Source code for rsatoolbox.vis.icon

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
icon object which can be plotted into an axis
"""

import os
import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.offsetbox import OffsetImage, AnnotationBbox, DrawingArea
import numpy as np
import PIL
import PIL.ImageOps
import PIL.ImageFilter
from PIL import UnidentifiedImageError
from rsatoolbox.rdm import RDMs
from rsatoolbox.util.pooling import pool_rdm


[docs]class Icon: """ Icon object, i.e. an object which can be plotted into an axis or as an axis label. Args: image (np.ndarray or PIL.Image or RDMs or Icon) the image to use as an icon arrays and images should give the image directly RDMs takes the average RDM from the object If an Icon is passed its image property is used string (String) string to place on the icon color (color definition) background / border color default: None -> no border or background marker (matplotlib markertype) sets what kind of symbol to plot cmap (color map) color map applied to the image border_type (String) - None : default, puts the color as a background where the alpha of the image is not 0 - 'pad' : pads the image with the border color -> square border - 'conv' : extends the area by convolving with a circle border_width (integer) width of the border make_square (bool) if set to true the image is first reshaped into a square circ_cut (flag) sets how the icon is cut into circular shape: - None : default, no cutting - 'cut' : sets alpha to 0 out of a circular aperture - 'cosine' : sets alpha to a raised cosine window - a number between 0 and 1 : a tukey window with the flat proportion of the aperture given by the number. For 0 this corresponds to the cosine window, for 1 it corresponds to 'cut'. resolution (one or two numbers): sets a resolution for the icon to which the image is resized prior to all processing. If only one number is provided, the image is resized to a square with that size marker_front (bool): switches whether the marker is plotted in front or behind the image. If True the marker is plotted unfilled in front If False the marker is plotted behind the image filled. default = True font_size (float) size of any annotation text font_name (str): annotation font font_color (np.ndarray) font color for annotations """ def __init__( self, image=None, string=None, color=None, marker=None, cmap=None, border_type=None, border_width=2, make_square=False, circ_cut=None, resolution=None, marker_front=True, markeredgewidth=2, font_size=None, font_name=None, font_color=None): self.final_image = None self.font_size = font_size self.font_name = font_name self.string = string self.font_color = font_color self.marker = marker self.marker_front = marker_front self.markeredgewidth = markeredgewidth self._make_square = make_square self._border_width = border_width self._border_type = border_type self._cmap = cmap self._color = color self._circ_cut = None self._resolution = None self.image = image if resolution is not None: self.resolution = resolution self.circ_cut = circ_cut @property def image(self): return self._image @image.setter def image(self, image): """ interprets image/converts it into an image""" if isinstance(image, Icon): self._image = image.image elif isinstance(image, RDMs): avg_rdm = pool_rdm(image) image = avg_rdm.get_matrices()[0] self._image = image / np.max(image) if self.resolution is None: self._resolution = np.array(100) elif image is not None: self._image = image else: self._image = None self.recompute_final_image() @property def string(self): return self._string @string.setter def string(self, string): if string is None or isinstance(string, str): self._string = string else: raise ValueError("String must be a string") @property def color(self): return self._color @color.setter def color(self, color): self._color = color self.recompute_final_image() @property def cmap(self): return self._cmap @cmap.setter def cmap(self, cmap): self._cmap = cmap self.recompute_final_image() @property def make_square(self): return self._make_square @make_square.setter def make_square(self, make_square): self._make_square = make_square self.recompute_final_image() @property def border_width(self): return self._border_width @border_width.setter def border_width(self, border_width): self._border_width = border_width self.recompute_final_image() @property def border_type(self): return self._border_type @border_type.setter def border_type(self, border_type): self._border_type = border_type self.recompute_final_image() @property def resolution(self): return self._resolution @resolution.setter def resolution(self, resolution): if resolution is not None: self._resolution = np.array(resolution) else: self._resolution = None self.recompute_final_image() @property def circ_cut(self): return self._circ_cut @circ_cut.setter def circ_cut(self, circ_cut): if circ_cut is None: self._circ_cut = None elif circ_cut == "cut": self._circ_cut = 1 elif circ_cut == "cosine": self._circ_cut = 0 elif 0 <= circ_cut <= 1: self._circ_cut = circ_cut else: raise ValueError("circ_cut must be in [0,1]") self.recompute_final_image()
