def velocity_plot(s,
width='15 kpc',
cmap1='hot',
cmap2='viridis',
stream=False):
import pynbody
import pynbody.plot.sph as sph
import matplotlib.pylab as plt
f, axs = plt.subplots(1, 2, figsize=(14, 6))
pynbody.analysis.angmom.faceon(s.g)
sph.velocity_image(s.g,
qty='temp',
width=width,
cmap=cmap1,
vector_color='cyan',
denoise=True,
vector_resolution=20,
subplot=axs[0],
show_cbar=False)
mode = 'stream' if stream else 'quiver'
pynbody.analysis.angmom.faceon(s.g)
sph.velocity_image(s.g,
width=width,
cmap=cmap2,
vector_color='black',
denoise=True,
units='Msol kpc^-2',
mode=mode,
vector_resolution=20,
subplot=axs[1],
show_cbar=False)
def tmp2(h1,
av_z=False,
vc='k',
rotate=False,
out_units="Msol yr**-1 pc**-2",
**kwargs):
import matplotlib.pylab as plt
from matplotlib.ticker import IndexLocator, FormatStrFormatter
from matplotlib.colors import Colormap, LinearSegmentedColormap
from matplotlib.patches import Circle
import pynbody
import numpy as np
from pynbody.plot import sph
from seren3.utils import plot_utils
def anno(ax, xy, rvir, color="lightsteelblue", facecolor="none", alpha=1):
e = Circle(xy=xy, radius=rvir)
ax.add_artist(e)
e.set_clip_box(ax.bbox)
e.set_edgecolor(color)
e.set_facecolor(facecolor) # "none" not None
e.set_alpha(alpha)
xy = (0, 0)
nrows = 3
# fig, axs = plt.subplots(nrows=nrows, ncols=1, figsize=(8,12))
# fig, axs = plt.subplots(nrows=1, ncols=nrows, figsize=(10,4))
import matplotlib.gridspec as gridspec
gs = gridspec.GridSpec(2, 6)
ax1 = plt.subplot(gs[0, 1:3])
ax2 = plt.subplot(gs[0, 3:5])
ax3 = plt.subplot(gs[1, 2:4])
axs = np.array([ax1, ax2, ax3])
# fig.subplots_adjust(hspace=0.001)
# fig.subplots_adjust(wspace=0.9)
def _load_s(h):
s = h.pynbody_snapshot(filt=False)
return s
if "s" in kwargs:
s = kwargs.pop("s")
else:
s = _load_s(h1)
if rotate:
# tx = pynbody.analysis.angmom.sideon(s[1].s[pynbody.filt.Sphere(radius='2 kpc')])
# tx.apply_to(s[0])
pynbody.analysis.angmom.sideon(s.s[pynbody.filt.Sphere(
radius='%f kpc' % (h1.rvir.in_units("kpc") / 4.))])
s.physical_units()
rvir = h1.rvir.in_units(s.g['pos'].units)
width = '%1.2f kpc' % (2.1 * rvir)
s.g['rad_flux_radial'].convert_units("s**-1 m**-2")
# s.g['rad_0_rho'].convert_units("s**-1 m**-2")
print s.g['rad_flux_radial'].units
for ax, field in zip(axs.flatten(),
["rho", "mass_flux_radial", "rad_flux_radial"]):
print "Rvir = %1.2f kpc" % rvir.in_units("kpc")
if field == "mass_flux_radial":
sph.velocity_image(s.g, qty="outflow_rate", units=out_units,\
width=width, av_z=av_z, cmap="RdBu_r", qtytitle=r"$\vec{F}_{\mathrm{M}_{\mathrm{gas}}}$",\
subplot=ax, quiverkey=False, vector_color=vc, edgecolor="k", vector_resolution=20, key_length="250 km s**-1", scale="2500 km s**-1", **kwargs)
# sph.velocity_image(s.g, qty="mass_flux_radial", units=out_units,\
# width=width, av_z=av_z, cmap="RdBu_r", qtytitle=r"$\vec{F}_{\mathrm{M}_{\mathrm{gas}}}$",\
# subplot=ax, quiverkey=False, vector_color=vc, vector_resolution=20, key_length="1000 km s**-1", **kwargs)
elif field == "rad_flux_radial":
cmap2 = plot_utils.load_custom_cmaps("blues_black_test")
sph.velocity_image(s.g, qty="rad_flux_radial", units="s**-1 m**-2",\
width=width, cmap=cmap2, qtytitle=r"$\vec{F}_{\mathrm{ion}}$",\
subplot=ax, quiverkey=False, vector_color=vc, edgecolor="k", vector_resolution=20, key_length="250 km s**-1", scale="2500 km s**-1", vmin=1e9, vmax=1e14, **kwargs)
# sph.velocity_image(s.g, qty="rad_0_rho", units="s**-1 m**-2",\
# width=width, cmap="RdBu_r", qtytitle=r"$\vec{F}_{\mathrm{ion}}$",\
# subplot=ax, quiverkey=False, vector_color=vc, vector_resolution=20, key_length="1000 km s**-1", vmin=1e8, vmax=1e12)
# sph.velocity_image(s.g, qty="temp", units="K",\
# width=width, av_z=av_z, cmap="jet", qtytitle=r"T",\
# subplot=ax, quiverkey=False, vector_color="k", vector_resolution=20, key_length="1000 km s**-1")
else:
sph.velocity_image(s.g, qty=field, width=width, cmap="RdBu_r", qtytitle=r"$\rho$$_{\mathrm{gas}}$",\
vector_resolution=20, vector_color=vc, key_x=0.38, key_y=0.815, key_color='yellow', key_length="250 km s**-1", scale="2500 km s**-1", units="Msol kpc**-2", subplot=ax, **kwargs)
anno(ax, xy, rvir)
anno(ax, xy, rvir / 4., color="r")
return s
def tmp(h1,
h2,
av_z=False,
vc='k',
rotate=False,
out_units="Msol yr**-1 pc**-2",
**kwargs):
import matplotlib.pylab as plt
from matplotlib.ticker import IndexLocator, FormatStrFormatter
from matplotlib.colors import Colormap, LinearSegmentedColormap
from matplotlib.patches import Circle
import pynbody
from pynbody.plot import sph
def anno(ax, xy, rvir, color="lightsteelblue", facecolor="none", alpha=1):
e = Circle(xy=xy, radius=rvir)
ax.add_artist(e)
e.set_clip_box(ax.bbox)
e.set_edgecolor(color)
e.set_facecolor(facecolor) # "none" not None
e.set_alpha(alpha)
xy = (0, 0)
nrows = 3
fig, axes = plt.subplots(nrows=nrows, ncols=2, figsize=(12, 16))
# fig.subplots_adjust(hspace=0.001)
# fig.subplots_adjust(wspace=0.9)
def _load_s(h):
s = h.pynbody_snapshot(filt=False)
return s
if "s" in kwargs:
s = kwargs.pop("s")
else:
s = [_load_s(hi) for hi in [h1, h2]]
if rotate:
# tx = pynbody.analysis.angmom.sideon(s[1].s[pynbody.filt.Sphere(radius='2 kpc')])
# tx.apply_to(s[0])
for s_h in s:
pynbody.analysis.angmom.sideon(
s_h.s[pynbody.filt.Sphere(radius='2 kpc')])
for row, field in zip(range(nrows),
["rho", "mass_flux_radial", "rad_flux_radial"]):
axs = axes[row, :]
print len(axs.flatten()), field
for h, s_h, ax in zip([h1, h2], s, axs.flatten()):
s_h.physical_units()
rvir = h.rvir.in_units(s_h.g['pos'].units)
width = '%1.2f kpc' % (2.1 * rvir)
s_h.g['rad_flux_radial'].convert_units("s**-1 m**-2")
s_h.g['rad_0_rho'].convert_units("s**-1 m**-2")
print "Rvir = %1.2f kpc" % rvir.in_units("kpc")
if field == "mass_flux_radial":
sph.velocity_image(s_h.g, qty="outflow_rate", units=out_units,\
width=width, av_z=av_z, cmap="RdBu_r", qtytitle=r"$\mathbf{F}_{\mathrm{M}_{\mathrm{gas}}}$",\
subplot=ax, quiverkey=False, vector_color=vc, vector_resolution=20, key_length="1000 km s**-1", **kwargs)
elif field == "rad_flux_radial":
# sph.velocity_image(s_h.g, qty="rad_flux_radial", units="s**-1 m**-2",\
# width=width, cmap="RdBu_r", qtytitle=r"$\vec{F}_{\mathrm{ion}}$",\
# subplot=ax, quiverkey=False, vector_color=vc, vector_resolution=20, key_length="1000 km s**-1")
sph.velocity_image(s_h.g, qty="rad_0_rho", units="s**-1 m**-2",\
width=width, cmap="RdBu_r", qtytitle=r"$\mathbf{F}_{\mathrm{ion}}$",\
subplot=ax, quiverkey=False, vector_color=vc, vector_resolution=20, key_length="1000 km s**-1", vmin=1e8, vmax=1e12)
# sph.velocity_image(s_h.g, qty="temp", units="K",\
# width=width, av_z=av_z, cmap="jet", qtytitle=r"T",\
# subplot=ax, quiverkey=False, vector_color="k", vector_resolution=20, key_length="1000 km s**-1")
else:
sph.velocity_image(s_h.g, qty=field, width=width, cmap="RdBu_r", qtytitle=r"$\rho$$_{\mathrm{gas}}$",\
vector_resolution=20, vector_color=vc, key_x=0.35, key_y=0.815, key_color='yellow', key_length="250 km s**-1", units="Msol kpc**-2", subplot=ax)
anno(ax, xy, rvir)
anno(ax, xy, rvir / 4., color="r")
return s
