def test_construct_weighted_hypergraph(self):
num_nodes = 7
num_nets = 4
hyperedge_indices = [0, 2, 6, 9, 12]
hyperedges = [0, 2, 0, 1, 3, 4, 3, 4, 6, 2, 5, 6]
node_weights = [1, 2, 3, 4, 5, 6, 7]
edge_weights = [11, 22, 33, 44]
k = 2
hypergraph = kahypar.Hypergraph(num_nodes, num_nets, hyperedge_indices,
hyperedges, k, edge_weights,
node_weights)
self.assertEqual(hypergraph.nodeWeight(0), 1)
self.assertEqual(hypergraph.nodeWeight(1), 2)
self.assertEqual(hypergraph.nodeWeight(2), 3)
self.assertEqual(hypergraph.nodeWeight(3), 4)
self.assertEqual(hypergraph.nodeWeight(4), 5)
self.assertEqual(hypergraph.nodeWeight(5), 6)
self.assertEqual(hypergraph.nodeWeight(6), 7)
self.assertEqual(hypergraph.edgeWeight(0), 11)
self.assertEqual(hypergraph.edgeWeight(1), 22)
self.assertEqual(hypergraph.edgeWeight(2), 33)
self.assertEqual(hypergraph.edgeWeight(3), 44)
def cut(self):
context = self._get_context()
num_nodes = self.num_of_nodes()
node_weights = [1] * num_nodes
k = 2
# Debug messages
# print("Creating hypergraph:")
# print(f"\t num_nodes: {num_nodes}")
# print(f"\t num_of_hyperedges: {self.num_of_hyperedges()}")
# print(f"\t net_indices: {self.net_indices}")
# print(f"\t nets: {self.nets}")
# print(f"\t net_weights: {self.net_weights}")
# print(f"\t node_weights: {node_weights}")
hypergraph = kahypar.Hypergraph(num_nodes, self.num_of_hyperedges(),
self.net_indices, self.nets, k,
self.net_weights, node_weights)
kahypar.partition(hypergraph, context)
left_partition = [
node for node in range(num_nodes) if hypergraph.blockID(node) == 0
]
right_partition = [
node for node in range(num_nodes) if hypergraph.blockID(node) == 1
]
# print(left_partition)
# print(right_partition)
# IDK what triggers this but a partition can be empty. In that case, tighten the imbalance restriction and retry
if len(left_partition) == 0 or len(right_partition) == 0:
self.set_epsilon(self.epsilon / 4)
return self.cut()
self.epsilon = self.startEpsilon
return set(self._to_lnum(left_partition)), set(
self._to_lnum(right_partition))
def hgpa(labels, nclass, random_state):
"""HyperGraph Partitioning Algorithm (HGPA).
Parameters
----------
labels: Labels generated by multiple clustering algorithms such as K-Means.
nclass: Number of classes in a consensus clustering label.
random_state: Used for reproducible results.
Return
-------
label_ce: Consensus clustering label obtained from HGPA.
"""
# Create hypergraph for kahypar
H = create_hypergraph(labels)
n_nodes, n_nets = H.shape
node_weights = [1] * n_nodes
edge_weights = [1] * n_nets
hyperedge_indices = [0]
hyperedges = []
HT = H.T
for i in range(n_nets):
h = HT.getrow(i)
idx_row, idx_col = h.nonzero()
hyperedges += list(idx_col)
hyperedge_indices.append(len(hyperedges))
hypergraph = kahypar.Hypergraph(n_nodes, n_nets, hyperedge_indices,
hyperedges, nclass, edge_weights,
node_weights)
# Settings for kahypar
context = kahypar.Context()
config_path = os.path.dirname(
__file__) + "/kahypar_config/km1_kKaHyPar_sea20.ini"
context.loadINIconfiguration(config_path)
if random_state is not None:
context.setSeed(random_state)
context.setK(nclass)
context.setEpsilon(0.03)
context.suppressOutput(True)
# Hypergraph partitioning
kahypar.partition(hypergraph, context)
label_ce = np.empty(n_nodes, dtype=int)
for i in range(n_nodes):
label_ce[i] = hypergraph.blockID(i)
return label_ce
def _init_hypergraph_tanner(self, graph, k=2):
nodes = list(range(1, graph.shape[0]))
edges = list(range(graph.shape[1]))
hyperedge_indices = [0]
hyperedges = []
edge_weights = []
for edge in range(graph.shape[1]):
