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Philipp Horstenkamp
2022-07-20 15:01:07 +02:00
parent aee5e8bbd9
commit e03f1c8be8
234 changed files with 21562 additions and 456 deletions
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pyrate/tests/plan/graph/__init__.py Normal file
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pyrate/tests/plan/graph/generate/__init__.py Normal file
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pyrate/tests/plan/graph/generate/example_files/geodesic_-M_s_-c_2_-f_2_ico.off Normal file
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3 37 115 116 0.90196 0.45098 0.00000
3 112 116 11 0.90196 0.45098 0.00000
3 6 60 117 0.90196 0.45098 0.00000
3 110 117 37 0.90196 0.45098 0.00000
3 118 7 77 0.90196 0.45098 0.00000
3 39 56 118 0.90196 0.45098 0.00000
3 118 119 39 0.90196 0.45098 0.00000
3 119 118 38 0.90196 0.45098 0.00000
3 38 120 119 0.90196 0.45098 0.00000
3 120 38 76 0.90196 0.45098 0.00000
3 121 39 119 0.90196 0.45098 0.00000
3 119 41 121 0.90196 0.45098 0.00000
3 41 119 120 0.90196 0.45098 0.00000
3 113 120 10 0.90196 0.45098 0.00000
3 11 57 121 0.90196 0.45098 0.00000
3 112 121 41 0.90196 0.45098 0.00000
1 0 0.38824 0.60000 0.30196
1 1 0.38824 0.60000 0.30196
1 2 0.38824 0.60000 0.30196
1 3 0.38824 0.60000 0.30196
1 4 0.38824 0.60000 0.30196
1 5 0.38824 0.60000 0.30196
1 6 0.38824 0.60000 0.30196
1 7 0.38824 0.60000 0.30196
1 8 0.38824 0.60000 0.30196
1 9 0.38824 0.60000 0.30196
1 10 0.38824 0.60000 0.30196
1 11 0.38824 0.60000 0.30196

205
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"""Tests the generated graphs are well-formed."""
# Standard Library
from contextlib import redirect_stdout
from io import StringIO
from math import isclose
# Testing
import unittest
# Typing
from typing import cast
# Hypothesis testing
from hypothesis import given
import hypothesis.strategies as st
# Scientific (testing)
import numpy as np
import numpy.testing
# Own geography
from pyrate.plan.geometry.geospatial import MEAN_EARTH_CIRCUMFERENCE
from pyrate.plan.geometry.helpers import haversine_numpy
# Module under test
from pyrate.plan.graph.generate import angular_distance_for
from pyrate.plan.graph.generate import create_earth_graph
from pyrate.plan.graph.generate import great_circle_distance_distance_for
from pyrate.plan.graph.generate import min_required_frequency
EXAMPLE_DISTANCES_KILOMETERS = [100000, 100000.0, 5000, 250] # smaller values take too long
class TestGridGeneration(unittest.TestCase):
"""Tests that a grid can be created and pruned."""
@staticmethod
def _calculate_distances(latitudes: np.ndarray, longitudes: np.ndarray, edges: np.ndarray) -> np.ndarray:
"""Calculates the distance of all edges. The `edges` index into the coordinate arrays."""
entries = [
(latitudes[node_1], longitudes[node_1], latitudes[node_2], longitudes[node_2])
for node_1, node_2 in edges
]
return haversine_numpy(*np.transpose(entries))
def test_create_earth_grid(self) -> None:
"""Ensures that the generated earth grids are formed correctly."""
