"""
Routines for plotting smoothed quantities
"""
import warnings
import matplotlib
import numpy as np
import pylab as p
from .. import config, sph, units as _units
from ..sph import renderers
def _width_in_sim_units(sim, width):
if isinstance(width, str) or issubclass(width.__class__, _units.UnitBase):
if isinstance(width, str):
width = _units.Unit(width)
width = width.in_units(sim['pos'].units, **sim.conversion_context())
return width
[docs]
def sideon_image(sim, *args, **kwargs):
"""Create an image of the given simulation, side-on to the disc of the passed halo.
This routine is a small wrapper around :func:`~pynbody.plot.sph.image` that rotates the simulation so that the disc
of the passed halo is side-on, makes the SPH image, then rotates the simulation back to its original orientation.
More flexible control over the orientation of the simulation can be achieved by using
:func:`~pynbody.analysis.angmom.sideon` in combination with :func:`~pynbody.plot.sph.image`.
"""
from ..analysis import angmom
with angmom.sideon(sim):
return image(sim, *args, **kwargs)
[docs]
def faceon_image(sim, *args, **kwargs):
"""Create an image of the given simulation, face-on to the disc of the passed halo.
This routine is a small wrapper around :func:`~pynbody.plot.sph.image` that rotates the simulation so that the disc
of the passed halo is face-on, makes the SPH image, then rotates the simulation back to its original orientation.
More flexible control over the orientation of the simulation can be achieved by using
:func:`~pynbody.analysis.angmom.faceon` in combination with :func:`~pynbody.plot.sph.image`.
"""
from ..analysis import angmom
with angmom.faceon(sim):
return image(sim, *args, **kwargs)
[docs]
def contour(sim, qty, width="10 kpc", resolution=None, units=None, axes=None, label=True, log=True, weight=None,
contour_kwargs=None, smooth_floor=0.0, _transform=None):
"""Create an image of the given quantity then turn it into contours.
Parameters
----------
sim : pynbody.snapshot.simsnap.SimSnap
The simulation snapshot to plot. The image is generated in the plane z=0, or
projected along the z axis.
qty : str | pynbody.array.SimArray
The name of the array to interpolate. Default is 'rho', which gives a density
image. Alternatively, an array can be passed in.
width : str or float, optional
The overall width and height of the plot. If a float, it is assumed
to be in units of sim['pos']. It can also be passed in as a string indicating
the units, e.g. '10 kpc'. (Default is '10 kpc')
resolution : int, optional
The number of pixels wide and tall. (Default is determined by the
:ref:`configuration file <configuration>`.)
units : str or pynbody.units.Unit, optional
The units of the output. Default is None, in which case the units of the input
quantity are used. If the units correspond to integrating the quantity along
a spatial dimension, the output is a projected image. For example, if the units
are 'Msol kpc^-2', and the quantity is 'rho', the output is a projected image of
the surface density.
axes : matplotlib.axes.Axes, optional
Axes instance on which the image will be shown; if None, the current pyplot figure is
used. (Default is False)
label : bool, optional
Whether to label the contours. (Default is True)
log : bool, optional
If True, the image is log-scaled before being contoured. (Default is True)
weight : str, optional
If set, the requested quantity is volume-averaged down the line of sight, weighted either
by volume (if weight is True) or by a specified quantity. (Default is None)
contour_kwargs : dict, optional
Additional keyword arguments to pass to the matplotlib contour function. (Default is None)
smooth_floor : float, optional
The minimum size of the smoothing kernel, either as a float or a unit string.
Setting this to a non-zero value makes smoother, clearer contours but loses fine detail.
Default is 0.0.
