def getimage(data, poss, temp, mass, hsml, num, norm, cmap):
print('There are', poss.shape[0], 'gas particles in the region')
# Set up particle objects
P1 = sph.Particles(poss, mass=temp * mass, hsml=hsml)
P2 = sph.Particles(poss, mass=mass, hsml=hsml)
# Initialise the scene
S1 = sph.Scene(P1)
S2 = sph.Scene(P2)
i = data[num]
i['xsize'] = 3840
i['ysize'] = 2160
i['roll'] = 0
S1.update_camera(**i)
S2.update_camera(**i)
R1 = sph.Render(S1)
R2 = sph.Render(S2)
R1.set_logscale()
R2.set_logscale()
img1 = R1.get_image()
img2 = R2.get_image()
img = img1 - img2
vmax = 7.5
vmin = 3.5
print("gas temperature", np.min(img), np.max(img))
# Convert images to rgb arrays
rgb = cmap(norm(img))
return rgb, R1.get_extent()
def __init__(self,
pos,
mass=None,
hsml=None,
nb=None,
logscale=True,
plot=True,
min_hsml=None,
max_hsml=None,
**kwargs):
if (mass is None):
mass = np.ones(len(pos[0, :]))
if (nb == None):
self._P = sph.Particles(pos, mass, hsml)
else:
self._P = sph.Particles(pos, mass, hsml, nb)
if ((min_hsml is not None) or (max_hsml is not None)):
hsml = self.get_hsml()
if (min_hsml is not None):
min_hsml = min_hsml
else:
min_hsml = np.min(hsml)
if (max_hsml is not None):
max_hsml = max_hsml
else:
max_hsml = np.max(hsml)
hsml = np.clip(hsml, min_hsml, max_hsml)
print 'Limiting smoothing lenght to the range [%.3f,%.3f]' % (
min_hsml, max_hsml)
self._P.set_hsml(hsml)
self._S = sph.Scene(self._P)
self._S.update_camera(**kwargs)
self._R = sph.Render(self._S)
if (logscale):
self._R.set_logscale()
self._img = self._R.get_image()
self._extent = self._R.get_extent()
if (plot):
self.imshow(aspect='auto')
return
else:
return
def plot_sph(x: pd.Series,
y: pd.Series,
w: pd.Series,
nb=32,
xsize=1000,
ysize=1000):
x_min = np.min(x)
x_max = np.max(x)
y_min = np.min(y)
y_max = np.max(y)
x0 = np.average((x_min, x_max))
y0 = np.average((y_min, y_max))
pos = np.zeros([len(df), 3])
pos[:, 0] = x
pos[:, 1] = y
w = w.to_numpy() * 100
particles = sph.Particles(pos, mass=w, nb=nb)
scene = sph.Scene(particles)
scene.update_camera(r="infinity",
x=x0,
y=y0,
z=0,
xsize=xsize,
ysize=ysize)
render = sph.Render(scene)
render.set_logscale()
img = render.get_image()
extent = render.get_extent()
for i, j in zip(range(4), [x0, x0, y0, y0]):
extent[i] += j
return img, extent
def myplot(x, y, nb=32, xsize=500, ysize=500):
"""This function reads in a set of data and smooths it using
nearest neighbors summing. It then outputs the smoothed data
with a measure of its extent. This output is then inputed to
Axes.imshow.
:param: x,y two columns of data such as particle positions
:param: nb smoothing size.
"""
xmin = np.min(x)
xmax = np.max(x)
ymin = np.min(y)
ymax = np.max(y)
x0 = (xmin + xmax) / 2.
y0 = (ymin + ymax) / 2.
pos = np.zeros([3, len(x)])
pos[0, :] = x
pos[1, :] = y
w = np.ones(len(x))
P = sph.Particles(pos, w, nb=nb)
S = sph.Scene(P)
S.update_camera(r='infinity', x=x0, y=y0, z=0, xsize=xsize, ysize=ysize)
R = sph.Render(S)
R.set_logscale()
img = R.get_image()
extent = R.get_extent()
for i, j in zip(xrange(4), [x0, x0, y0, y0]):
extent[i] += j
print extent, x0, y0
return img, extent
def getimage(data, poss, mass, hsml, num, max_pixel, cmap, Type="gas"):
print('There are', poss.shape[0], 'gas particles in the region')
# Set up particle objects
P = sph.Particles(poss, mass=mass, hsml=hsml)
print(np.min(mass))
# Initialise the scene
S = sph.Scene(P)
i = data[num]
i['xsize'] = 5000
i['ysize'] = 5000
i['roll'] = 0
S.update_camera(**i)
R = sph.Render(S)
R.set_logscale()
img = R.get_image()
if Type == "gas":
vmax =11
vmin = 6
print("gas", np.max(img))
# Convert images to rgb arrays
rgb = cmap(get_normalised_image(img, vmin=vmin, vmax=vmax))
else:
vmax = 21.6
vmin = 15.0
print("star", np.min(img[img != 0]), np.max(img))
rgb = img
return rgb, R.get_extent()
def myplot(x, y, nb=32, xsize=500, ysize=500): xmin = np.min(x) xmax = np.max(x) ymin = np.min(y) ymax = np.max(y) print xmin, xmax, ymin, ymax x0 = (xmin+xmax)/2. y0 = (ymin+ymax)/2. pos = np.zeros([3, len(x)]) pos[0,:] = x pos[1,:] = y w = np.ones(len(x)) P = sph.Particles(pos, w, nb=nb) S = sph.Scene(P) S.update_camera(r='infinity', x=x0, y=y0, z=0, xsize=xsize, ysize=ysize) R = sph.Render(S) R.set_logscale() img = R.get_image() extent = R.get_extent() for i, j in zip(xrange(4), [x0,x0,y0,y0]): extent[i] += j #print extent return img, extent
