def test_fail_connectors_order(self):
g = DeepGraph(v)
with pytest.raises(KeyError):
g.create_edges(connectors=[dsi, velo, dsf])
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi, velo, dsf])
def test_fail_common_output_rs(self):
g = DeepGraph(v)
with pytest.raises(AssertionError):
g.create_edges(connectors=[dsi, dsf], selectors=[dsf_velo_t])
g.create_edges_ft(('si', v.si.max()), connectors=[dsi, dsf],
selectors=[dsf_velo_t])
def test_fail_selector_ind_shape(self):
g = DeepGraph(v)
with pytest.raises(AssertionError):
g.create_edges(connectors=dsi, selectors=fail_ind_shape)
g.create_edges_ft(('si', v.si.max()), connectors=dsi,
selectors=fail_ind_shape)
def test_fail_selectors_order(self):
g = DeepGraph(v)
with pytest.raises(KeyError):
g.create_edges(selectors=[fail_selector_order, dsi_dsf_t])
g.create_edges_ft(('si', v.si.max()),
selectors=[fail_selector_order, dsi_dsf_t])
def test_ft_dt_min_chunk_size_hdf(self, tmpdir, min_chunk_size):
pytest.importorskip('tables')
# tmp hdf store
folder = str(tmpdir)
vo = v.drop('o', axis=1)
vs = pd.HDFStore(folder + 'vs.h5', mode='w')
vs.put('v', vo, format='t', data_columns=True, index=False)
e_true = e_full_true.copy()
e_true['dmcs'] = [
3, 6, 7, 7, 8, 12, 12, 3, 4, 4, 5, 9, 9, 1, 1, 2, 6, 6, 0, 1, 5, 5,
1, 5, 5, 4, 4, 0
]
e_true = e_true[e_true.dmcs <= 2][['dmcs']]
g = DeepGraph(vs)
g.create_edges_ft(ft_feature=('dtmcs', 2, 'h'),
min_chunk_size=min_chunk_size)
e_test = g.e.rename(columns={'ft_r': 'dmcs'})
e_test['dmcs'] = e_test.dmcs.astype(int)
assert_frame_equal(e_test.sort_index(axis=1),
e_true.sort_index(axis=1))
def test_hdf_key(self, tmpdir):
pytest.importorskip('tables')
# tmp hdf store
folder = str(tmpdir)
vo = v.drop('o', axis=1)
vs = pd.HDFStore(folder + 'vs.h5', mode='w')
vs.put('v', vo, format='t', data_columns=True, index=False)
e_true = e_full_true[(e_full_true.dsi <= 3) &
(e_full_true.dsf <= 1)]
g = DeepGraph(vs)
g.create_edges(selectors=[dsi_dsf_t], hdf_key='v')
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
selectors=[dsi_dsf_t], hdf_key='v')
e_test = g.e.drop('ft_r', axis=1)
vs.close()
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_step_size(self, step_size):
e_true = e_full_true.iloc[:, 0:0]
g = DeepGraph(v)
g.create_edges(step_size=step_size)
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
def test_ft_sf(self):
e_true = e_full_true[e_full_true.dsf <= 2.][['dsf']]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('sf', 2.))
e_test = g.e.rename(columns={'ft_r': 'dsf'})
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_from_pos(self, from_pos):
e_true = e_full_true.iloc[from_pos:, 0:0]
g = DeepGraph(v)
g.create_edges(from_pos=from_pos)
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
def test_ft_sf(self):
e_true = e_full_true[e_full_true.dsf <= 2.][['dsf']]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('sf', 2.))
