Add reflection table and interactive mode to xrd
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rasmusvt
parent
67ea048380
commit
a5c845fa54
3 changed files with 213 additions and 19 deletions
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@ -25,7 +25,9 @@ def prepare_plot(options={}):
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rc_params = options['rc_params']
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format_params = options['format_params']
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required_format_params = ['single_column_width', 'double_column_width', 'column_type', 'width_ratio', 'aspect_ratio', 'compress_width', 'compress_height', 'upscaling_factor', 'dpi']
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required_format_params = ['single_column_width', 'double_column_width', 'column_type', 'width_ratio', 'aspect_ratio',
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'width', 'height', 'compress_width', 'compress_height', 'upscaling_factor', 'dpi',
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'nrows', 'ncols', 'grid_ratio_height', 'grid_ratio_width']
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default_format_params = {
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'single_column_width': 8.3,
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@ -33,10 +35,16 @@ def prepare_plot(options={}):
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'column_type': 'single',
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'width_ratio': '1:1',
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'aspect_ratio': '1:1',
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'width': None,
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'height': None,
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'compress_width': 1,
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'compress_height': 1,
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'upscaling_factor': 1.0,
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'dpi': 600,
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'nrows': 1,
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'ncols': 1,
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'grid_ratio_height': None,
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'grid_ratio_width': None
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}
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format_params = aux.update_options(format_params, required_format_params, default_format_params)
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@ -48,13 +56,72 @@ def prepare_plot(options={}):
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# Update run commands if any is passed (will pass an empty dictionary if not passed)
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update_rc_params(rc_params)
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width = determine_width(format_params=format_params)
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height = determine_height(format_params=format_params, width=width)
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if not format_params['width']:
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width = determine_width(format_params=format_params)
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if not format_params['height']:
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height = determine_height(format_params=format_params, width=width)
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width, height = scale_figure(format_params=format_params, width=width, height=height)
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fig, ax = plt.subplots(figsize=(width, height), dpi=format_params['dpi'])
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if format_params['nrows'] == 1 and format_params['ncols'] == 1:
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fig, ax = plt.subplots(figsize=(width, height), dpi=format_params['dpi'])
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return fig, ax
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return fig, ax
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else:
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if not format_params['grid_ratio_height']:
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format_params['grid_ratio_height'] = [1 for i in range(format_params['nrows'])]
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if not format_params['grid_ratio_width']:
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format_params['grid-ratio_width'] = [1 for i in range(format_params['ncols'])]
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fig, axes = plt.subplots(nrows=format_params['nrows'], ncols=format_params['ncols'], figsize=(width,height),
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gridspec_kw={'height_ratios': format_params['grid_ratio_height'], 'width_ratios': format_params['grid_ratio_width']},
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facecolor='w', dpi=format_params['dpi'])
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return fig, axes
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def prepare_plots(options={}):
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rc_params = options['rc_params']
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format_params = options['format_params']
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required_options = ['single_column_width', 'double_column_width', 'column_type', 'width_ratio', 'aspect_ratio', 'compress_width', 'compress_height', 'upscaling_factor', 'dpi']
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default_options = {
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'single_column_width': 8.3,
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'double_column_width': 17.1,
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'column_type': 'single',
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'width_ratio': '1:1',
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'aspect_ratio': '1:1',
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'compress_width': 1,
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'compress_height': 1,
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'upscaling_factor': 1.0,
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'dpi': 600,
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}
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format_params = aux.update_options(format_params, required_options, default_options)
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# Reset run commands
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plt.rcdefaults()
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# Update run commands if any is passed (will pass an empty dictionary if not passed)
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update_rc_params(rc_params)
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width = determine_width(format_params)
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height = determine_height(format_params, width)
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width, height = scale_figure(options=format_params, width=width, height=height)
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if options['plot_kind'] == 'relative':
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fig, axes = plt.subplots(nrows=1, ncols=options['number_of_frames'], figsize=(width,height), facecolor='w', dpi=format_params['dpi'])
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elif options['plot_kind'] == 'absolute':
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fig, axes = plt.subplots(nrows=2, ncols=options['number_of_frames'], figsize=(width,height), gridspec_kw={'height_ratios': [1,5]}, facecolor='w', dpi=format_params['dpi'])
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return fig, axes
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def adjust_plot(fig, ax, options):
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@ -87,7 +87,7 @@ def integrate_1d(calibrant, bins, path=None, image=None, options=None):
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res = ai.integrate1d(image, bins, unit=options['unit'], filename=filename)
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if options['return']:
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return open_1d_data(filename)
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return read_diffractogram(filename)
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@ -222,7 +222,7 @@ def read_brml(path, options=None):
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return diffractogram
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def read_diffractogram(path, options=None):
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def read_diffractogram(path):
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@ -248,7 +248,7 @@ def read_diffractogram(path, options=None):
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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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diffractogram = read_diffractogram(path)
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elif kind == 'recx':
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diffractogram = read_brml(path, options=options)
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@ -5,8 +5,9 @@ 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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import ipywidgets as widgets
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import beamtime.xrd as xrd
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import beamtime.auxillary as aux
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import beamtime.plotting as btp
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@ -18,42 +19,168 @@ def plot_diffractogram(plot_data, options={}):
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plot_data (dict): Must include path = string to diffractogram data, and plot_kind = (recx, beamline, image)'''
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# Update options
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required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'scatter', 'plot_kind', 'rc_params', 'format_params']
