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 testDistanceBetweenCurves(self):
l1 = {'save_xd': array([[0.5,1,0], [1.5,1,0]]), 'lamb':array([0.0, 1.0])}
l2 = {'save_xd': array([[0,0,0], [1,0,0], [2,0,0]])}
x = arange(-1,1,0.005)
line = array(zip(x,x,x)) #not actually needed for calcualtion, but dummy argument to residuals_cal for now
residuals_calc = LPCResiduals(line, tube_radius = 0.2)
dist = residuals_calc._distanceBetweenCurves(l1,l2)
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 testResiduals(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) residuals_graph = residuals_calc.getGlobalResiduals(lpc_curve[0])
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])
class lpcAnalyser(object):
def __init__(self, filename):
'''
Constructor
'''
self._parser = lpcAnalysisParser(filename)
self._initReader()
self._initResiduals()
self._initPruner()
self._setOutputFilename()
self._initPurity()
def _initReader(self):
run_parameters = self._parser.getReadParameters()
if run_parameters['type'] == 'lpcAnalysisPickleReader':
self._reader = lpcAnalysisPickleReader(**run_parameters['params'])
else:
raise ValueError, 'Specified type of reader is not recognised'
def _initResiduals(self):
residual_parameters = self._parser.getResidualsParameters()
if residual_parameters['type'] == 'LPCResiduals':
tau_range = residual_parameters['params'].pop('tau_range')
self._residuals = LPCResiduals(**residual_parameters['params'])
self._residuals_runner = LPCResidualsRunner(self._residuals, tau_range)
else:
raise ValueError, 'Specified type of residuals calculator is not recognised'
def _initPruner(self):
pruner_parameters = self._parser.getPrunerParameters()
if pruner_parameters['type'] == 'lpcCurvePruner':
self._pruner = lpcCurvePruner(self._residuals_runner, **pruner_parameters['params'])
else:
raise ValueError, 'Specified type of residuals calculator is not recognised'
def _setOutputFilename(self):
misc = self._parser.getMiscParameters()
self._output_filename = misc['params']['output_filename']
def _initPurity(self):
self._purity = LPCPurityCalculator(self._residuals_runner)
def runAnalyser(self):
out_data = []
while 1:
try:
evt = self._reader.getNextEvent()
self._residuals.setDataPoints(evt[0]['Xi'])
self._residuals_runner.setLpcCurves(evt[0]['lpc_curve'])
self._residuals_runner.calculateResiduals(calc_residuals = False, calc_containment_matrix = False)
remaining_curves = self._pruner.pruneCurves()
#muon_proton_hits = truth_evt.getParticleHits([13, 2212])
#eff = LPCEfficiencyCalculator(remaining_curves, evt['data_range'], muon_proton_hits, tau) TODO - move from examples/toytracks
voxel_to_pdg_dictionary = evt[1].getParticlesInVoxelDict()
pur = self._purity.calculatePurity(remaining_curves, evt[0]['data_range'], voxel_to_pdg_dictionary)
out_data.append({'voxel_dict': voxel_to_pdg_dictionary, 'pur': pur})
except EOFError:
break
#TODO - factor this out into a class which enters the analysis configuration file
outfile = open(self._output_filename, 'w')
cPickle.dump(out_data, outfile, -1)
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 _initResiduals(self):
residual_parameters = self._parser.getResidualsParameters()
if residual_parameters['type'] == 'LPCResiduals':
tau_range = residual_parameters['params'].pop('tau_range')
self._residuals = LPCResiduals(**residual_parameters['params'])
self._residuals_runner = LPCResidualsRunner(self._residuals, tau_range)
else:
raise ValueError, 'Specified type of residuals calculator is not recognised'
def LPCEfficiencyCalculator(curves, data_range, particle_hits, tau):
#first rescale the curves then calculate the proton and muon efficiency
if data_range is None:
data_range = 1.0
muon_hits = array([[h[0][0], h[0][1], h[0][2]] for h in particle_hits[13]]) / data_range
proton_hits = array([[h[0][0], h[0][1], h[0][2]] for h in particle_hits[2212]]) / data_range
residuals_calc = LPCResiduals(muon_hits, tube_radius = 0.12)
residuals_runner = LPCResidualsRunner(curves, residuals_calc)
residuals_runner.setTauRange([tau])
muon_residuals = residuals_runner.calculateResiduals(True, False, False)
muon_coverage = max([len(muon_residuals['curve_residuals'][i]['coverage_indices'][tau]) for i in range(len(curves))])
muon_efficiency = float(muon_coverage) / len(muon_hits)
residuals_calc.setDataPoints(proton_hits)
proton_residuals = residuals_runner.calculateResiduals(True, False, False)
proton_coverage = max([len(proton_residuals['curve_residuals'][i]['coverage_indices'][tau]) for i in range(len(curves))])
proton_efficiency = float(proton_coverage) / len(proton_hits)
print 'residuals'