e_test = g.e.rename(columns={'ft_r': 'dsf'})
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_from_pos(self, from_pos):
e_true = e_full_true.iloc[from_pos:, 0:0]
g = DeepGraph(v)
g.create_edges(from_pos=from_pos)
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
def test_to_pos(self, to_pos):
e_true = e_full_true.iloc[:to_pos, 0:0]
g = DeepGraph(v)
g.create_edges(to_pos=to_pos)
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
def test_step_size(self, step_size):
e_true = e_full_true.iloc[:, 0:0]
g = DeepGraph(v)
g.create_edges(step_size=step_size)
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
def test_ft_max_pairs(self, max_pairs):
e_true = e_full_true[['dsi']]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('si', v.si.max()), max_pairs=max_pairs)
e_test = g.e.rename(columns={'ft_r': 'dsi'})
pdt.assert_frame_equal(e_test, e_true)
def test_to_pos(self, to_pos):
e_true = e_full_true.iloc[:to_pos, 0:0]
g = DeepGraph(v)
g.create_edges(to_pos=to_pos)
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
def test_ft_ftt_order(self):
e_true = e_full_true[e_full_true.dsf <= 1]
g = DeepGraph(v)
g.create_edges_ft(('si', v.si.max()), connectors=[dsi],
selectors=[dsf_velo_t, 'ft_selector'])
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_ft_si(self):
e_true = e_full_true[e_full_true.dsi <= 3][['dsi']]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('si', 3))
e_test = g.e.rename(columns={'ft_r': 'dsi'})
pdt.assert_frame_equal(e_test.sort_index(axis=1),
e_true.sort_index(axis=1))
def test_ft_sdt(self):
e_true = e_full_true[e_full_true.dsi <= 3][['dsi']]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('sdt', 3, 'h'))
e_test = g.e.rename(columns={'ft_r': 'dsi'})
e_test['dsi'] = e_test.dsi.astype(int)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_ft_sdt(self):
e_true = e_full_true[e_full_true.dsi <= 3][['dsi']]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('sdt', 3, 'h'))
e_test = g.e.rename(columns={'ft_r': 'dsi'})
e_test['dsi'] = e_test.dsi.astype(int)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_ft_r_dep_connector(self):
e_true = e_full_true[e_full_true.dsi <= 5]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('sdt', 5, 'h'), connectors=ft_r_dep)
e_test = g.e.rename(columns={'ft_r': 'dsi'})
e_test['dsi'] = e_test.dsi.astype(int)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_ft_max_pairs(self, max_pairs):
e_true = e_full_true[['dsi']]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('si', v.si.max()),
max_pairs=max_pairs)
e_test = g.e.rename(columns={'ft_r': 'dsi'})
pdt.assert_frame_equal(e_test, e_true)
def test_ft_r_dep_connector(self):
e_true = e_full_true[e_full_true.dsi <= 5]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('sdt', 5, 'h'),
connectors=ft_r_dep)
e_test = g.e.rename(columns={'ft_r': 'dsi'})
e_test['dsi'] = e_test.dsi.astype(int)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_ft_ftt_order(self):
e_true = e_full_true[e_full_true.dsf <= 1]
g = DeepGraph(v)
g.create_edges_ft(('si', v.si.max()), connectors=[dsi],
selectors=[dsf_velo_t, 'ft_selector'])
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort_index(axis=1),
e_true.sort_index(axis=1))
def test_ft_to_pos(self, ft_to_pos):
e_true = e_full_true[['dsi']]
s = e_true.index.get_level_values(0)
e_true = e_true[s < ft_to_pos]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('si', v.si.max()), to_pos=ft_to_pos)
e_test = g.e.rename(columns={'ft_r': 'dsi'})
pdt.assert_frame_equal(e_test, e_true)
def test_ft_to_pos(self, ft_to_pos):
e_true = e_full_true[['dsi']]
s = e_true.index.get_level_values(0)
e_true = e_true[s < ft_to_pos]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('si', v.si.max()),
to_pos=ft_to_pos)
e_test = g.e.rename(columns={'ft_r': 'dsi'})
pdt.assert_frame_equal(e_test, e_true)
def test_no_arguments(self):
