def plot_line(
y,
x,
as_subplot=False,
label=None,
plot_axis_type="semilogy",
vertical_lines=None,
vertical_line_labels=None,
units="arcsec",
kpc_per_arcsec=None,
figsize=(7, 7),
plot_legend=False,
title="Quantity vs Radius",
ylabel="Quantity",
titlesize=16,
xlabelsize=16,
ylabelsize=16,
xyticksize=16,
legend_fontsize=12,
output_path=None,
output_format="show",
output_filename="quantity_vs_radius",
):
plotter_util.setup_figure(figsize=figsize, as_subplot=as_subplot)
plotter_util.set_title(title=title, titlesize=titlesize)
if x is None:
x = np.arange(len(y))
plot_y_vs_x(y=y, x=x, plot_axis_type=plot_axis_type, label=label)
set_xy_labels_and_ticksize(
units=units,
kpc_per_arcsec=kpc_per_arcsec,
ylabel=ylabel,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
xyticksize=xyticksize,
)
plot_vertical_lines(
vertical_lines=vertical_lines,
vertical_line_labels=vertical_line_labels,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
)
set_legend(plot_legend=plot_legend, legend_fontsize=legend_fontsize)
plotter_util.output_figure(
array=None,
as_subplot=as_subplot,
output_path=output_path,
output_filename=output_filename,
output_format=output_format,
)
plotter_util.close_figure(as_subplot=as_subplot)
def plot_inversion_with_source_values(
inversion,
source_pixel_values,
plot_origin=True,
positions=None,
should_plot_centres=False,
should_plot_grid=False,
should_plot_border=False,
image_pixels=None,
source_pixels=None,
as_subplot=False,
units="arcsec",
kpc_per_arcsec=None,
figsize=(7, 7),
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,
title="Reconstructed Pixelization",
titlesize=16,
xlabelsize=16,
ylabelsize=16,
xyticksize=16,
output_path=None,
output_format="show",
output_filename="pixelization_source_values",
):
if isinstance(inversion.mapper, mappers.RectangularMapper):
reconstructed_pixelization = inversion.mapper.reconstructed_pixelization_from_solution_vector(
solution_vector=source_pixel_values)
origin = get_origin(image=reconstructed_pixelization,
plot_origin=plot_origin)
array_plotters.plot_array(
array=reconstructed_pixelization,
origin=origin,
positions=positions,
as_subplot=True,
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,
output_filename=output_filename,
)
mapper_plotters.plot_rectangular_mapper(
mapper=inversion.mapper,
should_plot_centres=should_plot_centres,
should_plot_grid=should_plot_grid,
should_plot_border=should_plot_border,
image_pixels=image_pixels,
source_pixels=source_pixels,
as_subplot=True,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
title=title,
titlesize=titlesize,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
xyticksize=xyticksize,
)
plotter_util.output_figure(
array=reconstructed_pixelization,
as_subplot=as_subplot,
output_path=output_path,
output_filename=output_filename,
output_format=output_format,
)
elif isinstance(inversion.mapper, mappers.VoronoiMapper):
mapper_plotters.plot_voronoi_mapper(
mapper=inversion.mapper,
source_pixel_values=source_pixel_values,
should_plot_centres=should_plot_centres,
should_plot_grid=should_plot_grid,
should_plot_border=should_plot_border,
image_pixels=image_pixels,
source_pixels=source_pixels,
as_subplot=True,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
title=title,
titlesize=titlesize,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
xyticksize=xyticksize,
)
plotter_util.output_figure(
array=None,
as_subplot=as_subplot,
output_path=output_path,
output_filename=output_filename,
output_format=output_format,
)
def plot_voronoi_mapper(
mapper,
source_pixel_values,
should_plot_centres=True,
should_plot_grid=True,
should_plot_border=False,
image_pixels=None,
source_pixels=None,
as_subplot=False,
units="arcsec",
kpc_per_arcsec=None,
xyticksize=16,
figsize=(7, 7),
title="Rectangular Mapper",
titlesize=16,
xlabelsize=16,
ylabelsize=16,
cb_ticksize=10,
cb_fraction=0.047,
cb_pad=0.01,
cb_tick_values=None,
cb_tick_labels=None,
output_path=None,
output_filename="voronoi_mapper",
output_format="show",
):
plotter_util.setup_figure(figsize=figsize, as_subplot=as_subplot)
set_axis_limits(mapper=mapper, units=units, kpc_per_arcsec=kpc_per_arcsec)
regions_SP, vertices_SP = voronoi_finite_polygons_2d(mapper.voronoi)
color_values = source_pixel_values[:] / np.max(source_pixel_values)
cmap = plt.get_cmap("jet")
set_colorbar(
cmap=cmap,
color_values=source_pixel_values,
cb_fraction=cb_fraction,
