Get HTXRD-plotter to a working state
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rasmusvt
parent
6247ce24bf
commit
83f4f6a155
1 changed files with 51 additions and 17 deletions
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@ -24,7 +24,7 @@ def plot_diffractogram(data, options={}):
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# Update options
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required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise', 'offset', 'offset_x', 'offset_y', 'offset_change',
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'reflections_plot', 'reflections_indices', 'reflections_data', 'heatmap', 'cmap', 'plot_kind', 'palettes', 'highlight', 'highlight_colours', 'interactive', 'rc_params', 'format_params', 'interactive_session_active']
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'reflections_plot', 'reflections_indices', 'reflections_data', 'heatmap', 'cmap', 'plot_kind', 'palettes', 'highlight', 'highlight_colours', 'interactive', 'rc_params', 'format_params', 'interactive_session_active', 'plot_diff']
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default_options = {
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'x_vals': '2th', 'y_vals': 'I',
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@ -51,6 +51,7 @@ def plot_diffractogram(data, options={}):
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'interactive_session_active': False,
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'rc_params': {},
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'format_params': {},
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'plot_diff': False,
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}
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if 'offset_y' not in options.keys():
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@ -86,15 +87,25 @@ def plot_diffractogram(data, options={}):
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if not isinstance(data['wavelength'], list):
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data['wavelength'] = [data['wavelength'] for _ in range(len(data['path']))]
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# LOAD DIFFRACTOGRAMS
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for index in range(len(data['path'])):
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diffractogram, wavelength = xrd.io.read_data(data=data, options=options, index=index)
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data['diffractogram'][index] = diffractogram
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data['wavelength'][index] = wavelength
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if 'htxrd' in data.keys() and data['htxrd']:
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data['diffractogram'], data['wavelength'] = xrd.io.read_htxrd(data=data, options=options, index=0)
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else:
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for index in range(len(data['path'])):
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diffractogram, wavelength = xrd.io.read_data(data=data, options=options, index=index)
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# FIXME This is a quick fix as the image is not reloaded when passing multiple beamline datasets. Should probably be handled in io?
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data['image'] = None
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data['diffractogram'][index] = diffractogram
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data['wavelength'][index] = wavelength
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# FIXME This is a quick fix as the image is not reloaded when passing multiple beamline datasets. Should probably be handled in io?
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data['image'] = None
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# Sets the xlim if this has not been specified
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@ -106,7 +117,12 @@ def plot_diffractogram(data, options={}):
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options['heatmap_loaded'] = True
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if options['heatmap']:
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options['xlim'] = [options['heatmap_xlim'][0], options['heatmap_xlim'][1]]
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xlim_start_frac, xlim_end_frac = options['xlim'][0] / data['diffractogram'][0][options['x_vals']].max(), options['xlim'][1] / data['diffractogram'][0][options['x_vals']].max()
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options['xlim'] = [options['heatmap_xlim'][0]*xlim_start_frac, options['heatmap_xlim'][1]*xlim_end_frac]
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if options['heatmap_reverse']:
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data['heatmap'] = data['heatmap'].iloc[::-1]
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data['heatmap_yticklabels'] = data['heatmap_yticklabels'][::-1]
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# If data was already loaded, only do a check to see if the data is in a list or not, and if not, put it in one. This is because it will be looped over later.
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else:
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@ -177,8 +193,12 @@ def plot_diffractogram(data, options={}):
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# Limit for when it is assumed that each diffractogram should have its own colour - after 8, the default colour palette is used up and starts a new.
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# FIXME Should probably allow for more than 8 if wanted - not a priority now
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if len(data['path']) < 8:
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colours = btp.generate_colours(options['palettes'])
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if len(data['path']) <= 8:
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if 'colours' in options.keys():
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colours = btp.generate_colours(options['colours'], kind='single')
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else:
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colours = btp.generate_colours(options['palettes'])
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# Generates the colours of a list of scans to highlight is passed. options['highlight'] and options['highlight_colour'] must be of equal length. Entries in highlight can either be a list or a single number,
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@ -254,6 +274,8 @@ def plot_diffractogram(data, options={}):
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options['ylabel'] = options['heatmap.ylabel']
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if not options['yunit'] or options['yunit'] == options['diff.yunit']:
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options['yunit'] = options['heatmap.yunit']
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ax.tick_params(axis='x', which='minor', bottom=False, top=False)
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ax.tick_params(axis='y', which='minor', left=False, right=False)
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@ -269,7 +291,7 @@ def plot_diffractogram(data, options={}):
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if options['highlight']:
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for i, highlight in enumerate(options['highlight']):
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if i < len(options['highlight'])-1 or len(options['highlight']) == 1:
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if i < len(options['highlight']) or len(options['highlight']) == 1:
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ax.axhline(y=highlight[1], c=options['highlight_colours'][i], ls='--', lw=0.5)
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@ -296,6 +318,14 @@ def plot_diffractogram(data, options={}):
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options['hide_y_ticklabels'] = True
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options['hide_y_ticks'] = True
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if options['plot_diff'] and len(data['path']) == 2:
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diff = data['diffractogram'][0]
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diff['I'] = diff['I'] - data['diffractogram'][1]['I']
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diff['I'] = diff['I'] - 0.5
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diff.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours))
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# Adjust the plot to make it prettier
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fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
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@ -418,6 +448,7 @@ def generate_heatmap(data, options={}):
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options['heatmap_xlim'] = xlims
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# Get temperatures if HTXRD-scans
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scan_numbers = []
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@ -463,6 +494,8 @@ def generate_heatmap(data, options={}):
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def determine_grid_layout(options):
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#aspect_ratio = int(options['format_params']['aspect_ratio'].split(':')[0]) / int(options['format_params']['aspect_ratio'].split(':')[1])
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nrows = 1 if not options['reflections_indices'] else 2
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if options['reflections_plot']:
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@ -470,7 +503,9 @@ def determine_grid_layout(options):
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nrows += 1
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options['format_params']['nrows'] = nrows
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options['format_params']['grid_ratio_height'] = [1 for i in range(nrows-1)]+[10]
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if not 'grid_ratio_height' in options['format_params'].keys():
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options['format_params']['grid_ratio_height'] = [0.6 for i in range(nrows-1)]+[10]
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return options
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@ -794,7 +829,8 @@ def plot_reflection_table(data, reflections_params, ax=None, options={}):
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'label': None
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}
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if 'colour' in data.keys():
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if 'colour' in reflections_params.keys():
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options['reflections_colour'] = reflections_params['colour']
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if 'min_alpha' in reflections_params.keys():
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options['min_alpha'] = reflections_params['min_alpha']
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@ -806,7 +842,6 @@ def plot_reflection_table(data, reflections_params, ax=None, options={}):
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options['wavelength'] = reflections_params['wavelength']
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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if not ax:
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_, ax = btp.prepare_plot(options)
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@ -826,8 +861,7 @@ def plot_reflection_table(data, reflections_params, ax=None, options={}):
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rel_intensity = (intensity / intensities.max())*(1-options['min_alpha']) + options['min_alpha']
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colour.append(rel_intensity)
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colours.append(colour)
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ax.vlines(x=reflections, ymin=-1, ymax=1, colors=colours, lw=0.5)
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