Plot multiple simulated diffractograms
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rasmusvt
parent
545c8212c5
commit
1126809c5a
1 changed files with 78 additions and 51 deletions
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@ -27,14 +27,16 @@ def plot_diffractogram(plot_data, options={}):
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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_plot': False,
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'reflections_indices': False,
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'reflections_data': None, # Should be passed as a dictionary on the form {path: rel_path, reflection_indices: number of indices, plot: boolean, colour: [r,g,b], min_alpha: 0-1]
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'xlim': None, 'ylim': None,
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'line': True, # whether or not to plot diffractogram as a line plot
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'scatter': False, # whether or not to plot individual data points
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'reflections_plot': False, # whether to plot reflections as a plot
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'reflections_indices': False, # whether to plot the reflection indices
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'reflections_data': None, # Should be passed as a list of dictionaries on the form {path: rel_path, reflection_indices: number of indices, 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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'interactive_session_active': False,
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'rc_params': {},
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'format_params': {},
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}
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@ -44,27 +46,20 @@ def plot_diffractogram(plot_data, options={}):
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if options['interactive']:
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options['interactive'] = False
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options['interactive_session_active'] = True
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plot_diffractogram_interactive(plot_data=plot_data, options=options)
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return
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if options['reflections_plot'] or options['reflections_indices']:
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if options['reflections_plot'] and options['reflections_indices']:
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options['format_params']['nrows'] = 3
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options['format_params']['grid_ratio_height'] = [2,1,10]
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elif options['reflections_plot']:
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options['format_params']['nrows'] = 2
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options['format_params']['grid_ratio_height'] = [1,10]
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elif options['reflections_indices']:
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options['format_params']['nrows'] = 2
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options['format_params']['grid_ratio_height'] = [2,10]
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else:
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options['format_params']['nrows'] = 1
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if options['reflections_data']:
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if not isinstance(options['reflections_data'], list):
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options['reflections_data'] = [options['reflections_data']]
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# Determine number of subplots and height ratios between them
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if len(options['reflections_data']) >= 1:
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options = determine_grid_layout(options=options)
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print(options['format_params']['nrows'])
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# Prepare plot, and read and process data
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@ -74,19 +69,17 @@ def plot_diffractogram(plot_data, options={}):
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# Assign the correct axes
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if options['reflections_plot'] or options['reflections_indices']:
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if options['reflections_plot'] and options['reflections_indices']:
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if options['reflections_indices']:
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indices_ax = ax[0]
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reflection_ax = ax[1]
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ax = ax[2]
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elif options['reflections_plot']:
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reflection_ax = ax[0]
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ax = ax[1]
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elif options['reflections_indices']:
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indices_ax = ax[0]
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ax = ax[1]
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if options['reflections_plot']:
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ref_axes = [axx for axx in ax[range(1,len(options['reflections_data'])+1)]]
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else:
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ref_axes = [axx for axx in ax[range(0,len(options['reflections_data']))]]
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ax = ax[-1]
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colours = btp.generate_colours(options['palettes'])
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@ -98,23 +91,50 @@ def plot_diffractogram(plot_data, options={}):
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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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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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if not options['xlim']:
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options['xlim'] = [diffractogram[options['x_vals']].min(), diffractogram[options['x_vals']].max()]
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fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
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# Make the reflection plots
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if options['reflections_plot'] and options['reflections_data']:
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options['xlim'] = ax.get_xlim()
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plot_reflection_table(plot_data=options['reflections_data'], ax=reflection_ax, options=options)
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for reference, axis in zip(options['reflections_data'], ref_axes):
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plot_reflection_table(plot_data=reference, ax=axis, options=options)
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# Print the reflection indices
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if options['reflections_indices'] and options['reflections_data']:
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options['xlim'] = ax.get_xlim()
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plot_reflection_indices(plot_data=options['reflections_data'], ax=indices_ax, options=options)
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for reference in options['reflections_data']:
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plot_reflection_indices(plot_data=reference, ax=indices_ax, options=options)
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return diffractogram, fig, ax
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def determine_grid_layout(options):
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nrows = 1 if not options['reflections_indices'] else 2
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if options['reflections_plot']:
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for reference in options['reflections_data']:
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nrows += 1
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options['format_params']['nrows'] = nrows
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options['format_params']['grid_ratio_height'] = [1 for i in range(nrows-1)]+[10]
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return options
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def plot_diffractogram_interactive(plot_data, options):
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if options['reflections_data']:
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@ -132,31 +152,38 @@ def plot_diffractogram_interactive(plot_data, options):
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display(w)
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def plot_reflection_indices(plot_data, ax, options={}):
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required_options = ['reflection_indices']
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def plot_reflection_indices(plot_data, ax, options={}):
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''' Print reflection indices 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 = ['reflection_indices', 'text_colour', 'hide_indices']
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default_options = {
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'reflection_indices': 3
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'reflection_indices': 3, # Number of reflection indices to plot, from highest intensity and working its way down
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'text_colour': 'black',
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'hide_indices': False
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}
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plot_data = update_options(options=plot_data, required_options=required_options, default_options=default_options)
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if not plot_data['hide_indices']:
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reflection_table = xrd.io.load_reflection_table(plot_data['path'])
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if plot_data['reflection_indices'] > 0:
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reflection_indices = reflection_table.nlargest(options['reflection_indices'], 'I')
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reflection_table = xrd.io.load_reflection_table(plot_data['path'])
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if plot_data['reflection_indices'] > 0:
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reflection_indices = reflection_table.nlargest(options['reflection_indices'], 'I')
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for i in range(plot_data['reflection_indices']):
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ax.text(s=f'({reflection_indices["h"].iloc[i]} {reflection_indices["k"].iloc[i]} {reflection_indices["l"].iloc[i]})', x=reflection_indices['2th'].iloc[i], y=0, fontsize=2.5, rotation=90, va='bottom', ha='center', c=plot_data['text_colour'])
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for i in range(plot_data['reflection_indices']):
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ax.text(s=f'({reflection_indices["h"].iloc[i]} {reflection_indices["k"].iloc[i]} {reflection_indices["l"].iloc[i]})', x=reflection_indices['2th'].iloc[i], y=0, fontsize=5, rotation=90, va='bottom', ha='center')
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if options['xlim']:
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ax.set_xlim(options['xlim'])
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ax.axis('off')
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if options['xlim']:
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ax.set_xlim(options['xlim'])
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ax.axis('off')
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return
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@ -212,7 +239,7 @@ def plot_reflection_table(plot_data, ax=None, options={}):
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ax.vlines(x=reflections, ymin=-1, ymax=1, colors=colours)
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ax.vlines(x=reflections, ymin=-1, ymax=1, colors=colours, lw=0.5)
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ax.set_ylim([-0.5,0.5])
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