def twoDisjointLinesWithMSClustering():
t = arange(-1,1,0.002)
x = map(lambda x: x + gauss(0,0.02)*(1-x*x), t)
y = map(lambda x: x + gauss(0,0.02)*(1-x*x), t)
z = map(lambda x: x + gauss(0,0.02)*(1-x*x), t)
line1 = array(zip(x,y,z))
line = vstack((line1, line1 + 3))
lpc = LPCImpl(start_points_generator = lpcMeanShift(ms_h = 1), h = 0.05, mult = None, it = 200, cross = False, scaled = False, convergence_at = 0.001)
lpc_curve = lpc.lpc(X=line)
#Plot results
fig = plt.figure()
ax = Axes3D(fig)
labels = lpc._startPointsGenerator._meanShift.labels_
labels_unique = unique(labels)
cluster_centers = lpc._startPointsGenerator._meanShift.cluster_centers_
n_clusters = len(labels_unique)
colors = cycle('bgrcmyk')
for k, col in zip(range(n_clusters), colors):
cluster_members = labels == k
cluster_center = cluster_centers[k]
ax.scatter(line[cluster_members, 0], line[cluster_members, 1], line[cluster_members, 2], c = col, alpha = 0.1)
ax.scatter([cluster_center[0]], [cluster_center[1]], [cluster_center[2]], c = 'b', marker= '^')
curve = lpc_curve[k]['save_xd']
ax.plot(curve[:,0],curve[:,1],curve[:,2], c = col, linewidth = 3)
plt.show()
def plot2():
fig5 = plt.figure()
x = map(lambda x: x + gauss(0,0.02)*(1-x*x), arange(-1,1,0.001))
y = map(lambda x: x + gauss(0,0.02)*(1-x*x), arange(-1,1,0.001))
z = map(lambda x: x + gauss(0,0.02)*(1-x*x), arange(-1,1,0.001))
line = array(zip(x,y,z))
lpc = LPCImpl(h = 0.05, mult = 2, it = 200, cross = False, scaled = False, convergence_at = 0.001)
lpc_curve = lpc.lpc(X=line)
ax = Axes3D(fig5)
ax.set_title('testNoisyLine2')
curve = lpc_curve[0]['save_xd']
ax.scatter(x,y,z, c = 'red')
ax.plot(curve[:,0],curve[:,1],curve[:,2])
saveToPdf(fig5, '/tmp/testNoisyLine2.pdf')
residuals_calc = LPCResiduals(line, tube_radius = 0.05, k = 10)
residual_diags = residuals_calc.getPathResidualDiags(lpc_curve[0])
fig6 = plt.figure()
#plt.plot(lpc_curve[0]['lamb'][1:], residual_diags['line_seg_num_NN'], drawstyle = 'step', linestyle = '--')
plt.plot(lpc_curve[0]['lamb'][1:], residual_diags['line_seg_mean_NN'])
plt.plot(lpc_curve[0]['lamb'][1:], residual_diags['line_seg_std_NN'])
saveToPdf(fig6, '/tmp/testNoisyLine2PathResiduals.pdf')
coverage_graph = residuals_calc.getCoverageGraph(lpc_curve[0], arange(0.001, .102, 0.005))
fig7 = plt.figure()
plt.plot(coverage_graph[0],coverage_graph[1])
saveToPdf(fig7, '/tmp/testNoisyLine2Coverage.pdf')
residual_graph = residuals_calc.getGlobalResiduals(lpc_curve[0])
fig8 = plt.figure()
plt.plot(residual_graph[0], residual_graph[1])
saveToPdf(fig8, '/tmp/testNoisyLine2Residuals.pdf')
fig9 = plt.figure()
plt.plot(range(len(lpc_curve[0]['lamb'])), lpc_curve[0]['lamb'])
saveToPdf(fig9, '/tmp/testNoisyLine2PathLength.pdf')
def helixHeteroscedasticDiags():
#Parameterise a helix (no noise)
fig5 = plt.figure()
t = arange(-1,1,0.0005)
x = map(lambda x: x + gauss(0,0.001 + 0.001*sin(2*pi*x)**2), (1 - t*t)*sin(4*pi*t))
y = map(lambda x: x + gauss(0,0.001 + 0.001*sin(2*pi*x)**2), (1 - t*t)*cos(4*pi*t))
z = map(lambda x: x + gauss(0,0.001 + 0.001*sin(2*pi*x)**2), t)
line = array(zip(x,y,z))
lpc = LPCImpl(h = 0.1, t0 = 0.1, mult = 1, it = 500, scaled = False, cross = False)
lpc_curve = lpc.lpc(X=line)
ax = Axes3D(fig5)
ax.set_title('helixHeteroscedastic')
curve = lpc_curve[0]['save_xd']
ax.scatter(x,y,z, c = 'red')
ax.plot(curve[:,0],curve[:,1],curve[:,2])
