Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/nx_shp.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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 import networkx as nx |
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15 |
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16 __all__ = ["read_shp", "write_shp"] |
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17 |
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18 |
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19 def read_shp(path, simplify=True, geom_attrs=True, strict=True): |
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20 """Generates a networkx.DiGraph from shapefiles. Point geometries are |
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21 translated into nodes, lines into edges. Coordinate tuples are used as |
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22 keys. Attributes are preserved, line geometries are simplified into start |
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23 and end coordinates. Accepts a single shapefile or directory of many |
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24 shapefiles. |
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25 |
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26 "The Esri Shapefile or simply a shapefile is a popular geospatial vector |
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27 data format for geographic information systems software [1]_." |
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28 |
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29 Parameters |
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30 ---------- |
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31 path : file or string |
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32 File, directory, or filename to read. |
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33 |
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34 simplify: bool |
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35 If True, simplify line geometries to start and end coordinates. |
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36 If False, and line feature geometry has multiple segments, the |
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37 non-geometric attributes for that feature will be repeated for each |
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38 edge comprising that feature. |
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39 |
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40 geom_attrs: bool |
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41 If True, include the Wkb, Wkt and Json geometry attributes with |
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42 each edge. |
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43 |
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44 NOTE: if these attributes are available, write_shp will use them |
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45 to write the geometry. If nodes store the underlying coordinates for |
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46 the edge geometry as well (as they do when they are read via |
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47 this method) and they change, your geomety will be out of sync. |
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48 |
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49 strict: bool |
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50 If True, raise NetworkXError when feature geometry is missing or |
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51 GeometryType is not supported. |
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52 If False, silently ignore missing or unsupported geometry in features. |
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53 |
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54 Returns |
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55 ------- |
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56 G : NetworkX graph |
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57 |
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58 Raises |
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59 ------ |
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60 ImportError |
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61 If ogr module is not available. |
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62 |
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63 RuntimeError |
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64 If file cannot be open or read. |
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65 |
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66 NetworkXError |
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67 If strict=True and feature is missing geometry or GeometryType is |
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68 not supported. |
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69 |
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70 Examples |
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71 -------- |
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72 >>> G = nx.read_shp("test.shp") # doctest: +SKIP |
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73 |
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74 References |
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75 ---------- |
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76 .. [1] https://en.wikipedia.org/wiki/Shapefile |
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77 """ |
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78 try: |
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79 from osgeo import ogr |
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80 except ImportError as e: |
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81 raise ImportError("read_shp requires OGR: http://www.gdal.org/") from e |
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82 |
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83 if not isinstance(path, str): |
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84 return |
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85 |
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86 net = nx.DiGraph() |
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87 shp = ogr.Open(path) |
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88 if shp is None: |
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89 raise RuntimeError(f"Unable to open {path}") |
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90 for lyr in shp: |
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91 fields = [x.GetName() for x in lyr.schema] |
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92 for f in lyr: |
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93 g = f.geometry() |
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94 if g is None: |
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95 if strict: |
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96 raise nx.NetworkXError("Bad data: feature missing geometry") |
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97 else: |
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98 continue |
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99 flddata = [f.GetField(f.GetFieldIndex(x)) for x in fields] |
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100 attributes = dict(zip(fields, flddata)) |
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101 attributes["ShpName"] = lyr.GetName() |
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102 # Note: Using layer level geometry type |
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103 if g.GetGeometryType() == ogr.wkbPoint: |
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104 net.add_node((g.GetPoint_2D(0)), **attributes) |
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105 elif g.GetGeometryType() in (ogr.wkbLineString, ogr.wkbMultiLineString): |
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106 for edge in edges_from_line(g, attributes, simplify, geom_attrs): |
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107 e1, e2, attr = edge |
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108 net.add_edge(e1, e2) |
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109 net[e1][e2].update(attr) |
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110 else: |
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111 if strict: |
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112 raise nx.NetworkXError( |
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113 "GeometryType {} not supported".format(g.GetGeometryType()) |
