def prediction_array(self, time, space_array):
# combine time with space dimension
space_array = self.space_class(space_array, copy=False)
t = DataArray(time * np.ones(space_array.ndata))
if space_array.original_shape is not None:
t.original_shape = space_array.original_shape
return t.adddim(space_array, type=self.data_class)
def test_cutoff(self):
x = DataArray(np.linspace(-5, 5, 100))
self.assertTrue(np.all(self.kernels[1].pdf(x)[x.toarray(0) < 0] == 0))
x = DataArray.from_meshgrid(
*np.meshgrid(
np.linspace(-5, 5, 50),
np.linspace(-5, 5, 50)
)
)
res = self.kernels[2].pdf(x)
self.assertTrue(np.all(res[x.toarray(0) < 0] == 0))
self.assertTrue(np.all(res[x.toarray(0) >= 0] > 0.))
def test_linkage_function(self):
lf = utils.linkage_func_separable(5., 10.)
self.assertTrue(lf(4, 9))
self.assertFalse(lf(5.01, 9))
self.assertFalse(lf(4, 10.01))
dt = DataArray(np.random.rand(10))
dd = DataArray(np.random.rand(10))
b_in = lf(dt, dd)
b_expct = (dt <= 5.) & (dd <= 10.)
self.assertTrue(np.all(b_in == b_expct))
lf = lambda dt, dd: (dt**2 + dd**2)**0.5 < 0.5
b_in = lf(dt, dd)
b_expct = (dt**2 + dd**2)**0.5 < 0.5
self.assertTrue(np.all(b_in == b_expct))
def plot_sepp_bg_surface(sepp_obj, domain=None, **kwargs):
k = sepp_obj.bg_kde
# if x_range is None:
# x_range = [min(sepp_obj.data.toarray(1)), max(sepp_obj.data.toarray(1))]
# y_range = [min(sepp_obj.data.toarray(2)), max(sepp_obj.data.toarray(2))]
# loc = DataArray.from_meshgrid(*np.meshgrid(
# np.linspace(x_range[0], x_range[1], npt),
# np.linspace(y_range[0], y_range[1], npt),
# ))
# z = k.partial_marginal_pdf(loc)
# if ax is None:
# fig = plt.figure()
# ax = fig.add_subplot(111)
# ax.contourf(loc.toarray(0), loc.toarray(1), z, 50)
# ax.set_aspect('equal')
# if domain is not None:
func = lambda x, y: k.partial_marginal_pdf(DataArray.from_meshgrid(x, y))
if domain is None:
xmin, xmax = min(sepp_obj.data.toarray(1)), max(
sepp_obj.data.toarray(1))
ymin, ymax = min(sepp_obj.data.toarray(2)), max(
sepp_obj.data.toarray(2))
domain = shapely_rectangle_from_vertices(xmin, ymin, xmax, ymax)
plot_surface_function_on_polygon(domain, func=func, **kwargs)
plt.axis('equal')
def predict(self, time, space_array, force_update=False):
"""
Generate a prediction from the trained model.
Supply single time and spatial sample points in separate arrays
If force_update=False then the spatial component is assumed unchanged, so only the time is altered.
This is important: updating the spatial sample points loses all cached net paths.
"""
if self.kde.targets_set and not force_update:
self.kde.update_target_times(time)
return self.kde.pdf()
else:
space_array = self.space_class(space_array, copy=False)
time_array = DataArray(np.ones(space_array.ndata) * time)
targets_array = time_array.adddim(space_array,
type=self.data_class)
return self.kde.pdf(targets=targets_array)
def test_marginal_cdf_values(self):
k = self.kernels[3]
x = DataArray(np.linspace(-5, 5, 100))
for i in range(3):
y = k.marginal_cdf(x, dim=i)
ye = self.expected_marginal_cdf(x, i)
self.assertTrue(np.all(np.abs(y - ye) < self.tol))
def marginal_icdf_optimise(k, y, dim=0, tol=1e-8):
n = 100
max_iter = 50
f = lambda x: np.abs(k.marginal_cdf(x, dim=dim) - y)
mean_bd = np.mean(k.bandwidths[:, dim])
minx = np.min(k.data[:, dim])
maxx = np.max(k.data[:, dim])
err = 1.
niter = 0
x0 = 0.