saveToPdf(fig5, '/tmp/helixHeteroscedastic.pdf')
residuals_calc = LPCResiduals(line, tube_radius = 0.2, k = 20)
residual_diags = residuals_calc.getPathResidualDiags(lpc_curve[0])
fig6 = plt.figure()
#plt.plot(lpc_curve[0]['lamb'][1:], residual_diags['line_seg_num_NN'], drawstyle = 'step', linestyle = '--')
plt.plot(lpc_curve[0]['lamb'][1:], residual_diags['line_seg_mean_NN'])
plt.plot(lpc_curve[0]['lamb'][1:], residual_diags['line_seg_std_NN'])
saveToPdf(fig6, '/tmp/helixHeteroscedasticPathResiduals.pdf')
coverage_graph = residuals_calc.getCoverageGraph(lpc_curve[0], arange(0.01, .052, 0.01))
fig7 = plt.figure()
plt.plot(coverage_graph[0],coverage_graph[1])
saveToPdf(fig7, '/tmp/helixHeteroscedasticCoverage.pdf')
residual_graph = residuals_calc.getGlobalResiduals(lpc_curve[0])
fig8 = plt.figure()
plt.plot(residual_graph[0], residual_graph[1])
saveToPdf(fig8, '/tmp/helixHeteroscedasticResiduals.pdf')
fig9 = plt.figure()
plt.plot(range(len(lpc_curve[0]['lamb'])), lpc_curve[0]['lamb'])
saveToPdf(fig9, '/tmp/helixHeteroscedasticPathLength.pdf')
def helixHeteroscedasticCrossingDemo():
#Parameterise a helix (no noise)
fig5 = plt.figure()
t = arange(-1,1,0.001)
x = map(lambda x: x + gauss(0,0.01 + 0.05*sin(8*pi*x)), (1 - t*t)*sin(4*pi*t))
y = map(lambda x: x + gauss(0,0.01 + 0.05*sin(8*pi*x)), (1 - t*t)*cos(4*pi*t))
z = map(lambda x: x + gauss(0,0.01 + 0.05*sin(8*pi*x)), t)
line = array(zip(x,y,z))
lpc = LPCImpl(h = 0.15, t0 = 0.1, mult = 2, it = 500, scaled = False)
lpc_curve = lpc.lpc(line)
ax = Axes3D(fig5)
ax.set_title('helixHeteroscedasticWithCrossing')
curve = lpc_curve[0]['save_xd']
ax.scatter(x,y,z, c = 'red')
ax.plot(curve[:,0],curve[:,1],curve[:,2])
saveToPdf(fig5, '/tmp/helixHeteroscedasticWithCrossing.pdf')
lpc.set_in_dict('cross', False, '_lpcParameters')
fig6 = plt.figure()
lpc_curve = lpc.lpc(X=line)
ax = Axes3D(fig6)
ax.set_title('helixHeteroscedasticWithoutCrossing')
curve = lpc_curve[0]['save_xd']
ax.scatter(x,y,z, c = 'red')
ax.plot(curve[:,0],curve[:,1],curve[:,2])
saveToPdf(fig6, '/tmp/helixHeteroscedasticWithoutCrossing.pdf')
def testNoisyLine2(self): x = map(lambda x: x + gauss(0,0.005), arange(-1,1,0.005)) y = map(lambda x: x + gauss(0,0.005), arange(-1,1,0.005)) z = map(lambda x: x + gauss(0,0.005), arange(-1,1,0.005)) line = array(zip(x,y,z)) lpc = LPCImpl(h = 0.2, convergence_at = 0.001, mult = 2) lpc_curve = lpc.lpc(X = line)
def testNoisyLine1(self): x = map(lambda x: x + gauss(0,0.002), arange(-1,1,0.001)) y = map(lambda x: x + gauss(0,0.002), arange(-1,1,0.001)) z = map(lambda x: x + gauss(0,0.02), arange(-1,1,0.001)) line = array(zip(x,y,z)) lpc = LPCImpl(h = 0.2, mult = 2) lpc_curve = lpc.lpc(X = line)
def testCoverage(self): x = map(lambda x: x + gauss(0,0.005 + 0.3*x*x), arange(-1,1,0.005)) y = map(lambda x: x + gauss(0,0.005 + 0.3*x*x), arange(-1,1,0.005)) z = map(lambda x: x + gauss(0,0.005 + 0.3*x*x), arange(-1,1,0.005)) line = array(zip(x,y,z)) lpc = LPCImpl(h = 0.05, convergence_at = 0.0001, it = 100, mult = 2) lpc_curve = lpc.lpc(X=line) residuals_calc = LPCResiduals(line, tube_radius = 1)
def testNoisyLine1Residuals(self): x = map(lambda x: x + gauss(0,0.005), arange(-1,1,0.005)) y = map(lambda x: x + gauss(0,0.005), arange(-1,1,0.005)) z = map(lambda x: x + gauss(0,0.005), arange(-1,1,0.005)) line = array(zip(x,y,z)) lpc = LPCImpl(h = 0.2, convergence_at = 0.0005, it = 500, mult = 2) lpc_curve = lpc.lpc(X=line) residuals_calc = LPCResiduals(line, tube_radius = 0.1) residual_diags = residuals_calc.getPathResidualDiags(lpc_curve[0])
