Commit 255a6d86 authored by jlaura's avatar jlaura
Browse files

Merge pull request #102 from Kelvinrr/mstchange 

changed mst to function with subgraphing and removed graph_masks
parents 5a69711f e46ef045

autocnet/fileio/io_utils.py

+9 −0
Original line number Diff line number Diff line
@@ -22,3 +22,12 @@ def delete_dir(dir): 
          Remove a directory

    """

    shutil.rmtree(dir)





def file_to_list(file):

    with open(file, 'r') as f:

        file_list = f.readlines()

        file_list = map(str.rstrip, file_list)

        file_list = filter(None, file_list)



    return file_list

autocnet/graph/network.py

+31 −34
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



from autocnet.fileio.io_gdal import GeoDataset

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
@@ -44,7 +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)
@@ -107,11 +108,8 @@ class CandidateGraph(nx.Graph): 
        : object

          A Network graph object

        """

        if not isinstance(filelist, list):

            with open(filelist, 'r') as f:

                filelist = f.readlines()

                filelist = map(str.rstrip, filelist)

                filelist = filter(None, filelist)

        if isinstance(filelist, str):

            filelist = io_utils.file_to_list(filelist)



        # TODO: Reject unsupported file formats + work with more file formats

        if basepath:
@@ -121,23 +119,28 @@ class CandidateGraph(nx.Graph): 


        # This is brute force for now, could swap to an RTree at some point.

        adjacency_dict = {}

        valid_datasets = []



        for i, j in itertools.permutations(datasets,2):

            if not i.file_name in adjacency_dict.keys():

        for i in datasets:

            adjacency_dict[i.file_name] = []

            if not j.file_name in adjacency_dict.keys():

                adjacency_dict[j.file_name] = []



            fp = i.footprint

            if fp and fp.IsValid():

                valid_datasets.append(i)

            else:

                warnings.warn('Missing or invalid geospatial data for {}'.format(i.base_name))



        # Grab the footprints and test for intersection

        for i, j in itertools.permutations(valid_datasets, 2):

            i_fp = i.footprint

            j_fp = j.footprint



            try:

                if j_fp and i_fp and i_fp.Intersects(j_fp):

                if i_fp.Intersects(j_fp):

                    adjacency_dict[i.file_name].append(j.file_name)

                    adjacency_dict[j.file_name].append(i.file_name)

            except:

                warnings.warn('No or incorrect geospatial information for {} and/or {}'.format(i, j))

                warnings.warn('Failed to calculated intersection between {} and {}'.format(i, j))



        return cls(adjacency_dict)
@@ -300,6 +303,11 @@ class CandidateGraph(nx.Graph): 
            descriptors = node.descriptors

            # Load the neighbors of the current node into the FLANN matcher

            neighbors = self.neighbors(i)



            # if node has no neighbors, skip

            if not neighbors:

                continue



            for n in neighbors:

                neighbor_descriptors = self.node[n].descriptors

                self._fl.add(neighbor_descriptors, n)
@@ -365,7 +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
@@ -376,20 +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:
@@ -406,11 +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

+47 −29
Original line number Diff line number Diff line
@@ -4,6 +4,10 @@ sys.path.insert(0, os.path.abspath('..')) 


import unittest



from unittest.mock import patch

from unittest.mock import PropertyMock

from osgeo import ogr



import numpy as np



from autocnet.examples import get_path
@@ -42,20 +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()
@@ -100,6 +108,21 @@ class TestCandidateGraph(unittest.TestCase): 
    def test_fromlist(self):

        mock_list = ['AS15-M-0295_SML.png', 'AS15-M-0296_SML.png', 'AS15-M-0297_SML.png',

                     'AS15-M-0298_SML.png', 'AS15-M-0299_SML.png', 'AS15-M-0300_SML.png']



        good_poly = ogr.CreateGeometryFromWkt('POLYGON ((30 10, 40 40, 20 40, 10 20, 30 10))')

        bad_poly = ogr.CreateGeometryFromWkt('POLYGON ((9999 10, 40 40, 20 40, 10 20, 30 10))')



        with patch('autocnet.fileio.io_gdal.GeoDataset.footprint', new_callable=PropertyMock) as patch_fp:

            patch_fp.return_value = good_poly

            n = network.CandidateGraph.from_filelist(mock_list, get_path('Apollo15'))

            self.assertEqual(n.number_of_nodes(), 6)

            self.assertEqual(n.number_of_edges(), 15)



            patch_fp.return_value = bad_poly

            n = network.CandidateGraph.from_filelist(mock_list, get_path('Apollo15'))

            self.assertEqual(n.number_of_nodes(), 6)

            self.assertEqual(n.number_of_edges(), 0)



        n = network.CandidateGraph.from_filelist(mock_list, get_path('Apollo15'))

        self.assertEqual(len(n.nodes()), 6)
@@ -137,14 +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"],
@@ -153,13 +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()))



        self.assertEqual(sorted(mst_graph.nodes()), sorted(graph.nodes()))

        self.assertEqual(len(mst_graph.edges()), len(graph.edges())-5)



        cls.mst_graph = cls.graph.copy()

        cls.mst_graph.remove_edges_from(removed_edges)



    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

File changed.

Preview size limit exceeded, changes collapsed.