_idx"] = "0: %s" % os.path.splitext(
os.path.basename(graphs[0]))[0]
base_graph["num_edges"] = "0: %d" % base_graph.ecount(
) # Keep track of all the graphs in a
del base_graph.es["weight"] # get rid of old attr
for time_slot, graph_fn in enumerate(graphs[1:]): # Note start index
g = igraph_io.read_arbitrary(graph_fn, informat="graphml")
base_graph += g.get_edgelist(
) # Add new edges to current graph at eid old_ecount:new_ecount
new_edges = [None] * ecount # Mask out all old edges
ecount = base_graph.ecount() # Update edge count
new_edges.extend(
g.es["weight"]
) # Assemble new edge weights for eids base.old_ecount:base.new_ecount
base_graph.es["weight%d" % (time_slot + 1)] = new_edges
base_graph["time_idx"] += ", %d: %s" % \
(time_slot+1, os.path.splitext(os.path.basename(graphs[time_slot+1]))[0])
base_graph["num_edges"] += ", %d: %d" % (time_slot + 1, g.ecount())
return base_graph
def main():
parser = argparse.ArgumentParser(
description="Verify that given a big graph I can\
obtain the equivalent small graph"
)
parser.add_argument("biggfn", action="store", help="The big graph filename")
parser.add_argument(
"--b",
"--bigformat",
default="graphml",
help="The format of\
the big graph",
)
parser.add_argument("smallgfn", action="store", help="The small graph filename")
parser.add_argument(
"--s",
"--smallformat",
default="graphml",
help="The format\
of the small graph",
)
parser.add_argument(
"-a",
"--atlasfn",
action="store",
default=os.path.join(os.path.dirname(__file__), "desikan_atlas.nii"),
help="The desikan atlas filename",
)
result = parser.parse_args()
gsmall = igraph_io.read_arbitrary(result.smallgfn, result.smallformat)
gbig = igraph_io.read_arbitrary(result.biggfn, result.bigformat)
atlas = Atlas(result.atlasfn)
verify(gsmall, gbig, atlas)
def make_mm_tensor_graphs(graphs, output):
"""
Serial writer for Weighted market martrix tensors to a single file.
Format:
Note that '# ' - is a comment
Example:
# 0:file_name0
# 1:file_name1
:
:
# N:file_nameN
source,target,graph#,weight
First there is a mapping from graph# 's (described below) to graph file names.
@param graphs: A list of fully qualified file names for graphs.
@param output: The name of the tensor graph output.
"""
f = open(output, "wb")
for idx, g_fn in enumerate(graphs):
f.write("# %d:%s\n" % (idx, os.path.basename(g_fn)))
f.write("\n")
for idx, g_fn in enumerate(graphs): # Note start index
g = igraph_io.read_arbitrary(g_fn, informat="graphml")
for edge in g.es:
f.write("%d,%d,%d,%d\n" %
(edge.source, edge.target, idx, edge["weight"]))
# Consider skipping a line here
f.close()
print "Mission complete"
def make_mm_tensor_graphs(graphs, output):
"""
Serial writer for Weighted market martrix tensors to a single file.
Format:
Note that '# ' - is a comment
Example:
# 0:file_name0
# 1:file_name1
:
:
# N:file_nameN
source,target,graph#,weight
First there is a mapping from graph# 's (described below) to graph file names.
@param graphs: A list of fully qualified file names for graphs.
@param output: The name of the tensor graph output.
"""
f = open(output, "wb")
for idx, g_fn in enumerate(graphs):
f.write("# %d:%s\n" % (idx, os.path.basename(g_fn)))
f.write("\n")
for idx, g_fn in enumerate(graphs): # Note start index
g = igraph_io.read_arbitrary(g_fn, informat="graphml")
for edge in g.es:
f.write("%d,%d,%d,%d\n" % (edge.source, edge.target, idx, edge["weight"]))
# Consider skipping a line here
f.close()
print "Mission complete"
