Add plot functionality to electrochemistry

beamtime/electrochemistry/io.py

@@ -4,6 +4,22 @@ import matplotlib.pyplot as plt
 import os
 
 
+def read_data(path, kind, options=None):
+
+	if kind == 'neware':
+		df = read_neware(path)
+		cycles = process_neware_data(df, options=options)
+
+	elif kind == 'batsmall':
+		df = read_batsmall(path)
+		cycles = process_batsmall_data(df=df, options=options)
+
+	elif kind == 'biologic':
+		df = read_biologic(path)
+		cycles = process_biologic_data(df=df, options=options)
+
+	return cycles
+
 def read_batsmall(path):
 	''' Reads BATSMALL-data into a DataFrame.
 
@@ -77,7 +93,7 @@ def read_biologic(path):
 
 
 
-def process_batsmall_data(df, units=None, splice_cycles=None, molecular_weight=None):
+def process_batsmall_data(df, options=None):
 	''' Takes BATSMALL-data in the form of a DataFrame and cleans the data up and converts units into desired units.
 	Splits up into individual charge and discharge DataFrames per cycle, and outputs a list where each element is a tuple with the Chg and DChg-data. E.g. cycles[10][0] gives the charge data for the 11th cycle.
 
@@ -94,12 +110,24 @@ def process_batsmall_data(df, units=None, splice_cycles=None, molecular_weight=N
 	cycles: A list with 
 	'''
 
+	required_options = ['splice_cycles', 'molecular_weight', 'reverse_discharge', 'units']
+	default_options = {'splice_cycles': None, 'molecular_weight': None, 'reverse_discharge': False, 'units': None}
+
+	if not options:
+		options = default_options
+	else:
+		for option in required_options:
+			if option not in options.keys():
+				options[option] = default_options[option]
+
 
 	# Complete set of new units and get the units used in the dataset, and convert values in the DataFrame from old to new.
-	new_units = set_units(units=units)
+	new_units = set_units(units=options['units'])
 	old_units = get_old_units(df, kind='batsmall')
 	df = unit_conversion(df=df, new_units=new_units, old_units=old_units, kind='batsmall')
 
+	options['units'] = new_units
+
 	# Replace NaN with empty string in the Comment-column and then remove all steps where the program changes - this is due to inconsistent values for current  
 	df[["comment"]] = df[["comment"]].fillna(value={'comment': ''})
 	df = df[df["comment"].str.contains("program")==False]
@@ -126,6 +154,18 @@ def process_batsmall_data(df, units=None, splice_cycles=None, molecular_weight=N
 		if chg_df.empty and dchg_df.empty:
 			continue
 
+		if options['reverse_discharge']:
+			max_capacity = dchg_df['capacity'].max() 
+			dchg_df['capacity'] = np.abs(dchg_df['capacity'] - max_capacity)
+
+			if 'specific_capacity' in df.columns:
+				max_capacity = dchg_df['specific_capacity'].max() 
+				dchg_df['specific_capacity'] = np.abs(dchg_df['specific_capacity'] - max_capacity)
+
+				if 'ions' in df.columns:
+					max_capacity = dchg_df['ions'].max() 
+					dchg_df['ions'] = np.abs(dchg_df['ions'] - max_capacity)
+
 		cycles.append((chg_df, dchg_df))
 
 
@@ -134,7 +174,7 @@ def process_batsmall_data(df, units=None, splice_cycles=None, molecular_weight=N
 	return cycles
 
 
-def process_neware_data(df, units=None, splice_cycles=None, active_material_weight=None, molecular_weight=None, reverse_discharge=False):
+def process_neware_data(df, options=None):
 
 	""" Takes data from NEWARE in a DataFrame as read by read_neware() and converts units, adds columns and splits into cycles.
 	
@@ -145,14 +185,27 @@ def process_neware_data(df, units=None, splice_cycles=None, active_material_weig
 	active_materiale_weight: weight of the active material (in mg) used in the cell. 
 	molecular_weight: the molar mass (in g mol^-1) of the active material, to calculate the number of ions extracted. Assumes one electron per Li+/Na+-ion """
 	
+	required_options = ['units', 'active_material_weight', 'molecular_weight', 'reverse_discharge', 'splice_cycles']
+	default_options = {'units': None, 'active_material_weight': None, 'molecular_weight': None, 'reverse_discharge': False, 'splice_cycles': None}
+
+	if not options:
+		options = default_options
+	else:
+		for option in required_options:
+			if option not in options.keys():
+				options[option] = default_options[option]
+
+
 	# Complete set of new units and get the units used in the dataset, and convert values in the DataFrame from old to new.
-	new_units = set_units(units=units)
+	new_units = set_units(units=options['units'])
 	old_units = get_old_units(df=df, kind='neware')
 	
-	df = add_columns(df=df, active_material_weight=active_material_weight, molecular_weight=molecular_weight, old_units=old_units, kind='neware')
+	df = add_columns(df=df, active_material_weight=options['active_material_weight'], molecular_weight=options['molecular_weight'], old_units=old_units, kind='neware')
 
 	df = unit_conversion(df=df, new_units=new_units, old_units=old_units, kind='neware')
 
