def map_kSZ_intensity(num_halo, redshift, simulation_type, nbins, rfov):
# Import data
path = extract.path_from_cluster_name(num_halo,
simulation_type=simulation_type)
file = extract.file_name_hdf5(
subject='groups', redshift=extract.redshift_floatTostr(redshift))
r200 = extract.group_r200(path, file)
print(r200)
group_CoP = extract.group_centre_of_potential(path, file)
file = extract.file_name_hdf5(
subject='particledata', redshift=extract.redshift_floatTostr(redshift))
# Gas particles
part_type = extract.particle_type('gas')
mass = extract.particle_masses(path, file, part_type)
coordinates = extract.particle_coordinates(path, file, part_type)
velocities = extract.particle_velocity(path, file, part_type)
temperatures = extract.particle_temperature(path, file, part_type)
group_number = extract.group_number(path, file, part_type)
subgroup_number = extract.subgroup_number(path, file, part_type)
tot_rest_frame, _ = profile.total_mass_rest_frame(path, file)
#gas_rest_frame, _ = profile.cluster_average_momentum(path, file, part_type)
# Retrieve coordinates & velocities
x = coordinates[:, 0] - group_CoP[0]
y = coordinates[:, 1] - group_CoP[1]
z = coordinates[:, 2] - group_CoP[2]
vx = velocities[:, 0] - tot_rest_frame[0]
vy = velocities[:, 1] - tot_rest_frame[1]
vz = velocities[:, 2] - tot_rest_frame[2]
h = extract.file_hubble_param(path, file)
# Rescale to comoving coordinates
x = profile.comoving_length(x, h, redshift)
y = profile.comoving_length(y, h, redshift)
z = profile.comoving_length(z, h, redshift)
r200 = profile.comoving_length(r200, h, redshift)
vx = profile.comoving_velocity(vx, h, redshift)
vy = profile.comoving_velocity(vy, h, redshift)
vz = profile.comoving_velocity(vz, h, redshift)
vx = profile.velocity_units(vx, unit_system='astro')
vy = profile.velocity_units(vy, unit_system='astro')
vz = profile.velocity_units(vz, unit_system='astro')
mass = profile.comoving_mass(mass, h, redshift)
mass = profile.mass_units(mass, unit_system='astro')
T = temperatures
# Compute radial distance
r = np.sqrt(x**2 + y**2 + z**2)
# Particle selection
index = np.where((r < 5 * r200) & (group_number > -1)
& (subgroup_number > -1) & (T > 10**5))[0]
mass, T = mass[index], T[index]
x, y, z = x[index], y[index], z[index]
vx, vy, vz = vx[index], vy[index], vz[index]
# Generate plot
plotpar.set_defaults_plot()
fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(20, 9))
# Convert to angular distances
#cosmo = {'omega_M_0' : 0.307, 'omega_lambda_0' : 0.693, 'h' : 0.6777}
#cosmo = cosmolopy.set_omega_k_0(cosmo)
redshift = extract.file_redshift(path, file)
#angular_distance = cosmolopy.angular_diameter_distance(redshift, z0 = 0, **cosmo)
cosmo = FlatLambdaCDM(H0=70, Om0=0.3)
angular_distance = cosmo.luminosity_distance(redshift)
print("angular_diameter_distance: ", angular_distance)
Mpc_to_arcmin = np.power(
np.pi, -1) * 180 * 60 / angular_distance * astropy.units.Mpc
x = x * Mpc_to_arcmin
y = y * Mpc_to_arcmin
z = z * Mpc_to_arcmin
r200 = r200 * Mpc_to_arcmin
# Bin data
cmap = [
plt.get_cmap('seismic'),
plt.get_cmap('seismic'),
plt.get_cmap('seismic_r')
]
#cmap = [mapgen.modified_spectral_cmap(Reversed = True), mapgen.modified_spectral_cmap(Reversed = True), mapgen.modified_spectral_cmap(Reversed = False)]
xlabel = [
r'$x\mathrm{/arcmin}$', r'$y\mathrm{/arcmin}$', r'$x\mathrm{/arcmin}$'
]
ylabel = [
r'$y\mathrm{/arcmin}$', r'$z\mathrm{/arcmin}$', r'$z\mathrm{/arcmin}$'
]
thirdAX = [r'$\bigotimes z$', r'$\bigotimes x$', r'$\bigodot y$']
cbarlabel = [
r'$\sum_{i} m_i v_{z, i}\ [\mathrm{M_\odot\ km\ s^{-1}}]$',
r'$\sum_{i} m_i v_{x, i}\ [\mathrm{M_\odot\ km\ s^{-1}}]$',
r'$\sum_{i} m_i v_{y, i}\ [\mathrm{M_\odot\ km\ s^{-1}}]$'
]
for i in [0, 1, 2]:
# Handle data
if i == 0:
x_Data = x
y_Data = y
weight = vz
elif i == 1:
x_Data = y
y_Data = z
weight = vx
elif i == 2:
x_Data = x
y_Data = z
weight = vy
x_bins = np.linspace(-rfov * r200, rfov * r200, nbins)
y_bins = np.linspace(-rfov * r200, rfov * r200, nbins)
Cx, Cy = mapgen.bins_meshify(x_Data, y_Data, x_bins, y_bins)
# line of sight momentum weights
count = mapgen.bins_evaluate(x_Data,
y_Data,
x_bins,
y_bins,
weights=mass * weight)
# convolution
kernel, _ = kernconv.nika2_kernel(x_bins, y_bins)
kernel = np.array(kernel)
kSZmap = convolve(count, kernel)
norm = mapgen.MidpointNormalize(vmin=kSZmap.min(),
vmax=kSZmap.max(),
midpoint=0)
img = axes[i].pcolor(Cx, Cy, kSZmap, cmap=cmap[i], norm=norm)
# Render elements in plots
axes[i].set_title(r'$\mathrm{MACSIS\ halo\ } %3d \qquad z = %8.3f$' %
(num_halo, redshift),
pad=94)
axes[i].set_aspect('equal')
axes[i].add_artist(
Circle((0, 0),
radius=r200,
color='black',
fill=False,
linestyle='--',
label=r'$R_{200}$'))
axes[i].add_artist(
Circle((0, 0),
radius=5 * r200,
color='black',
fill=False,
linewidth=0.5,
linestyle='-',
label=r'$R_{200}$'))
