def __init__(self, path, time_col):
shp = pysal.open(path + '.shp')
dbf = pysal.open(path + '.dbf')
# extract the spatial coordinates from the shapefile
x = []
y = []
n = 0
for i in shp:
count = 0
for j in i:
if count == 0:
x.append(j)
elif count == 1:
y.append(j)
count += 1
n += 1
self.n = n
x = np.array(x)
y = np.array(y)
self.x = np.reshape(x, (n, 1))
self.y = np.reshape(y, (n, 1))
self.space = np.hstack((self.x, self.y))
# extract the temporal information from the database
t = np.array(dbf.by_col(time_col))
line = np.ones((n, 1))
self.t = np.reshape(t, (n, 1))
self.time = np.hstack((self.t, line))
# close open objects
dbf.close()
shp.close()
def test_chi2(self):
import pysal
f = pysal.open(pysal.examples.get_path("usjoin.csv"))
pci = np.array([f.by_col[str(y)] for y in range(1929, 2010)])
pci = pci.transpose()
rpci = pci / (pci.mean(axis=0))
w = pysal.open(pysal.examples.get_path("states48.gal")).read()
w.transform = "r"
sm = pysal.Spatial_Markov(rpci, w, fixed=True, k=5)
chi = np.matrix(
[
[4.05598541e01, 6.44644317e-04, 1.60000000e01],
[5.54751974e01, 2.97033748e-06, 1.60000000e01],
[1.77528996e01, 3.38563882e-01, 1.60000000e01],
[4.00390961e01, 7.68422046e-04, 1.60000000e01],
[4.67966803e01, 7.32512065e-05, 1.60000000e01],
]
).getA()
obs = np.matrix(sm.chi2).getA()
np.testing.assert_array_almost_equal(obs, chi)
obs = np.matrix(
[
[4.61209613e02, 0.00000000e00, 4.00000000e00],
[1.48140694e02, 0.00000000e00, 4.00000000e00],
[6.33129261e01, 5.83089133e-13, 4.00000000e00],
[7.22778509e01, 7.54951657e-15, 4.00000000e00],
[2.32659201e02, 0.00000000e00, 4.00000000e00],
]
)
np.testing.assert_array_almost_equal(obs.getA(), np.matrix(sm.shtest).getA())
def test_chi2(self):
import pysal
f = pysal.open(pysal.examples.get_path("usjoin.csv"))
pci = np.array([f.by_col[str(y)] for y in range(1929, 2010)])
pci = pci.transpose()
rpci = pci / (pci.mean(axis=0))
w = pysal.open(pysal.examples.get_path("states48.gal")).read()
w.transform = "r"
sm = pysal.Spatial_Markov(rpci, w, fixed=True, k=5)
chi = np.matrix(
[
[4.06139105e01, 6.32961385e-04, 1.60000000e01],
[5.55485793e01, 2.88879565e-06, 1.60000000e01],
[1.77772638e01, 3.37100315e-01, 1.60000000e01],
[4.00925436e01, 7.54729084e-04, 1.60000000e01],
[4.68588786e01, 7.16364084e-05, 1.60000000e01],
]
).getA()
obs = np.matrix(sm.chi2).getA()
np.testing.assert_array_almost_equal(obs, chi)
obs = np.matrix(
[
[4.61209613e02, 0.00000000e00, 4.00000000e00],
[1.48140694e02, 0.00000000e00, 4.00000000e00],
[6.33129261e01, 5.83089133e-13, 4.00000000e00],
[7.22778509e01, 7.54951657e-15, 4.00000000e00],
[2.32659201e02, 0.00000000e00, 4.00000000e00],
]
)
np.testing.assert_array_almost_equal(obs.getA(), np.matrix(sm.shtest).getA())
def __init__(self, shapefile, idvariable=None, attribute=False):
self.points = {}
self.npoints = 0
if idvariable:
ids = get_ids(shapefile, idvariable)
else:
ids = None
pts = ps.open(shapefile)
# Get attributes if requested
if attribute == True:
dbname = os.path.splitext(shapefile)[0] + '.dbf'
db = ps.open(dbname)
else:
db = None
for i, pt in enumerate(pts):
if ids and db:
self.points[ids[i]] = {'coordinates':pt, 'properties':db[i]}
elif ids and not db:
self.points[ids[i]] = {'coordinates':pt, 'properties':None}
elif not ids and db:
self.points[i] = {'coordinates':pt, 'properties':db[i]}
else:
self.points[i] = {'coordinates':pt, 'properties':None}
pts.close()
if db:
db.close()
self.npoints = len(self.points.keys())
def _writeShp():
oShp = ps.open(out_shp, 'w')
shp = ps.open(pt_shp)
oDbf = ps.open(out_shp[:-3]+'dbf', 'w')
dbf = ps.open(pt_shp[:-3]+'dbf')
oDbf.header = dbf.header
col_name = 'in_poly'
col_spec = ('C', 14, 0)
if polyID_col:
col_name = polyID_col
#db = ps.open(poly_shp[:-3]+'dbf')
#col_spec = db.field_spec[db.header.index(polyID_col)]
oDbf.header.append(col_name)
oDbf.field_spec = dbf.field_spec
oDbf.field_spec.append(col_spec)
for poly, rec, i in zip(shp, dbf, correspondences):
oShp.write(poly)
rec.append(i)
oDbf.write(rec)
shp.close()
oShp.close()
dbf.close()
oDbf.close()
prj = open(pt_shp[:-3]+'prj').read()
oPrj = open(out_shp[:-3]+'prj', 'w')
oPrj.write(prj); oPrj.close()
t4 = time.time()
print '\t', t4-t3, ' seconds to write shapefile'
print 'Shapefile written to %s'%out_shp
def test():
# Test
shp = pysal.open(pysal.examples.get_path('NAT.shp'),'r')
dbf = pysal.open(pysal.examples.get_path('NAT.dbf'),'r')
show_map(shp)
ids = get_selected(shp)
print ids
w = pysal.rook_from_shapefile(pysal.examples.get_path('NAT.shp'))
moran_scatter_plot(shp, dbf, "HR90", w)
scatter_plot(shp, ["HR90", "PS90"])
scatter_plot_matrix(shp, ["HR90", "PS90"])
quantile_map(shp, dbf, "HC60", 5, basemap="leaflet_map")
select_ids = [i for i,v in enumerate(dbf.by_col["HC60"]) if v < 20.0]
select(shp, ids=select_ids)
quantile_map(shp, dbf, "HC60", 5)
lisa_map(shp, dbf, "HC60", w)
def __init__(self, path, time_col, infer_timestamp=False):
shp = pysal.open(path + '.shp')
dbf = pysal.open(path + '.dbf')
# extract the spatial coordinates from the shapefile
x = [coords[0] for coords in shp]
y = [coords[1] for coords in shp]
self.n = n = len(shp)
x = np.array(x)
y = np.array(y)
self.x = np.reshape(x, (n, 1))
self.y = np.reshape(y, (n, 1))
self.space = np.hstack((self.x, self.y))
# extract the temporal information from the database
if infer_timestamp:
col = dbf.by_col(time_col)
if isinstance(col[0], date):
day1 = min(col)
col = [(d - day1).days for d in col]
t = np.array(col)
else:
print("Unable to parse your time column as Python datetime \
objects, proceeding as integers.")
