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annotate planemo/lib/python3.7/site-packages/networkx/readwrite/nx_shp.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 """
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2 *********
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3 Shapefile
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4 *********
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5
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6 Generates a networkx.DiGraph from point and line shapefiles.
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7
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8 "The Esri Shapefile or simply a shapefile is a popular geospatial vector
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9 data format for geographic information systems software. It is developed
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10 and regulated by Esri as a (mostly) open specification for data
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11 interoperability among Esri and other software products."
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12 See https://en.wikipedia.org/wiki/Shapefile for additional information.
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13 """
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14 # Copyright (C) 2004-2019 by
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15 # Ben Reilly <benwreilly@gmail.com>
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16 # Aric Hagberg <hagberg@lanl.gov>
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17 # Dan Schult <dschult@colgate.edu>
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18 # Pieter Swart <swart@lanl.gov>
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19 # All rights reserved.
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20 # BSD license.
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21 import networkx as nx
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22 __author__ = """Ben Reilly (benwreilly@gmail.com)"""
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23 __all__ = ['read_shp', 'write_shp']
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24
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25
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26 def read_shp(path, simplify=True, geom_attrs=True, strict=True):
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27 """Generates a networkx.DiGraph from shapefiles. Point geometries are
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28 translated into nodes, lines into edges. Coordinate tuples are used as
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29 keys. Attributes are preserved, line geometries are simplified into start
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30 and end coordinates. Accepts a single shapefile or directory of many
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31 shapefiles.
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32
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33 "The Esri Shapefile or simply a shapefile is a popular geospatial vector
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34 data format for geographic information systems software [1]_."
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35
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36 Parameters
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37 ----------
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38 path : file or string
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39 File, directory, or filename to read.
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40
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41 simplify: bool
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42 If True, simplify line geometries to start and end coordinates.
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43 If False, and line feature geometry has multiple segments, the
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44 non-geometric attributes for that feature will be repeated for each
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45 edge comprising that feature.
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46
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47 geom_attrs: bool
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48 If True, include the Wkb, Wkt and Json geometry attributes with
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49 each edge.
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50
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51 NOTE: if these attributes are available, write_shp will use them
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52 to write the geometry. If nodes store the underlying coordinates for
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53 the edge geometry as well (as they do when they are read via
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54 this method) and they change, your geomety will be out of sync.
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55
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56 strict: bool
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57 If True, raise NetworkXError when feature geometry is missing or
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58 GeometryType is not supported.
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59 If False, silently ignore missing or unsupported geometry in features.
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60
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61 Returns
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62 -------
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63 G : NetworkX graph
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64
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65 Raises
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66 ------
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67 ImportError
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68 If ogr module is not available.
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69
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70 RuntimeError
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71 If file cannot be open or read.
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72
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73 NetworkXError
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74 If strict=True and feature is missing geometry or GeometryType is
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75 not supported.
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76
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77 Examples
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78 --------
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79 >>> G=nx.read_shp('test.shp') # doctest: +SKIP
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80
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81 References
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82 ----------
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83 .. [1] https://en.wikipedia.org/wiki/Shapefile
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84 """
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85 try:
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86 from osgeo import ogr
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87 except ImportError:
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88 raise ImportError("read_shp requires OGR: http://www.gdal.org/")
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89
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90 if not isinstance(path, str):
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91 return
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92
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93 net = nx.DiGraph()
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94 shp = ogr.Open(path)
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95 if shp is None:
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96 raise RuntimeError("Unable to open {}".format(path))
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97 for lyr in shp:
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98 fields = [x.GetName() for x in lyr.schema]
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99 for f in lyr:
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100 g = f.geometry()
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101 if g is None:
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102 if strict:
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103 raise nx.NetworkXError("Bad data: feature missing geometry")
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104 else:
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105 continue
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106 flddata = [f.GetField(f.GetFieldIndex(x)) for x in fields]
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107 attributes = dict(zip(fields, flddata))
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108 attributes["ShpName"] = lyr.GetName()
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109 # Note: Using layer level geometry type
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110 if g.GetGeometryType() == ogr.wkbPoint:
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111 net.add_node((g.GetPoint_2D(0)), **attributes)
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112 elif g.GetGeometryType() in (ogr.wkbLineString,
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113 ogr.wkbMultiLineString):
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114 for edge in edges_from_line(g, attributes, simplify,
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115 geom_attrs):
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116 e1, e2, attr = edge
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117 net.add_edge(e1, e2)
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118 net[e1][e2].update(attr)
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119 else:
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120 if strict:
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121 raise nx.NetworkXError("GeometryType {} not supported".