_transform : function, optional
A function to apply to the image before contouring. (Default is None)
"""
if resolution is None:
resolution = config['image-default-resolution']
if axes is None:
axes = p.gca()
if contour_kwargs is None:
contour_kwargs = {}
width = _width_in_sim_units(sim, width)
pixel_size = width / resolution
# width of image must be a pixel wider than the width of the final contour field, since the contours
# are based on the centres of the pixels not their edges
pipeline = renderers.make_render_pipeline(sim.s, quantity=qty, width=width + pixel_size,
weight = weight, out_units = units, resolution = resolution,
smooth_floor = smooth_floor)
im = pipeline.render()
if log:
im = np.log10(im)
if _transform:
im = _transform(im)
# width of image was expanded above, so this is now the positions of the centres
X = np.linspace(-width/2, width/2, resolution)
CS = axes.contour(X, X, im, **contour_kwargs)
if label:
axes.clabel(CS, fontsize=12, inline=True)
[docs]
def velocity_image(sim, qty='rho', vector_qty='vel', width="10 kpc", mode='quiver',
vector_color='black', vector_edgecolor='black', vector_resolution=40,
vector_scale=None, key=True, key_x=0.5, key_y=0.88,
key_color='k', key_edge_color='k', key_bg_color='w',
key_length="100 km s**-1",
stream_density=1.0, stream_linewidth = 1.0,
weight=None, restrict_depth=False,
**kwargs):
"""
Make an SPH image of the given simulation with velocity vectors overlaid on top.
Any keyword argument that can be passed to :func:`~pynbody.plot.sph.image` can also be passed
to this function. See that function for a full list of options.
Parameters
----------
sim : pynbody.snapshot.simsnap.SimSnap
The simulation snapshot to plot. The image is generated in the plane z=0, or
projected along the z axis.
qty : str | pynbody.array.SimArray
The name of the array to interpolate. Default is 'rho', which gives a density
image. Alternatively, an array can be passed in.
vector_qty : str
The name of the array to use for the vectors. Default is 'vel'.
width : str or float, optional
The overall width and height of the plot. If a float, it is assumed
to be in units of sim['pos']. It can also be passed in as a string indicating
the units, e.g. '10 kpc'. (Default is '10 kpc')
mode : str, optional
The type of plot to make. Options are 'quiver' or 'stream'. (Default is 'quiver')
vector_color : str, optional
The color of the velocity vectors. (Default is 'black')
vector_edgecolor : str, optional
The color for the edges of the velocity vectors. (Default is 'black')
vector_resolution : int, optional
The number of velocity vectors to generate in each dimension. (Default is 40)
vector_scale : str or float, optional
The length of a vector that would result in a displayed length of the
figure width/height. This can be provided as a unit string or a float, in which
case it is interpreted as having the same units as the vector array being plotted.
Default is None, in which case the vectors are scaled by matplotlib's quiver function.
This option is only used in 'quiver' mode.
key : bool, optional
Whether or not to inset a key showing the scale of the vectors.
Only used if in 'quiver' mode. (Default is True)
key_x : float, optional
The x position of the key in 'quiver' mode, if key is True. (Default is 0.5)
key_y : float, optional
The y position of the key in 'quiver' mode, if key is True. (Default is 0.88)
key_color : str, optional
The color of the key arrow/text in 'quiver' mode, if key is True. (Default is 'white')
key_edge_color : str, optional
The color of the border around the key in 'quiver' mode, if key is True. (Default is 'black')
key_bg_color : str, optional
The color of the background of the key in 'quiver' mode, if key is True. (Default is 'white')
key_length : str, optional
The velocity to use for the key in 'quiver' mode, if key is True. (Default is '100 km s**-1')
stream_density : float, optional
The density of stream lines in 'stream' mode. (Default is 1.0)
stream_linewidth : float, optional
The width of stream lines in 'stream' mode. (Default is 1.0)
**kwargs :
Any additional keyword arguments to pass to :func:`~pynbody.plot.sph.image`.
