def set_xy_labels(units, kpc_per_arcsec, xlabelsize, ylabelsize, xyticksize):
"""Set the x and y labels of the figure, and set the fontsize of those labels.
The x and y labels are always the distance scales, thus the labels are either arc-seconds or kpc and depend on the \
units the figure is plotted in.
Parameters
-----------
units : str
The units of the y / x axis of the plots, in arc-seconds ('arcsec') or kiloparsecs ('kpc').
kpc_per_arcsec : float
The conversion factor between arc-seconds and kiloparsecs, required to plot the units in kpc.
xlabelsize : int
The fontsize of the x axes label.
ylabelsize : int
The fontsize of the y axes label.
xyticksize : int
The font size of the x and y ticks on the figure axes.
"""
if units in 'arcsec' or kpc_per_arcsec is None:
plt.xlabel('x (arcsec)', fontsize=xlabelsize)
plt.ylabel('y (arcsec)', fontsize=ylabelsize)
elif units in 'kpc':
plt.xlabel('x (kpc)', fontsize=xlabelsize)
plt.ylabel('y (kpc)', fontsize=ylabelsize)
else:
raise exc.PlottingException(
'The units supplied to the plotted are not a valid string (must be pixels | '
'arcsec | kpc)')
plt.tick_params(labelsize=xyticksize)
def convert_grid_units(array, grid_arcsec, units, kpc_per_arcsec):
"""Convert the grid from its input units (arc-seconds) to the input unit (e.g. retain arc-seconds) or convert to \
another set of units (pixels or kilo parsecs).
Parameters
-----------
array : data_type.array.scaled_array.ScaledArray
The 2D array of data_type which is plotted, the shape of which is used for converting the grid to units of pixels.
grid_arcsec : ndarray or data_type.array.grids.Grid
The (y,x) coordinates of the grid in arc-seconds, in an array of shape (total_coordinates, 2).
units : str
The units of the y / x axis of the plots, in arc-seconds ('arcsec') or kiloparsecs ('kpc').
kpc_per_arcsec : float
The conversion factor between arc-seconds and kiloparsecs, required to plot the units in kpc.
"""
if units in "pixels":
return array.grid_arcsec_to_grid_pixels(grid_arcsec=grid_arcsec)
elif units in "arcsec" or kpc_per_arcsec is None:
return grid_arcsec
elif units in "kpc":
return grid_arcsec * kpc_per_arcsec
else:
raise exc.PlottingException(
"The units supplied to the plotter are not a valid string (must be pixels | "
"arcsec | kpc)")
def get_normalization_scale(norm, norm_min, norm_max, linthresh, linscale):
"""Get the normalization scale of the colormap. This will be scaled based on the input min / max normalization \
values.
For a 'symmetric_log' colormap, linthesh and linscale also change the colormap.
If norm_min / norm_max are not supplied, the minimum / maximum values of the array of data are used.
Parameters
-----------
array : data.array.scaled_array.ScaledArray
The 2D array of data which is plotted.
norm_min : float or None
The minimum array value the colormap map spans (all values below this value are plotted the same color).
norm_max : float or None
The maximum array value the colormap map spans (all values above this value are plotted the same color).
linthresh : float
For the 'symmetric_log' colormap normalization ,this specifies the range of values within which the colormap \
is linear.
linscale : float
For the 'symmetric_log' colormap normalization, this allowws the linear range set by linthresh to be stretched \
relative to the logarithmic range.
"""
if norm is 'linear':
return colors.Normalize(vmin=norm_min, vmax=norm_max)
elif norm is 'log':
if norm_min == 0.0:
norm_min = 1.e-4
return colors.LogNorm(vmin=norm_min, vmax=norm_max)
elif norm is 'symmetric_log':
return colors.SymLogNorm(linthresh=linthresh, linscale=linscale, vmin=norm_min, vmax=norm_max)
else:
raise exc.PlottingException('The normalization (norm) supplied to the plotter is not a valid string (must be '
'linear | log | symmetric_log')
def get_extent(array, units, kpc_per_arcsec, xticks_manual, yticks_manual):
"""Get the extent of the dimensions of the array in the units of the figure (e.g. arc-seconds or kpc).