def getimage(data, poss, hsml, num, boxsize):
print('There are', poss.shape[0], 'dark matter particles in the region')
# Set up particle objects
P = sph.Particles(poss, mass=np.ones(poss.shape[0]), hsml=hsml)
# Initialise the scene
S = sph.Scene(P)
i = data[num]
i['xsize'] = int(boxsize / hsml.max())
i['ysize'] = int(boxsize / hsml.max())
i['roll'] = 0
S.update_camera(**i)
R = sph.Render(S)
R.set_logscale()
img = R.get_image()
vmax = 7
vmin = 1
# Get colormaps
cmap = cmaps.twilight()
print(img.max())
# Convert images to rgb arrays
rgb = cmap(get_normalised_image(img, vmin=vmin, vmax=vmax))
return rgb, R.get_extent()
def getimage_stars(data, poss, mass, hsml, num, max_pixel, cmap, Type="gas"):
print('There are', poss.shape[0], 'gas particles in the region')
# Set up particle objects
P = sph.Particles(poss, mass=mass, hsml=hsml)
print(np.min(mass))
# Initialise the scene
S = sph.Scene(P)
i = data[num]
i['xsize'] = 3840
i['ysize'] = 2160
i['roll'] = 0
S.update_camera(**i)
R = sph.Render(S)
R.set_logscale()
img = R.get_image()
img = ndimage.gaussian_filter(img, sigma=(3, 3), order=0)
if Type == "gas":
vmax = 11
vmin = 6
print("gas", np.max(img))
else:
vmax = 13
vmin = 7.5
print("star", np.max(img))
# Convert images to rgb arrays
rgb = cmap(get_normalised_image(img, vmin=vmin, vmax=vmax))
return rgb, R.get_extent()
def plot_ledlow_contours(t, world2pixel, ngb=12, xsize=500, ysize=500):
""" Smooth galaxy positions of Ledlow+ (2005) to get contour lines
@param t : astropy.table.Table holding Ledlow data
@param world2pixel : aplpy.FITSFigure world2pixel function to map
RA,dec coordinates to Chandra mosaic pixels
@param ngb : number of neighbours to smooth over
@param xsize, ysize: size of the image (resolution?)
@return : img, extent """
ra = 15 * astropy.coordinates.Angle(t['RAJ2000'].filled(numpy.nan),
unit=u.degree)
dec = astropy.coordinates.Angle(t['DEJ2000'].filled(numpy.nan),
unit=u.degree)
ra, dec = world2pixel(ra,
dec) # convert ra, dec to xray mosaic pixel values
# Perform kernel density estimate
# https://docs.scipy.org/doc/scipy-0.18.1/reference/generated/scipy.stats.gaussian_kde.html
# X, Y = numpy.mgrid[xmax:xmin:300j, ymin:ymax:3000j]
# positions = numpy.vstack([X.ravel(), Y.ravel()])
# values = numpy.vstack([ra, dec])
# kernel = kde.gaussian_kde(values)
# Z = numpy.reshape(kernel(positions).T, X.shape)
# Z /= ((41.1-40.6)*60*(20.025-19.50)*60)
# pyplot.imshow(numpy.rot90(Z), cmap=pyplot.cm.gist_earth_r,
# extent=[xmax, xmin, ymin, ymax])
# cset = pyplot.contour(X, Y, Z, colors="w",
# levels=numpy.array([1,2,3,5,8,10])*Z.max()/10)
# pyplot.clabel(cset, inline=1, fontsize=10)
# https://stackoverflow.com/questions/2369492
xmin, xmax = ra.min(), ra.max()
ymin, ymax = dec.min(), dec.max()
x0 = (xmin + xmax) / 2.
y0 = (ymin + ymax) / 2.
pos = numpy.zeros([3, len(ra)])
pos[0, :] = ra
pos[1, :] = dec
w = numpy.ones(len(ra))
P = sphviewer.Particles(pos, w, nb=ngb)
S = sphviewer.Scene(P)
S.update_camera(r="infinity", x=x0, y=y0, z=0, xsize=xsize, ysize=ysize)
R = sphviewer.Render(S)
img = R.get_image()
extent = R.get_extent()
for i, j in zip(xrange(4), [x0, x0, y0, y0]):
extent[i] += j
img = 10 * img / numpy.max(img)
return img, extent
def getimage(data, poss, hsml, num, z, cmap):
print('There are', poss.shape[0], 'dark matter particles in the region')
# Set up particle objects
P = sph.Particles(poss, mass=np.ones(poss.shape[0]), hsml=hsml)
# Initialise the scene
S = sph.Scene(P)
i = data[num]
i['xsize'] = 3840
i['ysize'] = 2160
i['roll'] = 0
S.update_camera(**i)
print("Scene")
R = sph.Render(S)
print("Render")
R.set_logscale()
print("Logscale")
img = R.get_image()
print("Image")
print(img.max(),
np.percentile(img, 99.99),
np.percentile(img, 95),
np.percentile(img, 90),
np.percentile(img, 67.5),
np.percentile(img, 50))
vmax = 6.9
vmin = 0.1
# # Get colormaps
# cmap2 = cmr.torch_r(np.linspace(0, 1, 128))
# cmap3 = cmr.swamp(np.linspace(0, 1, 128))
#
# # combine them and build a new colormap
# colors = np.vstack((cmap2, cmap3))
# cmap = mcolors.LinearSegmentedColormap.from_list('colormap', colors)
hex_list = ["#000000", "#590925", "#6c1c55", "#7e2e84", "#ba4051",