t = np.array(col)
else:
t = np.array(dbf.by_col(time_col))
line = np.ones((n, 1))
self.t = np.reshape(t, (n, 1))
self.time = np.hstack((self.t, line))
# close open objects
dbf.close()
shp.close()
def test():
import pysal
road_shp = pysal.open('/Users/xun/Dropbox/dog_bites/phoenix.osm-roads.shp')
road_dbf = pysal.open('/Users/xun/Dropbox/dog_bites/phoenix.osm-roads.dbf')
import d3viz
d3viz.setup()
d3viz.show_map(road_shp, rebuild=True)
roadJsonFile = d3viz.get_json_path(road_shp)
import network_cluster
#roadJsonFile = '../test_data/man_road.geojson'
network = network_cluster.NetworkCluster(roadJsonFile)
# Segment the road network equally in 1,000 feet
network.SegmentNetwork(1000)
# Read into car accident points file
points_shp = pysal.open('/Users/xun/Dropbox/dog_bites/DogBitesOriginal/DogBitesOriginal.shp')
d3viz.add_layer(points_shp)
pointsJsonFile = d3viz.get_json_path(points_shp)
points = network_cluster.GetJsonPoints(pointsJsonFile, encoding='latin-1')
# Snap these points to nearest road segment
network.SnapPointsToNetwork(points)
def db(self, headerOnly=False):
if self.data['config']['other_missingValueCheck']:
pysal.MISSINGVALUE = self.data['config']['other_missingValue']
if 'fname' in self.data:
fileType = self.data['fname'].rsplit('.')[-1].lower()
self.fileType = fileType
if fileType == 'csv':
if headerOnly:
f = pysal.open(self.data['fname'], 'rU')
db = {}
db['header'] = f.header
f.close()
return db
else:
return pysal.open(self.data['fname'], 'rU')
elif fileType == 'dbf':
db = pysal.open(self.data['fname'], 'r')
header = []
# grab only the numeric fields.
if headerOnly:
for field, spec in zip(db.header, db.field_spec):
typ = spec[0].lower()
if typ in ['d', 'n', 'f']:
header.append(field)
return {'header': header}
else:
return db
else:
print "Unknown File Type"
return False
else:
return None
def test2():
#d6cd52286e5d3e9e08a5a42489180df3.shp
import pysal
shp = pysal.open('../www/tmp/d6cd52286e5d3e9e08a5a42489180df3.shp')
dbf = pysal.open('../www/tmp/d6cd52286e5d3e9e08a5a42489180df3.dbf')
w = pysal.queen_from_shapefile('../www/tmp/d6cd52286e5d3e9e08a5a42489180df3.shp')
#d3viz.moran_scatter_plot(shp, dbf, "dog_cnt", w)
import numpy as np
y = np.array(dbf.by_col["dog_cnt"])
lm = pysal.Moran_Local(y, w)
for i,j in enumerate(lm.q):
if lm.p_sim[i] >= 0.05:
print 0
else:
print j
import d3viz
d3viz.setup()
d3viz.show_map(shp)
d3viz.scatter_plot(shp, ["dog_cnt","home_cnt"])
d3viz.lisa_map(shp, "dog_cnt", lm)
def map_line_shp(shp_link, which='all'):
'''
Create a map object from a line shapefile
...
Arguments
---------
shp_link : str
Path to shapefile
which : str/list
Returns
-------
map : PatchCollection
Map object with the polygons from the shapefile
'''
shp = ps.open(shp_link)
if which == 'all':
db = ps.open(shp_link.replace('.shp', '.dbf'))
n = len(db.by_col(db.header[0]))
db.close()
which = [True] * n
patches = []
for inwhich, shape in zip(which, shp):
if inwhich:
for xy in shape.parts:
patches.append(xy)
lc = LineCollection(patches)
_ = _add_axes2col(lc, shp.bbox)
return lc
def test_d3viz():
import pysal
shp = pysal.open(pysal.examples.get_path('NAT.shp'),'r')
dbf = pysal.open(pysal.examples.get_path('NAT.dbf'),'r')
#shp = pysal.open('/Users/xun/github/PySAL-Viz/test_data/man_road.shp','r')
#dbf = pysal.open('/Users/xun/github/PySAL-Viz/test_data/man_road.dbf','r')
import d3viz
d3viz.setup()
d3viz.init_map(shp)
d3viz.show_map(shp)
d3viz.scatter_plot(shp, field_x="HR90", field_y="HC90")
w = pysal.queen_from_shapefile(pysal.examples.get_path('NAT.shp'))
d3viz.moran_scatter_plot(shp, dbf, "HR90", w)
d3viz.quantile_map(shp, "HR90", 5)
d3viz.quantile_map(shp, "HR90", 5, basemap="leaflet")
import numpy as np
y = np.array(dbf.by_col["HR90"])
lm = pysal.Moran_Local(y, w)
d3viz.lisa_map(shp, "HR90", lm)
def setUp(self):
db = pysal.open(pysal.examples.get_path("baltim.dbf"),'r')
self.ds_name = "baltim.dbf"
self.y_name = "PRICE"
self.y = np.array(db.by_col(self.y_name)).T
self.y.shape = (len(self.y),1)
self.x_names = ["NROOM","AGE","SQFT"]
self.x = np.array([db.by_col(var) for var in self.x_names]).T
ww = pysal.open(pysal.examples.get_path("baltim_q.gal"))
self.w = ww.read()
ww.close()
self.w_name = "baltim_q.gal"
self.w.transform = 'r'
self.regimes = db.by_col("CITCOU")
#Artficial:
n = 256
self.n2 = n/2
self.x_a1 = np.random.uniform(-10,10,(n,1))
self.x_a2 = np.random.uniform(1,5,(n,1))
self.q_a = self.x_a2 + np.random.normal(0,1,(n,1))
self.x_a = np.hstack((self.x_a1,self.x_a2))
self.y_a = np.dot(np.hstack((np.ones((n,1)),self.x_a)),np.array([[1],[0.5],[2]])) + np.random.normal(0,1,(n,1))
latt = int(np.sqrt(n))
self.w_a = pysal.lat2W(latt,latt)
self.w_a.transform='r'
self.regi_a = [0]*(n/2) + [1]*(n/2)
self.w_a1 = pysal.lat2W(latt/2,latt)
self.w_a1.transform='r'
def getHexShp(codeBook,outFile):
"""Create the hexagon shapeFile
Do NOT specify file extension in outFile"""
inCOD = open(codeBook)
inCOD = inCOD.readlines()
header = inCOD.pop(0)
dims,topo,cols,rows,neigh = header.split()
cols=int(cols)
rows=int(rows)
fieldSpec = [('N',20,10)]*int(dims)
fieldHead = ['plane%d'%i for i in range(int(dims))]
#hexpts=hexPts(x,y) #Orig WRONG!!!