axes[i].set_xlim(-rfov * r200, rfov * r200)
axes[i].set_ylim(-rfov * r200, rfov * r200)
axes[i].set_xlabel(xlabel[i])
axes[i].set_ylabel(ylabel[i])
axes[i].annotate(thirdAX[i], (0.03, 0.03),
textcoords='axes fraction',
size=15)
#if title:
# axes[i].set_title(r'$\mathrm{MACSIS\ halo\ } %3d \qquad z = %8.3f$' % (num_halo, redshift))
# Colorbar adjustments
ax2_divider = make_axes_locatable(axes[i])
cax2 = ax2_divider.append_axes("top", size="5%", pad="2%")
cbar = plt.colorbar(img, cax=cax2, orientation='horizontal')
cbar.set_label(cbarlabel[i], labelpad=-70)
#cax2.xaxis.set_tick_labels(['0',' ','0.5',' ','1',' ', '1.5',' ','2'])
cax2.xaxis.set_ticks_position("top")
print("run completed:", i)
#outfilename = 'parallel-out//I_kSZ_halo' + str(num_halo) +'_z016_' + str(nbins) + 'bins_' + str(rfov) + 'rfov.pdf'
#plt.savefig(outfilename)
plt.show()
def map_particles(num_halo, redshift, simulation_type = 'gas', output = 'show', title = True, save_name = 'Map_particles_gas', nbins = 400):
# Import data
path = extract.path_from_cluster_name(num_halo, simulation_type = simulation_type)
file = extract.file_name_hdf5(subject = 'groups', redshift = extract.redshift_floatTostr(redshift))
r200 = extract.group_r200(path, file)
group_CoP = extract.group_centre_of_potential(path, file)
file = extract.file_name_hdf5(subject = 'particledata', redshift = extract.redshift_floatTostr(redshift))
#print(r200)
h = extract.file_hubble_param(path, file)
# Gas particles
part_type = extract.particle_type('gas')
mass = extract.particle_masses(path, file, part_type)
coordinates = extract.particle_coordinates(path, file, part_type)
velocities = extract.particle_velocity(path, file, part_type)
group_number = extract.group_number(path, file, part_type)
subgroup_number = extract.subgroup_number(path, file, part_type)
tot_rest_frame, _ = profile.total_mass_rest_frame(path, file)
#gas_rest_frame, _ = profile.cluster_average_momentum(path, file, part_type)
# Retrieve coordinates & velocities
x = coordinates[:,0] - group_CoP[0]
y = coordinates[:,1] - group_CoP[1]
z = coordinates[:,2] - group_CoP[2]
vx = velocities[:,0] - tot_rest_frame[0]
vy = velocities[:,1] - tot_rest_frame[1]
vz = velocities[:,2] - tot_rest_frame[2]
# Rescale to comoving coordinates
x = profile.comoving_length(x, h, redshift)
y = profile.comoving_length(y, h, redshift)
z = profile.comoving_length(z, h, redshift)
r200 = profile.comoving_length(r200, h, redshift)
vx = profile.comoving_velocity(vx, h, redshift)
vy = profile.comoving_velocity(vy, h, redshift)
vz = profile.comoving_velocity(vz, h, redshift)
vx = profile.velocity_units(vx, unit_system = 'astro')
vy = profile.velocity_units(vy, unit_system = 'astro')
vz = profile.velocity_units(vz, unit_system = 'astro')
mass = profile.comoving_mass(mass, h, redshift)
mass = profile.mass_units(mass, unit_system = 'astro')
# Compute radial distance
r = np.sqrt(x**2+y**2+z**2)
# Select particles within 5*r200
index = np.where((r < 5*r200) & (group_number > -1) & (subgroup_number > -1))[0]
mass = mass[index]
x, y, z = x[index], y[index], z[index]
vx, vy, vz = vx[index], vy[index], vz[index]
# Generate plot
plotpar.set_defaults_plot()
fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(20, 7))
# Bin data
#nbins = 250
cmap = 'terrain_r'
################################################################################################
x_Data = x
y_Data = y
x_bins = np.linspace(np.min(x_Data), np.max(x_Data), nbins)
y_bins = np.linspace(np.min(y_Data), np.max(y_Data), nbins)
Cx, Cy = mapgen.bins_meshify(x_Data, y_Data, x_bins, y_bins)
count = mapgen.bins_evaluate(x_Data, y_Data, x_bins, y_bins, weights = None)
img = axes[0].pcolor(Cx, Cy, np.log10(count), cmap=cmap)
axes[0].set_xlabel(r'$x\mathrm{/Mpc}$')
axes[0].set_ylabel(r'$y\mathrm{/Mpc}$')
axes[0].annotate(r'$\bigotimes z$', (0.03, 0.03), textcoords='axes fraction', size = 15)
# Colorbar adjustments
ax2_divider = make_axes_locatable(axes[0])
cax2 = ax2_divider.append_axes("right", size="3%", pad="2%")
cbar = plt.colorbar(img, cax=cax2, orientation='vertical')
#cbar.set_label(r'$\log_{10}(N_{particles})$', labelpad=17)
#cax2.xaxis.set_tick_labels(['0',' ','0.5',' ','1',' ', '1.5',' ','2'])
cax2.xaxis.set_ticks_position("top")
x_Data = y
y_Data = z
x_bins = np.linspace(np.min(x_Data), np.max(x_Data), nbins)
y_bins = np.linspace(np.min(y_Data), np.max(y_Data), nbins)
Cx, Cy = mapgen.bins_meshify(x_Data, y_Data, x_bins, y_bins)
count = mapgen.bins_evaluate(x_Data, y_Data, x_bins, y_bins, weights = None)
img = axes[1].pcolor(Cx, Cy, np.log10(count), cmap=cmap)
axes[1].set_xlabel(r'$y\mathrm{/Mpc}$')
axes[1].set_ylabel(r'$z\mathrm{/Mpc}$')
axes[1].annotate(r'$\bigotimes x$', (0.03, 0.03), textcoords='axes fraction', size = 15)
# Colorbar adjustments
ax2_divider = make_axes_locatable(axes[1])