hyperedges += list(numpy.where(graph[1:, edge])[0])
hyperedge_indices.append(len(hyperedges))
edge_weights.append(1)
hp = kahypar.Hypergraph(len(nodes), len(edges), hyperedge_indices,
hyperedges, k, edge_weights, []), nodes, edges
return hp
def test_construct_hypergraph(self):
num_nodes = 7
num_nets = 4
hyperedge_indices = [0, 2, 6, 9, 12]
hyperedges = [0, 2, 0, 1, 3, 4, 3, 4, 6, 2, 5, 6]
k = 2
hypergraph = kahypar.Hypergraph(num_nodes, num_nets, hyperedge_indices,
hyperedges, k)
self.assertEqual(hypergraph.numNodes(), 7)
self.assertEqual(hypergraph.numEdges(), 4)
self.assertEqual(hypergraph.numPins(), 12)
def kahypar_subgraph_find_membership(
inputs,
output,
size_dict,
weight_nodes='const',
weight_edges='log',
fix_output_nodes=False,
parts=2,
imbalance=0.01,
compress=0,
seed=None,
profile=None,
mode='direct',
objective='cut',
quiet=True,
):
import kahypar as kahypar
if seed is None:
seed = random.randint(0, 2**31 - 1)
nv = len(inputs)
if parts >= nv:
return list(range(nv))
hg = get_hypergraph(inputs, output, size_dict, accel=False)
if compress:
hg.compress(compress)
winfo = to_sparse(hg, weight_nodes=weight_nodes, weight_edges=weight_edges)
hypergraph_kwargs = {
'num_nodes': hg.get_num_nodes(),
'num_edges': hg.get_num_edges(),
'index_vector': winfo['hyperedge_indices'],
'edge_vector': winfo['hyperedges'],
'k': parts,
}
edge_weights, node_weights = {
(False, False): (None, None),
(False, True): ([], winfo['node_weights']),
(True, False): (winfo['edge_weights'], []),
(True, True): (winfo['edge_weights'], winfo['node_weights']),
}[winfo['has_edge_weights'], winfo['has_node_weights']]
if edge_weights or node_weights:
hypergraph_kwargs['edge_weights'] = edge_weights
hypergraph_kwargs['node_weights'] = node_weights
hypergraph = kahypar.Hypergraph(**hypergraph_kwargs)
if fix_output_nodes:
# make sure all the output nodes (those with output indices) are in
# the same partition
onodes = tuple(hg.output_nodes())
if parts >= nv - len(onodes) + 1:
# too many partitions, simply group all outputs and return
groups = itertools.count(1)
return [0 if i in onodes else next(groups) for i in range(nv)]
for i in onodes:
hypergraph.fixNodeToBlock(i, 0)
# silences various warnings
mode = 'recursive'
if profile is None:
profile_mode = {'direct': 'k', 'recursive': 'r'}[mode]
profile = f"{objective}_{profile_mode}KaHyPar_sea20.ini"
context = kahypar.Context()
context.loadINIconfiguration(join(KAHYPAR_PROFILE_DIR, profile))
context.setK(parts)
context.setSeed(seed)
context.suppressOutput(quiet)
context.setEpsilon(imbalance * parts)
kahypar.partition(hypergraph, context)
return [hypergraph.blockID(i) for i in hypergraph.nodes()]
import os
import kahypar as kahypar
num_nodes = 7
num_nets = 4
hyperedge_indices = [0,2,6,9,12]
hyperedges = [0,2,0,1,3,4,3,4,6,2,5,6]
node_weights = [1,2,3,4,5,6,7]
edge_weights = [11,22,33,44]
k=2
hypergraph = kahypar.Hypergraph(num_nodes, num_nets, hyperedge_indices, hyperedges, k, edge_weights, node_weights)
context = kahypar.Context()
context.loadINIconfiguration("/home/ags/code/kahypar/config/km1_kKaHyPar_sea20.ini")
context.setK(k)
context.setEpsilon(0.03)
kahypar.partition(hypergraph, context)
def partition_hygr(self, h):
if (h._nverts <= self._tilesize):
return range(h._nverts)
tilesize = self._tilesize
nparts = int((h._nverts + tilesize - 1) / tilesize)
curnhygr = 1
kway_bound = nparts
totalcut = 0
gpvec = [0] * h._nverts
context = self._context
context.setK(2) # will always partition into 2
# nparts should be > 1 at this point
assert (nparts > 1)
if (nparts & (nparts - 1) != 0):