hexpts=hexPts(cols,rows)
polys=hexPoly(hexpts)# polygons
out = pysal.open(outFile+'.shp','w')
outd = pysal.open(outFile+'.dbf','w')
outd.header = fieldHead
outd.field_spec = fieldSpec
for line in inCOD:
outd.write(map(float,line.split()))
outd.close()
for bbox,poly in polys:
poly = map(pysal.cg.shapes.Point,poly)
poly = pysal.cg.shapes.Polygon(poly)
out.write(poly)
out.close()
return 'Shapefile created'
def map_poly_shp(shp_link, which='all'):
'''
Create a map object from a shapefile
...
Arguments
---------
shp_link : str
Path to shapefile
which : str/list
Returns
-------
map : PatchCollection
Map object with the polygons from the shapefile
'''
shp = ps.open(shp_link)
if which == 'all':
db = ps.open(shp_link.replace('.shp', '.dbf'))
n = len(db.by_col(db.header[0]))
db.close()
which = [True] * n
patches = []
for inwhich, shape in zip(which, shp):
if inwhich:
for ring in shape.parts:
xy = np.array(ring)
patches.append(xy)
return PolyCollection(patches)
def dl_merge(outname="tracts",sumlevel="140"):
os.chdir('/tmp')
outshp = pysal.open(outname+'.shp','w')
outdbf = pysal.open(outname+'.dbf','w')
for st in config.STATE_FIPS:
fname = name_template%(st)#,sumlevel)
if DEBUG: print fname
url = urllib.urlopen(base_url+fname)
dat = url.read()
if not os.path.exists(fname):
with open(fname,'wb') as o:
o.write(dat)
os.system('unzip '+fname)
shp = pysal.open(fname.replace('.zip','.shp'),'r')
for x in shp:
outshp.write(x)
dbf = pysal.open(fname.replace('.zip','.dbf'),'r')
outdbf.header = dbf.header
outdbf.field_spec = dbf.field_spec
for row in dbf:
outdbf.write(row)
os.remove(fname)
os.remove(fname.replace('.zip','.shp'))
os.remove(fname.replace('.zip','.shx'))
os.remove(fname.replace('.zip','.dbf'))
os.remove(fname.replace('.zip','.shp.xml'))
os.remove(fname.replace('.zip','.prj'))
outshp.close()
outdbf.close()
def test_sids(self):
w = pysal.open(pysal.examples.get_path("sids2.gal")).read()
f = pysal.open(pysal.examples.get_path("sids2.dbf"))
SIDR = np.array(f.by_col("SIDR74"))
mi = pysal.Moran(SIDR, w, two_tailed=False)
np.testing.assert_allclose(mi.I, 0.24772519320480135, atol=ATOL, rtol=RTOL)
self.assertAlmostEquals(mi.p_norm, 5.7916539074498452e-05)
def setUp(self):
f = pysal.open(pysal.examples.get_path("sids2.dbf"))
varnames = ['SIDR74', 'SIDR79', 'NWR74', 'NWR79']
self.names = varnames
vars = [np.array(f.by_col[var]) for var in varnames]
self.vars = vars
self.w = pysal.open(pysal.examples.get_path("sids2.gal")).read()
def map_point_shp(shp_link, which='all'):
'''
Create a map object from a point shapefile
...
Arguments
---------
shp_link : str
Path to shapefile
which : str/list
Returns
-------
map : PatchCollection
Map object with the points from the shapefile
'''
shp = ps.open(shp_link)
if which == 'all':
db = ps.open(shp_link.replace('.shp', '.dbf'))
n = len(db.by_col(db.header[0]))
db.close()
which = [True] * n
pts = []
for inwhich, pt in zip(which, shp):
if inwhich:
pts.append(pt)
pts = np.array(pts)
sc = plt.scatter(pts[:, 0], pts[:, 1])
_ = _add_axes2col(sc, shp.bbox)
return sc
def test_sids(self):
w = pysal.open(pysal.examples.get_path("sids2.gal")).read()
f = pysal.open(pysal.examples.get_path("sids2.dbf"))
SIDR = np.array(f.by_col("SIDR74"))
mi = pysal.Moran(SIDR, w)
self.assertAlmostEquals(mi.I, 0.24772519320480135)
self.assertAlmostEquals(mi.p_norm, 5.7916539074498452e-05)
def reader(shp_file_name, doubleEdges=True):
"""
Read a PySAL network (geographic graph) shapefile and create edges and
coordinates data structures
Parameters
----------
shp_file_name: Path to shapefile with .shp extension. Has to have been
created by contrib/spatialnet/
doubleEdges: Boolean if True create a twin for each edge
Returns
-------
coords: dict with key a node id and the value a pair of x,y coordinates
for the node's embedding in the plane
edges: list of edges (t,f) where t and f are ids of the nodes
"""
dir_name = os.path.dirname(shp_file_name)
base_name = os.path.basename(shp_file_name)
pre,suf = base_name.split(".")
shp_file = os.path.join(dir_name,pre+".shp")
dbf_file = os.path.join(dir_name,pre+".dbf")
sf = ps.open(shp_file)
df = ps.open(dbf_file)
edges = []
coords = {}
records = df.read()
df.close()
for record in records:
t = record[0]
f = record[1]
edges.append((t,f))
df.close()
i = 0
shps = sf.read()
sf.close()
for shp in shps:
t_xy, f_xy = shp.vertices
t = edges[i][0]
f = edges[i][1]
if t not in coords:
coords[t] = t_xy
if f not in coords:
coords[f] = f_xy
i += 1
if doubleEdges:
for edge in edges:
twin = edge[1],edge[0]
if twin not in edges:
edges.append(twin)
return coords, edges
def setUp(self):
self.filehandler = ps.open(ps.examples.get_path('columbus.dbf'))
self.df = self.filehandler.to_df()
self.filehandler.seek(0)
self.shapefile = ps.open(ps.examples.get_path('columbus.shp'))
self.csvhandler = ps.open(ps.examples.get_path('usjoin.csv'))
self.csv_df = self.csvhandler.to_df()
self.csvhandler.seek(0)
def test_network_from_allvertices(self):
shape = pysal.open(self.net)
dbf = pysal.open(self.net[:-3] + 'dbf')
graph = pynet.network_from_allvertices(shape, dbf)
neighbors = {(724432.38723173144, 877800.08747069736): 155.41097171058956,
(725247.70571468933, 877812.36851842562): 660.00000000003809}
start_point = (724587.78057580709, 877802.4281426128)
self.assertEqual(graph[start_point], neighbors)
def pip_xy_shp_multi(xy, poly_shp, polyID_col=None, out_shp=None,
empty=None):
'''
Point in polygon operation taking as input a points array and a polygon
shapefile (running on multicore)
...