for distance_km in EXAMPLE_DISTANCES_KILOMETERS:
with self.subTest(f"Test with distance {distance_km} km"):
distance = distance_km * 1000
# create a grid
graph = create_earth_graph(min_required_frequency(distance, in_meters=True))
self.assertIsNotNone(graph.node_radius)
actual_distance: float = cast(float, graph.node_radius) * 2
# the actual_distance must be a upper-bounded by he requested distance
self.assertLessEqual(actual_distance, distance)
self.assertLessEqual(actual_distance, MEAN_EARTH_CIRCUMFERENCE / 2)
# the shapes of the returned arrays must match
self.assertEqual(
graph.latitudes_radians.shape,
graph.longitudes_radians.shape,
"latitude and longitude must have the same shape",
)
self.assertEqual(
graph.latitudes_degrees.shape,
graph.longitudes_degrees.shape,
"latitude and longitude must have the same shape",
)
self.assertEqual(
graph.latitudes_radians.shape,
graph.longitudes_degrees.shape,
"radians and degrees must have the same shape",
)
self.assertGreaterEqual(len(graph), 12) # as it is based on slicing an icosahedron
# the edges must be valid indices into the edges
self.assertTrue(
np.all(graph.edges[:, :] >= 0) and np.all(graph.edges[:, :] < len(graph)),
"some edges reference non-existent points",
)
# check the actual coordinate value
if (
np.any(graph.latitudes_radians < -np.pi / 2)
or np.any(graph.longitudes_radians < -np.pi)
or np.any(graph.latitudes_radians >= +np.pi / 2)
or np.any(graph.longitudes_radians >= +np.pi)
):
print(
"latitude < min / 2:",
np.compress(graph.latitudes_radians < -np.pi / 2, graph.latitudes_radians),
)
print(
"longitude < min:",
np.compress(graph.longitudes_radians < -np.pi, graph.longitudes_radians),
)
print(
"latitude >= max / 2:",
np.compress(graph.latitudes_radians >= +np.pi / 2, graph.latitudes_radians),
)
print(
"longitude >= max:",
np.compress(graph.longitudes_radians >= +np.pi, graph.longitudes_radians),
)
self.fail("some points are outside of the allowed range")
# check the distances along the edges
distances = TestGridGeneration._calculate_distances(
graph.latitudes_radians, graph.longitudes_radians, graph.edges
)
numpy.testing.assert_allclose(distances, actual_distance, atol=10, rtol=0.2)
mean = np.mean(distances)
self.assertTrue(isclose(mean, actual_distance, rel_tol=0.1, abs_tol=10.0))
standard_deviation = np.std(distances)
self.assertLessEqual(standard_deviation / mean, 0.075)
def test_print_status(self) -> None:
"""This tests that logging being enabled actually logs something and does not crash."""
stdout_logging = StringIO()
with redirect_stdout(stdout_logging):
create_earth_graph(6, print_status=True)
logged_lines = list(stdout_logging.getvalue().splitlines())
self.assertEqual(len(logged_lines), 6, "we expect 6 lines of messages")
def test_find_neighbors(self) -> None:
"""Tests that result of the neighbor search is correct."""
for distance_km in EXAMPLE_DISTANCES_KILOMETERS:
with self.subTest(f"Test with distance {distance_km} km"):
# create a grid & determine neighbors
graph = create_earth_graph(min_required_frequency(distance_km * 1000, in_meters=True))
neighbors = graph.neighbors
count_per_node = np.count_nonzero(neighbors >= 0, axis=1)
# check the resulting number of entries
self.assertEqual(
np.sum(count_per_node),
graph.edges.shape[0] * 2,
"each edge must generate two entries in the neighbor table",
)
self.assertEqual(
np.count_nonzero(count_per_node == 5),
12,
"exactly twelve nodes must have exactly five neighbors "
"(the corners of the original icosahedron)",
)
self.assertEqual(
np.count_nonzero(count_per_node == 6),
len(graph) - 12,
"all but twelve nodes must have exactly six neighbors",
)
# check the range of values
valid_index = np.logical_and(neighbors >= 0, neighbors < len(graph))
self.assertTrue(
np.all(np.logical_xor(neighbors == -1, valid_index)),
"any value i may either be -1 (=null) or a valid index with 0 <= i < num_nodes",
)
class TestHelperMethods(unittest.TestCase):
"""Tests that the helpers (e.g. for computing minimum required frequencies) work correctly."""
@given(st.floats(min_value=1e-6, allow_infinity=False, allow_nan=False), st.booleans())
def test_right_order_of_magnitude(self, desired_distance: float, in_meters: bool) -> None:
"""Asserts that commuting a frequency and converting it to units is correct w.r.t. to each other."""
frequency = min_required_frequency(desired_distance, in_meters)
if in_meters:
actual_distance = great_circle_distance_distance_for(frequency)
else:
actual_distance = angular_distance_for(frequency)
self.assertLessEqual(actual_distance, desired_distance)
if frequency > 1:
if in_meters:
actual_distance_one_rougher = great_circle_distance_distance_for(frequency - 1)
else:
actual_distance_one_rougher = angular_distance_for(frequency - 1)
self.assertGreaterEqual(actual_distance_one_rougher, desired_distance)
def test_specific_values(self) -> None:
"""Asserts that commuting a frequency works correct for specific hand-chosen values."""
