Source code for topostats.theme

"""Custom Bruker Nanoscope colorscale."""

import logging

import matplotlib as mpl
import matplotlib.cm
import numpy as np
from matplotlib.colors import LinearSegmentedColormap, ListedColormap

from topostats.logs.logs import LOGGER_NAME

LOGGER = logging.getLogger(LOGGER_NAME)


[docs] class Colormap: """ Class for setting the Colormap. Parameters ---------- name : str Name of colormap to use. """ def __init__(self, name: str = "nanoscope"): """ Initialise the class. Parameters ---------- name : str Name of colormap to use. """ self.name = name self.cmap = None self.set_cmap(self.name)
[docs] def __str__(self) -> str: """ Return string representation of object. Returns ------- str String detailing the colormap. """ return f"TopoStats Colormap: {self.name}"
def set_cmap(self, name: str) -> None: """ Set the ColorMap. Parameters ---------- name : str Name of the colormap to return. """ if name.lower() == "nanoscope": self.cmap = self.nanoscope() elif name.lower() == "gwyddion": self.cmap = self.gwyddion() elif name.lower() == "blue": self.cmap = self.blue() elif name.lower() == "blue_purple_green": self.cmap = self.blue_purple_green() else: # Get one of the matplotlib colormaps self.cmap = mpl.colormaps[name] LOGGER.debug(f"[theme] Colormap set to : {name}")
[docs] def get_cmap(self) -> matplotlib.cm: """ Return the matplotlib.cm colormap object. Returns ------- matplotlib.cm Matplotlib Color map object. """ return self.cmap
[docs] @staticmethod def nanoscope() -> LinearSegmentedColormap: """ Matplotlib compatible colormap that replicates the Bruker Nanoscope colorscale. The colormap is implemented in Gwyddion's GwyGradient via 'Nanoscope.txt'. Returns ------- LinearSegmentedColormap MatplotLib LinearSegmentedColourmap that replicates Bruker Nanoscope colorscale. """ cdict = { "red": ( (0.0, 0.0, 0.0), (0.124464, 0.0, 0.0), (0.236052, 0.0670103, 0.0670103), (0.371245, 0.253338, 0.253338), (0.472103, 0.392344, 0.392344), (0.611588, 0.584587, 0.584587), (0.708155, 0.717678, 0.717678), (0.714052, 0.725806, 0.725806), (0.890558, 0.969072, 0.969072), (0.933476, 0.987464, 0.987464), (0.944709, 0.992278, 0.992278), (0.965682, 0.995207, 0.995207), (0.971401, 0.996006, 0.996006), (1, 1, 1), ), "green": ( (0.0, 0.0, 0.0), (0.124464, 0.0, 0.0), (0.236052, 0.0, 0.0), (0.371245, 0.0, 0.0), (0.472103, 0.0721649, 0.0721649), (0.611588, 0.334114, 0.334114), (0.708155, 0.515464, 0.515464), (0.714052, 0.527471, 0.527471), (0.890558, 0.886843, 0.886843), (0.933476, 0.974227, 0.974227), (0.944709, 0.980523, 0.980523), (0.965682, 0.992278, 0.992278), (0.971401, 0.993565, 0.993565), (1, 1, 1), ), "blue": ( (0.0, 0.0, 0.0), (0.124464, 0.0, 0.0), (0.236052, 0.0, 0.0), (0.371245, 0.0, 0.0), (0.472103, 0.0, 0.0), (0.611588, 0.0, 0.0), (0.708155, 0.252575, 0.252575), (0.714052, 0.268, 0.268), (0.890558, 0.76343, 0.76343), (0.933476, 0.883897, 0.883897), (0.944709, 0.915426, 0.915426), (0.965682, 0.974293, 0.974293), (0.971401, 0.990347, 0.990347), (1, 1, 1), ), } return LinearSegmentedColormap("nanoscope", cdict)
@staticmethod def gwyddion() -> LinearSegmentedColormap: """ Set RGBA colour map for the Gwyddion.net colour gradient. Returns ------- LinearSegmentedColormap The 'gwyddion' colormap. """ N = 4 # Number of values vals = np.ones((N, 4)) # Initialise the array to be full of 1.0 vals[0] = [0.0, 0.0, 0.0, 1] vals[1] = [168 / 256, 40 / 256, 15 / 256, 1.0] vals[2] = [243 / 256, 194 / 256, 93 / 256, 1.0] vals[3] = [1.0, 1.0, 1.0, 1.0] return LinearSegmentedColormap.from_list("gwyddion", vals, N=256) @staticmethod def blue() -> ListedColormap: """ Set RGBA colour map of just the colour blue. Returns ------- ListedColormap The 'blue' colormap. """ return ListedColormap([[32 / 256, 226 / 256, 205 / 256]], "blue", N=256) @staticmethod def blue_purple_green() -> ListedColormap: """ RGBA colour map of just the colour blue/purple/green. Returns ------- ListedColormap The 'blue/purple/green' colormap. """ return ListedColormap( [[0 / 256, 157 / 256, 229 / 256], [255 / 256, 100 / 256, 225 / 256], [0 / 256, 1, 139 / 256]], "blue_purple_green", N=3, )