def test_from_to_csv(self):
"""Test basic reading and writing functions."""
orig_file = os.path.join("tests", "data", "positionfixes.csv")
mod_file = os.path.join("tests", "data",
"positionfixes_mod_columns.csv")
tmp_file = os.path.join("tests", "data", "positionfixes_test_1.csv")
pfs = ti.read_positionfixes_csv(orig_file, sep=";", index_col="id")
column_mapping = {
"lat": "latitude",
"lon": "longitude",
"time": "tracked_at"
}
mod_pfs = ti.read_positionfixes_csv(mod_file,
sep=";",
index_col="id",
columns=column_mapping)
assert mod_pfs.equals(pfs)
pfs["tracked_at"] = pfs["tracked_at"].apply(
lambda d: d.isoformat().replace("+00:00", "Z"))
columns = [
"user_id", "tracked_at", "latitude", "longitude", "elevation",
"accuracy"
]
pfs.as_positionfixes.to_csv(tmp_file, sep=";", columns=columns)
assert filecmp.cmp(orig_file, tmp_file, shallow=False)
os.remove(tmp_file)
def test_read_positionfixes_csv_crs_parameter(self):
file = os.path.join('tests', 'data', 'positionfixes.csv')
pfs = ti.read_positionfixes_csv(file, sep=';', index_col="id")
crs = "EPSG:2056"
assert pfs.crs is None
pfs = ti.read_positionfixes_csv(file, sep=';', index_col="id", crs=crs)
assert pfs.crs == crs
def test_set_index(self):
"""Test if `index_col` can be set."""
file = os.path.join("tests", "data", "positionfixes.csv")
ind_name = "id"
pfs = ti.read_positionfixes_csv(file, sep=";", index_col=ind_name)
assert pfs.index.name == ind_name
pfs = ti.read_positionfixes_csv(file, sep=";", index_col=None)
assert pfs.index.name is None
def test_positionfixes_csv_index_col(self):
"""Test if `index_col` can be set."""
file = os.path.join('tests', 'data', 'positionfixes.csv')
ind_name = 'id'
pfs = ti.read_positionfixes_csv(file, sep=";", index_col=ind_name)
assert pfs.index.name == ind_name
pfs = ti.read_positionfixes_csv(file, sep=";", index_col=None)
assert pfs.index.name is None
def test_set_crs(self):
"""Test setting the crs when reading."""
file = os.path.join('tests', 'data', 'positionfixes.csv')
pfs = ti.read_positionfixes_csv(file, sep=';', index_col="id")
assert pfs.crs is None
crs = "EPSG:2056"
pfs = ti.read_positionfixes_csv(file, sep=';', index_col="id", crs=crs)
assert pfs.crs == crs
def test_dbscan_max(self):
"""Test with large epsilon parameter."""
pfs_file = os.path.join("tests", "data", "positionfixes.csv")
pfs = ti.read_positionfixes_csv(pfs_file,
sep=";",
tz="utc",
index_col="id")
_, sp = pfs.as_positionfixes.generate_staypoints(method="sliding",
gap_threshold=1e6,
dist_threshold=0,
time_threshold=0)
warn_string = "No locations can be generated, returning empty locs."