cb_pad=cb_pad,
cb_tick_values=cb_tick_values,
cb_tick_labels=cb_tick_labels,
)
for region, index in zip(regions_SP, range(mapper.pixels)):
polygon = vertices_SP[region]
col = cmap(color_values[index])
plt.fill(*zip(*polygon), alpha=0.7, facecolor=col, lw=0.0)
plotter_util.set_title(title=title, titlesize=titlesize)
grid_plotters.set_xy_labels(
units=units,
kpc_per_arcsec=kpc_per_arcsec,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
xyticksize=xyticksize,
)
plot_centres(
should_plot_centres=should_plot_centres,
mapper=mapper,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
)
plot_plane_grid(
should_plot_grid=should_plot_grid,
mapper=mapper,
as_subplot=True,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
pointsize=10,
xyticksize=xyticksize,
title=title,
titlesize=titlesize,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
)
plot_border(
should_plot_border=should_plot_border,
mapper=mapper,
as_subplot=True,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
pointsize=30,
xyticksize=xyticksize,
title=title,
titlesize=titlesize,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
)
mapper_grid = convert_grid(
grid=mapper.grid, units=units, kpc_per_arcsec=kpc_per_arcsec
)
point_colors = itertools.cycle(["y", "r", "k", "g", "m"])
plot_source_plane_image_pixels(
grid=mapper_grid, image_pixels=image_pixels, point_colors=point_colors
)
plot_source_plane_source_pixels(
grid=mapper_grid,
mapper=mapper,
source_pixels=source_pixels,
point_colors=point_colors,
)
plotter_util.output_figure(
None,
as_subplot=as_subplot,
output_path=output_path,
output_filename=output_filename,
output_format=output_format,
)
plotter_util.close_figure(as_subplot=as_subplot)
def plot_rectangular_mapper(
mapper,
should_plot_centres=False,
should_plot_grid=False,
should_plot_border=False,
image_pixels=None,
source_pixels=None,
as_subplot=False,
units="arcsec",
kpc_per_arcsec=None,
xyticksize=16,
figsize=(7, 7),
title="Rectangular Mapper",
titlesize=16,
xlabelsize=16,
ylabelsize=16,
output_path=None,
output_filename="rectangular_mapper",
output_format="show",
):
plotter_util.setup_figure(figsize=figsize, as_subplot=as_subplot)
set_axis_limits(mapper=mapper, units=units, kpc_per_arcsec=kpc_per_arcsec)
plot_rectangular_pixelization_lines(
mapper=mapper, units=units, kpc_per_arcsec=kpc_per_arcsec
)
plotter_util.set_title(title=title, titlesize=titlesize)
grid_plotters.set_xy_labels(
units=units,
kpc_per_arcsec=kpc_per_arcsec,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
xyticksize=xyticksize,
)
plot_centres(
should_plot_centres=should_plot_centres,
mapper=mapper,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
)
plot_plane_grid(
should_plot_grid=should_plot_grid,
mapper=mapper,
as_subplot=True,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
pointsize=10,
xyticksize=xyticksize,
title=title,
titlesize=titlesize,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
)
plot_border(
should_plot_border=should_plot_border,
mapper=mapper,
as_subplot=True,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
pointsize=30,
xyticksize=xyticksize,
title=title,
titlesize=titlesize,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
)
mapper_grid = convert_grid(
grid=mapper.grid, units=units, kpc_per_arcsec=kpc_per_arcsec
)
point_colors = itertools.cycle(["y", "r", "k", "g", "m"])
plot_source_plane_image_pixels(
grid=mapper_grid, image_pixels=image_pixels, point_colors=point_colors
)
plot_source_plane_source_pixels(
grid=mapper_grid,
mapper=mapper,
source_pixels=source_pixels,
point_colors=point_colors,
)
plotter_util.output_figure(
None,
as_subplot=as_subplot,
output_path=output_path,
output_filename=output_filename,
output_format=output_format,
)
plotter_util.close_figure(as_subplot=as_subplot)
def plot_array(
array,
origin=None,
mask=None,
extract_array_from_mask=False,
zoom_around_mask=False,
should_plot_border=False,
lines=None,
positions=None,
centres=None,
axis_ratios=None,
phis=None,
grid=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,
cb_tick_values=None,
cb_tick_labels=None,
title="Array",
titlesize=16,
xlabelsize=16,
ylabelsize=16,
xyticksize=16,
mask_pointsize=10,
border_pointsize=2,
position_pointsize=30,
grid_pointsize=1,
xticks_manual=None,
yticks_manual=None,
output_path=None,
output_format="show",
output_filename="array",
):
"""Plot an array of data_type as a figure.