Arguments
=========
xy : np.array
nx2 array with xy coordinates
poly_shp : str
Path to polygon shapefile
polyID_col : str
Name of the column in the polygon shapefile to be used as ID
in the output shape
out_shp : str
Path to the output shapefile where to write xy with a
column with correspondences appended (Optional, defaults to
None)
empty : str
String to insert if the point is not contained in any
polygon. Defaults to None
Returns
=======
correspondences : list
List of length len(xy) with the polygon ID where the
points are located
'''
t0 = time.time()
polys = ps.open(poly_shp)
if polyID_col:
polyIDs = ps.open(poly_shp[:-3]+'dbf').by_col(polyID_col)
pl = ps.cg.PolygonLocator(polys)
t1 = time.time()
print '\t', t1-t0, ' secs to build rtree'
parss = zip(xy, [pl]*xy.shape[0])
cores = mp.cpu_count()
pool = mp.Pool(cores)
correspondences = pool.map(_poly4xy, parss)
t2 = time.time()
print '\t', t2-t1, ' secs to get correspondences'
if polyID_col:
correspondences_names= []
for i in correspondences:
try:
correspondences_names.append(polyIDs[int(i)])
except:
correspondences_names.append(empty)
correspondences = correspondences_names
polys.close()
t3 = time.time()
print '\t', t3-t2, ' secs to convert correspondences'
if out_shp:
_writeShp()
return correspondences
def setUp(self):
sids = pysal.open(pysal.examples.get_path("sids2.shp"), "r")
self.sids = sids
self.d = np.array([i.centroid for i in sids])
self.w = knnW_from_array(self.d, k=5)
if not self.w.id_order_set:
self.w.id_order = self.w.id_order
sids_db = pysal.open(pysal.examples.get_path("sids2.dbf"), "r")
self.b, self.e = np.array(sids_db[:, 8]), np.array(sids_db[:, 9])
def moranI(self):
if (self.dlg.checkBox.checkState()==2 and self.dlg.rdButton_nm.isChecked()==True)or self.dlg.rdButton_sm.isChecked()==True:
self.w=pysal.open(os.path.join(os.path.dirname(__file__), 'default.gal')).read()
try:
self.w = pysal.open(self.dlg.txtSelect.text()).read()
except IOError, e:
print e.errno
print e
selectedFieldIndex = self.dlg.cmbBoxSelectField.currentIndex()
field= self.fieldsnumeric[selectedFieldIndex]
self.fieldName = field.name()
dbasefile=self.myfile[:-3]+'dbf'
dbase = pysal.open(dbasefile)
self.y = np.array(dbase.by_col[self.fieldName], dtype=('<f8'))
"""self.dlg.txtSelectSystemC.setPlainText("")
for i in self.y:
self.dlg.txtSelectSystemC.appendPlainText(str(i))"""
if self.w.n == self.y.size:
self.mi = pysal.Moran(self.y, self.w, two_tailed=False)
self.dlg.txtMoranI.setText(str(round(self.mi.I,5)))
self.dlg.txtMoranIp.setText(str(round(self.mi.p_norm,5)))
if self.mi.I >0.75 and self.mi.p_norm <0.05:
self.dlg.txtMoranIint.setText("I de Moran cercano a 1 y p value significativo (confianza 95%): posible autocorrelacion espacial")
elif self.mi.I <-0.75 and self.mi.p_norm <0.05:
self.dlg.txtMoranIint.setText("I de Moran cercano a -1 y p value significativo (confianza 95%): posible autocorrelacion espacial")
elif self.mi.I >-0.05 and self.mi.I <0.05:
self.dlg.txtMoranIint.setText("I de Moran cercano a 0: no existe autocorrelacion espacial")
elif self.mi.p_norm <0.05:
self.dlg.txtMoranIint.setText("p value significativo (confianza 95%): posible autocorrelacion espacial debil")
else:
self.dlg.txtMoranIint.setText("p value no significativo (confianza 95%): no existe autocorrelacion espacial")
"""lm = pysal.Moran_Local(y,w)"""
"""self.dlg.txtSelectSystemC2.appendPlainText(str(lm.p_sim))"""
"""self.dlg.txtOutput_2.setText(str(self.w.n)+' - '+str(self.y.size))"""
else:
QtGui.QMessageBox.warning(None,"Error","Oops! matrix has not been generated or not exists. Generate and try again...")
self.dlg.checkBox.setCheckState(0)
self.dlg.txtMoranI.clear()
self.dlg.txtMoranIp.clear()
self.dlg.txtMoranIint.clear()
"""self.dlg.txtSelectSystemC.setPlainText("")"""
self.dlg.groupBox_wm.setEnabled(True)
self.dlg.groupBox_mi.setEnabled(False)
self.dlg.widget_sm.setEnabled(False)
self.dlg.rdButton_sm.setChecked(0)
self.dlg.rdButton_nm.setChecked(1)
def test___init__(self):
import numpy as np
f = pysal.open(pysal.examples.get_path("usjoin.csv"))
pci = np.array([f.by_col[str(y)] for y in range(1929, 2010)]).transpose()
w = pysal.open(pysal.examples.get_path("states48.gal")).read()
lm = pysal.LISA_Markov(pci, w)
obs = np.array([1, 2, 3, 4])
np.testing.assert_array_almost_equal(obs, lm.classes)
"""
def test_write(self):
w = self.obj.read()
f = tempfile.NamedTemporaryFile(suffix='.gal')
fname = f.name
f.close()
o = pysal.open(fname, 'w')
o.write(w)
o.close()
wnew = pysal.open(fname, 'r').read()
self.assertEqual(wnew.pct_nonzero, w.pct_nonzero)
def test_network_from_endnodes(self):
shape = pysal.open(self.net)
dbf = pysal.open(self.net[:-3] + 'dbf')
def weight(geo_object, record):
return 1
graph = pynet.network_from_endnodes(shape, dbf, weight)
neighbors = {(724432.38723173144, 877800.08747069736): 1,
(725247.70571468933, 877812.36851842562): 1}
start_point = (724587.78057580709, 877802.4281426128)
self.assertEqual(graph[start_point], neighbors)
def __init__(self,parent=None,size=(600,600), style=wx.DEFAULT_FRAME_STYLE, geo=None, w=None):
wx.Frame.__init__(self,parent,size=size,style=style)
self.Bind
self.SetTitle("Weights Inspector")
if issubclass(type(geo),basestring):
geo = pysal.open(geo,'r')
self.geo = geo
if issubclass(type(w),basestring):
w = pysal.open(w,'r').read()
self.w = w
self.wm = WeightsMap(self,self.geo,self.w)
def OnSaveQueryToDBF(self, event):
try:
if self.query_data == None:
return
dlg = wx.FileDialog(
self,
message="Save query into new dbf files...",
defaultDir=os.getcwd(),
defaultFile='%s.dbf' %
(self.lisa_layer.name + '_dynamic_lisa'),
wildcard="shape file (*.dbf)|*.dbf|All files (*.*)|*.*",
style=wx.SAVE)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
path = dlg.GetPath()
dlg.Destroy()
dbf = self.lisa_layer.dbf
newDBF = pysal.open('%s.dbf' % path[:-4], 'w')
newDBF.header = []
newDBF.field_spec = []
for i in dbf.header:
newDBF.header.append(i)
for i in dbf.field_spec:
newDBF.field_spec.append(i)
for i in self.query_data.keys():
newDBF.header.append('T_%d' % (i + 1))
newDBF.field_spec.append(('N', 4, 0))
for i in range(dbf.n_records):
newRow = []
row = dbf.read_record(i)
newRow = [item for item in row]
for j in self.query_data.keys():
val = self.query_data[j][i]
newRow.append(int(val))
newDBF.write(newRow)
newDBF.close()
self.ShowMsgBox("Query results have been saved to a new dbf file.",
mtype='CAST information',
micon=wx.ICON_INFORMATION)
except:
self.ShowMsgBox(
"Saving query results to new dbf file failed. Please check if the dbf file already exists."
