Improve refinement plotting function
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rasmusthog
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36c6482928
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4cc6f4557f
1 changed files with 89 additions and 19 deletions
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@ -441,7 +441,8 @@ def generate_heatmap(data, options={}):
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xticks[xval] = xticks_xval
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options['x_tick_locators'] = None
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# FIXME COMMENTED OUT THIS LINE TO FIX SOMETHING - NOT SURE WHAT UNINTENDED CONSEQUENCES THAT MAY HAVE....
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#options['x_tick_locators'] = None
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heatmap = heatmap.reset_index().pivot_table(index='scan', columns='2th', values='I')
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@ -826,7 +827,8 @@ def plot_reflection_table(data, reflections_params, ax=None, options={}):
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'wavelength': 1.54059, # CuKalpha, [Å]
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'format_params': {},
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'rc_params': {},
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'label': None
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'label': None,
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'heatmap': False
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}
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@ -975,6 +977,16 @@ def plot_refinement(data, options={}):
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'r_wp': True,
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'r_exp': False,
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'wp': False,
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'wavelength': None,
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'xlabel': '2$\\theta$', 'xunit': '$^{\circ}$',
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'ylabel': 'Intensity', 'yunit': 'arb. u.',
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'text': [],
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'text_pos': [0.7, 0.9],
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'text_pos_increments': [0, -0.1],
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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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}
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options = aux.update_options(options=options, default_options=default_options, required_options=required_options)
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@ -1008,31 +1020,89 @@ def plot_refinement(data, options={}):
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for attr in results.keys():
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results[attr].append(result[attr].iloc[options['index']])
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fig, ax = plt.subplots(figsize=(20,10))
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# CREATE AND ASSIGN AXES
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df.plot(x='2th', y='Yobs', kind='scatter', ax=ax, c='black', marker='$\u25EF$')
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# Makes a list out of reflections_data if it only passed as a dict, as it will be looped through later
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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 the grid layout based on how many sets of reflections data has been passed
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if options['reflections_data'] and len(options['reflections_data']) >= 1:
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options = determine_grid_layout(options=options)
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# Create the Figure and Axes objects
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fig, ax = btp.prepare_plot(options=options)
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# Assign the correct axes to the indicies, reflections and figure itself
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if options['reflections_plot'] or options['reflections_indices']:
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if options['reflections_indices']:
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indices_ax = ax[0]
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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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df.plot.scatter(x='2th', y='Yobs', ax=ax, c='black', marker='$\u25EF$', s=plt.rcParams['lines.markersize']*10)
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df.plot(x='2th', y='Ycalc', ax=ax, c='red')
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df.plot(x='2th', y='diff', ax=ax)
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if options['r_wp']:
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ax.text(x=0.7*df['2th'].max(), y=0.7*df['Yobs'].max(), s='R$_{wp}$ = '+f'{r_wp}', fontsize=20)
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if options['r_exp']:
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ax.text(x=0.70*df['2th'].max(), y=0.60*df['Yobs'].max(), s='R$_{exp}$ = '+f'{r_exp}', fontsize=20)
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if options['sample']:
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options['text'].append([options['sample'], [options['text_pos'][0]*df['2th'].max(), options['text_pos'][1]*df['Yobs'].max()]])
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options['text_pos'][0] += options['text_pos_increments'][0]
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options['text_pos'][1] += options['text_pos_increments'][1]
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if options['wavelength']:
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options['text'].append([f'$\lambda$ = {options["wavelength"]} Å', [options['text_pos'][0]*df['2th'].max(), options['text_pos'][1]*df['Yobs'].max()]])
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options['text_pos'][0] += options['text_pos_increments'][0]
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options['text_pos'][1] += options['text_pos_increments'][1]
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if options['wp']:
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for i, (result, label) in enumerate(zip(data['results'], options['labels'])):
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ax.text(x=0.7*df['2th'].max(), y=(0.9-0.1*i)*df['Yobs'].max(), s=f'{label}: {np.round(float(results["wp"][i]), 2)}%', fontsize=20)
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options['text'].append([f'{label}: {np.round(float(results["wp"][i]), 1)}%', [options['text_pos'][0]*df['2th'].max(), options['text_pos'][1]*df['Yobs'].max()]])
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#ax.text(x=0.7*df['2th'].max(), y=ypos*df['Yobs'].max(), s=f'{label}: {np.round(float(results["wp"][i]), 2)}%', fontsize=20)
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options['text_pos'][0] += options['text_pos_increments'][0]
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options['text_pos'][1] += options['text_pos_increments'][1]
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if options['r_wp']:
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options['text'].append(['R$_{wp}$ = '+f'{np.round(r_wp, 2)}', [options['text_pos'][0]*df['2th'].max(), options['text_pos'][1]*df['Yobs'].max()]])
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options['text_pos'][0] += options['text_pos_increments'][0]
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options['text_pos'][1] += options['text_pos_increments'][1]
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#ax.text(x=0.7*df['2th'].max(), y=0.7*df['Yobs'].max(), s='R$_{wp}$ = '+f'{r_wp}')
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if options['r_exp']:
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options['text'].append(['R$_{exp}$ = '+f'{np.round(r_exp, 2)}', [options['text_pos'][0]*df['2th'].max(), options['text_pos'][1]*df['Yobs'].max()]])
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options['text_pos'][0] += options['text_pos_increments'][0]
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options['text_pos'][1] += options['text_pos_increments'][1]
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#ax.text(x=0.70*df['2th'].max(), y=0.60*df['Yobs'].max(), s='R$_{exp}$ = '+f'{r_exp}')
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if 'xlim' not in options.keys() or options['xlim'] == None:
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options['xlim'] = [df['2th'].min(), df['2th'].max()]
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fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
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# PLOT REFLECTION TABLES
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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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options['to_wavelength'] = options['wavelength'] # By default, the wavelength of the first diffractogram will be used for these.
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# Plot each reflection table in the relevant axis
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for reflections_params, axis in zip(options['reflections_data'], ref_axes):
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plot_reflection_table(data=data, reflections_params=reflections_params, ax=axis, options=options)
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if options['title']:
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ax.set_title(options['title'], size=30)
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if options['xlim']:
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ax.set_xlim(options['xlim'])
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else:
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ax.set_xlim([df['2th'].min(), df['2th'].max()])
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ax.tick_params(which='both', labelleft=False, left=False, labelsize=20, direction='in')
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ax.set_ylabel('Intensity [arb. u.]', size=20)
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ax.set_xlabel('2$\\theta$ [$^{\circ}$]', size=20)
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