Add translation of wavelengths and xlim updates
This commit is contained in:
rasmusvt
parent
a96210cf07
commit
9bb52fe819
3 changed files with 107 additions and 300 deletions
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@ -298,6 +298,7 @@ def ipywidgets_update(func, data, options={}, **kwargs):
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where key1, key2, key3 etc. are the values in the options-dictionary you want widget control of, and widget1, widget2, widget3 etc. are widgets to control these values, e.g. widgets.IntSlider(value=1, min=0, max=10)
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'''
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# Update the options-dictionary with the values from the widgets
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for key in kwargs:
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options[key] = kwargs[key]
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@ -306,6 +307,16 @@ def ipywidgets_update(func, data, options={}, **kwargs):
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func(data=data, options=options)
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def update_widgets(options):
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for widget in options['widgets'].values():
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if widget['state'] != options['x_vals']:
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for arg in widget[f'{options["x_vals"]}_default']:
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setattr(widget['w'], arg, widget[f'{options["x_vals"]}_default'][arg])
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widget['state'] = options['x_vals']
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def determine_width(format_params):
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@ -1,3 +1,4 @@
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from sympy import re
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import fabio, pyFAI
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import pandas as pd
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import numpy as np
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@ -293,23 +294,32 @@ def read_data(data, options={}):
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diffractogram = read_xy(data=data, options=options)
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diffractogram = translate_wavelengths(diffractogram=diffractogram, wavelength=data['wavelength'])
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diffractogram = translate_wavelengths(data=diffractogram, wavelength=data['wavelength'])
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return diffractogram
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def load_reflection_table(path):
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def load_reflection_table(data, options={}):
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required_options = ['wavelength', 'to_wavelength']
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default_options = {
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'wavelength': 1.54059,
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'to_wavelength': None
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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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# 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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reflections = pd.read_csv(data['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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with open(data['path'], 'r') as f:
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line = f.readline()
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headers = line.split()
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@ -323,11 +333,16 @@ def load_reflection_table(path):
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# Set the new modified headers as the headers of
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reflections.columns = headers
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reflections = translate_wavelengths(data=reflections, wavelength=options['wavelength'], to_wavelength=options['to_wavelength'])
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#print(reflections)
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return reflections
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def translate_wavelengths(diffractogram, wavelength):
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def translate_wavelengths(data, wavelength, to_wavelength=None):
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pd.options.mode.chained_assignment = None
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# Translate to CuKalpha
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cuka = 1.54059 # Å
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@ -335,11 +350,11 @@ def translate_wavelengths(diffractogram, wavelength):
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if cuka > wavelength:
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max_2th_cuka = 2*np.arcsin(wavelength/cuka) * 180/np.pi
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else:
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max_2th_cuka = diffractogram['2th'].max()
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max_2th_cuka = data['2th'].max()
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diffractogram['2th_cuka'] = np.NAN
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data['2th_cuka'] = np.NAN
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diffractogram['2th_cuka'].loc[diffractogram['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((diffractogram['2th']/2) * np.pi/180)) * 180/np.pi
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data['2th_cuka'].loc[data['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((data['2th']/2) * np.pi/180)) * 180/np.pi
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# Translate to MoKalpha
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moka = 0.71073 # Å
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@ -347,22 +362,36 @@ def translate_wavelengths(diffractogram, wavelength):
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if moka > wavelength:
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max_2th_moka = 2*np.arcsin(wavelength/moka) * 180/np.pi
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else:
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max_2th_moka = diffractogram['2th'].max()
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max_2th_moka = data['2th'].max()
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diffractogram['2th_moka'] = np.NAN
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data['2th_moka'] = np.NAN
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diffractogram['2th_moka'].loc[diffractogram['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((diffractogram['2th']/2) * np.pi/180)) * 180/np.pi
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data['2th_moka'].loc[data['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((data['2th']/2) * np.pi/180)) * 180/np.pi
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# Convert to other parameters
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diffractogram['d'] = wavelength / (2*np.sin(2*diffractogram['2th']) * 180/np.pi)
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diffractogram['1/d'] = 1/diffractogram['d']
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diffractogram['q'] = np.abs((4*np.pi/wavelength)*np.sin(diffractogram['2th']/2 * np.pi/180))