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122 format(g.GetGeometryType()))
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123
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124 return net
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125
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126
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127 def edges_from_line(geom, attrs, simplify=True, geom_attrs=True):
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128 """
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129 Generate edges for each line in geom
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130 Written as a helper for read_shp
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131
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132 Parameters
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133 ----------
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134
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135 geom: ogr line geometry
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136 To be converted into an edge or edges
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137
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138 attrs: dict
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139 Attributes to be associated with all geoms
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140
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141 simplify: bool
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142 If True, simplify the line as in read_shp
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143
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144 geom_attrs: bool
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145 If True, add geom attributes to edge as in read_shp
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146
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147
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148 Returns
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149 -------
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150 edges: generator of edges
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151 each edge is a tuple of form
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152 (node1_coord, node2_coord, attribute_dict)
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153 suitable for expanding into a networkx Graph add_edge call
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154 """
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155 try:
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156 from osgeo import ogr
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157 except ImportError:
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158 raise ImportError("edges_from_line requires OGR: http://www.gdal.org/")
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159
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160 if geom.GetGeometryType() == ogr.wkbLineString:
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161 if simplify:
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162 edge_attrs = attrs.copy()
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163 last = geom.GetPointCount() - 1
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164 if geom_attrs:
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165 edge_attrs["Wkb"] = geom.ExportToWkb()
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166 edge_attrs["Wkt"] = geom.ExportToWkt()
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167 edge_attrs["Json"] = geom.ExportToJson()
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168 yield (geom.GetPoint_2D(0), geom.GetPoint_2D(last), edge_attrs)
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169 else:
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170 for i in range(0, geom.GetPointCount() - 1):
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171 pt1 = geom.GetPoint_2D(i)
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172 pt2 = geom.GetPoint_2D(i + 1)
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173 edge_attrs = attrs.copy()
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174 if geom_attrs:
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175 segment = ogr.Geometry(ogr.wkbLineString)
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176 segment.AddPoint_2D(pt1[0], pt1[1])
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177 segment.AddPoint_2D(pt2[0], pt2[1])
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178 edge_attrs["Wkb"] = segment.ExportToWkb()
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179 edge_attrs["Wkt"] = segment.ExportToWkt()
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180 edge_attrs["Json"] = segment.ExportToJson()
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181 del segment
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182 yield (pt1, pt2, edge_attrs)
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183
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184 elif geom.GetGeometryType() == ogr.wkbMultiLineString:
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185 for i in range(geom.GetGeometryCount()):
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186 geom_i = geom.GetGeometryRef(i)
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187 for edge in edges_from_line(geom_i, attrs, simplify, geom_attrs):
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188 yield edge
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189
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190
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191 def write_shp(G, outdir):
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192 """Writes a networkx.DiGraph to two shapefiles, edges and nodes.
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193 Nodes and edges are expected to have a Well Known Binary (Wkb) or
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194 Well Known Text (Wkt) key in order to generate geometries. Also
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195 acceptable are nodes with a numeric tuple key (x,y).
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196
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197 "The Esri Shapefile or simply a shapefile is a popular geospatial vector
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198 data format for geographic information systems software [1]_."
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199
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200 Parameters
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201 ----------
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202 outdir : directory path
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203 Output directory for the two shapefiles.