while err > tol:
if niter > max_iter:
raise Exception(
"Failed to converge to optimum after %u iterations", max_iter)
xe = DataArray(np.linspace(minx, maxx, n))
ye = f(xe)
idx = np.argmin(ye)
if idx == 0:
# return xe[idx]
minx -= mean_bd
continue
if idx == (n - 1):
maxx += mean_bd
continue
err = ye[idx]
x0 = xe[idx]
minx = xe[idx - 1]
maxx = xe[idx + 1]
niter += 1
return float(x0)
def test_assess(self):
stk = hotspot.SKernelHistoric(1, bdwidth=0.3)
vb = validation.ValidationBase(self.data, stk)
vb.train_model()
# mock roc object with grid
mocroc = mock.create_autospec(roc.RocGrid)
mocroc.centroids = np.array([[0., 0.], [1., 1.]])
mocroc.sample_units = range(
2) # needs to have the correct length, contents not used
mocroc.sample_points = DataArray([[0., 0.], [1., 1.]])
vb.roc = mocroc
res = vb._iterate_run(pred_dt_plus=0.2,
true_dt_plus=None,
true_dt_minus=0.)
# set data
self.assertTrue(vb.roc.set_data.called)
self.assertEqual(vb.roc.set_data.call_count, 1)
self.assertTrue(
np.all(vb.roc.set_data.call_args[0] == vb.testing(
dt_plus=0.2)[:, 1:]))
# set prediction
self.assertTrue(vb.roc.set_prediction.called)
self.assertEqual(vb.roc.set_prediction.call_count, 1)
self.assertEqual(len(vb.roc.set_prediction.call_args[0]), 1)
t = (vb.cutoff_t + 0.2)
# expected prediction values at (0,0), (1,1)
pred_arg = DataArray(np.array([[t, 0., 0.], [t, 1., 1.]]))
pred_expctd = vb.model.predict(t, mocroc.sample_points)
self.assertTrue(
np.all(vb.roc.set_prediction.call_args[0][0] == pred_expctd))
# set grid
self.assertFalse(vb.roc.set_sample_units.called)
vb.set_sample_units(0.1)
self.assertTrue(vb.roc.set_sample_units.called)
self.assertEqual(vb.roc.set_sample_units.call_count, 1)
self.assertTupleEqual(vb.roc.set_sample_units.call_args[0], (0.1, ))
# evaluate
self.assertTrue(vb.roc.evaluate.called)
self.assertEqual(vb.roc.evaluate.call_count, 1)
def set_sample_points(self,
n_sample_per_grid,
respect_boundary=True,
*args,
**kwargs):
""" Generate n_sample_per_grid sample points per grid unit
Return n_sample_per_grid x self.ndata x 2 array, final dim is x, y """
if HAS_GEODJANGO and isinstance(self.poly, geos.GEOSGeometry):
point_class = geos.Point
else:
point_class = Point
if self.side_length is None:
# grid was supplied as an array
# slow version: need to iterate over the polygons
xres = np.empty((n_sample_per_grid, self.n_sample_units),
dtype=float)
yres = np.empty((n_sample_per_grid, self.n_sample_units),
dtype=float)
for i, p in enumerate(self.grid_polys):
xres[:, i], yres[:, i] = random_points_within_poly(
p, n_sample_per_grid)
else:
xmins = np.array([x[0] for x in self.sample_units])
ymins = np.array([x[1] for x in self.sample_units])
xres = np.random.rand(n_sample_per_grid, self.n_sample_units
) * self.side_length + xmins
yres = np.random.rand(n_sample_per_grid, self.n_sample_units
) * self.side_length + ymins
if respect_boundary:
# loop over grid squares that are incomplete
for i in np.where(np.array(self.full_grid_square) == False)[0]:
inside_idx = np.array([
point_class(x, y).within(self.poly)
for x, y in zip(xres[:, i], yres[:, i])
])
# pad empty parts with repeats of the centroid location
num_empty = n_sample_per_grid - sum(inside_idx)
if num_empty:
cx, cy = self.centroids[i]
rem_x = np.concatenate((xres[inside_idx,
i], cx * np.ones(num_empty)))
rem_y = np.concatenate((yres[inside_idx,
i], cy * np.ones(num_empty)))
xres[:, i] = rem_x
yres[:, i] = rem_y
xres = xres.flatten(order='F')
yres = yres.flatten(order='F')
self.sample_points = DataArray.from_args(xres, yres)
