Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
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317 lines
11 KiB
317 lines
11 KiB
4 years ago
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"""
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*********
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Shapefile
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*********
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Generates a networkx.DiGraph from point and line shapefiles.
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"The Esri Shapefile or simply a shapefile is a popular geospatial vector
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data format for geographic information systems software. It is developed
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and regulated by Esri as a (mostly) open specification for data
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interoperability among Esri and other software products."
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See https://en.wikipedia.org/wiki/Shapefile for additional information.
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"""
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import networkx as nx
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__all__ = ["read_shp", "write_shp"]
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def read_shp(path, simplify=True, geom_attrs=True, strict=True):
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"""Generates a networkx.DiGraph from shapefiles. Point geometries are
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translated into nodes, lines into edges. Coordinate tuples are used as
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keys. Attributes are preserved, line geometries are simplified into start
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and end coordinates. Accepts a single shapefile or directory of many
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shapefiles.
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"The Esri Shapefile or simply a shapefile is a popular geospatial vector
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data format for geographic information systems software [1]_."
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Parameters
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----------
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path : file or string
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File, directory, or filename to read.
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simplify: bool
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If True, simplify line geometries to start and end coordinates.
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If False, and line feature geometry has multiple segments, the
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non-geometric attributes for that feature will be repeated for each
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edge comprising that feature.
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geom_attrs: bool
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If True, include the Wkb, Wkt and Json geometry attributes with
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each edge.
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NOTE: if these attributes are available, write_shp will use them
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to write the geometry. If nodes store the underlying coordinates for
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the edge geometry as well (as they do when they are read via
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this method) and they change, your geomety will be out of sync.
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strict: bool
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If True, raise NetworkXError when feature geometry is missing or
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GeometryType is not supported.
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If False, silently ignore missing or unsupported geometry in features.
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Returns
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-------
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G : NetworkX graph
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Raises
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------
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ImportError
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If ogr module is not available.
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RuntimeError
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If file cannot be open or read.
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NetworkXError
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If strict=True and feature is missing geometry or GeometryType is
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not supported.
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Examples
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--------
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>>> G = nx.read_shp("test.shp") # doctest: +SKIP
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References
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----------
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.. [1] https://en.wikipedia.org/wiki/Shapefile
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"""
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try:
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from osgeo import ogr
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except ImportError as e:
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raise ImportError("read_shp requires OGR: http://www.gdal.org/") from e
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if not isinstance(path, str):
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return
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net = nx.DiGraph()
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shp = ogr.Open(path)
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if shp is None:
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raise RuntimeError(f"Unable to open {path}")
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for lyr in shp:
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fields = [x.GetName() for x in lyr.schema]
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for f in lyr:
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g = f.geometry()
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if g is None:
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if strict:
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raise nx.NetworkXError("Bad data: feature missing geometry")
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else:
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continue
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flddata = [f.GetField(f.GetFieldIndex(x)) for x in fields]
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attributes = dict(zip(fields, flddata))
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attributes["ShpName"] = lyr.GetName()
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# Note: Using layer level geometry type
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if g.GetGeometryType() == ogr.wkbPoint:
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net.add_node((g.GetPoint_2D(0)), **attributes)
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elif g.GetGeometryType() in (ogr.wkbLineString, ogr.wkbMultiLineString):
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for edge in edges_from_line(g, attributes, simplify, geom_attrs):
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e1, e2, attr = edge
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net.add_edge(e1, e2)
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net[e1][e2].update(attr)
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else:
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if strict:
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raise nx.NetworkXError(
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"GeometryType {} not supported".format(g.GetGeometryType())
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)
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return net
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def edges_from_line(geom, attrs, simplify=True, geom_attrs=True):
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"""
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Generate edges for each line in geom
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Written as a helper for read_shp
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Parameters
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----------
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geom: ogr line geometry
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To be converted into an edge or edges
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attrs: dict
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Attributes to be associated with all geoms
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simplify: bool
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If True, simplify the line as in read_shp
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geom_attrs: bool
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If True, add geom attributes to edge as in read_shp
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Returns
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-------
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edges: generator of edges
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each edge is a tuple of form
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(node1_coord, node2_coord, attribute_dict)
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suitable for expanding into a networkx Graph add_edge call
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"""
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try:
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from osgeo import ogr
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except ImportError as e:
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raise ImportError(
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"edges_from_line requires OGR: " "http://www.gdal.org/"
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) from e
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if geom.GetGeometryType() == ogr.wkbLineString:
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if simplify:
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edge_attrs = attrs.copy()
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last = geom.GetPointCount() - 1
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if geom_attrs:
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edge_attrs["Wkb"] = geom.ExportToWkb()
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edge_attrs["Wkt"] = geom.ExportToWkt()
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edge_attrs["Json"] = geom.ExportToJson()
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yield (geom.GetPoint_2D(0), geom.GetPoint_2D(last), edge_attrs)
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else:
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for i in range(0, geom.GetPointCount() - 1):
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pt1 = geom.GetPoint_2D(i)
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pt2 = geom.GetPoint_2D(i + 1)
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edge_attrs = attrs.copy()
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if geom_attrs:
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segment = ogr.Geometry(ogr.wkbLineString)
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segment.AddPoint_2D(pt1[0], pt1[1])
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segment.AddPoint_2D(pt2[0], pt2[1])
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edge_attrs["Wkb"] = segment.ExportToWkb()
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edge_attrs["Wkt"] = segment.ExportToWkt()
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edge_attrs["Json"] = segment.ExportToJson()
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del segment
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yield (pt1, pt2, edge_attrs)
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elif geom.GetGeometryType() == ogr.wkbMultiLineString:
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for i in range(geom.GetGeometryCount()):
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geom_i = geom.GetGeometryRef(i)
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yield from edges_from_line(geom_i, attrs, simplify, geom_attrs)
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def write_shp(G, outdir):
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"""Writes a networkx.DiGraph to two shapefiles, edges and nodes.
