#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Plotting utilities.
.. codeauthor:: Rasmus Handberg <rasmush@phys.au.dk>
"""
import logging
import os
import copy
import warnings
import numpy as np
from bottleneck import allnan, anynan
import matplotlib
from matplotlib.ticker import MaxNLocator
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
import astropy.visualization as viz
# Change to a non-GUI backend since this
# should be able to run on a cluster:
plt.switch_backend('Agg')
#--------------------------------------------------------------------------------------------------
[docs]
def plots_interactive(backend=('Qt5Agg', 'MacOSX', 'Qt4Agg', 'GTK3Agg', 'Qt5Cairo', 'GTK3Cairo', 'TkAgg')):
"""
Change plotting to using an interactive backend.
Parameters:
backend (str or list): Backend to change to. If not provided, will try different
interactive backends and use the first one that works.
.. codeauthor:: Rasmus Handberg <rasmush@phys.au.dk>
"""
logger = logging.getLogger(__name__)
logger.debug("Valid interactive backends: %s", matplotlib.rcsetup.interactive_bk)
if isinstance(backend, str):
backend = [backend]
for bckend in backend:
if bckend not in matplotlib.rcsetup.interactive_bk:
logger.warning("Interactive backend '%s' is not found", bckend)
continue
# Try to change the backend, and catch errors
# it it didn't work:
try:
plt.switch_backend(bckend)
except (ModuleNotFoundError, ImportError):
pass
else:
break
#--------------------------------------------------------------------------------------------------
[docs]
def plots_noninteractive():
"""
Change plotting to using a non-interactive backend, which can e.g. be used on a cluster.
Will set backend to 'Agg'.
.. codeauthor:: Rasmus Handberg <rasmush@phys.au.dk>
"""
plt.switch_backend('Agg')
#--------------------------------------------------------------------------------------------------
[docs]
def plot_image(image, ax=None, scale='log', cmap=None, origin='lower', xlabel=None,
ylabel=None, cbar=None, clabel='Flux ($e^{-}s^{-1}$)', cbar_ticks=None,
cbar_ticklabels=None, cbar_pad=None, cbar_size='5%', title=None,
percentile=95.0, vmin=None, vmax=None, offset_axes=None, color_bad='k', **kwargs):
"""
Utility function to plot a 2D image.
Parameters:
image (2d array): Image data.
ax (matplotlib.pyplot.axes, optional): Axes in which to plot.
Default (None) is to use current active axes.
scale (str or :py:class:`astropy.visualization.ImageNormalize` object, optional):
Normalization used to stretch the colormap.
Options: ``'linear'``, ``'sqrt'``, ``'log'``, ``'asinh'``, ``'histeq'``, ``'sinh'``
and ``'squared'``.
Can also be a :py:class:`astropy.visualization.ImageNormalize` object.
Default is ``'log'``.
origin (str, optional): The origin of the coordinate system.
xlabel (str, optional): Label for the x-axis.
ylabel (str, optional): Label for the y-axis.
cbar (string, optional): Location of color bar.
Choises are ``'right'``, ``'left'``, ``'top'``, ``'bottom'``.
Default is not to create colorbar.
clabel (str, optional): Label for the color bar.
cbar_size (float, optional): Fractional size of colorbar compared to axes. Default=0.03.
cbar_pad (float, optional): Padding between axes and colorbar.
title (str or None, optional): Title for the plot.
percentile (float, optional): The fraction of pixels to keep in color-trim.
If single float given, the same fraction of pixels is eliminated from both ends.
If tuple of two floats is given, the two are used as the percentiles.
Default=95.
cmap (matplotlib colormap, optional): Colormap to use. Default is the ``Blues`` colormap.
vmin (float, optional): Lower limit to use for colormap.
vmax (float, optional): Upper limit to use for colormap.
color_bad (str, optional): Color to apply to bad pixels (NaN). Default is black.
kwargs (dict, optional): Keyword arguments to be passed to :py:func:`matplotlib.pyplot.imshow`.
Returns:
:py:class:`matplotlib.image.AxesImage`: Image from returned
by :py:func:`matplotlib.pyplot.imshow`.
