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_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_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 phase_diagram(num_halo, redshift, output='show', title=True, save_name='Central_group_all_part_halo_'): # 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') 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 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='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 > 0))[0] density = density[index] temperature = temperature[index] # Bin data nbins = 600 x_Data = density y_Data = 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) 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) # Generate plot plotpar.set_defaults_plot() fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(7, 6)) img = axes.pcolor(Cx, Cy, np.log10(count + 1), cmap='viridis') axes.set_xscale('log') axes.set_yscale('log') axes.set_xlabel(r'$\rho/(M_\odot\ pc^{-3})$') axes.set_ylabel(r'$T/K$') if title: axes.set_title(r'$\mathrm{MACSIS\ halo\ } %3d \qquad z = %8.3f$' % (num_halo, redshift)) # Colorbar adjustments ax2_divider = make_axes_locatable(axes) 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") # Define output if output == 'show': plt.show() elif output == 'save': dir_name = 'Temperature-Density phase diagrams' if not exists(dir_name): makedirs(dir_name) plt.savefig(dir_name + '//' + save_name + 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 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")