cax2 = ax2_divider.append_axes("right", size="3%", pad="2%")
cbar = plt.colorbar(img, cax=cax2, orientation='vertical')
#cbar.set_label(r'$\log_{10}(N_{particles})$', labelpad=17)
#cax2.xaxis.set_tick_labels(['0',' ','0.5',' ','1',' ', '1.5',' ','2'])
cax2.xaxis.set_ticks_position("top")
x_Data = x
y_Data = z
x_bins = np.linspace(np.min(x_Data), np.max(x_Data), nbins)
y_bins = np.linspace(np.min(y_Data), np.max(y_Data), nbins)
Cx, Cy = mapgen.bins_meshify(x_Data, y_Data, x_bins, y_bins)
count = mapgen.bins_evaluate(x_Data, y_Data, x_bins, y_bins, weights = None)
img = axes[2].pcolor(Cx, Cy, np.log10(count), cmap=cmap)
axes[2].set_xlabel(r'$x\mathrm{/Mpc}$')
axes[2].set_ylabel(r'$z\mathrm{/Mpc}$')
axes[2].annotate(r'$\bigodot y$', (0.03, 0.03), textcoords='axes fraction', size = 15)
# Colorbar adjustments
ax2_divider = make_axes_locatable(axes[2])
cax2 = ax2_divider.append_axes("right", size="3%", pad="2%")
cbar = plt.colorbar(img, cax=cax2, orientation='vertical')
cbar.set_label(r'$\log_{10}(N_{particles})$', labelpad=17)
#cax2.xaxis.set_tick_labels(['0',' ','0.5',' ','1',' ', '1.5',' ','2'])
cax2.xaxis.set_ticks_position("top")
################################################################################################
# Plot r200 circle
for i in [0,1,2]:
axes[i].set_aspect('equal')
axes[i].add_artist(Circle((0,0), radius=r200, color = 'red', fill = False, linestyle = '--', label = r'$R_{200}$'))
axes[i].add_artist(Circle((0,0), radius=5*r200, color = 'black', fill = False, linewidth = 0.5,linestyle = '-', label = r'$R_{200}$'))
axes[i].set_xlim(-5.1*r200, 5.1*r200)
axes[i].set_ylim(-5.1*r200, 5.1*r200)
if title:
axes[i].set_title(r'$\mathrm{MACSIS\ halo\ } %3d \qquad z = %8.3f$' % (num_halo, redshift))
# Define output
if output == 'show':
plt.show()
elif output == 'save':
dir_name = 'Map particles'
if not exists(dir_name):
makedirs(dir_name)
plt.savefig(dir_name + '//'+save_name+'_partType'+part_type+'_halo'+str(num_halo)+'z'+str(redshift).replace(".", "")+'.pdf')
else:
print("[ERROR] The output type you are trying to select is not defined.")
exit(1)
def render_tSZ(axes,
num_halo,
redshift,
simulation_type,
projection=0,
nbins=100,
rfov=5,
cbar_color='inferno'):
# Import data
path = extract.path_from_cluster_name(num_halo,
simulation_type=simulation_type)
file = extract.file_name_hdf5(
subject='groups', redshift=extract.redshift_floatTostr(redshift))
r200 = extract.group_r200(path, file)
group_CoP = extract.group_centre_of_potential(path, file)
# Gas particles
file = extract.file_name_hdf5(
subject='particledata', redshift=extract.redshift_floatTostr(redshift))
part_type = extract.particle_type('gas')
mass = extract.particle_masses(path, file, part_type)
coordinates = extract.particle_coordinates(path, file, part_type)
velocities = extract.particle_velocity(path, file, part_type)
temperatures = extract.particle_temperature(path, file, part_type)
group_number = extract.group_number(path, file, part_type)
subgroup_number = extract.subgroup_number(path, file, part_type)
tot_rest_frame, _ = profile.total_mass_rest_frame(path, file)
# gas_rest_frame, _ = profile.cluster_average_momentum(path, file, part_type)
# Retrieve coordinates & velocities
x = coordinates[:, 0] - group_CoP[0]
y = coordinates[:, 1] - group_CoP[1]
z = coordinates[:, 2] - group_CoP[2]
vx = velocities[:, 0] - tot_rest_frame[0]
vy = velocities[:, 1] - tot_rest_frame[1]
vz = velocities[:, 2] - tot_rest_frame[2]
# Rescale to comoving coordinates
h = extract.file_hubble_param(path, file)
redshift = extract.file_redshift(path, file)
x = profile.comoving_length(x, h, redshift)
y = profile.comoving_length(y, h, redshift)
z = profile.comoving_length(z, h, redshift)
r200 = profile.comoving_length(r200, h, redshift)
vx = profile.comoving_velocity(vx, h, redshift)
vy = profile.comoving_velocity(vy, h, redshift)
vz = profile.comoving_velocity(vz, h, redshift)
vx = profile.velocity_units(vx, unit_system='SI')
vy = profile.velocity_units(vy, unit_system='SI')
vz = profile.velocity_units(vz, unit_system='SI')
mass = profile.comoving_mass(mass, h, redshift)
mass = profile.mass_units(mass, unit_system='SI')
T = temperatures
# Compute radial distance
r = np.sqrt(x**2 + y**2 + z**2)
# Particle selection
min_gn = 0
min_sgn = 0
min_T = 10**5
max_r = 5
index = np.where((r < max_r * r200) & (group_number >= min_gn)
& (subgroup_number >= min_sgn) & (T > min_T))[0]
mass, T = mass[index], T[index]
x, y, z = x[index], y[index], z[index]
vx, vy, vz = vx[index], vy[index], vz[index]
# Convert to angular distances
angular_distance = cosmo.angular_diameter_D(redshift)
Mpc_to_arcmin = np.power(np.pi, -1) * 180 * 60 / angular_distance
x = x * Mpc_to_arcmin
y = y * Mpc_to_arcmin
z = z * Mpc_to_arcmin
r200 = r200 * Mpc_to_arcmin
cmap = [cbar_color, cbar_color, cbar_color]