[docs] def recompute_final_image(self): """ computes the icon image from the parameters This function handles most of the image processing and must be run again if any properties are changed. If you use set to change properties this is automatically run. """ if self._image is None: self.final_image = None return if isinstance(self._image, np.ndarray): if self._image.dtype == np.uint8 or np.any(self._image > 1): # assume image is in uint8 0-255 range im = self._image / 255 else: im = self._image if self.cmap is not None: im = cm.get_cmap(self.cmap)(im) im = PIL.Image.fromarray((im * 255).astype(np.uint8)) else: # we hope it is a PIL image or equivalent im = self._image im = im.convert("RGBA") if self.make_square: new_size = max(im.width, im.height) if int(PIL.__version__[0]) >= 9: im = im.resize((new_size, new_size), PIL.Image.Resampling.NEAREST) else: im = im.resize((new_size, new_size), PIL.Image.NEAREST) if self.resolution is not None: if self.resolution.size == 1: if int(PIL.__version__[0]) >= 9: im = im.resize((self.resolution, self.resolution), PIL.Image.Resampling.NEAREST) else: im = im.resize((self.resolution, self.resolution), PIL.Image.NEAREST) else: if int(PIL.__version__[0]) >= 9: im = im.resize(self.resolution, PIL.Image.Resampling.NEAREST) else: im = im.resize(self.resolution, PIL.Image.NEAREST) if self.circ_cut is not None: middle = np.array(im.size) / 2 x = np.arange(im.size[0]) - middle[0] + 0.5 x = x / np.max(np.abs(x)) y = np.arange(im.size[1]) - middle[1] + 0.5 y = y / np.max(np.abs(y)) yy, xx = np.meshgrid(y, x) r = np.sqrt(xx ** 2 + yy ** 2) alpha = np.empty(r.shape) alpha[r > 1] = 0 alpha[r <= self.circ_cut] = 1 val = (r > self.circ_cut) & (r <= 1) alpha[val] = 0.5 + 0.5 * np.cos( np.pi * (r[val] - self.circ_cut) / (1 - self.circ_cut) ) alpha = alpha.T * np.array(im.getchannel("A")) alpha = PIL.Image.fromarray(np.uint8(alpha)) im.putalpha(alpha) if self.color is not None: if self.border_type is None: pass elif self.border_type == "alpha": bg_alpha = np.array(im.getchannel("A")) bg_alpha = bg_alpha > 0 bg_alpha = PIL.Image.fromarray(255 * np.uint8(bg_alpha)) bg = PIL.Image.new( "RGBA", im.size, color=tuple(np.uint8(255 * self.color)) ) bg.putalpha(bg_alpha) im = PIL.Image.alpha_composite(bg, im) elif self.border_type == "pad": im = PIL.ImageOps.expand(im, border=self.border_width, fill=self.color) elif self.border_type == "conv": im = PIL.ImageOps.expand( im, border=self.border_width, fill=(0, 0, 0, 0) ) bg_alpha = im.getchannel("A") bg_alpha = bg_alpha.filter(PIL.ImageFilter.BoxBlur(self.border_width)) bg_alpha = np.array(bg_alpha) bg_alpha = 255 * np.uint8(bg_alpha > 0) bg_alpha = PIL.Image.fromarray(bg_alpha) bg = PIL.Image.new( "RGBA", im.size, color=tuple(np.uint8(255 * self.color)) ) bg.putalpha(bg_alpha) im = PIL.Image.alpha_composite(bg, im) self.final_image = im
[docs] def plot(self, x, y, ax=None, size=None): """ plots the icon into an axis Args: x (float) x-position y (float) y-position ax (matplotlib axis) the axis to plot in size : float size of the icon scaling the image """ if ax is None: ax = plt.gca() if size is None: size = 1 if self.final_image is not None: imagebox = OffsetImage(self.final_image, zoom=size) ab = AnnotationBbox(imagebox, (x, y), frameon=False, pad=0) ax.add_artist(ab) zorder = ab.zorder else: zorder = 0 if self.marker: if self.final_image is not None: markersize = max(self.final_image.size) else: markersize = 50 markersize = markersize * size if self.marker_front: plt.plot( x, y, marker=self.marker, markeredgecolor=self.color, markerfacecolor=(0, 0, 0, 0), markersize=markersize, zorder=zorder + 0.1, markeredgewidth=self.markeredgewidth, ) else: plt.plot( x, y, marker=self.marker, markeredgecolor=self.color, markerfacecolor=self.color, markersize=markersize, zorder=zorder - 0.1, markeredgewidth=self.markeredgewidth, ) if self.string is not None: ax.annotate( self.string, (x, y), horizontalalignment="center", verticalalignment="center", zorder=zorder + 0.2, fontsize=self.font_size, fontname=self.font_name, color=self.font_color, )