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204
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205 Returns
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206 -------
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207 None
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208
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209 Examples
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210 --------
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211 nx.write_shp(digraph, '/shapefiles') # doctest +SKIP
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212
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213 References
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214 ----------
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215 .. [1] https://en.wikipedia.org/wiki/Shapefile
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216 """
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217 try:
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218 from osgeo import ogr
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219 except ImportError:
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220 raise ImportError("write_shp requires OGR: http://www.gdal.org/")
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221 # easier to debug in python if ogr throws exceptions
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222 ogr.UseExceptions()
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223
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224 def netgeometry(key, data):
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225 if 'Wkb' in data:
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226 geom = ogr.CreateGeometryFromWkb(data['Wkb'])
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227 elif 'Wkt' in data:
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228 geom = ogr.CreateGeometryFromWkt(data['Wkt'])
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229 elif type(key[0]).__name__ == 'tuple': # edge keys are packed tuples
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230 geom = ogr.Geometry(ogr.wkbLineString)
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231 _from, _to = key[0], key[1]
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232 try:
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233 geom.SetPoint(0, *_from)
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234 geom.SetPoint(1, *_to)
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235 except TypeError:
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236 # assume user used tuple of int and choked ogr
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237 _ffrom = [float(x) for x in _from]
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238 _fto = [float(x) for x in _to]
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239 geom.SetPoint(0, *_ffrom)
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240 geom.SetPoint(1, *_fto)
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241 else:
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242 geom = ogr.Geometry(ogr.wkbPoint)
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243 try:
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244 geom.SetPoint(0, *key)
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245 except TypeError:
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246 # assume user used tuple of int and choked ogr
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247 fkey = [float(x) for x in key]
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248 geom.SetPoint(0, *fkey)
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249
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250 return geom
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251
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252 # Create_feature with new optional attributes arg (should be dict type)
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253 def create_feature(geometry, lyr, attributes=None):
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254 feature = ogr.Feature(lyr.GetLayerDefn())
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255 feature.SetGeometry(g)
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256 if attributes is not None:
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257 # Loop through attributes, assigning data to each field
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258 for field, data in attributes.items():
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259 feature.SetField(field, data)
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260 lyr.CreateFeature(feature)
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261 feature.Destroy()
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262
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263 # Conversion dict between python and ogr types
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264 OGRTypes = {int: ogr.OFTInteger, str: ogr.OFTString, float: ogr.OFTReal}
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265
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266 # Check/add fields from attribute data to Shapefile layers
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267 def add_fields_to_layer(key, value, fields, layer):
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268 # Field not in previous edges so add to dict
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269 if type(value) in OGRTypes:
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270 fields[key] = OGRTypes[type(value)]
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271 else:
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272 # Data type not supported, default to string (char 80)
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273 fields[key] = ogr.OFTString
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274 # Create the new field
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275 newfield = ogr.FieldDefn(key, fields[key])
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276 layer.CreateField(newfield)
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277
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278
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279 drv = ogr.GetDriverByName("ESRI Shapefile")
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280 shpdir = drv.CreateDataSource(outdir)
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281 # delete pre-existing output first otherwise ogr chokes
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282 try:
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283 shpdir.DeleteLayer("nodes")
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284 except:
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285 pass
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286 nodes = shpdir.CreateLayer("nodes", None, ogr.wkbPoint)
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287
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288 # Storage for node field names and their data types
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289 node_fields = {}
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290
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291 def create_attributes(data, fields, layer):
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292 attributes = {} # storage for attribute data (indexed by field names)
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293 for key, value in data.items():
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294 # Reject spatial data not required for attribute table
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295 if (key != 'Json' and key != 'Wkt' and key != 'Wkb'
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296 and key != 'ShpName'):
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297 # Check/add field and data type to fields dict
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298 if key not in fields:
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299 add_fields_to_layer(key, value, fields, layer)
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300 # Store the data from new field to dict for CreateLayer()
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301 attributes[key] = value
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302 return attributes, layer
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303
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304 for n in G:
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305 data = G.nodes[n]
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306 g = netgeometry(n, data)
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307 attributes, nodes = create_attributes(data, node_fields, nodes)
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308 create_feature(g, nodes, attributes)
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309
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310 try:
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311 shpdir.DeleteLayer("edges")
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312 except:
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313 pass
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314 edges = shpdir.CreateLayer("edges", None, ogr.wkbLineString)
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315
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316 # New edge attribute write support merged into edge loop
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317 edge_fields = {} # storage for field names and their data types
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318
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319 for e in G.edges(data=True):
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320 data = G.get_edge_data(*e)
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321 g = netgeometry(e, data)
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322 attributes, edges = create_attributes(e[2], edge_fields, edges)
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323 create_feature(g, edges, attributes)
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324
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325 nodes, edges = None, None
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326
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327
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328 # fixture for pytest
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329 def setup_module(module):
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330 import pytest
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331 ogr = pytest.importorskip('ogr')