)
def get_points_array_from_shapefile(shapefile):
"""
Gets a data array of x and y coordinates from a given shapefile.
Parameters
----------
shapefile : string
name of a shape file including suffix
Returns
-------
points : array
(n, 2)
a data array of x and y coordinates
Notes
-----
If the given shape file includes polygons,
this function returns x and y coordinates of the polygons' centroids
Examples
--------
Point shapefile
>>> from pysal.weights.util import get_points_array_from_shapefile
>>> xy = get_points_array_from_shapefile(pysal.examples.get_path('juvenile.shp'))
>>> xy[:3]
array([[ 94., 93.],
[ 80., 95.],
[ 79., 90.]])
Polygon shapefile
>>> xy = get_points_array_from_shapefile(pysal.examples.get_path('columbus.shp'))
>>> xy[:3]
array([[ 8.82721847, 14.36907602],
[ 8.33265837, 14.03162401],
[ 9.01226541, 13.81971908]])
"""
f = pysal.open(shapefile)
if f.type.__name__ == 'Polygon':
data = np.array([shape.centroid for shape in f])
elif f.type.__name__ == 'Point':
data = np.array([shape for shape in f])
f.close()
return data
def _importArcData(filename):
"""Creates a new Layer from a shapefile (<file>.shp)
This function wraps and extends a core clusterPy function to utilize PySAL
W constructors and dbf readers.
Parameters
==========
filename: string
suffix of shapefile (fileName not fileName.shp)
Returns
=======
layer: clusterpy layer instance
"""
layer = _clusterpy.Layer()
layer.name = filename.split('/')[-1]
#print "Loading " + filename + ".dbf"
dbf = ps.open(filename+".dbf")
fields = dbf.header
#data, fields, specs = importDBF(filename + '.dbf')
data = {}
#print "Loading " + filename + ".shp"
if fields[0] != "ID":
fields = ["ID"] + fields
for y in range(dbf.n_records):
data[y] = [y] + dbf.by_row(y)
else:
for y in range(dbf.n_records):
data[y] = dbf.by_row_(y)
layer.fieldNames = fields
layer.Y = data
shpf = filename+".shp"
layer.shpType = 5
#print 'pysal reader'
layer.Wrook = ps.rook_from_shapefile(filename+".shp").neighbors
layer.Wqueen = ps.queen_from_shapefile(filename+".shp").neighbors
#print "Done"
return layer
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"r")
y = np.array(db.by_col("HOVAL"))
self.y = np.reshape(y, (49,1))
X = []
X.append(db.by_col("INC"))
self.X = np.array(X).T
self.X = np.hstack((np.ones(self.y.shape),self.X))
self.X = sparse.csr_matrix(self.X)
yd = []
yd.append(db.by_col("CRIME"))
self.yd = np.array(yd).T
q = []
q.append(db.by_col("DISCBD"))
self.q = np.array(q).T
self.w = pysal.rook_from_shapefile(pysal.examples.get_path("columbus.shp"))
self.w.transform = 'r'
def dbf2DF(dbfile):
"""
Reads in DBF files and returns Pandas DF.
dbfile : DBF file - Input to be imported
upper : Condition - If true, make column heads upper case
This block of code adapted from https://gist.github.com/ryan-hill/f90b1c68f60d12baea81
"""
#Pysal to open DBF
db = ps.open(dbfile)
#Convert dbf to dictionary
d = {col: db.by_col(col) for col in db.header}
#Convert to Pandas DF
pandasDF = pd.DataFrame(d)
db.close()
return pandasDF
def lisa_mapa(variavel, shapefile, p_thres=0.05, **kws):
w = ps.queen_from_shapefile(shapefile)
lisa = ps.Moran_Local(variavel, w)
fig = plt.figure(figsize=(9, 7))
shp = ps.open(shapefile)
base = maps.map_poly_shp(shp)
base = maps.base_lisa_cluster(base, lisa, p_thres=p_thres)
base.set_edgecolor('1')
base.set_linewidth(0.1)
ax = maps.setup_ax([base], [shp.bbox])
boxes, labels = maps.lisa_legend_components(lisa, p_thres=p_thres)
plt.legend(boxes, labels, fancybox=True, **kws)
plt.show()
def test_WSP2W(self):
sp = pysal.weights.lat2SW(2, 5)
wsp = pysal.weights.WSP(sp)
w = pysal.weights.WSP2W(wsp)
self.assertEquals(w.n, 10)
self.assertEquals(w[0], {1: 1, 5: 1})
w = pysal.open(pysal.examples.get_path('sids2.gal'), 'r').read()
wsp = pysal.weights.WSP(w.sparse, w.id_order)
w = pysal.weights.WSP2W(wsp)
self.assertEquals(w.n, 100)
self.assertEquals(w['37135'], {
'37001': 1.0,
'37033': 1.0,
'37037': 1.0,
'37063': 1.0,
'37145': 1.0
})
def df2dbf(df, dbf_path):
type2spec = {int: ('N', 20, 0),
np.int64: ('N', 20, 0),
np.int32: ('N', 20, 0),
float: ('N', 36, 15),
np.float32: ('N', 36, 15),
np.float64: ('N', 36, 15),
str: ('C', 14, 0)
}
types = [type(df[i].iloc[0]) for i in df.columns]
specs = [type2spec[t] for t in types]
db = ps.open(dbf_path, 'w')
db.header = list(df.columns)
db.field_spec = specs
for i, row in df.T.iteritems():
db.write(row)
db.close()
def write(self, filename=None, as_type='gal'):
"""
Write data (assumed pysal weight object) to gal binary weight files
:param filename: Base filename
:param as_type: gal
:return: location of file
"""
if not filename:
filename = self.uri
self.create_output_dir(filename)
if as_type == 'gal':
gal = pysal.open(filename, 'w')
gal.write(self.data)
gal.close()
else:
raise NotImplementedError('{} not a valid type'.format(as_type))
return self.uri
def dbf2DF(dbfile, upper=True):
'''
__author__ = "Ryan Hill <*****@*****.**>"
"Marc Weber <*****@*****.**>"
Reads and converts a dbf file to a pandas data frame using pysal.
