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Nov 16, 2021
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Data aug #210

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ee5b682
Merge pull request #207 from InsightLab/developer
mxaviersmp Jul 14, 2021
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adding examples and updating functions
Nov 15, 2021
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adding examples and updating functions
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adding examples and updating functions
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adding examples and updating functions
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adding examples and updating functions
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adding examples and updating functions
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adding examples and updating functions
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adding examples and updating functions
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adding examples and updating functions
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adding examples and updating functions
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adding examples and updating functions
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adding examples and updating functions
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8 changes: 8 additions & 0 deletions docs/api/pymove.utils.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,14 @@ pymove.utils.mem module
:undoc-members:
:show-inheritance:

pymove.utils.networkx module
----------------------------

.. automodule:: pymove.utils.networkx
:members:
:undoc-members:
:show-inheritance:

pymove.utils.trajectories module
--------------------------------

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577 changes: 271 additions & 306 deletions pymove/tests/test_utils_data_augmentation.py
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228 changes: 228 additions & 0 deletions pymove/tests/test_utils_networkx.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,228 @@
import json
import os

import pandas as pd
from networkx.classes.digraph import DiGraph
from networkx.testing import assert_graphs_equal
from numpy.testing import assert_equal

from pymove.utils.constants import (
DATETIME,
LATITUDE,
LOCAL_LABEL,
LONGITUDE,
PREV_LOCAL,
TID,
TRAJ_ID,
)
from pymove.utils.networkx import (
_populate_graph,
build_transition_graph_from_df,
build_transition_graph_from_dict,
graph_to_dict,
read_graph_json,
save_graph_as_json,
)

dict_graph = {
'nodes': {
'coords': { '85': (-3.8347478, -38.592189), '673': (-3.8235834, -38.590389),
'394': (-3.813889, -38.5904445), '263': (-3.9067654, -38.5907723),
'224': (-3.8857223, -38.5928892), '623': (-3.8828723, -38.5929789)},
'datetime': { '85': ['2017-09-02 22:00:27'], '673': ['2017-09-02 22:01:36'],
'394': ['2017-09-02 22:03:08'], '263': ['2017-09-02 22:03:46'],
'224': ['2017-09-02 22:07:19'], '623': ['2017-09-02 22:07:40']},
'freq_source': {'85': 1, '673': 0, '394': 0, '263': 0, '224': 0, '623': 0},
'freq_target': {'85': 0, '673': 0, '394': 0, '263': 0, '224': 0, '623': 1}},
'edges': {
'85': {'673': {'weight': 1, 'mean_times': '0 days 00:01:09'}},
'673': {'394': {'weight': 1, 'mean_times': '0 days 00:01:32'}},
'394': {'263': {'weight': 1, 'mean_times': '0 days 00:00:38'}},
'263': {'224': {'weight': 1, 'mean_times': '0 days 00:03:33'}},
'224': {'623': {'weight': 1, 'mean_times': '0 days 00:00:21'}},
'623': {}}}

list_data1 = {
TRAJ_ID: [[1, 1, 1, 1, 1, 1]],
DATETIME: [[pd.Timestamp('2017-09-02 22:00:27'),
pd.Timestamp('2017-09-02 22:01:36'),
pd.Timestamp('2017-09-02 22:03:08'),
pd.Timestamp('2017-09-02 22:03:46'),
pd.Timestamp('2017-09-02 22:07:19'),
pd.Timestamp('2017-09-02 22:07:40')]],
LOCAL_LABEL: [[85, 673, 394, 263, 224, 623]],
LATITUDE: [[-3.8347478, -3.8235834, -3.813889,
-3.9067654, -3.8857223, -3.8828723]],
LONGITUDE: [[-38.592189, -38.590389, -38.5904445,
-38.5907723, -38.5928892, -38.5929789]],
TID: [['12017090222', '12017090222', '12017090222',
'12017090222', '12017090222', '12017090222']]
}