# Taken from the implementation:
# The approximate angle between two edges on an icosahedron, in radians, about 63.4°
alpha = 1.1071487
# Contains pairs: (angular distance in radians, frequency)
table = [
(alpha + 1e-6, 1),
(alpha - 1e-9, 2),
(alpha / 9000.005, 9001),
]
for desired_angular_distance, desired_frequency in table:
computed_frequency = min_required_frequency(desired_angular_distance, in_meters=False)
self.assertEqual(desired_frequency, computed_frequency)

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pyrate/tests/plan/graph/generate/test_off_handler.py Normal file
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"""Tests the Aptiprism OFF file handler."""
# Standard library
import os.path
# Testing
import unittest
# Scientific
import numpy as np
# Module under test
from pyrate.plan.graph.generate import _parse_off_file
TEST_FILES_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), "example_files/"))
TEST_FILES = [
os.path.join(TEST_FILES_DIR, "geodestic_file_1.off"),
os.path.join(TEST_FILES_DIR, "geodestic_file_2.off"),
os.path.join(TEST_FILES_DIR, "geodesic_-M_s_-c_2_-f_2_ico.off"),
]
class TestOffHandler(unittest.TestCase):
"""Tests the Aptiprism OFF file handler using some examples."""
def test_with_example_files(self):
"""Tests the Aptiprism OFF file handler using three example files."""
for test_file in TEST_FILES:
with self.subTest(f'Test file "{test_file}"'):
# test that it does not crash
with open(test_file, "r", encoding="utf-8") as myfile:
source = myfile.read()
latitudes, longitudes, edges = _parse_off_file(source)
if "geodesic_-M_s_-c_2_-f_2_ico" in test_file:
self.assertEqual(
len(latitudes), 122, f"wrong total number of nodes: {len(latitudes)} instead of 122"
)
self.assertEqual(
edges.shape[0], 360, f"wrong total number of edges: {edges.shape[0]} instead of 360"
)
# the shapes of the returned arrays must match
self.assertEqual(
latitudes.shape, longitudes.shape, "latitude and longitude must have the same shape"
)
self.assertGreater(len(latitudes), 0, "no points found")
# the edges must be valid indices into the edges
self.assertTrue(
np.all(edges[:, :] >= 0) and np.all(edges[:, :] < len(latitudes)),
"some edges reference non-existent points",
)

166
pyrate/tests/plan/graph/test_geo_graph.py Normal file
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"""Asserts correct behaviour of the geo-referenced graph navigation.
See Also:
tests/common/raster_datasets/test_transformers_concrete.py
"""
# Standard library
from copy import deepcopy
import os.path
from tempfile import TemporaryDirectory
from unittest import TestCase
# Scientific
import numpy
from numpy import arange
from numpy import array
from numpy import empty
from numpy.testing import assert_array_equal
from pandas import DataFrame
# Graph generation / Module under test
from pyrate.common.raster_datasets import transformers_concrete
from pyrate.plan.graph import create_earth_graph
from pyrate.plan.graph import GeoNavigationGraph
from pyrate.plan.graph import min_required_frequency
# CI/Testing helpers
from ... import _open_test_geo_dataset
from .generate.test_graph_generation import EXAMPLE_DISTANCES_KILOMETERS
class TestGeoNavigationGraph(TestCase):
"""Tests properties specific to :class:`pyrate.plan.graph.GeoNavigationGraph`."""
def test_create_invalid_duplicate_argument_nodes(self) -> None:
"""Tests supplying nodes to from_coordinates_radians/from_coordinates_degrees raises an Exception."""
for function in [
GeoNavigationGraph.from_coordinates_degrees,
GeoNavigationGraph.from_coordinates_radians,
]:
with self.subTest(msg=f"function {str(function)}"):
with self.assertRaises(Exception): # noqa: H202
function( # type: ignore
latitudes=empty((0,)), longitudes=empty((0,)), edges=empty((0, 2)), nodes=DataFrame()
)
def test_node_radius_constructor(self) -> None:
"""Tests that only invalid inputs to node_radius raise exceptions."""