"#f6511d", "#ffb400", "#f7ec59", "#fbf6ac", "#ffffff"]
#cmap = get_continuous_cmap(hex_list, float_list=None)
img = ndimage.gaussian_filter(img, sigma=(3, 3), order=0)
# Convert images to rgb arrays
rgb = cmap(get_normalised_image(img, vmin=vmin, vmax=vmax))
return rgb, R.get_extent()
rl = 5
corte, = np.where((xn < rl) & (yn < rl) & (zn < rl) & (xn > -rl)
& (yn > -rl) & (zn > -rl))
#-----rango que tiene la escala de colores-----
vmin = 1.8
vmax = 6
# ----escala de colores que te guste (http://matplotlib.org/examples/color/colormaps_reference.html)---
cmap = 'magma'
nb1 = 100
# nb1 = 100
# npixel = 1000
npixel = 1000
particles = sph.Particles(pos[corte, :3], mstr[corte], nb=nb1)
escena = sph.Scene(particles)
escena.update_camera(r='infinity',
x=0,
y=0,
z=0,
extent=[-rl, rl, -rl, rl],
xsize=npixel,
ysize=npixel)
rend = sph.Render(escena)
extent = escena.get_extent()
rend.set_logscale()
ax[0, 0].imshow(rend.get_image(),
extent=extent,
origin='lower',
from pylab import *
import sphviewer
x, y, z, mass, den, fe = loadtxt(sys.argv[1],
unpack=True,
usecols=[1, 2, 3, 7, 9, 36],
skiprows=1,
delimiter=',')
pos = zeros(shape=(3, len(den)))
pos[0][:] = x
pos[1][:] = y
pos[2][:] = z
Particles = sphviewer.Particles(pos, fe)
for ii in range(200):
print sys.argv[1], ii
Scene = sphviewer.Scene(Particles)
camera = Scene.Camera.get_params()
theta = double(ii) / 200.0 * 360
radius = 1000 - double(ii)
Scene.update_camera(r=radius,
t=0,
p=theta,
xsize=1000,
ysize=1000,
x=0.0,
y=0.0,
z=0.0)
alpha *= 180. / np.pi
beta *= 180. / np.pi
print(alpha, beta)
for _orientation, _p, _t, _roll in zip([0, 1, 2, 3, 4, 5], beta, alpha,
[270, 180, 270, 0, 270, 90]):
print("#########\nRendering orientation %s\np=%s, t=%s, roll=%s\n##########"%\
(_orientation,_p,_t,_roll))
fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2, figsize=(10, 10))
if _orientation == 0:
mask = np.random.rand(len(halog_pos)) < 1
Pg = sph.Particles(halog_pos[mask], halog_mass[mask] * 1e10)
Pd = sph.Particles(halog_pos[mask], halog_dust[mask] * 1e10)
Psfr = sph.Particles(halog_pos[mask], halog_sfr[mask])
mask = np.random.rand(len(halos_pos)) < 1
Ps = sph.Particles(halos_pos[mask], halos_pmass[mask] * 1e10)
extent = 30
sm1, img1 = plot_dist(fig,
ax1,
Pg,
hcood,
cmaps.night(),
vmin=1e2,
extent=extent,
p=_p,
rl = 50
corte, = np.where((xn_drk < rl) & (yn_drk < rl) & (zn_drk < rl)
& (xn_drk > -rl) & (yn_drk > -rl) & (zn_drk > -rl))
#-----rango que tiene la escala de colores-----
vmin = 4.5
vmax = 6.7
# ----escala de colores que te guste (http://matplotlib.org/examples/color/colormaps_reference.html)---
cmap = 'viridis'
# nb1 = 300
nb1 = 25
npixel = 1000
particles = sph.Particles(pos2[corte, :3], mdrk[corte] * 1e10, nb=nb1)
escena = sph.Scene(particles)
escena.update_camera(r='infinity',
x=0,
y=0,
z=0,
extent=[-rl, rl, -rl, rl],
xsize=npixel,
ysize=npixel)
rend = sph.Render(escena)
extent = escena.get_extent()
rend.set_logscale()
ax[1, 0].imshow(rend.get_image(),
extent=extent,
origin='lower',
def select(self,centre,region_size): # Region size in Mpc
print 'Loading region...'
code_centre = centre * self.h/(self.a_0*1e3) # convert to h-less comoving code units
region_size *= self.h/self.a_0
# Point read_eagle to the data
snapfile = self.sim_path + 'snapshot_' + self.tag + '/snap_' + self.tag + '.0.hdf5'
# Open snapshot
snap = read.EagleSnapshot(snapfile)
# Select region of interest
snap.select_region(code_centre[0]-region_size/2.,
code_centre[0]+region_size/2.,
code_centre[1]-region_size/2.,
code_centre[1]+region_size/2.,
code_centre[2]-region_size/2.,
code_centre[2]+region_size/2.)
if self.property == 'stars':
pos = snap.read_dataset(4,'Coordinates') * self.a_0/self.h
smoothing_length = snap.read_dataset(4, 'SmoothingLength') * self.a_0 / self.h
quantity = snap.read_dataset(4, 'Mass') / self.h * 1e10
else:
pos = snap.read_dataset(0, 'Coordinates') * self.a_0 / self.h
smoothing_length = snap.read_dataset(0, 'SmoothingLength') * self.a_0 / self.h
if self.property == 'gas':
quantity = snap.read_dataset(0, 'Mass') / self.h / 1e10
elif self.property == 'xrays':
pids = snap.read_dataset(0, 'ParticleIDs')
quantity = self.xrays[np.searchsorted(self.xray_pids,pids)]
else:
raise IOError('Plot options are "gas","stars" or "xrays"')
print 'Wrapping box...'