This is used to set the extent of the array and thus the y / x axis limits.
Parameters
-----------
array : data.array.scaled_array.ScaledArray
The 2D array of data which is plotted.
units : str
The units of the y / x axis of the plots, in arc-seconds ('arcsec') or kiloparsecs ('kpc').
kpc_per_arcsec : float
The conversion factor between arc-seconds and kiloparsecs, required to plot the units in kpc.
xticks_manual : [] or None
If input, the xticks do not use the array's default xticks but instead overwrite them as these values.
yticks_manual : [] or None
If input, the yticks do not use the array's default yticks but instead overwrite them as these values.
"""
if xticks_manual is not None and yticks_manual is not None:
return np.asarray([xticks_manual[0], xticks_manual[3], yticks_manual[0], yticks_manual[3]])
if units in 'pixels':
return np.asarray([0, array.shape[1], 0, array.shape[0]])
elif units in 'arcsec' or kpc_per_arcsec is None:
return np.asarray([array.arc_second_minima[1], array.arc_second_maxima[1],
array.arc_second_minima[0], array.arc_second_maxima[0]])
elif units in 'kpc':
return list(map(lambda tick : tick*kpc_per_arcsec,
np.asarray([array.arc_second_minima[1], array.arc_second_maxima[1],
array.arc_second_minima[0], array.arc_second_maxima[0]])))
else:
raise exc.PlottingException('The units supplied to the plotted are not a valid string (must be pixels | '
'arcsec | kpc)')
def set_colorbar(cb_ticksize, cb_fraction, cb_pad, cb_tick_values,
cb_tick_labels):
"""Setup the colorbar of the figure, specifically its ticksize and the size is appears relative to the figure.
Parameters
-----------
cb_ticksize : int
The size of the tick labels on the colorbar.
cb_fraction : float
The fraction of the figure that the colorbar takes up, which resizes the colorbar relative to the figure.
cb_pad : float
Pads the color bar in the figure, which resizes the colorbar relative to the figure.
cb_tick_values : [float]
Manually specified values of where the colorbar tick labels appear on the colorbar.
cb_tick_labels : [float]
Manually specified labels of the color bar tick labels, which appear where specified by cb_tick_values.
"""
if cb_tick_values is None and cb_tick_labels is None:
cb = plt.colorbar(fraction=cb_fraction, pad=cb_pad)
elif cb_tick_values is not None and cb_tick_labels is not None:
cb = plt.colorbar(fraction=cb_fraction,
pad=cb_pad,
ticks=cb_tick_values)
cb.ax.set_yticklabels(cb_tick_labels)
else:
raise exc.PlottingException(
"Only 1 entry of cb_tick_values or cb_tick_labels was input. You must either supply"
"both the values and labels, or neither.")
cb.ax.tick_params(labelsize=cb_ticksize)
def plot_y_vs_x(y, x, plot_axis_type, label):
if plot_axis_type is "linear":
plt.plot(x, y, label=label)
elif plot_axis_type is "semilogy":
plt.semilogy(x, y, label=label)
elif plot_axis_type is "loglog":
plt.loglog(x, y, label=label)
else:
raise exc.PlottingException(
"The plot_axis_type supplied to the plotter is not a valid string (must be linear "
"| semilogy | loglog)")
def plot_model_image_of_planes(
fit, plot_foreground=False, plot_source=False, mask=None, extract_array_from_mask=False, zoom_around_mask=False,
positions=None, as_subplot=False,
units='arcsec', kpc_per_arcsec=None, figsize=(7, 7), aspect='equal',
cmap='jet', norm='linear', norm_min=None, norm_max=None, linthresh=0.05, linscale=0.01,
cb_ticksize=10, cb_fraction=0.047, cb_pad=0.01,
title='Fit Model Image', titlesize=16, xlabelsize=16, ylabelsize=16, xyticksize=16,
mask_pointsize=10, position_pointsize=10,
output_path=None, output_format='show', output_filename='fit_model_image_of_plane'):
"""Plot the model image of a specific plane of a lens fit.
Set *autolens.datas.array.plotters.array_plotters* for a description of all input parameters not described below.