e_true = e_full_true.iloc[:, 0:0]
g = DeepGraph(v)
g.create_edges()
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
g.create_edges_ft(('si', v.si.max()))
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test, e_true)
def test_connector(self):
e_true = e_full_true[['dsi']]
g = DeepGraph(v)
g.create_edges(connectors=dsi)
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
g.create_edges_ft(('si', v.si.max()),
connectors=dsi)
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test, e_true)
def test_connectors(self):
e_true = e_full_true[['dsf', 'dsi']]
g = DeepGraph(v)
g.create_edges(connectors=[dsi, dsf])
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi, dsf])
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
class TestAppendCP(object):
e = g.e.iloc[[0, 3]]
g = DeepGraph(v, e)
def test_defaults(self):
pytest.importorskip('scipy')
cp_true = np.array([0, 0, 0, 2, 1])
self.g.append_cp()
cp_test = g.v.cp.values
assert_allclose(cp_true, cp_test)
def test_consolidate_singles(self):
pytest.importorskip('scipy')
cp_true = np.array([1, 1, 1, 0, 0])
self.g.append_cp(consolidate_singles=True)
cp_test = g.v.cp.values
assert_allclose(cp_true, cp_test)
def test_selector(self):
e_true = e_full_true[(e_full_true.dsi <= 3) &
(e_full_true.dsf <= 1)]
g = DeepGraph(v)
g.create_edges(selectors=[dsi_dsf_t])
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
selectors=[dsi_dsf_t])
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_logging(self, tmpdir):
e_true = e_full_true.iloc[:, 0:0]
g = DeepGraph(v)
folder = str(tmpdir)
g.create_edges(verbose=True, logfile=folder+'lf.txt')
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
g.create_edges_ft(('si', v.si.max()),
verbose=True, logfile=folder+'lf.txt')
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_no_transfer_r(self):
e_true = e_full_true.drop('dsf', axis=1)
g = DeepGraph(v)
g.create_edges(connectors=[dsi, dsf, velo], no_transfer_rs='dsf')
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi, dsf, velo],
no_transfer_rs='dsf')
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_connector_selector(self):
e_true = e_full_true[e_full_true.dsi <= 3]
g = DeepGraph(v)
g.create_edges(connectors=[dsi, dsf, velo],
selectors=dsi_t)
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi, dsf, velo],
selectors=dsi_t)
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_hdf_step_size(self, tmpdir, step_size):
pytest.importorskip('tables')
# tmp hdf store
folder = str(tmpdir)
vo = v.drop('o', axis=1)
vs = pd.HDFStore(folder + 'vs.h5', mode='w')
vs.put('v', vo, format='t', index=False)
e_true = e_full_true[(e_full_true.dsi <= 3) & (e_full_true.dsf <= 1)]
g = DeepGraph(vs)
g.create_edges(selectors=[dsi_dsf_t], step_size=step_size, hdf_key='v')
e_test = g.e
vs.close()
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_r_dtype_dic(self):
e_true = e_full_true[['dsf', 'dsi']]
e_true['dsf'] = e_true.dsf.astype(np.uint8)
e_true['dsi'] = e_true.dsi.astype(np.float32)
r_dtype_dic = {'dsf': np.uint8, 'dsi': np.float32}
g = DeepGraph(v)
g.create_edges(connectors=[dsi, dsf], r_dtype_dic=r_dtype_dic)
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi, dsf], r_dtype_dic=r_dtype_dic)
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_transfer_feature(self):
e_true = e_full_true.iloc[:, 0:0]
s = e_true.index.get_level_values(0)
t = e_true.index.get_level_values(1)
e_true['f_s'] = v.loc[s, 'f'].values
e_true['f_t'] = v.loc[t, 'f'].values
g = DeepGraph(v)
g.create_edges(transfer_features='f')
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
transfer_features='f')
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_hdf_step_size(self, tmpdir, step_size):
pytest.importorskip('tables')
# tmp hdf store
folder = str(tmpdir)
vo = v.drop('o', axis=1)
vs = pd.HDFStore(folder + 'vs.h5', mode='w')
vs.put('v', vo, format='t', index=False)