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Nodes and edges are expected to have a Well Known Binary (Wkb) or
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Well Known Text (Wkt) key in order to generate geometries. Also
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acceptable are nodes with a numeric tuple key (x,y).
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"The Esri Shapefile or simply a shapefile is a popular geospatial vector
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data format for geographic information systems software [1]_."
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Parameters
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----------
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outdir : directory path
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Output directory for the two shapefiles.
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Returns
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-------
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None
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Examples
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--------
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nx.write_shp(digraph, '/shapefiles') # doctest +SKIP
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References
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----------
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.. [1] https://en.wikipedia.org/wiki/Shapefile
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"""
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try:
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from osgeo import ogr
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except ImportError as e:
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raise ImportError("write_shp requires OGR: http://www.gdal.org/") from e
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# easier to debug in python if ogr throws exceptions
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ogr.UseExceptions()
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def netgeometry(key, data):
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if "Wkb" in data:
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geom = ogr.CreateGeometryFromWkb(data["Wkb"])
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elif "Wkt" in data:
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geom = ogr.CreateGeometryFromWkt(data["Wkt"])
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elif type(key[0]).__name__ == "tuple": # edge keys are packed tuples
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geom = ogr.Geometry(ogr.wkbLineString)
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_from, _to = key[0], key[1]
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try:
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geom.SetPoint(0, *_from)
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geom.SetPoint(1, *_to)
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except TypeError:
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# assume user used tuple of int and choked ogr
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_ffrom = [float(x) for x in _from]
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_fto = [float(x) for x in _to]
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geom.SetPoint(0, *_ffrom)
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geom.SetPoint(1, *_fto)
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else:
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geom = ogr.Geometry(ogr.wkbPoint)
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try:
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geom.SetPoint(0, *key)
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except TypeError:
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# assume user used tuple of int and choked ogr
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fkey = [float(x) for x in key]
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geom.SetPoint(0, *fkey)
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return geom
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# Create_feature with new optional attributes arg (should be dict type)
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def create_feature(geometry, lyr, attributes=None):
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feature = ogr.Feature(lyr.GetLayerDefn())
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feature.SetGeometry(g)
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if attributes is not None:
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# Loop through attributes, assigning data to each field
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for field, data in attributes.items():
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feature.SetField(field, data)
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lyr.CreateFeature(feature)
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feature.Destroy()
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# Conversion dict between python and ogr types
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OGRTypes = {int: ogr.OFTInteger, str: ogr.OFTString, float: ogr.OFTReal}
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# Check/add fields from attribute data to Shapefile layers
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def add_fields_to_layer(key, value, fields, layer):
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# Field not in previous edges so add to dict
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if type(value) in OGRTypes:
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fields[key] = OGRTypes[type(value)]
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else:
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# Data type not supported, default to string (char 80)
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fields[key] = ogr.OFTString
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# Create the new field
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newfield = ogr.FieldDefn(key, fields[key])
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layer.CreateField(newfield)
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drv = ogr.GetDriverByName("ESRI Shapefile")
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shpdir = drv.CreateDataSource(outdir)
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# delete pre-existing output first otherwise ogr chokes
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try:
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shpdir.DeleteLayer("nodes")
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except:
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pass
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nodes = shpdir.CreateLayer("nodes", None, ogr.wkbPoint)
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# Storage for node field names and their data types
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node_fields = {}
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def create_attributes(data, fields, layer):
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attributes = {} # storage for attribute data (indexed by field names)
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for key, value in data.items():
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# Reject spatial data not required for attribute table
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if key != "Json" and key != "Wkt" and key != "Wkb" and key != "ShpName":
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# Check/add field and data type to fields dict
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if key not in fields:
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add_fields_to_layer(key, value, fields, layer)
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# Store the data from new field to dict for CreateLayer()
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attributes[key] = value
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return attributes, layer
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for n in G:
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data = G.nodes[n]
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g = netgeometry(n, data)
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attributes, nodes = create_attributes(data, node_fields, nodes)
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create_feature(g, nodes, attributes)
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try:
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shpdir.DeleteLayer("edges")
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except:
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pass
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edges = shpdir.CreateLayer("edges", None, ogr.wkbLineString)
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# New edge attribute write support merged into edge loop
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edge_fields = {} # storage for field names and their data types
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for e in G.edges(data=True):
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data = G.get_edge_data(*e)
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g = netgeometry(e, data)
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attributes, edges = create_attributes(e[2], edge_fields, edges)
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create_feature(g, edges, attributes)
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nodes, edges = None, None
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