Add plot functionality to electrochemistry
This commit is contained in:
rasmusvt
parent
4f255fd9d5
commit
43e6ef27c8
2 changed files with 433 additions and 33 deletions
|
|
@ -1,40 +1,373 @@
|
|||
import matplotlib.pyplot as plt
|
||||
from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator)
|
||||
|
||||
import pandas as pd
|
||||
import numpy as np
|
||||
import math
|
||||
|
||||
import beamtime.electrochemistry as ec
|
||||
|
||||
|
||||
def plot_gc(cycles, which_cycles='all', chg=True, dchg=True, colours=None, x='C', y='U'):
|
||||
def plot_gc(path, kind, options=None):
|
||||
|
||||
fig, ax = prepare_gc_plot()
|
||||
# Prepare plot, and read and process data
|
||||
fig, ax = prepare_gc_plot(options=options)
|
||||
cycles = ec.io.read_data(path=path, kind=kind, options=options)
|
||||
|
||||
|
||||
if which_cycles == 'all':
|
||||
which_cycles = [i for i, c in enumerate(cycles)]
|
||||
# Update options
|
||||
required_options = ['x_vals', 'y_vals', 'which_cycles', 'chg', 'dchg', 'colours', 'gradient']
|
||||
default_options = {'x_vals': 'capacity', 'y_vals': 'voltage', 'which_cycles': 'all', 'chg': True, 'dchg': True, 'colours': None, 'gradient': False}
|
||||
|
||||
if not colours:
|
||||
chg_colour = (40/255, 70/255, 75/255) # Dark Slate Gray #28464B
|
||||
dchg_colour = (239/255, 160/255, 11/255) # Marigold #EFA00B
|
||||
options = update_options(options=options, required_options=required_options, default_options=default_options)
|
||||
|
||||
# Update list of cycles to correct indices
|
||||
update_cycles_list(cycles=cycles, options=options)
|
||||
|
||||
colours = generate_colours(cycles=cycles, options=options)
|
||||
|
||||
print(len(options['which_cycles']))
|
||||
print(len(colours))
|
||||
|
||||
|
||||
|
||||
for i, cycle in enumerate(cycles):
|
||||
if i in options['which_cycles']:
|
||||
if options['chg']:
|
||||
cycle[0].plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=colours[i][0])
|
||||
|
||||
if options['dchg']:
|
||||
cycle[1].plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=colours[i][1])
|
||||
|
||||
|
||||
|
||||
fig, ax = prettify_gc_plot(fig=fig, ax=ax, options=options)
|
||||
|
||||
return cycles, fig, ax
|
||||
|
||||
|
||||
def update_options(options, required_options, default_options):
|
||||
|
||||
if not options:
|
||||
options = default_options
|
||||
|
||||
else:
|
||||
for option in required_options:
|
||||
if option not in options.keys():
|
||||
options[option] = default_options[option]
|
||||
|
||||
return options
|
||||
|
||||
def update_cycles_list(cycles, options):
|
||||
|
||||
if not options:
|
||||
options['which_cycles']
|
||||
|
||||
if options['which_cycles'] == 'all':
|
||||
options['which_cycles'] = [i for i in range(len(cycles))]
|
||||
|
||||
|
||||
elif type(options['which_cycles']) == list:
|
||||
options['which_cycles'] = [i-1 for i in options['which_cycles']]
