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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@ -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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@ -272,257 +306,6 @@ 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
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required_options = [
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'columns',
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'xticks', 'yticks',
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'units',
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'show_major_ticks', 'show_minor_ticks', 'show_tick_labels',
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'xlim', 'ylim',
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'hide_x_axis', 'hide_y_axis',
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'positions',
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'xlabel', 'ylabel',
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'sizes',
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'title'
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]
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# Define the default options
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default_options = {
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'columns': 1,
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'xticks': [10, 5], 'yticks': [10000, 5000],
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'units': {'2th': '$^o$', 'I': 'arb. u.'},
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'show_major_ticks': [True, False, True, False], 'show_minor_ticks': [True, False, True, False], 'show_tick_labels': [True, False, False, False],
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'xlim': None,'ylim': None,
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'hide_x_axis': False, 'hide_y_axis': False,
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'positions': {'xaxis': 'bottom', 'yaxis': 'left'},
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'xlabel': None, 'ylabel': None,
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'sizes': None,
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'title': None
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}
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options = update_options(options, required_options, default_options)
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##################################################################
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########################## DEFINE SIZES ##########################
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##################################################################
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# Define the required sizes
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required_sizes = [
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'labels',
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'legend',
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'title',
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'line', 'axes',
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'tick_labels',
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'major_ticks', 'minor_ticks']
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# Define default sizes
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default_sizes = {
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'labels': 30*options['columns'],
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'legend': 30*options['columns'],
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'title': 30*options['columns'],
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'line': 3*options['columns'],
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'axes': 3*options['columns'],
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'tick_labels': 30*options['columns'],
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'major_ticks': 20*options['columns'],
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'minor_ticks': 10*options['columns']
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}
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# Initialise dictionary if it doesn't exist
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if not options['sizes']:
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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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##################################################################
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########################## AXIS LABELS ###########################
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##################################################################
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if not options['xlabel']:
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options['xlabel'] = prettify_labels(options['x_vals']) + ' [{}]'.format(options['units'][options['x_vals']])
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else:
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options['xlabel'] = options['xlabel'] + ' [{}]'.format(options['units'][options['x_vals']])
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if not options['ylabel']:
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options['ylabel'] = prettify_labels(options['y_vals']) + ' [{}]'.format(options['units'][options['y_vals']])
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else:
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options['ylabel'] = options['ylabel'] + ' [{}]'.format(options['units'][options['y_vals']])
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ax.set_xlabel(options['xlabel'], size=options['sizes']['labels'])
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ax.set_ylabel(options['ylabel'], size=options['sizes']['labels'])
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##################################################################
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###################### TICK MARKS & LABELS #######################
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##################################################################
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ax.tick_params(
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direction='in',
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which='major',
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bottom=options['show_major_ticks'][0], labelbottom=options['show_tick_labels'][0],
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left=options['show_major_ticks'][1], labelleft=options['show_tick_labels'][1],
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top=options['show_major_ticks'][2], labeltop=options['show_tick_labels'][2],
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right=options['show_major_ticks'][3], labelright=options['show_tick_labels'][3],
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length=options['sizes']['major_ticks'],
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width=options['sizes']['axes'])
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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'])
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if options['positions']['yaxis'] == 'right':
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ax.yaxis.set_label_position("right")
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ax.yaxis.tick_right()
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if options['hide_x_axis']:
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ax.axes.xaxis.set_visible(False)
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if options['hide_y_axis']:
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ax.axes.yaxis.set_visible(False)
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# Otherwise apply user input
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if options['xticks']:
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major_xtick = options['xticks'][0]
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minor_xtick = options['xticks'][1]
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if options['yticks']:
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major_ytick = options['yticks'][0]
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minor_ytick = options['yticks'][1]
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# Apply values
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ax.xaxis.set_major_locator(MultipleLocator(major_xtick))
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ax.xaxis.set_minor_locator(MultipleLocator(minor_xtick))
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ax.yaxis.set_major_locator(MultipleLocator(major_ytick))
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ax.yaxis.set_minor_locator(MultipleLocator(minor_ytick))
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# SET FONTSIZE OF TICK LABELS
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plt.xticks(fontsize=options['sizes']['tick_labels'])
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plt.yticks(fontsize=options['sizes']['tick_labels'])
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##################################################################
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########################## AXES LIMITS ###########################
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##################################################################
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if options['xlim']:
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plt.xlim(options['xlim'])
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if options['ylim']:
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plt.ylim(options['ylim'])
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##################################################################
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############################# TITLE ##############################
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##################################################################
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if options['title']:
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ax.set_title(options['title'], size=options['sizes']['title'])
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##################################################################
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############################# LEGEND #############################
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##################################################################
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if ax.get_legend():
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ax.get_legend().remove()
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return fig, ax
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||||
def prettify_labels(label):
|
||||
|
||||
|
|
@ -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