text: # Copyright 2012 by Leighton Pritchard.  All rights reserved.
  #
  # This file is part of the Biopython distribution and governed by your
  # choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
  # Please see the LICENSE file that should have been included as part of this
  # package.
  """Generate RGB colours suitable for distinguishing categorical data.
  
  This module provides a class that implements a spiral 'path' through HSV
  colour space, permitting the selection of a number of points along that path,
  and returning the output in RGB colour space, suitable for use with ReportLab
  and other graphics packages.
  
  This approach to colour choice was inspired by Bang Wong's Points of View
  article: Color Coding, in Nature Methods _7_ 573 (https://doi.org/10.1038/nmeth0810-573).
  
  The module also provides helper functions that return a list for colours, or
  a dictionary of colours (if passed an iterable containing the names of
  categories to be coloured).
  """
  
  # standard library
  import colorsys    # colour format conversions
  from math import log, exp, floor, pi
  import random      # for jitter values
  
  
  class ColorSpiral(object):
      """Implement a spiral path through HSV colour space.
  
      This class provides functions for sampling points along a logarithmic
      spiral path through HSV colour space.
  
      The spiral is described by r = a * exp(b * t) where r is the distance
      from the axis of the HSV cylinder to the current point in the spiral,
      and t is the angle through which the spiral has turned to reach the
      current point. a and b are (positive, real) parameters that control the
      shape of the spiral.
  
       - a: the starting direction of the spiral
       - b: the number of revolutions about the axis made by the spiral
  
      We permit the spiral to move along the cylinder ('in V-space') between
      v_init and v_final, to give a gradation in V (essentially, brightness),
      along the path, where v_init, v_final are in [0,1].
  
      A brightness 'jitter' may also be provided as an absolute value in
      V-space, to aid in distinguishing consecutive colour points on the
      path.
      """
  
      def __init__(self, a=1, b=0.33, v_init=0.85, v_final=0.5,
                   jitter=0.05):
          """Initialize a logarithmic spiral path through HSV colour space.
  
          Arguments:
           - a - Parameter a for the spiral, controls the initial spiral
             direction. a > 0
           - b - parameter b for the spiral, controls the rate at which the
             spiral revolves around the axis. b > 0
           - v_init - initial value of V (brightness) for the spiral.
             v_init in [0,1]
           - v_final - final value of V (brightness) for the spiral
             v_final in [0,1]
           - jitter - the degree of V (brightness) jitter to add to each
             selected colour. The amount of jitter will be selected
             from a uniform random distribution [-jitter, jitter],
             and V will be maintained in [0,1].
  
          """
          # Initialize attributes
          self.a = a
          self.b = b
          self.v_init = v_init
          self.v_final = v_final
          self.jitter = jitter
  
      def get_colors(self, k, offset=0.1):
          """Generate k different RBG colours evenly-space on the spiral.
  
          A generator returning the RGB colour space values for k
          evenly-spaced points along the defined spiral in HSV space.
  
          Arguments:
           - k - the number of points to return
           - offset - how far along the spiral path to start.
  
          """
          # We use the offset to skip a number of similar colours near to HSV axis
          assert offset > 0 and offset < 1, "offset must be in (0,1)"
          v_rate = (self._v_final - self._v_init) / float(k)
          # Generator for colours: we have divided the arc length into sections
          # of equal length, and step along them
          for n in range(1, k + 1):
              # For each value of n, t indicates the angle through which the
              # spiral has turned, to this point
              t = (1. / self._b) * (log(n + (k * offset)) -
                                    log((1 + offset) * k * self._a))
              # Put 0 <= h <= 2*pi, where h is the angular part of the polar
              # co-ordinates for this point on the spiral
              h = t
              while h < 0:
                  h += 2 * pi
              h = (h - (floor(h / (2 * pi)) * pi))
              # Now put h in [0, 1] for colorsys conversion
              h = h / (2 * pi)
              # r is the radial distance of this point from the centre
              r = self._a * exp(self._b * t)
              # v is the brightness of this point, linearly interpolated
              # from self._v_init to self._v_final. Jitter size is sampled from
              # a uniform distribution
              if self._jitter:
                  jitter = random.random() * 2 * self._jitter - self._jitter
              else:
                  jitter = 0
              v = self._v_init + (n * v_rate + jitter)
              # We have arranged the arithmetic such that 0 <= r <= 1, so
              # we can use this value directly as s in HSV
              yield colorsys.hsv_to_rgb(h, r, max(0, min(v, 1)))
  
      def _get_a(self):
          return self._a
  
      def _set_a(self, value):
          self._a = max(0, value)
  
      def _get_b(self):
          return self._b
  
      def _set_b(self, value):
          self._b = max(0, value)
  
      def _get_v_init(self):
          return self._v_init
  
      def _set_v_init(self, value):
          self._v_init = max(0, min(1, value))
  
      def _get_v_final(self):
          return self._v_final
  
      def _set_v_final(self, value):
          self._v_final = max(0, min(1, value))
  
      def _get_jitter(self):
          return self._jitter
  
      def _set_jitter(self, value):
          self._jitter = max(0, min(1, value))
  
      a = property(_get_a, _set_a,
                   doc="Parameter controlling initial spiral direction (a > 0)")
      b = property(_get_b, _set_b,
                   doc="Parameter controlling rate spiral revolves around axis (b > 0)")
      v_init = property(_get_v_init, _set_v_init,
                        doc="Initial value of V (brightness) for the spiral (range 0 to 1)")
      v_final = property(_get_v_final, _set_v_final,
                         doc="Final value of V (brightness) for the spiral (range 0 to 1)")
      jitter = property(_get_jitter, _set_jitter,
                        doc="Degree of V (brightness) jitter to add to each color (range 0 to 1)")
  
  
  # Convenience functions for those who don't want to bother with a
  # ColorSpiral object
  def get_colors(k, **kwargs):
      """Return k colours selected by the ColorSpiral object, as a generator.
  
      Arguments:
       - k - the number of colours to return
       - kwargs - pass-through arguments to the ColorSpiral object
  
      """
      cs = ColorSpiral(**kwargs)
      return cs.get_colors(k)
  
  
  def get_color_dict(l, **kwargs):
      """Return a dictionary of colours using the provided values as keys.
  
      Returns a dictionary, keyed by the members of iterable l, with a
      colour assigned to each member.
  
      Arguments:
       - l - an iterable representing classes to be coloured
       - kwargs - pass-through arguments to the ColorSpiral object
  
      """
      cs = ColorSpiral(**kwargs)
      colors = cs.get_colors(len(l))
      dict = {}
      for item in l:
          dict[item] = next(colors)
      return dict
  