xlabel = [
r'$x\mathrm{/arcmin}$', r'$y\mathrm{/arcmin}$', r'$x\mathrm{/arcmin}$'
]
ylabel = [
r'$y\mathrm{/arcmin}$', r'$z\mathrm{/arcmin}$', r'$z\mathrm{/arcmin}$'
]
thirdAX = [r'$\bigotimes z$', r'$\bigotimes x$', r'$\bigodot y$']
cbarlabel = [r'$y_{tSZ}$', r'$y_{tSZ}$', r'$y_{tSZ}$']
# Compute angular bins
x_bins = np.linspace(-rfov * r200, rfov * r200, nbins)
y_bins = np.linspace(-rfov * r200, rfov * r200, nbins)
m_H = 1.6737236 * 10**(-27) # Hydrogen atom mass in kg
A_pix = (x_bins[1] - x_bins[0]) * (y_bins[1] - y_bins[0]) * (
3.0856776 * 10**22 / Mpc_to_arcmin)**2
tSZconst = sigma_T.value * k_B.value / (m_e.value * c.value**2 * m_H *
1.16)
# Set up index permutations
ijk = np.asarray([[0, 1, 2], [1, 2, 0], [0, 2, 1]])
# Set up vectors
pp_xyz = np.asarray([x, y, z])
# Prepare Kernel
kernel_Type = 'gauss'
kernel, fwhm = kernconv.nika2_kernel(x_bins,
y_bins,
kernel_Type=kernel_Type)
kernel = np.array(kernel)
# mass
mass = mass.astype(np.longdouble)
# Histogram calculation
Cx, Cy = mapgen.bins_meshify(pp_xyz[ijk[projection][0]],
pp_xyz[ijk[projection][1]], x_bins, y_bins)
weight = T.astype(np.longdouble)
# Histogram calculation
count_mT = mapgen.bins_evaluate(pp_xyz[ijk[projection][0]],
pp_xyz[ijk[projection][1]],
x_bins,
y_bins,
weights=mass * weight)
# Compute tSZ
tSZ = count_mT * tSZconst / A_pix
# Convolution
tSZmap = convolve(tSZ, kernel)
tSZmap[tSZmap == 0] = 10**-10
if axes is None:
return tSZmap
# Logarithmic normalization
tSZnorm = colors.LogNorm(vmin=10**-10, vmax=10**-3)
# Plot image
img = axes.pcolor(Cx, Cy, tSZmap, cmap=cmap[projection], norm=tSZnorm)
# Render elements in plots
axes.set_aspect('equal')
axes.add_artist(
Circle((0, 0),
radius=r200,
color='black',
fill=False,
linestyle='--',
label=r'$R_{200}$'))
axes.add_artist(
Circle((0, 0),
radius=5 * r200,
color='white',
fill=False,
linewidth=0.5,
linestyle='-',
label=r'$R_{200}$'))
axes.set_xlim(-rfov * r200, rfov * r200)
axes.set_ylim(-rfov * r200, rfov * r200)
axes.set_xlabel(xlabel[projection])
axes.set_ylabel(ylabel[projection])
axes.annotate(thirdAX[projection], (0.03, 0.03),
textcoords='axes fraction',
size=15,
color='w')
# Colorbar adjustments
ax2_divider = make_axes_locatable(axes)
cax2 = ax2_divider.append_axes("top", size="5%", pad="2%")
cbar = plt.colorbar(img, cax=cax2, orientation='horizontal')
cbar.set_label(cbarlabel[projection], labelpad=-70)
cax2.xaxis.set_ticks_position("top")
return tSZmap
def map_weighted_velocity(num_halo,
redshift,
simulation_type='gas',
output='show',
title=True,
save_name='Map_particles_gas',
plot_groups='FoF',
nbins=400):
# Import data
path = extract.path_from_cluster_name(num_halo,
simulation_type=simulation_type)
file = extract.file_name_hdf5(
subject='groups', redshift=extract.redshift_floatTostr(redshift))
r200 = extract.group_r200(path, file)
group_CoP = extract.group_centre_of_potential(path, file)
file = extract.file_name_hdf5(
subject='particledata', redshift=extract.redshift_floatTostr(redshift))
# Gas particles
part_type = extract.particle_type('gas')
mass = extract.particle_masses(path, file, part_type)
coordinates = extract.particle_coordinates(path, file, part_type)
velocities = extract.particle_velocity(path, file, part_type)
group_number = extract.group_number(path, file, part_type)
subgroup_number = extract.subgroup_number(path, file, part_type)
tot_rest_frame, _ = profile.total_mass_rest_frame(path, file)
#gas_rest_frame, _ = profile.cluster_average_momentum(path, file, part_type)
h = extract.file_hubble_param(path, file)
# Retrieve coordinates & velocities
x = coordinates[:, 0] - group_CoP[0]
y = coordinates[:, 1] - group_CoP[1]
z = coordinates[:, 2] - group_CoP[2]
vx = velocities[:, 0] - tot_rest_frame[0]
vy = velocities[:, 1] - tot_rest_frame[1]
vz = velocities[:, 2] - tot_rest_frame[2]
# Rescale to comoving coordinates
x = profile.comoving_length(x, h, redshift)
y = profile.comoving_length(y, h, redshift)
z = profile.comoving_length(z, h, redshift)
r200 = profile.comoving_length(r200, h, redshift)
vx = profile.comoving_velocity(vx, h, redshift)
vy = profile.comoving_velocity(vy, h, redshift)
vz = profile.comoving_velocity(vz, h, redshift)
vx = profile.velocity_units(vx, unit_system='astro')
vy = profile.velocity_units(vy, unit_system='astro')
vz = profile.velocity_units(vz, unit_system='astro')
mass = profile.comoving_mass(mass, h, redshift)
mass = profile.mass_units(mass, unit_system='astro')
# Compute radial distance
r = np.sqrt(x**2 + y**2 + z**2)
# Select particles within 5*r200
if plot_groups == 'FoF':
index = np.where((r < 5 * r200) & (group_number > -1)
& (subgroup_number > -1))[0]
elif plot_groups == 'subgroups':
index = np.where((r < 5 * r200) & (group_number > -1)
& (subgroup_number > 0))[0]
else:
print(
"[ERROR] The (sub)groups you are trying to plot are not defined.")