GeoNavigationGraph.from_coordinates_degrees(
latitudes=empty((0,)), longitudes=empty((0,)), edges=empty((0, 2)), node_radius=0
)
GeoNavigationGraph.from_coordinates_degrees(
latitudes=empty((0,)), longitudes=empty((0,)), edges=empty((0, 2)), node_radius=100_000
)
with self.assertRaises(Exception): # noqa: H202
GeoNavigationGraph.from_coordinates_degrees(
latitudes=empty((0,)), longitudes=empty((0,)), edges=empty((0, 2)), node_radius=-1e-9
)
def test_set_node_properties(self) -> None:
"""Tests that passing ``node_properties`` works."""
graph = GeoNavigationGraph.from_coordinates_radians(
latitudes=array([42]),
longitudes=array([21]),
edges=empty((0, 2)),
node_radius=100,
node_properties=DataFrame(data={"col1": [99], "col2": ["text"]}),
)
self.assertEqual(graph.node_radius, 100)
assert_array_equal(graph.node_properties["col1"], [99])
assert_array_equal(graph.node_properties["col2"], ["text"])
def test_read_write(self) -> None:
"""Tests that a *geo* navigation graph can be serialized and deserialized again."""
latitudes = array([49.8725144])
longitudes = array([8.6528707])
edges = empty((0, 2))
# `graph.neighbors` is cached, so we want to try it with and without the cached neighbors being set
for set_neighbors in [True, False]:
with self.subTest(f"neighbors set = {set_neighbors}"):
graph = GeoNavigationGraph.from_coordinates_degrees(
latitudes, longitudes, edges=edges, max_neighbors=42, node_radius=1000
)
if set_neighbors:
_ = graph.neighbors
with TemporaryDirectory() as directory:
path = os.path.join(directory, "some_file.hdf5")
graph.to_disk(path)
new_graph = GeoNavigationGraph.from_disk(path)
self.assertEqual(graph, new_graph)
assert_array_equal(new_graph.neighbors, graph.neighbors)
class TestNavigationGraphPruningGeo(TestCase):
"""Tests that navigation graphs can be pruned by testing it with earth graphs."""
def test_pruning_artificial(self) -> None:
"""Tests that pruning half of the points works as expected."""
for distance_km in EXAMPLE_DISTANCES_KILOMETERS:
with self.subTest(f"Test with distance {distance_km} km"):
# create a grid
graph = create_earth_graph(min_required_frequency(distance_km * 1000, in_meters=True))
# keep all nodes at even latitudes
keep_condition = arange(0, len(graph)) % 2 == 0
pruned_graph = deepcopy(graph)
pruned_graph.prune_nodes(keep_condition)
self.assertGreater(len(pruned_graph), 0, "some node must remain")
# test the reduction ratio
delta_nodes = len(pruned_graph) / len(graph)
delta_edges = pruned_graph.num_edges / graph.num_edges
self.assertAlmostEqual(delta_nodes, 0.5, msg="suspicious node count reduction")
# about a fifth of all edges should be removed since each of the removed nodes removed five
# edges
self.assertAlmostEqual(delta_edges, 1 / 5, delta=0.15, msg="suspicious edge count reduction")
# test the values in the edges, since they were rewritten as they point to new indices
self.assertTrue(numpy.all(pruned_graph.edges[:, :] >= 0), "indices must be non-negative")
self.assertTrue(
numpy.all(pruned_graph.edges[:, :] < len(pruned_graph)),
"some filtered edges reference (now) non-existent points",
)
def test_pruning_depth(self) -> None:
"""Supplements :meth`~test_pruning_artificial` by a real-world application.
Only checks application-specific properties and not, for example, the general shapes of the result.
"""
# create a grid
distance_meters = 500_000
graph = create_earth_graph(min_required_frequency(distance_meters, in_meters=True))
# fetch properties
mode = transformers_concrete.BathymetricTransformer.Modes.AVERAGE_DEPTH
graph.append_property(transformers_concrete.BathymetricTransformer(_open_test_geo_dataset(), [mode]))
# keep all nodes that are below sea level
keep_condition = (graph.node_properties[mode.column_name] < 0.0).to_numpy()
# Remove the now useless property
graph.clear_node_properties()
# perform pruning
pruned_graph = deepcopy(graph)
pruned_graph.prune_nodes(keep_condition)
# test the reduction ratio
delta_nodes = len(pruned_graph) / len(graph)
delta_edges = pruned_graph.num_edges / graph.num_edges
earth_fraction_water = 0.708 # see https://en.wikipedia.org/wiki/World_Ocean
# although we go by topography and not water coverage, this should still be fairly correct
self.assertAlmostEqual(
delta_nodes, earth_fraction_water, delta=0.1, msg="suspicious node count reduction"
)
self.assertAlmostEqual(
delta_edges, earth_fraction_water, delta=0.1, msg="suspicious edge count reduction"
)

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pyrate/tests/plan/graph/test_graph.py Normal file
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"""Asserts correct behaviour of the base classes for graph navigation.
