def test_write_pajek_no_coordinates(self):
net = readwrite.read_pajek(_fullpath("../networks/leu_by_genesets.net"))
net.coordinates = None
with NamedTemporaryFile("wt", suffix=".net", delete=False) as f:
try:
readwrite.write_pajek(f, net)
f.close()
net2 = readwrite.read_pajek(f.name)
np.testing.assert_equal(net2.nodes, net.nodes)
self.assertIsNone(net2.coordinates, net.coordinates)
finally:
os.remove(f.name)
def test_write_pajek(self):
net = readwrite.read_pajek(_fullpath("../networks/leu_by_genesets.net"))
with NamedTemporaryFile("wt", suffix=".net", delete=False) as f:
try:
readwrite.write_pajek(f, net)
f.close()
net2 = readwrite.read_pajek(f.name)
np.testing.assert_equal(net2.nodes, net.nodes)
np.testing.assert_equal(net2.coordinates, net.coordinates)
self.assertEqual(len(net2.edges), 1)
edges, edges2 = net.edges[0].edges, net2.edges[0].edges
np.testing.assert_equal(edges.indptr, edges2.indptr)
np.testing.assert_equal(edges.indices, edges2.indices)
np.testing.assert_almost_equal(edges.data, edges2.data)
finally:
os.remove(f.name)
def test_edge_list(self):
net = readwrite.read_pajek(_fullpath("test-arcslist.net"))
neighs = [(1, (2, 3, 6)), (2, (1, 4, 5, 6)), (5, (1, 2)),
(6, (2, 3, 4))]
self.assertEqual(net.number_of_edges(), sum(len(y) for _, y in neighs))
self.assertTrue(net.edges[0].directed)
for x, y in neighs:
np.testing.assert_equal(net.outgoing(x - 1), np.array(y) - 1)
def main():
from Orange.widgets.utils.widgetpreview import WidgetPreview
from orangecontrib.network.network.readwrite \
import read_pajek, transform_data_to_orange_table
from os.path import join, dirname
network = read_pajek(join(dirname(dirname(__file__)), 'networks', 'leu_by_genesets.net'))
#transform_data_to_orange_table(network)
WidgetPreview(OWNxExplorer).run(set_graph=network)
def main(): # pragma: no cover
from orangecontrib.network.network.readwrite import read_pajek
from os.path import join, dirname
from orangewidget.utils.widgetpreview import WidgetPreview
path = join(dirname(__file__), "..", "networks")
network = read_pajek(join(path, 'airtraffic.net'))
data = Table(join(path, 'airtraffic_items.tab'))
WidgetPreview(OWNxGroups).run(set_network=network, set_data=data)
def test_two_mode(self):
davis = readwrite.read_pajek(_fullpath("../networks/davis.net"))
self.assertEqual(davis.number_of_nodes(), 32)
self.assertEqual(list(davis.nodes), [
'EVELYN', 'LAURA', 'THERESA', 'BRENDA', 'CHARLOTTE', 'FRANCES',
'ELEANOR', 'PEARL', 'RUTH', 'VERNE', 'MYRNA', 'KATHERINE',
'SYLVIA', 'NORA', 'HELEN', 'DOROTHY', 'OLIVIA', 'FLORA', 'E1',
'E2', 'E3', 'E4', 'E5', 'E6', 'E7', 'E8', 'E9', 'E10', 'E11',
'E12', 'E13', 'E14'
])
self.assertEqual(davis.in_first_mode, 18)
def open_net_file(self, filename):
"""Read network from file."""
self.Error.clear()
self.Warning.clear()
self.Information.clear()
self.network = None
self.original_nodes = None
try:
self.network = read_pajek(filename)
except OSError as err:
self.Error.io_error(
filename,
"".join(format_exception_only(type(err), err)).rstrip())
except Exception: # pylint: disable=broad-except
self.Error.error_parsing_file(filename)
else:
self.original_nodes = self.network.nodes
self.read_auto_data(filename)
self.send_output()
domain = self.net.nodes.domain
# Tie a name for presenting clustering results to the widget instance
if self.cluster_feature is None:
self.cluster_feature = get_unique_names(domain, 'Cluster')
cd.add_results_to_items(self.net, labels, self.cluster_feature)
self.Outputs.items.send(self.net.nodes)
self.Outputs.network.send(self.net)
nclusters = len(set(labels.values()))
self.info.set_output_summary(nclusters, f"{nclusters} clusters")
@classmethod
def migrate_settings(cls, settings, version):
if version < 2:
rename_setting(settings, "autoApply", "auto_apply")
if hasattr(settings, "method"):
rename_setting(settings, "method", "attenuate")
if __name__ == "__main__":
from Orange.widgets.utils.widgetpreview import WidgetPreview
from orangecontrib.network.network.readwrite \
import read_pajek, transform_data_to_orange_table
from os.path import join, dirname
fname = join(dirname(dirname(__file__)), 'networks', 'leu_by_genesets.net')
network = read_pajek(fname)
transform_data_to_orange_table(network)
WidgetPreview(OWNxClustering).run(set_network=network)
callbacks=[self._progress_updater])
self._worker_thread = EmbedderThread(
lambda: self.embedder(self.network))
self._worker_thread.finished.connect(self.on_finished)
self.progressBarInit()
self.progressBarSet(1e-5)
self._worker_thread.start()
def on_finished(self):
output = self._worker_thread.result
self._worker_thread = None
self._progress_updater = None
self.progressBarFinished()
self.Outputs.items.send(output)
def onDeleteWidget(self):
if self._worker_thread is not None:
# prevent the callback from trying to access deleted widget object
self._progress_updater.widget = None
self._worker_thread.finished.disconnect()
self._worker_thread.quit()
super().onDeleteWidget()
if __name__ == "__main__":
from os.path import join, dirname
davis = join(dirname(__file__), "..", "networks", "davis.net")
network = readwrite.read_pajek(davis)
WidgetPreview(OWNxEmbedding).run(network)
def main_without_annotation():
net = readwrite.read_pajek("../networks/leu_by_genesets.net")
WidgetPreview(OWNxSave).run(net)
def test_write_pajek_multiple_edge_types(self):
net = readwrite.read_pajek(
_fullpath("../networks/leu_by_genesets.net"))
net.edges.append(net.edges[0])
with NamedTemporaryFile("wt", suffix=".net") as f:
self.assertRaises(TypeError, readwrite.write_pajek, f, net)
isDirected = 0
for edge in edges:
es = edge.edges
if edge.directed:
isDirected = 1
for i in range(es.shape[0]):
matrix = es[i].tocoo()
weight += matrix.data.tolist()
source += [i]*matrix.nnz
target += [r+c for r,c in zip(matrix.row, matrix.col)]
directed = np.array([isDirected]*len(source))
X =np.array([source,target,weight,directed]).T
domain = Domain([ContinuousVariable("source"),ContinuousVariable("target"),\
ContinuousVariable("weight"),ContinuousVariable("isDirected")],\
None, None)
edges = Table.from_numpy(domain,X,None,None,None)
self.edges = edges
# send the vertices & edges data table created to output signal
def send_output(self):
self.Outputs.vertices.send(self.vertices)
self.Outputs.edges.send(self.edges)
if __name__ == "__main__":
# Just for widget debugging
WidgetPreview(OWNx2Table).run(
read_pajek("D:/JetBrains/IdeaProjects/MyPyhton38/scripts/USAir97.net")
)