Parameters
-----------
array : data_type.array.scaled_array.ScaledArray
The 2D array of data_type which is plotted.
origin : (float, float).
The origin of the coordinate system of the array, which is plotted as an 'x' on the image if input.
mask : data_type.array.mask.Mask
The mask applied to the array, the edge of which is plotted as a set of points over the plotted array.
extract_array_from_mask : bool
The plotter array is extracted using the mask, such that masked values are plotted as zeros. This ensures \
bright features outside the mask do not impact the color map of the plot.
zoom_around_mask : bool
If True, the 2D region of the array corresponding to the rectangle encompassing all unmasked values is \
plotted, thereby zooming into the region of interest.
should_plot_border : bool
If a mask is supplied, its borders pixels (e.g. the exterior edge) is plotted if this is *True*.
positions : [[]]
Lists of (y,x) coordinates on the image which are plotted as colored dots, to highlight specific pixels.
grid : data_type.array.grids.Grid
A grid of (y,x) coordinates which may be plotted over the plotted array.
as_subplot : bool
Whether the array is plotted as part of a subplot, in which case the grid figure is not opened / closed.
units : str
The units of the y / x axis of the plots, in arc-seconds ('arcsec') or kiloparsecs ('kpc').
kpc_per_arcsec : float or None
The conversion factor between arc-seconds and kiloparsecs, required to plot the units in kpc.
figsize : (int, int)
The size of the figure in (rows, columns).
aspect : str
The aspect ratio of the array, specifically whether it is forced to be square ('equal') or adapts its size to \
the figure size ('auto').
cmap : str
The colormap the array is plotted using, which may be chosen from the standard matplotlib colormaps.
norm : str
The normalization of the colormap used to plot the image, specifically whether it is linear ('linear'), log \
('log') or a symmetric log normalization ('symmetric_log').
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.
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.
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.
mask_pointsize : int
The size of the points plotted to show the mask.
border_pointsize : int
The size of the points plotted to show the borders.
positions_pointsize : int
The size of the points plotted to show the input positions.
grid_pointsize : int
The size of the points plotted to show the grid.
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.
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.
'fits' - output to hard-disk as a fits file.'
Returns
--------
None
Examples
--------
array_plotters.plot_array(
array=image, origin=(0.0, 0.0), mask=circular_mask, extract_array_from_mask=True, zoom_around_mask=True,
should_plot_border=False, positions=[[1.0, 1.0], [2.0, 2.0]], grid=None, as_subplot=False,
units='arcsec', kpc_per_arcsec=None, figsize=(7,7), aspect='auto',
cmap='jet', norm='linear, norm_min=None, norm_max=None, linthresh=None, linscale=None,
cb_ticksize=10, cb_fraction=0.047, cb_pad=0.01, cb_tick_values=None, cb_tick_labels=None,
title='Image', titlesize=16, xlabelsize=16, ylabelsize=16, xyticksize=16,
mask_pointsize=10, border_pointsize=2, position_pointsize=10, grid_pointsize=10,
xticks_manual=None, yticks_manual=None,
output_path='/path/to/output', output_format='png', output_filename='image')
"""
if array is None or np.all(array == 0):
return
if extract_array_from_mask and mask is not None:
array = np.add(array,
0.0,
out=np.zeros_like(array),
where=np.asarray(mask) == 0)
if zoom_around_mask and mask is not None:
array = array.zoomed_scaled_array_around_mask(mask=mask, buffer=2)
zoom_offset_pixels = np.asarray(mask.zoom_offset_pixels)
zoom_offset_arcsec = np.asarray(mask.zoom_offset_arcsec)
else:
zoom_offset_pixels = None
zoom_offset_arcsec = None
if aspect is "square":
aspect = float(array.shape_arcsec[1]) / float(array.shape_arcsec[0])
fig = plot_figure(
array=array,
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,
xticks_manual=xticks_manual,
yticks_manual=yticks_manual,
)
plotter_util.set_title(title=title, titlesize=titlesize)
set_xy_labels_and_ticksize(
units=units,
kpc_per_arcsec=kpc_per_arcsec,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
