def test_lowScore(self):
a = CLT()
a.path_in = ["./data/vagus001.h5", "volume/data"]
a.path_out = ["/tmp/pores2.h5", "data"]
a.sigmaSmooth = 0.7
a.thresMembra = 1
a.sizeFilter = [20, 1000]
a.run()
res = a.res[::]
s = Score()
s.res = res
assert s.scoreTracer() == 0
def stest_simple(self):
a = CLT()
a.path_in = ["./data/vagus001.h5", "volume/data"]
a.path_out = ["/tmp/pores1.h5", "data"]
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [20, 1000]
a.run()
res = a.res[::]
s = Scorej()
s.res = res
assert p.scoreTracer() > 10
def test_lowScore(self):
a=CLT()
a.path_in = ["./data/vagus001.h5","volume/data"]
a.path_out = ["/tmp/pores2.h5","data"]
a.sigmaSmooth = 0.7
a.thresMembra = 1
a.sizeFilter = [20,1000]
a.run()
res = a.res[::]
s = Score()
s.res = res
assert s.scoreTracer() == 0
def stest_simple(self):
a=CLT()
a.path_in = ["./data/vagus001.h5","volume/data"]
a.path_out = ["/tmp/pores1.h5","data"]
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [20,1000]
a.run()
res = a.res[::]
s = Scorej()
s.res = res
assert p.scoreTracer() > 10
def test_Block_basic(self):
a=CLT()
a.path_in = ["./data/vagus001.h5","volume/data"]
a.path_out = ["/tmp/test.h5","data"]
a.Sub_Volume = [[0,100], [0,100], [0,17]]
a.blockSize = [50,50,50]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [20,1000]
a.run()
res = a.res[::]
score = a.getScore()
assert res.shape == (100,100,17)
def test_CLT_basic(self):
a=CLT()
a.path_in= ["./data/vagus001.h5","volume/data"]
a.path_out = ["/tmp/test.h5","data"]
a.Sub_Volume = [[0,50],[0,50],[0,50]]
a.blockSize = [25,25,25]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [20,1000]
#test if executing twice does not fail
a.run()
a.run()
def test_CLT_empty3(self):
a=CLT()
a.path_in= ["./data/vagus001.h5","volume/data"]
a.path_out = ["/tmp/test.h5","data"]
a.blockSize = [50,50,50]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = -1
a.sizeFilter = [0,10e10]
a.run()
res = a.res[::]
score = a.getScore()
# result is empty volume because everything was one large component
# (th<0), so the volume must be invalid
assert score == 0
assert numpy.all(res==0)
def test_CLT_empty2(self):
a=CLT()
a.path_in= ["./data/vagus001.h5","volume/data"]
a.path_out = ["/tmp/test.h5","data"]
a.blockSize = [50,50,50]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [10e5,10e6]
a.run()
res = a.res[::]
score = a.getScore()
# result is empty volume because size filter is abnormal
assert score == 0
assert numpy.all(res==0)
def test_CLT_basic(self):
a=CLT()
a.path_in= ["./data/vagus001.h5","volume/data"]
a.path_out = ["/tmp/test.h5","data"]
a.blockSize = [50,50,50]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [20,1000]
a.run()
res = a.res[::]
gaps = a.gaps[::]
score = a.getScore()
assert score>5 # mote than 5 start in the first 10 and end in the last 10 layer
assert numpy.sum(gaps!=0)>10 # there should be at least 10 gaps
assert len(numpy.unique(res))<30 # no more than 30 axons
assert len(numpy.unique(res))>15 # at least 15 axons
def test_Block_basic(self):
a = CLT()
a.path_in = ["./data/vagus001.h5", "volume/data"]
a.path_out = ["/tmp/test.h5", "data"]
a.Sub_Volume = [[0, 100], [0, 100], [0, 17]]
a.blockSize = [50, 50, 50]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [20, 1000]
a.run()
res = a.res[::]
score = a.getScore()
assert res.shape == (100, 100, 17)
def test_CLT_basic(self):
a = CLT()
a.path_in = ["./data/vagus001.h5", "volume/data"]
a.path_out = ["/tmp/test.h5", "data"]
a.Sub_Volume = [[0, 50], [0, 50], [0, 50]]
a.blockSize = [25, 25, 25]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [20, 1000]
#test if executing twice does not fail
a.run()
a.run()
def test_CLT_empty3(self):
a = CLT()
a.path_in = ["./data/vagus001.h5", "volume/data"]
a.path_out = ["/tmp/test.h5", "data"]
a.blockSize = [50, 50, 50]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = -1
a.sizeFilter = [0, 10e10]
a.run()
res = a.res[::]
score = a.getScore()
# result is empty volume because everything was one large component
# (th<0), so the volume must be invalid
assert score == 0
assert numpy.all(res == 0)
def test_CLT_empty2(self):
a = CLT()
a.path_in = ["./data/vagus001.h5", "volume/data"]
a.path_out = ["/tmp/test.h5", "data"]
a.blockSize = [50, 50, 50]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [10e5, 10e6]
a.run()
res = a.res[::]
score = a.getScore()
# result is empty volume because size filter is abnormal
assert score == 0
assert numpy.all(res == 0)
def test_CLT_basic(self):
a = CLT()
a.path_in = ["./data/vagus001.h5", "volume/data"]
a.path_out = ["/tmp/test.h5", "data"]
a.blockSize = [50, 50, 50]
a.helo = 10
a.sigmaSmooth = 0.7
a.thresMembra = 0.7
a.sizeFilter = [20, 1000]
a.run()
res = a.res[::]
gaps = a.gaps[::]
score = a.getScore()
assert score > 5 # mote than 5 start in the first 10 and end in the last 10 layer
assert numpy.sum(gaps != 0) > 10 # there should be at least 10 gaps
assert len(numpy.unique(res)) < 30 # no more than 30 axons
assert len(numpy.unique(res)) > 15 # at least 15 axons
