Add plot functionality for single diffractograms
This commit is contained in:
rasmusvt
parent
d6734184cc
commit
2b1b9b0d9b
3 changed files with 363 additions and 22 deletions
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@ -275,8 +275,8 @@ def prettify_gc_plot(fig, ax, options=None):
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# Otherwise apply user input
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# Otherwise apply user input
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else:
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else:
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major_xtick = options['yticks'][0]
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major_ytick = options['yticks'][0]
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minor_xtick = options['yticks'][1]
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minor_ytick = options['yticks'][1]
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# Apply values
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# Apply values
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@ -90,25 +90,7 @@ def integrate_1d(calibrant, bins, path=None, image=None, options=None):
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return open_1d_data(filename)
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return open_1d_data(filename)
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def open_1d_data(path, options=None):
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with open(path, 'r') as f:
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position = 0
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current_line = f.readline()
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while current_line[0] == '#':
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position = f.tell()
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current_line = f.readline()
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f.seek(position)
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df = pd.read_csv(f, header=None, delim_whitespace=True)
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df.columns = ['2th', 'I']
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return df
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@ -165,7 +147,7 @@ def view_integrator(calibrant):
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def read_brml(path, options=None):
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def read_brml(path, options=None):
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required_options = ['extract_folder']
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required_options = ['extract_folder', 'save_folder']
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default_options = {
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default_options = {
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'extract_folder': 'temp',
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'extract_folder': 'temp',
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'save_folder': None
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'save_folder': None
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@ -240,9 +222,43 @@ def read_brml(path, options=None):
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return diffractogram
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return diffractogram
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def read_diffractogram(path, options=None):
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with open(path, 'r') as f:
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position = 0
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current_line = f.readline()
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while current_line[0] == '#':
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position = f.tell()
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current_line = f.readline()
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f.seek(position)
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diffractogram = pd.read_csv(f, header=None, delim_whitespace=True)
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diffractogram.columns = ['2th', 'I']
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return diffractogram
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def read_data(path, kind, options=None):
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if kind == 'beamline':
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diffractogram = read_diffractogram(path, options=options)
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elif kind == 'recx':
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diffractogram = read_brml(path, options=options)
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elif kind == 'image':
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diffractogram = get_image_array(path)
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return diffractogram
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@ -1,2 +1,327 @@
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import matplotlib.pyplot as plt
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import matplotlib.pyplot as plt
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import numpy
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from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator)
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import pandas as pd
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import numpy as np
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import math
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import beamtime.xrd as xrd
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def plot_diffractogram(path, kind, options=None):
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# Prepare plot, and read and process data
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fig, ax = prepare_diffractogram_plot(options=options)
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diffractogram = xrd.io.read_data(path=path, kind=kind, options=options)
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# Update options
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required_options = ['x_vals', 'y_vals', 'scatter']
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default_options = {
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'x_vals': '2th',
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'y_vals': 'I',
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'scatter': False
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}
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options = update_options(options=options, required_options=required_options, default_options=default_options)
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if options['scatter']:
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diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, kind='scatter')
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else:
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diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax)
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fig, ax = prettify_diffractogram_plot(fig=fig, ax=ax, options=options)
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return diffractogram, fig, ax
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def prepare_diffractogram_plot(options=None):
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# First take care of the options for plotting - set any values not specified to the default values
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required_options = ['columns', 'width', 'height', 'format', 'dpi', 'facecolor']
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default_options = {'columns': 1, 'width': 14, 'format': 'golden_ratio', 'dpi': None, 'facecolor': 'w'}
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# Define the required sizes
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required_sizes = ['lines', 'axes']
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# If none are set at all, just pass the default_options
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if not options:
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options = default_options
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options['height'] = options['width'] * (math.sqrt(5) - 1) / 2
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options['figsize'] = (options['width'], options['height'])
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# Define default sizes
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default_sizes = {
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'lines': 3*options['columns'],
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'axes': 3*options['columns']
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}
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# Initialise dictionary if it doesn't exist
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if not 'sizes' in options.keys():
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options['sizes'] = {}
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# Update dictionary with default values where none is supplied
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for size in required_sizes:
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if size not in options['sizes']:
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options['sizes'][size] = default_sizes[size]
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# If options is passed, go through to fill out the rest.
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else:
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# Start by setting the width:
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if 'width' not in options.keys():
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options['width'] = default_options['width']
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# 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.
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if 'height' not in options.keys():
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if 'format' not in options.keys():
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options['height'] = options['width'] * (math.sqrt(5) - 1) / 2
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elif options['format'] == 'square':
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options['height'] = options['width']
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options['figsize'] = (options['width'], options['height'])
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# After height and width are set, go through the rest of the options to make sure that all the required options are filled
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for option in required_options:
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if option not in options.keys():
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options[option] = default_options[option]
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fig, ax = plt.subplots(figsize=(options['figsize']), dpi=options['dpi'], facecolor=options['facecolor'])
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plt.rc('lines', linewidth=options['sizes']['lines'])
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plt.rc('axes', linewidth=options['sizes']['axes'])
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return fig, ax
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def prettify_diffractogram_plot(fig, ax, options=None):
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##################################################################
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######################### UPDATE OPTIONS #########################
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##################################################################
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# Define the required options
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required_options = [
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'columns',
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'xticks', 'yticks',
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'units',
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'show_major_ticks', 'show_minor_ticks', 'show_tick_labels',
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'xlim', 'ylim',
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'hide_x_axis', 'hide_y_axis',
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'positions',
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'xlabel', 'ylabel',
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'sizes',
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'title'
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]
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# Define the default options
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default_options = {
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'columns': 1,
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'xticks': [10, 5], 'yticks': [10000, 5000],
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'units': {'2th': '$^o$', 'I': 'arb. u.'},
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'show_major_ticks': [True, False, True, False], 'show_minor_ticks': [True, False, True, False], 'show_tick_labels': [True, False, False, False],
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'xlim': None,'ylim': None,
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'hide_x_axis': False, 'hide_y_axis': False,
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'positions': {'xaxis': 'bottom', 'yaxis': 'left'},
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'xlabel': None, 'ylabel': None,
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'sizes': None,
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'title': None
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}
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options = update_options(options, required_options, default_options)
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##################################################################
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########################## DEFINE SIZES ##########################
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##################################################################
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# Define the required sizes
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required_sizes = [
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'labels',
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'legend',
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'title',
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'line', 'axes',
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'tick_labels',
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'major_ticks', 'minor_ticks']
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# Define default sizes
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default_sizes = {
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'labels': 30*options['columns'],
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'legend': 30*options['columns'],
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'title': 30*options['columns'],
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'line': 3*options['columns'],
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'axes': 3*options['columns'],
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'tick_labels': 30*options['columns'],
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'major_ticks': 20*options['columns'],
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'minor_ticks': 10*options['columns']
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}
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# Initialise dictionary if it doesn't exist
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if not options['sizes']:
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options['sizes'] = {}
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# Update dictionary with default values where none is supplied
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for size in required_sizes:
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if size not in options['sizes']:
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options['sizes'][size] = default_sizes[size]
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##################################################################
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########################## AXIS LABELS ###########################
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##################################################################
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if not options['xlabel']:
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options['xlabel'] = prettify_labels(options['x_vals']) + ' [{}]'.format(options['units'][options['x_vals']])
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else:
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options['xlabel'] = options['xlabel'] + ' [{}]'.format(options['units'][options['x_vals']])
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if not options['ylabel']:
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options['ylabel'] = prettify_labels(options['y_vals']) + ' [{}]'.format(options['units'][options['y_vals']])
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else:
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options['ylabel'] = options['ylabel'] + ' [{}]'.format(options['units'][options['y_vals']])
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ax.set_xlabel(options['xlabel'], size=options['sizes']['labels'])
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ax.set_ylabel(options['ylabel'], size=options['sizes']['labels'])
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##################################################################
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###################### TICK MARKS & LABELS #######################
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##################################################################
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ax.tick_params(
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direction='in',
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which='major',
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bottom=options['show_major_ticks'][0], labelbottom=options['show_tick_labels'][0],
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left=options['show_major_ticks'][1], labelleft=options['show_tick_labels'][1],
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top=options['show_major_ticks'][2], labeltop=options['show_tick_labels'][2],
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right=options['show_major_ticks'][3], labelright=options['show_tick_labels'][3],
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length=options['sizes']['major_ticks'],
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width=options['sizes']['axes'])
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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'])
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if options['positions']['yaxis'] == 'right':
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ax.yaxis.set_label_position("right")
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ax.yaxis.tick_right()
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if options['hide_x_axis']:
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ax.axes.xaxis.set_visible(False)
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if options['hide_y_axis']:
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ax.axes.yaxis.set_visible(False)
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# Otherwise apply user input
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if options['xticks']:
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major_xtick = options['xticks'][0]
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minor_xtick = options['xticks'][1]
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if options['yticks']:
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major_ytick = options['yticks'][0]
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minor_ytick = options['yticks'][1]
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# Apply values
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ax.xaxis.set_major_locator(MultipleLocator(major_xtick))
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ax.xaxis.set_minor_locator(MultipleLocator(minor_xtick))
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ax.yaxis.set_major_locator(MultipleLocator(major_ytick))
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ax.yaxis.set_minor_locator(MultipleLocator(minor_ytick))
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# SET FONTSIZE OF TICK LABELS
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plt.xticks(fontsize=options['sizes']['tick_labels'])
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plt.yticks(fontsize=options['sizes']['tick_labels'])
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##################################################################
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########################## AXES LIMITS ###########################
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##################################################################
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if options['xlim']:
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plt.xlim(options['xlim'])
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if options['ylim']:
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plt.ylim(options['ylim'])
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##################################################################
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############################# TITLE ##############################
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##################################################################
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if options['title']:
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ax.set_title(options['title'], size=options['sizes']['title'])
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##################################################################
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############################# LEGEND #############################
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##################################################################
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if ax.get_legend():
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ax.get_legend().remove()
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return fig, ax
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def prettify_labels(label):
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labels_dict = {
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'2th': '2$\\theta$',
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'I': 'Intensity'
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}
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return labels_dict[label]
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#def plot_diffractograms():
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#def plot_heatmap():
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def update_options(options, required_options, default_options):
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if not options:
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options = default_options
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else:
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for option in required_options:
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if option not in options.keys():
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options[option] = default_options[option]
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||||||
|
|
||||||
|
return options
|
||||||
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Add table
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Reference in a new issue