xyticksize=xyticksize,
)
plotter_util.set_colorbar(
cb_ticksize=cb_ticksize,
cb_fraction=cb_fraction,
cb_pad=cb_pad,
cb_tick_values=cb_tick_values,
cb_tick_labels=cb_tick_labels,
)
plot_origin(
array=array,
origin=origin,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
zoom_offset_arcsec=zoom_offset_arcsec,
)
plot_mask(
mask=mask,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
pointsize=mask_pointsize,
zoom_offset_pixels=zoom_offset_pixels,
)
plotter_util.plot_lines(line_lists=lines)
plot_border(
mask=mask,
should_plot_border=should_plot_border,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
pointsize=border_pointsize,
zoom_offset_arcsec=zoom_offset_arcsec,
)
plot_points(
points_arcsec=positions,
array=array,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
pointsize=position_pointsize,
zoom_offset_arcsec=zoom_offset_arcsec,
)
plot_grid(
grid_arcsec=grid,
array=array,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
pointsize=grid_pointsize,
zoom_offset_arcsec=zoom_offset_arcsec,
)
plot_centres(
array=array,
centres=centres,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
zoom_offset_arcsec=zoom_offset_arcsec,
)
plot_ellipses(
fig=fig,
array=array,
centres=centres,
axis_ratios=axis_ratios,
phis=phis,
units=units,
kpc_per_arcsec=kpc_per_arcsec,
zoom_offset_arcsec=zoom_offset_arcsec,
)
plotter_util.output_figure(
array,
as_subplot=as_subplot,
output_path=output_path,
output_filename=output_filename,
output_format=output_format,
)
plotter_util.close_figure(as_subplot=as_subplot)
def plot_grid(
grid,
colors=None,
axis_limits=None,
points=None,
lines=None,
as_subplot=False,
units="arcsec",
kpc_per_arcsec=None,
figsize=(12, 8),
pointsize=5,
pointcolor="k",
xyticksize=16,
cmap="jet",
cb_ticksize=10,
cb_fraction=0.047,
cb_pad=0.01,
cb_tick_values=None,
cb_tick_labels=None,
title="Grid",
titlesize=16,
xlabelsize=16,
ylabelsize=16,
symmetric_around_centre=True,
output_path=None,
output_format="show",
output_filename="grid",
):
"""Plot a grid of (y,x) Cartesian coordinates as a scatter plot of points.
Parameters
-----------
grid : data_type.array.grids.Grid
The (y,x) coordinates of the grid, in an array of shape (total_coordinates, 2).
axis_limits : []
The axis limits of the figure on which the grid is plotted, following [xmin, xmax, ymin, ymax].
points : []
A set of points that are plotted in a different colour for emphasis (e.g. to show the mappings between \
different planes).
as_subplot : bool
Whether the grid is plotted as part of a subplot, in which case the grid figure is not opened / closed.
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.
figsize : (int, int)
The size of the figure in (rows, columns).
pointsize : int
The size of the points plotted on the grid.
xyticksize : int
The font size of the x and y ticks on the figure axes.
title : str
The text of the title.
titlesize : int
The size of of the title of the figure.
xlabelsize : int
The fontsize of the x axes label.
ylabelsize : int
The fontsize of the y axes label.
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.
"""
plotter_util.setup_figure(figsize=figsize, as_subplot=as_subplot)
grid = convert_grid_units(grid_arcsec=grid,
units=units,
kpc_per_arcsec=kpc_per_arcsec)
if colors is not None:
plt.cm.get_cmap(cmap)
plt.scatter(
y=np.asarray(grid[:, 0]),
x=np.asarray(grid[:, 1]),
c=colors,
s=pointsize,
marker=".",
cmap=cmap,
)
if colors is not None:
plotter_util.set_colorbar(
cb_ticksize=cb_ticksize,
cb_fraction=cb_fraction,
cb_pad=cb_pad,
cb_tick_values=cb_tick_values,
cb_tick_labels=cb_tick_labels,
)
plotter_util.set_title(title=title, titlesize=titlesize)
set_xy_labels(
units=units,
kpc_per_arcsec=kpc_per_arcsec,
xlabelsize=xlabelsize,
ylabelsize=ylabelsize,
xyticksize=xyticksize,
)
set_axis_limits(
axis_limits=axis_limits,
grid=grid,
symmetric_around_centre=symmetric_around_centre,
)
plot_points(grid=grid, points=points, pointcolor=pointcolor)
plotter_util.plot_lines(line_lists=lines)
plt.tick_params(labelsize=xyticksize)
plotter_util.output_figure(
array=None,
as_subplot=as_subplot,
output_path=output_path,
output_filename=output_filename,
output_format=output_format,
)
plotter_util.close_figure(as_subplot=as_subplot)