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_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_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_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_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_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_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_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_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_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