rasmus/nafuma
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Add heatmap, lacks mapping between x-value and 2th

Browse source
This commit is contained in:
rasmusvt 2022-03-31 17:29:10 +02:00
parent bdce18d195
commit 6e851b494b
1 changed files with 24 additions and 9 deletions
Download patch file Download diff file Expand all files Collapse all files

21
beamtime/xrd/plot.py
View file

@ -1,3 +1,4 @@
import seaborn as sns
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator) from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator)
@ -20,7 +21,7 @@ def plot_diffractogram(data, options={}):
# Update options # Update options
required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise', 'offset', 'offset_x', 'offset_y', required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise', 'offset', 'offset_x', 'offset_y',
'reflections_plot', 'reflections_indices', 'reflections_data', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params', 'interactive_session_active'] 'reflections_plot', 'reflections_indices', 'reflections_data', 'heatmap', 'cmap', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params', 'interactive_session_active']
default_options = { default_options = {
'x_vals': '2th', 'x_vals': '2th',
@ -37,6 +38,8 @@ def plot_diffractogram(data, options={}):
'reflections_plot': False, # whether to plot reflections as a plot 'reflections_plot': False, # whether to plot reflections as a plot
'reflections_indices': False, # whether to plot the reflection indices 'reflections_indices': False, # whether to plot the reflection indices
'reflections_data': None, # Should be passed as a list of dictionaries on the form {path: rel_path, reflection_indices: number of indices, colour: [r,g,b], min_alpha: 0-1] 'reflections_data': None, # Should be passed as a list of dictionaries on the form {path: rel_path, reflection_indices: number of indices, colour: [r,g,b], min_alpha: 0-1]
'heatmap': False,
'cmap': 'viridis',
'plot_kind': None, 'plot_kind': None,
'palettes': [('qualitative', 'Dark2_8')], 'palettes': [('qualitative', 'Dark2_8')],
'interactive': False, 'interactive': False,
@ -70,12 +73,19 @@ def plot_diffractogram(data, options={}):
data['wavelength'][index] = wavelength data['wavelength'][index] = wavelength
else: else:
if not isinstance(data['diffractogram'], list): if not isinstance(data['diffractogram'], list):
data['diffractogram'] = [data['diffractogram']] data['diffractogram'] = [data['diffractogram']]
data['wavelength'] = [data['wavelength']] data['wavelength'] = [data['wavelength']]
if options['heatmap']:
data['heatmap'] = []
for diff in data['diffractogram']:
data['heatmap'].append(np.array(diff['I']))
data['heatmap'] = np.array(data['heatmap'])
data['heatmap'] = np.flipud(data['heatmap'])
# Sets the xlim if this has not bee specified # Sets the xlim if this has not bee specified
if not options['xlim']: if not options['xlim']:
options['xlim'] = [diffractogram[options['x_vals']].min(), diffractogram[options['x_vals']].max()] options['xlim'] = [diffractogram[options['x_vals']].min(), diffractogram[options['x_vals']].max()]
@ -130,6 +140,11 @@ def plot_diffractogram(data, options={}):
colours = btp.generate_colours(['black'], kind='single') colours = btp.generate_colours(['black'], kind='single')
# FIXME Must be changed to map the x-value to the 2th-value somehow
if options['heatmap']:
sns.heatmap(data['heatmap'], cmap=options['cmap'])
else:
for diffractogram in data['diffractogram']: for diffractogram in data['diffractogram']:
if options['line']: if options['line']:
diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours), zorder=1) diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours), zorder=1)
@ -168,7 +183,7 @@ def plot_diffractogram(data, options={}):
return diffractogram, fig, ax return data['diffractogram'], fig, ax
def determine_grid_layout(options): def determine_grid_layout(options):