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test_server.py
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test_server.py
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import os
import threading
import numpy as np
import pytest
from skimage import io
from scipy import ndimage as ndi
from gala import features, agglo, serve, evaluate as ev
D = os.path.dirname(os.path.abspath(__file__))
os.chdir(os.path.join(D, 'example-data/snemi-mini'))
@pytest.fixture
def dummy_data():
frag0 = np.arange(1, 17, dtype=int).reshape((4, 4))
gt0 = np.array([[1, 1, 2, 2], [1, 1, 2, 2], [3] * 4, [3] * 4], dtype=int)
frag, gt = (ndi.zoom(image, 4, order=0, mode='reflect')
for image in [frag0, gt0])
fman = features.base.Mock(frag, gt)
return frag, gt, fman
@pytest.fixture
def dummy_data2(dummy_data):
frag, gt, _ = dummy_data
frag[7, 7:9] = 17
frag[7:10, -1] = 18
fman = features.base.Mock(frag, gt)
return frag, gt, fman
def test_server(dummy_data):
frag, gt, fman = dummy_data
host, port = 'tcp://localhost', 5588
solver = serve.Solver(frag, feature_manager=fman,
port=port, host='tcp://*')
thread = threading.Thread(target=solver.listen, name='solver')
thread.start()
_, dst = serve.proofread(frag, gt, host=host, port=port, num_operations=2,
stop_when_finished=True, random_state=0)
result = np.array(dst)[frag]
# test: resulting segmentation should be improvement over fragments alone
assert (ev.vi(result, gt, ignore_x=[], ignore_y=[]) <
ev.vi(frag, gt, ignore_x=[], ignore_y=[]))
thread.join()
def test_server_imperfect_fragments(dummy_data2):
frag, gt, fman = dummy_data2
host, port = 'tcp://localhost', 5589
solver = serve.Solver(frag, feature_manager=fman,
port=port, host='tcp://*')
thread = threading.Thread(target=solver.listen, name='solver')
thread.start()
_, dst = serve.proofread(frag, gt, host=host, port=port, num_operations=2,
stop_when_finished=True, random_state=0)
result = np.array(dst)[frag]
# test: resulting segmentation should be improvement over fragments alone
assert (ev.vi(result, gt, ignore_x=[], ignore_y=[]) <
ev.vi(frag, gt, ignore_x=[], ignore_y=[]))
thread.join()
@pytest.fixture
def data():
frag, gt, pr = map(io.imread, sorted(os.listdir('.')))
return frag, gt, pr
@pytest.mark.skipif('GALA_TEST_FULL' not in os.environ,
reason=("Test takes too long; "
"set GALA_TEST_FULL env variable to run this."))
def test_server_long(data):
frag, gt, pr = data
host, port = 'tcp://localhost', 5590
solver = serve.Solver(frag, pr, port=port, host='tcp://*')
thread = threading.Thread(target=solver.listen, name='solver')
thread.start()
_, dst = serve.proofread(frag, gt, host=host, port=port,
stop_when_finished=True, random_state=0)
result = np.array(dst)[frag]
# test: resulting segmentation should be improvement over fragments alone
assert (ev.vi(result, gt, ignore_x=[], ignore_y=[]) <
ev.vi(frag, gt, ignore_x=[], ignore_y=[]))
thread.join()