with pytest.warns(UserWarning, match=warn_string):
_, locs_user = sp.as_staypoints.generate_locations(
method="dbscan",
epsilon=1e18,
num_samples=1000,
agg_level="user")
_, locs_data = sp.as_staypoints.generate_locations(
method="dbscan",
epsilon=1e18,
num_samples=1000,
agg_level="dataset")
# "With large epsilon, every user location is an outlier"
assert len(locs_user) == 0
assert len(locs_data) == 0
def test_positionfixes_from_to_csv(self):
orig_file = os.path.join('tests', 'data', 'positionfixes.csv')
mod_file = os.path.join('tests', 'data', 'positionfixes_mod_columns.csv')
tmp_file = os.path.join('tests', 'data', 'positionfixes_test.csv')
pfs = ti.read_positionfixes_csv(orig_file, sep=';', index_col="id")
column_mapping = {'lat': 'latitude', 'lon': 'longitude', 'time': 'tracked_at'}
mod_pfs = ti.read_positionfixes_csv(mod_file, sep=';', index_col="id", columns=column_mapping)
assert mod_pfs.equals(pfs)
pfs['tracked_at'] = pfs['tracked_at'].apply(lambda d: d.isoformat().replace('+00:00', 'Z'))
columns = ['user_id', 'tracked_at', 'latitude', 'longitude', 'elevation', 'accuracy']
pfs.as_positionfixes.to_csv(tmp_file, sep=';', columns=columns)
assert filecmp.cmp(orig_file, tmp_file, shallow=False)
os.remove(tmp_file)
def test_loop_read(self):
pfs = read_geolife(os.path.join('tests', 'data', 'geolife'))
tmp_file = os.path.join('tests', 'data', 'positionfixes_test.csv')
pfs.as_positionfixes.to_csv(tmp_file)
pfs2 = ti.read_positionfixes_csv(tmp_file, index_col='id')[pfs.columns]
os.remove(tmp_file)
assert np.isclose(0, (pfs.lat - pfs2.lat).abs().sum())
def test_positionfixes_plot(self):
tmp_file = 'tests/data/positionfixes_plot.png'
pfs = ti.read_positionfixes_csv('tests/data/positionfixes.csv',
sep=';')
pfs.as_positionfixes.plot(out_filename=tmp_file, plot_osm=False)
assert os.path.exists(tmp_file)
os.remove(tmp_file)
def test_loop_read(self):
"""Use read_geolife reader, store posfix as .csv, load them again."""
pfs, _ = read_geolife(os.path.join("tests", "data", "geolife"))
tmp_file = os.path.join("tests", "data", "positionfixes_test.csv")
pfs.as_positionfixes.to_csv(tmp_file)
pfs2 = ti.read_positionfixes_csv(tmp_file, index_col="id")[pfs.columns]
os.remove(tmp_file)
assert np.isclose(0, (pfs.lat - pfs2.lat).abs().sum())
def test_as_positionfixes_accessor(self):
orig_file = os.path.join('tests', 'data', 'positionfixes.csv')
pfs = ti.read_positionfixes_csv(orig_file, sep=';')
assert pfs.as_positionfixes
pfs = pfs.drop(['geom'], axis=1)
with pytest.raises(AttributeError):
pfs.as_positionfixes
def testdata_pfs_ids_geolife():
pfs_file = os.path.join('tests', 'data', 'geolife',
'geolife_positionfixes_with_ids.csv')
pfs = ti.read_positionfixes_csv(pfs_file, index_col='id')
pfs['staypoint_id'] = pfs['staypoint_id'].astype('Int64')
pfs['tripleg_id'] = pfs['tripleg_id'].astype('Int64')
pfs.geometry = pfs.geometry.set_crs(epsg=4326)
return pfs
def test_positionfixes_plot(self):
"""Use trackintel visualization function to plot positionfixes and check if file exists."""
tmp_file = os.path.join('tests', 'data', 'positionfixes_plot.png')
pfs_file = os.path.join('tests', 'data', 'positionfixes.csv')
pfs = ti.read_positionfixes_csv(pfs_file, sep=';', index_col='id', crs='EPSG:4326')
pfs.as_positionfixes.plot(out_filename=tmp_file, plot_osm=False)
assert os.path.exists(tmp_file)
os.remove(tmp_file)
def test_crs_warning(self):
"""Check if warning is raised for data without crs."""
