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Get HTXRD-plotter to a working state

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rasmusvt 2022-09-27 10:21:39 +02:00
parent 6247ce24bf
commit 83f4f6a155
1 changed files with 51 additions and 17 deletions
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50
nafuma/xrd/plot.py
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@ -24,7 +24,7 @@ def plot_diffractogram(data, options={}):
# Update options
required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise', 'offset', 'offset_x', 'offset_y', 'offset_change',
'reflections_plot', 'reflections_indices', 'reflections_data', 'heatmap', 'cmap', 'plot_kind', 'palettes', 'highlight', 'highlight_colours', 'interactive', 'rc_params', 'format_params', 'interactive_session_active']
'reflections_plot', 'reflections_indices', 'reflections_data', 'heatmap', 'cmap', 'plot_kind', 'palettes', 'highlight', 'highlight_colours', 'interactive', 'rc_params', 'format_params', 'interactive_session_active', 'plot_diff']
default_options = {
'x_vals': '2th', 'y_vals': 'I',
@ -51,6 +51,7 @@ def plot_diffractogram(data, options={}):
'interactive_session_active': False,
'rc_params': {},
'format_params': {},
'plot_diff': False,
}
if 'offset_y' not in options.keys():
@ -86,13 +87,23 @@ def plot_diffractogram(data, options={}):
if not isinstance(data['wavelength'], list):
data['wavelength'] = [data['wavelength'] for _ in range(len(data['path']))]
# LOAD DIFFRACTOGRAMS
if 'htxrd' in data.keys() and data['htxrd']:
data['diffractogram'], data['wavelength'] = xrd.io.read_htxrd(data=data, options=options, index=0)
else:
for index in range(len(data['path'])):
diffractogram, wavelength = xrd.io.read_data(data=data, options=options, index=index)
data['diffractogram'][index] = diffractogram
data['wavelength'][index] = wavelength
# FIXME This is a quick fix as the image is not reloaded when passing multiple beamline datasets. Should probably be handled in io?
data['image'] = None
@ -106,7 +117,12 @@ def plot_diffractogram(data, options={}):
options['heatmap_loaded'] = True
if options['heatmap']:
options['xlim'] = [options['heatmap_xlim'][0], options['heatmap_xlim'][1]]
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()
options['xlim'] = [options['heatmap_xlim'][0]*xlim_start_frac, options['heatmap_xlim'][1]*xlim_end_frac]
if options['heatmap_reverse']:
data['heatmap'] = data['heatmap'].iloc[::-1]
data['heatmap_yticklabels'] = data['heatmap_yticklabels'][::-1]
# 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.
else:
@ -177,7 +193,11 @@ def plot_diffractogram(data, options={}):
# 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.
# FIXME Should probably allow for more than 8 if wanted - not a priority now
if len(data['path']) < 8:
if len(data['path']) <= 8:
if 'colours' in options.keys():
colours = btp.generate_colours(options['colours'], kind='single')
else:
colours = btp.generate_colours(options['palettes'])
@ -255,6 +275,8 @@ def plot_diffractogram(data, options={}):
if not options['yunit'] or options['yunit'] == options['diff.yunit']:
options['yunit'] = options['heatmap.yunit']
ax.tick_params(axis='x', which='minor', bottom=False, top=False)
ax.tick_params(axis='y', which='minor', left=False, right=False)
@ -269,7 +291,7 @@ def plot_diffractogram(data, options={}):
if options['highlight']:
for i, highlight in enumerate(options['highlight']):
if i < len(options['highlight'])-1 or len(options['highlight']) == 1:
if i < len(options['highlight']) or len(options['highlight']) == 1:
ax.axhline(y=highlight[1], c=options['highlight_colours'][i], ls='--', lw=0.5)
@ -297,6 +319,14 @@ def plot_diffractogram(data, options={}):
options['hide_y_ticks'] = True
if options['plot_diff'] and len(data['path']) == 2:
diff = data['diffractogram'][0]
diff['I'] = diff['I'] - data['diffractogram'][1]['I']
diff['I'] = diff['I'] - 0.5
diff.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours))
# Adjust the plot to make it prettier
fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
@ -418,6 +448,7 @@ def generate_heatmap(data, options={}):
options['heatmap_xlim'] = xlims
# Get temperatures if HTXRD-scans
scan_numbers = []
@ -463,6 +494,8 @@ def generate_heatmap(data, options={}):
def determine_grid_layout(options):
#aspect_ratio = int(options['format_params']['aspect_ratio'].split(':')[0]) / int(options['format_params']['aspect_ratio'].split(':')[1])
nrows = 1 if not options['reflections_indices'] else 2
if options['reflections_plot']:
@ -470,7 +503,9 @@ def determine_grid_layout(options):
nrows += 1
options['format_params']['nrows'] = nrows
options['format_params']['grid_ratio_height'] = [1 for i in range(nrows-1)]+[10]
if not 'grid_ratio_height' in options['format_params'].keys():
options['format_params']['grid_ratio_height'] = [0.6 for i in range(nrows-1)]+[10]
return options
@ -794,7 +829,8 @@ def plot_reflection_table(data, reflections_params, ax=None, options={}):
'label': None
}
if 'colour' in data.keys():
if 'colour' in reflections_params.keys():
options['reflections_colour'] = reflections_params['colour']
if 'min_alpha' in reflections_params.keys():
options['min_alpha'] = reflections_params['min_alpha']
@ -807,7 +843,6 @@ def plot_reflection_table(data, reflections_params, ax=None, options={}):
options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
if not ax:
_, ax = btp.prepare_plot(options)
@ -829,7 +864,6 @@ def plot_reflection_table(data, reflections_params, ax=None, options={}):
ax.vlines(x=reflections, ymin=-1, ymax=1, colors=colours, lw=0.5)
ax.set_ylim([-0.5,0.5])