"""
if 'av_z' in kwargs:
weight = kwargs.pop('av_z')
warnings.warn("av_z is deprecated; use weight instead", DeprecationWarning)
vx_name, vy_name, _ = sim._array_name_ND_to_1D(vector_qty)
weight_for_vector = weight
if 'units' in kwargs and _units_imply_projection(sim, qty, _units.Unit(kwargs['units'])) and weight is None:
weight_for_vector = 'rho'
vel_pipeline = renderers.make_render_pipeline(sim, quantity=vx_name, width=width,
resolution=vector_resolution, weight=weight_for_vector,
restrict_depth=restrict_depth)
vx = vel_pipeline.render()
vel_pipeline.set_quantity(vy_name)
vy = vel_pipeline.render()
key_unit = _units.Unit(key_length)
if isinstance(width, str) or issubclass(width.__class__, _units.UnitBase):
if isinstance(width, str):
width = _units.Unit(width)
width = width.in_units(sim['pos'].units, **sim.conversion_context())
width = float(width)
pixel_size = width / float(vector_resolution)
X, Y = np.meshgrid(np.linspace(-width / 2 + pixel_size/2, width / 2 - pixel_size/2, vector_resolution),
np.linspace(-width / 2 + pixel_size/2, width / 2 - pixel_size/2, vector_resolution))
im = image(sim, qty=qty, width=width, weight=weight, restrict_depth=restrict_depth,
**kwargs)
axes = kwargs.get('axes', None)
if axes is None:
axes = p.gca()
if mode == 'quiver':
if vector_scale is None:
Q = axes.quiver(X, Y, vx, vy, color=vector_color, edgecolor=vector_edgecolor)
else:
if isinstance(vector_scale, str):
vector_scale = _units.Unit(vector_scale)
if _units.is_unit(vector_scale):
vector_scale = vector_scale.in_units(sim['vel'].units)
Q = axes.quiver(X, Y, vx, vy, scale=vector_scale, color=vector_color,
edgecolor=vector_edgecolor)
if key:
from . import util
qk = util.PynbodyQuiverKey(Q, key_x, key_y,
key_unit.in_units(sim['vel'].units, **sim.conversion_context()),
"$" + key_unit.latex() + "$",
color=key_color, labelcolor=key_color,
boxedgecolor=key_edge_color, boxfacecolor=key_bg_color)
qk.set_zorder(6)
p.gca().add_artist(qk)
elif mode == 'stream' :
Q = axes.streamplot(X, Y, vx, vy, color=vector_color, density=stream_density, linewidth=stream_linewidth)
axes.set_xlim(-width/2, width/2)
axes.set_ylim(-width/2, width/2)
return im
[docs]
def volume(sim, qty='rho', width=None, resolution=200,
color=(1.0,1.0,1.0),vmin=None,vmax=None,
dynamic_range=4.0,log=True,
create_figure=True):
"""Create a volume rendering of the given simulation using mayavi.
.. warning ::
This function requires mayavi to be installed. However, mayavi does not seem to be under
active development and is not compatible with the latest versions of python.
As a result, this function will probably be removed in future versions of pynbody.
For a more modern alternative, consider using `topsy <https://github.com/pynbody/topsy/>`_.
Parameters
----------
sim : pynbody.snapshot.simsnap.SimSnap
The simulation snapshot to visualize
qty : str, optional
The name of the array to interpolate. Default is 'rho', which gives a density image.
width : str or float, optional
The width of the cube to generate, centered on the origin. If None, the width is determined
by the extent of the simulation snapshot.
resolution : int, optional
The number of elements along each side of the cube. (Default is 200)
color : tuple, optional
The color of the volume rendering. The value of each voxel is used to set the opacity.
vmin : float, optional
The value for zero opacity. If None, this is inferred from vmax and dynamic_range.
vmax : float, optional
The value for full opacity. If None, the maximum value of the image is used.
dynamic_range : float, optional
The dynamic range in dex to use if vmin and vmax are not specified.