.. codeauthor:: Rasmus Handberg <rasmush@phys.au.dk>
"""
logger = logging.getLogger(__name__)
# Backward compatible settings:
make_cbar = kwargs.pop('make_cbar', None)
if make_cbar:
warnings.warn("'make_cbar' is deprecated. Use 'cbar' instead.", category=DeprecationWarning)
if not cbar:
cbar = make_cbar
# Special treatment for boolean arrays:
if isinstance(image, np.ndarray) and image.dtype == 'bool':
if vmin is None: vmin = 0
if vmax is None: vmax = 1
if cbar_ticks is None: cbar_ticks = [0, 1]
if cbar_ticklabels is None: cbar_ticklabels = ['False', 'True']
# Calculate limits of color scaling:
interval = None
if vmin is None or vmax is None:
if allnan(image):
logger.warning("Image is all NaN")
vmin = 0
vmax = 1
if cbar_ticks is None:
cbar_ticks = []
if cbar_ticklabels is None:
cbar_ticklabels = []
elif isinstance(percentile, (list, tuple, np.ndarray)):
interval = viz.AsymmetricPercentileInterval(percentile[0], percentile[1])
else:
interval = viz.PercentileInterval(percentile)
# Create ImageNormalize object with extracted limits:
if scale in ('log', 'linear', 'sqrt', 'asinh', 'histeq', 'sinh', 'squared'):
if scale == 'log':
stretch = viz.LogStretch()
elif scale == 'linear':
stretch = viz.LinearStretch()
elif scale == 'sqrt':
stretch = viz.SqrtStretch()
elif scale == 'asinh':
stretch = viz.AsinhStretch()
elif scale == 'histeq':
stretch = viz.HistEqStretch(image[np.isfinite(image)])
elif scale == 'sinh':
stretch = viz.SinhStretch()
elif scale == 'squared':
stretch = viz.SquaredStretch()
# Create ImageNormalize object. Very important to use clip=False if the image contains
# NaNs, otherwise NaN points will not be plotted correctly.
norm = viz.ImageNormalize(
data=image[np.isfinite(image)],
interval=interval,
vmin=vmin,
vmax=vmax,
stretch=stretch,
clip=not anynan(image))
elif isinstance(scale, (viz.ImageNormalize, matplotlib.colors.Normalize)):
norm = scale
else:
raise ValueError("scale {} is not available.".format(scale))
if offset_axes:
extent = (offset_axes[0]-0.5, offset_axes[0] + image.shape[1]-0.5, offset_axes[1]-0.5, offset_axes[1] + image.shape[0]-0.5)
else:
extent = (-0.5, image.shape[1]-0.5, -0.5, image.shape[0]-0.5)
if ax is None:
ax = plt.gca()
# Set up the colormap to use. If a bad color is defined,
# add it to the colormap:
if cmap is None:
cmap = copy.copy(plt.get_cmap('Blues'))
elif isinstance(cmap, str):
cmap = copy.copy(plt.get_cmap(cmap))
if color_bad:
cmap.set_bad(color_bad, 1.0)
# Plotting the image using all the settings set above:
im = ax.imshow(
image,
cmap=cmap,
norm=norm,
origin=origin,
extent=extent,
interpolation='nearest',
**kwargs)
if xlabel is not None:
ax.set_xlabel(xlabel)
if ylabel is not None:
ax.set_ylabel(ylabel)
if title is not None:
ax.set_title(title)
ax.set_xlim([extent[0], extent[1]])
ax.set_ylim([extent[2], extent[3]])
if cbar:
colorbar(im,
ax=ax,
loc=cbar,
size=cbar_size,
pad=cbar_pad,
label=clabel,
ticks=cbar_ticks,
ticklabels=cbar_ticklabels)
# Settings for ticks:
integer_locator = MaxNLocator(nbins=10, integer=True)
ax.xaxis.set_major_locator(integer_locator)
ax.xaxis.set_minor_locator(integer_locator)
ax.yaxis.set_major_locator(integer_locator)
ax.yaxis.set_minor_locator(integer_locator)
ax.tick_params(which='both', direction='out', pad=5)
ax.xaxis.tick_bottom()
ax.yaxis.tick_left()
return im
#--------------------------------------------------------------------------------------------------
[docs]
def plot_image_fit_residuals(fig, image, fit, residuals=None, percentile=95.0):
"""
Make a figure with three subplots showing the image, the fit and the
residuals. The image and the fit are shown with logarithmic scaling and a
common colorbar. The residuals are shown with linear scaling and a separate
colorbar.
Parameters:
fig (fig object): Figure object in which to make the subplots.
image (2D array): Image numpy array.
fit (2D array): Fitted image numpy array.
residuals (2D array, optional): Fitted image subtracted from image numpy array.
Returns:
list: List with Matplotlib subplot axes objects for each subplot.
