def main():
if MPI.COMM_WORLD.rank == 0:
print 'importing done'
pm = ParticleMesh(ns.BoxSize, ns.Nmesh, dtype='f4')
Ntot = paint_darkmatter(pm, ns.filename, TPMSnapshotFile)
if ns.remove_shotnoise:
shotnoise = pm.BoxSize ** 3 / Ntot
else:
shotnoise = 0
pm.r2c()
if MPI.COMM_WORLD.rank == 0:
print 'r2c done'
k, p = measurepower(pm, pm.complex, ns.binshift, ns.remove_cic, shotnoise)
if MPI.COMM_WORLD.rank == 0:
print 'measure power done'
if pm.comm.rank == 0:
if ns.output != '-':
myout = open(ns.output, 'w')
else:
myout = stdout
numpy.savetxt(myout, zip(k, p), '%0.7g')
myout.flush()
def main():
if MPI.COMM_WORLD.rank == 0:
print 'importing done'
pm = ParticleMesh(ns.BoxSize, ns.Nmesh, dtype='f4')
Ntot = paint_darkmatter(pm, ns.filename, TPMSnapshotFile)
if ns.remove_shotnoise:
shotnoise = pm.BoxSize**3 / Ntot
else:
shotnoise = 0
pm.r2c()
if MPI.COMM_WORLD.rank == 0:
print 'r2c done'
k, p = measurepower(pm, pm.complex, ns.binshift, ns.remove_cic, shotnoise)
if MPI.COMM_WORLD.rank == 0:
print 'measure power done'
if pm.comm.rank == 0:
if ns.output != '-':
myout = open(ns.output, 'w')
else:
myout = stdout
numpy.savetxt(myout, zip(k, p), '%0.7g')
myout.flush()
def do1d(pm, complex, ns, shotnoise):
result = measurepower(pm, complex, ns.binshift, ns.remove_cic, shotnoise)
if MPI.COMM_WORLD.rank == 0:
print 'measure'
if pm.comm.rank == 0:
storage = plugins.PowerSpectrumStorage.get(ns.mode, ns.output)
storage.write(result)
def main():
pm = ParticleMesh(ns.BoxSize, ns.Nmesh, dtype='f4')
if pm.comm.rank == 0:
hf = files.HaloFile(ns.halocatalogue)
nhalo = hf.nhalo
halopos = hf.read_pos()
halopos = pm.comm.bcast(halopos)
else:
halopos = pm.comm.bcast(None)
Ntot = 0
for round, (P, PL) in enumerate(izip(
files.read(pm.comm, ns.filename, files.TPMSnapshotFile,
columns=['Position'], bunchsize=ns.bunchsize),
files.read(pm.comm, ns.halolabel, files.HaloLabelFile,
columns=['Label'], bunchsize=ns.bunchsize),
)):
mask = PL['Label'] != 0
logging.info("Number of particles in halos is %d" % mask.sum())
P['Position'][mask] = halopos[PL['Label'][mask]]
P['Position'] *= ns.BoxSize
layout = pm.decompose(P['Position'])
tpos = layout.exchange(P['Position'])
#print tpos.shape
pm.paint(tpos)
npaint = pm.comm.allreduce(len(tpos), op=MPI.SUM)
nread = pm.comm.allreduce(len(P['Position']), op=MPI.SUM)
if pm.comm.rank == 0:
logging.info('round %d, npaint %d, nread %d' % (round, npaint, nread))
Ntot = Ntot + nread
if ns.remove_shotnoise:
shotnoise = pm.BoxSize ** 3 / Ntot
else:
shotnoise = 0
pm.r2c()
k, p = measurepower(pm, pm.complex, ns.binshift, ns.remove_cic, shotnoise)
if pm.comm.rank == 0:
if ns.output != '-':
myout = open(ns.output, 'w')
else:
myout = stdout
numpy.savetxt(myout, zip(k, p), '%0.7g')
myout.flush()
hf = files.HaloFile(ns.halocatalogue)
mass = hf.read_mass()
M1 = ((mass[1:] * 1.0)** 2).sum(dtype='f8') / (1.0 * Ntot) ** 2 * ns.BoxSize ** 3
logging.info("p[-inf] = %g, M1 = %g" % (p[-1], M1))
def main():
if MPI.COMM_WORLD.rank == 0:
print 'importing done'
pm = ParticleMesh(ns.BoxSize, ns.Nmesh, dtype='f4')