Default is 4.0
log : bool, optional
If True, the image is log-scaled before passing to mayavi. (Default is True)
create_figure : bool, optional
If True, create a new mayavi figure before rendering. (Default is True)
"""
import mayavi
from mayavi import mlab
from tvtk.util.ctf import ColorTransferFunction, PiecewiseFunction
if create_figure:
fig = mlab.figure(size=(500,500),bgcolor=(0,0,0))
grid_data = sph.to_3d_grid(sim,qty=qty,nx=resolution,
x2=None if width is None else width/2)
if log:
grid_data = np.log10(grid_data)
if vmin is None:
vmin = grid_data.max()-dynamic_range
if vmax is None:
vmax = grid_data.max()
else:
if vmin is None:
vmin = np.min(grid_data)
if vmax is None:
vmax = np.max(grid_data)
grid_data[grid_data<vmin]=vmin
grid_data[grid_data>vmax]=vmax
otf = PiecewiseFunction()
otf.add_point(vmin,0.0)
otf.add_point(vmax,1.0)
sf = mayavi.tools.pipeline.scalar_field(grid_data)
V = mlab.pipeline.volume(sf,color=color,vmin=vmin,vmax=vmax)
V.trait_get('volume_mapper')['volume_mapper'].blend_mode = 'maximum_intensity'
if color is None:
ctf = ColorTransferFunction()
ctf.add_rgb_point(vmin,107./255,124./255,132./255)
ctf.add_rgb_point(vmin+(vmax-vmin)*0.8,200./255,178./255,164./255)
ctf.add_rgb_point(vmin+(vmax-vmin)*0.9,1.0,210./255,149./255)
ctf.add_rgb_point(vmax,1.0,222./255,141./255)
V._volume_property.set_color(ctf)
V._ctf = ctf
V.update_ctf = True
V._otf = otf
V._volume_property.set_scalar_opacity(otf)
return V
def _units_imply_projection(sim, qty, units):
if isinstance(qty, str):
qty = sim[qty]
try:
qty.units.ratio(units, **sim.conversion_context())
# if this fails, perhaps we're requesting a projected image?
return False
except _units.UnitsException:
# if the following fails, there's no interpretation this routine
# can cope with. The error will be allowed to propagate.
qty.units.ratio(
units / (sim['x'].units), **sim.conversion_context())
return True
[docs]
def spherical_image(sim, qty='rho', nside=None, kernel=None, threaded=None, units=None,
weight=False, log=True, vmin=None, vmax=None, cmap=None, xsize=1600):
"""Make an SPH image on the sky around the origin.
.. note::
While pynbody does not require the healpy module to be installed, this function requires healpy to render
the healpix image onto a Mollweide projection.
To install healpy, use ``pip install healpy``.
Parameters
----------
sim : pynbody.snapshot.simsnap.SimSnap
The simulation snapshot to plot. The output will be a projected spherical image centred on the origin of the
particles in the snapshot.
qty : str | pynbody.array.SimArray
The name of the array to interpolate. Default is 'rho', which gives a density image. Alternatively, an array
can be passed in.
nside : int
The healpix nside resolution to use (must be power of 2)
kernel : str, optional
SPH kernel to use for smoothing; see :func:`~pynbody.sph.kernels.create_kernel` for options.
units : str or pynbody.units.Unit, optional
The units of the output. Default is None, in which case the units of the input quantity are used. Note that
unless using *weight*, the output is a projected angular image. For example, for density, the output unit
is mass per solid angle.
threaded : bool, optional
If True, use threads to parallelise the rendering. (Default is set in the config file).
weight : bool or str, optional
If True, the requested quantity is volume-averaged down the line of sight. If a string, the requested quantity
is averaged down the line of sight weighted by the named array (e.g. use 'rho' for density-weighted quantity).
log : bool, optional
If True, the image is log-scaled. (Default is True)
vmin : float, optional
The minimum value for the color scale. If None, the minimum value of the image.
vmax : float, optional
The maximum value for the color scale. If None, the maximum value of the image.
cmap : matplotlib.colors.Colormap or str, optional
Colormap to use. If None, the default colormap is used.
xsize : int, optional
The *xsize* parameter for healpy.mollview, which determines the resolution of the projection (i.e. does not
affect the resolution of the actual image, but the presentation.) Default is 1600.
"""
try:
import healpy as hp
except ImportError:
raise ImportError("healpy is required for spherical_image function. Install with: pip install healpy")
image = sph.render_spherical_image(sim, quantity=qty, nside=nside, kernel=kernel, out_units=units,
weight=weight, threaded=threaded)
unit = image.units
if unit is not None:
unit = f'${unit.latex()}$'
else:
unit = ''
hp.mollview(image, title=None, hold=True, norm='log' if log else None, unit=unit, cmap=cmap, min=vmin, max=vmax,
xsize=xsize)
[docs]
def image(sim, qty='rho', width="10 kpc", resolution=None, units=None, log=True,
vmin=None, vmax=None, weight=False, z_camera=None, clear=True, cmap=None,
title=None, colorbar_label=None, qtytitle=None, show_cbar=True, axes=None,
noplot=False, return_image=False, return_array=False,
fill_nan=True, fill_val=0.0, linthresh=None,
restrict_depth = False, threaded=True, approximate_fast=None, denoise=None,
kernel=None,
**kwargs):
"""
Make an image of the given simulation, using SPH or denoised-SPH interpolation.
Parameters
----------
sim : pynbody.snapshot.simsnap.SimSnap
The simulation snapshot to plot. The image is generated in the plane z=0, or
projected along the z axis.
qty : str | pynbody.array.SimArray
The name of the array to interpolate. Default is 'rho', which gives a density
image. Alternatively, an array can be passed in.
width : str or float, optional
The overall width and height of the plot. If a float, it is assumed
to be in units of sim['pos']. It can also be passed in as a string indicating
the units, e.g. '10 kpc'. (Default is '10 kpc')
resolution : int, optional
The number of pixels wide and tall. (Default is determined by the
:ref:`configuration file <configuration>`.)
units : str or pynbody.units.Unit, optional
The units of the output. Default is None, in which case the units of the input
quantity are used. If the units correspond to integrating the quantity along
a spatial dimension, the output is a projected image. For example, if the units
are 'Msol kpc^-2', and the quantity is 'rho', the output is a projected image of
the surface density.
log : bool, optional
If True, the image is log-scaled. (Default is True)
vmin : float, optional
The minimum value for the color scale. If None, the minimum value of the image.
vmax : float, optional
The maximum value for the color scale. If None, the maximum value of the image.
weight : bool or str, optional
If True, the requested quantity is volume-averaged down the line of sight. If a string, the
requested quantity is averaged down the line of sight weighted by the named array
(e.g. use 'rho' for density-weighted quantity).
restrict_depth : bool, optional
If True, restrict the depth of the image to the width of the image. (Default is False)
z_camera : float, optional
If set, a perspective image is rendered, as though the camera is a pinhole camera
at (0,0,z_camera). The frustrum is defined by the width of the image in the plane z=0.
clear : bool, optional
Whether to clear the axes before plotting. (Default is True)
cmap : matplotlib.colors.Colormap or str, optional
Colormap to use. If None, the default colormap is used.
title : str, optional
Plot title.
colorbar_label : str, optional
Colorbar label. If not provided, one will be generated from the quantity name and units.
show_cbar : bool, optional
Whether to automatically plot the colorbar. (Default is True)
axes : matplotlib.axes.Axes, optional
Axes instance on which the image will be shown; if None, the current pyplot figure is
used. (Default is False)
noplot : bool, optional
If True, the image is not displayed, only the image array is returned. This option therefore
implies return_array = True.
return_image : bool, optional
If True, the image instance returned by imshow is returned. (Default is False)
return_array : bool, optional
If True, the numpy array of the image is returned. (Default is False)
fill_nan : bool, optional
If any of the image values are NaN, replace with fill_val. (Default is True)
fill_val : float, optional
The fill value to use when replacing NaNs. (Default is 0.0)
linthresh : float, optional
If the image has negative and positive values and a log scaling is requested, the part
between -linthresh and linthresh is shown on a linear scale to avoid divergence at 0.
kernel : str, optional
SPH kernel to use for smoothing; see :func:`~pynbody.sph.kernels.create_kernel` for options.
approximate_fast : bool, optional
If True, speed up the image-making by rendering large kernels onto a lower-resolution image
first, which is then interpolated to the final resolution. (Default is set in the config file).
threaded : bool, optional
If True, use threads to parallelise the rendering. (Default is set in the config file).
qtytitle : str, optional
Deprecated alias for colorbar_label.
av_z : bool or str, optional
Deprecated alias for weight.