Arguments
---------
dbfile : a dbase (.dbf) file
'''
db = ps.open(dbfile)
cols = {col: db.by_col(col) for col in db.header}
db.close() #Close dbf
pandasDF = pd.DataFrame(cols)
if upper == True:
pandasDF.columns = pandasDF.columns.str.upper()
return pandasDF
def dbfdups(dbfpath, idvar):
"""checks duplicates in a dBase file
ID variable must be specified correctly
__author__ = "Luc Anselin <*****@*****.**> "
Arguments
---------
dbfpath : file path to dBase file
idvar : ID variable in dBase file
Returns
-------
a list with the duplicate IDs
"""
db = ps.open(dbfpath, 'r')
li = db.by_col(idvar)
return list(set([x for x in li if li.count(x) > 1]))
def on_inputbutton_clicked(self):
myFile1 = QFileDialog.getOpenFileName(self, "Select a shapefile","","comma_separatedfile(*.csv)")
if self.ui.inputbutton != None:
self.ui.inputline.setText(myFile1)
else:
pass
#create a new combobox(1)use pysal to open file(2) read in
#for saved shapefile to show columns
openfile=str(self.ui.inputline.text())
f=pysal.open(openfile)
#opendbf=openfile[:-3] + "dbf" #open the same file only with dbf
#f_dbf = pysal.open(opendbf)
self.fileheader=f.header #find columns, already in a list
for i in self.fileheader: #i is in a string
self.ui.startcombobox.addItem(i)
self.ui.endcombobox.addItem(i)
def test_process_weight(self):
"""Test Weight Process"""
with open(os.path.join(testfile_path, 'weight_process.json')) as inf:
body_text = inf.read().replace('{basepath}', testfile_path)
process = json.loads(body_text, object_hook=deserialize)
try:
process.compute()
output = process.output.read(format=formats.WEIGHT)
exp = pysal.open(
os.path.join(testfile_path, 'weight_process_result.gal'), 'r')
expected_w = exp.read()
exp.close()
self.assertEquals(expected_w.n, output.n)
self.assertIsNotNone(process.id)
self.assertIn(process.id, process.output.uri)
finally:
if process:
process.purge()
def generate_contours(self):
allPoly = ps.open(self.shp_link)
blobPoly = [None for i in range(len(np.unique(self.regions)))]
for i in range(len(allPoly)):
if(blobPoly[int(self.regions[i])] == None):
blobPoly[int(self.regions[i])] = pl.Polygon(allPoly[i].vertices)
else:
blobPoly[int(self.regions[i])] = blobPoly[int(self.regions[i])] + pl.Polygon(allPoly[i].vertices)
outputPoly = []
contours_to_blobs = []
counter = 0
for poly in blobPoly:
for i in range(len(poly)):
outputPoly.append(Polygon(poly.contour(i)))
contours_to_blobs.append(counter)
counter+=1
self.contours = outputPoly
self.contours_to_blobs = contours_to_blobs
def df2dbf(df, dbf_path, my_specs=None):
'''
Convert a pandas.DataFrame into a dbf.
__author__ = "Dani Arribas-Bel <*****@*****.**> "
...
Arguments
---------
df : DataFrame
Pandas dataframe object to be entirely written out to a dbf
dbf_path : str
Path to the output dbf. It is also returned by the function
my_specs : list
List with the field_specs to use for each column.
Defaults to None and applies the following scheme:
* int: ('N', 14, 0)
* float: ('N', 14, 14)
* str: ('C', 14, 0)
'''
if my_specs:
specs = my_specs
else:
type2spec = {
int: ('N', 20, 0),
np.int64: ('N', 20, 0),
np.int32: ('N', 20, 0),
np.int16: ('N', 20, 0),
np.int8: ('N', 20, 0),
float: ('N', 36, 15),
np.float64: ('N', 36, 15),
np.float32: ('N', 36, 15),
str: ('C', 14, 0)
}
types = [type(df[i].iloc[0]) for i in df.columns]
specs = [type2spec[t] for t in types]
db = ps.open(dbf_path, 'w')
db.header = list(df.columns)
db.field_spec = specs
for i, row in df.T.iteritems():
db.write(row)
db.close()
return dbf_path
def spw_from_shapefile(shapefile, norm=False):
polygons = ps.open(shapefile, 'r').read()
spolygons = list(map(asShape, polygons))
spolygons = [fix_mp(p) for p in spolygons]
perimeters = [p.length if norm else 1. for p in spolygons]
Wsrc = ps.queen_from_shapefile(shapefile)
new_weights, edges = {}, {}
for i in Wsrc.neighbors:
a = spolygons[i]
p = perimeters[i]
new_weights[i] = []
for j in Wsrc.neighbors[i]:
intersect = a.intersection(spolygons[j])
new_weights[i].append(intersect.length)
edges[i] = a.length - sum(new_weights[i]) # /a.length
return edges, ps.W(Wsrc.neighbors, new_weights)
def test_weight(self):
"""
Test WeightProcess for vector inputs
"""
vector_io = VectorFileIO(name='input',
uri=os.path.join(testfile_path,
'baghdad_hospitals.geojson'))
process = geo.WeightProcess('knnW', inputs=[vector_io])
try:
process.compute()
exp = pysal.open(
os.path.join(testfile_path, 'weight_process_result.gal'), 'r')
expected_w = exp.read()
exp.close()
actual = process.output.read(format=formats.WEIGHT)
self.assertEquals(expected_w.n, actual.n)
finally:
if process:
process.purge()
def Show(self):
try:
self.dialog.Fit()
if self.dialog.ShowModal() == wx.ID_OK:
path = self.txt_weight_path.GetValue()
name = os.path.splitext(os.path.basename(path))[0]
w = pysal.open(path).read()
data = {name:w.histogram}
data = dict([(w.id2i[id],len(nbs)) for id, nbs in w.neighbors.iteritems()])
hist_widget = PlotWidget(
self.main,
name,
{'Connectivity':data},
Histogram,
title="Histogram(%s) Connectivity of Weights" % name)
hist_widget.Show()
"""
shp = self.main.GetSHP(name)
if shp == None:
msg = "Please open shapefile \"%s\" first." % name
dlg = wx.MessageDialog(self.main, msg, 'Warning', wx.OK|wx.ICON_WARNING)
dlg.ShowModal()
dlg.Destroy()
else:
w = pysal.open(path).read()
data = {name:w.histogram}
data = dict([(w.id2i[id],len(nbs)) for id, nbs in w.neighbors.iteritems()])
hist_widget = PlotWidget(
self.main,
shp,
{'Connectivity':data},
Histogram,
title="Histogram(%s) Connectivity of Weights" % name)
hist_widget.Show()
"""
self.dialog.Destroy()
except Exception as err:
dlg = wx.MessageDialog(self.main,
"""Could not open weights file! Please select a valid weights file.