file = os.path.join("tests", "data", "positionfixes.csv")
pfs = ti.read_positionfixes_csv(file,
sep=";",
crs=None,
index_col=None)
with pytest.warns(UserWarning):
check_gdf_crs(pfs)
def test_extract_staypoints_sliding_min(self):
pfs = ti.read_positionfixes_csv('tests/data/positionfixes.csv',
sep=';')
spts = pfs.as_positionfixes.extract_staypoints(method='sliding',
dist_threshold=0,
time_threshold=0)
assert len(spts) == len(
pfs
), "With small thresholds, staypoint extraction should yield each positionfix"
def test_extract_triplegs_staypoint(self):
pfs = ti.read_positionfixes_csv('tests/data/positionfixes.csv', sep=';')
spts = pfs.as_positionfixes.extract_staypoints(method='sliding', dist_threshold=0, time_threshold=0)
tpls1 = pfs.as_positionfixes.extract_triplegs()
tpls2 = pfs.as_positionfixes.extract_triplegs(spts)
assert len(tpls1) > 0, "There should be more than zero triplegs"
assert len(tpls2) > 0, "There should be more than zero triplegs"
assert len(tpls1) == len(tpls2), "If we extract the staypoints in the same way, it should lead to " + \
"the same number of triplegs"
def test_read_positionfixes_gpd(self):
gdf = gpd.read_file(os.path.join('tests', 'data', 'positionfixes.geojson'))
gdf.set_index('id', inplace=True)
pfs_from_gpd = ti.io.from_geopandas.read_positionfixes_gpd(gdf, user_id='User', geom='geometry', tz='utc')
pfs_file = os.path.join('tests', 'data', 'positionfixes.csv')
pfs_from_csv = ti.read_positionfixes_csv(pfs_file, sep=';', tz='utc', index_col='id')
pd.testing.assert_frame_equal(pfs_from_gpd, pfs_from_csv, check_exact=False)
def test_transformation(self):
"""Check if data gets transformed."""
file = os.path.join("tests", "data", "positionfixes.csv")
pfs = ti.read_positionfixes_csv(file,
sep=";",
crs="EPSG:4326",
index_col=None)
pfs_2056 = pfs.to_crs("EPSG:2056")
_, pfs_4326 = check_gdf_crs(pfs_2056, transform=True)
assert_geodataframe_equal(pfs, pfs_4326, check_less_precise=True)
def test_loop_read(self):
"""Use read_geolife reader, store posfix as .csv, load them again."""
pfs, _ = read_geolife(os.path.join("tests", "data", "geolife"), print_progress=True)
saved_file = os.path.join("tests", "data", "positionfixes_test.csv")
pfs.as_positionfixes.to_csv(saved_file)
pfs_reRead = ti.read_positionfixes_csv(saved_file, index_col="id", crs="epsg:4326")
os.remove(saved_file)
assert_geoseries_equal(pfs.geometry, pfs_reRead.geometry)
def test_data():
"""Read tests data from files."""
pfs_file = os.path.join("examples", "data", "geolife_trajectory.csv")
pfs = ti.read_positionfixes_csv(pfs_file,
sep=";",
index_col=None,
crs="EPSG:4326")
pfs, stps = pfs.as_positionfixes.generate_staypoints(method="sliding")
return pfs, stps
def test_crs_warning(self):
"""Check if warning is raised for data without crs."""
file = os.path.join('tests', 'data', 'positionfixes.csv')
pfs = ti.read_positionfixes_csv(file,
sep=';',
crs=None,
index_col=None)
with pytest.warns(UserWarning):
ti.visualization.util.transform_gdf_to_wgs84(pfs)
def test_extract_staypoints_sliding_max(self):
pfs = ti.read_positionfixes_csv('tests/data/positionfixes.csv',
sep=';')
spts = pfs.as_positionfixes.extract_staypoints(
method='sliding',
dist_threshold=sys.maxsize,
time_threshold=sys.maxsize)
assert len(
spts
) == 0, "With large thresholds, staypoint extraction should not yield positionfixes"
def test_missing_link(self):
"""Test nan is assigned for missing link between stps and locs."""
pfs_file = os.path.join("tests", "data", "positionfixes.csv")
pfs = ti.read_positionfixes_csv(pfs_file, sep=";", tz="utc", index_col="id")
_, stps = pfs.as_positionfixes.generate_staypoints(method="sliding", dist_threshold=0, time_threshold=0)
stps, _ = stps.as_staypoints.generate_locations(
method="dbscan", epsilon=1e18, num_samples=1000, agg_level="user"
)
assert pd.isna(stps["location_id"]).any()
def test_transformation(self):
"""Check if data gets transformed."""