self.n_sample_point_per_unit = np.ones(
self.n_sample_units) * n_sample_per_grid
def test_pdf_values(self):
for i in range(self.min_nd, 4):
x = DataArray.from_meshgrid(
*np.meshgrid(
*[np.linspace(-5, 5, 50)] * i
)
)
y = self.kernels[i].pdf(x)
ye = self.expected_pdf(x)
self.assertTrue(np.all(np.abs(y - ye) < self.tol))
def plot_xy_kde(k, x_range, y_range, npt_1d=50, **kwargs):
x, y = np.meshgrid(np.linspace(x_range[0], x_range[1], npt_1d),
np.linspace(y_range[0], y_range[1], npt_1d))
loc = DataArray.from_meshgrid(x, y)
z = k.pdf(loc, normed=False)
fig = plt.figure()
ax = fig.add_subplot(111)
n_contours = kwargs.pop('n_contours', 40)
cax = ax.contourf(x, y, z, n_contours, cmap='binary')
if 'clim' in kwargs:
clim = kwargs.pop('clim')
cax.set_clim(clim)
ax.set_xlabel('X (m)')
ax.set_ylabel('Y (m)')
if kwargs.pop('colorbar', True):
fig.colorbar(cax)
return fig
def test_mvn3d(self):
mvn = kernels.MultivariateNormal([0, 0, 0], [1, 1, 1])
self.assertEqual(mvn.ndim, 3)
q = tplquad(partial(quad_pdf_fun, func=mvn.pdf), -5, 5, lambda x: -5, lambda x: 5, lambda x, y: -5, lambda x, y: 5)
self.assertAlmostEqual(q[0], 1.0, places=5)
# test with absolute values
x = np.meshgrid(*([np.linspace(-1, 1, 10)]*3))
x = np.vstack((x[0].flatten(), x[1].flatten(), x[2].flatten())).transpose().reshape(1000, 3)
y = mvn.pdf(x)
y_expct = multivariate_normal.pdf(x, mean=[0, 0, 0], cov=np.eye(3))
self.assertEqual(np.sum(np.abs((y - y_expct)).flatten()>1e-12), 0) # no single difference > 1e-12
# repeat with Data type
x = DataArray(x)
y = mvn.pdf(x)
self.assertEqual(np.sum(np.abs((y - y_expct)).flatten()>1e-12), 0) # no single difference > 1e-12
def update_target_times(self, target_times):
"""
Update the times attached to the (spatial) targets.
:param target_times: Either an iterable (in which case it must be possible to cast to a DataArray) or a scalar
(in which case all target times are set to this value)
"""
if hasattr(target_times, '__iter__'):
target_times = DataArray(target_times, copy=False)
self.logger.info("update_target_times with an iterable of len %d",
target_times.ndata)
if target_times.ndata != self.targets.ndata:
raise AttributeError(
"The number of data points does not match existing data in the supplied array"
)
self.targets.time = target_times
else:
self.logger.info("update_target_times with a fixed time %f",
target_times)
self.targets.data[:, 0] = target_times
def test_partials(self):
mvn = kernels.MultivariateNormal([0, 0, 0], [1, 2, 3])
arr = np.meshgrid(np.linspace(-15, 15, 20), np.linspace(-15, 15, 20))
xy = DataArray(np.concatenate([t[..., np.newaxis] for t in arr], axis=2))
# attempt to call with data of too few dims
with self.assertRaises(AttributeError):
p = mvn.partial_marginal_pdf(xy.getdim(0), dim=0)
p = mvn.partial_marginal_pdf(xy, dim=0) # should be marginal in 2nd and 3rd dims
p_expct = mvn.pdf(xy, dims=[1, 2])
self.assertTrue(np.all(np.abs(p - p_expct) < 1e-14))
p_expct = mvn.marginal_pdf(xy.getdim(0), dim=1) * mvn.marginal_pdf(xy.getdim(1), dim=2)
self.assertTrue(np.all(np.abs(p - p_expct) < 1e-14))
p = mvn.partial_marginal_pdf(xy, dim=1) # should be marginal in 1st and 3rd dims
p_expct = mvn.pdf(xy, dims=[0, 2])
self.assertTrue(np.all(np.abs(p - p_expct) < 1e-14))
# test directly
p_expct = mvn.marginal_pdf(xy.getdim(0), dim=0) * mvn.marginal_pdf(xy.getdim(1), dim=2)
self.assertTrue(np.all(np.abs(p - p_expct) < 1e-14))
def test_mvn1d(self):
mvn = kernels.MultivariateNormal([0], [1])
self.assertEqual(mvn.ndim, 1)
q = quad(partial(quad_pdf_fun, func=mvn.pdf), -5., 5.)