+	options['units'] = new_units
+
 
 	# Creates masks for charge and discharge curves
 	chg_mask = df['status'] == 'CC Chg'
@@ -176,7 +229,7 @@ def process_neware_data(df, units=None, splice_cycles=None, active_material_weig
 		if chg_df.empty and dchg_df.empty:
 			continue
 
-		if reverse_discharge:
+		if options['reverse_discharge']:
 			max_capacity = dchg_df['capacity'].max() 
 			dchg_df['capacity'] = np.abs(dchg_df['capacity'] - max_capacity)
 
@@ -195,19 +248,31 @@ def process_neware_data(df, units=None, splice_cycles=None, active_material_weig
 	return cycles
 
 
-def process_biologic_data(df, units=None, splice_cycles=None, active_material_weight=None, molecular_weight=None, reverse_discharge=False):
+def process_biologic_data(df, options=None):
+
+	required_options = ['units', 'active_material_weight', 'molecular_weight', 'reverse_discharge', 'splice_cycles']
+	default_options = {'units': None, 'active_material_weight': None, 'molecular_weight': None, 'reverse_discharge': False, 'splice_cycles': None}
+
+	if not options:
+		options = default_options
+	else:
+		for option in required_options:
+			if option not in options.keys():
+				options[option] = default_options[option]
 
 	# Pick out necessary columns
 	df = df[['Ns changes', 'Ns', 'time/s', 'Ewe/V', 'Energy charge/W.h', 'Energy discharge/W.h', '<I>/mA',  'Capacity/mA.h', 'cycle number']].copy()
 
 	# Complete set of new units and get the units used in the dataset, and convert values in the DataFrame from old to new.
-	new_units = set_units(units=units)
+	new_units = set_units(units=options['units'])
 	old_units = get_old_units(df=df, kind='biologic')
 	
-	df = add_columns(df=df, active_material_weight=active_material_weight, molecular_weight=molecular_weight, old_units=old_units, kind='biologic')
+	df = add_columns(df=df, active_material_weight=options['active_material_weight'], molecular_weight=options['molecular_weight'], old_units=old_units, kind='biologic')
 
 	df = unit_conversion(df=df, new_units=new_units, old_units=old_units, kind='biologic')
 
+	options['units'] = new_units
+
 
 	# Creates masks for charge and discharge curves
 	chg_mask = (df['status'] == 1) & (df['status_change'] != 1)
@@ -233,7 +298,7 @@ def process_biologic_data(df, units=None, splice_cycles=None, active_material_we
 		if chg_df.empty and dchg_df.empty:
 			continue
 
-		if reverse_discharge:
+		if options['reverse_discharge']:
 			max_capacity = dchg_df['capacity'].max() 
 			dchg_df['capacity'] = np.abs(dchg_df['capacity'] - max_capacity)
 
@@ -348,8 +413,8 @@ def unit_conversion(df, new_units, old_units, kind):
 def set_units(units=None):
 	
 	# Complete the list of units - if not all are passed, then default value will be used
-	required_units = ['time', 'current', 'voltage', 'capacity', 'mass', 'energy']
+	required_units = ['time', 'current', 'voltage', 'capacity', 'mass', 'energy', 'specific_capacity']
-	default_units = {'time': 'h', 'current': 'mA', 'voltage': 'V', 'capacity': 'mAh', 'mass': 'g', 'energy': 'mWh'}
+	default_units = {'time': 'h', 'current': 'mA', 'voltage': 'V', 'capacity': 'mAh', 'mass': 'g', 'energy': 'mWh', 'specific_capacity': None}
 
 	if not units:
 		units = default_units
@@ -359,6 +424,8 @@ def set_units(units=None):
 			if unit not in units.keys():
 				units[unit] = default_units[unit]
 
+	units['specific_capacity'] = r'{} {}'.format(units['capacity'], units['mass']) + '$^{-1}$'
+
 
 	return units
 

beamtime/electrochemistry/plot.py

@@ -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':
+	# Update options
-		which_cycles = [i for i, c in enumerate(cycles)]
+	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:
+	options = update_options(options=options, required_options=required_options, default_options=default_options)
-		chg_colour = (40/255, 70/255, 75/255) # Dark Slate Gray #28464B
+
-		dchg_colour = (239/255, 160/255, 11/255) # Marigold #EFA00B
+	# 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 cycles:
+	for i, cycle in enumerate(cycles):
-		if i in which_cycles:
+		if i in options['which_cycles']:
-			if chg:
+			if options['chg']:
-				cycle[0].plot(ax=ax)
+				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'])
+
+		if which_cycles[0] <= 0:
+			which_cycles[0] = 1
+
+		elif which_cycles[1] < 0:
+			which_cycles[1] = len(cycles)
 
 
-def prepare_gc_plot(figsize=(14,7), dpi=None):
+		options['which_cycles'] = [i-1 for i in range(which_cycles[0], which_cycles[1]+1)]
 
-	fig, ax = plt.subplots(figsize=figsize, dpi=dpi)
 
+	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 prettify_labels(label):
+	
+	labels_dict = {
+		'capacity': 'Capacity',
+		'specific_capacity': 'Specific capacity',
+		'voltage': 'Voltage',
+		'current': 'Current',
+		'energy': 'Energy',
+	}
+
+	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