exit(1)
mass = mass[index]
x, y, z = x[index], y[index], z[index]
vx, vy, vz = vx[index], vy[index], vz[index]
# Generate plot
plotpar.set_defaults_plot()
fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(20, 7))
# Bin data
#nbins = 800
cmap = mapgen.modified_spectral_cmap(Reversed=True)
xlabel = [r'$x\mathrm{/Mpc}$', r'$y\mathrm{/Mpc}$', r'$x\mathrm{/Mpc}$']
ylabel = [r'$y\mathrm{/Mpc}$', r'$z\mathrm{/Mpc}$', r'$z\mathrm{/Mpc}$']
thirdAX = [r'$\bigotimes z$', r'$\bigotimes x$', r'$\bigodot y$']
cbarlabel = [
r'$\sum_{i} m_i v_{z, i} / \sum_{i} m_i \ [\mathrm{km\ s^{-1}}]$',
r'$\sum_{i} m_i v_{x, i} / \sum_{i} m_i \ [\mathrm{km\ s^{-1}}]$',
r'$\sum_{i} m_i v_{y, i} / \sum_{i} m_i \ [\mathrm{km\ s^{-1}}]$'
]
for i in [0, 1, 2]:
# Handle data
if i == 0:
x_Data = x
y_Data = y
weight = vz
elif i == 1:
x_Data = y
y_Data = z
weight = vx
elif i == 2:
x_Data = x
y_Data = z
weight = vy
cmap = mapgen.modified_spectral_cmap(Reversed=False)
x_bins = np.linspace(np.min(x_Data), np.max(x_Data), nbins)
y_bins = np.linspace(np.min(y_Data), np.max(y_Data), nbins)
Cx, Cy = mapgen.bins_meshify(x_Data, y_Data, x_bins, y_bins)
# line of sight momentum weights
count_mv = mapgen.bins_evaluate(x_Data,
y_Data,
x_bins,
y_bins,
weights=mass * weight)
# mass weights
count_m = mapgen.bins_evaluate(x_Data,
y_Data,
x_bins,
y_bins,
weights=mass)
# average mass weighted velocity
count_m[count_m == 0] = 1
count = np.divide(count_mv, count_m)
norm = mapgen.MidpointNormalize(vmin=count.min(),
vmax=count.max(),
midpoint=0)
img = axes[i].pcolor(Cx, Cy, count, cmap=cmap, norm=norm)
# Render elements in plots
axes[i].set_aspect('equal')
axes[i].add_artist(
Circle((0, 0),
radius=r200,
color='black',
fill=False,
linestyle='--',
label=r'$R_{200}$'))
axes[i].add_artist(
Circle((0, 0),
radius=5 * r200,
color='black',
fill=False,
linewidth=0.5,
linestyle='-',
label=r'$R_{200}$'))
axes[i].set_xlim(-5.1 * r200, 5.1 * r200)
axes[i].set_ylim(-5.1 * r200, 5.1 * r200)
axes[i].set_xlabel(xlabel[i])
axes[i].set_ylabel(ylabel[i])
axes[i].annotate(thirdAX[i], (0.03, 0.03),
textcoords='axes fraction',
size=15)
if title:
axes[i].set_title(
r'$\mathrm{MACSIS\ halo\ } %3d \qquad z = %8.3f$' %
(num_halo, redshift))
# Colorbar adjustments
ax2_divider = make_axes_locatable(axes[i])
cax2 = ax2_divider.append_axes("right", size="3%", pad="2%")
cbar = plt.colorbar(img, cax=cax2, orientation='vertical')
cbar.set_label(cbarlabel[i], labelpad=17)
#cax2.xaxis.set_tick_labels(['0',' ','0.5',' ','1',' ', '1.5',' ','2'])
cax2.xaxis.set_ticks_position("top")
# Define output
if output == 'show':
plt.show()
elif output == 'save':
dir_name = 'Map mass weighted velocity'
if not exists(dir_name):
makedirs(dir_name)
plt.savefig(dir_name + '//' + save_name + '_partType' + part_type +
'_halo' + str(num_halo) + 'z' +
str(redshift).replace(".", "") + '.pdf')
else:
print(
"[ERROR] The output type you are trying to select is not defined.")