kway_bound = int(math.pow(2, int(math.log2(nparts)) + 1))
# each entry three elems: [hygr, curk, gcids, ne, pe]
# ne and pe include supernets
curlvl = [None]
nextlvl = [[None] * 5, [None] * 5]
curlvl[0] = [
h, nparts, [x for x in range(h._nverts)], h._nnets, h._npins
]
while (curnhygr != kway_bound):
lastid = 0
for i in range(curnhygr):
if (curlvl[i][1] == 1):
lastid += 1
continue
if (curlvl[i][0] is None):
continue
if (curnhygr > 1 and self._addMsgNets):
self._add_send_msg_nets(h, lastid, 2 * curnhygr, gpvec,
curlvl, i)
# compute target pw
curk = curlvl[i][1]
tpw = [None] * 2
if (curlvl[i][0]._nverts % tilesize != 0):
tmp = int((curk + 1) / 2)
tpw[0] = tmp * tilesize
tpw[1] = curlvl[i][0]._nverts - tpw[0]
else:
if (curk % 2 == 0):
tpw[0] = tpw[1] = (curk / 2) * tilesize
else:
tmp = int(curk / 2)
tpw[0] = (tmp + 1) * tilesize
tpw[1] = tmp * tilesize
tpw[0] = int(tpw[0])
tpw[1] = int(tpw[1])
# form kahypar hypergraph
hk = kahypar.Hypergraph(
curlvl[i][0]._nverts,
curlvl[i][3], # with msg nets
curlvl[i][0]._xpins,
curlvl[i][0]._pins,
2,
curlvl[i][0]._nwghts,
curlvl[i][0]._cwghts)
context.setCustomTargetBlockWeights(tpw)
context.suppressOutput(True)
# partition and get part vector
kahypar.partition(hk, context)
lpvec = [None] * curlvl[i][0]._nverts
for v in range(curlvl[i][0]._nverts):
lpvec[v] = hk.blockID(v)
# @TODO if tpw is not achieved, return id perm
curcut = kahypar.cut(hk)
totalcut += curcut
assert (hk.blockWeight(0) == tpw[0]
and hk.blockWeight(1) == tpw[1])
# update global partvec
for v in range(h._nverts): # orig hygr
if (gpvec[v] > lastid):
gpvec[v] += 1
for v in range(curlvl[i][0]._nverts):
if (lpvec[v] == 1):
gpvec[curlvl[i][2][v]] += 1
lastid += 2
left = 2 * i
right = 2 * i + 1
nextlvl[right][1] = int(curk / 2)
nextlvl[left][1] = nextlvl[right][1] + (curk % 2)
# bisect
self._bisect(curlvl, lpvec, nextlvl, i)
curnhygr = curnhygr * 2
# update curlvl and nextlvl
if (curnhygr != nparts):
curlvl = nextlvl
nextlvl = [[None] * 5 for i in range(2 * curnhygr)]
return gpvec
def kahypar_subgraph_find_membership(
inputs,
output,
size_dict,
weight_nodes='constant',
weight_edges='log',
fuse_output_inds=False,
parts=2,
imbalance=0.01,
seed=None,
profile=None,
mode='direct',
objective='cut',
quiet=True,
):
import kahypar as kahypar
if seed is None:
seed = random.randint(0, 2**31 - 1)
nv = len(inputs)
if parts >= nv:
return list(range(nv))
HG = HyperGraph(inputs, output, size_dict,
weight_edges=weight_edges,
weight_nodes=weight_nodes,
fuse_output_inds=fuse_output_inds)
hyperedge_indices, hyperedges = HG.to_sparse()
hypergraph_kwargs = {
'num_nodes': HG.num_vertices,
'num_edges': HG.num_edges,
'index_vector': hyperedge_indices,
'edge_vector': hyperedges,
'k': parts,
}
edge_weights, node_weights = {
(False, False): (None, None),
(False, True): ([], HG.node_weights),
(True, False): (HG.edge_weights, []),
(True, True): (HG.edge_weights, HG.node_weights),
}[HG.has_edge_weights, HG.has_node_weights]
if edge_weights or node_weights:
hypergraph_kwargs['edge_weights'] = edge_weights
hypergraph_kwargs['node_weights'] = node_weights
hypergraph = kahypar.Hypergraph(**hypergraph_kwargs)
if profile is None:
profile_mode = {'direct': 'k', 'recursive': 'r'}[mode]
profile = f"{objective}_{profile_mode}KaHyPar_dissertation.ini"
context = kahypar.Context()
context.loadINIconfiguration(join(KAHYPAR_PROFILE_DIR, profile))
context.setK(parts)
context.setSeed(seed)
context.suppressOutput(quiet)
context.setEpsilon(imbalance * parts)
kahypar.partition(hypergraph, context)
return [hypergraph.blockID(i) for i in hypergraph.nodes()]