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114 ) |
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115 |
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116 return net |
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117 |
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118 |
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119 def edges_from_line(geom, attrs, simplify=True, geom_attrs=True): |
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120 """ |
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121 Generate edges for each line in geom |
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122 Written as a helper for read_shp |
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123 |
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124 Parameters |
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125 ---------- |
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126 |
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127 geom: ogr line geometry |
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128 To be converted into an edge or edges |
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129 |
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130 attrs: dict |
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131 Attributes to be associated with all geoms |
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132 |
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133 simplify: bool |
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134 If True, simplify the line as in read_shp |
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135 |
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136 geom_attrs: bool |
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137 If True, add geom attributes to edge as in read_shp |
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138 |
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139 |
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140 Returns |
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141 ------- |
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142 edges: generator of edges |
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143 each edge is a tuple of form |
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144 (node1_coord, node2_coord, attribute_dict) |
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145 suitable for expanding into a networkx Graph add_edge call |
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146 """ |
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147 try: |
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148 from osgeo import ogr |
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149 except ImportError as e: |
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150 raise ImportError( |
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151 "edges_from_line requires OGR: " "http://www.gdal.org/" |
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152 ) from e |
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153 |
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154 if geom.GetGeometryType() == ogr.wkbLineString: |
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155 if simplify: |
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156 edge_attrs = attrs.copy() |
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157 last = geom.GetPointCount() - 1 |
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158 if geom_attrs: |
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159 edge_attrs["Wkb"] = geom.ExportToWkb() |
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160 edge_attrs["Wkt"] = geom.ExportToWkt() |
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161 edge_attrs["Json"] = geom.ExportToJson() |
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162 yield (geom.GetPoint_2D(0), geom.GetPoint_2D(last), edge_attrs) |
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163 else: |
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164 for i in range(0, geom.GetPointCount() - 1): |
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165 pt1 = geom.GetPoint_2D(i) |
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166 pt2 = geom.GetPoint_2D(i + 1) |
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167 edge_attrs = attrs.copy() |
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168 if geom_attrs: |
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169 segment = ogr.Geometry(ogr.wkbLineString) |
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170 segment.AddPoint_2D(pt1[0], pt1[1]) |
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171 segment.AddPoint_2D(pt2[0], pt2[1]) |
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172 edge_attrs["Wkb"] = segment.ExportToWkb() |
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173 edge_attrs["Wkt"] = segment.ExportToWkt() |
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174 edge_attrs["Json"] = segment.ExportToJson() |
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175 del segment |
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176 yield (pt1, pt2, edge_attrs) |
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177 |
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178 elif geom.GetGeometryType() == ogr.wkbMultiLineString: |
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179 for i in range(geom.GetGeometryCount()): |
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180 geom_i = geom.GetGeometryRef(i) |
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181 yield from edges_from_line(geom_i, attrs, simplify, geom_attrs) |
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182 |
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183 |
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184 def write_shp(G, outdir): |
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185 """Writes a networkx.DiGraph to two shapefiles, edges and nodes. |
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186 Nodes and edges are expected to have a Well Known Binary (Wkb) or |
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187 Well Known Text (Wkt) key in order to generate geometries. Also |
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188 acceptable are nodes with a numeric tuple key (x,y). |
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189 |
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190 "The Esri Shapefile or simply a shapefile is a popular geospatial vector |
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191 data format for geographic information systems software [1]_." |
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192 |
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193 Parameters |
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194 ---------- |
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195 outdir : directory path |
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196 Output directory for the two shapefiles. |
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197 |
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198 Returns |
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199 ------- |
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200 None |
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201 |
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202 Examples |
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203 -------- |
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204 nx.write_shp(digraph, '/shapefiles') # doctest +SKIP |
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205 |
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206 References |
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207 ---------- |
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208 .. [1] https://en.wikipedia.org/wiki/Shapefile |
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209 """ |
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210 try: |
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211 from osgeo import ogr |
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212 except ImportError as e: |
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213 raise ImportError("write_shp requires OGR: http://www.gdal.org/") from e |
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214 # easier to debug in python if ogr throws exceptions |
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215 ogr.UseExceptions() |
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216 |
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217 def netgeometry(key, data): |
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218 if "Wkb" in data: |
