How to use the gala.imio.read_h5_stack function in gala

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github janelia-flyem / gala / test / test_gala.py View on Github external
def setUp(self):
        self.probs2 = imio.read_h5_stack(rundir+'/test-05-probabilities.h5')
        self.probs1 = self.probs2[...,0]
        self.wss1 = imio.read_h5_stack(rundir+'/test-05-watershed.h5')
        self.f1, self.f2, self.f3 = features.moments.Manager(2, False), \
            features.histogram.Manager(3,compute_percentiles=[0.5]), \
            features.squiggliness.Manager(ndim=2)
        self.f4 = features.base.Composite(children=[self.f1, self.f2, self.f3])
github janelia-flyem / gala / test / test_gala.py View on Github external
def setUp(self):
        test_idxs = range(1,5)
        self.num_tests = len(test_idxs)
        pfns = [rundir+'/test-%02i-probabilities.h5'%i for i in test_idxs]
        wsfns = [rundir+'/test-%02i-watershed.h5'%i for i in test_idxs]
        self.probs = [imio.read_h5_stack(fn) for fn in pfns]
        self.wss = [imio.read_h5_stack(fn) for fn in wsfns]
        gtfns = [rundir+'/test-%02i-groundtruth.h5'%i for i in test_idxs]
        self.results = [imio.read_h5_stack(fn) for fn in gtfns]
github janelia-flyem / gala / benchmarks / bench_gala.py View on Github external
def trdata():
    wstr = imio.read_h5_stack(os.path.join(dd, 'train-ws.lzf.h5'))
    prtr = imio.read_h5_stack(os.path.join(dd, 'train-p1.lzf.h5'))
    gttr = imio.read_h5_stack(os.path.join(dd, 'train-gt.lzf.h5'))
    return wstr, prtr, gttr
github janelia-flyem / gala / benchmarks / bench_gala.py View on Github external
def trdata():
    wstr = imio.read_h5_stack(os.path.join(dd, 'train-ws.lzf.h5'))
    prtr = imio.read_h5_stack(os.path.join(dd, 'train-p1.lzf.h5'))
    gttr = imio.read_h5_stack(os.path.join(dd, 'train-gt.lzf.h5'))
    return wstr, prtr, gttr
github janelia-flyem / gala / benchmarks / bench_gala.py View on Github external
def tsdata():
    wsts = imio.read_h5_stack(os.path.join(dd, 'test-ws.lzf.h5'))
    prts = imio.read_h5_stack(os.path.join(dd, 'test-p1.lzf.h5'))
    gtts = imio.read_h5_stack(os.path.join(dd, 'test-gt.lzf.h5'))
    return wsts, prts, gtts
github janelia-flyem / gala / benchmarks / bench_gala.py View on Github external
def tsdata():
    wsts = imio.read_h5_stack(os.path.join(dd, 'test-ws.lzf.h5'))
    prts = imio.read_h5_stack(os.path.join(dd, 'test-p1.lzf.h5'))
    gtts = imio.read_h5_stack(os.path.join(dd, 'test-gt.lzf.h5'))
    return wsts, prts, gtts
github janelia-flyem / gala / benchmarks / bench_gala.py View on Github external
def trdata():
    wstr = imio.read_h5_stack(os.path.join(dd, 'train-ws.lzf.h5'))
    prtr = imio.read_h5_stack(os.path.join(dd, 'train-p1.lzf.h5'))
    gttr = imio.read_h5_stack(os.path.join(dd, 'train-gt.lzf.h5'))
    return wstr, prtr, gttr