/usr/share/pyshared/Epigrass/epigdal.py is in epigrass 2.0.4-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 | """
This module uses the GDAL and OGR Library to read maps in vaious formats and
export the results of Epigrass simulations to the formats supported by these libraries
copyright 2007 by Flavio Codeco Coelho
Licensed under the GPL.
"""
import locale, os#, pylab
from osgeo import ogr, gdal
from xml.dom import minidom, Node
from matplotlib.colors import rgb2hex, LogNorm
from matplotlib import cm
class World:
def __init__(self,filename,namefield='name',geocfield='geocode',outdir = '.'):
'''
Instantiate a world object.
Filename points to a file supported by OGR
'''
self.geocfield = geocfield
self.namefield = namefield
self.outdir = outdir
self.ds =ogr.Open(filename)
self.name = self.ds.GetName()
self.driver = self.ds.GetDriver()
self.centroids = []#centroid list (x,y,z) tuples
self.centdict = {} #keys are geocode, values are (x,y,z) tuples
self.geomdict = {} #keys are geocode, values are geometries
self.nlist = [] #nodelist: feature objects
self.nodesource = False #True if Node datasource has been created
self.edgesource = False #True if Edge datasource has been created
self.datasource = False #True if Data datasource has been created
self.layerlist = self.getLayerList()
def getLayerList(self):
"""
returns a list with the
available layers by name
"""
nlay = self.ds.GetLayerCount()
ln = []
for i in xrange(nlay):
l = self.ds.GetLayer(i)
ln.append(l.GetName())
return ln
def drawLayer(self,L):
'''
Draws a polygon layer using pylab
'''
N = 0
L.ResetReading()
feat = L.GetNextFeature()
while feat is not None:
field_count = L.GetLayerDefn().GetFieldCount()
geo = feat.GetGeometryRef()
if geo.GetGeometryCount()<2:
g1 = geo.GetGeometryRef( 0 )
x =[g1.GetX(i) for i in range(g1.GetPointCount()) ]
y =[g1.GetY(i) for i in range(g1.GetPointCount()) ]
pylab.plot(x,y,'-',hold=True)
for c in range( geo.GetGeometryCount()):
ring = geo.GetGeometryRef ( c )
for cnt in range( ring.GetGeometryCount()):
g1 = ring.GetGeometryRef( cnt )
x =[g1.GetX(i) for i in range(g1.GetPointCount()) ]
y =[g1.GetY(i) for i in range(g1.GetPointCount()) ]
pylab.plot(x,y,'-',hold=True)
feat = L.GetNextFeature()
pylab.xlabel("Longitude")
pylab.ylabel("Latitude")
pylab.grid(True)
pylab.show()
def getNodeList(self,l):
'''
Returns the centroid coordinates
l is an OGR layer.
'''
self.nlist=[]
f = l.GetNextFeature()
while f is not None:
g = f.GetGeometryRef()
self.geomdict[f.GetFieldAsInteger(self.geocfield)] = g
try:
c = g.Centroid()
self.nlist.append(f)
self.centdict[f.GetFieldAsInteger(self.geocfield)] = (c.GetX(),c.GetY(),c.GetZ())
except: #in case feature is not a polygon
print f.GetFID(),g.GetGeometryType()
f = l.GetNextFeature()
#print (2600501 in self.centdict)
def createNodeLayer(self):
"""
Creates a new shape file to represent network nodes.
The node layer will be based on the centroids of the
polygons belonging to the map layer associated with this
world instance.
namefield - name of the field containing polygon name
geocfield - name of the field containing geocode
"""
# Creates a new shape file to hold the data
if os.path.exists(os.path.join(self.outdir,'Nodes.shp')):
os.remove(os.path.join(self.outdir,'Nodes.shp'))
os.remove(os.path.join(self.outdir,'Nodes.shx'))
os.remove(os.path.join(self.outdir,'Nodes.dbf'))
if not self.nodesource:
dsn = self.driver.CreateDataSource(os.path.join(self.outdir,'Nodes.shp'))
self.nodesource = dsn
nl = dsn.CreateLayer("nodes",geom_type=ogr.wkbPoint)
#Create the fields
fi1 = ogr.FieldDefn("name")
fi2 = ogr.FieldDefn("geocode",field_type=ogr.OFTInteger)
fi3 = ogr.FieldDefn("x",field_type=ogr.OFTString)
fi4 = ogr.FieldDefn("y",field_type=ogr.OFTString)
nl.CreateField(fi1)
nl.CreateField(fi2)
nl.CreateField(fi3)
nl.CreateField(fi4)
#Add the features (points)
for f in self.nlist:
gc = f.GetFieldAsInteger(self.geocfield)
x = self.centdict[gc][0]
y = self.centdict[gc][1]
fe = ogr.Feature(nl.GetLayerDefn())
name = f.GetField(self.namefield)
fe.SetField('name',f.GetField(self.namefield))
fe.SetField('geocode',gc)
fe.SetField('x',str(x))
fe.SetField('y',str(y))
pt = ogr.Geometry(type=ogr.wkbPoint)
pt.AddPoint(x,y)
fe.SetGeometryDirectly(pt)
nl.CreateFeature(fe)
nl.SyncToDisk()
def createEdgeLayer(self,elist):
"""
Creates a new layer with edge information.
