import pandas as pd
from bokeh.plotting import figure, show
from bokeh.sampledata.periodic_table import elements
elements = elements.copy()
elements = elements[elements.group != "-"]
elements.sort_values('metal', inplace=True)
colormap = {
"alkali metal" : "#a6cee3",
"alkaline earth metal" : "#1f78b4",
"halogen" : "#fdbf6f",
"metal" : "#b2df8a",
"metalloid" : "#33a02c",
"noble gas" : "#bbbb88",
"nonmetal" : "#baa2a6",
"transition metal" : "#e08e79",
}
data=dict(
atomic_number=elements["atomic number"],
sym=elements["symbol"],
name=elements["name"],
atomic_mass = pd.to_numeric(elements['atomic mass'], errors="coerce"),
density=elements['density'],
metal=[x.title() for x in elements["metal"]],
type_color=[colormap[x] for x in elements["metal"]]
)
mass_format = '{0.00}'
import pandas as pd
from bokeh.plotting import figure, show
from bokeh.sampledata.periodic_table import elements
elements = elements.copy()
elements = elements[elements.group != "-"]
elements.sort_values('metal', inplace=True)
colormap = {
"alkali metal": "#a6cee3",
"alkaline earth metal": "#1f78b4",
"halogen": "#fdbf6f",
"metal": "#b2df8a",
"metalloid": "#33a02c",
"noble gas": "#bbbb88",
"nonmetal": "#baa2a6",
"transition metal": "#e08e79",
}
data = dict(atomic_number=elements["atomic number"],
sym=elements["symbol"],
name=elements["name"],
atomic_mass=pd.to_numeric(elements['atomic mass'],
errors="coerce"),
density=elements['density'],
metal=[x.title() for x in elements["metal"]],
type_color=[colormap[x] for x in elements["metal"]])
mass_format = '{0.00}'
Created on Thu May 30 15:17:41 2019
@author: Administrator
"""
from bokeh.io import output_file, show
from bokeh.plotting import figure
from bokeh.sampledata.periodic_table import elements
from bokeh.transform import dodge, factor_cmap
output_file("periodic.html")
periods = ["I", "II", "III", "IV", "V", "VI", "VII"]
groups = [str(x) for x in range(1, 19)]
df = elements.copy()
df["atomic mass"] = df["atomic mass"].astype(str)
df["group"] = df["group"].astype(str)
df["period"] = [periods[x - 1] for x in df.period]
df = df[df.group != "-"]
df = df[df.symbol != "Lr"]
df = df[df.symbol != "Lu"]
cmap = {
"alkali metal": "#a6cee3",
"alkaline earth metal": "#1f78b4",
"metal": "#d93b43",
"halogen": "#999d9a",
"metalloid": "#e08d49",
"noble gas": "#eaeaea",
"nonmetal": "#f1d4Af",
def report_html_periodic_table(logger, iteration=0):
# type: (Logger, int) -> ()
"""
reporting interactive (html) of periodic table to debug samples section
:param logger: The task.logger to use for sending the plots
:param iteration: The iteration number of the current reports
"""
output_file("periodic.html")
periods = ["I", "II", "III", "IV", "V", "VI", "VII"]
groups = [str(x) for x in range(1, 19)]
autompg_clean = elements.copy()
autompg_clean["atomic mass"] = autompg_clean["atomic mass"].astype(str)
autompg_clean["group"] = autompg_clean["group"].astype(str)
autompg_clean["period"] = [periods[x - 1] for x in autompg_clean.period]
autompg_clean = autompg_clean[autompg_clean.group != "-"]
autompg_clean = autompg_clean[autompg_clean.symbol != "Lr"]
autompg_clean = autompg_clean[autompg_clean.symbol != "Lu"]
cmap = {
"alkali metal": "#a6cee3",
"alkaline earth metal": "#1f78b4",
"metal": "#d93b43",
"halogen": "#999d9a",
"metalloid": "#e08d49",
"noble gas": "#eaeaea",
"nonmetal": "#f1d4Af",