|
||||
|
||||
|
||||
# Tuple is used to define an interval - as elements tuples can't be assigned, I convert it to a list here.
|
||||
elif type(options['which_cycles']) == tuple:
|
||||
which_cycles = list(options['which_cycles'])
|
||||
|
||||
for i, cycle in cycles:
|
||||
if i in which_cycles:
|
||||
if chg:
|
||||
cycle[0].plot(ax=ax)
|
||||
if which_cycles[0] <= 0:
|
||||
which_cycles[0] = 1
|
||||
|
||||
elif which_cycles[1] < 0:
|
||||
which_cycles[1] = len(cycles)
|
||||
|
||||
|
||||
options['which_cycles'] = [i-1 for i in range(which_cycles[0], which_cycles[1]+1)]
|
||||
|
||||
|
||||
return options
|
||||
|
||||
|
||||
def prepare_gc_plot(options=None):
|
||||
|
||||
|
||||
# First take care of the options for plotting - set any values not specified to the default values
|
||||
required_options = ['columns', 'width', 'height', 'format', 'dpi', 'facecolor']
|
||||
default_options = {'columns': 1, 'width': 14, 'format': 'golden_ratio', 'dpi': None, 'facecolor': 'w'}
|
||||
|
||||
# If none are set at all, just pass the default_options
|
||||
if not options:
|
||||
options = default_options
|
||||
options['height'] = options['width'] * (math.sqrt(5) - 1) / 2
|
||||
options['figsize'] = (options['width'], options['height'])
|
||||
|
||||
|
||||
# If options is passed, go through to fill out the rest.
|
||||
else:
|
||||
# Start by setting the width:
|
||||
if 'width' not in options.keys():
|
||||
options['width'] = default_options['width']
|
||||
|
||||
# Then set height - check options for format. If not given, set the height to the width scaled by the golden ratio - if the format is square, set the same. This should possibly allow for the tweaking of custom ratios later.
|
||||
if 'height' not in options.keys():
|
||||
if 'format' not in options.keys():
|
||||
options['height'] = options['width'] * (math.sqrt(5) - 1) / 2
|
||||
elif options['format'] == 'square':
|
||||
options['height'] = options['width']
|
||||
|
||||
options['figsize'] = (options['width'], options['height'])
|
||||
|
||||
# After height and width are set, go through the rest of the options to make sure that all the required options are filled
|
||||
for option in required_options:
|
||||
if option not in options.keys():
|
||||
options[option] = default_options[option]
|
||||
|
||||
fig, ax = plt.subplots(figsize=(options['figsize']), dpi=options['dpi'], facecolor=options['facecolor'])
|
||||
|
||||
linewidth = 1*options['columns']
|
||||
axeswidth = 3*options['columns']
|
||||
|
||||
plt.rc('lines', linewidth=linewidth)
|
||||
plt.rc('axes', linewidth=axeswidth)
|
||||
|
||||
return fig, ax
|
||||
|
||||
|
||||
def prettify_gc_plot(fig, ax, options=None):
|
||||
|
||||
|
||||
##################################################################
|
||||
######################### UPDATE OPTIONS #########################
|
||||
##################################################################
|
||||
|
||||
# Define the required options
|
||||
required_options = [
|
||||
'columns',
|
||||
'xticks', 'yticks',
|
||||
'show_major_ticks',
|
||||
'show_minor_ticks',
|
||||
'xlim', 'ylim',
|
||||
'hide_x_axis', 'hide_y_axis',
|
||||
'x_vals', 'y_vals',
|
||||
'xlabel', 'ylabel',
|
||||
'units', 'sizes',
|
||||
'title'
|
||||
]
|
||||
|
||||
|
||||
# Define the default options
|
||||
default_options = {
|
||||
'columns': 1,
|
||||
'xticks': None,
|
||||
'yticks': None,
|
||||
'show_major_ticks': [True, True, True, True],
|
||||
'show_minor_ticks': [True, True, True, True],
|
||||
'xlim': None,
|
||||
'ylim': None,
|
||||
'hide_x_axis': False,
|
||||
'hide_y_axis': False,
|
||||
'x_vals': 'specific_capacity',
|
||||
'y_vals': 'voltage',
|
||||
'xlabel': None,
|
||||
'ylabel': None,