e_true = e_full_true[(e_full_true.dsi <= 3) &
(e_full_true.dsf <= 1)]
g = DeepGraph(vs)
g.create_edges(selectors=[dsi_dsf_t], step_size=step_size,
hdf_key='v')
e_test = g.e
vs.close()
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_ft_sdt_hdf(self, tmpdir):
pytest.importorskip('tables')
# tmp hdf store
folder = str(tmpdir)
vo = v.drop('o', axis=1)
vs = pd.HDFStore(folder + 'vs.h5', mode='w')
vs.put('v', vo, format='t', data_columns=True, index=False)
e_true = e_full_true[(e_full_true.dsi <= 3) & (e_full_true.dsf <= 1)]
g = DeepGraph(vs)
g.create_edges_ft(ft_feature=('sdt', 3, 'h'),
selectors=dsi_dsf_t,
hdf_key='v')
e_test = g.e.drop('ft_r', axis=1)
vs.close()
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_ft_min_chunk_size(self, min_chunk_size):
e_true = e_full_true.copy()
e_true['dmcs'] = [3,6,7,7,8,12,12,3,4,4,5,9,9,1,1,2,6,6,0,1,5,5,1,
5,5,4,4,0]
e_true = e_true[e_true.dmcs <= 2][['dmcs']]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('mcs', 2),
min_chunk_size=min_chunk_size)
e_test = g.e.rename(columns={'ft_r': 'dmcs'})
e_test['dmcs'] = e_test.dmcs.astype(int)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(ft_feature=('dtmcs', 2, 'h'),
min_chunk_size=min_chunk_size)
e_test = g.e.rename(columns={'ft_r': 'dmcs'})
e_test['dmcs'] = e_test.dmcs.astype(int)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_fail_connectors_order(self):
g = DeepGraph(v)
with pytest.raises(KeyError):
g.create_edges(connectors=[dsi, velo, dsf])
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi, velo, dsf])
def test_fail_selectors_order(self):
g = DeepGraph(v)
with pytest.raises(KeyError):
g.create_edges(selectors=[fail_selector_order, dsi_dsf_t])
g.create_edges_ft(('si', v.si.max()),
selectors=[fail_selector_order, dsi_dsf_t])
def test_transfer_features(self):
e_true = e_full_true.iloc[:, 0:0]
s = e_true.index.get_level_values(0)
t = e_true.index.get_level_values(1)
e_true['f_s'] = v.loc[s, 'f'].values
e_true['f_t'] = v.loc[t, 'f'].values
e_true['s_s'] = v.loc[s, 's'].values
e_true['s_t'] = v.loc[t, 's'].values
e_true['o_s'] = v.loc[s, 'o'].values
e_true['o_t'] = v.loc[t, 'o'].values
g = DeepGraph(v)
g.create_edges(transfer_features=['f', 's', 'o'])
e_test = g.e
pdt.assert_frame_equal(e_test.sort_index(axis=1),
e_true.sort_index(axis=1))
g.create_edges_ft(('si', v.si.max()),
transfer_features=['f', 's', 'o'])
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort_index(axis=1),
e_true.sort_index(axis=1))
def test_fail_common_output_rs(self):
g = DeepGraph(v)
with pytest.raises(AssertionError):
g.create_edges(connectors=[dsi, dsf], selectors=[dsf_velo_t])
g.create_edges_ft(('si', v.si.max()), connectors=[dsi, dsf],
selectors=[dsf_velo_t])
def test_fail_selector_ind_shape(self):
g = DeepGraph(v)
with pytest.raises(AssertionError):
g.create_edges(connectors=dsi, selectors=fail_ind_shape)
g.create_edges_ft(('si', v.si.max()), connectors=dsi,
selectors=fail_ind_shape)
def test_ft_dt_min_chunk_size_hdf(self, tmpdir, min_chunk_size):
pytest.importorskip('tables')
# tmp hdf store
folder = str(tmpdir)
vo = v.drop('o', axis=1)
vs = pd.HDFStore(folder + 'vs.h5', mode='w')
vs.put('v', vo, format='t', data_columns=True, index=False)
e_true = e_full_true.copy()
e_true['dmcs'] = [3,6,7,7,8,12,12,3,4,4,5,9,9,1,1,2,6,6,0,1,5,5,1,
5,5,4,4,0]
e_true = e_true[e_true.dmcs <= 2][['dmcs']]
g = DeepGraph(vs)
g.create_edges_ft(ft_feature=('dtmcs', 2, 'h'),
min_chunk_size=min_chunk_size)
e_test = g.e.rename(columns={'ft_r': 'dmcs'})
e_test['dmcs'] = e_test.dmcs.astype(int)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_no_arguments(self):
e_true = e_full_true.iloc[:, 0:0]
g = DeepGraph(v)
g.create_edges()
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
g.create_edges_ft(('si', v.si.max()))
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test, e_true)