"transition metal": "#599d7A",
}
source = ColumnDataSource(autompg_clean)
p = figure(
plot_width=900,
plot_height=500,
title="Periodic Table (omitting LA and AC Series)",
x_range=groups,
y_range=list(reversed(periods)),
toolbar_location=None,
tools="hover",
)
p.rect(
"group",
"period",
0.95,
0.95,
source=source,
fill_alpha=0.6,
legend_label="metal",
color=factor_cmap("metal",
palette=list(cmap.values()),
factors=list(cmap.keys())),
)
text_props = {
"source": source,
"text_align": "left",
"text_baseline": "middle"
}
x = dodge("group", -0.4, range=p.x_range)
r = p.text(x=x, y="period", text="symbol", **text_props)
r.glyph.text_font_style = "bold"
r = p.text(x=x,
y=dodge("period", 0.3, range=p.y_range),
text="atomic number",
**text_props)
r.glyph.text_font_size = "8pt"
r = p.text(x=x,
y=dodge("period", -0.35, range=p.y_range),
text="name",
**text_props)
r.glyph.text_font_size = "5pt"
r = p.text(x=x,
y=dodge("period", -0.2, range=p.y_range),
text="atomic mass",
**text_props)
r.glyph.text_font_size = "5pt"
p.text(
x=["3", "3"],
y=["VI", "VII"],
text=["LA", "AC"],
text_align="center",
text_baseline="middle",
)
p.hover.tooltips = [
("Name", "@name"),
("Atomic number", "@{atomic number}"),
("Atomic mass", "@{atomic mass}"),
("Type", "@metal"),
("CPK color", "$color[hex, swatch]:CPK"),
("Electronic configuration", "@{electronic configuration}"),
]
p.outline_line_color = None
p.grid.grid_line_color = None
p.axis.axis_line_color = None
p.axis.major_tick_line_color = None
p.axis.major_label_standoff = 0
p.legend.orientation = "horizontal"
p.legend.location = "top_center"
save(p)
logger.report_media("html",
"periodic_html",
iteration=iteration,
local_path="periodic.html")
from bokeh.io import output_file, show
from bokeh.models import ColumnDataSource
from bokeh.plotting import figure
from bokeh.sampledata.periodic_table import elements
from bokeh.transform import dodge, factor_cmap
output_file("periodic.html")
periods = ["I", "II", "III", "IV", "V", "VI", "VII"]
groups = [str(x) for x in range(1, 19)]
df = elements.copy()
df["atomic mass"] = df["atomic mass"].astype(str)
df["group"] = df["group"].astype(str)
df["period"] = [periods[x-1] for x in df.period]
df = df[df.group != "-"]
df = df[df.symbol != "Lr"]
df = df[df.symbol != "Lu"]
cmap = {
"alkali metal" : "#a6cee3",
"alkaline earth metal" : "#1f78b4",
"metal" : "#d93b43",
"halogen" : "#999d9a",
"metalloid" : "#e08d49",
"noble gas" : "#eaeaea",
"nonmetal" : "#f1d4Af",
"transition metal" : "#599d7A",
}
source = ColumnDataSource(df)
def periodic_table():
periods = ["I", "II", "III", "IV", "V", "VI", "VII"]
groups = [str(x) for x in range(1, 19)]
df = elements.copy()
df["atomic mass"] = df["atomic mass"].astype(str)
df["group"] = df["group"].astype(str)
df["period"] = [periods[x - 1] for x in df.period]
df = df[df.group != "-"]
df = df[df.symbol != "Lr"]
df = df[df.symbol != "Lu"]
cmap = {
"alkali metal": "#a6cee3",
"alkaline earth metal": "#1f78b4",
"metal": "#d93b43",
"halogen": "#999d9a",
"metalloid": "#e08d49",
"noble gas": "#eaeaea",
"nonmetal": "#f1d4Af",
"transition metal": "#599d7A",
}
source = ColumnDataSource(df)
p = figure(title="Periodic Table (omitting LA and AC Series)",
plot_width=600,
plot_height=300,
tools="",
toolbar_location=None,
x_range=groups,
y_range=list(reversed(periods)))
p.rect("group",
"period",