|
||||
'units': None,
|
||||
'sizes': None,
|
||||
'title': None
|
||||
}
|
||||
|
||||
update_options(options, required_options, default_options)
|
||||
|
||||
|
||||
##################################################################
|
||||
########################## DEFINE SIZES ##########################
|
||||
##################################################################
|
||||
|
||||
# Define the required sizes
|
||||
required_sizes = [
|
||||
'labels',
|
||||
'legend',
|
||||
'title',
|
||||
'line', 'axes',
|
||||
'tick_labels',
|
||||
'major_ticks', 'minor_ticks']
|
||||
|
||||
|
||||
|
||||
# Define default sizes
|
||||
default_sizes = {
|
||||
'labels': 30*options['columns'],
|
||||
'legend': 30*options['columns'],
|
||||
'title': 30*options['columns'],
|
||||
'line': 3*options['columns'],
|
||||
'axes': 3*options['columns'],
|
||||
'tick_labels': 30*options['columns'],
|
||||
'major_ticks': 20*options['columns'],
|
||||
'minor_ticks': 10*options['columns']
|
||||
}
|
||||
|
||||
# Initialise dictionary if it doesn't exist
|
||||
if not options['sizes']:
|
||||
options['sizes'] = {}
|
||||
|
||||
|
||||
# Update dictionary with default values where none is supplied
|
||||
for size in required_sizes:
|
||||
if size not in options['sizes']:
|
||||
options['sizes'][size] = default_sizes[size]
|
||||
|
||||
|
||||
##################################################################
|
||||
########################## AXIS LABELS ###########################
|
||||
##################################################################
|
||||
|
||||
|
||||
if not options['xlabel']:
|
||||
print(options['x_vals'])
|
||||
print(options['units'])
|
||||
options['xlabel'] = prettify_labels(options['x_vals']) + ' [{}]'.format(options['units'][options['x_vals']])
|
||||
|
||||
else:
|
||||
options['xlabel'] = options['xlabel'] + ' [{}]'.format(options['units'][options['x_vals']])
|
||||
|
||||
|
||||
if not options['ylabel']:
|
||||
options['ylabel'] = prettify_labels(options['y_vals']) + ' [{}]'.format(options['units'][options['y_vals']])
|
||||
|
||||
else:
|
||||
options['ylabel'] = options['ylabel'] + ' [{}]'.format(options['units'][options['y_vals']])
|
||||
|
||||
ax.set_xlabel(options['xlabel'], size=options['sizes']['labels'])
|
||||
ax.set_ylabel(options['ylabel'], size=options['sizes']['labels'])
|
||||
|
||||
##################################################################
|
||||
###################### TICK MARKS & LABELS #######################
|
||||
##################################################################
|
||||
|
||||
ax.tick_params(direction='in', which='major', bottom=options['show_major_ticks'][0], left=options['show_major_ticks'][1], top=options['show_major_ticks'][2], right=options['show_major_ticks'][0], length=options['sizes']['major_ticks'], width=options['sizes']['axes'])
|
||||
ax.tick_params(direction='in', which='minor', bottom=options['show_minor_ticks'][0], left=options['show_minor_ticks'][1], top=options['show_minor_ticks'][2], right=options['show_minor_ticks'][0], length=options['sizes']['minor_ticks'], width=options['sizes']['axes'])
|
||||
|
||||
|
||||
|
||||
# DEFINE AND SET TICK DISTANCES
|
||||
|
||||
default_ticks = {
|
||||
'specific_capacity': [100, 50],
|
||||
'capacity': [0.1, 0.05],
|
||||
'voltage': [0.5, 0.25]
|
||||
}
|
||||
|
||||
|
||||
|
||||
# Set default tick distances for x-axis if not specified
|
||||
if not options['xticks']:
|
||||
|
||||
major_xtick = default_ticks[options['x_vals']][0]
|
||||
minor_xtick = default_ticks[options['x_vals']][1]
|
||||
|
||||
# Otherwise apply user input
|
||||
else:
|
||||
major_xtick = options['xticks'][0]
|
||||
minor_xtick = options['xticks'][1]