Parameters
-----------
fit : datas.fitting.fitting.AbstractFitter
The fit to the datas, which includes a list of every model image, residual_map, chi-squareds, etc.
plane_indexes : [int]
The plane from which the model image is generated.
"""
if plot_foreground:
if fit.tracer.total_planes == 2:
model_image = fit.model_image_of_planes[0]
else:
model_image = sum(fit.model_image_of_planes[0:-2])
elif plot_source:
model_image = fit.model_image_of_planes[-1]
else:
raise exc.PlottingException('Both plot_foreground and plot_source were False, one must be True')
array_plotters.plot_array(
array=model_image, mask=mask, extract_array_from_mask=extract_array_from_mask,
zoom_around_mask=zoom_around_mask, positions=positions, as_subplot=as_subplot,
units=units, kpc_per_arcsec=kpc_per_arcsec, figsize=figsize, aspect=aspect,
cmap=cmap, norm=norm, norm_min=norm_min, norm_max=norm_max, linthresh=linthresh, linscale=linscale,
cb_ticksize=cb_ticksize, cb_fraction=cb_fraction, cb_pad=cb_pad,
title=title, titlesize=titlesize, xlabelsize=xlabelsize, ylabelsize=ylabelsize, xyticksize=xyticksize,
mask_pointsize=mask_pointsize, position_pointsize=position_pointsize,
output_path=output_path, output_format=output_format, output_filename=output_filename)
def plot_vertical_lines(vertical_lines, vertical_line_labels, units,
kpc_per_arcsec):
if vertical_lines is [] or vertical_lines is None:
return
for vertical_line, vertical_line_label in zip(vertical_lines,
vertical_line_labels):
if units in "arcsec" or kpc_per_arcsec is None:
x_value_plot = vertical_line
elif units in "kpc":
x_value_plot = vertical_line
else:
raise exc.PlottingException(
"The units supplied to the plotter are not a valid string (must be pixels | "
"arcsec | kpc)")
plt.axvline(x=x_value_plot, label=vertical_line_label, linestyle="--")
def set_xy_labels_and_ticksize(units, kpc_per_arcsec, ylabel, xlabelsize,
ylabelsize, xyticksize):
"""Set the x and y labels of the figure, and set the fontsize of those labels.
The x label is always the distance scale / radius, thus the x-label is either arc-seconds or kpc and depending \
on the units the figure is plotted in.
The ylabel is the physical quantity being plotted and is passed as an input parameter.
Parameters
-----------
units : str
The units of the y / x axis of the plots, in arc-seconds ('arcsec') or kiloparsecs ('kpc').
kpc_per_arcsec : float
The conversion factor between arc-seconds and kiloparsecs, required to plot the units in kpc.
ylabel : str
The y-label of the figure, which is the physical quantitiy being plotted.
xlabelsize : int
The fontsize of the x axes label.
ylabelsize : int
The fontsize of the y axes label.
xyticksize : int
The font size of the x and y ticks on the figure axes.
"""
plt.ylabel(ylabel=ylabel, fontsize=ylabelsize)
if units in "arcsec" or kpc_per_arcsec is None:
plt.xlabel("x (arcsec)", fontsize=xlabelsize)
elif units in "kpc":
plt.xlabel("x (kpc)", fontsize=xlabelsize)
else:
raise exc.PlottingException(
"The units supplied to the plotter are not a valid string (must be pixels | "
"arcsec | kpc)")
plt.tick_params(labelsize=xyticksize)
def output_subplot_array(output_path, output_filename, output_format):
"""Output a figure which consists of a set of subplot,, either as an image on the screen or to the hard-disk as a \
.png file.
Parameters
-----------
output_path : str
The path on the hard-disk where the figure is output.
output_filename : str
The filename of the figure that is output.
output_format : str
The format the figue is output:
'show' - display on computer screen.
'png' - output to hard-disk as a png.