def _transition_graph():
expected_graph = DiGraph()
expected_graph.add_node('85', coords=(-3.8347478, -38.592189),
datetime=['2017-09-02 22:00:27'], freq_source=1, freq_target=0)
expected_graph.add_node('673', coords=(-3.8235834, -38.590389),
datetime=['2017-09-02 22:01:36'], freq_source=0, freq_target=0)
expected_graph.add_node('394', coords=(-3.813889, -38.5904445),
datetime=['2017-09-02 22:03:08'], freq_source=0, freq_target=0)
expected_graph.add_node('263', coords=(-3.9067654, -38.5907723),
datetime=['2017-09-02 22:03:46'], freq_source=0, freq_target=0)
expected_graph.add_node('224', coords=(-3.8857223, -38.5928892),
datetime=['2017-09-02 22:07:19'], freq_source=0, freq_target=0)
expected_graph.add_node('623', coords=(-3.8828723, -38.5929789),
datetime=['2017-09-02 22:07:40'], freq_source=0, freq_target=1)
expected_graph.add_edge( '85', '673', weight=1, mean_times='0 days 00:01:09')
expected_graph.add_edge('673', '394', weight=1, mean_times='0 days 00:01:32')
expected_graph.add_edge('394', '263', weight=1, mean_times='0 days 00:00:38')
expected_graph.add_edge('263', '224', weight=1, mean_times='0 days 00:03:33')
expected_graph.add_edge('224', '623', weight=1, mean_times='0 days 00:00:21')

return expected_graph


def test_populate_graph():
row = pd.DataFrame(list_data1).loc[0]

nodes = {'datetime': {}, 'coords': {}, 'freq_source': {}, 'freq_target': {}}
edges = {}

expected_nodes = {
'datetime': {'85': ['2017-09-02 22:00:27'], '673': ['2017-09-02 22:01:36'],
'394': ['2017-09-02 22:03:08'], '263': ['2017-09-02 22:03:46'],
'224': ['2017-09-02 22:07:19'], '623': ['2017-09-02 22:07:40']},
'coords': {'85': (-3.8347478, -38.592189), '673': (-3.8235834, -38.590389),
'394': (-3.813889, -38.5904445), '263': (-3.9067654, -38.5907723),
'224': (-3.8857223, -38.5928892), '623': (-3.8828723, -38.5929789)},
'freq_source': {'85': 1, '673': 0, '394': 0, '263': 0, '224': 0, '623': 0},
'freq_target': {'85': 0, '673': 0, '394': 0, '263': 0, '224': 0, '623': 1}}

expected_edges = {
'85': {'673': {'weight': 1, 'mean_times': '0 days 00:01:09'}},
'673': {'394': {'weight': 1, 'mean_times': '0 days 00:01:32'}},
'394': {'263': {'weight': 1, 'mean_times': '0 days 00:00:38'}},
'263': {'224': {'weight': 1, 'mean_times': '0 days 00:03:33'}},
'224': {'623': {'weight': 1, 'mean_times': '0 days 00:00:21'}}}

_populate_graph(row, nodes, edges)
nodes, edges

assert_equal(expected_nodes, nodes)
assert_equal(expected_edges, edges)


def test_build_transition_graph_from_dict():
expected_graph = _transition_graph()

graph = build_transition_graph_from_dict(dict_graph)

assert_graphs_equal(expected_graph, graph)


def test_build_transition_graph_from_df():
expected_graph = _transition_graph()

traj_df = pd.DataFrame(list_data1)

graph = build_transition_graph_from_df(traj_df)

assert_graphs_equal(expected_graph, graph)


def test_graph_to_dict():
graph = _transition_graph()

expected_dict = {
'nodes': {
'coords': { '85': (-3.8347478, -38.592189), '673': (-3.8235834, -38.590389),
'394': (-3.813889, -38.5904445), '263': (-3.9067654, -38.5907723),
'224': (-3.8857223, -38.5928892), '623': (-3.8828723, -38.5929789)},
'datetime': { '85': ['2017-09-02 22:00:27'], '673': ['2017-09-02 22:01:36'],
'394': ['2017-09-02 22:03:08'], '263': ['2017-09-02 22:03:46'],
'224': ['2017-09-02 22:07:19'], '623': ['2017-09-02 22:07:40']},
'freq_source': {'85': 1, '673': 0, '394': 0, '263': 0, '224': 0, '623': 0},
'freq_target': {'85': 0, '673': 0, '394': 0, '263': 0, '224': 0, '623': 1}},
'edges': {
'85': {'673': {'weight': 1, 'mean_times': '0 days 00:01:09'}},
'673': {'394': {'weight': 1, 'mean_times': '0 days 00:01:32'}},
'394': {'263': {'weight': 1, 'mean_times': '0 days 00:00:38'}},
'263': {'224': {'weight': 1, 'mean_times': '0 days 00:03:33'}},
'224': {'623': {'weight': 1, 'mean_times': '0 days 00:00:21'}},
'623': {}}}

