Source code for gammapy.image.plotting

# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""Helper functions and functions for plotting gamma-ray images."""
from collections import OrderedDict
import numpy as np
from astropy.coordinates import Angle

__all__ = [
    "colormap_hess",
    "colormap_milagro",
    "MapPanelPlotter",
    "illustrate_colormap",
    "grayify_colormap",
]

__doctest_requires__ = {("colormap_hess", "colormap_milagro"): ["matplotlib"]}


[docs]class MapPanelPlotter: """ Map panel plotter class. Given a `~matplotlib.pyplot.Figure` object this class creates axes objects using `~matplotlib.gridspec.GridSpec` and plots a given sky map onto these. An example of how this class is used can be found in the :gp-notebook:`hgps` notebook at the end. Parameters ---------- figure : `~matplotlib.pyplot.figure.` Figure instance. xlim : `~astropy.coordinates.Angle` Angle object specifying the longitude limits. ylim : `~astropy.coordinates.Angle` Angle object specifying the latitude limits. npanels : int Number of panels. **kwargs : dict Keyword arguments passed to `~matplotlib.gridspec.GridSpec`. """ def __init__(self, figure, xlim, ylim, npanels=4, **kwargs): from matplotlib.gridspec import GridSpec self.figure = figure self.parameters = OrderedDict(xlim=xlim, ylim=ylim, npanels=npanels) self.grid_spec = GridSpec(nrows=npanels, ncols=1, **kwargs) def _get_ax_extend(self, ax, panel): """Get width and height of the axis in world coordinates""" p = self.parameters # compute aspect ratio of the axis aspect = ax.bbox.width / ax.bbox.height # compute width and height in world coordinates height = np.abs(p["ylim"].diff()) width = aspect * height left, bottom = p["xlim"][0].wrap_at("180d"), p["ylim"][0] width_all = np.abs(p["xlim"].wrap_at("180d").diff()) xoverlap = ((p["npanels"] * width) - width_all) / (p["npanels"] - 1.0) if xoverlap < 0: raise ValueError( "No overlap between panels. Please reduce figure " "height or increase vertical space between the panels." ) left = left - panel * (width - xoverlap) return left[0], bottom, width, height def _set_ax_fov(self, ax, panel): left, bottom, width, height = self._get_ax_extend(ax, panel) # set fov xlim = Angle([left, left - width]) ylim = Angle([bottom, bottom + height]) xlim_pix, ylim_pix = ax.wcs.wcs_world2pix(xlim.deg, ylim.deg, 1) ax.set_xlim(*xlim_pix) ax.set_ylim(*ylim_pix) return ax
[docs] def plot_panel(self, map, panel=1, panel_fov=None, **kwargs): """ Plot sky map on one panel. Parameters ---------- map : `~gammapy.maps.WcsNDMap` Map to plot. panel : int Which panel to plot on (counted from top). """ if panel_fov is None: panel_fov = panel spec = self.grid_spec[panel] ax = self.figure.add_subplot(spec, projection=map.geom.wcs) try: ax = map.plot(ax=ax, **kwargs)[1] except AttributeError: ax = map.plot_rgb(ax=ax, **kwargs) ax = self._set_ax_fov(ax, panel_fov) return ax
[docs] def plot(self, map, **kwargs): """ Plot sky map on all panels. Parameters ---------- map : `~gammapy.maps.WcsNDMap` Map to plot. """ p = self.parameters axes = [] for panel in range(p["npanels"]): ax = self.plot_panel(map, panel=panel, **kwargs) axes.append(ax) return axes
[docs]def colormap_hess(transition=0.5, width=0.1): """Colormap often used in H.E.S.S. collaboration publications. This colormap goes black -> blue -> red -> yellow -> white. A sharp blue -> red -> yellow transition is often used for significance images with a value of red at ``transition ~ 5`` or ``transition ~ 7`` so that the following effect is achieved: - black, blue: non-significant features, not well visible - red: features at the detection threshold ``transition`` - yellow, white: significant features, very well visible The transition parameter is defined between 0 and 1. To calculate the value from data units an `~astropy.visualization.mpl_normalize.ImageNormalize` instance should be used (see example below). Parameters ---------- transition : float (default = 0.5) Value of the transition to red (between 0 and 1). width : float (default = 0.5) Width of the blue-red color transition (between 0 and 1). Returns ------- colormap : `matplotlib.colors.LinearSegmentedColormap` Colormap Examples -------- >>> from gammapy.image import colormap_hess >>> from astropy.visualization.mpl_normalize import ImageNormalize >>> from astropy.visualization import LinearStretch >>> normalize = ImageNormalize(vmin=-5, vmax=15, stretch=LinearStretch()) >>> transition = normalize(5) >>> cmap = colormap_hess(transition=transition) .. plot:: from gammapy.image import colormap_hess, illustrate_colormap import matplotlib.pyplot as plt cmap = colormap_hess() illustrate_colormap(cmap) plt.show() """ from matplotlib.colors import LinearSegmentedColormap # Compute normalised values (range 0 to 1) that # correspond to red, blue, yellow. red = float(transition) if width > red: blue = 0.1 * red else: blue = red - width yellow = 2.0 / 3.0 * (1 - red) + red black, white = 0, 1 # Create custom colormap # List entries: (value, (R, G, B)) colors = [ (black, "k"), (blue, (0, 0, 0.8)), (red, "r"), (yellow, (1.0, 1.0, 0)), (white, "w"), ] cmap = LinearSegmentedColormap.from_list(name="hess", colors=colors) return cmap
