def test_write_dx(tmpdir, nptype, dxtype, outfile, counts=100, ndim=3): # conversion from numpy array to DX file h, edges = np.histogramdd(np.random.random((counts, ndim)), bins=10) g = Grid(h, edges) # hack the grid to be a different dtype g.grid = g.grid.astype(nptype) assert_equal(g.grid.sum(), counts) with tmpdir.as_cwd(): g.export(outfile) g2 = Grid(outfile) # check that dxtype was written dx = gridData.OpenDX.field(0) dx.read(outfile) data = dx.components['data'] out_dxtype = data.type assert_almost_equal(g.grid, g2.grid, err_msg="written grid does not match original") assert_almost_equal(g.delta, g2.delta, decimal=6, err_msg="deltas of written grid do not match original") assert_equal(out_dxtype, dxtype)
def test_write_dx(tmpdir, nptype, dxtype, counts=100, ndim=3): # conversion from numpy array to DX file h, edges = np.histogramdd(np.random.random((counts, ndim)), bins=10) g = Grid(h, edges) # hack the grid to be a different dtype g.grid = g.grid.astype(nptype) assert_equal(g.grid.sum(), counts) with tmpdir.as_cwd(): outfile = "grid.dx" g.export(outfile) g2 = Grid(outfile) # check that dxtype was written dx = gridData.OpenDX.field(0) dx.read(outfile) data = dx.components['data'] out_dxtype = data.type assert_almost_equal(g.grid, g2.grid, err_msg="written grid does not match original") assert_almost_equal( g.delta, g2.delta, decimal=6, err_msg="deltas of written grid do not match original") assert_equal(out_dxtype, dxtype)
def _test_write_dx(counts=100, ndim=3, nptype="float32", dxtype="float"): h, edges = np.histogramdd(np.random.random((counts, ndim)), bins=10) g = Grid(h, edges) # hack the grid to be a different dtype g.grid = g.grid.astype(nptype) assert_equal(g.grid.sum(), counts) with tempdir.in_tempdir(): outfile = "grid.dx" g.export(outfile) g2 = Grid(outfile) # check that dxtype was written dx = gridData.OpenDX.field(0) dx.read(outfile) data = dx.components['data'] out_dxtype = data.type assert_almost_equal(g.grid, g2.grid, err_msg="written grid does not match original") assert_almost_equal( g.delta, g2.delta, decimal=6, err_msg="deltas of written grid do not match original") assert_equal(out_dxtype, dxtype)
def mask_generator(maskfile, referencefile=None, distance=5): if os.path.splitext(maskfile)[1] == ".pdb": mask = GridUtil.gen_distance_grid(referencefile, maskfile) else: mask = Grid(maskfile) mask.grid = mask.grid < distance return mask
def test_write_dx_ValueError(tmpdir, nptype, outfile, counts=100, ndim=3): h, edges = np.histogramdd(np.random.random((counts, ndim)), bins=10) g = Grid(h, edges) # hack the grid to be a different dtype g.grid = g.grid.astype(nptype) with pytest.raises(ValueError): with tmpdir.as_cwd(): g.export(outfile)
def test_write_dx_ValueError(tmpdir, nptype, counts=100, ndim=3): h, edges = np.histogramdd(np.random.random((counts, ndim)), bins=10) g = Grid(h, edges) # hack the grid to be a different dtype g.grid = g.grid.astype(nptype) with pytest.raises(ValueError): with tmpdir.as_cwd(): outfile = "grid.dx" g.export(outfile)