Add reflection table and interactive mode to xrd

beamtime/plotting.py

@@ -25,7 +25,9 @@ def prepare_plot(options={}):
     rc_params = options['rc_params']
     format_params = options['format_params']
     
-    required_format_params = ['single_column_width', 'double_column_width', 'column_type', 'width_ratio', 'aspect_ratio', 'compress_width', 'compress_height', 'upscaling_factor', 'dpi']
+    required_format_params = ['single_column_width', 'double_column_width', 'column_type', 'width_ratio', 'aspect_ratio', 
+    'width', 'height', 'compress_width', 'compress_height', 'upscaling_factor', 'dpi',
+    'nrows', 'ncols', 'grid_ratio_height', 'grid_ratio_width']
 
     default_format_params = {
     'single_column_width': 8.3,
@@ -33,10 +35,16 @@ def prepare_plot(options={}):
     'column_type': 'single',
     'width_ratio': '1:1',
     'aspect_ratio': '1:1',
+    'width': None,
+    'height': None,
     'compress_width': 1,
     'compress_height': 1,
     'upscaling_factor': 1.0,
     'dpi': 600,
+    'nrows': 1,
+    'ncols': 1,
+    'grid_ratio_height': None,
+    'grid_ratio_width': None
     }
     
     format_params = aux.update_options(format_params, required_format_params, default_format_params)
@@ -48,13 +56,72 @@ def prepare_plot(options={}):
     # Update run commands if any is passed (will pass an empty dictionary if not passed)
     update_rc_params(rc_params)
     
-    width = determine_width(format_params=format_params)
+    if not format_params['width']:
-    height = determine_height(format_params=format_params, width=width)
+        width = determine_width(format_params=format_params)
+    
+    if not format_params['height']:
+        height = determine_height(format_params=format_params, width=width)
+
     width, height = scale_figure(format_params=format_params, width=width, height=height)
     
-    fig, ax = plt.subplots(figsize=(width, height), dpi=format_params['dpi'])
+    if format_params['nrows'] == 1 and format_params['ncols'] == 1:
+        fig, ax = plt.subplots(figsize=(width, height), dpi=format_params['dpi'])
         
-    return fig, ax
+        return fig, ax
+
+    else:
+        if not format_params['grid_ratio_height']:
+            format_params['grid_ratio_height'] = [1 for i in range(format_params['nrows'])]
+
+        if not format_params['grid_ratio_width']:
+            format_params['grid-ratio_width'] = [1 for i in range(format_params['ncols'])]
+
+        fig, axes = plt.subplots(nrows=format_params['nrows'], ncols=format_params['ncols'], figsize=(width,height), 
+        gridspec_kw={'height_ratios': format_params['grid_ratio_height'], 'width_ratios': format_params['grid_ratio_width']}, 
+        facecolor='w', dpi=format_params['dpi'])
+
+        return fig, axes
+
+def prepare_plots(options={}):
+
+    rc_params = options['rc_params']
+    format_params = options['format_params']
+    
+    required_options = ['single_column_width', 'double_column_width', 'column_type', 'width_ratio', 'aspect_ratio', 'compress_width', 'compress_height', 'upscaling_factor', 'dpi']
+
+    default_options = {
+    'single_column_width': 8.3,
+    'double_column_width': 17.1,
+    'column_type': 'single',
+    'width_ratio': '1:1',
+    'aspect_ratio': '1:1',
+    'compress_width': 1,
+    'compress_height': 1,
+    'upscaling_factor': 1.0,
+    'dpi': 600, 
+    }
+    
+    format_params = aux.update_options(format_params, required_options, default_options)
+
+
+    # Reset run commands
+    plt.rcdefaults()
+    
+    # Update run commands if any is passed (will pass an empty dictionary if not passed)
+    update_rc_params(rc_params)
+    
+    width = determine_width(format_params)
+    height = determine_height(format_params, width)
+    width, height = scale_figure(options=format_params, width=width, height=height)
+
+
+    if options['plot_kind'] == 'relative':
+        fig, axes = plt.subplots(nrows=1, ncols=options['number_of_frames'], figsize=(width,height), facecolor='w', dpi=format_params['dpi'])
+
+    elif options['plot_kind'] == 'absolute':
+        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'])
+    
+    return fig, axes
 
 
 def adjust_plot(fig, ax, options):

beamtime/xrd/io.py

@@ -87,7 +87,7 @@ def integrate_1d(calibrant, bins, path=None, image=None, options=None):
     res = ai.integrate1d(image, bins, unit=options['unit'], filename=filename)
 
     if options['return']:
-        return open_1d_data(filename)
+        return read_diffractogram(filename)
     
 
 
@@ -222,7 +222,7 @@ def read_brml(path, options=None):
     return diffractogram
     
 
-def read_diffractogram(path, options=None):
+def read_diffractogram(path):
 
     
 
@@ -248,7 +248,7 @@ def read_diffractogram(path, options=None):
 def read_data(path, kind, options=None):
 
     if kind == 'beamline':
-        diffractogram = read_diffractogram(path, options=options)
+        diffractogram = read_diffractogram(path)
 
     elif kind == 'recx':
         diffractogram = read_brml(path, options=options)

beamtime/xrd/plot.py

@@ -5,8 +5,9 @@ import pandas as pd
 import numpy as np
 import math
 
-import beamtime.xrd as xrd
+import ipywidgets as widgets
 
+import beamtime.xrd as xrd
 import beamtime.auxillary as aux
 import beamtime.plotting as btp
 