region_size /= self.h/self.a_0
centre_mpc = centre /1e3
pos = ne.evaluate("pos-centre_mpc")
pos[pos[:,0]<(-1.*self.boxsize/2.),0] += self.boxsize
pos[pos[:,1]<(-1.*self.boxsize/2.),1] += self.boxsize
pos[pos[:,2]<(-1.*self.boxsize/2.),2] += self.boxsize
pos[pos[:,0]>self.boxsize/2.,0] -= self.boxsize
pos[pos[:,1]>self.boxsize/2.,1] -= self.boxsize
pos[pos[:,2]>self.boxsize/2.,2] -= self.boxsize
pos = ne.evaluate("pos+centre_mpc")
pos = pos.T
N = len(quantity)
pos *= 1e3 # convert to kpc
smoothing_length *= 1e3
print 'Creating scene...'
Particles = sphviewer.Particles(pos, quantity, hsml=smoothing_length)
self.Scene = sphviewer.Scene(Particles)
#-----rango que tiene la escala de colores-----
vmin=3
vmax=7
# ----escala de colores que te guste (http://matplotlib.org/examples/color/colormaps_reference.html)---
cmap='jet'
<<<<<<< HEAD
nb1 = 10
#nb1 = 100
=======
#nb1 = 5
nb1 = 100
>>>>>>> b29321f0c229ffcfec5b2b43354097e24d056487
particles=sph.Particles(pos[:3,corte],mstr[corte]*1e10,nb=nb1)
escena=sph.Scene(particles)
escena.update_camera(r='infinity',x=0,y=0,z=0,extent=[-rl,rl,-rl,rl])
rend=sph.Render(escena)
extent=escena.get_extent()
rend.set_logscale()
ax[0,0].imshow(rend.get_image(),extent=extent,origin='lower',cmap=cmap, vmin=vmin, vmax= vmax)
ax[0,0].set_xlim(-5,5)
ax[0,0].set_ylim(-5,5)
ax[0,0].set_xticks([])
ax[0,0].set_yticks([])
ax[0,0].set_yticklabels([])
ax[0,0].set_xticklabels([])
# ax[0,0].set_ylabel('$y\:[kpc]$', fontsize=40)
# ax[0,0].minorticks_on()
_radius = np.array(ad.to_dataframe('radius')) / _kpc
_x = np.array(ad.to_dataframe('x')) / _kpc
_y = np.array(ad.to_dataframe('y')) / _kpc
_z = np.array(ad.to_dataframe('z')) / _kpc
_coods = np.squeeze(np.array([_x, _z, _y])).T
radius = 15 # kpc
mask = _radius < radius
print("radius:", radius)
print("mass weighted temp:",
np.sum((_temp * _mass)[mask]) / np.sum(_mass[mask]))
extent = 15
img = [None, None]
for i, _weight in enumerate([_temp, _temp * (_mass / 1.99e38)]):
Pd = sph.Particles(_coods, _weight) # halog_dust[mask] * 1e10)
C = sph.Camera(x=0,
y=0,
z=0,
r='infinity',
zoom=1,
extent=[-extent, extent, -extent, extent],
xsize=512,
ysize=512)
S = sph.Scene(Pd, Camera=C)
R = sph.Render(S)
# R.set_logscale()
img[i] = R.get_image()
#if vmax is None:
# vmax = img.max()
def select(self, centre, region_size): # Region size in Mpc
if not self.quiet:
print 'Loading region...'
code_centre = centre * self.h / (
self.a_0 * 1e3) # convert to h-less comoving code units
code_region_size = region_size * self.h / self.a_0
centre_mpc = centre / 1e3
# Point read_eagle to the data
snapfile = self.sim_path + 'snapshot_' + self.tag + '/snap_' + self.tag + '.0.hdf5'
# Open snapshot
snap = read.EagleSnapshot(snapfile)
# Select region of interest
snap.select_region(code_centre[0] - code_region_size / 2.,
code_centre[0] + code_region_size / 2.,
code_centre[1] - code_region_size / 2.,
code_centre[1] + code_region_size / 2.,
code_centre[2] - code_region_size / 2.,
code_centre[2] + code_region_size / 2.)
if self.property == 'stars':
pos = snap.read_dataset(4, 'Coordinates') * self.a_0 / self.h
smoothing_length = snap.read_dataset(
4, 'SmoothingLength') * self.a_0 / self.h
quantity = snap.read_dataset(4, 'Mass') / self.h * 1e10
else:
pos = snap.read_dataset(0, 'Coordinates') * self.a_0 / self.h
smoothing_length = snap.read_dataset(
0, 'SmoothingLength') * self.a_0 / self.h
if self.property == 'gas':
quantity = snap.read_dataset(0, 'Mass') / self.h / 1e10
elif self.property == 'xrays':
pids = snap.read_dataset(0, 'ParticleIDs')
quantity = self.xrays[np.searchsorted(self.xray_pids, pids)]
elif self.property == 'entropy':
m_H_cgs = 1.6737e-24
weight = snap.read_dataset(0, 'Mass') / self.h / 1e10
temp = snap.read_dataset(0, 'Temperature')
abunds = np.zeros((len(temp), 11))
abunds[:, 0] = snap.read_dataset(
0, "SmoothedElementAbundance/Hydrogen")
abunds[:, 1] = snap.read_dataset(
0, "SmoothedElementAbundance/Helium")
abunds[:, 2] = snap.read_dataset(
0, "SmoothedElementAbundance/Carbon")
abunds[:, 3] = snap.read_dataset(
0, "SmoothedElementAbundance/Nitrogen")
abunds[:, 4] = snap.read_dataset(
0, "SmoothedElementAbundance/Oxygen")
abunds[:,
5] = snap.read_dataset(0,
"SmoothedElementAbundance/Neon")
abunds[:, 6] = snap.read_dataset(
0, "SmoothedElementAbundance/Magnesium")
abunds[:, 7] = snap.read_dataset(
0, "SmoothedElementAbundance/Silicon")
abunds[:, 8] = abunds[:, 7] * 0.6054160
abunds[:, 9] = abunds[:, 7] * 0.0941736
abunds[:, 10] = snap.read_dataset(
0, "SmoothedElementAbundance/Iron")
atomic_numbers = np.array(
[1., 2., 6., 7., 8., 10., 12., 14., 16., 20., 26.])
Xe = np.ones(len(abunds[:, 0]))
num_ratios = np.zeros(np.shape(abunds))
for col in range(len(abunds[0, :])):
num_ratios[:, col] = abunds[:, col] / abunds[:, 0]
for element in range(len(abunds[0, :]) - 1):
Xe += num_ratios[:,
element + 1] * atomic_numbers[element + 1]
density = snap.read_dataset(0, 'Density')
n_H = density * abunds[:, 0] / m_H_cgs # convert into nH cm^-3
n_e = n_H * Xe # electron density in cm^-3
quantity = temp / np.power(n_e, 2. / 3.)
else:
raise IOError(
'Plot options are "gas","ion", stars" or "xrays"')
if not self.quiet:
print 'Wrapping box...'
pos = ne.evaluate("pos-centre_mpc")
pos[pos[:, 0] < (-1. * self.boxsize / 2.), 0] += self.boxsize
pos[pos[:, 1] < (-1. * self.boxsize / 2.), 1] += self.boxsize
pos[pos[:, 2] < (-1. * self.boxsize / 2.), 2] += self.boxsize
pos[pos[:, 0] > self.boxsize / 2., 0] -= self.boxsize
pos[pos[:, 1] > self.boxsize / 2., 1] -= self.boxsize
pos[pos[:, 2] > self.boxsize / 2., 2] -= self.boxsize
pos = ne.evaluate("pos+centre_mpc")
# read_eagle loads in more than we actually asked for above. We need to mask to the region size again!
posmask = np.where(
(np.absolute(pos[:, 0] - centre_mpc[0]) < region_size / 2.)
& (np.absolute(pos[:, 1] - centre_mpc[1]) < region_size / 2.)
& (np.absolute(pos[:, 2] - centre_mpc[2]) < region_size / 2.))[0]
pos = pos[posmask, :]
smoothing_length = smoothing_length[posmask]
quantity = quantity[posmask]
N = len(quantity)
pos *= 1e3 # convert to kpc
smoothing_length *= 1e3
if not self.quiet:
print 'Creating scene...'
if self.property in [
'entropy',
]:
weight = weight[posmask]
Particles = sphviewer.Particles(pos, weight, hsml=smoothing_length)
self.weightScene = sphviewer.Scene(Particles)
Particles = sphviewer.Particles(pos,
quantity * weight,
hsml=smoothing_length)
self.propScene = sphviewer.Scene(Particles)
else:
if pos.size == 0:
self.Scene = None
else:
Particles = sphviewer.Particles(pos,
quantity,
hsml=smoothing_length)
self.Scene = sphviewer.Scene(Particles)
rl = 50
corte, = np.where((xn < rl) & (yn < rl) & (zn < rl) & (xn > -rl)
& (yn > -rl) & (zn > -rl))
#-----rango que tiene la escala de colores-----
vmin = 0.9
vmax = 6.7
# ----escala de colores que te guste (http://matplotlib.org/examples/color/colormaps_reference.html)---
cmap = 'magma'
# nb1 = 300
nb1 = 25
npixel = 1000
particles = sph.Particles(pos[corte, :3], mstr[corte] * 1e10, nb=nb1)
escena = sph.Scene(particles)
escena.update_camera(r='infinity',
x=0,
y=0,
z=0,
extent=[-rl, rl, -rl, rl],
xsize=npixel,
ysize=npixel)
rend = sph.Render(escena)
extent = escena.get_extent()
rend.set_logscale()
ax[1, 0].imshow(rend.get_image(),
extent=extent,
origin='lower',
# read in relevant columns from your file
x, y, z, mass, den = loadtxt(sys.argv[1],
unpack=True,
usecols=[1, 2, 3, 7, 9],
skiprows=1,
delimiter=',')
# set up arrays recognized by py-sphviewer
pos = zeros(shape=(3, len(den)))
pos[0][:] = x
pos[1][:] = y
pos[2][:] = z
# initialize sphviewer particles structure
Particles = sphviewer.Particles(pos, mass)
for ii in range(200):
print sys.argv[1], ii
# set up a scene
Scene = sphviewer.Scene(Particles)
camera = Scene.Camera.get_params()
# make a full rotation in 200 frames (theta in degrees)
theta = double(ii) / 200.0 * 360
# gradually ease in from 1000 to 800
radius = (1000 - double(ii)) * 6.957e10 # cm/Rsun
pmask[pmask] = (pgas[pmask, 1] < c[1] + dl)
pmask[pmask] = (pgas[pmask, 2] > c[2] - dl)
pmask[pmask] = (pgas[pmask, 2] < c[2] + dl)
# pmask = ((pgas[:,0] > coods[0]-dl) & (pgas[:,0] < coods[0]+dl) &\
# (pgas[:,1] > coods[1]-dl) & (pgas[:,1] < coods[1]+dl) &\
# (pgas[:,2] > coods[2]-dl) & (pgas[:,2] < coods[2]+dl))
print(len(pgas), np.sum(pmask))
if np.sum(pmask) == 0:
raise ValueError('No particles to plot')
ext = 500 # number of pixels in image
convers = ext / (2 * dl) # conversion factor
P = sph.Particles(pgas[pmask], mass=np.ones(np.sum(pmask)))
fig, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(15, 7))
for ax, t, p, c1, c2 in zip([ax1, ax2, ax3], [0, 0, 90], [0, 90, 90],
[0, 2, 2], [1, 1, 0]):
C = sph.Camera(r='infinity',
t=t,
p=p,
roll=0,
xsize=ext,
ysize=ext,
x=c[0],
y=c[1],
z=c[2],
def __init__(self, gn, prop,
sim='L0100N1504',
run='REFERENCE',
snapnum=28,
halotype='all'):
self.groupnumber = gn
self.property = prop
tag = snapdict[str(snapnum)][0]
try:
data = h5.File(
'/data5/arijdav1/saved_regions/' + sim + '_' + run + '/' + tag + '/' + halotype + '/group' + str(
gn) + '.hdf5', 'r')
except IOError:
print 'Invalid group number for this box.'
