changed mst to function with subgraphing and removed graph_masks (e46ef045) · Commits · aflab / astrogeology / Autocnet

autocnet/graph/network.py

+11 −23

Original line number	Diff line number	Diff line
		import itertools
		import math
		import os
		import warnings

		import dill as pickle
		import networkx as nx
		import numpy as np
		import pandas as pd
		import warnings

		from autocnet.fileio.io_gdal import GeoDataset
		from autocnet.fileio import io_utils
		from autocnet.fileio import io_hdf
		from autocnet.control.control import C
		from autocnet.fileio import io_hdf
		from autocnet.fileio import io_json
		from autocnet.matcher.matcher import FlannMatcher
		import autocnet.matcher.suppression_funcs as spf
		from autocnet.fileio import io_utils
		from autocnet.fileio.io_gdal import GeoDataset
		from autocnet.graph import markov_cluster
		from autocnet.graph.edge import Edge
		from autocnet.graph.node import Node
		from autocnet.graph import markov_cluster
		from autocnet.matcher.matcher import FlannMatcher
		from autocnet.vis.graph_view import plot_graph


		@@ -46,7 +46,6 @@ class CandidateGraph(nx.Graph):
		self.node_counter = 0
		node_labels = {}
		self.node_name_map = {}
		self.graph_masks = pd.DataFrame()

		for node_name in self.nodes():
		image_name = os.path.basename(node_name)
		@@ -374,7 +373,7 @@ class CandidateGraph(nx.Graph):
		"""
		_, self.clusters = func(self, args, *kwargs)

		def apply_func_to_edges(self, function, args, graph_mask_keys=[], *kwargs):
		def apply_func_to_edges(self, function, args, *kwargs):
		"""
		Iterates over edges using an optional mask and and applies the given function.
		If func is not an attribute of Edge, raises AttributeError
		@@ -385,20 +384,12 @@ class CandidateGraph(nx.Graph):
		graph_mask_keys : list
		of keys in graph_masks
		"""

		if graph_mask_keys:
		merged_graph_mask = self.graph_masks[graph_mask_keys].all(axis=1)
		edges_to_iter = merged_graph_mask[merged_graph_mask].index
		else:
		edges_to_iter = self.edges()

		if not isinstance(function, str):
		function = function.__name__

		for s, d in edges_to_iter:
		curr_edge = self.get_edge_data(s, d)
		for s, d, edge in self.edges_iter(data=True):
		try:
		func = getattr(curr_edge, function)
		func = getattr(edge, function)
		except:
		raise AttributeError(function, ' is not an attribute of Edge')
		else:
		@@ -415,11 +406,8 @@ class CandidateGraph(nx.Graph):
		boolean mask for edges in the minimum spanning tree
		"""

		graph_mask = pd.Series(False, index=self.edges())
		self.graph_masks['mst'] = graph_mask

		mst = nx.minimum_spanning_tree(self)
		self.graph_masks['mst'][mst.edges()] = True
		return self.create_edge_subgraph(mst.edges())

		def to_filelist(self):
		"""

autocnet/graph/tests/test_network.py

+28 −32

Original line number	Diff line number	Diff line
		@@ -6,14 +6,11 @@ import unittest

		from unittest.mock import patch
		from unittest.mock import PropertyMock
		from unittest.mock import MagicMock
		from osgeo import ogr
		import gdal

		import numpy as np

		from autocnet.examples import get_path
		from autocnet.fileio import io_gdal

		from .. import network

		@@ -49,20 +46,24 @@ class TestCandidateGraph(unittest.TestCase):

		def test_apply_func_to_edges(self):
		graph = self.graph.copy()
		graph.minimum_spanning_tree()
		mst_graph = graph.minimum_spanning_tree()

		try:
		graph.apply_func_to_edges('incorrect_func')
		except AttributeError:
		pass

		graph.extract_features(extractor_parameters={'nfeatures': 500})
		graph.match_features()
		graph.apply_func_to_edges("symmetry_check", graph_mask_keys=['mst'])
		mst_graph.extract_features(extractor_parameters={'nfeatures': 500})
		mst_graph.match_features()
		mst_graph.apply_func_to_edges("symmetry_check")

		self.assertFalse(graph[0][2].masks['symmetry'].all())
		self.assertFalse(graph[0][1].masks['symmetry'].all())

		try:
		self.assertTrue(graph[1][2].masks['symmetry'].all())
		except:
		pass

		def test_connected_subgraphs(self):
		subgraph_list = self.disconnected_graph.connected_subgraphs()
		@@ -159,14 +160,8 @@ class TestCandidateGraph(unittest.TestCase):

		self.assertEqual(test_sub_graph.edges(), sub_graph_from_matches.edges())

		def tearDown(self):
		pass


		class TestGraphMasks(unittest.TestCase):
		@classmethod
		def setUpClass(cls):
		cls.test_dict = {"0": ["4", "2", "1", "3"],
		def test_minimum_spanning_tree(self):
		test_dict = {"0": ["4", "2", "1", "3"],
		"1": ["0", "3", "2", "6", "5"],
		"2": ["1", "0", "3", "4", "7"],
		"3": ["2", "0", "1", "5"],
		@@ -175,13 +170,14 @@ class TestGraphMasks(unittest.TestCase):
		"6": ["1"],
		"7": ["2"]}

		cls.graph = network.CandidateGraph.from_adjacency(cls.test_dict)
		cls.graph.minimum_spanning_tree()
		removed_edges = cls.graph.graph_masks['mst'][cls.graph.graph_masks['mst'] == False].index
		graph = network.CandidateGraph.from_adjacency(test_dict)
		mst_graph = graph.minimum_spanning_tree()

		print(len(mst_graph.edges()))

		cls.mst_graph = cls.graph.copy()
		cls.mst_graph.remove_edges_from(removed_edges)
		self.assertEqual(sorted(mst_graph.nodes()), sorted(graph.nodes()))
		self.assertEqual(len(mst_graph.edges()), len(graph.edges())-5)

		def test_mst_output(self):
		self.assertEqual(sorted(self.mst_graph.nodes()), sorted(self.graph.nodes()))
		self.assertEqual(self.mst_graph.number_of_edges(), self.graph.number_of_edges()-5)
		No newline at end of file

		def tearDown(self):
		pass

notebooks/Tutorial with Visualization.ipynb

+121 −57

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