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diffractogram['q2'] = diffractogram['q']**2
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diffractogram['q4'] = diffractogram['q']**4
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data['d'] = wavelength / (2*np.sin((2*data['2th']*np.pi/180)/2))
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data['1/d'] = 1/data['d']
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data['q'] = np.abs((4*np.pi/wavelength)*np.sin(data['2th']/2 * np.pi/180))
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data['q2'] = data['q']**2
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data['q4'] = data['q']**4
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return diffractogram
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if to_wavelength:
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if to_wavelength > cuka:
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max_2th = 2*np.arcsin(cuka/to_wavelength) * 180/np.pi
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else:
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max_2th = data['2th_cuka'].max()
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data['2th'] = np.NAN
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data['2th'].loc[data['2th_cuka'] <= max_2th] = 2*np.arcsin(to_wavelength/cuka * np.sin((data['2th_cuka']/2) * np.pi/180)) * 180/np.pi
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return data
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@ -44,12 +44,13 @@ def plot_diffractogram(data, options={}):
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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if not 'diffractogram' in data.keys():
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diffractogram = xrd.io.read_data(data=data)
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diffractogram = xrd.io.read_data(data=data, options=options)
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data['diffractogram'] = diffractogram
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else:
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diffractogram = data['diffractogram']
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# Sets the xlim if this has not bee specified
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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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@ -62,6 +63,7 @@ def plot_diffractogram(data, options={}):
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return
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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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@ -93,9 +95,6 @@ def plot_diffractogram(data, options={}):
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colours = btp.generate_colours(options['palettes'])
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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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@ -104,8 +103,6 @@ def plot_diffractogram(data, options={}):
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fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
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@ -113,6 +110,7 @@ def plot_diffractogram(data, 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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options['to_wavelength'] = data['wavelength']
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for reference, axis in zip(options['reflections_data'], ref_axes):
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plot_reflection_table(data=reference, ax=axis, options=options)
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@ -120,10 +118,16 @@ def plot_diffractogram(data, 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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options['to_wavelength'] = data['wavelength']
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for reference in options['reflections_data']:
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plot_reflection_indices(data=reference, ax=indices_ax, options=options)
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if options['interactive_session_active']:
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btp.update_widgets(options=options)
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return diffractogram, fig, ax
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@ -145,25 +149,53 @@ def determine_grid_layout(options):
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def plot_diffractogram_interactive(data, options):
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options['widgets'] = {
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'xlim': {
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'w': widgets.FloatRangeSlider(value=[data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], min=data['diffractogram']['2th'].min(), max=data['diffractogram']['2th'].max(), step=0.5, layout=widgets.Layout(width='95%')),
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'2th_default': {'min': data['diffractogram']['2th'].min(), 'max': data['diffractogram']['2th'].max(), 'value': [data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], 'step': 0.5},
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'2th_cuka_default': {'min': data['diffractogram']['2th_cuka'].min(), 'max': data['diffractogram']['2th_cuka'].max(), 'value': [data['diffractogram']['2th_cuka'].min(), data['diffractogram']['2th_cuka'].max()], 'step': 0.5},
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'2th_moka_default': {'min': data['diffractogram']['2th_moka'].min(), 'max': data['diffractogram']['2th_moka'].max(), 'value': [data['diffractogram']['2th_moka'].min(), data['diffractogram']['2th_moka'].max()], 'step': 0.5},
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'd_default': {'min': data['diffractogram']['d'].min(), 'max': data['diffractogram']['d'].max(), 'value': [data['diffractogram']['d'].min(), data['diffractogram']['d'].max()], 'step': 0.5},
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'1/d_default': {'min': data['diffractogram']['1/d'].min(), 'max': data['diffractogram']['1/d'].max(), 'value': [data['diffractogram']['1/d'].min(), data['diffractogram']['1/d'].max()], 'step': 0.5},
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'q_default': {'min': data['diffractogram']['q'].min(), 'max': data['diffractogram']['q'].max(), 'value': [data['diffractogram']['q'].min(), data['diffractogram']['q'].max()], 'step': 0.5},
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'q2_default': {'min': data['diffractogram']['q2'].min(), 'max': data['diffractogram']['q2'].max(), 'value': [data['diffractogram']['q2'].min(), data['diffractogram']['q2'].max()], 'step': 0.5},
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'q4_default': {'min': data['diffractogram']['q4'].min(), 'max': data['diffractogram']['q4'].max(), 'value': [data['diffractogram']['q4'].min(), data['diffractogram']['q4'].max()], 'step': 0.5},
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'state': '2th'
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}
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}
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if options['reflections_data']:
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w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), data=widgets.fixed(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_plot=widgets.ToggleButton(value=True),
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reflections_indices=widgets.ToggleButton(value=False),
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x_vals=widgets.Dropdown(options=['2th', 'd', '1/d', 'q', 'q4', 'q4', '2th_cuka', '2th_moka'], value='2th', description='X-values'),