dict_graph = graph_to_dict(graph)

assert_equal(expected_dict, dict_graph)


def test_save_graph_as_json(tmpdir):

expected = {
'nodes': {
'coords': { '85': (-3.8347478, -38.592189), '673': (-3.8235834, -38.590389),
'394': (-3.813889, -38.5904445), '263': (-3.9067654, -38.5907723),
'224': (-3.8857223, -38.5928892), '623': (-3.8828723, -38.5929789)},
'datetime': { '85': ['2017-09-02 22:00:27'], '673': ['2017-09-02 22:01:36'],
'394': ['2017-09-02 22:03:08'], '263': ['2017-09-02 22:03:46'],
'224': ['2017-09-02 22:07:19'], '623': ['2017-09-02 22:07:40']},
'freq_source': {'85': 1, '673': 0, '394': 0, '263': 0, '224': 0, '623': 0},
'freq_target': {'85': 0, '673': 0, '394': 0, '263': 0, '224': 0, '623': 1}},
'edges': {
'85': {'673': {'weight': 1, 'mean_times': '0 days 00:01:09'}},
'673': {'394': {'weight': 1, 'mean_times': '0 days 00:01:32'}},
'394': {'263': {'weight': 1, 'mean_times': '0 days 00:00:38'}},
'263': {'224': {'weight': 1, 'mean_times': '0 days 00:03:33'}},
'224': {'623': {'weight': 1, 'mean_times': '0 days 00:00:21'}},
'623': {}}}

d = tmpdir.mkdir('utils')

file_write_default = d.join('test_save_graph.json')
filename_write_default = os.path.join(
file_write_default.dirname, file_write_default.basename
)

graph = _transition_graph()
save_graph_as_json(graph, filename_write_default)
saved_graph = read_graph_json(filename_write_default)

assert_equal(saved_graph, expected)


def test_read_graph_json(tmpdir):

expected = {
'nodes': {
'coords': { '85': (-3.8347478, -38.592189), '673': (-3.8235834, -38.590389),
'394': (-3.813889, -38.5904445), '263': (-3.9067654, -38.5907723),
'224': (-3.8857223, -38.5928892), '623': (-3.8828723, -38.5929789)},
'datetime': { '85': ['2017-09-02 22:00:27'], '673': ['2017-09-02 22:01:36'],
'394': ['2017-09-02 22:03:08'], '263': ['2017-09-02 22:03:46'],
'224': ['2017-09-02 22:07:19'], '623': ['2017-09-02 22:07:40']},
'freq_source': {'85': 1, '673': 0, '394': 0, '263': 0, '224': 0, '623': 0},
'freq_target': {'85': 0, '673': 0, '394': 0, '263': 0, '224': 0, '623': 1}},
'edges': {
'85': {'673': {'weight': 1, 'mean_times': '0 days 00:01:09'}},
'673': {'394': {'weight': 1, 'mean_times': '0 days 00:01:32'}},
'394': {'263': {'weight': 1, 'mean_times': '0 days 00:00:38'}},
'263': {'224': {'weight': 1, 'mean_times': '0 days 00:03:33'}},
'224': {'623': {'weight': 1, 'mean_times': '0 days 00:00:21'}},
'623': {}}}

d = tmpdir.mkdir('utils')

file_write_default = d.join('test_read_graph.json')
filename_write_default = os.path.join(
file_write_default.dirname, file_write_default.basename
)

graph = _transition_graph()

with open(filename_write_default, 'w') as f:
json.dump(dict_graph, f)

saved_graph = read_graph_json(filename_write_default)

assert_equal(saved_graph, expected)
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