exit(1)
def phase_diagram_master(redshift,
nbins=500,
output='save',
selection='all',
bg='w'):
master_density = []
master_temperature = []
for num_halo in np.arange(390):
print('Ímporting halo ' + str(num_halo))
# Import data
path = extract.path_from_cluster_name(num_halo, simulation_type='gas')
file = extract.file_name_hdf5(
subject='groups', redshift=extract.redshift_floatTostr(redshift))
r200 = extract.group_r200(path, file)
group_CoP = extract.group_centre_of_potential(path, file)
file = extract.file_name_hdf5(
subject='particledata',
redshift=extract.redshift_floatTostr(redshift))
# Gas particles
part_type = extract.particle_type('gas')
density = extract.particle_SPH_density(path, file, part_type)
coordinates = extract.particle_coordinates(path, file, part_type)
temperature = extract.particle_temperature(path, file, part_type)
group_number = extract.group_number(path, file, part_type)
subgroup_number = extract.subgroup_number(path, file, part_type)
# Retrieve coordinates
x = coordinates[:, 0] - group_CoP[0]
y = coordinates[:, 1] - group_CoP[1]
z = coordinates[:, 2] - group_CoP[2]
# Rescale to comoving coordinates
h = extract.file_hubble_param(path, file)
x = profile.comoving_length(x, h, redshift)
y = profile.comoving_length(y, h, redshift)
z = profile.comoving_length(z, h, redshift)
r200 = profile.comoving_length(r200, h, redshift)
density = profile.comoving_density(density, h, redshift)
density = profile.density_units(density, unit_system='nHcgs')
# Compute radial distance
r = np.sqrt(x**2 + y**2 + z**2)
index = 0
# Select particles within 5*r200
if selection.lower() == 'all':
index = np.where((r < 5 * r200) & (group_number == 1)
& (subgroup_number > -1))[0]
if selection.lower() == 'sub':
index = np.where((r < 5 * r200) & (group_number == 1)
& (subgroup_number > 0)
& (subgroup_number < 10000))[0]
if selection.lower() == 'icm':
index = np.where((r < 5 * r200) & (group_number == 1)
& (subgroup_number == 0))[0]
density = density[index]
temperature = temperature[index]
master_density.append(density)
master_temperature.append((temperature))
# Bin data
x_Data = np.concatenate(master_density)
y_Data = np.concatenate(master_temperature)
x_bins = np.logspace(np.min(np.log10(x_Data)), np.max(np.log10(x_Data)),
nbins)
y_bins = np.logspace(np.min(np.log10(y_Data)), np.max(np.log10(y_Data)),
nbins)
A_pix = (x_bins[1] - x_bins[0]) * (y_bins[1] - y_bins[0])
Cx, Cy = mapgen.bins_meshify(x_Data, y_Data, x_bins, y_bins)
count = mapgen.bins_evaluate(x_Data, y_Data, x_bins, y_bins,
weights=None) / A_pix
# Generate plot
plotpar.set_defaults_plot()
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(7, 7))
# Logarithmic normalization
norm = mpl.colors.LogNorm() # (vmin=10 ** -2, vmax=10 ** 1)
count2 = np.ma.masked_where(count == 0, count)
cmap = plt.get_cmap('CMRmap')
cmap.set_bad(color=bg, alpha=1)
img = axes.pcolormesh(Cx, Cy, count2, cmap=cmap, norm=norm)
axes.set_xscale('log')
axes.set_yscale('log')
axes.set_xlabel(r'$n_{\mathrm{H}}/\mathrm{cm}^{3}$')
#axes.set_xlabel(r'$\rho/(M_\odot\ kpc^{-3})$')
axes.set_ylabel(r'$T/\mathrm{K}$')
# Colorbar adjustments
ax2_divider = make_axes_locatable(axes)
cax2 = ax2_divider.append_axes("top", size="3%", pad="2%")
cbar = plt.colorbar(img, cax=cax2, orientation='horizontal')
cbar.set_label(
r'$N_{\mathrm{particles}} / (\mathrm{K}\ \mathrm{cm}^{-3})$',
labelpad=-70)
# cax2.xaxis.set_tick_labels(['0',' ','0.5',' ','1',' ', '1.5',' ','2'])
cax2.xaxis.set_ticks_position("top")
# Define output
if output == 'show':
plt.show()
elif output == 'save':
save_name = 'phase-diagram_nHcgs_halo' + str(10) + '_z' + str(
redshift).replace(
".", "") + '_nbins' + str(nbins) + '_' + selection + '.png'
dir_name = 'phase_diagrams_T-Rho_master390'
if not exists(dir_name): makedirs(dir_name)
plt.savefig(dir_name + '//' + save_name)
else:
print(
"[ERROR] The output type you are trying to select is not defined.")
exit(1)
def map_tSZ_intensity(num_halo,
redshift,
simulation_type,
nbins=100,
rfov=2,
output='show',
title=True,
plot_groups='FoF'):
# Import data
path = extract.path_from_cluster_name(num_halo,
simulation_type=simulation_type)
file = extract.file_name_hdf5(
subject='groups', redshift=extract.redshift_floatTostr(redshift))
r200 = extract.group_r200(path, file)
group_CoP = extract.group_centre_of_potential(path, file)
file = extract.file_name_hdf5(
subject='particledata', redshift=extract.redshift_floatTostr(redshift))
redshift_short = redshift
# Gas particles
part_type = extract.particle_type('gas')
mass = extract.particle_masses(path, file, part_type)
coordinates = extract.particle_coordinates(path, file, part_type)
velocities = extract.particle_velocity(path, file, part_type)
temperatures = extract.particle_temperature(path, file, part_type)
group_number = extract.group_number(path, file, part_type)
subgroup_number = extract.subgroup_number(path, file, part_type)
tot_rest_frame, _ = profile.total_mass_rest_frame(path, file)
#gas_rest_frame, _ = profile.cluster_average_momentum(path, file, part_type)
# Retrieve coordinates & velocities
x = coordinates[:, 0] - group_CoP[0]
y = coordinates[:, 1] - group_CoP[1]
z = coordinates[:, 2] - group_CoP[2]
vx = velocities[:, 0] - tot_rest_frame[0]
vy = velocities[:, 1] - tot_rest_frame[1]
vz = velocities[:, 2] - tot_rest_frame[2]
# Rescale to comoving coordinates
h = extract.file_hubble_param(path, file)
redshift = extract.file_redshift(path, file)
x = profile.comoving_length(x, h, redshift)
y = profile.comoving_length(y, h, redshift)
z = profile.comoving_length(z, h, redshift)
r200 = profile.comoving_length(r200, h, redshift)
vx = profile.comoving_velocity(vx, h, redshift)
vy = profile.comoving_velocity(vy, h, redshift)
vz = profile.comoving_velocity(vz, h, redshift)
vx = profile.velocity_units(vx, unit_system='SI')
vy = profile.velocity_units(vy, unit_system='SI')
vz = profile.velocity_units(vz, unit_system='SI')
mass = profile.comoving_mass(mass, h, redshift)
mass = profile.mass_units(mass, unit_system='SI')
T = temperatures
# Compute radial distance
r = np.sqrt(x**2 + y**2 + z**2)
# Particle selection
min_gn = 0
min_T = 10**5
max_r = 5
if plot_groups == 'FoF': min_sgn = 0
elif plot_groups == 'subgroups': min_sgn = 1
else:
print(
"[ERROR] The (sub)groups you are trying to plot are not defined.")