Details: """+ str(err.message), 'Warning', wx.OK|wx.ICON_WARNING)
dlg.ShowModal()
dlg.Destroy()
def dbf2DF(dbfile, mycols):
# Pysal to open DBF file
db = ps.open(dbfile)
# convert to a dictionary with key:value pairs
d = dict([(var, db.by_col(var)) for var in mycols])
# Convert to Pandas DF
pandasDF = pd.DataFrame(d)
# Make columns all uppercase
pandasDF.columns = map(str.upper, pandasDF.columns)
# close the dbf file
db.close()
# return the pandas data frame
return pandasDF
def get_shpdbf(filename, field):
"""
Extract a column from a shapefile (geom) or dbf (attribute)
"""
files = (os.path.join(UPLOAD_FOLDER, filename))
if field == 'thegeom':
geoms = []
with fiona.collection(files + '.shp', "r") as source:
for feat in source:
geoms.append(feat)
geojson = {"type": "FeatureCollection", "features": geoms}
response = {'status': 'success', 'data': {'geojson': geojson}}
else:
dbf = ps.open(files + '.dbf', 'r')
attr = dbf.by_col(field)
response = {'status': 'success', 'data': {field: attr}}
return jsonify(response)
def addGal2Layer(galfile, layer, contiguity='rook'):
"""
Attach an adjacency object to a layer
Parameters
==========
galfile: string
galfile
layer: clusterpy layer
contiguity: type of contguity ['rook'|'queen']
Returns
=======
None
Examples
========
>>> import pysal as ps
>>> import pysal.contrib.clusterpy as cp
>>> csvfile = ps.examples.get_path('mexico.csv')
>>> galfile = ps.examples.get_path('mexico.gal')
>>> mexico = cp.importCsvData(csvfile)
>>> cp.addRook2Layer(galfile, mexico)
>>> mexico.Wrook[0]
[31, 13]
"""
gal = ps.open(galfile).read().neighbors
w = {}
for key in gal:
w[int(key)] = list(map(int, gal[key]))
if contiguity.upper()== "ROOK":
layer.Wrook = w
elif contiguity.upper() == "QUEEN":
layer.Wqueen = w
else:
print('Unsupported contiguity type: ', contiguity)
def __init__(self, featureDataset, idField, countField, countFieldListFilePath):
'''
Constructor of MaxP. Note that isolated feature will not be joined with other features.
@param featureDataset - instance of FeatureDataSet in data.py of util package
@param idField - Primiary key field for spatial unit in the shapefile in featureDataset, not FID or ObjectID these kinds, should be sth. like GEOID etc.
@param countField - single field from the shapefile in featureDataset which will be used as constrain in max-p
@param countFieldListFilePath - paht to a file constaining a list of fields from the shapefile in featureDataset which will be used as parameters for max-p to compute SSD between regions
'''
index = []
count_values = []
targetCount_values = []
srcFeatureSet = featureDataset.dataPath
targetCountFields = read1ColText(countFieldListFilePath, False)
# Make sure the feature dataset is a shapefile
srcFeatureSetName = os.path.basename(srcFeatureSet)
if '.shp' not in srcFeatureSetName:
scratchFolder = os.path.join(os.path.dirname(os.path.dirname(srcFeatureSet)),'MaxPSrcData')
if not os.path.isdir(scratchFolder):
os.mkdir(scratchFolder)
scratchShapefileName = '%s.shp' % srcFeatureSetName
self._scratchShapefile = os.path.join(scratchFolder, scratchShapefileName)
if arcpy.Exists(self._scratchShapefile):
arcpy.Delete_management(self._scratchShapefile)
arcpy.FeatureClassToFeatureClass_conversion(srcFeatureSet, scratchFolder, scratchShapefileName)
else:
self._scratchShapefile = srcFeatureSet
# Generate pandas dataframe for ACS regionalization input
self._fieldList = [idField, countField]
self._fieldList.extend(targetCountFields)
with arcpy.da.SearchCursor(self._scratchShapefile, self._fieldList) as cursor: #@UndefinedVariable
for row in cursor:
index.append(row[0])
count_values.append(row[1])
targetCount_values.append(row[2:])
self._count_pdFrame = pd.DataFrame(count_values, index, [countField])
self._targetCount_pdFrame = pd.DataFrame(targetCount_values, index, targetCountFields)
self._targetMOE_pdFrame = np.empty(self._targetCount_pdFrame.shape)
self._targetMOE_pdFrame.fill(0.0)
self._targetMOE_pdFrame = pd.DataFrame(self._targetMOE_pdFrame, list(self._targetCount_pdFrame.index.values), list(self._targetCount_pdFrame.columns.values))
# Get pysal object from shapefile in featureDataset
self._w = ps.rook_from_shapefile(self._scratchShapefile, idVariable = idField)
self._shp = ps.open(self._scratchShapefile)
def __init__(self, shape_file_root, store_obj=False, dimension=2):
"""
"""
# Check that the rtree files are there, otherwise, create them
if not (os.path.exists(shape_file_root + '.idx')
and os.path.exists(shape_file_root + '.dat')):
print("Rtree data base does not exist. Create it now.")
