Example #1
0
def test_rstan_read_rdump():
    a = np.array([1, 3, 5])
    b = np.arange(10).reshape((-1, 2))
    c = np.arange(18).reshape([2, 3, 3])
    data = dict(**locals())
    tempdir = tempfile.mkdtemp()
    filename = os.path.join(tempdir, 'test_rdump.rdump')
    misc.stan_rdump(data, filename)
    d = misc.read_rdump(filename)
    np.testing.assert_equal(d['a'], a)
    np.testing.assert_equal(d['b'], b)
    np.testing.assert_equal(d['c'], c)
Example #2
0
 def test_rstan_read_rdump(self):
     a = np.array([1, 3, 5])
     b = np.arange(10).reshape((-1, 2))
     c = np.arange(18).reshape([2, 3, 3])
     data = dict(a=a, b=b, c=c)
     tempdir = tempfile.mkdtemp()
     filename = os.path.join(tempdir, 'test_rdump.rdump')
     misc.stan_rdump(data, filename)
     d = misc.read_rdump(filename)
     np.testing.assert_equal(d['a'], a)
     np.testing.assert_equal(d['b'], b)
     np.testing.assert_equal(d['c'], c)
Example #3
0
def main(args, logger):
    logger.info("Loading sequence depth file")
    df = load_multiple_depth_file(args["depth_file_path"])
    n_samples = len(args["depth_file_path"])
    n_length = df["location"].max()
    # Drop tuples those depth is 0 to reduce memory usage

    stan_data = {}
    stan_data["K"] = args["nmix"]
    df = df[df["depth"] != 0]
    n_iteration = len(df)
    stan_data["I"] = n_iteration
    stan_data["S"] = n_samples
    stan_data["L"] = n_length
    stan_data["SUBJECT"] = df["subject"].values
    stan_data["LOCATION"] = df["location"].values
    stan_data["DEPTH"] = df["depth"].values

    stan_rdump(stan_data, args["output_dest"])
Example #4
0
def test_stan_rdump():
    data = OrderedDict(x=1, y=0, z=[1, 2, 3], Phi=np.array([[1, 2], [3, 4]]))
    tempdir = tempfile.mkdtemp()
    filename = os.path.join(tempdir, 'test_rdump.rdump')
    misc.stan_rdump(data, filename)
    data_recovered = misc.read_rdump(filename)
    np.testing.assert_equal(data, data_recovered)

    data = OrderedDict(x=True, y=np.array([True, False]))
    data_expected = OrderedDict(x=1, y=np.array([1, 0]))
    misc.stan_rdump(data, filename)
    data_recovered = misc.read_rdump(filename)
    np.testing.assert_equal(data_recovered, data_expected)

    data = OrderedDict(x='foo')
    np.testing.assert_raises(ValueError, misc.stan_rdump, data, filename)

    data = OrderedDict(new=3)
    np.testing.assert_raises(ValueError, misc.stan_rdump, data, filename)
Example #5
0
def test_stan_rdump():
    data = OrderedDict(x=1, y=0, z=[1, 2, 3], Phi=np.array([[1, 2], [3, 4]]))
    tempdir = tempfile.mkdtemp()
    filename = os.path.join(tempdir, 'test_rdump.rdump')
    misc.stan_rdump(data, filename)
    data_recovered = misc.read_rdump(filename)
    np.testing.assert_equal(data, data_recovered)

    data = OrderedDict(x=True, y=np.array([True, False]))
    data_expected = OrderedDict(x=1, y=np.array([1, 0]))
    misc.stan_rdump(data, filename)
    data_recovered = misc.read_rdump(filename)
    np.testing.assert_equal(data_recovered, data_expected)

    data = OrderedDict(x='foo')
    np.testing.assert_raises(ValueError, misc.stan_rdump, data, filename)

    data = OrderedDict(new=3)
    np.testing.assert_raises(ValueError, misc.stan_rdump, data, filename)