def find_voids(snapshot, ptypes, grid, MAS, do_RSD, axis, threshold, Radii,
threads1, threads2, fout):
# read snapshot header and obtain BoxSize and redshift
head = readgadget.header(snapshot)
BoxSize = head.boxsize/1e3 #Mpc/h
redshift = head.redshift
# compute density field
delta = MASL.density_field_gadget(snapshot, ptypes, grid, MAS, do_RSD, axis)
delta /= np.mean(delta, dtype=np.float64); delta -= 1.0
# identify voids
V = VL.void_finder(delta, BoxSize, threshold, Radii,
threads1, threads2, void_field=False)
# void properties and void size function
void_pos = V.void_pos
void_radius = V.void_radius
VSF_R = V.Rbins # bins in radius
VSF = V.void_vsf # void size function
parameters = [grid, MAS, '%s'%ptypes, threshold, '%s'%Radii]
# save the results to file
f = h5py.File(fout, 'w')
f.create_dataset('parameters', data=parameters)
f.create_dataset('pos', data=void_pos)
f.create_dataset('radius', data=void_radius)
f.create_dataset('VSF_Rbins', data=VSF_R)
f.create_dataset('VSF', data=VSF)
f.close()
###########################################################################
fig = figure(figsize=(15, 7))
ax1 = fig.add_subplot(121)
ax2 = fig.add_subplot(122)
# create density field with random spheres
V = VL.random_spheres(BoxSize, Rmin, Rmax, Nvoids, dims)
delta = V.delta
# find voids
V2 = VL.void_finder(delta,
BoxSize,
threshold,
Rmax,
Rmin,
bins,
Omega_m,
threads,
void_field=True)
delta2 = V2.in_void
ax1.imshow(np.mean(delta[:, :, :], axis=0),
cmap=get_cmap('nipy_spectral'),
origin='lower',
vmin=-1,
vmax=0.0,
extent=[0, BoxSize, 0, BoxSize])
ax2.imshow(np.mean(delta2[:, :, :], axis=0),
cmap=get_cmap('nipy_spectral_r'),
head = readsnap.snapshot_header(snapshot)
BoxSize = head.boxsize / 1e3 #Mpc/h
Radii = Radii * BoxSize / grid
# read particle positions
pos = readsnap.read_block(snapshot, "POS ", parttype=1) / 1e3 #Mpc/h
# compute density field
delta = np.zeros((grid, grid, grid), dtype=np.float32)
MASL.MA(pos, delta, BoxSize, MAS)
delta /= np.mean(delta, dtype=np.float64)
delta -= 1.0
# find the void
V = VL.void_finder(delta,
BoxSize,
threshold,
Radii,
threads1,
threads2,
void_field=void_field)
# void properties
void_pos = V.void_pos #Mpc/h
void_radius = V.void_radius #Mpc/h
VSF_R = V.Rbins #VSF bins in radius
VSF = V.void_vsf #VSF
if void_field:
void_field = V.void_field #array with 0. Cells belonging to voids have 1
bins = 50 #number of radii between Rmin and Rmax to find voids
threads1 = 16 #openmp threads
threads2 = 4
f_out = 'Spheres_test.png'
###########################################################################
# create density field with random spheres
V = VL.random_spheres(BoxSize, Rmin, Rmax, Nvoids, dims)
delta = V.delta
# find voids
Radii = np.logspace(np.log10(Rmin), np.log10(Rmax), bins+1, dtype=np.float32)
V2 = VL.void_finder(delta, BoxSize, threshold, Radii,
threads1, threads2, void_field=True)
delta2 = V2.in_void
# print the positions and radius of the generated voids
pos1 = V.void_pos
R1 = V.void_radius
pos2 = V2.void_pos
R2 = V2.void_radius
print ' X Y Z R'
for i in xrange(Nvoids):
dx = pos1[i,0]-pos2[:,0]
dx[np.where(dx>BoxSize/2.0)] -= BoxSize
dx[np.where(dx<-BoxSize/2.0)]+= BoxSize