Returns
-------
matplotlib.image.AxesImage
The image instance returned by imshow, if return_image is True.
numpy.ndarray
The image array, if return_array is True or noplot is True.
"""
global config
if not noplot:
import matplotlib.pylab as plt
if axes:
p = axes
else:
p = plt
if qtytitle is not None:
warnings.warn("qtytitle is deprecated; use colorbar_label instead", DeprecationWarning)
colorbar_label = qtytitle
if kwargs.get('av_z', None) is not None:
weight = kwargs.pop('av_z')
warnings.warn("av_z is deprecated; use weight instead", DeprecationWarning)
if kwargs.get('ret_im', None) is not None:
return_image = kwargs.pop('ret_im')
warnings.warn("ret_im is deprecated; use return_image instead", DeprecationWarning)
if colorbar_label is None and isinstance(qty, str):
qtytitle = qty
else:
qtytitle = None
renderer = renderers.make_render_pipeline(sim, quantity=qty, width=width, resolution=resolution,
out_units=units, weight=weight, restrict_depth=restrict_depth,
kernel=kernel, z_camera=z_camera, threaded=threaded,
approximate_fast=approximate_fast, denoise=denoise)
# if width was provided e.g. as string, we'll need it as a float
width = renderer.geometry.width
if weight and qtytitle:
qtytitle = f"$\\langle${qtytitle}$\\rangle$"
elif renderer.is_projected and qtytitle is not None:
qtytitle = f"$\\int\\,${qtytitle}$\\,\\mathrm{{d}}z$"
im = renderer.render()
if fill_nan:
im[np.isnan(im)] = fill_val
if not noplot:
# set the log or linear normalizations
if log:
try:
im[np.where(im == 0)] = abs(im[np.where(abs(im != 0))]).min()
except ValueError:
raise ValueError("Failed to make a sensible logarithmic image. This probably means there are no particles in the view.")
# check if there are negative values -- if so, use the symmetric
# log normalization
if (vmin is None and (im < 0).any() ) or ((vmin is not None) and vmin<0):
# need to set the linear regime around zero -- set to by
# default start at 1/1000 of the log range
if linthresh is None:
linthresh = np.nanmax(abs(im)) / 1000.
norm = matplotlib.colors.SymLogNorm(
linthresh, vmin=vmin, vmax=vmax)
else:
norm = matplotlib.colors.LogNorm(vmin=vmin, vmax=vmax)
else:
norm = matplotlib.colors.Normalize(vmin=vmin, vmax=vmax)
#
# do the actual plotting
#
if clear and not axes:
p.clf()
ims = p.imshow(im[::-1, :].view(np.ndarray), extent=(-width / 2, width / 2, -width / 2, width / 2),
cmap=cmap, norm = norm)
u_st = sim['pos'].units.latex()
if not axes:
plt.xlabel("$x/%s$" % u_st)
plt.ylabel("$y/%s$" % u_st)
else:
p.set_xlabel("$x/%s$" % u_st)
p.set_ylabel("$y/%s$" % u_st)
if units is None:
units = im.units
if not isinstance(units, _units.UnitBase):
units = _units.Unit(units)
if units.latex() == "":
units=""
else:
units = "$"+units.latex()+"$"
if show_cbar:
colorbar = plt.colorbar(ims)
if colorbar_label is not None:
colorbar.set_label(colorbar_label)
elif qtytitle is not None:
colorbar.set_label(qtytitle+"/"+units)
if title is not None:
if not axes:
p.title(title)
else:
p.set_title(title)
if return_image and return_array:
return ims, im
elif return_image:
return ims
elif return_array or noplot:
return im