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xlim=widgets.FloatRangeSlider(value=options['xlim'], min=options['xlim'][0], max=options['xlim'][1], step=1, description='xlim', layout=widgets.Layout(width='1000px')))
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x_vals=widgets.Dropdown(options=['2th', 'd', '1/d', 'q', 'q2', 'q4', '2th_cuka', '2th_moka'], value='2th', description='X-values'),
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xlim=options['widgets']['xlim']['w'])
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else:
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w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), data=widgets.fixed(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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xlim=widgets.IntRangeSlider(value=options['xlim'], min=options['xlim'][0], max=options['xlim'][1], step=1, description='xlim'))
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xlim=options['widgets']['xlim']['w'])
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display(w)
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def update_widgets(options):
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for widget in options['widgets'].values():
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if widget['state'] != options['x_vals']:
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for arg in widget[f'{options["x_vals"]}_default']:
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setattr(widget['w'], arg, widget[f'{options["x_vals"]}_default'][arg])
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widget['state'] = options['x_vals']
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def plot_reflection_indices(data, ax, options={}):
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''' Print reflection indices from output generated by VESTA.
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@ -178,10 +210,10 @@ def plot_reflection_indices(data, ax, options={}):
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'hide_indices': False
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}
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data = update_options(options=data, required_options=required_options, default_options=default_options)
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data = aux.update_options(options=data, required_options=required_options, default_options=default_options)
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if not data['hide_indices']:
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reflection_table = xrd.io.load_reflection_table(data['path'])
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reflection_table = xrd.io.load_reflection_table(data=data, options=options)
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if data['reflection_indices'] > 0:
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@ -208,12 +240,13 @@ def plot_reflection_table(data, ax=None, options={}):
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Required contents of data:
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path (str): relative path to reflection table file'''
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required_options = ['reflection_indices', 'reflections_colour', 'min_alpha', 'format_params', 'rc_params', 'label']
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required_options = ['reflection_indices', 'reflections_colour', 'min_alpha', 'wavelength', 'format_params', 'rc_params', 'label']
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default_options = {
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'reflection_indices': 0, # Number of indices to print
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'reflections_colour': [0,0,0],
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'min_alpha': 0,
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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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@ -227,7 +260,8 @@ def plot_reflection_table(data, ax=None, options={}):
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options['reflection_indices'] = data['reflection_indices']
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if 'label' in data.keys():
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options['label'] = data['label']
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if 'wavelength' in data.keys():
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options['wavelength'] = data['wavelength']
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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@ -235,9 +269,9 @@ def plot_reflection_table(data, ax=None, options={}):
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if not ax:
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_, ax = btp.prepare_plot(options)
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reflection_table = xrd.io.load_reflection_table(data['path'])
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reflection_table = xrd.io.load_reflection_table(data=data, options=options)
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reflections, intensities = reflection_table['2th'], reflection_table['I']
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reflections, intensities = reflection_table[options['x_vals']], reflection_table['I']
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@ -273,257 +307,6 @@ def plot_reflection_table(data, ax=None, options={}):
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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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required_options = ['columns', 'width', 'height', 'format', 'dpi', 'facecolor']
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default_options = {'columns': 1, 'width': 14, 'format': 'golden_ratio', 'dpi': None, 'facecolor': 'w'}
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# Define the required sizes
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required_sizes = ['lines', 'axes']
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# If none are set at all, just pass the default_options
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if not options:
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options = default_options
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options['height'] = options['width'] * (math.sqrt(5) - 1) / 2
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options['figsize'] = (options['width'], options['height'])
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# Define default sizes
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default_sizes = {
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'lines': 3*options['columns'],
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'axes': 3*options['columns']
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}
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# Initialise dictionary if it doesn't exist
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if not 'sizes' in options.keys():
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options['sizes'] = {}
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# Update dictionary with default values where none is supplied
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for size in required_sizes:
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if size not in options['sizes']:
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options['sizes'][size] = default_sizes[size]
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# If options is passed, go through to fill out the rest.