def test_connectors(self):
e_true = e_full_true[['dsf', 'dsi']]
g = DeepGraph(v)
g.create_edges(connectors=[dsi, dsf])
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()), connectors=[dsi, dsf])
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_connector(self):
e_true = e_full_true[['dsi']]
g = DeepGraph(v)
g.create_edges(connectors=dsi)
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
g.create_edges_ft(('si', v.si.max()), connectors=dsi)
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test, e_true)
def test_selector(self):
e_true = e_full_true[(e_full_true.dsi <= 3) & (e_full_true.dsf <= 1)]
g = DeepGraph(v)
g.create_edges(selectors=[dsi_dsf_t])
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()), selectors=[dsi_dsf_t])
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_connector_selector(self):
e_true = e_full_true[e_full_true.dsi <= 3]
g = DeepGraph(v)
g.create_edges(connectors=[dsi, dsf, velo], selectors=dsi_t)
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi, dsf, velo],
selectors=dsi_t)
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_no_transfer_r(self):
e_true = e_full_true.drop('dsf', axis=1)
g = DeepGraph(v)
g.create_edges(connectors=[dsi, dsf, velo], no_transfer_rs='dsf')
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi, dsf, velo],
no_transfer_rs='dsf')
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_logging(self, tmpdir):
e_true = e_full_true.iloc[:, 0:0]
g = DeepGraph(v)
folder = str(tmpdir)
g.create_edges(verbose=True, logfile=folder+'lf.txt')
e_test = g.e
pdt.assert_frame_equal(e_test, e_true)
g.create_edges_ft(('si', v.si.max()),
verbose=True, logfile=folder+'lf.txt')
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort_index(axis=1),
e_true.sort_index(axis=1))
def test_r_dep_selector(self):
e_true = e_full_true[(e_full_true.dsi <= 3) & (e_full_true.dsf <= 1)]
g = DeepGraph(v)
g.create_edges(connectors=[dsi], selectors=[dsi_t, dsf_velo_t])
e_test = g.e
assert_frame_equal(e_test.sort_index(axis=1),
e_true.sort_index(axis=1))
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi],
selectors=[dsi_t, dsf_velo_t])
e_test = g.e.drop('ft_r', axis=1)
assert_frame_equal(e_test.sort_index(axis=1),
e_true.sort_index(axis=1))
def test_r_dtype_dic(self):
e_true = e_full_true[['dsf', 'dsi']]
e_true['dsf'] = e_true.dsf.astype(np.uint8)
e_true['dsi'] = e_true.dsi.astype(np.float32)
r_dtype_dic = {'dsf': np.uint8, 'dsi': np.float32}
g = DeepGraph(v)
g.create_edges(connectors=[dsi, dsf], r_dtype_dic=r_dtype_dic)
e_test = g.e
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(('si', v.si.max()),
connectors=[dsi, dsf],
r_dtype_dic=r_dtype_dic)
e_test = g.e.drop('ft_r', axis=1)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
def test_ft_min_chunk_size(self, min_chunk_size):
e_true = e_full_true.copy()
e_true['dmcs'] = [
3, 6, 7, 7, 8, 12, 12, 3, 4, 4, 5, 9, 9, 1, 1, 2, 6, 6, 0, 1, 5, 5,
1, 5, 5, 4, 4, 0
]
e_true = e_true[e_true.dmcs <= 2][['dmcs']]
g = DeepGraph(v)
g.create_edges_ft(ft_feature=('mcs', 2), min_chunk_size=min_chunk_size)
e_test = g.e.rename(columns={'ft_r': 'dmcs'})
e_test['dmcs'] = e_test.dmcs.astype(int)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
g.create_edges_ft(ft_feature=('dtmcs', 2, 'h'),
min_chunk_size=min_chunk_size)
e_test = g.e.rename(columns={'ft_r': 'dmcs'})
e_test['dmcs'] = e_test.dmcs.astype(int)
pdt.assert_frame_equal(e_test.sort(axis=1), e_true.sort(axis=1))
import pytest
import numpy as np
import pandas as pd
import pandas.util.testing as pdt
from numpy.testing import assert_allclose
from deepgraph import DeepGraph
# test node table
v = pd.DataFrame({'x': [-3.4,2.1,-1.1,0.9,2.3],
'time': [0,1,2,5,9],
'color': ['g','g','b','g','r'],
'size': [1,3,2,3,1]})
g = DeepGraph(v)
# create test edge table
def some_relations(ft_r,x_s,x_t,color_s,color_t,size_s,size_t):
dx = x_t - x_s