@@ -18,42 +19,168 @@ def plot_diffractogram(plot_data, options={}):
     plot_data (dict): Must include path = string to diffractogram data, and plot_kind = (recx, beamline, image)'''
 
     # Update options
-    required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'scatter', 'plot_kind', 'rc_params', 'format_params']
+    required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 
+    'reflections', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params']
 
     default_options = {
         'x_vals': '2th', 
         'y_vals': 'I',
         'ylabel': 'Intensity', 'xlabel': '2theta', 
         'xunit': 'deg', 'yunit': 'a.u.',
+        'line': True,
         'scatter': False,
+        'reflections': False,
+        'reflection_data': None, # Should be passed as a dictionary on the form {path: rel_path, colour: [r,g,b], min_alpha: 0-1]
         'plot_kind': None,
+        'palettes': [('qualitative', 'Dark2_8')],
+        'interactive': False,
         'rc_params': {},
-        'format_params': {}
+        'format_params': {},
         }
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
 
-    # Prepare plot, and read and process data
+    if options['interactive']:
-    fig, ax = btp.prepare_plot(options=options)
+        options['interactive'] = False
-    diffractogram = xrd.io.read_data(path=plot_data['path'], kind=plot_data['plot_kind'], options=options)
+        plot_diffractogram_interactive(plot_data=plot_data, options=options)
+        return
     
-    if options['scatter']:
+    # Make adjustments to parameters if reflections data is passed
-        ax.scatter(x= diffractogram[options['x_vals']], y = diffractogram[options['y_vals']])
+    if options['reflections']:
+        options['format_params']['nrows'] = 2
 
-        #diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, kind='scatter')
+        if not 'grid_ratio_height' in options['format_params'].keys():
+            options['format_params']['grid_ratio_height'] = [1,10]
 
     else:
-        diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax)
+        options['format_params']['nrows'] = 1
 
 
+    # Prepare plot, and read and process data
+
+    fig, ax = btp.prepare_plot(options=options)
+    
+    if options['reflections']:
+        reflection_ax = ax[0]
+        ax = ax[1]
+
+    colours = btp.generate_colours(options['palettes'])
+
+
+    diffractogram = xrd.io.read_data(path=plot_data['path'], kind=plot_data['plot_kind'], options=options)
+
+
+    if options['line']:
+        diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours), zorder=1)
+    
+    if options['scatter']:
+        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)]))
+
 
     fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
 
+    if options['reflections'] and options['reflection_data']:
+        plot_reflection_table(plot_data=options['reflection_data'], ax=reflection_ax, options=options)
+
 
     return diffractogram, fig, ax
 
 
+def plot_diffractogram_interactive(plot_data, options):
+
+    if options['reflections']:
+        w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), plot_data=widgets.fixed(plot_data), options=widgets.fixed(options), 
+        scatter=widgets.ToggleButton(value=False), 
+        line=widgets.ToggleButton(value=True), 
+        reflections=widgets.ToggleButton(value=True))
+    
+    else:
+        w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), plot_data=widgets.fixed(plot_data), options=widgets.fixed(options), 
+        scatter=widgets.ToggleButton(value=False), 
+        line=widgets.ToggleButton(value=True))
+    
+    
+    display(w)
+
+
+    
+def plot_reflection_table(plot_data, ax=None, options={}):
+    ''' Plots a reflection table from output generated by VESTA.
+    
+    Required contents of plot_data:
+    path (str): relative path to reflection table file'''
+
+    required_options = ['reflections_colour', 'min_alpha', 'format_params', 'rc_params']
+
+    default_options = {
+        'reflections_colour': [0,0,0],
+        'min_alpha': 0,
+        'format_params': {},
+        'rc_params': {}
+    }
+
+    if 'colour' in plot_data.keys():
+        options['reflections_colour'] = plot_data['colour']
+    if 'min_alpha' in plot_data.keys():
+        options['min_alpha'] = plot_data['min_alpha']
+
+
+    options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+
+    
+    
+    if not ax:
+        _, ax = btp.prepare_plot(options)
+
+    reflection_table = load_reflection_table(plot_data['path'])
+
+    reflections, intensities  = reflection_table['2th'], reflection_table['I']
+
+    for ref, intensity in zip(reflections, intensities):
+
+        rel_intensity = (intensity / intensities.max())*(1-options['min_alpha']) + options['min_alpha']
+
+
+        ax.axvline(x=ref, c=options['reflections_colour'], alpha=rel_intensity)
+        
+
+
+    ax.tick_params(which='both', bottom=False, labelbottom=False, right=False, labelright=False, left=False, labelleft=False, top=False, labeltop=False)
+    
+    if options['xlim']:
+        ax.set_xlim(options['xlim'])
+
+
+
+
+def load_reflection_table(path):
+
+    # 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
+    # that ensues from this formatting
+    reflections = pd.read_csv(path, delim_whitespace=True)
+
+    # Remove the extra column that appears from the headers issue
+    reflections.drop(reflections.columns[-1], axis=1, inplace=True)
+
+    with open(path, 'r') as f:
+        line = f.readline()
+
+        headers = line.split()
+
+        # Delete the fourth element which is '(Å)'
+        del headers[4]
+
+        # Change name of column to avoid using greek letters
+        headers[7] = '2th'
+
+    # Set the new modified headers as the headers of 
+    reflections.columns = headers
+
+    return reflections
+
+    
+
 
 def prepare_diffractogram_plot(options=None):
     # First take care of the options for plotting - set any values not specified to the default values