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else:
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# Start by setting the width:
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if 'width' not in options.keys():
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options['width'] = default_options['width']
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# Then set height - check options for format. If not given, set the height to the width scaled by the golden ratio - if the format is square, set the same. This should possibly allow for the tweaking of custom ratios later.
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if 'height' not in options.keys():
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if 'format' not in options.keys():
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options['height'] = options['width'] * (math.sqrt(5) - 1) / 2
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elif options['format'] == 'square':
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options['height'] = options['width']
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options['figsize'] = (options['width'], options['height'])
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# After height and width are set, go through the rest of the options to make sure that all the required options are filled
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for option in required_options:
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if option not in options.keys():
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options[option] = default_options[option]
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fig, ax = plt.subplots(figsize=(options['figsize']), dpi=options['dpi'], facecolor=options['facecolor'])
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plt.rc('lines', linewidth=options['sizes']['lines'])
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plt.rc('axes', linewidth=options['sizes']['axes'])
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return fig, ax
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def prettify_diffractogram_plot(fig, ax, options=None):
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##################################################################
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######################### UPDATE OPTIONS #########################
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##################################################################
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|
||||
# Define the required options
|
||||
required_options = [
|
||||
'columns',
|
||||
'xticks', 'yticks',
|
||||
'units',
|
||||
'show_major_ticks', 'show_minor_ticks', 'show_tick_labels',
|
||||
'xlim', 'ylim',
|
||||
'hide_x_axis', 'hide_y_axis',
|
||||
'positions',
|
||||
'xlabel', 'ylabel',
|
||||
'sizes',
|
||||
'title'
|
||||
]
|
||||
|
||||
|
||||
# Define the default options
|
||||
default_options = {
|
||||
'columns': 1,
|
||||
'xticks': [10, 5], 'yticks': [10000, 5000],
|
||||
'units': {'2th': '$^o$', 'I': 'arb. u.'},
|
||||
'show_major_ticks': [True, False, True, False], 'show_minor_ticks': [True, False, True, False], 'show_tick_labels': [True, False, False, False],
|
||||
'xlim': None,'ylim': None,
|
||||
'hide_x_axis': False, 'hide_y_axis': False,
|
||||
'positions': {'xaxis': 'bottom', 'yaxis': 'left'},
|
||||
'xlabel': None, 'ylabel': None,
|
||||
'sizes': None,
|
||||
'title': None
|
||||
}
|
||||
|
||||
options = update_options(options, required_options, default_options)
|
||||
|
||||
|
||||
|
||||
##################################################################
|
||||
########################## DEFINE SIZES ##########################
|
||||
##################################################################
|
||||
|
||||
# Define the required sizes
|
||||
required_sizes = [
|
||||
'labels',
|
||||
'legend',
|
||||
'title',
|
||||
'line', 'axes',
|
||||
'tick_labels',
|
||||
'major_ticks', 'minor_ticks']
|
||||
|
||||
|
||||
|
||||
# Define default sizes
|
||||
default_sizes = {
|
||||
'labels': 30*options['columns'],
|
||||
'legend': 30*options['columns'],
|
||||
'title': 30*options['columns'],
|
||||
'line': 3*options['columns'],
|
||||
'axes': 3*options['columns'],
|
||||
'tick_labels': 30*options['columns'],
|
||||
'major_ticks': 20*options['columns'],
|
||||
'minor_ticks': 10*options['columns']
|
||||
}
|
||||
|
||||
# Initialise dictionary if it doesn't exist
|
||||
if not options['sizes']:
|
||||
options['sizes'] = {}
|
||||
|
||||
|
||||
# Update dictionary with default values where none is supplied
|
||||
for size in required_sizes:
|
||||
if size not in options['sizes']:
|
||||
options['sizes'][size] = default_sizes[size]
