nafuma/beamtime/xrd/plot.py

import matplotlib.pyplot as plt
from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator)

import pandas as pd
import numpy as np
import math

import beamtime.xrd as xrd




def plot_diffractogram(path, kind, options=None):

    # Prepare plot, and read and process data
    fig, ax = prepare_diffractogram_plot(options=options)
    diffractogram = xrd.io.read_data(path=path, kind=kind, options=options)


    # Update options
    required_options = ['x_vals', 'y_vals', 'scatter']



    default_options = {
        'x_vals': '2th', 
        'y_vals': 'I', 
        'scatter': False
        }

    options = update_options(options=options, required_options=required_options, default_options=default_options)

    if options['scatter']:
        diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, kind='scatter')
    
    else:
        diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax)



    fig, ax = prettify_diffractogram_plot(fig=fig, ax=ax, options=options)


    return diffractogram, fig, ax



def prepare_diffractogram_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'}


    # Define the required sizes
    required_sizes = ['lines', 'axes']




    # 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'])

    
    # Define default sizes
    default_sizes = {
            'lines': 3*options['columns'],
            'axes': 3*options['columns']
    }

    # Initialise dictionary if it doesn't exist
    if not 'sizes' in options.keys():
        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]


    # 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'])


    plt.rc('lines', linewidth=options['sizes']['lines'])
    plt.rc('axes', linewidth=options['sizes']['axes'])

    return fig, ax

def prettify_diffractogram_plot(fig, ax, options=None):

    ##################################################################
    ######################### UPDATE OPTIONS #########################
    ##################################################################

    # Define the required options
    required_options = [
    'columns', 
    'xticks', 'yticks', 
    'units',
    'show_major_ticks', 'show_minor_ticks', 'show_tick_labels',
    'xlim', 'ylim',
    'hide_x_axis', 'hide_y_axis', 
    'positions', 
    'xlabel', 'ylabel', 
    'sizes',
    'title'
    ]


    # Define the default options
    default_options = {
        'columns': 1,
        'xticks': [10, 5], 'yticks': [10000, 5000],
        'units': {'2th': '$^o$', 'I': 'arb. u.'},
        'show_major_ticks': [True, False, True, False], 'show_minor_ticks': [True, False, True, False], 'show_tick_labels': [True, False, False, False],
        'xlim': None,'ylim': None,
        'hide_x_axis': False, 'hide_y_axis': False,
        'positions': {'xaxis': 'bottom', 'yaxis': 'left'},
        'xlabel': None, 'ylabel': None,
        'sizes': None,
        'title': None 	
    }

    options = 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']:
        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], labelbottom=options['show_tick_labels'][0],
        left=options['show_major_ticks'][1], labelleft=options['show_tick_labels'][1],
        top=options['show_major_ticks'][2], labeltop=options['show_tick_labels'][2],
        right=options['show_major_ticks'][3], labelright=options['show_tick_labels'][3],
        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'][3], length=options['sizes']['minor_ticks'], width=options['sizes']['axes'])



    if options['positions']['yaxis'] == 'right':
        ax.yaxis.set_label_position("right")
        ax.yaxis.tick_right()


    if options['hide_x_axis']:
        ax.axes.xaxis.set_visible(False)

    if options['hide_y_axis']:
        ax.axes.yaxis.set_visible(False)



    # Otherwise apply user input
    if options['xticks']:
        major_xtick = options['xticks'][0]
        minor_xtick = options['xticks'][1]


    if options['yticks']:

        major_ytick = options['yticks'][0]
        minor_ytick = 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'])

    ##################################################################
    ########################## AXES LIMITS ###########################
    ##################################################################

    if options['xlim']:
        plt.xlim(options['xlim'])

    if options['ylim']:
        plt.ylim(options['ylim'])

    ##################################################################
    ############################# TITLE ##############################
    ##################################################################

    if options['title']:
        ax.set_title(options['title'], size=options['sizes']['title'])

    ##################################################################
    ############################# LEGEND #############################
    ##################################################################

    if ax.get_legend():
        ax.get_legend().remove()

    return fig, ax



def prettify_labels(label):
	
	labels_dict = {
		'2th': '2$\\theta$',
        'I': 'Intensity'	
        }

	return labels_dict[label]

#def plot_diffractograms():




#def plot_heatmap():





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