exit(1)
index = np.where((r < max_r * r200) & (group_number >= min_gn)
& (subgroup_number >= min_sgn) & (T > min_T))[0]
mass, T = mass[index], T[index]
x, y, z = x[index], y[index], z[index]
vx, vy, vz = vx[index], vy[index], vz[index]
# Generate plot frame
plotpar.set_defaults_plot()
fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(20, 9))
# Convert to angular distances
angular_distance = cosmo.angular_diameter_D(redshift)
Mpc_to_arcmin = np.power(np.pi, -1) * 180 * 60 / angular_distance
x = x * Mpc_to_arcmin
y = y * Mpc_to_arcmin
z = z * Mpc_to_arcmin
r200 = r200 * Mpc_to_arcmin
# Bin data
cmap = ['Blues', 'Blues', 'Blues']
# cmap = [mapgen.modified_spectral_cmap(Reversed = True), mapgen.modified_spectral_cmap(Reversed = True), mapgen.modified_spectral_cmap(Reversed = False)]
xlabel = [
r'$x\mathrm{/arcmin}$', r'$y\mathrm{/arcmin}$', r'$x\mathrm{/arcmin}$'
]
ylabel = [
r'$y\mathrm{/arcmin}$', r'$z\mathrm{/arcmin}$', r'$z\mathrm{/arcmin}$'
]
thirdAX = [r'$\bigotimes z$', r'$\bigotimes x$', r'$\bigodot y$']
cbarlabel = [r'$y_{tSZ}$', r'$y_{tSZ}$', r'$y_{tSZ}$']
weight_function = r'$y_{tSZ} = - \frac{\sigma_T}{A_{pix} \mu_e m_H c} \sum_{i=0}^{N_{l.o.s.} m^{g}_i T^{g}_i}$'
for i in [0, 1, 2]:
# Handle data
if i == 0:
x_Data = x
y_Data = y
weight = T
elif i == 1:
x_Data = y
y_Data = z
weight = T
elif i == 2:
x_Data = x
y_Data = z
weight = T
# Compute angular bins
x_bins = np.linspace(-rfov * r200, rfov * r200, nbins)
y_bins = np.linspace(-rfov * r200, rfov * r200, nbins)
Cx, Cy = mapgen.bins_meshify(x_Data, y_Data, x_bins, y_bins)
from astropy.constants import c, sigma_T, k_B, m_e
m_H = 1.6737236 * 10**(-27) # Hydrogen atom mass in kg
A_pix = (x_bins[1] - x_bins[0]) * (y_bins[1] - y_bins[0]) * (
3.0856776 * 10**22 / Mpc_to_arcmin)**2
const = sigma_T.value * k_B.value / (m_e.value * c.value**2 * m_H *
1.16)
# line of sight momentum weights
mass = mass.astype(np.longdouble)
weight = weight.astype(np.longdouble)
count_mT = mapgen.bins_evaluate(x_Data,
y_Data,
x_bins,
y_bins,
weights=mass * weight)
# Compute tSZ
tSZ = count_mT * const / (A_pix)
# convolution
kernel_Type = 'gauss'
#kernel = Gaussian2DKernel(stddev=2)
kernel, fwhm = kernconv.nika2_kernel(x_bins,
y_bins,
kernel_Type=kernel_Type)
kernel = np.array(kernel)
tSZmap = convolve(tSZ, kernel)
# norm = mapgen.MidpointNormalize(vmin=tSZmap.min(), vmax=tSZmap.max(), midpoint=0)
c
# norm = colors.PowerNorm(gamma=0.2)
img = axes[i].pcolor(Cx, Cy, tSZmap, cmap=cmap[i], norm=norm)
# Render elements in plots
axes[i].set_aspect('equal')
axes[i].add_artist(
Circle((0, 0),
radius=r200,
color='black',
fill=False,
linestyle='--',
label=r'$R_{200}$'))
axes[i].add_artist(
Circle((0, 0),
radius=5 * r200,
color='black',
fill=False,
linewidth=0.5,
linestyle='-',
label=r'$R_{200}$'))
axes[i].set_xlim(-rfov * r200, rfov * r200)
axes[i].set_ylim(-rfov * r200, rfov * r200)
axes[i].set_xlabel(xlabel[i])
axes[i].set_ylabel(ylabel[i])
axes[i].annotate(thirdAX[i], (0.03, 0.03),
textcoords='axes fraction',
size=15)
if title and plot_groups == 'FoF':
axes[i].set_title(
r'$\mathrm{MACSIS\ halo\ } %3d \qquad z = %8.3f \qquad \mathrm{ICM + subhalos}$'
% (num_halo, redshift),
pad=94)
if title and plot_groups == 'subgroups':
axes[i].set_title(
r'$\mathrm{MACSIS\ halo\ } %3d \qquad z = %8.3f \qquad \mathrm{subhalos}$'
% (num_halo, redshift),
pad=94)
# Colorbar adjustments
ax2_divider = make_axes_locatable(axes[i])
cax2 = ax2_divider.append_axes("top", size="5%", pad="2%")
cbar = plt.colorbar(img, cax=cax2, orientation='horizontal')
cbar.set_label(cbarlabel[i], labelpad=-70)
#cax2.xaxis.set_tick_labels(['0',' ','0.5',' ','1',' ', '1.5',' ','2'])
cax2.xaxis.set_ticks_position("top")
print("Plot run completed:\t", i)
# Define output
if output == 'show':
plt.show()
elif output == 'save':
dir_name = 'tSZ maps'
if not exists(dir_name):
makedirs(dir_name)
save_name = 'tSZmap_' + plot_groups + '_halo' + str(
num_halo) + '_z' + str(redshift_short).replace(
".", "") + '_rfov' + str(rfov) + '_nbins' + str(nbins)
plt.savefig(dir_name + '//' + save_name + '.pdf')
# Generate metadata.txt
args = (num_halo, simulation_type, redshift, angular_distance, min_gn,
min_sgn, min_T, max_r, weight_function, nbins, rfov,
kernel_Type, fwhm, r200, r200 / Mpc_to_arcmin)
meta.metadata_file(args, dir_name + '//' + save_name)
else:
print(
"[ERROR] The output type you are trying to select is not defined.")