0.95,
0.95,
source=source,
fill_alpha=0.6,
legend="metal",
color=factor_cmap('metal',
palette=list(cmap.values()),
factors=list(cmap.keys())))
text_props = {
"source": source,
"text_align": "left",
"text_baseline": "middle"
}
x = dodge("group", -0.4, range=p.x_range)
r = p.text(x=x, y="period", text="symbol", **text_props)
r.glyph.text_font_style = "bold"
r = p.text(x=x,
y=dodge("period", 0.3, range=p.y_range),
text="atomic number",
**text_props)
r.glyph.text_font_size = "8pt"
r = p.text(x=x,
y=dodge("period", -0.35, range=p.y_range),
text="name",
**text_props)
r.glyph.text_font_size = "5pt"
r = p.text(x=x,
y=dodge("period", -0.2, range=p.y_range),
text="atomic mass",
**text_props)
r.glyph.text_font_size = "5pt"
p.text(x=["3", "3"],
y=["VI", "VII"],
text=["LA", "AC"],
text_align="center",
text_baseline="middle")
p.add_tools(
HoverTool(tooltips=[
("Name", "@name"),
("Atomic number", "@{atomic number}"),
("Atomic mass", "@{atomic mass}"),
("Type", "@metal"),
("CPK color", "$color[hex, swatch]:CPK"),
("Electronic configuration", "@{electronic configuration}"),
]))
p.outline_line_color = None
p.grid.grid_line_color = None
p.axis.axis_line_color = None
p.axis.major_tick_line_color = None
p.axis.major_label_standoff = 0
p.legend.orientation = "horizontal"
p.legend.location = "top_center"
return p
def plot_periodic_table():
output_file("periodic.html")
occurences = json.load(open('elements.json', 'r'))
periods = ["I", "II", "III", "IV", "V", "VI", "VII"]
groups = [str(x) for x in range(1, 19)]
df = elements.copy()
df["atomic mass"] = df["atomic mass"].astype(str)
df["group"] = df["group"].astype(str)
df["period"] = [periods[x - 1] for x in df.period]
df = df[df.group != "-"]
df = df[df.symbol != "Lr"]
df = df[df.symbol != "Lu"]
df['occurences'] = [
f'{round(occurences[x]/occurences["NumCandidates"] * 100, 2)}%'
for x in df.symbol
]
df['colors'] = [math.log(occurences[x] / 2 + 1) for x in df.symbol]
p = figure(title="Periodic Table (omitting LA and AC Series)",
plot_width=1000,
plot_height=450,
x_range=groups,
y_range=list(reversed(periods)))
#Use the field name of the column source
mapper = linear_cmap(field_name='colors',
palette=bokeh.palettes.Spectral6,
low=1,
high=max(df.colors))
r = p.rect("group",
"period",
0.95,
0.95,
source=df,
fill_alpha=0.6,
color=mapper)
color_bar = ColorBar(color_mapper=mapper['transform'],
width=8,
location=(0, 0))
p.add_layout(color_bar, 'right')
text_props = {
"source": df,
"text_align": "left",
"text_baseline": "middle"
}
x = dodge("group", -0.4, range=p.x_range)
p.text(x=x,
y="period",
text="symbol",
text_font_style="bold",
**text_props)
p.text(x=x,
y=dodge("period", 0.3, range=p.y_range),
text="atomic number",
text_font_size="11px",
**text_props)
p.text(x=x,
y=dodge("period", -0.35, range=p.y_range),
text="name",
text_font_size="7px",
**text_props)
p.text(x=x,
y=dodge("period", -0.2, range=p.y_range),
text="occurences",
text_font_size="7px",
**text_props)
p.text(x=["3", "3"],
y=["VI", "VII"],
text=["LA", "AC"],
text_align="center",
text_baseline="middle")
p.outline_line_color = None
p.grid.grid_line_color = None
p.axis.axis_line_color = None
p.axis.major_tick_line_color = None
p.axis.major_label_standoff = 0
p.legend.orientation = "horizontal"
p.legend.location = "top_center"
p.hover.renderers = [r] # only hover element boxes
show(p)
