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from __future__ import absolute_import, division
import six
import numpy as np
from numpy.testing import (assert_array_equal, assert_array_almost_equal,
assert_almost_equal)
import pytest
from gridData import Grid
def f_arithmetic(g):
return g + g - 2.5 * g / (g + 5.3)
@pytest.fixture(scope="class")
def data():
d = dict(
griddata=np.arange(1, 28).reshape(3, 3, 3),
origin=np.zeros(3),
delta=np.ones(3))
d['grid'] = Grid(d['griddata'], origin=d['origin'],
delta=d['delta'])
return d
class TestGrid(object):
@pytest.fixture
def pklfile(self, data, tmpdir):
g = data['grid']
fn = tmpdir.mkdir('grid').join('grid.dat')
g.save(fn) # always saves as pkl
return fn
def test_init(self, data):
g = Grid(data['griddata'], origin=data['origin'],
delta=1)
assert_array_equal(g.delta, data['delta'])
def test_init_wrong_origin(self, data):
with pytest.raises(TypeError):
Grid(data['griddata'], origin=np.ones(4), delta=data['delta'])
def test_init_wrong_delta(self, data):
with pytest.raises(TypeError):
Grid(data['griddata'], origin=data['origin'], delta=np.ones(4))
def test_empty_Grid(self):
g = Grid()
assert isinstance(g, Grid)
def test_init_missing_delta_ValueError(self, data):
with pytest.raises(ValueError):
Grid(data['griddata'], origin=data['origin'])
def test_init_missing_origin_ValueError(self, data):
with pytest.raises(ValueError):
Grid(data['griddata'], delta=data['delta'])
def test_init_wrong_data_exception(self):
with pytest.raises(IOError):
Grid("__does_not_exist__")
def test_load_wrong_fileformat_ValueError(self):
with pytest.raises(ValueError):
Grid(grid=True, file_format="xxx")
def test_equality(self, data):
assert data['grid'] == data['grid']
assert data['grid'] != 'foo'
g = Grid(data['griddata'], origin=data['origin'] + 1, delta=data['delta'])
assert data['grid'] != g
def test_addition(self, data):
g = data['grid'] + data['grid']
assert_array_equal(g.grid.flat, (2 * data['griddata']).flat)
g = 2 + data['grid']
assert_array_equal(g.grid.flat, (2 + data['griddata']).flat)
g = g + data['grid']
assert_array_equal(g.grid.flat, (2 + (2 * data['griddata'])).flat)
def test_subtraction(self, data):
g = data['grid'] - data['grid']
assert_array_equal(g.grid.flat, np.zeros(27))
g = 2 - data['grid']
assert_array_equal(g.grid.flat, (2 - data['griddata']).flat)
def test_multiplication(self, data):
g = data['grid'] * data['grid']
assert_array_equal(g.grid.flat, (data['griddata'] ** 2).flat)
g = 2 * data['grid']
assert_array_equal(g.grid.flat, (2 * data['griddata']).flat)
def test_division(self, data):
# __truediv__ is used in py3 by default and py2 if division
# is imported from __future__; to make testing easier lets call
# them explicitely
#
g = data['grid'].__truediv__(data['grid'])
assert_array_equal(g.grid.flat, np.ones(27))
g = data['grid'].__rtruediv__(2)
assert_array_equal(g.grid.flat, (2 / data['griddata']).flat)
@pytest.mark.skipif(not six.PY2, reason="classic division only in Python 2")
def test_classic_division(self, data):
# this is normally ONLY invoked in python 2 and will ONLY
# work in Python 2; we test the operator methods directly
# because '/' always performs truedivision in GridDataFormats
# (we use __future__.division everywhere, also in this test)
g = data['grid'].__div__(data['grid'])
assert_array_equal(g.grid.flat, np.ones(27, dtype=np.int64))
# performs floordivision
g = data['grid'].__rdiv__(2)
assert_array_equal(g.grid.flat, (2 // data['griddata']).flat)
# performs truedivision
# (note: '/' performs truedivision because of __future__.division!)
g = data['grid'].__rdiv__(2.0)
assert_array_equal(g.grid.flat, (2.0 / data['griddata']).flat)
@pytest.mark.skipif(six.PY2, reason="classic division present in Python 2")
def test_classic_division_NotImplementedError(self, data):
with pytest.raises(NotImplementedError):
data['grid'].__div__(2)
with pytest.raises(NotImplementedError):
data['grid'].__rdiv__(2)
def test_floordivision(self, data):
g = data['grid'].__floordiv__(data['grid'])
assert_array_equal(g.grid.flat, np.ones(27, dtype=np.int64))
g = 2 // data['grid']
assert_array_equal(g.grid.flat, (2 // data['griddata']).flat)
def test_power(self, data):
g = data['grid'] ** 2
assert_array_equal(g.grid.flat, (data['griddata'] ** 2).flat)
g = 2 ** data['grid']
assert_array_equal(g.grid.flat, (2 ** data['griddata']).flat)
def test_compatibility_type(self, data):
assert data['grid'].check_compatible(data['grid'])
assert data['grid'].check_compatible(3)
g = Grid(data['griddata'], origin=data['origin'] - 1, delta=data['delta'])
assert data['grid'].check_compatible(g)
def test_wrong_compatibile_type(self, data):
with pytest.raises(TypeError):
data['grid'].check_compatible("foo")
def test_non_orthonormal_boxes(self, data):
delta = np.eye(3)
with pytest.raises(NotImplementedError):
Grid(data['griddata'], origin=data['origin'], delta=delta)
def test_centers(self, data):
# this only checks the edges. If you know an alternative
# algorithm that isn't an exact duplicate of the one in
# g.centers to test this please implement it.
g = Grid(data['griddata'], origin=np.ones(3), delta=data['delta'])
centers = np.array(list(g.centers()))
assert_array_equal(centers[0], g.origin)
assert_array_equal(centers[-1] - g.origin,
(np.array(g.grid.shape) - 1) * data['delta'])
def test_resample_factor_failure(self, data):
pytest.importorskip('scipy')
with pytest.raises(ValueError):
g = data['grid'].resample_factor(0)
def test_resample_factor(self, data):
pytest.importorskip('scipy')
g = data['grid'].resample_factor(2)
assert_array_equal(g.delta, np.ones(3) * .5)
# zooming in by a factor of 2. Each subinterval is
# split in half, so 3 gridpoints (2 subintervals)
# becomes 5 gridpoints (4 subintervals)
assert_array_equal(g.grid.shape, np.ones(3) * 5)
# check that the values are identical with the
# correct stride.
assert_array_almost_equal(g.grid[::2, ::2, ::2],
data['grid'].grid)
def test_load_pickle(self, data, tmpdir):
g = data['grid']
fn = str(tmpdir.mkdir('grid').join('grid.pkl'))
g.save(fn)
h = Grid()
h.load(fn)
assert h == g
def test_init_pickle_pathobjects(self, data, tmpdir):
g = data['grid']
fn = tmpdir.mkdir('grid').join('grid.pickle')
g.save(fn)
h = Grid(fn)
assert h == g
@pytest.mark.parametrize("fileformat", ("pkl", "PKL", "pickle", "python"))
def test_load_fileformat(self, data, pklfile, fileformat):
h = Grid(pklfile, file_format="pkl")
assert h == data['grid']
# At the moment, reading the file with the wrong parser does not give
# good error messages.
@pytest.mark.xfail
@pytest.mark.parametrize("fileformat", ("ccp4", "plt", "dx"))
def test_load_wrong_fileformat(self, data, pklfile, fileformat):
with pytest.raises('ValueError'):
Grid(pklfile, file_format=fileformat)
# just check that we can export without stupid failures; detailed
# format checks in separate tests
@pytest.mark.parametrize("fileformat", ("dx", "pkl"))
def test_export(self, data, fileformat, tmpdir):
g = data['grid']
fn = tmpdir.mkdir('grid_export').join("grid.{}".format(fileformat))
g.export(fn) # check that path objects work
h = Grid(fn) # use format autodetection
assert g == h
@pytest.mark.parametrize("fileformat", ("ccp4", "plt"))
def test_export_not_supported(self, data, fileformat, tmpdir):
g = data['grid']
fn = tmpdir.mkdir('grid_export').join("grid.{}".format(fileformat))
with pytest.raises(ValueError):
g.export(fn)
def test_inheritance(data):
class DerivedGrid(Grid):
pass
dg = DerivedGrid(data['griddata'], origin=data['origin'],
delta=data['delta'])
result = f_arithmetic(dg)
assert isinstance(result, DerivedGrid)
ref = f_arithmetic(data['grid'])
assert_almost_equal(result.grid, ref.grid)
def test_anyarray(data):
ma = np.ma.MaskedArray(data['griddata'])
mg = Grid(ma, origin=data['origin'], delta=data['delta'])
assert isinstance(mg.grid, ma.__class__)
result = f_arithmetic(mg)
ref = f_arithmetic(data['grid'])
assert_almost_equal(result.grid, ref.grid)
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