exit(1)
def phase_diagram_master(axes, redshift, nbins = 400, max_halo=10, selection = 'all', bg='w'):
master_density = []
master_temperature = []
for num_halo in np.arange(max_halo):
print('Ímporting halo ' + str(num_halo))
# Import data
path = extract.path_from_cluster_name(num_halo, simulation_type='gas')
file = extract.file_name_hdf5(subject='groups', redshift=extract.redshift_floatTostr(redshift))
r200 = extract.group_r200(path, file)
group_CoP = extract.group_centre_of_potential(path, file)
file = extract.file_name_hdf5(subject='particledata', redshift=extract.redshift_floatTostr(redshift))
# Gas particles
part_type = extract.particle_type('gas')
density = extract.particle_SPH_density(path, file, part_type)/1.16 # Account for the fact that there are H/He atoms
coordinates = extract.particle_coordinates(path, file, part_type)
temperature = extract.particle_temperature(path, file, part_type)
group_number = extract.group_number(path, file, part_type)
subgroup_number = extract.subgroup_number(path, file, part_type)
# Retrieve coordinates
x = coordinates[:, 0] - group_CoP[0]
y = coordinates[:, 1] - group_CoP[1]
z = coordinates[:, 2] - group_CoP[2]
# Rescale to comoving coordinates
h = extract.file_hubble_param(path, file)
x = profile.comoving_length(x, h, redshift)
y = profile.comoving_length(y, h, redshift)
z = profile.comoving_length(z, h, redshift)
r200 = profile.comoving_length(r200, h, redshift)
density = profile.comoving_density(density, h, redshift)
density = profile.density_units(density, unit_system='nHcgs')
# Compute radial distance
r = np.sqrt(x ** 2 + y ** 2 + z ** 2)
index = 0
# Select particles within 5*r200
if selection.lower() == 'all':
index = np.where((r < 5 * r200) & (group_number == 1) & (subgroup_number > -1))[0]
if selection.lower() == 'sub':
index = np.where((r < 5 * r200) & (group_number == 1) & (subgroup_number > 0) & (subgroup_number < 10000))[0]
if selection.lower() == 'icm':
index = np.where((r < 5 * r200) & (group_number == 1) & (subgroup_number == 0))[0]
density = density[index]
temperature = temperature[index]
master_density.append(density)
master_temperature.append((temperature))
# Bin data
x_Data = np.concatenate(master_density)
y_Data = np.concatenate(master_temperature)
x_bins = np.logspace(np.min(np.log10(x_Data)), np.max(np.log10(x_Data)), nbins)
y_bins = np.logspace(np.min(np.log10(y_Data)), np.max(np.log10(y_Data)), nbins)
#A_pix = (x_bins[1:] - x_bins[:-1]) * (y_bins[1] - y_bins[0])
#Ex, Ey = np.meshgrid(x_bins, y_bins)
#A_pix = np.asarray([np.multiply((Ex[i][1:]-Ex[i][:-1]),(Ey[i+1][0]-Ey[i][0])) for i in range(np.shape(Ex)[0]-1)])
Cx, Cy = mapgen.bins_meshify(x_Data, y_Data, x_bins, y_bins)
#count = np.divide(mapgen.bins_evaluate(x_Data, y_Data, x_bins, y_bins, weights=None), A_pix)
count = mapgen.bins_evaluate(x_Data, y_Data, x_bins, y_bins, weights=None)
# Logarithmic normalization
norm = mpl.colors.LogNorm() # (vmin=10 ** -2, vmax=10 ** 1)
count2 = np.ma.masked_where(count == 0, count)
cmap = plt.get_cmap('CMRmap')
cmap.set_bad(color=bg, alpha=1)
img = axes.pcolormesh(Cx, Cy, count2, cmap=cmap, norm=norm)
axes.set_facecolor('k')
axes.set_xscale('log')
axes.set_yscale('log')
#axes.axvline(x=0.1, linewidth=1, color='w', linestyle='dotted')
axes.axhline(y=1e5, linewidth=1, color='w', linestyle='dashed')
#__M__ axes.axhline(y=1e5, linewidth=1, color='darkgrey', linestyle='dashed')
axes.set_xlabel(r'$n_{\mathrm{H}}/\mathrm{cm}^{3}$')
axes.set_xlim(2e-6, 1e3)
#axes.set_xlabel(r'$\rho/(M_\odot\ kpc^{-3})$')
if selection=='all':
axes.set_ylabel(r'$T/\mathrm{K}$')
t = axes.text(.15, 10 ** 9, r'$\mathrm{ICM\ +\ SUBHALOS}$', color='w', fontsize = 15)
#__M__t = axes.text(1, 10 ** 9, r'$\mathrm{ALL\ GAS}$', color='w', fontsize=15)
else:
axes.set_ylabel(r' ')
t = axes.text(.2, 10 ** 9, r'$\mathrm{SUBHALOS\ ONLY}$', color='w', fontsize = 15)
#__M__t = axes.text(.07, 10 ** 9, r'$\mathrm{SUBHALO\ GAS\ ONLY}$', color='w', fontsize=15)
t.set_bbox(dict(facecolor='k', alpha=0.9, edgecolor='grey'))
#__M__t.set_bbox(dict(facecolor='w', alpha=0.15, edgecolor='darkgrey'))
# Colorbar adjustments
ax2_divider = make_axes_locatable(axes)
cax2 = ax2_divider.append_axes("top", size="3%", pad="2%")
cbar = plt.colorbar(img, cax=cax2, orientation='horizontal')
#cbar.set_label(r'$N_{\mathrm{particles}} / (\mathrm{K}\ \mathrm{cm}^{-3})$', labelpad=-60)
cbar.set_label(r'$N_{\mathrm{particles}}$', labelpad=-60)
# cax2.xaxis.set_tick_labels(['0',' ','0.5',' ','1',' ', '1.5',' ','2'])
cax2.xaxis.set_ticks_position("top")