Ntot = paint_darkmatter(pm, ns.filename1, TPMSnapshotFile)
if MPI.COMM_WORLD.rank == 0:
print 'painting done'
pm.r2c()
if MPI.COMM_WORLD.rank == 0:
print 'r2c done'
complex = pm.complex.copy()
numpy.conjugate(complex, out=complex)
Ntot = paint_darkmatter(pm, ns.filename2, TPMSnapshotFile)
if MPI.COMM_WORLD.rank == 0:
print 'painting 2 done'
pm.r2c()
if MPI.COMM_WORLD.rank == 0:
print 'r2c 2 done'
complex *= pm.complex
complex **= 0.5
if MPI.COMM_WORLD.rank == 0:
print 'cross done'
k, p = measurepower(pm, complex, ns.binshift, ns.remove_cic, 0)
if MPI.COMM_WORLD.rank == 0:
print 'measure'
if pm.comm.rank == 0:
if ns.output != '-':
myout = open(ns.output, 'w')
else:
myout = stdout
numpy.savetxt(myout, zip(k, p), '%0.7g')
myout.flush()
def main():
if MPI.COMM_WORLD.rank == 0:
print "importing done"
pm = ParticleMesh(ns.BoxSize, ns.Nmesh, dtype="f4")
Ntot = paint_darkmatter(pm, ns.filename1, TPMSnapshotFile)
if MPI.COMM_WORLD.rank == 0:
print "painting done"
pm.r2c()
if MPI.COMM_WORLD.rank == 0:
print "r2c done"
complex = pm.complex.copy()
numpy.conjugate(complex, out=complex)
Ntot = paint_darkmatter(pm, ns.filename2, TPMSnapshotFile)
if MPI.COMM_WORLD.rank == 0:
print "painting 2 done"
pm.r2c()
if MPI.COMM_WORLD.rank == 0:
print "r2c 2 done"
complex *= pm.complex
complex **= 0.5
if MPI.COMM_WORLD.rank == 0:
print "cross done"
k, p = measurepower(pm, complex, ns.binshift, ns.remove_cic, 0)
if MPI.COMM_WORLD.rank == 0:
print "measure"
if pm.comm.rank == 0:
if ns.output != "-":
myout = open(ns.output, "w")
else:
myout = stdout
numpy.savetxt(myout, zip(k, p), "%0.7g")
myout.flush()
def main():
pm = ParticleMesh(ns.BoxSize, ns.Nmesh)
Ntot = paint_halos(pm, ns.halocatalogue, ns.BoxSize, ns.m0, ns.massmin, ns.massmax)
if ns.remove_shotnoise:
shotnoise = pm.BoxSize ** 3 / Ntot
else:
shotnoise = 0
pm.r2c()
k, p = measurepower(pm, pm.complex, ns.binshift, ns.remove_cic, shotnoise)
if pm.comm.rank == 0:
if ns.output != '-':
myout = open(ns.output, 'w')
else:
myout = stdout
numpy.savetxt(myout, zip(k, p), '%0.7g')
myout.flush()
def main():
pm = ParticleMesh(ns.BoxSize, ns.Nmesh)
Ntot = paint_halos(pm, ns.halocatalogue, ns.BoxSize, ns.m0, ns.massmin,
ns.massmax)
if ns.remove_shotnoise:
shotnoise = pm.BoxSize**3 / Ntot
else:
shotnoise = 0
pm.r2c()
k, p = measurepower(pm, pm.complex, ns.binshift, ns.remove_cic, shotnoise)
if pm.comm.rank == 0:
if ns.output != '-':
myout = open(ns.output, 'w')
else:
myout = stdout
numpy.savetxt(myout, zip(k, p), '%0.7g')
myout.flush()
def main():
if MPI.COMM_WORLD.rank == 0:
print 'importing done'
chain = [
TransferFunction.NormalizeDC,
TransferFunction.RemoveDC,
TransferFunction.Gaussian(1),
]
if ns.remove_cic == 'anisotropic':
chain.append(AnisotropicCIC)
if ns.remove_cic == 'isotropic':
chain.append(IsotropicCIC)
# setup the particle mesh object
pm = ParticleMesh(ns.BoxSize, ns.Nmesh, dtype='f4')
# paint first input
Ntot1 = ns.inputs[0].paint(ns, pm)
r1 = pm.real.copy()
# painting
if MPI.COMM_WORLD.rank == 0:
print 'painting done'
pm.r2c()
