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

Update smoothing function

Browse source
This commit is contained in:
rasmusvt 2022-06-21 19:04:04 +02:00
parent 1cf949e36b
commit 9e39135f00
1 changed files with 47 additions and 42 deletions
Download patch file Download diff file Expand all files Collapse all files

81
nafuma/xanes/calib.py
View file

@ -262,70 +262,75 @@ def smoothing(data: dict, options={}):
# FIXME Add logging # FIXME Add logging
# FIXME Add saving of files # FIXME Add saving of files
required_options = ['log', 'logfile', 'window_length','polyorder'] required_options = ['log', 'logfile', 'window_length','polyorder', 'save_default']
default_options = { default_options = {
'log': False, 'log': False,
'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_smoothing.log', 'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_smoothing.log',
'save_plots': False, 'save_plots': False,
'save_folder': './', 'save_folder': './',
'window_length': 3, 'window_length': 3,
'polyorder': 2 'polyorder': 2,
'save_default': False
} }
options = aux.update_options(options=options, required_options=required_options, default_options=default_options) options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
if options['save_default']:
data['xanes_data_smooth_default'] = data['xanes_data']['ZapEnergy']
# FIXME Add other types of filters # FIXME Add other types of filters
# FIXME Instead of assigning values directly to the data dictionary, these should be made into an own DataFrame that you can decide later what to do with - these variables should
# then be returned
for filename in data['path']: for filename in data['path']:
xanes_smooth = savgol_filter(data['xanes_data'][filename], options['window_length'], options['polyorder']) xanes_smooth = savgol_filter(data['xanes_data'][filename], options['window_length'], options['polyorder'])
default_smooth = savgol_filter(data['xanes_data'][filename], default_options['window_length'], default_options['polyorder']) if options['save_default']:
default_smooth = savgol_filter(data['xanes_data'][filename], default_options['window_length'], default_options['polyorder'])
data['xanes_data'][filename] = xanes_smooth
if options['save_default']:
data['xanes_data_smooth_default'][filename] = default_smooth
#printing the smoothed curves vs data if options['save_plots']:
if options['save_folder'] == True: if not os.path.isdir(options['save_folder']):
os.makedirs(options['save_folder'])
fig, (ax1,ax2) = plt.subplots(1,2,figsize=(15,5)) dst = os.path.join(options['save_folder'], os.path.basename(filename)) + '_smooth.png'
x_range_zoom=[6.54,6.55] #make into widget
y_range_zoom=[20000,80000] #make into widget
df_bkgd_sub.plot.scatter(x = "ZapEnergy",y=filenames, ax=ax1, color="Red") edge_pos = estimate_edge_position(data=data, options=options)
df_smooth.plot(x = "ZapEnergy",y=filenames, ax=ax1, color="Blue") intensity_midpoint = data['xanes_data'][filename].max() - data['xanes_data'][filename].min()
ax1.set_xlim(x_range_zoom)
ax1.set_ylim(y_range_zoom)
ax1.set_title("Smoothed curve (blue) vs data (red) used for further analysis")
df_bkgd_sub.plot.scatter(x = "ZapEnergy",y=filenames, ax=ax2, color="Red")
df_default.plot(x = "ZapEnergy",y=filenames, ax=ax2, color="Green")
ax2.set_xlim(x_range_zoom)
ax2.set_ylim(y_range_zoom)
ax2.set_title("Smoothed curve (green) vs data (red) using default window_length and polyorder")
# FIXME Clear up these two plotting functions if options['save_default']:
fig, (ax1, ax2) = plt.subplots(1,2,figsize=(20,5))
data['xanes_data'].plot(x='ZapEnergy', y=filename, color='black', ax=ax1)
xanes_smooth.plot(x='ZapEnergy', y=filename, color='red', ax=ax1)
ax1.set_xlim([edge_pos-0.5, edge_pos+0.5])
ax1.set_ylim([intensity_midpoint*0.98, intensity_midpoint*1.02])
if options['save_plots']: ax1.set_title(f'{os.path.basename(filename)} - Smooth', size=20)
if not os.path.isdir(options['save_folder']):
os.makedirs(options['save_folder'])
dst = os.path.join(options['save_folder'], os.path.basename(filename)) + '_pre_edge_fit.png' data['xanes_data_original'].plot(x='ZapEnergy', y=filename, color='black', ax=ax2)
data['xanes_data_smooth_default'].plot(x='ZapEnergy', y=filename, color='green', ax=ax2)
ax2.set_xlim([edge_pos-0.5, edge_pos+0.5])
ax2.set_ylim([intensity_midpoint*0.98, intensity_midpoint*1.02])
ax2.set_title(f'{os.path.basename(filename)} - Smooth (default values)', size=20)
fig, (ax1, ax2) = plt.subplots(1,2,figsize=(10,5)) elif not options['save_default']:
data['xanes_data_original'].plot(x='ZapEnergy', y=filename, color='black', ax=ax1) fig, ax = plt.subplots(figsize=(10,5))
pre_edge_fit_data.plot(x='ZapEnergy', y=filename, color='red', ax=ax1) data['xanes_data'].plot(x='ZapEnergy', y=filename, color='black', ax=ax1)
ax1.axvline(x = max(pre_edge_data['ZapEnergy']), ls='--') xanes_smooth.plot(x='ZapEnergy', y=filename, color='red', ax=ax1)
ax1.set_title(f'{os.path.basename(filename)} - Full view', size=20) ax1.set_xlim([edge_pos-0.5, edge_pos+0.5])
ax1.set_ylim([intensity_midpoint*0.98, intensity_midpoint*1.02])
data['xanes_data_original'].plot(x='ZapEnergy', y=filename, color='black', ax=ax2) ax1.set_title(f'{os.path.basename(filename)} - Smooth', size=20)
pre_edge_fit_data.plot(x='ZapEnergy', y=filename, color='red', ax=ax2)
ax2.axvline(x = max(pre_edge_data['ZapEnergy']), ls='--')
ax2.set_xlim([min(pre_edge_data['ZapEnergy']), max(pre_edge_data['ZapEnergy'])])
ax2.set_ylim([min(pre_edge_data[filename]), max(pre_edge_data[filename])])
ax2.set_title(f'{os.path.basename(filename)} - Fit region', size=20)
plt.savefig(dst, transparent=False) plt.savefig(dst, transparent=False)
plt.close() plt.close()
return xanes_smooth, default_smooth # FIXME See comment above about return values
return None