## fig = plt.figure()
## ax = fig.add_subplot(111)
## ax.xaxis.set_visible(False)
## ax.yaxis.set_visible(False)
## fileOut="img_log_ax_v-z=%.1lf-%i.pdf"% (z,i)
## titleStr = "v - z = %.1lf" % z# + "\n[%.2lf %.2lf %.2lf]"%(rx,ry,rz)
## print (titleStr)
## sph.image(impData.g,qty="v",width=smallbox,cmap="RdYlBu_r", denoise=True ,av_z=False, units="km s^-1",
## log=True, approximate_fast=False,subplot=ax,qtytitle=r"${\rm log}\, v\, {\rm km/s}$"
## ); #vmin=0.006, vmax=1.0,
## plt.savefig(fileOut,dpi=fig.dpi,bbox_inches='tight')
## plt.close(fig)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.xaxis.set_visible(False)
ax.yaxis.set_visible(False)
fileOut="img_log_ax_vt-z=%.1lf-%i.pdf"% (z,i)
titleStr = "$v_{t}$ @ z = %.1f" % z + "\nThin slice @ %s" % str(coords)
print(titleStr)
sph.velocity_image(impData.g, qty="tv", width=smallbox, cmap = "gist_ncar", units="km s^-1",
mode='quiver', quiverkey=False,qtytitle=r"${\rm log}\, v_{t}\, {\rm km/s}$",
density = 1.0, vector_resolution=40, vmax=1e3, subplot=ax,
show_cbar=True, vector_color='black')
plt.savefig(fileOut,dpi=fig.dpi,bbox_inches='tight')
plt.close(fig)
gc.collect()
del(s)
gc.collect()
# load the halos
h = s.halos()
# center on the largest halo and align the disk
pynbody.analysis.angmom.sideon(h[1])
# create the subplots
f, axs = plt.subplots(1, 2, figsize=(14, 6))
#create a simple slice showing the gas temperature, with velocity vectors overlaid
sph.velocity_image(h[1].g,
vector_color="cyan",
qty="temp",
width=50,
cmap="YlOrRd",
denoise=True,
approximate_fast=False,
subplot=axs[0],
show_cbar=False)
#you can also make a stream visualization instead of a quiver plot
pynbody.analysis.angmom.faceon(h[1])
s['pos'].convert_units('Mpc')
sph.velocity_image(s.g,
width='3 Mpc',
cmap="Greys_r",
mode='stream',
units='Msol kpc^-2',
density=2.0,
vector_resolution=100,
import pynbody
import pynbody.plot.sph as sph
import matplotlib.pylab as plt
# load the snapshot and set to physical units
s = pynbody.load('testdata/g15784.lr.01024.gz')
s.physical_units()
# load the halos
h = s.halos()
# center on the largest halo and align the disk
pynbody.analysis.angmom.sideon(h[1])
# create the subplots
f, axs = plt.subplots(1,2,figsize=(14,6))
#create a simple slice showing the gas temperature, with velocity vectors overlaid
sph.velocity_image(h[1].g, vector_color="cyan", qty="temp",width=50,cmap="YlOrRd",
denoise=True,approximate_fast=False, subplot=axs[0], show_cbar = False)
#you can also make a stream visualization instead of a quiver plot
pynbody.analysis.angmom.faceon(h[1])
s['pos'].convert_units('Mpc')
sph.velocity_image(s.g, width='3 Mpc', cmap = "Greys_r", mode='stream', units='Msol kpc^-2',
density = 2.0, vector_resolution=100, vmin=1e-1,subplot=axs[1],
show_cbar=False, vector_color='black')
subplot=sps[1],vmin=1e16,vmax=1e22,cmap='Greys');
sph.contour(outflow3_part.gas,units='m_p cm^-2', width=width, levels=levels,subplot=sps[2])
setp(ax3.get_yticklabels(), visible=False)
setp(ax3.set_ylabel(''))
for label in ax3.xaxis.get_ticklabels():
label.set_fontsize(8)
sps[3].axis('off')
ax3.set_title(ax3.get_title(),fontsize = 12)
ax3.add_artist(circle)
show()
#---------------------------------------------------------
sph.velocity_image(outflow1_part.gas,vector_color="cyan",qty="temp", width=xymax,cmap="YlOrRd", approximate_fast=False,fill_nan=True,fill_val = 0.0)
sph.image(s.gas,width=500)
#HI map
hiif = pynbody.analysis.ionfrac.calculate(s.gas,ion='hi')
s.gas['hiden'] = s.gas['rho']*s.gas['hydrogen']*hiif
s.gas['hiden'].units = s.gas['rho'].units
#shiim = sph.image(s.gas,qty='hiden',
# units='m_p cm^-2', width=5*xymax, clear=False,
# title='N$_{HI}$ cm$^{-2}$',
# vmin=1e12,vmax=1e20);
sim = sph.image(s.gas,
units='m_p cm^-2', width=5*xymax, clear=False,
title='N$_{gas}$ cm$^{-2}$',