if MPI.COMM_WORLD.rank == 0:
print 'r2c done'
# filter the field
pm.transfer(chain)
# do the cross power
do_cross = len(ns.inputs) > 1
if do_cross:
c1 = pm.complex.copy()
Ntot2 = ns.inputs[1].paint(ns, pm)
if MPI.COMM_WORLD.rank == 0:
print 'painting 2 done'
pm.r2c()
if MPI.COMM_WORLD.rank == 0:
print 'r2c 2 done'
# filter the field
pm.transfer(chain)
c2 = pm.complex.copy()
if MPI.COMM_WORLD.rank == 0:
print 'convolution done'
dot(pm, c2, c2)
c2 = pm.complex
# do the auto power
else:
c1 = pm.complex
c2 = pm.complex
Ntot2 = Ntot1
if ns.remove_shotnoise and not do_cross:
shotnoise = pm.BoxSize ** 3 / (1.0*Ntot1)
else:
shotnoise = 0
# only need one mu bin if 1d case is requested
if ns.mode == "1d": ns.Nmu = 1
# do the calculation
meta = {'box_size':pm.BoxSize, 'N1':Ntot1,
'N2':Ntot2, 'shot_noise': shotnoise}
result = measurepower(pm, c1, c2, ns.Nmu, binshift=ns.binshift,
shotnoise=shotnoise, los=ns.los)
# format the output appropriately
if ns.mode == "1d":
# this writes out 0 -> mean k, 2 -> mean power, 3 -> number of modes
meta['edges'] = result[-1][0] # write out kedges as metadata
result = map(numpy.ravel, (result[i] for i in [0, 2, 3]))
elif ns.mode == "2d":
result = dict(zip(['k','mu','power','modes','edges'], result))
if MPI.COMM_WORLD.rank == 0:
print 'measure'
storage = plugins.PowerSpectrumStorage.get(ns.mode, ns.output)
storage.write(result, **meta)
def main():
pm = ParticleMesh(ns.BoxSize, ns.Nmesh, dtype='f4')
if pm.comm.rank == 0:
hf = files.HaloFile(ns.halocatalogue)
nhalo = hf.nhalo
halopos = hf.read_pos()
halopos = pm.comm.bcast(halopos)
else:
halopos = pm.comm.bcast(None)
Ntot = 0
for round, (P, PL) in enumerate(
izip(
files.read(pm.comm,
ns.filename,
files.TPMSnapshotFile,
columns=['Position'],
bunchsize=ns.bunchsize),
files.read(pm.comm,
ns.halolabel,
files.HaloLabelFile,
columns=['Label'],
bunchsize=ns.bunchsize),
)):
mask = PL['Label'] != 0
logging.info("Number of particles in halos is %d" % mask.sum())
P['Position'][mask] = halopos[PL['Label'][mask]]
P['Position'] *= ns.BoxSize
layout = pm.decompose(P['Position'])
tpos = layout.exchange(P['Position'])
#print tpos.shape
pm.paint(tpos)
npaint = pm.comm.allreduce(len(tpos), op=MPI.SUM)
nread = pm.comm.allreduce(len(P['Position']), op=MPI.SUM)
if pm.comm.rank == 0:
logging.info('round %d, npaint %d, nread %d' %
(round, npaint, nread))
Ntot = Ntot + nread
if ns.remove_shotnoise:
shotnoise = pm.BoxSize**3 / Ntot
else:
shotnoise = 0
pm.r2c()
k, p = measurepower(pm, pm.complex, ns.binshift, ns.remove_cic, shotnoise)
if pm.comm.rank == 0:
if ns.output != '-':
myout = open(ns.output, 'w')
else:
myout = stdout
numpy.savetxt(myout, zip(k, p), '%0.7g')
myout.flush()
hf = files.HaloFile(ns.halocatalogue)
mass = hf.read_mass()
M1 = ((mass[1:] * 1.0)**
2).sum(dtype='f8') / (1.0 * Ntot)**2 * ns.BoxSize**3
logging.info("p[-inf] = %g, M1 = %g" % (p[-1], M1))
def compute_power(ns, comm=None):
"""
Compute the power spectrum. Given a `Namespace`, this is the function,
that computes and saves the power spectrum. It does all the work.