self.assertAlmostEqual(q[0], 1.0, places=5)
# test with absolute values
x = np.linspace(-1, 1, 10).reshape(10, 1)
y = mvn.pdf(x)
y_expct = norm.pdf(x)
for y1, y2 in zip(y, y_expct):
self.assertAlmostEqual(y1, y2)
# repeat with Data type
x = DataArray(np.linspace(-1, 1, 10))
y = mvn.pdf(x)
for y1, y2 in zip(y, y_expct):
self.assertAlmostEqual(y1, y2)
m = mvn.marginal_pdf(x)
self.assertListEqual(list(y), list(m))
c = mvn.marginal_cdf(np.array(0.))
self.assertAlmostEqual(c, 0.5)
def radial_spatial_triggering_plots(ppobj,
simobj=None,
xmax=None,
ymax=None,
cbar=True,
fmax=None,
vmax=None):
npt = 500
ci = 0.99
fig_kwargs = {
'figsize': (10, 5),
'dpi': 100,
'facecolor': 'w',
}
assert fmax is None or vmax is None, "Can specify EITHER vmax OR fmax"
xmax = xmax or ppobj.trigger_kde.marginal_icdf(ci, dim=1)
ymax = ymax or xmax
xy = DataArray.from_meshgrid(*np.meshgrid(np.linspace(-xmax, xmax, npt),
np.linspace(-ymax, ymax, npt)))
zxy1 = ppobj.trigger_kde.partial_marginal_pdf(xy,
normed=False) / ppobj.ndata
# zxy1 = ppobj.trigger_kde.partial_marginal_pdf(xy, normed=True)
if fmax is not None:
vmax = sorted(zxy1.flat)[int(zxy1.size * fmax)]
elif vmax is not None:
pass
else:
vmax = zxy1.max()
if simobj:
sx = simobj.trigger_params['sigma'][0]
sy = simobj.trigger_params['sigma'][1]
th = simobj.trigger_params['intensity']
# zxy2 = th / (np.sqrt(2 * np.pi) * sx * sy) * np.exp(
# -(xy.toarray(0) ** 2) / (2 * sx**2) - xy.toarray(1) ** 2 / (2 * sy ** 2)
# )
zxy2 = 1 / (2 * np.pi * sx *
sy) * np.exp(-(xy.toarray(0)**2) /
(2 * sx**2) - xy.toarray(1)**2 / (2 * sy**2))
vmax = max(zxy2.max(), vmax)
vmax *= 1.02
fig = plt.figure(**fig_kwargs)
if simobj:
ax1 = fig.add_subplot(121)
else:
ax1 = fig.add_subplot(111)
cont1 = ax1.contourf(xy.toarray(0),
xy.toarray(1),
zxy1,
50,
cmap=cm.coolwarm,
vmin=0,
vmax=vmax)
ax1.set_xlim([-xmax, xmax])
ax1.set_ylim([-ymax, ymax])
ax1.set_xlabel('X (metres)')
ax1.set_ylabel('Y (metres)')
ax1.set_aspect('equal')
# cax1 = plt.colorbar(cont, ax=ax1)
hbar = None
if simobj:
ax2 = fig.add_subplot(122)
cont2 = ax2.contourf(xy.toarray(0),
xy.toarray(1),
zxy2,
50,
cmap=cm.coolwarm,
vmin=0,
vmax=vmax)
ax2.yaxis.set_ticklabels([])
ax2.set_xlabel('X (metres)')
ax2.set_xlim([-xmax, xmax])
ax2.set_ylim([-ymax, ymax])
ax2.set_aspect('equal')
if cbar:
hbar = fig.colorbar(cont2, ax=[ax1, ax2])
else:
if cbar:
hbar = fig.colorbar(cont1, ax=ax1)
if cbar:
return hbar
def prediction_array(self, t):
n = self.roc.sample_points.ndata
ts = np.ones(n) * t
data_array = DataArray.from_args(ts).adddim(self.roc.sample_points,
type=self.data_class)
return data_array
def weighted_bg_mean_density(x, y):
xy = DataArray.from_meshgrid(x, y)
fxy = np.array(
[a.partial_marginal_pdf(xy) for a in res['weighted_backgrounds']])
return fxy.mean(axis=0).reshape(xy.original_shape)
def weighted_bg_rel_range(x, y):
xy = DataArray.from_meshgrid(x, y)
fxy = np.array(
[a.partial_marginal_pdf(xy) for a in res['weighted_backgrounds']])
fxy_mean = fxy.mean(axis=0)
return (fxy.ptp(axis=0) / fxy_mean).reshape(xy.original_shape)
nw = utils.NetworkWalker(itn_net,
targets,
max_distance=radius,
max_split=1e4)
k = NetworkKernelEqualSplitLinear(sources.getone(0), 200.)