v = dx / ft_r
same_color = color_s == color_t
larger_than = size_s > size_t
return dx, v, same_color, larger_than
g.create_edges_ft(('time', 5), connectors=some_relations)
g.e.rename(columns={'ft_r': 'dt'}, inplace=True)
class TestPartitionNodes(object):
def test_ft_fail_sorted(self):
g = DeepGraph(v)
with pytest.raises(AssertionError):
g.create_edges_ft(ft_feature=('f', 1))
class TestInterfaces(object):
e = g.e[['dx', 'dt', 'larger_than', 'same_color', 'v']]
e.iloc[0:5, 0] = np.nan
e.iloc[1, 1] = np.nan
e.iloc[2, 2] = np.nan
e.iloc[3, 3] = np.nan
e.iloc[4, 4] = np.nan
g = DeepGraph(v, e)
v_shift_ind = g.v.reset_index()
v_shift_ind['index'] += 2
v_shift_ind.set_index('index', inplace=True)
e_shift_ind = e.reset_index()
e_shift_ind['s'] += 2
e_shift_ind['t'] += 2
e_shift_ind.set_index(['s', 't'], inplace=True)
g_si = DeepGraph(v_shift_ind, e_shift_ind)
def test_return_cs_graph(self):
pytest.importorskip('scipy')
# relations = False
csgraph_true = np.array([[False, True, True, True, False],
[False, False, True, True, False],
[False, False, False, True, False],
[False, False, False, False, True],
[False, False, False, False, False]])
csgraph_test = self.g.return_cs_graph(relations=False).toarray()
csgraph_test_si = self.g_si.return_cs_graph(relations=False).toarray()
assert_allclose(csgraph_true, csgraph_test)
assert_allclose(csgraph_true, csgraph_test_si)
# relations = 'dt', dropna = True
csgraph_true = np.array([[0., 1., 0., 5., 0.], [0., 0., 1., 4., 0.],
[0., 0., 0., 3., 0.], [0., 0., 0., 0., 4.],
[0., 0., 0., 0., 0.]])
csgraph_test = self.g.return_cs_graph('dt', dropna=True).toarray()
csgraph_test_si = self.g_si.return_cs_graph('dt',
dropna=True).toarray()
assert_allclose(csgraph_true, csgraph_test)
assert_allclose(csgraph_true, csgraph_test_si)
# relations = 'dt', dropna = False
csgraph_true = np.array([[0., 1., np.nan, 5., 0.],
[0., 0., 1., 4., 0.], [0., 0., 0., 3., 0.],
[0., 0., 0., 0., 4.], [0., 0., 0., 0., 0.]])
csgraph_test = self.g.return_cs_graph('dt', dropna=False).toarray()
csgraph_test_si = self.g_si.return_cs_graph('dt',
dropna=False).toarray()
assert_allclose(csgraph_true, csgraph_test)
assert_allclose(csgraph_true, csgraph_test_si)
# relations = ['dx', 'dt]
csgraph_test = self.g.return_cs_graph(['dx', 'dt'], [True, False])
assert csgraph_test['dx'].nnz == 2
assert csgraph_test['dt'].nnz == 7
def test_return_nx_graph(self):
# only testing that return_nx_graph produces no errors
# work in progress!
pytest.importorskip('networkx')
pytest.importorskip('pandas', minversion="0.17.0")
self.g.return_nx_graph(False, False)
self.g.return_nx_graph(False, True)
self.g.return_nx_graph(True, False)
self.g.return_nx_graph('color', 'dx')
self.g.return_nx_graph(['color'], ['dx', 'dt'])
self.g_si.return_nx_graph(['color'], ['dx', 'dt'])
# test dropna
nxg = self.g.return_nx_graph(['color'], ['dx', 'dt'], dropna='none')
assert nxg.number_of_edges() == 7
nxg = self.g.return_nx_graph(['color'], ['dx', 'dt'], dropna='all')
assert nxg.number_of_edges() == 6
nxg = self.g.return_nx_graph(['color'], ['dx', 'dt'], dropna='any')
assert nxg.number_of_edges() == 2
def test_return_gt_graph(self):
# only testing that return_gt_graph produces no errors
# work in progress!
pytest.importorskip('graph_tool')
self.g.return_gt_graph(False, False)
self.g.return_gt_graph(False, True)
self.g.return_gt_graph(True, False)
self.g.return_gt_graph('color', 'dx')
self.g.return_gt_graph(['color'], ['dx', 'dt'])
self.g_si.return_gt_graph(['color'], ['dx', 'dt'],
node_indices=True,
edge_indices=True)
# test dropna
gtg = self.g.return_gt_graph(['color'], ['dx', 'dt'], dropna='none')
assert gtg.num_edges() == 7
gtg = self.g.return_gt_graph(['color'], ['dx', 'dt'], dropna='all')
assert gtg.num_edges() == 6
gtg = self.g.return_gt_graph(['color'], ['dx', 'dt'], dropna='any')
assert gtg.num_edges() == 2