See Also:
tests/common/raster_datasets/test_transformers_concrete.py
"""
# Standard library
from copy import deepcopy
import os.path
from tempfile import TemporaryDirectory
from unittest import TestCase
# Scientific
from numpy import array
from numpy import empty
from numpy import full
from numpy.testing import assert_array_equal
from pandas import DataFrame
from pandas.testing import assert_frame_equal
# Module under test
from pyrate.plan.graph import NavigationGraph
# Some examples:
_NODES = DataFrame(data={"property_1": [1, 2, 3], "property_2": [10, 20, 30]})
_EDGES = array([[0, 1], [1, 2]])
_NEIGHBORS = array([[1, -1], [0, 2], [1, -1]])
class TestNavigationGraph(TestCase):
"""Tests the very basic functionality like initialization, (de)serialization and finding neighbors."""
def test_empty(self) -> None:
"""Tests that a new instance can be created with and without neighbors."""
graph = NavigationGraph(DataFrame(), empty((0, 2)))
self.assertEqual(len(graph), 0)
self.assertEqual(graph.num_edges, 0)
# check that the correct neighbor table is returned
self.assertEqual(graph.neighbors.shape, (0, 0))
def test_create(self) -> None:
"""Tests that a new instance can be created with and without neighbors."""
for given_neighbors in [_NEIGHBORS, None]:
with self.subTest(f"neighbors given = {given_neighbors is not None}"):
graph = NavigationGraph(_NODES, _EDGES, given_neighbors)
assert_array_equal(graph.neighbors, _NEIGHBORS)
# repeated queries should return the same neighbors
assert_array_equal(graph.neighbors, graph.neighbors)
def test_read_write(self) -> None:
"""Tests that a navigation graph can be serialized and deserialized again."""
# `graph.neighbors` is cached, so we want to try it with and without the cached neighbors being set
for set_neighbors in [True, False]:
with self.subTest(f"neighbors set = {set_neighbors}"):
graph = NavigationGraph(_NODES, _EDGES, max_neighbors=42)
if set_neighbors:
_ = graph.neighbors
with TemporaryDirectory() as directory:
path = os.path.join(directory, "some_file.hdf5")
graph.to_disk(path)
new_graph = NavigationGraph.from_disk(path)
self.assertEqual(graph, new_graph)
assert_array_equal(new_graph.neighbors, _NEIGHBORS)
def test_max_neighbors_constructor(self) -> None:
"""Tests that only invalid inputs to max_neighbors raise exceptions."""
NavigationGraph(DataFrame(), empty((0, 2)), max_neighbors=0)
NavigationGraph(DataFrame(), empty((0, 2)), max_neighbors=10)
with self.assertRaises(Exception): # noqa: H202
NavigationGraph(DataFrame(), empty((0, 2)), max_neighbors=-2)
class TestNavigationGraphPruningArtificial(TestCase):
"""Tests that simple toy navigation graphs can be pruned."""
def test_pruning_no_nodes(self) -> None:
"""Tests that pruning no nodes works."""
old_graph = NavigationGraph(_NODES, _EDGES, _NEIGHBORS)
pruned_graph = deepcopy(old_graph)
retain_all = full((len(_NODES),), True)
pruned_graph.prune_nodes(retain_all)
self.assertEqual(old_graph, pruned_graph)
def test_pruning_all(self) -> None:
"""Tests that pruning all nodes works."""
old_graph = NavigationGraph(_NODES, _EDGES, _NEIGHBORS)
pruned_graph = deepcopy(old_graph)
retain_all = full((len(_NODES),), False)
pruned_graph.prune_nodes(retain_all)
self.assertNotEqual(old_graph, pruned_graph)
self.assertEqual(len(pruned_graph.nodes), 0)
self.assertEqual(len(pruned_graph.nodes.columns), 2, "the properties must be retained")
self.assertEqual(pruned_graph.edges.shape, (0, 2))
self.assertEqual(pruned_graph.neighbors.shape, (0, 0))
def test_pruning_very_simple(self) -> None:
"""Tests that pruning some nodes works as expected."""
old_graph = NavigationGraph(_NODES, _EDGES, _NEIGHBORS)
pruned_graph = deepcopy(old_graph)
keep_condition = array([True, True, False]) # only prune the last node
pruned_graph.prune_nodes(keep_condition)
self.assertNotEqual(old_graph, pruned_graph)
assert_frame_equal(pruned_graph.nodes, _NODES[:2])
assert_array_equal(pruned_graph.edges, _EDGES[:1])
assert_array_equal(pruned_graph.neighbors, _NEIGHBORS[:2, :1])