k.set_walker(nw)
z = k.pdf()
zn = z / max(z)
# plt.figure()
# itn_net.plot_network()
# plt.scatter(nodes[:, 0], nodes[:, 1], marker='x', s=15, c='k')
# plt.scatter(*targets.to_cartesian().separate, s=(zn * 20) ** 2)
# plt.scatter(*sources.getone(0).cartesian_coords, c='r', s=50)
# add time to sources and targets
times = DataArray(np.random.rand(num_pts))
sources_st = times.adddim(sources, type=NetworkSpaceTimeData)
targets_st = DataArray(np.ones(targets.ndata)).adddim(
targets, type=NetworkSpaceTimeData)
kst = NetworkTemporalKernelEqualSplit(
[sources_st.time.getone(0),
sources_st.space.getone(0)], [0.5, 200.])
kst.set_walker(nw)
zst = kst.pdf(target_times=targets_st.time)
zstn = zst / z.max()
# plt.figure()
# itn_net.plot_network()
# plt.scatter(nodes[:, 0], nodes[:, 1], marker='x', s=15, c='k')
# plt.scatter(*targets.to_cartesian().separate, s=(zstn * 20) ** 2)
def test_network_roc(self):
itn_net = load_test_network()
# lay down a few events on the network
net_point_array = []
edge_idx = [20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 100]
for i in edge_idx:
net_point_array.append(
itn_net.edges()[i].centroid) # midway along the edge
net_point_array = NetworkData(net_point_array)
# append to times to get full dataset
st_net_array = DataArray.from_args(
np.arange(net_point_array.ndata) / float(len(edge_idx))).adddim(
net_point_array, type=NetworkSpaceTimeData)
# test 1: Bowers kernel (decrease with time and distance)
stk = hotspot.STNetworkBowers(a=10., b=1.)
vb = validation.NetworkValidationBase(st_net_array, stk)
vb.set_sample_units(None) # the argument makes no difference here
vb.set_t_cutoff(0.5)
res = vb.run(time_step=0.1)
# on each step, the segment corresponding to the most recent event should have the highest prediction rank
for i in range(5):
self.assertTrue(
np.all(res['prediction_rank'][i][:(
i + 1)] == np.array(edge_idx[5:(i + 6)])[::-1]))
# test 2: binary mask kernel in space, decr in time
# exponential decrease with dt, zero when dd > 10
radius = 50.
