diff --git a/nafuma/xrd/plot.py b/nafuma/xrd/plot.py index 8f6d07c..6a11fd4 100644 --- a/nafuma/xrd/plot.py +++ b/nafuma/xrd/plot.py @@ -441,7 +441,8 @@ def generate_heatmap(data, options={}): xticks[xval] = xticks_xval - options['x_tick_locators'] = None + # FIXME COMMENTED OUT THIS LINE TO FIX SOMETHING - NOT SURE WHAT UNINTENDED CONSEQUENCES THAT MAY HAVE.... + #options['x_tick_locators'] = None heatmap = heatmap.reset_index().pivot_table(index='scan', columns='2th', values='I') @@ -826,7 +827,8 @@ def plot_reflection_table(data, reflections_params, ax=None, options={}): 'wavelength': 1.54059, # CuKalpha, [Å] 'format_params': {}, 'rc_params': {}, - 'label': None + 'label': None, + 'heatmap': False } @@ -975,6 +977,16 @@ def plot_refinement(data, options={}): 'r_wp': True, 'r_exp': False, 'wp': False, + 'wavelength': None, + 'xlabel': '2$\\theta$', 'xunit': '$^{\circ}$', + 'ylabel': 'Intensity', 'yunit': 'arb. u.', + 'text': [], + 'text_pos': [0.7, 0.9], + 'text_pos_increments': [0, -0.1], + 'reflections_plot': False, # whether to plot reflections as a plot + 'reflections_indices': False, # whether to plot the reflection indices + '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] + } options = aux.update_options(options=options, default_options=default_options, required_options=required_options) @@ -1008,31 +1020,89 @@ def plot_refinement(data, options={}): for attr in results.keys(): results[attr].append(result[attr].iloc[options['index']]) - fig, ax = plt.subplots(figsize=(20,10)) + # CREATE AND ASSIGN AXES - df.plot(x='2th', y='Yobs', kind='scatter', ax=ax, c='black', marker='$\u25EF$') + # Makes a list out of reflections_data if it only passed as a dict, as it will be looped through later + if options['reflections_data']: + if not isinstance(options['reflections_data'], list): + options['reflections_data'] = [options['reflections_data']] + + + # Determine the grid layout based on how many sets of reflections data has been passed + if options['reflections_data'] and len(options['reflections_data']) >= 1: + options = determine_grid_layout(options=options) + + # Create the Figure and Axes objects + fig, ax = btp.prepare_plot(options=options) + + # Assign the correct axes to the indicies, reflections and figure itself + if options['reflections_plot'] or options['reflections_indices']: + + if options['reflections_indices']: + indices_ax = ax[0] + + if options['reflections_plot']: + ref_axes = [axx for axx in ax[range(1,len(options['reflections_data'])+1)]] + + else: + ref_axes = [axx for axx in ax[range(0,len(options['reflections_data']))]] + + ax = ax[-1] + + df.plot.scatter(x='2th', y='Yobs', ax=ax, c='black', marker='$\u25EF$', s=plt.rcParams['lines.markersize']*10) df.plot(x='2th', y='Ycalc', ax=ax, c='red') df.plot(x='2th', y='diff', ax=ax) - if options['r_wp']: - ax.text(x=0.7*df['2th'].max(), y=0.7*df['Yobs'].max(), s='R$_{wp}$ = '+f'{r_wp}', fontsize=20) - - if options['r_exp']: - ax.text(x=0.70*df['2th'].max(), y=0.60*df['Yobs'].max(), s='R$_{exp}$ = '+f'{r_exp}', fontsize=20) + + if options['sample']: + options['text'].append([options['sample'], [options['text_pos'][0]*df['2th'].max(), options['text_pos'][1]*df['Yobs'].max()]]) + options['text_pos'][0] += options['text_pos_increments'][0] + options['text_pos'][1] += options['text_pos_increments'][1] + + if options['wavelength']: + options['text'].append([f'$\lambda$ = {options["wavelength"]} Å', [options['text_pos'][0]*df['2th'].max(), options['text_pos'][1]*df['Yobs'].max()]]) + options['text_pos'][0] += options['text_pos_increments'][0] + options['text_pos'][1] += options['text_pos_increments'][1] + if options['wp']: for i, (result, label) in enumerate(zip(data['results'], options['labels'])): - 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) + 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()]]) + + + #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) + options['text_pos'][0] += options['text_pos_increments'][0] + options['text_pos'][1] += options['text_pos_increments'][1] - if options['title']: - ax.set_title(options['title'], size=30) + if options['r_wp']: + 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()]]) + options['text_pos'][0] += options['text_pos_increments'][0] + options['text_pos'][1] += options['text_pos_increments'][1] + #ax.text(x=0.7*df['2th'].max(), y=0.7*df['Yobs'].max(), s='R$_{wp}$ = '+f'{r_wp}') + + if options['r_exp']: + 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()]]) + options['text_pos'][0] += options['text_pos_increments'][0] + options['text_pos'][1] += options['text_pos_increments'][1] + #ax.text(x=0.70*df['2th'].max(), y=0.60*df['Yobs'].max(), s='R$_{exp}$ = '+f'{r_exp}') - if options['xlim']: - ax.set_xlim(options['xlim']) - else: - ax.set_xlim([df['2th'].min(), df['2th'].max()]) - ax.tick_params(which='both', labelleft=False, left=False, labelsize=20, direction='in') - ax.set_ylabel('Intensity [arb. u.]', size=20) - ax.set_xlabel('2$\\theta$ [$^{\circ}$]', size=20) \ No newline at end of file + if 'xlim' not in options.keys() or options['xlim'] == None: + options['xlim'] = [df['2th'].min(), df['2th'].max()] + + + fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options) + + # PLOT REFLECTION TABLES + if options['reflections_plot'] and options['reflections_data']: + options['xlim'] = ax.get_xlim() + options['to_wavelength'] = options['wavelength'] # By default, the wavelength of the first diffractogram will be used for these. + + # Plot each reflection table in the relevant axis + for reflections_params, axis in zip(options['reflections_data'], ref_axes): + plot_reflection_table(data=data, reflections_params=reflections_params, ax=axis, options=options) + + + +