"""
if residuals is None:
residuals = image - fit
# Calculate common normalization for the first two subplots:
vmin_image, vmax_image = viz.PercentileInterval(percentile).get_limits(image)
vmin_fit, vmax_fit = viz.PercentileInterval(percentile).get_limits(fit)
vmin = np.nanmin([vmin_image, vmin_fit])
vmax = np.nanmax([vmax_image, vmax_fit])
norm = viz.ImageNormalize(vmin=vmin, vmax=vmax, stretch=viz.LogStretch())
# Add subplot with the image:
ax1 = fig.add_subplot(131)
im1 = plot_image(image, ax=ax1, scale=norm, cbar=None, title='Image')
# Add subplot with the fit:
ax2 = fig.add_subplot(132)
plot_image(fit, ax=ax2, scale=norm, cbar=None, title='PSF fit')
# Calculate the normalization for the third subplot:
vmin, vmax = viz.PercentileInterval(percentile).get_limits(residuals)
v = np.max(np.abs([vmin, vmax]))
# Add subplot with the residuals:
ax3 = fig.add_subplot(133)
im3 = plot_image(residuals, ax=ax3, scale='linear', cmap='seismic', vmin=-v, vmax=v, cbar=None, title='Residuals')
# Make the common colorbar for image and fit subplots:
cbar_ax12 = fig.add_axes([0.125, 0.2, 0.494, 0.03])
fig.colorbar(im1, cax=cbar_ax12, orientation='horizontal')
# Make the colorbar for the residuals subplot:
cbar_ax3 = fig.add_axes([0.7, 0.2, 0.205, 0.03])
fig.colorbar(im3, cax=cbar_ax3, orientation='horizontal')
# Add more space between subplots:
plt.subplots_adjust(wspace=0.4, hspace=0.4)
return [ax1, ax2, ax3]
#--------------------------------------------------------------------------------------------------
[docs]
def colorbar(im, ax=None, loc='right', pad=None, size='5%', label=None, ticks=None, ticklabels=None):
"""
Draw colorbar next to the given axes.
Returns:
:class:`matplotlib.colorbar.Colorbar`: Colorbar handle.
.. codeauthor:: Rasmus Handberg <rasmush@phys.au.dk>
"""
if ax is None:
ax = plt.gca()
fig = ax.figure
# Create new colorbar axes:
divider = make_axes_locatable(ax)
if loc == 'top':
pad = 0.05 if pad is None else pad
cax = divider.append_axes('top', size=size, pad=pad)
orientation = 'horizontal'
elif loc == 'bottom':
pad = 0.35 if pad is None else pad
cax = divider.append_axes('bottom', size=size, pad=pad)
orientation = 'horizontal'
elif loc == 'left':
pad = 0.35 if pad is None else pad
cax = divider.append_axes('left', size=size, pad=pad)
orientation = 'vertical'
else:
pad = 0.05 if pad is None else pad
cax = divider.append_axes('right', size=size, pad=pad)
orientation = 'vertical'
cb = fig.colorbar(im, cax=cax, orientation=orientation)
if loc == 'top':
cax.xaxis.set_ticks_position('top')
cax.xaxis.set_label_position('top')
elif loc == 'left':
cax.yaxis.set_ticks_position('left')
cax.yaxis.set_label_position('left')
if label is not None:
cb.set_label(label)
if ticks is not None:
cb.set_ticks(ticks)
if ticklabels is not None:
cb.set_ticklabels(ticklabels)
#cax.yaxis.set_major_locator(matplotlib.ticker.AutoLocator())
#cax.yaxis.set_minor_locator(matplotlib.ticker.AutoLocator())
cax.tick_params(which='both', direction='out', pad=5)
cb.set_alpha(1)
cb.draw_all()
return cb
#--------------------------------------------------------------------------------------------------
[docs]
def plot_outline(img, ax=None, threshold=0.5, **kwargs):
"""
Plot outline of pixel mask.
Parameters:
img (ndarray):
ax (:class:`matplotlib.pyplot.Axes`): Axes to plot outline into.
threshold (float): If ``img`` is not a boolean array, this is used for defining
the pixels which should be outlined. Ignored if ``img`` is boolean.
**kwargs: Additional keywords are passed to :func:`matplotlib.pyplot.plot`.
Returns:
narray or :class:`matplotlib.pyplot.Axes`:
.. codeauthor:: Rasmus Handberg <rasmush@phys.au.dk>
"""
# Special treatment for boolean arrays:
if isinstance(img, np.ndarray) and img.dtype == 'bool':
mapimg = img
else:
mapimg = (img > threshold)
ver_seg = np.where(mapimg[:,1:] != mapimg[:,:-1])
hor_seg = np.where(mapimg[1:,:] != mapimg[:-1,:])
lines = []
for p in zip(*hor_seg):
lines.append((p[1], p[0]+1))
lines.append((p[1]+1, p[0]+1))
lines.append((np.nan, np.nan))
# and the same for vertical segments
for p in zip(*ver_seg):
lines.append((p[1]+1, p[0]))
lines.append((p[1]+1, p[0]+1))
lines.append((np.nan, np.nan))
segments = np.array(lines, dtype='float64')
x0 = -0.5
x1 = img.shape[1] + x0
y0 = -0.5
y1 = img.shape[0] + y0
# now we need to know something about the image which is shown
# at this point let's assume it has extents (x0, y0)..(x1,y1) on the axis
# drawn with origin='lower'
# with this information we can rescale our points
segments[:,0] = x0 + (x1-x0) * segments[:,0] / mapimg.shape[1]
segments[:,1] = y0 + (y1-y0) * segments[:,1] / mapimg.shape[0]
if ax is None:
return segments
return ax.plot(segments[:,0], segments[:,1], **kwargs)
#--------------------------------------------------------------------------------------------------