file = os.path.join('tests', 'data', 'positionfixes.csv')
pfs = ti.read_positionfixes_csv(file,
sep=';',
crs='EPSG:4326',
index_col=None)
pfs_2056 = pfs.to_crs("EPSG:2056")
pfs_4326 = ti.visualization.util.transform_gdf_to_wgs84(pfs_2056)
assert_geodataframe_equal(pfs, pfs_4326, check_less_precise=True)
def test_staypoints_plot(self):
tmp_file = 'tests/data/staypoints_plot.png'
pfs = ti.read_positionfixes_csv('tests/data/positionfixes.csv',
sep=';')
stps = ti.read_staypoints_csv('tests/data/staypoints.csv', sep=';')
stps.as_staypoints.plot(out_filename=tmp_file,
radius=0.01,
positionfixes=pfs,
plot_osm=False)
assert os.path.exists(tmp_file)
os.remove(tmp_file)
def test_positionfixes_plot(self):
"""Use trackintel visualization function to plot positionfixes and check if the file exists."""
tmp_file = os.path.join("tests", "data", "positionfixes_plot.png")
pfs_file = os.path.join("tests", "data", "positionfixes.csv")
pfs = ti.read_positionfixes_csv(pfs_file,
sep=";",
index_col="id",
crs="EPSG:4326")
pfs.as_positionfixes.plot(out_filename=tmp_file, plot_osm=False)
assert os.path.exists(tmp_file)
os.remove(tmp_file)
def test_cluster_staypoints_dbscan_max(self):
pfs = ti.read_positionfixes_csv('tests/data/positionfixes.csv',
sep=';')
spts = pfs.as_positionfixes.extract_staypoints(method='sliding',
dist_threshold=0,
time_threshold=0)
_, clusters = spts.as_staypoints.extract_locations(method='dbscan',
epsilon=1e18,
num_samples=1000)
assert len(
clusters
) == 0, "With large hyperparameters, everything is an outlier"
def test_generate_staypoints_sliding_min(self):
pfs_file = os.path.join('tests', 'data', 'positionfixes.csv')
pfs = ti.read_positionfixes_csv(pfs_file,
sep=';',
tz='utc',
index_col='id')
pfs, stps = pfs.as_positionfixes.generate_staypoints(method='sliding',
dist_threshold=0,
time_threshold=0)
assert len(stps) == len(
pfs
), "With small thresholds, staypoint extraction should yield each positionfix"
def test_cluster_staypoints_dbscan_min(self):
pfs = ti.read_positionfixes_csv('tests/data/positionfixes.csv',
sep=';')
spts = pfs.as_positionfixes.extract_staypoints(method='sliding',
dist_threshold=0,
time_threshold=0)
_, clusters = spts.as_staypoints.extract_locations(method='dbscan',
epsilon=1e-18,
num_samples=0)
assert len(clusters) == len(
spts
), "With small hyperparameters, clustering should not reduce the number"
def test_set_datatime_tz(self):
"""Test setting the timezone infomation when reading."""
# check if tz is added to the datatime column
file = os.path.join('tests', 'data', 'positionfixes.csv')
pfs = ti.read_positionfixes_csv(file, sep=';', index_col="id")
assert pd.api.types.is_datetime64tz_dtype(pfs["tracked_at"])
# check if a timezone will be set after manually deleting the timezone
pfs['tracked_at'] = pfs['tracked_at'].dt.tz_localize(None)
assert not pd.api.types.is_datetime64tz_dtype(pfs["tracked_at"])
tmp_file = os.path.join('tests', 'data', 'positionfixes_test.csv')
pfs.as_positionfixes.to_csv(tmp_file, sep=';')
pfs = ti.read_positionfixes_csv(tmp_file, sep=';', index_col="id", tz = 'utc')
assert pd.api.types.is_datetime64tz_dtype(pfs["tracked_at"])
# check if a warning is raised if 'tz' is not provided
with pytest.warns(UserWarning):
ti.read_positionfixes_csv(tmp_file, sep=';', index_col="id")
os.remove(tmp_file)