|
||||
|
||||
|
||||
##################################################################
|
||||
########################## AXIS LABELS ###########################
|
||||
##################################################################
|
||||
|
||||
|
||||
if not options['xlabel']:
|
||||
options['xlabel'] = prettify_labels(options['x_vals']) + ' [{}]'.format(options['units'][options['x_vals']])
|
||||
|
||||
else:
|
||||
options['xlabel'] = options['xlabel'] + ' [{}]'.format(options['units'][options['x_vals']])
|
||||
|
||||
|
||||
if not options['ylabel']:
|
||||
options['ylabel'] = prettify_labels(options['y_vals']) + ' [{}]'.format(options['units'][options['y_vals']])
|
||||
|
||||
else:
|
||||
options['ylabel'] = options['ylabel'] + ' [{}]'.format(options['units'][options['y_vals']])
|
||||
|
||||
ax.set_xlabel(options['xlabel'], size=options['sizes']['labels'])
|
||||
ax.set_ylabel(options['ylabel'], size=options['sizes']['labels'])
|
||||
|
||||
##################################################################
|
||||
###################### TICK MARKS & LABELS #######################
|
||||
##################################################################
|
||||
|
||||
ax.tick_params(
|
||||
direction='in',
|
||||
which='major',
|
||||
bottom=options['show_major_ticks'][0], labelbottom=options['show_tick_labels'][0],
|
||||
left=options['show_major_ticks'][1], labelleft=options['show_tick_labels'][1],
|
||||
top=options['show_major_ticks'][2], labeltop=options['show_tick_labels'][2],
|
||||
right=options['show_major_ticks'][3], labelright=options['show_tick_labels'][3],
|
||||
length=options['sizes']['major_ticks'],
|
||||
width=options['sizes']['axes'])
|
||||
|
||||
|
||||
ax.tick_params(direction='in', which='minor', bottom=options['show_minor_ticks'][0], left=options['show_minor_ticks'][1], top=options['show_minor_ticks'][2], right=options['show_minor_ticks'][3], length=options['sizes']['minor_ticks'], width=options['sizes']['axes'])
|
||||
|
||||
|
||||
|
||||
if options['positions']['yaxis'] == 'right':
|
||||
ax.yaxis.set_label_position("right")
|
||||
ax.yaxis.tick_right()
|
||||
|
||||
|
||||
if options['hide_x_axis']:
|
||||
ax.axes.xaxis.set_visible(False)
|
||||
|
||||
if options['hide_y_axis']:
|
||||
ax.axes.yaxis.set_visible(False)
|
||||
|
||||
|
||||
|
||||
# Otherwise apply user input
|
||||
if options['xticks']:
|
||||
major_xtick = options['xticks'][0]
|
||||
minor_xtick = options['xticks'][1]
|
||||
|
||||
|
||||
if options['yticks']:
|
||||
|
||||
major_ytick = options['yticks'][0]
|
||||
minor_ytick = options['yticks'][1]
|
||||
|
||||
|
||||
# Apply values
|
||||
ax.xaxis.set_major_locator(MultipleLocator(major_xtick))
|
||||
ax.xaxis.set_minor_locator(MultipleLocator(minor_xtick))
|
||||
|
||||
ax.yaxis.set_major_locator(MultipleLocator(major_ytick))
|
||||
ax.yaxis.set_minor_locator(MultipleLocator(minor_ytick))
|
||||
|
||||
|
||||
|
||||
|
||||
# SET FONTSIZE OF TICK LABELS
|
||||
|
||||
plt.xticks(fontsize=options['sizes']['tick_labels'])
|
||||
plt.yticks(fontsize=options['sizes']['tick_labels'])
|
||||
|
||||
##################################################################
|
||||
########################## AXES LIMITS ###########################
|
||||
##################################################################
|
||||
|
||||
if options['xlim']:
|
||||
plt.xlim(options['xlim'])
|
||||
|
||||
if options['ylim']:
|
||||
plt.ylim(options['ylim'])
|
||||
|
||||
##################################################################
|
||||
############################# TITLE ##############################
|
||||
##################################################################
|
||||
|
||||
if options['title']:
|
||||
ax.set_title(options['title'], size=options['sizes']['title'])
|
||||
|
||||
##################################################################
|
||||
############################# LEGEND #############################
|
||||
##################################################################
|
||||
|
||||
if ax.get_legend():
|
||||
ax.get_legend().remove()
|
||||
|
||||
return fig, ax
|
||||
|
||||
|
||||
|
||||
def prettify_labels(label):
|
||||
|
||||
labels_dict = {
|
||||
|
|
@ -593,19 +376,3 @@ def reverse_diffractograms(diffractograms):
|
|||
return rev_diffractograms
|
||||
|
||||
#def plot_heatmap():
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
def update_options(options, required_options, default_options):
|
||||
|
||||
if not options:
|
||||
options = default_options
|
||||
|
||||
else:
|
||||
for option in required_options:
|
||||
if option not in options.keys():
|
||||
options[option] = default_options[option]
|
||||
|
||||
return options
|
||||
Loading…
Add table
Add a link
Reference in a new issue