"""
if output_format is 'show':
plt.show()
elif output_format is 'png':
plt.savefig(output_path + output_filename + '.png',
bbox_inches='tight')
elif output_format is 'fits':
raise exc.PlottingException(
'You cannot output a subplots with format .fits')
def plot_galaxy_data_array(
galaxy_data,
mask=None,
extract_array_from_mask=False,
zoom_around_mask=False,
positions=None,
as_subplot=False,
units="arcsec",
kpc_per_arcsec=None,
figsize=None,
aspect="square",
cmap="jet",
norm="linear",
norm_min=None,
norm_max=None,
linthresh=0.05,
linscale=0.01,
cb_ticksize=10,
cb_fraction=0.047,
cb_pad=0.01,
cb_tick_values=None,
cb_tick_labels=None,
titlesize=10,
xlabelsize=10,
ylabelsize=10,
xyticksize=10,
mask_pointsize=10,
position_pointsize=10.0,
grid_pointsize=1,
output_path=None,
output_filename="galaxy_data",
output_format="show",
):
if galaxy_data.use_image:
title = "Galaxy Data Image"
elif galaxy_data.use_convergence:
title = "Galaxy Data Convergence"
elif galaxy_data.use_potential:
title = "Galaxy Data Potential"
elif galaxy_data.use_deflections_y:
title = "Galaxy Data Deflections (y)"
elif galaxy_data.use_deflections_x:
title = "Galaxy Data Deflections (x)"
else:
raise exc.PlottingException(
"The galaxy data_type array does not have a True use_profile_type")
array_plotters.plot_array(
array=galaxy_data.image(return_in_2d=True),
mask=mask,
extract_array_from_mask=extract_array_from_mask,
zoom_around_mask=zoom_around_mask,
positions=positions,
as_subplot=as_subplot,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
figsize=figsize,
aspect=aspect,
cmap=cmap,
norm=norm,
norm_min=norm_min,
norm_max=norm_max,
linthresh=linthresh,
linscale=linscale,
cb_ticksize=cb_ticksize,
cb_fraction=cb_fraction,
cb_pad=cb_pad,
cb_tick_values=cb_tick_values,
cb_tick_labels=cb_tick_labels,
title=title,
titlesize=titlesize,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
xyticksize=xyticksize,
mask_pointsize=mask_pointsize,
position_pointsize=position_pointsize,
grid_pointsize=grid_pointsize,
output_path=output_path,
output_format=output_format,
output_filename=output_filename,
)
def plot_galaxy_data_array(galaxy_data,
mask=None,
extract_array_from_mask=False,
zoom_around_mask=False,
positions=None,
as_subplot=False,
units='arcsec',
kpc_per_arcsec=None,
figsize=None,
aspect='equal',
cmap='jet',
norm='linear',
norm_min=None,
norm_max=None,
linthresh=0.05,
linscale=0.01,
cb_ticksize=10,
cb_fraction=0.047,
cb_pad=0.01,
titlesize=10,
xlabelsize=10,
ylabelsize=10,
xyticksize=10,
mask_pointsize=10,
position_pointsize=10.0,
grid_pointsize=1,
output_path=None,
output_filename='galaxy_data',
output_format='show'):
if galaxy_data.use_intensities:
title = 'Galaxy Data Intensities'
elif galaxy_data.use_surface_density:
title = 'Galaxy Data Surface Density'
elif galaxy_data.use_potential:
title = 'Galaxy Data Potential'
elif galaxy_data.use_deflections_y:
title = 'Galaxy Data Deflections (y)'
elif galaxy_data.use_deflections_x:
title = 'Galaxy Data Deflections (x)'
else:
raise exc.PlottingException(
'The galaxy data array does not have a True use_profile_type')
array_plotters.plot_array(array=galaxy_data.image,
mask=mask,
extract_array_from_mask=extract_array_from_mask,
zoom_around_mask=zoom_around_mask,
positions=positions,
as_subplot=as_subplot,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
figsize=figsize,
aspect=aspect,
cmap=cmap,
norm=norm,
norm_min=norm_min,
norm_max=norm_max,
linthresh=linthresh,
linscale=linscale,
cb_ticksize=cb_ticksize,
cb_fraction=cb_fraction,
cb_pad=cb_pad,
title=title,
titlesize=titlesize,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
xyticksize=xyticksize,
mask_pointsize=mask_pointsize,
position_pointsize=position_pointsize,
grid_pointsize=grid_pointsize,
output_path=output_path,
output_format=output_format,
output_filename=output_filename)