def _tick_label( self, x, y, size, ax=None, linewidth=None, xybox=None, xycoords=None, box_alignment=None, horizontalalignment=None, verticalalignment=None, rotation=None, ): """ uses the icon as a ticklabel at location x Args: x (float) the horizontal position of the tick y (float) the vertical position of the tick size (float) scaling the size of the icon ax (matplotlib axis) the axis to put the label on """ ret_val = {} if ax is None: ax = plt.gca() tickline_color = self.color # np.any chokes on str input so need to test for this first if not (isinstance(tickline_color, str) or np.any(tickline_color)): tickline_color = [0.8, 0.8, 0.8] if self.final_image is not None: imagebox = OffsetImage(self.final_image, zoom=size, dpi_cor=True) ret_val['image'] = AnnotationBbox( imagebox, (x, y), xybox=xybox, xycoords=xycoords, box_alignment=box_alignment, boxcoords="offset points", bboxprops={"edgecolor": "none", "facecolor": "none"}, arrowprops={ "linewidth": linewidth, "color": tickline_color, "arrowstyle": "-", "shrinkA": 0, "shrinkB": 1, }, pad=0.0, annotation_clip=False, ) zorder = ret_val['image'].zorder ax.add_artist(ret_val['image']) else: zorder = 0 if self.marker: if self.final_image is not None: markersize = max(self.final_image.size) else: markersize = 50 markersize = markersize * size d = DrawingArea(markersize, markersize) if self.marker_front: zorder_marker = zorder + 0.1 else: zorder_marker = zorder - 0.1 d.set_zorder(zorder_marker) d.set_alpha(0) if self.marker_front: d.add_artist( plt.Line2D( [markersize / 2], [markersize / 2], marker=self.marker, markeredgecolor=self.color, markerfacecolor=(0, 0, 0, 0), markersize=markersize, markeredgewidth=self.markeredgewidth, transform=d.get_transform(), zorder=zorder_marker, ) ) else: d.add_artist( plt.Line2D( [markersize / 2], [markersize / 2], marker=self.marker, markeredgecolor=self.color, markerfacecolor=self.color, markersize=markersize, markeredgewidth=self.markeredgewidth, transform=d.get_transform(), zorder=zorder_marker, ) ) ret_val['marker'] = AnnotationBbox( d, (x, y), xybox=xybox, xycoords=xycoords, box_alignment=box_alignment, boxcoords="offset points", bboxprops={"edgecolor": "none", "facecolor": "none"}, arrowprops={ "linewidth": linewidth, "color": tickline_color, "arrowstyle": "-", "shrinkA": 0, "shrinkB": 1, }, pad=0.0, annotation_clip=False, ) ret_val['marker'].set_zorder(zorder_marker) ret_val['marker'].set_alpha(0) ax.add_artist(ret_val['marker']) if self.string is not None: ret_val['string'] = ax.annotate( self.string, (x, y), xytext=xybox, xycoords=xycoords, textcoords="offset points", horizontalalignment=horizontalalignment, verticalalignment=verticalalignment, arrowprops={ "linewidth": linewidth, "color": tickline_color, "arrowstyle": "-", "shrinkA": 0, "shrinkB": 1, }, zorder=zorder + 0.2, fontsize=self.font_size, fontname=self.font_name, color=self.font_color, rotation=rotation, ) return ret_val
[docs] def x_tick_label(self, x, size, offset, **kwarg): """ uses the icon as a ticklabel at location x Args: x (float) the position of the tick size (float) scaling the size of the icon offset (integer) how far the icon should be from the axis in axis units ax (matplotlib axis) the axis to put the label on """ return self._tick_label( x=x, y=0, size=size, xybox=(0, -offset), xycoords=("data", "axes fraction"), box_alignment=(0.5, 1), horizontalalignment="center", verticalalignment="bottom", rotation=90, **kwarg )
[docs] def y_tick_label(self, y, size, offset, **kwarg): """ uses the icon as a ticklabel at location x Args: y (float) the position of the tick size (float) scaling the size of the icon offset (integer) how far the icon should be from the axis in axis units ax (matplotlib axis) the axis to put the label on """ return self._tick_label( x=0, y=y, size=size, xybox=(-offset, 0), xycoords=("axes fraction", "data"), box_alignment=(1, 0.5), horizontalalignment="right", verticalalignment="center", rotation=0, **kwarg )
[docs]def icons_from_folder( folder, resolution=None, color=None, cmap=None, border_type=None, border_width=2, make_square=False, circ_cut=None, ): """ generates a dictionary of Icons for all images in a folder """ icons = dict() for filename in os.listdir(folder): try: im = PIL.Image.open(filename) icons[filename] = Icon( image=im, color=color, resolution=resolution, cmap=cmap, border_type=border_type, border_width=border_width, make_square=make_square, circ_cut=circ_cut, ) except ( FileNotFoundError, UnidentifiedImageError, IsADirectoryError, PermissionError, ): pass return icons