Parameters
----------
ns : argparse.Namespace
the parser namespace corresponding to the ``initialize_power_parser``
functions
comm : MPI.Communicator
the communicator to pass to the ``ParticleMesh`` object
"""
rank = comm.rank if comm is not None else MPI.COMM_WORLD.rank
# set logging level
logger.setLevel(ns.log_level)
if rank == 0:
logger.info('importing done')
chain = [TransferFunction.NormalizeDC, TransferFunction.RemoveDC]
if ns.remove_cic == 'anisotropic':
chain.append(AnisotropicCIC)
if ns.remove_cic == 'isotropic':
chain.append(IsotropicCIC)
# setup the particle mesh object, taking BoxSize from the painters
pm = ParticleMesh(ns.inputs[0].BoxSize, ns.Nmesh, dtype='f4', comm=comm)
# paint first input
Ntot1 = paint(ns.inputs[0], pm, ns)
# painting
if rank == 0:
logger.info('painting done')
pm.r2c()
if rank == 0:
logger.info('r2c done')
# filter the field
pm.transfer(chain)
# do the cross power
do_cross = len(ns.inputs) > 1 and ns.inputs[0] != ns.inputs[1]
if do_cross:
# crash if box size isn't the same
if not numpy.all(ns.inputs[0].BoxSize == ns.inputs[1].BoxSize):
raise ValueError("mismatch in box sizes for cross power measurement")
c1 = pm.complex.copy()
Ntot2 = paint(ns.inputs[1], pm, ns)
if rank == 0:
logger.info('painting 2 done')
pm.r2c()
if rank == 0:
logger.info('r2c 2 done')
# filter the field
pm.transfer(chain)
c2 = pm.complex
# do the auto power
else:
c1 = pm.complex
c2 = pm.complex
Ntot2 = Ntot1
if ns.remove_shotnoise and not do_cross:
shotnoise = pm.BoxSize.prod() / (1.0*Ntot1)
else:
shotnoise = 0
# only need one mu bin if 1d case is requested
if ns.mode == "1d": ns.Nmu = 1
# do the calculation
Lx, Ly, Lz = pm.BoxSize
meta = {'Lx':Lx, 'Ly':Ly, 'Lz':Lz, 'volume':Lx*Ly*Lz,
'N1':Ntot1, 'N2':Ntot2, 'shot_noise': shotnoise}
result = measurepower(pm, c1, c2, ns.Nmu, binshift=ns.binshift,
shotnoise=shotnoise, los=ns.los, dk=ns.dk,
kmin=ns.kmin, poles=ns.poles)
# format the output appropriately
if len(ns.poles):
pole_result, pkmu_result, edges = result
result = dict(zip(['k','mu','power','modes','edges'], pkmu_result+(edges,)))
elif ns.mode == "1d":
# this writes out 0 -> mean k, 2 -> mean power, 3 -> number of modes
meta['edges'] = result[-1][0] # write out kedges as metadata
result = map(numpy.ravel, (result[i] for i in [0, 2, 3]))
elif ns.mode == "2d":
result = dict(zip(['k','mu','power','modes','edges'], result))
if rank == 0:
# save the power
logger.info('measurement done; saving power to %s' %ns.output)
storage = plugins.PowerSpectrumStorage.new(ns.mode, ns.output)
storage.write(result, **meta)
# save the multipoles
if len(ns.poles):
if ns.pole_output is None:
raise RuntimeError("you specified multipoles to compute, but did not provide an output file name")
meta['edges'] = edges[0]
# format is k pole_0, pole_1, ...., modes_1d
logger.info('saving ell = %s multipoles to %s' %(",".join(map(str,ns.poles)), ns.pole_output))
result = [x for x in numpy.vstack(pole_result)]
storage = plugins.PowerSpectrumStorage.new('1d', ns.pole_output)
storage.write(result, **meta)