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| import re
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from matplotlib.collections import PatchCollection
from pymatgen.core.periodic_table import Element
class periodic_table(object):
"""
frame: str or dict, describe shapes of element cells.
str: patch class name under matplotlib.patches.
dict: {
"shape": patch class name,
"parms": width, height and other parms, needed for "shape",
"kparms": kparms, supported by "shape"
}
colors: dict, custom frame and background colors for elements.
{
"frame": str, list
"background": str, list, {"depend_on": data_key [, "cmp": color map, "cbar": True]}
}
if you use a gradient, color will based on the data from Element().data or you provide.
depend_on specify which data you want to use.
label: dict or function(not supported yet).
dict: {
"label1": [element symbols or atomic indexes],
...
}
or more detail:
dict: {
"label1": {
"elements": [element symbols or atomic indexes],
"color": not necessary
}
...
}
function: func(element symbol or atomic index) returns color and label
text: text content and format within element cells (not supported yet).
data: data beside pymatgen or you want overide for pymatgen
{symbol: {k1: v1, k2:v2}, ...}
"""
def __init__(self,
frame=None,
colors=None,
labels=None,
text=None,
data=None):
self.frame = frame or {}
if isinstance(self.frame, str):
self.frame = {"shape": self.frame or None}
self.frame.setdefault("shape", "Rectangle")
self.frame.setdefault("parms_orig", self.frame.get("parms", [1.0, 1.0]))
self.frame.setdefault("kparms", {})
self.colors = colors or {}
self.colors.setdefault("frame", "black")
self.colors.setdefault("background", "none")
if (not labels) or "background" in labels or "frame" in labels:
self.labels = labels or {}
else:
self.labels = {"background": labels}
self._text = text or None
self._data = {
Element.from_Z(i).symbol: {"Symbol": Element.from_Z(i).symbol, **Element.from_Z(i).data}
for i in range(1, 104)
}
if data:
[self._data[k].update(data[k]) for k in data]
def get_frame(self):
self.frame["parms"] = list(self.frame["parms_orig"])
if self.frame["shape"] == "FancyBboxPatch":
self.frame["kparms"].setdefault("boxstyle", "round, pad=0.1")
pad = float([*re.findall("pad=(\d+[.]\d+)", self.frame["kparms"]['boxstyle']), 0.3][0])
self.frame["parms"][0:2] = list(np.array(self.frame["parms_orig"][0:2]) - 2*pad)
try:
return getattr(mpatches, self.frame["shape"])
except AttributeError:
raise ValueError("Unsupported shape error")
def get_xys(self):
width_and_height = np.array(self.frame["parms_orig"][0:2])
text_shift = self.frame.get("text_shift",
np.array([0.5, 0.5]) * width_and_height)
if self.frame["shape"] == "FancyBboxPatch":
text_shift -= 0.10 * width_and_height
elements = [Element.from_Z(i) for i in range(1, 104)]
group_and_rows = [np.array([el.group, el.row]) for el in elements]
frame_xys = [
np.array([1, -1]) * gr * width_and_height for gr in group_and_rows
]
text_xys = [text_shift + fxy for fxy in frame_xys]
return frame_xys, text_xys
def get_colors_and_legend(self):
for v in self.colors.values():
if isinstance(v, list) and len(v) != len(self._data):
raise ValueError(
"Length of color list should be compatible with Elements.")
default_color_cycle = plt.rcParams['axes.prop_cycle'].by_key()['color']
default_edgecolor = ["black", self.colors["frame"]
][isinstance(self.colors["frame"], str)]
default_facecolor = ["none", self.colors["background"]
][isinstance(self.colors["background"], str)]
colors = {
"edgecolors":
self.colors.get("frame", default_edgecolor),
"facecolors":
[self.colors.get("background", default_facecolor),
None][isinstance(self.colors["background"], dict)]
}
legend_handles = []
for k, v in colors.items():
labels = self.labels.get({
"edgecolors": "frame",
"facecolors": "background"
}[k], None)
if labels:
if not v:
raise ValueError(
"Gradient mapped background can't be labelled.")
if isinstance(colors[k], str):
colors[k] = [colors[k]] * len(self._data)
if isinstance(list(labels.values())[0], list):
labels = {
lk: {
"elements": lv
}
for lk, lv in labels.items()
}
for i, l in enumerate(labels):
label = labels[l]
label.setdefault("label", l)
indexes = [Element(s).Z - 1 for s in label["elements"]]
label.setdefault("color", default_color_cycle[i])
for j in indexes:
colors[k][j] = label["color"]
label.setdefault("frame_kparms", {})
for lkk in ["edgecolor", "facecolor"]:
label["frame_kparms"].setdefault(lkk, "none")
label["frame_kparms"][k[0:-1]] = label["color"]
patch_legend = mpatches.Patch(
label=label["label"], **label["frame_kparms"])
legend_handles.append(patch_legend)
return colors, legend_handles
def get_plot(self, title=None, figsize=None, legend_kparms={}):
fig, ax = plt.subplots(figsize=figsize)
frame_xys, text_xys = self.get_xys()
colors, legend_handles = self.get_colors_and_legend()
frame = self.get_frame()
frames = [
frame(xy, *self.frame["parms"], **self.frame["kparms"])
for xy in frame_xys
]
collection = PatchCollection(frames, **colors)
ax.add_collection(collection)
[
ax.text(
*text_xys[i],
Element.from_Z(i + 1).symbol,
horizontalalignment="center",
verticalalignment="center",
family="Times New Roman",
size="x-large"
) for i in range(len(self._data))
]
if legend_handles:
legend_kparms.update({"handles": legend_handles})
legend_kparms.setdefault("loc", "upper center")
legend_kparms.setdefault("bbox_to_anchor", (0.41, 1.0))
legend_kparms.setdefault("fontsize", "x-large")
ax.legend(**legend_kparms)
if title:
plt.title(title, fontsize=28)
plt.axis('equal')
plt.axis('off')
plt.tight_layout()
return plt
def show(self, title=None, figsize=None):
plt = self.get_plot(title=title, figsize=figsize)
plt.show()
p = periodic_table(
frame={
"shape": "Rectangle",
"parms": [1.0, 1.25]
},
labels={
"background": {
"+1 Elements": ['Na', 'K', 'Rb', 'Ag', 'Cs', 'Tl', 'Cu'],
"+3 Elements": [
'Al', 'Sc', 'Cr', 'Fe', 'Co', 'Ga', 'Y', 'Ru', 'Rh', 'In',
'Sb', 'La', 'Ce', 'Gd', 'Ir', 'Bi'
],
"-2 Elements": ['O', 'S', 'Se', 'Te']
}
})
pplt = p.get_plot(figsize=(9, 5))
pplt.show()
plt.close()
p = periodic_table(
frame={
"shape": "FancyBboxPatch",
"parms": [1.0, 1.25]
},
labels={
"background": {
"+1 Elements": ['Na', 'K', 'Rb', 'Ag', 'Cs', 'Tl', 'Cu'],
"+3 Elements": [
'Al', 'Sc', 'Cr', 'Fe', 'Co', 'Ga', 'Y', 'Ru', 'Rh', 'In',
'Sb', 'La', 'Ce', 'Gd', 'Ir', 'Bi'
],
"-2 Elements": ['O', 'S', 'Se', 'Te']
}
})
pplt = p.get_plot(figsize=(9, 5))
pplt.savefig("periodic_table.pdf", transparent=True)
pplt.show()
|