elist is a list of tuples:
(sgeoc,dgeoc,fsd,fds)
"""
# Creates a new shape file to hold the data
if os.path.exists(os.path.join(self.outdir,'Edges.shp')):
os.remove(os.path.join(self.outdir,'Edges.shp'))
os.remove(os.path.join(self.outdir,'Edges.shx'))
os.remove(os.path.join(self.outdir,'Edges.dbf'))
if not self.edgesource:
dse = self.driver.CreateDataSource(os.path.join(self.outdir,'Edges.shp'))
self.edgesource = dse
el = dse.CreateLayer("edges",geom_type=ogr.wkbLineString)
#Create the fields
fi1 = ogr.FieldDefn("source_geocode",field_type=ogr.OFTInteger)
fi2 = ogr.FieldDefn("dest_geocode",field_type=ogr.OFTInteger)
fi3 = ogr.FieldDefn("flowSD",field_type=ogr.OFTReal)
fi3.SetPrecision(12)
fi4 = ogr.FieldDefn("flowDS",field_type=ogr.OFTReal)
fi4.SetPrecision(12)
el.CreateField(fi1)
el.CreateField(fi2)
el.CreateField(fi3)
el.CreateField(fi4)
#Add the features (lines)
for e in elist:
#print "setting edge fields"
fe = ogr.Feature(el.GetLayerDefn())
fe.SetField('source_geocode',e[0])
fe.SetField('dest_geocode',e[1])
fe.SetField('flowSD',e[2])
fe.SetField('flowSD',e[3])
line = ogr.Geometry(type=ogr.wkbLineString)
try:
#print "creating edge lines"
line.AddPoint(self.centdict[int(e[0])][0],self.centdict[int(e[0])][1])
line.AddPoint(self.centdict[int(e[1])][0],self.centdict[int(e[1])][1])
fe.SetGeometryDirectly(line)
el.CreateFeature(fe)
except: #node not in centdict
pass
el.SyncToDisk()
def createDataLayer(self,varlist, data):
"""
Creates a new shape to contain data about nodes.
varlist is the list of fields names associated with
the nodes.
data is a list of lists whose first element is the geocode
and the remaining elements are values of the fields, in the
same order as they appear in varlist.
"""
if os.path.exists(os.path.join(self.outdir,'Data.shp')):
os.remove(os.path.join(self.outdir,'Data.shp'))
os.remove(os.path.join(self.outdir,'Data.shx'))
os.remove(os.path.join(self.outdir,'Data.dbf'))
# Creates a new shape file to hold the data
if not self.datasource:
dsd = self.driver.CreateDataSource(os.path.join(self.outdir,'Data.shp'))
self.datasource = dsd
dl = dsd.CreateLayer("sim_results",geom_type=ogr.wkbPolygon)
#Create the fields
fi1 = ogr.FieldDefn("geocode",field_type=ogr.OFTInteger)
dl.CreateField(fi1)
for v in varlist:
#print "creating data fields"
fi = ogr.FieldDefn(v,field_type=ogr.OFTString)
fi.SetPrecision(12)
dl.CreateField(fi)
#Add the features (points)
for n,l in enumerate(data):
#Iterate over the lines of the data matrix.
gc = l[0]
try:
geom = self.geomdict[gc]
if geom.GetGeometryType() != 3: continue
#print geom.GetGeometryCount()
fe = ogr.Feature(dl.GetLayerDefn())
fe.SetField('geocode',gc)
for v,d in zip (varlist,l[1:]):
#print v,d
fe.SetField(v,str(d))
#Add the geometry
#print "cloning geometry"
clone = geom.Clone()
#print geom
#print "setting geometry"
fe.SetGeometry(clone)
#print "creating geom"
dl.CreateFeature(fe)
except: #Geocode not in polygon dictionary
pass
dl.SyncToDisk()
def genSitesFile(self,fname):
"""
This method generate a sites
csv file from the nodes extracted from the
map.