|
||||
|
||||
|
||||
# Set default tick distances for x-axis if not specified
|
||||
if not options['yticks']:
|
||||
|
||||
major_ytick = default_ticks[options['y_vals']][0]
|
||||
minor_ytick = default_ticks[options['y_vals']][1]
|
||||
|
||||
# Otherwise apply user input
|
||||
else:
|
||||
major_xtick = options['yticks'][0]
|
||||
minor_xtick = options['yticks'][1]
|
||||
|
||||
|
||||
# Apply values
|
||||
ax.xaxis.set_major_locator(MultipleLocator(major_xtick))
|
||||
ax.xaxis.set_minor_locator(MultipleLocator(minor_xtick))
|
||||
|
||||
ax.yaxis.set_major_locator(MultipleLocator(major_ytick))
|
||||
ax.yaxis.set_minor_locator(MultipleLocator(minor_ytick))
|
||||
|
||||
|
||||
# SET FONTSIZE OF TICK LABELS
|
||||
|
||||
plt.xticks(fontsize=options['sizes']['tick_labels'])
|
||||
plt.yticks(fontsize=options['sizes']['tick_labels'])
|
||||
|
||||
##################################################################
|
||||
############################# TITLE ##############################
|
||||
##################################################################
|
||||
|
||||
if options['title']:
|
||||
ax.set_title(options['title'], size=options['sizes']['title'])
|
||||
|
||||
##################################################################
|
||||
############################# LEGEND #############################
|
||||
##################################################################
|
||||
|
||||
ax.get_legend().remove()
|
||||
|
||||
return fig, ax
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
def prepare_gc_plot(figsize=(14,7), dpi=None):
|
||||
|
||||
fig, ax = plt.subplots(figsize=figsize, dpi=dpi)
|
||||
def prettify_labels(label):
|
||||
|
||||
labels_dict = {
|
||||
'capacity': 'Capacity',
|
||||
'specific_capacity': 'Specific capacity',
|
||||
'voltage': 'Voltage',
|
||||
'current': 'Current',
|
||||
'energy': 'Energy',
|
||||
}
|
||||
|
||||
return fig, ax
|
||||
return labels_dict[label]
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
def generate_colours(cycles, options):
|
||||
|
||||
# Assign colours from the options dictionary if it is defined, otherwise use standard colours.
|
||||
if options['colours']:
|
||||
charge_colour = options['colours'][0]
|
||||
discharge_colour = options['colours'][1]
|
||||
|
||||
else:
|
||||
charge_colour = (40/255, 70/255, 75/255) # Dark Slate Gray #28464B, coolors.co
|
||||
discharge_colour = (239/255, 160/255, 11/255) # Marigold #EFA00B, coolors.co
|
||||
|
||||
|
||||
|
||||
# If gradient is enabled, find start and end points for each colour
|
||||
if options['gradient']:
|
||||
|
||||
add_charge = min([(1-x)*0.75 for x in charge_colour])
|
||||
add_discharge = min([(1-x)*0.75 for x in discharge_colour])
|
||||
|
||||
charge_colour_start = charge_colour
|
||||
charge_colour_end = [x+add_charge for x in charge_colour]
|
||||
|
||||
discharge_colour_start = discharge_colour
|
||||
discharge_colour_end = [x+add_discharge for x in discharge_colour]
|
||||
|
||||
|
||||
|
||||
# Generate lists of colours
|
||||
colours = []
|
||||
|
||||
for cycle_number in range(0, len(cycles)):
|
||||
if options['gradient']:
|
||||
weight_start = (len(cycles) - cycle_number)/len(cycles)
|
||||
weight_end = cycle_number/len(cycles)
|
||||
|
||||
charge_colour = [weight_start*start_colour + weight_end*end_colour for start_colour, end_colour in zip(charge_colour_start, charge_colour_end)]
|
||||
discharge_colour = [weight_start*start_colour + weight_end*end_colour for start_colour, end_colour in zip(discharge_colour_start, discharge_colour_end)]
|
||||
|
||||
colours.append([charge_colour, discharge_colour])
|
||||
|
||||
return colours
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue