Merge pull request #111 from USGS-Astrogeology/revert-105-master (0d85cd16) · Commits · aflab / astrogeology / Autocnet

.travis.yml

+3 −9

Original line number	Original line	Diff line number	Diff line
	@@ -4,7 +4,6 @@ sudo: false
	branches:		branches:
	only:		only:
	- master		- master
	- dev

	python:		python:
	- "3.5"		- "3.5"
	@@ -28,9 +27,9 @@ install:
	- conda info -a		- conda info -a

	# Create a virtual env and install dependencies		# Create a virtual env and install dependencies
	# conda is explicitly included here to try to get it into a non-root env. It is NOT needed outside of CI testing and binstar upload.		- conda create -y -q -n test-env python=$TRAVIS_PYTHON_VERSION nose numpy pillow scipy pandas networkx scikit-image sqlalchemy numexpr dill cython pyyaml
	- conda install python=3.5 nose numpy pillow scipy pandas networkx scikit-image sqlalchemy numexpr dill cython pyyaml		# Activate the env
			- source activate test-env

	# Install the non-conda packages if required, requirements.txt duplicates are ignored		# Install the non-conda packages if required, requirements.txt duplicates are ignored
	- conda install -c https://conda.anaconda.org/jlaura opencv3=3.0.0		- conda install -c https://conda.anaconda.org/jlaura opencv3=3.0.0
	@@ -40,15 +39,11 @@ install:
	- pip install coverage		- pip install coverage
	- pip install coveralls		- pip install coveralls

	# Install libs to support upload to binstar
	- conda install anaconda-client binstar conda-build

	script:		script:
	- nosetests --with-coverage --cover-package=autocnet		- nosetests --with-coverage --cover-package=autocnet

	after_success:		after_success:
	- coveralls		- coveralls
	- python ci_support/upload_or_check_non_existence.py ci_support jlaura --channel=main

	notifications:		notifications:
	webhooks:		webhooks:
	@@ -65,4 +60,3 @@ notifications:
	- krodriguez@usgs.gov		- krodriguez@usgs.gov
	on_success: always		on_success: always
	on_failure: always		on_failure: always

autocnet/graph/edge.py

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -292,7 +292,7 @@ class Edge(dict, MutableMapping):
	raise AttributeError('This edge does not yet have any matches computed.')		raise AttributeError('This edge does not yet have any matches computed.')

	matches, mask = self._clean(clean_keys)		matches, mask = self._clean(clean_keys)
	domain = self.source.geodata.raster_size		domain = self.source.handle.raster_size

	# Massage the dataframe into the correct structure		# Massage the dataframe into the correct structure
	coords = self.source.get_keypoint_coordinates()		coords = self.source.get_keypoint_coordinates()

autocnet/graph/network.py

+23 −11

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

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

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


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

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

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

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

	def to_filelist(self):		def to_filelist(self):
	"""		"""

autocnet/graph/node.py

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -272,7 +272,7 @@ class Node(dict, MutableMapping):
	if not hasattr(self, '_keypoints'):		if not hasattr(self, '_keypoints'):
	raise AttributeError('No keypoints extracted for this node.')		raise AttributeError('No keypoints extracted for this node.')

	domain = self.geodata.raster_size		domain = self.handle.raster_size
	self._keypoints['strength'] = self._keypoints.apply(func, axis=1)		self._keypoints['strength'] = self._keypoints.apply(func, axis=1)

	if not hasattr(self, 'suppression'):		if not hasattr(self, 'suppression'):

autocnet/graph/tests/test_network.py

+32 −28

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

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

	import numpy as np		import numpy as np

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

	from .. import network		from .. import network

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

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

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

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

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

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

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

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

	def test_minimum_spanning_tree(self):		def tearDown(self):
	test_dict = {"0": ["4", "2", "1", "3"],		pass


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

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

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

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