write_shape_rtree_2D(shape_file_root, store_obj=store_obj)
rtree_time = os.path.getctime(shape_file_root + '.dat')
shape_time = os.path.getctime(shape_file_root + '.shp')
if shape_time > rtree_time:
warnings.warn('Shape file newer than rtree database,' +
' you may want to update/delete the old database')
self.shape = pysal.open(shape_file_root + '.shp')
p = rtree.index.Property()
p.dimension = dimension
p.overwrite = False
self.idx = rtree.index.Index(shape_file_root, properties=p)
def __init__(self, filename, name=None):
super(Morans, self).__init__()
self.filename = filename
self.shapefile = filename + '.shp'
self.dbf = filename + '.dbf'
if name:
self.name = name
else:
self.name = os.path.splitext(ntpath.basename(self.filename))[0]
self.results = {}
# Calculate the faster properties on init
self._threshold = pysal.min_threshold_dist_from_shapefile(
self.shapefile)
self._points_array = pysal.weights.util.get_points_array_from_shapefile(
self.shapefile)
self._data = pysal.open(self.dbf)
self._columns = self._data.by_col
def test_Headbanging_Median_Rate(self):
sids_d = np.array([i.centroid for i in self.sids])
sids_w = pysal.knnW(sids_d, k=5)
if not sids_w.id_order_set:
sids_w.id_order = sids_w.id_order
s_ht = sm.Headbanging_Triples(sids_d, sids_w, k=5)
sids_db = pysal.open(pysal.examples.get_path('sids2.dbf'), 'r')
s_e, s_b = np.array(sids_db[:, 9]), np.array(sids_db[:, 8])
sids_hb_r = sm.Headbanging_Median_Rate(s_e, s_b, s_ht)
sids_hb_rr5 = np.array([0.00075586, 0.,
0.0008285, 0.0018315, 0.00498891])
np.testing.assert_array_almost_equal(sids_hb_rr5, sids_hb_r.r[:5])
sids_hb_r2 = sm.Headbanging_Median_Rate(s_e, s_b, s_ht, iteration=5)
sids_hb_r2r5 = np.array([0.0008285, 0.00084331,
0.00086896, 0.0018315, 0.00498891])
np.testing.assert_array_almost_equal(sids_hb_r2r5, sids_hb_r2.r[:5])
sids_hb_r3 = sm.Headbanging_Median_Rate(s_e, s_b, s_ht, aw=s_b)
sids_hb_r3r5 = np.array([0.00091659, 0.,
0.00156838, 0.0018315, 0.00498891])
np.testing.assert_array_almost_equal(sids_hb_r3r5, sids_hb_r3.r[:5])
def dataframe_to_dbf(df, dbf_path, specs=None):
"""Given a pandas Dataframe, write a dbase database to ``dbf_path``.
:type df: pandas.Dataframe
:type dbf_path: basestring
:param specs: A list of column specifications for the dbase table. Each column is specified by a tuple (datatype,
size, decimal) - we support ``datatype in ('N', 'C')`` for strings, integers and floating point numbers, if
no specs are provided (see ``TYPE_MAPPING``)
:type specs: list[tuple(basestring, int, int)]
"""
if specs is None:
types = [type(df[i].iloc[0]) for i in df.columns]
specs = [TYPE_MAPPING[t] for t in types]
dbf = pysal.open(dbf_path, 'w', 'dbf')
dbf.header = list(df.columns)
dbf.field_spec = specs
for row in range(len(df)):
dbf.write(df.iloc[row])
dbf.close()
return dbf_path
def setUp(self):
data = pysal.open(pysal.examples.get_path('Tokyomortality.csv'), mode='Ur')
self.coords = list(zip(data.by_col('X_CENTROID'), data.by_col('Y_CENTROID')))
self.y = np.array(data.by_col('db2564')).reshape((-1,1))
self.off = np.array(data.by_col('eb2564')).reshape((-1,1))
OCC = np.array(data.by_col('OCC_TEC')).reshape((-1,1))
OWN = np.array(data.by_col('OWNH')).reshape((-1,1))
POP = np.array(data.by_col('POP65')).reshape((-1,1))
UNEMP = np.array(data.by_col('UNEMP')).reshape((-1,1))
self.X = np.hstack([OCC,OWN,POP,UNEMP])
self.BS_F = pysal.open(pysal.examples.get_path('tokyo_BS_F_listwise.csv'))
self.BS_NN = pysal.open(pysal.examples.get_path('tokyo_BS_NN_listwise.csv'))
self.GS_F = pysal.open(pysal.examples.get_path('tokyo_GS_F_listwise.csv'))
self.GS_NN = pysal.open(pysal.examples.get_path('tokyo_GS_NN_listwise.csv'))
self.BS_NN_OFF = pysal.open(pysal.examples.get_path('tokyo_BS_NN_OFF_listwise.csv'))
def dbf2df(dbf_path, index=None, cols=False, incl_index=False):
'''
Read a dbf file as a pandas.DataFrame, optionally selecting the index
variable and which columns are to be loaded.
__author__ = "Dani Arribas-Bel <*****@*****.**> "
...
Arguments
---------
dbf_path : str
Path to the DBF file to be read
index : str
Name of the column to be used as the index of the DataFrame
cols : list
List with the names of the columns to be read into the
DataFrame. Defaults to False, which reads the whole dbf
incl_index : Boolean
If True index is included in the DataFrame as a
column too. Defaults to False
Returns
-------
df : DataFrame
pandas.DataFrame object created
'''
db = ps.open(dbf_path)
if cols:
if incl_index:
cols.append(index)
vars_to_read = cols
else:
vars_to_read = db.header
data = dict([(var, db.by_col(var)) for var in vars_to_read])
if index:
index = db.by_col(index)
db.close()
return pd.DataFrame(data, index=index, columns=vars_to_read)
else:
db.close()
return pd.DataFrame(data, columns=vars_to_read)
def dataframe_to_dbf(df, dbf_path, specs=None):
if specs is None:
type2spec = {
int: ('N', 20, 0),
np.int64: ('N', 20, 0),
float: ('N', 36, 15),
np.float64: ('N', 36, 15),
unicode: ('C', 25, 0),
str: ('C', 25, 0)
}
types = [type(df[i].iloc[0]) for i in df.columns]
specs = [type2spec[t] for t in types]
dbf = pysal.open(dbf_path, 'w', 'dbf')
dbf.header = list(df.columns)
dbf.field_spec = specs
df_transpose = df.T
length = len(df_transpose.columns)
for row in range(length):
dbf.write(df_transpose[row])
dbf.close()
return dbf_path
def saveDataFrame2Dbf(data_frame_input, dbf_file, sep=","):
if six.PY2:
type2spec = {
int: ('N', 20, 0),
numpy.int64: ('N', 20, 0),
float: ('N', 36, 15),
numpy.float64: ('N', 36, 15),
str: ('C', 14, 0),
unicode: ('C', 14, 0)
}
else:
type2spec = {
int: ('N', 20, 0),
numpy.int64: ('N', 20, 0),
float: ('N', 36, 15),
numpy.float64: ('N', 36, 15),
str: ('C', 14, 0)
}
# Ecriture du contenu de la dataframe vers un fichier dbf
types = [
type(data_frame_input[i].iloc[0]) for i in data_frame_input.columns
]
specs = [type2spec[t] for t in types]
if six.PY2:
db_desc = pysal.open(dbf_file, 'w')
else:
if IS_libpysal:
db_desc = libpysal.io.fileio.FileIO.open(dbf_file, 'w')
else:
db_desc = pysal.lib.io.fileio.FileIO.open(dbf_file, 'w')
db_desc.header = list(data_frame_input.columns)
db_desc.field_spec = specs
for i, row in data_frame_input.T.iteritems():
db_desc.write(row)
db_desc.close()
return