exit()
if prop == 'stars':
pos = np.array(data['Stars/Coordinates']).T
smoothing_length = np.array(data['Stars/SmoothingLength'])
quantity = np.array(data['Stars/Mass']) * 1e10
else:
pos = np.array(data['Gas/Coordinates']).T
smoothing_length = np.array(data['Gas/SmoothingLength'])
if prop == 'gas':
quantity = np.array(data['Gas/Mass']) * 1e10
elif prop == 'hotgas':
quantity = np.array(data['Gas/Mass']) * 1e10
temp = np.array(data['Gas/Temperature'])
mask = np.where(temp > np.power(10., 5.5))[0]
column_pos = column_pos[mask]
smoothing_length = smoothing_length[mask]
quantity = quantity[mask]
elif prop == 'xrays':
quantity = np.array(
data['Gas/Xray_luminosity']) / 1e30 # make the numbers smaller so sphviewer can deal with them
else:
raise IOError('Plot options are "gas", "hotgas", "stars" or "xrays"')
N = len(quantity)
pos *= 1e3 # convert to kpc
smoothing_length *= 1e3
if prop == 'gas':
self.cmap = 'hot'
self.axlab = r'$\log\Sigma_g$ [$M_{\odot}$ $\mathrm{pc}^{-2}]$'
elif prop == 'hotgas':
self.cmap = 'hot'
self.axlab = r'$\log\Sigma_{\mathrm{g,hot}}$ [$M_{\odot}$ $\mathrm{pc}^{-2}]$'
elif prop == 'xrays':
self.cmap = 'gnuplot'
self.axlab = r'$\log\Sigma_{X,\mathrm{0.5-2keV}}$ [$\mathrm{erg}$ $\mathrm{s}^{-1}$ $\mathrm{pc}^{-2}]$'
elif prop == 'stars':
self.cmap = 'bone'
self.axlab = r'$\log\Sigma_*$ [$M_{\odot}$ $\mathrm{pc}^{-2}]$'
else:
raise IOError('Plot options are "gas", "hotgas", "stars" or "xrays"')
Particles = sphviewer.Particles(pos, quantity, hsml=smoothing_length)
self.Scene = sphviewer.Scene(Particles)
(norm_coods[:,1] < dx) & (norm_coods[:,1] > -dx) &\
(norm_coods[:,2] < dx) & (norm_coods[:,2] > -dx)
C = sph.Camera(x=0,
y=0,
z=0,
r='infinity',
extent=[-dx, dx, -dx, dx],
t=t,
p=p,
roll=0,
xsize=4000,
ysize=2250)
# Gas density
P = sph.Particles(norm_coods[coods_mask],
pmass[coods_mask] / pmass[coods_mask].min())
# hsml = hsml * 10)# * 2)
hsml = P.get_hsml()
## Create scene and render
S = sph.Scene(P, Camera=C)
R = sph.Render(S)
## Get image and plot
# R.set_logscale()
img = R.get_image()
print(img.min(), img.max())
cmap = sph_cmaps.desert() # plt.get_cmap('twilight')
img = cmap(vis_util.get_normalized_image(img, vmin=0, vmax=7))
pmask[pmask] = (pdark[pmask,2] > c[2]-dl)
pmask[pmask] = (pdark[pmask,2] < c[2]+dl)
# pmask = ((pdark[:,0] > coods[0]-dl) & (pdark[:,0] < coods[0]+dl) &\
# (pdark[:,1] > coods[1]-dl) & (pdark[:,1] < coods[1]+dl) &\
# (pdark[:,2] > coods[2]-dl) & (pdark[:,2] < coods[2]+dl))
print(len(pdark),np.sum(pmask))
# qv = QuickView(pdark[pmask],r='infinity',plot=False)
# qv.imshow()
ext=500 # number of pixels in image
convers = ext/(2*dl) # conversion factor
P = sph.Particles(pdark[pmask],mass=np.ones(np.sum(pmask)))
fig,(ax1,ax2,ax3) = plt.subplots(1,3,figsize=(15,7))
for ax,t,p,c1,c2 in zip([ax1,ax2,ax3],[0,0,90],[0,90,90],[0,2,2],[1,1,0]):
C = sph.Camera(r='infinity',t=t, p=p, roll=0, xsize=ext, ysize=ext,
x=c[0],y=c[1],z=c[2],extent=[-dl,dl,-dl,dl])
S = sph.Scene(P,C)
R = sph.Render(S)
img = np.log10(R.get_image())
extent = R.get_extent()
ax.imshow(img,cmap=cmaps.twilight())
pos *= 1e3 # convert to kpc
smoothing_length *= 1e3
if prop == 'gasmass':
cmap = 'hot'
axlab = r'$\log\Sigma_g$ [$M_{\odot}$ $\mathrm{kpc}^{-2}]$'
elif prop == 'xrays':
cmap = 'gnuplot'
axlab = r'$\log\Sigma_{X,\mathrm{0.5-2keV}}$ [$\mathrm{erg}$ $\mathrm{s}^{-1}$ $\mathrm{kpc}^{-2}]$'
elif prop == 'stars':
cmap = 'bone'
axlab = r'$\log\Sigma_*$ [$M_{\odot}$ $\mathrm{kpc}^{-2}]$'
else:
raise IOError('Plot options are "gasmass", "stars", "temperature" or "xrays"')
Particles = sphviewer.Particles(pos,quantity,hsml=smoothing_length)
Scene = sphviewer.Scene(Particles)
Scene.update_camera(x=0.,y=0.,z=0.,r='infinity',t=90.,extent=[-ext,ext,-ext,ext],xsize=res,ysize=res)
Render = sphviewer.Render(Scene)