[docs]def colormap_milagro(transition=0.5, width=0.0001, huestart=0.6): """Colormap often used in Milagro collaboration publications. This colormap is gray below ``transition`` and similar to the jet colormap above. A sharp gray -> color transition is often used for significance images with a transition value of ``transition ~ 5`` or ``transition ~ 7``, so that the following effect is achieved: - gray: non-significant features are not well visible - color: significant features at the detection threshold ``transition`` Note that this colormap is often criticised for over-exaggerating small differences in significance below and above the gray - color transition threshold. The transition parameter is defined between 0 and 1. To calculate the value from data units an `~astropy.visualization.mpl_normalize.ImageNormalize` instance should be used (see example below). Parameters ---------- transition : float (default = 0.5) Transition value (below: gray, above: color). width : float (default = 0.0001) Width of the transition huestart : float (default = 0.6) Hue of the color at ``transition`` Returns ------- colormap : `~matplotlib.colors.LinearSegmentedColormap` Colormap Examples -------- >>> from gammapy.image import colormap_milagro >>> from astropy.visualization.mpl_normalize import ImageNormalize >>> from astropy.visualization import LinearStretch >>> normalize = ImageNormalize(vmin=-5, vmax=15, stretch=LinearStretch()) >>> transition = normalize(5) >>> cmap = colormap_milagro(transition=transition) .. plot:: from gammapy.image import colormap_milagro, illustrate_colormap import matplotlib.pyplot as plt cmap = colormap_milagro() illustrate_colormap(cmap) plt.show() """ from colorsys import hls_to_rgb from matplotlib.colors import LinearSegmentedColormap # Compute normalised red, blue, yellow values transition = float(transition) # Create custom colormap # List entries: (value, (H, L, S)) colors = [ (0, (1, 1, 0)), (transition - width, (1, 0, 0)), (transition, (huestart, 0.4, 0.5)), (transition + width, (huestart, 0.4, 1)), (0.99, (0, 0.6, 1)), (1, (0, 1, 1)), ] # Convert HLS values to RGB values rgb_colors = [(val, hls_to_rgb(*hls)) for (val, hls) in colors] cmap = LinearSegmentedColormap.from_list(name="milagro", colors=rgb_colors) return cmap
[docs]def grayify_colormap(cmap, mode="hsp"): """ Return a grayscale version a the colormap. The grayscale conversion of the colormap is bases on perceived luminance of the colors. For the conversion either the `~skimage.color.rgb2gray` or a generic method called ``hsp`` [1]_ can be used. The code is loosely based on [2]_. Parameters ---------- cmap : str or `~matplotlib.colors.Colormap` Colormap name or instance. mode : {'skimage, 'hsp'} Grayscale conversion method. Either ``skimage`` or ``hsp``. References ---------- .. [1] Darel Rex Finley, "HSP Color Model - Alternative to HSV (HSB) and HSL" http://alienryderflex.com/hsp.html .. [2] Jake VanderPlas, "How Bad Is Your Colormap?" https://jakevdp.github.io/blog/2014/10/16/how-bad-is-your-colormap/ """ import matplotlib.pyplot as plt cmap = plt.cm.get_cmap(cmap) colors = cmap(np.arange(cmap.N)) if mode == "skimage": from skimage.color import rgb2gray # pylint:disable=import-error luminance = rgb2gray(np.array([colors])) colors[:, :3] = luminance[0][:, np.newaxis] elif mode == "hsp": rgb_weight = [0.299, 0.587, 0.114] luminance = np.sqrt(np.dot(colors[:, :3] ** 2, rgb_weight)) colors[:, :3] = luminance[:, np.newaxis] else: raise ValueError("Not a valid grayscale conversion mode.") return cmap.from_list(cmap.name + "_grayscale", colors, cmap.N)
[docs]def illustrate_colormap(cmap, **kwargs): """ Illustrate color distribution and perceived luminance of a colormap. Parameters ---------- cmap : str or `~matplotlib.colors.Colormap` Colormap name or instance. kwargs : dicts Keyword arguments passed to `grayify_colormap`. """ import matplotlib.pyplot as plt cmap = plt.cm.get_cmap(cmap) cmap_gray = grayify_colormap(cmap, **kwargs) figure = plt.figure(figsize=(8, 6)) v = np.linspace(0, 1, 4 * cmap.N) # Show colormap show_cmap = figure.add_axes([0.1, 0.8, 0.8, 0.1]) im = np.outer(np.ones(50), v) show_cmap.imshow(im, cmap=cmap, origin="lower") show_cmap.set_xticklabels([]) show_cmap.set_yticklabels([]) show_cmap.set_yticks([]) show_cmap.set_title("RGB & Gray Luminance of colormap {}".format(cmap.name)) # Show colormap gray show_cmap_gray = figure.add_axes([0.1, 0.72, 0.8, 0.09]) show_cmap_gray.imshow(im, cmap=cmap_gray, origin="lower") show_cmap_gray.set_xticklabels([]) show_cmap_gray.set_yticklabels([]) show_cmap_gray.set_yticks([]) # Plot RGB profiles plot_rgb = figure.add_axes([0.1, 0.1, 0.8, 0.6]) plot_rgb.plot(v, [cmap(_)[0] for _ in v], color="#A60628") plot_rgb.plot(v, [cmap(_)[1] for _ in v], color="#467821") plot_rgb.plot(v, [cmap(_)[2] for _ in v], color="#348ABD") plot_rgb.plot(v, [cmap_gray(_)[0] for _ in v], color="k", linestyle="--") plot_rgb.set_ylabel("Luminance") plot_rgb.set_ylim(-0.005, 1.005)