"""
f = open(fname,"w")
for fe in self.nlist:
gc = fe.GetFieldAsInteger(self.geocfield)
x = self.centdict[gc][0]
y = self.centdict[gc][1]
name = fe.GetField(self.namefield)
line = "%s,%s,%s,%s\n"%(x,y,name,gc)
#fe.SetField('name',f.GetField(self.namefield))
f.write(line)
f.close()
def closeSources(self):
"""
Close the data sources so that data is flushed and and files are closed
"""
if self.nodesource:
self.nodesource.Destroy()
#print "closed node files"
if self.edgesource:
self.edgesource.Destroy()
#print "closed edge files"
if self.datasource:
self.datasource.Destroy()
#print "closed data files"
class KmlGenerator:
"""
Generate a KML file for displaying data on
Google Maps/Earth
"""
def __init__(self):
self.doc = None
self.dnode = None #document node in the DOM
self.genRoot()
def genRoot(self):
"""
Generate a KML file root.
"""
self.kmldoc = doc = minidom.Document()
kml = doc.createElement("kml")
kml.setAttribute("xmlns","http://earth.google.com/kml/2.1")
doc.appendChild(kml)
d = doc.createElement("Document")
kml.appendChild(d)
nel = doc.createElement("name")
name = doc.createTextNode("KML Epigrass data file")
nel.appendChild(name)
d.appendChild(nel)
desc = doc.createElement("description")
d.appendChild(desc)
desc.appendChild(doc.createTextNode("Polygons with data"))
self.dnode = d
def addNodes(self,layer,names=None):
"""
Adds a node to the document.
d is the document element KML dom object.
layer is a layer with polygons
names is a dictionary of names indexed by geocode(int)
"""
doc = self.dnode
jet = cm.get_cmap("jet",50)
layer.ResetReading()
while 1:
f = layer.GetNextFeature()
if not f:#exit after the last feature
break
prevalence = float(f.GetField("prevalence"))
rgba = jet(prevalence)
bgrcol = list(rgba[:-1]) #rgb(list)
bgrcol.reverse() #turn it into bgr
hexcol = "#80"+rgb2hex(bgrcol)[1:] #abgr Alpha set to 128
g = f.GetGeometryRef()
if g.GetGeometryType() == 3:
if not names:
name = ""
else:
try:
name = names[f.GetFieldAsInteger("geocode")]
except KeyError:
print f.GetFieldAsInteger("geocode")
name = ""
description = "Prevalence: %s;\nTotal cases: %s;\nImported Cases: %s;"%(prevalence,f.GetField("totalcases"),f.GetField("arrivals"))
locale.setlocale(locale.LC_ALL,"C") #avoids conversion of decimal points
gml = g.ExportToGML() #extract the coordinates from the GML representation
coords = gml.split('<gml:coordinates>')[1].split('</gml:coordinates>')[0]
coords = " ".join([i+",0" for i in coords.split(" ")]) #add z coordinate
#create the kml elements
#placemark and sub elements
pm=self.kmldoc.createElement("Placemark")
nm = self.kmldoc.createElement("name")
nm.appendChild(self.kmldoc.createTextNode(name))
desc = self.kmldoc.createElement("description")
desc.appendChild(self.kmldoc.createTextNode(description))
pm.appendChild(nm)
pm.appendChild(desc)
#style and subelements
st=self.kmldoc.createElement("Style")
pm.appendChild(st)
ps = self.kmldoc.createElement("PolyStyle")
color = self.kmldoc.createElement("color")
color.appendChild(self.kmldoc.createTextNode(hexcol))
ps.appendChild(color)
fill = self.kmldoc.createElement("fill")
fill.appendChild(self.kmldoc.createTextNode("1"))
ps.appendChild(fill)
outline = self.kmldoc.createElement("outline")
outline.appendChild(self.kmldoc.createTextNode("1"))
ps.appendChild(outline)
st.appendChild(ps)
doc.appendChild(pm)
#Multigeometry
mg = self.kmldoc.createElement("MultiGeometry")
pm.appendChild(mg)
polygon = self.kmldoc.createElement("Polygon")
mg.appendChild(polygon)
ob = self.kmldoc.createElement("outerBoundaryIs")
polygon.appendChild(ob)
linr = self.kmldoc.createElement("LinearRing")
ob.appendChild(linr)
coordin = self.kmldoc.createElement("coordinates")
linr.appendChild(coordin)
coordin.appendChild(self.kmldoc.createTextNode(coords))
def writeToFile(self,dir):
"""
Writes the kml file to disk
"""
fullpath = os.path.join(dir,"Data.kml")
f=open(fullpath,"w")
f.write(self.kmldoc.toxml())
f.close()
if __name__=="__main__":
# opening data source
w = World('riozonas_LatLong.shp','nome_zonas','zona_trafe')
layer = w.ds.GetLayerByName(w.layerlist[0])
w.getNodeList(layer)
w.drawLayer(layer)
w.createNodeLayer()
w.nodesource.Destroy() #flush data to disk
## k = KmlGenerator()
## k.addNodes(w.datasource.GetLayer(0))
## k.writeToFile()
|