#Render.set_logscale()
img = Render.get_image()
sdensity_img = img/px_size**2
'''
# For quickly viewing the individual images
extent = Render.get_extent()
plt.figure()
plt.imshow(sdensity_img,cmap='hot',extent=extent, origin='lower')
plt.show()
def single_sphere(reg, snap, soft, num, part_type, cmap, vlims, runall=True):
if runall:
# Define path
path = '/cosma/home/dp004/dc-rope1/FLARES/FLARES-1/G-EAGLE_' + reg + '/data'
poss, masses, smls = get_particle_data(path, snap, part_type=part_type, soft=soft)
# Get the spheres centre
centre, radius, mindist = spherical_region(path, snap)
# Cutout particles
poss, masses, smls = cutout_particles(poss, masses, smls, centre, radius)
print('There are %i particles (type %s) in the region'%(len(masses),part_type))
# Set up particle objects
P = sph.Particles(poss, mass=masses, hsml=smls)
# Initialise the scene
S = sph.Scene(P)
targets = [[0,0,0]]#,0,0,0,0,0,0]
# Define the box size
lbox = (15 / 0.677) * 2
# Define anchors dict for camera parameters
anchors = {}
anchors['sim_times'] = [0.0, 'same', 'same', 'same', 'same', 'same', 'same', 'same', 'same']
anchors['id_frames'] = [0, 90, 180, 270, 360, 450, 540, 630, 720]
anchors['id_targets'] = [0, 'same', 'same', 'same', 'same', 'same', 'same', 'same', 'same']
anchors['r'] = [lbox * 3 / 4, 'same', 'same', 'same', 'same', 'same', 'same', 'same', 'same']
anchors['t'] = [0, 'same', 'same', 'same', 'same', 'same', 'same', 'same', 'same']
anchors['p'] = [0, 'pass', 'pass', 'pass', 'pass', 'pass', 'pass', 'pass', 360]
anchors['zoom'] = [1., 'same', 'same', 'same', 'same', 'same', 'same', 'same', 'same']
anchors['extent'] = [10, 'same', 'same', 'same', 'same', 'same', 'same', 'same', 'same']
# Define the camera trajectory
data = camera_tools.get_camera_trajectory(targets, anchors)
for N in np.arange(num*N_block,(num*N_block)+N_block):
print("N:",N,'| p:',data[N]['p'])
# Get images
if runall:
img, extent = getimage(snap, N, data, part_type=part_type, overwrite=True, P=P, S=S)
else:
img, extent = getimage(snap, N, data, part_type=part_type, overwrite=False)
rgb = apply_cmap(img,cmap,vlims)
fig = plt.figure(figsize=(16,9), frameon=False)
ax = fig.add_subplot(111)
# set extent to 16:9 ratio
ax.set_xlim(extent[0] * 16/9, extent[1] * 16/9)
ax.imshow(rgb, origin='lower', aspect='equal', extent=extent)
ax.tick_params(axis='both', left=False, top=False, right=False,
bottom=False, labelleft=False, labeltop=False,
labelright=False, labelbottom=False)
ax.set_facecolor(cmap(0.0)) # (0.95588623, 0.91961077, 0.95812116))
fname = 'plots/spheres/All/all_parts_animation_reg%s_snap%s_ptype%s_angle%05d.png'%(reg,snap,part_type,N)
print("Saving:",fname)
fig.savefig(fname, dpi=300, bbox_inches='tight')
plt.close(fig)
# beta[(z==0) & (x<0)] = -np.pi/2
alpha *= 180./np.pi
beta *= 180./np.pi
print(alpha,beta)
for ax,_orientation,_p,_t,_roll in zip(axes[:3,k], [0, 1, 4],
beta[[0,1,4]], alpha[[0,1,4]], [270,180,270]):
print("#########\nRendering orientation %s\np=%s, t=%s, roll=%s\n##########"%\
(_orientation,_p,_t,_roll))
if _orientation == 0:
mask = np.random.rand(len(halog_pos)) < 1
#Pg = sph.Particles(halog_pos[mask], halog_mass[mask] * 1e10)
Pd = sph.Particles(halog_pos[mask], halog_dust[mask] * 1e10)
# Psfr = sph.Particles(halog_pos[mask], halog_sfr[mask])
extent = 24.5
sm,img = plot_dist(fig, ax, Pd, hcood, cmaps.twilight(),
vmin=1e2, vmax=1e10, extent=extent, p=_p, t=_t, roll=_roll)
# sm4,img4 = plot_dist(fig, ax4, Psfr, hcood, cmaps.sunlight(),
# vmin=0.1, extent=extent, p=_p, t=_t, roll=_roll)
## ---- plot SEDs
# gidx = galaxies[k].GroupID
with h5py.File('sed_out_hires_test.h5','r') as f:
wav = f['%s/Wavelength'%gidx][:]
spec = f['%s/SED'%gidx][:]
def __init__(self, prop,
sim='L0100N1504',
run='REFERENCE',
snapnum=28):
print 'Initialising box for imaging...'