stk = hotspot.STNetworkFixedRadius(radius, 1.0)
vb = validation.NetworkValidationBase(st_net_array, stk)
vb.set_sample_units(None) # the argument makes no difference here
vb.set_t_cutoff(0.5)
res = vb.run(time_step=0.1, n_iter=1)
pvals = vb.roc.prediction_values
# check network distance from centroid to sources and verify non zero values
pvals_expctd_nonzero = []
for i, e in enumerate(vb.roc.sample_units):
if np.any([(e.centroid - x).length <= radius
for x in vb.training.toarray(1)]):
pvals_expctd_nonzero.append(i)
pvals_expctd_nonzero = np.array(pvals_expctd_nonzero)
self.assertTrue(
np.all(pvals.nonzero()[0] == np.array(pvals_expctd_nonzero)))
# test 3: repeat but with a mean version of the ROC
vb = validation.NetworkValidationMean(st_net_array, stk)
vb.set_sample_units(None, 10) # points are spaced ~10m apart
vb.set_t_cutoff(0.5)
res = vb.run(time_step=0.1, n_iter=1) # just one run this time
pvals2 = vb.roc.prediction_values
# check network distance from centroid to sources and verify non zero values
pvals_expctd_nonzero2 = []
for i, pt in enumerate(vb.sample_points.toarray(0)):
if np.any([(pt - x).length <= radius
for x in vb.training.toarray(1)]):
# find sample unit from sample point
this_sample_unit = bisect.bisect_right(
vb.roc.n_sample_point_per_unit.cumsum(), i)
if this_sample_unit not in pvals_expctd_nonzero2:
pvals_expctd_nonzero2.append(this_sample_unit)
self.assertTrue(
np.all(pvals2.nonzero()[0] == np.array(pvals_expctd_nonzero2)))
l_target = k.pdf(res_all.getrows(this_idx_target), normed=False)
l_sources.append(l_source)
l_targets.append(l_target)
kst[i,
j] = n / (nv * S * T) * np.sum(1 / (omega * l_source * l_target))
# plots
plt.figure()
plt.contourf(uu, vv, kst - np.pi * uu**2 * vv, 50)
plt.colorbar()
xy = DataArray.from_meshgrid(*np.meshgrid(
np.linspace(res_all.toarray(1).min(),
res_all.toarray(1).max(), 50),
np.linspace(res_all.toarray(2).min(),
res_all.toarray(2).max(), 50)))
zz = k.partial_marginal_pdf(xy, normed=False)
plt.figure()
plt.contourf(xy.toarray(0), xy.toarray(1), zz, 50)
plt.colorbar()
t = np.linspace(res_all.toarray(0).min(), res_all.toarray(0).max(), 500)
plt.figure()
plt.plot(t, k.marginal_pdf(t, dim=0, normed=False))
# simulation ONLY
if b_sim:
true_int = lambda xyz: 250 / (
(1 - np.exp(-1)) *
def create_network_with_crime_counts(
start_date=datetime.date(2011, 3, 1), domain_name='South'):
# load network, count crimes in 6mo and 12mo window, output shapefile
domains = chicago.get_chicago_side_polys()
domain = domains[domain_name]
end_date = start_date + datetime.timedelta(days=365)
crime_types = (
'THEFT',
'BURGLARY',
'HOMICIDE',
'BATTERY',
'ARSON',
'MOTOR VEHICLE THEFT',
'ASSAULT',
'ROBBERY',
)
time_window_filters = {
'6mo': lambda t: t <= 183,
'12mo': lambda t: t <= 365,
}
# get crime data
data, t0, cid = chicago.get_crimes_by_type(crime_type=crime_types,
start_date=start_date,
end_date=end_date,
domain=domain)
# get network
osm_file = os.path.join(
DATA_DIR, 'osm_chicago',
'%s_clipped.net' % consts.FILE_FRIENDLY_REGIONS[domain_name])
net = osm.OSMStreetNet.from_pickle(osm_file)
# snap crime data to network with maximum distance cutoff
netdata, failed = NetworkData.from_cartesian(net,
data[:, 1:],
radius=50,
return_failure_idx=True)
# get non-failed times
idx = sorted(set(range(data.shape[0])) - set(failed))
netdata = DataArray(data[idx, 0]).adddim(netdata,
type=NetworkSpaceTimeData)
# run over edges, count crimes in the two time windows
filters = {}
for filt_name, filt_func in time_window_filters.items():
filters[filt_name] = filt_func(netdata.toarray(0)).astype(int)
# add count attributes to all edges
for e in net.edges():
e.attrs['crimes_6mo'] = 0
e.attrs['crimes_12mo'] = 0
edge_counts = {}
for i, t in enumerate(netdata.space.toarray()):
t.edge.attrs['crimes_6mo'] += filters['6mo'][i]
t.edge.attrs['crimes_12mo'] += filters['12mo'][i]
net.save(consts.FILE_FRIENDLY_REGIONS[domain_name] +
'_network_crime_counts',
fmt='shp')