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219 geom = ogr.CreateGeometryFromWkb(data["Wkb"]) |
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220 elif "Wkt" in data: |
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221 geom = ogr.CreateGeometryFromWkt(data["Wkt"]) |
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222 elif type(key[0]).__name__ == "tuple": # edge keys are packed tuples |
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223 geom = ogr.Geometry(ogr.wkbLineString) |
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224 _from, _to = key[0], key[1] |
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225 try: |
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226 geom.SetPoint(0, *_from) |
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227 geom.SetPoint(1, *_to) |
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228 except TypeError: |
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229 # assume user used tuple of int and choked ogr |
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230 _ffrom = [float(x) for x in _from] |
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231 _fto = [float(x) for x in _to] |
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232 geom.SetPoint(0, *_ffrom) |
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233 geom.SetPoint(1, *_fto) |
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234 else: |
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235 geom = ogr.Geometry(ogr.wkbPoint) |
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236 try: |
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237 geom.SetPoint(0, *key) |
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238 except TypeError: |
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239 # assume user used tuple of int and choked ogr |
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240 fkey = [float(x) for x in key] |
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241 geom.SetPoint(0, *fkey) |
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242 |
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243 return geom |
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244 |
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245 # Create_feature with new optional attributes arg (should be dict type) |
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246 def create_feature(geometry, lyr, attributes=None): |
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247 feature = ogr.Feature(lyr.GetLayerDefn()) |
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248 feature.SetGeometry(g) |
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249 if attributes is not None: |
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250 # Loop through attributes, assigning data to each field |
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251 for field, data in attributes.items(): |
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252 feature.SetField(field, data) |
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253 lyr.CreateFeature(feature) |
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254 feature.Destroy() |
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255 |
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256 # Conversion dict between python and ogr types |
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257 OGRTypes = {int: ogr.OFTInteger, str: ogr.OFTString, float: ogr.OFTReal} |
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258 |
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259 # Check/add fields from attribute data to Shapefile layers |
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260 def add_fields_to_layer(key, value, fields, layer): |
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261 # Field not in previous edges so add to dict |
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262 if type(value) in OGRTypes: |
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263 fields[key] = OGRTypes[type(value)] |
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264 else: |
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265 # Data type not supported, default to string (char 80) |
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266 fields[key] = ogr.OFTString |
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267 # Create the new field |
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268 newfield = ogr.FieldDefn(key, fields[key]) |
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269 layer.CreateField(newfield) |
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270 |
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271 drv = ogr.GetDriverByName("ESRI Shapefile") |
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272 shpdir = drv.CreateDataSource(outdir) |
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273 # delete pre-existing output first otherwise ogr chokes |
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274 try: |
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275 shpdir.DeleteLayer("nodes") |
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276 except: |
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277 pass |
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278 nodes = shpdir.CreateLayer("nodes", None, ogr.wkbPoint) |
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279 |
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280 # Storage for node field names and their data types |
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281 node_fields = {} |
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282 |
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283 def create_attributes(data, fields, layer): |
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284 attributes = {} # storage for attribute data (indexed by field names) |
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285 for key, value in data.items(): |
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286 # Reject spatial data not required for attribute table |
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287 if key != "Json" and key != "Wkt" and key != "Wkb" and key != "ShpName": |
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288 # Check/add field and data type to fields dict |
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289 if key not in fields: |
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290 add_fields_to_layer(key, value, fields, layer) |
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291 # Store the data from new field to dict for CreateLayer() |
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292 attributes[key] = value |
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293 return attributes, layer |
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294 |
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295 for n in G: |
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296 data = G.nodes[n] |
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297 g = netgeometry(n, data) |
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298 attributes, nodes = create_attributes(data, node_fields, nodes) |
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299 create_feature(g, nodes, attributes) |
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300 |
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301 try: |
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302 shpdir.DeleteLayer("edges") |
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303 except: |
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304 pass |
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305 edges = shpdir.CreateLayer("edges", None, ogr.wkbLineString) |
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306 |
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307 # New edge attribute write support merged into edge loop |
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308 edge_fields = {} # storage for field names and their data types |
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309 |
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310 for e in G.edges(data=True): |
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311 data = G.get_edge_data(*e) |
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312 g = netgeometry(e, data) |
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313 attributes, edges = create_attributes(e[2], edge_fields, edges) |
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314 create_feature(g, edges, attributes) |
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315 |
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316 nodes, edges = None, None |