tag = snapdict[str(snapnum)][0]
sim_path = '/data5/simulations/EAGLE/' + sim + '/' + run + '/data/'
# Get volume information
boxsize = E.readAttribute('SNAP', sim_path, tag, "/Header/BoxSize")
h = E.readAttribute('SNAP', sim_path, tag, "/Header/HubbleParam")
a_0 = E.readAttribute('SNAP', sim_path, tag, "/Header/ExpansionFactor")
# Point read_eagle to the data
snapfile = sim_path + 'snapshot_' + tag + '/snap_' + tag + '.0.hdf5'
comm = MPI.COMM_WORLD
comm_rank = comm.Get_rank()
comm_size = comm.Get_size()
# Open snapshot
snap = read.EagleSnapshot(snapfile)
# Select region of interest
snap.select_region(0.,boxsize,0.,boxsize,0.,boxsize)
# Split selection between processors
# This assigns an equal number of hash cells to each processor.
snap.split_selection(comm_rank,comm_size)
if prop == 'stars':
#pos = load_array('Coordinates', 4, sim=sim, run=run, tag=tag).T
#smoothing_length = load_array('SmoothingLength', 4, sim=sim, run=run, tag=tag)
#quantity = load_array('Mass', 4, sim=sim, run=run, tag=tag) * 1e10
pos = snap.read_dataset(4,'Coordinates') * a_0/h
pos = pos.T
smoothing_length = snap.read_dataset(4, 'SmoothingLength') * a_0 / h
quantity = snap.read_dataset(4, 'Mass') / h * 1e10
else:
#pos = load_array('Coordinates', 0, sim=sim, run=run, tag=tag).T
#smoothing_length = load_array('SmoothingLength', 0, sim=sim, run=run, tag=tag)
pos = snap.read_dataset(0, 'Coordinates') * a_0 / h
print pos
pos = pos.T
smoothing_length = snap.read_dataset(0, 'SmoothingLength') * a_0 / h
if prop == 'gas':
quantity = snap.read_dataset(0, 'Mass') / h / 1e10
print quantity
elif prop == 'xrays':
pids = snap.read_dataset(0, 'ParticleIDs')
print 'Matching x-rays to particles'
xray_data = h5.File('/data6/arijdav1/Lx_matching/'+sim+'_'+run+'/'+tag+'.hdf5','r')
xrays = np.array(xray_data['Xray_luminosity']) / 1e30
xray_pids = np.array(xray_data['ParticleIDs'])
#match_sort = np.argsort(xray_pids)
#xrays = xrays[match_sort]
#xray_pids = xray_pids[match_sort]
quantity = xrays[np.searchsorted(xray_pids,pids)]
else:
raise IOError('Plot options are "gas","stars" or "xrays"')
N = len(quantity)
pos *= 1e3 # convert to kpc
smoothing_length *= 1e3
print N
Particles = sphviewer.Particles(pos, quantity, hsml=smoothing_length)
print Particles.get_pos()
print Particles.get_mass()
print Particles.get_hsml()
self.Scene = sphviewer.Scene(Particles)
self.sim = sim
self.run = run
self.tag = tag
self.property = prop
self.boxsize = boxsize / h
anchors['p'] = [0, 'pass', 'pass', 'pass', 'pass', 'pass', 900]
anchors['zoom'] = [1., 'same', 'same', 'same', 'same', 'same', 'same']
anchors['extent'] = [10, 'pass', 'pass', 'pass', 'pass', 'pass', 30]
data = get_camera_trajectory(targets, anchors)
n1 = 10000
cube1 = np.random.rand(3, n1)
cube1[1, :] -= 6
cube2 = np.random.rand(3, n1)
cube2[1, :] += 1
cubes = np.concatenate((cube1, cube2), axis=1)
mass = np.ones(n1+n1)
P = sph.Particles(cubes, mass)
S = sph.Scene(P)
h = 0
for i in data:
i['xsize'] = 200
i['ysize'] = 200
i['roll'] = 0
S = sph.Scene(P)
S.update_camera(**i)
print(S.Camera.get_params())
R = sph.Render(S)
img = R.get_image()
R.set_logscale()
plt.imsave('test/image_'+str('%d.png' % h), img,
vmin=0, vmax=6, cmap='cubehelix')
# sh_hmr = E.readArray("SUBFIND", sim, tag, "/Subhalo/HalfMassRad", numThreads=1)
## set centre of box
idx = np.argsort(sh_mstar)[::-1][0]
a, b, c = sh_cop[idx] # use most massive (mstar) halo
## Align with spin axis of galaxy
s = spin[idx]
t = np.arctan(s[0] / s[2]) * 180. / np.pi
p = np.arctan(s[1] / s[2]) * 180. / np.pi
## Create particle and camera objects
scaling = 1
P = sph.Particles(np.array(coods - [a, b, c]) * scaling, np.ones(len(coods)))
C = sph.Camera(x=0,
y=0,
z=0,
r=1,
zoom=1,
t=t,
p=p,
roll=0,
xsize=4000,
ysize=2250) # 16:9
S = sph.Scene(P, Camera=C)
## loop round object