def gaia():
gaia = array(readData('../resources/gaia.dat'))
lpc = LPCImpl(start_points_generator = lpcMeanShift(), mult = 1, scaled = False)
curve = lpc.lpc(X = gaia)
fig = plt.figure()
ax = Axes3D(fig)
ax.scatter(gaia[:,0], gaia[:,1], gaia[:,2], alpha = 0.3)
save_xd = curve[0]['save_xd']
ax.plot(save_xd[:,0], save_xd[:,1], save_xd[:,2])
def testNoisyLine2Residuals(self): #contains data that gets more scattered at each end of the line x = map(lambda x: x + gauss(0,0.005 + 0.3*x*x), arange(-1,1,0.005)) y = map(lambda x: x + gauss(0,0.005 + 0.3*x*x), arange(-1,1,0.005)) z = map(lambda x: x + gauss(0,0.005 + 0.3*x*x), arange(-1,1,0.005)) line = array(zip(x,y,z)) lpc = LPCImpl(h = 0.05, convergence_at = 0.001, it = 100, mult = 2) lpc_curve = lpc.lpc(X=line) residuals_calc = LPCResiduals(line, tube_radius = 1) residual_diags = residuals_calc.getPathResidualDiags(lpc_curve[0])
def calSpeedFlow():
calspeedflow = array(readData('../resources/calspeedflow.dat'))
print calspeedflow
lpc = LPCImpl(start_points_generator = lpcMeanShift(ms_h = 0.1), mult = 1)
lpc.lpc(X = calspeedflow)
curve = lpc.getCurve(unscale = True)
fig = plt.figure()
plt.scatter(calspeedflow[:,0], calspeedflow[:,1], alpha = 0.3)
save_xd = curve[0]['save_xd']
plt.plot(save_xd[:,0], save_xd[:,1])
def testResidualsRunner(self): x = map(lambda x: x + gauss(0,0.005 + 0.3*x*x), arange(-1,1,0.05)) y = map(lambda x: x + gauss(0,0.005 + 0.3*x*x), arange(-1,1,0.05)) z = map(lambda x: x + gauss(0,0.005 + 0.3*x*x), arange(-1,1,0.05)) line = array(zip(x,y,z)) lpc = LPCImpl(h = 0.2, convergence_at = 0.0001, it = 100, mult = 5) lpc_curve = lpc.lpc(X=line) residuals_calc = LPCResiduals(line, tube_radius = 0.15) residuals_runner = LPCResidualsRunner(lpc.getCurve(), residuals_calc) residuals_runner.setTauRange([0.05, 0.07]) residuals = residuals_runner.calculateResiduals() pprint(residuals)
def plot1():
fig1 = plt.figure()
x = map(lambda x: x + gauss(0,0.005), arange(-1,1,0.005))
y = map(lambda x: x + gauss(0,0.005), arange(-1,1,0.005))
z = map(lambda x: x + gauss(0,0.005), arange(-1,1,0.005))
line = array(zip(x,y,z))
lpc = LPCImpl(h = 0.05, mult = 2, scaled = False)
lpc_curve = lpc.lpc(X=line)
ax = Axes3D(fig1)
ax.set_title('testNoisyLine1')
curve = lpc_curve[0]['save_xd']
ax.scatter(curve[:,0],curve[:,1],curve[:,2],c = 'red')
return fig1
def helixRandom():
#Parameterise a helix (no noise)
fig4 = plt.figure()
t = arange(-1,1,0.001)
x = map(lambda x: x + gauss(0,0.01), (1 - t*t)*sin(4*pi*t))
y = map(lambda x: x + gauss(0,0.01), (1 - t*t)*cos(4*pi*t))
z = map(lambda x: x + gauss(0,0.01), t)
line = array(zip(x,y,z))
lpc = LPCImpl(h = 0.15, t0 = 0.2, mult = 2, it = 100, scaled = False)
lpc_curve = lpc.lpc(X=line)
ax = Axes3D(fig4)
ax.set_title('helixRandom')
curve = lpc_curve[0]['save_xd']
ax.scatter(x,y,z, c = 'red')
ax.plot(curve[:,0],curve[:,1],curve[:,2])
def testFollowXTwo(self): lpc = LPCImpl(h = [0.6, 0.7, 0.6], it = 10, convergence_at = 0.005, way = 'two') lpc.lpc(X = array([[.1,.2,.3], [.11,.22,.33], [.07,.18,.29]]))
def testLPCCalculation1(self): lpc = LPCImpl(h = [0.7, 0.7, 0.7], it = 10) lpc.lpc(X = array([[1.,2.,3.], [4.,5.,6.], [7.,8.,9.]]))