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required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter',
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'reflections', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params']
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default_options = {
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'x_vals': '2th',
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'y_vals': 'I',
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'ylabel': 'Intensity', 'xlabel': '2theta',
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'xunit': 'deg', 'yunit': 'a.u.',
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'line': True,
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'scatter': False,
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'reflections': False,
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'reflection_data': None, # Should be passed as a dictionary on the form {path: rel_path, colour: [r,g,b], min_alpha: 0-1]
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'plot_kind': None,
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'palettes': [('qualitative', 'Dark2_8')],
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'interactive': False,
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'rc_params': {},
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'format_params': {}
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'format_params': {},
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}
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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# Prepare plot, and read and process data
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fig, ax = btp.prepare_plot(options=options)
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diffractogram = xrd.io.read_data(path=plot_data['path'], kind=plot_data['plot_kind'], options=options)
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if options['interactive']:
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options['interactive'] = False
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plot_diffractogram_interactive(plot_data=plot_data, options=options)
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return
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if options['scatter']:
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ax.scatter(x= diffractogram[options['x_vals']], y = diffractogram[options['y_vals']])
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# Make adjustments to parameters if reflections data is passed
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if options['reflections']:
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options['format_params']['nrows'] = 2
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#diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, kind='scatter')
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if not 'grid_ratio_height' in options['format_params'].keys():
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options['format_params']['grid_ratio_height'] = [1,10]
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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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options['format_params']['nrows'] = 1
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# Prepare plot, and read and process data
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fig, ax = btp.prepare_plot(options=options)
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if options['reflections']:
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reflection_ax = ax[0]
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ax = ax[1]
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colours = btp.generate_colours(options['palettes'])
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diffractogram = xrd.io.read_data(path=plot_data['path'], kind=plot_data['plot_kind'], options=options)
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if options['line']:
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diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours), zorder=1)
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if options['scatter']:
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ax.scatter(x= diffractogram[options['x_vals']], y = diffractogram[options['y_vals']], c=[(1,1,1,0)], edgecolors=[next(colours)], linewidths=plt.rcParams['lines.markeredgewidth'], zorder=2) #, edgecolors=np.array([next(colours)]))
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fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
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if options['reflections'] and options['reflection_data']:
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plot_reflection_table(plot_data=options['reflection_data'], ax=reflection_ax, options=options)
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return diffractogram, fig, ax
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def plot_diffractogram_interactive(plot_data, options):
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if options['reflections']:
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w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), plot_data=widgets.fixed(plot_data), options=widgets.fixed(options),
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scatter=widgets.ToggleButton(value=False),
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line=widgets.ToggleButton(value=True),
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reflections=widgets.ToggleButton(value=True))
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else:
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w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), plot_data=widgets.fixed(plot_data), options=widgets.fixed(options),
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scatter=widgets.ToggleButton(value=False),
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line=widgets.ToggleButton(value=True))
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display(w)
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def plot_reflection_table(plot_data, ax=None, options={}):
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''' Plots a reflection table from output generated by VESTA.
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Required contents of plot_data:
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path (str): relative path to reflection table file'''
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required_options = ['reflections_colour', 'min_alpha', 'format_params', 'rc_params']
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default_options = {
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'reflections_colour': [0,0,0],
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'min_alpha': 0,
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'format_params': {},
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'rc_params': {}
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}
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if 'colour' in plot_data.keys():
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options['reflections_colour'] = plot_data['colour']
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if 'min_alpha' in plot_data.keys():
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options['min_alpha'] = plot_data['min_alpha']
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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if not ax:
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_, ax = btp.prepare_plot(options)
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reflection_table = load_reflection_table(plot_data['path'])
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reflections, intensities = reflection_table['2th'], reflection_table['I']
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for ref, intensity in zip(reflections, intensities):
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rel_intensity = (intensity / intensities.max())*(1-options['min_alpha']) + options['min_alpha']
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ax.axvline(x=ref, c=options['reflections_colour'], alpha=rel_intensity)
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ax.tick_params(which='both', bottom=False, labelbottom=False, right=False, labelright=False, left=False, labelleft=False, top=False, labeltop=False)
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if options['xlim']:
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ax.set_xlim(options['xlim'])
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def load_reflection_table(path):
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# VESTA outputs the file with a header that has a space between the parameter and units - so there is some extra code to rectify the issue
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# that ensues from this formatting
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reflections = pd.read_csv(path, delim_whitespace=True)
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# Remove the extra column that appears from the headers issue
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reflections.drop(reflections.columns[-1], axis=1, inplace=True)
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with open(path, 'r') as f:
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line = f.readline()
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headers = line.split()
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# Delete the fourth element which is '(Å)'
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del headers[4]
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# Change name of column to avoid using greek letters
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headers[7] = '2th'
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# Set the new modified headers as the headers of
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reflections.columns = headers
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return reflections
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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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